GapMind for Amino acid biosynthesis

 

Alignments for a candidate for preph-dehydratase in Pseudomonas fluorescens FW300-N2E3

Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate AO353_17845 AO353_17845 ArtI protein

Query= BRENDA::Q01269
         (268 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_17845
          Length = 261

 Score =  253 bits (645), Expect = 4e-72
 Identities = 129/250 (51%), Positives = 171/250 (68%), Gaps = 3/250 (1%)

Query: 12  LACLALLASASLQAQE--SRLDRILESGVLRVATTGDYKPFSYRTEEGGYAGFDVDMAQR 69
           L C  L  S    AQ   S LD+++E G L+V TTGDYKP++Y   EGGY G D+ MAQ 
Sbjct: 6   LLCSLLTFSVQAIAQNAPSHLDQVIERGHLKVCTTGDYKPYTYLRAEGGYEGIDIAMAQS 65

Query: 70  LAESLGAKLVVVPTSWPNLMRDFADDRFDIAMSGISINLERQRQAYFSIPYLRDGKTPIT 129
           LA+SL   +  VPT+W NLM DF  DR DI M GIS++LERQ++A FS     DGK P+ 
Sbjct: 66  LAKSLNVDVQWVPTTWKNLMTDFLADRCDIGMGGISVSLERQKKAAFSDTLGVDGKIPLV 125

Query: 130 LCSEEARFQTLEQIDQPGVTAIVNPGGTNEKFARANLKKARILVHPDNVTIFQQIVDGKA 189
            C ++ R+QT+EQ++Q  V  I   GGTNE FAR +L  A + + PDNVTIF+Q+++ KA
Sbjct: 126 RCEDKQRYQTVEQLNQSSVRLIEPAGGTNEVFARTHLPNATLTLFPDNVTIFEQLLENKA 185

Query: 190 DLMMTDAIEARLQSRLHPELCAVHPQQPFDFAEKAYLLPRDE-AFKRYVDQWLHIAEQSG 248
           D+M+TDA EAR Q +L P LCAV+P+Q   ++EKAYLLPRD+ A+K YVDQWLH+++ +G
Sbjct: 186 DVMITDASEARYQQKLKPGLCAVNPEQYLQYSEKAYLLPRDDVAWKAYVDQWLHLSKATG 245

Query: 249 LLRQRMEHWL 258
                +  WL
Sbjct: 246 AYDAVLAQWL 255


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: 214
Number of extensions: 5
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: 268
Length of database: 261
Length adjustment: 25
Effective length of query: 243
Effective length of database: 236
Effective search space:    57348
Effective search space used:    57348
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