Basic Search | Intermediate Search | Advanced SQL Search | Gene Image Map |  Home

Ureaplasma urealyticum Search Results

Record: 1 of 1  
MiniMap IGR106 IGR102 IGR107 IGR105 IGR103 IGR104 UU125 UU122 spoU, - UU124 cysS, - UU123 uvrB, - UU120 lig,DnlJ, - UU121 secA, - UU119 UU125 UU122 spoU, - UU124 cysS, - UU123 uvrB, - UU120 lig,DnlJ, - UU121 secA, - UU119 Type: tandem, Name:  - 89 Type: tandem, Name:  - 86 Type: tandem, Name:  - 91 Type: tandem, Name:  - 87 Type: tandem, Name:  - 88 Type: tandem, Name:  - 90 Type: tandem, Name:  - 432 UU125 UU122 spoU, - UU124 cysS, - UU123 uvrB, - UU120 lig,DnlJ, - UU121 secA, - UU119
* Calculated from Protein Sequence

Gene ID: UU121

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
lig  DnlJ  

Definition:
DNA ligase; Polydeoxyribonucleotide synthase (NAD+)

Gene Start:
159495

Gene Stop:
161516

Gene Length:
2022

Molecular Weight*:
77443

pI*:
6.20

Net Charge*:
-6.42

EC:
6.5.1.2  

Functional Class:
replication; DNA replication, restriction, modification, recombination, and repair  

Pathway: pathway table

Comment:
This protein catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double stranded DNA, using NAD as a coenzyme and as the energy source for the reaction. Lig is essential for DNA replication and repair of damaged DNA.

[Catalytic activity]:
NAD(+) + (Deoxyribonucleotide)(N) + (Deoxyribonucleotide)(M) =
AMP + nicotinamide nucleotide + (deoxyribonucleotide)(N+M).

Reference: Mol Gen Genet. 1986 Jul;204(1):1-7.

Blast Summary:  PSI-Blast Search
A gapped BLAST reveals a number of significant hits to DNA Ligase proteins. For example, residues 6-667 are 42% similar to the DNA ligase of M.pneumoniae (DNLJ_MYCPN). Other significant hits included (but were not limited to) the DNA ligases of M.genitalium (DNLJ_MYCGE), H.influenzae (DNLJ_HAEIN), R.prowazekki (pid:e1342996) and E.coli(DNLJ_ECOLI). By similarity, all of the above mentioned DNA ligases belong to the NAD-dependent DNA Ligase family.

A BLAST against the STDPRO database shows significant hits against the NAD-dependent DNA ligases of M.genitalium (MG254), C.trachomatis (CT146) and T.pallidum(TP0634).

COGS Summary:  COGS Search
The phylogenetic pattern of COG0272 is Ehgpc--u.
Cog name: NAD-dependent DNA ligase.
Functional class: L.
BeTs to e--pc--u.
Number of proteins in this genome belonging to this COG is 1



The phylogenetic pattern of is ehgpc-yu.
Cog name: BRCT domain type II.
Functional class: R.
BeTs to .
Number of proteins in this genome belonging to this COG is 1



Blocks Summary:  Blocks Search
Residues 10-51, 111-154, 193-215, 308-354, 244-290 and 356-383 rank in the 100.00th percentile to Block BL01055 (A,B,C,D,D and E respectively), described as NAD-dependent DNA ligase proteins.

Residues 304-310 rank in the 96.04th percentile to Block DM01834A, described as 8 Hydrogenase (Fe) Small Chain.



ProDom Summary:  Protein Domain Search
Residues 7-285 are 44% similar to a defined domain of O31498_BACSU, a DNA ligase.
Residues 286-481 are 49% similar, and residues 564-667 are 40% similar to a defined domain of DNLJ_MYCPN.
Residues 567-666 are 40% similar to a defined domain of DNLJ_HAEIN.

Paralogs:  Local Blast Search
No paralogs in U.u.

Pfam Summary:  Pfam Search
Residues 2 to 314 (E-value = 1.2e-136) place UU121 in the DNA_ligase_aden family which is described as NAD-dependent DNA ligase adenylation domain (PF01653)
Residues 316 to 398 (E-value = 5.8e-37) place UU121 in the DNA_ligase_OB family which is described as NAD-dependent DNA ligase OB-fold domain (PF03120)
Residues 402 to 430 (E-value = 4e-08) place UU121 in the DNA_ligase_ZBD family which is described as NAD-dependent DNA ligase C4 zinc finger domain (PF03119)
Residues 595 to 671 (E-value = 7e-06) place UU121 in the BRCT family which is described as BRCA1 C Terminus (BRCT) domain (PF00533)

PDB Hit:
gi|6573451|pdb|1B04|A Chain A, Structure Of The Adenylation Domain Of An Nad+ Dependent Ligase

Gene Protein Sequence:
MDKIKAKIDELKQKLDQWNYEYYVLDDPSVPDHVYDQTMRELIELENNYP
QFKTNNSPSVKVGGFVSEKFNKVKHKRPMLSLSNAFNDDDLKKFDQDNQN
ASVDLKGYVVEPKIDGLSISIIYKNAKLHQAITRGDGINGEDVTSNILTI
KDIPHYIDQKYKDYEIEVRGEVYMAFHDFYEMNDNLEESDKKFANPRNAA
AGTLRSLDNSIVAERKLSAFMYYLVNAQELGIKTHYESIQFLRDNKFKVS
DLIVKVDTINEVINQIDCYTKVRDKLSYMIDGIVIKINNLEVYDEIGYTS
KFPKWAIAYKFPANVVSSQLLEIINDVGRTGKISYVAKIKPILLDGSMVE
YATLHNFDFIKEKDIRINDEIKIYKAGDVIPYVDGVDLSKRLANSVPYEP
IINCPSCQSVLVRENDEVDQRCLNIYGCKKINIEKIVYFVSRNCMNIEGM
SDAIINKFYDANLIKNIADLYYLQKHKEFILTSDFKIKEKSFSNLINSIN
NSKKCSLEFLLTAFGIRHVGPNLAKKIAKQFKTMTALMHANFDELTNVDA
CGEKAALSLINWFNDEHNVSLVNQLQQVGVNMEYIDDFIYDDNINIIDEY
KNKTFVITGSFSISRDEIKTILEKYYHAKVKNSVSKKTDYVLVGTEAGTK
LEKAKLLGVKIIENEFWKKDNNF$

Gene Nucleotide Sequence:  Sequence Viewer
ATGGATAAAATAAAAGCTAAAATTGACGAATTAAAACAAAAACTAGACCA
ATGAAACTATGAATATTATGTTTTAGATGATCCAAGTGTGCCAGACCATG
TTTATGATCAAACAATGCGGGAGTTAATCGAACTTGAAAATAATTATCCT
CAATTTAAAACTAACAATTCACCAAGTGTAAAGGTTGGCGGCTTTGTTTC
AGAAAAATTTAATAAAGTAAAACATAAAAGACCAATGTTATCACTTTCAA
ATGCTTTTAATGATGATGATTTAAAAAAATTTGATCAAGATAATCAAAAT
GCTAGTGTCGATTTAAAAGGGTACGTAGTTGAACCTAAAATTGATGGTTT
AAGCATTTCTATTATTTATAAAAATGCCAAATTACACCAGGCAATTACAA
GAGGAGATGGGATTAATGGCGAAGATGTTACTTCCAATATTTTAACGATT
AAAGACATTCCTCACTATATTGATCAAAAATATAAAGACTACGAAATTGA
AGTTCGTGGTGAAGTCTATATGGCTTTTCATGATTTTTATGAAATGAATG
ATAATTTAGAAGAAAGTGATAAAAAATTTGCTAATCCAAGAAATGCTGCT
GCTGGAACATTAAGAAGTCTAGATAATTCAATTGTTGCAGAACGTAAATT
AAGTGCTTTTATGTATTATTTGGTTAATGCACAAGAACTAGGAATTAAAA
CGCATTATGAAAGTATTCAATTTTTAAGAGATAATAAATTTAAAGTTAGT
GATTTAATTGTTAAAGTCGATACAATTAATGAAGTTATTAATCAAATTGA
TTGTTATACTAAAGTGCGTGATAAACTTTCATATATGATTGATGGTATTG
TTATTAAAATTAATAATTTAGAAGTTTATGATGAGATTGGTTATACTTCT
AAATTTCCTAAATGAGCAATTGCTTATAAATTTCCAGCTAATGTTGTTAG
CTCACAATTACTAGAAATTATTAACGATGTTGGGCGTACAGGAAAAATCT
CATATGTTGCTAAAATTAAACCAATTTTATTAGATGGTAGTATGGTTGAA
TACGCTACTTTACATAACTTTGATTTTATTAAAGAAAAAGACATTCGAAT
TAATGATGAAATTAAAATTTATAAAGCAGGGGATGTAATTCCTTATGTTG
ATGGTGTTGATTTATCAAAACGTTTAGCAAATAGTGTACCTTATGAACCA
ATTATAAATTGCCCTTCATGCCAATCAGTTTTAGTACGTGAAAATGATGA
AGTTGACCAACGCTGCTTAAATATTTATGGATGTAAAAAAATCAATATTG
AAAAAATCGTTTATTTTGTTTCACGTAATTGCATGAATATTGAGGGAATG
AGTGATGCCATTATTAATAAATTTTATGATGCTAATTTAATTAAAAACAT
TGCAGATTTATACTATTTGCAAAAACACAAAGAATTTATTTTAACTAGTG
ATTTTAAAATTAAAGAAAAAAGTTTTAGTAATTTAATTAATAGTATTAAT
AATTCAAAAAAATGTTCTTTAGAATTTTTATTAACAGCTTTTGGAATTCG
TCATGTTGGACCAAATTTAGCTAAAAAAATAGCTAAACAATTTAAAACAA
TGACTGCTTTAATGCACGCTAATTTTGATGAATTAACTAATGTTGATGCA
TGTGGGGAAAAAGCAGCCTTATCATTAATTAATTGGTTTAATGATGAGCA
TAATGTTTCTTTAGTTAATCAATTACAACAAGTTGGTGTAAATATGGAAT
ATATTGATGATTTTATTTATGATGATAACATCAATATAATTGATGAATAT
AAAAATAAAACTTTTGTTATTACTGGTTCATTTAGTATTAGCCGTGATGA
AATTAAAACTATTTTAGAGAAATATTATCATGCAAAAGTTAAAAACAGTG
TTTCTAAAAAAACAGATTATGTTTTAGTTGGCACTGAAGCGGGTACGAAA
TTAGAAAAAGCTAAATTATTAGGTGTGAAAATTATTGAAAATGAATTTTG
AAAAAAGGATAATAATTTTTAA


Los Alamos National Laboratory     
Operated by the University of California for the National Nuclear Security Administration,
of the US Department of Energy.     Copyright © 2001 UC | Disclaimer/Privacy