Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_026127910.1 D471_RS0120555 homoserine kinase
Query= BRENDA::P07128 (309 letters) >NCBI__GCF_000341125.1:WP_026127910.1 Length = 318 Score = 200 bits (509), Expect = 3e-56 Identities = 116/270 (42%), Positives = 157/270 (58%), Gaps = 14/270 (5%) Query: 11 VTVTVPGSSANLGPGFDTLGLALSVYDTVEVEIIPSG-LEVEVFGEGQGEVPLDGSHLVV 69 +TV P +SANLGPGFD LGLA+ +Y+ + + + VEV GEG GEVPLD HLVV Sbjct: 1 MTVHAPATSANLGPGFDALGLAVRLYNRFDAALRDDDRINVEVTGEGAGEVPLDERHLVV 60 Query: 70 KAIRAGLKAADAEVPGLRVVCHNNIPQSRGLGSSAAAAVAGVAAANGLADFP-----LTQ 124 +A+R A ++PG+ + C NN+P +RGLGSS++A V GVAAA+ L + Sbjct: 61 RAMREAFDRAGEKLPGIDLTCVNNVPHARGLGSSSSAIVGGVAAASALLGRTGPGGGPDR 120 Query: 125 EQIVQLSSAFEGHPDNAAASVLGGAVVSWTNLSIDGKSQPQYAAVPLEVQDNIRATALVP 184 + I ++++ EGHPDN A V GG V++ + + AV L I VP Sbjct: 121 DWIYRIAADIEGHPDNVAPCVYGGYTVAY-------RGHEGWGAVSLAPDARILPVLCVP 173 Query: 185 NFHASTEAVRRVLPTEVTHIDARFNVSRVAVMIVALQQRPDLLWEGTRDRLHQPYRAEVL 244 ++ STE R +LP VTH DA FN R A+M A+ P+ L+ T DRLH+ YR + Sbjct: 174 SWRLSTERARGLLPERVTHADASFNAGRSALMTAAVCGHPETLYAATEDRLHESYREPAM 233 Query: 245 PITSEWVNRLRNR-GYAAYLSGAGPTAMVL 273 P T E + LR R G A +SGAGPT +VL Sbjct: 234 PRTLELIRDLRERDGLPAVVSGAGPTVLVL 263 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: 244 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: 318 Length adjustment: 27 Effective length of query: 282 Effective length of database: 291 Effective search space: 82062 Effective search space used: 82062 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_026127910.1 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.16267.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-64 201.8 0.0 6.7e-64 201.6 0.0 1.0 1 lcl|NCBI__GCF_000341125.1:WP_026127910.1 D471_RS0120555 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000341125.1:WP_026127910.1 D471_RS0120555 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 201.6 0.0 6.7e-64 6.7e-64 2 273 .. 2 273 .. 1 305 [. 0.89 Alignments for each domain: == domain 1 score: 201.6 bits; conditional E-value: 6.7e-64 TIGR00191 2 kvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkv 70 +v++Pa+sANlgpGfD lGla+ l+++++ +++ ++e +geg+ ++p++ + l+ +++ + lcl|NCBI__GCF_000341125.1:WP_026127910.1 2 TVHAPATSANLGPGFDALGLAVRLYNRFDAAL---RDDDRINVEVTGEGAGEVPLD-ERHLVVRAMREA 66 79**************************9888...3444447999999999*****.999********* PP TIGR00191 71 lkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelagl.....klskeelldlalllEgHpD 134 +++ g++++++ lt +++p +rGLGSS++aiv++v+aa +l+g + ++ + +a +EgHpD lcl|NCBI__GCF_000341125.1:WP_026127910.1 67 FDRAGEKLPGIDLTCVNNVPHARGLGSSSSAIVGGVAAASALLGRtgpggGPDRDWIYRIAADIEGHPD 135 ******************************************98733222579999************* PP TIGR00191 135 NvapallGGlqlavkedd.llevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshla 202 Nvap++ GG+++a + ++ v P ++++ vl +P +sT+ aR++LP++++ +d+ fn+ ++a lcl|NCBI__GCF_000341125.1:WP_026127910.1 136 NVAPCVYGGYTVAYRGHEgWGAVSLAP-DARILPVLCVPSWRLSTERARGLLPERVTHADASFNAGRSA 203 **************9888445555566.8**************************************** PP TIGR00191 203 vlvtAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.e 270 ++++A+ + ++ l+ a +Dr+h+ yRe +P e+ + +e l ++SGaGpt+l+l+ ++ e lcl|NCBI__GCF_000341125.1:WP_026127910.1 204 LMTAAVCGH--PETLYAATEDRLHESYREPAMPRTLELIRDLRERDGLPAVVSGAGPTVLVLCAVSEgE 270 *******99..899999*****************99999999999999***************877643 PP TIGR00191 271 eka 273 ++ lcl|NCBI__GCF_000341125.1:WP_026127910.1 271 ARE 273 332 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (318 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.81 // [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