Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_004314659.1 C665_RS13505 enoyl-CoA hydratase
Query= BRENDA::O87873 (258 letters) >NCBI__GCF_000310185.1:WP_004314659.1 Length = 260 Score = 79.3 bits (194), Expect = 7e-20 Identities = 80/265 (30%), Positives = 124/265 (46%), Gaps = 23/265 (8%) Query: 9 KVWLERDGSLLRLRLARP-KANIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPH-FSF 66 ++ L+ D + + L P K N V+AAM + A+ ++R V++ G + F+ Sbjct: 4 RIDLDIDQGIATVTLHNPTKLNAVNAAMWRGLSAAMARIAADDSVRCVIVRGAGENAFAA 63 Query: 67 GASVDEHMPDQCAQMLKSLH-------GLVREMLDSPVPILVALRGQCLGGGLEVAAAGN 119 G ++E + A + +LH + + D VP + A+RG C+GGGLE+A + Sbjct: 64 GGDIEEFRSVR-ATVDDALHYHEDLVASALNAIRDCAVPTVAAIRGACVGGGLEIAGCCD 122 Query: 120 LLFAAPDAKFGQPEIRLGV-FAPAASCLLPPRVGQACAEDLLWSGRSIDGAEGHRIGLID 178 + A A+FG P RLG P L VG A ++L GR +D E + GL+ Sbjct: 123 IRIAGESARFGAPINRLGFSMYPGEMAGLLALVGPAVVLEILLEGRILDAREALQKGLLT 182 Query: 179 VLAEDPEAAALRWFDEHIARLSASSLRF-AVRAARCDS--VPRIKQ--KLDTVEALYLEE 233 + +D R F+E A +SA +R A AR V R+ LD E + Sbjct: 183 RVVDDE-----RVFEE--AAVSAERIRAGAPLVARWHKQWVRRLTTGVALDEEEKRRAFD 235 Query: 234 LMASHDAVEGLKAFLEKRSANWENR 258 +A+ D EGL AF EKR+ + R Sbjct: 236 FLATADYREGLAAFSEKRAPVFRGR 260 Lambda K H 0.321 0.135 0.402 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: 177 Number of extensions: 12 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: 258 Length of database: 260 Length adjustment: 24 Effective length of query: 234 Effective length of database: 236 Effective search space: 55224 Effective search space used: 55224 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 (21.9 bits) S2: 47 (22.7 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