GapMind for Amino acid biosynthesis

 

Alignments for a candidate for thrC in Lentibacillus jeotgali Grbi

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_010529190.1 ON01_RS01240 threonine synthase

Query= BRENDA::O66740
         (352 letters)



>NCBI__GCF_000224785.1:WP_010529190.1
          Length = 353

 Score =  413 bits (1062), Expect = e-120
 Identities = 207/340 (60%), Positives = 262/340 (77%), Gaps = 4/340 (1%)

Query: 4   WQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSFK 63
           WQG+I+ Y+  LPV + TP ++L EGNT LI    L+  +G +  +Y K EG NPTGSFK
Sbjct: 3   WQGLIRHYQSNLPVTDRTPEISLQEGNTSLIHFSTLSEQLGIE--LYGKVEGANPTGSFK 60

Query: 64  DRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQAM 123
           DRGM LA++KA+E G  AVICASTGNTSASAAAYAARAG+RA +++PKG +A+GKL+QA+
Sbjct: 61  DRGMALAVAKAIEEGSNAVICASTGNTSASAAAYAARAGIRAIIVIPKGKIALGKLAQAV 120

Query: 124 IYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPDY 183
           +YGA ++ I G FDDAL IVRKI E  PV +VNSVNPYR+EGQKTAAFE+CD LG APD 
Sbjct: 121 MYGADIVEIDGNFDDALKIVRKISETAPVTLVNSVNPYRLEGQKTAAFEVCDVLGSAPDI 180

Query: 184 HFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIATAI 243
             IPVGNAGNI+AYWKGFK Y+E  K T LP+M G++AEGAA IV    ++NP+TIATAI
Sbjct: 181 LAIPVGNAGNISAYWKGFKEYHEM-KQTGLPQMFGFEAEGAAAIVGNEVVQNPETIATAI 239

Query: 244 KIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLIKLV 303
           +IGNP SWK A++A  ESGGKI +V+D+EI +A KL+A+ EGVF EP S AS+AG+I+  
Sbjct: 240 RIGNPASWKLAVQARDESGGKIGSVTDTEIAHAQKLLATQEGVFAEPGSCASIAGIIQQR 299

Query: 304 REGFFKGGEVVTCTLTGNGLKDPDTAI-KVCEEPITVPPD 342
           ++     G  V   LTGNGLKDP TAI ++ ++P+T+P D
Sbjct: 300 KQNTITEGSKVAAVLTGNGLKDPQTAIDQIDQDPVTLPND 339


Lambda     K      H
   0.317    0.136    0.400 

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: 453
Number of extensions: 15
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 352
Length of database: 353
Length adjustment: 29
Effective length of query: 323
Effective length of database: 324
Effective search space:   104652
Effective search space used:   104652
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_010529190.1 ON01_RS01240 (threonine synthase)
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))

# 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/TIGR00260.hmm
# target sequence database:        /tmp/gapView.296022.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00260  [M=340]
Accession:   TIGR00260
Description: thrC: threonine 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    6.3e-99  317.3   0.7    7.3e-99  317.1   0.7    1.0  1  NCBI__GCF_000224785.1:WP_010529190.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010529190.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.1   0.7   7.3e-99   7.3e-99       2     339 ..       8     322 ..       7     323 .. 0.97

  Alignments for each domain:
  == domain 1  score: 317.1 bits;  conditional E-value: 7.3e-99
                             TIGR00260   2 vryreilevt.ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgn 73 
                                             y++ l+vt  ++ ++l+eg+t+l+++ +l+e++g+ +ly k ++++Pt++FKDrg   +a +++ka e+g 
  NCBI__GCF_000224785.1:WP_010529190.1   8 RHYQSNLPVTdRTPEISLQEGNTSLIHFSTLSEQLGI-ELYGKVEGANPTGSFKDRG---MALAVAKAIEEGS 76 
                                           579999****999************************.*******************...************* PP

                             TIGR00260  74 etvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifed 146
                                           ++v+cA++G+t+a+aa a+a++a++++++++Pkgki+   +kl++a++++a +++i+G+FDda+++v++i e 
  NCBI__GCF_000224785.1:WP_010529190.1  77 NAVICASTGNTSASAA-AYAARAGIRAIIVIPKGKIA--LGKLAQAVMYGADIVEIDGNFDDALKIVRKISET 146
                                           ****************.********************..********************************99 PP

                             TIGR00260 147 keklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekkelg...lpiekla 215
                                            + +++nsvN   p+r+e+qkt+afe+++ lg  +pd +++pv+ +gn++a++kGf+e++e+    lp ++ +
  NCBI__GCF_000224785.1:WP_010529190.1 147 APVTLVNSVN---PYRLEGQKTAAFEVCDVLG-SAPDILAIPVGnAGNISAYWKGFKEYHEMKqtgLP-QMFG 214
                                           9999998888...*******************.9**********************9987665555**.**** PP

                             TIGR00260 216 iaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnledlkesvsdeeileaikkl 288
                                           ++aegaa iv +          +++eT++tA++ignp++++ a+++  +s+g++ ++    +d ei +a+k+l
  NCBI__GCF_000224785.1:WP_010529190.1 215 FEAEGAAAIVGNE-------VVQNPETIATAIRIGNPASWKLAVQARDESGGKIGSV----TDTEIAHAQKLL 276
                                           ******9999988.......7899*********************************....************ PP

                             TIGR00260 289 aeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdp 339
                                           a +eg+++ep +++++a+++++ +++   t+ ++  ++v ++ltgn+lkdp
  NCBI__GCF_000224785.1:WP_010529190.1 277 ATQEGVFAEPGSCASIAGIIQQRKQN---TITEG--SKVAAVLTGNGLKDP 322
                                           **************************...*****..99999********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (353 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: 21.51
//
[ok]

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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