Query 045896
Match_columns 520
No_of_seqs 133 out of 246
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 06:36:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045896.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045896hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5180 PBP1 Protein interacti 100.0 1E-36 2.3E-41 317.9 5.9 188 75-296 34-234 (654)
2 KOG2375 Protein interacting wi 100.0 5.7E-29 1.2E-33 273.4 18.9 316 3-336 7-339 (756)
3 PF06741 LsmAD: LsmAD domain; 99.9 3E-28 6.6E-33 201.0 6.0 71 223-294 1-72 (72)
4 PF14438 SM-ATX: Ataxin 2 SM d 99.8 2.5E-20 5.5E-25 153.7 5.6 76 64-143 1-77 (77)
5 KOG2375 Protein interacting wi 98.4 5.4E-08 1.2E-12 109.1 -1.0 208 62-298 223-443 (756)
6 cd01733 LSm10 The eukaryotic S 97.5 0.00075 1.6E-08 56.9 9.1 68 66-146 10-77 (78)
7 cd01724 Sm_D1 The eukaryotic S 97.5 0.00059 1.3E-08 59.0 8.5 72 65-149 1-72 (90)
8 cd01725 LSm2 The eukaryotic Sm 97.3 0.0019 4.1E-08 54.7 9.4 72 67-149 3-74 (81)
9 cd01726 LSm6 The eukaryotic Sm 97.3 0.0012 2.5E-08 53.7 7.6 63 69-144 4-66 (67)
10 cd01721 Sm_D3 The eukaryotic S 97.2 0.0021 4.6E-08 52.9 8.6 67 68-147 3-69 (70)
11 cd00600 Sm_like The eukaryotic 97.1 0.0014 3E-08 51.5 6.4 61 71-144 2-62 (63)
12 cd01731 archaeal_Sm1 The archa 97.0 0.0034 7.4E-08 51.1 8.0 63 69-144 4-66 (68)
13 PRK00737 small nuclear ribonuc 97.0 0.0035 7.7E-08 51.8 8.2 67 65-144 4-70 (72)
14 cd06168 LSm9 The eukaryotic Sm 97.0 0.0041 9E-08 52.2 8.3 70 70-146 5-74 (75)
15 cd01722 Sm_F The eukaryotic Sm 97.0 0.0048 1E-07 50.4 8.5 64 68-144 4-67 (68)
16 smart00651 Sm snRNP Sm protein 97.0 0.0032 7E-08 50.2 7.1 64 70-145 3-66 (67)
17 cd01723 LSm4 The eukaryotic Sm 96.9 0.006 1.3E-07 50.9 8.6 70 67-148 3-72 (76)
18 PF01423 LSM: LSM domain ; In 96.8 0.0037 8.1E-08 49.9 6.1 65 69-145 2-66 (67)
19 PF12701 LSM14: Scd6-like Sm d 96.7 0.01 2.2E-07 52.3 8.6 75 71-149 4-79 (96)
20 cd01717 Sm_B The eukaryotic Sm 96.4 0.017 3.6E-07 48.5 8.0 74 70-146 5-78 (79)
21 cd01719 Sm_G The eukaryotic Sm 96.3 0.019 4.1E-07 47.7 7.6 64 70-146 5-68 (72)
22 cd01736 LSm14_N LSm14 (also kn 96.3 0.015 3.2E-07 49.3 6.7 71 71-144 2-73 (74)
23 COG1958 LSM1 Small nuclear rib 96.2 0.027 5.8E-07 47.1 8.0 71 64-145 6-78 (79)
24 KOG1073 Uncharacterized mRNA-a 95.4 0.029 6.2E-07 59.7 6.1 75 69-148 3-80 (361)
25 cd01727 LSm8 The eukaryotic Sm 95.1 0.12 2.6E-06 42.9 7.8 68 70-146 4-71 (74)
26 cd01729 LSm7 The eukaryotic Sm 95.0 0.15 3.2E-06 43.4 8.2 71 70-145 7-77 (81)
27 cd01732 LSm5 The eukaryotic Sm 94.9 0.15 3.3E-06 42.9 7.9 69 67-145 5-73 (76)
28 PF11095 Gemin7: Gem-associate 94.7 0.12 2.6E-06 44.4 7.0 70 61-147 10-79 (80)
29 cd01730 LSm3 The eukaryotic Sm 94.6 0.19 4.1E-06 42.6 7.8 43 69-113 5-47 (82)
30 cd01728 LSm1 The eukaryotic Sm 94.5 0.15 3.3E-06 42.8 7.0 65 70-144 7-71 (74)
31 cd01720 Sm_D2 The eukaryotic S 91.7 1.2 2.5E-05 38.7 8.3 46 66-113 4-50 (87)
32 KOG1783 Small nuclear ribonucl 88.0 0.36 7.8E-06 41.0 2.2 43 69-113 10-52 (77)
33 KOG3293 Small nuclear ribonucl 85.1 1.1 2.3E-05 41.6 3.8 44 67-112 4-47 (134)
34 KOG3428 Small nuclear ribonucl 84.2 4.8 0.0001 36.7 7.4 70 65-148 2-71 (109)
35 KOG3448 Predicted snRNP core p 83.7 3.9 8.3E-05 36.1 6.4 43 69-113 6-48 (96)
36 KOG3482 Small nuclear ribonucl 82.3 3.5 7.7E-05 35.2 5.5 48 69-118 12-59 (79)
37 PF10842 DUF2642: Protein of u 81.6 3.8 8.1E-05 34.2 5.4 39 66-108 12-50 (66)
38 PF02237 BPL_C: Biotin protein 77.1 5.2 0.00011 30.6 4.6 31 74-107 2-32 (48)
39 cd01735 LSm12_N LSm12 belongs 72.9 8.7 0.00019 31.6 5.1 35 73-108 4-38 (61)
40 cd01718 Sm_E The eukaryotic Sm 72.9 20 0.00043 30.8 7.4 41 70-112 11-55 (79)
41 PF07073 ROF: Modulator of Rho 70.1 4.3 9.3E-05 34.9 2.9 38 70-107 12-51 (80)
42 PF06372 Gemin6: Gemin6 protei 68.0 9.4 0.0002 37.1 5.0 36 69-106 11-46 (166)
43 cd01734 YlxS_C YxlS is a Bacil 64.9 25 0.00055 29.6 6.5 55 70-145 20-78 (83)
44 PRK02001 hypothetical protein; 62.0 33 0.00071 32.8 7.3 73 59-144 76-148 (152)
45 PRK14638 hypothetical protein; 61.4 24 0.00052 33.4 6.3 43 59-106 86-128 (150)
46 PRK14642 hypothetical protein; 56.8 42 0.00091 33.5 7.4 71 69-147 94-179 (197)
47 PTZ00138 small nuclear ribonuc 52.2 60 0.0013 28.5 6.8 57 77-145 28-86 (89)
48 KOG3172 Small nuclear ribonucl 45.6 82 0.0018 29.0 6.7 64 73-149 13-76 (119)
49 PF02576 DUF150: Uncharacteris 43.5 34 0.00074 31.4 4.2 36 70-108 82-121 (141)
50 cd01716 Hfq Hfq, an abundant, 35.8 83 0.0018 26.0 4.8 31 74-107 10-40 (61)
51 PRK09618 flgD flagellar basal 34.3 68 0.0015 30.5 4.7 28 70-97 87-114 (142)
52 PRK14639 hypothetical protein; 33.6 74 0.0016 29.8 4.8 34 70-106 83-116 (140)
53 TIGR02383 Hfq RNA chaperone Hf 33.5 91 0.002 25.8 4.7 31 73-106 13-43 (61)
54 PRK14644 hypothetical protein; 33.3 76 0.0017 29.7 4.8 42 59-106 72-117 (136)
55 PRK00395 hfq RNA-binding prote 32.0 95 0.0021 27.0 4.7 34 71-107 15-48 (79)
56 PRK14641 hypothetical protein; 28.2 1.7E+02 0.0037 28.5 6.4 40 69-108 98-143 (173)
57 PRK14643 hypothetical protein; 27.2 1.6E+02 0.0036 28.3 6.1 29 70-98 99-131 (164)
58 PRK06792 flgD flagellar basal 26.1 1.1E+02 0.0024 30.5 4.8 27 71-97 114-140 (190)
59 COG1923 Hfq Uncharacterized ho 25.6 2E+02 0.0044 25.0 5.6 41 63-107 8-48 (77)
60 PRK11625 Rho-binding antitermi 24.4 1.2E+02 0.0025 26.6 4.0 27 70-96 18-44 (84)
61 PRK11911 flgD flagellar basal 23.6 1.2E+02 0.0027 28.8 4.4 28 70-97 88-115 (140)
62 PRK14633 hypothetical protein; 22.4 1.5E+02 0.0033 28.0 4.8 35 70-107 89-127 (150)
63 TIGR02603 CxxCH_TIGR02603 puta 22.4 1.3E+02 0.0028 27.4 4.2 30 76-108 58-87 (133)
64 PF11607 DUF3247: Protein of u 22.3 1.4E+02 0.003 27.0 4.1 31 64-94 16-47 (101)
65 COG4568 Rof Transcriptional an 21.5 1E+02 0.0022 27.0 3.0 28 70-97 18-45 (84)
66 PRK14640 hypothetical protein; 20.7 1.7E+02 0.0038 27.6 4.8 34 70-106 92-129 (152)
67 PRK14645 hypothetical protein; 20.2 1.7E+02 0.0038 27.9 4.7 42 59-106 88-129 (154)
68 PRK14632 hypothetical protein; 20.1 1.9E+02 0.0042 28.0 5.0 60 70-146 93-159 (172)
No 1
>COG5180 PBP1 Protein interacting with poly(A)-binding protein [RNA processing and modification]
Probab=100.00 E-value=1e-36 Score=317.85 Aligned_cols=188 Identities=33% Similarity=0.492 Sum_probs=137.7
Q ss_pred CceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEEEccccccc-
Q 045896 75 GLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVIAKDVAVTR- 153 (520)
Q Consensus 75 G~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~AkdV~ls~- 153 (520)
|..|-+.+.|| +..++.+. +.||+..+|++-.+ +.|...||+.++- +..|..
T Consensus 34 GS~I~~~~Tn~------~~~~nlEs-i~vv~~nprV~~~g-------------------Vs~s~sD~~t~~~-~~sl~~~ 86 (654)
T COG5180 34 GSIIGAFLTNE------DGKVNLES-IDVVETNPRVVFPG-------------------VSISESDIITVTK-MNSLQAE 86 (654)
T ss_pred cceeeeeeecC------Cccceeee-eeeeecCCccccCc-------------------cccccchhhhhhc-cchhhhh
Confidence 88888888887 33344543 56888888765542 2333344443321 111110
Q ss_pred -CCcc-----cccchhhhhccccceeccCCc-ccccccccccCCCCCCCCc----cccccccCCCCCCcccchhHhhhhh
Q 045896 154 -DGFA-----NELQSDKQRELMIDSLISQTR-HVEERELEPWIPDEDVPQL----PELENIFDDPWNSKKWDQFETNETL 222 (520)
Q Consensus 154 -D~~~-----~~~~~~~~~~FkTDTeIS~~~-~~~ERELq~W~pd~dd~~~----~sLE~~~d~~~~~~~WDQFeaNEkl 222 (520)
.... .........-|+||.+||+.. ..+||+|.+|.|++.+..+ ..||+ +.+.||||++||+|
T Consensus 87 ~en~~s~~gsa~~n~s~~rvfrTDv~ISg~~rE~keR~l~~w~p~p~aa~~~~~G~~le~------d~~~WdQFa~NeKl 160 (654)
T COG5180 87 KENDASERGSAAKNDSGWRVFRTDVEISGGPREIKERKLMPWAPLPKAADLEKSGKALEE------DCKDWDQFAANEKL 160 (654)
T ss_pred hccccccccccccccccceeeeecceecCCcchhhhhhhcccCCCccccCCccccchhhc------ccchHHHhhhhhhh
Confidence 0000 001112345699999999864 3559999999998765443 12443 23489999999999
Q ss_pred cCccccCCCCceeeeccCC-CchHHHHHHHHHHHHHHhcCCCcchhhhhhcCCcccCCCCCChhhcccccccCCC
Q 045896 223 FGVKTTFNEELYTTKLLRG-PQTEELEKEAARIAREIAGEDTQDLHLAEERGSSIHENLGIDEETRFSSVYRGTG 296 (520)
Q Consensus 223 FGVkSTFDE~LYTTkLDrs-p~ykereaeAeRIArEIE~s~t~n~HiaEERG~~~~~d~~~DEEdkYSaV~R~~~ 296 (520)
|||||+|||+|||++|||+ |.|++++.+|+|||+|||.+.|.|+|||||||+.+ +|++.||||+||+|+|..+
T Consensus 161 FgVkS~FDE~lYt~~idks~p~Yk~k~qeA~RIaKEIe~s~TtniHiaEeRGl~~-DDSGldeEDlYSgV~R~~d 234 (654)
T COG5180 161 FGVKSRFDEELYTEVIDKSSPSYKSKVQEARRIAKEIELSATTNIHIAEERGLGN-DDSGLDEEDLYSGVVRRGD 234 (654)
T ss_pred cCccccccHHHHhhhhccCChhhHHHHHHHHHHHHHHhhccccchhhhhhcCccc-cccCcchhhhhhhhhhhHH
Confidence 9999999999999999997 89999999999999999999999999999999976 4789999999999999643
No 2
>KOG2375 consensus Protein interacting with poly(A)-binding protein [RNA processing and modification]
Probab=99.96 E-value=5.7e-29 Score=273.36 Aligned_cols=316 Identities=29% Similarity=0.326 Sum_probs=221.7
Q ss_pred CccccCCCCCCCCCCCcccccccCCCcccCcccCCCCCCCCccccccccCCCCCcccCccchhHHHHHHhccCceEEEEE
Q 045896 3 NLQQVMPPKSTANGFGRRRGEREGGTRLESKSQSGKSNSGRVTTTGSVIGSKSGSCAVSSHDKLLYLASCLIGLSVEVQV 82 (520)
Q Consensus 3 ~~q~~~~~~~~~ng~~~rr~~r~~~~~~~nk~~~~~s~~~r~~~~~~~~g~~~g~~~s~~~dRLlyl~t~LIG~~VeVtv 82 (520)
.+.++-++..+.|++.+||..|.++.+..--.+..+ ..+-.+.. . .++..++|+|+++|.||..|.|+|
T Consensus 7 ~mk~~f~~~~ssn~~~~rr~~~~~~~~~~~p~~~~t---~~p~~~~s--~------~~~~~~~~~~~~~~s~g~~~~~~l 75 (756)
T KOG2375|consen 7 RMKPNFQPAASSNKLPGRRFSSGVGANGGKPAQSAT---PDPPNAES--I------ENPSRDSLAYKATDSIGPSVAVLL 75 (756)
T ss_pred cccccCCcccCCCCCccccccccccccCCCcccccC---CCCCCCCC--C------CCcchhhhhhhhcCCCCcccceec
Confidence 457788899999999999998887775443333333 22221111 1 667789999999999999999999
Q ss_pred ecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCC---cEEEEEcccccccCCcccc
Q 045896 83 KGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSE---LVQVIAKDVAVTRDGFANE 159 (520)
Q Consensus 83 kdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kD---IVqV~AkdV~ls~D~~~~~ 159 (520)
.+|..|.|||+.+++...++|+|.++-........+...+. .... ..++.|+..| |+++.++.-..-.+....+
T Consensus 76 ~ng~~~~gi~~s~N~~~~~gi~~~a~~~~~~~g~r~~~~r~-~~~~--~~~~~i~~~~~~eL~~~~~~~~~k~~~s~~~g 152 (756)
T KOG2375|consen 76 GNGSSYSGILVSNNPEQTVGIILVAADAKRRSGTRGSESRD-WMPD--PPTAGIPLEDELELTTSNAEQDEKATNSKSDG 152 (756)
T ss_pred cCCCCCcceeeecchhhcccccccccccccccccccccccc-cccC--CCcccCccccccchhhcccccchhhhcchhhc
Confidence 99999999999999998899999988765442122222222 1222 2566666555 3344333222211111111
Q ss_pred cch-----hhhhccccceeccCC--cccccccccccCCCCCCCCccccccccCCCCCCcccchhHhh---hhhcCccccC
Q 045896 160 LQS-----DKQRELMIDSLISQT--RHVEERELEPWIPDEDVPQLPELENIFDDPWNSKKWDQFETN---ETLFGVKTTF 229 (520)
Q Consensus 160 ~~~-----~~~~~FkTDTeIS~~--~~~~ERELq~W~pd~dd~~~~sLE~~~d~~~~~~~WDQFeaN---EklFGVkSTF 229 (520)
.+. .....|+||..+... ....|| |.+|.+++....+.-++.-....++. +||||++| .++|||.+||
T Consensus 153 v~~e~~~~~a~Ss~it~~~~~~~~~ee~~e~-l~p~~~~e~v~~~~~~~~~rl~~~~k-Gw~Qf~v~f~~~~~f~v~stF 230 (756)
T KOG2375|consen 153 VQSEKPDEAAYSSFITDSEGKGDEGEEEAER-LAPWIEDEVVPGGGIAEERRLENDNK-GWDQFEVNFHGSKKFNVMSTF 230 (756)
T ss_pred cccccccccccccccccccccccccccchhh-cCCCCcccccccccchhhcccccccC-CCCccchhhhhhhhhceeeee
Confidence 111 234568888887775 112234 55999988766665555444444554 99999999 9999999999
Q ss_pred CCCceeeeccCCCchHHHHHHHHHHHHHHhcCCCcchhhhhhcCCcccCCCCCChhhcccccccC-CCCCCCCCC-CCCc
Q 045896 230 NEELYTTKLLRGPQTEELEKEAARIAREIAGEDTQDLHLAEERGSSIHENLGIDEETRFSSVYRG-TGFDDSGYE-EDED 307 (520)
Q Consensus 230 DE~LYTTkLDrsp~ykereaeAeRIArEIE~s~t~n~HiaEERG~~~~~d~~~DEEdkYSaV~R~-~~~~~sg~~-~~~~ 307 (520)
||+||||+||+.+...+...+|+|||+||+...+...|.++||+...-+.+++|||++|+.|+|. -.+.+.++. ...+
T Consensus 231 de~ly~tk~d~~~kn~e~~e~a~Ria~ei~~~at~~~h~~ae~~~~gpd~~~I~ee~~ys~sd~~~~r~~~~~~~~~~qd 310 (756)
T KOG2375|consen 231 DEELYTTKLDKKVKNYEAYEGAERIAREIESLATSDAHHLAERRLGGPDREDIEEEDLYSRSDGPGVRFENEDFNEAMQD 310 (756)
T ss_pred ehhhhcceecccCCchhhHHHHHHhhccccccchhHHHHhhccCCCCcchhhhhhhhhcccccccchhhhhhhhhHHHHh
Confidence 99999999999854455599999999999999999999999998877777889999999966554 345666665 2457
Q ss_pred ccccCCCcc--ccCCCCCCccCcccchhccc
Q 045896 308 IVLNTHNNE--TFGDSSGSVDQISTDFAIAK 336 (520)
Q Consensus 308 ~~~~s~n~~--~f~~~~~s~~~~~~~~~~~~ 336 (520)
...+++++- .+++...++...+. .+++
T Consensus 311 ~~~d~i~~~~~kvn~~~k~~~~~~~--~sgk 339 (756)
T KOG2375|consen 311 KRNDKIAPLDQKVNDSTKSKALERW--NSGK 339 (756)
T ss_pred hhccccccccCCCCccccccccccc--cccc
Confidence 788888877 88887776655554 4444
No 3
>PF06741 LsmAD: LsmAD domain; InterPro: IPR009604 This entry represents a conserved region approximately 250 residues long located on eukaryotic ataxin-2 []. Ataxin-2 is a protein of unknown function, within which expansion of a polyglutamine tract (due to expansion of unstable CAG repeats in the coding region of the SCA2 gene) causes spinocerebellar ataxia type 2 (SCA2), a late-onset neurodegenerative disorder []. The expanded polyglutamine repeat in ataxin-2 causes disruption of the normal morphology of the Golgi complex and increased incidence of cell death []. Ataxin-2 is predicted to consist of mostly non-globular domains [].
Probab=99.95 E-value=3e-28 Score=201.04 Aligned_cols=71 Identities=54% Similarity=0.856 Sum_probs=67.3
Q ss_pred cCccccCCCCceeeeccCC-CchHHHHHHHHHHHHHHhcCCCcchhhhhhcCCcccCCCCCChhhcccccccC
Q 045896 223 FGVKTTFNEELYTTKLLRG-PQTEELEKEAARIAREIAGEDTQDLHLAEERGSSIHENLGIDEETRFSSVYRG 294 (520)
Q Consensus 223 FGVkSTFDE~LYTTkLDrs-p~ykereaeAeRIArEIE~s~t~n~HiaEERG~~~~~d~~~DEEdkYSaV~R~ 294 (520)
|||+|||||+||||+||++ |.|++++++|+|||+|||++.+.|+|++||||+ +..+.+.|||+|||+|+|+
T Consensus 1 FGV~stydE~lYTT~Ld~~~~~~k~~~~~A~riA~EIe~~~t~n~h~~eeR~~-~~~~~~~DEE~~YSaV~R~ 72 (72)
T PF06741_consen 1 FGVKSTYDENLYTTPLDRSDPDYKEREAEAERIAREIEGSTTSNIHVAEERGR-LEDDSGRDEEDKYSAVVRD 72 (72)
T ss_pred CCCCCccCchhceeeccCCCcchHHHHHHHHHHHHHHhccCCCCchhHHHhCc-cccCCCCCHHHhccceeCC
Confidence 9999999999999999998 799999999999999999999999999999998 4557788999999999995
No 4
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=99.81 E-value=2.5e-20 Score=153.66 Aligned_cols=76 Identities=43% Similarity=0.740 Sum_probs=49.0
Q ss_pred hhHHHHHHhccCceEEEEEecCCEEEEEEeecCCCC-CeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcE
Q 045896 64 DKLLYLASCLIGLSVEVQVKGGSVYAGIFHATSDEK-DFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELV 142 (520)
Q Consensus 64 dRLlyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~-dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIV 142 (520)
|||+|+++|+||++|+|+++||.+|+|||++++++. +++|+|||||.++++.... ......++.++|+|+++|||
T Consensus 1 dRl~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~----~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 1 DRLVYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSN----SDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp ---HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS----------EEEEEEE-GGGEEE-----
T ss_pred ChHHHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccccccc----CCccCCCCCceEEEeccccC
Confidence 799999999999999999999999999999999987 8999999999998854321 22333445599999999998
Q ss_pred E
Q 045896 143 Q 143 (520)
Q Consensus 143 q 143 (520)
|
T Consensus 77 ~ 77 (77)
T PF14438_consen 77 Q 77 (77)
T ss_dssp -
T ss_pred C
Confidence 6
No 5
>KOG2375 consensus Protein interacting with poly(A)-binding protein [RNA processing and modification]
Probab=98.36 E-value=5.4e-08 Score=109.10 Aligned_cols=208 Identities=15% Similarity=0.173 Sum_probs=153.9
Q ss_pred cchhHHHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCc
Q 045896 62 SHDKLLYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSEL 141 (520)
Q Consensus 62 ~~dRLlyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDI 141 (520)
...|+..+...|++.++++.++|+..|+|+|..+..-.+ .++.-+|.+....+.+.. ..++ .+.+++..+|.
T Consensus 223 ~f~v~stFde~ly~tk~d~~~kn~e~~e~a~Ria~ei~~--~at~~~h~~ae~~~~gpd-~~~I-----~ee~~ys~sd~ 294 (756)
T KOG2375|consen 223 KFNVMSTFDEELYTTKLDKKVKNYEAYEGAERIAREIES--LATSDAHHLAERRLGGPD-REDI-----EEEDLYSRSDG 294 (756)
T ss_pred hhceeeeeehhhhcceecccCCchhhHHHHHHhhccccc--cchhHHHHhhccCCCCcc-hhhh-----hhhhhcccccc
Confidence 356888889999999999999999999999999887544 334555554432232221 1222 37788888888
Q ss_pred EEEEEcccccccCCcccccchhhhhccccceeccCCcc----cccccccccCCCC--CCCCccccccccCCCCCCcccc-
Q 045896 142 VQVIAKDVAVTRDGFANELQSDKQRELMIDSLISQTRH----VEERELEPWIPDE--DVPQLPELENIFDDPWNSKKWD- 214 (520)
Q Consensus 142 VqV~AkdV~ls~D~~~~~~~~~~~~~FkTDTeIS~~~~----~~ERELq~W~pd~--dd~~~~sLE~~~d~~~~~~~WD- 214 (520)
.-+..+++.+. ....+.++|..|+-... -++..|++|.... .+.....++... ..+||
T Consensus 295 ~~~r~~~~~~~----------~~~qd~~~d~i~~~~~kvn~~~k~~~~~~~~sgk~~~N~s~~a~~~d~-----sn~~~~ 359 (756)
T KOG2375|consen 295 PGVRFENEDFN----------EAMQDKRNDKIAPLDQKVNDSTKSKALERWNSGKLLENASSYATPADA-----SNGWDE 359 (756)
T ss_pred cchhhhhhhhh----------HHHHhhhccccccccCCCCccccccccccccccccccccccccccchh-----hcCCCc
Confidence 88887777543 13456689999887432 3378899998754 122222333211 23675
Q ss_pred --hhHhhhhhcCccccCCCCc--eeeeccCC--CchHHHHHHHHHHHHHHhcCCCcchhhhhhcCCcccCCCCCChhhcc
Q 045896 215 --QFETNETLFGVKTTFNEEL--YTTKLLRG--PQTEELEKEAARIAREIAGEDTQDLHLAEERGSSIHENLGIDEETRF 288 (520)
Q Consensus 215 --QFeaNEklFGVkSTFDE~L--YTTkLDrs--p~ykereaeAeRIArEIE~s~t~n~HiaEERG~~~~~d~~~DEEdkY 288 (520)
||..|++-++++++|+--+ |+-.+.++ +.++.++++|..|+++|+...+....++.|. +.+.-||.+|
T Consensus 360 n~~~q~n~kn~~~~s~~~s~~~~~~~~sek~~se~~~qr~~~~~~~~~~~~~~~~~~~~~aaes------~s~~~~~~~p 433 (756)
T KOG2375|consen 360 NSMFQVNSKNYKSKSEVESSDMSTKKPSEKNESESFEQRKKRAVDLRRSETLGPQLGKKPAAES------DSGKAEEESP 433 (756)
T ss_pred ccccccccccccccccccccccccccccccccchhhhhhhhhhhhccccccccccccccccccc------cccccccCCC
Confidence 7999999999999999999 88888886 6799999999999999999999988888886 3457899999
Q ss_pred cccccCCCCC
Q 045896 289 SSVYRGTGFD 298 (520)
Q Consensus 289 SaV~R~~~~~ 298 (520)
..|+|.....
T Consensus 434 vt~~r~~~~~ 443 (756)
T KOG2375|consen 434 VTVQRKGGIE 443 (756)
T ss_pred cccccccccc
Confidence 9999987665
No 6
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=97.49 E-value=0.00075 Score=56.93 Aligned_cols=68 Identities=16% Similarity=0.256 Sum_probs=53.9
Q ss_pred HHHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEE
Q 045896 66 LLYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVI 145 (520)
Q Consensus 66 Llyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~ 145 (520)
|+-++..++|++|.|.+|||..|.|++.+++.- +-|+|+.|..+..+. .+ ... +++.|....|..|.
T Consensus 10 l~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~--MNl~L~~~~~~~~~~---~~---~~~-----~~v~IRG~nI~yI~ 76 (78)
T cd01733 10 LIILLQGLQGKVVTVELRNETTVTGRIASVDAF--MNIRLAKVTIIDRNG---KQ---VQV-----EEIMVTGRNIRYVH 76 (78)
T ss_pred HHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCC--ceeEEEEEEEEcCCC---ce---eEC-----CcEEEECCEEEEEE
Confidence 778889999999999999999999999999886 459999998775421 11 011 67888888888775
Q ss_pred E
Q 045896 146 A 146 (520)
Q Consensus 146 A 146 (520)
+
T Consensus 77 l 77 (78)
T cd01733 77 I 77 (78)
T ss_pred c
Confidence 4
No 7
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=97.48 E-value=0.00059 Score=59.04 Aligned_cols=72 Identities=21% Similarity=0.316 Sum_probs=57.9
Q ss_pred hHHHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEE
Q 045896 65 KLLYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQV 144 (520)
Q Consensus 65 RLlyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV 144 (520)
+|+.++..++|++|.|.+|||..|.|++.+++.- +-|+|+.|..+..+. .. . .-++++|....|..|
T Consensus 1 ~~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~--MNl~L~~a~~~~~~~---~~---~-----~~~~v~IRG~nI~yi 67 (90)
T cd01724 1 KLVRFLMKLTNETVTIELKNGTIVHGTITGVDPS--MNTHLKNVKLTLKGR---NP---V-----PLDTLSIRGNNIRYF 67 (90)
T ss_pred CHhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCc--eeEEEEEEEEEcCCC---ce---e-----EcceEEEeCCEEEEE
Confidence 3677888999999999999999999999999886 459999998775521 11 1 116789999999999
Q ss_pred EEccc
Q 045896 145 IAKDV 149 (520)
Q Consensus 145 ~AkdV 149 (520)
.+.|.
T Consensus 68 ~lPd~ 72 (90)
T cd01724 68 ILPDS 72 (90)
T ss_pred EcCCc
Confidence 88765
No 8
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=97.31 E-value=0.0019 Score=54.71 Aligned_cols=72 Identities=18% Similarity=0.201 Sum_probs=53.7
Q ss_pred HHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEEE
Q 045896 67 LYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVIA 146 (520)
Q Consensus 67 lyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~A 146 (520)
+.++..++|++|.|.+|||..|.|++.+++.-. -|+|+.|..+.... . .... .-+++.|...-|..|..
T Consensus 3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~M--Ni~L~n~~~~~~~~---~---~~~~---~~~~v~IRG~~I~~I~l 71 (81)
T cd01725 3 FSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYL--NIKLTNISVTDPEK---Y---PHML---SVKNCFIRGSVVRYVQL 71 (81)
T ss_pred hHHHHhCCCCEEEEEECCCcEEEEEEEEECCCc--ccEEEEEEEEcCCC---c---cccc---ccCeEEEECCEEEEEEe
Confidence 456788999999999999999999999999864 48999997654311 0 0011 11578999999998886
Q ss_pred ccc
Q 045896 147 KDV 149 (520)
Q Consensus 147 kdV 149 (520)
.+-
T Consensus 72 p~~ 74 (81)
T cd01725 72 PAD 74 (81)
T ss_pred Chh
Confidence 543
No 9
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=97.28 E-value=0.0012 Score=53.75 Aligned_cols=63 Identities=19% Similarity=0.336 Sum_probs=47.1
Q ss_pred HHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEE
Q 045896 69 LASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQV 144 (520)
Q Consensus 69 l~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV 144 (520)
++..++|++|.|.+++|..|+|++.+++.- +-++|+.|.....+. .+ ..+ ..++|...-|+.|
T Consensus 4 ~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~--mNlvL~~~~~~~~~~---~~---~~~-----~~v~IRG~~I~~I 66 (67)
T cd01726 4 FLKAIIGRPVVVKLNSGVDYRGILACLDGY--MNIALEQTEEYVNGQ---LK---NKY-----GDAFIRGNNVLYI 66 (67)
T ss_pred HHHhhCCCeEEEEECCCCEEEEEEEEEccc--eeeEEeeEEEEeCCc---ee---eEe-----CCEEEECCEEEEE
Confidence 467789999999999999999999999975 559999997755421 11 111 4577777777655
No 10
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=97.23 E-value=0.0021 Score=52.90 Aligned_cols=67 Identities=24% Similarity=0.262 Sum_probs=51.7
Q ss_pred HHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEEEc
Q 045896 68 YLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVIAK 147 (520)
Q Consensus 68 yl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~Ak 147 (520)
-++..++|++|.|.+|||..|.|++.+++.- +-++|+.|..+... +.. .. ..++.|....|..|...
T Consensus 3 ~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~--MNl~L~~~~~~~~~---g~~---~~-----~~~v~IRG~nI~~v~lP 69 (70)
T cd01721 3 KLLHEAEGHIVTVELKTGEVYRGKLIEAEDN--MNCQLKDVTVTARD---GRV---SQ-----LEQVYIRGSKIRFFILP 69 (70)
T ss_pred HHHhhCCCCEEEEEECCCcEEEEEEEEEcCC--ceeEEEEEEEECCC---CcE---eE-----cCcEEEeCCEEEEEEeC
Confidence 3567889999999999999999999999885 45999999865431 111 01 16788999999888764
No 11
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=97.14 E-value=0.0014 Score=51.47 Aligned_cols=61 Identities=20% Similarity=0.281 Sum_probs=47.1
Q ss_pred HhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEE
Q 045896 71 SCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQV 144 (520)
Q Consensus 71 t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV 144 (520)
..++|++|.|+++||..|.|+|.+++... -|+|+.|....... + ...+ ..++|....|+.|
T Consensus 2 ~~~~g~~V~V~l~~g~~~~G~L~~~D~~~--Ni~L~~~~~~~~~~---~---~~~~-----~~~~irG~~I~~I 62 (63)
T cd00600 2 KDLVGKTVRVELKDGRVLEGVLVAFDKYM--NLVLDDVEETIKEG---K---KRVL-----GLVLIRGDNVRLV 62 (63)
T ss_pred hHHCCCEEEEEECCCcEEEEEEEEECCCC--CEEECCEEEEecCC---c---EEEC-----CeEEEECCEEEEE
Confidence 35799999999999999999999999764 49999998765521 1 1112 5788888888766
No 12
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=97.05 E-value=0.0034 Score=51.06 Aligned_cols=63 Identities=19% Similarity=0.299 Sum_probs=48.4
Q ss_pred HHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEE
Q 045896 69 LASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQV 144 (520)
Q Consensus 69 l~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV 144 (520)
++..++|++|.|++++|..|.|+|.+++.- +-++|+.|.+...+. ++ ..+ ..++|....|+.|
T Consensus 4 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~--mNlvL~~~~e~~~~~---~~---~~l-----g~~~iRG~~I~~i 66 (68)
T cd01731 4 VLKDSLNKPVLVKLKGGKEVRGRLKSYDQH--MNLVLEDAEEIDDGE---PV---RKY-----GRVVIRGDNVLFI 66 (68)
T ss_pred HHHHhcCCEEEEEECCCCEEEEEEEEECCc--ceEEEeeEEEEecCC---eE---eEc-----CcEEEeCCEEEEE
Confidence 466789999999999999999999999986 449999998865421 11 111 4678888888766
No 13
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=97.04 E-value=0.0035 Score=51.78 Aligned_cols=67 Identities=22% Similarity=0.348 Sum_probs=50.4
Q ss_pred hHHHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEE
Q 045896 65 KLLYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQV 144 (520)
Q Consensus 65 RLlyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV 144 (520)
.-+.++..++|++|.|.++||..|.|++.+++.- +-++|+-|....++. . ...+ ..++|....|+.|
T Consensus 4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~--mNlvL~d~~e~~~~~---~---~~~l-----g~v~iRG~~V~~i 70 (72)
T PRK00737 4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIH--MNLVLDNAEEIQDGE---V---VRKL-----GKVVIRGDNVVYV 70 (72)
T ss_pred chHHHHHHhCCCEEEEEECCCCEEEEEEEEEccc--ceeEEeeEEEEcCCC---e---EeEc-----CcEEEeCCEEEEE
Confidence 3456677889999999999999999999999986 449999998765421 1 0011 4677888877766
No 14
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=97.00 E-value=0.0041 Score=52.22 Aligned_cols=70 Identities=19% Similarity=0.291 Sum_probs=50.6
Q ss_pred HHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEEE
Q 045896 70 ASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVIA 146 (520)
Q Consensus 70 ~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~A 146 (520)
+.+++|++|.|+++||..|.|+|.+++.... |||..|.+....+..... .+ ...-..++|+.+.|+.|.+
T Consensus 5 L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~N--ivL~~~~E~~~~~~~~~~--~~---~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 5 LRSLLGRTMRIHMTDGRTLVGVFLCTDRDCN--IILGSAQEYRPPPDSFSP--TE---PRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred HHHhcCCeEEEEEcCCeEEEEEEEEEcCCCc--EEecCcEEEEcccCccCC--cc---EEEeeeEEEeCCeEEEEEE
Confidence 5678999999999999999999999998655 999999886542211000 01 0011468899999988864
No 15
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=97.00 E-value=0.0048 Score=50.38 Aligned_cols=64 Identities=19% Similarity=0.239 Sum_probs=48.4
Q ss_pred HHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEE
Q 045896 68 YLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQV 144 (520)
Q Consensus 68 yl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV 144 (520)
-++..++|++|.|.++||..|.|++.+++.- +-|+|+.|.....+. .+ ..-..++|....|+.|
T Consensus 4 ~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~--mNi~L~~~~e~~~~~---~~--------~~lg~~~IRG~~I~~i 67 (68)
T cd01722 4 PFLNDLTGKPVIVKLKWGMEYKGTLVSVDSY--MNLQLANTEEYIDGK---ST--------GNLGEVLIRCNNVLYI 67 (68)
T ss_pred HHHHHcCCCEEEEEECCCcEEEEEEEEECCC--EEEEEeeEEEEeCCc---cc--------cCcCcEEEECCEEEEE
Confidence 3577889999999999999999999999975 569999997664421 11 1125678888777665
No 16
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=96.97 E-value=0.0032 Score=50.18 Aligned_cols=64 Identities=20% Similarity=0.268 Sum_probs=49.3
Q ss_pred HHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEE
Q 045896 70 ASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVI 145 (520)
Q Consensus 70 ~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~ 145 (520)
+..++|++|.|+++||..|.|+|.+++... -++|+.|....... .+ ...+ ..++|....|+.|.
T Consensus 3 L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~--NlvL~~~~e~~~~~--~~---~~~~-----~~~~IrG~~I~~i~ 66 (67)
T smart00651 3 LKKLIGKRVLVELKNGREYRGTLKGFDQFM--NLVLEDVEETVKDG--EK---KRKL-----GLVFIRGNNIVYII 66 (67)
T ss_pred hHHhCCcEEEEEECCCcEEEEEEEEECccc--cEEEccEEEEecCC--cE---EeEe-----CCEEEcCCEEEEEe
Confidence 567899999999999999999999999764 49999998876521 11 1112 56888888888764
No 17
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=96.92 E-value=0.006 Score=50.91 Aligned_cols=70 Identities=17% Similarity=0.185 Sum_probs=52.8
Q ss_pred HHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEEE
Q 045896 67 LYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVIA 146 (520)
Q Consensus 67 lyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~A 146 (520)
+.++..++|++|.|.++||..|.|++.+++.-. -++|+.|..+... |++ +. ...++.|..+-|..|..
T Consensus 3 l~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~m--Ni~L~~~~~~~~~---g~~-----~~--~~~~v~IRG~~I~~i~~ 70 (76)
T cd01723 3 LSLLKTAQNHPMLVELKNGETYNGHLVNCDNWM--NIHLREVICTSKD---GDK-----FW--KMPECYIRGNTIKYLRV 70 (76)
T ss_pred hHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCC--ceEEEeEEEECCC---CcE-----ee--eCCcEEEeCCEEEEEEc
Confidence 456788999999999999999999999999864 4899999876431 111 10 11568888888888865
Q ss_pred cc
Q 045896 147 KD 148 (520)
Q Consensus 147 kd 148 (520)
.+
T Consensus 71 p~ 72 (76)
T cd01723 71 PD 72 (76)
T ss_pred CH
Confidence 43
No 18
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=96.79 E-value=0.0037 Score=49.90 Aligned_cols=65 Identities=18% Similarity=0.216 Sum_probs=50.2
Q ss_pred HHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEE
Q 045896 69 LASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVI 145 (520)
Q Consensus 69 l~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~ 145 (520)
++..++|++|.|.++||..|.|+|.+++.. +-++|+-|..+..... ....+ ..++|....|+.|.
T Consensus 2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~--~Nl~L~~~~~~~~~~~-----~~~~~-----~~~~irG~~I~~I~ 66 (67)
T PF01423_consen 2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQF--MNLVLSDVTETIKNGP-----EKRSL-----GLVFIRGSNIRYIS 66 (67)
T ss_dssp HHHHTTTSEEEEEETTSEEEEEEEEEEETT--EEEEEEEEEEEETTES-----EEEEE-----EEEEEEGGGEEEEE
T ss_pred hhHHhCCcEEEEEEeCCEEEEEEEEEeech--heEEeeeEEEEECCCC-----cEeEC-----cEEEEECCEEEEEE
Confidence 466789999999999999999999999874 5599999998765321 01122 46888888887764
No 19
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=96.69 E-value=0.01 Score=52.31 Aligned_cols=75 Identities=20% Similarity=0.241 Sum_probs=52.5
Q ss_pred HhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCccccc-ccCCCCCceeEeCCCcEEEEEccc
Q 045896 71 SCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEF-VSKPPSKNFIIPSSELVQVIAKDV 149 (520)
Q Consensus 71 t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~-vsk~~~eTLII~~kDIVqV~AkdV 149 (520)
...||+.|.|..+++-+|+|+|+++++.. --|.|+.+|.--.. +.+....+ ..+...+.++|.+.||-++.+-..
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~-sTItL~nVr~~GtE---~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~ 79 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTED-STITLKNVRSFGTE---GRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEP 79 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTT-TEEEEEEEEETTET---TSS-SS---C-CSSSSEEEEETTTEEEEEECE-
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCC-CEEEeeeeeecCcC---CCCcCcccCCCCceeeEEEEEccccceEEEEcC
Confidence 35799999999999999999999999863 45999999975431 11100111 112223679999999999987443
No 20
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=96.43 E-value=0.017 Score=48.47 Aligned_cols=74 Identities=16% Similarity=0.236 Sum_probs=50.4
Q ss_pred HHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEEE
Q 045896 70 ASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVIA 146 (520)
Q Consensus 70 ~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~A 146 (520)
+..+||++|.|+++||..|.|+|.+++.... +||..|.+........... .....+..-..++|+...|+.|.+
T Consensus 5 l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~N--lVL~~~~E~~~~~~~~~~~-~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 5 MLQLINYRLRVTLQDGRQFVGQFLAFDKHMN--LVLSDCEEFRKVKKKKSKN-SEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred hHHHcCCEEEEEECCCcEEEEEEEEEcCccC--EEcCCEEEEEecccccccc-ccCcceeEeeeEEEcCCEEEEEEE
Confidence 4568999999999999999999999998654 8999998854322111000 000000111568999999988864
No 21
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=96.31 E-value=0.019 Score=47.73 Aligned_cols=64 Identities=16% Similarity=0.254 Sum_probs=49.5
Q ss_pred HHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEEE
Q 045896 70 ASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVIA 146 (520)
Q Consensus 70 ~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~A 146 (520)
+..+++++|.|.+++|..|.|+|.+++.-. -++|.-|.....+. .+ ..+ ..++|....|+.|.+
T Consensus 5 L~~~i~k~V~V~L~~g~~~~G~L~~~D~~m--NlvL~~~~E~~~~~---~~---~~l-----g~v~IRG~~I~~i~~ 68 (72)
T cd01719 5 LKKYMDKKLSLKLNGNRKVSGILRGFDPFM--NLVLDDAVEVNSGG---EK---NNI-----GMVVIRGNSIVMLEA 68 (72)
T ss_pred hHHhCCCeEEEEECCCeEEEEEEEEEcccc--cEEeccEEEEccCC---ce---eEe-----ceEEECCCEEEEEEc
Confidence 556899999999999999999999999754 49999998765321 11 111 568999999998875
No 22
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=96.27 E-value=0.015 Score=49.26 Aligned_cols=71 Identities=18% Similarity=0.220 Sum_probs=47.6
Q ss_pred HhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccc-cCCCCCceeEeCCCcEEE
Q 045896 71 SCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFV-SKPPSKNFIIPSSELVQV 144 (520)
Q Consensus 71 t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~v-sk~~~eTLII~~kDIVqV 144 (520)
...||+.+.+-.+..-+|+|+|+.++++. --|.|+.+|.--..--.+.. .++. +....+.++|...||-++
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~-sTi~L~nVr~fGTEgR~~~~--~~ipp~~~vyd~IvFrgsDIkDL 73 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTED-STIALKNVRSFGTEGRPTDG--PEIPPSDEVYDYIVFRGSDIKDL 73 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeecccc-CEEEeeeeEeecccCCCCCC--CccCCCCcceeEEEEcCCccccc
Confidence 35799999999999999999999999974 46999999875442111111 1110 111125577877777543
No 23
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=96.20 E-value=0.027 Score=47.12 Aligned_cols=71 Identities=21% Similarity=0.278 Sum_probs=53.0
Q ss_pred hhHHHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeec--CCCCCCCCcccccccCCCCCceeEeCCCc
Q 045896 64 DKLLYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIK--DGNFRGQKTVAEFVSKPPSKNFIIPSSEL 141 (520)
Q Consensus 64 dRLlyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk--~~s~~g~k~~~e~vsk~~~eTLII~~kDI 141 (520)
.+.+.++..++|++|.|.+++|..|.|++.+++.-. -++|..|..+. ++. .. .......++|....|
T Consensus 6 ~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~m--NlvL~d~~e~~~~~~~----~~-----~~~~~~~~~IRG~~I 74 (79)
T COG1958 6 PLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYM--NLVLDDVEEIISHDGE----KN-----VRRLGGEVLIRGDNI 74 (79)
T ss_pred CCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccce--eEEEeceEEEeccCCc----cc-----cceeccEEEEECCcE
Confidence 345778888999999999999999999999998864 48999999876 321 10 011224688888888
Q ss_pred EEEE
Q 045896 142 VQVI 145 (520)
Q Consensus 142 VqV~ 145 (520)
+.|.
T Consensus 75 ~~I~ 78 (79)
T COG1958 75 VLIS 78 (79)
T ss_pred EEEe
Confidence 7764
No 24
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=95.38 E-value=0.029 Score=59.66 Aligned_cols=75 Identities=21% Similarity=0.265 Sum_probs=55.9
Q ss_pred HHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCccccc---ccCCCCCceeEeCCCcEEEE
Q 045896 69 LASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEF---VSKPPSKNFIIPSSELVQVI 145 (520)
Q Consensus 69 l~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~---vsk~~~eTLII~~kDIVqV~ 145 (520)
+++..||..|.|.=|.--+|||||.+++++ |-.|.||.+|.--+. +.+..... ..| -.+.|||...||-+|.
T Consensus 3 ~~t~yIGS~ISLISk~DIRYEGILy~in~q-dSTlgLqnVRsfGTE---gRk~~~pq~p~~~k-Vy~YIlFRGSDIKDL~ 77 (361)
T KOG1073|consen 3 LVTSYIGSFISLISKNDIRYEGILYTINLQ-DSTLGLQNVRSFGTE---GRKTDGPQVPPDDK-VYDYILFRGSDIKDLI 77 (361)
T ss_pred cccccccceeEEeecccceeeeEEEecccc-ccceehhheeecccc---cCCCCCCcCCCCcc-ceeeEEecCcccceee
Confidence 356789999999999999999999999997 346889999875431 11111111 111 3367999999999999
Q ss_pred Ecc
Q 045896 146 AKD 148 (520)
Q Consensus 146 Akd 148 (520)
+.+
T Consensus 78 V~~ 80 (361)
T KOG1073|consen 78 VQE 80 (361)
T ss_pred ecc
Confidence 876
No 25
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=95.11 E-value=0.12 Score=42.92 Aligned_cols=68 Identities=18% Similarity=0.154 Sum_probs=48.5
Q ss_pred HHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEEE
Q 045896 70 ASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVIA 146 (520)
Q Consensus 70 ~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~A 146 (520)
+..+++++|.|.+++|..|.|+|.+++... -+||.-|.+.......+. + +..-.+++|....|+.|..
T Consensus 4 L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~--NlvL~~~~E~~~~~~~~~----~---~~~lG~~~iRG~~I~~i~~ 71 (74)
T cd01727 4 LEDYLNKTVSVITVDGRVIVGTLKGFDQAT--NLILDDSHERVYSSDEGV----E---QVVLGLYIIRGDNIAVVGE 71 (74)
T ss_pred HHHhcCCEEEEEECCCcEEEEEEEEEcccc--CEEccceEEEEecCCCCc----e---eeEeceEEECCCEEEEEEc
Confidence 456799999999999999999999998864 489999877533111111 1 0111568888888887754
No 26
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=95.00 E-value=0.15 Score=43.37 Aligned_cols=71 Identities=13% Similarity=0.127 Sum_probs=48.3
Q ss_pred HHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEE
Q 045896 70 ASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVI 145 (520)
Q Consensus 70 ~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~ 145 (520)
+..+||++|.|++++|..|.|+|.+++.-.. +||.-|.+.......... ..+. ...-..++|....|+.|.
T Consensus 7 L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mN--lvL~~~~E~~~~~~~~~~-~~~~--~~~lG~v~iRG~nV~~i~ 77 (81)
T cd01729 7 LSKYVDKKIRVKFQGGREVTGILKGYDQLLN--LVLDDTVEYLRDPDDPYK-LTDK--TRQLGLVVCRGTSVVLIS 77 (81)
T ss_pred HHHhcCCeEEEEECCCcEEEEEEEEEcCccc--EEecCEEEEEccCCcccc-cccc--eeEccEEEEcCCEEEEEe
Confidence 5667999999999999999999999988644 899999886542111100 0000 001145778888777764
No 27
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=94.88 E-value=0.15 Score=42.89 Aligned_cols=69 Identities=12% Similarity=0.166 Sum_probs=49.1
Q ss_pred HHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEE
Q 045896 67 LYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVI 145 (520)
Q Consensus 67 lyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~ 145 (520)
+-++..+++++|.|.+++|..|.|+|.+++.- +-+||.-|.+.......+. . ..-..++|....|+.|.
T Consensus 5 ~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~--mNlvL~da~E~~~~~~~~~-----~---~~lg~v~iRG~nV~~i~ 73 (76)
T cd01732 5 LELIDKCIGSRIWIVMKSDKEFVGTLLGFDDY--VNMVLEDVTEYEITPEGRK-----I---TKLDQILLNGNNICMLV 73 (76)
T ss_pred HHHHHHhCCCEEEEEECCCeEEEEEEEEeccc--eEEEEccEEEEEEcCCCce-----e---eEcCeEEEeCCeEEEEE
Confidence 34566779999999999999999999999886 4489999987652111111 0 01146788877777764
No 28
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=94.75 E-value=0.12 Score=44.40 Aligned_cols=70 Identities=10% Similarity=0.132 Sum_probs=48.6
Q ss_pred ccchhHHHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCC
Q 045896 61 SSHDKLLYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSE 140 (520)
Q Consensus 61 ~~~dRLlyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kD 140 (520)
-+++|+|.++..|+|++|++++.+.....|.|.+++.+...-.| ..+..+ ..+. +.=++...|
T Consensus 10 ~LRerfLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~V----s~L~TP--------lGv~-----~eAlLR~~D 72 (80)
T PF11095_consen 10 FLRERFLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQV----SNLQTP--------LGVQ-----PEALLRCSD 72 (80)
T ss_dssp HHHHHHHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEE----EEEETT--------TTEE-----EEEEEEGGG
T ss_pred HHHHHHHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEh----hhcCCC--------cccC-----hhheeecCC
Confidence 36899999999999999999999999999999999987532122 222221 1111 345778888
Q ss_pred cEEEEEc
Q 045896 141 LVQVIAK 147 (520)
Q Consensus 141 IVqV~Ak 147 (520)
|+.+.++
T Consensus 73 Vi~~~f~ 79 (80)
T PF11095_consen 73 VISISFD 79 (80)
T ss_dssp EEEEEE-
T ss_pred EEEEEec
Confidence 8888753
No 29
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=94.59 E-value=0.19 Score=42.56 Aligned_cols=43 Identities=21% Similarity=0.209 Sum_probs=36.1
Q ss_pred HHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecC
Q 045896 69 LASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKD 113 (520)
Q Consensus 69 l~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~ 113 (520)
++...++++|.|.+++|..|.|+|.+++.-. -+||.-|.+...
T Consensus 5 ~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~m--NlvL~d~~E~~~ 47 (82)
T cd01730 5 LIRLSLDERVYVKLRGDRELRGRLHAYDQHL--NMILGDVEETIT 47 (82)
T ss_pred HHHHhCCCEEEEEECCCCEEEEEEEEEccce--EEeccceEEEee
Confidence 3455699999999999999999999998864 488998887654
No 30
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=94.49 E-value=0.15 Score=42.76 Aligned_cols=65 Identities=17% Similarity=0.122 Sum_probs=45.8
Q ss_pred HHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEE
Q 045896 70 ASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQV 144 (520)
Q Consensus 70 ~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV 144 (520)
+...++++|.|.+++|..|.|+|.+++.-.. ++|.-|.+.-....... +..-..++|....|+.|
T Consensus 7 L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~N--lvL~d~~E~~~~~~~~~--------~~~lG~~viRG~~V~~i 71 (74)
T cd01728 7 LVDDLDKKVVVLLRDGRKLIGILRSFDQFAN--LVLQDTVERIYVGDKYG--------DIPRGIFIIRGENVVLL 71 (74)
T ss_pred HHHhcCCEEEEEEcCCeEEEEEEEEECCccc--EEecceEEEEecCCccc--------eeEeeEEEEECCEEEEE
Confidence 4567999999999999999999999998644 88999876532111000 11114677777777665
No 31
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=91.67 E-value=1.2 Score=38.72 Aligned_cols=46 Identities=13% Similarity=0.166 Sum_probs=37.7
Q ss_pred HHHHHHhc-cCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecC
Q 045896 66 LLYLASCL-IGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKD 113 (520)
Q Consensus 66 Llyl~t~L-IG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~ 113 (520)
|-+|-.|+ .|++|.|++++|..|.|.|.+++.- +-+||.-|.++..
T Consensus 4 l~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~h--mNlvL~d~~E~~~ 50 (87)
T cd01720 4 LSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRH--CNMVLENVKEMWT 50 (87)
T ss_pred HHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCc--cEEEEcceEEEee
Confidence 44555565 5999999999999999999999886 4589999988654
No 32
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=87.99 E-value=0.36 Score=41.03 Aligned_cols=43 Identities=19% Similarity=0.332 Sum_probs=32.5
Q ss_pred HHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecC
Q 045896 69 LASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKD 113 (520)
Q Consensus 69 l~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~ 113 (520)
++..+||++|.|.+.+|.-|.|++.+++-= +-|.|.-|-..-+
T Consensus 10 fl~~iiGr~V~VKl~sgvdyrG~l~~lDgy--mNiaLe~tee~~n 52 (77)
T KOG1783|consen 10 FLKAIIGRTVVVKLNSGVDYRGTLVCLDGY--MNIALESTEEYVN 52 (77)
T ss_pred HHHHHhCCeEEEEecCCccccceehhhhhH--HHHHHHHHHHHhc
Confidence 577899999999999999999999997642 2255555444333
No 33
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=85.08 E-value=1.1 Score=41.63 Aligned_cols=44 Identities=18% Similarity=0.204 Sum_probs=35.4
Q ss_pred HHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeec
Q 045896 67 LYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIK 112 (520)
Q Consensus 67 lyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk 112 (520)
|+|+...-|+++.|.+|||..|.|+|+.++.-.. |-|+-+-...
T Consensus 4 LsLL~~aq~~pmlvELKNget~nGhL~~cD~wMN--l~L~~Vi~ts 47 (134)
T KOG3293|consen 4 LSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMN--LHLREVICTS 47 (134)
T ss_pred hhHHHhcCCCeEEEEecCCCEecceeecchhhhh--cchheeEEec
Confidence 6788999999999999999999999999987533 5565554433
No 34
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=84.18 E-value=4.8 Score=36.65 Aligned_cols=70 Identities=20% Similarity=0.304 Sum_probs=52.1
Q ss_pred hHHHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEE
Q 045896 65 KLLYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQV 144 (520)
Q Consensus 65 RLlyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV 144 (520)
.|+-+++.+-+..|.|.++||++..|.+...+... -+.|+.+...-++ + .+.. +++.|-...|=++
T Consensus 2 klvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~M--n~~l~~v~~t~~~----~-----pv~l---~~lsirgnniRy~ 67 (109)
T KOG3428|consen 2 KLVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQM--NTHLKHVKMTVKG----E-----PVRL---DTLSIRGNNIRYY 67 (109)
T ss_pred hHHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhh--eeEEEEEEEecCC----C-----ceeE---EEEEeecceEEEE
Confidence 37788999999999999999999999999988754 3667766665442 1 1222 6777788888777
Q ss_pred EEcc
Q 045896 145 IAKD 148 (520)
Q Consensus 145 ~Akd 148 (520)
...|
T Consensus 68 ~lpD 71 (109)
T KOG3428|consen 68 ILPD 71 (109)
T ss_pred EccC
Confidence 7654
No 35
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=83.68 E-value=3.9 Score=36.14 Aligned_cols=43 Identities=19% Similarity=0.292 Sum_probs=33.7
Q ss_pred HHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecC
Q 045896 69 LASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKD 113 (520)
Q Consensus 69 l~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~ 113 (520)
++-.+||+.|.|.+||+--+.|++|++++= +-+-|...+.+..
T Consensus 6 fFkslvg~~V~VeLKnd~~i~GtL~svDqy--LNlkL~di~v~d~ 48 (96)
T KOG3448|consen 6 FFKSLVGKEVVVELKNDLSICGTLHSVDQY--LNLKLTDISVTDP 48 (96)
T ss_pred HHHHhcCCeEEEEEcCCcEEEEEecccchh--heeEEeeeEeeCc
Confidence 567799999999999999999999999873 2344555555544
No 36
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=82.29 E-value=3.5 Score=35.19 Aligned_cols=48 Identities=27% Similarity=0.328 Sum_probs=36.0
Q ss_pred HHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCC
Q 045896 69 LASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRG 118 (520)
Q Consensus 69 l~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g 118 (520)
++..|+|++|.|.+|=|..|.|.+.+.+.= |-+-|-.|...-++...+
T Consensus 12 FL~~l~gk~V~vkLKwg~eYkG~LvsvD~Y--mNlqL~~~eE~idG~~~g 59 (79)
T KOG3482|consen 12 FLNGLTGKPVLVKLKWGQEYKGTLVSVDNY--MNLQLANAEEYIDGVSTG 59 (79)
T ss_pred HHhhccCCeEEEEEecCcEEEEEEEEecch--hheehhhhhhhhcccccc
Confidence 467799999999999999999999997653 335566666544544443
No 37
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=81.64 E-value=3.8 Score=34.22 Aligned_cols=39 Identities=31% Similarity=0.432 Sum_probs=31.5
Q ss_pred HHHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeee
Q 045896 66 LLYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMA 108 (520)
Q Consensus 66 Llyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~A 108 (520)
+.-.+..+||+.|.|++.-|.+ .|+|..+.|| . |+|...
T Consensus 12 vyq~lq~liG~~vvV~T~~g~v-~G~L~~V~pD--h-Ivl~~~ 50 (66)
T PF10842_consen 12 VYQTLQSLIGQRVVVQTTRGSV-RGILVDVKPD--H-IVLEEN 50 (66)
T ss_pred HHHHHHHhcCCEEEEEEcCCcE-EEEEEeecCC--E-EEEEeC
Confidence 4456677999999999998887 9999999996 2 566553
No 38
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=77.14 E-value=5.2 Score=30.58 Aligned_cols=31 Identities=23% Similarity=0.485 Sum_probs=25.7
Q ss_pred cCceEEEEEecCCEEEEEEeecCCCCCeeEEEee
Q 045896 74 IGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKM 107 (520)
Q Consensus 74 IG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~ 107 (520)
+|++|.|.+ ++..++|++..++.++. ++|+.
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~--L~v~~ 32 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGA--LLVRT 32 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSE--EEEEE
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCE--EEEEE
Confidence 799999999 77888999999998764 55554
No 39
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=72.87 E-value=8.7 Score=31.61 Aligned_cols=35 Identities=20% Similarity=0.135 Sum_probs=29.1
Q ss_pred ccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeee
Q 045896 73 LIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMA 108 (520)
Q Consensus 73 LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~A 108 (520)
.||..|.+.+..|..++|-+-+++....+ +|||.+
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~-lIlk~~ 38 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKM-LILKCP 38 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcE-EEEECc
Confidence 68999999999999999999998876444 556653
No 40
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=72.86 E-value=20 Score=30.79 Aligned_cols=41 Identities=10% Similarity=0.096 Sum_probs=31.3
Q ss_pred HHhccCc--eEEEEEe--cCCEEEEEEeecCCCCCeeEEEeeeEeec
Q 045896 70 ASCLIGL--SVEVQVK--GGSVYAGIFHATSDEKDFGVILKMARLIK 112 (520)
Q Consensus 70 ~t~LIG~--~VeVtvk--dGsvYeGIF~t~S~~~dfgVVLK~Ar~vk 112 (520)
+-.++.. +|.|.++ +|..|.|+|.+++.-. -+||.-|.+..
T Consensus 11 l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~m--NlvL~d~~E~~ 55 (79)
T cd01718 11 IFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYM--NLVLDDAEEVH 55 (79)
T ss_pred HHHHHccCcEEEEEEEeCCCcEEEEEEEEEccce--eEEEcCEEEEe
Confidence 3345555 6777777 9999999999998853 48999987654
No 41
>PF07073 ROF: Modulator of Rho-dependent transcription termination (ROF); InterPro: IPR009778 This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo [].; PDB: 1SG5_A.
Probab=70.11 E-value=4.3 Score=34.88 Aligned_cols=38 Identities=21% Similarity=0.370 Sum_probs=24.1
Q ss_pred HHhccCceEEEEEecCCEEEEEEeecCC--CCCeeEEEee
Q 045896 70 ASCLIGLSVEVQVKGGSVYAGIFHATSD--EKDFGVILKM 107 (520)
Q Consensus 70 ~t~LIG~~VeVtvkdGsvYeGIF~t~S~--~~dfgVVLK~ 107 (520)
++||-+.+|.|+++||..++|+...+-. ++.-.++|..
T Consensus 12 iAC~~~~~v~L~l~dG~~~~g~A~dt~~~~~k~E~L~l~~ 51 (80)
T PF07073_consen 12 IACMYRYPVKLTLKDGEQIEGKALDTRTNAKKEECLVLEQ 51 (80)
T ss_dssp HHHTTTT-EEEE-TTT--EEESS-EEE---SSS-EEEEEE
T ss_pred HHHhcCCeEEEEEeCCCEEEEEEEEEEEecCceEEEEEec
Confidence 7899999999999999999999888643 3433455443
No 42
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=68.01 E-value=9.4 Score=37.05 Aligned_cols=36 Identities=17% Similarity=0.218 Sum_probs=27.2
Q ss_pred HHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEe
Q 045896 69 LASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILK 106 (520)
Q Consensus 69 l~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK 106 (520)
.++.+||++|.|++.| ..|.|.+.|++|-.. .|||-
T Consensus 11 ~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~-siVL~ 46 (166)
T PF06372_consen 11 EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSA-SIVLV 46 (166)
T ss_dssp HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT---EEEE
T ss_pred HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCC-eEEEE
Confidence 3567999999999999 999999999999754 34443
No 43
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=64.94 E-value=25 Score=29.63 Aligned_cols=55 Identities=22% Similarity=0.341 Sum_probs=38.7
Q ss_pred HHhccCceEEEEEe---cCC-EEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEE
Q 045896 70 ASCLIGLSVEVQVK---GGS-VYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVI 145 (520)
Q Consensus 70 ~t~LIG~~VeVtvk---dGs-vYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~ 145 (520)
+...+|..|.|+++ +|. .|.|++..++.+ .|+|..-. +. ...++.|+..||....
T Consensus 20 ~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~---~v~l~~~~--~~----------------~~~~~~i~~~~I~ka~ 78 (83)
T cd01734 20 FERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD---TVTLEVDI--KT----------------RGKTVEIPLDKIAKAR 78 (83)
T ss_pred HHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC---EEEEEEec--CC----------------CCeEEEEEhHHeeEEE
Confidence 46889999999998 664 799999998774 36665310 00 0146888888887664
No 44
>PRK02001 hypothetical protein; Validated
Probab=61.98 E-value=33 Score=32.75 Aligned_cols=73 Identities=15% Similarity=0.151 Sum_probs=44.6
Q ss_pred cCccchhHHHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeC
Q 045896 59 AVSSHDKLLYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPS 138 (520)
Q Consensus 59 ~s~~~dRLlyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~ 138 (520)
.+|+...- -+...+|+.|.|++.++..|.|++..++-+ .|+|..-...+++...+. ++..+.+.|+.
T Consensus 76 dRpL~~~~--~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~---~i~l~~~~~~~~~~~k~~--------~~~~~~~~i~~ 142 (152)
T PRK02001 76 TSPLKVPR--QYKKNIGRELEVLTKNGKKIEGELKSADEN---DITLEVKAREPKEGGKGK--------VTVEKEETITY 142 (152)
T ss_pred CCcCCCHH--HHHHhCCCEEEEEECCCCEEEEEEEEEeCC---EEEEEEcccccccccccc--------cccceeEEEEh
Confidence 45544322 245789999999999999999999998754 366653222211100011 11125677887
Q ss_pred CCcEEE
Q 045896 139 SELVQV 144 (520)
Q Consensus 139 kDIVqV 144 (520)
.+|...
T Consensus 143 ~~I~ka 148 (152)
T PRK02001 143 DDIKEA 148 (152)
T ss_pred HheeeE
Confidence 777654
No 45
>PRK14638 hypothetical protein; Provisional
Probab=61.45 E-value=24 Score=33.39 Aligned_cols=43 Identities=12% Similarity=0.136 Sum_probs=32.0
Q ss_pred cCccchhHHHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEe
Q 045896 59 AVSSHDKLLYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILK 106 (520)
Q Consensus 59 ~s~~~dRLlyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK 106 (520)
.+|+...- -+...+|+.|.|+++++..|.|++..++.+ .|+|.
T Consensus 86 dRpL~~~~--~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~---~i~l~ 128 (150)
T PRK14638 86 DRPLRGPK--DYVRFTGKLAKIVTKDGKTFIGRIESFVDG---TITIS 128 (150)
T ss_pred CCCCCCHH--HHHHhCCCEEEEEECCCcEEEEEEEEEeCC---EEEEE
Confidence 55554322 245889999999999999999999998753 35553
No 46
>PRK14642 hypothetical protein; Provisional
Probab=56.80 E-value=42 Score=33.47 Aligned_cols=71 Identities=14% Similarity=0.155 Sum_probs=44.3
Q ss_pred HHHhccCceEEEEEe-------------cCCEEEEEEeecCCCCCeeEEEeeeEe-e-cCCCCCCCCcccccccCCCCCc
Q 045896 69 LASCLIGLSVEVQVK-------------GGSVYAGIFHATSDEKDFGVILKMARL-I-KDGNFRGQKTVAEFVSKPPSKN 133 (520)
Q Consensus 69 l~t~LIG~~VeVtvk-------------dGsvYeGIF~t~S~~~dfgVVLK~Ar~-v-k~~s~~g~k~~~e~vsk~~~eT 133 (520)
=+...||..|.|+++ +...|+|+|..++.+ +|.|.+... . +.+...+.+ ... .+.+.
T Consensus 94 df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~---~i~l~~~~~~~~k~g~~~~k~-~~~----~~~~~ 165 (197)
T PRK14642 94 DFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG---GWQIVWSDEPPVKPGQRVSKK-RVP----APLQA 165 (197)
T ss_pred HHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC---EEEEEEeecccCCCccccccc-ccc----cccee
Confidence 367789999999998 678999999998653 465654322 1 111100100 000 11257
Q ss_pred eeEeCCCcEEEEEc
Q 045896 134 FIIPSSELVQVIAK 147 (520)
Q Consensus 134 LII~~kDIVqV~Ak 147 (520)
+-|+..+|-....+
T Consensus 166 ~~~~~~eik~a~l~ 179 (197)
T PRK14642 166 LGFTLDELREARLA 179 (197)
T ss_pred EEeehhheeeEEEE
Confidence 88999998877654
No 47
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=52.18 E-value=60 Score=28.52 Aligned_cols=57 Identities=7% Similarity=0.142 Sum_probs=37.9
Q ss_pred eEEEEEecC--CEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEE
Q 045896 77 SVEVQVKGG--SVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVI 145 (520)
Q Consensus 77 ~VeVtvkdG--svYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~ 145 (520)
+|.|.++++ ..|+|+|.+++.- +-|||.-|.++.... ..+ . .-..++|....|+.|.
T Consensus 28 ~V~i~l~~~~~r~~~G~L~gfD~~--mNlVL~d~~E~~~~~--~~~--~------~lG~ilIRGnnV~~I~ 86 (89)
T PTZ00138 28 RVQIWLYDHPNLRIEGKILGFDEY--MNMVLDDAEEVYTKK--NTR--K------DLGRILLKGDNITLIM 86 (89)
T ss_pred EEEEEEEeCCCcEEEEEEEEEccc--ceEEEccEEEEecCC--cee--e------EcCeEEEcCCEEEEEE
Confidence 566777674 7799999999885 349999998764311 010 0 1145777787777764
No 48
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=45.61 E-value=82 Score=28.97 Aligned_cols=64 Identities=22% Similarity=0.315 Sum_probs=41.5
Q ss_pred ccCceEEEEEecCCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcEEEEEccc
Q 045896 73 LIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELVQVIAKDV 149 (520)
Q Consensus 73 LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIVqV~AkdV 149 (520)
.-|+-|.|.+++|++|.|-+.-+.... -+.|...-.+.. .+..+. -+.+.|..+-|--++..|+
T Consensus 13 aqGhIVt~Et~tGe~YRGkliEaeDnm--Ncql~di~vT~~---dg~vs~--------le~V~IRGS~IRFlvlPdm 76 (119)
T KOG3172|consen 13 AQGHIVTVETKTGEVYRGKLIEAEDNM--NCQLRDITVTAR---DGRVSQ--------LEQVFIRGSKIRFLVLPDM 76 (119)
T ss_pred ccCcEEEEEecCCceeeeeeEEecccc--ccEEEEEEEEcc---CCccee--------eeeEEEecCeEEEEECchH
Confidence 469999999999999999999876543 244444333222 111111 1566777777777776655
No 49
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=43.47 E-value=34 Score=31.44 Aligned_cols=36 Identities=22% Similarity=0.451 Sum_probs=26.0
Q ss_pred HHhccCceEEEEEe----cCCEEEEEEeecCCCCCeeEEEeee
Q 045896 70 ASCLIGLSVEVQVK----GGSVYAGIFHATSDEKDFGVILKMA 108 (520)
Q Consensus 70 ~t~LIG~~VeVtvk----dGsvYeGIF~t~S~~~dfgVVLK~A 108 (520)
+...||..|.|+++ +...|.|++..++.+ .|+|+..
T Consensus 82 ~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~---~i~l~~~ 121 (141)
T PF02576_consen 82 FERFIGRKVKVKLKQPVNGRKEFEGKLLEVDED---EITLEVE 121 (141)
T ss_dssp HHHH-SEEEEEE-SS-SSS-SEEEEEEEEEETT---EEEEEEE
T ss_pred HHHhcCCeEEEEEeccCCCcEEEEEEEEEEeCC---EEEEEEC
Confidence 56889999999994 446799999998874 3777553
No 50
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=35.79 E-value=83 Score=26.01 Aligned_cols=31 Identities=19% Similarity=0.344 Sum_probs=26.1
Q ss_pred cCceEEEEEecCCEEEEEEeecCCCCCeeEEEee
Q 045896 74 IGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKM 107 (520)
Q Consensus 74 IG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~ 107 (520)
-..+|.|.+.||-+..|...+++. |.|.|..
T Consensus 10 ~~~~Vtv~L~NG~~l~G~I~~fD~---ftVll~~ 40 (61)
T cd01716 10 EKIPVTIYLVNGVQLKGQIESFDN---FTVLLES 40 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEcc---eEEEEEE
Confidence 356899999999999999999886 6677764
No 51
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=34.33 E-value=68 Score=30.55 Aligned_cols=28 Identities=29% Similarity=0.378 Sum_probs=25.2
Q ss_pred HHhccCceEEEEEecCCEEEEEEeecCC
Q 045896 70 ASCLIGLSVEVQVKGGSVYAGIFHATSD 97 (520)
Q Consensus 70 ~t~LIG~~VeVtvkdGsvYeGIF~t~S~ 97 (520)
...|||+.|.++..+|..+.|+..++..
T Consensus 87 a~slVGk~V~~~~~~g~~~tG~V~~V~~ 114 (142)
T PRK09618 87 YSELIGKEVEWEGEDGEIVSGTVTSVKQ 114 (142)
T ss_pred HHHHhCCEEEEEeCCCCEEEEEEEEEEE
Confidence 4579999999999999999999999874
No 52
>PRK14639 hypothetical protein; Provisional
Probab=33.55 E-value=74 Score=29.79 Aligned_cols=34 Identities=21% Similarity=0.308 Sum_probs=28.6
Q ss_pred HHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEe
Q 045896 70 ASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILK 106 (520)
Q Consensus 70 ~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK 106 (520)
+...+|..|.|++.++..|.|++..++-+ .|+|.
T Consensus 83 f~r~~G~~v~v~l~~~~~~~G~L~~~~~~---~i~l~ 116 (140)
T PRK14639 83 FAKSIGELVKITTNEKEKFEGKIVSVDDE---NITLE 116 (140)
T ss_pred HHHhCCCEEEEEECCCcEEEEEEEEEeCC---EEEEE
Confidence 56899999999999999999999998764 35553
No 53
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=33.49 E-value=91 Score=25.83 Aligned_cols=31 Identities=23% Similarity=0.385 Sum_probs=26.0
Q ss_pred ccCceEEEEEecCCEEEEEEeecCCCCCeeEEEe
Q 045896 73 LIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILK 106 (520)
Q Consensus 73 LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK 106 (520)
--..+|.|.+.||-+..|+..+++. |.|.|+
T Consensus 13 ~~~~~Vti~L~nG~~l~G~I~~fD~---ftVll~ 43 (61)
T TIGR02383 13 KERIPVTVFLVNGVQLKGVIESFDN---FTVLLE 43 (61)
T ss_pred HcCCcEEEEEeCCcEEEEEEEEEee---eEEEEE
Confidence 3467899999999999999999876 666665
No 54
>PRK14644 hypothetical protein; Provisional
Probab=33.31 E-value=76 Score=29.68 Aligned_cols=42 Identities=17% Similarity=0.215 Sum_probs=33.3
Q ss_pred cCccchhHHHHHHhccCceEEEEEecC----CEEEEEEeecCCCCCeeEEEe
Q 045896 59 AVSSHDKLLYLASCLIGLSVEVQVKGG----SVYAGIFHATSDEKDFGVILK 106 (520)
Q Consensus 59 ~s~~~dRLlyl~t~LIG~~VeVtvkdG----svYeGIF~t~S~~~dfgVVLK 106 (520)
.+|+..+ + +...||..|.|++++. ..|.|++..++.+ .|+|.
T Consensus 72 dRpL~~~--~-f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~---~i~l~ 117 (136)
T PRK14644 72 DMDYETD--E-LENHIGEIIDVSLNKEVNKTDFITGELLENNPE---TITLK 117 (136)
T ss_pred CCCCCHH--H-HHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC---EEEEE
Confidence 6777642 4 6788999999999988 8899999998764 36665
No 55
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=31.99 E-value=95 Score=27.02 Aligned_cols=34 Identities=18% Similarity=0.220 Sum_probs=28.1
Q ss_pred HhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEee
Q 045896 71 SCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKM 107 (520)
Q Consensus 71 t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~ 107 (520)
..--+.+|.|.+.||-+..|+..+++. |.|.|..
T Consensus 15 lr~~~~~VtifL~NG~~l~G~I~~fD~---ftVll~~ 48 (79)
T PRK00395 15 LRKERVPVTIYLVNGIKLQGQIESFDN---FVVLLRN 48 (79)
T ss_pred HHHcCCCEEEEEeCCcEEEEEEEEEcc---EEEEEEE
Confidence 345678999999999999999999876 7777753
No 56
>PRK14641 hypothetical protein; Provisional
Probab=28.23 E-value=1.7e+02 Score=28.54 Aligned_cols=40 Identities=15% Similarity=0.151 Sum_probs=28.9
Q ss_pred HHHhccCceEEEEEec----CCEEEEEEeecCCCC--CeeEEEeee
Q 045896 69 LASCLIGLSVEVQVKG----GSVYAGIFHATSDEK--DFGVILKMA 108 (520)
Q Consensus 69 l~t~LIG~~VeVtvkd----GsvYeGIF~t~S~~~--dfgVVLK~A 108 (520)
-+...+|+.|.|++++ ...|.|++..++.+. +-.|+|...
T Consensus 98 ~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~~~~~~~~~v~~~~~ 143 (173)
T PRK14641 98 QYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVSLTEGEGASIVLKPE 143 (173)
T ss_pred HHHHhCCCEEEEEEecccCCeEEEEEEEEeeecccCCCCcEEEEec
Confidence 3678999999999976 447999999997432 234555443
No 57
>PRK14643 hypothetical protein; Provisional
Probab=27.21 E-value=1.6e+02 Score=28.32 Aligned_cols=29 Identities=14% Similarity=0.051 Sum_probs=24.5
Q ss_pred HHhccCceEEEEEec----CCEEEEEEeecCCC
Q 045896 70 ASCLIGLSVEVQVKG----GSVYAGIFHATSDE 98 (520)
Q Consensus 70 ~t~LIG~~VeVtvkd----GsvYeGIF~t~S~~ 98 (520)
+...+|..|.|+++. ...|.|++..++-+
T Consensus 99 f~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 99 LVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred HHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 457889999999976 57899999999765
No 58
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=26.09 E-value=1.1e+02 Score=30.49 Aligned_cols=27 Identities=15% Similarity=0.106 Sum_probs=23.7
Q ss_pred HhccCceEEEEEecCCEEEEEEeecCC
Q 045896 71 SCLIGLSVEVQVKGGSVYAGIFHATSD 97 (520)
Q Consensus 71 t~LIG~~VeVtvkdGsvYeGIF~t~S~ 97 (520)
..|||+.|.+.-.+|..+.|+..++..
T Consensus 114 ~slIGK~V~~~~~dG~~vtG~V~sV~~ 140 (190)
T PRK06792 114 MKFLGKYVRGVSNDGKQVTGQVETVRL 140 (190)
T ss_pred HHhcCcEEEEEcCCCCEEEEEEEEEEE
Confidence 468999999988899999999998764
No 59
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=25.61 E-value=2e+02 Score=24.99 Aligned_cols=41 Identities=22% Similarity=0.242 Sum_probs=33.0
Q ss_pred chhHHHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEee
Q 045896 63 HDKLLYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILKM 107 (520)
Q Consensus 63 ~dRLlyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~ 107 (520)
-|.+++. ...-+-+|.|.+.||-+..|...+++. |.|.|+.
T Consensus 8 QD~fLn~-~Rk~~i~VtIfLvNG~~L~G~V~sfD~---f~VlL~~ 48 (77)
T COG1923 8 QDPFLNA-LRKEKIPVTIFLVNGFKLQGQVESFDN---FVVLLKN 48 (77)
T ss_pred chHHHHH-HHhcCCeEEEEEEcCEEEEEEEEeeee---EEEEEEc
Confidence 4666663 346788999999999999999999876 7777765
No 60
>PRK11625 Rho-binding antiterminator; Provisional
Probab=24.40 E-value=1.2e+02 Score=26.61 Aligned_cols=27 Identities=19% Similarity=0.278 Sum_probs=24.1
Q ss_pred HHhccCceEEEEEecCCEEEEEEeecC
Q 045896 70 ASCLIGLSVEVQVKGGSVYAGIFHATS 96 (520)
Q Consensus 70 ~t~LIG~~VeVtvkdGsvYeGIF~t~S 96 (520)
+.|+-+.+|.++++||...+|+...+-
T Consensus 18 lAC~~~~~l~l~l~dGe~~~g~A~D~~ 44 (84)
T PRK11625 18 LACQHHLMLTLELKDGEVLQAKASDLV 44 (84)
T ss_pred HHHhcCCeEEEEECCCCEEEEEEEeee
Confidence 677899999999999999999987754
No 61
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=23.65 E-value=1.2e+02 Score=28.82 Aligned_cols=28 Identities=21% Similarity=0.302 Sum_probs=24.2
Q ss_pred HHhccCceEEEEEecCCEEEEEEeecCC
Q 045896 70 ASCLIGLSVEVQVKGGSVYAGIFHATSD 97 (520)
Q Consensus 70 ~t~LIG~~VeVtvkdGsvYeGIF~t~S~ 97 (520)
...|||+.|.....+|..+.|+..++..
T Consensus 88 a~~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 88 AVNFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HHHhhCceeEEEecCCCEEEEEEEEEEE
Confidence 4579999999888999999999987654
No 62
>PRK14633 hypothetical protein; Provisional
Probab=22.39 E-value=1.5e+02 Score=27.97 Aligned_cols=35 Identities=23% Similarity=0.504 Sum_probs=27.2
Q ss_pred HHhccCceEEEEEe----cCCEEEEEEeecCCCCCeeEEEee
Q 045896 70 ASCLIGLSVEVQVK----GGSVYAGIFHATSDEKDFGVILKM 107 (520)
Q Consensus 70 ~t~LIG~~VeVtvk----dGsvYeGIF~t~S~~~dfgVVLK~ 107 (520)
+...+|+.|.|+++ ++..|.|++..++.+ .|.|..
T Consensus 89 f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~---~i~l~~ 127 (150)
T PRK14633 89 AQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN---NVILNL 127 (150)
T ss_pred HHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC---EEEEEE
Confidence 56889999999984 567899999998664 355643
No 63
>TIGR02603 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).
Probab=22.39 E-value=1.3e+02 Score=27.36 Aligned_cols=30 Identities=30% Similarity=0.482 Sum_probs=22.8
Q ss_pred ceEEEEEecCCEEEEEEeecCCCCCeeEEEeee
Q 045896 76 LSVEVQVKGGSVYAGIFHATSDEKDFGVILKMA 108 (520)
Q Consensus 76 ~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK~A 108 (520)
..+.|+++||.++.|++..-+. ..|+|+.+
T Consensus 58 ~~~~v~~~dG~~~~G~~~~e~~---~~~~l~~~ 87 (133)
T TIGR02603 58 EAYRVTLKDGRILSGIVASETA---DGVTVKMP 87 (133)
T ss_pred ccEEEEECCCCEEEEEEEecCC---CeEEEEcC
Confidence 3479999999999999988443 34667653
No 64
>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris. The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions []. ; PDB: 2E12_B.
Probab=22.33 E-value=1.4e+02 Score=27.03 Aligned_cols=31 Identities=32% Similarity=0.395 Sum_probs=26.1
Q ss_pred hhHHHHHHhccCc-eEEEEEecCCEEEEEEee
Q 045896 64 DKLLYLASCLIGL-SVEVQVKGGSVYAGIFHA 94 (520)
Q Consensus 64 dRLlyl~t~LIG~-~VeVtvkdGsvYeGIF~t 94 (520)
.||-+++.-|=|+ +|+++++||++..|++..
T Consensus 16 a~LE~lv~~L~ge~~V~l~L~DGs~l~Gtv~v 47 (101)
T PF11607_consen 16 ARLEHLVSELDGEERVELELDDGSMLRGTVAV 47 (101)
T ss_dssp HHHHHHHHCTTTT-EEEEEETTS-EEEEEECC
T ss_pred HHHHHHHhhcCCcceEEEEEcCCCeeeeeecc
Confidence 5788888888886 689999999999999865
No 65
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=21.49 E-value=1e+02 Score=26.98 Aligned_cols=28 Identities=21% Similarity=0.367 Sum_probs=24.5
Q ss_pred HHhccCceEEEEEecCCEEEEEEeecCC
Q 045896 70 ASCLIGLSVEVQVKGGSVYAGIFHATSD 97 (520)
Q Consensus 70 ~t~LIG~~VeVtvkdGsvYeGIF~t~S~ 97 (520)
+.|+--.++.+++|+|.+|+|.-..+-.
T Consensus 18 lACl~hl~l~L~lkdGev~~a~A~d~~~ 45 (84)
T COG4568 18 LACLHHLPLTLELKDGEVLQAKASDLQR 45 (84)
T ss_pred HHHhhhceEEEEEcCCeEEEEEehhhhh
Confidence 6788899999999999999999877643
No 66
>PRK14640 hypothetical protein; Provisional
Probab=20.73 E-value=1.7e+02 Score=27.63 Aligned_cols=34 Identities=15% Similarity=0.329 Sum_probs=26.8
Q ss_pred HHhccCceEEEEEe----cCCEEEEEEeecCCCCCeeEEEe
Q 045896 70 ASCLIGLSVEVQVK----GGSVYAGIFHATSDEKDFGVILK 106 (520)
Q Consensus 70 ~t~LIG~~VeVtvk----dGsvYeGIF~t~S~~~dfgVVLK 106 (520)
+...+|+.|.|+++ ++..|.|++..++-+ .|+|.
T Consensus 92 f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~---~v~l~ 129 (152)
T PRK14640 92 FEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD---MITLT 129 (152)
T ss_pred HHHhCCCeEEEEEecccCCceEEEEEEEEEeCC---EEEEE
Confidence 56899999999994 668899999998643 35554
No 67
>PRK14645 hypothetical protein; Provisional
Probab=20.20 E-value=1.7e+02 Score=27.88 Aligned_cols=42 Identities=19% Similarity=0.227 Sum_probs=29.9
Q ss_pred cCccchhHHHHHHhccCceEEEEEecCCEEEEEEeecCCCCCeeEEEe
Q 045896 59 AVSSHDKLLYLASCLIGLSVEVQVKGGSVYAGIFHATSDEKDFGVILK 106 (520)
Q Consensus 59 ~s~~~dRLlyl~t~LIG~~VeVtvkdGsvYeGIF~t~S~~~dfgVVLK 106 (520)
.+|+... .-+...+|..|.|++ ++..|.|++..++.+ .|+|.
T Consensus 88 dRpL~~~--~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~---~i~l~ 129 (154)
T PRK14645 88 KRPLFTA--RHFERFAGLKAKVRG-PGENFTGRIKAVSGD---QVTFD 129 (154)
T ss_pred CCCCCCH--HHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC---EEEEE
Confidence 4554332 235578999999975 889999999998653 35554
No 68
>PRK14632 hypothetical protein; Provisional
Probab=20.11 E-value=1.9e+02 Score=28.01 Aligned_cols=60 Identities=12% Similarity=0.140 Sum_probs=39.5
Q ss_pred HHhccCceEEEEEec-------CCEEEEEEeecCCCCCeeEEEeeeEeecCCCCCCCCcccccccCCCCCceeEeCCCcE
Q 045896 70 ASCLIGLSVEVQVKG-------GSVYAGIFHATSDEKDFGVILKMARLIKDGNFRGQKTVAEFVSKPPSKNFIIPSSELV 142 (520)
Q Consensus 70 ~t~LIG~~VeVtvkd-------GsvYeGIF~t~S~~~dfgVVLK~Ar~vk~~s~~g~k~~~e~vsk~~~eTLII~~kDIV 142 (520)
+...||+.|.|++++ ...|.|++..++-+ .|+|..-. +. +.+ ....++.|+..+|.
T Consensus 93 f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~---~i~l~~~~--~~----~~~--------~~~~~~~i~~~~I~ 155 (172)
T PRK14632 93 MSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD---TVVLRPEG--AP----APE--------AEEAVLRTSWQGVR 155 (172)
T ss_pred HHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC---EEEEEEcC--cc----ccc--------CCceeEEEEhHHcc
Confidence 568999999999986 56899999998643 36665310 10 000 01146788888887
Q ss_pred EEEE
Q 045896 143 QVIA 146 (520)
Q Consensus 143 qV~A 146 (520)
.+..
T Consensus 156 ka~l 159 (172)
T PRK14632 156 KANL 159 (172)
T ss_pred EEEE
Confidence 7654
Done!