Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate GFF1026 HP15_1005 acyl-CoA dehydrogenase domain protein
Query= metacyc::G1G01-166-MONOMER (393 letters) >FitnessBrowser__Marino:GFF1026 Length = 389 Score = 204 bits (520), Expect = 3e-57 Identities = 128/378 (33%), Positives = 196/378 (51%), Gaps = 18/378 (4%) Query: 19 LTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSGL 78 L E M+R+ FA ++APR E R+ + ++R+MG++GLLG T+ E+YGGS + Sbjct: 12 LGETLDMLREQINGFAASEIAPRAEEIDRNNEFPMDLWRKMGDMGLLGITVSEEYGGSDM 71 Query: 79 NYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFG 138 Y+ + + E+ R + S+L + I+ GTE QKQKYLPKL SGE IG Sbjct: 72 GYLAHVIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEEQKQKYLPKLVSGEHIGALA 131 Query: 139 LTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAG----DIRGF 194 ++EPN GSD SM A+ Y L G+KMWITN P A+ +V++AK D + F Sbjct: 132 MSEPNAGSDVISMKLTAKDEGDHYLLNGNKMWITNGPDANTYVIYAKTDTSAGSRGVTAF 191 Query: 195 VLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDV-RGLKGPFTCLNSARY 253 ++E+ G S K+G+R S T E+V + VP+EN+ V G K + L+ R Sbjct: 192 IVERDAPGFSRHQKLDKLGMRGSNTCELVFQDCKVPKENVLGGVGNGAKVLMSGLDYERL 251 Query: 254 GISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGR 313 +S G LG +A Y +R+QFG+ + +L+Q K+ADM T + A + Sbjct: 252 VLSGGPLGIMQAAMDVVVPYIRERKQFGQAIGEFELVQGKVADMYTWMNTAKSYVYMVAM 311 Query: 314 MKDEGTAAVEITSIMKRNSCGKALDIARMAR-------DMLGGNGISDEFGVARHLVNLE 366 D G ++++ G L A MA +LGGNG +E+ R L + + Sbjct: 312 SADRGAETT------RKDAAGAILYSAEMATKIALDAIQLLGGNGYINEYPTGRLLRDAK 365 Query: 367 VVNTYEGTHDVHALILGR 384 + GT ++ +++GR Sbjct: 366 LYEIGAGTSEIRRMLIGR 383 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: 354 Number of extensions: 12 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: 393 Length of database: 389 Length adjustment: 31 Effective length of query: 362 Effective length of database: 358 Effective search space: 129596 Effective search space used: 129596 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