BLASTX 2.2.10 [Oct-19-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 20060611S-049573 (1181 letters) Database: RefSeqSP 1040 sequences; 434,620 total letters Searching...done Score E Sequences producing significant alignments: (bits) Value Alignment gi|NP_998939.1| CD74 antigen [Sus scrofa] 111 4e-37 >ref|NP_998939.1| CD74 antigen [Sus scrofa] Length = 214 Score = 111 bits (278), Expect(3) = 4e-37 Identities = 60/97 (61%), Positives = 69/97 (71%) Frame = +2 Query: 239 MDDQRDLISNHEQLPMLVQRPGAPYSKCSRVSLYTGFSVQVVLLLCEHDTNCNIL*QLQG 418 M+DQRDLISNHEQLPML QRPGAP SKCSR +LYTGFSV V LLL T L Q QG Sbjct: 1 MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 60 Query: 419 RMYKLTITSHN*LIHSLHMKLHNHSNTMSHKRLTAPI 529 R+ KLT+TS N + SL MKL S +S R++AP+ Sbjct: 61 RLDKLTVTSQNLQLESLRMKLPKPSKPLSKMRVSAPM 97 Score = 48.9 bits (115), Expect(3) = 4e-37 Identities = 25/47 (53%), Positives = 32/47 (68%) Frame = +3 Query: 549 IEGP*PMRNFIRYYDMTQDHVIHLLLKNDSQAM*PNI*ERL**YLKH 689 +EGP PMRN +Y +MTQDHV+HLLLK+D + P + L LKH Sbjct: 104 MEGPEPMRNATKYGNMTQDHVMHLLLKSDPLGVYPKLKGSLPENLKH 150 Score = 28.9 bits (63), Expect(3) = 4e-37 Identities = 24/58 (41%), Positives = 27/58 (46%) Frame = +1 Query: 715 NWKLYQN*LRSVAHRFISS*TQLHETHTRSSVKTPTARLMIISSRLDEIKQDLSQFIL 888 NWKL++N LR F S L ET K P +SS L KQDL Q IL Sbjct: 159 NWKLFENWLRQWL-LFEMSKNSLEETPFEVPPKDP-LETEDLSSGLGVTKQDLGQVIL 214 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: 958,723 Number of Sequences: 1040 Number of extensions: 22264 Number of successful extensions: 62 Number of sequences better than 1.0e-05: 1 Number of HSP's better than 0.0 without gapping: 55 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): 62 length of database: 434,620 effective HSP length: 79 effective length of database: 352,460 effective search space used: 110672440 frameshift window, decay const: 40, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits)
Search to RefSeqBP
BLASTX 2.2.10 [Oct-19-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 20060611S-049573 (1181 letters) Database: RefSeqBP 33,508 sequences; 16,112,626 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value Alignment gi|NP_001029907.1| similar to CD74 antigen isoform b [Bos taurus] 106 5e-30 >ref|NP_001029907.1| similar to CD74 antigen isoform b [Bos taurus] Length = 204 Score = 106 bits (264), Expect(2) = 5e-30 Identities = 57/97 (58%), Positives = 66/97 (68%) Frame = +2 Query: 239 MDDQRDLISNHEQLPMLVQRPGAPYSKCSRVSLYTGFSVQVVLLLCEHDTNCNIL*QLQG 418 M+DQRDLISNHEQLPML QRPGA SKCSR +LYTGFSV V LLL T L Q QG Sbjct: 1 MEDQRDLISNHEQLPMLGQRPGAQESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 60 Query: 419 RMYKLTITSHN*LIHSLHMKLHNHSNTMSHKRLTAPI 529 R+ KLT+TS N + +L MKL + MS R+ P+ Sbjct: 61 RLDKLTVTSQNLQLENLRMKLPKPAKPMSQMRMATPM 97 Score = 43.9 bits (102), Expect(2) = 5e-30 Identities = 23/45 (51%), Positives = 29/45 (64%) Frame = +3 Query: 555 GP*PMRNFIRYYDMTQDHVIHLLLKNDSQAM*PNI*ERL**YLKH 689 GP PM+N +Y +MTQDHV+HLLLK D + P + L LKH Sbjct: 106 GPEPMKNATKYGNMTQDHVMHLLLKADPLKVYPQLKGSLPENLKH 150 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: 35,786,935 Number of Sequences: 33508 Number of extensions: 867090 Number of successful extensions: 2803 Number of sequences better than 1.0e-05: 1 Number of HSP's better than 0.0 without gapping: 2392 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): 2801 length of database: 16,112,626 effective HSP length: 103 effective length of database: 12,661,302 effective search space used: 3671777580 frameshift window, decay const: 40, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits)
Search to RefSeqCP
BLASTX 2.2.10 [Oct-19-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 20060611S-049573 (1181 letters) Database: RefSeqCP 33,732 sequences; 19,266,565 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value Alignment gi|XP_536468.2| PREDICTED: similar to HLA class II histocompati... 106 6e-27 >ref|XP_536468.2| PREDICTED: similar to HLA class II histocompatibility antigen, gamma chain (HLA-DR antigens associated invariant chain) (Ia antigen-associated invariant chain) (Ii) (p33) (CD74 antigen) [Canis familiaris] Length = 272 Score = 106 bits (264), Expect(2) = 6e-27 Identities = 57/97 (58%), Positives = 66/97 (68%) Frame = +2 Query: 239 MDDQRDLISNHEQLPMLVQRPGAPYSKCSRVSLYTGFSVQVVLLLCEHDTNCNIL*QLQG 418 M+DQRDLISNHEQLP+L QRPGAP SKCSR +LYTGFSV V LLL T L Q QG Sbjct: 1 MEDQRDLISNHEQLPILGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 60 Query: 419 RMYKLTITSHN*LIHSLHMKLHNHSNTMSHKRLTAPI 529 R+ KLT+TS N + SL MKL +S R+ P+ Sbjct: 61 RLDKLTVTSQNLQLESLRMKLPKPPKPLSKMRVATPM 97 Score = 33.9 bits (76), Expect(2) = 6e-27 Identities = 15/32 (46%), Positives = 21/32 (65%) Frame = +3 Query: 564 PMRNFIRYYDMTQDHVIHLLLKNDSQAM*PNI 659 P +N Y +MTQDHV+HLLL+ D + P + Sbjct: 111 PTQNATEYGNMTQDHVMHLLLEADPLKVYPKL 142 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: 41,999,979 Number of Sequences: 33732 Number of extensions: 1015864 Number of successful extensions: 3390 Number of sequences better than 1.0e-05: 1 Number of HSP's better than 0.0 without gapping: 2853 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): 3388 length of database: 19,266,565 effective HSP length: 105 effective length of database: 15,724,705 effective search space used: 4528715040 frameshift window, decay const: 40, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits)
Search to RefSeqHP
BLASTX 2.2.10 [Oct-19-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 20060611S-049573 (1181 letters) Database: RefSeqHP 39,411 sequences; 17,774,539 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value Alignment gi|NP_001020330.1| CD74 antigen isoform a [Homo sapiens] 103 8e-26 Alignment gi|NP_004346.1| CD74 antigen isoform b [Homo sapiens] 103 8e-26 Alignment gi|NP_001020329.1| CD74 antigen isoform c [Homo sapiens] 103 1e-25 >ref|NP_001020330.1| CD74 antigen isoform a [Homo sapiens] Length = 296 Score = 103 bits (258), Expect(2) = 8e-26 Identities = 55/97 (56%), Positives = 66/97 (68%) Frame = +2 Query: 239 MDDQRDLISNHEQLPMLVQRPGAPYSKCSRVSLYTGFSVQVVLLLCEHDTNCNIL*QLQG 418 MDDQRDLISN+EQLPML +RPGAP SKCSR +LYTGFS+ V LLL T L Q QG Sbjct: 17 MDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLYQQQG 76 Query: 419 RMYKLTITSHN*LIHSLHMKLHNHSNTMSHKRLTAPI 529 R+ KLT+TS N + +L MKL +S R+ P+ Sbjct: 77 RLDKLTVTSQNLQLENLRMKLPKPPKPVSKMRMATPL 113 Score = 32.3 bits (72), Expect(2) = 8e-26 Identities = 13/24 (54%), Positives = 18/24 (75%) Frame = +3 Query: 564 PMRNFIRYYDMTQDHVIHLLLKND 635 PM+N +Y +MT+DHV+HLL D Sbjct: 127 PMQNATKYGNMTEDHVMHLLQNAD 150 >ref|NP_004346.1| CD74 antigen isoform b [Homo sapiens] Length = 232 Score = 103 bits (258), Expect(2) = 8e-26 Identities = 55/97 (56%), Positives = 66/97 (68%) Frame = +2 Query: 239 MDDQRDLISNHEQLPMLVQRPGAPYSKCSRVSLYTGFSVQVVLLLCEHDTNCNIL*QLQG 418 MDDQRDLISN+EQLPML +RPGAP SKCSR +LYTGFS+ V LLL T L Q QG Sbjct: 17 MDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLYQQQG 76 Query: 419 RMYKLTITSHN*LIHSLHMKLHNHSNTMSHKRLTAPI 529 R+ KLT+TS N + +L MKL +S R+ P+ Sbjct: 77 RLDKLTVTSQNLQLENLRMKLPKPPKPVSKMRMATPL 113 Score = 32.3 bits (72), Expect(2) = 8e-26 Identities = 13/24 (54%), Positives = 18/24 (75%) Frame = +3 Query: 564 PMRNFIRYYDMTQDHVIHLLLKND 635 PM+N +Y +MT+DHV+HLL D Sbjct: 127 PMQNATKYGNMTEDHVMHLLQNAD 150 >ref|NP_001020329.1| CD74 antigen isoform c [Homo sapiens] Length = 160 Score = 103 bits (258), Expect(2) = 1e-25 Identities = 55/97 (56%), Positives = 66/97 (68%) Frame = +2 Query: 239 MDDQRDLISNHEQLPMLVQRPGAPYSKCSRVSLYTGFSVQVVLLLCEHDTNCNIL*QLQG 418 MDDQRDLISN+EQLPML +RPGAP SKCSR +LYTGFS+ V LLL T L Q QG Sbjct: 17 MDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLYQQQG 76 Query: 419 RMYKLTITSHN*LIHSLHMKLHNHSNTMSHKRLTAPI 529 R+ KLT+TS N + +L MKL +S R+ P+ Sbjct: 77 RLDKLTVTSQNLQLENLRMKLPKPPKPVSKMRMATPL 113 Score = 31.6 bits (70), Expect(2) = 1e-25 Identities = 12/20 (60%), Positives = 17/20 (85%) Frame = +3 Query: 564 PMRNFIRYYDMTQDHVIHLL 623 PM+N +Y +MT+DHV+HLL Sbjct: 127 PMQNATKYGNMTEDHVMHLL 146 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: 40,565,468 Number of Sequences: 39411 Number of extensions: 1014331 Number of successful extensions: 3200 Number of sequences better than 1.0e-05: 3 Number of HSP's better than 0.0 without gapping: 2703 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): 3196 length of database: 17,774,539 effective HSP length: 104 effective length of database: 13,675,795 effective search space used: 3952304755 frameshift window, decay const: 40, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits)
Search to RefSeqMP
BLASTX 2.2.10 [Oct-19-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 20060611S-049573 (1181 letters) Database: RefSeqMP 45,328 sequences; 21,768,885 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value Alignment gi|NP_034675.1| Ia-associated invariant chain [Mus musculus] 94 7e-23 >ref|NP_034675.1| Ia-associated invariant chain [Mus musculus] Length = 215 Score = 94.0 bits (232), Expect(2) = 7e-23 Identities = 53/97 (54%), Positives = 62/97 (63%) Frame = +2 Query: 239 MDDQRDLISNHEQLPMLVQRPGAPYSKCSRVSLYTGFSVQVVLLLCEHDTNCNIL*QLQG 418 MDDQRDLISNHEQLP+L RP P +CSR +LYTG SV V LLL T L Q QG Sbjct: 1 MDDQRDLISNHEQLPILGNRPREP-ERCSRGALYTGVSVLVALLLAGQATTAYFLYQQQG 59 Query: 419 RMYKLTITSHN*LIHSLHMKLHNHSNTMSHKRLTAPI 529 R+ KLTITS N + SL MKL + +S R+ P+ Sbjct: 60 RLDKLTITSQNLQLESLRMKLPKSAKPVSQMRMATPL 96 Score = 32.7 bits (73), Expect(2) = 7e-23 Identities = 12/23 (52%), Positives = 19/23 (82%) Frame = +3 Query: 564 PMRNFIRYYDMTQDHVIHLLLKN 632 P++N +Y +MTQDHV+HLL ++ Sbjct: 110 PVKNVTKYGNMTQDHVMHLLTRS 132 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: 48,010,624 Number of Sequences: 45328 Number of extensions: 1158124 Number of successful extensions: 3584 Number of sequences better than 1.0e-05: 1 Number of HSP's better than 0.0 without gapping: 3052 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): 3560 length of database: 21,768,885 effective HSP length: 106 effective length of database: 16,964,117 effective search space used: 4868701579 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)