Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_013842893.1 DESRU_RS14815 homoserine kinase
Query= BRENDA::P07128 (309 letters) >NCBI__GCF_000215085.1:WP_013842893.1 Length = 300 Score = 203 bits (516), Expect = 5e-57 Identities = 124/303 (40%), Positives = 178/303 (58%), Gaps = 16/303 (5%) Query: 7 VGRKVTVTVPGSSANLGPGFDTLGLALSVYDTVEVEIIPSGLEVEVFGEGQGEVPLDGSH 66 + V VTVP ++AN+GPGFD LG+AL +Y+ VE+ GL +E+ GEG G++ D + Sbjct: 1 MNNSVKVTVPATTANMGPGFDCLGMALKLYNQVEISPTDGGLAIEIQGEGAGDIRKDEGN 60 Query: 67 LVVKAIRAGLKAADAEVPGLRVVCHNNIPQSRGLGSSAAAAVAGVAAANGLADFPLTQEQ 126 +V KA+ + A PGL + N+IP +RGLGSSA+A V G+ AAN LA P T E+ Sbjct: 61 IVFKAVERLFQEAGRPCPGLVIKLTNHIPAARGLGSSASAIVGGLVAANRLAGDPFTPEK 120 Query: 127 IVQLSSAFEGHPDNAAASVLGGAVVSWTNLSIDGKSQPQYAAVPLEVQDNIRATALVPNF 186 ++ L++ EGHPDN A ++LGG ++S +GK P D + VP+F Sbjct: 121 LLALATELEGHPDNVAPALLGGIIISVVQ---EGKVHWLKITPP----DGLSTVVAVPDF 173 Query: 187 HASTEAVRRVLPTEVTHIDARFNVSRVAVMIVAL-QQRPDLLWEGTRDRLHQPYRAEVLP 245 ST A R VLP V+ DA FN+SR A+++ AL +R DLL D LHQPYR++++P Sbjct: 174 KLSTRAAREVLPKTVSLQDAVFNLSRSALLVGALCGKRLDLLQVAGEDLLHQPYRSQLVP 233 Query: 246 ITSEWVNRLRNRG-YAAYLSGAGPTAMVLSTEPIPD--KVLEDARESG-----IKVLELE 297 +E ++ R G LSGAGP + L+ P P +V+E++ + +KVLE Sbjct: 234 GMTEVISNARRAGALNVTLSGAGPAVIALTDGPNPQVAQVMENSFAAAGVKCLVKVLEPT 293 Query: 298 VAG 300 VAG Sbjct: 294 VAG 296 Lambda K H 0.315 0.132 0.377 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: 219 Number of extensions: 9 Number of successful extensions: 4 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: 309 Length of database: 300 Length adjustment: 27 Effective length of query: 282 Effective length of database: 273 Effective search space: 76986 Effective search space used: 76986 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_013842893.1 DESRU_RS14815 (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.3440.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-94 300.4 0.1 5.9e-94 300.3 0.1 1.0 1 lcl|NCBI__GCF_000215085.1:WP_013842893.1 DESRU_RS14815 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000215085.1:WP_013842893.1 DESRU_RS14815 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 300.3 0.1 5.9e-94 5.9e-94 1 301 [. 5 299 .. 5 300 .] 0.97 Alignments for each domain: == domain 1 score: 300.3 bits; conditional E-value: 5.9e-94 TIGR00191 1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakk 69 +kv+vPa++AN+gpGfD+lG+al+l++++ + + + +e++geg+ i k+ + N++ +++++ lcl|NCBI__GCF_000215085.1:WP_013842893.1 5 VKVTVPATTANMGPGFDCLGMALKLYNQVEISP----TDGGLAIEIQGEGAGDIRKD-EGNIVFKAVER 68 69*****************************99....44444699***********9.9********** PP TIGR00191 70 vlkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvap 138 ++++ g+ +++ ++++++ip++rGLGSSa+aiv++++aan lag +++ e+ll+la++lEgHpDNvap lcl|NCBI__GCF_000215085.1:WP_013842893.1 69 LFQEAGRPCPGLVIKLTNHIPAARGLGSSASAIVGGLVAANRLAGDPFTPEKLLALATELEGHPDNVAP 137 ********************************************************************* PP TIGR00191 139 allGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtA 207 allGG+ ++v ++ ++ lk+ + l +v+++P +++sT++aR+vLPk +s+qd+vfnls++a+lv A lcl|NCBI__GCF_000215085.1:WP_013842893.1 138 ALLGGIIISVVQEGKVHWLKITPPDGLSTVVAVPDFKLSTRAAREVLPKTVSLQDAVFNLSRSALLVGA 206 **********999988888886679******************************************** PP TIGR00191 208 lvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeekeekaqel 276 l k + dll++a +D +hqpyR++l+P++te+ a+ +gal++tlSGaGp+++al++ +++ aq + lcl|NCBI__GCF_000215085.1:WP_013842893.1 207 LCGK-RLDLLQVAGEDLLHQPYRSQLVPGMTEVISNARRAGALNVTLSGAGPAVIALTDGPNPQVAQVM 274 ****.**************************************************************** PP TIGR00191 277 leklakegieltvkvleldtdgaev 301 +++a +g ++ vkvle+ +gae+ lcl|NCBI__GCF_000215085.1:WP_013842893.1 275 ENSFAAAGVKCLVKVLEPTVAGAEI 299 ***********************98 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.37 // [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