Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate WP_011869127.1 MMARC5_RS07000 homoserine kinase
Query= SwissProt::Q6M0H5 (301 letters) >NCBI__GCF_000016125.1:WP_011869127.1 Length = 301 Score = 575 bits (1483), Expect = e-169 Identities = 286/301 (95%), Positives = 294/301 (97%) Query: 1 MKKVKVCSPGTSANLGPGYDIFGLALSNPYDIVEVEKTENGITISVEGEKAEEIPTNVDE 60 MKKVKVCSPGTSANLGPGYDIFGLALS PYDI+EVEKTE GI ISVEGEKAEEIPTNVDE Sbjct: 1 MKKVKVCSPGTSANLGPGYDIFGLALSKPYDILEVEKTEKGIIISVEGEKAEEIPTNVDE 60 Query: 61 NTAGVVAKKMIEDFKIESGIHIHIIKGIKPGSGLGSSSASCAGIAFALNELFELKLSKLE 120 NTAGVVAKKM+EDF I+SGIHIHI KGIKPGSGLGSSSASCAG+AFALNELFELKLSKLE Sbjct: 61 NTAGVVAKKMMEDFNIQSGIHIHINKGIKPGSGLGSSSASCAGVAFALNELFELKLSKLE 120 Query: 121 LVKYSSLGEAVAAGAPHADNVAPAIFGGFTLTTSYEPLEVLHIPVDLEVLVALPNIQVST 180 LVKYSSLGEAVAAGAPHADNVAPAIFGGFTLTTSY+PLEVLHIPVD+EVLVALPNIQVST Sbjct: 121 LVKYSSLGEAVAAGAPHADNVAPAIFGGFTLTTSYDPLEVLHIPVDIEVLVALPNIQVST 180 Query: 181 KTAREILPKEIPIKDMVNNVGKAAGMVYALYNNDLDLFGRYMSKDCVVEPCRANLIDGYT 240 KTAREILPKEIPIK MVNNVGKAAGMVYALYNNDL+LFGRYMSKDCVVEPCRANLIDGY Sbjct: 181 KTAREILPKEIPIKYMVNNVGKAAGMVYALYNNDLELFGRYMSKDCVVEPCRANLIDGYA 240 Query: 241 EVKEKVKDMVYGITISGSGPAIITIPKKEHVIDIENIFKEVWNCPVYYTKVGPGCYVEEI 300 EVKEKVKD+VYGITISGSGPAIITIPKKEHVIDIENIFKEVWNCPVYYTKVGPGCYVEEI Sbjct: 241 EVKEKVKDLVYGITISGSGPAIITIPKKEHVIDIENIFKEVWNCPVYYTKVGPGCYVEEI 300 Query: 301 E 301 E Sbjct: 301 E 301 Lambda K H 0.315 0.136 0.392 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: 426 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: 301 Length of database: 301 Length adjustment: 27 Effective length of query: 274 Effective length of database: 274 Effective search space: 75076 Effective search space used: 75076 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 bits)
Align candidate WP_011869127.1 MMARC5_RS07000 (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.7244.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-87 276.9 0.1 9.6e-87 276.6 0.1 1.0 1 lcl|NCBI__GCF_000016125.1:WP_011869127.1 MMARC5_RS07000 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016125.1:WP_011869127.1 MMARC5_RS07000 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 276.6 0.1 9.6e-87 9.6e-87 1 279 [. 4 281 .. 4 292 .. 0.94 Alignments for each domain: == domain 1 score: 276.6 bits; conditional E-value: 9.6e-87 TIGR00191 1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakk 69 +kv P++sANlgpG+D++Glals+ +++l +e++ e+ + ege++e+ip++ d+N + vakk lcl|NCBI__GCF_000016125.1:WP_011869127.1 4 VKVCSPGTSANLGPGYDIFGLALSKPYDILEVEKT--EKGII-ISVEGEKAEEIPTNVDENTAGVVAKK 69 68999*************************99933..33334.779*********************** PP TIGR00191 70 vlkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg......H 132 ++++++++ ++++++++k i+ g+GLGSS+a+ ++ + a+nel++lklsk el+++ +l E H lcl|NCBI__GCF_000016125.1:WP_011869127.1 70 MMEDFNIQ-SGIHIHINKGIKPGSGLGSSSASCAGVAFALNELFELKLSKLELVKYSSLGEAvaagapH 137 ********.************************************************************ PP TIGR00191 133 pDNvapallGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshl 201 +DNvapa++GG++l++++d levl++P +++v++++Pni+vsT+ aR++LPk+ + + +v+n+ ++ lcl|NCBI__GCF_000016125.1:WP_011869127.1 138 ADNVAPAIFGGFTLTTSYDP-LEVLHIP--VDIEVLVALPNIQVSTKTAREILPKEIPIKYMVNNVGKA 203 ********************.*******..69************************************* PP TIGR00191 202 avlvtAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek. 269 a++v+Al+++d ++++++++kD v +p R++li +++e+k+++k+ ++git+SG+Gp+i++++++e+ lcl|NCBI__GCF_000016125.1:WP_011869127.1 204 AGMVYALYNNDLELFGRYMSKDCVVEPCRANLIDGYAEVKEKVKDL-VYGITISGSGPAIITIPKKEHv 271 **********************************************.*******************994 PP TIGR00191 270 eekaqellek 279 +++ +e+ lcl|NCBI__GCF_000016125.1:WP_011869127.1 272 IDIENIFKEV 281 4444444444 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (301 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: 00:00:00.00 # Mc/sec: 11.34 // [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