Alignments for a candidate for aroE in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Phaeobacter inhibens BS107

Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate GFF3462 PGA1_c35150 shikimate dehydrogenase AroE

Query= reanno::Caulo:CCNA_00003
         (285 letters)



>FitnessBrowser__Phaeo:GFF3462
          Length = 277

 Score =  197 bits (502), Expect = 2e-55
 Identities = 108/269 (40%), Positives = 148/269 (55%)

Query: 11  VGGVCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRGGAVRGLNVTI 70
           + GV G P+ HS SP++H  W+   G+   YVP      + E  V  L      G N+TI
Sbjct: 8   LAGVIGSPVAHSRSPLVHGHWLRTYGIAGHYVPLHVEPGQLEEVVRSLPKMGFVGANITI 67

Query: 71  PFKERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAIQAPGFDVTAA 130
           P KE+ + +AD  +D A + GAAN L+F  DGS+ ADNTDG G +  +   AP +D    
Sbjct: 68  PHKEQIMEIADQVTDRATLIGAANTLIFRPDGSILADNTDGYGFITNLHQAAPDWDPATG 127

Query: 131 PVVILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAKGEDALPALLP 190
           P V+ GAGGA+R  +A+LL AG P I + NRT  RA      FG ++       +  ++ 
Sbjct: 128 PAVVFGAGGASRAVIASLLEAGVPEILLSNRTRERADQFRSEFGSRIQVVDWVQVGNVIE 187

Query: 191 EAGLIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEAAGRRTVDGLE 250
           +A L++N TSLG+ G       L     + VV D+VY PL+T+ L+ AE  G  TVDGL 
Sbjct: 188 QAALLVNTTSLGMVGKPRLRVPLDGLRSSTVVTDLVYTPLKTDMLQWAEDIGCTTVDGLG 247

Query: 251 MLLRQAIPTFETIYGQAPSPKIDVRVLAL 279
           MLL QA+P FE  +G+ P      R  AL
Sbjct: 248 MLLHQAVPGFERWFGKRPEVDAATREAAL 276


Lambda     K      H
   0.319    0.136    0.390 

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: 204
Number of extensions: 7
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: 285
Length of database: 277
Length adjustment: 26
Effective length of query: 259
Effective length of database: 251
Effective search space:    65009
Effective search space used:    65009
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 GFF3462 PGA1_c35150 (shikimate dehydrogenase AroE)
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.15333.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    4.6e-71  225.1   0.0    5.1e-71  224.9   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3462  PGA1_c35150 shikimate dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3462  PGA1_c35150 shikimate dehydrogenase AroE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.9   0.0   5.1e-71   5.1e-71       2     263 ..       8     272 ..       7     277 .] 0.93

  Alignments for each domain:
  == domain 1  score: 224.9 bits;  conditional E-value: 5.1e-71
                          TIGR00507   2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeiees 77 
                                        l gviG p++hS spl+h + l++ g++++Y+ ++ve+ +le+++  + + g+ G+n+T+P+Ke+++e++D+++++
  lcl|FitnessBrowser__Phaeo:GFF3462   8 LAGVIGSPVAHSRSPLVHGHWLRTYGIAGHYVPLHVEPGQLEEVVRSLPKMGFVGANITIPHKEQIMEIADQVTDR 83 
                                        679************************************************************************* PP

                          TIGR00507  78 akligavNTlk.ledgklvgynTDgiGlvssLek..lsklksekrvliiGAGGaakavaleLlka.dkeviiaNRt 149
                                        a liga NTl  + dg ++++nTDg+G++++L++   ++  +   +++ GAGGa++av+ +Ll+a   e+++ NRt
  lcl|FitnessBrowser__Phaeo:GFF3462  84 ATLIGAANTLIfRPDGSILADNTDGYGFITNLHQaaPDWDPATGPAVVFGAGGASRAVIASLLEAgVPEILLSNRT 159
                                        **********9889********************733444456789*******************5569******* PP

                          TIGR00507 150 vekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegklvvDlvynpletpllke 225
                                         e+a +  +++ +  +++ + +     ++  l++n+ts+g+ g+     v+ + l+++++v Dlvy pl+t +l++
  lcl|FitnessBrowser__Phaeo:GFF3462 160 RERADQFRSEFGSRIQVVDWVQVGNVIEQAALLVNTTSLGMVGKP-RLRVPLDGLRSSTVVTDLVYTPLKTDMLQW 234
                                        ***********9988888887777788999************987.99**************************** PP

                          TIGR00507 226 akkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfe 263
                                        a++ g+ ++dGlgMl +Qa+  Fe w+g  p+v+ + +
  lcl|FitnessBrowser__Phaeo:GFF3462 235 AEDIGCTTVDGLGMLLHQAVPGFERWFGKRPEVDAATR 272
                                        ********************************987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (277 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: 00:00:00.01
# Mc/sec: 7.06
//
[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