Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate PfGW456L13_2434 Phenylacetate degradation enoyl-CoA hydratase PaaA (EC 4.2.1.17)
Query= BRENDA::F4JML5 (301 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2434 Length = 257 Score = 168 bits (426), Expect = 1e-46 Identities = 99/250 (39%), Positives = 145/250 (58%), Gaps = 5/250 (2%) Query: 52 DSGIIEVNLDRPVTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVPGVFCAGADLKE 111 + G+ + L RP NA+ E+L L D R V++ F AGAD+KE Sbjct: 11 EPGVRLITLQRPQALNALTTELLGELAAELNIAQADPDTRAVVLTGSRKA-FAAGADIKE 69 Query: 112 RRTMSPSEVHTYVNSLRYM-FSFIEALSIPTIAAIEGAALGGGLEMALACDLRICGENAV 170 M+ ++ ++ R + I S P IAA+ G ALGGG E+A+ D+ I GE+A Sbjct: 70 ---MAERDLVGILDDPRQASWQAITRFSKPLIAAVNGFALGGGCELAMHADIIIAGEDAR 126 Query: 171 FGLPETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGLVNICVTAGEAH 230 FG PE L I+PGAGGTQRL R VG+S++ +++ TG IDA +A GLV+ Sbjct: 127 FGQPEINLGIMPGAGGTQRLLRAVGKSMAMQMVLTGESIDARQAQRVGLVSEVTQPEFTV 186 Query: 231 EKAIEMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEVEEMCYQKLLNTQDRLEGLAAF 290 E+A+ +A I K PLA+++AK+A+ + ++T++A+GL E + L T+DR EG+AAF Sbjct: 187 ERALHIAHSIAAKAPLAVRLAKEALLKAMDTDLATGLRFERHAFTVLAGTRDRDEGIAAF 246 Query: 291 AEKRKPLYTG 300 EKR P +TG Sbjct: 247 QEKRSPTFTG 256 Lambda K H 0.318 0.134 0.373 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: 160 Number of extensions: 7 Number of successful extensions: 2 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: 301 Length of database: 257 Length adjustment: 25 Effective length of query: 276 Effective length of database: 232 Effective search space: 64032 Effective search space used: 64032 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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