GapMind for Amino acid biosynthesis

 

Aligments for a candidate for trpD_1 in Desulfovibrio vulgaris Miyazaki F

Align Bifunctional protein TrpGD; EC 4.1.3.27; EC 2.4.2.18 (characterized)
to candidate 8501007 DvMF_1744 anthranilate phosphoribosyltransferase (RefSeq)

Query= SwissProt::P00904
         (531 letters)



>lcl|FitnessBrowser__Miya:8501007 DvMF_1744 anthranilate
           phosphoribosyltransferase (RefSeq)
          Length = 338

 Score =  190 bits (482), Expect = 8e-53
 Identities = 113/302 (37%), Positives = 166/302 (54%), Gaps = 6/302 (1%)

Query: 203 ILEKLYQAQTLSQQESHQLFSAVVRGELKPEQLAAALVSMKIRGEHPNEIAGAATALLEN 262
           ILE L     L+ + +   FS ++ GE+   Q  + L+ ++++GE P E+  A  A L  
Sbjct: 8   ILETLATGMDLAPELAEAGFSRLMDGEMTCAQAGSFLMGLRMKGETPQELTEAVRAALAR 67

Query: 263 AAPFPRPDYLFADIVGTGGDGSNSINISTASAFVAAACGLKVAKHGNRSVSSKSGSSDLL 322
           A      D    DIVGTGGDG +S N STA+A   A  G +V KHGNR+VSS  G++D +
Sbjct: 68  AVRVTGIDGPTIDIVGTGGDGRSSFNCSTATALTLAGMGHRVVKHGNRAVSSSCGAADAV 127

Query: 323 AAFGINLDMNADKSRQALDELGVCFLFAPKYHTGFRHAMPVRQQLKTRTLFNVLGPLINP 382
              G+ L+++ +  R  + +    FLFAP++H  FR+ MP+R++L  RTLFN+LGPL+NP
Sbjct: 128 EGLGLPLELDPEDVRALVAQRNFAFLFAPRFHPAFRNVMPIRRELGVRTLFNLLGPLLNP 187

Query: 383 AHPPLALIGVYSPELVLPIAETLRVLGYQRAAVVH-SGGMDEVSLHAPTIVAELH----- 436
           A P   L+GV   EL+  +A TL + G +RAAVVH +GG DE++   P  +  L      
Sbjct: 188 ARPSHMLLGVARAELLPLMARTLLLTGVRRAAVVHGAGGYDELTPMGPAHIMLLEGDGQG 247

Query: 437 DGEIKSYQLTAEDFGLTPYHQEQLAGGTPEENRDILTRLLQGKGDAAHEAAVAANVAMLM 496
            G +    +   D+G+     E+LA    +    +L  LL G G A     +  NV M +
Sbjct: 248 HGTLTEISVDPADYGIASCTPEELAVPDRDTAVRVLRELLSGGGPAPMRDMLMLNVGMAL 307

Query: 497 RL 498
            L
Sbjct: 308 HL 309


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: 473
Number of extensions: 26
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 531
Length of database: 338
Length adjustment: 32
Effective length of query: 499
Effective length of database: 306
Effective search space:   152694
Effective search space used:   152694
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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