Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate CCNA_02024 CCNA_02024 NADH-quinone oxidoreductase chain F
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Caulo:CCNA_02024 Length = 439 Score = 265 bits (676), Expect = 4e-75 Identities = 153/379 (40%), Positives = 216/379 (56%), Gaps = 12/379 (3%) Query: 175 VMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDPIK-----YVIVNADEGDPGAFMDRALI 229 ++ +K S LRGRGG GF KW P +K Y++VNADE +PG DR ++ Sbjct: 46 IIENMKNSGLRGRGGAGFSTGLKWSFM---PKEVKDGRPHYLVVNADESEPGTCKDREIM 102 Query: 230 EGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLAIRQASERGFVGKDILGSGF 289 +PH ++EG +I + A+ AH +IY+R EY E + AI+QA E VGK+ + G+ Sbjct: 103 RHDPHLLIEGCLIASRAMLAHACYIYIRGEYVFERERLEAAIKQAYEAKLVGKNNV-HGW 161 Query: 290 DFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAVKGVWDHPSVLNNVETWANV 349 DF + VH GAGA++CGE +AL+ +LEG+ G+PR K A G++ P+ +NNVE+ A Sbjct: 162 DFDIYVHHGAGAYICGEETALLESLEGKKGQPRLKPPFPAGAGLYGMPTTVNNVESIAVA 221 Query: 350 TQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPMGVTLRDIITKVGGGIPGG- 408 I+ +GA WF +G + GTK+F + G + VE M + R ++ GGI GG Sbjct: 222 GTILRRGAAWFAGFGRPNNAGTKLFCVSGHVNLPCNVEEAMSIPFRQLVEDHCGGIRGGW 281 Query: 409 KKFKAVQTGGPSGGCIP-EAMLDLPVDFDELTKAGSMMGSGGMIVMDEDTCMVDIARYFI 467 KAV GG S IP E DLP+DFD L S +G+ +IVMD+DT +V Sbjct: 282 GNLKAVIPGGSSVPMIPAEQCEDLPMDFDALRNLKSGLGTAAVIVMDKDTDLVRAIARLS 341 Query: 468 DFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIE-LLEELAESTGAALCALGKSA 526 F K ESCG+CTPCREG M V+ R+ G+ +I+ LL+ + G +CALG +A Sbjct: 342 YFYKHESCGQCTPCREGTGWMWRVMERMVTGEADPKEIDTLLDVTTQVEGHTICALGDAA 401 Query: 527 PNPVLSTIRYFRDEYEAHI 545 P+ R+FR E E I Sbjct: 402 AWPIQGLFRHFRHEVEERI 420 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: 761 Number of extensions: 33 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: 439 Length adjustment: 35 Effective length of query: 600 Effective length of database: 404 Effective search space: 242400 Effective search space used: 242400 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