Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate RR42_RS03755 RR42_RS03755 formate dehydrogenase
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Cup4G11:RR42_RS03755 Length = 517 Score = 330 bits (846), Expect = 9e-95 Identities = 190/519 (36%), Positives = 279/519 (53%), Gaps = 18/519 (3%) Query: 34 AGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYPEGICYLKVKPE 93 + LA GA V A E G + E+ G+ + E V + Y V PE Sbjct: 11 SSALAMGADAVARAIAREAAARGASIELVRNGSRGMFWLEPLVEVQTTAGRVAYGPVTPE 70 Query: 94 DVPEIVSHTIKEKKVVDRLLYEDPATGTRALR---ESDIPFYKNQQRNILSENLRLDSKS 150 DV + A G AL +IPF K Q+R + D S Sbjct: 71 DVAALFDAGFL-------------AGGAHALALGLTEEIPFLKGQERLTFARMGITDPLS 117 Query: 151 MDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDPIKY 210 + DY+A GY+ L++ L + ++ E+ S LRGRGG FP KW+ A PIKY Sbjct: 118 LADYIAHDGYAGLTRAL-TLDGAQIVQEVTDSGLRGRGGAAFPTGIKWQTVHQAQSPIKY 176 Query: 211 VIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLA 270 V+ NADEGD G F DR ++EG+P ++EG+ I AVGA G+IYVR EYP A+ + A Sbjct: 177 VVCNADEGDSGTFSDRMVMEGDPFMLIEGMTIAGLAVGAEHGYIYVRSEYPHAIAVLESA 236 Query: 271 IRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAV 330 I A G++G D+ GSG F + V GAGA+VCGE +AL+ +LEG+ G R K A+ Sbjct: 237 IGIAQAAGWLGDDLRGSGRRFRLDVRKGAGAYVCGEETALLESLEGKRGVVRAKPPLPAI 296 Query: 331 KGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPM 390 +G++ P+++NNV + A V I+ +GA ++ +G S GT F + G + GLVE Sbjct: 297 EGLFGKPTIINNVISLATVPVILARGAQFYRDFGMGRSRGTLPFQIAGNVRQGGLVEKAF 356 Query: 391 GVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMGSGGM 450 GVTLR+++ G G + +AVQ GGP G +P + LD P+D++ G+++G GG+ Sbjct: 357 GVTLRELLEGYGQGTRSARPIRAVQVGGPLGAYLPVSRLDTPMDYEAFAAFGAVLGHGGI 416 Query: 451 IVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIELLEE 510 +V D+ M ARY ++F ESCGKCTPCR G + + V+ +I G ++L+ + Sbjct: 417 VVFDDTVDMARQARYAMEFCAIESCGKCTPCRIGSTRGVEVIDKIIAGDQPVKHVKLVRD 476 Query: 511 LAES-TGAALCALGKSAPNPVLSTIRYFRDEYEAHIREK 548 L ++ G +LCA+G P PVLS + F +++ + K Sbjct: 477 LCDTMLGGSLCAMGGMTPYPVLSALDAFPEDFGVAVPAK 515 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: 846 Number of extensions: 38 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: 517 Length adjustment: 36 Effective length of query: 599 Effective length of database: 481 Effective search space: 288119 Effective search space used: 288119 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