Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_027458224.1 K420_RS0111660 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_000519045.1:WP_027458224.1 Length = 406 Score = 572 bits (1474), Expect = e-168 Identities = 298/406 (73%), Positives = 344/406 (84%), Gaps = 2/406 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MALIVQK+GGTSVG ERI+ VA++V KF G VVVVVSAMSGETN+LI LA ++ Sbjct: 1 MALIVQKYGGTSVGNPERIKNVAKRVAKFHAQGHQVVVVVSAMSGETNKLIALAKEVQAN 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 P PRELD + +TGEQVTI LLSMAL+ GVPA SYTG QV++LTDS TKARIL ID+ + Sbjct: 61 PNPRELDQICATGEQVTIGLLSMALMDIGVPARSYTGGQVKVLTDSTFTKARILSIDEAN 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 +RADL AG+VVVVAGFQGVD +GN+TTLGRGGSDT+GVALAAALKADECQIYTDVDGVYT Sbjct: 121 MRADLDAGKVVVVAGFQGVDADGNVTTLGRGGSDTSGVALAAALKADECQIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQ-EGPGTL 239 TDPRVVP+A++LD ITFEEMLEMASLGSKVLQIR+VEFAGKY V LRVL SFQ EG GTL Sbjct: 181 TDPRVVPEAKKLDTITFEEMLEMASLGSKVLQIRSVEFAGKYKVKLRVLSSFQDEGEGTL 240 Query: 240 ITIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNV 299 IT+ +E+++MEQPIISGIAFNRDEAKLT+ GVPDTPG+A++ILG I+ AN++VDMI+QNV Sbjct: 241 ITV-EEDKNMEQPIISGIAFNRDEAKLTMLGVPDTPGIAYQILGAIADANIDVDMIIQNV 299 Query: 300 AHDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVAS 359 HD TTDF+FTV+R D+ A IL+ A +GARE GD I KVS VGVGMRSH GVAS Sbjct: 300 GHDGTTDFSFTVNRGDFAKAQGILETVKAKLGAREITGDNKICKVSAVGVGMRSHPGVAS 359 Query: 360 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 405 +MF+ALA E INIQMISTSEIK+SVV++EKYLELAVR LH F LD Sbjct: 360 KMFKALADEGINIQMISTSEIKISVVLDEKYLELAVRVLHRTFGLD 405 Lambda K H 0.317 0.133 0.362 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: 556 Number of extensions: 16 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: 406 Length adjustment: 31 Effective length of query: 381 Effective length of database: 375 Effective search space: 142875 Effective search space used: 142875 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: 50 (23.9 bits)
Align candidate WP_027458224.1 K420_RS0111660 (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.17775.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-138 448.2 10.7 1.6e-138 448.0 10.7 1.0 1 lcl|NCBI__GCF_000519045.1:WP_027458224.1 K420_RS0111660 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000519045.1:WP_027458224.1 K420_RS0111660 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 448.0 10.7 1.6e-138 1.6e-138 1 405 [. 1 403 [. 1 405 [. 0.98 Alignments for each domain: == domain 1 score: 448.0 bits; conditional E-value: 1.6e-138 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + liVqK+GGtsvg+ erik++ak+v k +g++vvVVvSAms++t++l++la + ++ +++p lcl|NCBI__GCF_000519045.1:WP_027458224.1 1 MALIVQKYGGTSVGNPERIKNVAKRVAKFHAQGHQVVVVVSAMSGETNKLIALA------KEVQANPNP 63 579***************************************************......9******** PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re d++ ++GE++++ lls+al + gv a++++g++ +lTd++f++A+i +++ ++ L+ g++v lcl|NCBI__GCF_000519045.1:WP_027458224.1 64 RELDQICATGEQVTIGLLSMALMDIGVPARSYTGGQVKVLTDSTFTKARILSIDE-ANMRADLDAGKVV 131 ******************************************************9.99*********** PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vvaGF+G + +G++TtLGRGGSD++ ++laaalkAd+++iyTDV+GvyttDPrvv+eakk+d+i++eE+ lcl|NCBI__GCF_000519045.1:WP_027458224.1 132 VVAGFQGVDADGNVTTLGRGGSDTSGVALAAALKADECQIYTDVDGVYTTDPRVVPEAKKLDTITFEEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskeke.egTlitn....kkensslvkaialeknvarltv 271 le+A+lG kvl+ r++e+a ++kv+++v ss++ e egTlit ++e++ ++++ia++++ a+lt+ lcl|NCBI__GCF_000519045.1:WP_027458224.1 201 LEMASLGSKVLQIRSVEFAGKYKVKLRVLSSFQDEgEGTLITVeedkNMEQP-IISGIAFNRDEAKLTM 268 *********************************999*****98776666666.**************** PP TIGR00656 272 egegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesl 337 g+ + +gi+ +i +a+a+++i+vd+i+q ++ t+ s++v++ d +a+ +L++++ +++ +++ lcl|NCBI__GCF_000519045.1:WP_027458224.1 269 L--GVPDTPGIAYQILGAIADANIDVDMIIQNVGHdgtTDFSFTVNRGDFAKAQGILETVKAKLGAREI 335 *..9***************************9988888******************************* PP TIGR00656 338 eveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 ++++++vs+vg+g++++pGvas++fkal++++ini mis+se+kisv+ dek++e avr lh+++ lcl|NCBI__GCF_000519045.1:WP_027458224.1 336 TGDNKICKVSAVGVGMRSHPGVASKMFKALADEGINIQMISTSEIKISVVLDEKYLELAVRVLHRTFG 403 *****************************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (406 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.70 // [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