GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Pseudomonas fluorescens FW300-N2E2

Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate Pf6N2E2_5061 Quinate/shikimate 5-dehydrogenase I delta (EC 1.1.1.25)

Query= BRENDA::Q6PUG0
         (521 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5061
          Length = 285

 Score =  111 bits (277), Expect = 4e-29
 Identities = 89/282 (31%), Positives = 134/282 (47%), Gaps = 30/282 (10%)

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

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

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

Query: 408 ALAAAVS-----GEALPFENLASFQPEKGAILANATPIGMHPNKDRIPVSEASLKDYVVV 462
           ALA  ++     G A    +L++   E    L N TP+GM      +PV    L   + V
Sbjct: 168 ALANNLNQHFGVGRARAGHDLSAAMAEADG-LVNTTPMGM-AKLPGMPVPVELLHGQLWV 225

Query: 463 FDAVYTPRKTTLLKDAEAAGAITVSGVEMFLRQAIGQFHLFT 504
            + VY P +T LL++A A G  T+ G  M + QA+  F LF+
Sbjct: 226 AEIVYFPLETELLRNARALGCRTLDGGNMAVFQAVKAFELFS 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: 270
Number of extensions: 18
Number of successful extensions: 5
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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