Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate Ac3H11_1651 Homoserine kinase (EC 2.7.1.39)
Query= SwissProt::P29364 (316 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1651 Length = 316 Score = 209 bits (531), Expect = 9e-59 Identities = 127/318 (39%), Positives = 170/318 (53%), Gaps = 10/318 (3%) Query: 1 MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60 M+VFT + + L LG L + RGI G EN+N+F++ + G FVLTL ER + Sbjct: 1 MAVFTEVSNTEARELLRRLQLGELVELRGIEGGIENTNYFLTSDQGAFVLTLFERLTAEQ 60 Query: 61 LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120 LPF++ L+ L G+PVP ++G+ L + GKPA + +L G+ + P HC V Sbjct: 61 LPFYLYLMKHLAHGGVPVPDPRADKNGDILHTVCGKPAAVVNKLRGKSQLAPQGAHCAAV 120 Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALA--EIAALDA 178 G +L +H A R +P+ RGLPW E + P + E ALL LA A + Sbjct: 121 GTMLARMHLAGRDFDRRQPNLRGLPWWNETVPVVLPHIGEAQSALLRAELAYQNHVAAGS 180 Query: 179 ERPALPRANLHADLFRDNVLFDGPHLAGLIDFYNACSGWMLYDLAITLNDWCSN-TDGSL 237 ALP +HADLFRDNV+F+G L G DFY A L+DLA+ LNDWC + G+ Sbjct: 181 AYAALPCGPVHADLFRDNVMFEGEELTGFFDFYFAGVDTWLFDLAVCLNDWCIDLPTGAH 240 Query: 238 DPARARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRL----IAAEAFAGQDVLIH 293 D RA +L AY RP TA E E P+MLR +RFW+SRL + EA + H Sbjct: 241 DAERATRMLDAYQAVRPLTAAERELLPAMLRAGALRFWISRLWDFYLPREA---SMLTPH 297 Query: 294 DPAEFEIRLAQRQNVEIH 311 DP FE L R +H Sbjct: 298 DPTHFERVLRHRVAHPVH 315 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: 272 Number of extensions: 12 Number of successful extensions: 4 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: 316 Length adjustment: 27 Effective length of query: 289 Effective length of database: 289 Effective search space: 83521 Effective search space used: 83521 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 Ac3H11_1651 (Homoserine kinase (EC 2.7.1.39))
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.26864.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-100 321.1 0.0 4.3e-100 320.9 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651 Homoserine kinase (EC 2.7.1.39) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651 Homoserine kinase (EC 2.7.1.39) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 320.9 0.0 4.3e-100 4.3e-100 1 307 [] 1 308 [. 1 308 [. 0.97 Alignments for each domain: == domain 1 score: 320.9 bits; conditional E-value: 4.3e-100 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeL 62 mav+t+vs+ e ++ L lGel++l+Gi G+en+ny+lt d+g +vLtl+e+ + ae+L lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651 1 MAVFTEVSNTEARELLRRLQLGELVELRGIEGGIENTNYFLTSDQGAFVLTLFERLT-AEQL 61 9*******************************************************9.**** PP TIGR00938 63 PfflellthLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgev 124 Pf+l l++hLa+ g+pv+ p + ++G l ++ GkPaa+v+ L+G+s P+ ++c++vg + lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651 62 PFYLYLMKHLAHGGVPVPDPRADKNGDILHTVCGKPAAVVNKLRGKSQLAPQGAHCAAVGTM 123 ************************************************************** PP TIGR00938 125 laklhlagadfkeerkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflp.... 182 la++hlag df+ ++ n lr W+ ++ vl+++ e ++all++el++ +++ + lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651 124 LARMHLAGRDFDRRQPN-LRGLPWWNETVPV--VLPHIGEAQSALLRAELAYQNHVAAgsay 182 *****************.***********99..*******************9998752333 PP TIGR00938 183 rdLPrgvihadlfkdnvlldgdklkgvidfyfaCedallydlaiavndWcfea.ddkldaaa 243 LP g +hadlf+dnv+++g++l+g+ dfyfa d++l+dla+++ndWc++ + da++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651 183 AALPCGPVHADLFRDNVMFEGEELTGFFDFYFAGVDTWLFDLAVCLNDWCIDLpTGAHDAER 244 68**************************************************72568899** PP TIGR00938 244 akallkgyeavrpLseeekaafpvllrgaalrfllsrlldlvftqagelvvakdPaeferkL 305 a +l++y+avrpL++ e++ +p +lr++alrf++srl+d++ ++ + ++ dP++fer L lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651 245 ATRMLDAYQAVRPLTAAERELLPAMLRAGALRFWISRLWDFYLPREASMLTPHDPTHFERVL 306 *************************************************************9 PP TIGR00938 306 kv 307 ++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651 307 RH 308 86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (316 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: 6.62 // [ok]
This GapMind analysis is from Apr 09 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