Query 022221
Match_columns 300
No_of_seqs 207 out of 1061
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 08:57:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022221.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022221hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1677 CCCH-type Zn-finger pr 99.6 4.3E-16 9.3E-21 145.1 6.4 75 41-137 87-162 (332)
2 KOG1677 CCCH-type Zn-finger pr 99.6 4.1E-15 8.9E-20 138.5 11.3 81 34-138 126-207 (332)
3 COG5063 CTH1 CCCH-type Zn-fing 99.1 1.9E-10 4.1E-15 102.0 5.5 74 33-136 221-302 (351)
4 COG5063 CTH1 CCCH-type Zn-fing 99.0 7.2E-10 1.6E-14 98.4 5.7 32 265-296 270-302 (351)
5 KOG1595 CCCH-type Zn-finger pr 98.9 1.1E-09 2.3E-14 104.4 4.8 31 265-298 267-297 (528)
6 cd02396 PCBP_like_KH K homolog 98.9 2.6E-09 5.7E-14 75.6 4.1 64 179-242 1-65 (65)
7 PF00642 zf-CCCH: Zinc finger 98.8 6E-10 1.3E-14 64.7 0.0 26 267-292 1-27 (27)
8 PF00642 zf-CCCH: Zinc finger 98.8 7.6E-10 1.6E-14 64.2 0.1 26 38-63 1-26 (27)
9 KOG1676 K-homology type RNA bi 98.7 1.1E-08 2.4E-13 98.5 2.9 78 174-251 226-304 (600)
10 KOG1595 CCCH-type Zn-finger pr 98.6 1.3E-08 2.7E-13 97.2 2.7 67 36-139 232-298 (528)
11 KOG2192 PolyC-binding hnRNP-K 98.5 4.1E-08 9E-13 86.0 2.8 72 177-248 314-385 (390)
12 cd02394 vigilin_like_KH K homo 98.5 9.2E-08 2E-12 66.8 4.1 60 180-241 2-61 (62)
13 smart00356 ZnF_C3H1 zinc finge 98.5 9.7E-08 2.1E-12 55.2 2.1 26 267-292 2-27 (27)
14 KOG1040 Polyadenylation factor 98.5 8.7E-08 1.9E-12 87.9 2.7 56 37-132 74-129 (325)
15 cd00105 KH-I K homology RNA-bi 98.5 2.4E-07 5.1E-12 64.9 4.4 62 180-241 2-63 (64)
16 PF00013 KH_1: KH domain syndr 98.5 5E-08 1.1E-12 67.7 0.9 60 179-241 1-60 (60)
17 cd02393 PNPase_KH Polynucleoti 98.4 1.7E-07 3.8E-12 65.3 3.4 57 179-241 3-60 (61)
18 KOG2333 Uncharacterized conser 98.3 1.2E-07 2.6E-12 89.5 0.6 61 39-131 75-137 (614)
19 smart00356 ZnF_C3H1 zinc finge 98.3 3.9E-07 8.4E-12 52.6 2.2 26 37-63 1-26 (27)
20 KOG2193 IGF-II mRNA-binding pr 98.3 6.3E-07 1.4E-11 83.1 4.6 76 177-252 410-486 (584)
21 KOG2494 C3H1-type Zn-finger pr 98.0 3.4E-06 7.3E-11 76.3 2.8 67 33-136 30-97 (331)
22 KOG1676 K-homology type RNA bi 97.9 6.5E-06 1.4E-10 79.7 2.8 74 176-249 137-212 (600)
23 PF13014 KH_3: KH domain 97.9 8.4E-06 1.8E-10 52.6 2.3 42 188-229 1-43 (43)
24 KOG2190 PolyC-binding proteins 97.8 1.1E-05 2.4E-10 78.3 3.5 72 178-249 138-210 (485)
25 KOG2494 C3H1-type Zn-finger pr 97.8 1E-05 2.2E-10 73.2 1.8 27 270-297 72-98 (331)
26 KOG1492 C3H1-type Zn-finger pr 97.8 2.9E-05 6.3E-10 66.7 4.4 60 39-140 205-264 (377)
27 KOG2191 RNA-binding protein NO 97.7 2.2E-05 4.7E-10 71.1 3.4 73 178-250 132-207 (402)
28 smart00322 KH K homology RNA-b 97.7 2.8E-05 6.1E-10 54.2 3.1 65 178-244 3-67 (69)
29 KOG2191 RNA-binding protein NO 97.7 2.2E-05 4.8E-10 71.0 2.3 71 178-248 39-112 (402)
30 KOG1763 Uncharacterized conser 97.7 1.1E-05 2.3E-10 71.8 0.2 34 30-64 82-115 (343)
31 KOG2193 IGF-II mRNA-binding pr 97.5 3E-05 6.4E-10 72.3 0.9 71 179-249 494-566 (584)
32 KOG1040 Polyadenylation factor 97.4 0.0001 2.2E-09 67.9 3.4 54 39-132 104-157 (325)
33 COG5252 Uncharacterized conser 97.3 5.5E-05 1.2E-09 65.4 -0.5 36 30-66 75-110 (299)
34 COG5084 YTH1 Cleavage and poly 97.2 0.00078 1.7E-08 60.8 5.9 58 37-132 101-158 (285)
35 KOG0336 ATP-dependent RNA heli 97.2 0.00033 7.2E-09 65.7 3.5 85 158-245 27-111 (629)
36 TIGR03665 arCOG04150 arCOG0415 97.1 0.00015 3.2E-09 61.3 1.0 60 182-246 2-64 (172)
37 cd02395 SF1_like-KH Splicing f 97.0 0.00049 1.1E-08 54.6 2.3 62 187-248 15-96 (120)
38 KOG4791 Uncharacterized conser 96.9 0.00034 7.3E-09 66.3 1.4 23 42-65 5-27 (667)
39 PRK13763 putative RNA-processi 96.9 0.00042 9.1E-09 59.0 1.9 63 179-246 4-70 (180)
40 PF14608 zf-CCCH_2: Zinc finge 96.8 0.00082 1.8E-08 35.4 1.7 19 271-291 1-19 (19)
41 KOG2185 Predicted RNA-processi 96.8 0.00048 1E-08 64.1 1.0 24 270-293 141-164 (486)
42 TIGR03665 arCOG04150 arCOG0415 96.7 0.00051 1.1E-08 58.1 0.4 52 187-245 98-149 (172)
43 PRK13763 putative RNA-processi 96.2 0.0014 3.1E-08 55.8 0.4 52 187-245 104-155 (180)
44 PF14608 zf-CCCH_2: Zinc finge 96.2 0.0036 7.9E-08 32.9 1.7 19 110-131 1-19 (19)
45 KOG2190 PolyC-binding proteins 96.2 0.0097 2.1E-07 58.1 5.9 71 177-247 337-409 (485)
46 COG5152 Uncharacterized conser 96.1 0.0019 4.1E-08 54.7 0.7 30 36-65 137-166 (259)
47 KOG2192 PolyC-binding hnRNP-K 96.1 0.0012 2.6E-08 58.3 -0.5 70 179-248 124-194 (390)
48 KOG2185 Predicted RNA-processi 95.9 0.0034 7.5E-08 58.5 1.2 26 38-64 138-163 (486)
49 KOG2202 U2 snRNP splicing fact 95.8 0.0045 9.7E-08 54.6 1.5 29 42-70 17-45 (260)
50 KOG2333 Uncharacterized conser 95.4 0.0067 1.5E-07 58.1 1.3 27 107-133 75-103 (614)
51 KOG1492 C3H1-type Zn-finger pr 95.3 0.009 1.9E-07 51.6 1.8 29 38-67 231-259 (377)
52 COG5084 YTH1 Cleavage and poly 95.3 0.035 7.6E-07 50.3 5.5 30 106-136 102-131 (285)
53 TIGR02696 pppGpp_PNP guanosine 95.2 0.012 2.6E-07 59.8 2.5 65 177-247 577-642 (719)
54 KOG1039 Predicted E3 ubiquitin 95.2 0.018 3.8E-07 53.7 3.4 25 109-134 9-33 (344)
55 COG5152 Uncharacterized conser 95.2 0.0076 1.6E-07 51.1 0.9 29 267-295 139-168 (259)
56 KOG2202 U2 snRNP splicing fact 95.2 0.0055 1.2E-07 54.0 -0.0 31 262-292 145-175 (260)
57 TIGR03591 polynuc_phos polyrib 93.5 0.042 9E-07 56.2 2.1 63 178-246 551-614 (684)
58 KOG1813 Predicted E3 ubiquitin 93.0 0.029 6.3E-07 50.5 0.1 30 36-65 182-211 (313)
59 KOG0119 Splicing factor 1/bran 92.6 0.056 1.2E-06 52.0 1.4 70 178-247 138-230 (554)
60 KOG1763 Uncharacterized conser 91.9 0.042 9E-07 49.4 -0.3 35 263-297 86-120 (343)
61 KOG1813 Predicted E3 ubiquitin 91.5 0.056 1.2E-06 48.8 0.0 30 265-294 182-212 (313)
62 cd02134 NusA_KH NusA_K homolog 91.2 0.12 2.7E-06 35.7 1.5 36 178-213 25-60 (61)
63 PLN00207 polyribonucleotide nu 90.8 0.085 1.9E-06 55.0 0.6 64 177-246 684-749 (891)
64 KOG2113 Predicted RNA binding 90.6 0.66 1.4E-05 42.3 5.9 65 176-243 24-88 (394)
65 COG1094 Predicted RNA-binding 90.5 0.11 2.4E-06 44.3 0.9 52 188-246 112-163 (194)
66 KOG1039 Predicted E3 ubiquitin 89.8 0.12 2.6E-06 48.3 0.6 24 41-65 9-32 (344)
67 COG5252 Uncharacterized conser 89.4 0.085 1.8E-06 46.0 -0.7 34 265-298 81-114 (299)
68 PRK04163 exosome complex RNA-b 87.2 0.48 1E-05 42.0 2.7 60 179-244 146-206 (235)
69 KOG4791 Uncharacterized conser 86.3 0.66 1.4E-05 44.6 3.2 81 39-132 60-141 (667)
70 COG1185 Pnp Polyribonucleotide 84.4 0.7 1.5E-05 46.6 2.5 66 178-249 552-618 (692)
71 PF10650 zf-C3H1: Putative zin 83.9 0.69 1.5E-05 25.4 1.3 20 270-290 1-21 (23)
72 KOG2279 Kinase anchor protein 82.6 0.73 1.6E-05 45.1 1.8 71 177-247 139-209 (608)
73 TIGR03319 YmdA_YtgF conserved 82.0 0.82 1.8E-05 45.3 1.9 64 177-245 203-268 (514)
74 PRK00106 hypothetical protein; 81.4 0.96 2.1E-05 44.9 2.2 65 177-246 224-290 (535)
75 PRK12704 phosphodiesterase; Pr 80.7 1 2.2E-05 44.7 2.1 65 177-246 209-275 (520)
76 COG5176 MSL5 Splicing factor ( 80.6 0.72 1.6E-05 39.7 0.9 32 186-217 162-193 (269)
77 KOG2279 Kinase anchor protein 79.3 1.3 2.9E-05 43.4 2.3 68 177-244 295-365 (608)
78 PRK11824 polynucleotide phosph 78.5 0.93 2E-05 46.6 1.1 62 179-246 555-617 (693)
79 KOG0153 Predicted RNA-binding 77.6 1 2.2E-05 41.7 1.0 26 268-293 160-185 (377)
80 KOG1588 RNA-binding protein Sa 75.7 1.7 3.6E-05 38.9 1.7 38 178-215 92-135 (259)
81 KOG4369 RTK signaling protein 75.2 2.2 4.7E-05 45.6 2.6 72 179-250 1341-1413(2131)
82 PRK02821 hypothetical protein; 71.7 2.3 5E-05 30.9 1.3 31 177-207 30-60 (77)
83 PRK08406 transcription elongat 66.6 2.3 5E-05 34.6 0.5 38 178-215 99-136 (140)
84 PRK00468 hypothetical protein; 66.2 3.2 6.9E-05 30.0 1.1 30 178-207 30-59 (75)
85 PRK08406 transcription elongat 64.2 3.7 8.1E-05 33.4 1.3 38 179-216 33-70 (140)
86 KOG3273 Predicted RNA-binding 61.1 4.3 9.3E-05 34.9 1.2 53 186-245 177-229 (252)
87 PRK01064 hypothetical protein; 60.9 5.3 0.00011 29.1 1.5 30 177-206 29-58 (78)
88 KOG2814 Transcription coactiva 60.1 3.2 6.9E-05 38.3 0.2 72 180-253 59-131 (345)
89 PRK12705 hypothetical protein; 57.8 5.9 0.00013 39.2 1.6 40 178-217 198-238 (508)
90 KOG3702 Nuclear polyadenylated 57.4 54 0.0012 33.3 8.1 20 42-65 546-565 (681)
91 COG1837 Predicted RNA-binding 56.7 6.3 0.00014 28.5 1.2 30 177-206 29-58 (76)
92 KOG1067 Predicted RNA-binding 55.4 12 0.00025 37.3 3.2 62 179-247 598-660 (760)
93 PRK12328 nusA transcription el 54.4 8.3 0.00018 36.5 2.0 41 177-217 307-347 (374)
94 TIGR01952 nusA_arch NusA famil 53.0 5.6 0.00012 32.4 0.5 38 177-214 99-136 (141)
95 TIGR01953 NusA transcription t 52.7 7.8 0.00017 36.4 1.5 40 177-216 300-339 (341)
96 PF13184 KH_5: NusA-like KH do 52.5 6.8 0.00015 27.8 0.8 27 189-215 19-46 (69)
97 TIGR01952 nusA_arch NusA famil 52.1 7.7 0.00017 31.6 1.2 37 180-216 35-71 (141)
98 PF08098 ATX_III: Anemonia sul 50.9 8.3 0.00018 21.5 0.8 15 42-59 8-22 (27)
99 COG0195 NusA Transcription elo 50.6 7.4 0.00016 33.4 1.0 38 179-216 143-180 (190)
100 cd02414 jag_KH jag_K homology 50.5 11 0.00024 27.0 1.8 33 178-210 24-56 (77)
101 cd02410 archeal_CPSF_KH The ar 47.4 13 0.00027 30.5 1.7 40 178-217 76-115 (145)
102 COG1094 Predicted RNA-binding 46.6 18 0.00039 31.0 2.6 40 178-217 8-47 (194)
103 cd02413 40S_S3_KH K homology R 46.3 10 0.00022 27.7 1.0 30 179-208 31-60 (81)
104 KOG0153 Predicted RNA-binding 45.4 12 0.00025 34.9 1.4 28 39-67 160-187 (377)
105 cd02409 KH-II KH-II (K homolo 45.3 13 0.00029 25.0 1.5 30 182-211 29-58 (68)
106 PF07650 KH_2: KH domain syndr 43.1 4.6 9.9E-05 28.9 -1.3 32 180-211 27-58 (78)
107 PF10283 zf-CCHH: Zinc-finger 42.9 6.5 0.00014 22.3 -0.4 9 279-287 2-10 (26)
108 KOG2135 Proteins containing th 42.4 16 0.00035 35.4 1.9 51 5-64 186-236 (526)
109 PF13083 KH_4: KH domain; PDB: 39.6 5.7 0.00012 28.1 -1.2 32 177-208 28-59 (73)
110 PRK12329 nusA transcription el 38.1 16 0.00034 35.5 1.1 39 178-216 335-373 (449)
111 KOG3702 Nuclear polyadenylated 36.6 1.1E+02 0.0023 31.3 6.5 12 52-63 575-586 (681)
112 PRK09202 nusA transcription el 36.4 18 0.00039 35.6 1.2 39 177-215 301-339 (470)
113 PRK12327 nusA transcription el 34.9 20 0.00043 34.0 1.3 41 177-217 302-342 (362)
114 PRK06418 transcription elongat 34.4 22 0.00047 29.8 1.3 38 179-217 62-99 (166)
115 COG0092 RpsC Ribosomal protein 32.8 22 0.00047 31.4 1.1 27 179-205 52-78 (233)
116 COG1855 ATPase (PilT family) [ 31.6 28 0.00061 34.1 1.7 40 178-217 486-525 (604)
117 PRK13764 ATPase; Provisional 31.5 28 0.00061 35.3 1.8 41 177-217 480-520 (602)
118 cd02412 30S_S3_KH K homology R 30.5 21 0.00045 27.6 0.5 29 179-207 62-90 (109)
119 KOG3777 Uncharacterized conser 29.5 28 0.00061 33.7 1.3 26 36-64 167-192 (443)
120 KOG2874 rRNA processing protei 28.3 21 0.00045 32.4 0.2 44 191-241 162-205 (356)
121 cd02411 archeal_30S_S3_KH K ho 25.2 34 0.00075 25.0 0.9 28 180-207 40-67 (85)
122 COG5175 MOT2 Transcriptional r 24.8 27 0.00058 32.6 0.2 26 108-134 202-227 (480)
123 COG1908 FrhD Coenzyme F420-red 23.1 33 0.00071 27.2 0.4 17 277-294 59-75 (132)
124 COG0195 NusA Transcription elo 21.2 33 0.00071 29.4 0.1 34 184-217 82-115 (190)
125 KOG3777 Uncharacterized conser 20.2 56 0.0012 31.8 1.4 28 265-294 167-194 (443)
No 1
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.62 E-value=4.3e-16 Score=145.08 Aligned_cols=75 Identities=27% Similarity=0.567 Sum_probs=58.2
Q ss_pred ccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccccCcCC
Q 022221 41 KPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGC 120 (300)
Q Consensus 41 ~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~~~~~C 120 (300)
..|..|...+.|.++..|+|.|........+.. .......+..|||.+|.+|.+.+.|
T Consensus 87 ~~~~~~~~~~~~~~~s~~~~~~p~~~~~~~~~~----------------------~~~~~~~p~~~kt~lc~~~~~~g~c 144 (332)
T KOG1677|consen 87 GDCSAYLRTGVCGYGSSCRYNHPDLRLRPRPVR----------------------RSRGERKPERYKTPLCRSFRKSGTC 144 (332)
T ss_pred cccccccccCCCCCCCCCCccCcccccccCCcc----------------------ccccccCcccccCCcceeeecCccc
Confidence 789999999999999999999975332111100 0112234578999999999999999
Q ss_pred CC-CCCCccCCCccccCC
Q 022221 121 KF-GDKCHFAHGEWELGR 137 (300)
Q Consensus 121 ~~-g~~C~f~H~~~~~~~ 137 (300)
+| |++|+|+|+.++++.
T Consensus 145 ~y~ge~crfah~~~e~r~ 162 (332)
T KOG1677|consen 145 KYRGEQCRFAHGLEELRL 162 (332)
T ss_pred cccCchhhhcCCcccccc
Confidence 99 999999999988884
No 2
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.60 E-value=4.1e-15 Score=138.48 Aligned_cols=81 Identities=31% Similarity=0.577 Sum_probs=67.3
Q ss_pred CCCccccccccccccccccCC-CCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccc
Q 022221 34 TGIGSKSKPCTKFFSTSGCPF-GEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCN 112 (300)
Q Consensus 34 ~~~~~Kt~lC~~y~~~g~C~~-G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~ 112 (300)
....|||.+|+.|..+|.|+| |++|+|+|.+.++.... .......+.+|||++|.
T Consensus 126 ~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~~~------------------------~~~~~~~~~~~kt~lC~ 181 (332)
T KOG1677|consen 126 KPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRLPS------------------------SENQVGNPPKYKTKLCP 181 (332)
T ss_pred CcccccCCcceeeecCccccccCchhhhcCCcccccccc------------------------cchhhcCCCCCCCcCCC
Confidence 345799999999999999999 99999999987653111 12344567899999999
Q ss_pred ccccCcCCCCCCCCccCCCccccCCC
Q 022221 113 KYNSAEGCKFGDKCHFAHGEWELGRP 138 (300)
Q Consensus 113 ~~~~~~~C~~g~~C~f~H~~~~~~~~ 138 (300)
+|++.|.|+||.+|+|+|+..++...
T Consensus 182 ~f~~tG~C~yG~rC~F~H~~~~~~~~ 207 (332)
T KOG1677|consen 182 KFQKTGLCKYGSRCRFIHGEPEDRAS 207 (332)
T ss_pred ccccCCCCCCCCcCeecCCCcccccc
Confidence 99999999999999999999877754
No 3
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=99.06 E-value=1.9e-10 Score=101.98 Aligned_cols=74 Identities=22% Similarity=0.458 Sum_probs=60.6
Q ss_pred CCCCcccc--ccccccccccccCC---CCCCCCC---CCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 022221 33 PTGIGSKS--KPCTKFFSTSGCPF---GEGCHFL---HYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPP 104 (300)
Q Consensus 33 ~~~~~~Kt--~lC~~y~~~g~C~~---G~~C~F~---H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 104 (300)
+....||+ .||.-|-..|.|++ |+.|.|+ |+..++.. ...-.
T Consensus 221 ~n~~L~kt~~~lc~~ft~kg~~p~~~sG~~~q~a~~~HGlN~l~~------------------------------k~k~~ 270 (351)
T COG5063 221 QNKPLYKTNPELCESFTRKGTCPYWISGVKCQFACRGHGLNELKS------------------------------KKKKQ 270 (351)
T ss_pred ccchhhcCCHHHhhccCcCCCCccccccccccccccccccccccc------------------------------ccccc
Confidence 34456899 99999999999999 9999999 98654311 11235
Q ss_pred ccccccccccccCcCCCCCCCCccCCCccccC
Q 022221 105 AVKSRLCNKYNSAEGCKFGDKCHFAHGEWELG 136 (300)
Q Consensus 105 ~~kt~~C~~~~~~~~C~~g~~C~f~H~~~~~~ 136 (300)
+|||+.|.+|.+-|+|+||.+|-|+|+.+++-
T Consensus 271 ~frTePcinwe~sGyc~yg~Rc~F~hgd~~~i 302 (351)
T COG5063 271 NFRTEPCINWEKSGYCPYGLRCCFKHGDDSDI 302 (351)
T ss_pred ccccCCccchhhcccCccccccccccCChhhc
Confidence 89999999999999999999999999986554
No 4
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=98.97 E-value=7.2e-10 Score=98.36 Aligned_cols=32 Identities=41% Similarity=0.906 Sum_probs=29.0
Q ss_pred CCcccccccccc-cccccCCCCCcCCCCcchhc
Q 022221 265 NNFKTKLCENFA-KGSCTFGDRCHFAHGSEELR 296 (300)
Q Consensus 265 ~~ykt~~C~~~~-~G~C~~G~~C~faH~~~el~ 296 (300)
..|+|+.|.+|. -|.|+||-+|-|+||++++.
T Consensus 270 ~~frTePcinwe~sGyc~yg~Rc~F~hgd~~~i 302 (351)
T COG5063 270 QNFRTEPCINWEKSGYCPYGLRCCFKHGDDSDI 302 (351)
T ss_pred cccccCCccchhhcccCccccccccccCChhhc
Confidence 569999999999 79999999999999998864
No 5
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.91 E-value=1.1e-09 Score=104.42 Aligned_cols=31 Identities=35% Similarity=0.756 Sum_probs=28.5
Q ss_pred CCcccccccccccccccCCCCCcCCCCcchhccc
Q 022221 265 NNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKS 298 (300)
Q Consensus 265 ~~ykt~~C~~~~~G~C~~G~~C~faH~~~el~~~ 298 (300)
..|||++|++- |.|++ -.|.|||..+|||..
T Consensus 267 a~YRT~~CkDg--~~C~R-rvCfFAH~~eqLR~l 297 (528)
T KOG1595|consen 267 ARYRTRKCKDG--GYCPR-RVCFFAHSPEQLRPL 297 (528)
T ss_pred HHhccccccCC--CCCcc-ceEeeecChHHhccc
Confidence 56999999997 99999 999999999999864
No 6
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=98.86 E-value=2.6e-09 Score=75.57 Aligned_cols=64 Identities=27% Similarity=0.432 Sum_probs=57.6
Q ss_pred ceEEEeCccccceeccCCCccccchhcccCCeeEeccCCC-CCCccceeecCcHHHHHHHhhcce
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV-DPNLRNIELEGTFDQIKQASAMVR 242 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~-~~~~~~~~i~G~~~qi~~A~~~I~ 242 (300)
+.++.||...+|.|||++|.+|+.|++.|+++|.+.+... ...++.++|.|+++++..|..+|.
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence 3678999999999999999999999999999999976554 677899999999999999988763
No 7
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=98.83 E-value=6e-10 Score=64.67 Aligned_cols=26 Identities=62% Similarity=1.385 Sum_probs=21.2
Q ss_pred cccccccccc-cccccCCCCCcCCCCc
Q 022221 267 FKTKLCENFA-KGSCTFGDRCHFAHGS 292 (300)
Q Consensus 267 ykt~~C~~~~-~G~C~~G~~C~faH~~ 292 (300)
||+++|.+|+ +|.|+||++|+|+|++
T Consensus 1 ~k~~~C~~f~~~g~C~~G~~C~f~H~~ 27 (27)
T PF00642_consen 1 YKTKLCRFFMRTGTCPFGDKCRFAHGE 27 (27)
T ss_dssp TTSSB-HHHHHTS--TTGGGSSSBSSG
T ss_pred CccccChhhccCCccCCCCCcCccCCC
Confidence 6899999999 6999999999999974
No 8
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=98.81 E-value=7.6e-10 Score=64.25 Aligned_cols=26 Identities=46% Similarity=0.975 Sum_probs=21.6
Q ss_pred cccccccccccccccCCCCCCCCCCC
Q 022221 38 SKSKPCTKFFSTSGCPFGEGCHFLHY 63 (300)
Q Consensus 38 ~Kt~lC~~y~~~g~C~~G~~C~F~H~ 63 (300)
||+++|++|++.|.|++|++|+|+|+
T Consensus 1 ~k~~~C~~f~~~g~C~~G~~C~f~H~ 26 (27)
T PF00642_consen 1 YKTKLCRFFMRTGTCPFGDKCRFAHG 26 (27)
T ss_dssp TTSSB-HHHHHTS--TTGGGSSSBSS
T ss_pred CccccChhhccCCccCCCCCcCccCC
Confidence 69999998999999999999999996
No 9
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.66 E-value=1.1e-08 Score=98.46 Aligned_cols=78 Identities=33% Similarity=0.516 Sum_probs=70.3
Q ss_pred cccCcceEEEeCccccceeccCCCccccchhcccCCeeEec-cCCCCCCccceeecCcHHHHHHHhhcceeeEeccCCC
Q 022221 174 FGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIR-DHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGSG 251 (300)
Q Consensus 174 ~g~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~-~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~~~ 251 (300)
.+++.+.+|.||...||+||||+|++||.|+..||++|++. |+++.+.+|.+.|+|+.++|.+|..+|.+++...+..
T Consensus 226 ~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 226 GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence 34466899999999999999999999999999999999994 5666788999999999999999999999999877764
No 10
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.64 E-value=1.3e-08 Score=97.19 Aligned_cols=67 Identities=27% Similarity=0.538 Sum_probs=56.8
Q ss_pred CccccccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccc
Q 022221 36 IGSKSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYN 115 (300)
Q Consensus 36 ~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~ 115 (300)
.-|.-+.|..|. .|.|..||.|.|+|++.|-| .+|..|||++|+
T Consensus 232 yhYs~tpCPefr-kG~C~rGD~CEyaHgvfEcw--------------------------------LHPa~YRT~~Ck--- 275 (528)
T KOG1595|consen 232 YHYSSTPCPEFR-KGSCERGDSCEYAHGVFECW--------------------------------LHPARYRTRKCK--- 275 (528)
T ss_pred ccccCccCcccc-cCCCCCCCccccccceehhh--------------------------------cCHHHhcccccc---
Confidence 459999999995 59999999999999998764 245689999995
Q ss_pred cCcCCCCCCCCccCCCccccCCCC
Q 022221 116 SAEGCKFGDKCHFAHGEWELGRPT 139 (300)
Q Consensus 116 ~~~~C~~g~~C~f~H~~~~~~~~~ 139 (300)
.+++|+. .-|.|||.+++||...
T Consensus 276 Dg~~C~R-rvCfFAH~~eqLR~l~ 298 (528)
T KOG1595|consen 276 DGGYCPR-RVCFFAHSPEQLRPLP 298 (528)
T ss_pred CCCCCcc-ceEeeecChHHhcccC
Confidence 5678999 9999999999998543
No 11
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=98.54 E-value=4.1e-08 Score=85.95 Aligned_cols=72 Identities=33% Similarity=0.460 Sum_probs=66.7
Q ss_pred CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEecc
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNV 248 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~ 248 (300)
.+++++.||..+-|.||||+|..|++|.+.+|+.|.|......+.+++++|.|+.+|+++|++++++.+.+.
T Consensus 314 itTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 314 ITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred eeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 778999999999999999999999999999999999988777888999999999999999999998876543
No 12
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.54 E-value=9.2e-08 Score=66.82 Aligned_cols=60 Identities=28% Similarity=0.454 Sum_probs=53.8
Q ss_pred eEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcc
Q 022221 180 AKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMV 241 (300)
Q Consensus 180 ~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I 241 (300)
..+.||..+.+.|||++|.+|+.|++.++++|.+.+.. .....++|.|..+++..|..+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHHHHHHHHHh
Confidence 57899999999999999999999999999999997654 5568899999999999888765
No 13
>smart00356 ZnF_C3H1 zinc finger.
Probab=98.46 E-value=9.7e-08 Score=55.22 Aligned_cols=26 Identities=54% Similarity=1.230 Sum_probs=24.0
Q ss_pred cccccccccccccccCCCCCcCCCCc
Q 022221 267 FKTKLCENFAKGSCTFGDRCHFAHGS 292 (300)
Q Consensus 267 ykt~~C~~~~~G~C~~G~~C~faH~~ 292 (300)
+|+.+|.+|++|.|++|++|+|+|..
T Consensus 2 ~k~~~C~~~~~g~C~~g~~C~~~H~~ 27 (27)
T smart00356 2 YKTELCKFFKRGYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCCcCcCccCCCCCCCCCcCCCCcC
Confidence 68889999999999999999999973
No 14
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=98.45 E-value=8.7e-08 Score=87.95 Aligned_cols=56 Identities=29% Similarity=0.612 Sum_probs=46.9
Q ss_pred ccccccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccccc
Q 022221 37 GSKSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNS 116 (300)
Q Consensus 37 ~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~~ 116 (300)
..++++| +|+..|.|+.||.|.|+|.. ++ .|-+.|.||..
T Consensus 74 ~~~~~vc-K~~l~glC~kgD~C~Flhe~-~~--------------------------------------~k~rec~ff~~ 113 (325)
T KOG1040|consen 74 SRGKVVC-KHWLRGLCKKGDQCEFLHEY-DL--------------------------------------TKMRECKFFSL 113 (325)
T ss_pred cCCceee-hhhhhhhhhccCcCcchhhh-hh--------------------------------------ccccccccccc
Confidence 5789999 55577999999999999976 22 12345999999
Q ss_pred CcCCCCCCCCccCCCc
Q 022221 117 AEGCKFGDKCHFAHGE 132 (300)
Q Consensus 117 ~~~C~~g~~C~f~H~~ 132 (300)
.|.|..+..|-|.|+.
T Consensus 114 ~g~c~~~~~c~y~h~d 129 (325)
T KOG1040|consen 114 FGECTNGKDCPYLHGD 129 (325)
T ss_pred ccccccccCCcccCCC
Confidence 9999999999999987
No 15
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.45 E-value=2.4e-07 Score=64.85 Aligned_cols=62 Identities=31% Similarity=0.516 Sum_probs=56.0
Q ss_pred eEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcc
Q 022221 180 AKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMV 241 (300)
Q Consensus 180 ~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I 241 (300)
.++.||..+++.|||++|.+|+.|++.|++.|.+.....+.....+.+.|..+++..|..+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence 57899999999999999999999999999999997765566788999999999999988765
No 16
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=98.45 E-value=5e-08 Score=67.71 Aligned_cols=60 Identities=37% Similarity=0.599 Sum_probs=53.5
Q ss_pred ceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcc
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMV 241 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I 241 (300)
|.++.||..+++.|||++|.+|++|+..|++.|.+.+. + ....+.|.|++++++.|..+|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--~-~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--D-ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999765 3 456899999999999998764
No 17
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.44 E-value=1.7e-07 Score=65.34 Aligned_cols=57 Identities=23% Similarity=0.380 Sum_probs=50.6
Q ss_pred ceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCc-HHHHHHHhhcc
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGT-FDQIKQASAMV 241 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~-~~qi~~A~~~I 241 (300)
...+.||+.++|.|||++|++|++|+..|+++|.|.+. ..+.|.|. .+.++.|..+|
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~------g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDD------GTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCCC------CEEEEEeCCHHHHHHHHHHh
Confidence 46789999999999999999999999999999999762 46999997 88888888766
No 18
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=98.33 E-value=1.2e-07 Score=89.51 Aligned_cols=61 Identities=26% Similarity=0.666 Sum_probs=45.8
Q ss_pred ccccccccccc--cccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccccc
Q 022221 39 KSKPCTKFFST--SGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNS 116 (300)
Q Consensus 39 Kt~lC~~y~~~--g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~~ 116 (300)
+-+||.....+ ..|.|||+|+|.|++.....+.. +++ ..-|+.|..
T Consensus 75 ~n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~--------~Di------------------------g~~Cp~f~s 122 (614)
T KOG2333|consen 75 QNRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKA--------PDI------------------------GPSCPVFES 122 (614)
T ss_pred hhccChHhhcCCCccCcccccccccccHHHHHhccC--------ccc------------------------CCccceeec
Confidence 57799999877 68999999999999854321111 000 013999999
Q ss_pred CcCCCCCCCCccCCC
Q 022221 117 AEGCKFGDKCHFAHG 131 (300)
Q Consensus 117 ~~~C~~g~~C~f~H~ 131 (300)
.|.|+||.+|||+-.
T Consensus 123 ~G~Cp~G~~CRFl~a 137 (614)
T KOG2333|consen 123 LGFCPYGFKCRFLGA 137 (614)
T ss_pred cccCCccceeehhhc
Confidence 999999999999754
No 19
>smart00356 ZnF_C3H1 zinc finger.
Probab=98.31 E-value=3.9e-07 Score=52.64 Aligned_cols=26 Identities=35% Similarity=0.839 Sum_probs=23.2
Q ss_pred ccccccccccccccccCCCCCCCCCCC
Q 022221 37 GSKSKPCTKFFSTSGCPFGEGCHFLHY 63 (300)
Q Consensus 37 ~~Kt~lC~~y~~~g~C~~G~~C~F~H~ 63 (300)
.+|+.+|++| .+|.|.+|++|+|+|+
T Consensus 1 ~~k~~~C~~~-~~g~C~~g~~C~~~H~ 26 (27)
T smart00356 1 KYKTELCKFF-KRGYCPYGDRCKFAHP 26 (27)
T ss_pred CCCCCcCcCc-cCCCCCCCCCcCCCCc
Confidence 3688999777 8899999999999996
No 20
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=98.31 E-value=6.3e-07 Score=83.13 Aligned_cols=76 Identities=26% Similarity=0.291 Sum_probs=67.7
Q ss_pred CcceEEEeCccccceeccCCCccccchhcccCCeeEecc-CCCCCCccceeecCcHHHHHHHhhcceeeEeccCCCC
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD-HEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGSGS 252 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~-~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~~~~ 252 (300)
...+.+.||..++|+|||+.|.+||+|.+.+|+.|+|.. ..++..++++.|+|.+++..+|+..|...|.+.+.+.
T Consensus 410 ~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEenf~~ 486 (584)
T KOG2193|consen 410 QEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFFL 486 (584)
T ss_pred hhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhccCC
Confidence 567889999999999999999999999999999999965 4467788999999999999999999999888766543
No 21
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=98.00 E-value=3.4e-06 Score=76.27 Aligned_cols=67 Identities=19% Similarity=0.407 Sum_probs=47.4
Q ss_pred CCCCccccccccccccccccCCCCC-CCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccc
Q 022221 33 PTGIGSKSKPCTKFFSTSGCPFGEG-CHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLC 111 (300)
Q Consensus 33 ~~~~~~Kt~lC~~y~~~g~C~~G~~-C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C 111 (300)
..+-|...++|+.|. -++|..||+ |||+|..... .| ++-+-..|
T Consensus 30 kd~~wl~~eVCReF~-rn~C~R~d~~CkfaHP~~~~--~V--------------------------------~~g~v~aC 74 (331)
T KOG2494|consen 30 KDTKWLTLEVCREFL-RNTCSRGDRECKFAHPPKNC--QV--------------------------------SNGRVIAC 74 (331)
T ss_pred cccchhHHHHHHHHH-hccccCCCccccccCCCCCC--Cc--------------------------------cCCeEEEE
Confidence 445577788998885 599999999 9999964321 00 01122359
Q ss_pred cccccCcCCCCCCCCccCCCccccC
Q 022221 112 NKYNSAEGCKFGDKCHFAHGEWELG 136 (300)
Q Consensus 112 ~~~~~~~~C~~g~~C~f~H~~~~~~ 136 (300)
.-|++++ |.. ++|+|+|...+++
T Consensus 75 ~Ds~kgr-CsR-~nCkylHpp~hlk 97 (331)
T KOG2494|consen 75 FDSQKGR-CSR-ENCKYLHPPQHLK 97 (331)
T ss_pred eccccCc-cCc-ccceecCCChhhh
Confidence 8898888 964 5599999976554
No 22
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=97.89 E-value=6.5e-06 Score=79.72 Aligned_cols=74 Identities=27% Similarity=0.425 Sum_probs=64.1
Q ss_pred cCcceEEEeCccccceeccCCCccccchhcccCCeeEec-cCCC-CCCccceeecCcHHHHHHHhhcceeeEeccC
Q 022221 176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIR-DHEV-DPNLRNIELEGTFDQIKQASAMVRELIVNVG 249 (300)
Q Consensus 176 ~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~-~~~~-~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~ 249 (300)
..++.++.||+..+|+||||+|+.|++++..+++++.+. +... ...++.+.|+|++.+++.|..+|.++|.+..
T Consensus 137 ~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~ 212 (600)
T KOG1676|consen 137 VETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREED 212 (600)
T ss_pred cceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcc
Confidence 357888999999999999999999999999999999984 3332 2367999999999999999999999998533
No 23
>PF13014 KH_3: KH domain
Probab=97.88 E-value=8.4e-06 Score=52.56 Aligned_cols=42 Identities=40% Similarity=0.590 Sum_probs=35.6
Q ss_pred ccceeccCCCccccchhcccCCeeEecc-CCCCCCccceeecC
Q 022221 188 LAGAIIGKNGVNSKQICRLTGAKLSIRD-HEVDPNLRNIELEG 229 (300)
Q Consensus 188 ~~G~iiG~gG~~ik~i~~~Sga~i~i~~-~~~~~~~~~~~i~G 229 (300)
.+|+|||++|.+|++|++.|+++|.+.+ ...+...+.++|.|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 3689999999999999999999999976 44556678888765
No 24
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.85 E-value=1.1e-05 Score=78.31 Aligned_cols=72 Identities=24% Similarity=0.376 Sum_probs=64.5
Q ss_pred cceEEEeCccccceeccCCCccccchhcccCCeeEecc-CCCCCCccceeecCcHHHHHHHhhcceeeEeccC
Q 022221 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD-HEVDPNLRNIELEGTFDQIKQASAMVRELIVNVG 249 (300)
Q Consensus 178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~-~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~ 249 (300)
.+..+.||..++|.||||+|+.|++|++.|+++|.|.+ ..+..+++.+.|.|.++++.+|...|..+|.+..
T Consensus 138 v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~ 210 (485)
T KOG2190|consen 138 VTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENP 210 (485)
T ss_pred eEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcC
Confidence 46889999999999999999999999999999999954 5677888999999999999999999888876543
No 25
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=97.77 E-value=1e-05 Score=73.24 Aligned_cols=27 Identities=26% Similarity=0.691 Sum_probs=23.5
Q ss_pred ccccccccccccCCCCCcCCCCcchhcc
Q 022221 270 KLCENFAKGSCTFGDRCHFAHGSEELRK 297 (300)
Q Consensus 270 ~~C~~~~~G~C~~G~~C~faH~~~el~~ 297 (300)
-.|.+|++|.|.+ ++|+|.|+..+|+-
T Consensus 72 ~aC~Ds~kgrCsR-~nCkylHpp~hlkd 98 (331)
T KOG2494|consen 72 IACFDSQKGRCSR-ENCKYLHPPQHLKD 98 (331)
T ss_pred EEEeccccCccCc-ccceecCCChhhhh
Confidence 3699999999999 68999999888763
No 26
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=97.77 E-value=2.9e-05 Score=66.75 Aligned_cols=60 Identities=20% Similarity=0.492 Sum_probs=47.4
Q ss_pred ccccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccccCc
Q 022221 39 KSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAE 118 (300)
Q Consensus 39 Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~~~~ 118 (300)
...-|++|...|.|..|..|+|.|.... ..+|+.|+.+.
T Consensus 205 savycryynangicgkgaacrfvheptr-----------------------------------------kticpkflngr 243 (377)
T KOG1492|consen 205 SAVYCRYYNANGICGKGAACRFVHEPTR-----------------------------------------KTICPKFLNGR 243 (377)
T ss_pred ceeEEEEecCCCcccCCceeeeeccccc-----------------------------------------cccChHHhcCc
Confidence 4457988888999999999999996532 24699998887
Q ss_pred CCCCCCCCccCCCccccCCCCC
Q 022221 119 GCKFGDKCHFAHGEWELGRPTV 140 (300)
Q Consensus 119 ~C~~g~~C~f~H~~~~~~~~~~ 140 (300)
|..-++|...|..+..|.+.-
T Consensus 244 -cnkaedcnlsheldprripac 264 (377)
T KOG1492|consen 244 -CNKAEDCNLSHELDPRRIPAC 264 (377)
T ss_pred -cCchhcCCcccccCccccchh
Confidence 999999999997766665433
No 27
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.74 E-value=2.2e-05 Score=71.08 Aligned_cols=73 Identities=26% Similarity=0.316 Sum_probs=62.2
Q ss_pred cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCC---CCCccceeecCcHHHHHHHhhcceeeEeccCC
Q 022221 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV---DPNLRNIELEGTFDQIKQASAMVRELIVNVGS 250 (300)
Q Consensus 178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~---~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~~ 250 (300)
..+++.+|+..+|.||||+|.+||.+..+++++|+|....+ ...++.+++.|.+++..+|..+|-..+.+.+.
T Consensus 132 kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq 207 (402)
T KOG2191|consen 132 KQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ 207 (402)
T ss_pred ceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc
Confidence 45889999999999999999999999999999999984332 34469999999999999999988777766553
No 28
>smart00322 KH K homology RNA-binding domain.
Probab=97.72 E-value=2.8e-05 Score=54.20 Aligned_cols=65 Identities=31% Similarity=0.489 Sum_probs=54.8
Q ss_pred cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceee
Q 022221 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVREL 244 (300)
Q Consensus 178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~ 244 (300)
.+..+.||...++.+||++|.+|+.|...+++++.+..... ....+.|.|...++..|..+|...
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~ 67 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEI 67 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHH
Confidence 35788999999999999999999999999999999865332 567899999999998888776543
No 29
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.67 E-value=2.2e-05 Score=71.02 Aligned_cols=71 Identities=24% Similarity=0.361 Sum_probs=61.8
Q ss_pred cceEEEeCccccceeccCCCccccchhcccCCeeEecc-CC--CCCCccceeecCcHHHHHHHhhcceeeEecc
Q 022221 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD-HE--VDPNLRNIELEGTFDQIKQASAMVRELIVNV 248 (300)
Q Consensus 178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~-~~--~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~ 248 (300)
..+++.||...+|.||||||+.|.+++..++++|++.. .+ +..++|++-|.|+-+.+......|.+.|.+.
T Consensus 39 y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~ 112 (402)
T KOG2191|consen 39 YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREK 112 (402)
T ss_pred eEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHh
Confidence 56889999999999999999999999999999999953 33 6778899999999999988888877776553
No 30
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=97.66 E-value=1.1e-05 Score=71.79 Aligned_cols=34 Identities=35% Similarity=0.837 Sum_probs=29.5
Q ss_pred ccCCCCCccccccccccccccccCCCCCCCCCCCC
Q 022221 30 ENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYV 64 (300)
Q Consensus 30 ~~~~~~~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~ 64 (300)
...+.++..|+.+| -||..|.|..|+.|+|+|++
T Consensus 82 qkv~~gvDPKSvvC-afFk~g~C~KG~kCKFsHdl 115 (343)
T KOG1763|consen 82 QKVPKGVDPKSVVC-AFFKQGTCTKGDKCKFSHDL 115 (343)
T ss_pred cccccCCCchHHHH-HHHhccCCCCCCcccccchH
Confidence 34567888999999 66689999999999999976
No 31
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.51 E-value=3e-05 Score=72.27 Aligned_cols=71 Identities=25% Similarity=0.417 Sum_probs=60.8
Q ss_pred ceEEEeCccccceeccCCCccccchhcccCCeeEe-ccCCCCCCc-cceeecCcHHHHHHHhhcceeeEeccC
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-RDHEVDPNL-RNIELEGTFDQIKQASAMVRELIVNVG 249 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i-~~~~~~~~~-~~~~i~G~~~qi~~A~~~I~~~l~~~~ 249 (300)
...++||...+|.||||||.++.++++.|++.+.| ++..++.++ .++.|+|.+.+.++|+..|.+++.++-
T Consensus 494 ethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~iv~qvk 566 (584)
T KOG2193|consen 494 ETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHIVNQVK 566 (584)
T ss_pred eeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHHHHHHH
Confidence 34578999999999999999999999999999999 566666654 688999999999999998888875543
No 32
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=97.44 E-value=0.0001 Score=67.90 Aligned_cols=54 Identities=28% Similarity=0.557 Sum_probs=42.6
Q ss_pred ccccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccccCc
Q 022221 39 KSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAE 118 (300)
Q Consensus 39 Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~~~~ 118 (300)
|.+.|.+|...|.|..++.|.|.|..++. +.+.|++| +.|
T Consensus 104 k~rec~ff~~~g~c~~~~~c~y~h~dpqt---------------------------------------~~k~c~~~-~~g 143 (325)
T KOG1040|consen 104 KMRECKFFSLFGECTNGKDCPYLHGDPQT---------------------------------------AIKKCKWY-KEG 143 (325)
T ss_pred ccccccccccccccccccCCcccCCChhh---------------------------------------hhhccchh-hhc
Confidence 56679888899999999999999987422 24569666 455
Q ss_pred CCCCCCCCccCCCc
Q 022221 119 GCKFGDKCHFAHGE 132 (300)
Q Consensus 119 ~C~~g~~C~f~H~~ 132 (300)
+|+-|+.|++.|-.
T Consensus 144 ~c~~g~~c~~~h~~ 157 (325)
T KOG1040|consen 144 FCRGGPSCKKRHER 157 (325)
T ss_pred cCCCcchhhhhhhc
Confidence 69999999998844
No 33
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=97.26 E-value=5.5e-05 Score=65.39 Aligned_cols=36 Identities=25% Similarity=0.567 Sum_probs=29.5
Q ss_pred ccCCCCCccccccccccccccccCCCCCCCCCCCCCC
Q 022221 30 ENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPG 66 (300)
Q Consensus 30 ~~~~~~~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~~ 66 (300)
.....++..|+.+|..| ..+.|..|+.|+|+|+..+
T Consensus 75 q~iragvdpK~~vcalF-~~~~c~kg~~ckF~h~~ee 110 (299)
T COG5252 75 QVIRAGVDPKTVVCALF-LNKTCAKGDACKFAHGKEE 110 (299)
T ss_pred hhhccccCchhHHHHHh-ccCccccCchhhhhcchHH
Confidence 33567788999999555 6799999999999998643
No 34
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=97.17 E-value=0.00078 Score=60.84 Aligned_cols=58 Identities=29% Similarity=0.555 Sum_probs=43.4
Q ss_pred ccccccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccccc
Q 022221 37 GSKSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNS 116 (300)
Q Consensus 37 ~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~~ 116 (300)
.+...+| +++..|.|+.++.|.|+|+.+-.. . -.-.|++|-.
T Consensus 101 ~~s~V~c-~~~~~g~c~s~~~c~~lh~~d~~~------------------------------------s-~~~~c~~Fs~ 142 (285)
T COG5084 101 LSSSVVC-KFFLRGLCKSGFSCEFLHEYDLRS------------------------------------S-QGPPCRSFSL 142 (285)
T ss_pred ccCCccc-chhccccCcCCCccccccCCCccc------------------------------------c-cCCCcccccc
Confidence 4777889 555779999999999999764210 0 0223999977
Q ss_pred CcCCCCCCCCccCCCc
Q 022221 117 AEGCKFGDKCHFAHGE 132 (300)
Q Consensus 117 ~~~C~~g~~C~f~H~~ 132 (300)
.|.|..|..|.|.|.+
T Consensus 143 ~G~cs~g~~c~~~h~d 158 (285)
T COG5084 143 KGSCSSGPSCGYSHID 158 (285)
T ss_pred cceeccCCCCCccccC
Confidence 7779999999999976
No 35
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.16 E-value=0.00033 Score=65.72 Aligned_cols=85 Identities=22% Similarity=0.279 Sum_probs=62.3
Q ss_pred CCCcCCCCCCCCCccccccCcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHH
Q 022221 158 GGRLEPPPQSLGAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQA 237 (300)
Q Consensus 158 ~g~~~p~p~~~~~~~~~g~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A 237 (300)
+++|.-+.-.+.++++.+...++.+.|-..++|+|||++|++|+.||..++++|+|...+.. ..++|.|.-+...+|
T Consensus 27 g~~w~g~~~~~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e---~kv~ifg~~~m~~ka 103 (629)
T KOG0336|consen 27 GNYWAGHRDSRDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLE---VKVTIFGINHMRKKA 103 (629)
T ss_pred CCCccCCCCCCcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCce---eEEEEechHHHHHHH
Confidence 34444444444455666667788899999999999999999999999999999999875533 345577766666666
Q ss_pred hhcceeeE
Q 022221 238 SAMVRELI 245 (300)
Q Consensus 238 ~~~I~~~l 245 (300)
...|...+
T Consensus 104 ka~id~~~ 111 (629)
T KOG0336|consen 104 KASIDRGQ 111 (629)
T ss_pred HhhHhhhh
Confidence 65555444
No 36
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=97.14 E-value=0.00015 Score=61.30 Aligned_cols=60 Identities=25% Similarity=0.381 Sum_probs=51.8
Q ss_pred EEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceee---cCcHHHHHHHhhcceeeEe
Q 022221 182 ISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIEL---EGTFDQIKQASAMVRELIV 246 (300)
Q Consensus 182 ~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i---~G~~~qi~~A~~~I~~~l~ 246 (300)
+.||...+|+|||++|++|+.|+..++++|.|.+.. ..+.| .+++.++.+|..+|..+..
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~-----g~V~I~~~t~d~~~i~kA~~~I~~i~~ 64 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSET-----GEVKIEEEDEDPLAVMKAREVVKAIGR 64 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcCC-----ceEEEecCCCCHHHHHHHHHHHHHHHc
Confidence 578999999999999999999999999999997632 34666 7899999999999987654
No 37
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=96.95 E-value=0.00049 Score=54.58 Aligned_cols=62 Identities=27% Similarity=0.387 Sum_probs=47.6
Q ss_pred cccceeccCCCccccchhcccCCeeEeccCCCCC-----------------CccceeecC-c--HHHHHHHhhcceeeEe
Q 022221 187 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDP-----------------NLRNIELEG-T--FDQIKQASAMVRELIV 246 (300)
Q Consensus 187 ~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~-----------------~~~~~~i~G-~--~~qi~~A~~~I~~~l~ 246 (300)
..+|.|||.+|.+++.|+..|+++|.|++..+.. ..-.+.|++ + .+.+++|..+|..++.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 4678999999999999999999999997642110 114566666 4 5788999999998887
Q ss_pred cc
Q 022221 247 NV 248 (300)
Q Consensus 247 ~~ 248 (300)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 43
No 38
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.94 E-value=0.00034 Score=66.25 Aligned_cols=23 Identities=39% Similarity=0.804 Sum_probs=19.9
Q ss_pred cccccccccccCCCCCCCCCCCCC
Q 022221 42 PCTKFFSTSGCPFGEGCHFLHYVP 65 (300)
Q Consensus 42 lC~~y~~~g~C~~G~~C~F~H~~~ 65 (300)
.| +|+....|+++|.|.|.|...
T Consensus 5 dc-yff~ys~cKk~d~c~~rh~E~ 27 (667)
T KOG4791|consen 5 DC-YFFFYSTCKKGDSCPFRHCEA 27 (667)
T ss_pred cc-hhhhhhhhhccCcCcchhhHH
Confidence 48 777889999999999999753
No 39
>PRK13763 putative RNA-processing protein; Provisional
Probab=96.94 E-value=0.00042 Score=58.99 Aligned_cols=63 Identities=24% Similarity=0.310 Sum_probs=54.5
Q ss_pred ceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceee----cCcHHHHHHHhhcceeeEe
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIEL----EGTFDQIKQASAMVRELIV 246 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i----~G~~~qi~~A~~~I~~~l~ 246 (300)
...+.||+..+|.|||++|.+|+.|+..++++|.|.+.. ..+.| .+++.++.+|..+|..+..
T Consensus 4 ~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~-----g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSET-----GEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCC-----CeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 467899999999999999999999999999999997642 45566 4799999999999987765
No 40
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=96.81 E-value=0.00082 Score=35.40 Aligned_cols=19 Identities=42% Similarity=0.852 Sum_probs=16.4
Q ss_pred cccccccccccCCCCCcCCCC
Q 022221 271 LCENFAKGSCTFGDRCHFAHG 291 (300)
Q Consensus 271 ~C~~~~~G~C~~G~~C~faH~ 291 (300)
.|+||.. |+++++|.|.|+
T Consensus 1 ~Ck~~~~--C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN--CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC--CCCCCcCccCCc
Confidence 4888864 999999999996
No 41
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=96.77 E-value=0.00048 Score=64.08 Aligned_cols=24 Identities=46% Similarity=1.182 Sum_probs=21.8
Q ss_pred ccccccccccccCCCCCcCCCCcc
Q 022221 270 KLCENFAKGSCTFGDRCHFAHGSE 293 (300)
Q Consensus 270 ~~C~~~~~G~C~~G~~C~faH~~~ 293 (300)
..|.||+.|.|+|+++|||.||..
T Consensus 141 kpC~ffLeg~CRF~enCRfSHG~~ 164 (486)
T KOG2185|consen 141 KPCKFFLEGRCRFGENCRFSHGLD 164 (486)
T ss_pred ccchHhhccccccCcccccccCcc
Confidence 469999999999999999999853
No 42
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=96.67 E-value=0.00051 Score=58.05 Aligned_cols=52 Identities=29% Similarity=0.526 Sum_probs=47.9
Q ss_pred cccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeE
Q 022221 187 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELI 245 (300)
Q Consensus 187 ~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l 245 (300)
...|.|||++|.+++.|+..|+++|.|.+ +.+.|+|++++++.|...|..++
T Consensus 98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A~~~i~~li 149 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEELTGVSISVYG-------KTVGIIGDPEQVQIAREAIEMLI 149 (172)
T ss_pred HHHhhhcCCCcHHHHHHHHHHCCeEEEcC-------CEEEEECCHHHHHHHHHHHHHHH
Confidence 47899999999999999999999999975 56899999999999999998887
No 43
>PRK13763 putative RNA-processing protein; Provisional
Probab=96.20 E-value=0.0014 Score=55.77 Aligned_cols=52 Identities=29% Similarity=0.518 Sum_probs=46.8
Q ss_pred cccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeE
Q 022221 187 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELI 245 (300)
Q Consensus 187 ~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l 245 (300)
...|.|||++|.+++.|+..|+++|.|.+. .+.|.|++.++..|...|..++
T Consensus 104 r~~griIG~~G~~~k~ie~~t~~~i~i~~~-------~v~i~G~~~~~~~A~~~I~~li 155 (180)
T PRK13763 104 RIKGRIIGEGGKTRRIIEELTGVDISVYGK-------TVAIIGDPEQVEIAREAIEMLI 155 (180)
T ss_pred HHhhheeCCCcHHHHHHHHHHCcEEEEcCC-------EEEEEeCHHHHHHHHHHHHHHH
Confidence 468999999999999999999999999752 3889999999999999998877
No 44
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=96.16 E-value=0.0036 Score=32.91 Aligned_cols=19 Identities=37% Similarity=0.810 Sum_probs=15.6
Q ss_pred cccccccCcCCCCCCCCccCCC
Q 022221 110 LCNKYNSAEGCKFGDKCHFAHG 131 (300)
Q Consensus 110 ~C~~~~~~~~C~~g~~C~f~H~ 131 (300)
.|++|.. |++++.|.|.|.
T Consensus 1 ~Ck~~~~---C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN---CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC---CCCCCcCccCCc
Confidence 3887643 999999999995
No 45
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.16 E-value=0.0097 Score=58.13 Aligned_cols=71 Identities=25% Similarity=0.392 Sum_probs=61.5
Q ss_pred CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCC--CCCccceeecCcHHHHHHHhhcceeeEec
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV--DPNLRNIELEGTFDQIKQASAMVRELIVN 247 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~--~~~~~~~~i~G~~~qi~~A~~~I~~~l~~ 247 (300)
..+.++.||..++|.|||++|.+|.+|++.|++.|.|...+. ...+..++|.+...+...++..+...+..
T Consensus 337 ~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~ 409 (485)
T KOG2190|consen 337 TVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLSA 409 (485)
T ss_pred eeeeeeccCccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhccccccc
Confidence 467889999999999999999999999999999999976554 56789999999999998888888665533
No 46
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.12 E-value=0.0019 Score=54.69 Aligned_cols=30 Identities=30% Similarity=0.762 Sum_probs=26.3
Q ss_pred CccccccccccccccccCCCCCCCCCCCCC
Q 022221 36 IGSKSKPCTKFFSTSGCPFGEGCHFLHYVP 65 (300)
Q Consensus 36 ~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~ 65 (300)
+.|...+|.-|-.+|.|-|||.|+|+|...
T Consensus 137 iD~qpdVCKdyk~TGYCGYGDsCKflH~R~ 166 (259)
T COG5152 137 IDTQPDVCKDYKETGYCGYGDSCKFLHDRS 166 (259)
T ss_pred eecCcccccchhhcccccCCchhhhhhhhh
Confidence 356777999999999999999999999763
No 47
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=96.10 E-value=0.0012 Score=58.33 Aligned_cols=70 Identities=24% Similarity=0.357 Sum_probs=57.2
Q ss_pred ceEEEeCccccceeccCCCccccchhcccCCeeEecc-CCCCCCccceeecCcHHHHHHHhhcceeeEecc
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD-HEVDPNLRNIELEGTFDQIKQASAMVRELIVNV 248 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~-~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~ 248 (300)
.+++.|-++++|.|||++|++||+++..+.++++|.. --+.++++++.+.|.+..+......|.++|++.
T Consensus 124 e~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~ 194 (390)
T KOG2192|consen 124 ELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISES 194 (390)
T ss_pred hhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcC
Confidence 3567788999999999999999999999999999964 445678899999998887766666666665543
No 48
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=95.85 E-value=0.0034 Score=58.54 Aligned_cols=26 Identities=50% Similarity=1.083 Sum_probs=21.7
Q ss_pred cccccccccccccccCCCCCCCCCCCC
Q 022221 38 SKSKPCTKFFSTSGCPFGEGCHFLHYV 64 (300)
Q Consensus 38 ~Kt~lC~~y~~~g~C~~G~~C~F~H~~ 64 (300)
.-.++| .||..|.|+|+++|+|.|+.
T Consensus 138 ~sMkpC-~ffLeg~CRF~enCRfSHG~ 163 (486)
T KOG2185|consen 138 ESMKPC-KFFLEGRCRFGENCRFSHGL 163 (486)
T ss_pred hhhccc-hHhhccccccCcccccccCc
Confidence 356789 55578999999999999975
No 49
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=95.76 E-value=0.0045 Score=54.58 Aligned_cols=29 Identities=28% Similarity=0.626 Sum_probs=25.1
Q ss_pred cccccccccccCCCCCCCCCCCCCCCCcc
Q 022221 42 PCTKFFSTSGCPFGEGCHFLHYVPGGFKA 70 (300)
Q Consensus 42 lC~~y~~~g~C~~G~~C~F~H~~~~~~~~ 70 (300)
-|..|+++|.|++|+.|.=.|..|+..++
T Consensus 17 ~c~fy~k~gacR~gdrcsR~h~kpt~s~t 45 (260)
T KOG2202|consen 17 NCSFYFKIGACRHGDRCSRLHEKPTFSQT 45 (260)
T ss_pred ccchHHhhcccccccHHHHhhcccccchH
Confidence 39999999999999999999988776543
No 50
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=95.37 E-value=0.0067 Score=58.09 Aligned_cols=27 Identities=37% Similarity=0.837 Sum_probs=21.3
Q ss_pred ccccccccccC--cCCCCCCCCccCCCcc
Q 022221 107 KSRLCNKYNSA--EGCKFGDKCHFAHGEW 133 (300)
Q Consensus 107 kt~~C~~~~~~--~~C~~g~~C~f~H~~~ 133 (300)
+..+|+---.+ ..|.||++|+|.|..+
T Consensus 75 ~n~LCPsli~g~~~~C~f~d~Crf~HDi~ 103 (614)
T KOG2333|consen 75 QNRLCPSLIQGDISKCSFGDNCRFVHDIE 103 (614)
T ss_pred hhccChHhhcCCCccCcccccccccccHH
Confidence 45689876555 4599999999999863
No 51
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=95.31 E-value=0.009 Score=51.61 Aligned_cols=29 Identities=24% Similarity=0.591 Sum_probs=23.6
Q ss_pred cccccccccccccccCCCCCCCCCCCCCCC
Q 022221 38 SKSKPCTKFFSTSGCPFGEGCHFLHYVPGG 67 (300)
Q Consensus 38 ~Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~ 67 (300)
.+..+|.+|+ .|+|...+.|...|.+...
T Consensus 231 trkticpkfl-ngrcnkaedcnlsheldpr 259 (377)
T KOG1492|consen 231 TRKTICPKFL-NGRCNKAEDCNLSHELDPR 259 (377)
T ss_pred cccccChHHh-cCccCchhcCCcccccCcc
Confidence 3556899995 5999999999999987543
No 52
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=95.29 E-value=0.035 Score=50.30 Aligned_cols=30 Identities=27% Similarity=0.381 Sum_probs=24.4
Q ss_pred cccccccccccCcCCCCCCCCccCCCccccC
Q 022221 106 VKSRLCNKYNSAEGCKFGDKCHFAHGEWELG 136 (300)
Q Consensus 106 ~kt~~C~~~~~~~~C~~g~~C~f~H~~~~~~ 136 (300)
+....|++|..+. |+-++.|-|+|..+-+.
T Consensus 102 ~s~V~c~~~~~g~-c~s~~~c~~lh~~d~~~ 131 (285)
T COG5084 102 SSSVVCKFFLRGL-CKSGFSCEFLHEYDLRS 131 (285)
T ss_pred cCCcccchhcccc-CcCCCccccccCCCccc
Confidence 3455799998887 99999999999875554
No 53
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=95.20 E-value=0.012 Score=59.78 Aligned_cols=65 Identities=25% Similarity=0.316 Sum_probs=54.8
Q ss_pred CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEec
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIVN 247 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~~ 247 (300)
.....+.||++.++.|||.||.+|+.|+..||++|.|.+. ..+.|.+ +.+..++|..+|..++..
T Consensus 577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~------G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD------GTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC------cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 4456789999999999999999999999999999999763 4566666 667888999998888763
No 54
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.19 E-value=0.018 Score=53.72 Aligned_cols=25 Identities=36% Similarity=0.935 Sum_probs=22.0
Q ss_pred ccccccccCcCCCCCCCCccCCCccc
Q 022221 109 RLCNKYNSAEGCKFGDKCHFAHGEWE 134 (300)
Q Consensus 109 ~~C~~~~~~~~C~~g~~C~f~H~~~~ 134 (300)
.+|+||+++- |+||+.|+|.|....
T Consensus 9 tic~~~~~g~-c~~g~~cr~~h~~~~ 33 (344)
T KOG1039|consen 9 TICKYYQKGN-CKFGDLCRLSHSLPD 33 (344)
T ss_pred hhhhhccccc-ccccceeeeeccCch
Confidence 6799998886 999999999998753
No 55
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=95.17 E-value=0.0076 Score=51.09 Aligned_cols=29 Identities=28% Similarity=0.935 Sum_probs=24.6
Q ss_pred cccccccccc-cccccCCCCCcCCCCcchh
Q 022221 267 FKTKLCENFA-KGSCTFGDRCHFAHGSEEL 295 (300)
Q Consensus 267 ykt~~C~~~~-~G~C~~G~~C~faH~~~el 295 (300)
|-.-.|..|. +|.|-|||.|+|.|..++.
T Consensus 139 ~qpdVCKdyk~TGYCGYGDsCKflH~R~D~ 168 (259)
T COG5152 139 TQPDVCKDYKETGYCGYGDSCKFLHDRSDF 168 (259)
T ss_pred cCcccccchhhcccccCCchhhhhhhhhhh
Confidence 4445699998 9999999999999988754
No 56
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=95.16 E-value=0.0055 Score=54.04 Aligned_cols=31 Identities=29% Similarity=0.791 Sum_probs=26.8
Q ss_pred CCCCCcccccccccccccccCCCCCcCCCCc
Q 022221 262 SQSNNFKTKLCENFAKGSCTFGDRCHFAHGS 292 (300)
Q Consensus 262 ~~~~~ykt~~C~~~~~G~C~~G~~C~faH~~ 292 (300)
.+...++...|..|..+.|.+|..|-|+|-.
T Consensus 145 ~pvT~~rea~C~~~e~~~C~rG~~CnFmH~k 175 (260)
T KOG2202|consen 145 SPVTDFREAICGQFERTECSRGGACNFMHVK 175 (260)
T ss_pred cCcCchhhhhhcccccccCCCCCcCcchhhh
Confidence 3456788899999998899999999999954
No 57
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=93.48 E-value=0.042 Score=56.24 Aligned_cols=63 Identities=22% Similarity=0.357 Sum_probs=50.0
Q ss_pred cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEe
Q 022221 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIV 246 (300)
Q Consensus 178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~ 246 (300)
....+.||++.++.|||+||++|+.|...||++|.|.+. ..+.|.+ +...++.|...|..+..
T Consensus 551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd------G~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD------GTVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC------eEEEEEECcHHHHHHHHHHHHhhhc
Confidence 356689999999999999999999999999999999763 3445554 55677788777766643
No 58
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.98 E-value=0.029 Score=50.52 Aligned_cols=30 Identities=30% Similarity=0.716 Sum_probs=26.4
Q ss_pred CccccccccccccccccCCCCCCCCCCCCC
Q 022221 36 IGSKSKPCTKFFSTSGCPFGEGCHFLHYVP 65 (300)
Q Consensus 36 ~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~ 65 (300)
+.|--.+|.-|-.+|.|.|||.|+|.|+..
T Consensus 182 ~d~qpDicKdykeTgycg~gdSckFlh~r~ 211 (313)
T KOG1813|consen 182 IDYQPDICKDYKETGYCGYGDSCKFLHDRS 211 (313)
T ss_pred eecCchhhhhhHhhCcccccchhhhhhhhh
Confidence 357777999999999999999999999764
No 59
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=92.64 E-value=0.056 Score=51.95 Aligned_cols=70 Identities=33% Similarity=0.438 Sum_probs=50.6
Q ss_pred cceEEEeC------ccccceeccCCCccccchhcccCCeeEeccCC---------CCCC------c-cceeecC-cHHHH
Q 022221 178 ATAKISID------AKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE---------VDPN------L-RNIELEG-TFDQI 234 (300)
Q Consensus 178 ~t~~~~iP------~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~---------~~~~------~-~~~~i~G-~~~qi 234 (300)
...++.|| -..+|+|||..|.+.|.|..+|+++|.|+... .+.. + =.+-|+. +.+.+
T Consensus 138 ~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki 217 (554)
T KOG0119|consen 138 LHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKI 217 (554)
T ss_pred cccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHH
Confidence 34556664 46789999999999999999999999997511 1011 1 1234444 67788
Q ss_pred HHHhhcceeeEec
Q 022221 235 KQASAMVRELIVN 247 (300)
Q Consensus 235 ~~A~~~I~~~l~~ 247 (300)
++|..+|+.+|..
T Consensus 218 ~~Ai~vienli~~ 230 (554)
T KOG0119|consen 218 KKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999988864
No 60
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=91.93 E-value=0.042 Score=49.42 Aligned_cols=35 Identities=37% Similarity=0.758 Sum_probs=30.0
Q ss_pred CCCCcccccccccccccccCCCCCcCCCCcchhcc
Q 022221 263 QSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELRK 297 (300)
Q Consensus 263 ~~~~ykt~~C~~~~~G~C~~G~~C~faH~~~el~~ 297 (300)
...-+|+-+|-||..|.|.-|+.|.|+|...+-|.
T Consensus 86 ~gvDPKSvvCafFk~g~C~KG~kCKFsHdl~~~~k 120 (343)
T KOG1763|consen 86 KGVDPKSVVCAFFKQGTCTKGDKCKFSHDLAVERK 120 (343)
T ss_pred cCCCchHHHHHHHhccCCCCCCcccccchHHHhhh
Confidence 33567889999999999999999999999876654
No 61
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.48 E-value=0.056 Score=48.75 Aligned_cols=30 Identities=27% Similarity=0.967 Sum_probs=24.9
Q ss_pred CCcccccccccc-cccccCCCCCcCCCCcch
Q 022221 265 NNFKTKLCENFA-KGSCTFGDRCHFAHGSEE 294 (300)
Q Consensus 265 ~~ykt~~C~~~~-~G~C~~G~~C~faH~~~e 294 (300)
.-|-.-+|..|. ||.|-||+.|+|.|-...
T Consensus 182 ~d~qpDicKdykeTgycg~gdSckFlh~r~D 212 (313)
T KOG1813|consen 182 IDYQPDICKDYKETGYCGYGDSCKFLHDRSD 212 (313)
T ss_pred eecCchhhhhhHhhCcccccchhhhhhhhhh
Confidence 334556799998 999999999999997664
No 62
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=91.17 E-value=0.12 Score=35.70 Aligned_cols=36 Identities=31% Similarity=0.519 Sum_probs=32.0
Q ss_pred cceEEEeCccccceeccCCCccccchhcccCCeeEe
Q 022221 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI 213 (300)
Q Consensus 178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i 213 (300)
....+.++....|.+||++|.+|+.++..++.+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 567889999999999999999999999999877665
No 63
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=90.78 E-value=0.085 Score=54.96 Aligned_cols=64 Identities=17% Similarity=0.386 Sum_probs=51.3
Q ss_pred CcceEEEeCccccceeccCCCccccchhcccCCe-eEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEe
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAK-LSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIV 246 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~-i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~ 246 (300)
.....+.||+..++.|||.||.+|+.|...++++ |.|.+. ..+.|.+ +.+.++.|..+|..+..
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd------g~V~I~a~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD------GTVKITAKDLSSLEKSKAIISSLTM 749 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC------eeEEEEeCCHHHHHHHHHHHHHHhc
Confidence 3456789999999999999999999999999999 888763 3456665 66778888777666653
No 64
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=90.56 E-value=0.66 Score=42.33 Aligned_cols=65 Identities=12% Similarity=0.264 Sum_probs=54.6
Q ss_pred cCcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhccee
Q 022221 176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRE 243 (300)
Q Consensus 176 ~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~ 243 (300)
.+.++.+.+|...++.|.|++|..||.++..|..+|+--..+ .+.+|.++|-.+.++.|...|..
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~edv~~aRrei~s 88 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRHEDVRRARREIPS 88 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCchhHHHHhhcCcc
Confidence 567888999999999999999999999999999888764332 34788999999999988877754
No 65
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=90.52 E-value=0.11 Score=44.32 Aligned_cols=52 Identities=33% Similarity=0.554 Sum_probs=45.6
Q ss_pred ccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEe
Q 022221 188 LAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV 246 (300)
Q Consensus 188 ~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~ 246 (300)
..|.|||++|.+-+.|...|++.|.|.+.. +.|.|.+.+++.|...|..++.
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~t-------VaiiG~~~~v~iAr~AVemli~ 163 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGKT-------VAIIGGFEQVEIAREAVEMLIN 163 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCcE-------EEEecChhhhHHHHHHHHHHHc
Confidence 458899999999999999999999997754 8999999999988888877764
No 66
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.78 E-value=0.12 Score=48.26 Aligned_cols=24 Identities=33% Similarity=0.996 Sum_probs=21.9
Q ss_pred ccccccccccccCCCCCCCCCCCCC
Q 022221 41 KPCTKFFSTSGCPFGEGCHFLHYVP 65 (300)
Q Consensus 41 ~lC~~y~~~g~C~~G~~C~F~H~~~ 65 (300)
.+| +|+.-|.|+||+.|+|.|..+
T Consensus 9 tic-~~~~~g~c~~g~~cr~~h~~~ 32 (344)
T KOG1039|consen 9 TIC-KYYQKGNCKFGDLCRLSHSLP 32 (344)
T ss_pred hhh-hhcccccccccceeeeeccCc
Confidence 789 777889999999999999987
No 67
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=89.37 E-value=0.085 Score=46.04 Aligned_cols=34 Identities=47% Similarity=0.849 Sum_probs=30.2
Q ss_pred CCcccccccccccccccCCCCCcCCCCcchhccc
Q 022221 265 NNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKS 298 (300)
Q Consensus 265 ~~ykt~~C~~~~~G~C~~G~~C~faH~~~el~~~ 298 (300)
...|+..|-.|..+.|.-|+.|.|+|+.+|.|..
T Consensus 81 vdpK~~vcalF~~~~c~kg~~ckF~h~~ee~r~~ 114 (299)
T COG5252 81 VDPKTVVCALFLNKTCAKGDACKFAHGKEEARKT 114 (299)
T ss_pred cCchhHHHHHhccCccccCchhhhhcchHHHhhh
Confidence 4478899999999999999999999999887753
No 68
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=87.21 E-value=0.48 Score=42.03 Aligned_cols=60 Identities=17% Similarity=0.264 Sum_probs=48.8
Q ss_pred ceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceee
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVREL 244 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~ 244 (300)
-..+.||+.+++.+||++|..++.|...+++.|.+... ..++|.+ +.+....|..+|..+
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N------G~VwI~~~~~~~~~~a~~~I~~~ 206 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN------GRIWIKGPDEEDEEIAIEAIKKI 206 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC------cEEEEeeCCHHHHHHHHHHHHHH
Confidence 47789999999999999999999999999999999664 3677777 444667777766654
No 69
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=86.30 E-value=0.66 Score=44.61 Aligned_cols=81 Identities=15% Similarity=0.114 Sum_probs=42.7
Q ss_pred ccccccccccccc-cCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccccC
Q 022221 39 KSKPCTKFFSTSG-CPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSA 117 (300)
Q Consensus 39 Kt~lC~~y~~~g~-C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~~~ 117 (300)
..++| +|...+. |.. ++|-|-|..|.+...+.. .+..++-.-.++.....++++ ..-...|-+|+++
T Consensus 60 ~e~~C-Ywe~~p~gC~k-~~CgfRH~~pPLkg~l~~---~p~~pe~ev~~~~~SAq~~sV-------~~~p~P~l~~~K~ 127 (667)
T KOG4791|consen 60 SEIPC-YWENQPTGCQK-LNCGFRHNRPPLKGVLPT---VPESPEEEVKASQLSAQQNSV-------QSNPSPQLRSVKK 127 (667)
T ss_pred Ccccc-eeecCCCccCC-CccccccCCCchhhhccC---CCCCcccccccccccCCCccc-------ccCCchHHHHhhh
Confidence 34679 7766655 876 589999966544222211 111111000011111111122 2223458777766
Q ss_pred cCCCCCCCCccCCCc
Q 022221 118 EGCKFGDKCHFAHGE 132 (300)
Q Consensus 118 ~~C~~g~~C~f~H~~ 132 (300)
- |--+|.|.|+|..
T Consensus 128 ~-e~~~D~~s~Lh~P 141 (667)
T KOG4791|consen 128 V-ESSEDVPSPLHPP 141 (667)
T ss_pred h-hhhccccccCCCC
Confidence 4 9999999999976
No 70
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=84.42 E-value=0.7 Score=46.57 Aligned_cols=66 Identities=24% Similarity=0.374 Sum_probs=51.1
Q ss_pred cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcH-HHHHHHhhcceeeEeccC
Q 022221 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTF-DQIKQASAMVRELIVNVG 249 (300)
Q Consensus 178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~-~qi~~A~~~I~~~l~~~~ 249 (300)
....+.|++..+..+||++|..|+.|...++++|.|.+.. .+.|.++. ..+..|...|..+..+.+
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~IdieddG------tv~i~~s~~~~~~~ak~~I~~i~~e~e 618 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDG------TVKIAASDGESAKKAKERIEAITREVE 618 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCCC------cEEEEecchHHHHHHHHHHHHHHhhcc
Confidence 3566889999999999999999999999999999997432 35555543 567778777777665444
No 71
>PF10650 zf-C3H1: Putative zinc-finger domain; InterPro: IPR019607 This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger.
Probab=83.94 E-value=0.69 Score=25.44 Aligned_cols=20 Identities=35% Similarity=0.747 Sum_probs=16.7
Q ss_pred ccccccccc-cccCCCCCcCCC
Q 022221 270 KLCENFAKG-SCTFGDRCHFAH 290 (300)
Q Consensus 270 ~~C~~~~~G-~C~~G~~C~faH 290 (300)
.+|.|-++| .|.- +.|.|.|
T Consensus 1 ~lC~yEl~Gg~Cnd-~~C~~QH 21 (23)
T PF10650_consen 1 PLCPYELTGGVCND-PDCEFQH 21 (23)
T ss_pred CCCccccCCCeeCC-CCCCccc
Confidence 379998876 9987 6999998
No 72
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=82.59 E-value=0.73 Score=45.10 Aligned_cols=71 Identities=23% Similarity=0.427 Sum_probs=57.3
Q ss_pred CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVN 247 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~ 247 (300)
...+...+|+..++.|+||+|..+..++..++++|-++....+...+...|.+...-...|+.++.+.+.+
T Consensus 139 pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~e 209 (608)
T KOG2279|consen 139 PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSE 209 (608)
T ss_pred cccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccc
Confidence 34556788999999999999999999999999999998877666677777777766666777777666544
No 73
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=81.98 E-value=0.82 Score=45.31 Aligned_cols=64 Identities=27% Similarity=0.431 Sum_probs=44.3
Q ss_pred CcceEEEeCc-cccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeE
Q 022221 177 SATAKISIDA-KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELI 245 (300)
Q Consensus 177 ~~t~~~~iP~-~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l 245 (300)
.+...+.+|+ .+-|.||||.|.||+.+...||+-+.|++.+ ..+.+++ +|--.+-|...+..++
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~fdp~rreia~~~l~~li 268 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPVRREIARMALEKLI 268 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC-----CeEEecCCchHHHHHHHHHHHHHH
Confidence 3445578885 7789999999999999999999999998865 3444554 3322234444444443
No 74
>PRK00106 hypothetical protein; Provisional
Probab=81.40 E-value=0.96 Score=44.89 Aligned_cols=65 Identities=25% Similarity=0.375 Sum_probs=45.1
Q ss_pred CcceEEEeCc-cccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEe
Q 022221 177 SATAKISIDA-KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIV 246 (300)
Q Consensus 177 ~~t~~~~iP~-~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~ 246 (300)
.+...+.+|+ .+-|.||||.|.||+.+...||+-+.|++.+ ..+.+++ +|--.+-|...+..++.
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP-----EVVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC-----CeEEEeCCChHHHHHHHHHHHHHHH
Confidence 3445578885 7889999999999999999999999998765 3445555 33333344444444443
No 75
>PRK12704 phosphodiesterase; Provisional
Probab=80.67 E-value=1 Score=44.67 Aligned_cols=65 Identities=25% Similarity=0.405 Sum_probs=45.5
Q ss_pred CcceEEEeCc-cccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEe
Q 022221 177 SATAKISIDA-KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIV 246 (300)
Q Consensus 177 ~~t~~~~iP~-~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~ 246 (300)
.+...+.+|+ .+-|.||||.|.||+.+...||+-+.|++.+ ..+.+++ ++--.+.|...+..++.
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~~~~~rre~a~~~l~~l~~ 275 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPIRREIARLALEKLVQ 275 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC-----CeEEEecCChhhHHHHHHHHHHHHh
Confidence 3445578885 7889999999999999999999999998864 3445555 33333344444444433
No 76
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=80.65 E-value=0.72 Score=39.72 Aligned_cols=32 Identities=34% Similarity=0.599 Sum_probs=28.8
Q ss_pred ccccceeccCCCccccchhcccCCeeEeccCC
Q 022221 186 AKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 217 (300)
Q Consensus 186 ~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~ 217 (300)
...+|+|||..|.++++++..|+++|-|+...
T Consensus 162 ~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 162 SNFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred cceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 56789999999999999999999999997543
No 77
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=79.30 E-value=1.3 Score=43.36 Aligned_cols=68 Identities=15% Similarity=0.129 Sum_probs=57.5
Q ss_pred CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCc---cceeecCcHHHHHHHhhcceee
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNL---RNIELEGTFDQIKQASAMVREL 244 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~---~~~~i~G~~~qi~~A~~~I~~~ 244 (300)
..-.++.+|..++|.|||..|..++.+...+++.+.|..+...... .++.+.|..+.++.+..++...
T Consensus 295 l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egkqh~~n~vl~ml~~~ 365 (608)
T KOG2279|consen 295 LAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGKQHYENSVLEMLTVH 365 (608)
T ss_pred cccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecchhHHHHHHHhhhhcc
Confidence 4456789999999999999999999999999999999876544332 7888999999999998888743
No 78
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=78.46 E-value=0.93 Score=46.63 Aligned_cols=62 Identities=21% Similarity=0.346 Sum_probs=48.9
Q ss_pred ceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEe
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIV 246 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~ 246 (300)
...+.||+..++.+||.||.+|++|...++++|.+.+. ..+.+.+ +...+++|...|..+..
T Consensus 555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~------G~v~i~~~~~~~~~~a~~~I~~~~~ 617 (693)
T PRK11824 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD------GTVKIAATDGEAAEAAKERIEGITA 617 (693)
T ss_pred heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC------ceEEEEcccHHHHHHHHHHHHHhcc
Confidence 45678899999999999999999999999998888553 2445555 56677788887776654
No 79
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=77.61 E-value=1 Score=41.65 Aligned_cols=26 Identities=31% Similarity=0.855 Sum_probs=22.4
Q ss_pred ccccccccccccccCCCCCcCCCCcc
Q 022221 268 KTKLCENFAKGSCTFGDRCHFAHGSE 293 (300)
Q Consensus 268 kt~~C~~~~~G~C~~G~~C~faH~~~ 293 (300)
...+|.||..|+|++|+.|.|.|..-
T Consensus 160 ~p~Icsf~v~geckRG~ec~yrhEkp 185 (377)
T KOG0153|consen 160 RPHICSFFVKGECKRGAECPYRHEKP 185 (377)
T ss_pred CCccccceeeccccccccccccccCC
Confidence 34579999999999999999999653
No 80
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=75.71 E-value=1.7 Score=38.88 Aligned_cols=38 Identities=32% Similarity=0.512 Sum_probs=31.7
Q ss_pred cceEEEeCc------cccceeccCCCccccchhcccCCeeEecc
Q 022221 178 ATAKISIDA------KLAGAIIGKNGVNSKQICRLTGAKLSIRD 215 (300)
Q Consensus 178 ~t~~~~iP~------~~~G~iiG~gG~~ik~i~~~Sga~i~i~~ 215 (300)
.+.+|.||. ..||.|||..|..++.++..|+++|.|..
T Consensus 92 ~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG 135 (259)
T KOG1588|consen 92 LTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG 135 (259)
T ss_pred EEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence 345566653 47899999999999999999999999964
No 81
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=75.17 E-value=2.2 Score=45.64 Aligned_cols=72 Identities=17% Similarity=0.130 Sum_probs=58.8
Q ss_pred ceEEEeCccccceeccCCCccccchhcccCCeeEecc-CCCCCCccceeecCcHHHHHHHhhcceeeEeccCC
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD-HEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGS 250 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~-~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~~ 250 (300)
..++.+|...+..|||++|++|..++.-+|+.|.|.. ++.+..++.+.+-|.++....|-..|...+.+-+.
T Consensus 1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dpdv 1413 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIIDPDV 1413 (2131)
T ss_pred ccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeecCCc
Confidence 4557778888888999999999999999999999976 45556778889999999888887777766655443
No 82
>PRK02821 hypothetical protein; Provisional
Probab=71.71 E-value=2.3 Score=30.92 Aligned_cols=31 Identities=16% Similarity=0.384 Sum_probs=26.8
Q ss_pred CcceEEEeCccccceeccCCCccccchhccc
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLT 207 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~S 207 (300)
....++.+.+.-.|.||||+|.+++.|+..-
T Consensus 30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred cEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 4567888899999999999999999998754
No 83
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=66.56 E-value=2.3 Score=34.60 Aligned_cols=38 Identities=29% Similarity=0.403 Sum_probs=32.6
Q ss_pred cceEEEeCccccceeccCCCccccchhcccCCeeEecc
Q 022221 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD 215 (300)
Q Consensus 178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~ 215 (300)
....+.++....|.+|||+|.+++.++..++..+.|.+
T Consensus 99 ~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~~ 136 (140)
T PRK08406 99 KVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDIDD 136 (140)
T ss_pred EEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCeE
Confidence 45667889999999999999999999999988876643
No 84
>PRK00468 hypothetical protein; Provisional
Probab=66.24 E-value=3.2 Score=29.98 Aligned_cols=30 Identities=23% Similarity=0.391 Sum_probs=25.0
Q ss_pred cceEEEeCccccceeccCCCccccchhccc
Q 022221 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLT 207 (300)
Q Consensus 178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~S 207 (300)
....+.+.+.-.|.||||+|.+++.|+..-
T Consensus 30 ~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 30 VILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred EEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 445677889999999999999999988643
No 85
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=64.20 E-value=3.7 Score=33.37 Aligned_cols=38 Identities=21% Similarity=0.295 Sum_probs=32.8
Q ss_pred ceEEEeCccccceeccCCCccccchhcccCCeeEeccC
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH 216 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~ 216 (300)
.+-+.++...+|+.||++|++|+.+++..+.+|.|...
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~ 70 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY 70 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc
Confidence 45677789999999999999999999999988888543
No 86
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=61.07 E-value=4.3 Score=34.86 Aligned_cols=53 Identities=30% Similarity=0.479 Sum_probs=45.2
Q ss_pred ccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeE
Q 022221 186 AKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELI 245 (300)
Q Consensus 186 ~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l 245 (300)
...+|.|+|++|.+--.|...|..+|.+.+. .+.|.|.++.+..|...|..+|
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad~-------kIHiLG~~~niriAR~avcsLI 229 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLADS-------KIHILGAFQNIRIARDAVCSLI 229 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecCc-------eEEEeecchhhHHHHHhhHhhh
Confidence 4567899999999999999999999998764 3788999999998888777665
No 87
>PRK01064 hypothetical protein; Provisional
Probab=60.94 E-value=5.3 Score=29.09 Aligned_cols=30 Identities=30% Similarity=0.414 Sum_probs=24.9
Q ss_pred CcceEEEeCccccceeccCCCccccchhcc
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRL 206 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~ 206 (300)
.....+.+...-.|.+|||+|.+++.|+..
T Consensus 29 ~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 29 TIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred EEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 345567778888999999999999998874
No 88
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=60.07 E-value=3.2 Score=38.33 Aligned_cols=72 Identities=19% Similarity=0.223 Sum_probs=53.7
Q ss_pred eEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeec-CcHHHHHHHhhcceeeEeccCCCCC
Q 022221 180 AKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELE-GTFDQIKQASAMVRELIVNVGSGSG 253 (300)
Q Consensus 180 ~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~-G~~~qi~~A~~~I~~~l~~~~~~~p 253 (300)
..+.+++...+.|||+.|.+-+.+...+.+.|.+... ..+...+.|. +...++.+|...|..++.......|
T Consensus 59 ~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p--~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~s~p 131 (345)
T KOG2814|consen 59 SSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP--NTNKEEIKIIGISRNCVIQALERIAKLIDSDRKSFP 131 (345)
T ss_pred hhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC--CCCcceEEEeehhHHHHHHHHHHHHHHHHhhhhcCc
Confidence 3467789999999999999999999999999999542 2233334444 4778888888888888766554333
No 89
>PRK12705 hypothetical protein; Provisional
Probab=57.77 E-value=5.9 Score=39.20 Aligned_cols=40 Identities=33% Similarity=0.524 Sum_probs=33.8
Q ss_pred cceEEEeC-ccccceeccCCCccccchhcccCCeeEeccCC
Q 022221 178 ATAKISID-AKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 217 (300)
Q Consensus 178 ~t~~~~iP-~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~ 217 (300)
+...+.+| ..+-|.||||.|.||+.+...||.-+.|++.+
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp 238 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP 238 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc
Confidence 34446778 46779999999999999999999999998765
No 90
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=57.41 E-value=54 Score=33.29 Aligned_cols=20 Identities=25% Similarity=0.607 Sum_probs=14.4
Q ss_pred cccccccccccCCCCCCCCCCCCC
Q 022221 42 PCTKFFSTSGCPFGEGCHFLHYVP 65 (300)
Q Consensus 42 lC~~y~~~g~C~~G~~C~F~H~~~ 65 (300)
.|.++ -.|. ++.|.|+|...
T Consensus 546 ~Cky~---~~Ct-~a~Ce~~HPta 565 (681)
T KOG3702|consen 546 RCKYG---PACT-SAECEFAHPTA 565 (681)
T ss_pred cccCC---CcCC-chhhhhcCCcc
Confidence 58443 4677 88999999654
No 91
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=56.73 E-value=6.3 Score=28.55 Aligned_cols=30 Identities=27% Similarity=0.453 Sum_probs=25.0
Q ss_pred CcceEEEeCccccceeccCCCccccchhcc
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRL 206 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~ 206 (300)
....++.+-+.-.|-+|||+|.+++.|+..
T Consensus 29 ~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 29 TVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred eEEEEEEECcccccceecCCChhHHHHHHH
Confidence 344667888999999999999999998863
No 92
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=55.44 E-value=12 Score=37.30 Aligned_cols=62 Identities=19% Similarity=0.300 Sum_probs=47.7
Q ss_pred ceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEec
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIVN 247 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~~ 247 (300)
.+.+.++++..-.+||.+|...|.|...||+..++++.. ++|.. ++.....|++.|..++..
T Consensus 598 ~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe~t-------~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 598 LETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDEGT-------FSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred eeEEeecchhhheeecCccceeeeEeeeccceeeecCce-------EEEEecCHHHHHHHHHHHHHHhcC
Confidence 455778888899999999999999999999665554432 44443 677888899888887754
No 93
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=54.42 E-value=8.3 Score=36.53 Aligned_cols=41 Identities=24% Similarity=0.394 Sum_probs=36.6
Q ss_pred CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCC
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 217 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~ 217 (300)
.....+.||....+..||++|.|++-....+|.+|.|.+-+
T Consensus 307 ~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 307 EKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred CcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 45677899999999999999999999999999999997644
No 94
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=53.01 E-value=5.6 Score=32.42 Aligned_cols=38 Identities=24% Similarity=0.324 Sum_probs=32.2
Q ss_pred CcceEEEeCccccceeccCCCccccchhcccCCeeEec
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIR 214 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~ 214 (300)
.....+.+++...+..|||+|.|++.....++.++.|.
T Consensus 99 ~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 99 KKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 34566888999999999999999999999998877664
No 95
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=52.72 E-value=7.8 Score=36.37 Aligned_cols=40 Identities=23% Similarity=0.415 Sum_probs=35.9
Q ss_pred CcceEEEeCccccceeccCCCccccchhcccCCeeEeccC
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH 216 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~ 216 (300)
.....+.+|....+..||++|.|++-....||.+|.|.+.
T Consensus 300 ~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 300 KHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred CcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 3567889999999999999999999999999999999653
No 96
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=52.51 E-value=6.8 Score=27.75 Aligned_cols=27 Identities=37% Similarity=0.581 Sum_probs=22.5
Q ss_pred cceeccCCCccccchhccc-CCeeEecc
Q 022221 189 AGAIIGKNGVNSKQICRLT-GAKLSIRD 215 (300)
Q Consensus 189 ~G~iiG~gG~~ik~i~~~S-ga~i~i~~ 215 (300)
+|+.||++|.+|+.+++.. +.+|.+..
T Consensus 19 vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 19 VGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp HHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred ceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 7999999999999999999 88888854
No 97
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=52.09 E-value=7.7 Score=31.59 Aligned_cols=37 Identities=27% Similarity=0.414 Sum_probs=31.5
Q ss_pred eEEEeCccccceeccCCCccccchhcccCCeeEeccC
Q 022221 180 AKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH 216 (300)
Q Consensus 180 ~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~ 216 (300)
.-+.+....+|+.||++|++|+.+++..|-+|.|...
T Consensus 35 iifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey 71 (141)
T TIGR01952 35 VVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY 71 (141)
T ss_pred EEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc
Confidence 4467788899999999999999999888888888543
No 98
>PF08098 ATX_III: Anemonia sulcata toxin III family; InterPro: IPR012509 This entry occurs within the Anemonia sulcata toxin III (ATX III) neurotoxin family. ATX III is a neurotoxin that is produced by sea anemone; it adopts a compact structure containing four reverse turns and two other chain reversals, but no regular alpha-helix or beta-sheet. A hydrophobic patch found on the surface of the peptide may constitute part of the sodium channel binding surface [].; GO: 0019871 sodium channel inhibitor activity, 0009405 pathogenesis, 0042151 nematocyst; PDB: 1ANS_A.
Probab=50.87 E-value=8.3 Score=21.49 Aligned_cols=15 Identities=53% Similarity=1.499 Sum_probs=6.7
Q ss_pred cccccccccccCCCCCCC
Q 022221 42 PCTKFFSTSGCPFGEGCH 59 (300)
Q Consensus 42 lC~~y~~~g~C~~G~~C~ 59 (300)
|| +| .+.|++|.+|.
T Consensus 8 mc-~~--~~gC~WGQ~~~ 22 (27)
T PF08098_consen 8 MC-KY--TGGCPWGQNCY 22 (27)
T ss_dssp ----T--TTT-SSS-SS-
T ss_pred cc-ee--ecCCccccccc
Confidence 56 45 36699998874
No 99
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=50.64 E-value=7.4 Score=33.35 Aligned_cols=38 Identities=26% Similarity=0.365 Sum_probs=34.4
Q ss_pred ceEEEeCccccceeccCCCccccchhcccCCeeEeccC
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH 216 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~ 216 (300)
...+.||+...+.+||++|.+++-+.+.|+.++.|...
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~ 180 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence 57778999999999999999999999999999999653
No 100
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=50.47 E-value=11 Score=26.98 Aligned_cols=33 Identities=24% Similarity=0.353 Sum_probs=26.9
Q ss_pred cceEEEeCccccceeccCCCccccchhcccCCe
Q 022221 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAK 210 (300)
Q Consensus 178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~ 210 (300)
....+.+.....|.+|||.|..+..||-.....
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~ 56 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLV 56 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHHH
Confidence 346677888889999999999999999876543
No 101
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=47.35 E-value=13 Score=30.45 Aligned_cols=40 Identities=30% Similarity=0.444 Sum_probs=35.0
Q ss_pred cceEEEeCccccceeccCCCccccchhcccCCeeEeccCC
Q 022221 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 217 (300)
Q Consensus 178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~ 217 (300)
.+-++.|-....|.+||++|..+.+|...+|....|....
T Consensus 76 ~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp 115 (145)
T cd02410 76 DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP 115 (145)
T ss_pred CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence 3567888899999999999999999999999999885544
No 102
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=46.56 E-value=18 Score=31.03 Aligned_cols=40 Identities=33% Similarity=0.429 Sum_probs=35.1
Q ss_pred cceEEEeCccccceeccCCCccccchhcccCCeeEeccCC
Q 022221 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 217 (300)
Q Consensus 178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~ 217 (300)
....+.||....++|||..|...+.|...++.++.|+...
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~ 47 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKT 47 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEECCC
Confidence 4566899999999999999999999999999999886543
No 103
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=46.31 E-value=10 Score=27.73 Aligned_cols=30 Identities=20% Similarity=0.381 Sum_probs=25.6
Q ss_pred ceEEEeCccccceeccCCCccccchhcccC
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTG 208 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sg 208 (300)
...+.|-....|++||++|..+++|...-.
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~ 60 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQ 60 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHH
Confidence 367788889999999999999999987553
No 104
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=45.42 E-value=12 Score=34.93 Aligned_cols=28 Identities=29% Similarity=0.713 Sum_probs=22.0
Q ss_pred ccccccccccccccCCCCCCCCCCCCCCC
Q 022221 39 KSKPCTKFFSTSGCPFGEGCHFLHYVPGG 67 (300)
Q Consensus 39 Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~ 67 (300)
.-.+| .|+..|.|+.|+.|.|.|..+.+
T Consensus 160 ~p~Ic-sf~v~geckRG~ec~yrhEkp~d 187 (377)
T KOG0153|consen 160 RPHIC-SFFVKGECKRGAECPYRHEKPPD 187 (377)
T ss_pred CCccc-cceeeccccccccccccccCCCC
Confidence 34479 55566899999999999998743
No 105
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=45.33 E-value=13 Score=25.02 Aligned_cols=30 Identities=30% Similarity=0.465 Sum_probs=22.8
Q ss_pred EEeCccccceeccCCCccccchhcccCCee
Q 022221 182 ISIDAKLAGAIIGKNGVNSKQICRLTGAKL 211 (300)
Q Consensus 182 ~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i 211 (300)
+.+...-.|.+||+.|.+++.++..++..+
T Consensus 29 i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 29 IVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 344444579999999999999998876443
No 106
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=43.07 E-value=4.6 Score=28.95 Aligned_cols=32 Identities=38% Similarity=0.454 Sum_probs=26.2
Q ss_pred eEEEeCccccceeccCCCccccchhcccCCee
Q 022221 180 AKISIDAKLAGAIIGKNGVNSKQICRLTGAKL 211 (300)
Q Consensus 180 ~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i 211 (300)
..+.+-.+..|.+||++|++|+.|.......+
T Consensus 27 ~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 27 IIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp EEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred EEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 55677788999999999999999988665444
No 107
>PF10283 zf-CCHH: Zinc-finger (CX5CX6HX5H) motif; InterPro: IPR019406 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type Znf motif that in humans is part of the APLF (aprataxin- and PNK-like) forkead association domain-containing protein []. The Znf is highly conserved both in primary sequence and in the spacing between the putative zinc coordinating residues, and is configured CX5CX6HX5H. Many of the proteins containing this Znf are involved in DNA strand break repair and/or contain domains implicated in DNA metabolism. This Znf motif appears to be specialised for the non-covalent binding of poly ADP-ribose; Aprataxin also appears to covalently bind poly ADP-ribose, but not through its Znf motif [].; PDB: 2KQC_A 2KUO_A 2KQE_A 2KQD_A 2KQB_A.
Probab=42.94 E-value=6.5 Score=22.31 Aligned_cols=9 Identities=33% Similarity=1.309 Sum_probs=5.7
Q ss_pred cccCCCCCc
Q 022221 279 SCTFGDRCH 287 (300)
Q Consensus 279 ~C~~G~~C~ 287 (300)
.|+||.+|-
T Consensus 2 ~C~YG~~CY 10 (26)
T PF10283_consen 2 PCKYGAKCY 10 (26)
T ss_dssp E-TTGGG-S
T ss_pred CCCcchhhh
Confidence 599999993
No 108
>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]
Probab=42.43 E-value=16 Score=35.41 Aligned_cols=51 Identities=20% Similarity=0.201 Sum_probs=32.9
Q ss_pred CCCCCCCCCCCCCCCCCcccchhhhccCCCCCccccccccccccccccCCCCCCCCCCCC
Q 022221 5 GGRKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYV 64 (300)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~ 64 (300)
||++|-|.++-++++. |+. ....+|-...|..|...|.|..|+.|.+.|+.
T Consensus 186 ~~~rrsrsr~r~~~st-----rtg----p~ks~~s~~r~k~fee~g~~~r~el~p~~hg~ 236 (526)
T KOG2135|consen 186 HGHRRSRSRGRDPTST-----RTG----PEKSRNSENRRKFFEEFGVLERGELCPTHHGC 236 (526)
T ss_pred ccccccccccCCCccc-----ccC----cccccccHHhhhhhHhhceeeecccccccccc
Confidence 4555555555555543 100 11223445579778889999999999999975
No 109
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=39.62 E-value=5.7 Score=28.12 Aligned_cols=32 Identities=31% Similarity=0.455 Sum_probs=26.6
Q ss_pred CcceEEEeCccccceeccCCCccccchhcccC
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTG 208 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sg 208 (300)
.....+.+...-.|.||||.|.++..|+...+
T Consensus 28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 44567788888999999999999999987554
No 110
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=38.09 E-value=16 Score=35.50 Aligned_cols=39 Identities=33% Similarity=0.490 Sum_probs=35.2
Q ss_pred cceEEEeCccccceeccCCCccccchhcccCCeeEeccC
Q 022221 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH 216 (300)
Q Consensus 178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~ 216 (300)
....+.||....+..|||+|.|++-....|+.+|.|.+.
T Consensus 335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~ 373 (449)
T PRK12329 335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDS 373 (449)
T ss_pred cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccH
Confidence 456789999999999999999999999999999999653
No 111
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=36.55 E-value=1.1e+02 Score=31.29 Aligned_cols=12 Identities=25% Similarity=0.288 Sum_probs=6.7
Q ss_pred cCCCCCCCCCCC
Q 022221 52 CPFGEGCHFLHY 63 (300)
Q Consensus 52 C~~G~~C~F~H~ 63 (300)
|.|++.|.|.|.
T Consensus 575 k~fa~~~~ks~p 586 (681)
T KOG3702|consen 575 KKFASKCLKSHP 586 (681)
T ss_pred ccccccceeccc
Confidence 455666555553
No 112
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=36.45 E-value=18 Score=35.55 Aligned_cols=39 Identities=31% Similarity=0.437 Sum_probs=35.2
Q ss_pred CcceEEEeCccccceeccCCCccccchhcccCCeeEecc
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD 215 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~ 215 (300)
.....+.||....+..|||+|.|++..+..||.+|.|..
T Consensus 301 ~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 346778899999999999999999999999999999965
No 113
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=34.87 E-value=20 Score=33.96 Aligned_cols=41 Identities=29% Similarity=0.466 Sum_probs=36.1
Q ss_pred CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCC
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 217 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~ 217 (300)
.....+.+|....+..||++|.|++-....|+.+|.|.+..
T Consensus 302 ~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~ 342 (362)
T PRK12327 302 EKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES 342 (362)
T ss_pred CcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence 35677889999999999999999999999999999996543
No 114
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=34.39 E-value=22 Score=29.82 Aligned_cols=38 Identities=21% Similarity=0.297 Sum_probs=31.0
Q ss_pred ceEEEeCccccceeccCCCccccchhcccCCeeEeccCC
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 217 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~ 217 (300)
.+-+.|...- |..||++|.+++.++...|-+|.+....
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~s 99 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEKT 99 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEcC
Confidence 3445566666 9999999999999999999999996544
No 115
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=32.84 E-value=22 Score=31.42 Aligned_cols=27 Identities=30% Similarity=0.593 Sum_probs=24.1
Q ss_pred ceEEEeCccccceeccCCCccccchhc
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICR 205 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~ 205 (300)
.+.+.|-....|.|||++|++|..|..
T Consensus 52 ~~~V~I~aarPg~VIGk~G~~I~~L~~ 78 (233)
T COG0092 52 GTRVTIHAARPGLVIGKKGSNIEKLRK 78 (233)
T ss_pred ceEEEEEeCCCcceEcCCCccHHHHHH
Confidence 477888889999999999999998877
No 116
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=31.61 E-value=28 Score=34.07 Aligned_cols=40 Identities=28% Similarity=0.434 Sum_probs=35.0
Q ss_pred cceEEEeCccccceeccCCCccccchhcccCCeeEeccCC
Q 022221 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 217 (300)
Q Consensus 178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~ 217 (300)
...-+.+|...++.+|||+|.+|++|....|.+|.+...+
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 4466788999999999999999999999999999996533
No 117
>PRK13764 ATPase; Provisional
Probab=31.54 E-value=28 Score=35.29 Aligned_cols=41 Identities=24% Similarity=0.361 Sum_probs=36.0
Q ss_pred CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCC
Q 022221 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 217 (300)
Q Consensus 177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~ 217 (300)
...+.+.||...++.+|||+|.+|+.|....|..|.|....
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~ 520 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLD 520 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence 44566888999999999999999999999999999996544
No 118
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=30.54 E-value=21 Score=27.56 Aligned_cols=29 Identities=24% Similarity=0.461 Sum_probs=24.7
Q ss_pred ceEEEeCccccceeccCCCccccchhccc
Q 022221 179 TAKISIDAKLAGAIIGKNGVNSKQICRLT 207 (300)
Q Consensus 179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~S 207 (300)
.+.+.|-....|+|||+.|..|+.++...
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l 90 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKEL 90 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHH
Confidence 36778888889999999999999988754
No 119
>KOG3777 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.52 E-value=28 Score=33.74 Aligned_cols=26 Identities=27% Similarity=0.824 Sum_probs=21.1
Q ss_pred CccccccccccccccccCCCCCCCCCCCC
Q 022221 36 IGSKSKPCTKFFSTSGCPFGEGCHFLHYV 64 (300)
Q Consensus 36 ~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~ 64 (300)
..++-..| -| ..+|+||..|+|.|..
T Consensus 167 ~aq~~q~C-py--gkkctyg~kck~~h~~ 192 (443)
T KOG3777|consen 167 WAQNKQPC-PY--GKKCTYGGKCKFYHPE 192 (443)
T ss_pred hhhcccCC-Cc--ccccCCCCceeecccc
Confidence 45677789 66 5789999999999965
No 120
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=28.31 E-value=21 Score=32.41 Aligned_cols=44 Identities=25% Similarity=0.441 Sum_probs=32.7
Q ss_pred eeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcc
Q 022221 191 AIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMV 241 (300)
Q Consensus 191 ~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I 241 (300)
.|||..|.+++.|.-.|.+.|.|.... |.++|.+.....+...+
T Consensus 162 RLiGpng~TLKAlelLT~CYilVqG~T-------VsaiGpfkGlkevr~IV 205 (356)
T KOG2874|consen 162 RLIGPNGSTLKALELLTNCYILVQGNT-------VSAIGPFKGLKEVRKIV 205 (356)
T ss_pred HhcCCCchhHHHHHHHhhcEEEeeCcE-------EEeecCcchHHHHHHHH
Confidence 389999999999999999999996543 56667665544443333
No 121
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=25.17 E-value=34 Score=24.98 Aligned_cols=28 Identities=29% Similarity=0.580 Sum_probs=22.8
Q ss_pred eEEEeCccccceeccCCCccccchhccc
Q 022221 180 AKISIDAKLAGAIIGKNGVNSKQICRLT 207 (300)
Q Consensus 180 ~~~~iP~~~~G~iiG~gG~~ik~i~~~S 207 (300)
..+.|-....|.+||++|.++..+...-
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHH
Confidence 5666667888999999999999888743
No 122
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=24.79 E-value=27 Score=32.57 Aligned_cols=26 Identities=23% Similarity=0.545 Sum_probs=0.0
Q ss_pred cccccccccCcCCCCCCCCccCCCccc
Q 022221 108 SRLCNKYNSAEGCKFGDKCHFAHGEWE 134 (300)
Q Consensus 108 t~~C~~~~~~~~C~~g~~C~f~H~~~~ 134 (300)
|+-|..|+.+..|++++ |.|+|-..+
T Consensus 202 TKYCtsYLRn~~CpNp~-CMyLHEpg~ 227 (480)
T COG5175 202 TKYCTSYLRNAVCPNPD-CMYLHEPGP 227 (480)
T ss_pred hHHHHHHHcCCCCCCCC-eeeecCCCc
No 123
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=23.08 E-value=33 Score=27.17 Aligned_cols=17 Identities=29% Similarity=0.954 Sum_probs=14.1
Q ss_pred cccccCCCCCcCCCCcch
Q 022221 277 KGSCTFGDRCHFAHGSEE 294 (300)
Q Consensus 277 ~G~C~~G~~C~faH~~~e 294 (300)
.+.|++|+ |+|-||..-
T Consensus 59 v~GC~~ge-CHy~~GN~k 75 (132)
T COG1908 59 VAGCKIGE-CHYISGNYK 75 (132)
T ss_pred Eecccccc-eeeeccchH
Confidence 46899998 999998654
No 124
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=21.19 E-value=33 Score=29.41 Aligned_cols=34 Identities=26% Similarity=0.460 Sum_probs=28.3
Q ss_pred eCccccceeccCCCccccchhcccCCeeEeccCC
Q 022221 184 IDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 217 (300)
Q Consensus 184 iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~ 217 (300)
+-...+|+.||++|++|+.++..-+-+|.|....
T Consensus 82 ~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s 115 (190)
T COG0195 82 VKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS 115 (190)
T ss_pred cCcCchhhhccCCChHHHHHHHHhCCceEEEEeC
Confidence 3467789999999999999999999888885443
No 125
>KOG3777 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.24 E-value=56 Score=31.79 Aligned_cols=28 Identities=25% Similarity=0.528 Sum_probs=21.8
Q ss_pred CCcccccccccccccccCCCCCcCCCCcch
Q 022221 265 NNFKTKLCENFAKGSCTFGDRCHFAHGSEE 294 (300)
Q Consensus 265 ~~ykt~~C~~~~~G~C~~G~~C~faH~~~e 294 (300)
..++.+.|.|- -.|+||..|.|.|++..
T Consensus 167 ~aq~~q~Cpyg--kkctyg~kck~~h~~~~ 194 (443)
T KOG3777|consen 167 WAQNKQPCPYG--KKCTYGGKCKFYHPEIA 194 (443)
T ss_pred hhhcccCCCcc--cccCCCCceeecccccc
Confidence 44566779984 48999999999998753
Done!