Query 027188
Match_columns 227
No_of_seqs 330 out of 800
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 06:16:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027188.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027188hhsearch_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 1.7E-15 3.6E-20 137.1 4.2 41 25-65 122-163 (332)
2 cd02396 PCBP_like_KH K homolog 99.4 1.5E-13 3.3E-18 98.4 2.4 63 106-168 1-64 (65)
3 PF00013 KH_1: KH domain syndr 99.1 2.3E-11 5.1E-16 84.9 1.4 60 106-168 1-60 (60)
4 cd02394 vigilin_like_KH K homo 99.0 1E-10 2.3E-15 82.1 2.8 61 106-168 1-61 (62)
5 KOG1676 K-homology type RNA bi 99.0 2.4E-10 5.3E-15 112.1 4.7 85 98-182 223-308 (600)
6 cd00105 KH-I K homology RNA-bi 99.0 1.9E-10 4.1E-15 80.0 2.5 63 106-168 1-63 (64)
7 KOG1676 K-homology type RNA bi 99.0 2.8E-10 6.1E-15 111.7 4.5 75 106-180 319-395 (600)
8 COG5063 CTH1 CCCH-type Zn-fing 98.9 4E-10 8.6E-15 103.8 3.4 38 26-63 219-264 (351)
9 KOG2192 PolyC-binding hnRNP-K 98.9 1.8E-08 3.9E-13 92.3 11.5 71 103-173 313-383 (390)
10 cd02393 PNPase_KH Polynucleoti 98.9 8.6E-10 1.9E-14 78.7 1.7 57 106-168 3-60 (61)
11 PF00642 zf-CCCH: Zinc finger 98.8 1.1E-09 2.5E-14 66.9 -0.0 26 194-219 1-27 (27)
12 PF00642 zf-CCCH: Zinc finger 98.7 1.8E-09 3.9E-14 66.1 0.1 27 33-59 1-27 (27)
13 KOG2193 IGF-II mRNA-binding pr 98.7 3.9E-08 8.4E-13 94.3 6.4 75 105-179 411-486 (584)
14 smart00322 KH K homology RNA-b 98.6 2.3E-08 4.9E-13 68.2 3.1 66 105-172 3-68 (69)
15 KOG2191 RNA-binding protein NO 98.5 6.2E-08 1.4E-12 90.5 3.3 69 105-173 132-203 (402)
16 KOG1677 CCCH-type Zn-finger pr 98.5 6.8E-08 1.5E-12 87.7 2.8 41 25-65 167-207 (332)
17 PF13014 KH_3: KH domain 98.5 3.1E-08 6.6E-13 65.7 0.3 42 115-156 1-43 (43)
18 KOG2190 PolyC-binding proteins 98.5 1.3E-07 2.9E-12 91.9 4.5 72 105-176 138-210 (485)
19 COG5063 CTH1 CCCH-type Zn-fing 98.4 6.3E-07 1.4E-11 83.0 8.0 45 24-68 103-148 (351)
20 smart00356 ZnF_C3H1 zinc finge 98.4 1.4E-07 3.1E-12 56.2 1.9 27 193-219 1-27 (27)
21 KOG2193 IGF-II mRNA-binding pr 98.3 4.4E-07 9.5E-12 87.3 3.6 71 106-176 494-566 (584)
22 TIGR03665 arCOG04150 arCOG0415 98.2 6.3E-07 1.4E-11 75.9 2.7 60 109-173 2-64 (172)
23 cd02395 SF1_like-KH Splicing f 98.2 6E-07 1.3E-11 72.6 1.7 63 114-176 15-97 (120)
24 smart00356 ZnF_C3H1 zinc finge 98.2 1.1E-06 2.4E-11 52.3 2.3 27 32-59 1-27 (27)
25 KOG2191 RNA-binding protein NO 98.2 1.2E-06 2.5E-11 82.1 3.2 72 105-176 39-113 (402)
26 PRK13763 putative RNA-processi 98.1 2.1E-06 4.5E-11 73.4 3.5 64 105-173 3-70 (180)
27 TIGR03665 arCOG04150 arCOG0415 98.0 2.2E-06 4.8E-11 72.6 2.4 52 114-172 98-149 (172)
28 PRK13763 putative RNA-processi 97.8 7.6E-06 1.7E-10 69.9 2.1 52 115-173 105-156 (180)
29 KOG2190 PolyC-binding proteins 97.8 9.4E-06 2E-10 79.2 1.9 71 102-172 335-407 (485)
30 KOG1595 CCCH-type Zn-finger pr 97.7 2.4E-05 5.2E-10 76.7 2.8 34 189-225 264-297 (528)
31 TIGR02696 pppGpp_PNP guanosine 97.1 0.00034 7.3E-09 71.3 3.1 65 104-174 577-642 (719)
32 TIGR03591 polynuc_phos polyrib 97.1 0.00036 7.9E-09 70.5 2.9 63 105-173 551-614 (684)
33 KOG1595 CCCH-type Zn-finger pr 96.7 0.0016 3.4E-08 64.3 3.9 29 193-221 233-261 (528)
34 PLN00207 polyribonucleotide nu 96.6 0.0015 3.2E-08 68.1 3.0 65 103-173 683-749 (891)
35 KOG2185 Predicted RNA-processi 96.5 0.001 2.2E-08 64.1 1.1 25 196-220 140-164 (486)
36 cd02134 NusA_KH NusA_K homolog 96.4 0.00075 1.6E-08 48.1 -0.4 36 105-140 25-60 (61)
37 KOG2192 PolyC-binding hnRNP-K 96.1 0.0022 4.7E-08 59.4 1.2 70 105-174 123-193 (390)
38 KOG0119 Splicing factor 1/bran 96.1 0.0046 9.9E-08 60.8 3.1 62 113-174 152-230 (554)
39 PF14608 zf-CCCH_2: Zinc finge 95.9 0.0047 1E-07 35.1 1.5 19 198-218 1-19 (19)
40 COG1094 Predicted RNA-binding 95.8 0.005 1.1E-07 54.0 2.0 52 115-173 112-163 (194)
41 KOG0336 ATP-dependent RNA heli 95.6 0.017 3.6E-07 56.7 4.9 68 106-176 48-115 (629)
42 KOG2494 C3H1-type Zn-finger pr 95.5 0.0076 1.6E-07 56.5 1.9 26 198-224 73-98 (331)
43 PRK11824 polynucleotide phosph 95.4 0.01 2.2E-07 60.4 2.6 64 104-173 553-617 (693)
44 KOG1040 Polyadenylation factor 94.9 0.022 4.7E-07 53.5 3.1 31 31-63 73-103 (325)
45 KOG1040 Polyadenylation factor 94.4 0.013 2.8E-07 55.0 0.5 31 192-223 73-103 (325)
46 PF14608 zf-CCCH_2: Zinc finge 94.2 0.031 6.8E-07 31.6 1.5 18 37-57 1-18 (19)
47 PRK04163 exosome complex RNA-b 94.1 0.055 1.2E-06 48.0 3.7 65 100-170 139-205 (235)
48 KOG2185 Predicted RNA-processi 94.0 0.023 4.9E-07 55.1 1.1 32 36-68 141-176 (486)
49 COG1185 Pnp Polyribonucleotide 93.9 0.062 1.4E-06 54.8 4.2 66 105-176 552-618 (692)
50 KOG1763 Uncharacterized conser 93.6 0.018 3.9E-07 53.7 -0.3 34 191-224 87-120 (343)
51 COG5176 MSL5 Splicing factor ( 93.5 0.036 7.7E-07 49.9 1.4 43 103-145 146-194 (269)
52 COG5252 Uncharacterized conser 93.0 0.023 4.9E-07 51.8 -0.5 34 192-225 81-114 (299)
53 PF13184 KH_5: NusA-like KH do 92.8 0.059 1.3E-06 39.7 1.5 40 107-146 5-50 (69)
54 COG5152 Uncharacterized conser 92.7 0.043 9.4E-07 49.0 0.7 31 193-223 138-169 (259)
55 PRK08406 transcription elongat 92.6 0.053 1.2E-06 44.9 1.1 42 105-146 32-73 (140)
56 KOG2494 C3H1-type Zn-finger pr 91.9 0.045 9.8E-07 51.4 -0.1 25 196-220 37-62 (331)
57 PRK12328 nusA transcription el 91.5 0.091 2E-06 50.3 1.5 44 104-147 307-350 (374)
58 COG5152 Uncharacterized conser 91.1 0.089 1.9E-06 47.1 0.9 28 33-60 139-166 (259)
59 PRK08406 transcription elongat 91.1 0.054 1.2E-06 44.9 -0.4 39 104-142 98-136 (140)
60 KOG2279 Kinase anchor protein 90.9 0.12 2.7E-06 51.6 1.8 73 100-172 134-207 (608)
61 COG0195 NusA Transcription elo 90.8 0.08 1.7E-06 46.2 0.4 38 106-143 143-180 (190)
62 KOG2279 Kinase anchor protein 90.7 0.2 4.3E-06 50.2 3.0 70 105-176 68-138 (608)
63 TIGR01953 NusA transcription t 89.6 0.14 3.1E-06 48.2 0.9 40 104-143 300-339 (341)
64 PRK12704 phosphodiesterase; Pr 89.5 0.2 4.4E-06 49.5 2.0 63 105-173 210-275 (520)
65 TIGR01952 nusA_arch NusA famil 89.4 0.13 2.8E-06 43.0 0.4 40 103-142 98-137 (141)
66 PRK02821 hypothetical protein; 89.4 0.12 2.7E-06 39.0 0.3 31 104-134 30-60 (77)
67 KOG1588 RNA-binding protein Sa 89.1 0.15 3.3E-06 46.6 0.7 41 105-145 92-138 (259)
68 KOG4369 RTK signaling protein 88.7 0.16 3.5E-06 55.0 0.7 67 108-174 1343-1410(2131)
69 PRK00468 hypothetical protein; 88.6 0.14 2.9E-06 38.5 0.1 28 105-132 30-57 (75)
70 TIGR01952 nusA_arch NusA famil 88.6 0.11 2.4E-06 43.3 -0.4 39 109-147 37-75 (141)
71 TIGR03319 YmdA_YtgF conserved 88.4 0.48 1E-05 46.9 3.7 41 104-144 203-244 (514)
72 PRK12327 nusA transcription el 88.2 0.16 3.5E-06 48.3 0.2 41 104-144 302-342 (362)
73 COG1837 Predicted RNA-binding 87.1 0.19 4E-06 38.2 -0.0 30 103-132 28-57 (76)
74 PRK00106 hypothetical protein; 86.1 0.76 1.6E-05 45.9 3.6 41 104-144 224-265 (535)
75 KOG1813 Predicted E3 ubiquitin 85.7 0.26 5.7E-06 46.0 0.2 31 30-60 181-211 (313)
76 PRK12329 nusA transcription el 85.5 0.28 6.2E-06 48.0 0.4 40 105-144 335-374 (449)
77 KOG2814 Transcription coactiva 85.5 0.89 1.9E-05 43.2 3.6 72 107-180 59-131 (345)
78 PRK06418 transcription elongat 84.9 0.32 6.9E-06 41.8 0.3 41 105-146 61-101 (166)
79 PRK01064 hypothetical protein; 84.8 0.26 5.6E-06 37.4 -0.3 31 104-134 29-59 (78)
80 KOG1813 Predicted E3 ubiquitin 84.6 0.31 6.8E-06 45.5 0.2 33 190-222 180-213 (313)
81 PRK09202 nusA transcription el 84.1 0.38 8.3E-06 47.2 0.5 39 105-143 302-340 (470)
82 PF07650 KH_2: KH domain syndr 80.8 0.15 3.2E-06 37.2 -2.8 34 106-139 26-59 (78)
83 KOG2208 Vigilin [Lipid transpo 78.5 1.8 3.9E-05 44.9 3.1 72 104-177 346-417 (753)
84 KOG3273 Predicted RNA-binding 78.3 1.8 3.9E-05 38.9 2.7 53 114-173 178-230 (252)
85 KOG1763 Uncharacterized conser 77.3 0.67 1.5E-05 43.5 -0.3 32 32-64 89-120 (343)
86 KOG1924 RhoA GTPase effector D 77.1 12 0.00025 39.9 8.3 23 81-103 589-614 (1102)
87 COG5252 Uncharacterized conser 75.6 0.7 1.5E-05 42.4 -0.7 35 32-67 82-116 (299)
88 PRK12705 hypothetical protein; 74.4 2.2 4.7E-05 42.5 2.3 39 106-144 199-238 (508)
89 PRK13764 ATPase; Provisional 74.1 1.7 3.7E-05 44.0 1.6 42 104-145 480-521 (602)
90 cd02410 archeal_CPSF_KH The ar 74.0 2 4.4E-05 36.3 1.7 43 100-143 72-114 (145)
91 KOG2333 Uncharacterized conser 73.5 1.3 2.9E-05 44.3 0.6 26 195-220 75-103 (614)
92 KOG1039 Predicted E3 ubiquitin 73.3 1.4 3E-05 41.9 0.7 24 36-60 9-32 (344)
93 cd02409 KH-II KH-II (K homolo 73.2 0.59 1.3E-05 31.9 -1.4 32 107-138 27-58 (68)
94 KOG2202 U2 snRNP splicing fact 72.8 1.8 3.9E-05 39.7 1.3 29 190-218 146-174 (260)
95 COG0195 NusA Transcription elo 71.2 1.6 3.4E-05 38.2 0.5 39 109-147 80-118 (190)
96 PF13083 KH_4: KH domain; PDB: 66.7 0.79 1.7E-05 33.1 -2.0 31 104-134 28-58 (73)
97 KOG2333 Uncharacterized conser 66.0 2.5 5.4E-05 42.4 0.7 27 34-60 75-103 (614)
98 TIGR00436 era GTP-binding prot 61.1 2.1 4.5E-05 37.9 -0.8 28 105-132 221-249 (270)
99 KOG2202 U2 snRNP splicing fact 60.4 4.9 0.00011 37.0 1.5 31 26-57 143-173 (260)
100 COG1855 ATPase (PilT family) [ 59.6 4.7 0.0001 40.5 1.3 40 105-144 486-525 (604)
101 PF10650 zf-C3H1: Putative zin 59.6 5.5 0.00012 23.9 1.1 19 198-217 2-21 (23)
102 cd02414 jag_KH jag_K homology 57.8 2.5 5.5E-05 31.0 -0.7 31 105-135 24-54 (77)
103 cd02413 40S_S3_KH K homology R 57.4 2.3 4.9E-05 32.2 -1.0 33 106-138 31-63 (81)
104 COG1094 Predicted RNA-binding 57.3 10 0.00023 33.5 2.9 62 104-170 7-73 (194)
105 PRK15494 era GTPase Era; Provi 57.3 2.6 5.7E-05 39.0 -0.8 27 106-132 274-301 (339)
106 COG5084 YTH1 Cleavage and poly 56.8 6.6 0.00014 36.5 1.7 31 193-223 101-131 (285)
107 PRK00089 era GTPase Era; Revie 54.4 3.1 6.7E-05 36.9 -0.8 28 105-132 226-254 (292)
108 KOG1492 C3H1-type Zn-finger pr 52.2 7 0.00015 35.9 1.1 28 198-225 235-262 (377)
109 COG0092 RpsC Ribosomal protein 51.4 4.4 9.4E-05 36.8 -0.3 36 106-141 52-92 (233)
110 COG1159 Era GTPase [General fu 51.4 3.6 7.9E-05 38.5 -0.9 26 107-132 231-257 (298)
111 KOG2113 Predicted RNA binding 50.6 25 0.00054 33.8 4.4 64 103-169 24-87 (394)
112 cd02411 archeal_30S_S3_KH K ho 49.7 3.5 7.5E-05 31.0 -1.1 27 107-133 40-66 (85)
113 cd02412 30S_S3_KH K homology R 47.1 4 8.7E-05 32.1 -1.1 29 106-134 62-90 (109)
114 KOG3161 Predicted E3 ubiquitin 45.2 4.1 8.8E-05 42.1 -1.7 41 28-68 196-236 (861)
115 KOG0153 Predicted RNA-binding 44.1 10 0.00022 36.5 0.8 25 195-219 160-184 (377)
116 TIGR03675 arCOG00543 arCOG0054 44.0 12 0.00027 38.0 1.5 75 100-178 89-163 (630)
117 KOG1067 Predicted RNA-binding 41.7 29 0.00063 35.7 3.7 63 106-174 598-660 (760)
118 COG1908 FrhD Coenzyme F420-red 39.3 12 0.00026 31.2 0.5 17 45-62 60-76 (132)
119 PRK12327 nusA transcription el 39.2 9.9 0.00021 36.3 -0.0 34 114-147 245-279 (362)
120 PRK12328 nusA transcription el 38.4 12 0.00026 36.1 0.4 34 114-147 251-285 (374)
121 PRK12329 nusA transcription el 38.2 11 0.00025 37.1 0.2 34 114-147 277-311 (449)
122 KOG1492 C3H1-type Zn-finger pr 37.6 14 0.00031 33.9 0.8 23 36-58 207-229 (377)
123 COG1782 Predicted metal-depend 34.0 21 0.00045 36.3 1.3 74 100-177 95-168 (637)
124 TIGR01953 NusA transcription t 33.4 14 0.0003 35.0 -0.1 34 114-147 243-277 (341)
125 PRK04191 rps3p 30S ribosomal p 32.8 10 0.00022 33.4 -1.0 28 107-134 42-69 (207)
126 KOG1039 Predicted E3 ubiquitin 32.3 23 0.0005 33.8 1.2 25 195-219 248-274 (344)
127 KOG2208 Vigilin [Lipid transpo 31.9 31 0.00066 36.1 2.1 43 100-142 196-238 (753)
128 KOG4791 Uncharacterized conser 25.1 41 0.00089 34.0 1.6 33 37-71 34-67 (667)
129 PRK09202 nusA transcription el 24.7 27 0.00057 34.6 0.2 34 114-147 245-279 (470)
130 PF08352 oligo_HPY: Oligopepti 23.8 37 0.00081 23.5 0.8 13 45-57 49-61 (64)
131 PF10283 zf-CCHH: Zinc-finger 23.1 25 0.00054 21.7 -0.2 10 46-55 2-11 (26)
132 PF14611 SLS: Mitochondrial in 21.3 87 0.0019 26.7 2.7 61 112-177 33-93 (210)
133 PF02749 QRPTase_N: Quinolinat 21.1 75 0.0016 23.7 2.0 51 126-176 35-88 (88)
134 KOG3161 Predicted E3 ubiquitin 20.4 22 0.00049 37.0 -1.2 37 190-226 197-234 (861)
135 KOG4791 Uncharacterized conser 20.3 55 0.0012 33.2 1.4 26 196-222 61-87 (667)
No 1
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.56 E-value=1.7e-15 Score=137.11 Aligned_cols=41 Identities=37% Similarity=0.794 Sum_probs=37.4
Q ss_pred CCCCCCCCCcccccccccCCCCCCC-CCCCccCCCCcccCCC
Q 027188 25 PDGSSPPAVKSRLCNKYNSAEGCKF-GDKCHFAHGEWELGRP 65 (227)
Q Consensus 25 p~~~~~~~yKT~lC~~f~~~g~C~y-G~~C~FAHg~~ELr~p 65 (227)
.....+..|||.||..|..++.|.| |++|+|||+.+|||.+
T Consensus 122 ~~~~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~~ 163 (332)
T KOG1677|consen 122 RGERKPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRLP 163 (332)
T ss_pred ccccCcccccCCcceeeecCccccccCchhhhcCCccccccc
Confidence 4466788999999999999999999 9999999999999964
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=99.38 E-value=1.5e-13 Score=98.37 Aligned_cols=63 Identities=27% Similarity=0.451 Sum_probs=58.9
Q ss_pred ceeeehhhhhhhhhhccCCCcccccccccCCceeecccCC-CCcccccccccCHHHHHHHHHHH
Q 027188 106 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV-DPNLRNIELEGTFDQIKQASAMV 168 (227)
Q Consensus 106 t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es-~~~~r~i~ieGtfeqI~~As~mV 168 (227)
+.+|.||++++|.||||+|.++++|++.||+++.|.+.+. +.++|.|+|+|+++++++|..||
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 4689999999999999999999999999999999998775 78899999999999999999887
No 3
>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=99.10 E-value=2.3e-11 Score=84.93 Aligned_cols=60 Identities=37% Similarity=0.599 Sum_probs=54.9
Q ss_pred ceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHH
Q 027188 106 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMV 168 (227)
Q Consensus 106 t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV 168 (227)
|.+|.||.+++|.||||+|.++++|...||++|.|.++ + +...|.|+|+.++++.|..|+
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 67899999999999999999999999999999999876 3 455999999999999998875
No 4
>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=99.05 E-value=1e-10 Score=82.13 Aligned_cols=61 Identities=30% Similarity=0.461 Sum_probs=55.3
Q ss_pred ceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHH
Q 027188 106 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMV 168 (227)
Q Consensus 106 t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV 168 (227)
+.+|.||.+++|.|||++|.|+++|++.||++|.|.+.+ ..++.|.|.|+.+++..|..++
T Consensus 1 ~~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred CeEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHHHHHHHHHh
Confidence 357899999999999999999999999999999998865 4568899999999999998876
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.01 E-value=2.4e-10 Score=112.10 Aligned_cols=85 Identities=32% Similarity=0.501 Sum_probs=76.2
Q ss_pred ccccCCccceeeehhhhhhhhhhccCCCcccccccccCCceeec-ccCCCCcccccccccCHHHHHHHHHHHHHHHHhcC
Q 027188 98 AASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIR-DHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVG 176 (227)
Q Consensus 98 ~~~fg~s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~-~~es~~~~r~i~ieGtfeqI~~As~mV~elI~~~~ 176 (227)
....|++++.+|.||.+.||.||||+|++||-|...||+||.|+ |++...-||.+.|.|+.++|+.|..+|.++|...+
T Consensus 223 g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~ 302 (600)
T KOG1676|consen 223 GVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAE 302 (600)
T ss_pred CcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHh
Confidence 34567788999999999999999999999999999999999997 77766679999999999999999999999999888
Q ss_pred CCCCCC
Q 027188 177 SGSGHS 182 (227)
Q Consensus 177 ~~~~~~ 182 (227)
...+-.
T Consensus 303 ~~~~~~ 308 (600)
T KOG1676|consen 303 AGAGGG 308 (600)
T ss_pred ccCCCC
Confidence 765433
No 6
>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=99.00 E-value=1.9e-10 Score=79.99 Aligned_cols=63 Identities=32% Similarity=0.521 Sum_probs=58.0
Q ss_pred ceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHH
Q 027188 106 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMV 168 (227)
Q Consensus 106 t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV 168 (227)
+.+|.||..++|.|||++|.++++|.+.||+++.|.+...+.+++.|.|.|+.+++..|..++
T Consensus 1 ~~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred CEEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence 368999999999999999999999999999999999876667789999999999999998876
No 7
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.00 E-value=2.8e-10 Score=111.68 Aligned_cols=75 Identities=21% Similarity=0.408 Sum_probs=68.5
Q ss_pred ceeeehhhhhhhhhhccCCCcccccccccCCceeeccc-C-CCCcccccccccCHHHHHHHHHHHHHHHHhcCCCCC
Q 027188 106 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH-E-VDPNLRNIELEGTFDQIKQASAMVRELIVNVGSGSG 180 (227)
Q Consensus 106 t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~-e-s~~~~r~i~ieGtfeqI~~As~mV~elI~~~~~~~~ 180 (227)
..+|.||+++||+||||||+|||+|..+|||.+.|.-. + .|+++|.|+|.|+..||..|.+||++.+..+..+.+
T Consensus 319 ~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~~~n~~ 395 (600)
T KOG1676|consen 319 QFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDIAPNTP 395 (600)
T ss_pred eEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcccchHHHHHHHHHhcccCCCCC
Confidence 68999999999999999999999999999999999743 3 588999999999999999999999999998766554
No 8
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=98.95 E-value=4e-10 Score=103.78 Aligned_cols=38 Identities=37% Similarity=0.774 Sum_probs=32.7
Q ss_pred CCCCCCCCcc--cccccccCCCCCCC---CCCCccC---CCCcccC
Q 027188 26 DGSSPPAVKS--RLCNKYNSAEGCKF---GDKCHFA---HGEWELG 63 (227)
Q Consensus 26 ~~~~~~~yKT--~lC~~f~~~g~C~y---G~~C~FA---Hg~~ELr 63 (227)
.-++.+.||| .||..|...|.|+| |++|+|| ||..||.
T Consensus 219 ~e~n~~L~kt~~~lc~~ft~kg~~p~~~sG~~~q~a~~~HGlN~l~ 264 (351)
T COG5063 219 QEQNKPLYKTNPELCESFTRKGTCPYWISGVKCQFACRGHGLNELK 264 (351)
T ss_pred hhccchhhcCCHHHhhccCcCCCCcccccccccccccccccccccc
Confidence 3456789999 99999999999999 9999999 9855544
No 9
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=98.88 E-value=1.8e-08 Score=92.25 Aligned_cols=71 Identities=34% Similarity=0.470 Sum_probs=65.1
Q ss_pred CccceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHHHHHHH
Q 027188 103 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV 173 (227)
Q Consensus 103 ~s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV~elI~ 173 (227)
--+|+.++|+.++-|.||||||..||||...+||.|.|.+.-.+..+|+|.|+|+.+||++|+.++++-+.
T Consensus 313 PitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vk 383 (390)
T KOG2192|consen 313 PITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVK 383 (390)
T ss_pred ceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHH
Confidence 46899999999999999999999999999999999999986667778999999999999999998877554
No 10
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.86 E-value=8.6e-10 Score=78.74 Aligned_cols=57 Identities=23% Similarity=0.380 Sum_probs=51.9
Q ss_pred ceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccC-HHHHHHHHHHH
Q 027188 106 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGT-FDQIKQASAMV 168 (227)
Q Consensus 106 t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGt-feqI~~As~mV 168 (227)
+..|.||.+++|.||||||.++++|+..||++|.|.+. +.|.|+|+ .+.++.|.+||
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~------g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDD------GTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCCC------CEEEEEeCCHHHHHHHHHHh
Confidence 56789999999999999999999999999999999872 56999998 99999998876
No 11
>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=98.77 E-value=1.1e-09 Score=66.95 Aligned_cols=26 Identities=62% Similarity=1.385 Sum_probs=21.2
Q ss_pred cccccccccc-cccCCCCCCCcccCCc
Q 027188 194 FKTKLCENFA-KGSCTFGDRCHFAHGS 219 (227)
Q Consensus 194 ~KTklC~~f~-~G~C~~G~~C~FAHg~ 219 (227)
|||++|++|. .|.|+||++|+|+|++
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 5999999999999984
No 12
>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=98.74 E-value=1.8e-09 Score=66.08 Aligned_cols=27 Identities=52% Similarity=1.113 Sum_probs=22.7
Q ss_pred CcccccccccCCCCCCCCCCCccCCCC
Q 027188 33 VKSRLCNKYNSAEGCKFGDKCHFAHGE 59 (227)
Q Consensus 33 yKT~lC~~f~~~g~C~yG~~C~FAHg~ 59 (227)
|||++|++|..+|.|+||++|.|+|++
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 13
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=98.65 E-value=3.9e-08 Score=94.33 Aligned_cols=75 Identities=28% Similarity=0.315 Sum_probs=67.2
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceeecccC-CCCcccccccccCHHHHHHHHHHHHHHHHhcCCCC
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE-VDPNLRNIELEGTFDQIKQASAMVRELIVNVGSGS 179 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~e-s~~~~r~i~ieGtfeqI~~As~mV~elI~~~~~~~ 179 (227)
-+.+|.||++.+|+||||-|.+||||.|.+||.|+|--.| .|..+|.|.|+|++++.-.|+..|...|..-+...
T Consensus 411 e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEenf~~ 486 (584)
T KOG2193|consen 411 EQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFFL 486 (584)
T ss_pred hheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhccCC
Confidence 3568899999999999999999999999999999998766 58889999999999999999999988887666544
No 14
>smart00322 KH K homology RNA-binding domain.
Probab=98.64 E-value=2.3e-08 Score=68.25 Aligned_cols=66 Identities=30% Similarity=0.496 Sum_probs=58.7
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHHHHHH
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELI 172 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV~elI 172 (227)
.+.+|.|+....|.|||++|.++++|...||+++.+..... +.+.|.|.|+.++++.|..++.+.+
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 46789999999999999999999999999999999976543 5678999999999999999988764
No 15
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=98.51 E-value=6.2e-08 Score=90.47 Aligned_cols=69 Identities=28% Similarity=0.356 Sum_probs=63.0
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceeec-ccCC--CCcccccccccCHHHHHHHHHHHHHHHH
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIR-DHEV--DPNLRNIELEGTFDQIKQASAMVRELIV 173 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~-~~es--~~~~r~i~ieGtfeqI~~As~mV~elI~ 173 (227)
...||.||++-+|.||||||.+||+|.+++|+-|+|+ +.+. +..+|.|.+.|+|++..+|..||.++|.
T Consensus 132 kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~ 203 (402)
T KOG2191|consen 132 KQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQ 203 (402)
T ss_pred ceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhh
Confidence 3489999999999999999999999999999999999 5554 5557899999999999999999999887
No 16
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.48 E-value=6.8e-08 Score=87.66 Aligned_cols=41 Identities=37% Similarity=0.778 Sum_probs=36.8
Q ss_pred CCCCCCCCCcccccccccCCCCCCCCCCCccCCCCcccCCC
Q 027188 25 PDGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRP 65 (227)
Q Consensus 25 p~~~~~~~yKT~lC~~f~~~g~C~yG~~C~FAHg~~ELr~p 65 (227)
.....+.+|||++|.+|..+|.|+||.+|+|+|+..|++.-
T Consensus 167 ~~~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~~~~~~ 207 (332)
T KOG1677|consen 167 NQVGNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEPEDRAS 207 (332)
T ss_pred hhhcCCCCCCCcCCCccccCCCCCCCCcCeecCCCcccccc
Confidence 35567889999999999999999999999999999988853
No 17
>PF13014 KH_3: KH domain
Probab=98.48 E-value=3.1e-08 Score=65.67 Aligned_cols=42 Identities=40% Similarity=0.590 Sum_probs=37.3
Q ss_pred hhhhhhccCCCcccccccccCCceeecc-cCCCCccccccccc
Q 027188 115 LAGAIIGKNGVNSKQICRLTGAKLSIRD-HEVDPNLRNIELEG 156 (227)
Q Consensus 115 ~~G~IIGKgG~nikqI~~~TGaklsI~~-~es~~~~r~i~ieG 156 (227)
++|+||||+|.+|++|+..||++|.|.+ ...+.++|.|+|+|
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 4789999999999999999999999998 55677788898876
No 18
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=98.46 E-value=1.3e-07 Score=91.89 Aligned_cols=72 Identities=24% Similarity=0.387 Sum_probs=64.3
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceeecccC-CCCcccccccccCHHHHHHHHHHHHHHHHhcC
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE-VDPNLRNIELEGTFDQIKQASAMVRELIVNVG 176 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~e-s~~~~r~i~ieGtfeqI~~As~mV~elI~~~~ 176 (227)
.+.+|-|+++++|.||||+|..||+|++.|||+|.|+... ....+|.|.|.|.++.|+.|...|-..+....
T Consensus 138 v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~ 210 (485)
T KOG2190|consen 138 VTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENP 210 (485)
T ss_pred eEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcC
Confidence 4699999999999999999999999999999999999763 35558999999999999999998888777654
No 19
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=98.44 E-value=6.3e-07 Score=82.96 Aligned_cols=45 Identities=18% Similarity=0.236 Sum_probs=36.0
Q ss_pred CCCCCCC-CCCcccccccccCCCCCCCCCCCccCCCCcccCCCCCC
Q 027188 24 FPDGSSP-PAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRPTVP 68 (227)
Q Consensus 24 ~p~~~~~-~~yKT~lC~~f~~~g~C~yG~~C~FAHg~~ELr~p~~~ 68 (227)
-++...+ ..|||.+|..-..-..|.|+++|.|||.-.+++....+
T Consensus 103 ~~~a~~p~g~~kt~~l~ss~~~~~~~~p~~n~fahs~~issl~~~~ 148 (351)
T COG5063 103 GSNANKPYGLYKTEMLRSSTEIPYCRYPDKNPFAHSKAISSLAQTH 148 (351)
T ss_pred CCCccCccccccchhhhccccccccccCCCCcCCCccccccccccC
Confidence 4444444 78999999998888999999999999988887764444
No 20
>smart00356 ZnF_C3H1 zinc finger.
Probab=98.40 E-value=1.4e-07 Score=56.17 Aligned_cols=27 Identities=52% Similarity=1.195 Sum_probs=24.6
Q ss_pred ccccccccccccccCCCCCCCcccCCc
Q 027188 193 NFKTKLCENFAKGSCTFGDRCHFAHGS 219 (227)
Q Consensus 193 ~~KTklC~~f~~G~C~~G~~C~FAHg~ 219 (227)
.+|+.+|++|++|.|.+|++|+|+|..
T Consensus 1 ~~k~~~C~~~~~g~C~~g~~C~~~H~~ 27 (27)
T smart00356 1 KYKTELCKFFKRGYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCCCcCcCccCCCCCCCCCcCCCCcC
Confidence 378999999999999999999999973
No 21
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=98.30 E-value=4.4e-07 Score=87.26 Aligned_cols=71 Identities=23% Similarity=0.389 Sum_probs=62.5
Q ss_pred ceeeehhhhhhhhhhccCCCcccccccccCCceeecccC-CCCccc-ccccccCHHHHHHHHHHHHHHHHhcC
Q 027188 106 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE-VDPNLR-NIELEGTFDQIKQASAMVRELIVNVG 176 (227)
Q Consensus 106 t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~e-s~~~~r-~i~ieGtfeqI~~As~mV~elI~~~~ 176 (227)
-+.|+||.+.+|.||||||.|.+|+.++|+|.+.|-..+ .|.|+. .|+|.|+|...+.|+..+++++..+-
T Consensus 494 ethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~iv~qvk 566 (584)
T KOG2193|consen 494 ETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHIVNQVK 566 (584)
T ss_pred eeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHHHHHHH
Confidence 467899999999999999999999999999999996444 577766 78999999999999999999887554
No 22
>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=98.23 E-value=6.3e-07 Score=75.94 Aligned_cols=60 Identities=25% Similarity=0.381 Sum_probs=53.2
Q ss_pred eehhhhhhhhhhccCCCcccccccccCCceeecccCCCCccccccc---ccCHHHHHHHHHHHHHHHH
Q 027188 109 ISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIEL---EGTFDQIKQASAMVRELIV 173 (227)
Q Consensus 109 isV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~i---eGtfeqI~~As~mV~elI~ 173 (227)
|.||.+.+|+|||+||.+|++|...||+++.|.+.+ ..|.| .++++++..|..||..+..
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~-----g~V~I~~~t~d~~~i~kA~~~I~~i~~ 64 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSET-----GEVKIEEEDEDPLAVMKAREVVKAIGR 64 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcCC-----ceEEEecCCCCHHHHHHHHHHHHHHHc
Confidence 679999999999999999999999999999998742 45666 8999999999999988655
No 23
>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=98.19 E-value=6e-07 Score=72.62 Aligned_cols=63 Identities=25% Similarity=0.339 Sum_probs=51.0
Q ss_pred hhhhhhhccCCCcccccccccCCceeecccCCCCcc-----------------cccccccC---HHHHHHHHHHHHHHHH
Q 027188 114 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNL-----------------RNIELEGT---FDQIKQASAMVRELIV 173 (227)
Q Consensus 114 s~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~-----------------r~i~ieGt---feqI~~As~mV~elI~ 173 (227)
..+|.|||.+|.++|+|+..||++|.|++.+|.-.. -.|.|+++ .+.++.|..+|.+++.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 468999999999999999999999999987542211 24567774 5999999999999887
Q ss_pred hcC
Q 027188 174 NVG 176 (227)
Q Consensus 174 ~~~ 176 (227)
.+.
T Consensus 95 ~~~ 97 (120)
T cd02395 95 PAI 97 (120)
T ss_pred cCC
Confidence 443
No 24
>smart00356 ZnF_C3H1 zinc finger.
Probab=98.19 E-value=1.1e-06 Score=52.25 Aligned_cols=27 Identities=37% Similarity=0.858 Sum_probs=24.4
Q ss_pred CCcccccccccCCCCCCCCCCCccCCCC
Q 027188 32 AVKSRLCNKYNSAEGCKFGDKCHFAHGE 59 (227)
Q Consensus 32 ~yKT~lC~~f~~~g~C~yG~~C~FAHg~ 59 (227)
.+|+.+|+.| .+|.|++|+.|.|+|..
T Consensus 1 ~~k~~~C~~~-~~g~C~~g~~C~~~H~~ 27 (27)
T smart00356 1 KYKTELCKFF-KRGYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCCCcCcCc-cCCCCCCCCCcCCCCcC
Confidence 4799999999 78999999999999963
No 25
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=98.17 E-value=1.2e-06 Score=82.14 Aligned_cols=72 Identities=24% Similarity=0.345 Sum_probs=64.2
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceeeccc-C--CCCcccccccccCHHHHHHHHHHHHHHHHhcC
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH-E--VDPNLRNIELEGTFDQIKQASAMVRELIVNVG 176 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~-e--s~~~~r~i~ieGtfeqI~~As~mV~elI~~~~ 176 (227)
...||.|+...+|.||||||+.|.|+...||+.|+|+.+ + .+..+|++-|.|+.+.|...-.+|.++|+..-
T Consensus 39 y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p 113 (402)
T KOG2191|consen 39 YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKP 113 (402)
T ss_pred eEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhH
Confidence 678999999999999999999999999999999999854 3 57789999999999999988888877777543
No 26
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.11 E-value=2.1e-06 Score=73.36 Aligned_cols=64 Identities=23% Similarity=0.302 Sum_probs=56.7
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCccccccc----ccCHHHHHHHHHHHHHHHH
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIEL----EGTFDQIKQASAMVRELIV 173 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~i----eGtfeqI~~As~mV~elI~ 173 (227)
.+..|.||.+.+|.|||++|.+||.|...||++|.|.+.+ ..|.| .++++++..|..||+.+..
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~-----g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSET-----GEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCC-----CeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 3568999999999999999999999999999999998753 46666 4899999999999998765
No 27
>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=98.05 E-value=2.2e-06 Score=72.58 Aligned_cols=52 Identities=29% Similarity=0.526 Sum_probs=48.6
Q ss_pred hhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHHHHHH
Q 027188 114 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELI 172 (227)
Q Consensus 114 s~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV~elI 172 (227)
..+|.|||++|.+++.|+.+||++|.|.+ +.|.|.|++++++.|..+|.++|
T Consensus 98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A~~~i~~li 149 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEELTGVSISVYG-------KTVGIIGDPEQVQIAREAIEMLI 149 (172)
T ss_pred HHHhhhcCCCcHHHHHHHHHHCCeEEEcC-------CEEEEECCHHHHHHHHHHHHHHH
Confidence 37999999999999999999999999976 56999999999999999999988
No 28
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.84 E-value=7.6e-06 Score=69.88 Aligned_cols=52 Identities=29% Similarity=0.489 Sum_probs=47.8
Q ss_pred hhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHHHHHHH
Q 027188 115 LAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV 173 (227)
Q Consensus 115 ~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV~elI~ 173 (227)
..|.||||+|.+++.|..+||++|.|.++ .|.|.|++++++.|...|..++.
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~-------~v~i~G~~~~~~~A~~~I~~li~ 156 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGK-------TVAIIGDPEQVEIAREAIEMLIE 156 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCC-------EEEEEeCHHHHHHHHHHHHHHHc
Confidence 68999999999999999999999999763 38899999999999999998883
No 29
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.79 E-value=9.4e-06 Score=79.16 Aligned_cols=71 Identities=25% Similarity=0.392 Sum_probs=62.7
Q ss_pred CCccceeeehhhhhhhhhhccCCCcccccccccCCceeecccCC--CCcccccccccCHHHHHHHHHHHHHHH
Q 027188 102 GASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV--DPNLRNIELEGTFDQIKQASAMVRELI 172 (227)
Q Consensus 102 g~s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es--~~~~r~i~ieGtfeqI~~As~mV~elI 172 (227)
....++++.|+..++|.||||+|.+|.+|+++|||+|+|...+. ..+++.+.|.|.+++..-++..+...+
T Consensus 335 ~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~ 407 (485)
T KOG2190|consen 335 TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARL 407 (485)
T ss_pred cceeeeeeccCccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhccccc
Confidence 44578999999999999999999999999999999999998775 778899999999999988877665443
No 30
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=97.67 E-value=2.4e-05 Score=76.72 Aligned_cols=34 Identities=32% Similarity=0.684 Sum_probs=30.0
Q ss_pred CCCCccccccccccccccCCCCCCCcccCCccccccC
Q 027188 189 SQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKS 225 (227)
Q Consensus 189 ~~~~~~KTklC~~f~~G~C~~G~~C~FAHg~~ELr~~ 225 (227)
.++..|||++|+.- |.|+. --|.|||..+|||..
T Consensus 264 LHPa~YRT~~CkDg--~~C~R-rvCfFAH~~eqLR~l 297 (528)
T KOG1595|consen 264 LHPARYRTRKCKDG--GYCPR-RVCFFAHSPEQLRPL 297 (528)
T ss_pred cCHHHhccccccCC--CCCcc-ceEeeecChHHhccc
Confidence 35578999999987 89999 899999999999864
No 31
>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=97.09 E-value=0.00034 Score=71.31 Aligned_cols=65 Identities=25% Similarity=0.317 Sum_probs=55.6
Q ss_pred ccceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCccccccccc-CHHHHHHHHHHHHHHHHh
Q 027188 104 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIVN 174 (227)
Q Consensus 104 s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieG-tfeqI~~As~mV~elI~~ 174 (227)
.-..+|.||.++.|.|||.||.+||+|+..||++|.|.|.+ .|.|.+ +.++++.|..||..++..
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 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDDG------TVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecCc------EEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 45678899999999999999999999999999999998843 455544 788999999999887764
No 32
>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=97.05 E-value=0.00036 Score=70.52 Aligned_cols=63 Identities=22% Similarity=0.358 Sum_probs=52.5
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCccccccc-ccCHHHHHHHHHHHHHHHH
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIEL-EGTFDQIKQASAMVRELIV 173 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~i-eGtfeqI~~As~mV~elI~ 173 (227)
-..+|.||.++.|.|||+||.+||+|...||++|.|.|.+ .|.+ ..+-+.+..|..++..+..
T Consensus 551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG------~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDDG------TVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecCe------EEEEEECcHHHHHHHHHHHHhhhc
Confidence 4677899999999999999999999999999999998743 3344 3467788889888887754
No 33
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=96.68 E-value=0.0016 Score=64.28 Aligned_cols=29 Identities=45% Similarity=0.988 Sum_probs=24.6
Q ss_pred ccccccccccccccCCCCCCCcccCCccc
Q 027188 193 NFKTKLCENFAKGSCTFGDRCHFAHGSEE 221 (227)
Q Consensus 193 ~~KTklC~~f~~G~C~~G~~C~FAHg~~E 221 (227)
.|.-..|..|.+|.|.-||.|.||||.-|
T Consensus 233 hYs~tpCPefrkG~C~rGD~CEyaHgvfE 261 (528)
T KOG1595|consen 233 HYSSTPCPEFRKGSCERGDSCEYAHGVFE 261 (528)
T ss_pred cccCccCcccccCCCCCCCccccccceeh
Confidence 34455699999999999999999999766
No 34
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.57 E-value=0.0015 Score=68.12 Aligned_cols=65 Identities=18% Similarity=0.385 Sum_probs=55.5
Q ss_pred CccceeeehhhhhhhhhhccCCCcccccccccCCc-eeecccCCCCcccccccc-cCHHHHHHHHHHHHHHHH
Q 027188 103 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAK-LSIRDHEVDPNLRNIELE-GTFDQIKQASAMVRELIV 173 (227)
Q Consensus 103 ~s~t~kisV~as~~G~IIGKgG~nikqI~~~TGak-lsI~~~es~~~~r~i~ie-GtfeqI~~As~mV~elI~ 173 (227)
|.-...|.|+.+++|.|||.||.+||+|...||++ |.|.|.+ .|.|. -+.+.++.|..||.+++.
T Consensus 683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~ddg------~V~I~a~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDDG------TVKITAKDLSSLEKSKAIISSLTM 749 (891)
T ss_pred CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCCe------eEEEEeCCHHHHHHHHHHHHHHhc
Confidence 34577899999999999999999999999999999 9998853 34444 478899999999999876
No 35
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=96.47 E-value=0.001 Score=64.11 Aligned_cols=25 Identities=44% Similarity=1.127 Sum_probs=22.5
Q ss_pred cccccccccccCCCCCCCcccCCcc
Q 027188 196 TKLCENFAKGSCTFGDRCHFAHGSE 220 (227)
Q Consensus 196 TklC~~f~~G~C~~G~~C~FAHg~~ 220 (227)
-+.|.||..|.|+|+++|+|.||..
T Consensus 140 MkpC~ffLeg~CRF~enCRfSHG~~ 164 (486)
T KOG2185|consen 140 MKPCKFFLEGRCRFGENCRFSHGLD 164 (486)
T ss_pred hccchHhhccccccCcccccccCcc
Confidence 3579999999999999999999863
No 36
>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=96.35 E-value=0.00075 Score=48.12 Aligned_cols=36 Identities=31% Similarity=0.519 Sum_probs=33.2
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceee
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI 140 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI 140 (227)
..+++.|+....|.+|||+|.|+++++.++|.++.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 678999999999999999999999999999987755
No 37
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=96.12 E-value=0.0022 Score=59.44 Aligned_cols=70 Identities=24% Similarity=0.372 Sum_probs=54.4
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceeecccC-CCCcccccccccCHHHHHHHHHHHHHHHHh
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE-VDPNLRNIELEGTFDQIKQASAMVRELIVN 174 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~e-s~~~~r~i~ieGtfeqI~~As~mV~elI~~ 174 (227)
-..+|.|..|++|+|||+.|.+||++++.-.|.|+|...= ....+|.+.+.|.+.-+-.-...|..+|..
T Consensus 123 ce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e 193 (390)
T KOG2192|consen 123 CELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISE 193 (390)
T ss_pred hhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhc
Confidence 3567889999999999999999999999999999998532 344578888888776665555555555543
No 38
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.06 E-value=0.0046 Score=60.85 Aligned_cols=62 Identities=34% Similarity=0.463 Sum_probs=48.9
Q ss_pred hhhhhhhhccCCCcccccccccCCceeecccCC---------CCccc--------ccccccCHHHHHHHHHHHHHHHHh
Q 027188 113 AKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV---------DPNLR--------NIELEGTFDQIKQASAMVRELIVN 174 (227)
Q Consensus 113 as~~G~IIGKgG~nikqI~~~TGaklsI~~~es---------~~~~r--------~i~ieGtfeqI~~As~mV~elI~~ 174 (227)
-+.+|+|||-.|.+-|+|.+.|||||.|+-.+| |.+.+ -....-|.|.|+.|.++|+.+|..
T Consensus 152 ~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 152 INFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred cceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence 468999999999999999999999999997442 12211 112234889999999999998875
No 39
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=95.90 E-value=0.0047 Score=35.06 Aligned_cols=19 Identities=42% Similarity=0.852 Sum_probs=16.4
Q ss_pred cccccccccCCCCCCCcccCC
Q 027188 198 LCENFAKGSCTFGDRCHFAHG 218 (227)
Q Consensus 198 lC~~f~~G~C~~G~~C~FAHg 218 (227)
+|++|.. |+++++|.|+|.
T Consensus 1 ~Ck~~~~--C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN--CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC--CCCCCcCccCCc
Confidence 4887766 999999999994
No 40
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=95.82 E-value=0.005 Score=54.03 Aligned_cols=52 Identities=33% Similarity=0.554 Sum_probs=46.6
Q ss_pred hhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHHHHHHH
Q 027188 115 LAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV 173 (227)
Q Consensus 115 ~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV~elI~ 173 (227)
.-|.|||++|.+-+.|..+||+.|++.++. |.|-|+|++++.|..-|.-++.
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~t-------VaiiG~~~~v~iAr~AVemli~ 163 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGKT-------VAIIGGFEQVEIAREAVEMLIN 163 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCcE-------EEEecChhhhHHHHHHHHHHHc
Confidence 468999999999999999999999999854 8899999999999888877664
No 41
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=95.63 E-value=0.017 Score=56.68 Aligned_cols=68 Identities=21% Similarity=0.251 Sum_probs=54.0
Q ss_pred ceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHHHHHHHhcC
Q 027188 106 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVG 176 (227)
Q Consensus 106 t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV~elI~~~~ 176 (227)
..-++|-..+||.|||+||.+||.|+..|-.+|.|..-+. +-.|+|.|.-+-..+|.+.+..++....
T Consensus 48 plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~---e~kv~ifg~~~m~~kaka~id~~~~k~e 115 (629)
T KOG0336|consen 48 PLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDL---EVKVTIFGINHMRKKAKASIDRGQDKDE 115 (629)
T ss_pred chhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCc---eeEEEEechHHHHHHHHhhHhhhhhhhh
Confidence 3455678899999999999999999999999999987542 3467788888777788877766665443
No 42
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=95.46 E-value=0.0076 Score=56.54 Aligned_cols=26 Identities=27% Similarity=0.745 Sum_probs=22.8
Q ss_pred cccccccccCCCCCCCcccCCcccccc
Q 027188 198 LCENFAKGSCTFGDRCHFAHGSEELRK 224 (227)
Q Consensus 198 lC~~f~~G~C~~G~~C~FAHg~~ELr~ 224 (227)
.|..|.+|+|.. ++|+|+|...+|+.
T Consensus 73 aC~Ds~kgrCsR-~nCkylHpp~hlkd 98 (331)
T KOG2494|consen 73 ACFDSQKGRCSR-ENCKYLHPPQHLKD 98 (331)
T ss_pred EEeccccCccCc-ccceecCCChhhhh
Confidence 499999999998 67999999988874
No 43
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.37 E-value=0.01 Score=60.35 Aligned_cols=64 Identities=20% Similarity=0.335 Sum_probs=52.4
Q ss_pred ccceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCccccccccc-CHHHHHHHHHHHHHHHH
Q 027188 104 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIV 173 (227)
Q Consensus 104 s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieG-tfeqI~~As~mV~elI~ 173 (227)
.-...+.||.+..+.|||.||.+||+|...||+++.|.|.+ .|.+.+ +.+.++.|..|+..+..
T Consensus 553 p~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~G------~v~i~~~~~~~~~~a~~~I~~~~~ 617 (693)
T PRK11824 553 PRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDDG------TVKIAATDGEAAEAAKERIEGITA 617 (693)
T ss_pred chheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCCc------eEEEEcccHHHHHHHHHHHHHhcc
Confidence 34567788999999999999999999999999999997743 344443 77888899999988764
No 44
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=94.90 E-value=0.022 Score=53.51 Aligned_cols=31 Identities=29% Similarity=0.600 Sum_probs=26.9
Q ss_pred CCCcccccccccCCCCCCCCCCCccCCCCcccC
Q 027188 31 PAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELG 63 (227)
Q Consensus 31 ~~yKT~lC~~f~~~g~C~yG~~C~FAHg~~ELr 63 (227)
..+++..|++|.. |.|..||.|.|+|-. +|.
T Consensus 73 ~~~~~~vcK~~l~-glC~kgD~C~Flhe~-~~~ 103 (325)
T KOG1040|consen 73 DSRGKVVCKHWLR-GLCKKGDQCEFLHEY-DLT 103 (325)
T ss_pred ccCCceeehhhhh-hhhhccCcCcchhhh-hhc
Confidence 3899999999997 899999999999955 554
No 45
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=94.41 E-value=0.013 Score=54.97 Aligned_cols=31 Identities=29% Similarity=0.764 Sum_probs=27.8
Q ss_pred CccccccccccccccCCCCCCCcccCCccccc
Q 027188 192 NNFKTKLCENFAKGSCTFGDRCHFAHGSEELR 223 (227)
Q Consensus 192 ~~~KTklC~~f~~G~C~~G~~C~FAHg~~ELr 223 (227)
.+.++.+|++|+.|.|..||.|-|+|-. +|.
T Consensus 73 ~~~~~~vcK~~l~glC~kgD~C~Flhe~-~~~ 103 (325)
T KOG1040|consen 73 DSRGKVVCKHWLRGLCKKGDQCEFLHEY-DLT 103 (325)
T ss_pred ccCCceeehhhhhhhhhccCcCcchhhh-hhc
Confidence 3899999999999999999999999976 444
No 46
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=94.18 E-value=0.031 Score=31.65 Aligned_cols=18 Identities=39% Similarity=0.875 Sum_probs=14.9
Q ss_pred ccccccCCCCCCCCCCCccCC
Q 027188 37 LCNKYNSAEGCKFGDKCHFAH 57 (227)
Q Consensus 37 lC~~f~~~g~C~yG~~C~FAH 57 (227)
+|++|. .|.+++.|.|+|
T Consensus 1 ~Ck~~~---~C~~~~~C~f~H 18 (19)
T PF14608_consen 1 PCKFGP---NCTNGDNCPFSH 18 (19)
T ss_pred CCcCcC---CCCCCCcCccCC
Confidence 488553 499999999999
No 47
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.07 E-value=0.055 Score=48.04 Aligned_cols=65 Identities=17% Similarity=0.278 Sum_probs=49.3
Q ss_pred ccCC-ccceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCccccccccc-CHHHHHHHHHHHHH
Q 027188 100 SFGA-SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRE 170 (227)
Q Consensus 100 ~fg~-s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieG-tfeqI~~As~mV~e 170 (227)
.||. ..=..+.|+.++++.+||++|.+++.|...|++++.|-+++ .|.|.+ +.+.+..|.++|+.
T Consensus 139 ~lG~L~~G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~NG------~VwI~~~~~~~~~~a~~~I~~ 205 (235)
T PRK04163 139 GLGKIEGGTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQNG------RIWIKGPDEEDEEIAIEAIKK 205 (235)
T ss_pred CCCccCCCEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCCc------EEEEeeCCHHHHHHHHHHHHH
Confidence 4554 23456889999999999999999999999999999997754 455554 44466666666654
No 48
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=94.00 E-value=0.023 Score=55.09 Aligned_cols=32 Identities=31% Similarity=0.775 Sum_probs=26.0
Q ss_pred cccccccCCCCCCCCCCCccCCCC----cccCCCCCC
Q 027188 36 RLCNKYNSAEGCKFGDKCHFAHGE----WELGRPTVP 68 (227)
Q Consensus 36 ~lC~~f~~~g~C~yG~~C~FAHg~----~ELr~p~~~ 68 (227)
++|++|.. +.|+|+++|+|.||. .+||.=+.|
T Consensus 141 kpC~ffLe-g~CRF~enCRfSHG~~V~lsslr~yq~p 176 (486)
T KOG2185|consen 141 KPCKFFLE-GRCRFGENCRFSHGLDVPLSSLRNYQQP 176 (486)
T ss_pred ccchHhhc-cccccCcccccccCcccchhhcccCCCc
Confidence 68999886 899999999999985 567754444
No 49
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=93.95 E-value=0.062 Score=54.79 Aligned_cols=66 Identities=24% Similarity=0.363 Sum_probs=53.5
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCccccccccc-CHHHHHHHHHHHHHHHHhcC
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIVNVG 176 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieG-tfeqI~~As~mV~elI~~~~ 176 (227)
-...|.|+..+.+-|||+||..|++|...||+++.|.|.+ .|.|.+ +-+.++.|..+++++.....
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~IdieddG------tv~i~~s~~~~~~~ak~~I~~i~~e~e 618 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDG------TVKIAASDGESAKKAKERIEAITREVE 618 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCCC------cEEEEecchHHHHHHHHHHHHHHhhcc
Confidence 4567788999999999999999999999999999999654 344544 44788889888888775544
No 50
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=93.56 E-value=0.018 Score=53.70 Aligned_cols=34 Identities=38% Similarity=0.766 Sum_probs=30.0
Q ss_pred CCccccccccccccccCCCCCCCcccCCcccccc
Q 027188 191 SNNFKTKLCENFAKGSCTFGDRCHFAHGSEELRK 224 (227)
Q Consensus 191 ~~~~KTklC~~f~~G~C~~G~~C~FAHg~~ELr~ 224 (227)
..--|+.+|-+|..|.|.-|+.|.|+|++..-|+
T Consensus 87 gvDPKSvvCafFk~g~C~KG~kCKFsHdl~~~~k 120 (343)
T KOG1763|consen 87 GVDPKSVVCAFFKQGTCTKGDKCKFSHDLAVERK 120 (343)
T ss_pred CCCchHHHHHHHhccCCCCCCcccccchHHHhhh
Confidence 3566999999999999999999999999877664
No 51
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=93.47 E-value=0.036 Score=49.86 Aligned_cols=43 Identities=33% Similarity=0.495 Sum_probs=35.9
Q ss_pred Cccceeeehh------hhhhhhhhccCCCcccccccccCCceeecccCC
Q 027188 103 ASATAKISID------AKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV 145 (227)
Q Consensus 103 ~s~t~kisV~------as~~G~IIGKgG~nikqI~~~TGaklsI~~~es 145 (227)
+-.+-||.|| -..+|+|||-.|.+.||+.+.|+|||.|+-..+
T Consensus 146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gs 194 (269)
T COG5176 146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGS 194 (269)
T ss_pred ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccc
Confidence 3455677665 467999999999999999999999999997664
No 52
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=93.02 E-value=0.023 Score=51.82 Aligned_cols=34 Identities=47% Similarity=0.849 Sum_probs=30.6
Q ss_pred CccccccccccccccCCCCCCCcccCCccccccC
Q 027188 192 NNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKS 225 (227)
Q Consensus 192 ~~~KTklC~~f~~G~C~~G~~C~FAHg~~ELr~~ 225 (227)
..-||..|-.|..+.|.-|+.|.|+|+.+|-|+.
T Consensus 81 vdpK~~vcalF~~~~c~kg~~ckF~h~~ee~r~~ 114 (299)
T COG5252 81 VDPKTVVCALFLNKTCAKGDACKFAHGKEEARKT 114 (299)
T ss_pred cCchhHHHHHhccCccccCchhhhhcchHHHhhh
Confidence 4569999999999999999999999999988753
No 53
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=92.77 E-value=0.059 Score=39.70 Aligned_cols=40 Identities=30% Similarity=0.454 Sum_probs=29.8
Q ss_pred eeeehhhhh-----hhhhhccCCCccccccccc-CCceeecccCCC
Q 027188 107 AKISIDAKL-----AGAIIGKNGVNSKQICRLT-GAKLSIRDHEVD 146 (227)
Q Consensus 107 ~kisV~as~-----~G~IIGKgG~nikqI~~~T-GaklsI~~~es~ 146 (227)
+|+-|.... +|++||++|..+|.|++.. |.++.|.+-.+|
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~s~d 50 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEYSDD 50 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE--SS
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEcCCC
Confidence 455555555 8999999999999999999 999999876545
No 54
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=92.67 E-value=0.043 Score=49.00 Aligned_cols=31 Identities=26% Similarity=0.927 Sum_probs=26.1
Q ss_pred ccccccccccc-cccCCCCCCCcccCCccccc
Q 027188 193 NFKTKLCENFA-KGSCTFGDRCHFAHGSEELR 223 (227)
Q Consensus 193 ~~KTklC~~f~-~G~C~~G~~C~FAHg~~ELr 223 (227)
-|-...|+.|. +|+|-|||.|.|.|.-++.+
T Consensus 138 D~qpdVCKdyk~TGYCGYGDsCKflH~R~D~K 169 (259)
T COG5152 138 DTQPDVCKDYKETGYCGYGDSCKFLHDRSDFK 169 (259)
T ss_pred ecCcccccchhhcccccCCchhhhhhhhhhhh
Confidence 45567899998 89999999999999877543
No 55
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=92.57 E-value=0.053 Score=44.92 Aligned_cols=42 Identities=21% Similarity=0.281 Sum_probs=37.3
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCC
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVD 146 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~ 146 (227)
....+.|+...+|+.||++|.+|+-|+++.|.++.|.+...|
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d 73 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD 73 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC
Confidence 567788888999999999999999999999999999887654
No 56
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=91.86 E-value=0.045 Score=51.44 Aligned_cols=25 Identities=40% Similarity=1.042 Sum_probs=22.5
Q ss_pred cccccccccccCCCCCC-CcccCCcc
Q 027188 196 TKLCENFAKGSCTFGDR-CHFAHGSE 220 (227)
Q Consensus 196 TklC~~f~~G~C~~G~~-C~FAHg~~ 220 (227)
-++|+.|++|.|..||+ |+|||-..
T Consensus 37 ~eVCReF~rn~C~R~d~~CkfaHP~~ 62 (331)
T KOG2494|consen 37 LEVCREFLRNTCSRGDRECKFAHPPK 62 (331)
T ss_pred HHHHHHHHhccccCCCccccccCCCC
Confidence 46899999999999999 99999654
No 57
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=91.49 E-value=0.091 Score=50.27 Aligned_cols=44 Identities=23% Similarity=0.360 Sum_probs=39.2
Q ss_pred ccceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCC
Q 027188 104 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDP 147 (227)
Q Consensus 104 s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~ 147 (227)
.-.+.+.|+...-++.|||+|.|++...++||.+|-|..-++..
T Consensus 307 ~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~~~ 350 (374)
T PRK12328 307 EKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGSKE 350 (374)
T ss_pred CcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCCCc
Confidence 45788999999999999999999999999999999998766543
No 58
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=91.12 E-value=0.089 Score=47.05 Aligned_cols=28 Identities=29% Similarity=0.819 Sum_probs=24.6
Q ss_pred CcccccccccCCCCCCCCCCCccCCCCc
Q 027188 33 VKSRLCNKYNSAEGCKFGDKCHFAHGEW 60 (227)
Q Consensus 33 yKT~lC~~f~~~g~C~yG~~C~FAHg~~ 60 (227)
|.-..|+.|..+|.|-|||.|.|.|...
T Consensus 139 ~qpdVCKdyk~TGYCGYGDsCKflH~R~ 166 (259)
T COG5152 139 TQPDVCKDYKETGYCGYGDSCKFLHDRS 166 (259)
T ss_pred cCcccccchhhcccccCCchhhhhhhhh
Confidence 4556799999999999999999999654
No 59
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=91.10 E-value=0.054 Score=44.86 Aligned_cols=39 Identities=28% Similarity=0.397 Sum_probs=34.1
Q ss_pred ccceeeehhhhhhhhhhccCCCcccccccccCCceeecc
Q 027188 104 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD 142 (227)
Q Consensus 104 s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~ 142 (227)
.-.+.+.|+....|..|||+|.|++.++.++|.++-|.+
T Consensus 98 ~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~~ 136 (140)
T PRK08406 98 DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDIDD 136 (140)
T ss_pred cEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCeE
Confidence 346778899999999999999999999999999887644
No 60
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=90.89 E-value=0.12 Score=51.64 Aligned_cols=73 Identities=22% Similarity=0.392 Sum_probs=59.4
Q ss_pred ccCC-ccceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHHHHHH
Q 027188 100 SFGA-SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELI 172 (227)
Q Consensus 100 ~fg~-s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV~elI 172 (227)
+|.+ -.....+||..++++|||+||+.+..||+-++|||-+..++.+.-.|.+.|-+.......|..|+.+.+
T Consensus 134 ~~~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~ 207 (608)
T KOG2279|consen 134 LTENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKV 207 (608)
T ss_pred HhcCCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccc
Confidence 4443 234567899999999999999999999999999999999988877888888877766667777775444
No 61
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=90.84 E-value=0.08 Score=46.23 Aligned_cols=38 Identities=26% Similarity=0.365 Sum_probs=35.8
Q ss_pred ceeeehhhhhhhhhhccCCCcccccccccCCceeeccc
Q 027188 106 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH 143 (227)
Q Consensus 106 t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~ 143 (227)
.+.+.|+.+.-+.+|||+|.|++.+.++||.++.|..-
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~ 180 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence 78899999999999999999999999999999999764
No 62
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=90.71 E-value=0.2 Score=50.23 Aligned_cols=70 Identities=23% Similarity=0.327 Sum_probs=50.6
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCccccccccc-CHHHHHHHHHHHHHHHHhcC
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIVNVG 176 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieG-tfeqI~~As~mV~elI~~~~ 176 (227)
-..+|.|+...+=+||||+|.|||||+..|++|+.+.+.... +..+.+.+ -+.+..-|.+.+.+.+.+..
T Consensus 68 v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g--~e~~~~~~~~p~~v~~a~a~~~~~~~~~~ 138 (608)
T KOG2279|consen 68 IEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG--DERVLLISGFPVQVCKAKAAIHQILTENT 138 (608)
T ss_pred eeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC--cccchhhccCCCCCChHHHHHHHHHhcCC
Confidence 467899999999999999999999999999999999865432 23333333 55566656555555544433
No 63
>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=89.56 E-value=0.14 Score=48.21 Aligned_cols=40 Identities=23% Similarity=0.415 Sum_probs=36.8
Q ss_pred ccceeeehhhhhhhhhhccCCCcccccccccCCceeeccc
Q 027188 104 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH 143 (227)
Q Consensus 104 s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~ 143 (227)
.-.+.+.|+.+.-+..|||+|.|++..+.+||.+|-|.+.
T Consensus 300 ~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 300 KHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred CcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 3578999999999999999999999999999999999764
No 64
>PRK12704 phosphodiesterase; Provisional
Probab=89.50 E-value=0.2 Score=49.50 Aligned_cols=63 Identities=30% Similarity=0.544 Sum_probs=44.0
Q ss_pred cceeeehh-hhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHH--HHHHHHHHHHH
Q 027188 105 ATAKISID-AKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIK--QASAMVRELIV 173 (227)
Q Consensus 105 ~t~kisV~-as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~--~As~mV~elI~ 173 (227)
++.-+.+| ..+-|.||||.|.||+-+-..||+.|-|.|.. -.|.|+| |+-++ .|..-+..++.
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~-~~~~rre~a~~~l~~l~~ 275 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSG-FDPIRREIARLALEKLVQ 275 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC-----CeEEEec-CChhhHHHHHHHHHHHHh
Confidence 44455666 58999999999999999999999999998854 2334443 44444 45444445444
No 65
>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=89.37 E-value=0.13 Score=42.95 Aligned_cols=40 Identities=25% Similarity=0.351 Sum_probs=34.8
Q ss_pred CccceeeehhhhhhhhhhccCCCcccccccccCCceeecc
Q 027188 103 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD 142 (227)
Q Consensus 103 ~s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~ 142 (227)
....+.+.|+...-|..|||+|.|++....++|.++-|.+
T Consensus 98 ~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~~ 137 (141)
T TIGR01952 98 GKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDIDD 137 (141)
T ss_pred CCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCeE
Confidence 3456888999999999999999999999999999886653
No 66
>PRK02821 hypothetical protein; Provisional
Probab=89.35 E-value=0.12 Score=39.05 Aligned_cols=31 Identities=16% Similarity=0.384 Sum_probs=26.9
Q ss_pred ccceeeehhhhhhhhhhccCCCccccccccc
Q 027188 104 SATAKISIDAKLAGAIIGKNGVNSKQICRLT 134 (227)
Q Consensus 104 s~t~kisV~as~~G~IIGKgG~nikqI~~~T 134 (227)
....+|.|+.+-.|.||||+|.+++-|+-+-
T Consensus 30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred cEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 4678999999999999999999988877643
No 67
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=89.13 E-value=0.15 Score=46.63 Aligned_cols=41 Identities=29% Similarity=0.446 Sum_probs=34.7
Q ss_pred cceeeehh------hhhhhhhhccCCCcccccccccCCceeecccCC
Q 027188 105 ATAKISID------AKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV 145 (227)
Q Consensus 105 ~t~kisV~------as~~G~IIGKgG~nikqI~~~TGaklsI~~~es 145 (227)
-+.||.|| -..||.|+|--|-..|||+..||+||.|+-.+|
T Consensus 92 ~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgS 138 (259)
T KOG1588|consen 92 LTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGS 138 (259)
T ss_pred EEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCc
Confidence 45566665 357999999999999999999999999997664
No 68
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=88.70 E-value=0.16 Score=55.00 Aligned_cols=67 Identities=18% Similarity=0.151 Sum_probs=57.6
Q ss_pred eeehhhhhhhhhhccCCCcccccccccCCceeecc-cCCCCcccccccccCHHHHHHHHHHHHHHHHh
Q 027188 108 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD-HEVDPNLRNIELEGTFDQIKQASAMVRELIVN 174 (227)
Q Consensus 108 kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~-~es~~~~r~i~ieGtfeqI~~As~mV~elI~~ 174 (227)
|..||...+..|||+||.|+.-|+.-||+-|.|-. +++|-.+|-+.+.|.++..+.|-..|--+|-+
T Consensus 1343 k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1343 KGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred ccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeec
Confidence 56677777899999999999999999999999987 78888899999999999999887766555543
No 69
>PRK00468 hypothetical protein; Provisional
Probab=88.62 E-value=0.14 Score=38.53 Aligned_cols=28 Identities=25% Similarity=0.398 Sum_probs=24.9
Q ss_pred cceeeehhhhhhhhhhccCCCccccccc
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICR 132 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~ 132 (227)
...+|.|+.+-.|.||||+|.+++-|+-
T Consensus 30 ~~~~l~v~~~D~GrVIGk~Gr~i~AIRt 57 (75)
T PRK00468 30 VILELKVAPEDMGKVIGKQGRIAKAIRT 57 (75)
T ss_pred EEEEEEEChhhCcceecCCChhHHHHHH
Confidence 5678999999999999999999887765
No 70
>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=88.61 E-value=0.11 Score=43.29 Aligned_cols=39 Identities=26% Similarity=0.391 Sum_probs=34.2
Q ss_pred eehhhhhhhhhhccCCCcccccccccCCceeecccCCCC
Q 027188 109 ISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDP 147 (227)
Q Consensus 109 isV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~ 147 (227)
+.|....+|+.||++|.+++-|+++.|.++.|.+...|+
T Consensus 37 fvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D~ 75 (141)
T TIGR01952 37 FVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSENL 75 (141)
T ss_pred EEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCCH
Confidence 456777899999999999999999999999999876664
No 71
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=88.45 E-value=0.48 Score=46.88 Aligned_cols=41 Identities=29% Similarity=0.548 Sum_probs=34.6
Q ss_pred ccceeeehh-hhhhhhhhccCCCcccccccccCCceeecccC
Q 027188 104 SATAKISID-AKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 144 (227)
Q Consensus 104 s~t~kisV~-as~~G~IIGKgG~nikqI~~~TGaklsI~~~e 144 (227)
.++.-|.+| ..+-|.||||.|.||+-+-..||+.|-|.|..
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp 244 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP 244 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC
Confidence 344556666 58999999999999999999999999998754
No 72
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=88.15 E-value=0.16 Score=48.28 Aligned_cols=41 Identities=29% Similarity=0.466 Sum_probs=37.5
Q ss_pred ccceeeehhhhhhhhhhccCCCcccccccccCCceeecccC
Q 027188 104 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 144 (227)
Q Consensus 104 s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~e 144 (227)
.-.+.+.|+...-++.|||+|.|++..+.+||.++-|...+
T Consensus 302 ~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~ 342 (362)
T PRK12327 302 EKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES 342 (362)
T ss_pred CcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence 35788999999999999999999999999999999998754
No 73
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=87.06 E-value=0.19 Score=38.16 Aligned_cols=30 Identities=23% Similarity=0.405 Sum_probs=26.2
Q ss_pred CccceeeehhhhhhhhhhccCCCccccccc
Q 027188 103 ASATAKISIDAKLAGAIIGKNGVNSKQICR 132 (227)
Q Consensus 103 ~s~t~kisV~as~~G~IIGKgG~nikqI~~ 132 (227)
.+.+.+|+|+.+-.|.||||+|.+++-|+-
T Consensus 28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred CeEEEEEEECcccccceecCCChhHHHHHH
Confidence 356789999999999999999999887765
No 74
>PRK00106 hypothetical protein; Provisional
Probab=86.08 E-value=0.76 Score=45.93 Aligned_cols=41 Identities=27% Similarity=0.507 Sum_probs=34.8
Q ss_pred ccceeeehh-hhhhhhhhccCCCcccccccccCCceeecccC
Q 027188 104 SATAKISID-AKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 144 (227)
Q Consensus 104 s~t~kisV~-as~~G~IIGKgG~nikqI~~~TGaklsI~~~e 144 (227)
.++.-+.+| ..+-|.||||.|.||+-+-..||+.|-|-|..
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp 265 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP 265 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC
Confidence 345556666 58999999999999999999999999998754
No 75
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.74 E-value=0.26 Score=46.04 Aligned_cols=31 Identities=26% Similarity=0.698 Sum_probs=27.0
Q ss_pred CCCCcccccccccCCCCCCCCCCCccCCCCc
Q 027188 30 PPAVKSRLCNKYNSAEGCKFGDKCHFAHGEW 60 (227)
Q Consensus 30 ~~~yKT~lC~~f~~~g~C~yG~~C~FAHg~~ 60 (227)
..-|--.+|+.|..+|.|-||+.|.|.|...
T Consensus 181 ~~d~qpDicKdykeTgycg~gdSckFlh~r~ 211 (313)
T KOG1813|consen 181 RIDYQPDICKDYKETGYCGYGDSCKFLHDRS 211 (313)
T ss_pred eeecCchhhhhhHhhCcccccchhhhhhhhh
Confidence 3567778999999999999999999999543
No 76
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=85.54 E-value=0.28 Score=47.98 Aligned_cols=40 Identities=33% Similarity=0.478 Sum_probs=36.5
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceeecccC
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 144 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~e 144 (227)
-.+.+.|+.+..++.|||+|.|++..+.+||.++-|.+-+
T Consensus 335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~~ 374 (449)
T PRK12329 335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDSA 374 (449)
T ss_pred cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccHH
Confidence 4678999999999999999999999999999999998643
No 77
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=85.49 E-value=0.89 Score=43.16 Aligned_cols=72 Identities=19% Similarity=0.217 Sum_probs=57.8
Q ss_pred eeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccc-cCHHHHHHHHHHHHHHHHhcCCCCC
Q 027188 107 AKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELE-GTFDQIKQASAMVRELIVNVGSGSG 180 (227)
Q Consensus 107 ~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ie-GtfeqI~~As~mV~elI~~~~~~~~ 180 (227)
..|.|.+++.|.||||.|.+-|-|...|+.++.+-... .|.--|.|+ ++-++|.+|...+..+|.......|
T Consensus 59 ~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~--~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~s~p 131 (345)
T KOG2814|consen 59 SSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN--TNKEEIKIIGISRNCVIQALERIAKLIDSDRKSFP 131 (345)
T ss_pred hhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC--CCcceEEEeehhHHHHHHHHHHHHHHHHhhhhcCc
Confidence 45788999999999999999999999999999987543 233334444 4889999999999999998885444
No 78
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=84.88 E-value=0.32 Score=41.79 Aligned_cols=41 Identities=22% Similarity=0.293 Sum_probs=33.7
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCC
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVD 146 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~ 146 (227)
...=+.|...- |.-|||+|.|++.+++..|.++.|.++..|
T Consensus 61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~s~d 101 (166)
T PRK06418 61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEKTND 101 (166)
T ss_pred CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEcCCC
Confidence 34445555566 999999999999999999999999987655
No 79
>PRK01064 hypothetical protein; Provisional
Probab=84.75 E-value=0.26 Score=37.38 Aligned_cols=31 Identities=29% Similarity=0.387 Sum_probs=26.7
Q ss_pred ccceeeehhhhhhhhhhccCCCccccccccc
Q 027188 104 SATAKISIDAKLAGAIIGKNGVNSKQICRLT 134 (227)
Q Consensus 104 s~t~kisV~as~~G~IIGKgG~nikqI~~~T 134 (227)
....++.|+.+-.|.||||+|.+++-|+.+.
T Consensus 29 ~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 29 TIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred EEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 4578899999999999999999998887754
No 80
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.60 E-value=0.31 Score=45.52 Aligned_cols=33 Identities=24% Similarity=0.894 Sum_probs=27.3
Q ss_pred CCCccccccccccc-cccCCCCCCCcccCCcccc
Q 027188 190 QSNNFKTKLCENFA-KGSCTFGDRCHFAHGSEEL 222 (227)
Q Consensus 190 ~~~~~KTklC~~f~-~G~C~~G~~C~FAHg~~EL 222 (227)
...-|--.+|+.|. +|+|-|||.|.|.|.-.+.
T Consensus 180 ~~~d~qpDicKdykeTgycg~gdSckFlh~r~Dy 213 (313)
T KOG1813|consen 180 ERIDYQPDICKDYKETGYCGYGDSCKFLHDRSDY 213 (313)
T ss_pred ceeecCchhhhhhHhhCcccccchhhhhhhhhhc
Confidence 33567778999998 8999999999999976543
No 81
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=84.06 E-value=0.38 Score=47.18 Aligned_cols=39 Identities=31% Similarity=0.439 Sum_probs=36.2
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceeeccc
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH 143 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~ 143 (227)
..+.+.|+...-+..|||+|.|++..+++||.++-|.+.
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 578899999999999999999999999999999999763
No 82
>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=80.81 E-value=0.15 Score=37.23 Aligned_cols=34 Identities=35% Similarity=0.430 Sum_probs=28.3
Q ss_pred ceeeehhhhhhhhhhccCCCcccccccccCCcee
Q 027188 106 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLS 139 (227)
Q Consensus 106 t~kisV~as~~G~IIGKgG~nikqI~~~TGakls 139 (227)
...|.|.++.-|.||||+|.++++|.......|.
T Consensus 26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 4567788999999999999999999887665554
No 83
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=78.52 E-value=1.8 Score=44.88 Aligned_cols=72 Identities=19% Similarity=0.261 Sum_probs=62.9
Q ss_pred ccceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHHHHHHHhcCC
Q 027188 104 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGS 177 (227)
Q Consensus 104 s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV~elI~~~~~ 177 (227)
+--.++.+.+....-|+||+|.|+.-|.+.+..++.+.+.+ .+.+++.+.|..+-++.|..+|...+..+..
T Consensus 346 n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~--~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n 417 (753)
T KOG2208|consen 346 NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQG--SNNKKVVITGVSANDEKAVEDVEKIIAEILN 417 (753)
T ss_pred ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccccc--CCCCCeEEeccccchhHHHHHHHHHHHhhhc
Confidence 45677888999999999999999999999999999998733 4568999999999999999999888877765
No 84
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=78.35 E-value=1.8 Score=38.93 Aligned_cols=53 Identities=30% Similarity=0.483 Sum_probs=44.9
Q ss_pred hhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHHHHHHH
Q 027188 114 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV 173 (227)
Q Consensus 114 s~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV~elI~ 173 (227)
-.+|.|+||||-+---|...|-.+|.+.+. .|-|-|.|+-|+-|..-|-.||.
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad~-------kIHiLG~~~niriAR~avcsLIl 230 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLADS-------KIHILGAFQNIRIARDAVCSLIL 230 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecCc-------eEEEeecchhhHHHHHhhHhhhc
Confidence 457999999999988888888888888774 47899999999999887777664
No 85
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=77.32 E-value=0.67 Score=43.52 Aligned_cols=32 Identities=31% Similarity=0.568 Sum_probs=27.5
Q ss_pred CCcccccccccCCCCCCCCCCCccCCCCcccCC
Q 027188 32 AVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGR 64 (227)
Q Consensus 32 ~yKT~lC~~f~~~g~C~yG~~C~FAHg~~ELr~ 64 (227)
--|+.+|-.|. .|.|.-|++|.|+|++..-|.
T Consensus 89 DPKSvvCafFk-~g~C~KG~kCKFsHdl~~~~k 120 (343)
T KOG1763|consen 89 DPKSVVCAFFK-QGTCTKGDKCKFSHDLAVERK 120 (343)
T ss_pred CchHHHHHHHh-ccCCCCCCcccccchHHHhhh
Confidence 45999999876 599999999999999877765
No 86
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=77.10 E-value=12 Score=39.86 Aligned_cols=23 Identities=39% Similarity=0.720 Sum_probs=17.4
Q ss_pred CCCCCCCCCCCCCCccccc---ccCC
Q 027188 81 HGRMGGRLEPPPQSLGAAA---SFGA 103 (227)
Q Consensus 81 ~~~~~~~~~p~p~~~~~~~---~fg~ 103 (227)
+|+.+|...|||++|.++| -||-
T Consensus 589 ~g~~Gg~ppPP~~gm~pmaPvlP~gL 614 (1102)
T KOG1924|consen 589 GGFLGGPPPPPPPGMFPMAPVLPFGL 614 (1102)
T ss_pred CCCCCCCCCCCCCCcccccccCCCCC
Confidence 6788888888888887766 4554
No 87
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=75.62 E-value=0.7 Score=42.39 Aligned_cols=35 Identities=31% Similarity=0.636 Sum_probs=29.7
Q ss_pred CCcccccccccCCCCCCCCCCCccCCCCcccCCCCC
Q 027188 32 AVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRPTV 67 (227)
Q Consensus 32 ~yKT~lC~~f~~~g~C~yG~~C~FAHg~~ELr~p~~ 67 (227)
.-||..|-.|.. +.|.-|+.|.|+|+.+|.|.-+-
T Consensus 82 dpK~~vcalF~~-~~c~kg~~ckF~h~~ee~r~~eK 116 (299)
T COG5252 82 DPKTVVCALFLN-KTCAKGDACKFAHGKEEARKTEK 116 (299)
T ss_pred CchhHHHHHhcc-CccccCchhhhhcchHHHhhhcc
Confidence 458999999985 89999999999999888886443
No 88
>PRK12705 hypothetical protein; Provisional
Probab=74.43 E-value=2.2 Score=42.53 Aligned_cols=39 Identities=33% Similarity=0.528 Sum_probs=32.9
Q ss_pred ceeeehh-hhhhhhhhccCCCcccccccccCCceeecccC
Q 027188 106 TAKISID-AKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 144 (227)
Q Consensus 106 t~kisV~-as~~G~IIGKgG~nikqI~~~TGaklsI~~~e 144 (227)
+.-+.+| ..+-|.||||.|.||+-+-..||..|-|.|..
T Consensus 199 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp 238 (508)
T PRK12705 199 VSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP 238 (508)
T ss_pred eeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc
Confidence 3344445 68999999999999999999999999998865
No 89
>PRK13764 ATPase; Provisional
Probab=74.10 E-value=1.7 Score=44.03 Aligned_cols=42 Identities=24% Similarity=0.337 Sum_probs=38.1
Q ss_pred ccceeeehhhhhhhhhhccCCCcccccccccCCceeecccCC
Q 027188 104 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV 145 (227)
Q Consensus 104 s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es 145 (227)
...+.+.|+...++.||||+|.+|++|....|.+|.++..+.
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence 367889999999999999999999999999999999987654
No 90
>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=73.99 E-value=2 Score=36.29 Aligned_cols=43 Identities=30% Similarity=0.455 Sum_probs=38.5
Q ss_pred ccCCccceeeehhhhhhhhhhccCCCcccccccccCCceeeccc
Q 027188 100 SFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH 143 (227)
Q Consensus 100 ~fg~s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~ 143 (227)
.|+. .|-++.|-+..-|.||||+|.++.+|...||-...|.-.
T Consensus 72 ~Fd~-~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 72 YFDD-DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred EecC-CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 5665 678999999999999999999999999999999988654
No 91
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=73.51 E-value=1.3 Score=44.27 Aligned_cols=26 Identities=42% Similarity=1.136 Sum_probs=20.3
Q ss_pred ccccccccccc---cCCCCCCCcccCCcc
Q 027188 195 KTKLCENFAKG---SCTFGDRCHFAHGSE 220 (227)
Q Consensus 195 KTklC~~f~~G---~C~~G~~C~FAHg~~ 220 (227)
+..||.....| .|.|||+|+|.|..+
T Consensus 75 ~n~LCPsli~g~~~~C~f~d~Crf~HDi~ 103 (614)
T KOG2333|consen 75 QNRLCPSLIQGDISKCSFGDNCRFVHDIE 103 (614)
T ss_pred hhccChHhhcCCCccCcccccccccccHH
Confidence 56788888754 599999999988654
No 92
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.26 E-value=1.4 Score=41.88 Aligned_cols=24 Identities=38% Similarity=0.912 Sum_probs=21.5
Q ss_pred cccccccCCCCCCCCCCCccCCCCc
Q 027188 36 RLCNKYNSAEGCKFGDKCHFAHGEW 60 (227)
Q Consensus 36 ~lC~~f~~~g~C~yG~~C~FAHg~~ 60 (227)
.+|++|.. |.|.||++|+|.|..-
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 67999986 9999999999999765
No 93
>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=73.20 E-value=0.59 Score=31.85 Aligned_cols=32 Identities=28% Similarity=0.406 Sum_probs=24.2
Q ss_pred eeeehhhhhhhhhhccCCCcccccccccCCce
Q 027188 107 AKISIDAKLAGAIIGKNGVNSKQICRLTGAKL 138 (227)
Q Consensus 107 ~kisV~as~~G~IIGKgG~nikqI~~~TGakl 138 (227)
..+.+.....|.+|||+|.+++.|..+++..+
T Consensus 27 ~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 27 IIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 34444443579999999999999999887554
No 94
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=72.84 E-value=1.8 Score=39.74 Aligned_cols=29 Identities=28% Similarity=0.819 Sum_probs=26.4
Q ss_pred CCCccccccccccccccCCCCCCCcccCC
Q 027188 190 QSNNFKTKLCENFAKGSCTFGDRCHFAHG 218 (227)
Q Consensus 190 ~~~~~KTklC~~f~~G~C~~G~~C~FAHg 218 (227)
+-+.|+-.+|..|..+.|.+|..|.|.|-
T Consensus 146 pvT~~rea~C~~~e~~~C~rG~~CnFmH~ 174 (260)
T KOG2202|consen 146 PVTDFREAICGQFERTECSRGGACNFMHV 174 (260)
T ss_pred CcCchhhhhhcccccccCCCCCcCcchhh
Confidence 45789999999999889999999999994
No 95
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=71.24 E-value=1.6 Score=38.23 Aligned_cols=39 Identities=28% Similarity=0.458 Sum_probs=33.3
Q ss_pred eehhhhhhhhhhccCCCcccccccccCCceeecccCCCC
Q 027188 109 ISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDP 147 (227)
Q Consensus 109 isV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~ 147 (227)
..+....+|+.|||+|.+++.|++.-|.++-|.+...|+
T Consensus 80 ~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d~ 118 (190)
T COG0195 80 NVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSEDP 118 (190)
T ss_pred eecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCCH
Confidence 344567889999999999999999999999999877554
No 96
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=66.66 E-value=0.79 Score=33.14 Aligned_cols=31 Identities=32% Similarity=0.466 Sum_probs=25.9
Q ss_pred ccceeeehhhhhhhhhhccCCCccccccccc
Q 027188 104 SATAKISIDAKLAGAIIGKNGVNSKQICRLT 134 (227)
Q Consensus 104 s~t~kisV~as~~G~IIGKgG~nikqI~~~T 134 (227)
.....+.|+.+..|.||||.|.+++-|+.+.
T Consensus 28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~ 58 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLV 58 (73)
T ss_dssp TTEEEEEEESCCCHHHCTTHHHHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECCCCeeHHHHHHHH
Confidence 4567788899999999999999888777654
No 97
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=66.04 E-value=2.5 Score=42.44 Aligned_cols=27 Identities=37% Similarity=0.837 Sum_probs=23.0
Q ss_pred cccccccccCC--CCCCCCCCCccCCCCc
Q 027188 34 KSRLCNKYNSA--EGCKFGDKCHFAHGEW 60 (227)
Q Consensus 34 KT~lC~~f~~~--g~C~yG~~C~FAHg~~ 60 (227)
+..||...-.. ..|+||++|+|-|...
T Consensus 75 ~n~LCPsli~g~~~~C~f~d~Crf~HDi~ 103 (614)
T KOG2333|consen 75 QNRLCPSLIQGDISKCSFGDNCRFVHDIE 103 (614)
T ss_pred hhccChHhhcCCCccCcccccccccccHH
Confidence 57899988877 7899999999999643
No 98
>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=61.07 E-value=2.1 Score=37.93 Aligned_cols=28 Identities=39% Similarity=0.397 Sum_probs=23.6
Q ss_pred cceeeehh-hhhhhhhhccCCCccccccc
Q 027188 105 ATAKISID-AKLAGAIIGKNGVNSKQICR 132 (227)
Q Consensus 105 ~t~kisV~-as~~G~IIGKgG~nikqI~~ 132 (227)
..+.|.|+ .|+-+-||||+|..+|+|..
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~ 249 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGI 249 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHH
Confidence 34667777 78999999999999998875
No 99
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=60.41 E-value=4.9 Score=37.00 Aligned_cols=31 Identities=23% Similarity=0.675 Sum_probs=26.5
Q ss_pred CCCCCCCCcccccccccCCCCCCCCCCCccCC
Q 027188 26 DGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAH 57 (227)
Q Consensus 26 ~~~~~~~yKT~lC~~f~~~g~C~yG~~C~FAH 57 (227)
+-.+-..++-..|.-|..+ .|.+|..|.|-|
T Consensus 143 e~~pvT~~rea~C~~~e~~-~C~rG~~CnFmH 173 (260)
T KOG2202|consen 143 ELSPVTDFREAICGQFERT-ECSRGGACNFMH 173 (260)
T ss_pred eecCcCchhhhhhcccccc-cCCCCCcCcchh
Confidence 3344567899999999986 999999999999
No 100
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=59.63 E-value=4.7 Score=40.49 Aligned_cols=40 Identities=28% Similarity=0.434 Sum_probs=36.5
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccCCceeecccC
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE 144 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~e 144 (227)
..+-+.||....+.||||+|-+|++|....|-+|.+...+
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 5678889999999999999999999999999999998655
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=59.59 E-value=5.5 Score=23.92 Aligned_cols=19 Identities=37% Similarity=0.796 Sum_probs=16.3
Q ss_pred cccccccc-cCCCCCCCcccC
Q 027188 198 LCENFAKG-SCTFGDRCHFAH 217 (227)
Q Consensus 198 lC~~f~~G-~C~~G~~C~FAH 217 (227)
||.+-..| .|.- +.|.|-|
T Consensus 2 lC~yEl~Gg~Cnd-~~C~~QH 21 (23)
T PF10650_consen 2 LCPYELTGGVCND-PDCEFQH 21 (23)
T ss_pred CCccccCCCeeCC-CCCCccc
Confidence 79998887 8976 6899998
No 102
>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=57.82 E-value=2.5 Score=31.01 Aligned_cols=31 Identities=26% Similarity=0.407 Sum_probs=25.9
Q ss_pred cceeeehhhhhhhhhhccCCCcccccccccC
Q 027188 105 ATAKISIDAKLAGAIIGKNGVNSKQICRLTG 135 (227)
Q Consensus 105 ~t~kisV~as~~G~IIGKgG~nikqI~~~TG 135 (227)
...++.|+.+..|.+|||.|.+.+-|+.++.
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~ 54 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLAN 54 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHH
Confidence 3567888888899999999999988888754
No 103
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=57.39 E-value=2.3 Score=32.15 Aligned_cols=33 Identities=18% Similarity=0.390 Sum_probs=26.6
Q ss_pred ceeeehhhhhhhhhhccCCCcccccccccCCce
Q 027188 106 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKL 138 (227)
Q Consensus 106 t~kisV~as~~G~IIGKgG~nikqI~~~TGakl 138 (227)
..+|.|-++.-|.|||+.|.++++|...--..+
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~ 63 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRF 63 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHh
Confidence 467888899999999999999998887543333
No 104
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=57.33 E-value=10 Score=33.49 Aligned_cols=62 Identities=24% Similarity=0.324 Sum_probs=49.1
Q ss_pred ccceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCccccccc-----ccCHHHHHHHHHHHHH
Q 027188 104 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIEL-----EGTFDQIKQASAMVRE 170 (227)
Q Consensus 104 s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~i-----eGtfeqI~~As~mV~e 170 (227)
..+..+.||..-.|.+||+.|.--+.|-+.+|.+|.|...+ +.|.| +.++..+..|..+|+-
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~-----~~V~i~~~~~t~Dp~~~~ka~d~VkA 73 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKT-----GSVTIRTTRKTEDPLALLKARDVVKA 73 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECCC-----CeEEEEecCCCCChHHHHHHHHHHHH
Confidence 45667889999999999999999999999999999997654 23333 3477788888777754
No 105
>PRK15494 era GTPase Era; Provisional
Probab=57.26 E-value=2.6 Score=39.02 Aligned_cols=27 Identities=30% Similarity=0.425 Sum_probs=23.3
Q ss_pred ceeeehh-hhhhhhhhccCCCccccccc
Q 027188 106 TAKISID-AKLAGAIIGKNGVNSKQICR 132 (227)
Q Consensus 106 t~kisV~-as~~G~IIGKgG~nikqI~~ 132 (227)
.+.|.|+ .|+-+-||||+|..||+|..
T Consensus 274 ~~~i~v~~~sqk~iiiG~~g~~ik~i~~ 301 (339)
T PRK15494 274 NQVIVVSRESYKTIILGKNGSKIKEIGA 301 (339)
T ss_pred EEEEEECCCCceeEEEcCCcHHHHHHHH
Confidence 3678888 88999999999999998865
No 106
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=56.83 E-value=6.6 Score=36.52 Aligned_cols=31 Identities=26% Similarity=0.514 Sum_probs=22.2
Q ss_pred ccccccccccccccCCCCCCCcccCCccccc
Q 027188 193 NFKTKLCENFAKGSCTFGDRCHFAHGSEELR 223 (227)
Q Consensus 193 ~~KTklC~~f~~G~C~~G~~C~FAHg~~ELr 223 (227)
.+....|++|..|.|+-++.|.|+|+.+-++
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 4566677777777777777777777776544
No 107
>PRK00089 era GTPase Era; Reviewed
Probab=54.36 E-value=3.1 Score=36.88 Aligned_cols=28 Identities=36% Similarity=0.480 Sum_probs=23.2
Q ss_pred cceeeehh-hhhhhhhhccCCCccccccc
Q 027188 105 ATAKISID-AKLAGAIIGKNGVNSKQICR 132 (227)
Q Consensus 105 ~t~kisV~-as~~G~IIGKgG~nikqI~~ 132 (227)
-.+.|.|+ .|+-+-||||+|..||+|..
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~ 254 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGT 254 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHH
Confidence 34667777 78889999999999998876
No 108
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=52.25 E-value=7 Score=35.92 Aligned_cols=28 Identities=25% Similarity=0.727 Sum_probs=19.4
Q ss_pred cccccccccCCCCCCCcccCCccccccC
Q 027188 198 LCENFAKGSCTFGDRCHFAHGSEELRKS 225 (227)
Q Consensus 198 lC~~f~~G~C~~G~~C~FAHg~~ELr~~ 225 (227)
+|..|..|+|.-.++|...|..+.-|-|
T Consensus 235 icpkflngrcnkaedcnlsheldprrip 262 (377)
T KOG1492|consen 235 ICPKFLNGRCNKAEDCNLSHELDPRRIP 262 (377)
T ss_pred cChHHhcCccCchhcCCcccccCccccc
Confidence 5777777777777777777766665554
No 109
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=51.44 E-value=4.4 Score=36.76 Aligned_cols=36 Identities=31% Similarity=0.585 Sum_probs=29.2
Q ss_pred ceeeehhhhhhhhhhccCCCccccccc----ccCC-ceeec
Q 027188 106 TAKISIDAKLAGAIIGKNGVNSKQICR----LTGA-KLSIR 141 (227)
Q Consensus 106 t~kisV~as~~G~IIGKgG~nikqI~~----~TGa-klsI~ 141 (227)
..+|.|-+..-|.||||+|.+|.+|.. ++|. ++.|.
T Consensus 52 ~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I~ 92 (233)
T COG0092 52 GTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQIN 92 (233)
T ss_pred ceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceEE
Confidence 578999999999999999999887765 6776 45554
No 110
>COG1159 Era GTPase [General function prediction only]
Probab=51.38 E-value=3.6 Score=38.48 Aligned_cols=26 Identities=42% Similarity=0.579 Sum_probs=22.0
Q ss_pred eeeehh-hhhhhhhhccCCCccccccc
Q 027188 107 AKISID-AKLAGAIIGKNGVNSKQICR 132 (227)
Q Consensus 107 ~kisV~-as~~G~IIGKgG~nikqI~~ 132 (227)
+.|.|+ .|+=|-||||+|..+|+|-.
T Consensus 231 a~I~Ver~sQK~IiIGk~G~~iK~IG~ 257 (298)
T COG1159 231 ATIYVERESQKGIIIGKNGAMIKKIGT 257 (298)
T ss_pred EEEEEecCCccceEECCCcHHHHHHHH
Confidence 457787 78999999999999987765
No 111
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=50.59 E-value=25 Score=33.75 Aligned_cols=64 Identities=13% Similarity=0.267 Sum_probs=51.0
Q ss_pred CccceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHHH
Q 027188 103 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVR 169 (227)
Q Consensus 103 ~s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV~ 169 (227)
.+-|..+-|+-.+++.|+|.+|-.||.|+..|-.-++-=..+ .+-.+..+|-.+.++.|..-+.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~edv~~aRrei~ 87 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRHEDVRRARREIP 87 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCchhHHHHhhcCc
Confidence 456777888899999999999999999999998776654333 3457888999999988876553
No 112
>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=49.71 E-value=3.5 Score=30.97 Aligned_cols=27 Identities=30% Similarity=0.618 Sum_probs=22.6
Q ss_pred eeeehhhhhhhhhhccCCCcccccccc
Q 027188 107 AKISIDAKLAGAIIGKNGVNSKQICRL 133 (227)
Q Consensus 107 ~kisV~as~~G~IIGKgG~nikqI~~~ 133 (227)
.++.|.++.-|.|||++|.+++++...
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~ 66 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEI 66 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHH
Confidence 567777788999999999999887763
No 113
>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=47.14 E-value=4 Score=32.13 Aligned_cols=29 Identities=24% Similarity=0.461 Sum_probs=24.5
Q ss_pred ceeeehhhhhhhhhhccCCCccccccccc
Q 027188 106 TAKISIDAKLAGAIIGKNGVNSKQICRLT 134 (227)
Q Consensus 106 t~kisV~as~~G~IIGKgG~nikqI~~~T 134 (227)
..+|.|-++.-|.|||+.|.++++|....
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l 90 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKEL 90 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHH
Confidence 46788888999999999999998887643
No 114
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.25 E-value=4.1 Score=42.15 Aligned_cols=41 Identities=17% Similarity=0.304 Sum_probs=37.9
Q ss_pred CCCCCCcccccccccCCCCCCCCCCCccCCCCcccCCCCCC
Q 027188 28 SSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRPTVP 68 (227)
Q Consensus 28 ~~~~~yKT~lC~~f~~~g~C~yG~~C~FAHg~~ELr~p~~~ 68 (227)
...++|+|-+|......+.|+.+..|.|+|...|+.+|++.
T Consensus 196 amq~~vl~l~l~~Le~g~~~~Rk~lvmfvvq~le~~~pq~s 236 (861)
T KOG3161|consen 196 AMQSKVLTLMLRDLEQGGGCPRKTLVMFVVQQLELEKPQLS 236 (861)
T ss_pred chHHHHHHHHHHHHHhcCCccccceEEEEeeeccccchhhh
Confidence 34579999999999999999999999999999999999876
No 115
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=44.09 E-value=10 Score=36.50 Aligned_cols=25 Identities=32% Similarity=0.895 Sum_probs=21.9
Q ss_pred ccccccccccccCCCCCCCcccCCc
Q 027188 195 KTKLCENFAKGSCTFGDRCHFAHGS 219 (227)
Q Consensus 195 KTklC~~f~~G~C~~G~~C~FAHg~ 219 (227)
.-.+|.+|.+|.|+.|+.|-|-|-.
T Consensus 160 ~p~Icsf~v~geckRG~ec~yrhEk 184 (377)
T KOG0153|consen 160 RPHICSFFVKGECKRGAECPYRHEK 184 (377)
T ss_pred CCccccceeeccccccccccccccC
Confidence 3468999999999999999999943
No 116
>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=44.03 E-value=12 Score=38.00 Aligned_cols=75 Identities=20% Similarity=0.311 Sum_probs=50.7
Q ss_pred ccCCccceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHHHHHHHhcCCC
Q 027188 100 SFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGSG 178 (227)
Q Consensus 100 ~fg~s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV~elI~~~~~~ 178 (227)
.|+. .|-++.|.|..-|.||||+|.+..+|...||-...|.-...= +.=.+..--.-+++.+.-.++++..++..
T Consensus 89 ~f~~-~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~~---~~~~~~~~~~~~~~~~~~r~~~l~~~~~~ 163 (630)
T TIGR03675 89 YFDD-VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPPI---ESKTIKNIREYLRSESEERKEFLRKLGRR 163 (630)
T ss_pred EecC-CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCCC---CcHHHHHHHHHHHHhHHHHHHHHHHHHHh
Confidence 5665 678899999999999999999999999999999988654321 11112211222334445555666666553
No 117
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=41.68 E-value=29 Score=35.75 Aligned_cols=63 Identities=21% Similarity=0.268 Sum_probs=46.7
Q ss_pred ceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHHHHHHHh
Q 027188 106 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVN 174 (227)
Q Consensus 106 t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV~elI~~ 174 (227)
...+.|..+..-..||-||++.|-|...|| -++..|.++ .-.+--+.....+|.++|...+..
T Consensus 598 ~~tlkv~~sk~~~lIGp~G~~~kki~~EtG-ai~~vDe~t-----~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 598 LETLKVSPSKRATLIGPGGVLKKKIEVETG-AISQVDEGT-----FSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred eeEEeecchhhheeecCccceeeeEeeecc-ceeeecCce-----EEEEecCHHHHHHHHHHHHHHhcC
Confidence 445567788888999999999999999999 444444441 113345788888899888887764
No 118
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=39.34 E-value=12 Score=31.22 Aligned_cols=17 Identities=41% Similarity=1.269 Sum_probs=13.9
Q ss_pred CCCCCCCCCccCCCCccc
Q 027188 45 EGCKFGDKCHFAHGEWEL 62 (227)
Q Consensus 45 g~C~yG~~C~FAHg~~EL 62 (227)
.+|++|+ |||.||....
T Consensus 60 ~GC~~ge-CHy~~GN~ka 76 (132)
T COG1908 60 AGCKIGE-CHYISGNYKA 76 (132)
T ss_pred ecccccc-eeeeccchHH
Confidence 3999999 9999986543
No 119
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=39.21 E-value=9.9 Score=36.31 Aligned_cols=34 Identities=32% Similarity=0.513 Sum_probs=29.0
Q ss_pred hhhhhhhccCCCccccccccc-CCceeecccCCCC
Q 027188 114 KLAGAIIGKNGVNSKQICRLT-GAKLSIRDHEVDP 147 (227)
Q Consensus 114 s~~G~IIGKgG~nikqI~~~T-GaklsI~~~es~~ 147 (227)
+-+|+.||++|.+|+.|++.. |.+|-|.....|+
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~ 279 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDP 279 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCH
Confidence 358999999999999998766 9999998876554
No 120
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=38.43 E-value=12 Score=36.10 Aligned_cols=34 Identities=21% Similarity=0.353 Sum_probs=29.0
Q ss_pred hhhhhhhccCCCccccccccc-CCceeecccCCCC
Q 027188 114 KLAGAIIGKNGVNSKQICRLT-GAKLSIRDHEVDP 147 (227)
Q Consensus 114 s~~G~IIGKgG~nikqI~~~T-GaklsI~~~es~~ 147 (227)
+-+|+.||++|.+|+-|.+.- |.+|-|.....|+
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~ 285 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVP 285 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCH
Confidence 468999999999999998866 9999998876554
No 121
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=38.16 E-value=11 Score=37.11 Aligned_cols=34 Identities=26% Similarity=0.440 Sum_probs=28.8
Q ss_pred hhhhhhhccCCCccccccccc-CCceeecccCCCC
Q 027188 114 KLAGAIIGKNGVNSKQICRLT-GAKLSIRDHEVDP 147 (227)
Q Consensus 114 s~~G~IIGKgG~nikqI~~~T-GaklsI~~~es~~ 147 (227)
+-+|+.||++|.+|+.|.+.. |.||-|..-..|+
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp 311 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDP 311 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCH
Confidence 458999999999999998876 9999998766554
No 122
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=37.62 E-value=14 Score=33.94 Aligned_cols=23 Identities=35% Similarity=0.756 Sum_probs=21.1
Q ss_pred cccccccCCCCCCCCCCCccCCC
Q 027188 36 RLCNKYNSAEGCKFGDKCHFAHG 58 (227)
Q Consensus 36 ~lC~~f~~~g~C~yG~~C~FAHg 58 (227)
..|++|...|.|--|..|+|.|.
T Consensus 207 vycryynangicgkgaacrfvhe 229 (377)
T KOG1492|consen 207 VYCRYYNANGICGKGAACRFVHE 229 (377)
T ss_pred eEEEEecCCCcccCCceeeeecc
Confidence 35999999999999999999993
No 123
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=34.02 E-value=21 Score=36.33 Aligned_cols=74 Identities=26% Similarity=0.382 Sum_probs=49.1
Q ss_pred ccCCccceeeehhhhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHHHHHHHhcCC
Q 027188 100 SFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGS 177 (227)
Q Consensus 100 ~fg~s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV~elI~~~~~ 177 (227)
.|+. .|-++.|.+.+-|.||||+|.+..+|.+.||-.-.|--... .+.=.+..--+-+++...-.++++.+++.
T Consensus 95 ~Fd~-~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~PP---i~S~ti~~ir~~l~~~~~eR~~iL~~vg~ 168 (637)
T COG1782 95 YFDD-DTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTPP---IQSRTIKSIREILRSERKERREILRNVGR 168 (637)
T ss_pred EecC-CCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecCC---CchhhHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 5665 67888999999999999999999999999999988864331 11112222222333444444555555554
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=33.38 E-value=14 Score=35.01 Aligned_cols=34 Identities=29% Similarity=0.481 Sum_probs=29.0
Q ss_pred hhhhhhhccCCCccccccccc-CCceeecccCCCC
Q 027188 114 KLAGAIIGKNGVNSKQICRLT-GAKLSIRDHEVDP 147 (227)
Q Consensus 114 s~~G~IIGKgG~nikqI~~~T-GaklsI~~~es~~ 147 (227)
+-+|+.||++|.+|+-|++.- |.+|-|.....|+
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~ 277 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDP 277 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCH
Confidence 358999999999999998766 9999998876664
No 125
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=32.77 E-value=10 Score=33.39 Aligned_cols=28 Identities=29% Similarity=0.595 Sum_probs=22.6
Q ss_pred eeeehhhhhhhhhhccCCCccccccccc
Q 027188 107 AKISIDAKLAGAIIGKNGVNSKQICRLT 134 (227)
Q Consensus 107 ~kisV~as~~G~IIGKgG~nikqI~~~T 134 (227)
..|.|.++.-|.||||+|.+++++...-
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 5666777888999999999988877643
No 126
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.30 E-value=23 Score=33.77 Aligned_cols=25 Identities=40% Similarity=0.933 Sum_probs=20.8
Q ss_pred ccccccccc--cccCCCCCCCcccCCc
Q 027188 195 KTKLCENFA--KGSCTFGDRCHFAHGS 219 (227)
Q Consensus 195 KTklC~~f~--~G~C~~G~~C~FAHg~ 219 (227)
.-+.|++|. .|.|+||.+|-|.|-.
T Consensus 248 s~~~c~yf~~~~g~cPf~s~~~y~h~~ 274 (344)
T KOG1039|consen 248 SAKDCKYFSQGLGSCPFGSKCFYKHLL 274 (344)
T ss_pred hccchhhhcCCCCCCCCCCcccccccc
Confidence 346799998 4689999999999943
No 127
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=31.86 E-value=31 Score=36.05 Aligned_cols=43 Identities=28% Similarity=0.339 Sum_probs=38.4
Q ss_pred ccCCccceeeehhhhhhhhhhccCCCcccccccccCCceeecc
Q 027188 100 SFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD 142 (227)
Q Consensus 100 ~fg~s~t~kisV~as~~G~IIGKgG~nikqI~~~TGaklsI~~ 142 (227)
-+.-+.-.++.|+-.+...|||+||.|++=+...+...+-|.+
T Consensus 196 ~~~r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~ 238 (753)
T KOG2208|consen 196 KNERSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPD 238 (753)
T ss_pred ccceeEEEEeeccccchhhhccccccccccccccceeEEEccc
Confidence 4555788899999999999999999999999999999888874
No 128
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.15 E-value=41 Score=34.05 Aligned_cols=33 Identities=18% Similarity=0.493 Sum_probs=24.0
Q ss_pred ccccccCCCCCCCCCCCccCCCCcccC-CCCCCCCC
Q 027188 37 LCNKYNSAEGCKFGDKCHFAHGEWELG-RPTVPSYE 71 (227)
Q Consensus 37 lC~~f~~~g~C~yG~~C~FAHg~~ELr-~p~~~~~~ 71 (227)
-|++|...-.|+- -|.|-|++..+. .|..=+|+
T Consensus 34 ~C~~w~~~~~C~k--~C~YRHSe~~~kr~e~~CYwe 67 (667)
T KOG4791|consen 34 VCTLWQEGRCCRK--VCRYRHSEIDKKRSEIPCYWE 67 (667)
T ss_pred hhhhhhhcCcccc--cccchhhHHhhhcCcccceee
Confidence 4889988755654 799999887766 66665663
No 129
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=24.71 E-value=27 Score=34.56 Aligned_cols=34 Identities=29% Similarity=0.393 Sum_probs=28.4
Q ss_pred hhhhhhhccCCCccccccccc-CCceeecccCCCC
Q 027188 114 KLAGAIIGKNGVNSKQICRLT-GAKLSIRDHEVDP 147 (227)
Q Consensus 114 s~~G~IIGKgG~nikqI~~~T-GaklsI~~~es~~ 147 (227)
+-+|+.||++|.+|+-|.+.- |.+|-|..-..|+
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~ 279 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDDP 279 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCH
Confidence 358999999999999998766 9999998766554
No 130
>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=23.78 E-value=37 Score=23.46 Aligned_cols=13 Identities=38% Similarity=1.165 Sum_probs=11.0
Q ss_pred CCCCCCCCCccCC
Q 027188 45 EGCKFGDKCHFAH 57 (227)
Q Consensus 45 g~C~yG~~C~FAH 57 (227)
.+|+|..+|.||=
T Consensus 49 ~GC~f~~rC~~a~ 61 (64)
T PF08352_consen 49 NGCPFAPRCPYAT 61 (64)
T ss_pred CCCCccccchHhh
Confidence 3899999999873
No 131
>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=23.11 E-value=25 Score=21.65 Aligned_cols=10 Identities=50% Similarity=1.125 Sum_probs=5.7
Q ss_pred CCCCCCCCcc
Q 027188 46 GCKFGDKCHF 55 (227)
Q Consensus 46 ~C~yG~~C~F 55 (227)
.|+||.+|--
T Consensus 2 ~C~YG~~CYR 11 (26)
T PF10283_consen 2 PCKYGAKCYR 11 (26)
T ss_dssp E-TTGGG-S-
T ss_pred CCCcchhhhc
Confidence 4999999953
No 132
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=21.28 E-value=87 Score=26.66 Aligned_cols=61 Identities=20% Similarity=0.293 Sum_probs=48.1
Q ss_pred hhhhhhhhhccCCCcccccccccCCceeecccCCCCcccccccccCHHHHHHHHHHHHHHHHhcCC
Q 027188 112 DAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGS 177 (227)
Q Consensus 112 ~as~~G~IIGKgG~nikqI~~~TGaklsI~~~es~~~~r~i~ieGtfeqI~~As~mV~elI~~~~~ 177 (227)
.....-.+...+|.-..+|....|++|.+...+ ..|.|+|+...+..++..|.+++.++..
T Consensus 33 ~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~~-----~~i~I~g~k~~~~~i~~~i~~~l~~i~~ 93 (210)
T PF14611_consen 33 QPDEFFLLLTGNGRILENLAARNGAKIEVSRSE-----NRIRITGTKSTAEYIEASINEILSNIRT 93 (210)
T ss_pred cchheeeeecCCchHHHHHHHhcCceEEEecCC-----cEEEEEccHHHHHHHHHHHHHHHhhcEE
Confidence 344444566677777778877789999997654 4789999999999999999999987775
No 133
>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=21.13 E-value=75 Score=23.71 Aligned_cols=51 Identities=14% Similarity=0.214 Sum_probs=37.9
Q ss_pred cccccccccCCceeecccC-C--CCcccccccccCHHHHHHHHHHHHHHHHhcC
Q 027188 126 NSKQICRLTGAKLSIRDHE-V--DPNLRNIELEGTFDQIKQASAMVRELIVNVG 176 (227)
Q Consensus 126 nikqI~~~TGaklsI~~~e-s--~~~~r~i~ieGtfeqI~~As~mV~elI~~~~ 176 (227)
-..+|.+..|.++...-.+ . .+++..++++|+.+.|-.+++.+..++...|
T Consensus 35 ~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~~S 88 (88)
T PF02749_consen 35 EAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQRLS 88 (88)
T ss_dssp HHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHHHhC
Confidence 3666777777777665333 1 4567899999999999999999988887653
No 134
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.37 E-value=22 Score=36.98 Aligned_cols=37 Identities=19% Similarity=0.264 Sum_probs=32.4
Q ss_pred CCCccccccccccccc-cCCCCCCCcccCCccccccCC
Q 027188 190 QSNNFKTKLCENFAKG-SCTFGDRCHFAHGSEELRKSV 226 (227)
Q Consensus 190 ~~~~~KTklC~~f~~G-~C~~G~~C~FAHg~~ELr~~~ 226 (227)
....++|-+|...+.| .|..+..|.|+|...|+..+.
T Consensus 197 mq~~vl~l~l~~Le~g~~~~Rk~lvmfvvq~le~~~pq 234 (861)
T KOG3161|consen 197 MQSKVLTLMLRDLEQGGGCPRKTLVMFVVQQLELEKPQ 234 (861)
T ss_pred hHHHHHHHHHHHHHhcCCccccceEEEEeeeccccchh
Confidence 3479999999999975 589999999999999998764
No 135
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.30 E-value=55 Score=33.17 Aligned_cols=26 Identities=23% Similarity=0.361 Sum_probs=20.8
Q ss_pred ccccccccccc-CCCCCCCcccCCcccc
Q 027188 196 TKLCENFAKGS-CTFGDRCHFAHGSEEL 222 (227)
Q Consensus 196 TklC~~f~~G~-C~~G~~C~FAHg~~EL 222 (227)
-++|.+|.++. |.. ++|-|-|..-.|
T Consensus 61 e~~CYwe~~p~gC~k-~~CgfRH~~pPL 87 (667)
T KOG4791|consen 61 EIPCYWENQPTGCQK-LNCGFRHNRPPL 87 (667)
T ss_pred cccceeecCCCccCC-CccccccCCCch
Confidence 46899999988 876 899999965443
Done!