RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy516
(80 letters)
>1v54_I STA, cytochrome C oxidase polypeptide VIC; oxidoreductase; HET:
FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos
taurus} SCOP: f.23.3.1 PDB: 1oco_I* 1occ_I* 1ocz_I*
1ocr_I* 1v55_I* 2dyr_I* 2dys_I* 2eij_I* 2eik_I* 2eil_I*
2eim_I* 2ein_I* 2occ_I* 2ybb_T* 2zxw_I* 3abk_I* 3abl_I*
3abm_I* 3ag1_I* 3ag2_I* ...
Length = 73
Score = 87.6 bits (217), Expect = 4e-25
Identities = 27/70 (38%), Positives = 44/70 (62%)
Query: 7 TGKLPKPQLRNLLQSSIKVALVQGAVIAFGTAVAWKVLIMDPHKKAISEFYKTYDGEKDF 66
+ L KPQ+R LL ++ +V +++ G A +K + + KKA ++FY+ YD KDF
Sbjct: 1 STALAKPQMRGLLARRLRFHIVGAFMVSLGFATFYKFAVAEKRKKAYADFYRNYDSMKDF 60
Query: 67 ERMKKAGLFE 76
E M+KAG+F+
Sbjct: 61 EEMRKAGIFQ 70
>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 = 29.1 bits (64), Expect = 0.12
Identities = 12/78 (15%), Positives = 25/78 (32%), Gaps = 13/78 (16%)
Query: 1 MPAEAATGKLPKPQLRNLLQSSIKVALVQGAVIAFGTAVAWKVLIMDPHKKAISEFYKTY 60
+P E T N + SI ++ + + WK + D I
Sbjct: 318 LPREVLTT--------NPRRLSIIAESIRDGLATWDN---WKHVNCDKLTTIIESSLNVL 366
Query: 61 DGEKDFERM-KKAGLFEE 77
+ ++ +M + +F
Sbjct: 367 E-PAEYRKMFDRLSVFPP 383
>1y9j_A SEC1 family domain containing protein 1; membrane traffic, SLY1,
SM proteins, snares, protein protein transport; NMR
{Rattus norvegicus}
Length = 159
Score = 28.8 bits (64), Expect = 0.12
Identities = 11/50 (22%), Positives = 17/50 (34%), Gaps = 3/50 (6%)
Query: 15 LRNLLQSSIK--VALVQGAVIAFGTAVAWKVLIMDPH-KKAISEFYKTYD 61
+R ++K + V WKVLI D + IS +
Sbjct: 22 IRERQTVALKRMLNFNVPHVKNSPGEPVWKVLIYDRFGQDIISPLLSVKE 71
>1ceo_A Cellulase CELC; glycosyl hydrolase, family A/5 of glycosyl
hydrolases, cellulose degradation; 1.90A {Clostridium
thermocellum} SCOP: c.1.8.3 PDB: 1cen_A 1cec_A
Length = 343
Score = 28.0 bits (62), Expect = 0.24
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 46 MDPHKKAISEFYKTYDGEKDFERMKKAGL 74
+ ++ E + T+ EKD E + +AG
Sbjct: 14 ISQYQVFSKEHFDTFITEKDIETIAEAGF 42
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.8 bits (61), Expect = 0.25
Identities = 6/38 (15%), Positives = 15/38 (39%), Gaps = 5/38 (13%)
Query: 42 KVLIMDPHKKAISEFYKTYDG--EKDFERMKKAGLFEE 77
+ + KK + E+ + EK+ + A ++
Sbjct: 109 EQEWREKAKKDLEEWNQRQSEQVEKNKINNRIA---DK 143
>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 = 27.9 bits (61), Expect = 0.34
Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 5/49 (10%)
Query: 14 QLRNLLQSSIKVALVQGAVIAFGTAVAWKVLIMDPH-KKAISEFYKTYD 61
L++++ IK A+ WK++++D K +S K D
Sbjct: 9 GLKSVVWRKIKTAVFD----DCRKEGEWKIMLLDEFTTKLLSSCCKMTD 53
>1mqs_A SLY1 protein, SLY1P; SM-protein, snare, syntaxin,
endocytosis/exocytosis complex; 3.00A {Saccharomyces
cerevisiae} SCOP: e.25.1.1
Length = 671
Score = 27.7 bits (60), Expect = 0.37
Identities = 11/51 (21%), Positives = 18/51 (35%), Gaps = 3/51 (5%)
Query: 14 QLRNLLQSSIKVALVQGAV--IAFGTAVAWKVLIMDPH-KKAISEFYKTYD 61
++ L + + I + WKVLI+D IS + D
Sbjct: 29 KMLFLNKDLNNNDNITTITDDIFNQQEIIWKVLILDIKSTATISSVLRVND 79
>3tqk_A Phospho-2-dehydro-3-deoxyheptonate aldolase; transferase; 2.30A
{Francisella tularensis}
Length = 346
Score = 27.2 bits (61), Expect = 0.52
Identities = 6/13 (46%), Positives = 7/13 (53%)
Query: 37 TAVAWKVLIMDPH 49
T + WK I DP
Sbjct: 97 TTIGWKGFINDPD 109
>1of8_A Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited;
beta-alpha-barrel, lyase, synthase, synthetase; HET: PEP
G3P; 1.5A {Saccharomyces cerevisiae} SCOP: c.1.10.4 PDB:
1oab_A* 1of6_A* 1hfb_A* 1ofa_A* 1ofb_A 1ofo_A 1ofp_A
1ofq_A 1ofr_A* 1og0_A*
Length = 370
Score = 26.9 bits (60), Expect = 0.55
Identities = 8/13 (61%), Positives = 8/13 (61%)
Query: 37 TAVAWKVLIMDPH 49
T V WK LI DP
Sbjct: 115 TTVGWKGLINDPD 127
>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 = 26.8 bits (58), Expect = 0.58
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 8/29 (27%)
Query: 12 KPQLRNLLQSSIKV-------ALVQGAVI 33
K L+ L Q+S+K+ AL A +
Sbjct: 19 KQALKKL-QASLKLYADDSAPALAIKATM 46
>1n8f_A DAHP synthetase; (beta/alpha)8 barrel, metal binding protein; HET:
PEP; 1.75A {Escherichia coli} SCOP: c.1.10.4 PDB: 1gg1_A
1kfl_A* 1qr7_A*
Length = 350
Score = 26.8 bits (60), Expect = 0.64
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 37 TAVAWKVLIMDPH 49
T V WK LI DPH
Sbjct: 100 TTVGWKGLINDPH 112
>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 = 26.4 bits (57), Expect = 1.0
Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 14 QLRNLLQSSIKVALVQGAVIAFGTAVAWKVLIMDPH-KKAISEFYKTYD 61
L+ ++ I +++ WKVL++D + +S K D
Sbjct: 5 GLKAVVGEKIMHDVIK----KVKKKGEWKVLVVDQLSMRMLSSCCKMTD 49
>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 = 25.7 bits (55), Expect = 1.9
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 5/48 (10%)
Query: 15 LRNLLQSSIKVALVQGAVIAFGTAVAWKVLIMDPH-KKAISEFYKTYD 61
L+ + I +V A WKVLI+D + +S K ++
Sbjct: 3 LKTAVHEKIMNDVVL----AVKKNAEWKVLIVDQLSMRMVSACCKMHE 46
>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 = 25.4 bits (55), Expect = 2.2
Identities = 9/66 (13%), Positives = 21/66 (31%), Gaps = 22/66 (33%)
Query: 3 AEAATGK-LPKPQLRNLLQS----SIKVALV---QGAVIAFGTAVAWKVLIMDPHKKAIS 54
A + K L ++ + ++ + QG + ++ L
Sbjct: 129 ARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDY-----FEEL---------R 174
Query: 55 EFYKTY 60
+ Y+TY
Sbjct: 175 DLYQTY 180
Score = 24.6 bits (53), Expect = 4.1
Identities = 7/25 (28%), Positives = 8/25 (32%), Gaps = 11/25 (44%)
Query: 66 FERMKKAGLFE-----------EYT 79
FE +K GL EY
Sbjct: 1744 FEDLKSKGLIPADATFAGHSLGEYA 1768
>3otr_A Enolase; structural genomics, center for structural genomics of
infec diseases, csgid, alpha-beta barrel, TIM barrel;
2.75A {Toxoplasma gondii}
Length = 452
Score = 25.2 bits (56), Expect = 2.2
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 4/27 (14%)
Query: 42 KVLI-MDPHKKAISEFYKTYDGEKDFE 67
K+ I D A SEFYK + + D +
Sbjct: 246 KIKIAFDA---AASEFYKQDEKKYDLD 269
>1nnw_A Hypothetical protein; structural genomics, PSI, protein structure
initiative, southeast collaboratory for structural
genomics, secsg; 1.90A {Pyrococcus furiosus} SCOP:
d.159.1.5 PDB: 2gju_A
Length = 252
Score = 24.8 bits (53), Expect = 3.5
Identities = 9/35 (25%), Positives = 14/35 (40%)
Query: 44 LIMDPHKKAISEFYKTYDGEKDFERMKKAGLFEEY 78
++D YD + ER++ GL EE
Sbjct: 208 ALVDVDTLKPKFIEVEYDKKIIEERIRAEGLPEEI 242
>2xhe_A UNC18; exocytosis, exocytosis complex, snare, neuro fusion, SM
PROT choanoflagellates; 2.80A {Monosiga brevicollis}
Length = 650
Score = 24.9 bits (53), Expect = 3.7
Identities = 8/22 (36%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 41 WKVLIMDPH-KKAISEFYKTYD 61
WKVL++D + ISE + +
Sbjct: 25 WKVLVVDKPALRMISECARMSE 46
>3b40_A PVDM, probable dipeptidase; structural genomics, hydrolase,
PSI-2, protein structure initiative; 2.00A {Pseudomonas
aeruginosa}
Length = 417
Score = 24.5 bits (53), Expect = 4.3
Identities = 7/40 (17%), Positives = 13/40 (32%), Gaps = 7/40 (17%)
Query: 42 KVLIMDPH-------KKAISEFYKTYDGEKDFERMKKAGL 74
++L D +E K G+ D + + L
Sbjct: 21 RILSFDSRITVPLDFGTTGNEVDKDGPGQLDLVKAGRGRL 60
>3orf_A Dihydropteridine reductase; alpha-beta-alpha sandwich, rossmann
fold, oxidoreductase (AC NADH), NADH binding,
oxidoreductase; HET: NAD; 2.16A {Dictyostelium
discoideum}
Length = 251
Score = 24.2 bits (53), Expect = 4.9
Identities = 9/31 (29%), Positives = 11/31 (35%), Gaps = 7/31 (22%)
Query: 24 KVALVQGAVIAFGTAVA-------WKVLIMD 47
K LV G A G V W + +D
Sbjct: 23 KNILVLGGSGALGAEVVKFFKSKSWNTISID 53
>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides,
nucleotides, transferase; HET: 5GP; 1.85A {Coxiella
burnetii}
Length = 205
Score = 23.6 bits (52), Expect = 8.9
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 63 EKDFERMKKAGLFEEY 78
E F+ M K G F E+
Sbjct: 60 ETRFQAMVKEGAFLEH 75
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
0.318 0.133 0.380
Gapped
Lambda K H
0.267 0.0839 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,256,267
Number of extensions: 62785
Number of successful extensions: 224
Number of sequences better than 10.0: 1
Number of HSP's gapped: 224
Number of HSP's successfully gapped: 26
Length of query: 80
Length of database: 6,701,793
Length adjustment: 49
Effective length of query: 31
Effective length of database: 5,333,664
Effective search space: 165343584
Effective search space used: 165343584
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: 51 (23.2 bits)