Query psy15011
Match_columns 334
No_of_seqs 269 out of 590
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 18:08:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15011.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15011hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2874|consensus 100.0 6.6E-91 1.4E-95 657.5 15.6 241 5-333 37-277 (356)
2 COG1094 Predicted RNA-binding 100.0 2.6E-52 5.6E-57 377.8 15.6 164 71-273 6-173 (194)
3 KOG3273|consensus 100.0 8.9E-47 1.9E-51 344.7 11.2 178 64-280 63-247 (252)
4 PRK13763 putative RNA-processi 100.0 1.1E-34 2.5E-39 258.8 16.3 163 75-277 5-170 (180)
5 TIGR03665 arCOG04150 arCOG0415 100.0 3.8E-34 8.2E-39 253.6 15.6 164 77-282 2-168 (172)
6 KOG2874|consensus 99.9 9.1E-26 2E-30 214.9 0.8 64 19-82 68-131 (356)
7 COG1094 Predicted RNA-binding 98.4 2.5E-07 5.4E-12 85.2 3.8 64 18-81 18-82 (194)
8 PRK13763 putative RNA-processi 98.3 5.1E-06 1.1E-10 74.8 10.2 131 17-155 12-171 (180)
9 cd02395 SF1_like-KH Splicing f 98.3 2.8E-06 6E-11 72.6 7.8 92 175-283 16-113 (120)
10 TIGR03665 arCOG04150 arCOG0415 98.0 3.3E-06 7.1E-11 75.5 1.9 67 175-248 8-126 (172)
11 smart00322 KH K homology RNA-b 97.9 2.7E-05 5.8E-10 55.6 5.4 57 174-264 12-68 (69)
12 TIGR03319 YmdA_YtgF conserved 97.7 6.3E-05 1.4E-09 77.8 5.7 68 202-269 202-275 (514)
13 PF00013 KH_1: KH domain syndr 97.6 4.5E-05 9.7E-10 56.0 2.9 47 175-260 10-60 (60)
14 cd02394 vigilin_like_KH K homo 97.6 8.2E-05 1.8E-09 54.9 4.0 52 175-260 10-61 (62)
15 cd02393 PNPase_KH Polynucleoti 97.5 0.00011 2.4E-09 55.3 4.2 49 175-261 12-61 (61)
16 PRK12704 phosphodiesterase; Pr 97.5 0.00017 3.7E-09 74.8 6.8 61 210-270 217-282 (520)
17 cd00105 KH-I K homology RNA-bi 97.5 0.00016 3.4E-09 52.7 4.3 54 175-260 10-63 (64)
18 PRK00106 hypothetical protein; 97.3 0.00031 6.8E-09 73.3 5.7 59 210-269 232-296 (535)
19 KOG1676|consensus 97.3 0.0027 5.9E-08 66.8 11.7 233 28-269 75-392 (600)
20 PF13014 KH_3: KH domain 96.9 0.0017 3.7E-08 45.3 4.3 27 176-202 2-28 (43)
21 cd02396 PCBP_like_KH K homolog 96.5 0.0045 9.8E-08 46.6 4.6 55 175-260 10-64 (65)
22 KOG1676|consensus 95.8 0.026 5.6E-07 59.7 7.6 160 94-265 76-299 (600)
23 KOG1588|consensus 95.7 0.0068 1.5E-07 58.4 2.7 25 176-200 109-133 (259)
24 KOG2193|consensus 95.6 0.014 3.1E-07 60.0 4.6 81 176-256 210-342 (584)
25 KOG2193|consensus 95.2 0.016 3.6E-07 59.6 3.6 87 95-200 434-528 (584)
26 PRK12705 hypothetical protein; 95.2 0.032 7E-07 58.3 5.6 68 202-269 196-269 (508)
27 KOG2191|consensus 94.6 0.078 1.7E-06 53.3 6.2 88 175-262 49-200 (402)
28 PF13083 KH_4: KH domain; PDB: 92.6 0.011 2.4E-07 45.5 -2.7 24 176-199 40-63 (73)
29 PF13014 KH_3: KH domain 92.5 0.095 2.1E-06 36.4 2.1 26 216-241 3-28 (43)
30 KOG0119|consensus 90.6 0.66 1.4E-05 48.8 6.7 126 137-292 121-260 (554)
31 PRK02821 hypothetical protein; 89.9 0.23 5E-06 39.9 2.3 29 176-207 42-70 (77)
32 cd02414 jag_KH jag_K homology 89.3 0.23 4.9E-06 38.8 1.7 24 176-199 35-58 (77)
33 COG5176 MSL5 Splicing factor ( 89.0 0.97 2.1E-05 43.3 5.9 24 176-199 165-188 (269)
34 TIGR02696 pppGpp_PNP guanosine 88.7 0.62 1.4E-05 50.8 5.1 26 175-200 588-613 (719)
35 PRK01064 hypothetical protein; 88.7 0.24 5.2E-06 39.9 1.5 30 176-205 41-70 (78)
36 PRK04163 exosome complex RNA-b 87.9 0.74 1.6E-05 43.3 4.5 64 176-277 156-223 (235)
37 TIGR03591 polynuc_phos polyrib 87.9 0.61 1.3E-05 50.3 4.4 26 176-201 562-587 (684)
38 PRK00468 hypothetical protein; 87.8 0.3 6.6E-06 38.9 1.6 21 176-196 41-61 (75)
39 KOG2190|consensus 86.6 3.1 6.8E-05 43.5 8.5 97 174-270 52-212 (485)
40 cd02134 NusA_KH NusA_K homolog 85.7 0.76 1.6E-05 34.6 2.7 27 174-200 34-60 (61)
41 COG1837 Predicted RNA-binding 82.2 0.77 1.7E-05 37.0 1.5 19 176-194 41-59 (76)
42 KOG1588|consensus 81.4 0.86 1.9E-05 44.3 1.8 73 212-286 106-209 (259)
43 COG1847 Jag Predicted RNA-bind 81.0 0.51 1.1E-05 44.5 0.1 24 176-199 102-125 (208)
44 cd02409 KH-II KH-II (K homolo 80.9 1.6 3.6E-05 31.3 2.7 24 175-198 35-58 (68)
45 COG1159 Era GTPase [General fu 76.3 3.7 8.1E-05 40.7 4.5 54 126-190 187-255 (298)
46 KOG2190|consensus 73.4 3.6 7.8E-05 43.1 3.7 161 79-244 144-378 (485)
47 PRK12704 phosphodiesterase; Pr 71.7 1.8 3.8E-05 45.5 1.0 54 174-233 220-274 (520)
48 cd02395 SF1_like-KH Splicing f 70.6 1.6 3.4E-05 37.6 0.3 32 212-243 14-45 (120)
49 PLN00207 polyribonucleotide nu 70.2 3.3 7.1E-05 46.4 2.7 35 176-210 696-732 (891)
50 COG1185 Pnp Polyribonucleotide 69.6 6 0.00013 43.2 4.5 51 176-264 563-614 (692)
51 PRK08406 transcription elongat 69.5 4.8 0.0001 35.4 3.1 65 175-239 42-134 (140)
52 TIGR03319 YmdA_YtgF conserved 68.8 2.4 5.1E-05 44.5 1.2 59 174-245 214-274 (514)
53 KOG2192|consensus 67.8 15 0.00032 36.7 6.3 92 176-267 59-194 (390)
54 TIGR00436 era GTP-binding prot 67.6 13 0.00027 34.9 5.7 57 127-191 180-248 (270)
55 COG5176 MSL5 Splicing factor ( 67.1 7.4 0.00016 37.5 4.0 85 212-297 162-255 (269)
56 PRK15494 era GTPase Era; Provi 66.0 11 0.00023 37.1 5.1 56 127-190 232-299 (339)
57 PRK00106 hypothetical protein; 60.8 3.9 8.6E-05 43.3 1.1 59 174-245 235-295 (535)
58 KOG3273|consensus 58.8 17 0.00038 34.8 4.8 63 18-80 82-147 (252)
59 COG1097 RRP4 RNA-binding prote 58.6 13 0.00029 35.9 4.1 55 178-269 159-213 (239)
60 PRK11824 polynucleotide phosph 56.4 10 0.00023 41.1 3.4 24 176-199 565-588 (693)
61 KOG2191|consensus 53.1 9.5 0.00021 38.9 2.3 40 176-215 143-192 (402)
62 KOG2814|consensus 51.3 16 0.00036 36.9 3.6 24 176-199 68-91 (345)
63 cd00105 KH-I K homology RNA-bi 49.2 6.5 0.00014 28.2 0.3 30 213-242 9-38 (64)
64 PRK00089 era GTPase Era; Revie 47.6 29 0.00063 32.5 4.5 47 145-191 197-253 (292)
65 cd02134 NusA_KH NusA_K homolog 46.9 20 0.00043 26.9 2.7 29 211-239 32-60 (61)
66 PRK08406 transcription elongat 46.8 9.3 0.0002 33.6 1.0 25 176-200 110-134 (140)
67 PRK05568 flavodoxin; Provision 46.2 1.7E+02 0.0037 24.2 8.9 100 153-264 29-140 (142)
68 cd02394 vigilin_like_KH K homo 46.2 9.8 0.00021 27.7 0.9 31 213-243 9-39 (62)
69 COG1702 PhoH Phosphate starvat 46.1 31 0.00067 35.1 4.6 63 210-272 21-89 (348)
70 TIGR00112 proC pyrroline-5-car 45.9 17 0.00037 33.9 2.6 98 92-195 125-225 (245)
71 cd02393 PNPase_KH Polynucleoti 45.5 53 0.0011 24.5 4.8 35 96-135 26-60 (61)
72 smart00322 KH K homology RNA-b 45.3 8.5 0.00019 26.9 0.4 50 213-262 12-63 (69)
73 TIGR01952 nusA_arch NusA famil 39.6 28 0.00061 30.9 2.9 25 175-199 43-67 (141)
74 PRK12705 hypothetical protein; 39.6 12 0.00025 39.7 0.6 23 174-196 208-230 (508)
75 PF13083 KH_4: KH domain; PDB: 39.0 3 6.4E-05 32.0 -3.0 32 215-246 40-71 (73)
76 TIGR02696 pppGpp_PNP guanosine 36.3 85 0.0018 34.9 6.4 62 94-165 600-661 (719)
77 cd01104 HTH_MlrA-CarA Helix-Tu 36.1 63 0.0014 23.6 3.9 32 121-152 37-68 (68)
78 PRK01064 hypothetical protein; 36.1 16 0.00035 29.4 0.7 32 215-246 41-72 (78)
79 cd02396 PCBP_like_KH K homolog 35.8 14 0.0003 27.6 0.3 31 213-243 9-39 (65)
80 PF07650 KH_2: KH domain syndr 33.5 5.5 0.00012 30.6 -2.3 25 174-198 34-58 (78)
81 KOG0119|consensus 33.1 22 0.00047 37.9 1.3 30 213-242 153-182 (554)
82 cd01813 UBP_N UBP ubiquitin pr 32.5 23 0.00049 27.5 1.0 49 185-249 24-74 (74)
83 TIGR00762 DegV EDD domain prot 31.7 4.1E+02 0.0089 25.2 9.6 74 113-199 108-186 (275)
84 PRK07680 late competence prote 30.9 53 0.0012 30.7 3.4 97 91-194 141-242 (273)
85 TIGR01953 NusA transcription t 30.6 3.2E+02 0.0069 27.6 9.0 93 149-241 204-338 (341)
86 cd02410 archeal_CPSF_KH The ar 30.0 2.1E+02 0.0046 25.9 6.8 87 109-199 6-110 (145)
87 PRK00468 hypothetical protein; 28.3 28 0.0006 27.8 0.9 34 212-245 38-71 (75)
88 PF00403 HMA: Heavy-metal-asso 28.1 1.9E+02 0.0041 20.7 5.3 35 91-125 13-49 (62)
89 cd04764 HTH_MlrA-like_sg1 Heli 27.1 1.1E+02 0.0023 22.6 3.8 32 121-152 36-67 (67)
90 PF04459 DUF512: Protein of un 27.0 5.3E+02 0.012 24.2 9.4 126 10-201 67-199 (204)
91 PRK02821 hypothetical protein; 26.2 37 0.0008 27.3 1.3 32 212-246 39-70 (77)
92 COG1782 Predicted metal-depend 25.5 3.1E+02 0.0068 30.0 8.1 110 85-199 5-133 (637)
93 PRK10076 pyruvate formate lyas 25.5 3.7E+02 0.0081 25.0 7.9 85 107-197 35-127 (213)
94 COG1185 Pnp Polyribonucleotide 25.5 1E+02 0.0022 34.1 4.7 45 94-143 574-618 (692)
95 PF14748 P5CR_dimer: Pyrroline 24.0 19 0.00041 29.9 -0.8 56 136-195 30-86 (107)
96 PF13812 PPR_3: Pentatricopept 23.9 80 0.0017 19.4 2.3 21 133-153 6-26 (34)
97 COG1702 PhoH Phosphate starvat 22.3 92 0.002 31.8 3.5 35 177-211 27-61 (348)
98 TIGR00756 PPR pentatricopeptid 21.6 95 0.0021 18.6 2.3 21 133-153 5-25 (35)
99 cd04763 HTH_MlrA-like Helix-Tu 21.6 1.9E+02 0.0041 21.4 4.3 32 121-152 37-68 (68)
100 cd04735 OYE_like_4_FMN Old yel 21.5 6.5E+02 0.014 24.9 9.2 39 242-289 285-323 (353)
101 COG1707 ACT domain-containing 21.4 55 0.0012 30.8 1.6 59 200-263 81-139 (218)
102 PF08383 Maf_N: Maf N-terminal 21.3 66 0.0014 22.7 1.6 15 138-152 19-33 (35)
103 COG1847 Jag Predicted RNA-bind 21.3 39 0.00086 32.1 0.6 85 205-292 95-194 (208)
104 PF12776 Myb_DNA-bind_3: Myb/S 20.9 1.6E+02 0.0035 22.8 4.0 35 80-116 54-88 (96)
105 KOG4656|consensus 20.6 77 0.0017 30.7 2.4 58 92-152 22-83 (247)
106 PF12854 PPR_1: PPR repeat 20.6 1E+02 0.0022 20.3 2.4 21 133-153 12-32 (34)
107 TIGR03675 arCOG00543 arCOG0054 20.5 3.7E+02 0.008 29.3 7.7 92 106-201 20-129 (630)
108 PRK12327 nusA transcription el 20.2 1.4E+02 0.003 30.4 4.3 99 144-242 201-341 (362)
No 1
>KOG2874|consensus
Probab=100.00 E-value=6.6e-91 Score=657.48 Aligned_cols=241 Identities=71% Similarity=1.144 Sum_probs=232.4
Q ss_pred cccCCCCCCCCCCcccchhhhhHHHHHHHhhhcceeEeeeeecceEEEecccCCCcchhhhhhHHHhhhhccccCchhhH
Q psy15011 5 WSMKIPEFKKEDNPHEYLKECWPLVKNALELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEPLKE 84 (334)
Q Consensus 5 ~~~~~~~~~~~~~~~~ylke~w~~v~~~L~~~~i~~~ldl~egsmtV~Ttkkt~dPyiiikardlikl~sRsVpvP~~Re 84 (334)
|.++++.|+++|||+++++++ +| +|+| |.|||
T Consensus 37 d~wki~~Fs~edn~~g~~EeS----------Sf-----------atlF---------------------------PKYRE 68 (356)
T KOG2874|consen 37 DMWKIEKFSKEDNPHGFLEES----------SF-----------ATLF---------------------------PKYRE 68 (356)
T ss_pred hhhcccccCcccCccchhhhh----------hH-----------Hhhh---------------------------HHHHH
Confidence 334999999999999999998 77 7666 99999
Q ss_pred hHHhhhhhhHHHHHhhcceeEEEEccCCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCCHHHHHHhhhccceeeEEeccc
Q psy15011 85 EYLKECWPLVKNALELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEQAVRVLQDDISCDIIKIGN 164 (334)
Q Consensus 85 ~yLKe~W~~I~~~le~~~l~i~id~~~g~V~V~tt~kT~Dp~~i~KA~D~IkAi~rGF~~e~AlkLL~DDi~~dIIdIk~ 164 (334)
+||+++|+.|.++|++|++.|++|+.+|+|+|+||++|+|||+|+||+|+|++++||++++||+++|+||++||||+|+.
T Consensus 69 kYlke~wp~v~raL~e~~i~c~lDL~egsm~V~TtRkT~DPyIiikArdlIKLlaRsVp~eqAvkiLqDev~CdiIkIgn 148 (356)
T KOG2874|consen 69 KYLKECWPLVERALDEHHIKCVLDLVEGSMTVKTTRKTRDPYIIIKARDLIKLLARSVPFEQAVKILQDEVACDIIKIGN 148 (356)
T ss_pred HHHHHHHHHHHHHHHhcCcceEEeeccceeEEeecccccCceeeeeHHHHHHHHHcCCCHHHHHHHHhhccceeeeehhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCcchhccccceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCCccchhhhhhccceeeeeccEE
Q psy15011 165 LVQNKQRFVKRRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQTV 244 (334)
Q Consensus 165 ~v~n~~~l~R~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV 244 (334)
+++|+++|++||+||||++|.|++|||+||+|||+ |||+||
T Consensus 149 ~V~nkerFvKRRqRLiGpng~TLKAlelLT~CYil---------------------------------------VqG~TV 189 (356)
T KOG2874|consen 149 LVRNKERFVKRRQRLIGPNGSTLKALELLTNCYIL---------------------------------------VQGNTV 189 (356)
T ss_pred hhccHHHHHHHHHHhcCCCchhHHHHHHHhhcEEE---------------------------------------eeCcEE
Confidence 99999999999999999999999999999999999 999999
Q ss_pred EEecCCccHHHHHHHHHHHhcCCCchhHHHHHHHHHhhhcCCccccCCcccccccccccccccccCCcccccCCCCCCCC
Q psy15011 245 AALGPHKGLLQVRRIVEDTMKNIHPIYNIKALMIKRELAKDPKLKNENWERFLPNFKSKTLSKRKMPKKRKTKSEYTPFP 324 (334)
Q Consensus 245 ~iiG~~~~l~~ar~av~~li~g~hpiy~ik~l~~kr~l~~~~~~~~~~w~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~ 324 (334)
|+||+|.||++||++|+|||+|||||||||+|||||||+|||+|+||||+||||+|++||++++|.+ |.+.|++|||||
T Consensus 190 saiGpfkGlkevr~IV~DcM~NiHPiY~IK~LmiKRel~kd~~l~ne~W~rfLP~fkkknv~k~K~~-K~~~kk~ytpfP 268 (356)
T KOG2874|consen 190 SAIGPFKGLKEVRKIVEDCMKNIHPIYNIKTLMIKRELAKDPELANEDWSRFLPQFKKKNVKKRKPK-KVKGKKEYTPFP 268 (356)
T ss_pred EeecCcchHHHHHHHHHHHHhccchHHHHHHHHHHHHhhcChhhccccHHHHhHHhhhhhhhhcccc-cccCCCCCCCCC
Confidence 9999999999999999999999999999999999999999999999999999999999999877655 455699999999
Q ss_pred CCCCCCCCC
Q psy15011 325 PPQPESEAN 333 (334)
Q Consensus 325 ~~~~~~~~~ 333 (334)
|+||+|++|
T Consensus 269 p~q~~sKiD 277 (356)
T KOG2874|consen 269 PAQPPSKID 277 (356)
T ss_pred CCcCcchhh
Confidence 999999998
No 2
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=100.00 E-value=2.6e-52 Score=377.84 Aligned_cols=164 Identities=33% Similarity=0.477 Sum_probs=156.1
Q ss_pred hhhhccccCchhhHhHHhhhhhhHHHHHh-hcceeEEEEccCCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCCHHHHHH
Q psy15011 71 KLLSRSVPYEPLKEEYLKECWPLVKNALE-LHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEQAVR 149 (334)
Q Consensus 71 kl~sRsVpvP~~Re~yLKe~W~~I~~~le-~~~l~i~id~~~g~V~V~tt~kT~Dp~~i~KA~D~IkAi~rGF~~e~Alk 149 (334)
...++.|+||++|++||+..|..++++++ .++++|++|+++|+|+|+|+++|.||++++||+|+|+||+|||+||+|++
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~A~~ 85 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKALK 85 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHHHHH
Confidence 45678899999999999999999999996 56699999999999999999999999999999999999999999999999
Q ss_pred hhhccceeeEEecccccc-CcchhccccceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCCccchh
Q psy15011 150 VLQDDISCDIIKIGNLVQ-NKQRFVKRRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNGCTLKS 228 (334)
Q Consensus 150 LL~DDi~~dIIdIk~~v~-n~~~l~R~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g~~~~~ 228 (334)
||+||++||||||++++. +++||.|++|||||++|+||++||+||+|||+
T Consensus 86 LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~----------------------------- 136 (194)
T COG1094 86 LLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYIS----------------------------- 136 (194)
T ss_pred HhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEE-----------------------------
Confidence 999999999999999987 56679999999999999999999999999999
Q ss_pred hhhhccceeeeeccEEEEecCCccHHHHHHHHHHHhcCCCc--hhHH
Q psy15011 229 IELLTNCYMLVQGQTVAALGPHKGLLQVRRIVEDTMKNIHP--IYNI 273 (334)
Q Consensus 229 ~e~~~~~~~~V~g~tV~iiG~~~~l~~ar~av~~li~g~hp--iy~i 273 (334)
|||+||||||+|++++.||+||+|||+|+|| +|.-
T Consensus 137 ----------V~g~tVaiiG~~~~v~iAr~AVemli~G~~h~~Vy~f 173 (194)
T COG1094 137 ----------VYGKTVAIIGGFEQVEIAREAVEMLINGAPHGKVYKF 173 (194)
T ss_pred ----------EeCcEEEEecChhhhHHHHHHHHHHHcCCCchhHHHH
Confidence 9999999999999999999999999999988 8844
No 3
>KOG3273|consensus
Probab=100.00 E-value=8.9e-47 Score=344.68 Aligned_cols=178 Identities=21% Similarity=0.323 Sum_probs=165.8
Q ss_pred hhhhHH--HhhhhccccCchhhHhHHhhhhhhHHHHH-hhcceeEEEEccCCeEEEEcCCCCCChhHHHhHHHHHHHHhc
Q psy15011 64 IKARDM--IKLLSRSVPYEPLKEEYLKECWPLVKNAL-ELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSR 140 (334)
Q Consensus 64 ikardl--ikl~sRsVpvP~~Re~yLKe~W~~I~~~l-e~~~l~i~id~~~g~V~V~tt~kT~Dp~~i~KA~D~IkAi~r 140 (334)
.++..+ .+.++|+||+||||+++||++|+.||+++ |++++|++||++..+|+++++..|.||.+++|+.|||+||..
T Consensus 63 ~~a~~~~~~k~e~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmNlK~r~VelRt~~~t~D~s~Lqk~adfv~Af~l 142 (252)
T KOG3273|consen 63 LKAKRKRGGKIETRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMNLKARSVELRTCKDTEDPSALQKGADFVRAFIL 142 (252)
T ss_pred ccccccccCccceeeccCCcccCChHHHhhHhhhhHHHHhhhheeEeecccceeEeecCCCCCChHHHHHHHHHHHHHHh
Confidence 455444 67899999999999999999999999987 899999999999999999999999999999999999999999
Q ss_pred CCCHHHHHHhhh-ccceeeEEecccc-ccCcchhccccceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccc
Q psy15011 141 SVPYEQAVRVLQ-DDISCDIIKIGNL-VQNKQRFVKRRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSN 218 (334)
Q Consensus 141 GF~~e~AlkLL~-DDi~~dIIdIk~~-v~n~~~l~R~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~ 218 (334)
||+++||++||+ ||+|+|-+.|+++ +-.++|++|++|||+|++|+|+++|||.|+|+|+
T Consensus 143 GF~i~DAiALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIV------------------- 203 (252)
T KOG3273|consen 143 GFDIDDAIALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIV------------------- 203 (252)
T ss_pred CCcchhHHHHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEE-------------------
Confidence 999999999999 8999666666665 2377999999999999999999999999999999
Q ss_pred cCCCCccchhhhhhccceeeeeccEEEEecCCccHHHHHHHHHHHhcCCCc--hhHHHHHHHHH
Q psy15011 219 IGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQVRRIVEDTMKNIHP--IYNIKALMIKR 280 (334)
Q Consensus 219 ~g~~g~~~~~~e~~~~~~~~V~g~tV~iiG~~~~l~~ar~av~~li~g~hp--iy~ik~l~~kr 280 (334)
|+|.+|||+|.|+|+++||+|||+||+|++| +|+-.+.+..|
T Consensus 204 --------------------lad~kIHiLG~~~niriAR~avcsLIlGsppgkVy~~LR~vasR 247 (252)
T KOG3273|consen 204 --------------------LADSKIHILGAFQNIRIARDAVCSLILGSPPGKVYGNLRNVASR 247 (252)
T ss_pred --------------------ecCceEEEeecchhhHHHHHhhHhhhccCCchhHHHHHHHHHHh
Confidence 9999999999999999999999999999999 99999988776
No 4
>PRK13763 putative RNA-processing protein; Provisional
Probab=100.00 E-value=1.1e-34 Score=258.80 Aligned_cols=163 Identities=26% Similarity=0.340 Sum_probs=155.0
Q ss_pred ccccCchhhHhHHhhhhhhHHHHH-hhcceeEEEEccCCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCCHHHHHHhhhc
Q psy15011 75 RSVPYEPLKEEYLKECWPLVKNAL-ELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEQAVRVLQD 153 (334)
Q Consensus 75 RsVpvP~~Re~yLKe~W~~I~~~l-e~~~l~i~id~~~g~V~V~tt~kT~Dp~~i~KA~D~IkAi~rGF~~e~AlkLL~D 153 (334)
-.+++|++|..+|...|..+.+.| +++++++.+|..+|.|.|.|+. +.||.++++|+++|+||++||+||+|++++.|
T Consensus 5 ~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~~-~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~gd 83 (180)
T PRK13763 5 EYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTD-GEDPLAVLKARDIVKAIGRGFSPEKALRLLDD 83 (180)
T ss_pred EEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeCC-CCCHHHHHHHHHHHHHHhcCCCHHHHHHHhCC
Confidence 357899999999999999998887 6899999999999999999998 99999999999999999999999999999999
Q ss_pred cceeeEEeccccccCcchhccccceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCCccchhhhhhc
Q psy15011 154 DISCDIIKIGNLVQNKQRFVKRRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNGCTLKSIELLT 233 (334)
Q Consensus 154 Di~~dIIdIk~~v~n~~~l~R~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~ 233 (334)
+++++|++|.+|..+++|+.|++|||||++|+|+++||++|||+|.
T Consensus 84 ~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~---------------------------------- 129 (180)
T PRK13763 84 DYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDIS---------------------------------- 129 (180)
T ss_pred CceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEE----------------------------------
Confidence 9999999999998899999999999999999999999999999999
Q ss_pred cceeeeeccEEEEecCCccHHHHHHHHHHHhcC-CCc-hhHHHHHH
Q psy15011 234 NCYMLVQGQTVAALGPHKGLLQVRRIVEDTMKN-IHP-IYNIKALM 277 (334)
Q Consensus 234 ~~~~~V~g~tV~iiG~~~~l~~ar~av~~li~g-~hp-iy~ik~l~ 277 (334)
|+|++|+++|+++++..|+++|++|+.| +|+ +|+..+-.
T Consensus 130 -----i~~~~v~i~G~~~~~~~A~~~I~~li~g~~~~~~~~~l~~~ 170 (180)
T PRK13763 130 -----VYGKTVAIIGDPEQVEIAREAIEMLIEGAPHGTVYKFLERK 170 (180)
T ss_pred -----EcCCEEEEEeCHHHHHHHHHHHHHHHcCCCcHHHHHHHHHH
Confidence 9999999999999999999999999999 566 89877665
No 5
>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=3.8e-34 Score=253.63 Aligned_cols=164 Identities=25% Similarity=0.355 Sum_probs=153.7
Q ss_pred ccCchhhHhHHhhhhhhHHHHH-hhcceeEEEEccCCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCCHHHHHHhhhccc
Q psy15011 77 VPYEPLKEEYLKECWPLVKNAL-ELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEQAVRVLQDDI 155 (334)
Q Consensus 77 VpvP~~Re~yLKe~W~~I~~~l-e~~~l~i~id~~~g~V~V~tt~kT~Dp~~i~KA~D~IkAi~rGF~~e~AlkLL~DDi 155 (334)
+++|++|...|-..|....+.| +++++++++|..+|.|.|+ ..|.||+++++|+++|+||++||+|++|++|+.|++
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 6789999999999999998877 6899999999999999997 678999999999999999999999999999999999
Q ss_pred eeeEEeccccccCcchhccccceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCCccchhhhhhccc
Q psy15011 156 SCDIIKIGNLVQNKQRFVKRRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNGCTLKSIELLTNC 235 (334)
Q Consensus 156 ~~dIIdIk~~v~n~~~l~R~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~~~ 235 (334)
+++|++|.+|.++++||.|++|||||++|+|+++||++|+|+|+
T Consensus 80 ~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~------------------------------------ 123 (172)
T TIGR03665 80 MLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSIS------------------------------------ 123 (172)
T ss_pred eEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEE------------------------------------
Confidence 99999999998899999999999999999999999999999999
Q ss_pred eeeeeccEEEEecCCccHHHHHHHHHHHhcC-CCc-hhHHHHHHHHHhh
Q psy15011 236 YMLVQGQTVAALGPHKGLLQVRRIVEDTMKN-IHP-IYNIKALMIKREL 282 (334)
Q Consensus 236 ~~~V~g~tV~iiG~~~~l~~ar~av~~li~g-~hp-iy~ik~l~~kr~l 282 (334)
|+|++|+|+|++++++.|+++|++|+.| .|| +|+-.+-+ +|||
T Consensus 124 ---i~~~~v~i~G~~~~~~~A~~~i~~li~~~~~~~vy~~l~~~-~~~~ 168 (172)
T TIGR03665 124 ---VYGKTVGIIGDPEQVQIAREAIEMLIEGAPHGTVYKFLERK-RREL 168 (172)
T ss_pred ---EcCCEEEEECCHHHHHHHHHHHHHHHcCCCChhHHHHHHHH-HHHH
Confidence 9999999999999999999999999999 788 88876643 3444
No 6
>KOG2874|consensus
Probab=99.91 E-value=9.1e-26 Score=214.90 Aligned_cols=64 Identities=72% Similarity=1.137 Sum_probs=62.4
Q ss_pred ccchhhhhHHHHHHHhhhcceeEeeeeecceEEEecccCCCcchhhhhhHHHhhhhccccCchh
Q psy15011 19 HEYLKECWPLVKNALELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEPL 82 (334)
Q Consensus 19 ~~ylke~w~~v~~~L~~~~i~~~ldl~egsmtV~Ttkkt~dPyiiikardlikl~sRsVpvP~~ 82 (334)
.+||+||||+|++||++|+|+|.|||+||||+|+||++|||||+|++|||||++++||||||+.
T Consensus 68 EkYlke~wp~v~raL~e~~i~c~lDL~egsm~V~TtRkT~DPyIiikArdlIKLlaRsVp~eqA 131 (356)
T KOG2874|consen 68 EKYLKECWPLVERALDEHHIKCVLDLVEGSMTVKTTRKTRDPYIIIKARDLIKLLARSVPFEQA 131 (356)
T ss_pred HHHHHHHHHHHHHHHHhcCcceEEeeccceeEEeecccccCceeeeeHHHHHHHHHcCCCHHHH
Confidence 5799999999999999999999999999999999999999999999999999999999999965
No 7
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.38 E-value=2.5e-07 Score=85.16 Aligned_cols=64 Identities=41% Similarity=0.539 Sum_probs=60.8
Q ss_pred cccchhhhhHHHHHHHhhhc-ceeEeeeeecceEEEecccCCCcchhhhhhHHHhhhhccccCch
Q psy15011 18 PHEYLKECWPLVKNALELHF-IKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEP 81 (334)
Q Consensus 18 ~~~ylke~w~~v~~~L~~~~-i~~~ldl~egsmtV~Ttkkt~dPyiiikardlikl~sRsVpvP~ 81 (334)
.-+||...|+.+.+.++++. +.|++|+.+|+|++.|+++|.||+.+.+|+|+++..+|++|.+.
T Consensus 18 R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~ 82 (194)
T COG1094 18 RIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEK 82 (194)
T ss_pred hheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHH
Confidence 34799999999999999998 99999999999999999999999999999999999999999883
No 8
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.30 E-value=5.1e-06 Score=74.85 Aligned_cols=131 Identities=22% Similarity=0.272 Sum_probs=100.9
Q ss_pred CcccchhhhhHHHHHHH-hhhcceeEeeeeecceEEEecccCCCcchhhhhhHHHhhhhccccCch----hhHhHH----
Q psy15011 17 NPHEYLKECWPLVKNAL-ELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEP----LKEEYL---- 87 (334)
Q Consensus 17 ~~~~ylke~w~~v~~~L-~~~~i~~~ldl~egsmtV~Ttkkt~dPyiiikardlikl~sRsVpvP~----~Re~yL---- 87 (334)
+.-++|...|..+-+.| ++.++...+|..+|.++++|+. +.||+...+|++++..+++++++.. -...|.
T Consensus 12 ~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~~-~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~gd~y~~~Vi 90 (180)
T PRK13763 12 DRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTD-GEDPLAVLKARDIVKAIGRGFSPEKALRLLDDDYVLEVI 90 (180)
T ss_pred HHhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeCC-CCCHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCceEEEE
Confidence 34567888898888888 5666999999888999999998 9999999999999999999765331 111111
Q ss_pred -------------------hhhhhhHHHHHh-hcceeEEEEccCCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCCHHHH
Q psy15011 88 -------------------KECWPLVKNALE-LHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEQA 147 (334)
Q Consensus 88 -------------------Ke~W~~I~~~le-~~~l~i~id~~~g~V~V~tt~kT~Dp~~i~KA~D~IkAi~rGF~~e~A 147 (334)
-.-=....+.|+ .+++++.++. +.|.|. .||..+..|++.|.+|.+|++++.|
T Consensus 91 ~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~--~~v~i~-----G~~~~~~~A~~~I~~li~g~~~~~~ 163 (180)
T PRK13763 91 DLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG--KTVAII-----GDPEQVEIAREAIEMLIEGAPHGTV 163 (180)
T ss_pred EhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC--CEEEEE-----eCHHHHHHHHHHHHHHHcCCCcHHH
Confidence 111223445664 6888887774 557664 6999999999999999999999999
Q ss_pred HHhhhccc
Q psy15011 148 VRVLQDDI 155 (334)
Q Consensus 148 lkLL~DDi 155 (334)
+++|+++.
T Consensus 164 ~~~l~~~~ 171 (180)
T PRK13763 164 YKFLERKK 171 (180)
T ss_pred HHHHHHHH
Confidence 99999763
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=98.29 E-value=2.8e-06 Score=72.59 Aligned_cols=92 Identities=23% Similarity=0.191 Sum_probs=58.7
Q ss_pred ccceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCCccchhhhhhc-cceeee-eccEEEEecCC--
Q psy15011 175 RRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNGCTLKSIELLT-NCYMLV-QGQTVAALGPH-- 250 (334)
Q Consensus 175 ~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~-~~~~~V-~g~tV~iiG~~-- 250 (334)
-+|||||++|+|.+.||.-|||+|.|.|+.-.- ..+.-+.+. +++.-. .--+|.|.|+.
T Consensus 16 ~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~-----------------~~~~~~~~~~~~~~~~~eplhV~I~a~~~~ 78 (120)
T cd02395 16 FVGLILGPRGNTLKQLEKETGAKISIRGKGSMK-----------------DGKKEEELRGPKYAHLNEPLHVLITAETPP 78 (120)
T ss_pred eeEEEECCCChHHHHHHHHHCCEEEEecCcccc-----------------cccccccccCcccccCCCCcEEEEEeCCcH
Confidence 489999999999999999999999955531111 111111111 111111 11456666654
Q ss_pred -ccHHHHHHHHHHHhcCCCch-hHHHHHHHHHhhh
Q psy15011 251 -KGLLQVRRIVEDTMKNIHPI-YNIKALMIKRELA 283 (334)
Q Consensus 251 -~~l~~ar~av~~li~g~hpi-y~ik~l~~kr~l~ 283 (334)
+.+..|.+.|+.|+.-.||- .+.-.-.--+|||
T Consensus 79 ~e~~~~A~~~I~~ll~~~~~~~~~~~k~~ql~~la 113 (120)
T cd02395 79 EEALAKAVEAIEELLKPAIEGGNDELKREQLRELA 113 (120)
T ss_pred HHHHHHHHHHHHHHhccCCCccchHHHHHHHHHHH
Confidence 99999999999999999986 3333333344554
No 10
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=97.96 E-value=3.3e-06 Score=75.50 Aligned_cols=67 Identities=30% Similarity=0.318 Sum_probs=56.3
Q ss_pred ccceeeCCCcchHHHHHHhhceEEEecce--eeee--ecC--------------------Cc------------------
Q psy15011 175 RRQRLIGPNGCTLKSIELLTNCYMLVQGQ--TVAA--LGP--------------------HK------------------ 212 (334)
Q Consensus 175 ~rGRIIG~~GkTkkaIE~lT~~~I~V~gk--tV~I--IG~--------------------~~------------------ 212 (334)
++|.+||++|+|.+.|+..|||.|.+.+. +|.| .+. .+
T Consensus 8 kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~gd~y~~~Vi~I~ 87 (172)
T TIGR03665 8 RIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDYMLEVIDLK 87 (172)
T ss_pred HhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcCCcceEEEEEhh
Confidence 47899999999999999999999999985 6777 111 11
Q ss_pred ----------cccccccCCCCccchhhhhhccceeeeeccEEEEec
Q psy15011 213 ----------GLLQSNIGPNGCTLKSIELLTNCYMLVQGQTVAALG 248 (334)
Q Consensus 213 ----------~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~iiG 248 (334)
.+++|+||.+|.+++.||++||| .|.+-|
T Consensus 88 ~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~-------~i~i~~ 126 (172)
T TIGR03665 88 EYGKSPNALRRIKGRIIGEGGKTRRIIEELTGV-------SISVYG 126 (172)
T ss_pred hccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCC-------eEEEcC
Confidence 36899999999999999999986 777765
No 11
>smart00322 KH K homology RNA-binding domain.
Probab=97.90 E-value=2.7e-05 Score=55.59 Aligned_cols=57 Identities=19% Similarity=0.332 Sum_probs=45.6
Q ss_pred cccceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCCccchhhhhhccceeeeeccEEEEecCCccH
Q psy15011 174 KRRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGL 253 (334)
Q Consensus 174 R~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~iiG~~~~l 253 (334)
...|++||++|++.+.|+..|||+|.+.+.. . ...+|.+.|+.+++
T Consensus 12 ~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------------------~---------------~~~~v~i~g~~~~v 57 (69)
T smart00322 12 DKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------------------S---------------EERVVEITGPPENV 57 (69)
T ss_pred hhcceeECCCchHHHHHHHHHCCEEEECCCC-------------------C---------------CccEEEEEcCHHHH
Confidence 3468999999999999999999999821100 0 23789999999999
Q ss_pred HHHHHHHHHHh
Q psy15011 254 LQVRRIVEDTM 264 (334)
Q Consensus 254 ~~ar~av~~li 264 (334)
..|++.+.+.+
T Consensus 58 ~~a~~~i~~~~ 68 (69)
T smart00322 58 EKAAELILEIL 68 (69)
T ss_pred HHHHHHHHHHh
Confidence 99999998875
No 12
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=97.65 E-value=6.3e-05 Score=77.76 Aligned_cols=68 Identities=22% Similarity=0.397 Sum_probs=52.3
Q ss_pred ceeeeeec-CCccccccccCCCCccchhhhhhccceeeeeccE-EEEecCCccH--HHHHHHHHHHh-cC-CCc
Q psy15011 202 GQTVAALG-PHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQT-VAALGPHKGL--LQVRRIVEDTM-KN-IHP 269 (334)
Q Consensus 202 gktV~IIG-~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~t-V~iiG~~~~l--~~ar~av~~li-~g-~hp 269 (334)
+.||+.+- +.+.+||||||..|+--+++|.+||+++-|.+.. +-++-+|.-+ .+||.+++.|+ .| |||
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~fdp~rreia~~~l~~li~dgrihp 275 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPVRREIARMALEKLIQDGRIHP 275 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCCCeEEecCCchHHHHHHHHHHHHHHHcCCCCH
Confidence 44444443 4568888888888888888888888888888864 5557777777 78999999999 55 999
No 13
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=97.62 E-value=4.5e-05 Score=55.97 Aligned_cols=47 Identities=21% Similarity=0.372 Sum_probs=39.7
Q ss_pred ccceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCCccchhhhhhccceeeeec----cEEEEecCC
Q psy15011 175 RRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNGCTLKSIELLTNCYMLVQG----QTVAALGPH 250 (334)
Q Consensus 175 ~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g----~tV~iiG~~ 250 (334)
..|+|||++|++.+.||..|||.|. +.. .+|.|.|+.
T Consensus 10 ~~~~iIG~~G~~i~~I~~~t~~~I~---------------------------------------i~~~~~~~~v~I~G~~ 50 (60)
T PF00013_consen 10 LVGRIIGKKGSNIKEIEEETGVKIQ---------------------------------------IPDDDERDIVTISGSP 50 (60)
T ss_dssp HHHHHHTGGGHHHHHHHHHHTSEEE---------------------------------------EESTTEEEEEEEEESH
T ss_pred HcCEEECCCCCcHHHhhhhcCeEEE---------------------------------------EcCCCCcEEEEEEeCH
Confidence 3689999999999999999999999 543 488888988
Q ss_pred ccHHHHHHHH
Q psy15011 251 KGLLQVRRIV 260 (334)
Q Consensus 251 ~~l~~ar~av 260 (334)
+++..|++.|
T Consensus 51 ~~v~~A~~~I 60 (60)
T PF00013_consen 51 EQVEKAKKMI 60 (60)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHhhC
Confidence 8888888765
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=97.59 E-value=8.2e-05 Score=54.91 Aligned_cols=52 Identities=15% Similarity=0.295 Sum_probs=38.8
Q ss_pred ccceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCCccchhhhhhccceeeeeccEEEEecCCccHH
Q psy15011 175 RRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLL 254 (334)
Q Consensus 175 ~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~iiG~~~~l~ 254 (334)
..|+|||++|++.+.|+.-|||.|.|.+.. -....|.|.|+.+++.
T Consensus 10 ~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~----------------------------------~~~~~v~I~G~~~~v~ 55 (62)
T cd02394 10 LHRFIIGKKGSNIRKIMEETGVKIRFPDPG----------------------------------SKSDTITITGPKENVE 55 (62)
T ss_pred HhhhccCCCCCcHHHHHHHhCCEEEcCCCC----------------------------------CCCCEEEEEcCHHHHH
Confidence 367899999999999999999999822110 1137899999988888
Q ss_pred HHHHHH
Q psy15011 255 QVRRIV 260 (334)
Q Consensus 255 ~ar~av 260 (334)
.|+..|
T Consensus 56 ~A~~~i 61 (62)
T cd02394 56 KAKEEI 61 (62)
T ss_pred HHHHHh
Confidence 777665
No 15
>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=97.54 E-value=0.00011 Score=55.30 Aligned_cols=49 Identities=22% Similarity=0.344 Sum_probs=39.7
Q ss_pred ccceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCCccchhhhhhccceeeeeccEEEEecC-CccH
Q psy15011 175 RRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQTVAALGP-HKGL 253 (334)
Q Consensus 175 ~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~iiG~-~~~l 253 (334)
..|+|||++|+|.+.|+.-|||.|.|.+ +-+|.|.|+ .+++
T Consensus 12 ~ig~iIGkgG~~ik~I~~~tg~~I~i~~--------------------------------------~g~v~I~G~~~~~v 53 (61)
T cd02393 12 KIRDVIGPGGKTIKKIIEETGVKIDIED--------------------------------------DGTVYIAASDKEAA 53 (61)
T ss_pred heeeeECCCchHHHHHHHHHCCEEEeCC--------------------------------------CCEEEEEeCCHHHH
Confidence 3689999999999999999999998221 135888997 7888
Q ss_pred HHHHHHHH
Q psy15011 254 LQVRRIVE 261 (334)
Q Consensus 254 ~~ar~av~ 261 (334)
+.|++.|+
T Consensus 54 ~~A~~~I~ 61 (61)
T cd02393 54 EKAKKMIE 61 (61)
T ss_pred HHHHHHhC
Confidence 88887763
No 16
>PRK12704 phosphodiesterase; Provisional
Probab=97.53 E-value=0.00017 Score=74.75 Aligned_cols=61 Identities=21% Similarity=0.397 Sum_probs=51.2
Q ss_pred CCccccccccCCCCccchhhhhhccceeeeecc-EEEEecCCccHH--HHHHHHHHHhc-C-CCch
Q psy15011 210 PHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQ-TVAALGPHKGLL--QVRRIVEDTMK-N-IHPI 270 (334)
Q Consensus 210 ~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~-tV~iiG~~~~l~--~ar~av~~li~-g-~hpi 270 (334)
+.+.+||||||..|+--+.+|.+||+++-|.+. -|-+|-.|..++ .|+.+++.|+. | +||.
T Consensus 217 p~d~mkgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~~~~~rre~a~~~l~~l~~dg~i~P~ 282 (520)
T PRK12704 217 PNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPIRREIARLALEKLVQDGRIHPA 282 (520)
T ss_pred CCchhhcceeCCCcchHHHHHHHhCCeEEEcCCCCeEEEecCChhhHHHHHHHHHHHHhcCCcCCC
Confidence 567888888888888888888888888889885 566688888998 99999999994 4 9994
No 17
>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=97.48 E-value=0.00016 Score=52.72 Aligned_cols=54 Identities=19% Similarity=0.286 Sum_probs=40.2
Q ss_pred ccceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCCccchhhhhhccceeeeeccEEEEecCCccHH
Q psy15011 175 RRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLL 254 (334)
Q Consensus 175 ~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~iiG~~~~l~ 254 (334)
..|+|||++|++.+.|+..|+|.|.|.... . .-....|.+.|+.+++.
T Consensus 10 ~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~-------------------~-------------~~~~~~v~i~G~~~~v~ 57 (64)
T cd00105 10 LVGRIIGKGGSTIKEIREETGAKIKIPDSG-------------------S-------------GSEERIVTITGTPEAVE 57 (64)
T ss_pred hcceeECCCCHHHHHHHHHHCCEEEEcCCC-------------------C-------------CCCceEEEEEcCHHHHH
Confidence 468999999999999999999999922110 0 12346788888888888
Q ss_pred HHHHHH
Q psy15011 255 QVRRIV 260 (334)
Q Consensus 255 ~ar~av 260 (334)
.|+..|
T Consensus 58 ~a~~~i 63 (64)
T cd00105 58 KAKELI 63 (64)
T ss_pred HHHHHh
Confidence 877765
No 18
>PRK00106 hypothetical protein; Provisional
Probab=97.31 E-value=0.00031 Score=73.27 Aligned_cols=59 Identities=24% Similarity=0.426 Sum_probs=41.0
Q ss_pred CCccccccccCCCCccchhhhhhccceeeeecc--EEEEecCCccH--HHHHHHHHHHh-cC-CCc
Q psy15011 210 PHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQ--TVAALGPHKGL--LQVRRIVEDTM-KN-IHP 269 (334)
Q Consensus 210 ~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~--tV~iiG~~~~l--~~ar~av~~li-~g-~hp 269 (334)
+.+.+||||||..|+--+++|.+||+++-|.+. +|. +-.|.-+ .+||.+++.|+ .| |||
T Consensus 232 p~demkGriIGreGrNir~~E~~tGvdliiddtp~~v~-lS~fdpvRReiAr~~le~Li~dgrIhp 296 (535)
T PRK00106 232 PDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTPEVVV-LSGFDPIRREIARMTLESLIKDGRIHP 296 (535)
T ss_pred CChHhhcceeCCCcchHHHHHHHhCceEEEcCCCCeEE-EeCCChHHHHHHHHHHHHHHHcCCcCH
Confidence 445677777777777777777777777768773 444 4444444 58999999999 45 999
No 19
>KOG1676|consensus
Probab=97.25 E-value=0.0027 Score=66.85 Aligned_cols=233 Identities=15% Similarity=0.132 Sum_probs=149.5
Q ss_pred HHHHHHhhhcceeEeeeeecceEEEecccCCCcchhhhhhHHHhhh-hcc------------------ccCchhhHhHHh
Q psy15011 28 LVKNALELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLL-SRS------------------VPYEPLKEEYLK 88 (334)
Q Consensus 28 ~v~~~L~~~~i~~~ldl~egsmtV~Ttkkt~dPyiiikardlikl~-sRs------------------VpvP~~Re~yLK 88 (334)
.|...+-+++|...+.-..++.-.....-+=.|-.+=.|+.|+..+ +|+ +++|..|..-+-
T Consensus 75 qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlII 154 (600)
T KOG1676|consen 75 QIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAKQLIGEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLII 154 (600)
T ss_pred HhhhhhhhcCCccccCCCCCCcccccccccCCcccHHHHHHhhhhhhhccCCCCCccccCCccceeeeeccCccceeeEe
Confidence 4677777888776655555544444433344455555555565533 333 556666654443
Q ss_pred hhhhhHHHHH-hhcceeEEEEccCCeE--EEEcCCCCCChhHHHhHHHHHHHHhcCCCHHHHHHhhhccceeeEEecc-c
Q psy15011 89 ECWPLVKNAL-ELHFIKAELDVIEGSM--TVFTTRKTWDPYIIIKARDMIKLLSRSVPYEQAVRVLQDDISCDIIKIG-N 164 (334)
Q Consensus 89 e~W~~I~~~l-e~~~l~i~id~~~g~V--~V~tt~kT~Dp~~i~KA~D~IkAi~rGF~~e~AlkLL~DDi~~dIIdIk-~ 164 (334)
..=..--+-| +..++++-+.-..... ..++.+.|.||+.+..|+.+|.=|.+- -+|+.+-+.-.-. +
T Consensus 155 GKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e---------~~~~~~g~~~~~g~~ 225 (600)
T KOG1676|consen 155 GKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILRE---------EDDEVPGSGGHAGVR 225 (600)
T ss_pred ccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHh---------cccCCCccccccCcC
Confidence 3322222333 4566666554433321 457778899999999999999844441 0122332210000 0
Q ss_pred cccC--cch-hcc-ccceeeCCCcchHHHHHHhhceEEEe--------cceeeeeecCCcccc-----------------
Q psy15011 165 LVQN--KQR-FVK-RRQRLIGPNGCTLKSIELLTNCYMLV--------QGQTVAALGPHKGLL----------------- 215 (334)
Q Consensus 165 ~v~n--~~~-l~R-~rGRIIG~~GkTkkaIE~lT~~~I~V--------~gktV~IIG~~~~ik----------------- 215 (334)
...+ .+- .-| .-|-|||++|.|-|-|.+-||++|-+ -.+++.|+|.-++|.
T Consensus 226 ~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~ 305 (600)
T KOG1676|consen 226 GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGA 305 (600)
T ss_pred ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhccC
Confidence 0000 000 001 26899999999999999999999975 346799999873321
Q ss_pred ------------------------ccccCCCCccchhhhhhccceeeeec---------cEEEEecCCccHHHHHHHHHH
Q psy15011 216 ------------------------QSNIGPNGCTLKSIELLTNCYMLVQG---------QTVAALGPHKGLLQVRRIVED 262 (334)
Q Consensus 216 ------------------------~~~~g~~g~~~~~~e~~~~~~~~V~g---------~tV~iiG~~~~l~~ar~av~~ 262 (334)
+-+||.+|-+-|+|..-||.|+-+.= +|+.|-|+..+|..|+..|.+
T Consensus 306 ~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~ 385 (600)
T KOG1676|consen 306 GGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRD 385 (600)
T ss_pred CCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcccchHHHHHHHH
Confidence 34689999999999999998886654 599999999999999999999
Q ss_pred HhcCCCc
Q psy15011 263 TMKNIHP 269 (334)
Q Consensus 263 li~g~hp 269 (334)
-|-++-|
T Consensus 386 kvg~~~~ 392 (600)
T KOG1676|consen 386 KVGDIAP 392 (600)
T ss_pred HhcccCC
Confidence 9988654
No 20
>PF13014 KH_3: KH domain
Probab=96.88 E-value=0.0017 Score=45.26 Aligned_cols=27 Identities=30% Similarity=0.404 Sum_probs=24.8
Q ss_pred cceeeCCCcchHHHHHHhhceEEEecc
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYMLVQG 202 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~V~g 202 (334)
.|+|||++|.+.+.|+..|+|+|.|..
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 479999999999999999999999665
No 21
>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=96.52 E-value=0.0045 Score=46.57 Aligned_cols=55 Identities=18% Similarity=0.184 Sum_probs=39.8
Q ss_pred ccceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCCccchhhhhhccceeeeeccEEEEecCCccHH
Q psy15011 175 RRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLL 254 (334)
Q Consensus 175 ~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~iiG~~~~l~ 254 (334)
..|+|||++|.+.+.|+..|||.|.|.. +.. ..-....|-|.|+++++.
T Consensus 10 ~vg~iIG~~G~~i~~i~~~tga~I~i~~-------------------~~~------------~~~~~r~v~I~G~~~~v~ 58 (65)
T cd02396 10 QAGSIIGKGGSTIKEIREETGAKIRVSK-------------------SVL------------PGSTERVVTISGKPSAVQ 58 (65)
T ss_pred HcCeeECCCcHHHHHHHHHHCCEEEEcC-------------------CCC------------CCCCceEEEEEeCHHHHH
Confidence 3789999999999999999999999321 111 012234677888888887
Q ss_pred HHHHHH
Q psy15011 255 QVRRIV 260 (334)
Q Consensus 255 ~ar~av 260 (334)
.|...|
T Consensus 59 ~A~~~I 64 (65)
T cd02396 59 KALLLI 64 (65)
T ss_pred HHHHhh
Confidence 777654
No 22
>KOG1676|consensus
Probab=95.83 E-value=0.026 Score=59.75 Aligned_cols=160 Identities=13% Similarity=0.155 Sum_probs=113.7
Q ss_pred HHHHHhhcceeEEEEccCCeEEEEcCCCCCChhHHHhHHHHHHHH-hcCC---CHHHHHHhhhccceeeEEeccccccCc
Q psy15011 94 VKNALELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLL-SRSV---PYEQAVRVLQDDISCDIIKIGNLVQNK 169 (334)
Q Consensus 94 I~~~le~~~l~i~id~~~g~V~V~tt~kT~Dp~~i~KA~D~IkAi-~rGF---~~e~AlkLL~DDi~~dIIdIk~~v~n~ 169 (334)
|...+.+-++.+.+....+.+-.+.+..+..|..+..|+.++.=+ +||- +++++- +..-.++||-
T Consensus 76 I~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~~~~~~~~~q-----~~~~ttqeI~------ 144 (600)
T KOG1676|consen 76 IQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAKQLIGEVVSRGRPPGGFPDNQ-----GSVETTQEIL------ 144 (600)
T ss_pred hhhhhhhcCCccccCCCCCCcccccccccCCcccHHHHHHhhhhhhhccCCCCCccccC-----Cccceeeeec------
Confidence 444555667777777777777888888888888999898887644 3432 111100 0011122222
Q ss_pred chhccccceeeCCCcchHHHHHHhhceEEEe---------cceeeeeecCC-----------------------------
Q psy15011 170 QRFVKRRQRLIGPNGCTLKSIELLTNCYMLV---------QGQTVAALGPH----------------------------- 211 (334)
Q Consensus 170 ~~l~R~rGRIIG~~GkTkkaIE~lT~~~I~V---------~gktV~IIG~~----------------------------- 211 (334)
.=.-+-|-|||++|.|-+.+.+-|||.+.+ ++|.+-|+|+-
T Consensus 145 -IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~g~~~~~g 223 (600)
T KOG1676|consen 145 -IPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEVPGSGGHAG 223 (600)
T ss_pred -cCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCCCccccccC
Confidence 111236899999999999999999998765 33456777776
Q ss_pred --------------ccccccccCCCCccchhhhhhccceeee--------eccEEEEecCCccHHHHHHHHHHHhc
Q psy15011 212 --------------KGLLQSNIGPNGCTLKSIELLTNCYMLV--------QGQTVAALGPHKGLLQVRRIVEDTMK 265 (334)
Q Consensus 212 --------------~~ik~~~~g~~g~~~~~~e~~~~~~~~V--------~g~tV~iiG~~~~l~~ar~av~~li~ 265 (334)
..=-+-|||-+|.+-|.|-+=||+-|-+ --.++.|||+.+.+..|.+.|..++.
T Consensus 224 ~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~ 299 (600)
T KOG1676|consen 224 VRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIA 299 (600)
T ss_pred cCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHH
Confidence 1112347999999999999999999965 34689999999999999999999885
No 23
>KOG1588|consensus
Probab=95.73 E-value=0.0068 Score=58.43 Aligned_cols=25 Identities=36% Similarity=0.755 Sum_probs=23.8
Q ss_pred cceeeCCCcchHHHHHHhhceEEEe
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYMLV 200 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~V 200 (334)
.|||+|+.|.|.+.+|+-|+|+|+|
T Consensus 109 VGRILGPrGnSlkrLe~eTgCki~I 133 (259)
T KOG1588|consen 109 VGRILGPRGNSLKRLEEETGCKIMI 133 (259)
T ss_pred ccccccCCcchHHHHHHHHCCeEEE
Confidence 6999999999999999999999993
No 24
>KOG2193|consensus
Probab=95.60 E-value=0.014 Score=60.01 Aligned_cols=81 Identities=25% Similarity=0.330 Sum_probs=64.3
Q ss_pred cceeeCCCcchHHHHHHhhceEEEecc--------eeeeeecCC----------------------------------cc
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYMLVQG--------QTVAALGPH----------------------------------KG 213 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~V~g--------ktV~IIG~~----------------------------------~~ 213 (334)
.|-|||++|.|.+.|-.-|.|+|-|-. +-|.+.|-. .+
T Consensus 210 vgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~~k~~~e~pLk~lAHN~ 289 (584)
T KOG2193|consen 210 VGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAVDDKVAEEIPLKILAHNN 289 (584)
T ss_pred eEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHHhhhccchhhhcchhhhhhcc
Confidence 578999999999999999999998753 345555543 78
Q ss_pred ccccccCCCCccchhhhhhccceeeee----------ccEEEEecCCccHHHH
Q psy15011 214 LLQSNIGPNGCTLKSIELLTNCYMLVQ----------GQTVAALGPHKGLLQV 256 (334)
Q Consensus 214 ik~~~~g~~g~~~~~~e~~~~~~~~V~----------g~tV~iiG~~~~l~~a 256 (334)
+-+|.||.-|+..|-||.-|||.|+|- -.||-+-|..+..-.|
T Consensus 290 lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~A 342 (584)
T KOG2193|consen 290 LVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQA 342 (584)
T ss_pred hhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHH
Confidence 999999999999999999999999874 3566666644444333
No 25
>KOG2193|consensus
Probab=95.23 E-value=0.016 Score=59.58 Aligned_cols=87 Identities=18% Similarity=0.210 Sum_probs=55.0
Q ss_pred HHHHhhcceeEEEEc------cCCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCCHHHHHHhhhccce--eeEEeccccc
Q psy15011 95 KNALELHFIKAELDV------IEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEQAVRVLQDDIS--CDIIKIGNLV 166 (334)
Q Consensus 95 ~~~le~~~l~i~id~------~~g~V~V~tt~kT~Dp~~i~KA~D~IkAi~rGF~~e~AlkLL~DDi~--~dIIdIk~~v 166 (334)
+......|..+.+.. .++.|+| |.||.+.+||.-.|- + +|-++..+ -+-+.|..-+
T Consensus 434 Kql~RfagASiKIappE~pdvseRMViI-----tGppeaqfKAQgrif------g-----KikEenf~~Pkeevklethi 497 (584)
T KOG2193|consen 434 KQLSRFAGASIKIAPPEIPDVSERMVII-----TGPPEAQFKAQGRIF------G-----KIKEENFFLPKEEVKLETHI 497 (584)
T ss_pred HHHHHhccceeeecCCCCCCcceeEEEe-----cCChHHHHhhhhhhh------h-----hhhhhccCCchhhheeeeee
Confidence 333345666676643 3444444 589999999986542 1 22222222 1223333322
Q ss_pred cCcchhccccceeeCCCcchHHHHHHhhceEEEe
Q psy15011 167 QNKQRFVKRRQRLIGPNGCTLKSIELLTNCYMLV 200 (334)
Q Consensus 167 ~n~~~l~R~rGRIIG~~GkTkkaIE~lT~~~I~V 200 (334)
+ -=++..||+||++|+|-.-+.++|++.++|
T Consensus 498 r---VPs~~aGRvIGKGGktVnELQnlt~AeV~v 528 (584)
T KOG2193|consen 498 R---VPSSAAGRVIGKGGKTVNELQNLTSAEVVV 528 (584)
T ss_pred e---ccchhhhhhhccccccHHHHhccccceEEc
Confidence 2 234679999999999999999999999994
No 26
>PRK12705 hypothetical protein; Provisional
Probab=95.16 E-value=0.032 Score=58.26 Aligned_cols=68 Identities=21% Similarity=0.317 Sum_probs=43.6
Q ss_pred ceeeeeec-CCccccccccCCCCccchhhhhhccceeeeecc--EEEEec-CCccHHHHHHHHHHHhcC--CCc
Q psy15011 202 GQTVAALG-PHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQ--TVAALG-PHKGLLQVRRIVEDTMKN--IHP 269 (334)
Q Consensus 202 gktV~IIG-~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~--tV~iiG-~~~~l~~ar~av~~li~g--~hp 269 (334)
+.||+.+- +.+.+||||||-.|+--+++|.+||+++-|.+. .|.+.+ ++.-=..|+.+++.|+.. +||
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~~V~ls~fdp~rreia~~~l~~Li~dgri~p 269 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTPEAVVISSFNPIRREIARLTLEKLLADGRIHP 269 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCccchhhcccCccchHHHHHHHHHHHhcCCCCh
Confidence 34443332 345777777777777777777777777777764 333333 233446888999999844 899
No 27
>KOG2191|consensus
Probab=94.56 E-value=0.078 Score=53.25 Aligned_cols=88 Identities=16% Similarity=0.259 Sum_probs=67.7
Q ss_pred ccceeeCCCcchHHHHHHhhceEEEeccee----------eeeecCC---------------------------------
Q psy15011 175 RRQRLIGPNGCTLKSIELLTNCYMLVQGQT----------VAALGPH--------------------------------- 211 (334)
Q Consensus 175 ~rGRIIG~~GkTkkaIE~lT~~~I~V~gkt----------V~IIG~~--------------------------------- 211 (334)
+-|-|||++|.|-..+..-|||+|-+.-+. .-|-|+.
T Consensus 49 AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~k~v~~~~pqt~ 128 (402)
T KOG2191|consen 49 AAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVAKPVDILQPQTP 128 (402)
T ss_pred cccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCc
Confidence 357999999999999999999999765433 1222222
Q ss_pred cccc-----------ccccCCCCccchhhhhhccceeeee----------ccEEEEecCCccHHHHHHHHHH
Q psy15011 212 KGLL-----------QSNIGPNGCTLKSIELLTNCYMLVQ----------GQTVAALGPHKGLLQVRRIVED 262 (334)
Q Consensus 212 ~~ik-----------~~~~g~~g~~~~~~e~~~~~~~~V~----------g~tV~iiG~~~~l~~ar~av~~ 262 (334)
+++| +.+||.+|-+-|.+-+-+|++|.|+ ..-|-+.|++++...|.+.|..
T Consensus 129 ~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~ 200 (402)
T KOG2191|consen 129 DRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQ 200 (402)
T ss_pred cccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHH
Confidence 2333 5789999999999999999988776 5568899999988877665543
No 28
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=92.62 E-value=0.011 Score=45.47 Aligned_cols=24 Identities=38% Similarity=0.520 Sum_probs=21.9
Q ss_pred cceeeCCCcchHHHHHHhhceEEE
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYML 199 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~ 199 (334)
.||+||++|+|..||+.+++..+.
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~~~~~ 63 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVNAAAN 63 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHHHHHH
T ss_pred cceEECCCCeeHHHHHHHHHHHHH
Confidence 789999999999999999987765
No 29
>PF13014 KH_3: KH domain
Probab=92.51 E-value=0.095 Score=36.44 Aligned_cols=26 Identities=27% Similarity=0.310 Sum_probs=24.4
Q ss_pred ccccCCCCccchhhhhhccceeeeec
Q psy15011 216 QSNIGPNGCTLKSIELLTNCYMLVQG 241 (334)
Q Consensus 216 ~~~~g~~g~~~~~~e~~~~~~~~V~g 241 (334)
+++||.+|.+.+.|++.|||.|.|..
T Consensus 3 g~iIG~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 3 GRIIGKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred CeEECCCChHHHHHHHHhCcEEEECC
Confidence 57899999999999999999999977
No 30
>KOG0119|consensus
Probab=90.60 E-value=0.66 Score=48.77 Aligned_cols=126 Identities=17% Similarity=0.291 Sum_probs=76.9
Q ss_pred HHhcCCCHHHHHH---hhhccceeeEEeccccccCcchhccccceeeCCCcchHHHHHHhhceEEEecceeeeeecCCcc
Q psy15011 137 LLSRSVPYEQAVR---VLQDDISCDIIKIGNLVQNKQRFVKRRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKG 213 (334)
Q Consensus 137 Ai~rGF~~e~Alk---LL~DDi~~dIIdIk~~v~n~~~l~R~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ 213 (334)
.+.-||.+-.-.+ +++|-++ |++++|-. -.| .|=|||+.|.|.|-||.-|||+|.|-|+. +.
T Consensus 121 k~nP~fkpP~DYk~p~~~~~Kv~---IPvke~Pd--~NF---vGLiiGPRG~TqK~lE~etgAKI~IRGkg-----Sv-- 185 (554)
T KOG0119|consen 121 KLNPGFKPPADYKPPAKLHDKVY---IPVKEFPD--INF---VGLIIGPRGNTQKRLERETGAKIAIRGKG-----SV-- 185 (554)
T ss_pred HhCcCCCCCcccCccccccccee---cchhhcCC--cce---eEEEecCCccHHHHHHHHhCCeEEEeccc-----cc--
Confidence 3444554433222 3445566 55555522 233 57899999999999999999999966642 11
Q ss_pred ccccccCCCCccchh-------hhhhccceeeeeccEEEEecCCccHHHHHHHHHHHhcC--CCc--hhHHHHHHHHHhh
Q psy15011 214 LLQSNIGPNGCTLKS-------IELLTNCYMLVQGQTVAALGPHKGLLQVRRIVEDTMKN--IHP--IYNIKALMIKREL 282 (334)
Q Consensus 214 ik~~~~g~~g~~~~~-------~e~~~~~~~~V~g~tV~iiG~~~~l~~ar~av~~li~g--~hp--iy~ik~l~~kr~l 282 (334)
-.|+.+.+ .++=.-|+|+ .. .++.|+.|...|+.||.- .-| --..|++-+.++.
T Consensus 186 -------kEgk~~~~d~~~~~~~~epLH~~Is--ad------t~eki~~Ai~vienli~~av~~~e~~n~l~~~Qlrela 250 (554)
T KOG0119|consen 186 -------KEGKGRSDDLSYIPKENEPLHCLIS--AD------TQEKIKKAIAVIENLIQSAVSVPEGQNDLKRLQLRELA 250 (554)
T ss_pred -------cccccCCcccccccccccceeEEEe--cc------hHHHHHHHHHHHHHHHHhhccCccccccccHHHHHHHH
Confidence 12222222 2222223332 22 468899999999999974 233 3445566666666
Q ss_pred hcCCccccCC
Q psy15011 283 AKDPKLKNEN 292 (334)
Q Consensus 283 ~~~~~~~~~~ 292 (334)
.-++.+..++
T Consensus 251 ~lNgt~r~~d 260 (554)
T KOG0119|consen 251 RLNGTLRDDD 260 (554)
T ss_pred HhCCCCCccc
Confidence 6788888877
No 31
>PRK02821 hypothetical protein; Provisional
Probab=89.93 E-value=0.23 Score=39.89 Aligned_cols=29 Identities=21% Similarity=0.351 Sum_probs=22.7
Q ss_pred cceeeCCCcchHHHHHHhhceEEEecceeeee
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYMLVQGQTVAA 207 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~I 207 (334)
.||+||++|+|-+||=.+-.+- +|++|.+
T Consensus 42 ~GrVIGk~Gr~i~AIRtlv~a~---~~~~v~l 70 (77)
T PRK02821 42 LGKVIGRGGRTATALRTVVAAI---GGRGVRV 70 (77)
T ss_pred CcceeCCCCchHHHHHHHHHHh---cCCeEEE
Confidence 8999999999999998765543 5666553
No 32
>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=89.29 E-value=0.23 Score=38.83 Aligned_cols=24 Identities=33% Similarity=0.427 Sum_probs=21.6
Q ss_pred cceeeCCCcchHHHHHHhhceEEE
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYML 199 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~ 199 (334)
.|++||++|+|+.||+-+++..+.
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred CCeEECCCCccHHHHHHHHHHHHh
Confidence 589999999999999999987665
No 33
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=88.96 E-value=0.97 Score=43.29 Aligned_cols=24 Identities=38% Similarity=0.589 Sum_probs=23.0
Q ss_pred cceeeCCCcchHHHHHHhhceEEE
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYML 199 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~ 199 (334)
.|=|||+-|+|++.+|..|+|+|.
T Consensus 165 VGLliGPRG~Tlk~le~~s~akIa 188 (269)
T COG5176 165 VGLLIGPRGSTLKQLERISRAKIA 188 (269)
T ss_pred eEEEecCCcchHHHHHHHhCCeEE
Confidence 689999999999999999999998
No 34
>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=88.71 E-value=0.62 Score=50.81 Aligned_cols=26 Identities=23% Similarity=0.393 Sum_probs=23.4
Q ss_pred ccceeeCCCcchHHHHHHhhceEEEe
Q psy15011 175 RRQRLIGPNGCTLKSIELLTNCYMLV 200 (334)
Q Consensus 175 ~rGRIIG~~GkTkkaIE~lT~~~I~V 200 (334)
.+|.+||++|++-+.|..-|||.|.|
T Consensus 588 ki~~vIG~gGk~I~~i~~~tg~~Idi 613 (719)
T TIGR02696 588 KIGEVIGPKGKMINQIQDETGAEISI 613 (719)
T ss_pred HhhheeCCCcHhHHHHHHHHCCEEEE
Confidence 37899999999999999999999993
No 35
>PRK01064 hypothetical protein; Provisional
Probab=88.67 E-value=0.24 Score=39.86 Aligned_cols=30 Identities=27% Similarity=0.311 Sum_probs=22.6
Q ss_pred cceeeCCCcchHHHHHHhhceEEEecceee
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYMLVQGQTV 205 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~V~gktV 205 (334)
.||+||++|+|.++|-.+.++--.-.|++|
T Consensus 41 ~g~vIGk~G~~i~air~l~~~~~~~~~~rv 70 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLVSVASRNNVKV 70 (78)
T ss_pred ceEEECCCCccHHHHHHHHHHHHhhCCCEE
Confidence 799999999999999997665444333433
No 36
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=87.93 E-value=0.74 Score=43.29 Aligned_cols=64 Identities=20% Similarity=0.382 Sum_probs=42.1
Q ss_pred cceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCCccchhhhhhccceeeeeccEEEEecCCc-cHH
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHK-GLL 254 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~iiG~~~-~l~ 254 (334)
++|+||++|++.+.|...|+|.|. +|.| -.|.|-|+.. .+.
T Consensus 156 i~~lig~~g~~i~~l~~~~~~~I~-------------------ig~N-------------------G~VwI~~~~~~~~~ 197 (235)
T PRK04163 156 VPRVIGKKGSMINMLKEETGCDII-------------------VGQN-------------------GRIWIKGPDEEDEE 197 (235)
T ss_pred HHhhcCCCChhHhhhhhhhCcEEE-------------------EcCC-------------------cEEEEeeCCHHHHH
Confidence 456777777777777777777777 2322 3577777665 788
Q ss_pred HHHHHHHHHhcCCCc---hhHHHHHH
Q psy15011 255 QVRRIVEDTMKNIHP---IYNIKALM 277 (334)
Q Consensus 255 ~ar~av~~li~g~hp---iy~ik~l~ 277 (334)
.|.++|.++=.-.|= .=.+|.++
T Consensus 198 ~a~~~I~~~e~~~~~~~l~~~v~~~~ 223 (235)
T PRK04163 198 IAIEAIKKIEREAHTSGLTDRIKEFL 223 (235)
T ss_pred HHHHHHHHHHhhhhccChHHHHHHHH
Confidence 888888887766664 33444444
No 37
>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=87.91 E-value=0.61 Score=50.33 Aligned_cols=26 Identities=23% Similarity=0.406 Sum_probs=24.1
Q ss_pred cceeeCCCcchHHHHHHhhceEEEec
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYMLVQ 201 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~V~ 201 (334)
+|+|||++|++.+.|+.-|||.|.|.
T Consensus 562 I~~vIG~gGk~Ik~I~~~tg~~I~i~ 587 (684)
T TIGR03591 562 IRDVIGPGGKVIREITEETGAKIDIE 587 (684)
T ss_pred HHhhcCCCcHHHHHHHHHHCCEEEEe
Confidence 88999999999999999999999943
No 38
>PRK00468 hypothetical protein; Provisional
Probab=87.84 E-value=0.3 Score=38.92 Aligned_cols=21 Identities=24% Similarity=0.408 Sum_probs=18.0
Q ss_pred cceeeCCCcchHHHHHHhhce
Q psy15011 176 RQRLIGPNGCTLKSIELLTNC 196 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~ 196 (334)
.||+||++|+|-+||-.+-.+
T Consensus 41 ~GrVIGk~Gr~i~AIRtvv~a 61 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTVVKA 61 (75)
T ss_pred CcceecCCChhHHHHHHHHHH
Confidence 799999999999999875543
No 39
>KOG2190|consensus
Probab=86.57 E-value=3.1 Score=43.52 Aligned_cols=97 Identities=21% Similarity=0.242 Sum_probs=80.6
Q ss_pred cccceeeCCCcchHHHHHHhhceEEEecce-------eeeeec---------CC--------------------------
Q psy15011 174 KRRQRLIGPNGCTLKSIELLTNCYMLVQGQ-------TVAALG---------PH-------------------------- 211 (334)
Q Consensus 174 R~rGRIIG~~GkTkkaIE~lT~~~I~V~gk-------tV~IIG---------~~-------------------------- 211 (334)
+--|=|||++|.+-+-|=.-|+++|-|++. -|-|-| .-
T Consensus 52 kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~ 131 (485)
T KOG2190|consen 52 KEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDEAAEDNGE 131 (485)
T ss_pred ccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcccccccccccCCc
Confidence 346789999999999999888888888776 244445 10
Q ss_pred --------------ccccccccCCCCccchhhhhhccceeeeecc--------EEEEecCCccHHHHHHHHHHHhcCCCc
Q psy15011 212 --------------KGLLQSNIGPNGCTLKSIELLTNCYMLVQGQ--------TVAALGPHKGLLQVRRIVEDTMKNIHP 269 (334)
Q Consensus 212 --------------~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~--------tV~iiG~~~~l~~ar~av~~li~g~hp 269 (334)
...-+++||-+|+--++|.+.||+.|.|-+. .|=|-|....++.|-..|+.+|....|
T Consensus 132 ~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~~ 211 (485)
T KOG2190|consen 132 DASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENPP 211 (485)
T ss_pred cccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcCC
Confidence 2334789999999999999999999999988 688999999999999999999988665
Q ss_pred h
Q psy15011 270 I 270 (334)
Q Consensus 270 i 270 (334)
+
T Consensus 212 ~ 212 (485)
T KOG2190|consen 212 R 212 (485)
T ss_pred c
Confidence 5
No 40
>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=85.69 E-value=0.76 Score=34.60 Aligned_cols=27 Identities=15% Similarity=0.123 Sum_probs=23.9
Q ss_pred cccceeeCCCcchHHHHHHhhceEEEe
Q psy15011 174 KRRQRLIGPNGCTLKSIELLTNCYMLV 200 (334)
Q Consensus 174 R~rGRIIG~~GkTkkaIE~lT~~~I~V 200 (334)
.-.|+.||++|++-+.++.+++.+|-|
T Consensus 34 ~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 34 DQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred ccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 347899999999999999999988863
No 41
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=82.21 E-value=0.77 Score=37.02 Aligned_cols=19 Identities=32% Similarity=0.538 Sum_probs=16.8
Q ss_pred cceeeCCCcchHHHHHHhh
Q psy15011 176 RQRLIGPNGCTLKSIELLT 194 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT 194 (334)
.||+||++|+|-+||=-+-
T Consensus 41 ~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 41 MGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred ccceecCCChhHHHHHHHH
Confidence 8999999999999997643
No 42
>KOG1588|consensus
Probab=81.44 E-value=0.86 Score=44.28 Aligned_cols=73 Identities=22% Similarity=0.280 Sum_probs=50.3
Q ss_pred ccccccccCCCCccchhhhhhccceeeeeccE---------------------------EEEecCCc----cHHHHHHHH
Q psy15011 212 KGLLQSNIGPNGCTLKSIELLTNCYMLVQGQT---------------------------VAALGPHK----GLLQVRRIV 260 (334)
Q Consensus 212 ~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~t---------------------------V~iiG~~~----~l~~ar~av 260 (334)
=|--+||+|+.|-+.+-+|+-|||.|.|-|+- |.+.++.. -|..|..-|
T Consensus 106 fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI 185 (259)
T KOG1588|consen 106 FNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAPPAEAYARLAYALEEI 185 (259)
T ss_pred CccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHH
Confidence 46679999999999999999999999999862 55555543 355677778
Q ss_pred HHHhcCCCchhHHHHHHHHHhhhcCC
Q psy15011 261 EDTMKNIHPIYNIKALMIKRELAKDP 286 (334)
Q Consensus 261 ~~li~g~hpiy~ik~l~~kr~l~~~~ 286 (334)
+.++.=+|==+- .-.-=||||...
T Consensus 186 ~klL~P~~e~~d--k~~QL~ELa~ln 209 (259)
T KOG1588|consen 186 KKLLVPDHEDED--KREQLRELAILN 209 (259)
T ss_pred HHhcCCCCCCch--HHHHHHHHhhcC
Confidence 888765443222 222334665443
No 43
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=80.97 E-value=0.51 Score=44.50 Aligned_cols=24 Identities=42% Similarity=0.683 Sum_probs=23.1
Q ss_pred cceeeCCCcchHHHHHHhhceEEE
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYML 199 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~ 199 (334)
.|||||++|+|+.||+.|++.++.
T Consensus 102 ~~~LIG~~Gk~LdALQ~L~n~~l~ 125 (208)
T COG1847 102 AGRLIGKHGKTLDALQYLANLYLN 125 (208)
T ss_pred hhhhhccCCcchHHHHHHHHHHhh
Confidence 789999999999999999999988
No 44
>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=80.88 E-value=1.6 Score=31.33 Aligned_cols=24 Identities=17% Similarity=0.378 Sum_probs=21.1
Q ss_pred ccceeeCCCcchHHHHHHhhceEE
Q psy15011 175 RRQRLIGPNGCTLKSIELLTNCYM 198 (334)
Q Consensus 175 ~rGRIIG~~GkTkkaIE~lT~~~I 198 (334)
--|++||++|++..+++.+++-++
T Consensus 35 ~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 35 QPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CCceEECCCCccHHHHHHHHHHHc
Confidence 368999999999999999998554
No 45
>COG1159 Era GTPase [General function prediction only]
Probab=76.30 E-value=3.7 Score=40.70 Aligned_cols=54 Identities=22% Similarity=0.452 Sum_probs=36.7
Q ss_pred hHHHhHHHHHHHHhcCCCHHHHHHhhhccce----eeEEeccccccCcchhcc-----------ccceeeCCCcchHHHH
Q psy15011 126 YIIIKARDMIKLLSRSVPYEQAVRVLQDDIS----CDIIKIGNLVQNKQRFVK-----------RRQRLIGPNGCTLKSI 190 (334)
Q Consensus 126 ~~i~KA~D~IkAi~rGF~~e~AlkLL~DDi~----~dIIdIk~~v~n~~~l~R-----------~rGRIIG~~GkTkkaI 190 (334)
..=+.|.++|+ |+++..|+||+= .+|-+.+. +.+.+.+ .+|=|||++|...+.|
T Consensus 187 ~~rf~~aEiiR--------Ek~~~~l~eElPhsv~VeIe~~~~---~~~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~I 255 (298)
T COG1159 187 PERFLAAEIIR--------EKLLLLLREELPHSVAVEIEEFEE---REKGLLKIHATIYVERESQKGIIIGKNGAMIKKI 255 (298)
T ss_pred hHHHHHHHHHH--------HHHHHhcccccCceEEEEEEEEEe---cCCCeEEEEEEEEEecCCccceEECCCcHHHHHH
Confidence 34566888888 999999999843 55554443 2222222 3677899999888776
No 46
>KOG2190|consensus
Probab=73.43 E-value=3.6 Score=43.11 Aligned_cols=161 Identities=16% Similarity=0.094 Sum_probs=99.8
Q ss_pred CchhhHhHHhhhh-hhHHHHHhhcceeEEEEcc------CCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCCH-----HH
Q psy15011 79 YEPLKEEYLKECW-PLVKNALELHFIKAELDVI------EGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPY-----EQ 146 (334)
Q Consensus 79 vP~~Re~yLKe~W-~~I~~~le~~~l~i~id~~------~g~V~V~tt~kT~Dp~~i~KA~D~IkAi~rGF~~-----e~ 146 (334)
||.....+|-.-= ..|+.+.+.++.++++=.. +..|+|. ..|.++.+|--.|-+..+-+.+ -.
T Consensus 144 Vp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~Is-----G~~~av~~al~~Is~~L~~~~~~~~~~~~ 218 (485)
T KOG2190|consen 144 VPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTIS-----GEPDAVKKALVQISSRLLENPPRSPPPLV 218 (485)
T ss_pred echhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEc-----CchHHHHHHHHHHHHHHHhcCCcCCCCCC
Confidence 3444444443332 3456677889999987554 5566664 5677888888777766665321 11
Q ss_pred HHHhhhc-c-ceee-EEeccc-------c---ccCcch------hccccceeeCCCcchHHHHHHhhceEEEecceee--
Q psy15011 147 AVRVLQD-D-ISCD-IIKIGN-------L---VQNKQR------FVKRRQRLIGPNGCTLKSIELLTNCYMLVQGQTV-- 205 (334)
Q Consensus 147 AlkLL~D-D-i~~d-IIdIk~-------~---v~n~~~------l~R~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV-- 205 (334)
+-.-.+- - ..-. +..... + +...+. -.-..++++|++|-.-.++++-|+.-|.|++..-
T Consensus 219 st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~~ 298 (485)
T KOG2190|consen 219 STIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTDR 298 (485)
T ss_pred CcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCcc
Confidence 1111111 0 0000 001000 0 000011 0225799999999999999999999999988764
Q ss_pred ----eeecCC-------------------------------------ccccccccCCCCccchhhhhhccceeeeeccEE
Q psy15011 206 ----AALGPH-------------------------------------KGLLQSNIGPNGCTLKSIELLTNCYMLVQGQTV 244 (334)
Q Consensus 206 ----~IIG~~-------------------------------------~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV 244 (334)
.....+ .+..+++||.+|..--.|..+||+.|++++.-.
T Consensus 299 ~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~ 378 (485)
T KOG2190|consen 299 IVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEE 378 (485)
T ss_pred eeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCceEEccccc
Confidence 222222 355688999999999999999999999988764
No 47
>PRK12704 phosphodiesterase; Provisional
Probab=71.67 E-value=1.8 Score=45.51 Aligned_cols=54 Identities=19% Similarity=0.358 Sum_probs=45.0
Q ss_pred cccceeeCCCcchHHHHHHhhceEEEeccee-eeeecCCccccccccCCCCccchhhhhhc
Q psy15011 174 KRRQRLIGPNGCTLKSIELLTNCYMLVQGQT-VAALGPHKGLLQSNIGPNGCTLKSIELLT 233 (334)
Q Consensus 174 R~rGRIIG~~GkTkkaIE~lT~~~I~V~gkt-V~IIG~~~~ik~~~~g~~g~~~~~~e~~~ 233 (334)
--+|||||++|+..+++|.+|||.|.|+|.- +-+|-.|+.++.- -|+.++|.|-
T Consensus 220 ~mkgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~~~~~rre------~a~~~l~~l~ 274 (520)
T PRK12704 220 EMKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPIRRE------IARLALEKLV 274 (520)
T ss_pred hhhcceeCCCcchHHHHHHHhCCeEEEcCCCCeEEEecCChhhHH------HHHHHHHHHH
Confidence 4599999999999999999999999999984 5567777766554 4788999983
No 48
>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=70.58 E-value=1.6 Score=37.56 Aligned_cols=32 Identities=28% Similarity=0.449 Sum_probs=29.4
Q ss_pred ccccccccCCCCccchhhhhhccceeeeeccE
Q psy15011 212 KGLLQSNIGPNGCTLKSIELLTNCYMLVQGQT 243 (334)
Q Consensus 212 ~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~t 243 (334)
-|..+++||++|++.+.||+-|||.|+|.|..
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~g 45 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKG 45 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCc
Confidence 46779999999999999999999999999964
No 49
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=70.18 E-value=3.3 Score=46.43 Aligned_cols=35 Identities=29% Similarity=0.210 Sum_probs=27.9
Q ss_pred cceeeCCCcchHHHHHHhhceE-EEecc-eeeeeecC
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCY-MLVQG-QTVAALGP 210 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~-I~V~g-ktV~IIG~ 210 (334)
+|.+||++|+|.+.|..-||+. |.+.| -+|.|.|.
T Consensus 696 i~~vIG~GGktIk~I~eetg~~~Idi~ddg~V~I~a~ 732 (891)
T PLN00207 696 VNMIIGSGGKKVKSIIEETGVEAIDTQDDGTVKITAK 732 (891)
T ss_pred HHHHhcCCchhHHHHHHHHCCCccCcCCCeeEEEEeC
Confidence 7899999999999999999999 76544 34555553
No 50
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=69.59 E-value=6 Score=43.22 Aligned_cols=51 Identities=22% Similarity=0.270 Sum_probs=39.1
Q ss_pred cceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCCccchhhhhhccceeeeeccEEEEecCC-ccHH
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQTVAALGPH-KGLL 254 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~iiG~~-~~l~ 254 (334)
++=+||++|+|.++|-..||+.|.+ . .+.||.|.+.. +.++
T Consensus 563 I~dvIG~gGk~I~~I~eetg~~Idi-------------------------------------e-ddGtv~i~~s~~~~~~ 604 (692)
T COG1185 563 IRDVIGPGGKTIKAITEETGVKIDI-------------------------------------E-DDGTVKIAASDGESAK 604 (692)
T ss_pred HhhccCCcccchhhhhhhhCcEEEe-------------------------------------c-CCCcEEEEecchHHHH
Confidence 5578999999999999999999982 2 34677777766 6677
Q ss_pred HHHHHHHHHh
Q psy15011 255 QVRRIVEDTM 264 (334)
Q Consensus 255 ~ar~av~~li 264 (334)
.|++.|+++.
T Consensus 605 ~ak~~I~~i~ 614 (692)
T COG1185 605 KAKERIEAIT 614 (692)
T ss_pred HHHHHHHHHH
Confidence 7777777765
No 51
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=69.48 E-value=4.8 Score=35.38 Aligned_cols=65 Identities=17% Similarity=0.094 Sum_probs=44.2
Q ss_pred ccceeeCCCcchHHHHHHhhceEEEeccee------------------eee----------ecCCccccccccCCCCccc
Q psy15011 175 RRQRLIGPNGCTLKSIELLTNCYMLVQGQT------------------VAA----------LGPHKGLLQSNIGPNGCTL 226 (334)
Q Consensus 175 ~rGRIIG~~GkTkkaIE~lT~~~I~V~gkt------------------V~I----------IG~~~~ik~~~~g~~g~~~ 226 (334)
..|..+|++|+.-++|+++.|-+|-|-.-+ |.+ +==.++=.+..||.+|+.-
T Consensus 42 ~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d~~~fI~n~l~Pa~V~~v~I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni 121 (140)
T PRK08406 42 DMGLAIGKGGENVKRLEEKLGKDIELVEYSDDPEEFIKNIFAPAAVRSVTIKKKNGDKVAYVEVAPEDKGIAIGKNGKNI 121 (140)
T ss_pred CccccCCcCchHHHHHHHHhCCceEEEEcCCCHHHHHHHHcCCCEEEEEEEEecCCcEEEEEEECccccchhhCCCCHHH
Confidence 468999999999999999887555432211 111 1111233567788888888
Q ss_pred hhhhhhccceeee
Q psy15011 227 KSIELLTNCYMLV 239 (334)
Q Consensus 227 ~~~e~~~~~~~~V 239 (334)
+.++.|+|-++-|
T Consensus 122 ~la~~L~~~~~di 134 (140)
T PRK08406 122 ERAKDLAKRHFDI 134 (140)
T ss_pred HHHHHHhCCccCC
Confidence 8888888888766
No 52
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=68.83 E-value=2.4 Score=44.51 Aligned_cols=59 Identities=20% Similarity=0.360 Sum_probs=40.1
Q ss_pred cccceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCC--CccchhhhhhccceeeeeccEEE
Q psy15011 174 KRRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPN--GCTLKSIELLTNCYMLVQGQTVA 245 (334)
Q Consensus 174 R~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~--g~~~~~~e~~~~~~~~V~g~tV~ 245 (334)
-.+|||||++|+..+++|.+||| -|=|=-..+-+--|+.-+= --||.++|.| |.+..||
T Consensus 214 ~~kgriigreGrnir~~e~~tgv-------d~iiddtp~~v~ls~fdp~rreia~~~l~~l------i~dgrih 274 (514)
T TIGR03319 214 EMKGRIIGREGRNIRALETLTGV-------DLIIDDTPEAVILSGFDPVRREIARMALEKL------IQDGRIH 274 (514)
T ss_pred hhhccccCCCcchHHHHHHHhCc-------eEEEcCCCCeEEecCCchHHHHHHHHHHHHH------HHcCCCC
Confidence 35999999999999999999995 3333333344443433332 2378899998 6666665
No 53
>KOG2192|consensus
Probab=67.77 E-value=15 Score=36.71 Aligned_cols=92 Identities=22% Similarity=0.311 Sum_probs=68.8
Q ss_pred cceeeCCCcchHHHHHHhhceEEEeccee-----eeeecC-------------------------------Ccccccccc
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYMLVQGQT-----VAALGP-------------------------------HKGLLQSNI 219 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~V~gkt-----V~IIG~-------------------------------~~~ik~~~~ 219 (334)
-|-+||++|+..+++-.--++.|+|-|+. .+|--+ ++.+-+-+|
T Consensus 59 agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~ti~~ilk~iip~lee~f~~~~pce~rllihqs~ag~ii 138 (390)
T KOG2192|consen 59 AGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIETIGEILKKIIPTLEEGFQLPSPCELRLLIHQSLAGGII 138 (390)
T ss_pred ccceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHHHHHHHHHHHhhhhhhCCCCCCchhhhhhhhhhhcccee
Confidence 68999999999999999999999998875 222211 166778899
Q ss_pred CCCCccchhhhhh--------ccceeeeeccEEEEecCCccHHHHHHHHHHHhcCC
Q psy15011 220 GPNGCTLKSIELL--------TNCYMLVQGQTVAALGPHKGLLQVRRIVEDTMKNI 267 (334)
Q Consensus 220 g~~g~~~~~~e~~--------~~~~~~V~g~tV~iiG~~~~l~~ar~av~~li~g~ 267 (334)
|.||.--+-+-+- |+|-=---+.-|-+-|..+++-...++|.++++-+
T Consensus 139 grngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~ 194 (390)
T KOG2192|consen 139 GRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISES 194 (390)
T ss_pred cccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcC
Confidence 9999876665554 45555455666667788888888888888887653
No 54
>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=67.62 E-value=13 Score=34.90 Aligned_cols=57 Identities=23% Similarity=0.382 Sum_probs=32.9
Q ss_pred HHHhHHHHHHHHhcCCCHHHHHHhhhccce-eeEEeccccccCc-chh----------ccccceeeCCCcchHHHHH
Q psy15011 127 IIIKARDMIKLLSRSVPYEQAVRVLQDDIS-CDIIKIGNLVQNK-QRF----------VKRRQRLIGPNGCTLKSIE 191 (334)
Q Consensus 127 ~i~KA~D~IkAi~rGF~~e~AlkLL~DDi~-~dIIdIk~~v~n~-~~l----------~R~rGRIIG~~GkTkkaIE 191 (334)
.-+-+.++|+ |+.+..|++|+= +--+.+.++..+. ..+ .+.++-|||++|++.+.|-
T Consensus 180 ~~~~~~e~ir--------e~~~~~~~~e~p~~~~~~~~~~~~~~~~~~~i~~~i~v~~~s~k~iiig~~g~~ik~i~ 248 (270)
T TIGR00436 180 DRFKISEIIR--------EKIIRYTKEEIPHSVRVEIERKSFNEKGLLKIHALISVERESQKKIIIGKNGSMIKAIG 248 (270)
T ss_pred HHHHHHHHHH--------HHHHHhcccccCceEEEEEEEEEECCCCeEEEEEEEEECcCCceeEEEcCCcHHHHHHH
Confidence 3445667777 888889998832 2222222332111 111 1236889999999877753
No 55
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=67.06 E-value=7.4 Score=37.47 Aligned_cols=85 Identities=21% Similarity=0.359 Sum_probs=61.5
Q ss_pred ccccccccCCCCccchhhhhhccceeeeeccEEEEec-----CCccHHHHHHHHHHHhcCC--CchhHHHH--HHHHHhh
Q psy15011 212 KGLLQSNIGPNGCTLKSIELLTNCYMLVQGQTVAALG-----PHKGLLQVRRIVEDTMKNI--HPIYNIKA--LMIKREL 282 (334)
Q Consensus 212 ~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~iiG-----~~~~l~~ar~av~~li~g~--hpiy~ik~--l~~kr~l 282 (334)
.|.-+-+||+-|.|.+-+|+.|+|.|-|-|+.=-=-| .+++++-|.+.+.-||--. ..|++... +-+-||-
T Consensus 162 ~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n~I~~a 241 (269)
T COG5176 162 SNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREA 241 (269)
T ss_pred cceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHHHHHHH
Confidence 4566778999999999999999999998886422122 2567888888887777552 33444332 3456899
Q ss_pred hcCCccccCCccccc
Q psy15011 283 AKDPKLKNENWERFL 297 (334)
Q Consensus 283 ~~~~~~~~~~w~~~~ 297 (334)
+.+|+= .-+|+||-
T Consensus 242 ~~~PeG-qnDlkR~q 255 (269)
T COG5176 242 RRNPEG-QNDLKRFQ 255 (269)
T ss_pred hcCCcc-cchHHHHH
Confidence 999997 56899983
No 56
>PRK15494 era GTPase Era; Provisional
Probab=66.05 E-value=11 Score=37.05 Aligned_cols=56 Identities=20% Similarity=0.285 Sum_probs=32.9
Q ss_pred HHHhHHHHHHHHhcCCCHHHHHHhhhccce-eeEEeccccccCc-chh----------ccccceeeCCCcchHHHH
Q psy15011 127 IIIKARDMIKLLSRSVPYEQAVRVLQDDIS-CDIIKIGNLVQNK-QRF----------VKRRQRLIGPNGCTLKSI 190 (334)
Q Consensus 127 ~i~KA~D~IkAi~rGF~~e~AlkLL~DDi~-~dIIdIk~~v~n~-~~l----------~R~rGRIIG~~GkTkkaI 190 (334)
.-+-|.++|+ |+++..|++|+= +--+.+..+..+. +.+ ...++-|||++|++.+.|
T Consensus 232 ~~~~~~eiiR--------e~~~~~~~~EiP~~~~v~i~~~~~~~~~~~~i~~~i~v~~~sqk~iiiG~~g~~ik~i 299 (339)
T PRK15494 232 MRFIAAEITR--------EQLFLNLQKELPYKLTVQTEKWEDLKDKSVKINQVIVVSRESYKTIILGKNGSKIKEI 299 (339)
T ss_pred HHHHHHHHHH--------HHHHhhCCcccCceEEEEEEEEEEcCCCeEEEEEEEEECCCCceeEEEcCCcHHHHHH
Confidence 3455777888 999999999832 1112222222111 111 133778899999877664
No 57
>PRK00106 hypothetical protein; Provisional
Probab=60.82 E-value=3.9 Score=43.34 Aligned_cols=59 Identities=20% Similarity=0.322 Sum_probs=38.6
Q ss_pred cccceeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCC--ccchhhhhhccceeeeeccEEE
Q psy15011 174 KRRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNG--CTLKSIELLTNCYMLVQGQTVA 245 (334)
Q Consensus 174 R~rGRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g--~~~~~~e~~~~~~~~V~g~tV~ 245 (334)
--+|||||++|+..+++|.+||| -+=|=-..+-+--|+.-+=- -||.++|.| |.+..||
T Consensus 235 emkGriIGreGrNir~~E~~tGv-------dliiddtp~~v~lS~fdpvRReiAr~~le~L------i~dgrIh 295 (535)
T PRK00106 235 NMKGRIIGREGRNIRTLESLTGI-------DVIIDDTPEVVVLSGFDPIRREIARMTLESL------IKDGRIH 295 (535)
T ss_pred HhhcceeCCCcchHHHHHHHhCc-------eEEEcCCCCeEEEeCCChHHHHHHHHHHHHH------HHcCCcC
Confidence 35999999999999999999995 22222223333333322222 378889988 5566665
No 58
>KOG3273|consensus
Probab=58.79 E-value=17 Score=34.84 Aligned_cols=63 Identities=22% Similarity=0.415 Sum_probs=54.9
Q ss_pred cccc--hhhhhHHHHHHH-hhhcceeEeeeeecceEEEecccCCCcchhhhhhHHHhhhhccccCc
Q psy15011 18 PHEY--LKECWPLVKNAL-ELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYE 80 (334)
Q Consensus 18 ~~~y--lke~w~~v~~~L-~~~~i~~~ldl~egsmtV~Ttkkt~dPyiiikardlikl~sRsVpvP 80 (334)
||+| |++.|..|---+ +.-++..+.|+-..++++.|..-|.||-.--++.||++-..=+.+++
T Consensus 82 p~r~tplk~~W~kIytPive~lklqiRmNlK~r~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~ 147 (252)
T KOG3273|consen 82 PHRYTPLKDNWMKIYTPIVEHLKLQIRMNLKARSVELRTCKDTEDPSALQKGADFVRAFILGFDID 147 (252)
T ss_pred cccCChHHHhhHhhhhHHHHhhhheeEeecccceeEeecCCCCCChHHHHHHHHHHHHHHhCCcch
Confidence 5677 999998876655 45569999999999999999999999999999999999888888877
No 59
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=58.59 E-value=13 Score=35.90 Aligned_cols=55 Identities=22% Similarity=0.298 Sum_probs=39.9
Q ss_pred eeeCCCcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCCccchhhhhhccceeeeeccEEEEecCCccHHHHH
Q psy15011 178 RLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQVR 257 (334)
Q Consensus 178 RIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~iiG~~~~l~~ar 257 (334)
|+||++|...+.+...|+|.|. +|-||+--.++|+.. .-..|-
T Consensus 159 Rvig~~~sm~~~l~~~~~~~I~-------------------VG~NG~IWV~~~~~~------------------~e~~~~ 201 (239)
T COG1097 159 RVIGKKGSMLNMLKEKTGCEII-------------------VGQNGRIWVDGENES------------------LEELAI 201 (239)
T ss_pred eEecCCCcHHHHhhhhcCeEEE-------------------EecCCEEEecCCCcc------------------hHHHHH
Confidence 6999999999999999999999 566665444444433 356677
Q ss_pred HHHHHHhcCCCc
Q psy15011 258 RIVEDTMKNIHP 269 (334)
Q Consensus 258 ~av~~li~g~hp 269 (334)
.||..|=+-.|=
T Consensus 202 ~aI~~ie~ea~~ 213 (239)
T COG1097 202 EAIRKIEREAHT 213 (239)
T ss_pred HHHHHHhhhhhh
Confidence 777766555554
No 60
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=56.44 E-value=10 Score=41.12 Aligned_cols=24 Identities=29% Similarity=0.408 Sum_probs=22.2
Q ss_pred cceeeCCCcchHHHHHHhhceEEE
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYML 199 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~ 199 (334)
++.+||++|+|.+.|..-||+.|.
T Consensus 565 I~~vIG~gg~~ik~I~~~~~~~id 588 (693)
T PRK11824 565 IRDVIGPGGKTIREITEETGAKID 588 (693)
T ss_pred HHHHhcCCchhHHHHHHHHCCccc
Confidence 689999999999999999999888
No 61
>KOG2191|consensus
Probab=53.12 E-value=9.5 Score=38.85 Aligned_cols=40 Identities=20% Similarity=0.387 Sum_probs=34.0
Q ss_pred cceeeCCCcchHHHHHHhhceEEEec----------ceeeeeecCCcccc
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYMLVQ----------GQTVAALGPHKGLL 215 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~V~----------gktV~IIG~~~~ik 215 (334)
-|-|||++|.|-|+|.+-++|+|.|+ +.-|-+.|++++.+
T Consensus 143 ag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~ 192 (402)
T KOG2191|consen 143 AGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNM 192 (402)
T ss_pred ccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHH
Confidence 47899999999999999999999988 44488889886554
No 62
>KOG2814|consensus
Probab=51.27 E-value=16 Score=36.94 Aligned_cols=24 Identities=33% Similarity=0.331 Sum_probs=23.2
Q ss_pred cceeeCCCcchHHHHHHhhceEEE
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYML 199 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~ 199 (334)
.|-|+|++|+|++-||+-|+|+|.
T Consensus 68 ~~~lig~~g~trkkle~Etq~~i~ 91 (345)
T KOG2814|consen 68 IGWLIGKQGKTRKKLEEETQTNIF 91 (345)
T ss_pred hhhhhcccchHHHHHHHhhccceE
Confidence 789999999999999999999999
No 63
>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=49.17 E-value=6.5 Score=28.23 Aligned_cols=30 Identities=27% Similarity=0.354 Sum_probs=26.9
Q ss_pred cccccccCCCCccchhhhhhccceeeeecc
Q psy15011 213 GLLQSNIGPNGCTLKSIELLTNCYMLVQGQ 242 (334)
Q Consensus 213 ~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~ 242 (334)
..-+++||.+|...+.|++-|||.|.|...
T Consensus 9 ~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~ 38 (64)
T cd00105 9 SLVGRIIGKGGSTIKEIREETGAKIKIPDS 38 (64)
T ss_pred hhcceeECCCCHHHHHHHHHHCCEEEEcCC
Confidence 455789999999999999999999998874
No 64
>PRK00089 era GTPase Era; Reviewed
Probab=47.63 E-value=29 Score=32.53 Aligned_cols=47 Identities=28% Similarity=0.485 Sum_probs=26.3
Q ss_pred HHHHHhhhccce----eeEEecccc--cc-Ccchh---ccccceeeCCCcchHHHHH
Q psy15011 145 EQAVRVLQDDIS----CDIIKIGNL--VQ-NKQRF---VKRRQRLIGPNGCTLKSIE 191 (334)
Q Consensus 145 e~AlkLL~DDi~----~dIIdIk~~--v~-n~~~l---~R~rGRIIG~~GkTkkaIE 191 (334)
|+++..|++|+= .+|.+...- +. .-.-+ ...++=|||++|++.+.|-
T Consensus 197 e~~~~~l~~e~p~~~~v~~~~~~~~~~~~i~~~i~v~~~~~k~i~ig~~g~~i~~i~ 253 (292)
T PRK00089 197 EKLLRLLGDELPYSVAVEIEKFEERGLVRIEATIYVERDSQKGIIIGKGGAMLKKIG 253 (292)
T ss_pred HHHHhhCCccCCceEEEEEEEEEECCeEEEEEEEEEccCCceeEEEeCCcHHHHHHH
Confidence 899999998732 333333211 00 00001 1226889999999877753
No 65
>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=46.94 E-value=20 Score=26.93 Aligned_cols=29 Identities=17% Similarity=0.150 Sum_probs=25.3
Q ss_pred CccccccccCCCCccchhhhhhccceeee
Q psy15011 211 HKGLLQSNIGPNGCTLKSIELLTNCYMLV 239 (334)
Q Consensus 211 ~~~ik~~~~g~~g~~~~~~e~~~~~~~~V 239 (334)
.++=.+..||.+|+.-+.+++|+|.+|-|
T Consensus 32 ~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 32 PDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 34667889999999999999999998876
No 66
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=46.84 E-value=9.3 Score=33.57 Aligned_cols=25 Identities=20% Similarity=0.243 Sum_probs=22.8
Q ss_pred cceeeCCCcchHHHHHHhhceEEEe
Q psy15011 176 RQRLIGPNGCTLKSIELLTNCYMLV 200 (334)
Q Consensus 176 rGRIIG~~GkTkkaIE~lT~~~I~V 200 (334)
.|+.||++|++.++++.+++-++-|
T Consensus 110 ~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 110 KGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred cchhhCCCCHHHHHHHHHhCCccCC
Confidence 7899999999999999999988764
No 67
>PRK05568 flavodoxin; Provisional
Probab=46.20 E-value=1.7e+02 Score=24.21 Aligned_cols=100 Identities=11% Similarity=0.174 Sum_probs=59.9
Q ss_pred ccceeeEEeccccccCcchhccccceeeCC---------CcchHHHHHHhhceEEEecceeeeeecCCccccccccCCCC
Q psy15011 153 DDISCDIIKIGNLVQNKQRFVKRRQRLIGP---------NGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPNG 223 (334)
Q Consensus 153 DDi~~dIIdIk~~v~n~~~l~R~rGRIIG~---------~GkTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g~~g 223 (334)
+++.++++++.+.. ...+...-+=++|. .+..+..++.+-. ...|+.++++|.+-. ..|
T Consensus 29 ~g~~v~~~~~~~~~--~~~~~~~d~iilgsp~y~~~~~~~~~~~~f~~~~~~---~~~~k~~~~f~t~G~-------~~~ 96 (142)
T PRK05568 29 NGAEVKLLNVSEAS--VDDVKGADVVALGSPAMGDEVLEEGEMEPFVESISS---LVKGKKLVLFGSYGW-------GDG 96 (142)
T ss_pred CCCeEEEEECCCCC--HHHHHhCCEEEEECCccCcccccchhHHHHHHHhhh---hhCCCEEEEEEccCC-------CCC
Confidence 44667788877642 23565556666664 1456677776643 247899999999532 113
Q ss_pred ccch-hhhhhccceeeeeccEEEEecCC--ccHHHHHHHHHHHh
Q psy15011 224 CTLK-SIELLTNCYMLVQGQTVAALGPH--KGLLQVRRIVEDTM 264 (334)
Q Consensus 224 ~~~~-~~e~~~~~~~~V~g~tV~iiG~~--~~l~~ar~av~~li 264 (334)
.+-+ -.+.|.+..+.+-|..+-+-|.+ +.++.|++....+.
T Consensus 97 ~~~~~~~~~l~~~g~~~~~~~~~~~~~p~~~~l~~~~~~g~~l~ 140 (142)
T PRK05568 97 EWMRDWVERMEGYGANLVNEGLIVNNTPEGEGIEKCKALGEALA 140 (142)
T ss_pred hHHHHHHHHHHHCCCEEeCCcEEEecCCCHHHHHHHHHHHHHHH
Confidence 3434 33445666667777666666654 45666777666554
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=46.15 E-value=9.8 Score=27.75 Aligned_cols=31 Identities=19% Similarity=0.182 Sum_probs=28.0
Q ss_pred cccccccCCCCccchhhhhhccceeeeeccE
Q psy15011 213 GLLQSNIGPNGCTLKSIELLTNCYMLVQGQT 243 (334)
Q Consensus 213 ~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~t 243 (334)
..-+++||.+|...+.|++-|||.|.|....
T Consensus 9 ~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~ 39 (62)
T cd02394 9 KLHRFIIGKKGSNIRKIMEETGVKIRFPDPG 39 (62)
T ss_pred HHhhhccCCCCCcHHHHHHHhCCEEEcCCCC
Confidence 4557899999999999999999999998865
No 69
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=46.10 E-value=31 Score=35.13 Aligned_cols=63 Identities=19% Similarity=0.357 Sum_probs=43.2
Q ss_pred CCccccccccCCCCccchhhhhhccceeeeeccEEEEecCCccHHHHHHHHH--HHh----cCCCchhH
Q psy15011 210 PHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQVRRIVE--DTM----KNIHPIYN 272 (334)
Q Consensus 210 ~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~iiG~~~~l~~ar~av~--~li----~g~hpiy~ 272 (334)
+.++--....|++|...+-+|...|+.|..-|+++.+.|+...+..|++++. .+. .|++.+|.
T Consensus 21 ~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG~~~~i~g~~~~v~~A~~~l~~l~~~~~~~~g~~~~~~ 89 (348)
T COG1702 21 SDDNELVALFGPTDTNLSLLEIALGVSIVARGEAVRIIGARPLVDVATRVLLTLELLAEVRRGIASIYL 89 (348)
T ss_pred CCchhhhhhcCCCCccHHHHHHHhCcEEEeCCceEEEEechHHHHHHHHHHhHHHHHHHHhcccccCCH
Confidence 3344445555555666666666666666699999999999889999999888 332 45566554
No 70
>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=45.86 E-value=17 Score=33.89 Aligned_cols=98 Identities=16% Similarity=0.225 Sum_probs=64.7
Q ss_pred hhHHHHHhhcceeEEEEccCCeEEEEcCCCCCChhHHH-hHHHHH-HHHhcCCCHHHHHHhhhccceeeEEeccccc-cC
Q psy15011 92 PLVKNALELHFIKAELDVIEGSMTVFTTRKTWDPYIII-KARDMI-KLLSRSVPYEQAVRVLQDDISCDIIKIGNLV-QN 168 (334)
Q Consensus 92 ~~I~~~le~~~l~i~id~~~g~V~V~tt~kT~Dp~~i~-KA~D~I-kAi~rGF~~e~AlkLL~DDi~~dIIdIk~~v-~n 168 (334)
..+...++..|.-+.++ +..+..-|.--.--|..+. =+..++ .|+..||+.++|.++...=+. -...++ .+
T Consensus 125 ~~v~~lf~~~G~~~~v~--E~~~~~~talsgsgPA~~~~~~~al~~~~v~~Gl~~~~A~~lv~~~~~----G~a~l~~~~ 198 (245)
T TIGR00112 125 ALVLALFKAVGEVVELP--EALMDAVTALSGSGPAYVFLFIEALADAGVKQGLPRELALELAAQTVK----GAAKLLEES 198 (245)
T ss_pred HHHHHHHHhCCCEEEEC--HHHcchHHhhccCcHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH----HHHHHHHhc
Confidence 45667778888888887 4455444432223443222 222333 467899999999999975422 111222 35
Q ss_pred cchhccccceeeCCCcchHHHHHHhhc
Q psy15011 169 KQRFVKRRQRLIGPNGCTLKSIELLTN 195 (334)
Q Consensus 169 ~~~l~R~rGRIIG~~GkTkkaIE~lT~ 195 (334)
+.++...+.++.-|+|.|-.+|+.|-.
T Consensus 199 ~~~~~~l~~~v~spgGtT~~gl~~Le~ 225 (245)
T TIGR00112 199 GEHPALLKDQVTSPGGTTIAGLAVLEE 225 (245)
T ss_pred CCCHHHHHHcCCCCcHHHHHHHHHHHH
Confidence 578888899999999999999998754
No 71
>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=45.54 E-value=53 Score=24.55 Aligned_cols=35 Identities=23% Similarity=0.303 Sum_probs=27.5
Q ss_pred HHHhhcceeEEEEccCCeEEEEcCCCCCChhHHHhHHHHH
Q psy15011 96 NALELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMI 135 (334)
Q Consensus 96 ~~le~~~l~i~id~~~g~V~V~tt~kT~Dp~~i~KA~D~I 135 (334)
..-+++++++.++. +|.|.|.. .|+..+..|.++|
T Consensus 26 ~I~~~tg~~I~i~~-~g~v~I~G----~~~~~v~~A~~~I 60 (61)
T cd02393 26 KIIEETGVKIDIED-DGTVYIAA----SDKEAAEKAKKMI 60 (61)
T ss_pred HHHHHHCCEEEeCC-CCEEEEEe----CCHHHHHHHHHHh
Confidence 33468999999987 68999986 5677888888776
No 72
>smart00322 KH K homology RNA-binding domain.
Probab=45.34 E-value=8.5 Score=26.88 Aligned_cols=50 Identities=20% Similarity=0.114 Sum_probs=34.6
Q ss_pred cccccccCCCCccchhhhhhccceeeeeccE--EEEecCCccHHHHHHHHHH
Q psy15011 213 GLLQSNIGPNGCTLKSIELLTNCYMLVQGQT--VAALGPHKGLLQVRRIVED 262 (334)
Q Consensus 213 ~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~t--V~iiG~~~~l~~ar~av~~ 262 (334)
..-+.+||.+|+..+.++..||+.|.+.+.. ...+-=.-.-..+..|...
T Consensus 12 ~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~ 63 (69)
T smart00322 12 DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAEL 63 (69)
T ss_pred hhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHH
Confidence 5567899999999999999999999987653 4443333343344444333
No 73
>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=39.65 E-value=28 Score=30.86 Aligned_cols=25 Identities=24% Similarity=0.236 Sum_probs=21.3
Q ss_pred ccceeeCCCcchHHHHHHhhceEEE
Q psy15011 175 RRQRLIGPNGCTLKSIELLTNCYML 199 (334)
Q Consensus 175 ~rGRIIG~~GkTkkaIE~lT~~~I~ 199 (334)
-.|..+|++|+.-++|+++.|=+|-
T Consensus 43 ~vG~~IG~~G~rIk~i~el~gekId 67 (141)
T TIGR01952 43 EMGAAIGKGGENVKRLEELIGKSIE 67 (141)
T ss_pred CccccCCCCchHHHHHHHhcCCeeE
Confidence 4789999999999999999885554
No 74
>PRK12705 hypothetical protein; Provisional
Probab=39.55 E-value=12 Score=39.65 Aligned_cols=23 Identities=30% Similarity=0.527 Sum_probs=21.6
Q ss_pred cccceeeCCCcchHHHHHHhhce
Q psy15011 174 KRRQRLIGPNGCTLKSIELLTNC 196 (334)
Q Consensus 174 R~rGRIIG~~GkTkkaIE~lT~~ 196 (334)
--+|||||++|+..+++|.+||+
T Consensus 208 emkGriIGreGrNir~~E~~tGv 230 (508)
T PRK12705 208 AMKGRIIGREGRNIRAFEGLTGV 230 (508)
T ss_pred HhhccccCccchhHHHHHHhhCC
Confidence 45999999999999999999997
No 75
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=39.04 E-value=3 Score=31.96 Aligned_cols=32 Identities=28% Similarity=0.368 Sum_probs=26.0
Q ss_pred cccccCCCCccchhhhhhccceeeeeccEEEE
Q psy15011 215 LQSNIGPNGCTLKSIELLTNCYMLVQGQTVAA 246 (334)
Q Consensus 215 k~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~i 246 (334)
.+++||-+|++..+++-|.+.++.-+|+.|.+
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~~~~~~~~~~~~v 71 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVNAAANKHGKRVRV 71 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHHHHHHHT-SS-EE
T ss_pred cceEECCCCeeHHHHHHHHHHHHHhCCCEEEE
Confidence 78999999999999999999888777665543
No 76
>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=36.34 E-value=85 Score=34.86 Aligned_cols=62 Identities=13% Similarity=0.140 Sum_probs=46.2
Q ss_pred HHHHHhhcceeEEEEccCCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCCHHHHHHhhhccceeeEEecccc
Q psy15011 94 VKNALELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEQAVRVLQDDISCDIIKIGNL 165 (334)
Q Consensus 94 I~~~le~~~l~i~id~~~g~V~V~tt~kT~Dp~~i~KA~D~IkAi~rGF~~e~AlkLL~DDi~~dIIdIk~~ 165 (334)
|+.+.+++|++|.++- +|.|.|.. .|.-.+.+|.++|+.+...|.|+ .-+-+...|.+|.+|
T Consensus 600 I~~i~~~tg~~Idi~d-~G~V~I~a----~d~~~~~~A~~~I~~i~~~~~~~-----vG~i~~GkV~~I~df 661 (719)
T TIGR02696 600 INQIQDETGAEISIED-DGTVYIGA----ADGPSAEAARAMINAIANPTMPE-----VGERFLGTVVKTTAF 661 (719)
T ss_pred HHHHHHHHCCEEEEec-CcEEEEEe----CCHHHHHHHHHHHHHhhCcCcCC-----CCCEEEEEEEEEECc
Confidence 4455689999999986 79999987 68889999999999999875432 112244666666664
No 77
>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=36.11 E-value=63 Score=23.58 Aligned_cols=32 Identities=19% Similarity=0.190 Sum_probs=27.7
Q ss_pred CCCChhHHHhHHHHHHHHhcCCCHHHHHHhhh
Q psy15011 121 KTWDPYIIIKARDMIKLLSRSVPYEQAVRVLQ 152 (334)
Q Consensus 121 kT~Dp~~i~KA~D~IkAi~rGF~~e~AlkLL~ 152 (334)
...++-.+...+.+..+...||+++++.++|+
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 34677889999999999999999999999874
No 78
>PRK01064 hypothetical protein; Provisional
Probab=36.07 E-value=16 Score=29.43 Aligned_cols=32 Identities=25% Similarity=0.260 Sum_probs=26.3
Q ss_pred cccccCCCCccchhhhhhccceeeeeccEEEE
Q psy15011 215 LQSNIGPNGCTLKSIELLTNCYMLVQGQTVAA 246 (334)
Q Consensus 215 k~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~i 246 (334)
++++||-+|++..+|..+.+.-..=+|++|.+
T Consensus 41 ~g~vIGk~G~~i~air~l~~~~~~~~~~rv~l 72 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLVSVASRNNVKVSL 72 (78)
T ss_pred ceEEECCCCccHHHHHHHHHHHHhhCCCEEEE
Confidence 69999999999999999877666667776653
No 79
>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=35.75 E-value=14 Score=27.64 Aligned_cols=31 Identities=29% Similarity=0.269 Sum_probs=27.0
Q ss_pred cccccccCCCCccchhhhhhccceeeeeccE
Q psy15011 213 GLLQSNIGPNGCTLKSIELLTNCYMLVQGQT 243 (334)
Q Consensus 213 ~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~t 243 (334)
..-+++||.+|...+.|++-|||.|.|..+.
T Consensus 9 ~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~ 39 (65)
T cd02396 9 SQAGSIIGKGGSTIKEIREETGAKIRVSKSV 39 (65)
T ss_pred HHcCeeECCCcHHHHHHHHHHCCEEEEcCCC
Confidence 3457899999999999999999999997654
No 80
>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=33.49 E-value=5.5 Score=30.65 Aligned_cols=25 Identities=20% Similarity=0.246 Sum_probs=19.2
Q ss_pred cccceeeCCCcchHHHHHHhhceEE
Q psy15011 174 KRRQRLIGPNGCTLKSIELLTNCYM 198 (334)
Q Consensus 174 R~rGRIIG~~GkTkkaIE~lT~~~I 198 (334)
...|.+||++|++.+.|....+-.+
T Consensus 34 ~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 34 SQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CCccHhHHhhhHHHHHHHHHHHHHH
Confidence 3478999999999998877654443
No 81
>KOG0119|consensus
Probab=33.14 E-value=22 Score=37.92 Aligned_cols=30 Identities=30% Similarity=0.470 Sum_probs=26.8
Q ss_pred cccccccCCCCccchhhhhhccceeeeecc
Q psy15011 213 GLLQSNIGPNGCTLKSIELLTNCYMLVQGQ 242 (334)
Q Consensus 213 ~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~ 242 (334)
|.-+-+||+.|.|.|.+|+-||+-|-|-|+
T Consensus 153 NFvGLiiGPRG~TqK~lE~etgAKI~IRGk 182 (554)
T KOG0119|consen 153 NFVGLIIGPRGNTQKRLERETGAKIAIRGK 182 (554)
T ss_pred ceeEEEecCCccHHHHHHHHhCCeEEEecc
Confidence 445678999999999999999999999994
No 82
>cd01813 UBP_N UBP ubiquitin processing protease. The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.
Probab=32.48 E-value=23 Score=27.54 Aligned_cols=49 Identities=14% Similarity=0.090 Sum_probs=29.6
Q ss_pred chHHHHHHhhceEEEecceeeeeecCCccccccccC--CCCccchhhhhhccceeeeeccEEEEecC
Q psy15011 185 CTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIG--PNGCTLKSIELLTNCYMLVQGQTVAALGP 249 (334)
Q Consensus 185 kTkkaIE~lT~~~I~V~gktV~IIG~~~~ik~~~~g--~~g~~~~~~e~~~~~~~~V~g~tV~iiG~ 249 (334)
.-|..|+.+||+-.. +|+++| -+|+....=..|.-..|. .|++|..||+
T Consensus 24 ~lK~~i~~~tgvp~~---------------~QKLi~~~~~Gk~l~D~~~L~~~~i~-~g~~i~lmGs 74 (74)
T cd01813 24 DLKQFIKTLTGVLPE---------------RQKLLGLKVKGKPAEDDVKISALKLK-PNTKIMMMGT 74 (74)
T ss_pred HHHHHHHHHHCCCHH---------------HEEEEeecccCCcCCCCcCHHHcCCC-CCCEEEEEeC
Confidence 456777888875555 566666 245555543333333333 7888888884
No 83
>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=31.70 E-value=4.1e+02 Score=25.15 Aligned_cols=74 Identities=15% Similarity=0.127 Sum_probs=45.9
Q ss_pred eEEEEcCCCCCChhHHHhHHHHHHHHhcCCCHHHHHHhhhc---c--ceeeEEeccccccCcchhccccceeeCCCcchH
Q psy15011 113 SMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEQAVRVLQD---D--ISCDIIKIGNLVQNKQRFVKRRQRLIGPNGCTL 187 (334)
Q Consensus 113 ~V~V~tt~kT~Dp~~i~KA~D~IkAi~rGF~~e~AlkLL~D---D--i~~dIIdIk~~v~n~~~l~R~rGRIIG~~GkTk 187 (334)
.|.|--|+ +.-...-+-|....+++.-|.++++.++.|++ . .+|-+-|++.+ ++-||| +++.
T Consensus 108 ~i~ViDS~-~~s~~~g~~v~~a~~~~~~G~s~~eI~~~l~~~~~~~~~~f~v~~L~~L--------~~gGRi----s~~~ 174 (275)
T TIGR00762 108 KVTVIDSK-SASMGLGLLVLEAAKLAEEGKSLEEILAKLEELRERTKLYFVVDTLEYL--------VKGGRI----SKAA 174 (275)
T ss_pred CEEEECCh-HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcEEEEEECcHHHH--------HhcCCc----cHHH
Confidence 35444433 22333344455566777789999999999874 2 33555555544 345676 4566
Q ss_pred HHHHHhhceEEE
Q psy15011 188 KSIELLTNCYML 199 (334)
Q Consensus 188 kaIE~lT~~~I~ 199 (334)
..+-++-+.+-+
T Consensus 175 ~~~g~lL~ikPI 186 (275)
T TIGR00762 175 ALIGSLLNIKPI 186 (275)
T ss_pred HHHHHhhcceeE
Confidence 778888888766
No 84
>PRK07680 late competence protein ComER; Validated
Probab=30.85 E-value=53 Score=30.72 Aligned_cols=97 Identities=10% Similarity=0.082 Sum_probs=59.0
Q ss_pred hhhHHHHHhhcceeEEEEccCCeEEEEcCCCCCChhHHHhHH-HHHHH-Hh-cCCCHHHHHHhhhccce--eeEEecccc
Q psy15011 91 WPLVKNALELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKAR-DMIKL-LS-RSVPYEQAVRVLQDDIS--CDIIKIGNL 165 (334)
Q Consensus 91 W~~I~~~le~~~l~i~id~~~g~V~V~tt~kT~Dp~~i~KA~-D~IkA-i~-rGF~~e~AlkLL~DDi~--~dIIdIk~~ 165 (334)
...+...++..|....++. ..+..-+.--.--|..+.-.- -++.+ +. .||+.++|.+++-+=+. .+. +
T Consensus 141 ~~~~~~ll~~~G~~~~i~e--~~~~~~~~l~gs~pa~~~~~~~al~~~~~~~~Gl~~~~a~~~~~~~~~G~~~l-----~ 213 (273)
T PRK07680 141 QQKLERLFSNISTPLVIEE--DITRVSSDIVSCGPAFFSYLLQRFIDAAVEETNISKEEATTLASEMLIGMGKL-----L 213 (273)
T ss_pred HHHHHHHHHcCCCEEEECh--HhcchhhhhccchHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHH-----H
Confidence 3456677788887777763 323222211112232322222 24433 34 59999999999875322 111 1
Q ss_pred ccCcchhccccceeeCCCcchHHHHHHhh
Q psy15011 166 VQNKQRFVKRRQRLIGPNGCTLKSIELLT 194 (334)
Q Consensus 166 v~n~~~l~R~rGRIIG~~GkTkkaIE~lT 194 (334)
..++.|+.-.+.++.-|+|.|-..++.|=
T Consensus 214 ~~~~~~~~~l~~~v~spgG~T~~gl~~le 242 (273)
T PRK07680 214 EKGLYTLPTLQEKVCVKGGITGEGIKVLE 242 (273)
T ss_pred HhcCCCHHHHHHhCCCCChhHHHHHHHHH
Confidence 23557888899999999999999998774
No 85
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=30.62 E-value=3.2e+02 Score=27.56 Aligned_cols=93 Identities=18% Similarity=0.219 Sum_probs=58.9
Q ss_pred Hhhhc---cce---eeEEecccccc--------CcchhccccceeeCCCcchHHHHHHhh-ceEE--Eec----------
Q psy15011 149 RVLQD---DIS---CDIIKIGNLVQ--------NKQRFVKRRQRLIGPNGCTLKSIELLT-NCYM--LVQ---------- 201 (334)
Q Consensus 149 kLL~D---Di~---~dIIdIk~~v~--------n~~~l~R~rGRIIG~~GkTkkaIE~lT-~~~I--~V~---------- 201 (334)
+||+. +++ .+|..|.+-.+ +.+.=.-+.|..+|++|..-++|.+.. |=+| +-|
T Consensus 204 ~Lfe~EVPEI~dG~VeI~~iaR~pG~RtKvAV~s~~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~fi~n 283 (341)
T TIGR01953 204 ELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESNDENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIAN 283 (341)
T ss_pred HHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHHHHHH
Confidence 67763 455 55555544322 234455679999999999999986533 3222 111
Q ss_pred ---------------ceeeeeecCCccccccccCCCCccchhhhhhccceeeeec
Q psy15011 202 ---------------GQTVAALGPHKGLLQSNIGPNGCTLKSIELLTNCYMLVQG 241 (334)
Q Consensus 202 ---------------gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g 241 (334)
+.+.+.+-=.+.=+..-||-+|+--+-.-.|||..|-|+-
T Consensus 284 al~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 284 ALSPAKVISVEVLDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred hcCCceEEEEEEEcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 2223333334455667789999998889999999887764
No 86
>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=30.02 E-value=2.1e+02 Score=25.89 Aligned_cols=87 Identities=21% Similarity=0.276 Sum_probs=54.8
Q ss_pred ccCCeEEEEcCCCCCChhHHHhHHHHHHHHhc--------------CCCHHHHHHhhhccce--eeEEeccccccCcchh
Q psy15011 109 VIEGSMTVFTTRKTWDPYIIIKARDMIKLLSR--------------SVPYEQAVRVLQDDIS--CDIIKIGNLVQNKQRF 172 (334)
Q Consensus 109 ~~~g~V~V~tt~kT~Dp~~i~KA~D~IkAi~r--------------GF~~e~AlkLL~DDi~--~dIIdIk~~v~n~~~l 172 (334)
.+.=.+.|-| .||-.+..--|+|+-+|. =.++++|.++..+=+- -.|-||.=--..++-.
T Consensus 6 fEGPelviYt----k~P~~~~~~~dli~~lAk~lrKRIvvR~dps~l~~~e~A~~~I~~ivP~ea~i~di~Fd~~tGEV~ 81 (145)
T cd02410 6 FEGPELVVYT----KNPELFAEDGDLVKDLAKDLRKRIVIRPDPSVLKPPEEAIKIILEIVPEEAGITDIYFDDDTGEVI 81 (145)
T ss_pred eeCCeEEEEE----CCHHHHhcccHHHHHHHHHHhceEEEcCChhhcCCHHHHHHHHHHhCCCccCceeeEecCCCcEEE
Confidence 3334455554 778887776677777663 2467888887764211 2233332111234555
Q ss_pred ccc--cceeeCCCcchHHHHHHhhceEEE
Q psy15011 173 VKR--RQRLIGPNGCTLKSIELLTNCYML 199 (334)
Q Consensus 173 ~R~--rGRIIG~~GkTkkaIE~lT~~~I~ 199 (334)
..+ =|++||++|.+..-|-.-||=.-.
T Consensus 82 IeaeKPG~ViGk~g~~~reI~~~tgW~p~ 110 (145)
T cd02410 82 IEAEKPGLVIGKGGSTLREITRETGWAPK 110 (145)
T ss_pred EEEcCCeEEEecCchhHHHHHHHhCCeeE
Confidence 544 599999999999988888887665
No 87
>PRK00468 hypothetical protein; Provisional
Probab=28.25 E-value=28 Score=27.81 Aligned_cols=34 Identities=18% Similarity=0.229 Sum_probs=24.7
Q ss_pred ccccccccCCCCccchhhhhhccceeeeeccEEE
Q psy15011 212 KGLLQSNIGPNGCTLKSIELLTNCYMLVQGQTVA 245 (334)
Q Consensus 212 ~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~ 245 (334)
..=.+|+||-+|++-++|-.+-+.--.=+|+.|.
T Consensus 38 ~~D~GrVIGk~Gr~i~AIRtvv~aaa~k~~~rv~ 71 (75)
T PRK00468 38 PEDMGKVIGKQGRIAKAIRTVVKAAAIKENKRVV 71 (75)
T ss_pred hhhCcceecCCChhHHHHHHHHHHHHhcCCCEEE
Confidence 3345999999999999888776655445555554
No 88
>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=28.11 E-value=1.9e+02 Score=20.65 Aligned_cols=35 Identities=20% Similarity=0.110 Sum_probs=24.8
Q ss_pred hhhHHHHHh-hcce-eEEEEccCCeEEEEcCCCCCCh
Q psy15011 91 WPLVKNALE-LHFI-KAELDVIEGSMTVFTTRKTWDP 125 (334)
Q Consensus 91 W~~I~~~le-~~~l-~i~id~~~g~V~V~tt~kT~Dp 125 (334)
=..|.++|. .-|+ .+.+|..++.++|.......++
T Consensus 13 ~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~ 49 (62)
T PF00403_consen 13 AKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSI 49 (62)
T ss_dssp HHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCH
T ss_pred HHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCH
Confidence 345777774 4566 5899999999999985433343
No 89
>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=27.08 E-value=1.1e+02 Score=22.61 Aligned_cols=32 Identities=13% Similarity=0.218 Sum_probs=28.2
Q ss_pred CCCChhHHHhHHHHHHHHhcCCCHHHHHHhhh
Q psy15011 121 KTWDPYIIIKARDMIKLLSRSVPYEQAVRVLQ 152 (334)
Q Consensus 121 kT~Dp~~i~KA~D~IkAi~rGF~~e~AlkLL~ 152 (334)
.-.++..+...+.+..+...||++++...+|+
T Consensus 36 R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l~ 67 (67)
T cd04764 36 RYYTDEDIELLKKIKTLLEKGLSIKEIKEILN 67 (67)
T ss_pred eeeCHHHHHHHHHHHHHHHCCCCHHHHHHHhC
Confidence 34788899999999999999999999998874
No 90
>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=26.97 E-value=5.3e+02 Score=24.17 Aligned_cols=126 Identities=17% Similarity=0.261 Sum_probs=72.6
Q ss_pred CCCCCCCCcccchhhhhHHHHHHHhhhc-ceeEeeeeecceEEEecccCCCcchhhhhhHHHhhhhccccCchhhHhHHh
Q psy15011 10 PEFKKEDNPHEYLKECWPLVKNALELHF-IKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEPLKEEYLK 88 (334)
Q Consensus 10 ~~~~~~~~~~~ylke~w~~v~~~L~~~~-i~~~ldl~egsmtV~Ttkkt~dPyiiikardlikl~sRsVpvP~~Re~yLK 88 (334)
+.|.+-.|.=++++..+....++|.+.. ....+.++.|.+ | ..+|+
T Consensus 67 ~~fpQlenGVGm~r~f~~e~~~~l~~l~~~~~~v~ivTG~l----------------a-----------------~~~l~ 113 (204)
T PF04459_consen 67 EDFPQLENGVGMVRLFLDEWEEALRKLPKKPRRVTIVTGVL----------------A-----------------YPFLK 113 (204)
T ss_pred CCCcccCCCeeEhHHHHHHHHHHHhhcCCCCeeEEEEeeHH----------------H-----------------HHHHH
Confidence 3577777888899888888888887633 333333333332 1 12333
Q ss_pred hhhhhHHHHHhhcceeEEEEcc-----CCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCCHHHHHHhhhccceeeEEecc
Q psy15011 89 ECWPLVKNALELHFIKAELDVI-----EGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEQAVRVLQDDISCDIIKIG 163 (334)
Q Consensus 89 e~W~~I~~~le~~~l~i~id~~-----~g~V~V~tt~kT~Dp~~i~KA~D~IkAi~rGF~~e~AlkLL~DDi~~dIIdIk 163 (334)
+....+ .. ..++.+++-.. .++|+|. .++-++|+++++... +.. |.+=|-
T Consensus 114 ~~~~~l-~~--~~~~~v~V~~V~N~fFG~~ItVa---------GLLTg~Dii~~L~~~------------~~~-d~lllP 168 (204)
T PF04459_consen 114 PLVEKL-NR--IPGLEVEVVPVKNRFFGGTITVA---------GLLTGQDIIEQLKGK------------ELG-DLLLLP 168 (204)
T ss_pred HHHHHH-hc--cCCCeEEEEEeecCCCCCCeEEe---------eCccHHHHHHHhCcC------------CCC-CEEEEC
Confidence 333333 11 12444544333 5667775 488899999977651 111 122222
Q ss_pred ccccCcchhccc-cceeeCCCcchHHHHHHhhceEEEec
Q psy15011 164 NLVQNKQRFVKR-RQRLIGPNGCTLKSIELLTNCYMLVQ 201 (334)
Q Consensus 164 ~~v~n~~~l~R~-rGRIIG~~GkTkkaIE~lT~~~I~V~ 201 (334)
+.+.+. .++.+ +|.|..-|+...|+.|.|-
T Consensus 169 ------~~ml~~~~~~fL--DD~t~~el~~~lg~~v~vv 199 (204)
T PF04459_consen 169 ------DVMLRHGEGVFL--DDMTLEELEERLGVPVIVV 199 (204)
T ss_pred ------HHHhcCCCCccC--CCCcHHHHHHHhCCcEEEe
Confidence 222222 45555 7888899999888888743
No 91
>PRK02821 hypothetical protein; Provisional
Probab=26.23 E-value=37 Score=27.34 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=24.4
Q ss_pred ccccccccCCCCccchhhhhhccceeeeeccEEEE
Q psy15011 212 KGLLQSNIGPNGCTLKSIELLTNCYMLVQGQTVAA 246 (334)
Q Consensus 212 ~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~i 246 (334)
+.=.+|+||-+|++-++|-.+-..- .|+.|.+
T Consensus 39 ~~D~GrVIGk~Gr~i~AIRtlv~a~---~~~~v~l 70 (77)
T PRK02821 39 PDDLGKVIGRGGRTATALRTVVAAI---GGRGVRV 70 (77)
T ss_pred hhhCcceeCCCCchHHHHHHHHHHh---cCCeEEE
Confidence 3446899999999999888776554 7777664
No 92
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=25.48 E-value=3.1e+02 Score=29.98 Aligned_cols=110 Identities=23% Similarity=0.285 Sum_probs=70.8
Q ss_pred hHHhhhhhhHHHHHhhccee-EEEEccCCeEEEEcCCCCCChhHHHhHHHHHHHHhcC--------------CCHHHHHH
Q psy15011 85 EYLKECWPLVKNALELHFIK-AELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRS--------------VPYEQAVR 149 (334)
Q Consensus 85 ~yLKe~W~~I~~~le~~~l~-i~id~~~g~V~V~tt~kT~Dp~~i~KA~D~IkAi~rG--------------F~~e~Alk 149 (334)
.+|.+....|...+-. .++ .+++-+.=.+.|-+ .||-.+.+--|+|+-+|.- -++++|.+
T Consensus 5 ~~l~ei~~~i~~~~p~-~~~It~vefEGPelvvY~----k~P~~~~~~~dlik~lAk~lrKRI~iR~dPsvl~~~e~A~~ 79 (637)
T COG1782 5 EVLEEIRNKINEILPS-DVKITDVEFEGPELVVYT----KNPELFAKDGDLIKDLAKDLRKRIIIRPDPSVLKPPEEARK 79 (637)
T ss_pred HHHHHHHHHHHHhCCC-cCceEEEEecCCeEEEEe----cCHHHhccchhHHHHHHHHHhhceEeccCchhcCCHHHHHH
Confidence 3566666666666632 222 35677667777765 7888888766777776642 47899998
Q ss_pred hhhccce--eeEEeccccccCcchhccc--cceeeCCCcchHHHHHHhhceEEE
Q psy15011 150 VLQDDIS--CDIIKIGNLVQNKQRFVKR--RQRLIGPNGCTLKSIELLTNCYML 199 (334)
Q Consensus 150 LL~DDi~--~dIIdIk~~v~n~~~l~R~--rGRIIG~~GkTkkaIE~lT~~~I~ 199 (334)
+..+-+= .+|-|+.=--..++-+..+ =|-+||++|+|..-|-.-||-.=-
T Consensus 80 ~I~eivP~ea~i~~i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ 133 (637)
T COG1782 80 IILEIVPEEAGITDIYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPK 133 (637)
T ss_pred HHHHhCccccCceeEEecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcce
Confidence 8764321 2233322111234555433 588999999999999998886543
No 93
>PRK10076 pyruvate formate lyase II activase; Provisional
Probab=25.47 E-value=3.7e+02 Score=24.97 Aligned_cols=85 Identities=7% Similarity=-0.018 Sum_probs=43.7
Q ss_pred EEccCCeEEEEcCCCCCChhHHHhHHHHHHHHhc-------CCCHHHHHH-hhhccceeeEEeccccccCcchhccccce
Q psy15011 107 LDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSR-------SVPYEQAVR-VLQDDISCDIIKIGNLVQNKQRFVKRRQR 178 (334)
Q Consensus 107 id~~~g~V~V~tt~kT~Dp~~i~KA~D~IkAi~r-------GF~~e~Alk-LL~DDi~~dIIdIk~~v~n~~~l~R~rGR 178 (334)
++...|.|++...+.+--|-.+......++..+. |+-+.++++ |++ -+.+-.+||+.+ +.+...+.-|
T Consensus 35 ~~~sggGVt~SGGEPllq~~fl~~l~~~~k~~gi~~~leTnG~~~~~~~~~l~~-~~D~~l~DiK~~--d~~~~~~~tG- 110 (213)
T PRK10076 35 FRTSGGGVTLSGGEVLMQAEFATRFLQRLRLWGVSCAIETAGDAPASKLLPLAK-LCDEVLFDLKIM--DATQARDVVK- 110 (213)
T ss_pred hcCCCCEEEEeCchHHcCHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHH-hcCEEEEeeccC--CHHHHHHHHC-
Confidence 3445689999886555444333333333333222 444444444 554 333456777766 2233333333
Q ss_pred eeCCCcchHHHHHHhhceE
Q psy15011 179 LIGPNGCTLKSIELLTNCY 197 (334)
Q Consensus 179 IIG~~GkTkkaIE~lT~~~ 197 (334)
+.+..+++.|+.+...-
T Consensus 111 --~~~~~il~nl~~l~~~g 127 (213)
T PRK10076 111 --MNLPRVLENLRLLVSEG 127 (213)
T ss_pred --CCHHHHHHHHHHHHhCC
Confidence 44566777777766553
No 94
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=25.46 E-value=1e+02 Score=34.14 Aligned_cols=45 Identities=22% Similarity=0.304 Sum_probs=37.4
Q ss_pred HHHHHhhcceeEEEEccCCeEEEEcCCCCCChhHHHhHHHHHHHHhcCCC
Q psy15011 94 VKNALELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVP 143 (334)
Q Consensus 94 I~~~le~~~l~i~id~~~g~V~V~tt~kT~Dp~~i~KA~D~IkAi~rGF~ 143 (334)
|..+.+++++++.++ .+|+|.|.+ .|.-.+.+|++.|..+.+-|.
T Consensus 574 I~~I~eetg~~Idie-ddGtv~i~~----s~~~~~~~ak~~I~~i~~e~e 618 (692)
T COG1185 574 IKAITEETGVKIDIE-DDGTVKIAA----SDGESAKKAKERIEAITREVE 618 (692)
T ss_pred hhhhhhhhCcEEEec-CCCcEEEEe----cchHHHHHHHHHHHHHHhhcc
Confidence 345568999999999 899999987 567789999999998885444
No 95
>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=24.02 E-value=19 Score=29.88 Aligned_cols=56 Identities=18% Similarity=0.385 Sum_probs=38.1
Q ss_pred HHHhcCCCHHHHHHhhhccceeeEEeccccc-cCcchhccccceeeCCCcchHHHHHHhhc
Q psy15011 136 KLLSRSVPYEQAVRVLQDDISCDIIKIGNLV-QNKQRFVKRRQRLIGPNGCTLKSIELLTN 195 (334)
Q Consensus 136 kAi~rGF~~e~AlkLL~DDi~~dIIdIk~~v-~n~~~l~R~rGRIIG~~GkTkkaIE~lT~ 195 (334)
-++..|++.++|.++.-.-+. --..++ .++.++...+.++.-|+|-|-.+|+.|-.
T Consensus 30 a~v~~Gl~~~~A~~lv~~t~~----G~a~ll~~~~~~~~~l~~~v~tPgG~T~~gl~~L~~ 86 (107)
T PF14748_consen 30 AAVAQGLPREEARKLVAQTFI----GAAKLLEESGRSPAELRDEVTTPGGTTIAGLEVLEK 86 (107)
T ss_dssp HHHHTT--HHHHHHHHHHHHH----HHHHHHHHCSS-HHHHHHHHS-TTSHHHHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHHHHHH----HHHHHHHccCCCHHHHhhhccCCCCcHHHHHHHHHH
Confidence 357799999999999875422 112222 24568889999999999999999988753
No 96
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=23.87 E-value=80 Score=19.37 Aligned_cols=21 Identities=5% Similarity=0.298 Sum_probs=18.3
Q ss_pred HHHHHHhcCCCHHHHHHhhhc
Q psy15011 133 DMIKLLSRSVPYEQAVRVLQD 153 (334)
Q Consensus 133 D~IkAi~rGF~~e~AlkLL~D 153 (334)
-+++|+++.=.+++|+.+|++
T Consensus 6 ~ll~a~~~~g~~~~a~~~~~~ 26 (34)
T PF13812_consen 6 ALLRACAKAGDPDAALQLFDE 26 (34)
T ss_pred HHHHHHHHCCCHHHHHHHHHH
Confidence 468999999999999999974
No 97
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=22.32 E-value=92 Score=31.81 Aligned_cols=35 Identities=23% Similarity=0.496 Sum_probs=33.2
Q ss_pred ceeeCCCcchHHHHHHhhceEEEecceeeeeecCC
Q psy15011 177 QRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPH 211 (334)
Q Consensus 177 GRIIG~~GkTkkaIE~lT~~~I~V~gktV~IIG~~ 211 (334)
..+.|+.|.-++.||...|+.|..-|..+.|+|.-
T Consensus 27 ~~l~G~~~~~l~l~e~~~gv~i~~rG~~~~i~g~~ 61 (348)
T COG1702 27 VALFGPTDTNLSLLEIALGVSIVARGEAVRIIGAR 61 (348)
T ss_pred hhhcCCCCccHHHHHHHhCcEEEeCCceEEEEech
Confidence 37899999999999999999999999999999995
No 98
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=21.60 E-value=95 Score=18.64 Aligned_cols=21 Identities=19% Similarity=0.373 Sum_probs=18.2
Q ss_pred HHHHHHhcCCCHHHHHHhhhc
Q psy15011 133 DMIKLLSRSVPYEQAVRVLQD 153 (334)
Q Consensus 133 D~IkAi~rGF~~e~AlkLL~D 153 (334)
-+|.++++.-.+++|++++++
T Consensus 5 ~li~~~~~~~~~~~a~~~~~~ 25 (35)
T TIGR00756 5 TLIDGLCKAGRVEEALELFKE 25 (35)
T ss_pred HHHHHHHHCCCHHHHHHHHHH
Confidence 478899999999999999974
No 99
>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=21.57 E-value=1.9e+02 Score=21.36 Aligned_cols=32 Identities=9% Similarity=0.214 Sum_probs=27.4
Q ss_pred CCCChhHHHhHHHHHHHHhcCCCHHHHHHhhh
Q psy15011 121 KTWDPYIIIKARDMIKLLSRSVPYEQAVRVLQ 152 (334)
Q Consensus 121 kT~Dp~~i~KA~D~IkAi~rGF~~e~AlkLL~ 152 (334)
...+...+...+.+..+...||+++++.++|+
T Consensus 37 R~yt~~di~~l~~i~~l~~~g~~l~~i~~~l~ 68 (68)
T cd04763 37 RLFNDADIDRILEIKRWIDNGVQVSKVKKLLS 68 (68)
T ss_pred cccCHHHHHHHHHHHHHHHcCCCHHHHHHHhC
Confidence 44677788899999999999999999998874
No 100
>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=21.55 E-value=6.5e+02 Score=24.90 Aligned_cols=39 Identities=21% Similarity=0.206 Sum_probs=28.9
Q ss_pred cEEEEecCCccHHHHHHHHHHHhcCCCchhHHHHHHHHHhhhcCCccc
Q psy15011 242 QTVAALGPHKGLLQVRRIVEDTMKNIHPIYNIKALMIKRELAKDPKLK 289 (334)
Q Consensus 242 ~tV~iiG~~~~l~~ar~av~~li~g~hpiy~ik~l~~kr~l~~~~~~~ 289 (334)
..|.+.|.......|.+++.. |.+ ..|+-|-|..||.+.
T Consensus 285 iPVi~~Ggi~t~e~ae~~l~~---gaD------~V~~gR~liadPdl~ 323 (353)
T cd04735 285 LPLIAVGSINTPDDALEALET---GAD------LVAIGRGLLVDPDWV 323 (353)
T ss_pred CCEEEECCCCCHHHHHHHHHc---CCC------hHHHhHHHHhCccHH
Confidence 357778888888888888876 443 467788888888753
No 101
>COG1707 ACT domain-containing protein [General function prediction only]
Probab=21.38 E-value=55 Score=30.84 Aligned_cols=59 Identities=17% Similarity=0.201 Sum_probs=43.5
Q ss_pred ecceeeeeecCCccccccccCCCCccchhhhhhccceeeeeccEEEEecCCccHHHHHHHHHHH
Q psy15011 200 VQGQTVAALGPHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQVRRIVEDT 263 (334)
Q Consensus 200 V~gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~tV~iiG~~~~l~~ar~av~~l 263 (334)
||||.|-|||...++-+--.|-=+-|-+ -|+-|-.||| .|+-+.|+ ++|-.|.+||..|
T Consensus 81 iyGKRvIiiGGGAqVsqVA~GAIsEADR--HNiRGERISv--DTiPlVGE-E~laEAVkAV~rL 139 (218)
T COG1707 81 IYGKRVIIIGGGAQVSQVARGAISEADR--HNIRGERISV--DTIPLVGE-EELAEAVKAVARL 139 (218)
T ss_pred HhCcEEEEECCchhHHHHHHhhcchhhh--cccccceeee--ecccccCh-HHHHHHHHHHhcc
Confidence 5788888999888877766665554433 3677888888 48888887 5677888888765
No 102
>PF08383 Maf_N: Maf N-terminal region; InterPro: IPR013592 This region is found in various leucine zipper transcription factors of the Maf family. These are implicated in the regulation of insulin gene expression [], in erythroid differentiation [], and in differentiation of the neuroretina [].
Probab=21.34 E-value=66 Score=22.75 Aligned_cols=15 Identities=27% Similarity=0.184 Sum_probs=12.1
Q ss_pred HhcCCCHHHHHHhhh
Q psy15011 138 LSRSVPYEQAVRVLQ 152 (334)
Q Consensus 138 i~rGF~~e~AlkLL~ 152 (334)
=+.|++||||+..|-
T Consensus 19 e~l~LtpEDAvEaLi 33 (35)
T PF08383_consen 19 EALGLTPEDAVEALI 33 (35)
T ss_pred hhcCCCHHHHHHHHh
Confidence 367899999998873
No 103
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=21.31 E-value=39 Score=32.11 Aligned_cols=85 Identities=20% Similarity=0.353 Sum_probs=53.3
Q ss_pred eeeecCCccccccccCCCCccchhhhhhccceeeeec-cEEEEe---cCCcc------HHHHHHHHHHHhcC-----CCc
Q psy15011 205 VAALGPHKGLLQSNIGPNGCTLKSIELLTNCYMLVQG-QTVAAL---GPHKG------LLQVRRIVEDTMKN-----IHP 269 (334)
Q Consensus 205 V~IIG~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g-~tV~ii---G~~~~------l~~ar~av~~li~g-----~hp 269 (334)
|.|.|+. -++.||..|+++.+++.|+|.+..-++ +...++ |+|.. +++|.++....... ..|
T Consensus 95 ~~i~~~~---~~~LIG~~Gk~LdALQ~L~n~~l~~~~g~~~~v~ldv~~yRerR~e~L~~LA~~~A~rV~~tg~~v~L~p 171 (208)
T COG1847 95 VSIEGED---AGRLIGKHGKTLDALQYLANLYLNKIGGKFKRVTLDVGDYRERRKETLIKLAERAAERVLETGRSVELEP 171 (208)
T ss_pred EEecCCc---hhhhhccCCcchHHHHHHHHHHhhhhcCcceEEEEEhhhHHHHHHHHHHHHHHHHHHHHHhhCCeeecCC
Confidence 5666766 789999999999999999999887644 435554 44422 33444444444322 344
Q ss_pred hhHHHHHHHHHhhhcCCccccCC
Q psy15011 270 IYNIKALMIKRELAKDPKLKNEN 292 (334)
Q Consensus 270 iy~ik~l~~kr~l~~~~~~~~~~ 292 (334)
+-+-=+=+|-.=|.++|.+..+|
T Consensus 172 M~~~ERkIVH~~l~~~~~V~T~S 194 (208)
T COG1847 172 MPPFERKIVHTALSANPGVETYS 194 (208)
T ss_pred CCHHHHHHHHHHHHhcCCcceee
Confidence 54444555555566666655443
No 104
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=20.93 E-value=1.6e+02 Score=22.85 Aligned_cols=35 Identities=20% Similarity=0.015 Sum_probs=29.6
Q ss_pred chhhHhHHhhhhhhHHHHHhhcceeEEEEccCCeEEE
Q psy15011 80 EPLKEEYLKECWPLVKNALELHFIKAELDVIEGSMTV 116 (334)
Q Consensus 80 P~~Re~yLKe~W~~I~~~le~~~l~i~id~~~g~V~V 116 (334)
-..|.+.||..|..+..++.+.| .--|..++.|+.
T Consensus 54 lknk~~~lk~~y~~~~~l~~~sg--~gwd~~~~~i~a 88 (96)
T PF12776_consen 54 LKNKWKTLKKDYRIWKELRNHSG--FGWDPETGMITA 88 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCC--ceEcCCCCeEEC
Confidence 46789999999999999998777 778888887754
No 105
>KOG4656|consensus
Probab=20.60 E-value=77 Score=30.68 Aligned_cols=58 Identities=24% Similarity=0.196 Sum_probs=40.9
Q ss_pred hhHHHHHh-hcce-eEEEEccCCeEEEEcCCCCCChhHHHhHHH--HHHHHhcCCCHHHHHHhhh
Q psy15011 92 PLVKNALE-LHFI-KAELDVIEGSMTVFTTRKTWDPYIIIKARD--MIKLLSRSVPYEQAVRVLQ 152 (334)
Q Consensus 92 ~~I~~~le-~~~l-~i~id~~~g~V~V~tt~kT~Dp~~i~KA~D--~IkAi~rGF~~e~AlkLL~ 152 (334)
..|+..|+ --|+ ++++|+.++.|.|.++. -|..++.+-+ =.+|+.+||...+|++|+.
T Consensus 22 navk~~L~~V~Gi~~vevdle~q~v~v~ts~---p~s~i~~~le~tGr~Avl~G~G~psaval~a 83 (247)
T KOG4656|consen 22 NAVKACLKGVPGINSVEVDLEQQIVSVETSV---PPSEIQNTLENTGRDAVLRGAGKPSAVALLA 83 (247)
T ss_pred HHHHHHhccCCCcceEEEEhhhcEEEEEccC---ChHHHHHHHHhhChheEEecCCchhHHHHHH
Confidence 34555554 2222 58999999999999863 3455554432 2478899999999999997
No 106
>PF12854 PPR_1: PPR repeat
Probab=20.58 E-value=1e+02 Score=20.27 Aligned_cols=21 Identities=10% Similarity=0.259 Sum_probs=18.6
Q ss_pred HHHHHHhcCCCHHHHHHhhhc
Q psy15011 133 DMIKLLSRSVPYEQAVRVLQD 153 (334)
Q Consensus 133 D~IkAi~rGF~~e~AlkLL~D 153 (334)
-+|.++.+-=.+++|++||++
T Consensus 12 ~lI~~~Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 12 TLIDGYCKAGRVDEAFELFDE 32 (34)
T ss_pred HHHHHHHHCCCHHHHHHHHHh
Confidence 478999999999999999974
No 107
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=20.46 E-value=3.7e+02 Score=29.27 Aligned_cols=92 Identities=21% Similarity=0.309 Sum_probs=63.4
Q ss_pred EEEccCCeEEEEcCCCCCChhHHHhHHHHHHHHhcC--------------CCHHHHHHhhhccce--eeEEeccccccCc
Q psy15011 106 ELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRS--------------VPYEQAVRVLQDDIS--CDIIKIGNLVQNK 169 (334)
Q Consensus 106 ~id~~~g~V~V~tt~kT~Dp~~i~KA~D~IkAi~rG--------------F~~e~AlkLL~DDi~--~dIIdIk~~v~n~ 169 (334)
.++-+.=.+.|-| .||-.+.+--|+|+-++.- .++++|.++..+=+- -.|-||.=-...+
T Consensus 20 ~~~~egp~~~~~~----~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~f~~~~~ 95 (630)
T TIGR03675 20 DVEFEGPELVIYT----KNPELFAKDDDLVKELAKKLRKRIVIRPDPSVLLPPEEAIEKIKEIVPEEAGITDIYFDDVTG 95 (630)
T ss_pred EEEEeCCeEEEEe----CCHHHhccchHHHHHHHHHhhceEEEecChhhcCCHHHHHHHHHHhCCCcCCceeEEecCCCc
Confidence 4566666777765 7898888888888887743 468889888764221 2333433112245
Q ss_pred chhccc--cceeeCCCcchHHHHHHhhceEEEec
Q psy15011 170 QRFVKR--RQRLIGPNGCTLKSIELLTNCYMLVQ 201 (334)
Q Consensus 170 ~~l~R~--rGRIIG~~GkTkkaIE~lT~~~I~V~ 201 (334)
+-...+ =|.+||++|.|..-|-.-||=.-.|.
T Consensus 96 ~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~ 129 (630)
T TIGR03675 96 EVIIEAEKPGLVIGKGGSTLREITAETGWTPKVV 129 (630)
T ss_pred eEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEE
Confidence 666544 59999999999999999998777663
No 108
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=20.18 E-value=1.4e+02 Score=30.39 Aligned_cols=99 Identities=16% Similarity=0.129 Sum_probs=61.0
Q ss_pred HHHHHHhhhc---cce---eeEEecccccc--------CcchhccccceeeCCCcchHHHHHHhh-ceEEE--ec-----
Q psy15011 144 YEQAVRVLQD---DIS---CDIIKIGNLVQ--------NKQRFVKRRQRLIGPNGCTLKSIELLT-NCYML--VQ----- 201 (334)
Q Consensus 144 ~e~AlkLL~D---Di~---~dIIdIk~~v~--------n~~~l~R~rGRIIG~~GkTkkaIE~lT-~~~I~--V~----- 201 (334)
|+=-.+||+- +++ .+|..|.+-.+ +.+.-.-+.|..||++|..-++|.+.. |=+|- -|
T Consensus 201 p~~v~~Lfe~EVPEI~~G~VeIk~iaR~pG~RtKVAV~s~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~ 280 (362)
T PRK12327 201 PGLVKRLFELEVPEIYDGTVEIKSIAREAGDRTKIAVRSNNPNVDAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPA 280 (362)
T ss_pred HHHHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHH
Confidence 4445577774 455 44555443322 234445678999999999999995433 32222 11
Q ss_pred --------------------ceeeeeecCCccccccccCCCCccchhhhhhccceeeeecc
Q psy15011 202 --------------------GQTVAALGPHKGLLQSNIGPNGCTLKSIELLTNCYMLVQGQ 242 (334)
Q Consensus 202 --------------------gktV~IIG~~~~ik~~~~g~~g~~~~~~e~~~~~~~~V~g~ 242 (334)
+.+.+++-=.++=+..-||-+|+--+-...|||.+|-|...
T Consensus 281 ~fi~nal~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 281 EFVANALSPAKVVSVEVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred HHHHHhCCCceEEEEEEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 22233333334556677888888888888888888877654
Done!