Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_078430173.1 BK574_RS22615 aspartate kinase
Query= BRENDA::P08495 (408 letters) >NCBI__GCF_002019605.1:WP_078430173.1 Length = 409 Score = 518 bits (1334), Expect = e-151 Identities = 269/404 (66%), Positives = 327/404 (80%), Gaps = 1/404 (0%) Query: 1 MGLIVQKFGGTSVGSVEKIQNAANRAIAEKQKGHQVVVVVSAMGKSTDELVSLAKAISDQ 60 M +IVQK+GGTSVGSVE+I++ A R ++G+QVVVVVSAMGK+TD+LV+LA ISD+ Sbjct: 1 MSIIVQKYGGTSVGSVERIEHVAGRVAKTVEQGNQVVVVVSAMGKTTDQLVTLASEISDK 60 Query: 61 PSKREMDMLLATGEQVTISLLSMALQEKGYDAVSYTGWQAGIRTEAIHGNARITDIDTSV 120 PSKREMDMLL TGEQVTISLL+MALQ++G A+S TGWQAGI TE HG+ARI DI T Sbjct: 61 PSKREMDMLLTTGEQVTISLLAMALQQRGLGAISMTGWQAGIVTEENHGSARIIDIQTEK 120 Query: 121 LADQLEKGKIVIVAGFQGMTEDCEITTLGRGGSDTTAVALAAALKADKCDIYTDVPGVFT 180 + QL G +VIVAGFQG +E EITTLGRGGSDTTAVALAAALKA++CDIYTDV GV+T Sbjct: 121 METQLSLGNVVIVAGFQGSSEHGEITTLGRGGSDTTAVALAAALKAERCDIYTDVTGVYT 180 Query: 181 TDPRYVKSARKLEGISYDEMLELANLGAGVLHPRAVEFAKNYQVPLEVRSSTETEAGTLI 240 TDPRY+ ARKL ISYDEMLE+ANLGAGVLHPRAVEFAKNYQV L V SS E GTLI Sbjct: 181 TDPRYIDEARKLHSISYDEMLEMANLGAGVLHPRAVEFAKNYQVKLMVASSIVEEVGTLI 240 Query: 241 EEESSMEQNLIVRGIAFEDQITRVTIYGLTSGLTTLSTIFTTLAKRNINVDIIIQTQ-AE 299 EEE SMEQNL+VRGIAFE+ +T++T+ GL + + TLS +FT L+ INVDIIIQ Q AE Sbjct: 241 EEEVSMEQNLVVRGIAFENDVTKITVSGLPNEIGTLSDVFTLLSNHGINVDIIIQNQIAE 300 Query: 300 DKTGISFSVKTEDADQTVAVLEEYKDALEFEKIETESKLAKVSIVGSGMVSNPGVAAEMF 359 K+ +SFS ++T++VL+++++ L+FE++ E LAKVSI+GSGM+SNPGVAA+MF Sbjct: 301 QKSSVSFSTSRSSLEETLSVLKKHQEELQFEEVVHEGDLAKVSIIGSGMISNPGVAAQMF 360 Query: 360 AVLAQKNILIKMVSTSEIKVSTVVSENDMVKAVESLHDAFELSK 403 +LA+ ILIKMVSTSEIKVS +V E MV AVE+LH AF+L + Sbjct: 361 KILAEHEILIKMVSTSEIKVSALVEEGVMVPAVEALHRAFQLDE 404 Lambda K H 0.313 0.128 0.337 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: 447 Number of extensions: 15 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: 408 Length of database: 409 Length adjustment: 31 Effective length of query: 377 Effective length of database: 378 Effective search space: 142506 Effective search space used: 142506 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.9 bits)
Align candidate WP_078430173.1 BK574_RS22615 (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.12466.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-147 477.6 20.3 2e-147 477.4 20.3 1.0 1 lcl|NCBI__GCF_002019605.1:WP_078430173.1 BK574_RS22615 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_078430173.1 BK574_RS22615 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 477.4 20.3 2e-147 2e-147 1 406 [. 1 402 [. 1 403 [. 0.98 Alignments for each domain: == domain 1 score: 477.4 bits; conditional E-value: 2e-147 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 +++iVqK+GGtsvgs+eri+++a +v k++++g++vvVVvSAm+k+td+lv+la + isd++s+ lcl|NCBI__GCF_002019605.1:WP_078430173.1 1 MSIIVQKYGGTSVGSVERIEHVAGRVAKTVEQGNQVVVVVSAMGKTTDQLVTLA------SEISDKPSK 63 679***************************************************......89******* PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re+d+l+ +GE+++++ll++al+++g a++++g++agi+T++++g+A+i +++t e+++ +L g +v lcl|NCBI__GCF_002019605.1:WP_078430173.1 64 REMDMLLTTGEQVTISLLAMALQQRGLGAISMTGWQAGIVTEENHGSARIIDIQT-EKMETQLSLGNVV 131 *******************************************************.************* PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 +vaGF+G+ e+GeiTtLGRGGSD+tA++laaalkA+r++iyTDV GvyttDPr+++ea+k+++isy+E+ lcl|NCBI__GCF_002019605.1:WP_078430173.1 132 IVAGFQGSSEHGEITTLGRGGSDTTAVALAAALKAERCDIYTDVTGVYTTDPRYIDEARKLHSISYDEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn..kkensslvkaialeknvarltvege 274 le+A+lGa vlhpra+e+a++++v+++v ss +e gTli++ ++e++ +v++ia+e++v+++tv lcl|NCBI__GCF_002019605.1:WP_078430173.1 201 LEMANLGAGVLHPRAVEFAKNYQVKLMVASSIVEEVGTLIEEevSMEQNLVVRGIAFENDVTKITVS-- 267 ******************************************9999999******************.. PP TIGR00656 275 gmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleve 340 g+ ++ g+l+ +f++L++++invd+i+q + +s+s++ ++ ++e+ ++Lk+ ++++++e++ e lcl|NCBI__GCF_002019605.1:WP_078430173.1 268 GLPNEIGTLSDVFTLLSNHGINVDIIIQNQIAeqkSSVSFSTSRSSLEETLSVLKKHQEELQFEEVVHE 336 99************************9987434679********************************* PP TIGR00656 341 edlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 dla+vsi+g+g++++pGva+++fk l+e++i i+m+s+se+k+s lv+e ++ av++lh+++++ lcl|NCBI__GCF_002019605.1:WP_078430173.1 337 GDLAKVSIIGSGMISNPGVAAQMFKILAEHEILIKMVSTSEIKVSALVEEGVMVPAVEALHRAFQL 402 ***************************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (409 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7.95 // [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