Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_028314604.1 G491_RS0110795 aspartate kinase
Query= SwissProt::A4VJB4 (412 letters) >NCBI__GCF_000429905.1:WP_028314604.1 Length = 405 Score = 447 bits (1150), Expect = e-130 Identities = 230/405 (56%), Positives = 306/405 (75%), Gaps = 1/405 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60 M LIVQK+GGTSVG + RI++VA++V K D G+ +VVV+SAMSG T+ LI +A+ +S++ Sbjct: 1 MGLIVQKYGGTSVGDLVRIQEVAKRVAKTYDAGNQVVVVLSAMSGVTDHLIQMAEVLSDK 60 Query: 61 PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120 P RE+DV+++TGEQ T+ALLA+AL K G A S+ G+QVRILT++A ARIL + A Sbjct: 61 PNKREMDVLLATGEQTTVALLAIALEKMGYKAQSFLGHQVRILTNNAAQSARILDVQADP 120 Query: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 I+ + +VVVAGFQGVD GNITTLGRGGSDT+ VA+AAAL AD C+IYTDVDGVYT Sbjct: 121 IKDALADNAIVVVAGFQGVDGCGNITTLGRGGSDTSAVAVAAALGADSCEIYTDVDGVYT 180 Query: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLI 240 DPRVV+KA++L +T + MLEM+SLG+KVLQIR+VEFA K++VP+ V SF E GT+I Sbjct: 181 ADPRVVSKARKLKCVTHDVMLEMSSLGAKVLQIRSVEFAAKHNVPVHVRSSFNEEEGTMI 240 Query: 241 TLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVAH 300 E+ ME+ +++G+ F + +A++T+ VPD PGVA K+ ++ A + VDMI+QN Sbjct: 241 VC-EDRDMERMLVAGVTFVKTDARITVTKVPDEPGVAAKVFSAVADAGISVDMIIQNTRA 299 Query: 301 DNTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVASRM 360 N TD TFTV + DY +AL +++ IA E+GA GD NIAKVS+ GVGM+SH GVA++M Sbjct: 300 SNMTDITFTVPKTDYKDALVIVEKIAKEIGAESVAGDANIAKVSVTGVGMKSHHGVAAKM 359 Query: 361 FEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDA 405 F LA ++INI MISTSEI++S V+EEKY ELA + LHT F LDA Sbjct: 360 FSTLAAKSINIMMISTSEIRISCVVEEKYAELACQILHTEFGLDA 404 Lambda K H 0.317 0.133 0.357 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: 446 Number of extensions: 11 Number of successful extensions: 2 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: 412 Length of database: 405 Length adjustment: 31 Effective length of query: 381 Effective length of database: 374 Effective search space: 142494 Effective search space used: 142494 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: 50 (23.9 bits)
Align candidate WP_028314604.1 G491_RS0110795 (aspartate kinase)
to HMM TIGR00657 (aspartate kinase (EC 2.7.2.4))
# 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/TIGR00657.hmm # target sequence database: /tmp/gapView.10365.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00657 [M=442] Accession: TIGR00657 Description: asp_kinases: aspartate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-136 441.0 19.7 2.8e-133 431.2 19.7 2.0 1 lcl|NCBI__GCF_000429905.1:WP_028314604.1 G491_RS0110795 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429905.1:WP_028314604.1 G491_RS0110795 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 431.2 19.7 2.8e-133 2.8e-133 1 441 [. 1 401 [. 1 402 [. 0.98 Alignments for each domain: == domain 1 score: 431.2 bits; conditional E-value: 2.8e-133 TIGR00657 1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekelieki 69 m liVqK+GGtSvg+ ri++vak+v k++ gnqvvVV+SAm+gvTd+L+++ae +s+++ lcl|NCBI__GCF_000429905.1:WP_028314604.1 1 MGLIVQKYGGTSVGDLVRIQEVAKRVAKTYDAGNQVVVVLSAMSGVTDHLIQMAEVLSDKP-------- 61 679**********************************************************........ PP TIGR00657 70 rekhlealeelasqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllga 138 + +re+d++l++GE++++alla ale+ g+ka+s+lg lcl|NCBI__GCF_000429905.1:WP_028314604.1 62 ------------N--------------------KREMDVLLATGEQTTVALLAIALEKMGYKAQSFLGH 98 ............5....................8*********************************** PP TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkA 207 + ilt+++ ++A+ + +++++ ++++l + ivvvaGF+G++ g+ittLGRGGSD++A+++Aaal+A lcl|NCBI__GCF_000429905.1:WP_028314604.1 99 QVRILTNNAAQSAR-ILDVQADPIKDALADNAIVVVAGFQGVDGCGNITTLGRGGSDTSAVAVAAALGA 166 **************.****************************************************** PP TIGR00657 208 deveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpe 276 d +eiytDVdG+ytaDPr+v++Ar+l+ ++ + +lE++slGakvL+ r++e+a+++++p++v+s+fn+e lcl|NCBI__GCF_000429905.1:WP_028314604.1 167 DSCEIYTDVDGVYTADPRVVSKARKLKCVTHDVMLEMSSLGAKVLQIRSVEFAAKHNVPVHVRSSFNEE 235 ********************************************************************* PP TIGR00657 277 aeGTlivakskseeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlilqsssets.. 343 eGT+iv ++ ++e+ v ++++ k +a+++v +++++pg++a+vf+a+a+a+++vd+i+q++ ++ lcl|NCBI__GCF_000429905.1:WP_028314604.1 236 -EGTMIVCEDRDMERMLVAGVTFVKTDARITVTKVPDEPGVAAKVFSAVADAGISVDMIIQNTRASNmt 303 .**********9***************************************************966667 PP TIGR00657 344 .isfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeninie 411 i+f+v+k+d++ a + +k+ +e e+v + ++a+vs+ G gmks+ gvaak+f++La + ini+ lcl|NCBI__GCF_000429905.1:WP_028314604.1 304 dITFTVPKTDYKDALVIV-EKIAKEIGAESVAGDANIAKVSVTGVGMKSHHGVAAKMFSTLAAKSINIM 371 9*************9997.67************************************************ PP TIGR00657 412 missseikisvvvdekdaekavealheklv 441 mis+sei+is+vv+ek+ae a + lh ++ lcl|NCBI__GCF_000429905.1:WP_028314604.1 372 MISTSEIRISCVVEEKYAELACQILHTEFG 401 ***************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (405 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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06 # Mc/sec: 2.59 // [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