Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013842892.1 DESRU_RS14810 aspartate kinase
Query= BRENDA::P9WPX3 (421 letters) >NCBI__GCF_000215085.1:WP_013842892.1 Length = 404 Score = 400 bits (1029), Expect = e-116 Identities = 208/405 (51%), Positives = 297/405 (73%), Gaps = 9/405 (2%) Query: 3 LVVQKYGGSSVADAERIRRVAERIVATKKQGNDVVVVVSAMGDTTDDLLDLAQQVCPAPP 62 LVV+K+GGSSV D ERI+RVA R+V ++GN VVV VSAMGDTTDDL+ L +QV PP Sbjct: 2 LVVKKFGGSSVGDPERIKRVARRVVEEHQKGNQVVVAVSAMGDTTDDLISLMKQVTNNPP 61 Query: 63 PRELDMLLTAGERISNALVAMAIESLGAHARSFTGSQAGVITTGTHGNAKIIDVTPGRLQ 122 RE+DMLL+ GE+IS AL+AMAI LG+ S TG Q G+ T H AKI+ + GR++ Sbjct: 62 EREMDMLLSTGEQISIALLAMAIRDLGSDVVSLTGGQVGIYTDDVHTKAKILRIETGRVR 121 Query: 123 TALEEGRVVLVAGFQGVSQDTKDVTTLGRGGSDTTAVAMAAALGADVCEIYTDVDGIFSA 182 L +GRVV+VAGFQGV+ D D+TTLGRGGSDTTAVA+AAAL ADVCEI+TDVDG+++ Sbjct: 122 EELNQGRVVVVAGFQGVNPD-GDITTLGRGGSDTTAVALAAALRADVCEIFTDVDGVYTT 180 Query: 183 DPRIVRNARKLDTVTFEEMLEMAACGAKVLMLRCVEYARRHNIPVHVRSSYSDRPGTVVV 242 DPR+V ARKL ++++EMLE+A+ GA+VL R VE A+++ IP+HVR+S++ GT+V Sbjct: 181 DPRVVPEARKLSHISYDEMLELASLGAQVLHPRSVELAKQYGIPLHVRTSFNHMEGTIV- 239 Query: 243 GSIKDVP-MED-PILTGVAHDRSEAKVTIVGLPDIPGYAAKVFRAVADADVNIDMVLQNV 300 ++ P ME+ P+++GVAHD + AK+ + +PD PG A +F+A++ +N+DM++Q Sbjct: 240 ---EEAPDMENAPVVSGVAHDYNVAKIGLFDVPDKPGVAKTIFKALSKQSINVDMIIQ-- 294 Query: 301 SKVEDGKTDITFTCSRDVGPAAVEKLDSLRNEIGFSQLLYDDHIGKVSLIGAGMRSHPGV 360 S + + DI FT + D A++ ++++++E+GF +D+ + KVS++GAGM SHPGV Sbjct: 295 SAMRNNMNDIGFTTTIDDLRKALQIIEAIQDEVGFKGYTHDEDVAKVSIVGAGMISHPGV 354 Query: 361 TATFCEALAAVGVNIELISTSEIRISVLCRDTELDKAVVALHEAF 405 A EALA G+N+E+I+TSEI++S + + + +KAV ALH+ F Sbjct: 355 AADMFEALADEGINLEMITTSEIKVSCVIKRADTEKAVKALHKKF 399 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: 448 Number of extensions: 24 Number of successful extensions: 7 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: 404 Length adjustment: 31 Effective length of query: 390 Effective length of database: 373 Effective search space: 145470 Effective search space used: 145470 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_013842892.1 DESRU_RS14810 (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.373300.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-145 470.7 9.9 2.4e-145 470.5 9.9 1.0 1 NCBI__GCF_000215085.1:WP_013842892.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000215085.1:WP_013842892.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 470.5 9.9 2.4e-145 2.4e-145 2 405 .. 1 400 [. 1 402 [. 0.99 Alignments for each domain: == domain 1 score: 470.5 bits; conditional E-value: 2.4e-145 TIGR00656 2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerde 74 +l+V+KFGG+svg+ erik++a++v++e ++g++vvV vSAm+ +td l++l+ +++ +++ +re+d+ NCBI__GCF_000215085.1:WP_013842892.1 1 MLVVKKFGGSSVGDPERIKRVARRVVEEHQKGNQVVVAVSAMGDTTDDLISLM------KQVTNNPPEREMDM 67 79**************************************************9......8************* PP TIGR00656 75 lvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGat 147 l+s+GE++s+all++a+r+lg + ++l+g++ gi Tdd +++Aki +++t r+ e L++g +vvvaGF+G + NCBI__GCF_000215085.1:WP_013842892.1 68 LLSTGEQISIALLAMAIRDLGSDVVSLTGGQVGIYTDDVHTKAKILRIET-GRVREELNQGRVVVVAGFQGVN 139 **************************************************.********************** PP TIGR00656 148 eeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhp 220 +G+iTtLGRGGSD+tA++laaal Ad +ei+TDV+GvyttDPrvv+ea+k+ +isy+E+lelA+lGa+vlhp NCBI__GCF_000215085.1:WP_013842892.1 140 PDGDITTLGRGGSDTTAVALAAALRADVCEIFTDVDGVYTTDPRVVPEARKLSHISYDEMLELASLGAQVLHP 212 ************************************************************************* PP TIGR00656 221 ralelaveakvpilvrsskekeegTlitn..kkensslvkaialeknvarltvegegmlgkrgilaeifkaLa 291 r++ela+++++p+ vr s+++ egT +++ ++en ++v+++a++ nva++ ++ ++ +k+g++ +ifkaL+ NCBI__GCF_000215085.1:WP_013842892.1 213 RSVELAKQYGIPLHVRTSFNHMEGTIVEEapDMENAPVVSGVAHDYNVAKIGLF--DVPDKPGVAKTIFKALS 283 ****************************99999*99******************..***************** PP TIGR00656 292 eeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvas 361 +++invd+i+q+ + ++i ++ d+ +a +++++ +++++++ +ed+a+vsivgag++++pGva+ NCBI__GCF_000215085.1:WP_013842892.1 284 KQSINVDMIIQSAMRnnmNDIGFTTTIDDLRKALQIIEAIQDEVGFKGYTHDEDVAKVSIVGAGMISHPGVAA 356 ************99888899***************************************************** PP TIGR00656 362 eifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 +f+al++++in+ mi++se+k+s +++ +d+ekav++lh+k++ NCBI__GCF_000215085.1:WP_013842892.1 357 DMFEALADEGINLEMITTSEIKVSCVIKRADTEKAVKALHKKFV 400 ******************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (404 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: 00:00:00.00 # Mc/sec: 17.73 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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