Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate WP_086509117.1 BZY95_RS06295 formate dehydrogenase
Query= uniprot:Q39TW5 (635 letters) >NCBI__GCF_002151265.1:WP_086509117.1 Length = 516 Score = 344 bits (883), Expect = 5e-99 Identities = 194/509 (38%), Positives = 292/509 (57%), Gaps = 15/509 (2%) Query: 37 LASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYPEG--ICYLKVKPED 94 LA GA EV + E E G+ E+ G G P+V + I Y V PED Sbjct: 14 LALGADEVAQRIEAEAEARGV--EIELVRNGSRGLFWLEPLVEVETAAGRIAYGPVAPED 71 Query: 95 VPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIPFYKNQQRNILSENLRLDSKSMDDY 154 V + + E L + PA +IP+ + QQR S D S++DY Sbjct: 72 VAGLFDAGLLEGGEASSLC-QGPA--------EEIPYLQAQQRLTFSRIGVTDPLSLEDY 122 Query: 155 LAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDPIKYVIVN 214 A G+ L + L + P+ ++ E+K S LRGRGG FP KW+ +AP KY++ N Sbjct: 123 CAHDGFRGLRRAL-GLAPQAIVDEVKASGLRGRGGAAFPTGIKWQTVLDAPAAQKYIVCN 181 Query: 215 ADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLAIRQA 274 ADEGD G F DR ++E +P+ ++EG+ I AVGA +G++Y+R EYPLA E N AI +A Sbjct: 182 ADEGDSGTFADRLVMECDPYLLIEGMAIAGLAVGATQGYVYLRSEYPLAQEIFNEAIARA 241 Query: 275 SERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAVKGVW 334 G++G DILGSG F ++V +GAGA++CGE ++L+ +LEG+ G R K A++G++ Sbjct: 242 EAAGYLGGDILGSGRTFHLEVRLGAGAYICGEETSLLESLEGKRGMVRFKPPLPAIEGLF 301 Query: 335 DHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPMGVTL 394 P+V+NNV + A V I++ G + YG S GT L G + GLVE+ G TL Sbjct: 302 GQPTVVNNVLSLAAVPFILSDGGQAYADYGMGRSRGTLALQLAGNVQRGGLVELAFGTTL 361 Query: 395 RDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMGSGGMIVMD 454 R ++ + G G G+ +AVQ GGP G +PE+ DLP+D++ + G+++G GG+++ D Sbjct: 362 RQLMEEFGDGTFTGRPLRAVQVGGPLGAYLPESQWDLPLDYEAFAEVGAVLGHGGVVMFD 421 Query: 455 EDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIELLEELAES 514 + M + AR+ ++F ESCGKCTPCR G + + V+ RI G+ +E ++ LL +L E+ Sbjct: 422 DTVDMAEQARFAMEFCTVESCGKCTPCRIGAVRGVEVIDRIRAGERREANLILLADLCET 481 Query: 515 -TGAALCALGKSAPNPVLSTIRYFRDEYE 542 +LCA+G P PV S +++F D+ + Sbjct: 482 MVDGSLCAMGGMTPFPVQSVMKHFPDDLQ 510 Lambda K H 0.319 0.138 0.420 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: 838 Number of extensions: 52 Number of successful extensions: 3 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: 635 Length of database: 516 Length adjustment: 36 Effective length of query: 599 Effective length of database: 480 Effective search space: 287520 Effective search space used: 287520 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 (21.7 bits) S2: 53 (25.0 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