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= 029101
(199 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KYQ|A Chain A, Lipid-Induced Conformational Switch Controls Fusion
Activity Of Longin Domain Snare Ykt6
Length = 199
Score = 142 bits (358), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 90/202 (44%), Positives = 123/202 (60%), Gaps = 7/202 (3%)
Query: 1 MKITALLVL-KCNPDGSDPVVLATAMDVSHFGYFQRSSVKEFILFVARTVGKRTPPGQRQ 59
MK+ +L V K P V+L A DVS F +FQRSSV+EF+ F ++ + +R+ G R
Sbjct: 2 MKLYSLSVFYKGEPKA---VLLKAAYDVSSFSFFQRSSVQEFMTFTSQLIVERSAKGSRA 58
Query: 60 SVQHEEYKVHSYNR-NGLCVMGFMDDHYPVRSSFSLLNQVLDEYQKNFGE-SWRTAQADN 117
SV+ +EY H Y R + L + D YP R +F+LL +VLDE+ K W
Sbjct: 59 SVKEQEYLCHVYVRSDSLAGVVIADSEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGSPAT 118
Query: 118 MQPWPYLNEALNKYQDPAEADKLLKIQRELDETKIILHKTIDSVLARGEKLDSLVEKSSD 177
+ + L+ L++YQ+P EAD + K+Q ELDETKIILH T++S+L RGEKLD LV KS
Sbjct: 119 IH-YTALDGHLSRYQNPREADPMSKVQAELDETKIILHNTMESLLERGEKLDDLVSKSEV 177
Query: 178 LSAASQMFYKQAKKTNQCCTIL 199
L S+ FYK A+K N CC I+
Sbjct: 178 LGTQSKAFYKTARKQNSCCAIM 199
>pdb|3BW6|A Chain A, Crystal Structure Of The Longin Domain Of Yeast Ykt6
Length = 144
Score = 99.4 bits (246), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 55/144 (38%), Positives = 85/144 (59%), Gaps = 11/144 (7%)
Query: 1 MKITALLVLKCNPDGSDPVVLATAMDVSHFGYFQRSSVKEFILFVARTVGKRTPPGQRQS 60
M+I + V + G + L+ D+S FG+F+RSSV +F+ F A TV RT GQRQS
Sbjct: 5 MRIYYIGVFRSG--GEKALELSEVKDLSQFGFFERSSVGQFMTFFAETVASRTGAGQRQS 62
Query: 61 VQHEEYKVHSYNRN-GLCVMGFMDDHYPVRSSFSLLNQVLDEY-----QKNFGESWRTAQ 114
++ Y H Y R+ G+C + D YPVR +++LLN++LDEY ++ + + T
Sbjct: 63 IEEGNYIGHVYARSEGICGVLITDKEYPVRPAYTLLNKILDEYLVAHPKEEWADVTETND 122
Query: 115 ADNMQPWPYLNEALNKYQDPAEAD 138
A M+ L+ ++KYQDP++AD
Sbjct: 123 ALKMKQ---LDTYISKYQDPSQAD 143
>pdb|1IOU|A Chain A, Solution Structure Of Ykt6p (1-140)
pdb|1H8M|A Chain A, Solution Structure Of Ykt6
Length = 140
Score = 98.2 bits (243), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 54/144 (37%), Positives = 85/144 (59%), Gaps = 11/144 (7%)
Query: 1 MKITALLVLKCNPDGSDPVVLATAMDVSHFGYFQRSSVKEFILFVARTVGKRTPPGQRQS 60
M+I + V + G + L+ D+S FG+F+RSSV +F+ F A TV RT G+RQS
Sbjct: 1 MRIYYIGVFRSG--GEKALELSEVKDLSQFGFFERSSVGQFMTFFAETVASRTGAGERQS 58
Query: 61 VQHEEYKVHSYNRN-GLCVMGFMDDHYPVRSSFSLLNQVLDEY-----QKNFGESWRTAQ 114
++ Y H Y R+ G+C + D YPVR +++LLN++LDEY ++ + + T
Sbjct: 59 IEEGNYIGHVYARSEGICGVLITDKQYPVRPAYTLLNKILDEYLVAHPKEEWADVTETND 118
Query: 115 ADNMQPWPYLNEALNKYQDPAEAD 138
A M+ L+ ++KYQDP++AD
Sbjct: 119 ALKMKQ---LDTYISKYQDPSQAD 139
>pdb|4B93|A Chain A, Complex Of Vamp7 Cytoplasmic Domain With 2nd Ankyrin
Repeat Domain Of Varp
Length = 189
Score = 61.6 bits (148), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 39/147 (26%), Positives = 71/147 (48%), Gaps = 2/147 (1%)
Query: 41 FILFVARTVGKRTPPGQRQSVQHEEYKVHSYNRNGLCVMGFMDDHYPVRSSFSLLNQVLD 100
F+ + + K + + H Y H ++ + + DD + +FS LN+V
Sbjct: 26 FLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIVYLCITDDDFERSRAFSFLNEVKK 85
Query: 101 EYQKNFGESWRTA--QADNMQPWPYLNEALNKYQDPAEADKLLKIQRELDETKIILHKTI 158
+Q +G +TA A N + L L + + DK+++ Q ++DE K I+ + I
Sbjct: 86 RFQTTYGSRAQTALPYAMNSEFSSVLAAQLKHHSENKSLDKVMETQAQVDELKGIMVRNI 145
Query: 159 DSVLARGEKLDSLVEKSSDLSAASQMF 185
D V RGE+L+ L++K+ +L +S F
Sbjct: 146 DLVAQRGERLELLIDKTENLVDSSVTF 172
>pdb|1GL2|A Chain A, Crystal Structure Of An Endosomal Snare Core Complex
Length = 65
Score = 42.7 bits (99), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 35/57 (61%)
Query: 135 AEADKLLKIQRELDETKIILHKTIDSVLARGEKLDSLVEKSSDLSAASQMFYKQAKK 191
A D++ +Q E++ K I+ + ++ +LARGE LD L K+ DL A S+ F ++K
Sbjct: 6 AGNDRVRNLQSEVEGVKNIMTQNVERILARGENLDHLRNKTEDLEATSEHFKTTSQK 62
>pdb|2NPS|A Chain A, Crystal Structure Of The Early Endosomal Snare Complex
Length = 74
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 33/54 (61%)
Query: 138 DKLLKIQRELDETKIILHKTIDSVLARGEKLDSLVEKSSDLSAASQMFYKQAKK 191
DK+ +Q ++DE ++ + I V+ RGE+LD L +KS LS + F ++K+
Sbjct: 8 DKIKHVQNQVDEVIDVMQENITKVIERGERLDELQDKSESLSDNATAFSNRSKQ 61
>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 = 38.5 bits (88), Expect = 0.002, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 34/53 (64%)
Query: 142 KIQRELDETKIILHKTIDSVLARGEKLDSLVEKSSDLSAASQMFYKQAKKTNQ 194
++Q E+D+T I+ I+ V RGE+L S+ +K+ +L+ ++Q F + A + +
Sbjct: 6 ELQAEIDDTVGIMRDNINKVAERGERLTSIEDKADNLAVSAQGFKRGANRVRK 58
>pdb|1KIL|A Chain A, Three-Dimensional Structure Of The ComplexinSNARE COMPLEX
Length = 66
Score = 31.2 bits (69), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%)
Query: 139 KLLKIQRELDETKIILHKTIDSVLARGEKLDSLVEKSSDLSAASQMFYKQAKK 191
+L + Q ++DE I+ +D VL R +KL L +++ L A + F A K
Sbjct: 5 RLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAK 57
>pdb|1N7S|A Chain A, High Resolution Structure Of A Truncated Neuronal Snare
Complex
Length = 63
Score = 30.8 bits (68), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%)
Query: 139 KLLKIQRELDETKIILHKTIDSVLARGEKLDSLVEKSSDLSAASQMFYKQAKK 191
+L + Q ++DE I+ +D VL R +KL L +++ L A + F A K
Sbjct: 5 RLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAK 57
>pdb|2KOG|A Chain A, Lipid-Bound Synaptobrevin Solution Nmr Structure
Length = 119
Score = 30.8 bits (68), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%)
Query: 139 KLLKIQRELDETKIILHKTIDSVLARGEKLDSLVEKSSDLSAASQMFYKQAKK 191
+L + Q ++DE I+ +D VL R +KL L +++ L A + F A K
Sbjct: 34 RLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAK 86
>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 = 30.4 bits (67), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%)
Query: 139 KLLKIQRELDETKIILHKTIDSVLARGEKLDSLVEKSSDLSAASQMFYKQAKK 191
+L + Q ++DE I+ +D VL R +KL L +++ L A + F A K
Sbjct: 31 RLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAK 83
>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 = 30.4 bits (67), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%)
Query: 139 KLLKIQRELDETKIILHKTIDSVLARGEKLDSLVEKSSDLSAASQMFYKQAKK 191
+L + Q ++DE I+ +D VL R +KL L +++ L A + F A K
Sbjct: 6 RLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAK 58
>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 = 30.0 bits (66), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 31/73 (42%)
Query: 41 FILFVARTVGKRTPPGQRQSVQHEEYKVHSYNRNGLCVMGFMDDHYPVRSSFSLLNQVLD 100
F+ + + K + + H Y H ++ + + DD + +FS LN+V
Sbjct: 68 FLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIVYLCITDDDFERSRAFSFLNEVKK 127
Query: 101 EYQKNFGESWRTA 113
+Q +G +TA
Sbjct: 128 RFQTTYGSRAQTA 140
>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 = 30.0 bits (66), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 31/73 (42%)
Query: 41 FILFVARTVGKRTPPGQRQSVQHEEYKVHSYNRNGLCVMGFMDDHYPVRSSFSLLNQVLD 100
F+ + + K + + H Y H ++ + + DD + +FS LN+V
Sbjct: 78 FLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIVYLCITDDDFERSRAFSFLNEVKK 137
Query: 101 EYQKNFGESWRTA 113
+Q +G +TA
Sbjct: 138 RFQTTYGSRAQTA 150
>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 = 28.5 bits (62), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 21/31 (67%)
Query: 138 DKLLKIQRELDETKIILHKTIDSVLARGEKL 168
D++ +Q E++ K I+ + ++ +LARGE L
Sbjct: 280 DRVRNLQSEVEGVKNIMTQNVERILARGENL 310
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 28.1 bits (61), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 26/47 (55%)
Query: 136 EADKLLKIQRELDETKIILHKTIDSVLARGEKLDSLVEKSSDLSAAS 182
EA +LL+I + L I KTI+ A+G K D + S +SAAS
Sbjct: 78 EAAQLLQILQALHPPLTIDGKTINVEFAKGSKRDMASNEGSRISAAS 124
>pdb|4E8B|A Chain A, Crystal Structure Of 16s Rrna Methyltransferase Rsme From
E.Coli
Length = 251
Score = 27.3 bits (59), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 26/39 (66%)
Query: 143 IQRELDETKIILHKTIDSVLARGEKLDSLVEKSSDLSAA 181
++ ++D+ + LH + V++RGEK++ ++KS +L +
Sbjct: 67 LEGQIDDRESPLHIHLGQVMSRGEKMEFTIQKSIELGVS 105
>pdb|1QCF|A Chain A, Crystal Structure Of Hck In Complex With A Src Family-
Selective Tyrosine Kinase Inhibitor
pdb|2C0I|A Chain A, Src Family Kinase Hck With Bound Inhibitor A-420983
pdb|2C0I|B Chain B, Src Family Kinase Hck With Bound Inhibitor A-420983
pdb|2C0O|A Chain A, Src Family Kinase Hck With Bound Inhibitor A-770041
pdb|2C0O|B Chain B, Src Family Kinase Hck With Bound Inhibitor A-770041
pdb|2C0T|A Chain A, Src Family Kinase Hck With Bound Inhibitor A-641359
pdb|2C0T|B Chain B, Src Family Kinase Hck With Bound Inhibitor A-641359
Length = 454
Score = 27.3 bits (59), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 10/51 (19%)
Query: 55 PGQRQSVQHEEYKVHSYNRNGLCVMGFMDDHYPVRSSFSLLNQVLDEYQKN 105
P Q +V+H YK+ + + G + RS+FS L +++D Y+K
Sbjct: 117 PRQGDTVKH--YKIRTLDNGGFYI--------SPRSTFSTLQELVDHYKKG 157
>pdb|2DMW|A Chain A, Solution Structure Of The Longin Domain Of Synaptobrevin-
Like Protein 1
Length = 131
Score = 26.9 bits (58), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 14/73 (19%), Positives = 31/73 (42%)
Query: 41 FILFVARTVGKRTPPGQRQSVQHEEYKVHSYNRNGLCVMGFMDDHYPVRSSFSLLNQVLD 100
F+ + + K + + H Y H ++ + + DD + +F+ LN++
Sbjct: 32 FLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIVYLCITDDDFERSRAFNFLNEIKK 91
Query: 101 EYQKNFGESWRTA 113
+Q +G +TA
Sbjct: 92 RFQTTYGSRAQTA 104
>pdb|1AD5|A Chain A, Src Family Kinase Hck-Amp-Pnp Complex
pdb|1AD5|B Chain B, Src Family Kinase Hck-Amp-Pnp Complex
pdb|2HCK|A Chain A, Src Family Kinase Hck-Quercetin Complex
pdb|2HCK|B Chain B, Src Family Kinase Hck-Quercetin Complex
Length = 438
Score = 26.9 bits (58), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 10/51 (19%)
Query: 55 PGQRQSVQHEEYKVHSYNRNGLCVMGFMDDHYPVRSSFSLLNQVLDEYQKN 105
P Q +V+H YK+ + + G + RS+FS L +++D Y+K
Sbjct: 111 PRQGDTVKH--YKIRTLDNGGFYI--------SPRSTFSTLQELVDHYKKG 151
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
0.318 0.132 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,644,612
Number of Sequences: 62578
Number of extensions: 217179
Number of successful extensions: 633
Number of sequences better than 100.0: 60
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 42
Number of HSP's that attempted gapping in prelim test: 608
Number of HSP's gapped (non-prelim): 60
length of query: 199
length of database: 14,973,337
effective HSP length: 94
effective length of query: 105
effective length of database: 9,091,005
effective search space: 954555525
effective search space used: 954555525
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)