Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_013834616.1 THICY_RS00270 homoserine kinase
Query= curated2:Q9RAM6 (319 letters) >NCBI__GCF_000214825.1:WP_013834616.1 Length = 311 Score = 261 bits (668), Expect = 1e-74 Identities = 134/301 (44%), Positives = 186/301 (61%) Query: 1 MSVFTTVSFEQMQQWLKGYDLGELLDLQGIASGITNTNYFVTTDNGRYVLTLFEEHSAEE 60 MSV+T V+ EQ+ ++LK Y +G+L+ +GI++GI NTNYFV TD R+VLT+FE H E Sbjct: 1 MSVYTKVASEQLVEFLKHYSVGQLVSYKGISAGIENTNYFVDTDQSRFVLTIFEHHQPSE 60 Query: 61 LPNFLDLMTHLAERGIPCPHPVKNNAGRALGELNGKPAALVSCLAGRSLDNPMPQHCAAI 120 L FL++M +A+ GIP P NN+G LGEL GKPA LV+ L+G++L P C + Sbjct: 61 LGYFLNIMAFMADNGIPTALPQPNNSGGFLGELCGKPATLVARLSGQTLTFPTLPQCQVM 120 Query: 121 GEVLARMHIAGASFKAGMSNLRGQEWRIATAAKVAPFLDEENHRMLDAQLEFERTFDTRR 180 LAR H G+ F N R W T ++ L + + ++ ++ +++ D + Sbjct: 121 AATLARFHKVGSKFAEFRPNDRDILWAEETFKLISQRLTADQYSLIADEIAYQQAIDWQA 180 Query: 181 LPRGVIHADLFRDNVLMDGDKVGGVIDFYYACHDALLYDIAIAVNDWCVNADCTLDAVRV 240 LP+ VIHADLF DN + DG+ + G+ID YYAC A LYD+A+ VNDWC + L V Sbjct: 181 LPQSVIHADLFTDNAMFDGETLTGIIDLYYACQGACLYDLAVMVNDWCRDEMHQLKPEFV 240 Query: 241 RAFLDAYHAIRPLTGEEHAAWPGMLRVAAMRFWLSRLNDLYFPQAGELTHAKDPAYFERI 300 L AY IR LT +E A WP LR+AA+RF+LSRL D P+ GE+T K+P FE + Sbjct: 241 SKTLFAYQQIRQLTPQELACWPAALRMAALRFYLSRLKDAIMPRKGEMTMIKNPQVFEDL 300 Query: 301 L 301 L Sbjct: 301 L 301 Lambda K H 0.324 0.137 0.430 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: 277 Number of extensions: 11 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: 319 Length of database: 311 Length adjustment: 27 Effective length of query: 292 Effective length of database: 284 Effective search space: 82928 Effective search space used: 82928 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: 40 (21.5 bits) S2: 48 (23.1 bits)
Align candidate WP_013834616.1 THICY_RS00270 (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.22322.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-98 314.3 0.0 5.3e-98 314.1 0.0 1.0 1 lcl|NCBI__GCF_000214825.1:WP_013834616.1 THICY_RS00270 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214825.1:WP_013834616.1 THICY_RS00270 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 314.1 0.0 5.3e-98 5.3e-98 1 305 [. 1 301 [. 1 303 [. 0.98 Alignments for each domain: == domain 1 score: 314.1 bits; conditional E-value: 5.3e-98 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 m+vyt+v+ e+l +fL+ y +G+l+s kGi+ G+en+ny+++td+ r+vLt++e+++ + eL +fl+++ lcl|NCBI__GCF_000214825.1:WP_013834616.1 1 MSVYTKVASEQLVEFLKHYSVGQLVSYKGISAGIENTNYFVDTDQSRFVLTIFEHHQ-PSELGYFLNIM 68 9*******************************************************9.*********** PP TIGR00938 70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138 ++a++g+p+a p ++++G l+eL GkPa+lv+ L+G+ ++ Pt+ +c+ + ++la++h g++f e lcl|NCBI__GCF_000214825.1:WP_013834616.1 69 AFMADNGIPTALPQPNNSGGFLGELCGKPATLVARLSGQTLTFPTLPQCQVMAATLARFHKVGSKFAEF 137 ********************************************************************* PP TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdklk 207 r n r W ++ k + + l +++ +l+ +e+++ + ++ + LP++vihadlf dn ++dg+ l+ lcl|NCBI__GCF_000214825.1:WP_013834616.1 138 RPN-DRDILWAEETFKL--ISQRLTADQYSLIADEIAYQQAIDWQALPQSVIHADLFTDNAMFDGETLT 203 ***.5667899999999..999*********************************************** PP TIGR00938 208 gvidfyfaCedallydlaiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrf 276 g+id+y+aC++a lydla+ vndWc+++ ++l+ + + l +y+++r L+++e a +p +lr aalrf lcl|NCBI__GCF_000214825.1:WP_013834616.1 204 GIIDLYYACQGACLYDLAVMVNDWCRDEMHQLKPEFVSKTLFAYQQIRQLTPQELACWPAALRMAALRF 272 ************************************99999**************************** PP TIGR00938 277 llsrlldlvftqagelvvakdPaeferkL 305 +lsrl+d +++ ge++++k+P+ fe +L lcl|NCBI__GCF_000214825.1:WP_013834616.1 273 YLSRLKDAIMPRKGEMTMIKNPQVFEDLL 301 *************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (311 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: 8.72 // [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