GapMind for Amino acid biosynthesis

 

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

Align Homoserine kinase (EC:2.7.1.39) (characterized)
to candidate H281DRAFT_05614 H281DRAFT_05614 shikimate kinase

Query= reanno::Miya:8500213
         (185 letters)



>FitnessBrowser__Burk376:H281DRAFT_05614
          Length = 183

 Score = 75.5 bits (184), Expect = 5e-19
 Identities = 54/163 (33%), Positives = 79/163 (48%), Gaps = 3/163 (1%)

Query: 21  VSIIGMAGAGKTTVGRELALQLGWAHVDTDNLIEATYGTRLQAVADSMDKESFLDVEAGV 80
           V  +G+ GAGKTTVGR +A +L     D+D+ IEA  G R+  + +   +  F + EA V
Sbjct: 10  VFFVGLMGAGKTTVGRAIARRLDRPFFDSDHEIEARTGARIPVIFELEGEAGFREREASV 69

Query: 81  IRRI-GARRTVLSTGGSVVYRHEAMAHLAALGPLVYLDVSLPLILKRIAMNPDRGLAIA- 138
           I  + G  + VL+TGG  V R E    L + G ++YL  +   +  R   + +R L    
Sbjct: 70  ISELTGRDKIVLATGGGAVLRPENRQALQSRGVVIYLRANPHDLWLRTRRDKNRPLLQTE 129

Query: 139 -PGQTIEDLYNERIALYRRYATFTVAADALSPGGCATRIVAWL 180
            P   +E LY  R  LYR  A F +     S  G    ++  L
Sbjct: 130 DPKARLEALYEVRDPLYRECAHFVIETGRPSVNGLVNMVLMQL 172


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: 100
Number of extensions: 6
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: 185
Length of database: 183
Length adjustment: 19
Effective length of query: 166
Effective length of database: 164
Effective search space:    27224
Effective search space used:    27224
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 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