Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_066918738.1 ACG33_RS03535 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2397 (379 letters) >NCBI__GCF_001579945.1:WP_066918738.1 Length = 383 Score = 281 bits (720), Expect = 2e-80 Identities = 165/375 (44%), Positives = 224/375 (59%), Gaps = 5/375 (1%) Query: 6 DQNAIA---EMARQFAQERLKPFAEQWSREHRYPAEAIGEMAALGFFGMLVPEQWGGSDT 62 DQ+A+ E +F +ERL PA+ + EM A+G FG+ +PE++GG Sbjct: 4 DQDALRSLLETVSRFVRERLVQAERIVDETDEIPADIVAEMKAMGLFGLTIPEEYGGLGL 63 Query: 63 GYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKSDFLTPLARGEQIGAFA 122 +A+ + A ++ +G IL G +QK+ +L LA GE I +FA Sbjct: 64 TMEEEVLAMFVMGQTSPAFRSLFGTTVGIGSQGILMDGTPEQKARYLPRLATGELIASFA 123 Query: 123 LTEPQAGSDASSLRTRARRDGDHYVLNGAKQFITSGKHAGTVIVFAVTDPDA-GKGGISA 181 LTEP+AGSDA+SLRT A GD YVLNG K+FIT+ AG V A TDP + G GG+SA Sbjct: 124 LTEPEAGSDAASLRTSATLSGDSYVLNGTKRFITNAPLAGMFTVMARTDPGSKGAGGVSA 183 Query: 182 FIVPTDSPGYQVVRVEDKLGQHASDTCQIAFEDLRVPVANRLG-EEGEGYRIALANLEGG 240 FIV +PG ++ + + K+GQ + TC + FED RVP AN +G G G++ A+ LE G Sbjct: 184 FIVEAGTPGLRLGKRDRKMGQRGAWTCDVIFEDCRVPAANIIGGRPGLGFKTAMKVLEKG 243 Query: 241 RIGIAAQAVGMARAAFEAARDYARDRETFGKPIIEHQAVAFRLADMATQIAVARQMVHHA 300 RI IAA VG+A A YAR+R+ FG+ I E Q V LAD ++ AR M A Sbjct: 244 RIHIAAICVGVAERMLGDALRYARERKQFGQAIGEFQLVQAMLADSKAELYAARCMTLDA 303 Query: 301 AALREVGRPALVEASMAKLFASEMAEKVCSAAIQTLGGYGYLADFPVERIYRDVRVCQIY 360 A R+ G EAS AKLFASEM +V A+Q LGG GY+A++ +ER YRDVR+ +I+ Sbjct: 304 AQRRDRGENVSTEASCAKLFASEMCGRVADRAVQILGGAGYMAEYGIERFYRDVRLFRIF 363 Query: 361 EGTSDIQRLVISRNL 375 EGT+ IQ+LVI+RN+ Sbjct: 364 EGTTQIQQLVIARNM 378 Lambda K H 0.320 0.135 0.391 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: 355 Number of extensions: 16 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: 379 Length of database: 383 Length adjustment: 30 Effective length of query: 349 Effective length of database: 353 Effective search space: 123197 Effective search space used: 123197 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