Query 025258
Match_columns 255
No_of_seqs 221 out of 1302
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 04:03:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025258.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025258hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1403 McrA Restriction endon 99.8 3.4E-19 7.3E-24 142.0 8.5 141 107-250 1-142 (146)
2 PF13395 HNH_4: HNH endonuclea 99.4 1.4E-13 3E-18 98.0 1.9 45 181-225 1-53 (54)
3 cd00085 HNHc HNH nucleases; HN 99.3 1.1E-12 2.5E-17 89.4 4.0 52 169-221 3-57 (57)
4 smart00507 HNHc HNH nucleases. 99.2 2.6E-12 5.5E-17 86.2 2.2 49 169-218 2-52 (52)
5 TIGR01865 cas_Csn1 CRISPR-asso 99.2 6.9E-12 1.5E-16 129.7 5.7 61 168-228 571-640 (805)
6 PF01844 HNH: HNH endonuclease 99.2 1.1E-12 2.5E-17 88.6 -1.1 43 181-223 1-47 (47)
7 TIGR02646 conserved hypothetic 99.0 4.7E-10 1E-14 93.8 4.2 79 167-246 13-105 (144)
8 PRK11295 hypothetical protein; 99.0 4.3E-10 9.3E-15 92.0 3.7 61 167-227 13-79 (113)
9 PF14279 HNH_5: HNH endonuclea 97.4 6.4E-05 1.4E-09 56.9 1.2 45 181-228 1-48 (71)
10 COG3513 Predicted CRISPR-assoc 96.2 0.0018 3.9E-08 68.0 1.4 61 169-229 562-631 (1088)
11 PHA02565 49 recombination endo 96.0 0.0049 1.1E-07 53.3 2.9 55 167-224 9-69 (157)
12 smart00782 PhnA_Zn_Ribbon PhnA 95.7 0.0068 1.5E-07 42.7 1.8 44 173-219 2-45 (47)
13 COG3183 Predicted restriction 95.1 0.018 3.9E-07 53.7 3.3 59 166-224 183-255 (272)
14 PF05766 NinG: Bacteriophage L 95.0 0.037 7.9E-07 49.3 4.8 79 168-246 76-169 (189)
15 PF13391 HNH_2: HNH endonuclea 94.4 0.011 2.5E-07 42.0 0.1 40 181-220 1-58 (66)
16 COG3440 Predicted restriction 93.6 0.032 7E-07 52.7 1.3 55 165-219 179-240 (301)
17 PF06147 DUF968: Protein of un 92.7 0.18 4E-06 44.8 4.8 54 177-232 126-182 (200)
18 TIGR02986 restrict_Alw26I type 92.1 0.06 1.3E-06 52.8 1.0 47 179-226 245-292 (424)
19 TIGR03031 cas_csx12 CRISPR-ass 91.3 0.1 2.2E-06 53.8 1.7 38 173-210 755-800 (802)
20 PF09665 RE_Alw26IDE: Type II 86.9 0.19 4.2E-06 50.3 0.0 48 179-227 243-293 (511)
21 PF05198 IF3_N: Translation in 82.1 7.4 0.00016 29.7 6.8 56 94-158 9-64 (76)
22 PF14239 RRXRR: RRXRR protein 78.4 2.8 6.2E-05 37.1 3.9 34 100-133 1-34 (176)
23 PF05315 ICEA: ICEA Protein; 72.5 1.9 4.2E-05 39.3 1.4 71 148-222 70-152 (230)
24 PF02945 Endonuclease_7: Recom 70.5 2.1 4.5E-05 33.2 1.0 49 168-223 12-65 (81)
25 TIGR00168 infC translation ini 52.9 38 0.00081 29.5 5.7 56 94-158 4-59 (165)
26 PF08595 RXT2_N: RXT2-like, N- 51.4 13 0.00029 31.9 2.6 17 8-24 4-20 (149)
27 CHL00199 infC translation init 48.4 52 0.0011 29.4 5.9 57 93-158 20-76 (182)
28 PTZ00293 thymidine kinase; Pro 41.6 15 0.00032 33.3 1.4 59 179-241 138-200 (211)
29 PRK00028 infC translation init 39.0 88 0.0019 27.5 5.9 55 94-157 16-70 (177)
30 PF09257 BCMA-Tall_bind: BCMA, 33.5 10 0.00022 25.7 -0.6 20 206-225 7-26 (39)
31 COG0290 InfC Translation initi 33.0 1.4E+02 0.0031 26.6 6.2 40 93-132 14-53 (176)
32 PF14255 Cys_rich_CPXG: Cystei 32.3 15 0.00033 26.3 0.0 32 180-215 2-33 (52)
33 PF07510 DUF1524: Protein of u 31.6 17 0.00037 28.7 0.2 36 192-227 54-105 (142)
34 COG1435 Tdk Thymidine kinase [ 26.8 18 0.00038 32.8 -0.5 45 179-223 145-195 (201)
35 PF04231 Endonuclease_1: Endon 25.8 9.8 0.00021 34.5 -2.4 41 188-228 70-129 (218)
36 PF05605 zf-Di19: Drought indu 25.4 35 0.00075 23.8 0.9 38 177-219 1-40 (54)
37 PF13966 zf-RVT: zinc-binding 23.8 57 0.0012 24.4 1.9 19 177-196 58-76 (86)
38 PF07148 MalM: Maltose operon 23.1 72 0.0016 26.9 2.5 23 94-116 30-52 (135)
39 PF11672 DUF3268: Protein of u 22.0 24 0.00052 28.6 -0.5 40 179-222 3-43 (102)
40 KOG1829 Uncharacterized conser 20.5 62 0.0013 33.7 1.9 60 165-237 327-393 (580)
No 1
>COG1403 McrA Restriction endonuclease [Defense mechanisms]
Probab=99.79 E-value=3.4e-19 Score=142.05 Aligned_cols=141 Identities=27% Similarity=0.464 Sum_probs=123.6
Q ss_pred cceeeeeeHHHHHHHHHcCceeEEeecCCeeeCCCcceecCcEEEEecceehhhhcccCCHHHHHHHHHHCCCcccccCC
Q 025258 107 YRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQVVKRRRIKNNLSRKNLMYRDNFTCQYCSS 186 (255)
Q Consensus 107 y~Pl~~is~qrAi~l~~~gkAevl~~~~~~vrS~s~~~~vPsVIrL~~yv~~p~r~~~~~~~~R~~Vl~RD~~~CqYCG~ 186 (255)
|.|....+|++++..+..+.|..+..+. ..+++.....+|.+..+..+.+.+... .++.+|.+++.+|.+.|+||+.
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~r~~~~~~d~~~c~~c~~ 77 (146)
T COG1403 1 YNPLESKSIRPALDRLVSQRAKHVAEYP-CLASESKDLRRPSVTDLTGESKRPSEK--RPAKTRRAVLLRDNGLCQYCGS 77 (146)
T ss_pred CccccccchhHHHHHHhhcccccccCcc-eecceecccccCccceeeeeecccCCC--CchHHHHHHHccccccccccCC
Confidence 6788999999999999999999887654 455667788889999999887776543 3678999999999999999998
Q ss_pred CC-CCccceEEeCcCCCCCchhhHHHhchhhhhhhcCCCHHHHhhhhccCCCCCchHhHHHhhcc
Q 025258 187 RE-NLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEEANMQLSRVPKVLVRYLYHAVENH 250 (255)
Q Consensus 187 ~~-~ltVDHIiP~S~GG~~tweNLv~aC~~CN~~Kgnrtpeea~m~Ll~~P~~P~~~~~~~l~~~ 250 (255)
.. .+++|||+|.+.||.+.|+||+++|..||..|+++.+.+++|.+...|..|.......+...
T Consensus 78 ~~~~~~~dHiip~~~g~~~~~~Nl~~lc~~c~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 142 (146)
T COG1403 78 VGTDLEVDHIVPLSRGGASAWENLETLCERCHNKKGSRLPGKAGMKLRVKPRKPEVEKRKDLIRA 142 (146)
T ss_pred cCCCCceeeEeecccCCcchHHHHHHHHHhhcccccccchhhccCcccccccCCchhhhhhhhhc
Confidence 74 79999999999999999999999999999999999999999999999999998776665443
No 2
>PF13395 HNH_4: HNH endonuclease
Probab=99.38 E-value=1.4e-13 Score=98.00 Aligned_cols=45 Identities=49% Similarity=0.949 Sum_probs=42.1
Q ss_pred ccccCCC---C-----CCccceEEeCcCCCCCchhhHHHhchhhhhhhcCCCH
Q 025258 181 CQYCSSR---E-----NLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTL 225 (255)
Q Consensus 181 CqYCG~~---~-----~ltVDHIiP~S~GG~~tweNLv~aC~~CN~~Kgnrtp 225 (255)
|.|||+. . ..+||||+|+|.++.++++|||++|..||..|++++|
T Consensus 1 C~Y~g~~i~~~~l~~~~~~iDHiiP~s~~~~~s~~Nlvl~~~~~N~~K~~k~P 53 (54)
T PF13395_consen 1 CPYCGKPISIENLFKNKYEIDHIIPRSRGGDDSFWNLVLCCKECNRSKGNKTP 53 (54)
T ss_pred CCCCCCCCChhhcccCCceeEEEecccccCCCCcchhheECHHHhhcccccCC
Confidence 9999987 2 3799999999999999999999999999999999986
No 3
>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=99.33 E-value=1.1e-12 Score=89.43 Aligned_cols=52 Identities=42% Similarity=0.797 Sum_probs=47.7
Q ss_pred HHHHHHHHCCCcccccCCC---CCCccceEEeCcCCCCCchhhHHHhchhhhhhhc
Q 025258 169 SRKNLMYRDNFTCQYCSSR---ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKG 221 (255)
Q Consensus 169 ~R~~Vl~RD~~~CqYCG~~---~~ltVDHIiP~S~GG~~tweNLv~aC~~CN~~Kg 221 (255)
.|..++.|+ ++|+||+.. ..+++|||+|.+.||.++++||+++|..||..|+
T Consensus 3 ~r~~~~~~~-~~C~~c~~~~~~~~~~v~Hi~p~~~~~~~~~~Nl~~~c~~ch~~~~ 57 (57)
T cd00085 3 HRLVLLARD-GLCPYCGKPGGTEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKKH 57 (57)
T ss_pred HHHHHHHhC-CcCccCCCcCCCCCceEEeecchhhCCCCchHHhHHHHHHHhhccC
Confidence 578889998 899999984 6799999999999999999999999999999874
No 4
>smart00507 HNHc HNH nucleases.
Probab=99.25 E-value=2.6e-12 Score=86.18 Aligned_cols=49 Identities=41% Similarity=0.788 Sum_probs=45.1
Q ss_pred HHHHHHHHCCCcccccCCCC--CCccceEEeCcCCCCCchhhHHHhchhhhh
Q 025258 169 SRKNLMYRDNFTCQYCSSRE--NLTIDHVVPASRGGEWKWENLVAACFKCNS 218 (255)
Q Consensus 169 ~R~~Vl~RD~~~CqYCG~~~--~ltVDHIiP~S~GG~~tweNLv~aC~~CN~ 218 (255)
.|..++.|| +.|++||... .+++|||+|.+.||.++++||+++|..||.
T Consensus 2 ~~~~~~~r~-~~C~~C~~~~~~~~~v~Hi~p~~~~~~~~~~Nl~~~c~~ch~ 52 (52)
T smart00507 2 LRRLLLHRD-GVCAYCGKPASEGLEVDHIIPLSDGGNDDLDNLVLLCPKCHI 52 (52)
T ss_pred HHHHHHHHC-CCCcCCcCCCCCCeEEEecCChhcCCCCChHhCeecChhhCc
Confidence 477899999 9999999874 589999999999999999999999999994
No 5
>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=99.24 E-value=6.9e-12 Score=129.68 Aligned_cols=61 Identities=31% Similarity=0.418 Sum_probs=56.2
Q ss_pred HHHHHHHHHCCCcccccCCC---C------CCccceEEeCcCCCCCchhhHHHhchhhhhhhcCCCHHHH
Q 025258 168 LSRKNLMYRDNFTCQYCSSR---E------NLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEEA 228 (255)
Q Consensus 168 ~~R~~Vl~RD~~~CqYCG~~---~------~ltVDHIiP~S~GG~~tweNLv~aC~~CN~~Kgnrtpeea 228 (255)
..|-.++.+++++|+|||.+ . .++||||+|+|+||.|+|+|+|++|..||+.|++++|.++
T Consensus 571 ~~k~~L~~~q~~~C~Y~g~~i~~~~l~~~~~~~iDHIiP~s~~~dds~~N~vl~~~~~N~~K~~~tp~e~ 640 (805)
T TIGR01865 571 ILKLRLYYQQNGKCMYTGKEIDIDDLFDLSYYEIDHILPQSRSFDDSISNKVLVLASENQEKGDQTPYEA 640 (805)
T ss_pred HHHHHHHHHcCCcCCCCCCcCccccccCCCCCceeeecccccCCCCcHHHHHHHhHHHHhhccCCCHHHH
Confidence 45778999999999999987 2 4789999999999999999999999999999999999986
No 6
>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=99.21 E-value=1.1e-12 Score=88.60 Aligned_cols=43 Identities=42% Similarity=0.930 Sum_probs=31.8
Q ss_pred ccccCCC----CCCccceEEeCcCCCCCchhhHHHhchhhhhhhcCC
Q 025258 181 CQYCSSR----ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKK 223 (255)
Q Consensus 181 CqYCG~~----~~ltVDHIiP~S~GG~~tweNLv~aC~~CN~~Kgnr 223 (255)
|++||.. ..+++|||+|++.||.++++||+++|..||..|+++
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 8999987 468999999999999999999999999999999875
No 7
>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=98.97 E-value=4.7e-10 Score=93.78 Aligned_cols=79 Identities=18% Similarity=0.286 Sum_probs=62.2
Q ss_pred HHHHHHHHHHCCCcccccCCC---CCCccceEEeCcCCCC--CchhhHHHhchh---------hhhhhcCCCHHHHhhhh
Q 025258 167 NLSRKNLMYRDNFTCQYCSSR---ENLTIDHVVPASRGGE--WKWENLVAACFK---------CNSRKGKKTLEEANMQL 232 (255)
Q Consensus 167 ~~~R~~Vl~RD~~~CqYCG~~---~~ltVDHIiP~S~GG~--~tweNLv~aC~~---------CN~~Kgnrtpeea~m~L 232 (255)
+.+|..++..++++|.||+.. ..++|||++|++..+. .+|+||+++|.. ||..|++...... ..+
T Consensus 13 ~~i~~~L~~~~~~~C~YC~~~~~~~~~~ieH~~Pk~~~~~~~~~~~NL~~sC~~~n~~~~~~~Cn~~K~~~~~~~~-~~~ 91 (144)
T TIGR02646 13 DEVHNQLLQLQGGLCAYCEREIELLGSHIEHFRPKGAYPPLTLDWSNLFGSCHRESKQGNPLHCGRFKDNSCGSNN-FDE 91 (144)
T ss_pred HHHHHHHHHHhCCCcCccCCCcCCCCcceeeecccCCChhhhcChhhchhhccccCCCCCcccccccccccccccc-ccc
Confidence 468999999999999999984 6789999999998876 579999999999 8888865544322 344
Q ss_pred ccCCCCCchHhHHH
Q 025258 233 SRVPKVLVRYLYHA 246 (255)
Q Consensus 233 l~~P~~P~~~~~~~ 246 (255)
+..|..+...+++.
T Consensus 92 ~i~P~~~~~~~~f~ 105 (144)
T TIGR02646 92 LIDPLADDCEQLFT 105 (144)
T ss_pred ccCCCCCChHHhee
Confidence 55688777666553
No 8
>PRK11295 hypothetical protein; Provisional
Probab=98.96 E-value=4.3e-10 Score=91.99 Aligned_cols=61 Identities=20% Similarity=0.312 Sum_probs=53.4
Q ss_pred HHHHHHHHHHCCCcccccCCC------CCCccceEEeCcCCCCCchhhHHHhchhhhhhhcCCCHHH
Q 025258 167 NLSRKNLMYRDNFTCQYCSSR------ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEE 227 (255)
Q Consensus 167 ~~~R~~Vl~RD~~~CqYCG~~------~~ltVDHIiP~S~GG~~tweNLv~aC~~CN~~Kgnrtpee 227 (255)
.-.|+.++.++.+.|+.|++. ..++||||+|...|+.++.+||+++|..||..|+.+....
T Consensus 13 ~~~R~~~L~r~p~lC~~Cgr~~~~a~~~a~vVDHIip~~~gd~~D~sNLQ~LC~~CHn~kh~R~~~~ 79 (113)
T PRK11295 13 SGYREKALKLYPWVCGRCSREFVYSNLRELTVHHIDHDHDNNPEDGSNWELLCLYCHDHEHSKYTEA 79 (113)
T ss_pred HHHHHHHHHHCcchhhhhcChhccCCCCCceeeccCCCCCCCCCchhHHHHHhHHHHhHHHhhHHHh
Confidence 468999999999999999985 3579999999998988889999999999999998765543
No 9
>PF14279 HNH_5: HNH endonuclease
Probab=97.39 E-value=6.4e-05 Score=56.86 Aligned_cols=45 Identities=40% Similarity=0.826 Sum_probs=37.5
Q ss_pred ccccCCC---CCCccceEEeCcCCCCCchhhHHHhchhhhhhhcCCCHHHH
Q 025258 181 CQYCSSR---ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEEA 228 (255)
Q Consensus 181 CqYCG~~---~~ltVDHIiP~S~GG~~tweNLv~aC~~CN~~Kgnrtpeea 228 (255)
|.||++. ...+.+||+|-|.||...+.| .|..||+.-|.....+.
T Consensus 1 Ci~C~~~~~~~~~s~EHIIP~sLGG~~~~~~---vC~~CN~~~g~~vD~~l 48 (71)
T PF14279_consen 1 CIYCNKEKSESNFSEEHIIPESLGGKLKINN---VCDKCNNKFGSKVDAEL 48 (71)
T ss_pred CccCCCCCCccCCCccccCchhcCCcccccc---hhHHHhHHHhHHHHHHH
Confidence 8999987 345699999999999888877 89999999887665544
No 10
>COG3513 Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]
Probab=96.23 E-value=0.0018 Score=68.01 Aligned_cols=61 Identities=31% Similarity=0.357 Sum_probs=53.8
Q ss_pred HHHHHHHHCCCcccccCCC---------CCCccceEEeCcCCCCCchhhHHHhchhhhhhhcCCCHHHHh
Q 025258 169 SRKNLMYRDNFTCQYCSSR---------ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEEAN 229 (255)
Q Consensus 169 ~R~~Vl~RD~~~CqYCG~~---------~~ltVDHIiP~S~GG~~tweNLv~aC~~CN~~Kgnrtpeea~ 229 (255)
.+-.++.-++++|.|-|+. ...+||||+|.|+--.|+.+|.|..-..=|+-|||.+|-|+-
T Consensus 562 lKLrLY~~Q~gkcmYsgqei~I~rL~dk~~~eIDHi~P~Sr~~DDS~~NkVLv~s~~Nq~KgnqtP~e~~ 631 (1088)
T COG3513 562 LKLRLYYLQNGKCMYSGQEIDIHRLSDKGYYEIDHIVPQSRTWDDSIDNKVLVLSSENQEKGNQTPYEEF 631 (1088)
T ss_pred hHHHHHHHhcCcccccCcccchhhcccccceeeceeccccccccccccceeEEeccccccccCCCCHHHH
Confidence 3446788899999999986 248999999999999999999999999999999999987753
No 11
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=96.03 E-value=0.0049 Score=53.34 Aligned_cols=55 Identities=18% Similarity=0.290 Sum_probs=42.2
Q ss_pred HHHHHHHHHHCCCcccccCCC-----CCCccceEEeCcCCCCCchhh-HHHhchhhhhhhcCCC
Q 025258 167 NLSRKNLMYRDNFTCQYCSSR-----ENLTIDHVVPASRGGEWKWEN-LVAACFKCNSRKGKKT 224 (255)
Q Consensus 167 ~~~R~~Vl~RD~~~CqYCG~~-----~~ltVDHIiP~S~GG~~tweN-Lv~aC~~CN~~Kgnrt 224 (255)
+..++++++.++++|+.|+.+ ..+++||..|.+. ..+ .+ --.+|..||...|.-.
T Consensus 9 ~~~k~~l~e~Q~G~CaiC~~~l~~~~~~~~vDHDH~l~g--~~T-G~VRGLLC~~CN~~lG~~~ 69 (157)
T PHA02565 9 KEEKQKLFEAQNGICPLCKRELDGDVSKNHLDHDHELNG--PNA-GRVRGLLCNLCNALEGQMK 69 (157)
T ss_pred HHHHHHHHHHhCCcCCCCCCccCCCccccccCCCCCCCC--ccc-ccccccCchhhhhhhhhhh
Confidence 457889999999999999976 3579999987762 111 23 4579999999887764
No 12
>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=95.65 E-value=0.0068 Score=42.72 Aligned_cols=44 Identities=32% Similarity=0.523 Sum_probs=35.8
Q ss_pred HHHHCCCcccccCCCCCCccceEEeCcCCCCCchhhHHHhchhhhhh
Q 025258 173 LMYRDNFTCQYCSSRENLTIDHVVPASRGGEWKWENLVAACFKCNSR 219 (255)
Q Consensus 173 Vl~RD~~~CqYCG~~~~ltVDHIiP~S~GG~~tweNLv~aC~~CN~~ 219 (255)
++.|.+.+|..||....|.+-+|-|.+.| .-+|-+.+|..|+.+
T Consensus 2 L~~Rs~~kCELC~a~~~L~vy~Vpp~~~~---~~d~~iliC~tC~~Q 45 (47)
T smart00782 2 LLARCESKCELCGSDSPLVVYAVPPSSDV---TADNSVMLCDTCHSQ 45 (47)
T ss_pred hhHHcCCcccCcCCCCCceEEecCCCCCC---CccceeeechHHHHh
Confidence 57899999999998888998887665543 356779999999875
No 13
>COG3183 Predicted restriction endonuclease [Defense mechanisms]
Probab=95.15 E-value=0.018 Score=53.68 Aligned_cols=59 Identities=15% Similarity=0.302 Sum_probs=47.2
Q ss_pred CHHHHHHHHHHCCCcccccCCC----------CCCccceEEeCcCCC----CCchhhHHHhchhhhhhhcCCC
Q 025258 166 NNLSRKNLMYRDNFTCQYCSSR----------ENLTIDHVVPASRGG----EWKWENLVAACFKCNSRKGKKT 224 (255)
Q Consensus 166 ~~~~R~~Vl~RD~~~CqYCG~~----------~~ltVDHIiP~S~GG----~~tweNLv~aC~~CN~~Kgnrt 224 (255)
.+-.|++.+.-.+..|.-|+-. ...+|||++|.+.-+ -+...-|+++|+.||..-.-+.
T Consensus 183 na~~ra~~Ia~~G~vC~vC~fdF~k~YGe~gKgyIeVHH~~piae~e~~~~vnp~tDL~plCpNCH~mvHrr~ 255 (272)
T COG3183 183 NATLRAAAIAIHGTVCDVCEFDFQKKYGEIGKGYIEVHHKIPIAEFEGEYHVNPLTDLAPLCPNCHKMVHRRR 255 (272)
T ss_pred ChHHHHHHHHHhCceeeecCccHHHHhhhhccCeEEEeeccchhhhcCccccCchhhhhhcCccHHHHHhccC
Confidence 5667888888888999999864 468999999998532 2677899999999998665443
No 14
>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=95.02 E-value=0.037 Score=49.29 Aligned_cols=79 Identities=18% Similarity=0.318 Sum_probs=54.0
Q ss_pred HHHHHHHHHC-CCcccccCCC--CCCccceEEeCcCCCC--CchhhHHHhchhhhhhhcCCCHH----------HHhhhh
Q 025258 168 LSRKNLMYRD-NFTCQYCSSR--ENLTIDHVVPASRGGE--WKWENLVAACFKCNSRKGKKTLE----------EANMQL 232 (255)
Q Consensus 168 ~~R~~Vl~RD-~~~CqYCG~~--~~ltVDHIiP~S~GG~--~tweNLv~aC~~CN~~Kgnrtpe----------ea~m~L 232 (255)
...+.|..|| +..|..||.. ..++.-|...+..-.. -+..|+-..|..||..+++-..+ +.....
T Consensus 76 afn~~IR~RD~~~~CiSCG~~~~~~~dagHy~s~g~~~~lRF~~~N~~~qC~~CN~~~sgn~~~Yr~~Li~kiG~~~ve~ 155 (189)
T PF05766_consen 76 AFNKYIRLRDAGKPCISCGRKHGGQWDAGHYRSRGAAPELRFNEDNIHAQCKHCNRHLSGNIVEYRIGLIEKIGQERVEW 155 (189)
T ss_pred HHHHHHHHHhcCCCcccCCCcCCCCcccccccccccCcccccChhhHhHcCCccccccccCHHHHHHHHHHHHhHHHHHH
Confidence 4566777886 6799999986 5688999865532232 47899999999999999876433 223333
Q ss_pred ccCCCCCchHhHHH
Q 025258 233 SRVPKVLVRYLYHA 246 (255)
Q Consensus 233 l~~P~~P~~~~~~~ 246 (255)
|..|..|..++...
T Consensus 156 Le~~~~~~k~~~~e 169 (189)
T PF05766_consen 156 LEGPHEPRKWTIEE 169 (189)
T ss_pred HhcCCCCCCCCHHH
Confidence 44666666554443
No 15
>PF13391 HNH_2: HNH endonuclease
Probab=94.45 E-value=0.011 Score=41.97 Aligned_cols=40 Identities=23% Similarity=0.105 Sum_probs=32.9
Q ss_pred ccccCCCC-----CCccceEEeCcCC--CCC-----------chhhHHHhchhhhhhh
Q 025258 181 CQYCSSRE-----NLTIDHVVPASRG--GEW-----------KWENLVAACFKCNSRK 220 (255)
Q Consensus 181 CqYCG~~~-----~ltVDHIiP~S~G--G~~-----------tweNLv~aC~~CN~~K 220 (255)
|..||... .+++-||+|.+.+ +.+ +.+|..++|..+|..=
T Consensus 1 C~itg~~~~~~~~~~eaaHI~P~s~~~~~~~~~~~~~~~~~~~~~Ngl~L~~~lH~~f 58 (66)
T PF13391_consen 1 CVITGIRDPSPWELLEAAHIVPFSLGSWWMNNWFGEYANDWISPSNGLLLRPDLHKLF 58 (66)
T ss_pred CcCCcCCcCCCCCcEEEEEcccCccCCCchhhhhhhhhccCCCccEEEEcCHhHHHHH
Confidence 77888665 6899999999987 445 7889999999999753
No 16
>COG3440 Predicted restriction endonuclease [Defense mechanisms]
Probab=93.57 E-value=0.032 Score=52.73 Aligned_cols=55 Identities=16% Similarity=0.253 Sum_probs=46.9
Q ss_pred CCHHHHHHHHHHCCCcccccCCC-------CCCccceEEeCcCCCCCchhhHHHhchhhhhh
Q 025258 165 KNNLSRKNLMYRDNFTCQYCSSR-------ENLTIDHVVPASRGGEWKWENLVAACFKCNSR 219 (255)
Q Consensus 165 ~~~~~R~~Vl~RD~~~CqYCG~~-------~~ltVDHIiP~S~GG~~tweNLv~aC~~CN~~ 219 (255)
.....|+.|+.--+++|+.||-. ..+..-||.|...+|.+..-|-.++|...|..
T Consensus 179 rd~~fRk~V~~~Y~~RCalCG~e~~~~~~q~ii~~ahikp~~q~y~~~i~N~LaLC~nHh~~ 240 (301)
T COG3440 179 RDGAFRKIVLRQYDYRCALCGLEVLDFLEQNIIKAAHIKPFQQFYPDRIINGLALCKNHHWA 240 (301)
T ss_pred hhHHHHHHHHHHhcchhhhhcchhhhhhHHHHhhhhhcCcccccCcccccccchhchhhHHH
Confidence 35678999999999999999943 34566799999999999999999999888763
No 17
>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=92.73 E-value=0.18 Score=44.82 Aligned_cols=54 Identities=13% Similarity=0.237 Sum_probs=39.9
Q ss_pred CCCcccccCCCCCCccceEEeCcCCCC---CchhhHHHhchhhhhhhcCCCHHHHhhhh
Q 025258 177 DNFTCQYCSSRENLTIDHVVPASRGGE---WKWENLVAACFKCNSRKGKKTLEEANMQL 232 (255)
Q Consensus 177 D~~~CqYCG~~~~ltVDHIiP~S~GG~---~tweNLv~aC~~CN~~Kgnrtpeea~m~L 232 (255)
-.-.|..||++ .-.++|++..-.||. ..-..++++|+.||+...+ ..+.+.-+-
T Consensus 126 ~~~~C~iCGk~-~~d~hH~iG~g~~~~~~~~~d~~~ipLCr~hH~e~H~-g~~~Fe~ky 182 (200)
T PF06147_consen 126 KSRPCVICGKP-PADIHHIIGMGRGRMGIKHHDLFVIPLCREHHRELHR-GRKAFEQKY 182 (200)
T ss_pred ccCccccCCCC-ccccceeeccccCccccccCCCeehhccHHHHHHHhC-CHHHHHHHh
Confidence 34589999976 348999976655543 4567899999999999888 666655444
No 18
>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=92.13 E-value=0.06 Score=52.80 Aligned_cols=47 Identities=26% Similarity=0.395 Sum_probs=38.8
Q ss_pred CcccccCCC-CCCccceEEeCcCCCCCchhhHHHhchhhhhhhcCCCHH
Q 025258 179 FTCQYCSSR-ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLE 226 (255)
Q Consensus 179 ~~CqYCG~~-~~ltVDHIiP~S~GG~~tweNLv~aC~~CN~~Kgnrtpe 226 (255)
-.|+.|+.. ..+..|||-|.|.|-.+... .+++|..||+.|.+|.--
T Consensus 245 ~~~~~~~~~p~~~saDHIGPISlGF~h~P~-Fqplc~~cNSaKnnR~~l 292 (424)
T TIGR02986 245 CSIPECCKHPEKISADHIGPISLGFVHDPR-FQPLCSSCNSAKNDRLTL 292 (424)
T ss_pred ccCcccccCCCCCCccccCCcccccccCcc-ccccccccccccccceeH
Confidence 356678765 77999999999999887764 499999999999998543
No 19
>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=91.30 E-value=0.1 Score=53.78 Aligned_cols=38 Identities=24% Similarity=0.269 Sum_probs=28.5
Q ss_pred HHHHCCCcccccCCC--CCCccceEEeCcCCCC------CchhhHH
Q 025258 173 LMYRDNFTCQYCSSR--ENLTIDHVVPASRGGE------WKWENLV 210 (255)
Q Consensus 173 Vl~RD~~~CqYCG~~--~~ltVDHIiP~S~GG~------~tweNLv 210 (255)
|..-..+.|+|||.. ..-++|||+|+|.-+. ++..||.
T Consensus 755 Ik~fs~gIcpY~Ga~iG~~gEiDHI~PRSht~k~ygtvFN~E~NLI 800 (802)
T TIGR03031 755 IKNFSMGICPYKGASIGGQGEIDHIYPRSHSKKHYGTIFNSEVNLI 800 (802)
T ss_pred HHHHhccCCCCCCCCCCCcccccccccccccccccceeecCcccee
Confidence 444457899999987 5679999999998654 3455654
No 20
>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=86.91 E-value=0.19 Score=50.32 Aligned_cols=48 Identities=29% Similarity=0.510 Sum_probs=38.1
Q ss_pred Ccccc--cCCC-CCCccceEEeCcCCCCCchhhHHHhchhhhhhhcCCCHHH
Q 025258 179 FTCQY--CSSR-ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEE 227 (255)
Q Consensus 179 ~~CqY--CG~~-~~ltVDHIiP~S~GG~~tweNLv~aC~~CN~~Kgnrtpee 227 (255)
+.|+. |++. .-+..|||-|.|.|-.+... .+++|..||+.|.+|.--.
T Consensus 243 G~~~~~~~~~~~~~~SaDHIGPISlGF~h~P~-Fqplc~~cNSaKnnR~~ls 293 (511)
T PF09665_consen 243 GLCRFPNCGKEEECLSADHIGPISLGFVHRPR-FQPLCKSCNSAKNNRMYLS 293 (511)
T ss_pred CcccCCchhhhccccCccccCCcccccccCcc-ccccccccccccccceeHH
Confidence 55653 6654 56899999999999887765 4999999999999986443
No 21
>PF05198 IF3_N: Translation initiation factor IF-3, N-terminal domain; InterPro: IPR019814 Initiation factor 3 (IF-3) (gene infC) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-3 is thought to function as a fidelity factor during the assembly of the ternary initiation complex which consist of the 30S ribosomal subunit, the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit []. The chloroplast initiation factor IF-3(chl) is a protein that enhances the poly(A,U,G)-dependent binding of the initiator tRNA to chloroplast ribosomal 30s subunits in which the central section is evolutionary related to the sequence of bacterial IF-3 []. ; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1TIF_A.
Probab=82.08 E-value=7.4 Score=29.73 Aligned_cols=56 Identities=20% Similarity=0.255 Sum_probs=38.6
Q ss_pred ccccceEEEEcCCcceeeeeeHHHHHHHHHcCceeEEeecCCeeeCCCcceecCcEEEEecceeh
Q 025258 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQV 158 (255)
Q Consensus 94 ~l~~~~vLvLn~sy~Pl~~is~qrAi~l~~~gkAevl~~~~~~vrS~s~~~~vPsVIrL~~yv~~ 158 (255)
.+....|.|+|..++.+++++..+|+.+.-.-..+.|+.. ++.. |.|.+|..|-+.
T Consensus 9 ~I~~~~VrlI~~~g~~lGv~~~~eAl~~A~~~~lDLV~v~------~~~~---PPVcKi~dy~k~ 64 (76)
T PF05198_consen 9 EIRAPEVRLIDEDGEQLGVMSLREALRLAKEKGLDLVEVS------PNAD---PPVCKIMDYGKY 64 (76)
T ss_dssp G---SEEEEE-TTS-EEEEEEHHHHHHHHHHTT-EEEEEE------TTSS---S-EEEEE-HHHH
T ss_pred CcCCCEEEEECCCCcEeceEEHHHHHHHHHHcCCcEEEEc------CCCC---CCeEEEechHHH
Confidence 4567789999999999999999999999888888888753 3333 788888776433
No 22
>PF14239 RRXRR: RRXRR protein
Probab=78.37 E-value=2.8 Score=37.06 Aligned_cols=34 Identities=32% Similarity=0.224 Sum_probs=31.4
Q ss_pred EEEEcCCcceeeeeeHHHHHHHHHcCceeEEeec
Q 025258 100 GLVLDISYRPVNVVCWKRAICLEFMEKADVLEYY 133 (255)
Q Consensus 100 vLvLn~sy~Pl~~is~qrAi~l~~~gkAevl~~~ 133 (255)
|.|||.++.||.=+...+|=.|+-.|||.|+..+
T Consensus 1 VfVld~~gkPLmP~~p~rAR~LLk~GkA~V~r~~ 34 (176)
T PF14239_consen 1 VFVLDKNGKPLMPCHPARARKLLKQGKAKVVRRY 34 (176)
T ss_pred CeEECCCCCcCCCCCHHHHHHHHHCCCEEEEecC
Confidence 6899999999999999999999999999987643
No 23
>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=72.49 E-value=1.9 Score=39.29 Aligned_cols=71 Identities=18% Similarity=0.359 Sum_probs=43.6
Q ss_pred cEEEEecceehhhhcccCCHHHHHHHHHHC-CCcccccCCC-----CCCccceEEeCcCCC------CCchhhHHHhchh
Q 025258 148 AVLRVRHLLQVVKRRRIKNNLSRKNLMYRD-NFTCQYCSSR-----ENLTIDHVVPASRGG------EWKWENLVAACFK 215 (255)
Q Consensus 148 sVIrL~~yv~~p~r~~~~~~~~R~~Vl~RD-~~~CqYCG~~-----~~ltVDHIiP~S~GG------~~tweNLv~aC~~ 215 (255)
..|||..|- +.. +....+|+.|-.-. .-.|.+||.. ..+++||-.-+...- ..+.+-++++|..
T Consensus 70 d~IRLnG~n--~~~--~fnq~Ir~dIk~~yk~q~Cvm~g~~g~sent~ieiDHKd~rk~d~rvsd~~~q~~~dFQ~Lck~ 145 (230)
T PF05315_consen 70 DRIRLNGFN--TEK--VFNQNIRQDIKNYYKQQCCVMCGVRGNSENTKIEIDHKDGRKDDLRVSDMNTQTFDDFQPLCKA 145 (230)
T ss_pred HHHHHcCcC--chh--hhhhHHHHHHHHHHHhcCeeeecccCCCccceeeecccccccccchhcccchhhHHHHHHHHHH
Confidence 456777652 221 23445676653221 2479999974 567888874333221 1256789999999
Q ss_pred hhhhhcC
Q 025258 216 CNSRKGK 222 (255)
Q Consensus 216 CN~~Kgn 222 (255)
||..|..
T Consensus 146 ~N~~KRq 152 (230)
T PF05315_consen 146 CNDQKRQ 152 (230)
T ss_pred HhHHHHH
Confidence 9999843
No 24
>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=70.51 E-value=2.1 Score=33.23 Aligned_cols=49 Identities=24% Similarity=0.403 Sum_probs=31.7
Q ss_pred HHHHHHHHHCCCcccccCCC-----CCCccceEEeCcCCCCCchhhHHHhchhhhhhhcCC
Q 025258 168 LSRKNLMYRDNFTCQYCSSR-----ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKK 223 (255)
Q Consensus 168 ~~R~~Vl~RD~~~CqYCG~~-----~~ltVDHIiP~S~GG~~tweNLv~aC~~CN~~Kgnr 223 (255)
.-.+++++.++++|+.|+.+ ..+.+||=.. .| . . =-++|..||..-|.-
T Consensus 12 ~~~~~l~~~q~~~C~iC~~~~~~~~~~~~vDHdH~--tG-~--v--RGlLC~~CN~~lG~~ 65 (81)
T PF02945_consen 12 EEYEALLEEQGGRCAICGKPLPGESRKLVVDHDHK--TG-R--V--RGLLCRSCNTALGKV 65 (81)
T ss_dssp HHHHCCHHHTTTE-TTT-SEEETTCGGCEEEE-TT--TT-B--E--EEEEEHHHHHHHHHC
T ss_pred HHHHHHHHHhCCcCcCCCCCcccCCCcceecCCCC--CC-C--c--hhhhhhHHhhhhccc
Confidence 34567889999999999982 5678888641 11 1 0 015899999977655
No 25
>TIGR00168 infC translation initiation factor IF-3. render its expression particularly sensitive to excess of its gene product IF-3 thereby regulating its own expression
Probab=52.90 E-value=38 Score=29.49 Aligned_cols=56 Identities=14% Similarity=0.169 Sum_probs=43.6
Q ss_pred ccccceEEEEcCCcceeeeeeHHHHHHHHHcCceeEEeecCCeeeCCCcceecCcEEEEecceeh
Q 025258 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQV 158 (255)
Q Consensus 94 ~l~~~~vLvLn~sy~Pl~~is~qrAi~l~~~gkAevl~~~~~~vrS~s~~~~vPsVIrL~~yv~~ 158 (255)
++....|.+.|..++.+++++.++|+.+.-.-.-+.|+.. +... |.|-++-.|-+.
T Consensus 4 ~I~~~~Vrli~~dG~~lgv~~~~eAl~~A~~~~lDLVev~------~~a~---PPVckImdy~k~ 59 (165)
T TIGR00168 4 RIRFNEVRLIDENGEQLGIVSREEALEIAEEAGLDLVLIS------PNAK---PPVCKIMDYGKY 59 (165)
T ss_pred CcCCCEEEEECCCCcCCCcccHHHHHHHHHHcCCcEEEEC------CCCC---CCEEEEeeHHHH
Confidence 4667789999999999999999999999887777777643 2222 778888776533
No 26
>PF08595 RXT2_N: RXT2-like, N-terminal; InterPro: IPR013904 The entry represents the N-terminal region of RXT2-like proteins. In Saccharomyces cerevisiae (Baker's yeast), RXT2 has been demonstrated to be involved in conjugation with cellular fusion (mating) and invasive growth []. A high throughput localisation study has localised RXT2 to the nucleus [].
Probab=51.39 E-value=13 Score=31.93 Aligned_cols=17 Identities=18% Similarity=-0.019 Sum_probs=10.2
Q ss_pred cceeeeecCCCCeeeec
Q 025258 8 GGLNLLFNGDGSSFGVE 24 (255)
Q Consensus 8 ~~~~~~~~~~~~~~~~~ 24 (255)
=..||+.+.+.++-+-.
T Consensus 4 RGnKL~~~a~~V~~g~L 20 (149)
T PF08595_consen 4 RGNKLKQRAEFVHRGQL 20 (149)
T ss_pred cchhcchhccceecccc
Confidence 34566666666665554
No 27
>CHL00199 infC translation initiation factor 3; Provisional
Probab=48.41 E-value=52 Score=29.36 Aligned_cols=57 Identities=18% Similarity=0.153 Sum_probs=44.8
Q ss_pred cccccceEEEEcCCcceeeeeeHHHHHHHHHcCceeEEeecCCeeeCCCcceecCcEEEEecceeh
Q 025258 93 DELACFRGLVLDISYRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQV 158 (255)
Q Consensus 93 ~~l~~~~vLvLn~sy~Pl~~is~qrAi~l~~~gkAevl~~~~~~vrS~s~~~~vPsVIrL~~yv~~ 158 (255)
..+....|.|.|..++.+++++.++|+.+.-.-.-+.|+.. +... |.|-++..|-+.
T Consensus 20 e~I~~~~VrlI~~~G~~lGv~~~~eAl~~A~~~~lDLVeVs------~~a~---PPVCKImdygK~ 76 (182)
T CHL00199 20 ERIRFPKVRVIDDSGEQLGIFTSEQAIQLAANQGLDLVLVS------EKSD---PPVCRIIDYGKY 76 (182)
T ss_pred cccCCCEEEEECCCCcCCCceeHHHHHHHHHHcCCCEEEEC------CCCC---CCeEEEeehHHH
Confidence 35667889999999999999999999999887777777752 3333 788888777543
No 28
>PTZ00293 thymidine kinase; Provisional
Probab=41.59 E-value=15 Score=33.27 Aligned_cols=59 Identities=22% Similarity=0.420 Sum_probs=32.8
Q ss_pred CcccccCCCCCCccceEEe---C-cCCCCCchhhHHHhchhhhhhhcCCCHHHHhhhhccCCCCCch
Q 025258 179 FTCQYCSSRENLTIDHVVP---A-SRGGEWKWENLVAACFKCNSRKGKKTLEEANMQLSRVPKVLVR 241 (255)
Q Consensus 179 ~~CqYCG~~~~ltVDHIiP---~-S~GG~~tweNLv~aC~~CN~~Kgnrtpeea~m~Ll~~P~~P~~ 241 (255)
-.|..||++...+.= ++. . --||. +..++.|+.|+..|.....+...-..+..|..+..
T Consensus 138 aiC~~CG~~A~~t~R-~~~~~~~v~IGg~---e~Y~a~CR~c~~~~~~~~~~~~~~~~~~~~~~~~~ 200 (211)
T PTZ00293 138 AVCMFCGKEASFSKR-IVQSEQIELIGGE---DKYIATCRKCFRTKQLAEKELEKQDLVEFADFSNE 200 (211)
T ss_pred eEchhhCCcceeEEE-EcCCCCEEEECCc---ccEEehhhhhhhhhccchHhhhhchhhhhcccCcc
Confidence 589999977322211 111 0 11443 36889999999888777664443333333443333
No 29
>PRK00028 infC translation initiation factor IF-3; Reviewed
Probab=39.05 E-value=88 Score=27.49 Aligned_cols=55 Identities=18% Similarity=0.225 Sum_probs=42.7
Q ss_pred ccccceEEEEcCCcceeeeeeHHHHHHHHHcCceeEEeecCCeeeCCCcceecCcEEEEeccee
Q 025258 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQ 157 (255)
Q Consensus 94 ~l~~~~vLvLn~sy~Pl~~is~qrAi~l~~~gkAevl~~~~~~vrS~s~~~~vPsVIrL~~yv~ 157 (255)
.+....|.|+|..++.+++++..+|+.+.-.-.-+.|+. ++... |.|-++..|-+
T Consensus 16 ~I~~~~Vrli~~dG~~lgv~~~~eAl~~A~~~~lDLV~v------~~~~~---PPVckI~dy~k 70 (177)
T PRK00028 16 QIRAREVRLIGDDGEQLGIVSTREALELAEEAGLDLVEI------SPNAK---PPVCKIMDYGK 70 (177)
T ss_pred CcCCCEEEEECCCCcCCCceeHHHHHHHHHHcCCCEEEE------CCCCC---CCEEEEEeHHH
Confidence 467788999999999999999999999977666677764 23333 78888877643
No 30
>PF09257 BCMA-Tall_bind: BCMA, TALL-1 binding; InterPro: IPR015337 Cytokines can be grouped into a family on the basis of sequence, functional and structural similarities [, , ]. Tumor necrosis factor (TNF) (also known as TNF-alpha or cachectin) is a monocyte-derived cytotoxin that has been implicated in tumour regression, septic shock and cachexia [, ]. The protein is synthesised as a prohormone with an unusually long and atypical signal sequence, which is absent from the mature secreted cytokine []. A short hydrophobic stretch of amino acids serves to anchor the prohormone in lipid bilayers []. Both the mature protein and a partially-processed form of the hormone are secreted after cleavage of the propeptide []. There are a number of different families of TNF, but all these cytokines seem to form homotrimeric (or heterotrimeric in the case of LT-alpha/beta) complexes that are recognised by their specific receptors. Members of this entry, which are predominantly found in the tumour necrosis factor receptor superfamily member 17, BCMA, are required for binding to tumour necrosis factor ligand TALL-1 []. ; PDB: 2KN1_A 1OQD_R 1XU2_T.
Probab=33.49 E-value=10 Score=25.73 Aligned_cols=20 Identities=30% Similarity=0.605 Sum_probs=17.1
Q ss_pred hhhHHHhchhhhhhhcCCCH
Q 025258 206 WENLVAACFKCNSRKGKKTL 225 (255)
Q Consensus 206 weNLv~aC~~CN~~Kgnrtp 225 (255)
+++|..+|..||-+=++.+|
T Consensus 7 fD~LL~aCkPChLRCsn~tP 26 (39)
T PF09257_consen 7 FDRLLHACKPCHLRCSNNTP 26 (39)
T ss_dssp EETTTTEEEEHHHHHTSSS-
T ss_pred HHHHHHhcccceeecCCCCC
Confidence 58999999999999988765
No 31
>COG0290 InfC Translation initiation factor 3 (IF-3) [Translation, ribosomal structure and biogenesis]
Probab=33.03 E-value=1.4e+02 Score=26.62 Aligned_cols=40 Identities=15% Similarity=0.147 Sum_probs=32.7
Q ss_pred cccccceEEEEcCCcceeeeeeHHHHHHHHHcCceeEEee
Q 025258 93 DELACFRGLVLDISYRPVNVVCWKRAICLEFMEKADVLEY 132 (255)
Q Consensus 93 ~~l~~~~vLvLn~sy~Pl~~is~qrAi~l~~~gkAevl~~ 132 (255)
+++.-..|-+.+..++-+++++.++|+.|--.-..+.|+.
T Consensus 14 ~~Ir~~evrlIg~~GeqlGiv~~~eAL~lA~e~~LDLV~I 53 (176)
T COG0290 14 EEIRAREVRLIGEDGEQLGIVSIEEALKLAEEAGLDLVEI 53 (176)
T ss_pred ccccccEEEEECCCCcEEcceeHHHHHHHHHHcCCCEEEE
Confidence 4567788999999999999999999999966555565553
No 32
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=32.29 E-value=15 Score=26.34 Aligned_cols=32 Identities=28% Similarity=0.541 Sum_probs=22.6
Q ss_pred cccccCCCCCCccceEEeCcCCCCCchhhHHHhchh
Q 025258 180 TCQYCSSRENLTIDHVVPASRGGEWKWENLVAACFK 215 (255)
Q Consensus 180 ~CqYCG~~~~ltVDHIiP~S~GG~~tweNLv~aC~~ 215 (255)
.|+|||..-.+.+| .|.|+..-++-...+|++
T Consensus 2 ~CPyCge~~~~~iD----~s~~~Q~yiEDC~vCC~P 33 (52)
T PF14255_consen 2 QCPYCGEPIEILID----PSAGDQEYIEDCQVCCRP 33 (52)
T ss_pred CCCCCCCeeEEEEe----cCCCCeeEEeehhhcCCc
Confidence 69999976555444 456666777888888864
No 33
>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=31.57 E-value=17 Score=28.68 Aligned_cols=36 Identities=28% Similarity=0.283 Sum_probs=29.1
Q ss_pred cceEEeCcCCCC----------------CchhhHHHhchhhhhhhcCCCHHH
Q 025258 192 IDHVVPASRGGE----------------WKWENLVAACFKCNSRKGKKTLEE 227 (255)
Q Consensus 192 VDHIiP~S~GG~----------------~tweNLv~aC~~CN~~Kgnrtpee 227 (255)
+|||.|.+.... +...||+.+=..=|..++++.+.+
T Consensus 54 iEHI~Pq~~~~~~~~~~~~~~~~~~~~~~~igNL~LL~~~~N~~~~n~~f~~ 105 (142)
T PF07510_consen 54 IEHIFPQNPKKESKSEKDWDEEEREIYLNSIGNLTLLSKSLNSSISNKPFLE 105 (142)
T ss_pred eEeeccCCCCcccccccccCHHHHHHHhcccccEEEeccchhhccchhhhHH
Confidence 999999986542 567799999999998888887654
No 34
>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]
Probab=26.80 E-value=18 Score=32.81 Aligned_cols=45 Identities=22% Similarity=0.319 Sum_probs=26.3
Q ss_pred CcccccCCCCCC---ccceEEeCcCCCC---CchhhHHHhchhhhhhhcCC
Q 025258 179 FTCQYCSSRENL---TIDHVVPASRGGE---WKWENLVAACFKCNSRKGKK 223 (255)
Q Consensus 179 ~~CqYCG~~~~l---tVDHIiP~S~GG~---~tweNLv~aC~~CN~~Kgnr 223 (255)
-.|.+||++... .++..-+...|.. -.-++.++.|+.||...+..
T Consensus 145 aIC~~Cg~~At~~~Rl~~~~~a~~~~~~i~IGg~e~Y~a~CR~h~~~~~~~ 195 (201)
T COG1435 145 AICNVCGRKATRTLRLINGGPAVYEGPQILIGGNESYEARCRKHHKEPGKE 195 (201)
T ss_pred HHHHHhCCcceEEEEecCCCCCccCCCeEEECCCcceeehhhhhhhccccc
Confidence 489999987322 1222111111110 12678899999999877654
No 35
>PF04231 Endonuclease_1: Endonuclease I; InterPro: IPR007346 Bacterial periplasmic or secreted (3.1.21.1 from EC) Escherichia coli endonuclease I (EndoI) is a sequence independent endonuclease located in the periplasm. It is inhibited by different RNA species. It is thought to normally generate double strand breaks in DNA, except in the presence of high salt concentrations and RNA, when it generates single strand breaks in DNA. Its biological role is unknown []. Other family members are known to be extracellular []. This family also includes a non-specific, Mg2+-activated ribonuclease precursor (Q03091 from SWISSPROT) [].; GO: 0004518 nuclease activity; PDB: 1OUO_A 1OUP_B 2IVK_C 2VND_A 2PU3_A 2G7F_A 2G7E_A.
Probab=25.77 E-value=9.8 Score=34.48 Aligned_cols=41 Identities=29% Similarity=0.278 Sum_probs=29.9
Q ss_pred CCCccceEEeCcCCCCCc-------------------hhhHHHhchhhhhhhcCCCHHHH
Q 025258 188 ENLTIDHVVPASRGGEWK-------------------WENLVAACFKCNSRKGKKTLEEA 228 (255)
Q Consensus 188 ~~ltVDHIiP~S~GG~~t-------------------weNLv~aC~~CN~~Kgnrtpeea 228 (255)
..+..+||+|.|.+|... .-||.++=..+|..++|....+.
T Consensus 70 ~~~N~EHv~P~S~~~~~~~c~~ggr~~c~~~~~~~sDlH~L~pa~~~~Ns~RsN~~f~~~ 129 (218)
T PF04231_consen 70 DRWNREHVVPQSWFGKQFPCREGGRRCCESFRRMESDLHNLRPADGEVNSDRSNYPFGEV 129 (218)
T ss_dssp TSEEEEESS-HHHHHTTSHHHHHHHHHHHHHHHHHH-GGGEEEEEHHHHHHHTT-EE---
T ss_pred CccccceeeCHHHCCCCCcccccCcchhhccccccccccceeccccHhhccCCCCCcccc
Confidence 468999999999877543 45999999999999999875543
No 36
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=25.44 E-value=35 Score=23.78 Aligned_cols=38 Identities=34% Similarity=0.695 Sum_probs=21.0
Q ss_pred CCCcccccCCC--CCCccceEEeCcCCCCCchhhHHHhchhhhhh
Q 025258 177 DNFTCQYCSSR--ENLTIDHVVPASRGGEWKWENLVAACFKCNSR 219 (255)
Q Consensus 177 D~~~CqYCG~~--~~ltVDHIiP~S~GG~~tweNLv~aC~~CN~~ 219 (255)
+.+.|+||++. ..-=++|+.-.-.+... ...|+-|...
T Consensus 1 ~~f~CP~C~~~~~~~~L~~H~~~~H~~~~~-----~v~CPiC~~~ 40 (54)
T PF05605_consen 1 DSFTCPYCGKGFSESSLVEHCEDEHRSESK-----NVVCPICSSR 40 (54)
T ss_pred CCcCCCCCCCccCHHHHHHHHHhHCcCCCC-----CccCCCchhh
Confidence 45899999984 11124455433222211 2578888764
No 37
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=23.75 E-value=57 Score=24.42 Aligned_cols=19 Identities=32% Similarity=0.719 Sum_probs=14.5
Q ss_pred CCCcccccCCCCCCccceEE
Q 025258 177 DNFTCQYCSSRENLTIDHVV 196 (255)
Q Consensus 177 D~~~CqYCG~~~~ltVDHIi 196 (255)
....|..|+...+ +++|+.
T Consensus 58 ~~~~C~~C~~~~E-t~~Hlf 76 (86)
T PF13966_consen 58 VDPICPLCGNEEE-TIEHLF 76 (86)
T ss_pred cCCccccCCCccc-ccccee
Confidence 3579999997544 888986
No 38
>PF07148 MalM: Maltose operon periplasmic protein precursor (MalM); InterPro: IPR010794 This family consists of several maltose operon periplasmic protein precursor (MalM) sequences. The function of this family is unknown [].; GO: 0008643 carbohydrate transport, 0042597 periplasmic space
Probab=23.11 E-value=72 Score=26.86 Aligned_cols=23 Identities=22% Similarity=0.261 Sum_probs=19.5
Q ss_pred ccccceEEEEcCCcceeeeeeHH
Q 025258 94 ELACFRGLVLDISYRPVNVVCWK 116 (255)
Q Consensus 94 ~l~~~~vLvLn~sy~Pl~~is~q 116 (255)
++--+.||+||++|+|+..++..
T Consensus 30 ~vfaP~vliLD~~~~~~~~~~~~ 52 (135)
T PF07148_consen 30 SVFAPNVLILDENFQPVRTYPSS 52 (135)
T ss_pred cEEeeeEEEECCCCCEEEEcChH
Confidence 45568899999999999999854
No 39
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.98 E-value=24 Score=28.65 Aligned_cols=40 Identities=18% Similarity=0.369 Sum_probs=21.8
Q ss_pred CcccccCCCCCCc-cceEEeCcCCCCCchhhHHHhchhhhhhhcC
Q 025258 179 FTCQYCSSRENLT-IDHVVPASRGGEWKWENLVAACFKCNSRKGK 222 (255)
Q Consensus 179 ~~CqYCG~~~~lt-VDHIiP~S~GG~~tweNLv~aC~~CN~~Kgn 222 (255)
-.|.|||.+..+. -+-|-|..- +.|. ....|..|+..-|-
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~---~~~~-~~y~C~~C~AyVG~ 43 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRY---DDGP-YLYVCTPCDAYVGC 43 (102)
T ss_pred cccCCCCCeeEEcccchhcCccC---CCCc-eeEECCCCCceeee
Confidence 3799999874331 122222111 1232 34889999886543
No 40
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=20.52 E-value=62 Score=33.68 Aligned_cols=60 Identities=12% Similarity=0.084 Sum_probs=40.9
Q ss_pred CCHHHHHHHHHHCCCcccccCCCCCCccceEEeCcCCCCCchhhHH-------HhchhhhhhhcCCCHHHHhhhhccCCC
Q 025258 165 KNNLSRKNLMYRDNFTCQYCSSRENLTIDHVVPASRGGEWKWENLV-------AACFKCNSRKGKKTLEEANMQLSRVPK 237 (255)
Q Consensus 165 ~~~~~R~~Vl~RD~~~CqYCG~~~~ltVDHIiP~S~GG~~tweNLv-------~aC~~CN~~Kgnrtpeea~m~Ll~~P~ 237 (255)
.+...|+..+..++++|+-||..-.. +.|.+.. ..|..||..-..-.|...-+.+-..++
T Consensus 327 ~~~~~re~gL~aQ~~~CAgC~~~i~~-------------~~~~~~R~C~y~G~y~C~~Ch~~~~svIPARVl~~WDf~~y 393 (580)
T KOG1829|consen 327 HPAIPREKGLDAQNFRCAGCGHTIGP-------------DLEQRPRLCRYLGKYFCDCCHQNDKSVIPARVLHNWDFTKY 393 (580)
T ss_pred ccCcchhhhhhccCceecccCCCccc-------------ccccchhHhhhhhhhhCchhcccCcccccccceecccCccc
Confidence 35677999999999999999966210 3344433 469999998777666655555544443
Done!