Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011601854.1 FRAAL_RS02615 aspartate kinase
Query= BRENDA::P9WPX3 (421 letters) >NCBI__GCF_000058485.1:WP_011601854.1 Length = 422 Score = 571 bits (1472), Expect = e-167 Identities = 296/422 (70%), Positives = 350/422 (82%), Gaps = 1/422 (0%) Query: 1 MALVVQKYGGSSVADAERIRRVAERIVATKKQGNDVVVVVSAMGDTTDDLLDLAQQVCPA 60 MAL+V K+GGSSVADA+RI+RVAER+V ++ GNDVVVVVSAMGDTTD+LLDLA+QV P Sbjct: 1 MALLVAKFGGSSVADADRIKRVAERVVEARRDGNDVVVVVSAMGDTTDELLDLAEQVSPL 60 Query: 61 PPPRELDMLLTAGERISNALVAMAIESLGAHARSFTGSQAGVITTGTHGNAKIIDVTPGR 120 PP RELDMLLTAGERIS AL+AMAI +LGA ARSFTGSQAGVIT HG A+IIDVTPGR Sbjct: 61 PPARELDMLLTAGERISMALLAMAITTLGAEARSFTGSQAGVITDSVHGKARIIDVTPGR 120 Query: 121 LQTALEEGRVVLVAGFQGVSQDTKDVTTLGRGGSDTTAVAMAAALGADVCEIYTDVDGIF 180 ++ AL+EG + +VAGFQGVSQDTKD+TTLGRGGSDTTAVA+AAAL AD CEIYTDVDG+F Sbjct: 121 IRAALDEGAIAIVAGFQGVSQDTKDITTLGRGGSDTTAVALAAALHADACEIYTDVDGVF 180 Query: 181 SADPRIVRNARKLDTVTFEEMLEMAACGAKVLMLRCVEYARRHNIPVHVRSSYSDRPGTV 240 SADPRIV +AR++DT+++EEMLEMAACGAKVLMLRCVEYARR+++PVHVRSS++ +PGT Sbjct: 181 SADPRIVPDARRIDTISYEEMLEMAACGAKVLMLRCVEYARRYSVPVHVRSSFNAKPGTW 240 Query: 241 VVGSIKDVPMEDPILTGVAHDRSEAKVTIVGLPDIPGYAAKVFRAVADADVNIDMVLQNV 300 V + +E I+ GVAHD SEAKVT+VG PD PG AA VFRAVADADVN+DM++Q Sbjct: 241 VTEIPEAQLVEQAIIRGVAHDVSEAKVTVVGCPDKPGVAAAVFRAVADADVNLDMIVQVG 300 Query: 301 SKVEDGKTDITFTCSRDVGPAAVEKLDSLRNEIGFSQLLYDDHIGKVSLIGAGMRSHPGV 360 S G+TDI+FT + G A+ L ++ EIGF + LYDDHIGK+SLIGAGM+SHPGV Sbjct: 301 SVAGSGRTDISFTLPKTDGRTALTALAKVQGEIGFERTLYDDHIGKLSLIGAGMKSHPGV 360 Query: 361 TATFCEALAAVGVNIELISTSEIRISVLCRDTELDKAVVALHEAFGLGG-DEEATVYAGT 419 +A F ALA GVN+E+ISTSEIRISV+ RDT+L AV A+H AF LG D A VYAGT Sbjct: 361 SARFFGALADAGVNVEIISTSEIRISVVVRDTDLPGAVRAVHGAFELGDPDGGAVVYAGT 420 Query: 420 GR 421 GR Sbjct: 421 GR 422 Lambda K H 0.318 0.134 0.376 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: 571 Number of extensions: 19 Number of successful extensions: 5 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: 421 Length of database: 422 Length adjustment: 32 Effective length of query: 389 Effective length of database: 390 Effective search space: 151710 Effective search space used: 151710 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_011601854.1 FRAAL_RS02615 (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.5822.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-129 417.4 6.3 3.6e-129 417.2 6.3 1.0 1 lcl|NCBI__GCF_000058485.1:WP_011601854.1 FRAAL_RS02615 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000058485.1:WP_011601854.1 FRAAL_RS02615 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 417.2 6.3 3.6e-129 3.6e-129 2 406 .. 2 407 .. 1 408 [. 0.96 Alignments for each domain: == domain 1 score: 417.2 bits; conditional E-value: 3.6e-129 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 l V+KFGG+sv++ +rik++a++v+++ ++g++vvVVvSAm+ +tdel++la e++s + r lcl|NCBI__GCF_000058485.1:WP_011601854.1 2 ALLVAKFGGSSVADADRIKRVAERVVEARRDGNDVVVVVSAMGDTTDELLDLA------EQVSPLPPAR 64 789**************************************************......799******* PP TIGR00656 71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139 e d+l+ GE++s+all++a+ lg +a++++g +ag++Td+ +g+A+i ++ + r+ L+eg i + lcl|NCBI__GCF_000058485.1:WP_011601854.1 65 ELDMLLTAGERISMALLAMAITTLGAEARSFTGSQAGVITDSVHGKARIIDVTP-GRIRAALDEGAIAI 132 ******************************************************.************** PP TIGR00656 140 vaGFiGateeG.eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 vaGF+G ++ +iTtLGRGGSD+tA++laaal+Ad +eiyTDV+Gv+++DPr+v++a++id+isyeE+ lcl|NCBI__GCF_000058485.1:WP_011601854.1 133 VAGFQGVSQDTkDITTLGRGGSDTTAVALAAALHADACEIYTDVDGVFSADPRIVPDARRIDTISYEEM 201 ******9887638******************************************************** PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn....kkensslvkaialeknvarltve 272 le+A Gakvl r +e+a +++vp+ vrss++ + gT +t+ + ++ +++++a++ a++tv+ lcl|NCBI__GCF_000058485.1:WP_011601854.1 202 LEMAACGAKVLMLRCVEYARRYSVPVHVRSSFNAKPGTWVTEipeaQLVEQAIIRGVAHDVSEAKVTVV 270 ******************************************8776555568***************** PP TIGR00656 273 gegmlgkrgilaeifkaLaeeeinvdlisqtese.....tsislvvdeedvdeakkaLkeesgaaeles 336 g +k+g++a +f a+a++++n+d+i+q s t+is+++ ++d +a aL +++g++++e+ lcl|NCBI__GCF_000058485.1:WP_011601854.1 271 --GCPDKPGVAAAVFRAVADADVNLDMIVQVGSVagsgrTDISFTLPKTDGRTALTALAKVQGEIGFER 337 ..99************************99554334444****************************** PP TIGR00656 337 leveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 ++ + ++s++gag++++pGv ++ f al++ ++n+ is+se++isv+v+ d+ avr++h ++e lcl|NCBI__GCF_000058485.1:WP_011601854.1 338 TLYDDHIGKLSLIGAGMKSHPGVSARFFGALADAGVNVEIISTSEIRISVVVRDTDLPGAVRAVHGAFE 406 ******************************************************************998 PP TIGR00656 406 e 406 + lcl|NCBI__GCF_000058485.1:WP_011601854.1 407 L 407 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (422 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: 00:00:00.01 # Mc/sec: 11.75 // [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