Alignments for a candidate for thrC in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Dechlorosoma suillum PS

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate Dsui_2904 Dsui_2904 threonine synthase

Query= BRENDA::Q2SWH9
         (483 letters)



>FitnessBrowser__PS:Dsui_2904
          Length = 479

 Score =  638 bits (1646), Expect = 0.0
 Identities = 334/480 (69%), Positives = 378/480 (78%), Gaps = 4/480 (0%)

Query: 1   MNYISTRG-AGIGERHTFSDILLGGLAKDGGLYLPSEYPQVSADELARWRTLPYADLAFE 59
           M Y+STRG A      +F DILLGGLA DGGLYLP  YPQVS  EL  WR L YA+LAF 
Sbjct: 1   MRYLSTRGDAASSPTQSFCDILLGGLAPDGGLYLPETYPQVSRAELDAWRQLSYAELAFA 60

Query: 60  ILSKFCDDIAAADLRAITRRTYTADVYRHARRGGNAADITPLTTLGTENGAPVSLLELSN 119
           +LSKF DDI  ADL+AI  +TYTA VY HAR G NAAD+TP+  L  E G  ++L ELSN
Sbjct: 61  VLSKFIDDIPPADLKAICDKTYTAQVYCHARPGDNAADVTPIHWL--EQGK-LALQELSN 117

Query: 120 GPTLAFKDMAMQLLGNLFEYTLAKHGETLNILGATSGDTGSAAEYAMRGKEGVRVFMLSP 179
           GPTLAFKDMAMQLLGNLFEY LAK GE +NILGATSGDTGSAAEYAMRGK+GVRVFMLSP
Sbjct: 118 GPTLAFKDMAMQLLGNLFEYVLAKRGEEINILGATSGDTGSAAEYAMRGKKGVRVFMLSP 177

Query: 180 HKKMSAFQTAQMYSLQDPNIFNLAVNGVFDDCQDIVKAVSNDHAFKAQQKIGTVNSINWA 239
             KMSAFQ AQMYSLQD NI N+AV G+FDD QDIVKAVSND AFKA+ KIG VNSINWA
Sbjct: 178 DGKMSAFQRAQMYSLQDENIHNIAVRGMFDDAQDIVKAVSNDAAFKAKYKIGAVNSINWA 237

Query: 240 RVVAQVVYYFKGYFAATRSNDERVSFTVPSGNFGNVCAGHIARMMGLPIEKLVVATNEND 299
           RV AQ+VYYFKGYF AT +ND++V+F VPSGNFGN+CAGHIARMMGLPI KL++ATNEN+
Sbjct: 238 RVAAQIVYYFKGYFGATENNDQQVAFCVPSGNFGNICAGHIARMMGLPIGKLILATNENN 297

Query: 300 VLDEFFRTGAYRVRSAQDTYHTSSPSMDISKASNFERFVFDLLGRDPARVVQLFRDVEQK 359
           VLDEFF+TG YR R   +T+ TSSPSMDISKASNFERFVFDL+GRDPA+V +L+  V+  
Sbjct: 298 VLDEFFKTGVYRPRKTAETFVTSSPSMDISKASNFERFVFDLVGRDPAKVRELWAQVDAG 357

Query: 360 GGFDLAASGDFARVAEFGFVSGRSTHADRIATIRDVFERYRTMIDTHTADGLKVAREHLR 419
             FDL  +    ++A F FVSG S+HADR+ATIR  +E Y  MIDTHTADGLKVARE+  
Sbjct: 358 QAFDLRGTPYMDKLAGFAFVSGASSHADRLATIRSCWETYGVMIDTHTADGLKVARENPI 417

Query: 420 PGVPMVVLETAQPIKFGESIREALGQEPSRPAAFDGLEALPQRFEVVDANAQQVKDFIAA 479
            G+P VVLETA P KF E+IREALG+EP  PA   GLE L QR EV+D +   VK FI A
Sbjct: 418 AGMPTVVLETALPAKFAETIREALGREPEVPADLQGLEKLAQRVEVMDPDVNAVKAFIQA 477


Lambda     K      H
   0.320    0.135    0.392 

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: 657
Number of extensions: 17
Number of successful extensions: 2
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: 483
Length of database: 479
Length adjustment: 34
Effective length of query: 449
Effective length of database: 445
Effective search space:   199805
Effective search space used:   199805
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 Dsui_2904 Dsui_2904 (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.29117.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    3.3e-74  236.0   0.0    4.4e-74  235.6   0.0    1.1  1  lcl|FitnessBrowser__PS:Dsui_2904  Dsui_2904 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2904  Dsui_2904 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.6   0.0   4.4e-74   4.4e-74      37     332 ..     107     441 ..      76     448 .. 0.90

  Alignments for each domain:
  == domain 1  score: 235.6 bits;  conditional E-value: 4.4e-74
                         TIGR00260  37 aenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaaealagkanvkvvvLyPkgkisp 111
                                       + +l ++el+ gPtlaFKD+++q +++l++++l +  e   +l+AtsGdtg+aa +a++gk++v+v++L P+gk+s 
  lcl|FitnessBrowser__PS:Dsui_2904 107 QGKLALQELSNGPTLAFKDMAMQLLGNLFEYVLAKRGEeiNILGATSGDTGSAAEYAMRGKKGVRVFMLSPDGKMSA 183
                                       567899*************************9766555479************************************ PP

                         TIGR00260 112 v.keklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsinparieaqktyafeiveqlgkespdk 184
                                           ++    +en++ +a++G FDdaqd+vk++ +d     k+k+++vNsin+ar++aq++y+f       +++ ++
  lcl|FitnessBrowser__PS:Dsui_2904 184 FqRAQMYSLQDENIHNIAVRGMFDDAQDIVKAVSNDAAfkaKYKIGAVNSINWARVAAQIVYYFKGYFGATENNDQQ 260
                                       *99*******************************9665677*******************8888655555559999* PP

                         TIGR00260 185 vvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksgdlepkedk...eTlstAmdignpsnvera 258
                                       v++ vpsgnfg+i +G   ++++glpi kl  a++++ +++++f k+g   p+++     T s++mdi++ sn+er 
  lcl|FitnessBrowser__PS:Dsui_2904 261 VAFCVPSGNFGNICAG-HIARMMGLPIGKLILATNEN-NVLDEFFKTGVYRPRKTAetfVTSSPSMDISKASNFERF 335
                                       ****************.6667777************9.**********7777777633456799************9 PP

                         TIGR00260 259 le.larrslgnledlke...........................svsdeeileaikklaeeegyllephtavavaal 307
                                       ++ l+ r  +++ +l +                           + s ++ l +i+   e+ g+++++hta ++++ 
  lcl|FitnessBrowser__PS:Dsui_2904 336 VFdLVGRDPAKVRELWAqvdagqafdlrgtpymdklagfafvsgASSHADRLATIRSCWETYGVMIDTHTADGLKVA 412
                                       998***********98899************************99999***************************** PP

                         TIGR00260 308 kklvekg....vsatadpaKFeevvealt 332
                                       ++   +g    v  ta paKF+e++   +
  lcl|FitnessBrowser__PS:Dsui_2904 413 RENPIAGmptvVLETALPAKFAETIREAL 441
                                       *9999997753339********9988444 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (479 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: 9.52
//
[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