Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate CA265_RS23470 CA265_RS23470 homoserine kinase
Query= reanno::Pedo557:CA265_RS23470 (310 letters) >FitnessBrowser__Pedo557:CA265_RS23470 Length = 310 Score = 610 bits (1573), Expect = e-179 Identities = 310/310 (100%), Positives = 310/310 (100%) Query: 1 MKDSIKVFAPATVANVVCGFDVLGFAVNEPGDEVEMRFTDTPGVVIKGITGDDGRLPLDA 60 MKDSIKVFAPATVANVVCGFDVLGFAVNEPGDEVEMRFTDTPGVVIKGITGDDGRLPLDA Sbjct: 1 MKDSIKVFAPATVANVVCGFDVLGFAVNEPGDEVEMRFTDTPGVVIKGITGDDGRLPLDA 60 Query: 61 AKNTVSASVQHYLKHINRLDVGVEIELHKKMPIGSGLGSSSASTVAGLFAINKLMGDLLS 120 AKNTVSASVQHYLKHINRLDVGVEIELHKKMPIGSGLGSSSASTVAGLFAINKLMGDLLS Sbjct: 61 AKNTVSASVQHYLKHINRLDVGVEIELHKKMPIGSGLGSSSASTVAGLFAINKLMGDLLS 120 Query: 121 TKELVPFAMKGEELACGYGHADNVAPALLGGFVLVRSYDPLDVISLPTPAGMYAAIVYPE 180 TKELVPFAMKGEELACGYGHADNVAPALLGGFVLVRSYDPLDVISLPTPAGMYAAIVYPE Sbjct: 121 TKELVPFAMKGEELACGYGHADNVAPALLGGFVLVRSYDPLDVISLPTPAGMYAAIVYPE 180 Query: 181 VDVPTKDARQMIRSKVALKDAVTQWGNVAGLVSGLFMNDFDLIGRSMKDVLVEPTRSILI 240 VDVPTKDARQMIRSKVALKDAVTQWGNVAGLVSGLFMNDFDLIGRSMKDVLVEPTRSILI Sbjct: 181 VDVPTKDARQMIRSKVALKDAVTQWGNVAGLVSGLFMNDFDLIGRSMKDVLVEPTRSILI 240 Query: 241 PGFEEMRKLAMENGAIGFGISGSGPSVFSLTKDEETARKITKSQQQHLHKININSKAFVS 300 PGFEEMRKLAMENGAIGFGISGSGPSVFSLTKDEETARKITKSQQQHLHKININSKAFVS Sbjct: 241 PGFEEMRKLAMENGAIGFGISGSGPSVFSLTKDEETARKITKSQQQHLHKININSKAFVS 300 Query: 301 PVNAEGPKVL 310 PVNAEGPKVL Sbjct: 301 PVNAEGPKVL 310 Lambda K H 0.317 0.136 0.388 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: 558 Number of extensions: 17 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: 310 Length of database: 310 Length adjustment: 27 Effective length of query: 283 Effective length of database: 283 Effective search space: 80089 Effective search space used: 80089 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate CA265_RS23470 CA265_RS23470 (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.5021.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-70 221.5 0.0 6.2e-70 221.4 0.0 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS23470 CA265_RS23470 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS23470 CA265_RS23470 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 221.4 0.0 6.2e-70 6.2e-70 1 297 [. 5 305 .. 5 310 .] 0.88 Alignments for each domain: == domain 1 score: 221.4 bits; conditional E-value: 6.2e-70 TIGR00191 1 lkvkvPassANlgpGfDvlGlalslvlellvtedv.aqeskdksleaegegvekipkesdkNliyqva 67 +kv +Pa+ AN+ GfDvlG a+++ + + + + + + ++ + + ++p+++ kN + + lcl|FitnessBrowser__Pedo557:CA265_RS23470 5 IKVFAPATVANVVCGFDVLGFAVNEPGDEVEMRFTdTPGV---VIKGITGDDGRLPLDAAKNTVSASV 69 5899********************9988777773312222...34444444489************** PP TIGR00191 68 kkvlkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg.... 131 ++ lk+ ++ +v+++++k++p+g+GLGSS+a+ va++ a+n+l+g ls++el+ +a+ E+ lcl|FitnessBrowser__Pedo557:CA265_RS23470 70 QHYLKHINRLDVGVEIELHKKMPIGSGLGSSSASTVAGLFAINKLMGDLLSTKELVPFAMKGEElacg 137 ******99999****************************************************99*** PP TIGR00191 132 ..HpDNvapallGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfn 197 H+DNvapallGG++l+ ++d l v+++P+ + +++ +v+P+++v T++aR+++ ++ ++d+v + lcl|FitnessBrowser__Pedo557:CA265_RS23470 138 ygHADNVAPALLGGFVLVRSYDP-LDVISLPTPAGMYAAIVYPEVDVPTKDARQMIRSKVALKDAVTQ 204 **********************9.999999999*********************************** PP TIGR00191 198 lshlavlvtAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilala 265 ++a+lv l ++ dl+ mkD++ +p R+ liP+++e+++ a e+ga+g ++SG+Gp++++l+ lcl|FitnessBrowser__Pedo557:CA265_RS23470 205 WGNVAGLVSGLFMN-DFDLIGRSMKDVLVEPTRSILIPGFEEMRKLAMENGAIGFGISGSGPSVFSLT 271 **************.899999*********************************************** PP TIGR00191 266 eeek.eeka.qelleklakegieltvkvleldtd 297 ++e+ ++k ++ ++l+k +i+ + v ++ + lcl|FitnessBrowser__Pedo557:CA265_RS23470 272 KDEEtARKItKSQQQHLHKININSKAFVSPVNAE 305 **99644430333444444444444444555555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (310 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: 8.65 // [ok]
This GapMind analysis is from Apr 09 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