GapMind for Amino acid biosynthesis

 

Alignments for a candidate for preph-dehydratase in Pseudomonas fluorescens FW300-N2E3

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 AO353_02070 AO353_02070 prephenate dehydratase

Query= SwissProt::P27603
         (365 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_02070
          Length = 364

 Score =  632 bits (1630), Expect = 0.0
 Identities = 319/365 (87%), Positives = 341/365 (93%), Gaps = 1/365 (0%)

Query: 1   MSEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWV 60
           MSE  +LKALR+RID+LDE+IL+LISERARCAQEVARVK A+  + E  VFYRPEREA V
Sbjct: 1   MSE-QELKALRLRIDALDEKILELISERARCAQEVARVKMATLAEGEVPVFYRPEREAQV 59

Query: 61  LKHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVI 120
           LK +ME N+GPL NEEMARLFREIMSSCLALEQPL+VAYLGPEGTF+QAAA+KHFGH+VI
Sbjct: 60  LKRVMERNQGPLGNEEMARLFREIMSSCLALEQPLKVAYLGPEGTFTQAAAMKHFGHAVI 119

Query: 121 SKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL 180
           SKPMAAIDEVFREV AGAVNFGVVPVENSTEGAVNHTLDSFLEHD+VICGEVELRIHHHL
Sbjct: 120 SKPMAAIDEVFREVAAGAVNFGVVPVENSTEGAVNHTLDSFLEHDMVICGEVELRIHHHL 179

Query: 181 LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA 240
           LVGE TKTD I+RIYSHAQSLAQCRKWLDAHYPNVERVAVSSNA+AAKRVK EWNSAAIA
Sbjct: 180 LVGENTKTDSISRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNAEAAKRVKGEWNSAAIA 239

Query: 241 GDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 300
           GDMAA LYGL++LAEKIEDRP NSTRFL+IGSQEVPPTGDDKTSIIVSM NKPGALHELL
Sbjct: 240 GDMAAGLYGLTRLAEKIEDRPDNSTRFLMIGSQEVPPTGDDKTSIIVSMSNKPGALHELL 299

Query: 301 MPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360
           +PFH NGIDLTRIETRPSRSGKWTYVFFID +GHH+DPLIK VLEKI  EAVALKVLGSY
Sbjct: 300 VPFHDNGIDLTRIETRPSRSGKWTYVFFIDFVGHHRDPLIKAVLEKISQEAVALKVLGSY 359

Query: 361 PKAVL 365
           PKAVL
Sbjct: 360 PKAVL 364


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: 506
Number of extensions: 9
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: 365
Length of database: 364
Length adjustment: 29
Effective length of query: 336
Effective length of database: 335
Effective search space:   112560
Effective search space used:   112560
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