RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2378
(956 letters)
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 468 bits (1208), Expect = e-158
Identities = 149/266 (56%), Positives = 198/266 (74%), Gaps = 3/266 (1%)
Query: 1 MNMINSKYNKRKISIAPMMNLTDRHCRMFHRQITRYSWLYTEMFTTQAIL-GNKKHCLDF 59
M SK R+ S+APMM+ TDRHCR FHR ++R++ LYTEM TT AI+ G+++ L F
Sbjct: 1 MPEKMSKLPSRRFSVAPMMDWTDRHCRYFHRLLSRHALLYTEMVTTGAIIHGDRERLLAF 60
Query: 60 NAEEHPIAFQVGDNEPKKLAKSAKIIQKWGYDEINLNCGCPSNRVQNGFFGAILMTKPLL 119
+ EEHP+A Q+G ++P LA++AK+ + WGYDEINLN GCPS+RVQNG FGA LM +P L
Sbjct: 61 DPEEHPVALQLGGSDPADLAEAAKLAEDWGYDEINLNVGCPSDRVQNGRFGACLMAEPEL 120
Query: 120 VSDCIKAMRDSVEIDITVKHRIGIDDINSYDFVRDFVGTVSSAGCRTFIVHARNAFLKKL 179
V+DC+KAM+D+V I +TVKHRIGIDD +SY+F+ DFV TV+ AGC TFIVHAR A+LK L
Sbjct: 121 VADCVKAMKDAVSIPVTVKHRIGIDDQDSYEFLCDFVDTVAEAGCDTFIVHARKAWLKGL 180
Query: 180 NPKQNRKIPILKYNFVYNLKKDFPELEIIINGGIKTKKEIDLHLNYIDGVMLGREAYKNP 239
+PK+NR+IP L Y+ VY LK+DFP L I INGGIKT +E HL ++DGVM+GR AY NP
Sbjct: 181 SPKENREIPPLDYDRVYRLKRDFPHLTIEINGGIKTLEEAKEHLQHVDGVMIGRAAYHNP 240
Query: 240 FLMSNFDLNYYSNLPQYKIPTRIDII 265
+L++ D + +R +++
Sbjct: 241 YLLAEVDRELFGEPA--PPLSRSEVL 264
>gnl|CDD|236346 PRK08898, PRK08898, coproporphyrinogen III oxidase; Provisional.
Length = 394
Score = 430 bits (1109), Expect = e-143
Identities = 171/352 (48%), Positives = 230/352 (65%), Gaps = 35/352 (9%)
Query: 637 VKSFGNIDEKKYLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKL 696
K G I E YL+AL D+E +LP++ R++HT+FIGGGTPSL+S GLD LL +++ L
Sbjct: 43 WKDGGAIPEAAYLDALRADLEQALPLVWGRQVHTVFIGGGTPSLLSAAGLDRLLSDVRAL 102
Query: 697 LLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKY 756
L + ITLEANP TFE EKF + G+NRLSIGIQSFN+ +L LGR HD +A+
Sbjct: 103 LPLDPDAEITLEANPGTFEAEKFAQFRASGVNRLSIGIQSFNDAHLKALGRIHDGAEARA 162
Query: 757 AIEIAKQYFNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFKYP 816
AIEIA ++F+NFNLDL+YALP QTL E + D+ A+ + PPHLSLY LT+EPNT F K+P
Sbjct: 163 AIEIAAKHFDNFNLDLMYALPGQTLDEALADVETALAFGPPHLSLYHLTLEPNTLFAKFP 222
Query: 817 PLSMPSNDENAVMQDKITSLLKNNYYKNYEISAYSKTGYESQHNLNYWKFGDYLG----- 871
P ++P +D +A MQD I + L Y +YE+SAY+K G + +HNLNYW+FGDYLG
Sbjct: 223 P-ALPDDDASADMQDWIEARLAAAGYAHYEVSAYAKPGRQCRHNLNYWQFGDYLGIGAGA 281
Query: 872 -----------------------------NSIAKSKKIEKKCLIFEFMLNALRLKDGFSP 902
++ + +++ + L FEFMLNALRL DG
Sbjct: 282 HGKLSFPDRILRQMRYKHPATYLEQAKAGTAVQEEREVGARDLPFEFMLNALRLTDGVPA 341
Query: 903 NLFFERTGINIKIIESKLKNAEKLGLLKRNNKNIKPTSFGRYFLNDLQQIFL 954
+LF ERTG+ + IE +L AE+ GLL+R++ I+PT G+ FLNDLQ++FL
Sbjct: 342 HLFQERTGLPLAAIEPQLAAAEQRGLLERDHTRIRPTPLGQRFLNDLQELFL 393
>gnl|CDD|129825 TIGR00742, yjbN, tRNA dihydrouridine synthase A. This model
represents one branch of COG0042 (Predicted TIM-barrel
enzymes, possibly dehydrogenases, nifR3 family). It
represents a distinct subset by a set of shared unique
motifs, a conserved pattern of insertions/deletions
relative to other nifR3 homologs, and by subclustering
based on cross-genome bidirectional best hits. Members
are found in species as diverse as the proteobacteria, a
spirochete, a cyanobacterium, and Deinococcus
radiodurans. NifR3 itself, a protein of unknown function
associated with nitrogen regulation in Rhodobacter
capsulatus, is not a member of this branch. Members of
this family show a distant relationship to alpha/beta
(TIM) barrel enzymes such as dihydroorotate
dehydrogenase and glycolate oxidase [Protein synthesis,
tRNA and rRNA base modification].
Length = 318
Score = 345 bits (887), Expect = e-111
Identities = 142/256 (55%), Positives = 192/256 (75%), Gaps = 3/256 (1%)
Query: 11 RKISIAPMMNLTDRHCRMFHRQITRYSWLYTEMFTTQAIL-GNKKHCLDFNAEEHPIAFQ 69
+ S+APM++ TDRH R F R +++++ LYTEM T +AI+ G+KK L F+ EE P+A Q
Sbjct: 1 GRFSVAPMLDWTDRHFRYFLRLLSKHTLLYTEMITAKAIIHGDKKDILKFSPEESPVALQ 60
Query: 70 VGDNEPKKLAKSAKIIQKWGYDEINLNCGCPSNRVQNGFFGAILMTKPLLVSDCIKAMRD 129
+G ++P LAK AKI +K GYDEINLN GCPS+RVQNG FGA LM LV+DC+KAM++
Sbjct: 61 LGGSDPNDLAKCAKIAEKRGYDEINLNVGCPSDRVQNGNFGACLMGNADLVADCVKAMQE 120
Query: 130 SVEIDITVKHRIGIDDINSYDFVRDFVGTVSSAGCRTFIVHARNAFLKKLNPKQNRKIPI 189
+V I +TVKHRIGID ++SY+F+ DFV VS GC+ FIVHAR A+L L+PK+NR+IP
Sbjct: 121 AVNIPVTVKHRIGIDPLDSYEFLCDFVEIVSGKGCQNFIVHARKAWLSGLSPKENREIPP 180
Query: 190 LKYNFVYNLKKDFPELEIIINGGIKTKKEIDLHLNYIDGVMLGREAYKNPFLMSNFDLNY 249
L+Y VY LKKDFP L I INGGIK ++I HL+++DGVM+GREAY+NP+L++N D
Sbjct: 181 LRYERVYQLKKDFPHLTIEINGGIKNSEQIKQHLSHVDGVMVGREAYENPYLLANVDREI 240
Query: 250 YSNLPQYKIPTRIDII 265
++ +I TR +I+
Sbjct: 241 FN--ETDEILTRKEIV 254
>gnl|CDD|235550 PRK05660, PRK05660, HemN family oxidoreductase; Provisional.
Length = 378
Score = 345 bits (888), Expect = e-110
Identities = 133/346 (38%), Positives = 189/346 (54%), Gaps = 33/346 (9%)
Query: 641 GNIDEKKYLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFK 700
G + E +Y++ LL D++ LP++ R++H+IFIGGGTPSL S + LL ++ L F
Sbjct: 32 GEVPEDEYVDHLLADLDADLPLVQGREVHSIFIGGGTPSLFSAEAIQRLLDGVRARLPFA 91
Query: 701 KNISITLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEI 760
+ IT+EANP T E ++F Y G+NR+SIG+QSF+ + L LGR H +AK A ++
Sbjct: 92 PDAEITMEANPGTVEADRFVGYQRAGVNRISIGVQSFSEEKLKRLGRIHGPDEAKRAAKL 151
Query: 761 AKQY-FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFKYPPLS 819
A+ +FNLDL++ LP+Q+L E + DL AI +PPHLS Y LTIEPNT F PP
Sbjct: 152 AQGLGLRSFNLDLMHGLPDQSLEEALDDLRQAIALNPPHLSWYQLTIEPNTLFGSRPP-V 210
Query: 820 MPSNDENAVMQDKITSLLKNNYYKNYEISAYSKTGYESQHNLNYWKFGDYLG-------- 871
+P +D + ++ LL Y+ YE SAY+K GY+ QHNLNYW+FGDYLG
Sbjct: 211 LPDDDALWDIFEQGHQLLTAAGYQQYETSAYAKPGYQCQHNLNYWRFGDYLGIGCGAHGK 270
Query: 872 -----------------------NSIAKSKKIEKKCLIFEFMLNALRLKDGFSPNLFFER 908
+ + +E FEF +N RL + F
Sbjct: 271 LTFPDGRILRTWKTKHPRGYMQGRYLDGQRDVEAADRPFEFFMNRFRLLEAAPRADFEAY 330
Query: 909 TGINIKIIESKLKNAEKLGLLKRNNKNIKPTSFGRYFLNDLQQIFL 954
TG+ +I +L A G L + + T G+ FLNDL ++FL
Sbjct: 331 TGLPESVIRPQLDEALAQGYLTETADHWQITEHGKLFLNDLLELFL 376
>gnl|CDD|237587 PRK14019, PRK14019, bifunctional 3,4-dihydroxy-2-butanone
4-phosphate synthase/GTP cyclohydrolase II-like protein;
Provisional.
Length = 367
Score = 329 bits (846), Expect = e-104
Identities = 108/156 (69%), Positives = 133/156 (85%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNN 323
+I +D E+RENEGD++++++FVTP AINFM+K+ RGLIC+TLTE+ C QL L +MT +N
Sbjct: 19 VILVDEEDRENEGDLVMAAEFVTPEAINFMAKHGRGLICLTLTEERCEQLGLPLMTYRNG 78
Query: 324 SSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGGVL 383
+ +GTNFTVSIEAA GVTTGISA+DRA TI+ A ++ AKP DIVQPGHIFPL A+ GGVL
Sbjct: 79 TQYGTNFTVSIEAAEGVTTGISAADRARTIQAAVARDAKPEDIVQPGHIFPLMAQPGGVL 138
Query: 384 IRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMAR 419
+R GHTEAGCDL LAGLTP+AVICEI+ DDGTMAR
Sbjct: 139 VRAGHTEAGCDLAALAGLTPAAVICEIMKDDGTMAR 174
>gnl|CDD|223708 COG0635, HemN, Coproporphyrinogen III oxidase and related Fe-S
oxidoreductases [Coenzyme metabolism].
Length = 416
Score = 284 bits (728), Expect = 9e-87
Identities = 127/347 (36%), Positives = 184/347 (53%), Gaps = 37/347 (10%)
Query: 645 EKKYLEALLIDVELSLPII-LNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLL-LFKKN 702
+YL+ALL ++EL ++ R++ TI+ GGGTPSL+S L+ LLK +++L +
Sbjct: 64 VDEYLDALLEEIELVAALLGGQREVKTIYFGGGTPSLLSPEQLERLLKALRELFNDLDPD 123
Query: 703 ISITLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAK 762
IT+EANP T E EKF + G+NR+S+G+QSFN++ L LGR HD ++AK A+E+A+
Sbjct: 124 AEITIEANPGTVEAEKFKALKEAGVNRISLGVQSFNDEVLKALGRIHDEEEAKEAVELAR 183
Query: 763 QY-FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFKYP--PLS 819
+ F + N+DLIY LP QTL L DL A++ P HLSLYSL IEP T F + +
Sbjct: 184 KAGFTSINIDLIYGLPGQTLESLKEDLEQALELGPDHLSLYSLAIEPGTKFAQRKIKGKA 243
Query: 820 MPSNDENAVMQDKITSLLKNNYYKNYEISAYSKTGYESQHNLNYWKFGDYLG-------- 871
+P DE A M + + LL+ Y+ YEIS ++K G E +HNL YW+ DYLG
Sbjct: 244 LPDEDEKADMYELVEELLEKAGYRQYEISNFAKPGGECRHNLQYWETKDYLGIGAGAHGR 303
Query: 872 -----------------------NSIAKSKKIEKKCLIFEFMLNALRLKDGFSPNLFFER 908
+ + +++ LI E ++ LRL G ER
Sbjct: 304 IGGTRYQNKKNLKTYLEAVDEGGLPLVEGEELTPDDLIREALILGLRLNFGVDLAELEER 363
Query: 909 TGI-NIKIIESKLKNAEKLGLLKRNNKNIKPTSFGRYFLNDLQQIFL 954
GI I L GLL+ + ++ T GR L + + F
Sbjct: 364 FGIFKFAEILELLAELIADGLLELDGDRLRLTEKGRLLLRSIAEAFD 410
>gnl|CDD|216197 pfam00926, DHBP_synthase, 3,4-dihydroxy-2-butanone 4-phosphate
synthase. 3,4-Dihydroxy-2-butanone 4-phosphate is
biosynthesised from ribulose 5-phosphate and serves as
the biosynthetic precursor for the xylene ring of
riboflavin. Sometimes found as a bifunctional enzyme
with pfam00925.
Length = 193
Score = 267 bits (686), Expect = 7e-84
Identities = 96/174 (55%), Positives = 128/174 (73%), Gaps = 8/174 (4%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNN 323
+I +D E+RENEGD++++++ VTP ++NFM ++ARGLIC+ LTE+ +L L M +N
Sbjct: 14 VIVVDDEDRENEGDLVIAAEKVTPESVNFMIRHARGLICVALTEERADRLGLPPMVDRNT 73
Query: 324 SSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGGVL 383
FGT FTVS++A G TTGISA+DRA TI+ + A P D V+PGH+FPL+AK+GGVL
Sbjct: 74 DRFGTAFTVSVDAK-GTTTGISAADRALTIRALADPNAFPEDFVRPGHVFPLRAKEGGVL 132
Query: 384 IRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMAR-------AQEKNILHISV 430
R GHTEA DL +LAGLTP+AVICEILNDDGTMAR A+E + I++
Sbjct: 133 ERRGHTEAAVDLARLAGLTPAAVICEILNDDGTMARLPDLEEFAKEHGLPLITI 186
>gnl|CDD|223186 COG0108, RibB, 3,4-dihydroxy-2-butanone 4-phosphate synthase
[Coenzyme metabolism].
Length = 203
Score = 261 bits (670), Expect = 2e-81
Identities = 92/174 (52%), Positives = 120/174 (68%), Gaps = 8/174 (4%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNN 323
+I +D E+RENEGD+I +++ VTP I FM ++A GLIC+ LTE+ +L L M N
Sbjct: 19 VIVVDDEDRENEGDLIFAAEAVTPEQIAFMRRHASGLICVALTEERAKRLGLPPMVDNNT 78
Query: 324 SSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGGVL 383
+ GT FTVS++A TTGISA+DRA TI+ + AKPSD +PGH+FPL+AK GGVL
Sbjct: 79 DAHGTAFTVSVDARE-TTTGISAADRALTIRALADPGAKPSDFRRPGHVFPLRAKDGGVL 137
Query: 384 IRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMAR-------AQEKNILHISV 430
R GHTEA DL +LAGL P+ VICEI+NDDGTMAR A+E + I++
Sbjct: 138 ERRGHTEAAVDLARLAGLKPAGVICEIMNDDGTMARLPELEEFAKEHGLPVITI 191
>gnl|CDD|239200 cd02801, DUS_like_FMN, Dihydrouridine synthase-like (DUS-like)
FMN-binding domain. Members of this family catalyze the
reduction of the 5,6-double bond of a uridine residue on
tRNA. Dihydrouridine modification of tRNA is widely
observed in prokaryotes and eukaryotes, and also in some
archaea. Most dihydrouridines are found in the D loop of
t-RNAs. The role of dihydrouridine in tRNA is currently
unknown, but may increase conformational flexibility of
the tRNA. It is likely that different family members
have different substrate specificities, which may
overlap. 1VHN, a putative flavin oxidoreductase, has
high sequence similarity to DUS. The enzymatic
mechanism of 1VHN is not known at the present.
Length = 231
Score = 240 bits (614), Expect = 5e-73
Identities = 77/241 (31%), Positives = 129/241 (53%), Gaps = 20/241 (8%)
Query: 12 KISIAPMMNLTDRHCRMFHRQITRYSWLYTEMFTTQAILGNKK---HCLDFNAEEHPIAF 68
K+ +APM+ +TD R+ R+ +YTEM + +A+L + L N EE P+
Sbjct: 1 KLILAPMVGVTDLPFRLLCRRYG-ADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIV 59
Query: 69 QVGDNEPKKLAKSAKIIQKWGYDEINLNCGCPSNRVQNGFFGAILMTKPLLVSDCIKAMR 128
Q+G ++P+ LA++AKI+++ G D I+LN GCPS +V G GA L+ P LV++ ++A+R
Sbjct: 60 QLGGSDPETLAEAAKIVEELGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVR 119
Query: 129 DSVEIDITVKHRIGIDD-INSYDFVRDFVGTVSSAGCRTFIVHARNAFLKKLNPKQNRKI 187
++V I +TVK R+G DD + + + + AG VH R + R
Sbjct: 120 EAVPIPVTVKIRLGWDDEEETLELAK----ALEDAGASALTVHGRTR--------EQRYS 167
Query: 188 PILKYNFVYNLKKDFPELEIIINGGIKTKKEIDLHLNY--IDGVMLGREAYKNPFLMSNF 245
++++ + K+ + +I NG I + ++ L +DGVM+GR A NP+L
Sbjct: 168 GPADWDYIAEI-KEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREI 226
Query: 246 D 246
Sbjct: 227 K 227
>gnl|CDD|235119 PRK03353, ribB, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
Provisional.
Length = 217
Score = 235 bits (601), Expect = 2e-71
Identities = 86/159 (54%), Positives = 116/159 (72%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNN 323
++ LD E+RENEGD+I +++ +T + ++ G++C+ LTE+ QL L MM + N
Sbjct: 29 VMVLDDEDRENEGDMIFAAETMTVEQMALTIRHGSGIVCLCLTEERRKQLDLPMMVENNT 88
Query: 324 SSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGGVL 383
S +GT FTV+IEAA GVTTG+SA+DR TI+ A + AKPSD+ +PGH+FPL+A+ GGVL
Sbjct: 89 SQYGTAFTVTIEAAEGVTTGVSAADRITTIRAAIADGAKPSDLNRPGHVFPLRAQPGGVL 148
Query: 384 IRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARAQE 422
R GHTEA DL LAGL P+ V+CE+ NDDGTMARA E
Sbjct: 149 TRRGHTEATIDLMTLAGLKPAGVLCELTNDDGTMARAPE 187
>gnl|CDD|181774 PRK09311, PRK09311, bifunctional 3,4-dihydroxy-2-butanone
4-phosphate synthase/GTP cyclohydrolase II protein;
Provisional.
Length = 402
Score = 242 bits (619), Expect = 2e-71
Identities = 87/159 (54%), Positives = 116/159 (72%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNN 323
+I +D E+RENEGD+I +++ TP + FM ++ G +C+ LTE+ +L L M N
Sbjct: 20 VIVVDDEDRENEGDLIFAAEKATPELVAFMVRHTSGYVCVPLTEEDADRLDLPPMVAHNQ 79
Query: 324 SSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGGVL 383
S GT FTVS++AANGVTTGISA+DRA TI++ + +KP+D +PGH+FPL+AK GGVL
Sbjct: 80 DSHGTAFTVSVDAANGVTTGISAADRATTIRLLADPASKPADFTRPGHVFPLRAKPGGVL 139
Query: 384 IRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARAQE 422
R GHTEA DL +LAGL P+ VICEI+N+DGTMAR E
Sbjct: 140 RRAGHTEAAVDLARLAGLQPAGVICEIVNEDGTMARVPE 178
>gnl|CDD|171535 PRK12485, PRK12485, bifunctional 3,4-dihydroxy-2-butanone
4-phosphate synthase/GTP cyclohydrolase II-like protein;
Provisional.
Length = 369
Score = 240 bits (613), Expect = 3e-71
Identities = 108/214 (50%), Positives = 143/214 (66%), Gaps = 23/214 (10%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNN 323
++ +D E+RENEGD++L+++ AINFM++ ARGLIC+TLT++HC +L L+ M N
Sbjct: 19 VLLVDDEDRENEGDLLLAAERCDAQAINFMAREARGLICLTLTDEHCQRLGLEQMVPSNG 78
Query: 324 SSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGGVL 383
S F T FTVSIEAA GVTTGISA+DRA T+ A + A+P D+VQPGHIFPL+A++GGVL
Sbjct: 79 SVFSTAFTVSIEAATGVTTGISAADRARTVAAAVAPNARPEDLVQPGHIFPLRAREGGVL 138
Query: 384 IRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARAQEKNILHISVPGALEIPLALKNI 443
R GHTEAGCDL +LAG +P++VI E++NDDGTMAR + LE+ A K+
Sbjct: 139 TRAGHTEAGCDLARLAGFSPASVIVEVMNDDGTMARRPD-----------LEV-FAAKHG 186
Query: 444 IQIKKFNVLIAIGVIIRGETYHFELIANETISNI 477
I+I LI H+ L TI I
Sbjct: 187 IKIGTIADLI-----------HYRLSTEHTIKRI 209
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 234 bits (599), Expect = 8e-70
Identities = 95/272 (34%), Positives = 143/272 (52%), Gaps = 18/272 (6%)
Query: 1 MNMINSKYNKRKISIAPMMNLTDRHCRMFHRQITRYSWLYTEMFTTQAIL-GNKK--HCL 57
M I + ++ +APM +TD R R++ Y LYTEM + +A+L G KK L
Sbjct: 1 MLKIGLIELRNRVILAPMAGVTDLPFRRLARELGAYDLLYTEMVSAKALLHGRKKFLLLL 60
Query: 58 DFNAEEHPIAFQVGDNEPKKLAKSAKIIQKWGYDEINLNCGCPSNRVQNGFFGAILMTKP 117
D EE P+A Q+G ++P+ LA++AKI ++ G D I+LNCGCPS +V G GA L+ P
Sbjct: 61 DELEEERPVAVQLGGSDPELLAEAAKIAEELGADIIDLNCGCPSPKVVKGGAGAALLKNP 120
Query: 118 LLVSDCIKAMRDSVE-IDITVKHRIGIDDINSYDFVRDFVGTVS-SAGCRTFIVHARNAF 175
L+++ +KAM ++V I +TVK R+G DD D + + + AG VH R
Sbjct: 121 ELLAEIVKAMVEAVGDIPVTVKIRLGWDDD---DILALEIARILEDAGADALTVHGRTRA 177
Query: 176 LKKLNPKQNRKIPILKYNFVYNLKKDFPELEIIINGGIKTKKEIDLHLNYI--DGVMLGR 233
L P ++++ LK+ P + +I NG IK+ ++ L Y DGVM+GR
Sbjct: 178 QGYLGP--------ADWDYIKELKEAVPSIPVIANGDIKSLEDAKEMLEYTGADGVMIGR 229
Query: 234 EAYKNPFLMSNFDLNYYSNLPQYKIPTRIDII 265
A NP+L D L + +DI+
Sbjct: 230 GALGNPWLFRQIDYLETGELLPPTLAEVLDIL 261
>gnl|CDD|129630 TIGR00539, hemN_rel, putative oxygen-independent coproporphyrinogen
III oxidase. Experimentally determined examples of
oxygen-independent coproporphyrinogen III oxidase, an
enzyme that replaces HemF function under anaerobic
conditions, belong to a family of proteins described by
the model hemN. This model, hemN_rel, models a closely
related protein, shorter at the amino end and lacking
the region containing the motif PYRT[SC]YP found in
members of the hemN family. Several species, including
E. coli, Helicobacter pylori, Aquifex aeolicus, and
Chlamydia trachomatis, have members of both this family
and the E. coli hemN family. The member of this family
from Bacillus subtilis was shown to complement an
hemF/hemN double mutant of Salmonella typimurium and to
prevent accumulation of coproporphyrinogen III under
anaerobic conditions, but the exact role of this protein
is still uncertain. It is found in a number of species
that do not synthesize heme de novo [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 360
Score = 234 bits (599), Expect = 3e-69
Identities = 103/320 (32%), Positives = 151/320 (47%), Gaps = 37/320 (11%)
Query: 645 EKKYLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNIS 704
+++Y +AL D++ +L + +IFIGGGTP+ +S + L ++I + +
Sbjct: 29 KEEYTQALCQDLKHALSQTDQEPLESIFIGGGTPNTLSVEAFERLFESIYQHASLSDDCE 88
Query: 705 ITLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY 764
IT EANP E GINRLS+G+QSF + L LGR H +K AIE A +
Sbjct: 89 ITTEANPELITAEWCKGLKGAGINRLSLGVQSFRDDKLLFLGRQHSAKNIAPAIETALKS 148
Query: 765 -FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFKYPPLSMPSN 823
N +LDL+Y LP QTL+ L +L A + HLS Y+L++EPNT F K +P +
Sbjct: 149 GIENISLDLMYGLPLQTLNSLKEELKLAKELPINHLSAYALSVEPNTNFEKNAK-KLPDD 207
Query: 824 DENAVMQDKITSLLKNNYYKNYEISAYSKTGYESQHNLNYWKFGDYLG------------ 871
D A + + +L+ +K YE+S Y+K GY+ +HNL YW DYLG
Sbjct: 208 DSCAHFDEVVREILEGFGFKQYEVSNYAKAGYQVKHNLAYWGAKDYLGCGAGAHGCVANE 267
Query: 872 ---------NSIAK----------SKKIEKKCLIFEFMLNALRLKDGFSPNLFFERTGIN 912
N I K + K+ E + LR G + F E G++
Sbjct: 268 RFFAKKLIKNYIKDPLQRGVETLNEKNVPKQDKRLEKLFLGLRCVLGVEKSFFDENKGLS 327
Query: 913 IKIIESKLKNAEKLGLLKRN 932
+ K E +K N
Sbjct: 328 ----QVKFLIEENKAFIKNN 343
>gnl|CDD|216365 pfam01207, Dus, Dihydrouridine synthase (Dus). Members of this
family catalyze the reduction of the 5,6-double bond of
a uridine residue on tRNA. Dihydrouridine modification
of tRNA is widely observed in prokaryotes and
eukaryotes, and also in some archae. Most
dihydrouridines are found in the D loop of t-RNAs. The
role of dihydrouridine in tRNA is currently unknown, but
may increase conformational flexibility of the tRNA. It
is likely that different family members have different
substrate specificities, which may overlap. Dus 1 from
Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus
2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active
as a single subunit, requiring NADPH or NADH, and is
stimulated by the presence of FAD. Some family members
may be targeted to the mitochondria and even have a role
in mitochondria.
Length = 309
Score = 229 bits (587), Expect = 3e-68
Identities = 78/233 (33%), Positives = 121/233 (51%), Gaps = 16/233 (6%)
Query: 14 SIAPMMNLTDRHCRMFHRQITRYSWLYTEMFTTQAIL-GNKKHCLDFNAEEH--PIAFQV 70
+APM +TD R R+ + TEM T +A L K+ L E P+A Q+
Sbjct: 1 LLAPMAGVTDLPFRRLVREYGAGDLVVTEMVTAKAQLRPEKQRELMLPELEEPTPLAVQL 60
Query: 71 GDNEPKKLAKSAKIIQKWGYDEINLNCGCPSNRVQNGFFGAILMTKPLLVSDCIKAMRDS 130
G ++P LA++AK++ G D I++N GCP+ +V G GA L+ P LV+ +KA+ +
Sbjct: 61 GGSDPALLAEAAKLVADLGADIIDINMGCPAKKVTRGGAGAALLRDPDLVAQIVKAVVKA 120
Query: 131 VEIDITVKHRIGIDDINSYDFVRDFVGTVSSAGCRTFIVHARNAFLKKLNPKQNRKIPIL 190
V+I +TVK RIG D+ S++ + V AG + VH R QN + P
Sbjct: 121 VDIPVTVKIRIGWDE--SHENAVEIARRVEDAGAQALTVHGR-------TRAQNYEGPA- 170
Query: 191 KYNFVYNLKKDFPELEIIINGGIKTKKEIDLHLNYI--DGVMLGREAYKNPFL 241
++ + +K+ + +I NG I ++ L+Y DGVM+GR A NP+L
Sbjct: 171 DWDAIKQVKQAVS-IPVIANGDITDAEDAQRCLSYTGADGVMIGRGALGNPWL 222
>gnl|CDD|181629 PRK09057, PRK09057, coproporphyrinogen III oxidase; Provisional.
Length = 380
Score = 225 bits (575), Expect = 1e-65
Identities = 109/344 (31%), Positives = 168/344 (48%), Gaps = 41/344 (11%)
Query: 643 IDEKKYLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKN 702
ID+ ++ A L ++ R + +IF GGGTPSL+ + LL I +L +
Sbjct: 31 IDQARFAAAFLRELATEAARTGPRTLTSIFFGGGTPSLMQPETVAALLDAIARLWPVADD 90
Query: 703 ISITLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAK 762
I ITLEANP++ E +F Y G+NR+S+G+Q+ N+ L LGR H +A AI++A+
Sbjct: 91 IEITLEANPTSVEAGRFRGYRAAGVNRVSLGVQALNDADLRFLGRLHSVAEALAAIDLAR 150
Query: 763 QYFNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFF---KYPPLS 819
+ F + DLIYA P QTL+ +L A+ + HLSLY LTIE T F+ L
Sbjct: 151 EIFPRVSFDLIYARPGQTLAAWRAELKEALSLAADHLSLYQLTIEEGTAFYGLHAAGKLI 210
Query: 820 MPSNDENAVMQDKITSLLKNNYYKNYEISAYSKTGYESQHNLNYWKFGDYLG-------- 871
+P D A + + + YEIS +++ G ES+HNL YW++GDY G
Sbjct: 211 LPDEDLAADLYELTQEITAAAGLPAYEISNHARPGAESRHNLTYWRYGDYAGIGPGAHGR 270
Query: 872 -------NSIAKSKK---------------IEKKCLIF-----EFMLNALRLKDGFSPNL 904
++ A K IE++ L EF+L LRL++G
Sbjct: 271 LTLGGERHATATEKAPEAWLERVERNGHGIIEEERLDPEERADEFLLMGLRLREGIDLAR 330
Query: 905 FFERTGINIKIIESKLKNAEKLGLLKR-NNKNIKPTSFGRYFLN 947
+ +G + +L + + GL++R ++ T GR L+
Sbjct: 331 YAALSGRPLD--PERLADLIEEGLIERDGGSRLRATPAGRLVLD 372
>gnl|CDD|236465 PRK09319, PRK09319, bifunctional 3,4-dihydroxy-2-butanone
4-phosphate synthase/GTP cyclohydrolase II/unknown
domain fusion protein; Provisional.
Length = 555
Score = 229 bits (586), Expect = 3e-65
Identities = 91/161 (56%), Positives = 115/161 (71%), Gaps = 2/161 (1%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNN 323
++ +D ENRENEGD+I ++ F TP INFM+ ARGLIC+ +T + +L L +M +N
Sbjct: 21 VVVVDDENRENEGDLICAAQFATPEMINFMATEARGLICLAMTGERLDELDLPLMVDRNT 80
Query: 324 SSFGTNFTVSIEAA--NGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGG 381
S T FTVSI+A GV+TGISA DRA TI+VA + KP D+ +PGHIFPL+AK+GG
Sbjct: 81 DSNQTAFTVSIDAGPELGVSTGISAEDRARTIQVAINPDTKPEDLRRPGHIFPLRAKEGG 140
Query: 382 VLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARAQE 422
VL R GHTEA DL +LAGL P+ VICEI N DG+MAR E
Sbjct: 141 VLKRAGHTEAAVDLARLAGLYPAGVICEIQNPDGSMARLPE 181
>gnl|CDD|232999 TIGR00506, ribB, 3,4-dihydroxy-2-butanone 4-phosphate synthase.
Several members of the family are bifunctional,
involving both ribA and ribB function. In these cases,
ribA tends to be on the C-terminal end of the protein
and ribB tends to be on the N-terminal [Biosynthesis of
cofactors, prosthetic groups, and carriers, Riboflavin,
FMN, and FAD].
Length = 199
Score = 216 bits (553), Expect = 5e-65
Identities = 87/175 (49%), Positives = 118/175 (67%), Gaps = 8/175 (4%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNN 323
++ D E+RENEGD+I++++F+TP I FM ++A GLIC+ +T +L L M N
Sbjct: 18 VLVYDDEDRENEGDLIVAAEFITPEQIAFMRRHAGGLICVAITPDIADKLDLPPMVDINT 77
Query: 324 SSFGTNFTVSIEAANG-VTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGGV 382
S+ GT T +I A+ TGISA+DRA TI+ A + KPSD +PGH+FPL+A GGV
Sbjct: 78 SASGTASTFTITVAHRKTFTGISANDRALTIRAALADVVKPSDFRRPGHVFPLRAADGGV 137
Query: 383 LIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMAR-------AQEKNILHISV 430
L RGGHTEA DL +LAGL P+ VICE++NDDGTMAR A++ N+ IS+
Sbjct: 138 LTRGGHTEASVDLAELAGLKPAGVICEMMNDDGTMARKPELMEYAKKHNLKLISI 192
>gnl|CDD|236309 PRK08599, PRK08599, coproporphyrinogen III oxidase; Provisional.
Length = 377
Score = 220 bits (564), Expect = 3e-64
Identities = 112/348 (32%), Positives = 176/348 (50%), Gaps = 39/348 (11%)
Query: 643 IDEKKYLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKN 702
+DE YL+AL+ ++ + I K+ TI+IGGGTP+ +S L+ LL I + L
Sbjct: 30 VDE--YLDALIKEM-NTYAIRPFDKLKTIYIGGGTPTALSAEQLERLLTAIHRNLPLSGL 86
Query: 703 ISITLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAK 762
T EANP EK G+NR+S+G+Q+FN++ L +GRTH+ + AI AK
Sbjct: 87 EEFTFEANPGDLTKEKLQVLKDSGVNRISLGVQTFNDELLKKIGRTHNEEDVYEAIANAK 146
Query: 763 QY-FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFF---KYPPL 818
+ F+N ++DLIYALP QT+ + L A+ PH S YSL +EP T F+ + L
Sbjct: 147 KAGFDNISIDLIYALPGQTIEDFKESLAKALALDIPHYSAYSLILEPKTVFYNLMRKGKL 206
Query: 819 SMPSNDENAVMQDKITSLLKNNYYKNYEISAYSKTGYESQHNLNYWK------FG----- 867
+P D A M + + ++ + + YEIS ++K G+ES+HNL YW FG
Sbjct: 207 RLPGEDLEAEMYEYLMDEMEAHGFHQYEISNFAKPGFESRHNLTYWNNEEYYGFGAGASG 266
Query: 868 --------------DYL------GNSIAKSKKIEKKCLIFEFMLNALRLKDGFSPNLFFE 907
YL G + + KK + E M LR K G S F E
Sbjct: 267 YVNGVRYQNIGPIKHYLKAINEEGLPRLEEHVLTKKEQMEEEMFLGLRKKSGVSKARFEE 326
Query: 908 RTGINI-KIIESKLKNAEKLGLLKRNNKNIKPTSFGRYFLNDLQQIFL 954
+ G + + ++ ++ GLL+ ++ +++ T G++ N++ + FL
Sbjct: 327 KFGQSFEDVFGETIQELQEQGLLEEDDDHVRLTKKGKFLGNEVFEAFL 374
>gnl|CDD|181775 PRK09314, PRK09314, bifunctional 3,4-dihydroxy-2-butanone
4-phosphate synthase/GTP cyclohydrolase II protein;
Provisional.
Length = 339
Score = 212 bits (542), Expect = 2e-61
Identities = 108/280 (38%), Positives = 159/280 (56%), Gaps = 17/280 (6%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNN 323
+I +D E+RENEGD++ ++ F TP +NFM+ +ARGLIC++LT++ +L+L M KN
Sbjct: 19 LIMVDDEDRENEGDLVYAAIFSTPEKVNFMATHARGLICVSLTKELAKKLELPPMVSKNT 78
Query: 324 SSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGGVL 383
S+ T FTVSI+A TTGISA +R TIK+ + +KPSD V+PGHIFPL AK GGVL
Sbjct: 79 SNHETAFTVSIDAKEA-TTGISAFERDMTIKLLADDTSKPSDFVRPGHIFPLIAKDGGVL 137
Query: 384 IRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMAR-------AQEKNILHISVPGALEI 436
+R GHTE DL KLAGL P AVICEI+ +DGTMAR A++ N+ I V +E
Sbjct: 138 VRTGHTEGSVDLCKLAGLKPVAVICEIMKEDGTMARRDDLEDFAKKHNLKMIYVSDLVEY 197
Query: 437 PLALKNIIQIKKFNVLIAIGVIIRGETY--HFE----LIANETISNIMQISIKNNIPIIN 490
L +++I+ ++ G T+ H + I +
Sbjct: 198 RLKNESLIKEEEKEESEFAGFKAEKYTFLDHLQNEHIAFKFGEIKLTPNVKFHKIGSDFE 257
Query: 491 AILTT--ETIEQANSRILTKGEIIIFINHKNKSLVNLIKN 528
+ + + +A + G ++IF+N ++K N +K+
Sbjct: 258 LLTSDKFSELLKAIEYLKKNGGVLIFLNTESKE-NNQVKD 296
>gnl|CDD|167278 PRK01792, ribB, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
Provisional.
Length = 214
Score = 202 bits (514), Expect = 2e-59
Identities = 83/156 (53%), Positives = 110/156 (70%)
Query: 267 LDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNNSSF 326
LD E+RENEGD+I ++ +TP + + +Y G++C+ +T++ C QL L M + N S
Sbjct: 32 LDDEDRENEGDLIFPAETITPEQMAKLIRYGSGIVCLCITDELCQQLDLPPMVQHNTSVN 91
Query: 327 GTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGGVLIRG 386
T FTV+IEAA GV+TG+SA+DR TI+ A + AKPSD+ +PGH+FPL+A GGVL R
Sbjct: 92 KTAFTVTIEAAKGVSTGVSAADRVTTIQAAIADNAKPSDLHRPGHVFPLRAANGGVLTRR 151
Query: 387 GHTEAGCDLTKLAGLTPSAVICEILNDDGTMARAQE 422
GHTEA DL +LAG + VICEI NDDGTMAR E
Sbjct: 152 GHTEAAVDLARLAGYKEAGVICEITNDDGTMARTPE 187
>gnl|CDD|180263 PRK05799, PRK05799, coproporphyrinogen III oxidase; Provisional.
Length = 374
Score = 201 bits (514), Expect = 3e-57
Identities = 112/333 (33%), Positives = 161/333 (48%), Gaps = 40/333 (12%)
Query: 646 KKYLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISI 705
+Y++AL ++ S N+KI +IFIGGGTP+ +S L+ L + IKKL K+++
Sbjct: 33 MEYIKALSKEIRNS---TKNKKIKSIFIGGGTPTYLSLEALEILKETIKKLNK-KEDLEF 88
Query: 706 TLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY- 764
T+E NP TF EK +G+NRLSIG+Q++ N L LGR H ++ ++A++
Sbjct: 89 TVEGNPGTFTEEKLKILKSMGVNRLSIGLQAWQNSLLKYLGRIHTFEEFLENYKLARKLG 148
Query: 765 FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFKY---PPLSMP 821
FNN N+DL++ LPNQTL + L ++ +P H+S YSL IE T F+ L +P
Sbjct: 149 FNNINVDLMFGLPNQTLEDWKETLEKVVELNPEHISCYSLIIEEGTPFYNLYENGKLKLP 208
Query: 822 SNDENAVMQDKITSLLKNNYYKNYEISAYSKTGYESQHNLNYWKFGDYLG---------- 871
+E M LK Y YEIS ++K G E +HNL YW +Y+G
Sbjct: 209 DEEEEREMYHYTIEFLKEKGYHQYEISNFAKPGKECRHNLVYWDLEEYIGCGAGAHSYVN 268
Query: 872 -------NSIAK---------SKKIEKKCLIF-----EFMLNALRLKDGFSPNLFFERTG 910
++I K S E EFM LR G F +R G
Sbjct: 269 GKRYENISNIEKYIKEINENNSAVEEIHKNSIKDNMEEFMFMGLRKIKGICIEDFKKRFG 328
Query: 911 INI-KIIESKLKNAEKLGLLKRNNKNIKPTSFG 942
NI ++ + KLGLL I + G
Sbjct: 329 KNIYEVYGEVINKYIKLGLLIEKEGRIYLSERG 361
>gnl|CDD|215445 PLN02831, PLN02831, Bifunctional GTP cyclohydrolase II/
3,4-dihydroxy-2-butanone-4-phosphate synthase.
Length = 450
Score = 204 bits (520), Expect = 3e-57
Identities = 82/177 (46%), Positives = 121/177 (68%), Gaps = 10/177 (5%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMM--TKK 321
++ +D E+RENEGD+I+++ VTP A+ F+ K+ G++C+++ + +L+L +M +K+
Sbjct: 51 VVVVDDEDRENEGDLIMAASLVTPEAMAFLVKHGSGIVCVSMKGEDLDRLRLPLMVPSKE 110
Query: 322 NNSSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGG 381
N T FTV+++A +G TTG+SASDRA TI +S +KP D +PGHIFPL+ ++GG
Sbjct: 111 NEEKMATAFTVTVDAKHGTTTGVSASDRAKTILALASPDSKPEDFRRPGHIFPLRYREGG 170
Query: 382 VLIRGGHTEAGCDLTKLAGLTPSAVICEILND-DGTMAR-------AQEKNILHISV 430
VL R GHTEA DL LAGL P V+CEI+ND DG+MAR A+E + IS+
Sbjct: 171 VLKRAGHTEAAVDLAVLAGLPPVGVLCEIVNDEDGSMARLPQLRKFAEEHGLKIISI 227
>gnl|CDD|180630 PRK06582, PRK06582, coproporphyrinogen III oxidase; Provisional.
Length = 390
Score = 197 bits (503), Expect = 9e-56
Identities = 115/341 (33%), Positives = 167/341 (48%), Gaps = 42/341 (12%)
Query: 643 IDEKKYLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKN 702
ID ++L++ ++E II N+ I +IF GGGTPSL++ ++ ++ I L +
Sbjct: 38 IDHNQWLKSYEKEIEYFKDIIQNKYIKSIFFGGGTPSLMNPVIVEGIINKISNLAIIDNQ 97
Query: 703 ISITLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAK 762
ITLE NP++FE EKF ++ + GINR+SIG+QS L LGRTHD QA IE A
Sbjct: 98 TEITLETNPTSFETEKFKAFKLAGINRVSIGVQSLKEDDLKKLGRTHDCMQAIKTIEAAN 157
Query: 763 QYFNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYF---FKYPPLS 819
F + DLIYA QTL + +L A+Q + H+SLY LTIE T F FK L
Sbjct: 158 TIFPRVSFDLIYARSGQTLKDWQEELKQAMQLATSHISLYQLTIEKGTPFYKLFKEGNLI 217
Query: 820 MPSNDENAVMQDKITSLLKNNYYKNYEISAYSKTGYESQHNLNYWKFGDYLG-------- 871
+P +D A M + L++ Y YEIS Y+K G E HNL YW + YLG
Sbjct: 218 LPHSDAAAEMYEWTNHYLESKKYFRYEISNYAKIGQECLHNLTYWNYNSYLGIGPGAHSR 277
Query: 872 ----------------------------NSIAKSKKIEKKCLIFEFMLNALRLKDGFSPN 903
I + K+ + +I E ++ LRL G + +
Sbjct: 278 IIESSSSVSAIMMWHKPEKWLDAVKTKNVGIQTNTKLTHQEIIEEILMMGLRLSKGINIS 337
Query: 904 LFFERTGINIKIIES--KLKNAEKLGLLKRNNKNIKPTSFG 942
++ ++ I LK+ + L L++ + NI T G
Sbjct: 338 TLEQKLNTKLENILDMNNLKHYQALDLIRLDE-NIYLTDKG 377
>gnl|CDD|179162 PRK00910, ribB, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
Provisional.
Length = 218
Score = 186 bits (472), Expect = 1e-53
Identities = 81/159 (50%), Positives = 111/159 (69%)
Query: 264 IINLDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNN 323
++ LD E+RENEGDII S + +T + M + G++C+ LT+ +L+L M NN
Sbjct: 30 VLLLDDEDRENEGDIIYSVEHLTNAQMALMIRECSGIVCLCLTDAQADKLELPPMVVNNN 89
Query: 324 SSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAKKGGVL 383
S+ T FTVSIEA +GVTTG+SA DR TIK A++ +AKP D+ +PGH+FPL+A+ GGVL
Sbjct: 90 SANQTAFTVSIEAKHGVTTGVSAQDRVTTIKTAANPQAKPEDLARPGHVFPLRARAGGVL 149
Query: 384 IRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARAQE 422
R GHTE DL ++AGL P+ V+CE+ N DGTMA+ E
Sbjct: 150 ARRGHTEGTVDLMQMAGLQPAGVLCELTNPDGTMAKTPE 188
>gnl|CDD|180518 PRK06294, PRK06294, coproporphyrinogen III oxidase; Provisional.
Length = 370
Score = 184 bits (469), Expect = 2e-51
Identities = 95/268 (35%), Positives = 148/268 (55%), Gaps = 21/268 (7%)
Query: 620 SHYKIPYKVIINEAIELVKSFGNIDEKKYLEALLIDVELSLPIILNRKIHTIFIGGGTPS 679
S Y IPYK E V + N K+ L+ L P+ + I T+F GGGTPS
Sbjct: 24 SFYTIPYKE------ESVSLYCNAVLKEGLKKLA-------PLRCSHFIDTVFFGGGTPS 70
Query: 680 LISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNN 739
L+ L+++I K L ITLEANP + ++ GINR+SIG+Q+F++
Sbjct: 71 LVPP----ALIQDILKTLEAPHATEITLEANPENLSESYIRALALTGINRISIGVQTFDD 126
Query: 740 KYLNILGRTHDSKQAKYAIEIAKQY-FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPH 798
L +LGRTH S +A A++ ++ F+N ++DLIY LP Q+LS+ ++DL+ AI H
Sbjct: 127 PLLKLLGRTHSSSKAIDAVQECSEHGFSNLSIDLIYGLPTQSLSDFIVDLHQAITLPITH 186
Query: 799 LSLYSLTIEPNTYFFKYPPL---SMPSNDENAVMQDKITSLLKNNYYKNYEISAYSKTGY 855
+SLY+LTI+P+T F+K+ S+ + A M LL + + YE+++Y+K
Sbjct: 187 ISLYNLTIDPHTSFYKHRKRLLPSIADEEILAEMSLAAEELLTSQGFTRYELASYAKPQA 246
Query: 856 ESQHNLNYWKFGDYLGNSIAKSKKIEKK 883
+S+HN YW +LG ++ S+ +
Sbjct: 247 QSKHNTYYWTDRPFLGLGVSASQYLHGI 274
>gnl|CDD|134031 PRK00014, ribB, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
Provisional.
Length = 230
Score = 178 bits (453), Expect = 6e-51
Identities = 80/189 (42%), Positives = 112/189 (59%), Gaps = 11/189 (5%)
Query: 242 MSNFDLNYYSNLPQYKIPTRID-----------IINLDSENRENEGDIILSSDFVTPNAI 290
MSN S L TR++ +I +D +RENE D+I+++D +T +
Sbjct: 1 MSNVVPTPVSPLFAQPFATRLERALQHLRIGRPVILMDDFDRENEADLIVAADKLTVPVM 60
Query: 291 NFMSKYARGLICMTLTEKHCIQLKLDMMTKKNNSSFGTNFTVSIEAANGVTTGISASDRA 350
+ + G++C+ L + +L+L M N S + T FTVSIEA GVTTG+SA DR
Sbjct: 61 AQLIRDGSGIVCLCLPGETLDRLELPPMVDSNRSRYSTAFTVSIEAREGVTTGVSAVDRV 120
Query: 351 HTIKVASSKKAKPSDIVQPGHIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEI 410
TI+ A + A+ D+V PGH+FPL+A+ GGVL R GHTE DL LAGL P+ V+CE+
Sbjct: 121 TTIRAAIAPGARSGDVVSPGHVFPLRAQPGGVLTRRGHTEGSVDLAALAGLRPAGVLCEL 180
Query: 411 LNDDGTMAR 419
+N DGTM R
Sbjct: 181 MNADGTMMR 189
>gnl|CDD|236007 PRK07379, PRK07379, coproporphyrinogen III oxidase; Provisional.
Length = 400
Score = 177 bits (451), Expect = 2e-48
Identities = 86/232 (37%), Positives = 133/232 (57%), Gaps = 10/232 (4%)
Query: 646 KKYLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISI 705
++Y+E L E+++ + + T+F GGGTPSL+S L+ +L + + + I
Sbjct: 47 EEYVEVLC--QEIAITPSFGQPLQTVFFGGGTPSLLSVEQLERILTTLDQRFGIAPDAEI 104
Query: 706 TLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIE-IAKQY 764
+LE +P TF++E+ Y +G+NR+S+G+Q+F ++ L + GR+H K A++ I +
Sbjct: 105 SLEIDPGTFDLEQLQGYRSLGVNRVSLGVQAFQDELLALCGRSHRVKDIFAAVDLIHQAG 164
Query: 765 FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFKY--P---PLS 819
NF+LDLI LP+QTL + L AI +P HLS Y L +EP T F K P PL
Sbjct: 165 IENFSLDLISGLPHQTLEDWQASLEAAIALNPTHLSCYDLVLEPGTAFGKQYQPGKAPL- 223
Query: 820 MPSNDENAVMQDKITSLLKNNYYKNYEISAYSKTGYESQHNLNYWKFGDYLG 871
PS++ A M +L Y++YEIS Y+K GY+ +HN YW+ Y G
Sbjct: 224 -PSDETTAAMYRLAQEILTQAGYEHYEISNYAKPGYQCRHNRVYWENRPYYG 274
>gnl|CDD|181428 PRK08446, PRK08446, coproporphyrinogen III oxidase; Provisional.
Length = 350
Score = 170 bits (434), Expect = 1e-46
Identities = 91/231 (39%), Positives = 128/231 (55%), Gaps = 14/231 (6%)
Query: 645 EKKYLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNIS 704
+K+Y++AL +D++ L + KI ++FIGGGTPS +S + + + I L K+
Sbjct: 29 KKEYMQALCLDLKFELEQFTDEKIESVFIGGGTPSTVSAKFYEPIFEIISPYL--SKDCE 86
Query: 705 ITLEANP--STFE-IEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIA 761
IT EANP +T ++ + +G+NR+S G+QSFN L LGR H KQ AIE A
Sbjct: 87 ITTEANPNSATKAWLKGMKN---LGVNRISFGVQSFNEDKLKFLGRIHSQKQIIKAIENA 143
Query: 762 KQY-FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFKYPPLSM 820
K+ F N ++DLIY P L +L A + HLS YSLTIE NT FF+
Sbjct: 144 KKAGFENISIDLIYDTPLDNKKLLKEELKLAKELPINHLSAYSLTIEENTPFFEKN--HK 201
Query: 821 PSNDENAVMQDKITSLLKNNYYKNYEISAYSKTGYESQHNLNYWKFGDYLG 871
+DEN + L+ +K YEIS + K Y+ +HNL YW+ DYLG
Sbjct: 202 KKDDEN--LAKFFIEQLEELGFKQYEISNFGK-NYQCKHNLGYWQGKDYLG 249
>gnl|CDD|180172 PRK05628, PRK05628, coproporphyrinogen III oxidase; Validated.
Length = 375
Score = 147 bits (373), Expect = 2e-38
Identities = 73/230 (31%), Positives = 118/230 (51%), Gaps = 6/230 (2%)
Query: 648 YLEALLIDVELSLPIILN--RKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISI 705
YL+AL ++EL+ ++ + + T+F+GGGTPSL+ GL +L ++ +
Sbjct: 38 YLDALRAELELAAAVLGDPAPPVSTVFVGGGTPSLLGAEGLARVLDAVRDTFGLAPGAEV 97
Query: 706 TLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY- 764
T EANP + E F + G R+S+G+QS L +L RTH +A A A+
Sbjct: 98 TTEANPESTSPEFFAALRAAGFTRVSLGMQSAAPHVLAVLDRTHTPGRAVAAAREARAAG 157
Query: 765 FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYF---FKYPPLSMP 821
F + NLDLIY P ++ + L+ A++ H+S Y+L +E T + L P
Sbjct: 158 FEHVNLDLIYGTPGESDDDWRASLDAALEAGVDHVSAYALIVEDGTALARRVRRGELPAP 217
Query: 822 SNDENAVMQDKITSLLKNNYYKNYEISAYSKTGYESQHNLNYWKFGDYLG 871
+D A + + L + YE+S +++ G E +HNL YW+ GD+ G
Sbjct: 218 DDDVLADRYELADARLSAAGFDWYEVSNWARPGGECRHNLGYWRGGDWWG 267
>gnl|CDD|187742 cd09209, Lumazine_synthase-I, lumazine synthase
(6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes
the penultimate step in the biosynthesis of riboflavin
(vitamin B2); type-I. Type-I LS, also known as RibH1,
catalyzes the penultimate step in the biosynthesis of
riboflavin in plants and microorganisms. LS catalyse the
formation of 6,7-dimethyl-8-ribityllumazine by the
condensation of
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with
3,4-dihydroxy- 2-butanone-4-phosphate. Subsequently, the
lumazine intermediate dismutates to yield riboflavin and
5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione, in a
reaction catalyzed by riboflavin synthase synthase (RS);
RS belongs to a different family of the
Lumazine-synthase-like superfamily. Riboflavin is the
precursor of flavin mononucleotide (FMN) and flavin
adenine dinucleotide (FAD) which are essential cofactors
for the catalysis of a wide range of redox reactions.
These cofactors are also involved in many other
processes involving DNA repair, circadian time-keeping,
light sensing, and bioluminescence. Riboflavin is
biosynthesized in plants, fungi and certain
microorganisms; as animals lack the necessary enzymes to
produce this vitamin, they acquire it from dietary
sources. Type II LSs are distinct from type-I LS not
only in protein sequence, but in that they exhibit
different quaternary assemblies; type-I LSs form
pentamers. The pathogen Brucella spp. encode both a
Type-I LS and a Type-II LS called RibH1 and RibH2,
respectively. RibH1/type-I LS appears to be the
functional LS in Brucella spp., whereas RibH2/type-II LS
has much lower catalytic activity as LS. The pathogen
Brucella spp. have both a type-I LS and a type-II LS
called RibH1 and RibH2, respectively. RibH1/type-I LS
appears to be a functional LS in Brucella spp., whereas
RibH2/type-II LS has much lower catalytic activity as
LS.
Length = 133
Score = 131 bits (331), Expect = 2e-35
Identities = 40/101 (39%), Positives = 61/101 (60%), Gaps = 8/101 (7%)
Query: 420 AQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQ 479
+E+NI + VPGA EIPLA K + + K++ +IA+G +IRGET HF+ + NE +M+
Sbjct: 29 VKEENIDVVRVPGAFEIPLAAKRLARSGKYDAIIALGCVIRGETPHFDYVCNEVTRGLMR 88
Query: 480 ISIKNNIPIINAILTTETIEQANSRILTKGEIIIFINHKNK 520
+S++ +P+I +LTT+ EQA R K NK
Sbjct: 89 LSLETGVPVIFGVLTTDNEEQALERAGGK--------AGNK 121
>gnl|CDD|234606 PRK00061, ribH, 6,7-dimethyl-8-ribityllumazine synthase;
Provisional.
Length = 154
Score = 126 bits (319), Expect = 1e-33
Identities = 40/91 (43%), Positives = 59/91 (64%)
Query: 420 AQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQ 479
E+NI + VPGA EIPLA K + + K++ +IA+G +IRGET HF+ +ANE +
Sbjct: 43 VSEENIDVVRVPGAFEIPLAAKKLAESGKYDAVIALGAVIRGETPHFDYVANEVAKGLAD 102
Query: 480 ISIKNNIPIINAILTTETIEQANSRILTKGE 510
+S++ +P+ +LTT+TIEQA R TK
Sbjct: 103 VSLETGVPVGFGVLTTDTIEQAIERAGTKAG 133
>gnl|CDD|214792 smart00729, Elp3, Elongator protein 3, MiaB family, Radical SAM.
This superfamily contains MoaA, NifB, PqqE,
coproporphyrinogen III oxidase, biotin synthase and MiaB
families, and includes a representative in the
eukaryotic elongator subunit, Elp-3. Some members of the
family are methyltransferases.
Length = 216
Score = 125 bits (316), Expect = 1e-32
Identities = 59/186 (31%), Positives = 101/186 (54%), Gaps = 3/186 (1%)
Query: 647 KYLEALLIDVE-LSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISI 705
+YLEAL+ ++E L+ + T+FIGGGTP+L+S L+ LL+ I+++L K++ I
Sbjct: 30 RYLEALVREIELLAEKGEKEGLVGTVFIGGGTPTLLSPEQLEELLEAIREILGLAKDVEI 89
Query: 706 TLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQYF 765
T+E P T E + G+NR+S+G+QS +++ L + R H + A+E+ ++
Sbjct: 90 TIETRPDTLTEELLEALKEAGVNRVSLGVQSGDDEVLKAINRGHTVEDVLEAVELLREAG 149
Query: 766 N-NFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFK-YPPLSMPSN 823
+ DLI LP +T + L + P +S++ L+ P T K Y L P+
Sbjct: 150 PIKVSTDLIVGLPGETEEDFEETLKLLKELGPDRVSIFPLSPRPGTPLAKMYKRLKPPTK 209
Query: 824 DENAVM 829
+E A +
Sbjct: 210 EERAEL 215
>gnl|CDD|201491 pfam00885, DMRL_synthase, 6,7-dimethyl-8-ribityllumazine synthase.
This family includes the beta chain of 6,7-dimethyl-8-
ribityllumazine synthase EC:2.5.1.9, an enzyme involved
in riboflavin biosynthesis. The family also includes a
subfamily of distant archaebacterial proteins that may
also have the same function.
Length = 144
Score = 122 bits (309), Expect = 2e-32
Identities = 35/91 (38%), Positives = 58/91 (63%)
Query: 420 AQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQ 479
E++I + VPGA E+PLA K + + +++ ++A+G +IRG TYHF+ +A E +MQ
Sbjct: 34 VSEEDIDVVRVPGAFELPLAAKKLAKSGRYDAVVALGAVIRGGTYHFDYVAQEVSRGLMQ 93
Query: 480 ISIKNNIPIINAILTTETIEQANSRILTKGE 510
+S++ +P+ +LTT+T EQA R K
Sbjct: 94 VSLETGVPVGFGVLTTDTFEQALERAGGKAG 124
>gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family.
This model represents one branch of COG0042 (Predicted
TIM-barrel enzymes, possibly dehydrogenases, nifR3
family). This branch includes NifR3 itself, from
Rhodobacter capsulatus. It excludes a broadly
distributed but more sparsely populated subfamily that
contains sll0926 from Synechocystis PCC6803, HI0634 from
Haemophilus influenzae, and BB0225 from Borrelia
burgdorferi. It also excludes a shorter and more distant
archaeal subfamily.The function of nifR3, a member of
this family, is unknown, but it is found in an operon
with nitrogen-sensing two component regulators in
Rhodobacter capsulatus.Members of this family show a
distant relationship to alpha/beta (TIM) barrel enzymes
such as dihydroorotate dehydrogenase and glycolate
oxidase [Unknown function, General].
Length = 319
Score = 127 bits (320), Expect = 5e-32
Identities = 77/274 (28%), Positives = 122/274 (44%), Gaps = 53/274 (19%)
Query: 16 APMMNLTDRHCRMFHRQITRY--SWLYTEMFTTQAIL---GNKKHCLDFNAEEHPIAFQV 70
APM +TD F R + Y EM +++AI+ LD +E PI+ Q+
Sbjct: 13 APMAGVTDS---PFRRLVAEYGAGLTVCEMVSSEAIVYDSQRTMRLLDIAEDETPISVQL 69
Query: 71 GDNEPKKLAKSAKIIQKWGYDEINLNCGCPSNRVQNGFFGAILMTKPLLVSDCIKAMRDS 130
++P +A++AKI ++ G D I++N GCP ++ G+ L+ P L+ +KA+ D+
Sbjct: 70 FGSDPDTMAEAAKINEELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDA 129
Query: 131 VEIDITVKHRIGIDD--INSYDFVRDFVGTVSSAGCRTFIVHARNA-----------FLK 177
V+I +TVK RIG DD IN+ + R AG + +H R +
Sbjct: 130 VDIPVTVKIRIGWDDAHINAVEAAR----IAEDAGAQAVTLHGRTRAQGYSGEANWDIIA 185
Query: 178 KLNPKQNRKIPILKYNFVYNLKKDFPELEIIINGGIKTKKEIDLHLNY--IDGVMLGREA 235
++ KQ +IP +I NG I + ++ L DGVM+GR A
Sbjct: 186 RV--KQAVRIP------------------VIGNGDIFSPEDAKAMLETTGCDGVMIGRGA 225
Query: 236 YKNPFLMSN----FDLNYYSNLPQYKIPTRIDII 265
NP+L Y P + ++D I
Sbjct: 226 LGNPWLFRQIEQYLTTGKYKPPPTFA--EKLDAI 257
>gnl|CDD|233652 TIGR01951, nusB, transcription antitermination factor NusB. A
transcription antitermination complex active in many
bacteria was designated N-utilization substance (Nus) in
E. coli because of its interaction with phage lambda
protein N. This model represents NusB. Other components
are NusA and NusG. NusE is, in fact, ribosomal protein
S10 [Transcription, Transcription factors].
Length = 129
Score = 118 bits (299), Expect = 2e-31
Identities = 43/126 (34%), Positives = 68/126 (53%), Gaps = 7/126 (5%)
Query: 532 RHRAREFALQGIYQWLFNNMDVNLIETYIKEISNFYKVDKKYFYLILRGVINDINFLRYD 591
R +ARE ALQ +YQW + D+ I E + D++YF ++RGV+ + +
Sbjct: 1 RRKARELALQALYQWELSGNDLEEIIEEFLEEEELDEEDREYFRELVRGVLENQEEID-- 58
Query: 592 LSLII----DRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDEKK 647
LI D ++ L ++ +L + YEL +PYKV+INEA+EL K FG+ D K
Sbjct: 59 -ELISPHLEDWTLERLDPVDRAILRLAAYELLYRPDVPYKVVINEAVELAKKFGDDDSHK 117
Query: 648 YLEALL 653
++ +L
Sbjct: 118 FVNGVL 123
>gnl|CDD|223132 COG0054, RibH, Riboflavin synthase beta-chain [Coenzyme
metabolism].
Length = 152
Score = 119 bits (301), Expect = 3e-31
Identities = 41/97 (42%), Positives = 61/97 (62%), Gaps = 2/97 (2%)
Query: 416 TMAR--AQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANET 473
+ R A NI + VPGA EIPLA K + + K++ ++A+G +IRGETYHF+ +ANE
Sbjct: 37 ALKRHGADVDNIDVVRVPGAFEIPLAAKKLARTGKYDAVVALGAVIRGETYHFDYVANEV 96
Query: 474 ISNIMQISIKNNIPIINAILTTETIEQANSRILTKGE 510
+M +S++ +P+ +LTT+ IEQA R TK
Sbjct: 97 ARGLMDVSLETGVPVTFGVLTTDNIEQAIERAGTKAG 133
>gnl|CDD|234686 PRK00202, nusB, transcription antitermination protein NusB;
Reviewed.
Length = 137
Score = 117 bits (296), Expect = 9e-31
Identities = 44/128 (34%), Positives = 67/128 (52%), Gaps = 9/128 (7%)
Query: 531 PRHRAREFALQGIYQWLFNNMDVNLIETYIKEISNFYKVDKKYFYLILRGVINDINFLRY 590
R +ARE A+Q +YQW + D+ I + K D YF ++RGV+ +
Sbjct: 2 ARRKAREAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQA---- 57
Query: 591 DLSLII-----DRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDE 645
+L +I D ++ L +E +L + YEL +PYKV+INEAIEL K FG+ D
Sbjct: 58 ELDELISPYLKDWTLERLDPVERAILRLALYELLFRDDVPYKVVINEAIELAKKFGDEDS 117
Query: 646 KKYLEALL 653
K++ +L
Sbjct: 118 HKFVNGVL 125
>gnl|CDD|235641 PRK05904, PRK05904, coproporphyrinogen III oxidase; Provisional.
Length = 353
Score = 117 bits (294), Expect = 2e-28
Identities = 82/281 (29%), Positives = 130/281 (46%), Gaps = 27/281 (9%)
Query: 646 KKYLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISI 705
KK + L ++++ + ++ TI++GGGTP+ ++D LD LL IK + N
Sbjct: 35 KKIFKDFLKNIKMHIKNFKIKQFKTIYLGGGTPNCLNDQLLDILLSTIKPYV--DNNCEF 92
Query: 706 TLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIE-IAKQY 764
T+E NP + + +NR+S+G+QS NN L L RTH + +K AI + K
Sbjct: 93 TIECNPELITQSQINLLKKNKVNRISLGVQSMNNNILKQLNRTHTIQDSKEAINLLHKNG 152
Query: 765 FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFKYPPLSMPSND 824
N + D +Y LP L +L N+ +++ H+S YSL I+ + KY ++ +
Sbjct: 153 IYNISCDFLYCLPILKLKDLDEVFNFILKHKINHISFYSLEIKEGSILKKY-HYTIDEDK 211
Query: 825 ENAVMQDKITSLLKNNYYKNYEISAY-SKTGYESQHNLNYWKFGDYLG------------ 871
E + K NY + YE+S + + Y S+HNL YW+ D+
Sbjct: 212 EAEQLNYIKAKFNKLNYKR-YEVSNWTNNFKYISKHNLAYWRTKDWAAIGWGAHGFENNI 270
Query: 872 -----NSIAKSKKIEKKCLIFEF----MLNALRLKDGFSPN 903
SI I+K E ++ LRLKDG N
Sbjct: 271 EYFFDGSIQNWILIKKVLTDHELYQQILIMGLRLKDGLDLN 311
>gnl|CDD|236187 PRK08207, PRK08207, coproporphyrinogen III oxidase; Provisional.
Length = 488
Score = 111 bits (281), Expect = 1e-25
Identities = 66/231 (28%), Positives = 107/231 (46%), Gaps = 18/231 (7%)
Query: 648 YLEALLIDVELSLPII--LNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNIS- 704
YLEAL ++E + KI TI+ GGGTP+ ++ L+ LL+ I + KN+
Sbjct: 197 YLEALHYEIEEIGKYLKEKGLKITTIYFGGGTPTSLTAEELERLLEEIYENFPDVKNVKE 256
Query: 705 ITLEAN-PSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQ 763
T+EA P T EK G++R+SI Q+ N++ L +GR H + +A++
Sbjct: 257 FTVEAGRPDTITEEKLEVLKKYGVDRISINPQTMNDETLKAIGRHHTVEDIIEKFHLARE 316
Query: 764 Y-FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIE-PNTYFFKYPPLSMP 821
F+N N+DLI LP + L E+ L + +P L++++L I+ + +
Sbjct: 317 MGFDNINMDLIIGLPGEGLEEVKHTLEEIEKLNPESLTVHTLAIKRASRLTENKEKYKVA 376
Query: 822 SNDENAVMQDKITSLLKNNYYK------------NYEISAYSKTGYESQHN 860
+E M ++ K Y N E Y+K G ES +N
Sbjct: 377 DREEIEKMMEEAEEWAKELGYVPYYLYRQKNMLGNLENVGYAKPGKESIYN 427
>gnl|CDD|234473 TIGR04107, rSAM_HutW, putative heme utilization radical SAM enzyme
HutW. HutW is a radical SAM enzyme closely related to
HemN, the heme biosynthetic oxygen-independent
coproporphyrinogen oxidase. It belongs to operons
associated with heme uptake and utilization in Vibrio
cholerae and related species, but neither it not HutX
has been shown to be needed, as is HutZ, for heme
utilization. HutW failed to complement a Salmonella
enterica hemN mutant (PMID:15205415), suggesting a
related but distinct activity. Some members of this
family are fused to hutX.
Length = 420
Score = 105 bits (265), Expect = 5e-24
Identities = 56/172 (32%), Positives = 86/172 (50%), Gaps = 13/172 (7%)
Query: 647 KYLEALL--IDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNIS 704
Y +AL+ + E +LP+ + IH ++IGGGTP+ +S L L++ I++ L +
Sbjct: 70 AYTDALIAELAAEAALPLTQSGPIHAVYIGGGTPTALSADDLARLIRAIRRYLPLAPDCE 129
Query: 705 ITLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY 764
ITLE + F+ EK + G+NR SIG+QSF+ + LGR D ++ +E
Sbjct: 130 ITLEGRINGFDDEKADAALEAGVNRFSIGVQSFDTEVRRRLGRKDDREEVLARLEELSAL 189
Query: 765 FNNFN-----LDLIYALPNQTLSELMLDLNYAIQYSPPH-LSLYSLTIEPNT 810
+ +DLIY LP QT DL A + LY+L + P T
Sbjct: 190 ----DRAAVVIDLIYGLPGQTDEIWQQDLRIAAD-LGLDGVDLYALNLFPGT 236
>gnl|CDD|211550 TIGR00114, lumazine-synth, 6,7-dimethyl-8-ribityllumazine synthase.
This enzyme catalyzes the cyclo-ligation of
3,4-dihydroxy-2-butanone-4-P and
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione to
form 6,7-dimethyl-8-ribityllumazine, the immediate
precursor of riboflavin. Sometimes referred to as
riboflavin synthase, beta subunit, this should not be
confused with the alpha subunit which carries out the
subsequent reaction. Archaeal members of this family are
considered putative, although included in the seed and
scoring above the trusted cutoff [Biosynthesis of
cofactors, prosthetic groups, and carriers, Riboflavin,
FMN, and FAD].
Length = 138
Score = 98.2 bits (245), Expect = 6e-24
Identities = 42/90 (46%), Positives = 58/90 (64%)
Query: 420 AQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQ 479
A+ NI I VPGA E+PLA+K + + K++ +IA+G +IRG T HFE +A+E I
Sbjct: 31 AEVDNIDVIWVPGAFELPLAVKKLAESGKYDAVIALGTVIRGGTPHFEYVADEAAKGIAD 90
Query: 480 ISIKNNIPIINAILTTETIEQANSRILTKG 509
+++ P+I ILTTETIEQA R TK
Sbjct: 91 LALDYGKPVIFGILTTETIEQAIERAGTKA 120
>gnl|CDD|223852 COG0781, NusB, Transcription termination factor [Transcription].
Length = 151
Score = 97.8 bits (244), Expect = 1e-23
Identities = 41/138 (29%), Positives = 69/138 (50%), Gaps = 15/138 (10%)
Query: 527 KNKTPRHRAREFALQGIYQWLFNN------MDVNLIETYIKEISNFYKVDKKYFYLILRG 580
K R +ARE A+Q +YQW + + ++ E +++ + D +YF +++G
Sbjct: 5 PPKLTRRQARELAVQALYQWELSGSVSAEDILEDIEEEFVENELDIELADSEYFRSLVKG 64
Query: 581 VINDINFLRYDLSLII-----DRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIE 635
V+ + +L +I S+ L +E +L + YEL +PYKV+INEAIE
Sbjct: 65 VLENQE----ELDELISPHLKKWSLERLDLVERAILRLALYELLFRDDVPYKVVINEAIE 120
Query: 636 LVKSFGNIDEKKYLEALL 653
L K F D K++ +L
Sbjct: 121 LAKKFSGEDSHKFVNGVL 138
>gnl|CDD|181292 PRK08208, PRK08208, coproporphyrinogen III oxidase; Validated.
Length = 430
Score = 100 bits (252), Expect = 2e-22
Identities = 52/147 (35%), Positives = 81/147 (55%), Gaps = 2/147 (1%)
Query: 673 IGGGTPSLISDTGLDYLLKNIKKLL-LFKKNISITLEANPSTFEIEKFHSYSIIGINRLS 731
+GGGTP+L++ L+ L +++++L + NI ++E +P+T EK + G+NRLS
Sbjct: 97 VGGGTPTLLNAAELEKLFDSVERVLGVDLGNIPKSVETSPATTTAEKLALLAARGVNRLS 156
Query: 732 IGIQSFNNKYLNILGRTHDSKQAKYAIE-IAKQYFNNFNLDLIYALPNQTLSELMLDLNY 790
IG+QSF++ L+ L R A+E I F N+DLIY +P QT + M L+
Sbjct: 157 IGVQSFHDSELHALHRPQKRADVHQALEWIRAAGFPILNIDLIYGIPGQTHASWMESLDQ 216
Query: 791 AIQYSPPHLSLYSLTIEPNTYFFKYPP 817
A+ Y P L LY L + P T +
Sbjct: 217 ALVYRPEELFLYPLYVRPLTGLGRRAR 243
>gnl|CDD|236368 PRK09058, PRK09058, coproporphyrinogen III oxidase; Provisional.
Length = 449
Score = 101 bits (253), Expect = 2e-22
Identities = 51/177 (28%), Positives = 79/177 (44%), Gaps = 25/177 (14%)
Query: 648 YLEALL--IDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISI 705
Y +AL+ + +E P+ + IH ++ GGGTP+ +S L L+ +++ L + I
Sbjct: 93 YTDALIRELAMEADSPLTQSAPIHAVYFGGGTPTALSAEDLARLITALREYLPLAPDCEI 152
Query: 706 TLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQA----------- 754
TLE + F+ EK + G NR SIG+QSFN + GR D ++
Sbjct: 153 TLEGRINGFDDEKADAALDAGANRFSIGVQSFNTQVRRRAGRKDDREEVLARLEELVARD 212
Query: 755 KYAIEIAKQYFNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPH-LSLYSLTIEPNT 810
+ A+ DLI+ LP QT DL + LY+L + P T
Sbjct: 213 RAAVVC----------DLIFGLPGQTPEIWQQDLAIVRD-LGLDGVDLYALNLLPGT 258
>gnl|CDD|234435 TIGR03994, rSAM_HemZ, coproporphyrinogen dehydrogenase HemZ.
Members of this radical SAM protein family are HemZ, a
protein involved in coproporphyrinogen III
decarboxylation. Alternative names for this enzyme (EC
1.3.99.22) include coproporphyrinogen dehydrogenase and
oxygen-independent coproporphyrinogen III oxidase. The
family is related to, but distinct from HemN, and in
Bacillus subtilis was shown to be connected to peroxide
stress and catalase formation [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 401
Score = 100 bits (251), Expect = 2e-22
Identities = 70/231 (30%), Positives = 115/231 (49%), Gaps = 21/231 (9%)
Query: 648 YLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISITL 707
YL+AL ++E I+ K+ T++IGGGTP+ +S L+ LL I++ T+
Sbjct: 118 YLDALCKELEAVAKILKGLKLDTVYIGGGTPTTLSAEQLERLLGKIEENFDLSHLREFTV 177
Query: 708 EAN-PSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY-F 765
EA P + EK G+ R+SI Q+ N+K L+++GR H + K A +A++ F
Sbjct: 178 EAGRPDSITAEKLEVLKRHGVTRISINPQTMNDKTLDLIGRRHTVEDIKEAFALAREAGF 237
Query: 766 NNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEP----NTYFFKYPPLSMP 821
+N N+DLI LP +TL ++ L + +P +++++L I+ N KY +P
Sbjct: 238 DNINMDLIAGLPGETLEDVRDTLEQVKKLAPESITVHTLAIKRASRLNQEKDKY---QLP 294
Query: 822 SNDENAVMQDKITSLLKNN----YY--------KNYEISAYSKTGYESQHN 860
S ++ A M D ++ YY N E Y+K G E +N
Sbjct: 295 SFEDTAEMIDLAAEYARDMGMEPYYLYRQKNMAGNLENVGYAKPGKEGLYN 345
>gnl|CDD|129629 TIGR00538, hemN, oxygen-independent coproporphyrinogen III oxidase.
This model represents HemN, the oxygen-independent
coproporphyrinogen III oxidase that replaces HemF
function under anaerobic conditions. Several species,
including E. coli, Helicobacter pylori, and Aquifex
aeolicus, have both a member of this family and a member
of another, closely related family for which there is no
evidence of coproporphyrinogen III oxidase activity.
Members of this family have a perfectly conserved motif
PYRT[SC]YP in a region N-terminal to the region of
homology with the related uncharacterized protein
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Heme, porphyrin, and cobalamin].
Length = 455
Score = 98.7 bits (246), Expect = 2e-21
Identities = 55/202 (27%), Positives = 95/202 (47%), Gaps = 5/202 (2%)
Query: 645 EKKYLEALLIDVELSLPII-LNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNI 703
YL+AL ++ L P+ NR + + GGGTP+ +S + L+K I++ F +
Sbjct: 79 ADPYLDALEKEIALVAPLFDGNRHVSQLHWGGGTPTYLSPEQISRLMKLIRENFPFNADA 138
Query: 704 SITLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQ 763
I++E +P + + G NRLS G+Q FN + + R + + A++
Sbjct: 139 EISIEIDPRYITKDVIDALRDEGFNRLSFGVQDFNKEVQQAVNRIQPEEMIFELMNHARE 198
Query: 764 Y-FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFF--KYPPLSM 820
F + N+DLIY LP QT L + +P L++++ P K P ++
Sbjct: 199 AGFTSINIDLIYGLPKQTKESFAKTLEKVAELNPDRLAVFNYAHVPWVKPAQRKIPEAAL 258
Query: 821 PSNDEN-AVMQDKITSLLKNNY 841
PS +E ++Q+ I L + Y
Sbjct: 259 PSAEEKLDILQETIAFLTEAGY 280
>gnl|CDD|236464 PRK09318, PRK09318, bifunctional 3,4-dihydroxy-2-butanone
4-phosphate synthase/GTP cyclohydrolase II protein;
Provisional.
Length = 387
Score = 97.1 bits (242), Expect = 2e-21
Identities = 55/150 (36%), Positives = 76/150 (50%), Gaps = 10/150 (6%)
Query: 267 LDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTKKNNSSF 326
L NRENE D + + +T +NF Y +GL+C+T E+ LK +N
Sbjct: 16 LIDRNRENEADFVYPAQIITEEVVNFFLSYGKGLLCLTADEEDL--LKRGFFKLPSNGG- 72
Query: 327 GTNFTVSIEAANGVTTGISASDRAHTI-KVASSKKAKPSDIVQPGHIFPLQAKKGGVLIR 385
TNF + ++ G TGISAS+RA T K+A + PGH+ L G R
Sbjct: 73 ETNFFIPVDY--GTGTGISASERALTCRKLAEGLYV--HEFRYPGHVTLLGGI--GFNRR 126
Query: 386 GGHTEAGCDLTKLAGLTPSAVICEILNDDG 415
GHTEA +L++L G AVI EIL++ G
Sbjct: 127 RGHTEASLELSELLGFKRYAVIVEILDEKG 156
>gnl|CDD|178026 PLN02404, PLN02404, 6,7-dimethyl-8-ribityllumazine synthase.
Length = 141
Score = 87.9 bits (218), Expect = 2e-20
Identities = 28/83 (33%), Positives = 53/83 (63%)
Query: 422 EKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQIS 481
E+NI + VPG+ EIP+ + + + K++ ++ IG +IRG+T H++ +AN S ++
Sbjct: 40 EENIDVVWVPGSFEIPVVAQRLAKSGKYDAILCIGAVIRGDTTHYDAVANSAASGVLSAG 99
Query: 482 IKNNIPIINAILTTETIEQANSR 504
+ + +P I +LT + +EQA +R
Sbjct: 100 LNSGVPCIFGVLTCDDMEQALNR 122
>gnl|CDD|216253 pfam01029, NusB, NusB family. The NusB protein is involved in the
regulation of rRNA biosynthesis by transcriptional
antitermination.
Length = 126
Score = 85.7 bits (213), Expect = 8e-20
Identities = 32/124 (25%), Positives = 58/124 (46%), Gaps = 6/124 (4%)
Query: 533 HRAREFALQGIYQWLFNN--MDVNLIETYIKEISNFYKVDKKYFYLILRGVINDINFLRY 590
ARE ALQ +Y ++ L + ++ + D+ + ++ GV+ ++ L
Sbjct: 1 RNARELALQALYAVEERGASLNELLDKLLEADLD---ERDRAFATELVYGVLRNLEELDA 57
Query: 591 DLS-LIIDRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDEKKYL 649
+ L+ + + L ++ +L +G YEL IP V INEA+EL K FG ++
Sbjct: 58 LIEKLLENWPLERLDPVDRAILRLGLYELLYLDDIPPHVAINEAVELAKKFGGEKSAGFV 117
Query: 650 EALL 653
+L
Sbjct: 118 NGVL 121
>gnl|CDD|187740 cd08371, Lumazine_synthase-like, lumazine synthase and riboflavin
synthase; involved in the riboflavin (vitamin B2)
biosynthetic pathway. This superfamily contains
lumazine synthase (6,7-dimethyl-8-ribityllumazine
synthase, LS) and riboflavin synthase (RS). Both enzymes
play important roles in the riboflavin biosynthetic
pathway. Riboflavin is the precursor of flavin
mononucleotide (FMN) and flavin adenine dinucleotide
(FAD) which are essential cofactors for the catalysis of
a wide range of redox reactions. These cofactors are
also involved in many other processes involving DNA
repair, circadian time-keeping, light sensing, and
bioluminescence. Riboflavin is biosynthesized in plants,
fungi and certain microorganisms; as animals lack the
necessary enzymes to produce this vitamin, they acquire
it from dietary sources. In the final steps of the
riboflavin biosynthetic pathway, LS catalyzes the
condensation of the
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with
3,4-dihydroxy- 2-butanone-4-phosphate to release water,
inorganic phosphate and 6,7-dimethyl-8-ribityllumazine
(DMRL), and RS catalyzes a dismutation of DMRL which
yields riboflavin and
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In
the latter reaction, a four-carbon moiety is transferred
between two DMRL molecules serving as donor and
acceptor, respectively. Both the LS and RS catalyzed
reactions are thermodynamically irreversible and can
proceed in the absence of a catalyst. In bacteria and
eukaryotes, there are two types of LS: type-I LS forms
homo-pentamers or icosahedrally arranged dodecamers of
pentamers, type-II LS forms decamers (dimers of
pentamers). In archaea LSs and RSs appear to have
diverged early in the evolution of archaea from a common
ancestor.
Length = 129
Score = 84.8 bits (210), Expect = 2e-19
Identities = 34/92 (36%), Positives = 60/92 (65%), Gaps = 3/92 (3%)
Query: 422 EKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQIS 481
I+ ++VPGA EIPLA K +++ + ++ ++AIGV+I+GETYHFE++A+E +M +
Sbjct: 30 NIKIIVVTVPGAYEIPLAAKKLLEKEDYDAVVAIGVVIKGETYHFEIVAHEVSRGLMNLQ 89
Query: 482 IKNNIPIINAILTTETIE---QANSRILTKGE 510
++ + P+I +LT + E ++ KGE
Sbjct: 90 LETDKPVIFGVLTPDNAEEQADERAKRGNKGE 121
>gnl|CDD|236430 PRK09249, PRK09249, coproporphyrinogen III oxidase; Provisional.
Length = 453
Score = 87.9 bits (219), Expect = 5e-18
Identities = 54/210 (25%), Positives = 97/210 (46%), Gaps = 21/210 (10%)
Query: 645 EKKYLEALLIDVELSLPII-LNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNI 703
YL+AL ++ L ++ R + + GGGTP+ +S L L+ +++ F +
Sbjct: 79 ADPYLDALEKEIALVAALLGPGRPVSQLHWGGGTPTFLSPEQLRRLMALLREHFNFAPDA 138
Query: 704 SITLEANPSTFEIEKF-HSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAK 762
I++E +P ++E + G NRLS+G+Q F+ + + R + +E A+
Sbjct: 139 EISIEIDPRELDLEMLDALREL-GFNRLSLGVQDFDPEVQKAVNRIQPFEFTFALVEAAR 197
Query: 763 QY-FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTY-----FFK-- 814
+ F + N+DLIY LP QT L ++ P L++++ Y FK
Sbjct: 198 ELGFTSINIDLIYGLPKQTPESFARTLEKVLELRPDRLAVFN-------YAHVPWLFKAQ 250
Query: 815 --YPPLSMPSNDE-NAVMQDKITSLLKNNY 841
+PS +E A++Q I +L + Y
Sbjct: 251 RKIDEADLPSPEEKLAILQQTIETLTEAGY 280
>gnl|CDD|238342 cd00619, Terminator_NusB, Transcription termination factor NusB (N
protein-Utilization Substance B). NusB plays a key role
in the regulation of ribosomal RNA biosynthesis in
eubacteria by modulating the efficiency of
transcriptional antitermination. NusB along with other
Nus factors (NusA, NusE/S10 and NusG) forms the core
complex with the boxA element of the nut site of the
rRNA operons. These interactions help RNA polymerase to
counteract polarity during transcription of rRNA operons
and allow stable antitermination. The transcription
antitermination system can be appropriated by some
bacteriophages such as lambda, which use the system to
switch between the lysogenic and lytic modes of phage
propagation.
Length = 130
Score = 80.0 bits (198), Expect = 9e-18
Identities = 37/127 (29%), Positives = 67/127 (52%), Gaps = 9/127 (7%)
Query: 532 RHRAREFALQGIYQWLFNNMDVNLIETYIKEISNFYKVDKKYFYLILRGVINDINFLRYD 591
R RARE A+Q +Y W + + + ++ + K + ++RGV+ +I +
Sbjct: 1 RRRARELAVQALYAWELAPEILAEVVSLLELLQYKSKKVLPFALKLVRGVLENIE----E 56
Query: 592 LSLIIDR-----SINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDEK 646
+ +I++ S++ L+ +E +L + YEL +P+ V+INEAIEL K FG D
Sbjct: 57 IDELIEKHLRNWSLDRLAIVERAILRLAVYELLFLPDVPHPVVINEAIELAKRFGGDDSH 116
Query: 647 KYLEALL 653
K++ +L
Sbjct: 117 KFVNGVL 123
>gnl|CDD|181509 PRK08629, PRK08629, coproporphyrinogen III oxidase; Provisional.
Length = 433
Score = 79.3 bits (196), Expect = 2e-15
Identities = 76/339 (22%), Positives = 127/339 (37%), Gaps = 56/339 (16%)
Query: 646 KKYLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISI 705
+ Y +L E+ + L ++++GGGT +++ D L L+ KKL K+ +
Sbjct: 82 RAYFISL--RKEMEMVKELGYDFESMYVGGGTTTILEDE-LAKTLELAKKLFSIKE---V 135
Query: 706 TLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTH---DSKQAKYAIEIAK 762
+ E++P+ + K + I+RLSIG+QSFN+ L ++ R ++ I AK
Sbjct: 136 SCESDPNHLDPPKLKQLKGL-IDRLSIGVQSFNDDILKMVDRYEKFGSGQETFEKIMKAK 194
Query: 763 QYFNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFKYPPLSMPS 822
F N+DLI+ P QT L DL+ A + P ++ Y L T L
Sbjct: 195 GLFPIINVDLIFNFPGQTDEVLQHDLDIAKRLDPRQITTYPLMKSHQTRKSVKGSLGASQ 254
Query: 823 NDENAVMQDKITSLLKNNYYKNYEISAYSKTG------YESQHNLNYWKFGDYLGNSIAK 876
D I L Y + A+SK Y ++ +YLG
Sbjct: 255 KDNERQYYQIINELFG-QYNQL-SAWAFSKKNDEGFDEYVIDYD-------EYLGVGSGS 305
Query: 877 SKKIEKKCLIFEFMLN--ALRLKDGFSPN--------------LFFER---TGINIKIIE 917
++ + F L R+ G F ++IK
Sbjct: 306 FSFLDGTLYVNTFSLRDYQERIAAGQMGVIAQKNFSKKEVMQYRFLLGMFSGRLSIKYFR 365
Query: 918 SKLK-NAEK-----------LGLLKRNNKNIKPTSFGRY 944
N +K +G +K + ++ T FG+Y
Sbjct: 366 ETFGVNLDKALFKEMLLLKLIGAIKNDPGDLIVTDFGKY 404
>gnl|CDD|237356 PRK13347, PRK13347, coproporphyrinogen III oxidase; Provisional.
Length = 453
Score = 77.8 bits (192), Expect = 7e-15
Identities = 48/202 (23%), Positives = 89/202 (44%), Gaps = 9/202 (4%)
Query: 647 KYLEALLIDVELSLPIILN-RKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISI 705
Y+ AL+ ++ L + R++ + GGGTP++++ + L+ ++ F I
Sbjct: 82 AYVAALIREIRLVAASLPQRRRVSQLHWGGGTPTILNPDQFERLMAALRDAFDFAPEAEI 141
Query: 706 TLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY- 764
+E +P T E + + +G NR S G+Q F+ + + R + A+E+ +
Sbjct: 142 AVEIDPRTVTAEMLQALAALGFNRASFGVQDFDPQVQKAINRIQPEEMVARAVELLRAAG 201
Query: 765 FNNFNLDLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFK----YPPLSM 820
F + N DLIY LP+QT+ L+ I SP ++++ P K ++
Sbjct: 202 FESINFDLIYGLPHQTVESFRETLDKVIALSPDRIAVFGYAHVP--SRRKNQRLIDEAAL 259
Query: 821 PSNDENA-VMQDKITSLLKNNY 841
P +E + LL Y
Sbjct: 260 PDAEERLRQARAVADRLLAAGY 281
>gnl|CDD|235601 PRK05773, PRK05773, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
Validated.
Length = 219
Score = 73.6 bits (181), Expect = 1e-14
Identities = 57/185 (30%), Positives = 84/185 (45%), Gaps = 32/185 (17%)
Query: 268 DSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMT-------- 319
D + RE E D++ + VT +I + K A GLIC + L L+ +
Sbjct: 20 DFDGREEEVDMVFYAGAVTWKSIYTLRKNAGGLICYATSNSEGKTLGLNFLAEILKRHEL 79
Query: 320 -----KKNNSSFGTN--FTVSIEAANGVTTGISASDRAHTI----KVASSKKAKPSDIVQ 368
KK S+G F++ + TGIS DRA TI KV K P + +
Sbjct: 80 YRKLVKK--PSYGDEPAFSLWVNHVK-TKTGISDYDRALTIRELHKVVELAKTNPEEARE 136
Query: 369 --------PGHIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARA 420
PGH+ L + G+ R GHTE L + AGL PSAVI E+L++ ++++
Sbjct: 137 EFYENFYSPGHVPILIGR--GIRERRGHTELSIALAQAAGLEPSAVIAEMLDEKLSLSKE 194
Query: 421 QEKNI 425
+ K I
Sbjct: 195 KAKKI 199
>gnl|CDD|217866 pfam04055, Radical_SAM, Radical SAM superfamily. Radical SAM
proteins catalyze diverse reactions, including unusual
methylations, isomerisation, sulphur insertion, ring
formation, anaerobic oxidation and protein radical
formation.
Length = 165
Score = 71.0 bits (174), Expect = 3e-14
Identities = 30/118 (25%), Positives = 54/118 (45%), Gaps = 3/118 (2%)
Query: 668 IHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGI 727
+ + + GG P L+ D L + I ITLE N + + E G+
Sbjct: 45 VEVVILTGGEPLLLPDLVELLE---RLLKLREGEGIRITLETNGTLLDEELLEELKEAGL 101
Query: 728 NRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQYFNNFNLDLIYALPNQTLSELM 785
+R+SI +QS +++ L I+ R H ++ A+E+ ++ +D I LP + +L
Sbjct: 102 DRVSISLQSGDDEVLKIINRGHTFEEVLEALELLREAGIPVVVDNIVGLPGENDEDLE 159
>gnl|CDD|187744 cd09211, Lumazine_synthase_archaeal, lumazine synthase
(6,7-dimethyl-8-ribityllumazine synthase, LS); catalyzes
the penultimate step in the biosynthesis of riboflavin
(vitamin B2). Archaeal LS is an important enzyme in the
riboflavin biosynthetic pathway. Riboflavin is the
precursor of flavin mononucleotide (FMN) and flavin
adenine dinucleotide (FAD) which are essential cofactors
for the catalysis of a wide range of redox reactions.
These cofactors are also involved in many other
processes involving DNA repair, circadian time-keeping,
light sensing, and bioluminescence. In the final steps
of the riboflavin biosynthetic pathway LS catalyzes the
condensation of the
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with
3,4-dihydroxy- 2-butanone-4-phosphate to release water,
inorganic phosphate and 6,7-dimethyl-8-ribityllumazine
(DMRL), and riboflavin synthase (RS) catalyzes a
dismutation of DMRL which yields riboflavin and
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In
the latter reaction, a four-carbon moiety is transferred
between two DMRL molecules serving as donor and
acceptor, respectively. Both the LS and RS catalyzed
reactions are thermodynamically irreversible and can
proceed in the absence of a catalyst. LS from
Methanococcus jannaschii forms capsids with icosahedral
532 symmetry consisting of 60 subunits. Archaeal LSs
share sequence similarity with archaeal RSs, both appear
to have diverged early in the evolution of archaea from
a common ancestor.
Length = 131
Score = 60.4 bits (147), Expect = 8e-11
Identities = 21/61 (34%), Positives = 40/61 (65%)
Query: 428 ISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQISIKNNIP 487
+ VPG ++PLA+K +++ + ++ +G +I+GET H ELIAN+ I+ +S++ P
Sbjct: 35 LRVPGVFDMPLAVKKLLEKDDIDAVVTLGAVIKGETKHDELIANQAARKILDLSLEYGKP 94
Query: 488 I 488
+
Sbjct: 95 V 95
>gnl|CDD|238253 cd00447, NusB_Sun, RNA binding domain of NusB (N
protein-Utilization Substance B) and Sun (also known as
RrmB or Fmu) proteins. This family includes two
orthologous groups exemplified by the transcription
termination factor NusB and the N-terminal domain of the
rRNA-specific 5-methylcytidine transferase
(m5C-methyltransferase) Sun. The NusB protein plays a
key role in the regulation of ribosomal RNA biosynthesis
in eubacteria by modulating the efficiency of
transcriptional antitermination. NusB along with other
Nus factors (NusA, NusE/S10 and NusG) forms the core
complex with the boxA element of the nut site of the
rRNA operons. These interactions help RNA polymerase to
counteract polarity during transcription of rRNA operons
and allow stable antitermination. The transcription
antitermination system can be appropriated by some
bacteriophages such as lambda, which use the system to
switch between the lysogenic and lytic modes of phage
propagation. The m5C-methyltransferase Sun shares the
N-terminal non-catalytic RNA-binding domain with NusB.
Length = 129
Score = 59.3 bits (144), Expect = 1e-10
Identities = 34/123 (27%), Positives = 66/123 (53%), Gaps = 4/123 (3%)
Query: 534 RAREFALQGIYQWLFNNMD-VNLIETYIKEISNFYKVDKKYFYLILRGVINDINFLRYDL 592
ARE A Q +YQ N + + + ++++ K D+ + ++ GV+ ++ L +
Sbjct: 1 SAREIAFQALYQVEIRNGISLEAVLSALEKLQLA-KKDRPFALELVYGVLRNLPELDDII 59
Query: 593 SLIIDR-SINELSSIEYVVLLIGTYEL-KSHYKIPYKVIINEAIELVKSFGNIDEKKYLE 650
S ++ + ++ L ++ +L + YEL + Y +P V INEA+EL K FG+ D K++
Sbjct: 60 SPLLKKWLLDRLDKVDRAILRLLLYELYQLLYDVPPPVAINEAVELAKRFGDDDSAKFVN 119
Query: 651 ALL 653
+L
Sbjct: 120 GVL 122
>gnl|CDD|236713 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional.
Length = 312
Score = 59.1 bits (143), Expect = 4e-09
Identities = 39/113 (34%), Positives = 55/113 (48%), Gaps = 11/113 (9%)
Query: 65 PIAFQVGDNEPKKLAKSAK---IIQKWGYDEINLNCGCPSNRVQNGFFGAILMTKPLLVS 121
+ Q+ P+ LA++A + WG D LNCGCPS V GA L+ P L+
Sbjct: 64 LVRIQLLGQYPQWLAENAARAVELGSWGVD---LNCGCPSKTVNGSGGGATLLKDPELIY 120
Query: 122 DCIKAMRDSV--EIDITVKHRIGIDDINSYDFVRDFVGTVSSAGCRTFIVHAR 172
KAMR++V + +TVK R+G D S + + V AG +VH R
Sbjct: 121 QGAKAMREAVPAHLPVTVKVRLGWD---SGERKFEIADAVQQAGATELVVHGR 170
>gnl|CDD|187741 cd09208, Lumazine_synthase-II, lumazine synthase
(6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes
the penultimate step in the biosynthesis of riboflavin
(vitamin B2); type-II. Type-II LS also known as RibH2,
catalyzes the penultimate step in the biosynthesis of
riboflavin in plants and microorganisms. LS catalyses
the formation of 6,7-dimethyl-8-ribityllumazine by the
condensation of 5-amino-6-ribitylamino-
2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy-
2-butanone-4-phosphate. Subsequently, the lumazine
intermediate dismutates yielding riboflavin and
5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione, in a
reaction catalyzed by riboflavin synthase (RS); RS
belongs to a different family of the
Lumazine-synthase-like superfamily. Riboflavin is the
precursor of flavin mononucleotide (FMN) and flavin
adenine dinucleotide (FAD) which are essential cofactors
for the catalysis of a wide range of redox reactions.
These cofactors are also involved in many other
processes involving DNA repair, circadian time-keeping,
light sensing, and bioluminescence. Riboflavin is
biosynthesized in plants, fungi and certain
microorganisms; as animals lack the necessary enzymes to
produce this vitamin, they acquire it from dietary
sources. Type II LSs are distinct from type-I LS not
only in protein sequence, but in that they exhibit
different quaternary assemblies; type-II LSs form
decamers (dimers of pentamers). The pathogen Brucella
spp. have both a type-I LS and a type-II LS called RibH1
and RibH2, respectively. RibH1/type-I LS appears to be a
functional LS in Brucella spp., whereas RibH2/type-II LS
has much lower catalytic activity as LS and may be
regulated by a riboswitch that senses FMN, suggesting
that the type-II LSs may have evolved into very poor
catalysts or, that they may harbor a new, as-yet-unknown
function.
Length = 137
Score = 55.1 bits (133), Expect = 6e-09
Identities = 18/71 (25%), Positives = 38/71 (53%)
Query: 424 NILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQISIK 483
+ VPGA EIPL K + + ++ ++ +++ G Y E +A I +M++ ++
Sbjct: 35 EVDIFDVPGAFEIPLHAKRLARTGRYAAIVGAALVVDGGIYRHEFVAQAVIDGLMRVQLE 94
Query: 484 NNIPIINAILT 494
+P+ + +LT
Sbjct: 95 TEVPVFSVVLT 105
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 58.1 bits (140), Expect = 7e-09
Identities = 58/235 (24%), Positives = 106/235 (45%), Gaps = 25/235 (10%)
Query: 16 APMMNLTDRHCRMFHRQITRYSWLYTEMFTT--QAILGNKKHCLDFNAEEHPI-AFQVGD 72
APM +TDR R ++ +EM ++ Q +K + +E I Q+
Sbjct: 15 APMAGITDRPFRTLCYEMGA-GLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAG 73
Query: 73 NEPKKLAKSAKIIQKWGYDEINLNCGCPSNRVQNGFFGAILMTKPLLVSDCIKAMRDSVE 132
++PK++A +A+I + G I++N GCP+ +V G+ L+ P LV + + ++V+
Sbjct: 74 SDPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVD 133
Query: 133 IDITVKHRIGIDDINSYDFVRDFVGTVSSA---GCRTFIVHARN-AFLKKLNPKQNRKIP 188
+ +T+K R G + R+ V A G + +H R A L
Sbjct: 134 VPVTLKIRTGWAPEH-----RNCVEIAQLAEDCGIQALTIHGRTRACLFNGEA------- 181
Query: 189 ILKYNFVYNLKKDFPELEIIINGGIKTKKEIDLHLNYI--DGVMLGREAYKNPFL 241
+Y+ + +K+ + +I NG I + L+Y D +M+GR A P++
Sbjct: 182 --EYDSIRAVKQKV-SIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWI 233
>gnl|CDD|237096 PRK12419, PRK12419, riboflavin synthase subunit beta; Provisional.
Length = 158
Score = 49.3 bits (118), Expect = 1e-06
Identities = 18/65 (27%), Positives = 37/65 (56%)
Query: 430 VPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQISIKNNIPII 489
VPGA EIPL + + + ++ ++A +++ G Y E +A I +M++ + +P+
Sbjct: 51 VPGAFEIPLHAQTLAKTGRYAAIVAAALVVDGGIYRHEFVAQAVIDGLMRVQLDTEVPVF 110
Query: 490 NAILT 494
+ +LT
Sbjct: 111 SVVLT 115
>gnl|CDD|203555 pfam06969, HemN_C, HemN C-terminal domain. Members of this family
are all oxygen-independent coproporphyrinogen-III
oxidases (HemN). This enzyme catalyzes the
oxygen-independent conversion of coproporphyrinogen-III
to protoporphyrinogen-IX, one of the last steps in haem
biosynthesis. The function of this domain is unclear,
but comparison to other proteins containing a radical
SAM domain (pfam04055) suggest it may be a substrate
binding domain.
Length = 66
Score = 43.4 bits (103), Expect = 1e-05
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 885 LIFEFMLNALRLKDGFSPNLFFERTGI-NIKIIESKLKNAEKLGLLKRNNKNIKPTSFGR 943
+ E ++ LRL +G F +R G ++ +E L+ ++ GLL+ ++ ++ T GR
Sbjct: 6 RLRERLILGLRLTEGVDLAEFEQRFGGDFLEELEPLLEKLQEDGLLELDDGRLRLTPRGR 65
Query: 944 Y 944
Sbjct: 66 L 66
>gnl|CDD|223963 COG1032, COG1032, Fe-S oxidoreductase [Energy production and
conversion].
Length = 490
Score = 46.9 bits (111), Expect = 5e-05
Identities = 33/157 (21%), Positives = 64/157 (40%), Gaps = 9/157 (5%)
Query: 670 TIFIGGGTPSLISDTGLDYLLKNIKKLLLFK-KNISITL-EANPSTFEIEK-FHSYSIIG 726
IF+ G P+L + + L + + L K + I+ T E+ G
Sbjct: 252 DIFLYGS-PALNDEKRFELLSLELIERGLRKGCRVHISAPSLRADTVTDEELLKLLREAG 310
Query: 727 INRLSIGIQSFNNKYLNILGRTHDSKQA-KYAIEIAKQYFNNFNLDLIYALPNQTLSELM 785
+ R+ IGI+S + + L + + +++ + A++IAK++ L I LP +T ++
Sbjct: 311 LRRVYIGIESGSEELLKKINKGITTEEVLEEAVKIAKEHGLRVKLYFIVGLPGETEEDVK 370
Query: 786 LDLNYAIQ----YSPPHLSLYSLTIEPNTYFFKYPPL 818
+ A ++S P T + P L
Sbjct: 371 ETIELAKFIKKLGPKLYVSPSPFVPLPGTPLQEMPKL 407
>gnl|CDD|234440 TIGR04013, B12_SAM_MJ_1487, B12-binding domain/radical SAM domain
protein, MJ_1487 family. Members of this family have
both a B12 binding homology domain (pfam02310) and a
radical SAM domain (pfam04055), and occur only once per
genome. Some species with members of this family have a
related protein with similar domain architecture. This
protein is occurs largely in archaeal methanogens but
also in a few bacteria, including Thermotoga maritima
and Myxococcus xanthus [Unknown function, Enzymes of
unknown specificity].
Length = 382
Score = 37.2 bits (87), Expect = 0.031
Identities = 17/52 (32%), Positives = 30/52 (57%)
Query: 729 RLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQYFNNFNLDLIYALPNQT 780
RL IG QS +++ L + R H + + A+E+A ++ +D I+ LP +T
Sbjct: 268 RLHIGAQSGSDRVLKAIRRGHTVEDVERAVELALEHGFTPVVDFIFGLPGET 319
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 35.5 bits (83), Expect = 0.11
Identities = 29/123 (23%), Positives = 53/123 (43%), Gaps = 9/123 (7%)
Query: 535 AREFALQGIYQWLFNNMDVNL-IETYIKEISNFYKVDKKYFYLILRGVINDINFLRYDLS 593
ARE AL+ + + N N+ + +K+ S DK ++ G I L Y
Sbjct: 5 ARELALEVLIKVENNGAYSNIALNKVLKK-SELSDKDKALLTELVYGTIQRKLTLDY--- 60
Query: 594 LIIDRSINELSSIE---YVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDEKKYLE 650
+ I + ++ +L + Y+L K+P +NEA+E+ K G+ K++
Sbjct: 61 -YLAPFIKKRKKLDPWVRNLLRMSLYQLLYLDKVPDHAAVNEAVEIAKKRGHKGIAKFVN 119
Query: 651 ALL 653
+L
Sbjct: 120 GVL 122
>gnl|CDD|224164 COG1243, ELP3, Histone acetyltransferase [Transcription / Chromatin
structure and dynamics].
Length = 515
Score = 34.6 bits (80), Expect = 0.23
Identities = 25/120 (20%), Positives = 43/120 (35%), Gaps = 29/120 (24%)
Query: 667 KIHTIFIGGGTPSLISDTGLDY---LLKNIKKLLLF----------------KKNISITL 707
K+ I +GG +L L+Y LK K + + + IT+
Sbjct: 134 KVELIIMGGTFTAL----SLEYQEWFLKVALKAMNDFGYDLEEAQRKNETAELRCVGITI 189
Query: 708 EANPSTF---EIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY 764
E P +++ Y G+ R+ +G+QS + L R H + A + K
Sbjct: 190 ETRPDYIDEEHLDQMLKY---GVTRVELGVQSIYDDVLERTKRGHTVEDVVEATRLLKDA 246
>gnl|CDD|238343 cd00620, Methyltransferase_Sun, N-terminal RNA binding domain of
the methyltransferase Sun. The rRNA-specific
5-methylcytidine transferase Sun, also known as RrmB or
Fmu shares the RNA-binding non-catalytic domain with the
transcription termination factor NusB. The precise
biological role of this domain in Sun is unknown,
although it is likely to be involved in
sequence-specific RNA binding. The C-terminal
methyltransferase domain of Sun has been shown to
catalyze formation of m5C at position 967 of 16S rRNA in
Escherichia coli.
Length = 126
Score = 32.3 bits (74), Expect = 0.42
Identities = 13/78 (16%), Positives = 34/78 (43%), Gaps = 1/78 (1%)
Query: 580 GVINDINFLRYDLSLIIDRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKS 639
G + + L + ++ ++ + +L +G Y+L + +P ++E +E+ K
Sbjct: 47 GTLRWLALLDWIINPLLKKPDVGKDPDVRNLLRLGLYQLL-YLDVPPHAAVDETVEIAKI 105
Query: 640 FGNIDEKKYLEALLIDVE 657
++ + A+L E
Sbjct: 106 RKDLGRAGLVNAVLRRFE 123
>gnl|CDD|240091 cd04740, DHOD_1B_like, Dihydroorotate dehydrogenase (DHOD) class 1B
FMN-binding domain. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
Length = 296
Score = 32.1 bits (74), Expect = 1.1
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 79 AKSAKIIQKWGYDEINLNCGCPSNRVQNGFFGAILMTKPLLVSDCIKAMRDSVEIDITVK 138
+ A+ + G D I LN CP+ V+ G G T P V++ +KA++ + ++ + VK
Sbjct: 105 VEVAEKLADAGADAIELNISCPN--VKGG--GMAFGTDPEAVAEIVKAVKKATDVPVIVK 160
>gnl|CDD|182007 PRK09634, nusB, transcription antitermination protein NusB;
Provisional.
Length = 207
Score = 31.8 bits (73), Expect = 1.2
Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 11/43 (25%)
Query: 596 IDRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVK 638
IDR I L+ +E + L P V INEA+EL K
Sbjct: 149 IDRDILRLAVVEILFL-----------NTPAAVAINEAVELAK 180
>gnl|CDD|222441 pfam13898, DUF4205, Domain of unknown function (DUF4205). The
proteins in this family are uncharacterized but often
named FAM188B.
Length = 341
Score = 31.9 bits (73), Expect = 1.5
Identities = 14/56 (25%), Positives = 21/56 (37%), Gaps = 6/56 (10%)
Query: 238 NPFLMSN------FDLNYYSNLPQYKIPTRIDIINLDSENRENEGDIILSSDFVTP 287
NP L+S+ FDL YY L R+ + + + + D D P
Sbjct: 268 NPELLSDWKMERRFDLYYYDGLANQDEEIRLTVDTHSAADEADHNDQDGVRDLTPP 323
>gnl|CDD|165086 PHA02713, PHA02713, hypothetical protein; Provisional.
Length = 557
Score = 31.9 bits (72), Expect = 1.8
Identities = 31/87 (35%), Positives = 42/87 (48%), Gaps = 3/87 (3%)
Query: 187 IPILKYNFVYNLKKDFPELEIIINGGIKTKKEIDLH-LNYIDGVMLGREAYKNPFLMSNF 245
IPI+KY L + P L I + KT EI ++ D V L RE YK L+
Sbjct: 141 IPIVKY-IKRMLMSNIPTL-ITTDAFKKTVFEILFDIISTNDNVYLYREGYKVTILLKWL 198
Query: 246 DLNYYSNLPQYKIPTRIDIINLDSENR 272
+ NY + I + IDI NLD ++R
Sbjct: 199 EYNYITEEQLLCILSCIDIQNLDKKSR 225
>gnl|CDD|179586 PRK03512, PRK03512, thiamine-phosphate pyrophosphorylase;
Provisional.
Length = 211
Score = 31.2 bits (71), Expect = 1.9
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 5/46 (10%)
Query: 333 SIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAK 378
+I AA G+ G+S D ++ + A+PS I GH+FP Q K
Sbjct: 97 AIRAA-GLRLGVSTHDDM---EIDVALAARPSYIAL-GHVFPTQTK 137
>gnl|CDD|184628 PRK14331, PRK14331, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 437
Score = 31.3 bits (71), Expect = 3.0
Identities = 24/122 (19%), Positives = 50/122 (40%), Gaps = 27/122 (22%)
Query: 728 NRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQYFNN--FNLDLIYALPNQT----- 780
L + Q+ +++ L ++ R + ++ IE+ K+Y + F+ D+I P +T
Sbjct: 256 EHLHLPFQAGSDRILKLMDRGYTKEEYLEKIELLKEYIPDITFSTDIIVGFPTETEEDFE 315
Query: 781 -----LSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFKYPPLSMPSNDENAVMQDKITS 835
L ++ + ++ +YSP P T P M + + V ++
Sbjct: 316 ETLDVLKKVEFEQVFSFKYSP----------RPGT-----PAAYMEGQEPDEVKTKRMNR 360
Query: 836 LL 837
LL
Sbjct: 361 LL 362
>gnl|CDD|184353 PRK13832, PRK13832, plasmid partitioning protein; Provisional.
Length = 520
Score = 30.8 bits (70), Expect = 3.6
Identities = 21/63 (33%), Positives = 28/63 (44%), Gaps = 4/63 (6%)
Query: 366 IVQPGHIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVIC-EILNDDGTMARAQEKN 424
IVQP + P + G +I+ GH + AGL V+ E ND+G M E N
Sbjct: 40 IVQPPVVSPEEDGGNGYIIQAGHRRVKQAIA--AGLEEIEVLVTEAANDNGAMRSMVE-N 96
Query: 425 ILH 427
I
Sbjct: 97 IAR 99
>gnl|CDD|190601 pfam03323, GerA, Bacillus/Clostridium GerA spore germination
protein.
Length = 468
Score = 30.9 bits (71), Expect = 4.0
Identities = 14/59 (23%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 465 HFELIANETISNIMQISIKNNIPIINAILTTETIEQANSRILTKGEIIIFINHKNKSLV 523
+ EL E +I++ +K +PI + + +++ IL+ G ++FI+ ++K+L+
Sbjct: 51 NEELEEEEEKEDILEEILKKILPISE-VKEVDDLDEIIDSILS-GNTVLFIDGEDKALL 107
>gnl|CDD|218909 pfam06138, Chordopox_E11, Chordopoxvirus E11 protein. This family
consists of several Chordopoxvirus E11 proteins. The E11
gene of vaccinia virus encodes a 15-kDa polypeptide.
Mutations in the E11 gene makes the virus
temperature-sensitive due to either the fact that virus
infectivity requires a threshold level of active E11
protein or that E11 function is conditionally essential.
Length = 130
Score = 28.9 bits (65), Expect = 5.6
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 13/69 (18%)
Query: 555 LIETYIKEISNFYKVDKKYFYLILR-----------GVIN--DINFLRYDLSLIIDRSIN 601
I+ +I + + VDK FYL+++ G ++ + F +D L+ S N
Sbjct: 36 AIDYFISVLKKYIHVDKSTFYLVIKDKDIFYFKCDKGSVSQVENEFYTFDEELLFVDSYN 95
Query: 602 ELSSIEYVV 610
E++ IE+++
Sbjct: 96 EITGIEFII 104
>gnl|CDD|151502 pfam11056, UvsY, Recombination, repair and ssDNA binding protein
UvsY. UvsY protein enhances the rate of
single-stranded-DNA-dependant ATP hydrolysis by UvsX
protein. The enhancement of ATP hydrolysis by UvsY
protein is shown to result from the ability of UvsY
protein to increase the affinity of UvsX protein for
single-stranded DNA.
Length = 128
Score = 28.8 bits (65), Expect = 5.9
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 225 YIDGVMLGREAYKNPFLMSNFDLNYYSNLPQYKI 258
ID L E+ P L S + L YYS+ + KI
Sbjct: 7 KIDTTKLQTESANIPVLHSKW-LRYYSDAKKEKI 39
>gnl|CDD|239477 cd03382, PAP2_dolichyldiphosphatase, PAP2_like proteins,
dolichyldiphosphatase subfamily. Dolichyldiphosphatase
is a membrane-associated protein located in the
endoplasmic reticulum and hydrolyzes dolichyl
pyrophosphate, as well as dolichylmonophosphate at a low
rate. The enzyme is necessary for maintaining proper
levels of dolichol-linked oligosaccharides and protein
N-glycosylation, and might play a role in re-utilization
of the glycosyl carrier lipid for additional rounds of
lipid intermediate biosynthesis after its release during
protein N-glycosylation reactions.
Length = 159
Score = 29.2 bits (66), Expect = 6.3
Identities = 11/34 (32%), Positives = 21/34 (61%), Gaps = 3/34 (8%)
Query: 662 IILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKK 695
I+ R++ I++ G L+++ L+Y+LK I K
Sbjct: 36 ILFRRELEAIYLFIG---LLANEALNYVLKRIIK 66
>gnl|CDD|239244 cd02940, DHPD_FMN, Dihydropyrimidine dehydrogenase (DHPD)
FMN-binding domain. DHPD catalyzes the first step in
pyrimidine degradation: the NADPH-dependent reduction of
uracil and thymine to the corresponding
5,6-dihydropyrimidines. DHPD contains two FAD, two FMN,
and eight [4Fe-4S] clusters, arranged in two electron
transfer chains that pass the dimer interface twice. Two
of the Fe-S clusters show a hitherto unobserved
coordination involving a glutamine residue.
Length = 299
Score = 29.9 bits (68), Expect = 6.5
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 82 AKIIQKWGYDEINLNCGCPSNRVQNGFFGAILMTKPLLVSDCIKAMRDSVEIDITVKHRI 141
AK++++ G D + LN CP + G GA + P LV + + +R++V+I + K
Sbjct: 119 AKLVEEAGADALELNFSCPHGMPERG-MGAAVGQDPELVEEICRWVREAVKIPVIAKLTP 177
Query: 142 GIDDI 146
I DI
Sbjct: 178 NITDI 182
>gnl|CDD|224480 COG1564, THI80, Thiamine pyrophosphokinase [Coenzyme metabolism].
Length = 212
Score = 29.2 bits (66), Expect = 7.7
Identities = 21/85 (24%), Positives = 28/85 (32%), Gaps = 18/85 (21%)
Query: 654 IDVELSLPIILNRKIHTIFIGGGTPSLISDTG--LDYLLKNIK---KLLLFKKNISITLE 708
D+EL+L L R I I G G LD+ L N+ + I++
Sbjct: 78 TDLELALDEALERGADEIVILGA-------LGGRLDHALANLFLLLRPAKSGFKITLISG 130
Query: 709 AN------PSTFEIEKFHSYSIIGI 727
N P IEK Y
Sbjct: 131 QNLITPLPPGQHTIEKDPGYLYSIF 155
>gnl|CDD|163532 TIGR03820, lys_2_3_AblA, lysine-2,3-aminomutase. This model
describes lysine-2,3-aminomutase as found along with
beta-lysine acetyltransferase in a two-enzyme pathway
for making the compatible solute
N-epsilon-acetyl-beta-lysine. This compatible solute, or
osmolyte, is known to protect a number of methanogenic
archaea against salt stress. The trusted cutoff
distinguishes a tight clade with essentially full-length
homology from additional homologs that are shorter or
highly diverged in the C-terminal region. All members of
this family have the radical SAM motif CXXXCXXC, while
some but not all have a second copy of the motif in the
C-terminal region.
Length = 417
Score = 29.7 bits (67), Expect = 8.1
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 665 NRKIHTIFIGGGTPSLISDTGLDYLLKNIKKL 696
+I + + GG P L+SD LD++L ++ +
Sbjct: 153 TPQIRDVLLSGGDPLLLSDDYLDWILTELRAI 184
>gnl|CDD|232879 TIGR00218, manA, mannose-6-phosphate isomerase, class I. The names
phosphomannose isomerase and mannose-6-phosphate
isomerase are synonomous. This family contains two
rather deeply branched groups. One group contains an
experimentally determined phosphomannose isomerase of
Streptococcus mutans as well as three uncharacterized
paralogous proteins of Bacillus subtilis, all at more
than 50 % identity to each other, plus a more distant
homolog from Archaeoglobus fulgidus. The other group
contains members from E. coli, budding yeast, Borrelia
burgdorferi, etc [Energy metabolism, Sugars].
Length = 303
Score = 29.3 bits (66), Expect = 9.9
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 664 LNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIE 717
++ K F + ++S +K+ K L KK S + A+ F IE
Sbjct: 243 ISGKAE--FKQQQSALILSVLEGSGRIKSGGKTLPLKKGESFFIPAHLGPFTIE 294
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.138 0.397
Gapped
Lambda K H
0.267 0.0684 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 49,275,087
Number of extensions: 5084124
Number of successful extensions: 4684
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4577
Number of HSP's successfully gapped: 155
Length of query: 956
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 850
Effective length of database: 6,236,078
Effective search space: 5300666300
Effective search space used: 5300666300
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: 64 (28.5 bits)