Query 029223
Match_columns 197
No_of_seqs 197 out of 488
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 09:28:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029223.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029223hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3262 H/ACA small nucleolar 100.0 3.2E-53 6.9E-58 353.8 14.0 195 1-197 1-213 (215)
2 COG3277 GAR1 RNA-binding prote 99.9 5.4E-24 1.2E-28 162.5 9.0 92 50-141 1-92 (98)
3 PRK13149 H/ACA RNA-protein com 99.9 3.6E-23 7.8E-28 150.1 8.6 72 50-125 1-73 (73)
4 PF04410 Gar1: Gar1/Naf1 RNA b 99.9 5.5E-22 1.2E-26 161.3 7.3 99 41-142 14-115 (154)
5 KOG3262 H/ACA small nucleolar 98.8 2.9E-08 6.2E-13 84.1 9.5 121 6-134 12-143 (215)
6 KOG3428 Small nuclear ribonucl 98.5 1.6E-07 3.5E-12 73.0 4.9 67 64-136 6-79 (109)
7 KOG2236 Uncharacterized conser 98.3 4.1E-07 8.9E-12 85.5 3.4 78 49-126 207-287 (483)
8 PLN03134 glycine-rich RNA-bind 96.4 0.0022 4.7E-08 51.6 2.3 84 45-141 31-117 (144)
9 cd01724 Sm_D1 The eukaryotic S 94.1 0.11 2.3E-06 39.1 4.8 64 67-136 8-79 (90)
10 TIGR01661 ELAV_HUD_SF ELAV/HuD 94.0 0.011 2.4E-07 52.0 -0.8 79 49-140 270-351 (352)
11 TIGR01648 hnRNP-R-Q heterogene 92.7 0.11 2.5E-06 50.8 3.7 26 47-72 232-257 (578)
12 cd01721 Sm_D3 The eukaryotic S 91.4 0.29 6.3E-06 34.8 3.7 39 64-107 4-43 (70)
13 TIGR01659 sex-lethal sex-letha 91.3 0.13 2.9E-06 47.0 2.3 38 46-83 191-228 (346)
14 TIGR01659 sex-lethal sex-letha 90.7 0.057 1.2E-06 49.4 -0.7 43 43-85 102-144 (346)
15 KOG3172 Small nuclear ribonucl 90.1 1.9 4E-05 34.1 7.3 50 80-129 20-77 (119)
16 KOG3293 Small nuclear ribonucl 90.0 1 2.2E-05 36.3 5.9 30 79-108 16-46 (134)
17 KOG0116 RasGAP SH3 binding pro 89.8 0.56 1.2E-05 44.4 5.1 25 49-73 289-313 (419)
18 KOG0121 Nuclear cap-binding pr 89.1 0.14 2.9E-06 42.0 0.3 28 46-73 34-61 (153)
19 cd01725 LSm2 The eukaryotic Sm 88.1 0.77 1.7E-05 33.7 3.8 30 79-108 15-45 (81)
20 TIGR01649 hnRNP-L_PTB hnRNP-L/ 86.5 0.21 4.6E-06 47.0 0.0 35 47-81 1-35 (481)
21 cd01733 LSm10 The eukaryotic S 83.8 1.6 3.5E-05 31.8 3.6 30 79-108 23-53 (78)
22 cd01723 LSm4 The eukaryotic Sm 83.6 1.8 3.9E-05 31.2 3.7 37 66-107 7-44 (76)
23 KOG0415 Predicted peptidyl pro 83.4 0.72 1.6E-05 43.4 2.0 45 42-86 233-277 (479)
24 TIGR01661 ELAV_HUD_SF ELAV/HuD 82.4 0.38 8.3E-06 42.3 -0.2 38 47-84 2-39 (352)
25 TIGR01642 U2AF_lg U2 snRNP aux 79.5 0.89 1.9E-05 42.2 1.2 27 46-72 173-199 (509)
26 PF14578 GTP_EFTU_D4: Elongati 79.3 9 0.0002 28.5 6.3 73 45-124 2-81 (81)
27 PF05239 PRC: PRC-barrel domai 76.9 5.3 0.00012 27.7 4.3 23 76-98 10-32 (79)
28 TIGR01649 hnRNP-L_PTB hnRNP-L/ 76.5 0.62 1.3E-05 43.9 -0.8 40 45-84 391-432 (481)
29 KOG4454 RNA binding protein (R 71.3 0.36 7.8E-06 42.7 -3.5 31 46-76 7-37 (267)
30 PHA01365 hypothetical protein 69.8 4.6 0.0001 30.4 2.6 63 63-128 10-78 (91)
31 PF00076 RRM_1: RNA recognitio 68.9 1.3 2.9E-05 29.1 -0.4 32 51-82 1-32 (70)
32 PRK13828 rimM 16S rRNA-process 67.9 22 0.00047 29.0 6.5 33 75-107 85-117 (161)
33 TIGR01648 hnRNP-R-Q heterogene 67.5 1.8 3.9E-05 42.6 0.1 35 49-83 59-93 (578)
34 KOG0149 Predicted RNA-binding 67.4 1.7 3.7E-05 38.5 -0.1 52 49-108 13-64 (247)
35 PLN03121 nucleic acid binding 67.1 2.1 4.5E-05 38.0 0.4 52 47-109 4-55 (243)
36 KOG0122 Translation initiation 66.1 2.1 4.5E-05 38.3 0.2 81 47-138 188-269 (270)
37 cd04479 RPA3 RPA3: A subfamily 65.6 16 0.00034 27.6 4.9 55 47-107 15-72 (101)
38 KOG4205 RNA-binding protein mu 64.7 4.4 9.6E-05 37.0 2.0 42 47-88 96-137 (311)
39 KOG0148 Apoptosis-promoting RN 63.2 1.7 3.6E-05 39.6 -1.0 35 49-83 7-41 (321)
40 KOG0113 U1 small nuclear ribon 61.3 9.2 0.0002 35.2 3.4 91 44-142 97-193 (335)
41 TIGR02273 16S_RimM 16S rRNA pr 58.3 17 0.00037 29.4 4.3 33 75-107 100-132 (165)
42 cd01726 LSm6 The eukaryotic Sm 58.2 9.3 0.0002 26.7 2.3 37 65-106 5-42 (67)
43 COG0724 RNA-binding proteins ( 58.2 2.2 4.7E-05 33.9 -1.1 37 48-84 115-151 (306)
44 COG3881 PRC-barrel domain cont 57.4 68 0.0015 27.2 7.6 65 50-114 52-127 (176)
45 TIGR01642 U2AF_lg U2 snRNP aux 56.5 3.4 7.3E-05 38.4 -0.2 36 47-82 294-329 (509)
46 PRK00122 rimM 16S rRNA-process 55.8 21 0.00047 29.1 4.5 32 75-106 105-136 (172)
47 KOG0127 Nucleolar protein fibr 55.6 4.3 9.3E-05 40.2 0.3 81 47-138 291-378 (678)
48 PRK14592 rimM 16S rRNA-process 54.8 23 0.0005 28.9 4.5 32 75-106 97-128 (165)
49 PF05284 DUF736: Protein of un 53.2 49 0.0011 25.6 5.8 59 53-113 18-81 (107)
50 PF02470 MCE: mce related prot 52.3 79 0.0017 22.1 7.1 54 75-130 16-71 (81)
51 cd01731 archaeal_Sm1 The archa 51.0 21 0.00046 24.8 3.2 36 66-106 6-42 (68)
52 PF10246 MRP-S35: Mitochondria 50.8 22 0.00047 27.9 3.5 28 41-68 16-43 (104)
53 PRK14591 rimM 16S rRNA-process 50.8 38 0.00082 27.8 5.1 33 75-107 105-137 (169)
54 KOG0131 Splicing factor 3b, su 50.5 1.5 3.1E-05 37.8 -3.3 40 48-87 9-48 (203)
55 PF08669 GCV_T_C: Glycine clea 49.5 88 0.0019 22.5 6.5 27 70-96 29-55 (95)
56 PRK13829 rimM 16S rRNA-process 49.1 39 0.00084 27.6 4.9 34 75-109 94-127 (162)
57 KOG0105 Alternative splicing f 47.4 41 0.0009 29.4 5.0 71 47-134 5-79 (241)
58 TIGR01622 SF-CC1 splicing fact 46.5 5.3 0.00011 36.6 -0.6 28 45-72 183-210 (457)
59 COG1958 LSM1 Small nuclear rib 45.6 20 0.00043 25.7 2.4 49 79-128 21-73 (79)
60 COG0806 RimM RimM protein, req 44.0 59 0.0013 27.3 5.3 33 75-107 106-138 (174)
61 KOG0109 RNA-binding protein LA 43.5 8.9 0.00019 35.3 0.4 38 44-81 74-111 (346)
62 TIGR01622 SF-CC1 splicing fact 42.7 7.8 0.00017 35.5 -0.1 36 47-82 88-123 (457)
63 TIGR01645 half-pint poly-U bin 41.9 8.5 0.00018 38.3 -0.0 37 47-83 106-142 (612)
64 PF08661 Rep_fac-A_3: Replicat 38.0 60 0.0013 24.5 4.2 49 48-101 19-72 (109)
65 PRK14590 rimM 16S rRNA-process 37.5 61 0.0013 26.8 4.4 32 75-106 102-134 (171)
66 PF01176 eIF-1a: Translation i 37.5 1.1E+02 0.0023 21.2 5.0 27 83-112 1-27 (65)
67 cd01722 Sm_F The eukaryotic Sm 37.4 26 0.00056 24.5 1.9 27 79-105 15-42 (68)
68 PRK00737 small nuclear ribonuc 36.6 30 0.00065 24.5 2.1 38 64-106 8-46 (72)
69 PRK14594 rimM 16S rRNA-process 36.4 64 0.0014 26.4 4.4 32 75-107 102-133 (166)
70 PF01423 LSM: LSM domain ; In 35.4 32 0.00068 23.4 2.1 29 79-107 12-41 (67)
71 PRK14593 rimM 16S rRNA-process 35.4 1.1E+02 0.0025 25.3 5.8 33 75-108 109-141 (184)
72 TIGR01628 PABP-1234 polyadenyl 34.2 9 0.00019 36.5 -1.2 36 50-85 2-37 (562)
73 KOG4210 Nuclear localization s 34.1 19 0.00041 32.3 1.0 86 44-142 181-268 (285)
74 KOG0108 mRNA cleavage and poly 33.0 11 0.00025 35.9 -0.6 46 43-88 12-58 (435)
75 KOG4205 RNA-binding protein mu 33.0 25 0.00055 32.1 1.6 23 47-69 5-27 (311)
76 TIGR01645 half-pint poly-U bin 32.2 12 0.00025 37.4 -0.8 37 47-83 203-239 (612)
77 PHA02979 hypothetical protein; 31.0 18 0.00038 29.1 0.2 35 55-96 5-39 (140)
78 PLN03213 repressor of silencin 30.8 12 0.00027 36.9 -0.8 37 47-83 9-45 (759)
79 PLN03120 nucleic acid binding 30.5 21 0.00046 32.0 0.6 37 48-84 4-40 (260)
80 KOG0127 Nucleolar protein fibr 30.0 25 0.00054 35.0 1.1 54 49-112 6-61 (678)
81 COG1097 RRP4 RNA-binding prote 29.8 2.1E+02 0.0045 25.5 6.7 22 84-105 65-91 (239)
82 PF11380 DUF3184: Protein of u 29.7 30 0.00065 34.7 1.5 39 71-109 81-119 (691)
83 KOG1190 Polypyrimidine tract-b 29.2 21 0.00047 34.3 0.5 67 42-124 19-98 (492)
84 cd00600 Sm_like The eukaryotic 27.5 80 0.0017 20.9 3.0 28 79-106 10-38 (63)
85 PRK09010 single-stranded DNA-b 26.6 94 0.002 26.1 3.8 12 48-59 7-18 (177)
86 PRK12442 translation initiatio 25.5 1.1E+02 0.0025 23.1 3.7 8 89-96 11-18 (87)
87 KOG1004 Exosomal 3'-5' exoribo 25.5 1.2E+02 0.0027 26.7 4.4 10 115-124 108-117 (230)
88 TIGR02383 Hfq RNA chaperone Hf 25.5 30 0.00064 24.6 0.5 32 62-96 5-37 (61)
89 PF07290 DUF1449: Protein of u 25.2 85 0.0018 27.0 3.4 32 89-125 156-187 (202)
90 TIGR00523 eIF-1A eukaryotic/ar 24.4 2E+02 0.0043 22.0 5.0 24 84-110 18-41 (99)
91 smart00651 Sm snRNP Sm protein 24.4 73 0.0016 21.4 2.4 27 79-105 12-39 (67)
92 COG1532 Predicted RNA-binding 23.2 1.4E+02 0.003 21.0 3.5 36 59-96 13-48 (57)
93 KOG3973 Uncharacterized conser 22.5 2.3E+02 0.005 27.1 5.8 6 147-152 334-339 (465)
94 TIGR01628 PABP-1234 polyadenyl 22.5 27 0.00058 33.3 -0.2 35 48-82 88-122 (562)
95 cd00226 PRCH Photosynthetic re 22.4 2.9E+02 0.0063 24.7 6.2 34 75-108 148-184 (246)
96 smart00652 eIF1a eukaryotic tr 22.4 1.6E+02 0.0035 21.6 4.0 13 84-96 4-16 (83)
97 PF09475 Dot_icm_IcmQ: Dot/Icm 22.1 30 0.00064 29.5 0.0 50 76-135 93-142 (179)
98 PF14031 D-ser_dehydrat: Putat 22.0 2.6E+02 0.0056 20.7 5.1 29 98-128 51-79 (94)
99 cd01732 LSm5 The eukaryotic Sm 21.6 63 0.0014 23.4 1.6 37 64-105 7-44 (76)
100 COG5436 Predicted integral mem 21.3 89 0.0019 26.5 2.7 42 47-88 62-103 (182)
101 KOG0148 Apoptosis-promoting RN 21.2 41 0.00089 30.8 0.7 42 50-91 64-105 (321)
102 cd04717 BAH_polybromo BAH, or 20.6 1.8E+02 0.0039 22.1 4.1 20 86-105 21-41 (121)
103 PRK06341 single-stranded DNA-b 20.5 1.5E+02 0.0033 24.6 3.9 11 48-58 6-16 (166)
104 COG0468 RecA RecA/RadA recombi 20.3 35 0.00076 30.6 0.1 45 87-135 58-105 (279)
105 KOG0908 Thioredoxin-like prote 20.2 87 0.0019 28.5 2.5 43 54-96 155-197 (288)
No 1
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.2e-53 Score=353.81 Aligned_cols=195 Identities=65% Similarity=1.116 Sum_probs=139.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCC-CCCCCCCCCCcceEEeeceeeeccCceEecccccccCcc
Q 029223 1 MRPPRGGGGFRGGRDGGRGGRGG---GRFGGGGRGGGGRG-GFGFRDEGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYF 76 (197)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~gg~~gg~gg~-~~g~~~~gPPs~vl~lG~~sh~ce~dlV~K~~~~~VP~~ 76 (197)
|+|||++++++++++ =+++.++ +.|.++..-+|+++ ++.++|+.||++|++|++|+|+||+|||||+++++||||
T Consensus 1 ~~~~rgggg~~g~~g-fRgg~ggg~~gg~rgg~g~grgg~~~~~~~d~gpp~evvelg~flh~Cegd~Vck~~~~kIPyf 79 (215)
T KOG3262|consen 1 GGGPRGGGGGGGGGG-FRGGGGGGRGGGFRGGNGFGRGGRGGRGFQDQGPPEEVVELGKFLHMCEGDLVCKLTNKKIPYF 79 (215)
T ss_pred CCCCcCCCCCCCCCC-cccCCCCCCCCCcccCcccccCCcccCCcccCCCchhhhhhhhhhhhcCCceEEeeccccCCCC
Confidence 788998766655532 1221111 12222221123321 455789999999999999999999999999999999999
Q ss_pred cceEEccCCeeeeeeeEEecccCCceeEEeecCCccccccccCcEEEEcCCCCCcCCccCCCCCCCCCC----------C
Q 029223 77 NAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFLPQPKGQAQA----------G 146 (197)
Q Consensus 77 na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~d~v~a~s~~~GdklyIdp~klLPLdrflPkpk~~~g~----------g 146 (197)
||||||||++|||||||||+|||++|+||||+|.|+|+||+++||||||++|||||++|||+|....+. +
T Consensus 80 NAPIylenk~qIGKVDEIfG~i~d~~fsIK~~dgv~assfk~g~k~fi~p~KllPl~RFLP~p~~~kk~~~~~~~~~~~g 159 (215)
T KOG3262|consen 80 NAPIYLENKEQIGKVDEIFGPINDVHFSIKPSDGVQASSFKPGDKLFIDPDKLLPLDRFLPQPVGPKKPKGADRIKPGPG 159 (215)
T ss_pred CCceeecchhhhcchhhhcccccccEEEEecCCCceeecccCCCeEEecccccCcHhhcCCCCCCCCCcccccccCCCCC
Confidence 999999999999999999999999999999999999999999999999999999999999987533211 2
Q ss_pred CCCCCCC---CCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 029223 147 ARGGRGG---GGFRGRGG-GRGGGRGRGGGGGGFRGRGGPPRGGRGGGFRGRGRF 197 (197)
Q Consensus 147 grGggrg---~~~ggrgg-~~g~~~g~f~~~g~~~~~~~~~~g~~~~~~~~~~~~ 197 (197)
+++++++ .++++.++ +|++.+++|++.++.++++-+ |++.+++|++++|.
T Consensus 160 g~gg~rGgRg~~rGg~~grGrgg~~Gg~rgggg~rGG~~~-Rgg~ggg~rgrgR~ 213 (215)
T KOG3262|consen 160 GRGGGRGGRGGGRGGFGGRGRGGGGGGFRGGGGSRGGFRG-RGGHGGGFRGRGRG 213 (215)
T ss_pred CCCcCcCCCCCCcCCCCCCCCCCCCCcccCCCCCCCCccc-cCCCCCCCCCCCCC
Confidence 2222222 11222111 122233455555444444333 78888888887763
No 2
>COG3277 GAR1 RNA-binding protein involved in rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=5.4e-24 Score=162.52 Aligned_cols=92 Identities=38% Similarity=0.637 Sum_probs=86.9
Q ss_pred eEEeeceeeeccCceEecccccccCcccceEEccCCeeeeeeeEEecccCCceeEEeecCCccccccccCcEEEEcCCCC
Q 029223 50 VVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKL 129 (197)
Q Consensus 50 vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~d~v~a~s~~~GdklyIdp~kl 129 (197)
++.||+|+|.|+.++||...+..+|++||+|||++.++||+|+|||||||++|++||+++.+...+.+++|.+||.+++|
T Consensus 1 m~~lG~vlh~~~~g~vi~~~~~~iP~l~~~V~~~~~k~IG~V~dVfGPv~~PY~~Vkp~~~~~~~~~~vg~~lYi~~~k~ 80 (98)
T COG3277 1 MKRLGKVLHVCGTGMVIVRDNDRIPPLNAPVYDANLKRIGKVVDVFGPVDEPYILVKPDDRDVKLESLVGDTLYIPPDKL 80 (98)
T ss_pred CccceeEEEecCCceEEEeCCCCCCCCCCeeEecCCCEEEEEEEEEccCCCCEEEEeccccccccccccceEEEeccccc
Confidence 46799999999999999998889999999999999999999999999999999999999888867788999999999999
Q ss_pred CcCCccCCCCCC
Q 029223 130 LPLARFLPQPKG 141 (197)
Q Consensus 130 LPLdrflPkpk~ 141 (197)
++++|++|+++.
T Consensus 81 ~~~~r~~~~~k~ 92 (98)
T COG3277 81 IRKKRKLPRKKR 92 (98)
T ss_pred CcccccCccccc
Confidence 999999999886
No 3
>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed
Probab=99.89 E-value=3.6e-23 Score=150.15 Aligned_cols=72 Identities=29% Similarity=0.560 Sum_probs=67.8
Q ss_pred eEEeeceeeec-cCceEecccccccCcccceEEccCCeeeeeeeEEecccCCceeEEeecCCccccccccCcEEEEc
Q 029223 50 VVEVSSFLHAC-EGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYID 125 (197)
Q Consensus 50 vl~lG~~sh~c-e~dlV~K~~~~~VP~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~d~v~a~s~~~GdklyId 125 (197)
+.++|+|+|.| +++|||++ +++|+||++||++|+++||||+|||||||++|++||+++.+.|+ +++|++||.
T Consensus 1 Mk~~G~~~h~~~~g~lI~~~--~~~P~~n~~V~~~~~~~IGkV~dIfGPV~~pY~~Vk~~~~~~~~--~~g~k~yi~ 73 (73)
T PRK13149 1 MKRLGKVLHYAPKGKLIIRL--DKQPPIGSVVYDKKLKKIGKVVDVFGPVKEPYVLVKPDKKDPPE--LVGEKLYVR 73 (73)
T ss_pred CcEeEEEEEEcCCCCEEEEc--CCCCCCCCEeECCCCCEeEEEEEEECCCCCcEEEEEeCCCCCcc--ccCCEEEeC
Confidence 46899999999 78999999 78999999999999999999999999999999999999999987 789999984
No 4
>PF04410 Gar1: Gar1/Naf1 RNA binding region; InterPro: IPR007504 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. This entry represents Gar1 and Naf1. Naf1 is an RNA-binding protein required for the maturation of box H/ACA snoRNPs complex and ribosome biogenesis. During assembly of the H/ACA snoRNPs complex, it associates with the complex, disappearing during maturation of the complex being replaced by GAR1 to yield mature H/ACA snoRNPs complex. Naf1 reveals a striking structural homology with the core domain of archaeal Gar1 [].; GO: 0030515 snoRNA binding, 0031120 snRNA pseudouridine synthesis, 0042254 ribosome biogenesis; PDB: 2EY4_C 3MQK_C 2RFK_C 2HVY_B 3HAY_B 3U28_C 3UAI_C 2EQN_A 2V3M_F.
Probab=99.86 E-value=5.5e-22 Score=161.29 Aligned_cols=99 Identities=43% Similarity=0.760 Sum_probs=81.0
Q ss_pred CCCCCCCcceEEeeceeeeccCceEeccccc-ccCcccceEEccCCeeeeeeeEEecccCCceeEEe--ecCCccccccc
Q 029223 41 FRDEGPPAEVVEVSSFLHACEGDAVTKLTNE-KIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVK--MMEGIVATSYS 117 (197)
Q Consensus 41 ~~~~gPPs~vl~lG~~sh~ce~dlV~K~~~~-~VP~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK--~~d~v~a~s~~ 117 (197)
..+..|+.+++.||+|+|+|++.+||+++.. .||.+|+.|+++++++||+|+||||||++||++|| +++.+++.+++
T Consensus 14 ~~~~~~~~~i~~lG~v~~i~~~~vVvk~~~~~~vl~~~s~v~~edr~~iG~V~eiFGpV~~P~y~Vr~~~~~~~~~~~~~ 93 (154)
T PF04410_consen 14 DVEIGPPEEIKPLGTVSHIVENLVVVKSTPSKQVLDFGSVVCLEDRTKIGKVDEIFGPVNNPYYSVRFNSSEGIKAKSLK 93 (154)
T ss_dssp T-B--TTSSEEEEEEEEEEETTEEEEEE-SS-CEEBTT-EEEETTSBEEEEEEEEESESSS-EEEEE-SCHHHHHHHCCC
T ss_pred CcccCCCceEEEeeeEEEEeCCcEEEEeCCCCcCCCCCCEEECCCCCEeEEEeeEeCCCCceEEEEEeCCcccccccccc
Confidence 4577899999999999999999999999876 89999999999999999999999999999999999 78888888999
Q ss_pred cCcEEEEcCCCCCcCCccCCCCCCC
Q 029223 118 LGDKFYIDPSKLLPLARFLPQPKGQ 142 (197)
Q Consensus 118 ~GdklyIdp~klLPLdrflPkpk~~ 142 (197)
+++++|++++ |+++|||+++.+
T Consensus 94 ~g~~vy~~~~---~~~~~~~~~~~~ 115 (154)
T PF04410_consen 94 VGDKVYYDPD---PTSRFLPEPLKR 115 (154)
T ss_dssp TTSEEEEECC----GGGG-------
T ss_pred ccceEEECCC---chheeccccccc
Confidence 9999999988 899999887765
No 5
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=98.81 E-value=2.9e-08 Score=84.13 Aligned_cols=121 Identities=31% Similarity=0.450 Sum_probs=66.1
Q ss_pred CCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCC---CCcceEEeeceeeeccCceEec--ccccccCcccc
Q 029223 6 GGGGFRGGRDGGRGG--RGGGRFGGGGRGGGGRGGFGFRDEG---PPAEVVEVSSFLHACEGDAVTK--LTNEKIPYFNA 78 (197)
Q Consensus 6 ~~~~~~~~~~~~~~~--~~~~~~~gg~~gg~gg~~~g~~~~g---PPs~vl~lG~~sh~ce~dlV~K--~~~~~VP~~na 78 (197)
+..+||++..+++++ +++.+|+-++++.+. +.-+..+. +=.+.|...+=.-+|..+ ..| .+|.-|=..|.
T Consensus 12 g~~gfRgg~ggg~~gg~rgg~g~grgg~~~~~--~~d~gpp~evvelg~flh~Cegd~Vck~~-~~kIPyfNAPIylenk 88 (215)
T KOG3262|consen 12 GGGGFRGGGGGGRGGGFRGGNGFGRGGRGGRG--FQDQGPPEEVVELGKFLHMCEGDLVCKLT-NKKIPYFNAPIYLENK 88 (215)
T ss_pred CCCCcccCCCCCCCCCcccCcccccCCcccCC--cccCCCchhhhhhhhhhhhcCCceEEeec-cccCCCCCCceeecch
Confidence 345566665555432 222233333333333 33222322 333444444444455432 222 24555556788
Q ss_pred eEEccCCeeeeeeeEEecccCCc----eeEEeecCCccccccccCcEEEEcCCCCCcCCc
Q 029223 79 PIYLQNKTQIGKVDEIFGPINES----YFSVKMMEGIVATSYSLGDKFYIDPSKLLPLAR 134 (197)
Q Consensus 79 ~V~~knkt~IGkV~EIFGpIn~~----Y~sVK~~d~v~a~s~~~GdklyIdp~klLPLdr 134 (197)
.++-|.+++.|+|+||+.+|+.. ..|+|+.|.+.++ -|||.. -++|||.+-
T Consensus 89 ~qIGKVDEIfG~i~d~~fsIK~~dgv~assfk~g~k~fi~----p~KllP-l~RFLP~p~ 143 (215)
T KOG3262|consen 89 EQIGKVDEIFGPINDVHFSIKPSDGVQASSFKPGDKLFID----PDKLLP-LDRFLPQPV 143 (215)
T ss_pred hhhcchhhhcccccccEEEEecCCCceeecccCCCeEEec----ccccCc-HhhcCCCCC
Confidence 99999999999999999998864 3333555543322 356553 477888873
No 6
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=98.50 E-value=1.6e-07 Score=73.04 Aligned_cols=67 Identities=31% Similarity=0.454 Sum_probs=55.7
Q ss_pred eEecccccccCcccceEEccCCeee-eeeeEEecccCCceeEEeecCC---cccccccc---CcEEEEcCCCCCcCCccC
Q 029223 64 AVTKLTNEKIPYFNAPIYLQNKTQI-GKVDEIFGPINESYFSVKMMEG---IVATSYSL---GDKFYIDPSKLLPLARFL 136 (197)
Q Consensus 64 lV~K~~~~~VP~~na~V~~knkt~I-GkV~EIFGpIn~~Y~sVK~~d~---v~a~s~~~---GdklyIdp~klLPLdrfl 136 (197)
+|.++.++.| .|++||.+++ |+|+.||-.||..++.|++... +..+.+++ ..++||.||. |+||.+|
T Consensus 6 ~L~kl~~e~v-----tIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~~pv~l~~lsirgnniRy~~lpD~-l~ld~Ll 79 (109)
T KOG3428|consen 6 FLKKLLNERV-----TIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKGEPVRLDTLSIRGNNIRYYILPDS-LNLDTLL 79 (109)
T ss_pred HHHHhhCCeE-----EEEecCCcEEeeeEEEEEhhheeEEEEEEEecCCCceeEEEEEeecceEEEEEccCC-cCcceee
Confidence 4567777888 9999999999 9999999999999999987543 45554433 2789999999 9999998
No 7
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.30 E-value=4.1e-07 Score=85.54 Aligned_cols=78 Identities=21% Similarity=0.498 Sum_probs=65.6
Q ss_pred ceEEeeceeeeccCceEeccccc-ccCcccceEEccCCeeeeeeeEEecccCCceeEEeecCCcccc--ccccCcEEEEc
Q 029223 49 EVVEVSSFLHACEGDAVTKLTNE-KIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVAT--SYSLGDKFYID 125 (197)
Q Consensus 49 ~vl~lG~~sh~ce~dlV~K~~~~-~VP~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~d~v~a~--s~~~GdklyId 125 (197)
.++.||.|+.+++.++|++++.. .|--+-+.++++..+.||.|+||||||..+|..|+..+...+. .+.+++++|+-
T Consensus 207 ~~~plG~V~svv~~~VII~s~~~~~vlde~Svlf~edR~~lG~I~EiFGpV~~P~YvvRFnS~~e~~~~gi~ig~~vy~a 286 (483)
T KOG2236|consen 207 ELLPLGKVSSVVDQQVIIESTCNKEVLDEDSVLFLEDRTALGQIFEIFGPVKNPYYVVRFNSEEEISFLGICIGEKVYYA 286 (483)
T ss_pred ceechhHHHHHhhhceEEEeccCcccccccceEEeeccccchhhhhhhcccCCceEEEecCchhhhhhhccccCCeeEec
Confidence 78999999999999999998766 3446777888888889999999999999999999976554544 67788999887
Q ss_pred C
Q 029223 126 P 126 (197)
Q Consensus 126 p 126 (197)
|
T Consensus 287 p 287 (483)
T KOG2236|consen 287 P 287 (483)
T ss_pred C
Confidence 6
No 8
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=96.38 E-value=0.0022 Score=51.60 Aligned_cols=84 Identities=11% Similarity=0.094 Sum_probs=48.8
Q ss_pred CCCcceEEeeceeeeccCceEecccccccCcccceEEccCCe--eeeeeeEEecccCCceeEEeecCCccccccc-cCcE
Q 029223 45 GPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKT--QIGKVDEIFGPINESYFSVKMMEGIVATSYS-LGDK 121 (197)
Q Consensus 45 gPPs~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt--~IGkV~EIFGpIn~~Y~sVK~~d~v~a~s~~-~Gdk 121 (197)
.-.+..|+|++|.+.++++.|.++|++.-+..+..|..+..+ ..| |+ |++++..+ .|+.+. .=+.
T Consensus 31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG-----fa-----FV~F~~~e--~A~~Al~~lng 98 (144)
T PLN03134 31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRG-----FG-----FVNFNDEG--AATAAISEMDG 98 (144)
T ss_pred cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcce-----EE-----EEEECCHH--HHHHHHHHcCC
Confidence 346778999999999999999998876444444455444333 223 55 66665333 222221 1122
Q ss_pred EEEcCCCCCcCCccCCCCCC
Q 029223 122 FYIDPSKLLPLARFLPQPKG 141 (197)
Q Consensus 122 lyIdp~klLPLdrflPkpk~ 141 (197)
..|+..+ |.++...++++.
T Consensus 99 ~~i~Gr~-l~V~~a~~~~~~ 117 (144)
T PLN03134 99 KELNGRH-IRVNPANDRPSA 117 (144)
T ss_pred CEECCEE-EEEEeCCcCCCC
Confidence 3455554 667666555543
No 9
>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=94.09 E-value=0.11 Score=39.12 Aligned_cols=64 Identities=30% Similarity=0.436 Sum_probs=41.3
Q ss_pred cccccccCcccceEEccCCeee-eeeeEEecccCCceeEEeecC----CccccccccC---cEEEEcCCCCCcCCccC
Q 029223 67 KLTNEKIPYFNAPIYLQNKTQI-GKVDEIFGPINESYFSVKMME----GIVATSYSLG---DKFYIDPSKLLPLARFL 136 (197)
Q Consensus 67 K~~~~~VP~~na~V~~knkt~I-GkV~EIFGpIn~~Y~sVK~~d----~v~a~s~~~G---dklyIdp~klLPLdrfl 136 (197)
++..+.| .|.++|++.+ |++.+|+..||..+..++... .....++.+. .++.+.|+. |-++..|
T Consensus 8 ~l~g~~V-----~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~-l~~~~~l 79 (90)
T cd01724 8 KLTNETV-----TIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDS-LNLDTLL 79 (90)
T ss_pred hCCCCEE-----EEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCc-CCcchhh
Confidence 3444556 8899999877 999999999998888875421 1223333332 455666777 4444444
No 10
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=94.03 E-value=0.011 Score=52.02 Aligned_cols=79 Identities=15% Similarity=0.082 Sum_probs=54.1
Q ss_pred ceEEeeceeeeccCceEecccccccCcccceEEccCCe--eeeeeeEEecccCCceeEEe-ecCCccccccccCcEEEEc
Q 029223 49 EVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKT--QIGKVDEIFGPINESYFSVK-MMEGIVATSYSLGDKFYID 125 (197)
Q Consensus 49 ~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt--~IGkV~EIFGpIn~~Y~sVK-~~d~v~a~s~~~GdklyId 125 (197)
.+|||+||.+.|+++.|.++|+..-+..++.|+.+..+ ..| |+ |+++. .+++..|-....+ ..|+
T Consensus 270 ~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG-----~a-----FV~F~~~~~A~~Ai~~lnG--~~~~ 337 (352)
T TIGR01661 270 YCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKG-----YG-----FVSMTNYDEAAMAILSLNG--YTLG 337 (352)
T ss_pred cEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccc-----eE-----EEEECCHHHHHHHHHHhCC--CEEC
Confidence 37999999999999999999987666677777766543 334 55 66664 3444444332334 5566
Q ss_pred CCCCCcCCccCCCCC
Q 029223 126 PSKLLPLARFLPQPK 140 (197)
Q Consensus 126 p~klLPLdrflPkpk 140 (197)
.++ |-+++.++|++
T Consensus 338 gr~-i~V~~~~~~~~ 351 (352)
T TIGR01661 338 NRV-LQVSFKTNKAY 351 (352)
T ss_pred CeE-EEEEEccCCCC
Confidence 666 88888877765
No 11
>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=92.66 E-value=0.11 Score=50.79 Aligned_cols=26 Identities=12% Similarity=0.203 Sum_probs=22.5
Q ss_pred CcceEEeeceeeeccCceEecccccc
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLTNEK 72 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~~~~ 72 (197)
..++|+|+||++.|++|.|.++|++.
T Consensus 232 ~~k~LfVgNL~~~~tee~L~~~F~~f 257 (578)
T TIGR01648 232 KVKILYVRNLMTTTTEEIIEKSFSEF 257 (578)
T ss_pred cccEEEEeCCCCCCCHHHHHHHHHhc
Confidence 45789999999999999999988654
No 12
>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=91.42 E-value=0.29 Score=34.83 Aligned_cols=39 Identities=15% Similarity=0.146 Sum_probs=31.4
Q ss_pred eEecccccccCcccceEEccCCeee-eeeeEEecccCCceeEEee
Q 029223 64 AVTKLTNEKIPYFNAPIYLQNKTQI-GKVDEIFGPINESYFSVKM 107 (197)
Q Consensus 64 lV~K~~~~~VP~~na~V~~knkt~I-GkV~EIFGpIn~~Y~sVK~ 107 (197)
+|.++..+.| .|.+++.+.+ |++..++..||..+..++.
T Consensus 4 ~L~~~~g~~V-----~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~ 43 (70)
T cd01721 4 LLHEAEGHIV-----TVELKTGEVYRGKLIEAEDNMNCQLKDVTV 43 (70)
T ss_pred HHhhCCCCEE-----EEEECCCcEEEEEEEEEcCCceeEEEEEEE
Confidence 4455555566 8899999877 9999999999998888864
No 13
>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=91.34 E-value=0.13 Score=47.05 Aligned_cols=38 Identities=8% Similarity=0.022 Sum_probs=27.2
Q ss_pred CCcceEEeeceeeeccCceEecccccccCcccceEEcc
Q 029223 46 PPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQ 83 (197)
Q Consensus 46 PPs~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~k 83 (197)
..+.+|+|++|.+.++++.|.++|++.-....+.|+.+
T Consensus 191 ~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d 228 (346)
T TIGR01659 191 IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRD 228 (346)
T ss_pred cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeec
Confidence 34678999999999999888888766433344455443
No 14
>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=90.72 E-value=0.057 Score=49.42 Aligned_cols=43 Identities=14% Similarity=0.054 Sum_probs=32.6
Q ss_pred CCCCCcceEEeeceeeeccCceEecccccccCcccceEEccCC
Q 029223 43 DEGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNK 85 (197)
Q Consensus 43 ~~gPPs~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knk 85 (197)
+..+++.+|||++|.+.++++.|.++|++.-+...+.|+.+..
T Consensus 102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~ 144 (346)
T TIGR01659 102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYK 144 (346)
T ss_pred CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC
Confidence 3456789999999999999999999887755555555554433
No 15
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=90.09 E-value=1.9 Score=34.08 Aligned_cols=50 Identities=16% Similarity=0.183 Sum_probs=29.0
Q ss_pred EEccCCeee-eeeeEEecccCCceeEEeec--CC--ccccccccC---cEEEEcCCCC
Q 029223 80 IYLQNKTQI-GKVDEIFGPINESYFSVKMM--EG--IVATSYSLG---DKFYIDPSKL 129 (197)
Q Consensus 80 V~~knkt~I-GkV~EIFGpIn~~Y~sVK~~--d~--v~a~s~~~G---dklyIdp~kl 129 (197)
+++++.+.. ||+.|.-=.+|..+..|... |. .+++.+.+. ++|+|.|+-|
T Consensus 20 ~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdmL 77 (119)
T KOG3172|consen 20 VETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDML 77 (119)
T ss_pred EEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchHh
Confidence 344444443 99999999999988777542 21 112223332 4566666653
No 16
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=90.04 E-value=1 Score=36.29 Aligned_cols=30 Identities=17% Similarity=0.029 Sum_probs=25.6
Q ss_pred eEEccCCeee-eeeeEEecccCCceeEEeec
Q 029223 79 PIYLQNKTQI-GKVDEIFGPINESYFSVKMM 108 (197)
Q Consensus 79 ~V~~knkt~I-GkV~EIFGpIn~~Y~sVK~~ 108 (197)
-|++||.+++ |.++.++--||.++.+|-..
T Consensus 16 lvELKNget~nGhL~~cD~wMNl~L~~Vi~t 46 (134)
T KOG3293|consen 16 LVELKNGETYNGHLVNCDNWMNLHLREVICT 46 (134)
T ss_pred EEEecCCCEecceeecchhhhhcchheeEEe
Confidence 6888999888 99999999999998888653
No 17
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=89.76 E-value=0.56 Score=44.40 Aligned_cols=25 Identities=4% Similarity=-0.110 Sum_probs=18.6
Q ss_pred ceEEeeceeeeccCceEeccccccc
Q 029223 49 EVVEVSSFLHACEGDAVTKLTNEKI 73 (197)
Q Consensus 49 ~vl~lG~~sh~ce~dlV~K~~~~~V 73 (197)
.+|+|.+|.|++..++|.+.|...-
T Consensus 289 ~~i~V~nlP~da~~~~l~~~Fk~FG 313 (419)
T KOG0116|consen 289 LGIFVKNLPPDATPAELEEVFKQFG 313 (419)
T ss_pred cceEeecCCCCCCHHHHHHHHhhcc
Confidence 3489999999998888776665433
No 18
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=89.05 E-value=0.14 Score=42.00 Aligned_cols=28 Identities=11% Similarity=-0.001 Sum_probs=24.4
Q ss_pred CCcceEEeeceeeeccCceEeccccccc
Q 029223 46 PPAEVVEVSSFLHACEGDAVTKLTNEKI 73 (197)
Q Consensus 46 PPs~vl~lG~~sh~ce~dlV~K~~~~~V 73 (197)
--|.||+|||||+.+.++-|+++|...-
T Consensus 34 r~S~tvyVgNlSfyttEEqiyELFs~cG 61 (153)
T KOG0121|consen 34 RKSCTVYVGNLSFYTTEEQIYELFSKCG 61 (153)
T ss_pred hhcceEEEeeeeeeecHHHHHHHHHhcc
Confidence 4578999999999999999999987644
No 19
>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=88.14 E-value=0.77 Score=33.66 Aligned_cols=30 Identities=17% Similarity=0.265 Sum_probs=26.2
Q ss_pred eEEccCCeee-eeeeEEecccCCceeEEeec
Q 029223 79 PIYLQNKTQI-GKVDEIFGPINESYFSVKMM 108 (197)
Q Consensus 79 ~V~~knkt~I-GkV~EIFGpIn~~Y~sVK~~ 108 (197)
.|.+++++.+ |++.+|+..||..+..++..
T Consensus 15 ~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~ 45 (81)
T cd01725 15 TVELKNDLSIRGTLHSVDQYLNIKLTNISVT 45 (81)
T ss_pred EEEECCCcEEEEEEEEECCCcccEEEEEEEE
Confidence 8899999877 99999999999988888643
No 20
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=86.47 E-value=0.21 Score=47.05 Aligned_cols=35 Identities=14% Similarity=0.085 Sum_probs=27.5
Q ss_pred CcceEEeeceeeeccCceEecccccccCcccceEE
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIY 81 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~ 81 (197)
||.||+|++|.+.++++.|.++++..-+..+..|+
T Consensus 1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~ 35 (481)
T TIGR01649 1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMML 35 (481)
T ss_pred CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEE
Confidence 79999999999999999888888765444444444
No 21
>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=83.79 E-value=1.6 Score=31.85 Aligned_cols=30 Identities=20% Similarity=0.378 Sum_probs=26.2
Q ss_pred eEEccCCeee-eeeeEEecccCCceeEEeec
Q 029223 79 PIYLQNKTQI-GKVDEIFGPINESYFSVKMM 108 (197)
Q Consensus 79 ~V~~knkt~I-GkV~EIFGpIn~~Y~sVK~~ 108 (197)
.|.++|.+.+ |++.+++..||..+.+++..
T Consensus 23 ~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~ 53 (78)
T cd01733 23 TVELRNETTVTGRIASVDAFMNIRLAKVTII 53 (78)
T ss_pred EEEECCCCEEEEEEEEEcCCceeEEEEEEEE
Confidence 8999999877 99999999999988888643
No 22
>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=83.58 E-value=1.8 Score=31.20 Aligned_cols=37 Identities=16% Similarity=0.076 Sum_probs=29.2
Q ss_pred ecccccccCcccceEEccCCeee-eeeeEEecccCCceeEEee
Q 029223 66 TKLTNEKIPYFNAPIYLQNKTQI-GKVDEIFGPINESYFSVKM 107 (197)
Q Consensus 66 ~K~~~~~VP~~na~V~~knkt~I-GkV~EIFGpIn~~Y~sVK~ 107 (197)
.++..+.| .|.++|++.+ |++..++..||..+..++.
T Consensus 7 ~~~~g~~V-----~VeLkng~~~~G~L~~~D~~mNi~L~~~~~ 44 (76)
T cd01723 7 KTAQNHPM-----LVELKNGETYNGHLVNCDNWMNIHLREVIC 44 (76)
T ss_pred HhcCCCEE-----EEEECCCCEEEEEEEEEcCCCceEEEeEEE
Confidence 34445556 8899998877 9999999999988877754
No 23
>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=83.37 E-value=0.72 Score=43.37 Aligned_cols=45 Identities=16% Similarity=0.169 Sum_probs=32.3
Q ss_pred CCCCCCcceEEeeceeeeccCceEecccccccCcccceEEccCCe
Q 029223 42 RDEGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKT 86 (197)
Q Consensus 42 ~~~gPPs~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt 86 (197)
.+.-||++||||..|.-+++++-|--+|+..-+..++-|+-+.++
T Consensus 233 Ad~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~kt 277 (479)
T KOG0415|consen 233 ADVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKT 277 (479)
T ss_pred cccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccc
Confidence 466799999999999999888533333333345557778777776
No 24
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=82.37 E-value=0.38 Score=42.32 Aligned_cols=38 Identities=5% Similarity=-0.022 Sum_probs=30.6
Q ss_pred CcceEEeeceeeeccCceEecccccccCcccceEEccC
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQN 84 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~kn 84 (197)
|..+|||++|.+.++++-|.++|.+.-|.....|+.+.
T Consensus 2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~ 39 (352)
T TIGR01661 2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDK 39 (352)
T ss_pred CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcC
Confidence 67899999999999999999998876666666666543
No 25
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=79.52 E-value=0.89 Score=42.23 Aligned_cols=27 Identities=19% Similarity=0.129 Sum_probs=22.3
Q ss_pred CCcceEEeeceeeeccCceEecccccc
Q 029223 46 PPAEVVEVSSFLHACEGDAVTKLTNEK 72 (197)
Q Consensus 46 PPs~vl~lG~~sh~ce~dlV~K~~~~~ 72 (197)
..+.+|+|+||.+.++++.|.++|++.
T Consensus 173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~ 199 (509)
T TIGR01642 173 RQARRLYVGGIPPEFVEEAVVDFFNDL 199 (509)
T ss_pred ccccEEEEeCCCCCCCHHHHHHHHHHH
Confidence 346789999999999998888887653
No 26
>PF14578 GTP_EFTU_D4: Elongation factor Tu domain 4; PDB: 1G7R_A 1G7S_A 1G7T_A 1XE1_A.
Probab=79.33 E-value=9 Score=28.49 Aligned_cols=73 Identities=16% Similarity=0.250 Sum_probs=42.9
Q ss_pred CCCcceEEeeceeeeccCceEecccccccCcccceEEccCCeeeeeeeEEecc---cCC----ceeEEeecCCccccccc
Q 029223 45 GPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGP---INE----SYFSVKMMEGIVATSYS 117 (197)
Q Consensus 45 gPPs~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~IGkV~EIFGp---In~----~Y~sVK~~d~v~a~s~~ 117 (197)
-||+++..|=.+.+...+ +|+=.-.+=+-+.+.++ +...||+|.+|==. ++. .=++++.+... .++
T Consensus 2 ~~p~ki~Ilp~~vFr~~~-~IvG~V~~G~ik~G~~l---~G~~iG~I~sIe~~~k~v~~A~~G~eVai~Ieg~~---~i~ 74 (81)
T PF14578_consen 2 VRPGKIRILPVCVFRQSD-AIVGEVLEGIIKPGYPL---DGRKIGRIKSIEDNGKNVDEAKKGDEVAISIEGPT---QIK 74 (81)
T ss_dssp S-SEEEEEEEEEEECTCC-EEEEEEEEEEEETT-EE---CSSCEEEEEEEEETTEEESEEETT-EEEEEEET-----TB-
T ss_pred CCceEEEECCcCEEecCC-eEEEEEeeeEEeCCCcc---CCEEEEEEEEeEECCcCccccCCCCEEEEEEeCCc---cCC
Confidence 378999999999999888 66652223233567777 55569988887541 111 23445555543 567
Q ss_pred cCcEEEE
Q 029223 118 LGDKFYI 124 (197)
Q Consensus 118 ~GdklyI 124 (197)
++|.||+
T Consensus 75 eGDiLyV 81 (81)
T PF14578_consen 75 EGDILYV 81 (81)
T ss_dssp TT-EEEE
T ss_pred CCCEEeC
Confidence 7888886
No 27
>PF05239 PRC: PRC-barrel domain; InterPro: IPR007903 The PRC-barrel is an all beta barrel domain found in photosynthetic reaction centre subunit H of the purple bacteria. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the C terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain [].; PDB: 2QGG_A 3H9N_A 2WJN_H 2PRC_H 5PRC_H 2X5V_H 1DXR_H 1R2C_H 3G7F_H 1PRC_H ....
Probab=76.86 E-value=5.3 Score=27.72 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=19.8
Q ss_pred ccceEEccCCeeeeeeeEEeccc
Q 029223 76 FNAPIYLQNKTQIGKVDEIFGPI 98 (197)
Q Consensus 76 ~na~V~~knkt~IGkV~EIFGpI 98 (197)
++.+|++++.+.+|+|.||+-..
T Consensus 10 ~g~~V~~~~G~~iG~V~di~id~ 32 (79)
T PF05239_consen 10 IGKEVIDRDGEKIGKVKDIVIDP 32 (79)
T ss_dssp TTSEEEETTSCEEEEEEEEEEET
T ss_pred cCCEEEcCCCCEEEEEEEEEEeC
Confidence 57799999999999999996644
No 28
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=76.48 E-value=0.62 Score=43.92 Aligned_cols=40 Identities=13% Similarity=0.227 Sum_probs=29.9
Q ss_pred CCCcceEEeeceeeeccCceEeccccccc--CcccceEEccC
Q 029223 45 GPPAEVVEVSSFLHACEGDAVTKLTNEKI--PYFNAPIYLQN 84 (197)
Q Consensus 45 gPPs~vl~lG~~sh~ce~dlV~K~~~~~V--P~~na~V~~kn 84 (197)
.||+.+|+|.||.+.|+++.|.++|++.- ......|+.+.
T Consensus 391 ~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~ 432 (481)
T TIGR01649 391 QPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKD 432 (481)
T ss_pred CCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCC
Confidence 58999999999999999998888886532 23344555544
No 29
>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]
Probab=71.28 E-value=0.36 Score=42.68 Aligned_cols=31 Identities=10% Similarity=0.167 Sum_probs=26.2
Q ss_pred CCcceEEeeceeeeccCceEecccccccCcc
Q 029223 46 PPAEVVEVSSFLHACEGDAVTKLTNEKIPYF 76 (197)
Q Consensus 46 PPs~vl~lG~~sh~ce~dlV~K~~~~~VP~~ 76 (197)
|-+.||+|+||+.-+++++|.++|...-|++
T Consensus 7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~ 37 (267)
T KOG4454|consen 7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVY 37 (267)
T ss_pred chhhHHHHHhhhhhhhHHHHHHHhhccCceE
Confidence 4458999999999999999999988776543
No 30
>PHA01365 hypothetical protein
Probab=69.84 E-value=4.6 Score=30.43 Aligned_cols=63 Identities=21% Similarity=0.292 Sum_probs=37.3
Q ss_pred ceEeccccc-ccCcccceEEccCCeeeeeeeEEecccCCceeEEeecCCccccc----cccC-cEEEEcCCC
Q 029223 63 DAVTKLTNE-KIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATS----YSLG-DKFYIDPSK 128 (197)
Q Consensus 63 dlV~K~~~~-~VP~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~d~v~a~s----~~~G-dklyIdp~k 128 (197)
.+|||+|+. +|- ..+++-++.-+=+=+=||-++.+.|.-+-+-|.++..- .+.+ ..+|++|+|
T Consensus 10 rilqK~fkdskie---ki~~lps~~dv~~KYiif~r~s~~y~G~~vvdGiqIPFiAev~lngk~~iYLyP~K 78 (91)
T PHA01365 10 KLLQKCFKDSSID---VIFMSCNNLSPHKKYMIIDPESKYYIGYILTDGIKIPFIAEVWHNNTTRIYLDPRK 78 (91)
T ss_pred HHHHHHhCCCceE---EEEEecCCCCccccEEEEEEecceEEEEEEEcceeccEEeeeeeCCeEEEEEcccc
Confidence 367777654 232 13444444433333445778888888887777766432 2334 578999888
No 31
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=68.94 E-value=1.3 Score=29.08 Aligned_cols=32 Identities=3% Similarity=-0.043 Sum_probs=25.0
Q ss_pred EEeeceeeeccCceEecccccccCcccceEEc
Q 029223 51 VEVSSFLHACEGDAVTKLTNEKIPYFNAPIYL 82 (197)
Q Consensus 51 l~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~ 82 (197)
|+|++|.+.|+++-|.+++++.-+.....|..
T Consensus 1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~ 32 (70)
T PF00076_consen 1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMR 32 (70)
T ss_dssp EEEESETTTSSHHHHHHHHHTTSTEEEEEEEE
T ss_pred cEEcCCCCcCCHHHHHHHHHHhhhcccccccc
Confidence 68999999999999999887755554555555
No 32
>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional
Probab=67.89 E-value=22 Score=29.00 Aligned_cols=33 Identities=6% Similarity=0.055 Sum_probs=27.2
Q ss_pred cccceEEccCCeeeeeeeEEecccCCceeEEee
Q 029223 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (197)
Q Consensus 75 ~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~ 107 (197)
.++..|++++.+.+|+|.+|+=+-.+++..||.
T Consensus 85 LiG~~V~d~~g~~lG~V~~V~~~ga~dvlvV~~ 117 (161)
T PRK13828 85 LIGLAAVDTGGALLGRVKAVHNFGAGDILEIAP 117 (161)
T ss_pred ccCCEEEeCCCCEEEEEEEEccCCCccEEEEEE
Confidence 467899999999999999999866666677874
No 33
>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=67.54 E-value=1.8 Score=42.60 Aligned_cols=35 Identities=14% Similarity=0.140 Sum_probs=28.1
Q ss_pred ceEEeeceeeeccCceEecccccccCcccceEEcc
Q 029223 49 EVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQ 83 (197)
Q Consensus 49 ~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~k 83 (197)
..|||++|.+.+++|.|.++|++..+.....|+.+
T Consensus 59 ~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D 93 (578)
T TIGR01648 59 CEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD 93 (578)
T ss_pred CEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC
Confidence 78999999999999999999887666555555443
No 34
>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]
Probab=67.38 E-value=1.7 Score=38.53 Aligned_cols=52 Identities=10% Similarity=0.140 Sum_probs=39.1
Q ss_pred ceEEeeceeeeccCceEecccccccCcccceEEccCCeeeeeeeEEecccCCceeEEeec
Q 029223 49 EVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMM 108 (197)
Q Consensus 49 ~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~ 108 (197)
+-||||.|.|.+..|.+.+.|+.---.+-|.|+.|..+..-|- +| |+++|..
T Consensus 13 TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskG---yG-----fVTf~d~ 64 (247)
T KOG0149|consen 13 TKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKG---YG-----FVTFRDA 64 (247)
T ss_pred EEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccc---ee-----eEEeecH
Confidence 5689999999999999988887655556788999888755221 45 6777643
No 35
>PLN03121 nucleic acid binding protein; Provisional
Probab=67.12 E-value=2.1 Score=38.00 Aligned_cols=52 Identities=12% Similarity=-0.000 Sum_probs=38.3
Q ss_pred CcceEEeeceeeeccCceEecccccccCcccceEEccCCeeeeeeeEEecccCCceeEEeecC
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMME 109 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~d 109 (197)
...|++|+||++.++++-|.++|+..-+..+..|+.+.++. + |+ |++++-.+
T Consensus 4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~-g-----fA-----fVtF~d~~ 55 (243)
T PLN03121 4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYA-C-----TA-----YVTFKDAY 55 (243)
T ss_pred CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcc-e-----EE-----EEEECCHH
Confidence 34799999999999999999998876555666677665443 1 55 77886433
No 36
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=66.14 E-value=2.1 Score=38.34 Aligned_cols=81 Identities=16% Similarity=0.219 Sum_probs=49.0
Q ss_pred CcceEEeeceeeeccCceEecccccccCcccceEEccCCeeeeeeeEEecccCCceeEEee-cCCccccccccCcEEEEc
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKM-MEGIVATSYSLGDKFYID 125 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~-~d~v~a~s~~~GdklyId 125 (197)
-+.++.|-|||.++.++-|.+++....|... ||+..++..|.-.. |. |++++- ++++.|-..+.+--++
T Consensus 188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~r--vylardK~TG~~kG-FA-----FVtF~sRddA~rAI~~LnG~gyd-- 257 (270)
T KOG0122|consen 188 DEATVRVTNLSEDMREDDLEELFRPFGPITR--VYLARDKETGLSKG-FA-----FVTFESRDDAARAIADLNGYGYD-- 257 (270)
T ss_pred ccceeEEecCccccChhHHHHHhhccCccce--eEEEEccccCcccc-eE-----EEEEecHHHHHHHHHHccCcccc--
Confidence 4679999999999988766888777655533 34433333332111 66 888876 4455554444452222
Q ss_pred CCCCCcCCccCCC
Q 029223 126 PSKLLPLARFLPQ 138 (197)
Q Consensus 126 p~klLPLdrflPk 138 (197)
+-+|..+...|+
T Consensus 258 -~LILrvEwskP~ 269 (270)
T KOG0122|consen 258 -NLILRVEWSKPS 269 (270)
T ss_pred -eEEEEEEecCCC
Confidence 334677776555
No 37
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=65.63 E-value=16 Score=27.60 Aligned_cols=55 Identities=11% Similarity=0.169 Sum_probs=38.7
Q ss_pred CcceEEeeceeeeccCceEeccccc-ccCcccceEEccC--CeeeeeeeEEecccCCceeEEee
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLTNE-KIPYFNAPIYLQN--KTQIGKVDEIFGPINESYFSVKM 107 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~~~-~VP~~na~V~~kn--kt~IGkV~EIFGpIn~~Y~sVK~ 107 (197)
...|.+||++...-.+.++.++.+. +| .|.+.. ..++++.+||.|.++.. .+|+.
T Consensus 15 gk~V~ivGkV~~~~~~~~~~~~~Dg~~v-----~v~l~~~~~~~~~~~vEViG~V~~~-~~I~~ 72 (101)
T cd04479 15 GKTVRIVGKVEKVDGDSLTLISSDGVNV-----TVELNRPLDLPISGYVEVIGKVSPD-LTIRV 72 (101)
T ss_pred CCEEEEEEEEEEecCCeEEEEcCCCCEE-----EEEeCCCCCcccCCEEEEEEEECCC-CeEEE
Confidence 3578999999988766667776543 55 555544 45779999999988765 44444
No 38
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]
Probab=64.72 E-value=4.4 Score=36.98 Aligned_cols=42 Identities=7% Similarity=-0.016 Sum_probs=28.3
Q ss_pred CcceEEeeceeeeccCceEecccccccCcccceEEccCCeee
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQI 88 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~I 88 (197)
....+|||-|++.|+++.++..++..-...-+.|+++..++.
T Consensus 96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~ 137 (311)
T KOG4205|consen 96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSR 137 (311)
T ss_pred ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccc
Confidence 455889999999998888888776533334445555555544
No 39
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=63.23 E-value=1.7 Score=39.59 Aligned_cols=35 Identities=11% Similarity=0.114 Sum_probs=30.1
Q ss_pred ceEEeeceeeeccCceEecccccccCcccceEEcc
Q 029223 49 EVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQ 83 (197)
Q Consensus 49 ~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~k 83 (197)
.||+||||+.++++|+|..+|+..-|..++.|+.|
T Consensus 7 rtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~ 41 (321)
T KOG0148|consen 7 RTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD 41 (321)
T ss_pred ceEEeeccChhhHHHHHHHHHHhccccccceeehh
Confidence 69999999999999999999987777777777766
No 40
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]
Probab=61.29 E-value=9.2 Score=35.23 Aligned_cols=91 Identities=12% Similarity=0.164 Sum_probs=56.4
Q ss_pred CCCCcceEEeeceeeeccCceEecccccccCcccceEEccCCeeeeeeeEEecccCCceeEEeecCCcc-----cccccc
Q 029223 44 EGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIV-----ATSYSL 118 (197)
Q Consensus 44 ~gPPs~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~d~v~-----a~s~~~ 118 (197)
.+-|=.||||+.|+|.+.++-|-+.|+.--|.-+..++-+..|..=+- +. |+..+-+..++ |+-+++
T Consensus 97 ~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskG---YA-----FIeye~erdm~~AYK~adG~~I 168 (335)
T KOG0113|consen 97 IGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKG---YA-----FIEYEHERDMKAAYKDADGIKI 168 (335)
T ss_pred cCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccc---eE-----EEEeccHHHHHHHHHhccCcee
Confidence 456889999999999999999998888766665666666554433111 11 22223222222 233334
Q ss_pred C-cEEEEcCCCCCcCCccCCCCCCC
Q 029223 119 G-DKFYIDPSKLLPLARFLPQPKGQ 142 (197)
Q Consensus 119 G-dklyIdp~klLPLdrflPkpk~~ 142 (197)
. -.++||-+.--.+..+||+-.+.
T Consensus 169 dgrri~VDvERgRTvkgW~PRRLGG 193 (335)
T KOG0113|consen 169 DGRRILVDVERGRTVKGWLPRRLGG 193 (335)
T ss_pred cCcEEEEEecccccccccccccccC
Confidence 3 45777766656777788886653
No 41
>TIGR02273 16S_RimM 16S rRNA processing protein RimM. This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a PRC-barrel domain that it shares with other protein families (pfam05239) and a unique domain (pfam01782). This model describes the full-length protein. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide.
Probab=58.31 E-value=17 Score=29.44 Aligned_cols=33 Identities=18% Similarity=0.271 Sum_probs=28.2
Q ss_pred cccceEEccCCeeeeeeeEEecccCCceeEEee
Q 029223 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (197)
Q Consensus 75 ~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~ 107 (197)
.++..|++++.+.+|+|.||+-.-..++..|+.
T Consensus 100 LiG~~V~d~~~~~lG~V~~v~~~~a~dll~V~~ 132 (165)
T TIGR02273 100 LIGLEVVTEEGEELGKVVEILETGANDVLVVRS 132 (165)
T ss_pred hCCcEEEcCCCcEEEEEEEEecCCCccEEEEEE
Confidence 467899999999999999999977677788875
No 42
>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=58.22 E-value=9.3 Score=26.67 Aligned_cols=37 Identities=11% Similarity=0.163 Sum_probs=27.0
Q ss_pred EecccccccCcccceEEccCCeee-eeeeEEecccCCceeEEe
Q 029223 65 VTKLTNEKIPYFNAPIYLQNKTQI-GKVDEIFGPINESYFSVK 106 (197)
Q Consensus 65 V~K~~~~~VP~~na~V~~knkt~I-GkV~EIFGpIn~~Y~sVK 106 (197)
+.++..+.| .|.+++++.+ |++..++-.+|..+..++
T Consensus 5 L~~~~~~~V-----~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~ 42 (67)
T cd01726 5 LKAIIGRPV-----VVKLNSGVDYRGILACLDGYMNIALEQTE 42 (67)
T ss_pred HHhhCCCeE-----EEEECCCCEEEEEEEEEccceeeEEeeEE
Confidence 344445566 8889988766 999999997777666553
No 43
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=58.15 E-value=2.2 Score=33.86 Aligned_cols=37 Identities=8% Similarity=0.039 Sum_probs=28.9
Q ss_pred cceEEeeceeeeccCceEecccccccCcccceEEccC
Q 029223 48 AEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQN 84 (197)
Q Consensus 48 s~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~kn 84 (197)
..+|||++|.+.++++.|.++|.+..+.....|..++
T Consensus 115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~ 151 (306)
T COG0724 115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDR 151 (306)
T ss_pred CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeecc
Confidence 6999999999999999999988776655445554444
No 44
>COG3881 PRC-barrel domain containing protein [General function prediction only]
Probab=57.43 E-value=68 Score=27.15 Aligned_cols=65 Identities=12% Similarity=0.200 Sum_probs=36.9
Q ss_pred eEEeeceeeeccCceEeccccc-ccCcccc--------eEE-ccCCeeeeeeeEEecccCCc-eeEEeecCCcccc
Q 029223 50 VVEVSSFLHACEGDAVTKLTNE-KIPYFNA--------PIY-LQNKTQIGKVDEIFGPINES-YFSVKMMEGIVAT 114 (197)
Q Consensus 50 vl~lG~~sh~ce~dlV~K~~~~-~VP~~na--------~V~-~knkt~IGkV~EIFGpIn~~-Y~sVK~~d~v~a~ 114 (197)
.+.+.+++...++.++.....+ ..|.+|+ .+. ++..+..|.|.||+.-.+.- .+...+.+...|+
T Consensus 52 ~lp~~~i~Sig~k~Imi~vp~~~~~~~~ns~~ye~m~mk~~lt~dG~iLGmveDVyFdek~gkIvgyevS~GffAD 127 (176)
T COG3881 52 CLPVKNIVSIGSKMIMIYVPYKGSFIRFNSFTYEIMNMKVILTYDGTILGMVEDVYFDEKTGKIVGYEVSRGFFAD 127 (176)
T ss_pred eeeecceeeeccceEEEeccccceecccCchhhHhhcCceEeccCCcEeeeeeEEEEeccCCcEEEEEecCchhhh
Confidence 4556666665555444444333 2345555 333 36778889999999855542 3344555655554
No 45
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=56.53 E-value=3.4 Score=38.41 Aligned_cols=36 Identities=6% Similarity=-0.040 Sum_probs=27.0
Q ss_pred CcceEEeeceeeeccCceEecccccccCcccceEEc
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYL 82 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~ 82 (197)
+..+|||+||.+.++++.|.++|+..-+.....|+.
T Consensus 294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~ 329 (509)
T TIGR01642 294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIK 329 (509)
T ss_pred CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEe
Confidence 457899999999999998888877655544444443
No 46
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=55.83 E-value=21 Score=29.13 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=27.1
Q ss_pred cccceEEccCCeeeeeeeEEecccCCceeEEe
Q 029223 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVK 106 (197)
Q Consensus 75 ~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK 106 (197)
.++..|++++.+.+|+|.+|+=.-.+++..||
T Consensus 105 LiG~~V~d~~g~~lG~V~~v~~~~a~dll~I~ 136 (172)
T PRK00122 105 LIGLEVVDEDGEELGKVTDILETGANDVLVVL 136 (172)
T ss_pred hCCcEEEeCCCcEEEEEEEEccCCCceEEEEE
Confidence 46889999999999999999986666777775
No 47
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=55.55 E-value=4.3 Score=40.16 Aligned_cols=81 Identities=16% Similarity=0.116 Sum_probs=49.3
Q ss_pred CcceEEeeceeeeccCceEecccccccCcccceEEccCCeee--eeeeEEecccCCceeEEeecCCc----cccccccCc
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQI--GKVDEIFGPINESYFSVKMMEGI----VATSYSLGD 120 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~I--GkV~EIFGpIn~~Y~sVK~~d~v----~a~s~~~Gd 120 (197)
.+.||||=||+|.|+++.|...+..--+.-.|.|++...|.. |+ -|+.+|.+... .+.|-...+
T Consensus 291 ~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGt----------AFv~Fkt~~~~~~ci~~Aspa~e~ 360 (678)
T KOG0127|consen 291 EGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGT----------AFVKFKTQIAAQNCIEAASPASED 360 (678)
T ss_pred ccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccc----------eEEEeccHHHHHHHHHhcCccCCC
Confidence 347999999999999999999887654544555555555533 42 25555543322 222222234
Q ss_pred E-EEEcCCCCCcCCccCCC
Q 029223 121 K-FYIDPSKLLPLARFLPQ 138 (197)
Q Consensus 121 k-lyIdp~klLPLdrflPk 138 (197)
- |.|+ .++|-+...+++
T Consensus 361 g~~ll~-GR~Lkv~~Av~R 378 (678)
T KOG0127|consen 361 GSVLLD-GRLLKVTLAVTR 378 (678)
T ss_pred ceEEEe-ccEEeeeeccch
Confidence 4 4444 455888777655
No 48
>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional
Probab=54.81 E-value=23 Score=28.90 Aligned_cols=32 Identities=13% Similarity=0.235 Sum_probs=27.1
Q ss_pred cccceEEccCCeeeeeeeEEecccCCceeEEe
Q 029223 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVK 106 (197)
Q Consensus 75 ~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK 106 (197)
.++..|++++.+.+|+|.||+=+-.+++..|+
T Consensus 97 LiG~~V~~~~g~~lG~V~~v~~~ga~dvlvI~ 128 (165)
T PRK14592 97 LIGMEVKLEDNTIYGYIKKIYNFGSCDIIEIS 128 (165)
T ss_pred cCCcEEEcCCCCEEEEEEEEccCCCccEEEEE
Confidence 46789999999999999999996666667777
No 49
>PF05284 DUF736: Protein of unknown function (DUF736); InterPro: IPR007948 This family consists of several uncharacterised bacterial proteins of unknown function.
Probab=53.18 E-value=49 Score=25.57 Aligned_cols=59 Identities=14% Similarity=0.210 Sum_probs=35.0
Q ss_pred eeceeeeccCceEecc--cccccCcccceEEccC--CeeeeeeeEEeccc-CCceeEEeecCCccc
Q 029223 53 VSSFLHACEGDAVTKL--TNEKIPYFNAPIYLQN--KTQIGKVDEIFGPI-NESYFSVKMMEGIVA 113 (197)
Q Consensus 53 lG~~sh~ce~dlV~K~--~~~~VP~~na~V~~kn--kt~IGkV~EIFGpI-n~~Y~sVK~~d~v~a 113 (197)
|-+|+.+++-.+|-.. .+++.|-+ +|+..+ ...||-.-+=.... ..+|++||+++...+
T Consensus 18 I~TL~~~~~i~lvP~~~~~~e~aPdy--RV~~~~~~~~EvGaaW~~~~~~tg~~Ylsl~LddP~f~ 81 (107)
T PF05284_consen 18 IRTLTLDAKIRLVPNESKDSENAPDY--RVYAGPRGGVEVGAAWKKTSKDTGRDYLSLKLDDPSFP 81 (107)
T ss_pred EEEeEecccEEEEeCCCCCCCCCCCE--EEEecCCCCCceeeeehhhccccCCceEEEEEcCCCCC
Confidence 3345555544333332 34577744 555553 55677666656645 678999999987543
No 50
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=52.33 E-value=79 Score=22.12 Aligned_cols=54 Identities=19% Similarity=0.164 Sum_probs=31.7
Q ss_pred cccceEEccCCeeeeeeeEEec--ccCCceeEEeecCCccccccccCcEEEEcCCCCC
Q 029223 75 YFNAPIYLQNKTQIGKVDEIFG--PINESYFSVKMMEGIVATSYSLGDKFYIDPSKLL 130 (197)
Q Consensus 75 ~~na~V~~knkt~IGkV~EIFG--pIn~~Y~sVK~~d~v~a~s~~~GdklyIdp~klL 130 (197)
..+++|.. +.-+||+|++|-- .-+...+++++++.. ...+..+.+..|....||
T Consensus 16 ~~gs~V~~-~Gv~VG~V~~i~l~~~~~~v~v~~~i~~~~-~~~i~~~s~a~i~~~~ll 71 (81)
T PF02470_consen 16 SVGSPVRY-RGVEVGKVTSIELDPDGNRVRVTLRIDPDY-WHRIPDDSRASIRSSGLL 71 (81)
T ss_pred CCcCEEEE-CCEEEEEEEEEEEcCCCCEEEEEEEEcCCc-ceecCCCcEEEEEeCCch
Confidence 45778888 6778999999943 333345555666554 112334455555555544
No 51
>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=51.05 E-value=21 Score=24.79 Aligned_cols=36 Identities=11% Similarity=0.169 Sum_probs=25.1
Q ss_pred ecccccccCcccceEEccCCeee-eeeeEEecccCCceeEEe
Q 029223 66 TKLTNEKIPYFNAPIYLQNKTQI-GKVDEIFGPINESYFSVK 106 (197)
Q Consensus 66 ~K~~~~~VP~~na~V~~knkt~I-GkV~EIFGpIn~~Y~sVK 106 (197)
.++.+++| .|.+++++.+ |++..++-.+|..+..++
T Consensus 6 ~~~~~~~V-----~V~l~~g~~~~G~L~~~D~~mNlvL~~~~ 42 (68)
T cd01731 6 KDSLNKPV-----LVKLKGGKEVRGRLKSYDQHMNLVLEDAE 42 (68)
T ss_pred HHhcCCEE-----EEEECCCCEEEEEEEEECCcceEEEeeEE
Confidence 33444555 7888877666 999999987776665553
No 52
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 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 [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=50.83 E-value=22 Score=27.85 Aligned_cols=28 Identities=18% Similarity=0.414 Sum_probs=23.6
Q ss_pred CCCCCCCcceEEeeceeeeccCceEecc
Q 029223 41 FRDEGPPAEVVEVSSFLHACEGDAVTKL 68 (197)
Q Consensus 41 ~~~~gPPs~vl~lG~~sh~ce~dlV~K~ 68 (197)
+-+.++|+..+.+|++.|++++|+.+..
T Consensus 16 fi~lG~~~gk~V~G~I~hvv~ddLYIDf 43 (104)
T PF10246_consen 16 FIQLGDPEGKIVIGKIFHVVDDDLYIDF 43 (104)
T ss_pred hhhcCCccCCEEEEEEEEEecCceEEEe
Confidence 3467889999999999999999877765
No 53
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional
Probab=50.78 E-value=38 Score=27.78 Aligned_cols=33 Identities=15% Similarity=0.143 Sum_probs=26.8
Q ss_pred cccceEEccCCeeeeeeeEEecccCCceeEEee
Q 029223 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (197)
Q Consensus 75 ~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~ 107 (197)
.++..|++++.+.+|+|.||+=+-.++...|+.
T Consensus 105 LiG~~V~d~~g~~lG~V~~v~~~ga~dll~I~~ 137 (169)
T PRK14591 105 LIGCSVKNINNDSFGVVVDIIETGANEVLVCKE 137 (169)
T ss_pred ecCcEEEeCCCCEEEEEEEEeecCCceEEEEEc
Confidence 467899999999999999999865556567774
No 54
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]
Probab=50.52 E-value=1.5 Score=37.82 Aligned_cols=40 Identities=18% Similarity=0.093 Sum_probs=32.7
Q ss_pred cceEEeeceeeeccCceEecccccccCcccceEEccCCee
Q 029223 48 AEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQ 87 (197)
Q Consensus 48 s~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~ 87 (197)
..|++||+|-.-+.+++|++++-..-|.+|..|-.+..++
T Consensus 9 d~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~ 48 (203)
T KOG0131|consen 9 DATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQ 48 (203)
T ss_pred CceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcc
Confidence 4699999999999999999998777788777776555554
No 55
>PF08669 GCV_T_C: Glycine cleavage T-protein C-terminal barrel domain; InterPro: IPR013977 This entry shows glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. ; PDB: 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 3GIR_A 1WOO_A 1WOS_A 1WOR_A ....
Probab=49.48 E-value=88 Score=22.45 Aligned_cols=27 Identities=19% Similarity=0.292 Sum_probs=20.9
Q ss_pred ccccCcccceEEccCCeeeeeeeEEec
Q 029223 70 NEKIPYFNAPIYLQNKTQIGKVDEIFG 96 (197)
Q Consensus 70 ~~~VP~~na~V~~knkt~IGkV~EIFG 96 (197)
.+..|.-+++|+.++.+.||.|+..--
T Consensus 29 ~~~~~~~g~~v~~~~g~~vG~vTS~~~ 55 (95)
T PF08669_consen 29 GDAPPRGGEPVYDEDGKPVGRVTSGAY 55 (95)
T ss_dssp SSS--STTCEEEETTTEEEEEEEEEEE
T ss_pred CccCCCCCCEEEECCCcEEeEEEEEeE
Confidence 346788899999999999999998744
No 56
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional
Probab=49.06 E-value=39 Score=27.58 Aligned_cols=34 Identities=12% Similarity=0.304 Sum_probs=27.2
Q ss_pred cccceEEccCCeeeeeeeEEecccCCceeEEeecC
Q 029223 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMME 109 (197)
Q Consensus 75 ~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~d 109 (197)
.+...|+ ++.+.+|+|.+|+=+-.+++..|+..+
T Consensus 94 LiG~~V~-~~g~~lG~V~~v~~~ga~dvlvV~~~~ 127 (162)
T PRK13829 94 LRGLPVY-VDGEPLGEVVDVEDAGAQDLLVIRHVG 127 (162)
T ss_pred ccCeEEE-ECCEeeEEEEEEecCCCceEEEEEeCC
Confidence 4577889 888999999999986666777888644
No 57
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=47.44 E-value=41 Score=29.37 Aligned_cols=71 Identities=14% Similarity=0.108 Sum_probs=41.0
Q ss_pred CcceEEeeceeeeccCceEecccccccCcccceEEccCCeeeeeeeEEecccC---CceeEEeecCCcccccccc-CcEE
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPIN---ESYFSVKMMEGIVATSYSL-GDKF 122 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~IGkV~EIFGpIn---~~Y~sVK~~d~v~a~s~~~-Gdkl 122 (197)
-+..+.||||.-.+-+.-|..+|.+. |+|.||.=.+. .+|..|..++.-.|+.... .|-+
T Consensus 5 ~~~~iyvGNLP~diRekeieDlFyKy----------------g~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGY 68 (241)
T KOG0105|consen 5 NSRRIYVGNLPGDIREKEIEDLFYKY----------------GRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGY 68 (241)
T ss_pred ccceEEecCCCcchhhccHHHHHhhh----------------cceEEEEeccCCCCCCeeEEEecCccchhhhhhccccc
Confidence 45678889888777665454444321 34444433111 3588888777666654433 3555
Q ss_pred EEcCCCCCcCCc
Q 029223 123 YIDPSKLLPLAR 134 (197)
Q Consensus 123 yIdp~klLPLdr 134 (197)
-.|.-. |.++.
T Consensus 69 dydg~r-LRVEf 79 (241)
T KOG0105|consen 69 DYDGCR-LRVEF 79 (241)
T ss_pred ccCcce-EEEEe
Confidence 556666 66665
No 58
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=46.53 E-value=5.3 Score=36.64 Aligned_cols=28 Identities=7% Similarity=-0.014 Sum_probs=23.1
Q ss_pred CCCcceEEeeceeeeccCceEecccccc
Q 029223 45 GPPAEVVEVSSFLHACEGDAVTKLTNEK 72 (197)
Q Consensus 45 gPPs~vl~lG~~sh~ce~dlV~K~~~~~ 72 (197)
.|++.+|+|++|.+.++++.|.++|+..
T Consensus 183 ~p~~~~l~v~nl~~~~te~~l~~~f~~~ 210 (457)
T TIGR01622 183 IPNFLKLYVGNLHFNITEQELRQIFEPF 210 (457)
T ss_pred CCCCCEEEEcCCCCCCCHHHHHHHHHhc
Confidence 3567899999999999998888877653
No 59
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=45.63 E-value=20 Score=25.67 Aligned_cols=49 Identities=18% Similarity=0.175 Sum_probs=31.4
Q ss_pred eEEccCCeee-eeeeEEecccCCceeEEeec---CCccccccccCcEEEEcCCC
Q 029223 79 PIYLQNKTQI-GKVDEIFGPINESYFSVKMM---EGIVATSYSLGDKFYIDPSK 128 (197)
Q Consensus 79 ~V~~knkt~I-GkV~EIFGpIn~~Y~sVK~~---d~v~a~s~~~GdklyIdp~k 128 (197)
.|.+++.+.+ |++..++-.+|.....+... +..+. .......+||..+.
T Consensus 21 ~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~-~~~~~~~~~IRG~~ 73 (79)
T COG1958 21 LVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKN-VRRLGGEVLIRGDN 73 (79)
T ss_pred EEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccc-cceeccEEEEECCc
Confidence 7788888766 99999999888776666432 21110 12234567776665
No 60
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=44.05 E-value=59 Score=27.31 Aligned_cols=33 Identities=21% Similarity=0.292 Sum_probs=28.9
Q ss_pred cccceEEccCCeeeeeeeEEecccCCceeEEee
Q 029223 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (197)
Q Consensus 75 ~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~ 107 (197)
.+...|++++.+.+|+|+||+=+=+.++..||.
T Consensus 106 LiG~~V~~~~g~~lG~V~~i~~~Ga~Dvl~V~~ 138 (174)
T COG0806 106 LIGLEVVTEDGELLGKVTEILETGANDVLVVKA 138 (174)
T ss_pred ecCcEEEcCCCcEEEEEEEEeeCCCccEEEEEe
Confidence 357889999999999999999988888888886
No 61
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=43.48 E-value=8.9 Score=35.32 Aligned_cols=38 Identities=11% Similarity=0.196 Sum_probs=29.3
Q ss_pred CCCCcceEEeeceeeeccCceEecccccccCcccceEE
Q 029223 44 EGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIY 81 (197)
Q Consensus 44 ~gPPs~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~ 81 (197)
.+-++..++|||++..|+++-|-..|++.-|.++..|+
T Consensus 74 Ksk~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv 111 (346)
T KOG0109|consen 74 KSKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV 111 (346)
T ss_pred cCCCccccccCCCCccccCHHHhhhhcccCCceeeeee
Confidence 35688999999999999998777777777666555443
No 62
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=42.70 E-value=7.8 Score=35.53 Aligned_cols=36 Identities=6% Similarity=-0.104 Sum_probs=26.8
Q ss_pred CcceEEeeceeeeccCceEecccccccCcccceEEc
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYL 82 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~ 82 (197)
++.+|+|++|.+.++++-|.++|+..-+.....|+.
T Consensus 88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~ 123 (457)
T TIGR01622 88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIK 123 (457)
T ss_pred CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEee
Confidence 467999999999999988888876644444444444
No 63
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=41.89 E-value=8.5 Score=38.28 Aligned_cols=37 Identities=14% Similarity=0.005 Sum_probs=27.6
Q ss_pred CcceEEeeceeeeccCceEecccccccCcccceEEcc
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQ 83 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~k 83 (197)
....|||++|++.++++.|.++|...-+.....|..+
T Consensus 106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D 142 (612)
T TIGR01645 106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWD 142 (612)
T ss_pred CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeec
Confidence 4568999999999999999998876555444444443
No 64
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=38.03 E-value=60 Score=24.49 Aligned_cols=49 Identities=18% Similarity=0.299 Sum_probs=29.2
Q ss_pred cceEEeeceeeec--cCceEecccc-cccCcccceEEccCCe--eeeeeeEEecccCCc
Q 029223 48 AEVVEVSSFLHAC--EGDAVTKLTN-EKIPYFNAPIYLQNKT--QIGKVDEIFGPINES 101 (197)
Q Consensus 48 s~vl~lG~~sh~c--e~dlV~K~~~-~~VP~~na~V~~knkt--~IGkV~EIFGpIn~~ 101 (197)
..|..||++...- .+.+++++.+ .+| .|.+.... .+.+++||-|.++..
T Consensus 19 k~VrivGkv~~~~~~g~~~~l~~~d~~~V-----~v~l~~~~~~~~~~~vEviG~V~~~ 72 (109)
T PF08661_consen 19 KTVRIVGKVESVDPDGGSATLSTSDGGQV-----TVSLNPPSDEELSKYVEVIGKVNDD 72 (109)
T ss_dssp SEEEEEEEEEEE-TTSSEEEEE-TTS-EE-----EEEESS--SS---SEEEEEEEE-TT
T ss_pred CeEEEEEEEeeEcCCCCEEEEEcCCCCEE-----EEEeCCCCCCCCCCEEEEEEEEcCC
Confidence 3688899999877 5567777754 345 55555433 358889999977765
No 65
>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional
Probab=37.48 E-value=61 Score=26.75 Aligned_cols=32 Identities=3% Similarity=0.026 Sum_probs=24.9
Q ss_pred cccceEEccCCeeee-eeeEEecccCCceeEEe
Q 029223 75 YFNAPIYLQNKTQIG-KVDEIFGPINESYFSVK 106 (197)
Q Consensus 75 ~~na~V~~knkt~IG-kV~EIFGpIn~~Y~sVK 106 (197)
.++..|++++.+.+| +|.||+=.-.++...|+
T Consensus 102 LiG~~V~d~~g~~lGG~V~~v~~~~a~dllvV~ 134 (171)
T PRK14590 102 LIGLQAIDETGKPLNWKLTDVQDNPAHPILVFI 134 (171)
T ss_pred ccCcEEEeCCCCEeeeEEEEEecCCCceEEEEE
Confidence 467899999999997 99999985555555554
No 66
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=37.46 E-value=1.1e+02 Score=21.23 Aligned_cols=27 Identities=30% Similarity=0.509 Sum_probs=17.0
Q ss_pred cCCeeeeeeeEEecccCCceeEEeecCCcc
Q 029223 83 QNKTQIGKVDEIFGPINESYFSVKMMEGIV 112 (197)
Q Consensus 83 knkt~IGkV~EIFGpIn~~Y~sVK~~d~v~ 112 (197)
|..+.+++|.++.+.- ++.|+++|...
T Consensus 1 ee~e~~~~V~~~lG~~---~~~V~~~dg~~ 27 (65)
T PF01176_consen 1 EEGEVIGRVTEMLGNN---LFEVECEDGEE 27 (65)
T ss_dssp STTEEEEEEEEEESSS---EEEEEETTSEE
T ss_pred CCcEEEEEEEEECCCC---EEEEEeCCCCE
Confidence 3456677777777732 56666666544
No 67
>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=37.41 E-value=26 Score=24.52 Aligned_cols=27 Identities=11% Similarity=0.047 Sum_probs=21.2
Q ss_pred eEEccCCeee-eeeeEEecccCCceeEE
Q 029223 79 PIYLQNKTQI-GKVDEIFGPINESYFSV 105 (197)
Q Consensus 79 ~V~~knkt~I-GkV~EIFGpIn~~Y~sV 105 (197)
.|.++++..+ |++..++-.+|..+..+
T Consensus 15 ~V~Lk~g~~~~G~L~~~D~~mNi~L~~~ 42 (68)
T cd01722 15 IVKLKWGMEYKGTLVSVDSYMNLQLANT 42 (68)
T ss_pred EEEECCCcEEEEEEEEECCCEEEEEeeE
Confidence 7888888766 99999999776665555
No 68
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=36.65 E-value=30 Score=24.50 Aligned_cols=38 Identities=11% Similarity=0.113 Sum_probs=27.8
Q ss_pred eEecccccccCcccceEEccCCeee-eeeeEEecccCCceeEEe
Q 029223 64 AVTKLTNEKIPYFNAPIYLQNKTQI-GKVDEIFGPINESYFSVK 106 (197)
Q Consensus 64 lV~K~~~~~VP~~na~V~~knkt~I-GkV~EIFGpIn~~Y~sVK 106 (197)
+|.++.+++| .|.+++++.+ |++..++-.+|..+..++
T Consensus 8 ~L~~~~~k~V-----~V~lk~g~~~~G~L~~~D~~mNlvL~d~~ 46 (72)
T PRK00737 8 VLNNALNSPV-----LVRLKGGREFRGELQGYDIHMNLVLDNAE 46 (72)
T ss_pred HHHHhCCCEE-----EEEECCCCEEEEEEEEEcccceeEEeeEE
Confidence 4445555566 7888877655 999999998888777764
No 69
>PRK14594 rimM 16S rRNA-processing protein RimM; Provisional
Probab=36.42 E-value=64 Score=26.40 Aligned_cols=32 Identities=22% Similarity=0.341 Sum_probs=26.1
Q ss_pred cccceEEccCCeeeeeeeEEecccCCceeEEee
Q 029223 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (197)
Q Consensus 75 ~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~ 107 (197)
.++..|+++ .+.+|+|.+|+=.-.+++..||.
T Consensus 102 LiG~~V~~~-g~~lG~V~~v~~~ga~dll~V~~ 133 (166)
T PRK14594 102 LIGYAIVND-GKELGEVVSFFECLNSVLLEVKV 133 (166)
T ss_pred ccCeEEEEC-CEEEEEEEEEeeCCCcEEEEEEe
Confidence 467789986 78899999999977777778874
No 70
>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=35.40 E-value=32 Score=23.36 Aligned_cols=29 Identities=17% Similarity=0.071 Sum_probs=23.3
Q ss_pred eEEccCCeee-eeeeEEecccCCceeEEee
Q 029223 79 PIYLQNKTQI-GKVDEIFGPINESYFSVKM 107 (197)
Q Consensus 79 ~V~~knkt~I-GkV~EIFGpIn~~Y~sVK~ 107 (197)
.|.++++..+ |++..++-.+|..+..++.
T Consensus 12 ~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~ 41 (67)
T PF01423_consen 12 RVELKNGRTYRGTLVSFDQFMNLVLSDVTE 41 (67)
T ss_dssp EEEETTSEEEEEEEEEEETTEEEEEEEEEE
T ss_pred EEEEeCCEEEEEEEEEeechheEEeeeEEE
Confidence 7888888776 9999999977777666654
No 71
>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional
Probab=35.38 E-value=1.1e+02 Score=25.31 Aligned_cols=33 Identities=24% Similarity=0.296 Sum_probs=25.4
Q ss_pred cccceEEccCCeeeeeeeEEecccCCceeEEeec
Q 029223 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMM 108 (197)
Q Consensus 75 ~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~ 108 (197)
.+...|+++ .+.+|+|.||+=+-.+++..|+..
T Consensus 109 LiGl~V~~~-g~~lG~V~~v~~~ga~dvlvV~~~ 141 (184)
T PRK14593 109 LVGLSVVEE-NEILGKVIEIQRISQTDYFMVETT 141 (184)
T ss_pred ccCcEEEEC-CEEeEEEEEEccCCCceEEEEEec
Confidence 467788976 678999999998666666777753
No 72
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=34.25 E-value=9 Score=36.46 Aligned_cols=36 Identities=8% Similarity=0.014 Sum_probs=28.0
Q ss_pred eEEeeceeeeccCceEecccccccCcccceEEccCC
Q 029223 50 VVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNK 85 (197)
Q Consensus 50 vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knk 85 (197)
.|+|++|...++++.|.++|.+.-+..+..|..+..
T Consensus 2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~ 37 (562)
T TIGR01628 2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSV 37 (562)
T ss_pred eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC
Confidence 699999999999998888887665555666665544
No 73
>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]
Probab=34.12 E-value=19 Score=32.29 Aligned_cols=86 Identities=16% Similarity=0.159 Sum_probs=48.6
Q ss_pred CCCCcceEEeeceeeeccCceEeccccc--ccCcccceEEccCCeeeeeeeEEecccCCceeEEeecCCccccccccCcE
Q 029223 44 EGPPAEVVEVSSFLHACEGDAVTKLTNE--KIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDK 121 (197)
Q Consensus 44 ~gPPs~vl~lG~~sh~ce~dlV~K~~~~--~VP~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~d~v~a~s~~~Gdk 121 (197)
..++...++|++|+++.+.|.|.+.+.. .|..+..+.+.+.. +.+.|. |+.++..+..++ .+.. +.
T Consensus 181 ~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~-----~~kg~a-----~~~~~~~~~~~~-~~~~-~~ 248 (285)
T KOG4210|consen 181 SGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESG-----DSKGFA-----YVDFSAGNSKKL-ALND-QT 248 (285)
T ss_pred cCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCcc-----chhhhh-----hhhhhhchhHHH-Hhhc-cc
Confidence 4567777779999999999988855432 34332223332222 233355 555544333222 2332 44
Q ss_pred EEEcCCCCCcCCccCCCCCCC
Q 029223 122 FYIDPSKLLPLARFLPQPKGQ 142 (197)
Q Consensus 122 lyIdp~klLPLdrflPkpk~~ 142 (197)
-+|.... +.|++--|.|+..
T Consensus 249 ~~~~~~~-~~~~~~~~~~~~~ 268 (285)
T KOG4210|consen 249 RSIGGRP-LRLEEDEPRPKSD 268 (285)
T ss_pred CcccCcc-cccccCCCCcccc
Confidence 5666666 7788866777664
No 74
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]
Probab=33.02 E-value=11 Score=35.88 Aligned_cols=46 Identities=11% Similarity=0.051 Sum_probs=37.4
Q ss_pred CCCCCc-ceEEeeceeeeccCceEecccccccCcccceEEccCCeee
Q 029223 43 DEGPPA-EVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQI 88 (197)
Q Consensus 43 ~~gPPs-~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~I 88 (197)
..+|+. .+++||++.+...++.|..++.+..|.++...+++..+-.
T Consensus 12 ~~~~~~~~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~ 58 (435)
T KOG0108|consen 12 LNSPGLSSSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGK 58 (435)
T ss_pred ccCcccccceEecCCCCcccHHHHHHHHhccCccceeeecccccCCC
Confidence 345565 8999999999999999988888878888888887777644
No 75
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]
Probab=33.02 E-value=25 Score=32.14 Aligned_cols=23 Identities=0% Similarity=0.031 Sum_probs=18.1
Q ss_pred CcceEEeeceeeeccCceEeccc
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLT 69 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~ 69 (197)
.+..+|||.|+|.++++-|...+
T Consensus 5 ~~~KlfiGgisw~ttee~Lr~yf 27 (311)
T KOG4205|consen 5 ESGKLFIGGLSWETTEESLREYF 27 (311)
T ss_pred CCcceeecCcCccccHHHHHHHh
Confidence 45689999999999887665554
No 76
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=32.17 E-value=12 Score=37.36 Aligned_cols=37 Identities=5% Similarity=-0.072 Sum_probs=28.5
Q ss_pred CcceEEeeceeeeccCceEecccccccCcccceEEcc
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQ 83 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~k 83 (197)
....|||++|.+.++++.|.++|+..-+..++.|..+
T Consensus 203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D 239 (612)
T TIGR01645 203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARA 239 (612)
T ss_pred ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEec
Confidence 4568999999999999989888876555555566544
No 77
>PHA02979 hypothetical protein; Provisional
Probab=31.00 E-value=18 Score=29.12 Aligned_cols=35 Identities=29% Similarity=0.404 Sum_probs=21.8
Q ss_pred ceeeeccCceEecccccccCcccceEEccCCeeeeeeeEEec
Q 029223 55 SFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFG 96 (197)
Q Consensus 55 ~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~IGkV~EIFG 96 (197)
.||+.|+-|+-++| +.+..|..+++.+. ||.+||-
T Consensus 5 m~Sf~~diDLYtEC--erisdfYrRliN~~-----KiidiFi 39 (140)
T PHA02979 5 MFSFICDIDLYTEC--ERISDFYRRLINEE-----KIIDIFI 39 (140)
T ss_pred EEEeecCchhhhhh--hHHHHHHHHHhCcc-----eEEEEEh
Confidence 58899999988888 33444444444433 3556665
No 78
>PLN03213 repressor of silencing 3; Provisional
Probab=30.84 E-value=12 Score=36.86 Aligned_cols=37 Identities=8% Similarity=-0.057 Sum_probs=26.8
Q ss_pred CcceEEeeceeeeccCceEecccccccCcccceEEcc
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQ 83 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~k 83 (197)
....||||+|+|.++++-|...|.+.--..+..|+-+
T Consensus 9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE 45 (759)
T PLN03213 9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT 45 (759)
T ss_pred cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc
Confidence 4468999999999999888888876433344455533
No 79
>PLN03120 nucleic acid binding protein; Provisional
Probab=30.47 E-value=21 Score=31.98 Aligned_cols=37 Identities=11% Similarity=0.004 Sum_probs=27.4
Q ss_pred cceEEeeceeeeccCceEecccccccCcccceEEccC
Q 029223 48 AEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQN 84 (197)
Q Consensus 48 s~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~kn 84 (197)
..+|+|+||++.++++.|.+.|...-+..+..|..++
T Consensus 4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~ 40 (260)
T PLN03120 4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN 40 (260)
T ss_pred CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC
Confidence 4689999999999999898888764444444555444
No 80
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=29.98 E-value=25 Score=35.02 Aligned_cols=54 Identities=19% Similarity=0.305 Sum_probs=44.9
Q ss_pred ceEEeeceeeeccCceEecccccccCcccceEEccCCe--eeeeeeEEecccCCceeEEeecCCcc
Q 029223 49 EVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKT--QIGKVDEIFGPINESYFSVKMMEGIV 112 (197)
Q Consensus 49 ~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt--~IGkV~EIFGpIn~~Y~sVK~~d~v~ 112 (197)
.||||.++.+.+.++-+.+.|...-|+-.+.|++...+ ..| |+ |+++.|++.++
T Consensus 6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RG-----fg-----fVtFam~ED~q 61 (678)
T KOG0127|consen 6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRG-----FG-----FVTFAMEEDVQ 61 (678)
T ss_pred ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccC-----cc-----ceeeehHhHHH
Confidence 79999999999999999999988889999999987765 336 66 88888766544
No 81
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=29.80 E-value=2.1e+02 Score=25.48 Aligned_cols=22 Identities=27% Similarity=0.376 Sum_probs=14.8
Q ss_pred CCeeeeeeeEEecc-----cCCceeEE
Q 029223 84 NKTQIGKVDEIFGP-----INESYFSV 105 (197)
Q Consensus 84 nkt~IGkV~EIFGp-----In~~Y~sV 105 (197)
++..||+|.||+.. |+.+|.++
T Consensus 65 gD~VIG~I~~v~~~~W~VDI~sp~~A~ 91 (239)
T COG1097 65 GDVVIGKIIEVGPSGWKVDIGSPYPAL 91 (239)
T ss_pred CCEEEEEEEEEcccceEEEcCCccceE
Confidence 55667999999873 44455555
No 82
>PF11380 DUF3184: Protein of unknown function (DUF3184); InterPro: IPR021520 This eukaryotic family of proteins has no known function. ; GO: 0016772 transferase activity, transferring phosphorus-containing groups
Probab=29.70 E-value=30 Score=34.68 Aligned_cols=39 Identities=26% Similarity=0.386 Sum_probs=33.2
Q ss_pred cccCcccceEEccCCeeeeeeeEEecccCCceeEEeecC
Q 029223 71 EKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMME 109 (197)
Q Consensus 71 ~~VP~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~d 109 (197)
+..|-||+.++-.+...|=.+.|+|-.+|++|+-.|+-+
T Consensus 81 ~~lpTFNShaIE~~LhrIpgLSE~FIYfNDD~F~~rpV~ 119 (691)
T PF11380_consen 81 EALPTFNSHAIESQLHRIPGLSEHFIYFNDDYFFNRPVD 119 (691)
T ss_pred ccCCCcchHHHHHHHhcCCCccceeEEecCCEEEcCcCC
Confidence 356679999999999999889999999999999887643
No 83
>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]
Probab=29.19 E-value=21 Score=34.27 Aligned_cols=67 Identities=18% Similarity=0.257 Sum_probs=0.0
Q ss_pred CCCCC---CcceEEeeceeeeccCceEecccccccCcccceEEccCCeeeeeeeEEecccCCceeEEeecCCccccc---
Q 029223 42 RDEGP---PAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATS--- 115 (197)
Q Consensus 42 ~~~gP---Ps~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~d~v~a~s--- 115 (197)
.++.+ |++|+-|.++.|.|.++-|+.+.. +.|+|+.|.--.-..-..+.+.|...|.+
T Consensus 19 ~~~~~~~~pSkV~HlRnlp~e~tE~elI~Lg~----------------pFG~vtn~~~lkGknQAflem~d~~sAvtmv~ 82 (492)
T KOG1190|consen 19 YTQRSMAEPSKVVHLRNLPWEVTEEELISLGL----------------PFGKVTNLLMLKGKNQAFLEMADEESAVTMVN 82 (492)
T ss_pred cccccccCCcceeEeccCCccccHHHHHHhcc----------------cccceeeeeeeccchhhhhhhcchhhhhheee
Q ss_pred -------cccCcEEEE
Q 029223 116 -------YSLGDKFYI 124 (197)
Q Consensus 116 -------~~~GdklyI 124 (197)
...++.+||
T Consensus 83 ~y~~~~p~lr~~~~yi 98 (492)
T KOG1190|consen 83 YYTSVTPVLRGQPIYI 98 (492)
T ss_pred cccccCccccCcceee
No 84
>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=27.53 E-value=80 Score=20.85 Aligned_cols=28 Identities=14% Similarity=0.078 Sum_probs=20.4
Q ss_pred eEEccCCeee-eeeeEEecccCCceeEEe
Q 029223 79 PIYLQNKTQI-GKVDEIFGPINESYFSVK 106 (197)
Q Consensus 79 ~V~~knkt~I-GkV~EIFGpIn~~Y~sVK 106 (197)
.|.+++.+.+ |++..++.-+|..+.+++
T Consensus 10 ~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~ 38 (63)
T cd00600 10 RVELKDGRVLEGVLVAFDKYMNLVLDDVE 38 (63)
T ss_pred EEEECCCcEEEEEEEEECCCCCEEECCEE
Confidence 6777777655 999999986666655554
No 85
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=26.60 E-value=94 Score=26.11 Aligned_cols=12 Identities=17% Similarity=0.218 Sum_probs=8.7
Q ss_pred cceEEeeceeee
Q 029223 48 AEVVEVSSFLHA 59 (197)
Q Consensus 48 s~vl~lG~~sh~ 59 (197)
.+|+++|+|..+
T Consensus 7 N~V~LiGrLg~D 18 (177)
T PRK09010 7 NKVILVGNLGQD 18 (177)
T ss_pred eEEEEEEEeCCC
Confidence 467888887764
No 86
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=25.48 E-value=1.1e+02 Score=23.14 Aligned_cols=8 Identities=50% Similarity=0.821 Sum_probs=3.3
Q ss_pred eeeeEEec
Q 029223 89 GKVDEIFG 96 (197)
Q Consensus 89 GkV~EIFG 96 (197)
|+|+|++.
T Consensus 11 G~V~e~Lp 18 (87)
T PRK12442 11 GIVDEVLP 18 (87)
T ss_pred EEEEEECC
Confidence 44444433
No 87
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=25.47 E-value=1.2e+02 Score=26.74 Aligned_cols=10 Identities=30% Similarity=0.670 Sum_probs=7.6
Q ss_pred ccccCcEEEE
Q 029223 115 SYSLGDKFYI 124 (197)
Q Consensus 115 s~~~GdklyI 124 (197)
+++++|.+|.
T Consensus 108 nl~vGdliya 117 (230)
T KOG1004|consen 108 NLQVGDLIYA 117 (230)
T ss_pred ccccccEEEE
Confidence 5777888885
No 88
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=25.47 E-value=30 Score=24.55 Aligned_cols=32 Identities=25% Similarity=0.514 Sum_probs=22.4
Q ss_pred CceEecccccccCcccceEEccCCeee-eeeeEEec
Q 029223 62 GDAVTKLTNEKIPYFNAPIYLQNKTQI-GKVDEIFG 96 (197)
Q Consensus 62 ~dlV~K~~~~~VP~~na~V~~knkt~I-GkV~EIFG 96 (197)
++++-.+-.+++|. .||+.|+.++ |+|.+.+-
T Consensus 5 d~fln~~r~~~~~V---ti~L~nG~~l~G~I~~fD~ 37 (61)
T TIGR02383 5 DQFLNTLRKERIPV---TVFLVNGVQLKGVIESFDN 37 (61)
T ss_pred HHHHHHHHHcCCcE---EEEEeCCcEEEEEEEEEee
Confidence 33444444455654 9999999888 99998765
No 89
>PF07290 DUF1449: Protein of unknown function (DUF1449); InterPro: IPR010840 This family consists of several bacterial proteins of around 210 residues in length. The function of this family is unknown.
Probab=25.20 E-value=85 Score=26.96 Aligned_cols=32 Identities=22% Similarity=0.459 Sum_probs=23.4
Q ss_pred eeeeEEecccCCceeEEeecCCccccccccCcEEEEc
Q 029223 89 GKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYID 125 (197)
Q Consensus 89 GkV~EIFGpIn~~Y~sVK~~d~v~a~s~~~GdklyId 125 (197)
-+|.|-|+ |.+|+.|.+++. +.++.||+++|-
T Consensus 156 a~V~D~~G--q~hyv~veP~~~---~~~~~G~~VLlv 187 (202)
T PF07290_consen 156 ARVKDQFG--QLHYVMVEPEAG---EEFKQGTEVLLV 187 (202)
T ss_pred EEEEecCC--CEEEEEEeeCCC---CCCCCCCEEEEE
Confidence 46777777 458999988743 456789888775
No 90
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=24.44 E-value=2e+02 Score=21.98 Aligned_cols=24 Identities=17% Similarity=0.495 Sum_probs=14.0
Q ss_pred CCeeeeeeeEEecccCCceeEEeecCC
Q 029223 84 NKTQIGKVDEIFGPINESYFSVKMMEG 110 (197)
Q Consensus 84 nkt~IGkV~EIFGpIn~~Y~sVK~~d~ 110 (197)
+.+.+++|+++.|.- ++.|.+++.
T Consensus 18 e~e~~g~V~~~lG~~---~~~V~~~dG 41 (99)
T TIGR00523 18 EGEILGVIEQMLGAG---RVKVRCLDG 41 (99)
T ss_pred CCEEEEEEEEEcCCC---EEEEEeCCC
Confidence 556667777777722 445555443
No 91
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=24.36 E-value=73 Score=21.43 Aligned_cols=27 Identities=19% Similarity=0.119 Sum_probs=20.2
Q ss_pred eEEccCCeee-eeeeEEecccCCceeEE
Q 029223 79 PIYLQNKTQI-GKVDEIFGPINESYFSV 105 (197)
Q Consensus 79 ~V~~knkt~I-GkV~EIFGpIn~~Y~sV 105 (197)
.|.+++.+.+ |++..++-.+|..+..+
T Consensus 12 ~V~l~~g~~~~G~L~~~D~~~NlvL~~~ 39 (67)
T smart00651 12 LVELKNGREYRGTLKGFDQFMNLVLEDV 39 (67)
T ss_pred EEEECCCcEEEEEEEEECccccEEEccE
Confidence 7788777655 99999998776655544
No 92
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=23.24 E-value=1.4e+02 Score=20.99 Aligned_cols=36 Identities=22% Similarity=0.126 Sum_probs=20.2
Q ss_pred eccCceEecccccccCcccceEEccCCeeeeeeeEEec
Q 029223 59 ACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFG 96 (197)
Q Consensus 59 ~ce~dlV~K~~~~~VP~~na~V~~knkt~IGkV~EIFG 96 (197)
..++-+.++.+++.| ...-|..+.++..|+|++|+=
T Consensus 13 imEDV~~iev~~e~V--~a~Dilgd~ke~~G~vkriDl 48 (57)
T COG1532 13 IMEDVLYIEVTEEGV--VARDILGDEKEFEGQVKRIDL 48 (57)
T ss_pred EEeEEEEEEEecCcE--EEEeccCCceEecceEEEEEc
Confidence 344545555555554 122455566666688887764
No 93
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=22.55 E-value=2.3e+02 Score=27.08 Aligned_cols=6 Identities=50% Similarity=0.905 Sum_probs=2.4
Q ss_pred CCCCCC
Q 029223 147 ARGGRG 152 (197)
Q Consensus 147 grGggr 152 (197)
+|++++
T Consensus 334 grgggk 339 (465)
T KOG3973|consen 334 GRGGGK 339 (465)
T ss_pred CcCCCC
Confidence 344343
No 94
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=22.53 E-value=27 Score=33.28 Aligned_cols=35 Identities=6% Similarity=-0.016 Sum_probs=25.7
Q ss_pred cceEEeeceeeeccCceEecccccccCcccceEEc
Q 029223 48 AEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYL 82 (197)
Q Consensus 48 s~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~ 82 (197)
..+|+|.+|.+.++++.|.++|+..-..+...|..
T Consensus 88 ~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~ 122 (562)
T TIGR01628 88 VGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVAT 122 (562)
T ss_pred CCceEEcCCCccCCHHHHHHHHHhcCCcceeEeee
Confidence 35799999999999998888887644444444443
No 95
>cd00226 PRCH Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce ATP by ATP synthase. Subunit H is positioned mainly in the cytoplasm with one transmembrane alpha helix. Provides proton transfer pathway (water channels) connecting the terminal quinone electron acceptor of RC, to the aqueous phase. Found in photosynthetic bacteria: alpha, beta, and gamma proteobacteria.
Probab=22.43 E-value=2.9e+02 Score=24.70 Aligned_cols=34 Identities=18% Similarity=0.218 Sum_probs=25.8
Q ss_pred cccceEEccCCeeeeeeeEEeccc---CCceeEEeec
Q 029223 75 YFNAPIYLQNKTQIGKVDEIFGPI---NESYFSVKMM 108 (197)
Q Consensus 75 ~~na~V~~knkt~IGkV~EIFGpI---n~~Y~sVK~~ 108 (197)
....+|+..+++++|+|+||+--. .--|..|.+.
T Consensus 148 prGl~V~g~DGevvGtV~Dv~vD~~e~~iRYLeVdtg 184 (246)
T cd00226 148 PRGLPVVGADGEVAGKVTDLWVDRPEQLFRYLEVELA 184 (246)
T ss_pred CCCCEeEcCCCcEeEEEEEEEEcCCcceEEEEEEEcC
Confidence 346689999999999999998722 2248888763
No 96
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=22.40 E-value=1.6e+02 Score=21.63 Aligned_cols=13 Identities=23% Similarity=0.555 Sum_probs=6.3
Q ss_pred CCeeeeeeeEEec
Q 029223 84 NKTQIGKVDEIFG 96 (197)
Q Consensus 84 nkt~IGkV~EIFG 96 (197)
+.+.+++|++..|
T Consensus 4 e~q~~g~V~~~lG 16 (83)
T smart00652 4 DGQEIAQVVKMLG 16 (83)
T ss_pred CCcEEEEEEEEcC
Confidence 3444455555544
No 97
>PF09475 Dot_icm_IcmQ: Dot/Icm secretion system protein (dot_icm_IcmQ); InterPro: IPR013365 Proteins in this entry are the IcmQ component of Dot/Icm secretion systems, as found in the obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the literature now seems to favor calling this the Dot/Icm system. This protein was shown to be essential for translocation ().; PDB: 3FXE_A 3FXD_C.
Probab=22.12 E-value=30 Score=29.45 Aligned_cols=50 Identities=20% Similarity=0.474 Sum_probs=0.0
Q ss_pred ccceEEccCCeeeeeeeEEecccCCceeEEeecCCccccccccCcEEEEcCCCCCcCCcc
Q 029223 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARF 135 (197)
Q Consensus 76 ~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~d~v~a~s~~~GdklyIdp~klLPLdrf 135 (197)
+.-|||.......--|..=--.+|+-|++|...+ -|.+-+.+|+ +|+|+|
T Consensus 93 isRPIY~nE~dvk~~IksKenk~NEAYVaiyInq---------~dIl~~~~dk-~~~Dk~ 142 (179)
T PF09475_consen 93 ISRPIYANEEDVKAAIKSKENKLNEAYVAIYINQ---------SDILSLSPDK-IPTDKL 142 (179)
T ss_dssp ------------------------------------------------------------
T ss_pred hCCCCcCCHHHHHHHHHhhhcccceeEEEEEEch---------HhcccCCccc-cccccc
Confidence 3456666444433322222233444555554332 2334445566 677766
No 98
>PF14031 D-ser_dehydrat: Putative serine dehydratase domain; PDB: 3LLX_A 3ANV_A 3AWO_A 3AWN_A 3ANU_A 3GWQ_A.
Probab=22.01 E-value=2.6e+02 Score=20.71 Aligned_cols=29 Identities=28% Similarity=0.435 Sum_probs=15.5
Q ss_pred cCCceeEEeecCCccccccccCcEEEEcCCC
Q 029223 98 INESYFSVKMMEGIVATSYSLGDKFYIDPSK 128 (197)
Q Consensus 98 In~~Y~sVK~~d~v~a~s~~~GdklyIdp~k 128 (197)
+++..-.|++.+. .+.+++||+++|.|.-
T Consensus 51 ~seEHg~l~~~~~--~~~~~vGd~v~iiP~H 79 (94)
T PF14031_consen 51 LSEEHGILRLPDG--ADRLKVGDKVEIIPNH 79 (94)
T ss_dssp E-SS-EEEE-STT--GCGT-TT-EEEEEESS
T ss_pred eecceeEEECCCC--CCCCCCCCEEEEECCc
Confidence 3444455555554 3458999999998764
No 99
>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=21.65 E-value=63 Score=23.35 Aligned_cols=37 Identities=16% Similarity=0.162 Sum_probs=24.5
Q ss_pred eEecccccccCcccceEEccCCeee-eeeeEEecccCCceeEE
Q 029223 64 AVTKLTNEKIPYFNAPIYLQNKTQI-GKVDEIFGPINESYFSV 105 (197)
Q Consensus 64 lV~K~~~~~VP~~na~V~~knkt~I-GkV~EIFGpIn~~Y~sV 105 (197)
+|.++.++.| .|.+++++.+ |++..++.-+|.....+
T Consensus 7 ~L~~~~~~~V-----~V~l~~gr~~~G~L~g~D~~mNlvL~da 44 (76)
T cd01732 7 LIDKCIGSRI-----WIVMKSDKEFVGTLLGFDDYVNMVLEDV 44 (76)
T ss_pred HHHHhCCCEE-----EEEECCCeEEEEEEEEeccceEEEEccE
Confidence 3444445555 7777777765 99999998666654443
No 100
>COG5436 Predicted integral membrane protein [Function unknown]
Probab=21.34 E-value=89 Score=26.48 Aligned_cols=42 Identities=17% Similarity=0.266 Sum_probs=25.1
Q ss_pred CcceEEeeceeeeccCceEecccccccCcccceEEccCCeee
Q 029223 47 PAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQI 88 (197)
Q Consensus 47 Ps~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~I 88 (197)
|+..+.--.-+++..+-.|--....+|||.+..||+.|...+
T Consensus 62 ~dP~l~~a~C~fdvsegpvri~a~~nvpyWSvsiyds~~nn~ 103 (182)
T COG5436 62 PDPNLLYAFCRFDVSEGPVRIEAKGNVPYWSVSIYDSNGNNF 103 (182)
T ss_pred CCchhhhheeEeeccCCcEEEEecCCCceEEEEEEcCCCCce
Confidence 333444444555555543332223489999999999887644
No 101
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=21.25 E-value=41 Score=30.82 Aligned_cols=42 Identities=12% Similarity=-0.039 Sum_probs=33.4
Q ss_pred eEEeeceeeeccCceEecccccccCcccceEEccCCeeeeee
Q 029223 50 VVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKV 91 (197)
Q Consensus 50 vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~IGkV 91 (197)
-+||+-||-.++.+.|.++|..---.-+|.|+-+..|...|-
T Consensus 64 hvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKG 105 (321)
T KOG0148|consen 64 HVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKG 105 (321)
T ss_pred eEEehhcchhcchHHHHHHhccccccccceEeecccCCcccc
Confidence 378899998888888888887655567889999988877543
No 102
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=20.63 E-value=1.8e+02 Score=22.08 Aligned_cols=20 Identities=15% Similarity=0.300 Sum_probs=11.3
Q ss_pred eeeeeeeEEeccc-CCceeEE
Q 029223 86 TQIGKVDEIFGPI-NESYFSV 105 (197)
Q Consensus 86 t~IGkV~EIFGpI-n~~Y~sV 105 (197)
.-|++|.+|+=.. +..++.+
T Consensus 21 ~~i~~I~~i~~~~~g~~~~~~ 41 (121)
T cd04717 21 PIIFRIERLWKDEDGEKFFFG 41 (121)
T ss_pred CEEEEEeEEEECCCCCEEEEE
Confidence 3467777777644 3335554
No 103
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=20.52 E-value=1.5e+02 Score=24.63 Aligned_cols=11 Identities=9% Similarity=0.178 Sum_probs=7.0
Q ss_pred cceEEeeceee
Q 029223 48 AEVVEVSSFLH 58 (197)
Q Consensus 48 s~vl~lG~~sh 58 (197)
.+|+++|+|-.
T Consensus 6 N~V~LiGrLg~ 16 (166)
T PRK06341 6 NKVILIGNLGA 16 (166)
T ss_pred eEEEEEEEecC
Confidence 45677776654
No 104
>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]
Probab=20.30 E-value=35 Score=30.64 Aligned_cols=45 Identities=29% Similarity=0.390 Sum_probs=28.4
Q ss_pred eeeeeeEEecccCCceeEEeecCCcc--ccccccC-cEEEEcCCCCCcCCcc
Q 029223 87 QIGKVDEIFGPINESYFSVKMMEGIV--ATSYSLG-DKFYIDPSKLLPLARF 135 (197)
Q Consensus 87 ~IGkV~EIFGpIn~~Y~sVK~~d~v~--a~s~~~G-dklyIdp~klLPLdrf 135 (197)
+.|.|+|||||. .|=|..=.++ +...+++ ..+|||.+.-|+.+|+
T Consensus 58 ~~g~ItEiyG~~----gsGKT~lal~~~~~aq~~g~~a~fIDtE~~l~p~r~ 105 (279)
T COG0468 58 PRGRITEIYGPE----SSGKTTLALQLVANAQKPGGKAAFIDTEHALDPERA 105 (279)
T ss_pred ccceEEEEecCC----CcchhhHHHHHHHHhhcCCCeEEEEeCCCCCCHHHH
Confidence 458999999965 4444322222 2222344 7799999987776665
No 105
>KOG0908 consensus Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=20.22 E-value=87 Score=28.47 Aligned_cols=43 Identities=7% Similarity=0.065 Sum_probs=23.8
Q ss_pred eceeeeccCceEecccccccCcccceEEccCCeeeeeeeEEec
Q 029223 54 SSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFG 96 (197)
Q Consensus 54 G~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~IGkV~EIFG 96 (197)
.+|..+|+++++..++-.+++.+.+.-+.--++..+.++-++.
T Consensus 155 s~lesD~DeQl~isi~fnq~vk~hS~a~k~p~~~~~Pk~vkif 197 (288)
T KOG0908|consen 155 SNLESDCDEQLIISIPFNQAVKVHSIAIKGPANPLGPKTVKIF 197 (288)
T ss_pred cceecccccceEEEeeccCccceeeeecCCCCCCCCCeeEEEE
Confidence 5667788888777765445544444444333344454444443
Done!