Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_011513566.1 PCRYO_RS06325 acyl-CoA dehydrogenase
Query= reanno::SB2B:6937192 (389 letters) >NCBI__GCF_000013905.1:WP_011513566.1 Length = 384 Score = 251 bits (640), Expect = 3e-71 Identities = 129/374 (34%), Positives = 221/374 (59%), Gaps = 2/374 (0%) Query: 16 VDMLRDAVYEFAKGEIAPLAEKVDRDNAFPNELWAKFGDMGLLGVTVAEEYGGVNMGYLA 75 ++ + D + +F ++ P+ V ++ P+++ + ++GL G+T+ EEYGG+ + Sbjct: 8 LNQITDTIRQFVNNQLIPMEHWVAENDRLPDDIINQMRELGLFGLTIPEEYGGLGVTMEE 67 Query: 76 HVVAMEEISRASASIGLSYGAHSNLCVNQIYRNGNEAQRAKYLPKLISGEHIGALAMSEP 135 V E+ R S + G ++ + + + +G EAQ+ KYLP+L SGE IG+ ++EP Sbjct: 68 EVTLAFELGRTSPAFRSLIGTNNGIGSSGLVIDGTEAQKQKYLPRLASGEIIGSFCLTEP 127 Query: 136 NAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDAHTYVIYAKTD-LDKGPHGITAFIVE 194 ++GSD S+K A K+GD YI+NG K +ITN P+A + + A+TD +K GI+AFIVE Sbjct: 128 DSGSDAASLKTTAIKDGDTYIINGTKRYITNAPEAGVFTVMARTDPQNKRSGGISAFIVE 187 Query: 195 RGFKGFSQAQKLDKLGMRGSNTCELVFEDCEVPEENILGGLNN-GVKVLMSGLDYERVVL 253 G + + K+G +G++TC+++F++C VP + ++GG+ G K M LD R+ + Sbjct: 188 SDTPGITLGKIDKKMGQKGAHTCDVIFDNCIVPADALIGGVEGVGFKTAMKVLDKGRLHI 247 Query: 254 SGGPLGIMTACMDIVVPYVHERVQFGKSIGEFQLVQGKLADMYTGMNAAKSYVYNVARAC 313 + G T +D + Y ER QFG+ I FQL+Q LAD + AAKS V + +R Sbjct: 248 AAASTGAATRMLDDALHYAVERKQFGQPIANFQLIQAMLADSKAEIYAAKSMVLDASRLR 307 Query: 314 DRGETTRKDAAGVILYAAELATKMALDAIQLLGGNGYVNEYATGRLLRDAKLYEIGAGTS 373 D G+ +++ ++A E+ ++A A+Q+ GG GY+ +Y R RD +LY + GT+ Sbjct: 308 DEGKDVVTESSCAKMFATEMCGRVADRAVQIHGGAGYIADYGIERFYRDVRLYRLYEGTT 367 Query: 374 EIRRMLIGRELFNE 387 +I++++I R + E Sbjct: 368 QIQQIIIARNMIKE 381 Lambda K H 0.318 0.137 0.396 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: 385 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: 389 Length of database: 384 Length adjustment: 30 Effective length of query: 359 Effective length of database: 354 Effective search space: 127086 Effective search space used: 127086 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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