Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_012504855.1 PAES_RS01290 homoserine kinase
Query= reanno::Cola:Echvi_2001 (311 letters) >NCBI__GCF_000020625.1:WP_012504855.1 Length = 320 Score = 292 bits (748), Expect = 6e-84 Identities = 158/320 (49%), Positives = 208/320 (65%), Gaps = 12/320 (3%) Query: 1 MKKVTAFAPATVANVSCGFDILGFAVEEMGDKVTVSLADEPG----VRVVRIEGDGGRLP 56 MK VT FA AT+ NV+CGFD+LGFA++E GD+V ++L +E V + I GDGG LP Sbjct: 1 MKTVTGFASATIGNVACGFDVLGFAIKEPGDEVILTLHEESSSESPVSIKTIHGDGGALP 60 Query: 57 YEVDKNTCGVALKAFLA------AIDYKGGLEVELYKGLPLGSGMGSSAASSVAALEAAN 110 + KNT + FL ID++G +++EL K LPL SGMGSSAAS+ AAL AAN Sbjct: 61 RDPKKNTSSFVVLKFLEYLRNHKGIDFQGHIDLELKKNLPLSSGMGSSAASAAAALIAAN 120 Query: 111 QLLGNPLDKKALLPFAMKAEGVACGAEHADNVAPSLLGGFVLIRSYHPLDVTKLHVPKGL 170 +LLG P K L+ FA++ E VACG+ HADN AP++LG F+LIRSY+PLD+ + P L Sbjct: 121 ELLGGPCTKMELVHFAIEGERVACGSAHADNAAPAMLGNFILIRSYNPLDLITIPPPDQL 180 Query: 171 YCALVHPHLELNTADSRSVLRQQVPLKDAITQSGNIAGLVAGLYQEDMGLISRSLQDVIA 230 YC L HPH+EL TA +RSVL + + LK A Q GN+ L++GL D LI R+L DVIA Sbjct: 181 YCTLAHPHIELRTAYARSVLPRSISLKTATEQWGNVGALISGLLTSDYELIGRALVDVIA 240 Query: 231 EPSRSVLIPGFDEIKSAIKEVGALGVGISGSGPTTFILAPSREVAERASEICQEVFDKIG 290 EP R+ LIPGF ++K A GALG I+GSGP+ F + S AE+A + F I Sbjct: 241 EPKRATLIPGFYQVKEAALGAGALGCSIAGSGPSIFAFSSSAATAEKAGTAMRNAFLDID 300 Query: 291 --LEVDLYVSAVNTKGTYVI 308 LE D++VS V +G ++ Sbjct: 301 EHLEADIWVSPVCREGARIL 320 Lambda K H 0.317 0.136 0.383 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: 259 Number of extensions: 15 Number of successful extensions: 3 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: 311 Length of database: 320 Length adjustment: 27 Effective length of query: 284 Effective length of database: 293 Effective search space: 83212 Effective search space used: 83212 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_012504855.1 PAES_RS01290 (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.24678.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-64 202.6 0.0 3.8e-64 202.4 0.0 1.0 1 lcl|NCBI__GCF_000020625.1:WP_012504855.1 PAES_RS01290 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020625.1:WP_012504855.1 PAES_RS01290 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 202.4 0.0 3.8e-64 3.8e-64 7 286 .. 10 301 .. 5 320 .] 0.87 Alignments for each domain: == domain 1 score: 202.4 bits; conditional E-value: 3.8e-64 TIGR00191 7 assANlgpGfDvlGlalslvlellvtedvaqeskdk..sleaegegvekipkesdkNliyqvakkvlkk 73 a+ N++ GfDvlG a+++ + ++ + +s ++ s+++ + +p +++kN v++k+l+ lcl|NCBI__GCF_000020625.1:WP_012504855.1 10 ATIGNVACGFDVLGFAIKEPGDEVILTLHEESSSESpvSIKTIHGDGGALPRDPKKNTSSFVVLKFLEY 78 7889**************986655555444444444678888777779*********888888888776 PP TIGR00191 74 lgkr.....vkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg...... 131 l ++ + l+++k++pl++G+GSSaa+ +aa+iaanel+g +++k+el+++a++ E+ lcl|NCBI__GCF_000020625.1:WP_012504855.1 79 LRNHkgidfQGHIDLELKKNLPLSSGMGSSAASAAAALIAANELLGGPCTKMELVHFAIEGERvacgsa 147 66554555666789******************************************************* PP TIGR00191 132 HpDNvapallGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlsh 200 H+DN+apa+lG + l +++ l + +P ++l++ l+ P+ie+ Ta aR vLP++ s++ + + + lcl|NCBI__GCF_000020625.1:WP_012504855.1 148 HADNAAPAMLGNFILIRSYNP-LDLITIPPPDQLYCTLAHPHIELRTAYARSVLPRSISLKTATEQWGN 215 ******************999.888889889************************************** PP TIGR00191 201 lavlvtAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek 269 ++ l+ l + +l+ a+ D++++p+R++liP++ ++k+aa +galg + G+Gp+i+a+++ lcl|NCBI__GCF_000020625.1:WP_012504855.1 216 VGALISGLLTS-DYELIGRALVDVIAEPKRATLIPGFYQVKEAALGAGALGCSIAGSGPSIFAFSSSAA 283 ***********.7788888999*******************************************9999 PP TIGR00191 270 .eekaqelleklakegie 286 +eka +++ + + +e lcl|NCBI__GCF_000020625.1:WP_012504855.1 284 tAEKAGTAMRNAFLDIDE 301 899998888877666554 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (320 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: 10.16 // [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