GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Sphingomonas koreensis DSMZ 15582

Align sorbitol-6-phosphate dehydrogenase; EC 1.1.1.140 (characterized)
to candidate Ga0059261_2655 Ga0059261_2655 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= CharProtDB::CH_091827
         (259 letters)



>FitnessBrowser__Korea:Ga0059261_2655
          Length = 259

 Score =  130 bits (326), Expect = 4e-35
 Identities = 87/255 (34%), Positives = 136/255 (53%), Gaps = 6/255 (2%)

Query: 5   AVVIGGGQTLGAFLCHGLAAEGYRVAVVDIQSDKAANVAQEINAEYGESMAYGFGADATS 64
           AV+ GG + +G  +    A+EG  + +  I++D +   A++  A YG  +      D T 
Sbjct: 9   AVISGGNKGIGLAIAERFASEGANIVIGAIEADLSP--AEQALAGYGTGVV-AQRCDVTK 65

Query: 65  EQSVLALSRGVDEIFGRVDLLVYSAGIAKAAFISDFQLGDFDRSLQVNLVGYFLCAREFS 124
              V AL     E FG VD+ V +AG+   A + D   G++D +L VN  G FLC +E  
Sbjct: 66  ADDVRALFEAA-EAFGGVDIAVQNAGVITIAKVEDLTEGEWDLNLAVNTKGAFLCCQEAI 124

Query: 125 RLMIRDGIQGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHSLML 184
           R +   G  GR+I   S   + G      Y+A+KFG VG+TQSLA ++A  GITV+++  
Sbjct: 125 RRLRARGKPGRLINTASGQARDGFIFTPHYAASKFGVVGMTQSLAKEVATQGITVNAICP 184

Query: 185 GNLLKSPMFQSLLPQYATKLG-IKPDQVEQYYIDKVPLKRGCDYQDVLNMLLFYASPKAS 243
           G ++ + M+     ++   +G   P  + + ++  +P+KR     DV  ++ F AS  AS
Sbjct: 185 G-IIHTDMWDYNDREWGRLMGDYAPGALMEEWVQGIPMKRAGTGADVAALVAFLASADAS 243

Query: 244 YCTGQSINVTGGQVM 258
           Y TGQ+INV GG +M
Sbjct: 244 YITGQTINVDGGLIM 258


Lambda     K      H
   0.320    0.137    0.391 

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: 174
Number of extensions: 6
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: 259
Length adjustment: 24
Effective length of query: 235
Effective length of database: 235
Effective search space:    55225
Effective search space used:    55225
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 (21.8 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