Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate BPHYT_RS14990 BPHYT_RS14990 formate dehydrogenase subunit beta
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__BFirm:BPHYT_RS14990 Length = 520 Score = 321 bits (822), Expect = 6e-92 Identities = 192/517 (37%), Positives = 280/517 (54%), Gaps = 16/517 (3%) Query: 28 ISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYP-EG-I 85 I V + LA GA + A + E GL E+ G+ G P+V + EG I Sbjct: 4 IYVPRDSSALALGADALAQAIENEAARRGLAIELVRNGSR--GLLWLEPLVEVQTSEGRI 61 Query: 86 CYLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIPFYKNQQRNILSENLR 145 Y ++ DV + D E A R IP+ K QQR + Sbjct: 62 GYANIEAGDVSALF----------DAGFLEGGAHANRVGVVDAIPYLKKQQRLTFARIGI 111 Query: 146 LDSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAP 205 D S+DDY+A GG L L Q + + +S LRGRGG FPA KW R A Sbjct: 112 TDPLSIDDYVAHGGLEGLRNAL-QTDGDAACEALIESGLRGRGGAAFPAGIKWRTVRGAK 170 Query: 206 DPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVE 265 KY++ NADEGD G F DR ++E +P+ ++EG+II GA G IYVR EYP ++ Sbjct: 171 AAQKYIVCNADEGDSGTFSDRLVMESDPYVLIEGMIIAGVVTGATVGHIYVRSEYPHSIA 230 Query: 266 NINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKY 325 + AI +A G++G +LGS F + V GAGA+VCGE +AL+ +LEG+ G R K Sbjct: 231 TLEAAIAKARAAGWLGDRVLGSAHRFELFVAKGAGAYVCGEETALLESLEGKRGIVRAKP 290 Query: 326 IHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGL 385 A+ G++ P+V+NNV T A V I +GA ++ +G S GT F L G + GL Sbjct: 291 PVPALVGLFGQPTVINNVITLATVPIIFARGAAFYKDFGMGRSRGTLPFQLAGNVKQGGL 350 Query: 386 VEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMM 445 VE+ GVTLR+++ GGG G+ +AVQ GGP G +PE+ D+P+D++ G+++ Sbjct: 351 VELAFGVTLRELLYDYGGGTASGRPARAVQVGGPLGTYLPESQWDIPMDYEAYAAVGAVV 410 Query: 446 GSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDI 505 G GG++V D+ + + ++A+Y + F ESCGKCTPCR G + + V+ RI G + Sbjct: 411 GHGGLVVHDDTSNLAELAQYAMHFCALESCGKCTPCRIGSTRGVEVIGRIRNGDTSTRQV 470 Query: 506 ELLEELAES-TGAALCALGKSAPNPVLSTIRYFRDEY 541 +LL +L ++ +LCA+G P PVLS + +F +++ Sbjct: 471 QLLRDLCDTMVSGSLCAMGGMTPFPVLSALDHFPEDF 507 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: 818 Number of extensions: 47 Number of successful extensions: 4 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