Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate RR42_RS36370 RR42_RS36370 dihydrodipicolinate synthase
Query= curated2:A4YNH1 (314 letters) >FitnessBrowser__Cup4G11:RR42_RS36370 Length = 308 Score = 114 bits (286), Expect = 2e-30 Identities = 88/292 (30%), Positives = 135/292 (46%), Gaps = 15/292 (5%) Query: 15 SGLLSFPVTPFKADYSFDETTYRSNMDWLCGYDVAGLFAAGGTGEFFSLTAAEVPEVVKV 74 SG+ T FKADYS D M L V GL G GE S++A E V++ Sbjct: 9 SGVFPAVSTQFKADYSLDIEATHKVMCNLVADGVCGLVVCGTVGENTSMSAREKLAVIEA 68 Query: 75 AVDETKGRVPVLAGTG-YGTAIAREIAMSAEKAGADGLLLLPPYLMHAEQEGLAAHVEAV 133 A D +GRVPV+AG + TA AR++ A +AG DG++++P + A+ AAH + Sbjct: 69 AKDAARGRVPVIAGIAEFTTAFARDMVTEAARAGVDGVMVMPALVYSAKPHEAAAHFRDI 128 Query: 134 CKSVKIGVIVYNRD---NAILQPDTLARLCERCPNLVGYKDGIGDIELMTRVYTKMGDRL 190 + + V++YN + + PD L L + C N+V +KD GD + +GDR Sbjct: 129 ATATDLPVMLYNNPPVYRSDITPDILVSLAD-CENIVCFKDSSGDTRRFIDLRNAVGDRF 187 Query: 191 TYIGGLPTAETFALPYLDMGVTTYSSAVFNFVPEFATNFYAAVRKR--DHATIHAGLKDF 248 GL + L + +G + S + N P+ + R+R D A L + Sbjct: 188 VLFAGL---DDVVLESIAVGADGWISGMSNAFPKEGETLFRLARQRRFDEA---LALYRW 241 Query: 249 ILPLIAIRNRKKGYAVSIIKAGMKVIGRDSGPVRLPLTDLTEAEMAELTALV 300 +PL+ + R V IK ++ GR S R P L +A++ +V Sbjct: 242 FMPLLHLDARPD--LVQCIKLCEELTGRGSAVTRPPRMPLQGEALAQVMTVV 291 Lambda K H 0.320 0.136 0.392 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: 216 Number of extensions: 9 Number of successful extensions: 3 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: 314 Length of database: 308 Length adjustment: 27 Effective length of query: 287 Effective length of database: 281 Effective search space: 80647 Effective search space used: 80647 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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