Alignments for a candidate for thrC in Thermomonospora curvata DSM 43183

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Thermomonospora curvata DSM 43183

Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_012851176.1 TCUR_RS03920 threonine synthase

Query= curated2:Q58860
         (405 letters)



>NCBI__GCF_000024385.1:WP_012851176.1
          Length = 413

 Score =  254 bits (650), Expect = 2e-72
 Identities = 143/381 (37%), Positives = 223/381 (58%), Gaps = 12/381 (3%)

Query: 5   CIKCGKTYDVDEIIYTCE-CGGLLEIIYDYEEIKDKVSEEKLRKREIGVWRYLEYLPVKD 63
           C +CG++Y++    Y CE C G LEI YD+      V+ E +      +WRY   LPV  
Sbjct: 16  CRECGQSYELGPR-YACEQCFGPLEIAYDFAG----VTRESIESGPRNIWRYRGLLPVPA 70

Query: 64  ESKIVSLCEGG-TPLYRCNNLEKELGIKELYVKNEGANPTGSFKDRGMTVGVTRANELGV 122
             +     E G T L R ++L + LG+++L+VK++  NPT SFKDR + V +  A ELG 
Sbjct: 71  NVESTPNTEPGFTRLVRADHLAESLGMQKLWVKDDSGNPTHSFKDRVVAVALAAARELGF 130

Query: 123 EVVGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDDA 182
           +V+ C STGN + ++AA +AR+G +  V +P   +   K+     YG   + V+GN+DD 
Sbjct: 131 KVLACPSTGNLANAVAAAAARAGIRSAVFVP-ADLEQQKIITTAVYGGTFVTVRGNYDDV 189

Query: 183 LDMVKQLAKEKLIYLLNSIN--PFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNISA 240
             +  ++A E+  +   ++N  P+  EG KT+ +EI +QL W++PD++++PV +   ++ 
Sbjct: 190 NRLASEIAGEQEDWAFVNVNVRPYYAEGSKTLGYEIAEQLGWRLPDQIVIPVASGSQLTK 249

Query: 241 IWKGFKEFEITGIIDELP-KMTGIQADGAKPIVEAFRKRAKDIIPYKNPETIATAIRIGN 299
           I K F+EF   G++++ P K+ G QA G  P+  AF K   D++    P+TIA ++ IGN
Sbjct: 250 IDKAFQEFIKLGLVEDKPYKVFGAQATGCSPVAAAF-KAGHDVVRPVKPDTIAKSLAIGN 308

Query: 300 PVNAPKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLEEGI 359
           P + P  LD +  +GG  E V+D E+VE  +LLA  EGIF E A   ++A L+KL+  G 
Sbjct: 309 PADGPYVLDVVRRTGGAVEDVSDPEVVEGIRLLAATEGIFAETAGGVTVACLRKLIASGA 368

Query: 360 IDRDERIVCITTGHGLKDPDA 380
           +D +   V I +G GLK  DA
Sbjct: 369 LDPEAETVIINSGDGLKTLDA 389


Lambda     K      H
   0.317    0.137    0.395 

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: 455
Number of extensions: 27
Number of successful extensions: 7
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: 405
Length of database: 413
Length adjustment: 31
Effective length of query: 374
Effective length of database: 382
Effective search space:   142868
Effective search space used:   142868
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: 50 (23.9 bits)

Align candidate WP_012851176.1 TCUR_RS03920 (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.28986.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.1e-87  280.3   0.0    1.3e-87  280.1   0.0    1.0  1  lcl|NCBI__GCF_000024385.1:WP_012851176.1  TCUR_RS03920 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024385.1:WP_012851176.1  TCUR_RS03920 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.1   0.0   1.3e-87   1.3e-87       1     339 [.      59     387 ..      59     388 .. 0.97

  Alignments for each domain:
  == domain 1  score: 280.1 bits;  conditional E-value: 1.3e-87
                                 TIGR00260   1 vvryreilevt..ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltk 67 
                                               ++ryr +l+v+   +   + + g+t+l+r+++lae +g+++l+vk+++ +Pt +FKDr+   vav+l++
  lcl|NCBI__GCF_000024385.1:WP_012851176.1  59 IWRYRGLLPVPanVESTPNTEPGFTRLVRADHLAESLGMQKLWVKDDSGNPTHSFKDRV---VAVALAA 124
                                               8*********9644445567889************************************...******* PP

                                 TIGR00260  68 alelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDda 136
                                               a+elg ++++c ++G++++a+a a a++a+++  v++P++ ++  ++k++t+ +++ + + ++G++Dd+
  lcl|NCBI__GCF_000024385.1:WP_012851176.1 125 ARELGFKVLACPSTGNLANAVA-AAAARAGIRSAVFVPAD-LE--QQKIITTAVYGGTFVTVRGNYDDV 189
                                               **********************.*****************.99..************************ PP

                                 TIGR00260 137 qdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflek 204
                                               ++l  ei++++e + +++vN + p++ e++kt+ +ei+eqlg++ pd++v+pv+ ++ +++i k+f+e+
  lcl|NCBI__GCF_000024385.1:WP_012851176.1 190 NRLASEIAGEQEDWAFVNVN-VRPYYAEGSKTLGYEIAEQLGWRLPDQIVIPVAsGSQLTKIDKAFQEF 257
                                               ********************.55*******************************7789*********** PP

                                 TIGR00260 205 kelg....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnl 269
                                                +lg    +p +  +++a+g+++++ +f+ + d++   +++T++++++ignp++ +++l+++rr++g +
  lcl|NCBI__GCF_000024385.1:WP_012851176.1 258 IKLGlvedKPYKVFGAQATGCSPVAAAFKAGHDVVRPVKPDTIAKSLAIGNPADGPYVLDVVRRTGGAV 326
                                               ********9*9*****************9888************************************* PP

                                 TIGR00260 270 edlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkd 338
                                               ed+    sd e++e i++la++eg+++e++++v+va l+kl+++g    +dp+  +e+v + +g +lk+
  lcl|NCBI__GCF_000024385.1:WP_012851176.1 327 EDV----SDPEVVEGIRLLAATEGIFAETAGGVTVACLRKLIASG---ALDPE--AETVIINSGDGLKT 386
                                               ***....**************************************...*****..******9**99997 PP

                                 TIGR00260 339 p 339
                                                
  lcl|NCBI__GCF_000024385.1:WP_012851176.1 387 L 387
                                               5 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (413 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: 8.17
//
[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