GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Cronobacter universalis NCTC 9529

Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_007700802.1 AFK65_RS15785 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD

Query= SwissProt::Q92RN6
         (256 letters)



>NCBI__GCF_001277175.1:WP_007700802.1
          Length = 253

 Score =  136 bits (343), Expect = 4e-37
 Identities = 80/245 (32%), Positives = 135/245 (55%), Gaps = 4/245 (1%)

Query: 11  LRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQA 70
           L+ +  +VTG  +G+G  +    A  G  +  ++I   +     E+V A  G+    + A
Sbjct: 8   LQGKVAIVTGCDTGLGQGMALGLAEAGCDIVGINIVEPTETI--ERVTA-LGRRFLSLTA 64

Query: 71  DLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFMC 130
           DLR ++A+    + AVA+ G V VLVNNA    R+     +E+ WD+ +++N++ +FFM 
Sbjct: 65  DLRKIDAIPELIERAVAEFGHVDVLVNNAGLIRREDAINFSEQDWDDVMNLNIKSVFFMS 124

Query: 131 QAVAPHMQRQG-GGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRVN 189
           Q VA     QG GG I+N +S+        +P+Y+ +K+G++G+T+ +A +    NI VN
Sbjct: 125 QTVAKQFIAQGNGGKIINIASMLSFQGGIRVPSYTASKSGVMGITRLMANEWAKHNINVN 184

Query: 190 AILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTAQAM 249
           AI PG + T   ++L   E+  A + +R    R  +  DL+GP +FLAS +S  +    +
Sbjct: 185 AIAPGYMATNNTQQLRADEQRSAEILDRIPAGRWGLPSDLMGPVVFLASSASDYINGYTV 244

Query: 250 IIDGG 254
            +DGG
Sbjct: 245 AVDGG 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: 118
Number of extensions: 4
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: 253
Length adjustment: 24
Effective length of query: 232
Effective length of database: 229
Effective search space:    53128
Effective search space used:    53128
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