Align Benzoyl-CoA reductase, putative (characterized, see rationale)
to candidate WP_011385299.1 AMB_RS14710 aldehyde ferredoxin oxidoreductase
Query= uniprot:Q39TV8 (653 letters) >NCBI__GCF_000009985.1:WP_011385299.1 Length = 616 Score = 173 bits (438), Expect = 2e-47 Identities = 137/422 (32%), Positives = 191/422 (45%), Gaps = 24/422 (5%) Query: 6 TGYVLEVDLTKGSIERVATDPRDTELYLGGLGTNAKILWDRVPPEVEPFSPENLLIFAAG 65 TG L +DLT GS++ + YLG G K + V P+V+P SP N +IF G Sbjct: 4 TGKFLRIDLTNGSVKTEELNRAWARQYLGQRGLATKYFAEEVDPKVDPLSPANKMIFTTG 63 Query: 66 LLCGTPATGCNRTIVSTVSPQTKLMAFSMMGGFWAPELKYAGYDKIIFRGKSPELVYLYI 125 L GT A+ R V T P T +A S GGF+ ELK AG+D II G+SP+ VYL I Sbjct: 64 PLTGTAASTGGRYSVVTKGPLTNCIACSNSGGFFGNELKNAGWDMIIVEGRSPKPVYLSI 123 Query: 126 NNDKVEIRDASHLKGKGAIETAEIIKKELNEPRAQVAAIGKAGENRVFYASIEQG-RSSA 184 N+ VEIRDA+ GK ET +K +P +VA IG AGE V YA I +A Sbjct: 124 ENETVEIRDAAEFWGKTVWETENGLKARHQDPMLRVATIGAAGEKGVLYACIVNDLHRAA 183 Query: 185 SRGGIGAVMGDKGLKAVVVRGTKDLCVAKPEEYIGLCNEVLDYIKHREENPIPDVMPILA 244 R G+GAVMG K LKA+ VRGT+ + V P+ +I ++ K +N + L Sbjct: 184 GRSGVGAVMGSKNLKAIAVRGTRGVTVKDPDRFI---KATIEQKKVLADNAVTG--QGLP 238 Query: 245 GLGSPQEMKVHDEKWHTENFNWGNARTRRKDFWTDEVSHAWEKTMDKARTRLI-SCYNCP 303 G+ M V +E N+ + + E H T KA +C+ C Sbjct: 239 KYGTQVLMNVINEIGAMPTRNFKEVQFEGAHKISAEAMHEPRATDGKANLATNGACFGCT 298 Query: 304 MKCG-------ATISMEGLPTYMMKCFTKLTYTMAAYSDLDFGLRIAQKAT-------EY 349 + CG S+ P Y + + Y A D G+ + T E+ Sbjct: 299 IACGRISRMDPGHFSITSRPQY-KEPSGGVEYEAAWAMGSDCGVDDLEACTFANFMCNEH 357 Query: 350 GLDGFSAPQVMAFAFELLEKGILKDSDFPG--LPEGNEERFFYLLDKIVNRDGIGDILAN 407 G+D S +A A E+ E G++ G L G+ E + + +G G L Sbjct: 358 GIDPISFGSTLAAAMEMFEMGVITKEQTGGVELKFGSAEALVKMAELTGKGEGFGLELGQ 417 Query: 408 GT 409 G+ Sbjct: 418 GS 419 Score = 49.7 bits (117), Expect = 4e-10 Identities = 36/95 (37%), Positives = 46/95 (48%), Gaps = 11/95 (11%) Query: 552 PKFIAAGAGIEMDTEKLKKAAKRYRTLVRAFNIRRGMRRVDEQPPANHWKNRFPE----- 606 P+ AA G E E L + +R TL R FN+ GM D+ P K+ Sbjct: 523 PQIDAACEG-EWTPEILLEVGERIWTLERQFNLAAGMTAADDTLPKRLLKDAAKTGPAKG 581 Query: 607 ----LEKELLDSYYKLKGWNDDGIPTKETLDDLGL 637 LEK +L YY+L+GW DG+PT ETL L L Sbjct: 582 LTSGLEK-MLPEYYQLRGWTTDGVPTTETLKRLQL 615 Lambda K H 0.319 0.138 0.425 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: 904 Number of extensions: 46 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 653 Length of database: 616 Length adjustment: 38 Effective length of query: 615 Effective length of database: 578 Effective search space: 355470 Effective search space used: 355470 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