BLASTP 2.2.26 [Sep-21-2011]
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.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy3125
(163 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3BP6|A Chain A, Crystal Structure Of The Mouse Pd-1 Mutant And Pd-L2
Complex
pdb|3RNK|A Chain A, Crystal Structure Of The Complex Between Mouse Pd-1 Mutant
And Pd-L2 Igv Domain
pdb|3SBW|A Chain A, Crystal Structure Of The Complex Between The Extracellular
Domains Of Mouse Pd-1 Mutant And Human Pd-L1
pdb|3SBW|B Chain B, Crystal Structure Of The Complex Between The Extracellular
Domains Of Mouse Pd-1 Mutant And Human Pd-L1
Length = 117
Score = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 33 DARFSVIHPQNSDEWNMKIDYAQKRDAGIYEC-QVNTEPKMNM 74
DARF +I N +++M I ++ D+GIY C ++ PK+ +
Sbjct: 59 DARFQIIQLPNRHDFHMNILDTRRNDSGIYLCGAISLHPKLKI 101
Score = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 113 DARFSVIHPQNSDEWNMKIDYAQKRDAGIYEC-QVNTEPKMNM 154
DARF +I N +++M I ++ D+GIY C ++ PK+ +
Sbjct: 59 DARFQIIQLPNRHDFHMNILDTRRNDSGIYLCGAISLHPKLKI 101
>pdb|1I85|A Chain A, Crystal Structure Of The Ctla-4B7-2 Complex
pdb|1I85|B Chain B, Crystal Structure Of The Ctla-4B7-2 Complex
pdb|1NCN|A Chain A, The Receptor-Binding Domain Of Human B7-2
pdb|1NCN|B Chain B, The Receptor-Binding Domain Of Human B7-2
Length = 110
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 26/53 (49%), Gaps = 7/53 (13%)
Query: 29 TYTGDARFSVIHPQ-------NSDEWNMKIDYAQKRDAGIYECQVNTEPKMNM 74
Y G +F +H + +SD W +++ Q +D G+Y+C ++ + M
Sbjct: 44 VYLGKEKFDSVHSKYMGRTSFDSDSWTLRLHNLQIKDKGLYQCIIHHKKPTGM 96
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 26/53 (49%), Gaps = 7/53 (13%)
Query: 109 TYTGDARFSVIHPQ-------NSDEWNMKIDYAQKRDAGIYECQVNTEPKMNM 154
Y G +F +H + +SD W +++ Q +D G+Y+C ++ + M
Sbjct: 44 VYLGKEKFDSVHSKYMGRTSFDSDSWTLRLHNLQIKDKGLYQCIIHHKKPTGM 96
>pdb|1NPU|A Chain A, Crystal Structure Of The Extracellular Domain Of Murine
Pd-1
pdb|3BP5|A Chain A, Crystal Structure Of The Mouse Pd-1 And Pd-L2 Complex
Length = 117
Score = 31.2 bits (69), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 33 DARFSVIHPQNSDEWNMKIDYAQKRDAGIYEC-QVNTEPKMNM 74
DARF +I N +++M I ++ D+GIY C ++ PK +
Sbjct: 59 DARFQIIQLPNRHDFHMNILDTRRNDSGIYLCGAISLHPKAKI 101
Score = 31.2 bits (69), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 113 DARFSVIHPQNSDEWNMKIDYAQKRDAGIYEC-QVNTEPKMNM 154
DARF +I N +++M I ++ D+GIY C ++ PK +
Sbjct: 59 DARFQIIQLPNRHDFHMNILDTRRNDSGIYLCGAISLHPKAKI 101
>pdb|3RNQ|A Chain A, Crystal Structure Of The Complex Between The Extracellular
Domains Of Mouse Pd-1 Mutant And Pd-L2
Length = 117
Score = 30.8 bits (68), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 33 DARFSVIHPQNSDEWNMKIDYAQKRDAGIYEC-QVNTEPKMNM 74
DARF +I N +++M I ++ D+GIY C ++ PK +
Sbjct: 59 DARFQIIQLPNRHDFHMNILDTRRNDSGIYLCGAISRHPKAKI 101
Score = 30.8 bits (68), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 113 DARFSVIHPQNSDEWNMKIDYAQKRDAGIYEC-QVNTEPKMNM 154
DARF +I N +++M I ++ D+GIY C ++ PK +
Sbjct: 59 DARFQIIQLPNRHDFHMNILDTRRNDSGIYLCGAISRHPKAKI 101
>pdb|3BIK|B Chain B, Crystal Structure Of The Pd-1PD-L1 Complex
pdb|3BIK|C Chain C, Crystal Structure Of The Pd-1PD-L1 Complex
Length = 134
Score = 30.8 bits (68), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 33 DARFSVIHPQNSDEWNMKIDYAQKRDAGIYEC-QVNTEPKMNM 74
DARF +I N +++M I ++ D+GIY C ++ PK +
Sbjct: 69 DARFQIIQLPNRHDFHMNILDTRRNDSGIYLCGAISLHPKAKI 111
Score = 30.8 bits (68), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 113 DARFSVIHPQNSDEWNMKIDYAQKRDAGIYEC-QVNTEPKMNM 154
DARF +I N +++M I ++ D+GIY C ++ PK +
Sbjct: 69 DARFQIIQLPNRHDFHMNILDTRRNDSGIYLCGAISLHPKAKI 111
>pdb|3RRQ|A Chain A, Crystal Structure Of The Extracellular Domain Of Human
Pd-1
Length = 129
Score = 30.0 bits (66), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 33 DARFSVIHPQNSDEWNMKIDYAQKRDAGIYEC-QVNTEPKMNMAIMLNVDDR 83
D RF V N +++M + A++ D+G Y C ++ PK+ + L + R
Sbjct: 61 DCRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKLQIKESLRAELR 112
Score = 29.6 bits (65), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 113 DARFSVIHPQNSDEWNMKIDYAQKRDAGIYEC-QVNTEPKMNMAIMLNVD 161
D RF V N +++M + A++ D+G Y C ++ PK+ + L +
Sbjct: 61 DCRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKLQIKESLRAE 110
>pdb|2M2D|A Chain A, Human Programmed Cell Death 1 Receptor
Length = 118
Score = 30.0 bits (66), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 33 DARFSVIHPQNSDEWNMKIDYAQKRDAGIYEC-QVNTEPKMNMAIMLNVDDR 83
D+RF V N +++M + A++ D+G Y C ++ PK + L + R
Sbjct: 60 DSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELR 111
Score = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 113 DARFSVIHPQNSDEWNMKIDYAQKRDAGIYEC-QVNTEPKMNMAIMLNVD 161
D+RF V N +++M + A++ D+G Y C ++ PK + L +
Sbjct: 60 DSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAE 109
>pdb|3HXJ|A Chain A, Crystal Structure Of Pyrrolo-quinoline Quinone (pqq_dh)
From Methanococcus Maripaludis, Northeast Structural
Genomics Consortium Target Mrr86
pdb|3HXJ|B Chain B, Crystal Structure Of Pyrrolo-quinoline Quinone (pqq_dh)
From Methanococcus Maripaludis, Northeast Structural
Genomics Consortium Target Mrr86
pdb|3HXJ|C Chain C, Crystal Structure Of Pyrrolo-quinoline Quinone (pqq_dh)
From Methanococcus Maripaludis, Northeast Structural
Genomics Consortium Target Mrr86
pdb|3HXJ|D Chain D, Crystal Structure Of Pyrrolo-quinoline Quinone (pqq_dh)
From Methanococcus Maripaludis, Northeast Structural
Genomics Consortium Target Mrr86
Length = 330
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 25/110 (22%), Positives = 45/110 (40%), Gaps = 18/110 (16%)
Query: 30 YTGDARFSVIHPQNSDEWNMKIDY------AQKRDAGIYECQVNTEPKMNMAIMLNVDDR 83
Y G + I+P +++WN Y A D IY ++ AI + ++
Sbjct: 191 YFGSDKVYAINPDGTEKWNFYAGYWTVTRPAISEDGTIYVTSLDGHL---YAINPDGTEK 247
Query: 84 GR---GARLSAGPLLNFAFPDLLTTNIYTYTGDARFSVIHPQNSDEWNMK 130
R G R+ + P++ T IY + D I+P +++WN +
Sbjct: 248 WRFKTGKRIESSPVIG------NTDTIYFGSYDGHLYAINPDGTEKWNFE 291
>pdb|3V4Z|A Chain A, D-Alanine--D-Alanine Ligase From Yersinia Pestis
pdb|3V4Z|B Chain B, D-Alanine--D-Alanine Ligase From Yersinia Pestis
Length = 309
Score = 28.1 bits (61), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 40 HPQNSDEWNMKIDYAQKRDAGIYECQVNTEPKMNMAIMLNVDDRGRGARLS 90
H + W ++D Q RD Y +VNT P M ++ + R G S
Sbjct: 249 HALDCSGWG-RVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFS 298
>pdb|4AQ4|A Chain A, Substrate Bound Sn-Glycerol-3-Phosphate Binding
Periplasmic Protein Ugpb From Escherichia Coli
Length = 419
Score = 27.3 bits (59), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 10/45 (22%)
Query: 29 TYTGDARF--SVIHPQNSDEWNMKIDYAQ--------KRDAGIYE 63
TYTG A+F + P+N+ EW+ K Y R+ G YE
Sbjct: 301 TYTGVAKFLDFLAKPENAAEWHQKTGYLPITKAAYDLTREQGFYE 345
Score = 27.3 bits (59), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 10/45 (22%)
Query: 109 TYTGDARF--SVIHPQNSDEWNMKIDYAQ--------KRDAGIYE 143
TYTG A+F + P+N+ EW+ K Y R+ G YE
Sbjct: 301 TYTGVAKFLDFLAKPENAAEWHQKTGYLPITKAAYDLTREQGFYE 345
>pdb|2YWZ|A Chain A, Structure Of New Antigen Receptor Variable Domain From
Sharks
Length = 111
Score = 26.9 bits (58), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 18/79 (22%), Positives = 33/79 (41%), Gaps = 3/79 (3%)
Query: 12 VSWMRKRDLHILTTNIYTYTGDARFSVIHPQNSDEWNMKIDYAQKRDAGIYECQVNTEPK 71
+W R + +TN T + R+ + S ++++I + D+G Y+CQ + P
Sbjct: 34 TTWYR---TQLGSTNEKTISIGGRYDETVDKGSKSFSLRISDLRVEDSGTYKCQADYSPS 90
Query: 72 MNMAIMLNVDDRGRGARLS 90
L G G L+
Sbjct: 91 CYSYPSLESAVEGAGTVLT 109
Score = 26.2 bits (56), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 25/49 (51%)
Query: 102 LLTTNIYTYTGDARFSVIHPQNSDEWNMKIDYAQKRDAGIYECQVNTEP 150
L +TN T + R+ + S ++++I + D+G Y+CQ + P
Sbjct: 41 LGSTNEKTISIGGRYDETVDKGSKSFSLRISDLRVEDSGTYKCQADYSP 89
>pdb|2PN2|A Chain A, Crystal Structure Of A Putative Osmotic Stress Induced
And Detoxification Response Protein (Psyc_0566) From
Psychrobacter Arcticus 273-4 At 2.15 A Resolution
Length = 155
Score = 26.2 bits (56), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 24 TTNIYTYTGDARFSVIHPQNSDE 46
TT+ TY GD R S IH Q+++E
Sbjct: 21 TTSKVTYQGDLRTSAIHLQSNNE 43
Score = 26.2 bits (56), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 104 TTNIYTYTGDARFSVIHPQNSDE 126
TT+ TY GD R S IH Q+++E
Sbjct: 21 TTSKVTYQGDLRTSAIHLQSNNE 43
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.135 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,144,942
Number of Sequences: 62578
Number of extensions: 206533
Number of successful extensions: 950
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 917
Number of HSP's gapped (non-prelim): 36
length of query: 163
length of database: 14,973,337
effective HSP length: 91
effective length of query: 72
effective length of database: 9,278,739
effective search space: 668069208
effective search space used: 668069208
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)