Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate WP_013518171.1 ALIDE2_RS18060 homoserine kinase
Query= SwissProt::P29364 (316 letters) >NCBI__GCF_000204645.1:WP_013518171.1 Length = 316 Score = 221 bits (563), Expect = 2e-62 Identities = 134/315 (42%), Positives = 169/315 (53%), Gaps = 4/315 (1%) Query: 1 MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60 M+VFT + L LG L RGI G EN+N+FV+ E GE+VLTL ER + Sbjct: 1 MAVFTEVSSKEASDLLRRLQLGELLALRGIEGGIENTNYFVTSEQGEYVLTLFERLTFEQ 60 Query: 61 LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120 LPF++ L+ L G+PVP GE L + GKPA L +L G+ + P A HC V Sbjct: 61 LPFYLHLMKHLAHAGIPVPDPQADMHGEILHTVAGKPAALATKLRGKSQLAPQAAHCAAV 120 Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALA--EIAALDA 178 G LL +H A R ++P+ RGLPW E + P + ALL LA A + Sbjct: 121 GTLLARMHLAARDYERQQPNLRGLPWWNETVPVVLPHVGPGQAALLQSELAYQNHVAAGS 180 Query: 179 ERPALPRANLHADLFRDNVLFDGPHLAGLIDFYNACSGWMLYDLAITLNDWCSN-TDGSL 237 ALPR +HADLFRDNV+F+G L G DFY A L+DLA+ LNDWC + G Sbjct: 181 GYAALPRGPIHADLFRDNVMFEGTELTGCFDFYFAGVDTWLFDLAVCLNDWCIDLPTGRH 240 Query: 238 DPARARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQDVL-IHDPA 296 D R A+LAAY RP TA E E P+MLR +RFW+SRL +L HDPA Sbjct: 241 DGERTAAMLAAYQAVRPLTAAERELLPAMLRAGALRFWISRLWDFHLPRQASMLKPHDPA 300 Query: 297 EFEIRLAQRQNVEIH 311 FE L +R +H Sbjct: 301 HFERVLRERVRHPVH 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: 286 Number of extensions: 14 Number of successful extensions: 5 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 WP_013518171.1 ALIDE2_RS18060 (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.972.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-100 321.2 0.0 4.1e-100 321.0 0.0 1.0 1 lcl|NCBI__GCF_000204645.1:WP_013518171.1 ALIDE2_RS18060 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204645.1:WP_013518171.1 ALIDE2_RS18060 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 321.0 0.0 4.1e-100 4.1e-100 1 306 [. 1 307 [. 1 308 [. 0.97 Alignments for each domain: == domain 1 score: 321.0 bits; conditional E-value: 4.1e-100 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 mav+t+vs +e + L lGell+l+Gi G+en+ny++t ++g yvLtl+e+ + e+LPf+l+l+ lcl|NCBI__GCF_000204645.1:WP_013518171.1 1 MAVFTEVSSKEASDLLRRLQLGELLALRGIEGGIENTNYFVTSEQGEYVLTLFERLT-FEQLPFYLHLM 68 9*******************************************************9.*********** PP TIGR00938 70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138 +hLa+ g+pv+ p + G+ l ++aGkPaal L+G+s P+a++c++vg la++hla+ d++ + lcl|NCBI__GCF_000204645.1:WP_013518171.1 69 KHLAHAGIPVPDPQADMHGEILHTVAGKPAALATKLRGKSQLAPQAAHCAAVGTLLARMHLAARDYERQ 137 ********************************************************************* PP TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflp....rdLPrgvihadlfkdnvlldg 203 + n lr W+ ++ vl+++ +++aall++el++ +++ + LPrg ihadlf+dnv+++g lcl|NCBI__GCF_000204645.1:WP_013518171.1 138 QPN-LRGLPWWNETVPV--VLPHVGPGQAALLQSELAYQNHVAAgsgyAALPRGPIHADLFRDNVMFEG 203 ***.***********99..********************99876333357******************* PP TIGR00938 204 dklkgvidfyfaCedallydlaiavndWcfea.ddkldaaaakallkgyeavrpLseeekaafpvllrg 271 +l+g dfyfa d++l+dla+++ndWc++ ++ d +++ a+l +y+avrpL++ e++ +p +lr+ lcl|NCBI__GCF_000204645.1:WP_013518171.1 204 TELTGCFDFYFAGVDTWLFDLAVCLNDWCIDLpTGRHDGERTAAMLAAYQAVRPLTAAERELLPAMLRA 272 *******************************72578999****************************** PP TIGR00938 272 aalrfllsrlldlvftqagelvvakdPaeferkLk 306 +alrf++srl+d++ ++ + ++ dPa+fer L+ lcl|NCBI__GCF_000204645.1:WP_013518171.1 273 GALRFWISRLWDFHLPRQASMLKPHDPAHFERVLR 307 ********************************997 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 8.86 // [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