Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate WP_050750753.1 AMB_RS17165 NADP oxidoreductase
Query= uniprot:Q39TW5 (635 letters) >lcl|NCBI__GCF_000009985.1:WP_050750753.1 AMB_RS17165 NADP oxidoreductase Length = 619 Score = 268 bits (686), Expect = 4e-76 Identities = 162/491 (32%), Positives = 244/491 (49%), Gaps = 46/491 (9%) Query: 61 VNTKGTGCPGFCERGPIVMIYPEGICYLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATG 120 V+ T C G C++GP +++ I + + D ++V+ + ++ P Sbjct: 119 VSVDTTSCTGLCDQGPALLVNYRPITRMTAQRVD------------QIVELIRHKTP--- 163 Query: 121 TRALRESDIPFYKNQQRNILSENLRLDSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIK 180 L E F+K + +N+R + A G K +P++V+ +K Sbjct: 164 ---LAEWPAEFFK------VEDNIRRKDALLGADFAPGDALKALK-----SPQEVLDSVK 209 Query: 181 KSNLRGRGGGGFPAWRKWEESRNA----PDPIKYVIVNADEGDPGAFMDRALIEGNPHSI 236 +S LRGRGG GF +KW+ R A P YV+ NADEG+PG F DR L+ + Sbjct: 210 ESGLRGRGGAGFSTGQKWDFCRAAVGTGPHAAHYVVCNADEGEPGTFKDRVLLASYAGLV 269 Query: 237 LEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLAIRQASERGFVGKDILG-SGFDFTVKV 295 EG+ + Y +GA +G +Y+R EY +E +N + + +GK ILG +GFDF ++V Sbjct: 270 FEGMTVSGYVIGARKGIVYLRGEYRYLLEPLNAVLEKRRAAKLLGKSILGRTGFDFDIEV 329 Query: 296 HMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAVKGVWDHPSVLNNVETWANVTQIITK 355 H+GAGA+VCGE +AL+ +LEG+ G PR + G P+ +NNVET A+ I K Sbjct: 330 HLGAGAYVCGEETALLESLEGKRGVPRKRPPFPVTAGYLGQPTAVNNVETLASAALIAAK 389 Query: 356 GADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQ 415 GA W+ S GT S GTKI S+ G G+ E P GV + ++ G + +A Q Sbjct: 390 GAAWYKSIGTPKSAGTKILSISGDCERPGIYEYPYGVKVSQVLADC-----GARDTQACQ 444 Query: 416 TGGPSGGCIPEAMLDLPVDFDELTKAGSMMGSGGMIVMDEDTCMVDIARYFIDFLKDESC 475 G SG C+ + F+++ GS M + D M +AR F F ESC Sbjct: 445 IAGASGLCVAPNEFGRRIAFEDIPTGGSFM------IFDNTRDMFQVARNFAHFFVHESC 498 Query: 476 GKCTPCREGIRQMLAVLTRITVGKGKEGDI-ELLEELAESTGAALCALGKSAPNPVLSTI 534 G CTPCR G + + +I G G E DI ++ + A+ C LG++A N V T+ Sbjct: 499 GFCTPCRVGTTLLANAMDKIDEGHGGEYDINDIWRVIRTLKTASHCGLGQTAGNAVADTL 558 Query: 535 RYFRDEYEAHI 545 + FR YE + Sbjct: 559 QKFRPSYELRL 569 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: 1024 Number of extensions: 57 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: 619 Length adjustment: 38 Effective length of query: 597 Effective length of database: 581 Effective search space: 346857 Effective search space used: 346857 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: 54 (25.4 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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