Query 032576
Match_columns 137
No_of_seqs 177 out of 472
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 03:14:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032576.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032576hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00085 HNHc HNH nucleases; HN 98.7 8.2E-09 1.8E-13 63.4 3.0 32 105-136 12-49 (57)
2 PF01844 HNH: HNH endonuclease 98.6 4.9E-09 1.1E-13 64.2 0.1 30 107-136 1-37 (47)
3 smart00507 HNHc HNH nucleases. 98.5 3E-08 6.6E-13 59.8 0.5 33 105-137 11-48 (52)
4 PF13395 HNH_4: HNH endonuclea 98.3 2E-07 4.3E-12 60.5 1.5 30 107-136 1-41 (54)
5 TIGR01865 cas_Csn1 CRISPR-asso 98.2 7.8E-07 1.7E-11 83.7 3.4 33 105-137 582-626 (805)
6 COG1403 McrA Restriction endon 97.8 1E-05 2.3E-10 57.6 1.4 33 105-137 70-106 (146)
7 PRK11295 hypothetical protein; 97.6 1.4E-05 3.1E-10 60.1 0.3 34 103-136 23-65 (113)
8 TIGR02646 conserved hypothetic 97.4 0.00015 3.3E-09 54.9 3.1 33 105-137 25-65 (144)
9 TIGR03031 cas_csx12 CRISPR-ass 93.6 0.034 7.4E-07 52.6 1.6 29 99-127 755-788 (802)
10 PF13391 HNH_2: HNH endonuclea 90.8 0.086 1.9E-06 33.8 0.4 24 113-136 15-51 (66)
11 PF14279 HNH_5: HNH endonuclea 84.1 0.56 1.2E-05 32.4 1.2 25 107-131 1-31 (71)
12 COG3440 Predicted restriction 83.7 0.65 1.4E-05 40.4 1.7 33 105-137 193-235 (301)
13 COG3513 Predicted CRISPR-assoc 82.9 0.71 1.5E-05 45.4 1.8 31 105-135 572-614 (1088)
14 PHA02565 49 recombination endo 82.4 1.5 3.1E-05 35.1 3.1 18 105-122 21-46 (157)
15 PF06147 DUF968: Protein of un 51.4 8.9 0.00019 30.9 1.5 23 105-127 128-152 (200)
16 smart00782 PhnA_Zn_Ribbon PhnA 50.4 8.9 0.00019 24.7 1.1 32 102-136 5-39 (47)
17 PF07510 DUF1524: Protein of u 49.4 6.3 0.00014 28.0 0.3 13 115-127 54-66 (142)
18 PRK11788 tetratricopeptide rep 43.6 12 0.00026 30.5 1.1 28 85-113 350-377 (389)
19 PF05741 zf-nanos: Nanos RNA b 36.4 16 0.00036 24.3 0.7 21 93-113 20-42 (55)
20 PF12172 DUF35_N: Rubredoxin-l 35.0 17 0.00037 21.3 0.6 23 92-114 13-35 (37)
21 PF02945 Endonuclease_7: Recom 33.6 15 0.00034 25.9 0.2 8 105-112 23-30 (81)
22 PRK03824 hypA hydrogenase nick 29.3 78 0.0017 23.9 3.4 30 86-115 66-118 (135)
23 KOG3822 Succinyl-CoA:alpha-ket 28.3 39 0.00086 30.9 1.9 44 73-121 197-248 (516)
24 PF13154 DUF3991: Protein of u 28.3 61 0.0013 21.8 2.5 33 63-104 4-36 (77)
25 PF10005 DUF2248: Uncharacteri 27.2 61 0.0013 28.8 2.9 33 94-126 3-40 (343)
26 PF14206 Cys_rich_CPCC: Cystei 27.1 38 0.00082 24.0 1.3 26 104-130 20-48 (78)
27 PF14412 AHH: A nuclease famil 26.7 49 0.0011 23.2 1.9 16 107-122 9-25 (109)
28 PF14505 DUF4438: Domain of un 26.5 41 0.00088 28.9 1.6 30 91-120 2-39 (258)
29 PRK03681 hypA hydrogenase nick 26.1 51 0.0011 24.2 1.9 32 85-116 65-99 (114)
30 PRK11823 DNA repair protein Ra 25.8 37 0.00081 30.2 1.3 26 88-113 5-30 (446)
31 TIGR00100 hypA hydrogenase nic 25.3 56 0.0012 24.0 2.0 49 66-114 37-96 (115)
32 PF12639 Colicin-DNase: DNase/ 25.1 19 0.00042 26.5 -0.5 19 111-135 80-98 (110)
33 PF01927 Mut7-C: Mut7-C RNAse 24.8 25 0.00054 26.6 0.0 15 104-118 124-140 (147)
34 PF13248 zf-ribbon_3: zinc-rib 23.3 36 0.00078 18.8 0.5 17 96-112 8-24 (26)
35 COG1066 Sms Predicted ATP-depe 22.1 47 0.001 30.6 1.3 23 91-113 8-30 (456)
36 COG3183 Predicted restriction 21.6 26 0.00056 30.3 -0.5 35 103-137 194-245 (272)
37 PRK00564 hypA hydrogenase nick 20.9 56 0.0012 24.1 1.3 31 86-116 67-100 (117)
38 PRK12380 hydrogenase nickel in 20.7 80 0.0017 23.1 2.0 31 85-115 65-97 (113)
39 cd01121 Sms Sms (bacterial rad 20.6 45 0.00098 29.2 0.8 20 94-113 4-23 (372)
40 PF15446 zf-PHD-like: PHD/FYVE 20.1 57 0.0012 26.6 1.2 23 97-123 121-144 (175)
No 1
>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=98.73 E-value=8.2e-09 Score=63.37 Aligned_cols=32 Identities=41% Similarity=0.677 Sum_probs=29.5
Q ss_pred CCCCCCCC------CccceeeeccCCCCCchhhhhhhc
Q 032576 105 VGCPGCLC------HDYDHILPYSKGGKSTLENCQVLQ 136 (137)
Q Consensus 105 ~~C~~Cg~------~EiDHIiP~SkGG~t~~eNlqlLc 136 (137)
+.|.+|+. +++|||+|++.||.++.+||++||
T Consensus 12 ~~C~~c~~~~~~~~~~v~Hi~p~~~~~~~~~~Nl~~~c 49 (57)
T cd00085 12 GLCPYCGKPGGTEGLEVDHIIPLSDGGNNDLDNLVLLC 49 (57)
T ss_pred CcCccCCCcCCCCCceEEeecchhhCCCCchHHhHHHH
Confidence 47999985 599999999999999999999998
No 2
>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=98.65 E-value=4.9e-09 Score=64.20 Aligned_cols=30 Identities=47% Similarity=0.690 Sum_probs=21.3
Q ss_pred CCCCCC-------CccceeeeccCCCCCchhhhhhhc
Q 032576 107 CPGCLC-------HDYDHILPYSKGGKSTLENCQVLQ 136 (137)
Q Consensus 107 C~~Cg~-------~EiDHIiP~SkGG~t~~eNlqlLc 136 (137)
|++|+. +++|||+|++.||.++++||++||
T Consensus 1 C~~C~~~~~~~~~~~v~Hi~~~~~gg~~~~~Nl~~lC 37 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVHHIIPRSKGGKNDLENLILLC 37 (47)
T ss_dssp -TTT--B--GG-GEEEEESS-TTTT---STTTEEEEE
T ss_pred CCCCCCcCccCcceEeECcCchhcCCCCCHHHHHHHh
Confidence 677765 499999999999999999999998
No 3
>smart00507 HNHc HNH nucleases.
Probab=98.49 E-value=3e-08 Score=59.78 Aligned_cols=33 Identities=36% Similarity=0.572 Sum_probs=30.1
Q ss_pred CCCCCCCC-----CccceeeeccCCCCCchhhhhhhcC
Q 032576 105 VGCPGCLC-----HDYDHILPYSKGGKSTLENCQVLQV 137 (137)
Q Consensus 105 ~~C~~Cg~-----~EiDHIiP~SkGG~t~~eNlqlLc~ 137 (137)
+.|..|+. +++|||+|++.||.++.+||++||.
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p~~~~~~~~~~Nl~~~c~ 48 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIPLSDGGNDDLDNLVLLCP 48 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCChhcCCCCChHhCeecCh
Confidence 68999975 5999999999999999999999984
No 4
>PF13395 HNH_4: HNH endonuclease
Probab=98.33 E-value=2e-07 Score=60.50 Aligned_cols=30 Identities=37% Similarity=0.661 Sum_probs=26.6
Q ss_pred CCCCCC-----------CccceeeeccCCCCCchhhhhhhc
Q 032576 107 CPGCLC-----------HDYDHILPYSKGGKSTLENCQVLQ 136 (137)
Q Consensus 107 C~~Cg~-----------~EiDHIiP~SkGG~t~~eNlqlLc 136 (137)
|.+||. +++|||+|+|.||.+.+.|+.+.|
T Consensus 1 C~Y~g~~i~~~~l~~~~~~iDHiiP~s~~~~~s~~Nlvl~~ 41 (54)
T PF13395_consen 1 CPYCGKPISIENLFKNKYEIDHIIPRSRGGDDSFWNLVLCC 41 (54)
T ss_pred CCCCCCCCChhhcccCCceeEEEecccccCCCCcchhheEC
Confidence 677766 389999999999999999999876
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=98.22 E-value=7.8e-07 Score=83.67 Aligned_cols=33 Identities=24% Similarity=0.276 Sum_probs=30.2
Q ss_pred CCCCCCCCC------------ccceeeeccCCCCCchhhhhhhcC
Q 032576 105 VGCPGCLCH------------DYDHILPYSKGGKSTLENCQVLQV 137 (137)
Q Consensus 105 ~~C~~Cg~~------------EiDHIiP~SkGG~t~~eNlqlLc~ 137 (137)
+.|++||.. ++|||+|+|+||.++++|+.+.|.
T Consensus 582 ~~C~Y~g~~i~~~~l~~~~~~~iDHIiP~s~~~dds~~N~vl~~~ 626 (805)
T TIGR01865 582 GKCMYTGKEIDIDDLFDLSYYEIDHILPQSRSFDDSISNKVLVLA 626 (805)
T ss_pred CcCCCCCCcCccccccCCCCCceeeecccccCCCCcHHHHHHHhH
Confidence 889999872 799999999999999999999884
No 6
>COG1403 McrA Restriction endonuclease [Defense mechanisms]
Probab=97.77 E-value=1e-05 Score=57.56 Aligned_cols=33 Identities=39% Similarity=0.583 Sum_probs=29.0
Q ss_pred CCCCCCCC----CccceeeeccCCCCCchhhhhhhcC
Q 032576 105 VGCPGCLC----HDYDHILPYSKGGKSTLENCQVLQV 137 (137)
Q Consensus 105 ~~C~~Cg~----~EiDHIiP~SkGG~t~~eNlqlLc~ 137 (137)
+.|.+|+. .++|||+|.+.||.+..+|+++||.
T Consensus 70 ~~c~~c~~~~~~~~~dHiip~~~g~~~~~~Nl~~lc~ 106 (146)
T COG1403 70 GLCQYCGSVGTDLEVDHIVPLSRGGASAWENLETLCE 106 (146)
T ss_pred ccccccCCcCCCCceeeEeecccCCcchHHHHHHHHH
Confidence 57887765 4999999999999999999999983
No 7
>PRK11295 hypothetical protein; Provisional
Probab=97.62 E-value=1.4e-05 Score=60.13 Aligned_cols=34 Identities=18% Similarity=0.120 Sum_probs=30.0
Q ss_pred cCCCCCCCCCC---------ccceeeeccCCCCCchhhhhhhc
Q 032576 103 KLVGCPGCLCH---------DYDHILPYSKGGKSTLENCQVLQ 136 (137)
Q Consensus 103 ~~~~C~~Cg~~---------EiDHIiP~SkGG~t~~eNlqlLc 136 (137)
+.+.|..|+.. .+|||+|...|+.++.+|||.||
T Consensus 23 ~p~lC~~Cgr~~~~a~~~a~vVDHIip~~~gd~~D~sNLQ~LC 65 (113)
T PRK11295 23 YPWVCGRCSREFVYSNLRELTVHHIDHDHDNNPEDGSNWELLC 65 (113)
T ss_pred CcchhhhhcChhccCCCCCceeeccCCCCCCCCCchhHHHHHh
Confidence 33579999873 99999999999999999999999
No 8
>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=97.37 E-value=0.00015 Score=54.87 Aligned_cols=33 Identities=21% Similarity=0.077 Sum_probs=29.3
Q ss_pred CCCCCCCC------CccceeeeccCCCCCch--hhhhhhcC
Q 032576 105 VGCPGCLC------HDYDHILPYSKGGKSTL--ENCQVLQV 137 (137)
Q Consensus 105 ~~C~~Cg~------~EiDHIiP~SkGG~t~~--eNlqlLc~ 137 (137)
+.|.+|+. +++|||+|.+..+...+ +||.+.|.
T Consensus 25 ~~C~YC~~~~~~~~~~ieH~~Pk~~~~~~~~~~~NL~~sC~ 65 (144)
T TIGR02646 25 GLCAYCEREIELLGSHIEHFRPKGAYPPLTLDWSNLFGSCH 65 (144)
T ss_pred CCcCccCCCcCCCCcceeeecccCCChhhhcChhhchhhcc
Confidence 78999988 59999999999998877 79999884
No 9
>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=93.62 E-value=0.034 Score=52.64 Aligned_cols=29 Identities=28% Similarity=0.300 Sum_probs=23.4
Q ss_pred eeeecCCCCCCCCCC-----ccceeeeccCCCCC
Q 032576 99 VVFRKLVGCPGCLCH-----DYDHILPYSKGGKS 127 (137)
Q Consensus 99 vv~r~~~~C~~Cg~~-----EiDHIiP~SkGG~t 127 (137)
+.....|.||+||.. |+|||+|.|+-|++
T Consensus 755 Ik~fs~gIcpY~Ga~iG~~gEiDHI~PRSht~k~ 788 (802)
T TIGR03031 755 IKNFSMGICPYKGASIGGQGEIDHIYPRSHSKKH 788 (802)
T ss_pred HHHHhccCCCCCCCCCCCcccccccccccccccc
Confidence 344466899999985 99999999987764
No 10
>PF13391 HNH_2: HNH endonuclease
Probab=90.83 E-value=0.086 Score=33.75 Aligned_cols=24 Identities=29% Similarity=0.444 Sum_probs=18.5
Q ss_pred CccceeeeccCC--CCC-----------chhhhhhhc
Q 032576 113 HDYDHILPYSKG--GKS-----------TLENCQVLQ 136 (137)
Q Consensus 113 ~EiDHIiP~SkG--G~t-----------~~eNlqlLc 136 (137)
.|+-||+|++.+ +.. +.+|.-+|+
T Consensus 15 ~eaaHI~P~s~~~~~~~~~~~~~~~~~~~~~Ngl~L~ 51 (66)
T PF13391_consen 15 LEAAHIVPFSLGSWWMNNWFGEYANDWISPSNGLLLR 51 (66)
T ss_pred EEEEEcccCccCCCchhhhhhhhhccCCCccEEEEcC
Confidence 389999999987 555 566777775
No 11
>PF14279 HNH_5: HNH endonuclease
Probab=84.09 E-value=0.56 Score=32.36 Aligned_cols=25 Identities=40% Similarity=0.683 Sum_probs=20.2
Q ss_pred CCCCCCC------ccceeeeccCCCCCchhh
Q 032576 107 CPGCLCH------DYDHILPYSKGGKSTLEN 131 (137)
Q Consensus 107 C~~Cg~~------EiDHIiP~SkGG~t~~eN 131 (137)
|.+|..- ...||+|-|-||.....|
T Consensus 1 Ci~C~~~~~~~~~s~EHIIP~sLGG~~~~~~ 31 (71)
T PF14279_consen 1 CIYCNKEKSESNFSEEHIIPESLGGKLKINN 31 (71)
T ss_pred CccCCCCCCccCCCccccCchhcCCcccccc
Confidence 7788762 478999999999877765
No 12
>COG3440 Predicted restriction endonuclease [Defense mechanisms]
Probab=83.68 E-value=0.65 Score=40.39 Aligned_cols=33 Identities=21% Similarity=0.202 Sum_probs=29.7
Q ss_pred CCCCCCCC----------CccceeeeccCCCCCchhhhhhhcC
Q 032576 105 VGCPGCLC----------HDYDHILPYSKGGKSTLENCQVLQV 137 (137)
Q Consensus 105 ~~C~~Cg~----------~EiDHIiP~SkGG~t~~eNlqlLc~ 137 (137)
++|..||. -+.-||.|.+++|.+.+.|.-.||.
T Consensus 193 ~RCalCG~e~~~~~~q~ii~~ahikp~~q~y~~~i~N~LaLC~ 235 (301)
T COG3440 193 YRCALCGLEVLDFLEQNIIKAAHIKPFQQFYPDRIINGLALCK 235 (301)
T ss_pred chhhhhcchhhhhhHHHHhhhhhcCcccccCcccccccchhch
Confidence 78999994 1888999999999999999999984
No 13
>COG3513 Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]
Probab=82.89 E-value=0.71 Score=45.39 Aligned_cols=31 Identities=23% Similarity=0.293 Sum_probs=26.4
Q ss_pred CCCCCCCC------------CccceeeeccCCCCCchhhhhhh
Q 032576 105 VGCPGCLC------------HDYDHILPYSKGGKSTLENCQVL 135 (137)
Q Consensus 105 ~~C~~Cg~------------~EiDHIiP~SkGG~t~~eNlqlL 135 (137)
+.|-+-|. .|+|||+|.|.==.++.+|..+.
T Consensus 572 gkcmYsgqei~I~rL~dk~~~eIDHi~P~Sr~~DDS~~NkVLv 614 (1088)
T COG3513 572 GKCMYSGQEIDIHRLSDKGYYEIDHIVPQSRTWDDSIDNKVLV 614 (1088)
T ss_pred CcccccCcccchhhcccccceeeceeccccccccccccceeEE
Confidence 78888877 39999999999988999998764
No 14
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=82.38 E-value=1.5 Score=35.06 Aligned_cols=18 Identities=28% Similarity=0.392 Sum_probs=15.2
Q ss_pred CCCCCCCC--------Cccceeeecc
Q 032576 105 VGCPGCLC--------HDYDHILPYS 122 (137)
Q Consensus 105 ~~C~~Cg~--------~EiDHIiP~S 122 (137)
+.|+.|+. +++||..+.+
T Consensus 21 G~CaiC~~~l~~~~~~~~vDHDH~l~ 46 (157)
T PHA02565 21 GICPLCKRELDGDVSKNHLDHDHELN 46 (157)
T ss_pred CcCCCCCCccCCCccccccCCCCCCC
Confidence 78999986 3899998877
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=51.41 E-value=8.9 Score=30.90 Aligned_cols=23 Identities=26% Similarity=0.405 Sum_probs=17.4
Q ss_pred CCCCCCCCC--ccceeeeccCCCCC
Q 032576 105 VGCPGCLCH--DYDHILPYSKGGKS 127 (137)
Q Consensus 105 ~~C~~Cg~~--EiDHIiP~SkGG~t 127 (137)
..|..||.. ++|||+..-.||..
T Consensus 128 ~~C~iCGk~~~d~hH~iG~g~~~~~ 152 (200)
T PF06147_consen 128 RPCVICGKPPADIHHIIGMGRGRMG 152 (200)
T ss_pred CccccCCCCccccceeeccccCccc
Confidence 469999974 99999776655544
No 16
>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=50.44 E-value=8.9 Score=24.70 Aligned_cols=32 Identities=25% Similarity=0.237 Sum_probs=18.6
Q ss_pred ecCCCCCCCCCC---ccceeeeccCCCCCchhhhhhhc
Q 032576 102 RKLVGCPGCLCH---DYDHILPYSKGGKSTLENCQVLQ 136 (137)
Q Consensus 102 r~~~~C~~Cg~~---EiDHIiP~SkGG~t~~eNlqlLc 136 (137)
|..+.|..|+.- .+.++ |-+. ....+|..++|
T Consensus 5 Rs~~kCELC~a~~~L~vy~V-pp~~--~~~~d~~iliC 39 (47)
T smart00782 5 RCESKCELCGSDSPLVVYAV-PPSS--DVTADNSVMLC 39 (47)
T ss_pred HcCCcccCcCCCCCceEEec-CCCC--CCCccceeeec
Confidence 344789999984 33343 3333 34556666766
No 17
>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=49.42 E-value=6.3 Score=27.95 Aligned_cols=13 Identities=31% Similarity=0.549 Sum_probs=10.6
Q ss_pred cceeeeccCCCCC
Q 032576 115 YDHILPYSKGGKS 127 (137)
Q Consensus 115 iDHIiP~SkGG~t 127 (137)
+|||+|.+.....
T Consensus 54 iEHI~Pq~~~~~~ 66 (142)
T PF07510_consen 54 IEHIFPQNPKKES 66 (142)
T ss_pred eEeeccCCCCccc
Confidence 9999999976643
No 18
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=43.55 E-value=12 Score=30.46 Aligned_cols=28 Identities=25% Similarity=0.453 Sum_probs=23.2
Q ss_pred CCCCcchhccccCCeeeecCCCCCCCCCC
Q 032576 85 GRDPDRWRKDALGNVVFRKLVGCPGCLCH 113 (137)
Q Consensus 85 G~dp~r~R~Da~Gnvv~r~~~~C~~Cg~~ 113 (137)
..+|+ |+-+.||.+...-...||.|+.|
T Consensus 350 ~~~p~-~~c~~cg~~~~~~~~~c~~c~~~ 377 (389)
T PRK11788 350 KRKPR-YRCRNCGFTARTLYWHCPSCKAW 377 (389)
T ss_pred hCCCC-EECCCCCCCCccceeECcCCCCc
Confidence 44565 88888999988888899999988
No 19
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=36.38 E-value=16 Score=24.34 Aligned_cols=21 Identities=33% Similarity=0.491 Sum_probs=9.0
Q ss_pred ccccCCeeee--cCCCCCCCCCC
Q 032576 93 KDALGNVVFR--KLVGCPGCLCH 113 (137)
Q Consensus 93 ~Da~Gnvv~r--~~~~C~~Cg~~ 113 (137)
+|+.|.|++- ..+.|+.||..
T Consensus 20 k~~~G~v~CPvLr~y~Cp~CgAt 42 (55)
T PF05741_consen 20 KDPDGRVTCPVLRKYVCPICGAT 42 (55)
T ss_dssp B-TTS-B--TTGGG---TTT---
T ss_pred ECCCCCEeCHHHhcCcCCCCcCc
Confidence 6889998886 46789999985
No 20
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=35.00 E-value=17 Score=21.32 Aligned_cols=23 Identities=30% Similarity=0.505 Sum_probs=11.8
Q ss_pred hccccCCeeeecCCCCCCCCCCc
Q 032576 92 RKDALGNVVFRKLVGCPGCLCHD 114 (137)
Q Consensus 92 R~Da~Gnvv~r~~~~C~~Cg~~E 114 (137)
|=..+|.+++-....|+.|+..+
T Consensus 13 rC~~Cg~~~~pPr~~Cp~C~s~~ 35 (37)
T PF12172_consen 13 RCRDCGRVQFPPRPVCPHCGSDE 35 (37)
T ss_dssp E-TTT--EEES--SEETTTT---
T ss_pred EcCCCCCEecCCCcCCCCcCccc
Confidence 34668888888878888887644
No 21
>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=33.56 E-value=15 Score=25.86 Aligned_cols=8 Identities=25% Similarity=0.306 Sum_probs=5.4
Q ss_pred CCCCCCCC
Q 032576 105 VGCPGCLC 112 (137)
Q Consensus 105 ~~C~~Cg~ 112 (137)
+.|+.|+.
T Consensus 23 ~~C~iC~~ 30 (81)
T PF02945_consen 23 GRCAICGK 30 (81)
T ss_dssp TE-TTT-S
T ss_pred CcCcCCCC
Confidence 78999997
No 22
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.27 E-value=78 Score=23.91 Aligned_cols=30 Identities=23% Similarity=0.443 Sum_probs=22.6
Q ss_pred CCCcchhccccCCeeeec-----------------------CCCCCCCCCCcc
Q 032576 86 RDPDRWRKDALGNVVFRK-----------------------LVGCPGCLCHDY 115 (137)
Q Consensus 86 ~dp~r~R~Da~Gnvv~r~-----------------------~~~C~~Cg~~Ei 115 (137)
.-|.+|+=-.||...-.. ...||.||.+.+
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~ 118 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDF 118 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCc
Confidence 788899988899777553 356999987643
No 23
>KOG3822 consensus Succinyl-CoA:alpha-ketoacid-CoA transferase [Energy production and conversion]
Probab=28.30 E-value=39 Score=30.92 Aligned_cols=44 Identities=30% Similarity=0.563 Sum_probs=29.9
Q ss_pred HHHHHHhhhhccCCCCcchhccccCCeeeec---CCCCCCCCCC-----ccceeeec
Q 032576 73 KQQCWEKAEKVRGRDPDRWRKDALGNVVFRK---LVGCPGCLCH-----DYDHILPY 121 (137)
Q Consensus 73 k~~~w~k~~~v~G~dp~r~R~Da~Gnvv~r~---~~~C~~Cg~~-----EiDHIiP~ 121 (137)
-+++|..-..|.+ |+.|..||+++++ +.+-+.|..- |+.-|++.
T Consensus 197 EeaI~~DFAlvKa-----wkAD~~GNvvFr~sArNFN~PMCkAak~TvvEVEEIV~i 248 (516)
T KOG3822|consen 197 EEAIRADFALVKA-----WKADRAGNVVFRKSARNFNVPMCKAAKVTVVEVEEIVEI 248 (516)
T ss_pred hhhhhhhhhhhhh-----hhcCcccceeeehhhccCCcccchhccceEEEEeeeecc
Confidence 3556655555543 8999999999995 4456777662 66666653
No 24
>PF13154 DUF3991: Protein of unknown function (DUF3991)
Probab=28.26 E-value=61 Score=21.82 Aligned_cols=33 Identities=21% Similarity=0.274 Sum_probs=25.5
Q ss_pred CCCCCCCHHHHHHHHHhhhhccCCCCcchhccccCCeeeecC
Q 032576 63 ANPRSFPYSVKQQCWEKAEKVRGRDPDRWRKDALGNVVFRKL 104 (137)
Q Consensus 63 ~~~R~F~~~~k~~~w~k~~~v~G~dp~r~R~Da~Gnvv~r~~ 104 (137)
.+.|.+++++.+.+.++. .++.|.++|+++-..
T Consensus 4 ~~~RgI~~~~v~~~~~~g---------~i~~d~~~N~vF~~~ 36 (77)
T PF13154_consen 4 TEERGIDPEIVDAFINQG---------LIYQDKYGNVVFVGY 36 (77)
T ss_pred hhhcCcCHHHHHHHHHCC---------CEEEcCCccEEEEEE
Confidence 346899999999888866 355688999988754
No 25
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=27.22 E-value=61 Score=28.84 Aligned_cols=33 Identities=21% Similarity=0.383 Sum_probs=25.3
Q ss_pred cccCCeeeecCCCCCCCCCC-----ccceeeeccCCCC
Q 032576 94 DALGNVVFRKLVGCPGCLCH-----DYDHILPYSKGGK 126 (137)
Q Consensus 94 Da~Gnvv~r~~~~C~~Cg~~-----EiDHIiP~SkGG~ 126 (137)
+.|||.|+..+..|..|+.. +.-.+++....|.
T Consensus 3 ~~Cg~~v~FeNt~C~~Cg~~LGf~p~~~~~~al~~~~~ 40 (343)
T PF10005_consen 3 PNCGQPVFFENTRCLSCGSALGFDPDRREMVALEPDGD 40 (343)
T ss_pred CCCCCcceeCCCccccCCccccCCCCCCcEEeeccCCC
Confidence 46999999999999999872 6666666665433
No 26
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=27.10 E-value=38 Score=23.98 Aligned_cols=26 Identities=27% Similarity=0.521 Sum_probs=19.0
Q ss_pred CCCCCCCCCCcccee---eeccCCCCCchh
Q 032576 104 LVGCPGCLCHDYDHI---LPYSKGGKSTLE 130 (137)
Q Consensus 104 ~~~C~~Cg~~EiDHI---iP~SkGG~t~~e 130 (137)
...|+.|+ ||-|-+ -|-..||.+.++
T Consensus 20 ydIC~VC~-WEdD~~q~~~pd~~~G~N~~S 48 (78)
T PF14206_consen 20 YDICPVCF-WEDDGVQLRDPDYYGGANHMS 48 (78)
T ss_pred ceECCCCC-cccCCccccCCcccCCCCHHH
Confidence 35799996 888776 566678887554
No 27
>PF14412 AHH: A nuclease family of the HNH/ENDO VII superfamily with conserved AHH
Probab=26.68 E-value=49 Score=23.20 Aligned_cols=16 Identities=19% Similarity=0.133 Sum_probs=12.5
Q ss_pred CCCC-CCCccceeeecc
Q 032576 107 CPGC-LCHDYDHILPYS 122 (137)
Q Consensus 107 C~~C-g~~EiDHIiP~S 122 (137)
+... ..+++|||||..
T Consensus 9 ~~~p~~~~qaHHII~~~ 25 (109)
T PF14412_consen 9 GGKPSKGFQAHHIIPKN 25 (109)
T ss_pred CCCCCCCCccceecCcc
Confidence 4444 668999999987
No 28
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=26.51 E-value=41 Score=28.92 Aligned_cols=30 Identities=20% Similarity=0.142 Sum_probs=16.5
Q ss_pred hhccccCCeeeecC--------CCCCCCCCCccceeee
Q 032576 91 WRKDALGNVVFRKL--------VGCPGCLCHDYDHILP 120 (137)
Q Consensus 91 ~R~Da~Gnvv~r~~--------~~C~~Cg~~EiDHIiP 120 (137)
||+|..|+...... ..-.+|+.|..|||-|
T Consensus 2 yrv~~dG~p~ilP~~GGItyNv~vGD~a~g~agDHvEP 39 (258)
T PF14505_consen 2 YRVDHDGTPFILPGTGGITYNVRVGDSAFGWAGDHVEP 39 (258)
T ss_dssp EEE-TTSBEEE---EESEESS--TTSBSSS-BSSS---
T ss_pred ceeCCCCCEEeccccCcEEEeeeeCCccccccccccCC
Confidence 78888887776632 1125899999999988
No 29
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=26.06 E-value=51 Score=24.20 Aligned_cols=32 Identities=13% Similarity=0.144 Sum_probs=22.5
Q ss_pred CCCCcchhccccCCeeeec---CCCCCCCCCCccc
Q 032576 85 GRDPDRWRKDALGNVVFRK---LVGCPGCLCHDYD 116 (137)
Q Consensus 85 G~dp~r~R~Da~Gnvv~r~---~~~C~~Cg~~EiD 116 (137)
..-|.++|=-.||+.+... ...||.||...++
T Consensus 65 ~~~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~ 99 (114)
T PRK03681 65 EEQEAECWCETCQQYVTLLTQRVRRCPQCHGDMLR 99 (114)
T ss_pred EeeCcEEEcccCCCeeecCCccCCcCcCcCCCCcE
Confidence 3457777877899887664 2559999976443
No 30
>PRK11823 DNA repair protein RadA; Provisional
Probab=25.80 E-value=37 Score=30.20 Aligned_cols=26 Identities=19% Similarity=0.272 Sum_probs=22.2
Q ss_pred CcchhccccCCeeeecCCCCCCCCCC
Q 032576 88 PDRWRKDALGNVVFRKLVGCPGCLCH 113 (137)
Q Consensus 88 p~r~R~Da~Gnvv~r~~~~C~~Cg~~ 113 (137)
...|+=..||..-.+-.|+|+.|+.|
T Consensus 5 ~~~y~C~~Cg~~~~~~~g~Cp~C~~w 30 (446)
T PRK11823 5 KTAYVCQECGAESPKWLGRCPECGAW 30 (446)
T ss_pred CCeEECCcCCCCCcccCeeCcCCCCc
Confidence 34677788998888888999999999
No 31
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=25.32 E-value=56 Score=23.98 Aligned_cols=49 Identities=18% Similarity=0.165 Sum_probs=30.7
Q ss_pred CCCCHHHHHHHHHhhh---hc------cCCCCcchhccccCCeeeec--CCCCCCCCCCc
Q 032576 66 RSFPYSVKQQCWEKAE---KV------RGRDPDRWRKDALGNVVFRK--LVGCPGCLCHD 114 (137)
Q Consensus 66 R~F~~~~k~~~w~k~~---~v------~G~dp~r~R~Da~Gnvv~r~--~~~C~~Cg~~E 114 (137)
....++.-+-+|+-.. .+ ...-|.++|=..||+.+... ...||.||.+.
T Consensus 37 s~V~p~~L~faf~~~~~~t~~ega~L~I~~~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 37 SCVNPSQLQFAFEVVREGTVAEGAKLNIEDEPVECECEDCSEEVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred cccCHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcccCCCEEecCCcCccCcCCcCCC
Confidence 3445555556665432 22 23457778878888887763 45699998864
No 32
>PF12639 Colicin-DNase: DNase/tRNase domain of colicin-like bacteriocin; InterPro: IPR024622 This entry represents a C-terminal domain with endonuclease activity found in some colicin/pyocin bacteriocins, including colicin E2, E7, E9 and pyocin S1 and S2. The structure of this domain in colicin E7 has been described as a novel alpha/beta fold containing a Zn2+ ion [].; GO: 0004519 endonuclease activity; PDB: 3U43_B 2VLN_B 1V14_A 1V13_A 2GYK_B 1V15_C 2GZJ_F 2VLP_B 1FSJ_C 2GZG_B ....
Probab=25.07 E-value=19 Score=26.55 Aligned_cols=19 Identities=32% Similarity=0.471 Sum_probs=15.3
Q ss_pred CCCccceeeeccCCCCCchhhhhhh
Q 032576 111 LCHDYDHILPYSKGGKSTLENCQVL 135 (137)
Q Consensus 111 g~~EiDHIiP~SkGG~t~~eNlqlL 135 (137)
..++.||..+.+.| |||++
T Consensus 80 ~~~~~HH~~~i~~G------nl~lv 98 (110)
T PF12639_consen 80 KGYEWHHHQPISPG------NLQLV 98 (110)
T ss_dssp -B-EEEESSSGGGT------CEEEE
T ss_pred CcceEeccCcCCCC------eEEEc
Confidence 66899999999999 88875
No 33
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=24.80 E-value=25 Score=26.56 Aligned_cols=15 Identities=33% Similarity=0.689 Sum_probs=12.4
Q ss_pred CCCCCCCCC--Ccccee
Q 032576 104 LVGCPGCLC--HDYDHI 118 (137)
Q Consensus 104 ~~~C~~Cg~--~EiDHI 118 (137)
++.|+.|+. |+..|+
T Consensus 124 f~~C~~C~kiyW~GsH~ 140 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGSHW 140 (147)
T ss_pred EEECCCCCCEecccccH
Confidence 578999999 787775
No 34
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=23.29 E-value=36 Score=18.80 Aligned_cols=17 Identities=24% Similarity=0.395 Sum_probs=9.3
Q ss_pred cCCeeeecCCCCCCCCC
Q 032576 96 LGNVVFRKLVGCPGCLC 112 (137)
Q Consensus 96 ~Gnvv~r~~~~C~~Cg~ 112 (137)
+|+.+-.+..-|+.||.
T Consensus 8 Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 8 CGAEIDPDAKFCPNCGA 24 (26)
T ss_pred cCCcCCcccccChhhCC
Confidence 44544445555777763
No 35
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=22.10 E-value=47 Score=30.63 Aligned_cols=23 Identities=26% Similarity=0.396 Sum_probs=19.5
Q ss_pred hhccccCCeeeecCCCCCCCCCC
Q 032576 91 WRKDALGNVVFRKLVGCPGCLCH 113 (137)
Q Consensus 91 ~R~Da~Gnvv~r~~~~C~~Cg~~ 113 (137)
|--..||++--+=.++|+.|+.|
T Consensus 8 f~C~~CG~~s~KW~GkCp~Cg~W 30 (456)
T COG1066 8 FVCQECGYVSPKWLGKCPACGAW 30 (456)
T ss_pred EEcccCCCCCccccccCCCCCCc
Confidence 44567899888888999999999
No 36
>COG3183 Predicted restriction endonuclease [Defense mechanisms]
Probab=21.62 E-value=26 Score=30.32 Aligned_cols=35 Identities=17% Similarity=0.189 Sum_probs=22.4
Q ss_pred cCCCCCCCCC-------------CccceeeeccCCC----CCchhhhhhhcC
Q 032576 103 KLVGCPGCLC-------------HDYDHILPYSKGG----KSTLENCQVLQV 137 (137)
Q Consensus 103 ~~~~C~~Cg~-------------~EiDHIiP~SkGG----~t~~eNlqlLc~ 137 (137)
....|..|+. -|+||++|.+.=+ -+.+.-|..||+
T Consensus 194 ~G~vC~vC~fdF~k~YGe~gKgyIeVHH~~piae~e~~~~vnp~tDL~plCp 245 (272)
T COG3183 194 HGTVCDVCEFDFQKKYGEIGKGYIEVHHKIPIAEFEGEYHVNPLTDLAPLCP 245 (272)
T ss_pred hCceeeecCccHHHHhhhhccCeEEEeeccchhhhcCccccCchhhhhhcCc
Confidence 3456899965 2999999998433 223335666663
No 37
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.92 E-value=56 Score=24.07 Aligned_cols=31 Identities=10% Similarity=0.083 Sum_probs=21.7
Q ss_pred CCCcchhccccCCeeeec---CCCCCCCCCCccc
Q 032576 86 RDPDRWRKDALGNVVFRK---LVGCPGCLCHDYD 116 (137)
Q Consensus 86 ~dp~r~R~Da~Gnvv~r~---~~~C~~Cg~~EiD 116 (137)
.-|.++|=..||+.+-.. ...||.||.+.++
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~ 100 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNALDYGVCEKCHSKNVI 100 (117)
T ss_pred ecCCEEEhhhCCCccccCCccCCcCcCCCCCceE
Confidence 457778888899877663 2249999986443
No 38
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=20.67 E-value=80 Score=23.14 Aligned_cols=31 Identities=19% Similarity=0.130 Sum_probs=22.0
Q ss_pred CCCCcchhccccCCeeeec--CCCCCCCCCCcc
Q 032576 85 GRDPDRWRKDALGNVVFRK--LVGCPGCLCHDY 115 (137)
Q Consensus 85 G~dp~r~R~Da~Gnvv~r~--~~~C~~Cg~~Ei 115 (137)
..=|.++|=..||..+... ...||.||...+
T Consensus 65 ~~vp~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~ 97 (113)
T PRK12380 65 VYKPAQAWCWDCSQVVEIHQHDAQCPHCHGERL 97 (113)
T ss_pred EeeCcEEEcccCCCEEecCCcCccCcCCCCCCc
Confidence 3457788888888777663 345999987643
No 39
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=20.58 E-value=45 Score=29.15 Aligned_cols=20 Identities=30% Similarity=0.388 Sum_probs=16.3
Q ss_pred cccCCeeeecCCCCCCCCCC
Q 032576 94 DALGNVVFRKLVGCPGCLCH 113 (137)
Q Consensus 94 Da~Gnvv~r~~~~C~~Cg~~ 113 (137)
..||..-.+-.|+|+.|+.|
T Consensus 4 ~~cg~~~~~~~g~cp~c~~w 23 (372)
T cd01121 4 SECGYVSPKWLGKCPECGEW 23 (372)
T ss_pred CCCCCCCCCccEECcCCCCc
Confidence 45777777777899999999
No 40
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=20.07 E-value=57 Score=26.58 Aligned_cols=23 Identities=35% Similarity=0.782 Sum_probs=17.1
Q ss_pred CCeeeecCCCCCCCCC-CccceeeeccC
Q 032576 97 GNVVFRKLVGCPGCLC-HDYDHILPYSK 123 (137)
Q Consensus 97 Gnvv~r~~~~C~~Cg~-~EiDHIiP~Sk 123 (137)
-|||+ +|..|.. |+++|.-|++.
T Consensus 121 ~nVLF----RC~~C~RawH~~HLP~~~~ 144 (175)
T PF15446_consen 121 DNVLF----RCTSCHRAWHFEHLPPPSG 144 (175)
T ss_pred hheEE----ecCCccceeehhhCCCCcC
Confidence 36654 5888966 99999987653
Done!