GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Pseudomonas simiae WCS417

Align Bifunctional protein TrpGD; EC 4.1.3.27; EC 2.4.2.18 (characterized)
to candidate GFF5019 PS417_25715 anthranilate phosphoribosyltransferase

Query= SwissProt::P00904
         (531 letters)



>FitnessBrowser__WCS417:GFF5019
          Length = 349

 Score =  199 bits (506), Expect = 1e-55
 Identities = 126/336 (37%), Positives = 181/336 (53%), Gaps = 6/336 (1%)

Query: 200 LQPILEKLYQAQTLSQQESHQLFSAVVRGELKPEQLAAALVSMKIRGEHPNEIAGAATAL 259
           ++  L ++     LS  E   +   ++ G+    Q+ A +++M+++ E  +EI GA + +
Sbjct: 3   IKTALSRIVGHLDLSTAEMSDVMREIMTGQCTDAQIGAFMMAMRMKSESIDEIVGAVSVM 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 ADLLEAAGIYLNLTPVQVARCIDSVGIGFMFAQSHHGAMKHAAGPRKDLGLRTLFNMLGP 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 GEIKSYQLTAEDFGLTPYHQEQLAGGTP----EENRDILTRLLQGKGDAAHEAAVAANVA 493
            ++  Y +  ED G+       LA  +P    E  RD L R     G  A E  V    A
Sbjct: 243 DQVTEYWVEPEDLGMKSQSLHGLAVESPAASLELIRDALGRRKTENGQKAAEMIVLNAGA 302

Query: 494 MLMRLHGHEDLQANAQTVLEVLRSGSAYDRVTALAA 529
            L        L+       + L +G A +++  L A
Sbjct: 303 ALYAADHAYSLKEGVALAHDALHTGLAREKLEELGA 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 RKDLGLRTLFNMLGPLTNPAGVKHQVVGVFSQALCRPLAEVLQRLGSK 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: 400
Number of extensions: 21
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:

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