GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Paraburkholderia bryophila 376MFSha3.1

Align Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized)
to candidate H281DRAFT_04402 H281DRAFT_04402 carbamoyl-phosphate synthase small subunit

Query= curated2:Q9YGB2
         (192 letters)



>FitnessBrowser__Burk376:H281DRAFT_04402
          Length = 384

 Score = 68.9 bits (167), Expect = 1e-16
 Identities = 47/149 (31%), Positives = 71/149 (47%), Gaps = 13/149 (8%)

Query: 25  VKVVPNTITVGELRRLDPDGVIISPGPGHPLERREVGNSPEIVLEAGVPILGVCLGHQII 84
           V V+P   +  +   L+PDG+ +S GPG P        + + ++E G+P  G+CLGHQI+
Sbjct: 215 VTVLPAEASAADALALNPDGIFLSNGPGDPEPCDYAIAATKELIERGIPTFGICLGHQIM 274

Query: 85  ATAFGGKVGRVKP-RHGKASPVK--HDGKGVLRGIKNPLTAGRYHSLAV--LEVPREFDV 139
             A G +  ++K   HG   PVK   DG+ ++          + H  AV    +P    V
Sbjct: 275 GLALGARTVKMKTGHHGANHPVKDLDDGRVII--------TSQNHGFAVDADTLPANARV 326

Query: 140 SAVSLDDNVVMGIRHRKLPIEGLQFHPES 168
           + VSL D  + G      P    Q HPE+
Sbjct: 327 THVSLFDGTLQGFALSDKPAFCFQGHPEA 355


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: 196
Number of extensions: 15
Number of successful extensions: 4
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: 192
Length of database: 384
Length adjustment: 25
Effective length of query: 167
Effective length of database: 359
Effective search space:    59953
Effective search space used:    59953
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.

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