Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate AZOBR_RS31940 AZOBR_RS31940 NADH-quinone oxidoreductase subunit F
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__azobra:AZOBR_RS31940 Length = 561 Score = 298 bits (763), Expect = 4e-85 Identities = 175/526 (33%), Positives = 270/526 (51%), Gaps = 60/526 (11%) Query: 23 PTKPCISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYP 82 P + VC C +G +++ EL+ + +V C G C P V I Sbjct: 94 PPPVTVRVCDSLSCCMAGGEKLL----DELKAADMGPDVRVVRAPCMGACHNAPAVAI-- 147 Query: 83 EGICYLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIPFYKNQQRNILSE 142 H + E V+ ++ T +P Y Sbjct: 148 -----------------GHALHENATVESVVTAVKNGETHP----QLPTYV--------- 177 Query: 143 NLRLDSKSMDDYLAIGGYSALSKVLFQMTP-EDVMGEIKKSNLRGRGGGGFPAWRKWEES 201 S++ Y A GGY L+ L P +D++G+++ +NLRG GG GFP RKW Sbjct: 178 -------SLEQYKAEGGYRLLADCLTGNVPVDDILGKLEGANLRGLGGAGFPTGRKWRFV 230 Query: 202 RNAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYP 261 R+ P P + + VN DEG+PG F DR +E +PH LEG++IGA+ V A + +IY+R EYP Sbjct: 231 RHEPGP-RLMAVNGDEGEPGTFKDRYYLENDPHRFLEGMLIGAWVVEATDVYIYLRDEYP 289 Query: 262 LAVENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEP 321 E + I + G G + + GAGA++CGE SA++ ++EG+ G P Sbjct: 290 HIREVLEHEIAAVEKAGLAGHT--------RIHLRRGAGAYICGEESAMLESIEGKRGLP 341 Query: 322 RPKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKIT 381 R K +V G++ P+++NNVET + I+ KGADW+ S+G G G + +S+ G + Sbjct: 342 RHKPPFPSVVGLFGRPTLINNVETLFWIRDILEKGADWWGSHGRNGRKGLRSYSVSGHVK 401 Query: 382 NTGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKA 441 + G+ P GVT+R++I + GG+ G K GG SGG +P +M D+P+DF L + Sbjct: 402 DPGVKLAPAGVTIRELIDEYCGGMADGHTLKGYLPGGASGGILPASMDDIPLDFGTLEQH 461 Query: 442 GSMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGK 501 G +GS ++V+ + M + R +DF +DESCG+CTPCR G + +A++ K Sbjct: 462 GCFIGSAAVVVLSDQDDMRKVVRNLLDFFEDESCGQCTPCRVGTEKAVALI------KQP 515 Query: 502 EGDIELLEELAESTG-AALCALGKSAPNPVLSTIRYFRDEYEAHIR 546 D LL ELA G A++C LG++A NP+ S +++FRD+ +R Sbjct: 516 VWDEPLLTELARLMGTASICGLGQAAMNPLKSALKHFRDDLRGEVR 561 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: 944 Number of extensions: 54 Number of successful extensions: 5 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: 561 Length adjustment: 37 Effective length of query: 598 Effective length of database: 524 Effective search space: 313352 Effective search space used: 313352 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 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