RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8393
(98 letters)
>1y9j_A SEC1 family domain containing protein 1; membrane traffic, SLY1,
SM proteins, snares, protein protein transport; NMR
{Rattus norvegicus}
Length = 159
Score = 53.1 bits (127), Expect = 2e-10
Identities = 33/53 (62%), Positives = 42/53 (79%)
Query: 23 ALKQMMNFNEVQSKLSSSEPVWKILIFDRCGQDIISPVLSKNDLRELGVTLFL 75
ALK+M+NFN K S EPVWK+LI+DR GQDIISP+LS +LR++G+TL L
Sbjct: 29 ALKRMLNFNVPHVKNSPGEPVWKVLIYDRFGQDIISPLLSVKELRDMGITLHL 81
>1mqs_A SLY1 protein, SLY1P; SM-protein, snare, syntaxin,
endocytosis/exocytosis complex; 3.00A {Saccharomyces
cerevisiae} SCOP: e.25.1.1
Length = 671
Score = 52.4 bits (124), Expect = 1e-09
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 11/64 (17%)
Query: 23 ALKQMMNFNE-----------VQSKLSSSEPVWKILIFDRCGQDIISPVLSKNDLRELGV 71
A+ +M+ N+ + E +WK+LI D IS VL NDL + G+
Sbjct: 26 AILKMLFLNKDLNNNDNITTITDDIFNQQEIIWKVLILDIKSTATISSVLRVNDLLKAGI 85
Query: 72 TLFL 75
T+
Sbjct: 86 TVHS 89
>1epu_A S-SEC1; parallel beta-sheets, LEFT-hand turn connection, helical
BUN endocytosis-exocytosis complex; 2.40A {Loligo
pealei} SCOP: e.25.1.1 PDB: 1fvf_A 1fvh_A
Length = 591
Score = 44.6 bits (104), Expect = 7e-07
Identities = 9/40 (22%), Positives = 17/40 (42%)
Query: 36 KLSSSEPVWKILIFDRCGQDIISPVLSKNDLRELGVTLFL 75
WK+LI D+ ++S +++ G+TL
Sbjct: 17 LAVKKNAEWKVLIVDQLSMRMVSACCKMHEIMSEGITLVE 56
>1dn1_A NSEC1, syntaxin binding protein 1; protein-protein complex,
multi-subunit; 2.60A {Rattus norvegicus} SCOP: e.25.1.1
PDB: 3puj_A 3c98_A
Length = 594
Score = 43.0 bits (100), Expect = 3e-06
Identities = 9/39 (23%), Positives = 18/39 (46%)
Query: 36 KLSSSEPVWKILIFDRCGQDIISPVLSKNDLRELGVTLF 74
K + WK+L+ D+ ++S D+ G+T+
Sbjct: 20 KKVKKKGEWKVLVVDQLSMRMLSSCCKMTDIMTEGITIV 58
>2xhe_A UNC18; exocytosis, exocytosis complex, snare, neuro fusion, SM
PROT choanoflagellates; 2.80A {Monosiga brevicollis}
Length = 650
Score = 42.3 bits (98), Expect = 5e-06
Identities = 11/55 (20%), Positives = 23/55 (41%), Gaps = 7/55 (12%)
Query: 28 MNFNEVQSKL-------SSSEPVWKILIFDRCGQDIISPVLSKNDLRELGVTLFL 75
M+ + + WK+L+ D+ +IS +++ +LGVT+
Sbjct: 2 MSLKSAVKTVLTNSLRSVADGGDWKVLVVDKPALRMISECARMSEILDLGVTVVE 56
>3puk_A Syntaxin-binding protein 3; membrane trafficking, SM protein,
snare proteins, binding protein, endocytosis-exocytosis
complex; 3.05A {Mus musculus} PDB: 2pjx_A
Length = 592
Score = 41.4 bits (96), Expect = 1e-05
Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 1/53 (1%)
Query: 23 ALKQMMNFNEVQSKLSSSEPVWKILIFDRCGQDIISPVLSKNDLRELGVTLFL 75
++ V E WKI++ D ++S DL E G+T+
Sbjct: 12 SVVWRKIKTAVFDDCRK-EGEWKIMLLDEFTTKLLSSCCKMTDLLEEGITVIE 63
>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 = 30.7 bits (68), Expect = 0.038
Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 4/28 (14%)
Query: 63 KNDLRELGVTLFLYSAEVLDEEYSALCL 90
K L++L +L LY+ D+ AL +
Sbjct: 19 KQALKKLQASLKLYA----DDSAPALAI 42
>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 = 31.2 bits (70), Expect = 0.044
Identities = 18/99 (18%), Positives = 29/99 (29%), Gaps = 34/99 (34%)
Query: 19 QKSYALKQM---MNFNEVQSKLSSSEPVWKILIFDRCGQDIISPVLSKNDLRELGVT--- 72
+K +++ M F + +E IF + S ++ L T
Sbjct: 1679 EKGKRIRENYSAMIFETIVDGKLKTEK-----IFKEINEHSTSYTFR-SEKGLLSATQFT 1732
Query: 73 ---LFL--YSA-EVLDE----------------EYSALC 89
L L +A E L EY+AL
Sbjct: 1733 QPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALA 1771
Score = 25.0 bits (54), Expect = 5.4
Identities = 12/80 (15%), Positives = 22/80 (27%), Gaps = 25/80 (31%)
Query: 5 IIGLGQTQKGVVIIQKSYALKQM-MNFNEVQSKLSSSEPVWKILIFDRCGQDIISPVL-- 61
+IG+ Q + K + E++S L + Q +++ V
Sbjct: 240 LIGVIQ------LAHYVVTAKLLGFTPGELRSYLKGATG---------HSQGLVTAVAIA 284
Query: 62 ---SKNDLRELGVT----LF 74
S LF
Sbjct: 285 ETDSWESFFVSVRKAITVLF 304
>2iuk_A SEED lipoxygenase; iron, dioxygenase, metal-binding,
oxidoreductase, oxylipin biosynthesis, soybean
lipoxygenase-D, fatty acid biosynthesis; 2.4A {Glycine
max}
Length = 864
Score = 30.6 bits (68), Expect = 0.059
Identities = 14/76 (18%), Positives = 25/76 (32%), Gaps = 4/76 (5%)
Query: 9 GQTQKGVVIIQKSYALKQMMNFNEVQSKLSSSEPVWKILIFDRCGQDIISPVLSKNDLRE 68
GQ KG V++ L +FN + S I + + + +
Sbjct: 8 GQKIKGTVVLMPKNVL----DFNAITSIGKGGVIDTATGILGQGVSLVGGVIDTATSFLG 63
Query: 69 LGVTLFLYSAEVLDEE 84
+++ L SA D
Sbjct: 64 RNISMQLISATQTDGS 79
>1f8n_A Lipoxygenase-1; dioxygenase, metalloprotein, fatty acids,
oxidoreductase; 1.40A {Glycine max} SCOP: a.119.1.1
b.12.1.1 PDB: 1yge_A 2sbl_B 3pzw_A 1fgq_A 1fgr_A 3bnd_A
1fgt_A 1fgm_A 3bnb_A 1fgo_A 1y4k_A 3bne_A 3bnc_A
1ik3_A* 1hu9_A* 1jnq_A* 1lnh_A 1n8q_A* 1no3_A* 1rrh_A
...
Length = 839
Score = 26.3 bits (57), Expect = 1.9
Identities = 15/80 (18%), Positives = 24/80 (30%), Gaps = 27/80 (33%)
Query: 5 IIGLGQTQKGVVIIQKSYALKQMMNFNEVQSKLSSSEPVWKILIFDRCGQDIISPVLSKN 64
+ G KG V++ K + N S + D ++ L +
Sbjct: 1 MFSAGHKIKGTVVLMP----KNELEVNPDGSAV-----------------DNLNAFLGR- 38
Query: 65 DLRELGVTLFLYSAEVLDEE 84
V+L L SA D
Sbjct: 39 -----SVSLQLISATKADAH 53
>3fa4_A 2,3-dimethylmalate lyase; alpha/beta barrel, helix swapping; 2.18A
{Aspergillus niger} PDB: 3fa3_A
Length = 302
Score = 25.7 bits (57), Expect = 2.3
Identities = 4/19 (21%), Positives = 12/19 (63%)
Query: 58 SPVLSKNDLRELGVTLFLY 76
+P +S + +E+G + ++
Sbjct: 220 TPSISAAEAKEMGFRIIIF 238
>3lye_A Oxaloacetate acetyl hydrolase; (alpha/beta)8 barrel; 1.30A
{Cryphonectria parasitica} PDB: 3m0j_A* 3m0k_A
Length = 307
Score = 25.8 bits (57), Expect = 2.3
Identities = 3/19 (15%), Positives = 12/19 (63%)
Query: 58 SPVLSKNDLRELGVTLFLY 76
SP+++ + + +G + ++
Sbjct: 228 SPLITVEEAKAMGFRIMIF 246
>1xg4_A Probable methylisocitrate lyase; 2-methylisocitrate lyase/inhibitor
complex, isocitrate lyase superfamily; HET: ICT; 1.60A
{Escherichia coli} PDB: 1xg3_A* 1mum_A 1oqf_A 1ujq_A
1o5q_A
Length = 295
Score = 25.7 bits (57), Expect = 2.5
Identities = 6/19 (31%), Positives = 12/19 (63%)
Query: 58 SPVLSKNDLRELGVTLFLY 76
+P+ + ++LR V + LY
Sbjct: 216 TPLFTTDELRSAHVAMALY 234
>3ih1_A Methylisocitrate lyase; alpha-beta structure, TIM-barrel, center
for structural GENO infectious diseases, csgid; 2.00A
{Bacillus anthracis str} PDB: 3kz2_A
Length = 305
Score = 25.7 bits (57), Expect = 2.9
Identities = 4/19 (21%), Positives = 9/19 (47%)
Query: 58 SPVLSKNDLRELGVTLFLY 76
+P S + +G + +Y
Sbjct: 224 TPYYSAEEFANMGFQMVIY 242
>3eoo_A Methylisocitrate lyase; seattle structural genomics center for
infectious disease, ssgcid; 2.90A {Burkholderia
pseudomallei 1655}
Length = 298
Score = 25.7 bits (57), Expect = 3.0
Identities = 5/19 (26%), Positives = 12/19 (63%)
Query: 58 SPVLSKNDLRELGVTLFLY 76
+P+ + ++L+ V + LY
Sbjct: 220 TPLFTLDELKGANVDIALY 238
>1zlp_A PSR132, petal death protein; TIM-barrel, helix
swapping,2-ethyl-3-methylmalate lyase, 2-P methylmalate
lyase, lyase/PEP mutase superfamily; 2.70A {Dianthus
caryophyllus}
Length = 318
Score = 25.4 bits (56), Expect = 3.4
Identities = 4/19 (21%), Positives = 11/19 (57%)
Query: 58 SPVLSKNDLRELGVTLFLY 76
+P+ + + +E+G L +
Sbjct: 238 TPLHTPEEFKEMGFHLIAH 256
>2lmr_A ODIN, ankyrin repeat and SAM domain-containing protein; signaling
protein; NMR {Homo sapiens}
Length = 101
Score = 24.9 bits (54), Expect = 4.0
Identities = 6/20 (30%), Positives = 13/20 (65%)
Query: 54 QDIISPVLSKNDLRELGVTL 73
+ S V+ + DLR++G++
Sbjct: 57 HFLGSNVMEEQDLRDIGISD 76
>1xg7_A Hypothetical protein; southeast collaboratory for structural
genomics, secsg, hyperthermophIle, pyrococcus FU
protein structure initiative; 1.88A {Pyrococcus
furiosus} SCOP: a.96.1.6
Length = 250
Score = 25.0 bits (54), Expect = 4.7
Identities = 5/32 (15%), Positives = 14/32 (43%)
Query: 66 LRELGVTLFLYSAEVLDEEYSALCLMCLRMNC 97
++ +G+ E +D ++ AL + +
Sbjct: 16 IKGIGIEGAKEVEEKVDRQFYALQYLFRHQDP 47
>3b8i_A PA4872 oxaloacetate decarboxylase; alpha/beta barrel, helix
swapping, lyase; 1.90A {Pseudomonas aeruginosa}
Length = 287
Score = 24.6 bits (54), Expect = 5.7
Identities = 4/19 (21%), Positives = 7/19 (36%)
Query: 58 SPVLSKNDLRELGVTLFLY 76
+ L LGV + +
Sbjct: 215 PQLRDDARLARLGVRVVVN 233
>2j5b_A Tyrosyl-tRNA synthetase; ligase, protein biosynthesis, ATP-binding;
HET: TYE; 2.20A {Acanthamoeba polyphaga mimivirus}
Length = 348
Score = 24.6 bits (54), Expect = 6.9
Identities = 7/26 (26%), Positives = 14/26 (53%)
Query: 25 KQMMNFNEVQSKLSSSEPVWKILIFD 50
+M+ + + K+S S+P I + D
Sbjct: 221 HMLMSLSGPKKKMSKSDPQGAIFMDD 246
>2f3n_A SH3 and multiple ankyrin repeat domains 3; postsynaptic density,
SAM domain, shank, scaffolding protein, structural
protein; 2.10A {Rattus norvegicus} SCOP: a.60.1.2 PDB:
2f44_A
Length = 76
Score = 23.5 bits (51), Expect = 7.4
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 61 LSKNDLRELGVTLF 74
L+K D ELGVT
Sbjct: 39 LTKEDFVELGVTRV 52
>3p0j_A Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase,
AARS, tyrrs, pseudod translation, ATP-binding,
nucleotide-binding, ligase; HET: TYE; 2.89A {Leishmania
major} PDB: 3p0i_A* 3p0h_A*
Length = 690
Score = 24.4 bits (53), Expect = 8.1
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 27 MMNFNEVQSKLSSSEPVWKILIFD 50
+ + Q+K+S S+P I + D
Sbjct: 221 LAGLKQGQAKMSKSDPDSAIFMED 244
>3ln3_A Dihydrodiol dehydrogenase; putative reductase, structural genomics,
joint center for structural genomics, JCSG, protein
structure initiative, PSI-2; HET: MLY MSE NAD; 1.18A
{Mus musculus}
Length = 324
Score = 24.5 bits (53), Expect = 8.3
Identities = 8/33 (24%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 10 QTQKGVVIIQKSYALKQMMNFNEVQS-KLSSSE 41
Q+G+V + +S+ +M +V +LS +
Sbjct: 261 LIQRGIVPLAQSFXENEMRENLQVFGFQLSPED 293
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
0.324 0.138 0.410
Gapped
Lambda K H
0.267 0.0460 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,400,525
Number of extensions: 68597
Number of successful extensions: 237
Number of sequences better than 10.0: 1
Number of HSP's gapped: 237
Number of HSP's successfully gapped: 26
Length of query: 98
Length of database: 6,701,793
Length adjustment: 64
Effective length of query: 34
Effective length of database: 4,914,849
Effective search space: 167104866
Effective search space used: 167104866
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.1 bits)