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_011384980.1 AMB_RS13080 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >NCBI__GCF_000009985.1:WP_011384980.1 Length = 383 Score = 298 bits (763), Expect = 2e-85 Identities = 159/369 (43%), Positives = 229/369 (62%), Gaps = 2/369 (0%) Query: 9 QISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYA 68 Q+ D +F +ERL P + P E I EM +LG FG+ +PE++GG Sbjct: 10 QLLDTLSRFVRERLVPNEERIAEDDALPAEIIAEMKDLGLFGLSIPEEYGGLGLTMEEEV 69 Query: 69 MALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTEPQA 128 + EI A +I +N +G I+ G ++QK+++L LA+G ++ +FALTEP A Sbjct: 70 LCAFEIGQTSPAFRSIFGTNNGIGSQGIIIDGTEEQKQKYLPRLATGELIASFALTEPNA 129 Query: 129 GSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDP-SAGKRGISAFIVPTD 187 GSDA+SL+T AR +GDHY++NG K+FIT+ A + + A TDP + G GISAFIV D Sbjct: 130 GSDAASLRTTARKDGDHYIVNGTKRFITNAPEASIFTLMARTDPNNKGAGGISAFIVEAD 189 Query: 188 SPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGE-EGEGYKIALANLEGGRVGIAS 246 SPG + +++ K+GQ + TC ++FEDV+VP AN +G EG+G+K A+ L+ GR+ I++ Sbjct: 190 SPGLSLGKIDKKMGQKGAHTCDVIFEDVRVPAANIIGGIEGQGFKTAMKVLDRGRLHISA 249 Query: 247 QSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDS 306 VG++ + YA ER FGKPI E Q V LAD T+ AR MV AA +D Sbjct: 250 TCVGVSERLIRDSVKYAAERVQFGKPIGEFQLVQAMLADSRTEAYAARCMVLDAARKKDQ 309 Query: 307 GKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDI 366 G EA+ K+FASE ++ A+Q GG GY+SD+ +ER YRDVR+ +IYEGT+ I Sbjct: 310 GINVSTEAACCKMFASEAVGRIADRAVQVHGGAGYISDYGIERFYRDVRLFRIYEGTTQI 369 Query: 367 QRMVISRNL 375 Q++VI+RN+ Sbjct: 370 QQLVIARNM 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: 346 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: 375 Length of database: 383 Length adjustment: 30 Effective length of query: 345 Effective length of database: 353 Effective search space: 121785 Effective search space used: 121785 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 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