GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gatY in Caulobacter crescentus NA1000

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 CCNA_03360 CCNA_03360 tagatose-1,6-bisphosphate aldolase

Query= SwissProt::P0C8J6
         (284 letters)



>FitnessBrowser__Caulo:CCNA_03360
          Length = 363

 Score =  154 bits (388), Expect = 4e-42
 Identities = 109/326 (33%), Positives = 164/326 (50%), Gaps = 45/326 (13%)

Query: 4   VSTKQMLNNAQRGGYAVPAFNIHNLETMQVVVETAANLHAPVIIAGTPGTFTHAGTENLL 63
           ++ +Q+L++A    Y +PAFNI+N+E    ++E A  +++PVII  + G   +A    L 
Sbjct: 4   ITLRQLLDHAAEHEYGLPAFNINNMEQGLAIMEAADAVNSPVIIQASRGARNYANDIMLA 63

Query: 64  ALVSAMAKQYHH-PLAIHLDHHTKFDDIAQKVRSGVRSVMIDASHLPFAQ-------NIS 115
            ++ A+   Y H P+ +H DH       A  ++ G  SVM+D S +  A+       N+ 
Sbjct: 64  KMIDALVDIYPHIPVCMHQDHGNGPATCATAIQYGFTSVMMDGSLMEDAKTPASYEYNVE 123

Query: 116 RVKEVVDFCHRFDVSVEAELGQLG------GQEDDVQVNEA----DALYTNPAQAREFAE 165
             ++VV   H   VSVE ELG LG      G+ +D    E     D L T+P QA +F  
Sbjct: 124 VTRKVVQMAHSCGVSVEGELGVLGSLETGMGEAEDGHGFEGKLSHDELLTDPDQAVDFVA 183

Query: 166 ATGIDSLAVAIGTAHGMYA-----SAPALDFSRLENI-RQWVNLPLVLHGAS-------- 211
            TG+D+LA+A+GT+HG Y          L  + +E I R+  N  LV+HG+S        
Sbjct: 184 QTGVDALAIAMGTSHGAYKFTRKPDGDVLAMNVIEEIHRRLPNTHLVMHGSSSVPQDLQD 243

Query: 212 -------------GLSTKDIQQTIKLGICKINVATELKNAFSQALKNYLTEHPEATDPRD 258
                        G+  ++IQ+ IK G+ KINV T+ + A + A++  L E P   DPR 
Sbjct: 244 IINQYGGEMPQTWGVPVEEIQRGIKHGVRKINVDTDNRMAITGAIRKLLVEKPGEFDPRA 303

Query: 259 YLQSAKSAMRDVVSKVIADCGCEGRA 284
           YL+ AK AMR V      + G  G A
Sbjct: 304 YLKPAKEAMRKVCQARFVEFGSAGHA 329


Lambda     K      H
   0.318    0.131    0.376 

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: 241
Number of extensions: 13
Number of successful extensions: 5
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: 363
Length adjustment: 28
Effective length of query: 256
Effective length of database: 335
Effective search space:    85760
Effective search space used:    85760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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