Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_037572810.1 BS73_RS15290 homoserine kinase
Query= BRENDA::P07128 (309 letters) >NCBI__GCF_000744815.1:WP_037572810.1 Length = 332 Score = 212 bits (540), Expect = 8e-60 Identities = 121/283 (42%), Positives = 162/283 (57%), Gaps = 13/283 (4%) Query: 11 VTVTVPGSSANLGPGFDTLGLALSVYDTVEVEIIPSGLEVEVFGEGQGEVPLDGSHLVVK 70 V V VP ++ANLGPG+D+LGLALS+YD V V + S L V++ GEG +P D HL+V+ Sbjct: 11 VRVRVPATTANLGPGYDSLGLALSLYDDVVVRVAESDLHVDIAGEGADTLPRDERHLMVR 70 Query: 71 AIRAGLKAADAEVPGLRVVCHNNIPQSRGLGSSAAAAVAGVAAANGL---ADFPLTQEQI 127 ++RA + GL VVC N IP RGLGSS+AA VAG+ AA + L + Sbjct: 71 SMRAAFDLLGGQPRGLEVVCANRIPHGRGLGSSSAAIVAGLMAARAVTIGGPERLDDAGL 130 Query: 128 VQLSSAFEGHPDNAAASVLGGAVVSWTNLSIDGKSQPQYAAVPLEVQDNIRATALVPNFH 187 + L+S EGHPDN A +LGG ++WT D + A LE D + VP+ Sbjct: 131 LALASELEGHPDNVAPCLLGGFTIAWT----DSDGSERARAARLEPADGLVPVVFVPSQE 186 Query: 188 ASTEAVRRVLPTEVTHIDARFNVSRVAVMIVALQQRPDLLWEGTRDRLHQPYRAEVLPIT 247 TE R +LP +V H DA FN +R A+++ A+ + P LL+ T DRLHQ YRA +P + Sbjct: 187 VLTETARGLLPKQVPHADAAFNAARSALLVAAVTRDPRLLYPATEDRLHQDYRAPAMPGS 246 Query: 248 SEWVNRLRNRGYAAYLSGAGPTAMVL------STEPIPDKVLE 284 + V LR G A +SGAGPT + L S E D V+E Sbjct: 247 AALVGALRAEGVPAVISGAGPTVLALLGGERGSGEETSDAVVE 289 Lambda K H 0.315 0.132 0.377 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: 253 Number of extensions: 11 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: 309 Length of database: 332 Length adjustment: 28 Effective length of query: 281 Effective length of database: 304 Effective search space: 85424 Effective search space used: 85424 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_037572810.1 BS73_RS15290 (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.3816790.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-72 229.9 0.0 1.9e-72 229.6 0.0 1.0 1 NCBI__GCF_000744815.1:WP_037572810.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_037572810.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 229.6 0.0 1.9e-72 1.9e-72 1 301 [. 11 313 .. 11 315 .. 0.91 Alignments for each domain: == domain 1 score: 229.6 bits; conditional E-value: 1.9e-72 TIGR00191 1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkvlkk 73 ++v+vPa++ANlgpG+D+lGlalsl+++++v es+ + + ++geg++++p + + l+ + + ++ NCBI__GCF_000744815.1:WP_037572810.1 11 VRVRVPATTANLGPGYDSLGLALSLYDDVVVRV---AESDLH-VDIAGEGADTLPRD-ERHLMVRSMRAAFDL 78 68***************************9999...566665.99************.999************ PP TIGR00191 74 lgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanela...glklskeelldlalllEgHpDNvapallGG 143 lg ++ ++++ + ip grGLGSS+aaiva+++aa +++ + l+++ ll+la++lEgHpDNvap+llGG NCBI__GCF_000744815.1:WP_037572810.1 79 LGGQPRGLEVVCANRIPHGRGLGSSSAAIVAGLMAARAVTiggPERLDDAGLLALASELEGHPDNVAPCLLGG 151 *************************************997333478*************************** PP TIGR00191 144 lqlavkedd....llevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAlvskd 212 +++a ++ d + +P + l v+ +P ev T+ aR++LPk+++ +d+ fn++++a+lv+A++ + NCBI__GCF_000744815.1:WP_037572810.1 152 FTIAWTDSDgserARAARLEP-ADGLVPVVFVPSQEVLTETARGLLPKQVPHADAAFNAARSALLVAAVTRD- 222 *****9999888544555567.59***********************************************9. PP TIGR00191 213 kadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek...eekaqellekla. 281 + ll++a +Dr+hq yR+ +P+ +++ a +++g+ ++SGaGpt+lal e+ ee + ++ek+ NCBI__GCF_000744815.1:WP_037572810.1 223 -PRLLYPATEDRLHQDYRAPAMPGSAALVGALRAEGV-PAVISGAGPTVLALLGGERgsgEETSDAVVEKVLg 293 .99*************************999999986.568***********987776777777777877652 PP TIGR00191 282 kegieltvkvleldtdgaev 301 +g e + + l +d dga v NCBI__GCF_000744815.1:WP_037572810.1 294 FAGGEWSAHRLGIDLDGAAV 313 57888899999999999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (332 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: 27.46 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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