GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysE in Pseudomonas putida KT2440

Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate PP_1110 PP_1110 serine acetyltransferase

Query= BRENDA::P95231
         (229 letters)



>FitnessBrowser__Putida:PP_1110
          Length = 234

 Score =  113 bits (282), Expect = 4e-30
 Identities = 69/164 (42%), Positives = 93/164 (56%), Gaps = 11/164 (6%)

Query: 8   DIRAARERDPAAPTALEVIF-CYPGVHAVWGHRLAHWLWQR-------GARLLARAAAEF 59
           D++A   +DPAA   L  I   Y    AV  +RLAHW++         G + LA   +  
Sbjct: 59  DLQAFAMKDPAAGRDLVFIAKTYTSYSAVLHYRLAHWIYNNSAATYGAGGQCLAAMISRR 118

Query: 60  TRILTGVDIHPGAVIGARVFIDHATGVVIGETAEVGDDVTIYHGVTLGGSGM---VGGKR 116
            ++L+G +IH  + IGAR  IDH  G VIGET+ +GDD  +  GVTLG  G+       R
Sbjct: 119 GKMLSGAEIHFRSRIGARFIIDHGMGTVIGETSTIGDDCYVLGGVTLGARGISDNPSSPR 178

Query: 117 HPTVGDRVIIGAGAKVLGPIKIGEDSRIGANAVVVKPVPPSAVV 160
           HPT+G+RV IGA A VLG I +G+ + IG   +V K VP +A V
Sbjct: 179 HPTLGNRVQIGAFASVLGAIHVGDGAFIGPGCIVTKDVPAAARV 222


Lambda     K      H
   0.321    0.141    0.443 

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: 141
Number of extensions: 10
Number of successful extensions: 3
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: 229
Length of database: 234
Length adjustment: 23
Effective length of query: 206
Effective length of database: 211
Effective search space:    43466
Effective search space used:    43466
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 (21.8 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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