Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_013459322.1 SULKU_RS02335 homoserine kinase
Query= curated2:A6QBQ7 (292 letters) >NCBI__GCF_000183725.1:WP_013459322.1 Length = 293 Score = 365 bits (938), Expect = e-106 Identities = 174/292 (59%), Positives = 229/292 (78%) Query: 1 MLISVPATSANLGPGFDTLGLAVDLRNEIVIKPSKFLSLSTHGEGADNPKIKKNSLFLSI 60 M +SVPATSANLGPGFD+LGLAVDLRN++ + PS+F ++S GEG +NP++K N+LF+SI Sbjct: 1 MFVSVPATSANLGPGFDSLGLAVDLRNQVELVPSRFFAVSIKGEGENNPRLKGNNLFVSI 60 Query: 61 FNENYKRLSGKANNFRFEFTNRIPISRGLGSSSAVIVAALSGAYAMAGVKYNKREILNQA 120 FNE+Y+RL+ K NF+F F N+IP+SRGLGSSSAVIV+A+S A+ AGVK +KR ILN A Sbjct: 61 FNEHYRRLTQKRQNFKFTFYNQIPMSRGLGSSSAVIVSAISCAHEAAGVKVSKRRILNHA 120 Query: 121 LRYEHHPDNITPAVMGGFNVACVEGDRVYSKKRRMPDYLRAVVVVPNRTISTARSRTVLP 180 L YE HPDNITPAVMGGFN A VE +V+S+++ +PDYL+AVVV+PN+ ISTA+SRT LP Sbjct: 121 LVYESHPDNITPAVMGGFNAAMVEKQKVFSQQKHLPDYLKAVVVIPNKPISTAKSRTTLP 180 Query: 181 KMYRKEETVYSLSRAAYMTALFMSESWDLLRIASKDKLHQARRMKMMPELFDVQKLALKQ 240 K Y KE V++LS A F +E W++LR+A++D+ HQ RMKM+PELF VQK+A Sbjct: 181 KSYSKENAVFNLSHTAVTVGAFFNEDWEMLRLATQDRFHQKVRMKMLPELFAVQKMAYDN 240 Query: 241 GALMSTLSGSGSTFFNLAYEKDTDRIAQSLRARFPQFRVFVLALDNNGVITK 292 GALMSTLSGSGSTFFN+ Y++D +A +A F F + +L DN+G++ + Sbjct: 241 GALMSTLSGSGSTFFNMVYDQDAKMLADKFKAEFSDFEIKILGFDNDGLVVE 292 Lambda K H 0.320 0.134 0.376 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: 306 Number of extensions: 9 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: 292 Length of database: 293 Length adjustment: 26 Effective length of query: 266 Effective length of database: 267 Effective search space: 71022 Effective search space used: 71022 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: 48 (23.1 bits)
Align candidate WP_013459322.1 SULKU_RS02335 (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.26150.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-89 283.3 0.0 9.4e-89 283.2 0.0 1.0 1 lcl|NCBI__GCF_000183725.1:WP_013459322.1 SULKU_RS02335 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000183725.1:WP_013459322.1 SULKU_RS02335 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 283.2 0.0 9.4e-89 9.4e-89 3 302 .. 3 292 .. 1 293 [] 0.95 Alignments for each domain: == domain 1 score: 283.2 bits; conditional E-value: 9.4e-89 TIGR00191 3 vkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkvl 71 v+vPa+sANlgpGfD+lGla+ l++++ +++ + + + + ++geg e+ p +Nl+ ++++ + lcl|NCBI__GCF_000183725.1:WP_013459322.1 3 VSVPATSANLGPGFDSLGLAVDLRNQVELVP----SRFFA-VSIKGEG-ENNPRLKGNNLFVSIFNEHY 65 99*****************************....67766.7788888.77899999************ PP TIGR00191 72 kklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvapal 140 ++l ++ + +k+t ++ip++rGLGSS+a iv+a+ a e+ag k+sk ++l+ al++E HpDN++pa+ lcl|NCBI__GCF_000183725.1:WP_013459322.1 66 RRLTQKRQNFKFTFYNQIPMSRGLGSSSAVIVSAISCAHEAAGVKVSKRRILNHALVYESHPDNITPAV 134 ***9999************************************************************** PP TIGR00191 141 lGGlqlavkedd..llevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtA 207 +GG+++a+ e++ ++ ++P + lk+v+viPn +sTa++R LPk+ys +++vfnlsh av v A lcl|NCBI__GCF_000183725.1:WP_013459322.1 135 MGGFNAAMVEKQkvFSQQKHLP--DYLKAVVVIPNKPISTAKSRTTLPKSYSKENAVFNLSHTAVTVGA 201 ******9999995666777788..9******************************************** PP TIGR00191 208 lvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeekeekaqel 276 + ++ +++l++a +Dr+hq +R+k++Pel++++++a ++gal++tlSG+G+t++++ ++++ a+ l lcl|NCBI__GCF_000183725.1:WP_013459322.1 202 FFNE-DWEMLRLATQDRFHQKVRMKMLPELFAVQKMAYDNGALMSTLSGSGSTFFNMVYDQD---AKML 266 ****.899******************************************************...8889 PP TIGR00191 277 leklakegieltvkvleldtdgaeve 302 +k++ e+ ++++k+l +d+dg ve lcl|NCBI__GCF_000183725.1:WP_013459322.1 267 ADKFKAEFSDFEIKILGFDNDGLVVE 292 99********************8876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (293 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.26 // [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