Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_029133415.1 A3GO_RS0110840 aspartate kinase
Query= SwissProt::Q88EI9 (411 letters) >NCBI__GCF_000428045.1:WP_029133415.1 Length = 410 Score = 587 bits (1514), Expect = e-172 Identities = 309/411 (75%), Positives = 352/411 (85%), Gaps = 2/411 (0%) Query: 1 MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60 MALIVQK+GGTSVGSIERI+ VAEKV R GD +VVV+SAMSGETNRLI LAK I + Sbjct: 1 MALIVQKYGGTSVGSIERIQAVAEKVAAARNRGDQVVVVVSAMSGETNRLIALAKAIEEH 60 Query: 61 PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120 P RE+DV+VSTGEQVTIALL+MAL K PA SYTG QV ILTDS+H+KARI IDD K Sbjct: 61 PSAREMDVLVSTGEQVTIALLSMALHKIDCPAKSYTGGQVHILTDSAHSKARIQDIDDIK 120 Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 ++ADL G VVVVAGFQG+DE G+ITTLGRGGSDTT VALAAALKADECQI+TDVDGVYT Sbjct: 121 VKADLDAGCVVVVAGFQGIDEQGAITTLGRGGSDTTAVALAAALKADECQIFTDVDGVYT 180 Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLI 240 TDPRV P+ARR+ KI+FEEMLEMASLGSKVLQIR+VEFAGKYNVPLRVL SF+EG GTLI Sbjct: 181 TDPRVEPKARRMSKISFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLSSFEEGEGTLI 240 Query: 241 TIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAH 300 T E++ ME ISGIAFNRDEAKLTI GV D PGVA++ILGPIS +NIEVDMI+QN+ Sbjct: 241 TF-EDKGMENAKISGIAFNRDEAKLTILGVQDQPGVAYRILGPISDANIEVDMIIQNIGQ 299 Query: 301 DNTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASCM 360 D TTDFTFTVHRN+Y+KA S+L + A+++GAREVIGD I K+S+VGVGMRSHAG+AS M Sbjct: 300 DGTTDFTFTVHRNDYDKAVSILNDVAKDLGAREVIGDNAIVKISLVGVGMRSHAGIASSM 359 Query: 361 FEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLDA-PARQG 410 F AL+KE INI+MISTSEIK+SVV++EKYLEL VRALH AFDL A PA+ G Sbjct: 360 FAALSKEGINIRMISTSEIKISVVVDEKYLELGVRALHEAFDLAAEPAKIG 410 Lambda K H 0.316 0.133 0.358 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: 557 Number of extensions: 11 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: 411 Length of database: 410 Length adjustment: 31 Effective length of query: 380 Effective length of database: 379 Effective search space: 144020 Effective search space used: 144020 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_029133415.1 A3GO_RS0110840 (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.11587.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-137 445.0 13.4 1.5e-137 444.9 13.4 1.0 1 lcl|NCBI__GCF_000428045.1:WP_029133415.1 A3GO_RS0110840 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000428045.1:WP_029133415.1 A3GO_RS0110840 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 444.9 13.4 1.5e-137 1.5e-137 1 405 [. 1 401 [. 1 403 [. 0.98 Alignments for each domain: == domain 1 score: 444.9 bits; conditional E-value: 1.5e-137 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + liVqK+GGtsvgs+eri+++a++v ++ ++g++vvVVvSAms++t++l++la +ai++++s lcl|NCBI__GCF_000428045.1:WP_029133415.1 1 MALIVQKYGGTSVGSIERIQAVAEKVAAARNRGDQVVVVVSAMSGETNRLIALA------KAIEEHPSA 63 579***************************************************......9******** PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re+d lvs+GE++++alls+al++ + a++++g++ ilTd+ + +A+i++++ ++ L+ g +v lcl|NCBI__GCF_000428045.1:WP_029133415.1 64 REMDVLVSTGEQVTIALLSMALHKIDCPAKSYTGGQVHILTDSAHSKARIQDIDD-IKVKADLDAGCVV 131 ******************************************************9.9************ PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vvaGF+G +e+G iTtLGRGGSD+tA++laaalkAd+++i+TDV+GvyttDPrv ++a+++ kis+eE+ lcl|NCBI__GCF_000428045.1:WP_029133415.1 132 VVAGFQGIDEQGAITTLGRGGSDTTAVALAAALKADECQIFTDVDGVYTTDPRVEPKARRMSKISFEEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltveg 273 le+A+lG kvl+ ra+e+a +++vp++v ss+e+ egTlit +en +++ia++++ a+lt+ lcl|NCBI__GCF_000428045.1:WP_029133415.1 201 LEMASLGSKVLQIRAVEFAGKYNVPLRVLSSFEEGEGTLITFedkGMENA-KISGIAFNRDEAKLTIL- 267 ****************************************9865455555.9****************. PP TIGR00656 274 egmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaeleslev 339 g+ +++g++ +i + +++++i vd+i+q ++ t+ +++v+++d d+a+++L+++ ++++ +++ lcl|NCBI__GCF_000428045.1:WP_029133415.1 268 -GVQDQPGVAYRILGPISDANIEVDMIIQNIGQdgtTDFTFTVHRNDYDKAVSILNDVAKDLGAREVIG 335 .9***************************9998889********************************* PP TIGR00656 340 eedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 ++ + ++s+vg+g++++ G+as +f+al++++ini mis+se+kisv+vdek++e vr+lhe++ lcl|NCBI__GCF_000428045.1:WP_029133415.1 336 DNAIVKISLVGVGMRSHAGIASSMFAALSKEGINIRMISTSEIKISVVVDEKYLELGVRALHEAFD 401 ***************************************************************996 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7.71 // [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