Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate Pf1N1B4_2989 NAD-dependent formate dehydrogenase beta subunit
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2989 Length = 520 Score = 317 bits (813), Expect = 6e-91 Identities = 188/522 (36%), Positives = 283/522 (54%), Gaps = 24/522 (4%) Query: 26 PCISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMI-YPEG 84 PC S+ A GA EV A T+ L ++ T G P++ + P+G Sbjct: 8 PCDSLAR-----AVGADEVSVALATQARERNLPLDLQR--TSSRGLYWLEPLLEVDSPQG 60 Query: 85 -ICYLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIPFYKNQQRNILSEN 143 I + + DVP V+D L E A ++P+ K QQR + + Sbjct: 61 RIGFGPLTAADVPS----------VLDALQGEPSAHPLALGLVEELPYLKTQQRLLFARA 110 Query: 144 LRLDSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRN 203 S++DY A GG+ L++ + + E + S LRGRGG FPA KW R Sbjct: 111 GITQPLSLEDYRAHGGFEGLTQAI-ALGGEQTATAVFDSGLRGRGGAAFPAGIKWRTVRG 169 Query: 204 APDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLA 263 KY++ NADEGD G F DR L+EG+P ++EG+ I VGA G+IYVR EYP A Sbjct: 170 TQAAQKYIVCNADEGDSGTFADRMLMEGDPFLLIEGMAIAGITVGATYGYIYVRSEYPDA 229 Query: 264 VENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRP 323 V + A+ A G++G ++ GSG F ++V +GAGA++CGE +AL+ +LEG+ G R Sbjct: 230 VATLRAALNIARSAGYLGANVGGSGQAFDMEVRVGAGAYICGEETALLDSLEGKRGIVRA 289 Query: 324 KYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNT 383 K A++G++ P++++NV T A+V I+ KGA ++ YG S GT F L G I + Sbjct: 290 KPPIPALQGLFGLPTLVHNVLTLASVPLILAKGAQFYRDYGMGRSLGTMPFQLAGNIRHG 349 Query: 384 GLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGS 443 GLVE G+TLR+++ GGG G+ KA Q GGP G +P A D P+D++ G+ Sbjct: 350 GLVERAFGLTLRELVEDYGGGTASGRPLKAAQVGGPLGAWVPPAQFDTPLDYEAFAAIGA 409 Query: 444 MMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVG---KG 500 M+G GG++V D+ M +AR+ + F +ESCGKCTPCR G + + V+ R+ Sbjct: 410 MLGHGGVVVADDTLDMAHMARFAMQFCAEESCGKCTPCRIGSTRGVEVIDRLLAAPDQNS 469 Query: 501 KEGDIELLEELAESTG-AALCALGKSAPNPVLSTIRYFRDEY 541 ++ + +L++L ++ +LCALG PV S ++YF ++ Sbjct: 470 RDEQVIILKDLCDTLQYGSLCALGGMTSYPVASALKYFPADF 511 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: 806 Number of extensions: 36 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