Align Benzoyl-CoA reductase subunit A; 3-hydroxybenzoyl-CoA reductase subunit alpha; EC 1.3.7.8; EC 1.3.99.n1 (characterized)
to candidate WP_013417736.1 RVAN_RS00195 benzoyl-CoA reductase subunit A
Query= SwissProt::O87876 (438 letters) >NCBI__GCF_000166055.1:WP_013417736.1 Length = 430 Score = 626 bits (1614), Expect = 0.0 Identities = 314/436 (72%), Positives = 361/436 (82%), Gaps = 7/436 (1%) Query: 1 MECFVGIDLGSTTTKAVVMDDKGQVLGRGITNSRSNYDTAARVSKLEAFIDARLSLIRRE 60 M CF+GIDLGSTTTKAVVMD+ VLGRGITNSRSNYDTAA VSK EA +D RL+L RR Sbjct: 1 MRCFIGIDLGSTTTKAVVMDENQNVLGRGITNSRSNYDTAAAVSKQEALVDTRLTLFRRA 60 Query: 61 LDKEPAVAGRVDEIIDGLTRNFRREQFIEQLGDLEQTCVANVEGPRFAGKEKAIVGALTE 120 L+ P A + ++ GL RNFR QF+EQL DLE+TC+ NV+GPRFAG+EK ++ AL E Sbjct: 61 LEAVPGTADTAEAVLAGLERNFRHIQFVEQLEDLERTCIGNVKGPRFAGREKPVIEALAE 120 Query: 121 VFRRLREEEADKLFAPDAQRKSDFFRDLAGSRFMQIGEEVARANGVEFDHLLHMYDKSII 180 FRRLRE A + FAP +RKSDFFRDLAG FM GE V R G+ FD +L++YDKSII Sbjct: 121 TFRRLREHSATQ-FAPGFRRKSDFFRDLAGGDFMHNGEAVCREAGLAFDLILNIYDKSII 179 Query: 181 EVENRPPSADMNRKFRSAMERVRGEMSSALDTAALGAPIDAALEIDMSERYVVGTGYGRV 240 EVENRPP+ D+ KF A+E +LD + + AP+ AAL I + E YVVGTGYGRV Sbjct: 180 EVENRPPAGDIEGKFVRALEM------GSLDQSLIAAPVKAALSIPLEETYVVGTGYGRV 233 Query: 241 RLPFPKEHIRSEILCHGLGAHLMYPKTRTVLDIGGQDTKGIQIDDKGIVVNFQMNDRCAA 300 RLPFPKEHIRSEILCHGLGAH+MYP+TRTVLDIGGQDTKGIQ+D GIV NFQMNDRCAA Sbjct: 234 RLPFPKEHIRSEILCHGLGAHIMYPRTRTVLDIGGQDTKGIQVDPAGIVENFQMNDRCAA 293 Query: 301 GTGRYLGYVADEMNMGLHELGPLAMKSTKSIRINSTCTVFAGAELRDRLALGDKREDILA 360 G GRYLGY+ADEMNMGL ELGPLAM+STK +RINSTCTVFAGAELRDRLALG+KREDILA Sbjct: 294 GCGRYLGYIADEMNMGLQELGPLAMQSTKQVRINSTCTVFAGAELRDRLALGEKREDILA 353 Query: 361 GLHRAIMLRAMSIISRSGGITDQFTFTGGVAKNEAAVKELRQLVKENYGEVQINIDPDSI 420 GLHRAI+LRAMSI+SR+GG+ DQFTFTGGVAKNEAAV+ELR+L+KENYG+VQINI+PDSI Sbjct: 354 GLHRAIILRAMSILSRAGGVKDQFTFTGGVAKNEAAVRELRKLIKENYGDVQININPDSI 413 Query: 421 YTGALGASEFARRAVV 436 YTGALG + FA RAV+ Sbjct: 414 YTGALGGAAFAVRAVL 429 Lambda K H 0.320 0.137 0.385 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: 602 Number of extensions: 17 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: 438 Length of database: 430 Length adjustment: 32 Effective length of query: 406 Effective length of database: 398 Effective search space: 161588 Effective search space used: 161588 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 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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