RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2383
(391 letters)
>1olt_A Oxygen-independent coproporphyrinogen III oxidase; heme
biosynthesis, decarboxylase, radical SAM enzyme, 4Fe- 4
cluster; HET: SAM; 2.07A {Escherichia coli} SCOP:
c.1.28.2
Length = 457
Score = 272 bits (697), Expect = 7e-88
Identities = 82/396 (20%), Positives = 164/396 (41%), Gaps = 30/396 (7%)
Query: 16 PLSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILNRKIHTIFIG 75
PLSLY+H P+C K C +C + ++ +YL+AL ++ P+ R + + G
Sbjct: 52 PLSLYVHIPFCHKLCYFCGCNKIVTRQQHKADQYLDALEQEIVHRAPLFAGRHVSQLHWG 111
Query: 76 GGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIGI 135
GGTP+ ++ + L+K +++ F + I++E +P E++ G NRLS+G+
Sbjct: 112 GGTPTYLNKAQISRLMKLLRENFQFNADAEISIEVDPREIELDVLDHLRAEGFNRLSMGV 171
Query: 136 QSFNNKYLNILGRTHDSKQAKYAIEIAKQY-FNNFNLDLIYALPNQTLSELMLDLNYAIQ 194
Q FN + ++ R D + + A++ F + N+DLIY LP QT L +
Sbjct: 172 QDFNKEVQRLVNREQDEEFIFALLNHAREIGFTSTNIDLIYGLPKQTPESFAFTLKRVAE 231
Query: 195 YSPPHLSLYSLTIEPNTYFFKY--PPLSMPSNDENAVMQDKITSLLKNNYYKNYEISAYS 252
+P LS+++ P + + +PS + + + + L + Y+ + ++
Sbjct: 232 LNPDRLSVFNYAHLPTIFAAQRKIKDADLPSPQQKLDILQETIAFLTQSGYQFIGMDHFA 291
Query: 253 KTGYE----------SQHNLNY--WKFGDYLGIGAGSHSKLSFPNYIIRQIRYKNP---N 297
+ E ++ Y D LG+G + S I +N
Sbjct: 292 RPDDELAVAQREGVLHRNFQGYTTQGDTDLLGMGVSAISM-------IGDCYAQNQKELK 344
Query: 298 IYLKNIFSGNS-IAKSKKIEKKCLIFEFMLNALRLKDGFSPNLFFERTGINIKII----E 352
Y + + + + + + + I ++ +L + ++ +
Sbjct: 345 QYYQQVDEQGNALWRGIALTRDDCIRRDVIKSLICNFRLDYSPIEQQWDLLFADYFAEDL 404
Query: 353 SKLKNAEKLGLLKRNNKNIKPTSFGRYFLNDLQQIF 388
L K GL+ + K I+ T+ GR + ++ F
Sbjct: 405 KLLAPLAKDGLVDVDEKGIQVTAKGRLLIRNICMCF 440
>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 = 74.1 bits (181), Expect = 2e-14
Identities = 67/407 (16%), Positives = 137/407 (33%), Gaps = 71/407 (17%)
Query: 4 KRFNNLYIKKLPPLSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLI--DV---- 57
+ L + P + IK E+++ + K Y LL+ +V
Sbjct: 200 EMLQKLLYQIDPNWTSRSDHSSNIKL--RIHSIQAELRRLLKSKPYENCLLVLLNVQNAK 257
Query: 58 -----ELSLPIIL---NRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLE 109
LS I+L +++ T F+ T + IS L + L K + +
Sbjct: 258 AWNAFNLSCKILLTTRFKQV-TDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ 316
Query: 110 ANPSTFEIEKFH--SYSIIGINRLSIGIQSFNN-KYLNI--LGRTHDSKQAKYAIEIAKQ 164
P E+ + SII + G+ +++N K++N L +S ++
Sbjct: 317 DLPR--EVLTTNPRRLSIIA-ESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRK 373
Query: 165 YFNN---FNLDLIYALPNQTLSELMLDLNYA-IQYSPPHLSLYSLTIE-PNTYFFKYPPL 219
F+ F +P LS + D+ + + L YSL + P P +
Sbjct: 374 MFDRLSVFPPSA--HIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI 431
Query: 220 SM---PSNDENAVMQDKITSLLKNNYYKNYEISAYSKTGYESQHNLNYWKFGDYLG---I 273
+ + + I ++Y + + + Y+ ++G
Sbjct: 432 YLELKVKLENEYALHRSIV-----DHYNIPK--TFDSDDLIPPYLDQYFYS--HIGHHLK 482
Query: 274 GAGSHSKLS-FP------NYIIRQIRYK----NPNIYLKNIFSGNSIAKSKK-IEKKCLI 321
+++ F ++ ++IR+ N + + N + K I
Sbjct: 483 NIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTL--QQLKFYKPYICDNDPK 540
Query: 322 FEFMLNALRLKDGFSPNLFFERTGINIKIIESKLKNAEKLGLLKRNN 368
+E ++NA + D F P I +I SK + ++ L+ +
Sbjct: 541 YERLVNA--ILD-FLPK-------IEENLICSKYTDLLRIALMAEDE 577
Score = 33.7 bits (76), Expect = 0.13
Identities = 27/170 (15%), Positives = 42/170 (24%), Gaps = 42/170 (24%)
Query: 2 KYKRFNNLYIKKLPPLSL--YIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVEL 59
Y L P L Y + + H I+ + + +D
Sbjct: 452 HYNIPKTFDSDDLIPPYLDQYFYS--------HIGHHLKNIE-HPERMTLFRMVFLDFRF 502
Query: 60 SLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFE--- 116
L +KI I +T L +K I N +E
Sbjct: 503 -----LEQKIRHDSTAWNASGSILNTLQQ--------LKFYKPYIC----DNDPKYERLV 545
Query: 117 --IEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQ 164
I F I +KY ++L ++ E KQ
Sbjct: 546 NAILDF---------LPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQ 586
Score = 29.1 bits (64), Expect = 3.7
Identities = 36/283 (12%), Positives = 79/283 (27%), Gaps = 80/283 (28%)
Query: 115 FEI-EKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQYFNNFNLDL 173
FE E + Y I + F + +++ K ++ K + +D
Sbjct: 9 FETGEHQYQYKDI--------LSVFEDAFVDNF-------DCKDVQDMPKSILSKEEIDH 53
Query: 174 IYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFKYPPLSMPSNDENAVMQDK 233
I + L L ++L + E V Q
Sbjct: 54 IIMSKDAVSGTLRL--------------FWTLLSKQ----------------EEMV-QKF 82
Query: 234 ITSLLKNNYYKNYEISAYSKTGYESQHNLNYWKFGDYLGIGAGSHSKL-----SFPNY-I 287
+ +L+ NY + +S + Q ++ + + +L F Y +
Sbjct: 83 VEEVLRINY--KFLMSPIKTE--QRQPSMMTRMYIEQ-------RDRLYNDNQVFAKYNV 131
Query: 288 IRQIRYKNPNIYLKNIFSGNSIA--------KSKKIEKKCLIFEFMLNALRLKDGFSPNL 339
R Y L + ++ K+ + + + + +++ +
Sbjct: 132 SRLQPYLKLRQALLELRPAKNVLIDGVLGSGKT------WVALD-VCLSYKVQCKMDFKI 184
Query: 340 FFERTGINIKIIESKLKNAEKLGLLKRNNKNIKPTSFGRYFLN 382
F+ N E+ L+ +KL N + L
Sbjct: 185 FWLNLK-NCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLR 226
>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 = 50.8 bits (121), Expect = 5e-07
Identities = 60/374 (16%), Positives = 107/374 (28%), Gaps = 128/374 (34%)
Query: 16 PLSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKY---LEALLIDVELSLPIILNRKIHTI 72
P L F + S ++ + ++ L L + E + IH +
Sbjct: 57 PAELVGKF---------LGYVSSLVEPS-KVGQFDQVLNLCLTEFENC--YLEGNDIHAL 104
Query: 73 FIGGGTPSLISDTGLDYLLKNIKKLL------LFKKNISITLEANPSTFE---IEKFHSY 123
L+ + D L K+L+ ++N + F
Sbjct: 105 -----AAKLLQEN--DTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLV 157
Query: 124 SIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY--FNNFNLDLIYALPNQT 181
+I G G Q + Y E+ Y ++ DLI +T
Sbjct: 158 AIFG------G-QGNTDDYFE---------------ELRDLYQTYHVLVGDLIKFS-AET 194
Query: 182 LSELMLDLNYAIQYSPPHLSLYS-LT---IEPNTYFFKYPPLSMPSNDENAVMQDKITSL 237
LSEL+ A + L++ L P+ + P+S P + L
Sbjct: 195 LSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLI--------GVIQL 246
Query: 238 LKNNYYKNYEISAYSKTGYESQHNLNYWKFGDYLGIGAGSHSKLSFPNYIIRQIRYKNPN 297
+Y ++A + YL GA HS
Sbjct: 247 A------HYVVTA-------KLLGFTPGELRSYLK-GATGHS------------------ 274
Query: 298 IYLKNIFSGNSIAKSKKIEKKCLIFEF---MLNALRLKDGFSPNLF---------FERTG 345
+ + + +IA++ E F + A+ + LF + T
Sbjct: 275 ---QGLVTAVAIAETDSWE------SFFVSVRKAITV-------LFFIGVRCYEAYPNTS 318
Query: 346 INIKIIESKLKNAE 359
+ I+E L+N E
Sbjct: 319 LPPSILEDSLENNE 332
>2yx0_A Radical SAM enzyme; predicted tRNA modification enzyme, metal
binding protein, structural genomics, NPPSFA; 2.21A
{Pyrococcus horikoshii}
Length = 342
Score = 31.8 bits (71), Expect = 0.32
Identities = 35/275 (12%), Positives = 70/275 (25%), Gaps = 43/275 (15%)
Query: 2 KYKRFNNLY-IKKLPPLSLYIHFPWCIKKCPYCDFHSYE----------------IKKNI 44
++ Y I L + WC C +C ++++I
Sbjct: 56 RFCYKQKFYGIHSHRCLQMTPVLAWCTHNCIFCWRPMENFLGTELPQPWDDPAFIVEESI 115
Query: 45 SEKKYLEALLIDVELSLPIIL---NRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFK 101
++ L H G P L + L++ K
Sbjct: 116 KAQRKLLIGYKGNPKVDKKKFEEAWNPTHAAISLSGEPMLYPY--MGDLVEEFH-----K 168
Query: 102 KNISITLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEI 161
+ + + N + E + +L + I + + + N + + +
Sbjct: 169 RGFTTFIVTNGTIPERLEEMIKEDKLPTQLYVSITAPDIETYNSVNIPMIPDGWERILR- 227
Query: 162 AKQYFNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLT----IEPNTYFFKYP 217
L+L+ LP +T+ L L + + L +E Y F
Sbjct: 228 --------FLELMRDLPTRTVVRLTLVKGENMHSPEKYAKLILKARPMFVEAKAYMF-VG 278
Query: 218 PLSMPSNDENAVMQDKITSLLK--NNYYKNYEISA 250
N I + + Y I
Sbjct: 279 YSRNRLTINNMPSHQDIREFAEALVKHLPGYHIED 313
>2h9b_A HTH-type transcriptional regulator BENM; LTTR, transcriptional
activator, LYSR-type transcripti regulator; 1.80A
{Acinetobacter SP} PDB: 2h99_A 3k1m_A 3k1n_A 3k1p_A
2f7a_A* 2f6p_A 2f78_A 2f6g_A* 2f8d_A 2f97_A*
Length = 312
Score = 31.8 bits (73), Expect = 0.37
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 8/42 (19%)
Query: 348 IKIIESKLKNAEKLG--LLKRNNKNIKPTSFGRYFLNDLQQI 387
I+ +E E+LG LL+R ++ +K T G +F ++
Sbjct: 36 IQNLE------EELGIQLLERGSRPVKTTPEGHFFYQYAIKL 71
>2h98_A HTH-type transcriptional regulator CATM; BENM, LTTR; 1.80A
{Acinetobacter SP} PDB: 2h9q_A* 2f7b_A 2f7c_A* 3glb_A*
3m1e_A
Length = 313
Score = 31.4 bits (72), Expect = 0.40
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 8/42 (19%)
Query: 348 IKIIESKLKNAEKLG--LLKRNNKNIKPTSFGRYFLNDLQQI 387
I+ +E E+LG L +R + K T G +F QI
Sbjct: 36 IQKLE------EELGIQLFERGFRPAKVTEAGMFFYQHAVQI 71
>1ixc_A CBNR, LYSR-type regulatory protein; long alpha helix connecting DNA
binding and regulatory domai binding protein; 2.20A
{Cupriavidus necator} SCOP: a.4.5.37 c.94.1.1 PDB:
1iz1_A
Length = 294
Score = 31.4 bits (72), Expect = 0.40
Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 8/43 (18%)
Query: 348 IKIIESKLKNAEKLG--LLKRNNKNIKPTSFGRYFLNDLQQIF 388
++ +E LG LL+R+++ I+ T+ G FL D ++I
Sbjct: 36 MQALE------ADLGVVLLERSHRGIELTAAGHAFLEDARRIL 72
>1gte_A Dihydropyrimidine dehydrogenase; electron transfer, flavin,
iron-sulfur clusters, pyrimidine catabolism,
5-fluorouracil degradation, oxidoreductase; HET: FMN
FAD; 1.65A {Sus scrofa} SCOP: a.1.2.2 c.1.4.1 c.3.1.1
c.4.1.1 d.58.1.5 PDB: 1gt8_A* 1gth_A* 1h7w_A* 1h7x_A*
Length = 1025
Score = 29.0 bits (65), Expect = 3.0
Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 8/48 (16%)
Query: 24 PWCIKKCPYCDFHSYEIK---KNISEKKYLEAL-LIDVELSLPIILNR 67
C K CP H IK +IS K Y A +I + L +
Sbjct: 85 APCQKSCP---THLD-IKSFITSISNKNYYGAAKMIFSDNPLGLTCGM 128
>1i7d_A DNA topoisomerase III; decatenating enzyme, protein-DNA complex,
single-stranded DNA, isomerase/DNA complex; HET: DNA;
2.05A {Escherichia coli} SCOP: e.10.1.1 PDB: 2o5c_A*
2o54_A* 2o59_A* 2o19_A* 2o5e_A* 1d6m_A*
Length = 659
Score = 28.7 bits (65), Expect = 3.6
Identities = 9/33 (27%), Positives = 13/33 (39%), Gaps = 4/33 (12%)
Query: 350 IIESKLKNAEKLGLLKRNNKNIKPTSFGRYFLN 382
IIE L G L + + I T G+ +
Sbjct: 531 IIE-LLFKR---GFLTKKGRYIHSTDAGKALFH 559
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
0.320 0.139 0.408
Gapped
Lambda K H
0.267 0.0766 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,956,661
Number of extensions: 362271
Number of successful extensions: 889
Number of sequences better than 10.0: 1
Number of HSP's gapped: 874
Number of HSP's successfully gapped: 33
Length of query: 391
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 296
Effective length of database: 4,049,298
Effective search space: 1198592208
Effective search space used: 1198592208
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: 58 (26.0 bits)