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_2777 Echvi_2777 Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like

Query= BRENDA::P0A9T0
         (410 letters)



>FitnessBrowser__Cola:Echvi_2777
          Length = 630

 Score =  427 bits (1098), Expect = e-124
 Identities = 211/409 (51%), Positives = 289/409 (70%), Gaps = 4/409 (0%)

Query: 3   KVSLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSR 62
           K S  K +I  LL+E VH   +E ++  GY N+E    A+ +E+L E I++   IG+RS+
Sbjct: 225 KFSYPKSRINVLLLENVHPIGVEIMKQEGY-NVEVVSSAMSEEELCEKIKNVSIIGIRSK 283

Query: 63  THLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLL 122
           T +T+ V+  A +L+A+G FCIGTNQ+DL+   ++GI VFNAPFSNTRSV EL I E++ 
Sbjct: 284 TQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIF 343

Query: 123 LLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDI 182
           L+R + +   K H+G+WNK A+GSFE RGKKLGIIGYG+IG QL +LAE++GM V++YDI
Sbjct: 344 LMRNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDI 403

Query: 183 ENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGT 242
             +L LGNAT++  L +LL   D++SLHV      KN++  ++I  MK G++L+N SRG 
Sbjct: 404 VERLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGH 463

Query: 243 VVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQE 302
           VVD+PAL DAL S HLAGAA+DVFPTEP  N +PF S L    N +LTPHIGGST EAQE
Sbjct: 464 VVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQE 523

Query: 303 NIGLEVAGKLIKYSDNGSTLSAVNFPEVSLP-LHGGRRLMHIHENRPGVLTALNKIFAEQ 361
           NI   V GK+I+Y ++G+T ++VNFP + LP L    RL+HIH+N PGVL  +N++ A  
Sbjct: 524 NIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASY 583

Query: 362 GVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY 410
            +NI  QYL+T+ ++GYV+ DI  D+  +   + A+K I GTIR R+LY
Sbjct: 584 KINIVGQYLKTNEKIGYVITDI--DKRYSNDVIDALKEIEGTIRFRILY 630


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: 627
Number of extensions: 21
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: 410
Length of database: 630
Length adjustment: 34
Effective length of query: 376
Effective length of database: 596
Effective search space:   224096
Effective search space used:   224096
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: 52 (24.6 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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