Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_011384978.1 AMB_RS13070 enoyl-CoA hydratase
Query= BRENDA::F4JML5 (301 letters) >NCBI__GCF_000009985.1:WP_011384978.1 Length = 256 Score = 155 bits (392), Expect = 9e-43 Identities = 87/246 (35%), Positives = 139/246 (56%), Gaps = 3/246 (1%) Query: 55 IIEVNLDRPVTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVPGVFCAGADLKERRT 114 ++ + ++RP KNA+N E+ + L ++ D S R +++ F AGAD+K+ Sbjct: 13 VVLLRINRPDAKNALNGEVRRLLAEHMTTLGADPSVRAIVMTGNQEA-FAAGADIKDMAE 71 Query: 115 MSPSEVHTYVNSLRYMFSFIEALSIPTIAAIEGAALGGGLEMALACDLRICGENAVFGLP 174 + E+ N L ++ I P IAA+ G A GGG E+ + D+ + GENA F P Sbjct: 72 VGAIELMQRNNHL--LWRAIANCPKPVIAAVNGYAWGGGCELVMHADIIVAGENASFSQP 129 Query: 175 ETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGLVNICVTAGEAHEKAI 234 E + I+PGAGGTQRL+R VG+ + ++ TG+ I +EA GL ++ V E +KA+ Sbjct: 130 EVKVGIMPGAGGTQRLTRAVGKFKAMLMVMTGQAISGVEAGQMGLASVVVPDAEVVDKAL 189 Query: 235 EMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEVEEMCYQKLLNTQDRLEGLAAFAEKR 294 E+A+ I+ P+AI K+ + G + ++ + L +E +Q L + D+ EG+ AF EKR Sbjct: 190 EIAKTISRMPPVAIAQIKEVLLAGQDASLDTALMLERKAFQLLFASADQKEGMKAFIEKR 249 Query: 295 KPLYTG 300 KP Y G Sbjct: 250 KPTYQG 255 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: 148 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: 256 Length adjustment: 25 Effective length of query: 276 Effective length of database: 231 Effective search space: 63756 Effective search space used: 63756 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