254780514

254780514

type II restriction endonuclease

GeneID in NCBI database:8209509Locus tag:CLIBASIA_02005
Protein GI in NCBI database:254780514Protein Accession:YP_003064927.1
Gene range:-(763546, 763878)Protein Length:110aa
Gene description:type II restriction endonuclease
COG prediction:none
KEGG prediction:type II restriction endonuclease
SEED prediction:not defined as a protein in SEED
Pathway involved in KEGG:not defined
Subsystem involved in KEGG:not defined
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110
MQFNEIILKNISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTFVTHLMHKKKSGKALSLSIM
ccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEc
ccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHcccHHHHHHHHHcccccccccccEHEEEEEEHHHHHHHHHHHHHccccccEEEEEcc
MQFNEIILKNISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSntqsrrsrdgqEFEYIIYSLYNINTFVTHLMHKKKSGKALSLSIM
MQFNEIILknisnnyevPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTFVTHLMHKkksgkalslsim
MQFNEIILKNISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTFVTHLMHKKKSGKALSLSIM
***NEIILKNISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWV****************YIIYSLYNINTFVTHLMHKKKSGKALSLSIM
MQFNEIILKNISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTFVTHLM**************
MQFNEIILKNISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSNT******DGQEFEYIIYSLYNINTFVTHLMHKKKSGKALS****
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MQFNEIILKNISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTFVTHLMHKKKSGKALSLSIM
MQFNEIILKNISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTFVTHLMHKKKSGKALSLSIM
MQFNEIILKNISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTFVTHLMHKKKSGKALSLSIM

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target110 type II restriction endonuclease [Candidatus Liberibact
319407457 302 putative type II restriction endonuclease [Bartonella s 1 9e-17
150026186 298 type II restriction endonuclease [Flavobacterium psychr 1 3e-07
119026300 300 restriction endonuclease RKpn2kI [Bifidobacterium adole 2 0.001
283471714 306 type II restriction enzyme SsoII (Endonuclease SsoII)(R 2 0.001
>gi|319407457|emb|CBI81107.1| putative type II restriction endonuclease [Bartonella sp. 1-1C] Length = 302 Back     alignment and organism information
 Score = 90.1 bits (222), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 45/85 (52%), Positives = 54/85 (63%)

Query: 3   FNEIILKNISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEW 62
           FN  IL  IS  +E+PK +I+ELS +LF L   +   F+  L   FG Y  KI PY+Y  
Sbjct: 84  FNSAILMEISQQFEMPKRVISELSLKLFQLNVCDSQKFNEQLVNCFGQYAEKIIPYIYAL 143

Query: 63  VLSNTQSRRSRDGQEFEYIIYSLYN 87
            LSNTQSRRSR G+ FE IIY LYN
Sbjct: 144 CLSNTQSRRSRAGKTFEDIIYFLYN 168


Species: Bartonella sp. 1-1C
Genus: Bartonella
Family: Bartonellaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|150026186|ref|YP_001297012.1| type II restriction endonuclease [Flavobacterium psychrophilum JIP02/86] Length = 298 Back     alignment and organism information
>gi|119026300|ref|YP_910145.1| restriction endonuclease RKpn2kI [Bifidobacterium adolescentis ATCC 15703] Length = 300 Back     alignment and organism information
>gi|283471714|emb|CAQ50925.1| type II restriction enzyme SsoII (Endonuclease SsoII)(R.SsoII) [Staphylococcus aureus subsp. aureus ST398] Length = 306 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

No hit with e-value below 0.005

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 110 type II restriction endonuclease [Candidatus Liberibact
pfam09019164 EcoRII-C EcoRII C terminal. The C-terminal catalytic do 97.48
>pfam09019 EcoRII-C EcoRII C terminal Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target110 type II restriction endonuclease [Candidatus Liberibact
2gb7_A 305 Metal-Depleted Ecl18ki In Complex With Uncleaved, M 7e-13
>gi|110590214|pdb|2GB7|A Chain A, Metal-Depleted Ecl18ki In Complex With Uncleaved, Modified Dna Length = 305 Back     alignment and structure
 Score = 77.1 bits (188), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 4/64 (6%)

Query: 19  KMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEF 78
           K   T + + L + +       ++ +     +Y +    ++Y+  LSNTQSRRSR G+EF
Sbjct: 69  KEFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPT----HIYDLALSNTQSRRSRAGKEF 124

Query: 79  EYII 82
           E I+
Sbjct: 125 ESIL 128


Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target110 type II restriction endonuclease [Candidatus Liberibact
2gb7_A 305 R.ECL18KI; ECL18KI-DNA complex, type II restriction end 8e-04
1na6_A 404 Ecorii, restriction endonuclease ecorii; site-specific 0.003
>2gb7_A R.ECL18KI; ECL18KI-DNA complex, type II restriction endonuclease, nucleotide flipping, base extrusion, hydrolase/DNA complex; HET: DNA; 1.70A {Enterobacter cloacae} PDB: 2fqz_A* Length = 305 Back     alignment and structure
 Score = 37.3 bits (86), Expect = 8e-04
 Identities = 18/40 (45%), Positives = 25/40 (62%)

Query: 48  FGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYN 87
             D+  +   ++Y+  LSNTQSRRSR G+EFE I+  L  
Sbjct: 94  IRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMM 133


>1na6_A Ecorii, restriction endonuclease ecorii; site-specific restriction, mutation, replication, hydrolase; 2.10A {Escherichia coli} SCOP: b.142.1.1 c.52.1.22 PDB: 3hqg_A 3hqf_A Length = 404 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target110 type II restriction endonuclease [Candidatus Liberibact
2gb7_A 305 R.ECL18KI; ECL18KI-DNA complex, type II restriction end 99.42
3bm3_A 272 PSPGI restriction endonuclease; endonuclease-DNA comple 99.26
1na6_A 404 Ecorii, restriction endonuclease ecorii; site-specific 97.73
>2gb7_A R.ECL18KI; ECL18KI-DNA complex, type II restriction endonuclease, nucleotide flipping, base extrusion, hydrolase/DNA complex; HET: DNA; 1.70A {Enterobacter cloacae} PDB: 2fqz_A* Back     alignment and structure
Probab=99.42  E-value=1.7e-13  Score=98.82  Aligned_cols=71  Identities=30%  Similarity=0.327  Sum_probs=65.9

Q ss_pred             CHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             369999999996379642001579999999963212011044576310322355433045799999999739999
Q gi|254780514|r   17 VPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTF   91 (110)
Q Consensus        17 tPK~ll~~llselin~~t~K~~e~~etir~~~gdY~~~i~P~iy~l~lsntqsrrsrag~~fe~iiY~~Yn~~t~   91 (110)
                      .-+.+..++++.++|.+.+|++.+.++|+++|++|+.    +||.|++|++|||+||||+.||.+|.+++..+..
T Consensus        67 ~E~~~~~~~ls~~~d~~~~k~~~v~~~i~~~~~~~~d----~i~~L~lSv~QsRkSRAG~sfE~hle~if~~~GI  137 (305)
T 2gb7_A           67 FEKEFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPT----HIYDLALSNTQSRRSRAGKEFESILELLMMGAGI  137 (305)
T ss_dssp             HHHHHHHHHHHTTCCHHHHTTSCHHHHHHHHHHHCHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCH----HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCC
T ss_conf             8488899999853102110103699999877315818----9999998888746620204299999999997398



>3bm3_A PSPGI restriction endonuclease; endonuclease-DNA complex, restriction enzyme, PSPGI, base flipping, hydrolase/DNA complex; HET: DNA MSE CIT; 1.70A {Pyrococcus SP} Back     alignment and structure
>1na6_A Ecorii, restriction endonuclease ecorii; site-specific restriction, mutation, replication, hydrolase; 2.10A {Escherichia coli} SCOP: b.142.1.1 c.52.1.22 PDB: 3hqg_A 3hqf_A Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

No hit with e-value below 0.005

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target110 type II restriction endonuclease [Candidatus Liberibact
d1na6a2220 Restriction endonuclease EcoRII, C-terminal domain {Esc 97.54
>d1na6a2 c.52.1.22 (A:179-398) Restriction endonuclease EcoRII, C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Restriction endonuclease-like
family: Type II restriction endonuclease catalytic domain
domain: Restriction endonuclease EcoRII, C-terminal domain
species: Escherichia coli [TaxId: 562]
Probab=97.54  E-value=1.2e-05  Score=51.43  Aligned_cols=31  Identities=23%  Similarity=0.321  Sum_probs=28.2

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6310322355433045799999999739999
Q gi|254780514|r   61 EWVLSNTQSRRSRDGQEFEYIIYSLYNINTF   91 (110)
Q Consensus        61 ~l~lsntqsrrsrag~~fe~iiY~~Yn~~t~   91 (110)
                      .+.||++|+|+||||+.||.+++.|++-+..
T Consensus        75 ~~slSv~nrRKSRAG~sfE~hl~~if~~~gi  105 (220)
T d1na6a2          75 ALANSVSNRRKSRAGKSLELHLEHLFIEHGL  105 (220)
T ss_dssp             HHHHHHHHHHHHHSSSHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHCCC
T ss_conf             9999998877503305699999999996699



Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 110 type II restriction endonuclease [Candidatus Liber
2gb7_A_1-137137 (A:1-137) R.ECL18KI; ECL18KI-DNA complex, type II 4e-06
>2gb7_A (A:1-137) R.ECL18KI; ECL18KI-DNA complex, type II restriction endonuclease, nucleotide flipping, base extrusion, hydrolase/DNA complex; HET: DNA; 1.70A {Enterobacter cloacae} PDB: 2fqz_A*Length = 137 Back     alignment and structure
 Score = 45.0 bits (106), Expect = 4e-06
 Identities = 19/59 (32%), Positives = 31/59 (52%)

Query: 24  ELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYII 82
           E +T + +     +     +      D+  +   ++Y+  LSNTQSRRSR G+EFE I+
Sbjct: 70  EFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESIL 128


Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target110 type II restriction endonuclease [Candidatus Liberibact
2gb7_A_1-137137 R.ECL18KI; ECL18KI-DNA complex, type II restrictio 99.89
>2gb7_A (A:1-137) R.ECL18KI; ECL18KI-DNA complex, type II restriction endonuclease, nucleotide flipping, base extrusion, hydrolase/DNA complex; HET: DNA; 1.70A {Enterobacter cloacae} PDB: 2fqz_A* Back     alignment and structure
Probab=99.89  E-value=4.1e-24  Score=161.82  Aligned_cols=65  Identities=32%  Similarity=0.394  Sum_probs=61.6

Q ss_pred             CHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             369999999996379642001579999999963212011044576310322355433045799999999
Q gi|254780514|r   17 VPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSL   85 (110)
Q Consensus        17 tPK~ll~~llselin~~t~K~~e~~etir~~~gdY~~~i~P~iy~l~lsntqsrrsrag~~fe~iiY~~   85 (110)
                      --|.|++++++.|+|++++|+|+++|+|++||||||.    |||+|+|||||||||||||+||+||--+
T Consensus        67 ~Ek~Ft~k~ls~Lld~~~~K~m~~~e~Ik~f~~ey~~----~IY~L~LSNTQSRRSRAGKeFEaIiel~  131 (137)
T 2gb7_A           67 FEKEFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPT----HIYDLALSNTQSRRSRAGKEFESILELL  131 (137)
T ss_dssp             HHHHHHHHHHHTTCCHHHHTTSCHHHHHHHHHHHCHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCH----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             6455179999873004443115789999999850625----8999988888877731004399999999