Query 038314
Match_columns 565
No_of_seqs 127 out of 214
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 09:44:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038314.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038314hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5180 PBP1 Protein interacti 99.9 1.8E-26 3.9E-31 243.3 6.5 169 33-215 34-234 (654)
2 KOG2375 Protein interacting wi 99.8 6.1E-20 1.3E-24 203.7 20.3 183 17-201 52-272 (756)
3 PF14438 SM-ATX: Ataxin 2 SM d 99.8 4.2E-21 9.2E-26 158.9 5.3 75 22-96 1-77 (77)
4 PF06741 LsmAD: LsmAD domain; 99.7 9.5E-19 2.1E-23 146.1 3.8 48 152-201 1-49 (72)
5 KOG2375 Protein interacting wi 98.1 5.4E-05 1.2E-09 86.2 16.4 177 20-201 223-421 (756)
6 cd01733 LSm10 The eukaryotic S 97.4 0.0008 1.7E-08 57.2 8.4 68 24-99 10-77 (78)
7 cd01726 LSm6 The eukaryotic Sm 97.2 0.0013 2.7E-08 54.0 7.4 63 27-97 4-66 (67)
8 cd01724 Sm_D1 The eukaryotic S 97.2 0.0016 3.4E-08 56.9 8.0 72 23-102 1-72 (90)
9 cd00600 Sm_like The eukaryotic 97.1 0.0013 2.7E-08 52.0 6.0 61 29-97 2-62 (63)
10 PF01423 LSM: LSM domain ; In 97.1 0.0021 4.5E-08 51.7 7.3 65 27-98 2-66 (67)
11 PF12701 LSM14: Scd6-like Sm d 97.0 0.0029 6.4E-08 56.1 8.2 73 29-102 4-79 (96)
12 cd01725 LSm2 The eukaryotic Sm 97.0 0.0044 9.5E-08 52.9 8.8 71 25-101 3-73 (81)
13 cd06168 LSm9 The eukaryotic Sm 97.0 0.0041 8.9E-08 52.7 8.1 70 28-99 5-74 (75)
14 cd01722 Sm_F The eukaryotic Sm 97.0 0.0044 9.6E-08 51.0 8.0 63 27-97 5-67 (68)
15 cd01721 Sm_D3 The eukaryotic S 96.9 0.0043 9.4E-08 51.5 7.9 66 27-100 4-69 (70)
16 PRK00737 small nuclear ribonuc 96.9 0.0032 6.8E-08 52.5 6.9 68 23-98 4-71 (72)
17 smart00651 Sm snRNP Sm protein 96.8 0.0039 8.4E-08 50.0 6.6 64 28-98 3-66 (67)
18 cd01731 archaeal_Sm1 The archa 96.8 0.0049 1.1E-07 50.5 7.2 64 27-98 4-67 (68)
19 cd01736 LSm14_N LSm14 (also kn 96.7 0.0046 1E-07 52.9 6.5 68 29-97 2-73 (74)
20 PF07145 PAM2: Ataxin-2 C-term 96.6 0.00081 1.7E-08 43.5 1.1 18 344-361 1-18 (18)
21 cd01723 LSm4 The eukaryotic Sm 96.6 0.0098 2.1E-07 50.0 7.6 69 25-101 3-72 (76)
22 COG1958 LSM1 Small nuclear rib 96.5 0.0095 2.1E-07 50.2 7.2 71 22-98 6-78 (79)
23 cd01717 Sm_B The eukaryotic Sm 96.4 0.014 3E-07 49.3 7.5 70 28-99 5-78 (79)
24 cd01719 Sm_G The eukaryotic Sm 96.0 0.027 6E-07 47.2 7.2 65 28-100 5-69 (72)
25 KOG1073 Uncharacterized mRNA-a 95.8 0.014 3.1E-07 62.4 5.8 74 27-101 3-80 (361)
26 PF11095 Gemin7: Gem-associate 95.5 0.15 3.1E-06 44.5 9.6 70 19-100 10-79 (80)
27 cd01729 LSm7 The eukaryotic Sm 95.1 0.12 2.5E-06 44.4 7.9 69 28-98 7-77 (81)
28 cd01728 LSm1 The eukaryotic Sm 95.0 0.11 2.3E-06 44.1 7.2 65 28-97 7-71 (74)
29 cd01732 LSm5 The eukaryotic Sm 94.8 0.17 3.7E-06 43.1 7.9 68 27-99 7-74 (76)
30 cd01727 LSm8 The eukaryotic Sm 94.5 0.16 3.5E-06 42.5 7.2 68 28-99 4-71 (74)
31 cd01730 LSm3 The eukaryotic Sm 94.0 0.32 7E-06 41.5 8.1 68 28-97 6-80 (82)
32 cd01720 Sm_D2 The eukaryotic S 93.4 0.47 1E-05 41.6 8.2 73 24-98 4-84 (87)
33 KOG1783 Small nuclear ribonucl 85.7 0.55 1.2E-05 40.5 2.1 65 27-99 10-74 (77)
34 KOG3293 Small nuclear ribonucl 83.6 1.1 2.4E-05 42.0 3.3 40 25-66 4-43 (134)
35 PF10842 DUF2642: Protein of u 78.2 6.4 0.00014 33.3 5.7 43 20-66 8-50 (66)
36 KOG3482 Small nuclear ribonucl 76.9 8.6 0.00019 33.4 6.2 63 27-97 12-74 (79)
37 cd01718 Sm_E The eukaryotic Sm 72.3 18 0.00038 31.5 7.1 62 29-97 12-77 (79)
38 KOG3448 Predicted snRNP core p 72.3 4.8 0.0001 36.1 3.7 41 27-69 6-46 (96)
39 KOG3428 Small nuclear ribonucl 70.5 24 0.00051 32.7 7.8 73 24-105 3-76 (109)
40 PF07073 ROF: Modulator of Rho 65.8 4.4 9.4E-05 35.3 2.1 29 28-56 12-40 (80)
41 PTZ00138 small nuclear ribonuc 64.2 25 0.00053 31.3 6.4 57 35-98 28-86 (89)
42 PF02237 BPL_C: Biotin protein 63.8 20 0.00044 27.7 5.2 32 32-66 2-33 (48)
43 PF06372 Gemin6: Gemin6 protei 61.9 14 0.0003 36.3 4.9 60 27-100 11-70 (166)
44 TIGR02603 CxxCH_TIGR02603 puta 50.8 13 0.00028 34.1 2.6 61 34-113 58-118 (133)
45 PRK14642 hypothetical protein; 47.2 93 0.002 31.4 8.1 87 10-104 79-184 (197)
46 cd01734 YlxS_C YxlS is a Bacil 45.0 1E+02 0.0022 26.3 7.0 69 12-98 6-78 (83)
47 cd01735 LSm12_N LSm12 belongs 42.3 80 0.0017 26.4 5.7 37 30-67 3-39 (61)
48 PRK02001 hypothetical protein; 40.0 1.4E+02 0.0031 28.8 7.8 50 10-64 69-118 (152)
49 PRK09618 flgD flagellar basal 37.0 67 0.0014 30.9 5.1 29 28-56 87-115 (142)
50 KOG1780 Small Nuclear ribonucl 35.7 88 0.0019 27.5 5.1 67 28-102 9-75 (77)
51 PRK14638 hypothetical protein; 34.3 72 0.0016 30.5 4.9 50 10-64 79-128 (150)
52 TIGR02383 Hfq RNA chaperone Hf 32.7 94 0.002 26.1 4.7 30 32-64 14-43 (61)
53 cd01716 Hfq Hfq, an abundant, 32.2 1E+02 0.0022 25.9 4.8 30 33-65 11-40 (61)
54 PRK11625 Rho-binding antitermi 30.7 1.1E+02 0.0023 27.2 5.0 33 21-55 13-45 (84)
55 PRK00395 hfq RNA-binding prote 29.9 1.1E+02 0.0023 27.1 4.8 43 18-64 5-47 (79)
56 PRK11911 flgD flagellar basal 29.4 1.7E+02 0.0037 28.2 6.4 28 28-55 88-115 (140)
57 KOG3168 U1 snRNP component [Tr 29.3 27 0.00059 34.6 1.2 81 28-110 9-93 (177)
58 PF11607 DUF3247: Protein of u 26.4 1.2E+02 0.0026 27.9 4.5 32 21-52 15-47 (101)
59 PRK14639 hypothetical protein; 25.8 1.3E+02 0.0027 28.6 4.9 49 10-63 67-115 (140)
60 PF14153 Spore_coat_CotO: Spor 25.6 2.9E+02 0.0062 27.7 7.5 64 18-101 117-184 (185)
61 COG4568 Rof Transcriptional an 25.1 74 0.0016 28.2 3.0 28 28-55 18-45 (84)
62 PLN03200 cellulose synthase-in 24.7 2E+02 0.0044 38.2 7.8 47 15-66 1962-2008(2102)
63 PF02576 DUF150: Uncharacteris 24.2 1.8E+02 0.0038 27.0 5.5 52 10-66 66-121 (141)
64 PRK14641 hypothetical protein; 23.7 1.6E+02 0.0035 29.0 5.4 56 10-67 83-144 (173)
65 PRK14644 hypothetical protein; 23.5 1.4E+02 0.003 28.3 4.7 49 10-64 65-117 (136)
66 KOG4264 Nucleo-cytoplasmic pro 23.2 2.1E+02 0.0045 33.3 6.7 55 472-529 558-623 (694)
67 PRK06792 flgD flagellar basal 23.1 1.6E+02 0.0034 29.9 5.2 29 28-56 113-141 (190)
68 COG1923 Hfq Uncharacterized ho 22.3 2.6E+02 0.0057 24.7 5.7 45 18-66 5-49 (77)
69 KOG3172 Small nuclear ribonucl 21.9 2.6E+02 0.0057 26.2 5.9 63 31-102 13-76 (119)
No 1
>COG5180 PBP1 Protein interacting with poly(A)-binding protein [RNA processing and modification]
Probab=99.93 E-value=1.8e-26 Score=243.27 Aligned_cols=169 Identities=14% Similarity=0.028 Sum_probs=119.5
Q ss_pred CceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeee-------------ecCceEEEE-
Q 038314 33 GLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVI-------------LSADLVQVV- 98 (565)
Q Consensus 33 G~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI-------------~~kDIVqV~- 98 (565)
|..|.+.+.|| +..+++|+ +.||+..+|....|.+....+......-+-+ ..+++-++.
T Consensus 34 GS~I~~~~Tn~------~~~~nlEs-i~vv~~nprV~~~gVs~s~sD~~t~~~~~sl~~~~en~~s~~gsa~~n~s~~rv 106 (654)
T COG5180 34 GSIIGAFLTNE------DGKVNLES-IDVVETNPRVVFPGVSISESDIITVTKMNSLQAEKENDASERGSAAKNDSGWRV 106 (654)
T ss_pred cceeeeeeecC------Cccceeee-eeeeecCCccccCccccccchhhhhhccchhhhhhcccccccccccccccccee
Confidence 88999999997 44456654 6788998888754443211100000000000 011111111
Q ss_pred -EcCccCCCCCCCCCCCCccccccccCCCCCCCCCc-----ccCCCCCCCchhhhhccccccccccCCCCCCCcccccCC
Q 038314 99 -AKGVQLPADGIAGNFAGDDVVAVAGTVPPIDGQIS-----EAKRPIRSGLNKRRNQKRISVRNENGYFHGDGPIKAEKE 172 (565)
Q Consensus 99 -AkdV~Ls~D~isg~~~gd~erELq~WvPDedd~~~-----eLE~sn~~WDQFevNEkrFGVq~kSTYDEnLYTTkLDKd 172 (565)
-.|| +|+++...-++|+|.+|.|+..+... +||+.+..||||++||++||| |++|||+|||++|||+
T Consensus 107 frTDv-----~ISg~~rE~keR~l~~w~p~p~aa~~~~~G~~le~d~~~WdQFa~NeKlFgV--kS~FDE~lYt~~idks 179 (654)
T COG5180 107 FRTDV-----EISGGPREIKERKLMPWAPLPKAADLEKSGKALEEDCKDWDQFAANEKLFGV--KSRFDEELYTEVIDKS 179 (654)
T ss_pred eeecc-----eecCCcchhhhhhhcccCCCccccCCccccchhhcccchHHHhhhhhhhcCc--cccccHHHHhhhhccC
Confidence 1111 34444444467899999998766433 477888899999999999999 9999999999999996
Q ss_pred -chHHHHHHHHHHHHhhhhcCCCCCCcccc-----------cccccccccccccc
Q 038314 173 -HEEQMLSLKNMRNAMEVEHGKRDRMDVTK-----------IEEASVDSVNGRQV 215 (565)
Q Consensus 173 -~~ykereaeAeRIArEIEss~t~NiHLaE-----------~eea~~~~~~grq~ 215 (565)
+.|++|+.+|+|||+|||.+.|.|+||+| +||-+.+.|+.|.+
T Consensus 180 ~p~Yk~k~qeA~RIaKEIe~s~TtniHiaEeRGl~~DDSGldeEDlYSgV~R~~d 234 (654)
T COG5180 180 SPSYKSKVQEARRIAKEIELSATTNIHIAEERGLGNDDSGLDEEDLYSGVVRRGD 234 (654)
T ss_pred ChhhHHHHHHHHHHHHHHhhccccchhhhhhcCccccccCcchhhhhhhhhhhHH
Confidence 58999999999999999999999999999 68888888887654
No 2
>KOG2375 consensus Protein interacting with poly(A)-binding protein [RNA processing and modification]
Probab=99.84 E-value=6.1e-20 Score=203.67 Aligned_cols=183 Identities=18% Similarity=0.135 Sum_probs=128.0
Q ss_pred CCChHHHHHHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccC-CCCCCCcC-CCCceeeeeeecCc-
Q 038314 17 SSSLSEALLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKK-GKSNANVA-NGTVIETLVILSAD- 93 (565)
Q Consensus 17 ~~sl~DRLlfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~-G~s~anv~-sg~i~eTLVI~~kD- 93 (565)
..+..|+|+|+++|.||..|.+++.+|..|.|||++++.+..++|+|+++-.... +....... .....+++.|+..|
T Consensus 52 ~~~~~~~~~~~~~~s~g~~~~~~l~ng~~~~gi~~s~N~~~~~gi~~~a~~~~~~~g~r~~~~r~~~~~~~~~~i~~~~~ 131 (756)
T KOG2375|consen 52 ENPSRDSLAYKATDSIGPSVAVLLGNGSSYSGILVSNNPEQTVGIILVAADAKRRSGTRGSESRDWMPDPPTAGIPLEDE 131 (756)
T ss_pred CCcchhhhhhhhcCCCCcccceeccCCCCCcceeeecchhhcccccccccccccccccccccccccccCCCcccCccccc
Confidence 4567899999999999999999999999999999999999988888888654332 11111111 12334566666554
Q ss_pred --eEEEEEcCccCCCCCC--------------CCCCC-----C-ccccc---cccCCCCCCCCCc------ccCCCCCCC
Q 038314 94 --LVQVVAKGVQLPADGI--------------AGNFA-----G-DDVVA---VAGTVPPIDGQIS------EAKRPIRSG 142 (565)
Q Consensus 94 --IVqV~AkdV~Ls~D~i--------------sg~~~-----g-d~erE---Lq~WvPDedd~~~------eLE~sn~~W 142 (565)
|+++.++.-.+..+.. +..+. + +.|++ |.+|++++.-..+ .||.++++|
T Consensus 132 ~eL~~~~~~~~~k~~~s~~~gv~~e~~~~~a~Ss~it~~~~~~~~~ee~~e~l~p~~~~e~v~~~~~~~~~rl~~~~kGw 211 (756)
T KOG2375|consen 132 LELTTSNAEQDEKATNSKSDGVQSEKPDEAAYSSFITDSEGKGDEGEEEAERLAPWIEDEVVPGGGIAEERRLENDNKGW 211 (756)
T ss_pred cchhhcccccchhhhcchhhccccccccccccccccccccccccccccchhhcCCCCcccccccccchhhcccccccCCC
Confidence 3333222222211111 11000 1 11222 4489887655322 277888999
Q ss_pred chhhhh---ccccccccccCCCCCCCcccccCCchHHHHHHHHHHHHhhhhcCCCCCC-cccc
Q 038314 143 LNKRRN---QKRISVRNENGYFHGDGPIKAEKEHEEQMLSLKNMRNAMEVEHGKRDRM-DVTK 201 (565)
Q Consensus 143 DQFevN---EkrFGVq~kSTYDEnLYTTkLDKd~~ykereaeAeRIArEIEss~t~Ni-HLaE 201 (565)
|||++| +++|+| ++||||++|||+||+...-.+..++|+|||+|||...++.. |++|
T Consensus 212 ~Qf~v~f~~~~~f~v--~stFde~ly~tk~d~~~kn~e~~e~a~Ria~ei~~~at~~~h~~ae 272 (756)
T KOG2375|consen 212 DQFEVNFHGSKKFNV--MSTFDEELYTTKLDKKVKNYEAYEGAERIAREIESLATSDAHHLAE 272 (756)
T ss_pred Cccchhhhhhhhhce--eeeeehhhhcceecccCCchhhHHHHHHhhccccccchhHHHHhhc
Confidence 999999 999999 99999999999999976555559999999999999988655 6666
No 3
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=99.83 E-value=4.2e-21 Score=158.94 Aligned_cols=75 Identities=36% Similarity=0.616 Sum_probs=50.9
Q ss_pred HHHHHHHHhccCceEEEEEccCCEEEEEEEeeccCC-CeeEEEeccccccCCCCC-CCcCCCCceeeeeeecCceEE
Q 038314 22 EALLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEK-DYGIVLKKAKMSKKGKSN-ANVANGTVIETLVILSADLVQ 96 (565)
Q Consensus 22 DRLlfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~-d~gVVLK~AR~i~~G~s~-anv~sg~i~eTLVI~~kDIVq 96 (565)
|||+|+++|+||++|+||++||++|||||+++++++ +++|+||+||++.++..+ .+..++++.++|+|+++||||
T Consensus 1 dRl~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv~ 77 (77)
T PF14438_consen 1 DRLVYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVVQ 77 (77)
T ss_dssp ---HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE------
T ss_pred ChHHHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccCC
Confidence 899999999999999999999999999999999988 999999999999876543 344567889999999999986
No 4
>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=99.74 E-value=9.5e-19 Score=146.11 Aligned_cols=48 Identities=15% Similarity=0.151 Sum_probs=46.5
Q ss_pred cccccccCCCCCCCcccccCCc-hHHHHHHHHHHHHhhhhcCCCCCCcccc
Q 038314 152 ISVRNENGYFHGDGPIKAEKEH-EEQMLSLKNMRNAMEVEHGKRDRMDVTK 201 (565)
Q Consensus 152 FGVq~kSTYDEnLYTTkLDKd~-~ykereaeAeRIArEIEss~t~NiHLaE 201 (565)
||| +|||||+||||+|||++ +|++++++|+|||+|||++.+.|+|++|
T Consensus 1 FGV--~stydE~lYTT~Ld~~~~~~k~~~~~A~riA~EIe~~~t~n~h~~e 49 (72)
T PF06741_consen 1 FGV--KSTYDENLYTTPLDRSDPDYKEREAEAERIAREIEGSTTSNIHVAE 49 (72)
T ss_pred CCC--CCccCchhceeeccCCCcchHHHHHHHHHHHHHHhccCCCCchhHH
Confidence 999 99999999999999985 9999999999999999999999999977
No 5
>KOG2375 consensus Protein interacting with poly(A)-binding protein [RNA processing and modification]
Probab=98.14 E-value=5.4e-05 Score=86.17 Aligned_cols=177 Identities=10% Similarity=-0.054 Sum_probs=123.8
Q ss_pred hHHHHHHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEEE
Q 038314 20 LSEALLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVVA 99 (565)
Q Consensus 20 l~DRLlfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~A 99 (565)
+.-|+..+...|.+.++++.++|+..|+|+|+.+....+ -++..++.+.. ......++..|.+.+++...|..-+..
T Consensus 223 ~f~v~stFde~ly~tk~d~~~kn~e~~e~a~Ria~ei~~--~at~~~h~~ae-~~~~gpd~~~I~ee~~ys~sd~~~~r~ 299 (756)
T KOG2375|consen 223 KFNVMSTFDEELYTTKLDKKVKNYEAYEGAERIAREIES--LATSDAHHLAE-RRLGGPDREDIEEEDLYSRSDGPGVRF 299 (756)
T ss_pred hhceeeeeehhhhcceecccCCchhhHHHHHHhhccccc--cchhHHHHhhc-cCCCCcchhhhhhhhhcccccccchhh
Confidence 345777888999999999999999999999999876432 34444444422 111233456788999999999999998
Q ss_pred cCccCCC-------CCCC-C--CCCCc-cccccccCCCCCCCCC---cccC-CCCCCCch---hhhhccccccccccCCC
Q 038314 100 KGVQLPA-------DGIA-G--NFAGD-DVVAVAGTVPPIDGQI---SEAK-RPIRSGLN---KRRNQKRISVRNENGYF 161 (565)
Q Consensus 100 kdV~Ls~-------D~is-g--~~~gd-~erELq~WvPDedd~~---~eLE-~sn~~WDQ---FevNEkrFGVq~kSTYD 161 (565)
++.++.. |.+. . ...++ ++..|.+|....-..+ ..++ +..++||+ |..|++-|++ +++|+
T Consensus 300 ~~~~~~~~~qd~~~d~i~~~~~kvn~~~k~~~~~~~~sgk~~~N~s~~a~~~d~sn~~~~n~~~q~n~kn~~~--~s~~~ 377 (756)
T KOG2375|consen 300 ENEDFNEAMQDKRNDKIAPLDQKVNDSTKSKALERWNSGKLLENASSYATPADASNGWDENSMFQVNSKNYKS--KSEVE 377 (756)
T ss_pred hhhhhhHHHHhhhccccccccCCCCccccccccccccccccccccccccccchhhcCCCcccccccccccccc--ccccc
Confidence 8888762 1111 1 12222 3447889974331111 1233 55678985 9999999999 55555
Q ss_pred CC--CCcccccCC--chHHHHHHHHHHHHhhhhcCCCCCCcccc
Q 038314 162 HG--DGPIKAEKE--HEEQMLSLKNMRNAMEVEHGKRDRMDVTK 201 (565)
Q Consensus 162 En--LYTTkLDKd--~~ykereaeAeRIArEIEss~t~NiHLaE 201 (565)
-. -|+-.++|+ +.+++|+++|..|++||+...+...-++.
T Consensus 378 s~~~~~~~~sek~~se~~~qr~~~~~~~~~~~~~~~~~~~~~aa 421 (756)
T KOG2375|consen 378 SSDMSTKKPSEKNESESFEQRKKRAVDLRRSETLGPQLGKKPAA 421 (756)
T ss_pred ccccccccccccccchhhhhhhhhhhhccccccccccccccccc
Confidence 55 577777785 46899999999999999999987666555
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=97.43 E-value=0.0008 Score=57.24 Aligned_cols=68 Identities=15% Similarity=0.226 Sum_probs=54.3
Q ss_pred HHHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEEE
Q 038314 24 LLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVVA 99 (565)
Q Consensus 24 Llfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~A 99 (565)
|+-++..++|..|.|.+|||..|.|+|.+++. -+.++|+.|..+..+... .-.++++|.++.|.-|.+
T Consensus 10 l~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~--~MNl~L~~~~~~~~~~~~------~~~~~v~IRG~nI~yI~l 77 (78)
T cd01733 10 LIILLQGLQGKVVTVELRNETTVTGRIASVDA--FMNIRLAKVTIIDRNGKQ------VQVEEIMVTGRNIRYVHI 77 (78)
T ss_pred HHHHHHHCCCCEEEEEECCCCEEEEEEEEEcC--CceeEEEEEEEEcCCCce------eECCcEEEECCEEEEEEc
Confidence 77888999999999999999999999999876 468999999887542211 113678899998887653
No 7
>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=97.25 E-value=0.0013 Score=53.97 Aligned_cols=63 Identities=22% Similarity=0.282 Sum_probs=48.7
Q ss_pred HHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEE
Q 038314 27 ATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQV 97 (565)
Q Consensus 27 llt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV 97 (565)
++..++|++|.|.+|||..|+|+|.+++. -+.++|+.|.....+.. ..-...++|.+..|..|
T Consensus 4 ~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~--~mNlvL~~~~~~~~~~~------~~~~~~v~IRG~~I~~I 66 (67)
T cd01726 4 FLKAIIGRPVVVKLNSGVDYRGILACLDG--YMNIALEQTEEYVNGQL------KNKYGDAFIRGNNVLYI 66 (67)
T ss_pred HHHhhCCCeEEEEECCCCEEEEEEEEEcc--ceeeEEeeEEEEeCCce------eeEeCCEEEECCEEEEE
Confidence 45778999999999999999999999985 46899999977543221 11235788888888765
No 8
>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=97.21 E-value=0.0016 Score=56.88 Aligned_cols=72 Identities=19% Similarity=0.287 Sum_probs=57.6
Q ss_pred HHHHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEEEcCc
Q 038314 23 ALLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVVAKGV 102 (565)
Q Consensus 23 RLlfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~AkdV 102 (565)
+|+-++..++|+.|.|.+|||..|+|+|.+++. -+.++|+.|....++... .-.++++|.++.|.-|.+-|.
T Consensus 1 ~~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~--~MNl~L~~a~~~~~~~~~------~~~~~v~IRG~nI~yi~lPd~ 72 (90)
T cd01724 1 KLVRFLMKLTNETVTIELKNGTIVHGTITGVDP--SMNTHLKNVKLTLKGRNP------VPLDTLSIRGNNIRYFILPDS 72 (90)
T ss_pred CHhHHHHhCCCCEEEEEECCCCEEEEEEEEEcC--ceeEEEEEEEEEcCCCce------eEcceEEEeCCEEEEEEcCCc
Confidence 356778899999999999999999999999886 468999999877543211 123688999999999987763
No 9
>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=97.12 E-value=0.0013 Score=52.02 Aligned_cols=61 Identities=23% Similarity=0.328 Sum_probs=48.2
Q ss_pred HhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEE
Q 038314 29 MCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQV 97 (565)
Q Consensus 29 t~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV 97 (565)
..++|.+|.|+++||..|.|+|.+++.. +.++|+.+....... .....+.++|.++.|..|
T Consensus 2 ~~~~g~~V~V~l~~g~~~~G~L~~~D~~--~Ni~L~~~~~~~~~~------~~~~~~~~~irG~~I~~I 62 (63)
T cd00600 2 KDLVGKTVRVELKDGRVLEGVLVAFDKY--MNLVLDDVEETIKEG------KKRVLGLVLIRGDNVRLV 62 (63)
T ss_pred hHHCCCEEEEEECCCcEEEEEEEEECCC--CCEEECCEEEEecCC------cEEECCeEEEECCEEEEE
Confidence 4679999999999999999999999853 479999998765421 112346889999988876
No 10
>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=97.11 E-value=0.0021 Score=51.67 Aligned_cols=65 Identities=18% Similarity=0.253 Sum_probs=51.6
Q ss_pred HHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEE
Q 038314 27 ATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVV 98 (565)
Q Consensus 27 llt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~ 98 (565)
++..++|.+|.|.++||..|+|+|.+++. .+.++|+.|........ .......++|.++.|+.|.
T Consensus 2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~--~~Nl~L~~~~~~~~~~~-----~~~~~~~~~irG~~I~~I~ 66 (67)
T PF01423_consen 2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQ--FMNLVLSDVTETIKNGP-----EKRSLGLVFIRGSNIRYIS 66 (67)
T ss_dssp HHHHTTTSEEEEEETTSEEEEEEEEEEET--TEEEEEEEEEEEETTES-----EEEEEEEEEEEGGGEEEEE
T ss_pred hhHHhCCcEEEEEEeCCEEEEEEEEEeec--hheEEeeeEEEEECCCC-----cEeECcEEEEECCEEEEEE
Confidence 35778999999999999999999999985 57899999998755321 1112367889999998875
No 11
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.04 E-value=0.0029 Score=56.15 Aligned_cols=73 Identities=22% Similarity=0.332 Sum_probs=54.9
Q ss_pred HhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccC-CCC-CCC-cCCCCceeeeeeecCceEEEEEcCc
Q 038314 29 MCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKK-GKS-NAN-VANGTVIETLVILSADLVQVVAKGV 102 (565)
Q Consensus 29 t~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~-G~s-~an-v~sg~i~eTLVI~~kDIVqV~AkdV 102 (565)
...||+.|.+..|++-+|||+|++.+.+ +-.|.|+.+|.--. +.. ... ..+..+-+.++|.++||-++.+-..
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 DPYIGSKISLISKSDIRYEGILYSIDTE-DSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEP 79 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETT-TTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCC-CCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcC
Confidence 4579999999999999999999999986 45899999987521 111 011 1245677889999999999987554
No 12
>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=97.02 E-value=0.0044 Score=52.93 Aligned_cols=71 Identities=14% Similarity=0.098 Sum_probs=53.4
Q ss_pred HHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEEEcC
Q 038314 25 LFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVVAKG 101 (565)
Q Consensus 25 lfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~Akd 101 (565)
+-++..++|+.|.|.+|||..|+|++.+++.- +.++|+.|......... . .. -.+++.|.++.|..|...+
T Consensus 3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~--MNi~L~n~~~~~~~~~~-~--~~-~~~~v~IRG~~I~~I~lp~ 73 (81)
T cd01725 3 FSFFKTLVGKEVTVELKNDLSIRGTLHSVDQY--LNIKLTNISVTDPEKYP-H--ML-SVKNCFIRGSVVRYVQLPA 73 (81)
T ss_pred hHHHHhCCCCEEEEEECCCcEEEEEEEEECCC--cccEEEEEEEEcCCCcc-c--cc-ccCeEEEECCEEEEEEeCh
Confidence 34567899999999999999999999998864 57999999765321110 0 11 1268899999999888754
No 13
>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=96.97 E-value=0.0041 Score=52.71 Aligned_cols=70 Identities=16% Similarity=0.310 Sum_probs=51.3
Q ss_pred HHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEEE
Q 038314 28 TMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVVA 99 (565)
Q Consensus 28 lt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~A 99 (565)
+.+++|++|.|+++||..|.|+|.+++.. ..+||..|...............-....++|+++.|+.+++
T Consensus 5 L~~~l~~~v~V~l~dgR~~~G~l~~~D~~--~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 5 LRSLLGRTMRIHMTDGRTLVGVFLCTDRD--CNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred HHHhcCCeEEEEEcCCeEEEEEEEEEcCC--CcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 56789999999999999999999999864 57999999876433221000001124568889999998875
No 14
>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=96.96 E-value=0.0044 Score=51.02 Aligned_cols=63 Identities=21% Similarity=0.253 Sum_probs=49.4
Q ss_pred HHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEE
Q 038314 27 ATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQV 97 (565)
Q Consensus 27 llt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV 97 (565)
++..++|++|.|.++||..|.|.|.+++. -+.++|+.|.....+.. ..-...++|.+..|+.|
T Consensus 5 ~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~--~mNi~L~~~~e~~~~~~------~~~lg~~~IRG~~I~~i 67 (68)
T cd01722 5 FLNDLTGKPVIVKLKWGMEYKGTLVSVDS--YMNLQLANTEEYIDGKS------TGNLGEVLIRCNNVLYI 67 (68)
T ss_pred HHHHcCCCEEEEEECCCcEEEEEEEEECC--CEEEEEeeEEEEeCCcc------ccCcCcEEEECCEEEEE
Confidence 56788999999999999999999999985 47899999976543221 11236788999888765
No 15
>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=96.94 E-value=0.0043 Score=51.48 Aligned_cols=66 Identities=21% Similarity=0.256 Sum_probs=51.3
Q ss_pred HHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEEEc
Q 038314 27 ATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVVAK 100 (565)
Q Consensus 27 llt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~Ak 100 (565)
++..++|+.|.|.+|||..|.|.|.+++. -+.++|+.|....... .. . -.++++|.++.|..|..-
T Consensus 4 ~L~~~~g~~V~VeLk~g~~~~G~L~~~D~--~MNl~L~~~~~~~~~g---~~--~-~~~~v~IRG~nI~~v~lP 69 (70)
T cd01721 4 LLHEAEGHIVTVELKTGEVYRGKLIEAED--NMNCQLKDVTVTARDG---RV--S-QLEQVYIRGSKIRFFILP 69 (70)
T ss_pred HHhhCCCCEEEEEECCCcEEEEEEEEEcC--CceeEEEEEEEECCCC---cE--e-EcCcEEEeCCEEEEEEeC
Confidence 56788999999999999999999999886 4679999998653211 01 1 136889999999888753
No 16
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=96.92 E-value=0.0032 Score=52.49 Aligned_cols=68 Identities=22% Similarity=0.267 Sum_probs=51.8
Q ss_pred HHHHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEE
Q 038314 23 ALLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVV 98 (565)
Q Consensus 23 RLlfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~ 98 (565)
+-+-++..++|.+|.|.++||..|.|+|.+++. -+.++|+.|....++... .-...++|.++.|+.|.
T Consensus 4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~--~mNlvL~d~~e~~~~~~~------~~lg~v~iRG~~V~~i~ 71 (72)
T PRK00737 4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDI--HMNLVLDNAEEIQDGEVV------RKLGKVVIRGDNVVYVS 71 (72)
T ss_pred chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcc--cceeEEeeEEEEcCCCeE------eEcCcEEEeCCEEEEEc
Confidence 345567888999999999999999999999986 467999999876442110 11346888998888763
No 17
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=96.84 E-value=0.0039 Score=50.02 Aligned_cols=64 Identities=20% Similarity=0.268 Sum_probs=49.9
Q ss_pred HHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEE
Q 038314 28 TMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVV 98 (565)
Q Consensus 28 lt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~ 98 (565)
+..++|..|.|+++||..|.|+|.+++. .+.++|+.|........ .....+.++|.++.|+.|.
T Consensus 3 L~~~~~~~V~V~l~~g~~~~G~L~~~D~--~~NlvL~~~~e~~~~~~-----~~~~~~~~~IrG~~I~~i~ 66 (67)
T smart00651 3 LKKLIGKRVLVELKNGREYRGTLKGFDQ--FMNLVLEDVEETVKDGE-----KKRKLGLVFIRGNNIVYII 66 (67)
T ss_pred hHHhCCcEEEEEECCCcEEEEEEEEECc--cccEEEccEEEEecCCc-----EEeEeCCEEEcCCEEEEEe
Confidence 5788999999999999999999999885 46799999988754211 0112357888999888765
No 18
>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=96.83 E-value=0.0049 Score=50.54 Aligned_cols=64 Identities=19% Similarity=0.220 Sum_probs=49.5
Q ss_pred HHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEE
Q 038314 27 ATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVV 98 (565)
Q Consensus 27 llt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~ 98 (565)
++..++|++|.|.++||..|.|+|.+++.- +.++|+.|.....+... .-...++|.++.|+.|.
T Consensus 4 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~--mNlvL~~~~e~~~~~~~------~~lg~~~iRG~~I~~i~ 67 (68)
T cd01731 4 VLKDSLNKPVLVKLKGGKEVRGRLKSYDQH--MNLVLEDAEEIDDGEPV------RKYGRVVIRGDNVLFIS 67 (68)
T ss_pred HHHHhcCCEEEEEECCCCEEEEEEEEECCc--ceEEEeeEEEEecCCeE------eEcCcEEEeCCEEEEEc
Confidence 456789999999999999999999999863 67999999876442211 11247888999888763
No 19
>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=96.73 E-value=0.0046 Score=52.89 Aligned_cols=68 Identities=25% Similarity=0.384 Sum_probs=51.0
Q ss_pred HhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccC-CCCC--C-CcCCCCceeeeeeecCceEEE
Q 038314 29 MCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKK-GKSN--A-NVANGTVIETLVILSADLVQV 97 (565)
Q Consensus 29 t~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~-G~s~--a-nv~sg~i~eTLVI~~kDIVqV 97 (565)
...||+.+.+-.|++-+|||+|++.+++ +-.|.||..|.--. |... . -..+.++-+.++|.+.||-++
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~-~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkDL 73 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTE-DSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKDL 73 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccc-cCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccccc
Confidence 3579999999999999999999999997 46899999885421 1110 0 112456778899999998664
No 20
>PF07145 PAM2: Ataxin-2 C-terminal region; InterPro: IPR009818 This entry represents a conserved region approximately 250 residues long located towards the C terminus of 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 [].; PDB: 3NTW_B 1JH4_B 3KTR_B 3KUJ_B 3KUT_D 3KUS_D 1JGN_B 2RQG_A 2RQH_A.
Probab=96.65 E-value=0.00081 Score=43.51 Aligned_cols=18 Identities=56% Similarity=0.660 Sum_probs=13.7
Q ss_pred ccccccCCCCeeecCCCC
Q 038314 344 TKEFKLNPGAKIFSPSSV 361 (565)
Q Consensus 344 aKefKLNP~Ak~fsPsf~ 361 (565)
|+.+||||+||.|.|++.
T Consensus 1 a~~s~LNp~A~eFvP~~~ 18 (18)
T PF07145_consen 1 AKSSKLNPNAPEFVPSSK 18 (18)
T ss_dssp --SSSSSTTSSSS-TTTT
T ss_pred CcccccCCCCccccCCCC
Confidence 578999999999999873
No 21
>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=96.60 E-value=0.0098 Score=50.05 Aligned_cols=69 Identities=17% Similarity=0.174 Sum_probs=52.8
Q ss_pred HHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccC-CCCCCCcCCCCceeeeeeecCceEEEEEcC
Q 038314 25 LFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKK-GKSNANVANGTVIETLVILSADLVQVVAKG 101 (565)
Q Consensus 25 lfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~-G~s~anv~sg~i~eTLVI~~kDIVqV~Akd 101 (565)
+-++..++|++|.|.+|||..|.|++.+++. -+.++|+.|..++. |.. . ...++++|.++.|..|...+
T Consensus 3 l~~L~~~~g~~V~VeLkng~~~~G~L~~~D~--~mNi~L~~~~~~~~~g~~---~---~~~~~v~IRG~~I~~i~~p~ 72 (76)
T cd01723 3 LSLLKTAQNHPMLVELKNGETYNGHLVNCDN--WMNIHLREVICTSKDGDK---F---WKMPECYIRGNTIKYLRVPD 72 (76)
T ss_pred hHHHHhcCCCEEEEEECCCCEEEEEEEEEcC--CCceEEEeEEEECCCCcE---e---eeCCcEEEeCCEEEEEEcCH
Confidence 3467888999999999999999999999886 46799999987632 110 0 11257889999998887543
No 22
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=96.55 E-value=0.0095 Score=50.16 Aligned_cols=71 Identities=18% Similarity=0.188 Sum_probs=54.7
Q ss_pred HHHHHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEecccccc--CCCCCCCcCCCCceeeeeeecCceEEEE
Q 038314 22 EALLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSK--KGKSNANVANGTVIETLVILSADLVQVV 98 (565)
Q Consensus 22 DRLlfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~--~G~s~anv~sg~i~eTLVI~~kDIVqV~ 98 (565)
.+.+.++..++|++|.|.+|||..|.|+|.+++.- .-++|..|..+. ++... .......++|.++.|+.|.
T Consensus 6 ~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~--mNlvL~d~~e~~~~~~~~~----~~~~~~~~~IRG~~I~~I~ 78 (79)
T COG1958 6 PLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQY--MNLVLDDVEEIISHDGEKN----VRRLGGEVLIRGDNIVLIS 78 (79)
T ss_pred CCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccc--eeEEEeceEEEeccCCccc----cceeccEEEEECCcEEEEe
Confidence 34567788999999999999999999999999863 579999998875 32211 1223458899999988764
No 23
>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=96.42 E-value=0.014 Score=49.31 Aligned_cols=70 Identities=17% Similarity=0.323 Sum_probs=50.8
Q ss_pred HHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCC--C--cCCCCceeeeeeecCceEEEEE
Q 038314 28 TMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNA--N--VANGTVIETLVILSADLVQVVA 99 (565)
Q Consensus 28 lt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~a--n--v~sg~i~eTLVI~~kDIVqV~A 99 (565)
+..++|.+|.|+++||..|.|+|.+++.. ..+||..|.......... . ....-....++|.++.|+.|.+
T Consensus 5 l~~~l~~~V~V~l~dgR~~~G~L~~~D~~--~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 5 MLQLINYRLRVTLQDGRQFVGQFLAFDKH--MNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred hHHHcCCEEEEEECCCcEEEEEEEEEcCc--cCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 45689999999999999999999999864 569999987754322110 0 0001123578999999998875
No 24
>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=96.02 E-value=0.027 Score=47.18 Aligned_cols=65 Identities=18% Similarity=0.151 Sum_probs=50.7
Q ss_pred HHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEEEc
Q 038314 28 TMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVVAK 100 (565)
Q Consensus 28 lt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~Ak 100 (565)
+..++|++|.|.++||..|.|.|.+++. -+-++|..|....++.. ..-...++|.++.|+.|.+-
T Consensus 5 L~~~i~k~V~V~L~~g~~~~G~L~~~D~--~mNlvL~~~~E~~~~~~------~~~lg~v~IRG~~I~~i~~~ 69 (72)
T cd01719 5 LKKYMDKKLSLKLNGNRKVSGILRGFDP--FMNLVLDDAVEVNSGGE------KNNIGMVVIRGNSIVMLEAL 69 (72)
T ss_pred hHHhCCCeEEEEECCCeEEEEEEEEEcc--cccEEeccEEEEccCCc------eeEeceEEECCCEEEEEEcc
Confidence 4678999999999999999999999985 35799999977643211 11235789999999998753
No 25
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=95.83 E-value=0.014 Score=62.37 Aligned_cols=74 Identities=18% Similarity=0.345 Sum_probs=57.0
Q ss_pred HHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccC-CCCC--C-CcCCCCceeeeeeecCceEEEEEcC
Q 038314 27 ATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKK-GKSN--A-NVANGTVIETLVILSADLVQVVAKG 101 (565)
Q Consensus 27 llt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~-G~s~--a-nv~sg~i~eTLVI~~kDIVqV~Akd 101 (565)
+.+..||+.|.+.=|+--+|||||.+++++ |-.|.||.+|..-. +..+ . .....++-|.|||.+.||-+|.+.+
T Consensus 3 ~~t~yIGS~ISLISk~DIRYEGILy~in~q-dSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~ 80 (361)
T KOG1073|consen 3 LVTSYIGSFISLISKNDIRYEGILYTINLQ-DSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQE 80 (361)
T ss_pred cccccccceeEEeecccceeeeEEEecccc-ccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeecc
Confidence 356789999999999999999999999996 56799999886422 1111 1 1112237789999999999999887
No 26
>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=95.46 E-value=0.15 Score=44.45 Aligned_cols=70 Identities=17% Similarity=0.269 Sum_probs=50.4
Q ss_pred ChHHHHHHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEE
Q 038314 19 SLSEALLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVV 98 (565)
Q Consensus 19 sl~DRLlfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~ 98 (565)
-+++|+|.++..++|.+|++++.+.....|.|.+++.+...-.|=++- . + .| +.+.=++...||+.+.
T Consensus 10 ~LRerfLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~----T-P------lG-v~~eAlLR~~DVi~~~ 77 (80)
T PF11095_consen 10 FLRERFLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ----T-P------LG-VQPEALLRCSDVISIS 77 (80)
T ss_dssp HHHHHHHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE----T-T------TT-EEEEEEEEGGGEEEEE
T ss_pred HHHHHHHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC----C-C------cc-cChhheeecCCEEEEE
Confidence 489999999999999999999999999999999999876332322211 1 0 12 2355677999999887
Q ss_pred Ec
Q 038314 99 AK 100 (565)
Q Consensus 99 Ak 100 (565)
.+
T Consensus 78 f~ 79 (80)
T PF11095_consen 78 FD 79 (80)
T ss_dssp E-
T ss_pred ec
Confidence 64
No 27
>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=95.10 E-value=0.12 Score=44.37 Aligned_cols=69 Identities=12% Similarity=0.136 Sum_probs=49.7
Q ss_pred HHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCC-cC-CCCceeeeeeecCceEEEE
Q 038314 28 TMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNAN-VA-NGTVIETLVILSADLVQVV 98 (565)
Q Consensus 28 lt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~an-v~-sg~i~eTLVI~~kDIVqV~ 98 (565)
+..+||++|.|.++||..|.|+|.+++-- +.+||..|.....+..... .. ...-...++|.+..|+.|.
T Consensus 7 L~~~i~k~V~V~l~~gr~~~G~L~~~D~~--mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~ 77 (81)
T cd01729 7 LSKYVDKKIRVKFQGGREVTGILKGYDQL--LNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLIS 77 (81)
T ss_pred HHHhcCCeEEEEECCCcEEEEEEEEEcCc--ccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEe
Confidence 56789999999999999999999998864 5799999977644322110 00 0011256888999998875
No 28
>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=94.98 E-value=0.11 Score=44.14 Aligned_cols=65 Identities=15% Similarity=0.117 Sum_probs=46.9
Q ss_pred HHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEE
Q 038314 28 TMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQV 97 (565)
Q Consensus 28 lt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV 97 (565)
+...++.+|.|+++||..|.|+|++++.- ..++|..|......... ..+.....++|.++.|+.+
T Consensus 7 L~~~l~k~v~V~l~~gr~~~G~L~~fD~~--~NlvL~d~~E~~~~~~~---~~~~~lG~~viRG~~V~~i 71 (74)
T cd01728 7 LVDDLDKKVVVLLRDGRKLIGILRSFDQF--ANLVLQDTVERIYVGDK---YGDIPRGIFIIRGENVVLL 71 (74)
T ss_pred HHHhcCCEEEEEEcCCeEEEEEEEEECCc--ccEEecceEEEEecCCc---cceeEeeEEEEECCEEEEE
Confidence 45679999999999999999999999864 46899888654221111 0111235788888888865
No 29
>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=94.78 E-value=0.17 Score=43.07 Aligned_cols=68 Identities=12% Similarity=0.140 Sum_probs=49.8
Q ss_pred HHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEEE
Q 038314 27 ATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVVA 99 (565)
Q Consensus 27 llt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~A 99 (565)
++..++|++|.|.++||..|+|.|.+++-- +.+||..|......+.... ......++|.++.|+.|..
T Consensus 7 ~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~--mNlvL~da~E~~~~~~~~~---~~~lg~v~iRG~nV~~i~p 74 (76)
T cd01732 7 LIDKCIGSRIWIVMKSDKEFVGTLLGFDDY--VNMVLEDVTEYEITPEGRK---ITKLDQILLNGNNICMLVP 74 (76)
T ss_pred HHHHhCCCEEEEEECCCeEEEEEEEEeccc--eEEEEccEEEEEEcCCCce---eeEcCeEEEeCCeEEEEEC
Confidence 456679999999999999999999999864 5799999977642111100 1123578889999888763
No 30
>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=94.54 E-value=0.16 Score=42.46 Aligned_cols=68 Identities=16% Similarity=0.179 Sum_probs=49.4
Q ss_pred HHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEEE
Q 038314 28 TMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVVA 99 (565)
Q Consensus 28 lt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~A 99 (565)
+...++..|.|+++||..|.|+|.+++.. ..+||..|......... .. ......+++|.++.|+.|..
T Consensus 4 L~~~l~~~V~V~l~dgr~~~G~L~~~D~~--~NlvL~~~~E~~~~~~~-~~-~~~~lG~~~iRG~~I~~i~~ 71 (74)
T cd01727 4 LEDYLNKTVSVITVDGRVIVGTLKGFDQA--TNLILDDSHERVYSSDE-GV-EQVVLGLYIIRGDNIAVVGE 71 (74)
T ss_pred HHHhcCCEEEEEECCCcEEEEEEEEEccc--cCEEccceEEEEecCCC-Cc-eeeEeceEEECCCEEEEEEc
Confidence 45679999999999999999999999875 57999998765321111 10 01123678899999988764
No 31
>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=94.04 E-value=0.32 Score=41.53 Aligned_cols=68 Identities=12% Similarity=0.069 Sum_probs=46.4
Q ss_pred HHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCC----cCCCC---ceeeeeeecCceEEE
Q 038314 28 TMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNAN----VANGT---VIETLVILSADLVQV 97 (565)
Q Consensus 28 lt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~an----v~sg~---i~eTLVI~~kDIVqV 97 (565)
+...++.+|.|.++||..|.|+|.+++.- +.+||..|.....+..... ..... -...++|.++.|+.|
T Consensus 6 l~~~~~k~V~V~l~~gr~~~G~L~~fD~~--mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i 80 (82)
T cd01730 6 IRLSLDERVYVKLRGDRELRGRLHAYDQH--LNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV 80 (82)
T ss_pred HHHhCCCEEEEEECCCCEEEEEEEEEccc--eEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence 34559999999999999999999999864 5789988876544322111 00000 124577788887765
No 32
>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=93.43 E-value=0.47 Score=41.56 Aligned_cols=73 Identities=12% Similarity=0.133 Sum_probs=49.1
Q ss_pred HHHHHHhc-cCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCc-------CCCCceeeeeeecCceE
Q 038314 24 LLFATMCI-IGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANV-------ANGTVIETLVILSADLV 95 (565)
Q Consensus 24 Llfllt~L-IG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv-------~sg~i~eTLVI~~kDIV 95 (565)
|-+|-.++ .|.+|.|++++|..|.|.|.+++.- +.+||..|..+..+...... ...-....++|.++.|+
T Consensus 4 l~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~h--mNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv 81 (87)
T cd01720 4 LSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRH--CNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI 81 (87)
T ss_pred HHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCc--cEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence 34555565 5999999999999999999999864 57999998776543221100 00111345777777777
Q ss_pred EEE
Q 038314 96 QVV 98 (565)
Q Consensus 96 qV~ 98 (565)
.|.
T Consensus 82 ~Is 84 (87)
T cd01720 82 LVL 84 (87)
T ss_pred EEe
Confidence 654
No 33
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=85.66 E-value=0.55 Score=40.52 Aligned_cols=65 Identities=18% Similarity=0.238 Sum_probs=48.0
Q ss_pred HHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEEE
Q 038314 27 ATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVVA 99 (565)
Q Consensus 27 llt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~A 99 (565)
++..+||.+|.|.+.||.-|.|++.+.+ +=+.|.|.-+....+|+.... -..+.|.+..+..|..
T Consensus 10 fl~~iiGr~V~VKl~sgvdyrG~l~~lD--gymNiaLe~tee~~ngql~n~------ygdaFirGnnVlyIs~ 74 (77)
T KOG1783|consen 10 FLKAIIGRTVVVKLNSGVDYRGTLVCLD--GYMNIALESTEEYVNGQLKNK------YGDAFIRGNNVLYIST 74 (77)
T ss_pred HHHHHhCCeEEEEecCCccccceehhhh--hHHHHHHHHHHHHhcCccccc------ccceeeccccEEEEEe
Confidence 5688999999999999999999998765 345677888877666654321 1246777777776654
No 34
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=83.58 E-value=1.1 Score=42.02 Aligned_cols=40 Identities=20% Similarity=0.254 Sum_probs=32.8
Q ss_pred HHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEecc
Q 038314 25 LFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKA 66 (565)
Q Consensus 25 lfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~A 66 (565)
|+||...-|+++.|.+|||+.|.|+|+.|+.-. -+-|+..
T Consensus 4 LsLL~~aq~~pmlvELKNget~nGhL~~cD~wM--Nl~L~~V 43 (134)
T KOG3293|consen 4 LSLLKTAQNHPMLVELKNGETYNGHLVNCDNWM--NLHLREV 43 (134)
T ss_pred hhHHHhcCCCeEEEEecCCCEecceeecchhhh--hcchhee
Confidence 678899999999999999999999999988643 3444443
No 35
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=78.16 E-value=6.4 Score=33.28 Aligned_cols=43 Identities=28% Similarity=0.375 Sum_probs=33.6
Q ss_pred hHHHHHHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEecc
Q 038314 20 LSEALLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKA 66 (565)
Q Consensus 20 l~DRLlfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~A 66 (565)
.+--+.-.+..+||+.|.|.+..|++ +|+|....+|- |+|...
T Consensus 8 vdpyvyq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDh---Ivl~~~ 50 (66)
T PF10842_consen 8 VDPYVYQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDH---IVLEEN 50 (66)
T ss_pred cCHHHHHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCE---EEEEeC
Confidence 33445567889999999999998887 99999988863 566544
No 36
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=76.92 E-value=8.6 Score=33.44 Aligned_cols=63 Identities=24% Similarity=0.289 Sum_probs=43.9
Q ss_pred HHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEE
Q 038314 27 ATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQV 97 (565)
Q Consensus 27 llt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV 97 (565)
++-.|+|++|.|.+|=|..|+|.|.+.+. =+.+-|..|...-+|... +.+.|. .|.-.++.-|
T Consensus 12 FL~~l~gk~V~vkLKwg~eYkG~LvsvD~--YmNlqL~~~eE~idG~~~-----g~lGEi-lIRCNNvlyi 74 (79)
T KOG3482|consen 12 FLNGLTGKPVLVKLKWGQEYKGTLVSVDN--YMNLQLANAEEYIDGVST-----GNLGEI-LIRCNNVLYI 74 (79)
T ss_pred HHhhccCCeEEEEEecCcEEEEEEEEecc--hhheehhhhhhhhccccc-----ccceeE-EEEeccEEEE
Confidence 45789999999999999999999998664 355667777775455443 333343 4455555443
No 37
>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=72.27 E-value=18 Score=31.47 Aligned_cols=62 Identities=8% Similarity=0.167 Sum_probs=41.5
Q ss_pred HhccCc--eEEEEEc--cCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEE
Q 038314 29 MCIIGL--PVDVYIK--DGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQV 97 (565)
Q Consensus 29 t~LIG~--~VeVtvK--dGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV 97 (565)
-.++.. +|.|.++ +|..|+|+|.+++.- +.+||..|......... .. -...++|.++.|+.|
T Consensus 12 ~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~--mNlvL~d~~E~~~~~~~----~~-~lG~iliRGnnV~~I 77 (79)
T cd01718 12 FRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEY--MNLVLDDAEEVHLKTKT----RK-PLGRILLKGDNITLI 77 (79)
T ss_pred HHHHccCcEEEEEEEeCCCcEEEEEEEEEccc--eeEEEcCEEEEecCCce----Ee-EcCcEEEeCCEEEEE
Confidence 344555 6777777 999999999999864 57999998665321000 00 124678888888765
No 38
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=72.27 E-value=4.8 Score=36.06 Aligned_cols=41 Identities=15% Similarity=0.181 Sum_probs=31.0
Q ss_pred HHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccc
Q 038314 27 ATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMS 69 (565)
Q Consensus 27 llt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i 69 (565)
++..+||+.|.|-+|||--..|+||+.+. =+.+-|...+.+
T Consensus 6 fFkslvg~~V~VeLKnd~~i~GtL~svDq--yLNlkL~di~v~ 46 (96)
T KOG3448|consen 6 FFKSLVGKEVVVELKNDLSICGTLHSVDQ--YLNLKLTDISVT 46 (96)
T ss_pred HHHHhcCCeEEEEEcCCcEEEEEecccch--hheeEEeeeEee
Confidence 45789999999999999999999999764 233444444443
No 39
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=70.47 E-value=24 Score=32.73 Aligned_cols=73 Identities=22% Similarity=0.335 Sum_probs=54.1
Q ss_pred HHHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEEEcC-c
Q 038314 24 LLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVVAKG-V 102 (565)
Q Consensus 24 Llfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~Akd-V 102 (565)
|+-+++.+-+..|.|.+|||++.+|-+.+.+.- .-+.|+..+...+|. ..+ .+++-|.+++|-.+...| +
T Consensus 3 lvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~--Mn~~l~~v~~t~~~~----pv~---l~~lsirgnniRy~~lpD~l 73 (109)
T KOG3428|consen 3 LVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQ--MNTHLKHVKMTVKGE----PVR---LDTLSIRGNNIRYYILPDSL 73 (109)
T ss_pred HHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhh--heeEEEEEEEecCCC----cee---EEEEEeecceEEEEEccCCc
Confidence 677889999999999999999999999987763 356677766654421 111 378888888888888654 4
Q ss_pred cCC
Q 038314 103 QLP 105 (565)
Q Consensus 103 ~Ls 105 (565)
.++
T Consensus 74 ~ld 76 (109)
T KOG3428|consen 74 NLD 76 (109)
T ss_pred Ccc
Confidence 444
No 40
>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=65.82 E-value=4.4 Score=35.26 Aligned_cols=29 Identities=24% Similarity=0.477 Sum_probs=19.9
Q ss_pred HHhccCceEEEEEccCCEEEEEEEeeccC
Q 038314 28 TMCIIGLPVDVYIKDGSVYSGIFYTASVE 56 (565)
Q Consensus 28 lt~LIG~~VeVtvKdGsvYeGIF~TaS~e 56 (565)
++|+-+.+|.+++|||+.++|+...+...
T Consensus 12 iAC~~~~~v~L~l~dG~~~~g~A~dt~~~ 40 (80)
T PF07073_consen 12 IACMYRYPVKLTLKDGEQIEGKALDTRTN 40 (80)
T ss_dssp HHHTTTT-EEEE-TTT--EEESS-EEE--
T ss_pred HHHhcCCeEEEEEeCCCEEEEEEEEEEEe
Confidence 57999999999999999999998886543
No 41
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=64.15 E-value=25 Score=31.30 Aligned_cols=57 Identities=12% Similarity=0.194 Sum_probs=39.3
Q ss_pred eEEEEEccC--CEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEE
Q 038314 35 PVDVYIKDG--SVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVV 98 (565)
Q Consensus 35 ~VeVtvKdG--svYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~ 98 (565)
.|.|.++|+ ..|+|+|.+++.- +.+||..|.....+... .. -...++|.++.|+.|.
T Consensus 28 ~V~i~l~~~~~r~~~G~L~gfD~~--mNlVL~d~~E~~~~~~~----~~-~lG~ilIRGnnV~~I~ 86 (89)
T PTZ00138 28 RVQIWLYDHPNLRIEGKILGFDEY--MNMVLDDAEEVYTKKNT----RK-DLGRILLKGDNITLIM 86 (89)
T ss_pred EEEEEEEeCCCcEEEEEEEEEccc--ceEEEccEEEEecCCce----ee-EcCeEEEcCCEEEEEE
Confidence 567777675 6799999999864 57999999776431110 01 1246888999988875
No 42
>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=63.81 E-value=20 Score=27.66 Aligned_cols=32 Identities=16% Similarity=0.224 Sum_probs=25.2
Q ss_pred cCceEEEEEccCCEEEEEEEeeccCCCeeEEEecc
Q 038314 32 IGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKA 66 (565)
Q Consensus 32 IG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~A 66 (565)
+|++|.|.+ ++..++|++...+.++ ..+|+..
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G--~L~v~~~ 33 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDG--ALLVRTE 33 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTS--EEEEEET
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCC--EEEEEEC
Confidence 799999999 6677799999998876 3455443
No 43
>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=61.89 E-value=14 Score=36.25 Aligned_cols=60 Identities=22% Similarity=0.240 Sum_probs=38.1
Q ss_pred HHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEEEc
Q 038314 27 ATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVVAK 100 (565)
Q Consensus 27 llt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~Ak 100 (565)
....+||+.|.|++.| ..|.|.+.|+++.+.--|++++.. ++. ...-+|.+.-|-.|++-
T Consensus 11 ~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e---~~~----------~sv~~I~ghaVk~vevl 70 (166)
T PF06372_consen 11 EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE---DGK----------RSVKVIMGHAVKSVEVL 70 (166)
T ss_dssp HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T---TS-----------EEEEEE-GGGEEEEEEE
T ss_pred HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc---CCc----------eeEEEEEccceEEEEEc
Confidence 3467899999999999 999999999999875334443332 111 12456777777777653
No 44
>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=50.82 E-value=13 Score=34.14 Aligned_cols=61 Identities=23% Similarity=0.323 Sum_probs=39.1
Q ss_pred ceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEEEcCccCCCCCCCCCC
Q 038314 34 LPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVVAKGVQLPADGIAGNF 113 (565)
Q Consensus 34 ~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~AkdV~Ls~D~isg~~ 113 (565)
..+.|+++||.++.|++..-+ +..+.|+.+. | +...|+.+||.+......++--+++.+..
T Consensus 58 ~~~~v~~~dG~~~~G~~~~e~---~~~~~l~~~~----g------------~~~~i~~~~I~~~~~~~~S~MP~gl~~~L 118 (133)
T TIGR02603 58 EAYRVTLKDGRILSGIVASET---ADGVTVKMPG----G------------VEQSVPREEIKSREALPVSLMPEGLEMGL 118 (133)
T ss_pred ccEEEEECCCCEEEEEEEecC---CCeEEEEcCC----C------------cEEEEEHHHHHHhhcCCCCcCCchhhccC
Confidence 358999999999999998733 3467776542 1 24566677776666555554334444444
No 45
>PRK14642 hypothetical protein; Provisional
Probab=47.15 E-value=93 Score=31.44 Aligned_cols=87 Identities=16% Similarity=0.181 Sum_probs=51.5
Q ss_pred cccCCCCCCChHHHHHHHHHhccCceEEEEEc-------------cCCEEEEEEEeeccCCCeeEEEeccc--cccCCCC
Q 038314 10 ETTHSNNSSSLSEALLFATMCIIGLPVDVYIK-------------DGSVYSGIFYTASVEKDYGIVLKKAK--MSKKGKS 74 (565)
Q Consensus 10 ~~~~~~~~~sl~DRLlfllt~LIG~~VeVtvK-------------dGsvYeGIF~TaS~e~d~gVVLK~AR--~i~~G~s 74 (565)
|.+++--.+.|...-- +...+|..|.|+++ ++..|+|+|..++-+ +|.|.+-. ..+.|..
T Consensus 79 EVSSPGldRPLk~~~d--f~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~---~i~l~~~~~~~~k~g~~ 153 (197)
T PRK14642 79 EVSSPGIDRPLRHEQD--FERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG---GWQIVWSDEPPVKPGQR 153 (197)
T ss_pred EEeCCCCCCCCCCHHH--HHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC---EEEEEEeecccCCCccc
Confidence 4444444444443333 35778999999998 678999999988643 45554332 2222210
Q ss_pred CCCcCCC---CceeeeeeecCceEEEEEcC-ccC
Q 038314 75 NANVANG---TVIETLVILSADLVQVVAKG-VQL 104 (565)
Q Consensus 75 ~anv~sg---~i~eTLVI~~kDIVqV~Akd-V~L 104 (565)
...+ .+.+.+-|..+||-...++- ++|
T Consensus 154 ---~~k~~~~~~~~~~~~~~~eik~a~l~p~~~f 184 (197)
T PRK14642 154 ---VSKKRVPAPLQALGFTLDELREARLAPIVDF 184 (197)
T ss_pred ---cccccccccceeEEeehhheeeEEEEEEEec
Confidence 0001 22367888889888777653 444
No 46
>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=45.02 E-value=1e+02 Score=26.29 Aligned_cols=69 Identities=16% Similarity=0.202 Sum_probs=43.0
Q ss_pred cCCCCCCChHHHHHHHHHhccCceEEEEEc---cCC-EEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeee
Q 038314 12 THSNNSSSLSEALLFATMCIIGLPVDVYIK---DGS-VYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETL 87 (565)
Q Consensus 12 ~~~~~~~sl~DRLlfllt~LIG~~VeVtvK---dGs-vYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTL 87 (565)
+++--.+.|...--| ...+|..|.|+++ +|. .|.|.|..++-+ .|+|..-.+ +. .+++
T Consensus 6 SSPGl~RpL~~~~~~--~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~---~v~l~~~~~---~~----------~~~~ 67 (83)
T cd01734 6 SSPGAERPLKKEADF--ERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD---TVTLEVDIK---TR----------GKTV 67 (83)
T ss_pred cCCCCCCcCCCHHHH--HHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC---EEEEEEecC---CC----------CeEE
Confidence 333333444433333 5789999999998 664 799999998754 455543111 00 1467
Q ss_pred eeecCceEEEE
Q 038314 88 VILSADLVQVV 98 (565)
Q Consensus 88 VI~~kDIVqV~ 98 (565)
.|+-+||....
T Consensus 68 ~i~~~~I~ka~ 78 (83)
T cd01734 68 EIPLDKIAKAR 78 (83)
T ss_pred EEEhHHeeEEE
Confidence 78888877654
No 47
>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=42.29 E-value=80 Score=26.42 Aligned_cols=37 Identities=14% Similarity=0.043 Sum_probs=29.6
Q ss_pred hccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccc
Q 038314 30 CIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAK 67 (565)
Q Consensus 30 ~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR 67 (565)
..||..|.+++..|+.+||-+.+++.... -+|||.+-
T Consensus 3 f~iGs~V~~kTc~g~~ieGEV~afD~~tk-~lIlk~~s 39 (61)
T cd01735 3 FSVGSQVSCRTCFEQRLQGEVVAFDYPSK-MLILKCPS 39 (61)
T ss_pred cccccEEEEEecCCceEEEEEEEecCCCc-EEEEECcc
Confidence 35899999999999999999999887543 35566543
No 48
>PRK02001 hypothetical protein; Validated
Probab=40.00 E-value=1.4e+02 Score=28.81 Aligned_cols=50 Identities=24% Similarity=0.290 Sum_probs=36.9
Q ss_pred cccCCCCCCChHHHHHHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEe
Q 038314 10 ETTHSNNSSSLSEALLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLK 64 (565)
Q Consensus 10 ~~~~~~~~~sl~DRLlfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK 64 (565)
|.+++--.+.+...--| ...+|..|.|++.++..|.|.|..++-+ .|+|.
T Consensus 69 EVSSPGldRpL~~~~~f--~r~~G~~v~V~l~~~~~~~G~L~~~~~~---~i~l~ 118 (152)
T PRK02001 69 EVGSAGLTSPLKVPRQY--KKNIGRELEVLTKNGKKIEGELKSADEN---DITLE 118 (152)
T ss_pred EEeCCCCCCcCCCHHHH--HHhCCCEEEEEECCCCEEEEEEEEEeCC---EEEEE
Confidence 45555555555554444 4789999999999999999999998743 46554
No 49
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=37.01 E-value=67 Score=30.95 Aligned_cols=29 Identities=24% Similarity=0.270 Sum_probs=26.0
Q ss_pred HHhccCceEEEEEccCCEEEEEEEeeccC
Q 038314 28 TMCIIGLPVDVYIKDGSVYSGIFYTASVE 56 (565)
Q Consensus 28 lt~LIG~~VeVtvKdGsvYeGIF~TaS~e 56 (565)
...|||+.|.++..+|..++|+..+....
T Consensus 87 a~slVGk~V~~~~~~g~~~tG~V~~V~~~ 115 (142)
T PRK09618 87 YSELIGKEVEWEGEDGEIVSGTVTSVKQK 115 (142)
T ss_pred HHHHhCCEEEEEeCCCCEEEEEEEEEEEc
Confidence 47899999999999999999999998753
No 50
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=35.74 E-value=88 Score=27.48 Aligned_cols=67 Identities=19% Similarity=0.167 Sum_probs=48.0
Q ss_pred HHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCceEEEEEcCc
Q 038314 28 TMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSADLVQVVAKGV 102 (565)
Q Consensus 28 lt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kDIVqV~AkdV 102 (565)
+..+.-..+.|++.-|....|||+.++.= +.|||..+-.....-.+.+ +-..+|.+.-|+.+++.+.
T Consensus 9 LkkymdKki~lklnG~r~v~GiLrGyD~F--mNiVlde~vE~~~~~~~~~------ig~~vIrgnsiv~~eaL~~ 75 (77)
T KOG1780|consen 9 LKKYMDKKIVLKLNGGRKVTGILRGYDPF--MNIVLDETVEPNGDGDKNN------IGMVVIRGNSIVMVEALER 75 (77)
T ss_pred HHHhhhheEEEEeCCCcEEEEEEeccchH--HhhhhhhceeecCcCCcce------eeeEEEeccEEEEEeeccc
Confidence 35566788999999999999999998863 4578887766533111222 2356888899999887653
No 51
>PRK14638 hypothetical protein; Provisional
Probab=34.27 E-value=72 Score=30.48 Aligned_cols=50 Identities=16% Similarity=0.205 Sum_probs=36.3
Q ss_pred cccCCCCCCChHHHHHHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEe
Q 038314 10 ETTHSNNSSSLSEALLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLK 64 (565)
Q Consensus 10 ~~~~~~~~~sl~DRLlfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK 64 (565)
|.+++--.+.+...--| ...+|+.|.|+++++..|.|++..++-+ +|+|.
T Consensus 79 EVSSPGldRpL~~~~~f--~r~~G~~v~V~~~~~k~~~G~L~~~~~~---~i~l~ 128 (150)
T PRK14638 79 EVSSPGLDRPLRGPKDY--VRFTGKLAKIVTKDGKTFIGRIESFVDG---TITIS 128 (150)
T ss_pred EEeCCCCCCCCCCHHHH--HHhCCCEEEEEECCCcEEEEEEEEEeCC---EEEEE
Confidence 45555555555544444 4789999999999999999999998743 45553
No 52
>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=32.72 E-value=94 Score=26.13 Aligned_cols=30 Identities=20% Similarity=0.557 Sum_probs=25.2
Q ss_pred cCceEEEEEccCCEEEEEEEeeccCCCeeEEEe
Q 038314 32 IGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLK 64 (565)
Q Consensus 32 IG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK 64 (565)
=+.+|.|.+.||.+..|...+++ .|.|.|+
T Consensus 14 ~~~~Vti~L~nG~~l~G~I~~fD---~ftVll~ 43 (61)
T TIGR02383 14 ERIPVTVFLVNGVQLKGVIESFD---NFTVLLE 43 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEe---eeEEEEE
Confidence 35689999999999999999988 4677765
No 53
>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=32.20 E-value=1e+02 Score=25.93 Aligned_cols=30 Identities=20% Similarity=0.558 Sum_probs=25.2
Q ss_pred CceEEEEEccCCEEEEEEEeeccCCCeeEEEec
Q 038314 33 GLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKK 65 (565)
Q Consensus 33 G~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~ 65 (565)
..+|.|-+.||.+..|...+++ .|.|.|+.
T Consensus 11 ~~~Vtv~L~NG~~l~G~I~~fD---~ftVll~~ 40 (61)
T cd01716 11 KIPVTIYLVNGVQLKGQIESFD---NFTVLLES 40 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEc---ceEEEEEE
Confidence 4578999999999999999988 47777764
No 54
>PRK11625 Rho-binding antiterminator; Provisional
Probab=30.71 E-value=1.1e+02 Score=27.16 Aligned_cols=33 Identities=21% Similarity=0.240 Sum_probs=26.3
Q ss_pred HHHHHHHHHhccCceEEEEEccCCEEEEEEEeecc
Q 038314 21 SEALLFATMCIIGLPVDVYIKDGSVYSGIFYTASV 55 (565)
Q Consensus 21 ~DRLlfllt~LIG~~VeVtvKdGsvYeGIF~TaS~ 55 (565)
.|.|.- .|+-+.++.++++||...+|+-..+-.
T Consensus 13 yDyLEl--AC~~~~~l~l~l~dGe~~~g~A~D~~~ 45 (84)
T PRK11625 13 YDNLEL--ACQHHLMLTLELKDGEVLQAKASDLVS 45 (84)
T ss_pred hhHHHH--HHhcCCeEEEEECCCCEEEEEEEeeec
Confidence 455554 566999999999999999999877543
No 55
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=29.90 E-value=1.1e+02 Score=27.10 Aligned_cols=43 Identities=21% Similarity=0.411 Sum_probs=32.7
Q ss_pred CChHHHHHHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEe
Q 038314 18 SSLSEALLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLK 64 (565)
Q Consensus 18 ~sl~DRLlfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK 64 (565)
..+.|.++-.+ -.=+.+|+|.+.||.+..|+..+++ .|.|.|+
T Consensus 5 ~nlQd~fLn~l-r~~~~~VtifL~NG~~l~G~I~~fD---~ftVll~ 47 (79)
T PRK00395 5 QNLQDPFLNAL-RKERVPVTIYLVNGIKLQGQIESFD---NFVVLLR 47 (79)
T ss_pred cchHHHHHHHH-HHcCCCEEEEEeCCcEEEEEEEEEc---cEEEEEE
Confidence 34566665553 3457789999999999999999988 4777775
No 56
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=29.39 E-value=1.7e+02 Score=28.24 Aligned_cols=28 Identities=21% Similarity=0.247 Sum_probs=24.4
Q ss_pred HHhccCceEEEEEccCCEEEEEEEeecc
Q 038314 28 TMCIIGLPVDVYIKDGSVYSGIFYTASV 55 (565)
Q Consensus 28 lt~LIG~~VeVtvKdGsvYeGIF~TaS~ 55 (565)
...|||+.|.....+|..++|+..+...
T Consensus 88 a~~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 88 AVNFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HHHhhCceeEEEecCCCEEEEEEEEEEE
Confidence 4689999999888999999999987654
No 57
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=29.26 E-value=27 Score=34.59 Aligned_cols=81 Identities=17% Similarity=0.295 Sum_probs=50.5
Q ss_pred HHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEecccc---ccCCCCCCCcCCCCceeee-eeecCceEEEEEcCcc
Q 038314 28 TMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKM---SKKGKSNANVANGTVIETL-VILSADLVQVVAKGVQ 103 (565)
Q Consensus 28 lt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~---i~~G~s~anv~sg~i~eTL-VI~~kDIVqV~AkdV~ 103 (565)
++.+|-..+.|++.||..|-|-|.+++... .+||..+.. ++....+-+...+.-+--| +.....||..++.+-.
T Consensus 9 ml~~iNyr~rv~~qDgr~~ig~~~afDkhm--Nlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegpp 86 (177)
T KOG3168|consen 9 MLQHINYRMRVRLQDGRTFIGQFKAFDKHM--NLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPP 86 (177)
T ss_pred HHHhhcceEEEEeccCceeechhhhhHHHH--HHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCC
Confidence 467888999999999999999999998743 244443322 1111111111111111123 4467889999999987
Q ss_pred CCCCCCC
Q 038314 104 LPADGIA 110 (565)
Q Consensus 104 Ls~D~is 110 (565)
...|++.
T Consensus 87 p~s~s~~ 93 (177)
T KOG3168|consen 87 PPSDSFR 93 (177)
T ss_pred CCccccc
Confidence 7766655
No 58
>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=26.41 E-value=1.2e+02 Score=27.86 Aligned_cols=32 Identities=22% Similarity=0.234 Sum_probs=26.7
Q ss_pred HHHHHHHHHhccCc-eEEEEEccCCEEEEEEEe
Q 038314 21 SEALLFATMCIIGL-PVDVYIKDGSVYSGIFYT 52 (565)
Q Consensus 21 ~DRLlfllt~LIG~-~VeVtvKdGsvYeGIF~T 52 (565)
=.||.+++.-|=|. .|+++++||++..|....
T Consensus 15 Ia~LE~lv~~L~ge~~V~l~L~DGs~l~Gtv~v 47 (101)
T PF11607_consen 15 IARLEHLVSELDGEERVELELDDGSMLRGTVAV 47 (101)
T ss_dssp HHHHHHHHHCTTTT-EEEEEETTS-EEEEEECC
T ss_pred HHHHHHHHhhcCCcceEEEEEcCCCeeeeeecc
Confidence 46889998888886 699999999999998765
No 59
>PRK14639 hypothetical protein; Provisional
Probab=25.79 E-value=1.3e+02 Score=28.57 Aligned_cols=49 Identities=22% Similarity=0.262 Sum_probs=35.1
Q ss_pred cccCCCCCCChHHHHHHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEE
Q 038314 10 ETTHSNNSSSLSEALLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVL 63 (565)
Q Consensus 10 ~~~~~~~~~sl~DRLlfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVL 63 (565)
|.+++--.+.+...--| ...+|..|.|+++++..|.|++..++-+ +|.|
T Consensus 67 EVSSPGl~RpL~~~~~f--~r~~G~~v~v~l~~~~~~~G~L~~~~~~---~i~l 115 (140)
T PRK14639 67 EVSSPGLERKLSKIEHF--AKSIGELVKITTNEKEKFEGKIVSVDDE---NITL 115 (140)
T ss_pred EEeCCCCCCcCCCHHHH--HHhCCCEEEEEECCCcEEEEEEEEEeCC---EEEE
Confidence 44444444555443333 4789999999999999999999998754 4555
No 60
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=25.57 E-value=2.9e+02 Score=27.70 Aligned_cols=64 Identities=17% Similarity=0.263 Sum_probs=41.5
Q ss_pred CChHHHHHHHHHhccCc----eEEEEEccCCEEEEEEEeeccCCCeeEEEeccccccCCCCCCCcCCCCceeeeeeecCc
Q 038314 18 SSLSEALLFATMCIIGL----PVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSKKGKSNANVANGTVIETLVILSAD 93 (565)
Q Consensus 18 ~sl~DRLlfllt~LIG~----~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~~G~s~anv~sg~i~eTLVI~~kD 93 (565)
.++.||+.||+ .+-++ .|.|.++ +..|.||+..+.-+ .|.|+-.- ++ ++..|.-+|
T Consensus 117 M~~~EKI~fL~-~~P~~lp~i~C~i~t~-~~~Y~G~I~~~~~~---~v~i~~~~------------~~---~~~~i~~~~ 176 (185)
T PF14153_consen 117 MNIEEKIDFLI-NLPHHLPPIKCEIETK-DKSYRGIILSYDEG---EVSIMPFN------------QG---EEIEIPIDD 176 (185)
T ss_pred ccHHHHHHHHH-hCcccCCCCceEEEeC-CceEEEEEEeccCC---EEEEeccC------------CC---cceEeehhh
Confidence 45679999885 44443 5666655 57899999987753 34444331 11 466788899
Q ss_pred eEEEEEcC
Q 038314 94 LVQVVAKG 101 (565)
Q Consensus 94 IVqV~Akd 101 (565)
|+.|..-|
T Consensus 177 I~sI~~iG 184 (185)
T PF14153_consen 177 ITSIKMIG 184 (185)
T ss_pred eeeeeecc
Confidence 98887533
No 61
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=25.11 E-value=74 Score=28.20 Aligned_cols=28 Identities=25% Similarity=0.400 Sum_probs=24.2
Q ss_pred HHhccCceEEEEEccCCEEEEEEEeecc
Q 038314 28 TMCIIGLPVDVYIKDGSVYSGIFYTASV 55 (565)
Q Consensus 28 lt~LIG~~VeVtvKdGsvYeGIF~TaS~ 55 (565)
+.|+--..+.+++|||.+|+|.-+.+-.
T Consensus 18 lACl~hl~l~L~lkdGev~~a~A~d~~~ 45 (84)
T COG4568 18 LACLHHLPLTLELKDGEVLQAKASDLQR 45 (84)
T ss_pred HHHhhhceEEEEEcCCeEEEEEehhhhh
Confidence 5788889999999999999999877544
No 62
>PLN03200 cellulose synthase-interactive protein; Provisional
Probab=24.74 E-value=2e+02 Score=38.19 Aligned_cols=47 Identities=17% Similarity=0.112 Sum_probs=38.4
Q ss_pred CCCCChHHHHHHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEecc
Q 038314 15 NNSSSLSEALLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKA 66 (565)
Q Consensus 15 ~~~~sl~DRLlfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~A 66 (565)
.+..+++||-.+++-||.|.- .|+++.|.--+|.|++.|+ -|+|++-
T Consensus 1962 ~~~~~~~~~~~~~~~~~~G~L-~V~V~~a~nl~~~~~~sdP----yv~l~~g 2008 (2102)
T PLN03200 1962 SGPPRFHERAESLLQCLPGSL-TVTIKRGNNLKQSMGNTNA----FCKLTLG 2008 (2102)
T ss_pred hCCccHHHHHHHHHhhCCcce-EEEEeeccccccccCCCCC----eEEEEEC
Confidence 367899999999999999974 5788888887799998776 5667766
No 63
>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=24.21 E-value=1.8e+02 Score=27.02 Aligned_cols=52 Identities=23% Similarity=0.332 Sum_probs=30.7
Q ss_pred cccCCCCCCChHHHHHHHHHhccCceEEEEEc---cC-CEEEEEEEeeccCCCeeEEEecc
Q 038314 10 ETTHSNNSSSLSEALLFATMCIIGLPVDVYIK---DG-SVYSGIFYTASVEKDYGIVLKKA 66 (565)
Q Consensus 10 ~~~~~~~~~sl~DRLlfllt~LIG~~VeVtvK---dG-svYeGIF~TaS~e~d~gVVLK~A 66 (565)
|.+++--.+.+..+--| ...+|..|.|+++ +| ..|.|.+...+-+ .|+|+..
T Consensus 66 EVSSPG~~r~L~~~~~~--~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~---~i~l~~~ 121 (141)
T PF02576_consen 66 EVSSPGIDRPLKSPRDF--ERFIGRKVKVKLKQPVNGRKEFEGKLLEVDED---EITLEVE 121 (141)
T ss_dssp EEE--SSSS--SSHHHH--HHH-SEEEEEE-SS-SSS-SEEEEEEEEEETT---EEEEEEE
T ss_pred EEeCCCCCCcCCCHHHH--HHhcCCeEEEEEeccCCCcEEEEEEEEEEeCC---EEEEEEC
Confidence 34434444445433333 5789999999994 44 5799999998864 5777554
No 64
>PRK14641 hypothetical protein; Provisional
Probab=23.75 E-value=1.6e+02 Score=29.01 Aligned_cols=56 Identities=16% Similarity=0.124 Sum_probs=35.8
Q ss_pred cccCCCCCCChHHHHHHHHHhccCceEEEEEcc----CCEEEEEEEeeccCC--CeeEEEeccc
Q 038314 10 ETTHSNNSSSLSEALLFATMCIIGLPVDVYIKD----GSVYSGIFYTASVEK--DYGIVLKKAK 67 (565)
Q Consensus 10 ~~~~~~~~~sl~DRLlfllt~LIG~~VeVtvKd----GsvYeGIF~TaS~e~--d~gVVLK~AR 67 (565)
|.+++--.+.|..-- -+...+|+.|.|++++ ...|.|++..++.+. +-.|+|...+
T Consensus 83 EVSSPGldRpL~~~~--~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~~~~~~~~~v~~~~~~ 144 (173)
T PRK14641 83 MVSSPGLGEPIILPR--QYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVSLTEGEGASIVLKPEQ 144 (173)
T ss_pred EEeCCCCCCcCCCHH--HHHHhCCCEEEEEEecccCCeEEEEEEEEeeecccCCCCcEEEEecc
Confidence 444444444444322 2467899999999976 347999999998533 3455554443
No 65
>PRK14644 hypothetical protein; Provisional
Probab=23.49 E-value=1.4e+02 Score=28.30 Aligned_cols=49 Identities=18% Similarity=0.184 Sum_probs=37.4
Q ss_pred cccCCCCCCChHHHHHHHHHhccCceEEEEEccC----CEEEEEEEeeccCCCeeEEEe
Q 038314 10 ETTHSNNSSSLSEALLFATMCIIGLPVDVYIKDG----SVYSGIFYTASVEKDYGIVLK 64 (565)
Q Consensus 10 ~~~~~~~~~sl~DRLlfllt~LIG~~VeVtvKdG----svYeGIF~TaS~e~d~gVVLK 64 (565)
|.+++--.+.+..+ . +...+|..|.|++++. ..|.|++..++-+ .|+|.
T Consensus 65 EVSSPGldRpL~~~--~-f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~---~i~l~ 117 (136)
T PRK14644 65 DISSPGFDMDYETD--E-LENHIGEIIDVSLNKEVNKTDFITGELLENNPE---TITLK 117 (136)
T ss_pred EEECCCCCCCCCHH--H-HHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC---EEEEE
Confidence 56666667777753 3 5678999999999988 8899999998743 46664
No 66
>KOG4264 consensus Nucleo-cytoplasmic protein MLN51 [General function prediction only]
Probab=23.25 E-value=2.1e+02 Score=33.31 Aligned_cols=55 Identities=24% Similarity=0.316 Sum_probs=27.8
Q ss_pred ceEEecccCccc---C-CC-CCCCCCCCCCCCccccccccccCCcCCCce------eeeecCcccccCC
Q 038314 472 QLVYMQPVSNDL---G-VA-AMSPVSARPALTPHQVQFPKHQGNAAGQAL------QLCIPSPMVAGGL 529 (565)
Q Consensus 472 qlvYv~~~~~d~---g-~~-~~~~~~~~p~l~~~q~q~~k~qg~~~gq~~------~~~~~~p~~~~g~ 529 (565)
|-.||+|- -|| | .+ ...+-..-+-+++-+++|+-- .-.-|.. -.+|+|+.|+.|.
T Consensus 558 qg~yv~p~-a~lp~pg~~~y~~p~p~~n~~~~ppp~~~~pg--~pPpq~~q~l~~ptyfvpP~qmt~g~ 623 (694)
T KOG4264|consen 558 QGGYVSPN-ADLPSPGGGGYHGPPPHHNNHHNPPPKRFVPG--PPPPQVAQGLVVPTYFVPPPQMTRGS 623 (694)
T ss_pred cccccCCc-ccCCCCCcccCCCCCCCCCCCCCCCccccCCC--CCCccccccccccccccCccccccCC
Confidence 56677776 344 1 11 111122223466666776532 2222222 2567889998874
No 67
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=23.12 E-value=1.6e+02 Score=29.91 Aligned_cols=29 Identities=24% Similarity=0.231 Sum_probs=24.8
Q ss_pred HHhccCceEEEEEccCCEEEEEEEeeccC
Q 038314 28 TMCIIGLPVDVYIKDGSVYSGIFYTASVE 56 (565)
Q Consensus 28 lt~LIG~~VeVtvKdGsvYeGIF~TaS~e 56 (565)
...|||+.|.+.-.+|..++|+..+....
T Consensus 113 a~slIGK~V~~~~~dG~~vtG~V~sV~~~ 141 (190)
T PRK06792 113 GMKFLGKYVRGVSNDGKQVTGQVETVRLA 141 (190)
T ss_pred HHHhcCcEEEEEcCCCCEEEEEEEEEEEc
Confidence 35899999999889999999999987653
No 68
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=22.28 E-value=2.6e+02 Score=24.70 Aligned_cols=45 Identities=20% Similarity=0.351 Sum_probs=36.1
Q ss_pred CChHHHHHHHHHhccCceEEEEEccCCEEEEEEEeeccCCCeeEEEecc
Q 038314 18 SSLSEALLFATMCIIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKA 66 (565)
Q Consensus 18 ~sl~DRLlfllt~LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~A 66 (565)
..+.|.+++.+- .=+-+|.|.+.||-+-.|...++|. |.|.||.-
T Consensus 5 ~nlQD~fLn~~R-k~~i~VtIfLvNG~~L~G~V~sfD~---f~VlL~~~ 49 (77)
T COG1923 5 QNLQDPFLNALR-KEKIPVTIFLVNGFKLQGQVESFDN---FVVLLKNT 49 (77)
T ss_pred cccchHHHHHHH-hcCCeEEEEEEcCEEEEEEEEeeee---EEEEEEcC
Confidence 457788888744 4578999999999999999999884 77777643
No 69
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=21.93 E-value=2.6e+02 Score=26.21 Aligned_cols=63 Identities=22% Similarity=0.332 Sum_probs=39.9
Q ss_pred ccCceEEEEEccCCEEEEEEEeeccCCCeeEEEecccccc-CCCCCCCcCCCCceeeeeeecCceEEEEEcCc
Q 038314 31 IIGLPVDVYIKDGSVYSGIFYTASVEKDYGIVLKKAKMSK-KGKSNANVANGTVIETLVILSADLVQVVAKGV 102 (565)
Q Consensus 31 LIG~~VeVtvKdGsvYeGIF~TaS~e~d~gVVLK~AR~i~-~G~s~anv~sg~i~eTLVI~~kDIVqV~AkdV 102 (565)
.-|+-|++.+++|++|.|-+.-+.- .+.+.|...-.+. +|.. .-.|...|.++.|-=+++-|+
T Consensus 13 aqGhIVt~Et~tGe~YRGkliEaeD--nmNcql~di~vT~~dg~v-------s~le~V~IRGS~IRFlvlPdm 76 (119)
T KOG3172|consen 13 AQGHIVTVETKTGEVYRGKLIEAED--NMNCQLRDITVTARDGRV-------SQLEQVFIRGSKIRFLVLPDM 76 (119)
T ss_pred ccCcEEEEEecCCceeeeeeEEecc--ccccEEEEEEEEccCCcc-------eeeeeEEEecCeEEEEECchH
Confidence 4588999999999999999987643 2344444433221 1111 113677778877777665444
Done!