Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_099020245.1 CCS90_RS14235 acyl-CoA dehydrogenase
Query= metacyc::G1G01-166-MONOMER (393 letters) >NCBI__GCF_002591915.1:WP_099020245.1 Length = 386 Score = 164 bits (415), Expect = 4e-45 Identities = 114/372 (30%), Positives = 191/372 (51%), Gaps = 8/372 (2%) Query: 19 LTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSGL 78 L E+++ D+A +FA ++AP + + R GE+G LG PE+YGG GL Sbjct: 5 LNEDQQAFVDAAKEFAISEMAPLAAKWDEESIFPVDVIRNTGELGFLGIYSPEKYGGLGL 64 Query: 79 NYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFG 138 + + LI E+ + + + +++ + + + FG+E+ + + +L SGE + + Sbjct: 65 SRLDASLIFEEMSKHCTSTTAYLTIHNMCAWM-LTTFGSESLAETWGTQLTSGELLASYC 123 Query: 139 LTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAGDIRG---FV 195 LTEP HGSD G++ T A K D Y L GSK +I+ + ++ +V A+ RG F+ Sbjct: 124 LTEPGHGSDAGNLKTTAVKTDDTYVLNGSKTFISGAGSTEILIVMARTGEAGPRGVSCFM 183 Query: 196 LEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIF-PDVRGLKGPFTCLNSARYG 254 + G+S K+G + T I ++V +P E + + G K L+ R Sbjct: 184 VPADLAGISYGKKEDKMGWNSQPTRLITFEDVTIPAEYLIGQEGEGFKFAMKGLDGGRIN 243 Query: 255 ISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGRM 314 I+ +LG A+A + A+ Y L+R+QFG+ LA+ Q +Q KLADM TE+ A Q +RL + Sbjct: 244 IASCSLGTAQAALNQAQSYMLERKQFGQSLASFQALQFKLADMLTELIAARQ-MVRLAAV 302 Query: 315 K--DEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYE 372 K ++ A ++ KR + I A + GG G E+ + RH+ + V E Sbjct: 303 KLDNKHPQASAYCAMAKRFATDVCFQICDEALQLHGGYGYIKEYPLERHVRDTRVHRILE 362 Query: 373 GTHDVHALILGR 384 GT+++ LI+ R Sbjct: 363 GTNEIMRLIISR 374 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: 334 Number of extensions: 20 Number of successful extensions: 5 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: 386 Length adjustment: 30 Effective length of query: 363 Effective length of database: 356 Effective search space: 129228 Effective search space used: 129228 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