RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy130
(199 letters)
>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 = 204 bits (520), Expect = 2e-67
Identities = 125/198 (63%), Positives = 160/198 (80%)
Query: 1 MVKLFALNILYKAPTSAVMLKSSYDLQSFSFFQRGSVQEFMTFVSKTMVERSQTASRQSI 60
++KL++L++ YK AV+LK++YD+ SFSFFQR SVQEFMTF S+ +VERS SR S+
Sbjct: 1 LMKLYSLSVFYKGEPKAVLLKAAYDVSSFSFFQRSSVQEFMTFTSQLIVERSAKGSRASV 60
Query: 61 KEGEYMCHVFVRGDNLAGILVSDQEYPHRVAHTLITNVLNEFSKAVPPSSWPTGTEASIS 120
KE EY+CHV+VR D+LAG++++D EYP RVA TL+ VL+EFSK V WP G+ A+I
Sbjct: 61 KEQEYLCHVYVRSDSLAGVVIADSEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGSPATIH 120
Query: 121 FPQLPQYLARYQNPREADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSM 180
+ L +L+RYQNPREAD M+K+Q ELDETKIILHNT+E++L+RGEKLDDLVSKSE L
Sbjct: 121 YTALDGHLSRYQNPREADPMSKVQAELDETKIILHNTMESLLERGEKLDDLVSKSEVLGT 180
Query: 181 QSKAFYKTARKTNSCCSL 198
QSKAFYKTARK NSCC++
Sbjct: 181 QSKAFYKTARKQNSCCAI 198
>3bw6_A Synaptobrevin homolog YKT6; YKT6P, farnesylation, vacuole fusion,
snare, coiled coil, lipoprotein, membrane,
phosphoprotein; 2.50A {Saccharomyces cerevisiae} PDB:
1h8m_A 1iou_A
Length = 144
Score = 186 bits (473), Expect = 4e-61
Identities = 52/140 (37%), Positives = 86/140 (61%), Gaps = 2/140 (1%)
Query: 2 VKLFALNILYKAPTSAVMLKSSYDLQSFSFFQRGSVQEFMTFVSKTMVERSQTASRQSIK 61
++++ + + A+ L DL F FF+R SV +FMTF ++T+ R+ RQSI+
Sbjct: 5 MRIYYIGVFRSGGEKALELSEVKDLSQFGFFERSSVGQFMTFFAETVASRTGAGQRQSIE 64
Query: 62 EGEYMCHVFVRGDNLAGILVSDQEYPHRVAHTLITNVLNEFSKAVPPSSWPTGTEA--SI 119
EG Y+ HV+ R + + G+L++D+EYP R A+TL+ +L+E+ A P W TE ++
Sbjct: 65 EGNYIGHVYARSEGICGVLITDKEYPVRPAYTLLNKILDEYLVAHPKEEWADVTETNDAL 124
Query: 120 SFPQLPQYLARYQNPREADA 139
QL Y+++YQ+P +ADA
Sbjct: 125 KMKQLDTYISKYQDPSQADA 144
>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 = 125 bits (314), Expect = 2e-36
Identities = 34/184 (18%), Positives = 72/184 (39%), Gaps = 5/184 (2%)
Query: 15 TSAVMLKSSYDLQSFSFFQRGSVQEFMTFVSKTMVERSQTASRQSIKEGEYMCHVFVRGD 74
+ L +S +Q++ + + + ++ + + E M ++
Sbjct: 12 ADGLPLAASMQ---EDEQSGRDLQQYQSQAKQLFRKLNEQSPTRCTLEAGAMTFHYIIEQ 68
Query: 75 NLAGILVSDQEYPHRVAHTLITNVLNEFSKAVPPSSWPTGTEASIS--FPQLPQYLARYQ 132
+ +++ + +P ++A + ++ +EF + S + + Y
Sbjct: 69 GVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDTFIQKTKKLYI 128
Query: 133 NPREADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARKT 192
+ R + I EL + + I+ IE VLQRGE L L SK+ LS SK + + A+
Sbjct: 129 DSRARRNLGSINTELQDVQRIMVANIEEVLQRGEALSALDSKANNLSSLSKKYRQDAKYL 188
Query: 193 NSCC 196
N
Sbjct: 189 NMRS 192
>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 = 79.4 bits (196), Expect = 3e-20
Identities = 15/55 (27%), Positives = 32/55 (58%)
Query: 137 ADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARK 191
++Q E+D+T I+ + I V +RGE+L + K++ L++ ++ F + A +
Sbjct: 1 GSRTAELQAEIDDTVGIMRDNINKVAERGERLTSIEDKADNLAVSAQGFKRGANR 55
>1gl2_A Endobrevin; membrane protein, membrane fusion protein complex,
coiled coil, transmembrane; 1.9A {Rattus norvegicus}
SCOP: h.1.15.1
Length = 65
Score = 78.7 bits (194), Expect = 5e-20
Identities = 20/62 (32%), Positives = 32/62 (51%)
Query: 132 QNPREADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARK 191
D + +Q E++ K I+ +E +L RGE LD L +K+E L S+ F T++K
Sbjct: 3 HMSAGNDRVRNLQSEVEGVKNIMTQNVERILARGENLDHLRNKTEDLEATSEHFKTTSQK 62
Query: 192 TN 193
Sbjct: 63 VA 64
>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 = 77.1 bits (190), Expect = 2e-19
Identities = 14/56 (25%), Positives = 29/56 (51%)
Query: 136 EADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARK 191
+ + Q ++DE I+ ++ VL+R +KL +L +++ L + F +A K
Sbjct: 2 SNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAK 57
>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 = 76.1 bits (187), Expect = 8e-19
Identities = 19/61 (31%), Positives = 33/61 (54%)
Query: 133 NPREADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARKT 192
D + +Q ++DE ++ I V++RGE+LD+L KSE LS + AF +++
Sbjct: 3 MGPRNDKIKHVQNQVDEVIDVMQENITKVIERGERLDELQDKSESLSDNATAFSNRSKQL 62
Query: 193 N 193
Sbjct: 63 R 63
>1l4a_A Synaptobrevin; snare, snare complex, membrane fusion,
neurotransmission, endocytosis/exocytosis complex; 2.95A
{Loligo pealei} SCOP: h.1.15.1
Length = 80
Score = 75.0 bits (184), Expect = 2e-18
Identities = 13/60 (21%), Positives = 32/60 (53%)
Query: 132 QNPREADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARK 191
Q +++ + + Q +++E I+ ++ VL+R K+ +L +++ L + F +A K
Sbjct: 9 QPVQQSKRLQQTQAQVEEVVDIMRVNVDKVLERDSKISELDDRADALQAGASQFEASAGK 68
>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 = 70.1 bits (171), Expect = 2e-16
Identities = 16/66 (24%), Positives = 31/66 (46%)
Query: 129 ARYQNPREADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKT 188
A N + + Q ++DE I+ ++ VL+R +KL +L +++ L + F +
Sbjct: 21 APPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETS 80
Query: 189 ARKTNS 194
A K
Sbjct: 81 AAKLKR 86
>2kog_A Vesicle-associated membrane protein 2; synaptobrevin, VAMP2, DPC
micelle, snare, coiled coil, membrane fusion,
transmembrane; NMR {Rattus norvegicus}
Length = 119
Score = 68.6 bits (167), Expect = 1e-15
Identities = 16/65 (24%), Positives = 31/65 (47%)
Query: 129 ARYQNPREADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKT 188
A N + + Q ++DE I+ ++ VL+R +KL +L +++ L + F +
Sbjct: 24 APPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETS 83
Query: 189 ARKTN 193
A K
Sbjct: 84 AAKLK 88
>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 = 68.0 bits (166), Expect = 1e-15
Identities = 14/60 (23%), Positives = 29/60 (48%)
Query: 135 READAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARKTNS 194
+ + Q ++DE I+ ++ VL+R +KL +L +++ L + F +A K
Sbjct: 2 SHMRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKR 61
>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 = 41.2 bits (96), Expect = 1e-04
Identities = 31/185 (16%), Positives = 59/185 (31%), Gaps = 62/185 (33%)
Query: 36 SVQE----FMTFVSKTMVERSQTASRQSI-----KEGEYMCHVFVRGDN---LAGILVSD 83
+ E F+ +VS ++VE S+ + E E + ++ G++ LA L+ +
Sbjct: 56 TPAELVGKFLGYVS-SLVEPSKVGQFDQVLNLCLTEFE---NCYLEGNDIHALAAKLLQE 111
Query: 84 QEYPHRVAHTLITN------VLNEFSKAVPPSSW----PTGTEASISFPQLP-Q-----Y 127
+ LI N + S+ G A + Q Y
Sbjct: 112 NDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEG-NAQL-VAIFGGQGNTDDY 169
Query: 128 LARYQNPREADAMTKIQEELDETKIILHNT----IEAVLQR-GEKLDDLVSKSEGLSMQS 182
EEL + L+ T + +++ E L +L+ +
Sbjct: 170 F----------------EELRD----LYQTYHVLVGDLIKFSAETLSELIRTTLD---AE 206
Query: 183 KAFYK 187
K F +
Sbjct: 207 KVFTQ 211
Score = 38.5 bits (89), Expect = 0.001
Identities = 32/195 (16%), Positives = 58/195 (29%), Gaps = 77/195 (39%)
Query: 16 SAVMLKSSYDLQSF----------SFFQ--RGSVQEFMTFVSKTMVERSQTASRQSIKEG 63
+AV + + +SF FF R E + + ++ + S++
Sbjct: 279 TAVAIAETDSWESFFVSVRKAITVLFFIGVRC--YE--AYPNTSL---PPSILEDSLENN 331
Query: 64 E----YMCHVFVRGDNLAGILVSDQEYPHRVAHTL-------ITNVLNEFSKAV---PPS 109
E M + + + Q+Y ++ L I+ V N V PP
Sbjct: 332 EGVPSPM--LSISNLTQEQV----QDYVNKTNSHLPAGKQVEISLV-NGAKNLVVSGPPQ 384
Query: 110 S------------WPTGTEAS-ISFPQ---------LP-------QYLARYQNPREADAM 140
S P+G + S I F + LP L A
Sbjct: 385 SLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLV--------PAS 436
Query: 141 TKIQEELDETKIILH 155
I ++L + + +
Sbjct: 437 DLINKDLVKNNVSFN 451
Score = 36.2 bits (83), Expect = 0.006
Identities = 23/133 (17%), Positives = 44/133 (33%), Gaps = 38/133 (28%)
Query: 91 AHTLITNVLN----EFSKAVPPSSWPTGTEASISFPQ-LPQ------------------- 126
A++ L+ E VP +S+ ++ F + LP+
Sbjct: 3 AYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVG 62
Query: 127 ----YLARYQNPREADAMTKI-QEELD--ETKIILHNTIEAVLQRGEKLDD--LVSKSEG 177
Y++ P + ++ L E + N I A+ + + +D LV E
Sbjct: 63 KFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKEL 122
Query: 178 LSMQSKAFYKTAR 190
+ K + AR
Sbjct: 123 I----KNYIT-AR 130
Score = 27.7 bits (61), Expect = 3.1
Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 12/41 (29%)
Query: 137 ADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEG 177
AD M+ + + +E V RG + V + E
Sbjct: 1774 ADVMS------------IESLVEVVFYRGMTMQVAVPRDEL 1802
Score = 27.7 bits (61), Expect = 3.2
Identities = 12/83 (14%), Positives = 27/83 (32%), Gaps = 17/83 (20%)
Query: 131 YQNP-------READAMTKIQEELDETKIILHNTIEAVL----QRGEKLDDLVSK----- 174
Y+ AD K I+++N + + ++G+++ + S
Sbjct: 1636 YKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFET 1695
Query: 175 -SEGLSMQSKAFYKTARKTNSCC 196
+G K F + + S
Sbjct: 1696 IVDGKLKTEKIFKEINEHSTSYT 1718
>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 = 32.0 bits (72), Expect = 0.016
Identities = 11/38 (28%), Positives = 20/38 (52%)
Query: 154 LHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARK 191
L A+ +RG+KL DL ++ + + +F K A +
Sbjct: 20 LARARLALDERGQKLSDLEERTAAMMSSADSFSKHAHE 57
>2wam_A RV2714, conserved hypothetical alanine and leucine rich protein;
unknown function; 2.60A {Mycobacterium tuberculosis}
Length = 351
Score = 29.0 bits (64), Expect = 1.1
Identities = 13/52 (25%), Positives = 22/52 (42%)
Query: 125 PQYLARYQNPREADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSE 176
P YL + P A A+ + + ++ L EA + K+D+ V S
Sbjct: 242 PHYLTQTDYPAAAQALLEQVAKTGSLQLPLAVLAEAAAEVQAKIDEQVQASA 293
>3mnf_A PAC2 family protein; PSI2, MCSG, structural genomics, protein
structure initiativ midwest center for structural
genomics; 2.97A {Streptomyces avermitilis}
Length = 250
Score = 27.4 bits (60), Expect = 2.8
Identities = 12/52 (23%), Positives = 23/52 (44%)
Query: 125 PQYLARYQNPREADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSE 176
P Y+++ NP+ A+ E+L + +I L E +D L ++
Sbjct: 183 PHYVSQPPNPKATLALLNRLEDLIDVRIPLGELPEDARAWQVGVDQLAAEDS 234
>2p90_A Hypothetical protein CGL1923; structural genomics, PSI-2, MCSG
structure initiative; 2.35A {Corynebacterium glutamicum
atcc 13032} SCOP: c.56.8.1
Length = 319
Score = 26.7 bits (58), Expect = 5.1
Identities = 6/54 (11%), Positives = 18/54 (33%)
Query: 123 QLPQYLARYQNPREADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSE 176
+P Y++ P + + + + + L + +L + +S
Sbjct: 200 HVPHYVSASPYPAATLKLLQSIADSADLNLPLLALERDAEKVHRQLMEQTEESS 253
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
0.317 0.129 0.362
Gapped
Lambda K H
0.267 0.0506 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,733,432
Number of extensions: 149395
Number of successful extensions: 348
Number of sequences better than 10.0: 1
Number of HSP's gapped: 345
Number of HSP's successfully gapped: 21
Length of query: 199
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 110
Effective length of database: 4,216,824
Effective search space: 463850640
Effective search space used: 463850640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.5 bits)