GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pta in Dinoroseobacter shibae DFL-12

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate 3607217 Dshi_0633 Phosphate butyryltransferase (RefSeq)

Query= curated2:Q9X448
         (316 letters)



>lcl|FitnessBrowser__Dino:3607217 Dshi_0633 Phosphate
           butyryltransferase (RefSeq)
          Length = 471

 Score =  315 bits (808), Expect = 1e-90
 Identities = 169/292 (57%), Positives = 208/292 (71%)

Query: 12  YDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHRLD 71
           ++R+I  A    P  T V  P +  +L G I  AE  LITP+L+    +I   AAE  +D
Sbjct: 174 FERMILRAEPLPPFPTAVVAPEEPDALAGTILGAEHTLITPLLIGDPDRIAAAAAEKGID 233

Query: 72  LGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRISH 131
           L   EI+  PH  AAAA AV L+ EGR + +MKG LHTD L+  +     GLR  RR+SH
Sbjct: 234 LAPYEIIAEPHHKAAAACAVRLVHEGRAKAIMKGHLHTDVLLSAILKKDGGLRGTRRLSH 293

Query: 132 VFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVETVT 191
           VFVMDVPG    LFI+DAAINI PDL+ K DI QNAIDL +AIG+  P+V ILSAVETV 
Sbjct: 294 VFVMDVPGLDHPLFISDAAINIAPDLKTKADITQNAIDLALAIGVTMPKVGILSAVETVN 353

Query: 192 AKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILVVP 251
             IPST++AA L KMAERGQITGG+++GPLA DNA+D  AAR KGI S VAG A IL+VP
Sbjct: 354 PAIPSTLDAAILSKMAERGQITGGLVDGPLAMDNAVDLAAARTKGIISKVAGQADILIVP 413

Query: 252 DLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAAL 303
           ++EAGNMLAK LT+L HADA G+V+GA+ P++L SRAD+ + RLASCA+AAL
Sbjct: 414 NMEAGNMLAKQLTYLAHADAGGIVMGAQCPVILNSRADNDKARLASCAIAAL 465


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: 354
Number of extensions: 10
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: 316
Length of database: 471
Length adjustment: 30
Effective length of query: 286
Effective length of database: 441
Effective search space:   126126
Effective search space used:   126126
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: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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