Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_072906511.1 BUB13_RS05490 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_900142125.1:WP_072906511.1 Length = 411 Score = 505 bits (1300), Expect = e-147 Identities = 256/412 (62%), Positives = 326/412 (79%), Gaps = 2/412 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MAL+VQK+GGTSVGTVE+I VA +V K + G+DVVV+VSAM+GETNRL+ LA+++ E Sbjct: 1 MALVVQKYGGTSVGTVEKIRNVARRVAKTFDDGNDVVVIVSAMAGETNRLVALADEMCEF 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 P RE DV+VSTGEQVTIALLSM L G A SY G+Q+ ++TDSAH++ARI IDD Sbjct: 61 PSEREYDVLVSTGEQVTIALLSMCLQSMGYNAKSYLGSQIPVMTDSAHSRARIKSIDDKK 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 +R DLK G +++VAGFQG+D +GN+TTLGRGGSDT+ VA+AAALKAD C+IYTDVDGVYT Sbjct: 121 VREDLKNGTIIIVAGFQGIDDDGNVTTLGRGGSDTSAVAVAAALKADVCEIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240 TDPR+VP+AR+++KI++EEMLEMASLG+KVLQIR+VEFA KYNV + V +F + PGTL+ Sbjct: 181 TDPRMVPEARKIEKISYEEMLEMASLGAKVLQIRSVEFAKKYNVVVHVRSTFNDKPGTLV 240 Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300 +D+E ME ++SGIA+N+DEAK++I GVPD PG+A +I P+S AN+ VDMI+QNV+ Sbjct: 241 MKEDQE--METVLVSGIAYNKDEAKISIFGVPDQPGIAAQIFSPLSEANITVDMIIQNVS 298 Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360 D TD TFTV + D AL+I++ IGA + NI+K+SI+GVGMRSH+G+A Sbjct: 299 QDGKTDMTFTVLKTDCKKALKIVEDVMGKIGASGVKSNENISKISIIGVGMRSHSGIAQT 358 Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPARQGE 412 MFE LAKE INI+MISTSEIKVS +I+ KY ELAVR LH AF LD A + E Sbjct: 359 MFETLAKEGINIEMISTSEIKVSCIIDAKYTELAVRVLHEAFGLDKAAVEDE 410 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: 488 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: 411 Length adjustment: 31 Effective length of query: 381 Effective length of database: 380 Effective search space: 144780 Effective search space used: 144780 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_072906511.1 BUB13_RS05490 (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.521842.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-139 449.7 15.3 5.7e-139 449.5 15.3 1.0 1 NCBI__GCF_900142125.1:WP_072906511.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900142125.1:WP_072906511.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 449.5 15.3 5.7e-139 5.7e-139 1 405 [. 1 401 [. 1 403 [. 0.98 Alignments for each domain: == domain 1 score: 449.5 bits; conditional E-value: 5.7e-139 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 + l+VqK+GGtsvg +e+i+++a++v k+ +g++vvV+vSAm+++t++lv+la + + + +s+re d NCBI__GCF_900142125.1:WP_072906511.1 1 MALVVQKYGGTSVGTVEKIRNVARRVAKTFDDGNDVVVIVSAMAGETNRLVALA------DEMCEFPSEREYD 67 579***************************************************......6999********* PP TIGR00656 74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146 lvs+GE++++alls+ l+ g++a+++ g + +++Td+ + +A+ik+++ +++ e L++g+i++vaGF+G NCBI__GCF_900142125.1:WP_072906511.1 68 VLVSTGEQVTIALLSMCLQSMGYNAKSYLGSQIPVMTDSAHSRARIKSIDD-KKVREDLKNGTIIIVAGFQGI 139 **************************************************9.9******************** PP TIGR00656 147 teeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlh 219 + +G++TtLGRGGSD++A+++aaalkAd +eiyTDV+GvyttDPr+v+ea+ki+kisyeE+le+A+lGakvl+ NCBI__GCF_900142125.1:WP_072906511.1 140 DDDGNVTTLGRGGSDTSAVAVAAALKADVCEIYTDVDGVYTTDPRMVPEARKIEKISYEEMLEMASLGAKVLQ 212 ************************************************************************* PP TIGR00656 220 pralelaveakvpilvrsskekeegTlitn.kkens.slvkaialeknvarltvegegmlgkrgilaeifkaL 290 r++e+a++++v + vrs+++ + gTl+++ ++e++ lv++ia++k+ a+++++ g+ +++gi+a+if+ L NCBI__GCF_900142125.1:WP_072906511.1 213 IRSVEFAKKYNVVVHVRSTFNDKPGTLVMKeDQEMEtVLVSGIAYNKDEAKISIF--GVPDQPGIAAQIFSPL 283 *****************************974444446*****************..9*************** PP TIGR00656 291 aeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGva 360 +e++i vd+i+q s+ t+++++v ++d ++a k+ ++++g+++ + ++ +e++ ++si+g+g+++++G+a NCBI__GCF_900142125.1:WP_072906511.1 284 SEANITVDMIIQNVSQdgkTDMTFTVLKTDCKKALKIVEDVMGKIGASGVKSNENISKISIIGVGMRSHSGIA 356 ************9988888****************************************************** PP TIGR00656 361 seifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 + +f+ l++++ini mis+se+k+s ++d k++e avr lhe++ NCBI__GCF_900142125.1:WP_072906511.1 357 QTMFETLAKEGINIEMISTSEIKVSCIIDAKYTELAVRVLHEAFG 401 ******************************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (411 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 25.71 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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