GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Pantoea rwandensis LMG 26275

Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_084936983.1 HA51_RS22390 SDR family oxidoreductase

Query= uniprot:A0A4P7ABK7
         (254 letters)



>NCBI__GCF_002095475.1:WP_084936983.1
          Length = 246

 Score =  318 bits (815), Expect = 7e-92
 Identities = 160/247 (64%), Positives = 197/247 (79%), Gaps = 3/247 (1%)

Query: 8   LAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETHLLDVTDDD 67
           L GK VLITAA QGIG AS   FA +GA V+ +DI+ T L++L ++     + LDVTD  
Sbjct: 3   LHGKRVLITAAGQGIGLASARYFAEQGANVVGSDINITALQDLQNVT---PYRLDVTDRA 59

Query: 68  AIKALVAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVLPGMLAK 127
           AI+A V ++G VDVLFNCAG V +GN+L C ++ W F+ +LN  AMFH I+A LPGMLA+
Sbjct: 60  AIRAAVEELGPVDVLFNCAGVVHSGNLLACTEQEWQFALDLNVSAMFHMIQAFLPGMLAQ 119

Query: 128 KAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICPGTIESP 187
           K GSI+N++S ASSVKGVANRFAY A+KAAV+GLT+SVAADF++ GIRCNAICPGT++SP
Sbjct: 120 KKGSIINMSSVASSVKGVANRFAYSATKAAVIGLTRSVAADFIADGIRCNAICPGTVDSP 179

Query: 188 SLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNFTTGSIHM 247
           SL QRI+TQA+  GKSEDEV AAFVARQP+GRIG  EE+A LA YLASD SN+TTG+  +
Sbjct: 180 SLRQRIATQAQAEGKSEDEVYAAFVARQPIGRIGTVEEIAYLAAYLASDASNYTTGTAQV 239

Query: 248 IDGGWSN 254
           IDGGWSN
Sbjct: 240 IDGGWSN 246


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: 200
Number of extensions: 6
Number of successful extensions: 2
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: 246
Length adjustment: 24
Effective length of query: 230
Effective length of database: 222
Effective search space:    51060
Effective search space used:    51060
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