Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_011159805.1 TX73_RS21775 homoserine kinase
Query= reanno::Korea:Ga0059261_3253 (319 letters) >NCBI__GCF_000195775.1:WP_011159805.1 Length = 327 Score = 284 bits (727), Expect = 2e-81 Identities = 149/309 (48%), Positives = 197/309 (63%), Gaps = 3/309 (0%) Query: 1 MAVYTQVSAEALAGFLARYDVGELVSAKGIAEGVENSNYLVETTRDRFILTLYEKRVEAA 60 MAVYT V+A+ LA FL+RYD+G+L+S KGIAEGVENSN+L+ T+R FILTLYEKRV Sbjct: 1 MAVYTDVAADELADFLSRYDIGDLLSYKGIAEGVENSNFLLHTSRGYFILTLYEKRVARD 60 Query: 61 DLPYFMGLLDHLAAKGLPVPPAIKDRGGVEIQELNGRPACLIKFLSGISLSHPTPAQARA 120 DLP+F+ L+ HLA G+ P + DR G + L GRPA +I FL G+ P+ Sbjct: 61 DLPFFLSLMTHLADSGINCPQPVADREGRTLATLAGRPAAIISFLDGVWPRKPSVVHCAG 120 Query: 121 AGEAMAQMHRAVADFPLDRPNSMGVDTWQPLFEKCGHSLDQIVPGLYDDLGFAIARVVPA 180 G+A+A+MH A DF + R N++ V W+PLF D++ PGL D L ++ + Sbjct: 121 VGQALAKMHLAGRDFAMKRANALSVAGWRPLFAAAEARADEVQPGLRDFLAAELSYLESG 180 Query: 181 WTRNDFDRCAIHADLFPDNVLMRGDQVTGLIDFYFACTDIRVYDLAVMHSAWSFDA-HGR 239 +D + IHADLFPDNV GD+V+G+IDF FAC D+ YD+A+ +AW F+A H Sbjct: 181 VWPSDLPQGLIHADLFPDNVFFIGDEVSGIIDFTFACNDLLAYDVAICLNAWCFEADHAF 240 Query: 240 NYDPAVGDALIAGYEASFPLTEVERAAFPTLAAGACIRFSLSRAWDWLNTPADALVMRKD 299 N A AL++ Y PL E+AA P LA GA +RF L+R DWLN P ALV KD Sbjct: 241 NVTKA--RALLSAYTRERPLDAAEQAALPLLARGAALRFLLTRLVDWLNVPEGALVKPKD 298 Query: 300 PLAYVRRLK 308 P+ YVR+L+ Sbjct: 299 PMEYVRKLR 307 Lambda K H 0.323 0.138 0.429 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: 312 Number of extensions: 10 Number of successful extensions: 2 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: 319 Length of database: 327 Length adjustment: 28 Effective length of query: 291 Effective length of database: 299 Effective search space: 87009 Effective search space used: 87009 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 48 (23.1 bits)
Align candidate WP_011159805.1 TX73_RS21775 (homoserine kinase)
to HMM TIGR00938 (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/TIGR00938.hmm # target sequence database: /tmp/gapView.22088.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00938 [M=307] Accession: TIGR00938 Description: thrB_alt: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-125 404.5 0.0 1.7e-125 404.4 0.0 1.0 1 lcl|NCBI__GCF_000195775.1:WP_011159805.1 TX73_RS21775 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195775.1:WP_011159805.1 TX73_RS21775 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 404.4 0.0 1.7e-125 1.7e-125 1 307 [] 1 308 [. 1 308 [. 0.99 Alignments for each domain: == domain 1 score: 404.4 bits; conditional E-value: 1.7e-125 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 mavyt+v+ +el fL+ yd+G+lls kGiaeGvensn+ll t +g ++Ltlyekrv ++LPffl l+ lcl|NCBI__GCF_000195775.1:WP_011159805.1 1 MAVYTDVAADELADFLSRYDIGDLLSYKGIAEGVENSNFLLHTSRGYFILTLYEKRVARDDLPFFLSLM 69 9******************************************************************** PP TIGR00938 70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138 thLa+ g+ +++pv+ r+Gr+l +LaG+Paa+++fL+G +kP + +c+ vg+ lak+hlag df + lcl|NCBI__GCF_000195775.1:WP_011159805.1 70 THLADSGINCPQPVADREGRTLATLAGRPAAIISFLDGVWPRKPSVVHCAGVGQALAKMHLAGRDFAMK 138 ********************************************************************* PP TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkk.flprdLPrgvihadlfkdnvlldgdkl 206 r+n l+ + W++l+a+ +++++++l + l +el +l++ ++p dLP+g+ihadlf+dnv++ gd++ lcl|NCBI__GCF_000195775.1:WP_011159805.1 139 RANALSVAGWRPLFAAAEARADEVQPGLRDFLAAELSYLESgVWPSDLPQGLIHADLFPDNVFFIGDEV 207 *****************999*****************987549************************** PP TIGR00938 207 kgvidfyfaCedallydlaiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalr 275 +g+idf faC+d l+yd+ai++n+Wcfead+ +++++a+all +y + rpL + e+aa+p l+rgaalr lcl|NCBI__GCF_000195775.1:WP_011159805.1 208 SGIIDFTFACNDLLAYDVAICLNAWCFEADHAFNVTKARALLSAYTRERPLDAAEQAALPLLARGAALR 276 ********************************************************************* PP TIGR00938 276 fllsrlldlvftqagelvvakdPaeferkLkv 307 fll+rl+d+ + + g+lv++kdP e+ rkL++ lcl|NCBI__GCF_000195775.1:WP_011159805.1 277 FLLTRLVDWLNVPEGALVKPKDPMEYVRKLRF 308 *****************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (327 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: 7.50 // [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