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= 20060611C-004916
(916 letters)
Database: RefSeqSP
1040 sequences; 434,620 total letters
Searching...done
***** No hits found ******
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: 924,346
Number of Sequences: 1040
Number of extensions: 24146
Number of successful extensions: 107
Number of sequences better than 1.0e-05: 0
Number of HSP's better than 0.0 without gapping: 94
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): 105
length of database: 434,620
effective HSP length: 76
effective length of database: 355,580
effective search space used: 81072240
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= 20060611C-004916
(916 letters)
Database: RefSeqBP
33,508 sequences; 16,112,626 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001012698.2| major histocompatibility complex, class II, ... 283 1e-76
Alignment gi|XP_582099.2| PREDICTED: similar to major histocompatibility ... 238 6e-63
Alignment gi|NP_001029840.2| MHC class II antigen [Bos taurus] 211 5e-55
Alignment gi|NP_001012694.1| major histocompatibility complex, class II, ... 201 5e-52
Alignment gi|XP_876139.1| PREDICTED: similar to H-2 class II histocompati... 180 5e-50
Alignment gi|NP_001012697.1| major histocompatibility complex, class II, ... 183 1e-46
Alignment gi|NP_001013618.1| major histocompatibility complex, class II, ... 173 1e-45
Alignment gi|XP_874766.1| PREDICTED: similar to HLA class II histocompati... 107 4e-32
>ref|NP_001012698.2| major histocompatibility complex, class II, DRB3 [Bos taurus]
Length = 266
Score = 283 bits (725), Expect = 1e-76
Identities = 143/217 (65%), Positives = 159/217 (73%), Gaps = 30/217 (13%)
Frame = +2
Query: 71 MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 250
M+ L FS G WMAAL +ML+VL PPLA AR+ PHFL K ECHFFNGTERVR LDR+F
Sbjct: 1 MVCLYFSGGSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKGECHFFNGTERVRFLDRHF 60
Query: 251 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 430
YNG+E+VRFDSD GEFR VTE GRP+A++WNSQKDF+EQKRAEVD VCRHNY E+F V
Sbjct: 61 YNGEEFVRFDSDWGEFRAVTELGRPAAEHWNSQKDFLEQKRAEVDRVCRHNYGGVESFTV 120
Query: 431 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVE----------------------- 541
RR EP VTVYPAKTQPLQHHNLLVCSV GFYPGH+E
Sbjct: 121 QRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFYPGHIEVRWFRNGHEEEAGVISTGLIQNG 180
Query: 542 -----TMVMLETVPQSGEVYTCRVEHPSLTSP--VQW 631
TMVMLETVPQSGEVYTC+V+HP TSP V+W
Sbjct: 181 DWTFQTMVMLETVPQSGEVYTCQVDHPKRTSPITVEW 217
Score = 71.2 bits (173), Expect = 1e-12
Identities = 35/60 (58%), Positives = 39/60 (65%)
Frame = +1
Query: 604 PQPDEPRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQPTGLLS 783
P+ P TVEWRARS+SAQ KMMSG+ IYF+NQKGRP LQPTGLLS
Sbjct: 207 PKRTSPITVEWRARSDSAQSKMMSGVGGFVLGLLFLAVGLFIYFRNQKGRPTLQPTGLLS 266
>ref|XP_582099.2| PREDICTED: similar to major histocompatibility complex, class II,
DR beta 5 precursor [Bos taurus]
Length = 255
Score = 238 bits (606), Expect = 6e-63
Identities = 123/206 (59%), Positives = 139/206 (67%), Gaps = 30/206 (14%)
Frame = +2
Query: 104 MAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFDS 283
MAAL ++L+VLS P + AR+T PHF+ K EC F NG ER+R RY YN E V FDS
Sbjct: 1 MAALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQEDVHFDS 60
Query: 284 DVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTVY 463
DVGEF +TE GR A+YWN QKDFMEQ RA+VDT+CR NY+ +FL RR EP VTVY
Sbjct: 61 DVGEFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCRSNYQGIGSFLRQRRVEPTVTVY 120
Query: 464 PAKTQPLQHHNLLVCSVTGFYPGHVE----------------------------TMVMLE 559
PAKTQPLQHHNLLVCSV GFYPGH+E TMVMLE
Sbjct: 121 PAKTQPLQHHNLLVCSVNGFYPGHIEVRWFWNSHEEEAGVISTGLIQNGDWTFQTMVMLE 180
Query: 560 TVPQSGEVYTCRVEHPSLTSP--VQW 631
TVPQSGEVYTC+VEHPS TSP V+W
Sbjct: 181 TVPQSGEVYTCQVEHPSRTSPLTVEW 206
Score = 52.8 bits (125), Expect = 4e-07
Identities = 26/57 (45%), Positives = 33/57 (57%)
Frame = +1
Query: 604 PQPDEPRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQPTG 774
P P TVEWRA+S+SAQ K+MSGI I+ +++KG PALQP G
Sbjct: 196 PSRTSPLTVEWRAQSDSAQRKLMSGIGGFVLGLLFLGVGLFIHLRSKKGHPALQPIG 252
>ref|NP_001029840.2| MHC class II antigen [Bos taurus]
Length = 261
Score = 211 bits (538), Expect = 5e-55
Identities = 109/219 (49%), Positives = 133/219 (60%), Gaps = 30/219 (13%)
Frame = +2
Query: 65 SSMLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDR 244
S M+ L RG W A + + LV+LS P A RD+P F+ K C+F NGTERVR + R
Sbjct: 2 SGMVALWIPRGLWTAVVMVTLVMLSTPGAEGRDSPKDFVVQFKGLCYFTNGTERVRYVTR 61
Query: 245 YFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETF 424
Y YN +EYVRFDSD +R +T GRP A+YWNSQKDF+EQ RAE DTVCRHNY+
Sbjct: 62 YIYNQEEYVRFDSDWDLYRALTPLGRPDAEYWNSQKDFLEQTRAEADTVCRHNYQAELIT 121
Query: 425 LVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHV---------------------- 538
+ RR EP VT+ P++T+ L HHNLLVCSVT FYP +
Sbjct: 122 SLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLIR 181
Query: 539 ------ETMVMLETVPQSGEVYTCRVEHPSLTSP--VQW 631
+ +VMLE PQ G+VYTC VEHPSL SP V+W
Sbjct: 182 NGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPIMVEW 220
>ref|NP_001012694.1| major histocompatibility complex, class II, DQ beta [Bos taurus]
Length = 261
Score = 201 bits (512), Expect = 5e-52
Identities = 104/219 (47%), Positives = 133/219 (60%), Gaps = 30/219 (13%)
Frame = +2
Query: 65 SSMLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDR 244
S M+ L RG W AA+ + L VLS P A RD+P + +C+F NGTERVR + R
Sbjct: 2 SGMVALRIPRGLWTAAVMVTLAVLSTPGAEGRDSPQDTVVHFMGQCYFTNGTERVRYVTR 61
Query: 245 YFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETF 424
Y YN +E +DSDVGE+R VT+ GR A+YWNSQKD +EQ RAE+DTVCRHNY++
Sbjct: 62 YIYNQEETAYYDSDVGEYRAVTQLGRTLAEYWNSQKDILEQTRAELDTVCRHNYQLEVIT 121
Query: 425 LVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHV---------------------- 538
+ R+ EP VT+ ++T+ L HHNLLVCSVT FYPG +
Sbjct: 122 SLQRQVEPTVTISLSRTEALNHHNLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPLIR 181
Query: 539 ------ETMVMLETVPQSGEVYTCRVEHPSLTSP--VQW 631
+ +VMLE P+ G+VYTC VEHPSL SP V+W
Sbjct: 182 NGDWTFQILVMLEMTPKRGDVYTCHVEHPSLQSPISVEW 220
>ref|XP_876139.1| PREDICTED: similar to H-2 class II histocompatibility antigen, I-E
beta chain precursor [Bos taurus]
Length = 269
Score = 180 bits (457), Expect(2) = 5e-50
Identities = 91/174 (52%), Positives = 107/174 (61%), Gaps = 28/174 (16%)
Frame = +2
Query: 188 GKAECHFFNGTERVRLLDRYFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQ 367
GK+ECHF NGT++VR LDRY YN +E V+FDS VGE+R TE GRP+A+ WN +++
Sbjct: 4 GKSECHFSNGTQQVRFLDRYIYNREEQVQFDSLVGEYRARTEMGRPAAERWNRWPQALQR 63
Query: 368 KRAEVDTVCRHNYEISETFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVET- 544
RA V C NYE + V RR +P VTVYP K++PL HHNLLVCSV GFYPGH+E
Sbjct: 64 ARAAVHAYCASNYEFFASRTVQRRVQPTVTVYPVKSRPLWHHNLLVCSVNGFYPGHIEVR 123
Query: 545 ---------------------------MVMLETVPQSGEVYTCRVEHPSLTSPV 625
MVMLE VPQ GEVY C VEHPS TSPV
Sbjct: 124 WFRNGQEEEAGVVSTGLIPNGDWTFQIMVMLEIVPQGGEVYACHVEHPSRTSPV 177
Score = 36.2 bits (82), Expect(2) = 5e-50
Identities = 16/26 (61%), Positives = 19/26 (73%)
Frame = +1
Query: 604 PQPDEPRTVEWRARSESAQGKMMSGI 681
P P TVEWRA+ ES+Q KM+SGI
Sbjct: 171 PSRTSPVTVEWRAQDESSQEKMLSGI 196
>ref|NP_001012697.1| major histocompatibility complex, class II, DY beta [Bos taurus]
Length = 259
Score = 183 bits (465), Expect = 1e-46
Identities = 98/200 (49%), Positives = 120/200 (60%), Gaps = 30/200 (15%)
Frame = +2
Query: 122 MLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFDSDVGEFR 301
+ +VL P A RD P +F++ K C+F NGTE VRL+ R YN +E + FDSD+GEF
Sbjct: 19 VFLVLRIPEAHCRDAPKNFVYQFKGMCYFTNGTEHVRLVARQIYNKEEILHFDSDLGEFV 78
Query: 302 EVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTVYPAKTQP 481
VTE GR A+ WN+QKD + + RA VDT+CRHNY+ + F V RR EP VTV PA T+
Sbjct: 79 AVTELGRVCAEIWNTQKDLLAEFRAYVDTLCRHNYKETAGFTVQRRVEPTVTVSPASTEA 138
Query: 482 LQHHNLLVCSVTGFYPGHVETM----------------------------VMLETVPQSG 577
L HHNLLVCSVT FYP V+ VMLETVPQ G
Sbjct: 139 LNHHNLLVCSVTDFYPRQVKVKWFRNQQEQTAGVGFTPLTQNGDWTYQIHVMLETVPQLG 198
Query: 578 EVYTCRVEHPSLTSP--VQW 631
+VY C V+HPSL SP V+W
Sbjct: 199 DVYVCHVDHPSLQSPITVEW 218
>ref|NP_001013618.1| major histocompatibility complex, class II, DO beta [Bos taurus]
Length = 271
Score = 173 bits (439), Expect(2) = 1e-45
Identities = 86/203 (42%), Positives = 115/203 (56%), Gaps = 28/203 (13%)
Frame = +2
Query: 101 WMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFD 280
W+ + L + RD+P F+ KA+C+F NGTE+VR + R+ +N ++Y RFD
Sbjct: 8 WVVTFLSTALRLDASVTQGRDSPEDFVTQAKADCYFTNGTEKVRFVVRFIFNLEDYARFD 67
Query: 281 SDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTV 460
SD+G F +TE G+P A+ WN++ D + + RA VD +CR NY + F V RR +P VTV
Sbjct: 68 SDLGMFVALTELGKPDAERWNNRPDILARSRASVDMLCRRNYYLGAPFTVGRRVQPEVTV 127
Query: 461 YPAKTQPLQHHNLLVCSVTGFYPGHVETM----------------------------VML 556
YP KT LQH NLL+C VTGFYPG ++ VML
Sbjct: 128 YPEKTPALQHRNLLLCLVTGFYPGDIKVTWFRNGQEQREGIMSTGLIRNGDWTFQMTVML 187
Query: 557 ETVPQSGEVYTCRVEHPSLTSPV 625
P+ GEVYTC V+HPSL SPV
Sbjct: 188 AMTPELGEVYTCLVDHPSLLSPV 210
Score = 28.5 bits (62), Expect(2) = 1e-45
Identities = 14/45 (31%), Positives = 22/45 (48%)
Frame = +1
Query: 619 PRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGR 753
P +VEWRA+SE + K++SG ++ + KGR
Sbjct: 209 PVSVEWRAQSEYSWRKILSGAAAFLVGLVFFLVEIVVHIRAWKGR 253
>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 = 107 bits (266), Expect(2) = 4e-32
Identities = 80/221 (36%), Positives = 101/221 (45%), Gaps = 30/221 (13%)
Frame = +2
Query: 53 PLLFSSMLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVR 232
P LF+S + L FS+G WMAAL +M+ LSP L AR+T
Sbjct: 7 PFLFASTVCLYFSKGSWMAALLVMMG-LSPLLTWARETQ--------------------- 44
Query: 233 LLDRYFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRH--NY 406
Y +V DS + G+P A + D C H
Sbjct: 45 ------YKRTPWVVIDSQISAISH----GKPCALNGYRECDG-----------CFHPIGL 83
Query: 407 EISETFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVE--------------- 541
+ + + ++ EP VTVYPAKTQPLQH++LLVCSV GFY GHVE
Sbjct: 84 KANRDITLQKKVEPTVTVYPAKTQPLQHNHLLVCSVNGFYLGHVEVRWFWKGQEEEAGVI 143
Query: 542 -------------TMVMLETVPQSGEVYTCRVEHPSLTSPV 625
T+VMLETV QSGEVYTC++EHPS SP+
Sbjct: 144 STGLIQNGDWTFETIVMLETVLQSGEVYTCQLEHPSWRSPI 184
Score = 49.7 bits (117), Expect(2) = 4e-32
Identities = 25/58 (43%), Positives = 30/58 (51%)
Frame = +1
Query: 604 PQPDEPRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQPTGL 777
P P EWRA+S+SAQ KMMSG +F+NQKG LQPTG+
Sbjct: 178 PSWRSPIAEEWRAQSDSAQSKMMSGTGGFALGLLFLVVGLFTHFRNQKGHSGLQPTGI 235
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: 35,212,543
Number of Sequences: 33508
Number of extensions: 981028
Number of successful extensions: 4347
Number of sequences better than 1.0e-05: 8
Number of HSP's better than 0.0 without gapping: 3662
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): 4316
length of database: 16,112,626
effective HSP length: 101
effective length of database: 12,728,318
effective search space used: 2583848554
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= 20060611C-004916
(916 letters)
Database: RefSeqCP
33,732 sequences; 19,266,565 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami... 266 8e-84
Alignment gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca... 240 2e-70
Alignment gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati... 194 2e-52
Alignment gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati... 194 8e-50
>ref|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis familiaris]
Length = 266
Score = 266 bits (681), Expect(2) = 8e-84
Identities = 130/213 (61%), Positives = 152/213 (71%), Gaps = 28/213 (13%)
Frame = +2
Query: 71 MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 250
M+ LCF G WM AL ++L+VL+PP A ARDTPPHFL + K+EC+F NGTERVR ++RY
Sbjct: 1 MVCLCFLGGSWMTALMLILMVLNPPFAWARDTPPHFLEVAKSECYFTNGTERVRFVERYI 60
Query: 251 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 430
+N +E+VRFDSDVGEFR VTE GRP A+ WN QK+ +EQ+RA VDT CRHNY + E+F V
Sbjct: 61 HNREEFVRFDSDVGEFRAVTELGRPVAESWNGQKEILEQERATVDTYCRHNYGVIESFTV 120
Query: 431 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVET---------------------- 544
RR EP VTVYP KTQ LQHHNLLVCSV GFYPGH+E
Sbjct: 121 QRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNG 180
Query: 545 ------MVMLETVPQSGEVYTCRVEHPSLTSPV 625
+VMLE VPQSGEVYTC+VEHPSLTSPV
Sbjct: 181 DWTFQILVMLEIVPQSGEVYTCQVEHPSLTSPV 213
Score = 63.2 bits (152), Expect(2) = 8e-84
Identities = 32/60 (53%), Positives = 36/60 (60%)
Frame = +1
Query: 604 PQPDEPRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQPTGLLS 783
P P TVEWRA+S+SAQ KM+SGI IYF+NQKG LQPTGLLS
Sbjct: 207 PSLTSPVTVEWRAQSDSAQSKMLSGIGGFVLGLLFLAVGLFIYFRNQKGHSGLQPTGLLS 266
>ref|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Canis familiaris]
Length = 269
Score = 240 bits (613), Expect(2) = 2e-70
Identities = 122/219 (55%), Positives = 145/219 (66%), Gaps = 30/219 (13%)
Frame = +2
Query: 65 SSMLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDR 244
S + LC RGFW AA+ M+LVVLS P+A RD+P F+F KAEC+F NGTERVRLL +
Sbjct: 2 SGKMTLCIPRGFWTAAVMMILVVLSIPVAEGRDSPQDFVFQYKAECYFTNGTERVRLLTK 61
Query: 245 YFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETF 424
Y YN +E+VRFDSDVGEFR VTE GRP A+YWN QKD M++ RAE+DTVCRHNY E
Sbjct: 62 YIYNREEFVRFDSDVGEFRAVTELGRPDAEYWNRQKDEMDRVRAELDTVCRHNYGREELT 121
Query: 425 LVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHV---------------------- 538
+ RR EP VT++P+KT+ L HHNLLVCSVT FYPG +
Sbjct: 122 TLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLIR 181
Query: 539 ------ETMVMLETVPQSGEVYTCRVEHPSLTSP--VQW 631
+ +VMLE PQ G+VYTC VEH SL SP VQW
Sbjct: 182 NGDWTFQILVMLEMTPQRGDVYTCHVEHASLQSPITVQW 220
Score = 44.7 bits (104), Expect(2) = 2e-70
Identities = 24/54 (44%), Positives = 29/54 (53%)
Frame = +1
Query: 619 PRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQPTGLL 780
P TV+WRA+SESAQ KM+SGI I ++QKG P GLL
Sbjct: 215 PITVQWRAQSESAQSKMLSGIGGFVLGLIFLGLGLIIRHRSQKGSRGSPPAGLL 268
>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 = 194 bits (493), Expect(2) = 2e-52
Identities = 94/203 (46%), Positives = 123/203 (60%), Gaps = 28/203 (13%)
Frame = +2
Query: 101 WMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFD 280
WM AL + + L + RD+P F+ KA+C+F NGTE+V+ + R+ +N +EY RFD
Sbjct: 8 WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67
Query: 281 SDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTV 460
S VG F +TE G+P A+ WNSQ +E+ RA VD +CRHNYE+ F V R+ +P VTV
Sbjct: 68 SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127
Query: 461 YPAKTQPLQHHNLLVCSVTGFYPGHV----------------------------ETMVML 556
YP +T +QHHNLL+CSVTGFYPG + +TMVML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187
Query: 557 ETVPQSGEVYTCRVEHPSLTSPV 625
E P+ G+VYTC V HPSL SPV
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPV 210
Score = 30.4 bits (67), Expect(2) = 2e-52
Identities = 18/52 (34%), Positives = 24/52 (46%)
Frame = +1
Query: 619 PRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQPTG 774
P +VEWRA+S + KM+SGI I + QKG Q +G
Sbjct: 209 PVSVEWRAQSTYSWRKMLSGIAAFLLGLIFLLVGTVICLRAQKGYVETQFSG 260
>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 = 194 bits (494), Expect = 8e-50
Identities = 95/208 (45%), Positives = 126/208 (60%), Gaps = 30/208 (14%)
Frame = +2
Query: 101 WMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFD 280
WM AL + + L + RD+P F+ KA+C+F NGTE+V+ + R+ +N +EY RFD
Sbjct: 8 WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67
Query: 281 SDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTV 460
S VG F +TE G+P A+ WNSQ +E+ RA VD +CRHNYE+ F V R+ +P VTV
Sbjct: 68 SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127
Query: 461 YPAKTQPLQHHNLLVCSVTGFYPGHV----------------------------ETMVML 556
YP +T +QHHNLL+CSVTGFYPG + +TMVML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187
Query: 557 ETVPQSGEVYTCRVEHPSLTSP--VQWN 634
E P+ G+VYTC V HPSL SP V+W+
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPVSVEWS 215
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: 41,260,731
Number of Sequences: 33732
Number of extensions: 1144147
Number of successful extensions: 5253
Number of sequences better than 1.0e-05: 4
Number of HSP's better than 0.0 without gapping: 4292
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): 5223
length of database: 19,266,565
effective HSP length: 102
effective length of database: 15,825,901
effective search space used: 3196832002
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= 20060611C-004916
(916 letters)
Database: RefSeqHP
39,411 sequences; 17,774,539 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_002115.1| major histocompatibility complex, class II, DR ... 261 4e-70
Alignment gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati... 257 1e-68
Alignment gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati... 256 1e-68
Alignment gi|NP_002116.2| major histocompatibility complex, class II, DR ... 254 5e-68
Alignment gi|NP_072049.2| major histocompatibility complex, class II, DR ... 253 2e-67
Alignment gi|NP_068818.4| major histocompatibility complex, class II, DR ... 249 2e-66
Alignment gi|XP_949915.1| PREDICTED: similar to HLA class II histocompati... 226 2e-59
Alignment gi|NP_872355.1| major histocompatibility complex, class II, DQ ... 208 4e-54
Alignment gi|NP_002114.2| major histocompatibility complex, class II, DQ ... 207 8e-54
Alignment gi|NP_002112.3| major histocompatibility complex, class II, DP ... 207 1e-53
>ref|NP_002115.1| major histocompatibility complex, class II, DR beta 1 precursor
[Homo sapiens]
Length = 266
Score = 261 bits (668), Expect = 4e-70
Identities = 134/217 (61%), Positives = 155/217 (71%), Gaps = 30/217 (13%)
Frame = +2
Query: 71 MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 250
M+ L G M ALT+ L+VLS PLALA DT P FL+ K ECHFFNGTERVRLL+R
Sbjct: 1 MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCI 60
Query: 251 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 430
YN +E VRFDSDVGE+R VTE GRP A+YWNSQKD +EQ+RA VDT CRHNY + E+F V
Sbjct: 61 YNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTV 120
Query: 431 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVE----------------------- 541
RR EP+VTVYP+KTQPLQHHNLLVCSV+GFYPG +E
Sbjct: 121 QRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 542 -----TMVMLETVPQSGEVYTCRVEHPSLTSP--VQW 631
T+VMLETVP+SGEVYTC+VEHPS+TSP V+W
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEW 217
Score = 64.7 bits (156), Expect = 1e-10
Identities = 32/60 (53%), Positives = 35/60 (58%)
Frame = +1
Query: 604 PQPDEPRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQPTGLLS 783
P P TVEWRARSESAQ KM+SG+ IYF+NQKG LQPTG LS
Sbjct: 207 PSVTSPLTVEWRARSESAQSKMLSGVGGFVLGLLFLGAGLFIYFRNQKGHSGLQPTGFLS 266
>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 = 257 bits (656), Expect = 1e-68
Identities = 134/218 (61%), Positives = 153/218 (70%), Gaps = 30/218 (13%)
Frame = +2
Query: 71 MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 250
M+ L G MAALT+ L+VLS PLALA DT P FL K ECHFFNGTERVR L R
Sbjct: 1 MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60
Query: 251 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 430
YN +E VRFDSDVGE+R VTE GRP A+ WNSQKDF+E++RAEVDTVCRHNY + E+F V
Sbjct: 61 YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120
Query: 431 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVE----------------------- 541
RR P VTVYPAKTQPLQHHNLLVCSV+GFYPG +E
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 542 -----TMVMLETVPQSGEVYTCRVEHPSLTSP--VQWN 634
T+VMLETVP+SGEVYTC+VEHPS+ SP V+W+
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWS 218
>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 = 256 bits (655), Expect = 1e-68
Identities = 134/217 (61%), Positives = 152/217 (70%), Gaps = 30/217 (13%)
Frame = +2
Query: 71 MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 250
M+ L G MAALT+ L+VLS PLALA DT P FL K ECHFFNGTERVR L R
Sbjct: 1 MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60
Query: 251 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 430
YN +E VRFDSDVGE+R VTE GRP A+ WNSQKDF+E++RAEVDTVCRHNY + E+F V
Sbjct: 61 YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120
Query: 431 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVE----------------------- 541
RR P VTVYPAKTQPLQHHNLLVCSV+GFYPG +E
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 542 -----TMVMLETVPQSGEVYTCRVEHPSLTSP--VQW 631
T+VMLETVP+SGEVYTC+VEHPS+ SP V+W
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEW 217
Score = 63.9 bits (154), Expect = 2e-10
Identities = 32/60 (53%), Positives = 35/60 (58%)
Frame = +1
Query: 604 PQPDEPRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQPTGLLS 783
P P TVEWRARSESAQ KM+SG+ IYF+NQKG LQPTG LS
Sbjct: 207 PSVMSPLTVEWRARSESAQSKMLSGVGGFVLGLLFLGAGLFIYFRNQKGHSGLQPTGFLS 266
>ref|NP_002116.2| major histocompatibility complex, class II, DR beta 5 precursor
[Homo sapiens]
Length = 266
Score = 254 bits (650), Expect = 5e-68
Identities = 131/217 (60%), Positives = 151/217 (69%), Gaps = 30/217 (13%)
Frame = +2
Query: 71 MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 250
M+ L G +MA LT+ L+VLS PLALA DT P FL K ECHFFNGTERVR L R
Sbjct: 1 MVCLKLPGGSYMAKLTVTLMVLSSPLALAGDTRPRFLQQDKYECHFFNGTERVRFLHRDI 60
Query: 251 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 430
YN +E +RFDSDVGE+R VTE GRP A+YWNSQKDF+E +RA VDT CRHNY + E+F V
Sbjct: 61 YNQEEDLRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAAVDTYCRHNYGVGESFTV 120
Query: 431 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVE----------------------- 541
RR EP+VTVYPA+TQ LQHHNLLVCSV GFYPG +E
Sbjct: 121 QRRVEPKVTVYPARTQTLQHHNLLVCSVNGFYPGSIEVRWFRNSQEEKAGVVSTGLIQNG 180
Query: 542 -----TMVMLETVPQSGEVYTCRVEHPSLTSP--VQW 631
T+VMLETVP+SGEVYTC+VEHPS+TSP V+W
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEW 217
Score = 62.8 bits (151), Expect = 4e-10
Identities = 31/60 (51%), Positives = 35/60 (58%)
Frame = +1
Query: 604 PQPDEPRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQPTGLLS 783
P P TVEWRA+SESAQ KM+SG+ IYFKNQKG L PTGL+S
Sbjct: 207 PSVTSPLTVEWRAQSESAQSKMLSGVGGFVLGLLFLGAGLFIYFKNQKGHSGLHPTGLVS 266
>ref|NP_072049.2| major histocompatibility complex, class II, DR beta 3 precursor
[Homo sapiens]
Length = 266
Score = 253 bits (646), Expect = 2e-67
Identities = 130/217 (59%), Positives = 152/217 (70%), Gaps = 30/217 (13%)
Frame = +2
Query: 71 MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 250
M+ L G +AALT+ L+VLS LA A DT P FL L K+ECHFFNGTERVR LDRYF
Sbjct: 1 MVCLKLPGGSSLAALTVTLMVLSSRLAFAGDTRPRFLELRKSECHFFNGTERVRYLDRYF 60
Query: 251 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 430
+N +E++RFDSDVGE+R VTE GRP A+ WNSQKD +EQKR VD CRHNY + E+F V
Sbjct: 61 HNQEEFLRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGRVDNYCRHNYGVGESFTV 120
Query: 431 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVE----------------------- 541
RR P+VTVYPAKTQPLQHHNLLVCSV+GFYPG +E
Sbjct: 121 QRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 542 -----TMVMLETVPQSGEVYTCRVEHPSLTS--PVQW 631
T+VMLETVP+SGEVYTC+VEHPS+TS V+W
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSALTVEW 217
Score = 61.6 bits (148), Expect = 9e-10
Identities = 31/60 (51%), Positives = 34/60 (56%)
Frame = +1
Query: 604 PQPDEPRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQPTGLLS 783
P TVEWRARSESAQ KM+SG+ IYF+NQKG LQPTG LS
Sbjct: 207 PSVTSALTVEWRARSESAQSKMLSGVGGFVLGLLFLGAGLFIYFRNQKGHSGLQPTGFLS 266
>ref|NP_068818.4| major histocompatibility complex, class II, DR beta 4 precursor
[Homo sapiens]
Length = 266
Score = 249 bits (636), Expect = 2e-66
Identities = 127/218 (58%), Positives = 151/218 (69%), Gaps = 30/218 (13%)
Frame = +2
Query: 71 MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 250
M+ L G MAALT+ L VLS PLALA DT P FL K ECHF NGTERV L RY
Sbjct: 1 MVCLKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYI 60
Query: 251 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 430
YN +EY R++SD+GE++ VTE GRP A+YWNSQKD +E++RAEVDT CR+NY + E+F V
Sbjct: 61 YNQEEYARYNSDLGEYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVESFTV 120
Query: 431 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVE----------------------- 541
RR +P+VTVYP+KTQPLQHHNLLVCSV GFYPG +E
Sbjct: 121 QRRVQPKVTVYPSKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 542 -----TMVMLETVPQSGEVYTCRVEHPSLTSP--VQWN 634
T+VMLETVP+SGEVYTC+VEHPS+ SP VQW+
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSMMSPLTVQWS 218
Score = 62.0 bits (149), Expect = 7e-10
Identities = 31/60 (51%), Positives = 35/60 (58%)
Frame = +1
Query: 604 PQPDEPRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQPTGLLS 783
P P TV+W ARSESAQ KM+SG+ IYF+NQKG LQPTGLLS
Sbjct: 207 PSMMSPLTVQWSARSESAQSKMLSGVGGFVLGLLFLGTGLFIYFRNQKGHSGLQPTGLLS 266
>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 = 226 bits (576), Expect = 2e-59
Identities = 114/182 (62%), Positives = 129/182 (70%), Gaps = 30/182 (16%)
Frame = +2
Query: 176 FLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKD 355
FL K ECHFFNGTERVR L R YN +E VRFDSDVGE+R VTE GRP A+ WNSQKD
Sbjct: 54 FLKQDKFECHFFNGTERVRYLHRGIYNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKD 113
Query: 356 FMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGH 535
F+E++RAEVDTVCRHNY + E+F V RR P VTVYPAKTQPLQHHNLLVCSV+GFYPG
Sbjct: 114 FLERRRAEVDTVCRHNYGVGESFTVQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGS 173
Query: 536 VE----------------------------TMVMLETVPQSGEVYTCRVEHPSLTSP--V 625
+E T+VMLETVP+SGEVYTC+VEHPS+ SP V
Sbjct: 174 IEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTV 233
Query: 626 QW 631
+W
Sbjct: 234 EW 235
Score = 63.9 bits (154), Expect = 2e-10
Identities = 32/60 (53%), Positives = 35/60 (58%)
Frame = +1
Query: 604 PQPDEPRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQPTGLLS 783
P P TVEWRARSESAQ KM+SG+ IYF+NQKG LQPTG LS
Sbjct: 225 PSVMSPLTVEWRARSESAQSKMLSGVGGFVLGLLFLGAGLFIYFRNQKGHSGLQPTGFLS 284
>ref|NP_872355.1| major histocompatibility complex, class II, DQ beta 2 [Homo
sapiens]
Length = 231
Score = 208 bits (530), Expect = 4e-54
Identities = 109/209 (52%), Positives = 134/209 (64%), Gaps = 30/209 (14%)
Frame = +2
Query: 95 GFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVR 274
GFW AA+T+MLV+LS P+A ARD P FL K C+F NGTERVR + RY YN +EY R
Sbjct: 12 GFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVRGVARYIYNREEYGR 71
Query: 275 FDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRV 454
FDSDVGEF+ VTE GR S + WN+ KDF+EQ+RA VD VCRHNYE + R+ EP V
Sbjct: 72 FDSDVGEFQAVTELGR-SIEDWNNYKDFLEQERAAVDKVCRHNYEAELRTTLQRQVEPTV 130
Query: 455 TVYPAKTQPLQHHNLLVCSVTGFYPGHV----------------------------ETMV 550
T+ P++T+ L HHNLLVCSVT FYP + + +V
Sbjct: 131 TISPSRTEALNHHNLLVCSVTDFYPAQIKVQWFRNDQEETAGVVSTSLIRNGDWTFQILV 190
Query: 551 MLETVPQSGEVYTCRVEHPSLTSP--VQW 631
MLE PQ G++YTC+VEHPSL SP V+W
Sbjct: 191 MLEITPQRGDIYTCQVEHPSLQSPITVEW 219
>ref|NP_002114.2| major histocompatibility complex, class II, DQ beta 1 precursor
[Homo sapiens]
Length = 261
Score = 207 bits (528), Expect = 8e-54
Identities = 106/209 (50%), Positives = 132/209 (63%), Gaps = 30/209 (14%)
Frame = +2
Query: 95 GFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVR 274
G A +T+ML +LS P+A RD+P F++ K C+F NGTERVRL+ R YN +E VR
Sbjct: 12 GLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVR 71
Query: 275 FDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRV 454
FDSDVGEFR VT G P+A+YWNSQKD +E+KRA VD VCRHNY++ + RR EP V
Sbjct: 72 FDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTV 131
Query: 455 TVYPAKTQPLQHHNLLVCSVTGFYPGHV----------------------------ETMV 550
T+ P++T+ L HHNLLVCSVT FYP + + +V
Sbjct: 132 TISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILV 191
Query: 551 MLETVPQSGEVYTCRVEHPSLTSP--VQW 631
MLE PQ G+VYTC VEHPSL SP V+W
Sbjct: 192 MLEMTPQRGDVYTCHVEHPSLQSPITVEW 220
>ref|NP_002112.3| major histocompatibility complex, class II, DP beta 1 precursor
[Homo sapiens]
Length = 258
Score = 207 bits (526), Expect = 1e-53
Identities = 111/234 (47%), Positives = 141/234 (60%), Gaps = 30/234 (12%)
Frame = +2
Query: 110 ALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFDSDV 289
ALT +L+VL + R TP ++LF G+ EC+ FNGT+R L+RY YN +E+ RFDSDV
Sbjct: 14 ALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQR--FLERYIYNREEFARFDSDV 71
Query: 290 GEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTVYPA 469
GEFR VTE GRP+A+YWNSQKD +E+KRA D +CRHNYE+ + RR +PRV V P+
Sbjct: 72 GEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPMTLQRRVQPRVNVSPS 131
Query: 470 KTQPLQHHNLLVCSVTGFYPGHVET----------------------------MVMLETV 565
K PLQHHNLLVC VT FYPG ++ +VMLE
Sbjct: 132 KKGPLQHHNLLVCHVTDFYPGSIQVRWFLNGQEETAGVVSTNLIRNGDWTFQILVMLEMT 191
Query: 566 PQSGEVYTCRVEHPSLTSP--VQWNGGHGLNLLRAR**VGSGASSWVCSLLLWG 721
PQ G+VYTC+VEH SL SP V+W AR +GA +V L++ G
Sbjct: 192 PQQGDVYTCQVEHTSLDSPVTVEWKAQSD----SARSKTLTGAGGFVLGLIICG 241
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: 40,140,839
Number of Sequences: 39411
Number of extensions: 1155024
Number of successful extensions: 5805
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 4573
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): 5740
length of database: 17,774,539
effective HSP length: 102
effective length of database: 13,754,617
effective search space used: 2778432634
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= 20060611C-004916
(916 letters)
Database: RefSeqMP
45,328 sequences; 21,768,885 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_034512.1| histocompatibility 2, class II antigen E beta [... 253 3e-79
Alignment gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/... 212 6e-60
Alignment gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ... 191 1e-48
Alignment gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ... 175 3e-45
>ref|NP_034512.1| histocompatibility 2, class II antigen E beta [Mus musculus]
Length = 264
Score = 253 bits (646), Expect(2) = 3e-79
Identities = 124/202 (61%), Positives = 147/202 (72%), Gaps = 28/202 (13%)
Frame = +2
Query: 104 MAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFDS 283
+AA+ ++L VLSPP+AL RD+ P FL K+ECHF+NGT+RVR L RYFYN +E +RFDS
Sbjct: 10 VAAVILLLTVLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRFLKRYFYNLEENLRFDS 69
Query: 284 DVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTVY 463
DVGEFR VTE GRP A+ WNSQ + +++KRA VDT CRHNYEI + FLVPRR EP VTVY
Sbjct: 70 DVGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNFLVPRRVEPTVTVY 129
Query: 464 PAKTQPLQHHNLLVCSVTGFYPGHVE----------------------------TMVMLE 559
P KTQPL+HHNLLVCSV+ FYPG++E T+VMLE
Sbjct: 130 PTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLE 189
Query: 560 TVPQSGEVYTCRVEHPSLTSPV 625
TVPQSGEVYTC+VEHPSLT PV
Sbjct: 190 TVPQSGEVYTCQVEHPSLTDPV 211
Score = 61.6 bits (148), Expect(2) = 3e-79
Identities = 30/60 (50%), Positives = 37/60 (61%)
Frame = +1
Query: 604 PQPDEPRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQPTGLLS 783
P +P TVEW+A+S SAQ KM+SG+ IYF+NQKG+ LQPTGLLS
Sbjct: 205 PSLTDPVTVEWKAQSTSAQNKMLSGVGGFVLGLLFLRAGLFIYFRNQKGQSGLQPTGLLS 264
>ref|NP_001029150.1| H-2 class II histocompatibility antigen E-a/k beta-2 [Mus musculus]
Length = 287
Score = 212 bits (540), Expect(2) = 6e-60
Identities = 108/213 (50%), Positives = 140/213 (65%), Gaps = 28/213 (13%)
Frame = +2
Query: 71 MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 250
M+ L RG +AA+ + L++L+PP+ L RD P FL KAECH+FNG ERV + R+
Sbjct: 1 MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERVWSVTRFI 60
Query: 251 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 430
YN +E+ RF+SD G+F VTE GRP +Y N+QKD ++ RA VD CR+NY++ + F++
Sbjct: 61 YNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRASVDR-CRNNYDLVDIFML 119
Query: 431 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVE----------------------- 541
+AEP+VTVYPAKTQPL+HHNLLVCSV FYPG +E
Sbjct: 120 NLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNR 179
Query: 542 -----TMVMLETVPQSGEVYTCRVEHPSLTSPV 625
T+VMLE VP+ GEVYTC+VEHPSLTSPV
Sbjct: 180 DWTYQTLVMLEMVPRGGEVYTCQVEHPSLTSPV 212
Score = 37.7 bits (86), Expect(2) = 6e-60
Identities = 18/46 (39%), Positives = 22/46 (47%)
Frame = +1
Query: 604 PQPDEPRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKN 741
P P TVEWRARS SAQ K++SG+ Y +N
Sbjct: 206 PSLTSPVTVEWRARSTSAQNKLLSGVMGMALGLFILAVGLFFYLRN 251
>ref|NP_996988.1| histocompatibility 2, class II antigen A, beta 1 [Mus musculus]
Length = 265
Score = 191 bits (484), Expect = 1e-48
Identities = 99/207 (47%), Positives = 127/207 (61%), Gaps = 31/207 (14%)
Frame = +2
Query: 104 MAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFDS 283
++A ++L+VLS P D+ HF++ EC+F NGT+R+R + RY YN +EYVR+DS
Sbjct: 10 LSAAVVVLMVLSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRYVTRYIYNREEYVRYDS 69
Query: 284 DVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAE-PRVTV 460
DVGE R VTE GRP A+YWNSQ + +E+ RAE+DTVCRHNYE ET RR E P V +
Sbjct: 70 DVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRRLEQPNVVI 129
Query: 461 YPAKTQPLQHHNLLVCSVTGFYPGHV----------------------------ETMVML 556
++T+ L HHN LVCSVT FYP + + +VML
Sbjct: 130 SLSRTEALNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVML 189
Query: 557 ETVPQSGEVYTCRVEHPSLTSP--VQW 631
E P+ GEVYTC VEHPSL SP V+W
Sbjct: 190 EMTPRRGEVYTCHVEHPSLKSPITVEW 216
>ref|NP_034519.2| histocompatibility 2, O region beta locus [Mus musculus]
Length = 271
Score = 175 bits (443), Expect(2) = 3e-45
Identities = 88/206 (42%), Positives = 118/206 (57%), Gaps = 28/206 (13%)
Frame = +2
Query: 92 RGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYV 271
R W+ AL + L+ L + RD+P +F+ KA+C+F NGTE+V LL R+ +N +EY+
Sbjct: 5 RAPWVVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFIFNLEEYL 64
Query: 272 RFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPR 451
FDSD+G F +TE G P A WN + D +E RA V+ VCR Y++ F V R P
Sbjct: 65 HFDSDLGMFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGAPFTVERNVPPE 124
Query: 452 VTVYPAKTQPLQHHNLLVCSVTGFYPGHV----------------------------ETM 547
VTVYP +T LQ HNLL+CSVTGFYPG + +T
Sbjct: 125 VTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNGDWTFQTT 184
Query: 548 VMLETVPQSGEVYTCRVEHPSLTSPV 625
VMLE +P+ G++Y+C VEHP L PV
Sbjct: 185 VMLEMIPELGDIYSCLVEHPGLLRPV 210
Score = 26.2 bits (56), Expect(2) = 3e-45
Identities = 15/50 (30%), Positives = 21/50 (42%)
Frame = +1
Query: 619 PRTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQP 768
P +V W A+SE + K++SG I+ K QK QP
Sbjct: 209 PVSVAWMAQSEYSWKKILSGAAVFLLGLIVFLVGVVIHLKAQKASVETQP 258
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: 47,477,348
Number of Sequences: 45328
Number of extensions: 1318337
Number of successful extensions: 6093
Number of sequences better than 1.0e-05: 4
Number of HSP's better than 0.0 without gapping: 4982
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): 6068
length of database: 21,768,885
effective HSP length: 103
effective length of database: 17,100,101
effective search space used: 3437120301
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)