Alignments for a candidate for thrB in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Synechococcus elongatus PCC 7942

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate Synpcc7942_1440 Synpcc7942_1440 homoserine kinase

Query= curated2:Q31N99
         (306 letters)



>FitnessBrowser__SynE:Synpcc7942_1440
          Length = 306

 Score =  603 bits (1556), Expect = e-177
 Identities = 306/306 (100%), Positives = 306/306 (100%)

Query: 1   MRVRVAVPATTANLGPGFDCLGAALTLYNHFWFAPASTGELEITARGMDAEKISGDRDNL 60
           MRVRVAVPATTANLGPGFDCLGAALTLYNHFWFAPASTGELEITARGMDAEKISGDRDNL
Sbjct: 1   MRVRVAVPATTANLGPGFDCLGAALTLYNHFWFAPASTGELEITARGMDAEKISGDRDNL 60

Query: 61  VYRAFAAFFEKQEQPVPALKLEIELAVPLARGLGSSATAIVAGLVGANALAGSPWSNAQL 120
           VYRAFAAFFEKQEQPVPALKLEIELAVPLARGLGSSATAIVAGLVGANALAGSPWSNAQL
Sbjct: 61  VYRAFAAFFEKQEQPVPALKLEIELAVPLARGLGSSATAIVAGLVGANALAGSPWSNAQL 120

Query: 121 CDLATELEGHPDNVVPALLGGCRLAARDRQNQWAIADLDWHPDFIPVVAIPDFELSTEAA 180
           CDLATELEGHPDNVVPALLGGCRLAARDRQNQWAIADLDWHPDFIPVVAIPDFELSTEAA
Sbjct: 121 CDLATELEGHPDNVVPALLGGCRLAARDRQNQWAIADLDWHPDFIPVVAIPDFELSTEAA 180

Query: 181 RQVLPTQYSRSDAIFNAAHVGLVVRSLASGNGEWLAAALQDRLHQPYRQALIPGYAAVET 240
           RQVLPTQYSRSDAIFNAAHVGLVVRSLASGNGEWLAAALQDRLHQPYRQALIPGYAAVET
Sbjct: 181 RQVLPTQYSRSDAIFNAAHVGLVVRSLASGNGEWLAAALQDRLHQPYRQALIPGYAAVET 240

Query: 241 AALEAGAFGLVISGAGPTLLAISSPDRAEAVRQAMLTTWQATGLSVRAEILAIAESGTQI 300
           AALEAGAFGLVISGAGPTLLAISSPDRAEAVRQAMLTTWQATGLSVRAEILAIAESGTQI
Sbjct: 241 AALEAGAFGLVISGAGPTLLAISSPDRAEAVRQAMLTTWQATGLSVRAEILAIAESGTQI 300

Query: 301 EQETEN 306
           EQETEN
Sbjct: 301 EQETEN 306


Lambda     K      H
   0.318    0.132    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: 451
Number of extensions: 6
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: 306
Length of database: 306
Length adjustment: 27
Effective length of query: 279
Effective length of database: 279
Effective search space:    77841
Effective search space used:    77841
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate Synpcc7942_1440 Synpcc7942_1440 (homoserine kinase)
to HMM TIGR00191 (thrB: homoserine kinase (EC 2.7.1.39))

# 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/TIGR00191.hmm
# target sequence database:        /tmp/gapView.17757.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00191  [M=304]
Accession:   TIGR00191
Description: thrB: homoserine kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.7e-95  305.4   0.0    1.9e-95  305.2   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1440  Synpcc7942_1440 homoserine kinas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1440  Synpcc7942_1440 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.2   0.0   1.9e-95   1.9e-95       1     303 [.       3     302 ..       3     303 .. 0.96

  Alignments for each domain:
  == domain 1  score: 305.2 bits;  conditional E-value: 1.9e-95
                                 TIGR00191   1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakk 69 
                                               ++v vPa++ANlgpGfD+lG+al+l++++   +    ++ + +++a+g ++eki+ + ++Nl+y++++ 
  lcl|FitnessBrowser__SynE:Synpcc7942_1440   3 VRVAVPATTANLGPGFDCLGAALTLYNHFWFAP---ASTGELEITARGMDAEKISGD-RDNLVYRAFAA 67 
                                               68******************************9...667777899***********9.*********** PP

                                 TIGR00191  70 vlkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvap 138
                                               +++k+++ v+++kl++e  +pl+rGLGSSa+aiva+++ an+lag + s+++l dla++lEgHpDNv p
  lcl|FitnessBrowser__SynE:Synpcc7942_1440  68 FFEKQEQPVPALKLEIELAVPLARGLGSSATAIVAGLVGANALAGSPWSNAQLCDLATELEGHPDNVVP 136
                                               ********************************************************************* PP

                                 TIGR00191 139 allGGlqlavkedd.llevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvt 206
                                               allGG+ la ++ + +  + ++  ++++  v++iP +e+sT++aR+vLP +ysr+d++fn++h++++v 
  lcl|FitnessBrowser__SynE:Synpcc7942_1440 137 ALLGGCRLAARDRQnQWAIADLDWHPDFIPVVAIPDFELSTEAARQVLPTQYSRSDAIFNAAHVGLVVR 205
                                               ********998777556666777779******************************************* PP

                                 TIGR00191 207 AlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.eekaq 274
                                                l s+ + ++la a++Dr+hqpyR+ liP+++++++aa e+ga+g+++SGaGpt+la+++  + e   q
  lcl|FitnessBrowser__SynE:Synpcc7942_1440 206 SLASG-NGEWLAAALQDRLHQPYRQALIPGYAAVETAALEAGAFGLVISGAGPTLLAISSPDRaEAVRQ 273
                                               *****.*****************************************************9999799999 PP

                                 TIGR00191 275 elleklakegieltvkvleldtdgaevek 303
                                                +l +++  g  ++ ++l ++  g+++e+
  lcl|FitnessBrowser__SynE:Synpcc7942_1440 274 AMLTTWQATGLSVRAEILAIAESGTQIEQ 302
                                               ***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (306 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: 6.64
//
[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