Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_029934061.1 N746_RS0103890 aspartate kinase
Query= SwissProt::A4VJB4 (412 letters) >NCBI__GCF_000711195.1:WP_029934061.1 Length = 405 Score = 538 bits (1385), Expect = e-157 Identities = 276/404 (68%), Positives = 336/404 (83%), Gaps = 1/404 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60 MALIVQK+GGTSVGT+ERI+ VA+KV KF D G +VVV+SAMSGETNRL D+AK + E+ Sbjct: 1 MALIVQKYGGTSVGTLERIQNVAKKVSKFVDEGHQVVVVLSAMSGETNRLTDMAKTMQER 60 Query: 61 PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120 P RE+D++++TGEQVTIALL+MAL + G A+SYTG QV I TD HTKARI I+AQ+ Sbjct: 61 PSKREMDMLLTTGEQVTIALLSMALQQSGHDAISYTGWQVPIQTDEVHTKARIDSINAQK 120 Query: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 IQ + +VVVVAGFQGV G+I+TLGRGGSDTT VALAAALKA+ECQIYTDVDGVYT Sbjct: 121 IQDQLDLNKVVVVAGFQGVTANGDISTLGRGGSDTTAVALAAALKAEECQIYTDVDGVYT 180 Query: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLI 240 TDPR+V +A+RL+ ITF+EMLEMASLG+KVLQIR+VEFA KY VPLRVL S +EG GTLI Sbjct: 181 TDPRMVPEARRLETITFDEMLEMASLGAKVLQIRSVEFASKYKVPLRVLSSLKEGGGTLI 240 Query: 241 TLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVAH 300 T E++ ME+P+ISGIAFNRDE+KL + GVPD PGVA+ ILGPI+ AN+E+DMI+QN Sbjct: 241 T-SEDDQMEKPLISGIAFNRDESKLQVLGVPDKPGVAYAILGPIADANIEIDMIIQNQGQ 299 Query: 301 DNTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVASRM 360 D TTDFTFTVHRND +AL++L +++E+GARE + D IAKVS+VGVGMRSH G+ASRM Sbjct: 300 DGTTDFTFTVHRNDRAHALEILNAVSSEVGAREVVYDDTIAKVSLVGVGMRSHVGIASRM 359 Query: 361 FEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404 F+ LA ++INIQMI+T+EIK+SVVI E LE AV+ LH FELD Sbjct: 360 FKVLADKDINIQMIATTEIKISVVINESQLETAVKTLHEKFELD 403 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: 511 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_029934061.1 N746_RS0103890 (aspartate kinase)
to HMM TIGR00656 (aspartate kinase, monofunctional class (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/TIGR00656.hmm # target sequence database: /tmp/gapView.15129.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00656 [M=407] Accession: TIGR00656 Description: asp_kin_monofn: aspartate kinase, monofunctional class 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-141 457.7 13.6 2.2e-141 457.5 13.6 1.0 1 lcl|NCBI__GCF_000711195.1:WP_029934061.1 N746_RS0103890 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711195.1:WP_029934061.1 N746_RS0103890 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 457.5 13.6 2.2e-141 2.2e-141 1 406 [. 1 402 [. 1 403 [. 0.99 Alignments for each domain: == domain 1 score: 457.5 bits; conditional E-value: 2.2e-141 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + liVqK+GGtsvg eri+++ak+v k + eg++vvVV+SAms++t++l ++a +++++ +s+ lcl|NCBI__GCF_000711195.1:WP_029934061.1 1 MALIVQKYGGTSVGTLERIQNVAKKVSKFVDEGHQVVVVLSAMSGETNRLTDMA------KTMQERPSK 63 579**************************************************9......9******** PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re+d+l+ +GE++++alls+al++ g++a++++g++ +i Td+ +++A+i++++ +++ ++L+ +++v lcl|NCBI__GCF_000711195.1:WP_029934061.1 64 REMDMLLTTGEQVTIALLSMALQQSGHDAISYTGWQVPIQTDEVHTKARIDSINA-QKIQDQLDLNKVV 131 *******************************************************.************* PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vvaGF+G t +G+i tLGRGGSD+tA++laaalkA++++iyTDV+GvyttDPr+v+ea+++++i+++E+ lcl|NCBI__GCF_000711195.1:WP_029934061.1 132 VVAGFQGVTANGDISTLGRGGSDTTAVALAAALKAEECQIYTDVDGVYTTDPRMVPEARRLETITFDEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltveg 273 le+A+lGakvl+ r++e+a ++kvp++v ss ++ gTlit+ ++e++ l+++ia++++ ++l+v lcl|NCBI__GCF_000711195.1:WP_029934061.1 201 LEMASLGAKVLQIRSVEFASKYKVPLRVLSSLKEGGGTLITSeddQMEKP-LISGIAFNRDESKLQVL- 267 *****************************************988677777.*****************. PP TIGR00656 274 egmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaeleslev 339 g+ +k+g++ i + +a+++i +d+i+q +++ t+ +++v+++d +a ++L+++s +++ +++ + lcl|NCBI__GCF_000711195.1:WP_029934061.1 268 -GVPDKPGVAYAILGPIADANIEIDMIIQNQGQdgtTDFTFTVHRNDRAHALEILNAVSSEVGAREVVY 335 .9*****************************99999********************************* PP TIGR00656 340 eedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 + +a+vs+vg+g++++ G+as++fk+l++k+ini mi++ e+kisv+++e ++e av++lhek+e+ lcl|NCBI__GCF_000711195.1:WP_029934061.1 336 DDTIAKVSLVGVGMRSHVGIASRMFKVLADKDINIQMIATTEIKISVVINESQLETAVKTLHEKFEL 402 *****************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.51 // [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