GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Pseudomonas fluorescens FW300-N2C3

Align Bifunctional protein TrpGD; EC 4.1.3.27; EC 2.4.2.18 (characterized)
to candidate AO356_14435 AO356_14435 anthranilate phosphoribosyltransferase

Query= SwissProt::P00904
         (531 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_14435
          Length = 349

 Score =  203 bits (517), Expect = 7e-57
 Identities = 126/336 (37%), Positives = 182/336 (54%), Gaps = 6/336 (1%)

Query: 200 LQPILEKLYQAQTLSQQESHQLFSAVVRGELKPEQLAAALVSMKIRGEHPNEIAGAATAL 259
           ++  L ++     LS  E   +   ++ G+    Q+ A +++M+++ E  +EI GA + +
Sbjct: 3   IKTALSRIVGHLDLSTDEMRDVMREIMTGQCTDAQIGAFMMAMRMKSESIDEIVGAVSVM 62

Query: 260 LENAAPFPRPDYL-FADIVGTGGDGSNSINISTASAFVAAACGLKVAKHGNRSVSSKSGS 318
            E A            D+VGTGGDG+N  N+STAS+FV AA G  VAKHGNR+VS KSGS
Sbjct: 63  RELADKVELKTLDGVVDVVGTGGDGANIFNVSTASSFVVAAAGCTVAKHGNRAVSGKSGS 122

Query: 319 SDLLAAFGINLDMNADKSRQALDELGVCFLFAPKYHTGFRHAMPVRQQLKTRTLFNVLGP 378
           +DLL A GI L++   +  + +D +G+ F+FA  +H   +HA   R+ L  RTLFN+LGP
Sbjct: 123 ADLLEAAGIYLNLTPIQVARCIDNVGIGFMFAQTHHRAMKHAAAPRRDLGLRTLFNMLGP 182

Query: 379 LINPAHPPLALIGVYSPELVLPIAETLRVLGYQRAAVVHS-GGMDEVSLHAPTIVAELHD 437
           L NPA     ++GV+S  L  P+AE L+ LG +   VVHS  G+DE SL APT VAEL +
Sbjct: 183 LTNPAGVKHQVVGVFSQALCRPLAEVLQRLGSKHVLVVHSKDGLDEFSLAAPTFVAELKN 242

Query: 438 GEIKSYQLTAEDFGLTPYHQEQLAGGTPEEN----RDILTRLLQGKGDAAHEAAVAANVA 493
            +I  Y +  ED G+       LA   P ++    RD L R     G  A E  V    A
Sbjct: 243 DQISEYWVEPEDLGMKSQSLHGLAVDGPAQSLELIRDALGRRKTENGQKAAEMIVLNAGA 302

Query: 494 MLMRLHGHEDLQANAQTVLEVLRSGSAYDRVTALAA 529
            L        L+   +   + L +G A +++  L A
Sbjct: 303 ALYAADHASSLKQGVELAHDALHTGLAREKLEELGA 338



 Score = 25.4 bits (54), Expect = 0.004
 Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 2/48 (4%)

Query: 32  RNHIPAQTLIERLATMSNPVLMLSPGPGVPSEAGCMP--ELLTRLRGK 77
           R  +  +TL   L  ++NP  +     GV S+A C P  E+L RL  K
Sbjct: 168 RRDLGLRTLFNMLGPLTNPAGVKHQVVGVFSQALCRPLAEVLQRLGSK 215


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: 389
Number of extensions: 19
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: 2
Length of query: 531
Length of database: 349
Length adjustment: 32
Effective length of query: 499
Effective length of database: 317
Effective search space:   158183
Effective search space used:   158183
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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