Query 028336
Match_columns 210
No_of_seqs 174 out of 927
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 09:55:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028336.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028336hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1403 McrA Restriction endon 99.5 1.2E-14 2.7E-19 111.1 4.9 101 107-210 1-102 (146)
2 smart00507 HNHc HNH nucleases. 99.0 3.7E-10 8E-15 72.9 2.5 41 169-210 2-44 (52)
3 cd00085 HNHc HNH nucleases; HN 98.8 1.4E-09 3.1E-14 71.4 2.0 41 169-210 3-46 (57)
4 PF13395 HNH_4: HNH endonuclea 98.7 9.6E-09 2.1E-13 71.2 1.9 30 181-210 1-38 (54)
5 TIGR01865 cas_Csn1 CRISPR-asso 98.6 2E-08 4.3E-13 101.0 1.8 45 166-210 569-622 (805)
6 PF01844 HNH: HNH endonuclease 98.4 7.5E-08 1.6E-12 62.9 0.1 30 181-210 1-34 (47)
7 TIGR02646 conserved hypothetic 98.1 3.1E-06 6.7E-11 68.6 3.4 44 167-210 13-61 (144)
8 PRK11295 hypothetical protein; 97.7 2.1E-05 4.5E-10 63.2 2.1 44 166-209 12-61 (113)
9 PF14279 HNH_5: HNH endonuclea 96.5 0.0011 2.5E-08 48.9 1.3 28 181-208 1-31 (71)
10 TIGR03031 cas_csx12 CRISPR-ass 93.7 0.043 9.2E-07 55.3 2.4 30 174-203 756-787 (802)
11 COG3513 Predicted CRISPR-assoc 92.1 0.1 2.2E-06 54.3 2.6 42 169-210 562-612 (1088)
12 smart00782 PhnA_Zn_Ribbon PhnA 90.5 0.25 5.5E-06 34.1 2.5 33 173-205 2-34 (47)
13 PF14239 RRXRR: RRXRR protein 90.3 0.4 8.7E-06 41.3 4.2 34 100-133 1-34 (176)
14 PF05198 IF3_N: Translation in 85.3 4.2 9.1E-05 30.3 6.5 55 94-157 9-63 (76)
15 PF13391 HNH_2: HNH endonuclea 72.7 1.7 3.8E-05 29.6 0.9 21 181-201 1-26 (66)
16 COG3440 Predicted restriction 68.3 2.7 5.8E-05 39.2 1.3 45 165-209 179-230 (301)
17 TIGR00168 infC translation ini 66.5 16 0.00035 30.9 5.6 56 94-158 4-59 (165)
18 PF02945 Endonuclease_7: Recom 66.4 2.9 6.2E-05 31.7 1.0 29 167-195 11-44 (81)
19 CHL00199 infC translation init 56.3 32 0.00069 29.9 5.7 56 94-158 21-76 (182)
20 PRK00028 infC translation init 51.6 43 0.00092 28.6 5.7 55 94-157 16-70 (177)
21 PF05605 zf-Di19: Drought indu 47.6 8.8 0.00019 26.1 0.8 11 177-187 1-11 (54)
22 PF14255 Cys_rich_CPXG: Cystei 45.7 7.8 0.00017 27.2 0.3 15 180-194 2-16 (52)
23 PF13966 zf-RVT: zinc-binding 41.3 26 0.00056 25.5 2.5 30 169-199 47-79 (86)
24 PF07148 MalM: Maltose operon 40.9 25 0.00053 28.9 2.5 24 94-117 30-53 (135)
25 PF08595 RXT2_N: RXT2-like, N- 33.2 38 0.00081 28.5 2.5 16 9-24 5-20 (149)
26 COG0290 InfC Translation initi 30.4 1E+02 0.0022 26.9 4.8 55 94-157 15-69 (176)
27 COG1997 RPL43A Ribosomal prote 28.1 37 0.0008 26.7 1.5 19 169-187 26-44 (89)
28 PF06147 DUF968: Protein of un 26.5 44 0.00096 28.9 1.9 32 170-202 119-150 (200)
29 PF00571 CBS: CBS domain CBS d 26.1 1.2E+02 0.0026 19.3 3.5 31 92-122 25-55 (57)
30 COG3183 Predicted restriction 24.0 53 0.0012 30.4 2.0 34 166-199 183-226 (272)
31 PTZ00255 60S ribosomal protein 23.7 49 0.0011 25.9 1.5 20 168-187 26-45 (90)
32 PF13894 zf-C2H2_4: C2H2-type 22.4 29 0.00064 18.4 0.0 9 179-187 1-9 (24)
33 COG1996 RPC10 DNA-directed RNA 22.0 36 0.00078 23.9 0.4 15 173-187 19-33 (49)
34 PF04231 Endonuclease_1: Endon 21.7 18 0.0004 31.8 -1.4 18 188-205 70-87 (218)
No 1
>COG1403 McrA Restriction endonuclease [Defense mechanisms]
Probab=99.52 E-value=1.2e-14 Score=111.10 Aligned_cols=101 Identities=30% Similarity=0.519 Sum_probs=87.9
Q ss_pred CceeeeecHHHHHHHHHhCCeeEEEecCCeeeCCCcceecCeEEEEecceeeeeccccCChhhHHHHHhHcCCcccccCC
Q 028336 107 YRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQVVKRRRIKNNLSRKNLMYRDNFTCQYCSS 186 (210)
Q Consensus 107 y~Pl~~vswqrAi~Ll~~gkAevle~~~~~IrS~sg~~~vPsVIrL~~yv~~p~r~~~~~~~tR~~Vl~RD~~~CqYCG~ 186 (210)
|.|....+|++++..+..+.|..+..+. ...++.....+|.+..+..+...+... .++.+|.+++.||.+.|+|||.
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~r~~~~~~d~~~c~~c~~ 77 (146)
T COG1403 1 YNPLESKSIRPALDRLVSQRAKHVAEYP-CLASESKDLRRPSVTDLTGESKRPSEK--RPAKTRRAVLLRDNGLCQYCGS 77 (146)
T ss_pred CccccccchhHHHHHHhhcccccccCcc-eecceecccccCccceeeeeecccCCC--CchHHHHHHHccccccccccCC
Confidence 5788999999999999999999887654 455667788899999999887766543 5789999999999999999998
Q ss_pred Cc-CCeeCeeecCcCCCCCCcCcCC
Q 028336 187 RE-NLTIDHVVPASRGGEWKWENLV 210 (210)
Q Consensus 187 ~~-~LtvDHIIPrSrGG~dtweNLV 210 (210)
.. .+++|||||++.||.+.|+||+
T Consensus 78 ~~~~~~~dHiip~~~g~~~~~~Nl~ 102 (146)
T COG1403 78 VGTDLEVDHIVPLSRGGASAWENLE 102 (146)
T ss_pred cCCCCceeeEeecccCCcchHHHHH
Confidence 74 7999999999999999999974
No 2
>smart00507 HNHc HNH nucleases.
Probab=98.96 E-value=3.7e-10 Score=72.94 Aligned_cols=41 Identities=41% Similarity=0.784 Sum_probs=37.3
Q ss_pred hHHHHHhHcCCcccccCCCc--CCeeCeeecCcCCCCCCcCcCC
Q 028336 169 SRKNLMYRDNFTCQYCSSRE--NLTIDHVVPASRGGEWKWENLV 210 (210)
Q Consensus 169 tR~~Vl~RD~~~CqYCG~~~--~LtvDHIIPrSrGG~dtweNLV 210 (210)
.|..++.|| +.|+|||.+. .+++|||+|.+.||.++++||+
T Consensus 2 ~~~~~~~r~-~~C~~C~~~~~~~~~v~Hi~p~~~~~~~~~~Nl~ 44 (52)
T smart00507 2 LRRLLLHRD-GVCAYCGKPASEGLEVDHIIPLSDGGNDDLDNLV 44 (52)
T ss_pred HHHHHHHHC-CCCcCCcCCCCCCeEEEecCChhcCCCCChHhCe
Confidence 467899999 9999999885 4999999999999999999985
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=98.83 E-value=1.4e-09 Score=71.39 Aligned_cols=41 Identities=44% Similarity=0.799 Sum_probs=37.3
Q ss_pred hHHHHHhHcCCcccccCCC---cCCeeCeeecCcCCCCCCcCcCC
Q 028336 169 SRKNLMYRDNFTCQYCSSR---ENLTIDHVVPASRGGEWKWENLV 210 (210)
Q Consensus 169 tR~~Vl~RD~~~CqYCG~~---~~LtvDHIIPrSrGG~dtweNLV 210 (210)
.|..+++|| +.|+|||.. ..+++|||+|.+.||.++++||+
T Consensus 3 ~r~~~~~~~-~~C~~c~~~~~~~~~~v~Hi~p~~~~~~~~~~Nl~ 46 (57)
T cd00085 3 HRLVLLARD-GLCPYCGKPGGTEGLEVDHIIPLSDGGNNDLDNLV 46 (57)
T ss_pred HHHHHHHhC-CcCccCCCcCCCCCceEEeecchhhCCCCchHHhH
Confidence 578899999 999999984 67999999999999999999985
No 4
>PF13395 HNH_4: HNH endonuclease
Probab=98.66 E-value=9.6e-09 Score=71.17 Aligned_cols=30 Identities=53% Similarity=1.039 Sum_probs=27.5
Q ss_pred ccccCCC---cC-----CeeCeeecCcCCCCCCcCcCC
Q 028336 181 CQYCSSR---EN-----LTIDHVVPASRGGEWKWENLV 210 (210)
Q Consensus 181 CqYCG~~---~~-----LtvDHIIPrSrGG~dtweNLV 210 (210)
|.|||.+ .. .++|||+|+|++|.+++.|+|
T Consensus 1 C~Y~g~~i~~~~l~~~~~~iDHiiP~s~~~~~s~~Nlv 38 (54)
T PF13395_consen 1 CPYCGKPISIENLFKNKYEIDHIIPRSRGGDDSFWNLV 38 (54)
T ss_pred CCCCCCCCChhhcccCCceeEEEecccccCCCCcchhh
Confidence 9999987 33 799999999999999999997
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=98.57 E-value=2e-08 Score=100.97 Aligned_cols=45 Identities=31% Similarity=0.512 Sum_probs=39.8
Q ss_pred ChhhHHHHHhHcCCcccccCCC---c------CCeeCeeecCcCCCCCCcCcCC
Q 028336 166 NNLSRKNLMYRDNFTCQYCSSR---E------NLTIDHVVPASRGGEWKWENLV 210 (210)
Q Consensus 166 ~~~tR~~Vl~RD~~~CqYCG~~---~------~LtvDHIIPrSrGG~dtweNLV 210 (210)
....|..++.+++++|+|||.+ . .++||||||.|+||.|+|+|+|
T Consensus 569 ~~~~k~~L~~~q~~~C~Y~g~~i~~~~l~~~~~~~iDHIiP~s~~~dds~~N~v 622 (805)
T TIGR01865 569 KNILKLRLYYQQNGKCMYTGKEIDIDDLFDLSYYEIDHILPQSRSFDDSISNKV 622 (805)
T ss_pred hHHHHHHHHHHcCCcCCCCCCcCccccccCCCCCceeeecccccCCCCcHHHHH
Confidence 3456888999999999999987 2 4789999999999999999986
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=98.37 E-value=7.5e-08 Score=62.91 Aligned_cols=30 Identities=47% Similarity=1.043 Sum_probs=20.4
Q ss_pred ccccCCC----cCCeeCeeecCcCCCCCCcCcCC
Q 028336 181 CQYCSSR----ENLTIDHVVPASRGGEWKWENLV 210 (210)
Q Consensus 181 CqYCG~~----~~LtvDHIIPrSrGG~dtweNLV 210 (210)
|+|||.+ ..+++|||+|.+.||.++++||+
T Consensus 1 C~~C~~~~~~~~~~~v~Hi~~~~~gg~~~~~Nl~ 34 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVHHIIPRSKGGKNDLENLI 34 (47)
T ss_dssp -TTT--B--GG-GEEEEESS-TTTT---STTTEE
T ss_pred CCCCCCcCccCcceEeECcCchhcCCCCCHHHHH
Confidence 9999987 46899999999999999999984
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=98.06 E-value=3.1e-06 Score=68.58 Aligned_cols=44 Identities=23% Similarity=0.442 Sum_probs=38.4
Q ss_pred hhhHHHHHhHcCCcccccCCC---cCCeeCeeecCcCCCC--CCcCcCC
Q 028336 167 NLSRKNLMYRDNFTCQYCSSR---ENLTIDHVVPASRGGE--WKWENLV 210 (210)
Q Consensus 167 ~~tR~~Vl~RD~~~CqYCG~~---~~LtvDHIIPrSrGG~--dtweNLV 210 (210)
...|..|++..+++|.||+.. ..++|||++|++..+. -+|+||+
T Consensus 13 ~~i~~~L~~~~~~~C~YC~~~~~~~~~~ieH~~Pk~~~~~~~~~~~NL~ 61 (144)
T TIGR02646 13 DEVHNQLLQLQGGLCAYCEREIELLGSHIEHFRPKGAYPPLTLDWSNLF 61 (144)
T ss_pred HHHHHHHHHHhCCCcCccCCCcCCCCcceeeecccCCChhhhcChhhch
Confidence 468889999999999999984 6699999999998874 6789985
No 8
>PRK11295 hypothetical protein; Provisional
Probab=97.68 E-value=2.1e-05 Score=63.21 Aligned_cols=44 Identities=18% Similarity=0.255 Sum_probs=37.9
Q ss_pred ChhhHHHHHhHcCCcccccCCC------cCCeeCeeecCcCCCCCCcCcC
Q 028336 166 NNLSRKNLMYRDNFTCQYCSSR------ENLTIDHVVPASRGGEWKWENL 209 (210)
Q Consensus 166 ~~~tR~~Vl~RD~~~CqYCG~~------~~LtvDHIIPrSrGG~dtweNL 209 (210)
....|+.+|.|+.+.|+.|++. ..++||||+|...|+.+.-+||
T Consensus 12 ~~~~R~~~L~r~p~lC~~Cgr~~~~a~~~a~vVDHIip~~~gd~~D~sNL 61 (113)
T PRK11295 12 ESGYREKALKLYPWVCGRCSREFVYSNLRELTVHHIDHDHDNNPEDGSNW 61 (113)
T ss_pred HHHHHHHHHHHCcchhhhhcChhccCCCCCceeeccCCCCCCCCCchhHH
Confidence 4568999999999999999985 3579999999999988777776
No 9
>PF14279 HNH_5: HNH endonuclease
Probab=96.50 E-value=0.0011 Score=48.86 Aligned_cols=28 Identities=39% Similarity=0.921 Sum_probs=24.0
Q ss_pred ccccCCC---cCCeeCeeecCcCCCCCCcCc
Q 028336 181 CQYCSSR---ENLTIDHVVPASRGGEWKWEN 208 (210)
Q Consensus 181 CqYCG~~---~~LtvDHIIPrSrGG~dtweN 208 (210)
|.||++. ...|.+||||.|-||..++.|
T Consensus 1 Ci~C~~~~~~~~~s~EHIIP~sLGG~~~~~~ 31 (71)
T PF14279_consen 1 CIYCNKEKSESNFSEEHIIPESLGGKLKINN 31 (71)
T ss_pred CccCCCCCCccCCCccccCchhcCCcccccc
Confidence 8999987 446799999999999887766
No 10
>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=93.68 E-value=0.043 Score=55.33 Aligned_cols=30 Identities=23% Similarity=0.296 Sum_probs=24.3
Q ss_pred HhHcCCcccccCCC--cCCeeCeeecCcCCCC
Q 028336 174 MYRDNFTCQYCSSR--ENLTIDHVVPASRGGE 203 (210)
Q Consensus 174 l~RD~~~CqYCG~~--~~LtvDHIIPrSrGG~ 203 (210)
-.=..+.|+|||.. ..-++|||+|||+-|+
T Consensus 756 k~fs~gIcpY~Ga~iG~~gEiDHI~PRSht~k 787 (802)
T TIGR03031 756 KNFSMGICPYKGASIGGQGEIDHIYPRSHSKK 787 (802)
T ss_pred HHHhccCCCCCCCCCCCccccccccccccccc
Confidence 33357899999987 5679999999998665
No 11
>COG3513 Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]
Probab=92.09 E-value=0.1 Score=54.27 Aligned_cols=42 Identities=33% Similarity=0.505 Sum_probs=35.8
Q ss_pred hHHHHHhHcCCcccccCCC------cC---CeeCeeecCcCCCCCCcCcCC
Q 028336 169 SRKNLMYRDNFTCQYCSSR------EN---LTIDHVVPASRGGEWKWENLV 210 (210)
Q Consensus 169 tR~~Vl~RD~~~CqYCG~~------~~---LtvDHIIPrSrGG~dtweNLV 210 (210)
.+-.++.-+++.|.|-|+. .+ ..||||+|-|+-=.|+.+|.|
T Consensus 562 lKLrLY~~Q~gkcmYsgqei~I~rL~dk~~~eIDHi~P~Sr~~DDS~~NkV 612 (1088)
T COG3513 562 LKLRLYYLQNGKCMYSGQEIDIHRLSDKGYYEIDHIVPQSRTWDDSIDNKV 612 (1088)
T ss_pred hHHHHHHHhcCcccccCcccchhhcccccceeeceecccccccccccccee
Confidence 3456888999999999986 33 899999999998888888876
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=90.49 E-value=0.25 Score=34.09 Aligned_cols=33 Identities=27% Similarity=0.380 Sum_probs=27.5
Q ss_pred HHhHcCCcccccCCCcCCeeCeeecCcCCCCCC
Q 028336 173 LMYRDNFTCQYCSSRENLTIDHVVPASRGGEWK 205 (210)
Q Consensus 173 Vl~RD~~~CqYCG~~~~LtvDHIIPrSrGG~dt 205 (210)
++.|-+..|..||....|++-+|-|.+.|+.+.
T Consensus 2 L~~Rs~~kCELC~a~~~L~vy~Vpp~~~~~~d~ 34 (47)
T smart00782 2 LLARCESKCELCGSDSPLVVYAVPPSSDVTADN 34 (47)
T ss_pred hhHHcCCcccCcCCCCCceEEecCCCCCCCccc
Confidence 678999999999998889999987777666543
No 13
>PF14239 RRXRR: RRXRR protein
Probab=90.30 E-value=0.4 Score=41.30 Aligned_cols=34 Identities=32% Similarity=0.224 Sum_probs=31.5
Q ss_pred EEEEcCCCceeeeecHHHHHHHHHhCCeeEEEec
Q 028336 100 GLVLDISYRPVNVVCWKRAICLEFMEKADVLEYY 133 (210)
Q Consensus 100 VLVLNasy~Pl~~vswqrAi~Ll~~gkAevle~~ 133 (210)
|.|||.++.||.-+...+|=.|+-.|||.|+..+
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 6799999999999999999999999999888744
No 14
>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=85.34 E-value=4.2 Score=30.30 Aligned_cols=55 Identities=20% Similarity=0.266 Sum_probs=38.2
Q ss_pred ccCcceEEEEcCCCceeeeecHHHHHHHHHhCCeeEEEecCCeeeCCCcceecCeEEEEeccee
Q 028336 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQ 157 (210)
Q Consensus 94 ~~~~~rVLVLNasy~Pl~~vswqrAi~Ll~~gkAevle~~~~~IrS~sg~~~vPsVIrL~~yv~ 157 (210)
.+..+.|.++|.+++.+++++.++|+.+--.-..+.++.. ++.. |.|.+|..|-+
T Consensus 9 ~I~~~~VrlI~~~g~~lGv~~~~eAl~~A~~~~lDLV~v~------~~~~---PPVcKi~dy~k 63 (76)
T PF05198_consen 9 EIRAPEVRLIDEDGEQLGVMSLREALRLAKEKGLDLVEVS------PNAD---PPVCKIMDYGK 63 (76)
T ss_dssp G---SEEEEE-TTS-EEEEEEHHHHHHHHHHTT-EEEEEE------TTSS---S-EEEEE-HHH
T ss_pred CcCCCEEEEECCCCcEeceEEHHHHHHHHHHcCCcEEEEc------CCCC---CCeEEEechHH
Confidence 4566889999999999999999999999888888887753 2233 88999987743
No 15
>PF13391 HNH_2: HNH endonuclease
Probab=72.71 E-value=1.7 Score=29.59 Aligned_cols=21 Identities=38% Similarity=0.619 Sum_probs=17.8
Q ss_pred ccccCCCc-----CCeeCeeecCcCC
Q 028336 181 CQYCSSRE-----NLTIDHVVPASRG 201 (210)
Q Consensus 181 CqYCG~~~-----~LtvDHIIPrSrG 201 (210)
|..||... .++.-||+|.+.+
T Consensus 1 C~itg~~~~~~~~~~eaaHI~P~s~~ 26 (66)
T PF13391_consen 1 CVITGIRDPSPWELLEAAHIVPFSLG 26 (66)
T ss_pred CcCCcCCcCCCCCcEEEEEcccCccC
Confidence 77888766 6999999999976
No 16
>COG3440 Predicted restriction endonuclease [Defense mechanisms]
Probab=68.29 E-value=2.7 Score=39.15 Aligned_cols=45 Identities=16% Similarity=0.250 Sum_probs=36.9
Q ss_pred CChhhHHHHHhHcCCcccccCCC-------cCCeeCeeecCcCCCCCCcCcC
Q 028336 165 KNNLSRKNLMYRDNFTCQYCSSR-------ENLTIDHVVPASRGGEWKWENL 209 (210)
Q Consensus 165 ~~~~tR~~Vl~RD~~~CqYCG~~-------~~LtvDHIIPrSrGG~dtweNL 209 (210)
+..+.|+.|+.--+|+|+-||.. ..+.--||-|..++|.+..-|-
T Consensus 179 rd~~fRk~V~~~Y~~RCalCG~e~~~~~~q~ii~~ahikp~~q~y~~~i~N~ 230 (301)
T COG3440 179 RDGAFRKIVLRQYDYRCALCGLEVLDFLEQNIIKAAHIKPFQQFYPDRIING 230 (301)
T ss_pred hhHHHHHHHHHHhcchhhhhcchhhhhhHHHHhhhhhcCcccccCccccccc
Confidence 46789999999999999999954 3355569999999998887773
No 17
>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=66.51 E-value=16 Score=30.88 Aligned_cols=56 Identities=13% Similarity=0.120 Sum_probs=43.5
Q ss_pred ccCcceEEEEcCCCceeeeecHHHHHHHHHhCCeeEEEecCCeeeCCCcceecCeEEEEecceee
Q 028336 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQV 158 (210)
Q Consensus 94 ~~~~~rVLVLNasy~Pl~~vswqrAi~Ll~~gkAevle~~~~~IrS~sg~~~vPsVIrL~~yv~~ 158 (210)
.+..+.|.++|.++..+++++.++|+.+.-.---+.++... ... |.|-+|-.|.+.
T Consensus 4 ~I~~~~Vrli~~dG~~lgv~~~~eAl~~A~~~~lDLVev~~------~a~---PPVckImdy~k~ 59 (165)
T TIGR00168 4 RIRFNEVRLIDENGEQLGIVSREEALEIAEEAGLDLVLISP------NAK---PPVCKIMDYGKY 59 (165)
T ss_pred CcCCCEEEEECCCCcCCCcccHHHHHHHHHHcCCcEEEECC------CCC---CCEEEEeeHHHH
Confidence 35568899999999999999999999998776667776432 222 778898877543
No 18
>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=66.40 E-value=2.9 Score=31.70 Aligned_cols=29 Identities=21% Similarity=0.390 Sum_probs=20.4
Q ss_pred hhhHHHHHhHcCCcccccCCC-----cCCeeCee
Q 028336 167 NLSRKNLMYRDNFTCQYCSSR-----ENLTIDHV 195 (210)
Q Consensus 167 ~~tR~~Vl~RD~~~CqYCG~~-----~~LtvDHI 195 (210)
.....++++.++++|+.||.+ ..+-+||=
T Consensus 11 ~~~~~~l~~~q~~~C~iC~~~~~~~~~~~~vDHd 44 (81)
T PF02945_consen 11 PEEYEALLEEQGGRCAICGKPLPGESRKLVVDHD 44 (81)
T ss_dssp HHHHHCCHHHTTTE-TTT-SEEETTCGGCEEEE-
T ss_pred HHHHHHHHHHhCCcCcCCCCCcccCCCcceecCC
Confidence 345567899999999999982 56788885
No 19
>CHL00199 infC translation initiation factor 3; Provisional
Probab=56.26 E-value=32 Score=29.90 Aligned_cols=56 Identities=18% Similarity=0.159 Sum_probs=44.4
Q ss_pred ccCcceEEEEcCCCceeeeecHHHHHHHHHhCCeeEEEecCCeeeCCCcceecCeEEEEecceee
Q 028336 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQV 158 (210)
Q Consensus 94 ~~~~~rVLVLNasy~Pl~~vswqrAi~Ll~~gkAevle~~~~~IrS~sg~~~vPsVIrL~~yv~~ 158 (210)
.+..+.|.++|.+++.+++++.++|+.+...---+.++... ... |.|-++..|-+.
T Consensus 21 ~I~~~~VrlI~~~G~~lGv~~~~eAl~~A~~~~lDLVeVs~------~a~---PPVCKImdygK~ 76 (182)
T CHL00199 21 RIRFPKVRVIDDSGEQLGIFTSEQAIQLAANQGLDLVLVSE------KSD---PPVCRIIDYGKY 76 (182)
T ss_pred ccCCCEEEEECCCCcCCCceeHHHHHHHHHHcCCCEEEECC------CCC---CCeEEEeehHHH
Confidence 45678999999999999999999999998777777777533 222 788888877543
No 20
>PRK00028 infC translation initiation factor IF-3; Reviewed
Probab=51.61 E-value=43 Score=28.64 Aligned_cols=55 Identities=16% Similarity=0.201 Sum_probs=42.6
Q ss_pred ccCcceEEEEcCCCceeeeecHHHHHHHHHhCCeeEEEecCCeeeCCCcceecCeEEEEeccee
Q 028336 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQ 157 (210)
Q Consensus 94 ~~~~~rVLVLNasy~Pl~~vswqrAi~Ll~~gkAevle~~~~~IrS~sg~~~vPsVIrL~~yv~ 157 (210)
.+..+.|.++|.++..+++++..+|+.+.-.-.-+.++.. +... |.|-++-.|-+
T Consensus 16 ~I~~~~Vrli~~dG~~lgv~~~~eAl~~A~~~~lDLV~v~------~~~~---PPVckI~dy~k 70 (177)
T PRK00028 16 QIRAREVRLIGDDGEQLGIVSTREALELAEEAGLDLVEIS------PNAK---PPVCKIMDYGK 70 (177)
T ss_pred CcCCCEEEEECCCCcCCCceeHHHHHHHHHHcCCCEEEEC------CCCC---CCEEEEEeHHH
Confidence 4567899999999999999999999999766666666642 2233 78888877744
No 21
>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=47.56 E-value=8.8 Score=26.11 Aligned_cols=11 Identities=55% Similarity=1.368 Sum_probs=9.1
Q ss_pred cCCcccccCCC
Q 028336 177 DNFTCQYCSSR 187 (210)
Q Consensus 177 D~~~CqYCG~~ 187 (210)
|.++|.|||+.
T Consensus 1 ~~f~CP~C~~~ 11 (54)
T PF05605_consen 1 DSFTCPYCGKG 11 (54)
T ss_pred CCcCCCCCCCc
Confidence 56899999973
No 22
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=45.71 E-value=7.8 Score=27.25 Aligned_cols=15 Identities=33% Similarity=0.835 Sum_probs=11.7
Q ss_pred cccccCCCcCCeeCe
Q 028336 180 TCQYCSSRENLTIDH 194 (210)
Q Consensus 180 ~CqYCG~~~~LtvDH 194 (210)
.|+|||..-.+.+|.
T Consensus 2 ~CPyCge~~~~~iD~ 16 (52)
T PF14255_consen 2 QCPYCGEPIEILIDP 16 (52)
T ss_pred CCCCCCCeeEEEEec
Confidence 699999876666664
No 23
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=41.33 E-value=26 Score=25.53 Aligned_cols=30 Identities=30% Similarity=0.566 Sum_probs=20.8
Q ss_pred hHHHHHhH---cCCcccccCCCcCCeeCeeecCc
Q 028336 169 SRKNLMYR---DNFTCQYCSSRENLTIDHVVPAS 199 (210)
Q Consensus 169 tR~~Vl~R---D~~~CqYCG~~~~LtvDHIIPrS 199 (210)
++.++..| ....|..|+...+ |++|++=.-
T Consensus 47 t~~~l~~r~~~~~~~C~~C~~~~E-t~~Hlf~~C 79 (86)
T PF13966_consen 47 TKDNLQRRGIQVDPICPLCGNEEE-TIEHLFFHC 79 (86)
T ss_pred hhhhhhccCCccCCccccCCCccc-cccceeccC
Confidence 45555554 5689999997544 899987443
No 24
>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=40.91 E-value=25 Score=28.86 Aligned_cols=24 Identities=21% Similarity=0.246 Sum_probs=20.5
Q ss_pred ccCcceEEEEcCCCceeeeecHHH
Q 028336 94 ELACFRGLVLDISYRPVNVVCWKR 117 (210)
Q Consensus 94 ~~~~~rVLVLNasy~Pl~~vswqr 117 (210)
..-.|.||+||++++|+..++...
T Consensus 30 ~vfaP~vliLD~~~~~~~~~~~~~ 53 (135)
T PF07148_consen 30 SVFAPNVLILDENFQPVRTYPSSD 53 (135)
T ss_pred cEEeeeEEEECCCCCEEEEcChHH
Confidence 445689999999999999998764
No 25
>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=33.18 E-value=38 Score=28.47 Aligned_cols=16 Identities=19% Similarity=0.001 Sum_probs=9.8
Q ss_pred ceeeeecCCCCeeeec
Q 028336 9 GLNLLFNGDGSSFGVE 24 (210)
Q Consensus 9 ~~~~l~~~~~~~~~~~ 24 (210)
..||+.+.+.++-+-.
T Consensus 5 GnKL~~~a~~V~~g~L 20 (149)
T PF08595_consen 5 GNKLKQRAEFVHRGQL 20 (149)
T ss_pred chhcchhccceecccc
Confidence 4566666666665554
No 26
>COG0290 InfC Translation initiation factor 3 (IF-3) [Translation, ribosomal structure and biogenesis]
Probab=30.42 E-value=1e+02 Score=26.88 Aligned_cols=55 Identities=20% Similarity=0.246 Sum_probs=39.4
Q ss_pred ccCcceEEEEcCCCceeeeecHHHHHHHHHhCCeeEEEecCCeeeCCCcceecCeEEEEeccee
Q 028336 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQ 157 (210)
Q Consensus 94 ~~~~~rVLVLNasy~Pl~~vswqrAi~Ll~~gkAevle~~~~~IrS~sg~~~vPsVIrL~~yv~ 157 (210)
++..+.|.+++.+++-+++++.++|+.|-..---+.++. ||+.. |.|-++-.|-+
T Consensus 15 ~Ir~~evrlIg~~GeqlGiv~~~eAL~lA~e~~LDLV~I------spna~---PPVcKImDYGK 69 (176)
T COG0290 15 EIRAREVRLIGEDGEQLGIVSIEEALKLAEEAGLDLVEI------SPNAK---PPVCKIMDYGK 69 (176)
T ss_pred cccccEEEEECCCCcEEcceeHHHHHHHHHHcCCCEEEE------CCCCC---CCeeEeeeccc
Confidence 567788999999999999999999999955444455553 34444 55555555543
No 27
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=28.12 E-value=37 Score=26.65 Aligned_cols=19 Identities=16% Similarity=0.499 Sum_probs=15.4
Q ss_pred hHHHHHhHcCCcccccCCC
Q 028336 169 SRKNLMYRDNFTCQYCSSR 187 (210)
Q Consensus 169 tR~~Vl~RD~~~CqYCG~~ 187 (210)
.--+.-.|+.|.|..||+.
T Consensus 26 ~~ie~~~~~~~~Cp~C~~~ 44 (89)
T COG1997 26 KEIEAQQRAKHVCPFCGRT 44 (89)
T ss_pred HHHHHHHhcCCcCCCCCCc
Confidence 3345678999999999976
No 28
>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=26.55 E-value=44 Score=28.88 Aligned_cols=32 Identities=25% Similarity=0.523 Sum_probs=21.5
Q ss_pred HHHHHhHcCCcccccCCCcCCeeCeeecCcCCC
Q 028336 170 RKNLMYRDNFTCQYCSSRENLTIDHVVPASRGG 202 (210)
Q Consensus 170 R~~Vl~RD~~~CqYCG~~~~LtvDHIIPrSrGG 202 (210)
.+.+..=-.-.|..||++. -.++|+|..-+||
T Consensus 119 ~~yl~~v~~~~C~iCGk~~-~d~hH~iG~g~~~ 150 (200)
T PF06147_consen 119 EKYLYWVKSRPCVICGKPP-ADIHHIIGMGRGR 150 (200)
T ss_pred HHHHhhhccCccccCCCCc-cccceeeccccCc
Confidence 3444444456788899764 3899997766665
No 29
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=26.10 E-value=1.2e+02 Score=19.31 Aligned_cols=31 Identities=13% Similarity=0.017 Sum_probs=25.3
Q ss_pred ccccCcceEEEEcCCCceeeeecHHHHHHHH
Q 028336 92 FDELACFRGLVLDISYRPVNVVCWKRAICLE 122 (210)
Q Consensus 92 ~~~~~~~rVLVLNasy~Pl~~vswqrAi~Ll 122 (210)
+.......+.|+|.+++++++++.++-+..+
T Consensus 25 ~~~~~~~~~~V~d~~~~~~G~is~~dl~~~l 55 (57)
T PF00571_consen 25 MRKNGISRLPVVDEDGKLVGIISRSDLLKAL 55 (57)
T ss_dssp HHHHTSSEEEEESTTSBEEEEEEHHHHHHHH
T ss_pred HHHcCCcEEEEEecCCEEEEEEEHHHHHhhh
Confidence 3344577889999999999999999887765
No 30
>COG3183 Predicted restriction endonuclease [Defense mechanisms]
Probab=24.03 E-value=53 Score=30.39 Aligned_cols=34 Identities=18% Similarity=0.380 Sum_probs=28.3
Q ss_pred ChhhHHHHHhHcCCcccccCCC----------cCCeeCeeecCc
Q 028336 166 NNLSRKNLMYRDNFTCQYCSSR----------ENLTIDHVVPAS 199 (210)
Q Consensus 166 ~~~tR~~Vl~RD~~~CqYCG~~----------~~LtvDHIIPrS 199 (210)
.+..|+..+.=-+..|+-|+-. .-++++|++|.+
T Consensus 183 na~~ra~~Ia~~G~vC~vC~fdF~k~YGe~gKgyIeVHH~~pia 226 (272)
T COG3183 183 NATLRAAAIAIHGTVCDVCEFDFQKKYGEIGKGYIEVHHKIPIA 226 (272)
T ss_pred ChHHHHHHHHHhCceeeecCccHHHHhhhhccCeEEEeeccchh
Confidence 5677878888888999999964 348999999987
No 31
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=23.69 E-value=49 Score=25.89 Aligned_cols=20 Identities=10% Similarity=0.619 Sum_probs=16.4
Q ss_pred hhHHHHHhHcCCcccccCCC
Q 028336 168 LSRKNLMYRDNFTCQYCSSR 187 (210)
Q Consensus 168 ~tR~~Vl~RD~~~CqYCG~~ 187 (210)
...-++-.+..|.|.+||..
T Consensus 26 v~kie~~q~a~y~CpfCgk~ 45 (90)
T PTZ00255 26 IKKIEISQHAKYFCPFCGKH 45 (90)
T ss_pred HHHHHHHHhCCccCCCCCCC
Confidence 44557889999999999965
No 32
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=22.44 E-value=29 Score=18.41 Aligned_cols=9 Identities=33% Similarity=1.088 Sum_probs=5.7
Q ss_pred CcccccCCC
Q 028336 179 FTCQYCSSR 187 (210)
Q Consensus 179 ~~CqYCG~~ 187 (210)
|.|.+|+..
T Consensus 1 ~~C~~C~~~ 9 (24)
T PF13894_consen 1 FQCPICGKS 9 (24)
T ss_dssp EE-SSTS-E
T ss_pred CCCcCCCCc
Confidence 579999975
No 33
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=22.03 E-value=36 Score=23.89 Aligned_cols=15 Identities=33% Similarity=0.687 Sum_probs=11.4
Q ss_pred HHhHcCCcccccCCC
Q 028336 173 LMYRDNFTCQYCSSR 187 (210)
Q Consensus 173 Vl~RD~~~CqYCG~~ 187 (210)
+-.-+.-+|+|||..
T Consensus 19 ~~~~~~irCp~Cg~r 33 (49)
T COG1996 19 DQETRGIRCPYCGSR 33 (49)
T ss_pred hhccCceeCCCCCcE
Confidence 335567899999976
No 34
>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=21.74 E-value=18 Score=31.81 Aligned_cols=18 Identities=33% Similarity=0.381 Sum_probs=13.8
Q ss_pred cCCeeCeeecCcCCCCCC
Q 028336 188 ENLTIDHVVPASRGGEWK 205 (210)
Q Consensus 188 ~~LtvDHIIPrSrGG~dt 205 (210)
..++.+||+|.|.+|...
T Consensus 70 ~~~N~EHv~P~S~~~~~~ 87 (218)
T PF04231_consen 70 DRWNREHVVPQSWFGKQF 87 (218)
T ss_dssp TSEEEEESS-HHHHHTTS
T ss_pred CccccceeeCHHHCCCCC
Confidence 458899999999988653
Done!