Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate CA265_RS23555 CA265_RS23555 NADH-quinone oxidoreductase subunit F
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Pedo557:CA265_RS23555 Length = 455 Score = 311 bits (797), Expect = 4e-89 Identities = 172/427 (40%), Positives = 251/427 (58%), Gaps = 17/427 (3%) Query: 137 RNILSENLRLDS-KSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAW 195 R +L E++ + +++ Y GGY A+ K L +TPE+++ E+KKS LRGRGG GFP Sbjct: 3 RKLLLEHINVPGINTLEVYRQKGGYRAVEKALKTLTPEEIVEEVKKSGLRGRGGAGFPTG 62 Query: 196 RKWEESRNAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIY 255 KW +Y++ NADE +PG F DR L+ PH+++EG+I+ ++A+GA +IY Sbjct: 63 MKWSFLAKPEGVARYLVCNADESEPGTFKDRYLMTYIPHALIEGMIVSSFALGAKVSYIY 122 Query: 256 VRQEYPLAVENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALE 315 VR E + + AI +A G++GK+ILG+G+D + V G GA++CGE +AL+ +LE Sbjct: 123 VRGEMMPQIRILEKAIAEAKAAGWLGKNILGTGYDLELYVQPGGGAYICGEETALLESLE 182 Query: 316 GRAGEPRPKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFS 375 G+ G PR K A+ G++ P+V+NNVE+ A V II G D + G STGTK+ S Sbjct: 183 GKRGNPRIKPPFPAIAGLYGCPTVVNNVESIAAVVPIINDGGDEYAKIGIGRSTGTKLIS 242 Query: 376 LVGKITNTGLVEVPMGVTLRDII--TKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLP- 432 G + G+ E+ +G+ + + I + GGI GK+ KA GG S +P A L L Sbjct: 243 ASGNLVKPGVYEIELGLPVEEFIYSDEYCGGIANGKQLKATVAGGSSVPILP-ANLTLKY 301 Query: 433 -------VDFDELTK----AGSMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPC 481 + ++ L++ G+MMGSGG I DED C+V F F ESCG+C+PC Sbjct: 302 ANGEPRLMSYESLSEGGFATGTMMGSGGFIAFDEDQCIVRNTWNFSRFYHHESCGQCSPC 361 Query: 482 REGIRQMLAVLTRITVGKGKEGDIELLEELAES-TGAALCALGKSAPNPVLSTIRYFRDE 540 REG M VL +I G G D++LL ++ G +C LG +A PV S IR+FRDE Sbjct: 362 REGTGWMEKVLHKIEHGHGSMEDVDLLWDIQRKIEGNTICPLGDAAAWPVASAIRHFRDE 421 Query: 541 YEAHIRE 547 +E HI+E Sbjct: 422 FEWHIKE 428 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: 823 Number of extensions: 37 Number of successful extensions: 4 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: 455 Length adjustment: 35 Effective length of query: 600 Effective length of database: 420 Effective search space: 252000 Effective search space used: 252000 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: 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