Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate Echvi_1073 Echvi_1073 Acyl-CoA dehydrogenases
Query= BRENDA::B5UB85 (416 letters) >FitnessBrowser__Cola:Echvi_1073 Length = 599 Score = 231 bits (588), Expect = 6e-65 Identities = 141/403 (34%), Positives = 215/403 (53%), Gaps = 28/403 (6%) Query: 36 SEEQQQLRKMVFDFAQKELAPKAAEIDKENNFKELRPFWKKLGDLGLLGITASSDYGGTG 95 +EEQ+ + + DF E+ PK+ EID N + KK G+LGLLGI+ +Y G G Sbjct: 30 TEEQRMMAQACQDFIDTEILPKSEEIDSMKNPDLVPAILKKAGELGLLGISVPEEYQGLG 89 Query: 96 GKYSDHCVIMEELSRASGGIALSYGAHSNLCVNQINRNGTEEQKSKYLPKLCSGEHIGAL 155 ++ +I + + A+G + +YGAH+ + I GTEEQK KYLPKL +GE Sbjct: 90 MSFNTSMLIADIIG-AAGSFSTTYGAHTGIGTLPILYYGTEEQKKKYLPKLATGEWAACY 148 Query: 156 AMSEPGSGSDVVSMKLRAE--KKGDYYVLNGNKFWITNGPDADVLVVYAKTNWSTSKQQH 213 ++EP +GSD S K +A + G +Y+LNG K WI+NG AD+ +V+AK + Sbjct: 149 CLTEPDAGSDANSGKTKATLTEDGKHYLLNGQKMWISNGGFADLFIVFAKIG-----EDK 203 Query: 214 GISAFLIEKDYPGFSTAQKLDKLGMRGSNTGELVFEDCKVPAANLLGQENKGVYVLMSGL 273 ++AF++EKD+ G + ++ K+G++GS+T ++ F DCKVP N+L G + ++ L Sbjct: 204 NLTAFIVEKDFGGITMNEEEKKMGIKGSSTRQVFFNDCKVPVENMLSDRQNGFKIAVNIL 263 Query: 274 DLERLVLAAGPVGLMQAAIDTAFLYAHTRKQFGKNIGEFQLIQGKMADM----YTTLSAC 329 ++ R+ L AG +G + I A Y+ RKQFG +I F I+ K+A+M Y + S C Sbjct: 264 NIGRVKLGAGVLGGCRQVIKNALQYSSERKQFGVSINTFGAIKSKLAEMAVKTYVSESLC 323 Query: 330 RSYLYNVAKACDNGHVN---------------SKDCAGVILYCAEKATQVALDAIQILGG 374 N+ D + + +CA ++ +E V +QI GG Sbjct: 324 YRLGQNIEDRIDALMASGMEANQAKLKGVEQFAMECAIAKIHGSEVLDYVVDQGVQIYGG 383 Query: 375 NGYINDYPTGRILRDAKLYEIGAGTSEVRRML-IGRALNNEYK 416 GY D P R RDA++ I GT+E+ RML IG L K Sbjct: 384 MGYSADAPMERAYRDARISRIYEGTNEINRMLMIGMLLKRAMK 426 Lambda K H 0.318 0.135 0.399 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: 656 Number of extensions: 30 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 416 Length of database: 599 Length adjustment: 34 Effective length of query: 382 Effective length of database: 565 Effective search space: 215830 Effective search space used: 215830 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: 52 (24.6 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