Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate WP_010441027.1 G7G_RS0110000 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20676 (396 letters) >NCBI__GCF_000192475.1:WP_010441027.1 Length = 385 Score = 110 bits (276), Expect = 5e-29 Identities = 101/337 (29%), Positives = 173/337 (51%), Gaps = 31/337 (9%) Query: 65 GGTGWSSVQHYIFNEELQAAPAPQPLAFGV-SMVGPVIYTFGSEEQKKRFLPRIANVDDW 123 GG G+ SV Y Q A +G+ S+V I T+GSE+QK ++LP++A+ + Sbjct: 70 GGMGFDSVTLYE-----QTARGDAGWGYGIQSIVTHYITTYGSEDQKHKWLPKLASGEMI 124 Query: 124 WCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAKKQE 183 +EPG+GSD+ ++KT AEK G+ + + G K + T Q AD + +TD + + Sbjct: 125 GALAMTEPGTGSDVQAVKTTAEKDGNSYRLKGSKIFITNGQSADLVIVAAKTDKSL-GAK 183 Query: 184 GISFILVDMK-TKGI-TVRPIQTID-GGHEVNEVFFDDVEVPLENLVG-QENKGWDYAKF 239 G+S I V+ + T+G R ++ + G++ E+FF+DV+VP+ NL+G +E +G+ Sbjct: 184 GVSLIAVETEGTEGFRRGRNLEKLGMKGNDTAELFFEDVKVPMTNLLGPEEGQGFYQLMK 243 Query: 240 LLGNER--TGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALEL 297 L ER GI +G I + + ++ G+ V++ R KLA E + KA E+ Sbjct: 244 QLPWERLTIGIMALGAIDFAISETVKYVQERKAFGQRVMDFQNTRFKLA--ECKTKA-EV 300 Query: 298 TQLRVVADEGKHGKGKPNPA-SSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDDSN 356 + V GK G+ + A +S++K GSE+Q +++ G + + Sbjct: 301 LRSFVNDCIGKLEAGELDAATASMVKYWGSEVQNEIMHECLQLFGGYGFMMEY------- 353 Query: 357 ETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAV 393 IA Y + R IYGG+NE+ + +I +++ Sbjct: 354 -------PIARLYADARVQMIYGGTNEVMKELIARSL 383 Lambda K H 0.317 0.135 0.411 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: 337 Number of extensions: 13 Number of successful extensions: 2 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: 396 Length of database: 385 Length adjustment: 31 Effective length of query: 365 Effective length of database: 354 Effective search space: 129210 Effective search space used: 129210 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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