Align indolepyruvate ferredoxin oxidoreductase (subunit 2/2) (EC 1.2.7.8) (characterized)
to candidate WP_013257710.1 DEBA_RS04445 indolepyruvate ferredoxin oxidoreductase
Query= BRENDA::O07835 (647 letters) >NCBI__GCF_000143965.1:WP_013257710.1 Length = 646 Score = 414 bits (1065), Expect = e-120 Identities = 254/647 (39%), Positives = 370/647 (57%), Gaps = 42/647 (6%) Query: 14 GERVLLLGNHAIARGALEANIAVFAAYPGTPSSELTDTMAAVAKKAGVYMEYSTNEKVAF 73 G+ VLL GN AIARGALEA + AAYPG PSSE+ +A A+ AG++ E+STNEKVA Sbjct: 10 GQTVLLQGNEAIARGALEAGVQFAAAYPGNPSSEILQCLADSAQSAGIHAEWSTNEKVAL 69 Query: 74 ETALAAAWSGLRAMTAMKHVGLNVAADSFLSSVGMGV-EGGFVIMVADDPSMWSSQNEQD 132 E+A AA++ GLRAM +MK G+NVA D + GV GG V++ ADDPS SS NEQD Sbjct: 70 ESAAAASFCGLRAMASMKQNGVNVAQDFICNLTISGVGTGGLVLITADDPSGISSTNEQD 129 Query: 133 TRVYAKFANVPVLEPSSPHEAKEMTKYAFELSEKFKHFVILRTTTRSSHARGDVVLGELP 192 R A+ A +P+LEPS+P E + M K+AFELSE ++ V+ R+ +R SH RG+V G LP Sbjct: 130 ARFIARLACLPLLEPSTPDECRRMIKFAFELSEAIQNIVVFRSLSRLSHTRGNVAPGPLP 189 Query: 193 EEIKTGKRKFGKFKKDPTRFVDVPAHARKFHPLILEKIEKIREELNNCPFNWIEGKEDAK 252 + + + G+ F+ +P + H ++L+K+ K + + PFN +G + Sbjct: 190 GQKRAPHWRTGQ------NFITMPVMPK--HQIMLDKLAKAGQIMAESPFNPYDGPARPE 241 Query: 253 VGIIAPGLSYAYVKEALAWLGVED-VKILKLGTPFPVPYGLLGKFFDGLEKVLIVEELEP 311 + IIA G S+ Y EA +G+ED V + KLG +P+P LL + VL EE++P Sbjct: 242 LVIIASGSSWLYASEARQAMGLEDRVGLQKLGGTWPLPEALLLERLAASPAVLFAEEIDP 301 Query: 312 VVEEQVKT----WAYDKG-LRIPIHGKDLVPRVYEMTTRRAVEAIAKFLGLETPINFAE- 365 ++E+QV A + G R P + E++ R +A+ + L L TP + Sbjct: 302 IIEDQVMALYARHAAELGPKRFFGKASGHTPMIGELSPGRLAQAVGRILDLATPTVAPDY 361 Query: 366 IDEKYEKVSQIVPPRPPSLCPACPHRNSFFAIRK---AAGPKAIYPSDIGCYTLGVLPP- 421 ++ + +++VPPR CP CPHR SF++I++ A G + DIGCYTLG L Sbjct: 362 LERARQAAARLVPPREFGFCPGCPHRASFWSIKQVLAADGRDGLVSGDIGCYTLGALSTG 421 Query: 422 LRTVDTTVAMGASIGIGHGLSIAMNGSLAEEEHKEGKEKQIIVATIGDSTFYHTGLPALA 481 R V++ MG+ +G+G GL G L + Q ++ +GDSTF+H+GLP L Sbjct: 422 YRRVNSVHCMGSGLGVGSGL-----GQLGPQGF-----DQPVLTVVGDSTFFHSGLPGLI 471 Query: 482 NAIYNRSNVLIVVLDNLVTAMTGDQPNPGTGQTPHGM-GKRIPIEDVAKAMGADFVAVVD 540 NA +N ++ L+ +LDN TAMTG QP+P TGQT G G +I +E V +G + + D Sbjct: 472 NARWNGADFLLCILDNAATAMTGFQPHPATGQTATGRPGGQISLESVLDGLGVPY-RITD 530 Query: 541 PYDIKATYETIKKA-LEVEGVSVVVSRQVCALYKIGQMRRRGMKWPIYHVVEDKCTG--C 597 PYD+ AT +TI A L+ G ++ R+ CAL + +RG + V + C G C Sbjct: 531 PYDLAATQQTIYDALLDKGGARALILRRACALVQ----NKRGGHPYVMSVDQSVCRGEEC 586 Query: 598 ---KICINAYGCPAIYWDPETKKAKVDPTMCWGCGGCAQVCPFDAFE 641 + C + CP + +D KA++D +C GCG CAQ+CP A + Sbjct: 587 GCNRFCSRVFRCPGLIFDEAAGKARIDEVVCAGCGVCAQICPAGAIK 633 Lambda K H 0.319 0.136 0.412 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: 937 Number of extensions: 37 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: 647 Length of database: 646 Length adjustment: 38 Effective length of query: 609 Effective length of database: 608 Effective search space: 370272 Effective search space used: 370272 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: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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