Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate WP_013092990.1 BC1002_RS26025 homoserine kinase
Query= SwissProt::P29364 (316 letters) >NCBI__GCF_000092885.1:WP_013092990.1 Length = 331 Score = 221 bits (563), Expect = 2e-62 Identities = 135/330 (40%), Positives = 175/330 (53%), Gaps = 18/330 (5%) Query: 1 MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60 M+VFT + S L +++ YDLG + +FRGI+ G ENSNFF++ GE+VLT+ E+ + Sbjct: 1 MAVFTAVNESQLAEWMSHYDLGDVVEFRGISSGIENSNFFLTTTRGEYVLTIFEKLTAEQ 60 Query: 61 LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120 LPF+++L+ L +PVP + DG L GKPA + +L G E P HC EV Sbjct: 61 LPFYLDLMRHLAAHRVPVPDPMPRLDGALFGMLLGKPATIVTKLEGAPELAPGVEHCAEV 120 Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAAL--DA 178 G +L +H A R +P+ R LPW E + P L + R LLA LA A A Sbjct: 121 GHMLARMHLAGRDYPRYQPNLRSLPWWRETVPTILPYLEGEQRDLLASELAHQEAFFASA 180 Query: 179 ERPALPRANLHADLFRDNVLF--------DGPHLAGLIDFYNA-CSGWMLYDLAITLNDW 229 + A+P HADLFRDN +F L G DFY A C W L+D+A+T+NDW Sbjct: 181 DYAAMPSGPCHADLFRDNAMFAHAAPETGHEVRLGGFFDFYFAGCDKW-LFDVAVTVNDW 239 Query: 230 CSN-TDGSLDPARARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQ 288 C + G LD R ALL AY RPFT E HW MLR RFW+SRL Sbjct: 240 CVDLATGKLDTERTEALLRAYQTVRPFTVEENHHWGDMLRAGAYRFWVSRLYDFHLPRAA 299 Query: 289 DVL-IHDPAEFEIRLAQR----QNVEIHLP 313 ++L HDP FE L +R N IH P Sbjct: 300 ELLKPHDPGHFERILRERLLGVANPGIHTP 329 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: 308 Number of extensions: 15 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 WP_013092990.1 BC1002_RS26025 (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.27859.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-98 314.6 0.0 4.1e-98 314.4 0.0 1.0 1 lcl|NCBI__GCF_000092885.1:WP_013092990.1 BC1002_RS26025 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092885.1:WP_013092990.1 BC1002_RS26025 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 314.4 0.0 4.1e-98 4.1e-98 1 306 [. 1 315 [. 1 316 [. 0.95 Alignments for each domain: == domain 1 score: 314.4 bits; conditional E-value: 4.1e-98 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 mav+t v + +l ++++ ydlG++++++Gi++G+ensn++ltt++g yvLt++ek + ae+LPf+l+l+ lcl|NCBI__GCF_000092885.1:WP_013092990.1 1 MAVFTAVNESQLAEWMSHYDLGDVVEFRGISSGIENSNFFLTTTRGEYVLTIFEKLT-AEQLPFYLDLM 68 9*******************************************************9.*********** PP TIGR00938 70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138 +hLa++ +pv+ p+++ dG++ + L GkPa++v L+G P +e+c+evg++la++hlag d++ lcl|NCBI__GCF_000092885.1:WP_013092990.1 69 RHLAAHRVPVPDPMPRLDGALFGMLLGKPATIVTKLEGAPELAPGVEHCAEVGHMLARMHLAGRDYPRY 137 ********************************************************************* PP TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflpr....dLPrgvihadlfkdnvll.. 201 + n lr W+ ++ + +l+ le e+ +ll +el++ + f++ +P+g hadlf+dn ++ lcl|NCBI__GCF_000092885.1:WP_013092990.1 138 QPN-LRSLPWWRETVPT--ILPYLEGEQRDLLASELAHQEAFFASadyaAMPSGPCHADLFRDNAMFah 203 ***.***********99..******************99988764222279***************944 PP TIGR00938 202 ....dgdk..lkgvidfyfaCedallydlaiavndWcfe.addkldaaaakallkgyeavrpLseeeka 263 g++ l+g+ dfyfa d +l+d+a++vndWc++ a +kld++++ all +y++vrp++ ee+ lcl|NCBI__GCF_000092885.1:WP_013092990.1 204 aapeTGHEvrLGGFFDFYFAGCDKWLFDVAVTVNDWCVDlATGKLDTERTEALLRAYQTVRPFTVEENH 272 444224444589**************************96789************************** PP TIGR00938 264 afpvllrgaalrfllsrlldlvftqagelvvakdPaeferkLk 306 + +lr++a rf++srl d++ ++a el ++ dP +fer+L+ lcl|NCBI__GCF_000092885.1:WP_013092990.1 273 HWGDMLRAGAYRFWVSRLYDFHLPRAAELLKPHDPGHFERILR 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.46 // [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