Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_011319547.1 AVA_RS14135 homoserine kinase
Query= curated2:B2J7E8 (304 letters) >NCBI__GCF_000204075.1:WP_011319547.1 Length = 302 Score = 479 bits (1232), Expect = e-140 Identities = 240/301 (79%), Positives = 265/301 (88%) Query: 1 MSVVSAITVTVPATTANLGPGFDCIGAALKLYNEFRFTRLEEGGLIIHVSGTEAERVQTD 60 MSVVS++TV VP TTANLGPGFDCIGAAL +YN+F+FTRLE LII +G EAERV TD Sbjct: 1 MSVVSSVTVKVPGTTANLGPGFDCIGAALTIYNQFQFTRLETSELIIQATGAEAERVPTD 60 Query: 61 ESNLLYQAFVKFYQHIEQTPPTVKIEIKLGVPLARGLGSSATAIVGGLVAANQLEGATLS 120 ESNLLYQAFVK YQ+I+QTPP VK+EI+LGVPLARGLGSSATAIVGGLVAAN+L G LS Sbjct: 61 ESNLLYQAFVKLYQYIDQTPPGVKVEIELGVPLARGLGSSATAIVGGLVAANRLAGEPLS 120 Query: 121 QSQVMELAIAMEGHPDNVVPALLGGCRLAATSGTAWEICDVPWHKDVVPVVAIPNFELST 180 Q+QVMELAIA+EGHPDNVVPAL+GGCRLAAT WEICDVPWH D+VPV+AIP+FELST Sbjct: 121 QAQVMELAIAIEGHPDNVVPALVGGCRLAATGAMGWEICDVPWHGDIVPVLAIPDFELST 180 Query: 181 SEARGVLPTEVSRADAIFNTAHLGLLLRGLETGNGQWLKTALQDKLHQPYRKALIPSYDA 240 SEAR VLPTE SRADAIFNTAHLGLLLRGL+TG G+WL+ ALQDKLHQPYR+ALIP YDA Sbjct: 181 SEARRVLPTEYSRADAIFNTAHLGLLLRGLQTGKGEWLRAALQDKLHQPYRQALIPGYDA 240 Query: 241 VNIAAVSAGAYGMVISGAGPTLLALADQLHSEAVEAAMLAAWQEEGITAEVRSLSLDTQG 300 VN AAV+AGAYGMVISGAGPTLLALAD H+ AV AAM AW+E GI A VRSL+LDT G Sbjct: 241 VNTAAVAAGAYGMVISGAGPTLLALADVSHAAAVAAAMSTAWREAGIKAVVRSLALDTHG 300 Query: 301 A 301 A Sbjct: 301 A 301 Lambda K H 0.317 0.132 0.380 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: 363 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: 304 Length of database: 302 Length adjustment: 27 Effective length of query: 277 Effective length of database: 275 Effective search space: 76175 Effective search space used: 76175 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: 48 (23.1 bits)
Align candidate WP_011319547.1 AVA_RS14135 (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.3697081.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-97 312.5 0.0 1.2e-97 312.3 0.0 1.0 1 NCBI__GCF_000204075.1:WP_011319547.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000204075.1:WP_011319547.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 312.3 0.0 1.2e-97 1.2e-97 1 299 [. 7 301 .. 7 302 .] 0.98 Alignments for each domain: == domain 1 score: 312.3 bits; conditional E-value: 1.2e-97 TIGR00191 1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkvlkk 73 ++vkvP+++ANlgpGfD++G+al+ ++++ t e+ + ++a+g ++e++p++ + Nl+yq+++k+++ NCBI__GCF_000204075.1:WP_011319547.1 7 VTVKVPGTTANLGPGFDCIGAALTIYNQFQFTR---LETSELIIQATGAEAERVPTD-ESNLLYQAFVKLYQY 75 68*****************************99...888888899************.*************** PP TIGR00191 74 lgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvapallGGlql 146 ++ +++vk+++e +pl+rGLGSSa+aiv++++aan lag++ls++++++la+++EgHpDNv pal+GG+ l NCBI__GCF_000204075.1:WP_011319547.1 76 IDQTPPGVKVEIELGVPLARGLGSSATAIVGGLVAANRLAGEPLSQAQVMELAIAIEGHPDNVVPALVGGCRL 148 ************************************************************************* PP TIGR00191 147 avkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAlvskdkadllai 219 a + e+ +vP + ++ vl+iP +e+sT eaR vLP +ysr+d++fn++hl++l l ++ k ++l+ NCBI__GCF_000204075.1:WP_011319547.1 149 AATGAMGWEICDVPWHGDIVPVLAIPDFELSTSEARRVLPTEYSRADAIFNTAHLGLLLRGLQTG-KGEWLRA 220 **99999**********************************************************.******* PP TIGR00191 220 amkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.eekaqelleklakegieltvkv 291 a++D++hqpyR+ liP+++++++aa ++ga+g+++SGaGpt+lala+ ++ + a+ + + ++gi++ v+ NCBI__GCF_000204075.1:WP_011319547.1 221 ALQDKLHQPYRQALIPGYDAVNTAAVAAGAYGMVISGAGPTLLALADVSHaAAVAAAMSTAWREAGIKAVVRS 293 ************************************************997888888889999********** PP TIGR00191 292 leldtdga 299 l ldt+ga NCBI__GCF_000204075.1:WP_011319547.1 294 LALDTHGA 301 *****998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (302 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: 13.25 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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