Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate AO356_11475 AO356_11475 homoserine kinase
Query= SwissProt::P29364 (316 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_11475 Length = 316 Score = 449 bits (1154), Expect = e-131 Identities = 226/316 (71%), Positives = 252/316 (79%) Query: 1 MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60 MSVFTPL R LE FLAPY LGRL DF+GIA GSEN+NFF+SLE GEFVLTLVERGPVQ+ Sbjct: 1 MSVFTPLARPELETFLAPYGLGRLLDFQGIAAGSENTNFFISLEQGEFVLTLVERGPVQE 60 Query: 61 LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120 +PFFIELLDVLH+ LPVPYALRT DG ALR L GKPALLQPRLAG+H +Q NA HC +V Sbjct: 61 MPFFIELLDVLHDADLPVPYALRTTDGVALRELAGKPALLQPRLAGKHIKQANAQHCAQV 120 Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAALDAER 180 G+LL HLH ATR +++R +DRGL WM E+GA L L R LL AL EI+ Sbjct: 121 GELLAHLHLATRDNMIKRKTDRGLDWMQEEGAKLLSHLDTAPRQLLEAALDEISLKKVGI 180 Query: 181 PALPRANLHADLFRDNVLFDGPHLAGLIDFYNACSGWMLYDLAITLNDWCSNTDGSLDPA 240 ALPRAN+HADLFRDN +F+G HL GLIDFYNACSG MLYD+AI LNDWCS+ +G LD Sbjct: 181 LALPRANIHADLFRDNAMFEGTHLTGLIDFYNACSGPMLYDVAIALNDWCSDDNGVLDGP 240 Query: 241 RARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQDVLIHDPAEFEI 300 RARALL AYA RPFTA EA+ WP+MLRVACVRFWLSRLIAAE+FAGQDVLIHDP EF+ Sbjct: 241 RARALLGAYAALRPFTAAEAQLWPTMLRVACVRFWLSRLIAAESFAGQDVLIHDPMEFQQ 300 Query: 301 RLAQRQNVEIHLPFAL 316 RLAQRQ V LPFAL Sbjct: 301 RLAQRQTVHALLPFAL 316 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: 395 Number of extensions: 7 Number of successful extensions: 1 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 AO356_11475 AO356_11475 (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.2884.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-89 285.4 0.0 3.2e-89 285.2 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11475 AO356_11475 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11475 AO356_11475 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 285.2 0.0 3.2e-89 3.2e-89 1 306 [. 1 303 [. 1 304 [. 0.96 Alignments for each domain: == domain 1 score: 285.2 bits; conditional E-value: 3.2e-89 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLP 63 m+v+t ++ ele+fL y lG+ll+++Gia G en+n+++ ++g +vLtl e+ +e+P lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11475 1 MSVFTPLARPELETFLAPYGLGRLLDFQGIAAGSENTNFFISLEQGEFVLTLVERGP-VQEMP 62 9*****************************************************998.899** PP TIGR00938 64 fflellthLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevla 126 ff+ell+ L + +lpv+ ++++ dG al eLaGkPa l L+G+ +++ a++c++vge la lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11475 63 FFIELLDVLHDADLPVPYALRTTDGVALRELAGKPALLQPRLAGKHIKQANAQHCAQVGELLA 125 *************************************************************** PP TIGR00938 127 klhlagadfkeerkndlrleaWsilaakkfkvleqleeelaalldkelda..lkkflprdLPr 187 +lhla+ d +rk r +W + +k +l +l++ +ll++ ld lkk+ LPr lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11475 126 HLHLATRDNMIKRKT-DRGLDWMQEEGAK--LLSHLDTAPRQLLEAALDEisLKKVGILALPR 185 *******99999999.67889**999999..******************72256777889*** PP TIGR00938 188 gvihadlfkdnvlldgdklkgvidfyfaCedallydlaiavndWcfeaddkldaaaakallkg 250 + ihadlf+dn +++g +l+g+idfy aC++ +lyd+aia+ndWc + ++ ld +a+all++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11475 186 ANIHADLFRDNAMFEGTHLTGLIDFYNACSGPMLYDVAIALNDWCSDDNGVLDGPRARALLGA 248 *************************************************************** PP TIGR00938 251 yeavrpLseeekaafpvllrgaalrfllsrlldlvftqagelvvakdPaeferkLk 306 y a rp+++ e + +p++lr+a++rf+lsrl + ag+ v + dP ef+++L+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11475 249 YAALRPFTAAEAQLWPTMLRVACVRFWLSRLIAAE-SFAGQDVLIHDPMEFQQRLA 303 *******************************9865.57899999*********996 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 0.01s 00:00:00.01 Elapsed: 00:00:00.04 # Mc/sec: 2.24 // [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