RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2383
(391 letters)
>gnl|CDD|236346 PRK08898, PRK08898, coproporphyrinogen III oxidase; Provisional.
Length = 394
Score = 568 bits (1467), Expect = 0.0
Identities = 211/378 (55%), Positives = 282/378 (74%), Gaps = 3/378 (0%)
Query: 14 LPPLSLYIHFPWCIKKCPYCDFHSYEIKKN--ISEKKYLEALLIDVELSLPIILNRKIHT 71
LPPLSLY+HFPWC++KCPYCDF+S+E K I E YL+AL D+E +LP++ R++HT
Sbjct: 17 LPPLSLYVHFPWCVRKCPYCDFNSHEWKDGGAIPEAAYLDALRADLEQALPLVWGRQVHT 76
Query: 72 IFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRL 131
+FIGGGTPSL+S GLD LL +++ LL + ITLEANP TFE EKF + G+NRL
Sbjct: 77 VFIGGGTPSLLSAAGLDRLLSDVRALLPLDPDAEITLEANPGTFEAEKFAQFRASGVNRL 136
Query: 132 SIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQYFNNFNLDLIYALPNQTLSELMLDLNY 191
SIGIQSFN+ +L LGR HD +A+ AIEIA ++F+NFNLDL+YALP QTL E + D+
Sbjct: 137 SIGIQSFNDAHLKALGRIHDGAEARAAIEIAAKHFDNFNLDLMYALPGQTLDEALADVET 196
Query: 192 AIQYSPPHLSLYSLTIEPNTYFFKYPPLSMPSNDENAVMQDKITSLLKNNYYKNYEISAY 251
A+ + PPHLSLY LT+EPNT F K+PP ++P +D +A MQD I + L Y +YE+SAY
Sbjct: 197 ALAFGPPHLSLYHLTLEPNTLFAKFPP-ALPDDDASADMQDWIEARLAAAGYAHYEVSAY 255
Query: 252 SKTGYESQHNLNYWKFGDYLGIGAGSHSKLSFPNYIIRQIRYKNPNIYLKNIFSGNSIAK 311
+K G + +HNLNYW+FGDYLGIGAG+H KLSFP+ I+RQ+RYK+P YL+ +G ++ +
Sbjct: 256 AKPGRQCRHNLNYWQFGDYLGIGAGAHGKLSFPDRILRQMRYKHPATYLEQAKAGTAVQE 315
Query: 312 SKKIEKKCLIFEFMLNALRLKDGFSPNLFFERTGINIKIIESKLKNAEKLGLLKRNNKNI 371
+++ + L FEFMLNALRL DG +LF ERTG+ + IE +L AE+ GLL+R++ I
Sbjct: 316 EREVGARDLPFEFMLNALRLTDGVPAHLFQERTGLPLAAIEPQLAAAEQRGLLERDHTRI 375
Query: 372 KPTSFGRYFLNDLQQIFL 389
+PT G+ FLNDLQ++FL
Sbjct: 376 RPTPLGQRFLNDLQELFL 393
>gnl|CDD|235550 PRK05660, PRK05660, HemN family oxidoreductase; Provisional.
Length = 378
Score = 448 bits (1155), Expect = e-158
Identities = 168/379 (44%), Positives = 236/379 (62%), Gaps = 7/379 (1%)
Query: 13 KLPPLSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILNRKIHTI 72
KLPPLSLYIH PWC++KCPYCDF+S+ +K + E +Y++ LL D++ LP++ R++H+I
Sbjct: 3 KLPPLSLYIHIPWCVQKCPYCDFNSHALKGEVPEDEYVDHLLADLDADLPLVQGREVHSI 62
Query: 73 FIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLS 132
FIGGGTPSL S + LL ++ L F + IT+EANP T E ++F Y G+NR+S
Sbjct: 63 FIGGGTPSLFSAEAIQRLLDGVRARLPFAPDAEITMEANPGTVEADRFVGYQRAGVNRIS 122
Query: 133 IGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY-FNNFNLDLIYALPNQTLSELMLDLNY 191
IG+QSF+ + L LGR H +AK A ++A+ +FNLDL++ LP+Q+L E + DL
Sbjct: 123 IGVQSFSEEKLKRLGRIHGPDEAKRAAKLAQGLGLRSFNLDLMHGLPDQSLEEALDDLRQ 182
Query: 192 AIQYSPPHLSLYSLTIEPNTYFFKYPPLSMPSNDENAVMQDKITSLLKNNYYKNYEISAY 251
AI +PPHLS Y LTIEPNT F PP +P +D + ++ LL Y+ YE SAY
Sbjct: 183 AIALNPPHLSWYQLTIEPNTLFGSRPP-VLPDDDALWDIFEQGHQLLTAAGYQQYETSAY 241
Query: 252 SKTGYESQHNLNYWKFGDYLGIGAGSHSKLSFPN-YIIRQIRYKNPNIYLKNIFSGNSIA 310
+K GY+ QHNLNYW+FGDYLGIG G+H KL+FP+ I+R + K+P Y+ G +
Sbjct: 242 AKPGYQCQHNLNYWRFGDYLGIGCGAHGKLTFPDGRILRTWKTKHPRGYM----QGRYLD 297
Query: 311 KSKKIEKKCLIFEFMLNALRLKDGFSPNLFFERTGINIKIIESKLKNAEKLGLLKRNNKN 370
+ +E FEF +N RL + F TG+ +I +L A G L +
Sbjct: 298 GQRDVEAADRPFEFFMNRFRLLEAAPRADFEAYTGLPESVIRPQLDEALAQGYLTETADH 357
Query: 371 IKPTSFGRYFLNDLQQIFL 389
+ T G+ FLNDL ++FL
Sbjct: 358 WQITEHGKLFLNDLLELFL 376
>gnl|CDD|223708 COG0635, HemN, Coproporphyrinogen III oxidase and related Fe-S
oxidoreductases [Coenzyme metabolism].
Length = 416
Score = 362 bits (932), Expect = e-123
Identities = 159/390 (40%), Positives = 227/390 (58%), Gaps = 12/390 (3%)
Query: 8 NLYIKKLP-PLSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPII-L 65
Y+ LP PLSLYIH P+C+ KCPYCDF+S+ K+ +YL+ALL ++EL ++
Sbjct: 25 EAYMTALPKPLSLYIHIPFCVSKCPYCDFNSHVTKRGQPVDEYLDALLEEIELVAALLGG 84
Query: 66 NRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLL-LFKKNISITLEANPSTFEIEKFHSYS 124
R++ TI+ GGGTPSL+S L+ LLK +++L + IT+EANP T E EKF +
Sbjct: 85 QREVKTIYFGGGTPSLLSPEQLERLLKALRELFNDLDPDAEITIEANPGTVEAEKFKALK 144
Query: 125 IIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY-FNNFNLDLIYALPNQTLS 183
G+NR+S+G+QSFN++ L LGR HD ++AK A+E+A++ F + N+DLIY LP QTL
Sbjct: 145 EAGVNRISLGVQSFNDEVLKALGRIHDEEEAKEAVELARKAGFTSINIDLIYGLPGQTLE 204
Query: 184 ELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFKYP--PLSMPSNDENAVMQDKITSLLKNN 241
L DL A++ P HLSLYSL IEP T F + ++P DE A M + + LL+
Sbjct: 205 SLKEDLEQALELGPDHLSLYSLAIEPGTKFAQRKIKGKALPDEDEKADMYELVEELLEKA 264
Query: 242 YYKNYEISAYSKTGYESQHNLNYWKFGDYLGIGAGSHSKLSFPNYIIRQIRYKNPNIYLK 301
Y+ YEIS ++K G E +HNL YW+ DYLGIGAG+H ++ R KN YL+
Sbjct: 265 GYRQYEISNFAKPGGECRHNLQYWETKDYLGIGAGAHGRIGG----TRYQNKKNLKTYLE 320
Query: 302 NIFSGNS-IAKSKKIEKKCLIFEFMLNALRLKDGFSPNLFFERTGI-NIKIIESKLKNAE 359
+ G + + +++ LI E ++ LRL G ER GI I L
Sbjct: 321 AVDEGGLPLVEGEELTPDDLIREALILGLRLNFGVDLAELEERFGIFKFAEILELLAELI 380
Query: 360 KLGLLKRNNKNIKPTSFGRYFLNDLQQIFL 389
GLL+ + ++ T GR L + + F
Sbjct: 381 ADGLLELDGDRLRLTEKGRLLLRSIAEAFD 410
>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 = 300 bits (769), Expect = e-100
Identities = 124/353 (35%), Positives = 186/353 (52%), Gaps = 12/353 (3%)
Query: 17 LSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILNRKIHTIFIGG 76
+SLYIH P+C KC YCDF+SYE K + +++Y +AL D++ +L + +IFIGG
Sbjct: 1 MSLYIHIPFCENKCGYCDFNSYENK-SGPKEEYTQALCQDLKHALSQTDQEPLESIFIGG 59
Query: 77 GTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIGIQ 136
GTP+ +S + L ++I + + IT EANP E GINRLS+G+Q
Sbjct: 60 GTPNTLSVEAFERLFESIYQHASLSDDCEITTEANPELITAEWCKGLKGAGINRLSLGVQ 119
Query: 137 SFNNKYLNILGRTHDSKQAKYAIEIAKQY-FNNFNLDLIYALPNQTLSELMLDLNYAIQY 195
SF + L LGR H +K AIE A + N +LDL+Y LP QTL+ L +L A +
Sbjct: 120 SFRDDKLLFLGRQHSAKNIAPAIETALKSGIENISLDLMYGLPLQTLNSLKEELKLAKEL 179
Query: 196 SPPHLSLYSLTIEPNTYFFKYPPLSMPSNDENAVMQDKITSLLKNNYYKNYEISAYSKTG 255
HLS Y+L++EPNT F K +P +D A + + +L+ +K YE+S Y+K G
Sbjct: 180 PINHLSAYALSVEPNTNFEKNAK-KLPDDDSCAHFDEVVREILEGFGFKQYEVSNYAKAG 238
Query: 256 YESQHNLNYWKFGDYLGIGAGSHSKLSFPN-YIIRQIRYKNPNIYLKNIFSGNSIAKSKK 314
Y+ +HNL YW DYLG GAG+H ++ + + I+ + + + + N K
Sbjct: 239 YQVKHNLAYWGAKDYLGCGAGAHGCVANERFFAKKLIKNYIKDPLQRGVETLN----EKN 294
Query: 315 IEKKCLIFEFMLNALRLKDGFSPNLFFERTGINIKIIESKLKNAEKLGLLKRN 367
+ K+ E + LR G + F E G++ + K E +K N
Sbjct: 295 VPKQDKRLEKLFLGLRCVLGVEKSFFDENKGLS----QVKFLIEENKAFIKNN 343
>gnl|CDD|181629 PRK09057, PRK09057, coproporphyrinogen III oxidase; Provisional.
Length = 380
Score = 295 bits (758), Expect = 1e-97
Identities = 126/373 (33%), Positives = 203/373 (54%), Gaps = 8/373 (2%)
Query: 15 PPLSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILNRKIHTIFI 74
LY+H+P+C+ KCPYCDF+S+ ++ I + ++ A L ++ R + +IF
Sbjct: 3 GGFGLYVHWPFCLAKCPYCDFNSH-VRHAIDQARFAAAFLRELATEAARTGPRTLTSIFF 61
Query: 75 GGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIG 134
GGGTPSL+ + LL I +L +I ITLEANP++ E +F Y G+NR+S+G
Sbjct: 62 GGGTPSLMQPETVAALLDAIARLWPVADDIEITLEANPTSVEAGRFRGYRAAGVNRVSLG 121
Query: 135 IQSFNNKYLNILGRTHDSKQAKYAIEIAKQYFNNFNLDLIYALPNQTLSELMLDLNYAIQ 194
+Q+ N+ L LGR H +A AI++A++ F + DLIYA P QTL+ +L A+
Sbjct: 122 VQALNDADLRFLGRLHSVAEALAAIDLAREIFPRVSFDLIYARPGQTLAAWRAELKEALS 181
Query: 195 YSPPHLSLYSLTIEPNTYFF---KYPPLSMPSNDENAVMQDKITSLLKNNYYKNYEISAY 251
+ HLSLY LTIE T F+ L +P D A + + + YEIS +
Sbjct: 182 LAADHLSLYQLTIEEGTAFYGLHAAGKLILPDEDLAADLYELTQEITAAAGLPAYEISNH 241
Query: 252 SKTGYESQHNLNYWKFGDYLGIGAGSHSKLSFPNYIIRQIRYKNPNIYLKNI-FSGNSIA 310
++ G ES+HNL YW++GDY GIG G+H +L+ K P +L+ + +G+ I
Sbjct: 242 ARPGAESRHNLTYWRYGDYAGIGPGAHGRLTLGGERHATATEKAPEAWLERVERNGHGII 301
Query: 311 KSKKIEKKCLIFEFMLNALRLKDGFSPNLFFERTGINIKIIESKLKNAEKLGLLKR-NNK 369
+ ++++ + EF+L LRL++G + +G + +L + + GL++R
Sbjct: 302 EEERLDPEERADEFLLMGLRLREGIDLARYAALSGRPLD--PERLADLIEEGLIERDGGS 359
Query: 370 NIKPTSFGRYFLN 382
++ T GR L+
Sbjct: 360 RLRATPAGRLVLD 372
>gnl|CDD|236309 PRK08599, PRK08599, coproporphyrinogen III oxidase; Provisional.
Length = 377
Score = 268 bits (688), Expect = 3e-87
Identities = 134/384 (34%), Positives = 206/384 (53%), Gaps = 20/384 (5%)
Query: 16 PLSLYIHFPWCIKKCPYCDFHSYEIKKN-ISEKKYLEALLIDVELSLPIILNRKIHTIFI 74
P S YIH P+C C YCDF+ IK + E YL+AL+ ++ + I K+ TI+I
Sbjct: 1 PTSAYIHIPFCEHICYYCDFNKVFIKNQPVDE--YLDALIKEM-NTYAIRPFDKLKTIYI 57
Query: 75 GGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIG 134
GGGTP+ +S L+ LL I + L T EANP EK G+NR+S+G
Sbjct: 58 GGGTPTALSAEQLERLLTAIHRNLPLSGLEEFTFEANPGDLTKEKLQVLKDSGVNRISLG 117
Query: 135 IQSFNNKYLNILGRTHDSKQAKYAIEIAKQY-FNNFNLDLIYALPNQTLSELMLDLNYAI 193
+Q+FN++ L +GRTH+ + AI AK+ F+N ++DLIYALP QT+ + L A+
Sbjct: 118 VQTFNDELLKKIGRTHNEEDVYEAIANAKKAGFDNISIDLIYALPGQTIEDFKESLAKAL 177
Query: 194 QYSPPHLSLYSLTIEPNTYFF---KYPPLSMPSNDENAVMQDKITSLLKNNYYKNYEISA 250
PH S YSL +EP T F+ + L +P D A M + + ++ + + YEIS
Sbjct: 178 ALDIPHYSAYSLILEPKTVFYNLMRKGKLRLPGEDLEAEMYEYLMDEMEAHGFHQYEISN 237
Query: 251 YSKTGYESQHNLNYWKFGDYLGIGAGSHSKLSFPNYIIRQIRYKN--P-NIYLKNIFS-G 306
++K G+ES+HNL YW +Y G GAG+ ++ +RY+N P YLK I G
Sbjct: 238 FAKPGFESRHNLTYWNNEEYYGFGAGASGYVN-------GVRYQNIGPIKHYLKAINEEG 290
Query: 307 NSIAKSKKIEKKCLIFEFMLNALRLKDGFSPNLFFERTGINI-KIIESKLKNAEKLGLLK 365
+ + KK + E M LR K G S F E+ G + + ++ ++ GLL+
Sbjct: 291 LPRLEEHVLTKKEQMEEEMFLGLRKKSGVSKARFEEKFGQSFEDVFGETIQELQEQGLLE 350
Query: 366 RNNKNIKPTSFGRYFLNDLQQIFL 389
++ +++ T G++ N++ + FL
Sbjct: 351 EDDDHVRLTKKGKFLGNEVFEAFL 374
>gnl|CDD|180263 PRK05799, PRK05799, coproporphyrinogen III oxidase; Provisional.
Length = 374
Score = 252 bits (647), Expect = 3e-81
Identities = 141/371 (38%), Positives = 200/371 (53%), Gaps = 21/371 (5%)
Query: 16 PLSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILNRKIHTIFIG 75
+SLYIH P+C +KC YCDF SY K+++ + Y++AL ++ S N+KI +IFIG
Sbjct: 3 EISLYIHIPFCKQKCLYCDFPSYSGKEDLMME-YIKALSKEIRNS---TKNKKIKSIFIG 58
Query: 76 GGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIGI 135
GGTP+ +S L+ L + IKKL K+++ T+E NP TF EK +G+NRLSIG+
Sbjct: 59 GGTPTYLSLEALEILKETIKKLNK-KEDLEFTVEGNPGTFTEEKLKILKSMGVNRLSIGL 117
Query: 136 QSFNNKYLNILGRTHDSKQAKYAIEIAKQY-FNNFNLDLIYALPNQTLSELMLDLNYAIQ 194
Q++ N L LGR H ++ ++A++ FNN N+DL++ LPNQTL + L ++
Sbjct: 118 QAWQNSLLKYLGRIHTFEEFLENYKLARKLGFNNINVDLMFGLPNQTLEDWKETLEKVVE 177
Query: 195 YSPPHLSLYSLTIEPNTYFFKY---PPLSMPSNDENAVMQDKITSLLKNNYYKNYEISAY 251
+P H+S YSL IE T F+ L +P +E M LK Y YEIS +
Sbjct: 178 LNPEHISCYSLIIEEGTPFYNLYENGKLKLPDEEEEREMYHYTIEFLKEKGYHQYEISNF 237
Query: 252 SKTGYESQHNLNYWKFGDYLGIGAGSHSKLSFPNYIIRQIRYKN-PNI--YLKNIFSGNS 308
+K G E +HNL YW +Y+G GAG+HS + RY+N NI Y+K I NS
Sbjct: 238 AKPGKECRHNLVYWDLEEYIGCGAGAHS-------YVNGKRYENISNIEKYIKEINENNS 290
Query: 309 IAKSK-KIEKKCLIFEFMLNALRLKDGFSPNLFFERTGINI-KIIESKLKNAEKLGLLKR 366
+ K K + EFM LR G F +R G NI ++ + KLGLL
Sbjct: 291 AVEEIHKNSIKDNMEEFMFMGLRKIKGICIEDFKKRFGKNIYEVYGEVINKYIKLGLLIE 350
Query: 367 NNKNIKPTSFG 377
I + G
Sbjct: 351 KEGRIYLSERG 361
>gnl|CDD|180630 PRK06582, PRK06582, coproporphyrinogen III oxidase; Provisional.
Length = 390
Score = 251 bits (643), Expect = 2e-80
Identities = 137/368 (37%), Positives = 204/368 (55%), Gaps = 9/368 (2%)
Query: 17 LSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILNRKIHTIFIGG 76
LS+YIH+P+C+ KCPYCDF+S+ + I ++L++ ++E II N+ I +IF GG
Sbjct: 12 LSIYIHWPFCLSKCPYCDFNSH-VASTIDHNQWLKSYEKEIEYFKDIIQNKYIKSIFFGG 70
Query: 77 GTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIGIQ 136
GTPSL++ ++ ++ I L + ITLE NP++FE EKF ++ + GINR+SIG+Q
Sbjct: 71 GTPSLMNPVIVEGIINKISNLAIIDNQTEITLETNPTSFETEKFKAFKLAGINRVSIGVQ 130
Query: 137 SFNNKYLNILGRTHDSKQAKYAIEIAKQYFNNFNLDLIYALPNQTLSELMLDLNYAIQYS 196
S L LGRTHD QA IE A F + DLIYA QTL + +L A+Q +
Sbjct: 131 SLKEDDLKKLGRTHDCMQAIKTIEAANTIFPRVSFDLIYARSGQTLKDWQEELKQAMQLA 190
Query: 197 PPHLSLYSLTIEPNTYF---FKYPPLSMPSNDENAVMQDKITSLLKNNYYKNYEISAYSK 253
H+SLY LTIE T F FK L +P +D A M + L++ Y YEIS Y+K
Sbjct: 191 TSHISLYQLTIEKGTPFYKLFKEGNLILPHSDAAAEMYEWTNHYLESKKYFRYEISNYAK 250
Query: 254 TGYESQHNLNYWKFGDYLGIGAGSHSKLSFPNYIIRQIR-YKNPNIYLKNI-FSGNSIAK 311
G E HNL YW + YLGIG G+HS++ + + I + P +L + I
Sbjct: 251 IGQECLHNLTYWNYNSYLGIGPGAHSRIIESSSSVSAIMMWHKPEKWLDAVKTKNVGIQT 310
Query: 312 SKKIEKKCLIFEFMLNALRLKDGFSPNLFFERTGINIKIIES--KLKNAEKLGLLKRNNK 369
+ K+ + +I E ++ LRL G + + ++ ++ I LK+ + L L++ +
Sbjct: 311 NTKLTHQEIIEEILMMGLRLSKGINISTLEQKLNTKLENILDMNNLKHYQALDLIRLDE- 369
Query: 370 NIKPTSFG 377
NI T G
Sbjct: 370 NIYLTDKG 377
>gnl|CDD|180518 PRK06294, PRK06294, coproporphyrinogen III oxidase; Provisional.
Length = 370
Score = 211 bits (539), Expect = 5e-65
Identities = 123/374 (32%), Positives = 195/374 (52%), Gaps = 27/374 (7%)
Query: 16 PLSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLID-VELSLPIILNRKIHTIFI 74
PL+LYIH P+C KKC YC F++ K+ S Y A+L + ++ P+ + I T+F
Sbjct: 6 PLALYIHIPFCTKKCHYCSFYTIPYKEE-SVSLYCNAVLKEGLKKLAPLRCSHFIDTVFF 64
Query: 75 GGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIG 134
GGGTPSL+ L+++I K L ITLEANP + ++ GINR+SIG
Sbjct: 65 GGGTPSLVP----PALIQDILKTLEAPHATEITLEANPENLSESYIRALALTGINRISIG 120
Query: 135 IQSFNNKYLNILGRTHDSKQAKYAIEIAKQY-FNNFNLDLIYALPNQTLSELMLDLNYAI 193
+Q+F++ L +LGRTH S +A A++ ++ F+N ++DLIY LP Q+LS+ ++DL+ AI
Sbjct: 121 VQTFDDPLLKLLGRTHSSSKAIDAVQECSEHGFSNLSIDLIYGLPTQSLSDFIVDLHQAI 180
Query: 194 QYSPPHLSLYSLTIEPNTYFFKYPPL---SMPSNDENAVMQDKITSLLKNNYYKNYEISA 250
H+SLY+LTI+P+T F+K+ S+ + A M LL + + YE+++
Sbjct: 181 TLPITHISLYNLTIDPHTSFYKHRKRLLPSIADEEILAEMSLAAEELLTSQGFTRYELAS 240
Query: 251 YSKTGYESQHNLNYWKFGDYLGIGAGSHSKLSFPNYIIRQIRYKN-PNI--YLKNIFSGN 307
Y+K +S+HN YW +LG+G + L IR KN I YL+ +
Sbjct: 241 YAKPQAQSKHNTYYWTDRPFLGLGVSASQYLH-------GIRSKNLSRISHYLRALRKNL 293
Query: 308 SIAKS-KKIEKKCLIFEFMLNALRLKDGFSPNLFFERTGINIKIIESKLKNAEKLGLLKR 366
+S +++ I E + LRL +G F + + + L +
Sbjct: 294 PTQESSEELPPNERIKEALALRLRLCEGIPLADFPSE------LTSELIMHPIIQELFTK 347
Query: 367 NNKNIKPTSFGRYF 380
N++ + GR F
Sbjct: 348 NDQALSLNKKGRLF 361
>gnl|CDD|180172 PRK05628, PRK05628, coproporphyrinogen III oxidase; Validated.
Length = 375
Score = 204 bits (520), Expect = 3e-62
Identities = 108/377 (28%), Positives = 179/377 (47%), Gaps = 27/377 (7%)
Query: 16 PLSLYIHFPWCIKKCPYCDFHSY---EIKKNISEKKYLEALLIDVELSLPIILN--RKIH 70
P +Y+H P+C +C YCDF++Y E+ S YL+AL ++EL+ ++ + +
Sbjct: 2 PFGVYVHVPFCATRCGYCDFNTYTAAELGGGASPDGYLDALRAELELAAAVLGDPAPPVS 61
Query: 71 TIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINR 130
T+F+GGGTPSL+ GL +L ++ +T EANP + E F + G R
Sbjct: 62 TVFVGGGTPSLLGAEGLARVLDAVRDTFGLAPGAEVTTEANPESTSPEFFAALRAAGFTR 121
Query: 131 LSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY-FNNFNLDLIYALPNQTLSELMLDL 189
+S+G+QS L +L RTH +A A A+ F + NLDLIY P ++ + L
Sbjct: 122 VSLGMQSAAPHVLAVLDRTHTPGRAVAAAREARAAGFEHVNLDLIYGTPGESDDDWRASL 181
Query: 190 NYAIQYSPPHLSLYSLTIEPNTYF---FKYPPLSMPSNDENAVMQDKITSLLKNNYYKNY 246
+ A++ H+S Y+L +E T + L P +D A + + L + Y
Sbjct: 182 DAALEAGVDHVSAYALIVEDGTALARRVRRGELPAPDDDVLADRYELADARLSAAGFDWY 241
Query: 247 EISAYSKTGYESQHNLNYWKFGDYLGIGAGSHSKLSFPNYIIRQIRY---KNPNIYLKNI 303
E+S +++ G E +HNL YW+ GD+ G G G+HS + +R+ K+P Y +
Sbjct: 242 EVSNWARPGGECRHNLGYWRGGDWWGAGPGAHSH-------VGGVRWWNVKHPAAYAARL 294
Query: 304 FSGNS-IAKSKKIEKKCLIFEFMLNALRLKDGFSPNLFFERTGINIKIIESKLKNAEKLG 362
+G +A + ++ + E ++ LRL++G L ++ G
Sbjct: 295 AAGALPVAGREVLDAEDRHVERVMLGLRLREGLPLALLDAAE-------RARAARVVADG 347
Query: 363 LLKRNNKNIKPTSFGRY 379
LL + T GR
Sbjct: 348 LLAAEGGRLVLTLRGRL 364
>gnl|CDD|236007 PRK07379, PRK07379, coproporphyrinogen III oxidase; Provisional.
Length = 400
Score = 204 bits (520), Expect = 5e-62
Identities = 104/280 (37%), Positives = 153/280 (54%), Gaps = 20/280 (7%)
Query: 14 LPPLSLYIHFPWCIKKCPYCDFH--------SYEIKKNISEKKYLEALLIDVELSLPIIL 65
L P S YIH P+C ++C YCDF I E Y+E L E+++
Sbjct: 8 LLPTSAYIHIPFCRRRCFYCDFPISVVGDRTRGGTSGLIEE--YVEVLC--QEIAITPSF 63
Query: 66 NRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSI 125
+ + T+F GGGTPSL+S L+ +L + + + I+LE +P TF++E+ Y
Sbjct: 64 GQPLQTVFFGGGTPSLLSVEQLERILTTLDQRFGIAPDAEISLEIDPGTFDLEQLQGYRS 123
Query: 126 IGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIE-IAKQYFNNFNLDLIYALPNQTLSE 184
+G+NR+S+G+Q+F ++ L + GR+H K A++ I + NF+LDLI LP+QTL +
Sbjct: 124 LGVNRVSLGVQAFQDELLALCGRSHRVKDIFAAVDLIHQAGIENFSLDLISGLPHQTLED 183
Query: 185 LMLDLNYAIQYSPPHLSLYSLTIEPNTYFFKY--P---PLSMPSNDENAVMQDKITSLLK 239
L AI +P HLS Y L +EP T F K P PL PS++ A M +L
Sbjct: 184 WQASLEAAIALNPTHLSCYDLVLEPGTAFGKQYQPGKAPL--PSDETTAAMYRLAQEILT 241
Query: 240 NNYYKNYEISAYSKTGYESQHNLNYWKFGDYLGIGAGSHS 279
Y++YEIS Y+K GY+ +HN YW+ Y G G G+ S
Sbjct: 242 QAGYEHYEISNYAKPGYQCRHNRVYWENRPYYGFGMGAAS 281
>gnl|CDD|181428 PRK08446, PRK08446, coproporphyrinogen III oxidase; Provisional.
Length = 350
Score = 199 bits (508), Expect = 9e-61
Identities = 113/287 (39%), Positives = 157/287 (54%), Gaps = 17/287 (5%)
Query: 19 LYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILNRKIHTIFIGGGT 78
LYIH P+C KC YC F+SYE K+ +K+Y++AL +D++ L + KI ++FIGGGT
Sbjct: 3 LYIHIPFCESKCGYCAFNSYE-NKHDLKKEYMQALCLDLKFELEQFTDEKIESVFIGGGT 61
Query: 79 PSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIGIQSF 138
PS +S + + + I L K+ IT EANP++ +G+NR+S G+QSF
Sbjct: 62 PSTVSAKFYEPIFEIISPYL--SKDCEITTEANPNSATKAWLKGMKNLGVNRISFGVQSF 119
Query: 139 NNKYLNILGRTHDSKQAKYAIEIAKQY-FNNFNLDLIYALPNQTLSELMLDLNYAIQYSP 197
N L LGR H KQ AIE AK+ F N ++DLIY P L +L A +
Sbjct: 120 NEDKLKFLGRIHSQKQIIKAIENAKKAGFENISIDLIYDTPLDNKKLLKEELKLAKELPI 179
Query: 198 PHLSLYSLTIEPNTYFFKYPPLSMPSNDENAVMQDKITSLLKNNYYKNYEISAYSKTGYE 257
HLS YSLTIE NT FF+ +DEN + L+ +K YEIS + K Y+
Sbjct: 180 NHLSAYSLTIEENTPFFEKN--HKKKDDEN--LAKFFIEQLEELGFKQYEISNFGK-NYQ 234
Query: 258 SQHNLNYWKFGDYLGIGAGSHSKLSFPNYIIRQIRYKNPNI--YLKN 302
+HNL YW+ DYLG GAG+ ++ + Y N+ Y+KN
Sbjct: 235 CKHNLGYWQGKDYLGCGAGAVGFVANKRF------YPKKNLENYIKN 275
>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 = 150 bits (380), Expect = 2e-43
Identities = 70/218 (32%), Positives = 116/218 (53%), Gaps = 6/218 (2%)
Query: 16 PLSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVE-LSLPIILNRKIHTIFI 74
PL+LYI C ++C +C F S K +YLEAL+ ++E L+ + T+FI
Sbjct: 1 PLALYIITRGCPRRCTFCSFPSLRGK---LRSRYLEALVREIELLAEKGEKEGLVGTVFI 57
Query: 75 GGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIG 134
GGGTP+L+S L+ LL+ I+++L K++ IT+E P T E + G+NR+S+G
Sbjct: 58 GGGTPTLLSPEQLEELLEAIREILGLAKDVEITIETRPDTLTEELLEALKEAGVNRVSLG 117
Query: 135 IQSFNNKYLNILGRTHDSKQAKYAIEIAKQYFN-NFNLDLIYALPNQTLSELMLDLNYAI 193
+QS +++ L + R H + A+E+ ++ + DLI LP +T + L
Sbjct: 118 VQSGDDEVLKAINRGHTVEDVLEAVELLREAGPIKVSTDLIVGLPGETEEDFEETLKLLK 177
Query: 194 QYSPPHLSLYSLTIEPNTYFFK-YPPLSMPSNDENAVM 230
+ P +S++ L+ P T K Y L P+ +E A +
Sbjct: 178 ELGPDRVSIFPLSPRPGTPLAKMYKRLKPPTKEERAEL 215
>gnl|CDD|235641 PRK05904, PRK05904, coproporphyrinogen III oxidase; Provisional.
Length = 353
Score = 141 bits (356), Expect = 1e-38
Identities = 99/322 (30%), Positives = 154/322 (47%), Gaps = 21/322 (6%)
Query: 19 LYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILNRKIHTIFIGGGT 78
LYIH P+C C +CDF I K KK + L ++++ + ++ TI++GGGT
Sbjct: 9 LYIHIPFCQYICTFCDF--KRILKTPQTKKIFKDFLKNIKMHIKNFKIKQFKTIYLGGGT 66
Query: 79 PSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIGIQSF 138
P+ ++D LD LL IK + N T+E NP + + +NR+S+G+QS
Sbjct: 67 PNCLNDQLLDILLSTIKPYV--DNNCEFTIECNPELITQSQINLLKKNKVNRISLGVQSM 124
Query: 139 NNKYLNILGRTHDSKQAKYAIE-IAKQYFNNFNLDLIYALPNQTLSELMLDLNYAIQYSP 197
NN L L RTH + +K AI + K N + D +Y LP L +L N+ +++
Sbjct: 125 NNNILKQLNRTHTIQDSKEAINLLHKNGIYNISCDFLYCLPILKLKDLDEVFNFILKHKI 184
Query: 198 PHLSLYSLTIEPNTYFFKYPPLSMPSNDENAVMQDKITSLLKNNYYKNYEISAY-SKTGY 256
H+S YSL I+ + KY ++ + E + K NY + YE+S + + Y
Sbjct: 185 NHISFYSLEIKEGSILKKY-HYTIDEDKEAEQLNYIKAKFNKLNYKR-YEVSNWTNNFKY 242
Query: 257 ESQHNLNYWKFGDYLGIGAGSHSKLSFPNYIIRQIRYKNPNIYLKNIFSGNSIAKSKKIE 316
S+HNL YW+ D+ IG G+H ++N Y + N I K +
Sbjct: 243 ISKHNLAYWRTKDWAAIGWGAHG-------------FENNIEYFFDGSIQNWILIKKVLT 289
Query: 317 KKCLIFEFMLNALRLKDGFSPN 338
L + ++ LRLKDG N
Sbjct: 290 DHELYQQILIMGLRLKDGLDLN 311
>gnl|CDD|236187 PRK08207, PRK08207, coproporphyrinogen III oxidase; Provisional.
Length = 488
Score = 143 bits (364), Expect = 1e-38
Identities = 93/316 (29%), Positives = 145/316 (45%), Gaps = 38/316 (12%)
Query: 18 SLYIHFPWCIKKCPYCDFHSYEIKKNISEKK-YLEALLIDVELSLPII--LNRKIHTIFI 74
S+YI P+C +C YC F SY IK + YLEAL ++E + KI TI+
Sbjct: 165 SIYIGIPFCPTRCLYCSFPSYPIKGYKGLVEPYLEALHYEIEEIGKYLKEKGLKITTIYF 224
Query: 75 GGGTPSLISDTGLDYLLKNIKKLLLFKKNIS-ITLEAN-PSTFEIEKFHSYSIIGINRLS 132
GGGTP+ ++ L+ LL+ I + KN+ T+EA P T EK G++R+S
Sbjct: 225 GGGTPTSLTAEELERLLEEIYENFPDVKNVKEFTVEAGRPDTITEEKLEVLKKYGVDRIS 284
Query: 133 IGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY-FNNFNLDLIYALPNQTLSELMLDLNY 191
I Q+ N++ L +GR H + +A++ F+N N+DLI LP + L E+ L
Sbjct: 285 INPQTMNDETLKAIGRHHTVEDIIEKFHLAREMGFDNINMDLIIGLPGEGLEEVKHTLEE 344
Query: 192 AIQYSPPHLSLYSLTIE-PNTYFFKYPPLSMPSNDENAVMQDKITSLLKNNYYK------ 244
+ +P L++++L I+ + + +E M ++ K Y
Sbjct: 345 IEKLNPESLTVHTLAIKRASRLTENKEKYKVADREEIEKMMEEAEEWAKELGYVPYYLYR 404
Query: 245 ------NYEISAYSKTGYES---------QHNLNYWKFGDYLGIGAGSHSKLSFP--NYI 287
N E Y+K G ES + + +G+GAG+ SK FP N I
Sbjct: 405 QKNMLGNLENVGYAKPGKESIYNIQIMEEKQTI--------IGLGAGAVSKFVFPDENRI 456
Query: 288 IRQIRYKNPNIYLKNI 303
R K+P Y++ I
Sbjct: 457 ERFANPKDPKEYIERI 472
>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 = 137 bits (348), Expect = 8e-37
Identities = 98/310 (31%), Positives = 155/310 (50%), Gaps = 29/310 (9%)
Query: 18 SLYIHFPWCIKKCPYCDFHSYEI---KKNISEKKYLEALLIDVELSLPIILNRKIHTIFI 74
SLY+ P+C +C YC F SY I KK + E YL+AL ++E I+ K+ T++I
Sbjct: 86 SLYVGIPFCPTRCLYCSFTSYPIGKWKKRVDE--YLDALCKELEAVAKILKGLKLDTVYI 143
Query: 75 GGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEAN-PSTFEIEKFHSYSIIGINRLSI 133
GGGTP+ +S L+ LL I++ T+EA P + EK G+ R+SI
Sbjct: 144 GGGTPTTLSAEQLERLLGKIEENFDLSHLREFTVEAGRPDSITAEKLEVLKRHGVTRISI 203
Query: 134 GIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY-FNNFNLDLIYALPNQTLSELMLDLNYA 192
Q+ N+K L+++GR H + K A +A++ F+N N+DLI LP +TL ++ L
Sbjct: 204 NPQTMNDKTLDLIGRRHTVEDIKEAFALAREAGFDNINMDLIAGLPGETLEDVRDTLEQV 263
Query: 193 IQYSPPHLSLYSLTIEP----NTYFFKYPPLSMPSNDENAVMQDKITSLLKNN----YY- 243
+ +P +++++L I+ N KY +PS ++ A M D ++ YY
Sbjct: 264 KKLAPESITVHTLAIKRASRLNQEKDKY---QLPSFEDTAEMIDLAAEYARDMGMEPYYL 320
Query: 244 -------KNYEISAYSKTGYESQHN-LNYWKFGDYLGIGAGSHSKLSFP--NYIIRQIRY 293
N E Y+K G E +N L + + +GAG+ +KL FP I R
Sbjct: 321 YRQKNMAGNLENVGYAKPGKEGLYNILIMEEKQTIIALGAGASTKLVFPEGGRIERIENV 380
Query: 294 KNPNIYLKNI 303
K+ Y++ I
Sbjct: 381 KDVYEYIERI 390
>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 = 128 bits (323), Expect = 4e-33
Identities = 65/201 (32%), Positives = 99/201 (49%), Gaps = 14/201 (6%)
Query: 19 LYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALL--IDVELSLPIILNRKIHTIFIGG 76
LYIH P+C +C +C F + Y +AL+ + E +LP+ + IH ++IGG
Sbjct: 42 LYIHIPFCRTRCTFCGFFQNAWSPELGAA-YTDALIAELAAEAALPLTQSGPIHAVYIGG 100
Query: 77 GTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIGIQ 136
GTP+ +S L L++ I++ L + ITLE + F+ EK + G+NR SIG+Q
Sbjct: 101 GTPTALSADDLARLIRAIRRYLPLAPDCEITLEGRINGFDDEKADAALEAGVNRFSIGVQ 160
Query: 137 SFNNKYLNILGRTHDSKQAKYAIEIAKQYFNNFN-----LDLIYALPNQTLSELMLDLNY 191
SF+ + LGR D ++ +E + +DLIY LP QT DL
Sbjct: 161 SFDTEVRRRLGRKDDREEVLARLEELSAL----DRAAVVIDLIYGLPGQTDEIWQQDLRI 216
Query: 192 AIQYSPPH-LSLYSLTIEPNT 211
A + LY+L + P T
Sbjct: 217 AAD-LGLDGVDLYALNLFPGT 236
>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 = 127 bits (322), Expect = 5e-33
Identities = 102/422 (24%), Positives = 177/422 (41%), Gaps = 58/422 (13%)
Query: 4 KRFNNLYIKKLPPLSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPI 63
K P LSLY+H P+C K C +C + ++ YL+AL ++ L P+
Sbjct: 38 TAVARHNYPKTP-LSLYVHIPFCHKACYFCGCNVIITRQKHKADPYLDALEKEIALVAPL 96
Query: 64 I-LNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHS 122
NR + + GGGTP+ +S + L+K I++ F + I++E +P + +
Sbjct: 97 FDGNRHVSQLHWGGGTPTYLSPEQISRLMKLIRENFPFNADAEISIEIDPRYITKDVIDA 156
Query: 123 YSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY-FNNFNLDLIYALPNQT 181
G NRLS G+Q FN + + R + + A++ F + N+DLIY LP QT
Sbjct: 157 LRDEGFNRLSFGVQDFNKEVQQAVNRIQPEEMIFELMNHAREAGFTSINIDLIYGLPKQT 216
Query: 182 LSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFF--KYPPLSMPSNDEN-AVMQDKITSLL 238
L + +P L++++ P K P ++PS +E ++Q+ I L
Sbjct: 217 KESFAKTLEKVAELNPDRLAVFNYAHVPWVKPAQRKIPEAALPSAEEKLDILQETIAFLT 276
Query: 239 KNNY------------------------YKNYEISAYSKTGYESQHNLNYWKFGDYLGIG 274
+ Y ++N++ GY +Q K D LG G
Sbjct: 277 EAGYQFIGMDHFAKPDDELAVAQRKGELHRNFQ-------GYTTQ------KDTDLLGFG 323
Query: 275 AGSHSKLS---FPNYIIRQIRYKNPNIYLKNIFSGNSIAKSKKIEK---KCLIFEFMLNA 328
S S L N + YK + + G ++++ I + K L+ F L+
Sbjct: 324 VTSISMLGDCYAQNQKTLKQYYKAVDEGGNPVERGIALSQDDCIRREVIKSLMCNFKLDY 383
Query: 329 LRLKDGFSPNL--FFERTGINIKIIESKLKNAEKLGLLKRNNKNIKPTSFGRYFLNDLQQ 386
++++ F + +F + LK E+ GLL + K I+ T GR + ++
Sbjct: 384 SKIEEKFDLDFADYFAKE-------LELLKPLEEDGLLDVDEKGIEVTPKGRLLIRNIAM 436
Query: 387 IF 388
+F
Sbjct: 437 VF 438
>gnl|CDD|236368 PRK09058, PRK09058, coproporphyrinogen III oxidase; Provisional.
Length = 449
Score = 122 bits (308), Expect = 6e-31
Identities = 61/211 (28%), Positives = 94/211 (44%), Gaps = 34/211 (16%)
Query: 19 LYIHFPWCIKKCPYCDFHSYEIKKNISEKK----YLEALL--IDVELSLPIILNRKIHTI 72
LYIH P+C C +C F ++ N + Y +AL+ + +E P+ + IH +
Sbjct: 64 LYIHIPFCRTHCTFCGF--FQ---NAWNPEAVARYTDALIRELAMEADSPLTQSAPIHAV 118
Query: 73 FIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLS 132
+ GGGTP+ +S L L+ +++ L + ITLE + F+ EK + G NR S
Sbjct: 119 YFGGGTPTALSAEDLARLITALREYLPLAPDCEITLEGRINGFDDEKADAALDAGANRFS 178
Query: 133 IGIQSFNNKYLNILGRTHDSKQA-----------KYAIEIAKQYFNNFNLDLIYALPNQT 181
IG+QSFN + GR D ++ + A+ DLI+ LP QT
Sbjct: 179 IGVQSFNTQVRRRAGRKDDREEVLARLEELVARDRAAVVC----------DLIFGLPGQT 228
Query: 182 LSELMLDLNYAIQYSPPH-LSLYSLTIEPNT 211
DL + LY+L + P T
Sbjct: 229 PEIWQQDLAIVRD-LGLDGVDLYALNLLPGT 258
>gnl|CDD|181292 PRK08208, PRK08208, coproporphyrinogen III oxidase; Validated.
Length = 430
Score = 120 bits (303), Expect = 2e-30
Identities = 67/204 (32%), Positives = 106/204 (51%), Gaps = 2/204 (0%)
Query: 17 LSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILNRKIHTIFIGG 76
LSLYIH P+C +C +C+ + YL+AL+ E + + + +GG
Sbjct: 40 LSLYIHIPFCEMRCGFCNLFTRTGADAEFIDSYLDALIRQAEQVAEALAPARFASFAVGG 99
Query: 77 GTPSLISDTGLDYLLKNIKKLL-LFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIGI 135
GTP+L++ L+ L +++++L + NI ++E +P+T EK + G+NRLSIG+
Sbjct: 100 GTPTLLNAAELEKLFDSVERVLGVDLGNIPKSVETSPATTTAEKLALLAARGVNRLSIGV 159
Query: 136 QSFNNKYLNILGRTHDSKQAKYAIE-IAKQYFNNFNLDLIYALPNQTLSELMLDLNYAIQ 194
QSF++ L+ L R A+E I F N+DLIY +P QT + M L+ A+
Sbjct: 160 QSFHDSELHALHRPQKRADVHQALEWIRAAGFPILNIDLIYGIPGQTHASWMESLDQALV 219
Query: 195 YSPPHLSLYSLTIEPNTYFFKYPP 218
Y P L LY L + P T +
Sbjct: 220 YRPEELFLYPLYVRPLTGLGRRAR 243
>gnl|CDD|181509 PRK08629, PRK08629, coproporphyrinogen III oxidase; Provisional.
Length = 433
Score = 115 bits (290), Expect = 1e-28
Identities = 101/381 (26%), Positives = 165/381 (43%), Gaps = 51/381 (13%)
Query: 19 LYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILNRKIHTIFIGGGT 78
LY H P+C CPYC FH + K++ + + Y +L E+ + L ++++GGGT
Sbjct: 55 LYAHVPFCHTLCPYCSFHRFYFKEDKA-RAYFISL--RKEMEMVKELGYDFESMYVGGGT 111
Query: 79 PSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIGIQSF 138
+++ D L L+ KKL K+ ++ E++P+ + K + I+RLSIG+QSF
Sbjct: 112 TTILEDE-LAKTLELAKKLFSIKE---VSCESDPNHLDPPKLKQLKGL-IDRLSIGVQSF 166
Query: 139 NNKYLNILGRTH---DSKQAKYAIEIAKQYFNNFNLDLIYALPNQTLSELMLDLNYAIQY 195
N+ L ++ R ++ I AK F N+DLI+ P QT L DL+ A +
Sbjct: 167 NDDILKMVDRYEKFGSGQETFEKIMKAKGLFPIINVDLIFNFPGQTDEVLQHDLDIAKRL 226
Query: 196 SPPHLSLYSLTIEPNTYFFKYPPLSMPSNDENAVMQDKITSLLKNNYYKNYEISAYSKTG 255
P ++ Y L T L D I L Y + A+SK
Sbjct: 227 DPRQITTYPLMKSHQTRKSVKGSLGASQKDNERQYYQIINELFG-QYNQL-SAWAFSKKN 284
Query: 256 ------YESQHNLNYWKFGDYLGIGAGSHSKL---------SFPNYIIRQIRYKNPNIYL 300
Y ++ +YLG+G+GS S L S +Y R + I
Sbjct: 285 DEGFDEYVIDYD-------EYLGVGSGSFSFLDGTLYVNTFSLRDYQERIAAGQMGVIAQ 337
Query: 301 KNIFSGNSIAKSKKIEKKCL--IFEFMLNALRLKDGFSPNLFFERTGINIKIIESKLKNA 358
KN FS K + ++ + L +F L+ ++ F NL + +++ KL A
Sbjct: 338 KN-FS-----KKEVMQYRFLLGMFSGRLSIKYFRETFGVNL---DKALFKEMLLLKLIGA 388
Query: 359 EKLGLLKRNNKNIKPTSFGRY 379
+K + ++ T FG+Y
Sbjct: 389 -----IKNDPGDLIVTDFGKY 404
>gnl|CDD|236430 PRK09249, PRK09249, coproporphyrinogen III oxidase; Provisional.
Length = 453
Score = 110 bits (277), Expect = 1e-26
Identities = 65/240 (27%), Positives = 113/240 (47%), Gaps = 21/240 (8%)
Query: 16 PLSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPII-LNRKIHTIFI 74
PLSLY+H P+C C YC + + + YL+AL ++ L ++ R + +
Sbjct: 49 PLSLYVHIPFCRSLCYYCGCNKIITRDHEKADPYLDALEKEIALVAALLGPGRPVSQLHW 108
Query: 75 GGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKF-HSYSIIGINRLSI 133
GGGTP+ +S L L+ +++ F + I++E +P ++E + G NRLS+
Sbjct: 109 GGGTPTFLSPEQLRRLMALLREHFNFAPDAEISIEIDPRELDLEMLDALREL-GFNRLSL 167
Query: 134 GIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY-FNNFNLDLIYALPNQTLSELMLDLNYA 192
G+Q F+ + + R + +E A++ F + N+DLIY LP QT L
Sbjct: 168 GVQDFDPEVQKAVNRIQPFEFTFALVEAARELGFTSINIDLIYGLPKQTPESFARTLEKV 227
Query: 193 IQYSPPHLSLYSLTIEPNTY-----FFK----YPPLSMPSNDE-NAVMQDKITSLLKNNY 242
++ P L++++ Y FK +PS +E A++Q I +L + Y
Sbjct: 228 LELRPDRLAVFN-------YAHVPWLFKAQRKIDEADLPSPEEKLAILQQTIETLTEAGY 280
>gnl|CDD|237356 PRK13347, PRK13347, coproporphyrinogen III oxidase; Provisional.
Length = 453
Score = 108 bits (272), Expect = 5e-26
Identities = 84/397 (21%), Positives = 163/397 (41%), Gaps = 44/397 (11%)
Query: 15 PPLSLYIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILN-RKIHTIF 73
P+SLY+H P+C C +C ++ +++ + Y+ AL+ ++ L + R++ +
Sbjct: 49 EPVSLYLHVPFCRSLCWFCGCNTIITQRDAPVEAYVAALIREIRLVAASLPQRRRVSQLH 108
Query: 74 IGGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSI 133
GGGTP++++ + L+ ++ F I +E +P T E + + +G NR S
Sbjct: 109 WGGGTPTILNPDQFERLMAALRDAFDFAPEAEIAVEIDPRTVTAEMLQALAALGFNRASF 168
Query: 134 GIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY-FNNFNLDLIYALPNQTLSELMLDLNYA 192
G+Q F+ + + R + A+E+ + F + N DLIY LP+QT+ L+
Sbjct: 169 GVQDFDPQVQKAINRIQPEEMVARAVELLRAAGFESINFDLIYGLPHQTVESFRETLDKV 228
Query: 193 IQYSPPHLSLYSLTIEPNTYFFK----YPPLSMPSNDENA-VMQDKITSLLKNNYYK--- 244
I SP ++++ P K ++P +E + LL Y
Sbjct: 229 IALSPDRIAVFGYAHVP--SRRKNQRLIDEAALPDAEERLRQARAVADRLLAAGYVPIGL 286
Query: 245 ------NYEISAYSKTGYESQHNLNYW--KFGDYLGIGAGSHSKLSFPNYIIRQIRYKNP 296
+ E++ + G ++ Y + +G GA + S+ FP ++ I +
Sbjct: 287 DHFALPDDELAIAQREGRLHRNFQGYTTDRCETLIGFGASAISR--FPGGYVQNI--SSL 342
Query: 297 NIYLKNIFSGN-SIAKSKKIEKKCLI-----------FEFMLNALRLKDGFSPNLFFERT 344
Y + I +G I + + + F L A+ + GF F +
Sbjct: 343 KAYYRAIDAGRLPIERGYALSDDDRLRRAIIETLMCNFPVDLAAIAARHGFFARYFLDEL 402
Query: 345 GINIKIIESKLKNAEKLGLLKRNNKNIKPTSFGRYFL 381
++L+ GL+ + I+ T GR +
Sbjct: 403 --------ARLEPLAADGLVTIDGGGIRVTPEGRPLI 431
>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 = 89.5 bits (222), Expect = 3e-21
Identities = 39/167 (23%), Positives = 68/167 (40%), Gaps = 8/167 (4%)
Query: 20 YIHFPWCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILNRKIHTIFIGGGTP 79
I C +C YC F S + K E ++ + + + + GG P
Sbjct: 1 IIVTRGCNLRCTYCAFPSI-----RARGKGRELSPEEILEEAKELARLGVEVVILTGGEP 55
Query: 80 SLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIGIQSFN 139
L+ D L + I ITLE N + + E G++R+SI +QS +
Sbjct: 56 LLLPDLVELLE---RLLKLREGEGIRITLETNGTLLDEELLEELKEAGLDRVSISLQSGD 112
Query: 140 NKYLNILGRTHDSKQAKYAIEIAKQYFNNFNLDLIYALPNQTLSELM 186
++ L I+ R H ++ A+E+ ++ +D I LP + +L
Sbjct: 113 DEVLKIINRGHTFEEVLEALELLREAGIPVVVDNIVGLPGENDEDLE 159
>gnl|CDD|100105 cd01335, Radical_SAM, Radical SAM superfamily. Enzymes of this
family generate radicals by combining a 4Fe-4S cluster
and S-adenosylmethionine (SAM) in close proximity. They
are characterized by a conserved CxxxCxxC motif, which
coordinates the conserved iron-sulfur cluster.
Mechanistically, they share the transfer of a single
electron from the iron-sulfur cluster to SAM, which
leads to its reductive cleavage to methionine and a
5'-deoxyadenosyl radical, which, in turn, abstracts a
hydrogen from the appropriately positioned carbon atom.
Depending on the enzyme, SAM is consumed during this
process or it is restored and reused. Radical SAM
enzymes catalyze steps in metabolism, DNA repair, the
biosynthesis of vitamins and coenzymes, and the
biosynthesis of many antibiotics. Examples are biotin
synthase (BioB), lipoyl synthase (LipA), pyruvate
formate-lyase (PFL), coproporphyrinogen oxidase (HemN),
lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide
reductase (ARR), and MoaA, an enzyme of the
biosynthesis of molybdopterin.
Length = 204
Score = 58.1 bits (140), Expect = 6e-10
Identities = 39/193 (20%), Positives = 76/193 (39%), Gaps = 12/193 (6%)
Query: 25 WCIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISD 84
C C +C + + + S + E L I +E R + + + GG P L
Sbjct: 6 GCNLNCGFCSNPASKGRGPESPPEIEEILDIVLEA-----KERGVEVVILTGGEPLL--Y 58
Query: 85 TGLDYLLKNIKKLLLFKKNISITLEANPSTFEIEKFHSYSIIGINRLSIGIQSFNNK-YL 143
L LL+ +KK L I++E N + E +G++ + + + S + +
Sbjct: 59 PELAELLRRLKKEL---PGFEISIETNGTLLTEELLKELKELGLDGVGVSLDSGDEEVAD 115
Query: 144 NILGRTHDSKQAKYAIEIAKQYFNNFNLDLIYALPNQTLSELMLDLNYAIQ-YSPPHLSL 202
I G K+ A++ ++ + L+ L ++ + + +L + SP +SL
Sbjct: 116 KIRGSGESFKERLEALKELREAGLGLSTTLLVGLGDEDEEDDLEELELLAEFRSPDRVSL 175
Query: 203 YSLTIEPNTYFFK 215
+ L E T
Sbjct: 176 FRLLPEEGTPLEL 188
>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 = 43.8 bits (104), Expect = 4e-06
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 320 LIFEFMLNALRLKDGFSPNLFFERTGI-NIKIIESKLKNAEKLGLLKRNNKNIKPTSFGR 378
+ E ++ LRL +G F +R G ++ +E L+ ++ GLL+ ++ ++ T GR
Sbjct: 6 RLRERLILGLRLTEGVDLAEFEQRFGGDFLEELEPLLEKLQEDGLLELDDGRLRLTPRGR 65
Query: 379 Y 379
Sbjct: 66 L 66
>gnl|CDD|223963 COG1032, COG1032, Fe-S oxidoreductase [Energy production and
conversion].
Length = 490
Score = 47.2 bits (112), Expect = 9e-06
Identities = 38/204 (18%), Positives = 78/204 (38%), Gaps = 14/204 (6%)
Query: 26 CIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILNRKIHT--IFIGGGTPSLIS 83
C + C +C + + ++ +E + +E IF+ G P+L
Sbjct: 208 CPRGCRFCSITKHFKYRRRRPERVVEEIKELIEE---GGKRVVFFVDDIFLYGS-PALND 263
Query: 84 DTGLDYLLKNIKKLLLFK-KNISITL-EANPSTFEIEK-FHSYSIIGINRLSIGIQSFNN 140
+ + L + + L K + I+ T E+ G+ R+ IGI+S +
Sbjct: 264 EKRFELLSLELIERGLRKGCRVHISAPSLRADTVTDEELLKLLREAGLRRVYIGIESGSE 323
Query: 141 KYLNILGRTHDSKQA-KYAIEIAKQYFNNFNLDLIYALPNQTLSELMLDLNYAIQ----Y 195
+ L + + +++ + A++IAK++ L I LP +T ++ + A
Sbjct: 324 ELLKKINKGITTEEVLEEAVKIAKEHGLRVKLYFIVGLPGETEEDVKETIELAKFIKKLG 383
Query: 196 SPPHLSLYSLTIEPNTYFFKYPPL 219
++S P T + P L
Sbjct: 384 PKLYVSPSPFVPLPGTPLQEMPKL 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 = 37.6 bits (88), Expect = 0.009
Identities = 17/52 (32%), Positives = 30/52 (57%)
Query: 130 RLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQYFNNFNLDLIYALPNQT 181
RL IG QS +++ L + R H + + A+E+A ++ +D I+ LP +T
Sbjct: 268 RLHIGAQSGSDRVLKAIRRGHTVEDVERAVELALEHGFTPVVDFIFGLPGET 319
>gnl|CDD|224164 COG1243, ELP3, Histone acetyltransferase [Transcription / Chromatin
structure and dynamics].
Length = 515
Score = 35.0 bits (81), Expect = 0.072
Identities = 25/120 (20%), Positives = 43/120 (35%), Gaps = 29/120 (24%)
Query: 68 KIHTIFIGGGTPSLISDTGLDY---LLKNIKKLLLF----------------KKNISITL 108
K+ I +GG +L L+Y LK K + + + IT+
Sbjct: 134 KVELIIMGGTFTAL----SLEYQEWFLKVALKAMNDFGYDLEEAQRKNETAELRCVGITI 189
Query: 109 EANPSTF---EIEKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQY 165
E P +++ Y G+ R+ +G+QS + L R H + A + K
Sbjct: 190 ETRPDYIDEEHLDQMLKY---GVTRVELGVQSIYDDVLERTKRGHTVEDVVEATRLLKDA 246
>gnl|CDD|232891 TIGR00238, TIGR00238, KamA family protein. This model represents
essentially the whole of E. coli YjeK and of some of its
apparent orthologs. YodO in Bacillus subtilis, a family
member which is longer protein by an additional 100
residues, is characterized as a lysine 2,3-aminomutase
with iron, sulphide and pyridoxal 5'-phosphate groups.
The homolog MJ0634 from M. jannaschii is preceded by
nearly 200 C-terminal residues. This family shows
similarity to molybdenum cofactor biosynthesis protein
MoaA and related proteins. Note that the E. coli homolog
was expressed in E. coli and purified and found not to
display display lysine 2,3-aminomutase activity. Active
site residues are found in 100 residue extension in B.
subtilis. Name changed to KamA family protein [Energy
metabolism, Electron transport].
Length = 331
Score = 31.7 bits (72), Expect = 0.62
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 6/72 (8%)
Query: 26 CIKKCPYCDFHSYEIKKNISEKKYLEALLIDVELSLPIILNRKIHTIFIGGGTPSLISDT 85
C C YC + K+N KK + L + II I I GG P + D
Sbjct: 123 CAVNCRYCFRRHFPYKENPGNKKKWQKALDYIAEHPEII------EILISGGDPLMAKDH 176
Query: 86 GLDYLLKNIKKL 97
L++LLK ++++
Sbjct: 177 ELEWLLKRLEEI 188
>gnl|CDD|184628 PRK14331, PRK14331, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 437
Score = 31.3 bits (71), Expect = 0.81
Identities = 24/122 (19%), Positives = 50/122 (40%), Gaps = 27/122 (22%)
Query: 129 NRLSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQYFNN--FNLDLIYALPNQT----- 181
L + Q+ +++ L ++ R + ++ IE+ K+Y + F+ D+I P +T
Sbjct: 256 EHLHLPFQAGSDRILKLMDRGYTKEEYLEKIELLKEYIPDITFSTDIIVGFPTETEEDFE 315
Query: 182 -----LSELMLDLNYAIQYSPPHLSLYSLTIEPNTYFFKYPPLSMPSNDENAVMQDKITS 236
L ++ + ++ +YSP P T P M + + V ++
Sbjct: 316 ETLDVLKKVEFEQVFSFKYSP----------RPGT-----PAAYMEGQEPDEVKTKRMNR 360
Query: 237 LL 238
LL
Sbjct: 361 LL 362
>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 = 2.8
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 66 NRKIHTIFIGGGTPSLISDTGLDYLLKNIKKL 97
+I + + GG P L+SD LD++L ++ +
Sbjct: 153 TPQIRDVLLSGGDPLLLSDDYLDWILTELRAI 184
>gnl|CDD|181690 PRK09195, gatY, tagatose-bisphosphate aldolase; Reviewed.
Length = 284
Score = 29.3 bits (66), Expect = 2.9
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 10/41 (24%)
Query: 57 VELSLPIILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKL 97
EL P+I+ GTP S G +YLL +
Sbjct: 39 AELHSPVII----------AGTPGTFSYAGTEYLLAIVSAA 69
>gnl|CDD|237212 PRK12808, PRK12808, flagellin; Provisional.
Length = 476
Score = 29.5 bits (66), Expect = 3.1
Identities = 21/87 (24%), Positives = 36/87 (41%), Gaps = 8/87 (9%)
Query: 87 LDYLLKNI----KKLLLFKKNISI-TLEANPSTFEIE---KFHSYSIIGINRLSIGIQSF 138
+ Y+ N K LL +I+I TL+++ +I K + +GIN LSIG +
Sbjct: 121 ITYIADNTQFNDKNLLNSNSSINIQTLDSSDGDKQIGIDLKSATLEALGINDLSIGANTD 180
Query: 139 NNKYLNILGRTHDSKQAKYAIEIAKQY 165
+ + AK +E +
Sbjct: 181 IEAVSTKIAALDKNTIAKATVEAKAAF 207
>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 843
Score = 29.6 bits (67), Expect = 3.1
Identities = 17/102 (16%), Positives = 36/102 (35%), Gaps = 8/102 (7%)
Query: 224 NDENAVMQDKITSLLKNNYYKNYEISAYSKTGYESQHNLNYWKFGDYLGIGAGSHSKLSF 283
N E ++D + + E+ +TG +S +G Y+ + + +
Sbjct: 430 NIELDELRDLLN--NAKEWIAKLELEERERTGIKSLKIKYNKVYGYYIEVTKSNAKLVPD 487
Query: 284 PNYIIRQ-----IRYKNPNIYLKNIFSGNSIAKSKKIEKKCL 320
+YI RQ R+ P + ++ K +E +
Sbjct: 488 -DYIRRQTLKNAERFTTPELKELEEKLLDAEEKILALEYELF 528
>gnl|CDD|217934 pfam04157, EAP30, EAP30/Vps36 family. This family includes EAP30
as well as the Vps36 protein. Vps36 is involved in Golgi
to endosome trafficking. EAP30 is a subunit of the ELL
complex. The ELL is an 80-kDa RNA polymerase II
transcription factor. ELL interacts with three other
proteins to form the complex known as ELL complex. The
ELL complex is capable of increasing that catalytic rate
of transcription elongation, but is unable to repress
initiation of transcription by RNA polymerase II as is
the case of ELL. EAP30 is thought to lead to the
derepression of ELL's transcriptional inhibitory
activity.
Length = 219
Score = 29.2 bits (66), Expect = 3.4
Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 10/77 (12%)
Query: 288 IRQIRYKNPNIYLKNIFSGNSIAKSKKIEKKCLIFEFMLNALRLKDGFSPNLFFERTGIN 347
+ ++ + + ++++ KI L G + + E+ G +
Sbjct: 150 FKLVKIGSGVLVVQSVPKSELSEDQTKI----------LELAEELGGVTASELAEKLGWS 199
Query: 348 IKIIESKLKNAEKLGLL 364
I + L+ AEK GLL
Sbjct: 200 IGRAKEVLEKAEKEGLL 216
>gnl|CDD|224480 COG1564, THI80, Thiamine pyrophosphokinase [Coenzyme metabolism].
Length = 212
Score = 29.2 bits (66), Expect = 3.5
Identities = 21/85 (24%), Positives = 28/85 (32%), Gaps = 18/85 (21%)
Query: 55 IDVELSLPIILNRKIHTIFIGGGTPSLISDTG--LDYLLKNIK---KLLLFKKNISITLE 109
D+EL+L L R I I G G LD+ L N+ + I++
Sbjct: 78 TDLELALDEALERGADEIVILGA-------LGGRLDHALANLFLLLRPAKSGFKITLISG 130
Query: 110 AN------PSTFEIEKFHSYSIIGI 128
N P IEK Y
Sbjct: 131 QNLITPLPPGQHTIEKDPGYLYSIF 155
>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 = 28.4 bits (64), Expect = 4.5
Identities = 11/34 (32%), Positives = 21/34 (61%), Gaps = 3/34 (8%)
Query: 63 IILNRKIHTIFIGGGTPSLISDTGLDYLLKNIKK 96
I+ R++ I++ G L+++ L+Y+LK I K
Sbjct: 36 ILFRRELEAIYLFIG---LLANEALNYVLKRIIK 66
>gnl|CDD|233476 TIGR01574, miaB-methiolase, tRNA-N(6)-(isopentenyl)adenosine-37
thiotransferase enzyme MiaB. This model represents
homologs of the MiaB enzyme responsible for the
modification of the isopentenylated adenine-37 base of
most bacterial and eukaryotic tRNAs that read codons
beginning with uracil (all except tRNA(I,V) Ser).
Adenine-37 is next to the anticodon on the 3' side in
these tRNA's, and lack of modification at this site
leads to an increased spontaneous mutation frequency.
Isopentenylated A-37 is modified by methylthiolation at
position 2, either by MiaB alone or in concert with a
separate methylase yet to be discovered (MiaC?). MiaB
contains a 4Fe-4S cluster which is labile under
oxidizing conditions. Additionally, the sequence is
homologous (via PSI-BLAST searches) to the biotin
synthetase, BioB, which utilizes both an iron-sulfur
cluster and S-adenosym methionine (SAM) to generate a
radical which is responsible for initiating the
insertion of sulfur into the substrate. It is reasonable
to surmise that the methyl group of SAM becomes the
methyl group of the product, but this has not been
shown, and the possibility of a separate methylase
exists. This equivalog is a member of a subfamily
(TIGR00089) which contains several other hypothetical
equivalogs which are all probably enzymes with similar
function acting on different substrates. These enzymes
contain a TRAM domain (pfam01938) which is believed to
be responsible for binding to tRNAs. Hits to this model
span all major groups of bacteria and eukaryotes, but
not archaea, which are known to lack this particular
tRNA modification. The enzyme from Thermotoga maritima
has been cloned, expressed, spectroscopically
characterized and shown to complement the E. coli MiaB
enzyme [Protein synthesis, tRNA and rRNA base
modification].
Length = 438
Score = 29.0 bits (65), Expect = 4.9
Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 12/75 (16%)
Query: 135 IQSFNNKYLNILGRTHDSKQAKYAIEIAKQYFNNFNL--DLIYALPNQT----------L 182
+QS +++ L ++ R + + + + N ++ D+I P +T L
Sbjct: 264 VQSGSSEILKLMKRGYTREWYLNLVRKLRAACPNVSISTDIIVGFPGETEEDFEETLDLL 323
Query: 183 SELMLDLNYAIQYSP 197
E+ D ++ YSP
Sbjct: 324 REVEFDSAFSFIYSP 338
>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 = 28.9 bits (65), Expect = 5.0
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 65 LNRKIHTIFIGGGTPSLISDTGLDYLLKNIKKLLLFKKNISITLEANPSTFEIE 118
++ K F + ++S +K+ K L KK S + A+ F IE
Sbjct: 243 ISGKAE--FKQQQSALILSVLEGSGRIKSGGKTLPLKKGESFFIPAHLGPFTIE 294
>gnl|CDD|232820 TIGR00089, TIGR00089, radical SAM methylthiotransferase, MiaB/RimO
family. This subfamily contains the tRNA-i(6)A37
modification enzyme, MiaB (TIGR01574). The phylogenetic
tree indicates 4 distinct clades, one of which
corresponds to MiaB. The other three clades are modelled
by hypothetical equivalogs (TIGR01125, TIGR01579 and
TIGR01578). Together, the four models hit every sequence
hit by the subfamily model without any overlap between
them. This subfamily is aparrently a part of a larger
superfamily of enzymes utilizing both a 4Fe4S cluster
and S-adenosyl methionine (SAM) to initiate radical
reactions. MiaB acts on a particular isoprenylated
Adenine base of certain tRNAs causing thiolation at an
aromatic carbon, and probably also transferring a methyl
grouyp from SAM to the thiol. The particular substrate
of the three other clades is unknown but may be very
closely related.
Length = 429
Score = 28.7 bits (65), Expect = 5.3
Identities = 18/85 (21%), Positives = 38/85 (44%), Gaps = 6/85 (7%)
Query: 131 LSIGIQSFNNKYLNILGRTHDSKQAKYAIEIAKQYFNNFNL--DLIYALPNQTLSELM-- 186
L + +QS +++ L + R + ++ +E + + + D+I P +T +
Sbjct: 252 LHLPVQSGSDRILKRMNRKYTREEYLDIVEKIRAKIPDAAITTDIIVGFPGETEEDFEET 311
Query: 187 LDLNYAIQYSPPHLSLYSLTIEPNT 211
LDL +++ H +YS P T
Sbjct: 312 LDLVEEVKFDKLHSFIYSP--RPGT 334
>gnl|CDD|236303 PRK08579, PRK08579, anaerobic ribonucleoside triphosphate
reductase; Provisional.
Length = 625
Score = 28.6 bits (64), Expect = 6.5
Identities = 14/31 (45%), Positives = 15/31 (48%), Gaps = 10/31 (32%)
Query: 9 LYIKKLPPLSLYIHFPWCIKKCPYCDFHSYE 39
+YI KLP SLYI PYC HS
Sbjct: 67 IYIHKLP-YSLYI---------PYCTGHSIS 87
>gnl|CDD|236078 PRK07726, PRK07726, DNA topoisomerase III; Provisional.
Length = 658
Score = 28.6 bits (65), Expect = 6.8
Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 4/29 (13%)
Query: 350 IIESKLKNAEKLGLLKRNNKNIKPTSFGR 378
IIE KL K G L++ K I T G+
Sbjct: 521 IIE-KLF---KRGYLEKKGKYIHATDKGK 545
>gnl|CDD|182939 PRK11063, metQ, DL-methionine transporter substrate-binding
subunit; Provisional.
Length = 271
Score = 28.2 bits (63), Expect = 7.3
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 15/73 (20%)
Query: 155 AKYAIEIAKQYFNNFNLDLI----YALPNQTLSELMLDLNYAIQYSPPHLSL------YS 204
A+ A ++AK+ + +++L+ Y LPN+ LS+ +D N A Q+ P+L Y
Sbjct: 46 AEVAQKVAKEKYG-LDVELVTFNDYVLPNEALSKGDIDAN-AFQHK-PYLDQQIKDRGYK 102
Query: 205 LTIEPNTYFFKYP 217
L NT F YP
Sbjct: 103 LVAVGNT--FVYP 113
>gnl|CDD|236541 PRK09496, trkA, potassium transporter peripheral membrane
component; Reviewed.
Length = 453
Score = 28.5 bits (65), Expect = 7.3
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 341 FERTGINIKIIESKLKNAEKL 361
E+ G ++K+IE + AE+L
Sbjct: 250 LEKEGYSVKLIERDPERAEEL 270
>gnl|CDD|131081 TIGR02026, BchE, magnesium-protoporphyrin IX monomethyl ester
anaerobic oxidative cyclase. This model respresents the
cobalamin-dependent oxidative cyclase responsible for
forming the distinctive E-ring of the chlorin ring
system under anaerobic conditions. This step is
essential in the biosynthesis of both
bacteriochlorophyll and chlorophyll under anaerobic
conditions (a separate enzyme, AcsF, acts under aerobic
conditions). This model identifies two clades of
sequences, one from photosynthetic, non-cyanobacterial
bacteria and another including Synechocystis and several
non-photosynthetic bacteria. The function of the
Synechocystis gene is supported by gene clustering with
other photosynthetic genes, so the purpose of the gene
in the non-photosynthetic bacteria is uncertain. Note
that homologs of this gene are not found in plants which
rely solely on the aerobic cyclase.
Length = 497
Score = 28.3 bits (63), Expect = 7.6
Identities = 24/122 (19%), Positives = 46/122 (37%), Gaps = 6/122 (4%)
Query: 98 LLFKKNISITLEANPSTFEI----EKFHSYSIIGINRLSIGIQSFNNKYLNILGRTHDSK 153
++ + IS+T N +I + H Y G+ +S+G ++ L+ + +
Sbjct: 264 IIARNPISVTWGINTRVTDIVRDADILHLYRRAGLVHISLGTEAAAQATLDHFRKGTTTS 323
Query: 154 QAKYAIEIAKQYFNNFNL-DLIYALPNQTLSELMLDLNYAIQYSPPHLSLYSLTIEPNTY 212
K AI + +Q+ N + I N+T + + P + T P T
Sbjct: 324 TNKEAIRLLRQH-NILSEAQFITGFENETDETFEETYRQLLDWDPDQANWLMYTPWPFTS 382
Query: 213 FF 214
F
Sbjct: 383 LF 384
>gnl|CDD|133116 cd06906, M14_Nna1, Peptidase M14-like domain of ATP/GTP binding
proteins and cytosolic carboxypeptidases. Peptidase
M14-like domain of Nna-1 (Nervous system Nuclear protein
induced by Axotomy), also known as ATP/GTP binding
protein (AGTPBP-1) and cytosolic carboxypeptidase (CCP),
and related proteins. The Peptidase M14 family of
metallocarboxypeptidases are zinc-binding
carboxypeptidases (CPs) which hydrolyze single,
C-terminal amino acids from polypeptide chains, and have
a recognition site for the free C-terminal carboxyl
group, which is a key determinant of specificity. This
eukaryotic subgroup includes the mouse Nna1/CCP-1, and
-4 proteins, and the human Nna1/AGTPBP-1 protein.
Nna1-like proteins are active metallopeptidases that are
thought to act on cytosolic proteins such as
alpha-tubulin, to remove a C-terminal tyrosine. Nna1 is
widely expressed in the developing and adult nervous
systems, including cerebellar Purkinje and granule
neurons, miral cells of the olfactory bulb and retinal
photoreceptors. Nna1 is also induced in axotomized motor
neurons. Mutations in Nna1 cause Purkinje cell
degeneration (pcd). The Nna1 CP domain is required to
prevent the retinal photoreceptor loss and cerebellar
ataxia phenotypes of pcd mice, and a functional
zinc-binding domain is needed for Nna-1 to support
neuron survival in these mice. Nna1-like proteins from
the different phyla are highly diverse, but they all
contain a unique N-terminal conserved domain right
before the CP domain. It has been suggested that this
N-terminal domain might act as a folding domain.
Length = 278
Score = 27.8 bits (62), Expect = 9.1
Identities = 10/20 (50%), Positives = 14/20 (70%), Gaps = 2/20 (10%)
Query: 27 IKKCP--YCDFHSYEIKKNI 44
IK+ P YCD+H + KKN+
Sbjct: 148 IKRSPLVYCDYHGHSRKKNV 167
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
0.320 0.139 0.408
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: 20,453,131
Number of extensions: 2058676
Number of successful extensions: 2078
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1979
Number of HSP's successfully gapped: 103
Length of query: 391
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 292
Effective length of database: 6,546,556
Effective search space: 1911594352
Effective search space used: 1911594352
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: 60 (27.0 bits)