Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013429768.1 CALKRO_RS03695 aspartate kinase
Query= BRENDA::P08495 (408 letters) >NCBI__GCF_000166775.1:WP_013429768.1 Length = 409 Score = 419 bits (1077), Expect = e-122 Identities = 224/402 (55%), Positives = 297/402 (73%), Gaps = 2/402 (0%) Query: 1 MGLIVQKFGGTSVGSVEKIQNAANRAIAEKQKGHQVVVVVSAMGKSTDELVSLAKAISDQ 60 MG++VQK+GGTSV E+I AA RAI+E +KG++VVVVVSA G +TDEL+ AK I++ Sbjct: 1 MGIVVQKYGGTSVADKERIFRAARRAISEYEKGNKVVVVVSAQGDTTDELIEKAKEINEN 60 Query: 61 PSKREMDMLLATGEQVTISLLSMALQEKGYDAVSYTGWQAGIRTEAIHGNARITDIDTSV 120 PSKREMDMLL+TGEQ++I+L++MA+++ GY +S TGWQAGI+T++ + NARI +ID+ Sbjct: 61 PSKREMDMLLSTGEQISIALMAMAIEKLGYPVISLTGWQAGIKTDSHYSNARIIEIDSER 120 Query: 121 LADQLEKGKIVIVAGFQGMTEDCEITTLGRGGSDTTAVALAAALKADKCDIYTDVPGVFT 180 L +L+K IV+VAGFQG+ + +ITTLGRGGSDTTAVALAAALKADKC+IYTDV GV+T Sbjct: 121 LQRELDKRNIVVVAGFQGINKYDDITTLGRGGSDTTAVALAAALKADKCEIYTDVDGVYT 180 Query: 181 TDPRYVKSARKLEGISYDEMLELANLGAGVLHPRAVEFAKNYQVPLEVRSSTETEAGTLI 240 DPR V +A KL+ ISYDEMLELA LGA VLH R+VE AK Y +PL VRSS GT++ Sbjct: 181 ADPRIVPNASKLKEISYDEMLELATLGAKVLHNRSVELAKKYNIPLVVRSSFNDNEGTIV 240 Query: 241 EEESSMEQNLIVRGIAFEDQITRVTIYGLTSGLTTLSTIFTTLAKRNINVDIIIQTQAED 300 +E +S+E+ L+V G+A + I RV + G+ + IF+ LAK NINVDII+Q+ + Sbjct: 241 KEVNSVEK-LLVSGVACDKDIARVAVIGVENVPGKAFQIFSLLAKENINVDIILQSIGRE 299 Query: 301 KT-GISFSVKTEDADQTVAVLEEYKDALEFEKIETESKLAKVSIVGSGMVSNPGVAAEMF 359 KT ISF+V + QT+ VL + + + I +AKVSIVG+GMV+NPGVAA MF Sbjct: 300 KTKDISFTVSKSNLKQTLDVLTKNLHIIGAKDITYADNVAKVSIVGAGMVNNPGVAAMMF 359 Query: 360 AVLAQKNILIKMVSTSEIKVSTVVSENDMVKAVESLHDAFEL 401 L I I+M+STSEIK+S ++ E D KAV ++HD F+L Sbjct: 360 EALYDAGINIEMISTSEIKISVLIDEKDAEKAVRAIHDKFKL 401 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: 407 Number of extensions: 14 Number of successful extensions: 4 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_013429768.1 CALKRO_RS03695 (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.1916323.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-149 484.0 13.4 2.1e-149 483.8 13.4 1.0 1 NCBI__GCF_000166775.1:WP_013429768.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013429768.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 483.8 13.4 2.1e-149 2.1e-149 1 406 [. 1 401 [. 1 402 [. 0.99 Alignments for each domain: == domain 1 score: 483.8 bits; conditional E-value: 2.1e-149 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 + ++VqK+GGtsv+++eri +aa+++++e+++g+kvvVVvSA + +tdel+e a + i++++s+re+d NCBI__GCF_000166775.1:WP_013429768.1 1 MGIVVQKYGGTSVADKERIFRAARRAISEYEKGNKVVVVVSAQGDTTDELIEKA------KEINENPSKREMD 67 579***************************************************......9************ PP TIGR00656 74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146 +l+s+GE++s+al+++a+++lg+ ++l+g++agi Td+++ nA+i e++ erL L++ ivvvaGF+G NCBI__GCF_000166775.1:WP_013429768.1 68 MLLSTGEQISIALMAMAIEKLGYPVISLTGWQAGIKTDSHYSNARIIEIDS-ERLQRELDKRNIVVVAGFQGI 139 ***************************************************.********************* PP TIGR00656 147 teeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlh 219 ++ +iTtLGRGGSD+tA++laaalkAd++eiyTDV+Gvyt+DPr+v++a k+++isy+E+lelAtlGakvlh NCBI__GCF_000166775.1:WP_013429768.1 140 NKYDDITTLGRGGSDTTAVALAAALKADKCEIYTDVDGVYTADPRIVPNASKLKEISYDEMLELATLGAKVLH 212 ************************************************************************* PP TIGR00656 220 pralelaveakvpilvrsskekeegTlitn.kkensslvkaialeknvarltvegegmlgkrgilaeifkaLa 291 +r++ela+++++p++vrss++ +egT + + ++ ++ lv+++a +k++ar++v g+ + +g + +if++La NCBI__GCF_000166775.1:WP_013429768.1 213 NRSVELAKKYNIPLVVRSSFNDNEGTIVKEvNSVEKLLVSGVACDKDIARVAVI--GVENVPGKAFQIFSLLA 283 ****************************998777778*****************..99*************** PP TIGR00656 292 eeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvas 361 +e+invd+i q+ ++ +is++v++ +++++ ++L++ ++ +++ + ++a+vsivgag+v++pGva+ NCBI__GCF_000166775.1:WP_013429768.1 284 KENINVDIILQSIGRektKDISFTVSKSNLKQTLDVLTKNLHIIGAKDITYADNVAKVSIVGAGMVNNPGVAA 356 *************9989899***************************************************** PP TIGR00656 362 eifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 +f+al + +ini mis+se+kisvl+dekdaekavr++h+k+++ NCBI__GCF_000166775.1:WP_013429768.1 357 MMFEALYDAGINIEMISTSEIKISVLIDEKDAEKAVRAIHDKFKL 401 ******************************************986 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 14.73 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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