GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Desulfovibrio vulgaris Hildenborough

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate 209431 DVU0494 aminotransferase, class V

Query= BRENDA::P74281
         (384 letters)



>MicrobesOnline__882:209431
          Length = 389

 Score =  246 bits (629), Expect = 6e-70
 Identities = 133/364 (36%), Positives = 207/364 (56%), Gaps = 3/364 (0%)

Query: 1   MDNKQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLT 60
           M NK  L+ PGPTP+PE+V L MA+  I HR   F K++ E+   L+ L  T   VL L 
Sbjct: 1   MLNKPRLLTPGPTPLPERVRLVMAQDMIHHRKPAFKKLMGEVQEKLRILFGTSQPVLPLA 60

Query: 61  TSGTGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDF 120
            SG+GAM A++     PG++V+V   GKFG RW ++A   GL V  I  EWG+A+   + 
Sbjct: 61  CSGSGAMTAAVHGLFVPGEKVIVVEGGKFGQRWREIASLRGLEVVSIVVEWGRAVSLAEV 120

Query: 121 KTLLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAI 180
           +  L+A  D   K +++  SETSTGVL+ +  I A  +     L++ D ++++G +P  +
Sbjct: 121 EAALDAHPDA--KGVLMQLSETSTGVLHPVRGIAAVTRKRD-VLLVADGISAVGISPCPM 177

Query: 181 DDLGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSP 240
           D+ G+D + +GSQKG M+PPGL  +++S +AW+  +T     FY +L   + + ++  + 
Sbjct: 178 DEWGVDCLLTGSQKGLMLPPGLALIALSERAWRKADTVAPSCFYFNLPGERANCEKGQTL 237

Query: 241 FTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAASNAIT 300
           FT P++L+ GL  SL M    GL+ ++ +    T   R    AL L   AP+       +
Sbjct: 238 FTTPVSLIVGLGESLDMFLEAGLETVYRKQWALTMLARAGTAALGLAPLAPERFTWGLTS 297

Query: 301 AVAPLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEATL 360
            + P GV+  ++         + MAGGQDHLKG+I RIGH+G+V   DI++ + A+ + L
Sbjct: 298 VMLPAGVDGTRLLQVAADNHGVVMAGGQDHLKGRILRIGHMGWVDWADIVAGLHAVASGL 357

Query: 361 IELG 364
              G
Sbjct: 358 RTCG 361


Lambda     K      H
   0.317    0.134    0.386 

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: 341
Number of extensions: 14
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: 384
Length of database: 389
Length adjustment: 30
Effective length of query: 354
Effective length of database: 359
Effective search space:   127086
Effective search space used:   127086
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: 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