RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5227
(693 letters)
>3i9v_4 NADH-quinone oxidoreductase subunit 4; electron transport,
respiratory chain, cell flavoprotein, FMN, iron,
iron-sulfur, membrane; HET: FMN; 3.10A {Thermus
thermophilus} PDB: 2ybb_4* 2fug_4* 3iam_4* 3ias_4*
3m9s_4*
Length = 409
Score = 739 bits (1910), Expect = 0.0
Identities = 184/416 (44%), Positives = 256/416 (61%), Gaps = 27/416 (6%)
Query: 278 IEIKSYKLNFGPQHPAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLP 337
+ + LN GPQHP+ HGVLRL++ L GE V + PHIG LH EK E RTYLQ++
Sbjct: 21 LRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIGYLHTGFEKTMEHRTYLQNIT 80
Query: 338 YMDRLDYVSMMCNEHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDI 397
Y R+DY+ ++ AY +A+EKLL +P RA+ IRV+ +E++RL +HL+++G+ LD+
Sbjct: 81 YTPRMDYLHSFAHDLAYALAVEKLLGAVVPPRAETIRVILNELSRLASHLVFLGTGLLDL 140
Query: 398 GAMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKSSIIRNNKAT 457
GA+ YAFRERE +LD +E V+G R H Y R GGV DLPE
Sbjct: 141 GALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKEDLPE---------------- 184
Query: 458 KILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFT 517
+ ++ P IDEYE L ++ I+ +R G+GV+ PE A+ +G T
Sbjct: 185 ---------EFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLT 235
Query: 518 GPMLRGSGVKWDLRKKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIK 577
G LR SGV +D+RK PY Y FD+P+G+ GD +DR LVRI EMR+S KIIKQ ++
Sbjct: 236 GGSLRASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALE 295
Query: 578 WLRSNKGPVISNNNKITSPARINMKSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEF 637
L GPV N +IT P R ++++ME +I+HFK +TEGF+ P GE+Y E +GE
Sbjct: 296 RLEP--GPVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGEL 353
Query: 638 GIYLVSDGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVTIIGTQDIVFGEIDR 693
G Y+VSDG + PYR+K+R+P F +LQSL G + D+V II + D V G++DR
Sbjct: 354 GYYIVSDGGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR 409
>3i9v_6 NADH-quinone oxidoreductase subunit 6; electron transport,
respiratory chain, cell flavoprotein, FMN, iron,
iron-sulfur, membrane; HET: FMN; 3.10A {Thermus
thermophilus} PDB: 2ybb_6* 2fug_6* 3iam_6* 3ias_6*
3m9s_6*
Length = 181
Score = 280 bits (719), Expect = 3e-91
Identities = 77/126 (61%), Positives = 102/126 (80%), Gaps = 2/126 (1%)
Query: 27 DKLINWTRTSSMWPMTFGLACCAIEMMHAGASRYDLDRFGI-MFRPSPRQSDVMIVAGTL 85
+KL+ W R++S+WP TFGLACCAIEMM + +R DL RFG +FR SPRQ+DVMIVAG L
Sbjct: 25 EKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLARFGSEVFRASPRQADVMIVAGRL 84
Query: 86 CNKMAPALRKVYDQMTEPKWVISMGSCANGGGYYHYSYSVVRGCDRIVPVDVYIPGCPPT 145
KMAP +R+V++QM +PKWVISMG+CA+ GG ++ +Y++V+ D +VPVDVY+PGCPP
Sbjct: 85 SKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFN-NYAIVQNVDSVVPVDVYVPGCPPR 143
Query: 146 AEALLY 151
EAL+Y
Sbjct: 144 PEALIY 149
>3i9v_5 NADH-quinone oxidoreductase subunit 5; electron transport,
respiratory chain, cell flavoprotein, FMN, iron,
iron-sulfur, membrane; HET: FMN; 3.10A {Thermus
thermophilus} PDB: 2ybb_5* 2fug_5* 3iam_5* 3ias_5*
3m9s_5*
Length = 207
Score = 175 bits (446), Expect = 4e-51
Identities = 51/128 (39%), Positives = 70/128 (54%), Gaps = 13/128 (10%)
Query: 158 KILRDHVNFRFEQLIDLCGIDYSIYNKNINSDNSNKNLRFAIVLHLLSLNY-----NWRL 212
+ + + F L D+ G+DY Y + RFA+V L+SL R
Sbjct: 36 EEMAHYKAMGFNFLADIVGLDYLTYP-------DPRPERFAVVYELVSLPGWKDGDGSRF 88
Query: 213 RVRVFAENNELPRLHSITSLWSSANWYEREAFDLFGIFFDGHDDLRRLLTDYGFVGHPFR 272
VRV+ + PRL ++T LW SAN+ ERE +DLFGI F+GH DLR++LT GHP R
Sbjct: 89 FVRVYVPEED-PRLPTVTDLWGSANFLEREVYDLFGIVFEGHPDLRKILTPEDLEGHPLR 147
Query: 273 KDFPVIEI 280
KD+P+ E
Sbjct: 148 KDYPLGET 155
>3mcr_A NADH dehydrogenase, subunit C; structural genomics, joint center
for structural genomics, J protein structure initiative,
PSI-2; 2.65A {Thermobifida fusca}
Length = 213
Score = 151 bits (382), Expect = 4e-42
Identities = 33/108 (30%), Positives = 53/108 (49%), Gaps = 11/108 (10%)
Query: 152 DYYSTMKILRDHVNFRFEQLIDLCGIDYSIYNKNINSDNSNKNLRFAIVLHLLSLNYNWR 211
LRD RFE + + G+ Y ++ V L S+ +N+
Sbjct: 117 HLLDVATRLRDDPALRFELCLGVTGVHYP----------EDEGNELHAVYALRSITHNYE 166
Query: 212 LRVRVFAENNELPRLHSITSLWSSANWYEREAFDLFGIFFDGHDDLRR 259
+R+ V +++ P + SI S++ + +W+EREA+D FGI FDGH L R
Sbjct: 167 IRLEVSCPDSD-PHIPSIVSVYPTNDWHEREAWDFFGIIFDGHPALTR 213
>1cc1_S Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxidoreductase;
2.15A {Desulfomicrobium baculatum} SCOP: e.19.1.1
Length = 283
Score = 60.8 bits (147), Expect = 3e-10
Identities = 16/95 (16%), Positives = 36/95 (37%), Gaps = 11/95 (11%)
Query: 88 KMAPALRKVYDQMTEPKWVISMGSCANGGGYYHYSYSV--------VRGCDRIVPVDVYI 139
+ + D + +++G+C+ GG +V ++I + V +
Sbjct: 102 HEVTMMELIRDLAPKSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNV 161
Query: 140 PGCPPTAEALLYDYYSTMKILRDHVNFRFEQLIDL 174
PGCPP + ++ + + +N L +L
Sbjct: 162 PGCPPHPDWMV---GTLVAAWSHVLNPTEHPLPEL 193
>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 = 61.4 bits (148), Expect = 8e-10
Identities = 89/616 (14%), Positives = 167/616 (27%), Gaps = 174/616 (28%)
Query: 45 LACCAIE-MMHAGASRYDLDRFGIMFRPSPRQSDVMIVAGTLCNK--------MAPALRK 95
C ++ M + S+ ++D I+ + + TL +K + LR
Sbjct: 33 FDCKDVQDMPKSILSKEEIDH--IIMSKDAVSGTLRLF-WTLLSKQEEMVQKFVEEVLRI 89
Query: 96 VYDQMTEPKWVISMGSCANGGGYYHYSYSVVRGCDRIVPVDVYIPGCPPTAEALLYDYYS 155
Y + P Y + +V
Sbjct: 90 NYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRL--------------Q 135
Query: 156 TMKILRDHV-NFRFEQLIDLCGI--------------DYSIYNKN------INSDNSNK- 193
LR + R + + + G+ Y + K +N N N
Sbjct: 136 PYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSP 195
Query: 194 --------NLRFAIVLHLLSL-NYNWRLRVRVFAENNELPRLHSI----TSL------WS 234
L + I + S +++ +++R+ + EL RL L +
Sbjct: 196 ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQN 255
Query: 235 SANWYEREAFDLFGIFFDGHDDLRRLLT--DYG---FVGHPFRKDFPVIEIKSYKLNFGP 289
+ W AF+L + LLT F+ +
Sbjct: 256 AKAW---NAFNL---------SCKILLTTRFKQVTDFLSAATTTHISLDHHSM-----TL 298
Query: 290 QHPAAHGVLRLILELEG----EVVRKADP-HIGLLHRATEKLAEQRTYLQSLPYMDRLDY 344
+L L+ V +P + ++ E + + + D
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSII---AESIRD---------GLATWDN 346
Query: 345 VSMMCNEHAYVMAIEKLLNIKIP--IRAQYIR-VMFDE---ITRLLNHLMWIGSHSLDIG 398
+ N IE LN+ P R + R +F I +L L+W D+
Sbjct: 347 WKHV-NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVM 405
Query: 399 AMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDL---PEIMPQYKSSIIRNNK 455
+ L + L++ S + +Y +L E SI+ +
Sbjct: 406 VVVNKL----HKYSLVEKQPKESTISIP-------SIYLELKVKLENEYALHRSIVDHYN 454
Query: 456 ATKILNENRQGSLLDFIED--FTNRFP---KNIDEYETLLTDNRIWKQRLVGIGVVSPER 510
K + + L+ D F + KNI+ E + ++
Sbjct: 455 IPKTFDSD---DLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVF-------------- 497
Query: 511 ALSMGFTGPMLRGSGVKW-----------DLRKKQPYEIYNLLNFDIPIGKNGDSYDRYL 559
L F +R W L+ Y+ Y I N Y+R +
Sbjct: 498 -LDFRFLEQKIRHDSTAWNASGSILNTLQQLKF---YKPY--------ICDNDPKYERLV 545
Query: 560 VRIEE--MRQSNKIIK 573
I + + +I
Sbjct: 546 NAILDFLPKIEENLIC 561
Score = 59.5 bits (143), Expect = 3e-09
Identities = 44/317 (13%), Positives = 90/317 (28%), Gaps = 112/317 (35%)
Query: 45 LACCAI-EMMHAGASRYDLDRFGIMFRPSPRQSDV----MIVAGTLCNKMAPA-LRKVYD 98
I E + G + +D + + + I+ +L N + PA RK++D
Sbjct: 328 RRLSIIAESIRDGLATWD--NW--------KHVNCDKLTTIIESSL-NVLEPAEYRKMFD 376
Query: 99 QMTEPKWVISMGSCANGGGYYHYSYSVVRGCDRIVPVDVYIPGCPPTAEALLYDYYSTMK 158
+++ + P +IP +
Sbjct: 377 RLS------------------------------VFPPSAHIP-------------TILLS 393
Query: 159 IL-RDHVNFRFEQLIDLCGIDYSIYNKNINSDNSNKNLRFAIVLHLLSLNYNWRLRVRVF 217
++ D + +++ YS+ K I + + L
Sbjct: 394 LIWFDVIKSDVMVVVNKL-HKYSLVEKQ--------PKESTISIPSIYLELK-------- 436
Query: 218 AENNELPRLH-SITSLWSSANWYEREAF---DLFGIFFD--GH-----------DDLRRL 260
+ LH SI ++ ++ + L F+ GH R +
Sbjct: 437 VKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMV 496
Query: 261 LTDYGFVGHPFRKDFP-----------VIEIKSYKLNFGPQHPAAHGVLRLILE----LE 305
D+ F+ R D + ++K YK P ++ IL+ +E
Sbjct: 497 FLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIE 556
Query: 306 GEVVRKADPHIGLLHRA 322
++ + LL A
Sbjct: 557 ENLIC--SKYTDLLRIA 571
Score = 53.3 bits (127), Expect = 2e-07
Identities = 86/508 (16%), Positives = 157/508 (30%), Gaps = 161/508 (31%)
Query: 190 NSNKNLRFAIVLHLLSLNYNWRLRVRVFAENNELPRLHSITSLWSSANWYEREAFDLFG- 248
+ + + V +L +NY + L + E + P + + Y + L+
Sbjct: 73 SKQEEMVQKFVEEVLRINYKF-LMSPIKTEQRQ-PSMMTRM--------YIEQRDRLYND 122
Query: 249 --IFFDGH-------DDLRRLLTD---------YGFVGHPFRK---------DFPVIEIK 281
+F + LR+ L + G +G K + V
Sbjct: 123 NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLG--SGKTWVALDVCLSYKVQCKM 180
Query: 282 SYK---LNFGPQHPAAHGVL----RLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQ 334
+K LN + + VL +L+ +++ ++D + R AE R L+
Sbjct: 181 DFKIFWLNLKNCN-SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK 239
Query: 335 SLPYMDRL---DYVSMMCNEHAYVMAIEKLLNI--KIPIRAQYIRVMFDEITRLLNHLMW 389
S PY + L V N N+ KI + ++ +V H+
Sbjct: 240 SKPYENCLLVLLNV---QNA-----KAWNAFNLSCKILLTTRFKQVTDFLSAATTTHI-- 289
Query: 390 IGSHSLDIGAMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPE----IMPQ 445
SLD +M + E + LL Y +DLP P+
Sbjct: 290 ----SLDHHSMTLTP---DEVKSLL------------LKYL--DCRPQDLPREVLTTNPR 328
Query: 446 YKSSI---IRNNKAT----KILNENRQGSL----LDFIEDFTNR--------FPKNIDEY 486
S I IR+ AT K +N ++ ++ L+ +E R FP +
Sbjct: 329 RLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIP 388
Query: 487 ETLLTDNRIWKQRLVGIGVVSPERALSMGFTGPMLRGSGVKWDLRKKQPYEIYNLLNFDI 546
LL+ IW ++ M + + S V+ K+ I ++
Sbjct: 389 TILLS--LIWFD---------VIKSDVMVVVNKLHKYSLVEKQ-PKESTISIPSI----- 431
Query: 547 PIGKNGDSYDRYLVRIEEMRQSNKIIKQCIKWLRSNKGPVISNNNKITSPARINMKSNME 606
Y V++E ++ I ++ +++ + P
Sbjct: 432 --------YLELKVKLENEYALHRSIVDHYNIPKT------FDSDDLIPPY--------L 469
Query: 607 D------LIHHFK---------LFTEGF 619
D + HH K LF F
Sbjct: 470 DQYFYSHIGHHLKNIEHPERMTLFRMVF 497
Score = 49.1 bits (116), Expect = 5e-06
Identities = 80/501 (15%), Positives = 149/501 (29%), Gaps = 156/501 (31%)
Query: 65 FGIM---FRPSPRQSDVMIVAGTLCNKMAPALRKVYDQMTEPKWVISMGSCANGGGYYHY 121
F I + V+ + L ++ P D + K I H
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI------------HS 229
Query: 122 SYSVVRGCDRIVPVDVYIPGCPPTAEALLYDYYSTMKILRD-----HVN-F--------- 166
+ +R R++ Y LL +L + N F
Sbjct: 230 IQAELR---RLLKSKPY-------ENCLL--------VLLNVQNAKAWNAFNLSCKILLT 271
Query: 167 -RFEQLIDLCGIDYSIYNKNINSDNSNKNLRFAIVLHLLSLNYNWRLRVRVFAENNELPR 225
RF+Q+ D + +I+ D+ + L V LL + L R +LPR
Sbjct: 272 TRFKQVTDFLS---AATTTHISLDHHSMTLTPDEVKSLLL---KY-LDCRPQ----DLPR 320
Query: 226 ----------------LHSITSLWSSANW--YEREAFD-LFGIFFDGHD--DLRRLLTDY 264
+ + W NW + + + + + R++
Sbjct: 321 EVLTTNPRRLSIIAESIRDGLATWD--NWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRL 378
Query: 265 GFVGHPFRKDFPVIEIKSYKLNFGPQHPAAHGVLRLI-LELEGEVVRKADPHIGLLHRAT 323
F + P +L LI ++ V + LH+ +
Sbjct: 379 SV----FPPSAHI--------------PTI--LLSLIWFDVIKSDVMVV---VNKLHKYS 415
Query: 324 --EKLAEQRTYLQSLP--YMDRLDYVSMMCNEHAYVMAIEKLLNIKIPIRAQY-IRVMFD 378
EK ++ T S+P Y++ + H +++ Y I FD
Sbjct: 416 LVEKQPKESTI--SIPSIYLELKVKLENEYALHR------SIVD-------HYNIPKTFD 460
Query: 379 EITRLLNHL-----MWIGSHSLDIGAMGVLLYAFREREDLLDCYEAVSGARMHA--AYYR 431
+ +L IG H L + FR LD + + H A+
Sbjct: 461 SDDLIPPYLDQYFYSHIGHH-LKNIEHPERMTLFRMV--FLD-FRFLEQKIRHDSTAWNA 516
Query: 432 PGGVYRDLPEIMPQYKSSIIRNNKATKILNENRQGSLLDFIEDFTNRFPKNIDEYETLLT 491
G + L ++ YK I N + + L++ I DF + +N+ +
Sbjct: 517 SGSILNTLQQLK-FYKPYICDN--------DPKYERLVNAILDFLPKIEENLICSKYT-- 565
Query: 492 DNRIWKQRLVGIGVVSPERAL 512
L+ I +++ + A+
Sbjct: 566 -------DLLRIALMAEDEAI 579
Score = 43.3 bits (101), Expect = 3e-04
Identities = 23/141 (16%), Positives = 47/141 (33%), Gaps = 28/141 (19%)
Query: 470 DFIEDFTNRFPKNIDEYETL------LTD---NRIWKQ--------RLVGIGVVSPERAL 512
D + F + F N D + L+ + I RL + E +
Sbjct: 20 DILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMV 79
Query: 513 SMGFTGPMLRGS----GVKWDLRKKQPYEIYNLLNFDI-PIGKNGDSYDRYLV-RIEEMR 566
F +LR + ++QP + + + + + +Y V R++
Sbjct: 80 QK-FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYL 138
Query: 567 QSNKIIKQCIKWLRSNKGPVI 587
+ ++Q + LR K +I
Sbjct: 139 K----LRQALLELRPAKNVLI 155
>2wpn_A Periplasmic [nifese] hydrogenase, small subunit; metal-binding,
oxidoreductase, oxygen tolerance; HET: FSX SBY PSW;
2.04A {Desulfovibrio vulgaris}
Length = 317
Score = 57.4 bits (138), Expect = 4e-09
Identities = 21/118 (17%), Positives = 43/118 (36%), Gaps = 12/118 (10%)
Query: 81 VAGTLCNKMAPALRKVYDQMTEPKWVISMGSCANGGG----YYHYSYSV----VRGCDRI 132
+ G + + + + V+++G+CA GG + + G + I
Sbjct: 124 IIGEANHHEISMVDALKEFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGI 183
Query: 133 VPVDVYIPGCPPTAE----ALLYDYYSTMKILRDHVNFRFEQLIDLCGIDYSIYNKNI 186
V IPGCPP + ++ + K + +++D G + +NI
Sbjct: 184 KTPVVNIPGCPPHPDWIVGTVVLALDAIKKNGLEGGLAEVVKVLDSDGRPTPFFGRNI 241
>1h2a_S Hydrogenase; SO ligand, hydrogen metabolism, Mg center, MIR, MAD,
oxidoreductase; 1.80A {Desulfovibrio vulgaris str} SCOP:
e.19.1.1
Length = 317
Score = 57.0 bits (137), Expect = 7e-09
Identities = 24/157 (15%), Positives = 47/157 (29%), Gaps = 36/157 (22%)
Query: 31 NWTRTSSMWPMTFGLACCAIEMMHAGASRYD---LDRFGIMFRPSP-------------- 73
R S ++ C+ ++ A D LD + + +
Sbjct: 53 GPRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAALEQ 112
Query: 74 ----RQSDVMIVAGTLCNKMA---------PALRKVYDQMTEPKWVISMGSCANGGG--Y 118
+ +V G + L + + + VI+ G+CA GG
Sbjct: 113 AVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQA 172
Query: 119 YHYSYSVVRGCDRIVP----VDVYIPGCPPTAEALLY 151
+ + +G + + + I GCPP L+
Sbjct: 173 AKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVG 209
>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 = 56.2 bits (135), Expect = 4e-08
Identities = 103/606 (16%), Positives = 183/606 (30%), Gaps = 200/606 (33%)
Query: 120 HYSYSVVRGCDRIV-----PVDVYIPGCPPTAEALLYDYY--------------STMKIL 160
+ S ++ ++ P + + PT A L + ++L
Sbjct: 27 FFIASQLQ--EQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVL 84
Query: 161 RDHVNFRFEQLIDLCGIDYSIYN--KNINSDNSNKNLRFAIVLHLLSLNYNWRLRVRVFA 218
+ FE L G D I+ + +N ++ ++ NY + R+ A
Sbjct: 85 NLCLT-EFENCY-LEGND--IHALAAKLLQENDTTLVKTKELI----KNY---ITARIMA 133
Query: 219 ENNELPRLHSITSLWSSANWYEREAFDLFGIF---------FDGHDDLRRLLTDYGFVGH 269
+ + ++L+ + L IF F+ +LR L Y H
Sbjct: 134 -KRPFDKKSN-SALFRAV---GEGNAQLVAIFGGQGNTDDYFE---ELRDLYQTY----H 181
Query: 270 PFRKDFPVIEIKSYKLNFGPQHPAA------HGVLRLILELEGEVVRKAD---------- 313
D I+ + L+ + G L ++ LE
Sbjct: 182 VLVGDL--IKFSAETLSELIRTTLDAEKVFTQG-LNILEWLENPSNTPDKDYLLSIPISC 238
Query: 314 PHIGLL---H-RATEKL-----AEQRTYLQSLPYMDRLDYVSMMCNEHAYVMAI----EK 360
P IG++ H T KL E R+YL+ + V+ A +A E
Sbjct: 239 PLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQ-GLVT------AVAIAETDSWES 291
Query: 361 LLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFREREDLLDCYEAV 420
+ I V+F +IG + A ED L+ E V
Sbjct: 292 FFVSV----RKAITVLF-----------FIGVRCYE--AYPNTSLPPSILEDSLENNEGV 334
Query: 421 SGARMHAAYYRPGGVYRDLPEIMPQYKSSIIRNNKATKILNENRQ--------------- 465
M + + +L + Q + + + N L +Q
Sbjct: 335 PSP-MLS-------I-SNLTQ--EQVQDYVNKTNSH---LPAGKQVEISLVNGAKNLVVS 380
Query: 466 G---SLLDFIEDF-TNRFPKNIDEYETLLTDNRI-WKQRLVGIG-----VVSPERALSMG 515
G SL + P +D+ +RI + +R + V SP
Sbjct: 381 GPPQSLYGLNLTLRKAKAPSGLDQ-------SRIPFSERKLKFSNRFLPVASP------- 426
Query: 516 FTGPMLRG--SGVKWDLRKKQPYEIYNLLNFDIPI-----GKNGDSYDRYLV-RIEEMRQ 567
F +L + DL K +N + IP+ G + + RI +
Sbjct: 427 FHSHLLVPASDLINKDLVKNN--VSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDC-- 482
Query: 568 SNKIIKQCIKWLRSNK---------GP-------VISNNNKITSPARI----NMKSNMED 607
II+ +KW + + GP V+++ NK + R+ + N +D
Sbjct: 483 ---IIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINPDD 539
Query: 608 LIHHFK 613
FK
Sbjct: 540 DY-GFK 544
Score = 41.6 bits (97), Expect = 0.001
Identities = 85/563 (15%), Positives = 152/563 (26%), Gaps = 221/563 (39%)
Query: 227 HSI---TSLWSSANWYEREAF--------DLFGIFFDGHDDLR---RLLTDY-GFVGHPF 271
H + T+ + A+ +E F + F D+ L+ + G+V
Sbjct: 18 HVLLVPTASFFIASQL-QEQFNKILPEPTEGFA----ADDEPTTPAELVGKFLGYVSSLV 72
Query: 272 RKDFPVIEIKSYKLNFGPQHPAAHGVLRLIL-ELEGEVVRKADPHIGLLHRATEKLAEQR 330
+ VL L L E E
Sbjct: 73 EPS---------------KVGQFDQVLNLCLTEFE------------------------N 93
Query: 331 TYLQSLPYMDRLDYVSMMCNE-HAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMW 389
YL+ N+ HA + + + + + I+ +
Sbjct: 94 CYLEG--------------NDIHALAAKLLQENDTTLVKTKELIKNYI-TARIMAKRPFD 138
Query: 390 IGSHSLDIGAMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGG-----VY----RDLP 440
S+S L A E A++ A + GG Y RDL
Sbjct: 139 KKSNSA-------LFRAVGEGN-----------AQLVAIF---GGQGNTDDYFEELRDLY 177
Query: 441 EIMPQYKSSIIRNNKATKILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQR- 499
+ +I+ + + L+E L+ D F + ++ +L W +
Sbjct: 178 QTYHVLVGDLIKF--SAETLSE-----LIRTTLDAEKVFTQGLN----ILE----WLENP 222
Query: 500 ---------------LVGIGVV--------------SPE--RALSMGFTGPMLRGSGV-- 526
IGV+ +P R+ G TG G+
Sbjct: 223 SNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATG---HSQGLVT 279
Query: 527 --------KWDLRKKQPYEIYNLL------------NFDIPIGKNGDSYDR------YLV 560
W+ + +L N +P DS + ++
Sbjct: 280 AVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPML 339
Query: 561 RIEEMRQS--NKIIKQCIKWLRSNKGPVISNNNK-----ITSPARINMKSNMEDLIHHFK 613
I + Q + + L + K IS N ++ P + L +
Sbjct: 340 SISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQ--------SL-YGLN 390
Query: 614 LFTEGFYVPLGEIYSCVEHP--KGEFGI-YLVSDGANKPYRIKIRSPGFAH---LQSLSE 667
L P G S + K +F +L P + SP F H L S+
Sbjct: 391 LTLRKAKAPSGLDQSRIPFSERKLKFSNRFL-------P----VASP-F-HSHLLVPASD 437
Query: 668 MISGHMISDVVTIIGTQ-DI-VF 688
+I+ ++ + V+ I V+
Sbjct: 438 LINKDLVKNNVSFNAKDIQIPVY 460
Score = 41.6 bits (97), Expect = 0.001
Identities = 53/291 (18%), Positives = 90/291 (30%), Gaps = 106/291 (36%)
Query: 443 MPQYKSS-IIRN--NKATKILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQR 499
M YK+S ++ N+A + S+LD + + N P N+ +
Sbjct: 1633 MDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVIN--N--PVNLTIH------------- 1675
Query: 500 LVGIGVVSPERALSMGFTGPMLRGSGVKWDLRKKQPYEIYNLLNFDIPIGKNGDSYDRYL 559
F G +G K+ E Y+ + F+ D L
Sbjct: 1676 ----------------FGGE--KG---------KRIRENYSAMIFE-------TIVDGKL 1701
Query: 560 VRIEEMRQSNKIIKQCIKWLRSNKGPVISNNNKITSPARINM----KSNMEDLIHHFKLF 615
+ ++ N+ RS KG + + + T PA + K+ EDL L
Sbjct: 1702 KTEKIFKEINEHSTSYT--FRSEKGLL--SATQFTQPA---LTLMEKAAFEDLKSKG-LI 1753
Query: 616 TEGFYV---PLGEIYS---C-------------VEH---------PKGEFGIYLVSDGAN 647
LGE Y+ V + P+ E G A
Sbjct: 1754 PADATFAGHSLGE-YAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAI 1812
Query: 648 KPYRIKIRSPGFAH--LQSLSEMISGHMISDVVTII-----GTQDIVFGEI 691
P R+ + F+ LQ + E + +V I+ Q + G++
Sbjct: 1813 NPGRV---AASFSQEALQYVVERVGKRT-GWLVEIVNYNVENQQYVAAGDL 1859
Score = 31.2 bits (70), Expect = 1.5
Identities = 39/207 (18%), Positives = 56/207 (27%), Gaps = 102/207 (49%)
Query: 368 IRAQYIRVMFD--------------EITRLLNHLMWIGS--------------------- 392
IR Y ++F+ EI +
Sbjct: 1684 IRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAA 1743
Query: 393 ------------------HSLDIG---AM----GVLLYAFREREDLLD--------CYEA 419
HSL G A+ V+ + E L++ A
Sbjct: 1744 FEDLKSKGLIPADATFAGHSL--GEYAALASLADVM--SI---ESLVEVVFYRGMTMQVA 1796
Query: 420 V-------SGARMHAAYYRPGGVYRDLPEIMPQYKSSII-RNNKATK----ILN---ENR 464
V S M A PG V + QY ++ R K T I+N EN+
Sbjct: 1797 VPRDELGRSNYGMIAI--NPGRVAASFSQEALQY---VVERVGKRTGWLVEIVNYNVENQ 1851
Query: 465 Q----GSL--LDFIEDFTNRF-PKNID 484
Q G L LD + + N + ID
Sbjct: 1852 QYVAAGDLRALDTVTNVLNFIKLQKID 1878
>3ayx_B Membrane-bound hydrogenase small subunit; oxidoreductase,
membrane-bound NI-Fe hydrogenase; 1.18A {Hydrogenovibrio
marinus} PDB: 3ayy_B 3ayz_B
Length = 283
Score = 52.7 bits (126), Expect = 1e-07
Identities = 18/95 (18%), Positives = 34/95 (35%), Gaps = 16/95 (16%)
Query: 73 PRQSDVMIVAGTLCNKM---------APALRKVYDQMTEPKWVISMGSCANGGGYY--HY 121
+ + ++ V G P ++ + K +IS GSCA+ G
Sbjct: 73 YKGNYILAVEGNPPLNQDGMSCIIGGRPFSEQLKRMADDAKAIISWGSCASWGCVQAAKP 132
Query: 122 SYSVVRGCDRIVPVD-----VYIPGCPPTAEALLY 151
+ + + + + +PGCPP AE +
Sbjct: 133 NPTQATPVHKFLGGGYDKPIIKVPGCPPIAEVMTG 167
>1yqw_A Periplasmic [NIFE] hydrogenase small subunit; NI-Fe hydrogenase
unready state, oxidoreductase; 1.83A {Desulfovibrio
fructosovorans} PDB: 3cur_A 3cus_A 3h3x_A 1yrq_A 1frf_S
Length = 264
Score = 51.9 bits (124), Expect = 2e-07
Identities = 19/90 (21%), Positives = 32/90 (35%), Gaps = 12/90 (13%)
Query: 74 RQSDVMIVAGTLCNKMA---------PALRKVYDQMTEPKWVISMGSCANGGG--YYHYS 122
+ ++V G L P + + K +I +G+C+ GG +
Sbjct: 67 KDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPN 126
Query: 123 YSVVRGCDRIVPVDVY-IPGCPPTAEALLY 151
S +G + V IPGCPP +
Sbjct: 127 PSQAKGVSEALGVKTINIPGCPPNPINFVG 156
>1wui_S Periplasmic [NIFE] hydrogenase small subunit; high resolution
[NIFE]hydrogenase, oxidoreductase, NI-A state, unready
state; HET: NFC; 1.04A {Desulfovibrio vulgaris str}
SCOP: e.19.1.1 PDB: 1h2r_S 1ubj_S 1ubh_S 1ubl_S 1ubm_S
1ubo_S 1ubr_S 1ubt_S 1ubu_S 1wuh_S* 1ubk_S* 1wuj_S
1wuk_S 1wul_S 1e3d_A*
Length = 267
Score = 51.9 bits (124), Expect = 2e-07
Identities = 17/95 (17%), Positives = 33/95 (34%), Gaps = 15/95 (15%)
Query: 72 SPRQSDVMIVAGTLCNKMA---------PALRKVYDQMTEPKWVISMGSCANGGG--YYH 120
+ + +V G + L + + + VI+ G+CA GG
Sbjct: 65 NSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAAK 124
Query: 121 YSYSVVRGCDRIVP----VDVYIPGCPPTAEALLY 151
+ + +G + + + I GCPP L+
Sbjct: 125 PNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVG 159
>2wpn_B Periplasmic [nifese] hydrogenase, large subunit,
selenocysteine-containing; metal-binding,
oxidoreductase, oxygen tolerance; HET: FSX SBY PSW;
2.04A {Desulfovibrio vulgaris}
Length = 495
Score = 51.1 bits (122), Expect = 8e-07
Identities = 35/218 (16%), Positives = 62/218 (28%), Gaps = 44/218 (20%)
Query: 296 GVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMC----NE 351
G L+ + +E V A G+ R E + R D V +C
Sbjct: 29 GHLKAEVVVENGKVVDARLSGGMY-RGFETILRGR------DPRDASQIVQRICGVCPTA 81
Query: 352 H--AYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWI-GSHSLD------------ 396
H A V+A+++ K+P + R + L +H++ + D
Sbjct: 82 HSTASVLALDEAFGAKVPNNGRITRNLIFGANYLQSHILHFYHLSAQDFVQGPDTAPFVP 141
Query: 397 ------------IGAMGVLLY--AFREREDLLDCYEAVSGARMHAAYYRPGGVYRDL-PE 441
+ GV Y A R + G H GG E
Sbjct: 142 RFPKSDLRLSKELNKAGVDQYIEALEVRRICHEMVALFGGRMPHVQGQVVGGATEIPTKE 201
Query: 442 IMPQYKSSIIRNNKATKILNENRQGSLLDFIEDFTNRF 479
+ +Y + K + + + + + F
Sbjct: 202 KLVEYAARF---KKVRDFVEQKYVPVVYTIGSKYKDMF 236
>3rgw_S Membrane-bound hydrogenase (NIFE) small subunit H; [NIFE]
hydrogenase, high-resolution knallgasbacteria,
proteobacteria; 1.50A {Ralstonia eutropha}
Length = 339
Score = 50.9 bits (121), Expect = 8e-07
Identities = 19/108 (17%), Positives = 40/108 (37%), Gaps = 13/108 (12%)
Query: 57 ASRYDLDRFGIMFRPSPRQSDVMIVAGTLCNK---------MAPALRKVYDQMTEPKWVI 107
A+ + + + + ++ V G P + ++ + K +I
Sbjct: 51 AAGHQAEAILEEIMTKYKGNYILAVEGNPPLNQDGMSCIIGGRPFIEQLKYVAKDAKAII 110
Query: 108 SMGSCANGGGYY--HYSYSVVRGCDRIVPVD--VYIPGCPPTAEALLY 151
S GSCA+ G + + +++ + +PGCPP AE +
Sbjct: 111 SWGSCASWGCVQAAKPNPTQATPVHKVITDKPIIKVPGCPPIAEVMTG 158
>3uqy_S Hydrogenase-1 small chain; membrane-bound hydrogenase,
oxidoreductase; HET: LMT; 1.47A {Escherichia coli} PDB:
3usc_S* 3use_S*
Length = 335
Score = 49.7 bits (118), Expect = 2e-06
Identities = 15/92 (16%), Positives = 32/92 (34%), Gaps = 13/92 (14%)
Query: 73 PRQSDVMIVAGTLCNKMA---------PALRKVYDQMTEPKWVISMGSCANGGG--YYHY 121
++ V G P + K+ +I+ G+CA+ G
Sbjct: 67 YNGKYILAVEGNPPLGEQGMFCISSGRPFIEKLKRAAAGASAIIAWGTCASWGCVQAARP 126
Query: 122 SYSVVRGCDRIVP--VDVYIPGCPPTAEALLY 151
+ + D+++ + +PGCPP + +
Sbjct: 127 NPTQATPIDKVITDKPIIKVPGCPPIPDVMSA 158
>1yq9_A Periplasmic [NIFE] hydrogenase small subunit; oxidoreductase; 2.35A
{Desulfovibrio gigas} SCOP: e.19.1.1 PDB: 2frv_S 1frv_A
Length = 264
Score = 48.1 bits (114), Expect = 4e-06
Identities = 16/99 (16%), Positives = 32/99 (32%), Gaps = 15/99 (15%)
Query: 68 MFRPSPRQSDVMIVAGTLCNK---------MAPALRKVYDQMTEPKWVISMGSCANGGG- 117
+ + V ++ G + + + K VI++G+CA GG
Sbjct: 59 ALHEAIKGDFVCVIEGGIPMGDGGYWGKVGGRNMYDICAEVAPKAKAVIAIGTCATYGGV 118
Query: 118 -YYHYSYSVVRGCDRIVPV----DVYIPGCPPTAEALLY 151
+ + G + + + I GCPP +
Sbjct: 119 QAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVG 157
>3rko_A NADH-quinone oxidoreductase subunit A; complex I, proton pump,
membrane protein, Na ubiquinone, cytoplasmic membrane;
HET: LFA CA7; 3.00A {Escherichia coli}
Length = 147
Score = 45.5 bits (108), Expect = 6e-06
Identities = 9/27 (33%), Positives = 10/27 (37%)
Query: 1 MGRILGPYKPNPQKNSPYECGFKEFGD 27
G LG KN P+E G G
Sbjct: 33 GGWFLGGRARARSKNVPFESGIDSVGS 59
>1cc1_L Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxidoreductase;
2.15A {Desulfomicrobium baculatum} SCOP: e.18.1.1
Length = 498
Score = 45.0 bits (106), Expect = 7e-05
Identities = 33/234 (14%), Positives = 64/234 (27%), Gaps = 57/234 (24%)
Query: 296 GVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMC----NE 351
G L++ +E++ V A G+ R E++ R D V +C
Sbjct: 24 GHLKIEVEVKDGKVVDAKCSGGMF-RGFEQILRGR------DPRDSSQIVQRICGVCPTA 76
Query: 352 HAY--VMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWI------------------- 390
H VMA + +K+ + R + L +H++
Sbjct: 77 HCTASVMAQDDAFGVKVTTNGRITRNLIFGANYLQSHILHFYHLAALDYVKGPDVSPFVP 136
Query: 391 --------------GSHSLDIGAMGVLLY--AFREREDLLDCYEAVSGARMHAAYYRPGG 434
G+ + G+ Y A R + G H GG
Sbjct: 137 RYANADLLTDRIKDGAKADATNTYGLNQYLKALEIRRICHEMVAMFGGRMPHVQGMVVGG 196
Query: 435 VYRDLPEIMPQYKSSIIRNNKATKILNENRQGSLLDFIEDFTNRFPKNIDEYET 488
+ + + E ++ + +++ D +ET
Sbjct: 197 ATEIP---------TADKVAEYAARFKEVQKFVIEEYLPLIYTLGSVYTDLFET 241
>1wui_L Periplasmic [NIFE] hydrogenase large subunit; high resolution
[NIFE]hydrogenase, oxidoreductase, NI-A state, unready
state; HET: NFC; 1.04A {Desulfovibrio vulgaris str}
SCOP: e.18.1.1 PDB: 1ubj_L 1ubh_L 1ubl_L 1ubm_L 1ubo_L
1ubr_L 1ubt_L 1ubu_L 1wuh_L* 1ubk_L* 1wuj_L 1wuk_L
1wul_L 1h2r_L 1h2a_L
Length = 534
Score = 44.0 bits (103), Expect = 1e-04
Identities = 27/157 (17%), Positives = 51/157 (32%), Gaps = 20/157 (12%)
Query: 296 GVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMC----NE 351
G LR+ +E+E V+ A L R E + + R D + C
Sbjct: 17 GHLRIEVEVENGKVKNAYSS-STLFRGLEIILKGR------DPRDAQHFTQRTCGVCTYT 69
Query: 352 HAY--VMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFRE 409
HA ++ + + IP A YIR L+ ++ H + + L +
Sbjct: 70 HALASTRCVDNAVGVHIPKNATYIR-------NLVLGAQYLHDHIVHFYHLHALDFVDVT 122
Query: 410 REDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQY 446
D +A A + + + + + +
Sbjct: 123 AALKADPAKAAKVASSISPRKTTAADLKAVQDKLKTF 159
>3ayx_A Membrane-bound hydrogenase large subunit; oxidoreductase,
membrane-bound NI-Fe hydrogenase; 1.18A {Hydrogenovibrio
marinus} PDB: 3ayy_A 3ayz_A 3rgw_L
Length = 596
Score = 43.3 bits (101), Expect = 2e-04
Identities = 23/101 (22%), Positives = 41/101 (40%), Gaps = 12/101 (11%)
Query: 296 GVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMCN----- 350
G +R + ++ V + G + R E + R D +V +C
Sbjct: 29 GHMRCEVNVDENNVIQNAVSTGTMWRGLEVILRGR------DPRDAWAFVERICGVCTGC 82
Query: 351 -EHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWI 390
A V A+E L+IKIP A IR + + ++ +H++
Sbjct: 83 HALASVRAVEDALDIKIPHNATLIREIMAKTLQIHDHIVHF 123
>1e3d_B [NIFE] hydrogenase large subunit; molecular modelling, electron
transfer; HET: FSX; 1.8A {Desulfovibrio desulfuricans}
SCOP: e.18.1.1
Length = 542
Score = 42.8 bits (100), Expect = 3e-04
Identities = 31/157 (19%), Positives = 54/157 (34%), Gaps = 20/157 (12%)
Query: 296 GVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMC----NE 351
G LR+ +E+EG V+++A L R E + + R D + C
Sbjct: 25 GHLRIEVEVEGGVIKEARSC-ATLFRGIETILKGR------DPRDAQHFTQRTCGVCTYT 77
Query: 352 HAY--VMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFRE 409
HA +E +N IP A YIR L+ ++ H + + L +
Sbjct: 78 HALASTRCLEDAINKPIPANATYIR-------NLVLGNQFMHDHLVHFYHLHALDFVDVT 130
Query: 410 REDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQY 446
L D +A A + + + + +
Sbjct: 131 SALLADPAKAAKLANSISPRKATTEEFAAVQAKLKTF 167
>1yqw_Q Periplasmic [NIFE] hydrogenase large subunit; NI-Fe hydrogenase
unready state, oxidoreductase; 1.83A {Desulfovibrio
fructosovorans} PDB: 1yrq_H 3h3x_Q 3cus_Q 3cur_H 1frf_L
Length = 549
Score = 42.5 bits (99), Expect = 5e-04
Identities = 31/159 (19%), Positives = 56/159 (35%), Gaps = 21/159 (13%)
Query: 296 GVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMC----NE 351
G LR+++E+E V+ A L R E + + R D + C
Sbjct: 26 GHLRIMVEVENGKVKDAWSSSQLF-RGLEIILKGR------DPRDAQHFTQRACGVCTYV 78
Query: 352 HAY--VMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFRE 409
HA ++ + + IP A+ +R L+ ++ H + + L +
Sbjct: 79 HALASSRCVDDAVKVSIPANARMMR-------NLVMASQYLHDHLVHFYHLHALDWVDVT 131
Query: 410 REDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKS 448
D +A A A RPG + L + + K+
Sbjct: 132 AALKADPNKAAKLAASIAP-ARPGNSAKALKAVQDKLKA 169
>3myr_A Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydrogenase,
photosynthetic P sulfur bacterium, iron-sulfur cluster,
NI-A state; HET: SF4; 2.10A {Allochromatium vinosum}
Length = 269
Score = 41.5 bits (97), Expect = 5e-04
Identities = 17/89 (19%), Positives = 33/89 (37%), Gaps = 14/89 (15%)
Query: 77 DVMIVAGTLCNKMA----------PALRKVYDQMTEPKWVISMGSCANGGGYY--HYSYS 124
++IV G++ A + + + VI++G+CA GG + +
Sbjct: 68 YLVIVDGSIPGPDANPGFSTVAGHSNYSILMETVEHAAAVIAVGTCAAFGGLPQARPNPT 127
Query: 125 VVRGCDRIVPVD--VYIPGCPPTAEALLY 151
+V + +PGCPP +
Sbjct: 128 GAMSVMDLVRDKPVINVPGCPPIPMVITG 156
>1yq9_H Periplasmic [NIFE] hydrogenase large subunit; oxidoreductase; 2.35A
{Desulfovibrio gigas} SCOP: e.18.1.1 PDB: 2frv_L 1frv_B
Length = 536
Score = 40.5 bits (94), Expect = 0.001
Identities = 28/153 (18%), Positives = 50/153 (32%), Gaps = 20/153 (13%)
Query: 296 GVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMC----NE 351
G LR+ +E+EG ++ A L R E + + R D + C
Sbjct: 19 GHLRIEVEVEGGKIKNAWSMSTLF-RGLEMILKGR------DPRDAQHFTQRACGVCTYV 71
Query: 352 HAY--VMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFRE 409
HA V A++ + +KIP A +R L ++ H + + L +
Sbjct: 72 HALASVRAVDNCVGVKIPENATLMR-------NLTMGAQYMHDHLVHFYHLHALDWVNVA 124
Query: 410 REDLLDCYEAVSGARMHAAYYRPGGVYRDLPEI 442
D +A A + + +
Sbjct: 125 NALNADPAKAARLANDLSPRKTTTESLKAVQAK 157
>3myr_B Nickel-dependent hydrogenase large subunit; [NIFE] hydrogenase,
photosynthetic P sulfur bacterium, iron-sulfur cluster,
NI-A state; HET: SF4; 2.10A {Allochromatium vinosum}
Length = 561
Score = 39.8 bits (92), Expect = 0.003
Identities = 25/100 (25%), Positives = 44/100 (44%), Gaps = 13/100 (13%)
Query: 296 GVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMC----NE 351
G LR+ +++G + +A G + R E + + R D +V +C
Sbjct: 15 GHLRIEAQMDGATIAQAYSS-GTMVRGIETILKGR------DPRDAWAFVQRICGVCTLV 67
Query: 352 HAY--VMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMW 389
H V A+E L I++P+ AQ IR + + +H+M
Sbjct: 68 HGIASVRAVEDALRIELPLNAQLIRNLMIGAQYIHDHVMH 107
>3uqy_L Hydrogenase-1 large chain; membrane-bound hydrogenase,
oxidoreductase; HET: LMT; 1.47A {Escherichia coli} PDB:
3usc_L* 3use_L*
Length = 582
Score = 39.1 bits (90), Expect = 0.005
Identities = 24/101 (23%), Positives = 38/101 (37%), Gaps = 12/101 (11%)
Query: 296 GVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMC----NE 351
G +R + + + V G + R E + + R D +V +C
Sbjct: 29 GHMRCEVNINDQNVITNAVSCGTMFRGLEIILQGR------DPRDAWAFVERICGVCTGV 82
Query: 352 HAY--VMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWI 390
HA V AIE + IK+P A IR + +HL+
Sbjct: 83 HALASVYAIEDAIGIKVPDNANIIRNIMLATLWCHDHLVHF 123
>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 = 32.6 bits (73), Expect = 0.22
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 11/37 (29%)
Query: 573 KQCIKWLRSN-K--GPVISNNNKITSPARINMKSNME 606
KQ +K L+++ K ++PA + +K+ ME
Sbjct: 19 KQALKKLQASLKLYADD-------SAPA-LAIKATME 47
>2bvl_A Toxin B; glycosyltransferase; HET: GLC UDP TBR; 2.2A {Clostridium
difficile} SCOP: c.68.1.22 PDB: 2bvm_A* 2vkh_A* 2vkd_A*
2vl8_A*
Length = 543
Score = 33.6 bits (75), Expect = 0.22
Identities = 18/157 (11%), Positives = 51/157 (32%), Gaps = 2/157 (1%)
Query: 338 YMDRLDYVSMMCNEHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDI 397
+++ E ++ L+ + + +E + +
Sbjct: 186 FINYYKAQREENPELIIDDIVKTYLSNEYSKEIDELNTYIEESLNKITQNSGNDVRNFGE 245
Query: 398 GAMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKSSIIRN-NKA 456
G + + A S +A GG+Y D+ +++P + + + K
Sbjct: 246 FKNGESFNLYEQELVERWNLAAASDILRISALKEIGGMYLDV-DMLPGIQPDLFESIEKP 304
Query: 457 TKILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDN 493
+ + + + + L+ I + P+ E+ +L +
Sbjct: 305 SSVTVDFWEMTKLEAIMKYKEYIPEYTSEHFDMLDEE 341
>3rst_A Signal peptide peptidase SPPA; alpha/beta protein fold, signal
peptide digestion, bacterial membrane, hydrolase; 2.37A
{Bacillus subtilis}
Length = 240
Score = 28.7 bits (65), Expect = 5.1
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 5/28 (17%)
Query: 106 VISMGSCANGGGYYHYSYSVVRGCDRIV 133
+SMGS A GGYY + D+I
Sbjct: 83 YVSMGSMAASGGYY-----ISTAADKIF 105
>2zbx_A Cytochrome P450-SU1; beta prism, heme, iron, metal-binding,
monooxygenase, oxidoreductase; HET: HEM; 1.50A
{Streptomyces griseolus} PDB: 2zby_A* 2zbz_A* 3cv8_A*
3cv9_A*
Length = 412
Score = 28.7 bits (65), Expect = 6.3
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 5/52 (9%)
Query: 253 GHDDLRRLLTDYGFVGHPFRKDFPVIEIKSYKLNFGPQH-----PAAHGVLR 299
H+ R+LL D + +FP + + PQ P HG R
Sbjct: 56 KHEAARKLLGDPRLSSNRTDDNFPATSPRFEAVRESPQAFIGLDPPEHGTRR 107
>2y5n_A MYCG, P-450-like protein; oxidoreductase, mycinamicin biosynthesis;
HET: HEM MYV; 1.62A {Micromonospora griseorubida} PDB:
2y46_A* 2y5z_A* 2y98_A* 2yca_A* 2ygx_A*
Length = 417
Score = 28.8 bits (65), Expect = 6.8
Identities = 13/48 (27%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 253 GHDDLRRLLTDYGF-VGHPFRKDFPVIEIKSYKLNFGPQHPAAHGVLR 299
++D+R +L D F G +D P + K P H LR
Sbjct: 68 RYEDVRAVLGDGRFVRGPSMTRDEPRTRPEMVKGGLLSMDPPEHSRLR 115
>1jfb_A Nitric-oxide reductase cytochrome P450 55A1; cytochrome P450NOR,
atomic resolutio structural genomics/proteomics
initiative, RSGI; HET: HEM; 1.00A {Fusarium oxysporum}
SCOP: a.104.1.1 PDB: 1jfc_A* 1gej_A* 1ged_A* 1ehe_A*
1gei_A* 1rom_A* 2rom_A* 1ehf_A* 1cl6_A* 1ehg_A* 1cmj_A*
1f25_A* 1f24_A* 1xqd_A* 1f26_A* 1cmn_A* 1ulw_A*
Length = 404
Score = 28.3 bits (64), Expect = 8.1
Identities = 9/52 (17%), Positives = 14/52 (26%), Gaps = 5/52 (9%)
Query: 253 GHDDLRRLLTDYGFVGHPFRKDFPVIEIKSYKLNFGPQH-----PAAHGVLR 299
H D+ + T R+ FP + + P H R
Sbjct: 48 KHKDVCFVATSEKLSKVRTRQGFPELSASGKQAAKAKPTFVDMDPPEHMHQR 99
>3tyw_A Putative cytochrome P450; P450 monooxygenase, oxidoreductase; HET:
HEM; 2.90A {Streptomyces coelicolor}
Length = 417
Score = 28.4 bits (64), Expect = 8.8
Identities = 11/52 (21%), Positives = 17/52 (32%), Gaps = 5/52 (9%)
Query: 253 GHDDLRRLLTDYGFVGHPFRKDFPVIEIKSYKLNFGPQH-----PAAHGVLR 299
+DD+R LL+D R FP + + + H R
Sbjct: 60 RYDDVRELLSDPRVSADIRRPGFPALGEGEQEAGARFRPFIRTDAPEHTRYR 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
0.323 0.141 0.436
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 11,452,259
Number of extensions: 734574
Number of successful extensions: 1607
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1576
Number of HSP's successfully gapped: 50
Length of query: 693
Length of database: 6,701,793
Length adjustment: 100
Effective length of query: 593
Effective length of database: 3,909,693
Effective search space: 2318447949
Effective search space used: 2318447949
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: 61 (27.7 bits)