Alignments for a candidate for thrC in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Synechococcus elongatus PCC 7942

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate Synpcc7942_2612 Synpcc7942_2612 threonine synthase

Query= BRENDA::O66740
         (352 letters)



>FitnessBrowser__SynE:Synpcc7942_2612
          Length = 366

 Score =  428 bits (1101), Expect = e-124
 Identities = 211/351 (60%), Positives = 271/351 (77%), Gaps = 4/351 (1%)

Query: 4   WQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSFK 63
           W G+I+ Y+ YLPV + TPIVTL+EGNTPLI    +AR IG   ++++KY+GLNPTGSFK
Sbjct: 18  WPGLIEAYRDYLPVTDTTPIVTLHEGNTPLIPVPTIAREIGRGVEVFVKYDGLNPTGSFK 77

Query: 64  DRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQAM 123
           DRGMT+AI+KA EAG +AVICASTGNTSA+AAAYA R GLRA+VL+P G VA GKL+QA+
Sbjct: 78  DRGMTMAITKAKEAGAKAVICASTGNTSAAAAAYARRGGLRAFVLIPDGFVAQGKLAQAL 137

Query: 124 IYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPDY 183
           +YGA+VLAI+G FD AL IVR++   +PV +VNS+NPYR+EGQKTAAFE+ D LGEAPD+
Sbjct: 138 LYGAEVLAIKGNFDRALEIVREVANQYPVTLVNSLNPYRLEGQKTAAFELIDVLGEAPDW 197

Query: 184 HFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIATAI 243
             IP+GNAGNI+AYW GF+ Y+ +G   KLPRMMG+QA G+AP+V G  +++P TIATAI
Sbjct: 198 LCIPMGNAGNISAYWMGFQEYHAKGLSQKLPRMMGFQAAGSAPLVTGEIVQSPDTIATAI 257

Query: 244 KIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLIKLV 303
           +IGNP +W+ AL+  +ES G  +AV+D+EIL AY+++A  EG+FCEPASAASVAG++K  
Sbjct: 258 RIGNPANWQRALRVHEESNGAFNAVTDAEILDAYRMLAGQEGIFCEPASAASVAGMLKCK 317

Query: 304 REGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEPIT--VPPDFDEVVKVLGF 352
            E     G  + C LTGNGLKDP +AI+         + PD D V   +GF
Sbjct: 318 DE--IPDGATIVCVLTGNGLKDPSSAIEFSHTGFKAGIEPDLDIVAHTMGF 366


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: 475
Number of extensions: 18
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: 352
Length of database: 366
Length adjustment: 29
Effective length of query: 323
Effective length of database: 337
Effective search space:   108851
Effective search space used:   108851
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 Synpcc7942_2612 Synpcc7942_2612 (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.32031.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-104  336.0   0.0   1.5e-104  335.8   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2612  Synpcc7942_2612 threonine syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2612  Synpcc7942_2612 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.8   0.0  1.5e-104  1.5e-104       1     339 [.      22     338 ..      22     339 .. 0.96

  Alignments for each domain:
  == domain 1  score: 335.8 bits;  conditional E-value: 1.5e-104
                                 TIGR00260   1 vvryreilevt.ekdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltk 67 
                                               ++ yr +l+vt  +++v+l+eg+t+l+ +p++a+e+g   +++vk ++++Pt++FKDrg   +++++tk
  lcl|FitnessBrowser__SynE:Synpcc7942_2612  22 IEAYRDYLPVTdTTPIVTLHEGNTPLIPVPTIAREIGRgVEVFVKYDGLNPTGSFKDRG---MTMAITK 87 
                                               6789*******99*************************9********************...******* PP

                                 TIGR00260  68 alelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDda 136
                                               a+e+g+++v+cA++G+t+aaaa a+a++ +++++vL+P+g ++  ++kl++al ++a+vlaikG+FD a
  lcl|FitnessBrowser__SynE:Synpcc7942_2612  88 AKEAGAKAVICASTGNTSAAAA-AYARRGGLRAFVLIPDGFVA--QGKLAQALLYGAEVLAIKGNFDRA 153
                                               **********************.********************..************************ PP

                                 TIGR00260 137 qdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflek 204
                                               +++v+e++++ + +++ns N   p+r+e+qkt+afe+++ lg e+pd++++p++ +gn++a+++Gf+e+
  lcl|FitnessBrowser__SynE:Synpcc7942_2612 154 LEIVREVANQYPVTLVNSLN---PYRLEGQKTAAFELIDVLG-EAPDWLCIPMGnAGNISAYWMGFQEY 218
                                               ********776666666666...*******************.************************** PP

                                 TIGR00260 205 kelg....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnl 269
                                               + +g    lp ++++++a g+a+ v+           ++++T++tA++ignp+n++ral++ ++s+g +
  lcl|FitnessBrowser__SynE:Synpcc7942_2612 219 HAKGlsqkLP-RMMGFQAAGSAPLVTGE-------IVQSPDTIATAIRIGNPANWQRALRVHEESNGAF 279
                                               **********.**********9999987.......56789***************************** PP

                                 TIGR00260 270 edlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkd 338
                                               +++    +d+eil+a++ la +eg+++ep++a++va+++k  +     +++ +  +++v++ltgn+lkd
  lcl|FitnessBrowser__SynE:Synpcc7942_2612 280 NAV----TDAEILDAYRMLAGQEGIFCEPASAASVAGMLKCKD-----EIPDG--ATIVCVLTGNGLKD 337
                                               ***....*********************************987.....78999..*************9 PP

                                 TIGR00260 339 p 339
                                               p
  lcl|FitnessBrowser__SynE:Synpcc7942_2612 338 P 338
                                               8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (366 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: 8.69
//
[ok]

This GapMind analysis is from Apr 09 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