GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Pseudomonas fluorescens FW300-N2C3

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate AO356_27160 AO356_27160 dihydrodipicolinate synthase

Query= BRENDA::Q7D0E8
         (302 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27160
          Length = 297

 Score =  233 bits (594), Expect = 4e-66
 Identities = 139/299 (46%), Positives = 185/299 (61%), Gaps = 14/299 (4%)

Query: 5   FKGLSAFPITPADEAGRVDIEAFSALIARLDAAEVDSVGILGSTGIYMYLTREERRR--- 61
           F GLSAFP+TP DE G VD  AF+ L+ +L AA+VDS+G LGSTG Y YL+R ER R   
Sbjct: 2   FTGLSAFPLTPMDEQG-VDEIAFARLVQQLVAAKVDSIGALGSTGSYAYLSRAERFRVAQ 60

Query: 62  -AIEAAATILRGRRTLMAGIGALRTDEAVALAKDAEAAGADALLLAPVSYTPLTQEEAYH 120
            A+EAA  +      +M  IGALRT + + LA+DA+A G  ALLL PVSY  LTQ++ + 
Sbjct: 61  LAVEAAEDV-----PVMVSIGALRTRDVLLLAEDAQAVGVQALLLPPVSYQKLTQDDVFS 115

Query: 121 HFAAVAGATALPLAIYNNPTTTRFTFSDELLVRLAYIPNIRAIKMPLPADADYAGE--LA 178
            +  V+   ++PL +Y+NP TT F FSDEL  R+A +PN+R+IK+P   +A Y  +  + 
Sbjct: 116 MYEMVSANISVPLCVYDNPGTTHFEFSDELHRRIAELPNVRSIKIPGVPEAPYLAKERVE 175

Query: 179 RLRPKLSDDFAIGYSGDWGCTDATLAGGDTWYSVVAGLLPVPALQLMRAAQAGNAEEAKR 238
           RLR  +     IG SGD        AG D WYSV+ GL P  AL + RAA +G+A EA R
Sbjct: 176 RLRKLIPSHVTIGISGDASAAVGMNAGCDAWYSVMGGLFPNTALAITRAALSGDALEATR 235

Query: 239 LDATFQPLWALFKEF-GSIRVIYAAANILSLTVS-EPPRPILPLTSAERQRVEEALEAL 295
           L  + +PLWALF +F GS RVI  AA +   T S   P P+  +    R+++   +EAL
Sbjct: 236 LSESLKPLWALFSQFGGSFRVIATAAELRGFTHSASVPLPLRTIDGEGREQIAAVIEAL 294


Lambda     K      H
   0.319    0.133    0.381 

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: 173
Number of extensions: 6
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: 302
Length of database: 297
Length adjustment: 27
Effective length of query: 275
Effective length of database: 270
Effective search space:    74250
Effective search space used:    74250
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: 48 (23.1 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