Query 017154
Match_columns 376
No_of_seqs 244 out of 555
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 06:05:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017154.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017154hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2874 rRNA processing protei 100.0 6E-124 1E-128 893.3 25.0 336 11-347 18-354 (356)
2 COG1094 Predicted RNA-binding 100.0 3.7E-59 7.9E-64 428.1 17.0 180 45-224 3-185 (194)
3 KOG3273 Predicted RNA-binding 100.0 1.6E-45 3.4E-50 341.1 14.2 176 47-222 71-250 (252)
4 TIGR03665 arCOG04150 arCOG0415 100.0 4.2E-39 9.2E-44 289.0 17.4 166 54-222 2-169 (172)
5 PRK13763 putative RNA-processi 100.0 6.9E-39 1.5E-43 289.7 18.0 167 53-221 6-174 (180)
6 TIGR03319 YmdA_YtgF conserved 98.9 3.3E-09 7.1E-14 110.4 7.8 57 152-208 215-275 (514)
7 PRK00106 hypothetical protein; 98.8 4.1E-09 8.9E-14 110.4 6.3 68 133-208 225-296 (535)
8 PRK12704 phosphodiesterase; Pr 98.7 2.1E-08 4.6E-13 104.6 6.3 57 152-208 221-281 (520)
9 cd02395 SF1_like-KH Splicing f 98.5 3.1E-07 6.7E-12 79.6 7.9 71 152-223 16-114 (120)
10 smart00322 KH K homology RNA-b 98.3 1.2E-06 2.5E-11 63.5 5.5 52 151-202 12-68 (69)
11 PRK12705 hypothetical protein; 98.2 1.7E-06 3.7E-11 90.5 6.1 57 152-208 209-269 (508)
12 PF00013 KH_1: KH domain syndr 98.1 2E-06 4.2E-11 64.1 3.4 48 151-198 9-60 (60)
13 cd02393 PNPase_KH Polynucleoti 98.1 3.8E-06 8.2E-11 64.2 4.1 48 152-199 12-61 (61)
14 cd02394 vigilin_like_KH K homo 98.1 5.1E-06 1.1E-10 62.3 4.3 48 151-198 9-61 (62)
15 cd00105 KH-I K homology RNA-bi 98.0 8E-06 1.7E-10 60.4 4.8 47 152-198 10-63 (64)
16 cd02396 PCBP_like_KH K homolog 97.4 0.00025 5.4E-09 54.2 4.2 47 152-198 10-64 (65)
17 KOG1676 K-homology type RNA bi 97.2 0.00071 1.5E-08 72.1 7.1 144 51-203 140-299 (600)
18 PF13014 KH_3: KH domain 97.2 0.00061 1.3E-08 48.3 4.2 27 153-179 2-28 (43)
19 TIGR03665 arCOG04150 arCOG0415 96.9 0.0015 3.2E-08 59.5 5.0 53 152-204 8-65 (172)
20 PRK13763 putative RNA-processi 96.8 0.0016 3.4E-08 59.7 4.7 53 152-204 13-71 (180)
21 KOG1588 RNA-binding protein Sa 96.3 0.0026 5.7E-08 62.1 3.1 29 152-180 108-136 (259)
22 KOG2193 IGF-II mRNA-binding pr 96.0 0.022 4.9E-07 59.5 7.8 131 53-203 414-563 (584)
23 COG5176 MSL5 Splicing factor ( 95.5 0.031 6.7E-07 54.0 6.1 84 152-236 164-255 (269)
24 KOG0119 Splicing factor 1/bran 95.2 0.031 6.8E-07 59.1 5.6 109 115-231 122-260 (554)
25 COG1847 Jag Predicted RNA-bind 95.0 0.023 4.9E-07 54.2 3.5 79 153-231 102-194 (208)
26 PRK04163 exosome complex RNA-b 94.7 0.043 9.2E-07 52.3 4.7 54 153-207 156-211 (235)
27 TIGR02696 pppGpp_PNP guanosine 94.7 0.042 9.1E-07 60.4 5.3 53 152-204 588-642 (719)
28 KOG1676 K-homology type RNA bi 94.7 0.08 1.7E-06 57.0 7.1 122 70-203 75-209 (600)
29 TIGR03591 polynuc_phos polyrib 94.6 0.039 8.5E-07 60.1 4.6 53 152-204 561-615 (684)
30 PF13083 KH_4: KH domain; PDB: 94.1 0.0043 9.2E-08 48.5 -2.8 30 153-182 40-69 (73)
31 PRK01064 hypothetical protein; 91.8 0.09 1.9E-06 43.0 1.5 32 153-184 41-72 (78)
32 PRK02821 hypothetical protein; 91.5 0.14 3E-06 41.8 2.3 30 152-184 41-70 (77)
33 cd02134 NusA_KH NusA_K homolog 91.0 0.21 4.5E-06 38.3 2.7 26 152-177 35-60 (61)
34 cd02414 jag_KH jag_K homology 90.9 0.086 1.9E-06 41.8 0.6 26 153-178 35-60 (77)
35 KOG2193 IGF-II mRNA-binding pr 90.8 0.36 7.9E-06 50.8 5.1 83 79-179 227-317 (584)
36 PRK00468 hypothetical protein; 90.4 0.15 3.3E-06 41.3 1.6 31 153-183 41-71 (75)
37 PLN00207 polyribonucleotide nu 90.0 0.25 5.4E-06 55.7 3.3 58 152-210 695-757 (891)
38 COG1185 Pnp Polyribonucleotide 88.9 0.47 1E-05 52.1 4.4 52 153-204 563-616 (692)
39 cd02409 KH-II KH-II (K homolo 87.0 0.52 1.1E-05 34.5 2.4 24 152-175 35-58 (68)
40 KOG2190 PolyC-binding proteins 86.6 1.1 2.5E-05 47.4 5.5 144 52-204 45-208 (485)
41 KOG2191 RNA-binding protein NO 86.4 8.8 0.00019 39.7 11.3 148 50-208 39-208 (402)
42 COG1837 Predicted RNA-binding 85.0 0.47 1E-05 38.9 1.3 19 153-171 41-59 (76)
43 COG1097 RRP4 RNA-binding prote 84.9 1.8 3.9E-05 42.3 5.5 119 79-207 70-212 (239)
44 KOG2814 Transcription coactiva 84.2 1.2 2.6E-05 45.4 4.1 121 152-290 67-197 (345)
45 PRK11824 polynucleotide phosph 83.9 0.91 2E-05 49.8 3.3 52 153-204 565-618 (693)
46 COG1702 PhoH Phosphate starvat 83.5 1.9 4.2E-05 44.2 5.2 48 152-199 25-72 (348)
47 COG1094 Predicted RNA-binding 81.1 3.7 8E-05 39.1 5.8 62 152-213 18-87 (194)
48 cd02393 PNPase_KH Polynucleoti 75.2 5.4 0.00012 30.4 4.2 55 53-112 5-60 (61)
49 KOG1067 Predicted RNA-binding 64.4 4 8.7E-05 44.7 1.9 52 153-204 608-660 (760)
50 PRK08406 transcription elongat 63.8 3.6 7.8E-05 36.8 1.2 26 152-177 109-134 (140)
51 COG1159 Era GTPase [General fu 61.5 17 0.00036 36.8 5.6 62 105-177 189-273 (298)
52 TIGR00112 proC pyrroline-5-car 59.1 8.9 0.00019 36.3 3.0 99 68-172 124-225 (245)
53 PF00013 KH_1: KH domain syndr 58.6 32 0.00069 25.3 5.4 55 53-112 3-60 (60)
54 TIGR03278 methan_mark_10 putat 57.4 50 0.0011 34.4 8.4 139 87-238 73-235 (404)
55 PRK15494 era GTPase Era; Provi 55.6 23 0.00049 35.4 5.4 55 122-178 242-318 (339)
56 KOG2191 RNA-binding protein NO 55.4 13 0.00029 38.5 3.7 53 152-204 49-111 (402)
57 PRK10076 pyruvate formate lyas 55.2 82 0.0018 29.8 8.8 106 85-199 36-152 (213)
58 TIGR02696 pppGpp_PNP guanosine 54.4 31 0.00068 38.7 6.6 81 52-142 580-661 (719)
59 PF14611 SLS: Mitochondrial in 50.3 2.1E+02 0.0045 26.3 11.9 110 75-207 52-168 (210)
60 TIGR02517 type_II_gspD general 50.2 1.3E+02 0.0028 32.2 10.2 128 67-202 7-155 (594)
61 PF05598 DUF772: Transposase d 49.9 17 0.00036 28.1 2.7 61 97-160 2-67 (77)
62 cd00105 KH-I K homology RNA-bi 48.9 32 0.0007 25.0 4.0 56 52-112 2-63 (64)
63 PF07650 KH_2: KH domain syndr 47.3 2.7 5.8E-05 32.9 -2.1 24 152-175 35-58 (78)
64 PRK07680 late competence prote 46.2 22 0.00048 33.8 3.5 96 68-170 141-241 (273)
65 PRK00648 Maf-like protein; Rev 46.1 51 0.0011 30.8 5.8 54 161-215 53-111 (191)
66 KOG2190 PolyC-binding proteins 43.5 17 0.00036 38.9 2.4 32 150-181 346-377 (485)
67 PRK06928 pyrroline-5-carboxyla 41.2 69 0.0015 30.8 6.0 96 69-170 145-244 (277)
68 cd02394 vigilin_like_KH K homo 40.3 53 0.0012 24.2 4.1 55 53-112 3-61 (62)
69 cd01104 HTH_MlrA-CarA Helix-Tu 39.4 53 0.0011 24.4 4.0 32 98-129 37-68 (68)
70 PF14611 SLS: Mitochondrial in 39.2 67 0.0014 29.5 5.4 65 153-217 37-106 (210)
71 PF00403 HMA: Heavy-metal-asso 38.5 1.3E+02 0.0028 22.0 5.9 31 67-97 12-44 (62)
72 PRK04056 Maf-like protein; Rev 38.2 51 0.0011 30.6 4.5 40 175-215 63-107 (180)
73 COG0424 Maf Nucleotide-binding 36.2 55 0.0012 31.2 4.4 56 160-216 51-111 (193)
74 PRK01526 Maf-like protein; Rev 36.1 58 0.0012 30.9 4.5 40 175-215 72-116 (205)
75 PF14748 P5CR_dimer: Pyrroline 35.7 10 0.00022 32.0 -0.4 55 114-172 31-86 (107)
76 PRK11145 pflA pyruvate formate 35.4 2.3E+02 0.0049 26.4 8.4 107 89-201 72-188 (246)
77 cd02396 PCBP_like_KH K homolog 35.1 51 0.0011 25.0 3.3 57 51-112 1-64 (65)
78 PF15232 DUF4585: Domain of un 35.0 13 0.00028 30.7 0.1 24 261-284 2-25 (75)
79 TIGR00436 era GTP-binding prot 35.0 33 0.00072 32.6 2.8 26 152-177 232-265 (270)
80 KOG0336 ATP-dependent RNA heli 34.4 41 0.0009 36.3 3.6 51 152-202 57-111 (629)
81 PRK00148 Maf-like protein; Rev 33.7 81 0.0018 29.6 5.1 31 184-215 77-107 (194)
82 COG1782 Predicted metal-depend 33.6 1.4E+02 0.003 33.0 7.3 113 62-178 5-135 (637)
83 PRK14365 Maf-like protein; Pro 33.1 71 0.0015 30.1 4.6 40 175-215 65-109 (197)
84 TIGR02493 PFLA pyruvate format 32.5 3.1E+02 0.0067 25.2 8.6 108 89-202 67-184 (235)
85 COG0195 NusA Transcription elo 32.1 37 0.00081 32.1 2.6 31 151-181 151-181 (190)
86 TIGR00762 DegV EDD domain prot 31.7 4E+02 0.0087 25.6 9.6 103 90-202 108-214 (275)
87 cd02410 archeal_CPSF_KH The ar 31.5 2.5E+02 0.0054 25.9 7.6 91 84-178 4-112 (145)
88 TIGR02494 PFLE_PFLC glycyl-rad 31.3 3.2E+02 0.007 26.1 8.9 106 88-199 126-239 (295)
89 COG1185 Pnp Polyribonucleotide 31.3 70 0.0015 35.9 4.8 48 69-121 571-619 (692)
90 PRK00089 era GTPase Era; Revie 31.1 42 0.0009 32.0 2.8 27 152-178 237-271 (292)
91 cd04764 HTH_MlrA-like_sg1 Heli 31.0 79 0.0017 23.7 3.8 33 97-129 35-67 (67)
92 PRK00234 Maf-like protein; Rev 30.7 86 0.0019 29.4 4.7 32 183-215 77-108 (192)
93 COG1902 NemA NADH:flavin oxido 29.4 2.7E+02 0.0059 28.7 8.4 107 58-200 196-309 (363)
94 PRK08406 transcription elongat 29.3 45 0.00098 29.8 2.5 24 152-175 42-65 (140)
95 cd02395 SF1_like-KH Splicing f 28.8 1.9E+02 0.0042 25.3 6.3 50 69-122 25-99 (120)
96 PRK00078 Maf-like protein; Rev 28.8 93 0.002 29.1 4.6 40 175-215 66-110 (192)
97 PRK07634 pyrroline-5-carboxyla 28.1 59 0.0013 29.9 3.1 96 67-170 145-244 (245)
98 PRK14363 Maf-like protein; Pro 27.2 1E+02 0.0022 29.4 4.6 40 175-215 63-107 (204)
99 PRK14361 Maf-like protein; Pro 27.0 1.2E+02 0.0026 28.3 5.0 31 184-215 74-104 (187)
100 PRK04163 exosome complex RNA-b 26.8 1.5E+02 0.0033 28.4 5.7 67 45-117 141-208 (235)
101 PRK00032 Maf-like protein; Rev 26.6 1.1E+02 0.0024 28.6 4.7 31 184-215 79-109 (190)
102 cd04763 HTH_MlrA-like Helix-Tu 26.6 1.3E+02 0.0027 22.8 4.2 34 96-129 35-68 (68)
103 PTZ00431 pyrroline carboxylate 25.4 1.3E+02 0.0029 28.5 5.1 97 70-172 139-238 (260)
104 PRK14362 Maf-like protein; Pro 25.3 1.1E+02 0.0024 29.1 4.5 40 175-215 75-119 (207)
105 PRK00884 Maf-like protein; Rev 25.2 1.3E+02 0.0029 28.3 4.9 40 175-215 64-108 (194)
106 cd00555 Maf Nucleotide binding 24.7 1.3E+02 0.0029 27.7 4.8 31 184-215 76-106 (180)
107 cd04735 OYE_like_4_FMN Old yel 24.6 4.3E+02 0.0094 26.6 8.8 124 58-227 191-322 (353)
108 PRK14368 Maf-like protein; Pro 23.2 1.6E+02 0.0035 27.7 5.1 31 184-215 81-111 (193)
109 TIGR00172 maf MAF protein. Thi 22.7 1.7E+02 0.0037 27.2 5.1 31 184-215 79-109 (183)
110 PRK04425 Maf-like protein; Rev 22.6 1.6E+02 0.0034 27.9 4.9 40 175-215 67-111 (196)
111 PF04459 DUF512: Protein of un 22.6 2.1E+02 0.0045 27.3 5.7 95 53-180 101-201 (204)
112 PRK02478 Maf-like protein; Rev 22.0 1.8E+02 0.0039 27.4 5.1 31 184-215 85-115 (199)
113 PRK14367 Maf-like protein; Pro 22.0 1.5E+02 0.0032 28.1 4.6 31 184-215 85-115 (202)
114 TIGR01952 nusA_arch NusA famil 21.6 45 0.00098 30.1 1.1 27 153-179 111-137 (141)
115 PRK01839 Maf-like protein; Rev 21.6 1.7E+02 0.0036 27.9 4.9 31 184-215 97-127 (209)
116 PRK11880 pyrroline-5-carboxyla 21.5 1.1E+02 0.0023 28.8 3.6 104 65-173 138-244 (267)
117 PRK07679 pyrroline-5-carboxyla 21.5 1.5E+02 0.0032 28.4 4.6 100 67-172 145-247 (279)
118 PRK11901 hypothetical protein; 21.5 95 0.0021 32.0 3.4 26 177-202 278-305 (327)
119 PRK10629 EnvZ/OmpR regulon mod 21.4 1.8E+02 0.004 25.7 4.8 45 66-114 50-95 (127)
120 KOG4656 Copper chaperone for s 21.2 1.2E+02 0.0026 29.9 3.9 72 49-129 8-83 (247)
121 PRK14364 Maf-like protein; Pro 20.8 1.9E+02 0.0041 26.9 5.0 31 184-215 73-103 (181)
122 cd02412 30S_S3_KH K homology R 20.7 61 0.0013 27.5 1.6 22 152-173 71-92 (109)
123 smart00422 HTH_MERR helix_turn 20.5 1.6E+02 0.0035 21.7 3.8 31 99-129 38-68 (70)
124 PF06420 Mgm101p: Mitochondria 20.2 93 0.002 29.4 2.8 115 116-243 12-141 (171)
125 cd01105 HTH_GlnR-like Helix-Tu 20.2 1.4E+02 0.0031 24.1 3.6 34 98-131 38-71 (88)
126 PRK05412 putative nucleotide-b 20.0 3.4E+02 0.0074 25.5 6.4 121 62-201 13-148 (161)
No 1
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=6.2e-124 Score=893.33 Aligned_cols=336 Identities=66% Similarity=1.047 Sum_probs=312.7
Q ss_pred cccCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCcceeeeeeeecCcchHHHHHhhhHHHHHHHhhcceEEEEEcCcCe
Q 017154 11 KKHKGKHDKPKPWDEDPNIDHWKVEKFDPFWNEGGMLEVSSFSTLFPQYREKYLQEAWPMVKGALKEYGVSCELNLVEGS 90 (376)
Q Consensus 11 ~~~~~~~~~~kpwd~~~~id~wk~~~f~~edn~~g~~eessf~~lfPkyRe~yLKe~W~~I~k~Le~~~l~i~lDl~eGs 90 (376)
.+++.+|..++|||++++||+|+++.|+++|||+||+|+|||+||||+|||+||+++|+.|.++|++|+|.|.|||.+|+
T Consensus 18 ~~~k~~~e~~k~~~~~~~~d~wki~~Fs~edn~~g~~EeSSfatlFPKYREkYlke~wp~v~raL~e~~i~c~lDL~egs 97 (356)
T KOG2874|consen 18 ENKKPKPETDKPWDPDDNIDMWKIEKFSKEDNPHGFLEESSFATLFPKYREKYLKECWPLVERALDEHHIKCVLDLVEGS 97 (356)
T ss_pred hhcccccccCCCCCCCCcchhhcccccCcccCccchhhhhhHHhhhHHHHHHHHHHHHHHHHHHHHhcCcceEEeeccce
Confidence 35677889999999998899999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEcCCCCCChhHHHhHHHHHHHHhcCCChHHHHhhhccCceeEEEeccccccCchhhhhhhceecCCCCchHHHHHHH
Q 017154 91 MTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEMQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEIL 170 (376)
Q Consensus 91 V~V~Tt~kT~DP~~IlKArD~IkAiaRGF~~EqAlkLLeDDi~~dIIdI~~~v~nke~f~RrrgRIIG~~GkTkkaIE~L 170 (376)
|+|+||++|||||+|++|||||+++|||||++||++||+||++||||+|+++|+|+++|++||+||||+||.|++|||+|
T Consensus 98 m~V~TtRkT~DPyIiikArdlIKLlaRsVp~eqAvkiLqDev~CdiIkIgn~V~nkerFvKRRqRLiGpng~TLKAlelL 177 (356)
T KOG2874|consen 98 MTVKTTRKTRDPYIIIKARDLIKLLARSVPFEQAVKILQDEVACDIIKIGNLVRNKERFVKRRQRLIGPNGSTLKALELL 177 (356)
T ss_pred eEEeecccccCceeeeeHHHHHHHHHcCCCHHHHHHHHhhccceeeeehhhhhccHHHHHHHHHHhcCCCchhHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCceEEEeCcEEEEecCCccHHHHHHHHHHHhcCCCCchhHHHHHHHHHhhhcCcccccccccccchhhhcccccccccc
Q 017154 171 TGCYILVQGNTVAAMGSFKGLKQVRRIVEDCMQNKMHPVYHIKILMVKKELEKDPALANENWDRFLPKFKKKNVKQKKVK 250 (376)
Q Consensus 171 T~~~I~V~G~TVsIIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikelmiKreL~kd~~l~~e~W~rflP~fkk~~~~~~k~~ 250 (376)
|+|||+|||+|||+||+|.||++||++|+|||+| +||||||++|||||||++||+|+|||||||||+|+++|++++|++
T Consensus 178 T~CYilVqG~TVsaiGpfkGlkevr~IV~DcM~N-iHPiY~IK~LmiKRel~kd~~l~ne~W~rfLP~fkkknv~k~K~~ 256 (356)
T KOG2874|consen 178 TNCYILVQGNTVSAIGPFKGLKEVRKIVEDCMKN-IHPIYNIKTLMIKRELAKDPELANEDWSRFLPQFKKKNVKKRKPK 256 (356)
T ss_pred hhcEEEeeCcEEEeecCcchHHHHHHHHHHHHhc-cchHHHHHHHHHHHHhhcChhhccccHHHHhHHhhhhhhhhcccc
Confidence 9999999999999999999999999999999999 999999999999999999999999999999999999999999887
Q ss_pred c-cCCCCCCCCCCCCCCchhhhhhhccccccChhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCcccccc
Q 017154 251 S-KEKKPYTPFPPPPQPSKIDKLLESGEYFLSERKKESKKWQEKQEKQAEKTAENKRKRDAAFIPPEEPSRQNSCEAEDK 329 (376)
Q Consensus 251 ~-~~kk~~tpfpp~~~~~k~d~~~esgeyfl~~~~k~~~~~~~~~~~q~~~~~~~~~~r~~~~~~p~e~~~~~~~~~~~~ 329 (376)
+ +.||+||||||+|++||||+|||||||||+++++++++++|+.++|+++..+++++|.++|+||+|.+.....+...+
T Consensus 257 K~~~kk~ytpfPp~q~~sKiD~eleSGEYFl~~~~k~~kK~~e~~Ekq~e~~~er~~~r~k~fi~peE~~~~~~~~~~~~ 336 (356)
T KOG2874|consen 257 KVKGKKEYTPFPPAQPPSKIDKELESGEYFLRDEEKSRKKMQEKKEKQAEKRKERQEERMKAFIPPEEESRKPSNKKKEA 336 (356)
T ss_pred cccCCCCCCCCCCCcCcchhhhhhhcchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCccccccccccCCCC
Confidence 6 458999999999999999999999999999999999999999999999999999999999999999876442222222
Q ss_pred cchHHHHHHHHHHHHHHH
Q 017154 330 TNDVAAMAKSLKEKAKKL 347 (376)
Q Consensus 330 ~~~~~~~~~~~k~k~~~~ 347 (376)
.........+++.|++++
T Consensus 337 ~~~~~i~~~~~k~k~~ka 354 (356)
T KOG2874|consen 337 STETKIDVLSIKAKLKKA 354 (356)
T ss_pred CCcchHHHHHHHHhhhhc
Confidence 222222233456666554
No 2
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=100.00 E-value=3.7e-59 Score=428.13 Aligned_cols=180 Identities=32% Similarity=0.512 Sum_probs=170.9
Q ss_pred CcceeeeeeeecCcchHHHHHhhhHHHHHHHh-hcceEEEEEcCcCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCChHH
Q 017154 45 GMLEVSSFSTLFPQYREKYLQEAWPMVKGALK-EYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQ 123 (376)
Q Consensus 45 g~~eessf~~lfPkyRe~yLKe~W~~I~k~Le-~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD~IkAiaRGF~~Eq 123 (376)
++.+.++++|.||+||++||...|+.|+++|+ .++++|+||+.+|+|+|+||++|.||++++||+|||+||+||||||+
T Consensus 3 ~~~~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~ 82 (194)
T COG1094 3 EFAEKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEK 82 (194)
T ss_pred cccccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHH
Confidence 46788999999999999999999999999995 57799999999999999999999999999999999999999999999
Q ss_pred HHhhhccCceeEEEecccccc-CchhhhhhhceecCCCCchHHHHHHHhCceEEEeCcEEEEecCCccHHHHHHHHHHHh
Q 017154 124 AIKILDDEMQCDIIKIGNLVR-NKERFVKRRQHLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDCM 202 (376)
Q Consensus 124 AlkLLeDDi~~dIIdI~~~v~-nke~f~RrrgRIIG~~GkTkkaIE~LT~~~I~V~G~TVsIIG~~~~IkiAR~AIe~LI 202 (376)
|++||+||++||||||+++++ +++||.|++|||||++|+|+++||+||||||+|||+||||||+|+++++||+||+|||
T Consensus 83 A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~tVaiiG~~~~v~iAr~AVemli 162 (194)
T COG1094 83 ALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGKTVAIIGGFEQVEIAREAVEMLI 162 (194)
T ss_pred HHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCcEEEEecChhhhHHHHHHHHHHH
Confidence 999999999999999999998 5566999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCc-hhHHHHHHHHHhhhcC
Q 017154 203 QNKMHP-VYHIKILMVKKELEKD 224 (376)
Q Consensus 203 ~Gs~Hp-VY~ikelmiKreL~kd 224 (376)
+|++|+ ||.+|+...++...+.
T Consensus 163 ~G~~h~~Vy~fLer~~~~lk~~~ 185 (194)
T COG1094 163 NGAPHGKVYKFLERKERELKERE 185 (194)
T ss_pred cCCCchhHHHHHHHHHHHHHHHH
Confidence 999998 9999999886655544
No 3
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.6e-45 Score=341.07 Aligned_cols=176 Identities=18% Similarity=0.283 Sum_probs=167.1
Q ss_pred ceeeeeeeecCcchHHHHHhhhHHHHHHH-hhcceEEEEEcCcCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCChHHHH
Q 017154 47 LEVSSFSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAI 125 (376)
Q Consensus 47 ~eessf~~lfPkyRe~yLKe~W~~I~k~L-e~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD~IkAiaRGF~~EqAl 125 (376)
....+.+|.+|+||+++||++|+.|+.+| ++++++|+||+...+|+++|+..|.||..++|+.|||+||..||+++||+
T Consensus 71 ~k~e~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmNlK~r~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DAi 150 (252)
T KOG3273|consen 71 GKIETRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMNLKARSVELRTCKDTEDPSALQKGADFVRAFILGFDIDDAI 150 (252)
T ss_pred CccceeeccCCcccCChHHHhhHhhhhHHHHhhhheeEeecccceeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhHH
Confidence 33455689999999999999999999999 89999999999999999999999999999999999999999999999999
Q ss_pred hhhc-cCceeEEEecccccc-CchhhhhhhceecCCCCchHHHHHHHhCceEEEeCcEEEEecCCccHHHHHHHHHHHhc
Q 017154 126 KILD-DEMQCDIIKIGNLVR-NKERFVKRRQHLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDCMQ 203 (376)
Q Consensus 126 kLLe-DDi~~dIIdI~~~v~-nke~f~RrrgRIIG~~GkTkkaIE~LT~~~I~V~G~TVsIIG~~~~IkiAR~AIe~LI~ 203 (376)
+||+ ||+|+|.+.|+++.. .++|++|++|||+|++|+|++|||+.|.|+|+|+|.+|||||.|.||++||+|||.||+
T Consensus 151 ALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVlad~kIHiLG~~~niriAR~avcsLIl 230 (252)
T KOG3273|consen 151 ALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLADSKIHILGAFQNIRIARDAVCSLIL 230 (252)
T ss_pred HHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEecCceEEEeecchhhHHHHHhhHhhhc
Confidence 9999 999999999888764 78999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCc-hhHHHHHHHHHhhh
Q 017154 204 NKMHP-VYHIKILMVKKELE 222 (376)
Q Consensus 204 Gs~Hp-VY~ikelmiKreL~ 222 (376)
|++++ ||+.|+.+..|--+
T Consensus 231 GsppgkVy~~LR~vasRl~E 250 (252)
T KOG3273|consen 231 GSPPGKVYGNLRNVASRLKE 250 (252)
T ss_pred cCCchhHHHHHHHHHHhhhh
Confidence 98888 99999999987543
No 4
>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=100.00 E-value=4.2e-39 Score=288.96 Aligned_cols=166 Identities=23% Similarity=0.394 Sum_probs=159.2
Q ss_pred eecCcchHHHHHhhhHHHHHHH-hhcceEEEEEcCcCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCChHHHHhhhccCc
Q 017154 54 TLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEM 132 (376)
Q Consensus 54 ~lfPkyRe~yLKe~W~~I~k~L-e~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD~IkAiaRGF~~EqAlkLLeDDi 132 (376)
+.+|++|...|-..|+.+.+.| +++++.++||..+|.|.|+ ..|+||+++++|++||+||++||+|++|++||.|++
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~V~I~--~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~gd~y 79 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIE--EEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDY 79 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEe--cCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcCCcc
Confidence 5689999999999999999999 6899999999999999997 568999999999999999999999999999999999
Q ss_pred eeEEEeccccccCchhhhhhhceecCCCCchHHHHHHHhCceEEEeCcEEEEecCCccHHHHHHHHHHHhcCCCCc-hhH
Q 017154 133 QCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDCMQNKMHP-VYH 211 (376)
Q Consensus 133 ~~dIIdI~~~v~nke~f~RrrgRIIG~~GkTkkaIE~LT~~~I~V~G~TVsIIG~~~~IkiAR~AIe~LI~Gs~Hp-VY~ 211 (376)
+|+||+|.++.+++++|.+++|||||++|+|+++||.+|||+|+|+|++|+|+|+++++++||++|++||+|++|+ ||+
T Consensus 80 ~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~~~v~i~G~~~~~~~A~~~i~~li~~~~~~~vy~ 159 (172)
T TIGR03665 80 MLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYGKTVGIIGDPEQVQIAREAIEMLIEGAPHGTVYK 159 (172)
T ss_pred eEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcCCEEEEECCHHHHHHHHHHHHHHHcCCCChhHHH
Confidence 9999999999889999999999999999999999999999999999999999999999999999999999999999 999
Q ss_pred HHHHHHHHhhh
Q 017154 212 IKILMVKKELE 222 (376)
Q Consensus 212 ikelmiKreL~ 222 (376)
+|+.+. |||.
T Consensus 160 ~l~~~~-~~~~ 169 (172)
T TIGR03665 160 FLERKR-RELK 169 (172)
T ss_pred HHHHHH-HHHh
Confidence 999876 6653
No 5
>PRK13763 putative RNA-processing protein; Provisional
Probab=100.00 E-value=6.9e-39 Score=289.68 Aligned_cols=167 Identities=25% Similarity=0.392 Sum_probs=161.5
Q ss_pred eeecCcchHHHHHhhhHHHHHHH-hhcceEEEEEcCcCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCChHHHHhhhccC
Q 017154 53 STLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDE 131 (376)
Q Consensus 53 ~~lfPkyRe~yLKe~W~~I~k~L-e~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD~IkAiaRGF~~EqAlkLLeDD 131 (376)
.+.||++|..+|...|+.+.+.| +++|++|.+|..+|+|.|.||. |.||.++++|++||+||++||+||+|++++.|+
T Consensus 6 ~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~~-~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~gd~ 84 (180)
T PRK13763 6 YVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTD-GEDPLAVLKARDIVKAIGRGFSPEKALRLLDDD 84 (180)
T ss_pred EEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeCC-CCCHHHHHHHHHHHHHHhcCCCHHHHHHHhCCC
Confidence 57899999999999999999999 6899999999999999999998 999999999999999999999999999999999
Q ss_pred ceeEEEeccccccCchhhhhhhceecCCCCchHHHHHHHhCceEEEeCcEEEEecCCccHHHHHHHHHHHhcCCCCc-hh
Q 017154 132 MQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDCMQNKMHP-VY 210 (376)
Q Consensus 132 i~~dIIdI~~~v~nke~f~RrrgRIIG~~GkTkkaIE~LT~~~I~V~G~TVsIIG~~~~IkiAR~AIe~LI~Gs~Hp-VY 210 (376)
|+++||+|.++..++++|.|++|||||++|+|+++||++|||+|.|+|++|+|+|++++++.|+++|++|+.|++|+ ||
T Consensus 85 y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~~v~i~G~~~~~~~A~~~I~~li~g~~~~~~~ 164 (180)
T PRK13763 85 YVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGKTVAIIGDPEQVEIAREAIEMLIEGAPHGTVY 164 (180)
T ss_pred ceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCCEEEEEeCHHHHHHHHHHHHHHHcCCCcHHHH
Confidence 99999999999889999999999999999999999999999999999999999999999999999999999999999 99
Q ss_pred HHHHHHHHHhh
Q 017154 211 HIKILMVKKEL 221 (376)
Q Consensus 211 ~ikelmiKreL 221 (376)
++|+.... +|
T Consensus 165 ~~l~~~~~-~~ 174 (180)
T PRK13763 165 KFLERKKR-EL 174 (180)
T ss_pred HHHHHHHH-HH
Confidence 99999865 44
No 6
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=98.88 E-value=3.3e-09 Score=110.42 Aligned_cols=57 Identities=21% Similarity=0.519 Sum_probs=55.2
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeCcE-EEEecCCccH--HHHHHHHHHHh-cCCCCc
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQGNT-VAAMGSFKGL--KQVRRIVEDCM-QNKMHP 208 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G~T-VsIIG~~~~I--kiAR~AIe~LI-~Gs~Hp 208 (376)
.+|||||++|++.+++|.+|||.|+|.+.. +.+|.+|+++ ++||.+++.|| .|++||
T Consensus 215 ~kgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~fdp~rreia~~~l~~li~dgrihp 275 (514)
T TIGR03319 215 MKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPVRREIARMALEKLIQDGRIHP 275 (514)
T ss_pred hhccccCCCcchHHHHHHHhCceEEEcCCCCeEEecCCchHHHHHHHHHHHHHHHcCCCCH
Confidence 799999999999999999999999999988 8889999998 99999999999 999999
No 7
>PRK00106 hypothetical protein; Provisional
Probab=98.83 E-value=4.1e-09 Score=110.41 Aligned_cols=68 Identities=18% Similarity=0.459 Sum_probs=60.2
Q ss_pred eeEEEeccccccCchhhhhhhceecCCCCchHHHHHHHhCceEEEeCcE-EEEecCCccH--HHHHHHHHHHh-cCCCCc
Q 017154 133 QCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQGNT-VAAMGSFKGL--KQVRRIVEDCM-QNKMHP 208 (376)
Q Consensus 133 ~~dIIdI~~~v~nke~f~RrrgRIIG~~GkTkkaIE~LT~~~I~V~G~T-VsIIG~~~~I--kiAR~AIe~LI-~Gs~Hp 208 (376)
..-+|.|.+ .-.+|||||++|++.+|+|.+|||.|+|++.. +.+|.+|+++ ++||.+++.|| .|++||
T Consensus 225 tvs~v~lp~--------demkGriIGreGrNir~~E~~tGvdliiddtp~~v~lS~fdpvRReiAr~~le~Li~dgrIhp 296 (535)
T PRK00106 225 TITTVHLPD--------DNMKGRIIGREGRNIRTLESLTGIDVIIDDTPEVVVLSGFDPIRREIARMTLESLIKDGRIHP 296 (535)
T ss_pred eeeeEEcCC--------hHhhcceeCCCcchHHHHHHHhCceEEEcCCCCeEEEeCCChHHHHHHHHHHHHHHHcCCcCH
Confidence 355566654 23799999999999999999999999999977 7779999998 89999999999 999999
No 8
>PRK12704 phosphodiesterase; Provisional
Probab=98.69 E-value=2.1e-08 Score=104.57 Aligned_cols=57 Identities=21% Similarity=0.525 Sum_probs=54.9
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeCcE-EEEecCCccHH--HHHHHHHHHh-cCCCCc
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQGNT-VAAMGSFKGLK--QVRRIVEDCM-QNKMHP 208 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G~T-VsIIG~~~~Ik--iAR~AIe~LI-~Gs~Hp 208 (376)
.+|||||++|++.+++|.+|||.|+|++.. |.+|.+|+++. +|+.+++.|+ .|.+||
T Consensus 221 mkgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~~~~~rre~a~~~l~~l~~dg~i~P 281 (520)
T PRK12704 221 MKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPIRREIARLALEKLVQDGRIHP 281 (520)
T ss_pred hhcceeCCCcchHHHHHHHhCCeEEEcCCCCeEEEecCChhhHHHHHHHHHHHHhcCCcCC
Confidence 799999999999999999999999999986 88899999997 9999999999 999999
No 9
>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=98.53 E-value=3.1e-07 Score=79.56 Aligned_cols=71 Identities=23% Similarity=0.220 Sum_probs=60.3
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeCc------------------------EEEEecCC---ccHHHHHHHHHHHhcC
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQGN------------------------TVAAMGSF---KGLKQVRRIVEDCMQN 204 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G~------------------------TVsIIG~~---~~IkiAR~AIe~LI~G 204 (376)
.+||||||+|+|.+.||.-|||.|.|.|. +|.|.|+- +.+..|...|+.|+.-
T Consensus 16 ~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~~ 95 (120)
T cd02395 16 FVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLKP 95 (120)
T ss_pred eeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhcc
Confidence 68999999999999999999999999996 68999976 8899999999999986
Q ss_pred CCCch-hHHHHHHHHHhhhc
Q 017154 205 KMHPV-YHIKILMVKKELEK 223 (376)
Q Consensus 205 s~HpV-Y~ikelmiKreL~k 223 (376)
.|+- .+-+....-+||+.
T Consensus 96 -~~~~~~~~~k~~ql~~la~ 114 (120)
T cd02395 96 -AIEGGNDELKREQLRELAL 114 (120)
T ss_pred -CCCccchHHHHHHHHHHHH
Confidence 7775 55555555566653
No 10
>smart00322 KH K homology RNA-binding domain.
Probab=98.32 E-value=1.2e-06 Score=63.54 Aligned_cols=52 Identities=19% Similarity=0.324 Sum_probs=48.3
Q ss_pred hhhceecCCCCchHHHHHHHhCceEEEeC-----cEEEEecCCccHHHHHHHHHHHh
Q 017154 151 KRRQHLVGPNSSTLKALEILTGCYILVQG-----NTVAAMGSFKGLKQVRRIVEDCM 202 (376)
Q Consensus 151 RrrgRIIG~~GkTkkaIE~LT~~~I~V~G-----~TVsIIG~~~~IkiAR~AIe~LI 202 (376)
...|+|||++|.+.+.|+..|||.|.+.+ .+|.|.|+..++..|+..|.+++
T Consensus 12 ~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 12 DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred hhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 36799999999999999999999999988 67999999999999999999876
No 11
>PRK12705 hypothetical protein; Provisional
Probab=98.22 E-value=1.7e-06 Score=90.53 Aligned_cols=57 Identities=21% Similarity=0.506 Sum_probs=53.3
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeCcE-EEEecCCccH--HHHHHHHHHHh-cCCCCc
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQGNT-VAAMGSFKGL--KQVRRIVEDCM-QNKMHP 208 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G~T-VsIIG~~~~I--kiAR~AIe~LI-~Gs~Hp 208 (376)
.+|||||++|++.+++|.+||+.|+|.+.. +.+|-+|+.+ ++|+.+++.|| .|.+||
T Consensus 209 mkGriIGreGrNir~~E~~tGvdliiddtp~~V~ls~fdp~rreia~~~l~~Li~dgri~p 269 (508)
T PRK12705 209 MKGRIIGREGRNIRAFEGLTGVDLIIDDTPEAVVISSFNPIRREIARLTLEKLLADGRIHP 269 (508)
T ss_pred hhccccCccchhHHHHHHhhCCceEecCCccchhhcccCccchHHHHHHHHHHHhcCCCCh
Confidence 799999999999999999999999999977 6678888887 89999999999 999999
No 12
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=98.14 E-value=2e-06 Score=64.11 Aligned_cols=48 Identities=21% Similarity=0.382 Sum_probs=43.7
Q ss_pred hhhceecCCCCchHHHHHHHhCceEEEeC----cEEEEecCCccHHHHHHHH
Q 017154 151 KRRQHLVGPNSSTLKALEILTGCYILVQG----NTVAAMGSFKGLKQVRRIV 198 (376)
Q Consensus 151 RrrgRIIG~~GkTkkaIE~LT~~~I~V~G----~TVsIIG~~~~IkiAR~AI 198 (376)
...|+|||++|++++.||..|||.|.|.+ .+|.|.|+.+++..|++.|
T Consensus 9 ~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 9 SLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp HHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEESHHHHHHHHHHH
T ss_pred HHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEeCHHHHHHHHhhC
Confidence 36899999999999999999999999997 3799999999999998765
No 13
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.08 E-value=3.8e-06 Score=64.24 Aligned_cols=48 Identities=23% Similarity=0.395 Sum_probs=42.7
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeC-cEEEEecC-CccHHHHHHHHH
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQG-NTVAAMGS-FKGLKQVRRIVE 199 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G-~TVsIIG~-~~~IkiAR~AIe 199 (376)
..|+|||++|+|++.|+.-|||.|.|.. .+|.|.|+ .++++.|+..|+
T Consensus 12 ~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 12 KIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred heeeeECCCchHHHHHHHHHCCEEEeCCCCEEEEEeCCHHHHHHHHHHhC
Confidence 5799999999999999999999999998 45999998 778888887763
No 14
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.06 E-value=5.1e-06 Score=62.26 Aligned_cols=48 Identities=17% Similarity=0.338 Sum_probs=42.7
Q ss_pred hhhceecCCCCchHHHHHHHhCceEEEeC-----cEEEEecCCccHHHHHHHH
Q 017154 151 KRRQHLVGPNSSTLKALEILTGCYILVQG-----NTVAAMGSFKGLKQVRRIV 198 (376)
Q Consensus 151 RrrgRIIG~~GkTkkaIE~LT~~~I~V~G-----~TVsIIG~~~~IkiAR~AI 198 (376)
...|+|||++|.+.+.|+.-|||.|.|.. +.|.|.|+.+++..|+..|
T Consensus 9 ~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 9 KLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred HHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHHHHHHHHHHh
Confidence 35799999999999999999999999988 6799999988887777655
No 15
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.03 E-value=8e-06 Score=60.44 Aligned_cols=47 Identities=19% Similarity=0.362 Sum_probs=41.8
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeC-------cEEEEecCCccHHHHHHHH
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQG-------NTVAAMGSFKGLKQVRRIV 198 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G-------~TVsIIG~~~~IkiAR~AI 198 (376)
..++|||++|++++.|+..|||.|.|.. ..|.|.|+.+++..|+..|
T Consensus 10 ~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 10 LVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred hcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence 5799999999999999999999999977 4599999988888887765
No 16
>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=97.36 E-value=0.00025 Score=54.22 Aligned_cols=47 Identities=21% Similarity=0.322 Sum_probs=40.9
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeCc--------EEEEecCCccHHHHHHHH
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQGN--------TVAAMGSFKGLKQVRRIV 198 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G~--------TVsIIG~~~~IkiAR~AI 198 (376)
..|+|||++|.+.+.|+..|||.|.|..+ .|-|.|+.+++..|..-|
T Consensus 10 ~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 10 QAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred HcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 57999999999999999999999999864 378899988888777654
No 17
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=97.22 E-value=0.00071 Score=72.10 Aligned_cols=144 Identities=16% Similarity=0.199 Sum_probs=103.9
Q ss_pred eeeeecCcchHHHHHhhhHHHHHHH-hhcceEEEEEcCcCeE--EEEcCCCCCChhHHHhHHHHHHHHhcC----CChHH
Q 017154 51 SFSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSM--TVSTTRKTRDPYIIVKARDLIRLLSRS----VPAPQ 123 (376)
Q Consensus 51 sf~~lfPkyRe~yLKe~W~~I~k~L-e~~~l~i~lDl~eGsV--~V~Tt~kT~DP~~IlKArD~IkAiaRG----F~~Eq 123 (376)
+-.+++|..|...|-..=+..-+-| +..++.|.|.-..... .+++-+.|.||+.+..|+.||.=|.+. .+.+.
T Consensus 140 tqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~g~~ 219 (600)
T KOG1676|consen 140 TQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEVPGSG 219 (600)
T ss_pred eeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCCCccc
Confidence 3468999999999999888888889 6788888776553322 357778899999999999999877662 11110
Q ss_pred HHhhhc-cCceeEEEeccccccCchhhhhhhceecCCCCchHHHHHHHhCceEEEe--------CcEEEEecCCccHHHH
Q 017154 124 AIKILD-DEMQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQ--------GNTVAAMGSFKGLKQV 194 (376)
Q Consensus 124 AlkLLe-DDi~~dIIdI~~~v~nke~f~RrrgRIIG~~GkTkkaIE~LT~~~I~V~--------G~TVsIIG~~~~IkiA 194 (376)
--.. +...-.-++|. +=+ -.-|=|||++|.|.|-|.+-||++|-+- ..++.|||+.+.|..|
T Consensus 220 --~~~g~~~g~~~~~~V~-VPr------~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~A 290 (600)
T KOG1676|consen 220 --GHAGVRGGGSATREVK-VPR------SKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHA 290 (600)
T ss_pred --cccCcCccccceeEEe-ccc------cceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHH
Confidence 0000 11111111111 001 1368899999999999999999999773 2469999999999999
Q ss_pred HHHHHHHhc
Q 017154 195 RRIVEDCMQ 203 (376)
Q Consensus 195 R~AIe~LI~ 203 (376)
-+.|..||.
T Consensus 291 a~lI~eii~ 299 (600)
T KOG1676|consen 291 AELINEIIA 299 (600)
T ss_pred HHHHHHHHH
Confidence 999999984
No 18
>PF13014 KH_3: KH domain
Probab=97.17 E-value=0.00061 Score=48.27 Aligned_cols=27 Identities=26% Similarity=0.370 Sum_probs=25.5
Q ss_pred hceecCCCCchHHHHHHHhCceEEEeC
Q 017154 153 RQHLVGPNSSTLKALEILTGCYILVQG 179 (376)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~~I~V~G 179 (376)
-|+|||++|.|++.|+..|||+|.|..
T Consensus 2 vg~iIG~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 2 VGRIIGKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred cCeEECCCChHHHHHHHHhCcEEEECC
Confidence 379999999999999999999999987
No 19
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=96.88 E-value=0.0015 Score=59.47 Aligned_cols=53 Identities=21% Similarity=0.221 Sum_probs=48.3
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeCc--EEEE---ecCCccHHHHHHHHHHHhcC
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQGN--TVAA---MGSFKGLKQVRRIVEDCMQN 204 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G~--TVsI---IG~~~~IkiAR~AIe~LI~G 204 (376)
++|.|||++|+|.+.|+..|||.|.|... +|.| -|+...+..|++.|..+..|
T Consensus 8 kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 8 RIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRG 65 (172)
T ss_pred HhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence 67899999999999999999999999986 5777 57778899999999999988
No 20
>PRK13763 putative RNA-processing protein; Provisional
Probab=96.81 E-value=0.0016 Score=59.71 Aligned_cols=53 Identities=23% Similarity=0.231 Sum_probs=48.9
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeCc--EEEEe----cCCccHHHHHHHHHHHhcC
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQGN--TVAAM----GSFKGLKQVRRIVEDCMQN 204 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G~--TVsII----G~~~~IkiAR~AIe~LI~G 204 (376)
++|.|||++|+|.+.|+..|||.|.|... +|.|. ++...+..|++.|..+..|
T Consensus 13 kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g 71 (180)
T PRK13763 13 RIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTDGEDPLAVLKARDIVKAIGRG 71 (180)
T ss_pred HhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence 68999999999999999999999999986 48886 7888999999999999998
No 21
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.34 E-value=0.0026 Score=62.11 Aligned_cols=29 Identities=38% Similarity=0.710 Sum_probs=27.4
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeCc
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQGN 180 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G~ 180 (376)
-.|||+||.|.|++-||.-|||+|+|-|+
T Consensus 108 FVGRILGPrGnSlkrLe~eTgCki~IrGr 136 (259)
T KOG1588|consen 108 FVGRILGPRGNSLKRLEEETGCKIMIRGR 136 (259)
T ss_pred cccccccCCcchHHHHHHHHCCeEEEecC
Confidence 47999999999999999999999999985
No 22
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=95.99 E-value=0.022 Score=59.46 Aligned_cols=131 Identities=17% Similarity=0.198 Sum_probs=86.6
Q ss_pred eeecCcchHHHHHhhhHHHHHHH-hhcceEEEEEcC------cCeEEEEcCCCCCChhHHHhHHHHHH--HHhcC-CChH
Q 017154 53 STLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLV------EGSMTVSTTRKTRDPYIIVKARDLIR--LLSRS-VPAP 122 (376)
Q Consensus 53 ~~lfPkyRe~yLKe~W~~I~k~L-e~~~l~i~lDl~------eGsV~V~Tt~kT~DP~~IlKArD~Ik--AiaRG-F~~E 122 (376)
...+|..-...|-..-+.--+.| ...|..|.|..- +..|+| |.||.+.+||.--|- .---+ |.|.
T Consensus 414 ~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViI-----tGppeaqfKAQgrifgKikEenf~~Pk 488 (584)
T KOG2193|consen 414 RMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVII-----TGPPEAQFKAQGRIFGKIKEENFFLPK 488 (584)
T ss_pred eeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEe-----cCChHHHHhhhhhhhhhhhhhccCCch
Confidence 34556555555555555555555 567888877543 444444 589999999986542 11111 2222
Q ss_pred HHHhhhccCceeEEEeccccccCchhhhhhhceecCCCCchHHHHHHHhCceEEEe--------CcE-EEEecCCccHHH
Q 017154 123 QAIKILDDEMQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQ--------GNT-VAAMGSFKGLKQ 193 (376)
Q Consensus 123 qAlkLLeDDi~~dIIdI~~~v~nke~f~RrrgRIIG~~GkTkkaIE~LT~~~I~V~--------G~T-VsIIG~~~~Iki 193 (376)
. -++|..-++ .=+++.||+||++|+|..-|.+||++.++|- |.+ |-|||.|-.-..
T Consensus 489 e------------evklethir---VPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~ 553 (584)
T KOG2193|consen 489 E------------EVKLETHIR---VPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQN 553 (584)
T ss_pred h------------hheeeeeee---ccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchH
Confidence 2 233333332 2256899999999999999999999999993 334 888999988888
Q ss_pred HHHHHHHHhc
Q 017154 194 VRRIVEDCMQ 203 (376)
Q Consensus 194 AR~AIe~LI~ 203 (376)
|.+-|..+++
T Consensus 554 aQrki~~iv~ 563 (584)
T KOG2193|consen 554 AQRKIAHIVN 563 (584)
T ss_pred HHHHHHHHHH
Confidence 8887777763
No 23
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.47 E-value=0.031 Score=53.95 Aligned_cols=84 Identities=24% Similarity=0.337 Sum_probs=61.0
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeCcE-E-EEecC---CccHHHHHHHHHHHhcCCCC-chhHHH--HHHHHHhhhc
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQGNT-V-AAMGS---FKGLKQVRRIVEDCMQNKMH-PVYHIK--ILMVKKELEK 223 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G~T-V-sIIG~---~~~IkiAR~AIe~LI~Gs~H-pVY~ik--elmiKreL~k 223 (376)
-.|-||||-|+|++-+|..|+|+|.|-|.. | +.-|+ .++++-|-..+.-||....- .+.+.. .+-+-||-..
T Consensus 164 FVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n~I~~a~~ 243 (269)
T COG5176 164 FVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARR 243 (269)
T ss_pred eeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHHHHHHHhc
Confidence 579999999999999999999999999965 2 22222 45678888888888855332 244332 2234488999
Q ss_pred Ccccccccccccc
Q 017154 224 DPALANENWDRFL 236 (376)
Q Consensus 224 d~~l~~e~W~rfl 236 (376)
+|+= --+|.||-
T Consensus 244 ~PeG-qnDlkR~q 255 (269)
T COG5176 244 NPEG-QNDLKRFQ 255 (269)
T ss_pred CCcc-cchHHHHH
Confidence 9997 45899983
No 24
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=95.20 E-value=0.031 Score=59.10 Aligned_cols=109 Identities=20% Similarity=0.326 Sum_probs=74.0
Q ss_pred HhcCCChHHHHh---hhccCceeEEEeccccccCchhhhhhhceecCCCCchHHHHHHHhCceEEEeCcE----------
Q 017154 115 LSRSVPAPQAIK---ILDDEMQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQGNT---------- 181 (376)
Q Consensus 115 iaRGF~~EqAlk---LLeDDi~~dIIdI~~~v~nke~f~RrrgRIIG~~GkTkkaIE~LT~~~I~V~G~T---------- 181 (376)
+.-||-+..-.+ ++.|-++++|-+-.++ .-.|-|||+-|.|+|-||.-|||+|.|-|+-
T Consensus 122 ~nP~fkpP~DYk~p~~~~~Kv~IPvke~Pd~--------NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~ 193 (554)
T KOG0119|consen 122 LNPGFKPPADYKPPAKLHDKVYIPVKEFPDI--------NFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSD 193 (554)
T ss_pred hCcCCCCCcccCcccccccceecchhhcCCc--------ceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCc
Confidence 344554443333 3445565444333332 2478999999999999999999999999921
Q ss_pred -----------EE--Eec-CCccHHHHHHHHHHHhcCCCC-c-hhHHHHHHHHHhhhc-Cccccccc
Q 017154 182 -----------VA--AMG-SFKGLKQVRRIVEDCMQNKMH-P-VYHIKILMVKKELEK-DPALANEN 231 (376)
Q Consensus 182 -----------Vs--IIG-~~~~IkiAR~AIe~LI~Gs~H-p-VY~ikelmiKreL~k-d~~l~~e~ 231 (376)
.| |.+ +++.|+-|-.+|+.||.-+.- + .-+-+..+.-|||+. ++.|..++
T Consensus 194 d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~av~~~e~~n~l~~~Qlrela~lNgt~r~~d 260 (554)
T KOG0119|consen 194 DLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQSAVSVPEGQNDLKRLQLRELARLNGTLRDDD 260 (554)
T ss_pred ccccccccccceeEEEecchHHHHHHHHHHHHHHHHhhccCccccccccHHHHHHHHHhCCCCCccc
Confidence 12 222 346689999999999964333 4 777777777788764 77777776
No 25
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=94.96 E-value=0.023 Score=54.20 Aligned_cols=79 Identities=23% Similarity=0.423 Sum_probs=63.5
Q ss_pred hceecCCCCchHHHHHHHhCceEEEeCcE---EEE-ecCCcc------HHHHHHHHHHHh-cCCCC---chhHHHHHHHH
Q 017154 153 RQHLVGPNSSTLKALEILTGCYILVQGNT---VAA-MGSFKG------LKQVRRIVEDCM-QNKMH---PVYHIKILMVK 218 (376)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~~I~V~G~T---VsI-IG~~~~------IkiAR~AIe~LI-~Gs~H---pVY~ikelmiK 218 (376)
-|||||.+|+|+.||+.|++.++.-.+.+ |.+ +|.|.- +.+|-++..... .|..| |+-.+=+.++-
T Consensus 102 ~~~LIG~~Gk~LdALQ~L~n~~l~~~~g~~~~v~ldv~~yRerR~e~L~~LA~~~A~rV~~tg~~v~L~pM~~~ERkIVH 181 (208)
T COG1847 102 AGRLIGKHGKTLDALQYLANLYLNKIGGKFKRVTLDVGDYRERRKETLIKLAERAAERVLETGRSVELEPMPPFERKIVH 181 (208)
T ss_pred hhhhhccCCcchHHHHHHHHHHhhhhcCcceEEEEEhhhHHHHHHHHHHHHHHHHHHHHHhhCCeeecCCCCHHHHHHHH
Confidence 79999999999999999999998876644 444 677754 477777777776 66665 58888888998
Q ss_pred HhhhcCccccccc
Q 017154 219 KELEKDPALANEN 231 (376)
Q Consensus 219 reL~kd~~l~~e~ 231 (376)
.=|..+|.+.++|
T Consensus 182 ~~l~~~~~V~T~S 194 (208)
T COG1847 182 TALSANPGVETYS 194 (208)
T ss_pred HHHHhcCCcceee
Confidence 8899998887765
No 26
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.73 E-value=0.043 Score=52.30 Aligned_cols=54 Identities=20% Similarity=0.296 Sum_probs=47.3
Q ss_pred hceecCCCCchHHHHHHHhCceEEEeCcE-EEEecCCc-cHHHHHHHHHHHhcCCCC
Q 017154 153 RQHLVGPNSSTLKALEILTGCYILVQGNT-VAAMGSFK-GLKQVRRIVEDCMQNKMH 207 (376)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~~I~V~G~T-VsIIG~~~-~IkiAR~AIe~LI~Gs~H 207 (376)
++||||++|.+.+.|...|+|.|.|..|. |.|.|+-. .+..|.++|.+|=.- -|
T Consensus 156 i~~lig~~g~~i~~l~~~~~~~I~ig~NG~VwI~~~~~~~~~~a~~~I~~~e~~-~~ 211 (235)
T PRK04163 156 VPRVIGKKGSMINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIKKIERE-AH 211 (235)
T ss_pred HHhhcCCCChhHhhhhhhhCcEEEEcCCcEEEEeeCCHHHHHHHHHHHHHHHhh-hh
Confidence 78999999999999999999999999866 99988876 688999999888766 45
No 27
>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=94.72 E-value=0.042 Score=60.42 Aligned_cols=53 Identities=15% Similarity=0.261 Sum_probs=45.9
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeCc-EEEEecCC-ccHHHHHHHHHHHhcC
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQGN-TVAAMGSF-KGLKQVRRIVEDCMQN 204 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G~-TVsIIG~~-~~IkiAR~AIe~LI~G 204 (376)
.+|.|||++|+|.+.|..-|||.|.|.+. +|.|.|.- +.++.|+..|+.++..
T Consensus 588 ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 588 KIGEVIGPKGKMINQIQDETGAEISIEDDGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred HhhheeCCCcHhHHHHHHHHCCEEEEecCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 58999999999999999999999999984 58888844 5688899999988873
No 28
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=94.68 E-value=0.08 Score=56.99 Aligned_cols=122 Identities=17% Similarity=0.256 Sum_probs=90.5
Q ss_pred HHHHHHhhcceEEEEEcCcCeEEEEcCCCCCChhHHHhHHHHHHHH-hcCC---ChHHHHhhhccCceeEEEeccccccC
Q 017154 70 MVKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLL-SRSV---PAPQAIKILDDEMQCDIIKIGNLVRN 145 (376)
Q Consensus 70 ~I~k~Le~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD~IkAi-aRGF---~~EqAlkLLeDDi~~dIIdI~~~v~n 145 (376)
.|...+-+.++.+.+....+.+-.+.+..+..|..+..|+.||.=+ +||- +++++.- .......|.|-.
T Consensus 75 qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~~~~~~~~~q~---~~~ttqeI~IPa---- 147 (600)
T KOG1676|consen 75 QIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAKQLIGEVVSRGRPPGGFPDNQG---SVETTQEILIPA---- 147 (600)
T ss_pred HhhhhhhhcCCccccCCCCCCcccccccccCCcccHHHHHHhhhhhhhccCCCCCccccCC---ccceeeeeccCc----
Confidence 3555556678888888888888899999999999999999998765 5553 1121111 011122233332
Q ss_pred chhhhhhhceecCCCCchHHHHHHHhCceEEE-eCc--------EEEEecCCccHHHHHHHHHHHhc
Q 017154 146 KERFVKRRQHLVGPNSSTLKALEILTGCYILV-QGN--------TVAAMGSFKGLKQVRRIVEDCMQ 203 (376)
Q Consensus 146 ke~f~RrrgRIIG~~GkTkkaIE~LT~~~I~V-~G~--------TVsIIG~~~~IkiAR~AIe~LI~ 203 (376)
-+.|-|||++|-|.+-|.+-|||.+.+ +++ ++=|.|+.+.++.|+..|.++|.
T Consensus 148 -----~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~ 209 (600)
T KOG1676|consen 148 -----NKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILR 209 (600)
T ss_pred -----cceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHH
Confidence 257899999999999999999998654 432 57899999999999999999997
No 29
>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=94.58 E-value=0.039 Score=60.06 Aligned_cols=53 Identities=17% Similarity=0.317 Sum_probs=44.1
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeC-cEEEEecCC-ccHHHHHHHHHHHhcC
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQG-NTVAAMGSF-KGLKQVRRIVEDCMQN 204 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G-~TVsIIG~~-~~IkiAR~AIe~LI~G 204 (376)
.+|+|||++|+|.+.|+.-|||.|.|.+ .+|.|.+.- ..+..|.+.|..+...
T Consensus 561 kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 561 KIRDVIGPGGKVIREITEETGAKIDIEDDGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred HHHhhcCCCcHHHHHHHHHHCCEEEEecCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 4899999999999999999999999997 558887744 4578888888877653
No 30
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=94.14 E-value=0.0043 Score=48.46 Aligned_cols=30 Identities=30% Similarity=0.418 Sum_probs=24.1
Q ss_pred hceecCCCCchHHHHHHHhCceEEEeCcEE
Q 017154 153 RQHLVGPNSSTLKALEILTGCYILVQGNTV 182 (376)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~~I~V~G~TV 182 (376)
-|||||++|+|+.||+.|++.++.-+|..|
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~~~~~~~~~~~ 69 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVNAAANKHGKRV 69 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHHHHHHHT-SS-
T ss_pred cceEECCCCeeHHHHHHHHHHHHHhCCCEE
Confidence 699999999999999999988765555444
No 31
>PRK01064 hypothetical protein; Provisional
Probab=91.77 E-value=0.09 Score=42.99 Aligned_cols=32 Identities=19% Similarity=0.205 Sum_probs=25.6
Q ss_pred hceecCCCCchHHHHHHHhCceEEEeCcEEEE
Q 017154 153 RQHLVGPNSSTLKALEILTGCYILVQGNTVAA 184 (376)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~~I~V~G~TVsI 184 (376)
.||+||++|+|..+|-.+.++-..-+|..|.+
T Consensus 41 ~g~vIGk~G~~i~air~l~~~~~~~~~~rv~l 72 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLVSVASRNNVKVSL 72 (78)
T ss_pred ceEEECCCCccHHHHHHHHHHHHhhCCCEEEE
Confidence 69999999999999999877655556666553
No 32
>PRK02821 hypothetical protein; Provisional
Probab=91.47 E-value=0.14 Score=41.83 Aligned_cols=30 Identities=20% Similarity=0.287 Sum_probs=23.5
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeCcEEEE
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQGNTVAA 184 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G~TVsI 184 (376)
-.|||||++|+|.+||=.+-.+- +|..|.+
T Consensus 41 D~GrVIGk~Gr~i~AIRtlv~a~---~~~~v~l 70 (77)
T PRK02821 41 DLGKVIGRGGRTATALRTVVAAI---GGRGVRV 70 (77)
T ss_pred hCcceeCCCCchHHHHHHHHHHh---cCCeEEE
Confidence 38999999999999997754443 7777664
No 33
>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=90.96 E-value=0.21 Score=38.29 Aligned_cols=26 Identities=15% Similarity=0.172 Sum_probs=24.2
Q ss_pred hhceecCCCCchHHHHHHHhCceEEE
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILV 177 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V 177 (376)
-.|+.||++|++.+.++.++|.+|-|
T Consensus 35 ~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 35 QLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cceeeECCCCHHHHHHHHHHCCCeEE
Confidence 57999999999999999999998876
No 34
>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=90.87 E-value=0.086 Score=41.84 Aligned_cols=26 Identities=27% Similarity=0.308 Sum_probs=22.9
Q ss_pred hceecCCCCchHHHHHHHhCceEEEe
Q 017154 153 RQHLVGPNSSTLKALEILTGCYILVQ 178 (376)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~~I~V~ 178 (376)
-|+|||++|+|+.||+-|++..+.-.
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~~~~~~ 60 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANLVLNRN 60 (77)
T ss_pred CCeEECCCCccHHHHHHHHHHHHhhc
Confidence 49999999999999999999877644
No 35
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=90.82 E-value=0.36 Score=50.82 Aligned_cols=83 Identities=25% Similarity=0.317 Sum_probs=50.9
Q ss_pred ceEEEEEcC--------cCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCChHHHHhhhccCceeEEEeccccccCchhhh
Q 017154 79 GVSCELNLV--------EGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEMQCDIIKIGNLVRNKERFV 150 (376)
Q Consensus 79 ~l~i~lDl~--------eGsV~V~Tt~kT~DP~~IlKArD~IkAiaRGF~~EqAlkLLeDDi~~dIIdI~~~v~nke~f~ 150 (376)
.+.|++|.. +..++|-.|.. .--+|..+|--|.-. +| .+|++. +=|-|+-+.-|
T Consensus 227 qTqsriD~hrken~Gaaek~itvh~tpE-----g~s~Ac~~ILeimqk----EA---~~~k~~-~e~pLk~lAHN----- 288 (584)
T KOG2193|consen 227 QTQSRIDVHRKENAGAAEKIITVHSTPE-----GTSKACKMILEIMQK----EA---VDDKVA-EEIPLKILAHN----- 288 (584)
T ss_pred hhhheeeeeecccCCcccCceEEecCcc-----chHHHHHHHHHHHHH----hh---hccchh-hhcchhhhhhc-----
Confidence 345555543 67789987655 333454444333221 11 123332 33444444332
Q ss_pred hhhceecCCCCchHHHHHHHhCceEEEeC
Q 017154 151 KRRQHLVGPNSSTLKALEILTGCYILVQG 179 (376)
Q Consensus 151 RrrgRIIG~~GkTkkaIE~LT~~~I~V~G 179 (376)
...|||||+.|+.++-||--|||.|.|--
T Consensus 289 ~lvGRLIGKeGrnlKkIeq~TgTkITis~ 317 (584)
T KOG2193|consen 289 NLVGRLIGKEGRNLKKIEQDTGTKITISK 317 (584)
T ss_pred chhhhhhhhccccHHHHHhhcCCceeeee
Confidence 25799999999999999999999998753
No 36
>PRK00468 hypothetical protein; Provisional
Probab=90.42 E-value=0.15 Score=41.26 Aligned_cols=31 Identities=13% Similarity=0.234 Sum_probs=22.2
Q ss_pred hceecCCCCchHHHHHHHhCceEEEeCcEEE
Q 017154 153 RQHLVGPNSSTLKALEILTGCYILVQGNTVA 183 (376)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~~I~V~G~TVs 183 (376)
.|||||++|+|.+||-.+-.+-=.-+|..|.
T Consensus 41 ~GrVIGk~Gr~i~AIRtvv~aaa~k~~~rv~ 71 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTVVKAAAIKENKRVV 71 (75)
T ss_pred CcceecCCChhHHHHHHHHHHHHhcCCCEEE
Confidence 6999999999999998765443333444443
No 37
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=89.98 E-value=0.25 Score=55.74 Aligned_cols=58 Identities=19% Similarity=0.292 Sum_probs=49.5
Q ss_pred hhceecCCCCchHHHHHHHhCce-EEEeCc-EEEEec-CCccHHHHHHHHHHHhcCCCC-c-hh
Q 017154 152 RRQHLVGPNSSTLKALEILTGCY-ILVQGN-TVAAMG-SFKGLKQVRRIVEDCMQNKMH-P-VY 210 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~-I~V~G~-TVsIIG-~~~~IkiAR~AIe~LI~Gs~H-p-VY 210 (376)
.+|.|||++|+|.+.|..-||+. |-|.+. +|.|+| +.+.++.|...|..+... ++ + ||
T Consensus 695 ki~~vIG~GGktIk~I~eetg~~~Idi~ddg~V~I~a~d~~~i~~A~~~I~~l~~~-~~vG~iy 757 (891)
T PLN00207 695 KVNMIIGSGGKKVKSIIEETGVEAIDTQDDGTVKITAKDLSSLEKSKAIISSLTMV-PTVGDIY 757 (891)
T ss_pred HHHHHhcCCchhHHHHHHHHCCCccCcCCCeeEEEEeCCHHHHHHHHHHHHHHhcC-cCCCcEE
Confidence 47899999999999999999999 888884 599999 456689999999999875 44 3 77
No 38
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=88.92 E-value=0.47 Score=52.11 Aligned_cols=52 Identities=25% Similarity=0.355 Sum_probs=45.9
Q ss_pred hceecCCCCchHHHHHHHhCceEEEeC-cEEEEecCC-ccHHHHHHHHHHHhcC
Q 017154 153 RQHLVGPNSSTLKALEILTGCYILVQG-NTVAAMGSF-KGLKQVRRIVEDCMQN 204 (376)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~~I~V~G-~TVsIIG~~-~~IkiAR~AIe~LI~G 204 (376)
.+=+||++|+|+++|-..|||.|.|.+ .||.|.++. +.+..|++.|+++..-
T Consensus 563 I~dvIG~gGk~I~~I~eetg~~IdieddGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 563 IRDVIGPGGKTIKAITEETGVKIDIEDDGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred HhhccCCcccchhhhhhhhCcEEEecCCCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 456899999999999999999999987 679999988 5589999999998844
No 39
>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=87.01 E-value=0.52 Score=34.50 Aligned_cols=24 Identities=17% Similarity=0.331 Sum_probs=21.4
Q ss_pred hhceecCCCCchHHHHHHHhCceE
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYI 175 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I 175 (376)
--|++||++|+++.+|+.+++-++
T Consensus 35 ~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 35 QPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CCceEECCCCccHHHHHHHHHHHc
Confidence 369999999999999999999665
No 40
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=86.63 E-value=1.1 Score=47.43 Aligned_cols=144 Identities=18% Similarity=0.156 Sum_probs=90.1
Q ss_pred eeeecCcchHHHHHhhhHHHHHHH-hhcceEEEEEcC-----cCeEEEEcCCC----CCChhHHHhHHHHHHHHhcCCCh
Q 017154 52 FSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLV-----EGSMTVSTTRK----TRDPYIIVKARDLIRLLSRSVPA 121 (376)
Q Consensus 52 f~~lfPkyRe~yLKe~W~~I~k~L-e~~~l~i~lDl~-----eGsV~V~Tt~k----T~DP~~IlKArD~IkAiaRGF~~ 121 (376)
|.+|.|----.-+-..=+.+.+.| .+....++++.. ++-++|..++- .+--.++.+|.|+|-. .|.
T Consensus 45 ~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~---~~~- 120 (485)
T KOG2190|consen 45 YRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVF---KLE- 120 (485)
T ss_pred EEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhh---ccc-
Confidence 677777666666666667777777 455666666554 55666655210 0122467777776642 222
Q ss_pred HHHHhhhc-cCceeE-EEeccccccCchhhhhhhceecCCCCchHHHHHHHhCceEEEeCc--------EEEEecCCccH
Q 017154 122 PQAIKILD-DEMQCD-IIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQGN--------TVAAMGSFKGL 191 (376)
Q Consensus 122 EqAlkLLe-DDi~~d-IIdI~~~v~nke~f~RrrgRIIG~~GkTkkaIE~LT~~~I~V~G~--------TVsIIG~~~~I 191 (376)
++....-+ +...+. -+-++-+|. .-..|=|||++|...+-|.+.|||.|.|-+. .|-|-|..+.+
T Consensus 121 ~d~~~~~d~~~~~~~~~v~~RLlVp-----~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av 195 (485)
T KOG2190|consen 121 EDDEAAEDNGEDASGPEVTCRLLVP-----SSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAV 195 (485)
T ss_pred ccccccccCCccccCCceEEEEEec-----hhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHH
Confidence 00000000 000000 011222332 1247999999999999999999999999987 48889999999
Q ss_pred HHHHHHHHHHhcC
Q 017154 192 KQVRRIVEDCMQN 204 (376)
Q Consensus 192 kiAR~AIe~LI~G 204 (376)
..|-..|+.+|..
T Consensus 196 ~~al~~Is~~L~~ 208 (485)
T KOG2190|consen 196 KKALVQISSRLLE 208 (485)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999999966
No 41
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=86.37 E-value=8.8 Score=39.70 Aligned_cols=148 Identities=19% Similarity=0.219 Sum_probs=88.2
Q ss_pred eeeeeecCcchHHHHHhhhHHHHHHH-hhcceEEEEEcC-------cCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCCh
Q 017154 50 SSFSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLV-------EGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPA 121 (376)
Q Consensus 50 ssf~~lfPkyRe~yLKe~W~~I~k~L-e~~~l~i~lDl~-------eGsV~V~Tt~kT~DP~~IlKArD~IkAiaRGF~~ 121 (376)
....+|+|.|--.-|-.-=+..-.-| .+.+..|.|--. +-.|.+-+ ...-+|+-...||.==-|.-+-
T Consensus 39 y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~----Gt~eai~av~efI~dKire~p~ 114 (402)
T KOG2191|consen 39 YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQ----GTVEALNAVHEFIADKIREKPQ 114 (402)
T ss_pred eEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEe----ccHHHHHHHHHHHHHHHHHhHH
Confidence 66699999999988888778877778 578887777532 11222222 3334555555666544443332
Q ss_pred HHHH--hhhccCceeEEEe-ccccccCchhhhhhhceecCCCCchHHHHHHHhCceEEEe----------CcEEEEecCC
Q 017154 122 PQAI--KILDDEMQCDIIK-IGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQ----------GNTVAAMGSF 188 (376)
Q Consensus 122 EqAl--kLLeDDi~~dIId-I~~~v~nke~f~RrrgRIIG~~GkTkkaIE~LT~~~I~V~----------G~TVsIIG~~ 188 (376)
.++- .+|+--. -|-++ |+-++-|. -.|-|||++|.|.++|-+-++|+|.|+ ..-|-+.|.+
T Consensus 115 ~~~k~v~~~~pqt-~~r~kqikivvPNs-----tag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~ 188 (402)
T KOG2191|consen 115 AVAKPVDILQPQT-PDRIKQIKIVVPNS-----TAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEP 188 (402)
T ss_pred hhcCCccccCCCC-ccccceeEEeccCC-----cccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCH
Confidence 2221 1111000 11111 22222221 358899999999999999999999988 3347889999
Q ss_pred ccHHHHHHH-HHHHhcCCCCc
Q 017154 189 KGLKQVRRI-VEDCMQNKMHP 208 (376)
Q Consensus 189 ~~IkiAR~A-Ie~LI~Gs~Hp 208 (376)
+++..|-.. +..+-.- +|.
T Consensus 189 e~~~~A~~~IL~Ki~eD-pqs 208 (402)
T KOG2191|consen 189 EQNMKAVSLILQKIQED-PQS 208 (402)
T ss_pred HHHHHHHHHHHHHhhcC-Ccc
Confidence 887554444 4444444 553
No 42
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=84.96 E-value=0.47 Score=38.87 Aligned_cols=19 Identities=21% Similarity=0.426 Sum_probs=16.9
Q ss_pred hceecCCCCchHHHHHHHh
Q 017154 153 RQHLVGPNSSTLKALEILT 171 (376)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT 171 (376)
.||+||++|+|.+||=.+-
T Consensus 41 ~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 41 MGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred ccceecCCChhHHHHHHHH
Confidence 7999999999999997653
No 43
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=84.88 E-value=1.8 Score=42.34 Aligned_cols=119 Identities=18% Similarity=0.296 Sum_probs=73.7
Q ss_pred ceEEEEEcCcCeEEEEcCCCCCChh-HHHhHHHHHHHHhcCCC--hHHHHhhhc-cC-ceeEEEeccccc-----cCchh
Q 017154 79 GVSCELNLVEGSMTVSTTRKTRDPY-IIVKARDLIRLLSRSVP--APQAIKILD-DE-MQCDIIKIGNLV-----RNKER 148 (376)
Q Consensus 79 ~l~i~lDl~eGsV~V~Tt~kT~DP~-~IlKArD~IkAiaRGF~--~EqAlkLLe-DD-i~~dIIdI~~~v-----~nke~ 148 (376)
|.-+.+-.....|.|.+ || +++-+.++ +.|-|+ -.+--..|+ .| +++.|.++..-. .....
T Consensus 70 G~I~~v~~~~W~VDI~s------p~~A~L~ls~~---~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~ 140 (239)
T COG1097 70 GKIIEVGPSGWKVDIGS------PYPALLSLSDF---LRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEG 140 (239)
T ss_pred EEEEEEcccceEEEcCC------ccceEeehhhh---hcccccccccccccccccCCEEEEEEEEccCCCceEEEeecCC
Confidence 33444444455555543 22 34455555 556555 334445666 33 567776665321 12233
Q ss_pred hhhhh------------ceecCCCCchHHHHHHHhCceEEEeCcE-EEEecCCcc-HHHHHHHHHHHhcCCCC
Q 017154 149 FVKRR------------QHLVGPNSSTLKALEILTGCYILVQGNT-VAAMGSFKG-LKQVRRIVEDCMQNKMH 207 (376)
Q Consensus 149 f~Rrr------------gRIIG~~GkTkkaIE~LT~~~I~V~G~T-VsIIG~~~~-IkiAR~AIe~LI~Gs~H 207 (376)
+-+.+ =|+||++|+..+.|...|+|.|.|.=|- |.+=|.-+. ..+|-.||.+|=.- .|
T Consensus 141 ~GkL~~G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG~IWV~~~~~~~e~~~~~aI~~ie~e-a~ 212 (239)
T COG1097 141 LGKLKNGQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNGRIWVDGENESLEELAIEAIRKIERE-AH 212 (239)
T ss_pred CccccCCEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCCEEEecCCCcchHHHHHHHHHHHhhh-hh
Confidence 33333 2699999999999999999999998865 888888885 56777777666433 45
No 44
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=84.21 E-value=1.2 Score=45.45 Aligned_cols=121 Identities=20% Similarity=0.208 Sum_probs=74.2
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeC-----cEEEEec-CCccHHHHHHHHHHHh--cCCCCchhHHHHHHHHHhhhc
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQG-----NTVAAMG-SFKGLKQVRRIVEDCM--QNKMHPVYHIKILMVKKELEK 223 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G-----~TVsIIG-~~~~IkiAR~AIe~LI--~Gs~HpVY~ikelmiKreL~k 223 (376)
-.|-|||.+|+|++-||+-|+|.|.+-- .-|.|+| +-+++-.|.+=|.-+| .+..-|+-+++.+...
T Consensus 67 ~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~s~p~thflal~ln----- 141 (345)
T KOG2814|consen 67 FIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDSDRKSFPITHFLALPLN----- 141 (345)
T ss_pred HhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHhhhhcCchhhhhhhhcc-----
Confidence 4789999999999999999999999843 3355544 5567888888888888 4434567777776652
Q ss_pred Ccccccccccccc--hhhhccccccccccccCCCCCCCCCCCCCCchhhhhhhccccccChhHHHHHHH
Q 017154 224 DPALANENWDRFL--PKFKKKNVKQKKVKSKEKKPYTPFPPPPQPSKIDKLLESGEYFLSERKKESKKW 290 (376)
Q Consensus 224 d~~l~~e~W~rfl--P~fkk~~~~~~k~~~~~kk~~tpfpp~~~~~k~d~~~esgeyfl~~~~k~~~~~ 290 (376)
.-=-+|+..+|+ +-|...=. .-+....+|-+| +.+- |-=|-|-|-+...-.+..
T Consensus 142 -e~eVqe~f~~fke~~~~~esl~-------~~g~~~s~F~~p---~~~H--LTvgm~~L~~dd~vq~a~ 197 (345)
T KOG2814|consen 142 -EHEVQEGFLAFKELKPFIESLL-------DGGIDKSLFQGP---GTFH--LTVGMLKLLNDDDVQKAL 197 (345)
T ss_pred -hHHHHHHHHHHHhhhhhHHHhh-------ccchhhccccCC---ceee--EEEEEEEecChHHHHHHH
Confidence 111256666665 32221100 112344555433 3332 334666666665544443
No 45
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=83.88 E-value=0.91 Score=49.77 Aligned_cols=52 Identities=17% Similarity=0.293 Sum_probs=45.2
Q ss_pred hceecCCCCchHHHHHHHhCceEEEeC-cEEEEec-CCccHHHHHHHHHHHhcC
Q 017154 153 RQHLVGPNSSTLKALEILTGCYILVQG-NTVAAMG-SFKGLKQVRRIVEDCMQN 204 (376)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~~I~V~G-~TVsIIG-~~~~IkiAR~AIe~LI~G 204 (376)
++.+||++|+|.+.|..-||+.|-+.+ .+|.|.+ +-..+..|++.|..+...
T Consensus 565 I~~vIG~gg~~ik~I~~~~~~~idi~d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 565 IRDVIGPGGKTIREITEETGAKIDIEDDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred HHHHhcCCchhHHHHHHHHCCccccCCCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 689999999999999999999999987 5688888 456688999999888854
No 46
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=83.51 E-value=1.9 Score=44.18 Aligned_cols=48 Identities=27% Similarity=0.424 Sum_probs=44.9
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeCcEEEEecCCccHHHHHHHHH
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVE 199 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G~TVsIIG~~~~IkiAR~AIe 199 (376)
.-..|.|+.|..++.||...|+.|..-|+++.|+|....+..|++++.
T Consensus 25 ~~~~l~G~~~~~l~l~e~~~gv~i~~rG~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 25 ELVALFGPTDTNLSLLEIALGVSIVARGEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred hhhhhcCCCCccHHHHHHHhCcEEEeCCceEEEEechHHHHHHHHHHh
Confidence 356799999999999999999999999999999999889999999998
No 47
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=81.11 E-value=3.7 Score=39.10 Aligned_cols=62 Identities=21% Similarity=0.193 Sum_probs=49.5
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeCcE--EEEecC---Cc--cHHHHHHHHHHHhcCCCCc-hhHHH
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQGNT--VAAMGS---FK--GLKQVRRIVEDCMQNKMHP-VYHIK 213 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G~T--VsIIG~---~~--~IkiAR~AIe~LI~Gs~Hp-VY~ik 213 (376)
|.+=|||..|.+.++||..|+|.|.|+.++ |.|... .+ .+.-|++.|.-+=.|=.++ ...+|
T Consensus 18 R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~A~~LL 87 (194)
T COG1094 18 RIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKALKLL 87 (194)
T ss_pred hheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHHHHHHh
Confidence 677899999999999999999999999865 888765 23 3688999999888993333 55544
No 48
>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=75.18 E-value=5.4 Score=30.43 Aligned_cols=55 Identities=16% Similarity=0.237 Sum_probs=44.7
Q ss_pred eeecCcchHHHHHhhhHHHHHHH-hhcceEEEEEcCcCeEEEEcCCCCCChhHHHhHHHHH
Q 017154 53 STLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLI 112 (376)
Q Consensus 53 ~~lfPkyRe~yLKe~W~~I~k~L-e~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD~I 112 (376)
.+-+|+.+...|=.-=+...+.| +++++.+.++- +|.|.|.. .|+..+..|.++|
T Consensus 5 ~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-~g~v~I~G----~~~~~v~~A~~~I 60 (61)
T cd02393 5 TMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-DGTVYIAA----SDKEAAEKAKKMI 60 (61)
T ss_pred EEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-CCEEEEEe----CCHHHHHHHHHHh
Confidence 45678887777777777888888 67999999987 79999987 5678899998887
No 49
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=64.37 E-value=4 Score=44.72 Aligned_cols=52 Identities=19% Similarity=0.430 Sum_probs=46.2
Q ss_pred hceecCCCCchHHHHHHHhCceEEEeCcEEEEecCCcc-HHHHHHHHHHHhcC
Q 017154 153 RQHLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKG-LKQVRRIVEDCMQN 204 (376)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~~I~V~G~TVsIIG~~~~-IkiAR~AIe~LI~G 204 (376)
|.-||||+|..++-||.-||+.-.|++.|++|+-+-.. +..|++.|.-++.-
T Consensus 608 ~~~lIGp~G~~~kki~~EtGai~~vDe~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 608 RATLIGPGGVLKKKIEVETGAISQVDEGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred hheeecCccceeeeEeeeccceeeecCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 56799999999999999999999999999999987655 69999999888854
No 50
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=63.84 E-value=3.6 Score=36.76 Aligned_cols=26 Identities=12% Similarity=0.139 Sum_probs=23.7
Q ss_pred hhceecCCCCchHHHHHHHhCceEEE
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILV 177 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V 177 (376)
-.|+.||++|++.+++..|++-++-|
T Consensus 109 d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 109 DKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred ccchhhCCCCHHHHHHHHHhCCccCC
Confidence 37999999999999999999998866
No 51
>COG1159 Era GTPase [General function prediction only]
Probab=61.51 E-value=17 Score=36.80 Aligned_cols=62 Identities=21% Similarity=0.468 Sum_probs=41.1
Q ss_pred HHhHHHHHHHHhcCCChHHHHhhhccC----ceeEEEeccccccCchhhh-----------hhhceecCCCCchHHHH--
Q 017154 105 IVKARDLIRLLSRSVPAPQAIKILDDE----MQCDIIKIGNLVRNKERFV-----------KRRQHLVGPNSSTLKAL-- 167 (376)
Q Consensus 105 IlKArD~IkAiaRGF~~EqAlkLLeDD----i~~dIIdI~~~v~nke~f~-----------RrrgRIIG~~GkTkkaI-- 167 (376)
=+.|.++|+ |+++..|.|+ +..+|-+...- .+... ..+|=|||.+|.+++.|
T Consensus 189 rf~~aEiiR--------Ek~~~~l~eElPhsv~VeIe~~~~~---~~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~ 257 (298)
T COG1159 189 RFLAAEIIR--------EKLLLLLREELPHSVAVEIEEFEER---EKGLLKIHATIYVERESQKGIIIGKNGAMIKKIGT 257 (298)
T ss_pred HHHHHHHHH--------HHHHHhcccccCceEEEEEEEEEec---CCCeEEEEEEEEEecCCccceEECCCcHHHHHHHH
Confidence 445667776 9999999999 33566555542 11211 24778999999987776
Q ss_pred ------HHHhCceEEE
Q 017154 168 ------EILTGCYILV 177 (376)
Q Consensus 168 ------E~LT~~~I~V 177 (376)
|.+-+|.|.+
T Consensus 258 ~AR~~ie~l~~~kV~L 273 (298)
T COG1159 258 AARKDIEKLLGCKVYL 273 (298)
T ss_pred HHHHHHHHHhCCceEE
Confidence 6666666554
No 52
>TIGR00112 proC pyrroline-5-carboxylate reductase. This enzyme catalyzes the final step in proline biosynthesis. Among the four paralogs in Bacillus subtilis (proG, proH, proI, and comER), ComER is the most divergent and does not prevent proline auxotrophy from mutation of the other three. It is excluded from the seed and scores between the trusted and noise cutoffs.
Probab=59.13 E-value=8.9 Score=36.31 Aligned_cols=99 Identities=18% Similarity=0.271 Sum_probs=67.8
Q ss_pred hHHHHHHHhhcceEEEEEcCcCeEEEEcCCCCCChhHHH-hHHHHH-HHHhcCCChHHHHhhhccCceeEEEeccccc-c
Q 017154 68 WPMVKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIV-KARDLI-RLLSRSVPAPQAIKILDDEMQCDIIKIGNLV-R 144 (376)
Q Consensus 68 W~~I~k~Le~~~l~i~lDl~eGsV~V~Tt~kT~DP~~Il-KArD~I-kAiaRGF~~EqAlkLLeDDi~~dIIdI~~~v-~ 144 (376)
-..|...++..|..+.++ +..+.+-|.--.--|..+. =+..|+ .++..|++.++|.+|...=+. -...+. .
T Consensus 124 ~~~v~~lf~~~G~~~~v~--E~~~~~~talsgsgPA~~~~~~~al~~~~v~~Gl~~~~A~~lv~~~~~----G~a~l~~~ 197 (245)
T TIGR00112 124 RALVLALFKAVGEVVELP--EALMDAVTALSGSGPAYVFLFIEALADAGVKQGLPRELALELAAQTVK----GAAKLLEE 197 (245)
T ss_pred HHHHHHHHHhCCCEEEEC--HHHcchHHhhccCcHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH----HHHHHHHh
Confidence 356677778899988887 5666655543334554322 222333 467899999999999875421 011122 3
Q ss_pred CchhhhhhhceecCCCCchHHHHHHHhC
Q 017154 145 NKERFVKRRQHLVGPNSSTLKALEILTG 172 (376)
Q Consensus 145 nke~f~RrrgRIIG~~GkTkkaIE~LT~ 172 (376)
++.++...+.++.-|+|.|..+|+.|-.
T Consensus 198 ~~~~~~~l~~~v~spgGtT~~gl~~Le~ 225 (245)
T TIGR00112 198 SGEHPALLKDQVTSPGGTTIAGLAVLEE 225 (245)
T ss_pred cCCCHHHHHHcCCCCcHHHHHHHHHHHH
Confidence 5578999999999999999999998854
No 53
>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=58.57 E-value=32 Score=25.26 Aligned_cols=55 Identities=18% Similarity=0.135 Sum_probs=44.5
Q ss_pred eeecCcchHHHHHhhhHHHHHHH-hhcceEEEEEcC--cCeEEEEcCCCCCChhHHHhHHHHH
Q 017154 53 STLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLV--EGSMTVSTTRKTRDPYIIVKARDLI 112 (376)
Q Consensus 53 ~~lfPkyRe~yLKe~W~~I~k~L-e~~~l~i~lDl~--eGsV~V~Tt~kT~DP~~IlKArD~I 112 (376)
.+++|.....+|=.-=+..-+.| +++++.+.++-. ...|+|. .++..+..|+++|
T Consensus 3 ~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~-----G~~~~v~~A~~~I 60 (60)
T PF00013_consen 3 RIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTIS-----GSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEE-----ESHHHHHHHHHHH
T ss_pred EEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEE-----eCHHHHHHHHhhC
Confidence 57889999999999889988889 579999999765 3466664 4778999998876
No 54
>TIGR03278 methan_mark_10 putative methanogenesis marker protein 10. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The presence of motifs with seven invariant Cys residues in the N-terminal 50 residues, including three instances of CXXC, would be consistent with function as an oxidoreductase with FeS clusters. The exact function is unknown, but likely is linked to methanogenesis. In most genomes, the member of this family is encoded by a gene next to, and divergently transcribed from, the methyl coenzyme M reductase operon.
Probab=57.45 E-value=50 Score=34.41 Aligned_cols=139 Identities=15% Similarity=0.112 Sum_probs=80.4
Q ss_pred CcCeEEEEcCCCCCChhHHHhHHHHHHHHhc-C------------C-ChHHHHhhhccCceeEEEeccccccCchhhhhh
Q 017154 87 VEGSMTVSTTRKTRDPYIIVKARDLIRLLSR-S------------V-PAPQAIKILDDEMQCDIIKIGNLVRNKERFVKR 152 (376)
Q Consensus 87 ~eGsV~V~Tt~kT~DP~~IlKArD~IkAiaR-G------------F-~~EqAlkLLeDDi~~dIIdI~~~v~nke~f~Rr 152 (376)
..|.|++.+ ..+|..---..++++++.. | + +.+.+-+|++-.+..-.|+|..+ +.+ .
T Consensus 73 ~~ggVtisG---GGepl~~~~l~eLl~~lk~~gi~taI~~TnG~~l~~~e~~~~L~~~gld~v~iSvka~--dpe----~ 143 (404)
T TIGR03278 73 RDTKVTISG---GGDVSCYPELEELTKGLSDLGLPIHLGYTSGKGFDDPEIAEFLIDNGVREVSFTVFAT--DPE----L 143 (404)
T ss_pred CCCEEEEEC---CcccccCHHHHHHHHHHHhCCCCEEEeCCCCcccCCHHHHHHHHHcCCCEEEEecccC--CHH----H
Confidence 367888887 3566554444555555543 2 3 45556666654444444555554 222 3
Q ss_pred hceecC-CC-CchHHHHHHHhCceEEEeCcEEEEecCCccHHHHHHHHHHHh-cCCCCc--h--hHHHHHHHHHhhhcCc
Q 017154 153 RQHLVG-PN-SSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDCM-QNKMHP--V--YHIKILMVKKELEKDP 225 (376)
Q Consensus 153 rgRIIG-~~-GkTkkaIE~LT~~~I~V~G~TVsIIG~~~~IkiAR~AIe~LI-~Gs~Hp--V--Y~ikelmiKreL~kd~ 225 (376)
+.+++| ++ +..+.+|+.+.. .+.|....|.|=|--++-... ++|..+. .| ++| + ||.+.. .|=-|...+
T Consensus 144 h~kl~G~~~a~~ILe~L~~L~e-~~~v~~~ivlIPGiND~eel~-~ti~~L~~lg-~~~V~L~~y~~~g~-~ky~lg~~~ 219 (404)
T TIGR03278 144 RREWMKDPTPEASLQCLRRFCE-SCEVHAASVIIPGVNDGDVLW-KTCADLESWG-AKALILMRFANTEE-QGLILGNAP 219 (404)
T ss_pred HHHHhCCCCHHHHHHHHHHHHh-cCCEEEEEEEeCCccCcHHHH-HHHHHHHHCC-CCEEEEEecccccc-cccccCCcC
Confidence 444666 34 689999999998 588888888888877766654 6666665 35 555 2 332100 000122233
Q ss_pred c---cccccccccchh
Q 017154 226 A---LANENWDRFLPK 238 (376)
Q Consensus 226 ~---l~~e~W~rflP~ 238 (376)
. ...++|++|+..
T Consensus 220 ~~~~~~~~~~~e~~~~ 235 (404)
T TIGR03278 220 IIPGIKPHTVSEFKNI 235 (404)
T ss_pred cccCCCCCCHHHHHHH
Confidence 2 346788887755
No 55
>PRK15494 era GTPase Era; Provisional
Probab=55.57 E-value=23 Score=35.36 Aligned_cols=55 Identities=20% Similarity=0.254 Sum_probs=33.9
Q ss_pred HHHHhhhccCce----eEEEeccccccCchhh----------hhhhceecCCCCchHHHH--------HHHhCceEEEe
Q 017154 122 PQAIKILDDEMQ----CDIIKIGNLVRNKERF----------VKRRQHLVGPNSSTLKAL--------EILTGCYILVQ 178 (376)
Q Consensus 122 EqAlkLLeDDi~----~dIIdI~~~v~nke~f----------~RrrgRIIG~~GkTkkaI--------E~LT~~~I~V~ 178 (376)
|+++..|++++= +.|-...+-. + +.+ ...++=|||.+|++++.| |.+.||.|.+.
T Consensus 242 e~~~~~~~~EiP~~~~v~i~~~~~~~-~-~~~~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 242 EQLFLNLQKELPYKLTVQTEKWEDLK-D-KSVKINQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred HHHHhhCCcccCceEEEEEEEEEEcC-C-CeEEEEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 788888988832 3332222110 0 111 234788999999987765 77888877653
No 56
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=55.42 E-value=13 Score=38.47 Aligned_cols=53 Identities=25% Similarity=0.426 Sum_probs=39.9
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEe-------CcE--EEE-ecCCccHHHHHHHHHHHhcC
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQ-------GNT--VAA-MGSFKGLKQVRRIVEDCMQN 204 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~-------G~T--VsI-IG~~~~IkiAR~AIe~LI~G 204 (376)
+-|-|||++|.|...|..-|||+|-+- |.| |++ -|+.+.|..|.+-|.|-|.-
T Consensus 49 AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire 111 (402)
T KOG2191|consen 49 AAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIRE 111 (402)
T ss_pred cccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHH
Confidence 468899999999999999999999875 333 554 57777777666666555543
No 57
>PRK10076 pyruvate formate lyase II activase; Provisional
Probab=55.23 E-value=82 Score=29.81 Aligned_cols=106 Identities=8% Similarity=0.007 Sum_probs=59.1
Q ss_pred EcCcCeEEEEcCCCCCChhHHHhHHHHHHHH-hc---------CCChHHHHh-hhccCceeEEEeccccccCchhhhhhh
Q 017154 85 NLVEGSMTVSTTRKTRDPYIIVKARDLIRLL-SR---------SVPAPQAIK-ILDDEMQCDIIKIGNLVRNKERFVKRR 153 (376)
Q Consensus 85 Dl~eGsV~V~Tt~kT~DP~~IlKArD~IkAi-aR---------GF~~EqAlk-LLeDDi~~dIIdI~~~v~nke~f~Rrr 153 (376)
+...|.|++..+..+--|-.+ .++++++ .. |+-+..++. |+. -+.+-.+||+.+- .+...+.-
T Consensus 36 ~~sggGVt~SGGEPllq~~fl---~~l~~~~k~~gi~~~leTnG~~~~~~~~~l~~-~~D~~l~DiK~~d--~~~~~~~t 109 (213)
T PRK10076 36 RTSGGGVTLSGGEVLMQAEFA---TRFLQRLRLWGVSCAIETAGDAPASKLLPLAK-LCDEVLFDLKIMD--ATQARDVV 109 (213)
T ss_pred cCCCCEEEEeCchHHcCHHHH---HHHHHHHHHcCCCEEEECCCCCCHHHHHHHHH-hcCEEEEeeccCC--HHHHHHHH
Confidence 345689999874444333222 3444443 22 333444444 544 3445667777652 23333333
Q ss_pred ceecCCCCchHHHHHHHhCceEEEeCcEEEEecCCccHHHHHHHHH
Q 017154 154 QHLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVE 199 (376)
Q Consensus 154 gRIIG~~GkTkkaIE~LT~~~I~V~G~TVsIIG~~~~IkiAR~AIe 199 (376)
| +.++.++..|+.+...-+-|.=.|+.|=|-.++.+..+.++.
T Consensus 110 G---~~~~~il~nl~~l~~~g~~v~iR~~vIPg~nd~~e~i~~ia~ 152 (213)
T PRK10076 110 K---MNLPRVLENLRLLVSEGVNVIPRLPLIPGFTLSRENMQQALD 152 (213)
T ss_pred C---CCHHHHHHHHHHHHhCCCcEEEEEEEECCCCCCHHHHHHHHH
Confidence 4 556788888888877655554467777775566665555443
No 58
>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=54.37 E-value=31 Score=38.70 Aligned_cols=81 Identities=11% Similarity=0.168 Sum_probs=62.1
Q ss_pred eeeecCcchHHHHHhhhHHHHHHH-hhcceEEEEEcCcCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCChHHHHhhhcc
Q 017154 52 FSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDD 130 (376)
Q Consensus 52 f~~lfPkyRe~yLKe~W~~I~k~L-e~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD~IkAiaRGF~~EqAlkLLeD 130 (376)
..+-+|+.+..-|-.-=+.+-+.| +++|++|.++- +|.|.|.. .|.-.+.+|.++|+.|...|.|+ ..+
T Consensus 580 ~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-~G~V~I~a----~d~~~~~~A~~~I~~i~~~~~~~-----vG~ 649 (719)
T TIGR02696 580 ITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-DGTVYIGA----ADGPSAEAARAMINAIANPTMPE-----VGE 649 (719)
T ss_pred EEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-CcEEEEEe----CCHHHHHHHHHHHHHhhCcCcCC-----CCC
Confidence 356789988888877777777777 78999999995 89999987 77889999999999999974433 223
Q ss_pred CceeEEEecccc
Q 017154 131 EMQCDIIKIGNL 142 (376)
Q Consensus 131 Di~~dIIdI~~~ 142 (376)
-+...|.+|.++
T Consensus 650 i~~GkV~~I~df 661 (719)
T TIGR02696 650 RFLGTVVKTTAF 661 (719)
T ss_pred EEEEEEEEEECc
Confidence 344566666554
No 59
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=50.33 E-value=2.1e+02 Score=26.33 Aligned_cols=110 Identities=13% Similarity=0.203 Sum_probs=70.7
Q ss_pred HhhcceEEEEEcCcCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCChHHHHhhhccCceeEEEeccccccCchhhhhhhc
Q 017154 75 LKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEMQCDIIKIGNLVRNKERFVKRRQ 154 (376)
Q Consensus 75 Le~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD~IkAiaRGF~~EqAlkLLeDDi~~dIIdI~~~v~nke~f~Rrrg 154 (376)
+..+|..|++....+.|.|+.++. .+--+.+-|.-+. ..+..+.|++..+... +.....
T Consensus 52 ~~~~~~~I~~~~~~~~i~I~g~k~-----~~~~i~~~i~~~l-------------~~i~~~~i~l~~~~~~---~~~~~~ 110 (210)
T PF14611_consen 52 AARNGAKIEVSRSENRIRITGTKS-----TAEYIEASINEIL-------------SNIRTEEIDLSPIISK---HSEKKN 110 (210)
T ss_pred HHhcCceEEEecCCcEEEEEccHH-----HHHHHHHHHHHHH-------------hhcEEEEEecchhhhh---hccccc
Confidence 467899999999999999987553 2222222222111 3456778888876431 111111
Q ss_pred eecCCCCchHHHHHHHhCceEEEeCcE--EEEe-----cCCccHHHHHHHHHHHhcCCCC
Q 017154 155 HLVGPNSSTLKALEILTGCYILVQGNT--VAAM-----GSFKGLKQVRRIVEDCMQNKMH 207 (376)
Q Consensus 155 RIIG~~GkTkkaIE~LT~~~I~V~G~T--VsII-----G~~~~IkiAR~AIe~LI~Gs~H 207 (376)
+ --....+..|..+|+|||-..++. +.|. -.-..+..|++-+.-.+...+|
T Consensus 111 ~--~~~~~~l~~i~~~t~~~ie~~~~~~~~~i~~~~~~~~~~~~~~a~RlL~~a~~~~~~ 168 (210)
T PF14611_consen 111 S--QFTPDLLEEIQKLTNVYIEKNPDGNKLKISWLASPENEKRADRAKRLLLWALDYNPH 168 (210)
T ss_pred c--cccHHHHHHHHHHHcEEEEECCCCCeEEEEEEeeccccchHHHHHHHHHHhccCCcc
Confidence 2 123567889999999999988755 4444 3456689999988888864355
No 60
>TIGR02517 type_II_gspD general secretion pathway protein D. In Gram-negative bacteria, proteins that have first crossed the inner member by Sec-dependent protein transport can be exported across the outer membrane by type II secretion, also called the main terminal branch of the general secretion pathway. Members of this family are general secretion pathway protein D. In Yersinia enterocolitica, a second member of this family is part of a novel second type II secretion system specifically associated with virulence (See PubMed:12654803). This family is closely homologous to the type IV pilus outer membrane secretin PilQ (TIGR02515) and to the type III secretion system pore YscC/HrcC (TIGR02516).
Probab=50.19 E-value=1.3e+02 Score=32.16 Aligned_cols=128 Identities=15% Similarity=0.126 Sum_probs=69.8
Q ss_pred hhHHHHHHH-hhcceEEEEEcC-cCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCChHHHHhhhccCceeEEEecccccc
Q 017154 67 AWPMVKGAL-KEYGVSCELNLV-EGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEMQCDIIKIGNLVR 144 (376)
Q Consensus 67 ~W~~I~k~L-e~~~l~i~lDl~-eGsV~V~Tt~kT~DP~~IlKArD~IkAiaRGF~~EqAlkLLeDDi~~dIIdI~~~v~ 144 (376)
.|..|-+.+ +.+|+.+-+|.. .|.|++++ .+|...-.|.+++..+.+... +.+.+++-.+-|+.......
T Consensus 7 ~l~~vl~~~~~~~g~n~vid~~v~g~vtl~~----~~~v~~~eal~~l~~lL~~~g----l~~~~~g~~~~I~~~~~~~~ 78 (594)
T TIGR02517 7 DISTVVKAISDLTGKNFIIDPRVKGKITIIS----PRPVTEDEAYQLFLSALRAQG----FAVVPEGNGYKIVVPRAAAK 78 (594)
T ss_pred cHHHHHHHHHHHhCCeEEECCCCceEEEEEe----CCCCCHHHHHHHHHHHHHhCC----eEEEEeCCcEEEeCchHhcc
Confidence 456666666 679999999865 89999997 556666677777666544222 22333332222222211110
Q ss_pred -Cchhhhh----------hhceecCC-C---CchHHHHHHHh--CceEEEeC--cEEEEecCCccHHHHHHHHHHHh
Q 017154 145 -NKERFVK----------RRQHLVGP-N---SSTLKALEILT--GCYILVQG--NTVAAMGSFKGLKQVRRIVEDCM 202 (376)
Q Consensus 145 -nke~f~R----------rrgRIIG~-~---GkTkkaIE~LT--~~~I~V~G--~TVsIIG~~~~IkiAR~AIe~LI 202 (376)
....+.+ ..-|++=- . ......|+.+. ++.|.+.. +.|.|.|+...+..+++.|..+=
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~vi~L~~~~a~~v~~~L~~lls~~~~v~~d~~~N~liv~~~~~~l~~i~~li~~lD 155 (594)
T TIGR02517 79 LSPGPIEDGPAPGVGGDQFVTRVFPLRNISASELVPVLRPLVSPNGDVAAYPPTNTIVVTDYASNINRVARIIQQLD 155 (594)
T ss_pred cCCCccccCCCCCCCCCceEEEEEEeccCCHHHHHHHHHHhcCCCceEEEcCCCCEEEEEcCHHHHHHHHHHHHHhc
Confidence 0000000 00011100 0 11223333332 35677776 67999999999999998877653
No 61
>PF05598 DUF772: Transposase domain (DUF772); InterPro: IPR008490 This presumed domain is found at the N terminus of transposase insH and other related transposases.
Probab=49.87 E-value=17 Score=28.07 Aligned_cols=61 Identities=18% Similarity=0.319 Sum_probs=47.1
Q ss_pred CCCCChhHHHhHHHHHHHHhcCC-ChHHHHhhhccCc----eeEEEeccccccCchhhhhhhceecCCC
Q 017154 97 RKTRDPYIIVKARDLIRLLSRSV-PAPQAIKILDDEM----QCDIIKIGNLVRNKERFVKRRQHLVGPN 160 (376)
Q Consensus 97 ~kT~DP~~IlKArD~IkAiaRGF-~~EqAlkLLeDDi----~~dIIdI~~~v~nke~f~RrrgRIIG~~ 160 (376)
+...+|..++++ +|=+...|+ |..+....+.+++ +|. +++.+-+-+..-|.+-|.|+...+
T Consensus 2 Rp~~~~~~ml~~--ll~~~~~~~~S~r~l~~~l~~~~~~r~~~g-~~~~~~~pd~stl~rfr~rl~~~~ 67 (77)
T PF05598_consen 2 RPAYPPRMMLKA--LLLKYLFGLRSDRELEERLRDNLSFRYFCG-LSLEEPVPDHSTLSRFRKRLIQHG 67 (77)
T ss_pred cCCCCHHHHHHH--HHHHHHHhcchHHHHHhhHhhhhHHHHHHh-cccCCCCCChHHHHHHHHHHhhcc
Confidence 347899888888 555566798 9999999999883 488 777766666678888898888654
No 62
>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=48.92 E-value=32 Score=24.97 Aligned_cols=56 Identities=21% Similarity=0.199 Sum_probs=43.0
Q ss_pred eeeecCcchHHHHHhhhHHHHHHH-hhcceEEEEEcC-----cCeEEEEcCCCCCChhHHHhHHHHH
Q 017154 52 FSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLV-----EGSMTVSTTRKTRDPYIIVKARDLI 112 (376)
Q Consensus 52 f~~lfPkyRe~yLKe~W~~I~k~L-e~~~l~i~lDl~-----eGsV~V~Tt~kT~DP~~IlKArD~I 112 (376)
..+.+|.....+|-.-=+..-+.| +++++.+.++.. ...|.|..+ +..+..|..+|
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 357788888888888888888889 478999999875 456676653 67888888776
No 63
>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=47.34 E-value=2.7 Score=32.91 Aligned_cols=24 Identities=13% Similarity=0.148 Sum_probs=19.1
Q ss_pred hhceecCCCCchHHHHHHHhCceE
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYI 175 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I 175 (376)
..|.+||++|++++.|....+-.+
T Consensus 35 ~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 35 QPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CccHhHHhhhHHHHHHHHHHHHHH
Confidence 589999999999999866554444
No 64
>PRK07680 late competence protein ComER; Validated
Probab=46.21 E-value=22 Score=33.80 Aligned_cols=96 Identities=9% Similarity=0.118 Sum_probs=60.0
Q ss_pred hHHHHHHHhhcceEEEEEcCcCeEEEEcCCCCCChhHHHhHHH-HHHH-Hh-cCCChHHHHhhhccCce--eEEEecccc
Q 017154 68 WPMVKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARD-LIRL-LS-RSVPAPQAIKILDDEMQ--CDIIKIGNL 142 (376)
Q Consensus 68 W~~I~k~Le~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD-~IkA-ia-RGF~~EqAlkLLeDDi~--~dIIdI~~~ 142 (376)
...+...|+..|..+.++ +..+.+-|.--.--|..+.-.-+ |+.+ +. .||+.++|..++-+=+. ... +
T Consensus 141 ~~~~~~ll~~~G~~~~i~--e~~~~~~~~l~gs~pa~~~~~~~al~~~~~~~~Gl~~~~a~~~~~~~~~G~~~l-----~ 213 (273)
T PRK07680 141 QQKLERLFSNISTPLVIE--EDITRVSSDIVSCGPAFFSYLLQRFIDAAVEETNISKEEATTLASEMLIGMGKL-----L 213 (273)
T ss_pred HHHHHHHHHcCCCEEEEC--hHhcchhhhhccchHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHH-----H
Confidence 345666667788777776 34343333222233433333222 4433 44 59999999998874321 111 1
Q ss_pred ccCchhhhhhhceecCCCCchHHHHHHH
Q 017154 143 VRNKERFVKRRQHLVGPNSSTLKALEIL 170 (376)
Q Consensus 143 v~nke~f~RrrgRIIG~~GkTkkaIE~L 170 (376)
..++.++.-.+.++.-|+|.|..+|+.|
T Consensus 214 ~~~~~~~~~l~~~v~spgG~T~~gl~~l 241 (273)
T PRK07680 214 EKGLYTLPTLQEKVCVKGGITGEGIKVL 241 (273)
T ss_pred HhcCCCHHHHHHhCCCCChhHHHHHHHH
Confidence 2355799999999999999999999876
No 65
>PRK00648 Maf-like protein; Reviewed
Probab=46.15 E-value=51 Score=30.79 Aligned_cols=54 Identities=15% Similarity=0.124 Sum_probs=36.4
Q ss_pred CchHHHHHHHhCceEEEeCcEEE-----EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 161 SSTLKALEILTGCYILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 161 GkTkkaIE~LT~~~I~V~G~TVs-----IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
++.....+.+..-.|+|...||. |+|.+.+.+.|++-+..| .|+.|-||.-..+
T Consensus 53 ~Ka~~v~~~~~~~~~VI~aDTvV~~~g~ilgKP~~~~eA~~~L~~l-sG~~h~v~T~v~l 111 (191)
T PRK00648 53 LKAEAVRSDLFPDELIITADTIVWYDGKVLGKPKDEEEAVEMLRTL-SGKTHEVITGVCL 111 (191)
T ss_pred HHHHHHHHhhCCCCEEEEeCeEEEECCEEeCCCCCHHHHHHHHHHh-CCCCeEEEEEEEE
Confidence 34444444332334666666654 689999999999988777 6879987766554
No 66
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=43.51 E-value=17 Score=38.87 Aligned_cols=32 Identities=13% Similarity=0.217 Sum_probs=28.9
Q ss_pred hhhhceecCCCCchHHHHHHHhCceEEEeCcE
Q 017154 150 VKRRQHLVGPNSSTLKALEILTGCYILVQGNT 181 (376)
Q Consensus 150 ~RrrgRIIG~~GkTkkaIE~LT~~~I~V~G~T 181 (376)
....|.|||++|+..-.|..+||+.|.|++..
T Consensus 346 s~~igciiGk~G~~iseir~~tgA~I~I~~~~ 377 (485)
T KOG2190|consen 346 SDLIGCIIGKGGAKISEIRQRTGASISILNKE 377 (485)
T ss_pred ccccceeecccccchHHHHHhcCCceEEcccc
Confidence 34789999999999999999999999998855
No 67
>PRK06928 pyrroline-5-carboxylate reductase; Reviewed
Probab=41.22 E-value=69 Score=30.84 Aligned_cols=96 Identities=14% Similarity=0.269 Sum_probs=62.9
Q ss_pred HHHHHHHhhcceEEEEEcCcCeEEEEcCCCCCChhHHHh-HHHHHH-HHhc-CCChHHHHhhhccCceeEEEeccccc-c
Q 017154 69 PMVKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVK-ARDLIR-LLSR-SVPAPQAIKILDDEMQCDIIKIGNLV-R 144 (376)
Q Consensus 69 ~~I~k~Le~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlK-ArD~Ik-AiaR-GF~~EqAlkLLeDDi~~dIIdI~~~v-~ 144 (376)
..|...++..|....++ +..+.+-|.--.--|..+.- +.-|+. ++.. |++.++|.++.-.=+. --..+. .
T Consensus 145 ~~v~~l~~~~G~~~~v~--E~~~d~~tal~gsgPA~~~~~~~al~~a~~~~ggl~~~~a~~l~~~~~~----G~a~l~~~ 218 (277)
T PRK06928 145 SRLEETLSHFSHVMTIR--EENMDIASNLTSSSPGFIAAIFEEFAEAAVRNSSLSDEEAFQFLNFALA----GTGKLLVE 218 (277)
T ss_pred HHHHHHHHhCCCEEEEc--hhhCceeeeeecCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH----HHHHHHHc
Confidence 35566668889999887 45565555444455544432 223443 3333 6999999998874421 000111 3
Q ss_pred CchhhhhhhceecCCCCchHHHHHHH
Q 017154 145 NKERFVKRRQHLVGPNSSTLKALEIL 170 (376)
Q Consensus 145 nke~f~RrrgRIIG~~GkTkkaIE~L 170 (376)
++.|+.-.|.++.-|+|.|..+|+.|
T Consensus 219 ~~~~p~~l~~~v~spgGtT~~gl~~l 244 (277)
T PRK06928 219 EDYTFSGTIERVATKGGITAEGAEVI 244 (277)
T ss_pred cCCCHHHHHHhCCCCChHHHHHHHHH
Confidence 45789999999999999999999876
No 68
>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=40.27 E-value=53 Score=24.22 Aligned_cols=55 Identities=15% Similarity=0.166 Sum_probs=41.6
Q ss_pred eeecCcchHHHHHhhhHHHHHHH-hhcceEEEEEcC---cCeEEEEcCCCCCChhHHHhHHHHH
Q 017154 53 STLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLV---EGSMTVSTTRKTRDPYIIVKARDLI 112 (376)
Q Consensus 53 ~~lfPkyRe~yLKe~W~~I~k~L-e~~~l~i~lDl~---eGsV~V~Tt~kT~DP~~IlKArD~I 112 (376)
.+.+|.....+|=.-=+...+.| +++++.+.+... ++.|+|..+ +..+..|.++|
T Consensus 3 ~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-----~~~v~~A~~~i 61 (62)
T cd02394 3 EVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP-----KENVEKAKEEI 61 (62)
T ss_pred EEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC-----HHHHHHHHHHh
Confidence 45677777777777776777777 679999998875 689999763 56888887765
No 69
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=39.36 E-value=53 Score=24.42 Aligned_cols=32 Identities=22% Similarity=0.142 Sum_probs=28.2
Q ss_pred CCCChhHHHhHHHHHHHHhcCCChHHHHhhhc
Q 017154 98 KTRDPYIIVKARDLIRLLSRSVPAPQAIKILD 129 (376)
Q Consensus 98 kT~DP~~IlKArD~IkAiaRGF~~EqAlkLLe 129 (376)
..+++-.+...+.+..+...|||++++.++|+
T Consensus 37 r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~~ 68 (68)
T cd01104 37 RLYSEADVARLRLIRRLTSEGVRISQAAALAL 68 (68)
T ss_pred eecCHHHHHHHHHHHHHHHCCCCHHHHHHHhC
Confidence 35778899999999999999999999999874
No 70
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=39.21 E-value=67 Score=29.53 Aligned_cols=65 Identities=17% Similarity=0.126 Sum_probs=51.2
Q ss_pred hceecCCCCchHHHHHHHhCceEEEeC--cEEEEecCCccHHHHHHHHHHHhcCCCCc---hhHHHHHHH
Q 017154 153 RQHLVGPNSSTLKALEILTGCYILVQG--NTVAAMGSFKGLKQVRRIVEDCMQNKMHP---VYHIKILMV 217 (376)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~~I~V~G--~TVsIIG~~~~IkiAR~AIe~LI~Gs~Hp---VY~ikelmi 217 (376)
.-=|.+.+|..+..|-...||.|-|.. +.|.|-|+-..+..|...|..++.+..+- ++.+...+.
T Consensus 37 ~~LLl~~~~~~L~~l~~~~~~~I~~~~~~~~i~I~g~k~~~~~i~~~i~~~l~~i~~~~i~l~~~~~~~~ 106 (210)
T PF14611_consen 37 FFLLLTGNGRILENLAARNGAKIEVSRSENRIRITGTKSTAEYIEASINEILSNIRTEEIDLSPIISKHS 106 (210)
T ss_pred eeeeecCCchHHHHHHHhcCceEEEecCCcEEEEEccHHHHHHHHHHHHHHHhhcEEEEEecchhhhhhc
Confidence 445778899999888555699999955 68999999999999999999999984442 665554443
No 71
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=38.53 E-value=1.3e+02 Score=21.97 Aligned_cols=31 Identities=29% Similarity=0.270 Sum_probs=24.1
Q ss_pred hhHHHHHHHh-hcce-EEEEEcCcCeEEEEcCC
Q 017154 67 AWPMVKGALK-EYGV-SCELNLVEGSMTVSTTR 97 (376)
Q Consensus 67 ~W~~I~k~Le-~~~l-~i~lDl~eGsV~V~Tt~ 97 (376)
|=..|.++|. .-|+ .+.+|+.++.|+|....
T Consensus 12 C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~ 44 (62)
T PF00403_consen 12 CAKKVEKALSKLPGVKSVKVDLETKTVTVTYDP 44 (62)
T ss_dssp HHHHHHHHHHTSTTEEEEEEETTTTEEEEEEST
T ss_pred HHHHHHHHHhcCCCCcEEEEECCCCEEEEEEec
Confidence 3456888884 4576 58999999999998743
No 72
>PRK04056 Maf-like protein; Reviewed
Probab=38.18 E-value=51 Score=30.59 Aligned_cols=40 Identities=18% Similarity=0.190 Sum_probs=30.4
Q ss_pred EEEeCcEEE-----EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 175 ILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 175 I~V~G~TVs-----IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|...||. |+|.+.+.+.|++-+..| .|+.|-||.-..+
T Consensus 63 ~vI~aDTvV~~~g~ilgKP~~~~eA~~~L~~l-sg~~h~V~T~v~l 107 (180)
T PRK04056 63 NLLVADSVVSCGNKILRKAKDKEEAREMLKLQ-SGNEISVLTCMIL 107 (180)
T ss_pred EEEEeCEEEEECCEEecCCCCHHHHHHHHHHH-CCCcEEEEEEEEE
Confidence 555555544 789999999999988766 7879987766555
No 73
>COG0424 Maf Nucleotide-binding protein implicated in inhibition of septum formation [Cell division and chromosome partitioning]
Probab=36.21 E-value=55 Score=31.16 Aligned_cols=56 Identities=16% Similarity=0.255 Sum_probs=43.5
Q ss_pred CCchHHHHHHHh-CceEEEeCcEEEE----ecCCccHHHHHHHHHHHhcCCCCchhHHHHHH
Q 017154 160 NSSTLKALEILT-GCYILVQGNTVAA----MGSFKGLKQVRRIVEDCMQNKMHPVYHIKILM 216 (376)
Q Consensus 160 ~GkTkkaIE~LT-~~~I~V~G~TVsI----IG~~~~IkiAR~AIe~LI~Gs~HpVY~ikelm 216 (376)
..++..+.+.+. +|-|+-.|..|++ +|.+.+.+.|++-+..| .|+.|-||.-..++
T Consensus 51 ~~KA~~va~~~~~~~~VigaDtvv~ldgrilgKP~~~~eA~~~L~~l-SG~~h~v~T~v~li 111 (193)
T COG0424 51 EEKARAVAARLPPDALVIGADTVVVLDGRILGKPKDEEEAREMLRKL-SGRTHQVYTGVALI 111 (193)
T ss_pred HHHHHHHHHhCCCCCEEEecCeEEEECCEEecCCCCHHHHHHHHHHh-cCCeEEEEEEEEEE
Confidence 367778888887 8888877777774 78888899888777665 89899988765554
No 74
>PRK01526 Maf-like protein; Reviewed
Probab=36.13 E-value=58 Score=30.92 Aligned_cols=40 Identities=20% Similarity=0.323 Sum_probs=30.2
Q ss_pred EEEeCcEEE-----EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 175 ILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 175 I~V~G~TVs-----IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|...||. |+|.+.+.+.|++-+..| .|+.|-||.-.-+
T Consensus 72 ~VI~aDTvV~~~g~IlgKP~~~~eA~~mL~~l-sG~~h~V~Tgv~l 116 (205)
T PRK01526 72 IIIAADTVAAVGRRILPKATTYEEVKNCIKML-SGRRHRVYTGLCI 116 (205)
T ss_pred EEEEeCeEEEECCEEecCCCCHHHHHHHHHHh-CCCCeEEEEEEEE
Confidence 555555544 799999999999988777 7889987765544
No 75
>PF14748 P5CR_dimer: Pyrroline-5-carboxylate reductase dimerisation; PDB: 2RCY_D 3TRI_A 2IZZ_B 2GR9_B 2GRA_B 2GER_C 1YQG_A 2AG8_A 3GT0_A 2AMF_E ....
Probab=35.72 E-value=10 Score=31.96 Aligned_cols=55 Identities=18% Similarity=0.353 Sum_probs=37.7
Q ss_pred HHhcCCChHHHHhhhccCceeEEEeccccc-cCchhhhhhhceecCCCCchHHHHHHHhC
Q 017154 114 LLSRSVPAPQAIKILDDEMQCDIIKIGNLV-RNKERFVKRRQHLVGPNSSTLKALEILTG 172 (376)
Q Consensus 114 AiaRGF~~EqAlkLLeDDi~~dIIdI~~~v-~nke~f~RrrgRIIG~~GkTkkaIE~LT~ 172 (376)
++..|++.++|.+|.-.-+. --..+. .++.++...+.++.-|+|.|..+|+.|-.
T Consensus 31 ~v~~Gl~~~~A~~lv~~t~~----G~a~ll~~~~~~~~~l~~~v~tPgG~T~~gl~~L~~ 86 (107)
T PF14748_consen 31 AVAQGLPREEARKLVAQTFI----GAAKLLEESGRSPAELRDEVTTPGGTTIAGLEVLEK 86 (107)
T ss_dssp HHHTT--HHHHHHHHHHHHH----HHHHHHHHCSS-HHHHHHHHS-TTSHHHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHHHHHHH----HHHHHHHccCCCHHHHhhhccCCCCcHHHHHHHHHH
Confidence 57799999999998864321 111222 24569999999999999999999998753
No 76
>PRK11145 pflA pyruvate formate lyase-activating enzyme 1; Provisional
Probab=35.43 E-value=2.3e+02 Score=26.40 Aligned_cols=107 Identities=14% Similarity=0.017 Sum_probs=56.7
Q ss_pred CeEEEEcCCCCCChhHHHhHHHHHHHHh-------cCCCh---HHHHhhhccCceeEEEeccccccCchhhhhhhceecC
Q 017154 89 GSMTVSTTRKTRDPYIIVKARDLIRLLS-------RSVPA---PQAIKILDDEMQCDIIKIGNLVRNKERFVKRRQHLVG 158 (376)
Q Consensus 89 GsV~V~Tt~kT~DP~~IlKArD~IkAia-------RGF~~---EqAlkLLeDDi~~dIIdI~~~v~nke~f~RrrgRIIG 158 (376)
+.|++.....|-+|..+......++..+ -|+.+ +.+-.++. .+.+-.|+|..+. .+.+.+.+|.
T Consensus 72 ~~V~~sGGEPll~~~~~~~l~~~~k~~g~~i~l~TNG~~~~~~~~~~~ll~-~~d~v~islk~~~--~e~~~~~~g~--- 145 (246)
T PRK11145 72 GGVTASGGEAILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLD-VTDLVMLDLKQMN--DEIHQNLVGV--- 145 (246)
T ss_pred CeEEEeCccHhcCHHHHHHHHHHHHHcCCCEEEECCCCCCcchHHHHHHHH-hCCEEEECCCcCC--hhhcccccCC---
Confidence 4577765444444444433333333321 25532 44444443 2223456776653 2333344442
Q ss_pred CCCchHHHHHHHhCceEEEeCcEEEEecCCccHHHHHHHHHHH
Q 017154 159 PNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDC 201 (376)
Q Consensus 159 ~~GkTkkaIE~LT~~~I~V~G~TVsIIG~~~~IkiAR~AIe~L 201 (376)
.+..++.+|+.+....+-|.-.++.+-|-.+..+.+++.+.-|
T Consensus 146 ~~~~~l~~i~~l~~~g~~v~i~~~li~g~nd~~~ei~~l~~~l 188 (246)
T PRK11145 146 SNHRTLEFARYLAKRNQKTWIRYVVVPGWTDDDDSAHRLGEFI 188 (246)
T ss_pred ChHHHHHHHHHHHhCCCcEEEEEEEECCCCCCHHHHHHHHHHH
Confidence 4456777788877666666667787777777666666655444
No 77
>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=35.13 E-value=51 Score=24.97 Aligned_cols=57 Identities=19% Similarity=0.179 Sum_probs=43.9
Q ss_pred eeeeecCcchHHHHHhhhHHHHHHH-hhcceEEEEEcCc------CeEEEEcCCCCCChhHHHhHHHHH
Q 017154 51 SFSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVE------GSMTVSTTRKTRDPYIIVKARDLI 112 (376)
Q Consensus 51 sf~~lfPkyRe~yLKe~W~~I~k~L-e~~~l~i~lDl~e------GsV~V~Tt~kT~DP~~IlKArD~I 112 (376)
++.+++|..-..+|=.-.+..-+.| +++|+.+.+.... ..|+|. .+|..+..|..+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~-----G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTIS-----GKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEE-----eCHHHHHHHHHhh
Confidence 4678889988888888888888888 5789999887654 355664 5577888888776
No 78
>PF15232 DUF4585: Domain of unknown function (DUF4585)
Probab=35.02 E-value=13 Score=30.73 Aligned_cols=24 Identities=29% Similarity=0.540 Sum_probs=19.0
Q ss_pred CCCCCCchhhhhhhccccccChhH
Q 017154 261 PPPPQPSKIDKLLESGEYFLSERK 284 (376)
Q Consensus 261 pp~~~~~k~d~~~esgeyfl~~~~ 284 (376)
|.+++.+|+=+--+||+||+-+--
T Consensus 2 ~~~~tqrKvL~DP~SG~Yy~vd~P 25 (75)
T PF15232_consen 2 PYPATQRKVLQDPESGQYYVVDAP 25 (75)
T ss_pred CCCccCccEeecCCCCCEEEEecC
Confidence 456777888888999999997643
No 79
>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=34.97 E-value=33 Score=32.60 Aligned_cols=26 Identities=27% Similarity=0.570 Sum_probs=20.7
Q ss_pred hhceecCCCCchHHHH--------HHHhCceEEE
Q 017154 152 RRQHLVGPNSSTLKAL--------EILTGCYILV 177 (376)
Q Consensus 152 rrgRIIG~~GkTkkaI--------E~LT~~~I~V 177 (376)
.++-|||.+|++++.| |.+.||.|.+
T Consensus 232 ~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l 265 (270)
T TIGR00436 232 QKKIIIGKNGSMIKAIGIAARKDILELFDCDVFL 265 (270)
T ss_pred ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 4789999999988765 7777777765
No 80
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=34.40 E-value=41 Score=36.26 Aligned_cols=51 Identities=16% Similarity=0.179 Sum_probs=39.5
Q ss_pred hhceecCCCCchHHHHHHHhCceEEEeC-c---EEEEecCCccHHHHHHHHHHHh
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYILVQG-N---TVAAMGSFKGLKQVRRIVEDCM 202 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I~V~G-~---TVsIIG~~~~IkiAR~AIe~LI 202 (376)
.-|-+||.+|+..+-|.+-|+|+|-|-- . .|-|.|.-.--+.|..+|..++
T Consensus 57 mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~~~m~~kaka~id~~~ 111 (629)
T KOG0336|consen 57 MVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGINHMRKKAKASIDRGQ 111 (629)
T ss_pred hhheeeccCcchhhhhhcccceeEEEeccCceeEEEEechHHHHHHHHhhHhhhh
Confidence 3588999999999999999999997654 3 3666666555567777777766
No 81
>PRK00148 Maf-like protein; Reviewed
Probab=33.73 E-value=81 Score=29.60 Aligned_cols=31 Identities=10% Similarity=0.097 Sum_probs=25.0
Q ss_pred EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 184 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 184 IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|.+.+.+.|++-+..| .|+.|.||.-..+
T Consensus 77 Il~KP~~~eeA~~~L~~l-sG~~h~v~T~v~l 107 (194)
T PRK00148 77 LLGKPHTPEEAIERWQQM-SGRTGELYTGHAL 107 (194)
T ss_pred EecCCCCHHHHHHHHHHh-CCCCcEEEEEEEE
Confidence 789999999999977766 6889988875444
No 82
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=33.58 E-value=1.4e+02 Score=33.00 Aligned_cols=113 Identities=21% Similarity=0.253 Sum_probs=74.2
Q ss_pred HHHHhhhHHHHHHHhhcceEEEEEcCcCeEEEEcCCCCCChhHHHhHHHHHHHHhcC--------------CChHHHHhh
Q 017154 62 KYLQEAWPMVKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRS--------------VPAPQAIKI 127 (376)
Q Consensus 62 ~yLKe~W~~I~k~Le~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD~IkAiaRG--------------F~~EqAlkL 127 (376)
.+|.+.-..|...+-.----..++...=.+.|-| .+|-.+.+--|+|+-||.- .++++|.++
T Consensus 5 ~~l~ei~~~i~~~~p~~~~It~vefEGPelvvY~----k~P~~~~~~~dlik~lAk~lrKRI~iR~dPsvl~~~e~A~~~ 80 (637)
T COG1782 5 EVLEEIRNKINEILPSDVKITDVEFEGPELVVYT----KNPELFAKDGDLIKDLAKDLRKRIIIRPDPSVLKPPEEARKI 80 (637)
T ss_pred HHHHHHHHHHHHhCCCcCceEEEEecCCeEEEEe----cCHHHhccchhHHHHHHHHHhhceEeccCchhcCCHHHHHHH
Confidence 5677777778777732122236788788888887 8899988766888777642 478999988
Q ss_pred hccCce--eEEEeccccccCchhhhh--hhceecCCCCchHHHHHHHhCceEEEe
Q 017154 128 LDDEMQ--CDIIKIGNLVRNKERFVK--RRQHLVGPNSSTLKALEILTGCYILVQ 178 (376)
Q Consensus 128 LeDDi~--~dIIdI~~~v~nke~f~R--rrgRIIG~~GkTkkaIE~LT~~~I~V~ 178 (376)
..+=+= .+|-||.=--.+++.+.. -=|-+||++|+|++-|-.-||-.--|.
T Consensus 81 I~eivP~ea~i~~i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~iv 135 (637)
T COG1782 81 ILEIVPEEAGITDIYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIV 135 (637)
T ss_pred HHHhCccccCceeEEecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceee
Confidence 764321 222222210112343333 358899999999999999888754443
No 83
>PRK14365 Maf-like protein; Provisional
Probab=33.06 E-value=71 Score=30.10 Aligned_cols=40 Identities=13% Similarity=0.203 Sum_probs=29.9
Q ss_pred EEEeCcEEE-----EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 175 ILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 175 I~V~G~TVs-----IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|...||. |+|.+.+.+.|++-+.++ .|+.|-||.-..+
T Consensus 65 ~vI~aDTvV~~~g~Il~KP~~~~eA~~~L~~l-sg~~h~v~T~v~l 109 (197)
T PRK14365 65 IIISADTSVFCNGEVLGKPASPENAEEMLEKL-SGRKFLVITGLTV 109 (197)
T ss_pred EEEEeCeEEEECCEEecCCCCHHHHHHHHHHH-CCCceEEEEEEEE
Confidence 555555544 789999999999987766 7889987765544
No 84
>TIGR02493 PFLA pyruvate formate-lyase 1-activating enzyme. An iron-sulfur protein with a radical-SAM domain (pfam04055). A single glycine residue in EC 2.3.1.54, formate C-acetyltransferase (formate-pyruvate lyase), is oxidized to the corresponding radical by transfer of H from its CH2 to AdoMet with concomitant cleavage of the latter. The reaction requires Fe2+. The first stage is reduction of the AdoMet to give methionine and the 5'-deoxyadenosin-5-yl radical, which then abstracts a hydrogen radical from the glycine residue.
Probab=32.50 E-value=3.1e+02 Score=25.15 Aligned_cols=108 Identities=16% Similarity=0.108 Sum_probs=60.4
Q ss_pred CeEEEEcCCCCCChhHHHhHHHHHHHHhc-------CCC---hHHHHhhhccCceeEEEeccccccCchhhhhhhceecC
Q 017154 89 GSMTVSTTRKTRDPYIIVKARDLIRLLSR-------SVP---APQAIKILDDEMQCDIIKIGNLVRNKERFVKRRQHLVG 158 (376)
Q Consensus 89 GsV~V~Tt~kT~DP~~IlKArD~IkAiaR-------GF~---~EqAlkLLeDDi~~dIIdI~~~v~nke~f~RrrgRIIG 158 (376)
+.|++.....+-+|..+...-..++..+. |+- .+.+.++++ .+..-.|+|..+ +.+...+.+|.
T Consensus 67 ~~I~~~GGEPll~~~~~~~li~~~~~~g~~~~i~TNG~~~~~~~~~~~ll~-~~d~v~isl~~~--~~~~~~~~~g~--- 140 (235)
T TIGR02493 67 GGVTFSGGEPLLQPEFLSELFKACKELGIHTCLDTSGFLGGCTEAADELLE-YTDLVLLDIKHF--NPEKYKKLTGV--- 140 (235)
T ss_pred CeEEEeCcccccCHHHHHHHHHHHHHCCCCEEEEcCCCCCccHHHHHHHHH-hCCEEEEeCCCC--CHHHHHHHHCC---
Confidence 46777665555555444333333333221 321 355556665 222334555543 33444444443
Q ss_pred CCCchHHHHHHHhCceEEEeCcEEEEecCCccHHHHHHHHHHHh
Q 017154 159 PNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDCM 202 (376)
Q Consensus 159 ~~GkTkkaIE~LT~~~I~V~G~TVsIIG~~~~IkiAR~AIe~LI 202 (376)
..-+++.+|+.+.+..+.|.-.+|.+-|..++...+.+.+..+.
T Consensus 141 ~~~~v~~~i~~l~~~g~~~~v~~vv~~~~~~n~~ei~~l~~~~~ 184 (235)
T TIGR02493 141 SLQPTLDFAKYLAKRNKPIWIRYVLVPGYTDSEEDIEALAEFVK 184 (235)
T ss_pred CcHHHHHHHHHHHhCCCcEEEEEeeeCCcCCCHHHHHHHHHHHH
Confidence 34578999999887666665566665666678878877776665
No 85
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=32.07 E-value=37 Score=32.08 Aligned_cols=31 Identities=16% Similarity=0.214 Sum_probs=27.3
Q ss_pred hhhceecCCCCchHHHHHHHhCceEEEeCcE
Q 017154 151 KRRQHLVGPNSSTLKALEILTGCYILVQGNT 181 (376)
Q Consensus 151 RrrgRIIG~~GkTkkaIE~LT~~~I~V~G~T 181 (376)
.-+++.||++|+..+.+-.|||-+|-|..-.
T Consensus 151 ~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~~ 181 (190)
T COG0195 151 DQLSLAIGKGGQNVRLASQLTGWEIDIETIS 181 (190)
T ss_pred HHHhhccCcccHHHHHHHHHhCCEEEEEehh
Confidence 4589999999999999999999999887543
No 86
>TIGR00762 DegV EDD domain protein, DegV family. This family of proteins is related to DegV of Bacillus subtilis and includes paralogous sets in several species (B. subtilis, Deinococcus radiodurans, Mycoplasma pneumoniae) that are closer in percent identity to each than to most homologs from other species. This suggests both recent paralogy and diversity of function. DegV itself is encoded immediately downstream of DegU, a transcriptional regulator of degradation, but is itself uncharacterized. Crystallography suggested a lipid-binding site, while comparison of the crystal structure to dihydroxyacetone kinase and to a mannose transporter EIIA domain suggests a conserved domain, EDD, with phosphotransferase activity.
Probab=31.71 E-value=4e+02 Score=25.65 Aligned_cols=103 Identities=11% Similarity=0.161 Sum_probs=65.9
Q ss_pred eEEEEcCCCCCChhHHHhHHHHHHHHhcCCChHHHHhhhcc--CceeEEEeccccccCchhhhhhhceecCCCCchHHHH
Q 017154 90 SMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDD--EMQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKAL 167 (376)
Q Consensus 90 sV~V~Tt~kT~DP~~IlKArD~IkAiaRGF~~EqAlkLLeD--Di~~dIIdI~~~v~nke~f~RrrgRIIG~~GkTkkaI 167 (376)
.|.|--|+ +.....-+=|....+++.-|.++++.+..|++ +...-++=+.++ ...++-||| +.+...+
T Consensus 108 ~i~ViDS~-~~s~~~g~~v~~a~~~~~~G~s~~eI~~~l~~~~~~~~~~f~v~~L-----~~L~~gGRi----s~~~~~~ 177 (275)
T TIGR00762 108 KVTVIDSK-SASMGLGLLVLEAAKLAEEGKSLEEILAKLEELRERTKLYFVVDTL-----EYLVKGGRI----SKAAALI 177 (275)
T ss_pred CEEEECCh-HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcEEEEEECcH-----HHHHhcCCc----cHHHHHH
Confidence 45555444 33444455566677777889999999999873 222233333332 224566786 4566677
Q ss_pred HHHhCceEE--EeCcEEEEecCCccHHHHHHHHHHHh
Q 017154 168 EILTGCYIL--VQGNTVAAMGSFKGLKQVRRIVEDCM 202 (376)
Q Consensus 168 E~LT~~~I~--V~G~TVsIIG~~~~IkiAR~AIe~LI 202 (376)
-.+-+.+-+ +.+..+..+|...+.+-|.+.+.+.+
T Consensus 178 g~lL~ikPIi~~~~G~i~~~~k~Rg~kka~~~l~~~~ 214 (275)
T TIGR00762 178 GSLLNIKPILTVDDGKLVPIEKVRGRKKAIKKLVELV 214 (275)
T ss_pred HHhhcceeEEEEeCCEEEEeeccccHHHHHHHHHHHH
Confidence 777777744 45678899999999877766665555
No 87
>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=31.49 E-value=2.5e+02 Score=25.89 Aligned_cols=91 Identities=23% Similarity=0.288 Sum_probs=57.8
Q ss_pred EEcCcCeEEEEcCCCCCChhHHHhHHHHHHHHhc--------------CCChHHHHhhhccCce--eEEEeccccccCch
Q 017154 84 LNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSR--------------SVPAPQAIKILDDEMQ--CDIIKIGNLVRNKE 147 (376)
Q Consensus 84 lDl~eGsV~V~Tt~kT~DP~~IlKArD~IkAiaR--------------GF~~EqAlkLLeDDi~--~dIIdI~~~v~nke 147 (376)
++...=.+.|-| .||-.+..--|+|+-||. =.++++|.++..+=+- -.|-||.=-...++
T Consensus 4 vefEGPelviYt----k~P~~~~~~~dli~~lAk~lrKRIvvR~dps~l~~~e~A~~~I~~ivP~ea~i~di~Fd~~tGE 79 (145)
T cd02410 4 VEFEGPELVVYT----KNPELFAEDGDLVKDLAKDLRKRIVIRPDPSVLKPPEEAIKIILEIVPEEAGITDIYFDDDTGE 79 (145)
T ss_pred eEeeCCeEEEEE----CCHHHHhcccHHHHHHHHHHhceEEEcCChhhcCCHHHHHHHHHHhCCCccCceeeEecCCCcE
Confidence 445556677776 888888776778877764 2467888877663110 12222221011234
Q ss_pred hhhhh--hceecCCCCchHHHHHHHhCceEEEe
Q 017154 148 RFVKR--RQHLVGPNSSTLKALEILTGCYILVQ 178 (376)
Q Consensus 148 ~f~Rr--rgRIIG~~GkTkkaIE~LT~~~I~V~ 178 (376)
-...+ =|++||++|.|+.-|=.-||-.-.|.
T Consensus 80 V~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 80 VIIEAEKPGLVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred EEEEEcCCeEEEecCchhHHHHHHHhCCeeEEE
Confidence 43333 59999999999999988888866553
No 88
>TIGR02494 PFLE_PFLC glycyl-radical enzyme activating protein family. This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA, ), benzylsuccinate synthase (BssD, ), gycerol dehydratase (DhaB2, ) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0
Probab=31.33 E-value=3.2e+02 Score=26.12 Aligned_cols=106 Identities=17% Similarity=0.111 Sum_probs=52.0
Q ss_pred cCeEEEEcCCCCCChhHHHhHHHHHHHHh-------cCCCh-HHHHhhhccCceeEEEeccccccCchhhhhhhceecCC
Q 017154 88 EGSMTVSTTRKTRDPYIIVKARDLIRLLS-------RSVPA-PQAIKILDDEMQCDIIKIGNLVRNKERFVKRRQHLVGP 159 (376)
Q Consensus 88 eGsV~V~Tt~kT~DP~~IlKArD~IkAia-------RGF~~-EqAlkLLeDDi~~dIIdI~~~v~nke~f~RrrgRIIG~ 159 (376)
.+.|++.....+-.|-.+...-+.++..+ -|+-+ +..-+++. .+..-.|+|..+ +.+.+.+.+| +.
T Consensus 126 ~~~V~~sGGEPll~~~~l~~l~~~~k~~g~~~~i~TnG~~~~~~~~~ll~-~~d~~~isl~~~--~~~~~~~~~g---~~ 199 (295)
T TIGR02494 126 GGGVTLSGGEPLLQPEFALALLQACHERGIHTAVETSGFTPWETIEKVLP-YVDLFLFDIKHL--DDERHKEVTG---VD 199 (295)
T ss_pred CCcEEeeCcchhchHHHHHHHHHHHHHcCCcEeeeCCCCCCHHHHHHHHh-hCCEEEEeeccC--ChHHHHHHhC---CC
Confidence 45677776444444433322223333222 34444 34444553 222233566554 3345555555 24
Q ss_pred CCchHHHHHHHhCceEEEeCcEEEEecCCccHHHHHHHHH
Q 017154 160 NSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVE 199 (376)
Q Consensus 160 ~GkTkkaIE~LT~~~I~V~G~TVsIIG~~~~IkiAR~AIe 199 (376)
...++.+|+.|....+.+.=.++.+-|-.++.......+.
T Consensus 200 ~~~vl~~i~~l~~~~~~~~i~~~~v~~~n~~~~ei~~l~~ 239 (295)
T TIGR02494 200 NEPILENLEALAAAGKNVVIRIPVIPGFNDSEENIEAIAA 239 (295)
T ss_pred hHHHHHHHHHHHhCCCcEEEEeceeCCcCCCHHHHHHHHH
Confidence 4678888888877665443334434454455555554443
No 89
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=31.26 E-value=70 Score=35.91 Aligned_cols=48 Identities=23% Similarity=0.361 Sum_probs=39.2
Q ss_pred HHHHHHH-hhcceEEEEEcCcCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCCh
Q 017154 69 PMVKGAL-KEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPA 121 (376)
Q Consensus 69 ~~I~k~L-e~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD~IkAiaRGF~~ 121 (376)
+.+.+.| +++|+++.++ .+|+|.|.+ .|-..+.+|++.|..|.+-|.+
T Consensus 571 Gk~I~~I~eetg~~Idie-ddGtv~i~~----s~~~~~~~ak~~I~~i~~e~ev 619 (692)
T COG1185 571 GKTIKAITEETGVKIDIE-DDGTVKIAA----SDGESAKKAKERIEAITREVEV 619 (692)
T ss_pred ccchhhhhhhhCcEEEec-CCCcEEEEe----cchHHHHHHHHHHHHHHhhccc
Confidence 3444555 8999999999 899999998 5668999999999999965544
No 90
>PRK00089 era GTPase Era; Reviewed
Probab=31.08 E-value=42 Score=31.98 Aligned_cols=27 Identities=22% Similarity=0.474 Sum_probs=21.5
Q ss_pred hhceecCCCCchHHHH--------HHHhCceEEEe
Q 017154 152 RRQHLVGPNSSTLKAL--------EILTGCYILVQ 178 (376)
Q Consensus 152 rrgRIIG~~GkTkkaI--------E~LT~~~I~V~ 178 (376)
.++=|||.+|++++.| |.+.||.|.+.
T Consensus 237 ~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 237 QKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred ceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 4788999999988765 77888877653
No 91
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=30.96 E-value=79 Score=23.74 Aligned_cols=33 Identities=18% Similarity=0.217 Sum_probs=29.1
Q ss_pred CCCCChhHHHhHHHHHHHHhcCCChHHHHhhhc
Q 017154 97 RKTRDPYIIVKARDLIRLLSRSVPAPQAIKILD 129 (376)
Q Consensus 97 ~kT~DP~~IlKArD~IkAiaRGF~~EqAlkLLe 129 (376)
....++..+...+.+..+...|||+++...+|+
T Consensus 35 ~R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l~ 67 (67)
T cd04764 35 RRYYTDEDIELLKKIKTLLEKGLSIKEIKEILN 67 (67)
T ss_pred ceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHhC
Confidence 345888999999999999999999999988875
No 92
>PRK00234 Maf-like protein; Reviewed
Probab=30.70 E-value=86 Score=29.35 Aligned_cols=32 Identities=9% Similarity=0.071 Sum_probs=25.5
Q ss_pred EEecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 183 AAMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 183 sIIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
-|+|.+.+.+.|++-+..| .|+.|-||.-.-+
T Consensus 77 ~Il~KP~~~~eA~~mL~~l-sG~~h~V~T~v~l 108 (192)
T PRK00234 77 QILGKPHTFERAREQLLAA-SGQSVTFLTGLAL 108 (192)
T ss_pred EECCCCCCHHHHHHHHHHH-CCCcEEEEEEEEE
Confidence 3789999999999988776 7889987765544
No 93
>COG1902 NemA NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]
Probab=29.44 E-value=2.7e+02 Score=28.72 Aligned_cols=107 Identities=18% Similarity=0.180 Sum_probs=67.4
Q ss_pred cchHHHHHhhhHHHHHHHhhcc-eEEEEEcCcCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCChHHHHhhhc--cCce-
Q 017154 58 QYREKYLQEAWPMVKGALKEYG-VSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILD--DEMQ- 133 (376)
Q Consensus 58 kyRe~yLKe~W~~I~k~Le~~~-l~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD~IkAiaRGF~~EqAlkLLe--DDi~- 133 (376)
-+|..++.|+=..|..++.... |-++|...+-. +.. |.++++++.|++ .+.-
T Consensus 196 ENR~Rf~~EVv~aVr~~vg~~~~vg~Rls~~d~~----------~~~--------------g~~~~e~~~la~~L~~~G~ 251 (363)
T COG1902 196 ENRARFLLEVVDAVREAVGADFPVGVRLSPDDFF----------DGG--------------GLTIEEAVELAKALEEAGL 251 (363)
T ss_pred HHHHHHHHHHHHHHHHHhCCCceEEEEECccccC----------CCC--------------CCCHHHHHHHHHHHHhcCC
Confidence 4699999999999999996544 77777664320 111 888888888887 5555
Q ss_pred eEEEeccccccCc-hhhhhhhceecCCCCchHHH--HHHHhCceEEEeCcEEEEecCCccHHHHHHHHHH
Q 017154 134 CDIIKIGNLVRNK-ERFVKRRQHLVGPNSSTLKA--LEILTGCYILVQGNTVAAMGSFKGLKQVRRIVED 200 (376)
Q Consensus 134 ~dIIdI~~~v~nk-e~f~RrrgRIIG~~GkTkka--IE~LT~~~I~V~G~TVsIIG~~~~IkiAR~AIe~ 200 (376)
||+|++.+-.... ....... ++-.+-.+ |-.-++ -.|...|.......|..+|+.
T Consensus 252 ~d~i~vs~~~~~~~~~~~~~~-----~~~~~~~a~~i~~~~~-------~pvi~~G~i~~~~~Ae~~l~~ 309 (363)
T COG1902 252 VDYIHVSEGGYERGGTITVSG-----PGYQVEFAARIKKAVR-------IPVIAVGGINDPEQAEEILAS 309 (363)
T ss_pred ccEEEeecccccCCCCccccc-----cchhHHHHHHHHHhcC-------CCEEEeCCCCCHHHHHHHHHc
Confidence 8999998743321 1111110 22333333 222222 456677778888888888875
No 94
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=29.29 E-value=45 Score=29.81 Aligned_cols=24 Identities=25% Similarity=0.216 Sum_probs=20.0
Q ss_pred hhceecCCCCchHHHHHHHhCceE
Q 017154 152 RRQHLVGPNSSTLKALEILTGCYI 175 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~~I 175 (376)
..|..||++|+..++|+++.|-+|
T Consensus 42 ~vG~~IG~~G~rI~~i~e~lgekI 65 (140)
T PRK08406 42 DMGLAIGKGGENVKRLEEKLGKDI 65 (140)
T ss_pred CccccCCcCchHHHHHHHHhCCce
Confidence 458999999999999998886444
No 95
>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=28.80 E-value=1.9e+02 Score=25.26 Aligned_cols=50 Identities=16% Similarity=0.080 Sum_probs=36.7
Q ss_pred HHHHHHH-hhcceEEEEEcCc----------------------CeEEEEcCCCCCC--hhHHHhHHHHHHHHhcCCChH
Q 017154 69 PMVKGAL-KEYGVSCELNLVE----------------------GSMTVSTTRKTRD--PYIIVKARDLIRLLSRSVPAP 122 (376)
Q Consensus 69 ~~I~k~L-e~~~l~i~lDl~e----------------------GsV~V~Tt~kT~D--P~~IlKArD~IkAiaRGF~~E 122 (376)
+...+.| +++|+.|.|.-.. +.|.|.+ .| .-.+.+|..+|..|...+.++
T Consensus 25 G~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a----~~~~~e~~~~A~~~I~~ll~~~~~~ 99 (120)
T cd02395 25 GNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITA----ETPPEEALAKAVEAIEELLKPAIEG 99 (120)
T ss_pred ChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEe----CCcHHHHHHHHHHHHHHHhccCCCc
Confidence 3455567 6789888887542 7788876 55 578999999999888766544
No 96
>PRK00078 Maf-like protein; Reviewed
Probab=28.76 E-value=93 Score=29.10 Aligned_cols=40 Identities=18% Similarity=0.289 Sum_probs=29.5
Q ss_pred EEEeCcEEE-----EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 175 ILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 175 I~V~G~TVs-----IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|...||. |+|.+.+.+.|++-+..| .|+.|-||.-..+
T Consensus 66 lvI~aDTvV~~~g~ilgKP~~~eeA~~~L~~l-sG~~h~V~Tgv~l 110 (192)
T PRK00078 66 IVIGCDTIVAFNGKVLGKPKDEEDAFEMLKAL-SGNEHEVYSGIAI 110 (192)
T ss_pred EEEEeCeEEEECCEEeCCCCCHHHHHHHHHHH-CCCcEEEEEEEEE
Confidence 445555543 689999999999988877 6779988765444
No 97
>PRK07634 pyrroline-5-carboxylate reductase; Reviewed
Probab=28.06 E-value=59 Score=29.91 Aligned_cols=96 Identities=19% Similarity=0.178 Sum_probs=60.0
Q ss_pred hhHHHHHHHhhcceEEEEEcCcCeEEEEcCCCCCChhHHHhH-HHHHH-HHhcCCChHHHHhhhccCce--eEEEecccc
Q 017154 67 AWPMVKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKA-RDLIR-LLSRSVPAPQAIKILDDEMQ--CDIIKIGNL 142 (376)
Q Consensus 67 ~W~~I~k~Le~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKA-rD~Ik-AiaRGF~~EqAlkLLeDDi~--~dIIdI~~~ 142 (376)
....+...++..|..+.++ +..+..-|.--.-.|..+..- .-++. +...||+.++|.+++-.=+. .+ +
T Consensus 145 ~~~~v~~lf~~~G~~~~~~--e~~~~~~~a~~gs~pa~~~~~~~a~~~~~~~~Gl~~~~a~~~~~~~~~g~~~------~ 216 (245)
T PRK07634 145 HKETLQLILKGIGTSQLCT--EEEVHQLTAVTGSAPAFLYYFAESLIEATKSYGVDEETAKHLVIQMISGSAS------M 216 (245)
T ss_pred HHHHHHHHHHhCCCEEEEC--HHHcchHHhhhcchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH------H
Confidence 3455666667778888776 333444443333444332222 22333 45679999999999873321 11 1
Q ss_pred ccCchhhhhhhceecCCCCchHHHHHHH
Q 017154 143 VRNKERFVKRRQHLVGPNSSTLKALEIL 170 (376)
Q Consensus 143 v~nke~f~RrrgRIIG~~GkTkkaIE~L 170 (376)
..+..++.-.+.++.=|+|.|..+|..|
T Consensus 217 ~~~~~~~~~l~~~v~spgG~T~~gl~~l 244 (245)
T PRK07634 217 LEQTQDPANLREQVTTPGGSTAEGLKAL 244 (245)
T ss_pred HhCCCCHHHHHHhCCCCChHHHHHHHHh
Confidence 1223578889999999999999999865
No 98
>PRK14363 Maf-like protein; Provisional
Probab=27.19 E-value=1e+02 Score=29.36 Aligned_cols=40 Identities=18% Similarity=0.396 Sum_probs=29.9
Q ss_pred EEEeCcEEE-----EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 175 ILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 175 I~V~G~TVs-----IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
++|...||. |+|.+.+.+.|++-+..| .|+.|.||.-..+
T Consensus 63 lvI~aDTVV~~~g~IlgKP~~~eeA~~~L~~l-sG~~H~V~T~v~l 107 (204)
T PRK14363 63 LVIGSDTVVVLDGNILGKPESLEEAKGMLKKL-SGRWHVVYTGVAF 107 (204)
T ss_pred EEEEeCeEEEECCEEcCCCCCHHHHHHHHHHH-CCCCcEEEEEEEE
Confidence 444444543 789999999999988877 7779988766554
No 99
>PRK14361 Maf-like protein; Provisional
Probab=27.01 E-value=1.2e+02 Score=28.33 Aligned_cols=31 Identities=10% Similarity=0.080 Sum_probs=25.1
Q ss_pred EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 184 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 184 IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|.+.+.+.|++-+..| .|+.|-||.-..+
T Consensus 74 ilgKP~~~eeA~~~L~~l-sG~~h~V~T~v~l 104 (187)
T PRK14361 74 LLAKPADEAENEAFLRVL-SGRTHQVYTGVAV 104 (187)
T ss_pred EecCCCCHHHHHHHHHHh-CCCceEEEEEEEE
Confidence 699999999999988877 6879987665444
No 100
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=26.79 E-value=1.5e+02 Score=28.43 Aligned_cols=67 Identities=15% Similarity=0.072 Sum_probs=50.9
Q ss_pred CcceeeeeeeecCcchHHHHHhhhHHHHHHH-hhcceEEEEEcCcCeEEEEcCCCCCChhHHHhHHHHHHHHhc
Q 017154 45 GMLEVSSFSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSR 117 (376)
Q Consensus 45 g~~eessf~~lfPkyRe~yLKe~W~~I~k~L-e~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD~IkAiaR 117 (376)
|.++. -|.+-+|++...-|-.-=+.+-+.| +.+++.+.+.. +|.|.|.+ .|+-.+..|..+|+.+.+
T Consensus 141 G~L~~-G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-NG~VwI~~----~~~~~~~~a~~~I~~~e~ 208 (235)
T PRK04163 141 GKIEG-GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-NGRIWIKG----PDEEDEEIAIEAIKKIER 208 (235)
T ss_pred CccCC-CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-CcEEEEee----CCHHHHHHHHHHHHHHHh
Confidence 44442 4667788887777755556667777 67888888876 69999988 778899999999998876
No 101
>PRK00032 Maf-like protein; Reviewed
Probab=26.58 E-value=1.1e+02 Score=28.62 Aligned_cols=31 Identities=10% Similarity=0.157 Sum_probs=25.0
Q ss_pred EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 184 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 184 IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|.+.+.+.|++-+..| .|+.|-||.-..+
T Consensus 79 IlgKP~~~eeA~~~L~~l-sG~~h~v~T~v~l 109 (190)
T PRK00032 79 VLEKPRDAADAAAMLRAL-SGRTHQVMTAVAL 109 (190)
T ss_pred EecCCCCHHHHHHHHHHh-CCCCcEEEEEEEE
Confidence 789999999999988776 6879987765544
No 102
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=26.57 E-value=1.3e+02 Score=22.76 Aligned_cols=34 Identities=15% Similarity=0.189 Sum_probs=29.0
Q ss_pred CCCCCChhHHHhHHHHHHHHhcCCChHHHHhhhc
Q 017154 96 TRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILD 129 (376)
Q Consensus 96 t~kT~DP~~IlKArD~IkAiaRGF~~EqAlkLLe 129 (376)
.....+...|...+.+..+...||+++++..+|+
T Consensus 35 g~R~yt~~di~~l~~i~~l~~~g~~l~~i~~~l~ 68 (68)
T cd04763 35 GHRLFNDADIDRILEIKRWIDNGVQVSKVKKLLS 68 (68)
T ss_pred CCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHhC
Confidence 3445778899999999999999999999998874
No 103
>PTZ00431 pyrroline carboxylate reductase; Provisional
Probab=25.37 E-value=1.3e+02 Score=28.53 Aligned_cols=97 Identities=14% Similarity=0.184 Sum_probs=65.1
Q ss_pred HHHHHHhhcceEEEEEcCcCeEEEEcCCCCCChhHHHhH-HHHH-HHHhcCCChHHHHhhhccCceeEEEeccccc-cCc
Q 017154 70 MVKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKA-RDLI-RLLSRSVPAPQAIKILDDEMQCDIIKIGNLV-RNK 146 (376)
Q Consensus 70 ~I~k~Le~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKA-rD~I-kAiaRGF~~EqAlkLLeDDi~~dIIdI~~~v-~nk 146 (376)
.+...++..|..+.++ +..+.+-|.--.--|..+.-. ..|+ -++..|++.++|.+|.-.=+.= -..+. .+.
T Consensus 139 ~v~~l~~~~G~~~~v~--E~~~d~~ta~~gsgPA~~~~~~~al~~~~v~~Gl~~~~a~~l~~~~~~G----~a~ll~~~~ 212 (260)
T PTZ00431 139 KVIDIFSACGIIQEIK--EKDMDIATAISGCGPAYVFLFIESLIDAGVKNGLNRDVSKNLVLQTILG----SVHMVKASD 212 (260)
T ss_pred HHHHHHHhCCcEEEEC--hHHcchhhhhcCCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH----HHHHHHhcC
Confidence 5566667889999887 446766654433446443322 2333 4678999999999998754210 00111 245
Q ss_pred hhhhhhhceecCCCCchHHHHHHHhC
Q 017154 147 ERFVKRRQHLVGPNSSTLKALEILTG 172 (376)
Q Consensus 147 e~f~RrrgRIIG~~GkTkkaIE~LT~ 172 (376)
.++...|.++.=|+|.|..+|..|-.
T Consensus 213 ~~~~~l~~~v~spgG~T~~gl~~le~ 238 (260)
T PTZ00431 213 QPVQQLKDDVCSPGGITIVGLYTLEK 238 (260)
T ss_pred CCHHHHHHhCCCCChHHHHHHHHHHH
Confidence 68899999999999999999988754
No 104
>PRK14362 Maf-like protein; Provisional
Probab=25.29 E-value=1.1e+02 Score=29.07 Aligned_cols=40 Identities=13% Similarity=0.224 Sum_probs=29.3
Q ss_pred EEEeCcEEE-----EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 175 ILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 175 I~V~G~TVs-----IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
++|...||. |+|.+.+.+.|++-+..| .|+.|-||.-..+
T Consensus 75 ~VI~ADTvV~~~g~ilgKP~~~eeA~~~L~~l-sG~~H~V~Tgv~l 119 (207)
T PRK14362 75 LVIAADTVVALDGMILGKPADRADALSMLRRL-AGRTHEVVSACCV 119 (207)
T ss_pred EEEEeCeEEEeCCEEcCCCCCHHHHHHHHHHh-CCCceEEEEEEEE
Confidence 444444433 689999999999987776 6779987766555
No 105
>PRK00884 Maf-like protein; Reviewed
Probab=25.19 E-value=1.3e+02 Score=28.26 Aligned_cols=40 Identities=13% Similarity=0.196 Sum_probs=29.6
Q ss_pred EEEeCcEEE-----EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 175 ILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 175 I~V~G~TVs-----IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|...||. |+|.+.+.+.|++-+..| .|+.|-||.-..+
T Consensus 64 ~VI~aDTvV~~~g~ilgKP~~~eeA~~~L~~l-sG~~h~V~Tgv~l 108 (194)
T PRK00884 64 LIIGSDQVCVLDGEITGKPLTEENARAQLRKA-SGNIVTFYTGLAL 108 (194)
T ss_pred EEEEeCeEEEECCEEecCCCCHHHHHHHHHHH-CCCceEEEEEEEE
Confidence 444444533 789999999999988876 7889987765544
No 106
>cd00555 Maf Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or nucleic acid-binding protein with structural similarity to the hypoxanthine/xanthine NTP pyrophosphatase Ham1 from Methanococcus jannaschii, RNase H from Escherichia coli, and some other nucleotide or RNA-binding proteins.
Probab=24.69 E-value=1.3e+02 Score=27.72 Aligned_cols=31 Identities=23% Similarity=0.366 Sum_probs=24.6
Q ss_pred EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 184 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 184 IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|.+.+.+.|++-+.++ .|+.|.||.-.-+
T Consensus 76 il~KP~~~~eA~~~L~~l-sg~~h~v~T~v~l 106 (180)
T cd00555 76 ILGKPKDREEAREMLKRL-SGRTHEVYTGVAL 106 (180)
T ss_pred EEcCCCCHHHHHHHHHHH-cCCCcEEEEEEEE
Confidence 689999999999987776 6779987765444
No 107
>cd04735 OYE_like_4_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 4. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=24.62 E-value=4.3e+02 Score=26.56 Aligned_cols=124 Identities=10% Similarity=0.155 Sum_probs=69.0
Q ss_pred cchHHHHHhhhHHHHHHHh-----hcceEEEEEcCcCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCChHHHHhhhc--c
Q 017154 58 QYREKYLQEAWPMVKGALK-----EYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILD--D 130 (376)
Q Consensus 58 kyRe~yLKe~W~~I~k~Le-----~~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD~IkAiaRGF~~EqAlkLLe--D 130 (376)
-+|..++.++-..|.+++. ..-|.++|+..+. +.-|.++++++.++. +
T Consensus 191 enR~r~~~eii~~vr~~vg~~~~~~~~v~~R~s~~~~-------------------------~~~g~~~ee~~~i~~~L~ 245 (353)
T cd04735 191 ENRMRFPLAVVKAVQEVIDKHADKDFILGYRFSPEEP-------------------------EEPGIRMEDTLALVDKLA 245 (353)
T ss_pred HHHHHHHHHHHHHHHHHhccccCCCceEEEEECcccc-------------------------cCCCCCHHHHHHHHHHHH
Confidence 3688999999999999884 4557777764321 112555565555544 4
Q ss_pred CceeEEEeccccccCchhhhhhhceecCCC-CchHHHHHHHhCceEEEeCcEEEEecCCccHHHHHHHHHHHhcCCCCch
Q 017154 131 EMQCDIIKIGNLVRNKERFVKRRQHLVGPN-SSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDCMQNKMHPV 209 (376)
Q Consensus 131 Di~~dIIdI~~~v~nke~f~RrrgRIIG~~-GkTkkaIE~LT~~~I~V~G~TVsIIG~~~~IkiAR~AIe~LI~Gs~HpV 209 (376)
+.-+|.|+|+.-...... +..+.. ......|-...+ .+-.|...|.+.....|.++|.. | .+-
T Consensus 246 ~~GvD~I~Vs~g~~~~~~------~~~~~~~~~~~~~ik~~~~-----~~iPVi~~Ggi~t~e~ae~~l~~---g-aD~- 309 (353)
T cd04735 246 DKGLDYLHISLWDFDRKS------RRGRDDNQTIMELVKERIA-----GRLPLIAVGSINTPDDALEALET---G-ADL- 309 (353)
T ss_pred HcCCCEEEeccCcccccc------ccCCcchHHHHHHHHHHhC-----CCCCEEEECCCCCHHHHHHHHHc---C-CCh-
Confidence 445788888753221111 111111 112222322221 13458888999888888888875 3 221
Q ss_pred hHHHHHHHHHhhhcCccc
Q 017154 210 YHIKILMVKKELEKDPAL 227 (376)
Q Consensus 210 Y~ikelmiKreL~kd~~l 227 (376)
-++-|-|-.||.|
T Consensus 310 -----V~~gR~liadPdl 322 (353)
T cd04735 310 -----VAIGRGLLVDPDW 322 (353)
T ss_pred -----HHHhHHHHhCccH
Confidence 2344666666654
No 108
>PRK14368 Maf-like protein; Provisional
Probab=23.24 E-value=1.6e+02 Score=27.68 Aligned_cols=31 Identities=19% Similarity=0.134 Sum_probs=25.0
Q ss_pred EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 184 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 184 IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|.+.+...|++-+..| .|+.|-||.-.-+
T Consensus 81 ilgKP~~~~eA~~~L~~l-sG~~h~v~Tgv~l 111 (193)
T PRK14368 81 IMGKPKDEADAVRMLKKL-SGVPHEVITGFAV 111 (193)
T ss_pred EecCCCCHHHHHHHHHHh-CCCCcEEEEEEEE
Confidence 699999999999987776 6779987765544
No 109
>TIGR00172 maf MAF protein. This nonessential gene causes inhibition of septation when overexpressed. A member of the family is found in the Archaeon Pyrococcus horikoshii and another in the round worm Caenorhabditis elegans.
Probab=22.74 E-value=1.7e+02 Score=27.21 Aligned_cols=31 Identities=19% Similarity=0.274 Sum_probs=24.7
Q ss_pred EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 184 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 184 IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|.+.+.+.|++-+..| .|+.|-||.-.-+
T Consensus 79 ilgKP~~~~eA~~~L~~l-sG~~h~V~Tgv~l 109 (183)
T TIGR00172 79 IYGKPKDKEEAAEFLRKL-SGQEHEVYTAVAL 109 (183)
T ss_pred EecCCCCHHHHHHHHHHh-CCCCcEEEEEEEE
Confidence 689999999999987776 6778987765554
No 110
>PRK04425 Maf-like protein; Reviewed
Probab=22.64 E-value=1.6e+02 Score=27.86 Aligned_cols=40 Identities=18% Similarity=0.314 Sum_probs=29.9
Q ss_pred EEEeCcEEE-----EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 175 ILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 175 I~V~G~TVs-----IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|...||. |+|.+.+.+.|++-+.+| .|+.|-||.-..+
T Consensus 67 lvI~aDTvV~~~g~ilgKP~~~eeA~~~L~~l-sg~~h~v~T~v~l 111 (196)
T PRK04425 67 LIVGADQVAWCDGRQWGKPMNLANAQKMLMHL-SGREIEFYSALVL 111 (196)
T ss_pred EEEEeCeEEEECCEEecCCCCHHHHHHHHHHh-CCCcEEEEEEEEE
Confidence 444444433 699999999999988875 7889988776555
No 111
>PF04459 DUF512: Protein of unknown function (DUF512); InterPro: IPR007549 This is a domain of uncharacterised prokaryotic proteins. It is often found C-terminal to the radical SAM domain (IPR007197 from INTERPRO).
Probab=22.55 E-value=2.1e+02 Score=27.34 Aligned_cols=95 Identities=18% Similarity=0.279 Sum_probs=56.0
Q ss_pred eeecCcchHHHHHhhhHHHHHHHhhcceEEEEEcC-----cCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCChHHHHhh
Q 017154 53 STLFPQYREKYLQEAWPMVKGALKEYGVSCELNLV-----EGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKI 127 (376)
Q Consensus 53 ~~lfPkyRe~yLKe~W~~I~k~Le~~~l~i~lDl~-----eGsV~V~Tt~kT~DP~~IlKArD~IkAiaRGF~~EqAlkL 127 (376)
.++--.-=..+|+.....+ ..+ .++.+++-.. .++|+|. .++-++|+|.+|..+-.
T Consensus 101 ~ivTG~la~~~l~~~~~~l-~~~--~~~~v~V~~V~N~fFG~~ItVa---------GLLTg~Dii~~L~~~~~------- 161 (204)
T PF04459_consen 101 TIVTGVLAYPFLKPLVEKL-NRI--PGLEVEVVPVKNRFFGGTITVA---------GLLTGQDIIEQLKGKEL------- 161 (204)
T ss_pred EEEeeHHHHHHHHHHHHHH-hcc--CCCeEEEEEeecCCCCCCeEEe---------eCccHHHHHHHhCcCCC-------
Confidence 3333334455666655555 323 2555554433 6778884 68999999998876111
Q ss_pred hccCceeEEEeccccccCchhhhhh-hceecCCCCchHHHHHHHhCceEEEeCc
Q 017154 128 LDDEMQCDIIKIGNLVRNKERFVKR-RQHLVGPNSSTLKALEILTGCYILVQGN 180 (376)
Q Consensus 128 LeDDi~~dIIdI~~~v~nke~f~Rr-rgRIIG~~GkTkkaIE~LT~~~I~V~G~ 180 (376)
. |.+=|-+ .+.+- .++.+ +|.|..-|+.-.|+.|.|-..
T Consensus 162 -~-----d~lllP~------~ml~~~~~~fL--DD~t~~el~~~lg~~v~vv~~ 201 (204)
T PF04459_consen 162 -G-----DLLLLPD------VMLRHGEGVFL--DDMTLEELEERLGVPVIVVRG 201 (204)
T ss_pred -C-----CEEEECH------HHhcCCCCccC--CCCcHHHHHHHhCCcEEEeCC
Confidence 1 2222222 22222 45555 788999999988988887653
No 112
>PRK02478 Maf-like protein; Reviewed
Probab=22.02 E-value=1.8e+02 Score=27.44 Aligned_cols=31 Identities=19% Similarity=0.315 Sum_probs=24.9
Q ss_pred EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 184 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 184 IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|.+.+.+.|++-+..| .|+.|-||.-.-+
T Consensus 85 ilgKP~~~~eA~~~L~~l-sG~~h~V~T~v~l 115 (199)
T PRK02478 85 VFHKPKDMEEARRHLQKL-SGKTHQLNSAVVL 115 (199)
T ss_pred EecCCCCHHHHHHHHHHh-cCCCcEEEEEEEE
Confidence 789999999999887776 7889987765544
No 113
>PRK14367 Maf-like protein; Provisional
Probab=21.99 E-value=1.5e+02 Score=28.14 Aligned_cols=31 Identities=13% Similarity=0.205 Sum_probs=25.1
Q ss_pred EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 184 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 184 IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|.+.+.+.|++-+..| .|+.|-||.-..+
T Consensus 85 IlgKP~~~eeA~~~L~~l-sG~~h~V~Tgv~l 115 (202)
T PRK14367 85 ILGKPRSQAEAIEFLNRL-SGKQHTVLTAVCI 115 (202)
T ss_pred EecCCCCHHHHHHHHHHh-CCCCeEEEEEEEE
Confidence 799999999999987776 6779988765444
No 114
>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=21.61 E-value=45 Score=30.08 Aligned_cols=27 Identities=7% Similarity=0.083 Sum_probs=0.0
Q ss_pred hceecCCCCchHHHHHHHhCceEEEeC
Q 017154 153 RQHLVGPNSSTLKALEILTGCYILVQG 179 (376)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~~I~V~G 179 (376)
+++.||++|++.+-.-.||+-++=|.+
T Consensus 111 ~~~AIGk~G~Ni~la~~l~~~~~dI~~ 137 (141)
T TIGR01952 111 KGIAIGKGGKNIERAKELAKRHHDIDD 137 (141)
T ss_pred hhhhhCCCchhHHHHHHHhcCccCCeE
No 115
>PRK01839 Maf-like protein; Reviewed
Probab=21.59 E-value=1.7e+02 Score=27.89 Aligned_cols=31 Identities=10% Similarity=0.138 Sum_probs=25.1
Q ss_pred EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 184 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 184 IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|.+.+.+.|++-+..| .|+.|-||.-..+
T Consensus 97 IlgKP~~~eeA~~~L~~l-sg~~h~V~T~v~l 127 (209)
T PRK01839 97 ILGKPADAADALAMLTRL-AGRTHRVLTAVAV 127 (209)
T ss_pred EecCCCCHHHHHHHHHHh-CCCCcEEEEEEEE
Confidence 689999999999977766 7779987766555
No 116
>PRK11880 pyrroline-5-carboxylate reductase; Reviewed
Probab=21.55 E-value=1.1e+02 Score=28.78 Aligned_cols=104 Identities=20% Similarity=0.294 Sum_probs=65.0
Q ss_pred HhhhHHHHHHHhhcceEEEEEcCcCeEEEEcCCCCCCh-hHHHhHHHHHHH-HhcCCChHHHHhhhccCceeEEEecccc
Q 017154 65 QEAWPMVKGALKEYGVSCELNLVEGSMTVSTTRKTRDP-YIIVKARDLIRL-LSRSVPAPQAIKILDDEMQCDIIKIGNL 142 (376)
Q Consensus 65 Ke~W~~I~k~Le~~~l~i~lDl~eGsV~V~Tt~kT~DP-~~IlKArD~IkA-iaRGF~~EqAlkLLeDDi~~dIIdI~~~ 142 (376)
.+.+..+...++..|....++.. ..+..-+.--..-| |...=+..++.+ ...|++.++|.+++..=+. ...++
T Consensus 138 ~~~~~~v~~l~~~lG~~~~~~~e-~~~d~~~a~~~~~pa~~~~~~~~~~~~~~~~Gl~~~~a~~~~~~~~~----g~~~~ 212 (267)
T PRK11880 138 AEDRELVENLLSAFGKVVWVDDE-KQMDAVTAVSGSGPAYVFLFIEALADAGVKLGLPREQARKLAAQTVL----GAAKL 212 (267)
T ss_pred HHHHHHHHHHHHhCCeEEEECCh-HhcchHHHHhcChHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH----HHHHH
Confidence 35566777777888876667633 23333332212334 322334456664 5589999999988874321 00111
Q ss_pred c-cCchhhhhhhceecCCCCchHHHHHHHhCc
Q 017154 143 V-RNKERFVKRRQHLVGPNSSTLKALEILTGC 173 (376)
Q Consensus 143 v-~nke~f~RrrgRIIG~~GkTkkaIE~LT~~ 173 (376)
. ..+.++.-.+.++.=|+|.|..+|+.|-..
T Consensus 213 ~~~~~~~~~~l~~~v~tpgG~t~~gl~~l~~~ 244 (267)
T PRK11880 213 LLESGEHPAELRDNVTSPGGTTIAALRVLEEK 244 (267)
T ss_pred HHhcCCCHHHHHHhCCCCcHHHHHHHHHHHHC
Confidence 1 345688889999999999999999988643
No 117
>PRK07679 pyrroline-5-carboxylate reductase; Reviewed
Probab=21.48 E-value=1.5e+02 Score=28.36 Aligned_cols=100 Identities=14% Similarity=0.170 Sum_probs=59.9
Q ss_pred hhHHHHHHHhhcceEEEEEcCcCeEEEEcCCCCCCh-hHHHhHHHHH-HHHhcCCChHHHHhhhccCceeEEEecccc-c
Q 017154 67 AWPMVKGALKEYGVSCELNLVEGSMTVSTTRKTRDP-YIIVKARDLI-RLLSRSVPAPQAIKILDDEMQCDIIKIGNL-V 143 (376)
Q Consensus 67 ~W~~I~k~Le~~~l~i~lDl~eGsV~V~Tt~kT~DP-~~IlKArD~I-kAiaRGF~~EqAlkLLeDDi~~dIIdI~~~-v 143 (376)
....+...++..|-.+.++. ..+..-|..-..-| |...=+.-++ -+...|++.++|..++..-+.- -..+ .
T Consensus 145 ~~~~v~~l~~~~G~~~~v~e--~~~~~~~a~~Gsgpa~~~~~~eal~e~~~~~Gl~~~~a~~~~~~~~~g----sa~~~~ 218 (279)
T PRK07679 145 HIQTAKALFETIGLVSVVEE--EDMHAVTALSGSGPAYIYYVVEAMEKAAKKIGLKEDVAKSLILQTMIG----AAEMLK 218 (279)
T ss_pred HHHHHHHHHHhCCcEEEeCH--HHhhhHHHhhcCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH----HHHHHH
Confidence 34566666677787777763 23432232212222 2223333344 3688999999999999873110 0001 1
Q ss_pred cCchhhhhhhceecCCCCchHHHHHHHhC
Q 017154 144 RNKERFVKRRQHLVGPNSSTLKALEILTG 172 (376)
Q Consensus 144 ~nke~f~RrrgRIIG~~GkTkkaIE~LT~ 172 (376)
.+..+..-.+.++.-|+|.|..+|+.|-.
T Consensus 219 ~~~~~~~~l~~~v~spgg~t~~gl~~l~~ 247 (279)
T PRK07679 219 ASEKHPSILRKEITSPGGTTEAGIEVLQE 247 (279)
T ss_pred hcCCCHHHHHHhcCCCchHHHHHHHHHHH
Confidence 12346666788899999999999988764
No 118
>PRK11901 hypothetical protein; Reviewed
Probab=21.47 E-value=95 Score=32.01 Aligned_cols=26 Identities=15% Similarity=0.322 Sum_probs=21.9
Q ss_pred EeCcE--EEEecCCccHHHHHHHHHHHh
Q 017154 177 VQGNT--VAAMGSFKGLKQVRRIVEDCM 202 (376)
Q Consensus 177 V~G~T--VsIIG~~~~IkiAR~AIe~LI 202 (376)
.+|+. |.+.|.|.....|+.||..|=
T Consensus 278 RnGkpWYVVvyG~Y~Sr~eAk~Ai~sLP 305 (327)
T PRK11901 278 RDGKPWYVLVSGNYASSAEAKRAIATLP 305 (327)
T ss_pred ECCceEEEEEecCcCCHHHHHHHHHhCC
Confidence 45544 999999999999999999873
No 119
>PRK10629 EnvZ/OmpR regulon moderator; Provisional
Probab=21.41 E-value=1.8e+02 Score=25.75 Aligned_cols=45 Identities=13% Similarity=0.135 Sum_probs=37.3
Q ss_pred hhhHHHHHHHhhcceEE-EEEcCcCeEEEEcCCCCCChhHHHhHHHHHHH
Q 017154 66 EAWPMVKGALKEYGVSC-ELNLVEGSMTVSTTRKTRDPYIIVKARDLIRL 114 (376)
Q Consensus 66 e~W~~I~k~Le~~~l~i-~lDl~eGsV~V~Tt~kT~DP~~IlKArD~IkA 114 (376)
..=..|+..|++.||.+ .+...++++.|+- .|+..=++|+|+++.
T Consensus 50 ~~~~~v~~~L~~~gI~~ksi~~~~~~~~irf----~~~~~Ql~Ak~vL~~ 95 (127)
T PRK10629 50 PDGFYVYQHLDANGIHIKSITPENDSLLIRF----DSPEQSAAAKEVLDR 95 (127)
T ss_pred chHHHHHHHHHHCCCCcceEEeeCCEEEEEE----CCHHHHHHHHHHHHH
Confidence 34457888998889988 6888899999987 788888999999874
No 120
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=21.20 E-value=1.2e+02 Score=29.90 Aligned_cols=72 Identities=25% Similarity=0.289 Sum_probs=49.7
Q ss_pred eeeeeeecCcchHHHHHhhhHHHHHHHh-hcce-EEEEEcCcCeEEEEcCCCCCChhHHHhHHH--HHHHHhcCCChHHH
Q 017154 49 VSSFSTLFPQYREKYLQEAWPMVKGALK-EYGV-SCELNLVEGSMTVSTTRKTRDPYIIVKARD--LIRLLSRSVPAPQA 124 (376)
Q Consensus 49 essf~~lfPkyRe~yLKe~W~~I~k~Le-~~~l-~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD--~IkAiaRGF~~EqA 124 (376)
+..|+| |.+=| .|-..|+..|+ --|| ++++|+.++.|.|.|+ .-|..|+.+-+ =.+|+.+|+-..+|
T Consensus 8 ~~efaV--~M~ce----scvnavk~~L~~V~Gi~~vevdle~q~v~v~ts---~p~s~i~~~le~tGr~Avl~G~G~psa 78 (247)
T KOG4656|consen 8 EAEFAV--QMTCE----SCVNAVKACLKGVPGINSVEVDLEQQIVSVETS---VPPSEIQNTLENTGRDAVLRGAGKPSA 78 (247)
T ss_pred eEEEEE--echhH----HHHHHHHHHhccCCCcceEEEEhhhcEEEEEcc---CChHHHHHHHHhhChheEEecCCchhH
Confidence 445554 44444 44567888885 3444 6899999999999994 44555554432 25688889988899
Q ss_pred Hhhhc
Q 017154 125 IKILD 129 (376)
Q Consensus 125 lkLLe 129 (376)
+.|+.
T Consensus 79 val~a 83 (247)
T KOG4656|consen 79 VALLA 83 (247)
T ss_pred HHHHH
Confidence 98886
No 121
>PRK14364 Maf-like protein; Provisional
Probab=20.83 E-value=1.9e+02 Score=26.89 Aligned_cols=31 Identities=13% Similarity=0.171 Sum_probs=25.0
Q ss_pred EecCCccHHHHHHHHHHHhcCCCCchhHHHHH
Q 017154 184 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 215 (376)
Q Consensus 184 IIG~~~~IkiAR~AIe~LI~Gs~HpVY~ikel 215 (376)
|+|.+.+.+.|++-+.+| .|+.|-||.-..+
T Consensus 73 ilgKP~~~eeA~~~L~~l-sG~~h~V~Tgv~l 103 (181)
T PRK14364 73 IIGKPDSKQHAFDIWKQL-SGRWHDVFSGICI 103 (181)
T ss_pred EecCCCCHHHHHHHHHHh-CCCCeEEEEEEEE
Confidence 689999999999988777 6778987765544
No 122
>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=20.72 E-value=61 Score=27.51 Aligned_cols=22 Identities=14% Similarity=0.179 Sum_probs=17.7
Q ss_pred hhceecCCCCchHHHHHHHhCc
Q 017154 152 RRQHLVGPNSSTLKALEILTGC 173 (376)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~ 173 (376)
+=|.|||+.|+++..|..+...
T Consensus 71 rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 71 RPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred CCCcccCCchHHHHHHHHHHHH
Confidence 4689999999999998765444
No 123
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=20.51 E-value=1.6e+02 Score=21.73 Aligned_cols=31 Identities=13% Similarity=0.075 Sum_probs=27.5
Q ss_pred CCChhHHHhHHHHHHHHhcCCChHHHHhhhc
Q 017154 99 TRDPYIIVKARDLIRLLSRSVPAPQAIKILD 129 (376)
Q Consensus 99 T~DP~~IlKArD~IkAiaRGF~~EqAlkLLe 129 (376)
..++..+...+.+..+...|||++++-.+|+
T Consensus 38 ~y~~~dl~~l~~i~~lr~~g~~~~~i~~~l~ 68 (70)
T smart00422 38 LYSDEDLERLRFIKRLKELGFSLEEIKELLE 68 (70)
T ss_pred ecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 4788899999999999999999999988875
No 124
>PF06420 Mgm101p: Mitochondrial genome maintenance MGM101; InterPro: IPR009446 The mgm101 gene was identified as essential for maintenance of the mitochondrial genome in Saccharomyces cerevisiae []. Based on its DNA-binding activity, and experimental work with a temperature-sensitive mgm101 mutant, it has been proposed that the mgm101 gene product performs an essential function in the repair of oxidatively damaged mitochondrial DNA [].; GO: 0000002 mitochondrial genome maintenance, 0000262 mitochondrial chromosome
Probab=20.24 E-value=93 Score=29.37 Aligned_cols=115 Identities=30% Similarity=0.423 Sum_probs=69.3
Q ss_pred hcCCChHHHHhhhc--cCceeEEEeccccccCch-hhhhhhceecCCCCch-------HHHHHHHhCceEE-EeCcEEEE
Q 017154 116 SRSVPAPQAIKILD--DEMQCDIIKIGNLVRNKE-RFVKRRQHLVGPNSST-------LKALEILTGCYIL-VQGNTVAA 184 (376)
Q Consensus 116 aRGF~~EqAlkLLe--DDi~~dIIdI~~~v~nke-~f~RrrgRIIG~~GkT-------kkaIE~LT~~~I~-V~G~TVsI 184 (376)
..-|+.|.|--|+. |...+|| +-..+.=-++ ...|+-.|--|++|=- .-.=-.+|.-|-+ +.|.-||+
T Consensus 12 ~~pf~~e~~~~L~~pl~~~DiEI-KPDGliYLPEikYRRiLN~AFGpGgWgL~Prg~~~v~~k~v~ReyaLic~Gr~Vs~ 90 (171)
T PF06420_consen 12 SQPFSKEVADILLAPLDPEDIEI-KPDGLIYLPEIKYRRILNKAFGPGGWGLVPRGETIVTGKIVTREYALICHGRLVSQ 90 (171)
T ss_pred CCCCCHHHHHHHhCCCChhceeE-CCCceEEchHHHHHHHHHHhcCCCceeeeecCCceecCceEEEEEEEEEcCEEEEE
Confidence 35688888888877 5555665 2223322223 4566778888887632 2222234555544 46666887
Q ss_pred -ecCCc--cHHHHHHHHHHHhcCCCCchhHHHHHHHHHhhhcCccccccccc-ccchhhhccc
Q 017154 185 -MGSFK--GLKQVRRIVEDCMQNKMHPVYHIKILMVKKELEKDPALANENWD-RFLPKFKKKN 243 (376)
Q Consensus 185 -IG~~~--~IkiAR~AIe~LI~Gs~HpVY~ikelmiKreL~kd~~l~~e~W~-rflP~fkk~~ 243 (376)
+|.-+ +-.-.-.|++-|=.| .||. .-||=-++.|-|| +|+-+||+++
T Consensus 91 a~GEq~yf~~~~i~tA~EgcKSN---------ALmR---CCKDLGIaSELWDP~FIr~~k~~~ 141 (171)
T PF06420_consen 91 ARGEQDYFSPDSIPTATEGCKSN---------ALMR---CCKDLGIASELWDPRFIRKFKKKY 141 (171)
T ss_pred eeccccccCCCCCchHHHHHHHH---------HHHH---HHHHcCcchhhcChHHHHHHHHHh
Confidence 66422 112223456666555 4544 5678888999998 8999999884
No 125
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.19 E-value=1.4e+02 Score=24.13 Aligned_cols=34 Identities=12% Similarity=0.078 Sum_probs=30.4
Q ss_pred CCCChhHHHhHHHHHHHHhcCCChHHHHhhhccC
Q 017154 98 KTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDE 131 (376)
Q Consensus 98 kT~DP~~IlKArD~IkAiaRGF~~EqAlkLLeDD 131 (376)
..+++..|...+.+..+...|||++++.++|+.+
T Consensus 38 R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~~~ 71 (88)
T cd01105 38 RKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRR 71 (88)
T ss_pred eecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHc
Confidence 4588899999999999999999999999999843
No 126
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=20.02 E-value=3.4e+02 Score=25.47 Aligned_cols=121 Identities=16% Similarity=0.251 Sum_probs=74.7
Q ss_pred HHHHhhhHHHHHHHh-h---cceEEEEEcCcCeEEEEcCCCCCChhHHHhHHHHH--HHHhcCCChHHHHhhhccCceeE
Q 017154 62 KYLQEAWPMVKGALK-E---YGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLI--RLLSRSVPAPQAIKILDDEMQCD 135 (376)
Q Consensus 62 ~yLKe~W~~I~k~Le-~---~~l~i~lDl~eGsV~V~Tt~kT~DP~~IlKArD~I--kAiaRGF~~EqAlkLLeDDi~~d 135 (376)
.=|.++-....+.|. . .|..+++++.+..|++.+ .|-+-+--..|++ +++-||+++ +.|+-+-
T Consensus 13 qEv~NAv~qa~kEi~~RyDFKgs~a~iel~~~~i~l~a----~~d~kl~~v~diL~~kl~KR~i~~----k~ld~~~--- 81 (161)
T PRK05412 13 QEVDNAVDQANKEISTRFDFKGSKASIELKEEEITLTA----ESDFQLKQVKDILRSKLIKRGIDL----KALDYGK--- 81 (161)
T ss_pred HHHHHHHHHHHHHHhcccccCCCccEEEEcCCEEEEEe----CCHHHHHHHHHHHHHHHHHcCCCH----HHcCCCC---
Confidence 345666666777773 2 378888888888899987 6678888888888 488899984 3444210
Q ss_pred EEeccccccCchhhhhhhceecCCCCch----HHHH----HHHhCceEEEeCcEEEEecCC-ccHHHHHHHHHHH
Q 017154 136 IIKIGNLVRNKERFVKRRQHLVGPNSST----LKAL----EILTGCYILVQGNTVAAMGSF-KGLKQVRRIVEDC 201 (376)
Q Consensus 136 IIdI~~~v~nke~f~RrrgRIIG~~GkT----kkaI----E~LT~~~I~V~G~TVsIIG~~-~~IkiAR~AIe~L 201 (376)
.....+ -..|+.+-=..|-. ++.+ +.--.+...|||..|-+-|.- +.|+.|-..+...
T Consensus 82 ---~e~~sG-----~~vrq~i~lk~GI~~e~AKkIvK~IKd~klKVqa~IQGd~vRVtgKkrDDLQ~viallk~~ 148 (161)
T PRK05412 82 ---VEKASG-----KTVKQEVKLKQGIDQELAKKIVKLIKDSKLKVQAQIQGDQVRVTGKKRDDLQAVIALLRKA 148 (161)
T ss_pred ---ccccCC-----CEEEEEEehhhccCHHHHHHHHHHHHhcCCceeEEecCcEEEEecCCHhHHHHHHHHHHhc
Confidence 001111 11233332223322 2222 334568889999999999954 7787776655543
Done!