Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_015944056.1 DHAF_RS12290 homoserine kinase
Query= curated2:B8FU92 (297 letters) >NCBI__GCF_000021925.1:WP_015944056.1 Length = 297 Score = 572 bits (1474), Expect = e-168 Identities = 297/297 (100%), Positives = 297/297 (100%) Query: 1 MVRVRIPATSANLGPGFDCLGMALSLYNVVQIEAADSFQIALKGDYTAGIPGDETNLVWQ 60 MVRVRIPATSANLGPGFDCLGMALSLYNVVQIEAADSFQIALKGDYTAGIPGDETNLVWQ Sbjct: 1 MVRVRIPATSANLGPGFDCLGMALSLYNVVQIEAADSFQIALKGDYTAGIPGDETNLVWQ 60 Query: 61 SMCNLWEAIGFEIPTVSLELENNIPPTRGMGSSSAAIVGGLVAANEYAGGVLSKQQILQI 120 SMCNLWEAIGFEIPTVSLELENNIPPTRGMGSSSAAIVGGLVAANEYAGGVLSKQQILQI Sbjct: 61 SMCNLWEAIGFEIPTVSLELENNIPPTRGMGSSSAAIVGGLVAANEYAGGVLSKQQILQI 120 Query: 121 ANRIEGHPDNVAPALLGGVTLAVTAEASVIARTVHSQPQFMALAIVPDFYLSTEKSRNVL 180 ANRIEGHPDNVAPALLGGVTLAVTAEASVIARTVHSQPQFMALAIVPDFYLSTEKSRNVL Sbjct: 121 ANRIEGHPDNVAPALLGGVTLAVTAEASVIARTVHSQPQFMALAIVPDFYLSTEKSRNVL 180 Query: 181 PASISRADAVYNLSRTALLVEALIHENYELLKEGMQDRLHQNQRASLVPGLGETLQVALD 240 PASISRADAVYNLSRTALLVEALIHENYELLKEGMQDRLHQNQRASLVPGLGETLQVALD Sbjct: 181 PASISRADAVYNLSRTALLVEALIHENYELLKEGMQDRLHQNQRASLVPGLGETLQVALD 240 Query: 241 SGAYGSALSGSGPTILALVSSHRAEQVSQAMVDSLAAHGLTAKAYLLSVDSEGAAVI 297 SGAYGSALSGSGPTILALVSSHRAEQVSQAMVDSLAAHGLTAKAYLLSVDSEGAAVI Sbjct: 241 SGAYGSALSGSGPTILALVSSHRAEQVSQAMVDSLAAHGLTAKAYLLSVDSEGAAVI 297 Lambda K H 0.316 0.131 0.365 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: 416 Number of extensions: 5 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: 297 Length of database: 297 Length adjustment: 26 Effective length of query: 271 Effective length of database: 271 Effective search space: 73441 Effective search space used: 73441 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: 41 (21.6 bits) S2: 48 (23.1 bits)
Align candidate WP_015944056.1 DHAF_RS12290 (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.11624.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-91 291.0 0.2 4.4e-91 290.8 0.2 1.0 1 lcl|NCBI__GCF_000021925.1:WP_015944056.1 DHAF_RS12290 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021925.1:WP_015944056.1 DHAF_RS12290 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 290.8 0.2 4.4e-91 4.4e-91 1 301 [. 2 296 .. 2 297 .] 0.97 Alignments for each domain: == domain 1 score: 290.8 bits; conditional E-value: 4.4e-91 TIGR00191 1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakk 69 ++v++Pa+sANlgpGfD+lG+alsl++ + ++ + ++ ++ +g+ +++ip + + Nl+ q + + lcl|NCBI__GCF_000021925.1:WP_015944056.1 2 VRVRIPATSANLGPGFDCLGMALSLYNVVQIEA----A-DSFQIALKGDYTAGIPGD-ETNLVWQSMCN 64 689************************999888....3.33358999**********.9********** PP TIGR00191 70 vlkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvap 138 + + g +++ v l++e++ip +rG+GSS+aaiv++++aane ag lsk+++l++a +EgHpDNvap lcl|NCBI__GCF_000021925.1:WP_015944056.1 65 LWEAIGFEIPTVSLELENNIPPTRGMGSSSAAIVGGLVAANEYAGGVLSKQQILQIANRIEGHPDNVAP 133 ********************************************************************* PP TIGR00191 139 allGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtA 207 allGG++lav+ + +++ v s++++ +++++P + +sT+++R+vLP++ sr+d+v nls+ a+lv+A lcl|NCBI__GCF_000021925.1:WP_015944056.1 134 ALLGGVTLAVTAEASVIARTVHSQPQFMALAIVPDFYLSTEKSRNVLPASISRADAVYNLSRTALLVEA 202 **************9999999999********************************************* PP TIGR00191 208 lvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.eekaqe 275 l+++ + +ll+ m+Dr+hq R++l+P+l e q+a + ga+g++lSG+Gptilal + ++ e+ +q lcl|NCBI__GCF_000021925.1:WP_015944056.1 203 LIHE-NYELLKEGMQDRLHQNQRASLVPGLGETLQVALDSGAYGSALSGSGPTILALVSSHRaEQVSQA 270 ***9.********************************************************9999**** PP TIGR00191 276 lleklakegieltvkvleldtdgaev 301 ++++la +g ++ +l++d +ga v lcl|NCBI__GCF_000021925.1:WP_015944056.1 271 MVDSLAAHGLTAKAYLLSVDSEGAAV 296 ***********************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (297 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: 00:00:00.00 # Mc/sec: 10.73 // [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