Align Iron-sulfur cluster-binding oxidoreductase, CCG domain pair-containing, putative benzoyl-CoA reductase electron transfer protein (characterized, see rationale)
to candidate WP_086509107.1 BZY95_RS06235 DUF3483 domain-containing protein
Query= uniprot:Q39TW0 (387 letters) >NCBI__GCF_002151265.1:WP_086509107.1 Length = 675 Score = 194 bits (492), Expect = 8e-54 Identities = 125/403 (31%), Positives = 192/403 (47%), Gaps = 54/403 (13%) Query: 29 CYQCGLCDSVCPWNRVRQ-FSMRKIVRQGTFGLTE------------------------- 62 C QCG C++ CP Q + +K+++ G+ Sbjct: 251 CVQCGRCEAACPAFAAGQPLNPKKLIQDMVVGMAGGSDAHYAGSPYPDKPIGEHRGHPHG 310 Query: 63 ----------IEQEDIWRCSTCGTCPSRCPRGVNQIEAGVAMRR-IGAEYDVYPGHVGTI 111 ++ E +W C+TC C CP + ++A V MRR + E+ PG Sbjct: 311 PIVAREGTALVDAETLWSCTTCRACVEECPMMIEHVDAIVDMRRFLTLEHGNTPGKGA-- 368 Query: 112 RNVVASLTSEGNSLGGDRTQRGDWAKDL--PVKPYAEGMELLYFTGCYLSYDPRMRKVAA 169 V+ +L + N G D R WA DL P+ +++L + G + +D R ++ Sbjct: 369 -EVLDNLIATDNPGGFDPGSRMHWAADLNLPLMRDLGQVDVLLWLGDGV-FDMRNQRTLR 426 Query: 170 ATAAILNKAGVDFGILGSKESCCGESIRKTGNEELFKRLAKENIKQFIDNGVTKILVSSP 229 A +L AGVDF +LG++E G+ R+ G+E F+ LAK NI I+ P Sbjct: 427 ALVKVLRAAGVDFAVLGNEERDSGDVARRLGDEATFQSLAKRNIATLSQYRFQCIVTCDP 486 Query: 230 HCYHTFVNEY-----PEFKVNFEVVFISQYIGQLINEGRLQITGEFAKKVTYHDPCYLGR 284 H +H NEY P+F N+ V S YI +L GRL +VTYHDPCYLGR Sbjct: 487 HSFHVLKNEYGELGGPDFNANWVVRHHSTYIAELFEAGRLHFAPWKGGRVTYHDPCYLGR 546 Query: 285 HNGIYDEPRQVLQQVPGLELLEMADNRESSLCCGGGGGRIWMETPKEERFADLRIRQAVD 344 +NG ++ PR VL+ + G+E+ EM + S CCGGGGG + P ++R D+R+ + Sbjct: 547 YNGEFEAPRNVLRAL-GIEVKEMQRSGFRSRCCGGGGGAPITDIPGKQRIPDMRMNDVKE 605 Query: 345 VGATVLATSCPYCITNFTDSSLDLADHEKVEVKDLAEIILEVI 387 GA ++A CP C T + +D EV+D+AE++ + + Sbjct: 606 TGAELVAVGCPQC-TAMLEGVVDAT----AEVRDIAELVADAL 643 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: 630 Number of extensions: 32 Number of successful extensions: 6 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: 675 Length adjustment: 34 Effective length of query: 353 Effective length of database: 641 Effective search space: 226273 Effective search space used: 226273 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 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