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= 027705
(220 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 = 158 bits (399), Expect = 2e-39, Method: Compositional matrix adjust.
Identities = 77/187 (41%), Positives = 119/187 (63%), Gaps = 1/187 (0%)
Query: 1 MAILYALVARGTVVLAEFSAVTGNTGAVARRIIEKLPAESDSRVCFSQDRYIFHILRSDG 60
MAIL+A+VARGT +LA+ + GN V +I+ K+P+E++ ++ +S Y+FH + D
Sbjct: 2 MAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENN-KLTYSHGNYLFHYICQDR 60
Query: 61 LTFLCMANDTFGRRIPFSYLEDIQMRFMKNYGRVAHYAPAYAMNDEFSRVLHQQMEFFSS 120
+ +LC+ +D F R FS+L +++ RF YG A A YAMN EFS VL Q++ S
Sbjct: 61 IVYLCITDDDFERSRAFSFLNEVKKRFQTTYGSRAQTALPYAMNSEFSSVLAAQLKHHSE 120
Query: 121 NPSADTLNRVRGEVSEIRTIMVENIEKILERGDRIELLVDKTATMQDGAFHFRKQSKRLR 180
N S D + + +V E++ IMV NI+ + +RG+R+ELL+DKT + D + F+ S+ L
Sbjct: 121 NKSLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELLIDKTENLVDSSVTFKTTSRNLA 180
Query: 181 RALWMKN 187
RA+ MKN
Sbjct: 181 RAMCMKN 187
>pdb|2DMW|A Chain A, Solution Structure Of The Longin Domain Of Synaptobrevin-
Like Protein 1
Length = 131
Score = 109 bits (272), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 53/124 (42%), Positives = 80/124 (64%), Gaps = 1/124 (0%)
Query: 1 MAILYALVARGTVVLAEFSAVTGNTGAVARRIIEKLPAESDSRVCFSQDRYIFHILRSDG 60
MAIL+A+VARGT +LA+ + GN V +I+ K+P+E++ ++ +S Y+FH + D
Sbjct: 8 MAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENN-KLTYSHGNYLFHYICQDR 66
Query: 61 LTFLCMANDTFGRRIPFSYLEDIQMRFMKNYGRVAHYAPAYAMNDEFSRVLHQQMEFFSS 120
+ +LC+ +D F R F++L +I+ RF YG A AP YAMN EFS VL Q++ SS
Sbjct: 67 IVYLCITDDDFERSRAFNFLNEIKKRFQTTYGSRAQTAPPYAMNSEFSSVLAAQLKHHSS 126
Query: 121 NPSA 124
PS+
Sbjct: 127 GPSS 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 = 101 bits (251), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 50/121 (41%), Positives = 76/121 (62%), Gaps = 1/121 (0%)
Query: 1 MAILYALVARGTVVLAEFSAVTGNTGAVARRIIEKLPAESDSRVCFSQDRYIFHILRSDG 60
MAIL+A+VARGT +LA+ + GN V +I+ K+P+E++ ++ +S Y+FH + D
Sbjct: 54 MAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENN-KLTYSHGNYLFHYICQDR 112
Query: 61 LTFLCMANDTFGRRIPFSYLEDIQMRFMKNYGRVAHYAPAYAMNDEFSRVLHQQMEFFSS 120
+ +LC+ +D F R FS+L +++ RF YG A A YAMN EFS VL Q++ S
Sbjct: 113 IVYLCITDDDFERSRAFSFLNEVKKRFQTTYGSRAQTALPYAMNSEFSSVLAAQLKHHSE 172
Query: 121 N 121
N
Sbjct: 173 N 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 = 99.0 bits (245), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 48/116 (41%), Positives = 74/116 (63%), Gaps = 1/116 (0%)
Query: 1 MAILYALVARGTVVLAEFSAVTGNTGAVARRIIEKLPAESDSRVCFSQDRYIFHILRSDG 60
MAIL+A+VARGT +LA+ + GN V +I+ K+P+E++ ++ +S Y+FH + D
Sbjct: 44 MAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENN-KLTYSHGNYLFHYICQDR 102
Query: 61 LTFLCMANDTFGRRIPFSYLEDIQMRFMKNYGRVAHYAPAYAMNDEFSRVLHQQME 116
+ +LC+ +D F R FS+L +++ RF YG A A YAMN EFS VL Q++
Sbjct: 103 IVYLCITDDDFERSRAFSFLNEVKKRFQTTYGSRAQTALPYAMNSEFSSVLAAQLK 158
>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 = 65.9 bits (159), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 37/152 (24%), Positives = 77/152 (50%), Gaps = 2/152 (1%)
Query: 29 ARRIIEKLPAESDSRVCFSQDRYIFHILRSDGLTFLCMANDTFGRRIPFSYLEDIQMRFM 88
A+++ KL +S +R FH + G+ +L + F +++ F+YLED+ F
Sbjct: 38 AKQLFRKLNEQSPTRCTLEAGAMTFHYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFD 97
Query: 89 KNYG-RVAHYAPAYAMNDEFSRVLHQQMEFFSSNPSADTLNRVRGEVSEIRTIMVENIEK 147
+ +G +V + Y+ EF + + + + + + L + E+ +++ IMV NIE+
Sbjct: 98 EQHGKKVPTVSRPYSFI-EFDTFIQKTKKLYIDSRARRNLGSINTELQDVQRIMVANIEE 156
Query: 148 ILERGDRIELLVDKTATMQDGAFHFRKQSKRL 179
+L+RG+ + L K + + +R+ +K L
Sbjct: 157 VLQRGEALSALDSKANNLSSLSKKYRQDAKYL 188
>pdb|2NPS|A Chain A, Crystal Structure Of The Early Endosomal Snare Complex
Length = 74
Score = 60.5 bits (145), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 44/68 (64%)
Query: 119 SSNPSADTLNRVRGEVSEIRTIMVENIEKILERGDRIELLVDKTATMQDGAFHFRKQSKR 178
S P D + V+ +V E+ +M ENI K++ERG+R++ L DK+ ++ D A F +SK+
Sbjct: 2 SMGPRNDKIKHVQNQVDEVIDVMQENITKVIERGERLDELQDKSESLSDNATAFSNRSKQ 61
Query: 179 LRRALWMK 186
LRR +W +
Sbjct: 62 LRRQMWWR 69
>pdb|3KYQ|A Chain A, Lipid-Induced Conformational Switch Controls Fusion
Activity Of Longin Domain Snare Ykt6
Length = 199
Score = 58.5 bits (140), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 39/148 (26%), Positives = 72/148 (48%), Gaps = 23/148 (15%)
Query: 42 SRVCFSQDRYIFHI-LRSDGLTFLCMANDTFGRRIPFSYLEDIQMRFMKNYGRV------ 94
SR + Y+ H+ +RSD L + +A+ + R+ F+ LE + F K R+
Sbjct: 56 SRASVKEQEYLCHVYVRSDSLAGVVIADSEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGS 115
Query: 95 ---AHYAPAYAMNDEFSRVLHQQMEFFSSNP-SADTLNRVRGEVSEIRTIMVENIEKILE 150
HY A++ SR NP AD +++V+ E+ E + I+ +E +LE
Sbjct: 116 PATIHYT---ALDGHLSRY---------QNPREADPMSKVQAELDETKIILHNTMESLLE 163
Query: 151 RGDRIELLVDKTATMQDGAFHFRKQSKR 178
RG++++ LV K+ + + F K +++
Sbjct: 164 RGEKLDDLVSKSEVLGTQSKAFYKTARK 191
>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 = 55.1 bits (131), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 30/122 (24%), Positives = 62/122 (50%), Gaps = 2/122 (1%)
Query: 29 ARRIIEKLPAESDSRVCFSQDRYIFHILRSDGLTFLCMANDTFGRRIPFSYLEDIQMRFM 88
A+++ KL +S +R FH + G+ +L + F +++ F+YLED+ F
Sbjct: 37 AKQLFRKLNEQSPTRCTLEAGAMTFHYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFD 96
Query: 89 KNYG-RVAHYAPAYAMNDEFSRVLHQQMEFFSSNPSADTLNRVRGEVSEIRTIMVENIEK 147
+ +G +V + Y+ EF + + + + + + L + E+ +++ IMV NIE+
Sbjct: 97 EQHGKKVPTVSRPYSFI-EFDTFIQKTKKLYIDSRARRNLGSINTELQDVQRIMVANIEE 155
Query: 148 IL 149
+L
Sbjct: 156 VL 157
>pdb|1L4A|A Chain A, X-Ray Structure Of The Neuronal ComplexinSNARE COMPLEX
From The Squid Loligo Pealei
Length = 80
Score = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 35/61 (57%)
Query: 127 LNRVRGEVSEIRTIMVENIEKILERGDRIELLVDKTATMQDGAFHFRKQSKRLRRALWMK 186
L + + +V E+ IM N++K+LER +I L D+ +Q GA F + +L+R W K
Sbjct: 17 LQQTQAQVEEVVDIMRVNVDKVLERDSKISELDDRADALQAGASQFEASAGKLKRKFWWK 76
Query: 187 N 187
N
Sbjct: 77 N 77
>pdb|2KOG|A Chain A, Lipid-Bound Synaptobrevin Solution Nmr Structure
Length = 119
Score = 47.0 bits (110), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 35/61 (57%)
Query: 127 LNRVRGEVSEIRTIMVENIEKILERGDRIELLVDKTATMQDGAFHFRKQSKRLRRALWMK 186
L + + +V E+ IM N++K+LER ++ L D+ +Q GA F + +L+R W K
Sbjct: 35 LQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWWK 94
Query: 187 N 187
N
Sbjct: 95 N 95
>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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 35/61 (57%)
Query: 127 LNRVRGEVSEIRTIMVENIEKILERGDRIELLVDKTATMQDGAFHFRKQSKRLRRALWMK 186
L + + +V E+ IM N++K+LER ++ L D+ +Q GA F + +L+R W K
Sbjct: 7 LQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWWK 66
Query: 187 N 187
N
Sbjct: 67 N 67
>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 = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 35/61 (57%)
Query: 127 LNRVRGEVSEIRTIMVENIEKILERGDRIELLVDKTATMQDGAFHFRKQSKRLRRALWMK 186
L + + +V E+ IM N++K+LER ++ L D+ +Q GA F + +L+R W K
Sbjct: 32 LQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWWK 91
Query: 187 N 187
N
Sbjct: 92 N 92
>pdb|1KIL|A Chain A, Three-Dimensional Structure Of The ComplexinSNARE COMPLEX
Length = 66
Score = 46.2 bits (108), Expect = 1e-05, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 35/61 (57%)
Query: 127 LNRVRGEVSEIRTIMVENIEKILERGDRIELLVDKTATMQDGAFHFRKQSKRLRRALWMK 186
L + + +V E+ IM N++K+LER ++ L D+ +Q GA F + +L+R W K
Sbjct: 6 LQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWWK 65
Query: 187 N 187
N
Sbjct: 66 N 66
>pdb|1IFQ|A Chain A, Sec22b N-Terminal Domain
pdb|1IFQ|B Chain B, Sec22b N-Terminal Domain
Length = 138
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 34/65 (52%)
Query: 29 ARRIIEKLPAESDSRVCFSQDRYIFHILRSDGLTFLCMANDTFGRRIPFSYLEDIQMRFM 88
A+++ KL +S +R FH + G+ +L + F +++ F+YLED+ F
Sbjct: 48 AKQLFRKLNEQSPTRCTLEAGAXTFHYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFD 107
Query: 89 KNYGR 93
+ +G+
Sbjct: 108 EQHGK 112
>pdb|1N7S|A Chain A, High Resolution Structure Of A Truncated Neuronal Snare
Complex
Length = 63
Score = 42.4 bits (98), Expect = 2e-04, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 33/58 (56%)
Query: 127 LNRVRGEVSEIRTIMVENIEKILERGDRIELLVDKTATMQDGAFHFRKQSKRLRRALW 184
L + + +V E+ IM N++K+LER ++ L D+ +Q GA F + +L+R W
Sbjct: 6 LQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYW 63
>pdb|1GL2|A Chain A, Crystal Structure Of An Endosomal Snare Core Complex
Length = 65
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 37/57 (64%)
Query: 125 DTLNRVRGEVSEIRTIMVENIEKILERGDRIELLVDKTATMQDGAFHFRKQSKRLRR 181
D + ++ EV ++ IM +N+E+IL RG+ ++ L +KT ++ + HF+ S+++ R
Sbjct: 9 DRVRNLQSEVEGVKNIMTQNVERILARGENLDHLRNKTEDLEATSEHFKTTSQKVAR 65
>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 = 4e-04, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 34/55 (61%)
Query: 130 VRGEVSEIRTIMVENIEKILERGDRIELLVDKTATMQDGAFHFRKQSKRLRRALW 184
++ E+ + IM +NI K+ ERG+R+ + DK + A F++ + R+R+A+W
Sbjct: 7 LQAEIDDTVGIMRDNINKVAERGERLTSIEDKADNLAVSAQGFKRGANRVRKAMW 61
>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 = 30.4 bits (67), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 23/37 (62%)
Query: 119 SSNPSADTLNRVRGEVSEIRTIMVENIEKILERGDRI 155
S + D + ++ EV ++ IM +N+E+IL RG+ +
Sbjct: 274 SGSGHMDRVRNLQSEVEGVKNIMTQNVERILARGENL 310
>pdb|2FYT|A Chain A, Human Hmt1 Hnrnp Methyltransferase-Like 3 (S. Cerevisiae)
Protein
pdb|3SMQ|A Chain A, Crystal Structure Of Protein Arginine Methyltransferase 3
pdb|4HSG|A Chain A, Crystal Structure Of Human Prmt3 In Complex With An
Allosteric Inhibitor (Prmt3- Ktd)
Length = 340
Score = 28.1 bits (61), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 108 SRVLHQQMEFFSSNPSADTLNRVRGEVSEIRTIMVENIEKIL 149
S +L+Q M+ N DT+ ++G++ E+ + VE ++ I+
Sbjct: 96 SEILYQAMDIIRLNKLEDTITLIKGKIEEVH-LPVEKVDVII 136
>pdb|1F3L|A Chain A, Crystal Structure Of The Conserved Core Of Protein
Arginine Methyltransferase Prmt3
Length = 321
Score = 27.3 bits (59), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 108 SRVLHQQMEFFSSNPSADTLNRVRGEVSEIRTIMVENIEKIL 149
S +L+Q M+ N DT+ ++G++ E+ ++ VE ++ I+
Sbjct: 77 SEILYQAMDIIRLNKLEDTIVLIKGKIEEV-SLPVEKVDVII 117
>pdb|4AYW|A Chain A, Structure Of The Human Mitochondrial Abc Transporter,
Abcb10 (plate Form)
Length = 619
Score = 27.3 bits (59), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 107 FSRVLHQQMEFFSSNPSADTLNRVRGEVSEIRTIMVENIEKILERG 152
FS +L Q++ FF + + +NR+ + + + + EN+ L G
Sbjct: 133 FSSILRQEVAFFDKTRTGELINRLSSDTALLGRSVTENLSDGLRAG 178
>pdb|4AYT|A Chain A, Structure Of The Human Mitochondrial Abc Transporter,
Abcb10
pdb|4AYX|A Chain A, Structure Of The Human Mitochondrial Abc Transporter,
Abcb10 (Rod Form B)
pdb|3ZDQ|A Chain A, Structure Of The Human Mitochondrial Abc Transporter,
Abcb10 (nucleotide-free Form)
Length = 595
Score = 26.9 bits (58), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 107 FSRVLHQQMEFFSSNPSADTLNRVRGEVSEIRTIMVENIEKILERG 152
FS +L Q++ FF + + +NR+ + + + + EN+ L G
Sbjct: 102 FSSILRQEVAFFDKTRTGELINRLSSDTALLGRSVTENLSDGLRAG 147
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
0.326 0.136 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,054,335
Number of Sequences: 62578
Number of extensions: 184296
Number of successful extensions: 647
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 620
Number of HSP's gapped (non-prelim): 23
length of query: 220
length of database: 14,973,337
effective HSP length: 95
effective length of query: 125
effective length of database: 9,028,427
effective search space: 1128553375
effective search space used: 1128553375
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 bits)