GapMind for Amino acid biosynthesis

 

Alignments for a candidate for thrC in Pontibacter ramchanderi LP43

Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_101443628.1 BD749_RS05135 threonine synthase

Query= curated2:Q58860
         (405 letters)



>NCBI__GCF_002846395.1:WP_101443628.1
          Length = 400

 Score =  234 bits (596), Expect = 4e-66
 Identities = 136/378 (35%), Positives = 209/378 (55%), Gaps = 11/378 (2%)

Query: 5   CIKCGKTYDVDE--IIYTCECGGLLEIIYDYEEIKDKVSEEKLRKREIGVWRYLEYLPVK 62
           C  CG  Y   E   +  C C   L   Y  + + +K   E L  RE  +WRYLE LPV 
Sbjct: 17  CSNCGALYSPFEKQTVSAC-CQMPLLAGYAPDVLPEK---EALLTREGTMWRYLEMLPVL 72

Query: 63  DESKIVSLCEGGTPLYRCNNLEKELGIKELYVKNEGANPTGSFKDRGMTVGVTRANELGV 122
            +  IVSL EG TP+ +  NL ++  ++ L +K+EG NPTGSFK RG+++ +++A E GV
Sbjct: 73  HKENIVSLGEGYTPILQLANLARKYELRSLLLKDEGQNPTGSFKARGLSMAISKAKEHGV 132

Query: 123 EVVGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDDA 182
           E     + GN   ++AAY A++G +  V++P       +  +  +YGA+V+QV G  +D 
Sbjct: 133 EGCIIPTAGNAGVAMAAYCAKAGMRATVVMPRHTPKAFR-DECYWYGAEVVQVDGLINDC 191

Query: 183 LDMVKQL-AKEKLIYLLNSINPFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNISAI 241
              VK+L    +L+ +     P+RLEG+KT+ +EI +Q NWQ+PD ++ P G    +  I
Sbjct: 192 AAKVKELNTAGELLDVSTLKEPYRLEGKKTMGYEIAEQGNWQLPDVILYPAGGGTGLIGI 251

Query: 242 WKGFKEFEITGIIDE---LPKMTGIQADGAKPIVEAFRKRAKDIIPYKNPETIATAIRIG 298
           WK F+E +  G + E   LP+M  +QA+  +P+VE F  R  +   Y    TIA  + + 
Sbjct: 252 WKAFREMKKIGWLPEDAKLPRMVAVQAENCRPLVETFYGRQANAQNYMGKPTIANGLAVP 311

Query: 299 NPVNAPKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLEEG 358
            P+     L  +  SGG A +++++E++   K L   EG+FV P  A+     +KLL+ G
Sbjct: 312 RPLGEQLMLQTLQESGGTAISISEQEMITGLKELGSSEGLFVAPEGAAVWMAARKLLDTG 371

Query: 359 IIDRDERIVCITTGHGLK 376
            I  DE I+ + TG G K
Sbjct: 372 FIQYDEEILLLNTGSGQK 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: 442
Number of extensions: 19
Number of successful extensions: 4
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: 400
Length adjustment: 31
Effective length of query: 374
Effective length of database: 369
Effective search space:   138006
Effective search space used:   138006
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_101443628.1 BD749_RS05135 (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.1142866.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-54  171.8   0.0    1.3e-54  171.6   0.0    1.0  1  NCBI__GCF_002846395.1:WP_101443628.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002846395.1:WP_101443628.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.6   0.0   1.3e-54   1.3e-54       1     337 [.      62     389 ..      62     392 .. 0.95

  Alignments for each domain:
  == domain 1  score: 171.6 bits;  conditional E-value: 1.3e-54
                             TIGR00260   1 vvryreilevt.ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelg 72 
                                           ++ry e+l+v  ++++v+l eg t+ ++  +la++ +++ l +k+++ +Pt++FK rg   ++++++ka+e+g
  NCBI__GCF_002846395.1:WP_101443628.1  62 MWRYLEMLPVLhKENIVSLGEGYTPILQLANLARKYELRSLLLKDEGQNPTGSFKARG---LSMAISKAKEHG 131
                                           69*********9**********************************************...************ PP

                             TIGR00260  73 netvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeife 145
                                           +e  +  t G+ g a+a a+ +ka++++ v++P+  +   k        ++a+v++++G   d+ + vke+  
  NCBI__GCF_002846395.1:WP_101443628.1 132 VEGCIIPTAGNAGVAMA-AYCAKAGMRATVVMPRH-TP--KAFRDECYWYGAEVVQVDGLINDCAAKVKELNT 200
                                           *****************.****************9.44..3333456789*********************** PP

                             TIGR00260 146 dkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekkelg.......lp 210
                                             e l ++      p+r+e++kt+ +ei+eq +++ pd +  p + +  +  i+k+f e+k+ g       lp
  NCBI__GCF_002846395.1:WP_101443628.1 201 AGELLDVSTLK--EPYRLEGKKTMGYEIAEQGNWQLPDVILYPAGgGTGLIGIWKAFREMKKIGwlpedakLP 271
                                           ********999..9*******************************7667889********************* PP

                             TIGR00260 211 ieklaiaaegaadivrrflksg.dlepkedkeTlstAmdignpsnveralelarrslgnledlkesvsdeeil 282
                                            ++ a++ae++ + v+ f  ++ + +++  k T+++ +++ +p   + +l+  ++s+g + ++    s++e++
  NCBI__GCF_002846395.1:WP_101443628.1 272 -RMVAVQAENCRPLVETFYGRQaNAQNYMGKPTIANGLAVPRPLGEQLMLQTLQESGGTAISI----SEQEMI 339
                                           .*****************9998899999999****************************9999....****** PP

                             TIGR00260 283 eaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklk 337
                                              k+l  +eg+++ p +a+   a +kl++ g    ++++  ee+ +  tg ++k
  NCBI__GCF_002846395.1:WP_101443628.1 340 TGLKELGSSEGLFVAPEGAAVWMAARKLLDTG---FIQYD--EEILLLNTGSGQK 389
                                           ******************************99...99999..9988888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (400 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 17.70
//
[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