Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate WP_011513566.1 PCRYO_RS06325 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >NCBI__GCF_000013905.1:WP_011513566.1 Length = 384 Score = 285 bits (728), Expect = 2e-81 Identities = 151/369 (40%), Positives = 227/369 (61%), Gaps = 2/369 (0%) Query: 9 QISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYA 68 QI+D RQF +L P R P + I +M ELG FG+ +PE++GG Sbjct: 10 QITDTIRQFVNNQLIPMEHWVAENDRLPDDIINQMRELGLFGLTIPEEYGGLGVTMEEEV 69 Query: 69 MALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTEPQA 128 E+ A +++ +N +G ++ G + QK+++L LASG ++G+F LTEP + Sbjct: 70 TLAFELGRTSPAFRSLIGTNNGIGSSGLVIDGTEAQKQKYLPRLASGEIIGSFCLTEPDS 129 Query: 129 GSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRG-ISAFIVPTD 187 GSDA+SLKT A +GD Y++NG K++IT+ AGV V A TDP + G ISAFIV +D Sbjct: 130 GSDAASLKTTAIKDGDTYIINGTKRYITNAPEAGVFTVMARTDPQNKRSGGISAFIVESD 189 Query: 188 SPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGE-EGEGYKIALANLEGGRVGIAS 246 +PG + +++ K+GQ + TC ++F++ VP +G EG G+K A+ L+ GR+ IA+ Sbjct: 190 TPGITLGKIDKKMGQKGAHTCDVIFDNCIVPADALIGGVEGVGFKTAMKVLDKGRLHIAA 249 Query: 247 QSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDS 306 S G A + A YA ER+ FG+PI Q + LAD +I A+ MV A+ LRD Sbjct: 250 ASTGAATRMLDDALHYAVERKQFGQPIANFQLIQAMLADSKAEIYAAKSMVLDASRLRDE 309 Query: 307 GKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDI 366 GK + E+S AK+FA+EM +V A+Q GG GY++D+ +ER YRDVR+ ++YEGT+ I Sbjct: 310 GKDVVTESSCAKMFATEMCGRVADRAVQIHGGAGYIADYGIERFYRDVRLYRLYEGTTQI 369 Query: 367 QRMVISRNL 375 Q+++I+RN+ Sbjct: 370 QQIIIARNM 378 Lambda K H 0.319 0.134 0.389 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: 323 Number of extensions: 12 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: 375 Length of database: 384 Length adjustment: 30 Effective length of query: 345 Effective length of database: 354 Effective search space: 122130 Effective search space used: 122130 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: 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