Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate HSERO_RS07425 HSERO_RS07425 formate dehydrogenase subunit beta
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__HerbieS:HSERO_RS07425 Length = 520 Score = 342 bits (878), Expect = 2e-98 Identities = 194/511 (37%), Positives = 285/511 (55%), Gaps = 18/511 (3%) Query: 37 LASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYPEGICYLKVKPEDVP 96 LA GA EV AA E G + ++ G+ + E V + Y V PEDV Sbjct: 18 LALGANEVAAAITAEAHKRGQSIKLVRNGSRGMFWLEPLVEVATAAGRVAYGPVAPEDVA 77 Query: 97 EIVSHTIKEKKVVDRLLYEDPATGTRALR---ESDIPFYKNQQRNILSENLRLDSKSMDD 153 + + + G AL +I F KNQ+R + +D S++D Sbjct: 78 GLFDAGLLQG-------------GQHALHLGLTEEIAFLKNQERLTFARVGIIDPLSLED 124 Query: 154 YLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDPIKYVIV 213 YLA GY L L + TPE ++ E+ S LRGRGG FP KW+ A KYV+ Sbjct: 125 YLAHEGYVGLKNALAK-TPEAIVQEMIASGLRGRGGAAFPTGIKWQTVLRAQSAQKYVVC 183 Query: 214 NADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLAIRQ 273 NADEGD G F DR ++E +P +++EG+ I AVGA EG+IYVR EYP ++ + AI Sbjct: 184 NADEGDSGTFSDRMIMEDDPFTLIEGMTIAGVAVGATEGYIYVRSEYPHSIATLEQAIAI 243 Query: 274 ASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAVKGV 333 A +G++G DILGSG F ++V GAGA++CGE +A++ +LEG+ G R K A++G+ Sbjct: 244 AHAQGYLGDDILGSGKSFRLEVRKGAGAYICGEETAMLESLEGKRGVVRAKPPLPAIEGL 303 Query: 334 WDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPMGVT 393 + P+V+NN+ + A+V I+ +GAD++ ++G S GT F L G I GLVE G+T Sbjct: 304 FGKPTVINNLISLASVPVILARGADFYKNFGVGRSHGTLPFQLAGNIRQGGLVEKAFGLT 363 Query: 394 LRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMGSGGMIVM 453 LR ++ GGG G+ +AVQ GGP G +P++ D P+D++ G+M+G GG++ Sbjct: 364 LRQLLEDFGGGSASGRPIRAVQMGGPLGAYLPQSQFDTPLDYEAFAAIGAMIGHGGLVAF 423 Query: 454 DEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIELLEELAE 513 D+ M ARY + F ESCGKCTPCR G + + V+ +I + I LL+ L + Sbjct: 424 DDSVDMARQARYAMQFCAVESCGKCTPCRIGSTRGVEVIDKIIANDDRAQQIHLLKSLCD 483 Query: 514 S-TGAALCALGKSAPNPVLSTIRYFRDEYEA 543 + +LCA+G P PVLS + +F +++ A Sbjct: 484 TMVNGSLCAMGGMTPFPVLSALNHFPEDFGA 514 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: 823 Number of extensions: 47 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: 520 Length adjustment: 36 Effective length of query: 599 Effective length of database: 484 Effective search space: 289916 Effective search space used: 289916 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