Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_004316701.1 C665_RS14355 aspartate kinase
Query= SwissProt::A4VJB4 (412 letters) >NCBI__GCF_000310185.1:WP_004316701.1 Length = 410 Score = 530 bits (1364), Expect = e-155 Identities = 277/409 (67%), Positives = 330/409 (80%), Gaps = 2/409 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60 MALIVQK+GGTSVGT ER+ VA +V FR G +VVVVSAMSGETNRLI LA+ ++ Sbjct: 1 MALIVQKYGGTSVGTPERMRSVARRVANFRAQGHRVVVVVSAMSGETNRLIALARAVAPS 60 Query: 61 PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120 P RELDV+VSTGEQV+I LL MAL GVPA SYTG QVRILTDS HT+ARIL IDA Sbjct: 61 PRTRELDVVVSTGEQVSIGLLCMALDDLGVPARSYTGAQVRILTDSTHTRARILDIDAAP 120 Query: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 I++D+ AG VVVVAGFQGVD GNITTLGRGGSDTT VALAAAL+ADECQIYTDVDGVYT Sbjct: 121 IRKDLDAGGVVVVAGFQGVDAHGNITTLGRGGSDTTAVALAAALEADECQIYTDVDGVYT 180 Query: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGP--GT 238 DPR+V +A++LD + FEEMLE+ASLGSKVLQIRAVEFA KY V LRVL SF+E P GT Sbjct: 181 ADPRIVPEARKLDAVRFEEMLELASLGSKVLQIRAVEFAAKYKVKLRVLSSFEEDPGEGT 240 Query: 239 LITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNV 298 IT++E +ME+P+ISGIAF RDEAKLT+ GVPD PG+A++ILGPI+ A+++VDMI+QN Sbjct: 241 FITVEESSNMERPVISGIAFVRDEAKLTLTGVPDRPGIAYQILGPIADADIDVDMIIQNA 300 Query: 299 AHDNTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVAS 358 D +TD +FTV R D A++VL+G+ A +GAR D + KVS+VGVGMRSH GVA+ Sbjct: 301 PRDGSTDLSFTVARADLARAVKVLEGVQAHVGARSIESDDTMCKVSVVGVGMRSHPGVAA 360 Query: 359 RMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPA 407 +MF LA+E INIQMI+TSEI++SV I+EK+LE AVRALH A+ LD A Sbjct: 361 KMFRTLAEEGINIQMITTSEIRISVAIDEKHLERAVRALHKAYGLDVAA 409 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: 525 Number of extensions: 12 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: 410 Length adjustment: 31 Effective length of query: 381 Effective length of database: 379 Effective search space: 144399 Effective search space used: 144399 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_004316701.1 C665_RS14355 (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.11694.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-133 431.2 6.2 2.3e-133 431.0 6.2 1.0 1 lcl|NCBI__GCF_000310185.1:WP_004316701.1 C665_RS14355 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000310185.1:WP_004316701.1 C665_RS14355 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 431.0 6.2 2.3e-133 2.3e-133 1 405 [. 1 404 [. 1 406 [. 0.97 Alignments for each domain: == domain 1 score: 431.0 bits; conditional E-value: 2.3e-133 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + liVqK+GGtsvg er++ +a++v + +g++vvVVvSAms++t++l++la +a+ + lcl|NCBI__GCF_000310185.1:WP_004316701.1 1 MALIVQKYGGTSVGTPERMRSVARRVANFRAQGHRVVVVVSAMSGETNRLIALA------RAVAPSPRT 63 579***************************************************......899999*** PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re d +vs+GE++s+ ll +al +lgv a++++g++ ilTd+++++A+i +++ + + L+ g +v lcl|NCBI__GCF_000310185.1:WP_004316701.1 64 RELDVVVSTGEQVSIGLLCMALDDLGVPARSYTGAQVRILTDSTHTRARILDIDA-APIRKDLDAGGVV 131 *******************************************************.9************ PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vvaGF+G + +G+iTtLGRGGSD+tA++laaal+Ad+++iyTDV+Gvyt+DPr+v+ea+k+d + +eE+ lcl|NCBI__GCF_000310185.1:WP_004316701.1 132 VVAGFQGVDAHGNITTLGRGGSDTTAVALAAALEADECQIYTDVDGVYTADPRIVPEARKLDAVRFEEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskeke..egTlitn....kkensslvkaialeknvarlt 270 lelA+lG kvl+ ra+e+a ++kv+++v ss+e++ egT it ++e + ++++ia+ ++ a+lt lcl|NCBI__GCF_000310185.1:WP_004316701.1 201 LELASLGSKVLQIRAVEFAAKYKVKLRVLSSFEEDpgEGTFITVeessNMERP-VISGIAFVRDEAKLT 268 ********************************998889****98665555555.*************** PP TIGR00656 271 vegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaeles 336 ++ g+ +++gi+ +i + +a+++i+vd+i+q + t++s++v++ d+ +a+k+L+ ++ ++ +s lcl|NCBI__GCF_000310185.1:WP_004316701.1 269 LT--GVPDRPGIAYQILGPIADADIDVDMIIQNAPRdgsTDLSFTVARADLARAVKVLEGVQAHVGARS 335 **..9***************************9877888****************************** PP TIGR00656 337 leveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 +e + +++vs+vg+g++++pGva+++f l+e++ini mi++se++isv +dek +e+avr+lh+++ lcl|NCBI__GCF_000310185.1:WP_004316701.1 336 IESDDTMCKVSVVGVGMRSHPGVAAKMFRTLAEEGINIQMITTSEIRISVAIDEKHLERAVRALHKAYG 404 *****************************************************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (410 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: 00:00:00.01 # Mc/sec: 10.70 // [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