Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_012333698.1 M446_RS18850 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_000019365.1:WP_012333698.1 Length = 376 Score = 270 bits (690), Expect = 5e-77 Identities = 156/371 (42%), Positives = 226/371 (60%), Gaps = 5/371 (1%) Query: 12 LRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGGDYLALGI 71 +R T FA + P ++ FP E V +G +G G+ PE YGG D+++ + Sbjct: 9 IRDTARSFAQARLRPFAAEWDRDSRFPREAVAALGELGFLGMLVPEAYGGSAVDHVSYAL 68 Query: 72 ALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILGAFGLTEPDGG 131 A+EE+A D +V+ + S+ +PI FGT+AQK +L L G LGAF LTEP G Sbjct: 69 AIEEIAAGDGAVSTIMSVHNSVACVPILRFGTEAQKERFLVPLARGAQLGAFCLTEPGAG 128 Query: 132 SDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPDGKPLISSIIV 191 SDAGA TAR N +V++GTK FIT+ + L V AVT + GK IS+ IV Sbjct: 129 SDAGAV--TARARRVGNRYVLSGTKQFITSGRS--ADLAIVFAVTDPEA-GKRGISAFIV 183 Query: 192 PSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFLRILDEGRIAI 251 P+ TPG+ VA K+G ASDT ++ F D+ + LLG++G G L L+ GRI I Sbjct: 184 PTATPGYRVARIEHKLGQRASDTAQIVFEDMELTPDLLLGQEGEGLRIALSNLEGGRIGI 243 Query: 252 SALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMARVGWRDAASRL 311 +A A G+A+ + ++ YAGER FG+ + A+QA+ F++ADM + AR+ +AA Sbjct: 244 AAQAVGMARAAFEAALAYAGERETFGQKLTAHQAVAFRLADMATRIEAARLLVHNAARLR 303 Query: 312 VAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDSKILEIGEGTS 371 AG+P KEAA+AKL++S +A +A QIHGGYG++ +YPV R++RD ++ +I EGTS Sbjct: 304 DAGQPCLKEAAMAKLFASEMAEAVCSDAIQIHGGYGYLADYPVERIYRDVRVCQIYEGTS 363 Query: 372 EVQRMLIAREL 382 +VQR++I+R L Sbjct: 364 DVQRIVISRAL 374 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: 399 Number of extensions: 11 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: 386 Length of database: 376 Length adjustment: 30 Effective length of query: 356 Effective length of database: 346 Effective search space: 123176 Effective search space used: 123176 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