Alignments for a candidate for thrC in Sedimenticola selenatireducens DSM 17993

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Sedimenticola selenatireducens DSM 17993

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_029132662.1 A3GO_RS0106145 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>NCBI__GCF_000428045.1:WP_029132662.1
          Length = 460

 Score =  409 bits (1052), Expect = e-119
 Identities = 220/460 (47%), Positives = 299/460 (65%), Gaps = 7/460 (1%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           M+YVSTRG    + FS A++ GLA DGGL LP+ +PQ  A  ++      +  +A+ V+ 
Sbjct: 1   MRYVSTRGGIEPVTFSQAVMMGLATDGGLLLPESFPQIDATTLQRWAELPFKALAVEVMY 60

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120
           P+ G +I   + E++V E+Y +F H  V P+V+   +  +LELFHGPT AFKDVA+Q L 
Sbjct: 61  PYVGEDISRVELEKLVEESYASFSHPEVTPVVEV-GDLRILELFHGPTAAFKDVALQFLG 119

Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180
            + + +L + G R  I+GATSGDTG AAI    G++  DIFIL P GRVSP+Q+RQMT+ 
Sbjct: 120 NLFELLLERSGGRLNILGATSGDTGSAAIYGVRGQERIDIFILHPKGRVSPIQERQMTTV 179

Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTA--A 238
             +NVH ++I G FDD Q +VK +FNDL F    +L  VNSINWARI+ QVVYYF A   
Sbjct: 180 LDANVHNIAITGTFDDGQRIVKELFNDLAFKQEYTLGAVNSINWARILAQVVYYFYAWGR 239

Query: 239 LSLGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMR 298
           +S G  D+ V+F+VPTGNFGDIFAGYVA RMGLP+E+LI+ATN NDILSR + SG Y+  
Sbjct: 240 VSGGDVDQKVTFSVPTGNFGDIFAGYVAMRMGLPVERLILATNRNDILSRFVNSGVYQTG 299

Query: 299 GVAQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEF 358
            V  T SPSMDIQISSNFER L+    +D A VR LM  + + G   +  +  + + + F
Sbjct: 300 EVYPTISPSMDIQISSNFERYLYYLMDQDPAKVRALMDQMGREGKLEVPAEKRAEVAALF 359

Query: 359 SAGRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKASGTAPMVVLATAHPAKFPDA 418
            A   + +ET   I    ++ GY+LDPH+A+GV  A+E        + LATAHPAKF  A
Sbjct: 360 QAAAVSEEETRDQIRDTYAQTGYILDPHTAVGVHAAKEIPGA----ICLATAHPAKFGAA 415

Query: 419 VKAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVR 458
           VK A GVE + PA L  LM+++    VL  +  ++ ++++
Sbjct: 416 VKEAIGVESEPPASLQGLMEKETRCAVLEADAAVIRDFMK 455


Lambda     K      H
   0.320    0.135    0.389 

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: 535
Number of extensions: 24
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: 463
Length of database: 460
Length adjustment: 33
Effective length of query: 430
Effective length of database: 427
Effective search space:   183610
Effective search space used:   183610
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_029132662.1 A3GO_RS0106145 (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.28798.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    7.6e-92  294.0   0.0      1e-91  293.6   0.0    1.0  1  lcl|NCBI__GCF_000428045.1:WP_029132662.1  A3GO_RS0106145 threonine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000428045.1:WP_029132662.1  A3GO_RS0106145 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.6   0.0     1e-91     1e-91      12     331 ..      69     420 ..      58     426 .. 0.92

  Alignments for each domain:
  == domain 1  score: 293.6 bits;  conditional E-value: 1e-91
                                 TIGR00260  12 ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlc 78 
                                                 +l++l e s++ f  p+++  v++ +l ++elfhgPt aFKD++lqf+++l++ +le+      +l+
  lcl|NCBI__GCF_000428045.1:WP_029132662.1  69 RVELEKLVEESYASFSHPEVTPVVEVGDLRILELFHGPTAAFKDVALQFLGNLFELLLERSGGrlNILG 137
                                               5678999**************************************************998554459*** PP

                                 TIGR00260  79 AtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeife. 145
                                               AtsGdtg+aa+++ +g++ +++++L Pkg++sp+ + +++t+l+ n++ +ai+G+FDd q++vke+f+ 
  lcl|NCBI__GCF_000428045.1:WP_029132662.1 138 ATSGDTGSAAIYGVRGQERIDIFILHPKGRVSPIqERQMTTVLDANVHNIAITGTFDDGQRIVKELFNd 206
                                               **********************************999******************************96 PP

                                 TIGR00260 146 ..dkeklklnsvNsinparieaqk.tyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpi 211
                                                  k+++ l++vNsin+ari+aq+ +y++      g++  +kv+++vp gnfg+i++G+++++++ lp+
  lcl|NCBI__GCF_000428045.1:WP_029132662.1 207 laFKQEYTLGAVNSINWARILAQVvYYFYAWGRVSGGDVDQKVTFSVPTGNFGDIFAGYVAMRMG-LPV 274
                                               55566*******************666666667777799*************************9.**9 PP

                                 TIGR00260 212 eklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke..... 274
                                               e l  a++ + di+ rf +sg  ++ e   T+s++mdi ++sn+er l  l+ +  +++ +l       
  lcl|NCBI__GCF_000428045.1:WP_029132662.1 275 ERLILATNRN-DILSRFVNSGVYQTGEVYPTISPSMDIQISSNFERYLYyLMDQDPAKVRALMDqmgre 342
                                               9999999998.**********55555666******************999999999999999779999* PP

                                 TIGR00260 275 ....................svsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaK 323
                                                                   +vs+ee+ ++i+  +++ gy+l+phtav+v a k+   +   ata+paK
  lcl|NCBI__GCF_000428045.1:WP_029132662.1 343 gklevpaekraevaalfqaaAVSEEETRDQIRDTYAQTGYILDPHTAVGVHAAKEIPGAICLATAHPAK 411
                                               *****************************************************999887777******* PP

                                 TIGR00260 324 Feevve.al 331
                                               F  +v  a+
  lcl|NCBI__GCF_000428045.1:WP_029132662.1 412 FGAAVKeAI 420
                                               **9998554 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (460 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: 11.02
//
[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