Align homoserine kinase; EC 2.7.1.39 (characterized)
to candidate WP_012542912.1 KVAR_RS21885 homoserine kinase
Query= CharProtDB::CH_002113 (310 letters) >NCBI__GCF_000025465.1:WP_012542912.1 Length = 309 Score = 563 bits (1451), Expect = e-165 Identities = 274/308 (88%), Positives = 291/308 (94%) Query: 1 MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGRFADKLPSEP 60 MVKVYAPASSANMSVGFDVLGAAVTPVDG LLGD VTVEAAE FSL+NLGRFA KLP+ P Sbjct: 1 MVKVYAPASSANMSVGFDVLGAAVTPVDGTLLGDNVTVEAAEQFSLHNLGRFASKLPTAP 60 Query: 61 RENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLND 120 +ENIVYQCWE FCQE+GK +PV MTLEKNMPIGSGLGSSACSVVAAL+AMNE CGKPLN+ Sbjct: 61 QENIVYQCWESFCQEIGKTVPVTMTLEKNMPIGSGLGSSACSVVAALVAMNEFCGKPLNE 120 Query: 121 TRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWVLAYPGI 180 TR+LALMGE+EGRISGSIHYDNVAPC+LGGMQLMIEEN IISQQVPGFDEWLWVLAYPGI Sbjct: 121 TRMLALMGEMEGRISGSIHYDNVAPCYLGGMQLMIEENGIISQQVPGFDEWLWVLAYPGI 180 Query: 181 KVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQPELAAKLMKDVIAEPYRERLLP 240 KVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACY+RQP+LAAKLMKDVIAEPYR +LLP Sbjct: 181 KVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYTRQPQLAAKLMKDVIAEPYRTKLLP 240 Query: 241 GFRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVADWLGKNYLQNQEGFVHICRL 300 GF +ARQA EIGA A GISGSGPTLFALCDKP+TAQRVADWLG +YLQNQEGFVHICRL Sbjct: 241 GFSEARQATMEIGAQACGISGSGPTLFALCDKPDTAQRVADWLGAHYLQNQEGFVHICRL 300 Query: 301 DTAGARVL 308 DTAGARV+ Sbjct: 301 DTAGARVV 308 Lambda K H 0.321 0.136 0.412 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: 428 Number of extensions: 9 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: 310 Length of database: 309 Length adjustment: 27 Effective length of query: 283 Effective length of database: 282 Effective search space: 79806 Effective search space used: 79806 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_012542912.1 KVAR_RS21885 (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.4962.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-123 395.4 0.0 7e-123 395.3 0.0 1.0 1 lcl|NCBI__GCF_000025465.1:WP_012542912.1 KVAR_RS21885 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025465.1:WP_012542912.1 KVAR_RS21885 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 395.3 0.0 7e-123 7e-123 1 302 [. 2 308 .. 2 309 .] 0.99 Alignments for each domain: == domain 1 score: 395.3 bits; conditional E-value: 7e-123 TIGR00191 1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdk.sleaegegvekipkesdkNliyqvak 68 +kv++PassAN+++GfDvlG+a+++v++ l++++v++e++++ sl++ g++++k+p+ +++N++yq+++ lcl|NCBI__GCF_000025465.1:WP_012542912.1 2 VKVYAPASSANMSVGFDVLGAAVTPVDGTLLGDNVTVEAAEQfSLHNLGRFASKLPTAPQENIVYQCWE 70 69*************************************9999************************** PP TIGR00191 69 kvlkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg...... 131 ++++ gk pv +t+ek++p+g+GLGSSa+++vaa++a+ne++g++l+++++l+l++++Eg lcl|NCBI__GCF_000025465.1:WP_012542912.1 71 SFCQEIGKT-VPVTMTLEKNMPIGSGLGSSACSVVAALVAMNEFCGKPLNETRMLALMGEMEGrisgsi 138 *********.9********************************************************** PP TIGR00191 132 HpDNvapallGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlsh 200 H+DNvap++lGG+ql+++e+ +++++vP ++++ +vl++P+i+vsTaeaRa+LP++y+rqd++++++h lcl|NCBI__GCF_000025465.1:WP_012542912.1 139 HYDNVAPCYLGGMQLMIEENG-IISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRH 206 *********************.*********************************************** PP TIGR00191 201 lavlvtAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek 269 la++++A++++ +++l+a++mkD++++pyR+kl+P+++e +qa+ e ga + ++SG+Gpt++al+++ + lcl|NCBI__GCF_000025465.1:WP_012542912.1 207 LAGFIHACYTR-QPQLAAKLMKDVIAEPYRTKLLPGFSEARQATMEIGAQACGISGSGPTLFALCDKPD 274 ***********.********************************************************* PP TIGR00191 270 .eekaqelleklakegieltvkvleldtdgaeve 302 +++++++l ++ +++e++v++++ldt+ga+v+ lcl|NCBI__GCF_000025465.1:WP_012542912.1 275 tAQRVADWLGAHYLQNQEGFVHICRLDTAGARVV 308 *******************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (309 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: 11.24 // [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