Query 035039
Match_columns 75
No_of_seqs 12 out of 14
Neff 1.8
Searched_HMMs 46136
Date Fri Mar 29 08:42:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035039.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035039hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00301 Rubredoxin: Rubredoxi 66.5 2.5 5.4E-05 24.8 0.5 18 35-52 7-25 (47)
2 PF08953 DUF1899: Domain of un 63.8 2.5 5.3E-05 26.2 0.1 14 51-64 50-63 (65)
3 PF11584 Toxin_ToxA: Proteinac 61.6 1.2 2.7E-05 31.3 -1.7 14 46-59 88-101 (118)
4 cd09024 Aldose_epim_lacX Aldos 47.1 11 0.00023 26.9 1.2 36 20-63 218-253 (288)
5 PF06613 KorB_C: KorB C-termin 36.9 6.3 0.00014 25.0 -1.2 38 10-47 3-43 (60)
6 KOG0009 Ubiquitin-like/40S rib 34.5 9.6 0.00021 24.6 -0.6 18 22-39 31-48 (62)
7 PRK09647 RNA polymerase sigma 34.3 15 0.00032 25.1 0.3 17 40-56 3-26 (203)
8 PF13271 DUF4062: Domain of un 33.9 19 0.0004 21.7 0.6 11 29-39 58-68 (83)
9 PF04939 RRS1: Ribosome biogen 29.3 21 0.00045 25.7 0.3 16 22-37 93-115 (164)
10 cd03420 SirA_RHOD_Pry_redox Si 27.6 31 0.00067 20.2 0.8 13 53-65 4-16 (69)
11 PRK07308 flavodoxin; Validated 27.5 11 0.00023 24.1 -1.3 29 30-59 90-118 (146)
12 COG1773 Rubredoxin [Energy pro 26.7 23 0.0005 21.9 0.2 21 35-55 9-29 (55)
13 PF07038 DUF1324: Protein of u 25.9 18 0.00038 23.0 -0.5 9 55-63 9-17 (59)
14 COG4607 CeuA ABC-type enteroch 25.2 28 0.00061 28.0 0.4 18 34-51 215-233 (320)
15 PF07893 DUF1668: Protein of u 23.4 31 0.00068 25.9 0.3 9 53-61 287-295 (342)
16 cd03422 YedF YedF is a bacteri 22.6 43 0.00094 19.6 0.8 14 53-66 4-17 (69)
17 PRK10148 hypothetical protein; 22.5 32 0.00068 22.9 0.2 14 29-42 119-132 (147)
18 PF15584 Imm44: Immunity prote 22.1 39 0.00084 23.1 0.5 10 26-35 70-80 (94)
19 PF09664 DUF2399: Protein of u 21.8 38 0.00083 23.3 0.5 20 33-54 88-108 (152)
20 PF14309 DUF4378: Domain of un 21.4 21 0.00045 23.1 -0.8 13 21-33 54-66 (162)
21 PRK14782 lipoprotein signal pe 21.1 26 0.00056 24.2 -0.4 12 30-41 106-118 (157)
22 PRK05446 imidazole glycerol-ph 21.0 42 0.00091 26.1 0.6 22 33-59 253-280 (354)
23 PF07832 Bse634I: Cfr10I/Bse63 20.4 22 0.00047 28.1 -1.0 9 32-40 198-206 (280)
No 1
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=66.48 E-value=2.5 Score=24.84 Aligned_cols=18 Identities=39% Similarity=0.708 Sum_probs=12.6
Q ss_pred ccceeeccc-CchHHHhcC
Q 035039 35 YGWVFDEWK-DPSEEALAG 52 (75)
Q Consensus 35 YGWv~DEW~-DPae~ALaG 52 (75)
=|||||+.+ ||......|
T Consensus 7 CgyvYd~~~Gd~~~~i~pG 25 (47)
T PF00301_consen 7 CGYVYDPEKGDPENGIPPG 25 (47)
T ss_dssp TSBEEETTTBBGGGTB-TT
T ss_pred CCEEEcCCcCCcccCcCCC
Confidence 389999999 776654443
No 2
>PF08953 DUF1899: Domain of unknown function (DUF1899); InterPro: IPR015048 This set of proteins are found in various eukaryotic proteins. The function is unknown. ; PDB: 2B4E_A 2AQ5_A.
Probab=63.77 E-value=2.5 Score=26.20 Aligned_cols=14 Identities=50% Similarity=1.096 Sum_probs=8.7
Q ss_pred cCCCceeehhhhHH
Q 035039 51 AGGRGMFCIVPLAK 64 (75)
Q Consensus 51 aGGRGmFCilplAk 64 (75)
+||-|.|+++||.+
T Consensus 50 ~~GGG~~~Vlpl~~ 63 (65)
T PF08953_consen 50 SGGGGAFAVLPLNK 63 (65)
T ss_dssp -SSS--EEEEETT-
T ss_pred cCCccEEEEEeCCC
Confidence 56779999999976
No 3
>PF11584 Toxin_ToxA: Proteinaceous host-selective toxin ToxA; InterPro: IPR021635 ToxA is produced by particular Pyrenophora triticirepentis races and is a proteinaceous host-selective toxin. It is necessary and sufficient to cause cell death in sensitive wheat cultivars [].ToxA adopts a single-domain, beta-sandwich fold which has novel topology. The protein is directly involved in recognition events required for ToxA action. It is thought to be distantly related to FnIII proteins, gaining entry to the host via an integrin-like receptor []. ; PDB: 1ZLE_C 1ZLD_A.
Probab=61.55 E-value=1.2 Score=31.30 Aligned_cols=14 Identities=50% Similarity=1.018 Sum_probs=11.6
Q ss_pred hHHHhcCCCceeeh
Q 035039 46 SEEALAGGRGMFCI 59 (75)
Q Consensus 46 ae~ALaGGRGmFCi 59 (75)
+++||.-|||-||+
T Consensus 88 gdyaliqgrgsfcl 101 (118)
T PF11584_consen 88 GDYALIQGRGSFCL 101 (118)
T ss_dssp EEEEE-SEEEEEEE
T ss_pred cceeEEeccceEEE
Confidence 56899999999997
No 4
>cd09024 Aldose_epim_lacX Aldose 1-epimerase, similar to Lactococcus lactis lacX. Proteins similar to Lactococcus lactis lacX are uncharacterized members of aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen.
Probab=47.14 E-value=11 Score=26.93 Aligned_cols=36 Identities=25% Similarity=0.502 Sum_probs=26.6
Q ss_pred CCCcccccceeeeeeccceeecccCchHHHhcCCCceeehhhhH
Q 035039 20 SPSKLSSKRLLFDRRYGWVFDEWKDPSEEALAGGRGMFCIVPLA 63 (75)
Q Consensus 20 s~~~r~~rRL~fDRRYGWv~DEW~DPae~ALaGGRGmFCilplA 63 (75)
++...+.-++.||. |.|.- =|+.|. ++..|||=||.
T Consensus 218 ~~~~~~~v~l~~~~-~~~l~-vwt~~~------~~~~iciEP~t 253 (288)
T cd09024 218 SKKTGHGVTVDFDD-FPYLG-IWSKPN------GAPFVCIEPWY 253 (288)
T ss_pred cCCCCCEEEEEeCC-CCEEE-EeCCCC------CCCEEEEcCCC
Confidence 33334567778888 88865 788773 68899999985
No 5
>PF06613 KorB_C: KorB C-terminal beta-barrel domain; InterPro: IPR010575 This domain is found in several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This family is found in conjunction with IPR003115 from INTERPRO.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1IGQ_B 1IGU_A.
Probab=36.89 E-value=6.3 Score=25.04 Aligned_cols=38 Identities=24% Similarity=0.356 Sum_probs=22.1
Q ss_pred CccccccCCCCCCcccccceeeeee---ccceeecccCchH
Q 035039 10 SSKTSIPALSSPSKLSSKRLLFDRR---YGWVFDEWKDPSE 47 (75)
Q Consensus 10 s~k~~~~~lss~~~r~~rRL~fDRR---YGWv~DEW~DPae 47 (75)
+.|+.+|.+--.---|.-||+.+|| +||..=..-|-++
T Consensus 3 pdklKKaiv~V~~d~R~arllLnrRps~~G~~WiKyED~G~ 43 (60)
T PF06613_consen 3 PDKLKKAIVQVEHDGRPARLLLNRRPSSEGLAWIKYEDDGE 43 (60)
T ss_dssp TTB-SSEEEEEEETTEEEEE-TTB--SSTTEEEEEETTT--
T ss_pred hhhhhccEEEEEECCchhhhhhccCCCcCCeEEEEEccCCc
Confidence 4566666554444456789999999 8887666666444
No 6
>KOG0009 consensus Ubiquitin-like/40S ribosomal S30 protein fusion [Translation, ribosomal structure and biogenesis; Posttranslational modification, protein turnover, chaperones]
Probab=34.53 E-value=9.6 Score=24.55 Aligned_cols=18 Identities=33% Similarity=0.490 Sum_probs=14.8
Q ss_pred Ccccccceeeeeecccee
Q 035039 22 SKLSSKRLLFDRRYGWVF 39 (75)
Q Consensus 22 ~~r~~rRL~fDRRYGWv~ 39 (75)
.-|..+||.|.|||-=++
T Consensus 31 ~GRa~~Rlqy~rR~vn~~ 48 (62)
T KOG0009|consen 31 RGRAKKRLQYNRRFVNVV 48 (62)
T ss_pred cchHHHHhhhheeeEEee
Confidence 457889999999997655
No 7
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=34.29 E-value=15 Score=25.11 Aligned_cols=17 Identities=35% Similarity=0.923 Sum_probs=12.7
Q ss_pred ecccCchHH-------HhcCCCce
Q 035039 40 DEWKDPSEE-------ALAGGRGM 56 (75)
Q Consensus 40 DEW~DPae~-------ALaGGRGm 56 (75)
|.|+.|+++ |++|+-|.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~d 26 (203)
T PRK09647 3 DDWVEPSDELTGTAVFDATGDKAT 26 (203)
T ss_pred ccccCcccccccccccCCCCCCCC
Confidence 789999886 56777763
No 8
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=33.95 E-value=19 Score=21.73 Aligned_cols=11 Identities=45% Similarity=0.745 Sum_probs=9.2
Q ss_pred eeeeeecccee
Q 035039 29 LLFDRRYGWVF 39 (75)
Q Consensus 29 L~fDRRYGWv~ 39 (75)
+++-.||||+-
T Consensus 58 ~ilG~rYG~~~ 68 (83)
T PF13271_consen 58 LILGNRYGSVP 68 (83)
T ss_pred EeeccccCCCC
Confidence 56788999987
No 9
>PF04939 RRS1: Ribosome biogenesis regulatory protein (RRS1); InterPro: IPR007023 This is a family of eukaryotic ribosomal biogenesis regulatory proteins.; GO: 0042254 ribosome biogenesis, 0005634 nucleus
Probab=29.28 E-value=21 Score=25.72 Aligned_cols=16 Identities=31% Similarity=0.798 Sum_probs=12.5
Q ss_pred Ccccccceeee-------eeccc
Q 035039 22 SKLSSKRLLFD-------RRYGW 37 (75)
Q Consensus 22 ~~r~~rRL~fD-------RRYGW 37 (75)
.|+.+.||+|| +|||+
T Consensus 93 ~K~Kk~~lv~DE~~~eW~prwGy 115 (164)
T PF04939_consen 93 KKRKKSKLVYDEETGEWVPRWGY 115 (164)
T ss_pred ccccCcCccccccccchhhcccc
Confidence 47788899999 57775
No 10
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=27.61 E-value=31 Score=20.22 Aligned_cols=13 Identities=31% Similarity=0.562 Sum_probs=10.3
Q ss_pred CCceeehhhhHHH
Q 035039 53 GRGMFCIVPLAKA 65 (75)
Q Consensus 53 GRGmFCilplAk~ 65 (75)
-||..|-.|+-++
T Consensus 4 ~rG~~CP~Pvl~~ 16 (69)
T cd03420 4 ACGLQCPGPILKL 16 (69)
T ss_pred cCCCcCCHHHHHH
Confidence 4899999997543
No 11
>PRK07308 flavodoxin; Validated
Probab=27.50 E-value=11 Score=24.09 Aligned_cols=29 Identities=21% Similarity=0.029 Sum_probs=20.1
Q ss_pred eeeeeccceeecccCchHHHhcCCCceeeh
Q 035039 30 LFDRRYGWVFDEWKDPSEEALAGGRGMFCI 59 (75)
Q Consensus 30 ~fDRRYGWv~DEW~DPae~ALaGGRGmFCi 59 (75)
+.|+.|+| |-++.+.-++.|....+-++.
T Consensus 90 ~Gd~~y~~-~~~a~~~~~~~l~~~g~~~~~ 118 (146)
T PRK07308 90 SGDTFYDY-FCKSVDDFEAQFALTGATKGA 118 (146)
T ss_pred eCCCCHHH-HHHHHHHHHHHHHHcCCeEcc
Confidence 46888998 888888777777654444433
No 12
>COG1773 Rubredoxin [Energy production and conversion]
Probab=26.72 E-value=23 Score=21.86 Aligned_cols=21 Identities=29% Similarity=0.444 Sum_probs=15.4
Q ss_pred ccceeecccCchHHHhcCCCc
Q 035039 35 YGWVFDEWKDPSEEALAGGRG 55 (75)
Q Consensus 35 YGWv~DEW~DPae~ALaGGRG 55 (75)
=|||||+=+-+.+.-.++|.-
T Consensus 9 CG~vYd~e~Gdp~~gi~pgT~ 29 (55)
T COG1773 9 CGYVYDPEKGDPRCGIAPGTP 29 (55)
T ss_pred CceEeccccCCccCCCCCCCc
Confidence 399999998666666666654
No 13
>PF07038 DUF1324: Protein of unknown function (DUF1324); InterPro: IPR009757 This family consists of several Circovirus proteins of around 60 residues in length. The function of this family is unknown.
Probab=25.94 E-value=18 Score=23.03 Aligned_cols=9 Identities=56% Similarity=1.239 Sum_probs=7.3
Q ss_pred ceeehhhhH
Q 035039 55 GMFCIVPLA 63 (75)
Q Consensus 55 GmFCilplA 63 (75)
..|||.||+
T Consensus 9 srfcifplt 17 (59)
T PF07038_consen 9 SRFCIFPLT 17 (59)
T ss_pred eeeEEEEee
Confidence 379999985
No 14
>COG4607 CeuA ABC-type enterochelin transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=25.21 E-value=28 Score=28.00 Aligned_cols=18 Identities=33% Similarity=1.003 Sum_probs=14.0
Q ss_pred eccceeeccc-CchHHHhc
Q 035039 34 RYGWVFDEWK-DPSEEALA 51 (75)
Q Consensus 34 RYGWv~DEW~-DPae~ALa 51 (75)
||||+||+-. .|.++.+.
T Consensus 215 Rfg~ihd~~G~~pvd~~~~ 233 (320)
T COG4607 215 RFGWIHDDLGFTPVDENIK 233 (320)
T ss_pred cceeeecccCCCccccccc
Confidence 7899999988 77666553
No 15
>PF07893 DUF1668: Protein of unknown function (DUF1668); InterPro: IPR012871 The hypothetical proteins found in this family are expressed by Oryza sativa (Rice) and are of unknown function.
Probab=23.37 E-value=31 Score=25.87 Aligned_cols=9 Identities=67% Similarity=1.357 Sum_probs=7.6
Q ss_pred CCceeehhh
Q 035039 53 GRGMFCIVP 61 (75)
Q Consensus 53 GRGmFCilp 61 (75)
|.|.|||+=
T Consensus 287 G~grFCi~~ 295 (342)
T PF07893_consen 287 GSGRFCIVE 295 (342)
T ss_pred CCCCEEEEE
Confidence 799999863
No 16
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=22.58 E-value=43 Score=19.65 Aligned_cols=14 Identities=29% Similarity=0.316 Sum_probs=11.1
Q ss_pred CCceeehhhhHHHH
Q 035039 53 GRGMFCIVPLAKAC 66 (75)
Q Consensus 53 GRGmFCilplAk~l 66 (75)
-||..|=.|+-++-
T Consensus 4 ~rG~~CP~Pvi~~k 17 (69)
T cd03422 4 LRGEPCPYPAIATL 17 (69)
T ss_pred cCCCcCCHHHHHHH
Confidence 48999999987653
No 17
>PRK10148 hypothetical protein; Provisional
Probab=22.54 E-value=32 Score=22.88 Aligned_cols=14 Identities=21% Similarity=0.537 Sum_probs=11.2
Q ss_pred eeeeeeccceeecc
Q 035039 29 LLFDRRYGWVFDEW 42 (75)
Q Consensus 29 L~fDRRYGWv~DEW 42 (75)
--|..||||+.|-+
T Consensus 119 ~~wg~~~g~v~D~f 132 (147)
T PRK10148 119 TFWAHGFGKVTDKF 132 (147)
T ss_pred cchhhccEEEECCC
Confidence 46888999999864
No 18
>PF15584 Imm44: Immunity protein 44
Probab=22.07 E-value=39 Score=23.09 Aligned_cols=10 Identities=50% Similarity=1.042 Sum_probs=7.5
Q ss_pred ccceee-eeec
Q 035039 26 SKRLLF-DRRY 35 (75)
Q Consensus 26 ~rRL~f-DRRY 35 (75)
.=||+| |+||
T Consensus 70 ~WRLiWeD~RY 80 (94)
T PF15584_consen 70 RWRLIWEDKRY 80 (94)
T ss_pred EEEEEEecccc
Confidence 357887 8888
No 19
>PF09664 DUF2399: Protein of unknown function C-terminus (DUF2399); InterPro: IPR024465 This domain is found in archaeal, bacterial and eukaryotic proteins. Its function is unknown.
Probab=21.76 E-value=38 Score=23.28 Aligned_cols=20 Identities=30% Similarity=0.479 Sum_probs=15.2
Q ss_pred eeccceeeccc-CchHHHhcCCC
Q 035039 33 RRYGWVFDEWK-DPSEEALAGGR 54 (75)
Q Consensus 33 RRYGWv~DEW~-DPae~ALaGGR 54 (75)
.||||.+ |. ++.++..+=+.
T Consensus 88 ~r~~~~~--Wrm~~~dY~~~~~~ 108 (152)
T PF09664_consen 88 QRYGARP--WRMDAEDYLAALSA 108 (152)
T ss_pred HHhCCcc--ccCCHHHHHHhccc
Confidence 5899999 99 88888654443
No 20
>PF14309 DUF4378: Domain of unknown function (DUF4378)
Probab=21.42 E-value=21 Score=23.07 Aligned_cols=13 Identities=38% Similarity=0.496 Sum_probs=10.3
Q ss_pred CCcccccceeeee
Q 035039 21 PSKLSSKRLLFDR 33 (75)
Q Consensus 21 ~~~r~~rRL~fDR 33 (75)
...|.-|||+||.
T Consensus 54 ~~~~~~rkLLFD~ 66 (162)
T PF14309_consen 54 RWSRSDRKLLFDC 66 (162)
T ss_pred cccchhhhhHHHH
Confidence 4577889999993
No 21
>PRK14782 lipoprotein signal peptidase; Provisional
Probab=21.11 E-value=26 Score=24.16 Aligned_cols=12 Identities=50% Similarity=0.985 Sum_probs=8.8
Q ss_pred eeee-eccceeec
Q 035039 30 LFDR-RYGWVFDE 41 (75)
Q Consensus 30 ~fDR-RYGWv~DE 41 (75)
++|| +||.|.|=
T Consensus 106 liDRi~~G~VvDF 118 (157)
T PRK14782 106 VLDRVIYGYVLDF 118 (157)
T ss_pred HHHHhhcCceEEE
Confidence 3577 88888883
No 22
>PRK05446 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional
Probab=21.03 E-value=42 Score=26.11 Aligned_cols=22 Identities=36% Similarity=0.718 Sum_probs=16.1
Q ss_pred eeccceeecccCchHHHhc------CCCceeeh
Q 035039 33 RRYGWVFDEWKDPSEEALA------GGRGMFCI 59 (75)
Q Consensus 33 RRYGWv~DEW~DPae~ALa------GGRGmFCi 59 (75)
+|||| + =|-+|||+ +||+-|..
T Consensus 253 ~r~g~-~----~pmdeal~~~~~d~sgr~~~~~ 280 (354)
T PRK05446 253 GRFGF-V----LPMDECLARCALDISGRPYLVF 280 (354)
T ss_pred ceeee-c----cchhheeeEEEEECCCCCeeEE
Confidence 58998 3 38899986 68886554
No 23
>PF07832 Bse634I: Cfr10I/Bse634I restriction endonuclease; InterPro: IPR012415 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents Cfr10I and Bse634I restriction endonucleases. They exhibit a conserved tetrameric architecture that is of functional importance, wherein two dimers are arranged, back-to-back, with their putative DNA-binding clefts facing opposite directions. These clefts are formed between two monomers that interact, mainly via hydrophobic interactions supported by a few hydrogen bonds, to form a U-shaped dimer. Each monomer is folded to form a compact alpha-beta structure, whose core is made up of a five-stranded mixed beta-sheet. The monomer may be split into separate N-terminal and C-terminal subdomains at a hinge located in helix alpha3 []. Both Cfr10I and Bse634I recognise the double-stranded sequence RCCGGY and cleave after the purine R [].; PDB: 1CFR_A 3V21_B 1KNV_A 3V20_B 3V1Z_B 3MQY_A 3DVO_A 3MQ6_F 3DPG_B 3N7B_B ....
Probab=20.43 E-value=22 Score=28.08 Aligned_cols=9 Identities=44% Similarity=0.752 Sum_probs=7.8
Q ss_pred eeeccceee
Q 035039 32 DRRYGWVFD 40 (75)
Q Consensus 32 DRRYGWv~D 40 (75)
||||+|+|.
T Consensus 198 DRryQplhE 206 (280)
T PF07832_consen 198 DRRYQPLHE 206 (280)
T ss_dssp CCHHHHHHH
T ss_pred cccccchhh
Confidence 999999874
Done!