Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_046009782.1 OLEAN_RS14300 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_000967895.1:WP_046009782.1 Length = 407 Score = 592 bits (1527), Expect = e-174 Identities = 313/406 (77%), Positives = 344/406 (84%), Gaps = 1/406 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MAL VQK+GGTSVGTVERIE VA+KVK F +AG +V+ VSAMSGETNRLIGLAN I Sbjct: 1 MALYVQKYGGTSVGTVERIEHVADKVKSFHDAGHQMVIAVSAMSGETNRLIGLANSISSN 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 P PRE+DV+VSTGEQVTIALL++AL KRGV A S+TG QV I TDSAH KARI ID Sbjct: 61 PTPREMDVLVSTGEQVTIALLAIALQKRGVGAKSFTGWQVAIKTDSAHMKARIEDIDTVA 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 IR L AG V +VAGFQGVDG NITTLGRGGSDTTGVALAAAL ADE QIYTDVDGVYT Sbjct: 121 IRKQLDAGNVCIVAGFQGVDGENNITTLGRGGSDTTGVALAAALGADEAQIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240 TDPRVVP ARR++K+TFEEMLEMASLGSK+LQIRAVEFAGKY VPLRVL SF +GPGTLI Sbjct: 181 TDPRVVPNARRMEKVTFEEMLEMASLGSKILQIRAVEFAGKYKVPLRVLSSFDDGPGTLI 240 Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300 T+ +E+ S+E P+ISGIAFNRDEAK+T+ GVPD PGVA KIL PIS ANVEVDMIVQNVA Sbjct: 241 TM-EEDSSVENPVISGIAFNRDEAKVTVTGVPDIPGVASKILCPISDANVEVDMIVQNVA 299 Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360 D TTDFTFTV RNDY ALEILK TAA +GAR G +I KVS+VGVGMRSHAGVAS+ Sbjct: 300 EDGTTDFTFTVDRNDYAKALEILKNTAAELGARNVSGTDDICKVSMVGVGMRSHAGVASK 359 Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDA 406 MF+ LA ESINIQ I+TSEIK+SVVI EKYLELAVRALHTAF+LDA Sbjct: 360 MFKVLADESINIQAITTSEIKISVVIAEKYLELAVRALHTAFDLDA 405 Lambda K H 0.317 0.133 0.362 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: 537 Number of extensions: 17 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: 412 Length of database: 407 Length adjustment: 31 Effective length of query: 381 Effective length of database: 376 Effective search space: 143256 Effective search space used: 143256 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_046009782.1 OLEAN_RS14300 (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.8158.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-131 424.0 12.9 3.7e-131 423.8 12.9 1.0 1 lcl|NCBI__GCF_000967895.1:WP_046009782.1 OLEAN_RS14300 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000967895.1:WP_046009782.1 OLEAN_RS14300 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 423.8 12.9 3.7e-131 3.7e-131 2 406 .. 2 403 .. 1 404 [. 0.98 Alignments for each domain: == domain 1 score: 423.8 bits; conditional E-value: 3.7e-131 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 l VqK+GGtsvg +eri+++a++v++ g+++v+ vSAms++t++l+ la ++is++++pr lcl|NCBI__GCF_000967895.1:WP_046009782.1 2 ALYVQKYGGTSVGTVERIEHVADKVKSFHDAGHQMVIAVSAMSGETNRLIGLA------NSISSNPTPR 64 688*************************************************9......8********* PP TIGR00656 71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139 e+d lvs+GE++++all+ al+++gv a++++g++ +i Td+ + +A+i++++t + ++L+ g + + lcl|NCBI__GCF_000967895.1:WP_046009782.1 65 EMDVLVSTGEQVTIALLAIALQKRGVGAKSFTGWQVAIKTDSAHMKARIEDIDT-VAIRKQLDAGNVCI 132 ******************************************************.9************* PP TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208 vaGF+G + e +iTtLGRGGSD+t ++laaal Ad+ +iyTDV+GvyttDPrvv++a++++k+++eE+l lcl|NCBI__GCF_000967895.1:WP_046009782.1 133 VAGFQGVDGENNITTLGRGGSDTTGVALAAALGADEAQIYTDVDGVYTTDPRVVPNARRMEKVTFEEML 201 ********************************************************************* PP TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn....kkensslvkaialeknvarltveg 273 e+A+lG k+l+ ra+e+a ++kvp++v ss++ gTlit + en +++++ia++++ a++tv+ lcl|NCBI__GCF_000967895.1:WP_046009782.1 202 EMASLGSKILQIRAVEFAGKYKVPLRVLSSFDDGPGTLITMeedsSVEN-PVISGIAFNRDEAKVTVT- 268 ****************************************966633444.6*****************. PP TIGR00656 274 egmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaeleslev 339 g+ + +g++++i ++++++ vd+i+q +e t+ +++vd++d +a ++Lk++ +++ ++++ lcl|NCBI__GCF_000967895.1:WP_046009782.1 269 -GVPDIPGVASKILCPISDANVEVDMIVQNVAEdgtTDFTFTVDRNDYAKALEILKNTAAELGARNVSG 336 .9*****************************99999********************************* PP TIGR00656 340 eedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 d+++vs+vg+g++++ Gvas++fk+l+++ ini i++se+kisv++ ek++e avr+lh ++ + lcl|NCBI__GCF_000967895.1:WP_046009782.1 337 TDDICKVSMVGVGMRSHAGVASKMFKVLADESINIQAITTSEIKISVVIAEKYLELAVRALHTAFDL 403 ***************************************************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (407 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: 00:00:00.02 # Mc/sec: 7.69 // [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