Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate WP_074201903.1 BUQ81_RS08070 homoserine kinase
Query= SwissProt::P29364 (316 letters) >NCBI__GCF_900141795.1:WP_074201903.1 Length = 313 Score = 226 bits (577), Expect = 4e-64 Identities = 121/279 (43%), Positives = 158/279 (56%), Gaps = 2/279 (0%) Query: 1 MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60 MSV+T + L FL YDLG LR F GI+EG EN+N+FV E G +VLT+ E+ + Sbjct: 1 MSVYTTITEDELSQFLTRYDLGTLRSFEGISEGIENTNYFVDTEAGRYVLTIFEQHSFDE 60 Query: 61 LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120 LP+F+ ++ + E +P + + R+G L RL KPA L RL G QPN C + Sbjct: 61 LPYFLNIMAFMAEHAIPTAHPIADREGNYLNRLHDKPAALVQRLDGCGVEQPNVRQCAVM 120 Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAALDAER 180 G+ L H A R R +DR L W A + P L E+ +ALL LA A D Sbjct: 121 GETLARFHLAGRDFDGYRANDRDLSWAERTFAEIEPYLDEEDKALLRDELAYQQAQDWAH 180 Query: 181 PALPRANLHADLFRDNVLFDGPHLAGLIDFYNACSGWMLYDLAITLNDWCSNTDGSLDPA 240 LP+ +HADLF DN LF G LAG+ID Y AC+ LYDLA+ +NDW + + D Sbjct: 181 --LPQGVIHADLFTDNALFRGDELAGIIDLYYACNAPWLYDLAVMVNDWARDEENRYDLE 238 Query: 241 RARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRL 279 R RA++ AY RP T LE WP+ R+A +RFWLSRL Sbjct: 239 RVRAIMQAYQQVRPLTELEQAEWPAAQRMAALRFWLSRL 277 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: 252 Number of extensions: 15 Number of successful extensions: 2 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: 313 Length adjustment: 27 Effective length of query: 289 Effective length of database: 286 Effective search space: 82654 Effective search space used: 82654 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_074201903.1 BUQ81_RS08070 (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.15346.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-113 363.0 0.2 7.7e-113 362.8 0.2 1.0 1 lcl|NCBI__GCF_900141795.1:WP_074201903.1 BUQ81_RS08070 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900141795.1:WP_074201903.1 BUQ81_RS08070 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 362.8 0.2 7.7e-113 7.7e-113 1 306 [. 1 302 [. 1 303 [. 0.98 Alignments for each domain: == domain 1 score: 362.8 bits; conditional E-value: 7.7e-113 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 m+vyt+++++el++fL ydlG l s++Gi+eG+en+ny+++t+ gryvLt++e+++ +eLP+fl+++ lcl|NCBI__GCF_900141795.1:WP_074201903.1 1 MSVYTTITEDELSQFLTRYDLGTLRSFEGISEGIENTNYFVDTEAGRYVLTIFEQHS-FDELPYFLNIM 68 9********************************************************.9********** PP TIGR00938 70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138 ++ae+ +p+a+p++ r+G+ l+ L+ kPaalv+ L+G v++P +++c+ +ge+la++hlag df++ lcl|NCBI__GCF_900141795.1:WP_074201903.1 69 AFMAEHAIPTAHPIADREGNYLNRLHDKPAALVQRLDGCGVEQPNVRQCAVMGETLARFHLAGRDFDGY 137 ********************************************************************* PP TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdklk 207 r+nd r W + ++ + + l+ee++all++el++ + + +LP+gvihadlf dn l+ gd+l+ lcl|NCBI__GCF_900141795.1:WP_074201903.1 138 RAND-RDLSWAERTFAE--IEPYLDEEDKALLRDELAYQQAQDWAHLPQGVIHADLFTDNALFRGDELA 203 ***5.566899999988..99************************************************ PP TIGR00938 208 gvidfyfaCedallydlaiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrf 276 g+id+y+aC+ +lydla+ vndW++++++++d ++++a++++y++vrpL+e e+a +p ++r aalrf lcl|NCBI__GCF_900141795.1:WP_074201903.1 204 GIIDLYYACNAPWLYDLAVMVNDWARDEENRYDLERVRAIMQAYQQVRPLTELEQAEWPAAQRMAALRF 272 ********************************************************************* PP TIGR00938 277 llsrlldlvftqagelvvakdPaeferkLk 306 +lsrl+d v ++ g+l+++k+P f++ L lcl|NCBI__GCF_900141795.1:WP_074201903.1 273 WLSRLKDKVLPREGALTMIKNPDVFRQVLL 302 **************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (313 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.42 // [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