Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate HSERO_RS02240 HSERO_RS02240 homoserine kinase
Query= SwissProt::P29364 (316 letters) >FitnessBrowser__HerbieS:HSERO_RS02240 Length = 318 Score = 230 bits (586), Expect = 4e-65 Identities = 130/304 (42%), Positives = 177/304 (58%), Gaps = 6/304 (1%) Query: 1 MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60 M+VFTP+ L +L + LG +GI+ G ENSNFF+ E GE+VLTL E+ ++ Sbjct: 1 MAVFTPVSLEQLSDWLKHFPLGTATSIKGISSGIENSNFFIGTERGEYVLTLFEKLHIEQ 60 Query: 61 LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120 LPF++EL+ L E G+PVP + G + L KPA + +L G+ + P HC + Sbjct: 61 LPFYLELMRHLAERGIPVPAPVANDKGAIVSLLNDKPAAIVSKLEGQSQLDPQPVHCAAL 120 Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPAL--AEIAALDA 178 GD+L +H A + + +P+ RGL W LE + P LP + LLA + + A A Sbjct: 121 GDMLARMHLAAKDFKILQPNLRGLAWWLETTPTVLPFLPAELGRLLADEVQYQKDFAATA 180 Query: 179 ERPALPRANLHADLFRDNVLFDGPHLAGLIDFYNA-CSGWMLYDLAITLNDWCSNTD-GS 236 + ALPR +HADLFR+N +F G L+G+ DFY A C W L+DLA+T+NDWC + D G Sbjct: 181 DYRALPRGPVHADLFRNNAMFVGERLSGIFDFYFAGCDTW-LFDLAVTVNDWCVDLDTGV 239 Query: 237 LDPARARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQDVLI-HDP 295 LD AR A+LAAY RPF+ E W MLR A +RFWLSRL ++L HDP Sbjct: 240 LDLARTEAMLAAYRAVRPFSEAERIAWQPMLRAAALRFWLSRLYDFYMPRAAEMLTPHDP 299 Query: 296 AEFE 299 FE Sbjct: 300 THFE 303 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: 291 Number of extensions: 10 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: 318 Length adjustment: 27 Effective length of query: 289 Effective length of database: 291 Effective search space: 84099 Effective search space used: 84099 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 HSERO_RS02240 HSERO_RS02240 (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.31510.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-106 341.6 0.0 2.5e-106 341.4 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS02240 HSERO_RS02240 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS02240 HSERO_RS02240 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 341.4 0.0 2.5e-106 2.5e-106 1 306 [. 1 307 [. 1 308 [. 0.97 Alignments for each domain: == domain 1 score: 341.4 bits; conditional E-value: 2.5e-106 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflel 68 mav+t vs e+l+ +L+ + lG s+kGi++G+ensn+++ t++g yvLtl+ek e+LPf+lel lcl|FitnessBrowser__HerbieS:HSERO_RS02240 1 MAVFTPVSLEQLSDWLKHFPLGTATSIKGISSGIENSNFFIGTERGEYVLTLFEKLH-IEQLPFYLEL 67 9******************************************************99.9********* PP TIGR00938 69 lthLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfk 136 ++hLaerg+pv++pv++ +G+ +s L+ kPaa+v+ L+G+s P++ +c++ g++la++hla++dfk lcl|FitnessBrowser__HerbieS:HSERO_RS02240 68 MRHLAERGIPVPAPVANDKGAIVSLLNDKPAAIVSKLEGQSQLDPQPVHCAALGDMLARMHLAAKDFK 135 ******************************************************************** PP TIGR00938 137 eerkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflp....rdLPrgvihadlfkdnvl 200 + n lr aW+ +++ + vl++l +el++ll +e+++ k+f + r LPrg +hadlf++n + lcl|FitnessBrowser__HerbieS:HSERO_RS02240 136 ILQPN-LRGLAWWLETTPT--VLPFLPAELGRLLADEVQYQKDFAAtadyRALPRGPVHADLFRNNAM 200 *****.***********99..*****************99998864333389**************** PP TIGR00938 201 ldgdklkgvidfyfaCedallydlaiavndWcfeadd.kldaaaakallkgyeavrpLseeekaafpv 267 + g++l+g+ dfyfa d++l+dla++vndWc++ d+ ld a++ a+l +y+avrp+se e+ a+ lcl|FitnessBrowser__HerbieS:HSERO_RS02240 201 FVGERLSGIFDFYFAGCDTWLFDLAVTVNDWCVDLDTgVLDLARTEAMLAAYRAVRPFSEAERIAWQP 268 **********************************99636899************************** PP TIGR00938 268 llrgaalrfllsrlldlvftqagelvvakdPaeferkLk 306 +lr+aalrf+lsrl d+++++a e+ ++ dP++fer+L+ lcl|FitnessBrowser__HerbieS:HSERO_RS02240 269 MLRAAALRFWLSRLYDFYMPRAAEMLTPHDPTHFERILR 307 *************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (318 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: 00:00:00.00 # Mc/sec: 10.02 // [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