GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Rhodobacter maris JA276

Align Phosphate propanoyltransferase; Phosphate acyltransferase PduL; Phosphotransacylase PduL; PTAC; Propanediol utilization protein PduL; EC 2.3.1.222 (characterized)
to candidate WP_097070251.1 CRO22_RS11250 phosphate propanoyltransferase

Query= SwissProt::Q9XDN5
         (210 letters)



>NCBI__GCF_900217815.1:WP_097070251.1
          Length = 220

 Score =  175 bits (444), Expect = 5e-49
 Identities = 95/179 (53%), Positives = 120/179 (67%), Gaps = 2/179 (1%)

Query: 22  IPLGVSNRHIHLSAQDYERLF-PGHPISEKKALLQPGQYAAEQTVTLVGPKGQLKNVRLL 80
           +P+GVSNRHIHLS  D + LF PG  ++  KA+ QPGQYAAE+TV L GPKG++  VR+L
Sbjct: 34  VPVGVSNRHIHLSRPDMDILFGPGASLTRMKAMKQPGQYAAEETVILRGPKGEIGKVRVL 93

Query: 81  GPLRSVSQVEISRTDARTLGIAAPLRMSGNLKGTPGIRLVSPFAELELPSGVIVAQRHIH 140
           GPLR  +Q+E+S  D   LGI  P+RMSG L+G+ G+ +V P   +   +GVIVA RHIH
Sbjct: 94  GPLRKETQIEVSVADGFVLGIKPPMRMSGKLEGSAGLTVVGPKGAVVKDAGVIVALRHIH 153

Query: 141 MSPLDALILRVSHGDMVSVAIEGDDRGLIFNNVAIRVSPDMRLEMHIDTDEANAAGADN 199
           M+P DA  L + +GD V V + G  RG I  NVAIR       EMHID +EANA G  N
Sbjct: 154 MAPADASRLGLKNGDTVDVDVTG-PRGGIMRNVAIRSDEVSATEMHIDVEEANAFGLKN 211


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: 186
Number of extensions: 10
Number of successful extensions: 5
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: 220
Length adjustment: 22
Effective length of query: 188
Effective length of database: 198
Effective search space:    37224
Effective search space used:    37224
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