Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate Ac3H11_1447 NADH-ubiquinone oxidoreductase chain F (EC 1.6.5.3)
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1447 Length = 452 Score = 317 bits (811), Expect = 9e-91 Identities = 168/412 (40%), Positives = 249/412 (60%), Gaps = 8/412 (1%) Query: 150 SMDDYLAIGGYSALSKVLFQ-----MTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNA 204 S+ DY A GGY+AL K+L +T + V+ +K+S LRGRGG GFP KW + Sbjct: 39 SIKDYEARGGYAALRKILGTDGGEPLTQDQVIATVKESGLRGRGGAGFPTGLKWSFMPRS 98 Query: 205 PDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAV 264 KY++ N+DEG+PG DR +++ NPH ++EG+II AYA+G G+ Y+ E Sbjct: 99 FPGQKYLVCNSDEGEPGTCKDRDILQFNPHIVIEGMIIAAYAMGISVGYNYIHGEIFQTY 158 Query: 265 ENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPK 324 + A+ +A G++G ILGS F F + G GA++CGE +AL+ +LEG+ G+PR K Sbjct: 159 DRFEAALEEARAAGYLGDKILGSNFSFQLHAAHGFGAYICGEETALLESLEGKKGQPRFK 218 Query: 325 YIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTG 384 A G++ P+ +NN ET+A V II G + G + GTKIFS+ G + G Sbjct: 219 PPFPASFGLYGKPTTINNTETFAAVPWIIRNGGAAYLECGKPNNGGTKIFSVSGDVEKPG 278 Query: 385 LVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAML-DLPVDFDELTKAGS 443 EVP+G ++ ++ GG+ G++ KAV GG S +P +++ + +D+D + KAGS Sbjct: 279 NYEVPLGTPFAKLL-ELAGGVRKGRQLKAVIPGGSSAPVLPASIIMECTMDYDSIAKAGS 337 Query: 444 MMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEG 503 M+GSG +IVMD+ MV+ F ESCG+CTPCREG M V+ RI G+G++G Sbjct: 338 MLGSGAVIVMDDSRSMVESLLRLSYFYSHESCGQCTPCREGTGWMWRVIDRIQHGQGRDG 397 Query: 504 DIELLEELAES-TGAALCALGKSAPNPVLSTIRYFRDEYEAHIREKKCPALS 554 D+ LL +A++ G +CALG +A PV + I++FR E+EA IR++K P S Sbjct: 398 DLNLLNSVADNIQGRTICALGDAAAMPVRAMIKHFRPEFEALIRQEKTPQAS 449 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: 758 Number of extensions: 38 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: 452 Length adjustment: 35 Effective length of query: 600 Effective length of database: 417 Effective search space: 250200 Effective search space used: 250200 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