Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate Ga0059261_2519 Ga0059261_2519 aspartate kinase (EC 2.7.2.4)
Query= BRENDA::O69077 (412 letters) >FitnessBrowser__Korea:Ga0059261_2519 Length = 419 Score = 414 bits (1064), Expect = e-120 Identities = 229/414 (55%), Positives = 291/414 (70%), Gaps = 7/414 (1%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MA IV KFGGTS+ +ERI VA +VK EAG+ V VVVSAM+GET+RL+G + Sbjct: 1 MARIVMKFGGTSMAGIERIRNVANRVKAEWEAGNQVAVVVSAMAGETDRLVGFCREASPL 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 RE D +VS GEQVT LL++AL GVPA S+ G Q+ I T SAH ARI ID T Sbjct: 61 YDLREYDTVVSAGEQVTSGLLAIALQAIGVPARSWLGWQLPIHTSSAHASARIGTIDTTE 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 + A L G V V+ GFQG+ + +TTLGRGGSDT+ VA+AAA+KAD C IYTDVDGVYT Sbjct: 121 LNASLADGNVAVIPGFQGLAEDNRVTTLGRGGSDTSAVAVAAAMKADRCDIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEG----- 235 TDPR+VP+AR+L K+T+EEMLE+AS+G+KVLQ R+V A K V +RVL S ++ Sbjct: 181 TDPRIVPRARKLSKVTYEEMLELASVGAKVLQTRSVGLAMKEGVRVRVLSSLEDNRDEEG 240 Query: 236 -PGTLITIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDM 294 GTLI ++E +E+ +I+GIA +++EAK+T+ VPD PG I P++ A + VDM Sbjct: 241 HRGTLIVGEEEINDVERQLITGIAADKNEAKVTLTNVPDRPGAVGHIFTPLAEAGINVDM 300 Query: 295 IVQNVAH-DNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRS 353 IVQNVAH +TD TFTV R + AL++L+++ A IG I DT +AK+S+VGVGMRS Sbjct: 301 IVQNVAHATGSTDVTFTVPRAELARALDVLEKSKAPIGYDALIHDTKVAKISVVGVGMRS 360 Query: 354 HAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAP 407 HAGVA+ MFE L + INI I+TSEIKVSV+I E ELAVR LHTA+ LDAP Sbjct: 361 HAGVAATMFETLGERRINILAITTSEIKVSVLIHEDETELAVRVLHTAYGLDAP 414 Lambda K H 0.317 0.133 0.362 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: 468 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: 412 Length of database: 419 Length adjustment: 31 Effective length of query: 381 Effective length of database: 388 Effective search space: 147828 Effective search space used: 147828 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 Ga0059261_2519 Ga0059261_2519 (aspartate kinase (EC 2.7.2.4))
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.3828.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-132 427.9 8.1 4.2e-111 358.1 3.5 2.0 2 lcl|FitnessBrowser__Korea:Ga0059261_2519 Ga0059261_2519 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_2519 Ga0059261_2519 aspartate kinase (EC 2.7.2.4) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 72.6 0.1 1.8e-24 1.8e-24 1 59 [. 1 59 [. 1 62 [. 0.97 2 ! 358.1 3.5 4.2e-111 4.2e-111 104 440 .. 64 409 .. 60 411 .. 0.95 Alignments for each domain: == domain 1 score: 72.6 bits; conditional E-value: 1.8e-24 TIGR00657 1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvss 59 ma+iV+KFGGtS++ +eri++va++vk+e e gnqv+VVvSAmag Td+Lv +++++s+ lcl|FitnessBrowser__Korea:Ga0059261_2519 1 MARIVMKFGGTSMAGIERIRNVANRVKAEWEAGNQVAVVVSAMAGETDRLVGFCREASP 59 799****************************************************9986 PP == domain 2 score: 358.1 bits; conditional E-value: 4.2e-111 TIGR00657 104 reldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleegiiv 172 re+d+++s GE++++ lla al++ gv a+s+lg++ +i t+s++ +A+ + +i+t +l++ l g + lcl|FitnessBrowser__Korea:Ga0059261_2519 64 REYDTVVSAGEQVTSGLLAIALQAIGVPARSWLGWQLPIHTSSAHASAR-IGTIDTTELNASLADGNVA 131 89***********************************************.******************* PP TIGR00657 173 vvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEa 241 v+ GF+G+ e++++ttLGRGGSD++A+++Aaa+kAd+++iytDVdG+yt+DPrivp Ar+l +++yeE+ lcl|FitnessBrowser__Korea:Ga0059261_2519 132 VIPGFQGLAEDNRVTTLGRGGSDTSAVAVAAAMKADRCDIYTDVDGVYTTDPRIVPRARKLSKVTYEEM 200 ********************************************************************* PP TIGR00657 242 lELaslGakvLhprtlepamrakipivvkstfnpe.....aeGTlivaksk..seeepavkalsldknq 303 lELas+GakvL+ r++ +am+ +++++v s+ +++ GTliv++++ + e++ +++++ dkn+ lcl|FitnessBrowser__Korea:Ga0059261_2519 201 LELASVGAKVLQTRSVGLAMKEGVRVRVLSSLEDNrdeegHRGTLIVGEEEinDVERQLITGIAADKNE 269 ****************************999876522222469******9998667799********** PP TIGR00657 304 alvsvsgttmkpgilaevfgalaeakvnvdlilqsssets....isfvvdkedadkakellkkkvkeek 368 a+v++ ++++pg + ++f+ laea++nvd+i+q++ + + ++f+v++ ++ +a +l +k k+ lcl|FitnessBrowser__Korea:Ga0059261_2519 270 AKVTLTNVPDRPGAVGHIFTPLAEAGINVDMIVQNVAHATgstdVTFTVPRAELARALDVL-EKSKAPI 337 ***********************************994444678****************8.5699999 PP TIGR00657 369 aleevevekklalvslvGagmksapgvaakifeaLaeeniniemissseikisvvvdekdaekavealh 437 + ++k+a++s+vG gm+s+ gvaa++fe+L e+ ini +i +seik+sv+++e++ e av++lh lcl|FitnessBrowser__Korea:Ga0059261_2519 338 GYDALIHDTKVAKISVVGVGMRSHAGVAATMFETLGERRINILAITTSEIKVSVLIHEDETELAVRVLH 406 ********************************************************************* PP TIGR00657 438 ekl 440 ++ lcl|FitnessBrowser__Korea:Ga0059261_2519 407 TAY 409 998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (419 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: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 3.23 // [ok]
This GapMind analysis is from Apr 09 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