RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 010029
(520 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 = 588 bits (1518), Expect = 0.0
Identities = 219/505 (43%), Positives = 300/505 (59%), Gaps = 37/505 (7%)
Query: 37 FPIREATIKDLQLAFKQNKLTSRQLVEFYLGEIHRLN---PLLHGVIEVNPDALSQADKA 93
FP E + DLQ +L S L + YL I L+ P L VIE+NPDAL +A +
Sbjct: 6 FPYAETDVADLQARMTAGELDSTTLTQAYLQRIAALDRTGPRLRAVIELNPDALKEAAER 65
Query: 94 DYERKVKAAGSLRG-LHGIPILLKDNIATKDKMNTTAGSYALLRSVVPRDAGVVVKLRKA 152
D ER G LRG LHGIP+LLKDNI M T+AGS AL P DA +V +LR A
Sbjct: 66 DRER---RDGRLRGPLHGIPLLLKDNINAAP-MATSAGSLALQ-GFRPDDAYLVRRLRDA 120
Query: 153 GAIILGKASLSEWSNFRSSKAPSGFSGRGGQGKNPYVLSADPCGSSSGSAISVAANLAAV 212
GA++LGK +LSEW+NFR + + SG+S RGGQ +NPY +S PCGSSSGSA++VAANLA+V
Sbjct: 121 GAVVLGKTNLSEWANFRGNDSISGWSARGGQTRNPYRISHSPCGSSSGSAVAVAANLASV 180
Query: 213 SLGTETDGSILCPSSSNSVVGLKPTLGLTSRAGVIPITPRQDSVGPICRTVADAAYVLDA 272
++GTETDGSI+CP++ N VVGLKPT+GL SR G+IPI+ QD+ GP+ R+VADAA VL A
Sbjct: 181 AIGTETDGSIVCPAAINGVVGLKPTVGLVSRDGIIPISFSQDTAGPMARSVADAAAVLTA 240
Query: 273 IAGFDHYDPATRAASEYIPRGGYKQFLRPHGLKGKRLGIVRNPFFNFDEGSPLAQVFDHH 332
IAG D DPAT Y L P GL+GKR+G+++ P + + + +
Sbjct: 241 IAGRDDADPATATMPGRAVY-DYTARLDPQGLRGKRIGLLQTP---LLKYRGMPPLIEQA 296
Query: 333 LHTLRQEGALVIDHLEIGNINSLNSIANDETTAMLAEFKLAINAYLKELVTSPVRSLAEV 392
LR+ GA+V+ + + + A E T +L EFK + Y +P+RSLA++
Sbjct: 297 ATELRRAGAVVVP----VELPNQGAWAEAERTLLLYEFKAGLERYFNTH-RAPLRSLADL 351
Query: 393 IAFNNKFSDLEKIKEYGQDLLLSAEATDGIGKTE--KAAILNLERFTRDGFEKLMSTNNL 450
IAFN S E + +GQ+LL+ A+AT G+ +A +G + ++ + L
Sbjct: 352 IAFNQAHSKQE-LGLFGQELLVEADATAGLADPAYIRARSDARRLAGPEGIDAALAAHQL 410
Query: 451 DALVTPRSY---------------ASTLLAVGGFPGINVPAGYDSEGVPFGICFGGLKGT 495
DALV P + + + AV G+P + VP G +G+P G+ F G +
Sbjct: 411 DALVAPTTGVAWPIRSEGDDFPGESYSAAAVAGYPSLTVPMGQ-IDGLPVGLLFMGTAWS 469
Query: 496 EPKLIEIAYGFEQATKIRKPPSFKS 520
EPKLIE+AY +EQ T+ R+PP F +
Sbjct: 470 EPKLIEMAYAYEQRTRARRPPHFDT 494
>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 = 230 bits (588), Expect = 2e-70
Identities = 98/492 (19%), Positives = 167/492 (33%), Gaps = 106/492 (21%)
Query: 43 TIKDLQLAFKQNKLTSRQLVEFYLGEIHRLNPLLHGVIEVNPDALSQADKADYERKVKAA 102
++ DLQ + +L+ + I +H + + A A
Sbjct: 3 SLADLQRRIETGELSPNAAIAQSHAAIEAREKEVHAFVRHDKSA--------------RA 48
Query: 103 GSLRGLHGIPILLKDNIATKDKMNTTAGSYALLRSVVPRDAGVVVKLRKAGAIILGKASL 162
+ L GI + +KD I T + M T GS DA VV+ L++AGA I+GK +
Sbjct: 49 QASGPLRGIAVGIKDIIDTAN-MPTEMGSEIYRGWQPRSDAPVVMMLKRAGATIIGKTTT 107
Query: 163 SEWSNFRSSKAPSGFSGRGGQGKNPYVLSADPCGSSSGSAISVAANLAAVSLGTETDGSI 222
+ +++ + NP+ P G+SSGSA +V A + ++LGT+T GS+
Sbjct: 108 TAFASRDPTAT-----------LNPHNTGHSPGGASSGSAAAVGAGMIPLALGTQTGGSV 156
Query: 223 LCPSSSNSVVGLKPTLGLTSRAGVIPITPRQDSVGPICRTVADAAYVLDAIAGFDHYDPA 282
+ P++ +KP+ + GV + D+VG D A L A+ G +
Sbjct: 157 IRPAAYCGTAAIKPSFRMLPTVGVKCYSWALDTVGLFGARAEDLARGLLAMTGRSEFSGI 216
Query: 283 TRAASEYIPRGGYKQFLRPHGLKGKRLGIVRNPFFNFDEGSP-LAQVFDHHLHTLRQEGA 341
K R+G+VR F P Q + + GA
Sbjct: 217 V-------------------PAKAPRIGVVRQEF--AGAVEPAAEQGLQAAIKAAERAGA 255
Query: 342 LVID----HLEIGNINSLNSIANDETTAMLAEFKLAINAYLKELVTSPVRSLAEVIAFNN 397
V I + E LA + + + +R+ +
Sbjct: 256 SVQAIDLPEAVHEAWRIHPIIQDFEAHRALAWEF----SEHHDEIAPMLRASLD------ 305
Query: 398 KFSDLEKIKEYGQDLLLSAEATDGIGKTEKAAILNLERFTRDGFEKLMSTNNLDALVTPR 457
+ L+ + D +A + R R ++ +D L+T
Sbjct: 306 ------------ATVGLTPKEYD------EA--RRIGRRGRRELGEVFE--GVDVLLTYS 343
Query: 458 S------------------YASTLLAVGGFPGINVPAGYDSEGVPFGICFGGLKGTEPKL 499
+ TL+ G P +NVP G+P G+ G +
Sbjct: 344 APGTAPAKALASTGDPRYNRLWTLM---GNPCVNVPVL-KVGGLPIGVQVIARFGNDAHA 399
Query: 500 IEIAYGFEQATK 511
+ A+ E A
Sbjct: 400 LATAWFLEDALA 411
>2dc0_A Probable amidase; structural genomics, NPPSFA, national project on
protein structural and functional analyses; 2.00A
{Thermus thermophilus}
Length = 434
Score = 223 bits (572), Expect = 7e-68
Identities = 84/330 (25%), Positives = 135/330 (40%), Gaps = 42/330 (12%)
Query: 43 TIKDLQLAFKQNKLTSRQLVEFYLGEIHRLNPLLHGVIEVNPD-ALSQADKADYERKVKA 101
+ + + + + T L+E L + + ++ + A +A E
Sbjct: 2 DLLEAKRLLETGRTTPLALLEEALERAKAFQDR-NALAYLDEEAARKEALALTEEL---R 57
Query: 102 AGSLRG-LHGIPILLKDNIATKDKMNTTAGSYALLRSVVPRDAGVVVKLRKAGAIILGKA 160
G +RG LHG+P+ +KD K M T AG+ +P +A V +LR+AGA++ K
Sbjct: 58 RGQVRGPLHGLPLTVKDLFPVKG-MPTRAGT-KAPLPPLPEEARAVRRLREAGALLFAKT 115
Query: 161 SLSEWSNFRSSKAPSGFSGRGGQGKNPYVLSADPCGSSSGSAISVAANLAAVSLGTETDG 220
++ E + + G +N S GSS GSA++VA + SLGT+T G
Sbjct: 116 NMHEIA-LGITGENPWT----GPVRNAVDPSRQAGGSSGGSAVAVALGIGLASLGTDTGG 170
Query: 221 SILCPSSSNSVVGLKPTLGLTSRAGVIPITPRQDSVGPICRTVADAAYVLDAIAGFDHYD 280
SI P+ N VVG KP+ G S G +P++ D GP+ R+V DA ++ + +AG
Sbjct: 171 SIRIPAGFNGVVGFKPSYGRVSLEGALPLSRSTDHAGPLTRSVRDAHFLTEILAGESIPL 230
Query: 281 PATRAASEYIPRGGYKQFLRPHGLKGKRLGIVRNPFFNFDEGSPLAQVFDHHLHTLRQEG 340
G++ G+ + F G + + F L L
Sbjct: 231 E---------------------GVQNPVFGVPLD-FLEGRLGVEVRKAFTRLLEDLPALR 268
Query: 341 ALVIDHLEIGNINSLNSIANDETTAMLAEF 370
A V E+ SL E L +
Sbjct: 269 AEVR---EV----SLPLEGVYEVYTRLVRY 291
Score = 38.7 bits (91), Expect = 0.003
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 468 GFPGINVPAGYDSEGVPFGICFGGLKGTEPKLIEIAYGFEQAT 510
G P + +P EG+P G+ G G + K++ + E
Sbjct: 392 GVPTLALPFA-KVEGMPVGLQVVGAYGEDGKVLALGGWLEARL 433
>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 (558), Expect = 3e-65
Identities = 92/310 (29%), Positives = 151/310 (48%), Gaps = 19/310 (6%)
Query: 39 IREATIKDLQLAFKQNKLTSRQLVEFYLGEIHRLNPLLHGVIEVNPD-ALSQADKADYER 97
IR ++++L K K+ +V+ I +P + + ++ + A+ +A + D
Sbjct: 3 IRYESVENLLTLIKDKKIKPSDVVKDIYDAIEETDPTIKSFLALDKENAIKKAQELD--E 60
Query: 98 KVKAAGSLRGLHGIPILLKDNIATKDKMNTTAGSYALLRSVVPRDAGVVVKLRKAGAIIL 157
L GIP+ +KDNI T + TT S L V ++ V+ KL K A+++
Sbjct: 61 LQAKDQMDGKLFGIPMGIKDNIITNG-LETTCASKMLEGFVPIYESTVMEKLHKENAVLI 119
Query: 158 GKASLSEWSNFR--SSKAPSGFSGRGGQGKNPYVLSADPCGSSSGSAISVAANLAAVSLG 215
GK ++ E F S S F + NP+ A P GSS GSA +VAA L +SLG
Sbjct: 120 GKLNMDE---FAMGGSTETSYF----KKTVNPFDHKAVPGGSSGGSAAAVAAGLVPLSLG 172
Query: 216 TETDGSILCPSSSNSVVGLKPTLGLTSRAGVIPITPRQDSVGPICRTVADAAYVLDAIAG 275
++T GSI P++ VVG+KPT G SR G++ D +GP+ R V D A VL+AI+G
Sbjct: 173 SDTGGSIRQPAAYCGVVGMKPTYGRVSRFGLVAFASSLDQIGPLTRNVKDNAIVLEAISG 232
Query: 276 FDHYDPATRAASEYIPRGGYKQFLRPHGLKGKRLGIVRNPFFNFDEGSPLAQVFDHHLHT 335
D D +T S + + + +KG ++ + + + + + + + T
Sbjct: 233 ADVND-ST---SAPVDDVDFTSEIGK-DIKGLKVALPKE-YLGEGVADDVKEAVQNAVET 286
Query: 336 LRQEGALVID 345
L+ GA+V +
Sbjct: 287 LKSLGAVVEE 296
Score = 41.7 bits (99), Expect = 5e-04
Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 468 GFPGINVPAGYDSEGVPFGICFGGLKGTEPKLIEIAYGFEQATKI-RKPP 516
G PGI+VP G S G P G+ F G E L +AY +E +
Sbjct: 435 GLPGISVPCG-QSNGRPIGLQFIGKPFDEKTLYRVAYQYETQYNLHDVYE 483
>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 = 215 bits (549), Expect = 4e-64
Identities = 100/305 (32%), Positives = 153/305 (50%), Gaps = 27/305 (8%)
Query: 43 TIKDLQLAFKQNKLTSRQLVEFYLGEIHRLNPLLHGVIEVNPDALSQADKADYERKVKAA 102
+++ + +++ ++ + YL + L+P L + +N L +A+ D
Sbjct: 2 LAHEIRARVARGEVSPLEVAQAYLKRVQELDPGLGAFLSLNERLLEEAEAVDPGLP---- 57
Query: 103 GSLRGLHGIPILLKDNIATKDKMNTTAGSYALLRSVVPRDAGVVVKLRKAGAIILGKASL 162
L G+ + +KDNIAT+ + TTAGS L V P +A V +L+ GA++LGK +L
Sbjct: 58 -----LAGLVVAVKDNIATRG-LRTTAGSRLLENFVPPYEATAVARLKALGALVLGKTNL 111
Query: 163 SEWSNFR--SSKAPSGFSGRGGQGKNPYVLSADPCGSSSGSAISVAANLAAVSLGTETDG 220
E F SS S F KNP+ P GSS GSA ++AA+LA ++LG++T G
Sbjct: 112 DE---FGMGSSTEHSAF----FPTKNPFDPDRVPGGSSGGSAAALAADLAPLALGSDTGG 164
Query: 221 SILCPSSSNSVVGLKPTLGLTSRAGVIPITPRQDSVGPICRTVADAAYVLDAIAGFDHYD 280
S+ P++ V GLKPT G SR G+I D +GP+ R+V D A ++DA AG D D
Sbjct: 165 SVRQPAAFCGVYGLKPTYGRVSRFGLIAYASSLDQIGPMARSVRDLALLMDAAAGPDPLD 224
Query: 281 PATRAASEYIPRGGYKQFLRPHGLKGKRLGIVRNPFFNFDEGSPLAQVFDHHLHTLRQEG 340
AT PR +++ L L RLG+VR G + + + L R+ G
Sbjct: 225 -ATSLDLP--PR--FQEALEG-PLPPLRLGVVREALAGNSPG--VERALEEALKVFRELG 276
Query: 341 ALVID 345
V +
Sbjct: 277 LSVRE 281
Score = 42.1 bits (100), Expect = 4e-04
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 468 GFPGINVPAGYDSEGVPFGICFGGLKGTEPKLIEIAYGFEQATKI--RKPP 516
G P ++ PAG++ +P G+ G + +L+ A FE+AT K P
Sbjct: 417 GLPALSFPAGFE-GHLPVGLQLLAPWGEDERLLRAALAFEEATARAHLKAP 466
>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 = 213 bits (545), Expect = 2e-63
Identities = 99/310 (31%), Positives = 158/310 (50%), Gaps = 25/310 (8%)
Query: 39 IREATIKDLQLAFKQNKLTSRQLVEFYLGEIHRLNPLLHGVIEVNPD-ALSQADKADYER 97
+ + ++ +L+ K+ +++ +++VE + ++ + I AL QA+
Sbjct: 2 LWKKSLSELRELLKRGEVSPKEVVESFYDRYNQTEEKVKAYITPLYGKALKQAESLKERE 61
Query: 98 KVKAAGSLRGLHGIPILLKDNIATKDKMNTTAGSYALLRSVVPRDAGVVVKLRKAGAIIL 157
L GIPI +KDNI + TT S L V P DA V+ +L+KAGA+I+
Sbjct: 62 L--------PLFGIPIAVKDNILVEG-EKTTCASKILENFVAPYDATVIERLKKAGALIV 112
Query: 158 GKASLSEWSNFR--SSKAPSGFSGRGGQGKNPYVLSADPCGSSSGSAISVAANLAAVSLG 215
GK +L E F SS S F KNP+ L P GSS GSA SVA A VSLG
Sbjct: 113 GKTNLDE---FAMGSSTEYSAF----FPTKNPWDLERVPGGSSGGSAASVAVLSAPVSLG 165
Query: 216 TETDGSILCPSSSNSVVGLKPTLGLTSRAGVIPITPRQDSVGPICRTVADAAYVLDAIAG 275
++T GSI P+S V+G+KPT G SR G++ D +G R D A VL+ I+G
Sbjct: 166 SDTGGSIRQPASFCGVIGIKPTYGRVSRYGLVAFASSLDQIGVFGRRTEDVALVLEVISG 225
Query: 276 FDHYDPATRAASEYIPRGGYKQFLRPHGLKGKRLGIVRNPFFNFDEGSPLAQVFDHHLHT 335
+D D +T S +P + + ++ +KG ++G+ + FF ++ + + F++ +
Sbjct: 226 WDEKD-ST---SAKVPVPEWSEEVKK-EVKGLKIGLPKE-FFEYELQPQVKEAFENFIKE 279
Query: 336 LRQEGALVID 345
L +EG + +
Sbjct: 280 LEKEGFEIKE 289
Score = 41.4 bits (98), Expect = 5e-04
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 3/52 (5%)
Query: 468 GFPGINVPAGYDSEGVPFGICFGGLKGTEPKLIEIAYGFEQAT--KIRKPPS 517
G P I++P + +G+P G G E L++I+Y +EQ + P +
Sbjct: 428 GLPAISIPIAW-KDGLPVGGQLIGKHWDETTLLQISYLWEQKFKHYEKIPLT 478
>3a2q_A 6-aminohexanoate-cyclic-dimer hydrolase; alpha/beta fold, nylon
degradation; 1.80A {Arthrobacter SP} PDB: 3a2p_A
Length = 493
Score = 212 bits (543), Expect = 5e-63
Identities = 105/498 (21%), Positives = 177/498 (35%), Gaps = 62/498 (12%)
Query: 50 AFKQNKLTSRQLVEFYLGEIHRLNPLLHGVIEVNPD-ALSQADKADYERKVKAAGSLRGL 108
+ +++ +L+E + + +NP ++ VI + A +++ A
Sbjct: 16 LVRSGEISRTELLEATIAHVQAVNPEINAVIIPLFEKARRESELAS-----------GPF 64
Query: 109 HGIPILLKDNIATKDKMNTTAGSYALLRS--VVPRDAGVVVKLRKAGAIILGKASLSEWS 166
G+P LLKD T+ + S DA V ++R AG ++LGK + E
Sbjct: 65 AGVPYLLKDLTVVSQGDINTSSIKGMKESGYRADHDAYFVQRMRAAGFVLLGKTNTPEMG 124
Query: 167 NFRSSKAPSGFSGRGGQGKNPYVLSADPCGSSSGSAISVAANLAAVSLGTETDGSILCPS 226
N + G +NP+ L GSS GS +VAA L+ V+ G + G++ P+
Sbjct: 125 NQ-----VTTEPEAWGATRNPWNLGRSVGGSSGGSGAAVAAALSPVAHGNDAAGAVRIPA 179
Query: 227 SSNSVVGLKPTLGLTSRAGVIPITPRQD---SVGPICRTVADAAYVLDAIAGFDHYDPAT 283
S VVGLKPT G S ++ + G R+V D A +LD ++G D
Sbjct: 180 SVCGVVGLKPTRGRISPGPLVTDSDNVAGAAHEGLFARSVRDIAALLDVVSGHRPGDTFC 239
Query: 284 RAASEYIPRGGYKQFLRPHGLKGKRLGIVRNPFFNFDEGSP-LAQVFDHHLHTLRQEGAL 342
Y Q + R+G++ + P A L G
Sbjct: 240 APT----ASRPYAQGISE-NPGSLRVGVLTHNPVGDFALDPECAAAARGAAAALAALGHD 294
Query: 343 VID-----HLEIGNINSLNSIANDETTAMLAEFKLAIN-AYLKELVTSPVRSLAEVI--- 393
V D + + ++I + + I ++ V + +
Sbjct: 295 VNDAYPEALGDRSFLKDYSTICDVAIAREIERNGELIGRPLTEDDVEWTSWEMVKRADQV 354
Query: 394 ----------AFNNKFSDLEKIKEYGQDLLLS---AEATDGIGKTEKAAILNLERFTRDG 440
+E+ E G DLL+ T IG+ A +LE
Sbjct: 355 TGRAFAACVDELRYYAGKVERWWEAGWDLLILPTVTRQTPEIGELMLAKGTDLEGRQSAF 414
Query: 441 FEKLMSTNNLDALVTPRSYASTLLAVGGFPGINVPAGYDSEGVPFGICFGGLKGTEPKLI 500
+ + + G P I++P G S+G+P G+ G E L+
Sbjct: 415 ISGSLQM-------LAFTVPFNVS---GQPAISLPIGMSSDGMPIGVQIVAAYGREDLLL 464
Query: 501 EIAYGFEQAT--KIRKPP 516
++A E A R+P
Sbjct: 465 QVAAQLEGALPWVARRPQ 482
>3a1k_A Amidase; AS family enzyme, hydrolase; 2.17A {Rhodococcus SP} PDB:
3a1i_A
Length = 521
Score = 209 bits (534), Expect = 2e-61
Identities = 117/539 (21%), Positives = 175/539 (32%), Gaps = 119/539 (22%)
Query: 46 DLQLAFKQNKLTSRQLVEFYLGEIHRLNPLLHGVIEVNPD-ALSQADK----ADYERKVK 100
L + + +L + + A+ A + A Y
Sbjct: 21 TLDKTARLEWPALIDGALGSYDVVDQLYADEATPPTTSREHAVPSASENPLSAWYVTTSI 80
Query: 101 AAGSLRGLHGIPILLKDNIATKDKMNTTAGSYALLRSVVPRDAGVVVKLRKAGAIILGKA 160
S L G + +KDN+ + GS + RDA VV +L AGA + GKA
Sbjct: 81 PPTSDGVLTGRRVAIKDNVTVAG-VPMMNGSRTVEGFTPSRDATVVTRLLAAGATVAGKA 139
Query: 161 SLSEW----SNFRSSKAPSGFSGRGGQGKNPYVLSADPCGSSSGSAISVAANLAAVSLGT 216
+ S+F + P +NP+ + GSS GSA VA ++G
Sbjct: 140 VCEDLCFSGSSFTPASGPV---------RNPWDRQREAGGSSGGSAALVANGDVDFAIGG 190
Query: 217 ETDGSILCPSSSNSVVGLKPTLGLTSRAGVIPITPRQDSVGPICRTVADAAYVLDAIAGF 276
+ GSI P++ VVG KPT GL G PI D +GPI RTV DAA +L IAG
Sbjct: 191 DQGGSIRIPAAFCGVVGHKPTFGLVPYTGAFPIERTIDHLGPITRTVHDAALMLSVIAGR 250
Query: 277 DHYDPATRAASEYIPRGGYKQFLRPHGLKGKRLGIVRNPFFNFDEGSPLAQV---FDHHL 333
D DP +A S Y L + G R+GIVR F +V
Sbjct: 251 DGNDP-RQADSVEAGD--YLSTLDS-DVDGLRIGIVRE---GFGHAVSQPEVDDAVRAAA 303
Query: 334 HTLRQEGALVIDHLEIGNINSLNSIANDETTAMLAEFKLAINAYLKELVTSPVRSLAEVI 393
H+L + G + +N + A + + V +
Sbjct: 304 HSLTEIGC------TVEEVN-------------IPWHLHAFHIWN-------VIATDG-- 335
Query: 394 AFNNKF------------SDLEKIKEYGQDLLLSAEATDGIGKTEKAAIL---------- 431
D E + + + A+ + +T K L
Sbjct: 336 GAYQMLDGNGYGMNAEGLYDPELMAHFASRRIQHAD---ALSETVKLVALTGHHGITTLG 392
Query: 432 --------NLERFTRDGFEKLMSTNNLDALVTPRS-----------------YASTLLAV 466
NL R ++ + D LV P L +
Sbjct: 393 GASYGKARNLVPLARAAYDTALR--QFDVLVMPTLPYVASELPAKDVDRATFITKALGMI 450
Query: 467 G--------GFPGINVPAGYDSEGVPFGICFGGLKGTEPKLIEIAYGFEQAT-KIRKPP 516
G P ++VPAG G+P G+ G + ++ + FE+ P
Sbjct: 451 ANTAPFDVTGHPSLSVPAGL-VNGLPVGMMITGRHFDDATVLRVGRAFEKLRGAFPTPA 508
>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 (506), Expect = 7e-58
Identities = 94/308 (30%), Positives = 146/308 (47%), Gaps = 33/308 (10%)
Query: 41 EATIKDLQLAFKQNKLTSRQLVEFYLGEIHRLNPLLHGVIEVNPD-ALSQADKADYERKV 99
+ ++ K ++ +L + L I RL+P + I V + ++ + K
Sbjct: 6 DFRKLTIEECLKLSEEEREKLPQLSLETIKRLDPHVKAFISVRENVSVEKKGK------- 58
Query: 100 KAAGSLRGLHGIPILLKDNIATKDKMNTTAGSYALLRSVVPRDAGVVVKLRKAGAIILGK 159
GIP+ +KDNI T M TT S L DA VV K+++AG +++GK
Sbjct: 59 --------FWGIPVAIKDNILTLG-MRTTCASRILENYESVFDATVVKKMKEAGFVVVGK 109
Query: 160 ASLSEWSNFR--SSKAPSGFSGRGGQGKNPYVLSADPCGSSSGSAISVAANLAAVSLGTE 217
A+L E F SS S F +NP+ L P GSS GSA +V+A + +LG++
Sbjct: 110 ANLDE---FAMGSSTERSAF----FPTRNPWDLERVPGGSSGGSAAAVSAGMVVAALGSD 162
Query: 218 TDGSILCPSSSNSVVGLKPTLGLTSRAGVIPITPRQDSVGPICRTVADAAYVLDAIAGFD 277
T GS+ P+S VVG KPT GL SR G++ D +GPI +TV DAA +++ I+G D
Sbjct: 163 TGGSVRQPASLCGVVGYKPTYGLVSRYGLVAFASSLDQIGPITKTVRDAAILMEIISGRD 222
Query: 278 HYDPATRAASEYIPRGGYKQFLRPHGLKGKRLGIVRNPFFNFDEGSPLAQVFDHHLHTLR 337
D AT + + + G+ G + + + D +++ F+ L L
Sbjct: 223 END-ATTVNRKV----DFLSEIEE-GVSGMKFAVPEE-IYEHDIEEGVSERFEEALKLLE 275
Query: 338 QEGALVID 345
+ GA V
Sbjct: 276 RLGAKVER 283
Score = 41.8 bits (99), Expect = 5e-04
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 468 GFPGINVPAGYDSEGVPFGICFGGLKGTEPKLIEIAYGFEQATKIRKPP 516
G P I+VP G+ S +P G+ G + + K+ IA E+ + +
Sbjct: 420 GLPAISVPFGF-SNNLPVGVQVIGRRFADGKVFRIARAIEKNSPYNENG 467
>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 = 181 bits (462), Expect = 8e-51
Identities = 103/555 (18%), Positives = 178/555 (32%), Gaps = 87/555 (15%)
Query: 20 LLPTLLAISAQSNAIHAFPIREATIKDLQLAFKQNKLTSRQLVEFYLGEIHRLNPLLHGV 79
+ + Q+ + + + + L + +L+ + YLG+ +N + V
Sbjct: 49 MDKAVQRFRLQNPDLDSEALLTLPLLQLVQKLQSGELSPEAVFFTYLGKAWEVNKGTNCV 108
Query: 80 IEVNPDALSQADKADYERKVKAAGSLRGLHGIPILLKDNIATKDKMNTTAGSYALLRSVV 139
D E ++ A L+G+P+ LK+ + K ++T G
Sbjct: 109 TSYLTDC---------ETQLSQAPRQGLLYGVPVSLKECFSYKG-HDSTLGLSLNEGMPS 158
Query: 140 PRDAGVVVKLRKAGAIILGKASLSEWSNFRSSKAPSGFSGRGGQGKNPYVLSADPCGSSS 199
D VV L+ GA+ ++ + S + + GQ NP+ S P GSS
Sbjct: 159 ESDCVVVQVLKLQGAVPFVHTNVPQ-----SMFSYDCSNPLFGQTMNPWKSSKSPGGSSG 213
Query: 200 GSAISVAANLAAVSLGTETDGSILCPSSSNSVVGLKPTLGLTSRAGVIPITPRQDSV--- 256
G + + + + LGT+ GSI PS+ + GLKPT S++G+ Q +V
Sbjct: 214 GEGALIGSGGSPLGLGTDIGGSIRFPSAFCGICGLKPTGNRLSKSGLKGCVYGQTAVQLS 273
Query: 257 -GPICRTVADAAYVLDAIAGFDH--YDPATRAASEYIPRGGYKQFLRPHGLKGKRLGIVR 313
GP+ R V A L A+ DP +P +++ + + R+G
Sbjct: 274 LGPMARDVESLALCLKALLCEHLFTLDP-------TVPPLPFREEVYR-SSRPLRVGYYE 325
Query: 314 NPFFNFDEGSPLAQVFDHHLHTLRQEGALVID-----HLEIGNINSLNSIANDETTAMLA 368
+ + + L G +I + S + +D + L
Sbjct: 326 TDNY-TMPSPAMRRALIETKQRLEAAGHTLIPFLPNNIPYALEVLSTGGLFSDGGRSFLQ 384
Query: 369 EFKLAINAYLKELVTSPVRSLAEVIAFNNKFSDLEKIKEYGQDLLLSAEATDGIGKTEKA 428
FK + +R + + L+ + L + EK
Sbjct: 385 NFKGDFVDPCLGDLILILRLPSWFKRLLSLL--LKPLFPRLAAFLNNMRPRS----AEKL 438
Query: 429 AILNLERFT-RDGFEKLMSTNNLDALVTP---------------RSYASTLLA-VGGFPG 471
L E R NLD L+TP + + T+L FP
Sbjct: 439 WKLQHEIEMYRQSVIAQWKAMNLDVLLTPMLGPALDLNTPGRATGAVSYTMLYNCLDFPA 498
Query: 472 INVPAGY-----------------------------DSEGVPFGICFGGLKGTEPKLIEI 502
VP +S G+P + L E +
Sbjct: 499 GVVPVTTVTAEDDAQMELYKGYFGDIWDIILKKAMKNSVGLPVAVQCVALPWQEELCLRF 558
Query: 503 AYGFEQATKIRKPPS 517
EQ +K PS
Sbjct: 559 MREVEQLMTPQKQPS 573
>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 = 65.8 bits (160), Expect = 2e-11
Identities = 114/634 (17%), Positives = 191/634 (30%), Gaps = 223/634 (35%)
Query: 7 ATAILAFSLFSH------LLLPTLLAISAQSNAIHAFPIREATIKDLQ-----LAFKQNK 55
A + +L SH LL+PT ++ A ++E K L A ++
Sbjct: 3 AYSTRPLTL-SHGSLEHVLLVPT-------ASFFIASQLQEQFNKILPEPTEGFA-ADDE 53
Query: 56 LTSR-QLVEFYLGEIHRLNPLLHGVIEVNPDALSQADK------ADYERKVKAAGSLRG- 107
T+ +LV +LG + V P + Q D+ ++E L G
Sbjct: 54 PTTPAELVGKFLGYVSS---------LVEPSKVGQFDQVLNLCLTEFENCY-----LEGN 99
Query: 108 -LHGIPI-LLKDNIATKDKMNTTAGSYALLRSVVPRDAGVVVKLRKAGAIILGKASLSEW 165
+H + LL++N T K +Y R + R K S S
Sbjct: 100 DIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRP--------------FDKKSNSAL 145
Query: 166 SNFRSSKAPSG-----FSGRGGQGKN-PYV-----LSADPCGSSSGSAISVAANLAAVSL 214
FR+ + F GGQG Y L G I +A + +
Sbjct: 146 --FRAVGEGNAQLVAIF---GGQGNTDDYFEELRDLYQTY-HVLVGDLIKFSAETLSELI 199
Query: 215 GTETDGSILCPSSSNSVVGLK------------------PTLGLTSRAGVIPITPRQDSV 256
T D + N + L+ P +G+ A + +T +
Sbjct: 200 RTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYV-VTAKLLGF 258
Query: 257 GP------ICRTVADAAYVLDA--IAGFDHYDPATRAASEYIPRGGYKQFLRPHGLKGKR 308
P + + ++ A IA D ++ + + I L G++
Sbjct: 259 TPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAI------TVLFFIGVRCYE 312
Query: 309 --------LGIVRNPFFNFDEGSP----------LAQVFDH------HLHTLRQEGALVI 344
I+ + N +EG P QV D+ HL +
Sbjct: 313 AYPNTSLPPSILEDSLEN-NEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGK------- 364
Query: 345 DHLEIGNINSLNSIANDETTAMLAEFKLAINAYLKELVTSPVRSLAEVIAFNNKFSDLEK 404
+EI +N ++ +V+ P +SL N L K
Sbjct: 365 -QVEISLVNGAKNL----------------------VVSGPPQSLY---GLNLT---LRK 395
Query: 405 IK-EYGQD-----------------L---------LLSAEATDGIGKTEKAAILNLER-- 435
K G D L LL A+D I K ++
Sbjct: 396 AKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLL-VPASDLINKDLVKNNVSFNAKD 454
Query: 436 ------FTRDGFE-KLMSTNNLDALV------------TPRSYASTLLAVG--GFPGINV 474
T DG + +++S + + +V T + A+ +L G G G+ V
Sbjct: 455 IQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGV 514
Query: 475 PAGYDSEGVPFGICFGGLKGTEPKLIEIAYGFEQ 508
+ +G + G P + YGF+Q
Sbjct: 515 LTHRNKDGTGVRVIVAGTLDINP---DDDYGFKQ 545
Score = 46.2 bits (109), Expect = 3e-05
Identities = 60/357 (16%), Positives = 101/357 (28%), Gaps = 126/357 (35%)
Query: 88 SQA--------DKADYERKV--KAAGSLRGLHGIPIL--LKDNIATKDKMNTTAGS---- 131
SQ + + V +A + +G IL + +N
Sbjct: 1626 SQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIR 1685
Query: 132 --YALLRSVVPRDAGVVVKLRKAGAIILGKASLSEWSNFRSSKAPSGFSGRGGQGKNPYV 189
Y+ + D + + + + N S+ F G +
Sbjct: 1686 ENYSAMIFETIVDGKLKTE------------KIFKEINEHSTSYT--FRSEKG------L 1725
Query: 190 LS----ADPCGSSSGSAISVAANLAAVSLGTETDGSILCPSSSNSVV-GLKPTLG----L 240
LS P A+ AA ++ G I +++ G +LG L
Sbjct: 1726 LSATQFTQP-------AL-TLMEKAAFED-LKSKGLI----PADATFAGH--SLGEYAAL 1770
Query: 241 TSRAGVIPITPRQDSVGPICRTVADAAYVLDAIAGFDHYDPATRAASEYIPRGGYKQFLR 300
S A V+ I V+ Y RG Q
Sbjct: 1771 ASLADVMSI--------------ESLVEVV-------FY------------RGMTMQVAV 1797
Query: 301 PHGLKGK-RLGIVR-NPFFNFDEGSPLAQVFDHHLHTL-----RQEGALVIDHLEIGNIN 353
P G+ G++ NP G A L + ++ G LV EI N N
Sbjct: 1798 PRDELGRSNYGMIAINP------GRVAASFSQEALQYVVERVGKRTGWLV----EIVNYN 1847
Query: 354 SLNS---IANDETTAMLAEFKLAINAYLKELVTSPVRSLAEVIAFNNKFSDLEKIKE 407
N A D L +N ++K ++ + ++I S LE+++
Sbjct: 1848 VENQQYVAAGD--LRALDTVTNVLN-FIK------LQKI-DIIELQKSLS-LEEVEG 1893
Score = 29.2 bits (65), Expect = 4.4
Identities = 20/117 (17%), Positives = 43/117 (36%), Gaps = 31/117 (26%)
Query: 9 AILAFS--LFSHL----LLPTL-------L----AISAQSNAIHAFPIREATIKDLQLAF 51
A+ F L L+P L A+++ ++ I E+ ++ + F
Sbjct: 1735 ALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADV---MSI-ESLVE---VVF 1787
Query: 52 KQNKLTSRQLVEFYLGEIHRLNPLLHGVIEVNPDALSQA-DKADYERKVKAAGSLRG 107
+ + E+ R N +G+I +NP ++ + + + V+ G G
Sbjct: 1788 YRGMTMQVAVPR---DELGRSN---YGMIAINPGRVAASFSQEALQYVVERVGKRTG 1838
>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 = 0.005
Identities = 35/180 (19%), Positives = 62/180 (34%), Gaps = 33/180 (18%)
Query: 2 HCL------KMATAILAFSLFSHLLLPTLLAISAQSNAIHAFPIREATIKDLQLAFKQNK 55
+CL + A A AF+L +LL T ++ + A ++ + ++
Sbjct: 245 NCLLVLLNVQNAKAWNAFNLSCKILLTT--RFKQVTDFLSAATTTHISLDHHSMTLTPDE 302
Query: 56 LTSRQLVEFYLG--------EIHRLNPLLHGVI-EVNPDALSQAD---KADYERKVKA-A 102
+ L+ YL E+ NP +I E D L+ D + ++
Sbjct: 303 --VKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIE 360
Query: 103 GSLRGLHGIPILLKDN-----IATKDKMNTTAGSYALL-RSVVPRDAGVVV-KLRKAGAI 155
SL L P + + + +L+ V+ D VVV KL K +
Sbjct: 361 SSLNVLE--PAEYRKMFDRLSVFPPS-AHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLV 417
Score = 37.1 bits (85), Expect = 0.014
Identities = 31/243 (12%), Positives = 58/243 (23%), Gaps = 94/243 (38%)
Query: 299 LRP------HGLKG--KRLGIVRNPFFNFDEGSPLAQVFDHHLHTLRQEGALVIDH---- 346
LRP G+ G K + +A L V
Sbjct: 147 LRPAKNVLIDGVLGSGK---------------TWVA------LDVCLSYK--VQCKMDFK 183
Query: 347 ---LEIGNINSLNSIANDETTAMLAEFKLAINAYLKELVTSPVRSLAEVIAFNNKFSDLE 403
L + N NS ++ ML + I+ + + + L
Sbjct: 184 IFWLNLKNCNSPETV-----LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLL 238
Query: 404 KIKEYGQDLLLSAEATDGIGKTEKAAILNLERFTRDGFEKLMSTNNLDA-------LVTP 456
K K Y LL +L + + + +A L+T
Sbjct: 239 KSKPYENCLL----------------VL------LN----VQNAKAWNAFNLSCKILLTT 272
Query: 457 RSYASTLLAVGGFPGINVPAGYDSEGVPFGICFGGLKGTEPKLIEIAYGFEQATKIRK-- 514
R + + ++ + S + T ++ + + R
Sbjct: 273 R-FKQVTDFLSAATTTHISLDHHSMTL-----------TPDEVKSL---LLKYLDCRPQD 317
Query: 515 -PP 516
P
Sbjct: 318 LPR 320
Score = 31.0 bits (69), Expect = 1.1
Identities = 24/115 (20%), Positives = 40/115 (34%), Gaps = 21/115 (18%)
Query: 2 HCLKMATAILAFSLFSHLLLPTLLA-----ISAQSNAIHAFPIREATIKDLQLAFKQ--- 53
H LK +LF + L I S A +A T++ L+ +K
Sbjct: 480 H-LKNIEHPERMTLFRMVFLD--FRFLEQKIRHDSTAWNASGSILNTLQQLKF-YKPYIC 535
Query: 54 -NKLTSRQLVEFYLGEIHRLNPLLH-----GVIEVNPDALSQADKADYERKVKAA 102
N +LV L + ++ L ++ + AL D+A +E K
Sbjct: 536 DNDPKYERLVNAILDFLPKIEENLICSKYTDLLRI---ALMAEDEAIFEEAHKQV 587
Score = 30.6 bits (68), Expect = 1.6
Identities = 18/115 (15%), Positives = 31/115 (26%), Gaps = 37/115 (32%)
Query: 43 TIKDLQLAFKQNKLTS----RQLVEFYLGEIHRLNPLLHGVIEVNPDA---------LSQ 89
+I + L K R +V+ Y I + +I D L
Sbjct: 427 SIPSIYLELKVKLENEYALHRSIVDHY--NIPKTFD-SDDLIPPYLDQYFYSHIGHHLKN 483
Query: 90 ADKA-----------DY---ERKVKAAGSLRGLHG--IPILL-----KDNIATKD 123
+ D+ E+K++ + G + L K I D
Sbjct: 484 IEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDND 538
>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 = 34.9 bits (79), Expect = 0.021
Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 14/43 (32%)
Query: 337 RQEGALVIDHLEIGNINSLNSIANDETTAMLAEFKLAINAYLK 379
+Q + L+ SL A+D A LAI A ++
Sbjct: 19 KQA----LKKLQ----ASLKLYADDSAPA------LAIKATME 47
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 31.6 bits (71), Expect = 0.45
Identities = 13/52 (25%), Positives = 17/52 (32%), Gaps = 3/52 (5%)
Query: 468 GFPGINVPAGYDSEGVPFGICFGGLKGTEPKLIEIAYGFEQATKIRKPPSFK 519
G G+ + Y SE + P LI I G E + K K
Sbjct: 114 GSVGMAIQVNYSSEVKENSVDSDDKAKVPP-LIRIVSGLELSDT--KQKGKK 162
>3lml_A LIN1278 protein; structural genomics, PSI-2, protein structure
initiative, northeast structural genomics consortium,
NESG, LKR115; 3.30A {Listeria innocua}
Length = 460
Score = 29.4 bits (65), Expect = 2.9
Identities = 10/50 (20%), Positives = 14/50 (28%), Gaps = 2/50 (4%)
Query: 333 LHTLRQEGALVIDHLEIGNINSLNSIANDETTAMLAEFKLAINAYLKELV 382
L + + I ++ I DE AYL EL
Sbjct: 358 LDGINNDTRRNILDAIKERKDANTDIPADENGVQF--ILSMQTAYLNELQ 405
>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair,
DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A
{Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A*
Length = 377
Score = 27.9 bits (62), Expect = 9.3
Identities = 11/69 (15%), Positives = 23/69 (33%), Gaps = 5/69 (7%)
Query: 405 IKEYGQDLLLSAEATDGIGKTEKAAILNLERFTR-DGFEKLMSTNNLDALVTPRSYASTL 463
I +Y + + A + + + +R G++ + D LV+ R Y
Sbjct: 259 IMDYSSEEVEEETAQNILQDFITRREPSPISISRVLGYDVQQAAQLDDVLVSARGYR--- 315
Query: 464 LAVGGFPGI 472
+ I
Sbjct: 316 -LLKTVARI 323
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 0.135 0.386
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,896,251
Number of extensions: 503263
Number of successful extensions: 1125
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1063
Number of HSP's successfully gapped: 39
Length of query: 520
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 422
Effective length of database: 3,965,535
Effective search space: 1673455770
Effective search space used: 1673455770
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: 59 (27.0 bits)