Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate BPHYT_RS33645 BPHYT_RS33645 homoserine kinase
Query= SwissProt::P29364 (316 letters) >FitnessBrowser__BFirm:BPHYT_RS33645 Length = 331 Score = 222 bits (565), Expect = 1e-62 Identities = 133/318 (41%), Positives = 174/318 (54%), Gaps = 14/318 (4%) Query: 1 MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60 M+VFT + L +++ YDLG + +FRGI+ G ENSNFF++ GE+VLT+ E+ + Sbjct: 1 MAVFTAVTEPQLAEWMSHYDLGDVVEFRGISSGIENSNFFLTTTRGEYVLTIFEKLTAEQ 60 Query: 61 LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120 LPF+++L+ L +PVP + DG L GKPA + +L G E P HC EV Sbjct: 61 LPFYLDLMRHLAAHRVPVPDPMPREDGALFGTLHGKPAAIVTKLEGAPELAPGVEHCIEV 120 Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAAL--DA 178 G +L +H A R +P+ R LPW E + P L + R LL+ LA A A Sbjct: 121 GQMLARMHLAGRDYTGYQPNLRSLPWWRETVPTILPFLQGEQRELLSSELAHQEAFFASA 180 Query: 179 ERPALPRANLHADLFRDNVLF-----DGPH---LAGLIDFYNA-CSGWMLYDLAITLNDW 229 + ALP HADLFRDN +F D H L G DFY A C W L+D+A+T+NDW Sbjct: 181 DYAALPEGPCHADLFRDNAMFAHAAPDTGHEVRLGGFFDFYFAGCDKW-LFDVAVTVNDW 239 Query: 230 CSN-TDGSLDPARARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQ 288 C + G LD AR A+L AY RPFTA E HW MLR RFW+SRL Sbjct: 240 CVDLATGKLDNARTEAMLRAYQTVRPFTAEENRHWGDMLRAGAYRFWVSRLYDFYLPRAA 299 Query: 289 DVL-IHDPAEFEIRLAQR 305 ++L HDP FE L +R Sbjct: 300 ELLKPHDPGHFERILRER 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: 299 Number of extensions: 9 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: 331 Length adjustment: 28 Effective length of query: 288 Effective length of database: 303 Effective search space: 87264 Effective search space used: 87264 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 BPHYT_RS33645 BPHYT_RS33645 (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.19408.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-100 320.5 0.0 6.8e-100 320.3 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS33645 BPHYT_RS33645 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS33645 BPHYT_RS33645 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 320.3 0.0 6.8e-100 6.8e-100 1 306 [. 1 315 [. 1 316 [. 0.95 Alignments for each domain: == domain 1 score: 320.3 bits; conditional E-value: 6.8e-100 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflellt 70 mav+t v++ +l ++++ ydlG++++++Gi++G+ensn++ltt++g yvLt++ek + ae+LPf+l+l++ lcl|FitnessBrowser__BFirm:BPHYT_RS33645 1 MAVFTAVTEPQLAEWMSHYDLGDVVEFRGISSGIENSNFFLTTTRGEYVLTIFEKLT-AEQLPFYLDLMR 69 9*******************************************************9.************ PP TIGR00938 71 hLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkeerk 140 hLa++ +pv+ p++++dG++ ++L+GkPaa+v L+G P +e+c evg++la++hlag d+++ + lcl|FitnessBrowser__BFirm:BPHYT_RS33645 70 HLAAHRVPVPDPMPREDGALFGTLHGKPAAIVTKLEGAPELAPGVEHCIEVGQMLARMHLAGRDYTGYQP 139 ********************************************************************** PP TIGR00938 141 ndlrleaWsilaakkfkvleqleeelaalldkeldalkkflpr....dLPrgvihadlfkdnvll..... 201 n lr W+ ++ + +l++l+ e+ +ll++el++ + f++ LP+g hadlf+dn ++ lcl|FitnessBrowser__BFirm:BPHYT_RS33645 140 N-LRSLPWWRETVPT--ILPFLQGEQRELLSSELAHQEAFFASadyaALPEGPCHADLFRDNAMFahaap 206 *.***********99..******************9998876422227****************944444 PP TIGR00938 202 d.gdk..lkgvidfyfaCedallydlaiavndWcfe.addkldaaaakallkgyeavrpLseeekaafpv 267 d g++ l+g+ dfyfa d +l+d+a++vndWc++ a +kld+a++ a+l +y++vrp+++ee+ + lcl|FitnessBrowser__BFirm:BPHYT_RS33645 207 DtGHEvrLGGFFDFYFAGCDKWLFDVAVTVNDWCVDlATGKLDNARTEAMLRAYQTVRPFTAEENRHWGD 276 223445589**************************96789****************************** PP TIGR00938 268 llrgaalrfllsrlldlvftqagelvvakdPaeferkLk 306 +lr++a rf++srl d++ ++a el ++ dP +fer+L+ lcl|FitnessBrowser__BFirm:BPHYT_RS33645 277 MLRAGAYRFWVSRLYDFYLPRAAELLKPHDPGHFERILR 315 *************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (331 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: 11.68 // [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