GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Sinorhizobium meliloti 1021

Align Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized)
to candidate SMc01569 SMc01569 carbamoyl phosphate synthase small subunit

Query= curated2:Q9YGB2
         (192 letters)



>FitnessBrowser__Smeli:SMc01569
          Length = 401

 Score = 75.1 bits (183), Expect = 2e-18
 Identities = 51/156 (32%), Positives = 77/156 (49%), Gaps = 12/156 (7%)

Query: 18  YASLFDRVKVVPNTITVGELRRLDPDGVIISPGPGHPLERREVGNSPEI--VLEAGVPIL 75
           +A L  RV VVP   +  E+  L PDG+ +S GPG P    E    P I  +L+  +P+ 
Sbjct: 223 FAGLNCRVTVVPAQTSAEEVLALKPDGIFLSNGPGDPAATGEYA-VPVIQDLLKTDIPVF 281

Query: 76  GVCLGHQIIATAFGGKVGRV-KPRHGKASPVKHDGKGVLRGIKNPLTAGRYHSLAV--LE 132
           G+CLGHQ++A A G +  ++ +  HG   PVK    G +            H  AV    
Sbjct: 282 GICLGHQMLALALGARTEKMHQGHHGANHPVKDHTTGKVE------IVSMNHGFAVDANS 335

Query: 133 VPREFDVSAVSLDDNVVMGIRHRKLPIEGLQFHPES 168
           +P+  + + +SL D    G+R    P+  +Q HPE+
Sbjct: 336 LPQGVEQTHISLFDGTNCGLRVDGRPVFSVQHHPEA 371


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: 197
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: 192
Length of database: 401
Length adjustment: 25
Effective length of query: 167
Effective length of database: 376
Effective search space:    62792
Effective search space used:    62792
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 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