Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate YP_002825083.1 NGR_c05340 homoserine kinase
Query= reanno::Korea:Ga0059261_3253 (319 letters) >NCBI__GCF_000018545.1:YP_002825083.1 Length = 326 Score = 295 bits (755), Expect = 1e-84 Identities = 152/310 (49%), Positives = 203/310 (65%), Gaps = 2/310 (0%) Query: 1 MAVYTQVSAEALAGFLARYDVGELVSAKGIAEGVENSNYLVETTRDRFILTLYEKRVEAA 60 MAVYT ++ + LAGFLA YDVG L S KGIAEGVENSN+L+ TTR +ILTLYEKRV A Sbjct: 1 MAVYTDITEDELAGFLAAYDVGTLTSYKGIAEGVENSNFLLHTTRGSYILTLYEKRVNAD 60 Query: 61 DLPYFMGLLDHLAAKGLPVPPAIKDRGGVEIQELNGRPACLIKFLSGISLSHPTPAQARA 120 DLP+F+GL+ HLA +GL P + G + L+GRPA +I FL G+ L P R Sbjct: 61 DLPFFLGLMHHLAERGLSCPLPLPRADGALLGTLSGRPAAVISFLEGMWLRKPEAQHCRE 120 Query: 121 AGEAMAQMHRAVADFPLDRPNSMGVDTWQPLFEKCGHSLDQIVPGLYDDLGFAIARVVPA 180 G A+A MH A F L R N++ V W+PL+ D++ GL +D+ +A + Sbjct: 121 VGRALASMHEAGEGFALTRANALSVGGWRPLWRNSEARADEVQDGLKEDIAAELAYLEDH 180 Query: 181 WTRNDFDRCAIHADLFPDNVLMRGDQVTGLIDFYFACTDIRVYDLAVMHSAWSFDAHGRN 240 W RN + IHADLFPDNV GD+++GLIDFYFAC D YD+AV ++W F+ +G + Sbjct: 181 WPRN-LPQGVIHADLFPDNVFFLGDRLSGLIDFYFACNDFLAYDIAVCLNSWCFEKNG-S 238 Query: 241 YDPAVGDALIAGYEASFPLTEVERAAFPTLAAGACIRFSLSRAWDWLNTPADALVMRKDP 300 Y+ G AL++GYE+ LT E +A P LA G+ +RF L+R +DWL TPA ALV++KDP Sbjct: 239 YNITKGMALLSGYESVRKLTAEEVSALPLLARGSALRFFLTRLYDWLMTPAGALVVKKDP 298 Query: 301 LAYVRRLKHY 310 L Y+ +L+ + Sbjct: 299 LEYLTKLRFH 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: 301 Number of extensions: 13 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: 326 Length adjustment: 28 Effective length of query: 291 Effective length of database: 298 Effective search space: 86718 Effective search space used: 86718 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 YP_002825083.1 NGR_c05340 (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.19608.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-126 405.5 0.0 9e-126 405.3 0.0 1.0 1 lcl|NCBI__GCF_000018545.1:YP_002825083.1 NGR_c05340 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000018545.1:YP_002825083.1 NGR_c05340 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.3 0.0 9e-126 9e-126 1 306 [. 1 306 [. 1 307 [. 0.99 Alignments for each domain: == domain 1 score: 405.3 bits; conditional E-value: 9e-126 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 mavyt+++++el +fL yd+G l s kGiaeGvensn+ll t++g+y+Ltlyekrv+a++LPffl l+ lcl|NCBI__GCF_000018545.1:YP_002825083.1 1 MAVYTDITEDELAGFLAAYDVGTLTSYKGIAEGVENSNFLLHTTRGSYILTLYEKRVNADDLPFFLGLM 69 9******************************************************************** PP TIGR00938 70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138 +hLaergl+++ p+++ dG++l++L+G+Paa+++fL+G+ ++kP a++crevg la +h ag++f lcl|NCBI__GCF_000018545.1:YP_002825083.1 70 HHLAERGLSCPLPLPRADGALLGTLSGRPAAVISFLEGMWLRKPEAQHCREVGRALASMHEAGEGFALT 138 ********************************************************************* PP TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdklk 207 r+n l+ W++l + +++++++l++ + +el++l++ +pr+LP+gvihadlf+dnv++ gd+l+ lcl|NCBI__GCF_000018545.1:YP_002825083.1 139 RANALSVGGWRPLWRNSEARADEVQDGLKEDIAAELAYLEDHWPRNLPQGVIHADLFPDNVFFLGDRLS 207 ***************99999************************************************* PP TIGR00938 208 gvidfyfaCedallydlaiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrf 276 g+idfyfaC+d l+yd+a+++n Wcfe+++++++++ all gye+vr L++ee a+p l+rg+alrf lcl|NCBI__GCF_000018545.1:YP_002825083.1 208 GLIDFYFACNDFLAYDIAVCLNSWCFEKNGSYNITKGMALLSGYESVRKLTAEEVSALPLLARGSALRF 276 ********************************************************************* PP TIGR00938 277 llsrlldlvftqagelvvakdPaeferkLk 306 +l+rl d+ +t+ag+lvv kdP e+ kL+ lcl|NCBI__GCF_000018545.1:YP_002825083.1 277 FLTRLYDWLMTPAGALVVKKDPLEYLTKLR 306 **************************9998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.18 // [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