GapMind for Amino acid biosynthesis

 

Alignments for a candidate for thrB in Enterococcus termitis LMG 8895

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_069664979.1 BCR25_RS17885 homoserine kinase

Query= curated2:Q831T0
         (287 letters)



>NCBI__GCF_001730305.1:WP_069664979.1
          Length = 287

 Score =  417 bits (1072), Expect = e-121
 Identities = 205/287 (71%), Positives = 248/287 (86%)

Query: 1   MKIRVPATSANLGPGFDSCGIALSAYLTINVLGESEFWEIQHTLGEEISTNEENLLIQTA 60
           MKIRVPATSANLGPGFDSCGIALS YL+I VL  +E W+I H+LG +I +++ NLL+QTA
Sbjct: 1   MKIRVPATSANLGPGFDSCGIALSQYLSIEVLENAEEWKIIHSLGADIPSDKTNLLLQTA 60

Query: 61  LKIAPELTPKVIRMVSDIPLARGLGSSSSVIVAGIELANRLAHLNLSPKEKVRLATEMEG 120
           LK+AP L PKV++M SDIPLARGLGSSSSVIVAGIELANRL +LNLS KEK+R+ATE+EG
Sbjct: 61  LKLAPNLAPKVLKMTSDIPLARGLGSSSSVIVAGIELANRLGNLNLSQKEKLRIATEIEG 120

Query: 121 HPDNVAPAILGDFVVASHVENQVYHVKHHFPMCDVIAFIPEEPLFTEKSRAVLPEKLAYK 180
           HPDNVAPAI GDFVVAS+V+  V++VKHHFPMCDVIA++P+E L T +SR+VLP  + YK
Sbjct: 121 HPDNVAPAICGDFVVASYVDGDVHYVKHHFPMCDVIAYVPDEHLLTTESRSVLPNTMPYK 180

Query: 181 EAVAASSIANVMIAAILNGDLPLAGKMMEQDKWHETYRRSLVPHLKEIRRLTQQKGAYGS 240
           +AV ASSIANVMIAAILNG+LPLAG MME+D+WHE YRR LVPHL +IR L Q+ G YG+
Sbjct: 181 DAVKASSIANVMIAAILNGNLPLAGLMMEEDRWHEAYRRKLVPHLDQIRELGQKIGIYGA 240

Query: 241 FLSGAGPTVLILSPEERTNEIVQSLEKLSTKASIQIFNIDQEGVQVF 287
           FLSGAGPTVLIL+PEE T+++V++LEK+   A+I + +IDQEG QVF
Sbjct: 241 FLSGAGPTVLILTPEENTSQMVKALEKMPKSATINVLSIDQEGTQVF 287


Lambda     K      H
   0.317    0.133    0.375 

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: 328
Number of extensions: 8
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: 287
Length of database: 287
Length adjustment: 26
Effective length of query: 261
Effective length of database: 261
Effective search space:    68121
Effective search space used:    68121
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 (21.6 bits)
S2: 47 (22.7 bits)

Align candidate WP_069664979.1 BCR25_RS17885 (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.1082334.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.2e-76  241.7   0.1    4.7e-76  241.5   0.1    1.0  1  NCBI__GCF_001730305.1:WP_069664979.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069664979.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.5   0.1   4.7e-76   4.7e-76       1     301 [.       1     286 [.       1     287 [] 0.91

  Alignments for each domain:
  == domain 1  score: 241.5 bits;  conditional E-value: 4.7e-76
                             TIGR00191   1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkvlkk 73 
                                           +k++vPa+sANlgpGfD+ G+als++l++ v e   +++++k +++ g +   ip++ + Nl+ q+a+k++ +
  NCBI__GCF_001730305.1:WP_069664979.1   1 MKIRVPATSANLGPGFDSCGIALSQYLSIEVLE---NAEEWKIIHSLGAD---IPSD-KTNLLLQTALKLAPN 66 
                                           589*****************************9...55666645556555...****.9**********9987 PP

                             TIGR00191  74 lgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvapallGGlql 146
                                           l  +     l+++++ipl+rGLGSS++ iva++ +an l +l+ls++e+l +a+++EgHpDNvapa+ G +++
  NCBI__GCF_001730305.1:WP_069664979.1  67 LAPK----VLKMTSDIPLARGLGSSSSVIVAGIELANRLGNLNLSQKEKLRIATEIEGHPDNVAPAICGDFVV 135
                                           6655....78889**********************************************************99 PP

                             TIGR00191 147 avkedd..llevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAlvskdkadll 217
                                           a   d   + ++ + P     +v++ +P  ++ T e+R vLP+  +++d+v+++s ++v+++A+ +++ ++ +
  NCBI__GCF_001730305.1:WP_069664979.1 136 ASYVDGdvHYVKHHFP---MCDVIAYVPDEHLLTTESRSVLPNTMPYKDAVKASSIANVMIAAILNGNLPLAG 205
                                           8877773344555555...79**********************************************888888 PP

                             TIGR00191 218 aiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeekeekaqelleklakegieltvk 290
                                            ++ +Dr h+ yR+kl+P+l++i++  ++ g++g  lSGaGpt+l l+ ee+   ++++++ l k  + +t++
  NCBI__GCF_001730305.1:WP_069664979.1 206 LMMEEDRWHEAYRRKLVPHLDQIRELGQKIGIYGAFLSGAGPTVLILTPEEN---TSQMVKALEKMPKSATIN 275
                                           88889**********************************************9...888899999999999*** PP

                             TIGR00191 291 vleldtdgaev 301
                                           vl++d++g++v
  NCBI__GCF_001730305.1:WP_069664979.1 276 VLSIDQEGTQV 286
                                           ********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (287 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 15.26
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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