Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_043768783.1 U743_RS12745 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF1051 (387 letters) >NCBI__GCF_000733765.1:WP_043768783.1 Length = 375 Score = 271 bits (693), Expect = 2e-77 Identities = 145/368 (39%), Positives = 216/368 (58%), Gaps = 1/368 (0%) Query: 14 IDMLREQVQAFVAAEIAPRAEAIDQENLFPADMWRKFGEMGLLGVTVSEEYGGAGLGYLA 73 +++ R+ V+ F+ AE+AP + +++ + P ++WRK GE GLL V + EEYGGAG + Sbjct: 5 LELFRDNVKRFLEAEVAPHYDQWERDEILPREIWRKMGENGLLCVDMPEEYGGAGAPFSF 64 Query: 74 HVVAMEEISR-GSASVALSYGAHSNLCVNQINRNGNPEQKARYLPKLISGEHVGALAMSE 132 +EE SR G ++A + HS++ I G+ EQK YLPK+ +GE VGA+AM+E Sbjct: 65 SCAVVEEASRAGFTAIAGNLSVHSDIVAPYILHLGSEEQKQHYLPKMAAGECVGAIAMTE 124 Query: 133 PNAGSDVVSMKLRAEKRGDRYVLNGSKTWITNGPDANTYVIYAKTDLDKGAHGITAFIVE 192 P AGSD+ + RAE GD Y ++G KT+ITNG A+ V + KTD + GA G T F+V+ Sbjct: 125 PGAGSDLQGARTRAEADGDGYRISGQKTFITNGQHADVIVTFTKTDPNAGAKGTTLFLVD 184 Query: 193 RDWKGFSRGNKFDKLGMRGSNTCELFFDDVEVPQENVLGAENGGVKVLMSGLDYERVVLA 252 D +GF+RG +K+G +T ELF+ DV VP VLG GG LM L ER++LA Sbjct: 185 GDAEGFARGRNLEKIGQHAGDTSELFYQDVRVPASAVLGRVGGGFGHLMDELPRERLILA 244 Query: 253 GGPTGIMQSCLDVVVPYIHDRKQFGQSIGEFQFIQGKVADMYTQLNASRAYLYAVAQACD 312 G + CLD+ + Y+ +RK FG+ + Q + ++A M T L+ ++A+ ++ D Sbjct: 245 VGAVAAAEGCLDLTINYVQERKAFGKPLSAQQNTRFEIARMKTDLDVTKAFSEQCKRSFD 304 Query: 313 RGETTRKDAAGVILYTAENATQMALQAIQILGGNGYINEFPTGRLLRDAKLYEIGAGTSE 372 G AA T E ++A +Q+ GG GY+ E+P R DA++ I GTSE Sbjct: 305 AGSFDVPTAAMAKYATTEMQCRVADGCLQLFGGYGYMREYPVSRHYVDARVQRIYGGTSE 364 Query: 373 IRRMLIGR 380 I + +I R Sbjct: 365 IMKEIIAR 372 Lambda K H 0.318 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: 379 Number of extensions: 22 Number of successful extensions: 2 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: 387 Length of database: 375 Length adjustment: 30 Effective length of query: 357 Effective length of database: 345 Effective search space: 123165 Effective search space used: 123165 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