Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_026127686.1 D471_RS0113155 aspartate kinase
Query= BRENDA::P9WPX3 (421 letters) >NCBI__GCF_000341125.1:WP_026127686.1 Length = 423 Score = 572 bits (1473), Expect = e-167 Identities = 289/423 (68%), Positives = 353/423 (83%), Gaps = 2/423 (0%) Query: 1 MALVVQKYGGSSVADAERIRRVAERIVATKKQGNDVVVVVSAMGDTTDDLLDLAQQVCPA 60 MAL+VQKYGGSSVADAE I+RVA+RIVA KK G DVVVVVSAMGDTTD+LLDLA+QV P Sbjct: 1 MALIVQKYGGSSVADAEAIKRVAQRIVAQKKAGYDVVVVVSAMGDTTDELLDLAEQVSPM 60 Query: 61 PPPRELDMLLTAGERISNALVAMAIESLGAHARSFTGSQAGVITTGTHGNAKIIDVTPGR 120 PP RELDML+TAGER+S ALVAMAIE+LG ARSFTGSQAGVITT HGNAKIIDVTPGR Sbjct: 61 PPARELDMLVTAGERMSMALVAMAIENLGYEARSFTGSQAGVITTSLHGNAKIIDVTPGR 120 Query: 121 LQTALEEGRVVLVAGFQGVSQDTKDVTTLGRGGSDTTAVAMAAALGADVCEIYTDVDGIF 180 +Q A++EG + +VAGFQGVSQDTKD+T+LGRGGSDTTAVA+AAAL AD CEIY+DVDG+F Sbjct: 121 IQEAVDEGAICIVAGFQGVSQDTKDITSLGRGGSDTTAVALAAALEADACEIYSDVDGVF 180 Query: 181 SADPRIVRNARKLDTVTFEEMLEMAACGAKVLMLRCVEYARRHNIPVHVRSSYSDRPGTV 240 +ADPRIV +AR++ V++EEMLEMAACG K+L LRCVEYARR+NIP+HVRSS+S +PGT Sbjct: 181 TADPRIVPSARRIPQVSYEEMLEMAACGTKILHLRCVEYARRYNIPLHVRSSFSQKPGTW 240 Query: 241 VVGSIKDVP-MEDPILTGVAHDRSEAKVTIVGLPDIPGYAAKVFRAVADADVNIDMVLQN 299 VV +++ ME PI++GV+HDRSEAK+T+VG+PD G AA +F+A+ADA++NIDM++QN Sbjct: 241 VVSEVEESEGMEQPIISGVSHDRSEAKITVVGVPDKVGEAATIFKALADAEINIDMIVQN 300 Query: 300 VSKVEDGKTDITFTCSRDVGPAAVEKLDSLRNEIGFSQLLYDDHIGKVSLIGAGMRSHPG 359 VS V +TDI+FT ++ G AV L ++ ++GF L YDD IGKVSLIGAGMRS+PG Sbjct: 301 VSAVSTSRTDISFTVPKESGKVAVSSLKKVQEKVGFEALRYDDKIGKVSLIGAGMRSYPG 360 Query: 360 VTATFCEALAAVGVNIELISTSEIRISVLCRDTELDKAVVALHEAFGLGGDE-EATVYAG 418 VTA F +A+A G N+E+ISTSEIRISV+ ++++D AV A H F L D+ EA VY G Sbjct: 361 VTARFFDAVAGSGTNVEMISTSEIRISVIVEESQIDAAVQAAHSEFQLDADQVEAVVYGG 420 Query: 419 TGR 421 TGR Sbjct: 421 TGR 423 Lambda K H 0.318 0.134 0.376 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: 534 Number of extensions: 21 Number of successful extensions: 5 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: 421 Length of database: 423 Length adjustment: 32 Effective length of query: 389 Effective length of database: 391 Effective search space: 152099 Effective search space used: 152099 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_026127686.1 D471_RS0113155 (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.26507.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-130 419.7 11.0 7.5e-130 419.5 11.0 1.0 1 lcl|NCBI__GCF_000341125.1:WP_026127686.1 D471_RS0113155 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000341125.1:WP_026127686.1 D471_RS0113155 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 419.5 11.0 7.5e-130 7.5e-130 1 406 [. 1 408 [. 1 409 [. 0.97 Alignments for each domain: == domain 1 score: 419.5 bits; conditional E-value: 7.5e-130 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + liVqK+GG+sv++ e+ik++a+++++++k g++vvVVvSAm+ +tdel++la e++s + lcl|NCBI__GCF_000341125.1:WP_026127686.1 1 MALIVQKYGGSSVADAEAIKRVAQRIVAQKKAGYDVVVVVSAMGDTTDELLDLA------EQVSPMPPA 63 579***************************************************......79******* PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re d+lv GE++s+al+++a+++lg++a++++g +ag++T + +gnAki ++ + r+ e +eg i lcl|NCBI__GCF_000341125.1:WP_026127686.1 64 RELDMLVTAGERMSMALVAMAIENLGYEARSFTGSQAGVITTSLHGNAKIIDVTP-GRIQEAVDEGAIC 131 *******************************************************.************* PP TIGR00656 139 vvaGFiGateeG.eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeE 206 +vaGF+G ++ +iT LGRGGSD+tA++laaal+Ad +eiy DV+Gv+t+DPr+v++a++i+++syeE lcl|NCBI__GCF_000341125.1:WP_026127686.1 132 IVAGFQGVSQDTkDITSLGRGGSDTTAVALAAALEADACEIYSDVDGVFTADPRIVPSARRIPQVSYEE 200 *******9887638******************************************************* PP TIGR00656 207 alelAtlGakvlhpralelaveakvpilvrsskekeegTlitn......kkensslvkaialeknvarl 269 +le+A G k+lh r +e+a ++++p+ vrss++++ gT +++ +e++ +++++++++ a++ lcl|NCBI__GCF_000341125.1:WP_026127686.1 201 MLEMAACGTKILHLRCVEYARRYNIPLHVRSSFSQKPGTWVVSeveeseGMEQP-IISGVSHDRSEAKI 268 ******************************************977766566666.************** PP TIGR00656 270 tvegegmlgkrgilaeifkaLaeeeinvdlisqtese.....tsislvvdeedvdeakkaLkeesgaae 333 tv+ g+ +k g +a+ifkaLa++ein+d+i+q s t+is++v +e + a++ Lk+++++++ lcl|NCBI__GCF_000341125.1:WP_026127686.1 269 TVV--GVPDKVGEAATIFKALADAEINIDMIVQNVSAvstsrTDISFTVPKESGKVAVSSLKKVQEKVG 335 ***..9**************************9766555556*************************** PP TIGR00656 334 lesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhe 402 +e l ++ ++ +vs++gag+++ pGv+++ f a++ ++ n+ mis+se++isv+v+e + av++ h+ lcl|NCBI__GCF_000341125.1:WP_026127686.1 336 FEALRYDDKIGKVSLIGAGMRSYPGVTARFFDAVAGSGTNVEMISTSEIRISVIVEESQIDAAVQAAHS 404 ********************************************************************* PP TIGR00656 403 klee 406 ++++ lcl|NCBI__GCF_000341125.1:WP_026127686.1 405 EFQL 408 **97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (423 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: 10.67 // [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