Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate CA265_RS09630 CA265_RS09630 acyl-CoA dehydrogenase
Query= reanno::ANA3:7024494 (389 letters) >FitnessBrowser__Pedo557:CA265_RS09630 Length = 396 Score = 222 bits (565), Expect = 2e-62 Identities = 135/380 (35%), Positives = 204/380 (53%), Gaps = 5/380 (1%) Query: 5 YTSLNFGLGEEVDMLRDAVQDFAKHEIAPIAAKVDHDNAFPNEIWPVLGGMGLLGVTVPE 64 Y L+ L +E ++R +D+ K E++PI FP + L +G G T+P Sbjct: 15 YYLLDELLTDEHKLIRATARDWVKKEVSPIIEDYAQKAEFPKHLIKGLADIGAFGPTIPV 74 Query: 65 EYGGANMGYLAHVVAMEEISRASASIGLSYGAHSNLCVNQINRNGNAEQKAKYLPKLVSG 124 EYGGA + Y A+ + M+EI R + I + +L + I G+ EQ+ KYLPKL SG Sbjct: 75 EYGGAGLDYTAYGILMQEIERGDSGIRSTASVQGSLVMYPIYAYGSEEQRKKYLPKLASG 134 Query: 125 EHIGALAMSEPNAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDANTYVIYAKTDLTKG 184 E +G ++EP+ GS+ M + + G YILNG KMWI+N P A+ V++AK + K Sbjct: 135 EMMGCFGLTEPDHGSNPGGMVTNIKDAGSHYILNGAKMWISNAPFADIAVVWAKDESGK- 193 Query: 185 AHGITAFIVERGFKGFSQAQKLDKLGMRGSNTCELVFEDVEVPEENILGGLNNGVKVLMS 244 I IVERG +GFS + K +R S T ELVF++V+VP+ENI + +G+K + Sbjct: 194 ---IRGLIVERGMEGFSTPETHHKWSLRASATGELVFDNVKVPKENIFPEI-SGLKGPLG 249 Query: 245 GLDYERVVLSGGPLGIMNACMDIVVPYIHEREQFGKSIGEFQLVQGKLADMYTGMNAAKA 304 L+ R ++ G LG C D + Y ER QFGK IG FQL Q KLA+M T + + Sbjct: 250 CLNQARYGIAWGALGAAMDCYDTALRYSKERVQFGKPIGGFQLQQKKLAEMVTEITKGQL 309 Query: 305 YVYSVAKSCDRGETTRKDAAGAILYSAELATKMALDAIQLLGGNGYVNEYATGRLLRDAK 364 V+ + + + + A S E+A +A +A Q+LGG G EY+ R + + + Sbjct: 310 LVWRLGVLKSENRASAEQISMAKRNSVEIALDIARNARQMLGGMGITGEYSIMRHMMNLE 369 Query: 365 LYEIGAGTSEIRRMLIGREL 384 GT +I ++ G ++ Sbjct: 370 SVVTYEGTHDIHLLITGMDV 389 Lambda K H 0.316 0.135 0.388 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: 388 Number of extensions: 15 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: 396 Length adjustment: 31 Effective length of query: 358 Effective length of database: 365 Effective search space: 130670 Effective search space used: 130670 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 (21.6 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