Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_013074759.1 BTUS_RS03575 homoserine kinase
Query= curated2:Q3AAV5 (304 letters) >NCBI__GCF_000092905.1:WP_013074759.1 Length = 312 Score = 278 bits (712), Expect = 9e-80 Identities = 148/293 (50%), Positives = 191/293 (65%), Gaps = 3/293 (1%) Query: 2 VCVLIPATSANLGPGFDAVGMALSFYNEVSLGPSPKELEIEVFGDGAELISRDKNNLVYV 61 V V +PAT+ANLGPGFD++GMAL YNE+ L + L+ EV G GAE+I N++Y Sbjct: 3 VKVRVPATTANLGPGFDSLGMALQLYNEIELEIMDQGLQFEVTGAGAEMIPATSENVIYK 62 Query: 62 AITKIFERLGKTPRNLKLTLKNRVPLARGLGSSAAAIVGGLVAANAYLGNPLPKDELLRL 121 A+ +F++LG+ LKL N VP+ RGLGSSA AIVGGL AAN G PL D+LL L Sbjct: 63 AVQYVFDQLGRRRPGLKLRAHNAVPVTRGLGSSATAIVGGLAAANELCGRPLSADDLLEL 122 Query: 122 ATELEGHPDNVAPALLGGVVVSGFDRDKVKYLKLPVP-EVEVVVAIPKFQLKTADSRQIL 180 A +EGHPDNVA AL GG+VVSG +K +Y+KLPVP ++ VV +P+ L T DSR++L Sbjct: 123 AVAMEGHPDNVAAALFGGIVVSGKTGEKTRYVKLPVPQDLVCVVVVPEVPLATKDSRKVL 182 Query: 181 PAEIPFSQAVLNVNRVSFLIAAFCLKKYEYLQIGMEDYLHQPYRSQLIPGFYQVVEEAKK 240 P +PFS AV NVNRV L+ A E M+D LH+PYR LIPG + +K Sbjct: 183 PTSVPFSDAVHNVNRVGLLVGALATGDLETAGAAMDDVLHEPYRMSLIPGMGAAADAGRK 242 Query: 241 AGAYGVALSGSGPTVIALAREG--KAVGRAIEETFLNFGVEAEIIYTRPEERG 291 AGA GVALSGSGP++IA R G + VG A+ + + G+ A + RP+ RG Sbjct: 243 AGALGVALSGSGPSLIAFCRAGDEEPVGPAMIQAWAGAGLAAHSMVLRPDLRG 295 Lambda K H 0.318 0.139 0.396 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: 283 Number of extensions: 11 Number of successful extensions: 3 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: 304 Length of database: 312 Length adjustment: 27 Effective length of query: 277 Effective length of database: 285 Effective search space: 78945 Effective search space used: 78945 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_013074759.1 BTUS_RS03575 (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.21117.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-93 297.2 0.0 5.9e-93 297.0 0.0 1.0 1 lcl|NCBI__GCF_000092905.1:WP_013074759.1 BTUS_RS03575 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092905.1:WP_013074759.1 BTUS_RS03575 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 297.0 0.0 5.9e-93 5.9e-93 1 302 [. 3 299 .. 3 301 .. 0.96 Alignments for each domain: == domain 1 score: 297.0 bits; conditional E-value: 5.9e-93 TIGR00191 1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakk 69 +kv+vPa++ANlgpGfD+lG+al+l++e+ +++ ++ ++e +g g+e ip++ ++N+iy+++++ lcl|NCBI__GCF_000092905.1:WP_013074759.1 3 VKVRVPATTANLGPGFDSLGMALQLYNEIELEI----MDQGLQFEVTGAGAEMIPAT-SENVIYKAVQY 66 69*****************************99....34444599************.9********** PP TIGR00191 70 vlkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvap 138 v+++lg+r +++kl+ ++ +p++rGLGSSa+aiv++++aanel+g +ls +ll+la+++EgHpDNva+ lcl|NCBI__GCF_000092905.1:WP_013074759.1 67 VFDQLGRRRPGLKLRAHNAVPVTRGLGSSATAIVGGLAAANELCGRPLSADDLLELAVAMEGHPDNVAA 135 ********************************************************************* PP TIGR00191 139 allGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtA 207 al+GG++++ k +++ +k+P ++l +v+v+P++ + T+++R+vLP +++ +d+v n++++++lv A lcl|NCBI__GCF_000092905.1:WP_013074759.1 136 ALFGGIVVSGKTGEKTRYVKLPVPQDLVCVVVVPEVPLATKDSRKVLPTSVPFSDAVHNVNRVGLLVGA 204 ***********9999999999999********************************************* PP TIGR00191 208 lvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.eekaqe 275 l ++ + + am D++h+pyR++liP++ + a +++galg++lSG+Gp+++a+++ + e lcl|NCBI__GCF_000092905.1:WP_013074759.1 205 LATG-DLETAGAAMDDVLHEPYRMSLIPGMGAAADAGRKAGALGVALSGSGPSLIAFCRAGDeEPVGPA 272 ****.78888899***********************************************99777889* PP TIGR00191 276 lleklakegieltvkvleldtdgaeve 302 +++ +a +g ++++ vl++d g++v+ lcl|NCBI__GCF_000092905.1:WP_013074759.1 273 MIQAWAGAGLAAHSMVLRPDLRGVQVI 299 ************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (312 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.24 // [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