Align Iron-sulfur cluster-binding oxidoreductase, CCG domain pair-containing, putative benzoyl-CoA reductase electron transfer protein (characterized, see rationale)
to candidate WP_012965450.1 FERP_RS04705 (Fe-S)-binding protein
Query= uniprot:Q39TW0 (387 letters) >NCBI__GCF_000025505.1:WP_012965450.1 Length = 375 Score = 188 bits (478), Expect = 2e-52 Identities = 123/384 (32%), Positives = 196/384 (51%), Gaps = 37/384 (9%) Query: 24 DSLKYCYQCGLCDSVCP------WN----RVRQFSMRKIVRQGTFGLTEIEQE---DIWR 70 D C QC C VCP W R R + ++ ++R G ++++E D ++ Sbjct: 9 DEAFICAQCNFC-RVCPAFKHEDWESASPRGRIYLIKSLIR-GEIKPEDLDEEIIQDFFK 66 Query: 71 CSTCGTCPSRCPRGVNQIEAGVAMRR-IGAEYDVYPGHVGTIRNVVASLTSEGNSLGGDR 129 C+TCG C C + I+ R + E + P H + + + G G DR Sbjct: 67 CTTCGECEVVCQTEIPLIDVWEKARASLVKEGFILPAH----KRIGEAAKKTGCPYGEDR 122 Query: 130 TQRGDWAKDLPVKPYAEGMELLYFTGCYLSYDPRMRKVAAATAAILNKAGVDFGILGSKE 189 ++ DW D V +E E+ YF GC ++ R ++A T L KAG+DF + E Sbjct: 123 SR--DWWLDFEV---SEKAEVAYFAGCTATF--RTVEIAKNTVEFLKKAGIDFTYAKNDE 175 Query: 190 SCCGESIRKTGNEELFKRLAKENIKQFIDNGVTKILVSSPHCYHTFVNEYPE------FK 243 CCG + +TG E+ K+N +++ GV KI+ S CY T +YPE ++ Sbjct: 176 ICCGSPLLRTGQREIAYEFFKKNYEEWKRRGVKKIVTSCSGCYRTIKRDYPEIAKELGYE 235 Query: 244 VNFEVVFISQYIGQLINEGRLQITGEFAKKVTYHDPCYLGRHNGIYDEPRQVLQQVPGLE 303 +FEV +SQ I +LI G L++ + K VTYHDPC+LGRH +Y+EPR+VL+ + G + Sbjct: 236 WDFEVYHVSQLIHELIKSGELRLE-KLNKTVTYHDPCHLGRHMKVYEEPREVLKAL-GAD 293 Query: 304 LLEMADNRESSLCCGGGGGRIWMETPKEERFADLRIRQAVDVGATVLATSCPYCITNFTD 363 ++EM +NRE + CCG GGG + RI +A GA ++ + CP+C + Sbjct: 294 IVEMENNREEASCCGAGGGVKAQFKELAMKMGIDRISEAEKTGAELIVSCCPFCKLHLNQ 353 Query: 364 SSLDLADHEKVEVKDLAEIILEVI 387 ++ + + K+ V DL EI+ +++ Sbjct: 354 AAEE--KNSKLRVVDLIEIVNQLL 375 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: 450 Number of extensions: 36 Number of successful extensions: 6 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: 375 Length adjustment: 30 Effective length of query: 357 Effective length of database: 345 Effective search space: 123165 Effective search space used: 123165 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