Search to RefSeqBP_Rel49

BLASTX 2.2.24 [Aug-08-2010]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= ITT01_0086_H05
         (1093 letters)

Database: RefSeq49_BP.fasta 
           33,088 sequences; 17,681,374 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|XP_002702914.1| PREDICTED: BOLA-DQA2 protein-like [Bos tauru...   271   1e-72
Alignment   gi|NP_001012693.1| major histocompatibility complex, class II, ...   270   2e-72
Alignment   gi|NP_001013619.3| major histocompatibility complex, class II, ...   266   2e-71
Alignment   gi|NP_001073045.1| major histocompatibility complex, class II, ...   258   8e-69
Alignment   gi|NP_001012699.1| major histocompatibility complex, class II, ...   236   2e-62
Alignment   gi|NP_001012696.1| major histocompatibility complex, class II, ...   219   4e-57
Alignment   gi|NP_001012695.1| major histocompatibility complex, class II, ...   189   3e-48
Alignment   gi|NP_001192849.1| HLA class II histocompatibility antigen, DO ...   187   1e-47
Alignment   gi|XP_002697222.1| PREDICTED: MHC class II antigen-like [Bos ta...   187   1e-47
Alignment   gi|XP_002702869.1| PREDICTED: MHC class II antigen-like [Bos ta...   174   9e-44

>ref|XP_002702914.1| PREDICTED: BOLA-DQA2 protein-like [Bos taurus].
          Length = 254

 Score =  271 bits (692), Expect = 1e-72
 Identities = 132/186 (70%), Positives = 146/186 (78%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LP+FS+F S DPQ  LRNIA +KHNLNI+IK SN   A+N+VPEVTVF KSP++LGQPN
Sbjct: 70  RLPMFSQFASFDPQAILRNIAISKHNLNIMIKYSNFIPAINEVPEVTVFSKSPMVLGQPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLICH+DN FPPVINITWLKNGH+VTEG SETSFL K+DHSFLKI YLTFLPSDDD YDC
Sbjct: 130 TLICHMDN-FPPVINITWLKNGHAVTEGVSETSFLPKDDHSFLKIGYLTFLPSDDDVYDC 188

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPS 567
           KVEHW LD+PLLKHWEPE+PAPMSELTET                      QGLRSGG S
Sbjct: 189 KVEHWSLDEPLLKHWEPEVPAPMSELTETVVCALRLTVGLVGIVVGTIFIIQGLRSGGAS 248

Query: 568 RHQGSL 585
           RHQG L
Sbjct: 249 RHQGPL 254


>ref|NP_001012693.1| major histocompatibility complex, class II, DQ alpha 5 [Bos
           taurus].
          Length = 255

 Score =  270 bits (690), Expect = 2e-72
 Identities = 134/186 (72%), Positives = 145/186 (77%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           QLPLFS+  S DPQ ALRNIA  K +++ L K SN+TAA N+VPEVTVF KSPVMLGQPN
Sbjct: 70  QLPLFSRMLSFDPQLALRNIAIMKLHVDFLTKFSNSTAATNKVPEVTVFSKSPVMLGQPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLICHVDNIFPPVINITWL+NGHSVTEG SETSFL ++D+SFLKI YL FLPSDDD YDC
Sbjct: 130 TLICHVDNIFPPVINITWLRNGHSVTEGVSETSFLIRSDYSFLKIKYLAFLPSDDDIYDC 189

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPS 567
           KVEHWGLD+PLLKHWEPEIPAPMSELTET                      QGLRSG PS
Sbjct: 190 KVEHWGLDEPLLKHWEPEIPAPMSELTETVVCTLGLTMGLVGITVGTIFIIQGLRSGDPS 249

Query: 568 RHQGSL 585
           RHQG L
Sbjct: 250 RHQGPL 255


>ref|NP_001013619.3| major histocompatibility complex, class II, DQ alpha, type 1 [Bos
           taurus].
          Length = 255

 Score =  266 bits (681), Expect = 2e-71
 Identities = 129/186 (69%), Positives = 143/186 (76%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           QLP+F +  S + Q AL  IA AKH L++L KRSN T  +N+VPEVTVF KSP+MLGQPN
Sbjct: 70  QLPMFGELTSFEAQDALNEIAKAKHTLDVLTKRSNFTPVINEVPEVTVFSKSPMMLGQPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLICHVDNIFPPVINITWL+NGH+VTEG SETSFL K+D+SFLKI YLTFLPSDDD YDC
Sbjct: 130 TLICHVDNIFPPVINITWLRNGHAVTEGVSETSFLPKSDYSFLKIGYLTFLPSDDDVYDC 189

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPS 567
           KVEHWGLD+PLLKHWEPEIPAPMSELTET                      +GLRSGG S
Sbjct: 190 KVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLTVGLVGIVVGTVLIIRGLRSGGAS 249

Query: 568 RHQGSL 585
           RHQG L
Sbjct: 250 RHQGPL 255


>ref|NP_001073045.1| major histocompatibility complex, class II, DQ alpha, type 3 [Bos
           taurus].
          Length = 254

 Score =  258 bits (658), Expect = 8e-69
 Identities = 128/186 (68%), Positives = 141/186 (75%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LP+F K R   PQGALRNIA AKHNL++L K  N T  +N+VPEVTVF KSPVML QPN
Sbjct: 70  RLPMFDKLRFH-PQGALRNIAIAKHNLDVLTKLYNFTPVINEVPEVTVFSKSPVMLSQPN 128

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLICHVDNIFPPVINITWL+NGHSVTE  SETSFL ++D+S+LKISYL F PSDDD YDC
Sbjct: 129 TLICHVDNIFPPVINITWLRNGHSVTEHVSETSFLLRSDYSYLKISYLPFRPSDDDVYDC 188

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPS 567
           KVEHWGLD+PLLKHWEPEIPAPMSELTET                      +GLRS G S
Sbjct: 189 KVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLTVGLVGIVVGTVLITRGLRSSGAS 248

Query: 568 RHQGSL 585
           RHQG L
Sbjct: 249 RHQGPL 254


>ref|NP_001012699.1| major histocompatibility complex, class II, DQ alpha 2 [Bos
           taurus].
          Length = 268

 Score =  236 bits (603), Expect = 2e-62
 Identities = 109/135 (80%), Positives = 120/135 (88%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LP+FS+F   DPQ AL  IATAKHNL++L KRSN T  +N+VPEVTVF KSPVMLGQPN
Sbjct: 70  RLPMFSQFAGFDPQAALSEIATAKHNLDVLTKRSNFTPVINEVPEVTVFSKSPVMLGQPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLICHVDNIFPPVINITWLKNGH+VTEG SETSFL K+DHSFLKI YLTFLPSD+D YDC
Sbjct: 130 TLICHVDNIFPPVINITWLKNGHAVTEGVSETSFLPKDDHSFLKIGYLTFLPSDNDIYDC 189

Query: 388 KVEHWGLDKPLLKHW 432
           KVEHWGLD+PLLKHW
Sbjct: 190 KVEHWGLDEPLLKHW 204


>ref|NP_001012696.1| major histocompatibility complex, class II, DY alpha [Bos taurus].
          Length = 253

 Score =  219 bits (557), Expect = 4e-57
 Identities = 101/149 (67%), Positives = 120/149 (80%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LP FS     + Q ALRNI  +K NL+ILIK S+ T A +++PEV VFPKS V+LG PN
Sbjct: 68  RLPEFSNITKFEVQSALRNIVMSKRNLDILIKNSSFTPATSEIPEVAVFPKSSVVLGIPN 127

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLIC VDNIFPPVINITW  NGH V EG +ET+F  K+DHSFLK SYLTFLP+++DFYDC
Sbjct: 128 TLICQVDNIFPPVINITWFYNGHFVAEGIAETTFYPKSDHSFLKFSYLTFLPTNEDFYDC 187

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTET 474
           +VEHWGL++PL+KHWEPEIP P SELTET
Sbjct: 188 RVEHWGLEEPLVKHWEPEIPTPTSELTET 216


>ref|NP_001012695.1| major histocompatibility complex, class II, DR alpha [Bos taurus].
          Length = 253

 Score =  189 bits (481), Expect = 3e-48
 Identities = 89/148 (60%), Positives = 108/148 (72%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LP F  F S + QGAL N+A  K NL+I+IKRSNNT   N  PEVT+ P  PV LG+PN
Sbjct: 68  RLPEFGHFASFEAQGALANMAVMKANLDIMIKRSNNTPNTNVPPEVTLLPNKPVELGEPN 127

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLIC +D   PPVI++TWL+NG  VT+G S+T FL +NDH F K  YL FLP+ +D YDC
Sbjct: 128 TLICFIDKFSPPVISVTWLRNGKPVTDGVSQTVFLPRNDHLFRKFHYLPFLPTTEDVYDC 187

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTE 471
           KVEH GL++PLLKHWE E PAP+ E TE
Sbjct: 188 KVEHLGLNEPLLKHWEYEAPAPLPETTE 215


>ref|NP_001192849.1| HLA class II histocompatibility antigen, DO alpha chain [Bos
           taurus].
          Length = 250

 Score =  187 bits (475), Expect = 1e-47
 Identities = 87/149 (58%), Positives = 106/149 (71%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LP F  F   DPQ  L +IA  K +L  L+KRSN T A N  P V V PKS V LG+PN
Sbjct: 70  RLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNVSPRVAVLPKSHVQLGEPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
            LIC VD IFPPVINITWL+NGH VT+G +++SF ++ DH F K  YLTF+P  DDFYDC
Sbjct: 130 VLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFVPLVDDFYDC 189

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTET 474
           KVEHWGLD+PL +HWEP++P  + + T T
Sbjct: 190 KVEHWGLDQPLFQHWEPQVPTALPDTTGT 218


>ref|XP_002697222.1| PREDICTED: MHC class II antigen-like [Bos taurus].
          Length = 250

 Score =  187 bits (475), Expect = 1e-47
 Identities = 87/149 (58%), Positives = 106/149 (71%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LP F  F   DPQ  L +IA  K +L  L+KRSN T A N  P V V PKS V LG+PN
Sbjct: 70  RLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNVSPRVAVLPKSHVQLGEPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
            LIC VD IFPPVINITWL+NGH VT+G +++SF ++ DH F K  YLTF+P  DDFYDC
Sbjct: 130 VLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFVPLVDDFYDC 189

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTET 474
           KVEHWGLD+PL +HWEP++P  + + T T
Sbjct: 190 KVEHWGLDQPLFQHWEPQVPTALPDTTGT 218


>ref|XP_002702869.1| PREDICTED: MHC class II antigen-like [Bos taurus].
          Length = 224

 Score =  174 bits (442), Expect = 9e-44
 Identities = 82/135 (60%), Positives = 97/135 (71%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LP F  F   DPQ  L +IA  K +L  L+KRSN T A N  P V V PKS V LG+PN
Sbjct: 70  RLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNVSPRVAVLPKSHVQLGEPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
            LIC VD IFPPVINITWL+NGH VT+G +++SF ++ DH F K  YLTF+P  DDFYDC
Sbjct: 130 VLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFVPLVDDFYDC 189

Query: 388 KVEHWGLDKPLLKHW 432
           KVEHWGLD+PL +HW
Sbjct: 190 KVEHWGLDQPLFQHW 204


  Database: RefSeq49_BP.fasta
    Posted date:  Oct 17, 2011  1:42 PM
  Number of letters in database: 17,681,374
  Number of sequences in database:  33,088
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33088
Number of Hits to DB: 37,943,116
Number of extensions: 924726
Number of successful extensions: 2430
Number of sequences better than 1.0e-05: 51
Number of HSP's gapped: 2412
Number of HSP's successfully gapped: 51
Length of query: 364
Length of database: 17,681,374
Length adjustment: 104
Effective length of query: 260
Effective length of database: 14,240,222
Effective search space: 3702457720
Effective search space used: 3702457720
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)
Animal-Genome cDNA ITT01_0086_H05

Animal-Genome cDNA ITT01_0086_H05


Search to RefSeqHP_Rel49

BLASTX 2.2.24 [Aug-08-2010]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= ITT01_0086_H05
         (1093 letters)

Database: RefSeq49_HP.fasta 
           32,964 sequences; 18,297,164 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|XP_003119376.1| PREDICTED: HLA class II histocompatibility a...   276   2e-74
Alignment   gi|XP_003119375.1| PREDICTED: HLA class II histocompatibility a...   276   2e-74
Alignment   gi|XP_003119374.1| PREDICTED: HLA class II histocompatibility a...   276   2e-74
Alignment   gi|NP_002113.2| HLA class II histocompatibility antigen, DQ alp...   272   3e-73
Alignment   gi|XP_003120319.1| PREDICTED: HLA class II histocompatibility a...   268   9e-72
Alignment   gi|XP_003120318.1| PREDICTED: HLA class II histocompatibility a...   268   9e-72
Alignment   gi|XP_003120317.1| PREDICTED: HLA class II histocompatibility a...   268   9e-72
Alignment   gi|NP_064440.1| HLA class II histocompatibility antigen, DQ alp...   268   9e-72
Alignment   gi|XP_003119377.1| PREDICTED: HLA class II histocompatibility a...   238   7e-63
Alignment   gi|XP_003120320.1| PREDICTED: HLA class II histocompatibility a...   228   7e-60

>ref|XP_003119376.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
           chain-like isoform 3 [Homo sapiens].
          Length = 250

 Score =  276 bits (706), Expect = 2e-74
 Identities = 136/186 (73%), Positives = 145/186 (77%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           QLPLF +FR  DPQ AL NIA  KHNLNI+IKRSN+TAA N+VPEVTVF KSPV LGQPN
Sbjct: 65  QLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPN 124

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLTFLPSDD+ YDC
Sbjct: 125 TLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDC 184

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPS 567
           KVEHWGLD+PLLKHWEPEIP PMSELTET                      +GLRS G S
Sbjct: 185 KVEHWGLDEPLLKHWEPEIPTPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGAS 244

Query: 568 RHQGSL 585
           RHQG L
Sbjct: 245 RHQGPL 250


>ref|XP_003119375.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
           chain-like isoform 2 [Homo sapiens].
          Length = 255

 Score =  276 bits (706), Expect = 2e-74
 Identities = 136/186 (73%), Positives = 145/186 (77%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           QLPLF +FR  DPQ AL NIA  KHNLNI+IKRSN+TAA N+VPEVTVF KSPV LGQPN
Sbjct: 70  QLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLTFLPSDD+ YDC
Sbjct: 130 TLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDC 189

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPS 567
           KVEHWGLD+PLLKHWEPEIP PMSELTET                      +GLRS G S
Sbjct: 190 KVEHWGLDEPLLKHWEPEIPTPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGAS 249

Query: 568 RHQGSL 585
           RHQG L
Sbjct: 250 RHQGPL 255


>ref|XP_003119374.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
           chain-like isoform 1 [Homo sapiens].
          Length = 255

 Score =  276 bits (706), Expect = 2e-74
 Identities = 136/186 (73%), Positives = 145/186 (77%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           QLPLF +FR  DPQ AL NIA  KHNLNI+IKRSN+TAA N+VPEVTVF KSPV LGQPN
Sbjct: 70  QLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLTFLPSDD+ YDC
Sbjct: 130 TLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDC 189

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPS 567
           KVEHWGLD+PLLKHWEPEIP PMSELTET                      +GLRS G S
Sbjct: 190 KVEHWGLDEPLLKHWEPEIPTPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGAS 249

Query: 568 RHQGSL 585
           RHQG L
Sbjct: 250 RHQGPL 255


>ref|NP_002113.2| HLA class II histocompatibility antigen, DQ alpha 1 chain precursor
           [Homo sapiens].
          Length = 255

 Score =  272 bits (696), Expect = 3e-73
 Identities = 135/184 (73%), Positives = 143/184 (77%)
 Frame = +1

Query: 34  PLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTL 213
           P FSKF   DPQGALRN+A AKHNLNI+IKR N+TAA N+VPEVTVF KSPV LGQPNTL
Sbjct: 72  PEFSKFGGFDPQGALRNMAVAKHNLNIMIKRYNSTAATNEVPEVTVFSKSPVTLGQPNTL 131

Query: 214 ICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCKV 393
           IC VDNIFPPV+NITWL NG SVTEG SETSFLSK+DHSF KISYLTFLPS D+ YDCKV
Sbjct: 132 ICLVDNIFPPVVNITWLSNGQSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKV 191

Query: 394 EHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRH 573
           EHWGLD+PLLKHWEPEIPAPMSELTET                      QGLRS G SRH
Sbjct: 192 EHWGLDQPLLKHWEPEIPAPMSELTETVVCALGLSVGLMGIVVGTVFIIQGLRSVGASRH 251

Query: 574 QGSL 585
           QG L
Sbjct: 252 QGPL 255


>ref|XP_003120319.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
           chain-like isoform 3 [Homo sapiens].
          Length = 254

 Score =  268 bits (684), Expect = 9e-72
 Identities = 135/186 (72%), Positives = 144/186 (77%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LPLF + R  DPQ AL NIA  KHNLNILIKRSN+TAA N+VPEVTVF KSPV LGQPN
Sbjct: 70  KLPLFHRLRF-DPQFALTNIAVLKHNLNILIKRSNSTAATNEVPEVTVFSKSPVTLGQPN 128

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLTFLPS D+ YDC
Sbjct: 129 TLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDC 188

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPS 567
           KVEHWGLD+PLLKHWEPEIPAPMSELTET                      +GLRS G S
Sbjct: 189 KVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGAS 248

Query: 568 RHQGSL 585
           RHQG L
Sbjct: 249 RHQGPL 254


>ref|XP_003120318.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
           chain-like isoform 2 [Homo sapiens].
          Length = 249

 Score =  268 bits (684), Expect = 9e-72
 Identities = 135/186 (72%), Positives = 144/186 (77%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LPLF + R  DPQ AL NIA  KHNLNILIKRSN+TAA N+VPEVTVF KSPV LGQPN
Sbjct: 65  KLPLFHRLRF-DPQFALTNIAVLKHNLNILIKRSNSTAATNEVPEVTVFSKSPVTLGQPN 123

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLTFLPS D+ YDC
Sbjct: 124 TLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDC 183

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPS 567
           KVEHWGLD+PLLKHWEPEIPAPMSELTET                      +GLRS G S
Sbjct: 184 KVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGAS 243

Query: 568 RHQGSL 585
           RHQG L
Sbjct: 244 RHQGPL 249


>ref|XP_003120317.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
           chain-like isoform 1 [Homo sapiens].
          Length = 254

 Score =  268 bits (684), Expect = 9e-72
 Identities = 135/186 (72%), Positives = 144/186 (77%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LPLF + R  DPQ AL NIA  KHNLNILIKRSN+TAA N+VPEVTVF KSPV LGQPN
Sbjct: 70  KLPLFHRLRF-DPQFALTNIAVLKHNLNILIKRSNSTAATNEVPEVTVFSKSPVTLGQPN 128

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLTFLPS D+ YDC
Sbjct: 129 TLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDC 188

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPS 567
           KVEHWGLD+PLLKHWEPEIPAPMSELTET                      +GLRS G S
Sbjct: 189 KVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGAS 248

Query: 568 RHQGSL 585
           RHQG L
Sbjct: 249 RHQGPL 254


>ref|NP_064440.1| HLA class II histocompatibility antigen, DQ alpha 2 chain precursor
           [Homo sapiens].
          Length = 255

 Score =  268 bits (684), Expect = 9e-72
 Identities = 131/186 (70%), Positives = 143/186 (76%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           QLP+FSKF S DPQ ALRN+A  KH L  ++++SN+TAA N+VPEVTVF K PV LGQPN
Sbjct: 70  QLPMFSKFISFDPQSALRNMAVGKHTLEFMMRQSNSTAATNEVPEVTVFSKFPVTLGQPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLTFLPS D+ YDC
Sbjct: 130 TLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDC 189

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPS 567
           KVEHWGLD+PLLKHWEPEIPAPMSELTET                      QGLRS G S
Sbjct: 190 KVEHWGLDEPLLKHWEPEIPAPMSELTETLVCALGLSVGLMGIVVGTVFIIQGLRSVGAS 249

Query: 568 RHQGSL 585
           RHQG L
Sbjct: 250 RHQGLL 255


>ref|XP_003119377.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
           chain-like isoform 4 [Homo sapiens].
          Length = 208

 Score =  238 bits (607), Expect = 7e-63
 Identities = 112/135 (82%), Positives = 120/135 (88%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           QLPLF +FR  DPQ AL NIA  KHNLNI+IKRSN+TAA N+VPEVTVF KSPV LGQPN
Sbjct: 70  QLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLTFLPSDD+ YDC
Sbjct: 130 TLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDC 189

Query: 388 KVEHWGLDKPLLKHW 432
           KVEHWGLD+PLLKHW
Sbjct: 190 KVEHWGLDEPLLKHW 204


>ref|XP_003120320.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
           chain-like isoform 4 [Homo sapiens].
          Length = 207

 Score =  228 bits (581), Expect = 7e-60
 Identities = 110/135 (81%), Positives = 118/135 (87%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LPLF + R  DPQ AL NIA  KHNLNILIKRSN+TAA N+VPEVTVF KSPV LGQPN
Sbjct: 70  KLPLFHRLRF-DPQFALTNIAVLKHNLNILIKRSNSTAATNEVPEVTVFSKSPVTLGQPN 128

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLTFLPS D+ YDC
Sbjct: 129 TLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDC 188

Query: 388 KVEHWGLDKPLLKHW 432
           KVEHWGLD+PLLKHW
Sbjct: 189 KVEHWGLDEPLLKHW 203


  Database: RefSeq49_HP.fasta
    Posted date:  Oct 17, 2011  1:42 PM
  Number of letters in database: 18,297,164
  Number of sequences in database:  32,964
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 32964
Number of Hits to DB: 38,857,334
Number of extensions: 928814
Number of successful extensions: 2453
Number of sequences better than 1.0e-05: 52
Number of HSP's gapped: 2435
Number of HSP's successfully gapped: 52
Length of query: 364
Length of database: 18,297,164
Length adjustment: 104
Effective length of query: 260
Effective length of database: 14,868,908
Effective search space: 3865916080
Effective search space used: 3865916080
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)

Search to RefSeqCP_Rel49

BLASTX 2.2.24 [Aug-08-2010]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= ITT01_0086_H05
         (1093 letters)

Database: RefSeq49_CP.fasta 
           33,336 sequences; 18,874,504 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001011726.1| major histocompatibility complex, class II, ...   275   7e-74
Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis lupus fam...   186   3e-47
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...   184   1e-46
Alignment   gi|NP_001014403.1| major histocompatibility complex, class II, ...    68   1e-11
Alignment   gi|NP_001041564.1| major histocompatibility complex, class II, ...    68   2e-11
Alignment   gi|NP_001014768.1| DLA class II histocompatibility antigen, DR-...    68   2e-11
Alignment   gi|XP_535458.1| PREDICTED: similar to beta-2-microglobulin prec...    65   9e-11
Alignment   gi|XP_850148.1| PREDICTED: similar to beta-2-microglobulin prec...    65   9e-11
Alignment   gi|NP_001041592.1| major histocompatibility complex, class II, ...    60   3e-09
Alignment   gi|XP_849737.1| PREDICTED: similar to HLA class II histocompati...    59   6e-09

>ref|NP_001011726.1| major histocompatibility complex, class II, DQ alpha [Canis lupus
           familiaris].
          Length = 255

 Score =  275 bits (702), Expect = 7e-74
 Identities = 134/186 (72%), Positives = 144/186 (77%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LP+FS FRS DPQGALRN+A  K NLNI+ KRSN TAA N+VPEVTVF KSPVMLGQPN
Sbjct: 70  RLPVFSTFRSFDPQGALRNLAIIKQNLNIMTKRSNQTAATNEVPEVTVFSKSPVMLGQPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLIC VDNIFPPVIN+TWLKN HSVTEG SETSF +K DHSF KISYLTFLPS +D YDC
Sbjct: 130 TLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFSKISYLTFLPSAEDIYDC 189

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPS 567
           KVEHWGLD+PLLKHWEPE+P PMSELTET                      QGLRSGG S
Sbjct: 190 KVEHWGLDEPLLKHWEPEVPTPMSELTETVVCALGLAVGLVGIVMGTVFIIQGLRSGGTS 249

Query: 568 RHQGSL 585
           RHQG L
Sbjct: 250 RHQGPL 255


>ref|NP_001011723.1| MHC class II DR alpha chain [Canis lupus familiaris].
          Length = 254

 Score =  186 bits (472), Expect = 3e-47
 Identities = 89/148 (60%), Positives = 105/148 (70%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +L  F +F S + QGAL NIA  K NL+ +IKRSN+T   N  PEVTV   +PV LG+PN
Sbjct: 69  RLEEFGRFASFEAQGALANIAVDKANLDTMIKRSNHTPNTNVPPEVTVLSNTPVELGEPN 128

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
            LIC +D   PPVIN+TWL+NG+ VT G SET FL + DH F K  YL FLPS +D YDC
Sbjct: 129 ILICFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPREDHLFRKFHYLPFLPSAEDVYDC 188

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTE 471
           KVEHWGLD+PLLKHWE E P P+ E TE
Sbjct: 189 KVEHWGLDEPLLKHWEFEPPTPLPETTE 216


>ref|XP_850803.1| PREDICTED: similar to HLA class II histocompatibility antigen, DO
           alpha chain precursor (MHC class II antigen DOA) (MHC DZ
           alpha) (MHC DN-alpha) isoform 11 [Canis familiaris].
          Length = 227

 Score =  184 bits (467), Expect = 1e-46
 Identities = 86/156 (55%), Positives = 109/156 (69%), Gaps = 7/156 (4%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQV-------PEVTVFPKSP 186
           +LP F      DPQ  L +IA  K +L++L++RSN T A+N         P V V PK  
Sbjct: 40  RLPEFGNLAHFDPQNGLASIAVIKAHLDVLVERSNRTRAINGTHLSSPLPPRVAVLPKFR 99

Query: 187 VMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPS 366
           V LGQPN LIC VDNIFPPVINITWL+NG  ++EG ++TSF S+ DH F K  YLTF+PS
Sbjct: 100 VELGQPNVLICIVDNIFPPVINITWLRNGQIISEGVAQTSFYSQPDHLFRKFCYLTFVPS 159

Query: 367 DDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 474
            +D YDCKVEHWGL++PLL+HWEP++P P+ +  ET
Sbjct: 160 AEDMYDCKVEHWGLEEPLLRHWEPQVPIPVPDTIET 195


>ref|NP_001014403.1| major histocompatibility complex, class II, DQ beta 1 [Canis lupus
           familiaris].
          Length = 269

 Score = 68.2 bits (165), Expect = 1e-11
 Identities = 31/103 (30%), Positives = 46/103 (44%)
 Frame = +1

Query: 157 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 336
           P VT+FP    +L   N L+C V + +P  I + W +N    T G   T  +   D +F 
Sbjct: 129 PTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLIRNGDWTFQ 188

Query: 337 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 465
            +  L   P   D Y C VEH  L  P+   W  +  +  S++
Sbjct: 189 ILVMLEMTPQRGDVYTCHVEHASLQSPITVQWRAQSESAQSKM 231


>ref|NP_001041564.1| major histocompatibility complex, class II, DM alpha [Canis lupus
           familiaris].
          Length = 170

 Score = 67.8 bits (164), Expect = 2e-11
 Identities = 36/105 (34%), Positives = 52/105 (49%)
 Frame = +1

Query: 157 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 336
           P V VF   P+  G+PN L+C + N+FPP + + W  +   V EG   T   + +  SF 
Sbjct: 38  PMVDVFTLKPLEFGKPNMLVCFISNLFPPTLTVNWWHHLDPV-EGIGPTFVSAVDGFSFQ 96

Query: 337 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 471
             SYL F P+  D + C V H   +   + +W P    P S+L E
Sbjct: 97  AFSYLNFTPAPSDLFSCVVTHEIDNYTAIAYWVPHDALP-SDLLE 140


>ref|NP_001014768.1| DLA class II histocompatibility antigen, DR-1 beta chain precursor
           [Canis lupus familiaris].
          Length = 266

 Score = 67.8 bits (164), Expect = 2e-11
 Identities = 34/123 (27%), Positives = 55/123 (44%)
 Frame = +1

Query: 97  KHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGH 276
           +HN  ++    + T      P VTV+P     L   N L+C V+  +P  I + WL+NG 
Sbjct: 109 RHNYGVI---ESFTVQRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQ 165

Query: 277 SVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPM 456
               G   T  +   D +F  +  L  +P   + Y C+VEH  L  P+   W  +  +  
Sbjct: 166 EEEAGVVSTGLIRNGDWTFQILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWRAQSDSAQ 225

Query: 457 SEL 465
           S++
Sbjct: 226 SKM 228


>ref|XP_535458.1| PREDICTED: similar to beta-2-microglobulin precursor isoform 2
           [Canis familiaris].
          Length = 125

 Score = 65.5 bits (158), Expect = 9e-11
 Identities = 32/98 (32%), Positives = 52/98 (53%)
 Frame = +1

Query: 142 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 321
           AV   P++ V+ + P   G+PN L C+V    PP I I  LKNG  +    ++ SF    
Sbjct: 27  AVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SK 84

Query: 322 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 435
           D +F  + +  F P++ D + C+V+H  L +P +  W+
Sbjct: 85  DWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWD 122


>ref|XP_850148.1| PREDICTED: similar to beta-2-microglobulin precursor isoform 3
           [Canis familiaris].
          Length = 125

 Score = 65.5 bits (158), Expect = 9e-11
 Identities = 32/98 (32%), Positives = 52/98 (53%)
 Frame = +1

Query: 142 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 321
           AV   P++ V+ + P   G+PN L C+V    PP I I  LKNG  +    ++ SF    
Sbjct: 27  AVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SK 84

Query: 322 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 435
           D +F  + +  F P++ D + C+V+H  L +P +  W+
Sbjct: 85  DWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWD 122


>ref|NP_001041592.1| major histocompatibility complex, class II, DO beta [Canis lupus
           familiaris].
          Length = 270

 Score = 60.5 bits (145), Expect = 3e-09
 Identities = 30/95 (31%), Positives = 41/95 (43%)
 Frame = +1

Query: 157 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 336
           PEVTV+P+    +   N L+C V   +P  I I W +NG     G   T  +   D +F 
Sbjct: 123 PEVTVYPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQ 182

Query: 337 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPE 441
            +  L   P   D Y C V H  L  P+   W  +
Sbjct: 183 TMVMLEMTPELGDVYTCLVNHPSLLSPVSVEWRAQ 217


>ref|XP_849737.1| PREDICTED: similar to HLA class II histocompatibility antigen, DM
           beta chain precursor (MHC class II antigen DMB) [Canis
           familiaris].
          Length = 263

 Score = 59.3 bits (142), Expect = 6e-09
 Identities = 33/101 (32%), Positives = 50/101 (49%), Gaps = 1/101 (0%)
 Frame = +1

Query: 157 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN-DHSF 333
           P V V   +P    +   L C+V   +P  + I+W KNG  V    S  +    N D ++
Sbjct: 115 PTVQVAKSTPFNTKESVMLACYVWGFYPADVTISWRKNGQPVPSHSSALNMAQPNGDWTY 174

Query: 334 LKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPM 456
             +S+L   PS +D Y C VEH G  +P+ + W P + +PM
Sbjct: 175 QTVSHLATTPSYEDTYTCVVEHIGAPEPVCEDWTPGL-SPM 214


  Database: RefSeq49_CP.fasta
    Posted date:  Oct 17, 2011  1:42 PM
  Number of letters in database: 18,874,504
  Number of sequences in database:  33,336
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33336
Number of Hits to DB: 39,373,087
Number of extensions: 930836
Number of successful extensions: 2512
Number of sequences better than 1.0e-05: 20
Number of HSP's gapped: 2498
Number of HSP's successfully gapped: 20
Length of query: 364
Length of database: 18,874,504
Length adjustment: 104
Effective length of query: 260
Effective length of database: 15,407,560
Effective search space: 4005965600
Effective search space used: 4005965600
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)

Search to RefSeqMP_Rel49

BLASTX 2.2.24 [Aug-08-2010]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= ITT01_0086_H05
         (1093 letters)

Database: RefSeq49_MP.fasta 
           30,036 sequences; 15,617,559 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha...   249   3e-66
Alignment   gi|NP_034511.2| histocompatibility 2, class II antigen E alpha ...   183   2e-46
Alignment   gi|NP_032232.2| histocompatibility 2, O region alpha locus [Mus...   179   4e-45
Alignment   gi|NP_034516.3| class II histocompatibility antigen, M alpha ch...    72   6e-13
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...    71   2e-12
Alignment   gi|NP_033865.2| beta-2-microglobulin precursor [Mus musculus].        67   2e-11
Alignment   gi|NP_034512.2| H-2 class II histocompatibility antigen, I-E be...    64   2e-10
Alignment   gi|NP_034517.2| class II histocompatibility antigen, M beta 1 c...    64   3e-10
Alignment   gi|NP_001029150.1| histocompatibility 2, class II antigen E bet...    64   3e-10
Alignment   gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ...    64   3e-10

>ref|NP_034508.2| histocompatibility 2, class II antigen A, alpha precursor [Mus
           musculus].
          Length = 256

 Score =  249 bits (636), Expect = 3e-66
 Identities = 119/185 (64%), Positives = 134/185 (72%)
 Frame = +1

Query: 31  LPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNT 210
           LP F +  S DPQG L+NIA  KHNL +L KRSN+T A N+ P+ TVFPKSPV+LGQPNT
Sbjct: 72  LPEFGQLASFDPQGGLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNT 131

Query: 211 LICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCK 390
           LIC VDNIFPPVINITWL+N  SV +G  ETSF    D+SF K+SYLTF+PSDDD YDCK
Sbjct: 132 LICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCK 191

Query: 391 VEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSR 570
           VEHWGL++P+LKHWEPEIPAPMSELTET                      QGLRSGG SR
Sbjct: 192 VEHWGLEEPVLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTIFIIQGLRSGGTSR 251

Query: 571 HQGSL 585
           H G L
Sbjct: 252 HPGPL 256


>ref|NP_034511.2| histocompatibility 2, class II antigen E alpha precursor [Mus
           musculus].
          Length = 255

 Score =  183 bits (465), Expect = 2e-46
 Identities = 86/148 (58%), Positives = 106/148 (71%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +L  F+KF S + QGAL NIA  K NL+++ +RSNNT   N  PEVTV  +SPV LG+PN
Sbjct: 69  RLEEFAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPN 128

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
            LIC +D   PPV+N+TW +NG  VTEG SET FL ++DH F K  YLTFLPS DDFYDC
Sbjct: 129 ILICFIDKFSPPVVNVTWFRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDC 188

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTE 471
           +V+HWGL++PL KHWE E    + E TE
Sbjct: 189 EVDHWGLEEPLRKHWEFEEKTLLPETTE 216


>ref|NP_032232.2| histocompatibility 2, O region alpha locus [Mus musculus].
          Length = 250

 Score =  179 bits (453), Expect = 4e-45
 Identities = 83/149 (55%), Positives = 108/149 (72%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LP F  F  SD Q  L +I+  K +L+IL++RSN T AV+  P VTV PK+ V LG+PN
Sbjct: 70  RLPEFGDFAHSDFQSGLMSISMIKAHLDILVERSNRTRAVSVPPRVTVLPKTRVELGKPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
            LIC VD+IFPPVIN+TWL+N   +T+G ++TSF S+ +H F K  YLTF+PS +D YDC
Sbjct: 130 VLICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHRFRKFHYLTFVPSAEDVYDC 189

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTET 474
           KVEHWGLD PLL+HWEP++  P  +  ET
Sbjct: 190 KVEHWGLDTPLLQHWEPQVLTPPPDTIET 218


>ref|NP_034516.3| class II histocompatibility antigen, M alpha chain precursor [Mus
           musculus].
          Length = 261

 Score = 72.4 bits (176), Expect = 6e-13
 Identities = 49/158 (31%), Positives = 72/158 (45%), Gaps = 5/158 (3%)
 Frame = +1

Query: 13  NSEEQQLPLFSKFRSSDPQGALRNIATAKHNLNILI-----KRSNNTAAVNQVPEVTVFP 177
           N+   +LP F+++     QG    IA  K    +L+     K          +P   VF 
Sbjct: 76  NTRVPRLPDFAEWAQG--QGDASAIAFDKSFCEMLMREVSPKLEGQIPVSRGLPVAEVFT 133

Query: 178 KSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTF 357
             P+  G+PNTL+C + N+FPP + + W  +   V EG S TS  + +  +F   SYL F
Sbjct: 134 LKPLEFGKPNTLVCFISNLFPPTLTVNWQLHSAPV-EGASPTSISAVDGLTFQAFSYLNF 192

Query: 358 LPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 471
            P   D Y C V H       + +W P+   P S+L E
Sbjct: 193 TPEPFDLYSCTVTHEIDRYTAIAYWVPQNALP-SDLLE 229


>ref|NP_034519.2| histocompatibility 2, O region beta locus [Mus musculus].
          Length = 271

 Score = 70.9 bits (172), Expect = 2e-12
 Identities = 35/99 (35%), Positives = 48/99 (48%)
 Frame = +1

Query: 136 TAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLS 315
           T   N  PEVTV+P+   +L Q N L+C V   +P  I++ W +NG     G   T  + 
Sbjct: 116 TVERNVPPEVTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVR 175

Query: 316 KNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHW 432
             D +F     L  +P   D Y C VEH GL +P+   W
Sbjct: 176 NGDWTFQTTVMLEMIPELGDIYSCLVEHPGLLRPVSVAW 214


>ref|NP_033865.2| beta-2-microglobulin precursor [Mus musculus].
          Length = 119

 Score = 67.4 bits (163), Expect = 2e-11
 Identities = 33/102 (32%), Positives = 57/102 (55%), Gaps = 1/102 (0%)
 Frame = +1

Query: 142 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTE-GFSETSFLSK 318
           A+ + P++ V+ + P   G+PN L C+V    PP I I  LKNG  + +   S+ SF   
Sbjct: 20  AIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSF--S 77

Query: 319 NDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEI 444
            D SF  +++  F P++ D Y C+V+H  + +P   +W+ ++
Sbjct: 78  KDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM 119


>ref|NP_034512.2| H-2 class II histocompatibility antigen, I-E beta chain precursor
           [Mus musculus].
          Length = 264

 Score = 63.9 bits (154), Expect = 2e-10
 Identities = 29/103 (28%), Positives = 48/103 (46%)
 Frame = +1

Query: 157 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 336
           P VTV+P     L   N L+C V + +P  I + W +NG     G   T  +   D +F 
Sbjct: 124 PTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQ 183

Query: 337 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 465
            +  L  +P   + Y C+VEH  L  P+   W+ +  +  +++
Sbjct: 184 TLVMLETVPQSGEVYTCQVEHPSLTDPVTVEWKAQSTSAQNKM 226


>ref|NP_034517.2| class II histocompatibility antigen, M beta 1 chain precursor [Mus
           musculus].
          Length = 261

 Score = 63.5 bits (153), Expect = 3e-10
 Identities = 32/97 (32%), Positives = 47/97 (48%), Gaps = 1/97 (1%)
 Frame = +1

Query: 151 QVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN-DH 327
           + P V V   +P    +P  L C+V   +P  + ITW+KNG  V    ++      N D 
Sbjct: 113 RAPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDW 172

Query: 328 SFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEP 438
           ++  +SYL   PS  D Y C V+H G  +P+   W P
Sbjct: 173 TYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDWTP 209


>ref|NP_001029150.1| histocompatibility 2, class II antigen E beta2 [Mus musculus].
          Length = 287

 Score = 63.5 bits (153), Expect = 3e-10
 Identities = 29/103 (28%), Positives = 47/103 (45%)
 Frame = +1

Query: 157 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 336
           P+VTV+P     L   N L+C V + +P  I + W +NG     G   T  +   D ++ 
Sbjct: 125 PKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNRDWTYQ 184

Query: 337 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 465
            +  L  +P   + Y C+VEH  L  P+   W     +  ++L
Sbjct: 185 TLVMLEMVPRGGEVYTCQVEHPSLTSPVTVEWRARSTSAQNKL 227


>ref|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus musculus].
          Length = 261

 Score = 63.5 bits (153), Expect = 3e-10
 Identities = 32/97 (32%), Positives = 47/97 (48%), Gaps = 1/97 (1%)
 Frame = +1

Query: 151 QVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN-DH 327
           + P V V   +P    +P  L C+V   +P  + ITW+KNG  V    ++      N D 
Sbjct: 113 RAPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDW 172

Query: 328 SFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEP 438
           ++  +SYL   PS  D Y C V+H G  +P+   W P
Sbjct: 173 TYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDWTP 209


  Database: RefSeq49_MP.fasta
    Posted date:  Oct 17, 2011  1:42 PM
  Number of letters in database: 15,617,559
  Number of sequences in database:  30,036
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 30036
Number of Hits to DB: 33,207,832
Number of extensions: 792166
Number of successful extensions: 2208
Number of sequences better than 1.0e-05: 23
Number of HSP's gapped: 2198
Number of HSP's successfully gapped: 23
Length of query: 364
Length of database: 15,617,559
Length adjustment: 103
Effective length of query: 261
Effective length of database: 12,523,851
Effective search space: 3268725111
Effective search space used: 3268725111
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)

Search to RefSeqSP_Rel49

BLASTX 2.2.24 [Aug-08-2010]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= ITT01_0086_H05
         (1093 letters)

Database: RefSeq49_SP.fasta 
           24,897 sequences; 11,343,932 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001123696.1| SLA class II histocompatibility antigen, DQ ...   329   1e-90
Alignment   gi|NP_001107534.2| SLA class II histocompatibility antigen, DQ ...   304   7e-83
Alignment   gi|NP_001172072.1| src-like-adapter [Sus scrofa].                    205   4e-53
Alignment   gi|NP_001107178.1| MHC class II DR-alpha [Sus scrofa].               187   7e-48
Alignment   gi|NP_001004039.1| SLA-DM alpha chain [Sus scrofa].                   74   1e-13
Alignment   gi|NP_001107177.1| major histocompatibility complex, class II, ...    74   1e-13
Alignment   gi|NP_999143.1| beta-2-microglobulin precursor [Sus scrofa].          71   9e-13
Alignment   gi|NP_001107166.1| SLA class II histocompatibility antigen, DQ ...    66   4e-11
Alignment   gi|NP_001107536.2| MHC class II, DO beta [Sus scrofa].                64   1e-10
Alignment   gi|XP_003128397.1| PREDICTED: DLA class II histocompatibility a...    64   2e-10

>ref|NP_001123696.1| SLA class II histocompatibility antigen, DQ haplotype D alpha chain
           precursor [Sus scrofa].
          Length = 255

 Score =  329 bits (844), Expect = 1e-90
 Identities = 162/186 (87%), Positives = 162/186 (87%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           QLPLFSKF S DPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN
Sbjct: 70  QLPLFSKFTSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC
Sbjct: 130 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 189

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPS 567
           KVEHWGLDKPLLKHWEPEIPAPMSELTET                      QGLRSGGPS
Sbjct: 190 KVEHWGLDKPLLKHWEPEIPAPMSELTETVVCALGLIVGLVGIVVGTVFIIQGLRSGGPS 249

Query: 568 RHQGSL 585
           RHQGSL
Sbjct: 250 RHQGSL 255


>ref|NP_001107534.2| SLA class II histocompatibility antigen, DQ haplotype C alpha chain
           precursor [Sus scrofa].
          Length = 254

 Score =  304 bits (778), Expect = 7e-83
 Identities = 151/186 (81%), Positives = 157/186 (84%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LPLFS+F S DPQGALRNIAT KHNLNI+ KRSNNTAAVNQVPEVTVF KSPV+LGQPN
Sbjct: 70  RLPLFSEFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNQVPEVTVFSKSPVILGQPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
           TLICHVD+IFPPVINITWLKNGHSV +GFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC
Sbjct: 130 TLICHVDSIFPPVINITWLKNGHSV-KGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 188

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPS 567
           KVEHWGLDKPLLKHWEPEIPAPMSELTET                      QGL SGGPS
Sbjct: 189 KVEHWGLDKPLLKHWEPEIPAPMSELTETVVCALGLIVGLVGIVVGTVFIIQGLLSGGPS 248

Query: 568 RHQGSL 585
           RHQGSL
Sbjct: 249 RHQGSL 254


>ref|NP_001172072.1| src-like-adapter [Sus scrofa].
          Length = 250

 Score =  205 bits (521), Expect = 4e-53
 Identities = 94/149 (63%), Positives = 113/149 (75%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +LP FS F   DPQ  LR IA  + +L++L++RSN+T A N  P VTV PKSPV LGQPN
Sbjct: 70  RLPEFSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPN 129

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
            LIC VDNIFPPVINITWL NG +VTEG ++TSF ++ DHSF K  YLTF+PS  DFYDC
Sbjct: 130 VLICIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDC 189

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTET 474
           KVEHWGLD+PL  HWEP++  P+ + TET
Sbjct: 190 KVEHWGLDEPLFTHWEPQVTMPLPDTTET 218


>ref|NP_001107178.1| MHC class II DR-alpha [Sus scrofa].
          Length = 252

 Score =  187 bits (476), Expect = 7e-48
 Identities = 94/186 (50%), Positives = 110/186 (59%)
 Frame = +1

Query: 28  QLPLFSKFRSSDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 207
           +L  F  F S + QGAL NIA  K NL ILIKRSNNT   N  PEVTV    PV LG+PN
Sbjct: 67  RLEEFGHFASFEAQGALANIAVDKANLEILIKRSNNTPNTNVPPEVTVLSDKPVELGEPN 126

Query: 208 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 387
            LIC +D   PPV+N+TWL+NG  VT G SET FL + DH F K  YL F+PS +D YDC
Sbjct: 127 ILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDC 186

Query: 388 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXQGLRSGGPS 567
           +VEHWGLDKPLLKHWE E   P+ E TE                       +G+R G  +
Sbjct: 187 QVEHWGLDKPLLKHWEFEAQTPLPETTENTVCALGLIVALVGIIVGTVLIIKGVRKGNAT 246

Query: 568 RHQGSL 585
             +G L
Sbjct: 247 ERRGPL 252


>ref|NP_001004039.1| SLA-DM alpha chain [Sus scrofa].
          Length = 260

 Score = 73.9 bits (180), Expect = 1e-13
 Identities = 38/106 (35%), Positives = 56/106 (52%)
 Frame = +1

Query: 154 VPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSF 333
           +P   VF   P+  G+PNTL+C V N+FPP + +TW ++  +  EG   T   + +D SF
Sbjct: 126 LPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTW-EHHSAPVEGIGPTFVSATDDLSF 184

Query: 334 LKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 471
              SYL F P+  D + C V H       + +W P+   P S+L E
Sbjct: 185 QAFSYLNFTPTPSDLFSCVVTHELDGYVAISYWVPQNALP-SDLLE 229


>ref|NP_001107177.1| major histocompatibility complex, class II, DO alpha [Sus scrofa].
          Length = 260

 Score = 73.9 bits (180), Expect = 1e-13
 Identities = 38/106 (35%), Positives = 56/106 (52%)
 Frame = +1

Query: 154 VPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSF 333
           +P   VF   P+  G+PNTL+C V N+FPP + +TW ++  +  EG   T   + +D SF
Sbjct: 126 LPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTW-EHHSAPVEGIGPTFVSATDDLSF 184

Query: 334 LKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 471
              SYL F P+  D + C V H       + +W P+   P S+L E
Sbjct: 185 QAFSYLNFTPTPSDLFSCVVTHELDGYVAISYWVPQNALP-SDLLE 229


>ref|NP_999143.1| beta-2-microglobulin precursor [Sus scrofa].
          Length = 118

 Score = 71.2 bits (173), Expect = 9e-13
 Identities = 38/98 (38%), Positives = 53/98 (54%)
 Frame = +1

Query: 142 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 321
           AV + P+V V+ + P   G+PN L C+V    PP I I  LKNG  +    S+ SF    
Sbjct: 20  AVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SK 77

Query: 322 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 435
           D SF  + +  F P+  D Y C+V+H  LDKP +  W+
Sbjct: 78  DWSFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 115


>ref|NP_001107166.1| SLA class II histocompatibility antigen, DQ haplotype C beta chain
           precursor [Sus scrofa].
          Length = 261

 Score = 65.9 bits (159), Expect = 4e-11
 Identities = 34/123 (27%), Positives = 51/123 (41%)
 Frame = +1

Query: 97  KHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGH 276
           KHN  I       T      P VT+ P     L   N L+C V + +P  + + W +NG 
Sbjct: 112 KHNYQI---EEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQ 168

Query: 277 SVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPM 456
             T G   T  +   D ++  +  L       D Y C+VEH  L  P+L  W  +  +  
Sbjct: 169 EETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQNPILVEWRAQSESAQ 228

Query: 457 SEL 465
           S++
Sbjct: 229 SKM 231


>ref|NP_001107536.2| MHC class II, DO beta [Sus scrofa].
          Length = 277

 Score = 63.9 bits (154), Expect = 1e-10
 Identities = 33/103 (32%), Positives = 45/103 (43%)
 Frame = +1

Query: 157 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 336
           PEVTV P+    L   N L+C V   +P  I I W +NG    EG   T  +   D +F 
Sbjct: 136 PEVTVHPERTPSLQLRNLLLCSVTGFYPGAIEIRWFRNGQEQREGVLATGLIRNGDWTFQ 195

Query: 337 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 465
            +  L   P   D Y C V+H  L  P+   W  +     ++L
Sbjct: 196 TVVMLEMTPELGDVYTCLVDHPSLLSPVSVEWRAQSDCSWTKL 238


>ref|XP_003128397.1| PREDICTED: DLA class II histocompatibility antigen, DR-1 beta
           chain-like [Sus scrofa].
          Length = 321

 Score = 63.5 bits (153), Expect = 2e-10
 Identities = 28/95 (29%), Positives = 42/95 (44%)
 Frame = +1

Query: 157 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 336
           P VTV+P     L   N L+C V   +P  + + W +NG     G   T  +   D +F 
Sbjct: 126 PTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQ 185

Query: 337 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPE 441
            +  L  +P   + Y C+VEH  L  P+   W  +
Sbjct: 186 TMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRAQ 220


  Database: RefSeq49_SP.fasta
    Posted date:  Oct 17, 2011  1:42 PM
  Number of letters in database: 11,343,932
  Number of sequences in database:  24,897
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24897
Number of Hits to DB: 24,485,790
Number of extensions: 608541
Number of successful extensions: 1513
Number of sequences better than 1.0e-05: 27
Number of HSP's gapped: 1499
Number of HSP's successfully gapped: 27
Length of query: 364
Length of database: 11,343,932
Length adjustment: 100
Effective length of query: 264
Effective length of database: 8,854,232
Effective search space: 2337517248
Effective search space used: 2337517248
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)

Search to Sscrofa10_2

BLASTN 2.2.24 [Aug-08-2010]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= ITT01_0086_H05
         (1093 letters)

Database: Sscrofa_10.2.fasta 
           4582 sequences; 2,808,509,378 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Sscrofa_Chr07                                                         628   e-177

>Sscrofa_Chr07 
||          Length = 134764511

 Score =  628 bits (317), Expect = e-177
 Identities = 333/341 (97%)
 Strand = Plus / Plus

                                                                            
Query: 728      ggaacttaaggtgctgtgtcatctcagaattcatatgcccttggaatcctcttcctgacc 787
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29170461 ggaacttaaggtgctgtgtcatctcagaattcatatgcccttggaatcctcttcctgacc 29170520

                                                                            
Query: 788      ttctaggnnnnnnnncttttctcagttgttacctgttatgggatctctgagatatcccac 847
                |||||||        |||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29170521 ttctaggttttttttcttttctcagttgttacctgttatgggatctctgagatatcccac 29170580

                                                                            
Query: 848      tcggctacctgatccctcagtgaccctaaactaatatgtacatggaaacaataaatcact 907
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29170581 tcggctacctgatccctcagtgaccctaaactaatatgtacatggaaacaataaatcact 29170640

                                                                            
Query: 908      tcatgaggtttttgtactgaattctttcctgtctttcatctcaaggctgactaggaccat 967
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29170641 tcatgaggtttttgtactgaattctttcctgtctttcatctcaaggctgactaggaccat 29170700

                                                                            
Query: 968      ggtctcttgcacttcaggcccatttaatctcatttcccaggttatgcttcatgcccagta 1027
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29170701 ggtctcttgcacttcaggcccatttaatctcatttcccaggttatgcttcatgcccagta 29170760

                                                         
Query: 1028     acacaggagaagcatgtatagactgacaataaatattttgc 1068
                |||||||||||||||||||||||||||||||||||||||||
Sbjct: 29170761 acacaggagaagcatgtatagactgacaataaatattttgc 29170801



 Score =  559 bits (282), Expect = e-156
 Identities = 282/282 (100%)
 Strand = Plus / Plus

                                                                            
Query: 152      aggttcctgaggtgactgtgtttcccaagtctccagtgatgctgggtcagcccaacaccc 211
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29169480 aggttcctgaggtgactgtgtttcccaagtctccagtgatgctgggtcagcccaacaccc 29169539

                                                                            
Query: 212      tcatctgtcatgtggacaacatctttcctcctgtgatcaacatcacgtggttgaagaacg 271
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29169540 tcatctgtcatgtggacaacatctttcctcctgtgatcaacatcacgtggttgaagaacg 29169599

                                                                            
Query: 272      ggcactctgtcacagaaggtttttctgagaccagcttcctctccaaaaatgatcattcct 331
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29169600 ggcactctgtcacagaaggtttttctgagaccagcttcctctccaaaaatgatcattcct 29169659

                                                                            
Query: 332      tcctcaagatcagttatctcaccttcctcccttctgatgatgatttttatgactgcaaag 391
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29169660 tcctcaagatcagttatctcaccttcctcccttctgatgatgatttttatgactgcaaag 29169719

                                                          
Query: 392      tggagcactggggcctggataagccacttctgaaacactggg 433
                ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29169720 tggagcactggggcctggataagccacttctgaaacactggg 29169761



 Score =  345 bits (174), Expect = 3e-92
 Identities = 177/178 (99%)
 Strand = Plus / Plus

                                                                            
Query: 433      gaacctgagattccagcccccatgtcagagctgacagagacagtggtctgcgccctggga 492
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29170000 gaacctgagattccagcccccatgtcagagctgacagagacagtggtctgcgccctggga 29170059

                                                                            
Query: 493      ttgatcgtgggccttgtgggcatcgtggtgggcactgtcttcatcattcaaggcctgcgc 552
                |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
Sbjct: 29170060 ttgatcgtgggccttgtgggcatcgtggtgggcactgtcttcatcattcaaggcctacgc 29170119

                                                                          
Query: 553      tcaggtggtccctctagacaccaagggtccttgtgagtcacactccagaagggaaggt 610
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29170120 tcaggtggtccctctagacaccaagggtccttgtgagtcacactccagaagggaaggt 29170177



 Score =  238 bits (120), Expect = 5e-60
 Identities = 123/124 (99%)
 Strand = Plus / Plus

                                                                            
Query: 28       cagctgcctctgtttagcaaatttagaagttctgacccacagggtgcactgaggaacata 87
                ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||
Sbjct: 29168905 cagctgcctctgtttagcaaatttagaagttttgacccacagggtgcactgaggaacata 29168964

                                                                            
Query: 88       gctacggcaaaacataatttgaacatcctgattaaacgttccaacaacaccgcggctgtc 147
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29168965 gctacggcaaaacataatttgaacatcctgattaaacgttccaacaacaccgcggctgtc 29169024

                    
Query: 148      aatc 151
                ||||
Sbjct: 29169025 aatc 29169028



 Score =  165 bits (83), Expect = 6e-38
 Identities = 83/83 (100%)
 Strand = Plus / Plus

                                                                            
Query: 607      aggtgcactgcccgcctacaagagctgaagagtggatgtgctcaacgacctagaactatt 666
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29170340 aggtgcactgcccgcctacaagagctgaagagtggatgtgctcaacgacctagaactatt 29170399

                                       
Query: 667      ttctggccaaattcatcatatac 689
                |||||||||||||||||||||||
Sbjct: 29170400 ttctggccaaattcatcatatac 29170422



 Score = 65.9 bits (33), Expect = 4e-08
 Identities = 33/33 (100%)
 Strand = Plus / Plus

                                                 
Query: 1        tcattgctctacaactccgaagagcaacagctg 33
                |||||||||||||||||||||||||||||||||
Sbjct: 29164978 tcattgctctacaactccgaagagcaacagctg 29165010



 Score = 63.9 bits (32), Expect = 2e-07
 Identities = 32/32 (100%)
 Strand = Plus / Minus

                                                
Query: 379      tatgactgcaaagtggagcactggggcctgga 410
                ||||||||||||||||||||||||||||||||
Sbjct: 29547115 tatgactgcaaagtggagcactggggcctgga 29547084


  Database: Sscrofa_10.2.fasta
    Posted date:  Nov 16, 2011 10:34 AM
  Number of letters in database: 2,808,509,378
  Number of sequences in database:  4582
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Sequences: 4582
Number of Hits to DB: 32,621,837
Number of extensions: 210
Number of successful extensions: 210
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 210
Number of HSP's successfully gapped: 8
Length of query: 1093
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 1072
Effective length of database: 2,808,413,156
Effective search space: 3010618903232
Effective search space used: 3010618903232
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 50 (99.1 bits)
S1: 18 (36.2 bits)
S2: 30 (60.0 bits)