Query 008892
Match_columns 549
No_of_seqs 253 out of 360
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 17:53:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008892.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008892hhsearch_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 2.7E-39 5.9E-44 333.8 13.4 149 8-165 2-150 (361)
2 PF12701 LSM14: Scd6-like Sm d 100.0 2.8E-37 6.1E-42 268.6 8.9 94 9-106 2-95 (96)
3 cd01736 LSm14_N LSm14 (also kn 100.0 6.6E-36 1.4E-40 248.4 7.7 73 11-83 2-74 (74)
4 PF09532 FDF: FDF domain; Int 99.7 1.6E-19 3.6E-24 157.0 -4.3 98 405-507 1-103 (104)
5 cd00600 Sm_like The eukaryotic 97.8 4.3E-05 9.3E-10 60.4 5.9 61 11-82 2-62 (63)
6 PF14438 SM-ATX: Ataxin 2 SM d 97.8 2.1E-05 4.6E-10 65.5 3.6 68 11-81 8-77 (77)
7 cd01737 LSm16_N LSm16 belongs 96.6 0.0052 1.1E-07 50.4 5.9 61 10-83 1-62 (62)
8 KOG3973 Uncharacterized conser 96.5 0.0079 1.7E-07 63.9 7.9 9 384-392 186-194 (465)
9 PF01423 LSM: LSM domain ; In 96.4 0.0094 2E-07 47.9 6.0 63 11-83 4-66 (67)
10 KOG3973 Uncharacterized conser 96.1 0.011 2.3E-07 63.0 5.9 8 520-527 437-444 (465)
11 cd01719 Sm_G The eukaryotic Sm 95.6 0.038 8.2E-07 46.3 6.2 65 11-86 6-70 (72)
12 smart00651 Sm snRNP Sm protein 95.5 0.032 6.8E-07 44.8 5.5 63 11-83 4-66 (67)
13 cd01722 Sm_F The eukaryotic Sm 95.5 0.036 7.8E-07 45.6 5.8 61 11-82 7-67 (68)
14 PF05918 API5: Apoptosis inhib 95.1 0.006 1.3E-07 68.3 0.0 11 538-548 546-556 (556)
15 cd01717 Sm_B The eukaryotic Sm 95.0 0.072 1.6E-06 45.0 6.3 76 9-85 4-79 (79)
16 cd01731 archaeal_Sm1 The archa 95.0 0.065 1.4E-06 43.9 5.8 61 11-82 6-66 (68)
17 PRK00737 small nuclear ribonuc 94.9 0.057 1.2E-06 45.0 5.5 61 11-82 10-70 (72)
18 cd01726 LSm6 The eukaryotic Sm 94.9 0.062 1.3E-06 44.0 5.6 61 11-82 6-66 (67)
19 cd01728 LSm1 The eukaryotic Sm 94.9 0.07 1.5E-06 45.1 5.9 63 11-81 8-70 (74)
20 cd01723 LSm4 The eukaryotic Sm 94.9 0.067 1.5E-06 45.0 5.7 64 12-85 8-71 (76)
21 TIGR01648 hnRNP-R-Q heterogene 94.8 0.088 1.9E-06 59.6 8.1 30 400-429 269-298 (578)
22 cd01725 LSm2 The eukaryotic Sm 94.7 0.11 2.3E-06 44.5 6.5 65 12-85 8-72 (81)
23 cd01721 Sm_D3 The eukaryotic S 94.4 0.12 2.7E-06 42.8 6.2 63 11-84 6-68 (70)
24 COG1958 LSM1 Small nuclear rib 94.1 0.16 3.4E-06 42.8 6.4 65 11-83 13-78 (79)
25 KOG0921 Dosage compensation co 94.1 0.087 1.9E-06 62.0 6.3 18 466-483 1169-1191(1282)
26 cd06168 LSm9 The eukaryotic Sm 93.5 0.23 5E-06 42.1 6.2 69 11-84 6-74 (75)
27 cd01724 Sm_D1 The eukaryotic S 93.2 0.24 5.3E-06 43.3 6.2 64 12-86 8-71 (90)
28 KOG0116 RasGAP SH3 binding pro 92.6 0.15 3.3E-06 55.7 5.0 10 412-421 304-313 (419)
29 cd01733 LSm10 The eukaryotic S 92.4 0.4 8.6E-06 40.9 6.2 63 11-84 15-77 (78)
30 KOG0921 Dosage compensation co 91.1 0.34 7.4E-06 57.4 5.8 11 96-106 603-613 (1282)
31 cd01727 LSm8 The eukaryotic Sm 91.0 0.52 1.1E-05 39.4 5.3 65 10-83 4-70 (74)
32 cd01729 LSm7 The eukaryotic Sm 90.6 0.93 2E-05 38.8 6.6 70 11-83 8-77 (81)
33 cd01732 LSm5 The eukaryotic Sm 86.4 2.7 5.8E-05 35.7 6.6 65 11-83 9-73 (76)
34 PLN03134 glycine-rich RNA-bind 85.0 1 2.2E-05 42.0 3.8 28 398-425 74-101 (144)
35 KOG0116 RasGAP SH3 binding pro 82.9 1.5 3.3E-05 48.2 4.5 12 489-500 356-367 (419)
36 TIGR01659 sex-lethal sex-letha 82.4 2.2 4.7E-05 45.5 5.4 27 399-425 234-260 (346)
37 PRK11634 ATP-dependent RNA hel 81.2 2.2 4.8E-05 48.7 5.3 9 275-283 305-313 (629)
38 cd01720 Sm_D2 The eukaryotic S 80.1 6.6 0.00014 34.4 6.7 69 14-83 13-84 (87)
39 COG4371 Predicted membrane pro 75.4 4.2 9.2E-05 42.4 4.7 7 531-537 83-89 (334)
40 KOG3293 Small nuclear ribonucl 75.3 3.4 7.4E-05 38.6 3.7 13 471-483 51-63 (134)
41 TIGR01648 hnRNP-R-Q heterogene 75.0 4.4 9.5E-05 46.3 5.2 24 398-421 180-203 (578)
42 cd01730 LSm3 The eukaryotic Sm 72.7 13 0.00028 31.7 6.3 70 12-82 8-80 (82)
43 KOG2236 Uncharacterized conser 72.6 11 0.00024 42.1 7.3 25 189-213 456-481 (483)
44 TIGR01659 sex-lethal sex-letha 69.0 5.1 0.00011 42.7 3.8 32 398-429 147-178 (346)
45 PF12764 Gly-rich_Ago1: Glycin 68.4 5.4 0.00012 36.3 3.2 6 526-531 19-24 (104)
46 KOG3448 Predicted snRNP core p 66.8 14 0.00031 32.9 5.4 65 12-85 9-73 (96)
47 PF06372 Gemin6: Gemin6 protei 66.2 9.3 0.0002 37.3 4.6 60 11-87 13-72 (166)
48 KOG1073 Uncharacterized mRNA-a 65.3 15 0.00032 39.9 6.4 40 465-508 252-292 (361)
49 KOG2945 Predicted RNA-binding 63.7 5.5 0.00012 43.2 2.8 13 408-420 180-192 (365)
50 COG4907 Predicted membrane pro 51.3 11 0.00025 42.2 2.7 22 65-86 53-75 (595)
51 KOG3875 Peroxisomal biogenesis 49.1 18 0.00038 38.9 3.6 6 466-471 29-34 (362)
52 KOG0105 Alternative splicing f 48.8 17 0.00036 36.8 3.1 9 413-421 23-31 (241)
53 PRK06958 single-stranded DNA-b 48.6 24 0.00052 34.9 4.2 13 420-432 4-16 (182)
54 KOG3172 Small nuclear ribonucl 48.4 21 0.00045 32.9 3.5 28 500-527 79-106 (119)
55 PTZ00138 small nuclear ribonuc 44.7 53 0.0011 29.1 5.3 54 20-83 33-86 (89)
56 KOG2140 Uncharacterized conser 40.8 21 0.00045 41.0 2.7 21 404-426 384-404 (739)
57 cd01735 LSm12_N LSm12 belongs 40.5 55 0.0012 27.2 4.5 58 13-83 4-61 (61)
58 KOG1775 U6 snRNA-associated Sm 40.4 24 0.00052 30.8 2.5 62 11-82 13-76 (84)
59 PF02237 BPL_C: Biotin protein 38.6 51 0.0011 25.3 3.9 28 13-41 1-28 (48)
60 KOG2295 C2H2 Zn-finger protein 37.7 45 0.00098 38.3 4.7 7 511-517 576-582 (648)
61 PRK02001 hypothetical protein; 36.1 1.1E+02 0.0024 29.4 6.5 65 11-85 86-151 (152)
62 PF10842 DUF2642: Protein of u 35.5 53 0.0012 27.7 3.7 33 11-46 17-49 (66)
63 PRK14644 hypothetical protein; 35.0 60 0.0013 30.6 4.5 33 11-45 81-117 (136)
64 PF07076 DUF1344: Protein of u 34.7 36 0.00077 28.5 2.5 24 28-51 5-28 (61)
65 COG1512 Beta-propeller domains 34.1 47 0.001 34.8 3.9 8 426-434 90-97 (271)
66 PRK14642 hypothetical protein; 33.8 1.1E+02 0.0024 30.8 6.3 71 11-85 96-179 (197)
67 PRK14631 hypothetical protein; 33.5 64 0.0014 31.6 4.5 35 11-45 113-151 (174)
68 COG1512 Beta-propeller domains 33.3 42 0.00092 35.1 3.4 12 362-373 63-74 (271)
69 PF02576 DUF150: Uncharacteris 32.5 77 0.0017 29.3 4.7 31 12-44 84-118 (141)
70 PRK14638 hypothetical protein; 31.7 65 0.0014 30.7 4.1 33 11-45 96-128 (150)
71 COG4907 Predicted membrane pro 30.4 39 0.00084 38.2 2.7 13 27-39 52-64 (595)
72 cd01718 Sm_E The eukaryotic Sm 30.2 1.5E+02 0.0033 25.6 5.8 61 12-82 13-77 (79)
73 KOG1783 Small nuclear ribonucl 29.7 29 0.00064 30.0 1.3 62 11-83 12-73 (77)
74 PF12287 Caprin-1_C: Cytoplasm 28.1 62 0.0013 34.7 3.6 7 340-346 122-128 (316)
75 PRK14639 hypothetical protein; 27.7 93 0.002 29.4 4.4 35 11-47 84-118 (140)
76 KOG1995 Conserved Zn-finger pr 27.5 84 0.0018 34.3 4.5 8 468-475 136-143 (351)
77 PRK14633 hypothetical protein; 26.3 1E+02 0.0022 29.4 4.4 53 11-85 90-146 (150)
78 PF05084 GRA6: Granule antigen 25.6 69 0.0015 31.8 3.2 15 532-546 199-213 (215)
79 KOG4212 RNA-binding protein hn 22.9 1.1E+02 0.0023 34.8 4.3 29 399-427 85-113 (608)
80 PF00467 KOW: KOW motif; Inte 22.5 1.4E+02 0.0031 21.1 3.5 31 15-45 2-32 (32)
81 KOG0339 ATP-dependent RNA heli 22.4 81 0.0017 36.5 3.4 15 290-304 259-273 (731)
82 KOG3910 Helix loop helix trans 22.0 1.3E+03 0.028 26.9 16.4 24 170-195 198-221 (632)
83 COG0779 Uncharacterized protei 21.6 1.4E+02 0.003 28.9 4.4 33 11-45 95-131 (153)
No 1
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.7e-39 Score=333.77 Aligned_cols=149 Identities=43% Similarity=0.626 Sum_probs=123.6
Q ss_pred CCCCCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeeccC
Q 008892 8 NAPESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVKSS 87 (549)
Q Consensus 8 ~~~~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~v~~~ 87 (549)
+.+++|||++||||||.|||||||||+||++||||+|+||||||||||++++.+||+.++|||||||||+|||||.||+.
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 008892 88 PPPQKEEQIYQDPAIIQSQYAGISTNSPLLSSVVGKTLTESSSWQDTPTLTSKASAGSLLSHQPGTQVSQFSHPQAAQ 165 (549)
Q Consensus 88 p~~~~~~~~~~DPAI~~~~~p~~~~~s~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~plyQpg~~~~swg~s~~~~ 165 (549)
|+.+....++.+|+|. ...+.++..+.+....|.+..+.+-+....|..++.++|...+++|.....++
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 7643333355566652 22234444555566667777777777777799999999999999999866554
No 2
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=100.00 E-value=2.8e-37 Score=268.62 Aligned_cols=94 Identities=61% Similarity=0.998 Sum_probs=72.4
Q ss_pred CCCCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeeccCC
Q 008892 9 APESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVKSSP 88 (549)
Q Consensus 9 ~~~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~v~~~p 88 (549)
.+++|||++||||||++|||||+||+||.+++||+|+||||||||||+.+. +|||++++|+||+|||+|||||+||+.+
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 468999999999999999999999999999999999999999999998764 8999999999999999999999999987
Q ss_pred CCCCCccCCCCchhhhcc
Q 008892 89 PPQKEEQIYQDPAIIQSQ 106 (549)
Q Consensus 89 ~~~~~~~~~~DPAI~~~~ 106 (549)
++ ++.++|||||+.+
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 4578999999874
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=6.6e-36 Score=248.36 Aligned_cols=73 Identities=70% Similarity=1.151 Sum_probs=70.8
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~ 83 (549)
.+|||++||||||+||||||+||+||.+++||+|+||||||||||+.++++|||+++|||||||||+|||||+
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=99.71 E-value=1.6e-19 Score=156.95 Aligned_cols=98 Identities=36% Similarity=0.628 Sum_probs=42.4
Q ss_pred CCCCchhhHHHHHHhhchhhhhhcccccccCCCCCCccCCccccCCCCccccCccCCCCCCCCccCC-CcCCccCcCCCC
Q 008892 405 TKFTEEFDFEAMNEKFKKDEVWGYLGKAKQSGKPETIEDNTADQNSRGKEADGLVKNGDPKPAYRKD-DFFDTISCNSLN 483 (549)
Q Consensus 405 ~kf~~dFDFesaN~kFnK~ei~~~lgK~~~s~e~egeed~~~~~~~e~~E~~~~~~~~~~k~~YdK~-sFFD~IScn~~~ 483 (549)
++|++||||++||+||+|++||.++.+........... ....+. +............+|+|. +|||+|||+..+
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 58999999999999999999999997654421111100 000000 111111223445678875 999999999999
Q ss_pred CCCCCC-cc---cccccccccccccccc
Q 008892 484 RGTREG-QN---RFSERMRLDTETFGNF 507 (549)
Q Consensus 484 R~~r~g-R~---r~~eErklNtETFG~~ 507 (549)
|..+.+ |. +|.+||++|+||||..
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 974332 22 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=97.82 E-value=4.3e-05 Score=60.42 Aligned_cols=61 Identities=23% Similarity=0.361 Sum_probs=53.0
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccce
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDL 82 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL 82 (549)
..+||++|.+..+.+..|+|+|..+|. ...|.|+|+..+.+++ ....++.++.||+.|+.+
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 234678899999999876
No 6
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.77 E-value=2.1e-05 Score=65.49 Aligned_cols=68 Identities=15% Similarity=0.255 Sum_probs=45.1
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCC--CCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccc
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVG--DSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKD 81 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~--~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKD 81 (549)
..+||+++.+..|.+-+|||||+..+.+ +..|.|+.+|.-..+.... .-+...++-+.++|++.||-|
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 3589999999999999999999999998 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=96.64 E-value=0.0052 Score=50.41 Aligned_cols=61 Identities=28% Similarity=0.486 Sum_probs=47.3
Q ss_pred CCCccCceeEEeecCCee-EEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008892 10 PESYIGSFISLISKYEIR-YEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (549)
Q Consensus 10 ~~~~IGs~isLISk~~IR-YeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~ 83 (549)
++.+||+-+||-...++- |.|.+..||.++.||.|.+- |+-- | ..++-| |+||.-|||+|.
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 367999999999998874 99999999999999999872 1111 1 222223 899999999984
No 8
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=96.51 E-value=0.0079 Score=63.92 Aligned_cols=9 Identities=44% Similarity=0.689 Sum_probs=5.2
Q ss_pred cCCCCcCCC
Q 008892 384 TQLPLLPLP 392 (549)
Q Consensus 384 ~q~PlLPLP 392 (549)
...|||..|
T Consensus 186 ~~~PLlKkp 194 (465)
T KOG3973|consen 186 RSHPLLKKP 194 (465)
T ss_pred cCCchhcCc
Confidence 346676655
No 9
>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=96.38 E-value=0.0094 Score=47.93 Aligned_cols=63 Identities=21% Similarity=0.334 Sum_probs=52.6
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~ 83 (549)
..++|++|.+..+.+..|+|+|..+|. .--|.|+||.-+-.+++ ....++.++.||+.|.-++
T Consensus 4 ~~~~g~~V~V~l~~g~~~~G~L~~~D~-~~Nl~L~~~~~~~~~~~---------~~~~~~~~~irG~~I~~I~ 66 (67)
T PF01423_consen 4 QKLIGKRVRVELKNGRTYRGTLVSFDQ-FMNLVLSDVTETIKNGP---------EKRSLGLVFIRGSNIRYIS 66 (67)
T ss_dssp HHTTTSEEEEEETTSEEEEEEEEEEET-TEEEEEEEEEEEETTES---------EEEEEEEEEEEGGGEEEEE
T ss_pred HHhCCcEEEEEEeCCEEEEEEEEEeec-hheEEeeeEEEEECCCC---------cEeECcEEEEECCEEEEEE
Confidence 358999999999999999999999996 56699999988876654 3345678999999998765
No 10
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=96.05 E-value=0.011 Score=63.01 Aligned_cols=8 Identities=38% Similarity=0.563 Sum_probs=3.1
Q ss_pred CCCCCCCC
Q 008892 520 AGRGANYR 527 (549)
Q Consensus 520 ~gRGg~gr 527 (549)
+||+|+||
T Consensus 437 ggr~gggr 444 (465)
T KOG3973|consen 437 GGRDGGGR 444 (465)
T ss_pred CCCCCCCC
Confidence 33433333
No 11
>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=95.56 E-value=0.038 Score=46.27 Aligned_cols=65 Identities=18% Similarity=0.268 Sum_probs=52.0
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeecc
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVKS 86 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~v~~ 86 (549)
..||+++|.++-|.+..|+|+|..+| +---|.|.||..+-. + . ....++.++.||+.|.-+.-.+
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 57899999999999999999999999 567799999965531 1 1 1235788999999998876544
No 12
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=95.52 E-value=0.032 Score=44.79 Aligned_cols=63 Identities=19% Similarity=0.293 Sum_probs=50.4
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~ 83 (549)
..++|++|.+..+.+..|+|+|..+|. .-.|.|+|+.-+-.+. .....++.++.||+.|.-+.
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 468999999999999999999999996 5789999987665542 12335667889999987654
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=95.48 E-value=0.036 Score=45.59 Aligned_cols=61 Identities=18% Similarity=0.321 Sum_probs=47.9
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccce
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDL 82 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL 82 (549)
..++|++|.+.-|.+..|+|+|..+| +.--|.|+||.-+-- +. ....++.++.||+.|.-+
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 46799999999999999999999999 567899999854311 11 123478899999998754
No 14
>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=95.07 E-value=0.006 Score=68.33 Aligned_cols=11 Identities=36% Similarity=0.616 Sum_probs=0.0
Q ss_pred CCCCCCCCCCC
Q 008892 538 YGGRGHGGNMH 548 (549)
Q Consensus 538 ~~grg~g~~~~ 548 (549)
++|||+||||+
T Consensus 546 g~grg~~r~~~ 556 (556)
T PF05918_consen 546 GRGRGRGRGFW 556 (556)
T ss_dssp -----------
T ss_pred CCCCcccccCC
Confidence 34555566664
No 15
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=94.98 E-value=0.072 Score=44.97 Aligned_cols=76 Identities=14% Similarity=0.230 Sum_probs=57.0
Q ss_pred CCCCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeec
Q 008892 9 APESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVK 85 (549)
Q Consensus 9 ~~~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~v~ 85 (549)
.-..|||++|.+..+.+-.|+|+|..+|.. .-|.|.|+.-|-++.+...........-.+..++.||..|.-+.|+
T Consensus 4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~-~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v~ 79 (79)
T cd01717 4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKH-MNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTVE 79 (79)
T ss_pred hhHHHcCCEEEEEECCCcEEEEEEEEEcCc-cCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEEC
Confidence 346799999999999999999999999965 6788999988776554321011111223478899999999988763
No 16
>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=94.96 E-value=0.065 Score=43.88 Aligned_cols=61 Identities=11% Similarity=0.168 Sum_probs=48.3
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccce
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDL 82 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL 82 (549)
..++|++|.+..|.+-.|+|+|..+|.- --|.|+|+..+-.++ ...-++.++.||+.|.-+
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 4689999999999999999999999984 568899987654332 123467899999998654
No 17
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=94.94 E-value=0.057 Score=44.97 Aligned_cols=61 Identities=13% Similarity=0.195 Sum_probs=48.6
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccce
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDL 82 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL 82 (549)
..++|++|.+..|.+--|+|+|..+|. .--|.|+||..+-.+ . ...-++.++.||+.|.-+
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 467999999999999999999999998 567899998654321 1 113577899999998765
No 18
>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=94.94 E-value=0.062 Score=44.03 Aligned_cols=61 Identities=20% Similarity=0.376 Sum_probs=48.0
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccce
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDL 82 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL 82 (549)
..++|++|.+.-|.+.-|+|+|..+| +.=-|.|+||..+-..++ ...++.|+-||+.|.-+
T Consensus 6 ~~~~~~~V~V~Lk~g~~~~G~L~~~D-~~mNlvL~~~~~~~~~~~----------~~~~~~v~IRG~~I~~I 66 (67)
T cd01726 6 KAIIGRPVVVKLNSGVDYRGILACLD-GYMNIALEQTEEYVNGQL----------KNKYGDAFIRGNNVLYI 66 (67)
T ss_pred HhhCCCeEEEEECCCCEEEEEEEEEc-cceeeEEeeEEEEeCCce----------eeEeCCEEEECCEEEEE
Confidence 35799999999999999999999999 567789999865432111 22577899999998754
No 19
>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=94.91 E-value=0.07 Score=45.11 Aligned_cols=63 Identities=11% Similarity=0.120 Sum_probs=49.3
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccc
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKD 81 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKD 81 (549)
..||+++|.++-+.+..|.|+|..+| +.-.|.|.|+.-+-.++-+. .+.....|++||..|--
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 55789999986555443110 12357889999998743
No 20
>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=94.86 E-value=0.067 Score=44.98 Aligned_cols=64 Identities=23% Similarity=0.198 Sum_probs=51.7
Q ss_pred CccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeec
Q 008892 12 SYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVK 85 (549)
Q Consensus 12 ~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~v~ 85 (549)
.++|++|.+.-|.+..|+|+|..+|.- -.|.|+||.....+|.+ + ..++.++-||+.|+-+++-
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 67899999876554432 1 1357799999999988763
No 21
>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=94.77 E-value=0.088 Score=59.57 Aligned_cols=30 Identities=17% Similarity=0.229 Sum_probs=26.0
Q ss_pred cccCCCCCCchhhHHHHHHhhchhhhhhcc
Q 008892 400 SQYSTTKFTEEFDFEAMNEKFKKDEVWGYL 429 (549)
Q Consensus 400 ~~~~~~kf~~dFDFesaN~kFnK~ei~~~l 429 (549)
++|++++|++..|.+.|.+++|..+|.+..
T Consensus 269 rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~ 298 (578)
T TIGR01648 269 RDYAFVHFEDREDAVKAMDELNGKELEGSE 298 (578)
T ss_pred cCeEEEEeCCHHHHHHHHHHhCCCEECCEE
Confidence 579999999999999999999987776544
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=94.67 E-value=0.11 Score=44.49 Aligned_cols=65 Identities=17% Similarity=0.226 Sum_probs=52.0
Q ss_pred CccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeec
Q 008892 12 SYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVK 85 (549)
Q Consensus 12 ~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~v~ 85 (549)
..+|++|.+--|.+..|+|+|..+|.-= -|.|+||.....++.. .-..++.|..||+.|+.+++-
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 7899999876543321 123458899999999998873
No 23
>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=94.39 E-value=0.12 Score=42.80 Aligned_cols=63 Identities=24% Similarity=0.306 Sum_probs=51.4
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceee
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEV 84 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~v 84 (549)
...+|+.|.+--|.+..|.|+|..+|. .-.|.|+||.....+|+. .-++.++-||+.|+-+.+
T Consensus 6 ~~~~g~~V~VeLk~g~~~~G~L~~~D~-~MNl~L~~~~~~~~~g~~----------~~~~~v~IRG~nI~~v~l 68 (70)
T cd01721 6 HEAEGHIVTVELKTGEVYRGKLIEAED-NMNCQLKDVTVTARDGRV----------SQLEQVYIRGSKIRFFIL 68 (70)
T ss_pred hhCCCCEEEEEECCCcEEEEEEEEEcC-CceeEEEEEEEECCCCcE----------eEcCcEEEeCCEEEEEEe
Confidence 356899999999999999999999998 568999999864433321 245789999999998876
No 24
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=94.15 E-value=0.16 Score=42.78 Aligned_cols=65 Identities=18% Similarity=0.279 Sum_probs=51.2
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceeccc-CCCCCCCCCCCCCccccceEEEecCCcccee
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGT-EGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGT-EgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~ 83 (549)
..+|+++|.+.-|.+..|.|+|..+|..- -|.|.+|..... +|+.. .....+.++.||+.|+-|.
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 46899999999999999999999999874 578999998877 33321 2223348999999998764
No 25
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=94.13 E-value=0.087 Score=62.02 Aligned_cols=18 Identities=6% Similarity=0.026 Sum_probs=10.3
Q ss_pred CCccCC-----CcCCccCcCCCC
Q 008892 466 PAYRKD-----DFFDTISCNSLN 483 (549)
Q Consensus 466 ~~YdK~-----sFFD~IScn~~~ 483 (549)
..||.- |||++.-..-..
T Consensus 1169 aryDnG~~~n~SgyRRGgssysg 1191 (1282)
T KOG0921|consen 1169 ARYDNGPSNNNSGYRRGGSSYSG 1191 (1282)
T ss_pred ccccCCCccCccccccCCCCCCC
Confidence 456652 777776554433
No 26
>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=93.46 E-value=0.23 Score=42.12 Aligned_cols=69 Identities=19% Similarity=0.223 Sum_probs=52.5
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceee
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEV 84 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~v 84 (549)
..|||+++.++.+.+--|+|+|..+|.. .-|.|.|+. |-|.............+..|+-||..|..+.|
T Consensus 6 ~~~l~~~v~V~l~dgR~~~G~l~~~D~~-~NivL~~~~----E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 6 RSLLGRTMRIHMTDGRTLVGVFLCTDRD-CNIILGSAQ----EYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred HHhcCCeEEEEEcCCeEEEEEEEEEcCC-CcEEecCcE----EEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 5689999999999999999999999966 457899985 44432111112233478899999999998876
No 27
>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=93.23 E-value=0.24 Score=43.27 Aligned_cols=64 Identities=16% Similarity=0.153 Sum_probs=52.5
Q ss_pred CccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeecc
Q 008892 12 SYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVKS 86 (549)
Q Consensus 12 ~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~v~~ 86 (549)
.++|+.|.+--|.+..|+|+|..+|.- =-|.|+||..+-.+++ ..-|+.++.||+.|+-+++-+
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 28
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=92.65 E-value=0.15 Score=55.68 Aligned_cols=10 Identities=20% Similarity=0.514 Sum_probs=5.5
Q ss_pred hHHHHHHhhc
Q 008892 412 DFEAMNEKFK 421 (549)
Q Consensus 412 DFesaN~kFn 421 (549)
..++...+|-
T Consensus 304 ~l~~~Fk~FG 313 (419)
T KOG0116|consen 304 ELEEVFKQFG 313 (419)
T ss_pred HHHHHHhhcc
Confidence 3555556663
No 29
>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=92.41 E-value=0.4 Score=40.88 Aligned_cols=63 Identities=17% Similarity=0.306 Sum_probs=50.3
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceee
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEV 84 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~v 84 (549)
...+|+.|.+--|.+..|+|+|..+|.- =.|.|+||.-....+. ..-++.|+.||+.|+-+++
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 4789999975532221 1257899999999998765
No 30
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=91.13 E-value=0.34 Score=57.36 Aligned_cols=11 Identities=36% Similarity=0.468 Sum_probs=6.5
Q ss_pred CCCCchhhhcc
Q 008892 96 IYQDPAIIQSQ 106 (549)
Q Consensus 96 ~~~DPAI~~~~ 106 (549)
...||++-+..
T Consensus 603 ~~~dd~~~~~~ 613 (1282)
T KOG0921|consen 603 ILCDPSYNEST 613 (1282)
T ss_pred cccChhhcchh
Confidence 45667666543
No 31
>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=90.98 E-value=0.52 Score=39.41 Aligned_cols=65 Identities=20% Similarity=0.329 Sum_probs=49.2
Q ss_pred CCCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceec--ccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008892 10 PESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSF--GTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (549)
Q Consensus 10 ~~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsf--GTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~ 83 (549)
-..||+++|.++.+.+-.|+|+|..+|.. --|.|.++..+ .++ .+ + ....+..|+.||+.|--+.
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 45789999999999999999999999988 66888887443 221 11 1 1335789999999986544
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=90.64 E-value=0.93 Score=38.81 Aligned_cols=70 Identities=11% Similarity=0.158 Sum_probs=51.2
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~ 83 (549)
..||+++|.++-+.+-.|+|+|..+|.- --|.|.++..+-.+.- +..++.-....+..++.||..|--|.
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 5689999999999999999999999976 4688999865533211 11112223345789999999987654
No 33
>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=86.45 E-value=2.7 Score=35.73 Aligned_cols=65 Identities=23% Similarity=0.337 Sum_probs=48.1
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~ 83 (549)
..+++++|.+..|.+..|+|+|..+|.- -.|.|.|+..+= + ..++. ....++-|+.||..|.-+.
T Consensus 9 ~~~~~~~V~V~l~~gr~~~G~L~g~D~~-mNlvL~da~E~~-~--~~~~~----~~~~lg~v~iRG~nV~~i~ 73 (76)
T cd01732 9 DKCIGSRIWIVMKSDKEFVGTLLGFDDY-VNMVLEDVTEYE-I--TPEGR----KITKLDQILLNGNNICMLV 73 (76)
T ss_pred HHhCCCEEEEEECCCeEEEEEEEEeccc-eEEEEccEEEEE-E--cCCCc----eeeEcCeEEEeCCeEEEEE
Confidence 3468999999999999999999999975 578899985542 1 11111 1224788999999997653
No 34
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=84.98 E-value=1 Score=42.03 Aligned_cols=28 Identities=14% Similarity=0.192 Sum_probs=22.1
Q ss_pred cccccCCCCCCchhhHHHHHHhhchhhh
Q 008892 398 SQSQYSTTKFTEEFDFEAMNEKFKKDEV 425 (549)
Q Consensus 398 ~~~~~~~~kf~~dFDFesaN~kFnK~ei 425 (549)
+.++|++++|++..|.+.|.+++|..+|
T Consensus 74 ~~kGfaFV~F~~~e~A~~Al~~lng~~i 101 (144)
T PLN03134 74 RSRGFGFVNFNDEGAATAAISEMDGKEL 101 (144)
T ss_pred CcceEEEEEECCHHHHHHHHHHcCCCEE
Confidence 3678888888888888888888776555
No 35
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=82.86 E-value=1.5 Score=48.16 Aligned_cols=12 Identities=25% Similarity=0.216 Sum_probs=5.7
Q ss_pred Cccccccccccc
Q 008892 489 GQNRFSERMRLD 500 (549)
Q Consensus 489 gR~r~~eErklN 500 (549)
+|.-.-||++.+
T Consensus 356 ~~kl~Veek~~~ 367 (419)
T KOG0116|consen 356 GRKLNVEEKRPG 367 (419)
T ss_pred CeeEEEEecccc
Confidence 444444555443
No 36
>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=82.42 E-value=2.2 Score=45.47 Aligned_cols=27 Identities=4% Similarity=-0.011 Sum_probs=17.5
Q ss_pred ccccCCCCCCchhhHHHHHHhhchhhh
Q 008892 399 QSQYSTTKFTEEFDFEAMNEKFKKDEV 425 (549)
Q Consensus 399 ~~~~~~~kf~~dFDFesaN~kFnK~ei 425 (549)
.++|++++|++..|.++|.+++|+.++
T Consensus 234 ~kG~aFV~F~~~e~A~~Ai~~lng~~~ 260 (346)
T TIGR01659 234 PRGVAFVRFNKREEAQEAISALNNVIP 260 (346)
T ss_pred cceEEEEEECCHHHHHHHHHHhCCCcc
Confidence 346667777777777777776665444
No 37
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=81.20 E-value=2.2 Score=48.74 Aligned_cols=9 Identities=11% Similarity=-0.248 Sum_probs=4.6
Q ss_pred cccCCCCCC
Q 008892 275 AYMTDNNPN 283 (549)
Q Consensus 275 ~~~~~~~p~ 283 (549)
+..|.++|.
T Consensus 305 ~arGIDip~ 313 (629)
T PRK11634 305 AARGLDVER 313 (629)
T ss_pred HhcCCCccc
Confidence 455555554
No 38
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=80.11 E-value=6.6 Score=34.37 Aligned_cols=69 Identities=14% Similarity=0.185 Sum_probs=50.3
Q ss_pred cCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCC---CCCCCCccccceEEEecCCcccee
Q 008892 14 IGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDG---PQVLPSEKVYEYILFRGSDIKDLE 83 (549)
Q Consensus 14 IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~---~~Ipps~~vy~yIvFrgsDIKDL~ 83 (549)
.|++|-+.-|.+-.|.|+|..+|.. -.|.|.||..+-++.-+... .+.......+..|+.||..|.-|.
T Consensus 13 ~~~~V~V~lr~~r~~~G~L~~fD~h-mNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~Is 84 (87)
T cd01720 13 NNTQVLINCRNNKKLLGRVKAFDRH-CNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVILVL 84 (87)
T ss_pred CCCEEEEEEcCCCEEEEEEEEecCc-cEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEEEe
Confidence 3899999999999999999999975 67999999888665322111 111112334689999999987643
No 39
>COG4371 Predicted membrane protein [Function unknown]
Probab=75.44 E-value=4.2 Score=42.40 Aligned_cols=7 Identities=29% Similarity=0.605 Sum_probs=3.1
Q ss_pred CCCCCCC
Q 008892 531 GGGRRYG 537 (549)
Q Consensus 531 ~g~~g~g 537 (549)
|+|+|||
T Consensus 83 Y~GGGfg 89 (334)
T COG4371 83 YSGGGFG 89 (334)
T ss_pred CCCCCcC
Confidence 3334554
No 40
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=75.26 E-value=3.4 Score=38.62 Aligned_cols=13 Identities=31% Similarity=0.575 Sum_probs=8.7
Q ss_pred CCcCCccCcCCCC
Q 008892 471 DDFFDTISCNSLN 483 (549)
Q Consensus 471 ~sFFD~IScn~~~ 483 (549)
|.||..-.|=-+.
T Consensus 51 dkf~r~pEcYirG 63 (134)
T KOG3293|consen 51 DKFFRMPECYIRG 63 (134)
T ss_pred CceeecceeEEec
Confidence 3688777776654
No 41
>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=74.98 E-value=4.4 Score=46.28 Aligned_cols=24 Identities=4% Similarity=0.109 Sum_probs=18.9
Q ss_pred cccccCCCCCCchhhHHHHHHhhc
Q 008892 398 SQSQYSTTKFTEEFDFEAMNEKFK 421 (549)
Q Consensus 398 ~~~~~~~~kf~~dFDFesaN~kFn 421 (549)
+.++|++++|++..|.+.|.++++
T Consensus 180 KnRGFAFVeF~s~edAa~AirkL~ 203 (578)
T TIGR01648 180 KNRGFAFVEYESHRAAAMARRKLM 203 (578)
T ss_pred ccCceEEEEcCCHHHHHHHHHHhh
Confidence 467888888888888888877664
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=72.67 E-value=13 Score=31.74 Aligned_cols=70 Identities=11% Similarity=0.077 Sum_probs=48.4
Q ss_pred CccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCC---CCCCCCCccccceEEEecCCccce
Q 008892 12 SYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKD---GPQVLPSEKVYEYILFRGSDIKDL 82 (549)
Q Consensus 12 ~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~---~~~Ipps~~vy~yIvFrgsDIKDL 82 (549)
.+++++|.++.|.+-.|+|+|...|.. -.|.|.|+.-+-.+--... ...+......+..++.||..|.-|
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 43
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=72.62 E-value=11 Score=42.11 Aligned_cols=25 Identities=8% Similarity=0.065 Sum_probs=11.1
Q ss_pred CCCCCCC-CCccccCCCCCCcccccc
Q 008892 189 SPTPFQS-SSTVSSPLTGPNRIWTSE 213 (549)
Q Consensus 189 p~~~qq~-p~~ls~P~~~qq~~Q~p~ 213 (549)
||+++.+ |+..--|..-+++||.+-
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 44
>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=68.98 E-value=5.1 Score=42.71 Aligned_cols=32 Identities=16% Similarity=0.068 Sum_probs=27.6
Q ss_pred cccccCCCCCCchhhHHHHHHhhchhhhhhcc
Q 008892 398 SQSQYSTTKFTEEFDFEAMNEKFKKDEVWGYL 429 (549)
Q Consensus 398 ~~~~~~~~kf~~dFDFesaN~kFnK~ei~~~l 429 (549)
..++|++++|+++.|.+.|.+++|..++.+..
T Consensus 147 ~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~ 178 (346)
T TIGR01659 147 YSFGYAFVDFGSEADSQRAIKNLNGITVRNKR 178 (346)
T ss_pred ccCcEEEEEEccHHHHHHHHHHcCCCccCCce
Confidence 36799999999999999999999987776543
No 45
>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=68.40 E-value=5.4 Score=36.27 Aligned_cols=6 Identities=50% Similarity=0.695 Sum_probs=2.5
Q ss_pred CCCCCC
Q 008892 526 YRGRYG 531 (549)
Q Consensus 526 grGgy~ 531 (549)
||++|+
T Consensus 19 G~~~yG 24 (104)
T PF12764_consen 19 GRPGYG 24 (104)
T ss_pred CCCCCC
Confidence 344443
No 46
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=66.78 E-value=14 Score=32.90 Aligned_cols=65 Identities=15% Similarity=0.217 Sum_probs=50.7
Q ss_pred CccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeec
Q 008892 12 SYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVK 85 (549)
Q Consensus 12 ~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~v~ 85 (549)
..||+.+++-=|.|+-..|+|++||.= =.|.|.||++--.| +-|..-.|-+ +-.|||-|+-+++-
T Consensus 9 slvg~~V~VeLKnd~~i~GtL~svDqy-LNlkL~di~v~d~~-------kyPhm~Sv~n-cfIRGSvvrYv~l~ 73 (96)
T KOG3448|consen 9 SLVGKEVVVELKNDLSICGTLHSVDQY-LNLKLTDISVTDPD-------KYPHMLSVKN-CFIRGSVVRYVQLP 73 (96)
T ss_pred HhcCCeEEEEEcCCcEEEEEecccchh-heeEEeeeEeeCcc-------cCCCeeeeee-EEEeccEEEEEEeC
Confidence 579999999999999999999999975 35889999875443 2344444444 66799999998873
No 47
>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=66.22 E-value=9.3 Score=37.33 Aligned_cols=60 Identities=27% Similarity=0.506 Sum_probs=40.5
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeeccC
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVKSS 87 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~v~~~ 87 (549)
..|||+.+.+.... --|.|.||+||+.-.+|.|-| |...|+. .| .+-=|--||+++|.+.
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 4443331 11 3334777888888763
No 48
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=65.35 E-value=15 Score=39.93 Aligned_cols=40 Identities=20% Similarity=0.269 Sum_probs=30.4
Q ss_pred CCCccCC-CcCCccCcCCCCCCCCCCccccccccccccccccccc
Q 008892 465 KPAYRKD-DFFDTISCNSLNRGTREGQNRFSERMRLDTETFGNFQ 508 (549)
Q Consensus 465 k~~YdK~-sFFD~IScn~~~R~~r~gR~r~~eErklNtETFG~~s 508 (549)
+.+|++. .+|+++.-..-. +.+.++.+++.++..++....
T Consensus 252 ~~~~n~~s~r~~~~~~~~~~----n~~~~~~~~~~~~~~~q~~~~ 292 (361)
T KOG1073|consen 252 PSFYNQQSSRFTTISVSRVS----NTNSRNQEKRGLNNGGQSQQS 292 (361)
T ss_pred Cccccccccccccccccccc----cccccccccccccCCCccccc
Confidence 4678864 888877655543 568999999999998888766
No 49
>KOG2945 consensus Predicted RNA-binding protein [General function prediction only]
Probab=63.67 E-value=5.5 Score=43.19 Aligned_cols=13 Identities=23% Similarity=0.411 Sum_probs=8.3
Q ss_pred CchhhHHHHHHhh
Q 008892 408 TEEFDFEAMNEKF 420 (549)
Q Consensus 408 ~~dFDFesaN~kF 420 (549)
+.+||+.+.+.+.
T Consensus 180 krEf~r~sgsDr~ 192 (365)
T KOG2945|consen 180 KREFDRQSGSDRT 192 (365)
T ss_pred ceeeeeecccccc
Confidence 4678887765543
No 50
>COG4907 Predicted membrane protein [Function unknown]
Probab=51.26 E-value=11 Score=42.19 Aligned_cols=22 Identities=32% Similarity=0.413 Sum_probs=10.7
Q ss_pred CccccceEEEec-CCccceeecc
Q 008892 65 SEKVYEYILFRG-SDIKDLEVKS 86 (549)
Q Consensus 65 s~~vy~yIvFrg-sDIKDL~v~~ 86 (549)
-+++|.|++|.| .-|.-+++.|
T Consensus 53 ieeiysy~~~eG~~y~~~~rd~e 75 (595)
T COG4907 53 IEEIYSYIDAEGYGYITSLRDFE 75 (595)
T ss_pred eeeeeeeeeccccceEEEEeecc
Confidence 345566666665 3344444433
No 51
>KOG3875 consensus Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport]
Probab=49.11 E-value=18 Score=38.94 Aligned_cols=6 Identities=17% Similarity=0.850 Sum_probs=2.8
Q ss_pred CCccCC
Q 008892 466 PAYRKD 471 (549)
Q Consensus 466 ~~YdK~ 471 (549)
+.|+.+
T Consensus 29 p~f~~s 34 (362)
T KOG3875|consen 29 PGFQSS 34 (362)
T ss_pred cccccc
Confidence 345543
No 52
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=48.81 E-value=17 Score=36.79 Aligned_cols=9 Identities=22% Similarity=0.316 Sum_probs=3.5
Q ss_pred HHHHHHhhc
Q 008892 413 FEAMNEKFK 421 (549)
Q Consensus 413 FesaN~kFn 421 (549)
.|.-.-||.
T Consensus 23 ieDlFyKyg 31 (241)
T KOG0105|consen 23 IEDLFYKYG 31 (241)
T ss_pred HHHHHhhhc
Confidence 333333443
No 53
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=48.58 E-value=24 Score=34.94 Aligned_cols=13 Identities=31% Similarity=0.330 Sum_probs=7.4
Q ss_pred hchhhhhhccccc
Q 008892 420 FKKDEVWGYLGKA 432 (549)
Q Consensus 420 FnK~ei~~~lgK~ 432 (549)
+||=.|++.|++.
T Consensus 4 ~N~V~LiGrLg~D 16 (182)
T PRK06958 4 VNKVILVGNLGAD 16 (182)
T ss_pred ccEEEEEEEecCC
Confidence 4555566666553
No 54
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=48.43 E-value=21 Score=32.90 Aligned_cols=28 Identities=25% Similarity=0.195 Sum_probs=11.2
Q ss_pred cccccccccccCCCCCCCCCCCCCCCCC
Q 008892 500 DTETFGNFQQRANQGYGGYVAGRGANYR 527 (549)
Q Consensus 500 NtETFG~~s~r~rgg~ggrG~gRGg~gr 527 (549)
|---|+....+.-|+..+||+.|..+||
T Consensus 79 nAPmFkk~~~~~~g~~~~RG~~~~~~gr 106 (119)
T KOG3172|consen 79 NAPMFKKGKSRSLGGGPGRGRARRARGR 106 (119)
T ss_pred cCcccccccCCcCCCCCCccccccccCC
Confidence 3334554433333433344444433333
No 55
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=44.67 E-value=53 Score=29.09 Aligned_cols=54 Identities=19% Similarity=0.244 Sum_probs=37.6
Q ss_pred EeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008892 20 LISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (549)
Q Consensus 20 LISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~ 83 (549)
|..+.+..|+|+|..+|.-= -|.|.|+.-+= .+.. ....++.|+.||+.|.-+.
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 2335788999999997653
No 56
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=40.82 E-value=21 Score=40.99 Aligned_cols=21 Identities=29% Similarity=0.490 Sum_probs=15.3
Q ss_pred CCCCCchhhHHHHHHhhchhhhh
Q 008892 404 TTKFTEEFDFEAMNEKFKKDEVW 426 (549)
Q Consensus 404 ~~kf~~dFDFesaN~kFnK~ei~ 426 (549)
.-.|.-|-||+..-++| +.|.
T Consensus 384 L~vFk~dp~f~ene~ky--daik 404 (739)
T KOG2140|consen 384 LGVFKKDPNFEENEEKY--DAIK 404 (739)
T ss_pred hcccccCccHHHHHHHH--HHHH
Confidence 44677888888888888 4554
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=40.53 E-value=55 Score=27.18 Aligned_cols=58 Identities=21% Similarity=0.287 Sum_probs=42.8
Q ss_pred ccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008892 13 YIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (549)
Q Consensus 13 ~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~ 83 (549)
.||+++++.+-.+=++||.|...|..-..|.|+- -+.++++ ..-|+.+.+-+=|+|++
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=40.42 E-value=24 Score=30.77 Aligned_cols=62 Identities=29% Similarity=0.434 Sum_probs=47.4
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecc--cCCCCCCCCCCCCCccccceEEEecCCccce
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFG--TEGRKKDGPQVLPSEKVYEYILFRGSDIKDL 82 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfG--TEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL 82 (549)
+.-||+||-+|=|+|-.++|+|...|-=- .+.|++|.-|- +|||+- +-.+.|+..|..|-=|
T Consensus 13 DkcIgski~iimksdkE~~GtL~GFDd~V-NmvLeDvtEye~~~egr~~---------tk~~~iLLnGNni~mL 76 (84)
T KOG1775|consen 13 DKCIGSKIWIIMKSDKEFVGTLVGFDDFV-NMVLEDVTEYEITPEGRRM---------TKLDQILLNGNNITML 76 (84)
T ss_pred HHhcCceEEEEEccCceeeeEEechHHHH-HHHHHhhhheeeCCCccee---------eeeeeeeecCCcEEEE
Confidence 34699999999999999999999877432 35688887774 355532 3567899999988654
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=38.64 E-value=51 Score=25.30 Aligned_cols=28 Identities=11% Similarity=0.137 Sum_probs=22.6
Q ss_pred ccCceeEEeecCCeeEEEEeeeecCCCCe
Q 008892 13 YIGSFISLISKYEIRYEGVLYHLNVGDST 41 (549)
Q Consensus 13 ~IGs~isLISk~~IRYeGiL~~Id~~~sT 41 (549)
.||+.|+|.. .+-.|+|+...||.+-.=
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L 28 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGAL 28 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSEE
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCEE
Confidence 4899999999 555589999999876443
No 60
>KOG2295 consensus C2H2 Zn-finger protein [General function prediction only]
Probab=37.65 E-value=45 Score=38.33 Aligned_cols=7 Identities=43% Similarity=0.876 Sum_probs=3.6
Q ss_pred CCCCCCC
Q 008892 511 ANQGYGG 517 (549)
Q Consensus 511 ~rgg~gg 517 (549)
.||++||
T Consensus 576 ~r~~~gG 582 (648)
T KOG2295|consen 576 NRGPYGG 582 (648)
T ss_pred cCCCCCC
Confidence 3555555
No 61
>PRK02001 hypothetical protein; Validated
Probab=36.13 E-value=1.1e+02 Score=29.42 Aligned_cols=65 Identities=28% Similarity=0.276 Sum_probs=43.3
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEecccee-cccCCCCCCCCCCCCCccccceEEEecCCccceeec
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKS-FGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVK 85 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrs-fGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~v~ 85 (549)
..|||.+|.+..+..-+|+|+|..+|-+ .|+|. |.- =+-++++. . ....+-+.|.-++|+..+++
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--K-----VTVEKEETITYDDIKEAKVI 151 (152)
T ss_pred HHhCCCEEEEEECCCCEEEEEEEEEeCC--EEEEE-Eccccccccccc--c-----cccceeEEEEhHheeeEEEe
Confidence 3589999999998899999999999855 77774 220 01122221 1 12355677788888877664
No 62
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=35.49 E-value=53 Score=27.70 Aligned_cols=33 Identities=21% Similarity=0.309 Sum_probs=27.7
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEecc
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKN 46 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~n 46 (549)
.++||+++.+-+-.++ ++|+|..+.++ .|.|+.
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 63
>PRK14644 hypothetical protein; Provisional
Probab=35.04 E-value=60 Score=30.57 Aligned_cols=33 Identities=36% Similarity=0.314 Sum_probs=27.7
Q ss_pred CCccCceeEEeecCC----eeEEEEeeeecCCCCeEEec
Q 008892 11 ESYIGSFISLISKYE----IRYEGVLYHLNVGDSTIGLK 45 (549)
Q Consensus 11 ~~~IGs~isLISk~~----IRYeGiL~~Id~~~sTi~L~ 45 (549)
..|||.+|.+..+.. -+|+|+|..+|-+ +|+|.
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 468999999988776 7899999999854 78886
No 64
>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=34.73 E-value=36 Score=28.46 Aligned_cols=24 Identities=29% Similarity=0.401 Sum_probs=21.4
Q ss_pred EEEEeeeecCCCCeEEeccceecc
Q 008892 28 YEGVLYHLNVGDSTIGLKNVKSFG 51 (549)
Q Consensus 28 YeGiL~~Id~~~sTi~L~nVrsfG 51 (549)
-||+|..||.+.-||+|.+=++|=
T Consensus 5 veG~I~~id~~~~titLdDGksy~ 28 (61)
T PF07076_consen 5 VEGTIKSIDPETMTITLDDGKSYK 28 (61)
T ss_pred ceEEEEEEcCCceEEEecCCCEEE
Confidence 489999999999999999977764
No 65
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=34.10 E-value=47 Score=34.81 Aligned_cols=8 Identities=50% Similarity=1.087 Sum_probs=3.8
Q ss_pred hhccccccc
Q 008892 426 WGYLGKAKQ 434 (549)
Q Consensus 426 ~~~lgK~~~ 434 (549)
|+ +|+|++
T Consensus 90 W~-lG~k~~ 97 (271)
T COG1512 90 WK-LGDKAQ 97 (271)
T ss_pred cC-CCcccc
Confidence 44 554444
No 66
>PRK14642 hypothetical protein; Provisional
Probab=33.76 E-value=1.1e+02 Score=30.78 Aligned_cols=71 Identities=15% Similarity=0.264 Sum_probs=42.9
Q ss_pred CCccCceeEEeec-------------CCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecC
Q 008892 11 ESYIGSFISLISK-------------YEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGS 77 (549)
Q Consensus 11 ~~~IGs~isLISk-------------~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgs 77 (549)
..|||.+|.|..+ ..-+|+|+|..+|-+.-+|.+.. |-=+-+|-...-..+|. +-.-..|--+
T Consensus 96 ~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~~i~l~~~~-~~~~k~g~~~~k~~~~~---~~~~~~~~~~ 171 (197)
T PRK14642 96 ERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESGGWQIVWSD-EPPVKPGQRVSKKRVPA---PLQALGFTLD 171 (197)
T ss_pred HHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCCEEEEEEee-cccCCCccccccccccc---cceeEEeehh
Confidence 4589999999887 56789999999987633343332 11112221100112332 3444668889
Q ss_pred Cccceeec
Q 008892 78 DIKDLEVK 85 (549)
Q Consensus 78 DIKDL~v~ 85 (549)
|||+-+|.
T Consensus 172 eik~a~l~ 179 (197)
T PRK14642 172 ELREARLA 179 (197)
T ss_pred heeeEEEE
Confidence 99998774
No 67
>PRK14631 hypothetical protein; Provisional
Probab=33.47 E-value=64 Score=31.63 Aligned_cols=35 Identities=17% Similarity=0.393 Sum_probs=29.7
Q ss_pred CCccCceeEEeec----CCeeEEEEeeeecCCCCeEEec
Q 008892 11 ESYIGSFISLISK----YEIRYEGVLYHLNVGDSTIGLK 45 (549)
Q Consensus 11 ~~~IGs~isLISk----~~IRYeGiL~~Id~~~sTi~L~ 45 (549)
..|+|.+|.|..+ ..-+|.|+|..+|.++.+|+|.
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 68
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=33.28 E-value=42 Score=35.14 Aligned_cols=12 Identities=17% Similarity=0.094 Sum_probs=5.8
Q ss_pred cccccccCCCCC
Q 008892 362 KKDMAAMLPSSF 373 (549)
Q Consensus 362 ~kd~~~~~~~s~ 373 (549)
+.++.||.+.+.
T Consensus 63 ~~QiaVv~vpSt 74 (271)
T COG1512 63 GAQIAVVTVPST 74 (271)
T ss_pred CCeEEEEEecCC
Confidence 345555554433
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=32.47 E-value=77 Score=29.35 Aligned_cols=31 Identities=26% Similarity=0.406 Sum_probs=23.2
Q ss_pred CccCceeEEeec----CCeeEEEEeeeecCCCCeEEe
Q 008892 12 SYIGSFISLISK----YEIRYEGVLYHLNVGDSTIGL 44 (549)
Q Consensus 12 ~~IGs~isLISk----~~IRYeGiL~~Id~~~sTi~L 44 (549)
.|||.+|.+..+ ..-+|+|+|..++-+ +|+|
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 70
>PRK14638 hypothetical protein; Provisional
Probab=31.74 E-value=65 Score=30.73 Aligned_cols=33 Identities=18% Similarity=0.343 Sum_probs=28.2
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEec
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLK 45 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~ 45 (549)
..|+|++|.+..+..-+|+|+|..+|-+ +|+|.
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 71
>COG4907 Predicted membrane protein [Function unknown]
Probab=30.39 E-value=39 Score=38.23 Aligned_cols=13 Identities=8% Similarity=0.153 Sum_probs=6.5
Q ss_pred eEEEEeeeecCCC
Q 008892 27 RYEGVLYHLNVGD 39 (549)
Q Consensus 27 RYeGiL~~Id~~~ 39 (549)
..|+|...||.|.
T Consensus 52 ~ieeiysy~~~eG 64 (595)
T COG4907 52 EIEEIYSYIDAEG 64 (595)
T ss_pred eeeeeeeeeeccc
Confidence 3455555555553
No 72
>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=30.23 E-value=1.5e+02 Score=25.61 Aligned_cols=61 Identities=20% Similarity=0.350 Sum_probs=39.5
Q ss_pred CccCce--eEE--eecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccce
Q 008892 12 SYIGSF--ISL--ISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDL 82 (549)
Q Consensus 12 ~~IGs~--isL--ISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL 82 (549)
.|+.++ |.+ .-+.+..|+|+|..+|.-= -|.|.|+.=+ ... +. ....++.|+.||+.|.-|
T Consensus 13 ~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~m-NlvL~d~~E~----~~~-~~----~~~~lG~iliRGnnV~~I 77 (79)
T cd01718 13 RFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYM-NLVLDDAEEV----HLK-TK----TRKPLGRILLKGDNITLI 77 (79)
T ss_pred HHHccCcEEEEEEEeCCCcEEEEEEEEEccce-eEEEcCEEEE----ecC-Cc----eEeEcCcEEEeCCEEEEE
Confidence 355553 333 3459999999999999774 5888886322 111 11 112468899999988643
No 73
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=29.70 E-value=29 Score=30.01 Aligned_cols=62 Identities=23% Similarity=0.371 Sum_probs=41.6
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCcccee
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLE 83 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~ 83 (549)
..+||+++.+-=.+++-|.|+|..||-== -|+|+.- |--- ++ +. ...|.-...||+.|--|.
T Consensus 12 ~~iiGr~V~VKl~sgvdyrG~l~~lDgym-NiaLe~t-----ee~~-ng-ql---~n~ygdaFirGnnVlyIs 73 (77)
T KOG1783|consen 12 KAIIGRTVVVKLNSGVDYRGTLVCLDGYM-NIALEST-----EEYV-NG-QL---KNKYGDAFIRGNNVLYIS 73 (77)
T ss_pred HHHhCCeEEEEecCCccccceehhhhhHH-HHHHHHH-----HHHh-cC-cc---cccccceeeccccEEEEE
Confidence 46899999999999999999999998541 2445442 2111 11 11 235677778888876543
No 74
>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=28.14 E-value=62 Score=34.71 Aligned_cols=7 Identities=14% Similarity=0.207 Sum_probs=3.4
Q ss_pred Ccccccc
Q 008892 340 TPGQLVT 346 (549)
Q Consensus 340 tpgql~~ 346 (549)
.++|++|
T Consensus 122 ~~~q~fq 128 (316)
T PF12287_consen 122 SQPQVFQ 128 (316)
T ss_pred Ccccccc
Confidence 3455555
No 75
>PRK14639 hypothetical protein; Provisional
Probab=27.71 E-value=93 Score=29.36 Aligned_cols=35 Identities=20% Similarity=0.447 Sum_probs=29.3
Q ss_pred CCccCceeEEeecCCeeEEEEeeeecCCCCeEEeccc
Q 008892 11 ESYIGSFISLISKYEIRYEGVLYHLNVGDSTIGLKNV 47 (549)
Q Consensus 11 ~~~IGs~isLISk~~IRYeGiL~~Id~~~sTi~L~nV 47 (549)
..|+|.+|.+..+..-+|+|+|..+|-+ .|+|.++
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 4689999999988888999999998776 7777654
No 76
>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]
Probab=27.54 E-value=84 Score=34.27 Aligned_cols=8 Identities=25% Similarity=0.621 Sum_probs=3.7
Q ss_pred ccCCCcCC
Q 008892 468 YRKDDFFD 475 (549)
Q Consensus 468 YdK~sFFD 475 (549)
|+-.+|-.
T Consensus 136 ~agkdf~g 143 (351)
T KOG1995|consen 136 FAGKDFCG 143 (351)
T ss_pred hccccccC
Confidence 44445544
No 77
>PRK14633 hypothetical protein; Provisional
Probab=26.35 E-value=1e+02 Score=29.39 Aligned_cols=53 Identities=21% Similarity=0.391 Sum_probs=37.3
Q ss_pred CCccCceeEEeec----CCeeEEEEeeeecCCCCeEEeccceecccCCCCCCCCCCCCCccccceEEEecCCccceeec
Q 008892 11 ESYIGSFISLISK----YEIRYEGVLYHLNVGDSTIGLKNVKSFGTEGRKKDGPQVLPSEKVYEYILFRGSDIKDLEVK 85 (549)
Q Consensus 11 ~~~IGs~isLISk----~~IRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~~Ipps~~vy~yIvFrgsDIKDL~v~ 85 (549)
..|||++|.+..+ ..-+|+|+|..++-+ +|+|.. + +| +-+.|.-.+||..++.
T Consensus 90 ~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~--~i~l~~-~----~~---------------~~~~i~~~~I~ka~l~ 146 (150)
T PRK14633 90 QALVGFNVKAVTLAPVGSQTKFKGVLERVEGN--NVILNL-E----DG---------------KEISFDFDELKKLRVS 146 (150)
T ss_pred HHhCCCeEEEEEecccCCcEEEEEEEEEEeCC--EEEEEE-c----CC---------------cEEEEEhHHeeeEEEe
Confidence 4689999999884 568899999998654 777752 1 11 1256677778777663
No 78
>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=25.59 E-value=69 Score=31.82 Aligned_cols=15 Identities=53% Similarity=1.108 Sum_probs=8.1
Q ss_pred CCCCCCCCCCCCCCC
Q 008892 532 GGRRYGYGGRGHGGN 546 (549)
Q Consensus 532 g~~g~g~~grg~g~~ 546 (549)
|.-|+||+|||-|.|
T Consensus 199 G~Egrgyrgrgeggg 213 (215)
T PF05084_consen 199 GNEGRGYRGRGEGGG 213 (215)
T ss_pred cccccccCCCCCCCC
Confidence 334556666665544
No 79
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=22.90 E-value=1.1e+02 Score=34.76 Aligned_cols=29 Identities=24% Similarity=0.297 Sum_probs=25.4
Q ss_pred ccccCCCCCCchhhHHHHHHhhchhhhhh
Q 008892 399 QSQYSTTKFTEEFDFEAMNEKFKKDEVWG 427 (549)
Q Consensus 399 ~~~~~~~kf~~dFDFesaN~kFnK~ei~~ 427 (549)
.++-++.+|+.....++|.|+.||-++.+
T Consensus 85 ~rGcavVEFk~~E~~qKa~E~lnk~~~~G 113 (608)
T KOG4212|consen 85 ARGCAVVEFKDPENVQKALEKLNKYEVNG 113 (608)
T ss_pred cCCceEEEeeCHHHHHHHHHHhhhccccC
Confidence 56778999999999999999999988753
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=22.47 E-value=1.4e+02 Score=21.07 Aligned_cols=31 Identities=13% Similarity=0.161 Sum_probs=25.6
Q ss_pred CceeEEeecCCeeEEEEeeeecCCCCeEEec
Q 008892 15 GSFISLISKYEIRYEGVLYHLNVGDSTIGLK 45 (549)
Q Consensus 15 Gs~isLISk~~IRYeGiL~~Id~~~sTi~L~ 45 (549)
|..+.+|+=..--.+|++..||.+..+|.++
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
>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=22.40 E-value=81 Score=36.46 Aligned_cols=15 Identities=27% Similarity=0.189 Sum_probs=10.8
Q ss_pred CCCCCccccccccCC
Q 008892 290 SCPDTKATEAQISGR 304 (549)
Q Consensus 290 s~~~~~~i~~~is~K 304 (549)
|..++-.|+--.+||
T Consensus 259 sgrdvigIAktgSgk 273 (731)
T KOG0339|consen 259 SGRDVIGIAKTGSGK 273 (731)
T ss_pred ccccchheeeccCcc
Confidence 456777777777777
No 82
>KOG3910 consensus Helix loop helix transcription factor [Transcription]
Probab=21.96 E-value=1.3e+03 Score=26.92 Aligned_cols=24 Identities=17% Similarity=0.032 Sum_probs=18.6
Q ss_pred CCCCCCcccCCCCCCCCCCCCCCCCC
Q 008892 170 PSFPLPIYWQGYNGPSNNISPTPFQS 195 (549)
Q Consensus 170 sglaMPmywQGYy~p~~g~p~~~qq~ 195 (549)
+.+.|+-||-||-+ |..|||||..
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 5567888843
No 83
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.60 E-value=1.4e+02 Score=28.95 Aligned_cols=33 Identities=15% Similarity=0.335 Sum_probs=28.0
Q ss_pred CCccCceeEEee----cCCeeEEEEeeeecCCCCeEEec
Q 008892 11 ESYIGSFISLIS----KYEIRYEGVLYHLNVGDSTIGLK 45 (549)
Q Consensus 11 ~~~IGs~isLIS----k~~IRYeGiL~~Id~~~sTi~L~ 45 (549)
..|+|.+|.|.. ...-+|+|+|..+|.+. |+|.
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
Done!