Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_035235679.1 Q366_RS01730 aspartate kinase
Query= SwissProt::Q88EI9 (411 letters) >NCBI__GCF_000745975.1:WP_035235679.1 Length = 412 Score = 447 bits (1150), Expect = e-130 Identities = 231/410 (56%), Positives = 306/410 (74%), Gaps = 7/410 (1%) Query: 1 MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60 MAL VQKFGGTSV IERI +VA++V+K E D +VVVLSAM+G TN LI LA+Q ++ Sbjct: 1 MALRVQKFGGTSVADIERISKVADRVQKAHENKDQVVVVLSAMAGVTNNLISLARQASET 60 Query: 61 PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120 P RELDV+++TGEQ T AL+ M L RG+ A S+ G Q I TD KARI +ID Q Sbjct: 61 PDKRELDVLLATGEQTTAALMAMMLKSRGIKAKSFLGFQAGIHTDHMSGKARIREIDSQN 120 Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 +RA L EG +VVVAGFQG D++G ITTLGRGGSDT+ VA+AA+LKAD C+I+TDVDGVYT Sbjct: 121 LRAALDEGNIVVVAGFQGADDNGDITTLGRGGSDTSAVAIAASLKADVCEIFTDVDGVYT 180 Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLI 240 TDPR+ P+AR++ +I++EEMLEMA LG+KVLQIRSVEFA KYNVP+ V SF E GT++ Sbjct: 181 TDPRICPKARKISRISYEEMLEMAILGAKVLQIRSVEFAKKYNVPVHVRSSFNEEEGTMV 240 Query: 241 TIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQN--- 297 ++E E ME P++SGI + +EA++T + VPD PG++ + G ++ + I VDMI+QN Sbjct: 241 -VNESEDMESPVVSGITCDLNEARITFKRVPDQPGISATVFGALAEAGISVDMIIQNSRT 299 Query: 298 ---VAHDNTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHA 354 TD TFTV ++++ +A + E A +I A E+ T+IAK+S++G+GM+SH+ Sbjct: 300 GGETDPGGETDLTFTVTKDDFNRAMEISEKVADQINAGEIRTATEIAKISVIGLGMKSHS 359 Query: 355 GVASCMFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404 GVA+ MF+ALA+E+INI+MISTSEI++S V+ KY ELAVR LH AF LD Sbjct: 360 GVAAVMFKALAEENINIRMISTSEIRISCVILAKYAELAVRTLHAAFGLD 409 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: 441 Number of extensions: 14 Number of successful extensions: 3 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: 412 Length adjustment: 31 Effective length of query: 380 Effective length of database: 381 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_035235679.1 Q366_RS01730 (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.32231.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-136 441.1 13.1 2.3e-136 440.9 13.1 1.0 1 lcl|NCBI__GCF_000745975.1:WP_035235679.1 Q366_RS01730 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745975.1:WP_035235679.1 Q366_RS01730 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 440.9 13.1 2.3e-136 2.3e-136 2 405 .. 2 407 .. 1 409 [. 0.97 Alignments for each domain: == domain 1 score: 440.9 bits; conditional E-value: 2.3e-136 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 l VqKFGGtsv+++eri k+a++v k+ ++ ++vvVV+SAm++vt++l++la ++ s+ + +r lcl|NCBI__GCF_000745975.1:WP_035235679.1 2 ALRVQKFGGTSVADIERISKVADRVQKAHENKDQVVVVLSAMAGVTNNLISLA------RQASETPDKR 64 577**************************************************......89******** PP TIGR00656 71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139 e d l+++GE++++al++++l+ +g ka+++ g +agi Td g+A+i+e++ ++L L+eg ivv lcl|NCBI__GCF_000745975.1:WP_035235679.1 65 ELDVLLATGEQTTAALMAMMLKSRGIKAKSFLGFQAGIHTDHMSGKARIREIDS-QNLRAALDEGNIVV 132 ******************************************************.************** PP TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208 vaGF+Ga+ +G+iTtLGRGGSD++A+++aa+lkAd +ei+TDV+GvyttDPr+ ++a+ki +isyeE+l lcl|NCBI__GCF_000745975.1:WP_035235679.1 133 VAGFQGADDNGDITTLGRGGSDTSAVAIAASLKADVCEIFTDVDGVYTTDPRICPKARKISRISYEEML 201 ********************************************************************* PP TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltvege 274 e+A lGakvl+ r++e+a++++vp+ vrss+++eegT ++n ++e + +v++i+ + n ar+t + lcl|NCBI__GCF_000745975.1:WP_035235679.1 202 EMAILGAKVLQIRSVEFAKKYNVPVHVRSSFNEEEGTMVVNeseDMESP-VVSGITCDLNEARITFK-- 267 *****************************************66555555.*****************.. PP TIGR00656 275 gmlgkrgilaeifkaLaeeeinvdlisqtese.........tsislvvdeedvdeakkaLkeesgaael 334 + +++gi a++f+aLae++i+vd+i+q + t+++++v + d ++a ++ +++ ++++ lcl|NCBI__GCF_000745975.1:WP_035235679.1 268 RVPDQPGISATVFGALAEAGISVDMIIQNSRTggetdpggeTDLTFTVTKDDFNRAMEISEKVADQINA 336 **************************997743555778888***********************9999* PP TIGR00656 335 esleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhek 403 ++ + ++a++s++g g+++++Gva+ +fkal+e+nini mis+se++is ++ k+ae avr+lh++ lcl|NCBI__GCF_000745975.1:WP_035235679.1 337 GEIRTATEIAKISVIGLGMKSHSGVAAVMFKALAEENINIRMISTSEIRISCVILAKYAELAVRTLHAA 405 *******************************************************************99 PP TIGR00656 404 le 405 + lcl|NCBI__GCF_000745975.1:WP_035235679.1 406 FG 407 86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (412 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: 00:00:00.01 # Mc/sec: 11.73 // [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