Align Iron-sulfur cluster-binding oxidoreductase, CCG domain pair-containing, putative benzoyl-CoA reductase electron transfer protein (characterized, see rationale)
to candidate WP_004514581.1 GMET_RS10515 (Fe-S)-binding protein
Query= uniprot:Q39TW0 (387 letters) >NCBI__GCF_000012925.1:WP_004514581.1 Length = 387 Score = 799 bits (2063), Expect = 0.0 Identities = 387/387 (100%), Positives = 387/387 (100%) Query: 1 MGAIVETVTPYKEIIDVIKEKGGDSLKYCYQCGLCDSVCPWNRVRQFSMRKIVRQGTFGL 60 MGAIVETVTPYKEIIDVIKEKGGDSLKYCYQCGLCDSVCPWNRVRQFSMRKIVRQGTFGL Sbjct: 1 MGAIVETVTPYKEIIDVIKEKGGDSLKYCYQCGLCDSVCPWNRVRQFSMRKIVRQGTFGL 60 Query: 61 TEIEQEDIWRCSTCGTCPSRCPRGVNQIEAGVAMRRIGAEYDVYPGHVGTIRNVVASLTS 120 TEIEQEDIWRCSTCGTCPSRCPRGVNQIEAGVAMRRIGAEYDVYPGHVGTIRNVVASLTS Sbjct: 61 TEIEQEDIWRCSTCGTCPSRCPRGVNQIEAGVAMRRIGAEYDVYPGHVGTIRNVVASLTS 120 Query: 121 EGNSLGGDRTQRGDWAKDLPVKPYAEGMELLYFTGCYLSYDPRMRKVAAATAAILNKAGV 180 EGNSLGGDRTQRGDWAKDLPVKPYAEGMELLYFTGCYLSYDPRMRKVAAATAAILNKAGV Sbjct: 121 EGNSLGGDRTQRGDWAKDLPVKPYAEGMELLYFTGCYLSYDPRMRKVAAATAAILNKAGV 180 Query: 181 DFGILGSKESCCGESIRKTGNEELFKRLAKENIKQFIDNGVTKILVSSPHCYHTFVNEYP 240 DFGILGSKESCCGESIRKTGNEELFKRLAKENIKQFIDNGVTKILVSSPHCYHTFVNEYP Sbjct: 181 DFGILGSKESCCGESIRKTGNEELFKRLAKENIKQFIDNGVTKILVSSPHCYHTFVNEYP 240 Query: 241 EFKVNFEVVFISQYIGQLINEGRLQITGEFAKKVTYHDPCYLGRHNGIYDEPRQVLQQVP 300 EFKVNFEVVFISQYIGQLINEGRLQITGEFAKKVTYHDPCYLGRHNGIYDEPRQVLQQVP Sbjct: 241 EFKVNFEVVFISQYIGQLINEGRLQITGEFAKKVTYHDPCYLGRHNGIYDEPRQVLQQVP 300 Query: 301 GLELLEMADNRESSLCCGGGGGRIWMETPKEERFADLRIRQAVDVGATVLATSCPYCITN 360 GLELLEMADNRESSLCCGGGGGRIWMETPKEERFADLRIRQAVDVGATVLATSCPYCITN Sbjct: 301 GLELLEMADNRESSLCCGGGGGRIWMETPKEERFADLRIRQAVDVGATVLATSCPYCITN 360 Query: 361 FTDSSLDLADHEKVEVKDLAEIILEVI 387 FTDSSLDLADHEKVEVKDLAEIILEVI Sbjct: 361 FTDSSLDLADHEKVEVKDLAEIILEVI 387 Lambda K H 0.320 0.139 0.427 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: 783 Number of extensions: 21 Number of successful extensions: 5 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: 387 Length of database: 387 Length adjustment: 30 Effective length of query: 357 Effective length of database: 357 Effective search space: 127449 Effective search space used: 127449 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: 50 (23.9 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