Query 029597
Match_columns 191
No_of_seqs 186 out of 1194
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 15:28:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029597.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029597hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13395 HNH_4: HNH endonuclea 99.2 4E-12 8.7E-17 86.2 2.2 43 107-149 1-54 (54)
2 cd00085 HNHc HNH nucleases; HN 99.1 4.6E-11 1E-15 78.1 3.0 40 105-144 12-57 (57)
3 PF01844 HNH: HNH endonuclease 99.1 4.6E-12 9.9E-17 81.9 -1.8 40 107-146 1-47 (47)
4 TIGR01865 cas_Csn1 CRISPR-asso 98.9 9.7E-10 2.1E-14 108.6 5.3 52 99-150 576-639 (805)
5 smart00507 HNHc HNH nucleases. 98.8 8.9E-10 1.9E-14 70.7 0.6 42 99-141 6-52 (52)
6 PRK11295 hypothetical protein; 98.8 3E-09 6.5E-14 82.7 2.2 49 99-147 19-76 (113)
7 COG1403 McrA Restriction endon 98.7 7.4E-09 1.6E-13 79.1 3.6 52 99-150 64-119 (146)
8 PF14239 RRXRR: RRXRR protein 98.6 1.3E-08 2.9E-13 84.5 1.4 49 7-55 98-150 (176)
9 TIGR02646 conserved hypothetic 98.5 1.3E-07 2.9E-12 75.4 3.6 49 100-148 20-85 (144)
10 COG3513 Predicted CRISPR-assoc 95.8 0.0017 3.6E-08 64.9 -1.0 51 99-149 566-628 (1088)
11 PF14279 HNH_5: HNH endonuclea 95.4 0.0052 1.1E-07 44.1 0.6 39 107-148 1-45 (71)
12 TIGR02986 restrict_Alw26I type 94.9 0.012 2.6E-07 54.7 1.3 50 105-157 245-298 (424)
13 PHA02565 49 recombination endo 93.4 0.031 6.8E-07 45.9 0.9 46 99-146 15-68 (157)
14 COG3183 Predicted restriction 93.4 0.039 8.4E-07 48.8 1.5 59 99-157 190-267 (272)
15 PF06147 DUF968: Protein of un 93.2 0.071 1.5E-06 45.1 2.7 42 104-145 127-173 (200)
16 PF13391 HNH_2: HNH endonuclea 92.9 0.025 5.4E-07 38.3 -0.3 31 114-144 16-59 (66)
17 PF09665 RE_Alw26IDE: Type II 91.1 0.06 1.3E-06 51.1 -0.2 42 113-157 257-298 (511)
18 TIGR03031 cas_csx12 CRISPR-ass 89.7 0.17 3.6E-06 49.7 1.5 29 99-127 755-788 (802)
19 PF05766 NinG: Bacteriophage L 89.4 0.089 1.9E-06 44.5 -0.5 54 104-157 87-147 (189)
20 COG3440 Predicted restriction 89.0 0.11 2.3E-06 46.8 -0.3 44 99-142 187-240 (301)
21 smart00782 PhnA_Zn_Ribbon PhnA 86.8 0.59 1.3E-05 31.1 2.3 42 99-142 2-45 (47)
22 PF05315 ICEA: ICEA Protein; 41.4 29 0.00062 30.2 3.1 41 105-145 98-152 (230)
23 PF02945 Endonuclease_7: Recom 36.8 12 0.00027 27.4 0.2 42 98-146 16-65 (81)
24 PF07510 DUF1524: Protein of u 32.0 9.7 0.00021 28.7 -1.1 35 115-149 54-104 (142)
25 TIGR01211 ELP3 histone acetylt 25.0 27 0.00058 33.8 0.3 66 102-178 78-144 (522)
No 1
>PF13395 HNH_4: HNH endonuclease
Probab=99.23 E-value=4e-12 Score=86.17 Aligned_cols=43 Identities=42% Similarity=0.698 Sum_probs=39.7
Q ss_pred CCCCCC-----------CCcceEEecCCCCCChHhhHHHHhHHHHhhhcCCCcc
Q 029597 107 CPGCLC-----------HDYDHILPYSKGGKSTLENCQVLQATVNRSKGNRTEL 149 (191)
Q Consensus 107 C~~Cg~-----------~eVDHIiP~S~GG~d~~~NL~~LC~~CN~~K~n~~~~ 149 (191)
|.|||. .+||||+|+|.++.+++.||++.|..||..|++++|+
T Consensus 1 C~Y~g~~i~~~~l~~~~~~iDHiiP~s~~~~~s~~Nlvl~~~~~N~~K~~k~P~ 54 (54)
T PF13395_consen 1 CPYCGKPISIENLFKNKYEIDHIIPRSRGGDDSFWNLVLCCKECNRSKGNKTPF 54 (54)
T ss_pred CCCCCCCCChhhcccCCceeEEEecccccCCCCcchhheECHHHhhcccccCCC
Confidence 788885 3899999999999999999999999999999999874
No 2
>cd00085 HNHc HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.
Probab=99.11 E-value=4.6e-11 Score=78.11 Aligned_cols=40 Identities=38% Similarity=0.603 Sum_probs=37.0
Q ss_pred CCCCCCCC------CCcceEEecCCCCCChHhhHHHHhHHHHhhhc
Q 029597 105 VGCPGCLC------HDYDHILPYSKGGKSTLENCQVLQATVNRSKG 144 (191)
Q Consensus 105 ~~C~~Cg~------~eVDHIiP~S~GG~d~~~NL~~LC~~CN~~K~ 144 (191)
+.|++|+. +++|||+|++.||.++++||+++|..||..|+
T Consensus 12 ~~C~~c~~~~~~~~~~v~Hi~p~~~~~~~~~~Nl~~~c~~ch~~~~ 57 (57)
T cd00085 12 GLCPYCGKPGGTEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKKH 57 (57)
T ss_pred CcCccCCCcCCCCCceEEeecchhhCCCCchHHhHHHHHHHhhccC
Confidence 78999984 59999999999999999999999999999874
No 3
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=99.11 E-value=4.6e-12 Score=81.87 Aligned_cols=40 Identities=40% Similarity=0.639 Sum_probs=29.3
Q ss_pred CCCCCC-------CCcceEEecCCCCCChHhhHHHHhHHHHhhhcCC
Q 029597 107 CPGCLC-------HDYDHILPYSKGGKSTLENCQVLQATVNRSKGNR 146 (191)
Q Consensus 107 C~~Cg~-------~eVDHIiP~S~GG~d~~~NL~~LC~~CN~~K~n~ 146 (191)
|++|+. +++|||+|++.||.++++||+++|..||..|+++
T Consensus 1 C~~C~~~~~~~~~~~v~Hi~~~~~gg~~~~~Nl~~lC~~Ch~~k~~k 47 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVHHIIPRSKGGKNDLENLILLCPSCHRKKHDK 47 (47)
T ss_dssp -TTT--B--GG-GEEEEESS-TTTT---STTTEEEEEHHHHHHHH--
T ss_pred CCCCCCcCccCcceEeECcCchhcCCCCCHHHHHHHhHHHHHHhcCC
Confidence 778874 4899999999999999999999999999999874
No 4
>TIGR01865 cas_Csn1 CRISPR-associated protein, Csn1 family. CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas locus. The species range so far for this protein is animal pathogens and commensals only.
Probab=98.93 E-value=9.7e-10 Score=108.63 Aligned_cols=52 Identities=25% Similarity=0.361 Sum_probs=47.8
Q ss_pred hhhccCCCCCCCCCC------------CcceEEecCCCCCChHhhHHHHhHHHHhhhcCCCccc
Q 029597 99 VVFRKLVGCPGCLCH------------DYDHILPYSKGGKSTLENCQVLQATVNRSKGNRTELS 150 (191)
Q Consensus 99 vl~r~~~~C~~Cg~~------------eVDHIiP~S~GG~d~~~NL~~LC~~CN~~K~n~~~~~ 150 (191)
++..|++.|+|||.. +||||+|+|.||+|+++|++++|..||..|++++|+.
T Consensus 576 L~~~q~~~C~Y~g~~i~~~~l~~~~~~~iDHIiP~s~~~dds~~N~vl~~~~~N~~K~~~tp~e 639 (805)
T TIGR01865 576 LYYQQNGKCMYTGKEIDIDDLFDLSYYEIDHILPQSRSFDDSISNKVLVLASENQEKGDQTPYE 639 (805)
T ss_pred HHHHcCCcCCCCCCcCccccccCCCCCceeeecccccCCCCcHHHHHHHhHHHHhhccCCCHHH
Confidence 667899999999952 7999999999999999999999999999999999964
No 5
>smart00507 HNHc HNH nucleases.
Probab=98.82 E-value=8.9e-10 Score=70.66 Aligned_cols=42 Identities=31% Similarity=0.527 Sum_probs=37.6
Q ss_pred hhhccCCCCCCCCC-----CCcceEEecCCCCCChHhhHHHHhHHHHh
Q 029597 99 VVFRKLVGCPGCLC-----HDYDHILPYSKGGKSTLENCQVLQATVNR 141 (191)
Q Consensus 99 vl~r~~~~C~~Cg~-----~eVDHIiP~S~GG~d~~~NL~~LC~~CN~ 141 (191)
++.++ +.|++|+. +++|||+|++.||.++++||+++|..||.
T Consensus 6 ~~~r~-~~C~~C~~~~~~~~~v~Hi~p~~~~~~~~~~Nl~~~c~~ch~ 52 (52)
T smart00507 6 LLHRD-GVCAYCGKPASEGLEVDHIIPLSDGGNDDLDNLVLLCPKCHI 52 (52)
T ss_pred HHHHC-CCCcCCcCCCCCCeEEEecCChhcCCCCChHhCeecChhhCc
Confidence 55667 89999984 59999999999999999999999999984
No 6
>PRK11295 hypothetical protein; Provisional
Probab=98.77 E-value=3e-09 Score=82.65 Aligned_cols=49 Identities=12% Similarity=0.053 Sum_probs=42.1
Q ss_pred hhhccCCCCCCCCCC---------CcceEEecCCCCCChHhhHHHHhHHHHhhhcCCC
Q 029597 99 VVFRKLVGCPGCLCH---------DYDHILPYSKGGKSTLENCQVLQATVNRSKGNRT 147 (191)
Q Consensus 99 vl~r~~~~C~~Cg~~---------eVDHIiP~S~GG~d~~~NL~~LC~~CN~~K~n~~ 147 (191)
+|.++.+.|+.|+.. +||||+|...|+.++.+|||+||..||..++.+.
T Consensus 19 ~L~r~p~lC~~Cgr~~~~a~~~a~vVDHIip~~~gd~~D~sNLQ~LC~~CHn~kh~R~ 76 (113)
T PRK11295 19 ALKLYPWVCGRCSREFVYSNLRELTVHHIDHDHDNNPEDGSNWELLCLYCHDHEHSKY 76 (113)
T ss_pred HHHHCcchhhhhcChhccCCCCCceeeccCCCCCCCCCchhHHHHHhHHHHhHHHhhH
Confidence 455666789999873 8999999988999889999999999999997654
No 7
>COG1403 McrA Restriction endonuclease [Defense mechanisms]
Probab=98.74 E-value=7.4e-09 Score=79.13 Aligned_cols=52 Identities=35% Similarity=0.512 Sum_probs=46.3
Q ss_pred hhhccCCCCCCCCC----CCcceEEecCCCCCChHhhHHHHhHHHHhhhcCCCccc
Q 029597 99 VVFRKLVGCPGCLC----HDYDHILPYSKGGKSTLENCQVLQATVNRSKGNRTELS 150 (191)
Q Consensus 99 vl~r~~~~C~~Cg~----~eVDHIiP~S~GG~d~~~NL~~LC~~CN~~K~n~~~~~ 150 (191)
++.++.+.|.+|+. .++|||+|.+.||.+.++||+++|..||..|++.....
T Consensus 64 ~~~~d~~~c~~c~~~~~~~~~dHiip~~~g~~~~~~Nl~~lc~~c~~~k~~~~~~~ 119 (146)
T COG1403 64 VLLRDNGLCQYCGSVGTDLEVDHIVPLSRGGASAWENLETLCERCHNKKGSRLPGK 119 (146)
T ss_pred HHccccccccccCCcCCCCceeeEeecccCCcchHHHHHHHHHhhcccccccchhh
Confidence 56677789999974 58999999999999999999999999999999988753
No 8
>PF14239 RRXRR: RRXRR protein
Probab=98.60 E-value=1.3e-08 Score=84.51 Aligned_cols=49 Identities=12% Similarity=0.042 Sum_probs=44.5
Q ss_pred ccccc-CcccccCCCCCCCCCCCC--CccchhhcccccccH-Hhhhccccccc
Q 029597 7 PKRRK-STATRASSPSPSRRRGET--TVRSATLLDNELATE-EEISTLFTDLR 55 (191)
Q Consensus 7 ~~~~~-~~~~~~~~~r~~~r~~~~--~~~~~~l~~~~~~~~-~~~~~l~p~~~ 55 (191)
||+|| |++||||+|||+||+++. ||||.....+.++++ +++..|+||..
T Consensus 98 RR~RR~~rk~RyR~~RF~NR~r~~gwL~PSl~~rv~~~l~~v~~L~~~~PIt~ 150 (176)
T PF14239_consen 98 RRGRRYNRKTRYRKARFDNRKRPKGWLPPSLRHRVDTHLRWVKRLCKLLPITA 150 (176)
T ss_pred hhhcccccccccccccccccCCCCCCcCcCHHHHHHHHHHHHHHHHHhCCccc
Confidence 67888 899999999999999983 999998888889997 99999999986
No 9
>TIGR02646 conserved hypothetical protein TIGR02646. Members of this uncharacterized protein family are found exclusively in bacteria. Neighboring genes in various genomes are also uncharacterized or may annotated as similar to restriction system proteins.
Probab=98.46 E-value=1.3e-07 Score=75.42 Aligned_cols=49 Identities=16% Similarity=0.024 Sum_probs=40.1
Q ss_pred hhccCCCCCCCCC------CCcceEEecCCCCCC--hHhhHHHHhHH---------HHhhhcCCCc
Q 029597 100 VFRKLVGCPGCLC------HDYDHILPYSKGGKS--TLENCQVLQAT---------VNRSKGNRTE 148 (191)
Q Consensus 100 l~r~~~~C~~Cg~------~eVDHIiP~S~GG~d--~~~NL~~LC~~---------CN~~K~n~~~ 148 (191)
+..+++.|+||+. ++||||+|.+..+.. +|+||.++|.. ||..|++...
T Consensus 20 ~~~~~~~C~YC~~~~~~~~~~ieH~~Pk~~~~~~~~~~~NL~~sC~~~n~~~~~~~Cn~~K~~~~~ 85 (144)
T TIGR02646 20 LQLQGGLCAYCEREIELLGSHIEHFRPKGAYPPLTLDWSNLFGSCHRESKQGNPLHCGRFKDNSCG 85 (144)
T ss_pred HHHhCCCcCccCCCcCCCCcceeeecccCCChhhhcChhhchhhccccCCCCCccccccccccccc
Confidence 3456689999986 499999999988776 56999999999 8888865543
No 10
>COG3513 Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]
Probab=95.83 E-value=0.0017 Score=64.95 Aligned_cols=51 Identities=24% Similarity=0.334 Sum_probs=46.6
Q ss_pred hhhccCCCCCCCCC------------CCcceEEecCCCCCChHhhHHHHhHHHHhhhcCCCcc
Q 029597 99 VVFRKLVGCPGCLC------------HDYDHILPYSKGGKSTLENCQVLQATVNRSKGNRTEL 149 (191)
Q Consensus 99 vl~r~~~~C~~Cg~------------~eVDHIiP~S~GG~d~~~NL~~LC~~CN~~K~n~~~~ 149 (191)
+++.|++.|.|.|. .+||||+|.|.--+|+++|.++.-..=|+.|+|.+|.
T Consensus 566 LY~~Q~gkcmYsgqei~I~rL~dk~~~eIDHi~P~Sr~~DDS~~NkVLv~s~~Nq~KgnqtP~ 628 (1088)
T COG3513 566 LYYLQNGKCMYSGQEIDIHRLSDKGYYEIDHIVPQSRTWDDSIDNKVLVLSSENQEKGNQTPY 628 (1088)
T ss_pred HHHHhcCcccccCcccchhhcccccceeeceeccccccccccccceeEEeccccccccCCCCH
Confidence 35679999999996 2899999999999999999999999999999999985
No 11
>PF14279 HNH_5: HNH endonuclease
Probab=95.44 E-value=0.0052 Score=44.06 Aligned_cols=39 Identities=31% Similarity=0.549 Sum_probs=32.5
Q ss_pred CCCCCCC------CcceEEecCCCCCChHhhHHHHhHHHHhhhcCCCc
Q 029597 107 CPGCLCH------DYDHILPYSKGGKSTLENCQVLQATVNRSKGNRTE 148 (191)
Q Consensus 107 C~~Cg~~------eVDHIiP~S~GG~d~~~NL~~LC~~CN~~K~n~~~ 148 (191)
|.||... ...||||-|-||...+.| +|..||..-+...+
T Consensus 1 Ci~C~~~~~~~~~s~EHIIP~sLGG~~~~~~---vC~~CN~~~g~~vD 45 (71)
T PF14279_consen 1 CIYCNKEKSESNFSEEHIIPESLGGKLKINN---VCDKCNNKFGSKVD 45 (71)
T ss_pred CccCCCCCCccCCCccccCchhcCCcccccc---hhHHHhHHHhHHHH
Confidence 7888752 479999999999877766 99999999887765
No 12
>TIGR02986 restrict_Alw26I type II restriction endonuclease, Alw26I/Eco31I/Esp3I family. Members of this family are type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family. Characterized specificities of three members are GGTCTC, CGTCTC, and the shared subsequence GTCTC.
Probab=94.85 E-value=0.012 Score=54.67 Aligned_cols=50 Identities=30% Similarity=0.299 Sum_probs=38.3
Q ss_pred CCCCCCCC----CCcceEEecCCCCCChHhhHHHHhHHHHhhhcCCCccchhHHhhh
Q 029597 105 VGCPGCLC----HDYDHILPYSKGGKSTLENCQVLQATVNRSKGNRTELSRSDLIQK 157 (191)
Q Consensus 105 ~~C~~Cg~----~eVDHIiP~S~GG~d~~~NL~~LC~~CN~~K~n~~~~~~~el~~~ 157 (191)
..|+.|+. -..|||=|+|.|-...+ +.|++|..||.+|.++.. ..+++.+
T Consensus 245 ~~~~~~~~~p~~~saDHIGPISlGF~h~P-~Fqplc~~cNSaKnnR~~--lsDV~~L 298 (424)
T TIGR02986 245 CSIPECCKHPEKISADHIGPISLGFVHDP-RFQPLCSSCNSAKNDRLT--LSDVKTL 298 (424)
T ss_pred ccCcccccCCCCCCccccCCcccccccCc-ccccccccccccccccee--HHHHHHH
Confidence 34455554 38999999999988766 669999999999999985 3444444
No 13
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=93.45 E-value=0.031 Score=45.91 Aligned_cols=46 Identities=17% Similarity=0.143 Sum_probs=33.7
Q ss_pred hhhccCCCCCCCCC--------CCcceEEecCCCCCChHhhHHHHhHHHHhhhcCC
Q 029597 99 VVFRKLVGCPGCLC--------HDYDHILPYSKGGKSTLENCQVLQATVNRSKGNR 146 (191)
Q Consensus 99 vl~r~~~~C~~Cg~--------~eVDHIiP~S~GG~d~~~NL~~LC~~CN~~K~n~ 146 (191)
++..|++.|+.|+. ++|||..|.+.+.+. .=..+||..||...|.-
T Consensus 15 l~e~Q~G~CaiC~~~l~~~~~~~~vDHDH~l~g~~TG--~VRGLLC~~CN~~lG~~ 68 (157)
T PHA02565 15 LFEAQNGICPLCKRELDGDVSKNHLDHDHELNGPNAG--RVRGLLCNLCNALEGQM 68 (157)
T ss_pred HHHHhCCcCCCCCCccCCCccccccCCCCCCCCcccc--cccccCchhhhhhhhhh
Confidence 45567799999985 379999988632211 12679999999988865
No 14
>COG3183 Predicted restriction endonuclease [Defense mechanisms]
Probab=93.38 E-value=0.039 Score=48.84 Aligned_cols=59 Identities=17% Similarity=0.184 Sum_probs=43.0
Q ss_pred hhhccCCCCCCCCC------------C-CcceEEecCCCC--C--ChHhhHHHHhHHHHhhhcCCCc--cchhHHhhh
Q 029597 99 VVFRKLVGCPGCLC------------H-DYDHILPYSKGG--K--STLENCQVLQATVNRSKGNRTE--LSRSDLIQK 157 (191)
Q Consensus 99 vl~r~~~~C~~Cg~------------~-eVDHIiP~S~GG--~--d~~~NL~~LC~~CN~~K~n~~~--~~~~el~~~ 157 (191)
++.-....|..|+- + +|||++|.+.-+ . +...-|.++|+.||..-+..-+ .+..|++.+
T Consensus 190 ~Ia~~G~vC~vC~fdF~k~YGe~gKgyIeVHH~~piae~e~~~~vnp~tDL~plCpNCH~mvHrr~~~~lS~~elk~l 267 (272)
T COG3183 190 AIAIHGTVCDVCEFDFQKKYGEIGKGYIEVHHKIPIAEFEGEYHVNPLTDLAPLCPNCHKMVHRRRDRNLSVEELKIL 267 (272)
T ss_pred HHHHhCceeeecCccHHHHhhhhccCeEEEeeccchhhhcCccccCchhhhhhcCccHHHHHhccCCcCCCHHHHHHH
Confidence 45555577999973 1 999999998532 2 3456899999999999876554 466676655
No 15
>PF06147 DUF968: Protein of unknown function (DUF968); InterPro: IPR010373 This is a family of uncharacterised prophage proteins that are also found in bacteria and humans.
Probab=93.21 E-value=0.071 Score=45.07 Aligned_cols=42 Identities=19% Similarity=0.111 Sum_probs=32.5
Q ss_pred CCCCCCCCCC--CcceEEecCCCCCC---hHhhHHHHhHHHHhhhcC
Q 029597 104 LVGCPGCLCH--DYDHILPYSKGGKS---TLENCQVLQATVNRSKGN 145 (191)
Q Consensus 104 ~~~C~~Cg~~--eVDHIiP~S~GG~d---~~~NL~~LC~~CN~~K~n 145 (191)
...|..||.. +++|++....||.. .-..+.+||..||...++
T Consensus 127 ~~~C~iCGk~~~d~hH~iG~g~~~~~~~~~d~~~ipLCr~hH~e~H~ 173 (200)
T PF06147_consen 127 SRPCVICGKPPADIHHIIGMGRGRMGIKHHDLFVIPLCREHHRELHR 173 (200)
T ss_pred cCccccCCCCccccceeeccccCccccccCCCeehhccHHHHHHHhC
Confidence 3589999974 99999776544433 334899999999999888
No 16
>PF13391 HNH_2: HNH endonuclease
Probab=92.93 E-value=0.025 Score=38.28 Aligned_cols=31 Identities=23% Similarity=0.372 Sum_probs=25.4
Q ss_pred CcceEEecCCC--CCC-----------hHhhHHHHhHHHHhhhc
Q 029597 114 DYDHILPYSKG--GKS-----------TLENCQVLQATVNRSKG 144 (191)
Q Consensus 114 eVDHIiP~S~G--G~d-----------~~~NL~~LC~~CN~~K~ 144 (191)
++-||+|++.+ +.+ +.+|+.+||..+|..=.
T Consensus 16 eaaHI~P~s~~~~~~~~~~~~~~~~~~~~~Ngl~L~~~lH~~fd 59 (66)
T PF13391_consen 16 EAAHIVPFSLGSWWMNNWFGEYANDWISPSNGLLLRPDLHKLFD 59 (66)
T ss_pred EEEEcccCccCCCchhhhhhhhhccCCCccEEEEcCHhHHHHHC
Confidence 78899999986 555 67899999999998643
No 17
>PF09665 RE_Alw26IDE: Type II restriction endonuclease (RE_Alw26IDE); InterPro: IPR014328 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 type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family [], whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I).
Probab=91.06 E-value=0.06 Score=51.12 Aligned_cols=42 Identities=33% Similarity=0.248 Sum_probs=34.4
Q ss_pred CCcceEEecCCCCCChHhhHHHHhHHHHhhhcCCCccchhHHhhh
Q 029597 113 HDYDHILPYSKGGKSTLENCQVLQATVNRSKGNRTELSRSDLIQK 157 (191)
Q Consensus 113 ~eVDHIiP~S~GG~d~~~NL~~LC~~CN~~K~n~~~~~~~el~~~ 157 (191)
...|||=|+|.|-...+ +.+++|..||.+|.++.. ..+++.+
T Consensus 257 ~SaDHIGPISlGF~h~P-~Fqplc~~cNSaKnnR~~--lsDV~~L 298 (511)
T PF09665_consen 257 LSADHIGPISLGFVHRP-RFQPLCKSCNSAKNNRMY--LSDVKKL 298 (511)
T ss_pred cCccccCCcccccccCc-ccccccccccccccccee--HHHHHHH
Confidence 38999999999988766 669999999999999985 3444444
No 18
>TIGR03031 cas_csx12 CRISPR-associated protein, Csx12 family. Members of this family of CRISPR-associated (cas) protein are found, so far, in CRISPR/cas loci in Wolinella succinogenes DSM 1740, Legionella pneumophila str. Paris, and Francisella tularensis, where the last probably is an example of a degenerate CRISPR locus, having neither repeats nor a functional Cas1. The characteristic repeat length is 37 base pairs and period is about 72. One region of this large protein shows sequence similarity to PFAM model pfam01844, HNH endonuclease.
Probab=89.67 E-value=0.17 Score=49.73 Aligned_cols=29 Identities=28% Similarity=0.300 Sum_probs=23.2
Q ss_pred hhhccCCCCCCCCCC-----CcceEEecCCCCCC
Q 029597 99 VVFRKLVGCPGCLCH-----DYDHILPYSKGGKS 127 (191)
Q Consensus 99 vl~r~~~~C~~Cg~~-----eVDHIiP~S~GG~d 127 (191)
+.....+.|+|||+. ++|||+|+|+.+..
T Consensus 755 Ik~fs~gIcpY~Ga~iG~~gEiDHI~PRSht~k~ 788 (802)
T TIGR03031 755 IKNFSMGICPYKGASIGGQGEIDHIYPRSHSKKH 788 (802)
T ss_pred HHHHhccCCCCCCCCCCCcccccccccccccccc
Confidence 444567899999974 99999999986653
No 19
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=89.35 E-value=0.089 Score=44.47 Aligned_cols=54 Identities=20% Similarity=0.148 Sum_probs=42.0
Q ss_pred CCCCCCCCC-----CCcceEEecCCCCCC--hHhhHHHHhHHHHhhhcCCCccchhHHhhh
Q 029597 104 LVGCPGCLC-----HDYDHILPYSKGGKS--TLENCQVLQATVNRSKGNRTELSRSDLIQK 157 (191)
Q Consensus 104 ~~~C~~Cg~-----~eVDHIiP~S~GG~d--~~~NL~~LC~~CN~~K~n~~~~~~~el~~~ 157 (191)
+..|.+||. |+.-|......-... +..|+-..|..||..++.....+...|+..
T Consensus 87 ~~~CiSCG~~~~~~~dagHy~s~g~~~~lRF~~~N~~~qC~~CN~~~sgn~~~Yr~~Li~k 147 (189)
T PF05766_consen 87 GKPCISCGRKHGGQWDAGHYRSRGAAPELRFNEDNIHAQCKHCNRHLSGNIVEYRIGLIEK 147 (189)
T ss_pred CCCcccCCCcCCCCcccccccccccCcccccChhhHhHcCCccccccccCHHHHHHHHHHH
Confidence 468999996 588898776332333 567999999999999998877777777765
No 20
>COG3440 Predicted restriction endonuclease [Defense mechanisms]
Probab=89.04 E-value=0.11 Score=46.76 Aligned_cols=44 Identities=18% Similarity=0.136 Sum_probs=37.3
Q ss_pred hhhccCCCCCCCCC----------CCcceEEecCCCCCChHhhHHHHhHHHHhh
Q 029597 99 VVFRKLVGCPGCLC----------HDYDHILPYSKGGKSTLENCQVLQATVNRS 142 (191)
Q Consensus 99 vl~r~~~~C~~Cg~----------~eVDHIiP~S~GG~d~~~NL~~LC~~CN~~ 142 (191)
|+..-+++|+.||- -+.-||.|.+++|++.+.|...||..+|..
T Consensus 187 V~~~Y~~RCalCG~e~~~~~~q~ii~~ahikp~~q~y~~~i~N~LaLC~nHh~~ 240 (301)
T COG3440 187 VLRQYDYRCALCGLEVLDFLEQNIIKAAHIKPFQQFYPDRIINGLALCKNHHWA 240 (301)
T ss_pred HHHHhcchhhhhcchhhhhhHHHHhhhhhcCcccccCcccccccchhchhhHHH
Confidence 45556789999993 167899999999999999999999888865
No 21
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=86.80 E-value=0.59 Score=31.06 Aligned_cols=42 Identities=21% Similarity=0.178 Sum_probs=27.8
Q ss_pred hhhccCCCCCCCCCC--CcceEEecCCCCCChHhhHHHHhHHHHhh
Q 029597 99 VVFRKLVGCPGCLCH--DYDHILPYSKGGKSTLENCQVLQATVNRS 142 (191)
Q Consensus 99 vl~r~~~~C~~Cg~~--eVDHIiP~S~GG~d~~~NL~~LC~~CN~~ 142 (191)
++.|.+..|..|+.. ..-|-+|-+.+ ...+|.+++|..|+..
T Consensus 2 L~~Rs~~kCELC~a~~~L~vy~Vpp~~~--~~~d~~iliC~tC~~Q 45 (47)
T smart00782 2 LLARCESKCELCGSDSPLVVYAVPPSSD--VTADNSVMLCDTCHSQ 45 (47)
T ss_pred hhHHcCCcccCcCCCCCceEEecCCCCC--CCccceeeechHHHHh
Confidence 345667899999974 23333444333 3467889999999853
No 22
>PF05315 ICEA: ICEA Protein; InterPro: IPR007979 This family consists of several ICEA proteins from Helicobacter pylori, infection of which causes gastritis and peptic ulcer disease, and the bacteria is classified as a definite carcinogen of gastric cancer. ICEA1 is speculated to be associated with peptic ulcer disease and may have endonuclease activity [].
Probab=41.35 E-value=29 Score=30.16 Aligned_cols=41 Identities=22% Similarity=0.240 Sum_probs=26.6
Q ss_pred CCCCCCCCC--------CcceEEecCC------CCCChHhhHHHHhHHHHhhhcC
Q 029597 105 VGCPGCLCH--------DYDHILPYSK------GGKSTLENCQVLQATVNRSKGN 145 (191)
Q Consensus 105 ~~C~~Cg~~--------eVDHIiP~S~------GG~d~~~NL~~LC~~CN~~K~n 145 (191)
-.|++||.. ++||.--.-. =-+..++-.|+||..||..|..
T Consensus 98 q~Cvm~g~~g~sent~ieiDHKd~rk~d~rvsd~~~q~~~dFQ~Lck~~N~~KRq 152 (230)
T PF05315_consen 98 QCCVMCGVRGNSENTKIEIDHKDGRKDDLRVSDMNTQTFDDFQPLCKACNDQKRQ 152 (230)
T ss_pred cCeeeecccCCCccceeeecccccccccchhcccchhhHHHHHHHHHHHhHHHHH
Confidence 479999862 7888621100 0111456889999999999853
No 23
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=36.82 E-value=12 Score=27.36 Aligned_cols=42 Identities=21% Similarity=0.173 Sum_probs=26.0
Q ss_pred chhhccCCCCCCCCC--------CCcceEEecCCCCCChHhhHHHHhHHHHhhhcCC
Q 029597 98 NVVFRKLVGCPGCLC--------HDYDHILPYSKGGKSTLENCQVLQATVNRSKGNR 146 (191)
Q Consensus 98 nvl~r~~~~C~~Cg~--------~eVDHIiP~S~GG~d~~~NL~~LC~~CN~~K~n~ 146 (191)
.++..|.+.|+.|+. ..|||-. .-|. =--+||..||..-|.-
T Consensus 16 ~l~~~q~~~C~iC~~~~~~~~~~~~vDHdH---~tG~----vRGlLC~~CN~~lG~~ 65 (81)
T PF02945_consen 16 ALLEEQGGRCAICGKPLPGESRKLVVDHDH---KTGR----VRGLLCRSCNTALGKV 65 (81)
T ss_dssp CCHHHTTTE-TTT-SEEETTCGGCEEEE-T---TTTB----EEEEEEHHHHHHHHHC
T ss_pred HHHHHhCCcCcCCCCCcccCCCcceecCCC---CCCC----chhhhhhHHhhhhccc
Confidence 356677899999996 2677753 1121 1247999999987654
No 24
>PF07510 DUF1524: Protein of unknown function (DUF1524); InterPro: IPR011089 The family contains RloF from Campylobacter jejuni, its function and those of the other members are unknown.
Probab=32.03 E-value=9.7 Score=28.67 Aligned_cols=35 Identities=26% Similarity=0.435 Sum_probs=27.3
Q ss_pred cceEEecCCCCC----------------ChHhhHHHHhHHHHhhhcCCCcc
Q 029597 115 YDHILPYSKGGK----------------STLENCQVLQATVNRSKGNRTEL 149 (191)
Q Consensus 115 VDHIiP~S~GG~----------------d~~~NL~~LC~~CN~~K~n~~~~ 149 (191)
||||+|.+.... +.+.||++|=..=|..+++....
T Consensus 54 iEHI~Pq~~~~~~~~~~~~~~~~~~~~~~~igNL~LL~~~~N~~~~n~~f~ 104 (142)
T PF07510_consen 54 IEHIFPQNPKKESKSEKDWDEEEREIYLNSIGNLTLLSKSLNSSISNKPFL 104 (142)
T ss_pred eEeeccCCCCcccccccccCHHHHHHHhcccccEEEeccchhhccchhhhH
Confidence 999999975432 45669999999999888886653
No 25
>TIGR01211 ELP3 histone acetyltransferase, ELP3 family. The Saccharomyces cerevisiae member YPL086C has been characterized in vitro as an N-terminal acetyltransferase for all four core histones. It is a component of the RNA polymerase II holoenzyme, designated Elp3p for Elongator Protein 3. Members of this family are found in eukaryotes and archaea. These proteins are part of the larger set of GNAT acetyltransferases.
Probab=25.04 E-value=27 Score=33.79 Aligned_cols=66 Identities=17% Similarity=0.123 Sum_probs=33.1
Q ss_pred ccCCCCCCCCC-CCcceEEecCCCCCChHhhHHHHhHHHHhhhcCCCccchhHHhhhcCCccccCcccceeccccccc
Q 029597 102 RKLVGCPGCLC-HDYDHILPYSKGGKSTLENCQVLQATVNRSKGNRTELSRSDLIQKSSYCRVSGRDMDLLELSAYGN 178 (191)
Q Consensus 102 r~~~~C~~Cg~-~eVDHIiP~S~GG~d~~~NL~~LC~~CN~~K~n~~~~~~~el~~~s~~~~~~~~~~d~i~~~~~~~ 178 (191)
..|+.|.||-+ .+- --.|.|-=|. .++|....+..-+.+ .++.....++.-.+...|.||+++||.
T Consensus 78 cph~~c~~cp~~~~~-~~~~~sy~~~------ep~~~ra~~~~~dpy----~q~~~rl~~l~~~g~~~~kvE~i~~GG 144 (522)
T TIGR01211 78 CPHGKCLYCPGGPDS-ENSPQSYTGY------EPAAMRGRQNDYDPY----EQVTARLEQLEQIGHPVDKVELIIMGG 144 (522)
T ss_pred CCCCceEeCCCCCCc-CCCCcccCCC------CcHhHHHHHcCCCcH----HHHHHHHHHHHHhCCCCceEEEEEECC
Confidence 34567888843 221 1244443332 344554444433332 222222223333556778999999986
Done!