Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate WP_011767326.1 AZO_RS18100 homoserine kinase
Query= SwissProt::P29364 (316 letters) >NCBI__GCF_000061505.1:WP_011767326.1 Length = 317 Score = 231 bits (588), Expect = 2e-65 Identities = 133/301 (44%), Positives = 175/301 (58%), Gaps = 7/301 (2%) Query: 1 MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60 MSVFT + + L +L Y +GR + RGI+ G +NSNFFV+ G +VLTL E P + Sbjct: 1 MSVFTSVSDAELARWLQNYAIGRPVELRGISAGVQNSNFFVTTTLGRYVLTLFESIPRAE 60 Query: 61 LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120 LP+++ L+ L GLPVP + RD E L L +PA+L RL G P HC +V Sbjct: 61 LPYYLHLMAHLARHGLPVPAPIANRDNEYLDTLSERPAVLVMRLPGVSVMAPALQHCAKV 120 Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAALDAER 180 G +L LH A + + + RG W + LP + LL LA +D Sbjct: 121 GAMLAGLHLAGQSYGRRQDNPRGPAWRTATAEAVKRFLPAAEQRLLDDELAFQRGVDLA- 179 Query: 181 PALPRANLHADLFRDNVLFDGPHLAGLIDFYNACSGWMLYDLAITLNDWCSNTDGSLDPA 240 ALP +HADLFRDNVL+DG H+ G+IDFY A +L+D+A+T+NDWC+ DG LDPA Sbjct: 180 -ALPAGAIHADLFRDNVLWDGEHIGGVIDFYFAGYDALLFDVAVTVNDWCTEADGQLDPA 238 Query: 241 RARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAF---AGQDVLIHDPAE 297 R ALLAAY RPFT E WP +LR A +RFWLSR AA+ AG+ VL+ +P E Sbjct: 239 RCAALLAAYHAERPFTPAEHAAWPGVLRAAALRFWLSR--AADFHLPRAGEMVLVKNPDE 296 Query: 298 F 298 + Sbjct: 297 Y 297 Lambda K H 0.324 0.140 0.434 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: 297 Number of extensions: 8 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: 316 Length of database: 317 Length adjustment: 27 Effective length of query: 289 Effective length of database: 290 Effective search space: 83810 Effective search space used: 83810 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 48 (23.1 bits)
Align candidate WP_011767326.1 AZO_RS18100 (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.2665.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-114 367.8 0.0 2.7e-114 367.6 0.0 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011767326.1 AZO_RS18100 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000061505.1:WP_011767326.1 AZO_RS18100 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 367.6 0.0 2.7e-114 2.7e-114 1 306 [. 1 302 [. 1 303 [. 0.99 Alignments for each domain: == domain 1 score: 367.6 bits; conditional E-value: 2.7e-114 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 m+v+tsvsd el +L+ y +G++++l+Gi+ Gv+nsn+++tt+ gryvLtl+e eLP++l+l+ lcl|NCBI__GCF_000061505.1:WP_011767326.1 1 MSVFTSVSDAELARWLQNYAIGRPVELRGISAGVQNSNFFVTTTLGRYVLTLFESIP-RAELPYYLHLM 68 9******************************************************99.789******** PP TIGR00938 70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138 hLa +glpv++p+++rd + l++L+ +Pa+lv L+G sv P++++c++vg++la lhlag+++ + lcl|NCBI__GCF_000061505.1:WP_011767326.1 69 AHLARHGLPVPAPIANRDNEYLDTLSERPAVLVMRLPGVSVMAPALQHCAKVGAMLAGLHLAGQSYGRR 137 ********************************************************************9 PP TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdklk 207 ++n +r aW++++a+ v +l + +++lld+el++ + ++ LP g ihadlf+dnvl dg++++ lcl|NCBI__GCF_000061505.1:WP_011767326.1 138 QDN-PRGPAWRTATAEA--VKRFLPAAEQRLLDDELAFQRGVDLAALPAGAIHADLFRDNVLWDGEHIG 203 999.**********999..999*********************************************** PP TIGR00938 208 gvidfyfaCedallydlaiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrf 276 gvidfyfa dall+d+a++vndWc ead++ld a+ all +y+a rp+++ e+aa+p +lr+aalrf lcl|NCBI__GCF_000061505.1:WP_011767326.1 204 GVIDFYFAGYDALLFDVAVTVNDWCTEADGQLDPARCAALLAAYHAERPFTPAEHAAWPGVLRAAALRF 272 ********************************************************************* PP TIGR00938 277 llsrlldlvftqagelvvakdPaeferkLk 306 +lsr++d++ ++age+v +k+P e++ +L+ lcl|NCBI__GCF_000061505.1:WP_011767326.1 273 WLSRAADFHLPRAGEMVLVKNPDEYRDILR 302 **************************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (317 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 3.93 // [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