Query 008994
Match_columns 547
No_of_seqs 241 out of 360
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 19:06:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008994.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008994hhsearch_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 3.5E-39 7.6E-44 332.9 13.4 149 8-165 2-150 (361)
2 PF12701 LSM14: Scd6-like Sm d 100.0 2.5E-37 5.5E-42 268.8 8.9 94 9-106 2-95 (96)
3 cd01736 LSm14_N LSm14 (also kn 100.0 7.6E-36 1.6E-40 247.9 7.7 73 11-83 2-74 (74)
4 PF09532 FDF: FDF domain; Int 99.8 8.2E-23 1.8E-27 177.6 -2.6 98 403-505 1-103 (104)
5 cd00600 Sm_like The eukaryotic 97.8 4.6E-05 1E-09 60.2 5.8 61 11-82 2-62 (63)
6 PF14438 SM-ATX: Ataxin 2 SM d 97.8 2E-05 4.4E-10 65.6 3.6 68 11-81 8-77 (77)
7 cd01737 LSm16_N LSm16 belongs 96.7 0.0049 1.1E-07 50.5 5.9 61 10-83 1-62 (62)
8 PF01423 LSM: LSM domain ; In 96.3 0.01 2.2E-07 47.7 6.0 62 12-83 5-66 (67)
9 KOG3973 Uncharacterized conser 96.0 0.011 2.5E-07 62.8 6.0 10 537-546 376-385 (465)
10 PF05918 API5: Apoptosis inhib 95.9 0.0021 4.5E-08 71.9 0.0 8 538-545 548-555 (556)
11 KOG0921 Dosage compensation co 95.9 0.019 4.1E-07 67.3 7.3 18 337-354 1057-1074(1282)
12 KOG0116 RasGAP SH3 binding pro 95.6 0.012 2.7E-07 63.9 4.5 35 465-499 331-368 (419)
13 cd01719 Sm_G The eukaryotic Sm 95.5 0.04 8.6E-07 46.1 6.2 65 11-86 6-70 (72)
14 smart00651 Sm snRNP Sm protein 95.4 0.034 7.5E-07 44.6 5.4 63 11-83 4-66 (67)
15 cd01722 Sm_F The eukaryotic Sm 95.3 0.042 9.1E-07 45.2 5.7 61 11-82 7-67 (68)
16 KOG0921 Dosage compensation co 95.3 0.015 3.3E-07 68.0 4.2 19 464-482 1169-1192(1282)
17 cd01717 Sm_B The eukaryotic Sm 95.0 0.083 1.8E-06 44.6 6.6 75 10-85 5-79 (79)
18 PF05918 API5: Apoptosis inhib 95.0 0.0067 1.5E-07 67.9 0.0 9 531-540 546-554 (556)
19 cd01731 archaeal_Sm1 The archa 94.8 0.072 1.6E-06 43.6 5.7 61 11-82 6-66 (68)
20 cd01726 LSm6 The eukaryotic Sm 94.8 0.069 1.5E-06 43.8 5.6 60 12-82 7-66 (67)
21 cd01728 LSm1 The eukaryotic Sm 94.8 0.078 1.7E-06 44.8 5.9 63 11-81 8-70 (74)
22 PRK00737 small nuclear ribonuc 94.8 0.067 1.5E-06 44.5 5.4 61 11-82 10-70 (72)
23 cd01723 LSm4 The eukaryotic Sm 94.7 0.078 1.7E-06 44.6 5.7 64 12-85 8-71 (76)
24 cd01725 LSm2 The eukaryotic Sm 94.5 0.12 2.6E-06 44.1 6.5 65 12-85 8-72 (81)
25 cd01721 Sm_D3 The eukaryotic S 94.2 0.14 3.1E-06 42.5 6.2 62 12-84 7-68 (70)
26 COG1958 LSM1 Small nuclear rib 94.0 0.18 3.8E-06 42.5 6.4 65 11-83 13-78 (79)
27 cd06168 LSm9 The eukaryotic Sm 93.4 0.24 5.2E-06 42.0 6.1 70 11-85 6-75 (75)
28 TIGR01648 hnRNP-R-Q heterogene 93.2 0.2 4.4E-06 56.7 7.1 32 398-429 269-300 (578)
29 cd01724 Sm_D1 The eukaryotic S 93.0 0.27 5.9E-06 42.9 6.2 64 12-86 8-71 (90)
30 cd01733 LSm10 The eukaryotic S 92.0 0.47 1E-05 40.4 6.2 63 11-84 15-77 (78)
31 KOG1596 Fibrillarin and relate 90.9 0.38 8.2E-06 49.8 5.2 10 532-541 63-72 (317)
32 cd01729 LSm7 The eukaryotic Sm 90.4 1 2.2E-05 38.6 6.6 70 11-83 8-77 (81)
33 cd01727 LSm8 The eukaryotic Sm 90.3 0.65 1.4E-05 38.8 5.3 65 10-83 4-70 (74)
34 KOG1073 Uncharacterized mRNA-a 86.1 1.9 4.2E-05 46.5 6.9 40 463-506 252-292 (361)
35 cd01732 LSm5 The eukaryotic Sm 85.8 3 6.5E-05 35.4 6.6 64 12-83 10-73 (76)
36 PRK11634 ATP-dependent RNA hel 85.3 1.1 2.3E-05 51.2 4.8 10 275-284 305-314 (629)
37 KOG3293 Small nuclear ribonucl 85.2 0.96 2.1E-05 42.1 3.6 14 465-478 45-60 (134)
38 KOG3293 Small nuclear ribonucl 82.4 1.5 3.3E-05 40.9 3.6 16 465-480 59-76 (134)
39 COG4371 Predicted membrane pro 82.1 2 4.4E-05 44.7 4.8 15 522-536 76-90 (334)
40 TIGR01659 sex-lethal sex-letha 80.5 1.4 3.1E-05 46.8 3.2 37 392-428 143-179 (346)
41 KOG3172 Small nuclear ribonucl 79.9 1.6 3.4E-05 39.9 2.8 24 470-493 34-59 (119)
42 cd01720 Sm_D2 The eukaryotic S 79.3 6.8 0.00015 34.3 6.5 68 14-82 13-83 (87)
43 PRK11634 ATP-dependent RNA hel 77.1 2.8 6.1E-05 47.9 4.5 8 466-473 525-532 (629)
44 KOG2236 Uncharacterized conser 74.0 9.7 0.00021 42.5 7.3 25 189-213 456-481 (483)
45 cd01730 LSm3 The eukaryotic Sm 71.0 15 0.00032 31.4 6.3 70 12-82 8-80 (82)
46 KOG3448 Predicted snRNP core p 67.9 13 0.00029 33.1 5.4 64 12-84 9-72 (96)
47 KOG2945 Predicted RNA-binding 66.9 4.5 9.8E-05 43.8 2.9 7 407-413 181-187 (365)
48 PF06372 Gemin6: Gemin6 protei 66.9 8.9 0.00019 37.5 4.6 60 11-87 13-72 (166)
49 KOG3262 H/ACA small nucleolar 66.5 8.6 0.00019 38.5 4.5 7 421-427 95-101 (215)
50 TIGR01648 hnRNP-R-Q heterogene 66.2 6.5 0.00014 44.9 4.1 23 397-419 181-203 (578)
51 PF12764 Gly-rich_Ago1: Glycin 66.0 6.3 0.00014 35.8 3.2 8 524-531 19-26 (104)
52 KOG3172 Small nuclear ribonucl 56.4 11 0.00023 34.7 2.9 20 501-520 82-101 (119)
53 KOG2140 Uncharacterized conser 53.8 13 0.00028 42.5 3.6 26 400-427 382-407 (739)
54 PLN03134 glycine-rich RNA-bind 51.5 14 0.0003 34.6 2.9 30 395-424 73-102 (144)
55 COG4907 Predicted membrane pro 47.8 14 0.00031 41.5 2.8 22 65-86 53-75 (595)
56 PTZ00138 small nuclear ribonuc 41.3 64 0.0014 28.6 5.3 54 20-83 33-86 (89)
57 cd01735 LSm12_N LSm12 belongs 38.4 62 0.0014 26.9 4.5 58 13-83 4-61 (61)
58 KOG1775 U6 snRNA-associated Sm 38.3 27 0.00059 30.4 2.5 62 11-82 13-76 (84)
59 PF02237 BPL_C: Biotin protein 38.1 53 0.0011 25.2 3.8 27 13-40 1-27 (48)
60 PRK02001 hypothetical protein; 37.1 1.1E+02 0.0023 29.5 6.5 65 11-85 86-151 (152)
61 PF10842 DUF2642: Protein of u 36.7 49 0.0011 27.9 3.7 33 11-46 17-49 (66)
62 PF07076 DUF1344: Protein of u 35.4 34 0.00073 28.6 2.5 24 28-51 5-28 (61)
63 COG4907 Predicted membrane pro 35.3 30 0.00065 39.0 2.8 13 27-39 52-64 (595)
64 PRK14644 hypothetical protein; 35.0 60 0.0013 30.6 4.5 33 11-45 81-117 (136)
65 PRK14642 hypothetical protein; 34.8 1.1E+02 0.0023 30.9 6.3 71 11-85 96-179 (197)
66 PRK14631 hypothetical protein; 33.8 63 0.0014 31.7 4.5 35 11-45 113-151 (174)
67 PF02576 DUF150: Uncharacteris 33.1 75 0.0016 29.4 4.7 31 12-44 84-118 (141)
68 PRK14638 hypothetical protein; 32.2 62 0.0013 30.8 4.1 33 11-45 96-128 (150)
69 KOG1783 Small nuclear ribonucl 30.0 29 0.00063 30.0 1.3 62 11-83 12-73 (77)
70 COG1512 Beta-propeller domains 29.2 66 0.0014 33.7 4.0 16 414-433 83-98 (271)
71 COG1512 Beta-propeller domains 28.0 61 0.0013 34.0 3.5 9 410-418 145-153 (271)
72 PRK14639 hypothetical protein; 27.8 92 0.002 29.4 4.4 35 11-47 84-118 (140)
73 cd01718 Sm_E The eukaryotic Sm 27.6 1.8E+02 0.0039 25.2 5.8 60 13-82 14-77 (79)
74 PRK06958 single-stranded DNA-b 27.5 61 0.0013 32.1 3.3 12 419-430 5-16 (182)
75 KOG0339 ATP-dependent RNA heli 26.5 61 0.0013 37.4 3.4 15 290-304 259-273 (731)
76 PRK14633 hypothetical protein; 26.4 1E+02 0.0022 29.4 4.4 53 11-85 90-146 (150)
77 KOG3910 Helix loop helix trans 24.7 1.2E+03 0.025 27.3 16.4 24 170-195 198-221 (632)
78 cd01734 YlxS_C YxlS is a Bacil 24.2 2E+02 0.0043 24.4 5.4 56 11-85 21-80 (83)
79 PF05084 GRA6: Granule antigen 23.6 78 0.0017 31.4 3.1 37 508-544 172-213 (215)
80 PF00467 KOW: KOW motif; Inte 23.0 1.3E+02 0.0029 21.2 3.5 31 15-45 2-32 (32)
81 KOG1855 Predicted RNA-binding 22.5 2.3E+02 0.0051 31.9 6.8 33 398-430 286-318 (484)
82 PF12300 DUF3628: Protein of u 22.2 90 0.002 30.8 3.2 7 386-392 12-18 (180)
83 COG0779 Uncharacterized protei 21.7 1.4E+02 0.003 29.0 4.4 33 11-45 95-131 (153)
84 KOG2479 Translation initiation 20.9 1.1E+02 0.0024 34.5 3.9 7 417-423 34-40 (549)
85 PRK14634 hypothetical protein; 20.1 1.4E+02 0.003 28.7 4.0 33 11-45 96-132 (155)
No 1
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=3.5e-39 Score=332.87 Aligned_cols=149 Identities=43% Similarity=0.626 Sum_probs=123.7
Q ss_pred CCCCCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeeccC
Q 008994 8 NAPESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVKSS 87 (547)
Q Consensus 8 ~~~~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~v~~~ 87 (547)
+.+++|||++||||||.|||||||||+||++||||+|+||||||||||++++.+||+.++|||||||||+|||||.||+.
T Consensus 2 s~~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~ 81 (361)
T KOG1073|consen 2 SLVTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQET 81 (361)
T ss_pred CcccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccC
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCCCCccCCCCchhhhccCCCCCCCCCCccccccccccCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCcccc
Q 008994 88 PPPQKEEQIYQDPAIIQSQYAGISTNSPLLSSVVGKTLTESSSWQDTPTLTSKASAGSLLSHQPGTQVSQFSHPQAAQ 165 (547)
Q Consensus 88 p~~~~~~~~~~DPAI~~~~~p~~~~~s~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~plyQpg~~~~swg~s~~~~ 165 (547)
|+.+....++.+|+|. ...+.++..+.+....+.+..+.+-+....|..++.++|...+++|.....++
T Consensus 82 p~~~~~~~~p~~pp~p---------~~~~~~s~~s~~~~~~s~~~~~~~~~~~~~P~~~~~~~~~~~~g~~~~~~~~~ 150 (361)
T KOG1073|consen 82 PAGQIPCSLPVPPPMP---------PQSSIPSQQSGSDPKISFQFAQAGNPVIGNPQGLITTNPVPAEGSIYGSFQPP 150 (361)
T ss_pred cccCccccccCCCCCC---------cccccccccCCcccccccccccCCCcccCCcCccccCCCCccccccccccCCc
Confidence 7643333355666652 22244444555556667777777777777799999999999999999866554
No 2
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=100.00 E-value=2.5e-37 Score=268.82 Aligned_cols=94 Identities=61% Similarity=0.998 Sum_probs=72.4
Q ss_pred CCCCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeeccCC
Q 008994 9 APESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVKSSP 88 (547)
Q Consensus 9 ~~~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~v~~~p 88 (547)
.+++|||++||||||++|||||+||+||.+++||+|+||||||||||+++. +|||++++|+||+|||+|||||+||+.+
T Consensus 2 m~~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~-~ipp~~~v~~~I~Fr~sDIkdL~v~e~~ 80 (96)
T PF12701_consen 2 MADPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDR-EIPPSDEVYDYIVFRGSDIKDLKVIEPP 80 (96)
T ss_dssp -CCCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS----C-CSSSSEEEEETTTEEEEEECE-S
T ss_pred ccccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCc-ccCCCCceeeEEEEEccccceEEEEcCC
Confidence 578999999999999999999999999999999999999999999998864 8999999999999999999999999987
Q ss_pred CCCCCccCCCCchhhhcc
Q 008994 89 PPQKEEQIYQDPAIIQSQ 106 (547)
Q Consensus 89 ~~~~~~~~~~DPAI~~~~ 106 (547)
++ ++.++|||||+.+
T Consensus 81 ~~---~~~~~dpAiv~~~ 95 (96)
T PF12701_consen 81 PP---PPAPQDPAIVSVS 95 (96)
T ss_dssp -S---SSS----------
T ss_pred CC---CCCCCCCceeecC
Confidence 65 4578999999864
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=7.6e-36 Score=247.87 Aligned_cols=73 Identities=70% Similarity=1.151 Sum_probs=70.7
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~ 83 (547)
.+|||++||||||+||||||+||+||.+++||+|+||||||||||+.++++|||+++|||||||||+|||||+
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkDL~ 74 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKDLT 74 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccccC
Confidence 5899999999999999999999999999999999999999999999887789999999999999999999984
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=99.84 E-value=8.2e-23 Score=177.58 Aligned_cols=98 Identities=36% Similarity=0.628 Sum_probs=42.8
Q ss_pred CCCCchhhHHHHHhhhchhhhhhhccccccCCCCCCccCCcccccCCCcccCCccCCCCCCCCCCcc-ccccccCcccCC
Q 008994 403 TKFTEEFDFEAMNEKFKKDEVWGYLGKAKQSGKPETIEDNTADQNSRGKEADGLVKNGDPKPAYRKD-DFFDTISCNSLN 481 (547)
Q Consensus 403 ~kf~~DFDFeaaNaKFnKeei~~~lgK~~~s~~~~g~ed~~~~~~~e~~E~~~~~~~~~~k~~YdKd-sFFD~IS~e~~~ 481 (547)
|||++|||||+|||||+|++||+++.+........... ....+. +...........++|+|. +|||+|||++++
T Consensus 1 ik~~~DFDFes~NakF~K~~~~~e~~~~~~~~~~~~~~----~~~~~~-~~~~~~~~~~~~~~y~k~~sfFDnIS~e~~~ 75 (104)
T PF09532_consen 1 IKFDEDFDFESANAKFDKEEVFKELKKKDEKDEEDRLV----SENKEE-EEAEEENENDEEKYYDKKKSFFDNISCEAKD 75 (104)
T ss_dssp SSSSS---HCCCCCTSSCCHHCCHHHCC-------------------------------------B--B-------EEE-
T ss_pred CCCcCccCHHHHHHHhccccchhhhhcccccccccccc----cccccc-cccccccccCcccccccccccCcCCCccccc
Confidence 69999999999999999999999998764321111100 000110 111222233445677765 999999999999
Q ss_pred CCCcCC-cc---chhhhhcccccccCCC
Q 008994 482 RGTREG-QN---RFSERMRLDTETFGNF 505 (547)
Q Consensus 482 Rggr~G-R~---~~~EERk~ntETFG~~ 505 (547)
|....+ |. +|.|||++|+||||..
T Consensus 76 ~~~~~~~~~~~~~~~eer~~n~ETFG~~ 103 (104)
T PF09532_consen 76 RSEGNGPRRSGDDWREERKLNTETFGQS 103 (104)
T ss_dssp TT--EEE---HHHHHHHHHHH-HHTT--
T ss_pred ccCCcCCCcchhhHHHHHHhcccccCCC
Confidence 874332 32 4999999999999975
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=97.80 E-value=4.6e-05 Score=60.23 Aligned_cols=61 Identities=23% Similarity=0.361 Sum_probs=52.9
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccce
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDL 82 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL 82 (547)
..+||++|.+..+.+..|+|+|..+|. ...|.|+|+..+.+++ ....++.++.||+.|+.+
T Consensus 2 ~~~~g~~V~V~l~~g~~~~G~L~~~D~-~~Ni~L~~~~~~~~~~----------~~~~~~~~~irG~~I~~I 62 (63)
T cd00600 2 KDLVGKTVRVELKDGRVLEGVLVAFDK-YMNLVLDDVEETIKEG----------KKRVLGLVLIRGDNVRLV 62 (63)
T ss_pred hHHCCCEEEEEECCCcEEEEEEEEECC-CCCEEECCEEEEecCC----------cEEECCeEEEECCEEEEE
Confidence 468999999999999999999999994 4599999999999872 334678899999999876
No 6
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.78 E-value=2e-05 Score=65.59 Aligned_cols=68 Identities=15% Similarity=0.255 Sum_probs=45.2
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCC--CCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccc
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVG--DSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKD 81 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~--~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKD 81 (547)
..+||+++.+..|.+-+|||||+..+.+ +..|.|+.+|.-..+.... ..+-..++-+.++|++.||-|
T Consensus 8 ~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~---~~~~~~~~~~tlii~~~dvv~ 77 (77)
T PF14438_consen 8 TNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSN---SDPLSSEIVETLIIPAKDVVQ 77 (77)
T ss_dssp HTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS---------EEEEEEE-GGGEEE------
T ss_pred HhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccccccc---CCccCCCCCceEEEeccccCC
Confidence 3579999999999999999999999998 8999999999988876532 234577889999999999854
No 7
>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=96.65 E-value=0.0049 Score=50.51 Aligned_cols=61 Identities=28% Similarity=0.486 Sum_probs=47.2
Q ss_pred CCCccCceeEEeecCCee-EEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008994 10 PESYIGSFISLISKYEIR-YEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (547)
Q Consensus 10 ~~~~iGs~islISk~~IR-YeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~ 83 (547)
++.+||+-+||-...++- |.|.+..||.++.||.|.+- |+-- | ..++-| |+||.-|||+|.
T Consensus 1 a~dWiGs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~~~--~~ng--------i--k~~~~E-Vt~~~~DI~~L~ 62 (62)
T cd01737 1 AQDWLGSIVSINCGETLGVYQGLVSAVDQESQTISLAFP--FHNG--------V--KCLVPE-VTFRAGDIRELK 62 (62)
T ss_pred CCcccceEEEEecCCceEEEEEEEEEeCccceEEEEeec--ccCC--------c--cccCce-EEEEEcchhhcC
Confidence 367999999999988874 99999999999999999872 1111 1 222223 899999999984
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=96.34 E-value=0.01 Score=47.68 Aligned_cols=62 Identities=21% Similarity=0.330 Sum_probs=52.2
Q ss_pred CccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008994 12 SYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (547)
Q Consensus 12 ~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~ 83 (547)
.++|++|.+..+.+..|+|+|..+|. .--|.|+||.-+-.+++ ....++.++.||+.|.-++
T Consensus 5 ~~~g~~V~V~l~~g~~~~G~L~~~D~-~~Nl~L~~~~~~~~~~~---------~~~~~~~~~irG~~I~~I~ 66 (67)
T PF01423_consen 5 KLIGKRVRVELKNGRTYRGTLVSFDQ-FMNLVLSDVTETIKNGP---------EKRSLGLVFIRGSNIRYIS 66 (67)
T ss_dssp HTTTSEEEEEETTSEEEEEEEEEEET-TEEEEEEEEEEEETTES---------EEEEEEEEEEEGGGEEEEE
T ss_pred HhCCcEEEEEEeCCEEEEEEEEEeec-hheEEeeeEEEEECCCC---------cEeECcEEEEECCEEEEEE
Confidence 58999999999999999999999996 56699999988876654 3345678999999998765
No 9
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=96.02 E-value=0.011 Score=62.76 Aligned_cols=10 Identities=60% Similarity=1.255 Sum_probs=5.3
Q ss_pred CCCCCCCCCC
Q 008994 537 GGRGHGGNMH 546 (547)
Q Consensus 537 gGRG~g~~~~ 546 (547)
||||+|+||+
T Consensus 376 gG~GGGggyq 385 (465)
T KOG3973|consen 376 GGRGGGGGYQ 385 (465)
T ss_pred CCCCCCCCCc
Confidence 4555555653
No 10
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=95.90 E-value=0.0021 Score=71.88 Aligned_cols=8 Identities=50% Similarity=1.087 Sum_probs=0.0
Q ss_pred CCCCCCCC
Q 008994 538 GRGHGGNM 545 (547)
Q Consensus 538 GRG~g~~~ 545 (547)
|||+||||
T Consensus 548 grg~~r~~ 555 (556)
T PF05918_consen 548 GRGRGRGF 555 (556)
T ss_dssp --------
T ss_pred CCcccccC
Confidence 34444554
No 11
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=95.86 E-value=0.019 Score=67.26 Aligned_cols=18 Identities=33% Similarity=0.337 Sum_probs=11.2
Q ss_pred cccCccccccCCCCcccc
Q 008994 337 SLLTPGQLVTSRPPVLSS 354 (547)
Q Consensus 337 sL~tpgql~~~~~~~~sS 354 (547)
+||+|=|||-=++--|.|
T Consensus 1057 slVsPLQLLLF~SrKVqs 1074 (1282)
T KOG0921|consen 1057 SLVSPLQLLLFGSRKVQS 1074 (1282)
T ss_pred cccChHHHhhhhhhhccc
Confidence 577777777655544443
No 12
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=95.62 E-value=0.012 Score=63.92 Aligned_cols=35 Identities=11% Similarity=0.055 Sum_probs=20.2
Q ss_pred CCCccccccccCcccC-C--CCCcCCccchhhhhcccc
Q 008994 465 AYRKDDFFDTISCNSL-N--RGTREGQNRFSERMRLDT 499 (547)
Q Consensus 465 ~YdKdsFFD~IS~e~~-~--Rggr~GR~~~~EERk~nt 499 (547)
+|-.-+|||...-... . --.+++|....|||+.+-
T Consensus 331 ~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~~~~ 368 (419)
T KOG0116|consen 331 CFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKRPGF 368 (419)
T ss_pred ceEEEEEeecchhhhhhhcCccccCCeeEEEEeccccc
Confidence 4445567766433211 0 114677899999988554
No 13
>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=95.52 E-value=0.04 Score=46.11 Aligned_cols=65 Identities=18% Similarity=0.268 Sum_probs=52.0
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeecc
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVKS 86 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~v~~ 86 (547)
..||+++|.++-|.+..|+|+|..+| +---|.|.||..+-. + . ....++.++.||+.|.-+.-.+
T Consensus 6 ~~~i~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~E~~~-~-----~----~~~~lg~v~IRG~~I~~i~~~~ 70 (72)
T cd01719 6 KKYMDKKLSLKLNGNRKVSGILRGFD-PFMNLVLDDAVEVNS-G-----G----EKNNIGMVVIRGNSIVMLEALE 70 (72)
T ss_pred HHhCCCeEEEEECCCeEEEEEEEEEc-ccccEEeccEEEEcc-C-----C----ceeEeceEEECCCEEEEEEccc
Confidence 56899999999999999999999999 567799999965531 1 1 1235788999999998876544
No 14
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=95.44 E-value=0.034 Score=44.55 Aligned_cols=63 Identities=19% Similarity=0.293 Sum_probs=50.3
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~ 83 (547)
..++|++|.+..+.+..|+|+|..+|. .-.|.|+|+.-+-.+. .....++.++.||+.|.-+.
T Consensus 4 ~~~~~~~V~V~l~~g~~~~G~L~~~D~-~~NlvL~~~~e~~~~~---------~~~~~~~~~~IrG~~I~~i~ 66 (67)
T smart00651 4 KKLIGKRVLVELKNGREYRGTLKGFDQ-FMNLVLEDVEETVKDG---------EKKRKLGLVFIRGNNIVYII 66 (67)
T ss_pred HHhCCcEEEEEECCCcEEEEEEEEECc-cccEEEccEEEEecCC---------cEEeEeCCEEEcCCEEEEEe
Confidence 368999999999999999999999996 5789999987665542 12335667889999987654
No 15
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=95.34 E-value=0.042 Score=45.19 Aligned_cols=61 Identities=18% Similarity=0.321 Sum_probs=47.8
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccce
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDL 82 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL 82 (547)
..++|++|.+.-|.+..|+|+|..+| +.--|.|+||.-+-- +. ....++.++.||+.|.-+
T Consensus 7 ~~~~g~~V~V~Lk~g~~~~G~L~~~D-~~mNi~L~~~~e~~~------~~----~~~~lg~~~IRG~~I~~i 67 (68)
T cd01722 7 NDLTGKPVIVKLKWGMEYKGTLVSVD-SYMNLQLANTEEYID------GK----STGNLGEVLIRCNNVLYI 67 (68)
T ss_pred HHcCCCEEEEEECCCcEEEEEEEEEC-CCEEEEEeeEEEEeC------Cc----cccCcCcEEEECCEEEEE
Confidence 35799999999999999999999999 567899999854311 11 123478899999998754
No 16
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=95.33 E-value=0.015 Score=67.97 Aligned_cols=19 Identities=5% Similarity=0.008 Sum_probs=11.7
Q ss_pred CCCCcc-----ccccccCcccCCC
Q 008994 464 PAYRKD-----DFFDTISCNSLNR 482 (547)
Q Consensus 464 ~~YdKd-----sFFD~IS~e~~~R 482 (547)
..||.- |||.+-.+...+.
T Consensus 1169 aryDnG~~~n~SgyRRGgssysgG 1192 (1282)
T KOG0921|consen 1169 ARYDNGPSNNNSGYRRGGSSYSGG 1192 (1282)
T ss_pred ccccCCCccCccccccCCCCCCCC
Confidence 456653 7777766665543
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=94.98 E-value=0.083 Score=44.61 Aligned_cols=75 Identities=15% Similarity=0.235 Sum_probs=56.5
Q ss_pred CCCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeec
Q 008994 10 PESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVK 85 (547)
Q Consensus 10 ~~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~v~ 85 (547)
-..|||++|.+..+.+-.|+|+|..+|.. .-|.|.|+.-|-++.+...........-.+..++.||..|.-+.|+
T Consensus 5 l~~~l~~~V~V~l~dgR~~~G~L~~~D~~-~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v~ 79 (79)
T cd01717 5 MLQLINYRLRVTLQDGRQFVGQFLAFDKH-MNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTVE 79 (79)
T ss_pred hHHHcCCEEEEEECCCcEEEEEEEEEcCc-cCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEEC
Confidence 35799999999999999999999999965 6788999988776554321011111223478899999999988763
No 18
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=94.96 E-value=0.0067 Score=67.93 Aligned_cols=9 Identities=67% Similarity=1.154 Sum_probs=0.0
Q ss_pred CCCCCCCCCC
Q 008994 531 GRRYGYGGRG 540 (547)
Q Consensus 531 grGyG~gGRG 540 (547)
|||+|| |||
T Consensus 546 g~grg~-~r~ 554 (556)
T PF05918_consen 546 GRGRGR-GRG 554 (556)
T ss_dssp ----------
T ss_pred CCCCcc-ccc
Confidence 344444 454
No 19
>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=94.85 E-value=0.072 Score=43.62 Aligned_cols=61 Identities=11% Similarity=0.168 Sum_probs=48.2
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccce
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDL 82 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL 82 (547)
..++|++|.+..|.+-.|+|+|..+|.- --|.|+|+..+-.++ ...-++.++.||+.|.-+
T Consensus 6 ~~~~~~~V~V~l~~g~~~~G~L~~~D~~-mNlvL~~~~e~~~~~----------~~~~lg~~~iRG~~I~~i 66 (68)
T cd01731 6 KDSLNKPVLVKLKGGKEVRGRLKSYDQH-MNLVLEDAEEIDDGE----------PVRKYGRVVIRGDNVLFI 66 (68)
T ss_pred HHhcCCEEEEEECCCCEEEEEEEEECCc-ceEEEeeEEEEecCC----------eEeEcCcEEEeCCEEEEE
Confidence 3589999999999999999999999984 568899987654332 123467899999988644
No 20
>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=94.82 E-value=0.069 Score=43.75 Aligned_cols=60 Identities=20% Similarity=0.375 Sum_probs=47.5
Q ss_pred CccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccce
Q 008994 12 SYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDL 82 (547)
Q Consensus 12 ~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL 82 (547)
.++|++|.+.-|.+.-|+|+|..+| +.=-|.|+||..+-..++ ...++.|+-||+.|.-+
T Consensus 7 ~~~~~~V~V~Lk~g~~~~G~L~~~D-~~mNlvL~~~~~~~~~~~----------~~~~~~v~IRG~~I~~I 66 (67)
T cd01726 7 AIIGRPVVVKLNSGVDYRGILACLD-GYMNIALEQTEEYVNGQL----------KNKYGDAFIRGNNVLYI 66 (67)
T ss_pred hhCCCeEEEEECCCCEEEEEEEEEc-cceeeEEeeEEEEeCCce----------eeEeCCEEEECCEEEEE
Confidence 5799999999999999999999999 567789999865432111 22577899999998754
No 21
>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=94.78 E-value=0.078 Score=44.80 Aligned_cols=63 Identities=11% Similarity=0.120 Sum_probs=49.1
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccc
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKD 81 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKD 81 (547)
..||+++|.++.+.+..|.|+|..+| +.-.|.|.|+.-+-.++-.. .+.....|++||..|--
T Consensus 8 ~~~l~k~v~V~l~~gr~~~G~L~~fD-~~~NlvL~d~~E~~~~~~~~-------~~~~lG~~viRG~~V~~ 70 (74)
T cd01728 8 VDDLDKKVVVLLRDGRKLIGILRSFD-QFANLVLQDTVERIYVGDKY-------GDIPRGIFIIRGENVVL 70 (74)
T ss_pred HHhcCCEEEEEEcCCeEEEEEEEEEC-CcccEEecceEEEEecCCcc-------ceeEeeEEEEECCEEEE
Confidence 46899999999999999999999999 55789999986554443110 12357889999998743
No 22
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=94.76 E-value=0.067 Score=44.53 Aligned_cols=61 Identities=13% Similarity=0.195 Sum_probs=48.5
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccce
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDL 82 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL 82 (547)
..++|++|.+..|.+--|+|+|..+|. .--|.|+||..+-.+ . ...-++.++.||+.|.-+
T Consensus 10 ~~~~~k~V~V~lk~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~------~----~~~~lg~v~iRG~~V~~i 70 (72)
T PRK00737 10 NNALNSPVLVRLKGGREFRGELQGYDI-HMNLVLDNAEEIQDG------E----VVRKLGKVVIRGDNVVYV 70 (72)
T ss_pred HHhCCCEEEEEECCCCEEEEEEEEEcc-cceeEEeeEEEEcCC------C----eEeEcCcEEEeCCEEEEE
Confidence 357999999999999999999999998 567899998654321 1 113578899999998765
No 23
>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=94.69 E-value=0.078 Score=44.57 Aligned_cols=64 Identities=23% Similarity=0.198 Sum_probs=51.6
Q ss_pred CccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeec
Q 008994 12 SYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVK 85 (547)
Q Consensus 12 ~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~v~ 85 (547)
.++|++|.+.-|.+..|+|+|..+|.. -.|.|+||.....+|.+ + ..++.++-||+.|+-+++-
T Consensus 8 ~~~g~~V~VeLkng~~~~G~L~~~D~~-mNi~L~~~~~~~~~g~~-----~----~~~~~v~IRG~~I~~i~~p 71 (76)
T cd01723 8 TAQNHPMLVELKNGETYNGHLVNCDNW-MNIHLREVICTSKDGDK-----F----WKMPECYIRGNTIKYLRVP 71 (76)
T ss_pred hcCCCEEEEEECCCCEEEEEEEEEcCC-CceEEEeEEEECCCCcE-----e----eeCCcEEEeCCEEEEEEcC
Confidence 468999999999999999999999975 67899999876544432 1 1357799999999988763
No 24
>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=94.51 E-value=0.12 Score=44.09 Aligned_cols=65 Identities=17% Similarity=0.226 Sum_probs=51.9
Q ss_pred CccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeec
Q 008994 12 SYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVK 85 (547)
Q Consensus 12 ~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~v~ 85 (547)
..+|++|.+--|.+..|+|+|..+|.-= -|.|+||.....++.. .-..++.|..||+.|+-+++-
T Consensus 8 ~l~g~~V~VeLKng~~~~G~L~~vD~~M-Ni~L~n~~~~~~~~~~--------~~~~~~~v~IRG~~I~~I~lp 72 (81)
T cd01725 8 TLVGKEVTVELKNDLSIRGTLHSVDQYL-NIKLTNISVTDPEKYP--------HMLSVKNCFIRGSVVRYVQLP 72 (81)
T ss_pred hCCCCEEEEEECCCcEEEEEEEEECCCc-ccEEEEEEEEcCCCcc--------cccccCeEEEECCEEEEEEeC
Confidence 4589999999999999999999999764 7899999866543311 123458899999999998873
No 25
>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=94.23 E-value=0.14 Score=42.45 Aligned_cols=62 Identities=24% Similarity=0.308 Sum_probs=51.0
Q ss_pred CccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceee
Q 008994 12 SYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEV 84 (547)
Q Consensus 12 ~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~v 84 (547)
..+|+.|.+--|.+..|.|+|..+|. .-.|.|+||.....+|+. .-++.|+-||+.|+-+.+
T Consensus 7 ~~~g~~V~VeLk~g~~~~G~L~~~D~-~MNl~L~~~~~~~~~g~~----------~~~~~v~IRG~nI~~v~l 68 (70)
T cd01721 7 EAEGHIVTVELKTGEVYRGKLIEAED-NMNCQLKDVTVTARDGRV----------SQLEQVYIRGSKIRFFIL 68 (70)
T ss_pred hCCCCEEEEEECCCcEEEEEEEEEcC-CceeEEEEEEEECCCCcE----------eEcCcEEEeCCEEEEEEe
Confidence 56899999999999999999999998 568999999864433321 245789999999998876
No 26
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=93.98 E-value=0.18 Score=42.48 Aligned_cols=65 Identities=18% Similarity=0.279 Sum_probs=51.1
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceeccc-CCCCCCCCCCCCCccccceEEEecCCcccee
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGT-EGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGT-EgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~ 83 (547)
..+|+++|.+.-|.+..|.|+|..+|..- -|.|.||..... +|+.. .....+.++.||+.|+-|.
T Consensus 13 ~~~~~~~V~V~lk~g~~~~G~L~~~D~~m-NlvL~d~~e~~~~~~~~~-------~~~~~~~~~IRG~~I~~I~ 78 (79)
T COG1958 13 KKLLNKRVLVKLKNGREYRGTLVGFDQYM-NLVLDDVEEIISHDGEKN-------VRRLGGEVLIRGDNIVLIS 78 (79)
T ss_pred HHhhCCEEEEEECCCCEEEEEEEEEccce-eEEEeceEEEeccCCccc-------cceeccEEEEECCcEEEEe
Confidence 46889999999999999999999999874 578999998877 33321 2223448999999998764
No 27
>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=93.36 E-value=0.24 Score=41.95 Aligned_cols=70 Identities=19% Similarity=0.226 Sum_probs=52.8
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeec
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVK 85 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~v~ 85 (547)
..|||+++.++.+.+--|+|+|..+|.. .-|.|.|+. |-|.............+..|+-||..|.-+.|.
T Consensus 6 ~~~l~~~v~V~l~dgR~~~G~l~~~D~~-~NivL~~~~----E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v~ 75 (75)
T cd06168 6 RSLLGRTMRIHMTDGRTLVGVFLCTDRD-CNIILGSAQ----EYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEVE 75 (75)
T ss_pred HHhcCCeEEEEEcCCeEEEEEEEEEcCC-CcEEecCcE----EEEcccCccCCccEEEeeeEEEeCCeEEEEEEC
Confidence 4689999999999999999999999966 457899985 444321111122334788999999999988763
No 28
>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=93.19 E-value=0.2 Score=56.68 Aligned_cols=32 Identities=16% Similarity=0.180 Sum_probs=26.7
Q ss_pred CCCCCCCCCchhhHHHHHhhhchhhhhhhccc
Q 008994 398 SQYSTTKFTEEFDFEAMNEKFKKDEVWGYLGK 429 (547)
Q Consensus 398 ~~~~~~kf~~DFDFeaaNaKFnKeei~~~lgK 429 (547)
+.+++++|++.-|-+.|-+++|..+|.++.-+
T Consensus 269 rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~ 300 (578)
T TIGR01648 269 RDYAFVHFEDREDAVKAMDELNGKELEGSEIE 300 (578)
T ss_pred cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEE
Confidence 46999999999999999999988888765433
No 29
>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=93.02 E-value=0.27 Score=42.94 Aligned_cols=64 Identities=16% Similarity=0.153 Sum_probs=52.4
Q ss_pred CccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeecc
Q 008994 12 SYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVKS 86 (547)
Q Consensus 12 ~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~v~~ 86 (547)
.++|+.|.+--|.+..|+|+|..+|.- =-|.|+||..+-.++. ..-|+.++.||+.|+-+++-+
T Consensus 8 ~l~g~~V~VeLKng~~~~G~L~~vD~~-MNl~L~~a~~~~~~~~----------~~~~~~v~IRG~nI~yi~lPd 71 (90)
T cd01724 8 KLTNETVTIELKNGTIVHGTITGVDPS-MNTHLKNVKLTLKGRN----------PVPLDTLSIRGNNIRYFILPD 71 (90)
T ss_pred hCCCCEEEEEECCCCEEEEEEEEEcCc-eeEEEEEEEEEcCCCc----------eeEcceEEEeCCEEEEEEcCC
Confidence 568999999999999999999999976 4789999976643322 135788999999999998843
No 30
>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=92.01 E-value=0.47 Score=40.41 Aligned_cols=63 Identities=17% Similarity=0.306 Sum_probs=50.2
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceee
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEV 84 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~v 84 (547)
...+|+.|.+--|.+..|+|+|..+|.- =.|.|+||.-....+. ..-++.|+.||+.|+-+++
T Consensus 15 ~~l~g~~V~VeLKng~~~~G~L~~vD~~-MNl~L~~~~~~~~~~~----------~~~~~~v~IRG~nI~yI~l 77 (78)
T cd01733 15 QGLQGKVVTVELRNETTVTGRIASVDAF-MNIRLAKVTIIDRNGK----------QVQVEEIMVTGRNIRYVHI 77 (78)
T ss_pred HHCCCCEEEEEECCCCEEEEEEEEEcCC-ceeEEEEEEEEcCCCc----------eeECCcEEEECCEEEEEEc
Confidence 3568999999999999999999999976 4789999975432221 1257899999999998765
No 31
>KOG1596 consensus Fibrillarin and related nucleolar RNA-binding proteins [RNA processing and modification]
Probab=90.87 E-value=0.38 Score=49.84 Aligned_cols=10 Identities=50% Similarity=0.757 Sum_probs=4.6
Q ss_pred CCCCCCCCCC
Q 008994 532 RRYGYGGRGH 541 (547)
Q Consensus 532 rGyG~gGRG~ 541 (547)
||..+||||+
T Consensus 63 ~g~~~gg~~~ 72 (317)
T KOG1596|consen 63 RGESRGGRGG 72 (317)
T ss_pred cccCCCCccc
Confidence 3444455543
No 32
>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=90.39 E-value=1 Score=38.59 Aligned_cols=70 Identities=11% Similarity=0.158 Sum_probs=51.1
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~ 83 (547)
..||+++|.++-+.+-.|+|+|..+|.- --|.|.++..+-.+.- +..++.-....+..++.||..|--|.
T Consensus 8 ~~~i~k~V~V~l~~gr~~~G~L~~~D~~-mNlvL~~~~E~~~~~~--~~~~~~~~~~~lG~v~iRG~nV~~i~ 77 (81)
T cd01729 8 SKYVDKKIRVKFQGGREVTGILKGYDQL-LNLVLDDTVEYLRDPD--DPYKLTDKTRQLGLVVCRGTSVVLIS 77 (81)
T ss_pred HHhcCCeEEEEECCCcEEEEEEEEEcCc-ccEEecCEEEEEccCC--cccccccceeEccEEEEcCCEEEEEe
Confidence 4689999999999999999999999976 4688999865533211 11112223345789999999987654
No 33
>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=90.31 E-value=0.65 Score=38.83 Aligned_cols=65 Identities=20% Similarity=0.329 Sum_probs=49.1
Q ss_pred CCCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceec--ccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008994 10 PESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSF--GTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (547)
Q Consensus 10 ~~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsf--GTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~ 83 (547)
-..||+++|.++.+.+-.|+|+|..+|.. --|.|.++..+ .++ .. + ....+..|+.||+.|--+.
T Consensus 4 L~~~l~~~V~V~l~dgr~~~G~L~~~D~~-~NlvL~~~~E~~~~~~----~~--~--~~~~lG~~~iRG~~I~~i~ 70 (74)
T cd01727 4 LEDYLNKTVSVITVDGRVIVGTLKGFDQA-TNLILDDSHERVYSSD----EG--V--EQVVLGLYIIRGDNIAVVG 70 (74)
T ss_pred HHHhcCCEEEEEECCCcEEEEEEEEEccc-cCEEccceEEEEecCC----CC--c--eeeEeceEEECCCEEEEEE
Confidence 35789999999999999999999999988 66888887443 221 11 1 1335789999999986544
No 34
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.06 E-value=1.9 Score=46.46 Aligned_cols=40 Identities=20% Similarity=0.260 Sum_probs=27.1
Q ss_pred CCCCCcc-ccccccCcccCCCCCcCCccchhhhhcccccccCCCc
Q 008994 463 KPAYRKD-DFFDTISCNSLNRGTREGQNRFSERMRLDTETFGNFQ 506 (547)
Q Consensus 463 k~~YdKd-sFFD~IS~e~~~Rggr~GR~~~~EERk~ntETFG~~s 506 (547)
+..|+++ .+|+++.-... -+.+.+|.+++-++..++....
T Consensus 252 ~~~~n~~s~r~~~~~~~~~----~n~~~~~~~~~~~~~~~q~~~~ 292 (361)
T KOG1073|consen 252 PSFYNQQSSRFTTISVSRV----SNTNSRNQEKRGLNNGGQSQQS 292 (361)
T ss_pred Ccccccccccccccccccc----ccccccccccccccCCCccccc
Confidence 4567754 77776554432 3457889999888887777654
No 35
>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=85.85 E-value=3 Score=35.43 Aligned_cols=64 Identities=23% Similarity=0.328 Sum_probs=47.7
Q ss_pred CccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008994 12 SYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (547)
Q Consensus 12 ~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~ 83 (547)
.+++++|.+..|.+..|+|+|..+|.- -.|.|.|+..+= + ..++. ....++-|+.||..|.-+.
T Consensus 10 ~~~~~~V~V~l~~gr~~~G~L~g~D~~-mNlvL~da~E~~-~--~~~~~----~~~~lg~v~iRG~nV~~i~ 73 (76)
T cd01732 10 KCIGSRIWIVMKSDKEFVGTLLGFDDY-VNMVLEDVTEYE-I--TPEGR----KITKLDQILLNGNNICMLV 73 (76)
T ss_pred HhCCCEEEEEECCCeEEEEEEEEeccc-eEEEEccEEEEE-E--cCCCc----eeeEcCeEEEeCCeEEEEE
Confidence 468999999999999999999999975 578899985542 1 11111 1224788999999987653
No 36
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=85.25 E-value=1.1 Score=51.20 Aligned_cols=10 Identities=10% Similarity=-0.243 Sum_probs=5.3
Q ss_pred cccCCCCCCC
Q 008994 275 AYMTDNNPNT 284 (547)
Q Consensus 275 ~~~~~n~p~~ 284 (547)
+..|.++|..
T Consensus 305 ~arGIDip~V 314 (629)
T PRK11634 305 AARGLDVERI 314 (629)
T ss_pred HhcCCCcccC
Confidence 5555555543
No 37
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=85.25 E-value=0.96 Score=42.13 Aligned_cols=14 Identities=29% Similarity=0.610 Sum_probs=7.7
Q ss_pred CCCcc--ccccccCcc
Q 008994 465 AYRKD--DFFDTISCN 478 (547)
Q Consensus 465 ~YdKd--sFFD~IS~e 478 (547)
.|-|| +||..=.|=
T Consensus 45 ~ts~Dgdkf~r~pEcY 60 (134)
T KOG3293|consen 45 CTSEDGDKFFRMPECY 60 (134)
T ss_pred EeccCCCceeecceeE
Confidence 34443 677764554
No 38
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=82.44 E-value=1.5 Score=40.88 Aligned_cols=16 Identities=13% Similarity=0.198 Sum_probs=7.2
Q ss_pred CCCccc--cccccCcccC
Q 008994 465 AYRKDD--FFDTISCNSL 480 (547)
Q Consensus 465 ~YdKds--FFD~IS~e~~ 480 (547)
+|-+-+ -|=.|..+-+
T Consensus 59 cYirGttIkylri~d~ii 76 (134)
T KOG3293|consen 59 CYIRGTTIKYLRIPDEII 76 (134)
T ss_pred eEEecceeEEEeccHHHH
Confidence 565532 2334444444
No 39
>COG4371 Predicted membrane protein [Function unknown]
Probab=82.14 E-value=2 Score=44.65 Aligned_cols=15 Identities=27% Similarity=0.620 Sum_probs=7.4
Q ss_pred CCCCCCCCCCCCCCC
Q 008994 522 ANYRGRYGGGRRYGY 536 (547)
Q Consensus 522 grgRGgy~GgrGyG~ 536 (547)
|.++|+.|+|+|||.
T Consensus 76 GgY~gg~Y~GGGfgf 90 (334)
T COG4371 76 GGYSGGGYSGGGFGF 90 (334)
T ss_pred CCCCCCCCCCCCcCc
Confidence 334444444456665
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=80.48 E-value=1.4 Score=46.82 Aligned_cols=37 Identities=14% Similarity=0.014 Sum_probs=30.2
Q ss_pred CCCCCCCCCCCCCCCchhhHHHHHhhhchhhhhhhcc
Q 008994 392 PTPNLQSQYSTTKFTEEFDFEAMNEKFKKDEVWGYLG 428 (547)
Q Consensus 392 P~~~~~~~~~~~kf~~DFDFeaaNaKFnKeei~~~lg 428 (547)
+...+.+++++++|+++-|-+.|-+++|..+|.++--
T Consensus 143 ~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i 179 (346)
T TIGR01659 143 YKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRL 179 (346)
T ss_pred CCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCcee
Confidence 4445677899999999999999999999888876543
No 41
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=79.87 E-value=1.6 Score=39.92 Aligned_cols=24 Identities=21% Similarity=0.339 Sum_probs=13.1
Q ss_pred ccccccCcccCCCC--CcCCccchhh
Q 008994 470 DFFDTISCNSLNRG--TREGQNRFSE 493 (547)
Q Consensus 470 sFFD~IS~e~~~Rg--gr~GR~~~~E 493 (547)
..=||.+|...|-- .++||...-|
T Consensus 34 EaeDnmNcql~di~vT~~dg~vs~le 59 (119)
T KOG3172|consen 34 EAEDNMNCQLRDITVTARDGRVSQLE 59 (119)
T ss_pred EeccccccEEEEEEEEccCCcceeee
Confidence 56677777755421 3555544444
No 42
>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=79.30 E-value=6.8 Score=34.28 Aligned_cols=68 Identities=15% Similarity=0.202 Sum_probs=49.9
Q ss_pred cCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCC---CCCCCCccccceEEEecCCccce
Q 008994 14 IGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDG---PQVLPSEKVYEYILFRGSDIKDL 82 (547)
Q Consensus 14 iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~---~~Ipp~~~vy~yIvFrgsDIKDL 82 (547)
.|++|-+.-|.+-.|.|+|..+|.. -.|.|.||..+-++.-+... .+.......+..|+.||..|.-|
T Consensus 13 ~~~~V~V~lr~~r~~~G~L~~fD~h-mNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~I 83 (87)
T cd01720 13 NNTQVLINCRNNKKLLGRVKAFDRH-CNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVILV 83 (87)
T ss_pred CCCEEEEEEcCCCEEEEEEEEecCc-cEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEEE
Confidence 3899999999999999999999975 67999999888665322111 11111233468999999998754
No 43
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=77.06 E-value=2.8 Score=47.91 Aligned_cols=8 Identities=0% Similarity=0.293 Sum_probs=3.5
Q ss_pred CCcccccc
Q 008994 466 YRKDDFFD 473 (547)
Q Consensus 466 YdKdsFFD 473 (547)
|++-+|||
T Consensus 525 ~~~~s~v~ 532 (629)
T PRK11634 525 FASHSTIE 532 (629)
T ss_pred eCCceEEE
Confidence 44444444
No 44
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=73.97 E-value=9.7 Score=42.47 Aligned_cols=25 Identities=8% Similarity=0.065 Sum_probs=11.2
Q ss_pred CCCCCCC-CCccccCCCCCCcccccc
Q 008994 189 SPTPFQS-SSTVSSPLTGPNRIWTSE 213 (547)
Q Consensus 189 p~~~qq~-p~~ls~P~~~qq~~Q~p~ 213 (547)
||+++.+ |+..--|..-+++||.+-
T Consensus 456 P~~~~pppP~~pp~p~~~~~q~q~~~ 481 (483)
T KOG2236|consen 456 PHQQSPPPPPPPPPPNSPMNQMQNPS 481 (483)
T ss_pred ccccCCCCCCCCCCCCChhhcccCCC
Confidence 4444444 333333444445555543
No 45
>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=71.00 E-value=15 Score=31.39 Aligned_cols=70 Identities=11% Similarity=0.077 Sum_probs=48.2
Q ss_pred CccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCC---CCCCCCCccccceEEEecCCccce
Q 008994 12 SYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKD---GPQVLPSEKVYEYILFRGSDIKDL 82 (547)
Q Consensus 12 ~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~---~~~Ipp~~~vy~yIvFrgsDIKDL 82 (547)
.+++++|.++.|.+-.|+|+|...|.. -.|.|.|+.-+-.+--... ...+......+..++.||..|.-|
T Consensus 8 ~~~~k~V~V~l~~gr~~~G~L~~fD~~-mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i 80 (82)
T cd01730 8 LSLDERVYVKLRGDRELRGRLHAYDQH-LNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV 80 (82)
T ss_pred HhCCCEEEEEECCCCEEEEEEEEEccc-eEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence 358999999999999999999999976 4788999866533211110 010111223578899999988654
No 46
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=67.86 E-value=13 Score=33.07 Aligned_cols=64 Identities=16% Similarity=0.223 Sum_probs=50.3
Q ss_pred CccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceee
Q 008994 12 SYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEV 84 (547)
Q Consensus 12 ~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~v 84 (547)
..||+.+++-=|.|+-..|+|++||.= =.|.|.|||+--.| .-|..-.|-+ +-.|||-|+-+++
T Consensus 9 slvg~~V~VeLKnd~~i~GtL~svDqy-LNlkL~di~v~d~~-------kyPhm~Sv~n-cfIRGSvvrYv~l 72 (96)
T KOG3448|consen 9 SLVGKEVVVELKNDLSICGTLHSVDQY-LNLKLTDISVTDPD-------KYPHMLSVKN-CFIRGSVVRYVQL 72 (96)
T ss_pred HhcCCeEEEEEcCCcEEEEEecccchh-heeEEeeeEeeCcc-------cCCCeeeeee-EEEeccEEEEEEe
Confidence 579999999999999999999999975 35889999885443 2344444444 5679999999887
No 47
>KOG2945 consensus Predicted RNA-binding protein [General function prediction only]
Probab=66.91 E-value=4.5 Score=43.81 Aligned_cols=7 Identities=43% Similarity=0.729 Sum_probs=4.0
Q ss_pred chhhHHH
Q 008994 407 EEFDFEA 413 (547)
Q Consensus 407 ~DFDFea 413 (547)
.+||+.+
T Consensus 181 rEf~r~s 187 (365)
T KOG2945|consen 181 REFDRQS 187 (365)
T ss_pred eeeeeec
Confidence 4566654
No 48
>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=66.87 E-value=8.9 Score=37.46 Aligned_cols=60 Identities=27% Similarity=0.506 Sum_probs=40.7
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeeccC
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVKSS 87 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~v~~~ 87 (547)
..|||+.+.+.... --|.|.||+||+.-.+|.|-| |...|+. .| .+-=|--||+++|.+.
T Consensus 13 ~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~---~~e~~~~----------sv---~~I~ghaVk~vevl~~ 72 (166)
T PF06372_consen 13 QDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVN---FQEDGKR----------SV---KVIMGHAVKSVEVLSE 72 (166)
T ss_dssp HCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEE---E-TTS-E----------EE---EEE-GGGEEEEEEEE-
T ss_pred HHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEE---cccCCce----------eE---EEEEccceEEEEEccC
Confidence 57999999999998 889999999999999999985 4433331 11 3334778888888763
No 49
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=66.52 E-value=8.6 Score=38.48 Aligned_cols=7 Identities=43% Similarity=1.013 Sum_probs=3.1
Q ss_pred hhhhhhc
Q 008994 421 DEVWGYL 427 (547)
Q Consensus 421 eei~~~l 427 (547)
|||.+.+
T Consensus 95 DEIfG~i 101 (215)
T KOG3262|consen 95 DEIFGPI 101 (215)
T ss_pred hhhcccc
Confidence 4444444
No 50
>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=66.20 E-value=6.5 Score=44.92 Aligned_cols=23 Identities=4% Similarity=0.112 Sum_probs=16.6
Q ss_pred CCCCCCCCCCchhhHHHHHhhhc
Q 008994 397 QSQYSTTKFTEEFDFEAMNEKFK 419 (547)
Q Consensus 397 ~~~~~~~kf~~DFDFeaaNaKFn 419 (547)
.+.+++++|++.-|-+.|-.+++
T Consensus 181 nRGFAFVeF~s~edAa~AirkL~ 203 (578)
T TIGR01648 181 NRGFAFVEYESHRAAAMARRKLM 203 (578)
T ss_pred cCceEEEEcCCHHHHHHHHHHhh
Confidence 34788888888877777666654
No 51
>PF12764 Gly-rich_Ago1: Glycine-rich region of argonaut; InterPro: IPR024357 This domain is found in the N terminus of some argonaut proteins. Argonaut (AGO) proteins are involved in RNA-mediated post-transcriptional gene silencing [].
Probab=66.00 E-value=6.3 Score=35.79 Aligned_cols=8 Identities=63% Similarity=1.070 Sum_probs=3.7
Q ss_pred CCCCCCCC
Q 008994 524 YRGRYGGG 531 (547)
Q Consensus 524 gRGgy~Gg 531 (547)
||++|+|+
T Consensus 19 G~~~yGgg 26 (104)
T PF12764_consen 19 GRPGYGGG 26 (104)
T ss_pred CCCCCCCC
Confidence 44555443
No 52
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=56.40 E-value=11 Score=34.72 Aligned_cols=20 Identities=25% Similarity=0.193 Sum_probs=7.8
Q ss_pred ccCCCccCCCCCCCCCCCCC
Q 008994 501 TFGNFQQRANQGYGGYVAGR 520 (547)
Q Consensus 501 TFG~~sgR~rgGrgGrGrGR 520 (547)
-|+...+|.-++..+||+.|
T Consensus 82 mFkk~~~~~~g~~~~RG~~~ 101 (119)
T KOG3172|consen 82 MFKKGKSRSLGGGPGRGRAR 101 (119)
T ss_pred ccccccCCcCCCCCCccccc
Confidence 45543334433333333333
No 53
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=53.79 E-value=13 Score=42.51 Aligned_cols=26 Identities=23% Similarity=0.359 Sum_probs=19.7
Q ss_pred CCCCCCCchhhHHHHHhhhchhhhhhhc
Q 008994 400 YSTTKFTEEFDFEAMNEKFKKDEVWGYL 427 (547)
Q Consensus 400 ~~~~kf~~DFDFeaaNaKFnKeei~~~l 427 (547)
+..-.|+-|-||+..-+|| ++|..++
T Consensus 382 ~~L~vFk~dp~f~ene~ky--daikkei 407 (739)
T KOG2140|consen 382 KELGVFKKDPNFEENEEKY--DAIKKEI 407 (739)
T ss_pred hhhcccccCccHHHHHHHH--HHHHHHH
Confidence 4566789999999999999 5665443
No 54
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=51.52 E-value=14 Score=34.56 Aligned_cols=30 Identities=13% Similarity=0.122 Sum_probs=21.2
Q ss_pred CCCCCCCCCCCCchhhHHHHHhhhchhhhh
Q 008994 395 NLQSQYSTTKFTEEFDFEAMNEKFKKDEVW 424 (547)
Q Consensus 395 ~~~~~~~~~kf~~DFDFeaaNaKFnKeei~ 424 (547)
-+.+.+++++|++.-|-+.|=+++|..+|.
T Consensus 73 g~~kGfaFV~F~~~e~A~~Al~~lng~~i~ 102 (144)
T PLN03134 73 GRSRGFGFVNFNDEGAATAAISEMDGKELN 102 (144)
T ss_pred CCcceEEEEEECCHHHHHHHHHHcCCCEEC
Confidence 455678888888887777777777655543
No 55
>COG4907 Predicted membrane protein [Function unknown]
Probab=47.83 E-value=14 Score=41.46 Aligned_cols=22 Identities=32% Similarity=0.413 Sum_probs=10.8
Q ss_pred CccccceEEEec-CCccceeecc
Q 008994 65 SEKVYEYILFRG-SDIKDLEVKS 86 (547)
Q Consensus 65 ~~~vy~yIvFrg-sDIKDL~v~~ 86 (547)
-+++|.|++|.| .-|.-++..+
T Consensus 53 ieeiysy~~~eG~~y~~~~rd~e 75 (595)
T COG4907 53 IEEIYSYIDAEGYGYITSLRDFE 75 (595)
T ss_pred eeeeeeeeeccccceEEEEeecc
Confidence 345556666665 3344444433
No 56
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=41.34 E-value=64 Score=28.58 Aligned_cols=54 Identities=19% Similarity=0.244 Sum_probs=37.6
Q ss_pred EeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008994 20 LISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (547)
Q Consensus 20 lISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~ 83 (547)
|..+.+..|+|+|..+|.-= -|.|.|+.-+= .+.. ....++.|+.||..|.-+.
T Consensus 33 l~~~~~r~~~G~L~gfD~~m-NlVL~d~~E~~-----~~~~----~~~~lG~ilIRGnnV~~I~ 86 (89)
T PTZ00138 33 LYDHPNLRIEGKILGFDEYM-NMVLDDAEEVY-----TKKN----TRKDLGRILLKGDNITLIM 86 (89)
T ss_pred EEeCCCcEEEEEEEEEcccc-eEEEccEEEEe-----cCCc----eeeEcCeEEEcCCEEEEEE
Confidence 33556799999999999764 68899975331 1111 2335788999999997654
No 57
>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=38.42 E-value=62 Score=26.87 Aligned_cols=58 Identities=21% Similarity=0.287 Sum_probs=42.7
Q ss_pred ccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008994 13 YIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (547)
Q Consensus 13 ~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~ 83 (547)
.||+++++.+-.+=.+||.|...|..-..|.|+- -+.++++ ..-|+.+.+-+=|+|++
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~---~s~~~~~----------~~~dv~ivnls~~~dv~ 61 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKC---PSSSGKP----------NHADILLVNLSYVSEVE 61 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEEC---ccccCCC----------CcceEEEEEhhhEEecC
Confidence 5999999999999999999999999977777762 2222332 13456677777777763
No 58
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=38.26 E-value=27 Score=30.43 Aligned_cols=62 Identities=29% Similarity=0.431 Sum_probs=47.1
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecc--cCCCCCCCCCCCCCccccceEEEecCCccce
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFG--TEGRKKDGPQVLPSEKVYEYILFRGSDIKDL 82 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfG--TEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL 82 (547)
+.-||+||-+|=|+|-.++|+|...|-=- .+.|++|.-|- +|||+ -+-.+.|+..|..|-=|
T Consensus 13 DkcIgski~iimksdkE~~GtL~GFDd~V-NmvLeDvtEye~~~egr~---------~tk~~~iLLnGNni~mL 76 (84)
T KOG1775|consen 13 DKCIGSKIWIIMKSDKEFVGTLVGFDDFV-NMVLEDVTEYEITPEGRR---------MTKLDQILLNGNNITML 76 (84)
T ss_pred HHhcCceEEEEEccCceeeeEEechHHHH-HHHHHhhhheeeCCCcce---------eeeeeeeeecCCcEEEE
Confidence 34699999999999999999999876432 35688887774 35553 23567899999988654
No 59
>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=38.10 E-value=53 Score=25.22 Aligned_cols=27 Identities=11% Similarity=0.158 Sum_probs=22.2
Q ss_pred ccCceeEEeecCCeeEEEEeeeecCCCC
Q 008994 13 YIGSFISLISKYEIRYEGVLYHLNVGDS 40 (547)
Q Consensus 13 ~iGs~islISk~~IRYeGiL~~Id~~~s 40 (547)
.||+.|+|.. .+-.|+|+...||.+-.
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 55558999999987644
No 60
>PRK02001 hypothetical protein; Validated
Probab=37.09 E-value=1.1e+02 Score=29.55 Aligned_cols=65 Identities=28% Similarity=0.280 Sum_probs=43.5
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEecccee-cccCCCCCCCCCCCCCccccceEEEecCCccceeec
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKS-FGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVK 85 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrs-fGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~v~ 85 (547)
..|||.+|.+..+..-+|+|+|..+|-+ .|+|. |.- =+-++++. .....+-+.|.-++|+..+++
T Consensus 86 ~r~~G~~v~V~l~~~~~~~G~L~~~~~~--~i~l~-~~~~~~~~~~k~-------~~~~~~~~~i~~~~I~ka~l~ 151 (152)
T PRK02001 86 KKNIGRELEVLTKNGKKIEGELKSADEN--DITLE-VKAREPKEGGKG-------KVTVEKEETITYDDIKEAKVI 151 (152)
T ss_pred HHhCCCEEEEEECCCCEEEEEEEEEeCC--EEEEE-Eccccccccccc-------ccccceeEEEEhHheeeEEEe
Confidence 3589999999998899999999999855 67774 220 01122221 112355677888888887664
No 61
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=36.70 E-value=49 Score=27.89 Aligned_cols=33 Identities=21% Similarity=0.309 Sum_probs=27.6
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEecc
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKN 46 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~n 46 (547)
..+||+++.+-+-.++ ++|+|..+.++ .|.|+.
T Consensus 17 q~liG~~vvV~T~~g~-v~G~L~~V~pD--hIvl~~ 49 (66)
T PF10842_consen 17 QSLIGQRVVVQTTRGS-VRGILVDVKPD--HIVLEE 49 (66)
T ss_pred HHhcCCEEEEEEcCCc-EEEEEEeecCC--EEEEEe
Confidence 3579999999998887 79999999999 666653
No 62
>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=35.43 E-value=34 Score=28.58 Aligned_cols=24 Identities=29% Similarity=0.401 Sum_probs=21.4
Q ss_pred EEEEeeeecCCCCeEEeccceecc
Q 008994 28 YEGVLYHLNVGDSTIGLKNVKSFG 51 (547)
Q Consensus 28 YeGiL~~Id~~~sTi~L~nVrsfG 51 (547)
-||+|..||.+.-||+|.+=++|=
T Consensus 5 veG~I~~id~~~~titLdDGksy~ 28 (61)
T PF07076_consen 5 VEGTIKSIDPETMTITLDDGKSYK 28 (61)
T ss_pred ceEEEEEEcCCceEEEecCCCEEE
Confidence 489999999999999999977764
No 63
>COG4907 Predicted membrane protein [Function unknown]
Probab=35.28 E-value=30 Score=39.03 Aligned_cols=13 Identities=8% Similarity=0.153 Sum_probs=6.8
Q ss_pred eEEEEeeeecCCC
Q 008994 27 RYEGVLYHLNVGD 39 (547)
Q Consensus 27 RYeGiL~~Id~~~ 39 (547)
..|+|...||.|.
T Consensus 52 ~ieeiysy~~~eG 64 (595)
T COG4907 52 EIEEIYSYIDAEG 64 (595)
T ss_pred eeeeeeeeeeccc
Confidence 3455555555553
No 64
>PRK14644 hypothetical protein; Provisional
Probab=35.02 E-value=60 Score=30.56 Aligned_cols=33 Identities=36% Similarity=0.314 Sum_probs=27.8
Q ss_pred CCccCceeEEeecCC----eeEEEEeeeecCCCCeEEec
Q 008994 11 ESYIGSFISLISKYE----IRYEGVLYHLNVGDSTIGLK 45 (547)
Q Consensus 11 ~~~iGs~islISk~~----IRYeGiL~~Id~~~sTi~L~ 45 (547)
..|||.+|.+..+.. -+|+|+|..+|-+ +|+|.
T Consensus 81 ~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~--~i~l~ 117 (136)
T PRK14644 81 ENHIGEIIDVSLNKEVNKTDFITGELLENNPE--TITLK 117 (136)
T ss_pred HHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC--EEEEE
Confidence 468999999998776 7899999999854 78886
No 65
>PRK14642 hypothetical protein; Provisional
Probab=34.81 E-value=1.1e+02 Score=30.93 Aligned_cols=71 Identities=15% Similarity=0.260 Sum_probs=43.2
Q ss_pred CCccCceeEEeec-------------CCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecC
Q 008994 11 ESYIGSFISLISK-------------YEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGS 77 (547)
Q Consensus 11 ~~~iGs~islISk-------------~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgs 77 (547)
..|||.+|.|..+ ..-+|+|+|..+|-+.-+|.+.. |-=+-+|-...-..+| .+-.-..|--+
T Consensus 96 ~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~~i~l~~~~-~~~~k~g~~~~k~~~~---~~~~~~~~~~~ 171 (197)
T PRK14642 96 ERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESGGWQIVWSD-EPPVKPGQRVSKKRVP---APLQALGFTLD 171 (197)
T ss_pred HHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCCEEEEEEee-cccCCCcccccccccc---ccceeEEeehh
Confidence 4589999999887 56789999999987644443332 1111122110011233 23444668889
Q ss_pred Cccceeec
Q 008994 78 DIKDLEVK 85 (547)
Q Consensus 78 DIKDL~v~ 85 (547)
|||+-+|.
T Consensus 172 eik~a~l~ 179 (197)
T PRK14642 172 ELREARLA 179 (197)
T ss_pred heeeEEEE
Confidence 99998874
No 66
>PRK14631 hypothetical protein; Provisional
Probab=33.77 E-value=63 Score=31.68 Aligned_cols=35 Identities=17% Similarity=0.393 Sum_probs=29.7
Q ss_pred CCccCceeEEeec----CCeeEEEEeeeecCCCCeEEec
Q 008994 11 ESYIGSFISLISK----YEIRYEGVLYHLNVGDSTIGLK 45 (547)
Q Consensus 11 ~~~iGs~islISk----~~IRYeGiL~~Id~~~sTi~L~ 45 (547)
..|+|.+|.|..+ ..-+|.|+|..+|.++.+|+|.
T Consensus 113 ~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~~v~l~ 151 (174)
T PRK14631 113 QGYIGQQVALRLIAAVENRRKFQAKLLAVDLENEEIQVE 151 (174)
T ss_pred HHhCCCeEEEEEecccCCceEEEEEEEEeecCCCEEEEE
Confidence 4689999999985 4488999999999778899885
No 67
>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=33.08 E-value=75 Score=29.41 Aligned_cols=31 Identities=26% Similarity=0.406 Sum_probs=23.2
Q ss_pred CccCceeEEeec----CCeeEEEEeeeecCCCCeEEe
Q 008994 12 SYIGSFISLISK----YEIRYEGVLYHLNVGDSTIGL 44 (547)
Q Consensus 12 ~~iGs~islISk----~~IRYeGiL~~Id~~~sTi~L 44 (547)
.|||.+|.+..+ ..-+|+|+|..++-+ +|+|
T Consensus 84 ~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~--~i~l 118 (141)
T PF02576_consen 84 RFIGRKVKVKLKQPVNGRKEFEGKLLEVDED--EITL 118 (141)
T ss_dssp HH-SEEEEEE-SS-SSS-SEEEEEEEEEETT--EEEE
T ss_pred HhcCCeEEEEEeccCCCcEEEEEEEEEEeCC--EEEE
Confidence 589999999984 456799999999986 6666
No 68
>PRK14638 hypothetical protein; Provisional
Probab=32.23 E-value=62 Score=30.84 Aligned_cols=33 Identities=18% Similarity=0.343 Sum_probs=28.3
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEec
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLK 45 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~ 45 (547)
..|+|++|.+..+..-+|+|+|..+|-+ +|+|.
T Consensus 96 ~r~~G~~v~V~~~~~k~~~G~L~~~~~~--~i~l~ 128 (150)
T PRK14638 96 VRFTGKLAKIVTKDGKTFIGRIESFVDG--TITIS 128 (150)
T ss_pred HHhCCCEEEEEECCCcEEEEEEEEEeCC--EEEEE
Confidence 3589999999999999999999999854 67775
No 69
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=30.05 E-value=29 Score=30.04 Aligned_cols=62 Identities=23% Similarity=0.363 Sum_probs=41.6
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~ 83 (547)
..+||+++-+-=.+++-|.|+|..||-== .|+|+.- |---+ + +. ...|.-...||+.|--|.
T Consensus 12 ~~iiGr~V~VKl~sgvdyrG~l~~lDgym-NiaLe~t-----ee~~n-g-ql---~n~ygdaFirGnnVlyIs 73 (77)
T KOG1783|consen 12 KAIIGRTVVVKLNSGVDYRGTLVCLDGYM-NIALEST-----EEYVN-G-QL---KNKYGDAFIRGNNVLYIS 73 (77)
T ss_pred HHHhCCeEEEEecCCccccceehhhhhHH-HHHHHHH-----HHHhc-C-cc---cccccceeeccccEEEEE
Confidence 46899999999999999999999998641 2445442 21111 1 11 235677778888875543
No 70
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=29.19 E-value=66 Score=33.75 Aligned_cols=16 Identities=38% Similarity=0.738 Sum_probs=10.1
Q ss_pred HHhhhchhhhhhhccccccC
Q 008994 414 MNEKFKKDEVWGYLGKAKQS 433 (547)
Q Consensus 414 aNaKFnKeei~~~lgK~~~s 433 (547)
+|.-|+| |+ +|+|+++
T Consensus 83 a~rlfd~---W~-lG~k~~~ 98 (271)
T COG1512 83 ATRLFDK---WK-LGDKAQD 98 (271)
T ss_pred HHHHHHh---cC-CCccccC
Confidence 5666744 76 7776653
No 71
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=27.97 E-value=61 Score=33.99 Aligned_cols=9 Identities=11% Similarity=-0.023 Sum_probs=4.4
Q ss_pred hHHHHHhhh
Q 008994 410 DFEAMNEKF 418 (547)
Q Consensus 410 DFeaaNaKF 418 (547)
||..+=+++
T Consensus 145 ny~~gi~~~ 153 (271)
T COG1512 145 NYAGGLEAG 153 (271)
T ss_pred cHHHHHHHH
Confidence 355554554
No 72
>PRK14639 hypothetical protein; Provisional
Probab=27.80 E-value=92 Score=29.37 Aligned_cols=35 Identities=20% Similarity=0.447 Sum_probs=29.3
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccc
Q 008994 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNV 47 (547)
Q Consensus 11 ~~~iGs~islISk~~IRYeGiL~~Id~~~sTi~L~nV 47 (547)
..|+|.+|.+..+..-+|+|+|..+|-+ .|+|.++
T Consensus 84 ~r~~G~~v~v~l~~~~~~~G~L~~~~~~--~i~l~~~ 118 (140)
T PRK14639 84 AKSIGELVKITTNEKEKFEGKIVSVDDE--NITLENL 118 (140)
T ss_pred HHhCCCEEEEEECCCcEEEEEEEEEeCC--EEEEEEc
Confidence 4689999999988888999999998876 7777654
No 73
>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=27.60 E-value=1.8e+02 Score=25.19 Aligned_cols=60 Identities=20% Similarity=0.357 Sum_probs=39.0
Q ss_pred ccCce--eEE--eecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccce
Q 008994 13 YIGSF--ISL--ISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDL 82 (547)
Q Consensus 13 ~iGs~--isl--ISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL 82 (547)
|+.++ |.+ .-+.+..|+|+|..+|.-= -|.|.|+.=+ ... .. ....++.|+.||..|.-|
T Consensus 14 ~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~m-NlvL~d~~E~----~~~-~~----~~~~lG~iliRGnnV~~I 77 (79)
T cd01718 14 FLQSKQRVQIWLYEQTDLRIEGVIIGFDEYM-NLVLDDAEEV----HLK-TK----TRKPLGRILLKGDNITLI 77 (79)
T ss_pred HHccCcEEEEEEEeCCCcEEEEEEEEEccce-eEEEcCEEEE----ecC-Cc----eEeEcCcEEEeCCEEEEE
Confidence 45553 333 3459999999999999774 5888886322 111 11 112468899999988643
No 74
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=27.52 E-value=61 Score=32.13 Aligned_cols=12 Identities=33% Similarity=0.354 Sum_probs=5.4
Q ss_pred chhhhhhhcccc
Q 008994 419 KKDEVWGYLGKA 430 (547)
Q Consensus 419 nKeei~~~lgK~ 430 (547)
||=.|.++|++.
T Consensus 5 N~V~LiGrLg~D 16 (182)
T PRK06958 5 NKVILVGNLGAD 16 (182)
T ss_pred cEEEEEEEecCC
Confidence 333444555443
No 75
>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=26.55 E-value=61 Score=37.36 Aligned_cols=15 Identities=27% Similarity=0.189 Sum_probs=10.9
Q ss_pred CCCCCccccccccCC
Q 008994 290 SCPDTKATEAQISGR 304 (547)
Q Consensus 290 s~~~~~~i~~~is~K 304 (547)
|..++-.|+--.+||
T Consensus 259 sgrdvigIAktgSgk 273 (731)
T KOG0339|consen 259 SGRDVIGIAKTGSGK 273 (731)
T ss_pred ccccchheeeccCcc
Confidence 456777777777777
No 76
>PRK14633 hypothetical protein; Provisional
Probab=26.38 E-value=1e+02 Score=29.39 Aligned_cols=53 Identities=21% Similarity=0.371 Sum_probs=37.5
Q ss_pred CCccCceeEEeec----CCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeec
Q 008994 11 ESYIGSFISLISK----YEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVK 85 (547)
Q Consensus 11 ~~~iGs~islISk----~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~v~ 85 (547)
..|||++|.+..+ ..-+|+|+|..++-+ +|+|... +| +-+.|.-.+||..++.
T Consensus 90 ~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~--~i~l~~~-----~~---------------~~~~i~~~~I~ka~l~ 146 (150)
T PRK14633 90 QALVGFNVKAVTLAPVGSQTKFKGVLERVEGN--NVILNLE-----DG---------------KEISFDFDELKKLRVS 146 (150)
T ss_pred HHhCCCeEEEEEecccCCcEEEEEEEEEEeCC--EEEEEEc-----CC---------------cEEEEEhHHeeeEEEe
Confidence 4689999999884 568899999998654 7777521 01 1256777788777663
No 77
>KOG3910 consensus Helix loop helix transcription factor [Transcription]
Probab=24.71 E-value=1.2e+03 Score=27.31 Aligned_cols=24 Identities=17% Similarity=0.032 Sum_probs=18.6
Q ss_pred CCCCCCcccCCCCCCCCCCCCCCCCC
Q 008994 170 PSFPLPIYWQGYNGPSNNISPTPFQS 195 (547)
Q Consensus 170 sglaMPmywQGYy~p~~g~p~~~qq~ 195 (547)
+.+.|+-||-||-+ |..|||||..
T Consensus 198 s~~~~q~~~gg~ll--n~tphm~~ss 221 (632)
T KOG3910|consen 198 STGMMQPGFGGMLL--NSTPHMPQSS 221 (632)
T ss_pred ccccCCCCcccccC--CCCCCCcccc
Confidence 67889999999874 5567888833
No 78
>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=24.24 E-value=2e+02 Score=24.44 Aligned_cols=56 Identities=18% Similarity=0.275 Sum_probs=36.8
Q ss_pred CCccCceeEEeecC---C-eeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeec
Q 008994 11 ESYIGSFISLISKY---E-IRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVK 85 (547)
Q Consensus 11 ~~~iGs~islISk~---~-IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipp~~~vy~yIvFrgsDIKDL~v~ 85 (547)
..+||.+|.|..+. + -+|+|+|..+|-+ .|+|. +.- -+|. .-+.|.-.||+..+++
T Consensus 21 ~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~--~v~l~-~~~---~~~~-------------~~~~i~~~~I~ka~l~ 80 (83)
T cd01734 21 ERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD--TVTLE-VDI---KTRG-------------KTVEIPLDKIAKARLA 80 (83)
T ss_pred HHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC--EEEEE-Eec---CCCC-------------eEEEEEhHHeeEEEEE
Confidence 45899999998873 2 4799999999876 55553 210 0110 1367777888877653
No 79
>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=23.56 E-value=78 Score=31.44 Aligned_cols=37 Identities=35% Similarity=0.591 Sum_probs=0.0
Q ss_pred CCCCCC-----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 008994 508 RANQGY-----GGYVAGRGANYRGRYGGGRRYGYGGRGHGGN 544 (547)
Q Consensus 508 R~rgGr-----gGrGrGRGgrgRGgy~GgrGyG~gGRG~g~~ 544 (547)
|.++.| .|-|++--.++-.+.+|.-|+||.|||-|.|
T Consensus 172 RR~~rrsppepsgdgG~~~~G~~~~NGG~Egrgyrgrgeggg 213 (215)
T PF05084_consen 172 RRTGRRSPPEPSGDGGGNDAGNNAGNGGNEGRGYRGRGEGGG 213 (215)
T ss_pred HhhccCCCCCCCCCCCCCccccccCCCcccccccCCCCCCCC
No 80
>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=22.96 E-value=1.3e+02 Score=21.17 Aligned_cols=31 Identities=13% Similarity=0.161 Sum_probs=25.7
Q ss_pred CceeEEeecCCeeEEEEeeeecCCCCeEEec
Q 008994 15 GSFISLISKYEIRYEGVLYHLNVGDSTIGLK 45 (547)
Q Consensus 15 Gs~islISk~~IRYeGiL~~Id~~~sTi~L~ 45 (547)
|..+.+|+=..--.+|++..||.+..+|.++
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 6677777777777999999999999888763
No 81
>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]
Probab=22.47 E-value=2.3e+02 Score=31.94 Aligned_cols=33 Identities=12% Similarity=0.159 Sum_probs=24.0
Q ss_pred CCCCCCCCCchhhHHHHHhhhchhhhhhhcccc
Q 008994 398 SQYSTTKFTEEFDFEAMNEKFKKDEVWGYLGKA 430 (547)
Q Consensus 398 ~~~~~~kf~~DFDFeaaNaKFnKeei~~~lgK~ 430 (547)
|-.+++||++-.=-..|-|+.|.+-.|..-.|.
T Consensus 286 k~~AlvEye~~~~A~KA~e~~~~e~~wr~glkv 318 (484)
T KOG1855|consen 286 KECALVEYEEVEAARKARELLNPEQNWRMGLKV 318 (484)
T ss_pred hhhhhhhhhhhHHHHHHHHhhchhhhhhhcchh
Confidence 356788999887777777888777777654444
No 82
>PF12300 DUF3628: Protein of unknown function (DUF3628); InterPro: IPR022077 Proteins in this entry are DEAD Box RhlB RNA Helicases found in Xanthomonadaceae bacteria.; GO: 0016817 hydrolase activity, acting on acid anhydrides
Probab=22.22 E-value=90 Score=30.76 Aligned_cols=7 Identities=57% Similarity=0.800 Sum_probs=3.4
Q ss_pred CCCCCCC
Q 008994 386 LPLLPLP 392 (547)
Q Consensus 386 ~PlLPLP 392 (547)
+=|.|||
T Consensus 12 ELLtPLp 18 (180)
T PF12300_consen 12 ELLTPLP 18 (180)
T ss_pred HhccCCC
Confidence 3345555
No 83
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.69 E-value=1.4e+02 Score=28.96 Aligned_cols=33 Identities=15% Similarity=0.335 Sum_probs=28.0
Q ss_pred CCccCceeEEee----cCCeeEEEEeeeecCCCCeEEec
Q 008994 11 ESYIGSFISLIS----KYEIRYEGVLYHLNVGDSTIGLK 45 (547)
Q Consensus 11 ~~~iGs~islIS----k~~IRYeGiL~~Id~~~sTi~L~ 45 (547)
..|+|.+|.|.. ...-+|+|+|..+|.+. |+|.
T Consensus 95 ~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~--v~~~ 131 (153)
T COG0779 95 ARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET--VTLE 131 (153)
T ss_pred HHhcCcEEEEEEecccCCceEEEEEEEEEcCCe--EEEE
Confidence 458999999999 67889999999999884 6654
No 84
>KOG2479 consensus Translation initiation factor 3, subunit d (eIF-3d) [Translation, ribosomal structure and biogenesis]
Probab=20.93 E-value=1.1e+02 Score=34.53 Aligned_cols=7 Identities=29% Similarity=0.520 Sum_probs=4.4
Q ss_pred hhchhhh
Q 008994 417 KFKKDEV 423 (547)
Q Consensus 417 KFnKeei 423 (547)
.|.|-|=
T Consensus 34 pFsK~DR 40 (549)
T KOG2479|consen 34 PFSKSDR 40 (549)
T ss_pred ccccccc
Confidence 5777553
No 85
>PRK14634 hypothetical protein; Provisional
Probab=20.11 E-value=1.4e+02 Score=28.68 Aligned_cols=33 Identities=18% Similarity=0.362 Sum_probs=26.4
Q ss_pred CCccCceeEEeecCC----eeEEEEeeeecCCCCeEEec
Q 008994 11 ESYIGSFISLISKYE----IRYEGVLYHLNVGDSTIGLK 45 (547)
Q Consensus 11 ~~~iGs~islISk~~----IRYeGiL~~Id~~~sTi~L~ 45 (547)
..|+|.+|.|..+.. -+|+|+|..+|-+ .|+|.
T Consensus 96 ~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~--~v~l~ 132 (155)
T PRK14634 96 QTFRGFPVEVSHRDDDGSEQRLEGLLLERNED--HLQIN 132 (155)
T ss_pred HHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC--EEEEE
Confidence 458999999988754 4999999988755 77774
Done!