Query 011128
Match_columns 493
No_of_seqs 148 out of 200
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 08:25:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011128.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011128hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1073 Uncharacterized mRNA-a 100.0 1.1E-38 2.5E-43 322.0 15.0 145 16-202 3-149 (361)
2 PF12701 LSM14: Scd6-like Sm d 100.0 2.9E-36 6.3E-41 257.1 7.8 93 16-145 2-95 (96)
3 cd01736 LSm14_N LSm14 (also kn 100.0 8.6E-35 1.9E-39 238.8 7.6 70 17-86 1-71 (74)
4 cd00600 Sm_like The eukaryotic 97.8 4.2E-05 9E-10 58.7 5.2 58 18-86 2-60 (63)
5 PF14438 SM-ATX: Ataxin 2 SM d 97.8 1.3E-05 2.8E-10 65.1 2.1 66 18-86 8-76 (77)
6 PF01423 LSM: LSM domain ; In 96.4 0.006 1.3E-07 47.7 4.6 59 18-86 4-63 (67)
7 cd01719 Sm_G The eukaryotic Sm 95.9 0.016 3.5E-07 47.5 5.3 59 17-86 5-64 (72)
8 cd01737 LSm16_N LSm16 belongs 95.9 0.021 4.6E-07 46.7 5.7 56 18-86 2-59 (62)
9 cd01722 Sm_F The eukaryotic Sm 95.8 0.021 4.5E-07 46.0 5.5 58 18-86 7-65 (68)
10 smart00651 Sm snRNP Sm protein 95.6 0.021 4.6E-07 44.5 4.7 59 18-86 4-63 (67)
11 cd01731 archaeal_Sm1 The archa 95.6 0.022 4.8E-07 45.5 4.7 58 18-86 6-64 (68)
12 cd01726 LSm6 The eukaryotic Sm 95.6 0.025 5.3E-07 45.3 4.9 58 18-86 6-64 (67)
13 cd01728 LSm1 The eukaryotic Sm 95.5 0.034 7.5E-07 46.1 5.7 61 18-86 8-69 (74)
14 PRK00737 small nuclear ribonuc 95.4 0.026 5.7E-07 45.9 4.6 58 18-86 10-68 (72)
15 cd01717 Sm_B The eukaryotic Sm 94.3 0.13 2.8E-06 42.5 5.9 69 17-86 5-74 (79)
16 cd01725 LSm2 The eukaryotic Sm 94.2 0.13 2.7E-06 43.1 5.9 59 19-86 8-67 (81)
17 cd01723 LSm4 The eukaryotic Sm 94.2 0.092 2E-06 43.2 4.9 58 19-86 8-66 (76)
18 COG1958 LSM1 Small nuclear rib 94.0 0.15 3.2E-06 41.9 5.8 60 18-86 13-75 (79)
19 cd01727 LSm8 The eukaryotic Sm 93.2 0.18 3.9E-06 41.2 5.1 61 17-86 4-67 (74)
20 cd01721 Sm_D3 The eukaryotic S 93.2 0.19 4E-06 40.9 5.0 58 18-86 6-64 (70)
21 cd01724 Sm_D1 The eukaryotic S 93.1 0.19 4.2E-06 43.0 5.2 57 19-86 8-65 (90)
22 cd01729 LSm7 The eukaryotic Sm 92.8 0.33 7.2E-06 40.7 6.2 66 18-86 8-74 (81)
23 cd01733 LSm10 The eukaryotic S 90.7 0.51 1.1E-05 39.5 5.0 57 19-86 16-73 (78)
24 cd06168 LSm9 The eukaryotic Sm 88.3 1.4 2.9E-05 36.8 5.7 64 18-86 6-70 (75)
25 cd01732 LSm5 The eukaryotic Sm 87.5 1.4 3.1E-05 36.7 5.4 60 19-86 10-70 (76)
26 KOG1775 U6 snRNA-associated Sm 83.8 0.56 1.2E-05 40.4 1.3 59 18-86 13-74 (84)
27 cd01720 Sm_D2 The eukaryotic S 80.8 5 0.00011 34.5 6.0 65 21-86 13-81 (87)
28 cd01730 LSm3 The eukaryotic Sm 79.6 6.6 0.00014 32.8 6.2 67 19-86 8-78 (82)
29 PF06372 Gemin6: Gemin6 protei 73.2 5 0.00011 38.5 4.3 41 18-61 13-53 (166)
30 KOG1924 RhoA GTPase effector D 62.0 38 0.00081 40.0 8.9 9 254-262 606-614 (1102)
31 cd01718 Sm_E The eukaryotic Sm 50.3 35 0.00075 29.1 4.9 57 20-86 14-75 (79)
32 KOG3428 Small nuclear ribonucl 47.8 9.3 0.0002 34.8 1.1 33 22-55 12-44 (109)
33 PTZ00138 small nuclear ribonuc 46.9 38 0.00083 29.5 4.7 52 25-86 31-83 (89)
34 PF11208 DUF2992: Protein of u 46.7 3.6 7.9E-05 38.0 -1.6 44 32-86 7-50 (132)
35 PF02237 BPL_C: Biotin protein 43.9 39 0.00083 25.6 3.8 30 20-51 1-30 (48)
36 PRK14631 hypothetical protein; 40.0 41 0.00089 32.3 4.2 37 16-52 111-151 (174)
37 PRK14638 hypothetical protein; 38.8 44 0.00095 31.2 4.1 35 16-52 94-128 (150)
38 KOG1924 RhoA GTPase effector D 38.7 2.3E+02 0.0051 33.9 10.4 6 85-90 428-433 (1102)
39 KOG3344 40s ribosomal protein 38.3 18 0.0004 34.4 1.6 20 446-468 130-149 (150)
40 KOG3448 Predicted snRNP core p 38.1 68 0.0015 28.7 4.9 60 19-86 9-68 (96)
41 PRK14644 hypothetical protein; 37.8 49 0.0011 30.6 4.2 35 16-52 79-117 (136)
42 KOG2567 Uncharacterized conser 36.1 38 0.00081 33.2 3.3 39 426-468 119-158 (179)
43 KOG4849 mRNA cleavage factor I 33.4 3.1E+02 0.0067 30.2 9.7 26 14-46 70-95 (498)
44 KOG2236 Uncharacterized conser 33.2 3.1E+02 0.0066 30.8 9.8 15 83-97 267-283 (483)
45 KOG1783 Small nuclear ribonucl 31.5 28 0.00061 30.0 1.5 60 17-86 11-70 (77)
46 KOG3973 Uncharacterized conser 31.1 32 0.0007 37.2 2.2 9 451-459 352-360 (465)
47 KOG1659 Class 2 transcription 30.9 25 0.00054 35.4 1.3 15 457-471 135-149 (224)
48 cd01735 LSm12_N LSm12 belongs 29.6 1E+02 0.0022 25.3 4.4 33 20-52 4-36 (61)
49 PF00467 KOW: KOW motif; Inte 28.8 91 0.002 21.8 3.4 31 22-52 2-32 (32)
50 PRK14642 hypothetical protein; 27.4 75 0.0016 31.4 3.8 69 16-88 94-176 (197)
51 PRK14633 hypothetical protein; 26.2 93 0.002 29.0 4.0 35 16-52 88-126 (150)
52 PRK14634 hypothetical protein; 25.5 93 0.002 29.2 3.9 35 16-52 94-132 (155)
53 PF02576 DUF150: Uncharacteris 24.9 72 0.0016 28.8 3.0 33 17-51 82-118 (141)
54 PF07076 DUF1344: Protein of u 24.6 66 0.0014 26.7 2.4 21 35-55 5-25 (61)
55 PRK14641 hypothetical protein; 24.4 1.1E+02 0.0023 29.6 4.2 38 16-53 98-142 (173)
56 PRK02001 hypothetical protein; 23.8 1.1E+02 0.0023 29.0 4.0 65 16-90 84-150 (152)
57 PRK14643 hypothetical protein; 23.6 1.1E+02 0.0023 29.2 4.0 36 16-51 98-137 (164)
58 KOG4795 Protein associated wit 23.1 80 0.0017 32.6 3.2 18 77-94 72-93 (264)
59 PRK14632 hypothetical protein; 22.5 1.1E+02 0.0025 29.2 3.9 35 16-52 92-133 (172)
60 COG1588 POP4 RNase P/RNase MRP 20.8 86 0.0019 28.1 2.6 67 17-99 12-82 (95)
61 PF10842 DUF2642: Protein of u 20.8 1.3E+02 0.0028 25.1 3.5 33 18-53 17-49 (66)
62 PRK14639 hypothetical protein; 20.3 1.4E+02 0.003 27.6 3.9 36 16-53 82-117 (140)
63 cd01734 YlxS_C YxlS is a Bacil 20.1 1.4E+02 0.0031 24.8 3.6 35 16-52 19-57 (83)
No 1
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.1e-38 Score=322.04 Aligned_cols=145 Identities=43% Similarity=0.644 Sum_probs=117.6
Q ss_pred CCCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcccccccccc
Q 011128 16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITG 94 (493)
Q Consensus 16 ~~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK~~~~~~~g 94 (493)
.+++|||||||||||.|||||||||+||++||||+|+||| ||||||+++++++|+.++|||||||||||||
T Consensus 3 ~~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIK-------- 74 (361)
T KOG1073|consen 3 LVTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIK-------- 74 (361)
T ss_pred cccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccc--------
Confidence 5799999999999999999999999999999999999999 9999999999999999999999999999999
Q ss_pred cCCCCCCcccccccchhhccccCCCCceEecCCCCCCCCCCCCChhhhcccCCcccccccCCCC-CCCCCCCCCCCCCCC
Q 011128 95 DAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHNDPAIIQSHYSQAAIASTTLPS-GTGSLPDPTSQTSQL 173 (493)
Q Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~~~Dl~v~~~p~~~~~~~~~~dpai~~s~~~~~~~assslPs-~sGsl~~~ss~~~q~ 173 (493)
||+||+.|..+.....+.+|+|... .++++ .+++.+..+.+..+.
T Consensus 75 -------------------------DL~V~~~p~~~~~~~~p~~pp~p~~---------~~~~s~~s~~~~~~s~~~~~~ 120 (361)
T KOG1073|consen 75 -------------------------DLIVQETPAGQIPCSLPVPPPMPPQ---------SSIPSQQSGSDPKISFQFAQA 120 (361)
T ss_pred -------------------------eeeeccCcccCccccccCCCCCCcc---------cccccccCCcccccccccccC
Confidence 9999998765555667777777221 11222 344555555565555
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 011128 174 GLSRPPFQGNPPLYQPGGSLGAWGSSPMP 202 (493)
Q Consensus 174 g~p~P~fqg~~PlYQPg~~lg~wG~sPpp 202 (493)
+-+.-.++++++.+++....|.|.....+
T Consensus 121 ~~~~~~~P~~~~~~~~~~~~g~~~~~~~~ 149 (361)
T KOG1073|consen 121 GNPVIGNPQGLITTNPVPAEGSIYGSFQP 149 (361)
T ss_pred CCcccCCcCccccCCCCccccccccccCC
Confidence 55555566777788888888998887744
No 2
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=100.00 E-value=2.9e-36 Score=257.07 Aligned_cols=93 Identities=54% Similarity=0.916 Sum_probs=71.8
Q ss_pred CCCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcccccccccc
Q 011128 16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITG 94 (493)
Q Consensus 16 ~~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK~~~~~~~g 94 (493)
++++|||++||||||++|||||+||+||.+++||+|+||| ||||||+++. +|||++++||||+|||+|||
T Consensus 2 m~~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~-~ipp~~~v~~~I~Fr~sDIk-------- 72 (96)
T PF12701_consen 2 MADPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDR-EIPPSDEVYDYIVFRGSDIK-------- 72 (96)
T ss_dssp -CCCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS----C-CSSSSEEEEETTTEE--------
T ss_pred ccccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCc-ccCCCCceeeEEEEEccccc--------
Confidence 5789999999999999999999999999999999999999 9999999886 89999999999999999999
Q ss_pred cCCCCCCcccccccchhhccccCCCCceEecCCCCCCCCCCCCChhhhccc
Q 011128 95 DAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHNDPAIIQSH 145 (493)
Q Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~~~Dl~v~~~p~~~~~~~~~~dpai~~s~ 145 (493)
||+|++.++. ...++||||++.+
T Consensus 73 -------------------------dL~v~e~~~~---~~~~~dpAiv~~~ 95 (96)
T PF12701_consen 73 -------------------------DLKVIEPPPP---PPAPQDPAIVSVS 95 (96)
T ss_dssp -------------------------EEEECE-S-S---SSS----------
T ss_pred -------------------------eEEEEcCCCC---CCCCCCCceeecC
Confidence 9999998754 5579999999864
No 3
>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=100.00 E-value=8.6e-35 Score=238.84 Aligned_cols=70 Identities=60% Similarity=1.058 Sum_probs=68.1
Q ss_pred CCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 17 ~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
+.+|||++||||||+||||||+||+||.+++||+|+||| ||||||++++++|||+++|||||+|||+|||
T Consensus 1 ~~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIk 71 (74)
T cd01736 1 VTPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIK 71 (74)
T ss_pred CccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccc
Confidence 468999999999999999999999999999999999999 9999999988789999999999999999999
No 4
>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=97.79 E-value=4.2e-05 Score=58.74 Aligned_cols=58 Identities=19% Similarity=0.414 Sum_probs=49.9
Q ss_pred CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..++|++|.+..+.+..|+|+|..+| +...|.|+|+. +.++++ ...++.++.||+.|+
T Consensus 2 ~~~~g~~V~V~l~~g~~~~G~L~~~D-~~~Ni~L~~~~~~~~~~~----------~~~~~~~~irG~~I~ 60 (63)
T cd00600 2 KDLVGKTVRVELKDGRVLEGVLVAFD-KYMNLVLDDVEETIKEGK----------KRVLGLVLIRGDNVR 60 (63)
T ss_pred hHHCCCEEEEEECCCcEEEEEEEEEC-CCCCEEECCEEEEecCCc----------EEECCeEEEECCEEE
Confidence 46899999999999999999999999 45599999999 888733 233778999999998
No 5
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.76 E-value=1.3e-05 Score=65.05 Aligned_cols=66 Identities=23% Similarity=0.430 Sum_probs=43.3
Q ss_pred CccccceEEEEecCCceeEEEeeeecCC--CCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTE--ESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e--~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..+||+++.+..|.+-+|||||+..|.+ +..|.|+.+| -..+.... .-.-+.++-+.++|+++||-
T Consensus 8 ~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~---~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 8 TNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSN---SDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS---------EEEEEEE-GGGEEE-----
T ss_pred HhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccccccc---CCccCCCCCceEEEeccccC
Confidence 3579999999999999999999999998 8999999999 76665432 23566778888999999985
No 6
>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=96.36 E-value=0.006 Score=47.73 Aligned_cols=59 Identities=20% Similarity=0.382 Sum_probs=48.7
Q ss_pred CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..++|++|.+..+.+..|+|+|..+|. .--+.|+|+. .-.+++ ...-++.++.||+.|.
T Consensus 4 ~~~~g~~V~V~l~~g~~~~G~L~~~D~-~~Nl~L~~~~~~~~~~~---------~~~~~~~~~irG~~I~ 63 (67)
T PF01423_consen 4 QKLIGKRVRVELKNGRTYRGTLVSFDQ-FMNLVLSDVTETIKNGP---------EKRSLGLVFIRGSNIR 63 (67)
T ss_dssp HHTTTSEEEEEETTSEEEEEEEEEEET-TEEEEEEEEEEEETTES---------EEEEEEEEEEEGGGEE
T ss_pred HHhCCcEEEEEEeCCEEEEEEEEEeec-hheEEeeeEEEEECCCC---------cEeECcEEEEECCEEE
Confidence 358999999999999999999999995 6779999999 655554 2233577889999987
No 7
>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=95.93 E-value=0.016 Score=47.52 Aligned_cols=59 Identities=19% Similarity=0.331 Sum_probs=47.9
Q ss_pred CCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 17 ~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
...||+++|.++-|.+..|+|+|..+| +---|.|+|+. +--+++ ...+.-++-||+.|.
T Consensus 5 L~~~i~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~E~~~~~~----------~~~lg~v~IRG~~I~ 64 (72)
T cd01719 5 LKKYMDKKLSLKLNGNRKVSGILRGFD-PFMNLVLDDAVEVNSGGE----------KNNIGMVVIRGNSIV 64 (72)
T ss_pred hHHhCCCeEEEEECCCeEEEEEEEEEc-ccccEEeccEEEEccCCc----------eeEeceEEECCCEEE
Confidence 457899999999999999999999999 66778999997 531111 234677999999998
No 8
>cd01737 LSm16_N LSm16 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. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=95.90 E-value=0.021 Score=46.74 Aligned_cols=56 Identities=27% Similarity=0.529 Sum_probs=45.0
Q ss_pred CccccceEEEEecCCce-eEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 18 DSYIGSLISLTSKSEIR-YEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 18 ~~yIGskISLISKsdIR-YEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..|||+-+||-...++- |.|.+..||.++.||.|++-- -|- |+. +| | ++||.-|||
T Consensus 2 ~dWiGs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~~~~~ngi--k~~----~~------E-Vt~~~~DI~ 59 (62)
T cd01737 2 QDWLGSIVSINCGETLGVYQGLVSAVDQESQTISLAFPFHNGV--KCL----VP------E-VTFRAGDIR 59 (62)
T ss_pred CcccceEEEEecCCceEEEEEEEEEeCccceEEEEeecccCCc--ccc----Cc------e-EEEEEcchh
Confidence 67999999999998874 999999999999999998722 222 221 12 2 899999999
No 9
>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=95.84 E-value=0.021 Score=46.00 Aligned_cols=58 Identities=16% Similarity=0.264 Sum_probs=46.2
Q ss_pred CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..++|++|.+.-|.+..|+|+|..+| +.--|.|+|+. +--+++ ...++.++-||+.|.
T Consensus 7 ~~~~g~~V~V~Lk~g~~~~G~L~~~D-~~mNi~L~~~~e~~~~~~----------~~~lg~~~IRG~~I~ 65 (68)
T cd01722 7 NDLTGKPVIVKLKWGMEYKGTLVSVD-SYMNLQLANTEEYIDGKS----------TGNLGEVLIRCNNVL 65 (68)
T ss_pred HHcCCCEEEEEECCCcEEEEEEEEEC-CCEEEEEeeEEEEeCCcc----------ccCcCcEEEECCEEE
Confidence 35799999999999999999999999 57788999986 421111 123677899999987
No 10
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=95.62 E-value=0.021 Score=44.54 Aligned_cols=59 Identities=19% Similarity=0.326 Sum_probs=47.1
Q ss_pred CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..++|++|.+.-|.+..|+|+|..+|. .-.+.|+|+. ...++ ....-++.++.||+.|.
T Consensus 4 ~~~~~~~V~V~l~~g~~~~G~L~~~D~-~~NlvL~~~~e~~~~~---------~~~~~~~~~~IrG~~I~ 63 (67)
T smart00651 4 KKLIGKRVLVELKNGREYRGTLKGFDQ-FMNLVLEDVEETVKDG---------EKKRKLGLVFIRGNNIV 63 (67)
T ss_pred HHhCCcEEEEEECCCcEEEEEEEEECc-cccEEEccEEEEecCC---------cEEeEeCCEEEcCCEEE
Confidence 468999999999999999999999995 6788999988 55542 11223556888999887
No 11
>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=95.58 E-value=0.022 Score=45.55 Aligned_cols=58 Identities=12% Similarity=0.248 Sum_probs=46.6
Q ss_pred CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..++|++|.+..|.+-.|+|+|..+|. .--|.|+|+. +-.+++ ..-+..++.||+.|.
T Consensus 6 ~~~~~~~V~V~l~~g~~~~G~L~~~D~-~mNlvL~~~~e~~~~~~----------~~~lg~~~iRG~~I~ 64 (68)
T cd01731 6 KDSLNKPVLVKLKGGKEVRGRLKSYDQ-HMNLVLEDAEEIDDGEP----------VRKYGRVVIRGDNVL 64 (68)
T ss_pred HHhcCCEEEEEECCCCEEEEEEEEECC-cceEEEeeEEEEecCCe----------EeEcCcEEEeCCEEE
Confidence 358999999999999999999999997 5678899987 543332 122577899999987
No 12
>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=95.57 E-value=0.025 Score=45.35 Aligned_cols=58 Identities=19% Similarity=0.348 Sum_probs=46.4
Q ss_pred CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..++|++|.+.-|.+..|+|+|..+| +.=-|.|+|+. +-.++++ ..++.++-||+.|.
T Consensus 6 ~~~~~~~V~V~Lk~g~~~~G~L~~~D-~~mNlvL~~~~~~~~~~~~----------~~~~~v~IRG~~I~ 64 (67)
T cd01726 6 KAIIGRPVVVKLNSGVDYRGILACLD-GYMNIALEQTEEYVNGQLK----------NKYGDAFIRGNNVL 64 (67)
T ss_pred HhhCCCeEEEEECCCCEEEEEEEEEc-cceeeEEeeEEEEeCCcee----------eEeCCEEEECCEEE
Confidence 35799999999999999999999999 56778999987 5432221 13677999999987
No 13
>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=95.49 E-value=0.034 Score=46.07 Aligned_cols=61 Identities=11% Similarity=0.182 Sum_probs=48.6
Q ss_pred CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..||+++|.++-|.+-.|.|+|..+| +.-.|.|.|+. +-.++.+. .+.....+++||..|-
T Consensus 8 ~~~l~k~v~V~l~~gr~~~G~L~~fD-~~~NlvL~d~~E~~~~~~~~-------~~~~lG~~viRG~~V~ 69 (74)
T cd01728 8 VDDLDKKVVVLLRDGRKLIGILRSFD-QFANLVLQDTVERIYVGDKY-------GDIPRGIFIIRGENVV 69 (74)
T ss_pred HHhcCCEEEEEEcCCeEEEEEEEEEC-CcccEEecceEEEEecCCcc-------ceeEeeEEEEECCEEE
Confidence 57899999999999999999999999 56789999997 55444111 1223678999999886
No 14
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=95.39 E-value=0.026 Score=45.92 Aligned_cols=58 Identities=14% Similarity=0.248 Sum_probs=46.8
Q ss_pred CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..++|++|.+..|.+-.|+|+|..+|. .--|.|+|+. +-.+++ ..-++.++.||+.|.
T Consensus 10 ~~~~~k~V~V~lk~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~~----------~~~lg~v~iRG~~V~ 68 (72)
T PRK00737 10 NNALNSPVLVRLKGGREFRGELQGYDI-HMNLVLDNAEEIQDGEV----------VRKLGKVVIRGDNVV 68 (72)
T ss_pred HHhCCCEEEEEECCCCEEEEEEEEEcc-cceeEEeeEEEEcCCCe----------EeEcCcEEEeCCEEE
Confidence 467999999999999999999999997 6778999987 532211 123677999999987
No 15
>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=94.28 E-value=0.13 Score=42.51 Aligned_cols=69 Identities=13% Similarity=0.223 Sum_probs=51.5
Q ss_pred CCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 17 ~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
-..|||++|.+.-+.+=.|+|+|..+|. ...|.|.|+. +-++.++............+.-++.||..|.
T Consensus 5 l~~~l~~~V~V~l~dgR~~~G~L~~~D~-~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv 74 (79)
T cd01717 5 MLQLINYRLRVTLQDGRQFVGQFLAFDK-HMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIV 74 (79)
T ss_pred hHHHcCCEEEEEECCCcEEEEEEEEEcC-ccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEE
Confidence 4579999999999999999999999995 5778999998 7765543211111112224678999999987
No 16
>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=94.24 E-value=0.13 Score=43.09 Aligned_cols=59 Identities=17% Similarity=0.279 Sum_probs=46.5
Q ss_pred ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..+|++|.+--|.+..|+|+|..+|.- =-|.|+||. ...++.. ....++.|..||+.|+
T Consensus 8 ~l~g~~V~VeLKng~~~~G~L~~vD~~-MNi~L~n~~~~~~~~~~--------~~~~~~~v~IRG~~I~ 67 (81)
T cd01725 8 TLVGKEVTVELKNDLSIRGTLHSVDQY-LNIKLTNISVTDPEKYP--------HMLSVKNCFIRGSVVR 67 (81)
T ss_pred hCCCCEEEEEECCCcEEEEEEEEECCC-cccEEEEEEEEcCCCcc--------cccccCeEEEECCEEE
Confidence 358999999999999999999999964 468999998 6443321 1223578999999999
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=94.19 E-value=0.092 Score=43.20 Aligned_cols=58 Identities=22% Similarity=0.236 Sum_probs=47.1
Q ss_pred ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..+|++|.+--|.+..|+|+|..+|. .-.+.|+||. ...+|.+.. .++.++-||+.|+
T Consensus 8 ~~~g~~V~VeLkng~~~~G~L~~~D~-~mNi~L~~~~~~~~~g~~~~---------~~~~v~IRG~~I~ 66 (76)
T cd01723 8 TAQNHPMLVELKNGETYNGHLVNCDN-WMNIHLREVICTSKDGDKFW---------KMPECYIRGNTIK 66 (76)
T ss_pred hcCCCEEEEEECCCCEEEEEEEEEcC-CCceEEEeEEEECCCCcEee---------eCCcEEEeCCEEE
Confidence 46899999999999999999999996 5678999998 655554211 1466889999998
No 18
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=94.00 E-value=0.15 Score=41.93 Aligned_cols=60 Identities=18% Similarity=0.320 Sum_probs=47.3
Q ss_pred CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-ccc-CCCCCCCCCCCCCCCcee-EEEEecCCcc
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQ-KGEEKIGPQVPPSDKIYE-YILFRGSDIK 86 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGT-EgR~~~~~~IPPsd~Vye-yIvFRGSDIK 86 (493)
..++|++|.+.-|.+..|.|+|..+|.- --|.|+||. ... +|+.. ...+. .++-||+.|+
T Consensus 13 ~~~~~~~V~V~lk~g~~~~G~L~~~D~~-mNlvL~d~~e~~~~~~~~~--------~~~~~~~~~IRG~~I~ 75 (79)
T COG1958 13 KKLLNKRVLVKLKNGREYRGTLVGFDQY-MNLVLDDVEEIISHDGEKN--------VRRLGGEVLIRGDNIV 75 (79)
T ss_pred HHhhCCEEEEEECCCCEEEEEEEEEccc-eeEEEeceEEEeccCCccc--------cceeccEEEEECCcEE
Confidence 4678999999999999999999999975 456899999 665 33321 22244 7999999998
No 19
>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=93.25 E-value=0.18 Score=41.22 Aligned_cols=61 Identities=13% Similarity=0.259 Sum_probs=47.0
Q ss_pred CCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-c--ccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-L--EQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 17 ~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-f--GTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
-..||+++|.++-+.+-.|+|+|..+|.. --|.|.++. + .++.. . ....+..|+.||+.|-
T Consensus 4 L~~~l~~~V~V~l~dgr~~~G~L~~~D~~-~NlvL~~~~E~~~~~~~~----~----~~~~lG~~~iRG~~I~ 67 (74)
T cd01727 4 LEDYLNKTVSVITVDGRVIVGTLKGFDQA-TNLILDDSHERVYSSDEG----V----EQVVLGLYIIRGDNIA 67 (74)
T ss_pred HHHhcCCEEEEEECCCcEEEEEEEEEccc-cCEEccceEEEEecCCCC----c----eeeEeceEEECCCEEE
Confidence 46799999999999999999999999976 667888875 2 22111 0 1234788999999987
No 20
>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=93.19 E-value=0.19 Score=40.91 Aligned_cols=58 Identities=21% Similarity=0.359 Sum_probs=47.3
Q ss_pred CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
...+|++|.+--|.+..|+|+|..+|. .-.+.|+||. ...+|+. .-++.+.-||+.|+
T Consensus 6 ~~~~g~~V~VeLk~g~~~~G~L~~~D~-~MNl~L~~~~~~~~~g~~----------~~~~~v~IRG~nI~ 64 (70)
T cd01721 6 HEAEGHIVTVELKTGEVYRGKLIEAED-NMNCQLKDVTVTARDGRV----------SQLEQVYIRGSKIR 64 (70)
T ss_pred hhCCCCEEEEEECCCcEEEEEEEEEcC-CceeEEEEEEEECCCCcE----------eEcCcEEEeCCEEE
Confidence 356899999999999999999999997 6688999998 4444431 12577899999998
No 21
>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=93.10 E-value=0.19 Score=43.01 Aligned_cols=57 Identities=12% Similarity=0.233 Sum_probs=47.1
Q ss_pred ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..+|+.|.+--|.+..|+|+|..+|. .=-|.|+||. +-.+++. .-|+.++-||+.|+
T Consensus 8 ~l~g~~V~VeLKng~~~~G~L~~vD~-~MNl~L~~a~~~~~~~~~----------~~~~~v~IRG~nI~ 65 (90)
T cd01724 8 KLTNETVTIELKNGTIVHGTITGVDP-SMNTHLKNVKLTLKGRNP----------VPLDTLSIRGNNIR 65 (90)
T ss_pred hCCCCEEEEEECCCCEEEEEEEEEcC-ceeEEEEEEEEEcCCCce----------eEcceEEEeCCEEE
Confidence 46899999999999999999999996 4578999998 6544331 23788999999999
No 22
>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=92.84 E-value=0.33 Score=40.67 Aligned_cols=66 Identities=11% Similarity=0.214 Sum_probs=48.4
Q ss_pred CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..||+++|.+.-|.+-.|+|+|..+|. ---|.|.|+. +-.+... ..++.-....+.-++.||..|-
T Consensus 8 ~~~i~k~V~V~l~~gr~~~G~L~~~D~-~mNlvL~~~~E~~~~~~~--~~~~~~~~~~lG~v~iRG~nV~ 74 (81)
T cd01729 8 SKYVDKKIRVKFQGGREVTGILKGYDQ-LLNLVLDDTVEYLRDPDD--PYKLTDKTRQLGLVVCRGTSVV 74 (81)
T ss_pred HHhcCCeEEEEECCCcEEEEEEEEEcC-cccEEecCEEEEEccCCc--ccccccceeEccEEEEcCCEEE
Confidence 578999999999999999999999996 4567899986 4322111 1112223344788999999997
No 23
>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=90.71 E-value=0.51 Score=39.46 Aligned_cols=57 Identities=18% Similarity=0.373 Sum_probs=45.9
Q ss_pred ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..+|+.|.+--|.+..|+|+|..+|. .=.|.|+||. ...++.. .-++.|+-||+.|+
T Consensus 16 ~l~g~~V~VeLKng~~~~G~L~~vD~-~MNl~L~~~~~~~~~~~~----------~~~~~v~IRG~nI~ 73 (78)
T cd01733 16 GLQGKVVTVELRNETTVTGRIASVDA-FMNIRLAKVTIIDRNGKQ----------VQVEEIMVTGRNIR 73 (78)
T ss_pred HCCCCEEEEEECCCCEEEEEEEEEcC-CceeEEEEEEEEcCCCce----------eECCcEEEECCEEE
Confidence 45899999999999999999999996 4578999998 5333221 13788999999998
No 24
>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=88.28 E-value=1.4 Score=36.81 Aligned_cols=64 Identities=14% Similarity=0.288 Sum_probs=47.6
Q ss_pred CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..|||+++.++-+.+--|+|+|..+|. ..-|.|.|+. |-..... ........+.-++-||..|.
T Consensus 6 ~~~l~~~v~V~l~dgR~~~G~l~~~D~-~~NivL~~~~E~~~~~~~----~~~~~~r~lGlv~IrG~~Iv 70 (75)
T cd06168 6 RSLLGRTMRIHMTDGRTLVGVFLCTDR-DCNIILGSAQEYRPPPDS----FSPTEPRVLGLVMIPGHHIV 70 (75)
T ss_pred HHhcCCeEEEEEcCCeEEEEEEEEEcC-CCcEEecCcEEEEcccCc----cCCccEEEeeeEEEeCCeEE
Confidence 568999999999999999999999996 4567899986 4322111 01122235788999999998
No 25
>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=87.46 E-value=1.4 Score=36.73 Aligned_cols=60 Identities=25% Similarity=0.325 Sum_probs=45.5
Q ss_pred ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
.+++++|.+..|.+-.|+|+|..+|. --.+.|+|+. += + ..++. ...-++-++.||..|.
T Consensus 10 ~~~~~~V~V~l~~gr~~~G~L~g~D~-~mNlvL~da~E~~-~--~~~~~----~~~~lg~v~iRG~nV~ 70 (76)
T cd01732 10 KCIGSRIWIVMKSDKEFVGTLLGFDD-YVNMVLEDVTEYE-I--TPEGR----KITKLDQILLNGNNIC 70 (76)
T ss_pred HhCCCEEEEEECCCeEEEEEEEEecc-ceEEEEccEEEEE-E--cCCCc----eeeEcCeEEEeCCeEE
Confidence 46899999999999999999999995 5778999987 42 1 11111 1123677999999998
No 26
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=83.81 E-value=0.56 Score=40.38 Aligned_cols=59 Identities=25% Similarity=0.393 Sum_probs=46.8
Q ss_pred CccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-c--ccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-L--EQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-f--GTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
+.-||+||-+|=|+|-.++|+|...|-= -.+.|++|. | -+|||+... .+.|+.+|..|-
T Consensus 13 DkcIgski~iimksdkE~~GtL~GFDd~-VNmvLeDvtEye~~~egr~~tk---------~~~iLLnGNni~ 74 (84)
T KOG1775|consen 13 DKCIGSKIWIIMKSDKEFVGTLVGFDDF-VNMVLEDVTEYEITPEGRRMTK---------LDQILLNGNNIT 74 (84)
T ss_pred HHhcCceEEEEEccCceeeeEEechHHH-HHHHHHhhhheeeCCCcceeee---------eeeeeecCCcEE
Confidence 4569999999999999999999988742 235788988 5 457776432 678999999987
No 27
>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=80.81 E-value=5 Score=34.54 Aligned_cols=65 Identities=9% Similarity=0.172 Sum_probs=47.5
Q ss_pred ccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCC---CCCCCCCCceeEEEEecCCcc
Q 011128 21 IGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIG---PQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 21 IGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~---~~IPPsd~VyeyIvFRGSDIK 86 (493)
.|++|.+.-|.+-.|.|+|..+|. .-.|.|.|+. +-++..+... .+.......+..|+.||..|.
T Consensus 13 ~~~~V~V~lr~~r~~~G~L~~fD~-hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv 81 (87)
T cd01720 13 NNTQVLINCRNNKKLLGRVKAFDR-HCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI 81 (87)
T ss_pred CCCEEEEEEcCCCEEEEEEEEecC-ccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence 389999999999999999999996 6789999998 6555322111 111112223588999999987
No 28
>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=79.64 E-value=6.6 Score=32.81 Aligned_cols=67 Identities=9% Similarity=0.119 Sum_probs=46.1
Q ss_pred ccccceEEEEecCCceeEEEeeeecCCCCeeEecccc-cccC-CCCCCC--CCCCCCCCceeEEEEecCCcc
Q 011128 19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQK-GEEKIG--PQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTE-gR~~~~--~~IPPsd~VyeyIvFRGSDIK 86 (493)
.+++++|.++.|.+-.|+|+|...|. --.|.|.|+. +-.+ ...... ..+......+.-++.||..|.
T Consensus 8 ~~~~k~V~V~l~~gr~~~G~L~~fD~-~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv 78 (82)
T cd01730 8 LSLDERVYVKLRGDRELRGRLHAYDQ-HLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVI 78 (82)
T ss_pred HhCCCEEEEEECCCCEEEEEEEEEcc-ceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEE
Confidence 45899999999999999999999996 5678999987 4322 111100 001112224577889998886
No 29
>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=73.17 E-value=5 Score=38.48 Aligned_cols=41 Identities=27% Similarity=0.562 Sum_probs=30.3
Q ss_pred CccccceEEEEecCCceeEEEeeeecCCCCeeEecccccccCCC
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGE 61 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVRfGTEgR 61 (493)
..|+|+.+.+.... --|.|.||+||+.-.+|.|-| |.++|+
T Consensus 13 ~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~--~~e~~~ 53 (166)
T PF06372_consen 13 QDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVN--FQEDGK 53 (166)
T ss_dssp HCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEE--E-TTS-
T ss_pred HHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEE--cccCCc
Confidence 47999999999997 889999999999999999876 444444
No 30
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=62.04 E-value=38 Score=40.03 Aligned_cols=9 Identities=56% Similarity=1.051 Sum_probs=4.9
Q ss_pred CCCCCCCCC
Q 011128 254 MNPSLPTGV 262 (493)
Q Consensus 254 ~~~Slptg~ 262 (493)
+.+-||-|+
T Consensus 606 maPvlP~gL 614 (1102)
T KOG1924|consen 606 MAPVLPFGL 614 (1102)
T ss_pred ccccCCCCC
Confidence 444566665
No 31
>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=50.30 E-value=35 Score=29.11 Aligned_cols=57 Identities=21% Similarity=0.437 Sum_probs=37.5
Q ss_pred cccce--EEE--EecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 20 YIGSL--ISL--TSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 20 yIGsk--ISL--ISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
|+.++ |.+ .-+.+..|+|+|..+|.- --|.|.|+. +-.++ . ....++.|+-||+.|.
T Consensus 14 ~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~-mNlvL~d~~E~~~~~-----~----~~~~lG~iliRGnnV~ 75 (79)
T cd01718 14 FLQSKQRVQIWLYEQTDLRIEGVIIGFDEY-MNLVLDDAEEVHLKT-----K----TRKPLGRILLKGDNIT 75 (79)
T ss_pred HHccCcEEEEEEEeCCCcEEEEEEEEEccc-eeEEEcCEEEEecCC-----c----eEeEcCcEEEeCCEEE
Confidence 55553 333 346999999999999963 357888875 32111 0 0112677999999887
No 32
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=47.84 E-value=9.3 Score=34.77 Aligned_cols=33 Identities=9% Similarity=0.231 Sum_probs=19.8
Q ss_pred cceEEEEecCCceeEEEeeeecCCCCeeEecccc
Q 011128 22 GSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR 55 (493)
Q Consensus 22 GskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR 55 (493)
+.++.+=-|.+-+-+|+|..+|..=.+ -|.+|+
T Consensus 12 ~e~vtIeLkngt~v~G~I~~Vd~~Mn~-~l~~v~ 44 (109)
T KOG3428|consen 12 NERVTIELKNGTIVHGTIDSVDVQMNT-HLKHVK 44 (109)
T ss_pred CCeEEEEecCCcEEeeeEEEEEhhhee-EEEEEE
Confidence 345555556666666777777665444 466666
No 33
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=46.85 E-value=38 Score=29.53 Aligned_cols=52 Identities=21% Similarity=0.321 Sum_probs=35.4
Q ss_pred EEEEecCCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 25 ISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 25 ISLISKsdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
|.+..+.+.+|+|+|..+|.- --|.|.|+. +=. +.. ...-+..|+-||+.|.
T Consensus 31 i~l~~~~~r~~~G~L~gfD~~-mNlVL~d~~E~~~-----~~~----~~~~lG~ilIRGnnV~ 83 (89)
T PTZ00138 31 IWLYDHPNLRIEGKILGFDEY-MNMVLDDAEEVYT-----KKN----TRKDLGRILLKGDNIT 83 (89)
T ss_pred EEEEeCCCcEEEEEEEEEccc-ceEEEccEEEEec-----CCc----eeeEcCeEEEcCCEEE
Confidence 334456679999999999964 467888876 311 101 1223677999999987
No 34
>PF11208 DUF2992: Protein of unknown function (DUF2992); InterPro: IPR016787 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=46.67 E-value=3.6 Score=37.99 Aligned_cols=44 Identities=18% Similarity=0.294 Sum_probs=35.8
Q ss_pred CceeEEEeeeecCCCCeeEecccccccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 32 EIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 32 dIRYEGiL~~Id~e~sTIaL~nVRfGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
+-=|+|++-..| ++++....|.||.| |-..+||+||+.+..+++
T Consensus 7 g~FWvGv~E~~~--~~~~~v~rv~FG~E---------P~d~Ei~~fi~~~~~~L~ 50 (132)
T PF11208_consen 7 GPFWVGVFERHE--DGKYKVARVTFGAE---------PKDPEIYEFILKHWYKLR 50 (132)
T ss_pred CCcEEEEEEEEE--CCEEEEEEEeeCCC---------CCcHHHHHHHHHHHHHhc
Confidence 344899999886 68889989889976 455689999999888887
No 35
>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=43.92 E-value=39 Score=25.56 Aligned_cols=30 Identities=13% Similarity=0.305 Sum_probs=23.1
Q ss_pred cccceEEEEecCCceeEEEeeeecCCCCeeEe
Q 011128 20 YIGSLISLTSKSEIRYEGVLFNINTEESSIGL 51 (493)
Q Consensus 20 yIGskISLISKsdIRYEGiL~~Id~e~sTIaL 51 (493)
.||+.|++.. .+-.|+|+...||.+- -+-|
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G-~L~v 30 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDG-ALLV 30 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTS-EEEE
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCC-EEEE
Confidence 4899999999 5555899999998644 3433
No 36
>PRK14631 hypothetical protein; Provisional
Probab=39.99 E-value=41 Score=32.31 Aligned_cols=37 Identities=19% Similarity=0.434 Sum_probs=30.9
Q ss_pred CCCccccceEEEEec----CCceeEEEeeeecCCCCeeEec
Q 011128 16 SADSYIGSLISLTSK----SEIRYEGVLFNINTEESSIGLR 52 (493)
Q Consensus 16 ~~~~yIGskISLISK----sdIRYEGiL~~Id~e~sTIaL~ 52 (493)
+...|+|.+|.|..+ ..-+|+|+|..+|.++.+|+|.
T Consensus 111 df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~~v~l~ 151 (174)
T PRK14631 111 QLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLENEEIQVE 151 (174)
T ss_pred HHHHhCCCeEEEEEecccCCceEEEEEEEEeecCCCEEEEE
Confidence 445799999999985 4578999999999888888885
No 37
>PRK14638 hypothetical protein; Provisional
Probab=38.81 E-value=44 Score=31.19 Aligned_cols=35 Identities=14% Similarity=0.264 Sum_probs=29.2
Q ss_pred CCCccccceEEEEecCCceeEEEeeeecCCCCeeEec
Q 011128 16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLR 52 (493)
Q Consensus 16 ~~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~ 52 (493)
+...|+|++|.+..+..-+|+|+|..+|- .+|+|.
T Consensus 94 ~f~r~~G~~v~V~~~~~k~~~G~L~~~~~--~~i~l~ 128 (150)
T PRK14638 94 DYVRFTGKLAKIVTKDGKTFIGRIESFVD--GTITIS 128 (150)
T ss_pred HHHHhCCCEEEEEECCCcEEEEEEEEEeC--CEEEEE
Confidence 34578999999999999999999999984 566665
No 38
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=38.72 E-value=2.3e+02 Score=33.95 Aligned_cols=6 Identities=33% Similarity=0.988 Sum_probs=2.6
Q ss_pred cccccc
Q 011128 85 IKHCLL 90 (493)
Q Consensus 85 IK~~~~ 90 (493)
|+||||
T Consensus 428 IEecIS 433 (1102)
T KOG1924|consen 428 IEECIS 433 (1102)
T ss_pred HHHHHH
Confidence 345543
No 39
>KOG3344 consensus 40s ribosomal protein s10 [Translation, ribosomal structure and biogenesis]
Probab=38.34 E-value=18 Score=34.39 Aligned_cols=20 Identities=45% Similarity=0.652 Sum_probs=15.5
Q ss_pred CCCCCcccccCCCCCCCCcccCC
Q 011128 446 PYGAPTSTQYGYRGGRGRGRGRG 468 (493)
Q Consensus 446 ~~ga~~~~~~~~~~~rgrgrgrg 468 (493)
..||++.+...|| |||+||+
T Consensus 130 ~~gA~s~~~~~fr---g~g~g~~ 149 (150)
T KOG3344|consen 130 EGGAGSGTEPQFR---GRGFGRP 149 (150)
T ss_pred CCCCCcccccccc---ccCCCCC
Confidence 6899999999994 4555554
No 40
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=38.08 E-value=68 Score=28.67 Aligned_cols=60 Identities=17% Similarity=0.316 Sum_probs=44.5
Q ss_pred ccccceEEEEecCCceeEEEeeeecCCCCeeEecccccccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 19 ~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVRfGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
..||+.+++-=|.|+.-.|+|+.||.= =.+.|.|+|--.+.+ .|-.-.|-. +-.|||-|+
T Consensus 9 slvg~~V~VeLKnd~~i~GtL~svDqy-LNlkL~di~v~d~~k------yPhm~Sv~n-cfIRGSvvr 68 (96)
T KOG3448|consen 9 SLVGKEVVVELKNDLSICGTLHSVDQY-LNLKLTDISVTDPDK------YPHMLSVKN-CFIRGSVVR 68 (96)
T ss_pred HhcCCeEEEEEcCCcEEEEEecccchh-heeEEeeeEeeCccc------CCCeeeeee-EEEeccEEE
Confidence 469999999999999999999999974 347888988322222 344444444 556999888
No 41
>PRK14644 hypothetical protein; Provisional
Probab=37.84 E-value=49 Score=30.55 Aligned_cols=35 Identities=26% Similarity=0.386 Sum_probs=28.8
Q ss_pred CCCccccceEEEEecCC----ceeEEEeeeecCCCCeeEec
Q 011128 16 SADSYIGSLISLTSKSE----IRYEGVLFNINTEESSIGLR 52 (493)
Q Consensus 16 ~~~~yIGskISLISKsd----IRYEGiL~~Id~e~sTIaL~ 52 (493)
+...|+|++|.+..+.. -+|+|+|..+|- .+|+|.
T Consensus 79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~--~~i~l~ 117 (136)
T PRK14644 79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNP--ETITLK 117 (136)
T ss_pred HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeC--CEEEEE
Confidence 45678999999998776 789999999984 567775
No 42
>KOG2567 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.10 E-value=38 Score=33.18 Aligned_cols=39 Identities=44% Similarity=0.744 Sum_probs=19.9
Q ss_pred CCCCCCCCCC-cCCCCCCCCCCCCCCcccccCCCCCCCCcccCC
Q 011128 426 PPASDVQEPI-LPLPSTTERKPYGAPTSTQYGYRGGRGRGRGRG 468 (493)
Q Consensus 426 ~~~~e~q~Pi-LPLP~~~~qk~~ga~~~~~~~~~~~rgrgrgrg 468 (493)
+..+.-|+|+ -|.|++...-+ ...|-+.+|+|||||||+
T Consensus 119 ~~~~GyQ~P~~~p~p~~~~~~p----~~~~~~s~g~r~~gr~r~ 158 (179)
T KOG2567|consen 119 PTSPGYQPPNPQPHPRSQPRHP----YSPRKPSLGGRGRGRGRA 158 (179)
T ss_pred CCCCCccCCCCCCCCCCcccCC----ccccCCCCCCCCcCcccc
Confidence 4456677776 34442222111 112334677788777766
No 43
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=33.36 E-value=3.1e+02 Score=30.17 Aligned_cols=26 Identities=27% Similarity=0.262 Sum_probs=20.0
Q ss_pred CCCCCccccceEEEEecCCceeEEEeeeecCCC
Q 011128 14 SGSADSYIGSLISLTSKSEIRYEGVLFNINTEE 46 (493)
Q Consensus 14 ~~~~~~yIGskISLISKsdIRYEGiL~~Id~e~ 46 (493)
.+-...|-|+||++ |.|-|.-.-+++
T Consensus 70 ~~~~~s~~Grk~~~-------YvGNL~W~TTD~ 95 (498)
T KOG4849|consen 70 AKPATSSEGRKYCC-------YVGNLLWYTTDA 95 (498)
T ss_pred CCccccccCceEEE-------EecceeEEeccH
Confidence 45667889999988 999987666554
No 44
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.22 E-value=3.1e+02 Score=30.80 Aligned_cols=15 Identities=7% Similarity=0.056 Sum_probs=6.2
Q ss_pred CCccccc--ccccccCC
Q 011128 83 SDIKHCL--LTITGDAI 97 (493)
Q Consensus 83 SDIK~~~--~~~~g~~~ 97 (493)
.+=|||+ -|--|+.|
T Consensus 267 nS~~e~~~~gi~ig~~v 283 (483)
T KOG2236|consen 267 NSEEEISFLGICIGEKV 283 (483)
T ss_pred CchhhhhhhccccCCee
Confidence 3334453 33344443
No 45
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=31.47 E-value=28 Score=30.01 Aligned_cols=60 Identities=20% Similarity=0.339 Sum_probs=39.3
Q ss_pred CCccccceEEEEecCCceeEEEeeeecCCCCeeEecccccccCCCCCCCCCCCCCCCceeEEEEecCCcc
Q 011128 17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (493)
Q Consensus 17 ~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVRfGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK 86 (493)
-..+||+++-+-=.+++-|.|+|..||-= =.|+|+.-. --- ++. -...|.-...||+.|-
T Consensus 11 l~~iiGr~V~VKl~sgvdyrG~l~~lDgy-mNiaLe~te----e~~-ngq----l~n~ygdaFirGnnVl 70 (77)
T KOG1783|consen 11 LKAIIGRTVVVKLNSGVDYRGTLVCLDGY-MNIALESTE----EYV-NGQ----LKNKYGDAFIRGNNVL 70 (77)
T ss_pred HHHHhCCeEEEEecCCccccceehhhhhH-HHHHHHHHH----HHh-cCc----ccccccceeeccccEE
Confidence 35689999999999999999999999942 124444433 111 111 1123555667887776
No 46
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=31.11 E-value=32 Score=37.18 Aligned_cols=9 Identities=44% Similarity=0.464 Sum_probs=5.1
Q ss_pred cccccCCCC
Q 011128 451 TSTQYGYRG 459 (493)
Q Consensus 451 ~~~~~~~~~ 459 (493)
-|-+||.||
T Consensus 352 ~~eqgg~Rg 360 (465)
T KOG3973|consen 352 VLEQGGSRG 360 (465)
T ss_pred hhhccCCCC
Confidence 344567665
No 47
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=30.88 E-value=25 Score=35.45 Aligned_cols=15 Identities=60% Similarity=1.048 Sum_probs=11.1
Q ss_pred CCCCCCCcccCCCCc
Q 011128 457 YRGGRGRGRGRGNEV 471 (493)
Q Consensus 457 ~~~~rgrgrgrg~~~ 471 (493)
-||+||||||||.+.
T Consensus 135 ~~~~rg~Gtg~g~~~ 149 (224)
T KOG1659|consen 135 GSGGRGAGTGRGYKV 149 (224)
T ss_pred cccCcCCCcCCCccc
Confidence 356788888888776
No 48
>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=29.56 E-value=1e+02 Score=25.35 Aligned_cols=33 Identities=21% Similarity=0.274 Sum_probs=29.2
Q ss_pred cccceEEEEecCCceeEEEeeeecCCCCeeEec
Q 011128 20 YIGSLISLTSKSEIRYEGVLFNINTEESSIGLR 52 (493)
Q Consensus 20 yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~ 52 (493)
.||+++++.+-.+=++||.++..|..-.-+.|+
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk 36 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILK 36 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEE
Confidence 589999999999999999999999876666665
No 49
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=28.77 E-value=91 Score=21.80 Aligned_cols=31 Identities=13% Similarity=0.206 Sum_probs=25.6
Q ss_pred cceEEEEecCCceeEEEeeeecCCCCeeEec
Q 011128 22 GSLISLTSKSEIRYEGVLFNINTEESSIGLR 52 (493)
Q Consensus 22 GskISLISKsdIRYEGiL~~Id~e~sTIaL~ 52 (493)
|..+.+|+=..--.+|++..||.++.+|.++
T Consensus 2 Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~ve 32 (32)
T PF00467_consen 2 GDTVKVISGPFKGKIGKIVEIDRSKVRVTVE 32 (32)
T ss_dssp TSEEEESSSTTTTEEEEEEEEETTTTEEEES
T ss_pred CCEEEEeEcCCCCceEEEEEEECCCCEEEEC
Confidence 5667777777777999999999999888763
No 50
>PRK14642 hypothetical protein; Provisional
Probab=27.44 E-value=75 Score=31.41 Aligned_cols=69 Identities=16% Similarity=0.284 Sum_probs=39.5
Q ss_pred CCCccccceEEEEec-------------CCceeEEEeeeecCCCCeeEecccc-cccCCCCCCCCCCCCCCCceeEEEEe
Q 011128 16 SADSYIGSLISLTSK-------------SEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFR 81 (493)
Q Consensus 16 ~~~~yIGskISLISK-------------sdIRYEGiL~~Id~e~sTIaL~nVR-fGTEgR~~~~~~IPPsd~VyeyIvFR 81 (493)
+...|+|++|.+..+ ..-+|+|+|..+|-+.-+|.+.+ + =+-||-+..-..+|. +-.-..|-
T Consensus 94 df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~~i~l~~~~-~~~~k~g~~~~k~~~~~---~~~~~~~~ 169 (197)
T PRK14642 94 DFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESGGWQIVWSD-EPPVKPGQRVSKKRVPA---PLQALGFT 169 (197)
T ss_pred HHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCCEEEEEEee-cccCCCccccccccccc---cceeEEee
Confidence 345689999999887 56789999999986433333332 1 112221100012332 23345577
Q ss_pred cCCcccc
Q 011128 82 GSDIKHC 88 (493)
Q Consensus 82 GSDIK~~ 88 (493)
-+|||+|
T Consensus 170 ~~eik~a 176 (197)
T PRK14642 170 LDELREA 176 (197)
T ss_pred hhheeeE
Confidence 7888844
No 51
>PRK14633 hypothetical protein; Provisional
Probab=26.18 E-value=93 Score=29.03 Aligned_cols=35 Identities=20% Similarity=0.384 Sum_probs=27.6
Q ss_pred CCCccccceEEEEec----CCceeEEEeeeecCCCCeeEec
Q 011128 16 SADSYIGSLISLTSK----SEIRYEGVLFNINTEESSIGLR 52 (493)
Q Consensus 16 ~~~~yIGskISLISK----sdIRYEGiL~~Id~e~sTIaL~ 52 (493)
+...|+|++|.+..+ ..-+|+|+|..+|- .+|+|.
T Consensus 88 ~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~--~~i~l~ 126 (150)
T PRK14633 88 QAQALVGFNVKAVTLAPVGSQTKFKGVLERVEG--NNVILN 126 (150)
T ss_pred HHHHhCCCeEEEEEecccCCcEEEEEEEEEEeC--CEEEEE
Confidence 445799999999884 56889999999864 677774
No 52
>PRK14634 hypothetical protein; Provisional
Probab=25.51 E-value=93 Score=29.22 Aligned_cols=35 Identities=17% Similarity=0.432 Sum_probs=27.1
Q ss_pred CCCccccceEEEEecCC----ceeEEEeeeecCCCCeeEec
Q 011128 16 SADSYIGSLISLTSKSE----IRYEGVLFNINTEESSIGLR 52 (493)
Q Consensus 16 ~~~~yIGskISLISKsd----IRYEGiL~~Id~e~sTIaL~ 52 (493)
+...|+|+++.+..+.. -+|+|+|..+|- ..|+|.
T Consensus 94 ~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~--~~v~l~ 132 (155)
T PRK14634 94 DFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNE--DHLQIN 132 (155)
T ss_pred HHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeC--CEEEEE
Confidence 34578999999988754 499999998874 566664
No 53
>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=24.93 E-value=72 Score=28.81 Aligned_cols=33 Identities=24% Similarity=0.528 Sum_probs=23.7
Q ss_pred CCccccceEEEEec----CCceeEEEeeeecCCCCeeEe
Q 011128 17 ADSYIGSLISLTSK----SEIRYEGVLFNINTEESSIGL 51 (493)
Q Consensus 17 ~~~yIGskISLISK----sdIRYEGiL~~Id~e~sTIaL 51 (493)
...|||.+|.+..+ ..-+|+|+|..+|. .+|+|
T Consensus 82 ~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~--~~i~l 118 (141)
T PF02576_consen 82 FERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE--DEITL 118 (141)
T ss_dssp HHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET--TEEEE
T ss_pred HHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC--CEEEE
Confidence 34689999999984 45679999999997 55555
No 54
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=24.62 E-value=66 Score=26.74 Aligned_cols=21 Identities=29% Similarity=0.493 Sum_probs=19.0
Q ss_pred eEEEeeeecCCCCeeEecccc
Q 011128 35 YEGVLFNINTEESSIGLRNDR 55 (493)
Q Consensus 35 YEGiL~~Id~e~sTIaL~nVR 55 (493)
-||++..||++.-||+|.+=+
T Consensus 5 veG~I~~id~~~~titLdDGk 25 (61)
T PF07076_consen 5 VEGTIKSIDPETMTITLDDGK 25 (61)
T ss_pred ceEEEEEEcCCceEEEecCCC
Confidence 489999999999999999854
No 55
>PRK14641 hypothetical protein; Provisional
Probab=24.35 E-value=1.1e+02 Score=29.57 Aligned_cols=38 Identities=26% Similarity=0.351 Sum_probs=28.2
Q ss_pred CCCccccceEEEEecCCc----eeEEEeeeec---CCCCeeEecc
Q 011128 16 SADSYIGSLISLTSKSEI----RYEGVLFNIN---TEESSIGLRN 53 (493)
Q Consensus 16 ~~~~yIGskISLISKsdI----RYEGiL~~Id---~e~sTIaL~n 53 (493)
+...|+|.+|.+..+..+ +|+|+|..+| .++.+|+|.-
T Consensus 98 ~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~~~~~~~~~v~~~~ 142 (173)
T PRK14641 98 QYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVSLTEGEGASIVLKP 142 (173)
T ss_pred HHHHhCCCEEEEEEecccCCeEEEEEEEEeeecccCCCCcEEEEe
Confidence 345689999999887633 7999999998 3356676644
No 56
>PRK02001 hypothetical protein; Validated
Probab=23.77 E-value=1.1e+02 Score=28.96 Aligned_cols=65 Identities=18% Similarity=0.196 Sum_probs=42.3
Q ss_pred CCCccccceEEEEecCCceeEEEeeeecCCCCeeEecccc--cccCCCCCCCCCCCCCCCceeEEEEecCCcccccc
Q 011128 16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR--LEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLL 90 (493)
Q Consensus 16 ~~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~nVR--fGTEgR~~~~~~IPPsd~VyeyIvFRGSDIK~~~~ 90 (493)
+...|+|.++.+..+.+-+|+|+|..+|- .+|+|. +. =+-++++.. ....+-+.|.=++|+.+.+
T Consensus 84 ~f~r~~G~~v~V~l~~~~~~~G~L~~~~~--~~i~l~-~~~~~~~~~~k~~-------~~~~~~~~i~~~~I~ka~l 150 (152)
T PRK02001 84 QYKKNIGRELEVLTKNGKKIEGELKSADE--NDITLE-VKAREPKEGGKGK-------VTVEKEETITYDDIKEAKV 150 (152)
T ss_pred HHHHhCCCEEEEEECCCCEEEEEEEEEeC--CEEEEE-Ecccccccccccc-------cccceeEEEEhHheeeEEE
Confidence 34578999999999999999999999985 566664 22 112333211 1124556677778885433
No 57
>PRK14643 hypothetical protein; Provisional
Probab=23.57 E-value=1.1e+02 Score=29.22 Aligned_cols=36 Identities=8% Similarity=0.174 Sum_probs=28.9
Q ss_pred CCCccccceEEEEecC----CceeEEEeeeecCCCCeeEe
Q 011128 16 SADSYIGSLISLTSKS----EIRYEGVLFNINTEESSIGL 51 (493)
Q Consensus 16 ~~~~yIGskISLISKs----dIRYEGiL~~Id~e~sTIaL 51 (493)
+...|+|.++.+..+. .-+|+|+|..+|-++-+|.|
T Consensus 98 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l 137 (164)
T PRK14643 98 ELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRF 137 (164)
T ss_pred HHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEE
Confidence 4457899999998765 57899999999987666654
No 58
>KOG4795 consensus Protein associated with transcriptional elongation factor ELL [Transcription]
Probab=23.13 E-value=80 Score=32.59 Aligned_cols=18 Identities=33% Similarity=0.635 Sum_probs=14.7
Q ss_pred EEEEecCCc----ccccccccc
Q 011128 77 YILFRGSDI----KHCLLTITG 94 (493)
Q Consensus 77 yIvFRGSDI----K~~~~~~~g 94 (493)
.+||+|+-= |+||+||+-
T Consensus 72 ~tvFkGsked~k~KdcvLffd~ 93 (264)
T KOG4795|consen 72 KTVFKGSKEDPKDKDCVLFFDE 93 (264)
T ss_pred eeEeccccCCCCccceEEEEec
Confidence 589999865 789999983
No 59
>PRK14632 hypothetical protein; Provisional
Probab=22.51 E-value=1.1e+02 Score=29.17 Aligned_cols=35 Identities=26% Similarity=0.501 Sum_probs=27.5
Q ss_pred CCCccccceEEEEecCC-------ceeEEEeeeecCCCCeeEec
Q 011128 16 SADSYIGSLISLTSKSE-------IRYEGVLFNINTEESSIGLR 52 (493)
Q Consensus 16 ~~~~yIGskISLISKsd-------IRYEGiL~~Id~e~sTIaL~ 52 (493)
+...|||.+|.+..+.- -+|+|+|..+| +.+|+|.
T Consensus 92 ~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~--~~~i~l~ 133 (172)
T PRK14632 92 QMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVE--GDTVVLR 133 (172)
T ss_pred HHHHhCCCEEEEEEeccccccCCceEEEEEEEEEe--CCEEEEE
Confidence 34579999999988774 48999999997 4566665
No 60
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=20.83 E-value=86 Score=28.14 Aligned_cols=67 Identities=21% Similarity=0.454 Sum_probs=50.2
Q ss_pred CCccccceEEEEecCCceeEEEee-eecCCCCeeEecccccccCCCCCCCCCCCCCCCceeEEEEecCC---cccccccc
Q 011128 17 ADSYIGSLISLTSKSEIRYEGVLF-NINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSD---IKHCLLTI 92 (493)
Q Consensus 17 ~~~yIGskISLISKsdIRYEGiL~-~Id~e~sTIaL~nVRfGTEgR~~~~~~IPPsd~VyeyIvFRGSD---IK~~~~~~ 92 (493)
..++||-++.++--.+=-|+||=- -+|-..+|+.+.+ ++|. -.||-..-+|+ |++-| || |
T Consensus 12 ~hEliGl~vrVv~s~~~s~vGI~G~VVdETkNtLvi~t-----~~~~---~~VpK~~~vfe---f~~~~G~~vk-----V 75 (95)
T COG1588 12 RHELIGLEVRVVRSTNPSYVGIEGRVVDETKNTLVIDT-----GSRE---KVVPKDGAVFE---FEGPDGEKVK-----V 75 (95)
T ss_pred hHHhcCcEEEEEecCCCCccceeEEEEeeeccEEEEEC-----CCce---EEEecCcEEEE---EEcCCCcEEE-----E
Confidence 357999999999998888888753 4677888888876 6553 24777777777 56555 77 7
Q ss_pred cccCCCC
Q 011128 93 TGDAISG 99 (493)
Q Consensus 93 ~g~~~~~ 99 (493)
+|+.+-+
T Consensus 76 dG~lL~~ 82 (95)
T COG1588 76 DGRLLLG 82 (95)
T ss_pred cchhhhc
Confidence 8887655
No 61
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=20.77 E-value=1.3e+02 Score=25.15 Aligned_cols=33 Identities=21% Similarity=0.405 Sum_probs=26.5
Q ss_pred CccccceEEEEecCCceeEEEeeeecCCCCeeEecc
Q 011128 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRN 53 (493)
Q Consensus 18 ~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~n 53 (493)
..+||+++-+-+-.+. ++|+|.++.+ +.|.|+.
T Consensus 17 q~liG~~vvV~T~~g~-v~G~L~~V~p--DhIvl~~ 49 (66)
T PF10842_consen 17 QSLIGQRVVVQTTRGS-VRGILVDVKP--DHIVLEE 49 (66)
T ss_pred HHhcCCEEEEEEcCCc-EEEEEEeecC--CEEEEEe
Confidence 3579999999997777 7999999988 5566653
No 62
>PRK14639 hypothetical protein; Provisional
Probab=20.31 E-value=1.4e+02 Score=27.62 Aligned_cols=36 Identities=25% Similarity=0.531 Sum_probs=29.3
Q ss_pred CCCccccceEEEEecCCceeEEEeeeecCCCCeeEecc
Q 011128 16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRN 53 (493)
Q Consensus 16 ~~~~yIGskISLISKsdIRYEGiL~~Id~e~sTIaL~n 53 (493)
+...|+|.+|.+..+..-+|+|+|..+|- .+|+|.+
T Consensus 82 ~f~r~~G~~v~v~l~~~~~~~G~L~~~~~--~~i~l~~ 117 (140)
T PRK14639 82 HFAKSIGELVKITTNEKEKFEGKIVSVDD--ENITLEN 117 (140)
T ss_pred HHHHhCCCEEEEEECCCcEEEEEEEEEeC--CEEEEEE
Confidence 44579999999998888899999999886 5666644
No 63
>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=20.08 E-value=1.4e+02 Score=24.82 Aligned_cols=35 Identities=14% Similarity=0.446 Sum_probs=25.7
Q ss_pred CCCccccceEEEEecC----CceeEEEeeeecCCCCeeEec
Q 011128 16 SADSYIGSLISLTSKS----EIRYEGVLFNINTEESSIGLR 52 (493)
Q Consensus 16 ~~~~yIGskISLISKs----dIRYEGiL~~Id~e~sTIaL~ 52 (493)
+...|+|.+|.+..+. .-+|+|+|..+|-+ .|+|.
T Consensus 19 ~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~--~v~l~ 57 (83)
T cd01734 19 DFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD--TVTLE 57 (83)
T ss_pred HHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC--EEEEE
Confidence 3456899999998873 24699999998764 45553
Done!