Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_005458792.1 SACCYDRAFT_RS19470 homoserine kinase
Query= BRENDA::P07128 (309 letters) >NCBI__GCF_000244975.1:WP_005458792.1 Length = 306 Score = 245 bits (625), Expect = 1e-69 Identities = 145/300 (48%), Positives = 186/300 (62%), Gaps = 15/300 (5%) Query: 10 KVTVTVPGSSANLGPGFDTLGLALSVYDTVEVEIIPSGLEVEVFGEGQGE---VPLDGSH 66 K T+TVP S+ANLGPGFDT GLAL+++D VEVE+ SGL VEV G G+ VP D SH Sbjct: 2 KYTITVPASTANLGPGFDTFGLALALHDVVEVEVTGSGLSVEVIDAGAGDMSGVPTDESH 61 Query: 67 LVVKAIRAGLKAADAEVPGLRVVCHNNIPQSRGLGSSAAAAVAGVAAANGLADFPLTQEQ 126 LVV+A+R + D VPG+ + CHN IP +RGLGSSAAA VAGVAA LA + E Sbjct: 62 LVVRALRRACRHLDVAVPGVALRCHNAIPHARGLGSSAAAVVAGVAAGYALAGKDI-DEG 120 Query: 127 IVQLSSAFEGHPDNAAASVLGGAVVSWTNLSIDGKSQPQYAAVPLEVQDNIRATALVPNF 186 +QL+S FEGH DNAAAS+LGG VV+W +S + A L IR VP+ Sbjct: 121 ALQLASEFEGHADNAAASLLGGFVVAW-------QSGATFHAERLSPHSAIRPVVAVPDE 173 Query: 187 HASTEAVRRVLPTEVTHIDARFNVSRVAVMIVALQQRPDLLWEGTRDRLHQPYRAEVLPI 246 ++T+ R +LP V H DA F SR A+ + A+ RPDLL+ T DRLHQ YR P Sbjct: 174 RSATDQTRGLLPDYVPHGDAAFTASRSALAVHAVTTRPDLLFAATEDRLHQEYREPAYPA 233 Query: 247 TSEWVNRLRNRGYAAYLSGAGPTAMVLSTEPIPDKVLEDARESGIKVLELEVAGPVKVEV 306 + + LR+RG AA +SGAGPT + L+T I + E +G +V+EL + PV V + Sbjct: 234 SVRLMRALRSRGVAAVISGAGPTVLALTTTGI---LPEGVDVTGFEVMELPI-DPVGVRL 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: 248 Number of extensions: 12 Number of successful extensions: 4 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: 306 Length adjustment: 27 Effective length of query: 282 Effective length of database: 279 Effective search space: 78678 Effective search space used: 78678 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_005458792.1 SACCYDRAFT_RS19470 (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.30126.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-65 207.0 0.1 1.8e-65 206.8 0.1 1.0 1 lcl|NCBI__GCF_000244975.1:WP_005458792.1 SACCYDRAFT_RS19470 homoserine ki Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000244975.1:WP_005458792.1 SACCYDRAFT_RS19470 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 206.8 0.1 1.8e-65 1.8e-65 2 267 .. 4 263 .. 3 273 .. 0.92 Alignments for each domain: == domain 1 score: 206.8 bits; conditional E-value: 1.8e-65 TIGR00191 2 kvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkv 70 +++vPas+ANlgpGfD++Glal l + + v+ + + + a + +++++p++ + l+ +++ + lcl|NCBI__GCF_000244975.1:WP_005458792.1 4 TITVPASTANLGPGFDTFGLALALHDVVEVEV-TGSGLSVEVIDAGAGDMSGVPTD-ESHLVVRALRRA 70 69********************9988777766.43333333477777889******.999********* PP TIGR00191 71 lkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvapa 139 +++l+ +v++v+l+ ++ ip +rGLGSSaaa+va+v+a+ +lag+++++ l+la++ EgH+DN+a++ lcl|NCBI__GCF_000244975.1:WP_005458792.1 71 CRHLDVAVPGVALRCHNAIPHARGLGSSAAAVVAGVAAGYALAGKDIDEG-ALQLASEFEGHADNAAAS 138 ***********************************************975.79**************** PP TIGR00191 140 llGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAl 208 llGG+++a ++ + + ++ +s++ v+++P T ++R++LP ++ d+ f +s++a+ v+A+ lcl|NCBI__GCF_000244975.1:WP_005458792.1 139 LLGGFVVAWQSGATFHAERLSPHSAIRPVVAVPDERSATDQTRGLLPDYVPHGDAAFTASRSALAVHAV 207 *************8888887668********************************************** PP TIGR00191 209 vskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaee 267 +++ +dll a +Dr+hq yRe +P+ ++ +a + g+ + ++SGaGpt+lal++ lcl|NCBI__GCF_000244975.1:WP_005458792.1 208 TTR--PDLLFAATEDRLHQEYREPAYPASVRLMRALRSRGV-AAVISGAGPTVLALTTT 263 *99..9*****************************999986.678***********985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (306 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: 7.08 // [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