Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_029913072.1 P166_RS0111875 aspartate kinase
Query= SwissProt::A4VJB4 (412 letters) >NCBI__GCF_000711315.1:WP_029913072.1 Length = 408 Score = 533 bits (1373), Expect = e-156 Identities = 277/407 (68%), Positives = 336/407 (82%), Gaps = 3/407 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60 MALIVQK+GGTSVG+VERI+ VA KV KF D G +VV VSAMSGETNRL+ LAK++ ++ Sbjct: 1 MALIVQKYGGTSVGSVERIKNVANKVAKFVDEGHQVVVAVSAMSGETNRLMALAKEMQDE 60 Query: 61 PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120 P RELDV+++TGEQVTIALL+MAL ++G A+SYTG QV I T++ H KARI IDA + Sbjct: 61 PSRRELDVLLTTGEQVTIALLSMALQQKGYDAISYTGWQVPIHTNNVHFKARIEDIDADK 120 Query: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 + + G+VVVVAGFQGV +G+ITTLGRGGSDTT VALAAALKADECQIYTDVDGVYT Sbjct: 121 MMAQLNQGKVVVVAGFQGVTPEGDITTLGRGGSDTTAVALAAALKADECQIYTDVDGVYT 180 Query: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLI 240 TDPRVV +A+RLD IT++EMLE+ASLG+KVLQIR+VEFA KY VPLRVL S Q+G GTL+ Sbjct: 181 TDPRVVPEAKRLDVITYDEMLELASLGAKVLQIRSVEFASKYKVPLRVLSSLQDGGGTLL 240 Query: 241 TLDEE---ESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQN 297 +E+ ME+P+ISGIAF+RDEAKL I GVPD PGVA+KILGPIS AN+E+DMI+QN Sbjct: 241 ISEEDFEGLGMEKPLISGIAFSRDEAKLMILGVPDKPGVAYKILGPISDANIEIDMIIQN 300 Query: 298 VAHDNTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVA 357 D TTDFTFTV RND N A +++ IA+E+GARE + D I K+S+VGVGM+SH+G+A Sbjct: 301 QGIDGTTDFTFTVARNDLNMAKDIIKKIASELGARETLCDDTIVKISMVGVGMKSHSGIA 360 Query: 358 SRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404 S MF+ LA NINIQMI T+EIK+SVVI+E+YLE AV+ALH AFELD Sbjct: 361 STMFKTLADNNINIQMIGTTEIKISVVIDEQYLETAVKALHQAFELD 407 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: 504 Number of extensions: 9 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: 408 Length adjustment: 31 Effective length of query: 381 Effective length of database: 377 Effective search space: 143637 Effective search space used: 143637 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_029913072.1 P166_RS0111875 (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.1172330.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-139 451.7 10.1 1.4e-139 451.5 10.1 1.0 1 NCBI__GCF_000711315.1:WP_029913072.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000711315.1:WP_029913072.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 451.5 10.1 1.4e-139 1.4e-139 1 406 [. 1 406 [. 1 407 [. 0.98 Alignments for each domain: == domain 1 score: 451.5 bits; conditional E-value: 1.4e-139 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 + liVqK+GGtsvgs+erik++a++v k + eg++vvV vSAms++t++l++la + ++de+s+re d NCBI__GCF_000711315.1:WP_029913072.1 1 MALIVQKYGGTSVGSVERIKNVANKVAKFVDEGHQVVVAVSAMSGETNRLMALA------KEMQDEPSRRELD 67 579***************************************************......9************ PP TIGR00656 74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146 l+ +GE++++alls+al+++g++a++++g++ +i T++ + +A+i++++ +++ +L++g++vvvaGF+G NCBI__GCF_000711315.1:WP_029913072.1 68 VLLTTGEQVTIALLSMALQQKGYDAISYTGWQVPIHTNNVHFKARIEDIDA-DKMMAQLNQGKVVVVAGFQGV 139 ***************************************************.99******************* PP TIGR00656 147 teeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlh 219 t eG+iTtLGRGGSD+tA++laaalkAd+++iyTDV+GvyttDPrvv+eak++d i+y+E+lelA+lGakvl+ NCBI__GCF_000711315.1:WP_029913072.1 140 TPEGDITTLGRGGSDTTAVALAAALKADECQIYTDVDGVYTTDPRVVPEAKRLDVITYDEMLELASLGAKVLQ 212 ************************************************************************* PP TIGR00656 220 pralelaveakvpilvrsskekeegTlitn.......kkensslvkaialeknvarltvegegmlgkrgilae 285 r++e+a ++kvp++v ss + gTl+++ +e++ l+++ia++++ a+l + g+ +k+g++ + NCBI__GCF_000711315.1:WP_029913072.1 213 IRSVEFASKYKVPLRVLSSLQDGGGTLLISeedfeglGMEKP-LISGIAFSRDEAKLMIL--GVPDKPGVAYK 282 ***************************999899998889988.*****************..9********** PP TIGR00656 286 ifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglve 355 i + +++++i +d+i+q ++ t+ +++v+++d++ ak+++k+ +++ ++ + + ++s+vg+g+++ NCBI__GCF_000711315.1:WP_029913072.1 283 ILGPISDANIEIDMIIQNQGIdgtTDFTFTVARNDLNMAKDIIKKIASELGARETLCDDTIVKISMVGVGMKS 355 ******************986778************************************************* PP TIGR00656 356 apGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 ++G+as +fk l+++nini mi++ e+kisv++de+++e av++lh+++e+ NCBI__GCF_000711315.1:WP_029913072.1 356 HSGIASTMFKTLADNNINIQMIGTTEIKISVVIDEQYLETAVKALHQAFEL 406 *************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (408 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: 00:00:00.00 # Mc/sec: 24.47 // [ok]
This GapMind analysis is from Jul 25 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