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Neisseria gonorrhoeae Search Results

Record: 1 of 1  
MiniMap IGR0538 IGR0540 IGR0536 IGR0539 IGR0537 NG0643 truB, - NG0642 argD, - NG0646 res, - NG0640 lldD, - NG0639 clpX, - NG0645 NG0643 truB, - NG0642 argD, - NG0646 res, - NG0640 lldD, - NG0639 clpX, - NG0645 Type: tandem, Name:  - 31 truB, - NG0642 argD, - NG0646 res, - NG0640 rbfA, - NG0644 mod, - NG0641 mod, - NG0641 NG0643 rbfA, - NG0644 lldD, - NG0639 clpX, - NG0645
* Calculated from Protein Sequence

Gene ID: NG0641

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
mod  

Definition:
type III restriction/modification system modification methylase

Gene Start:
632343

Gene Stop:
630076

Gene Length:
2268

Molecular Weight*:
86031

pI*:
5.60

Net Charge*:
-11.39

EC:
3.1.21.5  

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

Pathway: pathway table

Secondary Evidence:
Su,P., Im,H., Hsieh,H., Kang'A,S. and Dunn,N.W. LlaFI, a type III restriction and modification system in Lactococcus lactis. Appl. Environ. Microbiol. 65 (2), 686-693 (1999) Medline: 99124607.

Comment:
From Medline (99124607): A type III restriction and modification (R/M) system, LlaFI, in Lactococcus lactis consists of two adjacent open reading frames (ORFs). The two ORFs exhibited significant similarity to type III restriction (Res) and modification (Mod) subunits. Both the N-terminal regions and the C-terminal regions of the Mod proteins are conserved, while the central regions are more variable. An S-adenosyl methionine (Ado-Met) binding motif (present in all adenine methyltransferases) was found in the N-terminal region of the Mod protein. LlaFI has cofactor requirements for activity that are characteristic of the previously described type III enzymes. ATP and Mg2+ are required for endonucleolytic activity; however, the activity is not strictly dependent on the presence of Ado-Met but is stimulated by it. This type III R/M system has been characterized not just in lactic acid bacteria but also in gram-positive bacteria.

See NG0640, subunit RES of the type III restriction/modification system enzyme. See also another res/mod system, NG0545, subunit Mod and NG0546, subunit Res.

Oklahoma ID: NGO.641c

Blast Summary:  PSI-Blast Search
Many significant hits to type III restriction/modification system modification methylase, subunit Mod, using gapped BLAST. Residues 188-756 in NG0641 have 62% similarity to U32786, H. influenzae putative type III restriction-modification enyme Mod.

Residues 259-756 in NG0641 have 54% similarity to residues 1-492 in AL162756, N. meningitidis Z2491 putative type III restriction/modification system modification methylase (11354118).

COGS Summary:  COGS Search
BeTs to 3 clades of COG2189
COG name: Adenine specific DNA methylase Mod
Functional Class:  L
The phylogenetic pattern of COG2189 is a----------hUJ-------
Number of proteins in this genome belonging to this COG is 2

Blocks Summary:  Blocks Search
***** PR00506 (D21 class N6 adenine-specific DNA methyltransferase signature) with a combined E-value of 4.4e-25.
    PR00506A    269-281
    PR00506B    303-322
    PR00506C    554-576
    PR00506D    577-591
***** IPB001091 (N-4 DNA methylase (N4-MTase)) with a combined E-value of 1.1e-08.
    IPB001091A    266-278
    IPB001091B    577-587


ProDom Summary:  Protein Domain Search
Residues 453-555 are 35% similar to a (MODIFICATION METHYLASE LLAFI) protein domain (PD210058) which is seen in Q9Z6H7_BBBBB.

Residues 558-618 are 83% similar to a (METHYLTRANSFERASE TRANSFERASE MODIFICATION METHYLASE) protein domain (PD000881) which is seen in P71366_HAEIN.

Residues 247-423 are 60% similar to a (METHYLTRANSFERASE MODIFICATION TRANSFERASE TYPE DNA) protein domain (PD096111) which is seen in Q9Z6H7_BBBBB.

Residues 1-136 are 94% similar to a (MODIFICATION METHYLTRANSFERASE METHYLASE LLAFI PLASMID) protein domain (PD084123) which is seen in YA58_HAEIN.

Residues 188-246 are 94% similar to a (TYPE III RESTRICTION-MODIFICATION ECOP15) protein domain (PD096112) which is seen in P71366_HAEIN.

Residues 619-743 are 92% similar to a (TYPE III ENZYME MODIFICATION METHYLTRANSFERASE) protein domain (PD093625) which is seen in P71366_HAEIN.



Paralogs:  Local Blast Search


NG0641 is paralogously related to NG0545 (site-specific DNA-methyltransferase; type III restriction-modification system methyltransferase, subunit mod) (2e-23), NG1379 (TonB protein) (6e-04), NG1056 (outer membrane antigenic lipoprotein b precursor) (6e-04) and NG0008 (modification methylase (DpnA)) (6e-04).


Pfam Summary:  Pfam Search
Residues 307 to 615 (E-value = 3.4e-23) place NG0641 in the N6_N4_Mtase family which is described as DNA methylase (PF01555)

Structural Feature(s):
Feature Type  Start  Stop
non-globular  
138  
187
non-globular  
365  
488
non-globular  
683  
756

PDB Hit:
pdb|1G60|1G60-A CRYSTAL STRUCTURE OF METHYLTRANSFERASE MBOII 54.7 6e-08
pdb|1EG2|1EG2-A CRYSTAL STRUCTURE OF RHODOBACTER SPHEROIDES (N6 66.0 2e-11

Gene Protein Sequence:
MKTGIQTELAQALLSHEKIWANEEKTILAKNILLDLVEKTDPSIIGLLLN
NDELKRHFFVEVNGVLVFKLQDFRFFLDKHSINNSYTKYANRIGLTDGNR
FLKDNSDIVLDFPFKDCVLNGGQSTEEGEEIYFKRNNSQPASQPASQPAS
QPASQPASQPASQPASQPASQPASQPASQPASQPASQLYTKLTRKRQEIF
FNQTLAFDEIDRLFDAKAFSKFSRHTADGKQPVGEIKRRSDGTPAENLII
KGNNLIAMHSLAKQFKGKVKLIYIDPPYNTETDSFAYNDKFSHSTWLTFM
KNRLEIAKELLKDDGLIFVQCDDKEQAYLKVLLDETFTRENFINCIAVKM
SEPSGNKMAHTSHRLPKIKEYILIYKNKNIKLNPIREQKSEWDNEYNIFL
ENFTQEDKKFIDLIVNSQTENKEINGNTLKEIDILLKKISPISVNQKLAQ
LNIKDNEVIKWKLDNAYRIVRTAASSSVKKLADEKKEICQQQFFSVISKR
DKLLYIVKSDYSKDAKAPRVQVLFAEDYLSISLCDLWTNINTTGLEAEGN
VELKNGKKPESLIETIIKLATNENDIVLDYHLGSGTTAAVAHKMNRQYIG
IEQMDYIETLAVERMKKVIDGEQGGISKAVNWQGGGEFVYAELSPFNETA
KQQILACENSDGIKTLFEGLCERHFLKYNVSVNEFSQIIEEPEFQSLALD
EQKQMMLEMLDLNQMYISLSEMDDEQFAGCLNDDDKALSRAFYQSVKHQA
EKKDGE

Gene Nucleotide Sequence:  Sequence Viewer
ATGAAGACAGGCATTCAAACCGAATTAGCCCAAGCCCTGCTATCACACGA
AAAAATATGGGCGAACGAAGAAAAAACCATTTTGGCCAAAAACATCCTGT
TGGATTTGGTGGAAAAAACCGACCCGTCCATTATCGGTTTGTTATTGAAT
AATGATGAGTTAAAACGCCATTTCTTTGTGGAAGTGAATGGTGTTTTGGT
GTTTAAATTGCAGGATTTTCGTTTTTTCTTGGACAAACACAGCATCAATA
ATTCCTACACAAAATACGCCAACCGCATTGGTTTGACGGACGGCAACCGC
TTTTTGAAAGACAATTCGGATATTGTGTTGGATTTTCCGTTTAAAGATTG
CGTATTGAATGGCGGACAAAGCACCGAAGAAGGCGAAGAAATTTATTTTA
AACGCAATAATAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGC
CAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCA
GCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGC
CAGCCAGCCAATTATACACCAAATTAACCAGAAAAAGACAAGAAATCTTT
TTTAATCAAACGCTTGCTTTTGATGAAATTGACCGGCTTTTTGACGCAAA
AGCATTCTCAAAATTCTCCCGCCACACCGCAGACGGCAAACAACCCGTTG
GCGAAATCAAACGCCGTTCAGACGGTACGCCAGCCGAAAATCTCATTATC
AAAGGCAATAATCTGATTGCCATGCATTCGCTTGCCAAGCAGTTTAAAGG
CAAAGTAAAGTTGATTTATATTGATCCACCGTATAATACAGAAACCGATA
GCTTTGCATATAACGATAAATTTTCACATTCCACTTGGCTAACATTTATG
AAAAATCGCTTGGAAATTGCGAAAGAGTTATTAAAAGATGATGGGCTAAT
CTTTGTTCAATGCGATGATAAGGAACAGGCTTATTTAAAAGTTTTATTAG
ATGAAACTTTTACAAGAGAAAATTTTATAAACTGCATTGCTGTAAAAATG
TCAGAGCCATCAGGTAACAAAATGGCACATACATCGCATAGACTACCAAA
GATAAAGGAATATATTCTTATCTATAAGAATAAAAATATAAAATTAAACC
CTATTAGAGAGCAAAAATCAGAATGGGACAATGAGTACAATATTTTTTTA
GAAAATTTTACACAAGAAGATAAAAAATTTATTGATTTAATAGTAAATAG
CCAAACAGAAAATAAAGAAATAAATGGTAATACTTTAAAAGAAATTGATA
TTCTTTTAAAGAAAATATCTCCTATTTCAGTTAATCAAAAATTAGCCCAA
TTAAATATTAAAGATAATGAAGTTATAAAATGGAAACTAGATAATGCGTA
TAGAATTGTAAGAACAGCAGCTAGTAGTAGCGTAAAAAAATTAGCAGATG
AAAAAAAAGAAATTTGCCAACAACAATTTTTTTCAGTTATTTCTAAACGA
GATAAATTATTGTATATCGTCAAGTCAGATTACTCAAAAGATGCAAAAGC
ACCACGAGTGCAGGTTTTGTTTGCAGAAGATTATTTGAGTATTAGTTTAT
GCGATTTATGGACAAATATAAATACCACAGGACTAGAAGCAGAAGGAAAT
GTAGAGTTAAAAAATGGTAAAAAGCCAGAAAGTTTAATTGAAACCATCAT
TAAACTAGCAACCAACGAAAACGACATCGTTCTAGACTACCACTTGGGCA
GTGGCACAACCGCCGCCGTCGCCCATAAAATGAACCGCCAATACATCGGC
ATTGAACAAATGGATTATATTGAAACGCTTGCCGTTGAACGCATGAAAAA
AGTAATTGACGGCGAGCAAGGCGGTATCTCAAAAGCTGTGAATTGGCAAG
GTGGTGGCGAGTTTGTTTATGCCGAACTTTCCCCATTTAACGAAACCGCA
AAACAACAAATTTTGGCGTGCGAAAATTCAGACGGCATCAAAACGCTGTT
TGAAGGTTTATGCGAACGCCATTTCTTGAAATACAACGTCAGCGTAAATG
AATTTAGCCAAATTATTGAAGAGCCTGAATTTCAATCCTTGGCATTAGAC
GAACAAAAACAAATGATGCTTGAAATGTTGGATTTAAATCAAATGTATAT
TTCATTATCCGAAATGGACGATGAACAATTTGCAGGCTGCCTGAATGATG
ATGATAAAGCGTTAAGCCGTGCGTTCTATCAATCAGTAAAACATCAAGCG
GAGAAAAAAGATGGCGAA


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