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= 029729
(189 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4B93|A Chain A, Complex Of Vamp7 Cytoplasmic Domain With 2nd Ankyrin
Repeat Domain Of Varp
Length = 189
Score = 95.9 bits (237), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 55/174 (31%), Positives = 91/174 (52%), Gaps = 8/174 (4%)
Query: 5 SLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYT 64
++++A VARG +LA++ GNF + Q L K+P+ NNK TY+ + F+Y+ +
Sbjct: 3 AILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIV 62
Query: 65 YCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDH 124
Y + D+ R +FL VK F + Y G +A TA +N EF L +++ H
Sbjct: 63 YLCITDDDFERSRAFSFLNEVKKRFQTTY-GSRAQTALPYAMNSEFSSVLAAQLKH---H 118
Query: 125 PE--EISKLAKVKAQVSEVKGVMMENIEKIG--GKRLSYWSIRLRTFISRHKTF 174
E + K+ + +AQV E+KG+M+ NI+ + G+RL + + TF
Sbjct: 119 SENKSLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELLIDKTENLVDSSVTF 172
>pdb|2DMW|A Chain A, Solution Structure Of The Longin Domain Of Synaptobrevin-
Like Protein 1
Length = 131
Score = 76.3 bits (186), Expect = 9e-15, Method: Compositional matrix adjust.
Identities = 40/124 (32%), Positives = 64/124 (51%), Gaps = 1/124 (0%)
Query: 2 SQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDN 61
S ++++A VARG +LA++ GNF + Q L K+P+ NNK TY+ + F+Y+ +
Sbjct: 6 SGMAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHGNYLFHYICQD 65
Query: 62 GYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYC 121
Y + D+ R FL +K F + Y G +A TAP +N EF L +++
Sbjct: 66 RIVYLCITDDDFERSRAFNFLNEIKKRFQTTY-GSRAQTAPPYAMNSEFSSVLAAQLKHH 124
Query: 122 VDHP 125
P
Sbjct: 125 SSGP 128
>pdb|4AFI|A Chain A, Complex Between Vamp7 Longin Domain And Fragment Of Delta-
Adaptin From Ap3
pdb|4AFI|B Chain B, Complex Between Vamp7 Longin Domain And Fragment Of Delta-
Adaptin From Ap3
Length = 173
Score = 73.2 bits (178), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 38/116 (32%), Positives = 62/116 (53%), Gaps = 1/116 (0%)
Query: 5 SLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYT 64
++++A VARG +LA++ GNF + Q L K+P+ NNK TY+ + F+Y+ +
Sbjct: 55 AILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIV 114
Query: 65 YCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQY 120
Y + D+ R +FL VK F + Y G +A TA +N EF L +++
Sbjct: 115 YLCITDDDFERSRAFSFLNEVKKRFQTTY-GSRAQTALPYAMNSEFSSVLAAQLKH 169
>pdb|2VX8|A Chain A, Vamp7 Longin Domain Hrb Peptide Complex
pdb|2VX8|B Chain B, Vamp7 Longin Domain Hrb Peptide Complex
pdb|2VX8|C Chain C, Vamp7 Longin Domain Hrb Peptide Complex
pdb|2VX8|D Chain D, Vamp7 Longin Domain Hrb Peptide Complex
Length = 169
Score = 73.2 bits (178), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 38/110 (34%), Positives = 59/110 (53%), Gaps = 1/110 (0%)
Query: 5 SLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYT 64
++++A VARG +LA++ GNF + Q L K+P+ NNK TY+ + F+Y+ +
Sbjct: 45 AILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIV 104
Query: 65 YCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKL 114
Y + D+ R +FL VK F + Y G +A TA +N EF L
Sbjct: 105 YLCITDDDFERSRAFSFLNEVKKRFQTTY-GSRAQTALPYAMNSEFSSVL 153
>pdb|3EGD|C Chain C, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec23a24A COMPLEXED WITH THE SNARE PROTEIN SEC22 AND
BOUND To The Transport Signal Sequence Of Vesicular
Stomatitis Virus Glycoprotein
pdb|3EGX|C Chain C, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec23a24A COMPLEXED WITH THE SNARE PROTEIN SEC22B AND
Bound To The Transport Signal Sequence Of The Snare
Protein Bet1
Length = 157
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 31/127 (24%), Positives = 62/127 (48%), Gaps = 3/127 (2%)
Query: 27 NFNSIAYQCLQKL-PASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERV 85
+ S A Q +KL S + T A TF+Y+++ G Y V+ + + +++ A+LE +
Sbjct: 32 QYQSQAKQLFRKLNEQSPTRCTLEAGAMTFHYIIEQGVCYLVLCEAAFPKKLAFAYLEDL 91
Query: 86 KDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVM 145
EF ++ G K T EF +++ + +D L + ++ +V+ +M
Sbjct: 92 HSEFDEQH-GKKVPTVSRPYSFIEFDTFIQKTKKLYIDSRAR-RNLGSINTELQDVQRIM 149
Query: 146 MENIEKI 152
+ NIE++
Sbjct: 150 VANIEEV 156
>pdb|2NUP|C Chain C, Crystal Structure Of The Human Sec23a24A HETERODIMER,
Complexed With The Snare Protein Sec22b
pdb|2NUT|C Chain C, Crystal Structure Of The Human Sec23a24A HETERODIMER,
Complexed With The Snare Protein Sec22b
Length = 196
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 31/127 (24%), Positives = 62/127 (48%), Gaps = 3/127 (2%)
Query: 27 NFNSIAYQCLQKL-PASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERV 85
+ S A Q +KL S + T A TF+Y+++ G Y V+ + + +++ A+LE +
Sbjct: 33 QYQSQAKQLFRKLNEQSPTRCTLEAGAMTFHYIIEQGVCYLVLCEAAFPKKLAFAYLEDL 92
Query: 86 KDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVM 145
EF ++ G K T EF +++ + +D L + ++ +V+ +M
Sbjct: 93 HSEFDEQH-GKKVPTVSRPYSFIEFDTFIQKTKKLYIDSRAR-RNLGSINTELQDVQRIM 150
Query: 146 MENIEKI 152
+ NIE++
Sbjct: 151 VANIEEV 157
>pdb|1IFQ|A Chain A, Sec22b N-Terminal Domain
pdb|1IFQ|B Chain B, Sec22b N-Terminal Domain
Length = 138
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 27 NFNSIAYQCLQKL-PASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERV 85
+ S A Q +KL S + T A TF+Y+++ G Y V+ + + +++ A+LE +
Sbjct: 43 QYQSQAKQLFRKLNEQSPTRCTLEAGAXTFHYIIEQGVCYLVLCEAAFPKKLAFAYLEDL 102
Query: 86 KDEFVSKYG 94
EF ++G
Sbjct: 103 HSEFDEQHG 111
>pdb|3KYQ|A Chain A, Lipid-Induced Conformational Switch Controls Fusion
Activity Of Longin Domain Snare Ykt6
Length = 199
Score = 30.4 bits (67), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 44/101 (43%), Gaps = 14/101 (13%)
Query: 57 YLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSK-----YGGGKAATAPANGLNKEFG 111
Y+ + V+AD ++ LE+V DEF + + G AT L+
Sbjct: 70 YVRSDSLAGVVIADSEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGSPATIHYTALD---- 125
Query: 112 PKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKI 152
L +Y +P E ++KV+A++ E K ++ +E +
Sbjct: 126 ---GHLSRY--QNPREADPMSKVQAELDETKIILHNTMESL 161
>pdb|3GTD|A Chain A, 2.4 Angstrom Crystal Structure Of Fumarate Hydratase From
Rickettsia Prowazekii
pdb|3GTD|B Chain B, 2.4 Angstrom Crystal Structure Of Fumarate Hydratase From
Rickettsia Prowazekii
Length = 482
Score = 30.4 bits (67), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 41/88 (46%), Gaps = 10/88 (11%)
Query: 37 QKLPASNNKFTYNCD-AHTFNYLVDNGYTYC------VVADESSG--RQIPMAFLERVKD 87
Q +PA NN TY D + ++ ++ G T+ + E SG QI A LER++D
Sbjct: 180 QLIPALNNLLTYLQDKSKDWDKIIKIGRTHLQDATPLTLKQEFSGYITQIEYA-LERIED 238
Query: 88 EFVSKYGGGKAATAPANGLNKEFGPKLK 115
Y + TA G+N + G +K
Sbjct: 239 ALKKVYLLAQGGTAVGTGINSKIGFDIK 266
>pdb|3B5N|A Chain A, Structure Of The Yeast Plasma Membrane Snare Complex
pdb|3B5N|E Chain E, Structure Of The Yeast Plasma Membrane Snare Complex
pdb|3B5N|I Chain I, Structure Of The Yeast Plasma Membrane Snare Complex
Length = 61
Score = 26.9 bits (58), Expect = 6.1, Method: Composition-based stats.
Identities = 11/32 (34%), Positives = 23/32 (71%), Gaps = 2/32 (6%)
Query: 129 SKLAKVKAQVSEVKGVMMENIEKIG--GKRLS 158
S+ A+++A++ + G+M +NI K+ G+RL+
Sbjct: 2 SRTAELQAEIDDTVGIMRDNINKVAERGERLT 33
>pdb|3I4I|A Chain A, Crystal Structure Of A Prokaryotic
Beta-1,3-1,4-Glucanase (Lichenase) Derived From A Mouse
Hindgut Metagenome
pdb|3I4I|B Chain B, Crystal Structure Of A Prokaryotic
Beta-1,3-1,4-Glucanase (Lichenase) Derived From A Mouse
Hindgut Metagenome
Length = 234
Score = 26.9 bits (58), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 1/70 (1%)
Query: 21 YTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMA 80
+T F F+ Q +K N +NC +N + +G + D+ P A
Sbjct: 21 FTHFGEGFDYYDSQLWEKADGWGNGGVFNCIWRAYNIELKDGILNLSITDDMPSSSKPYA 80
Query: 81 FLE-RVKDEF 89
E R +D+F
Sbjct: 81 GAEYRTRDKF 90
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
0.319 0.134 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,388,582
Number of Sequences: 62578
Number of extensions: 216137
Number of successful extensions: 619
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 8
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): 13
length of query: 189
length of database: 14,973,337
effective HSP length: 93
effective length of query: 96
effective length of database: 9,153,583
effective search space: 878743968
effective search space used: 878743968
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: 48 (23.1 bits)