Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate PfGW456L13_4886 NAD-dependent formate dehydrogenase beta subunit
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4886 Length = 519 Score = 318 bits (815), Expect = 4e-91 Identities = 188/523 (35%), Positives = 289/523 (55%), Gaps = 26/523 (4%) Query: 26 PCISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMI-YPEG 84 PC S+ A GA EV A ++ + L E+ T G P++ + P+G Sbjct: 7 PCDSLAR-----AVGADEVSVALISQAKERNLPLELQR--TSSRGLYWLEPLLEVDSPQG 59 Query: 85 -ICYLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALR-ESDIPFYKNQQRNILSE 142 I + + DVP ++ L +P++ AL ++ + K QQR + + Sbjct: 60 RIGFGPLTAADVPSVLD-----------ALQGEPSSHPLALGLVEELSYLKTQQRLLFAR 108 Query: 143 NLRLDSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESR 202 S+DDY A GG+ L++ + + E E+ S LRGRGG FPA KW R Sbjct: 109 AGITRPLSLDDYRAHGGFEGLTRAI-AVGGEQTATEVFDSGLRGRGGAAFPAGIKWRTVR 167 Query: 203 NAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPL 262 KY++ NADEGD G F DR L+EG+P ++EG+ I VGA G+IYVR EYP Sbjct: 168 ATEAVQKYIVCNADEGDSGTFADRMLMEGDPFLLIEGMAIAGITVGATYGYIYVRSEYPD 227 Query: 263 AVENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPR 322 AV + A+ A + G++G ++ GSG F ++V +GAGA++CGE +AL+ +LEG+ G R Sbjct: 228 AVATLRAALNIARDAGYLGANVGGSGLAFDMEVRVGAGAYICGEETALLDSLEGKRGIVR 287 Query: 323 PKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITN 382 K A+KG++ P++++NV T A+V I+ KGA ++ YG S GT F L G I + Sbjct: 288 AKPPIPALKGLFGLPTLVHNVLTLASVPLILAKGAQFYRDYGMGRSLGTMPFQLAGNIRH 347 Query: 383 TGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAG 442 GLVE G+TLR+++ GGG G+ KA Q GGP G +P + D P+D++ G Sbjct: 348 GGLVERAFGLTLRELVEDYGGGTASGRPLKAAQVGGPLGAWVPPSQFDTPLDYEAFAAIG 407 Query: 443 SMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITV---GK 499 +M+G GG++V D+ M +AR+ + F +ESCGKCTPCR G + + V+ R+ Sbjct: 408 AMLGHGGVVVADDSLDMAHMARFAMQFCAEESCGKCTPCRIGSTRGVEVIDRLLAAPDAS 467 Query: 500 GKEGDIELLEELAESTG-AALCALGKSAPNPVLSTIRYFRDEY 541 G++ + +L++L ++ +LCALG PV S +++F ++ Sbjct: 468 GRDEQVIILKDLCDTLQYGSLCALGGMVSFPVASALKHFPADF 510 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: 39 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: 519 Length adjustment: 36 Effective length of query: 599 Effective length of database: 483 Effective search space: 289317 Effective search space used: 289317 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