GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Pedobacter sp. GW460-11-11-14-LB5

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate CA265_RS15450 CA265_RS15450 3-oxoacyl-[acyl-carrier-protein] reductase

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



>FitnessBrowser__Pedo557:CA265_RS15450
          Length = 247

 Score =  120 bits (301), Expect = 3e-32
 Identities = 85/250 (34%), Positives = 125/250 (50%), Gaps = 16/250 (6%)

Query: 16  LKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAES-QLLVERLSADGHKACFERV 74
           L+GK  LVTG   GIG  I E FA QGA+V F  ++  E  + L + L + G K    R 
Sbjct: 4   LEGKTALVTGASKGIGRKIAEKFAEQGANVAFTYLSSVEKGEALEQELQSFGTKVKGYRS 63

Query: 75  DLTDVASLQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSVNLKHIFFCA 134
           D +  A  + +I  ++   G  DI+VNNA       +  ++E  WD+ +++NLK IF   
Sbjct: 64  DASKFAEAEQLINDIVAEFGTIDIVVNNAGITKDGLLMRMSEENWDDVININLKSIFNVT 123

Query: 135 QAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRATC 194
           +A    M     G  +N+GSI    G      Y   KA I G T+S+A++LG   IRA  
Sbjct: 124 KAASKVMMKARKGVFINMGSIVGTTGNGGQANYAASKAGIIGFTKSIAKELGSRNIRANV 183

Query: 195 VIPGNVRT-------PRQLKWYSPEGEAEIVAAQCLDGRLAPEDVAAMVLFLASDDARLV 247
           V PG +RT       P+ ++ +    E +I   +  +     ED+A + +FLASD +  V
Sbjct: 184 VAPGFIRTEMTDILDPKVVEGW----EKDIPLKRAGE----TEDIANVCVFLASDMSAYV 235

Query: 248 TGHSYFVDAG 257
           TG +  V  G
Sbjct: 236 TGQTLSVCGG 245


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: 124
Number of extensions: 5
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: 259
Length of database: 247
Length adjustment: 24
Effective length of query: 235
Effective length of database: 223
Effective search space:    52405
Effective search space used:    52405
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: 46 (22.3 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