Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate BWI76_RS13115 BWI76_RS13115 2,3-dehydroadipyl-CoA hydratase
Query= BRENDA::F4JML5 (301 letters) >FitnessBrowser__Koxy:BWI76_RS13115 Length = 255 Score = 156 bits (394), Expect = 5e-43 Identities = 89/247 (36%), Positives = 146/247 (59%), Gaps = 5/247 (2%) Query: 55 IIEVNLDRPVTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVPGVFCAGADLKERRT 114 ++++ L+RP +NA+N +L + + ++ D + V +I S F AGADL E Sbjct: 12 VLQLTLNRPQARNALNNALLMQIADVLDAAALDPTVGVCVI-SGNERFFAAGADLNE--- 67 Query: 115 MSPSEVHTYVNSLR-YMFSFIEALSIPTIAAIEGAALGGGLEMALACDLRICGENAVFGL 173 M+ +++ ++ +R +++ I+A S P IA++ G ALG G E+AL CDL + G+NA FGL Sbjct: 68 MAENDLPATLDDIRPRLWARIDAFSKPLIASVNGYALGAGCELALICDLIVAGDNARFGL 127 Query: 174 PETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGLVNICVTAGEAHEKA 233 PE L ++PGAGGTQRL R VG++++ ++ +G IDA +A GLV+ E A Sbjct: 128 PEITLGMMPGAGGTQRLIRSVGKALASRMVLSGESIDAHQALRAGLVSEVYPPALTDEYA 187 Query: 234 IEMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEVEEMCYQKLLNTQDRLEGLAAFAEK 293 + +A + PLA++ AK+++ E ++ +GL+ E + L T+DR EG+ AF K Sbjct: 188 LSLAATVARHSPLALRAAKQSLRLSQEVSLQAGLQQERQLFTLLSATEDRREGIDAFLHK 247 Query: 294 RKPLYTG 300 R + G Sbjct: 248 RTAEFKG 254 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: 144 Number of extensions: 6 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: 255 Length adjustment: 25 Effective length of query: 276 Effective length of database: 230 Effective search space: 63480 Effective search space used: 63480 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