BLASTX 2.2.10 [Oct-19-2004]
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= 20060611S-062187
(996 letters)
Database: RefSeqSP
1040 sequences; 434,620 total letters
Searching...done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_999143.1| beta 2-microglobulin [Sus scrofa] 44 6e-06
>ref|NP_999143.1| beta 2-microglobulin [Sus scrofa]
Length = 118
Score = 43.9 bits (102), Expect = 6e-06
Identities = 23/71 (32%), Positives = 37/71 (52%)
Frame = +2
Query: 485 NLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNGNWTYQVLVMLKMNLQRGDVYT 664
N L C + F+P Q++ +NG+K A L + +W++ +LV + D Y+
Sbjct: 41 NYLNCYVSGFHPPQIEIDLLKNGEKMNAE--QSDLSFSKDWSFYLLVHTEFTPNAVDQYS 98
Query: 665 CRVEHSTLQNP 697
CRV+H TL P
Sbjct: 99 CRVKHVTLDKP 109
Database: RefSeqSP
Posted date: Aug 1, 2006 7:14 PM
Number of letters in database: 434,620
Number of sequences in database: 1040
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 Hits to DB: 1,045,508
Number of Sequences: 1040
Number of extensions: 31205
Number of successful extensions: 200
Number of sequences better than 1.0e-05: 1
Number of HSP's better than 0.0 without gapping: 112
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 168
length of database: 434,620
effective HSP length: 77
effective length of database: 354,540
effective search space used: 90053160
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
Search to RefSeqBP
BLASTX 2.2.10 [Oct-19-2004]
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= 20060611S-062187
(996 letters)
Database: RefSeqBP
33,508 sequences; 16,112,626 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001029840.2| MHC class II antigen [Bos taurus] 247 1e-65
Alignment gi|NP_001012694.1| major histocompatibility complex, class II, ... 243 2e-64
Alignment gi|NP_001012697.1| major histocompatibility complex, class II, ... 177 1e-44
Alignment gi|NP_001012698.2| major histocompatibility complex, class II, ... 176 3e-44
Alignment gi|XP_582099.2| PREDICTED: similar to major histocompatibility ... 161 8e-40
Alignment gi|NP_001013618.1| major histocompatibility complex, class II, ... 157 9e-39
Alignment gi|XP_876139.1| PREDICTED: similar to H-2 class II histocompati... 149 3e-36
Alignment gi|XP_874766.1| PREDICTED: similar to HLA class II histocompati... 98 1e-20
Alignment gi|NP_001012399.1| hemochromatosis [Bos taurus] 57 2e-08
Alignment gi|NP_001035571.1| major histocompatibility complex, class II, ... 54 2e-07
>ref|NP_001029840.2| MHC class II antigen [Bos taurus]
Length = 261
Score = 247 bits (630), Expect = 1e-65
Identities = 125/219 (57%), Positives = 159/219 (72%)
Frame = +2
Query: 53 MSGMGALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVA 232
MSGM AL P+GL TA + V L L PG EG++SP+DFV F YF N T RVR V
Sbjct: 1 MSGMVALWIPRGLWTAVVMVTLVMLSTPGAEGRDSPKDFVVQFKGLCYFTNGTERVRYVT 60
Query: 233 RGVYNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKG 412
R +YNQ+E+V F+S+ +R TPLGRP Y N QKDFL Q R + + VC+ NYQ +
Sbjct: 61 RYIYNQEEYVRFDSDWDLYRALTPLGRPDAEYWNSQKDFLEQTRAEADTVCRHNYQAELI 120
Query: 413 PTLHRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLI 592
+L R+V+PTVTISPS+ +AL HNLLVC+ T+FYP+Q+K + FRN ++ETAG VS PLI
Sbjct: 121 TSLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLI 180
Query: 593 RNGNWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILGE 709
RNG+WT+Q+LVML+M QRGDVYTC VEH +LQ+PI+ E
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPIMVE 219
>ref|NP_001012694.1| major histocompatibility complex, class II, DQ beta [Bos taurus]
Length = 261
Score = 243 bits (620), Expect = 2e-64
Identities = 123/216 (56%), Positives = 157/216 (72%)
Frame = +2
Query: 53 MSGMGALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVA 232
MSGM ALR P+GL TAA+ V L L PG EG++SPQD V HF + YF N T RVR V
Sbjct: 1 MSGMVALRIPRGLWTAAVMVTLAVLSTPGAEGRDSPQDTVVHFMGQCYFTNGTERVRYVT 60
Query: 233 RGVYNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKG 412
R +YNQ+E ++S+VG +R T LGR Y N QKD L Q R + + VC+ NYQ++
Sbjct: 61 RYIYNQEETAYYDSDVGEYRAVTQLGRTLAEYWNSQKDILEQTRAELDTVCRHNYQLEVI 120
Query: 413 PTLHRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLI 592
+L RQV+PTVTIS S+ +AL HNLLVC+ T+FYP Q+K + F+NG++ETAG VS PLI
Sbjct: 121 TSLQRQVEPTVTISLSRTEALNHHNLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPLI 180
Query: 593 RNGNWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPI 700
RNG+WT+Q+LVML+M +RGDVYTC VEH +LQ+PI
Sbjct: 181 RNGDWTFQILVMLEMTPKRGDVYTCHVEHPSLQSPI 216
>ref|NP_001012697.1| major histocompatibility complex, class II, DY beta [Bos taurus]
Length = 259
Score = 177 bits (449), Expect = 1e-44
Identities = 92/195 (47%), Positives = 127/195 (65%)
Frame = +2
Query: 125 LGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGVYNQKEHVPFNSNVGNFRGGTP 304
L P +++P++FVY F YF N T VR VAR +YN++E + F+S++G F T
Sbjct: 23 LRIPEAHCRDAPKNFVYQFKGMCYFTNGTEHVRLVARQIYNKEEILHFDSDLGEFVAVTE 82
Query: 305 LGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTLHRQVQPTVTISPSKAKALTPH 484
LGR N QKD L + R + +C+ NY+ G T+ R+V+PTVT+SP+ +AL H
Sbjct: 83 LGRVCAEIWNTQKDLLAEFRAYVDTLCRHNYKETAGFTVQRRVEPTVTVSPASTEALNHH 142
Query: 485 NLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNGNWTYQVLVMLKMNLQRGDVYT 664
NLLVC+ T+FYP QVK + FRN Q++TAG PL +NG+WTYQ+ VML+ Q GDVY
Sbjct: 143 NLLVCSVTDFYPRQVKVKWFRNQQEQTAGVGFTPLTQNGDWTYQIHVMLETVPQLGDVYV 202
Query: 665 CRVEHSTLQNPILGE 709
C V+H +LQ+PI E
Sbjct: 203 CHVDHPSLQSPITVE 217
>ref|NP_001012698.2| major histocompatibility complex, class II, DRB3 [Bos taurus]
Length = 266
Score = 176 bits (446), Expect = 3e-44
Identities = 96/216 (44%), Positives = 132/216 (61%)
Frame = +2
Query: 62 MGALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGV 241
M L F G AAL VML L P + F+ ++ + +FFN T RVR + R
Sbjct: 1 MVCLYFSGGSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKGECHFFNGTERVRFLDRHF 60
Query: 242 YNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTL 421
YN +E V F+S+ G FR T LGRP + N QKDFL QKR + + VC+ NY + T+
Sbjct: 61 YNGEEFVRFDSDWGEFRAVTELGRPAAEHWNSQKDFLEQKRAEVDRVCRHNYGGVESFTV 120
Query: 422 HRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNG 601
R+V+PTVT+ P+K + L HNLLVC+ FYP ++ + FRNG +E AG +S LI+NG
Sbjct: 121 QRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFYPGHIEVRWFRNGHEEEAGVISTGLIQNG 180
Query: 602 NWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILGE 709
+WT+Q +VML+ Q G+VYTC+V+H +PI E
Sbjct: 181 DWTFQTMVMLETVPQSGEVYTCQVDHPKRTSPITVE 216
>ref|XP_582099.2| PREDICTED: similar to major histocompatibility complex, class II,
DR beta 5 precursor [Bos taurus]
Length = 255
Score = 161 bits (407), Expect = 8e-40
Identities = 86/204 (42%), Positives = 122/204 (59%)
Frame = +2
Query: 98 AALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGVYNQKEHVPFNSN 277
AAL V+L L P + + F++ F + F N R+R AR +YN +E V F+S+
Sbjct: 2 AALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQEDVHFDSD 61
Query: 278 VGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTLHRQVQPTVTISP 457
VG F T LGR Y N QKDF+ Q R K + +C+ NYQ R+V+PTVT+ P
Sbjct: 62 VGEFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCRSNYQGIGSFLRQRRVEPTVTVYP 121
Query: 458 SKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNGNWTYQVLVMLKM 637
+K + L HNLLVC+ FYP ++ + F N +E AG +S LI+NG+WT+Q +VML+
Sbjct: 122 AKTQPLQHHNLLVCSVNGFYPGHIEVRWFWNSHEEEAGVISTGLIQNGDWTFQTMVMLET 181
Query: 638 NLQRGDVYTCRVEHSTLQNPILGE 709
Q G+VYTC+VEH + +P+ E
Sbjct: 182 VPQSGEVYTCQVEHPSRTSPLTVE 205
>ref|NP_001013618.1| major histocompatibility complex, class II, DO beta [Bos taurus]
Length = 271
Score = 157 bits (398), Expect = 9e-39
Identities = 80/192 (41%), Positives = 117/192 (60%)
Frame = +2
Query: 125 LGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGVYNQKEHVPFNSNVGNFRGGTP 304
L A +G++SP+DFV YF N T +VR V R ++N +++ F+S++G F T
Sbjct: 19 LDASVTQGRDSPEDFVTQAKADCYFTNGTEKVRFVVRFIFNLEDYARFDSDLGMFVALTE 78
Query: 305 LGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTLHRQVQPTVTISPSKAKALTPH 484
LG+P N + D L + R + +C+ NY + T+ R+VQP VT+ P K AL
Sbjct: 79 LGKPDAERWNNRPDILARSRASVDMLCRRNYYLGAPFTVGRRVQPEVTVYPEKTPALQHR 138
Query: 485 NLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNGNWTYQVLVMLKMNLQRGDVYT 664
NLL+C T FYP +K FRNGQ++ G +S LIRNG+WT+Q+ VML M + G+VYT
Sbjct: 139 NLLLCLVTGFYPGDIKVTWFRNGQEQREGIMSTGLIRNGDWTFQMTVMLAMTPELGEVYT 198
Query: 665 CRVEHSTLQNPI 700
C V+H +L +P+
Sbjct: 199 CLVDHPSLLSPV 210
>ref|XP_876139.1| PREDICTED: similar to H-2 class II histocompatibility antigen, I-E
beta chain precursor [Bos taurus]
Length = 269
Score = 149 bits (377), Expect = 3e-36
Identities = 75/172 (43%), Positives = 107/172 (62%)
Frame = +2
Query: 194 YFFNETHRVRGVARGVYNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKG 373
+F N T +VR + R +YN++E V F+S VG +R T +GRP N L + R
Sbjct: 9 HFSNGTQQVRFLDRYIYNREEQVQFDSLVGEYRARTEMGRPAAERWNRWPQALQRARAAV 68
Query: 374 NPVCKPNYQIKKGPTLHRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNG 553
+ C NY+ T+ R+VQPTVT+ P K++ L HNLLVC+ FYP ++ + FRNG
Sbjct: 69 HAYCASNYEFFASRTVQRRVQPTVTVYPVKSRPLWHHNLLVCSVNGFYPGHIEVRWFRNG 128
Query: 554 QKETAGFVSPPLIRNGNWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILGE 709
Q+E AG VS LI NG+WT+Q++VML++ Q G+VY C VEH + +P+ E
Sbjct: 129 QEEEAGVVSTGLIPNGDWTFQIMVMLEIVPQGGEVYACHVEHPSRTSPVTVE 180
>ref|XP_874766.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DRB1-7 beta chain precursor (MHC class I antigen DRB1*7)
(DR-7) (DR7) [Bos taurus]
Length = 347
Score = 97.8 bits (242), Expect = 1e-20
Identities = 45/98 (45%), Positives = 70/98 (71%)
Frame = +2
Query: 416 TLHRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIR 595
TL ++V+PTVT+ P+K + L ++LLVC+ FY V+ + F GQ+E AG +S LI+
Sbjct: 90 TLQKKVEPTVTVYPAKTQPLQHNHLLVCSVNGFYLGHVEVRWFWKGQEEEAGVISTGLIQ 149
Query: 596 NGNWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILGE 709
NG+WT++ +VML+ LQ G+VYTC++EH + ++PI E
Sbjct: 150 NGDWTFETIVMLETVLQSGEVYTCQLEHPSWRSPIAEE 187
>ref|NP_001012399.1| hemochromatosis [Bos taurus]
Length = 356
Score = 57.0 bits (136), Expect = 2e-08
Identities = 47/175 (26%), Positives = 75/175 (42%), Gaps = 5/175 (2%)
Frame = +2
Query: 191 GYFFNETHRVRGVARGVYNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPK 370
G E + RG + Y+ ++H+ F ++R P + T K Q R
Sbjct: 131 GCELQEDNSTRGFWKYGYDGQDHLEFRPETLDWRAAEPRAQVTKLEWEVNKIRAKQNRAY 190
Query: 371 GNPVCKPNY----QIKKGPTLHRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQ 538
+ C ++ +GP L +QV P V ++ +LT L C NFYP + +
Sbjct: 191 LDRDCPEQLLHLLELGRGP-LEQQVPPLVKVTHHVTSSLTT---LRCRALNFYPQNITIR 246
Query: 539 GFRNGQKETAGFVSPP-LIRNGNWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPI 700
++ Q A + P ++ NG+ TYQ V L M Y+C+VEH L P+
Sbjct: 247 WLKDKQFLDAKEIKPEDVLPNGDGTYQAWVALAMLPGEEQRYSCQVEHPGLDQPL 301
>ref|NP_001035571.1| major histocompatibility complex, class II, DM beta-chain,
expressed [Bos taurus]
Length = 262
Score = 53.5 bits (127), Expect = 2e-07
Identities = 43/135 (31%), Positives = 57/135 (42%), Gaps = 1/135 (0%)
Frame = +2
Query: 347 FLNQKRPKGNPVCKPNYQIKKGPTLHRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQ 526
+L Q+ G C + Q HR PTV ++ + +L C FYP
Sbjct: 85 YLIQRLSNGLQNCAAHTQPFWSSLTHRTRPPTVQVAKTTPFNTRESVMLACYVWGFYPAD 144
Query: 527 VKFQGFRNGQKETAGFVSPPLIR-NGNWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPIL 703
V RNGQ+ + +I+ NG+WTYQ + L GD YTC VEH IL
Sbjct: 145 VAITWRRNGQEVLPHGRAWRIIQPNGDWTYQTVSHLATTPSFGDTYTCVVEHIGAPELIL 204
Query: 704 GECGHILNLPKQNAK 748
+ L LP Q K
Sbjct: 205 QDWTPGL-LPAQTVK 218
Database: RefSeqBP
Posted date: Aug 1, 2006 7:14 PM
Number of letters in database: 16,112,626
Number of sequences in database: 33,508
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 Hits to DB: 39,839,459
Number of Sequences: 33508
Number of extensions: 1254272
Number of successful extensions: 7032
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 4447
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 6482
length of database: 16,112,626
effective HSP length: 102
effective length of database: 12,694,810
effective search space used: 2907111490
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
Search to RefSeqHP
BLASTX 2.2.10 [Oct-19-2004]
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= 20060611S-062187
(996 letters)
Database: RefSeqHP
39,411 sequences; 17,774,539 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_002114.2| major histocompatibility complex, class II, DQ ... 246 3e-65
Alignment gi|NP_872355.1| major histocompatibility complex, class II, DQ ... 228 6e-60
Alignment gi|NP_002112.3| major histocompatibility complex, class II, DP ... 191 6e-49
Alignment gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati... 190 1e-48
Alignment gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati... 190 1e-48
Alignment gi|NP_002115.1| major histocompatibility complex, class II, DR ... 188 7e-48
Alignment gi|NP_002116.2| major histocompatibility complex, class II, DR ... 179 2e-45
Alignment gi|NP_068818.4| major histocompatibility complex, class II, DR ... 179 4e-45
Alignment gi|XP_949915.1| PREDICTED: similar to HLA class II histocompati... 178 6e-45
Alignment gi|NP_072049.2| major histocompatibility complex, class II, DR ... 168 8e-42
>ref|NP_002114.2| major histocompatibility complex, class II, DQ beta 1 precursor
[Homo sapiens]
Length = 261
Score = 246 bits (627), Expect = 3e-65
Identities = 125/219 (57%), Positives = 156/219 (71%)
Frame = +2
Query: 53 MSGMGALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVA 232
MS ALR P GL A +T+ML L P EG++SP+DFVY F YF N T RVR V+
Sbjct: 1 MSWKKALRIPGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVS 60
Query: 233 RGVYNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKG 412
R +YN++E V F+S+VG FR T LG P Y N QKD L +KR + VC+ NYQ++
Sbjct: 61 RSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELR 120
Query: 413 PTLHRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLI 592
TL R+V+PTVTISPS+ +AL HNLLVC+ T+FYP Q+K + FRN Q+ETAG VS PLI
Sbjct: 121 TTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLI 180
Query: 593 RNGNWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILGE 709
RNG+WT+Q+LVML+M QRGDVYTC VEH +LQ+PI E
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVE 219
>ref|NP_872355.1| major histocompatibility complex, class II, DQ beta 2 [Homo
sapiens]
Length = 231
Score = 228 bits (581), Expect = 6e-60
Identities = 118/219 (53%), Positives = 154/219 (70%)
Frame = +2
Query: 53 MSGMGALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVA 232
MS AL+ P G AA+TVML L P E ++ P+DF+ F YF N T RVRGVA
Sbjct: 1 MSWKMALQIPGGFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVRGVA 60
Query: 233 RGVYNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKG 412
R +YN++E+ F+S+VG F+ T LGR ++ N KDFL Q+R + VC+ NY+ +
Sbjct: 61 RYIYNREEYGRFDSDVGEFQAVTELGRSIEDW-NNYKDFLEQERAAVDKVCRHNYEAELR 119
Query: 413 PTLHRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLI 592
TL RQV+PTVTISPS+ +AL HNLLVC+ T+FYP Q+K Q FRN Q+ETAG VS LI
Sbjct: 120 TTLQRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVQWFRNDQEETAGVVSTSLI 179
Query: 593 RNGNWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILGE 709
RNG+WT+Q+LVML++ QRGD+YTC+VEH +LQ+PI E
Sbjct: 180 RNGDWTFQILVMLEITPQRGDIYTCQVEHPSLQSPITVE 218
>ref|NP_002112.3| major histocompatibility complex, class II, DP beta 1 precursor
[Homo sapiens]
Length = 258
Score = 191 bits (486), Expect = 6e-49
Identities = 98/205 (47%), Positives = 137/205 (66%)
Frame = +2
Query: 95 TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGVYNQKEHVPFNS 274
T ALT +L L V+G+ +P+++++ + Y FN T R + R +YN++E F+S
Sbjct: 12 TVALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQRF--LERYIYNREEFARFDS 69
Query: 275 NVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTLHRQVQPTVTIS 454
+VG FR T LGRP Y N QKD L +KR + +C+ NY++ TL R+VQP V +S
Sbjct: 70 DVGEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPMTLQRRVQPRVNVS 129
Query: 455 PSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNGNWTYQVLVMLK 634
PSK L HNLLVC T+FYP ++ + F NGQ+ETAG VS LIRNG+WT+Q+LVML+
Sbjct: 130 PSKKGPLQHHNLLVCHVTDFYPGSIQVRWFLNGQEETAGVVSTNLIRNGDWTFQILVMLE 189
Query: 635 MNLQRGDVYTCRVEHSTLQNPILGE 709
M Q+GDVYTC+VEH++L +P+ E
Sbjct: 190 MTPQQGDVYTCQVEHTSLDSPVTVE 214
>ref|XP_945926.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DRB1-9 beta chain precursor (MHC class I antigen DRB1*9)
(DR-9) (DR9) isoform 1 [Homo sapiens]
Length = 266
Score = 190 bits (483), Expect = 1e-48
Identities = 98/216 (45%), Positives = 141/216 (65%)
Frame = +2
Query: 62 MGALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGV 241
M L+ P G AALTV L L +P ++ F+ F+ +FFN T RVR + RG+
Sbjct: 1 MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60
Query: 242 YNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTL 421
YNQ+E+V F+S+VG +R T LGRP N QKDFL ++R + + VC+ NY + + T+
Sbjct: 61 YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120
Query: 422 HRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNG 601
R+V P VT+ P+K + L HNLLVC+ + FYP ++ + FRNGQ+E AG VS LI+NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 602 NWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILGE 709
+WT+Q LVML+ + G+VYTC+VEH ++ +P+ E
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVE 216
>ref|XP_949921.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DRB1-9 beta chain precursor (MHC class I antigen DRB1*9)
(DR-9) (DR9) isoform 3 [Homo sapiens]
Length = 325
Score = 190 bits (483), Expect = 1e-48
Identities = 98/216 (45%), Positives = 141/216 (65%)
Frame = +2
Query: 62 MGALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGV 241
M L+ P G AALTV L L +P ++ F+ F+ +FFN T RVR + RG+
Sbjct: 1 MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60
Query: 242 YNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTL 421
YNQ+E+V F+S+VG +R T LGRP N QKDFL ++R + + VC+ NY + + T+
Sbjct: 61 YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120
Query: 422 HRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNG 601
R+V P VT+ P+K + L HNLLVC+ + FYP ++ + FRNGQ+E AG VS LI+NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 602 NWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILGE 709
+WT+Q LVML+ + G+VYTC+VEH ++ +P+ E
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVE 216
>ref|NP_002115.1| major histocompatibility complex, class II, DR beta 1 precursor
[Homo sapiens]
Length = 266
Score = 188 bits (477), Expect = 7e-48
Identities = 97/216 (44%), Positives = 138/216 (63%)
Frame = +2
Query: 62 MGALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGV 241
M L+ P G ALTV L L +P ++ F++ F+ +FFN T RVR + R +
Sbjct: 1 MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCI 60
Query: 242 YNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTL 421
YNQ+E V F+S+VG +R T LGRP Y N QKD L Q+R + C+ NY + + T+
Sbjct: 61 YNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTV 120
Query: 422 HRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNG 601
R+V+P VT+ PSK + L HNLLVC+ + FYP ++ + FRNGQ+E AG VS LI+NG
Sbjct: 121 QRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 602 NWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILGE 709
+WT+Q LVML+ + G+VYTC+VEH ++ +P+ E
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVE 216
>ref|NP_002116.2| major histocompatibility complex, class II, DR beta 5 precursor
[Homo sapiens]
Length = 266
Score = 179 bits (455), Expect = 2e-45
Identities = 92/216 (42%), Positives = 135/216 (62%)
Frame = +2
Query: 62 MGALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGV 241
M L+ P G A LTV L L +P ++ F+ ++ +FFN T RVR + R +
Sbjct: 1 MVCLKLPGGSYMAKLTVTLMVLSSPLALAGDTRPRFLQQDKYECHFFNGTERVRFLHRDI 60
Query: 242 YNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTL 421
YNQ+E + F+S+VG +R T LGRP Y N QKDFL +R + C+ NY + + T+
Sbjct: 61 YNQEEDLRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAAVDTYCRHNYGVGESFTV 120
Query: 422 HRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNG 601
R+V+P VT+ P++ + L HNLLVC+ FYP ++ + FRN Q+E AG VS LI+NG
Sbjct: 121 QRRVEPKVTVYPARTQTLQHHNLLVCSVNGFYPGSIEVRWFRNSQEEKAGVVSTGLIQNG 180
Query: 602 NWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILGE 709
+WT+Q LVML+ + G+VYTC+VEH ++ +P+ E
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVE 216
>ref|NP_068818.4| major histocompatibility complex, class II, DR beta 4 precursor
[Homo sapiens]
Length = 266
Score = 179 bits (453), Expect = 4e-45
Identities = 91/213 (42%), Positives = 134/213 (62%)
Frame = +2
Query: 62 MGALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGV 241
M L+ P G AALTV L L +P ++ F+ + +F N T RV + R +
Sbjct: 1 MVCLKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYI 60
Query: 242 YNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTL 421
YNQ+E+ +NS++G ++ T LGRP Y N QKD L ++R + + C+ NY + + T+
Sbjct: 61 YNQEEYARYNSDLGEYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVESFTV 120
Query: 422 HRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNG 601
R+VQP VT+ PSK + L HNLLVC+ FYP ++ + FRNGQ+E AG VS LI+NG
Sbjct: 121 QRRVQPKVTVYPSKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 602 NWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPI 700
+WT+Q LVML+ + G+VYTC+VEH ++ +P+
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSMMSPL 213
>ref|XP_949915.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DRB1-9 beta chain precursor (MHC class I antigen DRB1*9)
(DR-9) (DR9) isoform 2 [Homo sapiens]
Length = 284
Score = 178 bits (452), Expect = 6e-45
Identities = 86/181 (47%), Positives = 125/181 (69%)
Frame = +2
Query: 167 FVYHFNFKGYFFNETHRVRGVARGVYNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKD 346
F+ F+ +FFN T RVR + RG+YNQ+E+V F+S+VG +R T LGRP N QKD
Sbjct: 54 FLKQDKFECHFFNGTERVRYLHRGIYNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKD 113
Query: 347 FLNQKRPKGNPVCKPNYQIKKGPTLHRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQ 526
FL ++R + + VC+ NY + + T+ R+V P VT+ P+K + L HNLLVC+ + FYP
Sbjct: 114 FLERRRAEVDTVCRHNYGVGESFTVQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGS 173
Query: 527 VKFQGFRNGQKETAGFVSPPLIRNGNWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILG 706
++ + FRNGQ+E AG VS LI+NG+WT+Q LVML+ + G+VYTC+VEH ++ +P+
Sbjct: 174 IEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTV 233
Query: 707 E 709
E
Sbjct: 234 E 234
>ref|NP_072049.2| major histocompatibility complex, class II, DR beta 3 precursor
[Homo sapiens]
Length = 266
Score = 168 bits (425), Expect = 8e-42
Identities = 92/216 (42%), Positives = 133/216 (61%)
Frame = +2
Query: 62 MGALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGV 241
M L+ P G AALTV L L + ++ F+ + +FFN T RVR + R
Sbjct: 1 MVCLKLPGGSSLAALTVTLMVLSSRLAFAGDTRPRFLELRKSECHFFNGTERVRYLDRYF 60
Query: 242 YNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTL 421
+NQ+E + F+S+VG +R T LGRP N QKD L QKR + + C+ NY + + T+
Sbjct: 61 HNQEEFLRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGRVDNYCRHNYGVGESFTV 120
Query: 422 HRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNG 601
R+V P VT+ P+K + L HNLLVC+ + FYP ++ + FRNGQ+E AG VS LI+NG
Sbjct: 121 QRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 602 NWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILGE 709
+WT+Q LVML+ + G+VYTC+VEH ++ + + E
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSALTVE 216
Database: RefSeqHP
Posted date: Aug 2, 2006 12:57 AM
Number of letters in database: 17,774,539
Number of sequences in database: 39,411
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 Hits to DB: 45,578,281
Number of Sequences: 39411
Number of extensions: 1494949
Number of successful extensions: 9006
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 5272
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 8195
length of database: 17,774,539
effective HSP length: 102
effective length of database: 13,754,617
effective search space used: 3149807293
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
Search to RefSeqCP
BLASTX 2.2.10 [Oct-19-2004]
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= 20060611S-062187
(996 letters)
Database: RefSeqCP
33,732 sequences; 19,266,565 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca... 229 4e-60
Alignment gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami... 181 1e-45
Alignment gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati... 170 2e-42
Alignment gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati... 170 2e-42
Alignment gi|XP_849737.1| PREDICTED: similar to HLA class II histocompati... 59 7e-09
>ref|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Canis familiaris]
Length = 269
Score = 229 bits (583), Expect = 4e-60
Identities = 115/216 (53%), Positives = 155/216 (71%)
Frame = +2
Query: 53 MSGMGALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVA 232
MSG L P+G TAA+ ++L L P EG++SPQDFV+ + + YF N T RVR +
Sbjct: 1 MSGKMTLCIPRGFWTAAVMMILVVLSIPVAEGRDSPQDFVFQYKAECYFTNGTERVRLLT 60
Query: 233 RGVYNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKG 412
+ +YN++E V F+S+VG FR T LGRP Y N QKD +++ R + + VC+ NY ++
Sbjct: 61 KYIYNREEFVRFDSDVGEFRAVTELGRPDAEYWNRQKDEMDRVRAELDTVCRHNYGREEL 120
Query: 413 PTLHRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLI 592
TL R+V+PTVTI PSK + L HNLLVC+ T+FYP Q+K + FRN Q++TAG VS PLI
Sbjct: 121 TTLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLI 180
Query: 593 RNGNWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPI 700
RNG+WT+Q+LVML+M QRGDVYTC VEH++LQ+PI
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHASLQSPI 216
>ref|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis familiaris]
Length = 266
Score = 181 bits (458), Expect = 1e-45
Identities = 96/216 (44%), Positives = 136/216 (62%)
Frame = +2
Query: 62 MGALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGV 241
M L F G AL ++L L P +++P F+ + YF N T RVR V R +
Sbjct: 1 MVCLCFLGGSWMTALMLILMVLNPPFAWARDTPPHFLEVAKSECYFTNGTERVRFVERYI 60
Query: 242 YNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTL 421
+N++E V F+S+VG FR T LGRP NGQK+ L Q+R + C+ NY + + T+
Sbjct: 61 HNREEFVRFDSDVGEFRAVTELGRPVAESWNGQKEILEQERATVDTYCRHNYGVIESFTV 120
Query: 422 HRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNG 601
R+V+PTVT+ P+K + L HNLLVC+ FYP ++ + RNGQ+E AG VS LIRNG
Sbjct: 121 QRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNG 180
Query: 602 NWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILGE 709
+WT+Q+LVML++ Q G+VYTC+VEH +L +P+ E
Sbjct: 181 DWTFQILVMLEIVPQSGEVYTCQVEHPSLTSPVTVE 216
>ref|XP_861384.1| PREDICTED: similar to HLA class II histocompatibility antigen, DO
beta chain precursor (MHC class II antigen DOB) isoform
2 [Canis familiaris]
Length = 228
Score = 170 bits (430), Expect = 2e-42
Identities = 84/200 (42%), Positives = 125/200 (62%)
Frame = +2
Query: 101 ALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGVYNQKEHVPFNSNV 280
AL V + GL + +G++SP+DFV YF N T +V+ V R ++N +E+ F+S+V
Sbjct: 11 ALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFDSHV 70
Query: 281 GNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTLHRQVQPTVTISPS 460
G F T LG+P N Q L + R + +C+ NY++ T+ R+VQP VT+ P
Sbjct: 71 GMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTVYPE 130
Query: 461 KAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNGNWTYQVLVMLKMN 640
+ ++ HNLL+C+ T FYP +K + FRNGQ+E G +S LIRNG+WT+Q +VML+M
Sbjct: 131 RTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVMLEMT 190
Query: 641 LQRGDVYTCRVEHSTLQNPI 700
+ GDVYTC V H +L +P+
Sbjct: 191 PELGDVYTCLVNHPSLLSPV 210
>ref|XP_850395.1| PREDICTED: similar to HLA class II histocompatibility antigen, DO
beta chain precursor (MHC class II antigen DOB) isoform
1 [Canis familiaris]
Length = 270
Score = 170 bits (430), Expect = 2e-42
Identities = 84/200 (42%), Positives = 125/200 (62%)
Frame = +2
Query: 101 ALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGVYNQKEHVPFNSNV 280
AL V + GL + +G++SP+DFV YF N T +V+ V R ++N +E+ F+S+V
Sbjct: 11 ALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFDSHV 70
Query: 281 GNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTLHRQVQPTVTISPS 460
G F T LG+P N Q L + R + +C+ NY++ T+ R+VQP VT+ P
Sbjct: 71 GMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTVYPE 130
Query: 461 KAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNGNWTYQVLVMLKMN 640
+ ++ HNLL+C+ T FYP +K + FRNGQ+E G +S LIRNG+WT+Q +VML+M
Sbjct: 131 RTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVMLEMT 190
Query: 641 LQRGDVYTCRVEHSTLQNPI 700
+ GDVYTC V H +L +P+
Sbjct: 191 PELGDVYTCLVNHPSLLSPV 210
>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 = 58.9 bits (141), Expect = 7e-09
Identities = 37/122 (30%), Positives = 54/122 (44%), Gaps = 1/122 (0%)
Frame = +2
Query: 338 QKDFLNQKRPKGNPVCKPNYQIKKGPTLHRQVQPTVTISPSKAKALTPHNLLVCAGTNFY 517
Q+++L+Q+ G C + Q G HR PTV ++ S +L C FY
Sbjct: 82 QQEYLHQRLSNGLQDCATHTQSFWGSLTHRTRPPTVQVAKSTPFNTKESVMLACYVWGFY 141
Query: 518 PTQVKFQGFRNGQKETAGFVSPPLIR-NGNWTYQVLVMLKMNLQRGDVYTCRVEHSTLQN 694
P V +NGQ + + + + NG+WTYQ + L D YTC VEH
Sbjct: 142 PADVTISWRKNGQPVPSHSSALNMAQPNGDWTYQTVSHLATTPSYEDTYTCVVEHIGAPE 201
Query: 695 PI 700
P+
Sbjct: 202 PV 203
Database: RefSeqCP
Posted date: Aug 1, 2006 9:25 PM
Number of letters in database: 19,266,565
Number of sequences in database: 33,732
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 Hits to DB: 46,896,981
Number of Sequences: 33732
Number of extensions: 1488156
Number of successful extensions: 8274
Number of sequences better than 1.0e-05: 5
Number of HSP's better than 0.0 without gapping: 5170
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 7688
length of database: 19,266,565
effective HSP length: 103
effective length of database: 15,792,169
effective search space used: 3600614532
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
Search to RefSeqMP
BLASTX 2.2.10 [Oct-19-2004]
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= 20060611S-062187
(996 letters)
Database: RefSeqMP
45,328 sequences; 21,768,885 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ... 198 6e-51
Alignment gi|NP_034512.1| histocompatibility 2, class II antigen E beta [... 167 2e-41
Alignment gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/... 158 7e-39
Alignment gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ... 157 2e-38
Alignment gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ... 57 2e-08
Alignment gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ... 56 5e-08
Alignment gi|NP_034319.1| Fc receptor, IgG, alpha chain transporter [Mus ... 50 5e-06
>ref|NP_996988.1| histocompatibility 2, class II antigen A, beta 1 [Mus musculus]
Length = 265
Score = 198 bits (504), Expect = 6e-51
Identities = 107/218 (49%), Positives = 145/218 (66%), Gaps = 4/218 (1%)
Frame = +2
Query: 68 ALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGVYN 247
AL+ P L +AA+ V++ L +PG EG +S + FVY F + YF N T R+R V R +YN
Sbjct: 2 ALQIPSLLLSAAVVVLMV-LSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRYVTRYIYN 60
Query: 248 QKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTLH- 424
++E+V ++S+VG R T LGRP Y N Q + L + R + + VC+ NY+ GP H
Sbjct: 61 REEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYE---GPETHT 117
Query: 425 ---RQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIR 595
R QP V IS S+ +AL HN LVC+ T+FYPTQ+K + FRNGQ+ET G S LIR
Sbjct: 118 SLRRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIR 177
Query: 596 NGNWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILGE 709
NG+WT+QVLVML+M +RG+VYTC VEH +L++PI E
Sbjct: 178 NGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVE 215
>ref|NP_034512.1| histocompatibility 2, class II antigen E beta [Mus musculus]
Length = 264
Score = 167 bits (423), Expect = 2e-41
Identities = 86/204 (42%), Positives = 131/204 (64%)
Frame = +2
Query: 98 AALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGVYNQKEHVPFNSN 277
AA+ ++L L P ++S F+ + + +F+N T RVR + R YN +E++ F+S+
Sbjct: 11 AAVILLLTVLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRFLKRYFYNLEENLRFDSD 70
Query: 278 VGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTLHRQVQPTVTISP 457
VG FR T LGRP N Q + L++KR + C+ NY+I + R+V+PTVT+ P
Sbjct: 71 VGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNFLVPRRVEPTVTVYP 130
Query: 458 SKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNGNWTYQVLVMLKM 637
+K + L HNLLVC+ ++FYP ++ + FRNG++E G VS L+RNG+WT+Q LVML+
Sbjct: 131 TKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLET 190
Query: 638 NLQRGDVYTCRVEHSTLQNPILGE 709
Q G+VYTC+VEH +L +P+ E
Sbjct: 191 VPQSGEVYTCQVEHPSLTDPVTVE 214
>ref|NP_001029150.1| H-2 class II histocompatibility antigen E-a/k beta-2 [Mus musculus]
Length = 287
Score = 158 bits (400), Expect = 7e-39
Identities = 88/216 (40%), Positives = 128/216 (59%)
Frame = +2
Query: 62 MGALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGV 241
M +L P+GL AA+ + L L P + ++ F+ + ++FN RV V R +
Sbjct: 1 MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERVWSVTRFI 60
Query: 242 YNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTL 421
YNQ+E FNS+ G F T LGRP Y N QKD L+ R + C+ NY + L
Sbjct: 61 YNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRASVDR-CRNNYDLVDIFML 119
Query: 422 HRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNG 601
+ + +P VT+ P+K + L HNLLVC+ +FYP ++ + FRNG++E G VS LI+N
Sbjct: 120 NLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNR 179
Query: 602 NWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILGE 709
+WTYQ LVML+M + G+VYTC+VEH +L +P+ E
Sbjct: 180 DWTYQTLVMLEMVPRGGEVYTCQVEHPSLTSPVTVE 215
>ref|NP_034519.2| histocompatibility 2, O region beta locus [Mus musculus]
Length = 271
Score = 157 bits (396), Expect = 2e-38
Identities = 85/213 (39%), Positives = 124/213 (58%)
Frame = +2
Query: 62 MGALRFPKGL*TAALTVMLGGLGAPGVEGKNSPQDFVYHFNFKGYFFNETHRVRGVARGV 241
MGA R P AL V L L + +EG++SP++FV YF N T +V + R +
Sbjct: 1 MGAGRAPW---VVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFI 57
Query: 242 YNQKEHVPFNSNVGNFRGGTPLGRPTPNY*NGQKDFLNQKRPKGNPVCKPNYQIKKGPTL 421
+N +E++ F+S++G F T LG P + N + D L R N VC+ Y++ T+
Sbjct: 58 FNLEEYLHFDSDLGMFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGAPFTV 117
Query: 422 HRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIRNG 601
R V P VT+ P + L HNLL+C+ T FYP + + FRNGQ+E +G +S L+RNG
Sbjct: 118 ERNVPPEVTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNG 177
Query: 602 NWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPI 700
+WT+Q VML+M + GD+Y+C VEH L P+
Sbjct: 178 DWTFQTTVMLEMIPELGDIYSCLVEHPGLLRPV 210
>ref|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus musculus]
Length = 261
Score = 57.4 bits (137), Expect = 2e-08
Identities = 37/125 (29%), Positives = 55/125 (44%), Gaps = 1/125 (0%)
Frame = +2
Query: 338 QKDFLNQKRPKGNPVCKPNYQIKKGPTLHRQVQPTVTISPSKAKALTPHNLLVCAGTNFY 517
+++ L Q+ G C + Q HR P+V ++ + +L C FY
Sbjct: 82 KEESLLQRLQNGLLDCASHTQPFWNALTHRTRAPSVRVAQTTPFNTREPVMLACYVWGFY 141
Query: 518 PTQVKFQGFRNGQKETAGFVSPPLIR-NGNWTYQVLVMLKMNLQRGDVYTCRVEHSTLQN 694
P V +NGQ + + NG+WTYQ + L + GDVYTC V+HS
Sbjct: 142 PADVTITWMKNGQLVPSHSNKEKTAQPNGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSE 201
Query: 695 PILGE 709
PI G+
Sbjct: 202 PIRGD 206
>ref|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus musculus]
Length = 261
Score = 56.2 bits (134), Expect = 5e-08
Identities = 32/97 (32%), Positives = 45/97 (46%), Gaps = 1/97 (1%)
Frame = +2
Query: 422 HRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAGFVSPPLIR-N 598
HR P+V ++ + +L C FYP V +NGQ + + N
Sbjct: 110 HRTRAPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPN 169
Query: 599 GNWTYQVLVMLKMNLQRGDVYTCRVEHSTLQNPILGE 709
G+WTYQ + L + GDVYTC V+HS PI G+
Sbjct: 170 GDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGD 206
>ref|NP_034319.1| Fc receptor, IgG, alpha chain transporter [Mus musculus]
Length = 365
Score = 49.7 bits (117), Expect = 5e-06
Identities = 45/165 (27%), Positives = 78/165 (47%), Gaps = 13/165 (7%)
Frame = +2
Query: 245 NQKEHVPFNSNVGNFRGGTP-------LGRPTPNY*NGQKDFLNQKRPK---GN-PVCKP 391
N +E + FN +GN+ G P L P+ + +FL P+ G+ +
Sbjct: 136 NGEEFMKFNPRIGNWTGEWPETEIVANLWMKQPDAARKESEFLLNSCPERLLGHLERGRR 195
Query: 392 NYQIKKGPTLHRQVQPTVTISPSKAKALTPHNLLVCAGTNFYPTQVKFQGFRNGQKETAG 571
N + K+ P++ + +P + S ++L CA +FYP ++KF+ RNG +G
Sbjct: 196 NLEWKEPPSMRLKARPGNSGS----------SVLTCAAFSFYPPELKFRFLRNGLASGSG 245
Query: 572 FVSPPLIRNGNWTYQVLVMLKMNLQRGDV--YTCRVEHSTLQNPI 700
S NG+ ++ +L+ ++RGD Y C+VEH L P+
Sbjct: 246 NCSTG--PNGDGSFHAWSLLE--VKRGDEHHYQCQVEHEGLAQPL 286
Database: RefSeqMP
Posted date: Aug 2, 2006 12:58 AM
Number of letters in database: 21,768,885
Number of sequences in database: 45,328
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 Hits to DB: 52,658,300
Number of Sequences: 45328
Number of extensions: 1625563
Number of successful extensions: 8698
Number of sequences better than 1.0e-05: 7
Number of HSP's better than 0.0 without gapping: 5559
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 8111
length of database: 21,768,885
effective HSP length: 104
effective length of database: 17,054,773
effective search space used: 3871433471
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)