Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_085772269.1 B1812_RS14765 acyl-CoA dehydrogenase family protein
Query= BRENDA::Q39QF5 (380 letters) >NCBI__GCF_002117405.1:WP_085772269.1 Length = 557 Score = 200 bits (509), Expect = 7e-56 Identities = 133/376 (35%), Positives = 202/376 (53%), Gaps = 15/376 (3%) Query: 15 VRDVATREIAPRALELDEKSLF-PEYARDLFAKLGLLNPLLPAAYGGTEMGVLTLALILE 73 +R A+ + P A E K+ + P A+LG+ +P +GG+ MG + + ++ E Sbjct: 183 MRKFASDNVTPFAQEWHAKNEYIPLEVISGLAELGVFGLTIPEEFGGSGMGKIAMCVVSE 242 Query: 74 ELGRVCASTALLLIAQTDGMLPIIHGGSPELKERYLRRFAGESTLLTALAATEPAAGSDL 133 EL R L I+ GG+ KE+YL + A L TA+ TEP GSDL Sbjct: 243 ELSRAYIGVGSLGTRSEIAGELILVGGTKAQKEKYLPKIAAGEILPTAVF-TEPNNGSDL 301 Query: 134 LAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPE-KGSKGISAFVVEK--GTP 190 ++TRAVR+GD Y + G K +IT+ ADV+ + T+PE KG KG+S + EK GT Sbjct: 302 AGLRTRAVREGDVYKVTGNKTWITHPVRADVMTLLVRTNPEEKGYKGLSMLLAEKPRGTD 361 Query: 191 -------GLVYGRNESKMGMRGSINSELFFENMEVPAENIIGA-EGTGFANLMQTLSTNR 242 G+ G E +G RG E+ F+ E PAEN++G EG GF LM+T + R Sbjct: 362 ENPFPAKGMTGGEIEV-LGYRGMKEFEIGFDGFETPAENLLGGVEGNGFKQLMETFESAR 420 Query: 243 VFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAA 302 + AA+A+G+AQ ALD+ +R+ ++R+QFGKP+ + + MA + +R +T +A Sbjct: 421 IQTAARALGVAQCALDLGLRYAKERIQFGKPLFSFPRIFDKIVAMAVEIHVARQITYFSA 480 Query: 303 ELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIY 362 DG K+ L MAK + + A +A+Q+ GG+G+ E V R++ DA++ I+ Sbjct: 481 R-QKDGGKRCDLEAGMAKLLGARVAWAAADNALQIHGGNGFALEYPVSRVLCDARILNIF 539 Query: 363 TGTNQITRMVTGRALL 378 G +I V R LL Sbjct: 540 EGAAEIQAQVIARRLL 555 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: 418 Number of extensions: 23 Number of successful extensions: 8 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: 380 Length of database: 557 Length adjustment: 33 Effective length of query: 347 Effective length of database: 524 Effective search space: 181828 Effective search space used: 181828 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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