Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_013554828.1 NITSA_RS09565 homoserine kinase
Query= curated2:A6QBQ7 (292 letters) >NCBI__GCF_000186245.1:WP_013554828.1 Length = 294 Score = 457 bits (1175), Expect = e-133 Identities = 232/293 (79%), Positives = 257/293 (87%), Gaps = 1/293 (0%) Query: 1 MLISVPATSANLGPGFDTLGLAVDLRNEIVIKPSKFLSLSTHGEGADNPKIKKNSLFLSI 60 M ISVPATSANLGPGFDTLGLA+DLRNEIVIKP++F S+ST GEGADNPKIKKNSLFL I Sbjct: 1 MFISVPATSANLGPGFDTLGLAIDLRNEIVIKPARFHSVSTKGEGADNPKIKKNSLFLHI 60 Query: 61 FNENYKRLS-GKANNFRFEFTNRIPISRGLGSSSAVIVAALSGAYAMAGVKYNKREILNQ 119 F+E Y++L+ GK FRFEFTNRIPISRGLGSSSAVIV+A++ A+ AGVKYNKR+ILN Sbjct: 61 FHEQYRKLTDGKRATFRFEFTNRIPISRGLGSSSAVIVSAITAAHLAAGVKYNKRKILNT 120 Query: 120 ALRYEHHPDNITPAVMGGFNVACVEGDRVYSKKRRMPDYLRAVVVVPNRTISTARSRTVL 179 ALRYEHHPDNITPAVMGGFNVAC+EG+RVYSKKRR+P YLRAV+VVP+RTIST RSR VL Sbjct: 121 ALRYEHHPDNITPAVMGGFNVACLEGERVYSKKRRLPSYLRAVLVVPDRTISTNRSRNVL 180 Query: 180 PKMYRKEETVYSLSRAAYMTALFMSESWDLLRIASKDKLHQARRMKMMPELFDVQKLALK 239 PKMY KEE VYSLSRAAYMTALFMSESWDLLRIA+KDK+HQ RRM+MMPELF+VQK AL Sbjct: 181 PKMYTKEEVVYSLSRAAYMTALFMSESWDLLRIAAKDKIHQERRMRMMPELFEVQKTALD 240 Query: 240 QGALMSTLSGSGSTFFNLAYEKDTDRIAQSLRARFPQFRVFVLALDNNGVITK 292 GALMSTLSGSGSTFFNLAY D ++A L RFPQFR+ LDN GVI K Sbjct: 241 HGALMSTLSGSGSTFFNLAYADDAKKLAAVLAERFPQFRIMTHGLDNVGVIGK 293 Lambda K H 0.320 0.134 0.376 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: 351 Number of extensions: 10 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: 292 Length of database: 294 Length adjustment: 26 Effective length of query: 266 Effective length of database: 268 Effective search space: 71288 Effective search space used: 71288 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_013554828.1 NITSA_RS09565 (homoserine kinase)
to HMM TIGR00191 (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/TIGR00191.hmm # target sequence database: /tmp/gapView.19204.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00191 [M=304] Accession: TIGR00191 Description: thrB: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-82 262.7 0.0 2e-82 262.4 0.0 1.0 1 lcl|NCBI__GCF_000186245.1:WP_013554828.1 NITSA_RS09565 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000186245.1:WP_013554828.1 NITSA_RS09565 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 262.4 0.0 2e-82 2e-82 3 291 .. 3 282 .. 1 291 [. 0.90 Alignments for each domain: == domain 1 score: 262.4 bits; conditional E-value: 2e-82 TIGR00191 3 vkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkvl 71 ++vPa+sANlgpGfD+lGla+ l++e+++++ + +++ + ++geg + pk ++ l+ +++++ + lcl|NCBI__GCF_000186245.1:WP_013554828.1 3 ISVPATSANLGPGFDTLGLAIDLRNEIVIKP----ARFHS-VSTKGEG-ADNPKIKKNSLFLHIFHEQY 65 89***************************99....77777.8889999.5568888999********99 PP TIGR00191 72 kklgkr.vkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvapa 139 +kl ++++ ++ ip++rGLGSS+a iv+a++aa +ag k++k ++l++al +E+HpDN++pa lcl|NCBI__GCF_000186245.1:WP_013554828.1 66 RKLTDGkRATFRFEFTNRIPISRGLGSSSAVIVSAITAAHLAAGVKYNKRKILNTALRYEHHPDNITPA 134 9986654699*********************************************************** PP TIGR00191 140 llGGlqlavkedd..llevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvt 206 ++GG+++a e + +++ ++P s l +vlv+P + +sT+ +R+vLPk y+ +++v ls++a +++ lcl|NCBI__GCF_000186245.1:WP_013554828.1 135 VMGGFNVACLEGErvYSKKRRLP--SYLRAVLVVPDRTISTNRSRNVLPKMYTKEEVVYSLSRAAYMTA 201 **********9997777888899..8*****************************************98 PP TIGR00191 207 AlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeekeekaqe 275 ++s+ +dll+ia kD++hq R++++Pel+e++++a ++gal++tlSG+G+t+++la+ +++k + lcl|NCBI__GCF_000186245.1:WP_013554828.1 202 LFMSE-SWDLLRIAAKDKIHQERRMRMMPELFEVQKTALDHGALMSTLSGSGSTFFNLAYADDAKKLA- 268 77777.*******************************************************9955544. PP TIGR00191 276 lleklakegieltvkv 291 +la+ + ++++ + lcl|NCBI__GCF_000186245.1:WP_013554828.1 269 --AVLAERFPQFRIMT 282 ..44455555555555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (294 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: 00:00:00.00 # Mc/sec: 10.09 // [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