GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Hafnia paralvei ATCC 29927

Align Phosphate propanoyltransferase; Phosphate acyltransferase PduL; Phosphotransacylase PduL; PTAC; Propanediol utilization protein PduL; EC 2.3.1.222 (characterized)
to candidate WP_008813240.1 M988_RS11440 phosphate propanoyltransferase

Query= SwissProt::Q9XDN5
         (210 letters)



>NCBI__GCF_001655005.1:WP_008813240.1
          Length = 216

 Score =  320 bits (820), Expect = 1e-92
 Identities = 162/206 (78%), Positives = 178/206 (86%)

Query: 1   MDKELLQSTVRKVLDEMRQRPIPLGVSNRHIHLSAQDYERLFPGHPISEKKALLQPGQYA 60
           M+K LL+  V K+LDEMR RPIPLGVSNRH+HLS QDY++LFP  P+ EKKALLQPGQ+A
Sbjct: 1   MEKTLLEPVVSKILDEMRLRPIPLGVSNRHLHLSVQDYQQLFPNQPLIEKKALLQPGQFA 60

Query: 61  AEQTVTLVGPKGQLKNVRLLGPLRSVSQVEISRTDARTLGIAAPLRMSGNLKGTPGIRLV 120
           AEQTVTLVGPKG LKNVR+LGPLRS SQVEISRTDARTLGI APLRMSGNL  TP IRLV
Sbjct: 61  AEQTVTLVGPKGSLKNVRILGPLRSHSQVEISRTDARTLGIHAPLRMSGNLDQTPAIRLV 120

Query: 121 SPFAELELPSGVIVAQRHIHMSPLDALILRVSHGDMVSVAIEGDDRGLIFNNVAIRVSPD 180
           SP+ ELELP GVIVAQRHIHMSPLDAL+ RV HGD V VAI+G  R LI ++VAIRVSP 
Sbjct: 121 SPYGELELPQGVIVAQRHIHMSPLDALLYRVKHGDCVQVAIQGSGRRLILDDVAIRVSPQ 180

Query: 181 MRLEMHIDTDEANAAGADNPHAFARL 206
           M+LEMHIDTDEANAAGAD+P AFA L
Sbjct: 181 MKLEMHIDTDEANAAGADDPAAFATL 206


Lambda     K      H
   0.319    0.136    0.388 

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: 250
Number of extensions: 11
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: 210
Length of database: 216
Length adjustment: 22
Effective length of query: 188
Effective length of database: 194
Effective search space:    36472
Effective search space used:    36472
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 (21.7 bits)
S2: 45 (21.9 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