Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_050464725.1 AKL27_RS20495 isovaleryl-CoA dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >NCBI__GCF_001189915.1:WP_050464725.1 Length = 394 Score = 263 bits (671), Expect = 8e-75 Identities = 142/377 (37%), Positives = 226/377 (59%), Gaps = 6/377 (1%) Query: 5 EEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTGY 64 E+ +R FA+ + P AAE DR +FP + +M +LG G+ E++GG GY Sbjct: 13 EDIAALRASVAAFAQAEIAPRAAEIDRSDQFPMDLWKKMGDLGVLGITAEEEYGGAAMGY 72 Query: 65 LAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFALT 124 LA+ + LEEI+ + H+++ I + G EQKAK+L+ L SG +GA A++ Sbjct: 73 LAHIIALEEISRASASVGLSYGAHSNLCVNQIKRNGTAEQKAKYLSKLISGDFIGALAMS 132 Query: 125 EPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184 EP AGSD S+K RA L+GD YVLNG K +IT+G +A V++V+A TDP+AG RG++AF+V Sbjct: 133 EPNAGSDVVSMKLRADLKGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGARGMTAFLV 192 Query: 185 PTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRVGI 244 G+SVA+ DKLG S T +++F+D +VP+ N LG G+G + ++ L+ R + Sbjct: 193 EKGFKGFSVAQKLDKLGMRGSHTGELVFQDCEVPLENVLGGIGKGVNVLMSGLDYERTVL 252 Query: 245 AAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYA---- 300 + +G+ +A + A Y +R FG+ I E Q + ++ADM + + + V+ Sbjct: 253 SGGPLGIMQACMDVAVPYIHDRKQFGQSIGEFQLMQGKIADMYSTMMACKAYVYAVGQAC 312 Query: 301 --AALRDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQ 358 AA D+ + +A+ A L+++E A + +Q LGG GY+N++P R++RD ++ + Sbjct: 313 DRAATPDAARALRKDAAGAILYSAEKATWMAGETIQILGGNGYINEYPAGRLWRDAKLYE 372 Query: 359 IYEGTSDIQRMVISRNL 375 I GTS+I+RM+I R L Sbjct: 373 IGAGTSEIRRMLIGREL 389 Lambda K H 0.320 0.134 0.388 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: 330 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: 394 Length adjustment: 30 Effective length of query: 345 Effective length of database: 364 Effective search space: 125580 Effective search space used: 125580 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