GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Xanthobacter autotrophicus Py2

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate WP_012115227.1 XAUT_RS16345 phosphate acetyltransferase

Query= curated2:Q9X448
         (316 letters)



>NCBI__GCF_000017645.1:WP_012115227.1
          Length = 327

 Score =  383 bits (984), Expect = e-111
 Identities = 209/300 (69%), Positives = 229/300 (76%)

Query: 11  KYDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHRL 70
           KYDRLIAAA+A       VAHPCDE SLG A+EAAE+GLI PILV P  KI   AA  RL
Sbjct: 21  KYDRLIAAAQALPKLRVAVAHPCDEASLGAALEAAELGLIEPILVGPPGKIAAAAAAARL 80

Query: 71  DLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRIS 130
           D+     V   HSH AAAKAV L+R G  + LMKGSLHTDELM  V A  TGLRT RRIS
Sbjct: 81  DISALRQVGAAHSHDAAAKAVELVRCGEADALMKGSLHTDELMSAVVARDTGLRTARRIS 140

Query: 131 HVFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVETV 190
           H FVMDVP H D L ITDAAINI P LE K  IVQNAIDL  A+   EPRVA+LSA+ETV
Sbjct: 141 HCFVMDVPSHPDPLIITDAAINIAPSLEDKSHIVQNAIDLANALKFDEPRVAVLSAMETV 200

Query: 191 TAKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILVV 250
              +PSTIEAAALCKMA+RGQITGG+++GPLA DNAID  +A IK I SPVAG A ILVV
Sbjct: 201 NPNVPSTIEAAALCKMADRGQITGGIVDGPLALDNAIDLGSAAIKHITSPVAGRANILVV 260

Query: 251 PDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAARRRA 310
           PDLEAGNMLAK+LTFL  ADAAG+VLGARVPI+LTSRADS  TRLASCAVA+L A  +RA
Sbjct: 261 PDLEAGNMLAKSLTFLAGADAAGIVLGARVPIILTSRADSKTTRLASCAVASLLADAQRA 320


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: 314
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: 327
Length adjustment: 28
Effective length of query: 288
Effective length of database: 299
Effective search space:    86112
Effective search space used:    86112
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 Apr 09 2024. 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