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= 038691
(221 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 = 140 bits (354), Expect = 4e-34, Method: Compositional matrix adjust.
Identities = 67/190 (35%), Positives = 112/190 (58%), Gaps = 2/190 (1%)
Query: 1 MGILYGMVARGNVVLAEFSAAQTNGNAIARQVIDKLPQGISDRILSYSHDHYIFHVKRTD 60
M IL+ +VARG +LA+ + N + Q++ K+P + L+YSH +Y+FH D
Sbjct: 2 MAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPS--ENNKLTYSHGNYLFHYICQD 59
Query: 61 NLTVLCMADDSFGWRIPFAFLEDIHQRFVRTYGRSIHSAAAYAMNDEFSRILSKQMDHYS 120
+ LC+ DD F F+FL ++ +RF TYG +A YAMN EFS +L+ Q+ H+S
Sbjct: 60 RIVYLCITDDDFERSRAFSFLNEVKKRFQTTYGSRAQTALPYAMNSEFSSVLAAQLKHHS 119
Query: 121 NDPNADRLNRLKGEMSHVRSVMIDNIEKIVERGDRLNLLVDKTATLHRNTVRFKRQARRY 180
+ + D++ + ++ ++ +M+ NI+ + +RG+RL LL+DKT L ++V FK +R
Sbjct: 120 ENKSLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELLIDKTENLVDSSVTFKTTSRNL 179
Query: 181 KSSVCWGNCK 190
++C N K
Sbjct: 180 ARAMCMKNIK 189
>pdb|2DMW|A Chain A, Solution Structure Of The Longin Domain Of Synaptobrevin-
Like Protein 1
Length = 131
Score = 97.8 bits (242), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 48/125 (38%), Positives = 73/125 (58%), Gaps = 2/125 (1%)
Query: 1 MGILYGMVARGNVVLAEFSAAQTNGNAIARQVIDKLPQGISDRILSYSHDHYIFHVKRTD 60
M IL+ +VARG +LA+ + N + Q++ K+P + L+YSH +Y+FH D
Sbjct: 8 MAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPS--ENNKLTYSHGNYLFHYICQD 65
Query: 61 NLTVLCMADDSFGWRIPFAFLEDIHQRFVRTYGRSIHSAAAYAMNDEFSRILSKQMDHYS 120
+ LC+ DD F F FL +I +RF TYG +A YAMN EFS +L+ Q+ H+S
Sbjct: 66 RIVYLCITDDDFERSRAFNFLNEIKKRFQTTYGSRAQTAPPYAMNSEFSSVLAAQLKHHS 125
Query: 121 NDPNA 125
+ P++
Sbjct: 126 SGPSS 130
>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 = 94.7 bits (234), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 46/122 (37%), Positives = 71/122 (58%), Gaps = 2/122 (1%)
Query: 1 MGILYGMVARGNVVLAEFSAAQTNGNAIARQVIDKLPQGISDRILSYSHDHYIFHVKRTD 60
M IL+ +VARG +LA+ + N + Q++ K+P + L+YSH +Y+FH D
Sbjct: 54 MAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPS--ENNKLTYSHGNYLFHYICQD 111
Query: 61 NLTVLCMADDSFGWRIPFAFLEDIHQRFVRTYGRSIHSAAAYAMNDEFSRILSKQMDHYS 120
+ LC+ DD F F+FL ++ +RF TYG +A YAMN EFS +L+ Q+ H+S
Sbjct: 112 RIVYLCITDDDFERSRAFSFLNEVKKRFQTTYGSRAQTALPYAMNSEFSSVLAAQLKHHS 171
Query: 121 ND 122
+
Sbjct: 172 EN 173
>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 = 89.7 bits (221), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 44/116 (37%), Positives = 67/116 (57%), Gaps = 2/116 (1%)
Query: 1 MGILYGMVARGNVVLAEFSAAQTNGNAIARQVIDKLPQGISDRILSYSHDHYIFHVKRTD 60
M IL+ +VARG +LA+ + N + Q++ K+P + L+YSH +Y+FH D
Sbjct: 44 MAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPS--ENNKLTYSHGNYLFHYICQD 101
Query: 61 NLTVLCMADDSFGWRIPFAFLEDIHQRFVRTYGRSIHSAAAYAMNDEFSRILSKQM 116
+ LC+ DD F F+FL ++ +RF TYG +A YAMN EFS +L+ Q+
Sbjct: 102 RIVYLCITDDDFERSRAFSFLNEVKKRFQTTYGSRAQTALPYAMNSEFSSVLAAQL 157
>pdb|3KYQ|A Chain A, Lipid-Induced Conformational Switch Controls Fusion
Activity Of Longin Domain Snare Ykt6
Length = 199
Score = 58.9 bits (141), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 70/144 (48%), Gaps = 15/144 (10%)
Query: 46 SYSHDHYIFHVK-RTDNLTVLCMADDSFGWRIPFAFLEDIHQRFVRTYGR---SIHSAAA 101
S Y+ HV R+D+L + +AD + R+ F LE + F + R + S A
Sbjct: 59 SVKEQEYLCHVYVRSDSLAGVVIADSEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGSPAT 118
Query: 102 ---YAMNDEFSRILSKQMDHYSNDPNADRLNRLKGEMSHVRSVMIDNIEKIVERGDRLNL 158
A++ SR Y N AD +++++ E+ + ++ + +E ++ERG++L+
Sbjct: 119 IHYTALDGHLSR--------YQNPREADPMSKVQAELDETKIILHNTMESLLERGEKLDD 170
Query: 159 LVDKTATLHRNTVRFKRQARRYKS 182
LV K+ L + F + AR+ S
Sbjct: 171 LVSKSEVLGTQSKAFYKTARKQNS 194
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 42/185 (22%), Positives = 84/185 (45%), Gaps = 10/185 (5%)
Query: 3 ILYGMVAR---GNVVLAEFSAAQTNG------NAIARQVIDKLPQGISDRILSYSHDHYI 53
+L M+AR G + A + +G + A+Q+ KL + R +
Sbjct: 3 VLLTMIARVADGLPLAASMQEDEQSGRDLQQYQSQAKQLFRKLNEQSPTRC-TLEAGAMT 61
Query: 54 FHVKRTDNLTVLCMADDSFGWRIPFAFLEDIHQRFVRTYGRSIHSAAAYAMNDEFSRILS 113
FH + L + + +F ++ FA+LED+H F +G+ + + + EF +
Sbjct: 62 FHYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDTFIQ 121
Query: 114 KQMDHYSNDPNADRLNRLKGEMSHVRSVMIDNIEKIVERGDRLNLLVDKTATLHRNTVRF 173
K Y + L + E+ V+ +M+ NIE++++RG+ L+ L K L + ++
Sbjct: 122 KTKKLYIDSRARRNLGSINTELQDVQRIMVANIEEVLQRGEALSALDSKANNLSSLSKKY 181
Query: 174 KRQAR 178
++ A+
Sbjct: 182 RQDAK 186
>pdb|2NPS|A Chain A, Crystal Structure Of The Early Endosomal Snare Complex
Length = 74
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 42/69 (60%)
Query: 123 PNADRLNRLKGEMSHVRSVMIDNIEKIVERGDRLNLLVDKTATLHRNTVRFKRQARRYKS 182
P D++ ++ ++ V VM +NI K++ERG+RL+ L DK+ +L N F ++++ +
Sbjct: 5 PRNDKIKHVQNQVDEVIDVMQENITKVIERGERLDELQDKSESLSDNATAFSNRSKQLRR 64
Query: 183 SVCWGNCKL 191
+ W CK+
Sbjct: 65 QMWWRGCKI 73
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 35/157 (22%), Positives = 68/157 (43%), Gaps = 10/157 (6%)
Query: 3 ILYGMVAR---GNVVLAEFSAAQTNG------NAIARQVIDKLPQGISDRILSYSHDHYI 53
+L M+AR G + A + +G + A+Q+ KL + R +
Sbjct: 2 VLLTMIARVADGLPLAASMQEDEQSGRDLQQYQSQAKQLFRKLNEQSPTRC-TLEAGAMT 60
Query: 54 FHVKRTDNLTVLCMADDSFGWRIPFAFLEDIHQRFVRTYGRSIHSAAAYAMNDEFSRILS 113
FH + L + + +F ++ FA+LED+H F +G+ + + + EF +
Sbjct: 61 FHYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDTFIQ 120
Query: 114 KQMDHYSNDPNADRLNRLKGEMSHVRSVMIDNIEKIV 150
K Y + L + E+ V+ +M+ NIE+++
Sbjct: 121 KTKKLYIDSRARRNLGSINTELQDVQRIMVANIEEVL 157
>pdb|1GL2|A Chain A, Crystal Structure Of An Endosomal Snare Core Complex
Length = 65
Score = 41.2 bits (95), Expect = 5e-04, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 34/54 (62%)
Query: 126 DRLNRLKGEMSHVRSVMIDNIEKIVERGDRLNLLVDKTATLHRNTVRFKRQARR 179
DR+ L+ E+ V+++M N+E+I+ RG+ L+ L +KT L + FK +++
Sbjct: 9 DRVRNLQSEVEGVKNIMTQNVERILARGENLDHLRNKTEDLEATSEHFKTTSQK 62
>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 = 41.2 bits (95), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 31/58 (53%)
Query: 127 RLNRLKGEMSHVRSVMIDNIEKIVERGDRLNLLVDKTATLHRNTVRFKRQARRYKSSV 184
R L+ E+ +M DNI K+ ERG+RL + DK L + FKR A R + ++
Sbjct: 3 RTAELQAEIDDTVGIMRDNINKVAERGERLTSIEDKADNLAVSAQGFKRGANRVRKAM 60
>pdb|1L4A|A Chain A, X-Ray Structure Of The Neuronal ComplexinSNARE COMPLEX
From The Squid Loligo Pealei
Length = 80
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%)
Query: 127 RLNRLKGEMSHVRSVMIDNIEKIVERGDRLNLLVDKTATLHRNTVRFKRQARRYKSSVCW 186
RL + + ++ V +M N++K++ER +++ L D+ L +F+ A + K W
Sbjct: 16 RLQQTQAQVEEVVDIMRVNVDKVLERDSKISELDDRADALQAGASQFEASAGKLKRKFWW 75
Query: 187 GNCKL 191
NCK+
Sbjct: 76 KNCKM 80
>pdb|3HD7|A Chain A, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup C 1 2 1
pdb|3HD7|E Chain E, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup C 1 2 1
pdb|3IPD|A Chain A, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup I 21 21 21
pdb|3IPD|E Chain E, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup I 21 21 21
Length = 91
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%)
Query: 127 RLNRLKGEMSHVRSVMIDNIEKIVERGDRLNLLVDKTATLHRNTVRFKRQARRYKSSVCW 186
RL + + ++ V +M N++K++ER +L+ L D+ L +F+ A + K W
Sbjct: 6 RLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWW 65
Query: 187 GNCKL 191
N K+
Sbjct: 66 KNLKM 70
>pdb|2KOG|A Chain A, Lipid-Bound Synaptobrevin Solution Nmr Structure
Length = 119
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%)
Query: 127 RLNRLKGEMSHVRSVMIDNIEKIVERGDRLNLLVDKTATLHRNTVRFKRQARRYKSSVCW 186
RL + + ++ V +M N++K++ER +L+ L D+ L +F+ A + K W
Sbjct: 34 RLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWW 93
Query: 187 GNCKL 191
N K+
Sbjct: 94 KNLKM 98
>pdb|1SFC|A Chain A, Neuronal Synaptic Fusion Complex
pdb|1SFC|E Chain E, Neuronal Synaptic Fusion Complex
pdb|1SFC|I Chain I, Neuronal Synaptic Fusion Complex
Length = 96
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%)
Query: 127 RLNRLKGEMSHVRSVMIDNIEKIVERGDRLNLLVDKTATLHRNTVRFKRQARRYKSSVCW 186
RL + + ++ V +M N++K++ER +L+ L D+ L +F+ A + K W
Sbjct: 31 RLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWW 90
Query: 187 GNCKL 191
N K+
Sbjct: 91 KNLKM 95
>pdb|1KIL|A Chain A, Three-Dimensional Structure Of The ComplexinSNARE COMPLEX
Length = 66
Score = 35.8 bits (81), Expect = 0.017, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 32/62 (51%)
Query: 127 RLNRLKGEMSHVRSVMIDNIEKIVERGDRLNLLVDKTATLHRNTVRFKRQARRYKSSVCW 186
RL + + ++ V +M N++K++ER +L+ L D+ L +F+ A + K W
Sbjct: 5 RLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWW 64
Query: 187 GN 188
N
Sbjct: 65 KN 66
>pdb|1IFQ|A Chain A, Sec22b N-Terminal Domain
pdb|1IFQ|B Chain B, Sec22b N-Terminal Domain
Length = 138
Score = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 30/66 (45%)
Query: 54 FHVKRTDNLTVLCMADDSFGWRIPFAFLEDIHQRFVRTYGRSIHSAAAYAMNDEFSRILS 113
FH + L + + +F ++ FA+LED+H F +G+ + + + EF +
Sbjct: 72 FHYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDTFIQ 131
Query: 114 KQMDHY 119
K Y
Sbjct: 132 KTKKLY 137
>pdb|3ZYM|A Chain A, Structure Of Calm (Picalm) In Complex With Vamp8
pdb|3ZYM|B Chain B, Structure Of Calm (Picalm) In Complex With Vamp8
pdb|3ZYM|C Chain C, Structure Of Calm (Picalm) In Complex With Vamp8
Length = 310
Score = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 24/37 (64%)
Query: 120 SNDPNADRLNRLKGEMSHVRSVMIDNIEKIVERGDRL 156
S + DR+ L+ E+ V+++M N+E+I+ RG+ L
Sbjct: 274 SGSGHMDRVRNLQSEVEGVKNIMTQNVERILARGENL 310
>pdb|1N7S|A Chain A, High Resolution Structure Of A Truncated Neuronal Snare
Complex
Length = 63
Score = 32.0 bits (71), Expect = 0.28, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 30/55 (54%)
Query: 127 RLNRLKGEMSHVRSVMIDNIEKIVERGDRLNLLVDKTATLHRNTVRFKRQARRYK 181
RL + + ++ V +M N++K++ER +L+ L D+ L +F+ A + K
Sbjct: 5 RLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLK 59
>pdb|3M2T|A Chain A, The Crystal Structure Of Dehydrogenase From
Chromobacterium Violaceum
pdb|3M2T|B Chain B, The Crystal Structure Of Dehydrogenase From
Chromobacterium Violaceum
Length = 359
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 92 YGRSIHSAAAYAMNDEFSRILSKQMDHYSNDPNADRLNRLKGEMSHVRSVMI 143
+ R + DEF L Q++HY+N P A L G S +RS ++
Sbjct: 130 FARPVRQLREXTQVDEFGETLHIQLNHYANKPRAP----LWGLDSTLRSFLL 177
>pdb|3ODG|A Chain A, Crystal Structure Of Xanthosine Phosphorylase Bound With
Xanthine From Yersinia Pseudotuberculosis
Length = 287
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 24/49 (48%)
Query: 1 MGILYGMVARGNVVLAEFSAAQTNGNAIARQVIDKLPQGISDRILSYSH 49
M I+ G V +VV SAA IA I L +G+SD +LS+
Sbjct: 213 MQIIGGDVVGMSVVPEVLSAAHCGLKVIALTAITNLAEGLSDVVLSHEQ 261
>pdb|3G7N|A Chain A, Crystal Structure Of A Triacylglycerol Lipase From
Penicillium Expansum At 1.3
pdb|3G7N|B Chain B, Crystal Structure Of A Triacylglycerol Lipase From
Penicillium Expansum At 1.3
Length = 258
Score = 27.3 bits (59), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 25/56 (44%)
Query: 11 GNVVLAEFSAAQTNGNAIARQVIDKLPQGISDRILSYSHDHYIFHVKRTDNLTVLC 66
GN A+F AQ V+D +P S ++++ H ++ T+ TV C
Sbjct: 165 GNQAWADFGTAQAGTFNRGNNVLDGVPNMYSSPLVNFKHYGTEYYSSGTEASTVKC 220
>pdb|2HE0|A Chain A, Crystal Structure Of A Human Notch1 Ankyrin Domain Mutant
pdb|2HE0|B Chain B, Crystal Structure Of A Human Notch1 Ankyrin Domain Mutant
Length = 253
Score = 26.9 bits (58), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 84 IHQRFVRTYGRSIHSAAAYAMNDEFSRILSKQMD 117
+H + RT ++H AAAY+ +D R+L D
Sbjct: 49 LHNQTDRTGATALHLAAAYSRSDAAKRLLEASAD 82
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
0.327 0.139 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,184,350
Number of Sequences: 62578
Number of extensions: 235216
Number of successful extensions: 680
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 26
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 649
Number of HSP's gapped (non-prelim): 26
length of query: 221
length of database: 14,973,337
effective HSP length: 95
effective length of query: 126
effective length of database: 9,028,427
effective search space: 1137581802
effective search space used: 1137581802
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 bits)