Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_073039273.1 BUB04_RS10965 aspartate kinase
Query= SwissProt::Q88EI9 (411 letters) >NCBI__GCF_900129305.1:WP_073039273.1 Length = 417 Score = 469 bits (1206), Expect = e-137 Identities = 241/404 (59%), Positives = 313/404 (77%), Gaps = 2/404 (0%) Query: 1 MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60 MAL+VQK+GGTSV +ERI VA +V + ++AGDDLVVVLSA +G+T+RLI+LA Q++ Sbjct: 1 MALVVQKYGGTSVADVERIRNVARRVIERKKAGDDLVVVLSARAGDTDRLIELAHQMSPH 60 Query: 61 PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120 P PRELDV+++TGEQ+TIAL +MA+ G AVS TG Q I+TD H ARI I+ Sbjct: 61 PDPRELDVLLATGEQITIALFSMAVKDMGFEAVSMTGYQAGIITDHHHGHARISWIETLP 120 Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 + LKEG++VVVAGFQG D+ G+ITTLGRGGSDTT VALAAALKAD C+IYTDV+GVYT Sbjct: 121 VVEKLKEGKIVVVAGFQGYDDEGNITTLGRGGSDTTAVALAAALKADACEIYTDVEGVYT 180 Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLI 240 TDP V +AR+L KI++EEMLEMAS+G+KVL IRSVEF KYNVP+ V SF + PGTL+ Sbjct: 181 TDPNVYSKARKLRKISYEEMLEMASMGAKVLHIRSVEFGMKYNVPIWVRSSFTDDPGTLV 240 Query: 241 TIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAH 300 T ++ E ME+ ++SG+ +N++EA++T+ VPD PG+AFKI PI+ + I VDMI+Q + Sbjct: 241 TAEDAE-MEKVVVSGVTYNKNEARVTVTDVPDVPGMAFKIFEPIAQAGINVDMIIQGSSG 299 Query: 301 -DNTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASC 359 + +FTV + +YE+ ++ E AREIGA V G+ IAK+S++GVGMRSH GVAS Sbjct: 300 VPGRANISFTVPKADYEQTVALAEKVAREIGAGPVHGNAHIAKISVIGVGMRSHTGVASL 359 Query: 360 MFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDL 403 MF++LAKE+INI MISTSEIK+S V++EKY ELAVR LH AF+L Sbjct: 360 MFDSLAKENINIHMISTSEIKISCVIDEKYTELAVRVLHDAFEL 403 Lambda K H 0.316 0.133 0.358 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: 538 Number of extensions: 18 Number of successful extensions: 4 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: 411 Length of database: 417 Length adjustment: 31 Effective length of query: 380 Effective length of database: 386 Effective search space: 146680 Effective search space used: 146680 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_073039273.1 BUB04_RS10965 (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.11382.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-142 461.8 6.8 1.2e-142 461.6 6.8 1.0 1 lcl|NCBI__GCF_900129305.1:WP_073039273.1 BUB04_RS10965 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900129305.1:WP_073039273.1 BUB04_RS10965 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 461.6 6.8 1.2e-142 1.2e-142 1 406 [. 1 403 [. 1 404 [. 0.98 Alignments for each domain: == domain 1 score: 461.6 bits; conditional E-value: 1.2e-142 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + l+VqK+GGtsv+++eri+++a++v++++k g++ vVV+SA ++ td+l+ela +++s ++ p lcl|NCBI__GCF_900129305.1:WP_073039273.1 1 MALVVQKYGGTSVADVERIRNVARRVIERKKAGDDLVVVLSARAGDTDRLIELA------HQMSPHPDP 63 579***************************************************......8******** PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re d l+++GE++++al+s+a+++ g +a++++g +agi+Td ++g+A+i+ ++t ++e L+eg+iv lcl|NCBI__GCF_900129305.1:WP_073039273.1 64 RELDVLLATGEQITIALFSMAVKDMGFEAVSMTGYQAGIITDHHHGHARISWIET-LPVVEKLKEGKIV 131 *******************************************************.9************ PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vvaGF+G + eG+iTtLGRGGSD+tA++laaalkAd +eiyTDVeGvyttDP+v ++a+k+ kisyeE+ lcl|NCBI__GCF_900129305.1:WP_073039273.1 132 VVAGFQGYDDEGNITTLGRGGSDTTAVALAAALKADACEIYTDVEGVYTTDPNVYSKARKLRKISYEEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltveg 273 le+A++Gakvlh r++e+ ++++vpi vrss+ + gTl+t+ ++e+ +v++++++kn ar+tv+ lcl|NCBI__GCF_900129305.1:WP_073039273.1 201 LEMASMGAKVLHIRSVEFGMKYNVPIWVRSSFTDDPGTLVTAedaEMEK-VVVSGVTYNKNEARVTVT- 267 *****************************************97544444.59****************. PP TIGR00656 274 egmlgkrgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaelesle 338 ++ + +g++ +if+ +a+++invd+i+q++s +is++v + d ++++++ +++ +++ ++ lcl|NCBI__GCF_900129305.1:WP_073039273.1 268 -DVPDVPGMAFKIFEPIAQAGINVDMIIQGSSGvpgrANISFTVPKADYEQTVALAEKVAREIGAGPVH 335 .*****************************98777779**********************99******* PP TIGR00656 339 veedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 + +a++s++g+g+++++Gvas +f l+++nini mis+se+kis ++dek++e avr lh+++e+ lcl|NCBI__GCF_900129305.1:WP_073039273.1 336 GNAHIAKISVIGVGMRSHTGVASLMFDSLAKENINIHMISTSEIKISCVIDEKYTELAVRVLHDAFEL 403 *****************************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (417 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: 10.49 // [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