Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate WP_011384980.1 AMB_RS13080 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-17424 (375 letters) >NCBI__GCF_000009985.1:WP_011384980.1 Length = 383 Score = 308 bits (790), Expect = 1e-88 Identities = 164/378 (43%), Positives = 239/378 (63%), Gaps = 4/378 (1%) Query: 2 LVNDEQ--QQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGG 59 ++ D++ Q+ D + F +ERL P E+ +D P E I EM +LGLFG+ +PE++GG Sbjct: 1 MIRDQEILNQLLDTLSRFVRERLVPNEERIAEDDALPAEIIAEMKDLGLFGLSIPEEYGG 60 Query: 60 SDTGYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLG 119 + EI A +I +N +G I+ G E+QK+++L LATG ++ Sbjct: 61 LGLTMEEEVLCAFEIGQTSPAFRSIFGTNNGIGSQGIIIDGTEEQKQKYLPRLATGELIA 120 Query: 120 AFALTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDP-EAGKRG 178 +FALTEP AGSDA+SL+T AR +GDHY++NG+K+FIT+ A + + A TDP G G Sbjct: 121 SFALTEPNAGSDAASLRTTARKDGDHYIVNGTKRFITNAPEASIFTLMARTDPNNKGAGG 180 Query: 179 ISAFIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGA-EGEGYKIALANL 237 ISAFIV DSPG + +++ K+GQ + TC ++F++V+VP AN +G EG+G+K A+ L Sbjct: 181 ISAFIVEADSPGLSLGKIDKKMGQKGAHTCDVIFEDVRVPAANIIGGIEGQGFKTAMKVL 240 Query: 238 EGGRIGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMV 297 + GR+ I++ VG++ + YA ER FGKP+ E Q V LAD T+ AR MV Sbjct: 241 DRGRLHISATCVGVSERLIRDSVKYAAERVQFGKPIGEFQLVQAMLADSRTEAYAARCMV 300 Query: 298 LHAAALRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVC 357 L AA +D G EA+ K+FASE ++ A+Q GG GY+SD+ +ER YRDVR+ Sbjct: 301 LDAARKKDQGINVSTEAACCKMFASEAVGRIADRAVQVHGGAGYISDYGIERFYRDVRLF 360 Query: 358 QIYEGTSDIQRMVIARNL 375 +IYEGT+ IQ++VIARN+ Sbjct: 361 RIYEGTTQIQQLVIARNM 378 Lambda K H 0.319 0.134 0.382 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: 18 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