Alignments for a candidate for thrC in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Echinicola vietnamensis KMM 6221, DSM 17526

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate Echvi_2002 Echvi_2002 threonine synthase

Query= BRENDA::P00934
         (428 letters)



>FitnessBrowser__Cola:Echvi_2002
          Length = 430

 Score =  344 bits (883), Expect = 3e-99
 Identities = 187/410 (45%), Positives = 271/410 (66%), Gaps = 8/410 (1%)

Query: 1   MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60
           MK Y+  +   +VS  +AV +GL  +QGL+ P  +P      ID++ +  F     +++ 
Sbjct: 1   MKFYSTNNKEHKVSLKEAVIKGLAPDQGLYMPERIPTLPADFIDQLPERSFQEIGYEVIG 60

Query: 61  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120
           A  G+++ +E ++E V    AF AP+  VE +V  LELFHGPTLAFKDFG RF +++++ 
Sbjct: 61  AIFGEDLSKEQIKELVDHTLAFDAPLVKVEEEVYTLELFHGPTLAFKDFGARFCSKLMSL 120

Query: 121 IAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETV 180
           +  D+ V +L ATSGDTG+AVA+ FY +P V+V+ILYP GK+S LQEK F TLG NI  +
Sbjct: 121 LVKDEKVRVLVATSGDTGSAVANGFYKVPGVEVIILYPSGKVSTLQEKQFTTLGENITAL 180

Query: 181 AIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETRNQ 240
            +DG FD CQ +VKQAF D++L  ++ L SANSINI+R + Q  YYF A ++LP +   +
Sbjct: 181 EVDGVFDDCQRMVKQAFLDKDLNESMLLTSANSINIARWIPQCLYYFYAYSRLP-KGHEK 239

Query: 241 LVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLSNA 300
           +V SVPSGNFG++ AG+LA+ +GLP++ F+AATNVN  VP FL    + P+ +  T+SN+
Sbjct: 240 VVFSVPSGNFGNIAAGMLAERMGLPIETFVAATNVNKIVPDFLKGVPFRPRPSLQTISNS 299

Query: 301 MDVSQPNNWPRVEELFRRKIWQLKEL--GYAAVDDETTQQTMRELK-ELGYTSEPHAAVA 357
           MDV  P+N+ R+ +L+  +  +LKE+  G+   DD TT++ M  +K   GY  +PH AVA
Sbjct: 300 MDVGNPSNFYRLLDLYGDES-KLKEMVKGF-FFDDATTREAMATVKAAAGYLMDPHGAVA 357

Query: 358 YRALRDQL--NPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERAD 405
           Y  L+  +  +PG  G+FL TAHP KF + VEA+  E + LP+ LA   D
Sbjct: 358 YLGLKAYMEEHPGYTGVFLETAHPGKFGDVVEAVHQEKVTLPERLAAFLD 407


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: 448
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: 428
Length of database: 430
Length adjustment: 32
Effective length of query: 396
Effective length of database: 398
Effective search space:   157608
Effective search space used:   157608
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 Echvi_2002 Echvi_2002 (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.8565.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    2.6e-91  292.3   0.0    3.1e-91  292.0   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2002  Echvi_2002 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2002  Echvi_2002 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.0   0.0   3.1e-91   3.1e-91      16     339 ..      70     399 ..      56     400 .. 0.91

  Alignments for each domain:
  == domain 1  score: 292.0 bits;  conditional E-value: 3.1e-91
                            TIGR00260  16 vdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgnetvlcAtsGdtgaaaa 89 
                                          ++++e + ++++++++  +v++ ++y +elfhgPtlaFKD+g +f ++l++ + ++ +  vl+AtsGdtg+a+a
  lcl|FitnessBrowser__Cola:Echvi_2002  70 EQIKELVDHTLAFDAPLVKVEE-EVYTLELFHGPTLAFKDFGARFCSKLMSLLVKDEKVRVLVATSGDTGSAVA 142
                                          5566777888999999999999.*************************************************** PP

                            TIGR00260  90 ealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsinp 160
                                          ++++  ++v+v++LyP+gk+s ++ek +t+l en++ l+++G FDd+q++vk++f dk     ++l s+Nsin+
  lcl|FitnessBrowser__Cola:Echvi_2002 143 NGFYKVPGVEVIILYPSGKVSTLQEKQFTTLGENITALEVDGVFDDCQRMVKQAFLDKDlneSMLLTSANSINI 216
                                          *******************************************************9665566************ PP

                            TIGR00260 161 arieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksgdl 234
                                          ar   q  y+f +  +l+ +  +kvv++vpsgnfg+i +G l+ +++ lp   +++aa++++ iv+ flk+  +
  lcl|FitnessBrowser__Cola:Echvi_2002 217 ARWIPQCLYYFYAYSRLP-KGHEKVVFSVPSGNFGNIAAGMLAERMG-LP-IETFVAATNVNKIVPDFLKGVPF 287
                                          ******************.999******************8888777.**.56788888888************ PP

                            TIGR00260 235 epkedkeTlstAmdignpsnveralelarrslgnledlkesvsdeeil.eaikklaeeegyllephtavavaal 307
                                           p+ +++T+s++md+gnpsn+ r+l+l   + +  e +k    d++++ ea+  + +  gyl++ph+ava+ +l
  lcl|FitnessBrowser__Cola:Echvi_2002 288 RPRPSLQTISNSMDVGNPSNFYRLLDLYGDESKLKEMVKGFFFDDATTrEAMATVKAAAGYLMDPHGAVAYLGL 361
                                          **************************99999999999998888887762566667777**************** PP

                            TIGR00260 308 kklvekg...vs...atadpaKFeevvealtgnklkdp 339
                                          k  +e+    ++    ta+p+KF +vvea+  +k   p
  lcl|FitnessBrowser__Cola:Echvi_2002 362 KAYMEEHpgyTGvflETAHPGKFGDVVEAVHQEKVTLP 399
                                          *****99865337899*************998887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (430 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: 8.86
//
[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