Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_086509213.1 BZY95_RS06815 2,3-dehydroadipyl-CoA hydratase PaaF
Query= BRENDA::F4JML5 (301 letters) >NCBI__GCF_002151265.1:WP_086509213.1 Length = 257 Score = 161 bits (408), Expect = 1e-44 Identities = 93/258 (36%), Positives = 142/258 (55%), Gaps = 11/258 (4%) Query: 48 LSGSDSGIIEVNLDRPVTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVPGVFCAGA 107 + G G++ + L RP NA+ +L L + QD R V+I F AGA Sbjct: 7 VEGPSRGVLRITLYRPEALNALTTALLAELAETLVAAEQDAEVRAVVITGS-QRAFAAGA 65 Query: 108 DLKERRTMSPSEVHTYVNSL----RYMFSFIEALSIPTIAAIEGAALGGGLEMALACDLR 163 D+KE H V L + ++ I S P +AA+ G LGGG E+A+ D+ Sbjct: 66 DIKEMAA------HDLVGMLEDPRQRHWASIARFSKPIVAAVNGFCLGGGCELAMHADIL 119 Query: 164 ICGENAVFGLPETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGLVNIC 223 I GE++ FG PE L I+PGAGGTQRL R VG++++ +++ TG I A A GL++ Sbjct: 120 IAGEDSRFGQPEINLGIMPGAGGTQRLVRAVGKALATQMVLTGEPISAHRALEAGLISEI 179 Query: 224 VTAGEAHEKAIEMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEVEEMCYQKLLNTQDR 283 A E+A+ +A+ I K PLA+++A++A+ + +T++ +GL E + L T+DR Sbjct: 180 TQPELAVERALAVAETIAAKAPLAVRLAREALHKAEDTDLTTGLRFERHAFTLLAGTRDR 239 Query: 284 LEGLAAFAEKRKPLYTGN 301 EG+ AF EKR +TG+ Sbjct: 240 EEGIRAFQEKRPATFTGH 257 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: 166 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: 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 Apr 09 2024. 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