RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2378
(956 letters)
>3b0p_A TRNA-dihydrouridine synthase; TIM barrel, oxidoreductase; HET: FMN;
1.70A {Thermus thermophilus} PDB: 3b0u_X* 3b0v_C*
Length = 350
Score = 444 bits (1145), Expect = e-149
Identities = 109/265 (41%), Positives = 171/265 (64%), Gaps = 10/265 (3%)
Query: 3 MINSKYNKRKISIAPMMNLTDRHCRMFHRQITRYSWLYTEMFTTQAIL-GNKKHCLDFNA 61
M++ ++S+APM++ TDRH R RQ++ LYTEM QA+L GN++ L F
Sbjct: 1 MLD-----PRLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRERLLAFRP 55
Query: 62 EEHPIAFQVGDNEPKKLAKSAKIIQKWGYDEINLNCGCPSNRVQNGFFGAILMTKPLLVS 121
EEHPIA Q+ ++PK LA++A+I + +GYDEINLN GCPS + Q G +GA L+ V
Sbjct: 56 EEHPIALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVR 115
Query: 122 DCIKAMRDSVEIDITVKHRIGIDDINSYDFVRDFVGTVSSAGCRTFIVHARNAFLKKLNP 181
+ +KAM ++V + +TVK R+G++ +Y + V ++ AG + F+VHAR+A L L+
Sbjct: 116 EILKAMGEAVRVPVTVKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHARSALL-ALST 174
Query: 182 KQNRKIPILKYNFVYNLKKDFPELEIIINGGIKTKKEIDLHLNYIDGVMLGREAYKNPFL 241
K NR+IP L++++V+ LK DFP+L + NGGI++ +E HL +DGVMLGR Y++PF+
Sbjct: 175 KANREIPPLRHDWVHRLKGDFPQLTFVTNGGIRSLEEALFHLKRVDGVMLGRAVYEDPFV 234
Query: 242 MSNFDLNYYSNLPQYKIPTRIDIIN 266
+ D + + P+R+++
Sbjct: 235 LEEADRRVFGL---PRRPSRLEVAR 256
>1g57_A DHBP synthase, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
riboflavine biosynthesis, skeletal rearrangement,
antimicrobial target; 1.40A {Escherichia coli} SCOP:
d.115.1.2 PDB: 1g58_A 1iez_A 3ls6_A 3lrj_A 3lqu_A 3h07_A
Length = 217
Score = 314 bits (807), Expect = e-101
Identities = 84/159 (52%), Positives = 115/159 (72%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNN 323
++ LD E+RENEGD+I ++ +T + ++ G++C+ +TE QL L MM + N
Sbjct: 29 VMVLDDEDRENEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNT 88
Query: 324 SSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGGVL 383
S++GT FTV+IEAA GVTTG+SA+DR T++ A + AKPSD+ +PGH+FPL+A+ GGVL
Sbjct: 89 SAYGTGFTVTIEAAEGVTTGVSAADRITTVRAAIADGAKPSDLNRPGHVFPLRAQAGGVL 148
Query: 384 IRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARAQE 422
RGGHTEA DL LAG P+ V+CE+ NDDGTMARA E
Sbjct: 149 TRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPE 187
>3mio_A DHBP synthase, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
riboflavin, ribulose-5-phosphate, FAD, FMN; 1.80A
{Mycobacterium tuberculosis} PDB: 3mgz_A 3mk5_A
Length = 206
Score = 303 bits (778), Expect = 3e-97
Identities = 75/176 (42%), Positives = 110/176 (62%), Gaps = 9/176 (5%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNN 323
+I +D E+RENEGD+I +++ TP + FM +Y G +C+ L C +L L M N
Sbjct: 20 VIVIDDEDRENEGDLIFAAEKATPEMVAFMVRYTSGYLCVPLDGAICDRLGLLPMYAVNQ 79
Query: 324 SSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGGVL 383
GT +TV+++A NG+ TGISASDRA T+++ + + D +PGH+ PL+AK GGVL
Sbjct: 80 DKHGTAYTVTVDARNGIGTGISASDRATTMRLLADPTSVADDFTRPGHVVPLRAKDGGVL 139
Query: 384 IRGGHTEAGCDLTKLAGLTPSAVICEILN--DDGTMAR-------AQEKNILHISV 430
R GHTEA DL ++AGL P+ ICEI++ D+G+MA A E + I++
Sbjct: 140 RRPGHTEAAVDLARMAGLQPAGAICEIVSQKDEGSMAHTDELRVFADEHGLALITI 195
>1tks_A 3,4-dihydroxy-2-butanone 4-phosphate synthase; riboflavin
biosynthesis, 3,4-dihydroxy-2-B 4-phosphate synthase,
synthetic gene, ISO; 1.60A {Candida albicans} SCOP:
d.115.1.2 PDB: 1tku_A* 2ris_A 2riu_A*
Length = 204
Score = 302 bits (776), Expect = 6e-97
Identities = 70/175 (40%), Positives = 109/175 (62%), Gaps = 8/175 (4%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNN 323
+I +D E+RENEGD+I++++ +T + F+ +Y+ G +C+ L+E+ QL+L M +
Sbjct: 21 LIVMDDEDRENEGDLIMAAELITQEKMAFLVRYSSGYVCVPLSEERANQLELPPMLANRS 80
Query: 324 SSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGGVL 383
GT +T++ + A G TTGISA DRA T + ++ +KP D ++PGHI PL+A G +
Sbjct: 81 DRHGTAYTITCDFAEGTTTGISAHDRALTTRSLANPNSKPQDFIKPGHILPLRAVPGLLK 140
Query: 384 IRGGHTEAGCDLTKLAGLTPSAVICEILND-DGTMAR-------AQEKNILHISV 430
R GHTEA L+ LAGL P+ VICE++ D DG M R ++ I I++
Sbjct: 141 KRRGHTEAAVQLSTLAGLQPAGVICELVRDEDGLMMRLDDCIQFGKKHGIKIINI 195
>1k4i_A 3,4-dihydroxy-2-butanone 4-phosphate synthase; riboflavin
biosynthesi antimicrobial target, structure-based
design, isomerase; 0.98A {Magnaporthe grisea} SCOP:
d.115.1.2 PDB: 1k49_A 1k4l_A 1k4o_A 1k4p_A
Length = 233
Score = 290 bits (744), Expect = 6e-92
Identities = 71/186 (38%), Positives = 103/186 (55%), Gaps = 19/186 (10%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNN 323
++ LD +RENE D+I++++ VT + FM +++ GLIC LT + L L M N
Sbjct: 28 VVVLDDPSRENEADLIIAAESVTTEQMAFMVRHSSGLICAPLTPERTTALDLPQMVTHNA 87
Query: 324 SSFGTNFTVSIEAA-NGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGGV 382
GT +TVS++A TTGISA DRA ++ ++ A+PS +PGH+FPL+A GGV
Sbjct: 88 DPRGTAYTVSVDAEHPSTTTGISAHDRALACRMLAAPDAQPSHFRRPGHVFPLRAVAGGV 147
Query: 383 LIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGT-----------MAR-------AQEKN 424
R GHTEAG +L +LAG P AVI EI++D M R A+
Sbjct: 148 RARRGHTEAGVELCRLAGKRPVAVISEIVDDGQEVEGRAVRAAPGMLRGDECVAFARRWG 207
Query: 425 ILHISV 430
+ ++
Sbjct: 208 LKVCTI 213
>1snn_A DHBP synthase, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
riboflavin biosynthesis, isomerase; HET: 5RP; 1.55A
{Methanocaldococcus jannaschii} SCOP: d.115.1.2 PDB:
1pvy_A* 1pvw_A
Length = 227
Score = 275 bits (706), Expect = 1e-86
Identities = 59/198 (29%), Positives = 88/198 (44%), Gaps = 32/198 (16%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMT---- 319
I+ DS+ RE E D++++S F+TP I M K A GLIC L C +L + M
Sbjct: 17 ILVYDSDEREGETDMVVASQFITPEHIRIMRKDAGGLICTALHPDICNKLGIPFMVDILE 76
Query: 320 --------------KKNNSSFGTNFTVSIEAANGVTTGISASDRAHTIKVA------SSK 359
++F+++I TGI+ +DRA TIK
Sbjct: 77 FASQKFKVLRELYPNDIPYDEKSSFSITINHR-KTFTGITDNDRAFTIKKLAELVKEGRF 135
Query: 360 KAKPSDIVQPGHIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMAR 419
+ PG + L+A +G V R GHTE L +LA L P ICE++ DDG
Sbjct: 136 NDFGKEFRSPGSVTLLRAAEGLVKNRQGHTEMTVALAELANLVPITTICEMMGDDGNAMS 195
Query: 420 -------AQEKNILHISV 430
A++ N++++S
Sbjct: 196 KNETKRYAEKHNLIYLSG 213
>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 = 203 bits (518), Expect = 4e-57
Identities = 67/359 (18%), Positives = 137/359 (38%), Gaps = 50/359 (13%)
Query: 645 EKKYLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNIS 704
+YL+AL ++ P+ R + + GGGTP+ ++ + L+K +++ F +
Sbjct: 82 ADQYLDALEQEIVHRAPLFAGRHVSQLHWGGGTPTYLNKAQISRLMKLLRENFQFNADAE 141
Query: 705 ITLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY 764
I++E +P E++ G NRLS+G+Q FN + ++ R D + + A++
Sbjct: 142 ISIEVDPREIELDVLDHLRAEGFNRLSMGVQDFNKEVQRLVNREQDEEFIFALLNHAREI 201
Query: 765 -FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFKY--PPLSMP 821
F + N+DLIY LP QT L + +P LS+++ P + + +P
Sbjct: 202 GFTSTNIDLIYGLPKQTPESFAFTLKRVAELNPDRLSVFNYAHLPTIFAAQRKIKDADLP 261
Query: 822 SNDENAVMQDKITSLLKNNYYKNYEISAYSKTGYE----------SQHNLNY--WKFGDY 869
S + + + + L + Y+ + +++ E ++ Y D
Sbjct: 262 SPQQKLDILQETIAFLTQSGYQFIGMDHFARPDDELAVAQREGVLHRNFQGYTTQGDTDL 321
Query: 870 LG---------------NS----------------IAKSKKIEKKCLIFEFMLNALRLKD 898
LG N + + + + I ++ +L
Sbjct: 322 LGMGVSAISMIGDCYAQNQKELKQYYQQVDEQGNALWRGIALTRDDCIRRDVIKSLICNF 381
Query: 899 GFSPNLFFERTGINIKII----ESKLKNAEKLGLLKRNNKNIKPTSFGRYFLNDLQQIF 953
+ ++ + L K GL+ + K I+ T+ GR + ++ F
Sbjct: 382 RLDYSPIEQQWDLLFADYFAEDLKLLAPLAKDGLVDVDEKGIQVTAKGRLLIRNICMCF 440
>3d3b_A Protein NUSB, N utilization substance protein B; NUSB, NUSE, NUT
site, phage lambda, lambdan antitermina antitermination;
HET: NHE; 1.30A {Escherichia coli} PDB: 3d3c_A 3imq_A
1ey1_A
Length = 141
Score = 125 bits (316), Expect = 1e-33
Identities = 47/127 (37%), Positives = 64/127 (50%)
Query: 527 KNKTPRHRAREFALQGIYQWLFNNMDVNLIETYIKEISNFYKVDKKYFYLILRGVINDIN 586
R RARE A+Q +Y W + D+ +E + VD YF +L GV +
Sbjct: 3 MEPAARRRARECAVQALYSWQLSQNDIADVEYQFLAEQDVKDVDVLYFRELLAGVATNTA 62
Query: 587 FLRYDLSLIIDRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDEK 646
+L + + R + EL +E VL I YEL +PYKV INEAIEL KSFG D
Sbjct: 63 YLDGLMKPYLSRLLEELGQVEKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSH 122
Query: 647 KYLEALL 653
K++ +L
Sbjct: 123 KFVNGVL 129
>1di0_A Lumazine synthase; transferase; 2.70A {Brucella abortus} SCOP:
c.16.1.1 PDB: 1t13_A* 1xn1_A
Length = 158
Score = 124 bits (314), Expect = 3e-33
Identities = 21/101 (20%), Positives = 44/101 (43%), Gaps = 5/101 (4%)
Query: 420 AQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQ 479
+ VPGA EIPL K + + ++ ++ +I G Y + +A I+ +MQ
Sbjct: 41 GGSVEVEIFDVPGAYEIPLHAKTLARTGRYAAIVGAAFVIDGGIYDHDFVATAVINGMMQ 100
Query: 480 ISIKNNIPIINAILTTETIEQANSRILTKGEIIIFINHKNK 520
+ ++ +P+++ +LT ++ + K K
Sbjct: 101 VQLETEVPVLSVVLTPHHFHESKEHHDFFHA-----HFKVK 136
>1kz1_A 6,7-dimethyl-8-ribityllumazine synthase; riboflavin biosynthesis,
ligand binding, transferase; 2.00A {Schizosaccharomyces
pombe} SCOP: c.16.1.1 PDB: 2a59_A* 2a58_A* 2a57_A*
1kyv_A* 1kyx_A* 1kyy_A* 1kz9_A 1kz4_A 1kz6_A
Length = 159
Score = 124 bits (314), Expect = 4e-33
Identities = 30/90 (33%), Positives = 51/90 (56%)
Query: 420 AQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQ 479
+ +NI SVPG+ E+P ++ I ++ +I IGV+I+G T HFE I+ + +M+
Sbjct: 49 VKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMR 108
Query: 480 ISIKNNIPIINAILTTETIEQANSRILTKG 509
+ + + +P+I +LT EQA R G
Sbjct: 109 VGLDSGVPVILGLLTVLNEEQALYRAGLNG 138
>1rvv_A Riboflavin synthase; transferase, flavoprotein; HET: INI; 2.40A
{Bacillus subtilis} SCOP: c.16.1.1 PDB: 1zis_A* 1vsw_A
1vsx_A 3jv8_A
Length = 154
Score = 123 bits (312), Expect = 5e-33
Identities = 36/89 (40%), Positives = 51/89 (57%)
Query: 420 AQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQ 479
+I VPGA EIP A K + + KK++ +I +G +IRG T H++ + NE I Q
Sbjct: 43 VDTNDIDVAWVPGAFEIPFAAKKMAETKKYDAIITLGTVIRGATTHYDYVCNEAAKGIAQ 102
Query: 480 ISIKNNIPIINAILTTETIEQANSRILTK 508
+ +P+I I+TTE IEQA R TK
Sbjct: 103 AANTTGVPVIFGIVTTENIEQAIERAGTK 131
>2obx_A DMRL synthase 1, 6,7-dimethyl-8-ribityllumazine synthase 1,
riboflavin S; alpha-beta, transferase; HET: INI; 2.53A
{Mesorhizobium loti}
Length = 157
Score = 122 bits (309), Expect = 2e-32
Identities = 18/85 (21%), Positives = 39/85 (45%)
Query: 420 AQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQ 479
+ VPGA EIPL + + + ++ ++ ++ G Y E +A+ I +M
Sbjct: 42 GDRFAVDVFDVPGAYEIPLHARTLAETGRYGAVLGTAFVVNGGIYRHEFVASAVIDGMMN 101
Query: 480 ISIKNNIPIINAILTTETIEQANSR 504
+ + +P+++A+LT +
Sbjct: 102 VQLSTGVPVLSAVLTPHNYHDSAEH 126
>3nq4_A 6,7-dimethyl-8-ribityllumazine synthase; 30MER, icosahedral,
flavodoxin like fold, transferase, DMRL riboflavin
biosynthesis, drug targe; 3.50A {Salmonella typhimurium}
PDB: 3mk3_A
Length = 156
Score = 122 bits (309), Expect = 2e-32
Identities = 33/89 (37%), Positives = 56/89 (62%)
Query: 420 AQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQ 479
++ NI + VPGA E+PLA + + + K++ ++A+G +IRG T HFE +A + +
Sbjct: 44 VKDDNITVVWVPGAYELPLATEALAKSGKYDAVVALGTVIRGGTAHFEYVAGGASNGLAS 103
Query: 480 ISIKNNIPIINAILTTETIEQANSRILTK 508
++ + +P+ +LTTE+IEQA R TK
Sbjct: 104 VAQDSGVPVAFGVLTTESIEQAIERAGTK 132
>2i0f_A 6,7-dimethyl-8-ribityllumazine synthase 1; lumazine synthase RIBH1,
transferase; 2.22A {Brucella abortus} PDB: 2f59_A
2o6h_A*
Length = 157
Score = 118 bits (299), Expect = 4e-31
Identities = 35/119 (29%), Positives = 60/119 (50%), Gaps = 22/119 (18%)
Query: 424 NILHISVPGALEIPLALKNIIQ-----IKKFNVLIAIGVIIRGETYHFELIANETISNIM 478
++VPGALEIP + + +++ +A+G +IRGETYHF++++NE+ +
Sbjct: 44 TYDVVTVPGALEIPATISFALDGADNGGTEYDGFVALGTVIRGETYHFDIVSNESCRALT 103
Query: 479 QISIKNNIPIINAILTTETIEQANSRILTKGEIIIFINHKNK---------SLVNLIKN 528
+S++ +I I N ILT E EQA + K+K +++ L K
Sbjct: 104 DLSVEESIAIGNGILTVENEEQAWVHARRE--------DKDKGGFAARAALTMIGLRKK 154
>1hqk_A 6,7-dimethyl-8-ribityllumazine synthase; analysi stability, vitamin
biosynthesis, transferase; 1.60A {Aquifex aeolicus}
SCOP: c.16.1.1 PDB: 1nqu_A* 1nqv_A* 1nqw_A* 1nqx_A*
Length = 154
Score = 118 bits (299), Expect = 4e-31
Identities = 34/91 (37%), Positives = 56/91 (61%)
Query: 420 AQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQ 479
+E++I + VPG+ EIP+A + + + + +IAIGV+IRG T HF+ IA+E +
Sbjct: 43 GREEDITLVRVPGSWEIPVAAGELARKEDIDAVIAIGVLIRGATPHFDYIASEVSKGLAN 102
Query: 480 ISIKNNIPIINAILTTETIEQANSRILTKGE 510
+S++ PI ++T +T+EQA R TK
Sbjct: 103 LSLELRKPITFGVITADTLEQAIERAGTKHG 133
>1c2y_A Protein (lumazine synthase); riboflavin biosynthesis, transferase;
HET: LMZ; 3.30A {Spinacia oleracea} SCOP: c.16.1.1
Length = 156
Score = 117 bits (295), Expect = 1e-30
Identities = 20/87 (22%), Positives = 51/87 (58%)
Query: 422 EKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQIS 481
++I + VPGA E+ + + + + K++ ++ +G +++G+T H++ + N S ++
Sbjct: 45 NEDIDVVWVPGAYELGVTAQALGKSGKYHAIVCLGAVVKGDTSHYDAVVNSASSGVLSAG 104
Query: 482 IKNNIPIINAILTTETIEQANSRILTK 508
+ + +P + +LT + ++QA +R K
Sbjct: 105 LNSGVPCVFGVLTCDNMDQAINRAGGK 131
>1vhn_A Putative flavin oxidoreducatase; structural genomics, unknown
function; HET: FMN; 1.59A {Thermotoga maritima} SCOP:
c.1.4.1
Length = 318
Score = 121 bits (305), Expect = 4e-30
Identities = 59/273 (21%), Positives = 111/273 (40%), Gaps = 45/273 (16%)
Query: 10 KRKISIAPMMNLTDRHCRMFHRQITRY---SWLYTEMFTTQAIL-GNKK-HCLDFNAEEH 64
+ K+ +APM TD F R + + ++EM + + L ++K L E
Sbjct: 4 EVKVGLAPMAGYTDS---AF-RTLAFEWGADFAFSEMVSAKGFLMNSQKTEELLPQPHER 59
Query: 65 PIAFQVGDNEPKKLAKSAKIIQKWGYDEINLNCGCPSNRVQNGFFGAILMTKPLLVSDCI 124
+A Q+ +EP +L+++A+I+ + Y I+LN GCP +V G L+ +
Sbjct: 60 NVAVQIFGSEPNELSEAARILSE-KYKWIDLNAGCPVRKVVKEGAGGALLKDLRHFRYIV 118
Query: 125 KAMRDSVEIDITVKHRIGIDDINSYDFVRDFVGTVSSAGCRTFIVHAR--------NAFL 176
+ +R SV +VK R+G + + R + G +H R A
Sbjct: 119 RELRKSVSGKFSVKTRLGWEKNEVEEIYR----ILVEEGVDEVFIHTRTVVQSFTGRA-- 172
Query: 177 KKLNPKQNRKIPILKYNFVYNLKKDFPELEIIINGGIKTKKEIDLHLNY--IDGVMLGRE 234
++ + L+K P ++G I T ++ L DG+++ R
Sbjct: 173 --------------EWKALSVLEKRIP---TFVSGDIFTPEDAKRALEESGCDGLLVARG 215
Query: 235 AYKNPFLMSNFDLNYYSNLPQYKIPTRIDIINL 267
A P++ + + +Y P+R +I+
Sbjct: 216 AIGRPWIFK--QIKDFLRSGKYSEPSREEILRT 246
>1eyv_A NUSB protein, N-utilizing substance protein B homolog; helical
bundle, structural genomics, PSI, protein structure
initiative; 1.60A {Mycobacterium tuberculosis} SCOP:
a.79.1.1
Length = 156
Score = 114 bits (288), Expect = 8e-30
Identities = 23/131 (17%), Positives = 55/131 (41%), Gaps = 4/131 (3%)
Query: 527 KNKTPRHRAREFALQGIYQWLFNNMDVNLI---ETYIKEISNFYKVDKKYFYLILRGVIN 583
K RH+AR+ A+ +++ + + + E Y + RGV
Sbjct: 5 KPVRGRHQARKRAVALLFEAEVRGISAAEVVDTRAALAEAKPDIARLHPYTAAVARGVSE 64
Query: 584 DINFLRYDLSLIIDR-SINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGN 642
+ ++ + +++ L +++ +L + +EL +P V+++EA++L K
Sbjct: 65 HAAHIDDLITAHLRGWTLDRLPAVDRAILRVSVWELLHAADVPEPVVVDEAVQLAKELST 124
Query: 643 IDEKKYLEALL 653
D ++ +L
Sbjct: 125 DDSPGFVNGVL 135
>1tzv_A NUSB protein, N utilization substance protein B homolog;
RNA-protein interaction, transcriptional
antitermination, transcription regulation; 1.35A
{Thermotoga maritima} SCOP: a.79.1.1 PDB: 1tzu_A 1tzt_A
1tzw_A 1tzx_A*
Length = 142
Score = 114 bits (287), Expect = 9e-30
Identities = 35/126 (27%), Positives = 63/126 (50%), Gaps = 1/126 (0%)
Query: 529 KTPRHRAREFALQGIYQWLFNNMDVNLIETYIKEISNFYKVDKKYFYLILRGVINDINFL 588
KTPR R R + ++Q F + + K K+ +RG+ +++ +
Sbjct: 2 KTPRRRMRLAVFKALFQHEFRRDEDLEQILEEILDETYDKKAKEDARRYIRGIKENLSMI 61
Query: 589 RYDLSLIIDR-SINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDEKK 647
+S +++ S+N LS ++ VL + TYEL IP +V I+EAIE+ K +G + K
Sbjct: 62 DDLISRYLEKWSLNRLSVVDRNVLRLATYELLFEKDIPIEVTIDEAIEIAKRYGTENSGK 121
Query: 648 YLEALL 653
++ +L
Sbjct: 122 FVNGIL 127
>1ejb_A Lumazine synthase; analysis, inhibitor complex, vitamin
biosynthesis transferase; HET: INJ; 1.85A {Saccharomyces
cerevisiae} SCOP: c.16.1.1 PDB: 2jfb_A
Length = 168
Score = 113 bits (285), Expect = 3e-29
Identities = 34/95 (35%), Positives = 53/95 (55%), Gaps = 5/95 (5%)
Query: 420 AQEKNILHISVPGALEIPLALKNIIQI-----KKFNVLIAIGVIIRGETYHFELIANETI 474
+E NI+ +VPG+ E+P K + K +V+I IGV+I+G T HFE I++ T
Sbjct: 47 VEENNIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLIKGSTMHFEYISDSTT 106
Query: 475 SNIMQISIKNNIPIINAILTTETIEQANSRILTKG 509
+M + K ++P+I +LT T EQA +R
Sbjct: 107 HALMNLQEKVDMPVIFGLLTCMTEEQALARAGIDE 141
>3r2d_A Protein NUSB, N utilization substance protein B; cross species
NUSB-NUSE-RNA interaction; 2.20A {Aquifex aeolicus} PDB:
2jr0_A 3r2c_A*
Length = 149
Score = 110 bits (278), Expect = 1e-28
Identities = 24/127 (18%), Positives = 49/127 (38%), Gaps = 2/127 (1%)
Query: 529 KTPRHRAREFALQGIYQWLFNNMDVNLIETYIKEISNFYKVD-KKYFYLILRGVINDINF 587
R AR+ A +Y+W + + + E N D +Y ++ + I
Sbjct: 2 MRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEE 61
Query: 588 LRYDLSLIIDR-SINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDEK 646
+ + + SI+ L +E L +G EL + + ++LVK + +
Sbjct: 62 IDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAG 121
Query: 647 KYLEALL 653
K++ +L
Sbjct: 122 KFVNGVL 128
>2c92_A 6,7-dimethyl-8-ribityllumazine synthase; transferase, riboflavin
biosynthesis, inhibitor binding; HET: TP6; 1.6A
{Mycobacterium tuberculosis} PDB: 1w29_A* 1w19_A*
2c94_A* 2c97_A* 2c9b_A* 2c9d_A* 2vi5_A*
Length = 160
Score = 110 bits (278), Expect = 2e-28
Identities = 28/89 (31%), Positives = 51/89 (57%), Gaps = 2/89 (2%)
Query: 416 TMARAQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETIS 475
A + + V GA+EIP+ + + + + ++A+GV+IRG+T HF+ + +
Sbjct: 42 VAAGCGLDDPTVVRVLGAIEIPVVAQELA--RNHDAVVALGVVIRGQTPHFDYVCDAVTQ 99
Query: 476 NIMQISIKNNIPIINAILTTETIEQANSR 504
+ ++S+ ++ PI N +LTT T EQA R
Sbjct: 100 GLTRVSLDSSTPIANGVLTTNTEEQALDR 128
>1c41_A Lumazine synthase; riboflavin biosynthesis, transferase; HET: LMZ;
3.10A {Magnaporthe grisea} SCOP: c.16.1.1
Length = 200
Score = 101 bits (254), Expect = 1e-24
Identities = 35/126 (27%), Positives = 56/126 (44%), Gaps = 36/126 (28%)
Query: 420 AQEKNILHISVPGALEIPLALKNIIQI--------------------------------- 446
+E NI+ SVPG+ E+P+A++ +
Sbjct: 46 VKESNIVVQSVPGSWELPIAVQRLYSASQLQTPSSGPSLSAGDLLGSSTTDLTALPTTTA 105
Query: 447 ---KKFNVLIAIGVIIRGETYHFELIANETISNIMQISIKNNIPIINAILTTETIEQANS 503
F+ LIAIGV+I+GET HFE IA+ +M++ + +P+I +LT T +QA +
Sbjct: 106 SSTGPFDALIAIGVLIKGETMHFEYIADSVSHGLMRVQLDTGVPVIFGVLTVLTDDQAKA 165
Query: 504 RILTKG 509
R
Sbjct: 166 RAGVIE 171
>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 = 81.1 bits (199), Expect = 1e-15
Identities = 92/624 (14%), Positives = 183/624 (29%), Gaps = 158/624 (25%)
Query: 423 KNILHISVPGAL------EIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELI---ANET 473
K+IL + + ++ K+I+ ++ + +I + G F + E
Sbjct: 19 KDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEM 78
Query: 474 ISNIMQISIKNNIPIINAILTTETIEQANSRILTKGEIIIFINHKNKSLVNLIKNKTPRH 533
+ ++ ++ N + + + TE + ++I +++ L N + +
Sbjct: 79 VQKFVEEVLRINYKFLMSPIKTEQRQ-------PSMMTRMYIEQRDR-LYNDNQVFAKYN 130
Query: 534 RAREFALQGIYQWLFNNMDVNLIETY----------IKEISNFYKVDKKY----FYLILR 579
+R + Q L + ++ YKV K F+L L+
Sbjct: 131 VSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLK 190
Query: 580 GVINDINFLRY--DLSLIIDRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELV 637
+ L L ID + S I + I+ +
Sbjct: 191 NCNSPETVLEMLQKLLYQIDPNWTSRSD--------------HSSNIKLR--IHSIQAEL 234
Query: 638 KSFGNIDEKKYLEALLI--DV---------ELSLPIIL---NRKIHTIFIGGGTPSLISD 683
+ + K Y LL+ +V LS I+L +++ T F+ T + IS
Sbjct: 235 RRL--LKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQV-TDFLSAATTTHISL 291
Query: 684 TGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFH--SYSIIGINRLSIGIQSFNN-K 740
L + L K + + P E+ + SII + G+ +++N K
Sbjct: 292 DHHSMTLTPDEVKSLLLKYLDCRPQDLPR--EVLTTNPRRLSIIA-ESIRDGLATWDNWK 348
Query: 741 YLNI--LGRTHDSKQAKYAIEIAKQYFNN---FNLDLIYALPNQTLSELMLDLNYAIQYS 795
++N L +S ++ F+ F +P LS + D
Sbjct: 349 HVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSA--HIPTILLSLIWFD-------- 398
Query: 796 PPHLSLYSLTIEPNTYFFKYPPLSMPSNDENAVMQDKITSLLKNNYYKNYEIS------- 848
+ +D V+ L K IS
Sbjct: 399 ------------------------VIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLE 434
Query: 849 -----------------AYSKTGYESQHNL------NYWKFGDYLGNSIAKSKKIEKKCL 885
Y+ +L Y+ ++G+ + + E+ L
Sbjct: 435 LKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYS--HIGHHLKNIEHPERMTL 492
Query: 886 I------FEFMLNALRLKDGFSPNLF--FERTGINIK-----IIESKLKNAEKLGLLKRN 932
F F+ +R D + N T +K I ++ K + +
Sbjct: 493 FRMVFLDFRFLEQKIR-HDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDF 551
Query: 933 NKNIKPTSFGRYFLNDLQQIFLNN 956
I+ DL +I L
Sbjct: 552 LPKIEENLI-CSKYTDLLRIALMA 574
Score = 76.0 bits (186), Expect = 4e-14
Identities = 119/788 (15%), Positives = 236/788 (29%), Gaps = 264/788 (33%)
Query: 183 QNRKI-PILKYNFVYNLK-KDFPELEIIINGGIKTKKEID---------LHLNYIDGVML 231
Q + I + + FV N KD ++ I +K+EID + +L
Sbjct: 17 QYKDILSVFEDAFVDNFDCKDVQDMP----KSILSKEEIDHIIMSKDAVSGTLRLFWTLL 72
Query: 232 --GREAYKNPFLMSNFDLNY---YSNL-PQYKIPTRIDIINLDSENRENEGDIILSSDFV 285
E + F+ +NY S + + + P+ + + ++ +R + + + V
Sbjct: 73 SKQEEMVQK-FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV 131
Query: 286 TPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNNSSFGTNFTVSIEAANGVTTGIS 345
+ R + ++L+ ++ + + V I+ G +G +
Sbjct: 132 S-----------R--------LQPYLKLRQALLELRPAKN------VLIDGVLG--SGKT 164
Query: 346 ASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSA 405
+ V S K + IF L L L L
Sbjct: 165 WV----ALDVCLSYKVQC---KMDFKIFWLNL--------KNCNSPETVLEMLQKL---- 205
Query: 406 VICEILNDDGTMARAQEKNI-LHISVPGALEIPLALKNIIQIKKF-NVLIAIGVIIRGET 463
++ + T NI L I I L+ +++ K + N L+ ++
Sbjct: 206 --LYQIDPNWTSRSDHSSNIKLRIH-----SIQAELRRLLKSKPYENCLL----VLLN-- 252
Query: 464 YHFELIANETISNIMQISIKNNIPIINAILTTETIEQANSRILTKGEIIIFINHKNKSLV 523
+ N N +S K +LTT + + + I ++H + +L
Sbjct: 253 -----VQNAKAWNAFNLSCK-------ILLTTRFKQVTDF-LSAATTTHISLDHHSMTL- 298
Query: 524 NLIKNKTPRHRAREFALQGIYQWLFNNMDVNLIETYIKEISNFYKVDKKYFYLI---LRG 580
TP ++L + + + + +I +R
Sbjct: 299 ------TPDEVKSLLL-----KYL--DCRPQDLPREVLTTNPRR------LSIIAESIRD 339
Query: 581 VINDINFLRY----DLSLIIDRSINELSSIE----YVVLLIGTYELKSHYKIPYKVIINE 632
+ + ++ L+ II+ S+N L E + L + IP +
Sbjct: 340 GLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV----FPPSAHIPTIL---- 391
Query: 633 AIELVKSFGNIDEKKYLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKN 692
L + ++ + DV + ++N K+H
Sbjct: 392 ---LSLIWFDVIK--------SDVMV----VVN-KLH----------------------- 412
Query: 693 IKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSK 752
K L+ K+ ST I SI L + ++ N L H S
Sbjct: 413 -KYSLVEKQP-------KESTISI-----PSIY----LELKVKLENEYAL------HRSI 449
Query: 753 QAKYAIEIAKQYFNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIE----P 808
Y I K + ++ L LD Y + HL
Sbjct: 450 VDHY--NIPKTFDSD------------DLIPPYLD-QYFYSHIGHHLKNIEHPERMTLFR 494
Query: 809 NTYF-FKYPPLSMPSNDENAVMQDKITSLLKNNYYKNYEISAYSKTGYESQ--HNLNYWK 865
+ F++ ++ KI ++ +A++ +G L ++K
Sbjct: 495 MVFLDFRF-------------LEQKI----------RHDSTAWNASGSILNTLQQLKFYK 531
Query: 866 FGDYLGNSIAKSKKIEKKCLIFEFMLNALRLKDGFSPNLFFERTGINIKIIESKLKNAEK 925
Y I +E ++NA + D F P I +I SK + +
Sbjct: 532 --PY----------ICDNDPKYERLVNA--ILD-FLPK-------IEENLICSKYTDLLR 569
Query: 926 LGLLKRNN 933
+ L+ +
Sbjct: 570 IALMAEDE 577
Score = 73.0 bits (178), Expect = 4e-13
Identities = 111/773 (14%), Positives = 203/773 (26%), Gaps = 255/773 (32%)
Query: 55 HCLDFNAEEHPIAFQ----------VGDNEPKKLAKSAK-IIQKWGYDEINLNCGCPSNR 103
H +DF EH ++ V + + K + K I+ K D I + +
Sbjct: 5 HHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHI-IMSKDAVSG 63
Query: 104 VQNGFFGAILMTKPLLVSDCIKAMRDSVEIDITVKHRIGIDDINSYDFVRDFVGTVSSAG 163
F+ L++K + K + + + I+ Y F+ + T
Sbjct: 64 TLRLFW--TLLSKQEEMVQ--KFVEEVLRIN--------------YKFLMSPIKTEQRQP 105
Query: 164 CRTFIVHARNAFLKKLNPKQNRKIPILKYNFVY----------NLKKDFPELEIIING-- 211
++++ + N KYN V L + P ++I+G
Sbjct: 106 SMM-----TRMYIEQRDRLYNDNQVFAKYN-VSRLQPYLKLRQALLELRPAKNVLIDGVL 159
Query: 212 GI-KTKKEIDLHLNYIDGVMLGREAYKNPFLMSNFDLN-YYSNLPQYKIPTRIDII--NL 267
G KT + + + + D ++ NL P + + L
Sbjct: 160 GSGKT--------------WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKL 205
Query: 268 -------DSENRENEGDIILSSDFVTPNAINFMS--KYARGLI----------------- 301
+ ++ +I L + + Y L+
Sbjct: 206 LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLS 265
Query: 302 CMTLTEKHCIQLKLDMMTKKNNSSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKA 361
C L +T + VT +SA+ H S
Sbjct: 266 CKIL------------LTTRFKQ---------------VTDFLSAATTTHISLDHHSMTL 298
Query: 362 KPSDIVQPGHIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARAQ 421
P ++ L K C L P V
Sbjct: 299 TPDEVKS------LLLKY-----------LDCRPQDL----PREV-LTT----------- 325
Query: 422 EKNILHISVPGAL--EIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQ 479
N +S+ + N + + I + L E +
Sbjct: 326 --NPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN------VLEPAEYRKMFDR 377
Query: 480 ISI--KN-NIPIIN-AILTTETIEQANSRILTKGEIIIFINHKNKSLVNLIKNKTPRHRA 535
+S+ + +IP I +++ + I+ ++ K SLV + K
Sbjct: 378 LSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLH--------KYSLVEK-QPKESTIS- 427
Query: 536 REFALQGIYQWLFNNMDVNLIETYIKEISNFYKVDKKYFYLILRGVINDINFLRYDLSLI 595
+ IY L ++ N + + I + Y + K + +D+ D
Sbjct: 428 ----IPSIYLELKVKLE-NEYALH-RSIVDHYNIPKTFDS-------DDLIPPYLD---- 470
Query: 596 IDRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDEKKYLEALLID 655
+Y IG + LK+ E E + F +L D
Sbjct: 471 -----------QYFYSHIG-HHLKN----------IEHPERMTLF----RMVFL-----D 499
Query: 656 VELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFE 715
L +KI I +T L +K I N +E
Sbjct: 500 FRF-----LEQKIRHDSTAWNASGSILNTLQQ--------LKFYKPYIC----DNDPKYE 542
Query: 716 -----IEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQ 763
I F I +KY ++L ++ E KQ
Sbjct: 543 RLVNAILDF---------LPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQ 586
Score = 48.7 bits (115), Expect = 1e-05
Identities = 49/375 (13%), Positives = 106/375 (28%), Gaps = 135/375 (36%)
Query: 23 DRHCRMFHRQITRYSWLYTEMFTTQAILGNKKHCLDFNAEEHPIAFQVGDNEPKKLAKSA 82
+ C++ TR+ + T H + + H + +
Sbjct: 263 NLSCKIL--LTTRFKQV-----TDFLSAATTTH---ISLDHHSMTLT--------PDEVK 304
Query: 83 KIIQKWGYDEINLNCGCPSNRVQNGFFGAILMTKPLLVSDCIKAMRDSVEIDITVKHRIG 142
++ K+ L+C + +L T P +S +++RD
Sbjct: 305 SLLLKY------LDCRPQDLPRE------VLTTNPRRLSIIAESIRD------------- 339
Query: 143 IDDINSYDFVRDFVGTVSSAGCRTFIVHARNAFLKKLNPKQNR-------------KIP- 188
+ ++D + C + L L P + R IP
Sbjct: 340 --GLATWDNWKHV-------NCDKLT-TIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPT 389
Query: 189 ----ILKYNFVYN--------------LKKDFPELEIIINGG-----IKTKKEIDLHLNY 225
++ ++ + + ++K E I I +K + E LH +
Sbjct: 390 ILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSI 449
Query: 226 IDGVMLGREAYKNPFLMSNFDLNY-YSNLP-------------------------QYKIP 259
+D + + + + D Y YS++ + KI
Sbjct: 450 VDHYNIPKTFDSDDLIPPYLD-QYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKI- 507
Query: 260 TRIDIINLDSENRENE--GDIILSSDFVTPNA----------INFMSKYARGLICMTLTE 307
R D ++ + ++ N ++F+ K LIC
Sbjct: 508 -RHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLIC----S 562
Query: 308 KHCIQLKLDMMTKKN 322
K+ L++ +M +
Sbjct: 563 KYTDLLRIALMAEDE 577
Score = 39.8 bits (92), Expect = 0.004
Identities = 45/309 (14%), Positives = 82/309 (26%), Gaps = 97/309 (31%)
Query: 36 YSWLY----TEMFTTQAILGNKKHCLD--FNAEEHPIAFQVGDNEP-KKLAKSAKIIQKW 88
Y +L TE + D +N + + V +P KL ++ ++
Sbjct: 91 YKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPA 150
Query: 89 GYDEINLN----CG--------CPSNRVQNGFFGAI------------LMTKPL--LVSD 122
+ ++ G C S +VQ I + + L L+
Sbjct: 151 KN--VLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQ 208
Query: 123 CIKAMRDSVEIDITVKHRIG---------------------IDDINSYDFVRDFVGTVSS 161
+ +K RI + ++ + F +
Sbjct: 209 IDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAF-----N 263
Query: 162 AGCRTFIVHARNAFL-KKLNPKQNRKIPILKYNFVYNLKKDFPELEIIINGGIKTKKE-I 219
C+ ++ R + L+ I + ++ T E
Sbjct: 264 LSCKI-LLTTRFKQVTDFLSAATTTHISLDHHSMTL------------------TPDEVK 304
Query: 220 DLHLNYIDGVM--LGREAYK-NPFLMSNF------DLNYYSNLPQYKIPTRIDII----- 265
L L Y+D L RE NP +S L + N II
Sbjct: 305 SLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN 364
Query: 266 NLDS-ENRE 273
L+ E R+
Sbjct: 365 VLEPAEYRK 373
>2b99_A Riboflavin synthase; lumazine riboflavin, transferase; HET: RDL;
2.22A {Methanocaldococcus jannaschii} PDB: 2b98_A*
Length = 156
Score = 67.3 bits (164), Expect = 4e-13
Identities = 22/124 (17%), Positives = 51/124 (41%), Gaps = 8/124 (6%)
Query: 422 EKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQIS 481
I+ +VPG ++P+A K +++ + ++++A+G+ G+ ++ A+E +M
Sbjct: 31 NIKIIRKTVPGIKDLPVACKKLLEEEGCDIVMALGMP--GKAEKDKVCAHEASLGLMLAQ 88
Query: 482 IKNNIPIINAILTTETIEQANSRILTKGEIIIFINHKNKSLVNLIKNKTPRHRAREFALQ 541
+ N II + E + + L + + N+ A +
Sbjct: 89 LMTNKHIIE--VFVHEDEAKDDKELDW----LAKRRAEEHAENVYYLLFKPEYLTRMAGK 142
Query: 542 GIYQ 545
G+ Q
Sbjct: 143 GLRQ 146
>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 = 57.8 bits (139), Expect = 2e-08
Identities = 67/393 (17%), Positives = 118/393 (30%), Gaps = 133/393 (33%)
Query: 598 RSINELS--SIEYVVLL-IGTY----ELK----SHYKIPYKVIINE-----AIELVKSF- 640
R + LS S+E+V+L+ ++ +L+ P + + ELV F
Sbjct: 7 RPLT-LSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFL 65
Query: 641 ----GNIDEKKY------LEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLL 690
++ K L L + E + IH + L+ + D L
Sbjct: 66 GYVSSLVEPSKVGQFDQVLNLCLTEFENC--YLEGNDIHAL-----AAKLLQEN--DTTL 116
Query: 691 KNIKKLL------LFKKNISITLEANPSTFE---IEKFHSYSIIGINRLSIGIQSFNNKY 741
K+L+ ++N + F +I G G Q + Y
Sbjct: 117 VKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFG------G-QGNTDDY 169
Query: 742 LNILGRTHDSKQAKYAIEIAKQY--FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHL 799
E+ Y ++ DLI +TLSEL+ A + L
Sbjct: 170 FE---------------ELRDLYQTYHVLVGDLIKFS-AETLSELIRTTLDAEKVFTQGL 213
Query: 800 SLYS-LT---IEPNTYFFKYPPLSMPSNDENAVMQDKITSLLKNNYYKNYEISAYSKTGY 855
++ L P+ + P+S P + L +Y ++A
Sbjct: 214 NILEWLENPSNTPDKDYLLSIPISCPLI--------GVIQLA------HYVVTA------ 253
Query: 856 ESQHNLNYWKFGDYL-GNS-----------IAKSKKIEKKCLIFEF---MLNALRLKDGF 900
+ YL G + IA++ E F + A+ +
Sbjct: 254 -KLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWE------SFFVSVRKAITV---- 302
Query: 901 SPNLF---------FERTGINIKIIESKLKNAE 924
LF + T + I+E L+N E
Sbjct: 303 ---LFFIGVRCYEAYPNTSLPPSILEDSLENNE 332
Score = 57.4 bits (138), Expect = 2e-08
Identities = 53/322 (16%), Positives = 104/322 (32%), Gaps = 106/322 (32%)
Query: 465 HFELIANETISNIMQISIKNNIPIINAILTTETIEQANSRILTKGEII-------IFINH 517
FE + ++ N+I +A L + +++ ++ ++ E+I I
Sbjct: 90 EFE-------NCYLE---GNDI---HA-LAAKLLQENDTTLVKTKELIKNYITARIMAKR 135
Query: 518 KNKSLVN--LIKNKTPRHRAREFAL---QGIYQWLFNNMDVNLIETYIKEISNFYKVDKK 572
N L + A+ A+ QG N + Y +E+ + Y+
Sbjct: 136 PFDKKSNSALFRA-VGEGNAQLVAIFGGQG------NT------DDYFEELRDLYQT--- 179
Query: 573 YFYLI------LRGVINDINFLRYDLSLIIDRSINELS---------SIEYVVL------ 611
Y L+ ++++ D + + +N L +Y++
Sbjct: 180 YHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCP 239
Query: 612 LIGTYELKSHYKIPYK----------------------VIINEAIELVKSFGNIDE--KK 647
LIG +L +HY + K ++ AI S+ + +K
Sbjct: 240 LIGVIQL-AHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRK 298
Query: 648 YLEALL-IDVE-------LSLPIILNRKIHTIFIGGGTPS---LISDTGLDYLLKNIKKL 696
+ L I V SLP + ++ G PS IS+ + + + K
Sbjct: 299 AITVLFFIGVRCYEAYPNTSLPPSILED--SLENNEGVPSPMLSISNLTQEQVQDYVNKT 356
Query: 697 ---LLFKKNISITLEAN-PSTF 714
L K + I+L N
Sbjct: 357 NSHLPAGKQVEISL-VNGAKNL 377
Score = 52.7 bits (126), Expect = 6e-07
Identities = 74/494 (14%), Positives = 130/494 (26%), Gaps = 178/494 (36%)
Query: 44 FTTQAILGNKKHCLDFNAEEHPIAFQVGDNEPKKLAKSAKIIQKWGYDEINLNCGCPSNR 103
F + GN + H +A ++ L K+ ++I+ Y + P ++
Sbjct: 91 FENCYLEGN---------DIHALAAKLLQENDTTLVKTKELIK--NYITARIMAKRPFDK 139
Query: 104 ---------VQNG------FFG-------------AILMTKPLLVSDCIKAMRDSVE--- 132
V G FG + T +LV D IK +++
Sbjct: 140 KSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELI 199
Query: 133 ---IDITVKHRIGIDDINSYDFVRDFVGTVSSAGCRTFIVHARNAFLKKLNPKQNRKIPI 189
+D G++ + +++ S+ + +++ + P+
Sbjct: 200 RTTLDAEKVFTQGLN-------ILEWLENPSNTPDKDYLLSIPISC------------PL 240
Query: 190 LK-------YNFVYNLKKDFPELEIIINGGIKTKKEI-------------DLHLNYIDGV 229
+ L EL + G + + ++ +
Sbjct: 241 IGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAI 300
Query: 230 ML-------GREAYKNPFLMSNFDLNYYSNLPQYKIPTRIDIINLDSENRENEGDIILSS 282
+ EAY P +P I L+ NEG
Sbjct: 301 TVLFFIGVRCYEAY-----------------PNTSLPPSI----LEDSLENNEG------ 333
Query: 283 DFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNNSSFGTNFTVSIEAANG--- 339
P+ M L+ + Q ++ K NS V I NG
Sbjct: 334 ---VPS-------------PM-LSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKN 376
Query: 340 -VTTGISAS-----DRAHTIKVA----------SSKKAKPSD----IVQPGH-------- 371
V +G S K S +K K S+ + P H
Sbjct: 377 LVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPAS 436
Query: 372 -IFPLQAKKGGVLIRGG-------HTEAGCDLTKLAG-LTPSAVICEILNDDGTMARAQE 422
+ K V T G DL L+G ++ V C I+ +
Sbjct: 437 DLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDC-IIRLPVKWETTTQ 495
Query: 423 KNILHISV--PGAL 434
HI PG
Sbjct: 496 FKATHILDFGPGGA 509
Score = 52.0 bits (124), Expect = 1e-06
Identities = 53/316 (16%), Positives = 101/316 (31%), Gaps = 98/316 (31%)
Query: 230 MLGREAYKN-PFLMSNFDL--NYYSNLPQYKIPTRIDIINLDSENRENEGDIILSSDFVT 286
M G + YK ++ N++ + + I +DI+ N ++ +
Sbjct: 1631 M-GMDLYKTSKAAQDVWNRADNHFKDTYGFSI---LDIV------INNPVNLTIHFGGEK 1680
Query: 287 PNAI--NFMSKYARGLICMTLTEKHCIQLKLDMMTKKNNSS--FG--------TNFT-VS 333
I N+ + +I T+ + K+ ++++S F T FT +
Sbjct: 1681 GKRIRENYSA-----MIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPA 1735
Query: 334 IEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPL-----QAKKGGVL----- 383
+ +A + SK P+D GH L A V+
Sbjct: 1736 L-----TLMEKAA------FEDLKSKGLIPADATFAGH--SLGEYAALASLADVMSIESL 1782
Query: 384 -----IRG-------GHTEAGCDLTKLAGLTPSAVICEILNDDGTMARAQEKNILHIS-- 429
RG E G + + P V + + A + + +
Sbjct: 1783 VEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVA-ASFSQE-----ALQYVVERVGKR 1836
Query: 430 VPGALEIPLALKNIIQIKKFNVLIAIG--VIIRGETYHFELIANETISNIM-QISIKNNI 486
+EI N +NV + G+ L A +T++N++ I ++ I
Sbjct: 1837 TGWLVEI--V--N------YNVE---NQQYVAAGD-----LRALDTVTNVLNFIKLQ-KI 1877
Query: 487 PII--NAILTTETIEQ 500
II L+ E +E
Sbjct: 1878 DIIELQKSLSLEEVEG 1893
Score = 45.0 bits (106), Expect = 1e-04
Identities = 56/357 (15%), Positives = 106/357 (29%), Gaps = 139/357 (38%)
Query: 541 QGI---------Y------QWLFNNMDVNLIETYIKEISNFYKVDKKYFYLILRGV---- 581
QG Y Q ++N D + +TY I + + + G
Sbjct: 1624 QGSQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKR 1683
Query: 582 INDINFLRYDLSLIIDRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINE------AI- 634
I + Y ++I + ++ E + I + ++ K +++ A+
Sbjct: 1684 IRE----NYS-AMIFETIVDGKLKTEKIFKEINEHSTSYTFRSE-KGLLSATQFTQPALT 1737
Query: 635 -------ELVKSFGNIDEKKYL------E--AL--LIDVELSLPIILNRKIHTIFIGGGT 677
E +KS G I E AL L DV +S+
Sbjct: 1738 LMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADV-MSI----------------- 1779
Query: 678 PSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHS-YSIIGINRLSIGIQS 736
++ ++F + +++ A P E S Y +I IN + S
Sbjct: 1780 ----ESL--------VE--VVFYRGMTMQ-VAVP---RDELGRSNYGMIAINPGRVAA-S 1820
Query: 737 FNNKYLNILGRTHDSKQAKYAIEIAKQYFNNFNLDLIYALPNQTLSELMLDLNYAIQYSP 796
F+ + L + K+ + +EI N+N + NQ Y
Sbjct: 1821 FSQEALQYVVER-VGKRTGWLVEIV-----NYN------VENQQ---------YVA---- 1855
Query: 797 PHLSLYSLTIEPNTYFFKYPPLSMPSNDENAVMQDKITSLLKNNYYKNYEISAYSKT 853
+ D A+ D +T++L + +I K+
Sbjct: 1856 -------------------------AGDLRAL--DTVTNVLNFIKLQKIDIIELQKS 1885
>1sqg_A SUN protein, FMU protein; rossmann-fold, mixed beta sheet,
methyltransferase-fold, RNA-binding domain; 1.65A
{Escherichia coli} SCOP: a.79.1.3 c.66.1.38 PDB: 1sqf_A
Length = 429
Score = 42.2 bits (100), Expect = 6e-04
Identities = 20/125 (16%), Positives = 53/125 (42%), Gaps = 5/125 (4%)
Query: 530 TPRHRAREFALQGIYQWLFNNMDVN-LIETYIKEISNFYKVDKKYFYLILRGVINDINFL 588
+ R A Q + Q + ++ ++ +++S DK + GV+ ++ L
Sbjct: 2 KKQRNLRSMAAQAVEQVVEQGQSLSNILPPLQQKVS---DKDKALLQELCFGVLRTLSQL 58
Query: 589 RYDLSLIIDRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDEKKY 648
+ ++ ++ R + + ++++G Y+L + +IP + E +E + K
Sbjct: 59 DWLINKLMARPMTGKQRTVHYLIMVGLYQLL-YTRIPPHAALAETVEGAIAIKRPQLKGL 117
Query: 649 LEALL 653
+ +L
Sbjct: 118 INGVL 122
>2yxl_A PH0851 protein, 450AA long hypothetical FMU protein; FMU-homolog,
methyltransferase, structural genomics, NPPSFA; HET:
SFG; 2.55A {Pyrococcus horikoshii}
Length = 450
Score = 35.7 bits (83), Expect = 0.070
Identities = 7/74 (9%), Positives = 17/74 (22%), Gaps = 2/74 (2%)
Query: 580 GVINDINFLRYDLSLIIDRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKS 639
++ + + I+ + L L + + P I
Sbjct: 59 DIMKKQGLIDKVIKEIVGVTPLILDPWLRAALRVAVDIA--LFHDPSSQTIKNLRWKASD 116
Query: 640 FGNIDEKKYLEALL 653
F + Y+
Sbjct: 117 FISSRTHPYVGMYF 130
>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 = 30.6 bits (70), Expect = 2.3
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 8/42 (19%)
Query: 913 IKIIESKLKNAEKLG--LLKRNNKNIKPTSFGRYFLNDLQQI 952
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 = 30.6 bits (70), Expect = 2.5
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 8/42 (19%)
Query: 913 IKIIESKLKNAEKLG--LLKRNNKNIKPTSFGRYFLNDLQQI 952
I+ +E E+LG L +R + K T G +F QI
Sbjct: 36 IQKLE------EELGIQLFERGFRPAKVTEAGMFFYQHAVQI 71
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 30.1 bits (67), Expect = 2.8
Identities = 18/98 (18%), Positives = 30/98 (30%), Gaps = 14/98 (14%)
Query: 3 MINSKYNKRKISIAPMMNLTDRHCRMFHRQITRYSWLYTEMFTTQAILGNKKHCLDFNAE 62
I Y+ + + + R ++ E+ T+ K L E
Sbjct: 119 AIQVNYSSEVKENSVDSDDKAKV-PPLIRIVSGL-----ELSDTKQ---KGKKFLVIAYE 169
Query: 63 EHP---IAFQVGDNEPKKLAKSAKIIQKWGYDEINLNC 97
P IA ++ NE + G DE+N C
Sbjct: 170 --PFENIAIELPPNEILFSENNDMDNNNDGVDELNKKC 205
>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 = 30.2 bits (69), Expect = 2.8
Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 8/43 (18%)
Query: 913 IKIIESKLKNAEKLG--LLKRNNKNIKPTSFGRYFLNDLQQIF 953
++ +E LG LL+R+++ I+ T+ G FL D ++I
Sbjct: 36 MQALE------ADLGVVLLERSHRGIELTAAGHAFLEDARRIL 72
>1kkh_A Mevalonate kinase; mixed beta sheet, phosphate-binding loop,
beta-alpha-beta, transferase; 2.40A {Methanocaldococcus
jannaschii} SCOP: d.14.1.5 d.58.26.3 PDB: 1vis_A
Length = 317
Score = 30.3 bits (69), Expect = 3.3
Identities = 9/52 (17%), Positives = 15/52 (28%)
Query: 204 ELEIIINGGIKTKKEIDLHLNYIDGVMLGREAYKNPFLMSNFDLNYYSNLPQ 255
L + +N Y + Y N + F +N S +P
Sbjct: 59 SLGLNLNEIKNINPNNFGDFKYCLCAIKNTLDYLNIEPKTGFKINISSKIPI 110
>2ex3_B Protein GP3, DNA terminal protein; DNA polymerase: protein primer
complex, transferase-replicat complex; HET: DNA; 3.00A
{Bacillus phage PHI29} SCOP: a.263.1.1
Length = 230
Score = 29.4 bits (65), Expect = 4.5
Identities = 23/93 (24%), Positives = 44/93 (47%), Gaps = 9/93 (9%)
Query: 216 KKEIDLHLNYIDGVMLGREAYKNPFLMSNFDLNYYSNLPQ---YKIPTRIDIINLDSENR 272
KK I L LN+I V E N F ++ + +P Y++ RI I+ E
Sbjct: 141 KKMIQLQLNFIKSV----EGSFNSFDAADELIEELKKIPPDDFYELFLRISEISF--EEF 194
Query: 273 ENEGDIILSSDFVTPNAINFMSKYARGLICMTL 305
++EG+ + + + ++++ +Y RG ++L
Sbjct: 195 DSEGNTVENVEGNVYKILSYLEQYRRGDFDLSL 227
>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 = 29.4 bits (66), Expect = 7.4
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 1/65 (1%)
Query: 82 AKIIQKWGYDEINLNCGCPSNRVQNGFFGAILMTKPLLVSDCIKAMRDSVEIDITVKHRI 141
++ + G D + LN CP + G G P LV + + +R +V+I K
Sbjct: 654 SRKAEASGADALELNLSCPHGMGERG-MGLACGQDPELVRNICRWVRQAVQIPFFAKLTP 712
Query: 142 GIDDI 146
+ DI
Sbjct: 713 NVTDI 717
>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 = 9.9
Identities = 9/33 (27%), Positives = 13/33 (39%), Gaps = 4/33 (12%)
Query: 915 IIESKLKNAEKLGLLKRNNKNIKPTSFGRYFLN 947
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
0.321 0.138 0.397
Gapped
Lambda K H
0.267 0.0400 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 14,562,072
Number of extensions: 925245
Number of successful extensions: 1956
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1912
Number of HSP's successfully gapped: 65
Length of query: 956
Length of database: 6,701,793
Length adjustment: 103
Effective length of query: 853
Effective length of database: 3,825,930
Effective search space: 3263518290
Effective search space used: 3263518290
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: 62 (28.5 bits)