Alignments for a candidate for thrC in Sulfurivirga caldicuralii DSM 17737

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Sulfurivirga caldicuralii DSM 17737

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_074201260.1 BUQ81_RS04885 threonine synthase

Query= BRENDA::O66740
         (352 letters)



>NCBI__GCF_900141795.1:WP_074201260.1
          Length = 359

 Score =  412 bits (1060), Expect = e-120
 Identities = 199/350 (56%), Positives = 268/350 (76%), Gaps = 2/350 (0%)

Query: 3   RWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSF 62
           R+ G+I++Y+  LPV ++T I++L EGNTPLI  +++ R +G    IY+KYEGLNPTGSF
Sbjct: 6   RYTGLIEKYRDRLPVHDDTRIISLGEGNTPLIRLNHIPRQLGKDVDIYVKYEGLNPTGSF 65

Query: 63  KDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQA 122
           KDRGMT+A++KAV+ G +A+ICASTGNTSA+AAAYAARAG+RA+VL+P G +A+GKL+QA
Sbjct: 66  KDRGMTMAVTKAVDEGAKAIICASTGNTSAAAAAYAARAGIRAFVLIPDGKIAMGKLAQA 125

Query: 123 MIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPD 182
           +++GA V+ I+G FDD + +V+++ ++ PV IVNS+NP R++GQKTAAFEI + LG APD
Sbjct: 126 LMHGAVVIQIKGNFDDGMRLVKEVADHAPVTIVNSINPNRLQGQKTAAFEIIEELGRAPD 185

Query: 183 YHFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIATA 242
           YH +PVGNAGNITA+W G+  YY +G +   PRM+G+QA G+AP VKG  + NP+T+ATA
Sbjct: 186 YHCLPVGNAGNITAHWMGYDEYYRDGIVGTRPRMVGYQASGSAPFVKGEMVDNPETVATA 245

Query: 243 IKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLIKL 302
           I+IG+P SW+ A    +ES G  DA SD EIL A KL+A  EGVFCEPASA SVAG ++ 
Sbjct: 246 IRIGHPQSWELAWNLQKESNGWFDACSDEEILAAQKLLAQAEGVFCEPASATSVAGAMRD 305

Query: 303 VREGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEP--ITVPPDFDEVVKVL 350
           ++ G    G  V CTLTG+GLKDPDTAI    +   +TV  + DEV + +
Sbjct: 306 IQNGKIPEGSTVVCTLTGHGLKDPDTAIAQSADTKVVTVAAEMDEVRRAI 355


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: 411
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: 359
Length adjustment: 29
Effective length of query: 323
Effective length of database: 330
Effective search space:   106590
Effective search space used:   106590
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_074201260.1 BUQ81_RS04885 (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.14778.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.8e-100  320.7   0.0     7e-100  320.4   0.0    1.1  1  lcl|NCBI__GCF_900141795.1:WP_074201260.1  BUQ81_RS04885 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900141795.1:WP_074201260.1  BUQ81_RS04885 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.4   0.0    7e-100    7e-100       1     340 []      11     330 ..      11     330 .. 0.97

  Alignments for each domain:
  == domain 1  score: 320.4 bits;  conditional E-value: 7e-100
                                 TIGR00260   1 vvryreilevt.ekdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltk 67 
                                               +++yr  l+v  ++++++l eg+t+l+r +++++++g+  ++yvk ++++Pt++FKDrg   +++++tk
  lcl|NCBI__GCF_900141795.1:WP_074201260.1  11 IEKYRDRLPVHdDTRIISLGEGNTPLIRLNHIPRQLGKdVDIYVKYEGLNPTGSFKDRG---MTMAVTK 76 
                                               689***********************************9********************...******* PP

                                 TIGR00260  68 alelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDda 136
                                               a ++g+++++cA++G+t+aaaa a+a++a+++++vL+P+gki+   +kl++al+++a v++ikG+FDd 
  lcl|NCBI__GCF_900141795.1:WP_074201260.1  77 AVDEGAKAIICASTGNTSAAAA-AYAARAGIRAFVLIPDGKIA--MGKLAQALMHGAVVIQIKGNFDDG 142
                                               **********************.********************..************************ PP

                                 TIGR00260 137 qdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflek 204
                                                +lvke++++ + + +ns+N   p r+++qkt+afei+e+lg ++pd  ++pv+ +gn++a ++G+ e+
  lcl|NCBI__GCF_900141795.1:WP_074201260.1 143 MRLVKEVADHAPVTIVNSIN---PNRLQGQKTAAFEIIEELG-RAPDYHCLPVGnAGNITAHWMGYDEY 207
                                               ********998877777777...*******************.9************************* PP

                                 TIGR00260 205 kelg....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnl 269
                                                + g    +p ++ + +a g+a++v+            ++eT++tA++ig+p ++e a++l ++s+g +
  lcl|NCBI__GCF_900141795.1:WP_074201260.1 208 YRDGivgtRP-RMVGYQASGSAPFVKGE-------MVDNPETVATAIRIGHPQSWELAWNLQKESNGWF 268
                                               ***9999999.**********9999877.......67889***************************** PP

                                 TIGR00260 270 edlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkd 338
                                               ++     sdeeil a+k+la+ eg+++ep++a++va+  + +++g   +++++  ++vv+ ltg++lkd
  lcl|NCBI__GCF_900141795.1:WP_074201260.1 269 DAC----SDEEILAAQKLLAQAEGVFCEPASATSVAGAMRDIQNG---KIPEG--STVVCTLTGHGLKD 328
                                               *99....**************************************...*****..************** PP

                                 TIGR00260 339 pe 340
                                               p+
  lcl|NCBI__GCF_900141795.1:WP_074201260.1 329 PD 330
                                               97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (359 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: 10.89
//
[ok]

This GapMind analysis is from Apr 10 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