Alignments for a candidate for aroE in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Dinoroseobacter shibae DFL-12

Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate 3610069 Dshi_3450 shikimate 5-dehydrogenase (RefSeq)

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



>FitnessBrowser__Dino:3610069
          Length = 278

 Score =  217 bits (552), Expect = 3e-61
 Identities = 116/269 (43%), Positives = 157/269 (58%)

Query: 11  VGGVCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRGGAVRGLNVTI 70
           + GV G PI HS SP +H  W+   G++  YVP              L     +G+NVT+
Sbjct: 8   IAGVIGNPITHSRSPHLHRHWLHVYGIEGYYVPLHVQGQDLAEVFHALPKLGFKGVNVTL 67

Query: 71  PFKERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAIQAPGFDVTAA 130
           PFKERA+ +AD  SD A + GAAN + F  DG++HADNTDG G +  +   APG+   AA
Sbjct: 68  PFKERAIELADRVSDRAALIGAANTITFQPDGTIHADNTDGYGFIENLRNGAPGWSPRAA 127

Query: 131 PVVILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAKGEDALPALLP 190
            +V+LGAGGAARG ++ALL AGAP + + NRT A+A+ L   FG +V       +   + 
Sbjct: 128 AIVVLGAGGAARGVLSALLEAGAPEVRLANRTRAKAEALRSDFGPRVTVVDWHGVSGTME 187

Query: 191 EAGLIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEAAGRRTVDGLE 250
           +A  ++N TSLG+ G      +L   P++AVV D+VY+PL T  L +A A G   VDGL 
Sbjct: 188 DAETLVNTTSLGMTGQPDLELNLDALPRSAVVTDIVYRPLMTPLLEQAVARGNPVVDGLG 247

Query: 251 MLLRQAIPTFETIYGQAPSPKIDVRVLAL 279
           MLL QA P FE  +G  P    ++R  AL
Sbjct: 248 MLLFQAAPGFERWFGVRPEITPELRAAAL 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: 226
Number of extensions: 10
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: 285
Length of database: 278
Length adjustment: 26
Effective length of query: 259
Effective length of database: 252
Effective search space:    65268
Effective search space used:    65268
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 3610069 Dshi_3450 (shikimate 5-dehydrogenase (RefSeq))
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.26970.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    2.3e-72  229.4   0.0    2.6e-72  229.2   0.0    1.0  1  lcl|FitnessBrowser__Dino:3610069  Dshi_3450 shikimate 5-dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3610069  Dshi_3450 shikimate 5-dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.2   0.0   2.6e-72   2.6e-72       2     260 ..       8     269 ..       7     277 .. 0.95

  Alignments for each domain:
  == domain 1  score: 229.2 bits;  conditional E-value: 2.6e-72
                         TIGR00507   2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeieesa 78 
                                       + gviGnpi hS sp +h + l+  g+e+ Y+ ++v+ ++l ++++++ +lg+kGvnvT+PfKe+++el+D+++++a
  lcl|FitnessBrowser__Dino:3610069   8 IAGVIGNPITHSRSPHLHRHWLHVYGIEGYYVPLHVQGQDLAEVFHALPKLGFKGVNVTLPFKERAIELADRVSDRA 84 
                                       689************************************************************************** PP

                         TIGR00507  79 kligavNTlk.ledgklvgynTDgiGlvssLek..lsklksekrvliiGAGGaakavaleLlka.dkeviiaNRtve 151
                                       +liga NT++   dg + ++nTDg+G++ +L++    +      ++++GAGGaa++v+ +Ll+a   ev +aNRt +
  lcl|FitnessBrowser__Dino:3610069  85 ALIGAANTITfQPDGTIHADNTDGYGFIENLRNgaPGWSPRAAAIVVLGAGGAARGVLSALLEAgAPEVRLANRTRA 161
                                       **********7789******************97445555578999******************6679********* PP

                         TIGR00507 152 kaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegklvvDlvynpletpllkeakk 228
                                       kae+l + +    +++ ++  +   +  + ++n+ts+g++g+  + e++ + l  +++v D+vy pl tpll+ a  
  lcl|FitnessBrowser__Dino:3610069 162 KAEALRSDFGPRVTVVDWHGVSGTMEDAETLVNTTSLGMTGQP-DLELNLDALPRSAVVTDIVYRPLMTPLLEQAVA 237
                                       ***********9*****************************98.99******************************* PP

                         TIGR00507 229 kgtkvidGlgMlvaQaalsFelwtgvepdvek 260
                                       +g +v+dGlgMl  Qaa  Fe w+gv p++  
  lcl|FitnessBrowser__Dino:3610069 238 RGNPVVDGLGMLLFQAAPGFERWFGVRPEITP 269
                                       ****************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (278 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 10.49
//
[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