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Treponema pallidum Search Results

Record: 1 of 1  
MiniMap IGR446 IGR445 IGR443 IGR444 TP0622 tprI, - TP0620 tprJ, - TP0621 TP0625 sbcD, - TP0626 TP0624 dniR,mltD, - TP0623 sbcC, - TP0627 TP0622 tprI, - TP0620 tprJ, - TP0621 TP0625 sbcD, - TP0626 TP0624 dniR,mltD, - TP0623 sbcC, - TP0627 Type: tandem, Name:  - 146 Type: tandem, Name:  - 143 Type: tandem, Name:  - 296 Type: tandem, Name:  - 144 Type: tandem, Name:  - 145 Type: tandem, Name:  - 147 TP0622 tprI, - TP0620 tprJ, - TP0621 TP0625 sbcD, - TP0626 TP0624 dniR,mltD, - TP0623 sbcC, - TP0627
* Calculated from Protein Sequence

Gene ID: TP0623

DNA Molecule Name:
1  

Genbank ID:
3322919

Gene Name:
dniR  mltD  

Definition:
possible membrane-bound lytic murein transglycosylase D (murein hydrolase D) (regulatory protein DnrI)

Gene Start:
676479

Gene Stop:
678815

Gene Length:
2337

Molecular Weight*:
84824

pI*:
11.06

Net Charge*:
52.08

EC:
3.2.1.-  

Functional Class:
Central intermediary metabolism; Polysaccharides  

Pathway: pathway table
Nucleotide metabolism; Aminosugars metabolism

Comment:
This protein is a murein-degrading enzyme. It may play a role in
recycling of muropeptides during cell elongation and/or cell division.

Reaction:
CLEAVAGE OF THE BETA-1,4-GLYCOSIDIC BOND BETWEEN N-ACETYLMURAMIC ACID
AND N-ACETYLGLUCOSAMINE RESIDUES, THEREBY CONSERVING THE ENERGY IN A
NEWLY SYNTHESIZED 1,6-ANHYDROBOND IN THE MURAMIC ACID RESIDUE.

TP0623 was assigned the EC 3.2.1.- in our original annotation. Comparison of our annotation with the annotation done by KEGGs leads us to re-examine
our original annotation.

Top 2 hit in gapped BALST were to MLTD (membrane-bound lytic murein transglycolase D precursor). MLTD entries in Swiss-Prot are given the EC
numbers 3.2.1.-. PSI-BLAST iterations were not informative in this case.

Looking at the BLAST results, we observed that the C-terminal (355-656aa) of TP0623 is the only region sharing similarity to the MLTD. This similiarity is shared over the entire length of the 2 MLTD database sequences.

The multiple sequences alignment of the MLTD sequences and TP0623 indicates that a possible start site for TP0623 is around 748bp position. If this is the correct start, then TP0623 would have significant similiarity to the 2 MLTD sequences over their entire length. However, there is no obvious ribosome binding site infront of this proposed start.

Finally, it should be noted that N-terminal of TP0623, as it is currently annotated, overlaps the N-terminal of TP0622 (which is coded from the opposite DNA strand) by 194 amino acids. Since these two Treponema proteins are coded in opposite directions, promoter sequences would be required within coding sequence.

TP0623 need to be revisited.


Blast Summary:  PSI-Blast Search
Gapped BLAST revealed a portion of the C-terminal region had
significant hits to membrane-bound lytic murein transglycosylase D
precursors, P60 proteins and a hypothetical protein. For example
residues 355-649 are 28% similar to MLTD_ECOLI, membrane-bound lytic
murein transglycosylase D of E. coli,(U70214).

COGS Summary:  COGS Search
BeTs to 5 clades of COG0741
COG name: Soluble lytic murein transglycosylase and related regulatory proteins
Functional Class:  M
The phylogenetic pattern of COG0741 is -----QVcEB-HUJ--oL--x
Number of proteins in this genome belonging to this COG is 2

Blocks Summary:  Blocks Search
Residues 401-425 and 466-473 represent significant (99%) similar to
blocks BL00922A,C, Prokaryotic transglycosylases proteins. Residues
in the region 700-718 represent a significant (99%) but unlikely
(proline rich region) hit to block PR00049D, WILM'S TUMOUR PROTEIN
SIGNATURE. Residues 60-76 represent a significant (99%) hit to block
PR00859C, PROKARYOTE METALLOTHIONEIN SIGNATURE.

ProDom Summary:  Protein Domain Search
Residues 506-594 are 24% similar to membrane-bound lytic murein
transglycosylase D of DNIR_ECOLI.

Paralogs:  Local Blast Search
This protein is paralogously related to TP0444 and TP0155 both of
which are conserved hypothetical proteins. Residues 605-779 are 27%
similar to TP0444 and residues 544-652 are 28% similar to TP0155.

Pfam Summary:  Pfam Search
Residues 378 to 493 (E-value = 1.2e-34) place TP0623 in the SLT family which is described as Transglycosylase SLT domain (PF01464)
Residues 607 to 650 (E-value = 3e-16) place TP0623 in the LysM family which is described as LysM domain (PF01476)
Residues 734 to 777 (E-value = 5.7e-16) place TP0623 in the LysM family which is described as LysM domain (PF01476)

Structural Feature(s):
Feature Type  Start  Stop
non-globular  
82  
177
non-globular  
243  
350
non-globular  
658  
729

PDB Hit:
none

Gene Protein Sequence:
MRARVRRSRQSACTSSGRRFFNRVSGGMISEKKSGSPGMSGYVPFSTSSS
AVRYGCAVLYSGTCQETASCGYTSCISAAHTRRYSRLCGVNPAGSRCMHA
AASRNEAGEAVSIKKSIFGSISFVRIARRSGTSSAVPRTGCAATSGAWDA
EETGSVPARVGTTFEELRQQRKTGISTKPTLTPMARSMLLVSAPIETRFY
LPAWQSCHLHKTPVVTVPTTYAYPAHRRFFSLYAVFNAHGASLVLPTQDM
LGWLPPRAKRAYRRLTVFLREIITARACSLFLFLLRCFPAGPCARARRLS
FLLFLCGAAACPPLWGAYAAHHALRAQSVPDTLIQRALVLGPLVHPLYPP
MQSFKEQYRSARYREYLSVVMQRSAPYRPFIEKLLRDAHLPVELLFLPVV
ESGFLERAVSKSGAVGIWQFMRNSIAGSAMRVSDWVDERRDPWKASVAAV
KKLQWNYTQLRDWPLALAAYNCGLGAIKRAIAQAGTADFWHLSERGFLRD
ETVRYVPKFLAVAEVLSRSHEHGIAWGAAHTPEETTTVTVSRAVDLNLLA
QAAGMDAQLLHTLNPALRYSITPPNAAYTLRVPSTHAQAVQAVLNRPGAV
LVHHTLHTIRSGDTLYALARRYGLGVDTLKAHNRAHSATHLKIGQKLIIP
TIRTGQTRRAPLRGAGTRAPGVMDQKEHAVPEVSALPSSSMTPPTPGGAD
TRAGADAPAPPSVPPPPESTAARATPAAPFVGKHVVQQGDTLWSLAKRYG
VSVENLAEENNLAVDATLSLGMILKTPRR

Gene Nucleotide Sequence:  Sequence Viewer
GTGCGTGCGCGCGTCAGGCGTTCTCGGCAATCTGCGTGTACCTCATCAGG
AAGGCGTTTTTTCAACAGAGTCAGCGGGGGAATGATATCCGAAAAAAAAT
CCGGTTCTCCAGGAATGAGCGGATACGTACCTTTTTCCACGTCATCGAGC
GCAGTCAGGTACGGATGCGCGGTGTTGTACAGCGGCACATGCCAAGAAAC
AGCTTCCTGCGGATATACAAGTTGCATAAGCGCAGCACACACGCGGAGGT
ACAGCCGATTGTGCGGTGTCAATCCGGCCGGATCGCGCTGTATGCACGCA
GCTGCCTCGCGCAATGAGGCAGGAGAAGCAGTTTCAATCAAGAAGAGTAT
CTTTGGATCCATCAGCTTTGTGCGAATTGCGCGTCGGTCCGGTACGTCAA
GCGCAGTGCCACGCACAGGATGCGCCGCCACCTCCGGCGCCTGGGATGCG
GAAGAAACCGGATCGGTACCTGCGCGCGTCGGCACCACCTTCGAAGAACT
GCGACAACAGAGAAAAACGGGTATCAGCACAAAACCGACACTCACCCCGA
TGGCGCGGTCAATGCTTTTAGTAAGCGCCCCCATAGAAACCCGTTTTTAC
CTCCCTGCATGGCAGTCGTGCCATTTACACAAAACGCCTGTTGTGACCGT
ACCGACAACGTACGCATACCCGGCGCACCGCCGCTTCTTTTCCCTTTACG
CGGTGTTCAACGCGCACGGCGCATCCCTTGTGCTCCCCACGCAAGACATG
CTAGGCTGGCTGCCACCGAGGGCGAAGAGAGCGTACAGGAGGTTAACGGT
TTTTTTGCGAGAAATCATTACCGCCCGTGCGTGTTCACTCTTCCTGTTTC
TCCTTCGTTGTTTCCCTGCTGGTCCCTGTGCGCGGGCGCGCCGGTTGTCC
TTCCTTCTGTTTCTCTGTGGTGCGGCAGCCTGCCCTCCGCTTTGGGGGGC
GTACGCAGCGCACCACGCGTTGCGCGCTCAGTCGGTACCTGACACCCTCA
TTCAGCGCGCGCTCGTGCTCGGTCCGCTCGTGCACCCCCTGTACCCGCCG
ATGCAGTCCTTCAAAGAACAGTACCGGAGCGCGCGTTACCGGGAATACCT
CTCTGTCGTTATGCAGCGGAGCGCGCCCTACCGCCCCTTTATCGAAAAAC
TGCTGCGCGACGCTCACCTTCCTGTCGAGCTGCTCTTTCTCCCCGTTGTC
GAATCGGGCTTTCTCGAACGGGCTGTCTCCAAATCCGGCGCAGTCGGCAT
TTGGCAGTTCATGCGCAATAGCATCGCAGGATCTGCCATGCGCGTGAGTG
ACTGGGTAGACGAACGGCGTGACCCCTGGAAGGCTTCCGTCGCCGCAGTC
AAAAAACTGCAGTGGAATTACACGCAGCTGCGTGACTGGCCCTTGGCCCT
CGCTGCGTACAACTGCGGTCTTGGCGCGATCAAGCGAGCCATTGCCCAGG
CAGGAACCGCCGATTTTTGGCATCTGAGTGAGCGCGGCTTTCTGCGCGAC
GAGACAGTCCGCTATGTCCCAAAGTTCCTTGCGGTTGCAGAAGTACTCAG
CCGGAGCCACGAGCACGGCATCGCCTGGGGAGCGGCACACACCCCCGAGG
AGACCACCACGGTTACCGTTTCGCGCGCGGTAGACTTAAACCTCTTGGCA
CAGGCAGCAGGGATGGATGCGCAATTGTTGCACACGCTCAACCCTGCACT
CCGCTATTCAATTACTCCCCCGAATGCAGCGTACACCCTCCGGGTGCCAA
GCACACATGCGCAGGCGGTCCAGGCAGTACTCAACCGCCCAGGCGCCGTG
CTCGTCCATCACACCCTGCACACCATCCGTTCAGGAGACACGCTTTACGC
ACTCGCCCGCCGCTATGGGTTGGGCGTCGATACGCTAAAAGCCCATAACC
GCGCACACAGCGCCACTCACCTGAAGATTGGACAAAAGCTCATCATTCCC
ACCATCCGGACTGGGCAGACCCGGCGCGCGCCCCTGCGGGGGGCAGGCAC
GCGTGCACCTGGAGTAATGGATCAGAAAGAGCATGCAGTGCCGGAAGTGT
CCGCACTTCCCTCGTCCTCAATGACGCCGCCGACGCCCGGGGGCGCGGAC
ACGCGCGCGGGAGCAGACGCGCCGGCACCCCCGAGCGTGCCACCACCGCC
GGAAAGCACAGCGGCGCGGGCAACCCCTGCAGCACCCTTTGTCGGCAAGC
ATGTAGTGCAGCAGGGGGATACCCTCTGGTCCTTAGCAAAGCGCTACGGC
GTTTCAGTAGAAAACCTGGCAGAGGAAAACAATCTAGCAGTAGACGCCAC
GCTCTCCTTGGGAATGATTCTCAAAACGCCGAGACGG


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