Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_019556780.1 F612_RS0105640 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_000381085.1:WP_019556780.1 Length = 408 Score = 529 bits (1362), Expect = e-155 Identities = 276/407 (67%), Positives = 337/407 (82%), Gaps = 2/407 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MALIVQK+GGTSVG VERI+ VA+KV +F E G VVVV+SAMSGETNRL +A ++ + Sbjct: 1 MALIVQKYGGTSVGNVERIQNVAKKVAQFVEDGHQVVVVLSAMSGETNRLTMMAKEMQTR 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 P RE+DV+++TGEQVTIALLSMAL +R PAVSYTG QV I+TD A++KARI ID Sbjct: 61 PCKREMDVLLTTGEQVTIALLSMALQQRDCPAVSYTGWQVPIITDDAYSKARIEKIDGQK 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 + L G+VVVVAGFQGV +G+ITTLGRGGSDTT VA+AAAL ADECQIYTDVDGVYT Sbjct: 121 MLEQLALGKVVVVAGFQGVTIDGDITTLGRGGSDTTAVAIAAALNADECQIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240 TDPRVVP+A+RLDKIT++EMLE+ASLG+KVLQIR+VEFA KY VPLRVL S ++G GTLI Sbjct: 181 TDPRVVPEAKRLDKITYDEMLELASLGAKVLQIRSVEFASKYKVPLRVLSSLKDGGGTLI 240 Query: 241 TIDD--EEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQN 298 T ++ ++ MEQP+ISGIAF+RDEAKL I GVPD PGVA++ILGPI+ AN+E+DMI+QN Sbjct: 241 TSEENFKDNEMEQPLISGIAFSRDEAKLMILGVPDKPGVAYQILGPIADANIEIDMIIQN 300 Query: 299 VAHDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVA 358 D TTDFTFT+ R D +ALEIL++TA ++GARE D +I K+S+VGVGM+SHAG+A Sbjct: 301 QGRDGTTDFTFTMSRLDAESALEILQKTANHLGAREVTMDDSIVKISMVGVGMKSHAGIA 360 Query: 359 SRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 405 S MF+ LA INIQMI T+EIK+SVVI+E YLE+AV++LH AFELD Sbjct: 361 STMFKTLADNEINIQMIGTTEIKISVVIDEAYLEIAVQSLHEAFELD 407 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: 495 Number of extensions: 14 Number of successful extensions: 3 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_019556780.1 F612_RS0105640 (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.13416.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-140 452.9 10.7 5.9e-140 452.8 10.7 1.0 1 lcl|NCBI__GCF_000381085.1:WP_019556780.1 F612_RS0105640 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000381085.1:WP_019556780.1 F612_RS0105640 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 452.8 10.7 5.9e-140 5.9e-140 1 406 [. 1 406 [. 1 407 [. 0.99 Alignments for each domain: == domain 1 score: 452.8 bits; conditional E-value: 5.9e-140 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + liVqK+GGtsvg++eri+++ak+v + +++g++vvVV+SAms++t++l +a + ++ + + lcl|NCBI__GCF_000381085.1:WP_019556780.1 1 MALIVQKYGGTSVGNVERIQNVAKKVAQFVEDGHQVVVVLSAMSGETNRLTMMA------KEMQTRPCK 63 579************************************************999......9******** PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re+d l+ +GE++++alls+al++++ a++++g++ +i+Tdd + +A+i++++ +++le+L+ g++v lcl|NCBI__GCF_000381085.1:WP_019556780.1 64 REMDVLLTTGEQVTIALLSMALQQRDCPAVSYTGWQVPIITDDAYSKARIEKIDG-QKMLEQLALGKVV 131 *******************************************************.9************ PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vvaGF+G t +G+iTtLGRGGSD+tA+++aaal+Ad+++iyTDV+GvyttDPrvv+eak++dki+y+E+ lcl|NCBI__GCF_000381085.1:WP_019556780.1 132 VVAGFQGVTIDGDITTLGRGGSDTTAVAIAAALNADECQIYTDVDGVYTTDPRVVPEAKRLDKITYDEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn.......kkensslvkaialeknvarl 269 lelA+lGakvl+ r++e+a ++kvp++v ss + gTlit+ ++e++ l+++ia++++ a+l lcl|NCBI__GCF_000381085.1:WP_019556780.1 201 LELASLGAKVLQIRSVEFASKYKVPLRVLSSLKDGGGTLITSeenfkdnEMEQP-LISGIAFSRDEAKL 268 *****************************************9999998777777.************** PP TIGR00656 270 tvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaele 335 + g+ +k+g++ +i + +a+++i +d+i+q +++ t+ ++++++ d+++a ++L+++ + ++ + lcl|NCBI__GCF_000381085.1:WP_019556780.1 269 MIL--GVPDKPGVAYQILGPIADANIEIDMIIQNQGRdgtTDFTFTMSRLDAESALEILQKTANHLGAR 335 ***..9*****************************99999***************************** PP TIGR00656 336 sleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekl 404 ++ ++ + ++s+vg+g++++ G+as +fk l++++ini mi++ e+kisv++de+++e av++lhe++ lcl|NCBI__GCF_000381085.1:WP_019556780.1 336 EVTMDDSIVKISMVGVGMKSHAGIASTMFKTLADNEINIQMIGTTEIKISVVIDEAYLEIAVQSLHEAF 404 ********************************************************************* PP TIGR00656 405 ee 406 e+ lcl|NCBI__GCF_000381085.1:WP_019556780.1 405 EL 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 6.96 // [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