Align aspartate kinase 1; EC 2.7.2.4 (characterized)
to candidate WP_092482509.1 BM299_RS05755 aspartate kinase
Query= CharProtDB::CH_090816 (404 letters) >NCBI__GCF_900115975.1:WP_092482509.1 Length = 408 Score = 384 bits (987), Expect = e-111 Identities = 206/408 (50%), Positives = 280/408 (68%), Gaps = 4/408 (0%) Query: 1 MKIIVQKFGGTSVKDDKGRKLALGHIKEAISEGYKVVVVVSAMGRKGDPYATDSLLGLLY 60 MK IV KFGGTS+ + R+ G I A EGY VVVVSA+GR+GDPYATD+L+ L+ Sbjct: 1 MKYIVLKFGGTSLVSPELRERVAGKIIAAKDEGYVPVVVVSAIGREGDPYATDTLISLVK 60 Query: 61 GDQSAISPREQDLLLSCGETISSVVFTSMLLDNGVKAAALTGAQAGFLTNDQHTNAKIIE 120 + RE D+L+SCGE IS VV + L G A LTGAQAG +T+ ++ A+I++ Sbjct: 61 QTYHDLPAREMDMLMSCGEIISGVVMAATLQAMGYPAVFLTGAQAGIITDRNYSGARILQ 120 Query: 121 MKPERLFSVLANHDAVVVAGFQGATEKGDTTTIGRGGSDTSAAALGAAVDAEYIDIFTDV 180 ++ + + VVVAGFQG TE G+ TT+GRGGSDT+AAALG A++A Y+DI+TDV Sbjct: 121 VQAKNVTRYTQEGYIVVVAGFQGTTEDGEITTLGRGGSDTTAAALGVALNAVYVDIYTDV 180 Query: 181 EGVMTADPRVVENAKPLPVVTYTEICNLAYQGAKVISPRAVEIAMQAKVPIRVRSTYSND 240 +G+MTADPR+V AK L V+TY EIC+LA++GAKV+ PRAVEIAMQ +P+RVRST+S+ Sbjct: 181 DGIMTADPRIVAEAKALEVITYDEICHLAHEGAKVVHPRAVEIAMQKSIPLRVRSTFSDS 240 Query: 241 KGTLVTSHHSSKVGS-DVF-ERLITGIAHVKDVTQF--KVPAKIGQYNVQTEVFKAMANA 296 GTLVT+ G+ D+ +R++TGI ++ + QF ++ A Q +F+A+A A Sbjct: 241 PGTLVTNSGEVYKGTIDITKDRIVTGITYISGIAQFIVRIGATGEGLKQQRRMFRALALA 300 Query: 297 GISVDFFNITPSEIVYTVAGNKTETAQRILMDMGYDPMVTRNCAKVSAVGAGIMGVPGVT 356 GIS+DF NI P +++TV + E A ++L + GY V CAKVSAVGAG+ GVPGV Sbjct: 301 GISIDFINILPEVVLFTVKDDVAEKAVKVLENTGYMSEVITGCAKVSAVGAGMSGVPGVI 360 Query: 357 SKIVSALSEKEIPILQSADSHTTIWVLVHEADMVPAVNALHEEFELSK 404 + IV AL++ +I ILQ DSHTT+WVLV +M AV ALH +F+L + Sbjct: 361 ADIVEALTKDDIQILQCNDSHTTVWVLVRREEMEKAVRALHRQFKLDQ 408 Lambda K H 0.316 0.131 0.364 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: 496 Number of extensions: 19 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: 404 Length of database: 408 Length adjustment: 31 Effective length of query: 373 Effective length of database: 377 Effective search space: 140621 Effective search space used: 140621 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_092482509.1 BM299_RS05755 (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.23899.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-127 410.6 9.9 4.3e-127 410.4 9.9 1.0 1 lcl|NCBI__GCF_900115975.1:WP_092482509.1 BM299_RS05755 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900115975.1:WP_092482509.1 BM299_RS05755 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 410.4 9.9 4.3e-127 4.3e-127 1 406 [. 1 406 [. 1 407 [. 0.96 Alignments for each domain: == domain 1 score: 410.4 bits; conditional E-value: 4.3e-127 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 ++ iV KFGGts+ s e ++++a ++++++ eg+ +vVVvSA+++++d +++ + l++l++++ ++ lcl|NCBI__GCF_900115975.1:WP_092482509.1 1 MKYIVLKFGGTSLVSPELRERVAGKIIAAKDEGYVPVVVVSAIGREGDPYATDT-LISLVKQTYHDLPA 68 578***************************************************.9************* PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re+d+l+s+GE +s ++++ l++ g+ a+ l+g++agi+Td ++ A+i +++ ++++ +eg+iv lcl|NCBI__GCF_900115975.1:WP_092482509.1 69 REMDMLMSCGEIISGVVMAATLQAMGYPAVFLTGAQAGIITDRNYSGARILQVQA-KNVTRYTQEGYIV 136 *******************************************************.9************ PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vvaGF+G+te+GeiTtLGRGGSD+tAa+l+ al+A +v+iyTDV+G++t+DPr+v eak ++ i+y+E+ lcl|NCBI__GCF_900115975.1:WP_092482509.1 137 VVAGFQGTTEDGEITTLGRGGSDTTAAALGVALNAVYVDIYTDVDGIMTADPRIVAEAKALEVITYDEI 205 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn.........kkensslvkaialeknva 267 + lA+ Gakv+hpra+e+a+++++p++vrs+++ + gTl+tn + ++++v++i++ ++a lcl|NCBI__GCF_900115975.1:WP_092482509.1 206 CHLAHEGAKVVHPRAVEIAMQKSIPLRVRSTFSDSPGTLVTNsgevykgtiDITKDRIVTGITYISGIA 274 ******************************************998888777666669************ PP TIGR00656 268 rltvegegmlgkrgilaeifkaLaeeeinvdlisqtesetsislvvdeedvdeakkaLkeesgaaeles 336 ++ v+ + + + ++f aLa ++i++d+i++ + + ++v++ +++a+k+L+++ lcl|NCBI__GCF_900115975.1:WP_092482509.1 275 QFIVRIGATGEGLKQQRRMFRALALAGISIDFINILP--EVVLFTVKDDVAEKAVKVLENTGYMS---- 337 *****777788899999********************..889999***************96333.... PP TIGR00656 337 leveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 ev ++a+vs+vgag++++pGv++ i++al +++i+il++ +s+t+++vlv+ +++ekavr+lh++++ lcl|NCBI__GCF_900115975.1:WP_092482509.1 338 -EVITGCAKVSAVGAGMSGVPGVIADIVEALTKDDIQILQCNDSHTTVWVLVRREEMEKAVRALHRQFK 405 .45668*************************************************************98 PP TIGR00656 406 e 406 + lcl|NCBI__GCF_900115975.1:WP_092482509.1 406 L 406 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (408 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 10.75 // [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