Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_011840308.1 RSPH17029_RS01585 acyl-CoA dehydrogenase family protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >NCBI__GCF_000015985.1:WP_011840308.1 Length = 555 Score = 233 bits (595), Expect = 7e-66 Identities = 144/383 (37%), Positives = 210/383 (54%), Gaps = 14/383 (3%) Query: 5 EEQTQIRDMARQFAEERLKPFAAEWD-REHRFPREAIDEMAELGFFGMLVPEQWGGCDTG 63 EE IRD R+FA+ER+ P A W R+ P E ++ +AE+G FG+ +PE++GG Sbjct: 173 EELEMIRDQFRRFADERVAPHAHGWHMRDELIPMEIVEALAEMGVFGLTIPEEFGGFGLS 232 Query: 64 YLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123 + + EE++ G ++ + + IL G D QKA +L LASG +L Sbjct: 233 KASMVVVSEELSRGYIGVGSL-GTRSEIAAELILCGGTDAQKAAWLPKLASGEILPTAVF 291 Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDP-SAGKRGISAF 182 TEP GSD SL+TRA +GD +V+NG K +IT V+ + A TDP + RG+S F Sbjct: 292 TEPNTGSDLGSLRTRAVKDGDEWVVNGNKTWITHAARTHVMTLLARTDPETTDYRGLSMF 351 Query: 183 IV---------PTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGE-EGEGYKI 232 + P +PG + +E LG +I F+ +V N LG EG+G+K Sbjct: 352 LAEKMPGTDADPFPTPGMTGGEIE-VLGYRGMKEYEIGFDGFRVKGENLLGGVEGQGFKQ 410 Query: 233 ALANLEGGRVGIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAV 292 + E R+ AA+A+G+A+ A E YA ER FGK +IE VA +LA MA +I V Sbjct: 411 LMQTFESARIQTAARAIGVAQNALEVGMQYAEERKQFGKALIEFPRVAGKLAMMAVEIMV 470 Query: 293 ARQMVHYAAALRDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYR 352 ARQ+ +++A +D GQ +EA MAKL + +A ALQ GG G+ ++ + RI Sbjct: 471 ARQLTYHSAWEKDHGQRCDLEAGMAKLLGARVAWAAADNALQIHGGNGFALEYQISRILC 530 Query: 353 DVRVCQIYEGTSDIQRMVISRNL 375 D R+ I+EG ++IQ VI+R L Sbjct: 531 DARILNIFEGAAEIQAQVIARRL 553 Score = 34.7 bits (78), Expect = 7e-06 Identities = 27/97 (27%), Positives = 45/97 (46%), Gaps = 5/97 (5%) Query: 237 LEGGRVGIAAQAVGMARAAFEAARDYARERSSF-----GKPIIEHQAVAFRLADMATQIA 291 L G + +A+ A+ A FE AR +ER + K + E Q A L+ +AT + Sbjct: 13 LLGDLLTLASDALPEVEALFETARSALKERVTTDGKVSSKALEEEQFAAHALSWLATYVE 72 Query: 292 VARQMVHYAAALRDSGQPALVEASMAKLFASEMAEKV 328 RQM +A L G+ +EA + ++ E ++ Sbjct: 73 SLRQMRAWAGRLETEGRFGEMEALILQIAFGEYLAQI 109 Lambda K H 0.320 0.134 0.388 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: 474 Number of extensions: 27 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 375 Length of database: 555 Length adjustment: 33 Effective length of query: 342 Effective length of database: 522 Effective search space: 178524 Effective search space used: 178524 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: 51 (24.3 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