Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate CCNA_01412 CCNA_01412 acyl-CoA dehydrogenase, short-chain specific
Query= BRENDA::B5UB85 (416 letters) >FitnessBrowser__Caulo:CCNA_01412 Length = 381 Score = 248 bits (633), Expect = 2e-70 Identities = 143/380 (37%), Positives = 221/380 (58%), Gaps = 7/380 (1%) Query: 33 FGLSEEQQQLRKMVFDFAQKELAPKAAEIDKENNFKELRPFWKKLGDLGLLGITASSDYG 92 F L+E+Q ++ FA+ +LAP +A+ D+ +F ++ +LG GI + D G Sbjct: 5 FALNEDQVAIQDAARAFAEGQLAPHSADWDENKHFPV--DVLRQAAELGFAGIYVNEDVG 62 Query: 93 GTGGKYSDHCVIMEELSRASGGIALSYGAHSNLCVNQINRNGTEEQKSKYLPKLCSGEHI 152 G+G D +I E LS +A H N+ I+R G+++ + +YLP+L + E I Sbjct: 63 GSGLSRLDASIIFEALSYGDVPVAAYLTIH-NMASWMIDRFGSDDLRQRYLPRLTTMELI 121 Query: 153 GALAMSEPGSGSDVVSMKLRAEKKGDYYVLNGNKFWITNGPDADVLVVYAKTNWSTSKQQ 212 + ++EPGSGSD +M+ A+ GD+YVLNG K +I+ G +D+ VV A+T +K Sbjct: 122 ASYCLTEPGSGSDAAAMRTTAKLDGDHYVLNGGKAFISGGGVSDIYVVMARTGGEGAK-- 179 Query: 213 HGISAFLIEKDYPGFSTAQKLDKLGMRGSNTGELVFEDCKVPAANLLGQENKGVYVLMSG 272 G+SAF++EK G S K+G T ++ F++C+VP AN +GQE +G M G Sbjct: 180 -GVSAFVVEKGMEGLSFGANERKMGWNAQPTAQVNFDNCRVPVANRIGQEGEGFRFAMMG 238 Query: 273 LDLERLVLAAGPVGLMQAAIDTAFLYAHTRKQFGKNIGEFQLIQGKMADMYTTLSACRSY 332 LD RL +A+ +G Q A+DTA Y TR QFG+ + +FQ +Q K+ADM T L A R Sbjct: 239 LDGGRLNIASCSLGGAQFALDTAKAYLETRNQFGRPLKDFQALQFKLADMATELEAARLM 298 Query: 333 LYNVAKACDNGHVN-SKDCAGVILYCAEKATQVALDAIQILGGNGYINDYPTGRILRDAK 391 + A A D+ H +K CA + + QVA DA+Q+ GG GY+ DYP R++RD + Sbjct: 299 VRRAAHALDSKHPEATKLCAMAKRFATDAGFQVANDALQLHGGYGYLQDYPLERLVRDLR 358 Query: 392 LYEIGAGTSEVRRMLIGRAL 411 +++I GT+E+ R++I R + Sbjct: 359 VHQILEGTNEIMRVIIAREM 378 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: 386 Number of extensions: 26 Number of successful extensions: 5 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: 416 Length of database: 381 Length adjustment: 31 Effective length of query: 385 Effective length of database: 350 Effective search space: 134750 Effective search space used: 134750 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 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