Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_011842516.1 RSPH17029_RS18350 indolepyruvate ferredoxin oxidoreductase family protein
Query= reanno::Cup4G11:RR42_RS19540 (1197 letters) >NCBI__GCF_000015985.1:WP_011842516.1 Length = 1119 Score = 957 bits (2474), Expect = 0.0 Identities = 531/1163 (45%), Positives = 710/1163 (61%), Gaps = 64/1163 (5%) Query: 21 SLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQSLWK 80 +L D+YT GR+ SG QAL RL + Q+ RDRA GL+TAG+++GYRGSPL D L + Sbjct: 13 ALTDRYTQASGRILASGAQALARLMIEQQRRDRADGLDTAGYVTGYRGSPLADFDGELMR 72 Query: 81 AKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRTSDVF 140 A + L+A I FQ GLNEDLAAT+VWGSQQ+++ P AR +GVF +WYGKGPG+DR+ D Sbjct: 73 AGRFLSASAIRFQPGLNEDLAATAVWGSQQIDLSPGARHDGVFALWYGKGPGIDRSMDAI 132 Query: 141 KHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDYGLHA 200 +HAN+AG+ GGVL+L GDDH A SST HQSE + + +P+L P+ V+EY+D+GL Sbjct: 133 RHANAAGTHPRGGVLLLMGDDHGAVSSTFPHQSEQVLISAMVPILSPAGVEEYIDFGLAG 192 Query: 201 WAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRWPDPPLEQE 260 +A+SR++G+WV KC TD+VE + S++L LP D LPPGGL+IRWPD L QE Sbjct: 193 FALSRFAGVWVGFKCQTDIVECTRSIDLPDPAARPALP-DMTLPPGGLSIRWPDDKLAQE 251 Query: 261 ARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGLDDETCAR 320 AR L+ K A A+ AN +DRI AR GI+ GKA+ D A A G+ E Sbjct: 252 AR-LEVKMEAVRAFAAANGLDRILGAGAGARRGIVATGKAWRDLTGAFARAGISPE---E 307 Query: 321 IGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDDVRPKVYG 380 G+RL KVG +WPL FAEGL+EILV+EEKR ++E ++ + YN R RP+++G Sbjct: 308 AGLRLLKVGLLWPLVPATLERFAEGLEEILVIEEKRPVIEDQIRAQFYN-RTGARPRIWG 366 Query: 381 KFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIAT--RLDKFELPADVRARIAARIA 438 K + P+ L+ + EL PA + +A RL LP Sbjct: 367 K-----------TTPEGAPLISSTAELDPAGLVPVLAAFLRLPPMTLP------------ 403 Query: 439 VIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWMDRSTSTF 498 EA A +P R+P+FCSGCPH+ ST +P+GSRA AGIGC + V MDR+ TF Sbjct: 404 --EAPAPAPGLP----FREPYFCSGCPHSVSTKLPDGSRATAGIGCSMLAVAMDRNVETF 457 Query: 499 SQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYKILYNDAVA 558 +QMGGEG WIG APF ++HVF ++GDGTYFHSGLLAIRA++AAGVN TYKIL+NDAVA Sbjct: 458 TQMGGEGANWIGHAPFTDERHVFVHMGDGTYFHSGLLAIRAAVAAGVNATYKILFNDAVA 517 Query: 559 MTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEVHHRDELDRIQ 618 MTGGQ DG L+V +Q+ AEG R++VV+ +EP ++ +LP+GV+V HRD L Q Sbjct: 518 MTGGQTHDGSLTVPAAVDQIRAEGVRELVVIAEEPAQWRG--RLPEGVKVLHRDRLQAEQ 575 Query: 619 RELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSVKSNCLSV 678 LREV G T +IYDQ CA EKRRRRKRG++P PA + I+ VCEGCGDCSV+SNC+++ Sbjct: 576 IRLREVEGVTCIIYDQVCAAEKRRRRKRGSHPKPAAQVMIHPGVCEGCGDCSVQSNCIAI 635 Query: 679 EPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGVSMDNLPALPQPA 738 EPLET+LG KRQ+N S+CN D SC+ GFCPSFVT EG Q ++P+ + LP P Sbjct: 636 EPLETDLGRKRQVNLSACNADLSCLKGFCPSFVTIEGGQ-RRPQLAPLPEALGHDLPPPV 694 Query: 739 LPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGAVLSHVQIA 798 +L+ G+GGTGV+T+ +L AAHL+ V VL+ GLAQK GAV++H++ A Sbjct: 695 ATTAGPAQALLLAGIGGTGVITVSAILAQAAHLDGLAVQVLNQTGLAQKNGAVMAHLRFA 754 Query: 799 AHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPTAEFIKNPK 858 LHA RI + EAD V+ D++ +A ++ GRTR + + TPTA F+++ Sbjct: 755 TDARALHAPRIGLAEADAVLAFDSVAAAAPKGLACIDPGRTRVVADRHVTPTAGFVRHST 814 Query: 859 WQFPGLSAEQDVRNAVGEACDFINASGLAVALIGDAIFTNPLVLGYAWQKGWLPLSLDAL 918 A +R+ G + + A+ LA+ GDAI N L+ G+A+Q G +PLS A+ Sbjct: 815 APREDTRAMDQLRSRAGARLETVPATELALRHFGDAIAANILLTGHAFQLGLIPLSEGAI 874 Query: 919 VRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVVKLPTSSGALLEK 978 ++AI +NG A E+N AF GR +A PE P ++ + + Sbjct: 875 LQAIRMNGGAAERNLEAFRAGRLLAARPE----------------AFAPAPPAAEPTVAE 918 Query: 979 LIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAAARNLSKLMAYKD 1038 L HLT +QDA YA F V R A G L A R +MA+KD Sbjct: 919 LRDRLVRHLTEWQDARYAARFERLVDRAAARVQGWTGGEAFL---RALMRGTHHVMAFKD 975 Query: 1039 EYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRDEK-GHLVKRRFGPSTM 1097 EYEVARL+ DP F + +FEG DY++ + L+PP + D + G K RFGP Sbjct: 976 EYEVARLHLDPAFHASVAREFEG----DYRIAYHLSPPFPGRTDARTGRPAKLRFGPWMQ 1031 Query: 1098 KLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRGLSAANHATAITLAS 1157 F +LA++K LRG FD FG+++ERR ERAL Y +EEL L+ + A A Sbjct: 1032 HGFRLLARMKRLRGTPFDPFGQSSERRAERALRERYIRRMEELLAALTPEDLPAATQEAE 1091 Query: 1158 LPDDIRGFGHVKDDNLAKVRTRW 1180 +RGFG VK NLA+ + W Sbjct: 1092 AVLAVRGFGPVKAGNLARWQAEW 1114 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: 3198 Number of extensions: 166 Number of successful extensions: 11 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: 1119 Length adjustment: 47 Effective length of query: 1150 Effective length of database: 1072 Effective search space: 1232800 Effective search space used: 1232800 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: 58 (26.9 bits)
This GapMind analysis is from Apr 10 2024. 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