GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Bacteroides thetaiotaomicron VPI-5482

Align phosphate acetyltransferase; EC 2.3.1.8 (characterized)
to candidate 352079 BT2551 phosphate butyryltransferase (NCBI ptt file)

Query= CharProtDB::CH_090885
         (294 letters)



>FitnessBrowser__Btheta:352079
          Length = 314

 Score =  165 bits (417), Expect = 1e-45
 Identities = 97/285 (34%), Positives = 160/285 (56%), Gaps = 5/285 (1%)

Query: 11  RGKGKKLAVAAANDDHVIEAVYRAWRERVCEPVLFGPEEEITRI--IEELVPEWKNPQII 68
           + + K++AV  AND +   A+ RA  E + E ++ G    + +   +++     K   I 
Sbjct: 17  QNRRKRIAVVCANDPNTEYAITRALEEGIAEFLMIGDSAILEKYPALKQYPDYVKTIHIE 76

Query: 69  DCPPEEAGRLAVEAVSKGECDFLMKGKIKTGDLMKIYLDERYGLRT-GKTMAMVSVMEIP 127
           D   +EA R AV  V +G  D LMKG I T +L+   LD+  GL   GK +  ++VMEIP
Sbjct: 77  DS--DEAAREAVRIVREGGADILMKGIINTDNLLHAILDKEKGLLPKGKILTHLAVMEIP 134

Query: 128 DFPRPLIISDPGMLISPTLEQKVDMIEHCVRVANVMGLETPKVAVVGAIEVVNPKMPITM 187
            + + L  SD  ++  PTL+Q+++MI + +      G+E P+VA++   E V+ K P ++
Sbjct: 135 TYHKLLFFSDAAVIPRPTLQQRIEMIWYAICTCRHFGIEQPRVALIHCTEKVSAKFPHSL 194

Query: 188 EAAILSKMNQRGQIKGCIVDGPFALDNVVSEEAAKKKGIQSPVAGKADILILPDIEAANI 247
           +   + ++ + G+    I+DGP  +     + +   KGI SP+ G+AD+LI P+IE+ N 
Sbjct: 195 DYVNIVELAEAGEFGNVIIDGPLDVRTACEQASGDIKGIVSPINGQADVLIFPNIESGNA 254

Query: 248 LYKALVFLAKAKSASTILGGKVPVVLTSRADSEETKFYSIALSAV 292
            YK++   A A  A  + G   PVVL SR+DS  +K+YSIA++ +
Sbjct: 255 FYKSVSLFANADMAGLLQGPICPVVLPSRSDSGLSKYYSIAMACL 299


Lambda     K      H
   0.319    0.136    0.386 

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: 235
Number of extensions: 12
Number of successful extensions: 2
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: 294
Length of database: 314
Length adjustment: 27
Effective length of query: 267
Effective length of database: 287
Effective search space:    76629
Effective search space used:    76629
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: 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