GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Salinicoccus carnicancri Crm

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_017548686.1 C792_RS0106680 glucose 1-dehydrogenase

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



>NCBI__GCF_000330705.1:WP_017548686.1
          Length = 243

 Score =  145 bits (366), Expect = 8e-40
 Identities = 86/240 (35%), Positives = 133/240 (55%), Gaps = 7/240 (2%)

Query: 25  RTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADELGDSKHKPLFLSCDLTD 84
           + V++TGG  G+GAS V+ F ++GA+V F D+D  AG  L DE+G      LF+  D+TD
Sbjct: 7   KVVIVTGGTGGMGASHVKKFVSEGAQVVFTDLDEGAGRVLQDEMGPQS---LFIKQDVTD 63

Query: 85  IDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQFFAAQAVM 144
            ++  K I + +  LGP+ VLVNNA  +          + +D  I VN +  F   +AV+
Sbjct: 64  SESWNKVIVETEKNLGPVNVLVNNAGVNYSEETEAFPEDEYDRVIEVNQKAVFLGMKAVI 123

Query: 145 EDMKAANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFNIRVNTLVPG 204
             MK A SGSIIN+ SI  +        Y  SK AV G+T+  A +LG + IRVN++ P 
Sbjct: 124 PSMKKAASGSIINISSIGGIRGRMESVAYSASKFAVTGMTKVGALELGKYGIRVNSVHPS 183

Query: 205 WVMTEKQKRLWLDDAGRRSIKEGQCIDAELEPADLARMALFLAADDSRMITAQDIVVDGG 264
            V T     L+ +  G +++   + +   L   +++ + L+LA+D+S   T  + V+DGG
Sbjct: 184 LVNT----GLFSESTGGKAVASDRPLGRVLTKEEVSALVLYLASDESSYTTGAEHVIDGG 239


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: 145
Number of extensions: 7
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: 266
Length of database: 243
Length adjustment: 24
Effective length of query: 242
Effective length of database: 219
Effective search space:    52998
Effective search space used:    52998
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: 47 (22.7 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