Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_086509502.1 BZY95_RS08430 acyl-CoA dehydrogenase
Query= reanno::WCS417:GFF2715 (375 letters) >NCBI__GCF_002151265.1:WP_086509502.1 Length = 385 Score = 258 bits (658), Expect = 3e-73 Identities = 140/365 (38%), Positives = 209/365 (57%), Gaps = 1/365 (0%) Query: 12 DAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAMAL 71 D R+F ++ + P W+ P+ ++ E G G+ +PE GG + +AL Sbjct: 14 DTIRRFLEQEVAPHYEAWEEAGEMPRSLWQQLGEAGLLGIDLPEALGGSGADFAIVQLAL 73 Query: 72 EEIAA-GDGACSTIMSVHNSVGCVPVLKFGNDQQKEQFLKPLASGAMLGAFALTEPQAGS 130 EEI+ G G ++ ++H ++ +L G Q+E++L +ASG +GA A+TEP AGS Sbjct: 74 EEISRQGFGGLASAYNIHANIVMPYLLHIGTPAQRERWLPAMASGETIGAIAMTEPGAGS 133 Query: 131 DASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPAAGKRGISAFIVPTDSPG 190 D +++KTRA + L+G K FIT+GQ A +VIV A TDPAAG RG+S F+V T G Sbjct: 134 DLAAMKTRASRTESGWRLDGSKLFITNGQIADLVIVCAKTDPAAGARGVSLFLVDTTLAG 193 Query: 191 YSVARVEDKLGQHASDTCQILFEDVKVPVANRLGEEGEGYKIALANLEGGRVGIASQAVG 250 +S + K+GQHASDT ++ F+D+++P LGE G G+ + L R+G+A+QA+G Sbjct: 194 FSRGQPIKKIGQHASDTAELFFDDLRLPEEALLGEAGAGFAYLMQELPRERLGVAAQALG 253 Query: 251 MARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGKPA 310 A DY RER +FG+ + E Q F LA++ QI + R A G+ Sbjct: 254 AMEGALALTLDYVRERRAFGRAVGEFQNTRFTLAEVRAQIDMGRAYFEQCVAKYRQGEMN 313 Query: 311 LVEASMAKLFASEMAEKVCSAALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQRMV 370 +A++ KL SEM + A LQ GGYGY ++P+ R Y D RV +Y GTS+I + V Sbjct: 314 GTDAAILKLQLSEMQCRTIDACLQLFGGYGYTREYPISRFYLDARVQTLYAGTSEIMKEV 373 Query: 371 ISRNL 375 I+R+L Sbjct: 374 IARSL 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: 331 Number of extensions: 15 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: 385 Length adjustment: 30 Effective length of query: 345 Effective length of database: 355 Effective search space: 122475 Effective search space used: 122475 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