GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Pseudomonas putida KT2440

Align Carbamoyl-phosphate synthase small chain; EC 6.3.5.5; Carbamoyl-phosphate synthetase glutamine chain (uncharacterized)
to candidate PP_0420 PP_0420 aminodeoxychorismate synthase / para-aminobenzoate synthase multi-enzyme complex

Query= curated2:Q8KGA2
         (366 letters)



>FitnessBrowser__Putida:PP_0420
          Length = 197

 Score = 85.1 bits (209), Expect = 1e-21
 Identities = 59/181 (32%), Positives = 91/181 (50%), Gaps = 17/181 (9%)

Query: 189 NIIRQLNAEGCKVTVV-NAKTTADEVLAMNPDGIFLSNGPGDPFAVTYAIDTIRELAARN 247
           N+++ L   G +V V+ N + T  ++ A+NP+ I +S GP  P     +I+ I   A + 
Sbjct: 14  NVVQYLGELGAEVKVIRNDEMTIAQIEALNPERIVVSPGPCTPSEAGVSIEAILHFAGK- 72

Query: 248 STLPIFGICLGHQLLSLAFGAKTYKLKFGHHGANHPVKN-------LLSNTIEITSQNHG 300
             LPI G+CLGHQ +  AFG    + +   HG   PV +        L+N + +T + H 
Sbjct: 73  --LPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVYHRDLGVFASLNNPLTVT-RYHS 129

Query: 301 FAVEMESLPGELELT----HKNLYDMTVEGIRHRELPCFSVQYHPEAAPGPHDSHYLFKE 356
             V+ E+LP  LE+T    H +     + G+RH+ L    VQ+HPE+       H LF  
Sbjct: 130 LVVKRETLPDCLEVTAWTSHADGSVDEIMGLRHKTLNIEGVQFHPESIL-TEQGHELFAN 188

Query: 357 F 357
           F
Sbjct: 189 F 189


Lambda     K      H
   0.317    0.134    0.387 

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: 190
Number of extensions: 11
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: 366
Length of database: 197
Length adjustment: 25
Effective length of query: 341
Effective length of database: 172
Effective search space:    58652
Effective search space used:    58652
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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