Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_017600363.1 D471_RS0120555 homoserine kinase
Query= BRENDA::P07128 (309 letters) >NCBI__GCF_000341125.1:WP_017600363.1 Length = 326 Score = 202 bits (514), Expect = 9e-57 Identities = 117/271 (43%), Positives = 158/271 (58%), Gaps = 14/271 (5%) Query: 10 KVTVTVPGSSANLGPGFDTLGLALSVYDTVEVEIIPSG-LEVEVFGEGQGEVPLDGSHLV 68 +VTV P +SANLGPGFD LGLA+ +Y+ + + + VEV GEG GEVPLD HLV Sbjct: 8 RVTVHAPATSANLGPGFDALGLAVRLYNRFDAALRDDDRINVEVTGEGAGEVPLDERHLV 67 Query: 69 VKAIRAGLKAADAEVPGLRVVCHNNIPQSRGLGSSAAAAVAGVAAANGLADFP-----LT 123 V+A+R A ++PG+ + C NN+P +RGLGSS++A V GVAAA+ L Sbjct: 68 VRAMREAFDRAGEKLPGIDLTCVNNVPHARGLGSSSSAIVGGVAAASALLGRTGPGGGPD 127 Query: 124 QEQIVQLSSAFEGHPDNAAASVLGGAVVSWTNLSIDGKSQPQYAAVPLEVQDNIRATALV 183 ++ I ++++ EGHPDN A V GG V++ + + AV L I V Sbjct: 128 RDWIYRIAADIEGHPDNVAPCVYGGYTVAY-------RGHEGWGAVSLAPDARILPVLCV 180 Query: 184 PNFHASTEAVRRVLPTEVTHIDARFNVSRVAVMIVALQQRPDLLWEGTRDRLHQPYRAEV 243 P++ STE R +LP VTH DA FN R A+M A+ P+ L+ T DRLH+ YR Sbjct: 181 PSWRLSTERARGLLPERVTHADASFNAGRSALMTAAVCGHPETLYAATEDRLHESYREPA 240 Query: 244 LPITSEWVNRLRNR-GYAAYLSGAGPTAMVL 273 +P T E + LR R G A +SGAGPT +VL Sbjct: 241 MPRTLELIRDLRERDGLPAVVSGAGPTVLVL 271 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: 251 Number of extensions: 14 Number of successful extensions: 5 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: 326 Length adjustment: 27 Effective length of query: 282 Effective length of database: 299 Effective search space: 84318 Effective search space used: 84318 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_017600363.1 D471_RS0120555 (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.676467.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-64 201.9 0.0 6e-64 201.7 0.0 1.0 1 NCBI__GCF_000341125.1:WP_017600363.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000341125.1:WP_017600363.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 201.7 0.0 6e-64 6e-64 1 273 [. 9 281 .. 9 313 .. 0.89 Alignments for each domain: == domain 1 score: 201.7 bits; conditional E-value: 6e-64 TIGR00191 1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkvlkk 73 ++v++Pa+sANlgpGfD lGla+ l+++++ +++ ++e +geg+ ++p++ + l+ +++ + +++ NCBI__GCF_000341125.1:WP_017600363.1 9 VTVHAPATSANLGPGFDALGLAVRLYNRFDAAL---RDDDRINVEVTGEGAGEVPLD-ERHLVVRAMREAFDR 77 689**************************9888...3444447999999999*****.999************ PP TIGR00191 74 lgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelagl.....klskeelldlalllEgHpDNvapall 141 g++++++ lt +++p +rGLGSS++aiv++v+aa +l+g + ++ + +a +EgHpDNvap++ NCBI__GCF_000341125.1:WP_017600363.1 78 AGEKLPGIDLTCVNNVPHARGLGSSSSAIVGGVAAASALLGRtgpggGPDRDWIYRIAADIEGHPDNVAPCVY 150 ***************************************98733222579999******************** PP TIGR00191 142 GGlqlavkedd.llevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAlvskdk 213 GG+++a + ++ v P ++++ vl +P +sT+ aR++LP++++ +d+ fn+ ++a++++A+ + NCBI__GCF_000341125.1:WP_017600363.1 151 GGYTVAYRGHEgWGAVSLAP-DARILPVLCVPSWRLSTERARGLLPERVTHADASFNAGRSALMTAAVCGH-- 220 *******9888445555566.8***********************************************99.. PP TIGR00191 214 adllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.eeka 273 ++ l+ a +Dr+h+ yRe +P e+ + +e l ++SGaGpt+l+l+ ++ e ++ NCBI__GCF_000341125.1:WP_017600363.1 221 PETLYAATEDRLHESYREPAMPRTLELIRDLRERDGLPAVVSGAGPTVLVLCAVSEgEARE 281 899999*****************99999999999999***************877643332 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (326 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: 00:00:00.04 # Mc/sec: 2.26 // [ok]
This GapMind analysis is from Jul 25 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