Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate WP_012116598.1 XAUT_RS23440 NADH-quinone oxidoreductase subunit NuoF
Query= uniprot:Q39TW5 (635 letters) >NCBI__GCF_000017645.1:WP_012116598.1 Length = 433 Score = 273 bits (697), Expect = 1e-77 Identities = 150/389 (38%), Positives = 226/389 (58%), Gaps = 11/389 (2%) Query: 164 SKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKW----EESRNAPDPIKYVIVNADEGD 219 +K + + + ++ E+K S LRGRGG GF KW ++S P Y++VNADE + Sbjct: 32 TKAILEKGRDWIINEMKTSGLRGRGGAGFSTGMKWSFMPKQSDGRPH---YLVVNADESE 88 Query: 220 PGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLAIRQASERGF 279 PG DR ++ +PH+++EG +I ++A+GAH +IYVR EY + + AI +A + G Sbjct: 89 PGTCKDREIMRNDPHTLIEGCLIASFAMGAHAAYIYVRGEYIFERKRLQAAIDEAYDAGL 148 Query: 280 VGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAVKGVWDHPSV 339 +GK + + F + VH GAGA++CGE +AL+ +LEG+ G PR K A G++ P+ Sbjct: 149 IGKSNIHD-YPFDLYVHHGAGAYICGEETALLESLEGKKGMPRLKPPFPANMGLYGCPTT 207 Query: 340 LNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPMGVTLRDIIT 399 +NNVE+ A I+ +GA WF+S G + GTK+FSL G + +VE M + R+++ Sbjct: 208 VNNVESIAVAPTILRRGAAWFSSIGRPNNVGTKLFSLAGHVNTPCVVEEAMSIPFRELVD 267 Query: 400 KVGGGIPGG-KKFKAVQTGGPSGGCIP-EAMLDLPVDFDELTKAGSMMGSGGMIVMDEDT 457 K GGG+ GG + GG S IP E DL +DFD S +G+ G++VMD+ T Sbjct: 268 KHGGGVRGGWDNLLGIIPGGASCPVIPAEQCADLIMDFDGTRAVKSSLGTAGVLVMDKST 327 Query: 458 CMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIE-LLEELAESTG 516 ++ F K ESCG+CTPCREG M V+ R+ G+ ++ +I+ LLE + G Sbjct: 328 DIIKAIARISAFFKHESCGQCTPCREGTGWMWRVVNRMAEGRAQKREIDMLLEVTTQIEG 387 Query: 517 AALCALGKSAPNPVLSTIRYFRDEYEAHI 545 +CALG +A PV IR++R E I Sbjct: 388 HTICALGDAAAWPVQGLIRHYRHVIEERI 416 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: 759 Number of extensions: 45 Number of successful extensions: 5 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: 433 Length adjustment: 35 Effective length of query: 600 Effective length of database: 398 Effective search space: 238800 Effective search space used: 238800 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