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) >NCBI__GCF_000009985.1:WP_050750753.1 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:
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