Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate SMc02525 SMc02525 NAD-dependent formate dehydrogenase subunit beta
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Smeli:SMc02525 Length = 518 Score = 326 bits (836), Expect = 1e-93 Identities = 188/511 (36%), Positives = 278/511 (54%), Gaps = 16/511 (3%) Query: 34 AGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYPEG--ICYLKVK 91 A LA GA +V+ A E+ GL + G+ + E P+V + G + Y VK Sbjct: 11 AAALALGAEKVVEAMAGEIAARGLDATIVRNGSRGMHWLE--PLVEVETAGGRVAYGPVK 68 Query: 92 PEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIPFYKNQQRNILSENLRLDSKSM 151 DV ++ D L A + +IPF K Q R + +D S+ Sbjct: 69 ASDVASLL----------DAGLISGGAHPLCLGKTEEIPFLKRQTRLTFARCGVIDPLSL 118 Query: 152 DDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDPIKYV 211 +DY A G L + + M P ++ E+ +S LRGRGG GFP KW+ A P KY+ Sbjct: 119 EDYRAHRGLLGLERAI-AMQPAAIVAEVTESGLRGRGGAGFPTGIKWKTVLEARGPRKYI 177 Query: 212 IVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLAI 271 + NADEGD G F DR ++EG+P ++EG+ I A GA +G+IY R EYP A+ ++ AI Sbjct: 178 VCNADEGDSGTFADRMIMEGDPFVLIEGMAIAGIATGATKGYIYTRSEYPHAIAVMSAAI 237 Query: 272 RQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAVK 331 A G +G +LGS F ++V GAGA+VCGE ++L+ +LEG+ G R K A K Sbjct: 238 EIARAAGVLGASVLGSAHAFDMEVRTGAGAYVCGEETSLLNSLEGKRGLVRAKPPLPAHK 297 Query: 332 GVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPMG 391 G++D P+V+NNV + A+V I+ KGA ++ +G S GT + G + + GL E G Sbjct: 298 GLFDRPTVINNVISLASVPVILDKGAGYYRDFGMGRSRGTIPLQIAGNVKHGGLFETAFG 357 Query: 392 VTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMGSGGMI 451 +TL +I+ ++GGG + KAVQ GGP G P A+ D P D++ ++G G++ Sbjct: 358 LTLGEIVDEIGGGTASARPVKAVQVGGPLGAYFPRALFDTPFDYEAFAARDGLIGHAGIV 417 Query: 452 VMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIELLEEL 511 V D+ M+ AR+ ++F ESCGKCTPCR G + + V RI G E + ELL +L Sbjct: 418 VFDDTADMLKQARFAMEFCAVESCGKCTPCRIGSTRGVEVADRIAAGIEPEKNRELLADL 477 Query: 512 AESTG-AALCALGKSAPNPVLSTIRYFRDEY 541 + +LCALG P PV+S + +F +++ Sbjct: 478 CNTMKFGSLCALGGFTPYPVMSAMTHFPEDF 508 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: 844 Number of extensions: 40 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: 518 Length adjustment: 36 Effective length of query: 599 Effective length of database: 482 Effective search space: 288718 Effective search space used: 288718 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