Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate GFF1026 PGA1_c10430 NADH-quinone oxidoreductase subunit F
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Phaeo:GFF1026 Length = 432 Score = 281 bits (718), Expect = 5e-80 Identities = 152/383 (39%), Positives = 233/383 (60%), Gaps = 11/383 (2%) Query: 175 VMGEIKKSNLRGRGGGGFPAWRKW----EESRNAPDPIKYVIVNADEGDPGAFMDRALIE 230 ++ +K S LRGRGG GFP KW +ES P Y+++NADE +PG DR ++ Sbjct: 43 IIQNMKDSGLRGRGGAGFPTGLKWSFMPKESDGRPS---YLVINADESEPGTCKDREIMR 99 Query: 231 GNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLAIRQASERGFVGKDILGSGFD 290 +PH+++EG +I ++A+ AH +IY+R EY E + AI + ++G +G++ GSG+D Sbjct: 100 HDPHTLIEGALIASFAMNAHTCYIYLRGEYIREREALQAAIDECYDQGLLGRNAAGSGWD 159 Query: 291 FTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAVKGVWDHPSVLNNVETWANVT 350 F V +H GAGA++CGE +AL+ +LEG+ G PR K A G++ P+ +NNVE+ A V Sbjct: 160 FDVLLHHGAGAYICGEETALIESLEGKKGMPRMKPPFPAGAGLYGCPTTVNNVESIAVVP 219 Query: 351 QIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPMGVTLRDIITKVGGGIPGG-K 409 I+ +G DWF +G + GTK+F++ G + N +VE M ++ ++I K GGI GG Sbjct: 220 TILRRGPDWFAGFGRQNNAGTKLFAISGHVNNPCVVEEAMSISFEELIEKHCGGIRGGWD 279 Query: 410 KFKAVQTGGPSGGCI-PEAMLDLPVDFDELT-KAGSMMGSGGMIVMDEDTCMVDIARYFI 467 AV GG S C+ E M D +DFD L + GS +G+ +IVMD++T ++ Sbjct: 280 NLLAVIPGGSSVPCVRGEKMKDAIMDFDYLRGELGSGLGTAAVIVMDKNTDIIKAIWRLS 339 Query: 468 DFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIELLEELAEST-GAALCALGKSA 526 F K ESCG+CTPCREG M+ V+ R+ G+ + +I++L ++ + G +CALG +A Sbjct: 340 KFYKHESCGQCTPCREGTGWMMRVMDRLVKGEAELEEIDMLWDVTKQVEGHTICALGDAA 399 Query: 527 PNPVLSTIRYFRDEYEAHIREKK 549 P+ IR FR+E E I+ +K Sbjct: 400 AWPIQGLIRNFREEIEDRIKAQK 422 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: 753 Number of extensions: 41 Number of successful extensions: 4 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: 432 Length adjustment: 35 Effective length of query: 600 Effective length of database: 397 Effective search space: 238200 Effective search space used: 238200 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