GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgD in Algiphilus aromaticivorans DG1253

Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate WP_043768161.1 U743_RS10725 4-hydroxy-tetrahydrodipicolinate synthase

Query= curated2:A4YNH1
         (314 letters)



>NCBI__GCF_000733765.1:WP_043768161.1
          Length = 293

 Score = 90.5 bits (223), Expect = 4e-23
 Identities = 93/294 (31%), Positives = 123/294 (41%), Gaps = 28/294 (9%)

Query: 22  VTPFKADYSFDETTYRSNMDWLCGYDVAGLFAAGGTGEFFSLTAAEVPEVVKVAVDETKG 81
           VTP  AD + D       + W      A + A G TGE  +L   E   V++  V     
Sbjct: 10  VTPMDADGAVDYEALDRLVAWHIEAGTAAIVAVGTTGESATLDNDEHIAVIRRVVAAADR 69

Query: 82  RVPVLAGTGYG-TAIAREIAMSAEKAGADGLLLLPPYLMHAEQEGLAAHVEAVCKSVKIG 140
           R+PV+AGTG   T+ A  +  +A   GAD  LL+ PY     QEGL  H  AV ++V I 
Sbjct: 70  RIPVIAGTGANATSEAIALTRAAADCGADAALLVTPYYNKPPQEGLYRHFRAVAEAVDIP 129

Query: 141 VIVYN---RDNAILQPDTLARLCERCPNLVGYKDGIGDIELMTRVY--TKMGDRLTYIGG 195
            I+YN   R    L P T+ RL E  PN++G K+ + D   +  +      GD   Y G 
Sbjct: 130 QILYNVPGRTGCDLLPVTVKRLAE-VPNIIGLKEALADEARIKELVGCGLPGDFALYSGD 188

Query: 196 LPTAETFALPYLDMGVTTYSSAVFNFVPEFATNFYAAVRKRDHATIH------AGL-KDF 248
             TA    L     G     S V N  P       AA    D A         AGL +D 
Sbjct: 189 DGTACGAML----AGFHGDVSVVANVAPAMMARMCAAATAGDRAAAEAADAELAGLHRDL 244

Query: 249 ILPLIAIRNRKKGYAVSIIKAGMKVIGRDSGPVRLPLTDLTEAEMAELTALVKA 302
            L    I  +   +A+ +I AG          +RLPL  L E     L A ++A
Sbjct: 245 FLQANPIPVKWALHAMGLIGAG----------IRLPLVPLAEEHHDTLRATLRA 288


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: 220
Number of extensions: 16
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: 293
Length adjustment: 27
Effective length of query: 287
Effective length of database: 266
Effective search space:    76342
Effective search space used:    76342
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 24 2021. 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