Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_012408880.1 NPUN_RS11540 homoserine kinase
Query= curated2:B2J7E8 (304 letters) >NCBI__GCF_000020025.1:WP_012408880.1 Length = 304 Score = 595 bits (1534), Expect = e-175 Identities = 304/304 (100%), Positives = 304/304 (100%) Query: 1 MSVVSAITVTVPATTANLGPGFDCIGAALKLYNEFRFTRLEEGGLIIHVSGTEAERVQTD 60 MSVVSAITVTVPATTANLGPGFDCIGAALKLYNEFRFTRLEEGGLIIHVSGTEAERVQTD Sbjct: 1 MSVVSAITVTVPATTANLGPGFDCIGAALKLYNEFRFTRLEEGGLIIHVSGTEAERVQTD 60 Query: 61 ESNLLYQAFVKFYQHIEQTPPTVKIEIKLGVPLARGLGSSATAIVGGLVAANQLEGATLS 120 ESNLLYQAFVKFYQHIEQTPPTVKIEIKLGVPLARGLGSSATAIVGGLVAANQLEGATLS Sbjct: 61 ESNLLYQAFVKFYQHIEQTPPTVKIEIKLGVPLARGLGSSATAIVGGLVAANQLEGATLS 120 Query: 121 QSQVMELAIAMEGHPDNVVPALLGGCRLAATSGTAWEICDVPWHKDVVPVVAIPNFELST 180 QSQVMELAIAMEGHPDNVVPALLGGCRLAATSGTAWEICDVPWHKDVVPVVAIPNFELST Sbjct: 121 QSQVMELAIAMEGHPDNVVPALLGGCRLAATSGTAWEICDVPWHKDVVPVVAIPNFELST 180 Query: 181 SEARGVLPTEVSRADAIFNTAHLGLLLRGLETGNGQWLKTALQDKLHQPYRKALIPSYDA 240 SEARGVLPTEVSRADAIFNTAHLGLLLRGLETGNGQWLKTALQDKLHQPYRKALIPSYDA Sbjct: 181 SEARGVLPTEVSRADAIFNTAHLGLLLRGLETGNGQWLKTALQDKLHQPYRKALIPSYDA 240 Query: 241 VNIAAVSAGAYGMVISGAGPTLLALADQLHSEAVEAAMLAAWQEEGITAEVRSLSLDTQG 300 VNIAAVSAGAYGMVISGAGPTLLALADQLHSEAVEAAMLAAWQEEGITAEVRSLSLDTQG Sbjct: 241 VNIAAVSAGAYGMVISGAGPTLLALADQLHSEAVEAAMLAAWQEEGITAEVRSLSLDTQG 300 Query: 301 AKSF 304 AKSF Sbjct: 301 AKSF 304 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: 458 Number of extensions: 5 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: 304 Length adjustment: 27 Effective length of query: 277 Effective length of database: 277 Effective search space: 76729 Effective search space used: 76729 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_012408880.1 NPUN_RS11540 (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.30676.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-97 309.6 0.0 9.5e-97 309.4 0.0 1.0 1 lcl|NCBI__GCF_000020025.1:WP_012408880.1 NPUN_RS11540 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020025.1:WP_012408880.1 NPUN_RS11540 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 309.4 0.0 9.5e-97 9.5e-97 2 300 .. 8 302 .. 7 304 .] 0.98 Alignments for each domain: == domain 1 score: 309.4 bits; conditional E-value: 9.5e-97 TIGR00191 2 kvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkv 70 +v+vPa++ANlgpGfD++G+al+l++e+ t e+ ++ g ++e++ ++ + Nl+yq+++k+ lcl|NCBI__GCF_000020025.1:WP_012408880.1 8 TVTVPATTANLGPGFDCIGAALKLYNEFRFTR---LEEGGLIIHVSGTEAERVQTD-ESNLLYQAFVKF 72 79****************************99...666666699999999***999.************ PP TIGR00191 71 lkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvapa 139 +++ ++ ++ vk++++ +pl+rGLGSSa+aiv++++aan+l g ls++++++la+++EgHpDNv pa lcl|NCBI__GCF_000020025.1:WP_012408880.1 73 YQHIEQTPPTVKIEIKLGVPLARGLGSSATAIVGGLVAANQLEGATLSQSQVMELAIAMEGHPDNVVPA 141 ********************************************************************* PP TIGR00191 140 llGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAl 208 llGG+ la ++ e+ +vP ++++ v++iPn+e+sT eaR+vLP ++sr+d++fn++hl++l l lcl|NCBI__GCF_000020025.1:WP_012408880.1 142 LLGGCRLAATSGTAWEICDVPWHKDVVPVVAIPNFELSTSEARGVLPTEVSRADAIFNTAHLGLLLRGL 210 ********************************************************************* PP TIGR00191 209 vskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.eekaqel 276 ++ + ++l++a++D++hqpyR+ liP +++++ aa +ga+g+++SGaGpt+lala++ + e ++ + lcl|NCBI__GCF_000020025.1:WP_012408880.1 211 ETG-NGQWLKTALQDKLHQPYRKALIPSYDAVNIAAVSAGAYGMVISGAGPTLLALADQLHsEAVEAAM 278 ***.*********************************************************99999*** PP TIGR00191 277 leklakegieltvkvleldtdgae 300 l +++egi ++v+ l+ldt+ga+ lcl|NCBI__GCF_000020025.1:WP_012408880.1 279 LAAWQEEGITAEVRSLSLDTQGAK 302 **********************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (304 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: 00:00:00.00 # Mc/sec: 9.53 // [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