Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate WP_050463180.1 AKL27_RS12600 homoserine kinase
Query= SwissProt::P29364 (316 letters) >NCBI__GCF_001189915.1:WP_050463180.1 Length = 318 Score = 226 bits (575), Expect = 7e-64 Identities = 124/304 (40%), Positives = 175/304 (57%), Gaps = 6/304 (1%) Query: 1 MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60 M+VFTP+ L +L + LG+ + +GI+ G ENSNFF++ + GE+VLTL E+ + Sbjct: 1 MAVFTPVSLDDLSGWLTQFSLGKAQAIKGISSGIENSNFFITTDSGEYVLTLFEKLTFEQ 60 Query: 61 LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120 LPF++EL+ L + G+ VP + + G + L GKPA + +L G + P HC EV Sbjct: 61 LPFYLELMRHLAQRGVLVPAPVANQQGSIINALNGKPASIVTKLEGESQLSPTPVHCAEV 120 Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPAL--AEIAALDA 178 G +L H+H A + + +P+ RGL W E + P LP + LL + E A A Sbjct: 121 GAMLAHMHLAAQDFTIRQPNLRGLSWWRETTPVVLPYLPADTQDLLRTEMQFQETFAASA 180 Query: 179 ERPALPRANLHADLFRDNVLFDGPHLAGLIDFYNA-CSGWMLYDLAITLNDWCSNTD-GS 236 LP +HADLFR+N +F L G DFY A C W L+DLA+T+NDWC + D G+ Sbjct: 181 TYAQLPNGPVHADLFRNNAMFVDTRLTGFFDFYFAGCDTW-LFDLAVTVNDWCIDVDSGA 239 Query: 237 LDPARARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQDVLI-HDP 295 LD RA+A++ AY RPF+A E + W MLR A +RFW+SRL ++L HDP Sbjct: 240 LDFPRAQAMMDAYHAVRPFSAAEQQAWQPMLRAAALRFWISRLYDFYLPRDAEMLTPHDP 299 Query: 296 AEFE 299 FE Sbjct: 300 GHFE 303 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: 281 Number of extensions: 10 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: 318 Length adjustment: 27 Effective length of query: 289 Effective length of database: 291 Effective search space: 84099 Effective search space used: 84099 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_050463180.1 AKL27_RS12600 (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.6847.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-104 335.5 0.0 1.8e-104 335.3 0.0 1.0 1 lcl|NCBI__GCF_001189915.1:WP_050463180.1 AKL27_RS12600 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001189915.1:WP_050463180.1 AKL27_RS12600 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 335.3 0.0 1.8e-104 1.8e-104 1 306 [. 1 307 [. 1 308 [. 0.97 Alignments for each domain: == domain 1 score: 335.3 bits; conditional E-value: 1.8e-104 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 mav+t vs ++l+++L + lG+ ++kGi++G+ensn+++ttd+g yvLtl+ek + e+LPf+lel+ lcl|NCBI__GCF_001189915.1:WP_050463180.1 1 MAVFTPVSLDDLSGWLTQFSLGKAQAIKGISSGIENSNFFITTDSGEYVLTLFEKLT-FEQLPFYLELM 68 9*******************************************************9.*********** PP TIGR00938 70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138 +hLa+rg+ v++pv++++G ++ L+GkPa++v L+G s Pt+ +c+evg++la++hla++df+ + lcl|NCBI__GCF_001189915.1:WP_050463180.1 69 RHLAQRGVLVPAPVANQQGSIINALNGKPASIVTKLEGESQLSPTPVHCAEVGAMLAHMHLAAQDFTIR 137 ********************************************************************* PP TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflpr....dLPrgvihadlfkdnvlldg 203 + n lr W+ +++ vl+ l +++++ll++e+++ ++f + +LP+g +hadlf++n ++ lcl|NCBI__GCF_001189915.1:WP_050463180.1 138 QPN-LRGLSWWRETTPV--VLPYLPADTQDLLRTEMQFQETFAASatyaQLPNGPVHADLFRNNAMFVD 203 ***.***********99..********************99976433338******************* PP TIGR00938 204 dklkgvidfyfaCedallydlaiavndWcfeadd.kldaaaakallkgyeavrpLseeekaafpvllrg 271 +l+g+ dfyfa d++l+dla++vndWc++ d+ ld +a+a++++y+avrp+s+ e++a+ +lr+ lcl|NCBI__GCF_001189915.1:WP_050463180.1 204 TRLTGFFDFYFAGCDTWLFDLAVTVNDWCIDVDSgALDFPRAQAMMDAYHAVRPFSAAEQQAWQPMLRA 272 *******************************995389******************************** PP TIGR00938 272 aalrfllsrlldlvftqagelvvakdPaeferkLk 306 aalrf++srl d++ ++ e+ ++ dP +fer+L+ lcl|NCBI__GCF_001189915.1:WP_050463180.1 273 AALRFWISRLYDFYLPRDAEMLTPHDPGHFERILR 307 *********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (318 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: 6.64 // [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