Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate AO356_22050 AO356_22050 NADH dehydrogenase
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_22050 Length = 451 Score = 309 bits (791), Expect = 2e-88 Identities = 170/424 (40%), Positives = 243/424 (57%), Gaps = 15/424 (3%) Query: 133 KNQQRNILSENLRLDSKS--MDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGG 190 ++ + + L+ LR D ++ +D+Y A GY+A K M +D++ +K S L+GRGG Sbjct: 14 RSAETHPLTWRLRDDGEAVWLDEYQAKNGYAAARKAFTDMAQDDIVQTVKDSGLKGRGGA 73 Query: 191 GFPAWRKW-----EESRNAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAY 245 GFP KW +ES N I+Y++ NADE +P + DR L+E PH ++EG++I A Sbjct: 74 GFPTGVKWGLMPKDESIN----IRYLLCNADEMEPNTWKDRMLMEQLPHLLIEGMLISAR 129 Query: 246 AVGAHEGFIYVRQEYPLAVENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCG 305 A+ + G+I++R EY A +++N A+ +A G +GK+ILGSGFDF + VH GAG ++CG Sbjct: 130 ALKTYRGYIFLRGEYTTAAKHLNRAVEEAKAAGLLGKNILGSGFDFELFVHTGAGRYICG 189 Query: 306 ESSALMTALEGRAGEPRPKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGT 365 E +AL+ +LEGR PR K A GVW P+ +NNVET NV II G DW+ S Sbjct: 190 EETALINSLEGRRANPRSKPPFPAAVGVWGKPTCVNNVETLCNVPAIIADGVDWYKSLAR 249 Query: 366 AGS--TGTKIFSLVGKITNTGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGC 423 GS GTK+ GK+ N GL E+P G+T R++ GG+ G K Q GG G Sbjct: 250 DGSEDMGTKLMGFSGKVKNPGLWELPFGITGRELFEDYAGGMRDGYTLKCWQPGGAGTGF 309 Query: 424 IPEAMLDLPVDFDELTKAGSMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCRE 483 + LD + + K G+ MG+G + +D+ MV + R +F ESCG CTPCR+ Sbjct: 310 LLPEHLDAQMYAGGIAKVGTRMGTGLAMAVDDSVNMVSLLRNMEEFFSRESCGFCTPCRD 369 Query: 484 GIRQMLAVLTRITVGKGKEGDIELLEELAE--STGAALCALGKSAPNPVLSTIRYFRDEY 541 G+ + +L I G+G+ GDIE L L G CA A P+ S I+YFR E+ Sbjct: 370 GLPWSVKLLRAIENGEGQAGDIETLLGLVGFLGPGKTFCAHAPGAVEPLGSAIKYFRPEF 429 Query: 542 EAHI 545 EA I Sbjct: 430 EAGI 433 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: 764 Number of extensions: 47 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: 451 Length adjustment: 35 Effective length of query: 600 Effective length of database: 416 Effective search space: 249600 Effective search space used: 249600 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 Apr 09 2024. 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