Animal-Genome cDNA 20060611C-005388


Search to RefSeqSP

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-005388
         (1119 letters)

Database: RefSeqSP 
           1040 sequences; 434,620 total letters

Searching...done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_998933.1| swine leukocyte antigen 7 [Sus scrofa]                74   6e-15
Alignment   gi|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa]                60   1e-10
Alignment   gi|NP_999143.1| beta 2-microglobulin [Sus scrofa]                     59   2e-10
Alignment   gi|NP_998996.1| CD1 antigen [Sus scrofa]                              55   3e-09

>ref|NP_998933.1| swine leukocyte antigen 7 [Sus scrofa]
          Length = 401

 Score = 73.9 bits (180), Expect = 6e-15
 Identities = 46/179 (25%), Positives = 80/179 (44%), Gaps = 5/179 (2%)
 Frame = +3

Query: 198 CHFFNGTERVRLLDRYFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAE 377
           C+       +R   ++ Y+G +Y+  + D+  +  V    + + + W  ++   EQ RA 
Sbjct: 122 CYVARDGRLLRGYSQFAYDGADYIVLNEDLRSWTAVGMAAQITRRKWE-EETVAEQSRAY 180

Query: 378 VDTVC---RHNYEISETFLVPRRAEPR--VTVYPAKTQPLQHHNLLVCSVTGFYPGHVEV 542
           ++  C    H Y  +    + R   P+  VT +P+    +     L C   GFYP  + +
Sbjct: 181 LEVACVQSLHRYLANGKETLQRSDPPKTHVTRHPSSDNKVT----LRCWALGFYPKEISL 236

Query: 543 RWFRNGQEEVAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEW 719
            W + GQ++   V      P+GD TF+    L   P   + YTC V+H  L  P+T+ W
Sbjct: 237 TWQQEGQDQSQDVEVVETRPSGDGTFRKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRW 295


>ref|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa]
          Length = 356

 Score = 59.7 bits (143), Expect = 1e-10
 Identities = 45/174 (25%), Positives = 74/174 (42%), Gaps = 11/174 (6%)
 Frame = +3

Query: 252 NGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRH----------- 398
           NG+E+++FD+ +G +       R     W  + D + +++  +   C H           
Sbjct: 136 NGEEFMKFDTKLGTWDGEWPEARTIGSKWMQEPDAVNKEKTFLLYSCPHRLLGHLERGRG 195

Query: 399 NYEISETFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAG 578
           N E  E   +  +A P        T P    ++L C    FYP  +++R+ RNG    +G
Sbjct: 196 NLEWKEPPSMRMKARPG-------TAP--GFSVLTCIAFSFYPPELQLRFLRNGLAAGSG 246

Query: 579 VVSTGLIPNGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESA 740
               G  PNGD +F     L         Y C V+H  L  P+TVE  + ++S+
Sbjct: 247 ESDIG--PNGDGSFHAWSSLTVKSGDEHHYCCVVQHAGLAQPLTVELESPAKSS 298


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

 Score = 58.9 bits (141), Expect = 2e-10
 Identities = 31/92 (33%), Positives = 49/92 (53%)
 Frame = +3

Query: 444 PRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNGDWTFQ 623
           P+V VY          N L C V+GF+P  +E+   +NG++  A    + L  + DW+F 
Sbjct: 25  PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAE--QSDLSFSKDWSFY 82

Query: 624 TMVMLETVPQSGEVYTCRVEHPSLTSPVTVEW 719
            +V  E  P + + Y+CRV+H +L  P  V+W
Sbjct: 83  LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKW 114


>ref|NP_998996.1| CD1 antigen [Sus scrofa]
          Length = 339

 Score = 55.1 bits (131), Expect = 3e-09
 Identities = 28/73 (38%), Positives = 39/73 (53%)
 Frame = +3

Query: 477 PLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNGDWTFQTMVMLETVPQS 656
           P   H +LVC V+GFYP  + V W R+ QE+  G     ++PN D T+   V L+     
Sbjct: 215 PSPGHLMLVCHVSGFYPKPIWVMWMRDEQEQ-PGTQQGDILPNADGTWYLRVTLDVAAGE 273

Query: 657 GEVYTCRVEHPSL 695
               +CRV+H SL
Sbjct: 274 ASGLSCRVKHSSL 286


  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: 1,166,209
Number of Sequences: 1040
Number of extensions: 32744
Number of successful extensions: 128
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 104
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): 122
length of database: 434,620
effective HSP length: 78
effective length of database: 353,500
effective search space used: 103929000
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-005388
         (1119 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, ...   413   e-115
Alignment   gi|XP_582099.2| PREDICTED: similar to major histocompatibility ...   343   2e-94
Alignment   gi|NP_001029840.2| MHC class II antigen [Bos taurus]                 306   2e-83
Alignment   gi|NP_001012694.1| major histocompatibility complex, class II, ...   295   6e-80
Alignment   gi|XP_876139.1| PREDICTED: similar to H-2 class II histocompati...   281   9e-76
Alignment   gi|NP_001012697.1| major histocompatibility complex, class II, ...   267   1e-71
Alignment   gi|NP_001013618.1| major histocompatibility complex, class II, ...   257   1e-68
Alignment   gi|XP_874766.1| PREDICTED: similar to HLA class II histocompati...   212   4e-55
Alignment   gi|NP_001029503.1| hypothetical protein LOC508800 [Bos taurus]        79   8e-15
Alignment   gi|NP_001012399.1| hemochromatosis [Bos taurus]                       77   2e-14

>ref|NP_001012698.2| major histocompatibility complex, class II, DRB3 [Bos taurus]
          Length = 266

 Score =  413 bits (1062), Expect = e-115
 Identities = 198/266 (74%), Positives = 218/266 (81%)
 Frame = +3

Query: 69  MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 248
           M+ L FS G WMAAL +ML+VL PPLA AR+  PHFL   K ECHFFNGTERVR LDR+F
Sbjct: 1   MVCLYFSGGSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKGECHFFNGTERVRFLDRHF 60

Query: 249 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 428
           YNG+E+VRFDSD GEFR VTE GRP+A++WNSQKDF+EQKRAEVD VCRHNY   E+F V
Sbjct: 61  YNGEEFVRFDSDWGEFRAVTELGRPAAEHWNSQKDFLEQKRAEVDRVCRHNYGGVESFTV 120

Query: 429 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNG 608
            RR EP VTVYPAKTQPLQHHNLLVCSV GFYPGH+EVRWFRNG EE AGV+STGLI NG
Sbjct: 121 QRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFYPGHIEVRWFRNGHEEEAGVISTGLIQNG 180

Query: 609 DWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 788
           DWTFQTMVMLETVPQSGEVYTC+V+HP  TSP+TVEWRARS+SAQ KMMSG+        
Sbjct: 181 DWTFQTMVMLETVPQSGEVYTCQVDHPKRTSPITVEWRARSDSAQSKMMSGVGGFVLGLL 240

Query: 789 XXXXXXXIYFKNQKGRPALQPTGLLS 866
                  IYF+NQKGRP LQPTGLLS
Sbjct: 241 FLAVGLFIYFRNQKGRPTLQPTGLLS 266


>ref|XP_582099.2| PREDICTED: similar to major histocompatibility complex, class II,
           DR beta 5 precursor [Bos taurus]
          Length = 255

 Score =  343 bits (879), Expect = 2e-94
 Identities = 167/252 (66%), Positives = 191/252 (75%)
 Frame = +3

Query: 102 MAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFDS 281
           MAAL ++L+VLS P + AR+T PHF+   K EC F NG ER+R   RY YN  E V FDS
Sbjct: 1   MAALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQEDVHFDS 60

Query: 282 DVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTVY 461
           DVGEF  +TE GR  A+YWN QKDFMEQ RA+VDT+CR NY+   +FL  RR EP VTVY
Sbjct: 61  DVGEFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCRSNYQGIGSFLRQRRVEPTVTVY 120

Query: 462 PAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNGDWTFQTMVMLE 641
           PAKTQPLQHHNLLVCSV GFYPGH+EVRWF N  EE AGV+STGLI NGDWTFQTMVMLE
Sbjct: 121 PAKTQPLQHHNLLVCSVNGFYPGHIEVRWFWNSHEEEAGVISTGLIQNGDWTFQTMVMLE 180

Query: 642 TVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFK 821
           TVPQSGEVYTC+VEHPS TSP+TVEWRA+S+SAQ K+MSGI               I+ +
Sbjct: 181 TVPQSGEVYTCQVEHPSRTSPLTVEWRAQSDSAQRKLMSGIGGFVLGLLFLGVGLFIHLR 240

Query: 822 NQKGRPALQPTG 857
           ++KG PALQP G
Sbjct: 241 SKKGHPALQPIG 252


>ref|NP_001029840.2| MHC class II antigen [Bos taurus]
          Length = 261

 Score =  306 bits (783), Expect = 2e-83
 Identities = 148/257 (57%), Positives = 179/257 (69%)
 Frame = +3

Query: 63  SSMLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDR 242
           S M+ L   RG W A + + LV+LS P A  RD+P  F+   K  C+F NGTERVR + R
Sbjct: 2   SGMVALWIPRGLWTAVVMVTLVMLSTPGAEGRDSPKDFVVQFKGLCYFTNGTERVRYVTR 61

Query: 243 YFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETF 422
           Y YN +EYVRFDSD   +R +T  GRP A+YWNSQKDF+EQ RAE DTVCRHNY+     
Sbjct: 62  YIYNQEEYVRFDSDWDLYRALTPLGRPDAEYWNSQKDFLEQTRAEADTVCRHNYQAELIT 121

Query: 423 LVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIP 602
            + RR EP VT+ P++T+ L HHNLLVCSVT FYP  ++VRWFRN +EE AGVVST LI 
Sbjct: 122 SLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLIR 181

Query: 603 NGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXX 782
           NGDWTFQ +VMLE  PQ G+VYTC VEHPSL SP+ VEWRA+SESAQ KM+SG+      
Sbjct: 182 NGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPIMVEWRAQSESAQSKMLSGVGGFVLG 241

Query: 783 XXXXXXXXXIYFKNQKG 833
                    I+ ++QKG
Sbjct: 242 LIFLGLGLIIHHRSQKG 258


>ref|NP_001012694.1| major histocompatibility complex, class II, DQ beta [Bos taurus]
          Length = 261

 Score =  295 bits (754), Expect = 6e-80
 Identities = 141/257 (54%), Positives = 180/257 (70%)
 Frame = +3

Query: 63  SSMLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDR 242
           S M+ L   RG W AA+ + L VLS P A  RD+P   +     +C+F NGTERVR + R
Sbjct: 2   SGMVALRIPRGLWTAAVMVTLAVLSTPGAEGRDSPQDTVVHFMGQCYFTNGTERVRYVTR 61

Query: 243 YFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETF 422
           Y YN +E   +DSDVGE+R VT+ GR  A+YWNSQKD +EQ RAE+DTVCRHNY++    
Sbjct: 62  YIYNQEETAYYDSDVGEYRAVTQLGRTLAEYWNSQKDILEQTRAELDTVCRHNYQLEVIT 121

Query: 423 LVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIP 602
            + R+ EP VT+  ++T+ L HHNLLVCSVT FYPG ++VRWF+NG+EE AG+VST LI 
Sbjct: 122 SLQRQVEPTVTISLSRTEALNHHNLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPLIR 181

Query: 603 NGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXX 782
           NGDWTFQ +VMLE  P+ G+VYTC VEHPSL SP++VEWRA+SESAQ KM+SG+      
Sbjct: 182 NGDWTFQILVMLEMTPKRGDVYTCHVEHPSLQSPISVEWRAQSESAQSKMLSGVGGFVLG 241

Query: 783 XXXXXXXXXIYFKNQKG 833
                    +  ++QKG
Sbjct: 242 LIFLGLGLIVRRRSQKG 258


>ref|XP_876139.1| PREDICTED: similar to H-2 class II histocompatibility antigen, I-E
           beta chain precursor [Bos taurus]
          Length = 269

 Score =  281 bits (718), Expect = 9e-76
 Identities = 132/193 (68%), Positives = 151/193 (78%)
 Frame = +3

Query: 186 GKAECHFFNGTERVRLLDRYFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQ 365
           GK+ECHF NGT++VR LDRY YN +E V+FDS VGE+R  TE GRP+A+ WN     +++
Sbjct: 4   GKSECHFSNGTQQVRFLDRYIYNREEQVQFDSLVGEYRARTEMGRPAAERWNRWPQALQR 63

Query: 366 KRAEVDTVCRHNYEISETFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVR 545
            RA V   C  NYE   +  V RR +P VTVYP K++PL HHNLLVCSV GFYPGH+EVR
Sbjct: 64  ARAAVHAYCASNYEFFASRTVQRRVQPTVTVYPVKSRPLWHHNLLVCSVNGFYPGHIEVR 123

Query: 546 WFRNGQEEVAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRA 725
           WFRNGQEE AGVVSTGLIPNGDWTFQ MVMLE VPQ GEVY C VEHPS TSPVTVEWRA
Sbjct: 124 WFRNGQEEEAGVVSTGLIPNGDWTFQIMVMLEIVPQGGEVYACHVEHPSRTSPVTVEWRA 183

Query: 726 RSESAQGKMMSGI 764
           + ES+Q KM+SGI
Sbjct: 184 QDESSQEKMLSGI 196


>ref|NP_001012697.1| major histocompatibility complex, class II, DY beta [Bos taurus]
          Length = 259

 Score =  267 bits (682), Expect = 1e-71
 Identities = 130/215 (60%), Positives = 156/215 (72%)
 Frame = +3

Query: 120 MLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFDSDVGEFR 299
           + +VL  P A  RD P +F++  K  C+F NGTE VRL+ R  YN +E + FDSD+GEF 
Sbjct: 19  VFLVLRIPEAHCRDAPKNFVYQFKGMCYFTNGTEHVRLVARQIYNKEEILHFDSDLGEFV 78

Query: 300 EVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTVYPAKTQP 479
            VTE GR  A+ WN+QKD + + RA VDT+CRHNY+ +  F V RR EP VTV PA T+ 
Sbjct: 79  AVTELGRVCAEIWNTQKDLLAEFRAYVDTLCRHNYKETAGFTVQRRVEPTVTVSPASTEA 138

Query: 480 LQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNGDWTFQTMVMLETVPQSG 659
           L HHNLLVCSVT FYP  V+V+WFRN QE+ AGV  T L  NGDWT+Q  VMLETVPQ G
Sbjct: 139 LNHHNLLVCSVTDFYPRQVKVKWFRNQQEQTAGVGFTPLTQNGDWTYQIHVMLETVPQLG 198

Query: 660 EVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGI 764
           +VY C V+HPSL SP+TVEWRA+SESAQ KM SGI
Sbjct: 199 DVYVCHVDHPSLQSPITVEWRAQSESAQSKMQSGI 233


>ref|NP_001013618.1| major histocompatibility complex, class II, DO beta [Bos taurus]
          Length = 271

 Score =  257 bits (656), Expect = 1e-68
 Identities = 120/246 (48%), Positives = 160/246 (65%)
 Frame = +3

Query: 99  WMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFD 278
           W+       + L   +   RD+P  F+   KA+C+F NGTE+VR + R+ +N ++Y RFD
Sbjct: 8   WVVTFLSTALRLDASVTQGRDSPEDFVTQAKADCYFTNGTEKVRFVVRFIFNLEDYARFD 67

Query: 279 SDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTV 458
           SD+G F  +TE G+P A+ WN++ D + + RA VD +CR NY +   F V RR +P VTV
Sbjct: 68  SDLGMFVALTELGKPDAERWNNRPDILARSRASVDMLCRRNYYLGAPFTVGRRVQPEVTV 127

Query: 459 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNGDWTFQTMVML 638
           YP KT  LQH NLL+C VTGFYPG ++V WFRNGQE+  G++STGLI NGDWTFQ  VML
Sbjct: 128 YPEKTPALQHRNLLLCLVTGFYPGDIKVTWFRNGQEQREGIMSTGLIRNGDWTFQMTVML 187

Query: 639 ETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYF 818
              P+ GEVYTC V+HPSL SPV+VEWRA+SE +  K++SG                ++ 
Sbjct: 188 AMTPELGEVYTCLVDHPSLLSPVSVEWRAQSEYSWRKILSGAAAFLVGLVFFLVEIVVHI 247

Query: 819 KNQKGR 836
           +  KGR
Sbjct: 248 RAWKGR 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 =  212 bits (540), Expect = 4e-55
 Identities = 125/272 (45%), Positives = 153/272 (56%), Gaps = 2/272 (0%)
 Frame = +3

Query: 51  PLLFSSMLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVR 230
           P LF+S + L FS+G WMAAL +M+  LSP L  AR+T                      
Sbjct: 7   PFLFASTVCLYFSKGSWMAALLVMMG-LSPLLTWARETQ--------------------- 44

Query: 231 LLDRYFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRH--NY 404
                 Y    +V  DS +         G+P A     + D            C H    
Sbjct: 45  ------YKRTPWVVIDSQISAISH----GKPCALNGYRECDG-----------CFHPIGL 83

Query: 405 EISETFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVV 584
           + +    + ++ EP VTVYPAKTQPLQH++LLVCSV GFY GHVEVRWF  GQEE AGV+
Sbjct: 84  KANRDITLQKKVEPTVTVYPAKTQPLQHNHLLVCSVNGFYLGHVEVRWFWKGQEEEAGVI 143

Query: 585 STGLIPNGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGI 764
           STGLI NGDWTF+T+VMLETV QSGEVYTC++EHPS  SP+  EWRA+S+SAQ KMMSG 
Sbjct: 144 STGLIQNGDWTFETIVMLETVLQSGEVYTCQLEHPSWRSPIAEEWRAQSDSAQSKMMSGT 203

Query: 765 XXXXXXXXXXXXXXXIYFKNQKGRPALQPTGL 860
                           +F+NQKG   LQPTG+
Sbjct: 204 GGFALGLLFLVVGLFTHFRNQKGHSGLQPTGI 235


>ref|NP_001029503.1| hypothetical protein LOC508800 [Bos taurus]
          Length = 299

 Score = 78.6 bits (192), Expect = 8e-15
 Identities = 54/211 (25%), Positives = 97/211 (45%), Gaps = 4/211 (1%)
 Frame = +3

Query: 117 MMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFDSDVGEF 296
           + +  LS  +   +D      F G   C   N  E       Y Y+G ++++FD ++  +
Sbjct: 93  IFMETLSDIMDYYKDREGSHTFQGAFGCELRNN-ESSGAFWGYAYDGQDFIKFDKEIPAW 151

Query: 297 REVTEFGRPSAKYWNSQKDFMEQKRAEVDTVC----RHNYEISETFLVPRRAEPRVTVYP 464
             +    + + + W ++  ++++ +A ++  C    R     S T L  R+  P V+V  
Sbjct: 152 VPLDPAAQNTKRKWEAEAVYVQRAKAYLEEECPGMLRRYLPYSRTHL-DRQESPSVSV-T 209

Query: 465 AKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNGDWTFQTMVMLET 644
               P  H   L C    FYP  + + W R G  + A      ++P+G+ T+Q+ V++  
Sbjct: 210 GHAAP-GHKRTLKCLAYDFYPRSIGLHWTRAGDAQEAES-GGDVLPSGNGTYQSWVVVGV 267

Query: 645 VPQSGEVYTCRVEHPSLTSPVTVEWRARSES 737
            P+    Y+C VEH SLT P+TV W  R ++
Sbjct: 268 PPEDQAPYSCHVEHRSLTRPLTVPWDPRQQA 298


>ref|NP_001012399.1| hemochromatosis [Bos taurus]
          Length = 356

 Score = 77.4 bits (189), Expect = 2e-14
 Identities = 51/180 (28%), Positives = 84/180 (46%), Gaps = 5/180 (2%)
 Frame = +3

Query: 240 RYFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCR----HNYE 407
           +Y Y+G +++ F  +  ++R      + +   W   K   +Q RA +D  C     H  E
Sbjct: 145 KYGYDGQDHLEFRPETLDWRAAEPRAQVTKLEWEVNKIRAKQNRAYLDRDCPEQLLHLLE 204

Query: 408 ISETFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQE-EVAGVV 584
           +    L  ++  P V V    T  L     L C    FYP ++ +RW ++ Q  +   + 
Sbjct: 205 LGRGPL-EQQVPPLVKVTHHVTSSL---TTLRCRALNFYPQNITIRWLKDKQFLDAKEIK 260

Query: 585 STGLIPNGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGI 764
              ++PNGD T+Q  V L  +P   + Y+C+VEHP L  P+T  W     S  G +++GI
Sbjct: 261 PEDVLPNGDGTYQAWVALAMLPGEEQRYSCQVEHPGLDQPLTATW---EPSLSGTLVTGI 317


  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: 44,551,578
Number of Sequences: 33508
Number of extensions: 1331583
Number of successful extensions: 5327
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 4355
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): 5270
length of database: 16,112,626
effective HSP length: 103
effective length of database: 12,661,302
effective search space used: 3405890238
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-005388
         (1119 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...   389   e-108
Alignment   gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca...   340   2e-93
Alignment   gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati...   282   4e-76
Alignment   gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati...   266   3e-71
Alignment   gi|XP_536867.2| PREDICTED: similar to Zinc-alpha-2-glycoprotein...    73   4e-13
Alignment   gi|XP_849737.1| PREDICTED: similar to HLA class II histocompati...    72   1e-12
Alignment   gi|NP_001018646.1| MHC class Ib [Canis familiaris]                    70   3e-12
Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]     70   4e-12
Alignment   gi|NP_001014767.1| MHC class I DLA-88 [Canis familiaris]              70   5e-12
Alignment   gi|XP_855624.1| PREDICTED: MHC class Ib [Canis familiaris]            68   1e-11

>ref|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis familiaris]
          Length = 266

 Score =  389 bits (998), Expect = e-108
 Identities = 185/266 (69%), Positives = 211/266 (79%)
 Frame = +3

Query: 69  MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 248
           M+ LCF  G WM AL ++L+VL+PP A ARDTPPHFL + K+EC+F NGTERVR ++RY 
Sbjct: 1   MVCLCFLGGSWMTALMLILMVLNPPFAWARDTPPHFLEVAKSECYFTNGTERVRFVERYI 60

Query: 249 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 428
           +N +E+VRFDSDVGEFR VTE GRP A+ WN QK+ +EQ+RA VDT CRHNY + E+F V
Sbjct: 61  HNREEFVRFDSDVGEFRAVTELGRPVAESWNGQKEILEQERATVDTYCRHNYGVIESFTV 120

Query: 429 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNG 608
            RR EP VTVYP KTQ LQHHNLLVCSV GFYPGH+EVRW RNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNG 180

Query: 609 DWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 788
           DWTFQ +VMLE VPQSGEVYTC+VEHPSLTSPVTVEWRA+S+SAQ KM+SGI        
Sbjct: 181 DWTFQILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWRAQSDSAQSKMLSGIGGFVLGLL 240

Query: 789 XXXXXXXIYFKNQKGRPALQPTGLLS 866
                  IYF+NQKG   LQPTGLLS
Sbjct: 241 FLAVGLFIYFRNQKGHSGLQPTGLLS 266


>ref|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Canis familiaris]
          Length = 269

 Score =  340 bits (871), Expect = 2e-93
 Identities = 165/267 (61%), Positives = 195/267 (73%)
 Frame = +3

Query: 63  SSMLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDR 242
           S  + LC  RGFW AA+ M+LVVLS P+A  RD+P  F+F  KAEC+F NGTERVRLL +
Sbjct: 2   SGKMTLCIPRGFWTAAVMMILVVLSIPVAEGRDSPQDFVFQYKAECYFTNGTERVRLLTK 61

Query: 243 YFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETF 422
           Y YN +E+VRFDSDVGEFR VTE GRP A+YWN QKD M++ RAE+DTVCRHNY   E  
Sbjct: 62  YIYNREEFVRFDSDVGEFRAVTELGRPDAEYWNRQKDEMDRVRAELDTVCRHNYGREELT 121

Query: 423 LVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIP 602
            + RR EP VT++P+KT+ L HHNLLVCSVT FYPG ++VRWFRN QE+ AGVVST LI 
Sbjct: 122 TLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLIR 181

Query: 603 NGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXX 782
           NGDWTFQ +VMLE  PQ G+VYTC VEH SL SP+TV+WRA+SESAQ KM+SGI      
Sbjct: 182 NGDWTFQILVMLEMTPQRGDVYTCHVEHASLQSPITVQWRAQSESAQSKMLSGIGGFVLG 241

Query: 783 XXXXXXXXXIYFKNQKGRPALQPTGLL 863
                    I  ++QKG     P GLL
Sbjct: 242 LIFLGLGLIIRHRSQKGSRGSPPAGLL 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 =  282 bits (722), Expect = 4e-76
 Identities = 133/253 (52%), Positives = 171/253 (67%)
 Frame = +3

Query: 99  WMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFD 278
           WM AL + +  L   +   RD+P  F+   KA+C+F NGTE+V+ + R+ +N +EY RFD
Sbjct: 8   WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67

Query: 279 SDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTV 458
           S VG F  +TE G+P A+ WNSQ   +E+ RA VD +CRHNYE+   F V R+ +P VTV
Sbjct: 68  SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127

Query: 459 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNGDWTFQTMVML 638
           YP +T  +QHHNLL+CSVTGFYPG ++++WFRNGQEE  GV+STGLI NGDWTFQTMVML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187

Query: 639 ETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYF 818
           E  P+ G+VYTC V HPSL SPV+VEWRA+S  +  KM+SGI               I  
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPVSVEWRAQSTYSWRKMLSGIAAFLLGLIFLLVGTVICL 247

Query: 819 KNQKGRPALQPTG 857
           + QKG    Q +G
Sbjct: 248 RAQKGYVETQFSG 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 =  266 bits (680), Expect = 3e-71
 Identities = 119/207 (57%), Positives = 152/207 (73%)
 Frame = +3

Query: 99  WMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFD 278
           WM AL + +  L   +   RD+P  F+   KA+C+F NGTE+V+ + R+ +N +EY RFD
Sbjct: 8   WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67

Query: 279 SDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTV 458
           S VG F  +TE G+P A+ WNSQ   +E+ RA VD +CRHNYE+   F V R+ +P VTV
Sbjct: 68  SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127

Query: 459 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNGDWTFQTMVML 638
           YP +T  +QHHNLL+CSVTGFYPG ++++WFRNGQEE  GV+STGLI NGDWTFQTMVML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187

Query: 639 ETVPQSGEVYTCRVEHPSLTSPVTVEW 719
           E  P+ G+VYTC V HPSL SPV+VEW
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPVSVEW 214


>ref|XP_536867.2| PREDICTED: similar to Zinc-alpha-2-glycoprotein precursor
           (Zn-alpha-2-glycoprotein) (Zn-alpha-2-GP) [Canis
           familiaris]
          Length = 315

 Score = 73.2 bits (178), Expect = 4e-13
 Identities = 53/219 (24%), Positives = 103/219 (47%), Gaps = 8/219 (3%)
 Frame = +3

Query: 117 MMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFDSDVGEF 296
           + +V L   +   +D      F G   C   N         RY Y+G  ++ F+ ++  +
Sbjct: 96  IFMVTLKDIMEYYKDKEGSHTFQGMFGCELQNNKNSGAFW-RYAYDGRNFIEFNKEIPAW 154

Query: 297 REVTEFGRPSAKYWNSQKDFMEQKRAEVDTVC----RHNYEISETFLVPRRAEPRVTVYP 464
                    + K W +++ ++++ +A ++  C    +   E  +T+L  R+  P V++  
Sbjct: 155 VPQDPAALNTKKKWEAEEVYVQRAKAYLEEECPVMLQRYLEYGKTYL-DRQEPPSVSITS 213

Query: 465 AKTQPLQHHNLLVCSVTGFYPGHVEVRWFR--NGQEEVAGVVSTGLIPNGDWTFQTMVML 638
             T   +    L C V+GFYP  +++ W +  + QE  +G     L+P+G+ T+Q  V++
Sbjct: 214 HGTP--EGIQTLKCWVSGFYPQEIDLHWIQADDTQETKSG---GALLPSGNNTYQAWVVM 268

Query: 639 ETVPQ--SGEVYTCRVEHPSLTSPVTVEWRARSESAQGK 749
              PQ  +   Y+C V+H SL+ P+TV W  R  + + +
Sbjct: 269 SASPQDLASFSYSCLVKHSSLSQPLTVLWDKRQGAVRAE 307


>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 = 72.0 bits (175), Expect = 1e-12
 Identities = 40/127 (31%), Positives = 61/127 (48%), Gaps = 1/127 (0%)
 Frame = +3

Query: 342 SQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGF 521
           +Q++++ Q+ +     C  + +     L  R   P V V  +     +   +L C V GF
Sbjct: 81  NQQEYLHQRLSNGLQDCATHTQSFWGSLTHRTRPPTVQVAKSTPFNTKESVMLACYVWGF 140

Query: 522 YPGHVEVRWFRNGQEEVAGVVSTGLI-PNGDWTFQTMVMLETVPQSGEVYTCRVEHPSLT 698
           YP  V + W +NGQ   +   +  +  PNGDWT+QT+  L T P   + YTC VEH    
Sbjct: 141 YPADVTISWRKNGQPVPSHSSALNMAQPNGDWTYQTVSHLATTPSYEDTYTCVVEHIGAP 200

Query: 699 SPVTVEW 719
            PV  +W
Sbjct: 201 EPVCEDW 207


>ref|NP_001018646.1| MHC class Ib [Canis familiaris]
          Length = 381

 Score = 70.5 bits (171), Expect = 3e-12
 Identities = 47/178 (26%), Positives = 81/178 (45%), Gaps = 7/178 (3%)
 Frame = +3

Query: 225 VRLLDRYFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNS------QKDFMEQKRAEVDT 386
           +R   R+ Y+G +Y+    D+  +       + + + W++      +K+F+E +  E   
Sbjct: 140 LRGYQRHAYDGLDYITLSEDLRSWIVEDPVAQITRRKWDAATVAENRKNFLEGRCLE--W 197

Query: 387 VCRHNYEISETFLVPRRAEPRVTVYPAKTQPLQHHNL-LVCSVTGFYPGHVEVRWFRNGQ 563
           + RH     ET    +RA+P  T      +P+  H + L C   GFYP  + + W R+G+
Sbjct: 198 LRRHLENGRETL---QRADPPKT--SVTRRPISEHEVTLKCWALGFYPAEITLTWQRDGE 252

Query: 564 EEVAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSES 737
           ++          P GD TFQ    +       + YTC + H SLT P+T+ W    +S
Sbjct: 253 DQTQDTELVETRPGGDGTFQKWAAVVVPSGEEQRYTCHILHKSLTKPITLRWEPPPQS 310


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

 Score = 70.1 bits (170), Expect = 4e-12
 Identities = 45/158 (28%), Positives = 68/158 (43%), Gaps = 1/158 (0%)
 Frame = +3

Query: 249 YNGDEYVRFDSDVGE-FREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFL 425
           ++GDE    D +  E    + EFGR ++         +   +A +DT+ + +     T  
Sbjct: 51  FDGDEIFHVDMEKKETVWRLEEFGRFASFEAQGALANIAVDKANLDTMIKRSNHTPNT-- 108

Query: 426 VPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPN 605
                 P VTV       L   N+L+C +  F P  + V W RNG     GV  T  +P 
Sbjct: 109 ---NVPPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPR 165

Query: 606 GDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEW 719
            D  F+    L  +P + +VY C+VEH  L  P+   W
Sbjct: 166 EDHLFRKFHYLPFLPSAEDVYDCKVEHWGLDEPLLKHW 203


>ref|NP_001014767.1| MHC class I DLA-88 [Canis familiaris]
          Length = 361

 Score = 69.7 bits (169), Expect = 5e-12
 Identities = 49/181 (27%), Positives = 76/181 (41%), Gaps = 7/181 (3%)
 Frame = +3

Query: 198 CHFFNGTERVRLLDRYFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAE 377
           C    G   +R   +  Y+G +Y+  + D+  +       + + + W +     E  R  
Sbjct: 125 CDLGPGGRLLRGYSQDAYDGADYIALNEDLRSWTAADTAAQITRRKWEAAGT-AEHDRNY 183

Query: 378 VDTVC----RHNYEISETFLVPRRAEP---RVTVYPAKTQPLQHHNLLVCSVTGFYPGHV 536
           ++T C    R   E+ +  L+  RAEP   RVT +P       H   L C   GFYP  +
Sbjct: 184 LETTCVEWLRRYLEMGKETLL--RAEPPSTRVTRHPIS----DHEVTLRCWALGFYPAEI 237

Query: 537 EVRWFRNGQEEVAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVE 716
            + W R+G+++          P GD TFQ    +       + YTC V+H  L  PVT  
Sbjct: 238 TLTWQRDGEDQTQDTEVVDTRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLAEPVTRR 297

Query: 717 W 719
           W
Sbjct: 298 W 298


>ref|XP_855624.1| PREDICTED: MHC class Ib [Canis familiaris]
          Length = 381

 Score = 68.2 bits (165), Expect = 1e-11
 Identities = 46/178 (25%), Positives = 80/178 (44%), Gaps = 7/178 (3%)
 Frame = +3

Query: 225 VRLLDRYFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNS------QKDFMEQKRAEVDT 386
           +R   R+ Y+G +Y+    D+  +       + + + W++      +K+F+E +  E   
Sbjct: 140 LRGYQRHAYDGLDYITLSEDLRSWIVEDPVAQITRRKWDAATVAENRKNFLEGRCLE--W 197

Query: 387 VCRHNYEISETFLVPRRAEPRVTVYPAKTQPLQHHNL-LVCSVTGFYPGHVEVRWFRNGQ 563
           + RH     ET    +RA+P  T      +P+  H + L C   GFYP  + + W R+G+
Sbjct: 198 LRRHLENGRETL---QRADPPKT--SVTRRPISEHEVTLKCWALGFYPAEITLTWQRDGE 252

Query: 564 EEVAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSES 737
           ++          P GD TFQ    +       + YTC + H SL  P+T+ W    +S
Sbjct: 253 DQTQDTELVETRPGGDGTFQKWAAVVVPSGEEQRYTCHILHKSLPKPITLRWEPPPQS 310


  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: 52,279,488
Number of Sequences: 33732
Number of extensions: 1559644
Number of successful extensions: 6344
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 5056
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): 6290
length of database: 19,266,565
effective HSP length: 104
effective length of database: 15,758,437
effective search space used: 4223261116
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-005388
         (1119 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 ...   386   e-107
Alignment   gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati...   381   e-106
Alignment   gi|NP_072049.2| major histocompatibility complex, class II, DR ...   378   e-105
Alignment   gi|NP_002116.2| major histocompatibility complex, class II, DR ...   375   e-104
Alignment   gi|NP_068818.4| major histocompatibility complex, class II, DR ...   370   e-103
Alignment   gi|XP_949915.1| PREDICTED: similar to HLA class II histocompati...   351   7e-97
Alignment   gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati...   334   7e-92
Alignment   gi|NP_002114.2| major histocompatibility complex, class II, DQ ...   306   2e-83
Alignment   gi|NP_002112.3| major histocompatibility complex, class II, DP ...   293   2e-79
Alignment   gi|NP_872355.1| major histocompatibility complex, class II, DQ ...   285   6e-77

>ref|NP_002115.1| major histocompatibility complex, class II, DR beta 1 precursor
           [Homo sapiens]
          Length = 266

 Score =  386 bits (992), Expect = e-107
 Identities = 188/266 (70%), Positives = 212/266 (79%)
 Frame = +3

Query: 69  MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 248
           M+ L    G  M ALT+ L+VLS PLALA DT P FL+  K ECHFFNGTERVRLL+R  
Sbjct: 1   MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCI 60

Query: 249 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 428
           YN +E VRFDSDVGE+R VTE GRP A+YWNSQKD +EQ+RA VDT CRHNY + E+F V
Sbjct: 61  YNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTV 120

Query: 429 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNG 608
            RR EP+VTVYP+KTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 609 DWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 788
           DWTFQT+VMLETVP+SGEVYTC+VEHPS+TSP+TVEWRARSESAQ KM+SG+        
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 789 XXXXXXXIYFKNQKGRPALQPTGLLS 866
                  IYF+NQKG   LQPTG LS
Sbjct: 241 FLGAGLFIYFRNQKGHSGLQPTGFLS 266


>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 =  381 bits (979), Expect = e-106
 Identities = 188/266 (70%), Positives = 209/266 (78%)
 Frame = +3

Query: 69  MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 248
           M+ L    G  MAALT+ L+VLS PLALA DT P FL   K ECHFFNGTERVR L R  
Sbjct: 1   MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60

Query: 249 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 428
           YN +E VRFDSDVGE+R VTE GRP A+ WNSQKDF+E++RAEVDTVCRHNY + E+F V
Sbjct: 61  YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120

Query: 429 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNG 608
            RR  P VTVYPAKTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 609 DWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 788
           DWTFQT+VMLETVP+SGEVYTC+VEHPS+ SP+TVEWRARSESAQ KM+SG+        
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 789 XXXXXXXIYFKNQKGRPALQPTGLLS 866
                  IYF+NQKG   LQPTG LS
Sbjct: 241 FLGAGLFIYFRNQKGHSGLQPTGFLS 266


>ref|NP_072049.2| major histocompatibility complex, class II, DR beta 3 precursor
           [Homo sapiens]
          Length = 266

 Score =  378 bits (970), Expect = e-105
 Identities = 184/266 (69%), Positives = 209/266 (78%)
 Frame = +3

Query: 69  MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 248
           M+ L    G  +AALT+ L+VLS  LA A DT P FL L K+ECHFFNGTERVR LDRYF
Sbjct: 1   MVCLKLPGGSSLAALTVTLMVLSSRLAFAGDTRPRFLELRKSECHFFNGTERVRYLDRYF 60

Query: 249 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 428
           +N +E++RFDSDVGE+R VTE GRP A+ WNSQKD +EQKR  VD  CRHNY + E+F V
Sbjct: 61  HNQEEFLRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGRVDNYCRHNYGVGESFTV 120

Query: 429 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNG 608
            RR  P+VTVYPAKTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 609 DWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 788
           DWTFQT+VMLETVP+SGEVYTC+VEHPS+TS +TVEWRARSESAQ KM+SG+        
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSALTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 789 XXXXXXXIYFKNQKGRPALQPTGLLS 866
                  IYF+NQKG   LQPTG LS
Sbjct: 241 FLGAGLFIYFRNQKGHSGLQPTGFLS 266


>ref|NP_002116.2| major histocompatibility complex, class II, DR beta 5 precursor
           [Homo sapiens]
          Length = 266

 Score =  375 bits (963), Expect = e-104
 Identities = 183/266 (68%), Positives = 207/266 (77%)
 Frame = +3

Query: 69  MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 248
           M+ L    G +MA LT+ L+VLS PLALA DT P FL   K ECHFFNGTERVR L R  
Sbjct: 1   MVCLKLPGGSYMAKLTVTLMVLSSPLALAGDTRPRFLQQDKYECHFFNGTERVRFLHRDI 60

Query: 249 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 428
           YN +E +RFDSDVGE+R VTE GRP A+YWNSQKDF+E +RA VDT CRHNY + E+F V
Sbjct: 61  YNQEEDLRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAAVDTYCRHNYGVGESFTV 120

Query: 429 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNG 608
            RR EP+VTVYPA+TQ LQHHNLLVCSV GFYPG +EVRWFRN QEE AGVVSTGLI NG
Sbjct: 121 QRRVEPKVTVYPARTQTLQHHNLLVCSVNGFYPGSIEVRWFRNSQEEKAGVVSTGLIQNG 180

Query: 609 DWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 788
           DWTFQT+VMLETVP+SGEVYTC+VEHPS+TSP+TVEWRA+SESAQ KM+SG+        
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRAQSESAQSKMLSGVGGFVLGLL 240

Query: 789 XXXXXXXIYFKNQKGRPALQPTGLLS 866
                  IYFKNQKG   L PTGL+S
Sbjct: 241 FLGAGLFIYFKNQKGHSGLHPTGLVS 266


>ref|NP_068818.4| major histocompatibility complex, class II, DR beta 4 precursor
           [Homo sapiens]
          Length = 266

 Score =  370 bits (951), Expect = e-103
 Identities = 179/266 (67%), Positives = 207/266 (77%)
 Frame = +3

Query: 69  MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 248
           M+ L    G  MAALT+ L VLS PLALA DT P FL   K ECHF NGTERV  L RY 
Sbjct: 1   MVCLKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYI 60

Query: 249 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 428
           YN +EY R++SD+GE++ VTE GRP A+YWNSQKD +E++RAEVDT CR+NY + E+F V
Sbjct: 61  YNQEEYARYNSDLGEYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVESFTV 120

Query: 429 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNG 608
            RR +P+VTVYP+KTQPLQHHNLLVCSV GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVQPKVTVYPSKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 609 DWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 788
           DWTFQT+VMLETVP+SGEVYTC+VEHPS+ SP+TV+W ARSESAQ KM+SG+        
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSMMSPLTVQWSARSESAQSKMLSGVGGFVLGLL 240

Query: 789 XXXXXXXIYFKNQKGRPALQPTGLLS 866
                  IYF+NQKG   LQPTGLLS
Sbjct: 241 FLGTGLFIYFRNQKGHSGLQPTGLLS 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 =  351 bits (900), Expect = 7e-97
 Identities = 168/231 (72%), Positives = 186/231 (80%)
 Frame = +3

Query: 174 FLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKD 353
           FL   K ECHFFNGTERVR L R  YN +E VRFDSDVGE+R VTE GRP A+ WNSQKD
Sbjct: 54  FLKQDKFECHFFNGTERVRYLHRGIYNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKD 113

Query: 354 FMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGH 533
           F+E++RAEVDTVCRHNY + E+F V RR  P VTVYPAKTQPLQHHNLLVCSV+GFYPG 
Sbjct: 114 FLERRRAEVDTVCRHNYGVGESFTVQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGS 173

Query: 534 VEVRWFRNGQEEVAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTV 713
           +EVRWFRNGQEE AGVVSTGLI NGDWTFQT+VMLETVP+SGEVYTC+VEHPS+ SP+TV
Sbjct: 174 IEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTV 233

Query: 714 EWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQPTGLLS 866
           EWRARSESAQ KM+SG+               IYF+NQKG   LQPTG LS
Sbjct: 234 EWRARSESAQSKMLSGVGGFVLGLLFLGAGLFIYFRNQKGHSGLQPTGFLS 284


>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 =  334 bits (857), Expect = 7e-92
 Identities = 162/217 (74%), Positives = 180/217 (82%)
 Frame = +3

Query: 69  MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 248
           M+ L    G  MAALT+ L+VLS PLALA DT P FL   K ECHFFNGTERVR L R  
Sbjct: 1   MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60

Query: 249 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 428
           YN +E VRFDSDVGE+R VTE GRP A+ WNSQKDF+E++RAEVDTVCRHNY + E+F V
Sbjct: 61  YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120

Query: 429 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNG 608
            RR  P VTVYPAKTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 609 DWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEW 719
           DWTFQT+VMLETVP+SGEVYTC+VEHPS+ SP+TVEW
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEW 217


>ref|NP_002114.2| major histocompatibility complex, class II, DQ beta 1 precursor
           [Homo sapiens]
          Length = 261

 Score =  306 bits (784), Expect = 2e-83
 Identities = 148/247 (59%), Positives = 179/247 (72%)
 Frame = +3

Query: 93  GFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVR 272
           G   A +T+ML +LS P+A  RD+P  F++  K  C+F NGTERVRL+ R  YN +E VR
Sbjct: 12  GLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVR 71

Query: 273 FDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRV 452
           FDSDVGEFR VT  G P+A+YWNSQKD +E+KRA VD VCRHNY++     + RR EP V
Sbjct: 72  FDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTV 131

Query: 453 TVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNGDWTFQTMV 632
           T+ P++T+ L HHNLLVCSVT FYP  ++VRWFRN QEE AGVVST LI NGDWTFQ +V
Sbjct: 132 TISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILV 191

Query: 633 MLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXI 812
           MLE  PQ G+VYTC VEHPSL SP+TVEWRA+SESAQ KM+SGI               I
Sbjct: 192 MLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVLGLIFLGLGLII 251

Query: 813 YFKNQKG 833
           + ++QKG
Sbjct: 252 HHRSQKG 258


>ref|NP_002112.3| major histocompatibility complex, class II, DP beta 1 precursor
           [Homo sapiens]
          Length = 258

 Score =  293 bits (749), Expect = 2e-79
 Identities = 137/218 (62%), Positives = 168/218 (77%)
 Frame = +3

Query: 108 ALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFDSDV 287
           ALT +L+VL   +   R TP ++LF G+ EC+ FNGT+R   L+RY YN +E+ RFDSDV
Sbjct: 14  ALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQR--FLERYIYNREEFARFDSDV 71

Query: 288 GEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTVYPA 467
           GEFR VTE GRP+A+YWNSQKD +E+KRA  D +CRHNYE+     + RR +PRV V P+
Sbjct: 72  GEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPMTLQRRVQPRVNVSPS 131

Query: 468 KTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNGDWTFQTMVMLETV 647
           K  PLQHHNLLVC VT FYPG ++VRWF NGQEE AGVVST LI NGDWTFQ +VMLE  
Sbjct: 132 KKGPLQHHNLLVCHVTDFYPGSIQVRWFLNGQEETAGVVSTNLIRNGDWTFQILVMLEMT 191

Query: 648 PQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSG 761
           PQ G+VYTC+VEH SL SPVTVEW+A+S+SA+ K ++G
Sbjct: 192 PQQGDVYTCQVEHTSLDSPVTVEWKAQSDSARSKTLTG 229


>ref|NP_872355.1| major histocompatibility complex, class II, DQ beta 2 [Homo
           sapiens]
          Length = 231

 Score =  285 bits (728), Expect = 6e-77
 Identities = 137/218 (62%), Positives = 163/218 (74%)
 Frame = +3

Query: 93  GFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVR 272
           GFW AA+T+MLV+LS P+A ARD P  FL   K  C+F NGTERVR + RY YN +EY R
Sbjct: 12  GFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVRGVARYIYNREEYGR 71

Query: 273 FDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRV 452
           FDSDVGEF+ VTE GR S + WN+ KDF+EQ+RA VD VCRHNYE      + R+ EP V
Sbjct: 72  FDSDVGEFQAVTELGR-SIEDWNNYKDFLEQERAAVDKVCRHNYEAELRTTLQRQVEPTV 130

Query: 453 TVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNGDWTFQTMV 632
           T+ P++T+ L HHNLLVCSVT FYP  ++V+WFRN QEE AGVVST LI NGDWTFQ +V
Sbjct: 131 TISPSRTEALNHHNLLVCSVTDFYPAQIKVQWFRNDQEETAGVVSTSLIRNGDWTFQILV 190

Query: 633 MLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQG 746
           MLE  PQ G++YTC+VEHPSL SP+TVEWR R     G
Sbjct: 191 MLEITPQRGDIYTCQVEHPSLQSPITVEWRPRGPPPAG 228


  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: 50,852,582
Number of Sequences: 39411
Number of extensions: 1570082
Number of successful extensions: 6953
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 5311
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): 6907
length of database: 17,774,539
effective HSP length: 103
effective length of database: 13,715,206
effective search space used: 3689390414
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-005388
         (1119 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 [...   372   e-103
Alignment   gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/...   305   6e-83
Alignment   gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ...   288   5e-78
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...   259   5e-69
Alignment   gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ...    76   6e-14
Alignment   gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ...    74   3e-13
Alignment   gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha...    70   4e-12
Alignment   gi|NP_038506.1| alpha-2-glycoprotein 1, zinc [Mus musculus]           68   2e-11
Alignment   gi|NP_001030080.1| hypothetical protein LOC547343 [Mus musculus]      68   2e-11
Alignment   gi|NP_032235.1| histocompatibility-2 complex class 1-like [Mus ...    68   2e-11

>ref|NP_034512.1| histocompatibility 2, class II antigen E beta [Mus musculus]
          Length = 264

 Score =  372 bits (954), Expect = e-103
 Identities = 174/255 (68%), Positives = 206/255 (80%)
 Frame = +3

Query: 102 MAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFDS 281
           +AA+ ++L VLSPP+AL RD+ P FL   K+ECHF+NGT+RVR L RYFYN +E +RFDS
Sbjct: 10  VAAVILLLTVLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRFLKRYFYNLEENLRFDS 69

Query: 282 DVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPRVTVY 461
           DVGEFR VTE GRP A+ WNSQ + +++KRA VDT CRHNYEI + FLVPRR EP VTVY
Sbjct: 70  DVGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNFLVPRRVEPTVTVY 129

Query: 462 PAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNGDWTFQTMVMLE 641
           P KTQPL+HHNLLVCSV+ FYPG++EVRWFRNG+EE  G+VSTGL+ NGDWTFQT+VMLE
Sbjct: 130 PTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLE 189

Query: 642 TVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFK 821
           TVPQSGEVYTC+VEHPSLT PVTVEW+A+S SAQ KM+SG+               IYF+
Sbjct: 190 TVPQSGEVYTCQVEHPSLTDPVTVEWKAQSTSAQNKMLSGVGGFVLGLLFLRAGLFIYFR 249

Query: 822 NQKGRPALQPTGLLS 866
           NQKG+  LQPTGLLS
Sbjct: 250 NQKGQSGLQPTGLLS 264


>ref|NP_001029150.1| H-2 class II histocompatibility antigen E-a/k beta-2 [Mus musculus]
          Length = 287

 Score =  305 bits (781), Expect = 6e-83
 Identities = 146/252 (57%), Positives = 184/252 (73%)
 Frame = +3

Query: 69  MLHLCFSRGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYF 248
           M+ L   RG  +AA+ + L++L+PP+ L RD  P FL   KAECH+FNG ERV  + R+ 
Sbjct: 1   MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERVWSVTRFI 60

Query: 249 YNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLV 428
           YN +E+ RF+SD G+F  VTE GRP  +Y N+QKD ++  RA VD  CR+NY++ + F++
Sbjct: 61  YNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRASVDR-CRNNYDLVDIFML 119

Query: 429 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNG 608
             +AEP+VTVYPAKTQPL+HHNLLVCSV  FYPG +EVRWFRNG+EE  GVVSTGLI N 
Sbjct: 120 NLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNR 179

Query: 609 DWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 788
           DWT+QT+VMLE VP+ GEVYTC+VEHPSLTSPVTVEWRARS SAQ K++SG+        
Sbjct: 180 DWTYQTLVMLEMVPRGGEVYTCQVEHPSLTSPVTVEWRARSTSAQNKLLSGVMGMALGLF 239

Query: 789 XXXXXXXIYFKN 824
                   Y +N
Sbjct: 240 ILAVGLFFYLRN 251


>ref|NP_996988.1| histocompatibility 2, class II antigen A, beta 1 [Mus musculus]
          Length = 265

 Score =  288 bits (738), Expect = 5e-78
 Identities = 143/255 (56%), Positives = 175/255 (68%), Gaps = 1/255 (0%)
 Frame = +3

Query: 102 MAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFDS 281
           ++A  ++L+VLS P     D+  HF++    EC+F NGT+R+R + RY YN +EYVR+DS
Sbjct: 10  LSAAVVVLMVLSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRYVTRYIYNREEYVRYDS 69

Query: 282 DVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAE-PRVTV 458
           DVGE R VTE GRP A+YWNSQ + +E+ RAE+DTVCRHNYE  ET    RR E P V +
Sbjct: 70  DVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRRLEQPNVVI 129

Query: 459 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNGDWTFQTMVML 638
             ++T+ L HHN LVCSVT FYP  ++VRWFRNGQEE  GV ST LI NGDWTFQ +VML
Sbjct: 130 SLSRTEALNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVML 189

Query: 639 ETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYF 818
           E  P+ GEVYTC VEHPSL SP+TVEWRA+SESA  KM+SGI               I  
Sbjct: 190 EMTPRRGEVYTCHVEHPSLKSPITVEWRAQSESAWSKMLSGIGGCVLGVIFLGLGLFIRH 249

Query: 819 KNQKGRPALQPTGLL 863
           ++QKG     P GLL
Sbjct: 250 RSQKGPRGPPPAGLL 264


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

 Score =  259 bits (661), Expect = 5e-69
 Identities = 124/254 (48%), Positives = 163/254 (64%)
 Frame = +3

Query: 90  RGFWMAALTMMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYV 269
           R  W+ AL + L+ L   +   RD+P +F+   KA+C+F NGTE+V LL R+ +N +EY+
Sbjct: 5   RAPWVVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFIFNLEEYL 64

Query: 270 RFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEISETFLVPRRAEPR 449
            FDSD+G F  +TE G P A  WN + D +E  RA V+ VCR  Y++   F V R   P 
Sbjct: 65  HFDSDLGMFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGAPFTVERNVPPE 124

Query: 450 VTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNGDWTFQTM 629
           VTVYP +T  LQ HNLL+CSVTGFYPG + V+WFRNGQEE +GV+STGL+ NGDWTFQT 
Sbjct: 125 VTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNGDWTFQTT 184

Query: 630 VMLETVPQSGEVYTCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXX 809
           VMLE +P+ G++Y+C VEHP L  PV+V W A+SE +  K++SG                
Sbjct: 185 VMLEMIPELGDIYSCLVEHPGLLRPVSVAWMAQSEYSWKKILSGAAVFLLGLIVFLVGVV 244

Query: 810 IYFKNQKGRPALQP 851
           I+ K QK     QP
Sbjct: 245 IHLKAQKASVETQP 258


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

 Score = 76.3 bits (186), Expect = 6e-14
 Identities = 52/172 (30%), Positives = 75/172 (43%), Gaps = 15/172 (8%)
 Frame = +3

Query: 249 YNGDEYVRFDSDVG-----EFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEIS 413
           +N D    +D DVG     EF  ++      +   N Q+  + + +  +     H     
Sbjct: 46  FNKDLLACWDPDVGKIVPCEFGVLSRLAEIISNILNEQESLIHRLQNGLQDCATHTQPFW 105

Query: 414 ETFLVPRRAEPRVTVYPAKTQPLQHHN--LLVCSVTGFYPGHVEVRWFRNGQ-------- 563
           +  L  R   P V V  A+T P       +L C V GFYP  V + W +NGQ        
Sbjct: 106 DV-LTHRTRAPSVRV--AQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNK 162

Query: 564 EEVAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEW 719
           E+ A        PNGDWT+QT+  L   P  G+VYTC V+H   + P+  +W
Sbjct: 163 EKTAQ-------PNGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207


>ref|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus musculus]
          Length = 261

 Score = 73.9 bits (180), Expect = 3e-13
 Identities = 51/172 (29%), Positives = 76/172 (44%), Gaps = 15/172 (8%)
 Frame = +3

Query: 249 YNGDEYVRFDSDVG-----EFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEIS 413
           +N D    +D DVG     EF  +  +    ++  N ++  +++ +  +     H     
Sbjct: 46  FNKDLLACWDPDVGKIVPCEFGVLYPWAENFSRILNKEESLLQRLQNGLLDCASHTQPFW 105

Query: 414 ETFLVPRRAEPRVTVYPAKTQPLQHHN--LLVCSVTGFYPGHVEVRWFRNGQ-------- 563
              L  R   P V V  A+T P       +L C V GFYP  V + W +NGQ        
Sbjct: 106 NA-LTHRTRAPSVRV--AQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNK 162

Query: 564 EEVAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEW 719
           E+ A        PNGDWT+QT+  L   P  G+VYTC V+H   + P+  +W
Sbjct: 163 EKTAQ-------PNGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207


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

 Score = 70.1 bits (170), Expect = 4e-12
 Identities = 46/161 (28%), Positives = 70/161 (43%), Gaps = 4/161 (2%)
 Frame = +3

Query: 249 YNGDEYVRFDSDVGE-FREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRHNYEI--SET 419
           ++GDE    D D  E    + EFG+ ++        F  Q   +   V +HN  +    +
Sbjct: 53  FDGDELFYVDLDKKETVWMLPEFGQLAS--------FDPQGGLQNIAVVKHNLGVLTKRS 104

Query: 420 FLVPRRAE-PRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGL 596
              P   E P+ TV+P     L   N L+C V   +P  + + W RN +    GV  T  
Sbjct: 105 NSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSF 164

Query: 597 IPNGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEW 719
             N D++F  +  L  +P   ++Y C+VEH  L  PV   W
Sbjct: 165 FVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHW 205


>ref|NP_038506.1| alpha-2-glycoprotein 1, zinc [Mus musculus]
          Length = 307

 Score = 68.2 bits (165), Expect = 2e-11
 Identities = 43/207 (20%), Positives = 90/207 (43%), Gaps = 6/207 (2%)
 Frame = +3

Query: 117 MMLVVLSPPLALARDTPPHFLFLGKAECHFFNGTERVRLLDRYFYNGDEYVRFDSDVGEF 296
           + LV L   +   +DT     F G   C   N      +  RY Y+G++++ F+ ++  +
Sbjct: 91  IFLVTLKDIMDYYKDTTGSHTFQGMFGCEITNNRSSGAVW-RYAYDGEDFIEFNKEIPAW 149

Query: 297 REVTEFGRPSAKYWNSQKDFMEQKRAEVDTVCRH------NYEISETFLVPRRAEPRVTV 458
             +      +   W ++K ++++ +A ++  C        NY  S       R +P    
Sbjct: 150 IPLDPAAANTKLKWEAEKVYVQRAKAYLEEECPEMLKRYLNYSRSHL----DRIDPPTVT 205

Query: 459 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVSTGLIPNGDWTFQTMVML 638
             ++  P   + +  C   GFYP  + + W     +++A     G+ PNG+ T+ +   +
Sbjct: 206 ITSRVIP-GGNRIFKCLAYGFYPQRISLHW-NKANKKLAFEPERGVFPNGNGTYLSWAEV 263

Query: 639 ETVPQSGEVYTCRVEHPSLTSPVTVEW 719
           E  PQ  + + C ++H   +  ++V+W
Sbjct: 264 EVSPQDIDPFFCLIDHRGFSQSLSVQW 290


>ref|NP_001030080.1| hypothetical protein LOC547343 [Mus musculus]
          Length = 362

 Score = 68.2 bits (165), Expect = 2e-11
 Identities = 46/170 (27%), Positives = 72/170 (42%), Gaps = 5/170 (2%)
 Frame = +3

Query: 225 VRLLDRYFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVC---- 392
           +R   +Y Y+G +Y+  + D+  +       + + + W  Q    E+KRA ++  C    
Sbjct: 134 LRGYQQYAYDGCDYIALNEDLKTWTAADTAAQITRRKWE-QAGAAERKRAYLEGTCVEWL 192

Query: 393 -RHNYEISETFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEE 569
            RH    +ET L     +  VT +P     +     L C   GFYP  + + W  NG+E 
Sbjct: 193 LRHLKNGNETLLRTDSPKAHVTHHPRSKGEVT----LRCWALGFYPADITLTWQLNGEEL 248

Query: 570 VAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYTCRVEHPSLTSPVTVEW 719
              +      P GD TFQ    +       + YTC V H  L  P+T+ W
Sbjct: 249 TQDMELVETRPAGDGTFQKWAAVVVPLGKEQNYTCHVHHEGLPEPLTLRW 298


>ref|NP_032235.1| histocompatibility-2 complex class 1-like [Mus musculus]
          Length = 341

 Score = 67.8 bits (164), Expect = 2e-11
 Identities = 40/153 (26%), Positives = 71/153 (46%), Gaps = 4/153 (2%)
 Frame = +3

Query: 240 RYFYNGDEYVRFDSDVGEFREVTEFGRPSAKYWNSQKDFMEQKRAEVDTVC----RHNYE 407
           +Y Y+G +++ F+ D   +  +      + + W +    ++ ++  ++  C    +   E
Sbjct: 129 QYAYDGQDFIIFNKDTLSWLAMDYVAHITKQAWEANLHELQYQKNWLEEECIAWLKRFLE 188

Query: 408 ISETFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEVAGVVS 587
                L  R   P V     +T P        C   GFYP  + + W +NG+E    V  
Sbjct: 189 YGRDTL-ERTEHPVVRTTRKETFP--GITTFFCRAHGFYPPEISMTWMKNGEEIAQEVDY 245

Query: 588 TGLIPNGDWTFQTMVMLETVPQSGEVYTCRVEH 686
            G++P+GD T+QT + +   PQS +VY+C VEH
Sbjct: 246 GGVLPSGDGTYQTWLSVNLDPQSNDVYSCHVEH 278


  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: 59,789,155
Number of Sequences: 45328
Number of extensions: 1768981
Number of successful extensions: 7453
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 5880
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): 7407
length of database: 21,768,885
effective HSP length: 105
effective length of database: 17,009,445
effective search space used: 4541521815
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)