GapMind for Amino acid biosynthesis

 

Alignments for a candidate for thrB in Rhizobium johnstonii 3841

Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_041936484.1 RL_RS22450 shikimate kinase

Query= metacyc::MONOMER-21144
         (185 letters)



>NCBI__GCF_000009265.1:WP_041936484.1
          Length = 196

 Score = 63.5 bits (153), Expect = 2e-15
 Identities = 45/137 (32%), Positives = 69/137 (50%), Gaps = 7/137 (5%)

Query: 23  IIGMAGAGKTTVGRELALQLGWAHVDTDNLIEATYGTRLQAVADSMDKESFLDVEAGVIR 82
           ++G+ GAGK++VGR +A QL    +D+D  IE      +  +  +  ++ F  +EA VI+
Sbjct: 27  LVGLMGAGKSSVGRIVASQLAIPFIDSDLEIERVSRMTIAELFAAYGEQEFRALEARVIK 86

Query: 83  RI---GARRTVLSTGGSVVYRHEAMAHLAALGPLVYLDVSLPLILKRIAMNPDRGLAIA- 138
           R+   G R  V+STGG          H+   G  V+L   L ++  R+A    R L    
Sbjct: 87  RLLKSGPR--VVSTGGGAFINDRTRKHIRKGGLSVWLKADLDVLWDRVAKRDTRPLLKTE 144

Query: 139 -PGQTIEDLYNERIALY 154
            P QT+E L N R  +Y
Sbjct: 145 NPKQTLEGLMNARYPIY 161


Lambda     K      H
   0.321    0.137    0.403 

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: 86
Number of extensions: 3
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: 185
Length of database: 196
Length adjustment: 20
Effective length of query: 165
Effective length of database: 176
Effective search space:    29040
Effective search space used:    29040
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: 44 (21.6 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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