GapMind for Amino acid biosynthesis

 

Aligments for a candidate for serA in Synechococcus elongatus PCC 7942

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate Synpcc7942_1347 Synpcc7942_1347 2-hydroxyacid dehydrogenase-like

Query= curated2:O27051
         (525 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_1347 Synpcc7942_1347
           2-hydroxyacid dehydrogenase-like
          Length = 331

 Score =  139 bits (350), Expect = 2e-37
 Identities = 88/269 (32%), Positives = 135/269 (50%), Gaps = 17/269 (6%)

Query: 60  IEAAPRLKI--IARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKI 117
           +EA   L +  +A    G + VD+ AA   G+ V+  P  +   VAEH+I L+L L RKI
Sbjct: 61  LEALAELGVEHVALRCAGFNQVDLSAAERLGLRVVRVPAYSPHAVAEHAIALILTLNRKI 120

Query: 118 AIADRSVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKE 177
             A    +EG +  +  +G +LNG T+GIIG GRIG+ +    + FG  ++ +D  +   
Sbjct: 121 HRAYARTREGNFALDGLVGFDLNGCTVGIIGTGRIGAVLTQILRGFGCHVLAHD-LVENP 179

Query: 178 AAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIID 237
                G   TDL+ L +E+ I+++H PLTP+T HL++ +    M+    ++N +RGG++D
Sbjct: 180 DCLAAGAVYTDLDQLWQEAQIISLHCPLTPQTYHLVNREAIAKMQPGTMLINTSRGGLVD 239

Query: 238 EDALYRALKDGEIAGAALDVFEEEPP--------------EGSPLLELENVVLTPHIGAS 283
             A+   LK   I    LDV+E+E P                  LL   NVV+T H    
Sbjct: 240 TQAVIEGLKLKRIGALGLDVYEQEEPLFFQDHSTEIIHDDVFQRLLTFPNVVITGHQAFL 299

Query: 284 TSEAQRDAAIIVANEIKTVFQGGAPRNVL 312
           T  A  + A    + +  + QG A  N L
Sbjct: 300 TDTALHNIAETTLSNLTDLEQGRACPNQL 328


Lambda     K      H
   0.316    0.135    0.366 

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: 337
Number of extensions: 13
Number of successful extensions: 3
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: 525
Length of database: 331
Length adjustment: 31
Effective length of query: 494
Effective length of database: 300
Effective search space:   148200
Effective search space used:   148200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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