Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate WP_012115455.1 XAUT_RS17550 NADH-quinone oxidoreductase subunit NuoF
Query= uniprot:Q39TW5 (635 letters) >NCBI__GCF_000017645.1:WP_012115455.1 Length = 520 Score = 327 bits (838), Expect = 8e-94 Identities = 185/519 (35%), Positives = 282/519 (54%), Gaps = 16/519 (3%) Query: 26 PCISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYPEG- 84 P I V A +A GA V + L G+T ++ G+ G P++ + E Sbjct: 4 PRIFVPNDATAVACGADRVARKLEAGLLARGITADITRNGSR--GLFWLEPLIEVETERG 61 Query: 85 -ICYLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIPFYKNQQRNILSEN 143 I Y VKP D+ +++ I D L +IP+ K Q R + Sbjct: 62 RIGYGPVKPSDIEDLLHAGILHG--ADHPLCVGLV--------DEIPYLKKQTRLTFARI 111 Query: 144 LRLDSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRN 203 +D S+ DY A GGY L + + + P + E+ +S LRGRGG GFP KW Sbjct: 112 GIIDPLSLTDYKAHGGYRGLERAI-TLGPSATVEEVVESGLRGRGGAGFPTGIKWRTVAA 170 Query: 204 APDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLA 263 AP +Y++ NADEGD G F DR ++E +P ++EG+ I AVGA +G++Y R EYPLA Sbjct: 171 APADQRYIVCNADEGDSGTFADRLIMEADPFCLIEGMTIAGLAVGATKGYVYSRSEYPLA 230 Query: 264 VENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRP 323 + AI +A E G +G +ILGSG F +++ MGAGA+VCGE +AL+ +LEG+ G R Sbjct: 231 FVVMEKAIEKAREAGLLGDNILGSGLSFDMEMRMGAGAYVCGEETALLESLEGKRGLVRA 290 Query: 324 KYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNT 383 K A KG++ P+V+NN+ + A V I+ KG ++ +G S GT + G I Sbjct: 291 KPPLPAHKGLFQKPTVINNLVSLATVPVILDKGGKYYRDFGMGRSRGTMPIQIAGNIKFG 350 Query: 384 GLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGS 443 GL E G+ L +++ +GGG G+ KAVQ GGP G +P D P D++ + Sbjct: 351 GLFETAFGIPLGELVYDIGGGTASGRPVKAVQAGGPLGAYLPTHQFDTPFDYEAFAAKDA 410 Query: 444 MMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEG 503 ++G GG++V D+ + D+A++ ++F ESCGKCTPCR G + + + ++ G+ +E Sbjct: 411 LIGHGGLVVFDDTADLADMAKFAMEFCAHESCGKCTPCRIGSTRGVETIDKVIAGEKREQ 470 Query: 504 DIELLEELAESTG-AALCALGKSAPNPVLSTIRYFRDEY 541 ++ LL +L + +LCALG P PVLS + +F +++ Sbjct: 471 NLALLTDLCHTMKLGSLCALGGFTPYPVLSALNHFPEDF 509 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: 867 Number of extensions: 48 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 Apr 09 2024. 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