GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Echinicola vietnamensis KMM 6221, DSM 17526

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate Echvi_3161 Echvi_3161 Lactate dehydrogenase and related dehydrogenases

Query= BRENDA::P0A9T0
         (410 letters)



>FitnessBrowser__Cola:Echvi_3161
          Length = 331

 Score =  105 bits (263), Expect = 1e-27
 Identities = 79/261 (30%), Positives = 126/261 (48%), Gaps = 13/261 (4%)

Query: 57  IGLRSRTHLTEDVINAAEKLVA--IGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAE 114
           I L S    + +V++   KL    I     G N VDL+ AA+  I V   P  +  ++AE
Sbjct: 47  IALFSNDDASSEVLDILHKLGIKFIALRSAGFNHVDLEKAAELNIKVARVPAYSPYAIAE 106

Query: 115 LVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLG 174
             +  +L L R + +A+ +     ++      F+  GK +G+IG G IG+ L  +    G
Sbjct: 107 HTMALILALNRRLIKAHNRVREQNFSLNGLTGFDLNGKTVGVIGTGKIGSVLVKILHGFG 166

Query: 175 MYVYFYDIENKLPLGNATQVQH--LSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPG 232
             +   DIE    L +   + +   + L   +D++SLHVP   STK+++  + I+LMK G
Sbjct: 167 CNILAQDIEESKDLIDKYGLIYSDCATLCKHADIISLHVPLKASTKHLINKEHIALMKSG 226

Query: 233 SLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPA---------TNSDPFTSPLCE 283
            +LIN SRG +VD  A+ + L +K +    +DV+  E              D   + L  
Sbjct: 227 VMLINTSRGGLVDTKAVIEGLKTKKIGYLGLDVYEEEEGLFFEDHSDDILQDDVIARLMT 286

Query: 284 FDNVLLTPHIGGSTQEAQENI 304
           F+NVL+T H    T+ A  NI
Sbjct: 287 FNNVLITSHQAFLTKTALTNI 307


Lambda     K      H
   0.318    0.135    0.383 

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: 280
Number of extensions: 19
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: 410
Length of database: 331
Length adjustment: 30
Effective length of query: 380
Effective length of database: 301
Effective search space:   114380
Effective search space used:   114380
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 (21.7 bits)
S2: 49 (23.5 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