RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6460
(198 letters)
>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP;
1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB:
1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D*
1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D*
2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...
Length = 482
Score = 382 bits (984), Expect = e-134
Identities = 153/168 (91%), Positives = 163/168 (97%)
Query: 30 QAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIIGAEH 89
QAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNI+G+EH
Sbjct: 312 QAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIVGSEH 371
Query: 90 YNIARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFQVAEVFTGH 149
Y++ARGVQKILQDYKSLQDIIAILGMDELSEEDKLTV+RARKIQRFLSQPFQVAEVFTGH
Sbjct: 372 YDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQPFQVAEVFTGH 431
Query: 150 AGKLVPLEETIKGFSEILAGKYDHLPEVAFYMVGPIEEVVAKAETLAK 197
GKLVPL+ETIKGF +ILAG+YDHLPE AFYMVGPIEE VAKA+ LA+
Sbjct: 432 LGKLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAE 479
>1fx0_B ATP synthase beta chain; latent ATPase, thermal stability,
potential tentoxin binding hydrolase; 3.20A {Spinacia
oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_B*
Length = 498
Score = 368 bits (948), Expect = e-128
Identities = 122/168 (72%), Positives = 138/168 (82%)
Query: 30 QAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIIGAEH 89
QA+YVPADDLTDPAPATTFAHLDATTVLSR +A GIYPAVDPLDSTS ++ P I+G EH
Sbjct: 325 QAVYVPADDLTDPAPATTFAHLDATTVLSRGLAAKGIYPAVDPLDSTSTMLQPRIVGEEH 384
Query: 90 YNIARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFQVAEVFTGH 149
Y IA+ V++ LQ YK LQDIIAILG+DELSEED+LTVARARKI+RFLSQPF VAEVFTG
Sbjct: 385 YEIAQRVKETLQRYKELQDIIAILGLDELSEEDRLTVARARKIERFLSQPFFVAEVFTGS 444
Query: 150 AGKLVPLEETIKGFSEILAGKYDHLPEVAFYMVGPIEEVVAKAETLAK 197
GK V L ETI+GF IL+G+ D LPE AFY+VG I+E AKA L
Sbjct: 445 PGKYVGLAETIRGFQLILSGELDSLPEQAFYLVGNIDEATAKAMNLEM 492
>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC
F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1
b.49.1.1 c.37.1.11
Length = 473
Score = 358 bits (921), Expect = e-124
Identities = 117/168 (69%), Positives = 134/168 (79%)
Query: 30 QAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIIGAEH 89
QAIYVPADD TDPAPATTF+HLDATT L R +AE+GIYPAVDPL STSR + P I+G EH
Sbjct: 304 QAIYVPADDYTDPAPATTFSHLDATTNLERKLAEMGIYPAVDPLVSTSRALAPEIVGEEH 363
Query: 90 YNIARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFQVAEVFTGH 149
Y +AR VQ+ L+ YK LQDIIAILGMDELS+EDKL V RAR+IQ FLSQ F VAE FTG
Sbjct: 364 YQVARKVQQTLERYKELQDIIAILGMDELSDEDKLVVHRARRIQFFLSQNFHVAEQFTGQ 423
Query: 150 AGKLVPLEETIKGFSEILAGKYDHLPEVAFYMVGPIEEVVAKAETLAK 197
G VP++ET++GF EIL GKYDHLPE F +VG IEEVV KA+ +
Sbjct: 424 PGSYVPVKETVRGFKEILEGKYDHLPEDRFRLVGRIEEVVEKAKAMGV 471
>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop,
phenylalanine mutant, hydrolase; 2.35A {Pyrococcus
horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A
3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A
3sdz_A
Length = 588
Score = 188 bits (478), Expect = 5e-57
Identities = 39/168 (23%), Positives = 64/168 (38%), Gaps = 15/168 (8%)
Query: 30 QAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDP------N 83
A+ P D ++P T + L +A +PA++ L S S +D
Sbjct: 390 GAVSPPGGDFSEPVVQNTLRVVKVFWALDADLARRRHFPAINWLTSYSLYVDAVKDWWHK 449
Query: 84 IIGAEHYNIARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQR-FLSQPFQV 142
I E + +LQ LQ+I+ I+G D L E ++ + AR ++ +L Q
Sbjct: 450 NIDPEWKAMRDKAMALLQKESELQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFD 509
Query: 143 AEVFTGHAGKLVPLEETIKGFSEILAGKYDHLPEVAFYMVGPIEEVVA 190
P E+ + +L YD E V P+EE+
Sbjct: 510 EVDTY------CPPEKQVTMMRVLL-NFYDKTMEAINRGV-PLEEIAK 549
>3gqb_A V-type ATP synthase alpha chain; A3B3, V-ATPase, ATP synthesis,
ATP-binding, hydrogen ION TRA hydrolase, ION transport;
2.80A {Thermus thermophilus HB8} PDB: 3a5c_A* 3a5d_A
3j0j_A* 1um2_C
Length = 578
Score = 182 bits (463), Expect = 7e-55
Identities = 29/167 (17%), Positives = 68/167 (40%), Gaps = 8/167 (4%)
Query: 30 QAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDP------N 83
A+ P D+++P +T + A L ++A +PA++ S S
Sbjct: 382 GAVSPPGGDMSEPVTQSTLRIVGAFWRLDASLAFRRHFPAINWNGSYSLFTSALDPWYRE 441
Query: 84 IIGAEHYNIARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQR-FLSQ-PFQ 141
+ ++ + + ++LQ LQ+I+ ++G D L + ++L + R I+ FL Q +
Sbjct: 442 NVAEDYPELRDAISELLQREAGLQEIVQLVGPDALQDAERLVIEVGRIIREDFLQQNAYH 501
Query: 142 VAEVFTGHAGKLVPLEETIKGFSEILAGKYDHLPEVAFYMVGPIEEV 188
+ ++ ++ + + E A + + +E +
Sbjct: 502 EVDAYSSMKKAYGIMKMILAFYKEAEAAIKRGVSIDEILQLPVLERI 548
>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis,
ATP-binding, hydrogen ION TRA hydrolase, ION transport;
2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D
3j0j_D*
Length = 464
Score = 122 bits (308), Expect = 3e-33
Identities = 36/141 (25%), Positives = 65/141 (46%), Gaps = 14/141 (9%)
Query: 32 IYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNI----IGA 87
+ +P DD T P P T + LSR + GIYP +DPL S SR+M+ +
Sbjct: 314 LSMPDDDRTHPIPDLTGYITEGQIQLSRELHRKGIYPPIDPLPSLSRLMNNGVGKGKTRE 373
Query: 88 EHYNIARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFQVAEVFT 147
+H ++ + + ++ ++AI+G D L+E D+ + A +RF Q +
Sbjct: 374 DHKQVSDQLYSAYANGVDIRKLVAIIGEDALTENDRRYLQFADAFERFFIN--QGQQN-- 429
Query: 148 GHAGKLVPLEETIKGFSEILA 168
+EE+++ +L+
Sbjct: 430 ------RSIEESLQIAWALLS 444
>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase,
A1AO, ATP synthesis, hydrogen ION transport, ION
transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A*
3b2q_A* 2rkw_A* 3eiu_A*
Length = 469
Score = 92.8 bits (231), Expect = 2e-22
Identities = 40/155 (25%), Positives = 70/155 (45%), Gaps = 24/155 (15%)
Query: 31 AIY---VPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIIG- 86
I +P DD+T P P + + V++R + GIYP ++ L S SR+M + IG
Sbjct: 308 QIPILSMPGDDITHPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLM-NSGIGA 366
Query: 87 ----AEHYNIARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVARARK-IQRFLSQPFQ 141
+H ++ + + + L+ ++AI+G + LSE D + A +F+ Q
Sbjct: 367 GKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGRN 426
Query: 142 VAEVFTGHAGKLVPLEETIKGFSEILAGKYDHLPE 176
+E+T++ +IL HLPE
Sbjct: 427 EN----------RTIEDTLEIGWQILT----HLPE 447
>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta
structure, hydrolase; HET: ADP; 2.40A {Salmonella
typhimurium}
Length = 438
Score = 85.9 bits (213), Expect = 4e-20
Identities = 37/144 (25%), Positives = 64/144 (44%), Gaps = 21/144 (14%)
Query: 31 AIY---VPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIIGA 87
A Y DD DP + A LD VLSR +AE G YPA+D S SR M +I
Sbjct: 306 AFYTVLTEGDDQQDPIADSARAILDGHIVLSRRLAEAGHYPAIDIEASISRAM-TALITE 364
Query: 88 EHYNIARGVQKILQDYKSLQDIIAI----LGMDELSEEDKLTVARARKIQRFLSQPFQVA 143
+HY R +++L ++ +D++++ G D + ++ + +++ FL Q
Sbjct: 365 QHYARVRLFKQLLSSFQRNRDLVSVGAYAKGSDPMLDK---AITLWPQLEAFLQQG---- 417
Query: 144 EVFTGHAGKLVPLEETIKGFSEIL 167
+ E++++ I
Sbjct: 418 ------IFERADWEDSLQALDLIF 435
>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*
Length = 347
Score = 84.2 bits (209), Expect = 9e-20
Identities = 39/145 (26%), Positives = 71/145 (48%), Gaps = 21/145 (14%)
Query: 31 AIY---VPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIIGA 87
AIY + +D++ DP + LD VL+R +AE +PA+D S SR+M N++ +
Sbjct: 217 AIYTVLLESDNVNDPIGDEVRSILDGHIVLTRELAEENHFPAIDIGLSASRVM-HNVVTS 275
Query: 88 EHYNIARGVQKILQDYKSLQDIIAI----LGMDELSEEDKLTVARARKIQRFLSQPFQVA 143
EH A +K++ YK+ + +I I +G D +++ + + IQ F+ Q
Sbjct: 276 EHLRAAAECKKLIATYKNPELLIRIGEYTMGQDPEADK---AIKNRKLIQNFIQQS---- 328
Query: 144 EVFTGHAGKLVPLEETIKGFSEILA 168
+ E+TI+ +++A
Sbjct: 329 ------TKDISSYEKTIESLFKVVA 347
>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 = 38.3 bits (88), Expect = 0.001
Identities = 18/130 (13%), Positives = 42/130 (32%), Gaps = 27/130 (20%)
Query: 70 VDPLDSTSRIMDPN-IIGAEH-------YNIARGVQKILQDYKSLQDIIAILGMDELSEE 121
++ L +DPN ++H + + + L K ++ + +L +
Sbjct: 199 LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVL--LNVQ-- 254
Query: 122 DKLTVARARKIQ-RFL--SQPFQVAEVFTGHAGKLVPLEETIKGFSE-----ILAGKY-- 171
+ A + + L ++ QV + + + L+ + +L KY
Sbjct: 255 NA-KAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLL-KYLD 312
Query: 172 ---DHLPEVA 178
LP
Sbjct: 313 CRPQDLPREV 322
Score = 28.3 bits (62), Expect = 2.1
Identities = 18/85 (21%), Positives = 31/85 (36%), Gaps = 19/85 (22%)
Query: 80 MDPNIIGAEHYNIARGVQKILQ----------DYKSLQDII-AILGMDELSE--EDKLTV 126
MD G Y + IL D K +QD+ +IL +E+ K V
Sbjct: 7 MDFET-GEHQY----QYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAV 61
Query: 127 ARARKI-QRFLSQPFQVAEVFTGHA 150
+ ++ LS+ ++ + F
Sbjct: 62 SGTLRLFWTLLSKQEEMVQKFVEEV 86
>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease,
nucleotide excision repair; 2.8A {Aeropyrum pernix}
SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A
Length = 219
Score = 36.0 bits (82), Expect = 0.004
Identities = 11/45 (24%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 97 QKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFQ 141
++IL+ + SL+ E+S+ + + RA +I++ L P++
Sbjct: 176 ERILERFGSLERFFT-ASKAEISKVEGIGEKRAEEIKKILMTPYK 219
>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 = 33.1 bits (75), Expect = 0.055
Identities = 33/216 (15%), Positives = 62/216 (28%), Gaps = 77/216 (35%)
Query: 38 DLTDPAPATTFAHLDATTVLSRA----IAELGIYPAVDPLDSTSRIMDPNIIGAEHYNIA 93
DL + A A V +RA G S I+ N + +
Sbjct: 1634 DLYKTSKA-------AQDVWNRADNHFKDTYGF--------SILDIVINNPVNLTIHFGG 1678
Query: 94 RGVQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKI-----QRFLS-----QP---- 139
++I ++Y ++ + G + + K + + LS QP
Sbjct: 1679 EKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTL 1738
Query: 140 -----FQVAE---------VFTGH-----------AGKLVPLEETIK-----GFSEILAG 169
F+ + F GH A + +E ++ G + +A
Sbjct: 1739 MEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVM-SIESLVEVVFYRGMTMQVAV 1797
Query: 170 KYDHLPEVAFYM--VGP-----------IEEVVAKA 192
D L + M + P ++ VV +
Sbjct: 1798 PRDELGRSNYGMIAINPGRVAASFSQEALQYVVERV 1833
Score = 28.5 bits (63), Expect = 1.8
Identities = 43/213 (20%), Positives = 64/213 (30%), Gaps = 59/213 (27%)
Query: 25 IFLPAQAIYVPADDLTDPAPATTFAHLDATTVLSR------AIAELGIYPAVDPLDSTSR 78
I + A YV L P ++L T S+ AIA D +S
Sbjct: 241 IGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIA------ETDSWESFFV 294
Query: 79 IMDPNI-----IGA---EHYNIARGVQKILQDYKSLQD-----IIAILGMDELSEEDKLT 125
+ I IG E Y IL+D + +++I + + +D +
Sbjct: 295 SVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYV- 353
Query: 126 VARARKIQRFLSQPFQVA---------EVFTGHAGKLVPLEETIKG-------------F 163
K L QV V +G L L T++ F
Sbjct: 354 ----NKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPF 409
Query: 164 SE-ILAGKYDHLPEVA--F---YMVGPIEEVVA 190
SE L LP VA F +V + +
Sbjct: 410 SERKLKFSNRFLP-VASPFHSHLLVPASDLINK 441
>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 = 31.5 bits (70), Expect = 0.10
Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 11/35 (31%)
Query: 20 LKRFSIFLPAQAIYVPADDLTDPAPATTFAHLDAT 54
LK+ L +Y D APA A + AT
Sbjct: 22 LKKLQASL---KLYAD-----DSAPA--LA-IKAT 45
Score = 25.7 bits (55), Expect = 8.4
Identities = 6/18 (33%), Positives = 6/18 (33%), Gaps = 7/18 (38%)
Query: 15 YQPDCLKRFSIFLPAQAI 32
Y D PA AI
Sbjct: 32 YADDSA-------PALAI 42
>3mtk_A Diguanylate cyclase/phosphodiesterase; structural genomics, PSI-2,
protein structure initiative; 2.24A
{Caldicellulosiruptor saccharolyticus}
Length = 178
Score = 30.1 bits (69), Expect = 0.34
Identities = 6/48 (12%), Positives = 13/48 (27%), Gaps = 8/48 (16%)
Query: 107 QDIIAILGMDE----LSEEDKLTVARARKIQRFLSQPFQVA--EVFTG 148
+ +G D E+ ++ L P+ V +
Sbjct: 77 GNKAFKIGFDRFAIICKSENISDFIE--RMLSQLLLPYNVNGNLIRVN 122
>3pjx_A Cyclic dimeric GMP binding protein; ggdef-EAL tandem domain,
C-DI-GMP receptor, lyase; 2.00A {Pseudomonas
fluorescens} PDB: 3pjw_A 3pju_A* 3pjt_A* 3pfm_A
Length = 430
Score = 30.5 bits (70), Expect = 0.35
Identities = 9/66 (13%), Positives = 24/66 (36%), Gaps = 11/66 (16%)
Query: 92 IARGVQKILQDYKSLQDIIAILGMDE-------LSEEDKLTVARARKIQRFLSQPFQVA- 143
+ + + Y Q+++ + E ++ E+ L +A+ + LS +
Sbjct: 78 VGEQLSRECAKYPETQNLVTRIRGGEFAVLAPGMTREEALQLAQ--SLDSALSSLYATGA 135
Query: 144 -EVFTG 148
+V
Sbjct: 136 TDVAAV 141
>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA
capture mechanism, ATP-binding, hydrolase,
nucleotide-binding, RN binding; 2.35A {Thermotoga
maritima}
Length = 427
Score = 28.7 bits (65), Expect = 1.4
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 56 VLSRAIAELGIYPAVDPLDSTSR 78
VLSR +A I+PA++ L S +R
Sbjct: 348 VLSRQLANKRIFPAINLLLSGTR 370
>3ice_A Transcription termination factor RHO; transcription, ATPase,
hexamer, helicase, RNA, RECA, OB fold ATP-binding,
hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli
k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A
Length = 422
Score = 28.3 bits (64), Expect = 1.9
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 56 VLSRAIAELGIYPAVDPLDSTSR 78
LSR IAE ++PA+D S +R
Sbjct: 347 HLSRKIAEKRVFPAIDYNRSGTR 369
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA
repair, endonuclease, helix-hairpin-helix, DNA binding
protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5
Length = 91
Score = 26.7 bits (59), Expect = 2.3
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 96 VQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPF 140
Q +L + SL+ +IA ++L+ L +AR++ L +PF
Sbjct: 45 SQTLLTTFGSLEQLIA-ASREDLALCPGLGPQKARRLFDVLHEPF 88
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase;
HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5
Length = 89
Score = 26.3 bits (58), Expect = 2.8
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 96 VQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPF 140
Q +L + SL+ +IA ++L+ L +AR++ L +PF
Sbjct: 32 SQTLLTTFGSLEQLIA-ASREDLALCPGLGPQKARRLFDVLHEPF 75
>3zwc_A Peroxisomal bifunctional enzyme; beta oxidation pathway,
oxidoreductase, lipid metabolism, LY isomerase,
peroxisome, fatty acid metabolism; HET: NAD HSC; 2.30A
{Rattus norvegicus} PDB: 3zw9_A* 3zw8_A* 3zwa_A* 3zwb_A*
2x58_A*
Length = 742
Score = 27.2 bits (61), Expect = 3.7
Identities = 10/64 (15%), Positives = 24/64 (37%), Gaps = 2/64 (3%)
Query: 113 LGM-DELSEEDKLTVARARKIQRFLSQPFQVAEVFTGHAGKLVPLEETIKGFSEILAGKY 171
LG+ D + + D + A Q+ + +P + +F L ++ + +Y
Sbjct: 185 LGILDAVVKSDPVEEAIKF-AQKIIDKPIEPRRIFNKPVPSLPNMDSVFAEAIAKVRKQY 243
Query: 172 DHLP 175
+
Sbjct: 244 PGVL 247
>3q8k_A Flap endonuclease 1; helix-3 turn-helix, hydrophobic wedge, 3' flap
binding site, hydrolase-DNA complex, DNA repair,
replication; HET: DNA; 2.20A {Homo sapiens} PDB: 3q8l_A*
3q8m_A*
Length = 341
Score = 27.1 bits (60), Expect = 4.1
Identities = 12/75 (16%), Positives = 30/75 (40%), Gaps = 7/75 (9%)
Query: 98 KILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFQVAEVFTGHAGKLVPLE 157
++Q +KS+++I+ L ++ + A ++ F EV + +L E
Sbjct: 247 DLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQL-------FLEPEVLDPESVELKWSE 299
Query: 158 ETIKGFSEILAGKYD 172
+ + + G+
Sbjct: 300 PNEEELIKFMCGEKQ 314
>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap
DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A
{Homo sapiens} SCOP: a.60.7.1 c.120.1.2
Length = 379
Score = 26.8 bits (59), Expect = 4.9
Identities = 12/75 (16%), Positives = 30/75 (40%), Gaps = 7/75 (9%)
Query: 98 KILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFQVAEVFTGHAGKLVPLE 157
++Q +KS+++I+ L ++ + A ++ F EV + +L E
Sbjct: 247 DLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQL-------FLEPEVLDPESVELKWSE 299
Query: 158 ETIKGFSEILAGKYD 172
+ + + G+
Sbjct: 300 PNEEELIKFMCGEKQ 314
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding
domain, homodimer, hydrolase; 1.45A {Pyrococcus
furiosus} SCOP: a.60.2.5
Length = 75
Score = 25.0 bits (55), Expect = 6.7
Identities = 9/48 (18%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 97 QKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFQVAE 144
+++L+ + S++ + + EL + + + A++I+R ++ P+ E
Sbjct: 28 RRLLKHFGSVERVFT-ASVAELMKVEGIGEKIAKEIRRVITAPYIEDE 74
>3oqb_A Oxidoreductase; structural genomics, protein structure INI NEW YORK
structural genomix research consortium, NYSGXRC, PSI-2;
2.60A {Bradyrhizobium japonicum}
Length = 383
Score = 26.3 bits (58), Expect = 7.3
Identities = 6/25 (24%), Positives = 9/25 (36%)
Query: 173 HLPEVAFYMVGPIEEVVAKAETLAK 197
H V + G ++ VV T
Sbjct: 205 HWRYVLDNLFGNVQSVVCIGNTDIP 229
>3db2_A Putative NADPH-dependent oxidoreductase; two domain protein,
rossman fold, putative dehydrogenase, ST genomics; 1.70A
{Desulfitobacterium hafniense dcb-2}
Length = 354
Score = 26.2 bits (58), Expect = 8.5
Identities = 3/20 (15%), Positives = 9/20 (45%)
Query: 178 AFYMVGPIEEVVAKAETLAK 197
+++GP+ V + +
Sbjct: 190 LQFLLGPVARVFNFGKPMYT 209
>3icl_A EAL/ggdef domain protein; structural genomics, PSI-2, protein
structure initiative, northeast structural genomics,
consortium, NESG; HET: MSE; 2.00A {Methylococcus
capsulatus}
Length = 171
Score = 25.5 bits (57), Expect = 8.9
Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 8/50 (16%)
Query: 107 QDIIAILGMDE----LSEEDKLTVAR--ARKIQRFLSQPFQVA--EVFTG 148
D +A +G D+ L+ A+KI L+QPF ++
Sbjct: 71 GDTVARIGGDKFTILLNGAKDTLNGALVAQKILDGLAQPFVFGAQQIVIS 120
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
0.321 0.137 0.396
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,149,593
Number of extensions: 194595
Number of successful extensions: 369
Number of sequences better than 10.0: 1
Number of HSP's gapped: 362
Number of HSP's successfully gapped: 35
Length of query: 198
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 109
Effective length of database: 4,216,824
Effective search space: 459633816
Effective search space used: 459633816
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 (21.8 bits)
S2: 55 (24.9 bits)