Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_086510406.1 BZY95_RS13300 isovaleryl-CoA dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >NCBI__GCF_002151265.1:WP_086510406.1 Length = 389 Score = 295 bits (755), Expect = 1e-84 Identities = 154/372 (41%), Positives = 232/372 (62%), Gaps = 2/372 (0%) Query: 5 EEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTGY 64 +E +RD FA + + P AAE D ++ FP + + ++G G+ VPE+ GG GY Sbjct: 14 DELNMLRDQVNAFARDEIAPRAAEIDEKNEFPNDLWQKFGDMGLLGITVPEEDGGTGMGY 73 Query: 65 LAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFG-NDEQKAKFLTPLASGAMLGAFAL 123 LA+ + +EEI+ + H+++ CV LK N EQKAK+L L SG +GA A+ Sbjct: 74 LAHCIAMEEISRASASVGLSYGAHSNL-CVNQLKINANAEQKAKYLPKLISGEHIGALAM 132 Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 +EP AGSD S+K RAR EGD Y+LNG K +IT+G +A V++V+A TDP AG +GI+AFI Sbjct: 133 SEPGAGSDVVSMKLRARQEGDKYILNGNKMWITNGPDADVLVVYAKTDPEAGSKGITAFI 192 Query: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRVG 243 + PG+S A+ DKLG S+TC+++F+D +VPV N LG+EG+G ++ ++ L+ R Sbjct: 193 IEKGMPGFSTAQKLDKLGMRGSNTCELVFQDCEVPVENVLGDEGKGVRVLMSGLDYERTV 252 Query: 244 IAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 +AA +G+ +AA + Y ER F + I E Q V ++ADM T + R ++ AA Sbjct: 253 LAAGPIGIMQAAMDVVVPYVHERKQFNQSIGEFQLVQGKIADMYTTLNACRAYLYAVAAA 312 Query: 304 RDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGT 363 D GQ + +A+ L+ +E A +V A+Q LGG GY+N++P R+ RD ++ +I GT Sbjct: 313 CDRGQTSRKDAAGVILYCAEKATQVALDAIQLLGGNGYINEYPTGRLLRDAKLYEIGAGT 372 Query: 364 SDIQRMVISRNL 375 S+I+RM+I R L Sbjct: 373 SEIRRMLIGREL 384 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: 333 Number of extensions: 15 Number of successful extensions: 1 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: 389 Length adjustment: 30 Effective length of query: 345 Effective length of database: 359 Effective search space: 123855 Effective search space used: 123855 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