Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_026607331.1 METAC_RS0112740 homoserine kinase
Query= reanno::Korea:Ga0059261_3253 (319 letters) >NCBI__GCF_000427445.1:WP_026607331.1 Length = 321 Score = 275 bits (703), Expect = 1e-78 Identities = 146/310 (47%), Positives = 195/310 (62%), Gaps = 2/310 (0%) Query: 1 MAVYTQVSAEALAGFLARYDVGELVSAKGIAEGVENSNYLVETTRDRFILTLYEKRVEAA 60 MAVYT+V LA FLA Y++G +++ KGIAEGVENSN+L+ FILTLYEKRV+ Sbjct: 1 MAVYTEVVDADLAAFLADYELGRVLALKGIAEGVENSNFLLHVEAGYFILTLYEKRVDER 60 Query: 61 DLPYFMGLLDHLAAKGLPVPPAIKDRGGVEIQELNGRPACLIKFLSGISLSHPTPAQARA 120 +LP+F+GL++HLAA+GL P ++ R GV + L GRPA ++ FL G+S S P A Sbjct: 61 NLPFFLGLMEHLAARGLTCPQPVRSRSGVALGRLAGRPAAIVTFLEGLSRSRPDAKDCAA 120 Query: 121 AGEAMAQMHRAVADFPLDRPNSMGVDTWQPLFEKCGHSLDQIVPGLYDDLGFAIARVVPA 180 GE++A++H A ADF R N++G+ W LFE D+ PGL + +A + Sbjct: 121 LGESLARLHLAGADFSGFRANALGLSAWPALFEPVRARADEGRPGLVSLIDGELAFLERN 180 Query: 181 WTRNDFDRCAIHADLFPDNVLMRGDQVTGLIDFYFACTDIRVYDLAVMHSAWSFDAHGRN 240 W R D IHADLFPDNVL GD+++GLIDFYFAC D YD+A+ +AW F+ G Sbjct: 181 WPR-DLPSGLIHADLFPDNVLFIGDKISGLIDFYFACVDAFAYDIAICLNAWCFEPDGA- 238 Query: 241 YDPAVGDALIAGYEASFPLTEVERAAFPTLAAGACIRFSLSRAWDWLNTPADALVMRKDP 300 ++ +LI YE L E A P LA GA +RF+L+R DWLN PA ALV KDP Sbjct: 239 FEIVKARSLIGAYERIRALRSDEAEALPILARGAALRFALTRLVDWLNVPAGALVHPKDP 298 Query: 301 LAYVRRLKHY 310 Y+R+L+ + Sbjct: 299 GEYIRKLEFH 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: 302 Number of extensions: 10 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_026607331.1 METAC_RS0112740 (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.9064.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-124 401.6 0.0 1.3e-124 401.4 0.0 1.0 1 lcl|NCBI__GCF_000427445.1:WP_026607331.1 METAC_RS0112740 homoserine kinas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000427445.1:WP_026607331.1 METAC_RS0112740 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 401.4 0.0 1.3e-124 1.3e-124 1 306 [. 1 306 [. 1 307 [. 0.99 Alignments for each domain: == domain 1 score: 401.4 bits; conditional E-value: 1.3e-124 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 mavyt+v d +l afL y+lG++l+lkGiaeGvensn+ll + g ++Ltlyekrv++ +LPffl l+ lcl|NCBI__GCF_000427445.1:WP_026607331.1 1 MAVYTEVVDADLAAFLADYELGRVLALKGIAEGVENSNFLLHVEAGYFILTLYEKRVDERNLPFFLGLM 69 9******************************************************************** PP TIGR00938 70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138 +hLa+rgl++++pv+sr+G al+ LaG+Paa+v fL+G+s ++P a+ c++ ge la+lhlagadf++ lcl|NCBI__GCF_000427445.1:WP_026607331.1 70 EHLAARGLTCPQPVRSRSGVALGRLAGRPAAIVTFLEGLSRSRPDAKDCAALGESLARLHLAGADFSGF 138 ********************************************************************* PP TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdklk 207 r+n l+l aW l++ + +++ ++l +l+d el++l++++prdLP+g+ihadlf+dnvl+ gdk++ lcl|NCBI__GCF_000427445.1:WP_026607331.1 139 RANALGLSAWPALFEPVRARADEGRPGLVSLIDGELAFLERNWPRDLPSGLIHADLFPDNVLFIGDKIS 207 *****************99************************************************** PP TIGR00938 208 gvidfyfaCedallydlaiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrf 276 g+idfyfaC da++yd+ai++n+Wcfe d+ +++++a++l+++ye++r+L + e +a+p+l+rgaalrf lcl|NCBI__GCF_000427445.1:WP_026607331.1 208 GLIDFYFACVDAFAYDIAICLNAWCFEPDGAFEIVKARSLIGAYERIRALRSDEAEALPILARGAALRF 276 ********************************************************************* PP TIGR00938 277 llsrlldlvftqagelvvakdPaeferkLk 306 l+rl+d+ + +ag+lv++kdP e+ rkL+ lcl|NCBI__GCF_000427445.1:WP_026607331.1 277 ALTRLVDWLNVPAGALVHPKDPGEYIRKLE 306 ****************************97 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.56 // [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