Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_077277469.1 B1C78_RS02020 aspartate kinase
Query= SwissProt::A4VJB4 (412 letters) >NCBI__GCF_002000365.1:WP_077277469.1 Length = 409 Score = 593 bits (1529), Expect = e-174 Identities = 308/406 (75%), Positives = 353/406 (86%), Gaps = 1/406 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60 MALIVQK+GGTSVG+VERI+ VA+KV +R G D+VVVVSAMSGET+RL+ LA+ I+ + Sbjct: 1 MALIVQKYGGTSVGSVERIQHVADKVLDYRRQGHDVVVVVSAMSGETDRLLGLARDINAR 60 Query: 61 PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120 P RELDV++STGEQVTIALLAMAL RG PA SYTG QV ILTDSAH KARI ID R Sbjct: 61 PEGRELDVLLSTGEQVTIALLAMALEGRGCPARSYTGAQVHILTDSAHNKARIRDIDGAR 120 Query: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 ++RD+ GRVVVVAGFQGVDE GNITTLGRGGSDTT VALAAALKADECQIYTDVDGVYT Sbjct: 121 VRRDLADGRVVVVAGFQGVDEHGNITTLGRGGSDTTAVALAAALKADECQIYTDVDGVYT 180 Query: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLI 240 TDPRV A A+RL++ITFEEMLEMASLGSKVLQIRAVEFAGKY+VPLRVL SFQEGPGTLI Sbjct: 181 TDPRVAANARRLERITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLSSFQEGPGTLI 240 Query: 241 TLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVAH 300 T EE+ MEQ +ISGIAFN++EA++TI GVPD PGVA++ILGPIS AN+EVDMIVQNV Sbjct: 241 TF-EEDGMEQALISGIAFNQNEAQVTILGVPDQPGVAWRILGPISDANIEVDMIVQNVGA 299 Query: 301 DNTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVASRM 360 D TTDFTFTVHRNDY+ AL +LQG+ ++ AR+ GD I K+S+VGVGMRSHAG+AS+M Sbjct: 300 DGTTDFTFTVHRNDYDKALAILQGLPEKLHARQISGDPKIVKISLVGVGMRSHAGIASKM 359 Query: 361 FEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAP 406 FEALA E INI+MISTSEIK+SVV++EKYLEL VRALH AFEL++P Sbjct: 360 FEALAGEGINIRMISTSEIKISVVVDEKYLELGVRALHDAFELESP 405 Lambda K H 0.317 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: 571 Number of extensions: 19 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: 409 Length adjustment: 31 Effective length of query: 381 Effective length of database: 378 Effective search space: 144018 Effective search space used: 144018 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_077277469.1 B1C78_RS02020 (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.6403.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-136 441.6 3.5 1.6e-136 441.4 3.5 1.0 1 lcl|NCBI__GCF_002000365.1:WP_077277469.1 B1C78_RS02020 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002000365.1:WP_077277469.1 B1C78_RS02020 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 441.4 3.5 1.6e-136 1.6e-136 1 406 [. 1 402 [. 1 403 [. 0.98 Alignments for each domain: == domain 1 score: 441.4 bits; conditional E-value: 1.6e-136 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + liVqK+GGtsvgs+eri+++a++vl+ ++g++vvVVvSAms++td+l+ la + i+ + lcl|NCBI__GCF_002000365.1:WP_077277469.1 1 MALIVQKYGGTSVGSVERIQHVADKVLDYRRQGHDVVVVVSAMSGETDRLLGLA------RDINARPEG 63 579***************************************************......89999**** PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re d l+s+GE++++all++al+ +g a++++g++ ilTd+ +++A+i++++ r+ L++g +v lcl|NCBI__GCF_002000365.1:WP_077277469.1 64 RELDVLLSTGEQVTIALLAMALEGRGCPARSYTGAQVHILTDSAHNKARIRDIDG-ARVRRDLADGRVV 131 *******************************************************.9************ PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vvaGF+G +e+G+iTtLGRGGSD+tA++laaalkAd+++iyTDV+GvyttDPrv +a+++++i++eE+ lcl|NCBI__GCF_002000365.1:WP_077277469.1 132 VVAGFQGVDEHGNITTLGRGGSDTTAVALAAALKADECQIYTDVDGVYTTDPRVAANARRLERITFEEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltveg 273 le+A+lG kvl+ ra+e+a +++vp++v ss+++ gTlit +e+ l+++ia+++n a++t+ lcl|NCBI__GCF_002000365.1:WP_077277469.1 201 LEMASLGSKVLQIRAVEFAGKYNVPLRVLSSFQEGPGTLITFeedGMEQA-LISGIAFNQNEAQVTIL- 267 ****************************************9865566666.*****************. PP TIGR00656 274 egmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaeleslev 339 g+ +++g++ +i + +++++i vd+i+q + t+ +++v+++d d+a ++L+ ++++ ++++ lcl|NCBI__GCF_002000365.1:WP_077277469.1 268 -GVPDQPGVAWRILGPISDANIEVDMIVQNVGAdgtTDFTFTVHRNDYDKALAILQGLPEKLHARQISG 335 .9***************************9876777********************************* PP TIGR00656 340 eedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 + ++ ++s+vg+g++++ G+as++f+al+ ++ini mis+se+kisv+vdek++e vr+lh+++e+ lcl|NCBI__GCF_002000365.1:WP_077277469.1 336 DPKIVKISLVGVGMRSHAGIASKMFEALAGEGINIRMISTSEIKISVVVDEKYLELGVRALHDAFEL 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.65 // [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