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= psy7169
(235 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1JWM|D Chain D, Crystal Structure Of The Complex Of The Mhc Class Ii
Molecule Hla-Dr1(Ha Peptide 306-318) With The
Superantigen Sec3
Length = 239
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 11/81 (13%)
Query: 46 HKTDVPARKLQELKLAFSEYYLSLILLQNY-----QNLNFTGFRKILKKHDK----LLNV 96
HK+ + +K + ++Y+S +++ +L + K LK +DK LLN
Sbjct: 12 HKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNISDKKLKNYDKVKTELLNE 71
Query: 97 DVGAKWRAEHVDI--SHFYVN 115
D+ K++ E VD+ S++YVN
Sbjct: 72 DLAKKYKDEVVDVYGSNYYVN 92
>pdb|2AQ3|B Chain B, Crystal Structure Of T-Cell Receptor V Beta Domain Variant
Complexed With Superantigen Sec3
pdb|2AQ3|D Chain D, Crystal Structure Of T-Cell Receptor V Beta Domain Variant
Complexed With Superantigen Sec3
pdb|2AQ3|F Chain F, Crystal Structure Of T-Cell Receptor V Beta Domain Variant
Complexed With Superantigen Sec3
pdb|2AQ3|H Chain H, Crystal Structure Of T-Cell Receptor V Beta Domain Variant
Complexed With Superantigen Sec3
Length = 237
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 11/81 (13%)
Query: 46 HKTDVPARKLQELKLAFSEYYLSLILLQNY-----QNLNFTGFRKILKKHDK----LLNV 96
HK+ + +K + ++Y+S +++ +L + K LK +DK LLN
Sbjct: 12 HKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNISDKKLKNYDKVKTELLNE 71
Query: 97 DVGAKWRAEHVDI--SHFYVN 115
D+ K++ E VD+ S++YVN
Sbjct: 72 DLAKKYKDEVVDVYGSNYYVN 92
>pdb|1JWS|D Chain D, Crystal Structure Of The Complex Of The Mhc Class Ii
Molecule Hla-Dr1 (Ha Peptide 306-318) With The
Superantigen Sec3 Variant 3b1
Length = 239
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 11/81 (13%)
Query: 46 HKTDVPARKLQELKLAFSEYYLSLILLQNYQ-----NLNFTGFRKILKKHDK----LLNV 96
HK+ + +K + ++Y+S +++ +L + K LK +DK LLN
Sbjct: 12 HKSSEFTGTMGNMKYLYDDHYVSATKVKSVDGMFNWDLIYNISDKKLKNYDKVKTELLNE 71
Query: 97 DVGAKWRAEHVDI--SHFYVN 115
D+ K++ E VD+ S++YVN
Sbjct: 72 DLAKKYKDEVVDVYGSNYYVN 92
>pdb|2IPK|D Chain D, Crystal Structure Of The Mhc Class Ii Molecule Hla-Dr1 In
Complex With The Fluorogenic Peptide, Acpkxvkqntlklat
(X3-
[5-(Dimethylamino)-1,3-Dioxo-1,
3-Dihydro-2h-Isoindol-2-Yl]- L-Alanine) And The
Superantigen, Sec3 Variant 3b2
Length = 240
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 11/81 (13%)
Query: 46 HKTDVPARKLQELKLAFSEYYLSLILLQNYQ-----NLNFTGFRKILKKHDK----LLNV 96
HK+ + +K + ++Y+S +++ +L + K LK +DK LLN
Sbjct: 13 HKSSEFTGTMGNMKYLYDDHYVSATKVKSVDSFFKWDLIYNISDKKLKNYDKVKTELLNE 72
Query: 97 DVGAKWRAEHVDI--SHFYVN 115
D+ K++ E VD+ S++YVN
Sbjct: 73 DLAKKYKDEVVDVYGSNYYVN 93
>pdb|1KLG|D Chain D, Crystal Structure Of Hla-Dr1TPI(23-37, Thr28-->ile Mutant)
Complexed With Staphylococcal Enterotoxin C3 Variant 3b2
(Sec3-3b2)
pdb|1KLU|D Chain D, Crystal Structure Of Hla-Dr1TPI(23-37) Complexed With
Staphylococcal Enterotoxin C3 Variant 3b2 (Sec3-3b2)
pdb|1JWU|D Chain D, Crystal Structure Of The Complex Of The Mhc Class Ii
Molecule Hla-Dr1 (Ha Peptide 306-318) With The
Superantigen Sec3 Variant 3b2
pdb|1PYW|D Chain D, Human Class Ii Mhc Protein Hla-Dr1 Bound To A Designed
Peptide Related To Influenza Virus Hemagglutinin,
Fvkqna(Maa)al, In Complex With Staphylococcal
Enterotoxin C3 Variant 3b2 (Sec3-3b2)
pdb|1SJE|D Chain D, Hla-Dr1 Complexed With A 16 Residue Hiv Capsid Peptide
Bound In A Hairpin Conformation
pdb|1SJH|D Chain D, Hla-Dr1 Complexed With A 13 Residue Hiv Capsid Peptide
pdb|1T5X|D Chain D, Hla-Dr1 In Complex With A Synthetic Peptide
(Aaysdqatplllspr) And The Superantigen Sec3-3b2
Length = 239
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 11/81 (13%)
Query: 46 HKTDVPARKLQELKLAFSEYYLSLILLQNYQ-----NLNFTGFRKILKKHDK----LLNV 96
HK+ + +K + ++Y+S +++ +L + K LK +DK LLN
Sbjct: 12 HKSSEFTGTMGNMKYLYDDHYVSATKVKSVDSFFKWDLIYNISDKKLKNYDKVKTELLNE 71
Query: 97 DVGAKWRAEHVDI--SHFYVN 115
D+ K++ E VD+ S++YVN
Sbjct: 72 DLAKKYKDEVVDVYGSNYYVN 92
>pdb|3BVG|A Chain A, Manipulating The Coupled Folding And Binding Process
Drives Affinity Maturation In A Protein-Protein Complex
Length = 237
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 11/81 (13%)
Query: 46 HKTDVPARKLQELKLAFSEYYLSLILLQNY-----QNLNFTGFRKILKKHDK----LLNV 96
HK+ + +K + ++Y+S +++ +L + K LK +DK LLN
Sbjct: 12 HKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNISDKKLKNYDKVKTELLNE 71
Query: 97 DVGAKWRAEHVDI--SHFYVN 115
D+ K++ E VD+ S++YVN
Sbjct: 72 DLAKKYKDEVVDVYGSNYYVN 92
>pdb|3BYT|B Chain B, A Complex Between A Variant Of Staphylococcal Enterotoxin
C3 And The Variable Domain Of The Murine T Cell Receptor
Beta Chain 8.2
pdb|3BYT|D Chain D, A Complex Between A Variant Of Staphylococcal Enterotoxin
C3 And The Variable Domain Of The Murine T Cell Receptor
Beta Chain 8.2
pdb|3BYT|F Chain F, A Complex Between A Variant Of Staphylococcal Enterotoxin
C3 And The Variable Domain Of The Murine T Cell Receptor
Beta Chain 8.2
pdb|3BYT|H Chain H, A Complex Between A Variant Of Staphylococcal Enterotoxin
C3 And The Variable Domain Of The Murine T Cell Receptor
Beta Chain 8.2
Length = 239
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 11/81 (13%)
Query: 46 HKTDVPARKLQELKLAFSEYYLSLILLQNY-----QNLNFTGFRKILKKHDK----LLNV 96
HK+ + +K + ++Y+S +++ +L + K LK +DK LLN
Sbjct: 12 HKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNISDKKLKNYDKVKTELLNE 71
Query: 97 DVGAKWRAEHVDI--SHFYVN 115
D+ K++ E VD+ S++YVN
Sbjct: 72 DLAKKYKDEVVDVYGSNYYVN 92
>pdb|2AQ2|B Chain B, Crystal Structure Of T-Cell Receptor V Beta Domain Variant
Complexed With Superantigen Sec3 Mutant
pdb|3BYY|B Chain B, Manipulating The Coupled Folding And Binding Process
Drives Affinity Maturation In A Protein-Protein Complex
Length = 237
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 11/81 (13%)
Query: 46 HKTDVPARKLQELKLAFSEYYLSLILLQNY-----QNLNFTGFRKILKKHDK----LLNV 96
HK+ + +K + ++Y+S +++ +L + K LK +DK LLN
Sbjct: 12 HKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNISDKKLKNYDKVKTELLNE 71
Query: 97 DVGAKWRAEHVDI--SHFYVN 115
D+ K++ E VD+ S++YVN
Sbjct: 72 DLAKKYKDEVVDVYGSNYYVN 92
>pdb|3BVM|A Chain A, Manipulating The Coupled Folding And Binding Process
Drives Affinity Maturation In A Protein-Protein Complex
Length = 237
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 11/81 (13%)
Query: 46 HKTDVPARKLQELKLAFSEYYLSLILLQNY-----QNLNFTGFRKILKKHDK----LLNV 96
HK+ + +K + ++Y+S +++ +L + K LK +DK LLN
Sbjct: 12 HKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNISDKKLKNYDKVKTELLNE 71
Query: 97 DVGAKWRAEHVDI--SHFYVN 115
D+ K++ E VD+ S++YVN
Sbjct: 72 DLAKKYKDEVVDVYGSNYYVN 92
>pdb|2AQ1|B Chain B, Crystal Structure Of T-Cell Receptor V Beta Domain Variant
Complexed With Superantigen Sec3 Mutant
pdb|2AQ1|D Chain D, Crystal Structure Of T-Cell Receptor V Beta Domain Variant
Complexed With Superantigen Sec3 Mutant
pdb|2AQ1|F Chain F, Crystal Structure Of T-Cell Receptor V Beta Domain Variant
Complexed With Superantigen Sec3 Mutant
pdb|2AQ1|H Chain H, Crystal Structure Of T-Cell Receptor V Beta Domain Variant
Complexed With Superantigen Sec3 Mutant
pdb|3BZD|B Chain B, Manipulating The Coupled Folding And Binding Process
Drives Affinity Maturation In A Protein-Protein Complex
Length = 237
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 11/81 (13%)
Query: 46 HKTDVPARKLQELKLAFSEYYLSLILLQNY-----QNLNFTGFRKILKKHDK----LLNV 96
HK+ + +K + ++Y+S +++ +L + K LK +DK LLN
Sbjct: 12 HKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNISDKKLKNYDKVKTELLNE 71
Query: 97 DVGAKWRAEHVDI--SHFYVN 115
D+ K++ E VD+ S++YVN
Sbjct: 72 DLAKKYKDEVVDVYGSNYYVN 92
>pdb|3BVZ|A Chain A, Manipulating The Coupled Folding And Binding Process
Drives Affinity Maturation In A Protein-Protein Complex
Length = 237
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 11/81 (13%)
Query: 46 HKTDVPARKLQELKLAFSEYYLSLILLQNY-----QNLNFTGFRKILKKHDK----LLNV 96
HK+ + +K + ++Y+S +++ +L + K LK +DK LLN
Sbjct: 12 HKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNISDKKLKNYDKVKTELLNE 71
Query: 97 DVGAKWRAEHVDI--SHFYVN 115
D+ K++ E VD+ S++YVN
Sbjct: 72 DLAKKYKDEVVDVYGSNYYVN 92
>pdb|1CQV|A Chain A, Crystal Structure Of Staphylococcal Enterotoxin C2 At 100k
Crystallized At Ph 5.0
pdb|1I4P|A Chain A, Crystal Structure Of Staphylococcal Enterotoxin C2 At 100k
Crystallized At Ph 5.5
pdb|1I4Q|A Chain A, Crystal Structure Of Staphylococcal Enterotoxin C2 At 100k
Crystallized At Ph 6.0
pdb|1I4R|A Chain A, Crystal Structure Of Staphylococcal Enterotoxin C2 At 100k
Crystallized At Ph 6.5
pdb|1I4X|A Chain A, Staphylococcal Enterotoxin C2, Monoclinic Form
Crystallized At Ph 8.0
pdb|1UNS|A Chain A, Identification Of A Secondary Zinc-Binding Site In
Staphylococcal Enterotoxin C2: Implications For
Superantigen Recognition
pdb|1SE2|A Chain A, Staphylococcal Enterotoxin C2, Monoclinic Form
pdb|1STE|A Chain A, Staphylococcal Enterotoxin C2 From Staphylococcus Aureus
Length = 239
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 11/81 (13%)
Query: 46 HKTDVPARKLQELKLAFSEYYLSLILLQNY-----QNLNFTGFRKILKKHDK----LLNV 96
HK+ + +K + ++Y+S + + +L + K LK +DK LLN
Sbjct: 12 HKSSEFTGTMGNMKYLYDDHYVSATKVMSVDKFLAHDLIYNISDKKLKNYDKVKTELLNE 71
Query: 97 DVGAKWRAEHVDI--SHFYVN 115
D+ K++ E VD+ S++YVN
Sbjct: 72 DLAKKYKDEVVDVYGSNYYVN 92
>pdb|3SRF|C Chain C, Human M1 Pyruvate Kinase
pdb|3SRF|A Chain A, Human M1 Pyruvate Kinase
pdb|3SRF|B Chain B, Human M1 Pyruvate Kinase
pdb|3SRF|D Chain D, Human M1 Pyruvate Kinase
pdb|3SRF|E Chain E, Human M1 Pyruvate Kinase
pdb|3SRF|F Chain F, Human M1 Pyruvate Kinase
pdb|3SRF|G Chain G, Human M1 Pyruvate Kinase
pdb|3SRF|H Chain H, Human M1 Pyruvate Kinase
Length = 551
Score = 28.1 bits (61), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 32/83 (38%)
Query: 129 VTSELEEGDRQKAMKRLRVPPLGEQQSPWTTFKVGLFLGCFAILFAIILLRVWTERIVAL 188
V +E Q A R R P + ++P T + L+ G F +L + W E +
Sbjct: 450 VLTESGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLR 509
Query: 189 SQILFKVGLFLGCFAILFAIILL 211
VG G F +I+L
Sbjct: 510 VNFAMNVGKARGFFKKGDVVIVL 532
>pdb|2IW0|A Chain A, Structure Of The Chitin Deacetylase From The Fungal
Pathogen Colletotrichum Lindemuthianum
Length = 254
Score = 27.7 bits (60), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 95 NVDVGAKWRAE-HVDISHFYVNKDINHLISETEATVTSELEEGDRQK---AMKRLRVP 148
N D + RA+ H+ SH Y + D+N L S + +LEE R+ A K +R P
Sbjct: 87 NPDTIRRMRADGHLVGSHTYAHPDLNTLSSADRISQMRQLEEATRRIDGFAPKYMRAP 144
>pdb|2V6E|A Chain A, Protelomerase Telk Complexed With Substrate Dna
pdb|2V6E|B Chain B, Protelomerase Telk Complexed With Substrate Dna
Length = 558
Score = 27.3 bits (59), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 118 INHLISETEATVTSELEEGDRQKAMK 143
IN L+SE EA S+ +GD+ K +K
Sbjct: 30 INSLVSEVEAIDASDRPQGDKTKKIK 55
>pdb|1ITW|A Chain A, Crystal Structure Of The Monomeric Isocitrate
Dehydrogenase In Complex With Isocitrate And Mn
pdb|1ITW|B Chain B, Crystal Structure Of The Monomeric Isocitrate
Dehydrogenase In Complex With Isocitrate And Mn
pdb|1ITW|C Chain C, Crystal Structure Of The Monomeric Isocitrate
Dehydrogenase In Complex With Isocitrate And Mn
pdb|1ITW|D Chain D, Crystal Structure Of The Monomeric Isocitrate
Dehydrogenase In Complex With Isocitrate And Mn
pdb|1J1W|A Chain A, Crystal Structure Of The Monomeric Isocitrate
Dehydrogenase In Complex With Nadp+
pdb|1J1W|B Chain B, Crystal Structure Of The Monomeric Isocitrate
Dehydrogenase In Complex With Nadp+
pdb|1J1W|C Chain C, Crystal Structure Of The Monomeric Isocitrate
Dehydrogenase In Complex With Nadp+
pdb|1J1W|D Chain D, Crystal Structure Of The Monomeric Isocitrate
Dehydrogenase In Complex With Nadp+
Length = 741
Score = 26.9 bits (58), Expect = 9.4, Method: Composition-based stats.
Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 10/92 (10%)
Query: 51 PARKLQELKLAFSEYYLSLILLQNYQ--------NLNFTGFRKILKKHDKLLNVDVGAKW 102
PARK+ E+ S +YL+L Q FTG K L ++ + ++ A
Sbjct: 647 PARKVGEIDNRGSHFYLALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAA- 705
Query: 103 RAEHVDISHFY-VNKDINHLISETEATVTSEL 133
+ + VDI+ +Y N D+ AT + L
Sbjct: 706 QGKPVDIAGYYHPNTDLTSKAMRPSATFNAAL 737
>pdb|1JCK|B Chain B, T-Cell Receptor Beta Chain Complexed With Sec3
Superantigen
pdb|1JCK|D Chain D, T-Cell Receptor Beta Chain Complexed With Sec3
Superantigen
pdb|1CK1|A Chain A, Structure Of Staphylococcal Enterotoxin C3
Length = 239
Score = 26.9 bits (58), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 11/81 (13%)
Query: 46 HKTDVPARKLQELKLAFSEYYLSLILLQNY-----QNLNFTGFRKILKKHDK----LLNV 96
HK+ + +K + ++Y+S +++ +L + K L +DK LLN
Sbjct: 12 HKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNINDKKLNNYDKVKTELLNE 71
Query: 97 DVGAKWRAEHVDI--SHFYVN 115
D+ K++ E VD+ S++YVN
Sbjct: 72 DLANKYKDEVVDVYGSNYYVN 92
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
0.324 0.137 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,637,900
Number of Sequences: 62578
Number of extensions: 201147
Number of successful extensions: 532
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 530
Number of HSP's gapped (non-prelim): 17
length of query: 235
length of database: 14,973,337
effective HSP length: 96
effective length of query: 139
effective length of database: 8,965,849
effective search space: 1246253011
effective search space used: 1246253011
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 50 (23.9 bits)