Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_011841236.1 RSPH17029_RS09050 acyl-CoA dehydrogenase family protein
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_000015985.1:WP_011841236.1 Length = 379 Score = 233 bits (595), Expect = 5e-66 Identities = 141/384 (36%), Positives = 214/384 (55%), Gaps = 8/384 (2%) Query: 1 MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYG 60 MD L+ E + + F + +AP + E P + ++ +GL G+ EE+G Sbjct: 1 MDFALSEEQQAIFDMARAFGAEEIAPHARAWEEAGTIPRTLWPKVAELGLGGVYVSEEHG 60 Query: 61 GMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEIL 120 G G L + E LA SVA L M I +G++ KA WLP +C+ L Sbjct: 61 GSGLGRLDATLVFEALAMACPSVAAFLSIHNMCAGM-IDRYGSEELKARWLPGICALTTL 119 Query: 121 GAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKP 180 ++ LTEP GSDA A RT R D + + ++GTK FI+ G +T+ G P Sbjct: 120 VSYCLTEPGAGSDAAALRT--RADATPEGYRLSGTKAFISGGGYS-DAYLTMCRTGGAGP 176 Query: 181 DGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQF 240 G IS+++VP+GTPG + K+GW A +TR++ F + VP L+GE+GRG+A Sbjct: 177 KG---ISTLLVPAGTPGLSFGGLEDKMGWRAQETRQVQFDECLVPTDLLVGEEGRGFAYA 233 Query: 241 LRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMA 300 + LD GR+ I+A A G AQ D + Y ER AFG+ + +QA+QF++A+ME+K A Sbjct: 234 MAGLDGGRLNIAATALGGAQAAFDATRAYMAERKAFGQRLDGFQALQFRLAEMEVKLQQA 293 Query: 301 RVGWRDAASRLVAGEP-FKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWR 359 R+ R AA +L G P K A+AKL + A + A + Q+HGGYG++ +Y + ++ R Sbjct: 294 RIFLRQAAWKLDQGAPDATKFCAMAKLAVTDSAFEVANQCLQLHGGYGYLADYGIEKIVR 353 Query: 360 DSKILEIGEGTSEVQRMLIARELG 383 D ++ +I EGT+E+ R+++AR LG Sbjct: 354 DLRVHQILEGTNEIMRVIVARALG 377 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: 418 Number of extensions: 15 Number of successful extensions: 5 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: 379 Length adjustment: 30 Effective length of query: 356 Effective length of database: 349 Effective search space: 124244 Effective search space used: 124244 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 Apr 10 2024. 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