Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_009779945.1 MED217_RS07745 acyl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2991 (396 letters) >NCBI__GCF_000152985.1:WP_009779945.1 Length = 602 Score = 231 bits (588), Expect = 6e-65 Identities = 135/389 (34%), Positives = 211/389 (54%), Gaps = 21/389 (5%) Query: 16 EDIDALRDAVRDFAQAEIAPRAADIDKSDQ-FPMDLWRKMGDLGVLGITVPEQYGGAAMG 74 E+ +++ V++F EI P + D ++ RK G+LG+LGI VP++Y G MG Sbjct: 34 EEQKMMKETVKEFVDREIVPNKERFEHKDYALTEEVMRKAGELGLLGIAVPDEYDGLGMG 93 Query: 75 YLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLISGEHVGALAM 134 +++ M+ + IS A+ S+ ++GAH+ + I G E QK KY+ KL +GE GA + Sbjct: 94 FVSTMLVCDYISGATGSIATAFGAHTGIGTMPITLYGTEEQKKKYVPKLATGEWFGAYCL 153 Query: 135 SEPGAGSDVISMKLKAE--DKGGYYLLNGSKMWITNGPDADTLVVYAKTEPELGARGVTA 192 +EPGAGSD S K KAE G Y +NG KMWI+N + +V+A+ E + + +T Sbjct: 154 TEPGAGSDANSGKTKAELSADGKSYKINGQKMWISNAGFCNLFIVFARIEDD---KNITG 210 Query: 193 FLIEK-GMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLMSGLDYE 251 F++E G S+ ++ KLG+ S T ++ F D VP EN+L G +G K+ M+ L+ Sbjct: 211 FIVENDSSNGISLGEEEKKLGIHSSSTRQVFFNDTVVPVENMLAGRGEGFKIAMNALNVG 270 Query: 252 RAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGRSFAYTV 311 R L L + ++D + Y ++R QF I +F I+ K+A+M T S +Y Sbjct: 271 RIKLAAACLDAQRRIIDMGVKYANERVQFKTPIAQFGAIKYKLAEMATNAYVCESASYRA 330 Query: 312 AKNLD-------MLGTDH-------VRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGY 357 AKN++ G H V + +C+ + + +E A EG+QIYGG G+ Sbjct: 331 AKNIEDRIAIRMADGNSHQEAELKGVEEYAIECSILKVAASEDMQNCADEGIQIYGGMGF 390 Query: 358 INEYPLGRLWRDAKLYEIGAGTSEIRRML 386 + P+ WRDA++ I GT+EI RML Sbjct: 391 SADAPMEAAWRDARISRIYEGTNEINRML 419 Lambda K H 0.318 0.136 0.400 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: 538 Number of extensions: 29 Number of successful extensions: 4 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: 602 Length adjustment: 34 Effective length of query: 362 Effective length of database: 568 Effective search space: 205616 Effective search space used: 205616 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 (21.7 bits) S2: 52 (24.6 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