Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate SMc01918 SMc01918 NADH dehydrogenase I subunit F
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Smeli:SMc01918 Length = 434 Score = 280 bits (717), Expect = 7e-80 Identities = 158/409 (38%), Positives = 241/409 (58%), Gaps = 12/409 (2%) Query: 146 LDSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKW----EES 201 L KS+ +A G + +K + + ++ E+K S LRGRGG GFP KW +ES Sbjct: 15 LKDKSLRGAMARGHWDG-TKQFLEKGRDWIINEVKASGLRGRGGAGFPTGLKWSFMPKES 73 Query: 202 RNAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYP 261 P Y++VNADE +PG DR ++ +PH+++EG +I ++A+GAH +IYVR E+ Sbjct: 74 DGRPH---YLVVNADESEPGTCKDRDIMRHDPHTLIEGCVIASFAMGAHAAYIYVRGEFI 130 Query: 262 LAVENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEP 321 E + AI + E G +GK+ G+D + VH GAGA++CGE +AL+ +LEG+ G+P Sbjct: 131 REREALQAAIDECYEYGLLGKNNK-LGYDIDIYVHHGAGAYICGEETALLESLEGKKGQP 189 Query: 322 RPKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKIT 381 R K A G++ P+ +NNVE+ A I+ +GA W+TS+G + GTK++S+ G + Sbjct: 190 RLKPPFPANMGLYGCPTTVNNVESIAVTPTILRRGAGWYTSFGRPNNHGTKLYSVSGHVN 249 Query: 382 NTGLVEVPMGVTLRDIITKVGGGIPGG-KKFKAVQTGGPSGGCIPEA-MLDLPVDFDELT 439 VE M + ++I K GGI GG AV GG S C+P A M D +D+D L Sbjct: 250 RPCTVEDAMSIPFHELIEKHCGGIRGGWDNLLAVIPGGSSVPCVPGAQMKDAIMDYDGLR 309 Query: 440 KAGSMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGK 499 + GS +G+ +IVMD+ T ++ F K ESCG+CTPCREG M+ V+ R+ G+ Sbjct: 310 ELGSGLGTAAVIVMDKSTDIIKAIWRLSAFYKHESCGQCTPCREGTGWMMRVMERMVQGR 369 Query: 500 GKEGDIELLEELAEST-GAALCALGKSAPNPVLSTIRYFRDEYEAHIRE 547 ++ +I++L ++ + G +CALG +A P+ I++FR E E I E Sbjct: 370 AQKREIDMLFDVTKQVEGHTICALGDAAAWPIQGLIKHFRPEMEKRIDE 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: 754 Number of extensions: 48 Number of successful extensions: 6 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: 434 Length adjustment: 35 Effective length of query: 600 Effective length of database: 399 Effective search space: 239400 Effective search space used: 239400 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