Alignments for a candidate for aroE in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Synechococcus elongatus PCC 7942

Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate Synpcc7942_2467 Synpcc7942_2467 shikimate 5-dehydrogenase

Query= curated2:Q8YVC1
         (289 letters)



>FitnessBrowser__SynE:Synpcc7942_2467
          Length = 288

 Score =  318 bits (816), Expect = 7e-92
 Identities = 161/287 (56%), Positives = 209/287 (72%), Gaps = 3/287 (1%)

Query: 2   ITGKTKLLGVIGHPVEHSLSPVMHNAAIAQLGLDYVYLPFPIAPDNLEAAIALLATIGVV 61
           +TG+T+LLG+IG P+EHSLSP++ NAAIA+LGLDY Y+PFP+   +L  A+A LA IGV 
Sbjct: 4   LTGRTRLLGIIGDPIEHSLSPLIQNAAIAELGLDYCYVPFPVKGADLATALAGLAAIGVQ 63

Query: 62  GFSVTIPHKQAIIPLLSEISPVAQAIGAVNTVTRQNNQWVGTNTDIEGFIAPLQTTYKRD 121
           GF+VTIPHKQA++PLLS++S +AQ++G+VNTV +    WVGTNTD+ GF+APLQ T + D
Sbjct: 64  GFNVTIPHKQAVMPLLSQVSELAQSVGSVNTVWQTEQGWVGTNTDVLGFLAPLQ-TLRSD 122

Query: 122 WSQQIAVILGNGGAARAVVAGCYQLGFAEIHVVGRNVQRLEEFRHSWENSPIAENLQVHT 181
           WS    V+LG GGAARAVVAGC QLG + I  V R+ Q+ + F+ SW +   A++L +H 
Sbjct: 123 WSGCRVVLLGCGGAARAVVAGCLQLGCSAIATVVRDAQKGDAFQQSWGDR--ADSLTIHD 180

Query: 182 WDYLAKLIPQANLLVNTTPIGMYPQVDESPLSAEELVNLQTGTIAYDLIYIPKPTQFLQK 241
           W  +  ++  A+L+VNTTP+GM P ++ SPL       L+  TIAYDLIY P PT+FLQ+
Sbjct: 181 WSDIPDVLSTADLVVNTTPLGMDPHIERSPLDNSAAQQLRPETIAYDLIYTPSPTRFLQQ 240

Query: 242 AQQQGAIIIDGLEMLVQQGVAALKIWLQQDDIPVDVMRQALIKHLGL 288
           A  QG   IDGLEMLVQQG A LKIW   + +PVD MR  L  HLGL
Sbjct: 241 AIAQGCHAIDGLEMLVQQGAAGLKIWTGAEAVPVDTMRSVLNAHLGL 287


Lambda     K      H
   0.320    0.136    0.403 

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: 291
Number of extensions: 9
Number of successful extensions: 3
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: 289
Length of database: 288
Length adjustment: 26
Effective length of query: 263
Effective length of database: 262
Effective search space:    68906
Effective search space used:    68906
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: 48 (23.1 bits)

Align candidate Synpcc7942_2467 Synpcc7942_2467 (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.27278.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    5.7e-67  211.7   0.0    6.5e-67  211.5   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2467  Synpcc7942_2467 shikimate 5-dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2467  Synpcc7942_2467 shikimate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.5   0.0   6.5e-67   6.5e-67       2     269 ..      10     285 ..       9     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: 211.5 bits;  conditional E-value: 6.5e-67
                                 TIGR00507   2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 
                                               llg+iG+pi+hS+spli+naa+++lgl++ Y+ f+v+  +l  al g+ a g++G+nvT+P+K++v++l
  lcl|FitnessBrowser__SynE:Synpcc7942_2467  10 LLGIIGDPIEHSLSPLIQNAAIAELGLDYCYVPFPVKGADLATALAGLAAIGVQGFNVTIPHKQAVMPL 78 
                                               68******************************************************************* PP

                                 TIGR00507  71 lDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka 139
                                               l +++e a+ +g+vNT+   +   vg nTD++G+++ L+ l    s+ rv+++G GGaa+av+   l+ 
  lcl|FitnessBrowser__SynE:Synpcc7942_2467  79 LSQVSELAQSVGSVNTVWQTEQGWVGTNTDVLGFLAPLQTLRSDWSGCRVVLLGCGGAARAVVAGCLQL 147
                                               ******************98889*****************988888**********************9 PP

                                 TIGR00507 140 dk.eviiaNRtvekaeelaerlqe.lgeilalsleeve..lkkvdliinatsaglsgeideaevka... 201
                                               ++ ++  + R  +k+ +  +       + +  + ++++  l++ dl++n+t++g+ ++i+  ++++   
  lcl|FitnessBrowser__SynE:Synpcc7942_2467 148 GCsAIATVVRDAQKGDAFQQSWGDrADSLTIHDWSDIPdvLSTADLVVNTTPLGMDPHIERSPLDNsaa 216
                                               872577889**9***8887776654555555566677633567****************9999976111 PP

                                 TIGR00507 202 ellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgve.pdvekvfealkekl 269
                                               + l+ +++++Dl+y p  t +l+ a  +g++ idGl+Mlv+Q+a   ++wtg e  +v+ ++++l+++l
  lcl|FitnessBrowser__SynE:Synpcc7942_2467 217 QQLRPETIAYDLIYTPSPTRFLQQAIAQGCHAIDGLEMLVQQGAAGLKIWTGAEaVPVDTMRSVLNAHL 285
                                               5678899**********************************************9889999999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (288 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: 7.32
//
[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