Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_041935467.1 RLEG_RS03240 homoserine kinase
Query= reanno::Korea:Ga0059261_3253 (319 letters) >NCBI__GCF_000023185.1:WP_041935467.1 Length = 321 Score = 285 bits (730), Expect = 8e-82 Identities = 144/310 (46%), Positives = 201/310 (64%), Gaps = 2/310 (0%) Query: 1 MAVYTQVSAEALAGFLARYDVGELVSAKGIAEGVENSNYLVETTRDRFILTLYEKRVEAA 60 MAVYT ++ + L FL YD G L+S KGIAEGVENSN+L+ T+RD ILTLYEKRVE + Sbjct: 1 MAVYTDIAEDDLKWFLTEYDAGTLLSYKGIAEGVENSNFLLHTSRDPLILTLYEKRVEKS 60 Query: 61 DLPYFMGLLDHLAAKGLPVPPAIKDRGGVEIQELNGRPACLIKFLSGISLSHPTPAQARA 120 DLP+F+G + HL+A+GL P + R G + L+GRPA LI FL G+ L P R Sbjct: 61 DLPFFLGFMQHLSARGLSCPLPLPRRDGALLGSLSGRPAALISFLEGMWLRKPEAKHCRE 120 Query: 121 AGEAMAQMHRAVADFPLDRPNSMGVDTWQPLFEKCGHSLDQIVPGLYDDLGFAIARVVPA 180 G+A+A+MH A F L R N++ +D W+ L+EK ++ GL ++ + + A Sbjct: 121 VGKALAEMHVAGDGFELKRANALSIDGWRGLWEKSEARAGEVESGLQTEIRSELDFLSAA 180 Query: 181 WTRNDFDRCAIHADLFPDNVLMRGDQVTGLIDFYFACTDIRVYDLAVMHSAWSFDAHGRN 240 W + IHADLFPDNV GDQ++GLIDFYFAC D+ YD+++ +AW F+ G Sbjct: 181 WP-SGLPAGVIHADLFPDNVFFLGDQLSGLIDFYFACNDLLAYDVSICLNAWCFEKDGA- 238 Query: 241 YDPAVGDALIAGYEASFPLTEVERAAFPTLAAGACIRFSLSRAWDWLNTPADALVMRKDP 300 Y+ G A++ GY++ PL+E E AA P L+ G+ +RF L+R +DWL TP A+V +KDP Sbjct: 239 YNITKGTAMLEGYQSVRPLSEAEIAALPVLSRGSALRFFLTRLYDWLTTPEGAMVTKKDP 298 Query: 301 LAYVRRLKHY 310 L Y+R+L+ + Sbjct: 299 LEYLRKLRFH 308 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: 298 Number of extensions: 12 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: 319 Length of database: 321 Length adjustment: 28 Effective length of query: 291 Effective length of database: 293 Effective search space: 85263 Effective search space used: 85263 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_041935467.1 RLEG_RS03240 (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.10277.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-123 396.4 0.0 5.3e-123 396.2 0.0 1.0 1 lcl|NCBI__GCF_000023185.1:WP_041935467.1 RLEG_RS03240 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023185.1:WP_041935467.1 RLEG_RS03240 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 396.2 0.0 5.3e-123 5.3e-123 1 307 [] 1 307 [. 1 307 [. 0.99 Alignments for each domain: == domain 1 score: 396.2 bits; conditional E-value: 5.3e-123 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 mavyt++++++l+ fL yd G lls kGiaeGvensn+ll t + +Ltlyekrv++ +LPffl ++ lcl|NCBI__GCF_000023185.1:WP_041935467.1 1 MAVYTDIAEDDLKWFLTEYDAGTLLSYKGIAEGVENSNFLLHTSRDPLILTLYEKRVEKSDLPFFLGFM 69 9******************************************************************** PP TIGR00938 70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138 +hL++rgl+++ p+++rdG++l++L+G+Paal++fL+G+ ++kP a++crevg+ la +h+ag++f+ + lcl|NCBI__GCF_000023185.1:WP_041935467.1 70 QHLSARGLSCPLPLPRRDGALLGSLSGRPAALISFLEGMWLRKPEAKHCREVGKALAEMHVAGDGFELK 138 ********************************************************************* PP TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdklk 207 r+n l+ + W+ l +k + ++e++l++++++eld+l+ +p LP gvihadlf+dnv++ gd+l+ lcl|NCBI__GCF_000023185.1:WP_041935467.1 139 RANALSIDGWRGLWEKSEARAGEVESGLQTEIRSELDFLSAAWPSGLPAGVIHADLFPDNVFFLGDQLS 207 *****************9999************************************************ PP TIGR00938 208 gvidfyfaCedallydlaiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrf 276 g+idfyfaC+d l+yd++i++n+Wcfe+d+ +++++ a+l+gy++vrpLse e aa+pvl rg+alrf lcl|NCBI__GCF_000023185.1:WP_041935467.1 208 GLIDFYFACNDLLAYDVSICLNAWCFEKDGAYNITKGTAMLEGYQSVRPLSEAEIAALPVLSRGSALRF 276 ********************************************************************* PP TIGR00938 277 llsrlldlvftqagelvvakdPaeferkLkv 307 +l+rl d+ +t+ g++v+ kdP e+ rkL++ lcl|NCBI__GCF_000023185.1:WP_041935467.1 277 FLTRLYDWLTTPEGAMVTKKDPLEYLRKLRF 307 ****************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (321 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: 8.56 // [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