RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 041105
(403 letters)
>1m22_A Peptide amidase, PAM; eleven-stranded beta sheet, covered double
layers of alpha helices on TOP and bottom, hydrolase;
HET: EPE; 1.40A {Stenotrophomonas maltophilia} SCOP:
c.117.1.1 PDB: 1m21_A*
Length = 503
Score = 476 bits (1228), Expect = e-167
Identities = 161/375 (42%), Positives = 226/375 (60%), Gaps = 18/375 (4%)
Query: 31 TESREFSVKEATIEDLQLAFKQNQLTSRQLVEMYIREIGRLN---PLLRGVIEVNPDAIN 87
+ + F E + DLQ +L S L + Y++ I L+ P LR VIE+NPDA+
Sbjct: 1 SRNVPFPYAETDVADLQARMTAGELDSTTLTQAYLQRIAALDRTGPRLRAVIELNPDALK 60
Query: 88 QADKADQERKAKAPRSQLGLHGIPILVKDNIATKDKMNTTAGSFALLGSVVPRDAFVVTK 147
+A + D+ER+ R LHGIP+L+KDNI M T+AGS AL G P DA++V +
Sbjct: 61 EAAERDRERRDGRLRG--PLHGIPLLLKDNINAAP-MATSAGSLALQG-FRPDDAYLVRR 116
Query: 148 LLEAGAIILGKASMSEWAHFRTFESPNGWCARTGQGKNPYVLSADPCGSSSGSAISVAAN 207
L +AGA++LGK ++SEWA+FR +S +GW AR GQ +NPY +S PCGSSSGSA++VAAN
Sbjct: 117 LRDAGAVVLGKTNLSEWANFRGNDSISGWSARGGQTRNPYRISHSPCGSSSGSAVAVAAN 176
Query: 208 MVAVSLGTDTDASILCPSGSNSVVGIKPTVGLISRDGVIPVSPRLDTVGPISKTVADTVY 267
+ +V++GT+TD SI+CP+ N VVG+KPTVGL+SRDG+IP+S DT GP++++VAD
Sbjct: 177 LASVAIGTETDGSIVCPAAINGVVGLKPTVGLVSRDGIIPISFSQDTAGPMARSVADAAA 236
Query: 268 VLDAIVGFDAKDEATREASKYIPPGGYKQFLKPHGLQGKRLGIVRNLGSNFTISSEVTEA 327
VL AI G D D AT Y L P GL+GKR+G+++ +
Sbjct: 237 VLTAIAGRDDADPATATMPGRAVY-DYTARLDPQGLRGKRIGLLQTP---LLKYRGMPPL 292
Query: 328 FEHHVRTLRQQGAILLDNFEINNLEAILNSIANGETLAILAAEFKQALNAYLQELVTSPV 387
E LR+ GA+++ E+ N A + E +L EFK L Y +P+
Sbjct: 293 IEQAATELRRAGAVVVP-VELPNQGAWAEA----ERT-LLLYEFKAGLERYFNTH-RAPL 345
Query: 388 RSLADVIAFNKMFPE 402
RSLAD+IAFN+ +
Sbjct: 346 RSLADLIAFNQAHSK 360
>1o9p_A Malonamidase E2; malonate; 1.8A {Bradyrhizobium japonicum} SCOP:
c.117.1.1 PDB: 1o9o_A 1obl_A 1och_A 1obk_A 1obi_A
1o9q_A* 1obj_A 1o9n_A 1ock_A 1ocl_A 1ocm_A
Length = 414
Score = 227 bits (581), Expect = 7e-71
Identities = 71/303 (23%), Positives = 112/303 (36%), Gaps = 46/303 (15%)
Query: 42 TIEDLQLAFKQNQLTSRQLVEMYIREIGRLNPLLRGVIEVNPDAINQADKADQERKAKAP 101
++ DLQ + +L+ + I + + + A +A P
Sbjct: 3 SLADLQRRIETGELSPNAAIAQSHAAIEAREKEVHAFVRHDKSA---------RAQASGP 53
Query: 102 RSQLGLHGIPILVKDNIATKDKMNTTAGSFALLGSVVPRDAFVVTKLLEAGAIILGKASM 161
L GI + +KD I T + M T GS G DA VV L AGA I+GK +
Sbjct: 54 -----LRGIAVGIKDIIDTAN-MPTEMGSEIYRGWQPRSDAPVVMMLKRAGATIIGKTTT 107
Query: 162 SEWAHFRTFESPNGWCARTGQGKNPYVLSADPCGSSSGSAISVAANMVAVSLGTDTDASI 221
+ +A NP+ P G+SSGSA +V A M+ ++LGT T S+
Sbjct: 108 TAFASRDP-----------TATLNPHNTGHSPGGASSGSAAAVGAGMIPLALGTQTGGSV 156
Query: 222 LCPSGSNSVVGIKPTVGLISRDGVIPVSPRLDTVGPISKTVADTVYVLDAIVGFDAKDEA 281
+ P+ IKP+ ++ GV S LDTVG D L A+ G
Sbjct: 157 IRPAAYCGTAAIKPSFRMLPTVGVKCYSWALDTVGLFGARAEDLARGLLAMTGRSEFSGI 216
Query: 282 TREASKYIPPGGYKQFLKPHGLQGKRLGIVRNLGSNFTISSEVTEAFEHHVRTLRQQGAI 341
+ R+G+VR + + + + ++ + GA
Sbjct: 217 V-------------------PAKAPRIGVVRQEFAG-AVEPAAEQGLQAAIKAAERAGAS 256
Query: 342 LLD 344
+
Sbjct: 257 VQA 259
>2dc0_A Probable amidase; structural genomics, NPPSFA, national project on
protein structural and functional analyses; 2.00A
{Thermus thermophilus}
Length = 434
Score = 224 bits (574), Expect = 2e-69
Identities = 83/304 (27%), Positives = 133/304 (43%), Gaps = 33/304 (10%)
Query: 42 TIEDLQLAFKQNQLTSRQLVEMYIREIGRLNPLLRGVIEVNPD-AINQADKADQERKAKA 100
+ + + + + T L+E + + ++ + A +A +E +
Sbjct: 2 DLLEAKRLLETGRTTPLALLEEALERAKAFQDR-NALAYLDEEAARKEALALTEELRRGQ 60
Query: 101 PRSQLGLHGIPILVKDNIATKDKMNTTAGSFALLGSVVPRDAFVVTKLLEAGAIILGKAS 160
R LHG+P+ VKD K M T AG+ +P +A V +L EAGA++ K +
Sbjct: 61 VRG--PLHGLPLTVKDLFPVKG-MPTRAGT-KAPLPPLPEEARAVRRLREAGALLFAKTN 116
Query: 161 MSEWAHFRTFESPNGWCARTGQGKNPYVLSADPCGSSSGSAISVAANMVAVSLGTDTDAS 220
M E A T E+P TG +N S GSS GSA++VA + SLGTDT S
Sbjct: 117 MHEIALGITGENPW-----TGPVRNAVDPSRQAGGSSGGSAVAVALGIGLASLGTDTGGS 171
Query: 221 ILCPSGSNSVVGIKPTVGLISRDGVIPVSPRLDTVGPISKTVADTVYVLDAIVGFDAKDE 280
I P+G N VVG KP+ G +S +G +P+S D GP++++V D ++ + + G E
Sbjct: 172 IRIPAGFNGVVGFKPSYGRVSLEGALPLSRSTDHAGPLTRSVRDAHFLTEILAGESIPLE 231
Query: 281 ATREASKYIPPGGYKQFLKPHGLQGKRLGIVRNLGSNFTISSEVTEAFEHHVRTLRQQGA 340
G+Q G+ + + EV +AF + L A
Sbjct: 232 ---------------------GVQNPVFGVPLDFLEG-RLGVEVRKAFTRLLEDLPALRA 269
Query: 341 ILLD 344
+ +
Sbjct: 270 EVRE 273
>3kfu_E Glutamyl-tRNA(Gln) amidotransferase subunit A; ASPRS, gatcab,
ATP-binding, aminoacyl-tRNA synthetase, ligas
nucleotide-binding, protein biosynthesis, ligase-RNA
comple; HET: H2U 5MU PSU; 3.00A {Thermus thermophilus}
Length = 471
Score = 218 bits (559), Expect = 7e-67
Identities = 91/311 (29%), Positives = 154/311 (49%), Gaps = 39/311 (12%)
Query: 42 TIEDLQLAFKQNQLTSRQLVEMYIREIGRLNPLLRGVIEVNPDAINQADKADQERKAKAP 101
+++ + +++ ++ + Y++ + L+P L + +N + +A+ D
Sbjct: 2 LAHEIRARVARGEVSPLEVAQAYLKRVQELDPGLGAFLSLNERLLEEAEAVDPGLP---- 57
Query: 102 RSQLGLHGIPILVKDNIATKDKMNTTAGSFALLGSVVPRDAFVVTKLLEAGAIILGKASM 161
L G+ + VKDNIAT+ + TTAGS L V P +A V +L GA++LGK ++
Sbjct: 58 -----LAGLVVAVKDNIATRG-LRTTAGSRLLENFVPPYEATAVARLKALGALVLGKTNL 111
Query: 162 SEWA--------HFRTFESPNGWCARTGQGKNPYVLSADPCGSSSGSAISVAANMVAVSL 213
E+ F KNP+ P GSS GSA ++AA++ ++L
Sbjct: 112 DEFGMGSSTEHSAF-------------FPTKNPFDPDRVPGGSSGGSAAALAADLAPLAL 158
Query: 214 GTDTDASILCPSGSNSVVGIKPTVGLISRDGVIPVSPRLDTVGPISKTVADTVYVLDAIV 273
G+DT S+ P+ V G+KPT G +SR G+I + LD +GP++++V D ++DA
Sbjct: 159 GSDTGGSVRQPAAFCGVYGLKPTYGRVSRFGLIAYASSLDQIGPMARSVRDLALLMDAAA 218
Query: 274 GFDAKDEATREASKYIPPGGYKQFLKPHGLQGKRLGIVRNLGSNFTISSEVTEAFEHHVR 333
G D D AT S +PP +++ L+ L RLG+VR + S V A E ++
Sbjct: 219 GPDPLD-AT---SLDLPP-RFQEALEG-PLPPLRLGVVREALAG--NSPGVERALEEALK 270
Query: 334 TLRQQGAILLD 344
R+ G + +
Sbjct: 271 VFRELGLSVRE 281
>3ip4_A Glutamyl-tRNA(Gln) amidotransferase subunit A; multi protein
complex, ligase, ATP-binding, nucleotide-bindi protein
biosynthesis; 1.90A {Staphylococcus aureus subsp} PDB:
2df4_A 2dqn_A* 2g5h_A 2g5i_A* 2f2a_A
Length = 485
Score = 218 bits (559), Expect = 8e-67
Identities = 92/317 (29%), Positives = 162/317 (51%), Gaps = 31/317 (9%)
Query: 37 SVKEATIEDLQLAFKQNQLTSRQLVEMYIREIGRLNPLLRGVIEVNPD-AINQADKADQE 95
S++ ++E+L K ++ +V+ I +P ++ + ++ + AI +A + D+
Sbjct: 2 SIRYESVENLLTLIKDKKIKPSDVVKDIYDAIEETDPTIKSFLALDKENAIKKAQELDEL 61
Query: 96 RKAKAPRSQLGLHGIPILVKDNIATKDKMNTTAGSFALLGSVVPRDAFVVTKLLEAGAII 155
+ +L GIP+ +KDNI T + TT S L G V ++ V+ KL + A++
Sbjct: 62 QAKDQMDGKLF--GIPMGIKDNIITNG-LETTCASKMLEGFVPIYESTVMEKLHKENAVL 118
Query: 156 LGKASMSEWA--------HFRTFESPNGWCARTGQGKNPYVLSADPCGSSSGSAISVAAN 207
+GK +M E+A +F + NP+ A P GSS GSA +VAA
Sbjct: 119 IGKLNMDEFAMGGSTETSYF-------------KKTVNPFDHKAVPGGSSGGSAAAVAAG 165
Query: 208 MVAVSLGTDTDASILCPSGSNSVVGIKPTVGLISRDGVIPVSPRLDTVGPISKTVADTVY 267
+V +SLG+DT SI P+ VVG+KPT G +SR G++ + LD +GP+++ V D
Sbjct: 166 LVPLSLGSDTGGSIRQPAAYCGVVGMKPTYGRVSRFGLVAFASSLDQIGPLTRNVKDNAI 225
Query: 268 VLDAIVGFDAKDEATREASKYIPPGGYKQFLKPHGLQGKRLGIVRNLGSNFTISSEVTEA 327
VL+AI G D D +T S + + + ++G ++ + + ++ +V EA
Sbjct: 226 VLEAISGADVND-ST---SAPVDDVDFTSEIGK-DIKGLKVALPKEYLGE-GVADDVKEA 279
Query: 328 FEHHVRTLRQQGAILLD 344
++ V TL+ GA++ +
Sbjct: 280 VQNAVETLKSLGAVVEE 296
>3h0l_A Glutamyl-tRNA(Gln) amidotransferase subunit A; multi protein
complex, ligase, protein biosynthesis; HET: ADP; 2.30A
{Aquifex aeolicus} PDB: 3h0m_A 3h0r_A*
Length = 478
Score = 217 bits (554), Expect = 4e-66
Identities = 94/314 (29%), Positives = 154/314 (49%), Gaps = 37/314 (11%)
Query: 40 EATIEDLQLAFKQNQLTSRQLVEMYIREIGRLNPLLRGVIEVNPD-AINQADKADQERKA 98
+ ++ +L+ K+ +++ +++VE + + ++ I A+ QA+ +
Sbjct: 4 KKSLSELRELLKRGEVSPKEVVESFYDRYNQTEEKVKAYITPLYGKALKQAESLKERELP 63
Query: 99 KAPRSQLGLHGIPILVKDNIATKDKMNTTAGSFALLGSVVPRDAFVVTKLLEAGAIILGK 158
L GIPI VKDNI + TT S L V P DA V+ +L +AGA+I+GK
Sbjct: 64 --------LFGIPIAVKDNILVEG-EKTTCASKILENFVAPYDATVIERLKKAGALIVGK 114
Query: 159 ASMSEWA--------HFRTFESPNGWCARTGQGKNPYVLSADPCGSSSGSAISVAANMVA 210
++ E+A F KNP+ L P GSS GSA SVA
Sbjct: 115 TNLDEFAMGSSTEYSAF-------------FPTKNPWDLERVPGGSSGGSAASVAVLSAP 161
Query: 211 VSLGTDTDASILCPSGSNSVVGIKPTVGLISRDGVIPVSPRLDTVGPISKTVADTVYVLD 270
VSLG+DT SI P+ V+GIKPT G +SR G++ + LD +G + D VL+
Sbjct: 162 VSLGSDTGGSIRQPASFCGVIGIKPTYGRVSRYGLVAFASSLDQIGVFGRRTEDVALVLE 221
Query: 271 AIVGFDAKDEATREASKYIPPGGYKQFLKPHGLQGKRLGIVRNLGSNFTISSEVTEAFEH 330
I G+D KD +T S +P + + +K ++G ++G+ + + +V EAFE+
Sbjct: 222 VISGWDEKD-ST---SAKVPVPEWSEEVKK-EVKGLKIGLPKEFFEY-ELQPQVKEAFEN 275
Query: 331 HVRTLRQQGAILLD 344
++ L ++G + +
Sbjct: 276 FIKELEKEGFEIKE 289
>3a1k_A Amidase; AS family enzyme, hydrolase; 2.17A {Rhodococcus SP} PDB:
3a1i_A
Length = 521
Score = 201 bits (513), Expect = 8e-60
Identities = 80/305 (26%), Positives = 120/305 (39%), Gaps = 15/305 (4%)
Query: 45 DLQLAFKQNQLTSRQLVEMYIREIGRLNPLLRGVIEVNPDAINQADKADQERKAKAPRSQ 104
L + + +L + + + + S
Sbjct: 21 TLDKTARLEWPALIDGALGSYDVVDQLYADEATPPTTSREHAVPSASENPLSAWYVTTSI 80
Query: 105 LG-----LHGIPILVKDNIATKDKMNTTAGSFALLGSVVPRDAFVVTKLLEAGAIILGKA 159
L G + +KDN+ + GS + G RDA VVT+LL AGA + GKA
Sbjct: 81 PPTSDGVLTGRRVAIKDNVTVAG-VPMMNGSRTVEGFTPSRDATVVTRLLAAGATVAGKA 139
Query: 160 SMSEWAHFRTFESPNGWCARTGQGKNPYVLSADPCGSSSGSAISVAANMVAVSLGTDTDA 219
+ F + A +G +NP+ + GSS GSA VA V ++G D
Sbjct: 140 VCEDLC----FSGSSFTPA-SGPVRNPWDRQREAGGSSGGSAALVANGDVDFAIGGDQGG 194
Query: 220 SILCPSGSNSVVGIKPTVGLISRDGVIPVSPRLDTVGPISKTVADTVYVLDAIVGFDAKD 279
SI P+ VVG KPT GL+ G P+ +D +GPI++TV D +L I G D D
Sbjct: 195 SIRIPAAFCGVVGHKPTFGLVPYTGAFPIERTIDHLGPITRTVHDAALMLSVIAGRDGND 254
Query: 280 EATREASKYIPPGGYKQFLKPHGLQGKRLGIVRNLGSNFTISSEVTEAFEHHVRTLRQQG 339
+ + G Y L + G R+GIVR + EV +A +L + G
Sbjct: 255 -PR--QADSVEAGDYLSTLDS-DVDGLRIGIVREGFGHAVSQPEVDDAVRAAAHSLTEIG 310
Query: 340 AILLD 344
+ +
Sbjct: 311 CTVEE 315
>2gi3_A Glutamyl-tRNA(Gln) amidotransferase subunit A; TM1272, structural
genomics, joint center for structura genomics, JCSG;
HET: MSE MPD; 1.80A {Thermotoga maritima} SCOP:
c.117.1.1 PDB: 3al0_A*
Length = 476
Score = 198 bits (505), Expect = 5e-59
Identities = 92/314 (29%), Positives = 148/314 (47%), Gaps = 45/314 (14%)
Query: 40 EATIEDLQLAFKQNQLTSRQLVEMYIREIGRLNPLLRGVIEVNPD-AINQADKADQERKA 98
+ ++ K ++ +L ++ + I RL+P ++ I V + ++ + K
Sbjct: 6 DFRKLTIEECLKLSEEEREKLPQLSLETIKRLDPHVKAFISVRENVSVEKKGK------- 58
Query: 99 KAPRSQLGLHGIPILVKDNIATKDKMNTTAGSFALLGSVVPRDAFVVTKLLEAGAIILGK 158
GIP+ +KDNI T M TT S L DA VV K+ EAG +++GK
Sbjct: 59 --------FWGIPVAIKDNILTLG-MRTTCASRILENYESVFDATVVKKMKEAGFVVVGK 109
Query: 159 ASMSEWA--------HFRTFESPNGWCARTGQGKNPYVLSADPCGSSSGSAISVAANMVA 210
A++ E+A F +NP+ L P GSS GSA +V+A MV
Sbjct: 110 ANLDEFAMGSSTERSAF-------------FPTRNPWDLERVPGGSSGGSAAAVSAGMVV 156
Query: 211 VSLGTDTDASILCPSGSNSVVGIKPTVGLISRDGVIPVSPRLDTVGPISKTVADTVYVLD 270
+LG+DT S+ P+ VVG KPT GL+SR G++ + LD +GPI+KTV D +++
Sbjct: 157 AALGSDTGGSVRQPASLCGVVGYKPTYGLVSRYGLVAFASSLDQIGPITKTVRDAAILME 216
Query: 271 AIVGFDAKDEATREASKYIPPGGYKQFLKPHGLQGKRLGIVRNLGSNFTISSEVTEAFEH 330
I G D D AT + + ++ G+ G + + + + I V+E FE
Sbjct: 217 IISGRDEND-AT---TVNRKV-DFLSEIEE-GVSGMKFAVPEEIYEH-DIEEGVSERFEE 269
Query: 331 HVRTLRQQGAILLD 344
++ L + GA +
Sbjct: 270 ALKLLERLGAKVER 283
>3a2q_A 6-aminohexanoate-cyclic-dimer hydrolase; alpha/beta fold, nylon
degradation; 1.80A {Arthrobacter SP} PDB: 3a2p_A
Length = 493
Score = 195 bits (497), Expect = 1e-57
Identities = 73/358 (20%), Positives = 129/358 (36%), Gaps = 32/358 (8%)
Query: 49 AFKQNQLTSRQLVEMYIREIGRLNPLLRGVIEVNPD-AINQADKADQERKAKAPRSQLGL 107
+ +++ +L+E I + +NP + VI + A +++ A P
Sbjct: 16 LVRSGEISRTELLEATIAHVQAVNPEINAVIIPLFEKARRESELAS------GP-----F 64
Query: 108 HGIPILVKDNIATKDKMNTTAGS--FALLGSVVPRDAFVVTKLLEAGAIILGKASMSEWA 165
G+P L+KD T+ G DA+ V ++ AG ++LGK + E
Sbjct: 65 AGVPYLLKDLTVVSQGDINTSSIKGMKESGYRADHDAYFVQRMRAAGFVLLGKTNTPEMG 124
Query: 166 HFRTFESPNGWCARTGQGKNPYVLSADPCGSSSGSAISVAANMVAVSLGTDTDASILCPS 225
+ T E G +NP+ L GSS GS +VAA + V+ G D ++ P+
Sbjct: 125 NQVTTEPE-----AWGATRNPWNLGRSVGGSSGGSGAAVAAALSPVAHGNDAAGAVRIPA 179
Query: 226 GSNSVVGIKPTVGLISRDGVIPVSPR---LDTVGPISKTVADTVYVLDAIVGFDAKDEAT 282
VVG+KPT G IS ++ S G +++V D +LD + G D
Sbjct: 180 SVCGVVGLKPTRGRISPGPLVTDSDNVAGAAHEGLFARSVRDIAALLDVVSGHRPGDTFC 239
Query: 283 REASKYIPPGGYKQFLKPHGLQGKRLGIV-RNLGSNFTISSEVTEAFEHHVRTLRQQGAI 341
Y Q + R+G++ N +F + E A L G
Sbjct: 240 APT----ASRPYAQGISE-NPGSLRVGVLTHNPVGDFALDPECAAAARGAAAALAALGHD 294
Query: 342 L----LDNFEINNLEAILNSIANGETLAILAAEFKQALNAYLQELVTSPVRSLADVIA 395
+ + + ++I + + + ++ V +
Sbjct: 295 VNDAYPEALGDRSFLKDYSTICDVAIAREIERNGELIGRPLTEDDVEWTSWEMVKRAD 352
>3ppm_A Fatty-acid amide hydrolase 1; protein-inhibitor complex, FAAH,
oxazole, oxadiazole, endoca degradation, membrane
protein; HET: JG1 1DO; 1.78A {Rattus norvegicus} PDB:
2wj2_A* 3k7f_A* 3k83_A* 3k84_A* 3lj6_A* 3lj7_A 3oj8_A*
2wj1_A* 3pr0_A* 2wap_A* 1mt5_A* 2vya_A* 3qk5_A* 3qj8_A*
3qj9_A* 3qkv_A*
Length = 573
Score = 178 bits (453), Expect = 9e-51
Identities = 74/393 (18%), Positives = 143/393 (36%), Gaps = 27/393 (6%)
Query: 10 IPIFSSLPLIILAVYSSGSPATESREFSVKEATIEDLQLAFKQNQLTSRQLVEMYIREIG 69
+SL + AV + ++ + L + +L+ + Y+ +
Sbjct: 40 QKQRASLETMDKAVQRFRLQNPDLDSEALLTLPLLQLVQKLQSGELSPEAVFFTYLGKAW 99
Query: 70 RLNPLLRGVIEVNPDAINQADKADQERKAKAPRSQLGLHGIPILVKDNIATKDKMNTTAG 129
+N V D + + ++APR L L+G+P+ +K+ + K ++T G
Sbjct: 100 EVNKGTNCVTSYLTDC--------ETQLSQAPRQGL-LYGVPVSLKECFSYKG-HDSTLG 149
Query: 130 SFALLGSVVPRDAFVVTKLLEAGAIILGKASMSEWAHFRTFESPNGWCARTGQGKNPYVL 189
G D VV L GA+ ++ + +++ N +T NP+
Sbjct: 150 LSLNEGMPSESDCVVVQVLKLQGAVPFVHTNVPQSM--FSYDCSNPLFGQT---MNPWKS 204
Query: 190 SADPCGSSSGSAISVAANMVAVSLGTDTDASILCPSGSNSVVGIKPTVGLISRDGVIPVS 249
S P GSS G + + + LGTD SI PS + G+KPT +S+ G+
Sbjct: 205 SKSPGGSSGGEGALIGSGGSPLGLGTDIGGSIRFPSAFCGICGLKPTGNRLSKSGLKGCV 264
Query: 250 PR----LDTVGPISKTVADTVYVLDAIVGFDAKDEATREASKYIPPGGYKQFLKPHGLQG 305
++GP+++ V L A++ +PP +++ + +
Sbjct: 265 YGQTAVQLSLGPMARDVESLALCLKALLCEHL-----FTLDPTVPPLPFREEVYR-SSRP 318
Query: 306 KRLGIVRNLGSNFTISSEVTEAFEHHVRTLRQQGAILLDNFEINNLEAILNSIANGETLA 365
R+G S + A + L G L+ F NN+ L ++ G +
Sbjct: 319 LRVGYYETDNY-TMPSPAMRRALIETKQRLEAAGHTLIP-FLPNNIPYALEVLSTGGLFS 376
Query: 366 ILAAEFKQALNAYLQELVTSPVRSLADVIAFNK 398
F Q + + + + ++ K
Sbjct: 377 DGGRSFLQNFKGDFVDPCLGDLILILRLPSWFK 409
>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 = 57.4 bits (138), Expect = 5e-09
Identities = 68/388 (17%), Positives = 117/388 (30%), Gaps = 102/388 (26%)
Query: 40 EATIEDLQLAFKQNQLTSRQLVEMYIREIG-RLNPLLRGVIEVNP------DAI----NQ 88
+ E+L+ ++ T LV I+ L+ L+R ++ + + N
Sbjct: 167 DDYFEELRDLYQ----TYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENP 222
Query: 89 ADKADQERKAKAPRSQLGLHGIPILVKDNIATKDKMNTTAGSF-ALLGSVVPRDAFVVTK 147
++ D++ P S L G+ L + K + T G + L +VT
Sbjct: 223 SNTPDKDYLLSIPIS-CPLIGVIQLAHYVVTAK-LLGFTPGELRSYLKGATGHSQGLVT- 279
Query: 148 LLEAGAIILGKASMSEWAHFRT---------FESPNGWC-ARTGQGKNPYVLSADPCGSS 197
A AI A W F F + R + L S
Sbjct: 280 ---AVAI----AETDSWESFFVSVRKAITVLF-----FIGVRCYEAYPNTSLPPSILEDS 327
Query: 198 SGSAISVAANMVAVSLGTDTDASILC---------PSGSNSVVGIKPTVGLI-SRDGVIP 247
+ V + M+++S T + P+ V I L+ ++
Sbjct: 328 LENNEGVPSPMLSIS-NL-TQEQVQDYVNKTNSHLPA--GKQVEI----SLVNGAKNLV- 378
Query: 248 VSPRLDTVGPISKTVADTVYVLDAIVGFDAKDEATREASKYIPPGGYKQFLKPHGLQGKR 307
VS GP ++Y L+ + R+A P G Q P + K
Sbjct: 379 VS------GP-----PQSLYGLNLTL---------RKAKA---PSGLDQSRIPFS-ERKL 414
Query: 308 LGIVRNLGSNFTISSEVTEAFEHHVRTLRQQGAILLDNFEINNLEAILNSIANGETLAIL 367
R L V F H L ++ + NN+ N + + I
Sbjct: 415 KFSNRFL--------PVASPF--HSHLLVPASDLINKDLVKNNVSF------NAKDIQIP 458
Query: 368 AAEFKQALNAYLQELVTSPVRSLADVIA 395
+ + L+ L S + D I
Sbjct: 459 VYDTFDGSD--LRVLSGSISERIVDCII 484
Score = 44.7 bits (105), Expect = 5e-05
Identities = 63/382 (16%), Positives = 118/382 (30%), Gaps = 127/382 (33%)
Query: 8 LNIPIFSSLPLIIL---AVY-----SSGSPATESREFSVKEAT--IEDLQLA-------- 49
L+IPI S PLI + A Y G E R +K AT + L A
Sbjct: 232 LSIPI--SCPLIGVIQLAHYVVTAKLLGFTPGELRS-YLKGATGHSQGLVTAVAIAETDS 288
Query: 50 ---FKQNQLTSRQLVEMYIREIGRLNPLLRG-----VIEVNPDAINQADKADQERKAKAP 101
F + R+ + + IG +R + P + + + ++ P
Sbjct: 289 WESFFVS---VRKAITVLFF-IG-----VRCYEAYPNTSLPPSILEDSLENNE----GVP 335
Query: 102 RSQLGLHGIPI-LVKDNIATKDKMNTTAG-----SFALLGSVVPRDAFVVT---KLLEAG 152
L + + V+D + +K N+ +L+ VV+ + L
Sbjct: 336 SPMLSISNLTQEQVQDYV---NKTNSHLPAGKQVEISLVNG---AKNLVVSGPPQSLYGL 389
Query: 153 AIILGKASMSEWAHFRTFESPNGWCARTGQGKNPYVLSA-DPCGSSSGSAISV------- 204
+ R ++P+G Q + P+ S S+ ++
Sbjct: 390 NL-----------TLRKAKAPSG----LDQSRIPF--SERKLKFSNRFLPVASPFHSHLL 432
Query: 205 --AANMVAVSLGTDT---DASIL-CP-----SGSNSVVGIKPTVGLISRDGVIPVSPRLD 253
A++++ L + +A + P GS+ ++ G IS V
Sbjct: 433 VPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSD----LRVLSGSISERIV-----DCI 483
Query: 254 TVGPI---SKTVADTVYVLDAIVGFDAKDEATREASKYIPPGGYKQF--LKPHGLQGKRL 308
P+ + T ++LD F PGG L G +
Sbjct: 484 IRLPVKWETTTQFKATHILD----FG--------------PGGASGLGVLTHRNKDGTGV 525
Query: 309 GIVRNLGSNFTISSEVTEAFEH 330
++ + I+ + F+
Sbjct: 526 RVI--VAGTLDINPDDDYGFKQ 545
Score = 42.3 bits (99), Expect = 3e-04
Identities = 49/325 (15%), Positives = 87/325 (26%), Gaps = 112/325 (34%)
Query: 90 DKADQERKAKAPRSQLGLHGIPILVKDNIATKDKMNTTAGSFAL------LGSVVPRDAF 143
++AD + G I +V +N + + D
Sbjct: 1647 NRAD-----NHFKDTYGF-SILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGK 1700
Query: 144 VVTKLLEAGAIILGKASMSEWAHFRTFESPNGWCARTG--QGKNPYVLSADPCGSSSGSA 201
+ T+ + +E + TF S G + T Q P +
Sbjct: 1701 LKTEKIFKEI--------NEHSTSYTFRSEKGLLSATQFTQ---PALT-----------L 1738
Query: 202 ISVAANMVAVSLGTDTDASILCPSG-SNSVVGIKPTVG----LISRDGVIPVSPRLDTVG 256
+ AA S G + G S +G L S V+ +
Sbjct: 1739 MEKAAFEDLKSKGLIPADATFA--GHS---------LGEYAALASLADVMSIE------- 1780
Query: 257 PISKTVADTVYVLDAIVGFDAKDEATREASKYIPPGGYKQFLKPHGLQGK-RLGIVRNLG 315
V V+ R G Q P G+ G++
Sbjct: 1781 -------SLVEVV-----------FYR--------GMTMQVAVPRDELGRSNYGMIAINP 1814
Query: 316 SNFTISSEVTEAFEHHVRTL-RQQGAILLDNFEINNLEAILNSIANGETLAILAAEFKQA 374
S EA ++ V + ++ G ++ EI N N + A + +A
Sbjct: 1815 GRVAASFS-QEALQYVVERVGKRTGWLV----EIVN----YNV--ENQQYVA-AGD-LRA 1861
Query: 375 LNAYLQELVTSPVRSLADVIAFNKM 399
L+ + +V+ F K+
Sbjct: 1862 LDT------------VTNVLNFIKL 1874
Score = 27.7 bits (61), Expect = 8.1
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 20/70 (28%)
Query: 35 EFS--VKEA---TIED-LQLAFKQNQLTSR-QLVEMYI--REIGRLNPLLRGVIEVNPDA 85
E++ A +IE +++ F R +++ + E+GR N G+I +NP
Sbjct: 1766 EYAALASLADVMSIESLVEVVFY------RGMTMQVAVPRDELGRSNY---GMIAINPGR 1816
Query: 86 INQADKADQE 95
+ A QE
Sbjct: 1817 V--AASFSQE 1824
>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 = 51.4 bits (122), Expect = 3e-07
Identities = 51/403 (12%), Positives = 119/403 (29%), Gaps = 130/403 (32%)
Query: 34 REFSVKEATIEDLQLAFKQNQLTSRQLVEMYIREIGRLNPLLR--GVIEVNPDAI----- 86
F K+ ++D ++ L+ + ++ I ++ LR + + +
Sbjct: 31 DNFDCKD--VQD----MPKSILSKEE-IDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFV 83
Query: 87 NQADKAD----QERKAKAPRSQLGLHGIPILVKDN-IATKDKMNTTAGSFALLGSVVPRD 141
+ + + R P ++ I +D++ FA V R
Sbjct: 84 EEVLRINYKFLMSPIKTEQRQ-------PSMMTRMYIEQRDRLYNDNQVFAKYN--VSRL 134
Query: 142 AFVV---TKLLE---AGAIIL-GKASMSEWAHFRTFESPNGWCARTGQGKNPYVLSADPC 194
+ LLE A +++ G + G GK ++ D C
Sbjct: 135 QPYLKLRQALLELRPAKNVLIDG---V------------------LGSGKT--WVALDVC 171
Query: 195 GSSSGSAISVAANMVA-VSLGT-DTDASILCPSGSNSVVGIKPTVGLISRDGVIPVSPRL 252
S + ++L ++ ++L + L+ + + P
Sbjct: 172 --LSYKVQCKMDFKIFWLNLKNCNSPETVL-----------EMLQKLLYQ-----IDPNW 213
Query: 253 DTVGPISKTVADTVYVLDAIVGFDAKDEATREASKYIPPGGYKQFLKPHGLQGKR-LGIV 311
+ S + ++ + E R KP+ + L ++
Sbjct: 214 TSRSDHSSNIKLRIH--------SIQAELRR-----------LLKSKPY----ENCLLVL 250
Query: 312 RNLGSNFTISSEVTEAFEHHVRTL---RQQGAI-LLDNFEINN--LEAILNSIANGETLA 365
N+ + ++ AF + L R + L + L+ ++ E +
Sbjct: 251 LNVQN-----AKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS 305
Query: 366 ILAAEFKQALNAYLQEL-----VTSPVRSLADVIAFNKMFPEL 403
+L + L+ Q+L T+P ++ + E
Sbjct: 306 LLL----KYLDCRPQDLPREVLTTNPR-----RLS---IIAES 336
Score = 40.6 bits (94), Expect = 8e-04
Identities = 52/406 (12%), Positives = 106/406 (26%), Gaps = 130/406 (32%)
Query: 32 ESREFSVKEATIEDLQLAFK------QNQLTSRQLV-EMYIREIGRLNPLLRGVIEVNPD 84
+E V++ E L++ +K + + ++ MYI + + L
Sbjct: 73 SKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQ---RDRLYNDNQVFAKY 129
Query: 85 AINQADKADQERKA--KA-PRSQLGLHGIPILVKDNIATKDKMNTTAGSFALLG-SV--- 137
+++ + R+A + P + + G + GS G +
Sbjct: 130 NVSRLQPYLKLRQALLELRPAKNVLIDG--------------V---LGS----GKTWVAL 168
Query: 138 -VPRDAFVVTKLLEAGAIILGKASMSEWAHFRTFESPNGWCARTGQGKNPYVLSADPCGS 196
V V K+ I W + + SP
Sbjct: 169 DVCLSYKVQCKM--DFKIF--------WLNLKNCNSPE---------------------- 196
Query: 197 SSGSAISVAANMVAVSLGTDTDASILCPSGSNSVVGIKPTVGLISRDGVIPVSPRLDTVG 256
+V + + D + + SN + I + R + S
Sbjct: 197 ------TVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRR---LLKSKPY---- 243
Query: 257 PISKTVADTVY---VLDAIVGFDAKDE---ATREAS--KYIPPGGYKQFLKPHGLQG--- 305
V V +A F+ + TR ++ H
Sbjct: 244 ENCLLVLLNVQNAKAWNA---FNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTP 300
Query: 306 -KRLGIVRN-LGSNFTISSEVTEAFEHHVRTLRQQGAIL------LDNFEINNLEAILNS 357
+ ++ L E + R L + DN++ N + +
Sbjct: 301 DEVKSLLLKYLDCRPQDLPR--EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI 358
Query: 358 IANGETLAIL-AAEFKQALNAYLQELVTSPVRSLADVIAFNKMFPE 402
I + +L +L AE+++ L +FP
Sbjct: 359 IES--SLNVLEPAEYRK----MFDRLS---------------VFPP 383
Score = 37.9 bits (87), Expect = 0.006
Identities = 27/188 (14%), Positives = 52/188 (27%), Gaps = 63/188 (33%)
Query: 18 LIILA-VYSS--------GSP--ATESREFSV---------KEATIEDLQLAFKQNQLTS 57
L++L V ++ T +R V +++ + ++
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLT-TRFKQVTDFLSAATTTHISLDHHSMTLTPDE--V 303
Query: 58 RQLVEMYI--------REIGRLNPLLRGVI----EVNPDAINQADKADQERKAKAPRSQL 105
+ L+ Y+ RE+ NP +I + + ++ S L
Sbjct: 304 KSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSL 363
Query: 106 -GLHGIPILVKDNIATKDKMNTTAGSFALLGSVVPRDAFVVTKLLEAGAIILGKASMSEW 164
L P + F L SV P A + T LL ++ W
Sbjct: 364 NVLE--PAEYRKM-------------FDRL-SVFPPSAHIPTILLS----LI-------W 396
Query: 165 AHFRTFES 172
+
Sbjct: 397 FDVIKSDV 404
Score = 32.1 bits (72), Expect = 0.43
Identities = 14/74 (18%), Positives = 27/74 (36%), Gaps = 21/74 (28%)
Query: 12 IF---SSLPLIILAVYSSGSPATESREF-------SV-----KEATIE--DLQLAFKQNQ 54
+F + +P I+L++ ++ S+ KE+TI + L K
Sbjct: 380 VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKL 439
Query: 55 LTS----RQLVEMY 64
R +V+ Y
Sbjct: 440 ENEYALHRSIVDHY 453
>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class
I, activator, RNA polymeras holoenzyme, sigma70, open
complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia
coli k-12}
Length = 613
Score = 28.8 bits (64), Expect = 4.0
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 61 VEMYIREIGRLNPLLRGVIEVN-PDAINQADKADQERKAKAPRS 103
V MY+RE+G + LL E++ I Q A+ P +
Sbjct: 98 VRMYMREMGTV-ELLTREGEIDIAKRIEDGINQVQCSVAEYPEA 140
>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 = 27.6 bits (60), Expect = 5.4
Identities = 7/34 (20%), Positives = 14/34 (41%), Gaps = 7/34 (20%)
Query: 347 EINNLEAILNSIANGETLAILAAEFKQALNAYLQ 380
+ L+A L A+ A+ A+ A ++
Sbjct: 21 ALKKLQASLKLYADDSAPAL-------AIKATME 47
>1v9m_A V-type ATP synthase subunit C; VOV1-ATPase, V-type ATPase, the C
subunit, thermus thermophi riken structural
genomics/proteomics initiative; 1.85A {Thermus
thermophilus} SCOP: f.40.1.1 PDB: 1r5z_A 3j0j_M*
Length = 323
Score = 27.3 bits (60), Expect = 8.5
Identities = 14/81 (17%), Positives = 28/81 (34%), Gaps = 6/81 (7%)
Query: 282 TREASKYIPPGGYKQFLKPHGLQGKRLGIVRNLGSNFTISSEVTEAFEHHVRTLRQQGAI 341
+ + + Y L GL ++R + R+ +
Sbjct: 33 FADFLRLLSETVYGGELAGQGLPDVDRAVLRTQAKLVG------DLPRLVTGEAREAVRL 86
Query: 342 LLDNFEINNLEAILNSIANGE 362
LL +++NL+A+L + A G
Sbjct: 87 LLLRNDLHNLQALLRAKATGR 107
>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA
complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1
Length = 438
Score = 27.6 bits (61), Expect = 9.2
Identities = 8/47 (17%), Positives = 20/47 (42%)
Query: 30 ATESREFSVKEATIEDLQLAFKQNQLTSRQLVEMYIREIGRLNPLLR 76
+ +E +E+ + ++++ V Y+ EIG++ L
Sbjct: 65 GPLEADLLPEEGLLEEEEEELSLPKVSTSDPVRQYLHEIGQVPLLTL 111
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 0.132 0.370
Gapped
Lambda K H
0.267 0.0646 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,947,329
Number of extensions: 368202
Number of successful extensions: 937
Number of sequences better than 10.0: 1
Number of HSP's gapped: 880
Number of HSP's successfully gapped: 25
Length of query: 403
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 307
Effective length of database: 4,021,377
Effective search space: 1234562739
Effective search space used: 1234562739
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: 58 (26.3 bits)