Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate RR42_RS00895 RR42_RS00895 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >FitnessBrowser__Cup4G11:RR42_RS00895 Length = 376 Score = 291 bits (746), Expect = 2e-83 Identities = 163/378 (43%), Positives = 236/378 (62%), Gaps = 5/378 (1%) Query: 5 LTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGG 64 LTPE E +R V +FA +AP + FP + RE+ +G +G+ PE+YGG G Sbjct: 3 LTPEQEMIRDAVRQFAQQEIAPHAAAWDRDKTFPQAVHRELAALGAYGVAVPEQYGGAGL 62 Query: 65 DYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILGAFG 124 DYL+L + LEE+A D + + + F ++AQK +WL L GE+LGAF Sbjct: 63 DYLSLALILEEIAAGDGGTSTVISVNNCPVCSMLMAFASEAQKQQWLVPLARGEMLGAFC 122 Query: 125 LTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPDGKP 184 LTEP GSDA A RT+A D +++V+NG K FIT+ + V AVT K GK Sbjct: 123 LTEPHVGSDAAALRTSAVRDG--DDYVLNGVKQFITSGKN--ADVAIVLAVTD-KAAGKR 177 Query: 185 LISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFLRIL 244 IS+ +VP+ TPG+ VA K+G ++SDT ++ F D RVPAAN+LGE+G GY L L Sbjct: 178 GISAFLVPTATPGYIVARLEEKLGQHSSDTAQILFEDCRVPAANMLGEEGAGYKMALSGL 237 Query: 245 DEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMARVGW 304 + GRI I++ + G+A+ D ++ YA ER +FG+ + A+QA+QF++ADM K +AR Sbjct: 238 EGGRIGIASQSIGMARAAFDAALAYAKERESFGQPLFAHQAVQFRLADMATKIEVARQMV 297 Query: 305 RDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDSKIL 364 AAS AG P KEAA+ KLY+S +A + A Q+ GGYG+++++PV R++RD ++ Sbjct: 298 WHAASLKDAGRPCLKEAAMGKLYASEMAEEVCSAAIQVFGGYGYVSDFPVERIYRDVRVC 357 Query: 365 EIGEGTSEVQRMLIAREL 382 +I EGTS++Q++LIAR L Sbjct: 358 QIYEGTSDIQKILIARAL 375 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: 17 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 17 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