GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Pseudomonas putida KT2440

Align Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized)
to candidate PP_4724 PP_4724 Carbamoyl-phosphate synthase small chain

Query= curated2:Q9YGB2
         (192 letters)



>FitnessBrowser__Putida:PP_4724
          Length = 378

 Score = 74.3 bits (181), Expect = 2e-18
 Identities = 50/148 (33%), Positives = 71/148 (47%), Gaps = 9/148 (6%)

Query: 24  RVKVVPNTITVGELRRLDPDGVIISPGPGHPLERREVGNSPEIVLEAGVPILGVCLGHQI 83
           RV VVP      E+  L+PDGV +S GPG P        + + +LE  +P+ G+CLGHQ+
Sbjct: 215 RVTVVPAQTPASEVLALNPDGVFLSNGPGDPEPCDYAIQAIKEILETEIPVFGICLGHQL 274

Query: 84  IATAFGGKVGRV-KPRHGKASPVKHDGKGVLRGIKNPLTAGRYHSLAVLEVPREFDVSAV 142
           +A A G K  ++    HG   PV+    GV+      +   + H  AV E     +V A+
Sbjct: 275 LALASGAKTVKMGHGHHGANHPVQDLDTGVV------MITSQNHGFAVDEATLPGNVRAI 328

Query: 143 --SLDDNVVMGIRHRKLPIEGLQFHPES 168
             SL D  + GI          Q HPE+
Sbjct: 329 HKSLFDGTLQGIERTDKSAFSFQGHPEA 356


Lambda     K      H
   0.320    0.141    0.422 

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: 198
Number of extensions: 12
Number of successful extensions: 2
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: 192
Length of database: 378
Length adjustment: 25
Effective length of query: 167
Effective length of database: 353
Effective search space:    58951
Effective search space used:    58951
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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