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) >NCBI__GCF_000009985.1:WP_011385160.1 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:
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