Alignments for a candidate for aroE in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Acidovorax sp. GW101-3H11

Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate Ac3H11_4044 Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25)

Query= SwissProt::Q9KVT3
         (278 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4044
          Length = 284

 Score =  233 bits (595), Expect = 3e-66
 Identities = 132/272 (48%), Positives = 166/272 (61%), Gaps = 7/272 (2%)

Query: 6   DQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGGRGCNVT 65
           D Y V GNP+ HS+SP IH  FA  T + + Y  + VP+DGF +  + F A+GGRGCNVT
Sbjct: 9   DLYCVMGNPVAHSRSPAIHARFAELTGEPIAYERRLVPMDGFAQGVRDFVAEGGRGCNVT 68

Query: 66  VPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQ-VLLKGA 124
           VPFK +A   A   +ER +LAGA NTL    DG I  DNTDG GLV D+     V L G 
Sbjct: 69  VPFKTDAPGLATACSERVQLAGAANTLTFRADGSIYADNTDGLGLVADITHNAGVPLAGR 128

Query: 125 TILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQS 184
            +LL+GAGGAA GVL PLL      ITV NRT AKA+ L E       ++    E L+ S
Sbjct: 129 DVLLVGAGGAAAGVLGPLLLAGARHITVANRTLAKAQALVESHRPLALLQKAELEALEPS 188

Query: 185 -----YDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAI 239
                +DVIIN+T++SL G    +   +    ++ YDMMYG     F  WAR HG A   
Sbjct: 189 AVTANFDVIINATASSLAGAGVPVPASVLRPGALAYDMMYGPAAQEFLDWARSHG-AVPR 247

Query: 240 DGLGMLVGQAAESFMLWRGLRPGTKQILRELR 271
           DGLGMLV QAAE+F+LWRG+RP + Q+L E++
Sbjct: 248 DGLGMLVEQAAEAFLLWRGVRPPSAQVLHEMQ 279


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: 213
Number of extensions: 10
Number of successful extensions: 4
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: 284
Length adjustment: 26
Effective length of query: 252
Effective length of database: 258
Effective search space:    65016
Effective search space used:    65016
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 Ac3H11_4044 (Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25))
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.17597.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
    8.2e-73  230.8   0.0    9.8e-73  230.6   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4044  Shikimate 5-dehydrogenase I alph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4044  Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.6   0.0   9.8e-73   9.8e-73       2     265 ..      10     278 ..       9     282 .. 0.96

  Alignments for each domain:
  == domain 1  score: 230.6 bits;  conditional E-value: 9.8e-73
                                        TIGR00507   2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPf 63 
                                                      l+ v+Gnp++hS sp+ih ++++ +g  + Y +  v+++ + + +  + a+g +G+nvTvPf
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4044  10 LYCVMGNPVAHSRSPAIHARFAELTGEPIAYERRLVPMDGFAQGVRDFVAEGGRGCNVTVPF 71 
                                                      799*********************************************************** PP

                                        TIGR00507  64 KeevlellDeieesakligavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvlii 123
                                                      K+ +  l+   +e+++l+ga NTl+ + dg ++++nTDg+Glv+++ +    + +++ vl++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4044  72 KTDAPGLATACSERVQLAGAANTLTfRADGSIYADNTDGLGLVADITHnAGVPLAGRDVLLV 133
                                                      *************************999*******************98888888******* PP

                                        TIGR00507 124 GAGGaakavaleLlka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkk....vd 180
                                                      GAGGaa +v+ +Ll a   ++++aNRt++ka++l+e  + l   ++ +le +e++     +d
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4044 134 GAGGAAAGVLGPLLLAgARHITVANRTLAKAQALVESHRPLALLQKAELEALEPSAvtanFD 195
                                                      ************99996789********************99999999999998765667** PP

                                        TIGR00507 181 liinatsaglsgeideaevkaellkegklvvDlvynpletpllkeakkkgtkvidGlgMlva 242
                                                      +iinat+++l g    ++v+a++l+ g+l++D++y p    +l +a+++g+   dGlgMlv+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4044 196 VIINATASSLAGAG--VPVPASVLRPGALAYDMMYGPAAQEFLDWARSHGAVPRDGLGMLVE 255
                                                      ************99..********************************************** PP

                                        TIGR00507 243 QaalsFelwtgvepdvekvfeal 265
                                                      Qaa +F lw+gv p+  +v + +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4044 256 QAAEAFLLWRGVRPPSAQVLHEM 278
                                                      *************9988887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (284 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: 00:00:00.00
# Mc/sec: 9.62
//
[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