GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-dehydrog in Phyllobacterium leguminum ORS 1419

Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_110751458.1 C7477_RS09530 SDR family oxidoreductase

Query= uniprot:A0A4P7ABK7
         (254 letters)



>NCBI__GCF_003217235.1:WP_110751458.1
          Length = 244

 Score =  276 bits (706), Expect = 3e-79
 Identities = 146/245 (59%), Positives = 179/245 (73%), Gaps = 7/245 (2%)

Query: 10  GKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETHLLDVTDDDAI 69
           GKTVL+TAA QGIG+A+   FAR GA V  TDI++  L  L    G+ T  LDV D  A+
Sbjct: 7   GKTVLVTAAGQGIGKATALAFARAGATVHTTDINEQALAALEGEPGISTRRLDVLDSAAV 66

Query: 70  KALVAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVLPGMLAKKA 129
              VA +G VDVLFNCAG+V +G+ILE  D   DF+F+LN ++M  TIRAVLPGM+    
Sbjct: 67  SQAVADIGAVDVLFNCAGFVHSGSILEIKDGDLDFAFDLNVRSMVRTIRAVLPGMIFNGG 126

Query: 130 GSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICPGTIESPSL 189
           G+IVN+AS ASS+KGV NRFAY  +KAAV+GLTKSVAAD+V QGIRCNAICPGT+ESPSL
Sbjct: 127 GAIVNMASVASSIKGVPNRFAYSVTKAAVIGLTKSVAADYVGQGIRCNAICPGTVESPSL 186

Query: 190 NQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNFTTGSIHMID 249
            +R+    K TG  E   RAAF++RQPMGRIG  EE+A LA+YLA   + +TTG  ++ID
Sbjct: 187 QERL----KATGDYE-AARAAFISRQPMGRIGTPEEIADLAVYLAG--ATYTTGQAYVID 239

Query: 250 GGWSN 254
           GGW N
Sbjct: 240 GGWVN 244


Lambda     K      H
   0.316    0.129    0.359 

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: 191
Number of extensions: 5
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: 254
Length of database: 244
Length adjustment: 24
Effective length of query: 230
Effective length of database: 220
Effective search space:    50600
Effective search space used:    50600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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