Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_015819433.1 TERTU_RS12405 aspartate kinase
Query= SwissProt::A4VJB4 (412 letters) >NCBI__GCF_000023025.1:WP_015819433.1 Length = 406 Score = 601 bits (1549), Expect = e-176 Identities = 311/405 (76%), Positives = 349/405 (86%), Gaps = 1/405 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60 M+LIVQKFGGTSVGT E+I+ VAEKV FRD G D+VVVVSAMSGETNRLI LA + E+ Sbjct: 1 MSLIVQKFGGTSVGTTEKIKAVAEKVAGFRDQGHDMVVVVSAMSGETNRLISLASDVQEK 60 Query: 61 PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120 P PRE+DV+VSTGEQVTIALL MAL +G A SYTG QV+ILTDSAH KARI ID Sbjct: 61 PDPREMDVLVSTGEQVTIALLCMALKAKGYDARSYTGGQVKILTDSAHMKARIQNIDVDN 120 Query: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 ++ D+ AGRVVVVAGFQGVDE GNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT Sbjct: 121 MRADLDAGRVVVVAGFQGVDEAGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 Query: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLI 240 TDPRVV A+RLDKITFEEMLEMAS GSKVLQIR+VEFAGKY VPLRVL SF +GPGTLI Sbjct: 181 TDPRVVDSARRLDKITFEEMLEMASQGSKVLQIRSVEFAGKYKVPLRVLSSFVDGPGTLI 240 Query: 241 TLDEE-ESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 299 TLDEE E+MEQP++SGIAFNRDEAK++I GVPD PGVA K+L PI AN+E+D+IVQNVA Sbjct: 241 TLDEENETMEQPVVSGIAFNRDEAKISILGVPDAPGVASKVLSPIGDANIEIDVIVQNVA 300 Query: 300 HDNTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVASR 359 DNT TFTVH+ND A VL G+A ++GARE +GD IAK+SIVGVGMRSHAGVAS+ Sbjct: 301 ADNTNAITFTVHKNDLEKAKSVLAGVAEDLGAREVVGDDKIAKISIVGVGMRSHAGVASK 360 Query: 360 MFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404 MF+ LA ENINIQMI+TSEIK++V+IEEKYLELAVRALH+AFELD Sbjct: 361 MFKTLANENINIQMITTSEIKITVIIEEKYLELAVRALHSAFELD 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: 573 Number of extensions: 21 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: 406 Length adjustment: 31 Effective length of query: 381 Effective length of database: 375 Effective search space: 142875 Effective search space used: 142875 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_015819433.1 TERTU_RS12405 (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.28953.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-138 446.4 15.8 5.6e-138 446.2 15.8 1.0 1 lcl|NCBI__GCF_000023025.1:WP_015819433.1 TERTU_RS12405 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023025.1:WP_015819433.1 TERTU_RS12405 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 446.2 15.8 5.6e-138 5.6e-138 1 406 [. 1 404 [. 1 405 [. 0.97 Alignments for each domain: == domain 1 score: 446.2 bits; conditional E-value: 5.6e-138 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 ++liVqKFGGtsvg +e+ik++a++v +g+++vVVvSAms++t++l++la + +++++ p lcl|NCBI__GCF_000023025.1:WP_015819433.1 1 MSLIVQKFGGTSVGTTEKIKAVAEKVAGFRDQGHDMVVVVSAMSGETNRLISLA------SDVQEKPDP 63 679***************************************************......89******* PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re+d lvs+GE++++all +al+++g++a++++g++ ilTd+ + +A+i+++++ ++ L+ g +v lcl|NCBI__GCF_000023025.1:WP_015819433.1 64 REMDVLVSTGEQVTIALLCMALKAKGYDARSYTGGQVKILTDSAHMKARIQNIDV-DNMRADLDAGRVV 131 *******************************************************.9************ PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vvaGF+G +e G+iTtLGRGGSD+t ++laaalkAd+++iyTDV+GvyttDPrvv++a+++dki++eE+ lcl|NCBI__GCF_000023025.1:WP_015819433.1 132 VVAGFQGVDEAGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTDPRVVDSARRLDKITFEEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn.....kkensslvkaialeknvarltv 271 le+A++G kvl+ r++e+a ++kvp++v ss+ gTlit ++e+ ++v++ia++++ a++++ lcl|NCBI__GCF_000023025.1:WP_015819433.1 201 LEMASQGSKVLQIRSVEFAGKYKVPLRVLSSFVDGPGTLITLdeeneTMEQ-PVVSGIAFNRDEAKISI 268 *****************************************9555444444.5**************** PP TIGR00656 272 egegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesl 337 g+ + +g+++++ + +++++i +d+i+q + ++i+++v+++d+++ak++L + ++++ +++ lcl|NCBI__GCF_000023025.1:WP_015819433.1 269 L--GVPDAPGVASKVLSPIGDANIEIDVIVQNVAAdntNAITFTVHKNDLEKAKSVLAGVAEDLGAREV 335 *..9***************************988778899***************************** PP TIGR00656 338 eveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 + ++a++sivg+g++++ Gvas++fk l+++nini mi++se+ki+v+++ek++e avr+lh+++e+ lcl|NCBI__GCF_000023025.1:WP_015819433.1 336 VGDDKIAKISIVGVGMRSHAGVASKMFKTLANENINIQMITTSEIKITVIIEEKYLELAVRALHSAFEL 404 *******************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (406 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7.89 // [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