Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_089301950.1 CHB84_RS13525 aspartate kinase
Query= BRENDA::P9WPX3 (421 letters) >NCBI__GCF_900188115.1:WP_089301950.1 Length = 421 Score = 597 bits (1538), Expect = e-175 Identities = 298/421 (70%), Positives = 358/421 (85%) Query: 1 MALVVQKYGGSSVADAERIRRVAERIVATKKQGNDVVVVVSAMGDTTDDLLDLAQQVCPA 60 MAL+VQKYGGSS+ A+RI+ VAERIV TKK GNDVVVV SAMGDTTDDLLDLA++V P Sbjct: 1 MALIVQKYGGSSLESADRIKSVAERIVETKKAGNDVVVVCSAMGDTTDDLLDLAERVNPT 60 Query: 61 PPPRELDMLLTAGERISNALVAMAIESLGAHARSFTGSQAGVITTGTHGNAKIIDVTPGR 120 PP RE+DMLLTAGERISNALVAMAI + GA A SF+GSQAGV+TT HGNA+I+DVTPGR Sbjct: 61 PPEREMDMLLTAGERISNALVAMAISAQGAEAWSFSGSQAGVVTTSAHGNARILDVTPGR 120 Query: 121 LQTALEEGRVVLVAGFQGVSQDTKDVTTLGRGGSDTTAVAMAAALGADVCEIYTDVDGIF 180 + AL EG V LVAGFQGVSQDTKDVTTLGRGGSDTTAVA+AAALGAD CEIY+DVDG++ Sbjct: 121 VTEALAEGYVALVAGFQGVSQDTKDVTTLGRGGSDTTAVALAAALGADECEIYSDVDGVY 180 Query: 181 SADPRIVRNARKLDTVTFEEMLEMAACGAKVLMLRCVEYARRHNIPVHVRSSYSDRPGTV 240 SADPRIV +ARK+DT+ +EEMLE+AA G+K+L LR VEYARR+ +P+ VRSSYS +PGT+ Sbjct: 181 SADPRIVSDARKIDTIPYEEMLELAATGSKILHLRAVEYARRYGVPLRVRSSYSSKPGTL 240 Query: 241 VVGSIKDVPMEDPILTGVAHDRSEAKVTIVGLPDIPGYAAKVFRAVADADVNIDMVLQNV 300 V GSI+++P+E ++TGV+HD SEAK+T+ +PD G AAK+FRAVADA+++IDMVLQNV Sbjct: 241 VTGSIEEIPVEQALITGVSHDTSEAKITVTDVPDYEGAAAKIFRAVADAEIDIDMVLQNV 300 Query: 301 SKVEDGKTDITFTCSRDVGPAAVEKLDSLRNEIGFSQLLYDDHIGKVSLIGAGMRSHPGV 360 S+ G TDITFT S+ AV+ L+ +R + GF +L D+++GKVSL+GAGMRSHPGV Sbjct: 301 SRTSSGVTDITFTLSKSNTEEAVKALERVREDAGFDSVLCDENVGKVSLVGAGMRSHPGV 360 Query: 361 TATFCEALAAVGVNIELISTSEIRISVLCRDTELDKAVVALHEAFGLGGDEEATVYAGTG 420 TATFCE+LA GVNIE+I+TSEIRISVL RD ++D AV ALH AFGLGGDEEA VYAG+G Sbjct: 361 TATFCESLANAGVNIEIINTSEIRISVLIRDADVDAAVQALHGAFGLGGDEEAVVYAGSG 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: 575 Number of extensions: 15 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_089301950.1 CHB84_RS13525 (aspartate kinase)
to HMM TIGR00657 (aspartate kinase (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/TIGR00657.hmm # target sequence database: /tmp/gapView.11179.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00657 [M=442] Accession: TIGR00657 Description: asp_kinases: aspartate kinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-138 448.2 7.8 2e-135 438.2 7.8 2.0 1 lcl|NCBI__GCF_900188115.1:WP_089301950.1 CHB84_RS13525 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900188115.1:WP_089301950.1 CHB84_RS13525 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 438.2 7.8 2e-135 2e-135 1 441 [. 1 406 [. 1 407 [. 0.98 Alignments for each domain: == domain 1 score: 438.2 bits; conditional E-value: 2e-135 TIGR00657 1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekelieki 69 maliVqK+GG+S+ +++rik va++++++k+ gn+vvVV+SAm+++Td+L++lae+v++ + lcl|NCBI__GCF_900188115.1:WP_089301950.1 1 MALIVQKYGGSSLESADRIKSVAERIVETKKAGNDVVVVCSAMGDTTDDLLDLAERVNPTP-------- 61 89***********************************************************........ PP TIGR00657 70 rekhlealeelasqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllga 138 + ere+d++l+ GE++S al+a+a++++g++a s++g+ lcl|NCBI__GCF_900188115.1:WP_089301950.1 62 ------------P--------------------EREMDMLLTAGERISNALVAMAISAQGAEAWSFSGS 98 ............7....................8*********************************** PP TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGat.ekgeittLGRGGSDltAallAaalk 206 +ag++t+s++g+A+ + +++ r++++l eg++ +vaGF+G++ +++++ttLGRGGSD+tA++lAaal+ lcl|NCBI__GCF_900188115.1:WP_089301950.1 99 QAGVVTTSAHGNAR-ILDVTPGRVTEALAEGYVALVAGFQGVSqDTKDVTTLGRGGSDTTAVALAAALG 166 **************.**************************9968899********************* PP TIGR00657 207 AdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnp 275 Ade+eiy DVdG+y+aDPriv++Ar++d+i yeE+lELa G+k+Lh r++e+a+r+++p++v+s+++ lcl|NCBI__GCF_900188115.1:WP_089301950.1 167 ADECEIYSDVDGVYSADPRIVSDARKIDTIPYEEMLELAATGSKILHLRAVEYARRYGVPLRVRSSYSS 235 ********************************************************************9 PP TIGR00657 276 eaeGTlivaksk..seeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlilqssset 342 + +GTl++++ + + e+ ++++s+d+++a+++v +++ g +a++f+a+a+a++++d++lq++s+t lcl|NCBI__GCF_900188115.1:WP_089301950.1 236 K-PGTLVTGSIEeiPVEQALITGVSHDTSEAKITVTDVPDYEGAAAKIFRAVADAEIDIDMVLQNVSRT 303 9.********999977779************************************************77 PP TIGR00657 343 s.....isfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaee 406 s i+f+++k+++++a+++l+ v+e++ + +v +++++ +vslvGagm+s+pgv+a+++e La++ lcl|NCBI__GCF_900188115.1:WP_089301950.1 304 SsgvtdITFTLSKSNTEEAVKALE-RVREDAGFDSVLCDENVGKVSLVGAGMRSHPGVTATFCESLANA 371 77899*****************95.7******************************************* PP TIGR00657 407 niniemissseikisvvvdekdaekavealheklv 441 ++nie+i +sei+isv++++ d+++av+alh ++ lcl|NCBI__GCF_900188115.1:WP_089301950.1 372 GVNIEIINTSEIRISVLIRDADVDAAVQALHGAFG 406 *******************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 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: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 3.56 // [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