GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Herbaspirillum seropedicae SmR1

Align shikimate dehydrogenase (EC 1.1.1.25); quinate/shikimate dehydrogenase (EC 1.1.1.282) (characterized)
to candidate HSERO_RS18795 HSERO_RS18795 shikimate dehydrogenase

Query= BRENDA::Q88JP1
         (269 letters)



>FitnessBrowser__HerbieS:HSERO_RS18795
          Length = 281

 Score =  136 bits (343), Expect = 4e-37
 Identities = 82/257 (31%), Positives = 129/257 (50%), Gaps = 7/257 (2%)

Query: 2   IRGSTELVAIVGSPIAQVKSPQNFNTWFNHNNCNLAMLPIDLHEAALDSFADTLRGWQNL 61
           I G+T +  ++G P+ QVK+P  FN +F H+  +  ++P  +               +N+
Sbjct: 4   ITGTTRIFPVIGWPVEQVKAPTLFNAYFEHHGIDARVIPFKIEPERYCEAVRMFMKTENV 63

Query: 62  RGCVVTVPYKQALANRVDGLSERAAALGSINVIRRERDGRLLGDNVDGAGFLGAAHKHGF 121
            G  V++P+K      V+  + RA   G+ N + R+ DG + GD +DG GF+ A  +   
Sbjct: 64  GGIFVSIPHKPMTLEAVEQSTLRARVAGACNAVYRDADGVIWGDLIDGEGFIRALARTAA 123

Query: 122 EPA----GKRALVIGCGGVGSAIAYALAEAGIASITLCDPSTARMGAVCELLGNGFPGLT 177
           +        RALV+G GGVG AI  +LA  G+A I++ D + A   A+       FP   
Sbjct: 124 DRPLVWNQTRALVVGTGGVGCAIVASLAAQGVAEISVFDTNRAGAEALLARAAAAFPATR 183

Query: 178 VSTQFSGLEDFDLVANASPVGMGTRAELPLSAALLATLQPDTLVADVVTSPEITPLLNRA 237
           V         FDL+ N +P+GM     +P +   L  ++ D +VAD     E++ LL +A
Sbjct: 184 VGFAQPDASGFDLLVNCTPLGMHVGDPMPFA---LEGVRRDAIVADCGMKIEMSQLLVQA 240

Query: 238 RQVGCRIQTGPEMAFAQ 254
           + +GCRIQ G EM   Q
Sbjct: 241 QALGCRIQKGKEMLIEQ 257


Lambda     K      H
   0.320    0.137    0.407 

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: 175
Number of extensions: 6
Number of successful extensions: 4
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: 269
Length of database: 281
Length adjustment: 25
Effective length of query: 244
Effective length of database: 256
Effective search space:    62464
Effective search space used:    62464
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