Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate WP_011385160.1 AMB_RS13985 NADH-quinone oxidoreductase subunit NuoF
Query= uniprot:Q39TW5 (635 letters) >lcl|NCBI__GCF_000009985.1:WP_011385160.1 AMB_RS13985 NADH-quinone oxidoreductase subunit NuoF Length = 427 Score = 281 bits (720), Expect = 3e-80 Identities = 150/380 (39%), Positives = 227/380 (59%), Gaps = 6/380 (1%) Query: 175 VMGEIKKSNLRGRGGGGFPAWRKWE--ESRNAPDPIKYVIVNADEGDPGAFMDRALIEGN 232 ++ E+K S LRGRGG GFP KW P P Y+++NADEG+PG DR ++ + Sbjct: 43 IIEEMKNSGLRGRGGAGFPTGVKWSFMPKTEGPRP-HYLVINADEGEPGTCKDREMMRFD 101 Query: 233 PHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLAIRQASERGFVGKDILGSGFDFT 292 PH ++EG +I ++A+GAH +IY+R E+ E++N+AI +A G +G + GSG+D Sbjct: 102 PHKLIEGALIASFAIGAHAAYIYIRGEFVREAEHLNIAIDEARAAGLLGPNACGSGWDCE 161 Query: 293 VKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAVKGVWDHPSVLNNVETWANVTQI 352 V VH GAGA++CGE SAL+ +LEG+ G+PR K A G++ P+ +NNVE+ A I Sbjct: 162 VYVHRGAGAYICGEESALIESLEGKKGQPRLKPPFPAGVGLYGCPTTVNNVESIAVAPTI 221 Query: 353 ITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPMGVTLRDIITKVGGGIPGG-KKF 411 + +GA WF+ G +TGTK+F + G + VE MG+ L+++I K GG+ GG Sbjct: 222 LRRGAAWFSGLGKPNNTGTKVFCISGHVNTPCNVEEEMGIPLKELIEKHAGGVRGGWDNL 281 Query: 412 KAVQTGGPSGGCIPEAML-DLPVDFDELTKAGSMMGSGGMIVMDEDTCMVDIARYFIDFL 470 A+ GG S + + ++ +DFD L S +G+ ++VMD+ T +V F Sbjct: 282 LAIIPGGSSVPMLTKQQCEEVTMDFDALRAMRSGLGTAAVMVMDKSTDLVRAIHRLSRFY 341 Query: 471 KDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIELLEELA-ESTGAALCALGKSAPNP 529 ESCG+CTPCREG M ++ R+ G + +I+LLEE++ + G +CALG +A P Sbjct: 342 WHESCGQCTPCREGTGWMSRMMGRMVTGDAELSEIDLLEEISRQIEGHTICALGDAAAWP 401 Query: 530 VLSTIRYFRDEYEAHIREKK 549 + IR FR E E I +++ Sbjct: 402 IQGLIRAFRPEMERRILDRQ 421 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: 763 Number of extensions: 41 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 635 Length of database: 427 Length adjustment: 35 Effective length of query: 600 Effective length of database: 392 Effective search space: 235200 Effective search space used: 235200 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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