GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Sphingobium czechense LL01

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate WP_066608841.1 V473_RS18950 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase

Query= curated2:Q9X448
         (316 letters)



>NCBI__GCF_001046645.1:WP_066608841.1
          Length = 473

 Score =  365 bits (937), Expect = e-105
 Identities = 191/294 (64%), Positives = 228/294 (77%)

Query: 12  YDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHRLD 71
           + RLI   R+  P  T +AHPC   ++  A  AAE GLI PIL+ PEA+IR  A +   D
Sbjct: 165 FRRLIEMTRSVEPVPTAIAHPCTTAAILAAAAAAEAGLIVPILIGPEARIRVAAKDAGKD 224

Query: 72  LGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRISH 131
           +G   ++DVPHSHAAAA+AV L+R G   LLMKGSLHTDELM  V  +ATGLRT+RRISH
Sbjct: 225 IGALRLIDVPHSHAAAARAVELVRSGEALLLMKGSLHTDELMGAVVPAATGLRTERRISH 284

Query: 132 VFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVETVT 191
            +++DVPGH   L ITDAAINI P LE K DI++NAIDL   IG+  P+VAILSAVETV 
Sbjct: 285 AYLLDVPGHPAPLIITDAAINIDPSLEDKADIIRNAIDLAHVIGIACPKVAILSAVETVN 344

Query: 192 AKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILVVP 251
             I ST++AAALCKMA+RGQI GGVL+GPLAFDNAI ++AA+ KGI SPVAG A++LVVP
Sbjct: 345 PAIRSTLDAAALCKMADRGQIVGGVLDGPLAFDNAISEKAAKDKGIVSPVAGRAEVLVVP 404

Query: 252 DLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYA 305
           +LEAGNMLAK LTFL  ADAAG+VLGARVPI+LTSRADS+RT +ASCA+A L A
Sbjct: 405 NLEAGNMLAKQLTFLGGADAAGVVLGARVPIILTSRADSLRTSVASCAIALLLA 458


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: 352
Number of extensions: 9
Number of successful extensions: 2
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: 473
Length adjustment: 30
Effective length of query: 286
Effective length of database: 443
Effective search space:   126698
Effective search space used:   126698
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