GapMind for Amino acid biosynthesis

 

Aligments for a candidate for aroD in Pseudomonas fluorescens FW300-N2C3

Align shikimate dehydrogenase (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate AO356_15590 AO356_15590 shikimate dehydrogenase

Query= BRENDA::Q6PUG0
         (521 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_15590
          Length = 285

 Score =  111 bits (277), Expect = 4e-29
 Identities = 91/282 (32%), Positives = 132/282 (46%), Gaps = 30/282 (10%)

Query: 236 MDTDTKVFGLISKPVGHSKGPILHNPTFRHVGYNGIYVPMFVDDLK-------EFFRVYS 288
           M   T + GLI   +  S+ P LH       G   +Y  + +D LK       +      
Sbjct: 3   MSNITVLAGLIGAGIQASRTPALHEQEGDAQGMRYLYRLIDLDALKLDSGALADLLVAAE 62

Query: 289 SPDFAGFSVGIPYKEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAI 348
             DF G ++  P K+A++   DE+ P A+ IGAVNT++ +  DGK IG+NTDC       
Sbjct: 63  RMDFTGLNITFPCKQAIIPLLDELSPEARGIGAVNTVVLK--DGKRIGHNTDC------- 113

Query: 349 EDALKVNGLTNGAAFLPSPLAGKLFVLVGAGGAGRALAFGAKSRRAE-IVIFDIDFDRAK 407
                  G   G       +A +  V +GAGGAG A+A        E + IFD++  RA+
Sbjct: 114 ------LGFAEGFRRGLGDVARQRVVQMGAGGAGAAVAHALLLEDVETLSIFDVEVSRAE 167

Query: 408 ALAAAVS-----GEALPFENLASFQPEKGAILANATPIGMHPNKDRIPVSEASLKDYVVV 462
           AL   ++     G A    +L S   E    L N TP+GM      +PV    L+  + V
Sbjct: 168 ALVNNLNQHFGPGRARAGHDLPSAMAEADG-LVNTTPMGM-AKLPGMPVPVELLRGTLWV 225

Query: 463 FDAVYTPRKTTLLKDAEAAGAITVSGVEMFLRQAIGQFHLFT 504
            + VY P +T LL++A A G  T+ G  M + QA+  F LF+
Sbjct: 226 AEIVYFPLETELLRNARAIGCRTLDGGNMAVFQAVKAFELFS 267


Lambda     K      H
   0.320    0.138    0.405 

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: 272
Number of extensions: 19
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: 521
Length of database: 285
Length adjustment: 30
Effective length of query: 491
Effective length of database: 255
Effective search space:   125205
Effective search space used:   125205
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: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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