Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_025273527.1 HALAL_RS0108145 aspartate kinase
Query= BRENDA::P9WPX3 (421 letters) >NCBI__GCF_000527155.1:WP_025273527.1 Length = 421 Score = 592 bits (1525), Expect = e-174 Identities = 288/421 (68%), Positives = 364/421 (86%) Query: 1 MALVVQKYGGSSVADAERIRRVAERIVATKKQGNDVVVVVSAMGDTTDDLLDLAQQVCPA 60 MALVVQKYGGSSV +A RI+RVAERIVAT+K GNDVVVVVSAMGDTTD+LLDLA V P Sbjct: 1 MALVVQKYGGSSVENATRIKRVAERIVATRKAGNDVVVVVSAMGDTTDELLDLADDVSPV 60 Query: 61 PPPRELDMLLTAGERISNALVAMAIESLGAHARSFTGSQAGVITTGTHGNAKIIDVTPGR 120 P PRELDML+TAGERIS +L+AMAI LG ARSFTGSQAG++TT HG+A+IIDVTPGR Sbjct: 61 PEPRELDMLVTAGERISMSLLAMAINDLGFQARSFTGSQAGMLTTAAHGDARIIDVTPGR 120 Query: 121 LQTALEEGRVVLVAGFQGVSQDTKDVTTLGRGGSDTTAVAMAAALGADVCEIYTDVDGIF 180 +Q++L+EG + +VAGFQGVS DTK +T+LGRGGSD TAVA+A+A+ ADVCEIY+DVDG++ Sbjct: 121 IQSSLDEGYITIVAGFQGVSPDTKAITSLGRGGSDVTAVALASAMEADVCEIYSDVDGVY 180 Query: 181 SADPRIVRNARKLDTVTFEEMLEMAACGAKVLMLRCVEYARRHNIPVHVRSSYSDRPGTV 240 +ADPRIV +A+KLDTVTFEEMLE+AA GAK+L LR VEYARR+ IP+HVRSSYS +PGT+ Sbjct: 181 TADPRIVPDAKKLDTVTFEEMLELAASGAKILYLRSVEYARRYGIPLHVRSSYSTKPGTI 240 Query: 241 VVGSIKDVPMEDPILTGVAHDRSEAKVTIVGLPDIPGYAAKVFRAVADADVNIDMVLQNV 300 V G ++D+P+E +++GVAHDRSEAKVT+ +PD PG AA +F+ +AD +++IDM++QNV Sbjct: 241 VAGHMEDLPVEQALISGVAHDRSEAKVTVTNVPDKPGAAASIFQIIADGEIDIDMIVQNV 300 Query: 301 SKVEDGKTDITFTCSRDVGPAAVEKLDSLRNEIGFSQLLYDDHIGKVSLIGAGMRSHPGV 360 S +G TDI+FT + G A+E+L ++E+G+ +++YD+++GK+SL+GAGMRSHPGV Sbjct: 301 STTGNGHTDISFTLPKADGRKAIEQLRKRQDELGYGKVIYDENVGKLSLVGAGMRSHPGV 360 Query: 361 TATFCEALAAVGVNIELISTSEIRISVLCRDTELDKAVVALHEAFGLGGDEEATVYAGTG 420 TATFC+AL+ GVNIE+ISTSEIRISV+CRDT+L++AV A+HEAF LGGDEEA VYAGTG Sbjct: 361 TATFCKALSDAGVNIEIISTSEIRISVVCRDTDLNEAVAAVHEAFDLGGDEEAVVYAGTG 420 Query: 421 R 421 R Sbjct: 421 R 421 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: 563 Number of extensions: 13 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: 421 Length of database: 421 Length adjustment: 32 Effective length of query: 389 Effective length of database: 389 Effective search space: 151321 Effective search space used: 151321 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_025273527.1 HALAL_RS0108145 (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.16150.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-127 411.0 6.2 3.1e-127 410.9 6.2 1.0 1 lcl|NCBI__GCF_000527155.1:WP_025273527.1 HALAL_RS0108145 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000527155.1:WP_025273527.1 HALAL_RS0108145 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 410.9 6.2 3.1e-127 3.1e-127 1 405 [. 1 406 [. 1 408 [. 0.97 Alignments for each domain: == domain 1 score: 410.9 bits; conditional E-value: 3.1e-127 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + l+VqK+GG+sv++ rik++a++++++ k g++vvVVvSAm+ +tdel++la + +s + p lcl|NCBI__GCF_000527155.1:WP_025273527.1 1 MALVVQKYGGSSVENATRIKRVAERIVATRKAGNDVVVVVSAMGDTTDELLDLA------DDVSPVPEP 63 579***************************************************......699****** PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 re d+lv GE++s++ll++a+++lg +a++++g +ag+lT + +g+A+i ++ + r+ + L+eg+i lcl|NCBI__GCF_000527155.1:WP_025273527.1 64 RELDMLVTAGERISMSLLAMAINDLGFQARSFTGSQAGMLTTAAHGDARIIDVTP-GRIQSSLDEGYIT 131 *******************************************************.************* PP TIGR00656 139 vvaGFiGateeGe.iTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeE 206 +vaGF+G + + iT LGRGGSD+tA++la+a++Ad +eiy DV+Gvyt+DPr+v++akk+d++++eE lcl|NCBI__GCF_000527155.1:WP_025273527.1 132 IVAGFQGVSPDTKaITSLGRGGSDVTAVALASAMEADVCEIYSDVDGVYTADPRIVPDAKKLDTVTFEE 200 ********9987549****************************************************** PP TIGR00656 207 alelAtlGakvlhpralelaveakvpilvrsskekeegTlitnkkens....slvkaialeknvarltv 271 +lelA Gak+l r++e+a ++++p+ vrss++++ gT + ++e l++++a+++ a++tv lcl|NCBI__GCF_000527155.1:WP_025273527.1 201 MLELAASGAKILYLRSVEYARRYGIPLHVRSSYSTKPGTIVAGHMEDLpveqALISGVAHDRSEAKVTV 269 *******************************************8876556668**************** PP TIGR00656 272 egegmlgkrgilaeifkaLaeeeinvdlisqtese.....tsislvvdeedvdeakkaLkeesgaaele 335 + ++ +k+g +a if+++a+ ei++d+i+q s t+is+++ + d +a + L+++++++++ lcl|NCBI__GCF_000527155.1:WP_025273527.1 270 T--NVPDKPGAAASIFQIIADGEIDIDMIVQNVSTtgnghTDISFTLPKADGRKAIEQLRKRQDELGYG 336 *..**************************99877667777***************************** PP TIGR00656 336 sleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekl 404 ++ ++e++ ++s+vgag++++pGv++ kal++ ++ni is+se++isv+ + d+++av ++he++ lcl|NCBI__GCF_000527155.1:WP_025273527.1 337 KVIYDENVGKLSLVGAGMRSHPGVTATFCKALSDAGVNIEIISTSEIRISVVCRDTDLNEAVAAVHEAF 405 *******************************************************************99 PP TIGR00656 405 e 405 lcl|NCBI__GCF_000527155.1:WP_025273527.1 406 D 406 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (421 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: 00:00:00.02 # Mc/sec: 7.98 // [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