Home Repository Download Help About Statistics Taxonomy Blastx
Links
PULDB
CAZy
dbCAN2
dbCAN-seq
run_dbcan
CAZypedia
PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0429

PubMed

21396969, J Biotechnol. 2011 Aug 20;155(1):20-33. doi: 10.1016/j.jbiotec.2010.12.018. Epub 2011 Mar 17.

Characterization method

sequence homology analysis

Genomic accession number

CP001832

Nucelotide position range

1073900-1119100

Substrate

O-antigen,unknown polysaccharide

Loci

SM11_pD1002-SM11_pD1043

Species

Sinorhizobium meliloti/382

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

wza SM11_pD1002 AEH83834.1 56 - 1394 (+) CP001832.1:1073956-1075294 -
rmlA2 SM11_pD1003 AEH83835.1 1481 - 2360 (+) CP001832.1:1075381-1076260 -
rmlC2 SM11_pD1004 AEH83836.1 2356 - 2941 (+) CP001832.1:1076256-1076841 -
rmlB2 SM11_pD1005 AEH83837.1 2937 - 4005 (+) CP001832.1:1076837-1077905 -
rmlD2 SM11_pD1006 AEH83838.1 4001 - 4931 (+) CP001832.1:1077901-1078831 -
wzx1 SM11_pD1007 AEH83839.1 4902 - 6411 (+) CP001832.1:1078802-1080311 -
- SM11_pD1008 AEH83840.1 6437 - 7631 (-) CP001832.1:1080337-1081531 -
- SM11_pD1009 AEH83841.1 7627 - 8602 (-) CP001832.1:1081527-1082502 -
- SM11_pD1010 AEH83842.1 8617 - 9322 (-) CP001832.1:1082517-1083222 -
- SM11_pD1011 AEH83843.1 9311 - 10418 (-) CP001832.1:1083211-1084318 -
- SM11_pD1012 AEH83844.1 10414 - 11452 (-) CP001832.1:1084314-1085352 -
- SM11_pD1013 AEH83845.1 11453 - 11954 (-) CP001832.1:1085353-1085854 -
- SM11_pD1014 AEH83846.1 12902 - 13037 (+) CP001832.1:1086802-1086937 -
- SM11_pD1015 AEH83847.1 13191 - 15402 (+) CP001832.1:1087091-1089302 -
- SM11_pD1016 AEH83848.1 15518 - 16202 (-) CP001832.1:1089418-1090102 -
- SM11_pD1017 AEH83849.1 16484 - 17075 (-) CP001832.1:1090384-1090975 -
- SM11_pD1018 AEH83850.1 17861 - 19418 (+) CP001832.1:1091761-1093318 -
- SM11_pD1019 AEH83851.1 19466 - 20261 (+) CP001832.1:1093366-1094161 -
- SM11_pD1020 AEH83852.1 20597 - 21341 (+) CP001832.1:1094497-1095241 -
- SM11_pD1021 AEH83853.1 22016 - 22451 (+) CP001832.1:1095916-1096351 -
- SM11_pD1022 AEH83854.1 22952 - 24302 (+) CP001832.1:1096852-1098202 -
- SM11_pD1023 AEH83855.1 24542 - 24719 (-) CP001832.1:1098442-1098619 -
- SM11_pD1024 AEH83856.1 25022 - 25271 (+) CP001832.1:1098922-1099171 -
- SM11_pD1025 AEH83857.1 25417 - 25546 (+) CP001832.1:1099317-1099446 -
- SM11_pD1026 AEH83858.1 25563 - 27099 (+) CP001832.1:1099463-1100999 -
- SM11_pD1027 AEH83859.1 27246 - 27450 (+) CP001832.1:1101146-1101350 -
- SM11_pD1028 AEH83860.1 27513 - 29673 (+) CP001832.1:1101413-1103573 -
glf SM11_pD1029 AEH83861.1 29763 - 30870 (-) CP001832.1:1103663-1104770 -
- SM11_pD1030 AEH83862.1 30870 - 31890 (-) CP001832.1:1104770-1105790 -
- SM11_pD1031 AEH83863.1 32559 - 32658 (-) CP001832.1:1106459-1106558 -
- SM11_pD1032 AEH83864.1 32949 - 33108 (-) CP001832.1:1106849-1107008 -
- SM11_pD1033 AEH83865.1 33429 - 34677 (-) CP001832.1:1107329-1108577 -
- SM11_pD1034 AEH83866.1 35313 - 36159 (+) CP001832.1:1109213-1110059 -
- SM11_pD1035 AEH83867.1 36387 - 37008 (+) CP001832.1:1110287-1110908 -
- SM11_pD1036 AEH83868.1 37169 - 37853 (-) CP001832.1:1111069-1111753 -
- SM11_pD1037 AEH83869.1 37855 - 38809 (-) CP001832.1:1111755-1112709 -
acpP SM11_pD1038 AEH83870.1 38824 - 39088 (-) CP001832.1:1112724-1112988 -
- SM11_pD1039 AEH83871.1 39138 - 40365 (-) CP001832.1:1113038-1114265 -
acsA SM11_pD1040 AEH83872.1 40361 - 41954 (-) CP001832.1:1114261-1115854 -
- SM11_pD1041 AEH83873.1 41967 - 42840 (-) CP001832.1:1115867-1116740 -
- SM11_pD1042 AEH83874.1 43043 - 44273 (+) CP001832.1:1116943-1118173 -
- SM11_pD1043 AEH83875.1 44244 - 45147 (+) CP001832.1:1118144-1119047 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

wza 57 - 1394 (+) TC: gnl|TC-DB|Q02728|1.B.18.1.1 No
rmlA2 1482 - 2360 (+) CDS No
rmlC2 2357 - 2941 (+) CDS No
rmlB2 2938 - 4005 (+) CDS No
rmlD2 4002 - 4931 (+) CDS No
wzx1 4903 - 6411 (+) CDS No
- 6438 - 7631 (-) CDS No
- 7628 - 8602 (-) CDS No
- 8618 - 9322 (-) CDS No
- 9312 - 10418 (-) TF: DBD-Pfam|ComK No
- 10415 - 11452 (-) CDS No
- 11454 - 11954 (-) CDS No
- 12903 - 13037 (+) CDS No
- 13192 - 15402 (+) CDS No
- 15519 - 16202 (-) TC: gnl|TC-DB|H8E4X1|9.B.18.1.2 No
- 16485 - 17075 (-) CDS No
- 17862 - 19418 (+) CDS No
- 19467 - 20261 (+) STP: STP|CbiA No
- 20598 - 21341 (+) CDS No
- 22017 - 22451 (+) CDS No
- 22953 - 24302 (+) CDS No
- 24543 - 24719 (-) CDS No
- 25023 - 25271 (+) CDS No
- 25418 - 25546 (+) CDS No
- 25564 - 27099 (+) CDS No
- 27247 - 27450 (+) CDS No
- 27514 - 29673 (+) CDS No
glf 29764 - 30870 (-) CDS No
- 30871 - 31890 (-) CAZyme: GT2_Glycos_transf_2|GT2 Yes
- 32560 - 32658 (-) other Yes
- 32950 - 33108 (-) other Yes
- 33430 - 34677 (-) other Yes
- 35314 - 36159 (+) other Yes
- 36388 - 37008 (+) other Yes
- 37170 - 37853 (-) other Yes
- 37856 - 38809 (-) CAZyme: GT2_Glycos_transf_2|GT2 Yes
acpP 38825 - 39088 (-) other Yes
- 39139 - 40365 (-) other Yes
acsA 40362 - 41954 (-) TC: gnl|TC-DB|P69451|4.C.1.1.4 Yes
- 41968 - 42840 (-) other Yes
- 43044 - 44273 (+) CAZyme: GT4 Yes
- 44245 - 45147 (+) CAZyme: GT2_Glycos_transf_2|GT2 Yes

PUL ID

PUL0429

PubMed

21396969, J Biotechnol. 2011 Aug 20;155(1):20-33. doi: 10.1016/j.jbiotec.2010.12.018. Epub 2011 Mar 17.

Title

The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome.

Author

Schneiker-Bekel S, Wibberg D, Bekel T, Blom J, Linke B, Neuweger H, Stiens M, Vorholter FJ, Weidner S, Goesmann A, Puhler A, Schluter A

Abstract

Isolates of the symbiotic nitrogen-fixing species Sinorhizobium meliloti usually contain a chromosome and two large megaplasmids encoding functions that are absolutely required for the specific interaction of the microsymbiont with corresponding host plants leading to an effective symbiosis. The complete genome sequence, including the megaplasmids pSmeSM11c (related to pSymA) and pSmeSM11d (related to pSymB), was established for the dominant, indigenous S. meliloti strain SM11 that had been isolated during a long-term field release experiment with genetically modified S. meliloti strains. The chromosome, the largest replicon of S. meliloti SM11, is 3,908,022bp in size and codes for 3785 predicted protein coding sequences. The size of megaplasmid pSmeSM11c is 1,633,319bp and it contains 1760 predicted protein coding sequences whereas megaplasmid pSmeSM11d is 1,632,395bp in size and comprises 1548 predicted coding sequences. The gene content of the SM11 chromosome is quite similar to that of the reference strain S. meliloti Rm1021. Comparison of pSmeSM11c to pSymA of the reference strain revealed that many gene regions of these replicons are variable, supporting the assessment that pSymA is a major hot-spot for intra-specific differentiation. Plasmids pSymA and pSmeSM11c both encode unique genes. Large gene regions of pSmeSM11c are closely related to corresponding parts of Sinorhizobium medicae WSM419 plasmids. Moreover, pSmeSM11c encodes further novel gene regions, e.g. additional plasmid survival genes (partition, mobilisation and conjugative transfer genes), acdS encoding 1-aminocyclopropane-1-carboxylate deaminase involved in modulation of the phytohormone ethylene level and genes having predicted functions in degradative capabilities, stress response, amino acid metabolism and associated pathways. In contrast to Rm1021 pSymA and pSmeSM11c, megaplasmid pSymB of strain Rm1021 and pSmeSM11d are highly conserved showing extensive synteny with only few rearrangements. Most remarkably, pSmeSM11b contains a new gene cluster predicted to be involved in polysaccharide biosynthesis. Compilation of the S. meliloti SM11 genome sequence contributes to an extension of the S. meliloti pan-genome.