Align 2-keto-4-carboxy-3-hexenedioate hydratase; KCH hydratase; EC 4.2.1.- (characterized)
to candidate BPHYT_RS30325 BPHYT_RS30325 4-oxalomesaconate hydratase
Query= SwissProt::G2IQQ5 (341 letters) >FitnessBrowser__BFirm:BPHYT_RS30325 Length = 349 Score = 462 bits (1188), Expect = e-135 Identities = 218/335 (65%), Positives = 251/335 (74%), Gaps = 1/335 (0%) Query: 3 MIIDCHGHYTVLPKAHDEWREQQKAAFKAGQPAPPYPEISDDEIRETIEANQLRLIKERG 62 MIIDCHGHYT P H+ WR QQ AA K G PP P I+DDEIRE+IE QLR+ ERG Sbjct: 1 MIIDCHGHYTTSPPQHEAWRAQQIAALKDGGTTPPRPVITDDEIRESIEGGQLRIQHERG 60 Query: 63 ADMTIFSPRASAMAPHVGDQSVAVPWAQACNNLIARVVDLFPETFAGVCMLPQSPEADMT 122 D+TIFSPRA+ M H+ W+ CN+L+ RV +LFP F GVC LPQ+P Sbjct: 61 TDLTIFSPRAAGMGHHLATAEANALWSSECNDLVHRVCELFPRNFVGVCQLPQAPGVAPA 120 Query: 123 SSIAELERCVNELGFIGCNLNPDPGGGHFKHPPLTDRFWYPFYEKMVELDVPAMIHVSGS 182 + I EL RCV ELGFIGCNLNPDP GGH+ PLTDR WYP YE MVELDVPAMIHVS S Sbjct: 121 NCIGELRRCVEELGFIGCNLNPDPSGGHWSGLPLTDRCWYPLYEAMVELDVPAMIHVSSS 180 Query: 183 CNPAMHATGAYYLAADTIAFMQLLQGNLFADFPTLRFIIPHGGGAVPYHWGRFRGLADML 242 CNP HATGA+Y+ DT AFMQLLQG+LFADFPTLRFIIPHGGGAVPYHWGR+RGLA + Sbjct: 181 CNPNFHATGAHYINGDTSAFMQLLQGDLFADFPTLRFIIPHGGGAVPYHWGRYRGLAQDM 240 Query: 243 KQPSLDTLLMNNVFFDTCVYHQPGINLLADVIDNKNILFGSEMVGAVRGIDPTTGHYFDD 302 K+P L L+ NVFFDTCVYHQPG LLA VI +NILF SE +GAV+GIDP TGHY+DD Sbjct: 241 KRPLLSEYLLKNVFFDTCVYHQPGAELLAKVIPVENILFASETIGAVQGIDPETGHYYDD 300 Query: 303 TKRYIDALD-ISDQERHAIFEGNTRRVFPRLDAKL 336 T+RYIDA++ +SD +R I+E N R V+PRL +L Sbjct: 301 TRRYIDAIEWLSDADRQRIYEDNARSVYPRLSRQL 335 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: 461 Number of extensions: 22 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: 341 Length of database: 349 Length adjustment: 29 Effective length of query: 312 Effective length of database: 320 Effective search space: 99840 Effective search space used: 99840 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