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= 039173
(265 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1KIL|D Chain D, Three-Dimensional Structure Of The ComplexinSNARE COMPLEX
Length = 66
Score = 31.2 bits (69), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 33/63 (52%)
Query: 172 RKMKQDQGLDVISEGLDTLKNLALDMNEELDRQVPLIDEIDTKVDKATSDLKNNNVRLKE 231
R+ + D+ L+ +S + L+++ALDM E+D Q ID I K D + + N R +
Sbjct: 4 RENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATK 63
Query: 232 TLL 234
L
Sbjct: 64 MLW 66
>pdb|1SFC|D Chain D, Neuronal Synaptic Fusion Complex
pdb|1SFC|H Chain H, Neuronal Synaptic Fusion Complex
pdb|1SFC|L Chain L, Neuronal Synaptic Fusion Complex
Length = 87
Score = 30.8 bits (68), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%)
Query: 172 RKMKQDQGLDVISEGLDTLKNLALDMNEELDRQVPLIDEIDTKVDKATSDLKNNNVRLKE 231
R+ + D+ L+ +S + L+++ALDM E+D Q ID I K D + + N R +
Sbjct: 23 RENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATK 82
Query: 232 TL 233
L
Sbjct: 83 ML 84
>pdb|1URQ|D Chain D, Crystal Structure Of Neuronal Q-Snares In Complex With
R-Snare Motif Of Tomosyn
Length = 69
Score = 30.8 bits (68), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%)
Query: 172 RKMKQDQGLDVISEGLDTLKNLALDMNEELDRQVPLIDEIDTKVDKATSDLKNNNVRLKE 231
R+ + D+ L+ +S + L+++ALDM E+D Q ID I K D + + N R +
Sbjct: 7 RENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATK 66
Query: 232 TL 233
L
Sbjct: 67 ML 68
>pdb|3HD7|D Chain D, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup C 1 2 1
pdb|3HD7|H Chain H, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup C 1 2 1
pdb|3IPD|D Chain D, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup I 21 21 21
pdb|3IPD|H Chain H, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup I 21 21 21
Length = 68
Score = 30.8 bits (68), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%)
Query: 172 RKMKQDQGLDVISEGLDTLKNLALDMNEELDRQVPLIDEIDTKVDKATSDLKNNNVRLKE 231
R+ + D+ L+ +S + L+++ALDM E+D Q ID I K D + + N R +
Sbjct: 6 RENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATK 65
Query: 232 TL 233
L
Sbjct: 66 ML 67
>pdb|1N7S|D Chain D, High Resolution Structure Of A Truncated Neuronal Snare
Complex
Length = 66
Score = 30.8 bits (68), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%)
Query: 172 RKMKQDQGLDVISEGLDTLKNLALDMNEELDRQVPLIDEIDTKVDKATSDLKNNNVRLKE 231
R+ + D+ L+ +S + L+++ALDM E+D Q ID I K D + + N R +
Sbjct: 4 RENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATK 63
Query: 232 TL 233
L
Sbjct: 64 ML 65
>pdb|3RK2|D Chain D, Truncated Snare Complex
pdb|3RK2|H Chain H, Truncated Snare Complex
pdb|3RK3|D Chain D, Truncated Snare Complex With Complexin
pdb|3RL0|D Chain D, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|H Chain H, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|L Chain L, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|P Chain P, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|T Chain T, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|X Chain X, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|BB Chain b, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|FF Chain f, Truncated Snare Complex With Complexin (P1)
Length = 65
Score = 30.8 bits (68), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%)
Query: 172 RKMKQDQGLDVISEGLDTLKNLALDMNEELDRQVPLIDEIDTKVDKATSDLKNNNVRLKE 231
R+ + D+ L+ +S + L+++ALDM E+D Q ID I K D + + N R +
Sbjct: 4 RENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATK 63
Query: 232 TL 233
L
Sbjct: 64 ML 65
>pdb|1XTG|B Chain B, Crystal Structure Of Neurotoxin BontA COMPLEXED WITH
Synaptosomal-Associated Protein 25
Length = 59
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 177 DQGLDVISEGLDTLKNLALDMNEELDRQVPLIDEIDTKVDKATSDLKNNNVRLKETL 233
D+ L+ +S + L+++ALDM E+D Q ID I K D + + N R + L
Sbjct: 2 DENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKML 58
>pdb|3ZUR|A Chain A, Crystal Structure Of An Engineered Botulinum Neurotoxin
Type A-Snare23 Derivative, Lc0-A-Snap25-Hn-A
pdb|3ZUR|B Chain B, Crystal Structure Of An Engineered Botulinum Neurotoxin
Type A-Snare23 Derivative, Lc0-A-Snap25-Hn-A
Length = 960
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 177 DQGLDVISEGLDTLKNLALDMNEELDRQVPLIDEIDTKVDKATSDLKNNNVRLKETL 233
D+ L+ +S + L+++ALDM E+D Q ID I K D + + N R + L
Sbjct: 453 DENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKML 509
>pdb|3HD7|B Chain B, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup C 1 2 1
pdb|3HD7|F Chain F, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup C 1 2 1
pdb|3IPD|B Chain B, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup I 21 21 21
pdb|3IPD|F Chain F, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup I 21 21 21
Length = 109
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%)
Query: 190 LKNLALDMNEELDRQVPLIDEIDTKVDKATSDLKNNNVRLKETLLKVRSSRNFCIDIILL 249
L ++ +DM ++ Q +ID I+ V+ A ++ K+ + +R I II+
Sbjct: 33 LHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSDTKKAVKYQSKARRKKIMIIIC 92
Query: 250 CVILGI 255
CVILGI
Sbjct: 93 CVILGI 98
>pdb|4IRY|B Chain B, Influenza A Virus Tail-loop Free Nucleoprotein At 2.8 A
Resolution
pdb|4IRY|A Chain A, Influenza A Virus Tail-loop Free Nucleoprotein At 2.8 A
Resolution
Length = 483
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 84 VPKLQKLARKKVKGLSKEEQETRHDLVLGLSERIEAI---PDGNTNATKANGGWATS 137
VP+ KL+ + V+ S E ET L L R AI GNTN +A GG +T
Sbjct: 353 VPR-GKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNTNQQRAGGGGSTG 408
>pdb|1ULR|A Chain A, Crystal Structure Of Tt0497 From Thermus Thermophilus Hb8
Length = 88
Score = 28.9 bits (63), Expect = 3.1, Method: Composition-based stats.
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 84 VPKLQKLARKKVKGLSKEEQETRHDLVLGLSERIEAIPDG 123
+P+L L + +V+G+ + L LGLS E +PDG
Sbjct: 1 MPRLVALVKGRVQGVGYRAFAQKKALELGLSGYAENLPDG 40
>pdb|2NPS|D Chain D, Crystal Structure Of The Early Endosomal Snare Complex
Length = 82
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 29/49 (59%)
Query: 176 QDQGLDVISEGLDTLKNLALDMNEELDRQVPLIDEIDTKVDKATSDLKN 224
QD+ L+++S + LKN++ + EL+ Q ++++ +++ S L N
Sbjct: 17 QDEQLELVSGSIGVLKNMSQRIGGELEEQAVMLEDFSHELESTQSRLDN 65
>pdb|3ZEY|L Chain L, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 142
Score = 28.1 bits (61), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 26/41 (63%), Gaps = 4/41 (9%)
Query: 87 LQKLARKKVKGLS----KEEQETRHDLVLGLSERIEAIPDG 123
+++LAR V+G+S +EE+E R D V +S +AI DG
Sbjct: 58 MKRLARGPVRGISLKLQEEERERRMDYVPEVSHVDQAIQDG 98
>pdb|3C8F|A Chain A, 4fe-4s-Pyruvate Formate-Lyase Activating Enzyme With
Partially Disordered Adomet
pdb|3CB8|A Chain A, 4fe-4s-Pyruvate Formate-Lyase Activating Enzyme In Complex
With Adomet And A Peptide Substrate
Length = 245
Score = 28.1 bits (61), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 185 EGLDTLKNLALDMNEELDRQVPLIDEIDTKVDKATSDLKNNNVRLKETLLKVRSSR 240
EG+ T LD N + R P+IDE+ D DLK N + + L+ V + R
Sbjct: 97 EGIHT----CLDTNGFVRRYDPVIDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHR 148
>pdb|4DG5|A Chain A, Crystal Structure Of Staphylococcal Phosphoglycerate
Kinase
Length = 403
Score = 27.3 bits (59), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 189 TLKNLALDMNEELDRQVPLIDEI-DTKVDKATSDLKNNNVRLKE 231
TL+ +A D++++LD++V + E K++ A DLK +V L E
Sbjct: 80 TLRPVAEDLSKKLDKEVVFVPETRGEKLEAAIKDLKEGDVLLVE 123
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
0.315 0.131 0.353
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,085,121
Number of Sequences: 62578
Number of extensions: 218801
Number of successful extensions: 627
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 609
Number of HSP's gapped (non-prelim): 23
length of query: 265
length of database: 14,973,337
effective HSP length: 97
effective length of query: 168
effective length of database: 8,903,271
effective search space: 1495749528
effective search space used: 1495749528
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)