Alignments for a candidate for thrC in Klebsiella variicola At-22

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Klebsiella variicola At-22

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_008807507.1 KVAR_RS21880 threonine synthase

Query= BRENDA::P00934
         (428 letters)



>NCBI__GCF_000025465.1:WP_008807507.1
          Length = 426

 Score =  780 bits (2014), Expect = 0.0
 Identities = 386/425 (90%), Positives = 405/425 (95%)

Query: 1   MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60
           MKLYNLKDHNEQVSFAQAVTQGLGK+QGLFFPHDLPEFSLTEID+ML  DFVTRSAKILS
Sbjct: 1   MKLYNLKDHNEQVSFAQAVTQGLGKHQGLFFPHDLPEFSLTEIDDMLAQDFVTRSAKILS 60

Query: 61  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120
           AFIGDEIPQ++L++RVRAAFAFPAPV+ V+ DVGCLELFHGPTLAFKDFGGRFMAQMLTH
Sbjct: 61  AFIGDEIPQDVLQQRVRAAFAFPAPVSKVQDDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120

Query: 121 IAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETV 180
           IAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETV
Sbjct: 121 IAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETV 180

Query: 181 AIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETRNQ 240
           AIDGDFDACQALVKQAFDDEELK  LGLNSANSINISRLLAQICYYFEA AQLPQE RNQ
Sbjct: 181 AIDGDFDACQALVKQAFDDEELKATLGLNSANSINISRLLAQICYYFEAAAQLPQEARNQ 240

Query: 241 LVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLSNA 300
           LV+SVPSGNFGDLTAGLLAKSLGLP+KRFIAATN NDTVPR+L  G+W+PKATQATLSNA
Sbjct: 241 LVISVPSGNFGDLTAGLLAKSLGLPIKRFIAATNANDTVPRYLQGGEWAPKATQATLSNA 300

Query: 301 MDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTSEPHAAVAYRA 360
           MDVSQPNNWPRVEELFRRKIW+L ELGYAAVDDETT+  MRELK +GY SEPHAA+A+RA
Sbjct: 301 MDVSQPNNWPRVEELFRRKIWRLSELGYAAVDDETTKAAMRELKAIGYISEPHAAIAWRA 360

Query: 361 LRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLPADFAAL 420
           LRDQL PGEYGLFLGTAHPAKFKESVE IL ETL LPKELA+RADLPLLSHNLPADFAAL
Sbjct: 361 LRDQLQPGEYGLFLGTAHPAKFKESVEEILQETLPLPKELADRADLPLLSHNLPADFAAL 420

Query: 421 RKLMM 425
           RKLMM
Sbjct: 421 RKLMM 425


Lambda     K      H
   0.319    0.135    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: 712
Number of extensions: 19
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: 428
Length of database: 426
Length adjustment: 32
Effective length of query: 396
Effective length of database: 394
Effective search space:   156024
Effective search space used:   156024
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_008807507.1 KVAR_RS21880 (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.20360.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-127  411.3   0.0   1.9e-127  411.1   0.0    1.0  1  lcl|NCBI__GCF_000025465.1:WP_008807507.1  KVAR_RS21880 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025465.1:WP_008807507.1  KVAR_RS21880 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.1   0.0  1.9e-127  1.9e-127       1     338 [.      52     396 ..      52     398 .. 0.97

  Alignments for each domain:
  == domain 1  score: 411.1 bits;  conditional E-value: 1.9e-127
                                 TIGR00260   1 vvryreilevt...ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavllt 66 
                                               v+r+++il+++   e+++  l+++++++f++p++ ++v+  ++ ++elfhgPtlaFKD+g++f+a++lt
  lcl|NCBI__GCF_000025465.1:WP_008807507.1  52 VTRSAKILSAFigdEIPQDVLQQRVRAAFAFPAPVSKVQD-DVGCLELFHGPTLAFKDFGGRFMAQMLT 119
                                               6899999999999999************************.**************************** PP

                                 TIGR00260  67 kalelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDd 135
                                               ++++++  t+l+AtsGdtgaa+a+a++g +nvkvv+LyP+gkisp++ekl+++l +n++++ai+GdFD+
  lcl|NCBI__GCF_000025465.1:WP_008807507.1 120 HIAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETVAIDGDFDA 188
                                               ********************************************************************* PP

                                 TIGR00260 136 aqdlvkeifedke...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGf 201
                                               +q+lvk++f+d+e    l+lns+Nsin++r++aq++y+fe+++ql++e+++++v++vpsgnfg++++G 
  lcl|NCBI__GCF_000025465.1:WP_008807507.1 189 CQALVKQAFDDEElkaTLGLNSANSINISRLLAQICYYFEAAAQLPQEARNQLVISVPSGNFGDLTAG- 256
                                               **********8777879***************************************************. PP

                                 TIGR00260 202 lekkelglpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnle 270
                                               l +k+lglp  k++iaa++a+d+v+r+l++g++ pk++++Tls+Amd+++p+n++r++el+rr+ + l 
  lcl|NCBI__GCF_000025465.1:WP_008807507.1 257 LLAKSLGLP-IKRFIAATNANDTVPRYLQGGEWAPKATQATLSNAMDVSQPNNWPRVEELFRRKIWRLS 324
                                               7788888**.899******************************************************** PP

                                 TIGR00260 271 dlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvs....atadpaKFeevvealtgnk 335
                                               +l+++++d+e+++a ++ ++  gy+ eph+a+a +al+++++ g +    +ta+paKF+e+ve ++ ++
  lcl|NCBI__GCF_000025465.1:WP_008807507.1 325 ELGYAAVDDETTKAAMRELKAIGYISEPHAAIAWRALRDQLQPGEYglflGTAHPAKFKESVEEILQET 393
                                               ********************************************555889*************888777 PP

                                 TIGR00260 336 lkd 338
                                               l  
  lcl|NCBI__GCF_000025465.1:WP_008807507.1 394 LPL 396
                                               765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (426 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: 8.36
//
[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