GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gatY in Shewanella oneidensis MR-1

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 200117 SO0933 fructose-bisphosphate aldolase, class II, Calvin cycle subtype (NCBI ptt file)

Query= SwissProt::P0C8J6
         (284 letters)



>lcl|FitnessBrowser__MR1:200117 SO0933 fructose-bisphosphate
           aldolase, class II, Calvin cycle subtype (NCBI ptt file)
          Length = 355

 Score =  171 bits (433), Expect = 2e-47
 Identities = 111/329 (33%), Positives = 175/329 (53%), Gaps = 45/329 (13%)

Query: 1   MYVVSTKQMLNNAQRGGYAVPAFNIHNLETMQVVVETAANLHAPVIIAGTPGTFTHAGTE 60
           M ++S +Q+L++A   GY VPAFN++NLE M+ +++ A    +PVI+  + G   +A  +
Sbjct: 1   MALISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQ 60

Query: 61  NLLALVSAMAKQYHH-PLAIHLDHHTKFDDIAQKVRSGVRSVMIDASHLP-------FAQ 112
            L  L++A  +QY   P+ IH DH T  D   + ++ G+ SVM+D S +        +  
Sbjct: 61  FLKYLMTAALEQYPDIPVCIHQDHGTDPDICQRSIQLGMSSVMMDGSLMADGKTPASYEY 120

Query: 113 NISRVKEVVDFCHRFDVSVEAELGQLG-------GQEDDVQ---VNEADALYTNPAQARE 162
           N+   +  V F H   VSVE E+G LG       G+ED V    V   D L T+P +A  
Sbjct: 121 NVDVTRRTVAFAHACGVSVEGEIGCLGSLETGTAGEEDGVGAEGVLSHDQLLTSPEEAAR 180

Query: 163 FAEATGIDSLAVAIGTAHGMY--ASAPALDFSRLENIRQW----VNLPLVLHGAS----- 211
           F   T +D+LA+AIGT+HG Y  +  P  D  R++ I++      N  LV+HG+S     
Sbjct: 181 FVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHGSSSVPQE 240

Query: 212 ----------------GLSTKDIQQTIKLGICKINVATELKNAFSQALKNYLTEHPEATD 255
                           G+  ++I + IK G+ K+N+ T+L+ A + A++ YL EHP   D
Sbjct: 241 WLKIINQYGGQIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKYLAEHPSEFD 300

Query: 256 PRDYLQSAKSAMRDVVSKVIADCGCEGRA 284
           PR +L+++  AM D+ +      GC G+A
Sbjct: 301 PRKFLKASMEAMADICTVRYEAFGCAGQA 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: 247
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: 355
Length adjustment: 27
Effective length of query: 257
Effective length of database: 328
Effective search space:    84296
Effective search space used:    84296
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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