GapMind for Amino acid biosynthesis

 

Aligments for a candidate for trpD_1 in Pedobacter sp. GW460-11-11-14-LB5

Align Bifunctional protein TrpGD; EC 4.1.3.27; EC 2.4.2.18 (characterized)
to candidate CA265_RS05010 CA265_RS05010 anthranilate phosphoribosyltransferase

Query= SwissProt::P00904
         (531 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS05010 CA265_RS05010
           anthranilate phosphoribosyltransferase
          Length = 329

 Score =  157 bits (397), Expect = 6e-43
 Identities = 95/299 (31%), Positives = 146/299 (48%), Gaps = 5/299 (1%)

Query: 200 LQPILEKLYQAQTLSQQESHQLFSAVVRGELKPEQLAAALVSMKIRGEHPNEIAGAATAL 259
           ++ IL  L++ ++ S++E+  +  ++  G     Q+AA + +  +R     E+ G   A+
Sbjct: 1   MKKILNHLFENKSFSREEAKNILISISEGAFNSSQIAAFITAYAMRNITVQELQGFRDAM 60

Query: 260 LENAAPFPRPDYLFADIVGTGGDGSNSINISTASAFVAAACGLKVAKHGNRSVSSKSGSS 319
           L+         Y   D+ GTGGDG ++ NIST S+FV A  G  VAKHGN  VSS  GSS
Sbjct: 61  LDMCVKVNLSGYDLIDLCGTGGDGKDTFNISTLSSFVVAGAGHHVAKHGNYGVSSGCGSS 120

Query: 320 DLLAAFGINLDMNADKSRQALDELGVCFLFAPKYHTGFRHAMPVRQQLKTRTLFNVLGPL 379
           +++   G     N D  ++ LD  G+CFL AP ++   +   P+R++L  +T FN+LGP+
Sbjct: 121 NVMEYLGYTFTNNEDTLKRNLDAAGICFLHAPLFNPAMKIVAPIRKELGVKTFFNMLGPM 180

Query: 380 INPAHPPLALIGVYSPELVLPIAETLRVLGYQRAAVVHSGGMDEVSLHAPTIVAELHDGE 439
           +NP  P   ++GV+S EL    A   +        V    G DEVSL            +
Sbjct: 181 VNPGQPKYQMVGVFSLELARLYAYLYQDTDKSYTIVHALEGYDEVSLTCDVKTFSNKGEQ 240

Query: 440 IKSYQLTAEDFGLTPYHQEQLAGG-TPEENRDILTRLLQGKGDAAHEAAVAANVAMLMR 497
           I    LT +D G        + GG T E +  I   +L GK        V  N A+ ++
Sbjct: 241 I----LTLQDMGFDKVEVNAIKGGDTVESSAKIFMDVLNGKATDVQNNVVLCNSALAIK 295


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: 342
Number of extensions: 15
Number of successful extensions: 1
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: 329
Length adjustment: 31
Effective length of query: 500
Effective length of database: 298
Effective search space:   149000
Effective search space used:   149000
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