Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate 15515 b1393 enoyl-CoA hydratase-isomerase (NCBI)
Query= BRENDA::F4JML5 (301 letters) >FitnessBrowser__Keio:15515 Length = 255 Score = 166 bits (420), Expect = 5e-46 Identities = 95/247 (38%), Positives = 147/247 (59%), Gaps = 5/247 (2%) Query: 55 IIEVNLDRPVTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVPGVFCAGADLKERRT 114 ++ + L+RP +NA+N +L L N E+ D S V +I F AGADL E Sbjct: 12 VLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNAR-FFAAGADLNE--- 67 Query: 115 MSPSEVHTYVNSLR-YMFSFIEALSIPTIAAIEGAALGGGLEMALACDLRICGENAVFGL 173 M+ ++ +N R +++ ++A + P IAA+ G ALG G E+AL CD+ + GENA FGL Sbjct: 68 MAEKDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFGL 127 Query: 174 PETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGLVNICVTAGEAHEKA 233 PE L I+PGAGGTQRL R VG+S++ +++ +G I A +A GLV+ + E A Sbjct: 128 PEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTLEYA 187 Query: 234 IEMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEVEEMCYQKLLNTQDRLEGLAAFAEK 293 +++A ++ PLA++ AK+A+ + E + +GL E + L T+DR EG++AF +K Sbjct: 188 LQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAFLQK 247 Query: 294 RKPLYTG 300 R P + G Sbjct: 248 RTPDFKG 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: 143 Number of extensions: 4 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