Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_019557832.1 F612_RS0111035 homoserine kinase
Query= curated2:Q0AHY7 (316 letters) >NCBI__GCF_000381085.1:WP_019557832.1 Length = 317 Score = 268 bits (686), Expect = 1e-76 Identities = 141/313 (45%), Positives = 191/313 (61%), Gaps = 9/313 (2%) Query: 1 MSVFTPVTKKQLAVWLQNYSLGSLTDLQGISSGIENTNYFVTTTQG----KFILTLFEKL 56 MSV+T V + QL +L+ Y +G L +GIS+GIENTNYFV T +F+LT+FE Sbjct: 1 MSVYTVVEENQLITFLEEYDVGFLESFEGISAGIENTNYFVNTRHNGQLKQFVLTIFEHH 60 Query: 57 TSTELPFYLNLMAYLSEQGIPCPKPIESQDHALLGTLNGKPASIVSFLPGQSMTQIREEQ 116 ELP++LN+MA+++E IP P+ + L L GKPAS+V+ L G + Q Sbjct: 61 DFEELPYFLNIMAFMAEHKIPTAHPMPTHSEGYLKELCGKPASLVTRLTGGGVDHPSVIQ 120 Query: 117 CAQVGEILAKMHLAGLNYNGKNRNPRGLDWWQTAAGTVMPFLSRSEQSLLDEELQFQIKQ 176 C +G+ LA H AGL Y N RG+DW Q+ + L+ E+ L+ EL +Q + Sbjct: 121 CGVMGKQLASFHQAGLEYEQCRANDRGIDWMQSTFDEINTHLTIEERDLITAELAYQNQI 180 Query: 177 RTTNLPQGIIHADLFRDNVLFTSTGIGGIIDFYFACNDALLYDLAITANDWCTL-----G 231 +LPQG+IHADLF DN LF + GIID Y+ACN A LYDLA+ NDWC + Sbjct: 181 DWAHLPQGVIHADLFCDNALFDGDELTGIIDLYYACNAAFLYDLAVMVNDWCRMNTENPA 240 Query: 232 DGVMDKARMHALVKAYQAARPLTAEEYPAWPAMLRAGALRFWLSRLYDYYLPRPGELTHK 291 D D++++ +V AYQ RPLT E AWPA LR ALRF+LSRL D +PR GE+T Sbjct: 241 DIHFDESKIATMVFAYQQQRPLTEAEQQAWPAALRLAALRFFLSRLQDKCMPREGEMTQI 300 Query: 292 KDPEYFRKILEYH 304 K+P+ F+K+L+ H Sbjct: 301 KNPDVFKKVLQIH 313 Lambda K H 0.320 0.136 0.415 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: 296 Number of extensions: 14 Number of successful extensions: 3 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: 317 Length adjustment: 27 Effective length of query: 289 Effective length of database: 290 Effective search space: 83810 Effective search space used: 83810 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_019557832.1 F612_RS0111035 (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.7369.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-97 310.7 0.1 6.5e-97 310.5 0.1 1.0 1 lcl|NCBI__GCF_000381085.1:WP_019557832.1 F612_RS0111035 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000381085.1:WP_019557832.1 F612_RS0111035 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 310.5 0.1 6.5e-97 6.5e-97 1 306 [. 1 311 [. 1 312 [. 0.95 Alignments for each domain: == domain 1 score: 310.5 bits; conditional E-value: 6.5e-97 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdk....gryvLtlyekrvkaeeLPff 65 m+vyt v +++l +fLe yd+G l s++Gi+ G+en+ny+++t + +++vLt++e++ eeLP+f lcl|NCBI__GCF_000381085.1:WP_019557832.1 1 MSVYTVVEENQLITFLEEYDVGFLESFEGISAGIENTNYFVNTRHngqlKQFVLTIFEHHD-FEELPYF 68 9*****************************************975222368********99.******* PP TIGR00938 66 lellthLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagad 134 l+++ ++ae+ +p+a+p+++++ l+eL GkPa+lv L+G v++P + +c +g+ la +h ag + lcl|NCBI__GCF_000381085.1:WP_019557832.1 69 LNIMAFMAEHKIPTAHPMPTHSEGYLKELCGKPASLVTRLTGGGVDHPSVIQCGVMGKQLASFHQAGLE 137 ********************************************************************* PP TIGR00938 135 fkeerkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldg 203 +++ r+n r +W + + + +l e+ +l+++el++ ++++ +LP+gvihadlf dn l+dg lcl|NCBI__GCF_000381085.1:WP_019557832.1 138 YEQCRAN-DRGIDWMQSTFDE--INTHLTIEERDLITAELAYQNQIDWAHLPQGVIHADLFCDNALFDG 203 *******.68889*9999888..8999999*************************************** PP TIGR00938 204 dklkgvidfyfaCedallydlaiavndWcfe.....addkldaaaakallkgyeavrpLseeekaafpv 267 d+l+g+id+y+aC+ a+lydla+ vndWc+ ad ++d+++ ++ +y+++rpL+e e++a+p lcl|NCBI__GCF_000381085.1:WP_019557832.1 204 DELTGIIDLYYACNAAFLYDLAVMVNDWCRMntenpADIHFDESKIATMVFAYQQQRPLTEAEQQAWPA 272 *****************************8433344789****************************** PP TIGR00938 268 llrgaalrfllsrlldlvftqagelvvakdPaeferkLk 306 +lr aalrf+lsrl+d +++ ge++++k+P f++ L+ lcl|NCBI__GCF_000381085.1:WP_019557832.1 273 ALRLAALRFFLSRLQDKCMPREGEMTQIKNPDVFKKVLQ 311 ************************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (317 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 8.52 // [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