GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapH in Cupriavidus basilensis 4G11

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase; EC 2.3.1.89 (characterized)
to candidate RR42_RS06325 RR42_RS06325 serine O-acetyltransferase

Query= SwissProt::O34981
         (236 letters)



>FitnessBrowser__Cup4G11:RR42_RS06325
          Length = 247

 Score = 58.5 bits (140), Expect = 1e-13
 Identities = 41/121 (33%), Positives = 59/121 (48%), Gaps = 5/121 (4%)

Query: 115 GASINIGSVIGEGTMID--MNVVLGGRATVGKNCHIGAGSVLAGVIEPPSAKP-VVIEDD 171
           G  I+ G+ +G    ID  M VV+G  A +G +C I  G  L G       K    +  +
Sbjct: 65  GIEIHPGAKVGRRVFIDHGMGVVVGETAEIGDDCTIYQGVTLGGTSLYKGVKRHPTLGAN 124

Query: 172 VVIGANAVVLEGVTVGKGAVVAAGAIVVNDVEPYTVVAGTPAKKIKDIDEKTKGKTEIKQ 231
           VV+ A A VL G T+G GA + + A+V+  V P     G PA+ I  + +   G+   KQ
Sbjct: 125 VVVSAGAKVLGGYTIGDGARIGSNAVVLKPVPPGATAVGIPARII--LPDAPSGQQGAKQ 182

Query: 232 E 232
           E
Sbjct: 183 E 183



 Score = 26.6 bits (57), Expect = 5e-04
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 40  KAFINGNTGVVFGEWSEI--QTAIEENQSKIEDYVVENDRRNSAIPMLDLKNIKARIEPG 97
           + FI+   GVV GE +EI     I +  +     + +  +R+  +    + +  A++  G
Sbjct: 77  RVFIDHGMGVVVGETAEIGDDCTIYQGVTLGGTSLYKGVKRHPTLGANVVVSAGAKVLGG 136

Query: 98  AIIRDQVEIGDNAVIM 113
             I D   IG NAV++
Sbjct: 137 YTIGDGARIGSNAVVL 152


Lambda     K      H
   0.313    0.134    0.364 

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: 135
Number of extensions: 11
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 236
Length of database: 247
Length adjustment: 23
Effective length of query: 213
Effective length of database: 224
Effective search space:    47712
Effective search space used:    47712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 46 (22.3 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