Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 202522 SO3415 aspartokinase I/homoserine dehydrogenase, threonine-sensitive (NCBI ptt file)
Query= BRENDA::P00561 (820 letters) >FitnessBrowser__MR1:202522 Length = 822 Score = 906 bits (2342), Expect = 0.0 Identities = 474/821 (57%), Positives = 590/821 (71%), Gaps = 10/821 (1%) Query: 1 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60 M+V+KFGGTS+AN +RF ADI+ A VATVLSAPA +TN L+ M+ + G+D Sbjct: 1 MKVMKFGGTSLANWQRFSMAADIVAKAATMEPVATVLSAPATVTNALLEMVNLAVKGEDY 60 Query: 61 LPNISDAERIFAELL-----TGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCP 115 P I ER+F L +GL++ Q A L + A+ + LHGI+LL +CP Sbjct: 61 SPVIQHVERVFTSLYQDAVSSGLSSTQSELLFAGLGA----QLARWQDRLHGITLLQECP 116 Query: 116 DSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIA 175 D I A ++ GE++S A+M V+ A+G +DP + L G LES VDIA S R Sbjct: 117 DGICAEIVVAGERLSAALMEQVMLAKGITSAQLDPRKLFLGRGRPLESVVDIAVSKPRFK 176 Query: 176 ASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTC 235 + + +M GFTA +E G++V LGRNGSDYSAAVLAACL A CEIWTDVDGVY Sbjct: 177 NLLLDEKRVWVMPGFTAADEDGKVVTLGRNGSDYSAAVLAACLDASSCEIWTDVDGVYNT 236 Query: 236 DPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLI 295 DPR V DA+LL +SYQEAMELSYFGAKVLHP+TI PIAQF IPC IKN+ NP APGTL+ Sbjct: 237 DPRVVADAKLLSQLSYQEAMELSYFGAKVLHPKTIAPIAQFHIPCYIKNSFNPDAPGTLV 296 Query: 296 GASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSE 355 D L VK ISNL+N MF VSGPGMKGMVGMA+R AA+SR+ +SV LITQSS E Sbjct: 297 SNLADASGLQVKAISNLDNQTMFDVSGPGMKGMVGMASRTLAAISRSGVSVSLITQSSCE 356 Query: 356 YSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAK 415 YSISFCV S+ + + A+++EF LE+K LLEP+ + LAI+S++GDGMRT +G++A+ Sbjct: 357 YSISFCVATSESAKVKLALEQEFELEIKSDLLEPIEMRHDLAIVSLIGDGMRTHKGVAAR 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 LK +HI +RVCG+ NS +L + G++L NWQ LA +++ +L Sbjct: 477 VGAGLLEQIKQQAIVLKEQHISIRVCGIVNSSKMLLDSAGIDLNNWQNLLADSQQSSDLP 536 Query: 536 RLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYA 595 L+ VKE LLNPV+VDCTSS+ V++QY + + G HVVTPNKKANT YY LR Sbjct: 537 ALLAWVKEQQLLNPVLVDCTSSEQVSNQYLEVMNAGMHVVTPNKKANTRDYAYYQALRQT 596 Query: 596 AEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSE 655 A RR+FLY+TNVGAGLPVI+NL+ LL AGD+L KF+GILSGSLS+IFGKLDEGMS SE Sbjct: 597 ALTQRRQFLYETNVGAGLPVIDNLKKLLFAGDKLHKFNGILSGSLSFIFGKLDEGMSLSE 656 Query: 656 ATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDV 715 AT LARE +TEPDPRDDLSGMDVARK+LILARE G +LEL+DI ++ VLP F+ GDV Sbjct: 657 ATKLAREKCFTEPDPRDDLSGMDVARKVLILAREVGLKLELSDIVVDSVLPESFDDSGDV 716 Query: 716 AAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGE 775 +FMA L + D AARVA+A+ +GKVLRYVG I E+G C V+IAEVD DPL+ VK GE Sbjct: 717 ESFMARLPEADAAIAARVAEAKAQGKVLRYVGQI-EEGACHVRIAEVDATDPLYSVKGGE 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: 1501 Number of extensions: 57 Number of successful extensions: 6 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 202522 SO3415 (aspartokinase I/homoserine dehydrogenase, threonine-sensitive (NCBI ptt file))
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.2630476.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-126 409.1 0.1 1.7e-126 408.8 0.1 1.1 1 FitnessBrowser__MR1:202522 Domain annotation for each sequence (and alignments): >> FitnessBrowser__MR1:202522 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 408.8 0.1 1.7e-126 1.7e-126 5 441 .. 3 461 .. 1 462 [. 0.91 Alignments for each domain: == domain 1 score: 408.8 bits; conditional E-value: 1.7e-126 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee....keliekirekhlealeelasq 83 V+KFGGtS++n +r++ +a+iv k+++ + +v++V+SA+a vT+aL+e+++ + ++e+ + +e+++++ ++ + + FitnessBrowser__MR1:202522 3 VMKFGGTSLANWQRFSMAADIVAKAATME-PVATVLSAPATVTNALLEMVNLAVKGEDyspvIQHVERVFTSLYQDAVSSG-- 82 9*************************777.************************999986665556666665555444444.. PP TIGR00657 84 alkeklkallekeleevkk...............ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrA 151 ++++++ l + +++ + + ++i+ GE+lSaal+ +++ ++g+ +++ l++++ l ++ +++ FitnessBrowser__MR1:202522 83 LSSTQSELLFAGLGAQLARwqdrlhgitllqecpDGICAEIVVAGERLSAALMEQVMLAKGITSAQ-LDPRKLFLGRGRPLES 164 44455555555555555445669999*******999*************************66655.699************* PP TIGR00657 152 kvleeikterlekl.leegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrl 233 +v + +++ r ++l l+e+ + v+ GF++a+e+g+++tLGR+GSD++Aa+lAa+l+A+ +ei+tDVdG+y +DPr+v +A++l FitnessBrowser__MR1:202522 165 VVDIAVSKPRFKNLlLDEKRVWVMPGFTAADEDGKVVTLGRNGSDYSAAVLAACLDASSCEIWTDVDGVYNTDPRVVADAKLL 247 *899998888887616778**************************************************************** PP TIGR00657 234 deisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk.. 314 ++sy+Ea+EL+++GakvLhp+t+ p++++ ip+ +k++fnp+a+GTl+ + + + +vka+s+ +nq++++vsg++mk FitnessBrowser__MR1:202522 248 SQLSYQEAMELSYFGAKVLHPKTIAPIAQFHIPCYIKNSFNPDAPGTLVSNLAD-ASGLQVKAISNLDNQTMFDVSGPGMKgm 329 ***************************************************988.556************************* PP TIGR00657 315 pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellk...kkvkeekaleevevekklalvslvGagmksapg 394 +g++++ + a+++ +v+v li+qss e+sisf+v +++ k k +l+ + + + + le++e+ ++la+vsl+G+gm++++g FitnessBrowser__MR1:202522 330 VGMASRTLAAISRSGVSVSLITQSSCEYSISFCVATSESAKVKLALEqefELEIKSDLLEPIEMRHDLAIVSLIGDGMRTHKG 412 **************************************8888888886777788999************************** PP TIGR00657 395 vaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441 vaa++f+aLa++ +ni +i+ sse++is+v+++++ ++av a h+ ++ FitnessBrowser__MR1:202522 413 VAARFFQALAQASVNIIAIAqgSSERSISTVIEQRKTKHAVAACHQGFF 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 22.28 // [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