GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroL in Desulfovibrio vulgaris Miyazaki F

Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate 8500213 DvMF_0971 shikimate kinase (RefSeq)

Query= curated2:Q31PU5
         (190 letters)



>FitnessBrowser__Miya:8500213
          Length = 185

 Score = 84.7 bits (208), Expect = 9e-22
 Identities = 51/147 (34%), Positives = 88/147 (59%), Gaps = 5/147 (3%)

Query: 14  LVGLMGSGKTTIGKLLAESLGYTYVDTDSLIENVTGRSIPEIFASDGEAGFRQIETQVLE 73
           ++G+ G+GKTT+G+ LA  LG+ +VDTD+LIE   G  +  +  S  +  F  +E  V+ 
Sbjct: 23  IIGMAGAGKTTVGRELALQLGWAHVDTDNLIEATYGTRLQAVADSMDKESFLDVEAGVIR 82

Query: 74  EVASYRRLVVATGGGIVIRPENWSYLQQ-GLVIWLDVPIPELLRRLEGDQNRPLLQTEAP 132
            + + RR V++TGG +V R E  ++L   G +++LDV +P +L+R+  + +R L    AP
Sbjct: 83  RIGA-RRTVLSTGGSVVYRHEAMAHLAALGPLVYLDVSLPLILKRIAMNPDRGL--AIAP 139

Query: 133 ATTLQALWEQRRDRYAQ-ADLRIAIEA 158
             T++ L+ +R   Y + A   +A +A
Sbjct: 140 GQTIEDLYNERIALYRRYATFTVAADA 166


Lambda     K      H
   0.316    0.134    0.376 

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: 89
Number of extensions: 2
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: 190
Length of database: 185
Length adjustment: 20
Effective length of query: 170
Effective length of database: 165
Effective search space:    28050
Effective search space used:    28050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 44 (21.6 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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