Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate AZOBR_RS14955 AZOBR_RS14955 formate dehydrogenase subunit beta
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__azobra:AZOBR_RS14955 Length = 521 Score = 333 bits (854), Expect = 1e-95 Identities = 192/516 (37%), Positives = 291/516 (56%), Gaps = 14/516 (2%) Query: 28 ISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYPEG-IC 86 I V A L+ GA E AA + E G+ + G+ + E + + PEG + Sbjct: 8 IYVPRDAAALSVGADETAAAIRAEATKRGIPLRIVRNGSRGMLWLET-LVEVETPEGRVA 66 Query: 87 YLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIPFYKNQQRNILSENLRL 146 Y V EDV + E D L L E IP++ Q+R + + Sbjct: 67 YGPVMAEDVAGLFDAGFLEG--ADHAL-------AHGLTEK-IPYFAKQERLTFARCGII 116 Query: 147 DSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPD 206 D S++DY GG+ L + L MTP +++ E+ +S LRGRGG GFP KW NA Sbjct: 117 DPLSVEDYRLHGGFRGLERAL-AMTPAEIVTEVTESGLRGRGGAGFPTGIKWNTVLNAKA 175 Query: 207 PIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVEN 266 KY+ NADEGD G F DR ++EG+P ++EG+ I A AVGA EG+IY+R EYP AV Sbjct: 176 DQKYICCNADEGDSGTFADRMIMEGDPFCLIEGMTIAAIAVGATEGYIYIRSEYPHAVAT 235 Query: 267 INLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYI 326 + AIR A + ++G +I G+G F + V +GAGA++CGE ++++ +LEG+ G R K Sbjct: 236 MREAIRLAYDEKWLGDEIHGTGHRFHLDVRVGAGAYICGEETSMLESLEGKRGTVRAKPP 295 Query: 327 HTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLV 386 A++G++ P+++NNV + +V I+ KGA+ + +G S GT F L G I + G+V Sbjct: 296 LPALEGLFGKPTIVNNVLSLTSVPIILDKGANHYRDFGVGRSRGTLAFQLAGNIKHGGIV 355 Query: 387 EVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMG 446 E GVTL +++ + GGG G+ +AVQ GGP G +P ++ +LP D++ +M+G Sbjct: 356 EKAFGVTLHELLYEFGGGTITGRPIRAVQAGGPLGAYLPPSLFELPKDYEAFAAVEAMVG 415 Query: 447 SGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIE 506 GG++V D+ M AR+ ++F ESCGKCTPCR G + + V+ I G+ + +I Sbjct: 416 HGGIVVFDDSVDMARQARFAMEFCAAESCGKCTPCRIGAVRGVEVMDNIIAGEKVQANIT 475 Query: 507 LLEELAE-STGAALCALGKSAPNPVLSTIRYFRDEY 541 LL +L E T +LCA+G P PV S +++F +++ Sbjct: 476 LLNDLCEVMTDGSLCAMGGMTPIPVRSALKHFPEDF 511 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: 868 Number of extensions: 58 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: 521 Length adjustment: 36 Effective length of query: 599 Effective length of database: 485 Effective search space: 290515 Effective search space used: 290515 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