GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Pseudomonas fluorescens FW300-N2E3

Align shikimate dehydrogenase (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate AO353_06175 AO353_06175 shikimate dehydrogenase

Query= BRENDA::Q6PUG0
         (521 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_06175
          Length = 284

 Score =  112 bits (280), Expect = 2e-29
 Identities = 90/279 (32%), Positives = 133/279 (47%), Gaps = 30/279 (10%)

Query: 239 DTKVFGLISKPVGHSKGPILHNPTFRHVGYNGIYVPMFVDDLK-------EFFRVYSSPD 291
           +T + GLI   +  S+ P LH       G   +Y  + +D LK       +        +
Sbjct: 5   NTVLAGLIGAGIQASRTPALHEREGDAQGLRYLYRLIDLDQLKLDSGALPDLLMSAERMN 64

Query: 292 FAGFSVGIPYKEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAIEDA 351
           F G ++  P K+A++   DE+ P A+ IGAVNT++ +  DGK IG+NTDC          
Sbjct: 65  FTGLNITFPCKQAIIPLLDELSPEARGIGAVNTVVLK--DGKRIGHNTDCLGFAEGFRRG 122

Query: 352 LKVNGLTNGAAFLPSPLAGKLFVLVGAGGAGRALAFGAKSRRA-EIVIFDIDFDRAKALA 410
           LK               A +  V +GAGGAG A+A    S    ++ IFD+D  RA++LA
Sbjct: 123 LK-------------DAARERVVQMGAGGAGAAVAHALLSEGVQQLSIFDVDVSRAQSLA 169

Query: 411 AAV-----SGEALPFENLASFQPEKGAILANATPIGMHPNKDRIPVSEASLKDYVVVFDA 465
             +     SG A    +L S   +    L N TP+GM      +PV    L+  + V + 
Sbjct: 170 NNLNQHFGSGRACAGSDLPSALAQADG-LVNTTPMGM-AKLPGMPVPVELLRAELWVAEI 227

Query: 466 VYTPRKTTLLKDAEAAGAITVSGVEMFLRQAIGQFHLFT 504
           VY P +T LL++A A G  T+ G  M + QA+  F LF+
Sbjct: 228 VYFPLETELLRNARALGCRTLDGGNMAVFQAVKAFELFS 266


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: 274
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: 284
Length adjustment: 30
Effective length of query: 491
Effective length of database: 254
Effective search space:   124714
Effective search space used:   124714
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:

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