Align palmitoyl-CoA hydrolase (EC 3.1.2.2) (characterized)
to candidate GFF3969 HP15_3909 carboxylesterase
Query= BRENDA::P33018 (278 letters) >FitnessBrowser__Marino:GFF3969 Length = 280 Score = 327 bits (838), Expect = 2e-94 Identities = 158/280 (56%), Positives = 200/280 (71%), Gaps = 6/280 (2%) Query: 1 MEMLEEHRCFEGWQQRWRHDSSTLNCPMTFSIFLPPPRDHTPP---PVLYWLSGLTCNDE 57 ME+L + FEG +R+RH S+TL C M F+++LPP + P PVLYWLSGLTC D+ Sbjct: 1 MELLSTNVSFEGEHRRYRHTSATLECDMEFAVYLPPVAVGSNPKKVPVLYWLSGLTCTDQ 60 Query: 58 NFTTKAGAQRVAAELGIVLVMPDTSPRGEKV-ANDDGYDLGQGAGFYLNATQPPWATHYR 116 NF KAGAQ+ AA+LG+ +V PDTSPRG + DD YD G GAGFY+NAT+ PWA HYR Sbjct: 61 NFMQKAGAQKRAAQLGMAIVCPDTSPRGVNLPGEDDSYDFGSGAGFYINATEQPWAPHYR 120 Query: 117 MYDYLRDELPALVQSQFNVSDRCAISGHSMGGHGALIMALKNPGKYTSVSAFAPIVNPCS 176 MYDY+ ELP L+++ V+D+ ++SGHSMGGHGALI ALKNPG+Y SVSAFAPI NP Sbjct: 121 MYDYVVKELPQLIENALPVTDKRSVSGHSMGGHGALICALKNPGRYASVSAFAPIANPTE 180 Query: 177 VPWGIKAFSSYLGEDKNAWLEWDSCALMYASNAQDAIPTLIDQGDNDQFLADQLQPAVLA 236 PWG KAF YLG+D +W EWD+ L+ A++ +P L+DQG D+FL QL P LA Sbjct: 181 CPWGQKAFKGYLGDDPRSWEEWDATLLI--PTARERLPLLVDQGTADEFLDSQLNPDALA 238 Query: 237 EAARQKAWPMTLRIQPGYDHSYYFIASFIEDHLRFHAQYL 276 +A + + LR+ GYDHSY+FIASFI+DHL HA+ L Sbjct: 239 DACEKFHHHINLRMHRGYDHSYFFIASFIDDHLDHHAKAL 278 Lambda K H 0.320 0.136 0.441 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: 325 Number of extensions: 9 Number of successful extensions: 4 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: 278 Length of database: 280 Length adjustment: 26 Effective length of query: 252 Effective length of database: 254 Effective search space: 64008 Effective search space used: 64008 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 (21.8 bits) S2: 47 (22.7 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