GapMind for Amino acid biosynthesis

 

Alignments for a candidate for preph-dehydratase in Pseudomonas simiae WCS417

Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate GFF1447 PS417_07360 ArtI protein

Query= BRENDA::Q01269
         (268 letters)



>FitnessBrowser__WCS417:GFF1447
          Length = 257

 Score =  246 bits (629), Expect = 3e-70
 Identities = 127/250 (50%), Positives = 177/250 (70%), Gaps = 3/250 (1%)

Query: 11  ALACLALLASASL-QAQESRLDRILESGVLRVATTGDYKPFSYRTEEGGYAGFDVDMAQR 69
           AL  LA LA+++L     S LD++L+ G L V TTGDYKP++    +G Y G D+ MA+ 
Sbjct: 6   ALCVLASLATSALADTTPSHLDQVLQRGTLTVCTTGDYKPYTSLRADGSYEGIDITMAES 65

Query: 70  LAESLGAKLVVVPTSWPNLMRDFADDRFDIAMSGISINLERQRQAYFSIPYLRDGKTPIT 129
           LA+SL AK+  VPT+W  LM DF   R DIA+ GIS++LERQ++A+FS     DGK P+ 
Sbjct: 66  LAKSLNAKIQWVPTTWKTLMPDFLAQRCDIAVGGISVSLERQKKAFFSQSLGVDGKIPLV 125

Query: 130 LCSEEARFQTLEQIDQPGVTAIVNPGGTNEKFARANLKKARILVHPDNVTIFQQIVDGKA 189
            C++  R+QT++QI+QP V  I   GGTNE FARA+L +A+I +H DNVTIF +++ GKA
Sbjct: 126 RCADVQRYQTVDQINQPQVRVIEPAGGTNEVFARAHLGQAQIRLH-DNVTIFDELLAGKA 184

Query: 190 DLMMTDAIEARLQSRLHPELCAVHPQQPFDFAEKAYLLPRDE-AFKRYVDQWLHIAEQSG 248
           D+M+TDA EAR Q +L P LCAV+P++   ++EKA+LLPRD+ A+K YVDQWLH+++ +G
Sbjct: 185 DVMITDASEARYQQKLKPGLCAVNPERQMQYSEKAFLLPRDDVAWKNYVDQWLHLSQATG 244

Query: 249 LLRQRMEHWL 258
                +  WL
Sbjct: 245 AYDAIVSQWL 254


Lambda     K      H
   0.322    0.135    0.406 

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: 207
Number of extensions: 8
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: 268
Length of database: 257
Length adjustment: 25
Effective length of query: 243
Effective length of database: 232
Effective search space:    56376
Effective search space used:    56376
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 (21.9 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