Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate N515DRAFT_0484 N515DRAFT_0484 glutaryl-CoA dehydrogenase
Query= reanno::ANA3:7024494 (389 letters) >FitnessBrowser__Dyella79:N515DRAFT_0484 Length = 389 Score = 211 bits (537), Expect = 3e-59 Identities = 124/373 (33%), Positives = 195/373 (52%), Gaps = 6/373 (1%) Query: 12 LGEEVDMLRDAVQDFAKHEIAPIAAKVDHDNAFPNEIWPVLGGMGLLGVTVPEEYGGANM 71 L +E M++D V F + PI FP E+ P + G+GLLG T+PE+YG A M Sbjct: 17 LTDEERMVQDTVGRFVDERVLPIIGDAFDQGRFPKELIPEIAGLGLLGATLPEQYGCAGM 76 Query: 72 GYLAHVVAMEEISRASASIGLSYGAHSNLCVNQINRNGNAEQKAKYLPKLVSGEHIGALA 131 +++ + +E+ R + + S+LC+ I G EQK YLPK+ +GE IG Sbjct: 77 NGVSYGLICQELERGDSGLRSFASVQSSLCMYPIYAYGTEEQKLHYLPKMAAGEIIGCFG 136 Query: 132 MSEPNAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDANTYVIYAKTDLTKGAHGITAF 191 ++EP+ GSD +MK +ARK+G +I+NG KMWITNG A+ +++A+T+ GI F Sbjct: 137 LTEPHGGSDPANMKTNARKDGGDWIINGAKMWITNGNLAHIAIVWAQTE-----DGIQGF 191 Query: 192 IVERGFKGFSQAQKLDKLGMRGSNTCELVFEDVEVPEENILGGLNNGVKVLMSGLDYERV 251 IV +GF+ + K+ +R S T L F+ V VPE N L + G+K + L R Sbjct: 192 IVPTDSQGFTAQEVHKKMSLRASVTSALFFDSVRVPEANRLPNV-KGLKGPLGCLTQARY 250 Query: 252 VLSGGPLGIMNACMDIVVPYIHEREQFGKSIGEFQLVQGKLADMYTGMNAAKAYVYSVAK 311 ++ GP+G AC+ V+ Y ER FG+ + Q +Q KLA+M + A+ + + Sbjct: 251 GITWGPIGAAQACLKEVLDYTQERVLFGRPLASNQAIQLKLAEMARRITMAQLLSLQLGR 310 Query: 312 SCDRGETTRKDAAGAILYSAELATKMALDAIQLLGGNGYVNEYATGRLLRDAKLYEIGAG 371 D G + A + +A +A + +LGG G E+ R + + G Sbjct: 311 LKDAGNMQPTQVSLAKWNNCRIAIDIARECRDILGGAGITTEHVAIRHALNLESVITYEG 370 Query: 372 TSEIRRMLIGREL 384 T + ++++GREL Sbjct: 371 TETVHQLVVGREL 383 Lambda K H 0.316 0.135 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: 337 Number of extensions: 14 Number of successful extensions: 3 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: 389 Length of database: 389 Length adjustment: 30 Effective length of query: 359 Effective length of database: 359 Effective search space: 128881 Effective search space used: 128881 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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