Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_012991396.1 THAL_RS01760 aspartate kinase
Query= SwissProt::C3JXY0 (413 letters) >NCBI__GCF_000025605.1:WP_012991396.1 Length = 414 Score = 416 bits (1068), Expect = e-121 Identities = 229/401 (57%), Positives = 292/401 (72%), Gaps = 4/401 (0%) Query: 3 LIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGDQQ 62 L+V KFGGTSVGS+ERI+ A KV G +VVV SAM+GET+RLI+LAK I D Sbjct: 4 LLVVKFGGTSVGSIERIKNAARKVIDKVQQGYKVVVVSSAMAGETDRLINLAKEI--DPL 61 Query: 63 PLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDDQK 122 P RELD++VSTGEQ IAL AM LN G PAVS G QV I+TDS HTKAR+ +I Q+ Sbjct: 62 PPERELDMLVSTGEQQAIALFAMVLNSMGYPAVSLCGWQVPIITDSVHTKARVRKIGVQR 121 Query: 123 IRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 182 ++ LK G + VVAGFQGV E ITTLGRGGSD T VALA AL AD C+IYTDV+GV+T Sbjct: 122 LKNILKEGYIPVVAGFQGVTEDWEITTLGRGGSDLTAVALAYALGAD-CEIYTDVEGVFT 180 Query: 183 TDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGTLI 242 DPR+V A+++ +I++EEMLEMASLG+KV+Q R+VEFA KYNV + V SF + GT I Sbjct: 181 ADPRIVPSARKIARISYEEMLEMASLGAKVMQARSVEFAMKYNVRIHVRSSFSDQEGTWI 240 Query: 243 TIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQNVSH 302 + EEE ME+ + I E+++T+ VPD PG+A++I + A+I VDMIVQNVSH Sbjct: 241 -VPEEEVMEKVAVRAITLETKESRITVVRVPDRPGIAYRIFKALGDAHIVVDMIVQNVSH 299 Query: 303 DNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVASRM 362 TD +FTV++ + AE I++ A+EIGA+EVV D +AKVS+VG+GM+S G A++M Sbjct: 300 QGYTDLSFTVNKADAPRAEEIVRKVAQEIGAQEVVRDDNVAKVSVVGIGMKSSYGTAAKM 359 Query: 363 FEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAF 403 FE L K +INI ISTSEIK+S +I++KY ELAVR LH+AF Sbjct: 360 FEVLYKNNINIMAISTSEIKISCLIDQKYGELAVRELHSAF 400 Lambda K H 0.316 0.133 0.357 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: 418 Number of extensions: 17 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: 413 Length of database: 414 Length adjustment: 31 Effective length of query: 382 Effective length of database: 383 Effective search space: 146306 Effective search space used: 146306 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_012991396.1 THAL_RS01760 (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.11274.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-137 444.5 7.6 2.2e-137 444.3 7.6 1.0 1 lcl|NCBI__GCF_000025605.1:WP_012991396.1 THAL_RS01760 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025605.1:WP_012991396.1 THAL_RS01760 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 444.3 7.6 2.2e-137 2.2e-137 2 406 .. 3 402 .. 2 403 .. 0.98 Alignments for each domain: == domain 1 score: 444.3 bits; conditional E-value: 2.2e-137 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 +l V+KFGGtsvgs+erik+aa++v++++++g+kvvVV SAm+++td+l++la + i + +r lcl|NCBI__GCF_000025605.1:WP_012991396.1 3 KLLVVKFGGTSVGSIERIKNAARKVIDKVQQGYKVVVVSSAMAGETDRLINLA------KEIDPLPPER 65 689**************************************************......89999***** PP TIGR00656 71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139 e d+lvs+GE+ ++al++++l+ g+ a++l g++ +i+Td+ +++A+++++ + +rL ++L+eg+i+v lcl|NCBI__GCF_000025605.1:WP_012991396.1 66 ELDMLVSTGEQQAIALFAMVLNSMGYPAVSLCGWQVPIITDSVHTKARVRKIGV-QRLKNILKEGYIPV 133 ******************************************************.************** PP TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208 vaGF+G te+ eiTtLGRGGSDltA++la+al Ad +eiyTDVeGv+t+DPr+v++a+ki++isyeE+l lcl|NCBI__GCF_000025605.1:WP_012991396.1 134 VAGFQGVTEDWEITTLGRGGSDLTAVALAYALGAD-CEIYTDVEGVFTADPRIVPSARKIARISYEEML 201 **********************************8.9******************************** PP TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitnkkens..slvkaialeknvarltvegeg 275 e+A+lGakv++ r++e+a++++v i vrss++ +egT i++++e v+ai+le + +r+tv+ lcl|NCBI__GCF_000025605.1:WP_012991396.1 202 EMASLGAKVMQARSVEFAMKYNVRIHVRSSFSDQEGTWIVPEEEVMekVAVRAITLETKESRITVV--R 268 ****************************************9544333479****************..* PP TIGR00656 276 mlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaeleslevee 341 + +++gi+ +ifkaL++++i vd+i+q s+ t++s++v++ d+++a+++ +++ ++++ +++ + lcl|NCBI__GCF_000025605.1:WP_012991396.1 269 VPDRPGIAYRIFKALGDAHIVVDMIVQNVSHqgyTDLSFTVNKADAPRAEEIVRKVAQEIGAQEVVRDD 337 ***************************9998899*********************************** PP TIGR00656 342 dlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 ++a+vs+vg g+++ G a+++f++l ++nini+ is+se+kis l+d+k+ e avr+lh++++e lcl|NCBI__GCF_000025605.1:WP_012991396.1 338 NVAKVSVVGIGMKSSYGTAAKMFEVLYKNNINIMAISTSEIKISCLIDQKYGELAVRELHSAFVE 402 **************************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (414 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.37 // [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