Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate PfGW456L13_596 Homoserine kinase (EC 2.7.1.39)
Query= SwissProt::P29364 (316 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_596 Length = 316 Score = 451 bits (1161), Expect = e-132 Identities = 225/316 (71%), Positives = 254/316 (80%) Query: 1 MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60 MSVFTPL R LEAFLAPY LGRL DF+GIA GSEN+NFF+SLE GEFVLTLVERGPVQ+ Sbjct: 1 MSVFTPLARPELEAFLAPYGLGRLLDFQGIAAGSENTNFFISLEQGEFVLTLVERGPVQE 60 Query: 61 LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120 +PFFIELLDVLH LPVPYALRT DG ALR L GKPALLQPRLAG+H +Q NA HC +V Sbjct: 61 MPFFIELLDVLHGADLPVPYALRTTDGVALRELAGKPALLQPRLAGKHIKQANAQHCAQV 120 Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAALDAER 180 G+LLGHLH AT+ +++R +DRGL WMLE+G L + + LL AL EI + Sbjct: 121 GELLGHLHLATQANMIKRKTDRGLDWMLEEGTQFLSHLGAEQKDLLQRALEEITRQKEKI 180 Query: 181 PALPRANLHADLFRDNVLFDGPHLAGLIDFYNACSGWMLYDLAITLNDWCSNTDGSLDPA 240 ALPRAN+HADLFRDN +F+G HL GLIDFYNACSG MLYD+AI LNDWCS+ +G +D Sbjct: 181 LALPRANIHADLFRDNAMFEGTHLTGLIDFYNACSGPMLYDVAIALNDWCSDDNGVIDGP 240 Query: 241 RARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQDVLIHDPAEFEI 300 RARALL AYA RPFTA EAE WP+MLRVACVRFWLSRLIAAE+FAGQDVLIHDP EF++ Sbjct: 241 RARALLGAYAALRPFTAAEAELWPTMLRVACVRFWLSRLIAAESFAGQDVLIHDPMEFQL 300 Query: 301 RLAQRQNVEIHLPFAL 316 RLAQRQ V LPFAL Sbjct: 301 RLAQRQTVNTPLPFAL 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: 394 Number of extensions: 9 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 PfGW456L13_596 (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.1206.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-87 278.6 0.0 3.8e-87 278.4 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_596 Homoserine kinase (EC 2.7.1.39) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_596 Homoserine kinase (EC 2.7.1.39) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 278.4 0.0 3.8e-87 3.8e-87 1 306 [. 1 303 [. 1 304 [. 0.96 Alignments for each domain: == domain 1 score: 278.4 bits; conditional E-value: 3.8e-87 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekr 56 m+v+t ++ eleafL y lG+ll+++Gia G en+n+++ ++g +vLtl e+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_596 1 MSVFTPLARPELEAFLAPYGLGRLLDFQGIAAGSENTNFFISLEQGEFVLTLVERG 56 9*****************************************************99 PP TIGR00938 57 vkaeeLPfflellthLaerglpvakpvksrdGralseLaGkPaalvefLkGssvak 112 +e+Pff+ell+ L +lpv+ ++++ dG al eLaGkPa l L+G+ +++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_596 57 P-VQEMPFFIELLDVLHGADLPVPYALRTTDGVALRELAGKPALLQPRLAGKHIKQ 111 8.899*************************************************** PP TIGR00938 113 PtaercrevgevlaklhlagadfkeerkndlrleaWsilaakkfkvleqleeelaa 168 a++c++vge l +lhla++ +rk r +W + + l +l +e+++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_596 112 ANAQHCAQVGELLGHLHLATQANMIKRKT-DRGLDWMLEEGTQ--FLSHLGAEQKD 164 ********************988888888.58889*9998888..9********** PP TIGR00938 169 lldkeldalkkflpr..dLPrgvihadlfkdnvlldgdklkgvidfyfaCedally 222 ll++ l+ +++ + LPr+ ihadlf+dn +++g +l+g+idfy aC++ +ly lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_596 165 LLQRALEEITRQKEKilALPRANIHADLFRDNAMFEGTHLTGLIDFYNACSGPMLY 220 *******998877764478************************************* PP TIGR00938 223 dlaiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrfll 278 d+aia+ndWc + ++ +d +a+all++y a rp+++ e + +p++lr+a++rf+l lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_596 221 DVAIALNDWCSDDNGVIDGPRARALLGAYAALRPFTAAEAELWPTMLRVACVRFWL 276 ******************************************************** PP TIGR00938 279 srlldlvftqagelvvakdPaeferkLk 306 srl + ag+ v + dP ef+ +L+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_596 277 SRLIAAE-SFAGQDVLIHDPMEFQLRLA 303 ***9865.57899999*******98886 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: 7.15 // [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