GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Phaeobacter inhibens BS107

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate GFF722 PGA1_c07370 putative short chain dehydrogenase

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



>FitnessBrowser__Phaeo:GFF722
          Length = 256

 Score =  217 bits (552), Expect = 2e-61
 Identities = 117/252 (46%), Positives = 159/252 (63%), Gaps = 4/252 (1%)

Query: 8   SAAAVYPSLKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSAD-G 66
           S  A++P LKG  V +TGGGSGIGA + EGF RQGA V F  +  +++   VER+ A+ G
Sbjct: 2   SDTAIFPDLKGASVFITGGGSGIGAALSEGFLRQGAKVAF--VGRSDATDFVERMEAETG 59

Query: 67  HKACFERVDLTDVASLQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSVN 126
           ++  F + D+TD+ +L+A I +  +  G    LVNNAAND RHA  ++ E +WD   ++N
Sbjct: 60  NRPLFIQCDITDIPALKAAIKQAAEAHGPITTLVNNAANDQRHATLDVDEEFWDWAQAIN 119

Query: 127 LKHIFFCAQAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLG 186
           LK  FF  QAV+P M+A GGG+IVN  SIS+ +G +    Y T  A I G+TRSLAR+ G
Sbjct: 120 LKAYFFACQAVLPGMQAAGGGSIVNFTSISYMMGNNGYPAYTTANAGINGMTRSLAREFG 179

Query: 187 RDGIRATCVIPGNVRTPRQL-KWYSPEGEAEIVAAQCLDGRLAPEDVAAMVLFLASDDAR 245
            D IR   + PG V T +QL +W +PE  A  +  QCL   LAP+D+    LFLAS  +R
Sbjct: 180 PDRIRVNALAPGWVLTDKQLDQWATPEALAAHLERQCLKDHLAPQDIVGSTLFLASATSR 239

Query: 246 LVTGHSYFVDAG 257
           +VTG +  VD G
Sbjct: 240 MVTGQTLVVDGG 251


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: 170
Number of extensions: 9
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: 256
Length adjustment: 24
Effective length of query: 235
Effective length of database: 232
Effective search space:    54520
Effective search space used:    54520
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