Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_069664979.1 BCR25_RS17885 homoserine kinase
Query= curated2:Q831T0 (287 letters) >NCBI__GCF_001730305.1:WP_069664979.1 Length = 287 Score = 417 bits (1072), Expect = e-121 Identities = 205/287 (71%), Positives = 248/287 (86%) Query: 1 MKIRVPATSANLGPGFDSCGIALSAYLTINVLGESEFWEIQHTLGEEISTNEENLLIQTA 60 MKIRVPATSANLGPGFDSCGIALS YL+I VL +E W+I H+LG +I +++ NLL+QTA Sbjct: 1 MKIRVPATSANLGPGFDSCGIALSQYLSIEVLENAEEWKIIHSLGADIPSDKTNLLLQTA 60 Query: 61 LKIAPELTPKVIRMVSDIPLARGLGSSSSVIVAGIELANRLAHLNLSPKEKVRLATEMEG 120 LK+AP L PKV++M SDIPLARGLGSSSSVIVAGIELANRL +LNLS KEK+R+ATE+EG Sbjct: 61 LKLAPNLAPKVLKMTSDIPLARGLGSSSSVIVAGIELANRLGNLNLSQKEKLRIATEIEG 120 Query: 121 HPDNVAPAILGDFVVASHVENQVYHVKHHFPMCDVIAFIPEEPLFTEKSRAVLPEKLAYK 180 HPDNVAPAI GDFVVAS+V+ V++VKHHFPMCDVIA++P+E L T +SR+VLP + YK Sbjct: 121 HPDNVAPAICGDFVVASYVDGDVHYVKHHFPMCDVIAYVPDEHLLTTESRSVLPNTMPYK 180 Query: 181 EAVAASSIANVMIAAILNGDLPLAGKMMEQDKWHETYRRSLVPHLKEIRRLTQQKGAYGS 240 +AV ASSIANVMIAAILNG+LPLAG MME+D+WHE YRR LVPHL +IR L Q+ G YG+ Sbjct: 181 DAVKASSIANVMIAAILNGNLPLAGLMMEEDRWHEAYRRKLVPHLDQIRELGQKIGIYGA 240 Query: 241 FLSGAGPTVLILSPEERTNEIVQSLEKLSTKASIQIFNIDQEGVQVF 287 FLSGAGPTVLIL+PEE T+++V++LEK+ A+I + +IDQEG QVF Sbjct: 241 FLSGAGPTVLILTPEENTSQMVKALEKMPKSATINVLSIDQEGTQVF 287 Lambda K H 0.317 0.133 0.375 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: 328 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: 287 Length of database: 287 Length adjustment: 26 Effective length of query: 261 Effective length of database: 261 Effective search space: 68121 Effective search space used: 68121 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: 47 (22.7 bits)
Align candidate WP_069664979.1 BCR25_RS17885 (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.1082334.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-76 241.7 0.1 4.7e-76 241.5 0.1 1.0 1 NCBI__GCF_001730305.1:WP_069664979.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001730305.1:WP_069664979.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 241.5 0.1 4.7e-76 4.7e-76 1 301 [. 1 286 [. 1 287 [] 0.91 Alignments for each domain: == domain 1 score: 241.5 bits; conditional E-value: 4.7e-76 TIGR00191 1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkvlkk 73 +k++vPa+sANlgpGfD+ G+als++l++ v e +++++k +++ g + ip++ + Nl+ q+a+k++ + NCBI__GCF_001730305.1:WP_069664979.1 1 MKIRVPATSANLGPGFDSCGIALSQYLSIEVLE---NAEEWKIIHSLGAD---IPSD-KTNLLLQTALKLAPN 66 589*****************************9...55666645556555...****.9**********9987 PP TIGR00191 74 lgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvapallGGlql 146 l + l+++++ipl+rGLGSS++ iva++ +an l +l+ls++e+l +a+++EgHpDNvapa+ G +++ NCBI__GCF_001730305.1:WP_069664979.1 67 LAPK----VLKMTSDIPLARGLGSSSSVIVAGIELANRLGNLNLSQKEKLRIATEIEGHPDNVAPAICGDFVV 135 6655....78889**********************************************************99 PP TIGR00191 147 avkedd..llevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAlvskdkadll 217 a d + ++ + P +v++ +P ++ T e+R vLP+ +++d+v+++s ++v+++A+ +++ ++ + NCBI__GCF_001730305.1:WP_069664979.1 136 ASYVDGdvHYVKHHFP---MCDVIAYVPDEHLLTTESRSVLPNTMPYKDAVKASSIANVMIAAILNGNLPLAG 205 8877773344555555...79**********************************************888888 PP TIGR00191 218 aiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeekeekaqelleklakegieltvk 290 ++ +Dr h+ yR+kl+P+l++i++ ++ g++g lSGaGpt+l l+ ee+ ++++++ l k + +t++ NCBI__GCF_001730305.1:WP_069664979.1 206 LMMEEDRWHEAYRRKLVPHLDQIRELGQKIGIYGAFLSGAGPTVLILTPEEN---TSQMVKALEKMPKSATIN 275 88889**********************************************9...888899999999999*** PP TIGR00191 291 vleldtdgaev 301 vl++d++g++v NCBI__GCF_001730305.1:WP_069664979.1 276 VLSIDQEGTQV 286 ********998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (287 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: 15.26 // [ok]
This GapMind analysis is from Jul 26 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