Align L-2-keto-3-deoxyarabonate dehydratase; L-KDA dehydratase; 2-dehydro-3-deoxy-L-arabinonate dehydratase; L-2-keto-3-deoxyarabinonate dehydratase; EC 4.2.1.43 (characterized)
to candidate WP_029001944.1 H537_RS0137415 dihydrodipicolinate synthase family protein
Query= SwissProt::Q1JUQ0 (309 letters) >NCBI__GCF_000430725.1:WP_029001944.1 Length = 309 Score = 482 bits (1241), Expect = e-141 Identities = 238/308 (77%), Positives = 263/308 (85%) Query: 1 MTSSSTPRHRGIFPVVPTTFADTGELDLASQKRAVDFMIDAGSDGLCILANFSEQFAITD 60 M + PR+RG+FPVVPTTF DTG LDL SQKRAVDFMIDAGSDGLCILANFSEQF + D Sbjct: 1 MAAIPAPRYRGVFPVVPTTFTDTGALDLDSQKRAVDFMIDAGSDGLCILANFSEQFLLAD 60 Query: 61 DERDVLTRTILEHVAGRVPVIVTTSHYSTQVCAARSLRAQQLGAAMVMAMPPYHGATFRV 120 +ER+VLTRT+LEHVA RVPVIVTT+H+ST+VC ARS RAQ GAAMVM MPPYHGATFRV Sbjct: 61 EEREVLTRTVLEHVASRVPVIVTTTHFSTEVCIARSRRAQAQGAAMVMVMPPYHGATFRV 120 Query: 121 PEAQIFEFYARVSDAIAIPIMVQDAPASGTALSAPFLARMAREIEQVAYFKIETPGAANK 180 PEA I FY R+SDA+ IP+MVQDAP SGT L A FLAR+ARE+ QV+YFKIETPGAANK Sbjct: 121 PEAAIESFYRRLSDALDIPVMVQDAPCSGTPLPAAFLARLAREVAQVSYFKIETPGAANK 180 Query: 181 LRELIRLGGDAIEGPWDGEEAITLLADLHAGATGAMTGGGFPDGIRPILEAWREGRHDDA 240 LRELIRLGG A+EGPWDGEE ITLLADL AGATGAMTG GFPD +R I++A R G D A Sbjct: 181 LRELIRLGGAAVEGPWDGEEGITLLADLEAGATGAMTGAGFPDAMRAIVDAHRAGGADAA 240 Query: 241 YARYQAWLPLINHENRQSGILTAKALMREGGVIASERPRHPMPELHPDTRAELLAIARRL 300 +A YQ WLPLINHENRQ+G L AKALM+EGGVIA E PRHP P LHP TR+EL+AIARRL Sbjct: 241 FALYQRWLPLINHENRQAGFLAAKALMKEGGVIACEAPRHPWPALHPATRSELIAIARRL 300 Query: 301 DPLVLRWA 308 DPLVLRWA Sbjct: 301 DPLVLRWA 308 Lambda K H 0.321 0.136 0.406 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: 375 Number of extensions: 6 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: 309 Length of database: 309 Length adjustment: 27 Effective length of query: 282 Effective length of database: 282 Effective search space: 79524 Effective search space used: 79524 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 (21.9 bits) S2: 48 (23.1 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