Alignments for a candidate for aroE in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Pseudomonas putida KT2440

Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate PP_0074 PP_0074 shikimate 5-dehydrogenase

Query= BRENDA::Q88RQ5
         (274 letters)



>FitnessBrowser__Putida:PP_0074
          Length = 274

 Score =  545 bits (1404), Expect = e-160
 Identities = 274/274 (100%), Positives = 274/274 (100%)

Query: 1   MDQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGGNVT 60
           MDQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGGNVT
Sbjct: 1   MDQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGGNVT 60

Query: 61  VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120
           VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK
Sbjct: 61  VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120

Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQEP 180
           RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQEP
Sbjct: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQEP 180

Query: 181 VDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGLG 240
           VDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGLG
Sbjct: 181 VDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGLG 240

Query: 241 MLAEQAAEAFFIWRGVRPDTAPVLAELRRQLARG 274
           MLAEQAAEAFFIWRGVRPDTAPVLAELRRQLARG
Sbjct: 241 MLAEQAAEAFFIWRGVRPDTAPVLAELRRQLARG 274


Lambda     K      H
   0.319    0.137    0.405 

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: 422
Number of extensions: 11
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: 274
Length of database: 274
Length adjustment: 25
Effective length of query: 249
Effective length of database: 249
Effective search space:    62001
Effective search space used:    62001
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: 47 (22.7 bits)

Align candidate PP_0074 PP_0074 (shikimate 5-dehydrogenase)
to HMM TIGR00507 (aroE: shikimate dehydrogenase (EC 1.1.1.25))

# 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/TIGR00507.hmm
# target sequence database:        /tmp/gapView.17187.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00507  [M=270]
Accession:   TIGR00507
Description: aroE: shikimate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    3.4e-83  264.9   0.0    3.8e-83  264.7   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_0074  PP_0074 shikimate 5-dehydrogenas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0074  PP_0074 shikimate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.7   0.0   3.8e-83   3.8e-83       3     269 ..       4     271 ..       2     272 .. 0.93

  Alignments for each domain:
  == domain 1  score: 264.7 bits;  conditional E-value: 3.8e-83
                           TIGR00507   3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeiees 77 
                                         + v+Gnpi hSksplih  +++q+g++leY  + ++++e+++   g++++g  G nvTvPfKee+++l+D ++++
  lcl|FitnessBrowser__Putida:PP_0074   4 YVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGS-GGNVTVPFKEEAFRLCDSLTPR 77 
                                         78************************************************95.77******************** PP

                           TIGR00507  78 akligavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka.dkeviiaNRt 149
                                         a+ +gavNTl  l dg l g+nTDg Glv +L        ++kr+li+GAGGa ++v+ ++l + +++++iaNRt
  lcl|FitnessBrowser__Putida:PP_0074  78 ARRAGAVNTLSkLADGTLQGDNTDGAGLVRDLTVnAGVELAGKRILILGAGGAVRGVLEPILAHkPQSLVIANRT 152
                                         **********99********************996444445*****************99776559********* PP

                           TIGR00507 150 vekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkeg.klvvDlvynpletpll 223
                                         vekae+la ++ elg ++a   + + ++ vd+iinatsa+l ge+  +++  +l+++g ++++D++y +  tp+ 
  lcl|FitnessBrowser__Putida:PP_0074 153 VEKAEQLAREFDELGPVVASGFAWL-QEPVDVIINATSASLAGEL--PPIADSLVEAGrTVCYDMMYGKEPTPFC 224
                                         ****************999885554.456****************..9999999988725889************ PP

                           TIGR00507 224 keakkkg.tkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269
                                         ++a k+g +kv+dGlgMl +Qaa +F +w+gv pd   v   l+++l
  lcl|FitnessBrowser__Putida:PP_0074 225 QWATKLGaAKVLDGLGMLAEQAAEAFFIWRGVRPDTAPVLAELRRQL 271
                                         *******99*****************************999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (274 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.19
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis