Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate Ac3H11_3809 tungsten-containing formate dehydrogenase beta subunit
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3809 Length = 635 Score = 268 bits (686), Expect = 4e-76 Identities = 175/521 (33%), Positives = 276/521 (52%), Gaps = 40/521 (7%) Query: 28 ISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYPEGICY 87 + VC C +GA E++AA L G +V C G CE+ P+ +++ C Sbjct: 119 LRVCDSLSCSLAGARELLAALPERLRAAG-QGDVQVLAVPCVGRCEQAPVAVVHQ---C- 173 Query: 88 LKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIPFYKNQQRNILSENLRLD 147 VP T+ E VV+ A +AL+ + +++I + +LR Sbjct: 174 ------PVPRATVDTVLE--VVESKPKRALARHPQALKAINFDVAALAEKSIPT-SLREV 224 Query: 148 SKSMDD---YLAIGGY-SALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRN 203 S + D Y A GGY +A + V +M E V+ ++ S LRG GG GFPA RKW R+ Sbjct: 225 SPAHTDLATYRAHGGYQTAAALVNGEMDAEAVLAAMEDSGLRGLGGAGFPAGRKWRIVRD 284 Query: 204 APDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLA 263 P P + + VN DEG+PG F DR +E +PH LEG++I A VG +IY+R EY Sbjct: 285 QPAP-RLMAVNIDEGEPGTFKDRTYLERDPHRFLEGVLIAAQVVGTEAIYIYLRDEY--- 340 Query: 264 VENINLAIRQASERGFVGKDILGSGFDFT---VKVHMGAGAFVCGESSALMTALEGRAGE 320 + ++QA D L + +++ GAGA++CGE SA++ ++EG+ GE Sbjct: 341 -HGCRVLLQQA-------LDDLRAEPPCPLPHIELRRGAGAYICGEESAMIESIEGKRGE 392 Query: 321 PRPKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKI 380 PR + + A G++ P++ +N ET V I+ +G WF S+G G G + FS+ G++ Sbjct: 393 PRMRPPYIAQVGLFGRPTLEHNFETLYWVRDIVERGPQWFASFGRHGRKGLRSFSVSGRV 452 Query: 381 TNTGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTK 440 + G+ P G+T++++I + GG+ G + A GG SGG +P ++ +P+DFD L Sbjct: 453 KHPGVKLAPAGITVQELIDEYCGGLLDGHQLYAYLPGGASGGILPASLNQIPLDFDTLQP 512 Query: 441 AGSMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKG 500 G +GS +IV+ + D A + F + ESCG+CTPCR G + T+ + Sbjct: 513 YGCFIGSAAVIVLSQHDRARDAALNVMRFFEHESCGQCTPCRVGTAK------AATLMEA 566 Query: 501 KEGDIELLEELAESTG-AALCALGKSAPNPVLSTIRYFRDE 540 + D +LL++LA+ G A++C LG++APNP+ +YF E Sbjct: 567 PQWDGDLLDDLAQVMGDASICGLGQAAPNPIRCIHKYFPHE 607 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: 946 Number of extensions: 49 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 635 Length of database: 635 Length adjustment: 38 Effective length of query: 597 Effective length of database: 597 Effective search space: 356409 Effective search space used: 356409 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: 54 (25.4 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