Align Iron-sulfur cluster-binding oxidoreductase, CCG domain pair-containing, putative benzoyl-CoA reductase electron transfer protein (characterized, see rationale)
to candidate BPHYT_RS25200 BPHYT_RS25200 (Fe-S)-binding protein
Query= uniprot:Q39TW0 (387 letters) >FitnessBrowser__BFirm:BPHYT_RS25200 Length = 637 Score = 192 bits (487), Expect = 3e-53 Identities = 126/396 (31%), Positives = 196/396 (49%), Gaps = 46/396 (11%) Query: 25 SLKYCYQCGLCDSVCPWNRVRQ-FSMRKIVRQGTFGL----------------------- 60 S C QCG C++ CP Q + +K+++ G+ Sbjct: 246 SFDACVQCGKCEAACPAFAAGQPLNPKKLIQDLVTGMVGGTDAQYAGSPTPGIPVGKHAG 305 Query: 61 --------TEIEQEDIWRCSTCGTCPSRCPRGVNQIEAGVAMRRIGAEYDVYPGHVGTIR 112 T IE + +W C+TC C CP + ++A V MRR + G I Sbjct: 306 APDKPLISTMIEADTLWSCTTCRACVQECPMLIEHVDAIVDMRRNQTLVEGSVPGKGPI- 364 Query: 113 NVVASLTSEGNSLGGDRTQRGDWAKDLPVKPYAEG--MELLYFTGCYLSYDPRMRKVAAA 170 +A+L G+S G D R DWA DL V+ G +++L G ++D R ++ A Sbjct: 365 -TLANLRETGSSNGYDIGARYDWAVDLQVQVAQPGRPVDVLLIAG-EGAFDMRYQRTLRA 422 Query: 171 TAAILNKAGVDFGILGSKESCCGESIRKTGNEELFKRLAKENIKQFIDNGVTKILVSSPH 230 +LN+AG+D+ +LG E+ G++ R+ G+E F++LA + I KI+ + PH Sbjct: 423 LVKVLNRAGIDYAVLGGVETDTGDTARRLGDEATFQQLALKLIGTLSQYSFRKIVTADPH 482 Query: 231 CYHTFVNEYPEFKVNFEVVFISQYIGQLINEGRL--QITGEFA-KKVTYHDPCYLGRHNG 287 H+ NEY +EV + I QL+ G+L + FA +K+TYHDPCYLGR+NG Sbjct: 483 VLHSLRNEYRALGGFYEVQHHTALIEQLVASGKLTPRAVAAFADRKITYHDPCYLGRYNG 542 Query: 288 IYDEPRQVLQQVPGLELLEMADNRESSLCCGGGGGRIWMETPKEERFADLRIRQAVDVGA 347 + PR++L+ + G++++EM N CCGGGGG + P + R D+RI A VGA Sbjct: 543 ETEAPRKLLKTI-GIKVVEMERNGMRGRCCGGGGGAPLTDIPGKRRIPDIRIDDAKTVGA 601 Query: 348 TVLATSCPYCITNFTDSSLDLADHEKVEVKDLAEII 383 ++A CP C + L+ + EV D+AE++ Sbjct: 602 EIVAVGCPNC-----TAMLEGVVGPRPEVLDVAELV 632 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: 569 Number of extensions: 33 Number of successful extensions: 7 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: 637 Length adjustment: 34 Effective length of query: 353 Effective length of database: 603 Effective search space: 212859 Effective search space used: 212859 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 17 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