Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate 3607889 Dshi_1297 acyl-CoA dehydrogenase domain protein (RefSeq)
Query= metacyc::G1G01-166-MONOMER (393 letters) >FitnessBrowser__Dino:3607889 Length = 387 Score = 206 bits (523), Expect = 1e-57 Identities = 124/371 (33%), Positives = 194/371 (52%), Gaps = 5/371 (1%) Query: 19 LTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSGL 78 L EE +R+ +++AQ+++ P E R A++ EMGE+GLLG T+ E YGG+G+ Sbjct: 10 LGEEVEALREMVHRWAQERVKPLAAETDRSNAFPNALWPEMGELGLLGITVDEAYGGAGM 69 Query: 79 NYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFG 138 Y+ + + E+ R + S+L + I GT+AQK+KYLPKL SG +G Sbjct: 70 GYLAHTVAVEEISRASASIGLSYGAHSNLCVNQIKLNGTDAQKEKYLPKLVSGAHVGALA 129 Query: 139 LTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDD--AGD--IRGF 194 ++E GSD M RA K + YRL G+K WITN P AD VV+AK D AG I F Sbjct: 130 MSEAGAGSDVVGMKLRAEKRNDHYRLNGTKYWITNGPDADTLVVYAKTDPEAGSKGITAF 189 Query: 195 VLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIF-PDVRGLKGPFTCLNSARY 253 ++EK G S K+G+R S T E++ ++V VP EN+ + RG+ + L+ R Sbjct: 190 LIEKEMAGFSTSPHFDKLGMRGSNTAELIFEDVEVPFENVLGEEGRGVAVLMSGLDYERV 249 Query: 254 GISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGR 313 +S +G C Y +R+QFG P+ QL+Q K+ADM T + A + + Sbjct: 250 VLSGVNIGIMAGCLDEVMPYMTERRQFGEPIGNFQLMQGKIADMYTAMNSARAYAYEVAK 309 Query: 314 MKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYEG 373 D G + + + + + +A A +GG G ++ VAR + +++ G Sbjct: 310 ACDRGEVTRQDAAACVLYASEEGMKVAHQAVQAMGGAGFLNDSPVARMFRDAKLMEIGAG 369 Query: 374 THDVHALILGR 384 T ++ +++GR Sbjct: 370 TSEIRRMLVGR 380 Lambda K H 0.320 0.137 0.413 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: 13 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: 393 Length of database: 387 Length adjustment: 31 Effective length of query: 362 Effective length of database: 356 Effective search space: 128872 Effective search space used: 128872 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 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