Align palmitoyl-CoA hydrolase (EC 3.1.2.2) (characterized)
to candidate RR42_RS28645 RR42_RS28645 S-formylglutathione hydrolase
Query= BRENDA::P33018 (278 letters) >FitnessBrowser__Cup4G11:RR42_RS28645 Length = 283 Score = 273 bits (698), Expect = 3e-78 Identities = 144/283 (50%), Positives = 186/283 (65%), Gaps = 8/283 (2%) Query: 1 MEMLEEHRCFEGWQQRWRHDSSTLNCPMTFSIFLPPPRDHTPP---PVLYWLSGLTCNDE 57 +E+L EH CF G Q+ +RH S+T+ PM FS+FLP P P L++L+GLTC +E Sbjct: 2 LELLSEHGCFGGVQRFYRHASATIGLPMRFSVFLPAQALVQPEQRLPALFYLAGLTCTEE 61 Query: 58 NFTTKAGAQRVAAELGIVLVMPDTSPRGEKVAND-DGYDLGQGAGFYLNATQPPWATHYR 116 F KAGAQR AAE G++LV PDTSPR +A + + +D G GAGFYL+ATQ PW+ H+R Sbjct: 62 TFMIKAGAQRYAAEHGLILVAPDTSPRDTGIAGEAESWDFGVGAGFYLDATQAPWSQHWR 121 Query: 117 MYDYLRDELPALVQSQFNV-SDRCAISGHSMGGHGALIMALKNPGKYTSVSAFAPIVNPC 175 M Y+ EL LV + + R I GHSMGGHGAL++A ++PG++ SVSAFAPI P Sbjct: 122 MESYVTQELFDLVTTVLPADAQRVGIFGHSMGGHGALVLAQRHPGRFRSVSAFAPIAAPT 181 Query: 176 SVPWGIKAFSSYLGEDKNAWLEWDSCALMYASNAQDAIP--TLIDQGDNDQFLADQLQPA 233 PWG KAFS YLG D+ +W ++D+ ALM A A+ P L+DQG D+FLADQL P Sbjct: 182 RCPWGEKAFSRYLGTDRASWEQYDASALM-ARQAKAPFPRGILVDQGLADKFLADQLHPE 240 Query: 234 VLAEAARQKAWPMTLRIQPGYDHSYYFIASFIEDHLRFHAQYL 276 V A P+ LR GYDH YYFI++ +E+HLR HA L Sbjct: 241 VFEAACAAIGQPLLLRRHEGYDHGYYFISTLMENHLRHHAAQL 283 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: 296 Number of extensions: 11 Number of successful extensions: 5 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: 283 Length adjustment: 26 Effective length of query: 252 Effective length of database: 257 Effective search space: 64764 Effective search space used: 64764 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