GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Desulfovibrio vulgaris Hildenborough

Align Bifunctional protein TrpGD; EC 4.1.3.27; EC 2.4.2.18 (characterized)
to candidate 209403 DVU0467 anthranilate phosphoribosyltransferase

Query= SwissProt::P00904
         (531 letters)



>MicrobesOnline__882:209403
          Length = 332

 Score =  204 bits (520), Expect = 3e-57
 Identities = 122/302 (40%), Positives = 170/302 (56%), Gaps = 2/302 (0%)

Query: 203 ILEKLYQAQTLSQQESHQLFSAVVRGELKPEQLAAALVSMKIRGEHPNEIAGAATALLEN 262
           ILE L     L  + +   F++++ G++ P Q  + L+ ++++GE  +E+  A  A L  
Sbjct: 7   ILETLATGCDLHPEMAGAGFASLMDGDMTPAQAGSFLMGLRMKGETADEMTEAVRAALAR 66

Query: 263 AAPFPRPDYLFADIVGTGGDGSNSINISTASAFVAAACGLKVAKHGNRSVSSKSGSSDLL 322
           A      D    DIVGTGGDG +S N STA+A   A  G KV KHGNR+VSS  GS+D +
Sbjct: 67  AVTVRGVDAPSIDIVGTGGDGRSSFNCSTATALTLAGMGHKVVKHGNRAVSSSCGSADAI 126

Query: 323 AAFGINLDMNADKSRQALDELGVCFLFAPKYHTGFRHAMPVRQQLKTRTLFNVLGPLINP 382
              G+ L+++A      L E G  FLFAP++H  FRH MP+R++L  RTLFN+LGPL+NP
Sbjct: 127 EGLGLPLEVDAADVPAMLHERGFAFLFAPRFHPAFRHVMPIRRELGVRTLFNLLGPLLNP 186

Query: 383 AHPPLALIGVYSPELVLPIAETLRVLGYQRAAVVH-SGGMDEVSLHAPTIVAELHDGEIK 441
           A P   L+GV    L+  +AETLR  G  RAAVV  +GG DE++   P  V  L DG + 
Sbjct: 187 ARPTHMLLGVARESLMPLMAETLRRTGAARAAVVFGAGGYDELTPLGPARVLFLRDGIVS 246

Query: 442 SYQLTAEDFGLTPYHQEQLAGGTPEENRDILTRLLQGKGDAAHEAAVAANVAMLMRLHGH 501
            +++    +G+ P   E L     EE   +L  LL G G  A    +  NV M + L  H
Sbjct: 247 EHEVDPARYGIAPCTPEDLVVRDREEAVRVLRELLSGAGPQAMRDMLVFNVGMALHLL-H 305

Query: 502 ED 503
           +D
Sbjct: 306 DD 307


Lambda     K      H
   0.318    0.134    0.388 

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: 443
Number of extensions: 22
Number of successful extensions: 2
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: 531
Length of database: 332
Length adjustment: 32
Effective length of query: 499
Effective length of database: 300
Effective search space:   149700
Effective search space used:   149700
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