Query psy2081
Match_columns 380
No_of_seqs 275 out of 832
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 23:49:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2081.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2081hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2814|consensus 100.0 6.5E-56 1.4E-60 421.4 14.7 285 90-380 56-345 (345)
2 PLN00108 unknown protein; Prov 100.0 1.7E-49 3.7E-54 372.5 21.0 211 159-380 30-254 (257)
3 PF10469 AKAP7_NLS: AKAP7 2'5' 100.0 1.4E-43 2.9E-48 328.2 20.0 205 165-380 1-209 (209)
4 COG1514 LigT 2'-5' RNA ligase 100.0 4.4E-28 9.4E-33 219.6 19.5 178 165-380 1-178 (180)
5 TIGR02258 2_5_ligase 2'-5' RNA 100.0 4.2E-27 9.2E-32 212.2 20.1 179 165-380 1-179 (179)
6 PRK15124 2'-5' RNA ligase; Pro 100.0 6.8E-27 1.5E-31 211.3 18.6 170 165-380 5-174 (176)
7 PRK13679 hypothetical protein; 99.8 1.9E-17 4.2E-22 148.5 16.3 166 166-380 2-167 (168)
8 PHA02574 57B hypothetical prot 99.7 6.2E-17 1.3E-21 142.0 10.7 111 164-315 8-118 (149)
9 PF13563 2_5_RNA_ligase2: 2'-5 99.4 1.5E-12 3.3E-17 113.3 9.1 130 205-365 21-151 (153)
10 cd02393 PNPase_KH Polynucleoti 99.4 1.3E-12 2.8E-17 98.0 6.7 59 92-153 3-61 (61)
11 cd02394 vigilin_like_KH K homo 99.3 3.2E-12 6.9E-17 95.7 5.6 60 93-153 2-62 (62)
12 PF05213 Corona_NS2A: Coronavi 99.3 1E-10 2.2E-15 106.4 13.3 166 163-377 4-176 (248)
13 PF00013 KH_1: KH domain syndr 99.2 4.7E-12 1E-16 94.2 2.1 60 92-152 1-60 (60)
14 PF02834 LigT_PEase: LigT like 99.1 1.7E-10 3.7E-15 91.8 6.3 87 171-270 1-87 (87)
15 cd00105 KH-I K homology RNA-bi 99.0 4.6E-10 9.9E-15 83.9 6.2 59 93-152 2-63 (64)
16 cd02395 SF1_like-KH Splicing f 98.9 3.4E-09 7.4E-14 90.1 7.4 61 99-159 14-96 (120)
17 smart00322 KH K homology RNA-b 98.9 9.3E-09 2E-13 76.5 8.2 65 91-156 3-68 (69)
18 cd02396 PCBP_like_KH K homolog 98.9 4.5E-09 9.8E-14 79.6 6.2 59 93-152 2-64 (65)
19 PF13014 KH_3: KH domain 98.8 1.1E-08 2.4E-13 71.1 4.6 39 101-139 1-43 (43)
20 PRK13763 putative RNA-processi 98.6 6.6E-08 1.4E-12 87.9 6.3 66 90-157 2-70 (180)
21 TIGR03665 arCOG04150 arCOG0415 98.5 1.1E-07 2.5E-12 85.8 4.6 62 95-158 2-65 (172)
22 KOG1676|consensus 98.5 2.9E-07 6.3E-12 95.0 7.5 144 89-236 228-387 (600)
23 TIGR02696 pppGpp_PNP guanosine 98.4 3.4E-07 7.3E-12 98.1 7.4 65 91-158 578-642 (719)
24 KOG0119|consensus 98.2 1.9E-06 4.1E-11 87.2 6.6 70 90-159 137-231 (554)
25 TIGR03591 polynuc_phos polyrib 98.2 1.3E-06 2.8E-11 94.4 5.6 65 91-158 551-615 (684)
26 PRK13763 putative RNA-processi 98.2 5.1E-06 1.1E-10 75.6 8.3 55 100-159 104-158 (180)
27 TIGR03665 arCOG04150 arCOG0415 98.2 6E-06 1.3E-10 74.6 7.9 55 100-159 98-152 (172)
28 COG1185 Pnp Polyribonucleotide 97.9 1.3E-05 2.8E-10 84.7 6.0 67 91-160 552-618 (692)
29 PLN00207 polyribonucleotide nu 97.9 8.7E-06 1.9E-10 89.2 4.4 66 90-158 684-750 (891)
30 PRK04163 exosome complex RNA-b 97.9 3.3E-05 7.1E-10 73.2 7.6 64 93-159 147-210 (235)
31 KOG2191|consensus 97.9 0.00011 2.4E-09 71.4 11.1 70 86-156 34-109 (402)
32 KOG1676|consensus 97.8 9.4E-05 2E-09 76.8 10.3 139 89-236 137-298 (600)
33 COG5176 MSL5 Splicing factor ( 97.8 2.7E-05 5.9E-10 71.1 4.9 73 87-159 144-222 (269)
34 KOG1588|consensus 97.8 0.0001 2.3E-09 69.8 8.7 40 91-130 92-137 (259)
35 KOG2113|consensus 97.8 1.7E-05 3.7E-10 76.4 3.3 65 89-154 24-88 (394)
36 KOG2193|consensus 97.7 2.8E-05 6E-10 77.6 4.1 75 91-166 199-277 (584)
37 PRK11824 polynucleotide phosph 97.6 4.5E-05 9.7E-10 82.8 3.6 64 92-158 555-618 (693)
38 KOG2192|consensus 97.5 0.00026 5.6E-09 67.1 7.2 68 91-159 315-385 (390)
39 PF09749 HVSL: Uncharacterised 97.4 0.0027 5.8E-08 60.3 13.3 141 165-315 40-188 (239)
40 KOG2191|consensus 97.4 0.00039 8.4E-09 67.7 7.1 77 92-174 133-215 (402)
41 COG1094 Predicted RNA-binding 97.4 0.00061 1.3E-08 62.1 7.8 56 100-160 111-166 (194)
42 KOG2190|consensus 97.3 0.00061 1.3E-08 70.8 7.5 68 91-159 138-209 (485)
43 COG1094 Predicted RNA-binding 97.3 0.0007 1.5E-08 61.7 6.8 65 90-156 7-75 (194)
44 KOG0336|consensus 97.2 0.00028 6E-09 70.9 3.4 73 86-159 42-114 (629)
45 KOG2208|consensus 97.1 0.00082 1.8E-08 73.6 5.9 104 87-193 344-449 (753)
46 PF07823 CPDase: Cyclic phosph 97.0 0.011 2.3E-07 54.5 12.0 178 166-380 4-196 (196)
47 PF02834 LigT_PEase: LigT like 96.9 0.00064 1.4E-08 53.7 2.9 76 277-372 8-87 (87)
48 KOG2193|consensus 96.9 0.0013 2.8E-08 65.9 5.3 70 90-160 492-566 (584)
49 TIGR03319 YmdA_YtgF conserved 96.7 0.0041 8.8E-08 65.4 7.2 68 91-160 204-272 (514)
50 PRK12704 phosphodiesterase; Pr 96.6 0.0051 1.1E-07 64.8 7.6 69 91-161 210-279 (520)
51 PRK00106 hypothetical protein; 96.6 0.0053 1.1E-07 64.6 7.4 68 91-160 225-293 (535)
52 KOG1067|consensus 96.5 0.0026 5.7E-08 66.0 4.2 69 87-159 593-661 (760)
53 COG1097 RRP4 RNA-binding prote 96.1 0.0093 2E-07 56.2 5.5 64 93-159 148-211 (239)
54 cd02134 NusA_KH NusA_K homolog 96.0 0.013 2.8E-07 43.7 4.9 37 90-126 24-60 (61)
55 KOG2192|consensus 95.7 0.07 1.5E-06 50.9 9.5 66 87-153 44-110 (390)
56 PRK12705 hypothetical protein; 95.3 0.021 4.6E-07 59.8 4.7 68 91-160 198-266 (508)
57 KOG2190|consensus 93.9 0.099 2.1E-06 54.6 5.8 101 93-193 45-167 (485)
58 KOG2814|consensus 93.2 0.028 6.1E-07 55.1 0.4 151 208-375 128-279 (345)
59 PF14611 SLS: Mitochondrial in 93.0 0.71 1.5E-05 42.6 9.4 67 92-161 27-93 (210)
60 KOG2113|consensus 92.8 0.081 1.7E-06 51.6 2.7 71 86-156 110-181 (394)
61 KOG2208|consensus 91.9 0.13 2.8E-06 56.7 3.3 46 83-128 701-746 (753)
62 PRK02821 hypothetical protein; 91.4 0.27 5.7E-06 38.6 3.8 35 86-121 27-61 (77)
63 PRK00468 hypothetical protein; 91.0 0.33 7.2E-06 37.9 3.9 31 89-119 28-58 (75)
64 TIGR03223 Phn_opern_protn puta 90.9 2.6 5.5E-05 39.9 10.5 139 208-380 56-226 (228)
65 KOG3273|consensus 90.2 0.17 3.7E-06 46.5 1.9 55 100-159 178-232 (252)
66 cd02409 KH-II KH-II (K homolo 90.0 0.79 1.7E-05 33.6 5.2 34 91-124 25-58 (68)
67 PRK01064 hypothetical protein; 89.5 0.59 1.3E-05 36.8 4.2 33 88-120 27-59 (78)
68 COG1837 Predicted RNA-binding 89.4 0.45 9.7E-06 37.2 3.4 32 88-119 27-58 (76)
69 COG1855 ATPase (PilT family) [ 89.1 0.28 6.1E-06 50.6 2.7 45 82-128 479-523 (604)
70 PRK13764 ATPase; Provisional 88.1 0.4 8.7E-06 51.5 3.2 45 82-128 474-518 (602)
71 KOG2279|consensus 87.8 0.49 1.1E-05 49.5 3.4 105 84-191 61-167 (608)
72 PRK08406 transcription elongat 87.3 0.72 1.6E-05 40.3 3.8 40 88-127 96-135 (140)
73 KOG2874|consensus 87.1 1 2.2E-05 43.6 4.8 50 102-160 160-209 (356)
74 cd02413 40S_S3_KH K homology R 85.3 0.82 1.8E-05 36.1 2.9 44 82-128 24-67 (81)
75 PF13083 KH_4: KH domain; PDB: 85.1 0.42 9.1E-06 36.6 1.1 34 91-124 29-62 (73)
76 PF13184 KH_5: NusA-like KH do 84.2 0.61 1.3E-05 35.7 1.6 35 92-126 4-44 (69)
77 PRK08406 transcription elongat 83.9 1.2 2.6E-05 38.9 3.5 36 92-127 33-68 (140)
78 cd02414 jag_KH jag_K homology 82.8 2 4.3E-05 33.3 4.0 36 92-127 25-60 (77)
79 TIGR01952 nusA_arch NusA famil 81.2 1.6 3.4E-05 38.3 3.2 40 88-127 97-136 (141)
80 KOG2279|consensus 79.4 1 2.2E-05 47.2 1.6 70 87-156 136-207 (608)
81 PF07650 KH_2: KH domain syndr 74.7 1 2.2E-05 34.8 0.1 43 80-125 17-59 (78)
82 TIGR01952 nusA_arch NusA famil 74.4 4 8.7E-05 35.7 3.8 36 92-127 34-69 (141)
83 KOG3102|consensus 71.8 14 0.00031 34.5 6.8 98 207-320 119-219 (269)
84 PF10283 zf-CCHH: Zinc-finger 71.6 1 2.2E-05 27.9 -0.4 14 27-40 4-17 (26)
85 cd02412 30S_S3_KH K homology R 70.0 5.1 0.00011 33.3 3.3 40 82-124 55-94 (109)
86 cd02411 archeal_30S_S3_KH K ho 69.0 8.9 0.00019 30.3 4.4 40 82-124 32-71 (85)
87 PHA02977 hypothetical protein; 68.2 27 0.00059 30.7 7.4 90 211-314 71-170 (201)
88 COG5166 Uncharacterized conser 66.9 4.3 9.3E-05 42.5 2.6 65 92-156 450-522 (657)
89 TIGR01953 NusA transcription t 65.4 7.1 0.00015 39.2 3.8 40 89-128 299-338 (341)
90 COG0195 NusA Transcription elo 64.4 6.9 0.00015 36.0 3.2 36 92-127 143-178 (190)
91 COG0092 RpsC Ribosomal protein 63.9 8.5 0.00018 36.4 3.8 42 82-126 45-86 (233)
92 PRK06418 transcription elongat 63.1 8.6 0.00019 34.6 3.5 35 92-127 62-96 (166)
93 PF06299 DUF1045: Protein of u 59.6 50 0.0011 29.6 7.7 112 221-364 13-152 (160)
94 PRK12328 nusA transcription el 59.0 8.3 0.00018 39.1 3.0 42 89-130 306-347 (374)
95 PRK12327 nusA transcription el 58.8 11 0.00025 38.0 3.9 41 88-128 300-340 (362)
96 PF00352 TBP: Transcription fa 54.1 38 0.00083 26.6 5.6 37 120-159 48-85 (86)
97 PRK09202 nusA transcription el 52.0 12 0.00025 39.3 2.9 37 91-127 302-338 (470)
98 COG5255 Uncharacterized protei 51.3 65 0.0014 30.1 7.1 31 278-314 154-184 (239)
99 PF08975 2H-phosphodiest: Doma 50.0 21 0.00047 30.3 3.6 48 166-217 14-61 (118)
100 PF13382 Adenine_deam_C: Adeni 49.8 38 0.00082 30.6 5.4 78 131-219 64-150 (171)
101 PTZ00084 40S ribosomal protein 49.5 35 0.00076 32.1 5.3 43 82-127 38-80 (220)
102 PRK12329 nusA transcription el 49.2 18 0.00039 37.5 3.6 38 91-128 335-372 (449)
103 COG0195 NusA Transcription elo 47.9 19 0.00041 33.1 3.2 35 92-126 77-111 (190)
104 COG1702 PhoH Phosphate starvat 47.6 45 0.00098 33.5 6.0 57 99-160 23-81 (348)
105 cd02410 archeal_CPSF_KH The ar 47.2 18 0.0004 31.8 2.9 33 94-126 79-111 (145)
106 PRK15031 5-carboxymethyl-2-hyd 45.4 26 0.00056 30.1 3.5 46 208-253 60-105 (126)
107 KOG3102|consensus 42.5 75 0.0016 29.8 6.2 86 162-258 167-257 (269)
108 PF07823 CPDase: Cyclic phosph 41.6 39 0.00086 30.9 4.4 39 267-314 3-44 (196)
109 PF08302 tRNA_lig_CPD: Fungal 41.6 2.3E+02 0.005 27.2 9.8 15 220-234 25-39 (257)
110 COG1135 AbcC ABC-type metal io 41.1 35 0.00076 34.0 4.0 93 93-189 25-129 (339)
111 TIGR01008 rpsC_E_A ribosomal p 40.9 43 0.00094 30.9 4.5 40 82-124 32-71 (195)
112 PF02962 CHMI: 5-carboxymethyl 38.9 37 0.0008 29.1 3.4 28 209-236 60-87 (124)
113 PRK04191 rps3p 30S ribosomal p 37.7 1.5E+02 0.0033 27.5 7.7 42 82-126 34-75 (207)
114 COG3638 ABC-type phosphate/pho 37.5 50 0.0011 31.7 4.4 113 92-235 22-135 (258)
115 TIGR03675 arCOG00543 arCOG0054 35.8 1.1E+02 0.0023 33.4 7.2 35 93-127 95-129 (630)
116 CHL00048 rps3 ribosomal protei 35.4 80 0.0017 29.5 5.4 42 82-126 60-101 (214)
117 PTZ00179 60S ribosomal protein 32.4 1.1E+02 0.0025 28.0 5.8 49 119-169 125-174 (189)
118 TIGR01009 rpsC_bact ribosomal 31.2 71 0.0015 29.8 4.3 39 82-123 56-94 (211)
119 TIGR03693 ocin_ThiF_like putat 30.2 6.7E+02 0.014 27.5 11.8 131 120-275 390-530 (637)
120 PRK13679 hypothetical protein; 30.2 3.8E+02 0.0082 23.5 12.5 106 112-234 16-136 (168)
121 PF09749 HVSL: Uncharacterised 29.9 1.1E+02 0.0024 28.8 5.4 66 163-235 138-208 (239)
122 PF03808 Glyco_tran_WecB: Glyc 29.7 1.7E+02 0.0038 25.9 6.5 68 211-291 48-125 (172)
123 PRK13731 conjugal transfer sur 29.0 81 0.0018 30.1 4.2 58 258-316 43-101 (243)
124 cd06533 Glyco_transf_WecG_TagA 29.0 1.7E+02 0.0037 26.0 6.3 68 211-291 46-123 (171)
125 PLN00062 TATA-box-binding prot 28.4 86 0.0019 28.5 4.2 32 131-162 145-177 (179)
126 COG0331 FabD (acyl-carrier-pro 28.3 4E+02 0.0087 26.3 9.3 83 103-190 134-218 (310)
127 COG0799 Uncharacterized homolo 28.0 3.7E+02 0.008 22.7 7.6 60 225-298 7-66 (115)
128 COG1782 Predicted metal-depend 27.1 43 0.00094 35.4 2.3 34 93-126 101-134 (637)
129 PRK15245 type III effector pho 26.7 3.4E+02 0.0073 25.5 7.7 79 208-298 103-194 (241)
130 TIGR00436 era GTP-binding prot 26.4 64 0.0014 30.7 3.2 27 91-117 221-248 (270)
131 KOG4369|consensus 25.7 29 0.00063 40.1 0.8 62 94-156 1343-1408(2131)
132 KOG3302|consensus 25.5 87 0.0019 28.9 3.7 40 120-162 158-198 (200)
133 PRK12327 nusA transcription el 24.1 58 0.0013 33.0 2.5 38 91-128 231-274 (362)
134 COG1847 Jag Predicted RNA-bind 23.2 82 0.0018 29.4 3.1 43 83-126 84-126 (208)
135 PRK15494 era GTPase Era; Provi 22.8 86 0.0019 31.2 3.5 25 92-116 274-299 (339)
136 PF08921 DUF1904: Domain of un 22.4 3.5E+02 0.0075 22.5 6.4 74 218-297 7-88 (108)
137 PRK00310 rpsC 30S ribosomal pr 21.7 3.1E+02 0.0066 26.0 6.8 39 82-123 56-94 (232)
138 TIGR01953 NusA transcription t 21.6 74 0.0016 32.0 2.7 37 91-127 229-271 (341)
139 PRK09256 hypothetical protein; 21.3 1.2E+02 0.0027 26.3 3.7 31 131-161 66-100 (138)
140 PRK00089 era GTPase Era; Revie 21.3 61 0.0013 31.0 2.0 25 92-116 227-252 (292)
141 KOG1423|consensus 21.0 1.1E+02 0.0023 30.7 3.6 28 92-119 329-357 (379)
142 COG0851 MinE Septum formation 20.6 2E+02 0.0043 23.2 4.4 19 143-161 13-31 (88)
143 COG1159 Era GTPase [General fu 20.5 53 0.0011 32.4 1.3 30 87-116 223-255 (298)
144 PRK11538 ribosome-associated p 20.5 4.9E+02 0.011 21.4 7.4 60 225-298 7-66 (105)
145 cd04516 TBP_eukaryotes eukaryo 20.4 1.7E+02 0.0037 26.4 4.6 38 120-160 46-84 (174)
146 cd00652 TBP_TLF TATA box bindi 20.3 3E+02 0.0065 24.7 6.1 37 121-160 47-84 (174)
147 COG4604 CeuD ABC-type enteroch 20.2 1.2E+02 0.0025 28.8 3.4 44 93-140 20-63 (252)
148 PF14611 SLS: Mitochondrial in 20.2 2.5E+02 0.0055 25.5 5.8 73 83-157 84-164 (210)
No 1
>KOG2814|consensus
Probab=100.00 E-value=6.5e-56 Score=421.45 Aligned_cols=285 Identities=33% Similarity=0.554 Sum_probs=259.0
Q ss_pred ceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCC-CCcEEEeeCCHHHHHHHHHHHHHHhhhhcccCCccee
Q psy2081 90 QYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQ-TGDIIISSYSERGIASAKRRLDLLLVFARKKIPYTHL 168 (380)
Q Consensus 90 ~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~-~~~i~I~g~~~~~v~~A~~~I~~iv~~~rkk~~~thF 168 (380)
.|..+++|+++|++.|||++|.|+++||+||+|+|-+|++++ .+.|+|+|.++.+|.+|.+||..++++.|++.|+|||
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~s~p~thf 135 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDSDRKSFPITHF 135 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHhhhhcCchhhh
Confidence 599999999999999999999999999999999999999995 5899999999999999999999999999999999999
Q ss_pred eeccCCChhHHHHHHHHHHHHhcccC-cCCCCccccccCCCCceeeEEeeccCCchhHHHHHHHHHhhcccccccccccC
Q psy2081 169 LSIPMNVPNIQENFAKFKATVLSDFS-RCRGIEESLFQEPGRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPILRSQ 247 (380)
Q Consensus 169 IaIpl~~~~I~~~~~~fq~~v~~~~~-~~~gi~~~~fv~p~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~~~~ 247 (380)
+|+|++..+|++.|..|++.....++ ...|++.+.|++|..+||||+|+.++++++|++|++.|+.+.+++. ...+..
T Consensus 136 lal~lne~eVqe~f~~fke~~~~~esl~~~g~~~s~F~~p~~~HLTvgm~~L~~dd~vq~a~e~les~~~e~~-~~~~~k 214 (345)
T KOG2814|consen 136 LALPLNEHEVQEGFLAFKELKPFIESLLDGGIDKSLFQGPGTFHLTVGMLKLLNDDDVQKALEILESTFQEIR-IDVGEK 214 (345)
T ss_pred hhhhcchHHHHHHHHHHHhhhhhHHHhhccchhhccccCCceeeEEEEEEEecChHHHHHHHHHHHHHHHHHH-hccCCC
Confidence 99999987999999999944333222 3567999999999999999999999999999999999999854443 455679
Q ss_pred ceEEEecceecCCCCCCceeEEEEEecC--ChHHHHHHH-HHHHHHHHHCCCccccccCCCceeeEEEeecccccccCCC
Q psy2081 248 RIKINLKGLEIMNDDPAEVDILYAKVVD--DSGLVQKLC-DDVVQYFISQHLISKAYQKYDTVKMHVTLMNSKYRMRQNP 324 (380)
Q Consensus 248 pf~l~l~Glg~F~ddp~~~rVLya~v~d--~~~~Lq~L~-~~l~~~f~~~Gl~~~~~~e~r~fkpHiTL~nt~~r~~~~~ 324 (380)
|+.+.++|+++|||+|..++||||+|++ ....|+..+ +.|..+|.++|+.. ++++++++|+||||++||+.+.
T Consensus 215 p~~i~lkG~~~mnddP~~~kVLYAkv~~~~~e~~l~~~~~~~i~~~f~~~~li~---k~~~~~kLH~TvmNsryrk~~~- 290 (345)
T KOG2814|consen 215 PLFIDLKGLDKMNDDPSLTKVLYAKVEPDDYEKFLQHRCGERILERFVASGLIK---KESSSLKLHCTVMNSRYRKNGG- 290 (345)
T ss_pred ceeeeccchhhhcCCHhHheeeeeeccCcchHHHHHHHHHHHHHHHHHHhcchh---ccccccEEEEEEehhhhhhcCC-
Confidence 9999999999999999999999999993 357888888 99999999999999 7999999999999999998754
Q ss_pred CCCCCccccCcCCHHHHHHHhCCceeceEEeeEEEEEEeeecCCCCceeeeEEEeC
Q psy2081 325 SSDTNSEKRSTFNAKDILESLGDFEFGETFVYCVHLSQRHTHDMDGYFKPSAVISL 380 (380)
Q Consensus 325 ~~~~~~~~r~~fda~~il~~~~~~~fG~~~v~~I~L~~s~~~~~~g~Y~~~~~i~L 380 (380)
.++..+....||+++||+.|++|.||++.+.++|+++....+++|||.+.++++|
T Consensus 291 -~~g~~K~~~~Fdar~ilk~fg~f~fg~~~~~eih~~~~~~~d~ng~y~~~gsi~f 345 (345)
T KOG2814|consen 291 -EPGLVKESESFDAREILKAFGQFLFGELKLQEIHLSVRFAADQNGNYNECGSIPF 345 (345)
T ss_pred -CcchhhHhhhccHHHHHHHHhhHhHhhcccceeeeeeeeccccccchhhhcCCCC
Confidence 3333466778999999999999999999999999999999999999999999987
No 2
>PLN00108 unknown protein; Provisional
Probab=100.00 E-value=1.7e-49 Score=372.45 Aligned_cols=211 Identities=28% Similarity=0.522 Sum_probs=193.7
Q ss_pred hcccCCcceeeeccCC-ChhHHHHHHHHHHHHhcccCc----------CCCCccccccCCCCceeeEEeeccCCchhHHH
Q psy2081 159 ARKKIPYTHLLSIPMN-VPNIQENFAKFKATVLSDFSR----------CRGIEESLFQEPGRLHITMGMLMLADSVERDQ 227 (380)
Q Consensus 159 ~rkk~~~thFIaIpl~-~~~I~~~~~~fq~~v~~~~~~----------~~gi~~~~fv~p~~LHLTL~~L~l~~~~ev~~ 227 (380)
..++.+|||||||||. +++|++.+.+||+.|+..++. +.|+++++|++|.+|||||+||.|.+++++++
T Consensus 30 ~~~~~~~THFlavPL~~~p~i~~~~~~Fk~~Vl~~~~~~~~~f~~~l~~~gid~siF~~p~~LHLTLgmL~L~~~eev~k 109 (257)
T PLN00108 30 QAHREVFTHFVSLPLAIYPDLKKNIEAFQNSVLGNNDKDPLKFQSTLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVK 109 (257)
T ss_pred cccCCCCCeEEEEEcCCCHHHHHHHHHHHHHHHhccccccccccccccccCCCHHHcCCCCceEEEEEEEEcCCHHHHHH
Confidence 3457899999999995 899999999999999986552 45899999999999999999999999999999
Q ss_pred HHHHHHhhcccccccccccCceEEEecceecCCCCCCceeEEEEEecC--ChHHHHHHHHHHHHHHHHCCCccccccCC-
Q psy2081 228 AVEVLQKCGNNIILPILRSQRIKINLKGLEIMNDDPAEVDILYAKVVD--DSGLVQKLCDDVVQYFISQHLISKAYQKY- 304 (380)
Q Consensus 228 A~~~L~~~~~~~i~~~~~~~pf~l~l~Glg~F~ddp~~~rVLya~v~d--~~~~Lq~L~~~l~~~f~~~Gl~~~~~~e~- 304 (380)
|.++|++|. ..|+++++.+|+.|+|+||++|||||++++||||+|++ +.++||++|+.|.+.|+++||+. ++.
T Consensus 110 A~~~L~s~~-~~i~~~l~~~pl~I~lkGL~~Mnddps~~~VLYA~Ve~~~~~~rLq~~ad~i~~~F~~aGL~~---~d~~ 185 (257)
T PLN00108 110 AQNILKSIC-SNVRQALKDRPVFIRLRGLDCMNGSLDKTRVLYAPVEEVGHEGRLLNACHVIIDAFENAGFAG---KDAK 185 (257)
T ss_pred HHHHHHHHH-HHHHHhhCCCCeEEEEEeehhcCCCcccceEEEEeccccCchhHHHHHHHHHHHHHHHcCCcc---cccC
Confidence 999999995 77888888899999999999999999999999999983 35799999999999999999997 454
Q ss_pred CceeeEEEeecccccccCCCCCCCCccccCcCCHHHHHHHhCCceeceEEeeEEEEEEeeecCCCCceeeeEEEeC
Q psy2081 305 DTVKMHVTLMNSKYRMRQNPSSDTNSEKRSTFNAKDILESLGDFEFGETFVYCVHLSQRHTHDMDGYFKPSAVISL 380 (380)
Q Consensus 305 r~fkpHiTL~nt~~r~~~~~~~~~~~~~r~~fda~~il~~~~~~~fG~~~v~~I~L~~s~~~~~~g~Y~~~~~i~L 380 (380)
+++|||+||||++||+... +++.+|||++|+++|++++||.+.|++||||++++.+.+|||++.++++|
T Consensus 186 ~~vKLH~TlmNt~~rk~k~-------~k~~sFDA~~Il~~f~d~~FG~~~i~~vhls~r~s~~~dGyY~~~~sl~~ 254 (257)
T PLN00108 186 SRLKLHATLMNASYRKDKS-------KKMDTFDAREIHKEFENKDWGTYLIREAHISQRYKYDPNGYFHCCASLPF 254 (257)
T ss_pred cceeeEeEEechhhhhccc-------CccccccHHHHHHhccCcccceEEecEEEEEeecccCCCCCEEEEEEeec
Confidence 6999999999999987643 57789999999999999999999999999999999999999999999987
No 3
>PF10469 AKAP7_NLS: AKAP7 2'5' RNA ligase-like domain; InterPro: IPR019510 This entry represents the N-terminal nuclear localisation signal-containing domain found in the cyclic AMP-dependent protein kinase A (PKA) anchor protein, AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes []. This domain carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein []. Binding to the regulatory subunits RI and RII of PKA is mediated via the RI-RII subunit-binding domain at the C terminus.
Probab=100.00 E-value=1.4e-43 Score=328.24 Aligned_cols=205 Identities=38% Similarity=0.612 Sum_probs=178.5
Q ss_pred cceeeeccCCChhHHHHHHHHHHHHhcccCcCCCCccccccCCCCceeeEEeeccCCchhHHHHHHHHHhhccccccccc
Q psy2081 165 YTHLLSIPMNVPNIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPIL 244 (380)
Q Consensus 165 ~thFIaIpl~~~~I~~~~~~fq~~v~~~~~~~~gi~~~~fv~p~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~ 244 (380)
||||||||+++++|++.+.+||+.|+..+ ++++.++|++|++|||||+||++.+++++++|+++|+++.+.+.+.+.
T Consensus 1 pthFl~ipl~~~~i~~~~~~fq~~v~~~~---~~~~~~~~i~~~~lHlTL~vl~L~~~~~i~~a~~~L~~~~~~i~~~~~ 77 (209)
T PF10469_consen 1 PTHFLCIPLNSPEIQEKFKEFQNEVLSKD---PGLDESAFIPPEKLHLTLGVLSLDTDEEIEKAKEALKSLKQEIKDQLQ 77 (209)
T ss_pred CCeEEEEECCCHHHHHHHHHHHHHHHhhc---CCCCHHHcCCcccceEEEEEeeCCCHHHHHHHHHHHHHHHHHHhhhcc
Confidence 79999999999999999999999999765 478889999999999999999999999999999999999654443322
Q ss_pred ccCceEEEecceecCCCCCCceeEEEEEecCC--hHHHHHHHHHHHHHHHHCCCccccccCCC-ceeeEEEeeccccccc
Q psy2081 245 RSQRIKINLKGLEIMNDDPAEVDILYAKVVDD--SGLVQKLCDDVVQYFISQHLISKAYQKYD-TVKMHVTLMNSKYRMR 321 (380)
Q Consensus 245 ~~~pf~l~l~Glg~F~ddp~~~rVLya~v~d~--~~~Lq~L~~~l~~~f~~~Gl~~~~~~e~r-~fkpHiTL~nt~~r~~ 321 (380)
..+|+.|+|+|+++||+||+++|||||+|.++ ...|++|++.|.+.|.++||... ++.+ +|+||+||||++|+..
T Consensus 78 ~~~~~~i~l~Gl~~f~~d~~~~~VLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~--~~~~~~~~~H~Tl~n~~~~~~ 155 (209)
T PF10469_consen 78 NPPPLKITLKGLGYFNDDPSKARVLYAKVSEDSNSERLQELANKLRERFQEAGLLVT--DDRRFSFKPHITLMNTSYRKK 155 (209)
T ss_pred CCCCceEEeeechhhCCCCCcceEEEEcccccchHHHHHHHHHHHHHHHHHcCCccc--cccCCCcceEEEEEecccccc
Confidence 24999999999999998899999999999943 69999999999999999999983 2233 3899999999999632
Q ss_pred CCCCCCCCccccCcCCHHHHHHHhCCceeceEEeeEEEEEEeeecCC-CCceeeeEEEeC
Q psy2081 322 QNPSSDTNSEKRSTFNAKDILESLGDFEFGETFVYCVHLSQRHTHDM-DGYFKPSAVISL 380 (380)
Q Consensus 322 ~~~~~~~~~~~r~~fda~~il~~~~~~~fG~~~v~~I~L~~s~~~~~-~g~Y~~~~~i~L 380 (380)
.. .+...+||++++++.|++++||.+.|++|+||+|+..+. +|||.++++|+|
T Consensus 156 ~~------~~~~~~~d~~~~~~~~~~~~fG~~~v~~i~Lc~m~~~~~~dg~Y~~~~~i~l 209 (209)
T PF10469_consen 156 KK------RRQGNKFDASELLEKYKDFDFGEQPVEEIQLCSMGSTKPSDGYYQCIASIPL 209 (209)
T ss_pred cc------ccccCccccHHHHHHcCCCccceEEECEEEEEeCCCCCCCCCeEEEEEEecC
Confidence 11 022267999999999999999999999999999988875 999999999987
No 4
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=4.4e-28 Score=219.55 Aligned_cols=178 Identities=20% Similarity=0.256 Sum_probs=158.0
Q ss_pred cceeeeccCCChhHHHHHHHHHHHHhcccCcCCCCccccccCCCCceeeEEeeccCCchhHHHHHHHHHhhccccccccc
Q psy2081 165 YTHLLSIPMNVPNIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPIL 244 (380)
Q Consensus 165 ~thFIaIpl~~~~I~~~~~~fq~~v~~~~~~~~gi~~~~fv~p~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~ 244 (380)
+++||||+++ +++++.+..++..+... . ...|++++++||||.|||.++++.++.++++|.++. .
T Consensus 1 ~RlFiAl~~p-~~i~~~i~~~~~~~~~~------~-~~k~v~~en~HiTL~flGev~e~~~~~l~~~l~~i~-------~ 65 (180)
T COG1514 1 MRLFIALDPP-AEIAERLARIRARLKGA------R-AIKWVEPENLHITLKFLGEVDEDKADELIEALARIA-------A 65 (180)
T ss_pred CeeEEEecCC-HHHHHHHHHHHHhcCcc------c-ccccccccCceEEEEccCCcCchHHHHHHHHHHHhh-------c
Confidence 4799999998 68999999999988753 1 457999999999999999999999999999998884 1
Q ss_pred ccCceEEEecceecCCCCCCceeEEEEEecCChHHHHHHHHHHHHHHHHCCCccccccCCCceeeEEEeecccccccCCC
Q psy2081 245 RSQRIKINLKGLEIMNDDPAEVDILYAKVVDDSGLVQKLCDDVVQYFISQHLISKAYQKYDTVKMHVTLMNSKYRMRQNP 324 (380)
Q Consensus 245 ~~~pf~l~l~Glg~F~ddp~~~rVLya~v~d~~~~Lq~L~~~l~~~f~~~Gl~~~~~~e~r~fkpHiTL~nt~~r~~~~~ 324 (380)
.. ||.|+++|+|.|+ ++..|||+|+++.+ .+.|.+|++.|...+...||.. +.++|.||+||++.+. +
T Consensus 66 ~~-~f~i~l~g~g~F~-~~~~~rvi~~~v~~-~~~L~~L~~~l~~~~~~~g~~~----~~r~F~PHvTl~r~k~-~---- 133 (180)
T COG1514 66 PE-PFPITLDGAGSFP-NPRRPRVIWVGVEE-TEELRALAEELERALARLGLRP----EERPFVPHVTLARVKS-K---- 133 (180)
T ss_pred CC-ceEEEEeeEcccC-CCCCCcEEEEcCCC-cHHHHHHHHHHHHHHHhcCCCC----CCCCcCCCEEEEeecc-c----
Confidence 23 9999999999999 69999999999995 7899999999999999999997 7899999999996543 1
Q ss_pred CCCCCccccCcCCHHHHHHHhCCceeceEEeeEEEEEEeeecCCCCceeeeEEEeC
Q psy2081 325 SSDTNSEKRSTFNAKDILESLGDFEFGETFVYCVHLSQRHTHDMDGYFKPSAVISL 380 (380)
Q Consensus 325 ~~~~~~~~r~~fda~~il~~~~~~~fG~~~v~~I~L~~s~~~~~~g~Y~~~~~i~L 380 (380)
-...+++..+.+..||++.|++++|++|.+++.++.|+++.+++|
T Consensus 134 -----------~~~~~~~~~~~~~~~~~~~vd~~~L~~S~l~~~gp~Y~~~~~~~L 178 (180)
T COG1514 134 -----------DKLVEALGEFKNVEFGEMEVDRFSLYSSTLTPGGPIYETLKEFPL 178 (180)
T ss_pred -----------chhhhhhhhhccccccceEeeEEEEEEEeeCCCCCEEEEEEEEec
Confidence 124578889999999999999999999999999999999999886
No 5
>TIGR02258 2_5_ligase 2'-5' RNA ligase. This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles.
Probab=99.95 E-value=4.2e-27 Score=212.18 Aligned_cols=179 Identities=21% Similarity=0.312 Sum_probs=154.1
Q ss_pred cceeeeccCCChhHHHHHHHHHHHHhcccCcCCCCccccccCCCCceeeEEeeccCCchhHHHHHHHHHhhccccccccc
Q psy2081 165 YTHLLSIPMNVPNIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPIL 244 (380)
Q Consensus 165 ~thFIaIpl~~~~I~~~~~~fq~~v~~~~~~~~gi~~~~fv~p~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~ 244 (380)
+|+|+||+++. ++++.+.++++.+....+ ...|++++++||||.|++..++++++.+.+.|.++.
T Consensus 1 ~R~FiAl~~p~-~~~~~l~~~~~~l~~~~~------~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~-------- 65 (179)
T TIGR02258 1 MRLFIAIDLPP-EIREQLSRIQRKLKSPLD------GIKWVPPENLHITLKFLGEVDEEQVEELEDALAKIA-------- 65 (179)
T ss_pred CeEEEEecCCH-HHHHHHHHHHHHhhccCC------CcEECChHHCEEEEEEccCCCHHHHHHHHHHHHHhc--------
Confidence 48999999995 699999999999875322 357999999999999999999999999999888763
Q ss_pred ccCceEEEecceecCCCCCCceeEEEEEecCChHHHHHHHHHHHHHHHHCCCccccccCCCceeeEEEeecccccccCCC
Q psy2081 245 RSQRIKINLKGLEIMNDDPAEVDILYAKVVDDSGLVQKLCDDVVQYFISQHLISKAYQKYDTVKMHVTLMNSKYRMRQNP 324 (380)
Q Consensus 245 ~~~pf~l~l~Glg~F~ddp~~~rVLya~v~d~~~~Lq~L~~~l~~~f~~~Gl~~~~~~e~r~fkpHiTL~nt~~r~~~~~ 324 (380)
..+|.+.+.|+++|+ +++.++|||+++++ .+.|.+|++.+.+.+...|+.. +.++|+|||||++....
T Consensus 66 -~~~f~l~l~~~~~F~-~~~~~~vl~l~~~~-~~~L~~L~~~l~~~~~~~g~~~----~~~~f~PHiTlar~~~~----- 133 (179)
T TIGR02258 66 -EPPFTLKLEGIGVFG-NPKRPRVLWAGVEQ-SEELTQLHADLERELAKLGFSK----EERPFTPHITLARKKSG----- 133 (179)
T ss_pred -CCCeEEEEeeeeeCC-CCCCCeEEEEeeCC-CHHHHHHHHHHHHHHHHcCCCC----CCCCcCCCEEEEEecCC-----
Confidence 356999999999999 68889999999985 4599999999999999999975 77899999999953211
Q ss_pred CCCCCccccCcCCHHHHHHHhCCceeceEEeeEEEEEEeeecCCCCceeeeEEEeC
Q psy2081 325 SSDTNSEKRSTFNAKDILESLGDFEFGETFVYCVHLSQRHTHDMDGYFKPSAVISL 380 (380)
Q Consensus 325 ~~~~~~~~r~~fda~~il~~~~~~~fG~~~v~~I~L~~s~~~~~~g~Y~~~~~i~L 380 (380)
. .+..++++.+..+.++.+.|++|+|++|.+++.|+.|+++++++|
T Consensus 134 -------~---~~~~~~~~~~~~~~~~~~~v~~i~L~~S~~~~~g~~Y~~l~~~~l 179 (179)
T TIGR02258 134 -------K---PGVPEFLQEFANEEFGSFHVDEFHLYSSTLTPGGPIYEPLARFQL 179 (179)
T ss_pred -------c---HhHHHHHHHhCCCCCCceEeeEEEEEEeeccCCCCcceEEEEEcC
Confidence 0 234567888888889999999999999999999999999999987
No 6
>PRK15124 2'-5' RNA ligase; Provisional
Probab=99.95 E-value=6.8e-27 Score=211.26 Aligned_cols=170 Identities=12% Similarity=0.125 Sum_probs=141.5
Q ss_pred cceeeeccCCChhHHHHHHHHHHHHhcccCcCCCCccccccCCCCceeeEEeeccCCchhHHHHHHHHHhhccccccccc
Q psy2081 165 YTHLLSIPMNVPNIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPIL 244 (380)
Q Consensus 165 ~thFIaIpl~~~~I~~~~~~fq~~v~~~~~~~~gi~~~~fv~p~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~ 244 (380)
.|+|+||+++ +++++.+.++++.+.... ...|++|+++||||.|||.+++++++.+.+++.++
T Consensus 5 ~RlFiAl~~p-~~~~~~l~~~~~~~~~~~-------~~rwv~~~nlHiTL~FlG~v~~~~~~~l~~~l~~~--------- 67 (176)
T PRK15124 5 KRLFFAIDLP-DEIRQQIIHWRATHFPPE-------AGRPVAAANLHLTLAFLGEVSAEKQQALSQLAGRI--------- 67 (176)
T ss_pred eEEEEEeCCC-HHHHHHHHHHHHHhcccc-------CcccccccccEEEEEecCCCCHHHHHHHHHHHHhc---------
Confidence 5999999999 479999999998775421 35799999999999999999999999888888766
Q ss_pred ccCceEEEecceecCCCCCCceeEEEEEecCChHHHHHHHHHHHHHHHHCCCccccccCCCceeeEEEeecccccccCCC
Q psy2081 245 RSQRIKINLKGLEIMNDDPAEVDILYAKVVDDSGLVQKLCDDVVQYFISQHLISKAYQKYDTVKMHVTLMNSKYRMRQNP 324 (380)
Q Consensus 245 ~~~pf~l~l~Glg~F~ddp~~~rVLya~v~d~~~~Lq~L~~~l~~~f~~~Gl~~~~~~e~r~fkpHiTL~nt~~r~~~~~ 324 (380)
..+||.|.++|+|+|++ |||||++++++.+.|..|++.|.+.+..+|+.. |.++|+|||||+|.+. ...
T Consensus 68 ~~~pF~l~l~~~g~Fp~----prvlwlg~~~~~~~L~~L~~~l~~~l~~~G~~~----e~r~f~PHiTLaR~~~--~~~- 136 (176)
T PRK15124 68 RQPGFTLTLDDAGQWPR----SRVVWLGMRQPPRGLLQLANMLRSQAARSGCYQ----SPQPFHPHITLLRDAS--RPV- 136 (176)
T ss_pred ccCCeEEEECcccCcCC----CCEEEEEcCCCCHHHHHHHHHHHHHHHHcCCCC----CCCCCCCCEeeccCCC--Ccc-
Confidence 24799999999999983 899999998667899999999999999999976 8899999999985321 100
Q ss_pred CCCCCccccCcCCHHHHHHHhCCceeceEEeeEEEEEEeeecCCCCceeeeEEEeC
Q psy2081 325 SSDTNSEKRSTFNAKDILESLGDFEFGETFVYCVHLSQRHTHDMDGYFKPSAVISL 380 (380)
Q Consensus 325 ~~~~~~~~r~~fda~~il~~~~~~~fG~~~v~~I~L~~s~~~~~~g~Y~~~~~i~L 380 (380)
... . ..+.+ .+.|++|+|++|.+++.|+.|+++++++|
T Consensus 137 ----------~~~-----~--~~~~~-~~~v~~~~L~~S~l~~~g~~Y~~l~~~~L 174 (176)
T PRK15124 137 ----------AIP-----P--PGFNW-SFPVTEFTLYASSFARGRTRYTPLQRWPL 174 (176)
T ss_pred ----------ccc-----C--CCCCC-ceEcCEEEEEEEeccCCCCEEEEEEEEeC
Confidence 011 0 11233 48899999999999999999999999987
No 7
>PRK13679 hypothetical protein; Provisional
Probab=99.76 E-value=1.9e-17 Score=148.48 Aligned_cols=166 Identities=14% Similarity=0.135 Sum_probs=125.6
Q ss_pred ceeeeccCCChhHHHHHHHHHHHHhcccCcCCCCccccccCCCCceeeEEeeccCCchhHHHHHHHHHhhcccccccccc
Q psy2081 166 THLLSIPMNVPNIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPILR 245 (380)
Q Consensus 166 thFIaIpl~~~~I~~~~~~fq~~v~~~~~~~~gi~~~~fv~p~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~~ 245 (380)
.|||||+++. .+++.+.++++.+... ..+++| ||||.|++..++++++++.+.|+++. ..
T Consensus 2 ~~~iai~~p~-~~~~~l~~~~~~~~~~---------~~~v~p---HITL~f~g~~~~~~~~~l~~~l~~~~-------~~ 61 (168)
T PRK13679 2 KYGIVLFPSK-KIQDFANSYRKRYDPH---------YALIPP---HITLKEPFEISDEQLDSIVEELRAIA-------SE 61 (168)
T ss_pred eeEEEEcCCH-HHHHHHHHHHHhhCcc---------cccCCC---ceEEecCCCCCHHHHHHHHHHHHHHH-------hc
Confidence 6999999995 6999999998776421 236777 99999999999999999999888773 13
Q ss_pred cCceEEEecceecCCCCCCceeEEEEEecCChHHHHHHHHHHHHHHHHCCCccccccCCCceeeEEEeecccccccCCCC
Q psy2081 246 SQRIKINLKGLEIMNDDPAEVDILYAKVVDDSGLVQKLCDDVVQYFISQHLISKAYQKYDTVKMHVTLMNSKYRMRQNPS 325 (380)
Q Consensus 246 ~~pf~l~l~Glg~F~ddp~~~rVLya~v~d~~~~Lq~L~~~l~~~f~~~Gl~~~~~~e~r~fkpHiTL~nt~~r~~~~~~ 325 (380)
..||.+++.|+++|+ .+ ++|||++++. .+.|++|++.|...+. + . .+.++|.|||||++....
T Consensus 62 ~~pf~l~l~~~~~F~-~~--~~vl~l~~~~-~~~L~~L~~~l~~~~~--~--~---~~~~~f~PHiTlar~~~~------ 124 (168)
T PRK13679 62 TKPFTLHVTKVSSFA-PT--NNVIYFKVEK-TEELEELHERLHSGDF--Y--G---EAEYAFVPHITIGQGLSD------ 124 (168)
T ss_pred CCCEEEEEeccccCC-CC--CCEEEEEccC-CHHHHHHHHHHHhccc--c--c---ccCCCCCCeEEeeCCCCc------
Confidence 489999999999998 33 5899999984 6899999999987553 1 2 356889999999953211
Q ss_pred CCCCccccCcCCHHHHHHHhCCceeceEEeeEEEEEEeeecCCCCceeeeEEEeC
Q psy2081 326 SDTNSEKRSTFNAKDILESLGDFEFGETFVYCVHLSQRHTHDMDGYFKPSAVISL 380 (380)
Q Consensus 326 ~~~~~~~r~~fda~~il~~~~~~~fG~~~v~~I~L~~s~~~~~~g~Y~~~~~i~L 380 (380)
...-++.+.++. .++.+ .+.|++|+|+.+. .++-|..+.+++|
T Consensus 125 -------~~~~~~~~~l~~-~~~~~-~~~v~~i~L~~~~---~~~~w~~~~~~~~ 167 (168)
T PRK13679 125 -------DEHEDVLGQLKM-ADVDH-EETIDRFHLLYQL---ENGSWTVYETFRL 167 (168)
T ss_pred -------HHHHHHHHHHhc-CCcce-eEEECeEEEEEEC---CCCeEEEEEEeeC
Confidence 111223344434 55666 7899999999442 3788999998876
No 8
>PHA02574 57B hypothetical protein; Provisional
Probab=99.70 E-value=6.2e-17 Score=142.03 Aligned_cols=111 Identities=13% Similarity=0.044 Sum_probs=90.3
Q ss_pred CcceeeeccCCChhHHHHHHHHHHHHhcccCcCCCCccccccCCCCceeeEEeeccCCchhHHHHHHHHHhhcccccccc
Q psy2081 164 PYTHLLSIPMNVPNIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPI 243 (380)
Q Consensus 164 ~~thFIaIpl~~~~I~~~~~~fq~~v~~~~~~~~gi~~~~fv~p~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~ 243 (380)
..|.|+||+++. ++++.+.++|+.+. ...||++++|||||.| +++.+.....
T Consensus 8 ~~RlF~Al~~~~-~~r~~L~~lq~~l~----------~~r~V~~enLHlTL~F----~~~~v~~l~~------------- 59 (149)
T PHA02574 8 SQGTYVAAKFSE-ATLDALERLQRTLR----------IPNPVPRDKLHSTIVY----SRVYVPFIPA------------- 59 (149)
T ss_pred cceEEEEEcCCH-HHHHHHHHHHHhcc----------CCcccCHHHCEEEEec----CHHHhHHHhc-------------
Confidence 578999999985 89999999998842 1569999999999999 3444443311
Q ss_pred cccCceEEEecceecCCCCCCceeEEEEEecCChHHHHHHHHHHHHHHHHCCCccccccCCCceeeEEEeec
Q psy2081 244 LRSQRIKINLKGLEIMNDDPAEVDILYAKVVDDSGLVQKLCDDVVQYFISQHLISKAYQKYDTVKMHVTLMN 315 (380)
Q Consensus 244 ~~~~pf~l~l~Glg~F~ddp~~~rVLya~v~d~~~~Lq~L~~~l~~~f~~~Gl~~~~~~e~r~fkpHiTL~n 315 (380)
..+||.+.++|+|+|+ ++. +||||++++ ++.|..|++.+.+.+.+ . +.++|+||+||+|
T Consensus 60 -~~~~F~l~l~glG~F~-~~~-~rvlWlg~~--~~~L~~L~~~l~~~l~~----~----~~r~F~PHITLaR 118 (149)
T PHA02574 60 -SGSTEVASSGHLEVWE-TQD-KNALVLVLE--SEYLQCRHKYARALGAT----H----DFDDYTPHITLSY 118 (149)
T ss_pred -cCCCeEEEeccccccC-CCC-CCEEEEEeC--CHHHHHHHHHHHHHhhc----C----CCCCcCCcEEEee
Confidence 3489999999999997 323 799999997 79999999999999988 2 3457999999984
No 9
>PF13563 2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB: 1IUH_A.
Probab=99.38 E-value=1.5e-12 Score=113.31 Aligned_cols=130 Identities=17% Similarity=0.177 Sum_probs=78.0
Q ss_pred cCCCCceeeEEeeccCCchhHHHHHHHHHhhcccccccccccCceEEEecceecCCCCCCceeEEEEEecCChHHHHHHH
Q psy2081 205 QEPGRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPILRSQRIKINLKGLEIMNDDPAEVDILYAKVVDDSGLVQKLC 284 (380)
Q Consensus 205 v~p~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~~~~pf~l~l~Glg~F~ddp~~~rVLya~v~d~~~~Lq~L~ 284 (380)
......||||.+.+..++.. +.+.+.|..+. ...+||.|+|.|+++|+ . +.+|||+.+. +++.|.+|+
T Consensus 21 ~~~~~pHITL~~~~~~~~~~-~~~~~~l~~~~-------~~~~~f~l~l~~~~~F~-~--~~~vi~l~~~-~~~~L~~L~ 88 (153)
T PF13563_consen 21 YPRWPPHITLAFPFDIDDSL-DELVEALARLA-------AGFPPFELRLDGFGSFP-G--KGRVIFLNVE-PSPELEALH 88 (153)
T ss_dssp --GGG-EEEEEEEEE--GGG-HHHHHHHHHHH-------HHS--EEEEEEEEEEES-S--SSSSEEEEEE-E-HHHHHHH
T ss_pred CCCCCCEeEEEecCcccccH-HHHHHHHHHHH-------ccCCCeEEEEccEEEcC-C--CCCEEEEEcC-CCHHHHHHH
Confidence 44455999999999876643 55555565552 13488999999999998 3 3459999996 579999999
Q ss_pred HHHHHHHHHCCCccccccCCCceeeEEEeecccccccCCCCCCCCccccCcCCHHHHHHHhC-CceeceEEeeEEEEEEe
Q psy2081 285 DDVVQYFISQHLISKAYQKYDTVKMHVTLMNSKYRMRQNPSSDTNSEKRSTFNAKDILESLG-DFEFGETFVYCVHLSQR 363 (380)
Q Consensus 285 ~~l~~~f~~~Gl~~~~~~e~r~fkpHiTL~nt~~r~~~~~~~~~~~~~r~~fda~~il~~~~-~~~fG~~~v~~I~L~~s 363 (380)
+.|.+.|...+... ...++|.|||||++..... ....+++.+. ......+.|++|.|+++
T Consensus 89 ~~l~~~~~~~~~~~---~~~~~~~PHiTia~~~~~~----------------~~~~~~~~~~~~~~~~~~~v~~l~L~~~ 149 (153)
T PF13563_consen 89 RALREALRPFGFKQ---DSYRPFRPHITIARRLSPK----------------QAAEAIEKLQSEFPPISFTVDELALVRS 149 (153)
T ss_dssp HHHHHHHHHHHGGG---GGGS----EEEEEEESS---------------------------------EEEEE-EEEEEEE
T ss_pred HHHHHHHHHcCCcc---ccCCCcceEEEEeccCCcc----------------hhHHHHHHHhCcCCCcEEEEeEEEEEEE
Confidence 99999999998876 2338999999999532211 1123445442 22334589999999987
Q ss_pred ee
Q psy2081 364 HT 365 (380)
Q Consensus 364 ~~ 365 (380)
..
T Consensus 150 ~~ 151 (153)
T PF13563_consen 150 DG 151 (153)
T ss_dssp E-
T ss_pred CC
Confidence 64
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=99.37 E-value=1.3e-12 Score=98.03 Aligned_cols=59 Identities=24% Similarity=0.361 Sum_probs=55.0
Q ss_pred EEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHH
Q psy2081 92 KYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLD 153 (380)
Q Consensus 92 ~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~ 153 (380)
..++.||+++++.|||++|+++|+|+++|||+|+|++ ++.|.|+|.++++++.|+++|+
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---CCEEEEEeCCHHHHHHHHHHhC
Confidence 5689999999999999999999999999999999986 5789999988999999999874
No 11
>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=99.31 E-value=3.2e-12 Score=95.71 Aligned_cols=60 Identities=33% Similarity=0.538 Sum_probs=54.5
Q ss_pred EEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCC-CCcEEEeeCCHHHHHHHHHHHH
Q psy2081 93 YQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQ-TGDIIISSYSERGIASAKRRLD 153 (380)
Q Consensus 93 ~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~-~~~i~I~g~~~~~v~~A~~~I~ 153 (380)
.++.||+++|+.|||++|+++++|+++|||+|+||+.+. ++.|+|+|+ +++|..|+++|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP-KENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC-HHHHHHHHHHhC
Confidence 578999999999999999999999999999999998653 478999997 899999998873
No 12
>PF05213 Corona_NS2A: Coronavirus NS2A protein; InterPro: IPR007878 This entry is represented by Coronavirus non-structural protein 2A (32kDa); it is a family of uncharacterised viral proteins. Members have a phosphoesterase module (2H) [] and are predicted to be involved in RNA modification. The viral group of 2H phosphoesterases contains proteins from two unrelated virus types: the type C rotaviruses (VP3 protein, IPR011181 from INTERPRO) that are double stranded multipartite RNA viruses and the coronaviruses (NS2 protein, this group) that are positive strand RNA viruses. Given that these viruses have vertebrate hosts, it is likely that the 2H phosphoesterase domain was derived from the host by one of virus groups followed by rapid sequence divergence []. Subsequently, it may have been exchanged between the viral families. Although the direction of the exchange is not clear, it is possible that a double stranded replicative form of a subgenomic RNA transcript of the coronavirus NS2 was stabilised by a rotavirus and incorporated into its multiple double stranded RNA genome []. These proteins can be utilised as novel drug targets because of their predicted RNA modification role.
Probab=99.25 E-value=1e-10 Score=106.38 Aligned_cols=166 Identities=17% Similarity=0.279 Sum_probs=122.6
Q ss_pred CCcceeeeccCCC-hhHHHHHHHHHHHHhcccCcCCCCccccccCCCCceeeEEeeccCCchhHHHHHHHHHhhcccccc
Q psy2081 163 IPYTHLLSIPMNV-PNIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVERDQAVEVLQKCGNNIIL 241 (380)
Q Consensus 163 ~~~thFIaIpl~~-~~I~~~~~~fq~~v~~~~~~~~gi~~~~fv~p~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~ 241 (380)
..|||||.+|+.+ ..+..++..+|-.+++. |+|-++-.-| ||||+||-+ .++++..+..+|+++..++
T Consensus 4 D~P~HFin~Pl~~f~~f~~~~~~LQ~~~~~e-----G~d~k~QkaP---HlSl~mL~I-sd~~i~~V~~~iq~ViddM-- 72 (248)
T PF05213_consen 4 DKPTHFINFPLVQFEGFMLNFKDLQFQLLEE-----GVDCKLQKAP---HLSLGMLDI-SDEDIPDVETAIQKVIDDM-- 72 (248)
T ss_pred CCCCceeeccchhhhhHHHHHHHHHHHHHHc-----CCCccccccC---eeEEEEEEc-ChhhhhhHHHHHHHHHHHh--
Confidence 4689999999986 67999999999999875 5665543333 999999976 7888999887887764322
Q ss_pred cccccCceEEEecceecCCCCCCceeEEEEEecCChHHHHHHHHHHHHHHHHCCCccccccCCCceeeEEEeeccccccc
Q psy2081 242 PILRSQRIKINLKGLEIMNDDPAEVDILYAKVVDDSGLVQKLCDDVVQYFISQHLISKAYQKYDTVKMHVTLMNSKYRMR 321 (380)
Q Consensus 242 ~~~~~~pf~l~l~Glg~F~ddp~~~rVLya~v~d~~~~Lq~L~~~l~~~f~~~Gl~~~~~~e~r~fkpHiTL~nt~~r~~ 321 (380)
.- ....+++..-..++ |.+-|.|+ .++.|++.|...|.+.|+.. ...|.+.||+||+...-..
T Consensus 73 --~~-~~~~it~tnp~MLg------~~yV~nV~----Gv~slh~ki~n~~~~kgit~---gQSRmwIPHiTia~~~~~a- 135 (248)
T PF05213_consen 73 --VW-FEGDITFTNPHMLG------RCYVANVK----GVLSLHDKIVNVFRKKGITF---GQSRMWIPHITIAQLNDAA- 135 (248)
T ss_pred --hc-ccceEEecCceeec------cEEEEecc----cHHHHHHHHHHHHHHhCcCc---Ccccccccceehhhhhchh-
Confidence 11 22267777766665 56666665 68899999999999999998 7899999999998432110
Q ss_pred CCCCCCCCccccCcCCHHHHHHHhCCceec-eEEe-----eEEEEEEeeecCCCCceeeeEE
Q psy2081 322 QNPSSDTNSEKRSTFNAKDILESLGDFEFG-ETFV-----YCVHLSQRHTHDMDGYFKPSAV 377 (380)
Q Consensus 322 ~~~~~~~~~~~r~~fda~~il~~~~~~~fG-~~~v-----~~I~L~~s~~~~~~g~Y~~~~~ 377 (380)
.+ .+ + .+|+ +.++ .++.|-+.+....+|+|..+.+
T Consensus 136 ----------v~--I~-------~--~qFny~~~~n~~~~~rle~VKlGa~K~dgfYe~i~s 176 (248)
T PF05213_consen 136 ----------VR--IK-------E--KQFNYKITINPSSPARLEFVKLGAEKKDGFYESIVS 176 (248)
T ss_pred ----------eE--ec-------c--ceeeeEeeccCCChhcCeEEEcCCcccCceeeeehh
Confidence 01 00 1 2344 3555 7889999999999999998865
No 13
>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=99.21 E-value=4.7e-12 Score=94.17 Aligned_cols=60 Identities=32% Similarity=0.475 Sum_probs=54.2
Q ss_pred EEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHH
Q psy2081 92 KYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRL 152 (380)
Q Consensus 92 ~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I 152 (380)
+..|.||.+++++|||++|+++++|+++|+|+|+||+.++...|+|+| ++++|.+|+++|
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 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISG-SPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEE-SHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEe-CHHHHHHHHhhC
Confidence 578999999999999999999999999999999999764234899999 799999999886
No 14
>PF02834 LigT_PEase: LigT like Phosphoesterase; InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases. These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.
Probab=99.09 E-value=1.7e-10 Score=91.83 Aligned_cols=87 Identities=14% Similarity=0.239 Sum_probs=70.5
Q ss_pred ccCCChhHHHHHHHHHHHHhcccCcCCCCccccccCCCCceeeEEeeccCCchhHHHHHHHHHhhcccccccccccCceE
Q psy2081 171 IPMNVPNIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPILRSQRIK 250 (380)
Q Consensus 171 Ipl~~~~I~~~~~~fq~~v~~~~~~~~gi~~~~fv~p~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~~~~pf~ 250 (380)
|+++ +++++.+.++++.+.+.+. -....|++|.++||||.|+|..+++++.+.++.|.... ....||.
T Consensus 1 i~~p-~~~~~~L~~l~~~l~~~~~----~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~-------~~~~~f~ 68 (87)
T PF02834_consen 1 IDLP-EEIKEQLNQLQERLRQALP----PLGIRWVRPFNPHITLAFLGEVPPDQLPELIEALANIA-------SRFPPFT 68 (87)
T ss_dssp EE-T-HHHHHHHHHHHHHHHHHCC----SCTEEEGSCGGSEEEEEEEEEESHHHHHHHHHHHHHHH-------CCCB-EE
T ss_pred CCCC-HHHHHHHHHHHHHHhhhcc----ccCCcccCCCCCeEEEEeCCCCCHHHHHHHHHHHHhhh-------ccCCCeE
Confidence 4555 4799999999999996543 12346889999999999999999999999999998873 2358999
Q ss_pred EEecceecCCCCCCceeEEE
Q psy2081 251 INLKGLEIMNDDPAEVDILY 270 (380)
Q Consensus 251 l~l~Glg~F~ddp~~~rVLy 270 (380)
+.+.|+++|+ +...+||+|
T Consensus 69 ~~~~~~~~f~-s~~~~rvi~ 87 (87)
T PF02834_consen 69 LTVDGFGLFP-SRLRPRVIW 87 (87)
T ss_dssp EEEEEEEEEE-EEETCEEEE
T ss_pred EEEeEEEEeC-CCCCCCCcC
Confidence 9999999999 555899999
No 15
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.04 E-value=4.6e-10 Score=83.92 Aligned_cols=59 Identities=29% Similarity=0.432 Sum_probs=52.8
Q ss_pred EEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCC---CCcEEEeeCCHHHHHHHHHHH
Q psy2081 93 YQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQ---TGDIIISSYSERGIASAKRRL 152 (380)
Q Consensus 93 ~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~---~~~i~I~g~~~~~v~~A~~~I 152 (380)
..+.||..++++|||++|+++++|+++|+|+|.||..+. ...|.|.|. .+++..|+..|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~-~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT-PEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcC-HHHHHHHHHHh
Confidence 578999999999999999999999999999999997542 457999996 89999998876
No 16
>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=98.91 E-value=3.4e-09 Score=90.06 Aligned_cols=61 Identities=30% Similarity=0.486 Sum_probs=54.1
Q ss_pred CCCcceeeCCCCchHHHHHHHhCceEEcCCCC--------------------CCCcEEEeeCC--HHHHHHHHHHHHHHh
Q psy2081 99 KSFYPFIIGVKGSTKRRIESETNTQLSIPRQG--------------------QTGDIIISSYS--ERGIASAKRRLDLLL 156 (380)
Q Consensus 99 ~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~--------------------~~~~i~I~g~~--~~~v~~A~~~I~~iv 156 (380)
..|+|.|||++|+|+|+|+++|||+|.|...+ +.+.|.|+|.+ .+++.+|++.|+.|+
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 36889999999999999999999999998653 22789999999 999999999999998
Q ss_pred hhh
Q psy2081 157 VFA 159 (380)
Q Consensus 157 ~~~ 159 (380)
...
T Consensus 94 ~~~ 96 (120)
T cd02395 94 KPA 96 (120)
T ss_pred ccC
Confidence 744
No 17
>smart00322 KH K homology RNA-binding domain.
Probab=98.88 E-value=9.3e-09 Score=76.55 Aligned_cols=65 Identities=28% Similarity=0.402 Sum_probs=58.2
Q ss_pred eEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCC-CCCcEEEeeCCHHHHHHHHHHHHHHh
Q psy2081 91 YKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQG-QTGDIIISSYSERGIASAKRRLDLLL 156 (380)
Q Consensus 91 ~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~-~~~~i~I~g~~~~~v~~A~~~I~~iv 156 (380)
++..+.||..+++.+||++|+++++|+++|+++|.++... ....|.|.|+ ..++..|+..|...+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~-~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGP-PENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcC-HHHHHHHHHHHHHHh
Confidence 6789999999999999999999999999999999998644 3468999997 899999999988765
No 18
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=98.87 E-value=4.5e-09 Score=79.59 Aligned_cols=59 Identities=24% Similarity=0.281 Sum_probs=52.2
Q ss_pred EEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCC--C--CcEEEeeCCHHHHHHHHHHH
Q psy2081 93 YQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQ--T--GDIIISSYSERGIASAKRRL 152 (380)
Q Consensus 93 ~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~--~--~~i~I~g~~~~~v~~A~~~I 152 (380)
..+.||.+.++.|||++|+++++|+++|||+|++++... . -.|+|+|. .+++..|..+|
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~-~~~v~~A~~~I 64 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK-PSAVQKALLLI 64 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeC-HHHHHHHHHhh
Confidence 578999999999999999999999999999999987543 1 36899995 89999998876
No 19
>PF13014 KH_3: KH domain
Probab=98.76 E-value=1.1e-08 Score=71.07 Aligned_cols=39 Identities=36% Similarity=0.545 Sum_probs=33.7
Q ss_pred CcceeeCCCCchHHHHHHHhCceEEcCC---CCCC-CcEEEee
Q psy2081 101 FYPFIIGVKGSTKRRIESETNTQLSIPR---QGQT-GDIIISS 139 (380)
Q Consensus 101 ~~~~IIG~~G~t~k~ie~eT~~~I~ip~---~~~~-~~i~I~g 139 (380)
+|++|||++|+++++|+++|+|+|+||+ ++.+ ..|+|+|
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 5899999999999999999999999998 3332 4788887
No 20
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.61 E-value=6.6e-08 Score=87.92 Aligned_cols=66 Identities=29% Similarity=0.388 Sum_probs=60.6
Q ss_pred ceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEe---eCCHHHHHHHHHHHHHHhh
Q psy2081 90 QYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIIS---SYSERGIASAKRRLDLLLV 157 (380)
Q Consensus 90 ~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~---g~~~~~v~~A~~~I~~iv~ 157 (380)
.+..++.||++.++.|||++|+++|.|+++||++|+|.. +++.|.|. +.+++++.+|++.|+.|+.
T Consensus 2 ~~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~--~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 2 MMMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS--ETGEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred CceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC--CCCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 467899999999999999999999999999999999974 44899998 7789999999999999986
No 21
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.50 E-value=1.1e-07 Score=85.75 Aligned_cols=62 Identities=27% Similarity=0.378 Sum_probs=56.0
Q ss_pred EEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEE--eeCCHHHHHHHHHHHHHHhhh
Q psy2081 95 CHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIII--SSYSERGIASAKRRLDLLLVF 158 (380)
Q Consensus 95 v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I--~g~~~~~v~~A~~~I~~iv~~ 158 (380)
+.||++.++.|||++|+++|+|+++||++|+|.. +++.|.| .+.++.++.+|++.|..+...
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~--~~g~V~I~~~t~d~~~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS--ETGEVKIEEEDEDPLAVMKAREVVKAIGRG 65 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc--CCceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence 6799999999999999999999999999999964 3488999 566899999999999998763
No 22
>KOG1676|consensus
Probab=98.47 E-value=2.9e-07 Score=95.00 Aligned_cols=144 Identities=13% Similarity=0.151 Sum_probs=95.6
Q ss_pred CceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEc-CCCCCC---CcEEEeeCCHHHHHHHHHHHHHHhhhhcccC-
Q psy2081 89 GQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSI-PRQGQT---GDIIISSYSERGIASAKRRLDLLLVFARKKI- 163 (380)
Q Consensus 89 g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~i-p~~~~~---~~i~I~g~~~~~v~~A~~~I~~iv~~~rkk~- 163 (380)
++-+..|.||...+|.||||+|++||+|..+|||||+| |..+-+ -.+.|.|. ++.|+.|.+.|..||++.....
T Consensus 228 ~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~-~d~ie~Aa~lI~eii~~~~~~~~ 306 (600)
T KOG1676|consen 228 GSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGT-VDQIEHAAELINEIIAEAEAGAG 306 (600)
T ss_pred ccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecC-HHHHHHHHHHHHHHHHHHhccCC
Confidence 34488999999999999999999999999999999999 433312 46999995 9999999999999998886552
Q ss_pred ------Cc----ceeeeccCCCh-hHHHHHHHHHHHHhcccCcCCCCccccccCCCCceeeEEeeccCCchhHHHHHHHH
Q psy2081 164 ------PY----THLLSIPMNVP-NIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVERDQAVEVL 232 (380)
Q Consensus 164 ------~~----thFIaIpl~~~-~I~~~~~~fq~~v~~~~~~~~gi~~~~fv~p~~LHLTL~~L~l~~~~ev~~A~~~L 232 (380)
.| ...+.||-..- -|+++-.+-...+..+.+...++... -+-.+.-.-+..+.. ++.+|+-|++++
T Consensus 307 ~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~--~p~~~~~ektf~IrG-~~~QIdhAk~LI 383 (600)
T KOG1676|consen 307 GGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ--PPNGNPKEKTFVIRG-DKRQIDHAKQLI 383 (600)
T ss_pred CCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC--CCCCCccceEEEEec-CcccchHHHHHH
Confidence 11 45667776421 12333333333333332211112111 111333444444454 788899999998
Q ss_pred Hhhc
Q psy2081 233 QKCG 236 (380)
Q Consensus 233 ~~~~ 236 (380)
+.-.
T Consensus 384 r~kv 387 (600)
T KOG1676|consen 384 RDKV 387 (600)
T ss_pred HHHh
Confidence 8764
No 23
>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=98.45 E-value=3.4e-07 Score=98.06 Aligned_cols=65 Identities=22% Similarity=0.290 Sum_probs=61.2
Q ss_pred eEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhh
Q psy2081 91 YKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVF 158 (380)
Q Consensus 91 ~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~ 158 (380)
-..++.||++.++.|||+||.+||+|+++||++|+|. ++|.|.|.|.+++.+++|+++|+.++..
T Consensus 578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~---d~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE---DDGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe---cCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 4789999999999999999999999999999999995 4799999999999999999999999874
No 24
>KOG0119|consensus
Probab=98.23 E-value=1.9e-06 Score=87.23 Aligned_cols=70 Identities=29% Similarity=0.443 Sum_probs=60.8
Q ss_pred ceEEEEEcCC------CCcceeeCCCCchHHHHHHHhCceEEcCCCCC-------------------CCcEEEeeCCHHH
Q psy2081 90 QYKYQCHIPK------SFYPFIIGVKGSTKRRIESETNTQLSIPRQGQ-------------------TGDIIISSYSERG 144 (380)
Q Consensus 90 ~~~~~v~Vp~------~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~-------------------~~~i~I~g~~~~~ 144 (380)
++.-+|.||. .|+|+|||+.|.|.|+||+|||++|.|-..+. .-.+.|++.+.+.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 6777888884 78999999999999999999999999976321 1258999999999
Q ss_pred HHHHHHHHHHHhhhh
Q psy2081 145 IASAKRRLDLLLVFA 159 (380)
Q Consensus 145 v~~A~~~I~~iv~~~ 159 (380)
|.+|...|+.|+.+.
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999999875
No 25
>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=98.22 E-value=1.3e-06 Score=94.37 Aligned_cols=65 Identities=18% Similarity=0.208 Sum_probs=60.2
Q ss_pred eEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhh
Q psy2081 91 YKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVF 158 (380)
Q Consensus 91 ~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~ 158 (380)
-..++.||++.++.|||++|++||+|+++||++|+|- ++|.|.|.+.+.+.+.+|+++|+.++..
T Consensus 551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~---ddG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE---DDGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe---cCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 4778999999999999999999999999999999994 4799999999999999999999999653
No 26
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.20 E-value=5.1e-06 Score=75.56 Aligned_cols=55 Identities=25% Similarity=0.318 Sum_probs=49.4
Q ss_pred CCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhh
Q psy2081 100 SFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFA 159 (380)
Q Consensus 100 ~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~ 159 (380)
..+|.|||++|+|+|.||+.|+|+|+|+. ..|.|.| +.++++.|++.|+.|+...
T Consensus 104 r~~griIG~~G~~~k~ie~~t~~~i~i~~----~~v~i~G-~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 104 RIKGRIIGEGGKTRRIIEELTGVDISVYG----KTVAIIG-DPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred HHhhheeCCCcHHHHHHHHHHCcEEEEcC----CEEEEEe-CHHHHHHHHHHHHHHHcCC
Confidence 36899999999999999999999999974 4599999 5999999999999999554
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=98.17 E-value=6e-06 Score=74.57 Aligned_cols=55 Identities=25% Similarity=0.291 Sum_probs=50.2
Q ss_pred CCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhh
Q psy2081 100 SFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFA 159 (380)
Q Consensus 100 ~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~ 159 (380)
...+.|||++|+|++.||..|+|+|.|+. ..|.|.| +.++++.|++.|+.|+...
T Consensus 98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~----~~v~i~G-~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEELTGVSISVYG----KTVGIIG-DPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred HHHhhhcCCCcHHHHHHHHHHCCeEEEcC----CEEEEEC-CHHHHHHHHHHHHHHHcCC
Confidence 36899999999999999999999999974 6899999 6999999999999999555
No 28
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.93 E-value=1.3e-05 Score=84.65 Aligned_cols=67 Identities=21% Similarity=0.245 Sum_probs=62.4
Q ss_pred eEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhhc
Q psy2081 91 YKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFAR 160 (380)
Q Consensus 91 ~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~r 160 (380)
-..++.|+++.++.+||++|.+|++|-++||++|+|. ++|.|.|.+.+.+.+.+|+++|+.++.+..
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie---ddGtv~i~~s~~~~~~~ak~~I~~i~~e~e 618 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE---DDGTVKIAASDGESAKKAKERIEAITREVE 618 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec---CCCcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence 4789999999999999999999999999999999995 689999999999999999999999996663
No 29
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.90 E-value=8.7e-06 Score=89.21 Aligned_cols=66 Identities=17% Similarity=0.228 Sum_probs=61.2
Q ss_pred ceEEEEEcCCCCcceeeCCCCchHHHHHHHhCce-EEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhh
Q psy2081 90 QYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQ-LSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVF 158 (380)
Q Consensus 90 ~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~-I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~ 158 (380)
--..++.||++.++.|||+||.|||+|+++||+. |+|- ++|.|.|.|.+.+.+++|+++|+.|+..
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~---ddg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ---DDGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC---CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 3578999999999999999999999999999999 9994 5799999999999999999999999853
No 30
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.90 E-value=3.3e-05 Score=73.20 Aligned_cols=64 Identities=27% Similarity=0.268 Sum_probs=59.7
Q ss_pred EEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhh
Q psy2081 93 YQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFA 159 (380)
Q Consensus 93 ~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~ 159 (380)
..+.||+.+++.+||++|.+++.|.++|++.|.| +.+|.|.|.|++.+.+.+|.+.|+.+-.++
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~i---g~NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIV---GQNGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEE---cCCcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 4588999999999999999999999999999999 678999999999999999999999987766
No 31
>KOG2191|consensus
Probab=97.89 E-value=0.00011 Score=71.41 Aligned_cols=70 Identities=21% Similarity=0.312 Sum_probs=56.4
Q ss_pred ccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCC------CcEEEeeCCHHHHHHHHHHHHHHh
Q psy2081 86 GKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQT------GDIIISSYSERGIASAKRRLDLLL 156 (380)
Q Consensus 86 ~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~------~~i~I~g~~~~~v~~A~~~I~~iv 156 (380)
.+.++|.+.|-||..-.+.||||+|+||.+|+.|||++|++.+..+. ..+.|+|. -+++....+-|..-+
T Consensus 34 ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt-~eai~av~efI~dKi 109 (402)
T KOG2191|consen 34 GEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGT-VEALNAVHEFIADKI 109 (402)
T ss_pred CCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEecc-HHHHHHHHHHHHHHH
Confidence 35566999999999999999999999999999999999999875432 36888895 677776655554443
No 32
>KOG1676|consensus
Probab=97.84 E-value=9.4e-05 Score=76.84 Aligned_cols=139 Identities=14% Similarity=0.180 Sum_probs=93.5
Q ss_pred CceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCC-----CcEEEeeCCHHHHHHHHHHHHHHhhhhcc--
Q psy2081 89 GQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQT-----GDIIISSYSERGIASAKRRLDLLLVFARK-- 161 (380)
Q Consensus 89 g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~-----~~i~I~g~~~~~v~~A~~~I~~iv~~~rk-- 161 (380)
+..+..|.||.+..+.||||+|+|+|.|.+.+||++.+-..+.. -.+.|+| +...|+.|+..+..|+.+-.+
T Consensus 137 ~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritG-dp~~ve~a~~lV~dil~e~~~~~ 215 (600)
T KOG1676|consen 137 VETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITG-DPDKVEQAKQLVADILREEDDEV 215 (600)
T ss_pred cceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecC-CHHHHHHHHHHHHHHHHhcccCC
Confidence 44688999999999999999999999999999999988654432 2699999 599999999999999974321
Q ss_pred -----------cCCcceeeeccCCC-hhHHHHHHHHHHHHhcccCcCCCCcccc-ccC---CCCceeeEEeeccCCchhH
Q psy2081 162 -----------KIPYTHLLSIPMNV-PNIQENFAKFKATVLSDFSRCRGIEESL-FQE---PGRLHITMGMLMLADSVER 225 (380)
Q Consensus 162 -----------k~~~thFIaIpl~~-~~I~~~~~~fq~~v~~~~~~~~gi~~~~-fv~---p~~LHLTL~~L~l~~~~ev 225 (380)
-...+.-|-||-.. --|+++-.+....|..+.+ . ++ |.+ |...-=|+..+| +.+.+
T Consensus 216 ~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG----~--KIQfkpDd~p~speR~~~IiG--~~d~i 287 (600)
T KOG1676|consen 216 PGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETG----A--KIQFKPDDDPSSPERPAQIIG--TVDQI 287 (600)
T ss_pred CccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccC----c--eeEeecCCCCCCccceeeeec--CHHHH
Confidence 01112223333221 2345555555555555432 1 11 222 222334555566 57889
Q ss_pred HHHHHHHHhhc
Q psy2081 226 DQAVEVLQKCG 236 (380)
Q Consensus 226 ~~A~~~L~~~~ 236 (380)
+.|.+++.++.
T Consensus 288 e~Aa~lI~eii 298 (600)
T KOG1676|consen 288 EHAAELINEII 298 (600)
T ss_pred HHHHHHHHHHH
Confidence 99999988874
No 33
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=97.80 E-value=2.7e-05 Score=71.09 Aligned_cols=73 Identities=25% Similarity=0.407 Sum_probs=62.0
Q ss_pred cCCceEEEEEcC------CCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhh
Q psy2081 87 KDGQYKYQCHIP------KSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFA 159 (380)
Q Consensus 87 ~~g~~~~~v~Vp------~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~ 159 (380)
...+|+-.+.|| ..|+|.|||+.|.|+|+||+.|+|+|-|-..+..-+..|.+..++....|.+-|.-||..-
T Consensus 144 rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~ad 222 (269)
T COG5176 144 RPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEAD 222 (269)
T ss_pred CcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcc
Confidence 456789999999 4789999999999999999999999999877766677777777888888888888887544
No 34
>KOG1588|consensus
Probab=97.78 E-value=0.0001 Score=69.81 Aligned_cols=40 Identities=28% Similarity=0.520 Sum_probs=34.8
Q ss_pred eEEEEEcCC------CCcceeeCCCCchHHHHHHHhCceEEcCCCC
Q psy2081 91 YKYQCHIPK------SFYPFIIGVKGSTKRRIESETNTQLSIPRQG 130 (380)
Q Consensus 91 ~~~~v~Vp~------~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~ 130 (380)
-+..|.||. .|+|.|+|++|.|+|+||++|+|+|-|-..|
T Consensus 92 ~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrg 137 (259)
T KOG1588|consen 92 LTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRG 137 (259)
T ss_pred EEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCC
Confidence 456677775 5999999999999999999999999997765
No 35
>KOG2113|consensus
Probab=97.77 E-value=1.7e-05 Score=76.37 Aligned_cols=65 Identities=15% Similarity=0.316 Sum_probs=62.2
Q ss_pred CceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHH
Q psy2081 89 GQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDL 154 (380)
Q Consensus 89 g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~ 154 (380)
++.+.++.||..+.+.|.|++|.++|.|..+|+|+|.-|++++...+.++|. .+.|..||..|..
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~-~edv~~aRrei~s 88 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGR-HEDVRRARREIPS 88 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCCcceeccC-chhHHHHhhcCcc
Confidence 6789999999999999999999999999999999999999999999999996 8999999999988
No 36
>KOG2193|consensus
Probab=97.72 E-value=2.8e-05 Score=77.59 Aligned_cols=75 Identities=17% Similarity=0.289 Sum_probs=64.1
Q ss_pred eEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCC----CcEEEeeCCHHHHHHHHHHHHHHhhhhcccCCcc
Q psy2081 91 YKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQT----GDIIISSYSERGIASAKRRLDLLLVFARKKIPYT 166 (380)
Q Consensus 91 ~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~----~~i~I~g~~~~~v~~A~~~I~~iv~~~rkk~~~t 166 (380)
|-+.+-||..|++.|||+.|+|||.|-..|.++|+|-+.... -.|+|-| ++++..+|+.+|..|+..-..+...+
T Consensus 199 ~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~-tpEg~s~Ac~~ILeimqkEA~~~k~~ 277 (584)
T KOG2193|consen 199 WPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHS-TPEGTSKACKMILEIMQKEAVDDKVA 277 (584)
T ss_pred cceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEec-CccchHHHHHHHHHHHHHhhhccchh
Confidence 778899999999999999999999999999999999765443 3688888 48999999999999996665555555
No 37
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.58 E-value=4.5e-05 Score=82.78 Aligned_cols=64 Identities=25% Similarity=0.325 Sum_probs=59.2
Q ss_pred EEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhh
Q psy2081 92 KYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVF 158 (380)
Q Consensus 92 ~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~ 158 (380)
...+.||++.++.+||+||.|+|+|.++||++|+| .++|.|.|.+.+.+.+++|+++|+.++..
T Consensus 555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi---~d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDI---EDDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred heeecCCHHHHHHHhcCCchhHHHHHHHHCCcccc---CCCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 56889999999999999999999999999999998 35799999999999999999999999854
No 38
>KOG2192|consensus
Probab=97.51 E-value=0.00026 Score=67.07 Aligned_cols=68 Identities=25% Similarity=0.283 Sum_probs=55.6
Q ss_pred eEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCC--CCC-CcEEEeeCCHHHHHHHHHHHHHHhhhh
Q psy2081 91 YKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQ--GQT-GDIIISSYSERGIASAKRRLDLLLVFA 159 (380)
Q Consensus 91 ~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~--~~~-~~i~I~g~~~~~v~~A~~~I~~iv~~~ 159 (380)
.+..|.||+++-+.|||++|..|++|..|.|+.|.|..+ +.. -.|+|+| ++..+..|.--++.-|...
T Consensus 315 tTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItG-TqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 315 TTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG-TQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred eeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEec-cHHHHhhHHHHHHHHHHhh
Confidence 367899999999999999999999999999999999653 333 4689999 4888988876666555443
No 39
>PF09749 HVSL: Uncharacterised conserved protein; InterPro: IPR019146 This entry is of proteins of approximately 300 residues conserved from plants to humans. It contains two conserved motifs, HxSL and FHVSL. The function is unknown.
Probab=97.44 E-value=0.0027 Score=60.25 Aligned_cols=141 Identities=16% Similarity=0.211 Sum_probs=92.6
Q ss_pred cceeeeccCC-ChhHHHHHHHHHHHHhcccCcCC----CCccccccCCCCceeeEEeeccCCchhHHHHHHHHHhhcccc
Q psy2081 165 YTHLLSIPMN-VPNIQENFAKFKATVLSDFSRCR----GIEESLFQEPGRLHITMGMLMLADSVERDQAVEVLQKCGNNI 239 (380)
Q Consensus 165 ~thFIaIpl~-~~~I~~~~~~fq~~v~~~~~~~~----gi~~~~fv~p~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~ 239 (380)
+..||-||.. +..+.+.+.++.+.+.+.+.... ....+-.-.+..|||+|.=---+...+++.-.+.|++..
T Consensus 40 w~t~vYi~~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~s~lg~~~~lHISLSr~~~lr~~~id~f~~~lr~~l--- 116 (239)
T PF09749_consen 40 WPTHVYIEWPPSEDQRELLEKLISKANSICPKLHSEFEPLLYSDLGSPDPLHISLSRTFPLRTHQIDPFVDSLRQAL--- 116 (239)
T ss_pred cceEEEEEecCcHHHHHHHHHHHHHHHhhhhhhhhhcccccccccCCCCCeEEEeCCCccccHHHHHHHHHHHHHHH---
Confidence 4455556654 34566666666666655442100 000111124688999986444445577777777777652
Q ss_pred cccccccCceEEEecceecCCCCCCceeEEEE-EecCChH-HHHHHHHHHHHHHHHCCCccccccCC-CceeeEEEeec
Q psy2081 240 ILPILRSQRIKINLKGLEIMNDDPAEVDILYA-KVVDDSG-LVQKLCDDVVQYFISQHLISKAYQKY-DTVKMHVTLMN 315 (380)
Q Consensus 240 i~~~~~~~pf~l~l~Glg~F~ddp~~~rVLya-~v~d~~~-~Lq~L~~~l~~~f~~~Gl~~~~~~e~-r~fkpHiTL~n 315 (380)
. .....+|.+.+.++.+|. +..+.|...+ .|..+.. .|..|.+.|.+.+.+.|+.. -+ ..-.+||.||-
T Consensus 117 -~-~~~~~~F~v~f~~~~~~~-N~e~TR~FL~l~V~~~~~~~l~~l~~~i~~~l~~~~lp~----~Y~~~~~fHvSIAw 188 (239)
T PF09749_consen 117 -R-SSNIRPFYVSFSGLDVYT-NDEKTRSFLALRVSEGSNNELKRLLDRINEVLKEFGLPP----FYDEDPSFHVSIAW 188 (239)
T ss_pred -h-hcCCceEEEEeCceEEEe-cCCCCeEEEEEEecccccHHHHHHHHHHHHHHHHhCCCc----ccCCCCCCEEEEEE
Confidence 0 024589999999999998 6777774332 2434433 39999999999999999986 66 78999999993
No 40
>KOG2191|consensus
Probab=97.41 E-value=0.00039 Score=67.69 Aligned_cols=77 Identities=17% Similarity=0.138 Sum_probs=60.5
Q ss_pred EEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCC------CcEEEeeCCHHHHHHHHHHHHHHhhhhcccCCc
Q psy2081 92 KYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQT------GDIIISSYSERGIASAKRRLDLLLVFARKKIPY 165 (380)
Q Consensus 92 ~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~------~~i~I~g~~~~~v~~A~~~I~~iv~~~rkk~~~ 165 (380)
++.+-||.+--+.||||+|+|+|.+.++.++.|+|-.+... -.|++.|. .+...+|..+|..-|.+= |
T Consensus 133 qikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge-~e~~~~A~~~IL~Ki~eD-----p 206 (402)
T KOG2191|consen 133 QIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGE-PEQNMKAVSLILQKIQED-----P 206 (402)
T ss_pred eeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCC-HHHHHHHHHHHHHHhhcC-----C
Confidence 58899999999999999999999999999999999543332 35777885 899999999987776443 3
Q ss_pred ceeeeccCC
Q psy2081 166 THLLSIPMN 174 (380)
Q Consensus 166 thFIaIpl~ 174 (380)
.|=-||-++
T Consensus 207 qs~scln~s 215 (402)
T KOG2191|consen 207 QSGSCLNIS 215 (402)
T ss_pred cccceeccc
Confidence 444444443
No 41
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.39 E-value=0.00061 Score=62.14 Aligned_cols=56 Identities=25% Similarity=0.269 Sum_probs=50.3
Q ss_pred CCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhhc
Q psy2081 100 SFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFAR 160 (380)
Q Consensus 100 ~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~r 160 (380)
...|.|||++|.|++-||+-|+|.|.+ ....|.|.|. .++|+.|++.|+.|+....
T Consensus 111 R~kgRIIG~~GkTr~~IE~lt~~~I~V----~g~tVaiiG~-~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 111 RIKGRIIGREGKTRRAIEELTGVYISV----YGKTVAIIGG-FEQVEIAREAVEMLINGAP 166 (194)
T ss_pred HhhceeeCCCchHHHHHHHHhCCeEEE----eCcEEEEecC-hhhhHHHHHHHHHHHcCCC
Confidence 456899999999999999999999999 4468999995 8999999999999997774
No 42
>KOG2190|consensus
Probab=97.29 E-value=0.00061 Score=70.83 Aligned_cols=68 Identities=19% Similarity=0.242 Sum_probs=58.0
Q ss_pred eEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCC---CC-CCcEEEeeCCHHHHHHHHHHHHHHhhhh
Q psy2081 91 YKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQ---GQ-TGDIIISSYSERGIASAKRRLDLLLVFA 159 (380)
Q Consensus 91 ~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~---~~-~~~i~I~g~~~~~v~~A~~~I~~iv~~~ 159 (380)
.++.+-||....|.||||+|+.||+|.++|+++|.+-+. .. .-.|+|.|. ...|.+|...|-.++-+.
T Consensus 138 v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~-~~av~~al~~Is~~L~~~ 209 (485)
T KOG2190|consen 138 VTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGE-PDAVKKALVQISSRLLEN 209 (485)
T ss_pred eEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCc-hHHHHHHHHHHHHHHHhc
Confidence 688999999999999999999999999999999999442 11 235999996 899999999888887653
No 43
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.27 E-value=0.0007 Score=61.75 Aligned_cols=65 Identities=25% Similarity=0.346 Sum_probs=58.1
Q ss_pred ceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeC----CHHHHHHHHHHHHHHh
Q psy2081 90 QYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSY----SERGIASAKRRLDLLL 156 (380)
Q Consensus 90 ~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~----~~~~v~~A~~~I~~iv 156 (380)
.+...+.||+...+.+||+.|++.+.||+.|+|+|.+.. +++.|.|... ++-.+.+|++-|+.|-
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~--~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIg 75 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS--KTGSVTIRTTRKTEDPLALLKARDVVKAIG 75 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC--CCCeEEEEecCCCCChHHHHHHHHHHHHHh
Confidence 356779999999999999999999999999999999975 6688888765 8899999999998886
No 44
>KOG0336|consensus
Probab=97.18 E-value=0.00028 Score=70.90 Aligned_cols=73 Identities=22% Similarity=0.226 Sum_probs=62.6
Q ss_pred ccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhh
Q psy2081 86 GKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFA 159 (380)
Q Consensus 86 ~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~ 159 (380)
..+|.+...+.|-+.++|.+||++|++|++|+..|+|+|+|-..+....|+|.|. +.--.+|+.-|+..++..
T Consensus 42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~-~~m~~kaka~id~~~~k~ 114 (629)
T KOG0336|consen 42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGI-NHMRKKAKASIDRGQDKD 114 (629)
T ss_pred cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCceeEEEEech-HHHHHHHHhhHhhhhhhh
Confidence 4556688899999999999999999999999999999999987555678999995 777788888888887543
No 45
>KOG2208|consensus
Probab=97.05 E-value=0.00082 Score=73.55 Aligned_cols=104 Identities=15% Similarity=0.271 Sum_probs=85.6
Q ss_pred cCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCC-CcEEEeeCCHHHHHHHHHHHHHHhhhhcccCCc
Q psy2081 87 KDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQT-GDIIISSYSERGIASAKRRLDLLLVFARKKIPY 165 (380)
Q Consensus 87 ~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~-~~i~I~g~~~~~v~~A~~~I~~iv~~~rkk~~~ 165 (380)
.++ +...+.|.+.++.+++|++|+.+.+|+++++|.|++|.++++ ..|+++|. ..++.+|.+.++.++.+...+ ..
T Consensus 344 ~nn-~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~-~~~~~ka~~~v~~~~~ei~n~-~~ 420 (753)
T KOG2208|consen 344 ENN-ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGV-SANDEKAVEDVEKIIAEILNS-IV 420 (753)
T ss_pred ccc-eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEecc-ccchhHHHHHHHHHHHhhhcc-cc
Confidence 344 899999999999999999999999999999999999997766 57999996 789999999999999999764 34
Q ss_pred ceeeeccCC-ChhHHHHHHHHHHHHhccc
Q psy2081 166 THLLSIPMN-VPNIQENFAKFKATVLSDF 193 (380)
Q Consensus 166 thFIaIpl~-~~~I~~~~~~fq~~v~~~~ 193 (380)
++-+-||-. +..|.+.-....+.++..|
T Consensus 421 ~~~~~iP~k~~~~iig~~g~~i~~I~~k~ 449 (753)
T KOG2208|consen 421 KEEVQIPTKSHKRIIGTKGALINYIMGKH 449 (753)
T ss_pred cceeecCccchhhhhccccccHHHHHhhc
Confidence 555556654 4556666666677777765
No 46
>PF07823 CPDase: Cyclic phosphodiesterase-like protein; InterPro: IPR012386 2',3' Cyclic nucleotide phosphodiesterases (CPDases) are enzymes that catalyse at least two distinct steps in the splicing of tRNA introns in eukaryotes. The active site is characterised by two conserved histidine residues []. The enzyme has six cysteine residues, four of which are involved in forming two intra-molecular disulphide bridges. One of these bridges is involved in the catalytic activity of the enzyme as it opens when CPDase is semi-reduced []. Proteins in this entryand belong to 3.1.4.37 from EC and catalyse the reaction Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate. ; GO: 0004112 cyclic-nucleotide phosphodiesterase activity; PDB: 1JH7_A 1JH6_B 1FSI_B.
Probab=97.01 E-value=0.011 Score=54.54 Aligned_cols=178 Identities=16% Similarity=0.129 Sum_probs=82.4
Q ss_pred ceeeeccCCChhHHHHHHHHHHHHhcccCcCCCCccccccCCCCceeeEEee-ccCCchhHHHHHHHHHhhccccccccc
Q psy2081 166 THLLSIPMNVPNIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGML-MLADSVERDQAVEVLQKCGNNIILPIL 244 (380)
Q Consensus 166 thFIaIpl~~~~I~~~~~~fq~~v~~~~~~~~gi~~~~fv~p~~LHLTL~~L-~l~~~~ev~~A~~~L~~~~~~~i~~~~ 244 (380)
..+++-|-++ .....+..+...+...++ |- .++--=|+||.-- ...+.+++ .+.|.++..
T Consensus 4 SlWl~P~~~~-~~~~~L~~lI~~L~~~~~---~~-----~p~F~PHiTL~s~i~~~~~~~~---~~~L~~~~~------- 64 (196)
T PF07823_consen 4 SLWLVPPPGS-PLYERLKTLISSLASLFP---GS-----PPPFEPHITLTSGISLDSSDDV---QKVLDSAAA------- 64 (196)
T ss_dssp EEEEEE-T---TTHHHHHHHHHHHHHHST-----------------EEEEEEEEE--HHHH---HHHHHHHHH-------
T ss_pred EEEEcCCCCc-cHHHHHHHHHHHHHHHCC---CC-----CCCcCCeEEEeCCCccCCHHHH---HHHHHHHHH-------
Confidence 3444444433 577888888888877654 11 1223349999772 22233444 444555421
Q ss_pred ccCce-----EEEecceecCCCCCCceeEEEEEecCChHHHHHHHHHHHHHHHHCCCcc--ccccCCCceeeEEEeeccc
Q psy2081 245 RSQRI-----KINLKGLEIMNDDPAEVDILYAKVVDDSGLVQKLCDDVVQYFISQHLIS--KAYQKYDTVKMHVTLMNSK 317 (380)
Q Consensus 245 ~~~pf-----~l~l~Glg~F~ddp~~~rVLya~v~d~~~~Lq~L~~~l~~~f~~~Gl~~--~~~~e~r~fkpHiTL~nt~ 317 (380)
..+++ .++++++.. ...-=+=+|+.++ .++.|..|++.+++.|....=.. .......+|.||+.|+
T Consensus 65 ~~~~~~~~~~~v~~~~v~~---g~~yfq~vyl~v~-~t~~L~~l~~~~r~~~~~~~~~~~~~~~~~~~~y~PHlSLl--- 137 (196)
T PF07823_consen 65 ALKPLPKNHFTVRFDKVAS---GDKYFQCVYLEVE-KTPELMSLAQIARELFVEGPPDEVKAAEWPREPYMPHLSLL--- 137 (196)
T ss_dssp H-B-E-----EEEEEEEEE---EEETTEEEEEEE----HHHHHHHCHHHHCT----------T----S----EEEEE---
T ss_pred hccCcccceeEEEeeeEee---CCeEEEEEEEEec-CChhHHHHHHHHHHHhhhccccccccccccCCCCCCeEEEE---
Confidence 12444 777776643 1122356899998 56899999999999886431000 0002346899999998
Q ss_pred ccccCCCCCCCCccccCcCCHHHHHHHhCCc-------eeceEEeeEEEEEEeeecCCCCceeeeEEEeC
Q psy2081 318 YRMRQNPSSDTNSEKRSTFNAKDILESLGDF-------EFGETFVYCVHLSQRHTHDMDGYFKPSAVISL 380 (380)
Q Consensus 318 ~r~~~~~~~~~~~~~r~~fda~~il~~~~~~-------~fG~~~v~~I~L~~s~~~~~~g~Y~~~~~i~L 380 (380)
|..-.. ..+ -.+..+.+...+. ....|.+.+|.|++.... =.-..+++++.|
T Consensus 138 Y~d~~~-------~e~--~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~lv~t~g~--v~~W~~l~~~~l 196 (196)
T PF07823_consen 138 YGDLPP-------EEK--AEAAEIAQRIDDALGVDSGISGLGWEGGELKLVRTDGP--VEEWEVLASVDL 196 (196)
T ss_dssp -----H-------HHH--HHHHHHHHHH-TT------GTT-EEEEEEEEEEE--TT---TT-EEEEEEE-
T ss_pred EcCCCc-------ccH--HHHHHHHHHhcccccccccCCCCCEeccEEEEEEcCCC--CCcEEEEEEEeC
Confidence 643211 011 1123344454444 334578999999985443 456777777765
No 47
>PF02834 LigT_PEase: LigT like Phosphoesterase; InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases. These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.
Probab=96.94 E-value=0.00064 Score=53.73 Aligned_cols=76 Identities=13% Similarity=0.072 Sum_probs=53.7
Q ss_pred hHHHHHHHHHHHHHHHHCCCccccccCCCceeeEEEeecccccccCCCCCCCCccccCcCCHHHHHHHhCCc--eec--e
Q psy2081 277 SGLVQKLCDDVVQYFISQHLISKAYQKYDTVKMHVTLMNSKYRMRQNPSSDTNSEKRSTFNAKDILESLGDF--EFG--E 352 (380)
Q Consensus 277 ~~~Lq~L~~~l~~~f~~~Gl~~~~~~e~r~fkpHiTL~nt~~r~~~~~~~~~~~~~r~~fda~~il~~~~~~--~fG--~ 352 (380)
.+.|.++++.+.+.+...|+.. + +++.||+||+... .. ..-.+..+.+..... .+. .
T Consensus 8 ~~~L~~l~~~l~~~~~~~~~r~----~-~~~~~HiTL~flg---~~-----------~~~~~~~l~~~l~~~~~~~~~f~ 68 (87)
T PF02834_consen 8 KEQLNQLQERLRQALPPLGIRW----V-RPFNPHITLAFLG---EV-----------PPDQLPELIEALANIASRFPPFT 68 (87)
T ss_dssp HHHHHHHHHHHHHHCCSCTEEE----G-SCGGSEEEEEEEE---EE-----------SHHHHHHHHHHHHHHHCCCB-EE
T ss_pred HHHHHHHHHHHhhhccccCCcc----c-CCCCCeEEEEeCC---CC-----------CHHHHHHHHHHHHhhhccCCCeE
Confidence 4789999999999999999987 5 8999999998432 10 011244555555444 222 3
Q ss_pred EEeeEEEEEEeeecCCCCce
Q psy2081 353 TFVYCVHLSQRHTHDMDGYF 372 (380)
Q Consensus 353 ~~v~~I~L~~s~~~~~~g~Y 372 (380)
+.++++.++.+.. +.+..|
T Consensus 69 ~~~~~~~~f~s~~-~~rvi~ 87 (87)
T PF02834_consen 69 LTVDGFGLFPSRL-RPRVIW 87 (87)
T ss_dssp EEEEEEEEEEEEE-TCEEEE
T ss_pred EEEeEEEEeCCCC-CCCCcC
Confidence 8999999999988 565555
No 48
>KOG2193|consensus
Probab=96.91 E-value=0.0013 Score=65.94 Aligned_cols=70 Identities=17% Similarity=0.282 Sum_probs=57.2
Q ss_pred ceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCC---CCCC--cEEEeeCCHHHHHHHHHHHHHHhhhhc
Q psy2081 90 QYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQ---GQTG--DIIISSYSERGIASAKRRLDLLLVFAR 160 (380)
Q Consensus 90 ~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~---~~~~--~i~I~g~~~~~v~~A~~~I~~iv~~~r 160 (380)
+....+.||..-.|.||||||.|.++|+.-|++.+.||+. +++. .|.|+|. -=+-..|..+|..|+.+..
T Consensus 492 klethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGh-fyatq~aQrki~~iv~qvk 566 (584)
T KOG2193|consen 492 KLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGH-FYATQNAQRKIAHIVNQVK 566 (584)
T ss_pred eeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeech-hhcchHHHHHHHHHHHHHH
Confidence 4577899999999999999999999999999999999984 2332 4778884 4456678888888887664
No 49
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.68 E-value=0.0041 Score=65.44 Aligned_cols=68 Identities=24% Similarity=0.295 Sum_probs=59.6
Q ss_pred eEEEEEcCC-CCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhhc
Q psy2081 91 YKYQCHIPK-SFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFAR 160 (380)
Q Consensus 91 ~~~~v~Vp~-~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~r 160 (380)
....|++|. ++-|.|||+.|.+||-+|.-||+.|-|.. ..+.|+|+|-++-.-+-|+.-++.|+.+-|
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd--tp~~v~ls~fdp~rreia~~~l~~li~dgr 272 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--TPEAVILSGFDPVRREIARMALEKLIQDGR 272 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC--CCCeEEecCCchHHHHHHHHHHHHHHHcCC
Confidence 467889998 78899999999999999999999999963 345788999888888999999999998776
No 50
>PRK12704 phosphodiesterase; Provisional
Probab=96.62 E-value=0.0051 Score=64.78 Aligned_cols=69 Identities=23% Similarity=0.272 Sum_probs=59.0
Q ss_pred eEEEEEcCC-CCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhhcc
Q psy2081 91 YKYQCHIPK-SFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFARK 161 (380)
Q Consensus 91 ~~~~v~Vp~-~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~rk 161 (380)
....|++|. ++-|.|||+.|.+||-+|.-||+.|-|.. ..+.|+|+|-++-.-+.|+.-++.++.+.+-
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd--tp~~v~ls~~~~~rre~a~~~l~~l~~dg~i 279 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--TPEAVILSGFDPIRREIARLALEKLVQDGRI 279 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC--CCCeEEEecCChhhHHHHHHHHHHHHhcCCc
Confidence 466889998 78899999999999999999999999963 3467899997777777899999999887753
No 51
>PRK00106 hypothetical protein; Provisional
Probab=96.60 E-value=0.0053 Score=64.64 Aligned_cols=68 Identities=24% Similarity=0.300 Sum_probs=59.6
Q ss_pred eEEEEEcCC-CCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhhc
Q psy2081 91 YKYQCHIPK-SFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFAR 160 (380)
Q Consensus 91 ~~~~v~Vp~-~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~r 160 (380)
....|++|. ++-|.|||+.|.+||-+|.-||+.|-|.. ..+.|+|+|-++-.-+-|+.-++.|+.+-|
T Consensus 225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--tp~~v~lS~fdpvRReiAr~~le~Li~dgr 293 (535)
T PRK00106 225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD--TPEVVVLSGFDPIRREIARMTLESLIKDGR 293 (535)
T ss_pred eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC--CCCeEEEeCCChHHHHHHHHHHHHHHHcCC
Confidence 467889998 78899999999999999999999999963 345789999888888999999999997775
No 52
>KOG1067|consensus
Probab=96.49 E-value=0.0026 Score=66.01 Aligned_cols=69 Identities=20% Similarity=0.209 Sum_probs=61.1
Q ss_pred cCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhh
Q psy2081 87 KDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFA 159 (380)
Q Consensus 87 ~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~ 159 (380)
..+-...++.|+++....+||++|-.+|+|+.|||+.-++ ++++++|.++++...++|++.|..|+..-
T Consensus 593 ~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v----De~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 593 EYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV----DEGTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred ccCceeeEEeecchhhheeecCccceeeeEeeeccceeee----cCceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 4455688999999999999999999999999999977666 46899999999999999999999888543
No 53
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=96.14 E-value=0.0093 Score=56.17 Aligned_cols=64 Identities=27% Similarity=0.290 Sum_probs=55.9
Q ss_pred EEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhh
Q psy2081 93 YQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFA 159 (380)
Q Consensus 93 ~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~ 159 (380)
.-+.||+.++..+||++|+-++-|.++|+|+|-+ |.+|-|.|.|++......|...|..+=.++
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~V---G~NG~IWV~~~~~~~e~~~~~aI~~ie~ea 211 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIV---GQNGRIWVDGENESLEELAIEAIRKIEREA 211 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEE---ecCCEEEecCCCcchHHHHHHHHHHHhhhh
Confidence 4588999999999999999999999999999999 789999999987666777777777775554
No 54
>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=96.04 E-value=0.013 Score=43.74 Aligned_cols=37 Identities=16% Similarity=0.260 Sum_probs=34.6
Q ss_pred ceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEc
Q psy2081 90 QYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSI 126 (380)
Q Consensus 90 ~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~i 126 (380)
.....+.||+.-.+..|||+|.+++.++..++-+|++
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3688999999999999999999999999999998876
No 55
>KOG2192|consensus
Probab=95.75 E-value=0.07 Score=50.95 Aligned_cols=66 Identities=15% Similarity=0.223 Sum_probs=51.8
Q ss_pred cCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCC-CCcEEEeeCCHHHHHHHHHHHH
Q psy2081 87 KDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQ-TGDIIISSYSERGIASAKRRLD 153 (380)
Q Consensus 87 ~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~-~~~i~I~g~~~~~v~~A~~~I~ 153 (380)
..+++.+.+-+.+.--+.||||+|++||+|..++++.|++|..+. +-.++|++. .+.|-.-...|.
T Consensus 44 k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad-~~ti~~ilk~ii 110 (390)
T KOG2192|consen 44 KRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISAD-IETIGEILKKII 110 (390)
T ss_pred hhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCCCceeEEEecc-HHHHHHHHHHHh
Confidence 456688899999999999999999999999999999999997443 246788874 555554444433
No 56
>PRK12705 hypothetical protein; Provisional
Probab=95.27 E-value=0.021 Score=59.77 Aligned_cols=68 Identities=28% Similarity=0.300 Sum_probs=57.0
Q ss_pred eEEEEEcCC-CCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhhc
Q psy2081 91 YKYQCHIPK-SFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFAR 160 (380)
Q Consensus 91 ~~~~v~Vp~-~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~r 160 (380)
....|++|. ++-|.|||+.|.+||.+|..||+.|.|+. ....|+|.+-++..-+.|+..++.|+..-+
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--tp~~V~ls~fdp~rreia~~~l~~Li~dgr 266 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD--TPEAVVISSFNPIRREIARLTLEKLLADGR 266 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC--CccchhhcccCccchHHHHHHHHHHHhcCC
Confidence 466788887 78889999999999999999999999964 335688888778888889988888886654
No 57
>KOG2190|consensus
Probab=93.91 E-value=0.099 Score=54.64 Aligned_cols=101 Identities=17% Similarity=0.139 Sum_probs=69.1
Q ss_pred EEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCC--CC-CCcEEEee--------CCHHHHHHHHHHHHHHhh----
Q psy2081 93 YQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQ--GQ-TGDIIISS--------YSERGIASAKRRLDLLLV---- 157 (380)
Q Consensus 93 ~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~--~~-~~~i~I~g--------~~~~~v~~A~~~I~~iv~---- 157 (380)
..+-.+-...|.|||++|.++++|..+|+++|.|-.. |. +..|+|+| +..+++.+|-++|-...+
T Consensus 45 ~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~ 124 (485)
T KOG2190|consen 45 YRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDE 124 (485)
T ss_pred EEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccccccc
Confidence 4555667889999999999999999999888888543 22 24788888 137889999888866421
Q ss_pred ------hhcccCCcceeeeccCCC-hhHHHHHHHHHHHHhccc
Q psy2081 158 ------FARKKIPYTHLLSIPMNV-PNIQENFAKFKATVLSDF 193 (380)
Q Consensus 158 ------~~rkk~~~thFIaIpl~~-~~I~~~~~~fq~~v~~~~ 193 (380)
...++.+.+.=+-+|-.+ ..|.++-.....+|.+.+
T Consensus 125 ~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~T 167 (485)
T KOG2190|consen 125 AAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREET 167 (485)
T ss_pred ccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhc
Confidence 112333446667777552 235666666666666654
No 58
>KOG2814|consensus
Probab=93.23 E-value=0.028 Score=55.12 Aligned_cols=151 Identities=12% Similarity=0.017 Sum_probs=95.4
Q ss_pred CCceeeEEeeccCCchhHHHHHHHHHhhcccccccccccCceEEEecceecCCCCCCceeEEEEEecCChHHHHHHHHHH
Q psy2081 208 GRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPILRSQRIKINLKGLEIMNDDPAEVDILYAKVVDDSGLVQKLCDDV 287 (380)
Q Consensus 208 ~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~~~~pf~l~l~Glg~F~ddp~~~rVLya~v~d~~~~Lq~L~~~l 287 (380)
-++|+|+.+.-.+++.+|+.-...+++.. ..+..++...-...-|+|.+.|+ -.|-.+++-+ .+.+|+.++.+
T Consensus 128 ~s~p~thflal~lne~eVqe~f~~fke~~-~~~esl~~~g~~~s~F~~p~~~H-----LTvgm~~L~~-dd~vq~a~e~l 200 (345)
T KOG2814|consen 128 KSFPITHFLALPLNEHEVQEGFLAFKELK-PFIESLLDGGIDKSLFQGPGTFH-----LTVGMLKLLN-DDDVQKALEIL 200 (345)
T ss_pred hcCchhhhhhhhcchHHHHHHHHHHHhhh-hhHHHhhccchhhccccCCceee-----EEEEEEEecC-hHHHHHHHHHH
Confidence 47889888877789999999988888552 23333333333455568888887 4677777764 58899999999
Q ss_pred HHHHHHCCCccccccCCCceeeEEEeecccccccCCCCCCCCccccCcCCHHHHHHHhCCceeceEEeeEEEEEEeeecC
Q psy2081 288 VQYFISQHLISKAYQKYDTVKMHVTLMNSKYRMRQNPSSDTNSEKRSTFNAKDILESLGDFEFGETFVYCVHLSQRHTHD 367 (380)
Q Consensus 288 ~~~f~~~Gl~~~~~~e~r~fkpHiTL~nt~~r~~~~~~~~~~~~~r~~fda~~il~~~~~~~fG~~~v~~I~L~~s~~~~ 367 (380)
...|.+.+... .+..-|.+|-+++.. ++++. ++.--+.+-.+-+..+.+ +.-+|.+.+..++.|.+....
T Consensus 201 es~~~e~~~~~---~~kp~~i~lkG~~~m--nddP~-~~kVLYAkv~~~~~e~~l----~~~~~~~i~~~f~~~~li~k~ 270 (345)
T KOG2814|consen 201 ESTFQEIRIDV---GEKPLFIDLKGLDKM--NDDPS-LTKVLYAKVEPDDYEKFL----QHRCGERILERFVASGLIKKE 270 (345)
T ss_pred HHHHHHHHhcc---CCCceeeeccchhhh--cCCHh-HheeeeeeccCcchHHHH----HHHHHHHHHHHHHHhcchhcc
Confidence 99999988887 578889999999843 33322 000001222222323333 233555566666666666654
Q ss_pred -CCCceeee
Q psy2081 368 -MDGYFKPS 375 (380)
Q Consensus 368 -~~g~Y~~~ 375 (380)
+..+|++.
T Consensus 271 ~~~~kLH~T 279 (345)
T KOG2814|consen 271 SSSLKLHCT 279 (345)
T ss_pred ccccEEEEE
Confidence 34555554
No 59
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=93.01 E-value=0.71 Score=42.61 Aligned_cols=67 Identities=9% Similarity=0.195 Sum_probs=58.1
Q ss_pred EEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhhcc
Q psy2081 92 KYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFARK 161 (380)
Q Consensus 92 ~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~rk 161 (380)
.+.+.+++..+-+|....|..++.|-...|++|.+.. +.+.|.|+|. +..+..+...|..++...+.
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~--~~~~i~I~g~-k~~~~~i~~~i~~~l~~i~~ 93 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR--SENRIRITGT-KSTAEYIEASINEILSNIRT 93 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec--CCcEEEEEcc-HHHHHHHHHHHHHHHhhcEE
Confidence 4566667899999999999999999888899999965 5679999995 89999999999999988763
No 60
>KOG2113|consensus
Probab=92.75 E-value=0.081 Score=51.57 Aligned_cols=71 Identities=20% Similarity=0.299 Sum_probs=62.5
Q ss_pred ccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHH-HHHHHHh
Q psy2081 86 GKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAK-RRLDLLL 156 (380)
Q Consensus 86 ~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~-~~I~~iv 156 (380)
...|+-+..+.+|....+.+.|.+|++++++++-|++.|.-|-+..+...-++|-.+..+++|+ ..|+..+
T Consensus 110 s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~~~~Vf~Vtg~~~nC~kra~s~eie~ta 181 (394)
T KOG2113|consen 110 SASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRCGEPVFCVTGAPKNCVKRARSCEIEQTA 181 (394)
T ss_pred cccCCCceeeeccceeeeeccccccCccchheecccceEeeeccCCCceEEEecCCcchhhhccccchhhhh
Confidence 3567778899999999999999999999999999999999998777788999997677799998 7777665
No 61
>KOG2208|consensus
Probab=91.85 E-value=0.13 Score=56.65 Aligned_cols=46 Identities=33% Similarity=0.549 Sum_probs=41.2
Q ss_pred eeeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCC
Q psy2081 83 IYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPR 128 (380)
Q Consensus 83 i~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~ 128 (380)
+.....+..+.++.||-++|+.|||++|++.|.++.++++.|.+|.
T Consensus 701 ~~~~~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 701 IALEAKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred cccccccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence 4444556678899999999999999999999999999999999997
No 62
>PRK02821 hypothetical protein; Provisional
Probab=91.41 E-value=0.27 Score=38.62 Aligned_cols=35 Identities=14% Similarity=0.224 Sum_probs=29.4
Q ss_pred ccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhC
Q psy2081 86 GKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETN 121 (380)
Q Consensus 86 ~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~ 121 (380)
.+++ ....+.|.++-.|.||||+|.+++.|..--.
T Consensus 27 ~~~~-~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 27 NRRG-RTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CCCc-EEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 3444 7899999999999999999999999876533
No 63
>PRK00468 hypothetical protein; Provisional
Probab=90.98 E-value=0.33 Score=37.85 Aligned_cols=31 Identities=13% Similarity=0.165 Sum_probs=26.9
Q ss_pred CceEEEEEcCCCCcceeeCCCCchHHHHHHH
Q psy2081 89 GQYKYQCHIPKSFYPFIIGVKGSTKRRIESE 119 (380)
Q Consensus 89 g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~e 119 (380)
+.....+.|.++-.|.||||+|.|++.|..-
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 3367889999999999999999999988654
No 64
>TIGR03223 Phn_opern_protn putative phosphonate metabolism protein. This family of proteins is observed in the vicinity of other caharacterized genes involved in the catabolism of phosphonates via the3 C-P lyase system (GenProp0232), its function is unknown. These proteins are members of the somewhat broader pfam06299 model "Protein of unknown function (DUF1045)" which contains proteins found in a different genomic context as well.
Probab=90.94 E-value=2.6 Score=39.88 Aligned_cols=139 Identities=17% Similarity=0.149 Sum_probs=73.7
Q ss_pred CCceeeEEe-eccC---CchhHHHHHHHHHhhcccccccccccCceEE---EecceecCCCCCCceeEEEEEecCChHHH
Q psy2081 208 GRLHITMGM-LMLA---DSVERDQAVEVLQKCGNNIILPILRSQRIKI---NLKGLEIMNDDPAEVDILYAKVVDDSGLV 280 (380)
Q Consensus 208 ~~LHLTL~~-L~l~---~~~ev~~A~~~L~~~~~~~i~~~~~~~pf~l---~l~Glg~F~ddp~~~rVLya~v~d~~~~L 280 (380)
--+|.||+- +.+- ++.++..|.+.+.+- ..||.| .+.-++-|- =+.+...++.|
T Consensus 56 YGfHaTLKaPFrLa~g~~~a~L~~al~~fA~~----------~~pf~i~~L~l~~Lg~Fl---------AL~P~~~~~~L 116 (228)
T TIGR03223 56 YGFHATLKAPFRLAPGVTEAELLAAVAAFAAT----------RAPFALPPLRVALLGGFL---------ALRPAAPCPAL 116 (228)
T ss_pred cccceeecCCcccCCCCCHHHHHHHHHHHHhc----------CCCccCCcceeeeeCCEE---------EEeeCCCCHHH
Confidence 358999874 3332 234455554444332 245544 334443332 11123457999
Q ss_pred HHHHHHHHHHHHHC---------------CCccccc---c------CCCceeeEEEeecccccccCCCCCCCCccccCcC
Q psy2081 281 QKLCDDVVQYFISQ---------------HLISKAY---Q------KYDTVKMHVTLMNSKYRMRQNPSSDTNSEKRSTF 336 (380)
Q Consensus 281 q~L~~~l~~~f~~~---------------Gl~~~~~---~------e~r~fkpHiTL~nt~~r~~~~~~~~~~~~~r~~f 336 (380)
+.|++.+++.|... ||..... . =-+.|..||||-. +-... .+ -
T Consensus 117 ~~LAa~~V~~~d~fRAPls~aelaRRr~~~Ls~~Q~~~L~~WGYPYV~deFrFHmTLTg---~l~~~--------~~--~ 183 (228)
T TIGR03223 117 QALAAACVRELDPFRAPLTEAELARRRPDQLTPRQRALLERWGYPYVLEEFRFHMTLTG---RLDEE--------ER--A 183 (228)
T ss_pred HHHHHHHHHhhhhccCCCCHHHHhhcCccCCCHHHHHHHHHcCCCceecceEEEEEecC---CCChH--------HH--H
Confidence 99999999999542 2221000 0 0246999999952 11110 00 0
Q ss_pred CHHHHHH-HhCCceeceEEeeEEEEEEeeecCCCCceeeeEEEeC
Q psy2081 337 NAKDILE-SLGDFEFGETFVYCVHLSQRHTHDMDGYFKPSAVISL 380 (380)
Q Consensus 337 da~~il~-~~~~~~fG~~~v~~I~L~~s~~~~~~g~Y~~~~~i~L 380 (380)
.+...++ .|...--..+.|+.|.||.-. ..|.-++.+..++|
T Consensus 184 ~~~~~l~~~~~~~l~~p~~id~laLf~e~--~~g~pF~~~~~~~l 226 (228)
T TIGR03223 184 AVLARLEARFAPLLADPLAVDGLALFVEP--EPGAPFRLIARVAL 226 (228)
T ss_pred HHHHHHHHHhhhccCCCeeeeeEEEEecc--CCCCCcEEEEeecC
Confidence 1223333 344444456899999998542 23455777776665
No 65
>KOG3273|consensus
Probab=90.22 E-value=0.17 Score=46.46 Aligned_cols=55 Identities=25% Similarity=0.205 Sum_probs=47.1
Q ss_pred CCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhh
Q psy2081 100 SFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFA 159 (380)
Q Consensus 100 ~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~ 159 (380)
.-+|.|+|++|.|+=.||+-|.|+|.+- +..|-|-|. -+++.-|++.|=.|+-..
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVla----d~kIHiLG~-~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLA----DSKIHILGA-FQNIRIARDAVCSLILGS 232 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEec----CceEEEeec-chhhHHHHHhhHhhhccC
Confidence 4578999999999999999999999993 567999994 788999999988877443
No 66
>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=89.97 E-value=0.79 Score=33.56 Aligned_cols=34 Identities=18% Similarity=0.239 Sum_probs=29.1
Q ss_pred eEEEEEcCCCCcceeeCCCCchHHHHHHHhCceE
Q psy2081 91 YKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQL 124 (380)
Q Consensus 91 ~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I 124 (380)
....+.+...-.+.+||++|.+++.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 5667777776789999999999999999999665
No 67
>PRK01064 hypothetical protein; Provisional
Probab=89.53 E-value=0.59 Score=36.75 Aligned_cols=33 Identities=24% Similarity=0.256 Sum_probs=28.5
Q ss_pred CCceEEEEEcCCCCcceeeCCCCchHHHHHHHh
Q psy2081 88 DGQYKYQCHIPKSFYPFIIGVKGSTKRRIESET 120 (380)
Q Consensus 88 ~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT 120 (380)
++.....+.|.++-.|.+||++|.|++.|..-.
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 344788999999999999999999999997653
No 68
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=89.42 E-value=0.45 Score=37.24 Aligned_cols=32 Identities=16% Similarity=0.193 Sum_probs=28.1
Q ss_pred CCceEEEEEcCCCCcceeeCCCCchHHHHHHH
Q psy2081 88 DGQYKYQCHIPKSFYPFIIGVKGSTKRRIESE 119 (380)
Q Consensus 88 ~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~e 119 (380)
++.....+.|.++-.|.+|||+|.|++.|..-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 44578999999999999999999999998653
No 69
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=89.07 E-value=0.28 Score=50.57 Aligned_cols=45 Identities=20% Similarity=0.477 Sum_probs=39.2
Q ss_pred ceeeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCC
Q psy2081 82 DIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPR 128 (380)
Q Consensus 82 ~i~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~ 128 (380)
+++....+ ...+.||...++.+|||+|.++++||...|.+|++-.
T Consensus 479 eVe~~gd~--~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~ 523 (604)
T COG1855 479 EVEVVGDG--RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP 523 (604)
T ss_pred eEEEecCC--eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence 55655444 7889999999999999999999999999999999944
No 70
>PRK13764 ATPase; Provisional
Probab=88.09 E-value=0.4 Score=51.48 Aligned_cols=45 Identities=20% Similarity=0.363 Sum_probs=39.5
Q ss_pred ceeeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCC
Q psy2081 82 DIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPR 128 (380)
Q Consensus 82 ~i~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~ 128 (380)
+++...++ +..+.||...++.+|||+|.++++||...|..|+|-.
T Consensus 474 ~~~~~~~~--~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 474 EVEVVSDN--KAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred EEEEecCC--eEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 45555555 7889999999999999999999999999999999944
No 71
>KOG2279|consensus
Probab=87.75 E-value=0.49 Score=49.48 Aligned_cols=105 Identities=16% Similarity=0.238 Sum_probs=70.0
Q ss_pred eeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCC-CcEEEeeCCHHHHHHHHHHHHHHhhhhccc
Q psy2081 84 YLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQT-GDIIISSYSERGIASAKRRLDLLLVFARKK 162 (380)
Q Consensus 84 ~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~-~~i~I~g~~~~~v~~A~~~I~~iv~~~rkk 162 (380)
++....+...++-||.+++..|+|+.|+.++.|+..|+.+|.+...+.. -.+-+.+.-+..|..|+..|-.++...
T Consensus 61 e~e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~--- 137 (608)
T KOG2279|consen 61 EQKPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTEN--- 137 (608)
T ss_pred ecCchhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHhcC---
Confidence 4444566788999999999999999999999999999999999653322 234444434566777777766655333
Q ss_pred CCcceeeeccCC-ChhHHHHHHHHHHHHhc
Q psy2081 163 IPYTHLLSIPMN-VPNIQENFAKFKATVLS 191 (380)
Q Consensus 163 ~~~thFIaIpl~-~~~I~~~~~~fq~~v~~ 191 (380)
.++..=+++|.. ++.|.....+.+.++..
T Consensus 138 ~pvk~~lsvpqr~~~~i~grgget~~si~~ 167 (608)
T KOG2279|consen 138 TPVSEQLSVPQRSVGRIIGRGGETIRSICK 167 (608)
T ss_pred Ccccccccchhhhcccccccchhhhcchhc
Confidence 244444445544 34455555555555544
No 72
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=87.32 E-value=0.72 Score=40.27 Aligned_cols=40 Identities=15% Similarity=0.199 Sum_probs=35.8
Q ss_pred CCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcC
Q psy2081 88 DGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIP 127 (380)
Q Consensus 88 ~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip 127 (380)
++.-...+.|++.-.+..|||+|.+++.++.-++-.++|-
T Consensus 96 ~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 96 NGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred CCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 3346778999999999999999999999999999999883
No 73
>KOG2874|consensus
Probab=87.08 E-value=1 Score=43.55 Aligned_cols=50 Identities=20% Similarity=0.244 Sum_probs=39.5
Q ss_pred cceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhhc
Q psy2081 102 YPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFAR 160 (380)
Q Consensus 102 ~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~r 160 (380)
...+||++|+|++.||--|+|.|-+ ..++|.+.|+ -.++..++. ||.+.-
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilV----qG~TVsaiGp-fkGlkevr~----IV~DcM 209 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILV----QGNTVSAIGP-FKGLKEVRK----IVEDCM 209 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEe----eCcEEEeecC-cchHHHHHH----HHHHHH
Confidence 3479999999999999999999998 4578999997 566665554 555554
No 74
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=85.31 E-value=0.82 Score=36.12 Aligned_cols=44 Identities=16% Similarity=0.265 Sum_probs=34.5
Q ss_pred ceeeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCC
Q psy2081 82 DIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPR 128 (380)
Q Consensus 82 ~i~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~ 128 (380)
+|+.+.++ +.+.|-...-+.+||++|+++++|.++-.....++.
T Consensus 24 eI~Rt~~~---i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~ 67 (81)
T cd02413 24 EVRVTPTR---TEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE 67 (81)
T ss_pred EEEEcCCe---EEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence 67766543 555666667799999999999999999888887753
No 75
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=85.14 E-value=0.42 Score=36.60 Aligned_cols=34 Identities=18% Similarity=0.091 Sum_probs=29.2
Q ss_pred eEEEEEcCCCCcceeeCCCCchHHHHHHHhCceE
Q psy2081 91 YKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQL 124 (380)
Q Consensus 91 ~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I 124 (380)
-...+.|..+-.|.||||+|.|++.|+.-++.-+
T Consensus 29 ~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~ 62 (73)
T PF13083_consen 29 DTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA 62 (73)
T ss_dssp TEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred eEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence 6788888999999999999999999987665443
No 76
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=84.21 E-value=0.61 Score=35.74 Aligned_cols=35 Identities=20% Similarity=0.283 Sum_probs=27.6
Q ss_pred EEEEEcCCCC-----cceeeCCCCchHHHHHHHh-CceEEc
Q psy2081 92 KYQCHIPKSF-----YPFIIGVKGSTKRRIESET-NTQLSI 126 (380)
Q Consensus 92 ~~~v~Vp~~~-----~~~IIG~~G~t~k~ie~eT-~~~I~i 126 (380)
+..+-|-+.- .|..||++|+.++.|+++. |-+|++
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdv 44 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDV 44 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEE
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEE
Confidence 4555566665 8999999999999999999 888887
No 77
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=83.86 E-value=1.2 Score=38.89 Aligned_cols=36 Identities=14% Similarity=0.270 Sum_probs=32.3
Q ss_pred EEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcC
Q psy2081 92 KYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIP 127 (380)
Q Consensus 92 ~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip 127 (380)
++-+-|++...|..||++|++++.|++..|-+|++=
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv 68 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV 68 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence 667778888999999999999999999999898883
No 78
>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=82.82 E-value=2 Score=33.34 Aligned_cols=36 Identities=19% Similarity=0.229 Sum_probs=30.6
Q ss_pred EEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcC
Q psy2081 92 KYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIP 127 (380)
Q Consensus 92 ~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip 127 (380)
...++|..+-.+.+||++|.|+..|+--++.-++-.
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~~ 60 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNRN 60 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhhc
Confidence 566778888899999999999999999888766653
No 79
>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=81.22 E-value=1.6 Score=38.29 Aligned_cols=40 Identities=15% Similarity=0.138 Sum_probs=36.5
Q ss_pred CCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcC
Q psy2081 88 DGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIP 127 (380)
Q Consensus 88 ~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip 127 (380)
+|.....+.||++-++..|||+|.+++...+-|+-+++|-
T Consensus 97 ~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 97 NGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 5667888999999999999999999999999999999884
No 80
>KOG2279|consensus
Probab=79.42 E-value=1 Score=47.23 Aligned_cols=70 Identities=23% Similarity=0.294 Sum_probs=55.4
Q ss_pred cCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCC--cEEEeeCCHHHHHHHHHHHHHHh
Q psy2081 87 KDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTG--DIIISSYSERGIASAKRRLDLLL 156 (380)
Q Consensus 87 ~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~--~i~I~g~~~~~v~~A~~~I~~iv 156 (380)
.+.-++....||...++.|+|++|.|++.|+.-.+.+|.+...|..| .+.+.+..+.-++.|+..|..=+
T Consensus 136 ~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~ 207 (608)
T KOG2279|consen 136 ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKV 207 (608)
T ss_pred cCCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccc
Confidence 55668999999999999999999999999999999999998766654 34444434666777777665544
No 81
>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=74.72 E-value=1 Score=34.80 Aligned_cols=43 Identities=28% Similarity=0.315 Sum_probs=35.1
Q ss_pred ccceeeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEE
Q psy2081 80 DLDIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLS 125 (380)
Q Consensus 80 ~~~i~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ 125 (380)
.+.|+.+. ....+.+-.+.-+.+||++|+++++|.++.+-.+.
T Consensus 17 ~i~I~r~~---~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 17 DIEIERTP---DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp EEEEEESS---SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred eEEEEEcC---CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 35666533 46778888899999999999999999999887775
No 82
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=74.43 E-value=4 Score=35.74 Aligned_cols=36 Identities=14% Similarity=0.192 Sum_probs=33.0
Q ss_pred EEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcC
Q psy2081 92 KYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIP 127 (380)
Q Consensus 92 ~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip 127 (380)
+.-+-|.+...|..||++|++++.|++..|-+|+|=
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV 69 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI 69 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE
Confidence 788889999999999999999999998899888873
No 83
>KOG3102|consensus
Probab=71.81 E-value=14 Score=34.51 Aligned_cols=98 Identities=14% Similarity=0.243 Sum_probs=68.1
Q ss_pred CCCceeeEEeeccCCchhHHHHHHHHHhhcccccccccccCceEEEecceecCCCCCCceeE-EEEEec-CChHHHHHHH
Q psy2081 207 PGRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPILRSQRIKINLKGLEIMNDDPAEVDI-LYAKVV-DDSGLVQKLC 284 (380)
Q Consensus 207 p~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~~~~pf~l~l~Glg~F~ddp~~~rV-Lya~v~-d~~~~Lq~L~ 284 (380)
-..+||.|.==.-+.-.++.....+|++.- .....|-+++.++.+|- +..+.|. |-+.+. .+.+.+.++.
T Consensus 119 ~~~fHlSLsr~VvLr~HqI~~fi~~L~~~l-------~s~~rf~~t~n~~~iyt-N~e~TRtFi~leitt~~~~~~~~~i 190 (269)
T KOG3102|consen 119 GREFHLSLSRNVVLRVHQINSFISMLRQKL-------QSQKRFLITFNKWEIYT-NDEHTRTFISLEITTSGLSEISKQI 190 (269)
T ss_pred cceEEEeeccceEEEeehhhHHHHHHHHHH-------hhhhhheEeecceEEEe-ccccceeEEEEEechhhHHHHHHHH
Confidence 467999886443345566777777777652 23477899999999998 4555554 334444 3457777777
Q ss_pred HHHHHHHHHCCCccccccCC-CceeeEEEeecccccc
Q psy2081 285 DDVVQYFISQHLISKAYQKY-DTVKMHVTLMNSKYRM 320 (380)
Q Consensus 285 ~~l~~~f~~~Gl~~~~~~e~-r~fkpHiTL~nt~~r~ 320 (380)
+.+.+-+....|.. -+ ++ .+|+.|+ |..
T Consensus 191 ~~vd~Vm~~~nL~~----FY~DP-sfHiSL~---Wcv 219 (269)
T KOG3102|consen 191 DAVDEVMKLHNLPE----FYKDP-SFHISLV---WCV 219 (269)
T ss_pred HHHHHHHHHcCchh----hhcCC-CCCceEE---EEe
Confidence 88888888888875 34 44 8999997 654
No 84
>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=71.63 E-value=1 Score=27.94 Aligned_cols=14 Identities=29% Similarity=0.385 Sum_probs=8.4
Q ss_pred EecCeeeeeCCCCC
Q psy2081 27 IIDGRRYRVNPSWP 40 (380)
Q Consensus 27 ~~~~r~yr~~~~~~ 40 (380)
+.|..|||+|+.+.
T Consensus 4 ~YG~~CYRkNp~H~ 17 (26)
T PF10283_consen 4 KYGAKCYRKNPQHF 17 (26)
T ss_dssp TTGGG-S--SCCHH
T ss_pred CcchhhhcCCHHHH
Confidence 35788999999874
No 85
>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=70.02 E-value=5.1 Score=33.29 Aligned_cols=40 Identities=25% Similarity=0.285 Sum_probs=29.7
Q ss_pred ceeeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceE
Q psy2081 82 DIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQL 124 (380)
Q Consensus 82 ~i~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I 124 (380)
+|+.+.+. +.|.|-..+-|.|||++|+++++|.+.....+
T Consensus 55 ~I~R~~~~---i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~~ 94 (109)
T cd02412 55 EIERKADR---VEVTIHTARPGIIIGKKGAGIEKLRKELQKLL 94 (109)
T ss_pred EEEEcCCC---EEEEEEeCCCCcccCCchHHHHHHHHHHHHHh
Confidence 56654433 55555666679999999999999999876654
No 86
>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=69.01 E-value=8.9 Score=30.27 Aligned_cols=40 Identities=18% Similarity=0.174 Sum_probs=29.3
Q ss_pred ceeeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceE
Q psy2081 82 DIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQL 124 (380)
Q Consensus 82 ~i~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I 124 (380)
+|+.+.++ ....+++ .+-|.+||++|+++++|.+.-.-.+
T Consensus 32 eI~r~~~~-i~V~I~t--~~pg~iIGk~G~~I~~l~~~l~k~~ 71 (85)
T cd02411 32 EILRTPLG-TQITIYA--ERPGMVIGRGGKNIRELTEILETKF 71 (85)
T ss_pred EEEEcCCc-EEEEEEE--CCCCceECCCchhHHHHHHHHHHHh
Confidence 56655444 5666666 7889999999999999988754443
No 87
>PHA02977 hypothetical protein; Provisional
Probab=68.20 E-value=27 Score=30.70 Aligned_cols=90 Identities=17% Similarity=0.070 Sum_probs=52.3
Q ss_pred eeeEEeeccCCchhHHHHHHHHHhhcccccccccccCceEEEecceecCCCCC------CceeEEEEEecCChHHHHHHH
Q psy2081 211 HITMGMLMLADSVERDQAVEVLQKCGNNIILPILRSQRIKINLKGLEIMNDDP------AEVDILYAKVVDDSGLVQKLC 284 (380)
Q Consensus 211 HLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~~~~pf~l~l~Glg~F~ddp------~~~rVLya~v~d~~~~Lq~L~ 284 (380)
|+||+.-.--..+..+.-++..... .-+.+.+.-+..=+||... ...+-+-++++ .++.|..|.
T Consensus 71 hitlgian~dq~~~f~~fk~~~~d~---------dl~sis~~cke~icfpqs~askelga~g~avvmkle-~sddlkalr 140 (201)
T PHA02977 71 HITLGIANKDQCDNFENFKELIKDI---------DLQSISFTCKEEICFPQSNASKELGAKGCAVVMKLE-ASDDLKALR 140 (201)
T ss_pred ceeeeccCccHhHHHHHHHHHhhcc---------cceeEEEEeeeeEeccccchhhhhCcCccEEEEEEE-echHHHHHH
Confidence 9998776432223334444444333 2356777778888888422 23455666776 467887777
Q ss_pred HHHHHHHH----HCCCccccccCCCceeeEEEee
Q psy2081 285 DDVVQYFI----SQHLISKAYQKYDTVKMHVTLM 314 (380)
Q Consensus 285 ~~l~~~f~----~~Gl~~~~~~e~r~fkpHiTL~ 314 (380)
+.+....- -.|=.. -..+..||+|+.
T Consensus 141 nvl~n~vp~pkdifg~i~----~d~~w~phitig 170 (201)
T PHA02977 141 NVLFNAVPCPKDIFGDIL----SDNPWCPHITIG 170 (201)
T ss_pred HHhhcccCCcHHhhcccc----cCCCCCCceEEE
Confidence 76644221 012222 346899999997
No 88
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=66.94 E-value=4.3 Score=42.48 Aligned_cols=65 Identities=17% Similarity=0.174 Sum_probs=45.1
Q ss_pred EEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCC---CCC---CcEEEeeC--CHHHHHHHHHHHHHHh
Q psy2081 92 KYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQ---GQT---GDIIISSY--SERGIASAKRRLDLLL 156 (380)
Q Consensus 92 ~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~---~~~---~~i~I~g~--~~~~v~~A~~~I~~iv 156 (380)
..++-||...|+.|||.||..+++....-++-|++-.. +.+ ..|.|..+ ++.++..|+.-...+|
T Consensus 450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V 522 (657)
T COG5166 450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKV 522 (657)
T ss_pred heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHH
Confidence 46778888999999999999999999999999988431 111 35777775 3344444443333333
No 89
>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=65.35 E-value=7.1 Score=39.17 Aligned_cols=40 Identities=15% Similarity=0.219 Sum_probs=36.6
Q ss_pred CceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCC
Q psy2081 89 GQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPR 128 (380)
Q Consensus 89 g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~ 128 (380)
..-...+.||.+-.+.-||++|.++|---.-||.+|+|=+
T Consensus 299 ~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 299 DKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred CCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 3368999999999999999999999999999999999943
No 90
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=64.45 E-value=6.9 Score=36.00 Aligned_cols=36 Identities=19% Similarity=0.209 Sum_probs=34.5
Q ss_pred EEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcC
Q psy2081 92 KYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIP 127 (380)
Q Consensus 92 ~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip 127 (380)
...+.||.+-.+..||++|.+++...+-||.+|+|-
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~ 178 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE 178 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence 888999999999999999999999999999999994
No 91
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=63.88 E-value=8.5 Score=36.43 Aligned_cols=42 Identities=19% Similarity=0.218 Sum_probs=31.8
Q ss_pred ceeeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEc
Q psy2081 82 DIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSI 126 (380)
Q Consensus 82 ~i~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~i 126 (380)
+|+.+.. .+.|.|-...-|.+||++|+.+++|.++....+..
T Consensus 45 eIeR~~~---~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~ 86 (233)
T COG0092 45 EIERTPK---GTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGK 86 (233)
T ss_pred EEEecCC---ceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCC
Confidence 6777733 45555666778999999999999998886655555
No 92
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=63.11 E-value=8.6 Score=34.60 Aligned_cols=35 Identities=9% Similarity=0.117 Sum_probs=29.4
Q ss_pred EEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcC
Q psy2081 92 KYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIP 127 (380)
Q Consensus 92 ~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip 127 (380)
.+-+-|.+-. |.-||++|.++|++++..|-+|.+=
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence 4555565566 9999999999999999999999883
No 93
>PF06299 DUF1045: Protein of unknown function (DUF1045); InterPro: IPR009389 This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
Probab=59.64 E-value=50 Score=29.58 Aligned_cols=112 Identities=14% Similarity=0.107 Sum_probs=61.8
Q ss_pred CchhHHHHHHHHHhhcccccccccccCceE---EEecceecCCCCCCceeEEEEEecCChHHHHHHHHHHHHHHHHCCCc
Q psy2081 221 DSVERDQAVEVLQKCGNNIILPILRSQRIK---INLKGLEIMNDDPAEVDILYAKVVDDSGLVQKLCDDVVQYFISQHLI 297 (380)
Q Consensus 221 ~~~ev~~A~~~L~~~~~~~i~~~~~~~pf~---l~l~Glg~F~ddp~~~rVLya~v~d~~~~Lq~L~~~l~~~f~~~Gl~ 297 (380)
++.++.+|.+.+..-. .||. +.+.-+|-| |=+-+.+.++.|+.|++.++..|-..-=.
T Consensus 13 ~~~~L~~a~~~~a~~~----------~pf~l~~L~v~~lg~F---------lALvp~~~~~~L~~LAa~cV~~~d~fRAP 73 (160)
T PF06299_consen 13 SEADLLAALAAFAARF----------APFELPGLEVARLGGF---------LALVPAGPCPALQALAAACVRAFDPFRAP 73 (160)
T ss_pred CHHHHHHHHHHHhccC----------CCccCCceeEeeECCE---------EEEeeCCCCHHHHHHHHHHHHhhhhccCC
Confidence 5666766666665432 3332 445555544 22334445799999999999999753211
Q ss_pred ccc-c-----------c------------CCCceeeEEEeecccccccCCCCCCCCccccCcCCHHHHHH-HhCCceece
Q psy2081 298 SKA-Y-----------Q------------KYDTVKMHVTLMNSKYRMRQNPSSDTNSEKRSTFNAKDILE-SLGDFEFGE 352 (380)
Q Consensus 298 ~~~-~-----------~------------e~r~fkpHiTL~nt~~r~~~~~~~~~~~~~r~~fda~~il~-~~~~~~fG~ 352 (380)
.++ + . =-+.|..||||-. +-.. ..+. .+...++ .|...--..
T Consensus 74 ls~aelaRR~~~~Ls~~Q~~~L~rWGYPYV~deFRFHmTLTg---~l~~--------~~~~--~~~~~l~~~f~~~l~~p 140 (160)
T PF06299_consen 74 LSEAELARRRPAGLSPRQRANLERWGYPYVMDEFRFHMTLTG---RLDP--------AERA--RVEAALEAHFAPLLPEP 140 (160)
T ss_pred CChHHHhhcCcccCCHHHHHHHHHhCCCceeCcCEeeEEeCC---CCCH--------HHHH--HHHHHHHHHHHhhcCCC
Confidence 110 0 0 0246999999952 2111 0110 1222333 355554467
Q ss_pred EEeeEEEEEEee
Q psy2081 353 TFVYCVHLSQRH 364 (380)
Q Consensus 353 ~~v~~I~L~~s~ 364 (380)
+.|+.|.|+.-.
T Consensus 141 ~~id~laLf~e~ 152 (160)
T PF06299_consen 141 LRIDSLALFGEP 152 (160)
T ss_pred eeecceEEEecc
Confidence 899999998543
No 94
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=58.98 E-value=8.3 Score=39.09 Aligned_cols=42 Identities=17% Similarity=0.110 Sum_probs=37.6
Q ss_pred CceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCC
Q psy2081 89 GQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQG 130 (380)
Q Consensus 89 g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~ 130 (380)
..-...+.||..-++.-||++|.++|---.-||.+|+|-+.+
T Consensus 306 ~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 306 EEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred CCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 335889999999999999999999999999999999996544
No 95
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=58.77 E-value=11 Score=38.04 Aligned_cols=41 Identities=17% Similarity=0.244 Sum_probs=37.1
Q ss_pred CCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCC
Q psy2081 88 DGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPR 128 (380)
Q Consensus 88 ~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~ 128 (380)
...-...+.||..-.+.-||++|.++|---.-||.+|+|=+
T Consensus 300 ~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 300 EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 44468899999999999999999999999999999999954
No 96
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=54.11 E-value=38 Score=26.61 Aligned_cols=37 Identities=22% Similarity=0.237 Sum_probs=28.8
Q ss_pred hCceEEcCCCCCCCcEEEee-CCHHHHHHHHHHHHHHhhhh
Q psy2081 120 TNTQLSIPRQGQTGDIIISS-YSERGIASAKRRLDLLLVFA 159 (380)
Q Consensus 120 T~~~I~ip~~~~~~~i~I~g-~~~~~v~~A~~~I~~iv~~~ 159 (380)
.++.+.|= .+|.|+|+| .+.+.+..|.++|..++.+.
T Consensus 48 p~~t~~IF---~sGki~itGaks~~~~~~a~~~i~~~L~~~ 85 (86)
T PF00352_consen 48 PKATVLIF---SSGKIVITGAKSEEEAKKAIEKILPILQKL 85 (86)
T ss_dssp TTEEEEEE---TTSEEEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred CcEEEEEE---cCCEEEEEecCCHHHHHHHHHHHHHHHHHc
Confidence 35666664 368999999 48999999999988887654
No 97
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=52.04 E-value=12 Score=39.28 Aligned_cols=37 Identities=19% Similarity=0.232 Sum_probs=35.2
Q ss_pred eEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcC
Q psy2081 91 YKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIP 127 (380)
Q Consensus 91 ~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip 127 (380)
-...+.||..-.+.-|||+|.++|...+-||.+|+|=
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~ 338 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIM 338 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEE
Confidence 5889999999999999999999999999999999994
No 98
>COG5255 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.34 E-value=65 Score=30.10 Aligned_cols=31 Identities=16% Similarity=0.205 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHCCCccccccCCCceeeEEEee
Q psy2081 278 GLVQKLCDDVVQYFISQHLISKAYQKYDTVKMHVTLM 314 (380)
Q Consensus 278 ~~Lq~L~~~l~~~f~~~Gl~~~~~~e~r~fkpHiTL~ 314 (380)
..|.++.+.+.+ .+|+.. .+.+.+..|+||.
T Consensus 154 ~~l~~~Rd~ls~---~~g~r~---P~HDaY~FHITlg 184 (239)
T COG5255 154 KILEEWRDYLSE---KFGYRH---PDHDAYQFHITLG 184 (239)
T ss_pred HHHHHHHHHHhh---hhcccC---CCCcceEEEEEee
Confidence 445444444433 468998 4889999999997
No 99
>PF08975 2H-phosphodiest: Domain of unknown function (DUF1868); InterPro: IPR015069 This family consist of hypothetical bacterial proteins. ; PDB: 2FSQ_A.
Probab=49.97 E-value=21 Score=30.26 Aligned_cols=48 Identities=8% Similarity=0.013 Sum_probs=29.3
Q ss_pred ceeeeccCCChhHHHHHHHHHHHHhcccCcCCCCccccccCCCCceeeEEee
Q psy2081 166 THLLSIPMNVPNIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGML 217 (380)
Q Consensus 166 thFIaIpl~~~~I~~~~~~fq~~v~~~~~~~~gi~~~~fv~p~~LHLTL~~L 217 (380)
+.|||=--...+....+..+++.+++.. ..+.-.|.||+.+|+|+.=.
T Consensus 14 NTvIchl~~~s~~~~al~~i~~~l~~~~----~~~k~a~lP~sS~HMTVf~G 61 (118)
T PF08975_consen 14 NTVICHLPQDSPFYAALLAIQQRLRESP----FADKLAFLPPSSYHMTVFEG 61 (118)
T ss_dssp EEEEEEB-TTSHHHHHHHHHHHHHHTSG----GGGGEEE--GGG-EEEEEEE
T ss_pred CeEEeecCCCChHHHHHHHHHHHHHhCc----cccceEecCcchhhhhhhcc
Confidence 4566642223467778888888888643 23445689999999998543
No 100
>PF13382 Adenine_deam_C: Adenine deaminase C-terminal domain; PDB: 3T8L_B 3T81_A 3NQB_A.
Probab=49.76 E-value=38 Score=30.60 Aligned_cols=78 Identities=15% Similarity=0.169 Sum_probs=52.3
Q ss_pred CCCcEEEeeCCHHHHHHHHHHHHHHhhhh--cccCCcceeeeccCC-------ChhHHHHHHHHHHHHhcccCcCCCCcc
Q psy2081 131 QTGDIIISSYSERGIASAKRRLDLLLVFA--RKKIPYTHLLSIPMN-------VPNIQENFAKFKATVLSDFSRCRGIEE 201 (380)
Q Consensus 131 ~~~~i~I~g~~~~~v~~A~~~I~~iv~~~--rkk~~~thFIaIpl~-------~~~I~~~~~~fq~~v~~~~~~~~gi~~ 201 (380)
++..|++.|.+.+....|..++..+-.-. .........+.+|+. -+++.+.+.++.+.+.+. |
T Consensus 64 DshniiviG~~~~dm~~A~n~l~~~gGG~vvv~~g~v~a~lpLpi~GlmS~~~~eev~~~~~~l~~~~~~l-----G--- 135 (171)
T PF13382_consen 64 DSHNIIVIGTNDEDMALAANRLIEMGGGIVVVDDGEVLAELPLPIAGLMSDLPAEEVARQLEELEEALREL-----G--- 135 (171)
T ss_dssp TT--EEEEESSHHHHHHHHHHHHHTTSEEEEEETTEEEEEEE-TBTTTBBSS-HHHHHHHHHHHHHHHHTT-----S---
T ss_pred CCCCEEEEECCHHHHHHHHHHHHHhCCCEEEEECCEEEEEEeccccceecCCCHHHHHHHHHHHHHHHHHc-----C---
Confidence 45689999999999999999988865322 123345778888863 257888998888877753 2
Q ss_pred ccccCCCCceeeEEeecc
Q psy2081 202 SLFQEPGRLHITMGMLML 219 (380)
Q Consensus 202 ~~fv~p~~LHLTL~~L~l 219 (380)
| +..+.-+||.||.+
T Consensus 136 --~-~~~~p~~tlsflsl 150 (171)
T PF13382_consen 136 --C-PFDDPFMTLSFLSL 150 (171)
T ss_dssp ----BTTTBSGGGGGTT-
T ss_pred --C-CCCCHHHHHHHhhc
Confidence 1 22366788888875
No 101
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=49.51 E-value=35 Score=32.13 Aligned_cols=43 Identities=14% Similarity=0.179 Sum_probs=31.4
Q ss_pred ceeeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcC
Q psy2081 82 DIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIP 127 (380)
Q Consensus 82 ~i~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip 127 (380)
+|+.+.++ ..+.++ ...-+.|||++|..+++|.++-.-.+.++
T Consensus 38 eI~Rt~~~-i~V~I~--tarPg~vIG~~G~~i~~l~~~L~k~~~~~ 80 (220)
T PTZ00084 38 EVRVTPIR-TEIIIR--ATRTREVLGDKGRRIRELTSLLQKRFGFP 80 (220)
T ss_pred EEEEcCCc-EEEEEE--ECCCccEEcCCchHHHHHHHHHHHHhCCC
Confidence 67776554 444444 45569999999999999998877666553
No 102
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=49.22 E-value=18 Score=37.49 Aligned_cols=38 Identities=18% Similarity=0.240 Sum_probs=35.5
Q ss_pred eEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCC
Q psy2081 91 YKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPR 128 (380)
Q Consensus 91 ~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~ 128 (380)
-...+.||..-.+.-|||+|.++|---.-||.+|+|-+
T Consensus 335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 57899999999999999999999999999999999943
No 103
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=47.91 E-value=19 Score=33.11 Aligned_cols=35 Identities=14% Similarity=0.185 Sum_probs=30.5
Q ss_pred EEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEc
Q psy2081 92 KYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSI 126 (380)
Q Consensus 92 ~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~i 126 (380)
..+..+-..-.|..||++|++++.|.++.|-+|+|
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdV 111 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDV 111 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEE
Confidence 56666777788999999999999999999977776
No 104
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=47.62 E-value=45 Score=33.49 Aligned_cols=57 Identities=16% Similarity=0.066 Sum_probs=46.2
Q ss_pred CCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHHHHHHHHHH--HHhhhhc
Q psy2081 99 KSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLD--LLLVFAR 160 (380)
Q Consensus 99 ~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~--~iv~~~r 160 (380)
....-.+.|+.|..++.||..+|+.|.-+ ...+.|+|. +..|..|...+. .+....+
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~r----G~~~~i~g~-~~~v~~A~~~l~~l~~~~~~~ 81 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVAR----GEAVRIIGA-RPLVDVATRVLLTLELLAEVR 81 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEeC----CceEEEEec-hHHHHHHHHHHhHHHHHHHHh
Confidence 34556689999999999999999999974 357999996 558999999998 5555544
No 105
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=47.17 E-value=18 Score=31.76 Aligned_cols=33 Identities=30% Similarity=0.299 Sum_probs=28.5
Q ss_pred EEEcCCCCcceeeCCCCchHHHHHHHhCceEEc
Q psy2081 94 QCHIPKSFYPFIIGVKGSTKRRIESETNTQLSI 126 (380)
Q Consensus 94 ~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~i 126 (380)
.+.|-...-|.+||++|.++++|-.+||-+-.+
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~v 111 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKV 111 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEE
Confidence 455556778999999999999999999998776
No 106
>PRK15031 5-carboxymethyl-2-hydroxymuconate delta-isomerase; Provisional
Probab=45.41 E-value=26 Score=30.11 Aligned_cols=46 Identities=13% Similarity=0.144 Sum_probs=31.4
Q ss_pred CCceeeEEeeccCCchhHHHHHHHHHhhcccccccccccCceEEEe
Q psy2081 208 GRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPILRSQRIKINL 253 (380)
Q Consensus 208 ~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~~~~pf~l~l 253 (380)
.=+|+||.++.+-++++.+.+.+.|-++......++.+...+.|++
T Consensus 60 ~Fihv~l~i~~GRs~e~k~~l~~~l~~~l~~~~~~~~~~~~~~LS~ 105 (126)
T PRK15031 60 AFVHMTLKIGAGRSLESRQEVGEMLFALIKAHFAALMESRYLALSF 105 (126)
T ss_pred cEEEEEeeecCCCCHHHHHHHHHHHHHHHHHHhhhhhcccceEEEE
Confidence 4689999999999999988888877766444443333333344444
No 107
>KOG3102|consensus
Probab=42.53 E-value=75 Score=29.84 Aligned_cols=86 Identities=12% Similarity=0.208 Sum_probs=45.2
Q ss_pred cCCcceeeeccCCCh---hHHHHHHHHHHHHhcccCcCCCCccccccCCCCceeeEEeeccCCchhHH-HHHHHHHhhcc
Q psy2081 162 KIPYTHLLSIPMNVP---NIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVERD-QAVEVLQKCGN 237 (380)
Q Consensus 162 k~~~thFIaIpl~~~---~I~~~~~~fq~~v~~~~~~~~gi~~~~fv~p~~LHLTL~~L~l~~~~ev~-~A~~~L~~~~~ 237 (380)
..+-+.||++|+... +|-+.+.. .++|++.+ ++. ..++.| .+|+.|....+--...++ +....|+++.
T Consensus 167 ~e~TRtFi~leitt~~~~~~~~~i~~-vd~Vm~~~----nL~-~FY~DP-sfHiSL~WcvGD~rt~L~g~~l~EL~~l~- 238 (269)
T KOG3102|consen 167 DEHTRTFISLEITTSGLSEISKQIDA-VDEVMKLH----NLP-EFYKDP-SFHISLVWCVGDIRTSLKGAVLVELRKLR- 238 (269)
T ss_pred cccceeEEEEEechhhHHHHHHHHHH-HHHHHHHc----Cch-hhhcCC-CCCceEEEEeccHHHhhhhHHHHHHHHHH-
Confidence 345689999999842 22223333 45555543 243 233456 999999988653333333 3333333332
Q ss_pred cccccc-cccCceEEEecceec
Q psy2081 238 NIILPI-LRSQRIKINLKGLEI 258 (380)
Q Consensus 238 ~~i~~~-~~~~pf~l~l~Glg~ 258 (380)
+-. ...--|.+++.|+.+
T Consensus 239 ---dg~~~~~~~l~v~~~~i~C 257 (269)
T KOG3102|consen 239 ---DGGCVQNRILTVKFCGIEC 257 (269)
T ss_pred ---hccchhheeEEEeeeeEEE
Confidence 100 011335677777776
No 108
>PF07823 CPDase: Cyclic phosphodiesterase-like protein; InterPro: IPR012386 2',3' Cyclic nucleotide phosphodiesterases (CPDases) are enzymes that catalyse at least two distinct steps in the splicing of tRNA introns in eukaryotes. The active site is characterised by two conserved histidine residues []. The enzyme has six cysteine residues, four of which are involved in forming two intra-molecular disulphide bridges. One of these bridges is involved in the catalytic activity of the enzyme as it opens when CPDase is semi-reduced []. Proteins in this entryand belong to 3.1.4.37 from EC and catalyse the reaction Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate. ; GO: 0004112 cyclic-nucleotide phosphodiesterase activity; PDB: 1JH7_A 1JH6_B 1FSI_B.
Probab=41.65 E-value=39 Score=30.93 Aligned_cols=39 Identities=15% Similarity=0.139 Sum_probs=17.7
Q ss_pred eEEEEEecCC---hHHHHHHHHHHHHHHHHCCCccccccCCCceeeEEEee
Q psy2081 267 DILYAKVVDD---SGLVQKLCDDVVQYFISQHLISKAYQKYDTVKMHVTLM 314 (380)
Q Consensus 267 rVLya~v~d~---~~~Lq~L~~~l~~~f~~~Gl~~~~~~e~r~fkpHiTL~ 314 (380)
--||+-+..+ .+.|+.|-..|...|-. ..-.|-||+||.
T Consensus 3 ~SlWl~P~~~~~~~~~L~~lI~~L~~~~~~---------~~p~F~PHiTL~ 44 (196)
T PF07823_consen 3 YSLWLVPPPGSPLYERLKTLISSLASLFPG---------SPPPFEPHITLT 44 (196)
T ss_dssp EEEEEEE-T--TTHHHHHHHHHHHHHHST------------------EEEE
T ss_pred EEEEEcCCCCccHHHHHHHHHHHHHHHCCC---------CCCCcCCeEEEe
Confidence 3589988743 35565555555444331 124799999997
No 109
>PF08302 tRNA_lig_CPD: Fungal tRNA ligase phosphodiesterase domain; InterPro: IPR015965 This entry represents a phosphodiesterase domain found in fungal tRNA ligases []. Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation
Probab=41.64 E-value=2.3e+02 Score=27.17 Aligned_cols=15 Identities=20% Similarity=0.169 Sum_probs=10.5
Q ss_pred CCchhHHHHHHHHHh
Q psy2081 220 ADSVERDQAVEVLQK 234 (380)
Q Consensus 220 ~~~~ev~~A~~~L~~ 234 (380)
.+++++++|.+.-..
T Consensus 25 Ps~e~id~A~~~Al~ 39 (257)
T PF08302_consen 25 PSDEEIDEAFQKALN 39 (257)
T ss_pred CCHHHHHHHHHHHHh
Confidence 368888888766555
No 110
>COG1135 AbcC ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=41.09 E-value=35 Score=33.99 Aligned_cols=93 Identities=20% Similarity=0.322 Sum_probs=58.8
Q ss_pred EEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEee-----CCHHHHHHHHHHHHHHhhhhcccCCcce
Q psy2081 93 YQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISS-----YSERGIASAKRRLDLLLVFARKKIPYTH 167 (380)
Q Consensus 93 ~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g-----~~~~~v~~A~~~I~~iv~~~rkk~~~th 167 (380)
++++|++--+=-|||..|+=+.-|-+-.+ ...-|+ +|.|.|.| -+...+..+|++|-.|-..+.--...|.
T Consensus 25 vsL~I~~GeI~GIIG~SGAGKSTLiR~iN-~Le~Pt---sG~v~v~G~di~~l~~~~Lr~~R~~IGMIFQhFnLLssrTV 100 (339)
T COG1135 25 VSLEIPKGEIFGIIGYSGAGKSTLLRLIN-LLERPT---SGSVFVDGQDLTALSEAELRQLRQKIGMIFQHFNLLSSRTV 100 (339)
T ss_pred ceEEEcCCcEEEEEcCCCCcHHHHHHHHh-ccCCCC---CceEEEcCEecccCChHHHHHHHhhccEEeccccccccchH
Confidence 67889998888899999986554433221 112232 34444444 4788899999999888765543333455
Q ss_pred e--eeccCC-----ChhHHHHHHHHHHHH
Q psy2081 168 L--LSIPMN-----VPNIQENFAKFKATV 189 (380)
Q Consensus 168 F--IaIpl~-----~~~I~~~~~~fq~~v 189 (380)
| ||+||- ..++..+..++.+-|
T Consensus 101 ~~NvA~PLeiag~~k~ei~~RV~elLelV 129 (339)
T COG1135 101 FENVAFPLELAGVPKAEIKQRVAELLELV 129 (339)
T ss_pred HhhhhhhHhhcCCCHHHHHHHHHHHHHHc
Confidence 5 777874 245666666655543
No 111
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=40.88 E-value=43 Score=30.92 Aligned_cols=40 Identities=18% Similarity=0.223 Sum_probs=28.8
Q ss_pred ceeeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceE
Q psy2081 82 DIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQL 124 (380)
Q Consensus 82 ~i~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I 124 (380)
+|+.+.++ ..+.++ ...-+.+||++|+++++|.++-.-.+
T Consensus 32 eI~r~~~~-~~I~I~--~~rPg~vIG~~g~~i~~l~~~l~k~~ 71 (195)
T TIGR01008 32 DVRVTPLG-TKVIIF--AERPGLVIGRGGRRIRELTEKLQKKF 71 (195)
T ss_pred EEEEcCCc-EEEEEE--ECCCceEECCCchHHHHHHHHHHHHh
Confidence 67766554 444444 45569999999999999988865543
No 112
>PF02962 CHMI: 5-carboxymethyl-2-hydroxymuconate isomerase; InterPro: IPR004220 5-carboxymethyl-2-hydroxymuconate isomerase transforms 5-carboxymethyl-2-hydroxy-muconic acid into 5-oxo-pent-3-ene-1,2,5-tricarboxylic acid during the third step of the homoprotocatechuate catabolic pathway []. Homoprotocatechuate (HPC; 3,4-dihydroxyphenylacetate) is catabolized to Krebs cycle intermediates via extradiol (meta-) cleavage and the necessary enzymes are chromosomally encoded in a variety of bacteria []. 5-carboxymethyl-2-hydroxymuconate isomerase is probably a dimer of two identical subunits []. A comparison of the N-terminal half of the isomerase/decarboxylase sequence from the pathway (both encoded by the gene hpcE), with the second half showed significant similarity. This suggests that a duplication may have occurred to produce a bifunctional gene [].; PDB: 3E6Q_H 1OTG_B.
Probab=38.87 E-value=37 Score=29.05 Aligned_cols=28 Identities=18% Similarity=0.185 Sum_probs=21.8
Q ss_pred CceeeEEeeccCCchhHHHHHHHHHhhc
Q psy2081 209 RLHITMGMLMLADSVERDQAVEVLQKCG 236 (380)
Q Consensus 209 ~LHLTL~~L~l~~~~ev~~A~~~L~~~~ 236 (380)
=+|+||.+|.+-++++.+++.+.|-++.
T Consensus 60 FvHv~l~il~GRs~e~k~~l~~~l~~~l 87 (124)
T PF02962_consen 60 FVHVTLRILAGRSEEQKKALSEALLAVL 87 (124)
T ss_dssp EEEEEEEEETT--HHHHHHHHHHHHHHH
T ss_pred EEEEEeeecCCCCHHHHHHHHHHHHHHH
Confidence 5899999999999998888877776654
No 113
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=37.71 E-value=1.5e+02 Score=27.46 Aligned_cols=42 Identities=14% Similarity=0.166 Sum_probs=31.0
Q ss_pred ceeeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEc
Q psy2081 82 DIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSI 126 (380)
Q Consensus 82 ~i~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~i 126 (380)
+|+.+.++ ....+++ ..-+.+||++|+++++|.+.-+-...+
T Consensus 34 eI~Rt~~~-i~I~I~t--a~PGivIGk~G~~I~klk~~Lkk~~~~ 75 (207)
T PRK04191 34 EIKKTPLG-TRITIYA--ERPGMVIGRGGKNIRELTEILEKKFGL 75 (207)
T ss_pred EEEEcCCc-EEEEEEE--CCCCeEECCCchhHHHHHHHHHHHhCC
Confidence 55555444 5666666 778999999999999999887665443
No 114
>COG3638 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=37.53 E-value=50 Score=31.68 Aligned_cols=113 Identities=16% Similarity=0.239 Sum_probs=64.3
Q ss_pred EEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeCCHHHH-HHHHHHHHHHhhhhcccCCcceeee
Q psy2081 92 KYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGI-ASAKRRLDLLLVFARKKIPYTHLLS 170 (380)
Q Consensus 92 ~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~~~~~v-~~A~~~I~~iv~~~rkk~~~thFIa 170 (380)
-+.+.||+--+-.|||+.|+=+.-|-.--+--+++ ..|+|.+.|.+..+. .++.++++.-+.= .|=.
T Consensus 22 ~Vnl~I~~GE~VaiIG~SGaGKSTLLR~lngl~d~----t~G~i~~~g~~i~~~~~k~lr~~r~~iGm--------IfQ~ 89 (258)
T COG3638 22 DVNLEINQGEMVAIIGPSGAGKSTLLRSLNGLVDP----TSGEILFNGVQITKLKGKELRKLRRDIGM--------IFQQ 89 (258)
T ss_pred eEeEEeCCCcEEEEECCCCCcHHHHHHHHhcccCC----CcceEEecccchhccchHHHHHHHHhcee--------Eecc
Confidence 46788999999999999999988888776665554 346777777422111 1112222111110 1111
Q ss_pred ccCCChhHHHHHHHHHHHHhcccCcCCCCccccccCCCCceeeEEeeccCCchhHHHHHHHHHhh
Q psy2081 171 IPMNVPNIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVERDQAVEVLQKC 235 (380)
Q Consensus 171 Ipl~~~~I~~~~~~fq~~v~~~~~~~~gi~~~~fv~p~~LHLTL~~L~l~~~~ev~~A~~~L~~~ 235 (380)
+.+...+.-+.+-+....+ ..++|. .+|++.+.++...|.++|+.+
T Consensus 90 -----~nLv~r~sv~~NVl~grl~-----~~s~~~---------slfglfsk~dk~~Al~aLerv 135 (258)
T COG3638 90 -----FNLVPRLSVLENVLLGRLG-----YTSTWR---------SLFGLFSKEDKAQALDALERV 135 (258)
T ss_pred -----CCcccccHHHHHHHhhhcc-----cchHHH---------HHhCCCCHHHHHHHHHHHHHc
Confidence 1234444444444433221 112222 256777889999999999886
No 115
>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=35.78 E-value=1.1e+02 Score=33.43 Aligned_cols=35 Identities=29% Similarity=0.241 Sum_probs=30.0
Q ss_pred EEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcC
Q psy2081 93 YQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIP 127 (380)
Q Consensus 93 ~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip 127 (380)
-.|-|-...-|.+||++|+|+++|-.+||-+-.+-
T Consensus 95 ~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~ 129 (630)
T TIGR03675 95 GEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVV 129 (630)
T ss_pred ceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEE
Confidence 35667778889999999999999999999987763
No 116
>CHL00048 rps3 ribosomal protein S3
Probab=35.36 E-value=80 Score=29.54 Aligned_cols=42 Identities=17% Similarity=0.155 Sum_probs=30.2
Q ss_pred ceeeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEc
Q psy2081 82 DIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSI 126 (380)
Q Consensus 82 ~i~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~i 126 (380)
+|+.+..+ ..+.++ ....+.|||++|+++++|.+.-.-.+..
T Consensus 60 ~I~r~~~~-~~I~I~--~~~Pg~vIG~~g~~i~~l~~~L~k~~~~ 101 (214)
T CHL00048 60 EIQRKIDL-IQVIIY--TGFPKLLIERKGRGIEELQINLQKELNS 101 (214)
T ss_pred EEEEcCCe-EEEEEE--ECCCceEECCCcHhHHHHHHHHHHHhCC
Confidence 67776554 444444 5667999999999999998886554433
No 117
>PTZ00179 60S ribosomal protein L9; Provisional
Probab=32.38 E-value=1.1e+02 Score=27.97 Aligned_cols=49 Identities=6% Similarity=0.118 Sum_probs=34.6
Q ss_pred HhCceEEcCCC-CCCCcEEEeeCCHHHHHHHHHHHHHHhhhhcccCCcceee
Q psy2081 119 ETNTQLSIPRQ-GQTGDIIISSYSERGIASAKRRLDLLLVFARKKIPYTHLL 169 (380)
Q Consensus 119 eT~~~I~ip~~-~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~rkk~~~thFI 169 (380)
-.|++|..|++ ...+.|+|+|.+++.|-.-...|+...... . ..+|.|+
T Consensus 125 p~gv~v~~~~~~~~k~~i~i~G~DKq~Vgq~AA~i~~~~~~~-~-~d~r~f~ 174 (189)
T PTZ00179 125 ADTVKVYRTDPSKVKDELVLEGNDLEQVSREAAVMHQLCLVK-K-KDIRKFL 174 (189)
T ss_pred CCCEEEEecCCcccCCEEEEEeCCHHHHHHHHHHHHHhhccc-C-CCccEee
Confidence 34666666654 333689999999999999999999976333 2 2346675
No 118
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=31.18 E-value=71 Score=29.83 Aligned_cols=39 Identities=21% Similarity=0.278 Sum_probs=28.0
Q ss_pred ceeeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCce
Q psy2081 82 DIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQ 123 (380)
Q Consensus 82 ~i~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~ 123 (380)
+|+.+.++ ..+.++ ....+.|||++|..+++|.+.-...
T Consensus 56 eI~rt~~~-i~I~I~--~~~pg~vIG~~g~~i~~l~~~l~~~ 94 (211)
T TIGR01009 56 EIERPADK-IRVTIH--TARPGIVIGKKGSEIEKLRKDLQKL 94 (211)
T ss_pred EEEEcCCc-eEEEEE--eCCCcceeCCCchHHHHHHHHHHHH
Confidence 67776555 454444 4555999999999999998775443
No 119
>TIGR03693 ocin_ThiF_like putative thiazole-containing bacteriocin maturation protein. Members of this protein family are found in a three-gene operon in Bacillus anthracis and related Bacillus species, where the other two genes are clearly identified with maturation of a putative thiazole-containing bacteriocin precursor. While there is no detectable pairwise sequence similarity between members of this family and the proposed cyclodehydratases such as SagC of Streptococcus pyogenes (see family TIGR03603), both families show similarity through PSI-BLAST to ThiF, a protein involved in biosynthesis of the thiazole moiety for thiamine biosynthesis. This family, therefore, may contribute to cyclodehydratase function in heterocycle-containing bacteriocin biosyntheses. In Bacillus licheniformis ATCC 14580, the bacteriocin precursor gene is adjacent to the gene for this protein.
Probab=30.25 E-value=6.7e+02 Score=27.49 Aligned_cols=131 Identities=11% Similarity=0.102 Sum_probs=73.2
Q ss_pred hCceEEcCCCCCC------CcEEEeeC--CHHHHHHHHHHHHHHhhhhcccCCccee-eeccCCChhHHHHHHHHHHHHh
Q psy2081 120 TNTQLSIPRQGQT------GDIIISSY--SERGIASAKRRLDLLLVFARKKIPYTHL-LSIPMNVPNIQENFAKFKATVL 190 (380)
Q Consensus 120 T~~~I~ip~~~~~------~~i~I~g~--~~~~v~~A~~~I~~iv~~~rkk~~~thF-IaIpl~~~~I~~~~~~fq~~v~ 190 (380)
+.|+|++..+..+ ..++..|- +.+.-+++..-|+.-|++.-.+.-|.++ ++|-.-..-.-+.+..+|+.+.
T Consensus 390 ~~~~~~~~~p~~~gp~~~l~~~~~~g~th~earreagl~gie~y~~~~~~~~~~~~~~~~ig~get~~e~~~ral~~~~~ 469 (637)
T TIGR03693 390 AQCFIQTADPLSDGPAELLPEITCSGLTHNEARREAGLTGIEMYAAEILHRLIPEHGDFAIAAGETLAEGVLRALEKCLE 469 (637)
T ss_pred hhceEEecCCCCCCcccccCCceecccchHHHHHhhchhhHHHHHHHHHHhhcCcccCceeecchhHHHHHHHHHHHHHH
Confidence 6789999777665 35777774 3445566777888877776555556666 6665543222223333333333
Q ss_pred cccCcCCCCccccccCCCCceeeEEeeccCCchhHHHHHHHHHhhcccccccccccCceEEEe-cceecCCCCCCceeEE
Q psy2081 191 SDFSRCRGIEESLFQEPGRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPILRSQRIKINL-KGLEIMNDDPAEVDIL 269 (380)
Q Consensus 191 ~~~~~~~gi~~~~fv~p~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~~~~pf~l~l-~Glg~F~ddp~~~rVL 269 (380)
...- +. +.-..--+|..-|+.+.++.-.--.++|..+. ..| +|-+ ..+--|| |+
T Consensus 470 ~~~~------~~--~~~~~~~~~~~~~~~i~d~~~~fy~~~l~~~~---------~~p-~~~~~~~~~~fp-------v~ 524 (637)
T TIGR03693 470 HKLC------ER--IKHGKEEISLVDLDDIEDKHCAFYLDALATIH---------EAP-EIALGEEIEGFP-------VA 524 (637)
T ss_pred HHHH------HH--HhcCCCceeEEecccchhhHHHHHHHHHHHhc---------cCC-ccccccccccCC-------EE
Confidence 2210 00 11222335555666666666665555665542 222 3333 3455677 99
Q ss_pred EEEecC
Q psy2081 270 YAKVVD 275 (380)
Q Consensus 270 ya~v~d 275 (380)
|+++.+
T Consensus 525 w~~~~~ 530 (637)
T TIGR03693 525 WAGIND 530 (637)
T ss_pred EEeeCC
Confidence 999984
No 120
>PRK13679 hypothetical protein; Provisional
Probab=30.15 E-value=3.8e+02 Score=23.47 Aligned_cols=106 Identities=12% Similarity=0.074 Sum_probs=54.1
Q ss_pred hHHHHHHHhCceEEcCCCCCCCcEEEe--e-CCHHHHHHHHHHHHHHhhhhcc----------cC--CcceeeeccCCCh
Q psy2081 112 TKRRIESETNTQLSIPRQGQTGDIIIS--S-YSERGIASAKRRLDLLLVFARK----------KI--PYTHLLSIPMNVP 176 (380)
Q Consensus 112 t~k~ie~eT~~~I~ip~~~~~~~i~I~--g-~~~~~v~~A~~~I~~iv~~~rk----------k~--~~thFIaIpl~~~ 176 (380)
.+.++++..+....-. ...|++. | -+.+.+....+.++.+.+.... -. .-..|+.+. +.
T Consensus 16 ~l~~~~~~~~~~~~~v----~pHITL~f~g~~~~~~~~~l~~~l~~~~~~~~pf~l~l~~~~~F~~~~~vl~l~~~-~~- 89 (168)
T PRK13679 16 FANSYRKRYDPHYALI----PPHITLKEPFEISDEQLDSIVEELRAIASETKPFTLHVTKVSSFAPTNNVIYFKVE-KT- 89 (168)
T ss_pred HHHHHHHhhCcccccC----CCceEEecCCCCCHHHHHHHHHHHHHHHhcCCCEEEEEeccccCCCCCCEEEEEcc-CC-
Confidence 4556666665443321 1378775 3 3556666666666666542110 00 112233332 12
Q ss_pred hHHHHHHHHHHHHhcccCcCCCCccccccCCCCceeeEEeeccCCchhHHHHHHHHHh
Q psy2081 177 NIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVERDQAVEVLQK 234 (380)
Q Consensus 177 ~I~~~~~~fq~~v~~~~~~~~gi~~~~fv~p~~LHLTL~~L~l~~~~ev~~A~~~L~~ 234 (380)
+.+.++.+.+..... +... ..+-.-|+||+ ....+++..+|.+.|+.
T Consensus 90 ---~~L~~L~~~l~~~~~---~~~~---~~~f~PHiTla--r~~~~~~~~~~~~~l~~ 136 (168)
T PRK13679 90 ---EELEELHERLHSGDF---YGEA---EYAFVPHITIG--QGLSDDEHEDVLGQLKM 136 (168)
T ss_pred ---HHHHHHHHHHHhccc---cccc---CCCCCCeEEee--CCCCcHHHHHHHHHHhc
Confidence 355555555554321 0000 12455799999 55577888888777754
No 121
>PF09749 HVSL: Uncharacterised conserved protein; InterPro: IPR019146 This entry is of proteins of approximately 300 residues conserved from plants to humans. It contains two conserved motifs, HxSL and FHVSL. The function is unknown.
Probab=29.87 E-value=1.1e+02 Score=28.81 Aligned_cols=66 Identities=18% Similarity=0.309 Sum_probs=39.0
Q ss_pred CCcceeeeccCCChh---HHHHHHHHHHHHhcccCcCCCCcccccc-CCCCceeeEEeeccCCchhHHHHH-HHHHhh
Q psy2081 163 IPYTHLLSIPMNVPN---IQENFAKFKATVLSDFSRCRGIEESLFQ-EPGRLHITMGMLMLADSVERDQAV-EVLQKC 235 (380)
Q Consensus 163 ~~~thFIaIpl~~~~---I~~~~~~fq~~v~~~~~~~~gi~~~~fv-~p~~LHLTL~~L~l~~~~ev~~A~-~~L~~~ 235 (380)
..-|.|+++++..+. +...+.. .+.++..+ |.+ .|- ....+|++|+..-....+++.+.. +.+...
T Consensus 138 e~TR~FL~l~V~~~~~~~l~~l~~~-i~~~l~~~----~lp--~~Y~~~~~fHvSIAw~~~~~~~~l~~~~~~~~~~~ 208 (239)
T PF09749_consen 138 EKTRSFLALRVSEGSNNELKRLLDR-INEVLKEF----GLP--PFYDEDPSFHVSIAWTLGDPSEELKESSLKILQEP 208 (239)
T ss_pred CCCeEEEEEEecccccHHHHHHHHH-HHHHHHHh----CCC--cccCCCCCCEEEEEEECCCchHHHHHHHHHHHHHH
Confidence 456899999998432 3333333 33444433 333 255 788999999998765555555543 444443
No 122
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=29.67 E-value=1.7e+02 Score=25.91 Aligned_cols=68 Identities=10% Similarity=0.028 Sum_probs=42.8
Q ss_pred eeeEEeeccCCchhHHHHHHHHHhhcccccccccccCceEEEecceecCCC----------CCCceeEEEEEecCChHHH
Q psy2081 211 HITMGMLMLADSVERDQAVEVLQKCGNNIILPILRSQRIKINLKGLEIMND----------DPAEVDILYAKVVDDSGLV 280 (380)
Q Consensus 211 HLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~~~~pf~l~l~Glg~F~d----------dp~~~rVLya~v~d~~~~L 280 (380)
+.++.++|. +++.+++|.+.|++... .+.+.-.--++|+. +.+.|++||+++. +++=
T Consensus 48 ~~~ifllG~-~~~~~~~~~~~l~~~yP----------~l~ivg~~~g~f~~~~~~~i~~~I~~~~pdiv~vglG--~PkQ 114 (172)
T PF03808_consen 48 GKRIFLLGG-SEEVLEKAAANLRRRYP----------GLRIVGYHHGYFDEEEEEAIINRINASGPDIVFVGLG--APKQ 114 (172)
T ss_pred CCeEEEEeC-CHHHHHHHHHHHHHHCC----------CeEEEEecCCCCChhhHHHHHHHHHHcCCCEEEEECC--CCHH
Confidence 567888887 66778888888888752 22233233344431 4578999999997 4454
Q ss_pred HHHHHHHHHHH
Q psy2081 281 QKLCDDVVQYF 291 (380)
Q Consensus 281 q~L~~~l~~~f 291 (380)
..+.....+.+
T Consensus 115 E~~~~~~~~~l 125 (172)
T PF03808_consen 115 ERWIARHRQRL 125 (172)
T ss_pred HHHHHHHHHHC
Confidence 45555554433
No 123
>PRK13731 conjugal transfer surface exclusion protein TraT; Provisional
Probab=28.98 E-value=81 Score=30.10 Aligned_cols=58 Identities=9% Similarity=0.107 Sum_probs=45.3
Q ss_pred cCCCCCCceeEEEEEecCCh-HHHHHHHHHHHHHHHHCCCccccccCCCceeeEEEeecc
Q psy2081 258 IMNDDPAEVDILYAKVVDDS-GLVQKLCDDVVQYFISQHLISKAYQKYDTVKMHVTLMNS 316 (380)
Q Consensus 258 ~F~ddp~~~rVLya~v~d~~-~~Lq~L~~~l~~~f~~~Gl~~~~~~e~r~fkpHiTL~nt 316 (380)
+|= ||..-|++|+.|.+-+ ..+..|...|...+...|+...++.+.-.|-+++.|++.
T Consensus 43 IfL-dP~~~ktVyv~vrNTSd~~~~~l~~~i~~~L~~kGY~iv~~P~~A~Y~lQaNVL~~ 101 (243)
T PRK13731 43 IWL-EPASERTVFLQIKNTSDKDMSGLQGKIADAVKAKGYQVVTSPDKAYYWIQANVLKA 101 (243)
T ss_pred EEE-cCCCCceEEEEEeeCCCcchHHHHHHHHHHHHhCCeEEecChhhceeeeeeeehhc
Confidence 455 5666899999999544 456679999999999999998655555678888888765
No 124
>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.
Probab=28.97 E-value=1.7e+02 Score=25.98 Aligned_cols=68 Identities=13% Similarity=0.041 Sum_probs=43.8
Q ss_pred eeeEEeeccCCchhHHHHHHHHHhhcccccccccccCceEEEecceecCCC----------CCCceeEEEEEecCChHHH
Q psy2081 211 HITMGMLMLADSVERDQAVEVLQKCGNNIILPILRSQRIKINLKGLEIMND----------DPAEVDILYAKVVDDSGLV 280 (380)
Q Consensus 211 HLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~~~~pf~l~l~Glg~F~d----------dp~~~rVLya~v~d~~~~L 280 (380)
+.++.++|. +++.+++|.+.|++.... +.+.-.--++|++ +...|++||++.. +++=
T Consensus 46 ~~~v~llG~-~~~~~~~~~~~l~~~yp~----------l~i~g~~~g~~~~~~~~~i~~~I~~~~pdiv~vglG--~PkQ 112 (171)
T cd06533 46 GLRVFLLGA-KPEVLEKAAERLRARYPG----------LKIVGYHHGYFGPEEEEEIIERINASGADILFVGLG--APKQ 112 (171)
T ss_pred CCeEEEECC-CHHHHHHHHHHHHHHCCC----------cEEEEecCCCCChhhHHHHHHHHHHcCCCEEEEECC--CCHH
Confidence 677888886 677788998888887522 1222112334432 2456999999997 5565
Q ss_pred HHHHHHHHHHH
Q psy2081 281 QKLCDDVVQYF 291 (380)
Q Consensus 281 q~L~~~l~~~f 291 (380)
..+.....+.+
T Consensus 113 E~~~~~~~~~l 123 (171)
T cd06533 113 ELWIARHKDRL 123 (171)
T ss_pred HHHHHHHHHHC
Confidence 66666666655
No 125
>PLN00062 TATA-box-binding protein; Provisional
Probab=28.38 E-value=86 Score=28.51 Aligned_cols=32 Identities=25% Similarity=0.293 Sum_probs=27.5
Q ss_pred CCCcEEEee-CCHHHHHHHHHHHHHHhhhhccc
Q psy2081 131 QTGDIIISS-YSERGIASAKRRLDLLLVFARKK 162 (380)
Q Consensus 131 ~~~~i~I~g-~~~~~v~~A~~~I~~iv~~~rkk 162 (380)
.+|.|+|+| .+.+.+..|.+.|..++.+.++.
T Consensus 145 ~sGkvvitGaks~~~~~~ai~~i~p~L~~~~~~ 177 (179)
T PLN00062 145 VSGKIVITGAKVREEIYTAFENIYPVLTEFRKR 177 (179)
T ss_pred CCCEEEEEecCCHHHHHHHHHHHHHHHHHhccC
Confidence 368999999 47899999999999999888754
No 126
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=28.31 E-value=4e+02 Score=26.33 Aligned_cols=83 Identities=16% Similarity=0.209 Sum_probs=52.3
Q ss_pred ceeeCCCCchHHHHHHHhCce--EEcCCCCCCCcEEEeeCCHHHHHHHHHHHHHHhhhhcccCCcceeeeccCCChhHHH
Q psy2081 103 PFIIGVKGSTKRRIESETNTQ--LSIPRQGQTGDIIISSYSERGIASAKRRLDLLLVFARKKIPYTHLLSIPMNVPNIQE 180 (380)
Q Consensus 103 ~~IIG~~G~t~k~ie~eT~~~--I~ip~~~~~~~i~I~g~~~~~v~~A~~~I~~iv~~~rkk~~~thFIaIpl~~~~I~~ 180 (380)
..++|---+.++++=++++-. +.|-.-+..+.|+|+|. ++.|++|....+..-+ ++..+ .=++.|.-++-+..
T Consensus 134 aav~gl~~e~v~~~~~~~~~~~~v~iaN~N~~~QiVIsG~-~~ale~a~~~~~~~g~---kr~i~-l~vs~pfHs~lm~p 208 (310)
T COG0331 134 AAVLGLDDEQVEKACEEAAQGTVVEIANYNSPGQIVISGT-KEALEKAAEILKEAGA---KRAIP-LPVSGPFHSPLMKP 208 (310)
T ss_pred HHHcCCCHHHHHHHHHHhccCCeEEEeeeCCCCcEEEECC-HHHHHHHHHHHHHhhh---hhhcc-cCCCchhhhhhhHH
Confidence 357777777788887777643 66655455689999996 8999999887776652 22222 33444444444555
Q ss_pred HHHHHHHHHh
Q psy2081 181 NFAKFKATVL 190 (380)
Q Consensus 181 ~~~~fq~~v~ 190 (380)
...+|...+.
T Consensus 209 a~~~~~~~l~ 218 (310)
T COG0331 209 AADELAEALE 218 (310)
T ss_pred HHHHHHHHHH
Confidence 5555554443
No 127
>COG0799 Uncharacterized homolog of plant Iojap protein [Function unknown]
Probab=28.04 E-value=3.7e+02 Score=22.74 Aligned_cols=60 Identities=17% Similarity=0.195 Sum_probs=43.7
Q ss_pred HHHHHHHHHhhcccccccccccCceEEEecceecCCCCCCceeEEEEEecCChHHHHHHHHHHHHHHHHCCCcc
Q psy2081 225 RDQAVEVLQKCGNNIILPILRSQRIKINLKGLEIMNDDPAEVDILYAKVVDDSGLVQKLCDDVVQYFISQHLIS 298 (380)
Q Consensus 225 v~~A~~~L~~~~~~~i~~~~~~~pf~l~l~Glg~F~ddp~~~rVLya~v~d~~~~Lq~L~~~l~~~f~~~Gl~~ 298 (380)
+..+.++|.+.+ ......|.++|...+-| ..+-|.-. ++-.++.+++.+.+.+.++|+..
T Consensus 7 ~~~i~~alddkK--------AeDIv~lDv~~~s~~tD-----yfVIatg~-s~rhv~Aiad~i~~~~k~~g~~~ 66 (115)
T COG0799 7 LEVIVEALDDKK--------AEDIVVLDVSGKSSLTD-----YFVIATGN-SSRHVKAIADNVKEELKEAGEVP 66 (115)
T ss_pred HHHHHHHHHhcc--------CCCeEEEEccCCccccc-----EEEEEEeC-chHHHHHHHHHHHHHHHHcCCCc
Confidence 455556665553 34667899999999987 33333332 36789999999999999999876
No 128
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=27.12 E-value=43 Score=35.42 Aligned_cols=34 Identities=32% Similarity=0.271 Sum_probs=29.3
Q ss_pred EEEEcCCCCcceeeCCCCchHHHHHHHhCceEEc
Q psy2081 93 YQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSI 126 (380)
Q Consensus 93 ~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~i 126 (380)
-.+-|-...-|.+||+.|+|.++|-.+||-+-.|
T Consensus 101 GEViIea~KPGlvigk~g~~~reI~~~tgW~p~i 134 (637)
T COG1782 101 GEVIIEAKKPGLVIGKGGSTLREITAETGWAPKI 134 (637)
T ss_pred ceEEEEecCCceEEecCchHHHHHHHHhCCccee
Confidence 4566777888999999999999999999988665
No 129
>PRK15245 type III effector phosphothreonine lyase; Provisional
Probab=26.65 E-value=3.4e+02 Score=25.53 Aligned_cols=79 Identities=15% Similarity=0.180 Sum_probs=48.8
Q ss_pred CCceeeEEeeccCCchhHHHHHHHHHhhcccccccccccCce-EEEecceecCCC----CCCceeEEEEEec-CC-----
Q psy2081 208 GRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPILRSQRI-KINLKGLEIMND----DPAEVDILYAKVV-DD----- 276 (380)
Q Consensus 208 ~~LHLTL~~L~l~~~~ev~~A~~~L~~~~~~~i~~~~~~~pf-~l~l~Glg~F~d----dp~~~rVLya~v~-d~----- 276 (380)
+++||.+ ..++|..|-++|..+. .....|+ .-++..+..-.. .-++-=.||+++. ++
T Consensus 103 DK~HiSV------~~~qv~qAF~als~lL------fSeDSPiDKWKVTDM~rv~qqsRV~~GAQfTLYvKpd~edsqYsa 170 (241)
T PRK15245 103 DKFHISV------ARDQVPQAFQALSGLL------FSEDSPVDKWKVTDMERVSQQSRVGLGAQFTLYVKPDQENSQYSA 170 (241)
T ss_pred ceEEEEe------cHHHHHHHHHHhhhhh------cCCCCCcceeeeccccccCccchhcccceEEEEecCccccccCCH
Confidence 6899975 6788999999988763 1123443 223332222110 0111234999997 21
Q ss_pred --hHHHHHHHHHHHHHHHHCCCcc
Q psy2081 277 --SGLVQKLCDDVVQYFISQHLIS 298 (380)
Q Consensus 277 --~~~Lq~L~~~l~~~f~~~Gl~~ 298 (380)
..+...+-..|+..|..+|+..
T Consensus 171 ~~l~k~r~Fie~lE~~L~~~gi~p 194 (241)
T PRK15245 171 SFLHKTRQFIECLESRLSENGVIS 194 (241)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCC
Confidence 1456677788899999999976
No 130
>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=26.43 E-value=64 Score=30.69 Aligned_cols=27 Identities=22% Similarity=0.265 Sum_probs=20.8
Q ss_pred eEEEEEcCCCCc-ceeeCCCCchHHHHH
Q psy2081 91 YKYQCHIPKSFY-PFIIGVKGSTKRRIE 117 (380)
Q Consensus 91 ~~~~v~Vp~~~~-~~IIG~~G~t~k~ie 117 (380)
....+.|+++-+ +-|||++|+++|+|-
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~ 248 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIG 248 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHH
Confidence 355777887666 477899999999873
No 131
>KOG4369|consensus
Probab=25.70 E-value=29 Score=40.14 Aligned_cols=62 Identities=13% Similarity=0.064 Sum_probs=48.4
Q ss_pred EEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCC-CCC---CcEEEeeCCHHHHHHHHHHHHHHh
Q psy2081 94 QCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQ-GQT---GDIIISSYSERGIASAKRRLDLLL 156 (380)
Q Consensus 94 ~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~-~~~---~~i~I~g~~~~~v~~A~~~I~~iv 156 (380)
.+.||---...+||++|.++..+..-||+.|.|-+- +++ ..+.+.|. ...+.-|..-|..++
T Consensus 1343 k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~-p~~~r~a~~~I~~~i 1408 (2131)
T KOG4369|consen 1343 KGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGR-PPSQRVATSPIGLPI 1408 (2131)
T ss_pred ccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCC-Chhhhhhhcccccee
Confidence 456777778899999999999999999999999873 332 26777774 666777777676665
No 132
>KOG3302|consensus
Probab=25.53 E-value=87 Score=28.93 Aligned_cols=40 Identities=23% Similarity=0.229 Sum_probs=32.1
Q ss_pred hCceEEcCCCCCCCcEEEee-CCHHHHHHHHHHHHHHhhhhccc
Q psy2081 120 TNTQLSIPRQGQTGDIIISS-YSERGIASAKRRLDLLLVFARKK 162 (380)
Q Consensus 120 T~~~I~ip~~~~~~~i~I~g-~~~~~v~~A~~~I~~iv~~~rkk 162 (380)
+++.+.|= .+|.|+++| .+++.+..|.+.|.-++.++|++
T Consensus 158 pkv~l~IF---~tG~VvvtgA~~~~~i~~Ai~~IyPil~~frk~ 198 (200)
T KOG3302|consen 158 PKVVLLIF---VTGKVVVTGAKVREETYEAIENIYPILLEFRKK 198 (200)
T ss_pred CcEEEEEe---cCCEEEEEecccHHHHHHHHHHHhHHHHHhhhc
Confidence 35555552 368999999 47889999999999999998765
No 133
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=24.07 E-value=58 Score=33.01 Aligned_cols=38 Identities=18% Similarity=0.191 Sum_probs=30.8
Q ss_pred eEEEEEcCC-----CCcceeeCCCCchHHHHHHHh-CceEEcCC
Q psy2081 91 YKYQCHIPK-----SFYPFIIGVKGSTKRRIESET-NTQLSIPR 128 (380)
Q Consensus 91 ~~~~v~Vp~-----~~~~~IIG~~G~t~k~ie~eT-~~~I~ip~ 128 (380)
++..+.|-+ +-.|..||++|++++.|.++. |-+|+|=.
T Consensus 231 ~RtKVAV~s~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv~ 274 (362)
T PRK12327 231 DRTKIAVRSNNPNVDAKGACVGPKGQRVQNIVSELKGEKIDIID 274 (362)
T ss_pred ceeEEEEEcCCCCCCchheeECCCChhHHHHHHHhCCCeEEEEE
Confidence 677777754 457899999999999999998 88888743
No 134
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=23.23 E-value=82 Score=29.40 Aligned_cols=43 Identities=21% Similarity=0.207 Sum_probs=34.5
Q ss_pred eeeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCceEEc
Q psy2081 83 IYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSI 126 (380)
Q Consensus 83 i~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~i 126 (380)
|.....| -...+.|..+-.+.|||+.|.|+..||--++.-++-
T Consensus 84 i~v~~~~-~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 84 ITVSEEG-RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEeecC-cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 3333344 467778888889999999999999999999988776
No 135
>PRK15494 era GTPase Era; Provisional
Probab=22.85 E-value=86 Score=31.18 Aligned_cols=25 Identities=24% Similarity=0.437 Sum_probs=20.3
Q ss_pred EEEEEcCCCCcc-eeeCCCCchHHHH
Q psy2081 92 KYQCHIPKSFYP-FIIGVKGSTKRRI 116 (380)
Q Consensus 92 ~~~v~Vp~~~~~-~IIG~~G~t~k~i 116 (380)
..++.|+++-++ -|||++|+++|+|
T Consensus 274 ~~~i~v~~~sqk~iiiG~~g~~ik~i 299 (339)
T PRK15494 274 NQVIVVSRESYKTIILGKNGSKIKEI 299 (339)
T ss_pred EEEEEECCCCceeEEEcCCcHHHHHH
Confidence 367888876665 7899999999987
No 136
>PF08921 DUF1904: Domain of unknown function (DUF1904); InterPro: IPR015017 This entry represents a family of hypothetical bacterial proteins. ; PDB: 1U9D_B.
Probab=22.36 E-value=3.5e+02 Score=22.50 Aligned_cols=74 Identities=11% Similarity=0.102 Sum_probs=34.8
Q ss_pred ccCCchhHHHHHHHH-HhhcccccccccccCceEEEecceecCCCCCCc-----eeEEEEEecCChHHHH-HHHHHHHHH
Q psy2081 218 MLADSVERDQAVEVL-QKCGNNIILPILRSQRIKINLKGLEIMNDDPAE-----VDILYAKVVDDSGLVQ-KLCDDVVQY 290 (380)
Q Consensus 218 ~l~~~~ev~~A~~~L-~~~~~~~i~~~~~~~pf~l~l~Glg~F~ddp~~-----~rVLya~v~d~~~~Lq-~L~~~l~~~ 290 (380)
++++.+.+....+.| .+++ ++++ +...-|+|..-...+|-+.+.. +-|+|..= .+..| ++|..|.+.
T Consensus 7 rGi~~e~v~~~S~~LideLa-~i~~--~p~e~ftlE~i~s~~i~~G~~~~~~pfVEV~WF~R---~qe~qd~vA~~It~~ 80 (108)
T PF08921_consen 7 RGIEEEQVQELSKELIDELA-EICG--CPRENFTLEWINSTFIFDGEISEGYPFVEVLWFDR---GQEVQDKVAQAITEH 80 (108)
T ss_dssp ESS-HHHHHHHHHHHHHHHH-HHHT----GGG-EEEE-------TT-B-----EEEEEES------HHHHHHHHHHHHHH
T ss_pred ecCCHHHHHHHhHHHHHHHH-HHHC--CCcceEEEEEeceEEEEcCcccccceeEEEEEecC---CHHHHHHHHHHHHHH
Confidence 445777777666553 3342 2221 2346788888877777655554 45555432 35555 788888888
Q ss_pred HHH-CCCc
Q psy2081 291 FIS-QHLI 297 (380)
Q Consensus 291 f~~-~Gl~ 297 (380)
+.+ .|..
T Consensus 81 v~~~~g~~ 88 (108)
T PF08921_consen 81 VKKANGYQ 88 (108)
T ss_dssp HHHH-TT-
T ss_pred HHhcCCCC
Confidence 888 6654
No 137
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=21.74 E-value=3.1e+02 Score=26.00 Aligned_cols=39 Identities=18% Similarity=0.233 Sum_probs=28.2
Q ss_pred ceeeccCCceEEEEEcCCCCcceeeCCCCchHHHHHHHhCce
Q psy2081 82 DIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQ 123 (380)
Q Consensus 82 ~i~~~~~g~~~~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~ 123 (380)
+|+.+.++ ..+.+++ ...+.|||++|..+++|.+.-...
T Consensus 56 eI~R~~~~-i~I~I~~--~rP~~iiG~~g~~i~~l~~~L~~~ 94 (232)
T PRK00310 56 EIERPAKR-VRVTIHT--ARPGIVIGKKGAEIEKLRKELEKL 94 (232)
T ss_pred EEEEcCCe-EEEEEEE--CCCccccCCCcHHHHHHHHHHHHH
Confidence 56665544 5555555 556899999999999998875543
No 138
>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=21.63 E-value=74 Score=31.96 Aligned_cols=37 Identities=22% Similarity=0.300 Sum_probs=29.9
Q ss_pred eEEEEEcCC-----CCcceeeCCCCchHHHHHHHh-CceEEcC
Q psy2081 91 YKYQCHIPK-----SFYPFIIGVKGSTKRRIESET-NTQLSIP 127 (380)
Q Consensus 91 ~~~~v~Vp~-----~~~~~IIG~~G~t~k~ie~eT-~~~I~ip 127 (380)
++..+.|-+ +-.|..||++|++++.|.++. |=+|+|=
T Consensus 229 ~RtKvAV~s~~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv 271 (341)
T TIGR01953 229 YRTKIAVESNDENIDPVGACVGPKGSRIQAISKELNGEKIDII 271 (341)
T ss_pred ceeEEEEEcCCCCCCcceeeECCCCchHHHHHHHhCCCeEEEE
Confidence 666676643 457899999999999999998 7778773
No 139
>PRK09256 hypothetical protein; Provisional
Probab=21.29 E-value=1.2e+02 Score=26.34 Aligned_cols=31 Identities=35% Similarity=0.350 Sum_probs=22.4
Q ss_pred CCCcEEEeeC----CHHHHHHHHHHHHHHhhhhcc
Q psy2081 131 QTGDIIISSY----SERGIASAKRRLDLLLVFARK 161 (380)
Q Consensus 131 ~~~~i~I~g~----~~~~v~~A~~~I~~iv~~~rk 161 (380)
.+|.++|+.. ...+.+.|.+++..++.+...
T Consensus 66 ~~g~l~i~~~~~RSQ~~Nr~~al~kL~~~i~~~~~ 100 (138)
T PRK09256 66 KDGVIVIKAQEFRSQERNREDALERLVALIREALK 100 (138)
T ss_pred CCCcEEEEECCcCCHHHHHHHHHHHHHHHHHHHhh
Confidence 3567788762 457788898988888877643
No 140
>PRK00089 era GTPase Era; Reviewed
Probab=21.25 E-value=61 Score=31.03 Aligned_cols=25 Identities=20% Similarity=0.303 Sum_probs=19.3
Q ss_pred EEEEEcCCCCc-ceeeCCCCchHHHH
Q psy2081 92 KYQCHIPKSFY-PFIIGVKGSTKRRI 116 (380)
Q Consensus 92 ~~~v~Vp~~~~-~~IIG~~G~t~k~i 116 (380)
...+.|.++-+ +-|||++|+++|+|
T Consensus 227 ~~~i~v~~~~~k~i~ig~~g~~i~~i 252 (292)
T PRK00089 227 EATIYVERDSQKGIIIGKGGAMLKKI 252 (292)
T ss_pred EEEEEEccCCceeEEEeCCcHHHHHH
Confidence 45677776555 57889999999987
No 141
>KOG1423|consensus
Probab=21.00 E-value=1.1e+02 Score=30.70 Aligned_cols=28 Identities=21% Similarity=0.350 Sum_probs=21.9
Q ss_pred EEEEEcCCCCcc-eeeCCCCchHHHHHHH
Q psy2081 92 KYQCHIPKSFYP-FIIGVKGSTKRRIESE 119 (380)
Q Consensus 92 ~~~v~Vp~~~~~-~IIG~~G~t~k~ie~e 119 (380)
...+.+|+.-.+ .|||+||..|++|-++
T Consensus 329 ~~~v~~pK~s~~klliGkgG~ki~qI~~~ 357 (379)
T KOG1423|consen 329 QVEVVCPKNSQKKLLIGKGGKKISQIGTR 357 (379)
T ss_pred EEEEEcCCCcceeEEEcCCCccHHHHHHH
Confidence 456778886655 7899999999998655
No 142
>COG0851 MinE Septum formation topological specificity factor [Cell division and chromosome partitioning]
Probab=20.64 E-value=2e+02 Score=23.19 Aligned_cols=19 Identities=37% Similarity=0.564 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHhhhhcc
Q psy2081 143 RGIASAKRRLDLLLVFARK 161 (380)
Q Consensus 143 ~~v~~A~~~I~~iv~~~rk 161 (380)
....-|++|++.|++.-|.
T Consensus 13 ~Sa~~AkeRLQiilA~eR~ 31 (88)
T COG0851 13 NSAETAKERLQLILAHERA 31 (88)
T ss_pred CcHHHHHHHHHHhhhhhhh
Confidence 3467799999999998873
No 143
>COG1159 Era GTPase [General function prediction only]
Probab=20.49 E-value=53 Score=32.35 Aligned_cols=30 Identities=23% Similarity=0.379 Sum_probs=21.4
Q ss_pred cCCceEE--EEEcCCCC-cceeeCCCCchHHHH
Q psy2081 87 KDGQYKY--QCHIPKSF-YPFIIGVKGSTKRRI 116 (380)
Q Consensus 87 ~~g~~~~--~v~Vp~~~-~~~IIG~~G~t~k~i 116 (380)
..|.+.+ .+.|+.+= -+-|||++|+.+|+|
T Consensus 223 ~~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~I 255 (298)
T COG1159 223 EKGLLKIHATIYVERESQKGIIIGKNGAMIKKI 255 (298)
T ss_pred CCCeEEEEEEEEEecCCccceEECCCcHHHHHH
Confidence 3454433 57777654 457899999999988
No 144
>PRK11538 ribosome-associated protein; Provisional
Probab=20.49 E-value=4.9e+02 Score=21.42 Aligned_cols=60 Identities=18% Similarity=0.264 Sum_probs=40.5
Q ss_pred HHHHHHHHHhhcccccccccccCceEEEecceecCCCCCCceeEEEEEecCChHHHHHHHHHHHHHHHHCCCcc
Q psy2081 225 RDQAVEVLQKCGNNIILPILRSQRIKINLKGLEIMNDDPAEVDILYAKVVDDSGLVQKLCDDVVQYFISQHLIS 298 (380)
Q Consensus 225 v~~A~~~L~~~~~~~i~~~~~~~pf~l~l~Glg~F~ddp~~~rVLya~v~d~~~~Lq~L~~~l~~~f~~~Gl~~ 298 (380)
+..++++|.+.+ +..-..+.+++...|-| -.+-|.-. +...++.|++.|.+.+.+.|+..
T Consensus 7 ~~~i~~~l~dkK--------a~DI~vlDv~~~~~~~D-----y~VIatg~-S~rh~~aia~~v~~~~k~~~~~~ 66 (105)
T PRK11538 7 QDFVIDKIDDLK--------GQDIIALDVQGKSSITD-----CMIICTGT-SSRHVMSIADHVVQESRAAGLLP 66 (105)
T ss_pred HHHHHHHHHHcC--------CCCeEEEECCCCCcccC-----EEEEEEeC-CHHHHHHHHHHHHHHHHHcCCCC
Confidence 445666666653 23445788898877774 22223322 46889999999999999888764
No 145
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=20.44 E-value=1.7e+02 Score=26.40 Aligned_cols=38 Identities=18% Similarity=0.179 Sum_probs=28.7
Q ss_pred hCceEEcCCCCCCCcEEEee-CCHHHHHHHHHHHHHHhhhhc
Q psy2081 120 TNTQLSIPRQGQTGDIIISS-YSERGIASAKRRLDLLLVFAR 160 (380)
Q Consensus 120 T~~~I~ip~~~~~~~i~I~g-~~~~~v~~A~~~I~~iv~~~r 160 (380)
-++.+.|= .+|.++||| .+.+.+..|.++|..++....
T Consensus 46 Pk~t~lIF---~SGKiviTGaks~e~a~~a~~~i~~~L~~~g 84 (174)
T cd04516 46 PKTTALIF---SSGKMVCTGAKSEDDSKLAARKYARIIQKLG 84 (174)
T ss_pred CcEEEEEE---CCCeEEEEecCCHHHHHHHHHHHHHHHHHcC
Confidence 44555554 368999998 688888888888888876664
No 146
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=20.30 E-value=3e+02 Score=24.74 Aligned_cols=37 Identities=24% Similarity=0.255 Sum_probs=27.9
Q ss_pred CceEEcCCCCCCCcEEEee-CCHHHHHHHHHHHHHHhhhhc
Q psy2081 121 NTQLSIPRQGQTGDIIISS-YSERGIASAKRRLDLLLVFAR 160 (380)
Q Consensus 121 ~~~I~ip~~~~~~~i~I~g-~~~~~v~~A~~~I~~iv~~~r 160 (380)
++.+.|= .+|.|+||| .+.+.+..|.++|..++....
T Consensus 47 ~~t~lIf---~sGKivitGaks~~~~~~a~~~~~~~L~~~g 84 (174)
T cd00652 47 KTTALIF---SSGKMVITGAKSEEDAKLAARKYARILQKLG 84 (174)
T ss_pred cEEEEEE---CCCEEEEEecCCHHHHHHHHHHHHHHHHHcC
Confidence 4566664 368999999 588888888888887776654
No 147
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=20.23 E-value=1.2e+02 Score=28.76 Aligned_cols=44 Identities=30% Similarity=0.367 Sum_probs=32.0
Q ss_pred EEEEcCCCCcceeeCCCCchHHHHHHHhCceEEcCCCCCCCcEEEeeC
Q psy2081 93 YQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSY 140 (380)
Q Consensus 93 ~~v~Vp~~~~~~IIG~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g~ 140 (380)
+++.||+--+-.|||+.|+-+.-|=.--.-=+.. ++|.|.|.|.
T Consensus 20 isl~i~~g~iTs~IGPNGAGKSTLLS~~sRL~~~----d~G~i~i~g~ 63 (252)
T COG4604 20 VSLDIPKGGITSIIGPNGAGKSTLLSMMSRLLKK----DSGEITIDGL 63 (252)
T ss_pred ceeeecCCceeEEECCCCccHHHHHHHHHHhccc----cCceEEEeee
Confidence 5789999999999999998776664333222222 5688999884
No 148
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=20.21 E-value=2.5e+02 Score=25.51 Aligned_cols=73 Identities=16% Similarity=-0.000 Sum_probs=49.7
Q ss_pred eeeccCCceEEEEEcCCCCcceeeC----CCCchHHHHHHHhCceEEcCCCCCCCcEEEee----CCHHHHHHHHHHHHH
Q psy2081 83 IYLGKDGQYKYQCHIPKSFYPFIIG----VKGSTKRRIESETNTQLSIPRQGQTGDIIISS----YSERGIASAKRRLDL 154 (380)
Q Consensus 83 i~~~~~g~~~~~v~Vp~~~~~~IIG----~~G~t~k~ie~eT~~~I~ip~~~~~~~i~I~g----~~~~~v~~A~~~I~~ 154 (380)
|....+.-.+.+|.+|.-...+-.+ .....++.|++.|+|.|.... +.+.+.|.+ ..+..++.|++-+..
T Consensus 84 i~~~l~~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~--~~~~~~i~~~~~~~~~~~~~~a~RlL~~ 161 (210)
T PF14611_consen 84 INEILSNIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNP--DGNKLKISWLASPENEKRADRAKRLLLW 161 (210)
T ss_pred HHHHHhhcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECC--CCCeEEEEEEeeccccchHHHHHHHHHH
Confidence 4444455456677777543332222 246779999999999999864 334567776 678889999988877
Q ss_pred Hhh
Q psy2081 155 LLV 157 (380)
Q Consensus 155 iv~ 157 (380)
.+.
T Consensus 162 a~~ 164 (210)
T PF14611_consen 162 ALD 164 (210)
T ss_pred hcc
Confidence 763
Done!