Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_111393797.1 CLV31_RS14820 acyl-CoA dehydrogenase
Query= BRENDA::B0EVL5 (395 letters) >NCBI__GCF_003253485.1:WP_111393797.1 Length = 379 Score = 223 bits (567), Expect = 9e-63 Identities = 134/377 (35%), Positives = 201/377 (53%), Gaps = 5/377 (1%) Query: 16 LDSQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYG 75 ++ QLT+ V+++AR ++Q LLP V + K +MG+LG LG + +Y Sbjct: 1 MNFQLTEEHLAVQEAAREFAQSELLPGVIDRDSEAKFPHEQIKKMGDLGFLGMMVDPKYN 60 Query: 76 GSGMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGEWV 135 G GM+ + Y + E+ ++D+ MSV +SLV + ++GSEE KQKYL +LATGE + Sbjct: 61 GGGMDTISYVIAMEELSKIDASASVSMSVNNSLVCWGLEKYGSEEQKQKYLTRLATGEIL 120 Query: 136 GCFGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKDDAG----D 191 G F L+EP GSD S T A Y L+G K WITN A V++V A+ DA Sbjct: 121 GAFCLSEPEAGSDATSQRTSAEWNGDHYVLNGTKNWITNGSTASVYLVIAQTDASKGHKG 180 Query: 192 IRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTVR-GLKGPFTCLN 250 I F++EKGW+G K+G+R S T ++ +V P EN G LN Sbjct: 181 ISVFLVEKGWEGFVIGKKEDKLGIRGSDTHSLMFTDVKVPAENRIGEEGFGFTFAMETLN 240 Query: 251 SARYGIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQGCL 310 R GIA ALG A YE A Y+ +RK FG+P++ +Q IQ KLADM T+I Sbjct: 241 GGRIGIAAQALGIASGAYELALAYSKERKAFGKPISQHQAIQFKLADMATQIEAARLLVY 300 Query: 311 RLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLEVVN 370 + LKD+G +++ K + ++++ A + GG G E+ + R + + ++ Sbjct: 301 KAAWLKDQGEDYAHASAMAKLYASEVAMNVTVEAVQVHGGYGYVKEYHVERLMRDAKITQ 360 Query: 371 TYEGTHDIHALILGRAI 387 YEGT +I +++ R I Sbjct: 361 IYEGTSEIQRIVISRGI 377 Lambda K H 0.319 0.136 0.409 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: 336 Number of extensions: 20 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: 395 Length of database: 379 Length adjustment: 30 Effective length of query: 365 Effective length of database: 349 Effective search space: 127385 Effective search space used: 127385 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