Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_092481851.1 BM299_RS01675 homoserine kinase
Query= curated2:B9ML57 (307 letters) >NCBI__GCF_900115975.1:WP_092481851.1 Length = 300 Score = 272 bits (695), Expect = 8e-78 Identities = 141/301 (46%), Positives = 194/301 (64%), Gaps = 3/301 (0%) Query: 1 MISVKVPASSANLGAGFDCMGVALKLYNIIEVEEIEKGLIITSSPDDPS-IAKDENNLVF 59 MI V+VPA++ANLG GFDC+G+AL+LYNI+E +I +GL+I D + ++E NLV+ Sbjct: 1 MIRVQVPATTANLGPGFDCLGMALELYNIVEFSKISRGLVIEVEGDGAEELPRNEKNLVY 60 Query: 60 RAMKTVFDEVGWYPRGLRINLINEIPLTRGLGSSAACISGGIYAANLLCGGKLSEEEMIY 119 RA + VF+ P GLRI L+N IP+ RGLGSSA+ I GGI AAN++CG LS EM+ Sbjct: 61 RAARRVFERACRVPEGLRIKLVNNIPVGRGLGSSASAIVGGIIAANVMCGANLSMREMLN 120 Query: 120 LAAKMEGHPDNSTPAMIGGLVFAVLEDKKVNYIKFVVPARLKFAVFIPDFQLSTEYARNI 179 LA MEGHPDN PA++GGL+ + ++ + K +P LK V IPDF ++T R Sbjct: 121 LACSMEGHPDNIAPALLGGLIIYTSVEGEITWTKIDLPPALKAVVAIPDFIMNTRDTREA 180 Query: 180 LPKYIEFKDAVFNIGRATLFASAITTGNYELLPAATQDRLHQPYRKKLIPDFDKIVNLSL 239 LP+ + +DAV+NIGRA L +A+ G+ +L A DRLHQPYR+ IP F K+++ + Sbjct: 181 LPQLVTMRDAVYNIGRAALLVAALQKGDLSILGTAMDDRLHQPYRQGAIPGFKKVISAAR 240 Query: 240 EAGAKGAFLSGAGPSIIALVDENYEIFEQNVKNALASMDLVANWDFMILEADNSGATVFS 299 AGA+G LSGAGP+I+AL D N+E+ + +KN + A MIL GA Sbjct: 241 LAGARGVALSGAGPTIVALADGNFELIAEVMKNTFRECGVGAR--TMILAPGPVGARALE 298 Query: 300 V 300 V Sbjct: 299 V 299 Lambda K H 0.319 0.137 0.391 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: 272 Number of extensions: 16 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: 307 Length of database: 300 Length adjustment: 27 Effective length of query: 280 Effective length of database: 273 Effective search space: 76440 Effective search space used: 76440 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_092481851.1 BM299_RS01675 (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.32363.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-89 284.1 0.0 5.6e-89 283.9 0.0 1.0 1 lcl|NCBI__GCF_900115975.1:WP_092481851.1 BM299_RS01675 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900115975.1:WP_092481851.1 BM299_RS01675 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 283.9 0.0 5.6e-89 5.6e-89 1 285 [. 2 280 .. 2 298 .. 0.92 Alignments for each domain: == domain 1 score: 283.9 bits; conditional E-value: 5.6e-89 TIGR00191 1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakk 69 ++v+vPa++ANlgpGfD+lG+al+l++ + + ++ +e eg+g+e++p + +kNl+y++a + lcl|NCBI__GCF_900115975.1:WP_092481851.1 2 IRVQVPATTANLGPGFDCLGMALELYNIVEFSK---ISRGLV-IEVEGDGAEELPRN-EKNLVYRAARR 65 58************************9777766...666666.9************9.*********** PP TIGR00191 70 vlkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvap 138 v+++ + ++++++++ ++ip+grGLGSSa+aiv+++iaan ++g +ls e+l+la +EgHpDN+ap lcl|NCBI__GCF_900115975.1:WP_092481851.1 66 VFERACRVPEGLRIKLVNNIPVGRGLGSSASAIVGGIIAANVMCGANLSMREMLNLACSMEGHPDNIAP 134 ********************************************************************* PP TIGR00191 139 allGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtA 207 allGGl + ++ + ++ +k+ ++lk+v++iP + ++T+++R+ LP+ ++++d+v n ++a+lv+A lcl|NCBI__GCF_900115975.1:WP_092481851.1 135 ALLGGLIIYTSVEGEITWTKIDLPPALKAVVAIPDFIMNTRDTREALPQLVTMRDAVYNIGRAALLVAA 203 ********99999866666655559******************************************** PP TIGR00191 208 lvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeekeekaqel 276 l ++ +l +am Dr+hqpyR+ iP+++++ aa+ +ga g++lSGaGpti+ala+ ++e +a+ + lcl|NCBI__GCF_900115975.1:WP_092481851.1 204 LQKG-DLSILGTAMDDRLHQPYRQGAIPGFKKVISAARLAGARGVALSGAGPTIVALADGNFELIAEVM 271 ****.77888899*************************************************9999998 PP TIGR00191 277 leklakegi 285 ++++ + g lcl|NCBI__GCF_900115975.1:WP_092481851.1 272 KNTFRECGV 280 888876555 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.52 // [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