GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Sinorhizobium meliloti 1021

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate SMc02849 SMc02849 2-hydroxyacid dehydrogenase

Query= curated2:O27051
         (525 letters)



>FitnessBrowser__Smeli:SMc02849
          Length = 334

 Score =  191 bits (486), Expect = 3e-53
 Identities = 120/305 (39%), Positives = 175/305 (57%), Gaps = 14/305 (4%)

Query: 18  SELEEVAEVVVNTTITPE---ELLDAIKDFDAIVVRSRTKVTREVIE-AAPRLKIIARAG 73
           + + E+ +  +N   TP    EL+ A+K  D +V     ++   +IE A P+LK+IA   
Sbjct: 21  TRMRELFDAELNIDDTPRSQPELVAAVKRADVLVPTVTDRIDAALIEQAGPQLKLIAAFS 80

Query: 74  VGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIA-----IADRSVKEGK 128
            GVDN+DV AA  +GI V N P   +   A+ ++ L+LA+ R++A     + DR  +   
Sbjct: 81  NGVDNIDVDAAARKGITVTNTPNVLTEDTADMTMALILAVPRRLAEGAQVLTDRKGEWAG 140

Query: 129 WEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEM-GVTVT 187
           W     +G  + GK +GI+GMGRIG+ V  R KAFG+ I  ++ +  K   EEM   T  
Sbjct: 141 WSPTWMLGRRIAGKRIGIVGMGRIGTAVARRAKAFGLSIHYHNRHRVKPETEEMLEATYW 200

Query: 188 D-LETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALK 246
           D L+ +L   DIV+++ P TP T HL+S     LM+  ++IVN ARGGIIDE AL ++L+
Sbjct: 201 DSLDQMLARVDIVSVNCPSTPATYHLLSARRLALMRPDSYIVNTARGGIIDEAALIKSLR 260

Query: 247 DGEIAGAALDVFEEEPPEGSPLLELE---NVVLTPHIGASTSEAQRDAAIIVANEIKTVF 303
           +G+IAGA LDVFE EP     L++L     VVL PH+ ++T E + D    V   I+T F
Sbjct: 261 EGKIAGAGLDVFENEPCVNPKLIKLAGEGKVVLLPHMSSATLEGRIDMGEKVVINIRTFF 320

Query: 304 QGGAP 308
            G  P
Sbjct: 321 DGHRP 325


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: 408
Number of extensions: 16
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: 525
Length of database: 334
Length adjustment: 32
Effective length of query: 493
Effective length of database: 302
Effective search space:   148886
Effective search space used:   148886
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 (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