Align palmitoyl-CoA hydrolase (EC 3.1.2.2) (characterized)
to candidate AZOBR_RS16510 AZOBR_RS16510 S-formylglutathione hydrolase
Query= BRENDA::P33018 (278 letters) >FitnessBrowser__azobra:AZOBR_RS16510 Length = 287 Score = 347 bits (889), Expect = e-100 Identities = 169/283 (59%), Positives = 206/283 (72%), Gaps = 8/283 (2%) Query: 1 MEMLEEHRCFEGWQQRWRHDSSTLNCPMTFSIFLPPPRDHTPP----PVLYWLSGLTCND 56 + + +RCF GW +R+RH S+ L+C M F+++LPP + PV YWLSGLTC D Sbjct: 5 LTQIAANRCFGGWHKRFRHRSAVLDCDMVFAVYLPPQAESGTKSGKVPVFYWLSGLTCTD 64 Query: 57 ENFTTKAGAQRVAAELGIVLVMPDTSPRGEKVAND-DG-YDLGQGAGFYLNATQPPWATH 114 ENF KAGA R+AAELGI +V PDTSPRG V D DG +D G GAGFY+NAT+ PWA H Sbjct: 65 ENFMQKAGAMRMAAELGIAIVAPDTSPRGPDVPGDPDGAWDFGLGAGFYVNATREPWAKH 124 Query: 115 YRMYDYLRDELPALVQSQFNVSDRCAISGHSMGGHGALIMALKNPGKYTSVSAFAPIVNP 174 YRM+DY+ ELP LV+++ V+DR +ISGHSMGGHGAL+ AL+NPG+Y +VSAFAPI NP Sbjct: 125 YRMHDYVVRELPELVEAELPVTDRRSISGHSMGGHGALVCALRNPGRYCAVSAFAPIGNP 184 Query: 175 CSVPWGIKAFSSYLGEDKNAWLEWDSCALMYASNAQDAIPTLIDQGDNDQFLADQLQPAV 234 SVPWG KAF + G D AWLEWDSCAL+ A + +P L+DQGD D FL QL+P Sbjct: 185 ASVPWGEKAFERFFGTDYAAWLEWDSCALL--GRASEKLPILVDQGDADSFLEKQLKPEN 242 Query: 235 LAEAARQKAWPMTLRIQPGYDHSYYFIASFIEDHLRFHAQYLL 277 L AA P+TLR+QPGYDHSY+FIASFI+DHLR HA LL Sbjct: 243 LQRAAAAAGHPLTLRMQPGYDHSYFFIASFIDDHLRHHAAALL 285 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: 321 Number of extensions: 8 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: 287 Length adjustment: 26 Effective length of query: 252 Effective length of database: 261 Effective search space: 65772 Effective search space used: 65772 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