Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_011989422.1 CKL_RS04215 homoserine kinase
Query= curated2:A5N6I0 (300 letters) >NCBI__GCF_000016505.1:WP_011989422.1 Length = 300 Score = 594 bits (1531), Expect = e-175 Identities = 300/300 (100%), Positives = 300/300 (100%) Query: 1 MAKVKVRIPATTANMGPGFDTLGMALKLYNEIEVEEINGKTQIYNNGLKSEEDFGNNLIY 60 MAKVKVRIPATTANMGPGFDTLGMALKLYNEIEVEEINGKTQIYNNGLKSEEDFGNNLIY Sbjct: 1 MAKVKVRIPATTANMGPGFDTLGMALKLYNEIEVEEINGKTQIYNNGLKSEEDFGNNLIY 60 Query: 61 KSIIETMNKGGYSYKGFKINVVKCDVPISRGLGSSSACIVGGIKIANEIMGNKLELKDMI 120 KSIIETMNKGGYSYKGFKINVVKCDVPISRGLGSSSACIVGGIKIANEIMGNKLELKDMI Sbjct: 61 KSIIETMNKGGYSYKGFKINVVKCDVPISRGLGSSSACIVGGIKIANEIMGNKLELKDMI 120 Query: 121 DLATKIEGHPDNVVPAMVGGMVVSLKTGEDIKYSKIDLPKQLKFVAMIPSFQVNTALSRK 180 DLATKIEGHPDNVVPAMVGGMVVSLKTGEDIKYSKIDLPKQLKFVAMIPSFQVNTALSRK Sbjct: 121 DLATKIEGHPDNVVPAMVGGMVVSLKTGEDIKYSKIDLPKQLKFVAMIPSFQVNTALSRK 180 Query: 181 VLPKSYLKEECIFNISRCAMLVSALYNGEFDKLRTCFQDKIHQPYRKNLIKNSDDIFKKA 240 VLPKSYLKEECIFNISRCAMLVSALYNGEFDKLRTCFQDKIHQPYRKNLIKNSDDIFKKA Sbjct: 181 VLPKSYLKEECIFNISRCAMLVSALYNGEFDKLRTCFQDKIHQPYRKNLIKNSDDIFKKA 240 Query: 241 VEFGSIGEFISGSGSTLMAVLNKNEDEFVISIKRYLSGLQDKWNVILLEPDLEGVRIVKI 300 VEFGSIGEFISGSGSTLMAVLNKNEDEFVISIKRYLSGLQDKWNVILLEPDLEGVRIVKI Sbjct: 241 VEFGSIGEFISGSGSTLMAVLNKNEDEFVISIKRYLSGLQDKWNVILLEPDLEGVRIVKI 300 Lambda K H 0.318 0.137 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: 489 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: 300 Length of database: 300 Length adjustment: 27 Effective length of query: 273 Effective length of database: 273 Effective search space: 74529 Effective search space used: 74529 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 WP_011989422.1 CKL_RS04215 (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.7011.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-84 268.4 0.0 3.5e-84 268.2 0.0 1.0 1 lcl|NCBI__GCF_000016505.1:WP_011989422.1 CKL_RS04215 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016505.1:WP_011989422.1 CKL_RS04215 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 268.2 0.0 3.5e-84 3.5e-84 1 303 [. 4 299 .. 4 300 .] 0.93 Alignments for each domain: == domain 1 score: 268.2 bits; conditional E-value: 3.5e-84 TIGR00191 1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakk 69 +kv++Pa++AN+gpGfD+lG+al+l++e+ v+e ++ k++ + ++g + ++ +Nliy+ + + lcl|NCBI__GCF_000016505.1:WP_011989422.1 4 VKVRIPATTANMGPGFDTLGMALKLYNEIEVEE---INGKTQ-IYNNGLK---SEEDFGNNLIYKSIIE 65 69*****************************99...333333.3344433...2345589********* PP TIGR00191 70 vlkklgkrvkpvkltv.ekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNva 137 +++k g + k++k++v + ++p++rGLGSS+a iv+++ ane++g+kl+ ++++dla+ +EgHpDNv lcl|NCBI__GCF_000016505.1:WP_011989422.1 66 TMNKGGYSYKGFKINVvKCDVPISRGLGSSSACIVGGIKIANEIMGNKLELKDMIDLATKIEGHPDNVV 134 **************972569************************************************* PP TIGR00191 138 pallGGlqlavkedd..llevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavl 204 pa++GG+++++k + + ++++P ++lk+v++iP ++v+Ta +R+vLPk+y ++++fn s+ a+l lcl|NCBI__GCF_000016505.1:WP_011989422.1 135 PAMVGGMVVSLKTGEdiKYSKIDLP--KQLKFVAMIPSFQVNTALSRKVLPKSYLKEECIFNISRCAML 201 ************9985566677777..8***************************************** PP TIGR00191 205 vtAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeekeeka 273 v Al+++ + d l+++ +D++hqpyR++li + ++i ++a e g +g +SG+G+t++a+ +++++e + lcl|NCBI__GCF_000016505.1:WP_011989422.1 202 VSALYNG-EFDKLRTCFQDKIHQPYRKNLIKNSDDIFKKAVEFGSIGEFISGSGSTLMAVLNKNEDEFV 269 *******.99*********************************************************** PP TIGR00191 274 qelleklakegieltvkvleldtdgaevek 303 +++ l+ +++ +v +le+d +g++++k lcl|NCBI__GCF_000016505.1:WP_011989422.1 270 ISIKRYLSGLQDKWNVILLEPDLEGVRIVK 299 ***************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (300 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: 11.00 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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:
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