RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12122
(412 letters)
>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 = 50.0 bits (119), Expect = 1e-06
Identities = 38/259 (14%), Positives = 69/259 (26%), Gaps = 86/259 (33%)
Query: 132 LDEVCLMRLRIGHTKITHSFLFRREDPPVCDKCNVPLTVEHIVLSCRKMRFRPNSFLNST 191
+D L + H + H L VP T + S + +F T
Sbjct: 1 MDAYSTRPLTLSHGSLEHVLL-------------VP-TASFFIASQLQEQFN-KILPEPT 45
Query: 192 LSDVLKDDPDSVATL-MRFLKRNNFPKELYRRSGLYPGSPG----------------FYR 234
D+P + A L +FL Y S + P G +
Sbjct: 46 EGFAADDEPTTPAELVGKFLG--------YVSSLVEPSKVGQFDQVLNLCLTEFENCYLE 97
Query: 235 GED---------------LKRVQSVM---YRGYEGVGAPNFRRPSHSKEAKTVILCASRS 276
G D L + + ++ P F + S+S
Sbjct: 98 GNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRP-FDKKSNSA------------ 144
Query: 277 DCLMTSTFAENAECFIHL---GIPAVY------LYTDTVYSSVLHLFCELRPACILENSD 327
L + NA+ G Y LY Y ++ + + E
Sbjct: 145 --LFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLY--QTYHVLVGDLIKFSAETLSELIR 200
Query: 328 VARDRKRILIYQKTVSLKS 346
D ++ ++ + +++
Sbjct: 201 TTLDAEK--VFTQGLNILE 217
Score = 41.2 bits (96), Expect = 6e-04
Identities = 29/158 (18%), Positives = 51/158 (32%), Gaps = 50/158 (31%)
Query: 20 APRR-----PPKSLWGQKTNLIFFLCPKSPKYGKVSYNHVGIAGNEAADREAKSTLGS-- 72
+ PP+SL+G L P ++ + E K +
Sbjct: 373 GAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPF------------SERKLKFSNRF 420
Query: 73 -PIT---HNRLL---LEEIRS-LTRKHFLQTWNSTWAATN---PTHITHN--KLRRIKSS 119
P+ H+ LL + I L + + ++ A + P + T + LR + S
Sbjct: 421 LPVASPFHSHLLVPASDLINKDLVKNNV------SFNAKDIQIPVYDTFDGSDLRVLSGS 474
Query: 120 ISPWSTSCQKSRL-DEVCLMRL---RIGHTKITHSFLF 153
IS R+ D + + + K TH F
Sbjct: 475 ISE--------RIVDCIIRLPVKWETTTQFKATHILDF 504
Score = 39.3 bits (91), Expect = 0.002
Identities = 71/465 (15%), Positives = 128/465 (27%), Gaps = 165/465 (35%)
Query: 50 SYNHVGIAGNEAADREAKSTL------------------GSPITHNRLLLEEIRSL--TR 89
+Y I D+++ S L G+ + EE+R L T
Sbjct: 125 NYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDY----FEELRDLYQTY 180
Query: 90 KHFLQTWNSTWAATNPTHITHNKLRRIKSSISPWSTSCQKSRLDEVCLMRLRIGHTKITH 149
+ + L + + + L+
Sbjct: 181 HVLVGDL---------IKFSAETLSELIRTTLDAEKVFTQG-LN--------------IL 216
Query: 150 SFLFRREDPPVCDK-CNVPLTV--------EHIVLSCRKMRFRPNSFLN--STLSDVLK- 197
+L + P D ++P++ H V++ + + F P + + +
Sbjct: 217 EWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQG 276
Query: 198 ----------DDPDS----VATLMRFLKRNNF-----PKELYRRSGLYP----------- 227
D +S V + L F E Y + L P
Sbjct: 277 LVTAVAIAETDSWESFFVSVRKAITVL----FFIGVRCYEAYPNTSLPPSILEDSLENNE 332
Query: 228 GSPGF---YRGEDLKRVQSVMYRGYEGVGAPNFRRPSHSK-------EAKTVILCASRSD 277
G P ++VQ V N P+ + AK +++
Sbjct: 333 GVPSPMLSISNLTQEQVQDY-------VNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQS 385
Query: 278 CLMT-STFAENAECFIHLG---IP---------AVYLYTDTVYSSVLHLFCELRPACILE 324
L + A+ L IP +L + + S L L PA L
Sbjct: 386 -LYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHL-----LVPASDLI 439
Query: 325 NSDVARDRK-------RILIY---------QKTVSLKSETIHQAFRVGQEW----VFKAH 364
N D+ ++ +I +Y + S+ + R+ +W FKA
Sbjct: 440 NKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKAT 499
Query: 365 HI------NSPSLG------KAGKRQQHAIAWMVDGQPS---GYQ 394
HI + LG K G + +A +D P G++
Sbjct: 500 HILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINPDDDYGFK 544
Score = 31.9 bits (72), Expect = 0.41
Identities = 38/227 (16%), Positives = 58/227 (25%), Gaps = 93/227 (40%)
Query: 47 GKVSYNHVGIAGN--EAADREAKSTLGSPITHNRLLLEEIRSLTRKHFLQTWNSTWAATN 104
G Y A + AD K T G I L+ + N
Sbjct: 1632 GMDLYKTSKAAQDVWNRADNHFKDTYGFSI------LDIVI-----------------NN 1668
Query: 105 PTHIT-HNKLRRIKSSISPWSTSCQKSRLDEVCLMRLRIGHTKITHSFLFRREDPPVCDK 163
P ++T H +K + R+R ++ + E D
Sbjct: 1669 PVNLTIHF--------------GGEKGK-------RIRENYSAMI------FETIV--DG 1699
Query: 164 CNVPLTV-EHIVLSCRKMRFR-PNSFLNST------LSDVLKDDPDSVATLMRFLK-RNN 214
+ + I FR L++T L+ + A LK +
Sbjct: 1700 KLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLM------EKA-AFEDLKSKGL 1752
Query: 215 FPK----------E---LYRRSGLYPGSPGFYRGEDLKRVQSVMYRG 248
P E L + + E L V V YRG
Sbjct: 1753 IPADATFAGHSLGEYAALASLADVMS----I---ESLVEV--VFYRG 1790
>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 = 40.6 bits (94), Expect = 0.001
Identities = 43/261 (16%), Positives = 85/261 (32%), Gaps = 63/261 (24%)
Query: 130 SRLDEVCLMRLRIGHTKITHSFLFRREDPPVC----DKCNV--PLTVEHIVLSCRKM--- 180
SR D ++LRI + L + + C NV LSC+ +
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL--NVQNAKAWNAFNLSCKILLTT 272
Query: 181 RFRPNS-FLNS------TLSDVLK--DDPDSVATLMRFL--KRNNFPKELYRRSGLYPGS 229
RF+ + FL++ +L + + L+++L + + P+E+ +
Sbjct: 273 RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSI 332
Query: 230 PGFYRGEDLKRVQSVMYRGYEGVGAPNFRRPSHSKEAKTVILCASRSDCLMTSTFAENAE 289
+ L N++ + K + L AE +
Sbjct: 333 IAESIRDGLATWD-------------NWKHVNCDKLTTII------ESSLNVLEPAEYRK 373
Query: 290 CFIHLG-------IPA---VYLYTDTVYSSVLHLFCELRPACILENSDVARDRK--RILI 337
F L IP ++ D + S V+ + +L ++E + K I I
Sbjct: 374 MFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVE-----KQPKESTISI 428
Query: 338 YQKTVSLKSE-----TIHQAF 353
+ LK + +H++
Sbjct: 429 PSIYLELKVKLENEYALHRSI 449
>1cjx_A 4-hydroxyphenylpyruvate dioxygenase; oxidoreductase, iron; 2.40A
{Pseudomonas fluorescens} SCOP: d.32.1.3 d.32.1.3
Length = 357
Score = 30.5 bits (68), Expect = 1.1
Identities = 11/99 (11%), Positives = 30/99 (30%), Gaps = 7/99 (7%)
Query: 166 VPLTVEHIVLSCRKMRFRPNSFLNSTLSDVLKDDPDSVATLMRFLKRNNFPKELYRRSGL 225
V + +V + ++ F+ + + + + + L S +
Sbjct: 241 VAFLTDDLVKTWDALKKIGMRFMTAPPDTYYEMLEGRLPDHGEPVDQLQARGILLDGSSV 300
Query: 226 YPGSPGFYRGEDLKRVQSVMY------RGYEGVGAPNFR 258
G + + ++ +G +G G NF+
Sbjct: 301 -EGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFK 338
>3g9k_L Capsule biosynthesis protein CAPD; CAPD protein, the great lakes
regional C excellence, GLRCE, capsule
biogenesis/degradation; HET: GLU; 1.79A {Bacillus
anthracis} PDB: 3ga9_L*
Length = 323
Score = 28.3 bits (64), Expect = 4.6
Identities = 12/49 (24%), Positives = 17/49 (34%), Gaps = 21/49 (42%)
Query: 228 GSPGFYRGE--------------DLKRVQSVM-------YRGYEGVGAP 255
G+ GFY G D+K + + Y GY+ AP
Sbjct: 189 GAKGFYEGGVARAISKTAKISLEDIKGYKVEVRKPVKGNYMGYDVYTAP 237
>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO
enzyme, structural genomics, protein structure
initiative; NMR {Desulfitobacterium hafniense dcb-2}
PDB: 2kw4_A
Length = 147
Score = 27.3 bits (61), Expect = 5.5
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 53 HVGIAGNEAADREAKSTLGSP 73
H G N+ D +AKS LG
Sbjct: 118 HSGNEFNDYVDMKAKSALGIR 138
>3gms_A Putative NADPH:quinone reductase; structural genomics, putative
quinone oxidoreductase, unknown function, PSI-2; 1.76A
{Bacillus thuringiensis}
Length = 340
Score = 27.9 bits (63), Expect = 6.3
Identities = 4/19 (21%), Positives = 6/19 (31%), Gaps = 1/19 (5%)
Query: 214 NFPKELYRRSGLYPGSPGF 232
N +L +G Y
Sbjct: 45 NPS-DLIPITGAYAHRIPL 62
>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of
RNA/DNA hybrid; 1.40A {Uncultured organism}
Length = 140
Score = 26.7 bits (60), Expect = 7.5
Identities = 4/19 (21%), Positives = 7/19 (36%)
Query: 48 KVSYNHVGIAGNEAADREA 66
+ + H+ N AD
Sbjct: 113 NLVFVHIPREKNARADELV 131
>1yb5_A Quinone oxidoreductase; medium-chain dehydrogenase/reductase,
quinon reduction, structural genomics, structural
genomics consort; HET: NAP; 1.85A {Homo sapiens} SCOP:
b.35.1.2 c.2.1.1
Length = 351
Score = 27.5 bits (62), Expect = 8.1
Identities = 8/19 (42%), Positives = 8/19 (42%), Gaps = 1/19 (5%)
Query: 214 NFPKELYRRSGLYPGSPGF 232
N E Y RSG Y P
Sbjct: 70 NPV-ETYIRSGTYSRKPLL 87
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 0.137 0.425
Gapped
Lambda K H
0.267 0.0810 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,338,273
Number of extensions: 366411
Number of successful extensions: 648
Number of sequences better than 10.0: 1
Number of HSP's gapped: 643
Number of HSP's successfully gapped: 13
Length of query: 412
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 316
Effective length of database: 4,021,377
Effective search space: 1270755132
Effective search space used: 1270755132
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 (22.0 bits)
S2: 58 (26.0 bits)