Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 5208568 Shew_1079 bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq)
Query= BRENDA::P00561 (820 letters) >FitnessBrowser__PV4:5208568 Length = 822 Score = 913 bits (2359), Expect = 0.0 Identities = 469/818 (57%), Positives = 596/818 (72%), Gaps = 4/818 (0%) Query: 1 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60 M+V+KFGGTS+AN +RF A I+ ++A + A VLSAPA +TN L+ M++ ++G D Sbjct: 1 MKVMKFGGTSLANWQRFNSAAQIVLASAAEQPTAVVLSAPATVTNGLLEMVDLAVAGDDF 60 Query: 61 LPNISDAERIFAELLTGLAAAQ--PGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSI 118 P +S +F + L G AA++ G L+ + + + L G+ LLG+CPD++ Sbjct: 61 FPVLSQVHEVF-KTLYGQAASEVLSGEQSDSLEAVLAAQLKHWQDKLQGVVLLGECPDAV 119 Query: 119 NAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASR 178 A ++ GE++S A+M ++ A G + + P + +A G LES VDIA S +R A Sbjct: 120 RAEIVVGGERLSAALMEQLMLAAGVSANQLVPQQLFVAHGPALESVVDIAASKQRFAELS 179 Query: 179 IPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPR 238 + A + +M GFTAG++ G +V LGRNGSDYSAAVL+AC+ A CCEIWTDVDGVY DPR Sbjct: 180 LDAHQVWVMPGFTAGDKDGRVVTLGRNGSDYSAAVLSACIDASCCEIWTDVDGVYNTDPR 239 Query: 239 QVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGAS 298 V DA+LL +SYQEAMELSYFGAKVLHP+TI PIAQ+ IPC I+N+ NPQAPGTL+ Sbjct: 240 VVADAKLLTQLSYQEAMELSYFGAKVLHPKTIAPIAQYHIPCYIRNSFNPQAPGTLVSNQ 299 Query: 299 RDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSI 358 DE L VK ISNL+ MF ++GPGMKGMVGMA+R A+SR+ +SV LITQSSSEYSI Sbjct: 300 VDETGLNVKAISNLDEQTMFDIAGPGMKGMVGMASRTLGAISRSGVSVSLITQSSSEYSI 359 Query: 359 SFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFA 418 SFCV D R A+++EF LELK +LE +A+ LAI+S++GDGMRT +G++ KFF Sbjct: 360 SFCVATQDAERVRVALEQEFELELKSEILEQIAMRHNLAIVSLIGDGMRTHKGVAGKFFQ 419 Query: 419 ALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGG 478 ALA+AN+NIVAIAQGSSERSIS V+ + HQ LF+ ++VF++G G VG Sbjct: 420 ALAQANVNIVAIAQGSSERSISAVIELRKTKHAIAACHQSLFDVQHYLDVFLVGCGNVGA 479 Query: 479 ALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLI 538 LLEQ+K+Q LK +HI +RVCGVANS+ +L + G++L +WQ LA +++ +L +++ Sbjct: 480 GLLEQIKQQTEMLKAQHITVRVCGVANSRHMLLDAKGIDLNHWQGLLADSQQACDLDKML 539 Query: 539 RLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEK 598 K+ LLNPV+VDCTS++AV+DQY + G HVVTPNKKANT DYY LR A Sbjct: 540 AWAKDQQLLNPVLVDCTSNEAVSDQYVAVMNAGLHVVTPNKKANTRDYDYYRALRQTALH 599 Query: 599 SRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATT 658 RR+FLY+T VGAGLPVI+NL+ LL AGD+L KF+GILSGSLSYIFG LDEGMS SEAT Sbjct: 600 QRRQFLYETTVGAGLPVIDNLKKLLFAGDKLQKFNGILSGSLSYIFGMLDEGMSLSEATG 659 Query: 659 LAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAF 718 +ARE +TEPDPRDDLSGMDVARK+LILARE G ++EL+DI++E VLP+ F+A GDV F Sbjct: 660 IAREKCFTEPDPRDDLSGMDVARKVLILAREVGMQIELSDIQVESVLPSHFDASGDVETF 719 Query: 719 MANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENAL 778 MANLS LD A RV A+ GKVLRYVG IDE+G CRVKIAEVD DPL+ VK GENAL Sbjct: 720 MANLSALDGELAERVNSAKAAGKVLRYVGQIDEEG-CRVKIAEVDAKDPLYSVKGGENAL 778 Query: 779 AFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSW 816 AFYS YYQP+P VLRGYGAG +VTAAGVFADLLRTL+W Sbjct: 779 AFYSRYYQPIPFVLRGYGAGTEVTAAGVFADLLRTLNW 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: 1515 Number of extensions: 40 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 5208568 Shew_1079 (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.2189.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-128 416.0 1.1 1.3e-128 415.7 1.1 1.1 1 lcl|FitnessBrowser__PV4:5208568 Shew_1079 bifunctional aspartoki Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5208568 Shew_1079 bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 415.7 1.1 1.3e-128 1.3e-128 5 441 .. 3 461 .. 1 462 [. 0.92 Alignments for each domain: == domain 1 score: 415.7 bits; conditional E-value: 1.3e-128 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee....keliekirekhleale 78 V+KFGGtS++n +r++ +a+iv+++++++ + +VV+SA+a vT+ L+e+++ + +++ +++++++++ + +++ lcl|FitnessBrowser__PV4:5208568 3 VMKFGGTSLANWQRFNSAAQIVLASAAEQ-PTAVVLSAPATVTNGLLEMVDLAVAGDDffpvLSQVHEVFKTLYGQAA 79 9*************************666.***************************998886777778888777777 PP TIGR00657 79 ela.sqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleelgvkavsllgaeagil 143 ++ s + + l+a+l+++l++ + ++ +++i+ GE+lSaal+ +++ + gv a +l+ ++ + lcl|FitnessBrowser__PV4:5208568 80 SEVlSGEQSDSLEAVLAAQLKHWQDklqgvvllgecpDAVRAEIVVGGERLSAALMEQLMLAAGVSANQLVP-QQLFV 156 77767777777777777777776668999***********************************77777765.55667 PP TIGR00657 144 tdsefgrAkvleeikterl.eklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiy 220 +++ ++++v + ++++r e l++ ++ v+ GF++ +++g+++tLGR+GSD++Aa+l a+++A+++ei+tDVdG+y lcl|FitnessBrowser__PV4:5208568 157 AHGPALESVVDIAASKQRFaELSLDAHQVWVMPGFTAGDKDGRVVTLGRNGSDYSAAVLSACIDASCCEIWTDVDGVY 234 777777777566666666515567888*************************************************** PP TIGR00657 221 taDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavkals 298 +DPr+v +A++l ++sy+Ea+EL+++GakvLhp+t+ p++++ ip+ ++++fnp+a+GTl+ ++ + e +vka+s lcl|FitnessBrowser__PV4:5208568 235 NTDPRVVADAKLLTQLSYQEAMELSYFGAKVLHPKTIAPIAQYHIPCYIRNSFNPQAPGTLVSNQVD-ETGLNVKAIS 311 *****************************************************************88.666******* PP TIGR00657 299 ldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellk...kkvkeekale 371 + ++q++++++g++mk +g++++ +ga+++ +v+v li+qssse+sisf+v ++da++ +l+ + +++ + le lcl|FitnessBrowser__PV4:5208568 312 NLDEQTMFDIAGPGMKgmVGMASRTLGAISRSGVSVSLITQSSSEYSISFCVATQDAERVRVALEqefELELKSEILE 389 **********************************************************9999998777788999**** PP TIGR00657 372 evevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441 ++ + ++la+vsl+G+gm++++gva+k+f+aLa++n+ni++i+ sse++is v++ ++ ++a+ a h+ l+ lcl|FitnessBrowser__PV4:5208568 390 QIAMRHNLAIVSLIGDGMRTHKGVAGKFFQALAQANVNIVAIAqgSSERSISAVIELRKTKHAIAACHQSLF 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 18.60 // [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