Align Iron-sulfur cluster-binding oxidoreductase, CCG domain pair-containing, putative benzoyl-CoA reductase electron transfer protein (characterized, see rationale)
to candidate WP_111608784.1 DK187_RS18275 (Fe-S)-binding protein
Query= uniprot:Q39TW0 (387 letters) >NCBI__GCF_003259225.1:WP_111608784.1 Length = 640 Score = 187 bits (475), Expect = 7e-52 Identities = 120/395 (30%), Positives = 190/395 (48%), Gaps = 51/395 (12%) Query: 29 CYQCGLCDSVCPWNRVRQ-FSMRKIVRQGTFGLTE------------------------- 62 C QCG C++VCP Q + +K+++ G Sbjct: 248 CVQCGRCEAVCPAFAAGQPLNPKKLIQDMVVGFAGGTDENYAGSPYPGIDLGHAKGAPNQ 307 Query: 63 ------IEQEDIWRCSTCGTCPSRCPRGVNQIEAGVAMRR-IGAEYDVYPGH-VGTIRNV 114 I + +W C+TC C CP + ++A V MRR + E P + N+ Sbjct: 308 IITDGLIHPDTLWSCTTCRACVEECPMMIEHVDAIVDMRRFLTLEKGSTPNKGAQVLENI 367 Query: 115 VASLTSEGNSLGGDRTQRGDWAKD--LPVKPYAEGMELLYFTGCYLSYDPRMRKVAAATA 172 +A+ N G R WA D LPV + ++L++ ++D R +++ A Sbjct: 368 IAT----DNPNGYAPASRTHWAADQNLPVMKDVKQADVLFWVSDG-AFDMRSQRILRAFV 422 Query: 173 AILNKAGVDFGILGSKESCCGESIRKTGNEELFKRLAKENIKQFIDNGVTKILVSSPHCY 232 ++ A VD ILG +E G+ R+ G++ F+ LAK N+ KI+ + PH + Sbjct: 423 KLMKAANVDVAILGDEELDSGDVARRLGDDATFQSLAKRNLATLSTYQFNKIVTTDPHAF 482 Query: 233 HTFVNEYPEFKV----NFEVVFISQYIGQLINEGRLQITGEFAKKVTYHDPCYLGRHNGI 288 H NEY +F N EV+ + ++ +L+ +G LQ+ KVTYHDPCYLGR+NG Sbjct: 483 HCLKNEYGDFGSDALQNVEVLHHTTFLNRLVKDGLLQLEPFKGGKVTYHDPCYLGRYNGE 542 Query: 289 YDEPRQVLQQVPGLELLEMADNRESSLCCGGGGGRIWMETPKEERFADLRIRQAVDVGAT 348 Y+ PR++L + G+++ EM ++ S CCGGGGG + P E R AD+R+ V GA+ Sbjct: 543 YEAPRELLASL-GIDVAEMERSKFRSRCCGGGGGAPITDIPGERRIADMRMEDVVSTGAS 601 Query: 349 VLATSCPYCITNFTDSSLDLADHEKVEVKDLAEII 383 ++A C C + L+ + VKD+AEI+ Sbjct: 602 MVAVGCQQC-----TAMLEGVVEPRPVVKDIAEIL 631 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: 581 Number of extensions: 34 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: 640 Length adjustment: 34 Effective length of query: 353 Effective length of database: 606 Effective search space: 213918 Effective search space used: 213918 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