Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_050655857.1 C1M55_RS09530 acyl-CoA dehydrogenase
Query= BRENDA::Q3JP94 (395 letters) >NCBI__GCF_002893965.1:WP_050655857.1 Length = 380 Score = 189 bits (480), Expect = 1e-52 Identities = 121/380 (31%), Positives = 189/380 (49%), Gaps = 6/380 (1%) Query: 12 LLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQ 71 L+ Q+ D + RD A LAP+V E + E +F +G+ GLL PE+ Sbjct: 6 LMPSQEARDLIELTRDVADKV----LAPKVNEYEKAEKYPDGVFPALGQAGLLSLPYPEE 61 Query: 72 YGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGE 131 +GG Y Y + E+ + +SV S L P+F FG+D QK ++LP + G Sbjct: 62 FGGGDQPYEVYLQVLEEIASRWAAVAVAVSVHS-LSCFPLFTFGTDEQKNRWLPDMLGGN 120 Query: 132 WIGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRD 191 IG + L+E GSD ++ +A GGY ++GSK WITN AD + ++A+ +DG Sbjct: 121 TIGAYSLSEAQAGSDAAALSCKATPTDGGYRVNGSKAWITNGGKADFYNLFARTSDDGSR 180 Query: 192 EIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENIL-PHVKGLRGPFTCL 250 + +++K +GLS K+GLRA T D+AF+PEE ++ +GL F+ L Sbjct: 181 GVSCLLVDKDAEGLSFGKPEEKMGLRAVPTASANYDDAFIPEERLIGQRGQGLPIAFSAL 240 Query: 251 NSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGV 310 +S R GIA A+G A+ A Y +RK FG+ + +Q + LADM + Sbjct: 241 DSGRLGIAAVAVGIAQGALDDAVAYAKERKAFGKRIIDHQGLGFVLADMAAAVDSARATY 300 Query: 311 LRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVV 370 L R +D G S+ K + A+ + A + GG G + +F V R++ ++ Sbjct: 301 LDAARRRDAGVPYSRNASVAKLVATDAAMKVTTDAVQVFGGYGYTQDFPVERYMREAKIT 360 Query: 371 NTYEGTHDIHALILGRAQTG 390 +EGT+ I L++ R G Sbjct: 361 QIFEGTNQIQRLVIARQLAG 380 Lambda K H 0.320 0.138 0.414 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: 388 Number of extensions: 16 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: 380 Length adjustment: 30 Effective length of query: 365 Effective length of database: 350 Effective search space: 127750 Effective search space used: 127750 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