Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_111393848.1 CLV31_RS15640 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_003253485.1:WP_111393848.1 Length = 401 Score = 219 bits (558), Expect = 1e-61 Identities = 133/383 (34%), Positives = 210/383 (54%), Gaps = 12/383 (3%) Query: 1 MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYG 60 +D LT E + +R ++ +F ++P I D+ ++ FPYEIV++ G +G FG P EYG Sbjct: 23 LDDLLTEEQKLIRSSIRDFVKKEISPYIEDWAQKAHFPYEIVKKFGEVGAFGPQLPVEYG 82 Query: 61 GMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEIL 120 G DY++ G+ ++E+ R DS + T SL PI+ FGT+ Q+ ++LPRL SGE+L Sbjct: 83 CGGLDYISYGLIMQEIERGDSGMRSTASVQGSLVMYPIYKFGTEEQRLKYLPRLASGELL 142 Query: 121 GAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKP 180 G FGLTEPD GS+ T + + + +++NG K +I+NS + V + Sbjct: 143 GCFGLTEPDHGSNPSGMVTNFK--DMGDHYLLNGAKMWISNSPK-----ADIAVVWAKNE 195 Query: 181 DGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLL-GEQGRGYAQ 239 +G+ I +IV G GF+ ++K AS T EL F +V+VP NLL G+ G G Sbjct: 196 EGR--IQGLIVERGMEGFSTPETHNKWSLRASCTGELVFDNVKVPKENLLPGKTGLGAP- 252 Query: 240 FLRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHM 299 + LD R I+ A G A C + + +YA ER FG+ IG +Q Q K+A+M + Sbjct: 253 -MMCLDSARFGIAWGAIGAAMDCYESARRYAAERIQFGKPIGGFQLTQKKLAEMLTEITK 311 Query: 300 ARVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWR 359 A++ + G+ ++AK + +A++ AREA QIHGG G EYP+ R Sbjct: 312 AQLLAWKVGKMMNEGKAKTVHISMAKRNNVEMALNIAREARQIHGGMGITGEYPIMRHMM 371 Query: 360 DSKILEIGEGTSEVQRMLIAREL 382 + + + EGT ++ +++ E+ Sbjct: 372 NLESVITYEGTHDIHLLILGNEI 394 Lambda K H 0.318 0.136 0.402 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: 411 Number of extensions: 19 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: 386 Length of database: 401 Length adjustment: 31 Effective length of query: 355 Effective length of database: 370 Effective search space: 131350 Effective search space used: 131350 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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