GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Bacteroides thetaiotaomicron VPI-5482

Align Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized)
to candidate 353791 BT4265 GMP synthase (glutamine-hydrolyzing) (NCBI ptt file)

Query= curated2:Q02003
         (198 letters)



>FitnessBrowser__Btheta:353791
          Length = 507

 Score = 66.2 bits (160), Expect = 9e-16
 Identities = 44/141 (31%), Positives = 68/141 (48%), Gaps = 5/141 (3%)

Query: 48  SPGPGWPADAGKMETLIQQFAGQKPILGICLGFQAIVEVFGGKLRLAHQVMHGKNSQVRQ 107
           SP   +  DA K++  + +  G+ PILGIC G Q +     GK+  A    +G+      
Sbjct: 52  SPFSVYDKDAFKVD--LSEIRGKYPILGICYGAQFMAYTNNGKVEPAGTREYGRAHLTSF 109

Query: 108 TSGNLIFNHLPSKFLVMRYHSIVMDEAVALPDFAITAVATDDGEIMAIENEKEQIYGLQF 167
              N++F  +     V   H    D   A+PD      +TD  +I A + E E+++G+QF
Sbjct: 110 CKDNVLFKGVRENTQVWMSHG---DTITAIPDNFKKIASTDKVDIAAYQVEGEKVWGVQF 166

Query: 168 HPESIGTLDGMTMIENFVNQV 188
           HPE   + DG  ++ NFV  V
Sbjct: 167 HPEVFHSEDGTQILRNFVVDV 187


Lambda     K      H
   0.318    0.136    0.389 

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: 209
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 198
Length of database: 507
Length adjustment: 27
Effective length of query: 171
Effective length of database: 480
Effective search space:    82080
Effective search space used:    82080
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: 48 (23.1 bits)

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

Links

Downloads

Related tools

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