Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate NP_662905.1 CT2030 bifunctional aspartokinase I/homoserine dehydrogenase I
Query= reanno::Cola:Echvi_2000 (815 letters) >NCBI__GCF_000006985.1:NP_662905.1 Length = 818 Score = 679 bits (1753), Expect = 0.0 Identities = 368/821 (44%), Positives = 521/821 (63%), Gaps = 13/821 (1%) Query: 1 MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60 M++ KFGGSSIA+ I V II ++ + +V SA G VT+ L + A +A + + Sbjct: 1 MRVFKFGGSSIASAAKISNVAGIIRRELKSTPLVVVVSAIGKVTDMLAETAALAGNGDAA 60 Query: 61 YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV 120 Y L+ + H I+++L + S T++ EL D+ HG++L++E S++++ V Sbjct: 61 YRDKLEGIASLHGGIIRELFGTEA-SAEETWLGEMMAELNDVLHGVFLLRELSDKSLALV 119 Query: 121 LSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSHD 180 LS+GERLS I++ + G VDAR ++ TDD AKV+ T KLI + F+S D Sbjct: 120 LSYGERLSCRIVSRYMHVSGTPAECVDARSVIVTDDNHCFAKVDRLATGKLIHERFRSFD 179 Query: 181 DIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVYT 240 + V+TGFI S G T +GR GSD+TA+I AAL AE+V IWTDV G +ADP+ V Sbjct: 180 VLPVVTGFIASAPDGSVTNLGRGGSDFTATILGAALHAEEVWIWTDVDGFYSADPKRVPD 239 Query: 241 AFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDSGEG 300 A IP++SY EAMELSH GAKV+ P +QP MK IP+ IKN+F P++ GTRI ++ Sbjct: 240 ARVIPEISYAEAMELSHAGAKVLHPLAVQPVMKAGIPLRIKNSFNPEKPGTRIGIEAAGA 299 Query: 301 KI----IKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSIC 356 + + G++S++++ +L++ G G+ V G + R F LA + INII ISQASSE SI Sbjct: 300 EALPGTVTGLTSINHVVLLSLSGSGMAGVPGTASRLFTCLARHSINIIFISQASSEQSIS 359 Query: 357 VAIASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQA 416 +AIA AS AK V+EEEF EI+ +D + + ++A++AVVG M +PG S ++F+ Sbjct: 360 LAIAPGQASMAKKVLEEEFAREIEERRIDPVSVRRNLAMVAVVGNKMLGHPGVSAQLFET 419 Query: 417 LGRNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGK 476 LG+N VNV A+AQG++E+NIS VI AD KALN +HE+FFLS KV H+F+VG G I K Sbjct: 420 LGKNGVNVIAVAQGANEMNISLVIDSADENKALNCVHESFFLSMRKV-HVFIVGTGTIAK 478 Query: 477 ALTKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLA----TVGPPDENDEPMDM 532 +L I + LQ+E LD+ + G+AN+R M G DL ++ P + ++ + Sbjct: 479 SLISQIRRHRATLQKELGLDVVVAGLANTRSMCIEPAGIDLEHWHDSLKPRESHE---GI 535 Query: 533 DKFIGTMTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKK 592 ++I + E N N++ VDCTAS+ VA+ Y +L + + + T NK +GP + Y+K+ Sbjct: 536 GQYIRLIQERNLHNTIVVDCTASRQVAECYPALLRANISVATANKLGMAGPWDLYRKIMD 595 Query: 593 LAGQRGVRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFS 652 +F YETNV AGLPVINTL DL SGD + IE VLSG++++IF+EL KG FS Sbjct: 596 ALRSSNAKFLYETNVGAGLPVINTLNDLKNSGDKIVCIEGVLSGTLSFIFNELRKGGRFS 655 Query: 653 EVVAQAKEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAAS 712 E+V +AKE GYTEPDPRDDLSG D ARK+LILGRE G L + DVE QS+VPE S Sbjct: 656 EIVRKAKESGYTEPDPRDDLSGADFARKLLILGRELGYQLEYADVECQSLVPEPLRGEMS 715 Query: 713 VPEFFKKLQKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSD 772 EF +L D + + A ++G + + L +GKAKVGL + E P L GS+ Sbjct: 716 PAEFLDQLSSIDDWYVDEMASAASEGMTIAYTGELRDGKAKVGLKRVPLESPVAGLNGSE 775 Query: 773 NMILFTTERYNDFPMIVRGPGAGADVTAAGVFADIIRLGNY 813 N+++FTTERY P++V+GPGAG +VTA GVFADI+R+ +Y Sbjct: 776 NLVVFTTERYLKTPLVVKGPGAGGEVTAGGVFADILRIASY 816 Lambda K H 0.317 0.134 0.375 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: 1326 Number of extensions: 53 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: 815 Length of database: 818 Length adjustment: 41 Effective length of query: 774 Effective length of database: 777 Effective search space: 601398 Effective search space used: 601398 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: 56 (26.2 bits)
Align candidate NP_662905.1 CT2030 (bifunctional aspartokinase I/homoserine dehydrogenase I)
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.10351.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.3e-125 403.1 0.0 1.2e-124 402.7 0.0 1.1 1 lcl|NCBI__GCF_000006985.1:NP_662905.1 CT2030 bifunctional aspartokinas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000006985.1:NP_662905.1 CT2030 bifunctional aspartokinase I/homoserine dehydrogenase I # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 402.7 0.0 1.2e-124 1.2e-124 5 441 .. 3 460 .. 1 461 [. 0.93 Alignments for each domain: == domain 1 score: 402.7 bits; conditional E-value: 1.2e-124 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhl 74 V KFGG+S++++ +i++va i+ +e ++ + vVVvSA+++vTd L e+a + +++ +++e i + h lcl|NCBI__GCF_000006985.1:NP_662905.1 3 VFKFGGSSIASAAKISNVAGIIRRELKST-PLVVVVSAIGKVTDMLAETAALAGNGDAayRDKLEGIASLHG 73 89************************555.***********************9999989999********9 PP TIGR00657 75 ealeela.sqalk.eklkallekeleevkk.........ereldlilsvGEklSaallaaaleelgvkavsl 135 ++ el +a++ e++ + +el+ v + +++l+l+ls+GE+lS+++++ +++ g +++ lcl|NCBI__GCF_000006985.1:NP_662905.1 74 GIIRELFgTEASAeETWLGEMMAELNDVLHgvfllrelsDKSLALVLSYGERLSCRIVSRYMHVSG-TPAEC 144 9999988755444044555666666666668999********************************.999** PP TIGR00657 136 lgaeagiltdsefgrAkvleeikterlek.lleegiivvvaGFiGatekgeittLGRGGSDltAallAaalk 206 ++a+++i+td+++ Akv + ++ + + + + + ++++vv+GFi++ ++g++t LGRGGSD+tA++l+aal+ lcl|NCBI__GCF_000006985.1:NP_662905.1 145 VDARSVIVTDDNHCFAKVDRLATGKLIHErFRSFDVLPVVTGFIASAPDGSVTNLGRGGSDFTATILGAALH 216 *****************666666665554055556************************************* PP TIGR00657 207 AdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeae 278 A+ev+i+tDVdG y+aDP+ vp+Ar ++eisy+Ea+EL++ GakvLhp +++p+m+a+ip+++k++fnpe++ lcl|NCBI__GCF_000006985.1:NP_662905.1 217 AEEVWIWTDVDGFYSADPKRVPDARVIPEISYAEAMELSHAGAKVLHPLAVQPVMKAGIPLRIKNSFNPEKP 288 ************************************************************************ PP TIGR00657 279 GTlivaksk..seeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisf 346 GT i+ + + + v++l++ ++ +l+s+sg++m+ pg+++++f++la++++n++ i+q sse+sis+ lcl|NCBI__GCF_000006985.1:NP_662905.1 289 GTRIGIEAAgaEALPGTVTGLTSINHVVLLSLSGSGMAgvPGTASRLFTCLARHSINIIFISQASSEQSISL 360 *****999976556678******************************************************* PP TIGR00657 347 vvdkedadkakellk...kkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis. 414 ++ +a+ ak++l+ + ee+ + +v+v ++la+v++vG++m ++pgv a++fe+L ++++n+ +++ lcl|NCBI__GCF_000006985.1:NP_662905.1 361 AIAPGQASMAKKVLEeefAREIEERRIDPVSVRRNLAMVAVVGNKMLGHPGVSAQLFETLGKNGVNVIAVAq 432 *************9977766789999*********************************************9 PP TIGR00657 415 .sseikisvvvdekdaekavealheklv 441 ++e++is+v+d+ d +ka++++he ++ lcl|NCBI__GCF_000006985.1:NP_662905.1 433 gANEMNISLVIDSADENKALNCVHESFF 460 9************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (818 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: 17.41 // [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