Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_013258112.1 DEBA_RS06440 acyl-CoA dehydrogenase
Query= reanno::WCS417:GFF2715 (375 letters) >NCBI__GCF_000143965.1:WP_013258112.1 Length = 382 Score = 336 bits (861), Expect = 7e-97 Identities = 171/372 (45%), Positives = 247/372 (66%), Gaps = 1/372 (0%) Query: 5 EEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGY 64 EEQL + + A +FA + LKP AA +D+ H P E + + ELGF G+ +PE++GG Y Sbjct: 7 EEQLMVKETAARFADDELKPKAAHYDKTHEHPAEFVEALGELGFMGIAIPEEYGGAGMDY 66 Query: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPVLKFGNDQQKEQFLKPLASGAMLGAFALT 124 ++Y +AL EI+ GD + IMSV NS+ P+ FG D+QK+ FL P+ASG LG + LT Sbjct: 67 VSYVLALSEISRGDASVGVIMSVCNSLYGFPLNSFGTDEQKKAFLTPVASGKKLGCYGLT 126 Query: 125 EPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPAAGKRGISAFIV 184 E AGSD ++++T A L+G+ +VLNG K+FIT+G A +V A+TD AAG +GIS+F+V Sbjct: 127 EAGAGSDPAAMRTTAVLDGNEWVLNGEKKFITNGNVASYAVVAAITDKAAGAKGISSFVV 186 Query: 185 PTD-SPGYSVARVEDKLGQHASDTCQILFEDVKVPVANRLGEEGEGYKIALANLEGGRVG 243 + + G+SV +E+K+G AS T +++FED ++P N LG+ G G K L L GR+G Sbjct: 187 DLENTKGFSVGFIEEKMGICASGTSELVFEDARIPKENLLGQLGGGLKQMLMTLNSGRIG 246 Query: 244 IASQAVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 I SQA+G+ RA E A YA+ERE FGKPI QA+ ++LAD+AT + A ++ AA L Sbjct: 247 IGSQALGIGRAVLEEAVAYAKEREQFGKPIAAMQAIQWKLADIATHLDAAELLLLRAAWL 306 Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSAALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363 D ++A+M K++AS+ A +Q LGGYGY ++ +ER RD ++ QIYEGT Sbjct: 307 EDQHANFEMQAAMGKMYASDAAMAAAIEGVQVLGGYGYCKEYAMERHMRDAKITQIYEGT 366 Query: 364 SDIQRMVISRNL 375 ++I R+VI+RNL Sbjct: 367 NEIMRLVIARNL 378 Lambda K H 0.319 0.134 0.387 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: 385 Number of extensions: 14 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: 375 Length of database: 382 Length adjustment: 30 Effective length of query: 345 Effective length of database: 352 Effective search space: 121440 Effective search space used: 121440 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: 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