Alignments for a candidate for thrC in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Dyella japonica UNC79MFTsu3.2

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate N515DRAFT_0575 N515DRAFT_0575 threonine synthase

Query= reanno::Dyella79:N515DRAFT_0575
         (441 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0575
          Length = 441

 Score =  892 bits (2306), Expect = 0.0
 Identities = 441/441 (100%), Positives = 441/441 (100%)

Query: 1   MSEPLLYHSTRGAAHGAGIGEAIAAGLAPDGGLYVPEALPSRRPDDFDPDGTLADTAARL 60
           MSEPLLYHSTRGAAHGAGIGEAIAAGLAPDGGLYVPEALPSRRPDDFDPDGTLADTAARL
Sbjct: 1   MSEPLLYHSTRGAAHGAGIGEAIAAGLAPDGGLYVPEALPSRRPDDFDPDGTLADTAARL 60

Query: 61  LRPFFAGHALAAELPAICAEAFCFDAPLRPLPQHPGAAMLELFHGPSAAFKDFGARFLAS 120
           LRPFFAGHALAAELPAICAEAFCFDAPLRPLPQHPGAAMLELFHGPSAAFKDFGARFLAS
Sbjct: 61  LRPFFAGHALAAELPAICAEAFCFDAPLRPLPQHPGAAMLELFHGPSAAFKDFGARFLAS 120

Query: 121 CFRRLRKAGEAPLTILVATSGDTGAAVAAAFHRQPGVEVVILYPDGLVSPRQAHQLGCFG 180
           CFRRLRKAGEAPLTILVATSGDTGAAVAAAFHRQPGVEVVILYPDGLVSPRQAHQLGCFG
Sbjct: 121 CFRRLRKAGEAPLTILVATSGDTGAAVAAAFHRQPGVEVVILYPDGLVSPRQAHQLGCFG 180

Query: 181 DNVRALRVAGRFDDCQRMVKAALNDTALQAQRPLSSANSISLGRLLPQMAYYAHASLRWW 240
           DNVRALRVAGRFDDCQRMVKAALNDTALQAQRPLSSANSISLGRLLPQMAYYAHASLRWW
Sbjct: 181 DNVRALRVAGRFDDCQRMVKAALNDTALQAQRPLSSANSISLGRLLPQMAYYAHASLRWW 240

Query: 241 REHRRPLNFIVPTGNLGNALAAVWVREMGLPVGAIELACNANETLPDYFAGTPYAPRAAV 300
           REHRRPLNFIVPTGNLGNALAAVWVREMGLPVGAIELACNANETLPDYFAGTPYAPRAAV
Sbjct: 241 REHRRPLNFIVPTGNLGNALAAVWVREMGLPVGAIELACNANETLPDYFAGTPYAPRAAV 300

Query: 301 ATLANAMDVGAPSNFERLRWTFPYDDDLRGQLSSHSVDDDTIRATVRRHALEHGEVFCPH 360
           ATLANAMDVGAPSNFERLRWTFPYDDDLRGQLSSHSVDDDTIRATVRRHALEHGEVFCPH
Sbjct: 301 ATLANAMDVGAPSNFERLRWTFPYDDDLRGQLSSHSVDDDTIRATVRRHALEHGEVFCPH 360

Query: 361 TATAMHRLDLRQEKADWAVVSTAHAAKFESVVEPLIGRGVAVPPALQAMLARPAQAEAIE 420
           TATAMHRLDLRQEKADWAVVSTAHAAKFESVVEPLIGRGVAVPPALQAMLARPAQAEAIE
Sbjct: 361 TATAMHRLDLRQEKADWAVVSTAHAAKFESVVEPLIGRGVAVPPALQAMLARPAQAEAIE 420

Query: 421 ASDDALKQWLLPQPAHVRRLG 441
           ASDDALKQWLLPQPAHVRRLG
Sbjct: 421 ASDDALKQWLLPQPAHVRRLG 441


Lambda     K      H
   0.322    0.136    0.420 

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: 937
Number of extensions: 23
Number of successful extensions: 1
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: 441
Length of database: 441
Length adjustment: 32
Effective length of query: 409
Effective length of database: 409
Effective search space:   167281
Effective search space used:   167281
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate N515DRAFT_0575 N515DRAFT_0575 (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.2124.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-69  220.9   0.0    1.6e-69  220.6   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0575  N515DRAFT_0575 threonine synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0575  N515DRAFT_0575 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.6   0.0   1.6e-69   1.6e-69      42     335 ..      99     399 ..      71     403 .. 0.87

  Alignments for each domain:
  == domain 1  score: 220.6 bits;  conditional E-value: 1.6e-69
                                    TIGR00260  42 vkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaaealagkanvkvvvLyP 105
                                                  ++elfhgP+ aFKD+g +f+a+ + +++++g++  t+l+AtsGdtgaa+a a+ ++++v+vv+LyP
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0575  99 MLELFHGPSAAFKDFGARFLASCFRRLRKAGEAplTILVATSGDTGAAVAAAFHRQPGVEVVILYP 164
                                                  789*************************************************************** PP

                                    TIGR00260 106 kgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsinparieaqk. 167
                                                  +g +sp +   +     n++ l + G FDd+q++vk++++d     +  l+s+Nsi  +r++ q+ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0575 165 DGLVSPRQAHQLGCFGDNVRALRVAGRFDDCQRMVKAALNDTAlqaQRPLSSANSISLGRLLPQMa 230
                                                  *******5555566899**********************9666666999****************5 PP

                                    TIGR00260 168 tyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksgd 233
                                                  +ya+  +     e++  + + vp gn+g++l++    + +glp+  +  a + + ++++ +  +  
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0575 231 YYAHASLRWWR-EHRRPLNFIVPTGNLGNALAAVWVRE-MGLPVGAIELACNAN-ETLPDYFAGTP 293
                                                  55555444444.*********************55555.55**********998.99999999999 PP

                                    TIGR00260 234 lepkedkeTlstAmdignpsnveralelarrslgnledlke.svsdeeileaikklaeeegyllep 298
                                                    p++ ++Tl++Amd+g psn+er+ + +   +    +l + sv d+ i  ++++ a e+g +  p
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0575 294 YAPRAAVATLANAMDVGAPSNFERLRWTFPYDDDLRGQLSShSVDDDTIRATVRRHALEHGEVFCP 359
                                                  9**************************88777666666655267777777788999999**999** PP

                                    TIGR00260 299 htavavaalkklvekg...vsatadpaKFeevvealtgnk 335
                                                  hta+a+  l    ek    v +ta+ aKFe vve l g +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0575 360 HTATAMHRLDLRQEKAdwaVVSTAHAAKFESVVEPLIGRG 399
                                                  ******999655555547666*************988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (441 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: 00:00:00.01
# Mc/sec: 10.52
//
[ok]

This GapMind analysis is from Apr 09 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