Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_028310466.1 H566_RS0104240 homoserine kinase
Query= curated2:A4G1V8 (322 letters) >NCBI__GCF_000482785.1:WP_028310466.1 Length = 331 Score = 332 bits (850), Expect = 1e-95 Identities = 170/330 (51%), Positives = 215/330 (65%), Gaps = 13/330 (3%) Query: 1 MAVFTPVSLDDLTTWITQFDLGRALAIKGISSGIENSNFFITTER----GEYVLTVFEKL 56 MAVFTPVS + W+ Q+DLG ++I+GI SGIENSNFF T G +VLT+FE L Sbjct: 1 MAVFTPVSPAEAADWLRQYDLGELVSIEGIGSGIENSNFFFNTTSADNGGRFVLTIFENL 60 Query: 57 TFEQLPFYLNLMRHLAEGGVSVPAPVANRNGSIINALHGKPASIVTKLEGHCQLAPQPVH 116 QLPFYL M LA GV+VP P+ +R G+I+ ++ GKP + T+L+G +L PQP H Sbjct: 61 EPAQLPFYLEFMAALAARGVAVPRPIPDRTGAILQSIKGKPCCLATRLKGEFELDPQPEH 120 Query: 117 CAAVGAMLACMHLAAEDFE-----IRQPNLRGLEWWNEVTPIVMPYLSDSNEQLLATEII 171 C +G +A MH ++ + QPNLRGL+W + P V +L LL E+ Sbjct: 121 CRQLGRTIAQMHAGGLAYQEARPQLMQPNLRGLDWQQAMLPKVAEWLPADLADLLRDELA 180 Query: 172 SQNAFADSDVFRELPNGPIHADLFRNNVMFEGEQ----LTGFFDFYFAGCDTWLFDVAVT 227 Q + LP GP+HAD+FRNNV+F+G + L G FDFYFAG D+++FD+AV Sbjct: 181 VQAGHQSGAQYASLPRGPVHADIFRNNVLFDGTRAAPHLGGVFDFYFAGVDSFIFDLAVA 240 Query: 228 VNDWCIDDDSGELDQARVRAMLDAYHAIRPFTDAEQGAWQTMLRASALRFWLSRLYDFHM 287 VNDW ID DSG +D AR A++ AY A RPFTDAE+ AW LRA ALRFW+SRLYDF+ Sbjct: 241 VNDWAIDLDSGAIDAARADALIAAYAAERPFTDAERAAWPLALRAGALRFWVSRLYDFYR 300 Query: 288 PRDAEMLTPHDPAHFERILRLRIAQTAPAL 317 PR+AE LTPHDP HFERILRLR A AL Sbjct: 301 PREAETLTPHDPTHFERILRLRRAGPGCAL 330 Lambda K H 0.324 0.137 0.431 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: 370 Number of extensions: 16 Number of successful extensions: 4 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: 322 Length of database: 331 Length adjustment: 28 Effective length of query: 294 Effective length of database: 303 Effective search space: 89082 Effective search space used: 89082 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 (21.6 bits) S2: 48 (23.1 bits)
Align candidate WP_028310466.1 H566_RS0104240 (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.30424.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-91 293.0 0.0 1.6e-91 292.8 0.0 1.0 1 lcl|NCBI__GCF_000482785.1:WP_028310466.1 H566_RS0104240 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000482785.1:WP_028310466.1 H566_RS0104240 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 292.8 0.0 1.6e-91 1.6e-91 1 306 [. 1 320 [. 1 321 [. 0.92 Alignments for each domain: == domain 1 score: 292.8 bits; conditional E-value: 1.6e-91 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdk....gryvLtlyekrvkaeeLPff 65 mav+t vs e +L ydlGel+s++Gi +G+ensn++ +t++ gr+vLt++e+ + +LPf+ lcl|NCBI__GCF_000482785.1:WP_028310466.1 1 MAVFTPVSPAEAADWLRQYDLGELVSIEGIGSGIENSNFFFNTTSadngGRFVLTIFENLE-PAQLPFY 68 9****************************************997544558**********9.99***** PP TIGR00938 66 lellthLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagad 134 le++ La+rg++v++p++ r G+ l++++GkP +l LkG P++e+cr+ g + a++h g lcl|NCBI__GCF_000482785.1:WP_028310466.1 69 LEFMAALAARGVAVPRPIPDRTGAILQSIKGKPCCLATRLKGEFELDPQPEHCRQLGRTIAQMHAGGLA 137 ******************************************9999******************99977 PP TIGR00938 135 fkee....rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkf....lprdLPrgvihadlf 195 ++e ++ +lr +W+ ++ k v+e l ++la+ll++el++ + +LPrg +had+f lcl|NCBI__GCF_000482785.1:WP_028310466.1 138 YQEArpqlMQPNLRGLDWQQAMLPK--VAEWLPADLADLLRDELAVQAGHqsgaQYASLPRGPVHADIF 204 7765122256679999**9999988..*****************98754411115578*********** PP TIGR00938 196 kdnvlldgdk....lkgvidfyfaCedallydlaiavndWcfeadd.kldaaaakallkgyeavrpLse 259 ++nvl+dg + l+gv dfyfa d++++dla+avndW+++ d+ +daa+a al+ +y a rp+++ lcl|NCBI__GCF_000482785.1:WP_028310466.1 205 RNNVLFDGTRaaphLGGVFDFYFAGVDSFIFDLAVAVNDWAIDLDSgAIDAARADALIAAYAAERPFTD 273 *******986555599***************************985389******************** PP TIGR00938 260 eekaafpvllrgaalrfllsrlldlvftqagelvvakdPaeferkLk 306 e+aa+p +lr++alrf++srl d++ ++ e ++ dP++fer+L+ lcl|NCBI__GCF_000482785.1:WP_028310466.1 274 AERAAWPLALRAGALRFWVSRLYDFYRPREAETLTPHDPTHFERILR 320 *********************************************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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.03 // [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