GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Nocardiopsis gilva YIM 90087

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_094932655.1 CDO52_RS21950 SDR family oxidoreductase

Query= reanno::BFirm:BPHYT_RS16920
         (266 letters)



>NCBI__GCF_002263495.1:WP_094932655.1
          Length = 693

 Score =  125 bits (314), Expect = 2e-33
 Identities = 78/245 (31%), Positives = 128/245 (52%), Gaps = 6/245 (2%)

Query: 25  RTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADELGDSKHKPLFLSCDLTD 84
           R  ++TG A GIGA+     AA G  VA  D+  S  +   DE+       + L  D++D
Sbjct: 6   RVAIVTGAARGIGAATARRLAADGRSVAVIDLKESDAQRTVDEITADGGTAIGLGADVSD 65

Query: 85  IDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQFFAAQAVM 144
            D +  A+  V   LGP  +LVNNA   + + + +++ + +D  + V++R  F  A+A  
Sbjct: 66  ADQVAAAVGQVAERLGPPTILVNNAGVLRDNLLFKMSEDDWDTVMNVHLRGSFLMARAAQ 125

Query: 145 EDMKAANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFNIRVNTLVPG 204
           + M A N G I+NL S S    N G   Y  +K+ +QG T+ LA +LG F +  N + PG
Sbjct: 126 QHMVAENWGRIVNLSSSS-AQGNRGQANYSTAKAGLQGFTKTLAIELGKFGVTCNAVAPG 184

Query: 205 WVMTEKQK----RLWLD-DAGRRSIKEGQCIDAELEPADLARMALFLAADDSRMITAQDI 259
           +++T+  K    R+ +D +  +++  EG  +    +P D+A    FL ++ S  ++ Q I
Sbjct: 185 FIVTDMTKATAARVGMDYEDFKKAAAEGIPVRRVGQPEDIANTVSFLTSEASGFVSGQVI 244

Query: 260 VVDGG 264
            V GG
Sbjct: 245 YVAGG 249


Lambda     K      H
   0.320    0.134    0.388 

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: 379
Number of extensions: 21
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: 266
Length of database: 693
Length adjustment: 32
Effective length of query: 234
Effective length of database: 661
Effective search space:   154674
Effective search space used:   154674
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: 51 (24.3 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