Align 2-keto-4-carboxy-3-hexenedioate hydratase; KCH hydratase; EC 4.2.1.- (characterized)
to candidate Ga0059261_0527 Ga0059261_0527 Predicted metal-dependent hydrolase of the TIM-barrel fold
Query= SwissProt::G2IQQ5 (341 letters) >FitnessBrowser__Korea:Ga0059261_0527 Length = 339 Score = 637 bits (1644), Expect = 0.0 Identities = 298/339 (87%), Positives = 319/339 (94%) Query: 3 MIIDCHGHYTVLPKAHDEWREQQKAAFKAGQPAPPYPEISDDEIRETIEANQLRLIKERG 62 +IIDCHGHYTVLPK HD WRE+QKAAFKAG PPYPEISDDEIRETIEANQLRLI+ERG Sbjct: 1 VIIDCHGHYTVLPKGHDAWREEQKAAFKAGTTPPPYPEISDDEIRETIEANQLRLIRERG 60 Query: 63 ADMTIFSPRASAMAPHVGDQSVAVPWAQACNNLIARVVDLFPETFAGVCMLPQSPEADMT 122 AD+TIFSPRASAMAPHVGD++VA WA CN+LIARVV LFPE FAGVCMLPQSP+A M Sbjct: 61 ADLTIFSPRASAMAPHVGDEAVATEWAMRCNDLIARVVKLFPERFAGVCMLPQSPKAGMA 120 Query: 123 SSIAELERCVNELGFIGCNLNPDPGGGHFKHPPLTDRFWYPFYEKMVELDVPAMIHVSGS 182 +SIAELERCV ELGFIGCNLNPDPGGGHF HPPLTDR+WYPFYEKMVELDVPAMIHVSGS Sbjct: 121 NSIAELERCVTELGFIGCNLNPDPGGGHFTHPPLTDRYWYPFYEKMVELDVPAMIHVSGS 180 Query: 183 CNPAMHATGAYYLAADTIAFMQLLQGNLFADFPTLRFIIPHGGGAVPYHWGRFRGLADML 242 CNPAMHATG YY+AADT+AFMQLL+GNLFADFPTLRFIIPHGGGAVPYHWGR+RGLADML Sbjct: 181 CNPAMHATGGYYIAADTVAFMQLLEGNLFADFPTLRFIIPHGGGAVPYHWGRYRGLADML 240 Query: 243 KQPSLDTLLMNNVFFDTCVYHQPGINLLADVIDNKNILFGSEMVGAVRGIDPTTGHYFDD 302 K+P+LDT LMNN+FFDTCVYHQPGI+LLADVI NKNILFGSEMVGAVRGIDPTTGHYFDD Sbjct: 241 KKPALDTHLMNNIFFDTCVYHQPGIDLLADVIANKNILFGSEMVGAVRGIDPTTGHYFDD 300 Query: 303 TKRYIDALDISDQERHAIFEGNTRRVFPRLDAKLKARGL 341 TKRY+DAL+ISD ERHAIFEGN RRVFPRLDA+LKARGL Sbjct: 301 TKRYVDALEISDTERHAIFEGNARRVFPRLDAQLKARGL 339 Lambda K H 0.323 0.140 0.442 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: 585 Number of extensions: 18 Number of successful extensions: 1 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: 341 Length of database: 339 Length adjustment: 28 Effective length of query: 313 Effective length of database: 311 Effective search space: 97343 Effective search space used: 97343 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 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