Query 027432
Match_columns 223
No_of_seqs 314 out of 1648
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 09:50:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027432.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027432hhsearch_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 8.4E-16 1.8E-20 138.4 4.2 40 20-59 122-162 (332)
2 cd02396 PCBP_like_KH K homolog 99.5 2.4E-14 5.2E-19 100.2 6.3 64 99-162 1-65 (65)
3 KOG2192 PolyC-binding hnRNP-K 99.4 1.3E-11 2.8E-16 107.6 14.0 74 95-168 312-385 (390)
4 KOG1676 K-homology type RNA bi 99.3 1.5E-12 3.2E-17 123.3 7.1 78 94-171 226-304 (600)
5 cd02394 vigilin_like_KH K homo 99.3 3.2E-12 7E-17 88.2 5.9 62 99-162 1-62 (62)
6 PF00013 KH_1: KH domain syndr 99.3 1.4E-12 3.1E-17 89.4 3.7 60 99-161 1-60 (60)
7 cd00105 KH-I K homology RNA-bi 99.3 8.5E-12 1.8E-16 85.8 6.6 64 99-162 1-64 (64)
8 cd02393 PNPase_KH Polynucleoti 99.3 8.6E-12 1.9E-16 86.5 5.8 58 99-162 3-61 (61)
9 KOG2191 RNA-binding protein NO 99.2 3.1E-11 6.8E-16 107.6 7.1 74 97-170 131-207 (402)
10 COG5063 CTH1 CCCH-type Zn-fing 99.1 2.3E-11 4.9E-16 107.4 3.0 33 187-219 269-302 (351)
11 KOG2191 RNA-binding protein NO 99.0 3.7E-10 8E-15 100.9 7.0 74 97-170 38-114 (402)
12 KOG2190 PolyC-binding proteins 99.0 3.2E-10 6.9E-15 107.4 7.0 73 97-169 137-210 (485)
13 KOG1676 K-homology type RNA bi 99.0 6.9E-10 1.5E-14 105.4 6.4 74 96-169 137-212 (600)
14 PF00642 zf-CCCH: Zinc finger 99.0 9.3E-11 2E-15 68.5 0.3 27 28-54 1-27 (27)
15 smart00322 KH K homology RNA-b 99.0 3.2E-09 6.9E-14 72.4 7.4 66 98-165 3-68 (69)
16 PF13014 KH_3: KH domain 98.9 1.8E-09 3.8E-14 69.5 4.2 42 108-149 1-43 (43)
17 KOG2193 IGF-II mRNA-binding pr 98.8 6.9E-09 1.5E-13 95.4 6.9 76 96-171 409-485 (584)
18 PF00642 zf-CCCH: Zinc finger 98.8 5.8E-10 1.3E-14 65.1 -0.3 26 190-215 1-27 (27)
19 KOG2193 IGF-II mRNA-binding pr 98.7 1.8E-08 3.9E-13 92.7 4.6 70 98-167 199-269 (584)
20 cd02395 SF1_like-KH Splicing f 98.6 8.7E-08 1.9E-12 75.2 6.1 70 100-169 2-97 (120)
21 TIGR03665 arCOG04150 arCOG0415 98.6 5.5E-08 1.2E-12 80.7 4.5 63 102-169 2-67 (172)
22 KOG1677 CCCH-type Zn-finger pr 98.6 6.4E-08 1.4E-12 87.2 4.9 34 187-220 127-162 (332)
23 PRK13763 putative RNA-processi 98.5 1.2E-07 2.6E-12 79.2 5.5 65 98-167 3-71 (180)
24 COG5063 CTH1 CCCH-type Zn-fing 98.5 1.9E-07 4.1E-12 82.8 6.3 44 20-63 104-148 (351)
25 TIGR03665 arCOG04150 arCOG0415 98.5 1.6E-07 3.5E-12 77.8 4.8 55 107-168 98-152 (172)
26 smart00356 ZnF_C3H1 zinc finge 98.4 1.6E-07 3.4E-12 54.1 2.0 27 189-215 1-27 (27)
27 smart00356 ZnF_C3H1 zinc finge 98.4 2E-07 4.2E-12 53.7 2.1 26 27-53 1-26 (27)
28 PRK13763 putative RNA-processi 98.3 6.6E-07 1.4E-11 74.7 5.0 56 107-169 104-159 (180)
29 KOG2192 PolyC-binding hnRNP-K 98.3 4.2E-07 9E-12 79.7 3.8 72 99-170 124-196 (390)
30 KOG2190 PolyC-binding proteins 98.3 3E-06 6.5E-11 80.6 9.1 70 97-166 42-120 (485)
31 KOG1595 CCCH-type Zn-finger pr 98.2 4.5E-07 9.8E-12 85.7 2.4 31 187-220 266-296 (528)
32 KOG0336 ATP-dependent RNA heli 98.2 2.6E-06 5.7E-11 79.0 6.7 93 74-169 23-115 (629)
33 TIGR02696 pppGpp_PNP guanosine 98.0 1.5E-05 3.3E-10 78.7 7.2 65 97-167 577-642 (719)
34 TIGR03591 polynuc_phos polyrib 97.8 3.4E-05 7.5E-10 76.4 5.6 68 97-170 550-618 (684)
35 KOG1595 CCCH-type Zn-finger pr 97.6 4.5E-05 9.7E-10 72.4 3.8 31 188-218 232-262 (528)
36 KOG0119 Splicing factor 1/bran 97.5 0.00024 5.1E-09 67.0 6.3 74 97-170 137-233 (554)
37 PLN00207 polyribonucleotide nu 97.4 0.00018 3.9E-09 72.8 4.7 68 97-170 684-753 (891)
38 COG1094 Predicted RNA-binding 97.3 0.0005 1.1E-08 57.9 5.4 56 108-170 112-167 (194)
39 COG1185 Pnp Polyribonucleotide 97.3 0.00045 9.7E-09 67.6 5.6 69 97-171 551-620 (692)
40 KOG2494 C3H1-type Zn-finger pr 97.2 0.00016 3.5E-09 65.0 1.6 28 192-220 71-98 (331)
41 cd02134 NusA_KH NusA_K homolog 96.8 0.0014 2.9E-08 45.2 3.3 36 98-133 25-60 (61)
42 PRK11824 polynucleotide phosph 96.7 0.0016 3.4E-08 64.9 4.0 67 98-170 554-621 (693)
43 COG5176 MSL5 Splicing factor ( 96.6 0.0028 6.2E-08 54.1 4.5 76 95-170 145-243 (269)
44 KOG2185 Predicted RNA-processi 96.6 0.00072 1.6E-08 62.5 1.0 30 191-220 139-172 (486)
45 PRK04163 exosome complex RNA-b 96.5 0.0059 1.3E-07 53.0 5.8 66 99-170 146-212 (235)
46 PF14608 zf-CCCH_2: Zinc finge 96.3 0.0025 5.4E-08 34.0 1.5 18 32-52 1-18 (19)
47 KOG1040 Polyadenylation factor 96.3 0.0039 8.5E-08 56.7 3.7 32 26-59 73-104 (325)
48 PF14608 zf-CCCH_2: Zinc finge 96.2 0.003 6.5E-08 33.7 1.6 19 194-214 1-19 (19)
49 KOG4369 RTK signaling protein 96.2 0.0022 4.7E-08 66.0 1.5 74 97-170 1339-1413(2131)
50 KOG2333 Uncharacterized conser 96.2 0.0038 8.2E-08 59.2 3.0 25 29-53 75-101 (614)
51 KOG2279 Kinase anchor protein 96.1 0.0042 9E-08 59.5 2.8 75 96-171 66-140 (608)
52 KOG2279 Kinase anchor protein 96.0 0.0029 6.2E-08 60.6 1.6 71 99-169 141-211 (608)
53 KOG2185 Predicted RNA-processi 95.8 0.0038 8.2E-08 57.9 1.1 29 30-59 140-172 (486)
54 TIGR03319 YmdA_YtgF conserved 95.6 0.029 6.3E-07 54.1 6.3 66 97-167 203-270 (514)
55 PRK12704 phosphodiesterase; Pr 95.4 0.043 9.3E-07 53.0 6.9 67 97-168 209-277 (520)
56 KOG2202 U2 snRNP splicing fact 95.4 0.01 2.2E-07 52.0 2.4 28 187-214 147-174 (260)
57 COG5252 Uncharacterized conser 95.4 0.0083 1.8E-07 52.1 1.7 34 188-221 81-114 (299)
58 KOG1588 RNA-binding protein Sa 95.3 0.016 3.6E-07 50.9 3.4 71 96-166 90-190 (259)
59 PRK00106 hypothetical protein; 95.2 0.049 1.1E-06 52.8 6.5 66 97-167 224-291 (535)
60 KOG2814 Transcription coactiva 95.0 0.031 6.7E-07 50.7 4.4 70 98-169 57-127 (345)
61 KOG2113 Predicted RNA binding 95.0 0.03 6.5E-07 50.6 4.1 67 94-163 22-88 (394)
62 KOG3273 Predicted RNA-binding 94.9 0.018 3.9E-07 49.0 2.4 58 106-170 177-234 (252)
63 COG5152 Uncharacterized conser 94.9 0.0097 2.1E-07 50.5 0.8 36 28-63 139-174 (259)
64 PRK00468 hypothetical protein; 94.8 0.024 5.3E-07 40.8 2.6 30 97-126 29-58 (75)
65 KOG2494 C3H1-type Zn-finger pr 94.8 0.0067 1.4E-07 54.8 -0.5 25 192-216 37-62 (331)
66 PRK02821 hypothetical protein; 94.7 0.028 6.1E-07 40.7 2.7 31 97-127 30-60 (77)
67 PRK08406 transcription elongat 94.6 0.062 1.3E-06 43.2 4.6 37 98-134 32-68 (140)
68 COG5152 Uncharacterized conser 93.8 0.022 4.8E-07 48.3 0.7 30 189-218 138-168 (259)
69 COG1837 Predicted RNA-binding 93.8 0.052 1.1E-06 39.3 2.5 30 97-126 29-58 (76)
70 PRK01064 hypothetical protein; 93.7 0.066 1.4E-06 38.9 2.9 30 97-126 29-58 (78)
71 KOG1067 Predicted RNA-binding 93.7 0.16 3.4E-06 49.4 6.1 67 97-170 596-663 (760)
72 KOG1763 Uncharacterized conser 93.6 0.016 3.5E-07 51.7 -0.6 33 188-220 88-120 (343)
73 PF13184 KH_5: NusA-like KH do 93.0 0.09 1.9E-06 37.2 2.6 36 99-134 4-45 (69)
74 COG1094 Predicted RNA-binding 93.0 0.18 3.9E-06 42.6 4.8 69 97-170 7-80 (194)
75 KOG1040 Polyadenylation factor 92.9 0.033 7.2E-07 50.7 0.4 28 188-215 73-100 (325)
76 PRK12705 hypothetical protein; 92.7 0.13 2.8E-06 49.6 4.1 41 97-137 197-238 (508)
77 PRK08406 transcription elongat 91.4 0.13 2.8E-06 41.3 2.1 38 97-134 98-135 (140)
78 KOG1763 Uncharacterized conser 91.2 0.055 1.2E-06 48.4 -0.3 34 26-60 88-121 (343)
79 KOG1492 C3H1-type Zn-finger pr 90.9 0.14 3E-06 44.5 1.9 22 31-52 207-228 (377)
80 cd02409 KH-II KH-II (K homolo 90.8 0.3 6.5E-06 32.8 3.2 34 98-131 25-58 (68)
81 KOG1813 Predicted E3 ubiquitin 90.6 0.087 1.9E-06 47.2 0.4 39 25-63 181-219 (313)
82 TIGR01952 nusA_arch NusA famil 90.5 0.27 5.8E-06 39.6 3.1 36 99-134 34-69 (141)
83 PF13083 KH_4: KH domain; PDB: 90.4 0.1 2.2E-06 36.8 0.5 32 96-127 27-58 (73)
84 KOG2208 Vigilin [Lipid transpo 90.2 0.44 9.6E-06 48.1 5.0 72 97-170 346-417 (753)
85 PF07650 KH_2: KH domain syndr 89.9 0.12 2.6E-06 36.8 0.5 34 98-131 25-58 (78)
86 COG5252 Uncharacterized conser 89.8 0.071 1.5E-06 46.4 -0.8 36 27-63 82-117 (299)
87 COG5084 YTH1 Cleavage and poly 89.6 0.46 1E-05 42.6 4.1 32 26-58 100-131 (285)
88 cd02414 jag_KH jag_K homology 88.7 0.45 9.7E-06 34.0 2.9 33 97-129 23-55 (77)
89 COG0195 NusA Transcription elo 87.6 0.43 9.2E-06 40.4 2.5 37 99-135 143-179 (190)
90 PRK13764 ATPase; Provisional 87.5 0.47 1E-05 46.7 3.1 40 97-136 480-519 (602)
91 PRK06418 transcription elongat 87.5 0.93 2E-05 37.5 4.3 37 98-135 61-97 (166)
92 TIGR01952 nusA_arch NusA famil 86.8 0.42 9.1E-06 38.5 1.9 38 97-134 99-136 (141)
93 COG1855 ATPase (PilT family) [ 86.0 0.58 1.3E-05 44.8 2.7 39 97-135 485-523 (604)
94 cd02413 40S_S3_KH K homology R 85.8 0.78 1.7E-05 33.4 2.7 33 98-130 30-62 (81)
95 TIGR01953 NusA transcription t 85.0 0.83 1.8E-05 42.0 3.1 39 97-135 300-338 (341)
96 KOG1039 Predicted E3 ubiquitin 85.0 0.32 7E-06 44.7 0.5 24 31-55 9-32 (344)
97 KOG1813 Predicted E3 ubiquitin 84.7 0.31 6.6E-06 43.8 0.1 30 188-217 182-212 (313)
98 PRK12328 nusA transcription el 83.6 1.2 2.5E-05 41.5 3.5 39 96-134 306-344 (374)
99 KOG2874 rRNA processing protei 80.8 2.5 5.4E-05 37.9 4.3 53 111-170 162-214 (356)
100 PRK09202 nusA transcription el 80.2 1.5 3.3E-05 41.9 3.0 39 97-135 301-339 (470)
101 PF10650 zf-C3H1: Putative zin 79.5 1.2 2.6E-05 24.9 1.2 21 193-214 1-22 (23)
102 cd02412 30S_S3_KH K homology R 79.3 1.3 2.9E-05 33.8 1.9 30 98-127 61-90 (109)
103 cd02411 archeal_30S_S3_KH K ho 78.6 1.9 4.1E-05 31.3 2.5 28 99-126 39-66 (85)
104 PRK12327 nusA transcription el 78.2 1.9 4.2E-05 39.9 2.9 40 96-135 301-340 (362)
105 COG0092 RpsC Ribosomal protein 78.0 1.8 4E-05 37.6 2.6 36 98-133 51-91 (233)
106 PRK12329 nusA transcription el 77.5 1.8 3.8E-05 41.2 2.5 39 97-135 334-372 (449)
107 COG0195 NusA Transcription elo 76.3 2.3 4.9E-05 36.0 2.6 35 100-134 78-112 (190)
108 PF14611 SLS: Mitochondrial in 74.6 11 0.00024 31.6 6.4 67 99-170 27-93 (210)
109 cd02410 archeal_CPSF_KH The ar 74.4 2.1 4.6E-05 34.7 1.9 38 98-135 76-113 (145)
110 KOG4791 Uncharacterized conser 71.9 4.1 8.9E-05 39.1 3.4 22 193-214 119-140 (667)
111 KOG2202 U2 snRNP splicing fact 71.1 1.9 4.2E-05 38.0 1.0 27 26-53 148-174 (260)
112 KOG2208 Vigilin [Lipid transpo 70.5 4.2 9.2E-05 41.2 3.4 67 99-166 421-487 (753)
113 KOG2333 Uncharacterized conser 70.4 1.8 4E-05 41.6 0.8 22 32-53 116-137 (614)
114 COG1097 RRP4 RNA-binding prote 69.4 10 0.00022 33.2 5.1 37 99-135 147-183 (239)
115 COG5084 YTH1 Cleavage and poly 62.0 4.9 0.00011 36.1 1.7 31 189-219 101-131 (285)
116 TIGR00436 era GTP-binding prot 54.2 6.2 0.00013 34.4 1.1 28 100-127 223-251 (270)
117 PRK15494 era GTPase Era; Provi 53.5 9.6 0.00021 34.6 2.2 27 100-126 275-302 (339)
118 KOG3161 Predicted E3 ubiquitin 52.3 2.7 5.8E-05 41.7 -1.6 36 187-222 198-234 (861)
119 PRK04191 rps3p 30S ribosomal p 51.1 12 0.00026 31.9 2.3 28 100-127 42-69 (207)
120 CHL00048 rps3 ribosomal protei 50.9 13 0.00028 31.9 2.5 30 98-127 66-95 (214)
121 TIGR03675 arCOG00543 arCOG0054 50.7 10 0.00022 37.6 2.1 40 97-136 92-131 (630)
122 PRK12327 nusA transcription el 50.3 11 0.00024 34.9 2.1 28 107-134 245-273 (362)
123 TIGR01008 rpsC_E_A ribosomal p 49.5 13 0.00028 31.5 2.3 28 99-126 39-66 (195)
124 TIGR01953 NusA transcription t 49.1 13 0.00027 34.3 2.3 28 107-134 243-271 (341)
125 PRK12329 nusA transcription el 48.8 11 0.00024 35.9 1.9 27 107-133 277-304 (449)
126 PRK00089 era GTPase Era; Revie 48.5 8.5 0.00018 33.7 1.0 27 101-127 229-256 (292)
127 KOG1492 C3H1-type Zn-finger pr 48.4 7.1 0.00015 34.0 0.5 21 194-214 208-229 (377)
128 PRK12328 nusA transcription el 48.3 11 0.00024 35.2 1.7 28 107-134 251-279 (374)
129 COG1782 Predicted metal-depend 47.9 11 0.00023 36.8 1.6 37 98-134 99-135 (637)
130 COG1847 Jag Predicted RNA-bind 47.8 14 0.0003 31.7 2.1 35 97-131 90-124 (208)
131 PTZ00084 40S ribosomal protein 47.4 14 0.00031 31.9 2.2 28 99-126 45-72 (220)
132 COG1159 Era GTPase [General fu 46.3 8.8 0.00019 34.7 0.8 27 101-127 232-259 (298)
133 KOG4369 RTK signaling protein 45.1 11 0.00024 40.2 1.3 69 99-167 782-850 (2131)
134 KOG1423 Ras-like GTPase ERA [C 43.4 20 0.00044 33.0 2.6 31 98-128 328-359 (379)
135 PRK09202 nusA transcription el 42.8 16 0.00034 35.2 1.9 27 107-133 245-272 (470)
136 COG1908 FrhD Coenzyme F420-red 42.3 9.8 0.00021 30.1 0.4 17 40-57 60-76 (132)
137 KOG0153 Predicted RNA-binding 39.6 13 0.00029 34.2 0.9 22 193-214 162-183 (377)
138 COG1702 PhoH Phosphate starvat 38.1 65 0.0014 29.8 5.1 56 105-167 22-79 (348)
139 PF10283 zf-CCHH: Zinc-finger 36.9 10 0.00022 21.8 -0.2 9 41-49 2-10 (26)
140 TIGR01009 rpsC_bact ribosomal 36.7 26 0.00056 30.0 2.1 28 99-126 63-90 (211)
141 PRK00310 rpsC 30S ribosomal pr 30.0 39 0.00084 29.4 2.2 30 98-127 62-91 (232)
142 KOG2113 Predicted RNA binding 29.5 53 0.0012 30.1 3.0 59 97-158 114-173 (394)
143 PF02749 QRPTase_N: Quinolinat 26.4 1.3E+02 0.0028 21.6 4.1 50 118-167 34-86 (88)
144 KOG3161 Predicted E3 ubiquitin 26.4 1.1E+02 0.0023 30.9 4.7 39 25-63 198-236 (861)
145 KOG1039 Predicted E3 ubiquitin 25.2 37 0.00081 31.3 1.3 23 193-215 250-274 (344)
146 PF08352 oligo_HPY: Oligopepti 22.4 40 0.00086 22.5 0.7 12 41-52 50-61 (64)
No 1
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.58 E-value=8.4e-16 Score=138.44 Aligned_cols=40 Identities=33% Similarity=0.711 Sum_probs=37.3
Q ss_pred CCCCCCCccccccCcccccccCCCC-CCCCCCcccccccCC
Q 027432 20 PASNGPTVVKSRMCNRLNSAEGCKF-GDKCHFAHGEWELGK 59 (223)
Q Consensus 20 ~~~~~~~~~kt~~C~~~~~~g~C~~-g~~C~faH~~~el~~ 59 (223)
....++..|||.||..|...|.|.| |++|+|||+.+||+.
T Consensus 122 ~~~~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~ 162 (332)
T KOG1677|consen 122 RGERKPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRL 162 (332)
T ss_pred ccccCcccccCCcceeeecCccccccCchhhhcCCcccccc
Confidence 4567788999999999999999999 999999999999996
No 2
>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=99.52 E-value=2.4e-14 Score=100.21 Aligned_cols=64 Identities=31% Similarity=0.483 Sum_probs=58.7
Q ss_pred eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCC-CCCceEEEEcCCHHHHHHHHHHHH
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEA-DPNLRNIELEGSFEQIKQASAMVR 162 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~-~~~~r~v~I~G~~~~i~~A~~lI~ 162 (223)
+++++||.+.+|.|||++|.+|++|+++|||+|++.+... +..+|.|+|.|+++++++|..+|.
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 4789999999999999999999999999999999976554 678899999999999999999873
No 3
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.37 E-value=1.3e-11 Score=107.61 Aligned_cols=74 Identities=31% Similarity=0.523 Sum_probs=69.9
Q ss_pred CCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhc
Q 027432 95 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI 168 (223)
Q Consensus 95 g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~ 168 (223)
|..+|..+.||.++-|.||||||++|++|++++||.|.|.+...+..+|+++|+|+.+||+.|+.|+++.+++.
T Consensus 312 GPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 312 GPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred CceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 55788999999999999999999999999999999999999888899999999999999999999999998754
No 4
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.35 E-value=1.5e-12 Score=123.28 Aligned_cols=78 Identities=33% Similarity=0.517 Sum_probs=71.6
Q ss_pred CCCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEe-ccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCCC
Q 027432 94 FGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPA 171 (223)
Q Consensus 94 ~g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I-~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~~ 171 (223)
.+.+.+.+|.||.+.||+||||+|++||+|+.+||++|++ .|.++.+.||++.|.|+.++|+.|.+||.++|++.+.+
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 4556799999999999999999999999999999999999 46666888999999999999999999999999987765
No 5
>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=99.32 E-value=3.2e-12 Score=88.16 Aligned_cols=62 Identities=27% Similarity=0.440 Sum_probs=56.2
Q ss_pred eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHH
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVR 162 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~ 162 (223)
+.++.||.+++|.|||++|++|++|++++|++|++.+.. ..++.|+|+|+.+++..|+.+|.
T Consensus 1 ~~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred CeEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHHHHHHHHHhC
Confidence 367999999999999999999999999999999997654 56789999999999999999873
No 6
>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=99.31 E-value=1.4e-12 Score=89.36 Aligned_cols=60 Identities=43% Similarity=0.635 Sum_probs=55.2
Q ss_pred eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHH
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMV 161 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI 161 (223)
|.++.||.+.+|.|||++|++|++|+++||++|++.+. + ....|+|+|+.++++.|+.+|
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 67899999999999999999999999999999999766 3 455999999999999999986
No 7
>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=99.29 E-value=8.5e-12 Score=85.82 Aligned_cols=64 Identities=36% Similarity=0.580 Sum_probs=58.5
Q ss_pred eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHH
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVR 162 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~ 162 (223)
+.++.||.+.++.|||++|++|++|+++||++|.|.+...+..++.|+|.|+.+++..|..+|.
T Consensus 1 ~~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred CEEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHhC
Confidence 3689999999999999999999999999999999987665678899999999999999998873
No 8
>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=99.27 E-value=8.6e-12 Score=86.45 Aligned_cols=58 Identities=26% Similarity=0.416 Sum_probs=53.2
Q ss_pred eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCC-HHHHHHHHHHHH
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGS-FEQIKQASAMVR 162 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~-~~~i~~A~~lI~ 162 (223)
+..+.||.+++|.|||++|++|++|+++||++|.|.+ ++.|+|+|+ .++++.|+.+|.
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCHHHHHHHHHHhC
Confidence 5789999999999999999999999999999999976 357999998 999999999873
No 9
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.20 E-value=3.1e-11 Score=107.64 Aligned_cols=74 Identities=32% Similarity=0.351 Sum_probs=66.0
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc-C--CCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-H--EADPNLRNIELEGSFEQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~-~--~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~ 170 (223)
..+++|+||++.+|.||||||.+||.|++++|++|+|+. . .....+|+|+++|+++++.+|..+|.++|.+.+.
T Consensus 131 ~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq 207 (402)
T KOG2191|consen 131 IKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ 207 (402)
T ss_pred cceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc
Confidence 356899999999999999999999999999999999973 2 3445689999999999999999999999987654
No 10
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=99.13 E-value=2.3e-11 Score=107.38 Aligned_cols=33 Identities=39% Similarity=0.818 Sum_probs=30.2
Q ss_pred CcccccccCcccc-CCcCCCCCCCccccCccccC
Q 027432 187 SSNFKTKLCGNFA-KGSCTFGDRCHFAHGAAELR 219 (223)
Q Consensus 187 ~~~~kt~~C~~~~-~g~C~~g~~C~faH~~~elr 219 (223)
..+|||+.|.+|. .|.|+||-+|.|+||.+++-
T Consensus 269 ~~~frTePcinwe~sGyc~yg~Rc~F~hgd~~~i 302 (351)
T COG5063 269 KQNFRTEPCINWEKSGYCPYGLRCCFKHGDDSDI 302 (351)
T ss_pred ccccccCCccchhhcccCccccccccccCChhhc
Confidence 3789999999999 79999999999999998864
No 11
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.05 E-value=3.7e-10 Score=100.88 Aligned_cols=74 Identities=23% Similarity=0.362 Sum_probs=67.1
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC---CCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~---~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~ 170 (223)
..-++|+||+..+|.||||||++|.+++.++||+|+++++ -++..||++.|.|+-+.+....++|.++|++...
T Consensus 38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~ 114 (402)
T KOG2191|consen 38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQ 114 (402)
T ss_pred ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHH
Confidence 3678999999999999999999999999999999999643 3677899999999999999999999999987553
No 12
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.05 E-value=3.2e-10 Score=107.37 Aligned_cols=73 Identities=27% Similarity=0.447 Sum_probs=67.8
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEec-cCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR-DHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG 169 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~-~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~ 169 (223)
..+.+++||.+.+|.||||+|+.||+|++.|||+|+|. +..+...+|.|+|.|.+++|.+|...|..+|.+..
T Consensus 137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~ 210 (485)
T KOG2190|consen 137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENP 210 (485)
T ss_pred ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcC
Confidence 45799999999999999999999999999999999994 55788889999999999999999999999998853
No 13
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.98 E-value=6.9e-10 Score=105.41 Aligned_cols=74 Identities=27% Similarity=0.453 Sum_probs=65.1
Q ss_pred CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEe-ccCCCC-CCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432 96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEAD-PNLRNIELEGSFEQIKQASAMVRELIVRIG 169 (223)
Q Consensus 96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I-~~~~~~-~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~ 169 (223)
..+|.+|.||++++|+||||+|++||++++++|+++.+ .|.... ..++.+.|+|++++|+.|+.||.++|.+..
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 35789999999999999999999999999999999888 444433 367999999999999999999999999633
No 14
>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=98.98 E-value=9.3e-11 Score=68.50 Aligned_cols=27 Identities=48% Similarity=1.062 Sum_probs=22.7
Q ss_pred cccccCcccccccCCCCCCCCCCcccc
Q 027432 28 VKSRMCNRLNSAEGCKFGDKCHFAHGE 54 (223)
Q Consensus 28 ~kt~~C~~~~~~g~C~~g~~C~faH~~ 54 (223)
|||++|++|..+|.|+||++|+|+|++
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 799999999999999999999999974
No 15
>smart00322 KH K homology RNA-binding domain.
Probab=98.96 E-value=3.2e-09 Score=72.42 Aligned_cols=66 Identities=32% Similarity=0.562 Sum_probs=59.1
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhh
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELI 165 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i 165 (223)
.+.++.||...+|.|||++|.+|++|++.+|++|.+..... ....|+|.|+.++++.|..+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHHh
Confidence 46889999999999999999999999999999999964432 5688999999999999999998765
No 16
>PF13014 KH_3: KH domain
Probab=98.90 E-value=1.8e-09 Score=69.48 Aligned_cols=42 Identities=43% Similarity=0.692 Sum_probs=37.8
Q ss_pred cccceecCCCcchhhhhhhcCCeEEecc-CCCCCCceEEEEcC
Q 027432 108 LAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEG 149 (223)
Q Consensus 108 ~vG~IIGkgG~~Ik~I~~~SGa~I~I~~-~~~~~~~r~v~I~G 149 (223)
.+|+|||++|++|++|+++|||+|+|.+ ..++..++.|+|+|
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 4789999999999999999999999976 56677889999987
No 17
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=98.83 E-value=6.9e-09 Score=95.39 Aligned_cols=76 Identities=26% Similarity=0.272 Sum_probs=68.9
Q ss_pred CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC-CCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCCC
Q 027432 96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH-EADPNLRNIELEGSFEQIKQASAMVRELIVRIGPA 171 (223)
Q Consensus 96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~-~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~~ 171 (223)
...++++.||...||+|||+.|.+||+|.+.+||.|+|... -++..+|.|+|+|++++.-+|+..|..+|.+...+
T Consensus 409 e~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEenf~ 485 (584)
T KOG2193|consen 409 EQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFF 485 (584)
T ss_pred chhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhccC
Confidence 36778999999999999999999999999999999999543 46678999999999999999999999999987754
No 18
>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=98.82 E-value=5.8e-10 Score=65.13 Aligned_cols=26 Identities=62% Similarity=1.364 Sum_probs=21.2
Q ss_pred cccccCcccc-CCcCCCCCCCccccCc
Q 027432 190 FKTKLCGNFA-KGSCTFGDRCHFAHGA 215 (223)
Q Consensus 190 ~kt~~C~~~~-~g~C~~g~~C~faH~~ 215 (223)
|||++|++|. .|.|++|++|+|+|+.
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 7999999999 5999999999999974
No 19
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=98.68 E-value=1.8e-08 Score=92.69 Aligned_cols=70 Identities=27% Similarity=0.427 Sum_probs=64.5
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhcCCeEEe-ccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhh
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRNIELEGSFEQIKQASAMVRELIVR 167 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I-~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~ 167 (223)
-.++++||...+|+||||.|.+||+|..+|-++|.+ .....+..|++++|.|++|+..+|..+|+++|..
T Consensus 199 ~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqk 269 (584)
T KOG2193|consen 199 WPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQK 269 (584)
T ss_pred cceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHH
Confidence 457899999999999999999999999999999999 4556678899999999999999999999999964
No 20
>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=98.61 E-value=8.7e-08 Score=75.15 Aligned_cols=70 Identities=26% Similarity=0.374 Sum_probs=54.4
Q ss_pred EEEEecc------ccccceecCCCcchhhhhhhcCCeEEeccCCCC-----------------CCceEEEEcC-C--HHH
Q 027432 100 AKISVDA------SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEAD-----------------PNLRNIELEG-S--FEQ 153 (223)
Q Consensus 100 ~~i~VP~------~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~-----------------~~~r~v~I~G-~--~~~ 153 (223)
.+|+||. +++|.|||.+|.+||+|+++|||+|.|....+. ...--|.|++ + .++
T Consensus 2 ~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~ 81 (120)
T cd02395 2 EKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEA 81 (120)
T ss_pred CEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHH
Confidence 3555554 678999999999999999999999999654111 0114677877 4 699
Q ss_pred HHHHHHHHHhhhhhcC
Q 027432 154 IKQASAMVRELIVRIG 169 (223)
Q Consensus 154 i~~A~~lI~~~i~~~~ 169 (223)
+++|..+|.+++....
T Consensus 82 ~~~A~~~I~~ll~~~~ 97 (120)
T cd02395 82 LAKAVEAIEELLKPAI 97 (120)
T ss_pred HHHHHHHHHHHhccCC
Confidence 9999999999998544
No 21
>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=98.58 E-value=5.5e-08 Score=80.65 Aligned_cols=63 Identities=24% Similarity=0.415 Sum_probs=55.3
Q ss_pred EEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEE---cCCHHHHHHHHHHHHhhhhhcC
Q 027432 102 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIEL---EGSFEQIKQASAMVRELIVRIG 169 (223)
Q Consensus 102 i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I---~G~~~~i~~A~~lI~~~i~~~~ 169 (223)
+.||.+.+|.|||+||++|+.|+++||++|+|.+. +..|.| +++++++++|+.+|.++...++
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~ 67 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLAVMKAREVVKAIGRGFS 67 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHHHHHHHHHHHHHHcCCC
Confidence 57999999999999999999999999999999753 246777 7899999999999999877433
No 22
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.56 E-value=6.4e-08 Score=87.24 Aligned_cols=34 Identities=47% Similarity=1.094 Sum_probs=32.0
Q ss_pred CcccccccCcccc-CCcCCC-CCCCccccCccccCc
Q 027432 187 SSNFKTKLCGNFA-KGSCTF-GDRCHFAHGAAELRK 220 (223)
Q Consensus 187 ~~~~kt~~C~~~~-~g~C~~-g~~C~faH~~~elr~ 220 (223)
+..|||.+|++|. .|.|+| |++|+|||+.+|||-
T Consensus 127 p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~ 162 (332)
T KOG1677|consen 127 PERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRL 162 (332)
T ss_pred cccccCCcceeeecCccccccCchhhhcCCcccccc
Confidence 5789999999999 799999 999999999999994
No 23
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.54 E-value=1.2e-07 Score=79.16 Aligned_cols=65 Identities=23% Similarity=0.321 Sum_probs=57.8
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEc----CCHHHHHHHHHHHHhhhhh
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE----GSFEQIKQASAMVRELIVR 167 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~----G~~~~i~~A~~lI~~~i~~ 167 (223)
....+.||.+.+|.|||++|++|+.|++++|++|+|.+. +..|.|. ++++++++|+.+|.+++..
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g 71 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLAVLKARDIVKAIGRG 71 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence 356899999999999999999999999999999999753 2567784 8999999999999998874
No 24
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=98.51 E-value=1.9e-07 Score=82.83 Aligned_cols=44 Identities=23% Similarity=0.295 Sum_probs=36.6
Q ss_pred CCCCCC-CccccccCcccccccCCCCCCCCCCcccccccCCCccc
Q 027432 20 PASNGP-TVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAI 63 (223)
Q Consensus 20 ~~~~~~-~~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~~~~~ 63 (223)
++..++ ..|||.+|..-..-+.|.|+++|.|||...+++-.-.+
T Consensus 104 ~~a~~p~g~~kt~~l~ss~~~~~~~~p~~n~fahs~~issl~~~~ 148 (351)
T COG5063 104 SNANKPYGLYKTEMLRSSTEIPYCRYPDKNPFAHSKAISSLAQTH 148 (351)
T ss_pred CCccCccccccchhhhccccccccccCCCCcCCCccccccccccC
Confidence 555566 89999999988778999999999999998888764444
No 25
>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=98.48 E-value=1.6e-07 Score=77.81 Aligned_cols=55 Identities=29% Similarity=0.469 Sum_probs=50.6
Q ss_pred ccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhc
Q 027432 107 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI 168 (223)
Q Consensus 107 ~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~ 168 (223)
..+|.|||++|++++.|++.||++|+|.+ +.|.|.|++++++.|+.+|.+++...
T Consensus 98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEELTGVSISVYG-------KTVGIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred HHHhhhcCCCcHHHHHHHHHHCCeEEEcC-------CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence 47899999999999999999999999974 67999999999999999999999654
No 26
>smart00356 ZnF_C3H1 zinc finger.
Probab=98.40 E-value=1.6e-07 Score=54.09 Aligned_cols=27 Identities=52% Similarity=1.177 Sum_probs=24.5
Q ss_pred ccccccCccccCCcCCCCCCCccccCc
Q 027432 189 NFKTKLCGNFAKGSCTFGDRCHFAHGA 215 (223)
Q Consensus 189 ~~kt~~C~~~~~g~C~~g~~C~faH~~ 215 (223)
.+|+.+|++|+.|.|.+|++|+|+|..
T Consensus 1 ~~k~~~C~~~~~g~C~~g~~C~~~H~~ 27 (27)
T smart00356 1 KYKTELCKFFKRGYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCCCcCcCccCCCCCCCCCcCCCCcC
Confidence 368999999999999999999999963
No 27
>smart00356 ZnF_C3H1 zinc finger.
Probab=98.38 E-value=2e-07 Score=53.68 Aligned_cols=26 Identities=35% Similarity=0.856 Sum_probs=23.7
Q ss_pred ccccccCcccccccCCCCCCCCCCccc
Q 027432 27 VVKSRMCNRLNSAEGCKFGDKCHFAHG 53 (223)
Q Consensus 27 ~~kt~~C~~~~~~g~C~~g~~C~faH~ 53 (223)
.+|+.+|++| ..|.|++|++|+|+|.
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 4789999999 7799999999999995
No 28
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.33 E-value=6.6e-07 Score=74.73 Aligned_cols=56 Identities=29% Similarity=0.457 Sum_probs=50.2
Q ss_pred ccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432 107 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG 169 (223)
Q Consensus 107 ~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~ 169 (223)
..+|+|||++|++++.|++.||++|+|.+ +.|.|.|++++++.|..+|.+++....
T Consensus 104 r~~griIG~~G~~~k~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A~~~I~~li~g~~ 159 (180)
T PRK13763 104 RIKGRIIGEGGKTRRIIEELTGVDISVYG-------KTVAIIGDPEQVEIAREAIEMLIEGAP 159 (180)
T ss_pred HHhhheeCCCcHHHHHHHHHHCcEEEEcC-------CEEEEEeCHHHHHHHHHHHHHHHcCCC
Confidence 46899999999999999999999999964 349999999999999999999996543
No 29
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=98.33 E-value=4.2e-07 Score=79.71 Aligned_cols=72 Identities=22% Similarity=0.341 Sum_probs=65.3
Q ss_pred eEEEEeccccccceecCCCcchhhhhhhcCCeEEecc-CCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~-~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~ 170 (223)
.++++|..+++|.|||++|+.||++++.+.|+++|.. -.+.+.+|+|.|.|.+..|-.+.+.|.+.|.+.+.
T Consensus 124 e~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pi 196 (390)
T KOG2192|consen 124 ELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPI 196 (390)
T ss_pred hhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCc
Confidence 3689999999999999999999999999999999964 46778899999999999999999999999987664
No 30
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=98.29 E-value=3e-06 Score=80.60 Aligned_cols=70 Identities=23% Similarity=0.285 Sum_probs=65.4
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC---------CHHHHHHHHHHHHhhhh
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG---------SFEQIKQASAMVRELIV 166 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G---------~~~~i~~A~~lI~~~i~ 166 (223)
..+.|++++...+|.||||.|..||+|+.++.++|.|.+...+..+|+|+|+| ..+++.+|..+|...+.
T Consensus 42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~ 120 (485)
T KOG2190|consen 42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLE 120 (485)
T ss_pred cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccc
Confidence 34489999999999999999999999999999999999889999999999999 99999999999998766
No 31
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.25 E-value=4.5e-07 Score=85.65 Aligned_cols=31 Identities=32% Similarity=0.733 Sum_probs=28.4
Q ss_pred CcccccccCccccCCcCCCCCCCccccCccccCc
Q 027432 187 SSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRK 220 (223)
Q Consensus 187 ~~~~kt~~C~~~~~g~C~~g~~C~faH~~~elr~ 220 (223)
+..|||++|++- |.|+. --|-|||..+|||.
T Consensus 266 Pa~YRT~~CkDg--~~C~R-rvCfFAH~~eqLR~ 296 (528)
T KOG1595|consen 266 PARYRTRKCKDG--GYCPR-RVCFFAHSPEQLRP 296 (528)
T ss_pred HHHhccccccCC--CCCcc-ceEeeecChHHhcc
Confidence 469999999997 89999 78999999999985
No 32
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=98.22 E-value=2.6e-06 Score=79.03 Aligned_cols=93 Identities=19% Similarity=0.182 Sum_probs=71.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHH
Q 027432 74 VPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQ 153 (223)
Q Consensus 74 ~~~r~~g~~~~~~~~~~~~s~g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~ 153 (223)
..+|..+|.-...++-+++..+..-..-+.|-+++||.|||+||++||.||..++++|+|.+-+. +..|+|.|.-.-
T Consensus 23 ~v~rg~~w~g~~~~~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~---e~kv~ifg~~~m 99 (629)
T KOG0336|consen 23 RVNRGNYWAGHRDSRDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDL---EVKVTIFGINHM 99 (629)
T ss_pred ecCCCCCccCCCCCCcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCc---eeEEEEechHHH
Confidence 34555555544444444444555667788899999999999999999999999999999965433 577999999998
Q ss_pred HHHHHHHHHhhhhhcC
Q 027432 154 IKQASAMVRELIVRIG 169 (223)
Q Consensus 154 i~~A~~lI~~~i~~~~ 169 (223)
-.+|...|...+...+
T Consensus 100 ~~kaka~id~~~~k~e 115 (629)
T KOG0336|consen 100 RKKAKASIDRGQDKDE 115 (629)
T ss_pred HHHHHhhHhhhhhhhh
Confidence 8899999988876443
No 33
>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=97.98 E-value=1.5e-05 Score=78.73 Aligned_cols=65 Identities=23% Similarity=0.306 Sum_probs=58.9
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhh
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVR 167 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~ 167 (223)
....++.||.+++|.|||.||.+||.|+++||++|.|.+ +..|.|.+ +.+++++|+.+|..++..
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 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 456789999999999999999999999999999999976 36788877 699999999999999984
No 34
>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=97.77 E-value=3.4e-05 Score=76.38 Aligned_cols=68 Identities=22% Similarity=0.343 Sum_probs=58.1
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhcCC
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~~~ 170 (223)
....++.||.+++|.|||+||++||.|.++||++|.|.+ +..|.|.+ +.+.+++|..+|..+......
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~~~~~~~a~~~I~~~~~~~~~ 618 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDGEAAEAAIKMIEGITAEPEV 618 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECcHHHHHHHHHHHHhhhccccc
Confidence 456789999999999999999999999999999999976 25566655 689999999999999775443
No 35
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=97.63 E-value=4.5e-05 Score=72.38 Aligned_cols=31 Identities=42% Similarity=0.905 Sum_probs=26.8
Q ss_pred cccccccCccccCCcCCCCCCCccccCcccc
Q 027432 188 SNFKTKLCGNFAKGSCTFGDRCHFAHGAAEL 218 (223)
Q Consensus 188 ~~~kt~~C~~~~~g~C~~g~~C~faH~~~el 218 (223)
-.|.-..|-.|.+|.|..||.|.||||.-|-
T Consensus 232 yhYs~tpCPefrkG~C~rGD~CEyaHgvfEc 262 (528)
T KOG1595|consen 232 YHYSSTPCPEFRKGSCERGDSCEYAHGVFEC 262 (528)
T ss_pred ccccCccCcccccCCCCCCCccccccceehh
Confidence 4566678999999999999999999998763
No 36
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.47 E-value=0.00024 Score=67.03 Aligned_cols=74 Identities=30% Similarity=0.426 Sum_probs=56.6
Q ss_pred cceEEEEecc------ccccceecCCCcchhhhhhhcCCeEEeccC---------CC------CCCc-eEEEEcC-CHHH
Q 027432 97 SATAKISVDA------SLAGAIIGKGGVNSKQICRQTGAKLSIRDH---------EA------DPNL-RNIELEG-SFEQ 153 (223)
Q Consensus 97 ~~t~~i~VP~------~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~---------~~------~~~~-r~v~I~G-~~~~ 153 (223)
..+.+|.||. ++||+|||-.|.++|+|.++|||+|.|+-. .. ...+ =-+.|++ +.|.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 5667888884 789999999999999999999999999531 00 0011 2244555 6999
Q ss_pred HHHHHHHHHhhhhhcCC
Q 027432 154 IKQASAMVRELIVRIGP 170 (223)
Q Consensus 154 i~~A~~lI~~~i~~~~~ 170 (223)
|++|.++|..+|.+...
T Consensus 217 i~~Ai~vienli~~av~ 233 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSAVS 233 (554)
T ss_pred HHHHHHHHHHHHHhhcc
Confidence 99999999999987443
No 37
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.38 E-value=0.00018 Score=72.76 Aligned_cols=68 Identities=19% Similarity=0.355 Sum_probs=59.2
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCe-EEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhcCC
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAK-LSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~-I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~~~ 170 (223)
....++.||.++++.|||.||.+||.|.+++|++ |.|.+ +..|.|.+ +.+.+++|+.+|.++..+...
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~~~i~~A~~~I~~l~~~~~v 753 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDLSSLEKSKAIISSLTMVPTV 753 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCHHHHHHHHHHHHHHhcCcCC
Confidence 4567899999999999999999999999999999 88876 35677877 799999999999999875443
No 38
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.27 E-value=0.0005 Score=57.94 Aligned_cols=56 Identities=30% Similarity=0.475 Sum_probs=50.5
Q ss_pred cccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432 108 LAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 108 ~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~ 170 (223)
..|.|||++|.+-+.|.+-||+.|.|.. ..|.|.|.+++++.|+..|..++.....
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g-------~tVaiiG~~~~v~iAr~AVemli~G~~h 167 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYG-------KTVAIIGGFEQVEIAREAVEMLINGAPH 167 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeC-------cEEEEecChhhhHHHHHHHHHHHcCCCc
Confidence 4699999999999999999999999964 4699999999999999999999986553
No 39
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.25 E-value=0.00045 Score=67.62 Aligned_cols=69 Identities=25% Similarity=0.379 Sum_probs=61.0
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCC-HHHHHHHHHHHHhhhhhcCCC
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGS-FEQIKQASAMVRELIVRIGPA 171 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~-~~~i~~A~~lI~~~i~~~~~~ 171 (223)
....++.|+.+++.-+||+||.+|++|.+++|++|+|.+ +..|.|.++ .+.++.|+..|.++.++++.+
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied------dGtv~i~~s~~~~~~~ak~~I~~i~~e~evg 620 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED------DGTVKIAASDGESAKKAKERIEAITREVEVG 620 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC------CCcEEEEecchHHHHHHHHHHHHHHhhcccc
Confidence 456788999999999999999999999999999999974 345888775 699999999999999988875
No 40
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=97.18 E-value=0.00016 Score=65.02 Aligned_cols=28 Identities=25% Similarity=0.609 Sum_probs=23.8
Q ss_pred cccCccccCCcCCCCCCCccccCccccCc
Q 027432 192 TKLCGNFAKGSCTFGDRCHFAHGAAELRK 220 (223)
Q Consensus 192 t~~C~~~~~g~C~~g~~C~faH~~~elr~ 220 (223)
--.|.++.+|.|.... |+|+|.-.+|+.
T Consensus 71 v~aC~Ds~kgrCsR~n-CkylHpp~hlkd 98 (331)
T KOG2494|consen 71 VIACFDSQKGRCSREN-CKYLHPPQHLKD 98 (331)
T ss_pred EEEEeccccCccCccc-ceecCCChhhhh
Confidence 3469999999999875 999999888764
No 41
>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=96.81 E-value=0.0014 Score=45.22 Aligned_cols=36 Identities=33% Similarity=0.528 Sum_probs=33.4
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhcCCeEEe
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI 133 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I 133 (223)
....+.|+.+..|..|||+|.||+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 678899999999999999999999999999988765
No 42
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.69 E-value=0.0016 Score=64.86 Aligned_cols=67 Identities=21% Similarity=0.327 Sum_probs=56.8
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhcCC
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~~~ 170 (223)
....+.|+.+.++.+||.||.+||+|.+++|++|.|.+ +..|.|.+ +.+.+++|..+|..+..+...
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~~~~~~~a~~~I~~~~~~~~v 621 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDGEAAEAAKERIEGITAEPEV 621 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEcccHHHHHHHHHHHHHhcccCcC
Confidence 44677889999999999999999999999999988854 35577777 689999999999999876444
No 43
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.62 E-value=0.0028 Score=54.06 Aligned_cols=76 Identities=21% Similarity=0.196 Sum_probs=51.6
Q ss_pred CCcceEEEEec------cccccceecCCCcchhhhhhhcCCeEEeccCCCC-----CCc------------eEEEEcCCH
Q 027432 95 GASATAKISVD------ASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEAD-----PNL------------RNIELEGSF 151 (223)
Q Consensus 95 g~~~t~~i~VP------~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~-----~~~------------r~v~I~G~~ 151 (223)
+...+.+++|| .+.||+|||..|.++|++++.|+|+|.|.-.-.. ..+ ....+....
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adse 224 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSE 224 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchh
Confidence 45677889988 4789999999999999999999999999532110 001 111222334
Q ss_pred HHHHHHHHHHHhhhhhcCC
Q 027432 152 EQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 152 ~~i~~A~~lI~~~i~~~~~ 170 (223)
+.+..+...+++.|.+...
T Consensus 225 dki~~~ik~~~n~I~~a~~ 243 (269)
T COG5176 225 DKICRLIKSQLNAIREARR 243 (269)
T ss_pred hhHHHHHHHHHHHHHHHhc
Confidence 5666677777777766544
No 44
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=96.62 E-value=0.00072 Score=62.50 Aligned_cols=30 Identities=43% Similarity=1.015 Sum_probs=25.1
Q ss_pred ccccCccccCCcCCCCCCCccccCc----cccCc
Q 027432 191 KTKLCGNFAKGSCTFGDRCHFAHGA----AELRK 220 (223)
Q Consensus 191 kt~~C~~~~~g~C~~g~~C~faH~~----~elr~ 220 (223)
-.++|.+|+.|.|.|+++|||.||. ++||+
T Consensus 139 sMkpC~ffLeg~CRF~enCRfSHG~~V~lsslr~ 172 (486)
T KOG2185|consen 139 SMKPCKFFLEGRCRFGENCRFSHGLDVPLSSLRN 172 (486)
T ss_pred hhccchHhhccccccCcccccccCcccchhhccc
Confidence 3468999999999999999999985 45554
No 45
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.47 E-value=0.0059 Score=53.02 Aligned_cols=66 Identities=15% Similarity=0.227 Sum_probs=55.6
Q ss_pred eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhcCC
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~~~ 170 (223)
-..+.||.++++.+||++|.+|+.|.+.+++.|.|.++ ..|.|++ +.+.+..|..+|.++-++...
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N------G~VwI~~~~~~~~~~a~~~I~~~e~~~~~ 212 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN------GRIWIKGPDEEDEEIAIEAIKKIEREAHT 212 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC------cEEEEeeCCHHHHHHHHHHHHHHHhhhhc
Confidence 46789999999999999999999999999999999652 4566766 577999999999987766543
No 46
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=96.30 E-value=0.0025 Score=34.01 Aligned_cols=18 Identities=39% Similarity=0.877 Sum_probs=15.3
Q ss_pred cCcccccccCCCCCCCCCCcc
Q 027432 32 MCNRLNSAEGCKFGDKCHFAH 52 (223)
Q Consensus 32 ~C~~~~~~g~C~~g~~C~faH 52 (223)
+|++|.. |.++++|.|+|
T Consensus 1 ~Ck~~~~---C~~~~~C~f~H 18 (19)
T PF14608_consen 1 PCKFGPN---CTNGDNCPFSH 18 (19)
T ss_pred CCcCcCC---CCCCCcCccCC
Confidence 4886653 99999999999
No 47
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=96.29 E-value=0.0039 Score=56.69 Aligned_cols=32 Identities=31% Similarity=0.549 Sum_probs=27.9
Q ss_pred CccccccCcccccccCCCCCCCCCCcccccccCC
Q 027432 26 TVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGK 59 (223)
Q Consensus 26 ~~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~ 59 (223)
..+++.+|++|.. |.|..||.|.|+|-. +|.+
T Consensus 73 ~~~~~~vcK~~l~-glC~kgD~C~Flhe~-~~~k 104 (325)
T KOG1040|consen 73 DSRGKVVCKHWLR-GLCKKGDQCEFLHEY-DLTK 104 (325)
T ss_pred ccCCceeehhhhh-hhhhccCcCcchhhh-hhcc
Confidence 3889999999999 899999999999965 5554
No 48
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=96.22 E-value=0.003 Score=33.70 Aligned_cols=19 Identities=42% Similarity=0.812 Sum_probs=16.1
Q ss_pred cCccccCCcCCCCCCCccccC
Q 027432 194 LCGNFAKGSCTFGDRCHFAHG 214 (223)
Q Consensus 194 ~C~~~~~g~C~~g~~C~faH~ 214 (223)
+|++|.. |+++++|.|+|.
T Consensus 1 ~Ck~~~~--C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN--CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC--CCCCCcCccCCc
Confidence 4887765 999999999994
No 49
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=96.17 E-value=0.0022 Score=66.02 Aligned_cols=74 Identities=18% Similarity=0.174 Sum_probs=64.6
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc-CCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~-~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~ 170 (223)
....++.||...+..|||+||.||..++..+|+.|.|.+ ...+..||.+.+.|.++.++.|..+|.-.|-+...
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dpdv 1413 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIIDPDV 1413 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeecCCc
Confidence 344678899999999999999999999999999999987 45557799999999999999999999888866554
No 50
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=96.16 E-value=0.0038 Score=59.24 Aligned_cols=25 Identities=40% Similarity=1.030 Sum_probs=21.8
Q ss_pred ccccCcccccc--cCCCCCCCCCCccc
Q 027432 29 KSRMCNRLNSA--EGCKFGDKCHFAHG 53 (223)
Q Consensus 29 kt~~C~~~~~~--g~C~~g~~C~faH~ 53 (223)
+..||...... ..|.|||+|+|.|.
T Consensus 75 ~n~LCPsli~g~~~~C~f~d~Crf~HD 101 (614)
T KOG2333|consen 75 QNRLCPSLIQGDISKCSFGDNCRFVHD 101 (614)
T ss_pred hhccChHhhcCCCccCccccccccccc
Confidence 46799998887 68999999999993
No 51
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=96.07 E-value=0.0042 Score=59.49 Aligned_cols=75 Identities=25% Similarity=0.388 Sum_probs=61.0
Q ss_pred CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCCC
Q 027432 96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPA 171 (223)
Q Consensus 96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~~ 171 (223)
.....++.|+.+.|-.||||+|++|++|+..++++|.+.+...+ .++.-.+.|-+.++..|+.++..++.+.++.
T Consensus 66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g-~e~~~~~~~~p~~v~~a~a~~~~~~~~~~pv 140 (608)
T KOG2279|consen 66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG-DERVLLISGFPVQVCKAKAAIHQILTENTPV 140 (608)
T ss_pred hheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC-cccchhhccCCCCCChHHHHHHHHHhcCCcc
Confidence 35567899999999999999999999999999999999754322 3444555668889999999999988776654
No 52
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=96.04 E-value=0.0029 Score=60.57 Aligned_cols=71 Identities=25% Similarity=0.440 Sum_probs=62.5
Q ss_pred eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG 169 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~ 169 (223)
...+.+|...++.|||++|++++.|+..++|+|.++........+.+.|.+...-...|+.++.+.+.+.+
T Consensus 141 k~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~ede 211 (608)
T KOG2279|consen 141 SEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDE 211 (608)
T ss_pred cccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchh
Confidence 35678999999999999999999999999999999877666667999999988888899999999886543
No 53
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=95.76 E-value=0.0038 Score=57.86 Aligned_cols=29 Identities=31% Similarity=0.774 Sum_probs=24.7
Q ss_pred cccCcccccccCCCCCCCCCCcccc----cccCC
Q 027432 30 SRMCNRLNSAEGCKFGDKCHFAHGE----WELGK 59 (223)
Q Consensus 30 t~~C~~~~~~g~C~~g~~C~faH~~----~el~~ 59 (223)
-++|++|.. |.|+|+.+|+|.||. ++||+
T Consensus 140 MkpC~ffLe-g~CRF~enCRfSHG~~V~lsslr~ 172 (486)
T KOG2185|consen 140 MKPCKFFLE-GRCRFGENCRFSHGLDVPLSSLRN 172 (486)
T ss_pred hccchHhhc-cccccCcccccccCcccchhhccc
Confidence 467999998 899999999999985 56665
No 54
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.55 E-value=0.029 Score=54.09 Aligned_cols=66 Identities=24% Similarity=0.370 Sum_probs=50.1
Q ss_pred cceEEEEecc-ccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhh
Q 027432 97 SATAKISVDA-SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVR 167 (223)
Q Consensus 97 ~~t~~i~VP~-~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~ 167 (223)
.++-.+.+|+ ++-|.||||.|.||+.+..-||+.|-|+|.. ..|+|++ +|---+.|+..+..+|..
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC-----CeEEecCCchHHHHHHHHHHHHHHHc
Confidence 3455678898 5559999999999999999999999997643 3577887 565555666666666643
No 55
>PRK12704 phosphodiesterase; Provisional
Probab=95.40 E-value=0.043 Score=53.02 Aligned_cols=67 Identities=22% Similarity=0.331 Sum_probs=51.0
Q ss_pred cceEEEEecc-ccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhc
Q 027432 97 SATAKISVDA-SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRI 168 (223)
Q Consensus 97 ~~t~~i~VP~-~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~ 168 (223)
.++-.+.+|+ ++-|.||||.|.||+.+..-||+.|-|+|.+ ..|.|+| ++-.-+.|...+..++...
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~~~~~rre~a~~~l~~l~~dg 277 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPIRREIARLALEKLVQDG 277 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC-----CeEEEecCChhhHHHHHHHHHHHHhcC
Confidence 3455678888 5569999999999999999999999997653 3577887 5555456777777666543
No 56
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=95.40 E-value=0.01 Score=52.00 Aligned_cols=28 Identities=32% Similarity=0.950 Sum_probs=25.7
Q ss_pred CcccccccCccccCCcCCCCCCCccccC
Q 027432 187 SSNFKTKLCGNFAKGSCTFGDRCHFAHG 214 (223)
Q Consensus 187 ~~~~kt~~C~~~~~g~C~~g~~C~faH~ 214 (223)
-..|+-..|..|..+.|.+|..|.|.|-
T Consensus 147 vT~~rea~C~~~e~~~C~rG~~CnFmH~ 174 (260)
T KOG2202|consen 147 VTDFREAICGQFERTECSRGGACNFMHV 174 (260)
T ss_pred cCchhhhhhcccccccCCCCCcCcchhh
Confidence 3778999999999999999999999994
No 57
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=95.36 E-value=0.0083 Score=52.08 Aligned_cols=34 Identities=47% Similarity=0.835 Sum_probs=30.0
Q ss_pred cccccccCccccCCcCCCCCCCccccCccccCcC
Q 027432 188 SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKT 221 (223)
Q Consensus 188 ~~~kt~~C~~~~~g~C~~g~~C~faH~~~elr~~ 221 (223)
..-||..|-.|..+.|.-|+.|.|+|+.+|.|..
T Consensus 81 vdpK~~vcalF~~~~c~kg~~ckF~h~~ee~r~~ 114 (299)
T COG5252 81 VDPKTVVCALFLNKTCAKGDACKFAHGKEEARKT 114 (299)
T ss_pred cCchhHHHHHhccCccccCchhhhhcchHHHhhh
Confidence 3459999999999999999999999998887753
No 58
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=95.31 E-value=0.016 Score=50.87 Aligned_cols=71 Identities=30% Similarity=0.421 Sum_probs=50.4
Q ss_pred CcceEEEEecc------ccccceecCCCcchhhhhhhcCCeEEeccCC------------CCC--------CceEEEEcC
Q 027432 96 ASATAKISVDA------SLAGAIIGKGGVNSKQICRQTGAKLSIRDHE------------ADP--------NLRNIELEG 149 (223)
Q Consensus 96 ~~~t~~i~VP~------~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~------------~~~--------~~r~v~I~G 149 (223)
...+.+|+||- +.||.|||..|.++|+|+++|||+|.|.-.. .+. -...|+..+
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~ 169 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEA 169 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeC
Confidence 35678888886 5899999999999999999999999994210 000 014566666
Q ss_pred CHH----HHHHHHHHHHhhhh
Q 027432 150 SFE----QIKQASAMVRELIV 166 (223)
Q Consensus 150 ~~~----~i~~A~~lI~~~i~ 166 (223)
++. -+..|++.|..+|.
T Consensus 170 p~~ea~~rl~~AleeI~klL~ 190 (259)
T KOG1588|consen 170 PPAEAYARLAYALEEIKKLLV 190 (259)
T ss_pred CHHHHHHHHHHHHHHHHHhcC
Confidence 654 34467777776663
No 59
>PRK00106 hypothetical protein; Provisional
Probab=95.17 E-value=0.049 Score=52.79 Aligned_cols=66 Identities=23% Similarity=0.335 Sum_probs=51.2
Q ss_pred cceEEEEecc-ccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhh
Q 027432 97 SATAKISVDA-SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVR 167 (223)
Q Consensus 97 ~~t~~i~VP~-~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~ 167 (223)
.++-.+.+|+ ++-|.||||-|.||+.+..-||+.|-|+|.+ ..|+|+| +|---+.|+..+..++..
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP-----EVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC-----CeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 4455688898 5569999999999999999999999997643 3577888 666666666666666654
No 60
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.04 E-value=0.031 Score=50.72 Aligned_cols=70 Identities=24% Similarity=0.252 Sum_probs=56.8
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEc-CCHHHHHHHHHHHHhhhhhcC
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE-GSFEQIKQASAMVRELIVRIG 169 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~-G~~~~i~~A~~lI~~~i~~~~ 169 (223)
-...+.|+++..|.|||+.|.+.+.|+++++++|.+..... +...|+|. +..++|.+|..-|..+|....
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~--n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT--NKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC--CcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 34568999999999999999999999999999999965432 23344444 478999999999999987765
No 61
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=94.96 E-value=0.03 Score=50.56 Aligned_cols=67 Identities=16% Similarity=0.305 Sum_probs=56.6
Q ss_pred CCCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHh
Q 027432 94 FGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRE 163 (223)
Q Consensus 94 ~g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~ 163 (223)
.+..-+..+.||...|+.|.|++|.+||.|+.+|..+|+-.... .+-++.++|..+.++.|+..|..
T Consensus 22 ~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~edv~~aRrei~s 88 (394)
T KOG2113|consen 22 IGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRHEDVRRARREIPS 88 (394)
T ss_pred CCCccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCchhHHHHhhcCcc
Confidence 34567788899999999999999999999999999998763221 23679999999999999998876
No 62
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=94.92 E-value=0.018 Score=48.99 Aligned_cols=58 Identities=31% Similarity=0.474 Sum_probs=51.6
Q ss_pred cccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432 106 ASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 106 ~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~ 170 (223)
+..+|.|+||+|.+--.|.+.|.++|.+.+ ..|-|-|.+++++.|+..|..+|...++
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad-------~kIHiLG~~~niriAR~avcsLIlGspp 234 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD-------SKIHILGAFQNIRIARDAVCSLILGSPP 234 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecC-------ceEEEeecchhhHHHHHhhHhhhccCCc
Confidence 567899999999999999999999999965 3589999999999999999999976554
No 63
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.90 E-value=0.0097 Score=50.50 Aligned_cols=36 Identities=19% Similarity=0.581 Sum_probs=29.2
Q ss_pred cccccCcccccccCCCCCCCCCCcccccccCCCccc
Q 027432 28 VKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAI 63 (223)
Q Consensus 28 ~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~~~~~ 63 (223)
|..-.|+.|..+|.|-|||.|.|.|..+.....+..
T Consensus 139 ~qpdVCKdyk~TGYCGYGDsCKflH~R~D~KtGWkL 174 (259)
T COG5152 139 TQPDVCKDYKETGYCGYGDSCKFLHDRSDFKTGWKL 174 (259)
T ss_pred cCcccccchhhcccccCCchhhhhhhhhhhhccccc
Confidence 445679999999999999999999988766654333
No 64
>PRK00468 hypothetical protein; Provisional
Probab=94.84 E-value=0.024 Score=40.84 Aligned_cols=30 Identities=30% Similarity=0.353 Sum_probs=26.8
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhh
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQ 126 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~ 126 (223)
...+++.|..+-+|.||||+|.+|+.|+.-
T Consensus 29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 29 SVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred eEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 456789999999999999999999999874
No 65
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=94.77 E-value=0.0067 Score=54.78 Aligned_cols=25 Identities=40% Similarity=1.000 Sum_probs=22.4
Q ss_pred cccCccccCCcCCCCCC-CccccCcc
Q 027432 192 TKLCGNFAKGSCTFGDR-CHFAHGAA 216 (223)
Q Consensus 192 t~~C~~~~~g~C~~g~~-C~faH~~~ 216 (223)
-++||.|++|.|+.||+ |+|||--.
T Consensus 37 ~eVCReF~rn~C~R~d~~CkfaHP~~ 62 (331)
T KOG2494|consen 37 LEVCREFLRNTCSRGDRECKFAHPPK 62 (331)
T ss_pred HHHHHHHHhccccCCCccccccCCCC
Confidence 37899999999999999 99999544
No 66
>PRK02821 hypothetical protein; Provisional
Probab=94.68 E-value=0.028 Score=40.72 Aligned_cols=31 Identities=23% Similarity=0.418 Sum_probs=27.5
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhc
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQT 127 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~S 127 (223)
.....+.|..+-+|.||||+|.+|+.|+.--
T Consensus 30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred cEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 4568899999999999999999999999753
No 67
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=94.57 E-value=0.062 Score=43.18 Aligned_cols=37 Identities=27% Similarity=0.400 Sum_probs=33.6
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhcCCeEEec
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR 134 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~ 134 (223)
..+.+.|+...+|+.||++|++|+.|++..|-+|.|-
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv 68 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV 68 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence 4677888999999999999999999999999999884
No 68
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=93.83 E-value=0.022 Score=48.35 Aligned_cols=30 Identities=27% Similarity=0.908 Sum_probs=25.7
Q ss_pred ccccccCcccc-CCcCCCCCCCccccCcccc
Q 027432 189 NFKTKLCGNFA-KGSCTFGDRCHFAHGAAEL 218 (223)
Q Consensus 189 ~~kt~~C~~~~-~g~C~~g~~C~faH~~~el 218 (223)
.|.-.+|+.|. +|+|-|||.|.|.|..++.
T Consensus 138 D~qpdVCKdyk~TGYCGYGDsCKflH~R~D~ 168 (259)
T COG5152 138 DTQPDVCKDYKETGYCGYGDSCKFLHDRSDF 168 (259)
T ss_pred ecCcccccchhhcccccCCchhhhhhhhhhh
Confidence 45667899999 8999999999999987643
No 69
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=93.79 E-value=0.052 Score=39.26 Aligned_cols=30 Identities=27% Similarity=0.365 Sum_probs=27.0
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhh
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQ 126 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~ 126 (223)
...+++.|..+-+|.||||+|.+|+.|+.-
T Consensus 29 ~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 29 TVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred eEEEEEEECcccccceecCCChhHHHHHHH
Confidence 456889999999999999999999999864
No 70
>PRK01064 hypothetical protein; Provisional
Probab=93.71 E-value=0.066 Score=38.91 Aligned_cols=30 Identities=30% Similarity=0.348 Sum_probs=26.8
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhh
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQ 126 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~ 126 (223)
....++.|..+..|.+|||+|.+|+.|+.-
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 456789999999999999999999999874
No 71
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=93.67 E-value=0.16 Score=49.40 Aligned_cols=67 Identities=21% Similarity=0.302 Sum_probs=55.7
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhcCC
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~~~ 170 (223)
.-..++.|+.+..-.+||.+|.+.|.|..+||+.-++++ ..++|.. ++..+++|+.+|..++.....
T Consensus 596 P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe-------~t~~i~A~~~~am~~Ak~~I~~i~~~~~~ 663 (760)
T KOG1067|consen 596 PVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDE-------GTFSIFAPTQAAMEEAKEFIDGIIKDDQV 663 (760)
T ss_pred ceeeEEeecchhhheeecCccceeeeEeeeccceeeecC-------ceEEEEecCHHHHHHHHHHHHHHhcCccc
Confidence 345678899999999999999999999999997766653 4566766 799999999999999976443
No 72
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=93.56 E-value=0.016 Score=51.74 Aligned_cols=33 Identities=42% Similarity=0.835 Sum_probs=28.8
Q ss_pred cccccccCccccCCcCCCCCCCccccCccccCc
Q 027432 188 SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRK 220 (223)
Q Consensus 188 ~~~kt~~C~~~~~g~C~~g~~C~faH~~~elr~ 220 (223)
.--|+.+|-+|..|.|.-|+.|.|+|....-|+
T Consensus 88 vDPKSvvCafFk~g~C~KG~kCKFsHdl~~~~k 120 (343)
T KOG1763|consen 88 VDPKSVVCAFFKQGTCTKGDKCKFSHDLAVERK 120 (343)
T ss_pred CCchHHHHHHHhccCCCCCCcccccchHHHhhh
Confidence 445899999999999999999999998876554
No 73
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=92.97 E-value=0.09 Score=37.20 Aligned_cols=36 Identities=33% Similarity=0.520 Sum_probs=28.9
Q ss_pred eEEEEecccc-----ccceecCCCcchhhhhhhc-CCeEEec
Q 027432 99 TAKISVDASL-----AGAIIGKGGVNSKQICRQT-GAKLSIR 134 (223)
Q Consensus 99 t~~i~VP~~~-----vG~IIGkgG~~Ik~I~~~S-Ga~I~I~ 134 (223)
-.++.|-+.. +|+.||++|++|+.|.++. |.+|.|-
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 3466677766 9999999999999999999 9999883
No 74
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=92.95 E-value=0.18 Score=42.65 Aligned_cols=69 Identities=22% Similarity=0.318 Sum_probs=55.6
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEc-----CCHHHHHHHHHHHHhhhhhcCC
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE-----GSFEQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~-----G~~~~i~~A~~lI~~~i~~~~~ 170 (223)
.....+.||...++.+||+.|+..+.|.+.+++++.|+.. +..|+|. .+|-.+.+|..+|..+=..+++
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~p 80 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPP 80 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCH
Confidence 3456799999999999999999999999999999999643 2445553 3688999999998887665554
No 75
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=92.95 E-value=0.033 Score=50.71 Aligned_cols=28 Identities=29% Similarity=0.718 Sum_probs=26.1
Q ss_pred cccccccCccccCCcCCCCCCCccccCc
Q 027432 188 SNFKTKLCGNFAKGSCTFGDRCHFAHGA 215 (223)
Q Consensus 188 ~~~kt~~C~~~~~g~C~~g~~C~faH~~ 215 (223)
..+++.+|++|+.|.|+.||.|-|+|-.
T Consensus 73 ~~~~~~vcK~~l~glC~kgD~C~Flhe~ 100 (325)
T KOG1040|consen 73 DSRGKVVCKHWLRGLCKKGDQCEFLHEY 100 (325)
T ss_pred ccCCceeehhhhhhhhhccCcCcchhhh
Confidence 4789999999999999999999999966
No 76
>PRK12705 hypothetical protein; Provisional
Probab=92.71 E-value=0.13 Score=49.59 Aligned_cols=41 Identities=27% Similarity=0.414 Sum_probs=34.2
Q ss_pred cceEEEEecccc-ccceecCCCcchhhhhhhcCCeEEeccCC
Q 027432 97 SATAKISVDASL-AGAIIGKGGVNSKQICRQTGAKLSIRDHE 137 (223)
Q Consensus 97 ~~t~~i~VP~~~-vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~ 137 (223)
.+.-.+.+|++- -|.||||-|.||+.+...||..|-|+|..
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp 238 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP 238 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc
Confidence 344567788854 49999999999999999999999997654
No 77
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=91.40 E-value=0.13 Score=41.28 Aligned_cols=38 Identities=24% Similarity=0.281 Sum_probs=33.2
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEec
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR 134 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~ 134 (223)
.....+.|+.+..|..|||+|.|++.++.-++-++.|.
T Consensus 98 ~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 98 DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred cEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 34567789999999999999999999999999887664
No 78
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=91.16 E-value=0.055 Score=48.42 Aligned_cols=34 Identities=32% Similarity=0.481 Sum_probs=29.1
Q ss_pred CccccccCcccccccCCCCCCCCCCcccccccCCC
Q 027432 26 TVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKP 60 (223)
Q Consensus 26 ~~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~~ 60 (223)
.--|+.+|-+|.. |.|.-|++|.|+|....-+..
T Consensus 88 vDPKSvvCafFk~-g~C~KG~kCKFsHdl~~~~k~ 121 (343)
T KOG1763|consen 88 VDPKSVVCAFFKQ-GTCTKGDKCKFSHDLAVERKK 121 (343)
T ss_pred CCchHHHHHHHhc-cCCCCCCcccccchHHHhhhc
Confidence 4458999998887 899999999999998877763
No 79
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=90.92 E-value=0.14 Score=44.49 Aligned_cols=22 Identities=32% Similarity=0.686 Sum_probs=20.5
Q ss_pred ccCcccccccCCCCCCCCCCcc
Q 027432 31 RMCNRLNSAEGCKFGDKCHFAH 52 (223)
Q Consensus 31 ~~C~~~~~~g~C~~g~~C~faH 52 (223)
-.|++|...|-|-.|..|+|.|
T Consensus 207 vycryynangicgkgaacrfvh 228 (377)
T KOG1492|consen 207 VYCRYYNANGICGKGAACRFVH 228 (377)
T ss_pred eEEEEecCCCcccCCceeeeec
Confidence 3599999999999999999999
No 80
>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=90.79 E-value=0.3 Score=32.78 Aligned_cols=34 Identities=26% Similarity=0.318 Sum_probs=26.4
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhcCCeE
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKL 131 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I 131 (223)
....+.+.....|.+||++|.+++.|+...+-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 3445555555689999999999999999887544
No 81
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.59 E-value=0.087 Score=47.16 Aligned_cols=39 Identities=21% Similarity=0.488 Sum_probs=31.4
Q ss_pred CCccccccCcccccccCCCCCCCCCCcccccccCCCccc
Q 027432 25 PTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAI 63 (223)
Q Consensus 25 ~~~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~~~~~ 63 (223)
..-|---+|+.|..+|.|-|||.|.|.|........+..
T Consensus 181 ~~d~qpDicKdykeTgycg~gdSckFlh~r~DyK~GWqi 219 (313)
T KOG1813|consen 181 RIDYQPDICKDYKETGYCGYGDSCKFLHDRSDYKAGWQI 219 (313)
T ss_pred eeecCchhhhhhHhhCcccccchhhhhhhhhhcccccee
Confidence 356777899999999999999999999987766544333
No 82
>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=90.54 E-value=0.27 Score=39.64 Aligned_cols=36 Identities=31% Similarity=0.441 Sum_probs=31.9
Q ss_pred eEEEEeccccccceecCCCcchhhhhhhcCCeEEec
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR 134 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~ 134 (223)
-.-+.|....+|+.||++|++|+.|++..|-+|.|-
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV 69 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI 69 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE
Confidence 455788888999999999999999999999998883
No 83
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=90.44 E-value=0.1 Score=36.80 Aligned_cols=32 Identities=25% Similarity=0.343 Sum_probs=27.8
Q ss_pred CcceEEEEeccccccceecCCCcchhhhhhhc
Q 027432 96 ASATAKISVDASLAGAIIGKGGVNSKQICRQT 127 (223)
Q Consensus 96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~S 127 (223)
......+.|..+..|.||||.|.+++.||.-.
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~ 58 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLV 58 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHH
Confidence 35678899999999999999999999998754
No 84
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=90.22 E-value=0.44 Score=48.11 Aligned_cols=72 Identities=19% Similarity=0.253 Sum_probs=61.7
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~ 170 (223)
...+.+.|-......|+||+|.+|.+|++.+.+.|.+.. .+..+..+++.|....+++|...+...+.+...
T Consensus 346 n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n 417 (753)
T KOG2208|consen 346 NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVSANDEKAVEDVEKIIAEILN 417 (753)
T ss_pred ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccccchhHHHHHHHHHHHhhhc
Confidence 355678888999999999999999999999999999965 234467899999999999999999988887654
No 85
>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=89.87 E-value=0.12 Score=36.78 Aligned_cols=34 Identities=35% Similarity=0.462 Sum_probs=28.7
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhcCCeE
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKL 131 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I 131 (223)
....+.+-.+..|.|||++|++|+.|.+...-.+
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 4577889999999999999999999988765444
No 86
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=89.77 E-value=0.071 Score=46.43 Aligned_cols=36 Identities=33% Similarity=0.531 Sum_probs=30.4
Q ss_pred ccccccCcccccccCCCCCCCCCCcccccccCCCccc
Q 027432 27 VVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAI 63 (223)
Q Consensus 27 ~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~~~~~ 63 (223)
--||..|-.|.. +.|.-|+.|.|+|+.+|.|..--.
T Consensus 82 dpK~~vcalF~~-~~c~kg~~ckF~h~~ee~r~~eK~ 117 (299)
T COG5252 82 DPKTVVCALFLN-KTCAKGDACKFAHGKEEARKTEKP 117 (299)
T ss_pred CchhHHHHHhcc-CccccCchhhhhcchHHHhhhccc
Confidence 348899999988 799999999999998888875444
No 87
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=89.62 E-value=0.46 Score=42.57 Aligned_cols=32 Identities=25% Similarity=0.313 Sum_probs=27.3
Q ss_pred CccccccCcccccccCCCCCCCCCCcccccccC
Q 027432 26 TVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELG 58 (223)
Q Consensus 26 ~~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~ 58 (223)
..+..-.|++|.. |.|+-++.|.|+|+..-++
T Consensus 100 ~~~s~V~c~~~~~-g~c~s~~~c~~lh~~d~~~ 131 (285)
T COG5084 100 VLSSSVVCKFFLR-GLCKSGFSCEFLHEYDLRS 131 (285)
T ss_pred cccCCcccchhcc-ccCcCCCccccccCCCccc
Confidence 3588889999999 8999999999999765554
No 88
>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=88.75 E-value=0.45 Score=33.96 Aligned_cols=33 Identities=18% Similarity=0.296 Sum_probs=27.4
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCC
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGA 129 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa 129 (223)
.....+.|..+..|.||||.|+++..||.-...
T Consensus 23 ~~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~ 55 (77)
T cd02414 23 GDTVEVNISGDDIGLLIGKRGKTLDALQYLANL 55 (77)
T ss_pred CCEEEEEEecCCCCeEECCCCccHHHHHHHHHH
Confidence 345678888899999999999999999876543
No 89
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=87.65 E-value=0.43 Score=40.36 Aligned_cols=37 Identities=30% Similarity=0.402 Sum_probs=34.6
Q ss_pred eEEEEeccccccceecCCCcchhhhhhhcCCeEEecc
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~ 135 (223)
...+.||.+..+..|||+|.|++-+.+-||.++.|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 6788899999999999999999999999999999964
No 90
>PRK13764 ATPase; Provisional
Probab=87.55 E-value=0.47 Score=46.71 Aligned_cols=40 Identities=28% Similarity=0.405 Sum_probs=36.3
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH 136 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~ 136 (223)
.....+.||...++.+|||+|.+|++|.+..|.+|.|...
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 4567899999999999999999999999999999999543
No 91
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=87.51 E-value=0.93 Score=37.53 Aligned_cols=37 Identities=27% Similarity=0.402 Sum_probs=31.6
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~ 135 (223)
..+-++|-... |.-|||+|.+|+.+++..|-+|.|-+
T Consensus 61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 44567777777 99999999999999999999998843
No 92
>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=86.80 E-value=0.42 Score=38.49 Aligned_cols=38 Identities=26% Similarity=0.307 Sum_probs=33.4
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEec
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR 134 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~ 134 (223)
.....+.|+.+..+..|||+|.|++...+-++-++.|.
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 45677889999999999999999999999998887664
No 93
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=86.01 E-value=0.58 Score=44.78 Aligned_cols=39 Identities=28% Similarity=0.495 Sum_probs=35.4
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~ 135 (223)
.....+.||...++.+|||+|.+|++|.+..|-+|.|..
T Consensus 485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~ 523 (604)
T COG1855 485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP 523 (604)
T ss_pred CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence 345778999999999999999999999999999999954
No 94
>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=85.80 E-value=0.78 Score=33.37 Aligned_cols=33 Identities=12% Similarity=0.306 Sum_probs=27.7
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhcCCe
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAK 130 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~ 130 (223)
...++.|-+..-|.|||++|.+|++|++.-...
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~ 62 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKR 62 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHH
Confidence 347889999999999999999999998865433
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=85.03 E-value=0.83 Score=41.96 Aligned_cols=39 Identities=26% Similarity=0.430 Sum_probs=35.9
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~ 135 (223)
.....+.||.+..+..|||+|.|++-..+-+|.+|.|..
T Consensus 300 ~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 300 KHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred CcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 467889999999999999999999999999999999953
No 96
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.01 E-value=0.32 Score=44.69 Aligned_cols=24 Identities=33% Similarity=0.804 Sum_probs=21.6
Q ss_pred ccCcccccccCCCCCCCCCCccccc
Q 027432 31 RMCNRLNSAEGCKFGDKCHFAHGEW 55 (223)
Q Consensus 31 ~~C~~~~~~g~C~~g~~C~faH~~~ 55 (223)
.+|++|.. |.|.||+.|+|.|..-
T Consensus 9 tic~~~~~-g~c~~g~~cr~~h~~~ 32 (344)
T KOG1039|consen 9 TICKYYQK-GNCKFGDLCRLSHSLP 32 (344)
T ss_pred hhhhhccc-ccccccceeeeeccCc
Confidence 67998888 8999999999999765
No 97
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.68 E-value=0.31 Score=43.77 Aligned_cols=30 Identities=27% Similarity=0.958 Sum_probs=26.4
Q ss_pred cccccccCcccc-CCcCCCCCCCccccCccc
Q 027432 188 SNFKTKLCGNFA-KGSCTFGDRCHFAHGAAE 217 (223)
Q Consensus 188 ~~~kt~~C~~~~-~g~C~~g~~C~faH~~~e 217 (223)
.-|.-.+|+.|. +|.|-||+.|.|-|..+.
T Consensus 182 ~d~qpDicKdykeTgycg~gdSckFlh~r~D 212 (313)
T KOG1813|consen 182 IDYQPDICKDYKETGYCGYGDSCKFLHDRSD 212 (313)
T ss_pred eecCchhhhhhHhhCcccccchhhhhhhhhh
Confidence 567778999999 899999999999997653
No 98
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=83.62 E-value=1.2 Score=41.51 Aligned_cols=39 Identities=21% Similarity=0.331 Sum_probs=35.9
Q ss_pred CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEec
Q 027432 96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR 134 (223)
Q Consensus 96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~ 134 (223)
......+.||.+..++.|||+|.|++-..+-+|.+|.|.
T Consensus 306 ~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~ 344 (374)
T PRK12328 306 EEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELN 344 (374)
T ss_pred CCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence 346788999999999999999999999999999999994
No 99
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=80.84 E-value=2.5 Score=37.92 Aligned_cols=53 Identities=21% Similarity=0.396 Sum_probs=45.9
Q ss_pred ceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432 111 AIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 111 ~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~ 170 (223)
.+||..|.++|.|.--|.+.|-|.- ..|++.|.+..++++..++.+++....+
T Consensus 162 RLiGpng~TLKAlelLT~CYilVqG-------~TVsaiGpfkGlkevr~IV~DcM~NiHP 214 (356)
T KOG2874|consen 162 RLIGPNGSTLKALELLTNCYILVQG-------NTVSAIGPFKGLKEVRKIVEDCMKNIHP 214 (356)
T ss_pred HhcCCCchhHHHHHHHhhcEEEeeC-------cEEEeecCcchHHHHHHHHHHHHhccch
Confidence 5899999999999999999998853 4689999999999999999988866443
No 100
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=80.18 E-value=1.5 Score=41.94 Aligned_cols=39 Identities=28% Similarity=0.363 Sum_probs=35.7
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~ 135 (223)
.....+.||.+..+..|||+|.|++...+-+|.+|.|..
T Consensus 301 ~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 357889999999999999999999999999999999943
No 101
>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=79.49 E-value=1.2 Score=24.88 Aligned_cols=21 Identities=38% Similarity=0.676 Sum_probs=16.9
Q ss_pred ccCccccCC-cCCCCCCCccccC
Q 027432 193 KLCGNFAKG-SCTFGDRCHFAHG 214 (223)
Q Consensus 193 ~~C~~~~~g-~C~~g~~C~faH~ 214 (223)
.||.+...| .|...+ |.|-|-
T Consensus 1 ~lC~yEl~Gg~Cnd~~-C~~QHf 22 (23)
T PF10650_consen 1 PLCPYELTGGVCNDPD-CEFQHF 22 (23)
T ss_pred CCCccccCCCeeCCCC-CCcccc
Confidence 379998887 898765 999983
No 102
>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=79.29 E-value=1.3 Score=33.76 Aligned_cols=30 Identities=20% Similarity=0.478 Sum_probs=25.9
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhc
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQT 127 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~S 127 (223)
..++|.|-+..-|.|||+.|++|++|++..
T Consensus 61 ~~i~I~I~t~rPg~vIG~~G~~i~~L~~~l 90 (109)
T cd02412 61 DRVEVTIHTARPGIIIGKKGAGIEKLRKEL 90 (109)
T ss_pred CCEEEEEEeCCCCcccCCchHHHHHHHHHH
Confidence 347788899999999999999999988754
No 103
>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=78.62 E-value=1.9 Score=31.34 Aligned_cols=28 Identities=29% Similarity=0.578 Sum_probs=23.7
Q ss_pred eEEEEeccccccceecCCCcchhhhhhh
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQ 126 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~ 126 (223)
..++.|-...-|.+||++|.+|+++++.
T Consensus 39 ~i~V~I~t~~pg~iIGk~G~~I~~l~~~ 66 (85)
T cd02411 39 GTQITIYAERPGMVIGRGGKNIRELTEI 66 (85)
T ss_pred cEEEEEEECCCCceECCCchhHHHHHHH
Confidence 3667777789999999999999998875
No 104
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=78.17 E-value=1.9 Score=39.92 Aligned_cols=40 Identities=30% Similarity=0.416 Sum_probs=36.2
Q ss_pred CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc
Q 027432 96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135 (223)
Q Consensus 96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~ 135 (223)
......+.||.+..+..|||+|.|++--.+-+|.+|.|..
T Consensus 301 ~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 301 EEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred CCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 3467889999999999999999999999999999999953
No 105
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=77.98 E-value=1.8 Score=37.62 Aligned_cols=36 Identities=25% Similarity=0.545 Sum_probs=28.9
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhh----cCC-eEEe
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQ----TGA-KLSI 133 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~----SGa-~I~I 133 (223)
...+|.|-+..-|.||||+|++|++|++. +|. .++|
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I 91 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQI 91 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceE
Confidence 46788999999999999999999988764 555 3444
No 106
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=77.49 E-value=1.8 Score=41.17 Aligned_cols=39 Identities=33% Similarity=0.435 Sum_probs=35.7
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~ 135 (223)
.....+.||.+..++.|||+|.|++--..-+|-+|.|.+
T Consensus 334 ~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 334 GRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred CcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 456789999999999999999999999999999999954
No 107
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=76.34 E-value=2.3 Score=35.99 Aligned_cols=35 Identities=29% Similarity=0.426 Sum_probs=29.7
Q ss_pred EEEEeccccccceecCCCcchhhhhhhcCCeEEec
Q 027432 100 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR 134 (223)
Q Consensus 100 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~ 134 (223)
..+.+-.+.+|+.||++|++|+.|+++-|-+|.|-
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVV 112 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVV 112 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEE
Confidence 44455567889999999999999999999888883
No 108
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=74.63 E-value=11 Score=31.59 Aligned_cols=67 Identities=13% Similarity=0.215 Sum_probs=55.3
Q ss_pred eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP 170 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~ 170 (223)
...+.+.....-+|...+|..+++|....|++|.+... +..+.|+|+...++.+...|.+++.....
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k~~~~~i~~~i~~~l~~i~~ 93 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTKSTAEYIEASINEILSNIRT 93 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccHHHHHHHHHHHHHHHhhcEE
Confidence 34566677788889999999999998889999999543 35799999999999999999999875443
No 109
>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=74.43 E-value=2.1 Score=34.65 Aligned_cols=38 Identities=32% Similarity=0.551 Sum_probs=33.8
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~ 135 (223)
.+=.+.|-...-|.+||++|.++++|..++|=+-.|-.
T Consensus 76 ~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 76 DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 45678899999999999999999999999999988843
No 110
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=71.90 E-value=4.1 Score=39.11 Aligned_cols=22 Identities=14% Similarity=-0.248 Sum_probs=20.0
Q ss_pred ccCccccCCcCCCCCCCccccC
Q 027432 193 KLCGNFAKGSCTFGDRCHFAHG 214 (223)
Q Consensus 193 ~~C~~~~~g~C~~g~~C~faH~ 214 (223)
..|.+|.++.|.-+|-|.|.|-
T Consensus 119 ~P~l~~~K~~e~~~D~~s~Lh~ 140 (667)
T KOG4791|consen 119 SPQLRSVKKVESSEDVPSPLHP 140 (667)
T ss_pred chHHHHhhhhhhhccccccCCC
Confidence 4699999999999999999994
No 111
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=71.13 E-value=1.9 Score=37.97 Aligned_cols=27 Identities=26% Similarity=0.701 Sum_probs=24.0
Q ss_pred CccccccCcccccccCCCCCCCCCCccc
Q 027432 26 TVVKSRMCNRLNSAEGCKFGDKCHFAHG 53 (223)
Q Consensus 26 ~~~kt~~C~~~~~~g~C~~g~~C~faH~ 53 (223)
..++-..|..|..+ .|.+|..|.|.|-
T Consensus 148 T~~rea~C~~~e~~-~C~rG~~CnFmH~ 174 (260)
T KOG2202|consen 148 TDFREAICGQFERT-ECSRGGACNFMHV 174 (260)
T ss_pred Cchhhhhhcccccc-cCCCCCcCcchhh
Confidence 56788899999985 9999999999994
No 112
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=70.55 E-value=4.2 Score=41.21 Aligned_cols=67 Identities=13% Similarity=0.290 Sum_probs=46.6
Q ss_pred eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhh
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIV 166 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~ 166 (223)
...+.||......|||.+|..|.+|...++. ++|...+.......+++.|....+..+..++..+..
T Consensus 421 ~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~-v~i~f~~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~ 487 (753)
T KOG2208|consen 421 KEEVQIPTKSHKRIIGTKGALINYIMGKHGG-VHIKFQNNNNSSDMVTIRGISKDVEKSVSLLKALKA 487 (753)
T ss_pred cceeecCccchhhhhccccccHHHHHhhcCc-EEEecCCCCcccccceEeccccccchhHHHHHhhhh
Confidence 4568999999999999999999999999995 555433334444556666655555454444444444
No 113
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=70.39 E-value=1.8 Score=41.58 Aligned_cols=22 Identities=32% Similarity=0.658 Sum_probs=19.7
Q ss_pred cCcccccccCCCCCCCCCCccc
Q 027432 32 MCNRLNSAEGCKFGDKCHFAHG 53 (223)
Q Consensus 32 ~C~~~~~~g~C~~g~~C~faH~ 53 (223)
-|..|.+.|.|+||-+|+|+-+
T Consensus 116 ~Cp~f~s~G~Cp~G~~CRFl~a 137 (614)
T KOG2333|consen 116 SCPVFESLGFCPYGFKCRFLGA 137 (614)
T ss_pred ccceeeccccCCccceeehhhc
Confidence 4999999999999999999753
No 114
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=69.39 E-value=10 Score=33.19 Aligned_cols=37 Identities=19% Similarity=0.309 Sum_probs=33.3
Q ss_pred eEEEEeccccccceecCCCcchhhhhhhcCCeEEecc
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~ 135 (223)
-.-+.|+..+|-.+||++|+.++-+.+.+++.|.|..
T Consensus 147 G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~ 183 (239)
T COG1097 147 GQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ 183 (239)
T ss_pred CEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec
Confidence 3568999999999999999999999999999988843
No 115
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=61.98 E-value=4.9 Score=36.10 Aligned_cols=31 Identities=26% Similarity=0.454 Sum_probs=24.7
Q ss_pred ccccccCccccCCcCCCCCCCccccCccccC
Q 027432 189 NFKTKLCGNFAKGSCTFGDRCHFAHGAAELR 219 (223)
Q Consensus 189 ~~kt~~C~~~~~g~C~~g~~C~faH~~~elr 219 (223)
.+-...|++|..|.|+-++.|.|.|+.+-++
T Consensus 101 ~~s~V~c~~~~~g~c~s~~~c~~lh~~d~~~ 131 (285)
T COG5084 101 LSSSVVCKFFLRGLCKSGFSCEFLHEYDLRS 131 (285)
T ss_pred ccCCcccchhccccCcCCCccccccCCCccc
Confidence 4566778888888888888888888877655
No 116
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=54.23 E-value=6.2 Score=34.36 Aligned_cols=28 Identities=43% Similarity=0.395 Sum_probs=21.1
Q ss_pred EEEEecc-ccccceecCCCcchhhhhhhc
Q 027432 100 AKISVDA-SLAGAIIGKGGVNSKQICRQT 127 (223)
Q Consensus 100 ~~i~VP~-~~vG~IIGkgG~~Ik~I~~~S 127 (223)
..|.|.. +.-+.|||++|+.||+|....
T Consensus 223 ~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 223 ALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 3455554 455899999999999997743
No 117
>PRK15494 era GTPase Era; Provisional
Probab=53.47 E-value=9.6 Score=34.64 Aligned_cols=27 Identities=33% Similarity=0.417 Sum_probs=20.9
Q ss_pred EEEEecc-ccccceecCCCcchhhhhhh
Q 027432 100 AKISVDA-SLAGAIIGKGGVNSKQICRQ 126 (223)
Q Consensus 100 ~~i~VP~-~~vG~IIGkgG~~Ik~I~~~ 126 (223)
..|+|.. +.-+.|||++|+.||+|...
T Consensus 275 ~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 275 QVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 3456665 55689999999999998764
No 118
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.29 E-value=2.7 Score=41.68 Aligned_cols=36 Identities=22% Similarity=0.300 Sum_probs=32.0
Q ss_pred CcccccccCccccC-CcCCCCCCCccccCccccCcCC
Q 027432 187 SSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAELRKTA 222 (223)
Q Consensus 187 ~~~~kt~~C~~~~~-g~C~~g~~C~faH~~~elr~~~ 222 (223)
.+.|+|-+|+.... |.|+.+..|.|+|...|+.++.
T Consensus 198 q~~vl~l~l~~Le~g~~~~Rk~lvmfvvq~le~~~pq 234 (861)
T KOG3161|consen 198 QSKVLTLMLRDLEQGGGCPRKTLVMFVVQQLELEKPQ 234 (861)
T ss_pred HHHHHHHHHHHHHhcCCccccceEEEEeeeccccchh
Confidence 38999999999996 5599999999999999998764
No 119
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=51.12 E-value=12 Score=31.94 Aligned_cols=28 Identities=29% Similarity=0.590 Sum_probs=23.3
Q ss_pred EEEEeccccccceecCCCcchhhhhhhc
Q 027432 100 AKISVDASLAGAIIGKGGVNSKQICRQT 127 (223)
Q Consensus 100 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~S 127 (223)
.++.|-...-|.+||++|.+|+++++.-
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~L 69 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEIL 69 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHH
Confidence 5666777889999999999999887653
No 120
>CHL00048 rps3 ribosomal protein S3
Probab=50.91 E-value=13 Score=31.93 Aligned_cols=30 Identities=7% Similarity=0.144 Sum_probs=25.0
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhc
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQT 127 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~S 127 (223)
...+|.|=...-|.|||++|.+|++|++.-
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 346778888889999999999999988653
No 121
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=50.72 E-value=10 Score=37.64 Aligned_cols=40 Identities=28% Similarity=0.488 Sum_probs=34.8
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH 136 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~ 136 (223)
..+-++.|-+.+-|+||||+|.++++|..++|=+..|-..
T Consensus 92 ~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 92 DVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred CCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 3456788999999999999999999999999999888443
No 122
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=50.32 E-value=11 Score=34.95 Aligned_cols=28 Identities=29% Similarity=0.481 Sum_probs=24.6
Q ss_pred ccccceecCCCcchhhhhhhc-CCeEEec
Q 027432 107 SLAGAIIGKGGVNSKQICRQT-GAKLSIR 134 (223)
Q Consensus 107 ~~vG~IIGkgG~~Ik~I~~~S-Ga~I~I~ 134 (223)
+-+|+.||++|++|+.|.+.. |-+|.|-
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv 273 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDII 273 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEE
Confidence 567999999999999998887 8899883
No 123
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=49.55 E-value=13 Score=31.53 Aligned_cols=28 Identities=25% Similarity=0.517 Sum_probs=24.5
Q ss_pred eEEEEeccccccceecCCCcchhhhhhh
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQ 126 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~ 126 (223)
..++.|-...-|.|||++|.+|++|++.
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~ 66 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEK 66 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHH
Confidence 4778888899999999999999988764
No 124
>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=49.11 E-value=13 Score=34.26 Aligned_cols=28 Identities=29% Similarity=0.495 Sum_probs=24.7
Q ss_pred ccccceecCCCcchhhhhhhc-CCeEEec
Q 027432 107 SLAGAIIGKGGVNSKQICRQT-GAKLSIR 134 (223)
Q Consensus 107 ~~vG~IIGkgG~~Ik~I~~~S-Ga~I~I~ 134 (223)
+-+|+.||++|++|+.|.++. |-+|.|-
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv 271 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDII 271 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEE
Confidence 557999999999999999887 8899883
No 125
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=48.82 E-value=11 Score=35.87 Aligned_cols=27 Identities=26% Similarity=0.505 Sum_probs=24.3
Q ss_pred ccccceecCCCcchhhhhhhc-CCeEEe
Q 027432 107 SLAGAIIGKGGVNSKQICRQT-GAKLSI 133 (223)
Q Consensus 107 ~~vG~IIGkgG~~Ik~I~~~S-Ga~I~I 133 (223)
+-+|+.||++|++|+.|.+.. |-+|.|
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDV 304 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDV 304 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEE
Confidence 568999999999999999887 888888
No 126
>PRK00089 era GTPase Era; Reviewed
Probab=48.46 E-value=8.5 Score=33.68 Aligned_cols=27 Identities=44% Similarity=0.609 Sum_probs=20.1
Q ss_pred EEEecc-ccccceecCCCcchhhhhhhc
Q 027432 101 KISVDA-SLAGAIIGKGGVNSKQICRQT 127 (223)
Q Consensus 101 ~i~VP~-~~vG~IIGkgG~~Ik~I~~~S 127 (223)
.|.|.. +.-+.|||++|+.||+|....
T Consensus 229 ~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 229 TIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 345543 455899999999999987643
No 127
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=48.36 E-value=7.1 Score=34.03 Aligned_cols=21 Identities=33% Similarity=0.899 Sum_probs=18.6
Q ss_pred cCcccc-CCcCCCCCCCccccC
Q 027432 194 LCGNFA-KGSCTFGDRCHFAHG 214 (223)
Q Consensus 194 ~C~~~~-~g~C~~g~~C~faH~ 214 (223)
.|++|. .|.|--|.-|||.|-
T Consensus 208 ycryynangicgkgaacrfvhe 229 (377)
T KOG1492|consen 208 YCRYYNANGICGKGAACRFVHE 229 (377)
T ss_pred EEEEecCCCcccCCceeeeecc
Confidence 599998 799999999999984
No 128
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=48.32 E-value=11 Score=35.15 Aligned_cols=28 Identities=21% Similarity=0.421 Sum_probs=24.7
Q ss_pred ccccceecCCCcchhhhhhhc-CCeEEec
Q 027432 107 SLAGAIIGKGGVNSKQICRQT-GAKLSIR 134 (223)
Q Consensus 107 ~~vG~IIGkgG~~Ik~I~~~S-Ga~I~I~ 134 (223)
+-+|+.||++|++|+.|.++. |-+|.|-
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI 279 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCI 279 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEE
Confidence 567999999999999998887 8899883
No 129
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=47.86 E-value=11 Score=36.77 Aligned_cols=37 Identities=32% Similarity=0.528 Sum_probs=32.8
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhcCCeEEec
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR 134 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~ 134 (223)
.+-.+.|-+.+-|+||||+|++.+.|..++|-.-.|-
T Consensus 99 ~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~iv 135 (637)
T COG1782 99 DTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIV 135 (637)
T ss_pred CCceEEEEecCCceEEecCchHHHHHHHHhCCcceee
Confidence 4557888999999999999999999999999887774
No 130
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=47.80 E-value=14 Score=31.73 Aligned_cols=35 Identities=23% Similarity=0.303 Sum_probs=28.2
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeE
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKL 131 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I 131 (223)
..++.+.|-.+..+.|||+.|.++..||--+.+.+
T Consensus 90 ~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l 124 (208)
T COG1847 90 GRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYL 124 (208)
T ss_pred CcEEEEEecCCchhhhhccCCcchHHHHHHHHHHh
Confidence 34566788888899999999999999987665543
No 131
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=47.45 E-value=14 Score=31.92 Aligned_cols=28 Identities=14% Similarity=0.332 Sum_probs=24.3
Q ss_pred eEEEEeccccccceecCCCcchhhhhhh
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQ 126 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~ 126 (223)
..++.|-...-|.|||++|..|++|++.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~ 72 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSL 72 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHH
Confidence 4678888888999999999999988765
No 132
>COG1159 Era GTPase [General function prediction only]
Probab=46.34 E-value=8.8 Score=34.68 Aligned_cols=27 Identities=41% Similarity=0.513 Sum_probs=20.8
Q ss_pred EEEecc-ccccceecCCCcchhhhhhhc
Q 027432 101 KISVDA-SLAGAIIGKGGVNSKQICRQT 127 (223)
Q Consensus 101 ~i~VP~-~~vG~IIGkgG~~Ik~I~~~S 127 (223)
.|+|.. +.=|.||||+|+.||+|....
T Consensus 232 ~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 232 TIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred EEEEecCCccceEECCCcHHHHHHHHHH
Confidence 356664 455899999999999987643
No 133
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=45.14 E-value=11 Score=40.22 Aligned_cols=69 Identities=6% Similarity=-0.017 Sum_probs=57.3
Q ss_pred eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhh
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR 167 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~ 167 (223)
.++..++...+.+||+.++.+|+-|+.-+++++.|.....-..|+.++|.+.-...+-+..||...+..
T Consensus 782 niehrdkkgf~plImaatagh~tvV~~llk~ha~veaQsdrtkdt~lSlacsggr~~vvelLl~~gank 850 (2131)
T KOG4369|consen 782 NIEHRDKKGFVPLIMAATAGHITVVQDLLKAHADVEAQSDRTKDTMLSLACSGGRTRVVELLLNAGANK 850 (2131)
T ss_pred cccccccccchhhhhhcccCchHHHHHHHhhhhhhhhhcccccCceEEEecCCCcchHHHHHHHhhccc
Confidence 356778889999999999999999999999999997665566789999998877777777777666543
No 134
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=43.39 E-value=20 Score=32.96 Aligned_cols=31 Identities=23% Similarity=0.349 Sum_probs=24.0
Q ss_pred ceEEEEeccc-cccceecCCCcchhhhhhhcC
Q 027432 98 ATAKISVDAS-LAGAIIGKGGVNSKQICRQTG 128 (223)
Q Consensus 98 ~t~~i~VP~~-~vG~IIGkgG~~Ik~I~~~SG 128 (223)
.+.++.+|.. ..-.||||||..|++|.++-+
T Consensus 328 I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 328 IQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 4567788864 457799999999999987543
No 135
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=42.77 E-value=16 Score=35.17 Aligned_cols=27 Identities=30% Similarity=0.505 Sum_probs=24.2
Q ss_pred ccccceecCCCcchhhhhhhc-CCeEEe
Q 027432 107 SLAGAIIGKGGVNSKQICRQT-GAKLSI 133 (223)
Q Consensus 107 ~~vG~IIGkgG~~Ik~I~~~S-Ga~I~I 133 (223)
+-+|+.||++|++|+.|.+.. |-+|.|
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idi 272 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDI 272 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEE
Confidence 457999999999999999887 889988
No 136
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=42.31 E-value=9.8 Score=30.06 Aligned_cols=17 Identities=41% Similarity=1.269 Sum_probs=13.7
Q ss_pred cCCCCCCCCCCccccccc
Q 027432 40 EGCKFGDKCHFAHGEWEL 57 (223)
Q Consensus 40 g~C~~g~~C~faH~~~el 57 (223)
.+|++|+ |||-||....
T Consensus 60 ~GC~~ge-CHy~~GN~ka 76 (132)
T COG1908 60 AGCKIGE-CHYISGNYKA 76 (132)
T ss_pred ecccccc-eeeeccchHH
Confidence 4899999 9999985433
No 137
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=39.61 E-value=13 Score=34.25 Aligned_cols=22 Identities=36% Similarity=0.976 Sum_probs=20.4
Q ss_pred ccCccccCCcCCCCCCCccccC
Q 027432 193 KLCGNFAKGSCTFGDRCHFAHG 214 (223)
Q Consensus 193 ~~C~~~~~g~C~~g~~C~faH~ 214 (223)
.+|.+|.+|.|+.|+.|-|.|-
T Consensus 162 ~Icsf~v~geckRG~ec~yrhE 183 (377)
T KOG0153|consen 162 HICSFFVKGECKRGAECPYRHE 183 (377)
T ss_pred ccccceeecccccccccccccc
Confidence 5899999999999999999994
No 138
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=38.09 E-value=65 Score=29.79 Aligned_cols=56 Identities=18% Similarity=0.249 Sum_probs=46.0
Q ss_pred ccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHH--hhhhh
Q 027432 105 DASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVR--ELIVR 167 (223)
Q Consensus 105 P~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~--~~i~~ 167 (223)
+.+.+-.|.|..+.+++.|.+..|++|.... +.++|.|+...++.|...+. +.+..
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG-------~~~~i~g~~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVARG-------EAVRIIGARPLVDVATRVLLTLELLAE 79 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeCC-------ceEEEEechHHHHHHHHHHhHHHHHHH
Confidence 3667788999999999999999999987753 45889999778888888888 55544
No 139
>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=36.91 E-value=10 Score=21.78 Aligned_cols=9 Identities=56% Similarity=1.368 Sum_probs=5.5
Q ss_pred CCCCCCCCC
Q 027432 41 GCKFGDKCH 49 (223)
Q Consensus 41 ~C~~g~~C~ 49 (223)
.|+||.+|-
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 489999993
No 140
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=36.71 E-value=26 Score=30.01 Aligned_cols=28 Identities=18% Similarity=0.514 Sum_probs=24.0
Q ss_pred eEEEEeccccccceecCCCcchhhhhhh
Q 027432 99 TAKISVDASLAGAIIGKGGVNSKQICRQ 126 (223)
Q Consensus 99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~ 126 (223)
..+|.|-...-|.|||+.|.+|++|++.
T Consensus 63 ~i~I~I~~~~pg~vIG~~g~~i~~l~~~ 90 (211)
T TIGR01009 63 KIRVTIHTARPGIVIGKKGSEIEKLRKD 90 (211)
T ss_pred ceEEEEEeCCCcceeCCCchHHHHHHHH
Confidence 3678888888899999999999998854
No 141
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=30.01 E-value=39 Score=29.37 Aligned_cols=30 Identities=17% Similarity=0.489 Sum_probs=24.5
Q ss_pred ceEEEEeccccccceecCCCcchhhhhhhc
Q 027432 98 ATAKISVDASLAGAIIGKGGVNSKQICRQT 127 (223)
Q Consensus 98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~S 127 (223)
...+|.|-...-|.|||++|.+|++|++.-
T Consensus 62 ~~i~I~I~~~rP~~iiG~~g~~i~~l~~~L 91 (232)
T PRK00310 62 KRVRVTIHTARPGIVIGKKGAEIEKLRKEL 91 (232)
T ss_pred CeEEEEEEECCCccccCCCcHHHHHHHHHH
Confidence 346777778888999999999999887653
No 142
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=29.51 E-value=53 Score=30.14 Aligned_cols=59 Identities=20% Similarity=0.263 Sum_probs=43.4
Q ss_pred cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHH-HHHHH
Q 027432 97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQ-IKQAS 158 (223)
Q Consensus 97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~-i~~A~ 158 (223)
..+....||...+|+|.|..|.+|+.|++.+...|.-.-. ..+-++.+.|-+.. +++|.
T Consensus 114 qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~---~~~~Vf~Vtg~~~nC~kra~ 173 (394)
T KOG2113|consen 114 QTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR---CGEPVFCVTGAPKNCVKRAR 173 (394)
T ss_pred CCceeeeccceeeeeccccccCccchheecccceEeeecc---CCCceEEEecCCcchhhhcc
Confidence 4567788999999999999999999999999988765211 12345666776555 44443
No 143
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=26.45 E-value=1.3e+02 Score=21.65 Aligned_cols=50 Identities=16% Similarity=0.271 Sum_probs=38.1
Q ss_pred cchhhhhhhcCCeEEeccCC---CCCCceEEEEcCCHHHHHHHHHHHHhhhhh
Q 027432 118 VNSKQICRQTGAKLSIRDHE---ADPNLRNIELEGSFEQIKQASAMVRELIVR 167 (223)
Q Consensus 118 ~~Ik~I~~~SGa~I~I~~~~---~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~ 167 (223)
.-+..|-+..+.+++..-.+ -..++.++++.|+..++-.|...++++|..
T Consensus 34 ~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~ 86 (88)
T PF02749_consen 34 EEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQR 86 (88)
T ss_dssp HHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 35667777778888774332 224679999999999999999999998864
No 144
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.41 E-value=1.1e+02 Score=30.91 Aligned_cols=39 Identities=26% Similarity=0.304 Sum_probs=35.3
Q ss_pred CCccccccCcccccccCCCCCCCCCCcccccccCCCccc
Q 027432 25 PTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAI 63 (223)
Q Consensus 25 ~~~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~~~~~ 63 (223)
.++|+|-+|....+.+.|+.+..|.|+|...||..+-+.
T Consensus 198 q~~vl~l~l~~Le~g~~~~Rk~lvmfvvq~le~~~pq~s 236 (861)
T KOG3161|consen 198 QSKVLTLMLRDLEQGGGCPRKTLVMFVVQQLELEKPQLS 236 (861)
T ss_pred HHHHHHHHHHHHHhcCCccccceEEEEeeeccccchhhh
Confidence 369999999999999999999999999999999986543
No 145
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.24 E-value=37 Score=31.33 Aligned_cols=23 Identities=43% Similarity=0.983 Sum_probs=19.7
Q ss_pred ccCcccc--CCcCCCCCCCccccCc
Q 027432 193 KLCGNFA--KGSCTFGDRCHFAHGA 215 (223)
Q Consensus 193 ~~C~~~~--~g~C~~g~~C~faH~~ 215 (223)
+.|++|. .|.|+||..|-+.|-.
T Consensus 250 ~~c~yf~~~~g~cPf~s~~~y~h~~ 274 (344)
T KOG1039|consen 250 KDCKYFSQGLGSCPFGSKCFYKHLL 274 (344)
T ss_pred cchhhhcCCCCCCCCCCcccccccc
Confidence 5799998 5779999999999943
No 146
>PF08352 oligo_HPY: Oligopeptide/dipeptide transporter, C-terminal region; InterPro: IPR013563 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry features a region found towards the C terminus of oligopeptide ABC transporter ATP binding proteins, immediately following the ATP-binding domain (IPR003439 from INTERPRO). All characterised members appear able to be involved in the transport of oligopeptides or dipeptides. Some are important for sporulation or antibiotic resistance. Some dipeptide transporters also act on the haem precursor delta-aminolevulinic acid. ; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0015833 peptide transport
Probab=22.40 E-value=40 Score=22.52 Aligned_cols=12 Identities=42% Similarity=1.237 Sum_probs=10.4
Q ss_pred CCCCCCCCCCcc
Q 027432 41 GCKFGDKCHFAH 52 (223)
Q Consensus 41 ~C~~g~~C~faH 52 (223)
+|+|..+|.||=
T Consensus 50 GC~f~~rC~~a~ 61 (64)
T PF08352_consen 50 GCPFAPRCPYAT 61 (64)
T ss_pred CCCccccchHhh
Confidence 899999999873
Done!