GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_1431
          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.

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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