GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Pseudomonas fluorescens FW300-N2E2

Align phosphoribosylanthranilate isomerase; EC 5.3.1.24 (characterized)
to candidate Pf6N2E2_71 Phosphoribosylanthranilate isomerase (EC 5.3.1.24)

Query= CharProtDB::CH_021917
         (235 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_71
          Length = 210

 Score =  196 bits (499), Expect = 2e-55
 Identities = 106/216 (49%), Positives = 141/216 (65%), Gaps = 10/216 (4%)

Query: 20  PRTRIKLCGLSRPDDVLHAAALGADAIGLVFYAKSPRAVTIAQAAELARLAPPFVSVVGL 79
           P  R K+CG++R +D L A   GADAIGLVFYAKSPRAVT+ QA  + +  PPFV+ VGL
Sbjct: 2   PVVRSKICGITRVEDALAAVEAGADAIGLVFYAKSPRAVTVQQARAIIQALPPFVTPVGL 61

Query: 80  FVNATAAEIEAVVRDVPLTLLQFHGDETPEQCDALGRAARLPWVRAVRVGPSTQSADLVE 139
           FVNA+  E+  ++  VPL LLQFHGDE P  C+   R    P+++A+RV       D+  
Sbjct: 62  FVNASRCELGEILDAVPLGLLQFHGDEAPADCEGWHR----PYIKALRV---KAGDDIAA 114

Query: 140 SSLHYSKARGLLFDTLVPDY-GGSGKVFDWSLIPAELARRAVLSGGLNAQNVGDAIRQLR 198
           S   ++ A G+L D  V    GG+G+ FDWSL+P  L +  +L+GGL   NV  AIRQ+R
Sbjct: 115 SCAAFASASGILLDAYVEGVPGGTGEAFDWSLVPQGLDKPIILAGGLTVDNVAQAIRQVR 174

Query: 199 PFAVDVSSGIEVEGAKGVKDHARMAAFVRAVRDADA 234
           P+AVDVS G  VE  KG+KD A++ AF+ AVR + +
Sbjct: 175 PYAVDVSGG--VEQGKGIKDPAKIRAFMAAVRSSQS 208


Lambda     K      H
   0.319    0.134    0.384 

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: 159
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: 235
Length of database: 210
Length adjustment: 22
Effective length of query: 213
Effective length of database: 188
Effective search space:    40044
Effective search space used:    40044
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: 45 (21.9 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