GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Pseudomonas simiae WCS417

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate GFF1039 PS417_05265 short-chain dehydrogenase

Query= reanno::Korea:Ga0059261_1894
         (259 letters)



>FitnessBrowser__WCS417:GFF1039
          Length = 253

 Score =  116 bits (290), Expect = 5e-31
 Identities = 84/245 (34%), Positives = 123/245 (50%), Gaps = 8/245 (3%)

Query: 19  KRVLVTGGGSGIGAGIVEGFARQGADVT--FFDIAGAESQLLVERLSADGHKACFERVDL 76
           K  L+TG  SGIG  +   +AR G  V   ++     + Q  V  +   G +     +D+
Sbjct: 4   KVALITGAASGIGQALAVAYARNGVAVVGGYYPADPHDPQTTVSLVEEAGGECLMLPLDV 63

Query: 77  TDVASLQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSVNLKHIFFCAQA 136
            D AS+ A+ A+ I+  G  D  V NA    R  + E+T+A WDE L+V+L  +    +A
Sbjct: 64  GDTASVDALAAQTIQHFGRLDYAVANAGLLRRAPLLEMTDALWDEMLNVDLTGVMRTFRA 123

Query: 137 VVPAMRARGGGAIVNLGSISWHL-GLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRATCV 195
               M+   GGA+V + SI+  + G  +   Y   KA + GL RSLA +L   GIR   V
Sbjct: 124 ATRHMQE--GGALVAISSIAGGVYGWQEHSHYAAAKAGVPGLCRSLAVELAAKGIRCNAV 181

Query: 196 IPGNVRTPRQL---KWYSPEGEAEIVAAQCLDGRLAPEDVAAMVLFLASDDARLVTGHSY 252
           IPG + TP+ L       PEG A+   A  L      ++VA++V FL SD +  +TG S 
Sbjct: 182 IPGLIETPQSLDAKNSLGPEGLAKAARAIPLGRVGRADEVASLVQFLTSDASSYLTGQSI 241

Query: 253 FVDAG 257
            +D G
Sbjct: 242 VIDGG 246


Lambda     K      H
   0.321    0.137    0.409 

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: 132
Number of extensions: 8
Number of successful extensions: 4
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: 259
Length of database: 253
Length adjustment: 24
Effective length of query: 235
Effective length of database: 229
Effective search space:    53815
Effective search space used:    53815
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 17 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