Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate WP_011426948.1 RHE_RS19125 NADH-quinone oxidoreductase subunit NuoF
Query= uniprot:Q39TW5 (635 letters) >NCBI__GCF_000092045.1:WP_011426948.1 Length = 420 Score = 383 bits (983), Expect = e-110 Identities = 187/402 (46%), Positives = 262/402 (65%), Gaps = 2/402 (0%) Query: 151 MDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDPIKY 210 + Y A GGY AL KVL + TP++V+ +K+SNLRGRGG GF KW KY Sbjct: 18 LSTYEAGGGYQALVKVLREYTPDEVVELVKRSNLRGRGGAGFLTGMKWSFVPKQSSKPKY 77 Query: 211 VIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLA 270 + NADEG+PG F DR L+E +PH ++EGL + AYA+GA ++Y+R EY A+ + A Sbjct: 78 LCCNADEGEPGTFKDRILMERDPHQLIEGLAVSAYAIGAKTAYVYIRGEYVTAIRRLEQA 137 Query: 271 IRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAV 330 I +A +G++G ILGS F+FTV +H GAGA++CGE +A++ +LEGR +PR K AV Sbjct: 138 IAEAHAKGYLGSRILGSDFNFTVHIHCGAGAYICGEETAMLESLEGRRAQPRLKPPFPAV 197 Query: 331 KGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPM 390 G++ P+V+NNVET A V I+ +G+DWF G S G K++ + G++ GL E+PM Sbjct: 198 AGLYASPTVINNVETLACVPHIVVRGSDWFRDIGPEKSPGPKLYCVSGQVRKPGLYELPM 257 Query: 391 GVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMGSGGM 450 G+ LR+++ GG P G++ KAV GG S IPE LD+ +DFD L AGSM+GS G+ Sbjct: 258 GIPLRELVDHAGGP-PPGRRIKAVIPGGVSAPVIPEHGLDVGMDFDSLAAAGSMLGSAGV 316 Query: 451 IVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIELLEE 510 IV+D TCMV +A I+F ESCGKCTPCREG+ ++ +L RI G G GD+E L+ Sbjct: 317 IVIDNSTCMVKVATRIIEFFHHESCGKCTPCREGLNWVVKILRRIEAGDGAPGDLEQLDM 376 Query: 511 LAEST-GAALCALGKSAPNPVLSTIRYFRDEYEAHIREKKCP 551 L + G CALG A + + +++FR+E+ AHI E++CP Sbjct: 377 LCKGIFGNTFCALGDGAAMGLRAALKHFREEFVAHIEERRCP 418 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: 764 Number of extensions: 46 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: 420 Length adjustment: 35 Effective length of query: 600 Effective length of database: 385 Effective search space: 231000 Effective search space used: 231000 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: 52 (24.6 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