RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7110
(86 letters)
>2nps_D Syntaxin-6; vesicle fusion, snare complex, early endosomal snare
complex, VTI1A, VAMP4, transport protein; 2.50A {Homo
sapiens}
Length = 82
Score = 41.3 bits (97), Expect = 1e-06
Identities = 13/74 (17%), Positives = 32/74 (43%), Gaps = 5/74 (6%)
Query: 11 GNYYEPVPNQFDGGDAIHQENEQLTSDLRNKIQALKSLTIDIGTEVKYQNEHLLRGMDDD 70
G++ + + + + ++ + I LK+++ IG E++ Q +L +
Sbjct: 1 GSHMASMTGG----NNMGRMQDEQLELVSGSIGVLKNMSQRIGGELEEQAV-MLEDFSHE 55
Query: 71 FDRTGGFLNNSMAR 84
+ T L+N M +
Sbjct: 56 LESTQSRLDNVMKK 69
>1n7s_D SNAP-25A; neuronal snare protein complex, four helix bundle,
transport protein; 1.45A {Rattus norvegicus} SCOP:
h.1.15.1 PDB: 3rk2_D 3rk3_D 3rl0_D 1kil_D 3hd7_D*
3hd9_D 3ipd_D 1urq_D 1xtg_B
Length = 66
Score = 35.5 bits (82), Expect = 1e-04
Identities = 13/61 (21%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 24 GDAIHQENEQLTSDLRNKIQALKSLTIDIGTEVKYQNEHLLRGMDDDFDRTGGFLNNSMA 83
G A E ++ + I L+ + +D+G E+ QN + R + + D ++ +
Sbjct: 1 GSARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDR-IMEKADSNKTRIDEANQ 59
Query: 84 R 84
R
Sbjct: 60 R 60
>1sfc_D Protein (SNAP-25B), protein (synaptobrevin 2); membrane fusion
protein complex, transport protein; 2.40A {Rattus
norvegicus} SCOP: h.1.15.1
Length = 87
Score = 35.6 bits (82), Expect = 2e-04
Identities = 17/84 (20%), Positives = 35/84 (41%), Gaps = 6/84 (7%)
Query: 1 MDNRMRRQHAGNYYEPVPNQFDGGDAIHQENEQLTSDLRNKIQALKSLTIDIGTEVKYQN 60
+D R + +G + V N DA E ++ + I L+ + +D+G E+ QN
Sbjct: 2 VDEREQMAISGGFIRRVTN-----DARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQN 56
Query: 61 EHLLRGMDDDFDRTGGFLNNSMAR 84
+ + + D ++ + R
Sbjct: 57 R-QIDRIMEKADSNKTRIDEANQR 79
>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 = 36.6 bits (84), Expect = 3e-04
Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 13/75 (17%)
Query: 16 PVPNQFDGGDAIHQENEQLTSDLRNKIQALKSLTIDIGTEVKYQNEHLLRGMDDDFDRTG 75
PV + FDG D + + ++ + + + L + T +++ H+L DF G
Sbjct: 458 PVYDTFDGSD-LRVLSGSISERI---VDCIIRLPVKWETTTQFKATHIL-----DFGPGG 508
Query: 76 ----GFLNNSMARGT 86
G L + GT
Sbjct: 509 ASGLGVLTHRNKDGT 523
>1gl2_D Syntaxin 8, vesicle transport V-snare protein VTI1-like 1;
membrane protein, membrane fusion protein complex,
coiled coil, transmembrane; 1.9A {Rattus norvegicus}
SCOP: h.1.15.1
Length = 65
Score = 32.4 bits (74), Expect = 0.002
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 24 GDAIHQENEQLTSDLRNKIQALKSLTIDIGTEVKYQNEHLLRGMDDDFDRTGGFLNNSMA 83
G + +++ L L + I K + +IG E+ QNE ++ + + + T L
Sbjct: 1 GSHMQEQDAGL-DALSSIISRQKQMGQEIGNELDEQNE-IIDDLANLVENTDEKLRTEAR 58
Query: 84 R 84
R
Sbjct: 59 R 59
>1l4a_D S-SNAP25 fusion protein; snare, snare complex, membrane fusion,
neurotransmission, endocytosis/exocytosis complex;
2.95A {Loligo pealei} SCOP: h.1.15.1
Length = 87
Score = 30.7 bits (69), Expect = 0.013
Identities = 14/69 (20%), Positives = 29/69 (42%), Gaps = 5/69 (7%)
Query: 1 MDNRMRRQHAGNYYEPVPNQFDGGDAIHQENEQLTSDLRNKIQALKSLTIDIGTEVKYQN 60
+ ++ + Y + N DA + E ++ + I L+++ ID+G E+ QN
Sbjct: 3 VGDQNGMGPSSGYVTRITN-----DAREDDMENNMKEVSSMIGNLRNMAIDMGNEIGSQN 57
Query: 61 EHLLRGMDD 69
+ R
Sbjct: 58 RQVDRIQQK 66
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 28.2 bits (63), Expect = 0.24
Identities = 13/46 (28%), Positives = 17/46 (36%), Gaps = 9/46 (19%)
Query: 24 GDAIHQENEQLTSDLRN-KIQALKSLTIDIGTEVKYQNEHLLRGMD 68
E E+ D + KI L IG + Y L RG+D
Sbjct: 279 VGETWSEFEKNFEDFKVGKINIL------IGVQAYYGK--LTRGVD 316
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 27.2 bits (59), Expect = 0.49
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 5/30 (16%)
Query: 29 QENEQLTSDLRNKIQALKS---LTIDIGTE 55
Q ++L + L K+ A S L I E
Sbjct: 20 QALKKLQASL--KLYADDSAPALAIKATME 47
>1ney_A TIM, triosephosphate isomerase; yeast, DHAP, dihydroxyacetone
phosphate, michaelis complex; HET: FTR 13P; 1.20A
{Saccharomyces cerevisiae} SCOP: c.1.1.1 PDB: 1nf0_A*
1i45_A* 1ypi_A 2ypi_A 7tim_A* 3ypi_A*
Length = 247
Score = 24.5 bits (54), Expect = 5.2
Identities = 8/45 (17%), Positives = 17/45 (37%)
Query: 14 YEPVPNQFDGGDAIHQENEQLTSDLRNKIQALKSLTIDIGTEVKY 58
YEPV G A ++ + + + +R + + + Y
Sbjct: 163 YEPVXAIGTGLAATPEDAQDIHASIRKFLASKLGDKAASELRILY 207
>1ub2_A Catalase-peroxidase; KATG, cyanobacteria, oxidoreductase; HET:
HEM; 2.40A {Synechococcus elongatus} SCOP: a.93.1.3
a.93.1.3
Length = 720
Score = 24.3 bits (53), Expect = 6.0
Identities = 7/39 (17%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 4 RMRRQHAGNYYEPVPNQFDGGDAIHQENEQLTSDLRNKI 42
+ QH P+ F+ + + + + L DL+ +
Sbjct: 33 DILSQHD-RKTNPMGPDFNYQEEVQKLDAALKQDLQALM 70
>2fvg_A Endoglucanase; TM1049, structural genomics, joint center for
structural genomics, JCSG, protein structure initiative,
PS hydrolase; 2.01A {Thermotoga maritima} SCOP: b.49.3.1
c.56.5.4
Length = 340
Score = 24.5 bits (54), Expect = 6.0
Identities = 13/61 (21%), Positives = 19/61 (31%), Gaps = 10/61 (16%)
Query: 23 GGDAIHQENEQLTSDLRNKIQALKSLTIDIGTEVKYQNEHLLR-G----MDDDFDRTGGF 77
G IH L D N ++L ID G + + + G D+ G
Sbjct: 106 GYRPIH-----LQRDEENTPPRFENLRIDFGFSSADEAKKYVSIGDYVSFVSDYIEKNGR 160
Query: 78 L 78
Sbjct: 161 A 161
>3q4g_A NH(3)-dependent NAD(+) synthetase; structural genomics, csgid,
center for structural genomics O infectious diseases,
alpha beta; 2.40A {Vibrio cholerae}
Length = 279
Score = 24.3 bits (53), Expect = 6.0
Identities = 7/57 (12%), Positives = 19/57 (33%)
Query: 29 QENEQLTSDLRNKIQALKSLTIDIGTEVKYQNEHLLRGMDDDFDRTGGFLNNSMARG 85
Q++E + I+ S++++I V + + + +G
Sbjct: 88 QKDEDEAQLALSFIRPTHSVSVNIKAGVDGLHAASHHALANTGLIPSDPAKVDFIKG 144
>3rza_A Tripeptidase; phosphorylase/hydrolase-like, structural genomics,
joint CEN structural genomics, JCSG, protein structure
initiative; HET: CIT PG4 PGE; 2.10A {Staphylococcus
aureus subsp}
Length = 396
Score = 24.2 bits (53), Expect = 6.2
Identities = 6/20 (30%), Positives = 9/20 (45%)
Query: 16 PVPNQFDGGDAIHQENEQLT 35
P G + IH NE++
Sbjct: 354 PSVILGVGYEKIHTTNERMP 373
>2lfc_A Fumarate reductase, flavoprotein subunit; structural genomics,
northeast structural genomics consortiu PSI-biology; NMR
{Lactobacillus plantarum}
Length = 160
Score = 24.2 bits (53), Expect = 6.5
Identities = 6/20 (30%), Positives = 10/20 (50%)
Query: 60 NEHLLRGMDDDFDRTGGFLN 79
++ G D DF R +L+
Sbjct: 120 QGYVQDGHDHDFGRDPKYLH 139
>3dpi_A NAD+ synthetase; ssgcid, decode, structural genomics, PSI, protein
structure initiative; 2.20A {Burkholderia pseudomallei}
Length = 285
Score = 23.9 bits (52), Expect = 8.1
Identities = 12/58 (20%), Positives = 19/58 (32%), Gaps = 2/58 (3%)
Query: 29 QENEQLTSDLRNKIQALKSLTIDIGTEVKYQNEHLLRGMDDDFDRTGGFLN--NSMAR 84
Q +E ++A ++LT+D+ L G D N AR
Sbjct: 92 QHDEADARRALAFVRADETLTVDVKPAADAMLAALAAGGLAYLDHAQQDFVLGNIKAR 149
>4at0_A 3-ketosteroid-delta4-5alpha-dehydrogenase; oxidoreductase,
dehydogenase, steroid catabolism; HET: FAD; 1.60A
{Rhodococcus jostii} PDB: 4at2_A*
Length = 510
Score = 23.8 bits (52), Expect = 8.7
Identities = 4/19 (21%), Positives = 8/19 (42%)
Query: 60 NEHLLRGMDDDFDRTGGFL 78
N+H G D + ++
Sbjct: 410 NKHAAEGSDPLLHKKSEWV 428
>3tx1_A UDP-N-acetylenolpyruvoylglucosamine reductase; structural
genomics, center for structural genomics of infec
diseases, csgid; HET: FAD; 2.69A {Listeria
monocytogenes}
Length = 322
Score = 23.6 bits (52), Expect = 9.1
Identities = 9/37 (24%), Positives = 17/37 (45%)
Query: 50 IDIGTEVKYQNEHLLRGMDDDFDRTGGFLNNSMARGT 86
+D+GTE Y + + + F LN +++ T
Sbjct: 11 VDLGTENLYFQSNAMNNLQTKFPHIAIKLNEPLSKYT 47
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
0.316 0.135 0.389
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,328,954
Number of extensions: 64007
Number of successful extensions: 160
Number of sequences better than 10.0: 1
Number of HSP's gapped: 158
Number of HSP's successfully gapped: 22
Length of query: 86
Length of database: 6,701,793
Length adjustment: 54
Effective length of query: 32
Effective length of database: 5,194,059
Effective search space: 166209888
Effective search space used: 166209888
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 (21.6 bits)
S2: 51 (23.4 bits)