Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_066607952.1 V473_RS17395 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >NCBI__GCF_001046645.1:WP_066607952.1 Length = 381 Score = 234 bits (598), Expect = 2e-66 Identities = 150/371 (40%), Positives = 206/371 (55%), Gaps = 9/371 (2%) Query: 13 DMVRDVATR----EIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMGVLTL 68 DM+RD A R IAP A E+D K FP +LGL + GG +G L Sbjct: 13 DMIRDSAARFSADRIAPLAAEIDAKDWFPRELWPAMGELGLHGITVSEEDGGLGLGYLEH 72 Query: 69 ALILEELGRVCASTALLLIAQTDGML-PIIHGGSPELKERYLRRFAGESTLLTALAATEP 127 + EE+ R AS L A ++ + I G+ E K +YL + + +LA +E Sbjct: 73 VVAQEEVARASASIGLSYGAHSNLCVNQIRRWGNAEQKAKYLPKLISGDHV-GSLAMSEA 131 Query: 128 AAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAFVVEK 187 AGSD+++MK +A ++GD+Y++NG K +ITN AD +VVYA T +GSKGI+ F++EK Sbjct: 132 GAGSDVVSMKLKAEKKGDRYILNGTKFWITNAPYADTLVVYAKTG--EGSKGITTFLIEK 189 Query: 188 GTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRVFCAA 247 G G+ KMGMRGS +EL F++ EVP ENI+G G LM L R A Sbjct: 190 DMKGFSIGQKIDKMGMRGSPTAELVFDDCEVPEENIMGPLNGGVGILMSGLDYERTVLAG 249 Query: 248 QAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAELLDD 307 +GI Q LD + + ++R QFG+PI +Q VADM A+ ++R A D Sbjct: 250 IQLGIMQACLDTVLPYVRERQQFGRPIGAFQLMQAKVADMYVALNSARAYVYAVARACDS 309 Query: 308 GDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIYTGTNQ 367 G K + A +AS+ AM+V +AVQ LGG+GY K+ VER MRDAKL I GTN+ Sbjct: 310 G-KTTRFDAAGAILLASENAMKVALEAVQALGGAGYTKDWPVERYMRDAKLLDIGAGTNE 368 Query: 368 ITRMVTGRALL 378 I RM+ GR L+ Sbjct: 369 IRRMLIGRELI 379 Lambda K H 0.319 0.134 0.371 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: 323 Number of extensions: 14 Number of successful extensions: 4 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: 380 Length of database: 381 Length adjustment: 30 Effective length of query: 350 Effective length of database: 351 Effective search space: 122850 Effective search space used: 122850 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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