Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate RR42_RS34245 RR42_RS34245 indolepyruvate ferredoxin oxidoreductase
Query= reanno::Cup4G11:RR42_RS19540 (1197 letters) >FitnessBrowser__Cup4G11:RR42_RS34245 Length = 1186 Score = 1776 bits (4601), Expect = 0.0 Identities = 886/1199 (73%), Positives = 1007/1199 (83%), Gaps = 16/1199 (1%) Query: 1 MNAPLTPPVSDAIRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTA 60 MNAPL S A + ALA+VSL+DKYTLE+GRVY+SGTQALVRLPMLQ+ RD AAGLNTA Sbjct: 1 MNAPL----SSAQQDALASVSLDDKYTLEKGRVYLSGTQALVRLPMLQKARDLAAGLNTA 56 Query: 61 GFISGYRGSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFE 120 GFISGYRGSPLG +DQ+LWKAK+HLAA D+VFQ G+NEDLAAT+VWG+QQVN++PDA + Sbjct: 57 GFISGYRGSPLGGVDQALWKAKKHLAASDVVFQPGVNEDLAATAVWGTQQVNLFPDATRD 116 Query: 121 GVFGMWYGKGPGVDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKAC 180 GVF MWYGKGPGVDR+ DV KHANSAGS++HGGVL+LAGDDHAAKSS++AHQSEH+ A Sbjct: 117 GVFSMWYGKGPGVDRSIDVLKHANSAGSAKHGGVLLLAGDDHAAKSSSVAHQSEHVLLAS 176 Query: 181 GLPVLYPSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQD 240 G+PVLYPSNVQEYLDYGLH WAMSRYSGLWVSMKCVTDVVES+ASVE+DP RV IVLP+D Sbjct: 177 GIPVLYPSNVQEYLDYGLHGWAMSRYSGLWVSMKCVTDVVESTASVEVDPDRVRIVLPED 236 Query: 241 FILPPGGLNIRWPDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKA 300 F +P GGLNIRWPDPPL QEARLLD+KWYA LAY+RANK++R+ +DSP+ARFGIMT GKA Sbjct: 237 FAMPEGGLNIRWPDPPLAQEARLLDHKWYAALAYIRANKLNRVVLDSPNARFGIMTAGKA 296 Query: 301 YLDTRQALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIME 360 YLD RQAL++LGLDD+TC RIGIR++KVGCVWPL+AH AR FA GL+EILVVEEKRQI+E Sbjct: 297 YLDVRQALSDLGLDDDTCRRIGIRVFKVGCVWPLDAHDAREFATGLEEILVVEEKRQILE 356 Query: 361 YALKEELYNWRDDVRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRL 420 YALKEELYNWRDDVRPKVYGKFDE+ N GGEWS+P+ NWLLPAHYELSPA+IA+AIATRL Sbjct: 357 YALKEELYNWRDDVRPKVYGKFDERGNHGGEWSLPRGNWLLPAHYELSPALIAKAIATRL 416 Query: 421 DKFELPADVRARIAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALA 480 +K +LP DVR RIAAR+A+IEAKE+ A PR++ ERKPWFCSGCPHNTST VPEGSRALA Sbjct: 417 EKSDLPTDVRERIAARVALIEAKEREAARPRISVERKPWFCSGCPHNTSTRVPEGSRALA 476 Query: 481 GIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRAS 540 GIGCHYM +WMDR+T TFSQMGGEGVAW GQ F G+KHVF NLGDGTYFHSGLLA+RAS Sbjct: 477 GIGCHYMAMWMDRNTDTFSQMGGEGVAWTGQMHFTGEKHVFVNLGDGTYFHSGLLAVRAS 536 Query: 541 IAAGVNITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAI 600 IAA NITYKIL+NDAVAMTGGQP+DG L+V +A+QV AEGA KIVVVTDEPEKY Sbjct: 537 IAAKANITYKILFNDAVAMTGGQPVDGVLTVPQIAHQVLAEGASKIVVVTDEPEKYGDGG 596 Query: 601 KLPQGVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFIND 660 LP V VHHRD+LD IQ +LR+ G TILIYDQTCATEKRRRRKRGT DPAKRAFIND Sbjct: 597 MLPASVTVHHRDQLDEIQVQLRDTAGVTILIYDQTCATEKRRRRKRGTMADPAKRAFIND 656 Query: 661 AVCEGCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKK 720 AVCEGCGDCSVKSNCLSVEPLET LGTKR+INQSSCNKDFSCVNGFCPSFVTAEGAQV+K Sbjct: 657 AVCEGCGDCSVKSNCLSVEPLETPLGTKRKINQSSCNKDFSCVNGFCPSFVTAEGAQVRK 716 Query: 721 PERHG--VSMDNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTV 778 P G ++ + ALPQPALP LE PYGVLVTGVGGTGVVTIGGLLGMAAHLE KGVTV Sbjct: 717 PAAAGGKGALADFSALPQPALPTLERPYGVLVTGVGGTGVVTIGGLLGMAAHLEQKGVTV 776 Query: 779 LDMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGR 838 LDMAGLAQKGGAV+SHVQIA P LHATRIA GEA LVIGCDAIVSA +V+SKT++ Sbjct: 777 LDMAGLAQKGGAVISHVQIAPTPAALHATRIATGEARLVIGCDAIVSASPEVLSKTRIDV 836 Query: 839 TRAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVGEACDFINASGLAVALIGDAIFTN 898 T A +N+A TPTA+FIKNP W+FPG SAEQD+R +VG+AC FI+A+ AV L+ D+I++N Sbjct: 837 TAAAINSADTPTADFIKNPNWKFPGASAEQDLRASVGDACAFIDANAWAVKLLADSIYSN 896 Query: 899 PLVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRN 958 PL+LG+AWQKGW+PL ++LVRAIELNG AVEKN AFDWGR++AH E +L +L+ Sbjct: 897 PLLLGFAWQKGWVPLRRESLVRAIELNGVAVEKNLLAFDWGRYLAHHGE--AALAAQLQI 954 Query: 959 TAEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGK 1018 T A+VV +P + L+ +I R LTAYQ+ AYA +R V VRAAE VG Sbjct: 955 TPR-AQVVAMPET----LDSVIRQREALLTAYQNPAYAARYRAAVESVRAAEKR-VGANP 1008 Query: 1019 PLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLM 1078 LPL EA ARNL+KLMAYKDEYEVARLY DP FLDKLR QFEGEPGRDYQL+F LAPPL+ Sbjct: 1009 RLPLAEAVARNLAKLMAYKDEYEVARLYADPAFLDKLRAQFEGEPGRDYQLSFHLAPPLL 1068 Query: 1079 AKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLE 1138 AKRD GHLVKRRFGP+ + F +LA+ KGLRG FDVFGKTAERR ER LI +Y A+ E Sbjct: 1069 AKRDSHGHLVKRRFGPAMLTAFRLLARAKGLRGTAFDVFGKTAERRAERKLIEDYIAMAE 1128 Query: 1139 ELTRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHPETAQRVA 1197 E L+A TA+ LASLPDDIRGFGHVK+ N+ K R ALL Q+R A RVA Sbjct: 1129 EFGATLNADRLDTAVALASLPDDIRGFGHVKEANMEKAAARRVALLAQYR--GAAARVA 1185 Lambda K H 0.319 0.135 0.407 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 3478 Number of extensions: 131 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 1197 Length of database: 1186 Length adjustment: 47 Effective length of query: 1150 Effective length of database: 1139 Effective search space: 1309850 Effective search space used: 1309850 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 (21.7 bits) S2: 59 (27.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory