Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate N515DRAFT_0576 N515DRAFT_0576 homoserine kinase
Query= reanno::Dyella79:N515DRAFT_0576 (330 letters) >FitnessBrowser__Dyella79:N515DRAFT_0576 Length = 330 Score = 644 bits (1661), Expect = 0.0 Identities = 330/330 (100%), Positives = 330/330 (100%) Query: 1 MNAQLAAQNPEPMARSPQRALSAQALAPASVGNVGIGFDILGHSVAGAGDRARVRRIDEP 60 MNAQLAAQNPEPMARSPQRALSAQALAPASVGNVGIGFDILGHSVAGAGDRARVRRIDEP Sbjct: 1 MNAQLAAQNPEPMARSPQRALSAQALAPASVGNVGIGFDILGHSVAGAGDRARVRRIDEP 60 Query: 61 VVRIAAIEGCVVDLPLDPAQNTAGMALMALRKALGLRHGFELVLHKGIALGSGMGGSASS 120 VVRIAAIEGCVVDLPLDPAQNTAGMALMALRKALGLRHGFELVLHKGIALGSGMGGSASS Sbjct: 61 VVRIAAIEGCVVDLPLDPAQNTAGMALMALRKALGLRHGFELVLHKGIALGSGMGGSASS 120 Query: 121 CVAALVAANALLERPLPMESLYGFALEGEAVASGGRHGDNVGPMLLGGLVLATRDRLVRV 180 CVAALVAANALLERPLPMESLYGFALEGEAVASGGRHGDNVGPMLLGGLVLATRDRLVRV Sbjct: 121 CVAALVAANALLERPLPMESLYGFALEGEAVASGGRHGDNVGPMLLGGLVLATRDRLVRV 180 Query: 181 PVPDAWHCALVHPHMVLETRKARAALAGAYQLGEFVAQSANLSLMLAGCWQGDAGLVREG 240 PVPDAWHCALVHPHMVLETRKARAALAGAYQLGEFVAQSANLSLMLAGCWQGDAGLVREG Sbjct: 181 PVPDAWHCALVHPHMVLETRKARAALAGAYQLGEFVAQSANLSLMLAGCWQGDAGLVREG 240 Query: 241 LNDVLVEPRRAPLIPGFARVKQAAMDHRAMGASISGAGPSVFGWFEQRDEAKAAAAAMAA 300 LNDVLVEPRRAPLIPGFARVKQAAMDHRAMGASISGAGPSVFGWFEQRDEAKAAAAAMAA Sbjct: 241 LNDVLVEPRRAPLIPGFARVKQAAMDHRAMGASISGAGPSVFGWFEQRDEAKAAAAAMAA 300 Query: 301 AFAEAGLDSDTLVSPIAGPSAALIDVERKA 330 AFAEAGLDSDTLVSPIAGPSAALIDVERKA Sbjct: 301 AFAEAGLDSDTLVSPIAGPSAALIDVERKA 330 Lambda K H 0.320 0.134 0.394 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: 468 Number of extensions: 7 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: 330 Length of database: 330 Length adjustment: 28 Effective length of query: 302 Effective length of database: 302 Effective search space: 91204 Effective search space used: 91204 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
Align candidate N515DRAFT_0576 N515DRAFT_0576 (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.3446.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-55 171.7 0.0 1.1e-54 171.3 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0576 N515DRAFT_0576 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0576 N515DRAFT_0576 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 171.3 0.0 1.1e-54 1.1e-54 5 275 .. 27 295 .. 24 318 .. 0.90 Alignments for each domain: == domain 1 score: 171.3 bits; conditional E-value: 1.1e-54 TIGR00191 5 vPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkv 70 +Pas N+g GfD+lG ++ + + + + + a v +p+++ +N + +++ + lcl|FitnessBrowser__Dyella79:N515DRAFT_0576 27 APASVGNVGIGFDILGHSVAGAGDRARVRRIDEPVV--RIAAIEGCVVDLPLDPAQNTAGMALMAL 90 8******************98766555553333333..34444445588***************** PP TIGR00191 71 lkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg..... 131 k lg r ++++l ++k i lg+G+G Sa++ vaa++aan+l++ +l e l +al+ E lcl|FitnessBrowser__Dyella79:N515DRAFT_0576 91 RKALGLR-HGFELVLHKGIALGSGMGGSASSCVAALVAANALLERPLPMESLYGFALEGEAvasgg 155 *******.****************************************************9***** PP TIGR00191 132 .HpDNvapallGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvf 196 H DNv+p llGGl+la+++ + ++vP +++++ lv P++ + T++aRa L ay++ + v+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0576 156 rHGDNVGPMLLGGLVLATRDRL--VRVPVP--DAWHCALVHPHMVLETRKARAALAGAYQLGEFVA 217 ***************9998776..556666..9********************************* PP TIGR00191 197 nlshlavlvtAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptil 262 ++++l+++ + + ++ a l++ ++D++ +p R+ liP+++++kqaa ++ a+g +SGaGp+++ lcl|FitnessBrowser__Dyella79:N515DRAFT_0576 218 QSANLSLMLAGCWQG-DAGLVREGLNDVLVEPRRAPLIPGFARVKQAAMDHRAMGASISGAGPSVF 282 ***************.8999********************************************** PP TIGR00191 263 alaeeekeekaqe 275 e+ +e ka+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0576 283 GWFEQRDEAKAAA 295 9999999666654 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (330 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: 00:00:00.01 # Mc/sec: 9.25 // [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