Alignments for a candidate for aroE in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Shewanella oneidensis MR-1

Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate 199237 SO0040 shikimate 5-dehydrogenase (NCBI ptt file)

Query= SwissProt::Q9KVT3
         (278 letters)



>FitnessBrowser__MR1:199237
          Length = 287

 Score =  284 bits (726), Expect = 2e-81
 Identities = 146/277 (52%), Positives = 188/277 (67%), Gaps = 6/277 (2%)

Query: 5   IDQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGGRGCNV 64
           +D+YAVFG+PI HSKSPFIH  FA  TQ+S+ Y A   P+DGF  + K FF+ GG+G NV
Sbjct: 8   VDRYAVFGHPIGHSKSPFIHGQFAALTQESLTYEAILAPIDGFEASLKSFFSSGGKGANV 67

Query: 65  TVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQVLLKGA 124
           TVPFKE+A+   D L+  A LAGAVNTL  L DG I GDNTDG GLV DL++    L+  
Sbjct: 68  TVPFKEQAFALCDSLSAEAALAGAVNTLSLLADGSIRGDNTDGLGLVADLISHLGSLQHK 127

Query: 125 TILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGE------VKAQAF 178
            +LL+GAGGAARG + PLL+     + +TNRT  KA+ L ++ +   E      ++A + 
Sbjct: 128 RVLLVGAGGAARGCILPLLNAGVGQLVITNRTQTKAKDLVDIFSQLEEGIYKDKLQALSM 187

Query: 179 EQLKQSYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQA 238
            +L   ++++INSTSASL GELP +   I  S +VCYDMMYG   T FNQWA Q G A+ 
Sbjct: 188 SELTGEFELVINSTSASLAGELPPLPQSIIGSTTVCYDMMYGAMPTAFNQWALQQGAAKV 247

Query: 239 IDGLGMLVGQAAESFMLWRGLRPGTKQILRELRKNLE 275
           IDGLGMLVGQAA+SF LWR + P T  +L+ LR+ L+
Sbjct: 248 IDGLGMLVGQAAKSFALWRTVEPDTAVVLKLLREKLQ 284


Lambda     K      H
   0.320    0.135    0.392 

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: 203
Number of extensions: 4
Number of successful extensions: 2
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: 278
Length of database: 287
Length adjustment: 26
Effective length of query: 252
Effective length of database: 261
Effective search space:    65772
Effective search space used:    65772
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 199237 SO0040 (shikimate 5-dehydrogenase (NCBI ptt file))
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.29700.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
      1e-86  276.4   0.0    1.2e-86  276.3   0.0    1.0  1  lcl|FitnessBrowser__MR1:199237  SO0040 shikimate 5-dehydrogenase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199237  SO0040 shikimate 5-dehydrogenase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.3   0.0   1.2e-86   1.2e-86       3     269 ..      11     283 ..       9     284 .. 0.96

  Alignments for each domain:
  == domain 1  score: 276.3 bits;  conditional E-value: 1.2e-86
                       TIGR00507   3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeieesakli 81 
                                     ++v+G+pi hSksp+ih ++++ ++  l+Y a+ ++i+ +e  l+ +++ g kG+nvTvPfKe++++l+D ++ +a+l+
  lcl|FitnessBrowser__MR1:199237  11 YAVFGHPIGHSKSPFIHGQFAALTQESLTYEAILAPIDGFEASLKSFFSSGGKGANVTVPFKEQAFALCDSLSAEAALA 89 
                                     9****************************************************************************** PP

                       TIGR00507  82 gavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka.dkeviiaNRtvekaeela 157
                                     gavNTl  l dg + g+nTDg+Glv++L   l  l+ +krvl++GAGGaa++ +l+Ll+a   +++i+NRt+ ka++l+
  lcl|FitnessBrowser__MR1:199237  90 GAVNTLSlLADGSIRGDNTDGLGLVADLIShLGSLQ-HKRVLLVGAGGAARGCILPLLNAgVGQLVITNRTQTKAKDLV 167
                                     *******99*******************999*****.***********************5579*************** PP

                       TIGR00507 158 erlqe......lgeilalsleevelkkvdliinatsaglsgeideaevkaellkegklvvDlvynpletpllkeakkkg 230
                                     + + +        + +als++e+   +++l+in+tsa+l ge+  ++++++++ + ++++D++y  + t++ ++a ++g
  lcl|FitnessBrowser__MR1:199237 168 DIFSQleegiyKDKLQALSMSELTG-EFELVINSTSASLAGEL--PPLPQSIIGSTTVCYDMMYGAMPTAFNQWALQQG 243
                                     ****988888556678999988865.6****************..********************************** PP

                       TIGR00507 231 .tkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269
                                      +kvidGlgMlv Qaa+sF lw+ vepd  +v + l+ekl
  lcl|FitnessBrowser__MR1:199237 244 aAKVIDGLGMLVGQAAKSFALWRTVEPDTAVVLKLLREKL 283
                                     99********************************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (287 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.01
//
[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