Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_052664755.1 NITAL_RS03510 aspartate kinase
Query= BRENDA::P9WPX3 (421 letters) >NCBI__GCF_000969705.1:WP_052664755.1 Length = 415 Score = 479 bits (1232), Expect = e-140 Identities = 247/410 (60%), Positives = 316/410 (77%), Gaps = 3/410 (0%) Query: 1 MALVVQKYGGSSVADAERIRRVAERIVATKKQGNDVVVVVSAMGDTTDDLLDLAQQVCPA 60 MA+VVQKYGG+SV D +R++RVA+R+ T + GN VVVVSAMG TTDDL+ +AQ++ A Sbjct: 1 MAIVVQKYGGTSVGDTDRMKRVADRVARTHRDGNQTVVVVSAMGKTTDDLVAMAQRISDA 60 Query: 61 PPPRELDMLLTAGERISNALVAMAIESLGAHARSFTGSQAGVITTGTHGNAKIIDVTPGR 120 PP RELD+LLT+GERIS +L+AMA+ G A+SFTGSQAG+IT HG A+I+++TPGR Sbjct: 61 PPQRELDILLTSGERISMSLLAMALAEHGVPAKSFTGSQAGIITDAVHGKARILEITPGR 120 Query: 121 LQTALEEGRVVLVAGFQGVSQDTKDVTTLGRGGSDTTAVAMAAALGADVCEIYTDVDGIF 180 +Q AL+EG VV+VAGFQGVSQDTKD+T+LGRGGSDTTAVA+AAALGADVCEIYTDVDG+F Sbjct: 121 VQEALDEGNVVIVAGFQGVSQDTKDITSLGRGGSDTTAVALAAALGADVCEIYTDVDGVF 180 Query: 181 SADPRIVRNARKLDTVTFEEMLEMAACGAKVLMLRCVEYARRHNIPVHVRSSYSDRPGTV 240 +ADPRIV ARKL V++EE LEM A GA VL R VE+ R H + +HVRSS+S PGT Sbjct: 181 TADPRIVATARKLSYVSYEEALEMTAHGAGVLQTRSVEFGRNHGVRIHVRSSFSYTPGT- 239 Query: 241 VVGSIKDVPMEDPILTGVAHDRSEAKVTIVGLPDIPGYAAKVFRAVADADVNIDMVLQNV 300 VG ++ +ED I++GVAHD SEAKVT++ + D PG AAK+F +ADA +NIDM++QNV Sbjct: 240 WVGPREESTVEDAIISGVAHDTSEAKVTVMKVSDQPGIAAKLFSTLADAKINIDMIVQNV 299 Query: 301 SKVEDGKTDITFTCSRDVGPAAVEKLDSLRNEIGFSQLLYDDHIGKVSLIGAGMRSHPGV 360 S DG+TDI+FT R A L+ IG +L D+++ KVSL+GAGM++HPGV Sbjct: 300 S--ADGRTDISFTLPRGDTNQARAILEPYAEAIGAEGVLVDENVAKVSLVGAGMKTHPGV 357 Query: 361 TATFCEALAAVGVNIELISTSEIRISVLCRDTELDKAVVALHEAFGLGGD 410 A AL+A GVNIE+ISTS IR+SV+ +++ AV+A+HEAFGL D Sbjct: 358 AARMFSALSAAGVNIEMISTSTIRVSVVIAKDQVEPAVLAVHEAFGLSED 407 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: 521 Number of extensions: 20 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: 415 Length adjustment: 32 Effective length of query: 389 Effective length of database: 383 Effective search space: 148987 Effective search space used: 148987 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_052664755.1 NITAL_RS03510 (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.31823.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-132 427.0 13.6 4.5e-132 426.8 13.6 1.0 1 lcl|NCBI__GCF_000969705.1:WP_052664755.1 NITAL_RS03510 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000969705.1:WP_052664755.1 NITAL_RS03510 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 426.8 13.6 4.5e-132 4.5e-132 1 406 [. 1 404 [. 1 405 [. 0.97 Alignments for each domain: == domain 1 score: 426.8 bits; conditional E-value: 4.5e-132 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + ++VqK+GGtsvg+++r+k++a++v ++ ++g++ vVVvSAm+k+td lv++a + isd++ + lcl|NCBI__GCF_000969705.1:WP_052664755.1 1 MAIVVQKYGGTSVGDTDRMKRVADRVARTHRDGNQTVVVVSAMGKTTDDLVAMA------QRISDAPPQ 63 579***************************************************......79******* PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re d l+ GE++s++ll++al e+gv a++++g +agi+Td+ +g+A+i e+ + r+ e L+eg +v lcl|NCBI__GCF_000969705.1:WP_052664755.1 64 RELDILLTSGERISMSLLAMALAEHGVPAKSFTGSQAGIITDAVHGKARILEITP-GRVQEALDEGNVV 131 *******************************************************.************* PP TIGR00656 139 vvaGFiGateeG.eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeE 206 +vaGF+G ++ +iT LGRGGSD+tA++laaal Ad +eiyTDV+Gv+t+DPr+v +a+k+ ++syeE lcl|NCBI__GCF_000969705.1:WP_052664755.1 132 IVAGFQGVSQDTkDITSLGRGGSDTTAVALAAALGADVCEIYTDVDGVFTADPRIVATARKLSYVSYEE 200 *******9887638******************************************************* PP TIGR00656 207 alelAtlGakvlhpralelaveakvpilvrsskekeegTlitnkkens...slvkaialeknvarltve 272 ale+ +Ga vl+ r++e+ + +v i vrss++ gT + +++e +++++a++ a++tv+ lcl|NCBI__GCF_000969705.1:WP_052664755.1 201 ALEMTAHGAGVLQTRSVEFGRNHGVRIHVRSSFSYTPGTWVGPREESTvedAIISGVAHDTSEAKVTVM 269 ******************************************9555555559***************** PP TIGR00656 273 gegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesle 338 ++ +++gi+a++f++La+++in+d+i+q s t+is+++ + d+++a ++L+ + +a++ e + lcl|NCBI__GCF_000969705.1:WP_052664755.1 270 --KVSDQPGIAAKLFSTLADAKINIDMIVQNVSAdgrTDISFTLPRGDTNQARAILEPYAEAIGAEGVL 336 ..****************************9876677******************************** PP TIGR00656 339 veedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 v+e++a+vs+vgag++ +pGva+++f+al+ ++ni mis+s +++sv++ + ++e av ++he++ + lcl|NCBI__GCF_000969705.1:WP_052664755.1 337 VDENVAKVSLVGAGMKTHPGVAARMFSALSAAGVNIEMISTSTIRVSVVIAKDQVEPAVLAVHEAFGL 404 ****************************************************************9965 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (415 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: 9.46 // [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