GapMind for Amino acid biosynthesis

 

Aligments for a candidate for preph-dehydratase in Dyella japonica UNC79MFTsu3.2

Align Bifunctional chorismate mutase/prephenate dehydratase; Chorismate mutase-prephenate dehydratase; P-protein; EC 5.4.99.5; EC 4.2.1.51 (characterized)
to candidate N515DRAFT_1431 N515DRAFT_1431 chorismate mutase

Query= SwissProt::P27603
         (365 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1431 N515DRAFT_1431
           chorismate mutase
          Length = 362

 Score =  375 bits (963), Expect = e-108
 Identities = 188/358 (52%), Positives = 259/358 (72%), Gaps = 4/358 (1%)

Query: 7   LKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHIME 66
           L+ +R RIDS+D +I +LISERA  AQEVARVK A     +   +YRPEREA VL+ +++
Sbjct: 8   LEQVRERIDSIDRQIQELISERAGWAQEVARVKGAGLSAID---YYRPEREAHVLRMVVD 64

Query: 67  LNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPMAA 126
            N+GPL + EM RLFREIMSSCLA E PL+V +LGPEGTFS+ A  KHFGH+    P+ +
Sbjct: 65  RNRGPLSDTEMVRLFREIMSSCLAQEDPLKVGFLGPEGTFSEQAVRKHFGHAAYGLPLGS 124

Query: 127 IDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGETT 186
           I+EVF+EV AG  +FGVVPVENS +G +  TLD FL  +  ICGE+ELR+H   L  +  
Sbjct: 125 IEEVFQEVAAGHADFGVVPVENSGQGMIQITLDMFLTSEATICGEIELRVHQ-CLHSQGG 183

Query: 187 KTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMAAQ 246
           + + I R+Y+HAQSL QC+ WL  + P+VE +AVSSNA+AA+  +   ++AAIAG+ A +
Sbjct: 184 RMEDIKRVYAHAQSLQQCKTWLRINLPDVECIAVSSNAEAARMARHADDAAAIAGETAGR 243

Query: 247 LYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPFHSN 306
           +YGL  LA  IEDR  N+TRFL+IG    PP+G+D+TS+++++ +KPGAL+++L PF  +
Sbjct: 244 VYGLKTLATGIEDRADNTTRFLVIGRSLFPPSGNDRTSLLITVNDKPGALYDVLSPFAKH 303

Query: 307 GIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPKAV 364
            + L RIE+RP+ +GKW Y FFID  GH QD  I+  ++++G  A  ++VLGSYP A+
Sbjct: 304 DVSLNRIESRPAHTGKWQYAFFIDVSGHVQDAPIQAAMQEMGGAAAQVRVLGSYPVAL 361


Lambda     K      H
   0.319    0.133    0.390 

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: 365
Number of extensions: 11
Number of successful extensions: 3
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: 365
Length of database: 362
Length adjustment: 29
Effective length of query: 336
Effective length of database: 333
Effective search space:   111888
Effective search space used:   111888
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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