Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_011610781.1 TERY_RS04735 homoserine kinase
Query= curated2:B2J7E8 (304 letters) >NCBI__GCF_000014265.1:WP_011610781.1 Length = 305 Score = 405 bits (1042), Expect = e-118 Identities = 197/302 (65%), Positives = 246/302 (81%), Gaps = 1/302 (0%) Query: 1 MSVVSAITVTVPATTANLGPGFDCIGAALKLYNEFRFTRLEEGGLI-IHVSGTEAERVQT 59 M+ +S+ITV+VPATTANLGPGFDC+GAA+ LYN F+F+ + + I V+G EA +V T Sbjct: 1 MTTLSSITVSVPATTANLGPGFDCLGAAISLYNRFKFSIADSAIEVKITVTGKEAPKVST 60 Query: 60 DESNLLYQAFVKFYQHIEQTPPTVKIEIKLGVPLARGLGSSATAIVGGLVAANQLEGATL 119 D +NL YQAFVK Y++I QTPP V +EI LGVPLARGLGSSATAIVGGL+ ANQL G+ L Sbjct: 61 DRNNLAYQAFVKLYEYINQTPPCVLVEIDLGVPLARGLGSSATAIVGGLLGANQLAGSPL 120 Query: 120 SQSQVMELAIAMEGHPDNVVPALLGGCRLAATSGTAWEICDVPWHKDVVPVVAIPNFELS 179 SQ++VM LAIA+EGHPDNVVPALLGGCRL A++ W +CD+PWH D+VPVVAIP+FELS Sbjct: 121 SQTEVMNLAIAIEGHPDNVVPALLGGCRLTASTSKGWVVCDIPWHPDIVPVVAIPDFELS 180 Query: 180 TSEARGVLPTEVSRADAIFNTAHLGLLLRGLETGNGQWLKTALQDKLHQPYRKALIPSYD 239 T+EAR V+PTE R+DAIFN AHLG+LLRGLETG G+WL+ +QDK+HQPYRK+LI Y+ Sbjct: 181 TTEARRVIPTEYIRSDAIFNCAHLGILLRGLETGYGEWLQAGMQDKIHQPYRKSLIKGYE 240 Query: 240 AVNIAAVSAGAYGMVISGAGPTLLALADQLHSEAVEAAMLAAWQEEGITAEVRSLSLDTQ 299 V AA++AGAY MVISGAGPTLLAL + L S V AAM AW+ +G+ +V++L ++T+ Sbjct: 241 YVRSAALNAGAYEMVISGAGPTLLALTNSLTSSKVIAAMTGAWENQGVVTQVQALEINTR 300 Query: 300 GA 301 GA Sbjct: 301 GA 302 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: 317 Number of extensions: 7 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: 304 Length of database: 305 Length adjustment: 27 Effective length of query: 277 Effective length of database: 278 Effective search space: 77006 Effective search space used: 77006 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_011610781.1 TERY_RS04735 (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.11536.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-93 296.9 0.0 6.8e-93 296.8 0.0 1.0 1 lcl|NCBI__GCF_000014265.1:WP_011610781.1 TERY_RS04735 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000014265.1:WP_011610781.1 TERY_RS04735 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 296.8 0.0 6.8e-93 6.8e-93 2 299 .. 8 302 .. 7 305 .] 0.96 Alignments for each domain: == domain 1 score: 296.8 bits; conditional E-value: 6.8e-93 TIGR00191 2 kvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkv 70 +v+vPa++ANlgpGfD+lG+a+sl++++ + a ++ + +++ +g+++ k++++ ++Nl+yq+++k+ lcl|NCBI__GCF_000014265.1:WP_011610781.1 8 TVSVPATTANLGPGFDCLGAAISLYNRFKFSI--ADSAIEVKITVTGKEAPKVSTD-RNNLAYQAFVKL 73 79**************************9998..4444444599************.************ PP TIGR00191 71 lkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvapa 139 ++ ++ ++ v ++++ +pl+rGLGSSa+aiv++++ an+lag +ls++e+++la+++EgHpDNv pa lcl|NCBI__GCF_000014265.1:WP_011610781.1 74 YEYINQTPPCVLVEIDLGVPLARGLGSSATAIVGGLLGANQLAGSPLSQTEVMNLAIAIEGHPDNVVPA 142 ********************************************************************* PP TIGR00191 140 llGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAl 208 llGG+ l+ + + +v ++P ++++ v++iP +e+sT eaR v+P +y r+d++fn +hl++l l lcl|NCBI__GCF_000014265.1:WP_011610781.1 143 LLGGCRLTASTSKGWVVCDIPWHPDIVPVVAIPDFELSTTEARRVIPTEYIRSDAIFNCAHLGILLRGL 211 ***********999******************************************************* PP TIGR00191 209 vskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.eekaqel 276 ++ ++l+ m+D++hqpyR++li +++ ++ aa ++ga+ +++SGaGpt+lal++ + + + + lcl|NCBI__GCF_000014265.1:WP_011610781.1 212 ETG-YGEWLQAGMQDKIHQPYRKSLIKGYEYVRSAALNAGAYEMVISGAGPTLLALTNSLTsSKVIAAM 279 ***.********************************************************966666778 PP TIGR00191 277 leklakegieltvkvleldtdga 299 + ++g ++v+ le++t ga lcl|NCBI__GCF_000014265.1:WP_011610781.1 280 TGAWENQGVVTQVQALEINTRGA 302 88999999*********999997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (305 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: 00:00:00.01 # Mc/sec: 7.69 // [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