Align Iron-sulfur cluster-binding oxidoreductase, CCG domain pair-containing, putative benzoyl-CoA reductase electron transfer protein (characterized, see rationale)
to candidate AO356_13910 AO356_13910 (Fe-S)-binding protein
Query= uniprot:Q39TW0 (387 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_13910 Length = 649 Score = 194 bits (494), Expect = 5e-54 Identities = 120/395 (30%), Positives = 193/395 (48%), Gaps = 47/395 (11%) Query: 29 CYQCGLCDSVCPWNRVRQ-FSMRKIVRQGTFGLTE------------------------- 62 C QCG C++ CP Q + +K+++ GL Sbjct: 245 CVQCGKCEAACPAFAAGQPLNPKKLIQDMVVGLAGGTDAKFAGSPYPGKPVGEHAGNPHQ 304 Query: 63 ------IEQEDIWRCSTCGTCPSRCPRGVNQIEAGVAMRR-IGAEYDVYPGH-VGTIRNV 114 ++ E +W C+TC C CP + ++A V MRR + E P + N+ Sbjct: 305 PIVNGLVDAETLWSCTTCRACVEECPMMIEHVDAIVDMRRHLTLEKGATPNKGAEVLENL 364 Query: 115 VASLTSEGNSLGGDRTQRGDWAKDLPVKPYAE--GMELLYFTGCYLSYDPRMRKVAAATA 172 +A+ G + GG R +WA DL + +E ++L++ G ++D R ++ A Sbjct: 365 IATDNPGGFAPGG----RMNWAADLNLNLLSEKKSTDVLFWVGDG-AFDMRNQRTLRAFV 419 Query: 173 AILNKAGVDFGILGSKESCCGESIRKTGNEELFKRLAKENIKQFIDNGVTKILVSSPHCY 232 +L A +DF +LG +E G+ R+ G+E F+ LAK NI+ +I+ PH + Sbjct: 420 KVLKAAKIDFAVLGLEERDSGDVARRLGDEATFQLLAKRNIQTLAKYSFNRIVTCDPHSF 479 Query: 233 HTFVNEYPEFKVNFEVVFISQYIGQLINEGRLQITGEFAKKVTYHDPCYLGRHNGIYDEP 292 H NEY F N+ V S Y+ ++I+ G L + VTYHDPCYLGR+NG Y+ P Sbjct: 480 HVLKNEYGAFDGNYLVQHHSTYLAEIIDAGALNLGQHKGDSVTYHDPCYLGRYNGEYEAP 539 Query: 293 RQVLQQVPGLELLEMADNRESSLCCGGGGGRIWMETPKEERFADLRIRQAVDVGATVLAT 352 RQVL+ + G+E+ EM + S CCGGGGG + P ++R D+R+ + GA ++A Sbjct: 540 RQVLRAL-GIEVKEMQRSGFRSRCCGGGGGAPITDIPGKQRIPDMRMDDIRETGAELVAV 598 Query: 353 SCPYCITNFTDSSLDLADHEKVEVKDLAEIILEVI 387 CP C + L+ + +KD+AE++ + + Sbjct: 599 GCPQC-----TAMLEGVVEPRPMIKDIAELVADAL 628 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: 606 Number of extensions: 34 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 387 Length of database: 649 Length adjustment: 34 Effective length of query: 353 Effective length of database: 615 Effective search space: 217095 Effective search space used: 217095 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 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