GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Herbaspirillum seropedicae SmR1

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate HSERO_RS01300 HSERO_RS01300 phosphate acetyltransferase

Query= curated2:Q9X448
         (316 letters)



>FitnessBrowser__HerbieS:HSERO_RS01300
          Length = 319

 Score =  321 bits (823), Expect = 1e-92
 Identities = 174/299 (58%), Positives = 212/299 (70%)

Query: 11  KYDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHRL 70
           +YD+LI  A         V HPC   +L GA+EA + GL  P+LV PE +IR +A    +
Sbjct: 12  RYDQLIRDALGAQAMRVAVVHPCSPEALQGALEARDEGLFDPVLVGPETRIRRIAEAADI 71

Query: 71  DLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRIS 130
            L    IV   HSHAAAA+AV +   G    LMKGSLH+DEL+  V   A+GLRT+RRIS
Sbjct: 72  SLQGLPIVPAEHSHAAAARAVEMAVAGEVGALMKGSLHSDELLGAVVGGASGLRTERRIS 131

Query: 131 HVFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVETV 190
           HV+ M +P +   L ITDAAINI P L  KRDI QNAIDL   +G+  P VA+L+AVETV
Sbjct: 132 HVYAMAIPAYPKPLIITDAAINIAPTLAHKRDICQNAIDLLHVMGVPRPHVAVLAAVETV 191

Query: 191 TAKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILVV 250
              +PST++AAAL  MA R QITG +++GPLAFDNAI  +AA +KGI SPVAG A IL+V
Sbjct: 192 NPAMPSTLDAAALTVMATRHQITGALVDGPLAFDNAISLQAASVKGIVSPVAGSADILLV 251

Query: 251 PDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAARRR 309
           PDLEAGNMLAK L +L+ ADAAGLVLGARVPI+LTSRADS+R RLAS A+A L A+R+R
Sbjct: 252 PDLEAGNMLAKQLIYLSQADAAGLVLGARVPIILTSRADSLRVRLASSALARLVASRQR 310


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: 265
Number of extensions: 12
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: 319
Length adjustment: 27
Effective length of query: 289
Effective length of database: 292
Effective search space:    84388
Effective search space used:    84388
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: 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