Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_012676051.1 PERMA_RS05395 homoserine kinase
Query= curated2:C0QQC5 (300 letters) >NCBI__GCF_000021565.1:WP_012676051.1 Length = 300 Score = 588 bits (1517), Expect = e-173 Identities = 300/300 (100%), Positives = 300/300 (100%) Query: 1 MKVLKVKVPATTANLGAGFDTLGLALTLYNEFIVEEHDGVVIETEPKNEFLEIPENNLFI 60 MKVLKVKVPATTANLGAGFDTLGLALTLYNEFIVEEHDGVVIETEPKNEFLEIPENNLFI Sbjct: 1 MKVLKVKVPATTANLGAGFDTLGLALTLYNEFIVEEHDGVVIETEPKNEFLEIPENNLFI 60 Query: 61 QVIKYACERRGKTFHGAKLKQINRVPVARGLGSSATAIVGAIVVSSAVSKTELTDDIFFD 120 QVIKYACERRGKTFHGAKLKQINRVPVARGLGSSATAIVGAIVVSSAVSKTELTDDIFFD Sbjct: 61 QVIKYACERRGKTFHGAKLKQINRVPVARGLGSSATAIVGAIVVSSAVSKTELTDDIFFD 120 Query: 121 IAYRFEPHPDNLIPAWKGGFITALKDREKTYYNSIDFPEDIKAVVVIPEFELSTEKARSV 180 IAYRFEPHPDNLIPAWKGGFITALKDREKTYYNSIDFPEDIKAVVVIPEFELSTEKARSV Sbjct: 121 IAYRFEPHPDNLIPAWKGGFITALKDREKTYYNSIDFPEDIKAVVVIPEFELSTEKARSV 180 Query: 181 LPERIPLRDGIFNVQRVSLFLSALQNRRYDLLRVAMEDRFHQPYRKKLIPNFDRVVQNGY 240 LPERIPLRDGIFNVQRVSLFLSALQNRRYDLLRVAMEDRFHQPYRKKLIPNFDRVVQNGY Sbjct: 181 LPERIPLRDGIFNVQRVSLFLSALQNRRYDLLRVAMEDRFHQPYRKKLIPNFDRVVQNGY 240 Query: 241 DAGALGVSLSGAGSAILALADRNFEEIGKAMTEGFSEAGIRSEYKILDIDREGANLEILE 300 DAGALGVSLSGAGSAILALADRNFEEIGKAMTEGFSEAGIRSEYKILDIDREGANLEILE Sbjct: 241 DAGALGVSLSGAGSAILALADRNFEEIGKAMTEGFSEAGIRSEYKILDIDREGANLEILE 300 Lambda K H 0.320 0.138 0.392 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: 445 Number of extensions: 13 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: 300 Length of database: 300 Length adjustment: 27 Effective length of query: 273 Effective length of database: 273 Effective search space: 74529 Effective search space used: 74529 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_012676051.1 PERMA_RS05395 (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.4321.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-87 278.4 0.0 3.3e-87 278.1 0.0 1.0 1 lcl|NCBI__GCF_000021565.1:WP_012676051.1 PERMA_RS05395 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021565.1:WP_012676051.1 PERMA_RS05395 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 278.1 0.0 3.3e-87 3.3e-87 1 301 [. 4 296 .. 4 298 .. 0.94 Alignments for each domain: == domain 1 score: 278.1 bits; conditional E-value: 3.3e-87 TIGR00191 1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakk 69 lkvkvPa++ANlg GfD+lGlal+l++e++v+e ++ + +e+e ++ + +++Nl+ qv+k+ lcl|NCBI__GCF_000021565.1:WP_012676051.1 4 LKVKVPATTANLGAGFDTLGLALTLYNEFIVEE-------HDGVVIETEPKNEFLEIPENNLFIQVIKY 65 69*****************************99.......22244444444555555667********* PP TIGR00191 70 vlkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvap 138 +++ gk ++ kl+ + +p++rGLGSSa+aiv+a++ ++ +++l++ d+a E HpDN p lcl|NCBI__GCF_000021565.1:WP_012676051.1 66 ACERRGKTFHGAKLKQINRVPVARGLGSSATAIVGAIVVSSAVSKTELTDDIFFDIAYRFEPHPDNLIP 134 ********************************************************************* PP TIGR00191 139 allGGlqlavkedd..llevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlv 205 a GG+ +a+k+ + +++ P +++k+v+viP++e+sT++aR vLP++ +++d +fn+++++++ lcl|NCBI__GCF_000021565.1:WP_012676051.1 135 AWKGGFITALKDREktYYNSIDFP--EDIKAVVVIPEFELSTEKARSVLPERIPLRDGIFNVQRVSLFL 201 **********99883445566666..9****************************************** PP TIGR00191 206 tAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeekeekaq 274 Al ++ + dll++am+Dr+hqpyR+kliP+++++ q ++galg+ lSGaG++ilala+ ++ee+ + lcl|NCBI__GCF_000021565.1:WP_012676051.1 202 SALQNR-RYDLLRVAMEDRFHQPYRKKLIPNFDRVVQNGYDAGALGVSLSGAGSAILALADRNFEEIGK 269 ******.************************************************************** PP TIGR00191 275 elleklakegieltvkvleldtdgaev 301 + e ++++gi+ + k+l++d +ga++ lcl|NCBI__GCF_000021565.1:WP_012676051.1 270 AMTEGFSEAGIRSEYKILDIDREGANL 296 ************************987 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.80 // [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