GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Granulicella mallensis MP5ACTX8

Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_014264488.1 ACIX8_RS06265 glucose 1-dehydrogenase

Query= SwissProt::Q92RN6
         (256 letters)



>NCBI__GCF_000178955.2:WP_014264488.1
          Length = 256

 Score =  117 bits (294), Expect = 2e-31
 Identities = 81/250 (32%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 9   PDLRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIA--AESSLALCEKVAAQTGQAPH 66
           P L+ R  +VTG GSGIG A+ E  A++GA    VD     + + A  +K+ A  G+A  
Sbjct: 2   PTLQGRVAVVTGSGSGIGQAIAERLAKEGANCV-VDYRDHIDQAQATADKITAAGGKAI- 59

Query: 67  FIQADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHL 126
            ++AD+  +       ++A  +LGS  +LVNNA  +       VTE  +D  L+VNL+  
Sbjct: 60  LVRADVSVLSDCTNLVEQAWQQLGSCDILVNNAGIEKGADFWDVTEADYDAVLNVNLKGA 119

Query: 127 FFMCQAVAPHMQ-RQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDN 185
           FF+ QA    ++  +  G ++N SS+   +  P    Y  +K  +  L + LA +LGP  
Sbjct: 120 FFLTQAFVRKLRDAKKPGRVINISSVHEDMVFPHFSTYCASKGAMRMLMRDLAVELGPLG 179

Query: 186 IRVNAILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMT 245
           I VN I PG + T     L   +  +  +     L R+   +++ G   FLASD +A +T
Sbjct: 180 ITVNNIAPGAVNTPINTSLLANKPKLEALLANIPLGRLANPEEIAGLAAFLASDDAAYVT 239

Query: 246 AQAMIIDGGV 255
               +IDGG+
Sbjct: 240 GSTYVIDGGL 249


Lambda     K      H
   0.321    0.133    0.377 

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: 129
Number of extensions: 9
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: 256
Length of database: 256
Length adjustment: 24
Effective length of query: 232
Effective length of database: 232
Effective search space:    53824
Effective search space used:    53824
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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