Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_084276585.1 B8779_RS05980 aspartate kinase
Query= SwissProt::Q88EI9 (411 letters) >NCBI__GCF_900176045.1:WP_084276585.1 Length = 401 Score = 448 bits (1153), Expect = e-130 Identities = 229/402 (56%), Positives = 313/402 (77%), Gaps = 3/402 (0%) Query: 3 LIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQPV 62 LIVQK+GGTSVGS+ERIE VA++V K +EAG+D+VVV+SAMSGETN+LID AK + P Sbjct: 2 LIVQKYGGTSVGSLERIENVAKRVAKTKEAGNDVVVVVSAMSGETNKLIDYAKHFSPTPS 61 Query: 63 PRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQKIR 122 R++D+++S+GE+VT ALL++AL + G P V+ TG Q I+TD SH ARI +I+ + ++ Sbjct: 62 RRDMDLLLSSGERVTAALLSIALNEMGFPTVAMTGRQAGIVTDKSHTVARIEKINPEPMQ 121 Query: 123 ADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTD 182 LKEG+++VVAGFQG+ E G +TTLGRGGSD T VA+A AL AD+C+IY+DVDGVYTTD Sbjct: 122 NALKEGKIIVVAGFQGITEDGQVTTLGRGGSDLTAVAIAGALGADKCEIYSDVDGVYTTD 181 Query: 183 PRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLITI 242 PR+ P+A++L+KI+++EMLE+ASLG+KVLQ RSVE A K V + SF + PGT+IT Sbjct: 182 PRIEPKAKKLDKISYDEMLELASLGAKVLQNRSVELAKKLGVVIEARSSFNDNPGTIIT- 240 Query: 243 DEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAHDN 302 EE+ ME+P++SGIA ++++A++++RGV D PG+A +I ++ NI VDMIVQ + D Sbjct: 241 KEEDIMEKPLVSGIALDKNQARVSLRGVKDRPGIAAEIFKALANENINVDMIVQTIGEDG 300 Query: 303 TTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASCMFE 362 T+ FTV +NE E + V+E E +V D +AKVSIVGVGM+SH+GVAS FE Sbjct: 301 KTNLDFTVPQNELELVKKVMEQFKDEY--EKVEYDPDVAKVSIVGVGMKSHSGVASKAFE 358 Query: 363 ALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404 +AKE+INI+MISTSEIK+S++++EKY ELAVRALH A++LD Sbjct: 359 TMAKENINIEMISTSEIKISMIIDEKYGELAVRALHAAYELD 400 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: 467 Number of extensions: 16 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: 411 Length of database: 401 Length adjustment: 31 Effective length of query: 380 Effective length of database: 370 Effective search space: 140600 Effective search space used: 140600 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_084276585.1 B8779_RS05980 (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.7676.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-148 479.5 10.2 5e-148 479.4 10.2 1.0 1 lcl|NCBI__GCF_900176045.1:WP_084276585.1 B8779_RS05980 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176045.1:WP_084276585.1 B8779_RS05980 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 479.4 10.2 5e-148 5e-148 2 406 .. 1 399 [. 1 400 [. 0.98 Alignments for each domain: == domain 1 score: 479.4 bits; conditional E-value: 5e-148 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 +liVqK+GGtsvgs eri+++ak+v k+++ g++vvVVvSAms++t++l++ a + +s +s+r lcl|NCBI__GCF_900176045.1:WP_084276585.1 1 MLIVQKYGGTSVGSLERIENVAKRVAKTKEAGNDVVVVVSAMSGETNKLIDYA------KHFSPTPSRR 63 79***************************************************......9********* PP TIGR00656 71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139 +d+l+s GE++++alls al+e g ++a++g +agi+Td++++ A+i+++++ e + + L+eg+i+v lcl|NCBI__GCF_900176045.1:WP_084276585.1 64 DMDLLLSSGERVTAALLSIALNEMGFPTVAMTGRQAGIVTDKSHTVARIEKINP-EPMQNALKEGKIIV 131 ******************************************************.9************* PP TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208 vaGF+G te+G++TtLGRGGSDltA+++a al Ad++eiy DV+GvyttDPr+ ++akk+dkisy+E+l lcl|NCBI__GCF_900176045.1:WP_084276585.1 132 VAGFQGITEDGQVTTLGRGGSDLTAVAIAGALGADKCEIYSDVDGVYTTDPRIEPKAKKLDKISYDEML 200 ********************************************************************* PP TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltvege 274 elA+lGakvl++r++ela++ +v i+ rss++ + gT it+ +e++ lv++ial+kn+ar++++ lcl|NCBI__GCF_900176045.1:WP_084276585.1 201 ELASLGAKVLQNRSVELAKKLGVVIEARSSFNDNPGTIITKeedIMEKP-LVSGIALDKNQARVSLR-- 266 ****************************************976445666.*****************.. PP TIGR00656 275 gmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleve 340 g+ +++gi+aeifkaLa+e+invd+i+qt +e t+++++v +++++ kk++++++ +e+e++e++ lcl|NCBI__GCF_900176045.1:WP_084276585.1 267 GVKDRPGIAAEIFKALANENINVDMIVQTIGEdgkTNLDFTVPQNELELVKKVMEQFK--DEYEKVEYD 333 99****************************99999*******************9996..7888***** PP TIGR00656 341 edlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 d+a+vsivg+g+++++Gvas++f+ ++++nini mis+se+kis+++dek+ e avr+lh+++e+ lcl|NCBI__GCF_900176045.1:WP_084276585.1 334 PDVAKVSIVGVGMKSHSGVASKAFETMAKENINIEMISTSEIKISMIIDEKYGELAVRALHAAYEL 399 ***************************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (401 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: 00:00:00.02 # Mc/sec: 7.88 // [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