GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacE in Azohydromonas australica DSM 1124

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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