Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_089322638.1 CHB58_RS03055 aspartate kinase
Query= SwissProt::Q88EI9 (411 letters) >NCBI__GCF_900188395.1:WP_089322638.1 Length = 403 Score = 468 bits (1205), Expect = e-136 Identities = 242/402 (60%), Positives = 309/402 (76%), Gaps = 1/402 (0%) Query: 3 LIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQPV 62 L+VQKFGGTS+GSI+RI+ VA +V + + G+D+VVV+SAMSGET+RLI L K+IT +P Sbjct: 2 LVVQKFGGTSMGSIDRIKHVASRVIEEKSKGNDVVVVVSAMSGETDRLIQLVKEITSEPS 61 Query: 63 PRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQKIR 122 R++D +V+TGEQV+ LL++ L G AVS TG Q I TD + KARIL+ID +IR Sbjct: 62 ERDMDFVVATGEQVSAGLLSITLNSLGYDAVSLTGWQAGIKTDKAFTKARILEIDTDRIR 121 Query: 123 ADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTD 182 LK G++VV+ GFQG+ E G ITTLGRGGSDT+ VA+AAALKAD C IYTDVDGVYT D Sbjct: 122 NYLKNGKIVVITGFQGITEEGDITTLGRGGSDTSAVAIAAALKADRCDIYTDVDGVYTAD 181 Query: 183 PRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLITI 242 PR+V AR+++ I++EEMLE+ASLG+KVLQIRSVEFA KY VPLRV +F GTLI Sbjct: 182 PRIVENARKIDVISYEEMLELASLGAKVLQIRSVEFAMKYKVPLRVRSTFTTDEGTLIK- 240 Query: 243 DEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAHDN 302 +E+ ME+ ++ GIA N++EA++T+ VPD PG+A K+ ++ +NI VDMIVQNV+ D Sbjct: 241 EEDAEMEKVVVRGIAHNKNEARITVERVPDKPGIAAKLFEALAEANIPVDMIVQNVSVDG 300 Query: 303 TTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASCMFE 362 TD +FTV +N+ KAQ + E A EIGAR VI D KIAKVSIVG+GMR+HAGVA +F+ Sbjct: 301 YTDISFTVDKNDISKAQKITEKVAEEIGARGVITDDKIAKVSIVGLGMRNHAGVAGKVFD 360 Query: 363 ALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404 LAK INI MISTSEIK+S ++EEK+ ELAVR LH AF+LD Sbjct: 361 TLAKYGINILMISTSEIKISCIIEEKFTELAVRVLHEAFNLD 402 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: 474 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: 411 Length of database: 403 Length adjustment: 31 Effective length of query: 380 Effective length of database: 372 Effective search space: 141360 Effective search space used: 141360 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_089322638.1 CHB58_RS03055 (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.19248.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-151 489.8 16.8 3.8e-151 489.6 16.8 1.0 1 lcl|NCBI__GCF_900188395.1:WP_089322638.1 CHB58_RS03055 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900188395.1:WP_089322638.1 CHB58_RS03055 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 489.6 16.8 3.8e-151 3.8e-151 2 406 .. 1 401 [. 1 402 [. 0.98 Alignments for each domain: == domain 1 score: 489.6 bits; conditional E-value: 3.8e-151 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 +l+VqKFGGts+gs++rik++a++v++e+++g++vvVVvSAms++td+l++l+ + i +e+s+r lcl|NCBI__GCF_900188395.1:WP_089322638.1 1 MLVVQKFGGTSMGSIDRIKHVASRVIEEKSKGNDVVVVVSAMSGETDRLIQLV------KEITSEPSER 63 79***************************************************......899******* PP TIGR00656 71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139 +d +v++GE++s+ lls l+ lg++a++l+g++agi Td+ f++A+i e++t r+ + L++g+ivv lcl|NCBI__GCF_900188395.1:WP_089322638.1 64 DMDFVVATGEQVSAGLLSITLNSLGYDAVSLTGWQAGIKTDKAFTKARILEIDT-DRIRNYLKNGKIVV 131 ******************************************************.************** PP TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208 ++GF+G teeG+iTtLGRGGSD++A+++aaalkAdr++iyTDV+Gvyt+DPr+ve+a+kid isyeE+l lcl|NCBI__GCF_900188395.1:WP_089322638.1 132 ITGFQGITEEGDITTLGRGGSDTSAVAIAAALKADRCDIYTDVDGVYTADPRIVENARKIDVISYEEML 200 ********************************************************************* PP TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltvege 274 elA+lGakvl+ r++e+a+++kvp++vrs++ ++egTli + ++e+ +v++ia++kn ar+tve lcl|NCBI__GCF_900188395.1:WP_089322638.1 201 ELASLGAKVLQIRSVEFAMKYKVPLRVRSTFTTDEGTLIKEedaEMEK-VVVRGIAHNKNEARITVE-- 266 ***************************************997544444.59****************.. PP TIGR00656 275 gmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleve 340 + +k+gi+a++f+aLae++i vd+i+q s t+is++vd++d+ +a+k+ +++ ++++ + + ++ lcl|NCBI__GCF_900188395.1:WP_089322638.1 267 RVPDKPGIAAKLFEALAEANIPVDMIVQNVSVdgyTDISFTVDKNDISKAQKITEKVAEEIGARGVITD 335 ****************************9987889********************************** PP TIGR00656 341 edlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 ++a+vsivg g++++ Gva+++f l++ +inilmis+se+kis +++ek +e avr lhe++ + lcl|NCBI__GCF_900188395.1:WP_089322638.1 336 DKIAKVSIVGLGMRNHAGVAGKVFDTLAKYGINILMISTSEIKISCIIEEKFTELAVRVLHEAFNL 401 ***************************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (403 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: 00:00:00.02 # Mc/sec: 7.08 // [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