RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15613
(219 letters)
>3vny_A Beta-glucuronidase; TIM barrel, greek-KEY, glycoside hydrolase
family 79, hydrol; 1.50A {Acidobacterium capsulatum}
PDB: 3vnz_A* 3vo0_A*
Length = 488
Score = 68.4 bits (166), Expect = 1e-13
Identities = 26/123 (21%), Positives = 45/123 (36%), Gaps = 12/123 (9%)
Query: 100 NLPFLCSGETGSCVGGGVEGLTDTFAASFLWIDKLGLAARLGVSVVVRQSLEFGNYSLLD 159
LPF ET SC GG +G++DTFAA+ D + A G + + G Y
Sbjct: 280 GLPFRL-TETNSCYQGGKQGVSDTFAAALWAGDLMYQQAAAGST---GINFHGGGYGWYT 335
Query: 160 ------WNTLEPNPDWWLSVLYKRLVDPRVLNISV--PLSHRTLRLYVQCSPAHNITVFG 211
+ P+++ +L+ + ++L + + L Y +
Sbjct: 336 PVAGTPEDGFIARPEYYGMLLFAQAGAGQLLGAKLTDNSAAPLLTAYALRGTDGRTRIAL 395
Query: 212 INS 214
N
Sbjct: 396 FNK 398
>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 = 38.7 bits (89), Expect = 0.001
Identities = 43/240 (17%), Positives = 73/240 (30%), Gaps = 70/240 (29%)
Query: 1 MNLGYYLNRSDNISAYLNPDTFDLLTYQITRMKNITAKHYEN---HVELPPLWLAELWSG 57
+NL N + + L L YQI + H N + L L
Sbjct: 187 LNLKNC-NSPETVLEMLQ-----KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS 240
Query: 58 ITAESCLLETGPKV-------DLINGSFHLIIIRCQIHLIT----CLLDSEWLNLPFLCS 106
E+CLL V N +F+ + C+I L+T + D FL +
Sbjct: 241 KPYENCLL-----VLLNVQNAKAWN-AFN---LSCKI-LLTTRFKQVTD-------FLSA 283
Query: 107 GETGS-CVGGGVEGLTD----TFAASFLWIDKLGLAAR------LGVSVVVRQSLEFGNY 155
T + LT + +L L +S++ +
Sbjct: 284 ATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT 343
Query: 156 SLLDWNTLEPNPDWWLSVLYKRLVDPRVLNISV----PLSHRTLRLYVQCS--PAH-NIT 208
W D W V +L ++ S+ P +R +++ + S P +I
Sbjct: 344 ----W-------DNWKHVNCDKLT--TIIESSLNVLEPAEYR--KMFDRLSVFPPSAHIP 388
Score = 32.1 bits (72), Expect = 0.13
Identities = 16/109 (14%), Positives = 32/109 (29%), Gaps = 34/109 (31%)
Query: 13 ISAYL--NPDTFD-LLTYQITRMKNITA------------KHYEN------HVELPPLWL 51
I+ + T+D ++ I K ++ +P + L
Sbjct: 333 IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILL 392
Query: 52 AELWSGITAE-----------SCLLETGPKVDLINGSFHLIIIRCQIHL 89
+ +W + L+E PK I S I + ++ L
Sbjct: 393 SLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTI--SIPSIYLELKVKL 439
Score = 29.8 bits (66), Expect = 0.79
Identities = 13/72 (18%), Positives = 23/72 (31%), Gaps = 24/72 (33%)
Query: 163 LEPNPDWWLSVLYKRLVDP------------RVLNISVPLS---------HRTLR--LYV 199
L N + +S + P R+ N + + + LR L
Sbjct: 87 LRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALL- 145
Query: 200 QCSPAHNITVFG 211
+ PA N+ + G
Sbjct: 146 ELRPAKNVLIDG 157
>1dpe_A Dipeptide-binding protein; peptide transport, periplasmic,
chemotaxis binding proteins for active transport; 2.00A
{Escherichia coli K12} SCOP: c.94.1.1 PDB: 1dpp_A
Length = 507
Score = 28.0 bits (63), Expect = 2.6
Identities = 11/61 (18%), Positives = 23/61 (37%), Gaps = 12/61 (19%)
Query: 138 ARLGVSVVVRQSLEFGNY-----------SLLDWNTLEPNPDWWLSVLYKRLVDPRVLNI 186
A++GV + + E+G Y ++ W +PD + + + + N
Sbjct: 373 AKVGVQAKIV-TYEWGEYLKRAKDGEHQTVMMGWTGDNGDPDNFFATEFSCAASEQGSNY 431
Query: 187 S 187
S
Sbjct: 432 S 432
>1ugp_A NitrIle hydratase alpha subunit; complex, N-butyric acid,
non-corrin cobalt, hydration, lyase; HET: BUA; 1.63A
{Pseudonocardia thermophila} SCOP: d.149.1.1 PDB: 1ire_A
1ugr_A 1ugq_A 1ugs_A
Length = 203
Score = 26.9 bits (59), Expect = 4.8
Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 13/72 (18%)
Query: 120 LTDTFAASFLWIDKLGLAARLGVSVVVRQSLEFGNYSLL-------DWNTLEPNPDWWLS 172
L D A +LG+ G ++ ++ + ++ ++ W L P+W+
Sbjct: 72 LADGTEA----CKELGIGGLQGEDMMWVENTDEVHHVVVCTLASCYPWPVLGLPPNWFKE 127
Query: 173 VLYK-RLV-DPR 182
Y+ R+V +PR
Sbjct: 128 PQYRSRVVREPR 139
>3fmw_A Oxygenase; mithramycin, baeyer-villiger, flavin binding protein,
oxidoreductase; HET: FAD; 2.89A {Streptomyces
argillaceus}
Length = 570
Score = 27.4 bits (61), Expect = 5.0
Identities = 11/34 (32%), Positives = 12/34 (35%), Gaps = 11/34 (32%)
Query: 113 VGGGVEGLTDTFAASFLWIDKLGLAARLGVSVVV 146
VGGG GL A L GV +V
Sbjct: 55 VGGGPVGLM---LAGEL--------RAGGVGALV 77
>2qa1_A PGAE, polyketide oxygenase PGAE; FAD, angucycline, aromatic
hydroxylase, oxidored; HET: FAD; 1.80A {Streptomyces}
Length = 500
Score = 26.9 bits (60), Expect = 6.3
Identities = 11/34 (32%), Positives = 12/34 (35%), Gaps = 11/34 (32%)
Query: 113 VGGGVEGLTDTFAASFLWIDKLGLAARLGVSVVV 146
VG G G+ A L GV VVV
Sbjct: 17 VGAGPAGMM---LAGEL--------RLAGVEVVV 39
>2qa2_A CABE, polyketide oxygenase CABE; FAD, angucycline, aromatic
hydroxylase, oxidored; HET: FAD; 2.70A {Streptomyces}
Length = 499
Score = 26.5 bits (59), Expect = 7.5
Identities = 11/34 (32%), Positives = 12/34 (35%), Gaps = 11/34 (32%)
Query: 113 VGGGVEGLTDTFAASFLWIDKLGLAARLGVSVVV 146
VG G GL A L GV V+V
Sbjct: 18 VGAGPAGLM---LAGEL--------RLGGVDVMV 40
>3ano_A AP-4-A phosphorylase; diadenosine polyphosphate, HIT transferase;
HET: PG4; 1.89A {Mycobacterium tuberculosis}
Length = 218
Score = 26.5 bits (58), Expect = 7.5
Identities = 6/41 (14%), Positives = 14/41 (34%)
Query: 35 ITAKHYENHVELPPLWLAELWSGITAESCLLETGPKVDLIN 75
+ + +L L AEL + +++ + N
Sbjct: 110 VPYRRVSELEDLTDLESAELMAFTQKAIRVIKNVSRPHGFN 150
>2noo_A NIKA, nickel-binding periplasmic protein; nickel-bound, transport,
iodine, hydrolase; HET: TYI; 1.65A {Escherichia coli
K12} PDB: 3mvx_A* 3dp8_A* 3e3k_A* 1zlq_A* 3mvw_A*
3mvy_A* 3mvz_A* 3mw0_A* 3mz9_A* 1uiu_A 1uiv_A 3mzb_A*
3qim_A
Length = 502
Score = 26.6 bits (59), Expect = 7.9
Identities = 6/49 (12%), Positives = 13/49 (26%), Gaps = 12/49 (24%)
Query: 138 ARLGVSVVVRQSLEFGNY-----------SLLDWNTLEPNPDWWLSVLY 175
++G V + E + +P +LS +
Sbjct: 365 RQIGADVSL-IGEEESSIXARQRDGRFGMIFHRTAGAPADPHAFLSSMR 412
>1vk4_A PFKB carbohydrate kinase TM0415; structural genomics, JCSG, protein
structure initiative, joint center for structural G
transferase; 1.91A {Thermotoga maritima} SCOP: c.72.1.1
Length = 298
Score = 26.2 bits (58), Expect = 8.9
Identities = 6/33 (18%), Positives = 13/33 (39%), Gaps = 7/33 (21%)
Query: 122 DTFAASFLWIDKLGLAARLGVSVVVRQSLEFGN 154
DT A+F L + + + ++ +F
Sbjct: 246 DTCTAAF-------LVGFVFKKMSIEKATKFAA 271
>3tpa_A Heme-binding protein A; glutathione binding protein, SBP; 2.00A
{Haemophilus parasuis 29755}
Length = 521
Score = 26.1 bits (58), Expect = 10.0
Identities = 9/49 (18%), Positives = 20/49 (40%), Gaps = 12/49 (24%)
Query: 138 ARLGVSVVVRQSLEFGNY-----------SLLDWNTLEPNPDWWLSVLY 175
A++GV + + E+ ++ W + +PD +L L+
Sbjct: 380 AKIGVKAKL-VTHEWADFNKRTREGEFAAGTYGWTSRNGDPDNFLFPLF 427
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
0.323 0.140 0.451
Gapped
Lambda K H
0.267 0.0462 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,538,288
Number of extensions: 205008
Number of successful extensions: 406
Number of sequences better than 10.0: 1
Number of HSP's gapped: 404
Number of HSP's successfully gapped: 19
Length of query: 219
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 129
Effective length of database: 4,188,903
Effective search space: 540368487
Effective search space used: 540368487
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.6 bits)