RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5723
(162 letters)
>1n7s_A Vesicle-associated membrane protein 2; neuronal snare protein
complex, four helix bundle, transport protein; 1.45A
{Rattus norvegicus} SCOP: h.1.15.1 PDB: 1kil_A 3rk2_A
3rk3_A 3rl0_A 3fii_B 3g94_B
Length = 63
Score = 59.4 bits (144), Expect = 6e-13
Identities = 38/49 (77%), Positives = 44/49 (89%)
Query: 92 SKLSESQKQVDEVVGIMRVNVEKVLERDQKLSELDNRANALQQGASQFE 140
+L ++Q QVDEVV IMRVNV+KVLERDQKLSELD+RA+ALQ GASQFE
Sbjct: 4 RRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFE 52
Score = 56.3 bits (136), Expect = 1e-11
Identities = 36/55 (65%), Positives = 42/55 (76%)
Query: 27 AAQKRLQQTQAQVDEVVDIMKTNVEKVLERDQKLSELDDRAGNLGKMDGGFAGNS 81
+ +RLQQTQAQVDEVVDIM+ NV+KVLERDQKLSELDDRA L F ++
Sbjct: 1 GSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSA 55
>2kog_A Vesicle-associated membrane protein 2; synaptobrevin, VAMP2, DPC
micelle, snare, coiled coil, membrane fusion,
transmembrane; NMR {Rattus norvegicus}
Length = 119
Score = 60.5 bits (146), Expect = 7e-13
Identities = 41/71 (57%), Positives = 48/71 (67%)
Query: 11 AGDDGIVGGPRTPQQIAAQKRLQQTQAQVDEVVDIMKTNVEKVLERDQKLSELDDRAGNL 70
A G G P P + + +RLQQTQAQVDEVVDIM+ NV+KVLERDQKLSELDDRA L
Sbjct: 14 AAPAGEGGPPAPPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADAL 73
Query: 71 GKMDGGFAGNS 81
F ++
Sbjct: 74 QAGASQFETSA 84
Score = 56.3 bits (135), Expect = 3e-11
Identities = 39/62 (62%), Positives = 45/62 (72%)
Query: 79 GNSSGRQQKSDPKSKLSESQKQVDEVVGIMRVNVEKVLERDQKLSELDNRANALQQGASQ 138
G +L ++Q QVDEVV IMRVNV+KVLERDQKLSELD+RA+ALQ GASQ
Sbjct: 20 GGPPAPPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQ 79
Query: 139 FE 140
FE
Sbjct: 80 FE 81
>3b5n_A Synaptobrevin homolog 1; snare complex, syntaxin, synaptobrevin,
SNAP-25, SSO1P, SNC1P, SEC9P, SSO1, SNC1, coiled coil;
1.60A {Saccharomyces cerevisiae} SCOP: h.1.15.1
Length = 61
Score = 59.0 bits (143), Expect = 9e-13
Identities = 19/49 (38%), Positives = 34/49 (69%)
Query: 92 SKLSESQKQVDEVVGIMRVNVEKVLERDQKLSELDNRANALQQGASQFE 140
S+ +E Q ++D+ VGIMR N+ KV ER ++L+ ++++A+ L A F+
Sbjct: 2 SRTAELQAEIDDTVGIMRDNINKVAERGERLTSIEDKADNLAVSAQGFK 50
Score = 52.8 bits (127), Expect = 2e-10
Identities = 19/47 (40%), Positives = 31/47 (65%)
Query: 31 RLQQTQAQVDEVVDIMKTNVEKVLERDQKLSELDDRAGNLGKMDGGF 77
R + QA++D+ V IM+ N+ KV ER ++L+ ++D+A NL GF
Sbjct: 3 RTAELQAEIDDTVGIMRDNINKVAERGERLTSIEDKADNLAVSAQGF 49
>3hd7_A Vesicle-associated membrane protein 2; membrane protein,
coiled-coil, 4-helical bundle, cell juncti cytoplasmic
vesicle, membrane, phosphoprotein; HET: GGG; 3.40A
{Rattus norvegicus} PDB: 3hd9_A 3ipd_A
Length = 91
Score = 59.2 bits (143), Expect = 1e-12
Identities = 38/51 (74%), Positives = 44/51 (86%)
Query: 90 PKSKLSESQKQVDEVVGIMRVNVEKVLERDQKLSELDNRANALQQGASQFE 140
+L ++Q QVDEVV IMRVNV+KVLERDQKLSELD+RA+ALQ GASQFE
Sbjct: 3 HMRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFE 53
Score = 58.8 bits (142), Expect = 2e-12
Identities = 36/55 (65%), Positives = 42/55 (76%)
Query: 27 AAQKRLQQTQAQVDEVVDIMKTNVEKVLERDQKLSELDDRAGNLGKMDGGFAGNS 81
+ +RLQQTQAQVDEVVDIM+ NV+KVLERDQKLSELDDRA L F ++
Sbjct: 2 SHMRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSA 56
>1l4a_A Synaptobrevin; snare, snare complex, membrane fusion,
neurotransmission, endocytosis/exocytosis complex; 2.95A
{Loligo pealei} SCOP: h.1.15.1
Length = 80
Score = 58.8 bits (142), Expect = 2e-12
Identities = 38/62 (61%), Positives = 46/62 (74%)
Query: 79 GNSSGRQQKSDPKSKLSESQKQVDEVVGIMRVNVEKVLERDQKLSELDNRANALQQGASQ 138
G G Q +L ++Q QV+EVV IMRVNV+KVLERD K+SELD+RA+ALQ GASQ
Sbjct: 2 GPPQGPPQPVQQSKRLQQTQAQVEEVVDIMRVNVDKVLERDSKISELDDRADALQAGASQ 61
Query: 139 FE 140
FE
Sbjct: 62 FE 63
Score = 54.2 bits (130), Expect = 9e-11
Identities = 36/55 (65%), Positives = 41/55 (74%)
Query: 23 PQQIAAQKRLQQTQAQVDEVVDIMKTNVEKVLERDQKLSELDDRAGNLGKMDGGF 77
PQ + KRLQQTQAQV+EVVDIM+ NV+KVLERD K+SELDDRA L F
Sbjct: 8 PQPVQQSKRLQQTQAQVEEVVDIMRVNVDKVLERDSKISELDDRADALQAGASQF 62
>1sfc_A VAMP 2, protein (synaptobrevin 2); membrane fusion protein
complex, transport protein; 2.40A {Rattus norvegicus}
SCOP: h.1.15.1
Length = 96
Score = 57.4 bits (138), Expect = 9e-12
Identities = 41/71 (57%), Positives = 48/71 (67%)
Query: 11 AGDDGIVGGPRTPQQIAAQKRLQQTQAQVDEVVDIMKTNVEKVLERDQKLSELDDRAGNL 70
A G G P P + + +RLQQTQAQVDEVVDIM+ NV+KVLERDQKLSELDDRA L
Sbjct: 11 AAPAGEGGPPAPPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADAL 70
Query: 71 GKMDGGFAGNS 81
F ++
Sbjct: 71 QAGASQFETSA 81
Score = 55.1 bits (132), Expect = 6e-11
Identities = 39/62 (62%), Positives = 45/62 (72%)
Query: 79 GNSSGRQQKSDPKSKLSESQKQVDEVVGIMRVNVEKVLERDQKLSELDNRANALQQGASQ 138
G +L ++Q QVDEVV IMRVNV+KVLERDQKLSELD+RA+ALQ GASQ
Sbjct: 17 GGPPAPPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQ 76
Query: 139 FE 140
FE
Sbjct: 77 FE 78
>2nps_A VAMP-4, vesicle-associated membrane protein 4; vesicle fusion,
snare complex, early endosomal snare complex, VTI1A,
VAMP4, transport protein; 2.50A {Mus musculus}
Length = 74
Score = 54.5 bits (131), Expect = 6e-11
Identities = 19/48 (39%), Positives = 32/48 (66%)
Query: 93 KLSESQKQVDEVVGIMRVNVEKVLERDQKLSELDNRANALQQGASQFE 140
K+ Q QVDEV+ +M+ N+ KV+ER ++L EL +++ +L A+ F
Sbjct: 9 KIKHVQNQVDEVIDVMQENITKVIERGERLDELQDKSESLSDNATAFS 56
Score = 49.5 bits (118), Expect = 4e-09
Identities = 18/44 (40%), Positives = 31/44 (70%)
Query: 27 AAQKRLQQTQAQVDEVVDIMKTNVEKVLERDQKLSELDDRAGNL 70
+++ Q QVDEV+D+M+ N+ KV+ER ++L EL D++ +L
Sbjct: 5 PRNDKIKHVQNQVDEVIDVMQENITKVIERGERLDELQDKSESL 48
>1gl2_A Endobrevin; membrane protein, membrane fusion protein complex,
coiled coil, transmembrane; 1.9A {Rattus norvegicus}
SCOP: h.1.15.1
Length = 65
Score = 54.0 bits (130), Expect = 8e-11
Identities = 16/53 (30%), Positives = 27/53 (50%)
Query: 88 SDPKSKLSESQKQVDEVVGIMRVNVEKVLERDQKLSELDNRANALQQGASQFE 140
S ++ Q +V+ V IM NVE++L R + L L N+ L+ + F+
Sbjct: 5 SAGNDRVRNLQSEVEGVKNIMTQNVERILARGENLDHLRNKTEDLEATSEHFK 57
Score = 52.1 bits (125), Expect = 3e-10
Identities = 15/48 (31%), Positives = 27/48 (56%)
Query: 23 PQQIAAQKRLQQTQAQVDEVVDIMKTNVEKVLERDQKLSELDDRAGNL 70
A R++ Q++V+ V +IM NVE++L R + L L ++ +L
Sbjct: 2 SHMSAGNDRVRNLQSEVEGVKNIMTQNVERILARGENLDHLRNKTEDL 49
>3fie_C Fragment of vesicle-associated membrane protein 2; BONT F, VAMP,
inhibitor, complex structure, acetylation, cell
junction, hydrolase; 2.10A {Clostridium botulinum}
Length = 38
Score = 52.5 bits (125), Expect = 2e-10
Identities = 25/35 (71%), Positives = 30/35 (85%)
Query: 23 PQQIAAQKRLQQTQAQVDEVVDIMKTNVEKVLERD 57
P + + +RLQQTQAQVDEVVDIM+ NV+KVLERD
Sbjct: 2 PPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERD 36
Score = 41.3 bits (96), Expect = 3e-06
Identities = 20/34 (58%), Positives = 24/34 (70%)
Query: 86 QKSDPKSKLSESQKQVDEVVGIMRVNVEKVLERD 119
+L ++Q QVDEVV IMRVNV+KVLERD
Sbjct: 3 PNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERD 36
>3kyq_A YKT6, synaptobrevin homolog YKT6; V-snare homolog, lipid binding,
cytoplasmic vesicle, ER-GOLG transport, golgi apparatus,
lipoprotein; HET: DPV; 2.44A {Rattus norvegicus}
Length = 199
Score = 51.0 bits (121), Expect = 1e-08
Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 1/91 (1%)
Query: 51 EKVLER-DQKLSELDDRAGNLGKMDGGFAGNSSGRQQKSDPKSKLSESQKQVDEVVGIMR 109
EKVL+ +++ +D G+ + R Q +S+ Q ++DE I+
Sbjct: 96 EKVLDEFSKQVDRIDWPVGSPATIHYTALDGHLSRYQNPREADPMSKVQAELDETKIILH 155
Query: 110 VNVEKVLERDQKLSELDNRANALQQGASQFE 140
+E +LER +KL +L +++ L + F
Sbjct: 156 NTMESLLERGEKLDDLVSKSEVLGTQSKAFY 186
Score = 45.2 bits (106), Expect = 1e-06
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 28 AQKRLQQTQAQVDEVVDIMKTNVEKVLERDQKLSELDDRAGNLGKMDGGFAGNSSGRQQK 87
+ + QA++DE I+ +E +LER +KL +L ++ LG F + R+Q
Sbjct: 136 EADPMSKVQAELDETKIILHNTMESLLERGEKLDDLVSKSEVLGTQSKAFYKTA--RKQN 193
Query: 88 S 88
S
Sbjct: 194 S 194
>2nut_C Vesicle-trafficking protein SEC22B; human copii SEC23/24 complexed
with SEC22, protein transport; 2.30A {Homo sapiens} PDB:
2nup_C 3egd_C 3egx_C 1ifq_A
Length = 196
Score = 46.4 bits (109), Expect = 5e-07
Identities = 17/57 (29%), Positives = 30/57 (52%)
Query: 84 RQQKSDPKSKLSESQKQVDEVVGIMRVNVEKVLERDQKLSELDNRANALQQGASQFE 140
S + L ++ +V IM N+E+VL+R + LS LD++AN L + ++
Sbjct: 126 LYIDSRARRNLGSINTELQDVQRIMVANIEEVLQRGEALSALDSKANNLSSLSKKYR 182
Score = 39.9 bits (92), Expect = 1e-04
Identities = 17/58 (29%), Positives = 31/58 (53%)
Query: 24 QQIAAQKRLQQTQAQVDEVVDIMKTNVEKVLERDQKLSELDDRAGNLGKMDGGFAGNS 81
A++ L ++ +V IM N+E+VL+R + LS LD +A NL + + ++
Sbjct: 128 IDSRARRNLGSINTELQDVQRIMVANIEEVLQRGEALSALDSKANNLSSLSKKYRQDA 185
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 34.1 bits (77), Expect = 0.015
Identities = 19/122 (15%), Positives = 45/122 (36%), Gaps = 16/122 (13%)
Query: 35 TQAQVDEVVDIMKTNVEKV------LERDQKLSELDDRAGNLGKMDGGFAGNSSGRQQKS 88
++ ++D ++ + K V L Q+ + + +++ F S + ++
Sbjct: 47 SKEEIDHII-MSKDAVSGTLRLFWTLLSKQE-EMVQKFVEEVLRINYKFLM-SPIKTEQR 103
Query: 89 DPKSKLSESQKQVDEVVGIMRVNVEKVLERDQKLSELDNRANALQQGASQFEHVPTFHGL 148
P +Q D + +V + + R Q +L R AL + ++V G
Sbjct: 104 QPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKL--R-QALLE-LRPAKNV-LIDG- 157
Query: 149 SM 150
+
Sbjct: 158 -V 158
Score = 30.6 bits (68), Expect = 0.21
Identities = 17/127 (13%), Positives = 37/127 (29%), Gaps = 25/127 (19%)
Query: 20 PRTPQQIAAQKRLQQTQAQVDEVVDIM----KTN-VEKVLERDQKLSELDDRAGNLGKMD 74
R + ++ L + + + ++D + KT V K+ KMD
Sbjct: 132 SRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVC-LSYKV---------QCKMD 181
Query: 75 GGFAGNSSGRQQKSD----PKSKL-----SESQKQVDEVVGIMRVNVEKVLERDQKLSEL 125
+ + KL + D I ++ + + ++L +
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNI-KLRIHSIQAELRRLLKS 240
Query: 126 DNRANAL 132
N L
Sbjct: 241 KPYENCL 247
>1urq_A M-tomosyn isoform; transport protein, tomosyn-snare complex,
exocytosis, four helical bundle, coiled coil; 2.0A
{Rattus norvegicus} SCOP: h.1.15.1
Length = 63
Score = 30.8 bits (69), Expect = 0.032
Identities = 14/50 (28%), Positives = 21/50 (42%)
Query: 90 PKSKLSESQKQVDEVVGIMRVNVEKVLERDQKLSELDNRANALQQGASQF 139
+ + VVG + + ER QKLS+L+ R A+ A F
Sbjct: 2 SHGGIEGVKGAASGVVGELARARLALDERGQKLSDLEERTAAMMSSADSF 51
Score = 27.0 bits (59), Expect = 0.81
Identities = 11/47 (23%), Positives = 21/47 (44%)
Query: 32 LQQTQAQVDEVVDIMKTNVEKVLERDQKLSELDDRAGNLGKMDGGFA 78
++ + VV + + ER QKLS+L++R + F+
Sbjct: 6 IEGVKGAASGVVGELARARLALDERGQKLSDLEERTAAMMSSADSFS 52
>3al9_A Plexin-A2; beta-propeller, membrane protein, signaling protein;
HET: NAG; 2.10A {Mus musculus} PDB: 3al8_B*
Length = 539
Score = 27.7 bits (60), Expect = 2.2
Identities = 7/23 (30%), Positives = 9/23 (39%)
Query: 135 GASQFEHVPTFHGLSMSRQINHL 157
G + TFH + NHL
Sbjct: 1 GTTGMPQYSTFHSENRDWTFNHL 23
>3a8u_X Omega-amino acid--pyruvate aminotransferase; large pleated sheet,
transaminase, pyridox phosphate; HET: PLP; 1.40A
{Pseudomonas putida}
Length = 449
Score = 27.1 bits (61), Expect = 2.9
Identities = 4/21 (19%), Positives = 10/21 (47%)
Query: 35 TQAQVDEVVDIMKTNVEKVLE 55
+D + D + + K+L+
Sbjct: 429 KPQDLDRLFDAVGEVLNKLLD 449
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 27.3 bits (60), Expect = 3.0
Identities = 12/78 (15%), Positives = 24/78 (30%), Gaps = 26/78 (33%)
Query: 8 PGGAGDDGIVGGPRTPQQIAAQKRLQQTQAQVDEVVDIMKTNVEKVLERDQKLSELDDRA 67
G + G++ P ++AA +Q + VV+ + ++E
Sbjct: 1801 ELGRSNYGMIA--INPGRVAAS----FSQEALQYVVERVGKRTGWLVE-----------I 1843
Query: 68 GNLGKMDGGFAGNSSGRQ 85
N N +Q
Sbjct: 1844 VNY---------NVENQQ 1852
>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch
recognition, mismatched unpaired DNA binding protein-DNA
complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A*
2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*
Length = 934
Score = 26.5 bits (59), Expect = 5.0
Identities = 10/38 (26%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 28 AQKRLQQTQAQ-VDEVVDIMKTNVEKVLERDQKLSELD 64
+ ++ Q V E+V+I VE + + L++LD
Sbjct: 566 NKTEYEEAQDAIVKEIVNISSGYVEPMQTLNDVLAQLD 603
>3nui_A Pyruvate transaminase; amino transferase, transferase; 2.00A
{Vibrio fluvialis}
Length = 478
Score = 26.0 bits (58), Expect = 7.0
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 35 TQAQVDEVVDIMKTNVEKVLER 56
T+AQ+DE+ D ++ ++KV
Sbjct: 444 TEAQMDEMFDKLEKALDKVFAE 465
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.309 0.129 0.345
Gapped
Lambda K H
0.267 0.0599 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,263,884
Number of extensions: 125296
Number of successful extensions: 320
Number of sequences better than 10.0: 1
Number of HSP's gapped: 319
Number of HSP's successfully gapped: 49
Length of query: 162
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 76
Effective length of database: 4,300,587
Effective search space: 326844612
Effective search space used: 326844612
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (24.5 bits)