Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_013817476.1 METME_RS03820 aspartate kinase
Query= SwissProt::Q88EI9 (411 letters) >NCBI__GCF_000214665.1:WP_013817476.1 Length = 408 Score = 584 bits (1505), Expect = e-171 Identities = 308/405 (76%), Positives = 349/405 (86%), Gaps = 2/405 (0%) Query: 1 MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60 MAL V KFGGTSVG++ERI+ VAEKVKK +AGD +VVV+SAMSGETNRL+ LAK++ Q Sbjct: 1 MALYVYKFGGTSVGTVERIKAVAEKVKKSHDAGDQIVVVVSAMSGETNRLVALAKEMQVQ 60 Query: 61 PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120 P RELDV++STGEQVTIALL+MAL GV A SYTG QV+ILTDS+H KARI +ID+ Sbjct: 61 PTDRELDVLLSTGEQVTIALLSMALHNVGVDARSYTGAQVKILTDSAHTKARIREIDEAN 120 Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 +RADL GRVVVVAGFQGVDE G+ITTLGRGGSDTTGVALAAALKADEC IYTDVDGVYT Sbjct: 121 MRADLDAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECHIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLI 240 TDPRVVP+ARRLE+ITFEEMLEMASLGSKVLQIRSVEFAGKYNV LRVL SF EG GTLI Sbjct: 181 TDPRVVPKARRLEQITFEEMLEMASLGSKVLQIRSVEFAGKYNVKLRVLSSFMEGNGTLI 240 Query: 241 TIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAH 300 T +E E ME+ +ISGIAFNRDEAKLT+ GVPD PGVA KILGP++A NIEVDMIVQN++ Sbjct: 241 TYEESE-MERALISGIAFNRDEAKLTLTGVPDLPGVASKILGPVAAENIEVDMIVQNISA 299 Query: 301 DNTTDFTFTVHRNEYEKAQSVLENTAREIGAR-EVIGDTKIAKVSIVGVGMRSHAGVASC 359 TTDFTFTV+RN++ +A+SVLE E+G ++IGD I KVSIVGVGMRSHAG+AS Sbjct: 300 HGTTDFTFTVNRNDFARAKSVLEGLRNELGGNTQIIGDNSIVKVSIVGVGMRSHAGIAST 359 Query: 360 MFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404 MF+ LA E INIQMISTSEIK+SVV++EKYLELAVRALH AFDLD Sbjct: 360 MFKTLADEGINIQMISTSEIKISVVVDEKYLELAVRALHKAFDLD 404 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: 561 Number of extensions: 16 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: 411 Length of database: 408 Length adjustment: 31 Effective length of query: 380 Effective length of database: 377 Effective search space: 143260 Effective search space used: 143260 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_013817476.1 METME_RS03820 (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.12393.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-134 434.6 15.0 2.2e-134 434.4 15.0 1.0 1 lcl|NCBI__GCF_000214665.1:WP_013817476.1 METME_RS03820 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214665.1:WP_013817476.1 METME_RS03820 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 434.4 15.0 2.2e-134 2.2e-134 2 406 .. 2 403 .. 1 404 [. 0.97 Alignments for each domain: == domain 1 score: 434.4 bits; conditional E-value: 2.2e-134 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 l V KFGGtsvg +erik++a++v+k+ g++ vVVvSAms++t++lv+la + ++ ++++r lcl|NCBI__GCF_000214665.1:WP_013817476.1 2 ALYVYKFGGTSVGTVERIKAVAEKVKKSHDAGDQIVVVVSAMSGETNRLVALA------KEMQVQPTDR 64 688**************************************************......9********* PP TIGR00656 71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139 e d l+s+GE++++alls+al++ gv+a++++g++ ilTd+ +++A+i+e++ ++ L+ g +vv lcl|NCBI__GCF_000214665.1:WP_013817476.1 65 ELDVLLSTGEQVTIALLSMALHNVGVDARSYTGAQVKILTDSAHTKARIREIDE-ANMRADLDAGRVVV 132 *****************************************************9.99************ PP TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208 vaGF+G +e+G+iTtLGRGGSD+t ++laaalkAd+++iyTDV+GvyttDPrvv++a+++++i++eE+l lcl|NCBI__GCF_000214665.1:WP_013817476.1 133 VAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECHIYTDVDGVYTTDPRVVPKARRLEQITFEEML 201 ********************************************************************* PP TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn.kkens.slvkaialeknvarltvegeg 275 e+A+lG kvl+ r++e+a +++v+++v ss+ + +gTlit ++e++ l+++ia++++ a+lt++ g lcl|NCBI__GCF_000214665.1:WP_013817476.1 202 EMASLGSKVLQIRSVEFAGKYNVKLRVLSSFMEGNGTLITYeESEMErALISGIAFNRDEAKLTLT--G 268 ***************************************9864444446*****************..9 PP TIGR00656 276 mlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaae.lesleve 340 + + +g++++i + +a e+i vd+i+q s t+ +++v+++d +ak++L+ ++++ +++ + lcl|NCBI__GCF_000214665.1:WP_013817476.1 269 VPDLPGVASKILGPVAAENIEVDMIVQNISAhgtTDFTFTVNRNDFARAKSVLEGLRNELGgNTQIIGD 337 ***************************9988888********************99888877899999* PP TIGR00656 341 edlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 + + +vsivg+g++++ G+as +fk l++++ini mis+se+kisv+vdek++e avr+lh+++ + lcl|NCBI__GCF_000214665.1:WP_013817476.1 338 NSIVKVSIVGVGMRSHAGIASTMFKTLADEGINIQMISTSEIKISVVVDEKYLELAVRALHKAFDL 403 **************************************************************9976 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.68 // [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