Align 2-keto-4-carboxy-3-hexenedioate hydratase; KCH hydratase; EC 4.2.1.- (characterized)
to candidate RR42_RS28355 RR42_RS28355 amidohydrolase
Query= SwissProt::G2IQQ5 (341 letters) >FitnessBrowser__Cup4G11:RR42_RS28355 Length = 334 Score = 221 bits (563), Expect = 2e-62 Identities = 129/340 (37%), Positives = 187/340 (55%), Gaps = 11/340 (3%) Query: 3 MIIDCHGHYTVLPKAHDEWREQQKAAFKAGQPAPPY-PEISDDEIRETIEANQLRLIKER 61 MIID H H + P++ + A G+ P P++ D +R+ E ++ + + Sbjct: 1 MIIDSHAHIVMPPESF-----RYMAELVGGRANPSTTPKVPDASVRKVAE-ELVQSMDKV 54 Query: 62 GADMTIFSPRASAMAPHVGDQSVAVPWAQACNNLIARVVDLFPETFAGVCMLPQ-SPEAD 120 G D+ SPR V V W++ CN+LIAR V LFP+ F GV LPQ E+ Sbjct: 55 GTDVQFISPRPYLQMHSVKPGRVTELWSRHCNDLIARFVALFPDRFRGVAGLPQYMNESP 114 Query: 121 MTSSIAELERCVNELGFIGCNLNPDPGGGHFKHPP-LTDRFWYPFYEKMVELDVPAMIHV 179 ++ ELERCV ELGF+GC +NPDP G PP L D FWYP Y+ M +LDVP +IH Sbjct: 115 ALRAVPELERCVKELGFVGCLINPDPTEGEGPTPPGLGDPFWYPLYDAMTQLDVPGLIHS 174 Query: 180 SGSCNPAMHATGAYYLAADTIAFMQLLQGNLFADFPTLRFIIPHGGGAVPYHWGRFRGLA 239 +GSC+ A + ++ ++IA + LL +F +P L+ ++ HGGGA+PY GRFR + Sbjct: 175 AGSCS-ARESYTLKFINEESIAIVSLLGSKVFDTYPGLKIVVAHGGGAIPYQMGRFRSWS 233 Query: 240 DMLKQPSLDTLLMNNVFFDTCVYHQPGINLLADVIDNKNILFGSEMVGAVRGIDPTTGHY 299 + + ++FDTC Y + I LL V N+LFG+E G DP +G Sbjct: 234 VRKGETVSFDEQLKRLYFDTCNYSKEAIELLLKVAGTDNVLFGTEKPGTGSARDPVSGRD 293 Query: 300 FDDTKRYIDALD-ISDQERHAIFEGNTRRVFPRLDAKLKA 338 +DD K I+++D +S+Q+R IFE N RV+ R K +A Sbjct: 294 YDDMKPVIESIDWLSEQQRRNIFECNCTRVYSRAFRKDEA 333 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: 337 Number of extensions: 20 Number of successful extensions: 6 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: 334 Length adjustment: 28 Effective length of query: 313 Effective length of database: 306 Effective search space: 95778 Effective search space used: 95778 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