Query 007191
Match_columns 613
No_of_seqs 237 out of 308
Neff 3.7
Searched_HMMs 46136
Date Thu Mar 28 20:11:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007191.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007191hhsearch_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 6.3E-39 1.4E-43 333.6 25.7 156 16-222 3-160 (361)
2 PF12701 LSM14: Scd6-like Sm d 100.0 1E-34 2.2E-39 255.1 7.8 93 16-145 2-95 (96)
3 cd01736 LSm14_N LSm14 (also kn 100.0 2.5E-33 5.4E-38 235.9 7.5 70 17-86 1-71 (74)
4 PF09532 FDF: FDF domain; Int 99.7 5.8E-20 1.3E-24 160.8 -4.2 94 476-569 1-103 (104)
5 cd00600 Sm_like The eukaryotic 97.5 0.0002 4.4E-09 57.1 5.3 58 18-86 2-60 (63)
6 PF14438 SM-ATX: Ataxin 2 SM d 97.5 7E-05 1.5E-09 63.0 2.3 66 18-86 8-76 (77)
7 KOG0921 Dosage compensation co 95.7 0.01 2.2E-07 70.1 4.2 9 135-143 603-611 (1282)
8 PF01423 LSM: LSM domain ; In 95.4 0.026 5.6E-07 45.8 4.7 59 18-86 4-63 (67)
9 cd01737 LSm16_N LSm16 belongs 95.3 0.048 1E-06 45.7 5.9 56 18-86 2-59 (62)
10 cd01731 archaeal_Sm1 The archa 94.4 0.084 1.8E-06 43.7 5.2 58 18-86 6-64 (68)
11 smart00651 Sm snRNP Sm protein 94.4 0.07 1.5E-06 43.2 4.7 59 18-86 4-63 (67)
12 cd01728 LSm1 The eukaryotic Sm 94.3 0.11 2.4E-06 44.5 5.7 62 17-86 7-69 (74)
13 cd01722 Sm_F The eukaryotic Sm 93.9 0.14 3E-06 42.7 5.5 58 18-86 7-65 (68)
14 cd01726 LSm6 The eukaryotic Sm 93.8 0.13 2.9E-06 42.6 5.2 58 18-86 6-64 (67)
15 cd01719 Sm_G The eukaryotic Sm 93.7 0.14 3.1E-06 43.4 5.3 60 16-86 4-64 (72)
16 PRK00737 small nuclear ribonuc 93.6 0.13 2.9E-06 43.3 5.0 58 18-86 10-68 (72)
17 cd01717 Sm_B The eukaryotic Sm 92.3 0.34 7.4E-06 41.4 5.7 70 16-86 4-74 (79)
18 COG1958 LSM1 Small nuclear rib 92.2 0.38 8.3E-06 41.0 5.8 60 18-86 13-75 (79)
19 TIGR01648 hnRNP-R-Q heterogene 91.8 0.13 2.9E-06 58.6 3.5 8 591-598 394-401 (578)
20 KOG3973 Uncharacterized conser 91.7 0.31 6.6E-06 53.0 5.7 9 431-439 186-194 (465)
21 cd01723 LSm4 The eukaryotic Sm 91.4 0.41 8.9E-06 40.8 5.1 58 19-86 8-66 (76)
22 cd01725 LSm2 The eukaryotic Sm 91.2 0.58 1.3E-05 40.5 6.0 59 19-86 8-67 (81)
23 KOG0921 Dosage compensation co 91.2 0.2 4.4E-06 59.7 4.2 11 557-567 1181-1191(1282)
24 cd01727 LSm8 The eukaryotic Sm 90.6 0.51 1.1E-05 39.9 4.9 62 16-86 3-67 (74)
25 cd01724 Sm_D1 The eukaryotic S 90.3 0.63 1.4E-05 41.2 5.5 57 19-86 8-65 (90)
26 cd01729 LSm7 The eukaryotic Sm 90.1 0.88 1.9E-05 39.4 6.2 67 17-86 7-74 (81)
27 KOG3973 Uncharacterized conser 89.9 0.32 6.8E-06 52.9 3.9 9 580-588 436-444 (465)
28 KOG0116 RasGAP SH3 binding pro 89.6 0.39 8.4E-06 53.1 4.4 14 575-588 377-390 (419)
29 TIGR01648 hnRNP-R-Q heterogene 89.0 0.95 2.1E-05 51.9 7.1 16 477-492 275-290 (578)
30 cd01721 Sm_D3 The eukaryotic S 88.9 0.98 2.1E-05 38.0 5.4 58 18-86 6-64 (70)
31 PF07172 GRP: Glycine rich pro 87.5 1 2.2E-05 40.5 4.9 12 588-599 73-84 (95)
32 KOG0105 Alternative splicing f 87.4 0.65 1.4E-05 47.1 4.0 27 583-609 85-111 (241)
33 cd01733 LSm10 The eukaryotic S 87.3 1.4 3E-05 38.1 5.5 58 18-86 15-73 (78)
34 COG4371 Predicted membrane pro 85.9 1 2.2E-05 47.5 4.5 33 566-598 58-90 (334)
35 KOG2945 Predicted RNA-binding 85.0 1.5 3.3E-05 47.9 5.5 27 464-490 164-191 (365)
36 cd06168 LSm9 The eukaryotic Sm 83.1 3.1 6.8E-05 35.8 5.6 65 17-86 5-70 (75)
37 cd01732 LSm5 The eukaryotic Sm 82.4 3.6 7.8E-05 35.5 5.7 61 18-86 9-70 (76)
38 KOG0116 RasGAP SH3 binding pro 80.8 1.7 3.7E-05 48.2 4.0 8 586-593 394-401 (419)
39 PLN03134 glycine-rich RNA-bind 80.5 1.3 2.9E-05 41.7 2.7 27 533-561 90-116 (144)
40 TIGR01659 sex-lethal sex-letha 77.6 3 6.6E-05 44.8 4.6 29 533-561 249-277 (346)
41 cd01720 Sm_D2 The eukaryotic S 74.2 9.3 0.0002 33.9 6.0 65 21-86 13-81 (87)
42 cd01730 LSm3 The eukaryotic Sm 73.9 11 0.00024 32.6 6.2 67 19-86 8-78 (82)
43 PRK11634 ATP-dependent RNA hel 67.0 7.5 0.00016 45.0 4.8 12 533-544 539-550 (629)
44 PF06372 Gemin6: Gemin6 protei 64.2 9.7 0.00021 37.7 4.4 36 17-53 12-47 (166)
45 KOG1073 Uncharacterized mRNA-a 51.1 29 0.00062 38.3 5.6 45 526-574 251-296 (361)
46 KOG2044 5'-3' exonuclease HKE1 50.6 34 0.00073 41.3 6.4 30 581-610 899-928 (931)
47 PRK11634 ATP-dependent RNA hel 47.6 19 0.00042 41.7 3.9 16 525-540 520-535 (629)
48 COG1512 Beta-propeller domains 42.4 26 0.00057 37.1 3.6 8 484-491 146-153 (271)
49 KOG1775 U6 snRNA-associated Sm 41.1 23 0.00049 31.5 2.4 59 18-86 13-74 (84)
50 KOG2236 Uncharacterized conser 40.1 53 0.0011 37.5 5.6 8 21-28 211-218 (483)
51 PF11208 DUF2992: Protein of u 39.5 6.8 0.00015 37.4 -1.1 46 32-88 7-52 (132)
52 PTZ00138 small nuclear ribonuc 37.9 61 0.0013 29.1 4.7 52 25-86 31-83 (89)
53 cd01718 Sm_E The eukaryotic Sm 34.3 93 0.002 27.4 5.2 58 19-86 13-75 (79)
54 PRK14644 hypothetical protein; 33.8 61 0.0013 31.0 4.3 35 16-52 79-117 (136)
55 PF12287 Caprin-1_C: Cytoplasm 32.1 48 0.001 36.0 3.7 8 386-393 122-129 (316)
56 PRK14633 hypothetical protein; 31.7 67 0.0014 31.0 4.2 35 16-52 88-126 (150)
57 PF02237 BPL_C: Biotin protein 30.8 76 0.0016 24.8 3.7 27 20-47 1-27 (48)
58 PRK14642 hypothetical protein; 30.0 1.1E+02 0.0023 31.4 5.5 34 17-52 95-141 (197)
59 KOG3448 Predicted snRNP core p 30.0 60 0.0013 29.7 3.3 60 19-86 9-68 (96)
60 PRK14631 hypothetical protein; 29.8 72 0.0016 31.7 4.2 37 16-52 111-151 (174)
61 PF05084 GRA6: Granule antigen 29.7 50 0.0011 33.3 3.1 16 589-606 198-213 (215)
62 PRK14639 hypothetical protein; 28.6 85 0.0018 30.0 4.3 36 16-53 82-117 (140)
63 PRK14634 hypothetical protein; 28.5 78 0.0017 30.8 4.1 35 16-52 94-132 (155)
64 PF05084 GRA6: Granule antigen 27.5 72 0.0016 32.2 3.7 16 582-598 197-212 (215)
65 KOG1924 RhoA GTPase effector D 27.2 5.4E+02 0.012 31.9 11.1 10 107-116 445-454 (1102)
66 PRK14638 hypothetical protein; 26.5 86 0.0019 30.3 4.0 35 16-52 94-128 (150)
67 PRK02001 hypothetical protein; 25.0 1.1E+02 0.0023 30.0 4.3 65 16-90 84-150 (152)
68 cd01734 YlxS_C YxlS is a Bacil 24.9 1.1E+02 0.0024 26.3 4.1 34 17-52 20-57 (83)
69 PF02576 DUF150: Uncharacteris 24.8 88 0.0019 29.3 3.7 33 17-51 82-118 (141)
70 cd01735 LSm12_N LSm12 belongs 24.7 1.4E+02 0.003 25.3 4.4 33 20-52 4-36 (61)
71 PRK14632 hypothetical protein; 24.3 1E+02 0.0022 30.5 4.2 35 16-52 92-133 (172)
72 KOG1924 RhoA GTPase effector D 24.2 3.3E+02 0.0071 33.6 8.7 6 534-539 977-982 (1102)
73 KOG1783 Small nuclear ribonucl 23.1 49 0.0011 29.3 1.5 58 18-86 12-70 (77)
74 PF15320 RAM: mRNA cap methyla 22.3 1.2E+02 0.0026 27.0 3.8 36 570-605 35-70 (81)
75 PF00467 KOW: KOW motif; Inte 21.5 1.5E+02 0.0033 21.3 3.6 31 22-52 2-32 (32)
76 KOG3293 Small nuclear ribonucl 20.4 1.2E+02 0.0026 29.2 3.6 6 533-538 73-78 (134)
77 PF15098 TMEM89: TMEM89 protei 20.3 61 0.0013 31.0 1.6 34 185-218 4-39 (134)
78 PRK14647 hypothetical protein; 20.0 1.4E+02 0.003 29.0 4.1 35 16-52 93-136 (159)
79 KOG0339 ATP-dependent RNA heli 20.0 1E+02 0.0022 36.2 3.6 17 376-392 343-359 (731)
No 1
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=6.3e-39 Score=333.64 Aligned_cols=156 Identities=41% Similarity=0.614 Sum_probs=126.7
Q ss_pred CCcccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccccccccccc
Q 007191 16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITG 94 (613)
Q Consensus 16 ~~~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK~~~~~~~~ 94 (613)
.+++||||+||||||.|||||||||+||++||||+|+||| ||||||++++++||+.++|||||||||||||
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 6899999999999999999999999999999999999999 9999999999999999999999999999999
Q ss_pred cCCCCCCcccccccceecccccCCCCceeecCCCCCCCCCCCCChhhhhccCCCccccccCCCC-CCCCCCCCCCCCCCC
Q 007191 95 DAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHNDPAIIQSHYSQAAIASTTLPS-GTGSLPDPTSQTSQL 173 (613)
Q Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~~~dl~v~~~p~~~~~~~~~~dpai~~~~~~~pa~~s~s~Ps-~~g~~~~~ss~~~~~ 173 (613)
||+||+.|+.+..-.++.+|+|.. .+++++ .+++.+..+.+..+.
T Consensus 75 -------------------------DL~V~~~p~~~~~~~~p~~pp~p~---------~~~~~s~~s~~~~~~s~~~~~~ 120 (361)
T KOG1073|consen 75 -------------------------DLIVQETPAGQIPCSLPVPPPMPP---------QSSIPSQQSGSDPKISFQFAQA 120 (361)
T ss_pred -------------------------eeeeccCcccCccccccCCCCCCc---------ccccccccCCcccccccccccC
Confidence 999999877655556677777722 233443 456666777777665
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccCCCCC
Q 007191 174 GLSRPPFQGNPPLYQPGGSLGAWGSSPMPTTNGAGLAMPMYWQGFYGSP 222 (613)
Q Consensus 174 g~~~p~f~~~~P~yqPg~~~g~wg~sp~p~an~~glaMpmYwqGyy~pp 222 (613)
+.+.-.+...++.++|...+|+|.....+ |++|.|+...+
T Consensus 121 ~~~~~~~P~~~~~~~~~~~~g~~~~~~~~---------~~~~~~~~~~~ 160 (361)
T KOG1073|consen 121 GNPVIGNPQGLITTNPVPAEGSIYGSFQP---------PSQPPGGFADS 160 (361)
T ss_pred CCcccCCcCccccCCCCccccccccccCC---------cccCCCCcCCC
Confidence 55555666677889999999999988743 35676655443
No 2
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=100.00 E-value=1e-34 Score=255.09 Aligned_cols=93 Identities=54% Similarity=0.916 Sum_probs=71.7
Q ss_pred CCcccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccccccccccc
Q 007191 16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLLTITG 94 (613)
Q Consensus 16 ~~~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK~~~~~~~~ 94 (613)
++++|||++||||||++|||||+||+||++++||+|+||| ||||||+++. +|||++++|+||+|||+|||
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 9999999875 89999999999999999999
Q ss_pred cCCCCCCcccccccceecccccCCCCceeecCCCCCCCCCCCCChhhhhcc
Q 007191 95 DAISGPRLSQTRDWTLRSVIRKDIQDLQVKSSPPVQTTTSIHNDPAIIQSH 145 (613)
Q Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~~~dl~v~~~p~~~~~~~~~~dpai~~~~ 145 (613)
||+|++.++. ...++|||||+++
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 4579999999864
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=2.5e-33 Score=235.86 Aligned_cols=70 Identities=60% Similarity=1.058 Sum_probs=68.1
Q ss_pred CcccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 17 ~~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
|.+|||++||||||+||||||+||+||++++||+|+||| ||||||+.++++|||+++|||||||||+|||
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 9999999887789999999999999999999
No 4
>PF09532 FDF: FDF domain; InterPro: IPR019050 This motif is found in the C-terminal region of Sm-like proteins []. Sm and Sm-like proteins of the Lsm (like Sm) domain family are generally involved in essential RNA-processing tasks.; PDB: 4A53_A 2WAX_B 3D3K_A 2WAY_B 3D3J_A.
Probab=99.73 E-value=5.8e-20 Score=160.76 Aligned_cols=94 Identities=37% Similarity=0.650 Sum_probs=42.0
Q ss_pred ccccccccHHHHhhhhchhhhhhcccCCCCcCCCC-CC---CccccccCCCCCCCCCcccc-cchhcccccccccCCCCC
Q 007191 476 TRFTEDFDFIAMNEKFNKDEVWGHLGKSNKALDDG-DN---YEDEEDVGSSKHENKPVYVK-DDFFDSLSCDALNRGSHN 550 (613)
Q Consensus 476 ~kF~eDFDFea~NeKFnKDEv~g~LgK~~~~~~De-dD---~~ee~~~e~~~~e~k~~YdK-~sFFDnIScn~ldr~GRn 550 (613)
++|++||||+++|+||+|++||.+|.+........ .. ...+...+........+|+| ++|||+|||+.++|....
T Consensus 1 ik~~~DFDFes~NakF~K~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~k~~sfFDnIS~e~~~~~~~~ 80 (104)
T PF09532_consen 1 IKFDEDFDFESANAKFDKEEVFKELKKKDEKDEEDRLVSENKEEEEAEEENENDEEKYYDKKKSFFDNISCEAKDRSEGN 80 (104)
T ss_dssp SSSSS---HCCCCCTSSCCHHCCHHHCC--------------------------------B--B-------EEE-TT--E
T ss_pred CCCcCccCHHHHHHHhccccchhhhhcccccccccccccccccccccccccccCcccccccccccCcCCCcccccccCCc
Confidence 58999999999999999999999987764322111 00 01111112222344567777 899999999999875433
Q ss_pred C-CC---cccccccCccCccCCC
Q 007191 551 G-RP---RFSEQVRRDTETFGDF 569 (613)
Q Consensus 551 ~-Rl---dfseeRk~dtETFG~~ 569 (613)
+ |. +|.++|++|+||||..
T Consensus 81 ~~~~~~~~~~eer~~n~ETFG~~ 103 (104)
T PF09532_consen 81 GPRRSGDDWREERKLNTETFGQS 103 (104)
T ss_dssp EE---HHHHHHHHHHH-HHTT--
T ss_pred CCCcchhhHHHHHHhcccccCCC
Confidence 2 33 4999999999999974
No 5
>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=97.49 E-value=0.0002 Score=57.08 Aligned_cols=58 Identities=17% Similarity=0.361 Sum_probs=50.2
Q ss_pred cccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 18 ~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
..++|++|.+..+.+..|+|+|..+| +...|.|+|+. +.++ .....++.++.||+.|+
T Consensus 2 ~~~~g~~V~V~l~~g~~~~G~L~~~D-~~~Ni~L~~~~~~~~~----------~~~~~~~~~~irG~~I~ 60 (63)
T cd00600 2 KDLVGKTVRVELKDGRVLEGVLVAFD-KYMNLVLDDVEETIKE----------GKKRVLGLVLIRGDNVR 60 (63)
T ss_pred hHHCCCEEEEEECCCcEEEEEEEEEC-CCCCEEECCEEEEecC----------CcEEECCeEEEECCEEE
Confidence 46899999999999999999999999 55599999999 8876 23455778999999998
No 6
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.45 E-value=7e-05 Score=62.98 Aligned_cols=66 Identities=23% Similarity=0.430 Sum_probs=43.2
Q ss_pred cccccceeEEEecCCceeEEEeeeecCC--CCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 18 DSYIGSLISLTSKSEIRYEGVLFNINTE--ESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 18 ~~~IGs~ISLISks~IRYeGiL~~Id~e--~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
..+||+++.+..|.+-+|||||+..+++ +..|.|+.+| -.++.... .-+-..++-+.++|+++||-
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 4579999999999999999999999998 8999999999 66554432 23456788889999999985
No 7
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=95.65 E-value=0.01 Score=70.08 Aligned_cols=9 Identities=33% Similarity=0.442 Sum_probs=3.9
Q ss_pred CCCChhhhh
Q 007191 135 IHNDPAIIQ 143 (613)
Q Consensus 135 ~~~dpai~~ 143 (613)
+..||++-+
T Consensus 603 ~~~dd~~~~ 611 (1282)
T KOG0921|consen 603 ILCDPSYNE 611 (1282)
T ss_pred cccChhhcc
Confidence 344444443
No 8
>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=95.44 E-value=0.026 Score=45.83 Aligned_cols=59 Identities=20% Similarity=0.382 Sum_probs=48.5
Q ss_pred cccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 18 ~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
..++|++|.+..+.+..|+|+|..+|. .--|.|+||. .-.+++ ....+..++.||+.|.
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 468999999999999999999999994 6779999998 654433 3344577889999987
No 9
>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=95.32 E-value=0.048 Score=45.67 Aligned_cols=56 Identities=23% Similarity=0.456 Sum_probs=45.2
Q ss_pred cccccceeEEEecCCce-eEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 18 DSYIGSLISLTSKSEIR-YEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 18 ~~~IGs~ISLISks~IR-YeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
..|||+-+||-...++- |.|.+..||.++-||.|.+-- -|- ..++-| ++||.-|||
T Consensus 2 ~dWiGs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~~~~~ngi------------k~~~~E-Vt~~~~DI~ 59 (62)
T cd01737 2 QDWLGSIVSINCGETLGVYQGLVSAVDQESQTISLAFPFHNGV------------KCLVPE-VTFRAGDIR 59 (62)
T ss_pred CcccceEEEEecCCceEEEEEEEEEeCccceEEEEeecccCCc------------cccCce-EEEEEcchh
Confidence 57999999999998884 999999999999999998722 222 222333 899999999
No 10
>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=94.44 E-value=0.084 Score=43.74 Aligned_cols=58 Identities=12% Similarity=0.253 Sum_probs=46.7
Q ss_pred cccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 18 ~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
..++|++|.+..|.+-.|+|+|..+|. .--|.|+|+. +-.++ ...-+..++.||+.|.
T Consensus 6 ~~~~~~~V~V~l~~g~~~~G~L~~~D~-~mNlvL~~~~e~~~~~----------~~~~lg~~~iRG~~I~ 64 (68)
T cd01731 6 KDSLNKPVLVKLKGGKEVRGRLKSYDQ-HMNLVLEDAEEIDDGE----------PVRKYGRVVIRGDNVL 64 (68)
T ss_pred HHhcCCEEEEEECCCCEEEEEEEEECC-cceEEEeeEEEEecCC----------eEeEcCcEEEeCCEEE
Confidence 468999999999999999999999995 6778999987 54322 1223567899999987
No 11
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=94.44 E-value=0.07 Score=43.20 Aligned_cols=59 Identities=19% Similarity=0.326 Sum_probs=47.3
Q ss_pred cccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 18 ~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
..++|++|.+.-+.+..|+|+|..+|. .-.|.|+|+. .-.+. .....++.++.||+.|.
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 468999999999999999999999994 6889999987 55432 12334556888999887
No 12
>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=94.26 E-value=0.11 Score=44.47 Aligned_cols=62 Identities=11% Similarity=0.180 Sum_probs=49.4
Q ss_pred CcccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 17 ~~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
-..||+++|.++-|.+-.|.|+|..+| +...|.|.|+. +-.++-+ . .+.....+++||..|-
T Consensus 7 L~~~l~k~v~V~l~~gr~~~G~L~~fD-~~~NlvL~d~~E~~~~~~~-~------~~~~lG~~viRG~~V~ 69 (74)
T cd01728 7 LVDDLDKKVVVLLRDGRKLIGILRSFD-QFANLVLQDTVERIYVGDK-Y------GDIPRGIFIIRGENVV 69 (74)
T ss_pred HHHhcCCEEEEEEcCCeEEEEEEEEEC-CcccEEecceEEEEecCCc-c------ceeEeeEEEEECCEEE
Confidence 457899999999999999999999999 67789999997 5544311 0 1234678999999886
No 13
>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=93.93 E-value=0.14 Score=42.69 Aligned_cols=58 Identities=19% Similarity=0.320 Sum_probs=46.6
Q ss_pred cccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 18 ~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
..++|++|.+.-|.+..|+|+|..+| +.--|.|+||. +- . +. ....++.++-||+.|.
T Consensus 7 ~~~~g~~V~V~Lk~g~~~~G~L~~~D-~~mNi~L~~~~e~~-~-----~~----~~~~lg~~~IRG~~I~ 65 (68)
T cd01722 7 NDLTGKPVIVKLKWGMEYKGTLVSVD-SYMNLQLANTEEYI-D-----GK----STGNLGEVLIRCNNVL 65 (68)
T ss_pred HHcCCCEEEEEECCCcEEEEEEEEEC-CCEEEEEeeEEEEe-C-----Cc----cccCcCcEEEECCEEE
Confidence 45799999999999999999999999 67889999986 42 1 11 1234677899999987
No 14
>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=93.81 E-value=0.13 Score=42.58 Aligned_cols=58 Identities=19% Similarity=0.348 Sum_probs=46.6
Q ss_pred cccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 18 ~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
..++|++|.+.-|.+.-|+|+|..+| ..--|.|+|+. +-..+ ....++.++-||+.|.
T Consensus 6 ~~~~~~~V~V~Lk~g~~~~G~L~~~D-~~mNlvL~~~~~~~~~~----------~~~~~~~v~IRG~~I~ 64 (67)
T cd01726 6 KAIIGRPVVVKLNSGVDYRGILACLD-GYMNIALEQTEEYVNGQ----------LKNKYGDAFIRGNNVL 64 (67)
T ss_pred HhhCCCeEEEEECCCCEEEEEEEEEc-cceeeEEeeEEEEeCCc----------eeeEeCCEEEECCEEE
Confidence 35799999999999999999999999 67889999987 43211 1224677999999987
No 15
>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=93.73 E-value=0.14 Score=43.38 Aligned_cols=60 Identities=17% Similarity=0.305 Sum_probs=48.8
Q ss_pred CCcccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 16 ~~~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
....||+++|.++-|.+..|+|+|..+| +---|.|+||. +-- + . ....+.-++-||+.|.
T Consensus 4 ~L~~~i~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~E~~~-~-----~----~~~~lg~v~IRG~~I~ 64 (72)
T cd01719 4 ELKKYMDKKLSLKLNGNRKVSGILRGFD-PFMNLVLDDAVEVNS-G-----G----EKNNIGMVVIRGNSIV 64 (72)
T ss_pred hhHHhCCCeEEEEECCCeEEEEEEEEEc-ccccEEeccEEEEcc-C-----C----ceeEeceEEECCCEEE
Confidence 3467999999999999999999999999 77889999997 531 1 1 1235677999999998
No 16
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=93.64 E-value=0.13 Score=43.29 Aligned_cols=58 Identities=14% Similarity=0.255 Sum_probs=46.9
Q ss_pred cccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 18 ~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
..++|++|.+..|.+--|+|+|..+|. .--|.|+|+. +-.+ . ...-++.++.||+.|.
T Consensus 10 ~~~~~k~V~V~lk~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~------~----~~~~lg~v~iRG~~V~ 68 (72)
T PRK00737 10 NNALNSPVLVRLKGGREFRGELQGYDI-HMNLVLDNAEEIQDG------E----VVRKLGKVVIRGDNVV 68 (72)
T ss_pred HHhCCCEEEEEECCCCEEEEEEEEEcc-cceeEEeeEEEEcCC------C----eEeEcCcEEEeCCEEE
Confidence 467999999999999999999999996 7789999987 5321 1 1134677999999987
No 17
>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=92.29 E-value=0.34 Score=41.41 Aligned_cols=70 Identities=13% Similarity=0.225 Sum_probs=52.1
Q ss_pred CCcccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 16 ~~~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
....|||++|.+.-+.+=.|+|+|..+| +...|.|.|+. +-++.+...........-.+.-++.||..|.
T Consensus 4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D-~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv 74 (79)
T cd01717 4 KMLQLINYRLRVTLQDGRQFVGQFLAFD-KHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIV 74 (79)
T ss_pred hhHHHcCCEEEEEECCCcEEEEEEEEEc-CccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEE
Confidence 4578999999999999999999999999 56779999998 7765543210101111224677999999887
No 18
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=92.16 E-value=0.38 Score=40.96 Aligned_cols=60 Identities=18% Similarity=0.320 Sum_probs=47.1
Q ss_pred cccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-ccc-CCCCCCCCCCCCCCCcee-eEEEEcCccc
Q 007191 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQ-KGEEKIGPQVPPSDKIYE-YILFRGSDIK 86 (613)
Q Consensus 18 ~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGT-EgR~~~~~~Ipps~~vye-yIvFrgsDIK 86 (613)
..+++++|.+.-|.+..|.|+|..+|. .--|.|.||. ... +++.. ...+. .++.||+.|+
T Consensus 13 ~~~~~~~V~V~lk~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~~~~~--------~~~~~~~~~IRG~~I~ 75 (79)
T COG1958 13 KKLLNKRVLVKLKNGREYRGTLVGFDQ-YMNLVLDDVEEIISHDGEKN--------VRRLGGEVLIRGDNIV 75 (79)
T ss_pred HHhhCCEEEEEECCCCEEEEEEEEEcc-ceeEEEeceEEEeccCCccc--------cceeccEEEEECCcEE
Confidence 568999999999999999999999995 4568899998 665 33221 23333 7999999998
No 19
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=91.80 E-value=0.13 Score=58.61 Aligned_cols=8 Identities=63% Similarity=1.252 Sum_probs=4.1
Q ss_pred CCCCCCCC
Q 007191 591 YHGRGYGY 598 (613)
Q Consensus 591 y~GRGygy 598 (613)
|||++|||
T Consensus 394 ~~~~~~~~ 401 (578)
T TIGR01648 394 YYGDYYGY 401 (578)
T ss_pred ccCccccc
Confidence 35555554
No 20
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=91.69 E-value=0.31 Score=52.98 Aligned_cols=9 Identities=33% Similarity=0.663 Sum_probs=4.7
Q ss_pred cCCCCCCCC
Q 007191 431 VQEPILPLP 439 (613)
Q Consensus 431 ~q~PlLPlP 439 (613)
...|||-.|
T Consensus 186 ~~~PLlKkp 194 (465)
T KOG3973|consen 186 RSHPLLKKP 194 (465)
T ss_pred cCCchhcCc
Confidence 345666544
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=91.38 E-value=0.41 Score=40.77 Aligned_cols=58 Identities=22% Similarity=0.245 Sum_probs=46.6
Q ss_pred ccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 19 ~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
..+|++|.+.-|.+..|+|+|..+|. .-.|.|+||. ...+|.+ + ..++.++-||+.|+
T Consensus 8 ~~~g~~V~VeLkng~~~~G~L~~~D~-~mNi~L~~~~~~~~~g~~-----~----~~~~~v~IRG~~I~ 66 (76)
T cd01723 8 TAQNHPMLVELKNGETYNGHLVNCDN-WMNIHLREVICTSKDGDK-----F----WKMPECYIRGNTIK 66 (76)
T ss_pred hcCCCEEEEEECCCCEEEEEEEEEcC-CCceEEEeEEEECCCCcE-----e----eeCCcEEEeCCEEE
Confidence 46899999999999999999999994 7789999998 5444322 1 12466899999998
No 22
>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=91.23 E-value=0.58 Score=40.50 Aligned_cols=59 Identities=19% Similarity=0.325 Sum_probs=46.5
Q ss_pred ccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 19 ~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
..+|++|.+--|.+..|+|+|..+|. .--|.|+||. ...++- ..-..++.|..||+.|+
T Consensus 8 ~l~g~~V~VeLKng~~~~G~L~~vD~-~MNi~L~n~~~~~~~~~--------~~~~~~~~v~IRG~~I~ 67 (81)
T cd01725 8 TLVGKEVTVELKNDLSIRGTLHSVDQ-YLNIKLTNISVTDPEKY--------PHMLSVKNCFIRGSVVR 67 (81)
T ss_pred hCCCCEEEEEECCCcEEEEEEEEECC-CcccEEEEEEEEcCCCc--------ccccccCeEEEECCEEE
Confidence 35899999999999999999999995 5579999998 543221 11233578999999999
No 23
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=91.22 E-value=0.2 Score=59.73 Aligned_cols=11 Identities=18% Similarity=0.090 Sum_probs=6.1
Q ss_pred ccccCccCccC
Q 007191 557 EQVRRDTETFG 567 (613)
Q Consensus 557 eeRk~dtETFG 567 (613)
-.|+.+--+||
T Consensus 1181 gyRRGgssysg 1191 (1282)
T KOG0921|consen 1181 GYRRGGSSYSG 1191 (1282)
T ss_pred ccccCCCCCCC
Confidence 34555555665
No 24
>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=90.56 E-value=0.51 Score=39.95 Aligned_cols=62 Identities=15% Similarity=0.292 Sum_probs=47.8
Q ss_pred CCcccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-c--ccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-L--EQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 16 ~~~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-f--GTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
....||+++|.++-+.+-.|+|+|..+|.. --|.|.++. + .++ .+. ....+..|+.||+.|-
T Consensus 3 ~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~-~NlvL~~~~E~~~~~~----~~~----~~~~lG~~~iRG~~I~ 67 (74)
T cd01727 3 TLEDYLNKTVSVITVDGRVIVGTLKGFDQA-TNLILDDSHERVYSSD----EGV----EQVVLGLYIIRGDNIA 67 (74)
T ss_pred hHHHhcCCEEEEEECCCcEEEEEEEEEccc-cCEEccceEEEEecCC----CCc----eeeEeceEEECCCEEE
Confidence 456899999999999999999999999965 678899875 3 221 110 1235788999999987
No 25
>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=90.31 E-value=0.63 Score=41.22 Aligned_cols=57 Identities=12% Similarity=0.232 Sum_probs=46.9
Q ss_pred ccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 19 ~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
.++|+.|.+--|.+..|+|+|..+|. .--|.|+||. +-.++. ..-|+.++.||+.|+
T Consensus 8 ~l~g~~V~VeLKng~~~~G~L~~vD~-~MNl~L~~a~~~~~~~~----------~~~~~~v~IRG~nI~ 65 (90)
T cd01724 8 KLTNETVTIELKNGTIVHGTITGVDP-SMNTHLKNVKLTLKGRN----------PVPLDTLSIRGNNIR 65 (90)
T ss_pred hCCCCEEEEEECCCCEEEEEEEEEcC-ceeEEEEEEEEEcCCCc----------eeEcceEEEeCCEEE
Confidence 46899999999999999999999994 5689999998 543221 134788999999999
No 26
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=90.14 E-value=0.88 Score=39.43 Aligned_cols=67 Identities=10% Similarity=0.205 Sum_probs=49.0
Q ss_pred CcccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 17 ~~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
-..||+++|.++-|.+-.|+|+|..+|. ---|.|.|+. +-.+.-. ...+.-....+..++.||..|-
T Consensus 7 L~~~i~k~V~V~l~~gr~~~G~L~~~D~-~mNlvL~~~~E~~~~~~~--~~~~~~~~~~lG~v~iRG~nV~ 74 (81)
T cd01729 7 LSKYVDKKIRVKFQGGREVTGILKGYDQ-LLNLVLDDTVEYLRDPDD--PYKLTDKTRQLGLVVCRGTSVV 74 (81)
T ss_pred HHHhcCCeEEEEECCCcEEEEEEEEEcC-cccEEecCEEEEEccCCc--ccccccceeEccEEEEcCCEEE
Confidence 4578999999999999999999999994 6678899986 4322111 1111223345788999999987
No 27
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=89.89 E-value=0.32 Score=52.88 Aligned_cols=9 Identities=44% Similarity=0.612 Sum_probs=3.4
Q ss_pred CCCCCCCCC
Q 007191 580 GPYRGGRSR 588 (613)
Q Consensus 580 Gg~rGg~gR 588 (613)
||+|+|+||
T Consensus 436 gggr~gggr 444 (465)
T KOG3973|consen 436 GGGRDGGGR 444 (465)
T ss_pred CCCCCCCCC
Confidence 333333334
No 28
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=89.59 E-value=0.39 Score=53.11 Aligned_cols=14 Identities=57% Similarity=0.900 Sum_probs=5.9
Q ss_pred CCCCCCCCCCCCCC
Q 007191 575 GRGGRGPYRGGRSR 588 (613)
Q Consensus 575 GrGGRGg~rGg~gR 588 (613)
||++++|+||++||
T Consensus 377 ~~~~~~g~~~~~gr 390 (419)
T KOG0116|consen 377 GRGNRGGGRGPGGR 390 (419)
T ss_pred cccCCCCCCCCCCC
Confidence 44444444443333
No 29
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=89.00 E-value=0.95 Score=51.94 Aligned_cols=16 Identities=19% Similarity=0.374 Sum_probs=6.2
Q ss_pred cccccccHHHHhhhhc
Q 007191 477 RFTEDFDFIAMNEKFN 492 (613)
Q Consensus 477 kF~eDFDFea~NeKFn 492 (613)
+|++.-|-+++-+++|
T Consensus 275 eF~s~e~A~kAi~~ln 290 (578)
T TIGR01648 275 HFEDREDAVKAMDELN 290 (578)
T ss_pred EeCCHHHHHHHHHHhC
Confidence 3333334344333333
No 30
>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=88.95 E-value=0.98 Score=37.98 Aligned_cols=58 Identities=21% Similarity=0.359 Sum_probs=47.1
Q ss_pred cccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 18 ~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
...+|+.|.+--|.+..|.|+|..+|. .-.|.|+||. ...+|+. .-++.++-||+.|+
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 356899999999999999999999996 7789999997 4433321 23577999999998
No 31
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=87.53 E-value=1 Score=40.52 Aligned_cols=12 Identities=50% Similarity=0.985 Sum_probs=5.7
Q ss_pred CCCCCCCCCCCC
Q 007191 588 RGSYHGRGYGYA 599 (613)
Q Consensus 588 RGgy~GRGygy~ 599 (613)
+|+|.|.|+|+.
T Consensus 73 gGgygGgG~G~~ 84 (95)
T PF07172_consen 73 GGGYGGGGGGYG 84 (95)
T ss_pred CCCCCCCCCCCC
Confidence 345555444443
No 32
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=87.41 E-value=0.65 Score=47.06 Aligned_cols=27 Identities=33% Similarity=0.438 Sum_probs=16.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 007191 583 RGGRSRGSYHGRGYGYAPRGRGYGYGM 609 (613)
Q Consensus 583 rGg~gRGgy~GRGygy~gRg~g~~~~~ 609 (613)
.+.+.||+|.|+|.|.+|+|+.++-|-
T Consensus 85 ~s~~~~G~y~gggrgGgg~gg~rgpps 111 (241)
T KOG0105|consen 85 SSSDRRGSYSGGGRGGGGGGGRRGPPS 111 (241)
T ss_pred cccccccccCCCCCCCCCCCcccCCcc
Confidence 444556677777777677777776443
No 33
>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=87.34 E-value=1.4 Score=38.09 Aligned_cols=58 Identities=17% Similarity=0.367 Sum_probs=46.2
Q ss_pred cccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 18 ~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
...+|+.|.+--|.+..|.|+|.++|. .-.|.|+||. ....+. ..-++.|+-||+.|+
T Consensus 15 ~~l~g~~V~VeLKng~~~~G~L~~vD~-~MNl~L~~~~~~~~~~~----------~~~~~~v~IRG~nI~ 73 (78)
T cd01733 15 QGLQGKVVTVELRNETTVTGRIASVDA-FMNIRLAKVTIIDRNGK----------QVQVEEIMVTGRNIR 73 (78)
T ss_pred HHCCCCEEEEEECCCCEEEEEEEEEcC-CceeEEEEEEEEcCCCc----------eeECCcEEEECCEEE
Confidence 346899999999999999999999994 5689999998 532111 114788999999998
No 34
>COG4371 Predicted membrane protein [Function unknown]
Probab=85.93 E-value=1 Score=47.46 Aligned_cols=33 Identities=42% Similarity=0.870 Sum_probs=21.8
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 007191 566 FGDFPRYHGGRGGRGPYRGGRSRGSYHGRGYGY 598 (613)
Q Consensus 566 FG~~~r~rGGrGGRGg~rGg~gRGgy~GRGygy 598 (613)
|+-.+.+-++|.+||+-+|+|+.|+|-|.|||.
T Consensus 58 fraps~~sr~YS~~gpsGGgY~gg~Y~GGGfgf 90 (334)
T COG4371 58 FRAPSGYSRGYSGGGPSGGGYSGGGYSGGGFGF 90 (334)
T ss_pred CCCCCCCCCCcCCCCCCCCCCCCCCCCCCCcCc
Confidence 433344445666777777777777888888874
No 35
>KOG2945 consensus Predicted RNA-binding protein [General function prediction only]
Probab=85.04 E-value=1.5 Score=47.91 Aligned_cols=27 Identities=26% Similarity=0.323 Sum_probs=13.7
Q ss_pred CCCCCCCCc-cccccccccccHHHHhhh
Q 007191 464 GRGRGNELS-RSATRFTEDFDFIAMNEK 490 (613)
Q Consensus 464 GrGrg~~~~-k~~~kF~eDFDFea~NeK 490 (613)
|+||++... .+.+.-+.+||+..-+++
T Consensus 164 G~Grg~~g~~~~~~~~krEf~r~sgsDr 191 (365)
T KOG2945|consen 164 GGGRGNWGDDGDDITGKREFDRQSGSDR 191 (365)
T ss_pred CccCCCCCccccccccceeeeeeccccc
Confidence 445555543 222222357887765544
No 36
>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=83.06 E-value=3.1 Score=35.80 Aligned_cols=65 Identities=14% Similarity=0.277 Sum_probs=48.1
Q ss_pred CcccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 17 ~~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
...|||+++.++-+.+--|+|+|..+|. ..-|.|.|+. |-+.... ........+..|+-||..|.
T Consensus 5 L~~~l~~~v~V~l~dgR~~~G~l~~~D~-~~NivL~~~~E~~~~~~~----~~~~~~r~lGlv~IrG~~Iv 70 (75)
T cd06168 5 LRSLLGRTMRIHMTDGRTLVGVFLCTDR-DCNIILGSAQEYRPPPDS----FSPTEPRVLGLVMIPGHHIV 70 (75)
T ss_pred HHHhcCCeEEEEEcCCeEEEEEEEEEcC-CCcEEecCcEEEEcccCc----cCCccEEEeeeEEEeCCeEE
Confidence 3578999999999999999999999994 5668899986 4322111 11122335778999999887
No 37
>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=82.44 E-value=3.6 Score=35.47 Aligned_cols=61 Identities=26% Similarity=0.360 Sum_probs=46.2
Q ss_pred cccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 18 ~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
..+++++|.+..|.+-.|+|+|..+| +--.|.|+|+. += + ..++. ....+.-|+.||..|.
T Consensus 9 ~~~~~~~V~V~l~~gr~~~G~L~g~D-~~mNlvL~da~E~~-~--~~~~~----~~~~lg~v~iRG~nV~ 70 (76)
T cd01732 9 DKCIGSRIWIVMKSDKEFVGTLLGFD-DYVNMVLEDVTEYE-I--TPEGR----KITKLDQILLNGNNIC 70 (76)
T ss_pred HHhCCCEEEEEECCCeEEEEEEEEec-cceEEEEccEEEEE-E--cCCCc----eeeEcCeEEEeCCeEE
Confidence 34689999999999999999999999 46789999987 42 1 11111 1223677999999988
No 38
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=80.83 E-value=1.7 Score=48.23 Aligned_cols=8 Identities=38% Similarity=0.597 Sum_probs=3.8
Q ss_pred CCCCCCCC
Q 007191 586 RSRGSYHG 593 (613)
Q Consensus 586 ~gRGgy~G 593 (613)
.+|||++|
T Consensus 394 ~~~gg~~~ 401 (419)
T KOG0116|consen 394 GGRGGGRG 401 (419)
T ss_pred CCCCCCcC
Confidence 34555444
No 39
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=80.51 E-value=1.3 Score=41.68 Aligned_cols=27 Identities=7% Similarity=0.030 Sum_probs=18.7
Q ss_pred cchhcccccccccCCCCCCCCcccccccC
Q 007191 533 DDFFDSLSCDALNRGSHNGRPRFSEQVRR 561 (613)
Q Consensus 533 ~sFFDnIScn~ldr~GRn~RldfseeRk~ 561 (613)
..+.+.++...+ .+|..+++|+++|..
T Consensus 90 ~~Al~~lng~~i--~Gr~l~V~~a~~~~~ 116 (144)
T PLN03134 90 TAAISEMDGKEL--NGRHIRVNPANDRPS 116 (144)
T ss_pred HHHHHHcCCCEE--CCEEEEEEeCCcCCC
Confidence 466666666655 377788888887654
No 40
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=77.61 E-value=3 Score=44.82 Aligned_cols=29 Identities=17% Similarity=0.190 Sum_probs=17.7
Q ss_pred cchhcccccccccCCCCCCCCcccccccC
Q 007191 533 DDFFDSLSCDALNRGSHNGRPRFSEQVRR 561 (613)
Q Consensus 533 ~sFFDnIScn~ldr~GRn~RldfseeRk~ 561 (613)
..+.+.|++..++..++..+++|++++..
T Consensus 249 ~~Ai~~lng~~~~g~~~~l~V~~a~~~~~ 277 (346)
T TIGR01659 249 QEAISALNNVIPEGGSQPLTVRLAEEHGK 277 (346)
T ss_pred HHHHHHhCCCccCCCceeEEEEECCcccc
Confidence 35666666665543345567788877654
No 41
>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=74.20 E-value=9.3 Score=33.92 Aligned_cols=65 Identities=11% Similarity=0.206 Sum_probs=47.2
Q ss_pred ccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCC--CCCCC-CCCceeeEEEEcCccc
Q 007191 21 IGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIG--PQVPP-SDKIYEYILFRGSDIK 86 (613)
Q Consensus 21 IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~--~~Ipp-s~~vyeyIvFrgsDIK 86 (613)
.|++|-+.-|.+-.|.|+|..+| +...|.|.|+. +-++.-+... .+-+. ....+..|+.||..|.
T Consensus 13 ~~~~V~V~lr~~r~~~G~L~~fD-~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv 81 (87)
T cd01720 13 NNTQVLINCRNNKKLLGRVKAFD-RHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI 81 (87)
T ss_pred CCCEEEEEEcCCCEEEEEEEEec-CccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence 38999999999999999999999 47889999998 6554322111 01111 2223588999999887
No 42
>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=73.95 E-value=11 Score=32.62 Aligned_cols=67 Identities=9% Similarity=0.119 Sum_probs=46.0
Q ss_pred ccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccC-CCCCCC--CCCCCCCCceeeEEEEcCccc
Q 007191 19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQK-GEEKIG--PQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 19 ~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTE-gR~~~~--~~Ipps~~vyeyIvFrgsDIK 86 (613)
.+++++|.++.|.+-.|+|+|...|. .-.|.|.|+. +-.+ ...... ..+......+.-++.||..|.
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 45899999999999999999999994 6689999987 4322 111100 001111224567889998876
No 43
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=66.96 E-value=7.5 Score=44.97 Aligned_cols=12 Identities=0% Similarity=0.254 Sum_probs=6.5
Q ss_pred cchhcccccccc
Q 007191 533 DDFFDSLSCDAL 544 (613)
Q Consensus 533 ~sFFDnIScn~l 544 (613)
+.+++.|....+
T Consensus 539 ~~~~~~~~~~~~ 550 (629)
T PRK11634 539 GEVLQHFTRTRI 550 (629)
T ss_pred HHHHHHhccccc
Confidence 456666654443
No 44
>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=64.20 E-value=9.7 Score=37.71 Aligned_cols=36 Identities=28% Similarity=0.480 Sum_probs=29.0
Q ss_pred CcccccceeEEEecCCceeEEEeeeecCCCCeeeecc
Q 007191 17 ADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRN 53 (613)
Q Consensus 17 ~~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~n 53 (613)
...|||+.+.+.... --|.|.||+||+.-.+|.|-|
T Consensus 12 ~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~ 47 (166)
T PF06372_consen 12 WQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVN 47 (166)
T ss_dssp HHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEE
T ss_pred HHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEE
Confidence 357999999999997 889999999999999999976
No 45
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=51.11 E-value=29 Score=38.33 Aligned_cols=45 Identities=16% Similarity=0.192 Sum_probs=30.6
Q ss_pred CCCcccc-cchhcccccccccCCCCCCCCcccccccCccCccCCCCCCCC
Q 007191 526 NKPVYVK-DDFFDSLSCDALNRGSHNGRPRFSEQVRRDTETFGDFPRYHG 574 (613)
Q Consensus 526 ~k~~YdK-~sFFDnIScn~ldr~GRn~RldfseeRk~dtETFG~~~r~rG 574 (613)
+..+|++ ..+|+++.-..- -+.+.++.+++-.++-++....+.+|
T Consensus 251 ~~~~~n~~s~r~~~~~~~~~----~n~~~~~~~~~~~~~~~q~~~~~~~~ 296 (361)
T KOG1073|consen 251 KPSFYNQQSSRFTTISVSRV----SNTNSRNQEKRGLNNGGQSQQSGRPG 296 (361)
T ss_pred CCcccccccccccccccccc----ccccccccccccccCCCcccccCCCC
Confidence 4567885 677776655433 24577888889898888887665443
No 46
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=50.64 E-value=34 Score=41.30 Aligned_cols=30 Identities=27% Similarity=0.388 Sum_probs=14.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 007191 581 PYRGGRSRGSYHGRGYGYAPRGRGYGYGMS 610 (613)
Q Consensus 581 g~rGg~gRGgy~GRGygy~gRg~g~~~~~~ 610 (613)
+++|+.+.++|+..||||+.+++++--++.
T Consensus 899 ~~~~~~~~~~~~r~~~~~g~k~~~~~~gnP 928 (931)
T KOG2044|consen 899 GRGGGNGPRGYQRPPYGGGSKGGGGYQGNP 928 (931)
T ss_pred CCCCCCCCCccccCCcCCccccCCCCCCCC
Confidence 344444444555567776644444333333
No 47
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=47.58 E-value=19 Score=41.70 Aligned_cols=16 Identities=6% Similarity=0.117 Sum_probs=9.7
Q ss_pred CCCCcccccchhcccc
Q 007191 525 ENKPVYVKDDFFDSLS 540 (613)
Q Consensus 525 e~k~~YdK~sFFDnIS 540 (613)
..-..||+-+|||-=.
T Consensus 520 g~i~i~~~~s~v~~~~ 535 (629)
T PRK11634 520 GNIKLFASHSTIELPK 535 (629)
T ss_pred CcEEEeCCceEEEcCh
Confidence 3445677777776433
No 48
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=42.40 E-value=26 Score=37.10 Aligned_cols=8 Identities=13% Similarity=-0.151 Sum_probs=3.4
Q ss_pred HHHHhhhh
Q 007191 484 FIAMNEKF 491 (613)
Q Consensus 484 Fea~NeKF 491 (613)
|...-+++
T Consensus 146 y~~gi~~~ 153 (271)
T COG1512 146 YAGGLEAG 153 (271)
T ss_pred HHHHHHHH
Confidence 44444443
No 49
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=41.13 E-value=23 Score=31.51 Aligned_cols=59 Identities=27% Similarity=0.412 Sum_probs=45.9
Q ss_pred cccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cc--cCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LE--QKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 18 ~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fG--TEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
+.-||+||-+|=|+|-.++|+|...|-= -.+.|++|. |- +|||+. +-.+.|+..|..|-
T Consensus 13 DkcIgski~iimksdkE~~GtL~GFDd~-VNmvLeDvtEye~~~egr~~---------tk~~~iLLnGNni~ 74 (84)
T KOG1775|consen 13 DKCIGSKIWIIMKSDKEFVGTLVGFDDF-VNMVLEDVTEYEITPEGRRM---------TKLDQILLNGNNIT 74 (84)
T ss_pred HHhcCceEEEEEccCceeeeEEechHHH-HHHHHHhhhheeeCCCccee---------eeeeeeeecCCcEE
Confidence 4569999999999999999999988732 236788888 64 466543 33577999999987
No 50
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.10 E-value=53 Score=37.45 Aligned_cols=8 Identities=25% Similarity=0.563 Sum_probs=3.3
Q ss_pred ccceeEEE
Q 007191 21 IGSLISLT 28 (613)
Q Consensus 21 IGs~ISLI 28 (613)
||..+|++
T Consensus 211 lG~V~svv 218 (483)
T KOG2236|consen 211 LGKVSSVV 218 (483)
T ss_pred hhHHHHHh
Confidence 44444443
No 51
>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=39.46 E-value=6.8 Score=37.39 Aligned_cols=46 Identities=17% Similarity=0.281 Sum_probs=37.9
Q ss_pred CceeEEEeeeecCCCCeeeecccccccCCCCCCCCCCCCCCCceeeEEEEcCccccc
Q 007191 32 EIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHC 88 (613)
Q Consensus 32 ~IRYeGiL~~Id~e~sTv~L~nVrfGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK~~ 88 (613)
+-=|+|++-..+ ++++....|.||.| |-..+||+||+.+..+|+++
T Consensus 7 g~FWvGv~E~~~--~~~~~v~rv~FG~E---------P~d~Ei~~fi~~~~~~L~f~ 52 (132)
T PF11208_consen 7 GPFWVGVFERHE--DGKYKVARVTFGAE---------PKDPEIYEFILKHWYKLRFS 52 (132)
T ss_pred CCcEEEEEEEEE--CCEEEEEEEeeCCC---------CCcHHHHHHHHHHHHHhcCC
Confidence 344899999987 88999999999954 56779999999999888833
No 52
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=37.88 E-value=61 Score=29.15 Aligned_cols=52 Identities=21% Similarity=0.321 Sum_probs=35.9
Q ss_pred eEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 25 ISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 25 ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
|.|..+.+..|+|+|..+|. ---|.|.|+. +=. +.. ....+..|+.||+.|.
T Consensus 31 i~l~~~~~r~~~G~L~gfD~-~mNlVL~d~~E~~~-----~~~----~~~~lG~ilIRGnnV~ 83 (89)
T PTZ00138 31 IWLYDHPNLRIEGKILGFDE-YMNMVLDDAEEVYT-----KKN----TRKDLGRILLKGDNIT 83 (89)
T ss_pred EEEEeCCCcEEEEEEEEEcc-cceEEEccEEEEec-----CCc----eeeEcCeEEEcCCEEE
Confidence 34445668999999999994 4578899876 311 111 1234677999999987
No 53
>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=34.30 E-value=93 Score=27.37 Aligned_cols=58 Identities=21% Similarity=0.428 Sum_probs=38.0
Q ss_pred ccccce--eEE--EecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 19 SYIGSL--ISL--TSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 19 ~~IGs~--ISL--ISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
.|+..+ |.+ .-+.+..|+|+|..+|. ---|.|.|+. +-.+ +. ....+..|+.||..|.
T Consensus 13 ~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~-~mNlvL~d~~E~~~~-----~~----~~~~lG~iliRGnnV~ 75 (79)
T cd01718 13 RFLQSKQRVQIWLYEQTDLRIEGVIIGFDE-YMNLVLDDAEEVHLK-----TK----TRKPLGRILLKGDNIT 75 (79)
T ss_pred HHHccCcEEEEEEEeCCCcEEEEEEEEEcc-ceeEEEcCEEEEecC-----Cc----eEeEcCcEEEeCCEEE
Confidence 355553 333 34699999999999994 3468898875 4211 01 1123567999999887
No 54
>PRK14644 hypothetical protein; Provisional
Probab=33.77 E-value=61 Score=30.98 Aligned_cols=35 Identities=26% Similarity=0.380 Sum_probs=29.1
Q ss_pred CCcccccceeEEEecCC----ceeEEEeeeecCCCCeeeec
Q 007191 16 SADSYIGSLISLTSKSE----IRYEGVLFNINTEESSIGLR 52 (613)
Q Consensus 16 ~~~~~IGs~ISLISks~----IRYeGiL~~Id~e~sTv~L~ 52 (613)
.-..|||.+|.+..+.. -.|+|+|..+| +.+|+|.
T Consensus 79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~--~~~i~l~ 117 (136)
T PRK14644 79 ELENHIGEIIDVSLNKEVNKTDFITGELLENN--PETITLK 117 (136)
T ss_pred HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEe--CCEEEEE
Confidence 35678999999988776 78999999998 6678886
No 55
>PF12287 Caprin-1_C: Cytoplasmic activation/proliferation-associated protein-1 C term; InterPro: IPR022070 This family of proteins is found in eukaryotes. Proteins in this family are typically between 343 and 708 amino acids in length. This family is the C-terminal region of caprin-1. Caprin-1 is a protein involved in regulating cellular proliferation. In mutated phenotypes, the G1 phase of the cell cycle is greatly lengthened, impairing normal proliferation. The C-terminal region of caprin-1 contains RGG motifs which are characteristic of RNA binding domains. It is possible that caprin-1 functions through an RNA binding mechanism.
Probab=32.09 E-value=48 Score=35.98 Aligned_cols=8 Identities=25% Similarity=0.389 Sum_probs=4.3
Q ss_pred CCCcccCC
Q 007191 386 TPGQLLQP 393 (613)
Q Consensus 386 tpgqllq~ 393 (613)
.++|+.|.
T Consensus 122 ~~~q~fq~ 129 (316)
T PF12287_consen 122 SQPQVFQS 129 (316)
T ss_pred Cccccccc
Confidence 34566663
No 56
>PRK14633 hypothetical protein; Provisional
Probab=31.70 E-value=67 Score=31.01 Aligned_cols=35 Identities=20% Similarity=0.387 Sum_probs=28.2
Q ss_pred CCcccccceeEEEec----CCceeEEEeeeecCCCCeeeec
Q 007191 16 SADSYIGSLISLTSK----SEIRYEGVLFNINTEESSIGLR 52 (613)
Q Consensus 16 ~~~~~IGs~ISLISk----s~IRYeGiL~~Id~e~sTv~L~ 52 (613)
+...|||.+|.+..+ ..-+|+|+|..+| +.+|+|.
T Consensus 88 ~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~--~~~i~l~ 126 (150)
T PRK14633 88 QAQALVGFNVKAVTLAPVGSQTKFKGVLERVE--GNNVILN 126 (150)
T ss_pred HHHHhCCCeEEEEEecccCCcEEEEEEEEEEe--CCEEEEE
Confidence 345689999999884 5688999999997 6777775
No 57
>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=30.83 E-value=76 Score=24.77 Aligned_cols=27 Identities=15% Similarity=0.336 Sum_probs=21.7
Q ss_pred cccceeEEEecCCceeEEEeeeecCCCC
Q 007191 20 YIGSLISLTSKSEIRYEGVLFNINTEES 47 (613)
Q Consensus 20 ~IGs~ISLISks~IRYeGiL~~Id~e~s 47 (613)
.||+.|+|.. .+-.++|+...||.+-.
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~ 27 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGA 27 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSE
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCE
Confidence 4899999999 55558999999985443
No 58
>PRK14642 hypothetical protein; Provisional
Probab=29.99 E-value=1.1e+02 Score=31.36 Aligned_cols=34 Identities=18% Similarity=0.382 Sum_probs=26.4
Q ss_pred CcccccceeEEEec-------------CCceeEEEeeeecCCCCeeeec
Q 007191 17 ADSYIGSLISLTSK-------------SEIRYEGVLFNINTEESSIGLR 52 (613)
Q Consensus 17 ~~~~IGs~ISLISk-------------s~IRYeGiL~~Id~e~sTv~L~ 52 (613)
-..|||.+|.|..+ ..-+|+|+|..+|- ..|+|.
T Consensus 95 f~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~--~~i~l~ 141 (197)
T PRK14642 95 FERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAES--GGWQIV 141 (197)
T ss_pred HHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcC--CEEEEE
Confidence 34689999999887 45789999999984 455553
No 59
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=29.97 E-value=60 Score=29.65 Aligned_cols=60 Identities=17% Similarity=0.314 Sum_probs=44.8
Q ss_pred ccccceeEEEecCCceeEEEeeeecCCCCeeeecccccccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 19 SYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDRLEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 19 ~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVrfGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
..||+.+++-=|.|+--.|+|++||.= =.|.|.||+--.+ ..-|..-.|-. +-.|||-|+
T Consensus 9 slvg~~V~VeLKnd~~i~GtL~svDqy-LNlkL~di~v~d~------~kyPhm~Sv~n-cfIRGSvvr 68 (96)
T KOG3448|consen 9 SLVGKEVVVELKNDLSICGTLHSVDQY-LNLKLTDISVTDP------DKYPHMLSVKN-CFIRGSVVR 68 (96)
T ss_pred HhcCCeEEEEEcCCcEEEEEecccchh-heeEEeeeEeeCc------ccCCCeeeeee-EEEeccEEE
Confidence 579999999999999999999999953 4588999883222 22344444444 566999888
No 60
>PRK14631 hypothetical protein; Provisional
Probab=29.77 E-value=72 Score=31.68 Aligned_cols=37 Identities=19% Similarity=0.434 Sum_probs=30.9
Q ss_pred CCcccccceeEEEec----CCceeEEEeeeecCCCCeeeec
Q 007191 16 SADSYIGSLISLTSK----SEIRYEGVLFNINTEESSIGLR 52 (613)
Q Consensus 16 ~~~~~IGs~ISLISk----s~IRYeGiL~~Id~e~sTv~L~ 52 (613)
+-..|+|.+|.|..+ ..-+|.|+|..+|.++.+|+|.
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 345689999999985 4478999999999888888885
No 61
>PF05084 GRA6: Granule antigen protein (GRA6); InterPro: IPR008119 Toxoplasma gondii is an obligate intracellular apicomplexan protozoan parasite, with a complex lifestyle involving varied hosts []. It has two phases of growth: an intestinal phase in feline hosts, and an extra-intestinal phase in other mammals. Oocysts from infected cats develop into tachyzoites, and eventually, bradyzoites and zoitocysts in the extraintestinal host []. Transmission of the parasite occurs through contact with infected cats or raw/undercooked meat; in immunocompromised individuals, it can cause severe and often lethal toxoplasmosis. Acute infection in healthy humans can sometimes also cause tissue damage []. The protozoan utilises a variety of secretory and antigenic proteins to invade a host and gain access to the intracellular environment []. These originate from distinct organelles in the T. gondii cell termed micronemes, rhoptries, and dense granules. They are released at specific times during invasion to ensure the proteins are allocated to their correct target destinations []. Dense granule antigens (GRAs) are released from the T. gondii tachyzoite while still encapsulated in a host vacuole. Gra6, one of these moieties, is associated with the parasitophorous vacuole []. It possesses a hydrophobic central region flanked by two hydrophilic domains, and is present as a single copy gene in the Toxoplasma gondii genome []. Gra6 shares a similar function with Gra2, in that it is rapidly targeted to a network of membranous tubules that connect with the vacuolar membrane []. Indeed, these two proteins, together with Gra4, form a multimeric complex that stabilises the parasite within the vacuole.
Probab=29.67 E-value=50 Score=33.29 Aligned_cols=16 Identities=56% Similarity=1.049 Sum_probs=8.4
Q ss_pred CCCCCCCCCCCCCCCCCC
Q 007191 589 GSYHGRGYGYAPRGRGYG 606 (613)
Q Consensus 589 Ggy~GRGygy~gRg~g~~ 606 (613)
||..|| ||.|||-|.|
T Consensus 198 GG~Egr--gyrgrgeggg 213 (215)
T PF05084_consen 198 GGNEGR--GYRGRGEGGG 213 (215)
T ss_pred Cccccc--ccCCCCCCCC
Confidence 444444 4566666554
No 62
>PRK14639 hypothetical protein; Provisional
Probab=28.55 E-value=85 Score=30.03 Aligned_cols=36 Identities=25% Similarity=0.556 Sum_probs=29.8
Q ss_pred CCcccccceeEEEecCCceeEEEeeeecCCCCeeeecc
Q 007191 16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRN 53 (613)
Q Consensus 16 ~~~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~n 53 (613)
+...|+|.+|.+..+..-+|+|+|..+| +.+|+|.+
T Consensus 82 ~f~r~~G~~v~v~l~~~~~~~G~L~~~~--~~~i~l~~ 117 (140)
T PRK14639 82 HFAKSIGELVKITTNEKEKFEGKIVSVD--DENITLEN 117 (140)
T ss_pred HHHHhCCCEEEEEECCCcEEEEEEEEEe--CCEEEEEE
Confidence 4457899999999888889999999998 56777754
No 63
>PRK14634 hypothetical protein; Provisional
Probab=28.53 E-value=78 Score=30.77 Aligned_cols=35 Identities=20% Similarity=0.450 Sum_probs=27.7
Q ss_pred CCcccccceeEEEecCCc----eeEEEeeeecCCCCeeeec
Q 007191 16 SADSYIGSLISLTSKSEI----RYEGVLFNINTEESSIGLR 52 (613)
Q Consensus 16 ~~~~~IGs~ISLISks~I----RYeGiL~~Id~e~sTv~L~ 52 (613)
+-..|+|.+|.+..+..+ +|+|+|..+| +..|+|.
T Consensus 94 ~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~--~~~v~l~ 132 (155)
T PRK14634 94 DFQTFRGFPVEVSHRDDDGSEQRLEGLLLERN--EDHLQIN 132 (155)
T ss_pred HHHHhCCCeEEEEEecCCCCeEEEEEEEEEEe--CCEEEEE
Confidence 345689999999887554 8999999988 6677774
No 64
>PF05084 GRA6: Granule antigen protein (GRA6); InterPro: IPR008119 Toxoplasma gondii is an obligate intracellular apicomplexan protozoan parasite, with a complex lifestyle involving varied hosts []. It has two phases of growth: an intestinal phase in feline hosts, and an extra-intestinal phase in other mammals. Oocysts from infected cats develop into tachyzoites, and eventually, bradyzoites and zoitocysts in the extraintestinal host []. Transmission of the parasite occurs through contact with infected cats or raw/undercooked meat; in immunocompromised individuals, it can cause severe and often lethal toxoplasmosis. Acute infection in healthy humans can sometimes also cause tissue damage []. The protozoan utilises a variety of secretory and antigenic proteins to invade a host and gain access to the intracellular environment []. These originate from distinct organelles in the T. gondii cell termed micronemes, rhoptries, and dense granules. They are released at specific times during invasion to ensure the proteins are allocated to their correct target destinations []. Dense granule antigens (GRAs) are released from the T. gondii tachyzoite while still encapsulated in a host vacuole. Gra6, one of these moieties, is associated with the parasitophorous vacuole []. It possesses a hydrophobic central region flanked by two hydrophilic domains, and is present as a single copy gene in the Toxoplasma gondii genome []. Gra6 shares a similar function with Gra2, in that it is rapidly targeted to a network of membranous tubules that connect with the vacuolar membrane []. Indeed, these two proteins, together with Gra4, form a multimeric complex that stabilises the parasite within the vacuole.
Probab=27.47 E-value=72 Score=32.21 Aligned_cols=16 Identities=44% Similarity=0.765 Sum_probs=9.6
Q ss_pred CCCCCCCCCCCCCCCCC
Q 007191 582 YRGGRSRGSYHGRGYGY 598 (613)
Q Consensus 582 ~rGg~gRGgy~GRGygy 598 (613)
-+|.-|| ||+|||-|.
T Consensus 197 NGG~Egr-gyrgrgegg 212 (215)
T PF05084_consen 197 NGGNEGR-GYRGRGEGG 212 (215)
T ss_pred CCccccc-ccCCCCCCC
Confidence 3344445 788887663
No 65
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=27.21 E-value=5.4e+02 Score=31.93 Aligned_cols=10 Identities=20% Similarity=0.292 Sum_probs=5.0
Q ss_pred ccceeccccc
Q 007191 107 DWTLRSVIRK 116 (613)
Q Consensus 107 ~~~~~~~~~~ 116 (613)
||+-|.++..
T Consensus 445 df~yr~~l~i 454 (1102)
T KOG1924|consen 445 DFKYRFRLDI 454 (1102)
T ss_pred CcchhhcccC
Confidence 5555554433
No 66
>PRK14638 hypothetical protein; Provisional
Probab=26.46 E-value=86 Score=30.30 Aligned_cols=35 Identities=14% Similarity=0.290 Sum_probs=29.5
Q ss_pred CCcccccceeEEEecCCceeEEEeeeecCCCCeeeec
Q 007191 16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLR 52 (613)
Q Consensus 16 ~~~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~ 52 (613)
+-..|+|.+|.+..+..-+|+|+|..+| +.+|+|.
T Consensus 94 ~f~r~~G~~v~V~~~~~k~~~G~L~~~~--~~~i~l~ 128 (150)
T PRK14638 94 DYVRFTGKLAKIVTKDGKTFIGRIESFV--DGTITIS 128 (150)
T ss_pred HHHHhCCCEEEEEECCCcEEEEEEEEEe--CCEEEEE
Confidence 3456899999999999999999999998 5667775
No 67
>PRK02001 hypothetical protein; Validated
Probab=25.01 E-value=1.1e+02 Score=29.98 Aligned_cols=65 Identities=20% Similarity=0.215 Sum_probs=42.0
Q ss_pred CCcccccceeEEEecCCceeEEEeeeecCCCCeeeecccc--cccCCCCCCCCCCCCCCCceeeEEEEcCccccccc
Q 007191 16 SADSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR--LEQKGEEKIGPQVPPSDKIYEYILFRGSDIKHCLL 90 (613)
Q Consensus 16 ~~~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr--fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK~~~~ 90 (613)
+-..|+|.+|.+..+..-+|+|+|..+| +.+|+|. +. =+-++++.. ....+-+.|.=++|+.+.+
T Consensus 84 ~f~r~~G~~v~V~l~~~~~~~G~L~~~~--~~~i~l~-~~~~~~~~~~k~~-------~~~~~~~~i~~~~I~ka~l 150 (152)
T PRK02001 84 QYKKNIGRELEVLTKNGKKIEGELKSAD--ENDITLE-VKAREPKEGGKGK-------VTVEKEETITYDDIKEAKV 150 (152)
T ss_pred HHHHhCCCEEEEEECCCCEEEEEEEEEe--CCEEEEE-Ecccccccccccc-------cccceeEEEEhHheeeEEE
Confidence 3456899999999988999999999998 5677774 22 112222211 1124456667777774433
No 68
>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=24.93 E-value=1.1e+02 Score=26.34 Aligned_cols=34 Identities=15% Similarity=0.432 Sum_probs=25.6
Q ss_pred CcccccceeEEEecC----CceeEEEeeeecCCCCeeeec
Q 007191 17 ADSYIGSLISLTSKS----EIRYEGVLFNINTEESSIGLR 52 (613)
Q Consensus 17 ~~~~IGs~ISLISks----~IRYeGiL~~Id~e~sTv~L~ 52 (613)
-..|||.+|.+..+. .-+|+|+|..+|- ..|+|.
T Consensus 20 ~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~--~~v~l~ 57 (83)
T cd01734 20 FERAVGKYVHVKLYQPIDGQKEFEGTLLGVDD--DTVTLE 57 (83)
T ss_pred HHHhCCCEEEEEEEcccCCeEEEEEEEEeEeC--CEEEEE
Confidence 456899999998873 2369999999984 556654
No 69
>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=24.76 E-value=88 Score=29.31 Aligned_cols=33 Identities=27% Similarity=0.565 Sum_probs=24.1
Q ss_pred CcccccceeEEEec----CCceeEEEeeeecCCCCeeee
Q 007191 17 ADSYIGSLISLTSK----SEIRYEGVLFNINTEESSIGL 51 (613)
Q Consensus 17 ~~~~IGs~ISLISk----s~IRYeGiL~~Id~e~sTv~L 51 (613)
..-|||.+|.+..+ ..-+|+|+|..+| +.+|+|
T Consensus 82 ~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~--~~~i~l 118 (141)
T PF02576_consen 82 FERFIGRKVKVKLKQPVNGRKEFEGKLLEVD--EDEITL 118 (141)
T ss_dssp HHHH-SEEEEEE-SS-SSS-SEEEEEEEEEE--TTEEEE
T ss_pred HHHhcCCeEEEEEeccCCCcEEEEEEEEEEe--CCEEEE
Confidence 45689999999984 4567999999999 466666
No 70
>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=24.71 E-value=1.4e+02 Score=25.32 Aligned_cols=33 Identities=21% Similarity=0.274 Sum_probs=29.5
Q ss_pred cccceeEEEecCCceeEEEeeeecCCCCeeeec
Q 007191 20 YIGSLISLTSKSEIRYEGVLFNINTEESSIGLR 52 (613)
Q Consensus 20 ~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~ 52 (613)
.||+++++.+-.+=.+||.|+..|..-.-|.|+
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk 36 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILK 36 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEE
Confidence 589999999999999999999999886667675
No 71
>PRK14632 hypothetical protein; Provisional
Probab=24.33 E-value=1e+02 Score=30.49 Aligned_cols=35 Identities=26% Similarity=0.518 Sum_probs=28.0
Q ss_pred CCcccccceeEEEecCCc-------eeEEEeeeecCCCCeeeec
Q 007191 16 SADSYIGSLISLTSKSEI-------RYEGVLFNINTEESSIGLR 52 (613)
Q Consensus 16 ~~~~~IGs~ISLISks~I-------RYeGiL~~Id~e~sTv~L~ 52 (613)
+-..|||.+|.+..+.-+ +|+|+|..+| +.+|+|.
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 345689999999888744 8999999997 6677775
No 72
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=24.19 E-value=3.3e+02 Score=33.64 Aligned_cols=6 Identities=33% Similarity=1.093 Sum_probs=3.2
Q ss_pred chhccc
Q 007191 534 DFFDSL 539 (613)
Q Consensus 534 sFFDnI 539 (613)
.||-.|
T Consensus 977 EFFaDi 982 (1102)
T KOG1924|consen 977 EFFADI 982 (1102)
T ss_pred HHHHHH
Confidence 555544
No 73
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=23.10 E-value=49 Score=29.25 Aligned_cols=58 Identities=21% Similarity=0.378 Sum_probs=39.5
Q ss_pred cccccceeEEEecCCceeEEEeeeecCCCCeeeecccc-cccCCCCCCCCCCCCCCCceeeEEEEcCccc
Q 007191 18 DSYIGSLISLTSKSEIRYEGVLFNINTEESSIGLRNDR-LEQKGEEKIGPQVPPSDKIYEYILFRGSDIK 86 (613)
Q Consensus 18 ~~~IGs~ISLISks~IRYeGiL~~Id~e~sTv~L~nVr-fGTEgR~~~~~~Ipps~~vyeyIvFrgsDIK 86 (613)
..+||+++-+-=.+.+-|.|+|..||-= -.|+|+.-. |- ++. -...|.-...||+.|-
T Consensus 12 ~~iiGr~V~VKl~sgvdyrG~l~~lDgy-mNiaLe~tee~~------ngq----l~n~ygdaFirGnnVl 70 (77)
T KOG1783|consen 12 KAIIGRTVVVKLNSGVDYRGTLVCLDGY-MNIALESTEEYV------NGQ----LKNKYGDAFIRGNNVL 70 (77)
T ss_pred HHHhCCeEEEEecCCccccceehhhhhH-HHHHHHHHHHHh------cCc----ccccccceeeccccEE
Confidence 5689999999999999999999999932 234555433 21 222 1234555667887775
No 74
>PF15320 RAM: mRNA cap methylation, RNMT-activating mini protein
Probab=22.34 E-value=1.2e+02 Score=26.98 Aligned_cols=36 Identities=19% Similarity=0.128 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 007191 570 PRYHGGRGGRGPYRGGRSRGSYHGRGYGYAPRGRGY 605 (613)
Q Consensus 570 ~r~rGGrGGRGg~rGg~gRGgy~GRGygy~gRg~g~ 605 (613)
+..|+|+++|+++..++.+..++|++..++..++++
T Consensus 35 W~~r~~gn~r~~~~r~~~~r~~rg~~~r~~~~~~~r 70 (81)
T PF15320_consen 35 WNSRRGGNQRGRGNRYRDNRRFRGRDGRRGWQRRNR 70 (81)
T ss_pred cccCCCCCCCCCCCccccCCCCCCCCCCCCCCCCCc
No 75
>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=21.55 E-value=1.5e+02 Score=21.28 Aligned_cols=31 Identities=13% Similarity=0.206 Sum_probs=26.0
Q ss_pred cceeEEEecCCceeEEEeeeecCCCCeeeec
Q 007191 22 GSLISLTSKSEIRYEGVLFNINTEESSIGLR 52 (613)
Q Consensus 22 Gs~ISLISks~IRYeGiL~~Id~e~sTv~L~ 52 (613)
|..+.+|+=..--.+|++..||.+..+|.++
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 6677788877888999999999999888763
No 76
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=20.41 E-value=1.2e+02 Score=29.19 Aligned_cols=6 Identities=33% Similarity=0.789 Sum_probs=2.4
Q ss_pred cchhcc
Q 007191 533 DDFFDS 538 (613)
Q Consensus 533 ~sFFDn 538 (613)
|...|.
T Consensus 73 d~iid~ 78 (134)
T KOG3293|consen 73 DEIIDK 78 (134)
T ss_pred HHHHHH
Confidence 344443
No 77
>PF15098 TMEM89: TMEM89 protein family
Probab=20.28 E-value=61 Score=30.95 Aligned_cols=34 Identities=44% Similarity=0.918 Sum_probs=29.5
Q ss_pred CC-CCCCCCCCCCCCCC-CCCCCCCCcccccccccC
Q 007191 185 PL-YQPGGSLGAWGSSP-MPTTNGAGLAMPMYWQGF 218 (613)
Q Consensus 185 P~-yqPg~~~g~wg~sp-~p~an~~glaMpmYwqGy 218 (613)
|+ ||=|-.+++||=.| .-.+-+.+|.-|=||-|-
T Consensus 4 PlWYQvgLDLqPWGCqPn~le~C~~sLgcpG~wmgl 39 (134)
T PF15098_consen 4 PLWYQVGLDLQPWGCQPNSLEGCGSSLGCPGYWMGL 39 (134)
T ss_pred chhhhhcccccccCCCCCChhhhccCCCCCcccccc
Confidence 55 78898999999999 777788999999999774
No 78
>PRK14647 hypothetical protein; Provisional
Probab=20.05 E-value=1.4e+02 Score=29.03 Aligned_cols=35 Identities=14% Similarity=0.342 Sum_probs=27.7
Q ss_pred CCcccccceeEEEecC---------CceeEEEeeeecCCCCeeeec
Q 007191 16 SADSYIGSLISLTSKS---------EIRYEGVLFNINTEESSIGLR 52 (613)
Q Consensus 16 ~~~~~IGs~ISLISks---------~IRYeGiL~~Id~e~sTv~L~ 52 (613)
+...|+|.+|.+..+. .-+|.|+|..+| +..|+|.
T Consensus 93 ~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~--~~~v~l~ 136 (159)
T PRK14647 93 DYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLA--DGVVTIA 136 (159)
T ss_pred HHHHhCCcEEEEEEeccccccccCCceEEEEEEEeec--CCEEEEE
Confidence 4456899999999864 468999999998 5667664
No 79
>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=20.04 E-value=1e+02 Score=36.15 Aligned_cols=17 Identities=35% Similarity=0.696 Sum_probs=8.4
Q ss_pred ccCCCCCcccCCCcccC
Q 007191 376 LNDGIMPSLVTPGQLLQ 392 (613)
Q Consensus 376 ~~~~p~P~lvtpgqllq 392 (613)
+++.+-=.+.|||-|+.
T Consensus 343 Lk~g~EivVaTPgRlid 359 (731)
T KOG0339|consen 343 LKEGAEIVVATPGRLID 359 (731)
T ss_pred hhcCCeEEEechHHHHH
Confidence 33444444556665543
Done!