Aligments for a candidate for aroE in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Aligments for a candidate for aroE in Escherichia coli BW25113

Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate 17344 b3281 dehydroshikimate reductase, NAD(P)-binding (NCBI)

Query= BRENDA::P15770
         (272 letters)



>lcl|FitnessBrowser__Keio:17344 b3281 dehydroshikimate reductase,
           NAD(P)-binding (NCBI)
          Length = 272

 Score =  541 bits (1394), Expect = e-159
 Identities = 272/272 (100%), Positives = 272/272 (100%)

Query: 1   METYAVFGNPIAHSKSPFIHQQFAQQLNIEHPYGRVLAPINDFINTLNAFFSAGGKGANV 60
           METYAVFGNPIAHSKSPFIHQQFAQQLNIEHPYGRVLAPINDFINTLNAFFSAGGKGANV
Sbjct: 1   METYAVFGNPIAHSKSPFIHQQFAQQLNIEHPYGRVLAPINDFINTLNAFFSAGGKGANV 60

Query: 61  TVPFKEEAFARADELTERAALAGAVNTLMRLEDGRLLGDNTDGVGLLSDLERLSFIRPGL 120
           TVPFKEEAFARADELTERAALAGAVNTLMRLEDGRLLGDNTDGVGLLSDLERLSFIRPGL
Sbjct: 61  TVPFKEEAFARADELTERAALAGAVNTLMRLEDGRLLGDNTDGVGLLSDLERLSFIRPGL 120

Query: 121 RILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDELEGHE 180
           RILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDELEGHE
Sbjct: 121 RILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDELEGHE 180

Query: 181 FDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNADGLGM 240
           FDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNADGLGM
Sbjct: 181 FDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNADGLGM 240

Query: 241 LVAQAAHAFLLWHGVLPDVEPVIKQLQEELSA 272
           LVAQAAHAFLLWHGVLPDVEPVIKQLQEELSA
Sbjct: 241 LVAQAAHAFLLWHGVLPDVEPVIKQLQEELSA 272


Lambda     K      H
   0.321    0.138    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: 394
Number of extensions: 10
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: 272
Length of database: 272
Length adjustment: 25
Effective length of query: 247
Effective length of database: 247
Effective search space:    61009
Effective search space used:    61009
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 17344 b3281 (dehydroshikimate reductase, NAD(P)-binding (NCBI))
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.12545.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.8e-116  373.4   0.0   3.1e-116  373.2   0.0    1.0  1  lcl|FitnessBrowser__Keio:17344  b3281 dehydroshikimate reductase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17344  b3281 dehydroshikimate reductase, NAD(P)-binding (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.2   0.0  3.1e-116  3.1e-116       2     269 ..       3     270 ..       2     271 .. 0.99

  Alignments for each domain:
  == domain 1  score: 373.2 bits;  conditional E-value: 3.1e-116
                       TIGR00507   2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeieesakl 80 
                                     +++v+Gnpi+hSksp+ih+++++ql++e++Y ++ ++i+++ ++l++++++g kG+nvTvPfKee+++++De++e+a+l
  lcl|FitnessBrowser__Keio:17344   3 TYAVFGNPIAHSKSPFIHQQFAQQLNIEHPYGRVLAPINDFINTLNAFFSAGGKGANVTVPFKEEAFARADELTERAAL 81 
                                     89***************************************************************************** PP

                       TIGR00507  81 igavNTlk.ledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlkadkeviiaNRtvekaeelae 158
                                     +gavNTl+ ledg+l+g+nTDg+Gl+s+Le+ls++++++r+l+iGAGGa+++v+l+Ll+ d++v+i+NRtv++aeela+
  lcl|FitnessBrowser__Keio:17344  82 AGAVNTLMrLEDGRLLGDNTDGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAK 160
                                     ********9********************************************************************** PP

                       TIGR00507 159 rlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegklvvDlvynpletpllkeakkkg.tkvidG 236
                                      ++++g+i+als++e+e +++dliinats+g+sg+i  ++++++l++ g++++D++y++++tp+l++++++g ++++dG
  lcl|FitnessBrowser__Keio:17344 161 LFAHTGSIQALSMDELEGHEFDLIINATSSGISGDI--PAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGsKRNADG 237
                                     ************************************..**********************************899**** PP

                       TIGR00507 237 lgMlvaQaalsFelwtgvepdvekvfealkekl 269
                                     lgMlvaQaa++F lw+gv+pdve v+++l+e+l
  lcl|FitnessBrowser__Keio:17344 238 LGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEEL 270
                                     ******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (272 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.30
//
[ok]

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:

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, 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

GapMind for Amino acid biosynthesis