Alignments for a candidate for aroE in Thermocrinis albus DSM 14484

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Thermocrinis albus DSM 14484

Align Shikimate dehydrogenase (NADP(+)); SD; SDH; EC 1.1.1.25 (characterized)
to candidate WP_012992013.1 THAL_RS04965 shikimate dehydrogenase

Query= SwissProt::O67049
         (269 letters)



>NCBI__GCF_000025605.1:WP_012992013.1
          Length = 259

 Score =  282 bits (722), Expect = 4e-81
 Identities = 138/259 (53%), Positives = 191/259 (73%), Gaps = 8/259 (3%)

Query: 8   LYGVIGFPVKHSLSPVFQNALIRYAGLNAVYLAFEINPEELKKAFEGFKALKVKGINVTV 67
           LYG+IG+PV HSLSPVFQN  +RY G++A+Y+ FE+ PE+L +A +G K L V+G+NVT+
Sbjct: 3   LYGLIGYPVSHSLSPVFQNFALRYLGVDAIYVPFEVKPEDLSEAIKGLKVLGVRGVNVTI 62

Query: 68  PFKEEIIPLLDYVEDTAKEIGAVNTVKFENGKAYGYNTDWIGFLKSLKSLIPEVKEKSIL 127
           P KE ++ L+D+++   + IGA NT+  E+G    YNTDWIGFLKSL  +  ++ +   L
Sbjct: 63  PHKERVLDLVDWMDHHTEVIGAANTLLLEDGIIKAYNTDWIGFLKSLWDM--QLSKGKAL 120

Query: 128 VLGAGGASRAVIYALVKEGAKVFLWNRTKEKAIKLAQKFPLEVVNSPEEVIDKVQVIVNT 187
           +LGAGG+SRAV YAL +EG +V+LWNRTKEKA+ LA++F L+VV+ PEEV+  V +IVNT
Sbjct: 121 LLGAGGSSRAVAYALRQEGWEVYLWNRTKEKAVSLAERFQLQVVDRPEEVVKHVDLIVNT 180

Query: 188 TSVGLKDKDPEIFNYDLIKKDHVVVDII-YKETKLLKKAKEKGAKLFDGLPMLLWQGIEA 246
           T       +  +F+Y LI   H ++DII Y+ET L+++AKE GAK  DGLPMLL+QG+E+
Sbjct: 181 T-----PSEEPLFDYQLIDSHHSILDIIYYRETALIRRAKEVGAKYSDGLPMLLYQGLES 235

Query: 247 FKIWNGCEVPYSVAERSVR 265
            +IW GC VPY +   SVR
Sbjct: 236 LRIWTGCSVPYKLVLESVR 254


Lambda     K      H
   0.318    0.138    0.396 

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: 269
Number of extensions: 14
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: 269
Length of database: 259
Length adjustment: 25
Effective length of query: 244
Effective length of database: 234
Effective search space:    57096
Effective search space used:    57096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate WP_012992013.1 THAL_RS04965 (shikimate 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.19607.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.5e-72  229.3   0.0    2.9e-72  229.0   0.0    1.0  1  lcl|NCBI__GCF_000025605.1:WP_012992013.1  THAL_RS04965 shikimate dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025605.1:WP_012992013.1  THAL_RS04965 shikimate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.0   0.0   2.9e-72   2.9e-72       2     266 ..       3     254 ..       2     258 .. 0.95

  Alignments for each domain:
  == domain 1  score: 229.0 bits;  conditional E-value: 2.9e-72
                                 TIGR00507   2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 
                                               l+g+iG+p+ hS+sp+ +n al+ lg++  Y+ fev++e+l++a++g+k lg++GvnvT+P+Ke+vl+l
  lcl|NCBI__GCF_000025605.1:WP_012992013.1   3 LYGLIGYPVSHSLSPVFQNFALRYLGVDAIYVPFEVKPEDLSEAIKGLKVLGVRGVNVTIPHKERVLDL 71 
                                               79******************************************************************* PP

                                 TIGR00507  71 lDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka 139
                                               +D ++++ ++iga NTl ledg + +ynTD iG+++sL    +l  + ++l++GAGG+++ava +L ++
  lcl|NCBI__GCF_000025605.1:WP_012992013.1  72 VDWMDHHTEVIGAANTLLLEDGIIKAYNTDWIGFLKSLWD-MQLS-KGKALLLGAGGSSRAVAYALRQE 138
                                               **************************************99.5565.6889******************* PP

                                 TIGR00507 140 dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegk 208
                                               + ev + NRt+eka  laer+q     + ++  e   k+vdli+n+t++      +e+  + +l+++ +
  lcl|NCBI__GCF_000025605.1:WP_012992013.1 139 GWEVYLWNRTKEKAVSLAERFQL----QVVDRPEEVVKHVDLIVNTTPS------EEPLFDYQLIDSHH 197
                                               **********************9....888888999999********96......3566899******* PP

                                 TIGR00507 209 lvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealk 266
                                                ++D++y    t+l++ ak++g+k +dGl Ml +Q++ s ++wtg   +++ v e ++
  lcl|NCBI__GCF_000025605.1:WP_012992013.1 198 SILDIIYYRE-TALIRRAKEVGAKYSDGLPMLLYQGLESLRIWTGCSVPYKLVLESVR 254
                                               *******987.************************************99999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (259 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: 00:00:00.00
# Mc/sec: 9.21
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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