BBa_K371001 1 BBa_K371001 pduAB(Propanediol utilization gene A+B)[RBS+pduA+RBS+pduB] 2010-08-26T11:00:00Z 2015-05-08T01:12:15Z pduJK come from Citrobacter Freundii genenom(NBRC NO.12681) Pdu, a abbreviation of propanediol utilization, is name of operon which is used for degradation propanediol to generate energy. Pdu operon consist of 21 genes. Some of these genes encode a series proteins which assemble to a large icosahedral protein complex. PduAB consist of pdu A and pdu B wich their corresponding natural RBS, which got from Citrobacter Freundii by PCR. PduAB, together with others struture part of pdu operon such as pdu JK, can be used to construct a empty proteinous microcompartment in bacteria. false false _498_ 0 3984 9 It's complicated true The sequencing result show that the gene of pduAB has some silent mutations, which have no effect on the function of protein. false Yang Zhang annotation2078684 1 stop codon range2078684 1 1110 1112 annotation2078681 1 stop codon range2078681 1 298 300 annotation2078682 1 pduB coding sequence range2078682 1 300 1112 annotation2078680 1 start codon range2078680 1 300 302 annotation2078683 1 RBS range2078683 1 285 292 annotation2078685 1 start codon range2078685 1 19 21 annotation2078678 1 RBS range2078678 1 6 11 annotation2078679 1 pduA coding sequence range2078679 1 19 300 BBa_K371004 1 BBa_K371004 pduN(Propanediol utilization gene N)[RBS+pduN] 2010-08-26T11:00:00Z 2015-05-08T01:12:15Z pduJK come from Citrobacter Freundii genenom(NBRC NO.12681) Pdu, a abbreviation of propanediol utilization, is name of operon which is used for degradation propanediol to generate energy. Pdu operon consist of 21 genes, which belongs to a kind of BMC(bacterial microcompartment).Some of these genes encode a series proteins which assemble to a large icosahedral protein complex. PduN consist of pdu N wich their natural RBS, which got from Citrobacter Freundii by PCR. PduN, together with others struture part of pdu operon, can be used to construct a empty proteinous microcompartment in bacteria. false false _498_ 0 3984 9 It's complicated true There are some silent mutation in sequencing result of pduN. false Yang Zhang annotation2078722 1 stop codon range2078722 1 292 294 annotation2078725 1 pduN conding sequence range2078725 1 19 294 annotation2078724 1 RBS range2078724 1 4 12 annotation2078723 1 start codon range2078723 1 19 21 BBa_K371007 1 BBa_K371007 pduAB+pduJK+pduN+pduTUV 2010-08-26T11:00:00Z 2015-05-08T01:12:16Z All these genes come from the strain of Citrobacter Freundi(NBRC NO.12681) by PCR This part consists of four basic part, pduAB, pduJK, pduN and pduTUV. This part encode all proteins used for construct pdu BMC(bacterial microcompartment). All these genes belong to pdu operon, which consist of 21 genes. Some of these genes encode enzymes involved in the utilization of propanediol as carbon resource. Other genes like pduA encode structure proteins, which by unknown method assemble into a large icosahedral protein complex. There are also other similar type of metabolic protein complex, such as carboxysome and ethanolamine utilization complex. They are all belong to BMC(bacterial microcompartment). false false _498_ 0 3984 9 It's complicated true Because the natural sequence of pdu A, pduB and pduJ has a PstI restriction site. Site-mutation method has been applied to remove thess site to meet the RFC10 standard. The sequencing result of some gene shows some silent mutation when compare with the reference sequence we got from NCBI. But these are also few error mutation in pduK and pduTUV. We think the difference between our result and the reference come deprive from the devergence of bacterial strain. We are still do experiment do certify that our system can work well. false Yang Zhang component2084051 1 BBa_K371000 component2084069 1 BBa_K371005 component2084042 1 BBa_K371001 component2084056 1 BBa_K371004 annotation2084056 1 BBa_K371004 range2084056 1 1912 2205 annotation2084051 1 BBa_K371000 range2084051 1 1121 1903 annotation2084042 1 BBa_K371001 range2084042 1 1 1112 annotation2084069 1 BBa_K371005 range2084069 1 2214 3609 BBa_K371000 1 BBa_K371000 pduJK(Propanediol utilization gene J+K)[RBS+pduJ+RBS+pduK] 2010-08-26T11:00:00Z 2015-05-08T01:12:15Z pduAb come from Citrobacter Freundii genenom(NBRC NO.12681) Pdu, a abbreviation of propanediol utilization, is name of operon which is used for degradation propanediol to generate energy. Pdu operon consist of 21 genes. Some of these genes encode a series proteins which assemble to a large icosahedral protein complex. PduAB consist of pdu A and pdu B wich their natural RBS, which got from Citrobacter Freundii by PCR. PduAB, together with others struture part of pdu operon, can be used to construct a empty proteinous microcompartment in bacteria. false false _498_ 0 3984 9 It's complicated true The sequence results of pduAB, which we got by PCR from Citrobacter Freundii(NBRC NO.12681), are different from the sequence we found on the papar. We suspect that the strain we used is not same with the papar. false Yang Zhang annotation2078676 1 start codon range2078676 1 319 321 annotation2078670 1 pduJ RBS range2078670 1 5 12 annotation2078675 1 pduK RBS range2078675 1 307 312 annotation2078672 1 pduJ coding sequence range2078672 1 19 294 annotation2078677 1 stop codon range2078677 1 781 783 annotation2078674 1 stop codon range2078674 1 292 294 annotation2078671 1 start codon range2078671 1 19 21 annotation2078673 1 pduK coding sequence range2078673 1 319 783 BBa_K371005 1 BBa_K371005 pduTUV(Propanediol utilization gene T+U+V)[RBS+pduT+RBS+pduU+RBS+pduV] 2010-08-26T11:00:00Z 2015-05-08T01:12:16Z pduJK come from Citrobacter Freundii genenom(NBRC NO.12681) Pdu, a abbreviation of propanediol utilization, is name of operon which is used for degradation propanediol to generate energy. Pdu operon consist of 21 genes, which belongs to a kind of BMC(bacterial microcompartment).Some of these genes encode a series proteins which assemble to a large icosahedral protein complex. PduTUV consist of pduT, pduU and pduV wich their corresponding natural RBS, which got from Citrobacter Freundii by PCR. PduTUV, together with other struture parts of pdu operon, can be used to construct a empty proteinous microcompartment in bacteria. false false _498_ 0 3984 9 It's complicated true Sequencing result shows that there are several silent mutation in pduT and pduU. PduV has some error mutation. We are still working on the function assay to certify whether the mutation pduV still function well. false Yang Zhang annotation2078727 1 pduU coding sequence range2078727 1 589 939 annotation2078731 1 RBS range2078731 1 931 937 annotation2078726 1 stop codon range2078726 1 1393 1396 annotation2078737 1 pduT coding sequence range2078737 1 35 589 annotation2078729 1 RBS range2078729 1 23 28 annotation2078735 1 stop codon range2078735 1 587 589 annotation2078734 1 start codon range2078734 1 944 946 annotation2078730 1 RBS range2078730 1 576 582 annotation2078728 1 pduV coding sequence range2078728 1 944 1396 annotation2078733 1 start codon range2078733 1 589 591 annotation2078732 1 start codon range2078732 1 35 47 annotation2078736 1 stop codon range2078736 1 937 939 BBa_K371005_sequence 1 ctgagcaatccatcacggtaataagaggttaatcatgtctcaggctatagggattttagaactcaccagcattgccaaaggaatggaagctggcgatgccatgttaaaaagcgcgaatgtgaatttactggtcagcaagaccatctgcccgggaaaatttctactcatgctcggtggtgacgtaggtgccgtacaacaggcgattgccactggaacatctcttgctggcgatatgctcgttgatagtctggtactccccaacattcatgccagcgtactacccgcaatcagcggactaaacagcgtagataagcgtcaggcagttggtattgtcgaaacatggagcgttgctgcctgcatctgcgccgccgaccgggcggttaaagcctccaacgtcacgctggtccgcgtccgtatggcatttggtattggcggcaagtgttacatggtcgtagctggcgatgtatccgatgtgaataacgcggtgacggttgccagtgaaagtgcgggtgaaaaaggcctgctggtttaccgctcggtcatcccccgtccacacgaaagcatgtggcgacaaatggtggaaggataatggaaagacaacccaccacggatcgtatgattcaggaatatgttcctggcaaacaggtcacgttggcgcaccttatcgccaatcccggtaaggatttgttcaagaaactgggattacctgattcggtttctgcgatcggtattctgaccattacccctagcgaagcctcaatcatcgcctgtgatatcgccacgaaatcaggggcggtagagattggttttctcgaccggtttaccggcgcggtggtactgacgggcgatgtttcagccgttgagtacgcgctgaaacaggtaacccgaacgctgggcgaaatgatgcgttttaccgcgtgtcccatcacccggacgtaatctcgtgaaacgtatcatgctaattggccccagccagtgcggtaaaacgtcgctcacacagtgcatgcgcggagaggtgctccactatcagaagacccaggccatagtctggtcacctacgacaatagacacaccgggtgaatatcttgagaaccgctgcctgtacagtgcgctgctggccagcgcctgtgaagcggacattattgcgctggtactcaatgctgacgcgccgtggtcaccattttctcccggttttaccggaccaatgaaccgacccgttattggcctcgttaccaaagccgatttagccaacccgcagcgtatttctcttgtggagagttggttagctcaggctggtgcgcaaaaagtatttgtcaccagcgcgctggagaataccggggtcgatgagatgttcatttttctgaatgcaaaggaatcttcctgtctcacaaaataa BBa_K371001_sequence 1 aacccaggcgaggtctttatgcaacaagaagcgttaggaatggtagaaaccaaaggcttgacagcagccatagaggccgcagatgcaatggtgaagtcagccaatgtaatgctggtcggctacgaaaaaattggttcggggctggtaacagttattgtccgcggcgatgtcggcgcagtcaaagcagcaacagatgccggtgccgccgcagcccgtaatgtgggagaagtgaaagccgtacacgttatcccacgcccgcataccgatgtagaaaaaatcttaccgaagggaattagctaatgagcagcaatgaactggttgaacagatcatggcgcaggtgattgctcgcgtggcaacgccggaacagcaggctatcccagaaaataatcacccaacacgagaaacggctatggcagagaaaagctgtagtttaacggagtttgtcggtaccgcgattggcgacaccgtcggtctggtaatcgccaacgtagacagtgccctactggacgcaatgaaacttgaaaaacgctatcgctccattggcatccttggcgcccgtactggtgcgggtccacacatcatggccgctgatgaagcggtgaaagccaccaatactgaagtcgtcagtattgagttaccacgtgataccaaaggcggcgcaggtcatggctcgctgattattcttggcggcaacgatgtttccgacgtgaaacgcggcattgaagtcgcactgaaagagctggatcgcacctttggcgacgtttatgccaacgaagccggtcacatcgaaatgcaatacaccgcacgcgccagctacgcacttgaaaaagcctttggcgcaccgattggtcgtgcctgtggcgtcatcgtcggcgcaccagcatccgttggtgtcctgatggctgatactgccctgaaatccgccaacgtggaagttgtggcttacagctcccctgctcatggcaccagcttcagtaacgaagccattctggttatttcgggtgactctggcgctgttcgtcaggctgttatctctgcccgtgaaatcggtaaaaccgtactcgggaccctcggctcagagccgaaaaacgatcgtccgtcctacatctga BBa_K371000_sequence 1 ccacaggagaaaagcagtatgaataacgcactgggactggttgaaacaaaagggcttgtcggcgctattgaagccgctgatgccatggtgaaatccgcaaacgtgcagttggttggttacgaaaaaatcggctctggcctgatcaacgttatggttcgcggtgatgtcggcgcggtgaaagcagccgtagatgctggaagcgcagcagcaagcgccgttggtgaggtgaaatcctgccacgttatcccgcgtccgcacagcgacgttgaagccattttacctaaatccgcataagtcgttgcaaccaaggagcacagcgtgaagcaatcactgggattacttgaagttagtggtctggcattagccatcagttgcgcggacgtcatggcgaaagccgcctccatcacgctggtgggcctcgaaaaaaccaacggctcaggctggacggtgatcaagataatcggggatgtggcctccgtccaggcggccatttccactggtgtcagtttcgctgaccagcgagatggactggtggctcacaaagtcatttccagacccggggacgggatcctgtcgcatagcgttgtcctggagcctgaaccaacgcccgaccccataccagccataccacatgaagaaatccctgaggaccatgcggcacccgaagcaccgcaagatgcagaattgattagctgcaatttgtgtcttgatcctgcctgccctcgccaaaaaggtgagccgcgcacactttgtcttcactccggcaaacgaggtgaagcgtga BBa_K371004_sequence 1 attaagcaggagtgagctatgcatctggcacgggttacaggcgttgtggtttccacgcaaaaatctccatcactggtgggaaaaaaactgttgctggtacgtcgggtaagtgctgacggagagcttcctgcgtctccagtgagtggagatgaagtcgctgttgattctgtcggcgcggggaccggcgaactggtattactcagcagcgggtccagcgccagacacgttttttccggcccgaatgaggccattgatctggctatcgtcggcattgtcgacacgctttctcgttag BBa_K371007_sequence 1 aacccaggcgaggtctttatgcaacaagaagcgttaggaatggtagaaaccaaaggcttgacagcagccatagaggccgcagatgcaatggtgaagtcagccaatgtaatgctggtcggctacgaaaaaattggttcggggctggtaacagttattgtccgcggcgatgtcggcgcagtcaaagcagcaacagatgccggtgccgccgcagcccgtaatgtgggagaagtgaaagccgtacacgttatcccacgcccgcataccgatgtagaaaaaatcttaccgaagggaattagctaatgagcagcaatgaactggttgaacagatcatggcgcaggtgattgctcgcgtggcaacgccggaacagcaggctatcccagaaaataatcacccaacacgagaaacggctatggcagagaaaagctgtagtttaacggagtttgtcggtaccgcgattggcgacaccgtcggtctggtaatcgccaacgtagacagtgccctactggacgcaatgaaacttgaaaaacgctatcgctccattggcatccttggcgcccgtactggtgcgggtccacacatcatggccgctgatgaagcggtgaaagccaccaatactgaagtcgtcagtattgagttaccacgtgataccaaaggcggcgcaggtcatggctcgctgattattcttggcggcaacgatgtttccgacgtgaaacgcggcattgaagtcgcactgaaagagctggatcgcacctttggcgacgtttatgccaacgaagccggtcacatcgaaatgcaatacaccgcacgcgccagctacgcacttgaaaaagcctttggcgcaccgattggtcgtgcctgtggcgtcatcgtcggcgcaccagcatccgttggtgtcctgatggctgatactgccctgaaatccgccaacgtggaagttgtggcttacagctcccctgctcatggcaccagcttcagtaacgaagccattctggttatttcgggtgactctggcgctgttcgtcaggctgttatctctgcccgtgaaatcggtaaaaccgtactcgggaccctcggctcagagccgaaaaacgatcgtccgtcctacatctgatactagagccacaggagaaaagcagtatgaataacgcactgggactggttgaaacaaaagggcttgtcggcgctattgaagccgctgatgccatggtgaaatccgcaaacgtgcagttggttggttacgaaaaaatcggctctggcctgatcaacgttatggttcgcggtgatgtcggcgcggtgaaagcagccgtagatgctggaagcgcagcagcaagcgccgttggtgaggtgaaatcctgccacgttatcccgcgtccgcacagcgacgttgaagccattttacctaaatccgcataagtcgttgcaaccaaggagcacagcgtgaagcaatcactgggattacttgaagttagtggtctggcattagccatcagttgcgcggacgtcatggcgaaagccgcctccatcacgctggtgggcctcgaaaaaaccaacggctcaggctggacggtgatcaagataatcggggatgtggcctccgtccaggcggccatttccactggtgtcagtttcgctgaccagcgagatggactggtggctcacaaagtcatttccagacccggggacgggatcctgtcgcatagcgttgtcctggagcctgaaccaacgcccgaccccataccagccataccacatgaagaaatccctgaggaccatgcggcacccgaagcaccgcaagatgcagaattgattagctgcaatttgtgtcttgatcctgcctgccctcgccaaaaaggtgagccgcgcacactttgtcttcactccggcaaacgaggtgaagcgtgatactagagattaagcaggagtgagctatgcatctggcacgggttacaggcgttgtggtttccacgcaaaaatctccatcactggtgggaaaaaaactgttgctggtacgtcgggtaagtgctgacggagagcttcctgcgtctccagtgagtggagatgaagtcgctgttgattctgtcggcgcggggaccggcgaactggtattactcagcagcgggtccagcgccagacacgttttttccggcccgaatgaggccattgatctggctatcgtcggcattgtcgacacgctttctcgttagtactagagctgagcaatccatcacggtaataagaggttaatcatgtctcaggctatagggattttagaactcaccagcattgccaaaggaatggaagctggcgatgccatgttaaaaagcgcgaatgtgaatttactggtcagcaagaccatctgcccgggaaaatttctactcatgctcggtggtgacgtaggtgccgtacaacaggcgattgccactggaacatctcttgctggcgatatgctcgttgatagtctggtactccccaacattcatgccagcgtactacccgcaatcagcggactaaacagcgtagataagcgtcaggcagttggtattgtcgaaacatggagcgttgctgcctgcatctgcgccgccgaccgggcggttaaagcctccaacgtcacgctggtccgcgtccgtatggcatttggtattggcggcaagtgttacatggtcgtagctggcgatgtatccgatgtgaataacgcggtgacggttgccagtgaaagtgcgggtgaaaaaggcctgctggtttaccgctcggtcatcccccgtccacacgaaagcatgtggcgacaaatggtggaaggataatggaaagacaacccaccacggatcgtatgattcaggaatatgttcctggcaaacaggtcacgttggcgcaccttatcgccaatcccggtaaggatttgttcaagaaactgggattacctgattcggtttctgcgatcggtattctgaccattacccctagcgaagcctcaatcatcgcctgtgatatcgccacgaaatcaggggcggtagagattggttttctcgaccggtttaccggcgcggtggtactgacgggcgatgtttcagccgttgagtacgcgctgaaacaggtaacccgaacgctgggcgaaatgatgcgttttaccgcgtgtcccatcacccggacgtaatctcgtgaaacgtatcatgctaattggccccagccagtgcggtaaaacgtcgctcacacagtgcatgcgcggagaggtgctccactatcagaagacccaggccatagtctggtcacctacgacaatagacacaccgggtgaatatcttgagaaccgctgcctgtacagtgcgctgctggccagcgcctgtgaagcggacattattgcgctggtactcaatgctgacgcgccgtggtcaccattttctcccggttttaccggaccaatgaaccgacccgttattggcctcgttaccaaagccgatttagccaacccgcagcgtatttctcttgtggagagttggttagctcaggctggtgcgcaaaaagtatttgtcaccagcgcgctggagaataccggggtcgatgagatgttcatttttctgaatgcaaaggaatcttcctgtctcacaaaataa igem2sbol 1 iGEM to SBOL conversion Conversion of the iGEM parts registry to SBOL2.1 James Alastair McLaughlin Chris J. Myers 2017-03-06T15:00:00.000Z