GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Rhodobacter ovatus JA234

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate WP_097031787.1 CRO07_RS16700 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase

Query= curated2:Q9X448
         (316 letters)



>NCBI__GCF_900207575.1:WP_097031787.1
          Length = 464

 Score =  316 bits (809), Expect = 8e-91
 Identities = 169/298 (56%), Positives = 212/298 (71%)

Query: 11  KYDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHRL 70
           ++   +  ARA  P    V HPC ++++ GAIE  + GL+ PIL+ P AKIR  AAE  +
Sbjct: 162 RWQGFVEEARALPPVRAAVVHPCSKSAILGAIEVRDEGLLDPILIGPGAKIRAAAAEAGV 221

Query: 71  DLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRIS 130
            L    I +  HSHAAAA+AV L   G  ++L+KGSLH+DEL+  V + + GLRT+RRIS
Sbjct: 222 SLDGFRIEETEHSHAAAARAVELAACGNVQVLVKGSLHSDELLAAVVSKSGGLRTERRIS 281

Query: 131 HVFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVETV 190
           HV+ MDVP +   + +TDAAINI P LE KRDI QNA+DL   +G  +P+VA+L+AVETV
Sbjct: 282 HVYAMDVPAYRKPVIVTDAAINIAPTLEHKRDICQNAVDLMRLLGRDQPKVAVLAAVETV 341

Query: 191 TAKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILVV 250
            A +P+T++AAAL  MA RGQITG +++GPLAFDNAI  EA   KGI S VAG A ILVV
Sbjct: 342 NATMPATLDAAALTVMAARGQITGALVDGPLAFDNAISPEAVATKGIVSQVAGEADILVV 401

Query: 251 PDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAARR 308
           PDLEAGNMLAK L +   A AAGLVLGARVPIVLTSRAD +  R+AS A+A L A R+
Sbjct: 402 PDLEAGNMLAKQLIYFAGATAAGLVLGARVPIVLTSRADPLSARIASAALAKLVAVRK 459


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: 331
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: 464
Length adjustment: 30
Effective length of query: 286
Effective length of database: 434
Effective search space:   124124
Effective search space used:   124124
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 24 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