GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gatY in Klebsiella michiganensis M5al

Align D-tagatose-1,6-bisphosphate aldolase subunit GatY; TBPA; TagBP aldolase; D-tagatose-bisphosphate aldolase class II; Tagatose-bisphosphate aldolase; EC 4.1.2.40 (characterized)
to candidate BWI76_RS00545 BWI76_RS00545 putative class-II ketose-bisphosphate aldolase

Query= SwissProt::Q8VS16
         (284 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS00545 BWI76_RS00545 putative
           class-II ketose-bisphosphate aldolase
          Length = 280

 Score =  181 bits (458), Expect = 2e-50
 Identities = 101/266 (37%), Positives = 152/266 (57%), Gaps = 2/266 (0%)

Query: 8   NMLLK-AQRLGY-AVPAFNIHNLETMQVVVETAAELRSPLILAGTPGTYSYAGTGNVVAI 65
           N +LK AQ   + A+ +FN+H +E +    + A +  SPL++  + GT  Y G   +V  
Sbjct: 7   NAILKIAQERNFKAIGSFNLHCIEMLPAFFKAAQQSHSPLMIQISTGTAEYLGYRLLVDA 66

Query: 66  ARDLAKIWDLPLAVHLDHHEDLADITRKVQAGIRSVMIDGSHSPFEENVALVKSVVELSH 125
            R LA+  ++P  +HLDH  D++ I   + AG  SVM DGSH   EEN+   + VVE++ 
Sbjct: 67  VRSLAESENVPTCLHLDHCSDISAIETAMDAGFTSVMYDGSHLDLEENIGNTRIVVEMAR 126

Query: 126 RYDASVEAELGRLGGVEDDLGVDAKDALYTNPEQGREFVARTGIDSLAVVIGTAHGLYAA 185
             + +VE ELG +GG ED   V A+D  +T  E  + FV  T +D LAV +GT HGLY  
Sbjct: 127 PRNITVEGELGAIGGSEDGKAVAAEDICFTTVEDAKRFVEETRVDMLAVSVGTVHGLYTG 186

Query: 186 EPKLGFAALPPISERVDVPLVLHGASKLPDSDIRRAISLGVCKVNVATELKIAFSDALKH 245
           + ++    L  IS    VPLVLHG + + D D+R+A++ G+ KVNV TE+ + + D  K 
Sbjct: 187 KAQIQHQRLKEISAATGVPLVLHGGTGVSDEDMRQAVTEGINKVNVGTEMNVQWVDRCKT 246

Query: 246 YFEENPDANEPRHYMKPAKAAMKDVV 271
            FE+    +  R ++ PA  A+  V+
Sbjct: 247 TFEKGKVNDSVRKFLIPANNAVTHVL 272


Lambda     K      H
   0.319    0.135    0.389 

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: 197
Number of extensions: 7
Number of successful extensions: 1
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: 284
Length of database: 280
Length adjustment: 26
Effective length of query: 258
Effective length of database: 254
Effective search space:    65532
Effective search space used:    65532
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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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