Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate WP_068166709.1 HTA01S_RS01325 homoserine kinase
Query= SwissProt::P29364 (316 letters) >NCBI__GCF_001592305.1:WP_068166709.1 Length = 336 Score = 211 bits (538), Expect = 1e-59 Identities = 128/317 (40%), Positives = 168/317 (52%), Gaps = 12/317 (3%) Query: 1 MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHG----EFVLTLVERG 56 M+V+T + A L LG L + RGI G EN+N+F + E VLT+ ER Sbjct: 1 MAVYTEVAFGEAAALLHRLSLGDLTELRGIQGGIENTNYFATTVRDGVAHEHVLTVFERL 60 Query: 57 PVQDLPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHH 116 + LP+++ L+ L G+PVP GE L ++GKPA + +L G E P H Sbjct: 61 SFEQLPYYLHLMKYLAGQGIPVPEPAADERGEILHSVQGKPAAVVNKLRGHSELAPTEAH 120 Query: 117 CQEVGDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALA--EIA 174 C+ VGD+L +H A RG + +P+ RGLPW E + P L E AL+ LA Sbjct: 121 CRAVGDMLARMHLAGRGFEMSQPNLRGLPWWNETVPVVLPHLGESQAALIRTELAYQNHV 180 Query: 175 ALDAERPALPRANLHADLFRDNVLFDGPHLAGLIDFYNACSGWMLYDLAITLNDWC---- 230 A + ALPR +HADLFRDNV+FD L G DFY A + L+DLA+ LNDWC Sbjct: 181 AAGSAYTALPRGPVHADLFRDNVMFDDGELTGFFDFYFAGNDSFLFDLAVCLNDWCILHA 240 Query: 231 -SNTDGSLDPARARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQD 289 DG D RARA++AAY RP + E + P+MLR +RFWLSRL Sbjct: 241 ADERDGQHDAGRARAMIAAYQAVRPLSMAERQLLPAMLRAGALRFWLSRLWDWHLPRDAS 300 Query: 290 VL-IHDPAEFEIRLAQR 305 +L HDP FE L +R Sbjct: 301 MLKPHDPTHFERVLRER 317 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: 14 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: 336 Length adjustment: 28 Effective length of query: 288 Effective length of database: 308 Effective search space: 88704 Effective search space used: 88704 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_068166709.1 HTA01S_RS01325 (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.23489.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-96 308.5 0.0 3.1e-96 308.3 0.0 1.0 1 lcl|NCBI__GCF_001592305.1:WP_068166709.1 HTA01S_RS01325 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001592305.1:WP_068166709.1 HTA01S_RS01325 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 308.3 0.0 3.1e-96 3.1e-96 1 306 [. 1 315 [. 1 316 [. 0.95 Alignments for each domain: == domain 1 score: 308.3 bits; conditional E-value: 3.1e-96 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdk....gryvLtlyekrvkaeeLPff 65 mavyt+v++ e a L+ lG+l +l+Gi G+en+ny+ tt + +vLt++e+ + e+LP++ lcl|NCBI__GCF_001592305.1:WP_068166709.1 1 MAVYTEVAFGEAAALLHRLSLGDLTELRGIQGGIENTNYFATTVRdgvaHEHVLTVFERLS-FEQLPYY 68 9*****************************************9652222589********9.******* PP TIGR00938 66 lellthLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagad 134 l+l+++La +g+pv++p + + G+ l +++GkPaa+v+ L+G+s Pt ++cr+vg++la++hlag + lcl|NCBI__GCF_001592305.1:WP_068166709.1 69 LHLMKYLAGQGIPVPEPAADERGEILHSVQGKPAAVVNKLRGHSELAPTEAHCRAVGDMLARMHLAGRG 137 ********************************************************************* PP TIGR00938 135 fkeerkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflp....rdLPrgvihadlfkdnv 199 f+ ++ n lr W+ ++ vl++l e +aal+++el++ +++ + LPrg +hadlf+dnv lcl|NCBI__GCF_001592305.1:WP_068166709.1 138 FEMSQPN-LRGLPWWNETVPV--VLPHLGESQAALIRTELAYQNHVAAgsayTALPRGPVHADLFRDNV 203 *******.***********99..*******************999865333368*************** PP TIGR00938 200 lldgdklkgvidfyfaCedallydlaiavndWcf.....eaddkldaaaakallkgyeavrpLseeeka 263 ++d ++l+g+ dfyfa +d++l+dla+++ndWc+ e d++ da +a+a++ +y+avrpLs e++ lcl|NCBI__GCF_001592305.1:WP_068166709.1 204 MFDDGELTGFFDFYFAGNDSFLFDLAVCLNDWCIlhaadERDGQHDAGRARAMIAAYQAVRPLSMAERQ 272 *********************************75555467899************************* PP TIGR00938 264 afpvllrgaalrfllsrlldlvftqagelvvakdPaeferkLk 306 +p +lr++alrf+lsrl+d++ ++ + ++ dP++fer L+ lcl|NCBI__GCF_001592305.1:WP_068166709.1 273 LLPAMLRAGALRFWLSRLWDWHLPRDASMLKPHDPTHFERVLR 315 ****************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (336 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.16 // [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