GapMind for Amino acid biosynthesis

 

Aligments for a candidate for cmutase in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_2520 Chorismate mutase I (EC 5.4.99.5) / Prephenate dehydratase (EC 4.2.1.51)

Query= SwissProt::P27603
         (365 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2520 Chorismate mutase I
           (EC 5.4.99.5) / Prephenate dehydratase (EC 4.2.1.51)
          Length = 364

 Score =  635 bits (1637), Expect = 0.0
 Identities = 319/365 (87%), Positives = 341/365 (93%), Gaps = 1/365 (0%)

Query: 1   MSEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWV 60
           MSE  +LKALR+RID+LDE++L+LISERARCAQEVARVK AS  + E  VFYRPEREA V
Sbjct: 1   MSE-QELKALRLRIDALDEKVLELISERARCAQEVARVKMASLAEGEVPVFYRPEREAQV 59

Query: 61  LKHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVI 120
           LK +ME NKGPL NEEMARLFREIMSSCLALEQPL+VAYLGPEGTF+QAAA+KHFGH+VI
Sbjct: 60  LKRVMERNKGPLGNEEMARLFREIMSSCLALEQPLKVAYLGPEGTFTQAAAMKHFGHAVI 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+DPL+K VLEKI  EAVALKVLGSY
Sbjct: 300 VPFHDNGIDLTRIETRPSRSGKWTYVFFIDFVGHHRDPLVKGVLEKISQEAVALKVLGSY 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: 503
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)

Align candidate Pf6N2E2_2520 (Chorismate mutase I (EC 5.4.99.5) / Prephenate dehydratase (EC 4.2.1.51))
to HMM TIGR01807 (pheA: chorismate mutase (EC 5.4.99.5))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01807.hmm
# target sequence database:        /tmp/gapView.6982.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01807  [M=76]
Accession:   TIGR01807
Description: CM_P2: chorismate mutase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
    1.2e-34  104.8   2.9    1.2e-34  104.8   1.3    1.9  2  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2520  Chorismate mutase I (EC 5.4.99.5


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2520  Chorismate mutase I (EC 5.4.99.5) / Prephenate dehydratase (EC 4.2.1.5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   1.3   1.2e-34   1.2e-34       1      76 []       6      84 ..       6      84 .. 0.93
   2 ?   -3.0   0.0      0.51      0.51      67      75 ..     125     133 ..     122     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 1.2e-34
                                      TIGR01807  1 LkelRnkiDaiDdrildLlseRaklakavgelKkks...aseaviYRPeREaavlrrlkelnkGpL 63
                                                   Lk+lR +iDa+D+++l+L+seRa++a++v+++K +s    +  v+YRPeREa+vl+r++e+nkGpL
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2520  6 LKALRLRIDALDEKVLELISERARCAQEVARVKMASlaeGEVPVFYRPEREAQVLKRVMERNKGPL 71
                                                   799********************************9633333579********************* PP

                                      TIGR01807 64 dqeavarifrEim 76
                                                    +e++ar+frEim
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2520 72 GNEEMARLFREIM 84
                                                   ************9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.51
                                      TIGR01807  67 avarifrEi 75 
                                                    a++ +frE+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2520 125 AIDEVFREV 133
                                                    789999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (76 nodes)
Target sequences:                          1  (364 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 7.39
//
[ok]

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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