Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate WP_004300679.1 C665_RS03910 homoserine kinase
Query= SwissProt::P29364 (316 letters) >NCBI__GCF_000310185.1:WP_004300679.1 Length = 318 Score = 236 bits (601), Expect = 7e-67 Identities = 137/306 (44%), Positives = 177/306 (57%), Gaps = 12/306 (3%) Query: 1 MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60 MSVFTP+ S L +L Y +GRL + GI+ G +NSNFFV+ G +VLTL E P + Sbjct: 1 MSVFTPVPESVLADWLKDYAIGRLVELEGISAGVQNSNFFVTTTLGRYVLTLFEGIPRAE 60 Query: 61 LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120 LP+++ L+ L GLPVP + R E L L+ +PA L RL+GR E P HC V Sbjct: 61 LPYYLHLMAHLSRHGLPVPGPIANRHNEYLGTLQERPAALVVRLSGRSEMSPGLAHCGRV 120 Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAALDAER 180 G +L LH A + + + RG W L P LP + LL +A A +D Sbjct: 121 GAMLAGLHLAGQSYGRRQENPRGAAWRAATAQVLRPFLPADEQTLLDAEIAFQATIDV-- 178 Query: 181 PALPRANLHADLFRDNVLFD-----GPHLAGLIDFYNACSGWMLYDLAITLNDWCSNTDG 235 ALP +HADLFRDNVL+D G + G+IDFY A +L+D+A+T+NDWCS DG Sbjct: 179 AALPAGAIHADLFRDNVLWDTDADGGVRIGGVIDFYFAGYDALLFDVAVTVNDWCSTPDG 238 Query: 236 SLDPARARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAF---AGQDVLI 292 LD RA ALL AY RPFT E WP+MLR A +RFW+SR AA+ AG+ VL+ Sbjct: 239 GLDAERAAALLDAYHAERPFTDAERAAWPAMLRAAALRFWMSR--AADFHLPRAGEMVLV 296 Query: 293 HDPAEF 298 DP E+ Sbjct: 297 KDPNEY 302 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: 308 Number of extensions: 14 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: 316 Length of database: 318 Length adjustment: 27 Effective length of query: 289 Effective length of database: 291 Effective search space: 84099 Effective search space used: 84099 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_004300679.1 C665_RS03910 (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.27894.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-108 347.0 0.0 5.7e-108 346.8 0.0 1.0 1 lcl|NCBI__GCF_000310185.1:WP_004300679.1 C665_RS03910 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000310185.1:WP_004300679.1 C665_RS03910 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 346.8 0.0 5.7e-108 5.7e-108 1 306 [. 1 307 [. 1 308 [. 0.97 Alignments for each domain: == domain 1 score: 346.8 bits; conditional E-value: 5.7e-108 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 m+v+t v + l +L+ y +G+l++l+Gi+ Gv+nsn+++tt+ gryvLtl+e eLP++l+l+ lcl|NCBI__GCF_000310185.1:WP_004300679.1 1 MSVFTPVPESVLADWLKDYAIGRLVELEGISAGVQNSNFFVTTTLGRYVLTLFEGIP-RAELPYYLHLM 68 9******************************************************99.789******** PP TIGR00938 70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138 hL+ +glpv+ p+++r + l++L+ +Paalv L+G+s P +++c +vg++la lhlag+++ + lcl|NCBI__GCF_000310185.1:WP_004300679.1 69 AHLSRHGLPVPGPIANRHNEYLGTLQERPAALVVRLSGRSEMSPGLAHCGRVGAMLAGLHLAGQSYGRR 137 ********************************************************************* PP TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdk.. 205 ++n +r +aW+ ++a+ + ++l +++++lld+e+++ +++ LP g ihadlf+dnvl d+d lcl|NCBI__GCF_000310185.1:WP_004300679.1 138 QEN-PRGAAWRAATAQV--LRPFLPADEQTLLDAEIAFQATIDVAALPAGAIHADLFRDNVLWDTDAdg 203 ***.*********9999..99*****************************************9977433 PP TIGR00938 206 ...lkgvidfyfaCedallydlaiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrg 271 ++gvidfyfa dall+d+a++vndWc + d+ lda++a all++y+a rp+++ e+aa+p +lr+ lcl|NCBI__GCF_000310185.1:WP_004300679.1 204 gvrIGGVIDFYFAGYDALLFDVAVTVNDWCSTPDGGLDAERAAALLDAYHAERPFTDAERAAWPAMLRA 272 44589**************************************************************** PP TIGR00938 272 aalrfllsrlldlvftqagelvvakdPaeferkLk 306 aalrf++sr++d++ ++age+v +kdP+e++ +L+ lcl|NCBI__GCF_000310185.1:WP_004300679.1 273 AALRFWMSRAADFHLPRAGEMVLVKDPNEYRDILR 307 *******************************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (318 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: 7.34 // [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