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= psy12593
(122 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2BC4|A Chain A, Crystal Structure Of Hla-Dm
pdb|2BC4|C Chain C, Crystal Structure Of Hla-Dm
Length = 211
Score = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 11/89 (12%)
Query: 8 YPHQGQFQEVLQDVFCAESTMATTPFPRSAGFKGILESVQDFYFDVMNNRSDPRV---KD 64
+P Q L V+C + + S G + Q F+FD N PR+ D
Sbjct: 9 WPDDLQNHTFLHTVYCQDGS-------PSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFAD 61
Query: 65 WFLMSGPLPTVCICLSYA-FIVKIVGPKL 92
W G P + + ++++ +GPKL
Sbjct: 62 WAQEQGDAPAILFDKEFCEWMIQQIGPKL 90
>pdb|4FQX|C Chain C, Crystal Structure Of Hla-Dm Bound To Hla-Dr1
pdb|4GBX|C Chain C, Crystal Structure Of An Immune Complex At Ph 6.5
Length = 203
Score = 29.6 bits (65), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 11/89 (12%)
Query: 8 YPHQGQFQEVLQDVFCAESTMATTPFPRSAGFKGILESVQDFYFDVMNNRSDPRV---KD 64
+P Q L V+C + + S G + Q F+FD N PR+ D
Sbjct: 9 WPDDLQNHTFLHTVYCQDGS-------PSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFAD 61
Query: 65 WFLMSGPLPTVCICLSYA-FIVKIVGPKL 92
W G P + + ++++ +GPKL
Sbjct: 62 WAQEQGDAPAILFDKEFCEWMIQQIGPKL 90
>pdb|4GMG|A Chain A, Nadp+ Bound Structure Of A Thiazolinyl Imine Reductase
From Yersinia Enterocolitica (Irp3)
pdb|4GMG|B Chain B, Nadp+ Bound Structure Of A Thiazolinyl Imine Reductase
From Yersinia Enterocolitica (Irp3)
pdb|4GMG|C Chain C, Nadp+ Bound Structure Of A Thiazolinyl Imine Reductase
From Yersinia Enterocolitica (Irp3)
pdb|4GMG|D Chain D, Nadp+ Bound Structure Of A Thiazolinyl Imine Reductase
From Yersinia Enterocolitica (Irp3)
Length = 385
Score = 28.9 bits (63), Expect = 0.78, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 2 YWVSTYYPHQGQFQEVLQDVFCAESTMATTP 32
YW++T+YPH + L+D +A TP
Sbjct: 142 YWINTFYPHTRAGRTWLRDAQQLRRCLAKTP 172
>pdb|4GMF|A Chain A, Apo Structure Of A Thiazolinyl Imine Reductase From
Yersinia Enterocolitica (Irp3)
pdb|4GMF|B Chain B, Apo Structure Of A Thiazolinyl Imine Reductase From
Yersinia Enterocolitica (Irp3)
pdb|4GMF|C Chain C, Apo Structure Of A Thiazolinyl Imine Reductase From
Yersinia Enterocolitica (Irp3)
pdb|4GMF|D Chain D, Apo Structure Of A Thiazolinyl Imine Reductase From
Yersinia Enterocolitica (Irp3)
Length = 372
Score = 28.9 bits (63), Expect = 0.84, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 2 YWVSTYYPHQGQFQEVLQDVFCAESTMATTP 32
YW++T+YPH + L+D +A TP
Sbjct: 122 YWINTFYPHTRAGRTWLRDAQQLRRCLAKTP 152
>pdb|4I0P|A Chain A, Hla-do In Complex With Hla-dm
pdb|4I0P|E Chain E, Hla-do In Complex With Hla-dm
Length = 188
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 34/84 (40%), Gaps = 11/84 (13%)
Query: 13 QFQEVLQDVFCAESTMATTPFPRSAGFKGILESVQDFYFDVMNNRSDPRV---KDWFLMS 69
Q L V+C + + S G + Q F+FD N PR+ DW
Sbjct: 2 QNHTFLHTVYCQDGS-------PSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADWAQEQ 54
Query: 70 GPLPTVCICLSYA-FIVKIVGPKL 92
G P + + ++++ +GPKL
Sbjct: 55 GDAPAILFDKEFCEWMIQQIGPKL 78
>pdb|3CF6|E Chain E, Structure Of Epac2 In Complex With Cyclic-Amp And Rap
Length = 694
Score = 25.8 bits (55), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 16 EVLQDVFCAESTMATTPFPRSAGFKGILESVQD 48
EVL V+C + T T P +A K ++ +V D
Sbjct: 352 EVLFKVYCIDHTYTTIRVPVAASVKEVISAVAD 384
>pdb|2BYV|E Chain E, Structure Of The Camp Responsive Exchange Factor Epac2 In
Its Auto-Inhibited State
Length = 999
Score = 25.8 bits (55), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 16 EVLQDVFCAESTMATTPFPRSAGFKGILESVQD 48
EVL V+C + T T P +A K ++ +V D
Sbjct: 657 EVLFKVYCIDHTYTTIRVPVAASVKEVISAVAD 689
>pdb|4F7Z|A Chain A, Conformational Dynamics Of Exchange Protein Directly
Activated By Camp
Length = 999
Score = 25.4 bits (54), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 16 EVLQDVFCAESTMATTPFPRSAGFKGILESVQD 48
EVL V+C + T T P +A K ++ +V D
Sbjct: 657 EVLFKVYCIDHTYTTIRVPVAASVKEVISAVAD 689
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
0.328 0.141 0.460
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,714,842
Number of Sequences: 62578
Number of extensions: 126018
Number of successful extensions: 334
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 329
Number of HSP's gapped (non-prelim): 8
length of query: 122
length of database: 14,973,337
effective HSP length: 84
effective length of query: 38
effective length of database: 9,716,785
effective search space: 369237830
effective search space used: 369237830
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 bits)