Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 7023927 Shewana3_1139 bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq)
Query= BRENDA::P00561 (820 letters) >FitnessBrowser__ANA3:7023927 Length = 822 Score = 919 bits (2374), Expect = 0.0 Identities = 476/821 (57%), Positives = 595/821 (72%), Gaps = 10/821 (1%) Query: 1 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60 M+V+KFGGTS+AN +RF ADI+ A+ VATVLSAPA +TN L+ M++ + G+D Sbjct: 1 MKVMKFGGTSLANWQRFSMAADIVAKAAKAEPVATVLSAPATVTNALLEMVDVAVKGEDY 60 Query: 61 LPNISDAERIFAELL-----TGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCP 115 P I ER+F L +GL+++Q A L + A+ + L GI+LL +CP Sbjct: 61 SPVIQHVERVFTSLYQDAVSSGLSSSQSEVLFAGLSV----QLARWQDRLRGITLLQECP 116 Query: 116 DSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIA 175 D + A ++ GE++S A+M V+ A+G +DP E L G LES VDIA S R Sbjct: 117 DGVRAEIVVAGERLSAALMEQVMLAKGITSAQLDPRELFLGRGRPLESVVDIAVSKPRFK 176 Query: 176 ASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTC 235 + + +M GFTA +E G++V LGRNGSDYSAAVLAACL A CEIWTDVDGVY Sbjct: 177 NLALDEKRVWVMPGFTAADEDGKVVTLGRNGSDYSAAVLAACLDASSCEIWTDVDGVYNT 236 Query: 236 DPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLI 295 DPR V DA+LL +SYQEAMELSYFGAKVLHP+TI PIAQF IPC IKN+ NP APGTL+ Sbjct: 237 DPRVVTDAKLLSQLSYQEAMELSYFGAKVLHPKTIAPIAQFHIPCYIKNSFNPDAPGTLV 296 Query: 296 GASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSE 355 DE L VK ISNL+N MF VSGPGMKGMVGMA+R AA+SR+ +SV LITQSS E Sbjct: 297 SNQADESGLQVKAISNLDNQTMFDVSGPGMKGMVGMASRTLAAISRSGVSVSLITQSSCE 356 Query: 356 YSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAK 415 YSISFCV SD + + A+++EF LE+K LLEP+ + LAI+S++GDGMRT +G++A+ Sbjct: 357 YSISFCVATSDAAKVKSALEQEFELEIKSDLLEPIEMRHDLAIVSLIGDGMRTHKGVAAR 416 Query: 416 FFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGG 475 FF ALA+A++NI+AIAQGSSERSIS V+ V HQ F+ Q ++VF++G G Sbjct: 417 FFQALAQASVNIIAIAQGSSERSISTVIEQRKTKHAVAACHQGFFDVQQYLDVFLVGCGN 476 Query: 476 VGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLG 535 VG LLEQ+K Q S LK +HI +RVCG+ NS +L + G++L NWQ LA +++P +L Sbjct: 477 VGAGLLEQIKHQASVLKEQHISIRVCGIVNSSKMLLDSAGIDLNNWQNLLADSQQPSDLS 536 Query: 536 RLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYA 595 L+ VKE LLNPV+VDCTSS V++QY + + G HVVTPNKKANT YY LR Sbjct: 537 ALLAWVKEQQLLNPVLVDCTSSDQVSNQYLEVMNAGMHVVTPNKKANTRDYAYYQALRQT 596 Query: 596 AEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSE 655 A K RR+FLY+TNVGAGLPVI+NL+ LL AGD+L KF+GILSGSLS+IFGKLDEGM+ SE Sbjct: 597 ALKQRRQFLYETNVGAGLPVIDNLKKLLFAGDKLHKFNGILSGSLSFIFGKLDEGMTLSE 656 Query: 656 ATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDV 715 AT LARE +TEPDPRDDLSGMDVARK+LILARE G +LEL+DI ++ VLP +F+ GDV Sbjct: 657 ATKLAREKCFTEPDPRDDLSGMDVARKVLILAREVGLKLELSDIVVDSVLPDDFDDSGDV 716 Query: 716 AAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGE 775 +FMA L++ D AARVA+A+ +GKVLRYVG I E+G C V+I EVD DPL+ VK GE Sbjct: 717 ESFMARLTEADAAIAARVAEAKAQGKVLRYVGQI-EEGACYVRITEVDATDPLYSVKGGE 775 Query: 776 NALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSW 816 NALAFYS YYQP+P VLRGYGAG +VTAAG FAD+LRTL+W Sbjct: 776 NALAFYSRYYQPIPFVLRGYGAGTEVTAAGAFADVLRTLNW 816 Lambda K H 0.319 0.135 0.384 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: 1487 Number of extensions: 53 Number of successful extensions: 5 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: 820 Length of database: 822 Length adjustment: 42 Effective length of query: 778 Effective length of database: 780 Effective search space: 606840 Effective search space used: 606840 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 56 (26.2 bits)
Align candidate 7023927 Shewana3_1139 (bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq))
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.9958.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-129 418.6 0.4 2.3e-129 418.2 0.4 1.1 1 lcl|FitnessBrowser__ANA3:7023927 Shewana3_1139 bifunctional aspar Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7023927 Shewana3_1139 bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 418.2 0.4 2.3e-129 2.3e-129 5 441 .. 3 461 .. 1 462 [. 0.92 Alignments for each domain: == domain 1 score: 418.2 bits; conditional E-value: 2.3e-129 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee....keliekirekhleal 77 V+KFGGtS++n +r++ +a+iv k+++ + +v++V+SA+a vT+aL+e+++ + ++e+ + +e+++++ ++ + lcl|FitnessBrowser__ANA3:7023927 3 VMKFGGTSLANWQRFSMAADIVAKAAKAE-PVATVLSAPATVTNALLEMVDVAVKGEDyspvIQHVERVFTSLYQDA 78 9************************9666.**********************9999998666566666666665555 PP TIGR00657 78 eela.sqalkeklkallekeleevkk...............ereldlilsvGEklSaallaaaleelgvkavsllga 138 + s + +++ l + +++ + + +++i+ GE+lSaal+ +++ ++g+ +++ l++ lcl|FitnessBrowser__ANA3:7023927 79 VSSGlS---SSQSEVLFAGLSVQLARwqdrlrgitllqecpDGVRAEIVVAGERLSAALMEQVMLAKGITSAQ-LDP 151 444444...455555555555555555669999***********************************76665.699 PP TIGR00657 139 eagiltdsefgrAkvleeikterlek.lleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiyt 214 ++ l ++ ++++v + +++ r ++ +l+e+ + v+ GF++a+e+g+++tLGR+GSD++Aa+lAa+l+A+ +ei+t lcl|FitnessBrowser__ANA3:7023927 152 RELFLGRGRPLESVVDIAVSKPRFKNlALDEKRVWVMPGFTAADEDGKVVTLGRNGSDYSAAVLAACLDASSCEIWT 228 9999**********888888887766268999********************************************* PP TIGR00657 215 DVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseee 291 DVdG+y +DPr+v +A++l ++sy+Ea+EL+++GakvLhp+t+ p++++ ip+ +k++fnp+a+GTl+ ++ + e+ lcl|FitnessBrowser__ANA3:7023927 229 DVDGVYNTDPRVVTDAKLLSQLSYQEAMELSYFGAKVLHPKTIAPIAQFHIPCYIKNSFNPDAPGTLVSNQAD-ESG 304 ***********************************************************************98.666 PP TIGR00657 292 pavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellk...kk 363 +vka+s+ +nq++++vsg++mk +g++++ + a+++ +v+v li+qss e+sisf+v ++da k k++l+ + lcl|FitnessBrowser__ANA3:7023927 305 LQVKAISNLDNQTMFDVSGPGMKgmVGMASRTLAAISRSGVSVSLITQSSCEYSISFCVATSDAAKVKSALEqefEL 381 **********************************************************************9977777 PP TIGR00657 364 vkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdekdaekavealhe 438 + + + le++e+ ++la+vsl+G+gm++++gvaa++f+aLa++ +ni +i+ sse++is+v+++++ ++av a h+ lcl|FitnessBrowser__ANA3:7023927 382 EIKSDLLEPIEMRHDLAIVSLIGDGMRTHKGVAARFFQALAQASVNIIAIAqgSSERSISTVIEQRKTKHAVAACHQ 458 88999************************************************************************ PP TIGR00657 439 klv 441 ++ lcl|FitnessBrowser__ANA3:7023927 459 GFF 461 987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (822 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 12.06 // [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