Alignments for a candidate for aroE in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Pseudomonas simiae WCS417

Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate GFF24 PS417_00125 shikimate dehydrogenase

Query= BRENDA::Q88RQ5
         (274 letters)



>FitnessBrowser__WCS417:GFF24
          Length = 272

 Score =  439 bits (1128), Expect = e-128
 Identities = 213/272 (78%), Positives = 245/272 (90%)

Query: 1   MDQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGGNVT 60
           MD+YVVFGNPIGHSKSPLIHR+FAEQTG+ L+Y+TLLAPL++FS CAR FF+QG G NVT
Sbjct: 1   MDRYVVFGNPIGHSKSPLIHRMFAEQTGEQLDYSTLLAPLEDFSGCAREFFQQGRGANVT 60

Query: 61  VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120
           VPFKE+A+RL +SLT RA+RAGAVNTLSKLADG+L GDNTDGAGLVRDLTVNAG+ L GK
Sbjct: 61  VPFKEDAYRLANSLTERAQRAGAVNTLSKLADGSLLGDNTDGAGLVRDLTVNAGLNLQGK 120

Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQEP 180
           RIL+LGAGGAVRG LEP+LA +P SL+IANRTVEKAE LA  FD+LGPV ASGF WL+EP
Sbjct: 121 RILLLGAGGAVRGALEPLLAEQPASLIIANRTVEKAEMLAELFDDLGPVSASGFDWLREP 180

Query: 181 VDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGLG 240
           VDVIINATSASL+G++PPIA SL+E G+T CYDMMY KEPT FC+WAT+ GA+  +DGLG
Sbjct: 181 VDVIINATSASLSGDVPPIASSLIEPGKTFCYDMMYAKEPTAFCRWATEHGASVAMDGLG 240

Query: 241 MLAEQAAEAFFIWRGVRPDTAPVLAELRRQLA 272
           ML EQAAEAF++WRGVRPD+APVLAELRRQLA
Sbjct: 241 MLVEQAAEAFYLWRGVRPDSAPVLAELRRQLA 272


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: 325
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: 272
Length adjustment: 25
Effective length of query: 249
Effective length of database: 247
Effective search space:    61503
Effective search space used:    61503
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 GFF24 PS417_00125 (shikimate 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.32642.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    2.9e-80  255.3   0.0    3.2e-80  255.1   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF24  PS417_00125 shikimate dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF24  PS417_00125 shikimate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.1   0.0   3.2e-80   3.2e-80       3     269 ..       4     271 ..       2     272 .] 0.93

  Alignments for each domain:
  == domain 1  score: 255.1 bits;  conditional E-value: 3.2e-80
                         TIGR00507   3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeieesak 79 
                                       + v+Gnpi hSksplih  +++q+g +l Y  + +++e+++    +++++g +G+nvTvPfKe +++l+  ++e+a+
  lcl|FitnessBrowser__WCS417:GFF24   4 YVVFGNPIGHSKSPLIHRMFAEQTGEQLDYSTLLAPLEDFSGCAREFFQQG-RGANVTVPFKEDAYRLANSLTERAQ 79 
                                       78************************************************9.8************************ PP

                         TIGR00507  80 ligavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka.dkeviiaNRtveka 153
                                        +gavNTl  l dg l+g+nTDg Glv +L        ++kr+l++GAGGa ++++ +Ll + + ++iiaNRtveka
  lcl|FitnessBrowser__WCS417:GFF24  80 RAGAVNTLSkLADGSLLGDNTDGAGLVRDLTVnAGLNLQGKRILLLGAGGAVRGALEPLLAEqPASLIIANRTVEKA 156
                                       ********99********************9954433359*****************988664899*********** PP

                         TIGR00507 154 eelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegk.lvvDlvynpletpllkeakkk 229
                                       e lae +  lg + a   + +  + vd+iinatsa+lsg++  +++ ++l++ gk +++D++y++  t++ ++a ++
  lcl|FitnessBrowser__WCS417:GFF24 157 EMLAELFDDLGPVSASGFDWL-REPVDVIINATSASLSGDV--PPIASSLIEPGKtFCYDMMYAKEPTAFCRWATEH 230
                                       ***********9988775554.567****************..********99862689****************** PP

                         TIGR00507 230 g.tkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269
                                       g +  +dGlgMlv+Qaa +F lw+gv pd   v   l+++l
  lcl|FitnessBrowser__WCS417:GFF24 231 GaSVAMDGLGMLVEQAAEAFYLWRGVRPDSAPVLAELRRQL 271
                                       *55668************************99999988877 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 8.54
//
[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