RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7154
(385 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 = 463 bits (1194), Expect = e-163
Identities = 101/279 (36%), Positives = 168/279 (60%), Gaps = 20/279 (7%)
Query: 51 LFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMHAAYVRPGGV 110
+ E++R+ +H++ +GT LD+GA+TPFF+ F ERE +++ +E +G R H Y+R GGV
Sbjct: 119 ILNELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGV 178
Query: 111 ALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVGIVSAEDALNYGFSGVM 170
D+P + ++ + R+DE E + E+ ++ +R + VG++ E A++ G +G
Sbjct: 179 KEDLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGS 238
Query: 171 LRGSGIKWDLRKVQPYDGYENFEFDIPIGTHGNV-----IGMKEMRQSLRIVEQAINKMP 225
LR SG+ +D+RK PY GYE + FD+P+G G+V + ++EMR+S++I++QA+ ++
Sbjct: 239 LRASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLE 298
Query: 226 GGEVRTDDMKISTPSRSEMK---------------GYPVPPGATYTAVEAPKGEFGVYLV 270
G VR + +I+ P R ++ G+ P G Y E+ +GE G Y+V
Sbjct: 299 PGPVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIV 358
Query: 271 SDGTSKPYRCKIKAPGFAHLAALEKIGKGSFLADIVAII 309
SDG S PYR K++AP F +L +L KG + D+VAII
Sbjct: 359 SDGGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAII 397
Score = 149 bits (378), Expect = 2e-41
Identities = 33/70 (47%), Positives = 45/70 (64%)
Query: 305 IVAIIDPHIGLLHRGTEKLIEYKTYTQALPYFDRLDYVSMMCNEQCYSLAVEKLLNIEVP 364
V + PHIG LH G EK +E++TY Q + Y R+DY+ ++ Y+LAVEKLL VP
Sbjct: 51 EVLEVVPHIGYLHTGFEKTMEHRTYLQNITYTPRMDYLHSFAHDLAYALAVEKLLGAVVP 110
Query: 365 LRAKYIRVMF 374
RA+ IRV+
Sbjct: 111 PRAETIRVIL 120
Score = 52.1 bits (126), Expect = 1e-07
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 5/40 (12%)
Query: 28 EKQIRNMVINFGPQHPAAHGVLLLFAE-----ITRILNHI 62
E + M +N GPQHP+ HGVL L + ++ HI
Sbjct: 20 ELRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHI 59
>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 = 39.1 bits (90), Expect = 0.002
Identities = 38/274 (13%), Positives = 76/274 (27%), Gaps = 105/274 (38%)
Query: 15 WKIINWN----------DNLVPVE--KQIRNMVINFGPQH---PAAHGVLLLF------A 53
WK +N + + L P E K + + F P P +L L +
Sbjct: 347 WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV-F-PPSAHIPTI--LLSLIWFDVIKS 402
Query: 54 EITRILNHI------------MAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMH 101
++ ++N + + ++ E + K+ Y +H
Sbjct: 403 DVMVVVNKLHKYSLVEKQPKESTISIPSI----------YLELKVKLENEYA------LH 446
Query: 102 A----AYVRPGGVALDIPIGLLDD--IYHFIS--TFSARLDEVEDMLTENRLWIQRTKDV 153
Y P D I D Y I + E + ++
Sbjct: 447 RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFR--MVF------- 497
Query: 154 GIVSAEDALNYGFSGVMLRGSGIKW-----------DLRKVQPY------------DGYE 190
L++ F +R W L+ +PY +
Sbjct: 498 --------LDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAIL 549
Query: 191 NF----EFDIPIGTHGNVIGMKEMRQSLRIVEQA 220
+F E ++ + +++ + M + I E+A
Sbjct: 550 DFLPKIEENLICSKYTDLLRIALMAEDEAIFEEA 583
>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 = 35.4 bits (81), Expect = 0.040
Identities = 43/266 (16%), Positives = 75/266 (28%), Gaps = 84/266 (31%)
Query: 88 M-MEFYERASGAR---------MHAAYVRPGGVALDI----PIGLLDDIYHFISTFSARL 133
M M+ Y+ + A+ Y G LDI P+ L HF R+
Sbjct: 1631 MGMDLYKTSKAAQDVWNRADNHFKDTY---GFSILDIVINNPVNL---TIHFGGEKGKRI 1684
Query: 134 DE-VEDMLTENRLWIQRTKDVGIVSAE--DALNYGFSGVMLRGSGIKWDLRK---VQP-- 185
E M+ E D + + + +N + R K L QP
Sbjct: 1685 RENYSAMIFET------IVDGKLKTEKIFKEINEHSTSYTFRSE--KGLLSATQFTQPAL 1736
Query: 186 ----YDGYENF--EFDIPIGT----H-----------GNVIGMKEMRQSLRIVEQ---AI 221
+E+ + IP H +V+ ++ + + +V +
Sbjct: 1737 TLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESL---VEVVFYRGMTM 1793
Query: 222 NK-MPGGEVRTDDMKISTPSRSEMKGYPVPPGATYTAVEAPKGEFGVYLVSDGTSKPYRC 280
+P E+ RS + PG + ++ V V T
Sbjct: 1794 QVAVPRDEL----------GRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWL--V 1841
Query: 281 KI---KAPGF-----AHLAALEKIGK 298
+I L AL+ +
Sbjct: 1842 EIVNYNVENQQYVAAGDLRALDTVTN 1867
Score = 33.1 bits (75), Expect = 0.18
Identities = 23/98 (23%), Positives = 37/98 (37%), Gaps = 25/98 (25%)
Query: 60 NHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMHAA--------YVRPGG-- 109
N+ M A++ G + F E + ++E + +G + YV G
Sbjct: 1806 NYGMI----AINPGRVAASFSQ-EALQYVVERVGKRTGWLVEIVNYNVENQQYV-AAGDL 1859
Query: 110 VALDIPIGLLD-------DIYHFISTFSARLDEVEDML 140
ALD +L+ DI + S L+EVE L
Sbjct: 1860 RALDTVTNVLNFIKLQKIDIIELQKSLS--LEEVEGHL 1895
Score = 27.7 bits (61), Expect = 9.1
Identities = 13/68 (19%), Positives = 24/68 (35%), Gaps = 21/68 (30%)
Query: 18 INWNDNLVPVEKQIRNM---VINFGPQHPAAHGVLLLFAEITRILN----HIMAVGTHAL 70
+ W E + +++FGP + GVL R + ++ GT L
Sbjct: 488 VKW-------ETTTQFKATHILDFGPGGASGLGVL-----THRNKDGTGVRVIVAGT--L 533
Query: 71 DVGAMTPF 78
D+ +
Sbjct: 534 DINPDDDY 541
>1cc1_L Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxidoreductase;
2.15A {Desulfomicrobium baculatum} SCOP: e.18.1.1
Length = 498
Score = 33.0 bits (75), Expect = 0.15
Identities = 20/130 (15%), Positives = 37/130 (28%), Gaps = 13/130 (10%)
Query: 85 REKMMEFYERASGARMHAAYVRPGGVALDIPIGLLDDIYHFISTFSARLDEVEDMLTENR 144
R E G H + GG + + + E L
Sbjct: 172 RRICHEMVAMFGGRMPHVQGMVVGGATEIPTADKVAEYAARFKEVQKFVIEEYLPLIYTL 231
Query: 145 LWIQRTKDVGIVSAEDALNYGF-------------SGVMLRGSGIKWDLRKVQPYDGYEN 191
+ + ++ + +G GV + G ++D + V+ Y G+
Sbjct: 232 GSVYTDLFETGIGWKNVIAFGVFPEDDDYKTFLLKPGVYIDGKDEEFDSKLVKEYVGHSF 291
Query: 192 FEFDIPIGTH 201
F+ P G H
Sbjct: 292 FDHSAPGGLH 301
>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 = 32.2 bits (73), Expect = 0.32
Identities = 16/122 (13%), Positives = 30/122 (24%), Gaps = 13/122 (10%)
Query: 85 REKMMEFYERASGARMHAAYVRPGGVALDIPIGLLDDIYHFISTF-----SARLDEVEDM 139
R E G H GG L + + V +
Sbjct: 169 RRICHEMVALFGGRMPHVQGQVVGGATEIPTKEKLVEYAARFKKVRDFVEQKYVPVVYTI 228
Query: 140 LTENRLWIQRTKDVGIVSA--------EDALNYGFSGVMLRGSGIKWDLRKVQPYDGYEN 191
++ + + + + GV +G + +D K++ Y Y
Sbjct: 229 GSKYKDMFKVGQGFKAALCVGAFPLDNSGKKHLFMPGVYAKGKDMPFDPSKIKEYVKYSW 288
Query: 192 FE 193
F
Sbjct: 289 FA 290
Score = 28.3 bits (63), Expect = 4.9
Identities = 12/72 (16%), Positives = 25/72 (34%), Gaps = 12/72 (16%)
Query: 314 GLLHRGTEKLIEYKTYTQALPYFDRLDYVSMMCN------EQCYSLAVEKLLNIEVPLRA 367
G ++RG E ++ + D V +C LA+++ +VP
Sbjct: 49 GGMYRGFETILRGR------DPRDASQIVQRICGVCPTAHSTASVLALDEAFGAKVPNNG 102
Query: 368 KYIRVMFTFYQW 379
+ R + +
Sbjct: 103 RITRNLIFGANY 114
>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 = 32.1 bits (72), Expect = 0.34
Identities = 17/67 (25%), Positives = 29/67 (43%)
Query: 313 IGLLHRGTEKLIEYKTYTQALPYFDRLDYVSMMCNEQCYSLAVEKLLNIEVPLRAKYIRV 372
G + RG E ++ + A + +R+ V C+ AVE L+I++P A IR
Sbjct: 49 TGTMWRGLEVILRGRDPRDAWAFVERICGVCTGCHALASVRAVEDALDIKIPHNATLIRE 108
Query: 373 MFTFYQW 379
+
Sbjct: 109 IMAKTLQ 115
>3uqy_L Hydrogenase-1 large chain; membrane-bound hydrogenase,
oxidoreductase; HET: LMT; 1.47A {Escherichia coli} PDB:
3usc_L* 3use_L*
Length = 582
Score = 31.4 bits (70), Expect = 0.55
Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 12/73 (16%)
Query: 313 IGLLHRGTEKLIEYKTYTQALPYFDRLDYVSMMCN------EQCYSLAVEKLLNIEVPLR 366
G + RG E +++ + D +V +C A+E + I+VP
Sbjct: 49 CGTMFRGLEIILQGR------DPRDAWAFVERICGVCTGVHALASVYAIEDAIGIKVPDN 102
Query: 367 AKYIRVMFTFYQW 379
A IR + W
Sbjct: 103 ANIIRNIMLATLW 115
>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 = 30.9 bits (69), Expect = 0.77
Identities = 14/66 (21%), Positives = 27/66 (40%)
Query: 314 GLLHRGTEKLIEYKTYTQALPYFDRLDYVSMMCNEQCYSLAVEKLLNIEVPLRAKYIRVM 373
L RG E +++ + A + R V + + V+ + + +P A YIR +
Sbjct: 37 STLFRGLEIILKGRDPRDAQHFTQRTCGVCTYTHALASTRCVDNAVGVHIPKNATYIRNL 96
Query: 374 FTFYQW 379
Q+
Sbjct: 97 VLGAQY 102
Score = 27.8 bits (61), Expect = 7.9
Identities = 14/110 (12%), Positives = 27/110 (24%), Gaps = 12/110 (10%)
Query: 41 QHPAAHGVLLLFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARM 100
+ G L F + H ++ A + + K
Sbjct: 157 KTFVETGQLGPFTNAYFLGGHPAYYLDPETNLIATAHYLEALRLQVKAARAMAVFGAKNP 216
Query: 101 HAAYVRPGGVALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRT 150
H + GGV + R+ E E + E + ++
Sbjct: 217 HTQFTVVGGVTCYDALTP------------QRIAEFEALWKETKAFVDEV 254
>1e3d_B [NIFE] hydrogenase large subunit; molecular modelling, electron
transfer; HET: FSX; 1.8A {Desulfovibrio desulfuricans}
SCOP: e.18.1.1
Length = 542
Score = 29.4 bits (65), Expect = 2.6
Identities = 14/73 (19%), Positives = 25/73 (34%), Gaps = 12/73 (16%)
Query: 313 IGLLHRGTEKLIEYKTYTQALPYFDRLDYVSMMCN------EQCYSLAVEKLLNIEVPLR 366
L RG E +++ + D + C + +E +N +P
Sbjct: 44 CATLFRGIETILKGR------DPRDAQHFTQRTCGVCTYTHALASTRCLEDAINKPIPAN 97
Query: 367 AKYIRVMFTFYQW 379
A YIR + Q+
Sbjct: 98 ATYIRNLVLGNQF 110
Score = 27.4 bits (60), Expect = 10.0
Identities = 7/69 (10%), Positives = 20/69 (28%), Gaps = 12/69 (17%)
Query: 82 FEEREKMMEFYERASGARMHAAYVRPGGVALDIPIGLLDDIYHFISTFSARLDEVEDMLT 141
+ ++ + H + GGV + R+ + ++
Sbjct: 206 LRAQVEVAKGMAVFGAKNPHTQFTVAGGVTCYEALT------------PERIKQFRELYV 253
Query: 142 ENRLWIQRT 150
+ R +I+
Sbjct: 254 KARAFIEEV 262
>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 = 29.0 bits (64), Expect = 2.7
Identities = 19/73 (26%), Positives = 30/73 (41%), Gaps = 12/73 (16%)
Query: 313 IGLLHRGTEKLIEYKTYTQALPYFDRLDYVSMMCN------EQCYSLAVEKLLNIEVPLR 366
G + RG E +++ + D +V +C AVE L IE+PL
Sbjct: 34 SGTMVRGIETILKGR------DPRDAWAFVQRICGVCTLVHGIASVRAVEDALRIELPLN 87
Query: 367 AKYIRVMFTFYQW 379
A+ IR + Q+
Sbjct: 88 AQLIRNLMIGAQY 100
>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 = 28.6 bits (63), Expect = 4.0
Identities = 12/73 (16%), Positives = 26/73 (35%), Gaps = 12/73 (16%)
Query: 313 IGLLHRGTEKLIEYKTYTQALPYFDRLDYVSMMCN------EQCYSLAVEKLLNIEVPLR 366
+ L RG E +++ + D + C AV+ + +++P
Sbjct: 38 MSTLFRGLEMILKGR------DPRDAQHFTQRACGVCTYVHALASVRAVDNCVGVKIPEN 91
Query: 367 AKYIRVMFTFYQW 379
A +R + Q+
Sbjct: 92 ATLMRNLTMGAQY 104
>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 = 28.2 bits (62), Expect = 4.6
Identities = 13/66 (19%), Positives = 27/66 (40%)
Query: 314 GLLHRGTEKLIEYKTYTQALPYFDRLDYVSMMCNEQCYSLAVEKLLNIEVPLRAKYIRVM 373
L RG E +++ + A + R V + S V+ + + +P A+ +R +
Sbjct: 46 SQLFRGLEIILKGRDPRDAQHFTQRACGVCTYVHALASSRCVDDAVKVSIPANARMMRNL 105
Query: 374 FTFYQW 379
Q+
Sbjct: 106 VMASQY 111
>2epj_A Glutamate-1-semialdehyde 2,1-aminomutase; PLP enzyme, GSA,
structural genomics, NPPSFA; HET: PMP; 1.70A {Aeropyrum
pernix} PDB: 2zsl_A* 2zsm_A*
Length = 434
Score = 27.9 bits (63), Expect = 6.5
Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 202 GNVIGMKEMRQSLRIVEQAINKMPGGEVRTDDMKISTPSRSEMKGYPV 249
G++ + +S + E+ PGG +++P R+ +K YP
Sbjct: 1 GHMDVLASGEKSRMLFERTKELFPGG--------VNSPVRAAVKPYPF 40
>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 = 26.8 bits (58), Expect = 7.4
Identities = 12/77 (15%), Positives = 19/77 (24%), Gaps = 48/77 (62%)
Query: 218 EQAINKMPGGEVRTDDMKISTPSRSEMKGYPVPPGATYTAVEAPKGEFGVYLVSDGTSKP 277
+QA+ K+ ++ +K Y A D
Sbjct: 19 KQALKKL----------------QASLKLY------------AD----------D----- 35
Query: 278 YRCKIKAPGFAHLAALE 294
AP A A +E
Sbjct: 36 -----SAPALAIKATME 47
>3nvo_A Zinc transport protein ZNTB; alpha-beta-alpha sandwich, zinc efflux
system, membrane, TRA protein; 2.30A {Salmonella
enterica} PDB: 3nwi_A
Length = 264
Score = 27.1 bits (60), Expect = 9.0
Identities = 10/40 (25%), Positives = 19/40 (47%)
Query: 106 RPGGVALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRL 145
GG +D+ L D FI ++ ++ED L + ++
Sbjct: 144 DCGGWLVDVCDALTDHASEFIEELHDKIIDLEDNLLDQQI 183
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
0.322 0.139 0.423
Gapped
Lambda K H
0.267 0.0787 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,341,843
Number of extensions: 402180
Number of successful extensions: 1045
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1038
Number of HSP's successfully gapped: 34
Length of query: 385
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 290
Effective length of database: 4,049,298
Effective search space: 1174296420
Effective search space used: 1174296420
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.0 bits)