GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Desulfovibrio vulgaris Hildenborough

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate 209573 DVU0627 phosphotransbutyrylase

Query= curated2:Q9X448
         (316 letters)



>MicrobesOnline__882:209573
          Length = 343

 Score =  198 bits (503), Expect = 2e-55
 Identities = 119/313 (38%), Positives = 179/313 (57%), Gaps = 10/313 (3%)

Query: 7   AQPSKYDRLIAAA-RAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVA 65
           A P   D ++AA  R   P    VA   +  +L   +EA +MG+  P+LV   A   ++A
Sbjct: 30  AAPRTLDDIVAAVVRRGIPVRVAVAACAEPNALAAVLEARDMGMAVPVLVGDIAATESIA 89

Query: 66  AEHRLDLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRT 125
            E  L L   E+ D P    A  +AV  +R G  ++LMKG ++TD L+  V    +GL  
Sbjct: 90  TERGLSLEGCEVEDEPVPVKAVQRAVDRVRTGGADVLMKGLVNTDVLLRVVLNRVSGLSA 149

Query: 126 QRRISHVFVMDVPG--------HTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLG 177
              +SHV V  +P          +  + ITDAA+NI P++E K  IV+NAI +  ++G+ 
Sbjct: 150 GGLLSHVAVCSLPATCGGEASASSRLVCITDAAVNISPNMERKLGIVRNAICVARSLGIP 209

Query: 178 EPRVAILSAVETVTAK-IPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKG 236
            PRVA+L+A E V    +P+T++A  + +MA++G+    ++ GP+A D AI  + A  KG
Sbjct: 210 SPRVAMLAATEKVMLPAMPATLDAQIVARMADQGEFGDAMVAGPMALDVAISPDIAARKG 269

Query: 237 INSPVAGHAQILVVPDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLA 296
           ++ PVAG A IL  PD+E+GN+L K+LT L H + AG++ G   P+V+ SR DS R++L 
Sbjct: 270 VSHPVAGRADILCAPDIESGNILYKSLTTLAHVEMAGILTGTTAPVVVPSRGDSRRSKLL 329

Query: 297 SCAVAALYAARRR 309
           S A+AA  A   R
Sbjct: 330 SLALAAYVAMECR 342


Lambda     K      H
   0.320    0.133    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: 224
Number of extensions: 7
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: 316
Length of database: 343
Length adjustment: 28
Effective length of query: 288
Effective length of database: 315
Effective search space:    90720
Effective search space used:    90720
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 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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