Alignments for a candidate for aroB in Thermomonospora curvata DSM 43183

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Thermomonospora curvata DSM 43183

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_012853277.1 TCUR_RS14550 3-dehydroquinate synthase

Query= BRENDA::P9WPX9
         (362 letters)



>NCBI__GCF_000024385.1:WP_012853277.1
          Length = 358

 Score =  393 bits (1010), Expect = e-114
 Identities = 205/348 (58%), Positives = 250/348 (71%), Gaps = 1/348 (0%)

Query: 10  VQVAVDPPYPVVIGTGLLDELEDLLADRHK-VAVVHQPGLAETAEEIRKRLAGKGVDAHR 68
           + V  + PY VVIGTG+L+EL  LL ++ + VAVVH   L E A  + K L   G  A  
Sbjct: 6   ITVRGESPYEVVIGTGVLEELPGLLGEKVRTVAVVHDEALPEIAGPVCKALEEAGYTACP 65

Query: 69  IEIPDAEAGKDLPVVGFIWEVLGRIGIGRKDALVSLGGGAATDVAGFAAATWLRGVSIVH 128
           + +P  EA K++ V+  +W    R+G+ R DA+V +GGGA TD+AGFAAA+WLRGV  V 
Sbjct: 66  LPVPSGEAAKEIGVLAGLWSDFARLGVTRSDAVVGVGGGATTDLAGFAAASWLRGVRAVL 125

Query: 129 LPTTLLGMVDAAVGGKTGINTDAGKNLVGAFHQPLAVLVDLATLQTLPRDEMICGMAEVV 188
           +PTTLLGMVDAAVGGKTGIN   GKNLVGAFH P  VL +L+ L T+P  + I G+AEV+
Sbjct: 126 VPTTLLGMVDAAVGGKTGINIAEGKNLVGAFHPPSGVLCELSALATMPHQDYISGLAEVI 185

Query: 189 KAGFIADPVILDLIEADPQAALDPAGDVLPELIRRAITVKAEVVAADEKESELREILNYG 248
           KAGFIADP IL+L+EADP  A  P G    EL+ RA+ VKAEVV+AD +ES LREILNYG
Sbjct: 186 KAGFIADPKILELVEADPAGAASPTGTHTRELVERAVRVKAEVVSADLRESGLREILNYG 245

Query: 249 HTLGHAIERRERYRWRHGAAVSVGLVFAAELARLAGRLDDATAQRHRTILSSLGLPVSYD 308
           HTLGHAIE+ E YR+RHG AV++G+V+AAELARL GRLD AT +RHRT+L+S+GLP  Y 
Sbjct: 246 HTLGHAIEKAEDYRFRHGHAVAIGMVYAAELARLTGRLDAATVERHRTVLTSVGLPTGYR 305

Query: 309 PDALPQLLEIMAGDKKTRAGVLRFVVLDGLAKPGRMVGPDPGLLVTAY 356
            DA P L E M  DKK R   LR VVLDGLA+PGR+ GP   LL  AY
Sbjct: 306 ADAWPALREGMRVDKKARGATLRLVVLDGLARPGRLEGPADELLAAAY 353


Lambda     K      H
   0.320    0.139    0.406 

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: 414
Number of extensions: 9
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: 362
Length of database: 358
Length adjustment: 29
Effective length of query: 333
Effective length of database: 329
Effective search space:   109557
Effective search space used:   109557
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: 49 (23.5 bits)

Align candidate WP_012853277.1 TCUR_RS14550 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

# 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/TIGR01357.hmm
# target sequence database:        /tmp/gapView.891458.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01357  [M=344]
Accession:   TIGR01357
Description: aroB: 3-dehydroquinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.5e-106  340.0   0.0   9.9e-106  339.7   0.0    1.0  1  NCBI__GCF_000024385.1:WP_012853277.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000024385.1:WP_012853277.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.7   0.0  9.9e-106  9.9e-106       1     328 [.      14     338 ..      14     352 .. 0.94

  Alignments for each domain:
  == domain 1  score: 339.7 bits;  conditional E-value: 9.9e-106
                             TIGR01357   1 ykvkvgegllkklveelaekasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklld 73 
                                           y+v++g+g+l++l   l ek +++ v++de++ + +a  + +al+++g+++  l vp+ge +K++ ++a l++
  NCBI__GCF_000024385.1:WP_012853277.1  14 YEVVIGTGVLEELPGLLGEKVRTVAVVHDEALPE-IAGPVCKALEEAGYTACPLPVPSGEAAKEIGVLAGLWS 85 
                                           689***************9666666666666655.667777777788************************** PP

                             TIGR01357  74 qlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyq 146
                                             ++ +++r++++v++GGG+ +DlaGF+Aa++lRG+r v vPTtll+mvD++vGGKtgin ++gkNl+Gaf+ 
  NCBI__GCF_000024385.1:WP_012853277.1  86 DFARLGVTRSDAVVGVGGGATTDLAGFAAASWLRGVRAVLVPTTLLGMVDAAVGGKTGINIAEGKNLVGAFHP 158
                                           ************************************************************************* PP

                             TIGR01357 147 PkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVe 219
                                           P+ Vl++l+ l+t+p++ +++G+aEviK g+iad +++e +e   +    + +  +++el++r+++vKaevV+
  NCBI__GCF_000024385.1:WP_012853277.1 159 PSGVLCELSALATMPHQDYISGLAEVIKAGFIADPKILELVEADPAGAA-SPTGTHTRELVERAVRVKAEVVS 230
                                           ******************************************9888555.5678******************* PP

                             TIGR01357 220 eDekesglRalLNfGHtlgHaiEallkyklsHGeaVaiGmvveaklseklgllkaellerlvallkklglptk 292
                                           +D +esglR++LN+GHtlgHaiE++ +y+++HG+aVaiGmv++a+l++ +g l+a  +er++++l ++glpt 
  NCBI__GCF_000024385.1:WP_012853277.1 231 ADLRESGLREILNYGHTLGHAIEKAEDYRFRHGHAVAIGMVYAAELARLTGRLDAATVERHRTVLTSVGLPTG 303
                                           ************************************************************************* PP

                             TIGR01357 293 lkkklsveellkallkDKKnegskiklvlleeiGka 328
                                           ++   +  +l + +  DKK++g +++lv+l+ ++++
  NCBI__GCF_000024385.1:WP_012853277.1 304 YRA-DAWPALREGMRVDKKARGATLRLVVLDGLARP 338
                                           **7.8999**********************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (358 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: 23.92
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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