Query 021811
Match_columns 307
No_of_seqs 228 out of 545
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 05:51:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021811.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021811hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2874 rRNA processing protei 100.0 5E-104 1E-108 740.2 22.1 252 1-253 77-329 (356)
2 COG1094 Predicted RNA-binding 100.0 1.5E-52 3.3E-57 375.4 17.0 154 2-155 29-185 (194)
3 TIGR03665 arCOG04150 arCOG0415 100.0 3.5E-37 7.6E-42 269.6 17.6 148 2-152 20-168 (172)
4 PRK13763 putative RNA-processi 100.0 3.3E-36 7.2E-41 265.4 17.4 147 2-149 25-172 (180)
5 KOG3273 Predicted RNA-binding 100.0 6.7E-35 1.5E-39 264.5 11.7 150 4-153 98-250 (252)
6 TIGR03319 YmdA_YtgF conserved 99.0 7E-10 1.5E-14 112.4 7.9 69 63-139 203-275 (514)
7 PRK00106 hypothetical protein; 99.0 8.6E-10 1.9E-14 112.5 6.3 69 63-139 224-296 (535)
8 PRK12704 phosphodiesterase; Pr 98.8 5E-09 1.1E-13 106.4 6.3 57 83-139 221-281 (520)
9 cd02395 SF1_like-KH Splicing f 98.6 1.7E-07 3.7E-12 79.1 7.3 71 83-154 16-114 (120)
10 smart00322 KH K homology RNA-b 98.4 7.1E-07 1.5E-11 62.9 5.2 52 82-133 12-68 (69)
11 PRK12705 hypothetical protein; 98.4 5.1E-07 1.1E-11 92.0 6.1 69 63-139 197-269 (508)
12 PF00013 KH_1: KH domain syndr 98.2 1.2E-06 2.7E-11 63.4 3.6 48 82-129 9-60 (60)
13 cd02394 vigilin_like_KH K homo 98.2 2.7E-06 5.8E-11 62.0 4.4 48 82-129 9-61 (62)
14 cd02393 PNPase_KH Polynucleoti 98.2 2.1E-06 4.5E-11 63.9 3.8 49 82-130 11-61 (61)
15 cd00105 KH-I K homology RNA-bi 98.1 5E-06 1.1E-10 59.9 4.5 48 82-129 9-63 (64)
16 cd02396 PCBP_like_KH K homolog 97.4 0.00024 5.3E-09 52.8 4.5 47 83-129 10-64 (65)
17 PF13014 KH_3: KH domain 97.3 0.00039 8.4E-09 47.9 4.0 26 85-110 3-28 (43)
18 TIGR03665 arCOG04150 arCOG0415 97.0 0.001 2.2E-08 58.8 5.0 53 83-135 8-65 (172)
19 PRK13763 putative RNA-processi 97.0 0.001 2.2E-08 59.3 4.8 53 83-135 13-71 (180)
20 KOG1588 RNA-binding protein Sa 96.6 0.0015 3.2E-08 62.2 3.0 29 83-111 108-136 (259)
21 KOG1676 K-homology type RNA bi 96.3 0.011 2.5E-07 61.7 7.5 123 3-134 162-299 (600)
22 COG5176 MSL5 Splicing factor ( 95.9 0.018 4E-07 54.1 6.0 84 83-167 164-255 (269)
23 COG1847 Jag Predicted RNA-bind 95.4 0.014 3E-07 54.2 3.5 79 84-162 102-194 (208)
24 KOG0119 Splicing factor 1/bran 95.4 0.023 5.1E-07 58.6 5.2 109 46-162 122-260 (554)
25 PRK04163 exosome complex RNA-b 95.2 0.028 6E-07 52.1 4.8 55 83-138 155-211 (235)
26 KOG2193 IGF-II mRNA-binding pr 95.1 0.065 1.4E-06 54.8 7.4 114 2-134 433-563 (584)
27 KOG1676 K-homology type RNA bi 95.1 0.049 1.1E-06 57.1 6.7 121 2-134 76-209 (600)
28 TIGR02696 pppGpp_PNP guanosine 95.0 0.031 6.7E-07 59.8 5.0 53 83-135 588-642 (719)
29 PF13083 KH_4: KH domain; PDB: 94.9 0.0026 5.7E-08 48.3 -2.4 31 84-114 40-70 (73)
30 TIGR03591 polynuc_phos polyrib 94.7 0.042 9.1E-07 58.2 5.0 52 83-134 561-614 (684)
31 PRK01064 hypothetical protein; 92.3 0.066 1.4E-06 42.6 1.2 32 84-115 41-72 (78)
32 cd02414 jag_KH jag_K homology 92.0 0.053 1.1E-06 41.9 0.4 26 84-109 35-60 (77)
33 KOG2193 IGF-II mRNA-binding pr 91.9 0.43 9.3E-06 49.1 6.8 82 11-110 228-317 (584)
34 PRK02821 hypothetical protein; 91.7 0.12 2.6E-06 41.1 2.1 66 40-115 3-70 (77)
35 cd02134 NusA_KH NusA_K homolog 91.7 0.14 3.1E-06 38.1 2.4 26 83-108 35-60 (61)
36 PLN00207 polyribonucleotide nu 90.8 0.19 4.2E-06 55.1 3.3 58 83-141 695-757 (891)
37 PRK00468 hypothetical protein; 90.7 0.13 2.9E-06 40.5 1.5 31 84-114 41-71 (75)
38 COG1185 Pnp Polyribonucleotide 89.7 0.38 8.3E-06 51.5 4.3 52 84-135 563-616 (692)
39 cd02409 KH-II KH-II (K homolo 88.5 0.35 7.6E-06 34.4 2.1 23 84-106 36-58 (68)
40 KOG2814 Transcription coactiva 86.7 1 2.3E-05 44.7 4.9 121 83-221 67-197 (345)
41 PRK11824 polynucleotide phosph 86.2 0.63 1.4E-05 49.6 3.3 53 83-135 564-618 (693)
42 COG1837 Predicted RNA-binding 85.8 0.39 8.5E-06 38.3 1.2 19 84-102 41-59 (76)
43 KOG2190 PolyC-binding proteins 85.6 1.3 2.8E-05 45.8 5.1 53 83-135 148-208 (485)
44 COG1097 RRP4 RNA-binding prote 85.4 1.6 3.5E-05 41.6 5.2 99 36-138 91-212 (239)
45 COG1702 PhoH Phosphate starvat 84.4 1.8 3.9E-05 43.2 5.3 48 83-130 25-72 (348)
46 COG1094 Predicted RNA-binding 84.1 3.3 7.1E-05 38.4 6.5 61 83-144 18-87 (194)
47 KOG2191 RNA-binding protein NO 83.1 1.9 4E-05 43.3 4.8 55 83-138 142-207 (402)
48 TIGR00112 proC pyrroline-5-car 75.2 2.1 4.6E-05 39.3 2.4 96 2-103 127-225 (245)
49 KOG1067 Predicted RNA-binding 72.3 2.1 4.6E-05 45.6 1.8 53 83-135 607-660 (760)
50 PRK08406 transcription elongat 70.3 2.3 5E-05 36.9 1.3 27 83-109 109-135 (140)
51 TIGR03278 methan_mark_10 putat 70.2 24 0.00052 35.7 8.6 139 18-169 73-235 (404)
52 PF05598 DUF772: Transposase d 69.1 6.6 0.00014 29.4 3.4 61 28-91 2-67 (77)
53 PF14611 SLS: Mitochondrial in 63.7 82 0.0018 28.1 9.9 113 3-138 49-168 (210)
54 PRK10076 pyruvate formate lyas 61.6 72 0.0016 29.3 9.3 105 17-130 37-152 (213)
55 PRK06928 pyrroline-5-carboxyla 61.1 15 0.00032 34.3 4.9 94 2-101 147-244 (277)
56 cd02393 PNPase_KH Polynucleoti 59.1 27 0.00058 25.8 5.0 37 2-43 24-60 (61)
57 PF00403 HMA: Heavy-metal-asso 58.8 31 0.00067 24.5 5.2 27 2-28 16-44 (62)
58 PRK07680 late competence prote 57.8 8.8 0.00019 35.4 2.7 93 2-101 144-241 (273)
59 KOG2191 RNA-binding protein NO 55.4 13 0.00027 37.7 3.5 53 83-135 49-111 (402)
60 PF07650 KH_2: KH domain syndr 51.7 2.4 5.3E-05 32.2 -1.7 24 83-106 35-58 (78)
61 TIGR02517 type_II_gspD general 47.4 1.8E+02 0.0039 30.2 10.5 109 3-133 13-155 (594)
62 TIGR02696 pppGpp_PNP guanosine 45.8 60 0.0013 35.6 6.9 62 2-73 600-661 (719)
63 KOG2190 PolyC-binding proteins 45.7 14 0.00031 38.3 2.2 31 82-112 347-377 (485)
64 PTZ00431 pyrroline carboxylate 45.1 40 0.00087 31.1 4.9 96 2-103 140-238 (260)
65 PRK07634 pyrroline-5-carboxyla 43.0 16 0.00036 32.5 2.0 92 2-101 149-244 (245)
66 PF14611 SLS: Mitochondrial in 42.8 53 0.0011 29.3 5.2 64 84-147 37-105 (210)
67 cd02410 archeal_CPSF_KH The ar 41.9 1.1E+02 0.0023 27.5 6.8 90 14-109 3-112 (145)
68 cd01104 HTH_MlrA-CarA Helix-Tu 41.5 49 0.0011 23.8 4.0 32 29-60 37-68 (68)
69 PF14748 P5CR_dimer: Pyrroline 41.5 6.8 0.00015 32.1 -0.6 56 44-103 30-86 (107)
70 PF15232 DUF4585: Domain of un 41.4 8.8 0.00019 30.8 0.0 24 192-215 2-25 (75)
71 COG0195 NusA Transcription elo 39.3 26 0.00056 32.2 2.7 31 82-112 151-181 (190)
72 COG1185 Pnp Polyribonucleotide 38.1 50 0.0011 36.0 4.9 46 2-52 574-619 (692)
73 PRK04056 Maf-like protein; Rev 36.1 56 0.0012 29.5 4.3 40 106-146 63-107 (180)
74 COG0424 Maf Nucleotide-binding 35.6 56 0.0012 30.2 4.2 55 91-146 51-110 (193)
75 TIGR02494 PFLE_PFLC glycyl-rad 35.5 3.2E+02 0.007 25.3 9.4 107 19-131 126-240 (295)
76 PRK11145 pflA pyruvate formate 34.3 2.7E+02 0.0059 25.1 8.4 107 20-132 72-188 (246)
77 PRK06476 pyrroline-5-carboxyla 33.5 1.1E+02 0.0023 28.0 5.7 98 2-103 136-235 (258)
78 PRK12491 pyrroline-5-carboxyla 33.4 67 0.0014 30.2 4.5 95 2-103 147-245 (272)
79 PRK08406 transcription elongat 33.3 36 0.00078 29.5 2.5 24 83-106 42-65 (140)
80 PRK00148 Maf-like protein; Rev 32.6 83 0.0018 28.7 4.8 31 115-146 77-107 (194)
81 PRK01526 Maf-like protein; Rev 32.4 69 0.0015 29.5 4.3 52 94-146 60-116 (205)
82 TIGR02493 PFLA pyruvate format 32.3 3.6E+02 0.0078 23.9 10.1 108 20-133 67-184 (235)
83 PF04459 DUF512: Protein of un 32.1 1.4E+02 0.0031 27.6 6.3 80 2-111 112-201 (204)
84 PF00013 KH_1: KH domain syndr 32.0 1.1E+02 0.0024 21.7 4.5 37 2-43 22-60 (60)
85 PRK10629 EnvZ/OmpR regulon mod 31.8 95 0.0021 26.7 4.8 40 2-45 55-95 (127)
86 cd02394 vigilin_like_KH K homo 31.7 1.2E+02 0.0025 21.7 4.6 37 2-43 22-61 (62)
87 cd04764 HTH_MlrA-like_sg1 Heli 31.5 81 0.0017 23.0 3.8 33 28-60 35-67 (67)
88 KOG0336 ATP-dependent RNA heli 31.1 48 0.001 34.9 3.3 51 83-133 57-111 (629)
89 PRK07679 pyrroline-5-carboxyla 30.9 64 0.0014 29.9 3.9 95 2-103 149-247 (279)
90 PF13721 SecD-TM1: SecD export 30.5 1E+02 0.0022 25.3 4.6 40 2-45 51-91 (101)
91 PRK14361 Maf-like protein; Pro 29.8 97 0.0021 28.1 4.8 31 115-146 74-104 (187)
92 PRK00234 Maf-like protein; Rev 29.6 89 0.0019 28.4 4.5 32 114-146 77-108 (192)
93 PRK14365 Maf-like protein; Pro 29.2 86 0.0019 28.7 4.4 46 99-146 59-109 (197)
94 PRK00884 Maf-like protein; Rev 28.6 1E+02 0.0022 28.2 4.7 40 106-146 64-108 (194)
95 PRK00648 Maf-like protein; Rev 28.4 98 0.0021 28.1 4.5 40 106-146 67-111 (191)
96 TIGR01952 nusA_arch NusA famil 27.9 31 0.00067 30.2 1.2 27 84-110 111-137 (141)
97 cd04763 HTH_MlrA-like Helix-Tu 27.9 1.2E+02 0.0026 22.1 4.3 34 27-60 35-68 (68)
98 PRK00078 Maf-like protein; Rev 26.1 1.1E+02 0.0023 27.9 4.4 40 106-146 66-110 (192)
99 PRK14368 Maf-like protein; Pro 25.5 1.3E+02 0.0029 27.5 4.8 52 93-146 55-111 (193)
100 PRK14363 Maf-like protein; Pro 24.8 1.1E+02 0.0024 28.2 4.3 41 105-146 62-107 (204)
101 COG1159 Era GTPase [General fu 24.8 70 0.0015 31.6 3.1 53 53-108 198-273 (298)
102 PF13184 KH_5: NusA-like KH do 24.5 1.1E+02 0.0023 23.7 3.5 35 82-122 17-51 (69)
103 cd02395 SF1_like-KH Splicing f 24.2 3E+02 0.0066 23.3 6.5 48 2-53 28-99 (120)
104 PRK02478 Maf-like protein; Rev 24.1 1.5E+02 0.0032 27.2 4.9 31 115-146 85-115 (199)
105 PRK14364 Maf-like protein; Pro 23.9 1.5E+02 0.0031 26.8 4.8 31 115-146 73-103 (181)
106 TIGR00436 era GTP-binding prot 23.9 62 0.0013 29.9 2.5 26 83-108 232-265 (270)
107 cd02412 30S_S3_KH K homology R 23.7 49 0.0011 27.2 1.6 23 83-105 71-93 (109)
108 PF04365 DUF497: Protein of un 23.5 34 0.00074 26.7 0.6 32 41-72 6-37 (80)
109 COG2608 CopZ Copper chaperone 23.3 2E+02 0.0044 21.7 4.8 38 2-39 20-59 (71)
110 smart00422 HTH_MERR helix_turn 23.0 1.4E+02 0.0031 21.3 3.8 31 30-60 38-68 (70)
111 COG0134 TrpC Indole-3-glycerol 22.8 52 0.0011 31.7 1.8 72 28-103 114-195 (254)
112 PRK00032 Maf-like protein; Rev 22.6 1.4E+02 0.0031 27.1 4.4 31 115-146 79-109 (190)
113 cd00555 Maf Nucleotide binding 22.5 1.6E+02 0.0036 26.3 4.8 31 115-146 76-106 (180)
114 KOG3088 Secretory carrier memb 22.4 1.6E+02 0.0034 29.4 4.9 22 185-206 29-54 (313)
115 PRK14362 Maf-like protein; Pro 22.3 1.3E+02 0.0029 27.7 4.3 53 92-146 62-119 (207)
116 cd01105 HTH_GlnR-like Helix-Tu 21.8 1.3E+02 0.0028 23.6 3.6 34 29-62 38-71 (88)
117 TIGR00172 maf MAF protein. Thi 21.6 1.8E+02 0.0039 26.3 4.9 31 115-146 79-109 (183)
118 PRK04425 Maf-like protein; Rev 21.3 1.7E+02 0.0036 26.8 4.7 40 106-146 67-111 (196)
119 TIGR03675 arCOG00543 arCOG0054 21.1 2.6E+02 0.0057 30.0 6.7 93 13-109 19-129 (630)
120 PRK12327 nusA transcription el 20.9 80 0.0017 31.7 2.7 30 83-112 313-342 (362)
121 PRK00089 era GTPase Era; Revie 20.8 75 0.0016 29.3 2.4 27 83-109 237-271 (292)
122 KOG4656 Copper chaperone for s 20.5 1.3E+02 0.0028 28.9 3.8 46 12-60 36-83 (247)
123 PRK11901 hypothetical protein; 20.1 1.1E+02 0.0024 30.7 3.4 26 108-133 278-305 (327)
124 PLN02688 pyrroline-5-carboxyla 20.0 31 0.00067 31.4 -0.3 55 45-103 187-242 (266)
No 1
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.6e-104 Score=740.19 Aligned_cols=252 Identities=72% Similarity=1.124 Sum_probs=246.8
Q ss_pred CHHHHHhhhccEEEEEcCCCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHhhhccCceeEEEEcCccccChhhH
Q 021811 1 MVKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEMQCDIIKIGNLVRNKERF 80 (307)
Q Consensus 1 ~v~~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~ilKArD~IkAIaRGF~~E~AlkLLeDd~~~dIIdI~~~~~nke~f 80 (307)
+|++||++|+|.|.||+.+|+|+|+||++|||||+|++|||||++++||||+|||++||+||++||||+|+++++|+++|
T Consensus 77 ~v~raL~e~~i~c~lDL~egsm~V~TtRkT~DPyIiikArdlIKLlaRsVp~eqAvkiLqDev~CdiIkIgn~V~nkerF 156 (356)
T KOG2874|consen 77 LVERALDEHHIKCVLDLVEGSMTVKTTRKTRDPYIIIKARDLIKLLARSVPFEQAVKILQDEVACDIIKIGNLVRNKERF 156 (356)
T ss_pred HHHHHHHhcCcceEEeeccceeEEeecccccCceeeeeHHHHHHHHHcCCCHHHHHHHHhhccceeeeehhhhhccHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhccccCCCCchHHHHHHHhCceEEEeCceEEEecCCCcHHHHHHHHHHHhcCCCchhHHHHHHHHHHhhhcCccccc
Q 021811 81 VKRRQHLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDCMQNKMHPVYHIKILMVKKELEKDPALAN 160 (307)
Q Consensus 81 ~RrrgRIIG~~GkTkkaIE~LT~~yI~V~G~TVsIIG~~~~IkiAR~aIedlI~g~iHpVY~ikelmiKReL~kd~~l~~ 160 (307)
++||+|||||||.|++|||+||+|||+|||+|||+||+|.||++||++|+|||+| +||||||++|||||||++||+|+|
T Consensus 157 vKRRqRLiGpng~TLKAlelLT~CYilVqG~TVsaiGpfkGlkevr~IV~DcM~N-iHPiY~IK~LmiKRel~kd~~l~n 235 (356)
T KOG2874|consen 157 VKRRQRLIGPNGSTLKALELLTNCYILVQGNTVSAIGPFKGLKEVRKIVEDCMKN-IHPIYNIKTLMIKRELAKDPELAN 235 (356)
T ss_pred HHHHHHhcCCCchhHHHHHHHhhcEEEeeCcEEEeecCcchHHHHHHHHHHHHhc-cchHHHHHHHHHHHHhhcChhhcc
Confidence 9999999999999999999999999999999999999999999999999999999 999999999999999999999999
Q ss_pred ccccccchhccccccccccccc-cCCCCCCCCCCCCCCchhhhhhhccccccCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 021811 161 ENWDRFLPKFKKKNVKQKKVKS-KEKKPYTPFPPPPQPSKIDKLLESGEYFLSERKKESKKWQEKQEKQAEKTAENKRKR 239 (307)
Q Consensus 161 e~W~rflp~fkk~~~~~~k~~~-~~kk~~tpfpp~~~~~k~d~~~esgeyfl~~~~k~~~~~~~~~~~q~~~~~~~~~~r 239 (307)
||||||||+|+++|++++|+++ +.||+||||||+|++||||+|||||||||+++++++++++|+.++|+++..+++++|
T Consensus 236 e~W~rfLP~fkkknv~k~K~~K~~~kk~ytpfPp~q~~sKiD~eleSGEYFl~~~~k~~kK~~e~~Ekq~e~~~er~~~r 315 (356)
T KOG2874|consen 236 EDWSRFLPQFKKKNVKKRKPKKVKGKKEYTPFPPAQPPSKIDKELESGEYFLRDEEKSRKKMQEKKEKQAEKRKERQEER 315 (356)
T ss_pred ccHHHHhHHhhhhhhhhcccccccCCCCCCCCCCCcCcchhhhhhhcchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999876 558999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCCCCCCCCCC
Q 021811 240 DAAFIPPEEPSRQN 253 (307)
Q Consensus 240 ~~~~~~p~e~~~~~ 253 (307)
.++|+||+|.+...
T Consensus 316 ~k~fi~peE~~~~~ 329 (356)
T KOG2874|consen 316 MKAFIPPEEESRKP 329 (356)
T ss_pred hhccCCCccccccc
Confidence 99999999987654
No 2
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=100.00 E-value=1.5e-52 Score=375.42 Aligned_cols=154 Identities=32% Similarity=0.544 Sum_probs=144.7
Q ss_pred HHHHHhhhc-cEEEEEcCCCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHhhhccCceeEEEEcCcccc-Chhh
Q 021811 2 VKGALKEYG-VSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEMQCDIIKIGNLVR-NKER 79 (307)
Q Consensus 2 v~~~le~~~-i~i~lDl~egsV~V~tt~kT~DP~~ilKArD~IkAIaRGF~~E~AlkLLeDd~~~dIIdI~~~~~-nke~ 79 (307)
|.++++++. ++|+||+.+|+|+|+||++|.||+.++||+|+|+||+||||||+|++||+||++||||||+++++ +++|
T Consensus 29 v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~ 108 (194)
T COG1094 29 VKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDH 108 (194)
T ss_pred chHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHHHHHHhcCCcEEEEEEHHHhccCchhh
Confidence 456666665 99999999999999999999999999999999999999999999999999999999999999998 5566
Q ss_pred HhhhhccccCCCCchHHHHHHHhCceEEEeCceEEEecCCCcHHHHHHHHHHHhcCCCch-hHHHHHHHHHHhhhcC
Q 021811 80 FVKRRQHLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDCMQNKMHP-VYHIKILMVKKELEKD 155 (307)
Q Consensus 80 f~RrrgRIIG~~GkTkkaIE~LT~~yI~V~G~TVsIIG~~~~IkiAR~aIedlI~g~iHp-VY~ikelmiKReL~kd 155 (307)
|.|++|||||+||+|+++||+||||||+|||+||||||+|+++.+||+||+|||+|++|+ ||.+|+...++...+.
T Consensus 109 l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~tVaiiG~~~~v~iAr~AVemli~G~~h~~Vy~fLer~~~~lk~~~ 185 (194)
T COG1094 109 LRRIKGRIIGREGKTRRAIEELTGVYISVYGKTVAIIGGFEQVEIAREAVEMLINGAPHGKVYKFLERKERELKERE 185 (194)
T ss_pred hhHhhceeeCCCchHHHHHHHHhCCeEEEeCcEEEEecChhhhHHHHHHHHHHHcCCCchhHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999888 9999999888666554
No 3
>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=3.5e-37 Score=269.60 Aligned_cols=148 Identities=24% Similarity=0.425 Sum_probs=141.0
Q ss_pred HHHHHhhhccEEEEEcCCCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHhhhccCceeEEEEcCccccChhhHh
Q 021811 2 VKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEMQCDIIKIGNLVRNKERFV 81 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~ilKArD~IkAIaRGF~~E~AlkLLeDd~~~dIIdI~~~~~nke~f~ 81 (307)
|..+-+++|+.+++|..+|.|.|+ ..|+||+++++|++||++|++||+|++|++||.|+++++||+|.+|..++++|.
T Consensus 20 Ik~I~~~tgv~I~Id~~~g~V~I~--~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~gd~y~~~Vi~I~~~~~~~~~~~ 97 (172)
T TIGR03665 20 KKEIEERTGVKLDIDSETGEVKIE--EEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDYMLEVIDLKEYGKSPNALR 97 (172)
T ss_pred HHHHHHHhCcEEEEEcCCceEEEe--cCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcCCcceEEEEEhhhccCCHHHHH
Confidence 566779999999999999999997 568999999999999999999999999999999999999999999988999999
Q ss_pred hhhccccCCCCchHHHHHHHhCceEEEeCceEEEecCCCcHHHHHHHHHHHhcCCCch-hHHHHHHHHHHhh
Q 021811 82 KRRQHLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDCMQNKMHP-VYHIKILMVKKEL 152 (307)
Q Consensus 82 RrrgRIIG~~GkTkkaIE~LT~~yI~V~G~TVsIIG~~~~IkiAR~aIedlI~g~iHp-VY~ikelmiKReL 152 (307)
+++|||||++|+|+++||.+|||+|+|+|++|+|+|+++++++||++|++||+|++|+ ||++|+.+.. ||
T Consensus 98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~~~v~i~G~~~~~~~A~~~i~~li~~~~~~~vy~~l~~~~~-~~ 168 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEELTGVSISVYGKTVGIIGDPEQVQIAREAIEMLIEGAPHGTVYKFLERKRR-EL 168 (172)
T ss_pred HHHhhhcCCCcHHHHHHHHHHCCeEEEcCCEEEEECCHHHHHHHHHHHHHHHcCCCChhHHHHHHHHHH-HH
Confidence 9999999999999999999999999999999999999999999999999999999999 9999998654 44
No 4
>PRK13763 putative RNA-processing protein; Provisional
Probab=100.00 E-value=3.3e-36 Score=265.37 Aligned_cols=147 Identities=24% Similarity=0.417 Sum_probs=142.4
Q ss_pred HHHHHhhhccEEEEEcCCCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHhhhccCceeEEEEcCccccChhhHh
Q 021811 2 VKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEMQCDIIKIGNLVRNKERFV 81 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~ilKArD~IkAIaRGF~~E~AlkLLeDd~~~dIIdI~~~~~nke~f~ 81 (307)
|+.+.+++|+++.+|..+|+|.|.||. |.||+.+++|+++|+||++||+||+|++++.|+|+++||+|.+|..++++|.
T Consensus 25 Ik~I~e~tg~~I~i~~~~g~V~I~~~~-~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~gd~y~~~Vi~i~~~~~~~~~~~ 103 (180)
T PRK13763 25 KKEIEERTGVKLEIDSETGEVIIEPTD-GEDPLAVLKARDIVKAIGRGFSPEKALRLLDDDYVLEVIDLSDYGDSPNALR 103 (180)
T ss_pred HHHHHHHHCcEEEEECCCCeEEEEeCC-CCCHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCceEEEEEhhhccCChhHHH
Confidence 566778999999999999999999998 9999999999999999999999999999999999999999999988999999
Q ss_pred hhhccccCCCCchHHHHHHHhCceEEEeCceEEEecCCCcHHHHHHHHHHHhcCCCch-hHHHHHHHHH
Q 021811 82 KRRQHLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDCMQNKMHP-VYHIKILMVK 149 (307)
Q Consensus 82 RrrgRIIG~~GkTkkaIE~LT~~yI~V~G~TVsIIG~~~~IkiAR~aIedlI~g~iHp-VY~ikelmiK 149 (307)
|++|||||++|+|+++||++|||+|.|+|++|+|+|++++++.|+++|++|+.|++|+ ||++|+....
T Consensus 104 r~~griIG~~G~~~k~ie~~t~~~i~i~~~~v~i~G~~~~~~~A~~~I~~li~g~~~~~~~~~l~~~~~ 172 (180)
T PRK13763 104 RIKGRIIGEGGKTRRIIEELTGVDISVYGKTVAIIGDPEQVEIAREAIEMLIEGAPHGTVYKFLERKKR 172 (180)
T ss_pred HHhhheeCCCcHHHHHHHHHHCcEEEEcCCEEEEEeCHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999 9999999866
No 5
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.7e-35 Score=264.49 Aligned_cols=150 Identities=19% Similarity=0.282 Sum_probs=143.5
Q ss_pred HHHhhhccEEEEEcCCCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHhhhc-cCceeEEEEcCcccc-ChhhHh
Q 021811 4 GALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILD-DEMQCDIIKIGNLVR-NKERFV 81 (307)
Q Consensus 4 ~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~ilKArD~IkAIaRGF~~E~AlkLLe-Dd~~~dIIdI~~~~~-nke~f~ 81 (307)
=+++.+++++++|+...+|+++||..|.||..++|+.|||+||..||+++||+.||+ ||+|+|.+.|+++.. .++|++
T Consensus 98 Pive~lklqiRmNlK~r~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DAiALlrlddlflesFEi~dVKtL~GdHls 177 (252)
T KOG3273|consen 98 PIVEHLKLQIRMNLKARSVELRTCKDTEDPSALQKGADFVRAFILGFDIDDAIALLRLDDLFLESFEIKDVKTLKGDHLS 177 (252)
T ss_pred HHHHhhhheeEeecccceeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhHHHHHhhhhhhheeeeecccccccchhHH
Confidence 468999999999999999999999999999999999999999999999999999999 999999999999875 789999
Q ss_pred hhhccccCCCCchHHHHHHHhCceEEEeCceEEEecCCCcHHHHHHHHHHHhcCCCch-hHHHHHHHHHHhhh
Q 021811 82 KRRQHLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDCMQNKMHP-VYHIKILMVKKELE 153 (307)
Q Consensus 82 RrrgRIIG~~GkTkkaIE~LT~~yI~V~G~TVsIIG~~~~IkiAR~aIedlI~g~iHp-VY~ikelmiKReL~ 153 (307)
|..|||+|++|+|+.|||+.|.++|+|+|.+|||+|.|.+|++||+|||.||.|++++ ||+-|+.+..|--+
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad~kIHiLG~~~niriAR~avcsLIlGsppgkVy~~LR~vasRl~E 250 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLADSKIHILGAFQNIRIARDAVCSLILGSPPGKVYGNLRNVASRLKE 250 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecCceEEEeecchhhHHHHHhhHhhhccCCchhHHHHHHHHHHhhhh
Confidence 9999999999999999999999999999999999999999999999999999998777 99999999987543
No 6
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=99.00 E-value=7e-10 Score=112.36 Aligned_cols=69 Identities=19% Similarity=0.503 Sum_probs=61.1
Q ss_pred ceeEEEEcCccccChhhHhhhhccccCCCCchHHHHHHHhCceEEEeCce-EEEecCCCcH--HHHHHHHHHHh-cCCCc
Q 021811 63 MQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQGNT-VAAMGSFKGL--KQVRRIVEDCM-QNKMH 138 (307)
Q Consensus 63 ~~~dIIdI~~~~~nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~V~G~T-VsIIG~~~~I--kiAR~aIedlI-~g~iH 138 (307)
...-+|.|.+ + -.+|||||++|++.+++|.+|||+|+|+|+. +.+|.+|+++ ++||.+++.|| +|++|
T Consensus 203 ~~~~~v~lp~---d-----~~kgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~fdp~rreia~~~l~~li~dgrih 274 (514)
T TIGR03319 203 TTVSVVNLPN---D-----EMKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPVRREIARMALEKLIQDGRIH 274 (514)
T ss_pred heeeeEEcCC---h-----hhhccccCCCcchHHHHHHHhCceEEEcCCCCeEEecCCchHHHHHHHHHHHHHHHcCCCC
Confidence 3455666653 1 3799999999999999999999999999988 8889999999 99999999999 99999
Q ss_pred h
Q 021811 139 P 139 (307)
Q Consensus 139 p 139 (307)
|
T Consensus 275 p 275 (514)
T TIGR03319 275 P 275 (514)
T ss_pred H
Confidence 9
No 7
>PRK00106 hypothetical protein; Provisional
Probab=98.95 E-value=8.6e-10 Score=112.49 Aligned_cols=69 Identities=17% Similarity=0.472 Sum_probs=61.1
Q ss_pred ceeEEEEcCccccChhhHhhhhccccCCCCchHHHHHHHhCceEEEeCce-EEEecCCCcH--HHHHHHHHHHh-cCCCc
Q 021811 63 MQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQGNT-VAAMGSFKGL--KQVRRIVEDCM-QNKMH 138 (307)
Q Consensus 63 ~~~dIIdI~~~~~nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~V~G~T-VsIIG~~~~I--kiAR~aIedlI-~g~iH 138 (307)
...-++.|.+ + -.+|||||++|++.+++|.+|||+|+|+|+. +.+|.+|+++ ++||.+++.|| +|+||
T Consensus 224 ~tvs~v~lp~---d-----emkGriIGreGrNir~~E~~tGvdliiddtp~~v~lS~fdpvRReiAr~~le~Li~dgrIh 295 (535)
T PRK00106 224 QTITTVHLPD---D-----NMKGRIIGREGRNIRTLESLTGIDVIIDDTPEVVVLSGFDPIRREIARMTLESLIKDGRIH 295 (535)
T ss_pred heeeeEEcCC---h-----HhhcceeCCCcchHHHHHHHhCceEEEcCCCCeEEEeCCChHHHHHHHHHHHHHHHcCCcC
Confidence 3456666664 1 3799999999999999999999999999987 7789999998 89999999999 99999
Q ss_pred h
Q 021811 139 P 139 (307)
Q Consensus 139 p 139 (307)
|
T Consensus 296 p 296 (535)
T PRK00106 296 P 296 (535)
T ss_pred H
Confidence 9
No 8
>PRK12704 phosphodiesterase; Provisional
Probab=98.82 E-value=5e-09 Score=106.40 Aligned_cols=57 Identities=21% Similarity=0.525 Sum_probs=55.0
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeCce-EEEecCCCcHH--HHHHHHHHHh-cCCCch
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQGNT-VAAMGSFKGLK--QVRRIVEDCM-QNKMHP 139 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G~T-VsIIG~~~~Ik--iAR~aIedlI-~g~iHp 139 (307)
.+|||||++|++.+++|.+|||+|+|+|+. |.+|.+|+++. +|+.+++.|+ +|.+||
T Consensus 221 mkgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~~~~~rre~a~~~l~~l~~dg~i~P 281 (520)
T PRK12704 221 MKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPIRREIARLALEKLVQDGRIHP 281 (520)
T ss_pred hhcceeCCCcchHHHHHHHhCCeEEEcCCCCeEEEecCChhhHHHHHHHHHHHHhcCCcCC
Confidence 799999999999999999999999999987 88899999997 9999999999 999999
No 9
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.57 E-value=1.7e-07 Score=79.06 Aligned_cols=71 Identities=23% Similarity=0.220 Sum_probs=60.2
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeCc------------------------eEEEecCC---CcHHHHHHHHHHHhcC
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQGN------------------------TVAAMGSF---KGLKQVRRIVEDCMQN 135 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G~------------------------TVsIIG~~---~~IkiAR~aIedlI~g 135 (307)
.+||||||+|+|.+.||.-|||.|.|.|. +|.|.|+- +.+..|...|+.|+.-
T Consensus 16 ~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~~ 95 (120)
T cd02395 16 FVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLKP 95 (120)
T ss_pred eeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhcc
Confidence 68999999999999999999999999996 68899876 8899999999999987
Q ss_pred CCchh-HHHHHHHHHHhhhc
Q 021811 136 KMHPV-YHIKILMVKKELEK 154 (307)
Q Consensus 136 ~iHpV-Y~ikelmiKReL~k 154 (307)
.|+- .+-+....-+||+.
T Consensus 96 -~~~~~~~~~k~~ql~~la~ 114 (120)
T cd02395 96 -AIEGGNDELKREQLRELAL 114 (120)
T ss_pred -CCCccchHHHHHHHHHHHH
Confidence 7775 55555555566653
No 10
>smart00322 KH K homology RNA-binding domain.
Probab=98.37 E-value=7.1e-07 Score=62.92 Aligned_cols=52 Identities=19% Similarity=0.324 Sum_probs=48.1
Q ss_pred hhhccccCCCCchHHHHHHHhCceEEEeC-----ceEEEecCCCcHHHHHHHHHHHh
Q 021811 82 KRRQHLVGPNSSTLKALEILTGCYILVQG-----NTVAAMGSFKGLKQVRRIVEDCM 133 (307)
Q Consensus 82 RrrgRIIG~~GkTkkaIE~LT~~yI~V~G-----~TVsIIG~~~~IkiAR~aIedlI 133 (307)
...|+|||++|.+++.|+..|||.|.+.+ .+|.+.|+..++..|+..|.+++
T Consensus 12 ~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 12 DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred hhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 36799999999999999999999999988 67999999999999999998876
No 11
>PRK12705 hypothetical protein; Provisional
Probab=98.37 E-value=5.1e-07 Score=92.03 Aligned_cols=69 Identities=19% Similarity=0.487 Sum_probs=59.4
Q ss_pred ceeEEEEcCccccChhhHhhhhccccCCCCchHHHHHHHhCceEEEeCce-EEEecCCCcH--HHHHHHHHHHh-cCCCc
Q 021811 63 MQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQGNT-VAAMGSFKGL--KQVRRIVEDCM-QNKMH 138 (307)
Q Consensus 63 ~~~dIIdI~~~~~nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~V~G~T-VsIIG~~~~I--kiAR~aIedlI-~g~iH 138 (307)
....++.|.+ + -.+|||||++|++.+++|.+||+.|+|.|.. +.+|-.|+.+ ++|+.+++.|| .|.+|
T Consensus 197 ~tvs~v~lp~---d-----emkGriIGreGrNir~~E~~tGvdliiddtp~~V~ls~fdp~rreia~~~l~~Li~dgri~ 268 (508)
T PRK12705 197 LSVSVVPIPS---D-----AMKGRIIGREGRNIRAFEGLTGVDLIIDDTPEAVVISSFNPIRREIARLTLEKLLADGRIH 268 (508)
T ss_pred heeeeeecCC---h-----HhhccccCccchhHHHHHHhhCCceEecCCccchhhcccCccchHHHHHHHHHHHhcCCCC
Confidence 3455666653 1 3799999999999999999999999999977 6678889887 89999999999 99999
Q ss_pred h
Q 021811 139 P 139 (307)
Q Consensus 139 p 139 (307)
|
T Consensus 269 p 269 (508)
T PRK12705 269 P 269 (508)
T ss_pred h
Confidence 9
No 12
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=98.21 E-value=1.2e-06 Score=63.45 Aligned_cols=48 Identities=21% Similarity=0.382 Sum_probs=43.6
Q ss_pred hhhccccCCCCchHHHHHHHhCceEEEeC----ceEEEecCCCcHHHHHHHH
Q 021811 82 KRRQHLVGPNSSTLKALEILTGCYILVQG----NTVAAMGSFKGLKQVRRIV 129 (307)
Q Consensus 82 RrrgRIIG~~GkTkkaIE~LT~~yI~V~G----~TVsIIG~~~~IkiAR~aI 129 (307)
...++|||++|++++.||..|||.|.|.+ .+|.|.|+.+++..|++.|
T Consensus 9 ~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 9 SLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp HHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEESHHHHHHHHHHH
T ss_pred HHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEeCHHHHHHHHhhC
Confidence 46899999999999999999999999997 3799999999999998765
No 13
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.16 E-value=2.7e-06 Score=62.04 Aligned_cols=48 Identities=17% Similarity=0.338 Sum_probs=42.6
Q ss_pred hhhccccCCCCchHHHHHHHhCceEEEeC-----ceEEEecCCCcHHHHHHHH
Q 021811 82 KRRQHLVGPNSSTLKALEILTGCYILVQG-----NTVAAMGSFKGLKQVRRIV 129 (307)
Q Consensus 82 RrrgRIIG~~GkTkkaIE~LT~~yI~V~G-----~TVsIIG~~~~IkiAR~aI 129 (307)
...++|||++|.+++.|+.-|||.|.|.. +.|.|.|+.+++..|+..|
T Consensus 9 ~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 9 KLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred HHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHHHHHHHHHHh
Confidence 46799999999999999999999999988 6699999988887777654
No 14
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.15 E-value=2.1e-06 Score=63.95 Aligned_cols=49 Identities=22% Similarity=0.390 Sum_probs=43.0
Q ss_pred hhhccccCCCCchHHHHHHHhCceEEEeC-ceEEEecC-CCcHHHHHHHHH
Q 021811 82 KRRQHLVGPNSSTLKALEILTGCYILVQG-NTVAAMGS-FKGLKQVRRIVE 130 (307)
Q Consensus 82 RrrgRIIG~~GkTkkaIE~LT~~yI~V~G-~TVsIIG~-~~~IkiAR~aIe 130 (307)
...|+|||++|+|++.|+.-|||.|.|.. .+|.|.|+ .++++.|+..|+
T Consensus 11 ~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 11 DKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred hheeeeECCCchHHHHHHHHHCCEEEeCCCCEEEEEeCCHHHHHHHHHHhC
Confidence 36799999999999999999999999997 45999998 778888887663
No 15
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.08 E-value=5e-06 Score=59.87 Aligned_cols=48 Identities=19% Similarity=0.355 Sum_probs=42.0
Q ss_pred hhhccccCCCCchHHHHHHHhCceEEEeC-------ceEEEecCCCcHHHHHHHH
Q 021811 82 KRRQHLVGPNSSTLKALEILTGCYILVQG-------NTVAAMGSFKGLKQVRRIV 129 (307)
Q Consensus 82 RrrgRIIG~~GkTkkaIE~LT~~yI~V~G-------~TVsIIG~~~~IkiAR~aI 129 (307)
...++|||++|++++.|+..|||.|.|.. ..|.|.|+.+++..|+..|
T Consensus 9 ~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 9 SLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred hhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence 35699999999999999999999999977 4599999988888877665
No 16
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=97.41 E-value=0.00024 Score=52.82 Aligned_cols=47 Identities=21% Similarity=0.322 Sum_probs=40.7
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeCc--------eEEEecCCCcHHHHHHHH
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQGN--------TVAAMGSFKGLKQVRRIV 129 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G~--------TVsIIG~~~~IkiAR~aI 129 (307)
..|+|||++|.+.+.|+..|||.|.|..+ .|-|.|+++++..|..-|
T Consensus 10 ~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 10 QAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred HcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 57999999999999999999999999854 378899988888777654
No 17
>PF13014 KH_3: KH domain
Probab=97.27 E-value=0.00039 Score=47.95 Aligned_cols=26 Identities=27% Similarity=0.410 Sum_probs=25.1
Q ss_pred ccccCCCCchHHHHHHHhCceEEEeC
Q 021811 85 QHLVGPNSSTLKALEILTGCYILVQG 110 (307)
Q Consensus 85 gRIIG~~GkTkkaIE~LT~~yI~V~G 110 (307)
|+|||++|.|++.|+..|||+|.|..
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 78999999999999999999999987
No 18
>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=97.01 E-value=0.001 Score=58.85 Aligned_cols=53 Identities=21% Similarity=0.221 Sum_probs=48.1
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeCc--eEEE---ecCCCcHHHHHHHHHHHhcC
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQGN--TVAA---MGSFKGLKQVRRIVEDCMQN 135 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G~--TVsI---IG~~~~IkiAR~aIedlI~g 135 (307)
+.|.|||++|+|.+.|+..|||.|.|... +|.| -++...+..|++.|..+..|
T Consensus 8 kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 8 RIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRG 65 (172)
T ss_pred HhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence 67899999999999999999999999986 5777 47778899999999999988
No 19
>PRK13763 putative RNA-processing protein; Provisional
Probab=96.97 E-value=0.001 Score=59.30 Aligned_cols=53 Identities=23% Similarity=0.231 Sum_probs=48.8
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeCc--eEEEe----cCCCcHHHHHHHHHHHhcC
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQGN--TVAAM----GSFKGLKQVRRIVEDCMQN 135 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G~--TVsII----G~~~~IkiAR~aIedlI~g 135 (307)
+.|.|||++|.|.+.|+..|||.|.|... +|.|. ++...+..|++.|..+..|
T Consensus 13 kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g 71 (180)
T PRK13763 13 RIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTDGEDPLAVLKARDIVKAIGRG 71 (180)
T ss_pred HhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence 68999999999999999999999999976 48886 7888999999999999998
No 20
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.60 E-value=0.0015 Score=62.20 Aligned_cols=29 Identities=38% Similarity=0.710 Sum_probs=27.3
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeCc
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQGN 111 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G~ 111 (307)
-.|||+||.|.|++.||.-|||.|+|-|+
T Consensus 108 FVGRILGPrGnSlkrLe~eTgCki~IrGr 136 (259)
T KOG1588|consen 108 FVGRILGPRGNSLKRLEEETGCKIMIRGR 136 (259)
T ss_pred cccccccCCcchHHHHHHHHCCeEEEecC
Confidence 36999999999999999999999999986
No 21
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=96.29 E-value=0.011 Score=61.67 Aligned_cols=123 Identities=17% Similarity=0.231 Sum_probs=83.8
Q ss_pred HHHHhhhccEEEEEcCCCeE--EEEcCCCCCChHHHHhHHHHHHHHHcC----CChHHHHhhhc-cCceeEEEEcCcccc
Q 021811 3 KGALKEYGVSCELNLVEGSM--TVSTTRKTRDPYIIVKARDLIRLLSRS----VPAPQAIKILD-DEMQCDIIKIGNLVR 75 (307)
Q Consensus 3 ~~~le~~~i~i~lDl~egsV--~V~tt~kT~DP~~ilKArD~IkAIaRG----F~~E~AlkLLe-Dd~~~dIIdI~~~~~ 75 (307)
..+=+..|++|.|.-+.... .+++-+.|.||+.+..|+.||.=|.+. .+.+. --.. +...-.-+++. +=|
T Consensus 162 kqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~g~~--~~~g~~~g~~~~~~V~-VPr 238 (600)
T KOG1676|consen 162 KQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEVPGSG--GHAGVRGGGSATREVK-VPR 238 (600)
T ss_pred HHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCCCccc--cccCcCccccceeEEe-ccc
Confidence 44556778888777654422 356777899999999999999877662 11110 0001 11111111111 001
Q ss_pred ChhhHhhhhccccCCCCchHHHHHHHhCceEEEe--------CceEEEecCCCcHHHHHHHHHHHhc
Q 021811 76 NKERFVKRRQHLVGPNSSTLKALEILTGCYILVQ--------GNTVAAMGSFKGLKQVRRIVEDCMQ 134 (307)
Q Consensus 76 nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~V~--------G~TVsIIG~~~~IkiAR~aIedlI~ 134 (307)
+ --|=|||++|.|.|-|.+-||++|-+- ..++.|||+.+.|..|-+.|..||.
T Consensus 239 ~------~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~ 299 (600)
T KOG1676|consen 239 S------KVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIA 299 (600)
T ss_pred c------ceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHH
Confidence 1 358899999999999999999999874 2469999999999999999999983
No 22
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.86 E-value=0.018 Score=54.13 Aligned_cols=84 Identities=23% Similarity=0.334 Sum_probs=61.8
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeCce-E-EEec---CCCcHHHHHHHHHHHhcCCCc-hhHHHH--HHHHHHhhhc
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQGNT-V-AAMG---SFKGLKQVRRIVEDCMQNKMH-PVYHIK--ILMVKKELEK 154 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G~T-V-sIIG---~~~~IkiAR~aIedlI~g~iH-pVY~ik--elmiKReL~k 154 (307)
-.|-||||.|+|++.+|..|+|.|.|-|.. | ..-| ..++++-+-..+.-||.-..- .+.+.. .+-+-||-..
T Consensus 164 FVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n~I~~a~~ 243 (269)
T COG5176 164 FVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARR 243 (269)
T ss_pred eeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHHHHHHHhc
Confidence 568999999999999999999999999965 2 1222 245788888888888855332 344432 2334578999
Q ss_pred Ccccccccccccc
Q 021811 155 DPALANENWDRFL 167 (307)
Q Consensus 155 d~~l~~e~W~rfl 167 (307)
+|+= --+|.||-
T Consensus 244 ~PeG-qnDlkR~q 255 (269)
T COG5176 244 NPEG-QNDLKRFQ 255 (269)
T ss_pred CCcc-cchHHHHH
Confidence 9997 55899984
No 23
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=95.43 E-value=0.014 Score=54.20 Aligned_cols=79 Identities=23% Similarity=0.423 Sum_probs=63.8
Q ss_pred hccccCCCCchHHHHHHHhCceEEEeCce---EEE-ecCCCc------HHHHHHHHHHHh-cCCCc---hhHHHHHHHHH
Q 021811 84 RQHLVGPNSSTLKALEILTGCYILVQGNT---VAA-MGSFKG------LKQVRRIVEDCM-QNKMH---PVYHIKILMVK 149 (307)
Q Consensus 84 rgRIIG~~GkTkkaIE~LT~~yI~V~G~T---VsI-IG~~~~------IkiAR~aIedlI-~g~iH---pVY~ikelmiK 149 (307)
-|||||.+|+|+.||+.|++.++.-.+.+ |.+ +|.|.- +..|-++..... .|.+| |+-.+=+.++-
T Consensus 102 ~~~LIG~~Gk~LdALQ~L~n~~l~~~~g~~~~v~ldv~~yRerR~e~L~~LA~~~A~rV~~tg~~v~L~pM~~~ERkIVH 181 (208)
T COG1847 102 AGRLIGKHGKTLDALQYLANLYLNKIGGKFKRVTLDVGDYRERRKETLIKLAERAAERVLETGRSVELEPMPPFERKIVH 181 (208)
T ss_pred hhhhhccCCcchHHHHHHHHHHhhhhcCcceEEEEEhhhHHHHHHHHHHHHHHHHHHHHHhhCCeeecCCCCHHHHHHHH
Confidence 79999999999999999999999886544 444 677754 467777777776 67665 68888888998
Q ss_pred HhhhcCccccccc
Q 021811 150 KELEKDPALANEN 162 (307)
Q Consensus 150 ReL~kd~~l~~e~ 162 (307)
.-|..+|.+.++|
T Consensus 182 ~~l~~~~~V~T~S 194 (208)
T COG1847 182 TALSANPGVETYS 194 (208)
T ss_pred HHHHhcCCcceee
Confidence 8999999888776
No 24
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=95.36 E-value=0.023 Score=58.56 Aligned_cols=109 Identities=21% Similarity=0.299 Sum_probs=73.9
Q ss_pred HHcCCChHHHHh---hhccCceeEEEEcCccccChhhHhhhhccccCCCCchHHHHHHHhCceEEEeCce----------
Q 021811 46 LSRSVPAPQAIK---ILDDEMQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQGNT---------- 112 (307)
Q Consensus 46 IaRGF~~E~Alk---LLeDd~~~dIIdI~~~~~nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~V~G~T---------- 112 (307)
+.-||-+..=.+ ++.|-++++|=+-.++ | -.|-|||+.|.|+|-||.-|||+|.|-|+-
T Consensus 122 ~nP~fkpP~DYk~p~~~~~Kv~IPvke~Pd~--N------FvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~ 193 (554)
T KOG0119|consen 122 LNPGFKPPADYKPPAKLHDKVYIPVKEFPDI--N------FVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSD 193 (554)
T ss_pred hCcCCCCCcccCcccccccceecchhhcCCc--c------eeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCc
Confidence 445555443333 3456666544433332 2 468999999999999999999999999921
Q ss_pred -------------EEEec-CCCcHHHHHHHHHHHhcCC-Cch-hHHHHHHHHHHhhh-cCccccccc
Q 021811 113 -------------VAAMG-SFKGLKQVRRIVEDCMQNK-MHP-VYHIKILMVKKELE-KDPALANEN 162 (307)
Q Consensus 113 -------------VsIIG-~~~~IkiAR~aIedlI~g~-iHp-VY~ikelmiKReL~-kd~~l~~e~ 162 (307)
+-|.+ +++.|+-|-.+|+.||.-+ .-| .-+-+..+.-|||+ -++.+..++
T Consensus 194 d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~av~~~e~~n~l~~~Qlrela~lNgt~r~~d 260 (554)
T KOG0119|consen 194 DLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQSAVSVPEGQNDLKRLQLRELARLNGTLRDDD 260 (554)
T ss_pred ccccccccccceeEEEecchHHHHHHHHHHHHHHHHhhccCccccccccHHHHHHHHHhCCCCCccc
Confidence 12222 3456888999999999543 335 76777777777776 477887777
No 25
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.21 E-value=0.028 Score=52.08 Aligned_cols=55 Identities=20% Similarity=0.307 Sum_probs=47.6
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeCce-EEEecCCC-cHHHHHHHHHHHhcCCCc
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQGNT-VAAMGSFK-GLKQVRRIVEDCMQNKMH 138 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G~T-VsIIG~~~-~IkiAR~aIedlI~g~iH 138 (307)
..+||||++|.+++.|...|+|.|.|..|. |.|.|+.. .+..|.++|.+|=.- -|
T Consensus 155 ~i~~lig~~g~~i~~l~~~~~~~I~ig~NG~VwI~~~~~~~~~~a~~~I~~~e~~-~~ 211 (235)
T PRK04163 155 KVPRVIGKKGSMINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIKKIERE-AH 211 (235)
T ss_pred HHHhhcCCCChhHhhhhhhhCcEEEEcCCcEEEEeeCCHHHHHHHHHHHHHHHhh-hh
Confidence 378899999999999999999999999866 88988876 688899999888766 56
No 26
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=95.13 E-value=0.065 Score=54.84 Aligned_cols=114 Identities=19% Similarity=0.247 Sum_probs=74.0
Q ss_pred HHHHHhhhccEEEEEcCC-----CeEEEEcCCCCCChHHHHhHHHHHH--HHHc-CCChHHHHhhhccCceeEEEEcCcc
Q 021811 2 VKGALKEYGVSCELNLVE-----GSMTVSTTRKTRDPYIIVKARDLIR--LLSR-SVPAPQAIKILDDEMQCDIIKIGNL 73 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~e-----gsV~V~tt~kT~DP~~ilKArD~Ik--AIaR-GF~~E~AlkLLeDd~~~dIIdI~~~ 73 (307)
|+.+....|..+.|..-+ -.|.+. |.||...+||.--|- .--- .|.|.. -++|..-
T Consensus 433 IKql~RfagASiKIappE~pdvseRMViI----tGppeaqfKAQgrifgKikEenf~~Pke------------evkleth 496 (584)
T KOG2193|consen 433 IKQLSRFAGASIKIAPPEIPDVSERMVII----TGPPEAQFKAQGRIFGKIKEENFFLPKE------------EVKLETH 496 (584)
T ss_pred HHHHHHhccceeeecCCCCCCcceeEEEe----cCChHHHHhhhhhhhhhhhhhccCCchh------------hheeeee
Confidence 344455667777765432 233344 489999999975442 1111 222222 2333333
Q ss_pred ccChhhHhhhhccccCCCCchHHHHHHHhCceEEEe--------Cce-EEEecCCCcHHHHHHHHHHHhc
Q 021811 74 VRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQ--------GNT-VAAMGSFKGLKQVRRIVEDCMQ 134 (307)
Q Consensus 74 ~~nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~V~--------G~T-VsIIG~~~~IkiAR~aIedlI~ 134 (307)
++ .=.+..||+||++|+|..-|.+||++.++|- |.+ |-|||.|-.-..|.+-|..+++
T Consensus 497 ir---VPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~iv~ 563 (584)
T KOG2193|consen 497 IR---VPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHIVN 563 (584)
T ss_pred ee---ccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHHHH
Confidence 33 1235899999999999999999999999993 334 7789999888888777776653
No 27
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=95.12 E-value=0.049 Score=57.10 Aligned_cols=121 Identities=18% Similarity=0.270 Sum_probs=91.6
Q ss_pred HHHHHhhhccEEEEEcCCCeEEEEcCCCCCChHHHHhHHHHHHHH-HcCC---ChHHHHhhhccCceeEEEEcCccccCh
Q 021811 2 VKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLL-SRSV---PAPQAIKILDDEMQCDIIKIGNLVRNK 77 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~ilKArD~IkAI-aRGF---~~E~AlkLLeDd~~~dIIdI~~~~~nk 77 (307)
|...+.+.|+.+.+....+.+-.+.+..+..|..+-.|+.||.=+ +||- +++++-- ......-|.|-. +
T Consensus 76 I~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~~~~~~~~~q~---~~~ttqeI~IPa---~- 148 (600)
T KOG1676|consen 76 IQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAKQLIGEVVSRGRPPGGFPDNQG---SVETTQEILIPA---N- 148 (600)
T ss_pred hhhhhhhcCCccccCCCCCCcccccccccCCcccHHHHHHhhhhhhhccCCCCCccccCC---ccceeeeeccCc---c-
Confidence 456677788888888888888889999999999999999998765 5653 2222111 011222333332 2
Q ss_pred hhHhhhhccccCCCCchHHHHHHHhCceEEE-eC-c-------eEEEecCCCcHHHHHHHHHHHhc
Q 021811 78 ERFVKRRQHLVGPNSSTLKALEILTGCYILV-QG-N-------TVAAMGSFKGLKQVRRIVEDCMQ 134 (307)
Q Consensus 78 e~f~RrrgRIIG~~GkTkkaIE~LT~~yI~V-~G-~-------TVsIIG~~~~IkiAR~aIedlI~ 134 (307)
+-|-|||++|-|.+.|.+-|||.+.+ ++ + ++=|.|+.+.++.|+..|.|+|.
T Consensus 149 -----k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~ 209 (600)
T KOG1676|consen 149 -----KCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILR 209 (600)
T ss_pred -----ceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHH
Confidence 57899999999999999999998654 43 2 57899999999999999999997
No 28
>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=95.00 E-value=0.031 Score=59.84 Aligned_cols=53 Identities=15% Similarity=0.250 Sum_probs=45.9
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeC-ceEEEecCC-CcHHHHHHHHHHHhcC
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQG-NTVAAMGSF-KGLKQVRRIVEDCMQN 135 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G-~TVsIIG~~-~~IkiAR~aIedlI~g 135 (307)
.++.|||++|+|.+.|..-|||.|.|.+ .+|.|.|.- +.++.|+..|+.+...
T Consensus 588 ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 588 KIGEVIGPKGKMINQIQDETGAEISIEDDGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred HhhheeCCCcHhHHHHHHHHCCEEEEecCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 5899999999999999999999999998 558888854 5688899999988873
No 29
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=94.91 E-value=0.0026 Score=48.27 Aligned_cols=31 Identities=29% Similarity=0.398 Sum_probs=24.8
Q ss_pred hccccCCCCchHHHHHHHhCceEEEeCceEE
Q 021811 84 RQHLVGPNSSTLKALEILTGCYILVQGNTVA 114 (307)
Q Consensus 84 rgRIIG~~GkTkkaIE~LT~~yI~V~G~TVs 114 (307)
-|||||++|+|+.||+.|++.++.-+|..|.
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~~~~~~~~~~~~ 70 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVNAAANKHGKRVR 70 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHHHHHHHT-SS-E
T ss_pred cceEECCCCeeHHHHHHHHHHHHHhCCCEEE
Confidence 6999999999999999999887765555443
No 30
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=94.68 E-value=0.042 Score=58.25 Aligned_cols=52 Identities=17% Similarity=0.317 Sum_probs=43.6
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeC-ceEEEecCC-CcHHHHHHHHHHHhc
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQG-NTVAAMGSF-KGLKQVRRIVEDCMQ 134 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G-~TVsIIG~~-~~IkiAR~aIedlI~ 134 (307)
.+++|||++|+|.+.|+.-|||.|.|.+ .+|.|.+.- ..+..|.+.|..+..
T Consensus 561 kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 561 KIRDVIGPGGKVIREITEETGAKIDIEDDGTVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred HHHhhcCCCcHHHHHHHHHHCCEEEEecCeEEEEEECcHHHHHHHHHHHHhhhc
Confidence 5899999999999999999999999996 558887744 446888888887764
No 31
>PRK01064 hypothetical protein; Provisional
Probab=92.28 E-value=0.066 Score=42.58 Aligned_cols=32 Identities=19% Similarity=0.205 Sum_probs=26.1
Q ss_pred hccccCCCCchHHHHHHHhCceEEEeCceEEE
Q 021811 84 RQHLVGPNSSTLKALEILTGCYILVQGNTVAA 115 (307)
Q Consensus 84 rgRIIG~~GkTkkaIE~LT~~yI~V~G~TVsI 115 (307)
.||+||++|+|..+|-.+.++-..-+|..|.+
T Consensus 41 ~g~vIGk~G~~i~air~l~~~~~~~~~~rv~l 72 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLVSVASRNNVKVSL 72 (78)
T ss_pred ceEEECCCCccHHHHHHHHHHHHhhCCCEEEE
Confidence 69999999999999999877665556666553
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=91.97 E-value=0.053 Score=41.86 Aligned_cols=26 Identities=27% Similarity=0.308 Sum_probs=23.1
Q ss_pred hccccCCCCchHHHHHHHhCceEEEe
Q 021811 84 RQHLVGPNSSTLKALEILTGCYILVQ 109 (307)
Q Consensus 84 rgRIIG~~GkTkkaIE~LT~~yI~V~ 109 (307)
-|+|||++|+|+.||+-|++..+.-.
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~~~~~~ 60 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANLVLNRN 60 (77)
T ss_pred CCeEECCCCccHHHHHHHHHHHHhhc
Confidence 49999999999999999999877644
No 33
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=91.93 E-value=0.43 Score=49.10 Aligned_cols=82 Identities=26% Similarity=0.339 Sum_probs=51.1
Q ss_pred cEEEEEcC--------CCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHhhhccCceeEEEEcCccccChhhHhh
Q 021811 11 VSCELNLV--------EGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEMQCDIIKIGNLVRNKERFVK 82 (307)
Q Consensus 11 i~i~lDl~--------egsV~V~tt~kT~DP~~ilKArD~IkAIaRGF~~E~AlkLLeDd~~~dIIdI~~~~~nke~f~R 82 (307)
+.|++|.. +..+||-.|.+. .-+|..+|--|.-. +| .+|++. +=|-|+-+.-| .
T Consensus 228 TqsriD~hrken~Gaaek~itvh~tpEg-----~s~Ac~~ILeimqk----EA---~~~k~~-~e~pLk~lAHN-----~ 289 (584)
T KOG2193|consen 228 TQSRIDVHRKENAGAAEKIITVHSTPEG-----TSKACKMILEIMQK----EA---VDDKVA-EEIPLKILAHN-----N 289 (584)
T ss_pred hhheeeeeecccCCcccCceEEecCccc-----hHHHHHHHHHHHHH----hh---hccchh-hhcchhhhhhc-----c
Confidence 34566654 567888876553 33444333322211 11 122322 44555555544 3
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeC
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQG 110 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G 110 (307)
.-|||||+.|+.++-||--|||.|.|.-
T Consensus 290 lvGRLIGKeGrnlKkIeq~TgTkITis~ 317 (584)
T KOG2193|consen 290 LVGRLIGKEGRNLKKIEQDTGTKITISK 317 (584)
T ss_pred hhhhhhhhccccHHHHHhhcCCceeeee
Confidence 6799999999999999999999998753
No 34
>PRK02821 hypothetical protein; Provisional
Probab=91.75 E-value=0.12 Score=41.08 Aligned_cols=66 Identities=15% Similarity=0.280 Sum_probs=38.9
Q ss_pred HHHHHHHHcCCC-hHHHHhhhccC-ceeEEEEcCccccChhhHhhhhccccCCCCchHHHHHHHhCceEEEeCceEEE
Q 021811 40 RDLIRLLSRSVP-APQAIKILDDE-MQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQGNTVAA 115 (307)
Q Consensus 40 rD~IkAIaRGF~-~E~AlkLLeDd-~~~dIIdI~~~~~nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~V~G~TVsI 115 (307)
.+||..|++++= .++++.+-..+ --..+|.|.- ++ .=.|||||++|+|.+||=.+-.+- +|+.|.+
T Consensus 3 ~~lv~~ivk~LVd~Pe~V~V~~~~~~~~~~i~l~v---~~----~D~GrVIGk~Gr~i~AIRtlv~a~---~~~~v~l 70 (77)
T PRK02821 3 ADAVEHLVRGIVDNPDDVRVDSHTNRRGRTLEVRV---HP----DDLGKVIGRGGRTATALRTVVAAI---GGRGVRV 70 (77)
T ss_pred HHHHHHHHHHhCCCCCeEEEEEEECCCcEEEEEEE---Ch----hhCcceeCCCCchHHHHHHHHHHh---cCCeEEE
Confidence 467777776642 33455543311 0112344432 22 248999999999999998755543 7777664
No 35
>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=91.68 E-value=0.14 Score=38.05 Aligned_cols=26 Identities=15% Similarity=0.172 Sum_probs=24.1
Q ss_pred hhccccCCCCchHHHHHHHhCceEEE
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILV 108 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V 108 (307)
-.|+.||++|++.+.++.++|.+|-|
T Consensus 35 ~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 35 QLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cceeeECCCCHHHHHHHHHHCCCeEE
Confidence 57999999999999999999998876
No 36
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=90.79 E-value=0.19 Score=55.14 Aligned_cols=58 Identities=19% Similarity=0.280 Sum_probs=49.3
Q ss_pred hhccccCCCCchHHHHHHHhCce-EEEeC-ceEEEecC-CCcHHHHHHHHHHHhcCCCc-h-hH
Q 021811 83 RRQHLVGPNSSTLKALEILTGCY-ILVQG-NTVAAMGS-FKGLKQVRRIVEDCMQNKMH-P-VY 141 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~y-I~V~G-~TVsIIG~-~~~IkiAR~aIedlI~g~iH-p-VY 141 (307)
.++.|||++|+|.+.|..-||+. |-+.+ .+|.|+|. .+.++.|...|..+... ++ + +|
T Consensus 695 ki~~vIG~GGktIk~I~eetg~~~Idi~ddg~V~I~a~d~~~i~~A~~~I~~l~~~-~~vG~iy 757 (891)
T PLN00207 695 KVNMIIGSGGKKVKSIIEETGVEAIDTQDDGTVKITAKDLSSLEKSKAIISSLTMV-PTVGDIY 757 (891)
T ss_pred HHHHHhcCCchhHHHHHHHHCCCccCcCCCeeEEEEeCCHHHHHHHHHHHHHHhcC-cCCCcEE
Confidence 58899999999999999999999 98887 45999984 56689999999999865 44 3 77
No 37
>PRK00468 hypothetical protein; Provisional
Probab=90.69 E-value=0.13 Score=40.47 Aligned_cols=31 Identities=13% Similarity=0.234 Sum_probs=22.4
Q ss_pred hccccCCCCchHHHHHHHhCceEEEeCceEE
Q 021811 84 RQHLVGPNSSTLKALEILTGCYILVQGNTVA 114 (307)
Q Consensus 84 rgRIIG~~GkTkkaIE~LT~~yI~V~G~TVs 114 (307)
.||+||++|+|.+||-.+-.+-=.=+|..|.
T Consensus 41 ~GrVIGk~Gr~i~AIRtvv~aaa~k~~~rv~ 71 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTVVKAAAIKENKRVV 71 (75)
T ss_pred CcceecCCChhHHHHHHHHHHHHhcCCCEEE
Confidence 6999999999999998865543333444443
No 38
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=89.68 E-value=0.38 Score=51.49 Aligned_cols=52 Identities=25% Similarity=0.355 Sum_probs=45.9
Q ss_pred hccccCCCCchHHHHHHHhCceEEEeC-ceEEEecCC-CcHHHHHHHHHHHhcC
Q 021811 84 RQHLVGPNSSTLKALEILTGCYILVQG-NTVAAMGSF-KGLKQVRRIVEDCMQN 135 (307)
Q Consensus 84 rgRIIG~~GkTkkaIE~LT~~yI~V~G-~TVsIIG~~-~~IkiAR~aIedlI~g 135 (307)
.+=+||++|+|+++|-..|||.|.+.+ .||.|.++. +.+..|++.|+++..-
T Consensus 563 I~dvIG~gGk~I~~I~eetg~~IdieddGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 563 IRDVIGPGGKTIKAITEETGVKIDIEDDGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred HhhccCCcccchhhhhhhhCcEEEecCCCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 556899999999999999999999986 679999988 5579999999998844
No 39
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=88.46 E-value=0.35 Score=34.39 Aligned_cols=23 Identities=17% Similarity=0.323 Sum_probs=21.1
Q ss_pred hccccCCCCchHHHHHHHhCceE
Q 021811 84 RQHLVGPNSSTLKALEILTGCYI 106 (307)
Q Consensus 84 rgRIIG~~GkTkkaIE~LT~~yI 106 (307)
-|++||++|+++.+|+.+++-++
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 68999999999999999999665
No 40
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=86.74 E-value=1 Score=44.70 Aligned_cols=121 Identities=20% Similarity=0.196 Sum_probs=75.2
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEe-----CceEEEec-CCCcHHHHHHHHHHHh--cCCCchhHHHHHHHHHHhhhc
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQ-----GNTVAAMG-SFKGLKQVRRIVEDCM--QNKMHPVYHIKILMVKKELEK 154 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~-----G~TVsIIG-~~~~IkiAR~aIedlI--~g~iHpVY~ikelmiKReL~k 154 (307)
-.|-|||.+|+|++-||+-|+|.|.+- ...|.|+| .-+++-.|.+=|.-+| .+..-|+-+++.+...
T Consensus 67 ~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~s~p~thflal~ln----- 141 (345)
T KOG2814|consen 67 FIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDSDRKSFPITHFLALPLN----- 141 (345)
T ss_pred HhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHhhhhcCchhhhhhhhcc-----
Confidence 478999999999999999999999984 23355544 5566888888888888 4434577777777654
Q ss_pred Ccccccccccccc--hhccccccccccccccCCCCCCCCCCCCCCchhhhhhhccccccCchHHHHHHH
Q 021811 155 DPALANENWDRFL--PKFKKKNVKQKKVKSKEKKPYTPFPPPPQPSKIDKLLESGEYFLSERKKESKKW 221 (307)
Q Consensus 155 d~~l~~e~W~rfl--p~fkk~~~~~~k~~~~~kk~~tpfpp~~~~~k~d~~~esgeyfl~~~~k~~~~~ 221 (307)
.-=-+|+..+|. +-|...=. .-+....+|-+|- .+ -|-=|-|-|-+...-++..
T Consensus 142 -e~eVqe~f~~fke~~~~~esl~-------~~g~~~s~F~~p~---~~--HLTvgm~~L~~dd~vq~a~ 197 (345)
T KOG2814|consen 142 -EHEVQEGFLAFKELKPFIESLL-------DGGIDKSLFQGPG---TF--HLTVGMLKLLNDDDVQKAL 197 (345)
T ss_pred -hHHHHHHHHHHHhhhhhHHHhh-------ccchhhccccCCc---ee--eEEEEEEEecChHHHHHHH
Confidence 111256666666 33322100 1233445554433 32 2334666666665555443
No 41
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=86.17 E-value=0.63 Score=49.61 Aligned_cols=53 Identities=17% Similarity=0.304 Sum_probs=45.2
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeC-ceEEEec-CCCcHHHHHHHHHHHhcC
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQG-NTVAAMG-SFKGLKQVRRIVEDCMQN 135 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G-~TVsIIG-~~~~IkiAR~aIedlI~g 135 (307)
.++.+||++|+|++.|..-||+.|-+.+ .+|.|.+ +-..+..|++.|+.+...
T Consensus 564 kI~~vIG~gg~~ik~I~~~~~~~idi~d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 564 KIRDVIGPGGKTIREITEETGAKIDIEDDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred HHHHHhcCCchhHHHHHHHHCCccccCCCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 3689999999999999999999999986 5688888 456688899999888754
No 42
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=85.80 E-value=0.39 Score=38.29 Aligned_cols=19 Identities=21% Similarity=0.426 Sum_probs=17.0
Q ss_pred hccccCCCCchHHHHHHHh
Q 021811 84 RQHLVGPNSSTLKALEILT 102 (307)
Q Consensus 84 rgRIIG~~GkTkkaIE~LT 102 (307)
.||+||++|+|.+||=.+-
T Consensus 41 ~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 41 MGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred ccceecCCChhHHHHHHHH
Confidence 7999999999999998753
No 43
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=85.56 E-value=1.3 Score=45.77 Aligned_cols=53 Identities=21% Similarity=0.271 Sum_probs=48.2
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeCc--------eEEEecCCCcHHHHHHHHHHHhcC
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQGN--------TVAAMGSFKGLKQVRRIVEDCMQN 135 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G~--------TVsIIG~~~~IkiAR~aIedlI~g 135 (307)
..|=|||++|...+-|.+.|||.|.|-+. .|-|-|..+.++.|-..|+.+|..
T Consensus 148 q~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~ 208 (485)
T KOG2190|consen 148 QVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLE 208 (485)
T ss_pred heeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHh
Confidence 47899999999999999999999999987 388889999999999999999965
No 44
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=85.37 E-value=1.6 Score=41.56 Aligned_cols=99 Identities=18% Similarity=0.285 Sum_probs=63.8
Q ss_pred HHhHHHHHHHHHcCCC--hHHHHhhhc-cC-ceeEEEEcCccc-----cChhhHhhhh------------ccccCCCCch
Q 021811 36 IVKARDLIRLLSRSVP--APQAIKILD-DE-MQCDIIKIGNLV-----RNKERFVKRR------------QHLVGPNSST 94 (307)
Q Consensus 36 ilKArD~IkAIaRGF~--~E~AlkLLe-Dd-~~~dIIdI~~~~-----~nke~f~Rrr------------gRIIG~~GkT 94 (307)
.+-+.++ +.|-|+ -.+--..|+ .| +++.|-++..-- ...+.|-+.+ =|+||++|+.
T Consensus 91 ~L~ls~~---~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p~kVpRvig~~~sm 167 (239)
T COG1097 91 LLSLSDF---LRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPPSKVPRVIGKKGSM 167 (239)
T ss_pred Eeehhhh---hcccccccccccccccccCCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEchhhcceEecCCCcH
Confidence 4444454 556555 233445566 33 556666665321 1223333333 2699999999
Q ss_pred HHHHHHHhCceEEEeCce-EEEecCCCc-HHHHHHHHHHHhcCCCc
Q 021811 95 LKALEILTGCYILVQGNT-VAAMGSFKG-LKQVRRIVEDCMQNKMH 138 (307)
Q Consensus 95 kkaIE~LT~~yI~V~G~T-VsIIG~~~~-IkiAR~aIedlI~g~iH 138 (307)
.+.|...|+|.|.|.=|- |.+=|+-+. -.+|-.||.+|=.- .|
T Consensus 168 ~~~l~~~~~~~I~VG~NG~IWV~~~~~~~e~~~~~aI~~ie~e-a~ 212 (239)
T COG1097 168 LNMLKEKTGCEIIVGQNGRIWVDGENESLEELAIEAIRKIERE-AH 212 (239)
T ss_pred HHHhhhhcCeEEEEecCCEEEecCCCcchHHHHHHHHHHHhhh-hh
Confidence 999999999999998765 888888886 56677777666433 45
No 45
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=84.44 E-value=1.8 Score=43.23 Aligned_cols=48 Identities=27% Similarity=0.424 Sum_probs=44.9
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeCceEEEecCCCcHHHHHHHHH
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVE 130 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G~TVsIIG~~~~IkiAR~aIe 130 (307)
.-..|.|+.|..++.||...|+.|..-|+++.++|....+..|++++.
T Consensus 25 ~~~~l~G~~~~~l~l~e~~~gv~i~~rG~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 25 ELVALFGPTDTNLSLLEIALGVSIVARGEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred hhhhhcCCCCccHHHHHHHhCcEEEeCCceEEEEechHHHHHHHHHHh
Confidence 456799999999999999999999999999999999889999999988
No 46
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=84.07 E-value=3.3 Score=38.41 Aligned_cols=61 Identities=23% Similarity=0.268 Sum_probs=49.5
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeCce--EEEecC---CCc--HHHHHHHHHHHhcCCCch--hHHHH
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQGNT--VAAMGS---FKG--LKQVRRIVEDCMQNKMHP--VYHIK 144 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G~T--VsIIG~---~~~--IkiAR~aIedlI~g~iHp--VY~ik 144 (307)
|-+=|||+.|.+.+.||..|+|.|.|+.++ |.|... .++ +.-|++.|.-+=.| -.| ...+|
T Consensus 18 R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG-F~pe~A~~LL 87 (194)
T COG1094 18 RIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRG-FPPEKALKLL 87 (194)
T ss_pred hheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcC-CCHHHHHHHh
Confidence 667899999999999999999999999865 888765 344 68899999998899 444 55544
No 47
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=83.06 E-value=1.9 Score=43.34 Aligned_cols=55 Identities=16% Similarity=0.288 Sum_probs=41.6
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEe----------CceEEEecCCCcHHHHH-HHHHHHhcCCCc
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQ----------GNTVAAMGSFKGLKQVR-RIVEDCMQNKMH 138 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~----------G~TVsIIG~~~~IkiAR-~aIedlI~g~iH 138 (307)
-.|-|||++|.|.++|-+-++|+|.|+ ..-|-+.|.++++..|- .++..+-+- +|
T Consensus 142 tag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eD-pq 207 (402)
T KOG2191|consen 142 TAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQED-PQ 207 (402)
T ss_pred cccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcC-Cc
Confidence 358899999999999999999999998 23377899998875444 444444444 55
No 48
>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=75.24 E-value=2.1 Score=39.29 Aligned_cols=96 Identities=19% Similarity=0.275 Sum_probs=66.3
Q ss_pred HHHHHhhhccEEEEEcCCCeEEEEcCCCCCChHHHH-hHHHHH-HHHHcCCChHHHHhhhccCceeEEEEcCccc-cChh
Q 021811 2 VKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIV-KARDLI-RLLSRSVPAPQAIKILDDEMQCDIIKIGNLV-RNKE 78 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~il-KArD~I-kAIaRGF~~E~AlkLLeDd~~~dIIdI~~~~-~nke 78 (307)
|+.+++..|..+.++ +..+.+-|.--.--|..+. =+..|+ .++..|++.++|.++...-+. -...+. .++.
T Consensus 127 v~~lf~~~G~~~~v~--E~~~~~~talsgsgPA~~~~~~~al~~~~v~~Gl~~~~A~~lv~~~~~----G~a~l~~~~~~ 200 (245)
T TIGR00112 127 VLALFKAVGEVVELP--EALMDAVTALSGSGPAYVFLFIEALADAGVKQGLPRELALELAAQTVK----GAAKLLEESGE 200 (245)
T ss_pred HHHHHHhCCCEEEEC--HHHcchHHhhccCcHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH----HHHHHHHhcCC
Confidence 677889999999887 5666665543334454322 222333 467899999999999875421 011122 3557
Q ss_pred hHhhhhccccCCCCchHHHHHHHhC
Q 021811 79 RFVKRRQHLVGPNSSTLKALEILTG 103 (307)
Q Consensus 79 ~f~RrrgRIIG~~GkTkkaIE~LT~ 103 (307)
++...+.++.-|+|.|..+|+.|-.
T Consensus 201 ~~~~l~~~v~spgGtT~~gl~~Le~ 225 (245)
T TIGR00112 201 HPALLKDQVTSPGGTTIAGLAVLEE 225 (245)
T ss_pred CHHHHHHcCCCCcHHHHHHHHHHHH
Confidence 8999999999999999999998853
No 49
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=72.27 E-value=2.1 Score=45.63 Aligned_cols=53 Identities=19% Similarity=0.439 Sum_probs=46.7
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeCceEEEecCCCc-HHHHHHHHHHHhcC
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKG-LKQVRRIVEDCMQN 135 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G~TVsIIG~~~~-IkiAR~aIedlI~g 135 (307)
-|.-||||+|..++-||.-||+.-.|++.|++|+-+... +..|++.|.-++.-
T Consensus 607 k~~~lIGp~G~~~kki~~EtGai~~vDe~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 607 KRATLIGPGGVLKKKIEVETGAISQVDEGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred hhheeecCccceeeeEeeeccceeeecCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 356799999999999999999999999999999987765 69999999988844
No 50
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=70.35 E-value=2.3 Score=36.90 Aligned_cols=27 Identities=11% Similarity=0.145 Sum_probs=24.2
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEe
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQ 109 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~ 109 (307)
-.|+.||++|++.++++.|+|-++-|.
T Consensus 109 d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 109 DKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred ccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 379999999999999999999998663
No 51
>TIGR03278 methan_mark_10 putative methanogenesis marker protein 10. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The presence of motifs with seven invariant Cys residues in the N-terminal 50 residues, including three instances of CXXC, would be consistent with function as an oxidoreductase with FeS clusters. The exact function is unknown, but likely is linked to methanogenesis. In most genomes, the member of this family is encoded by a gene next to, and divergently transcribed from, the methyl coenzyme M reductase operon.
Probab=70.15 E-value=24 Score=35.70 Aligned_cols=139 Identities=15% Similarity=0.112 Sum_probs=80.8
Q ss_pred CCCeEEEEcCCCCCChHHHHhHHHHHHHHHc-C------------C-ChHHHHhhhccCceeEEEEcCccccChhhHhhh
Q 021811 18 VEGSMTVSTTRKTRDPYIIVKARDLIRLLSR-S------------V-PAPQAIKILDDEMQCDIIKIGNLVRNKERFVKR 83 (307)
Q Consensus 18 ~egsV~V~tt~kT~DP~~ilKArD~IkAIaR-G------------F-~~E~AlkLLeDd~~~dIIdI~~~~~nke~f~Rr 83 (307)
..|-|++.+ ..+|..---..++++++.. | + +++.+-+|++-.+..-.|+|..+ +++ .
T Consensus 73 ~~ggVtisG---GGepl~~~~l~eLl~~lk~~gi~taI~~TnG~~l~~~e~~~~L~~~gld~v~iSvka~--dpe----~ 143 (404)
T TIGR03278 73 RDTKVTISG---GGDVSCYPELEELTKGLSDLGLPIHLGYTSGKGFDDPEIAEFLIDNGVREVSFTVFAT--DPE----L 143 (404)
T ss_pred CCCEEEEEC---CcccccCHHHHHHHHHHHhCCCCEEEeCCCCcccCCHHHHHHHHHcCCCEEEEecccC--CHH----H
Confidence 357888887 4566554445566665544 3 3 44555555553333344555543 333 3
Q ss_pred hccccC-CC-CchHHHHHHHhCceEEEeCceEEEecCCCcHHHHHHHHHHHh-cCCCch--h--HHHHHHHHHHhhhcCc
Q 021811 84 RQHLVG-PN-SSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDCM-QNKMHP--V--YHIKILMVKKELEKDP 156 (307)
Q Consensus 84 rgRIIG-~~-GkTkkaIE~LT~~yI~V~G~TVsIIG~~~~IkiAR~aIedlI-~g~iHp--V--Y~ikelmiKReL~kd~ 156 (307)
+.+++| ++ +..+.+|+.+.. .+.+....|.|=|--++-... ++|..+. .| ++| + ||.... .|=-|...|
T Consensus 144 h~kl~G~~~a~~ILe~L~~L~e-~~~v~~~ivlIPGiND~eel~-~ti~~L~~lg-~~~V~L~~y~~~g~-~ky~lg~~~ 219 (404)
T TIGR03278 144 RREWMKDPTPEASLQCLRRFCE-SCEVHAASVIIPGVNDGDVLW-KTCADLESWG-AKALILMRFANTEE-QGLILGNAP 219 (404)
T ss_pred HHHHhCCCCHHHHHHHHHHHHh-cCCEEEEEEEeCCccCcHHHH-HHHHHHHHCC-CCEEEEEecccccc-cccccCCcC
Confidence 445677 45 689999999998 588888888888877766654 6666666 35 555 2 332100 000122333
Q ss_pred c---cccccccccchh
Q 021811 157 A---LANENWDRFLPK 169 (307)
Q Consensus 157 ~---l~~e~W~rflp~ 169 (307)
. ...++|++|+..
T Consensus 220 ~~~~~~~~~~~e~~~~ 235 (404)
T TIGR03278 220 IIPGIKPHTVSEFKNI 235 (404)
T ss_pred cccCCCCCCHHHHHHH
Confidence 3 346788887765
No 52
>PF05598 DUF772: Transposase domain (DUF772); InterPro: IPR008490 This presumed domain is found at the N terminus of transposase insH and other related transposases.
Probab=69.10 E-value=6.6 Score=29.42 Aligned_cols=61 Identities=18% Similarity=0.303 Sum_probs=48.7
Q ss_pred CCCCChHHHHhHHHHHHHHHcCC-ChHHHHhhhccC----ceeEEEEcCccccChhhHhhhhccccCCC
Q 021811 28 RKTRDPYIIVKARDLIRLLSRSV-PAPQAIKILDDE----MQCDIIKIGNLVRNKERFVKRRQHLVGPN 91 (307)
Q Consensus 28 ~kT~DP~~ilKArD~IkAIaRGF-~~E~AlkLLeDd----~~~dIIdI~~~~~nke~f~RrrgRIIG~~ 91 (307)
+.+++|..++++ +|=+...|+ |..+....+.++ ++|. +++.+-+.+..-|.+-|.|+...+
T Consensus 2 Rp~~~~~~ml~~--ll~~~~~~~~S~r~l~~~l~~~~~~r~~~g-~~~~~~~pd~stl~rfr~rl~~~~ 67 (77)
T PF05598_consen 2 RPAYPPRMMLKA--LLLKYLFGLRSDRELEERLRDNLSFRYFCG-LSLEEPVPDHSTLSRFRKRLIQHG 67 (77)
T ss_pred cCCCCHHHHHHH--HHHHHHHhcchHHHHHhhHhhhhHHHHHHh-cccCCCCCChHHHHHHHHHHhhcc
Confidence 447899999888 455566788 999999999988 4488 777777777889999999988664
No 53
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=63.71 E-value=82 Score=28.09 Aligned_cols=113 Identities=12% Similarity=0.193 Sum_probs=71.8
Q ss_pred HHHHhhhccEEEEEcCCCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHhhhccCceeEEEEcCccccChhhHhh
Q 021811 3 KGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEMQCDIIKIGNLVRNKERFVK 82 (307)
Q Consensus 3 ~~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~ilKArD~IkAIaRGF~~E~AlkLLeDd~~~dIIdI~~~~~nke~f~R 82 (307)
+.++..+|..|++....+.|.|..++. .+--+.+-|.-+ =..+..+.|++..+..+ +..
T Consensus 49 ~~l~~~~~~~I~~~~~~~~i~I~g~k~-----~~~~i~~~i~~~-------------l~~i~~~~i~l~~~~~~---~~~ 107 (210)
T PF14611_consen 49 ENLAARNGAKIEVSRSENRIRITGTKS-----TAEYIEASINEI-------------LSNIRTEEIDLSPIISK---HSE 107 (210)
T ss_pred HHHHHhcCceEEEecCCcEEEEEccHH-----HHHHHHHHHHHH-------------HhhcEEEEEecchhhhh---hcc
Confidence 444578899999999999999987543 222222222211 13456778888876531 111
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeCce--EEEe-----cCCCcHHHHHHHHHHHhcCCCc
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQGNT--VAAM-----GSFKGLKQVRRIVEDCMQNKMH 138 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G~T--VsII-----G~~~~IkiAR~aIedlI~g~iH 138 (307)
...+ --....+..|..+|+|||-..++. +.|. -....+..|++-+.-.+...+|
T Consensus 108 ~~~~--~~~~~~l~~i~~~t~~~ie~~~~~~~~~i~~~~~~~~~~~~~~a~RlL~~a~~~~~~ 168 (210)
T PF14611_consen 108 KKNS--QFTPDLLEEIQKLTNVYIEKNPDGNKLKISWLASPENEKRADRAKRLLLWALDYNPH 168 (210)
T ss_pred cccc--cccHHHHHHHHHHHcEEEEECCCCCeEEEEEEeeccccchHHHHHHHHHHhccCCcc
Confidence 1111 123567889999999999988755 4443 3455688899888888864355
No 54
>PRK10076 pyruvate formate lyase II activase; Provisional
Probab=61.57 E-value=72 Score=29.30 Aligned_cols=105 Identities=9% Similarity=0.006 Sum_probs=59.1
Q ss_pred cCCCeEEEEcCCCCCChHHHHhHHHHHHHH-Hc---------CCChHHHHh-hhccCceeEEEEcCccccChhhHhhhhc
Q 021811 17 LVEGSMTVSTTRKTRDPYIIVKARDLIRLL-SR---------SVPAPQAIK-ILDDEMQCDIIKIGNLVRNKERFVKRRQ 85 (307)
Q Consensus 17 l~egsV~V~tt~kT~DP~~ilKArD~IkAI-aR---------GF~~E~Alk-LLeDd~~~dIIdI~~~~~nke~f~Rrrg 85 (307)
...|.|++..+..+--|-.+ .++++++ .+ |+-+..++. |+. -+.+-.+||+.+- .+...+.-|
T Consensus 37 ~sggGVt~SGGEPllq~~fl---~~l~~~~k~~gi~~~leTnG~~~~~~~~~l~~-~~D~~l~DiK~~d--~~~~~~~tG 110 (213)
T PRK10076 37 TSGGGVTLSGGEVLMQAEFA---TRFLQRLRLWGVSCAIETAGDAPASKLLPLAK-LCDEVLFDLKIMD--ATQARDVVK 110 (213)
T ss_pred CCCCEEEEeCchHHcCHHHH---HHHHHHHHHcCCCEEEECCCCCCHHHHHHHHH-hcCEEEEeeccCC--HHHHHHHHC
Confidence 34689999874443333222 3444444 23 333444444 444 3445667777652 233333333
Q ss_pred cccCCCCchHHHHHHHhCceEEEeCceEEEecCCCcHHHHHHHHH
Q 021811 86 HLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVE 130 (307)
Q Consensus 86 RIIG~~GkTkkaIE~LT~~yI~V~G~TVsIIG~~~~IkiAR~aIe 130 (307)
+.++.+++.|+.+....+-|.=.|+.|=|-.++.+..+.+..
T Consensus 111 ---~~~~~il~nl~~l~~~g~~v~iR~~vIPg~nd~~e~i~~ia~ 152 (213)
T PRK10076 111 ---MNLPRVLENLRLLVSEGVNVIPRLPLIPGFTLSRENMQQALD 152 (213)
T ss_pred ---CCHHHHHHHHHHHHhCCCcEEEEEEEECCCCCCHHHHHHHHH
Confidence 556788888888877655555467777776666666655443
No 55
>PRK06928 pyrroline-5-carboxylate reductase; Reviewed
Probab=61.05 E-value=15 Score=34.33 Aligned_cols=94 Identities=14% Similarity=0.276 Sum_probs=63.0
Q ss_pred HHHHHhhhccEEEEEcCCCeEEEEcCCCCCChHHHHh-HHHHHH-HHHc-CCChHHHHhhhccCceeEEEEcCccc-cCh
Q 021811 2 VKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVK-ARDLIR-LLSR-SVPAPQAIKILDDEMQCDIIKIGNLV-RNK 77 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~ilK-ArD~Ik-AIaR-GF~~E~AlkLLeDd~~~dIIdI~~~~-~nk 77 (307)
|+.+++..|....++ |..+.+-|.--.--|..+.- +.-|+. ++.. |++.++|.++.-.=+.= -..+. ..+
T Consensus 147 v~~l~~~~G~~~~v~--E~~~d~~tal~gsgPA~~~~~~~al~~a~~~~ggl~~~~a~~l~~~~~~G----~a~l~~~~~ 220 (277)
T PRK06928 147 LEETLSHFSHVMTIR--EENMDIASNLTSSSPGFIAAIFEEFAEAAVRNSSLSDEEAFQFLNFALAG----TGKLLVEED 220 (277)
T ss_pred HHHHHHhCCCEEEEc--hhhCceeeeeecCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHH----HHHHHHccC
Confidence 678889999999997 45566555443455544332 223444 3333 69999999988744210 00111 245
Q ss_pred hhHhhhhccccCCCCchHHHHHHH
Q 021811 78 ERFVKRRQHLVGPNSSTLKALEIL 101 (307)
Q Consensus 78 e~f~RrrgRIIG~~GkTkkaIE~L 101 (307)
.++.-.|.++.-|+|.|..+|+.|
T Consensus 221 ~~p~~l~~~v~spgGtT~~gl~~l 244 (277)
T PRK06928 221 YTFSGTIERVATKGGITAEGAEVI 244 (277)
T ss_pred CCHHHHHHhCCCCChHHHHHHHHH
Confidence 788999999999999999999876
No 56
>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=59.15 E-value=27 Score=25.83 Aligned_cols=37 Identities=24% Similarity=0.452 Sum_probs=30.4
Q ss_pred HHHHHhhhccEEEEEcCCCeEEEEcCCCCCChHHHHhHHHHH
Q 021811 2 VKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLI 43 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~ilKArD~I 43 (307)
|+.+-+++|+.+.++- +|.|.|.. .|+..+..|.++|
T Consensus 24 ik~I~~~tg~~I~i~~-~g~v~I~G----~~~~~v~~A~~~I 60 (61)
T cd02393 24 IKKIIEETGVKIDIED-DGTVYIAA----SDKEAAEKAKKMI 60 (61)
T ss_pred HHHHHHHHCCEEEeCC-CCEEEEEe----CCHHHHHHHHHHh
Confidence 4566788999999987 69999986 6678899988876
No 57
>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=58.81 E-value=31 Score=24.53 Aligned_cols=27 Identities=33% Similarity=0.460 Sum_probs=21.3
Q ss_pred HHHHHhhh-cc-EEEEEcCCCeEEEEcCC
Q 021811 2 VKGALKEY-GV-SCELNLVEGSMTVSTTR 28 (307)
Q Consensus 2 v~~~le~~-~i-~i~lDl~egsV~V~tt~ 28 (307)
|+++|... |+ .+.+|+.++.++|....
T Consensus 16 v~~~l~~~~GV~~v~vd~~~~~v~v~~~~ 44 (62)
T PF00403_consen 16 VEKALSKLPGVKSVKVDLETKTVTVTYDP 44 (62)
T ss_dssp HHHHHHTSTTEEEEEEETTTTEEEEEEST
T ss_pred HHHHHhcCCCCcEEEEECCCCEEEEEEec
Confidence 56677665 66 69999999999999743
No 58
>PRK07680 late competence protein ComER; Validated
Probab=57.79 E-value=8.8 Score=35.43 Aligned_cols=93 Identities=10% Similarity=0.138 Sum_probs=58.4
Q ss_pred HHHHHhhhccEEEEEcCCCeEEEEcCCCCCChHHHHhHHH-HHHH-HH-cCCChHHHHhhhccCce--eEEEEcCccccC
Q 021811 2 VKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARD-LIRL-LS-RSVPAPQAIKILDDEMQ--CDIIKIGNLVRN 76 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~ilKArD-~IkA-Ia-RGF~~E~AlkLLeDd~~--~dIIdI~~~~~n 76 (307)
+..+|+..|..+.++ +..+.+-|.--.--|..+.-.-+ |+.+ +. .||+.++|..++-+=+. ... +..+
T Consensus 144 ~~~ll~~~G~~~~i~--e~~~~~~~~l~gs~pa~~~~~~~al~~~~~~~~Gl~~~~a~~~~~~~~~G~~~l-----~~~~ 216 (273)
T PRK07680 144 LERLFSNISTPLVIE--EDITRVSSDIVSCGPAFFSYLLQRFIDAAVEETNISKEEATTLASEMLIGMGKL-----LEKG 216 (273)
T ss_pred HHHHHHcCCCEEEEC--hHhcchhhhhccchHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHH-----HHhc
Confidence 566788888777776 33343333221223433332222 4433 44 59999999998874321 111 1235
Q ss_pred hhhHhhhhccccCCCCchHHHHHHH
Q 021811 77 KERFVKRRQHLVGPNSSTLKALEIL 101 (307)
Q Consensus 77 ke~f~RrrgRIIG~~GkTkkaIE~L 101 (307)
+.++.-.+.++.-|+|.|...|+.|
T Consensus 217 ~~~~~~l~~~v~spgG~T~~gl~~l 241 (273)
T PRK07680 217 LYTLPTLQEKVCVKGGITGEGIKVL 241 (273)
T ss_pred CCCHHHHHHhCCCCChhHHHHHHHH
Confidence 5789999999999999999999876
No 59
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=55.40 E-value=13 Score=37.66 Aligned_cols=53 Identities=25% Similarity=0.428 Sum_probs=40.2
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEe-------Cce--EE-EecCCCcHHHHHHHHHHHhcC
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQ-------GNT--VA-AMGSFKGLKQVRRIVEDCMQN 135 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~-------G~T--Vs-IIG~~~~IkiAR~aIedlI~g 135 (307)
.-|-|||++|.|...|..-|||+|-+- |.| |+ |-|+.+.|..|.+-|.|-|.-
T Consensus 49 AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire 111 (402)
T KOG2191|consen 49 AAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIRE 111 (402)
T ss_pred cccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHH
Confidence 457899999999999999999999874 344 55 457777777766666665543
No 60
>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=51.69 E-value=2.4 Score=32.20 Aligned_cols=24 Identities=13% Similarity=0.148 Sum_probs=19.5
Q ss_pred hhccccCCCCchHHHHHHHhCceE
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYI 106 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI 106 (307)
..|.+||++|++++.|....+-.+
T Consensus 35 ~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 35 QPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CccHhHHhhhHHHHHHHHHHHHHH
Confidence 589999999999998877655544
No 61
>TIGR02517 type_II_gspD general secretion pathway protein D. In Gram-negative bacteria, proteins that have first crossed the inner member by Sec-dependent protein transport can be exported across the outer membrane by type II secretion, also called the main terminal branch of the general secretion pathway. Members of this family are general secretion pathway protein D. In Yersinia enterocolitica, a second member of this family is part of a novel second type II secretion system specifically associated with virulence (See PubMed:12654803). This family is closely homologous to the type IV pilus outer membrane secretin PilQ (TIGR02515) and to the type III secretion system pore YscC/HrcC (TIGR02516).
Probab=47.41 E-value=1.8e+02 Score=30.20 Aligned_cols=109 Identities=17% Similarity=0.216 Sum_probs=67.0
Q ss_pred HHHHhhhccEEEEEcC-CCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHhhhccC-------------------
Q 021811 3 KGALKEYGVSCELNLV-EGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDE------------------- 62 (307)
Q Consensus 3 ~~~le~~~i~i~lDl~-egsV~V~tt~kT~DP~~ilKArD~IkAIaRGF~~E~AlkLLeDd------------------- 62 (307)
+-..+..|+.+-+|.. .|.|++++ .+|+..-.|.+++..+.+... +.+..++
T Consensus 13 ~~~~~~~g~n~vid~~v~g~vtl~~----~~~v~~~eal~~l~~lL~~~g----l~~~~~g~~~~I~~~~~~~~~~~~~~ 84 (594)
T TIGR02517 13 KAISDLTGKNFIIDPRVKGKITIIS----PRPVTEDEAYQLFLSALRAQG----FAVVPEGNGYKIVVPRAAAKLSPGPI 84 (594)
T ss_pred HHHHHHhCCeEEECCCCceEEEEEe----CCCCCHHHHHHHHHHHHHhCC----eEEEEeCCcEEEeCchHhcccCCCcc
Confidence 4455788999999865 89999997 556666677776665543222 1222222
Q ss_pred ------------ceeEEEEcCccccChhhHhhhhccccCCCCchHHHHHHHhCceEEEeC--ceEEEecCCCcHHHHHHH
Q 021811 63 ------------MQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQG--NTVAAMGSFKGLKQVRRI 128 (307)
Q Consensus 63 ------------~~~dIIdI~~~~~nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~V~G--~TVsIIG~~~~IkiAR~a 128 (307)
+...+|.+... +.+.+......++++ ++.|.+.. |.+.+.|+...+..+++.
T Consensus 85 ~~~~~~~~~~~~~~~~vi~L~~~--~a~~v~~~L~~lls~------------~~~v~~d~~~N~liv~~~~~~l~~i~~l 150 (594)
T TIGR02517 85 EDGPAPGVGGDQFVTRVFPLRNI--SASELVPVLRPLVSP------------NGDVAAYPPTNTIVVTDYASNINRVARI 150 (594)
T ss_pred ccCCCCCCCCCceEEEEEEeccC--CHHHHHHHHHHhcCC------------CceEEEcCCCCEEEEEcCHHHHHHHHHH
Confidence 22334444432 222333333333333 35677776 679999999999999988
Q ss_pred HHHHh
Q 021811 129 VEDCM 133 (307)
Q Consensus 129 IedlI 133 (307)
|..+=
T Consensus 151 i~~lD 155 (594)
T TIGR02517 151 IQQLD 155 (594)
T ss_pred HHHhc
Confidence 77653
No 62
>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=45.80 E-value=60 Score=35.60 Aligned_cols=62 Identities=13% Similarity=0.242 Sum_probs=47.0
Q ss_pred HHHHHhhhccEEEEEcCCCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHhhhccCceeEEEEcCcc
Q 021811 2 VKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEMQCDIIKIGNL 73 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~ilKArD~IkAIaRGF~~E~AlkLLeDd~~~dIIdI~~~ 73 (307)
|+.+.+++|++|.++- +|.|.|.. .|.-.+.+|.++|+.|...|.|+ ..+-+...|.+|.+|
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 6778899999999996 79999996 78889999999999999975433 122244555555543
No 63
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=45.68 E-value=14 Score=38.32 Aligned_cols=31 Identities=13% Similarity=0.235 Sum_probs=28.7
Q ss_pred hhhccccCCCCchHHHHHHHhCceEEEeCce
Q 021811 82 KRRQHLVGPNSSTLKALEILTGCYILVQGNT 112 (307)
Q Consensus 82 RrrgRIIG~~GkTkkaIE~LT~~yI~V~G~T 112 (307)
...|.|||++|...-.|..+||+.|.|++..
T Consensus 347 ~~igciiGk~G~~iseir~~tgA~I~I~~~~ 377 (485)
T KOG2190|consen 347 DLIGCIIGKGGAKISEIRQRTGASISILNKE 377 (485)
T ss_pred cccceeecccccchHHHHHhcCCceEEcccc
Confidence 4789999999999999999999999998755
No 64
>PTZ00431 pyrroline carboxylate reductase; Provisional
Probab=45.09 E-value=40 Score=31.12 Aligned_cols=96 Identities=14% Similarity=0.163 Sum_probs=65.7
Q ss_pred HHHHHhhhccEEEEEcCCCeEEEEcCCCCCChHHHHhHH-HHH-HHHHcCCChHHHHhhhccCceeEEEEcCcc-ccChh
Q 021811 2 VKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKAR-DLI-RLLSRSVPAPQAIKILDDEMQCDIIKIGNL-VRNKE 78 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~ilKAr-D~I-kAIaRGF~~E~AlkLLeDd~~~dIIdI~~~-~~nke 78 (307)
|..+++..|..+.++ +..+.+-|.--.--|..+.--- .++ -++..|+|.++|.++.-.=+.= -..+ .....
T Consensus 140 v~~l~~~~G~~~~v~--E~~~d~~ta~~gsgPA~~~~~~~al~~~~v~~Gl~~~~a~~l~~~~~~G----~a~ll~~~~~ 213 (260)
T PTZ00431 140 VIDIFSACGIIQEIK--EKDMDIATAISGCGPAYVFLFIESLIDAGVKNGLNRDVSKNLVLQTILG----SVHMVKASDQ 213 (260)
T ss_pred HHHHHHhCCcEEEEC--hHHcchhhhhcCCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH----HHHHHHhcCC
Confidence 678889999999997 4467766644334464433222 233 4678999999999998754210 0011 12446
Q ss_pred hHhhhhccccCCCCchHHHHHHHhC
Q 021811 79 RFVKRRQHLVGPNSSTLKALEILTG 103 (307)
Q Consensus 79 ~f~RrrgRIIG~~GkTkkaIE~LT~ 103 (307)
++...|.++.=|+|.|...|..|-.
T Consensus 214 ~~~~l~~~v~spgG~T~~gl~~le~ 238 (260)
T PTZ00431 214 PVQQLKDDVCSPGGITIVGLYTLEK 238 (260)
T ss_pred CHHHHHHhCCCCChHHHHHHHHHHH
Confidence 8889999999999999999988753
No 65
>PRK07634 pyrroline-5-carboxylate reductase; Reviewed
Probab=42.98 E-value=16 Score=32.55 Aligned_cols=92 Identities=20% Similarity=0.204 Sum_probs=58.7
Q ss_pred HHHHHhhhccEEEEEcCCCeEEEEcCCCCCChHHHHhH-HHHHH-HHHcCCChHHHHhhhccCce--eEEEEcCccccCh
Q 021811 2 VKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKA-RDLIR-LLSRSVPAPQAIKILDDEMQ--CDIIKIGNLVRNK 77 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~ilKA-rD~Ik-AIaRGF~~E~AlkLLeDd~~--~dIIdI~~~~~nk 77 (307)
|+.+++..|..+.++ +..+..-|.--+-.|..+..- ..++. +...||+.++|.+++-.=+. .+. ..+.
T Consensus 149 v~~lf~~~G~~~~~~--e~~~~~~~a~~gs~pa~~~~~~~a~~~~~~~~Gl~~~~a~~~~~~~~~g~~~~------~~~~ 220 (245)
T PRK07634 149 LQLILKGIGTSQLCT--EEEVHQLTAVTGSAPAFLYYFAESLIEATKSYGVDEETAKHLVIQMISGSASM------LEQT 220 (245)
T ss_pred HHHHHHhCCCEEEEC--HHHcchHHhhhcchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH------HhCC
Confidence 567788888888776 333444443333444332222 22333 45679999999999874311 111 1123
Q ss_pred hhHhhhhccccCCCCchHHHHHHH
Q 021811 78 ERFVKRRQHLVGPNSSTLKALEIL 101 (307)
Q Consensus 78 e~f~RrrgRIIG~~GkTkkaIE~L 101 (307)
.++...+.++.=|+|.|..+|..|
T Consensus 221 ~~~~~l~~~v~spgG~T~~gl~~l 244 (245)
T PRK07634 221 QDPANLREQVTTPGGSTAEGLKAL 244 (245)
T ss_pred CCHHHHHHhCCCCChHHHHHHHHh
Confidence 577889999999999999999865
No 66
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=42.83 E-value=53 Score=29.29 Aligned_cols=64 Identities=17% Similarity=0.132 Sum_probs=50.9
Q ss_pred hccccCCCCchHHHHHHHhCceEEEeC--ceEEEecCCCcHHHHHHHHHHHhcCCCc---hhHHHHHHH
Q 021811 84 RQHLVGPNSSTLKALEILTGCYILVQG--NTVAAMGSFKGLKQVRRIVEDCMQNKMH---PVYHIKILM 147 (307)
Q Consensus 84 rgRIIG~~GkTkkaIE~LT~~yI~V~G--~TVsIIG~~~~IkiAR~aIedlI~g~iH---pVY~ikelm 147 (307)
.-=|.+.+|..+..|-...||.|-|.. +.|.|-|+-..++.|...|..++.+..+ +++.+...+
T Consensus 37 ~~LLl~~~~~~L~~l~~~~~~~I~~~~~~~~i~I~g~k~~~~~i~~~i~~~l~~i~~~~i~l~~~~~~~ 105 (210)
T PF14611_consen 37 FFLLLTGNGRILENLAARNGAKIEVSRSENRIRITGTKSTAEYIEASINEILSNIRTEEIDLSPIISKH 105 (210)
T ss_pred eeeeecCCchHHHHHHHhcCceEEEecCCcEEEEEccHHHHHHHHHHHHHHHhhcEEEEEecchhhhhh
Confidence 455778899999988555699999954 6799999999999999999999998444 266554443
No 67
>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=41.92 E-value=1.1e+02 Score=27.47 Aligned_cols=90 Identities=23% Similarity=0.333 Sum_probs=59.4
Q ss_pred EEEcCCCeEEEEcCCCCCChHHHHhHHHHHHHHHc--------------CCChHHHHhhhcc----CceeEEEEcCcccc
Q 021811 14 ELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSR--------------SVPAPQAIKILDD----EMQCDIIKIGNLVR 75 (307)
Q Consensus 14 ~lDl~egsV~V~tt~kT~DP~~ilKArD~IkAIaR--------------GF~~E~AlkLLeD----d~~~dIIdI~~~~~ 75 (307)
.++.+.=.+.|.| .||-.+..--|+|+-||. =.++++|.++..+ |--+.=|.-..-
T Consensus 3 ~vefEGPelviYt----k~P~~~~~~~dli~~lAk~lrKRIvvR~dps~l~~~e~A~~~I~~ivP~ea~i~di~Fd~~-- 76 (145)
T cd02410 3 DVEFEGPELVVYT----KNPELFAEDGDLVKDLAKDLRKRIVIRPDPSVLKPPEEAIKIILEIVPEEAGITDIYFDDD-- 76 (145)
T ss_pred eeEeeCCeEEEEE----CCHHHHhcccHHHHHHHHHHhceEEEcCChhhcCCHHHHHHHHHHhCCCccCceeeEecCC--
Confidence 3556666788886 899888887788887764 2467888887763 211111111111
Q ss_pred ChhhHhh--hhccccCCCCchHHHHHHHhCceEEEe
Q 021811 76 NKERFVK--RRQHLVGPNSSTLKALEILTGCYILVQ 109 (307)
Q Consensus 76 nke~f~R--rrgRIIG~~GkTkkaIE~LT~~yI~V~ 109 (307)
.++.... .=|++||++|.|++-|-.-||-.-.|.
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEE
Confidence 2233333 359999999999999988998876664
No 68
>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=41.50 E-value=49 Score=23.83 Aligned_cols=32 Identities=22% Similarity=0.142 Sum_probs=27.9
Q ss_pred CCCChHHHHhHHHHHHHHHcCCChHHHHhhhc
Q 021811 29 KTRDPYIIVKARDLIRLLSRSVPAPQAIKILD 60 (307)
Q Consensus 29 kT~DP~~ilKArD~IkAIaRGF~~E~AlkLLe 60 (307)
..+++-.+...+.+..+...|||++++.++|+
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 35778889999999999999999999999874
No 69
>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=41.48 E-value=6.8 Score=32.08 Aligned_cols=56 Identities=18% Similarity=0.343 Sum_probs=37.8
Q ss_pred HHHHcCCChHHHHhhhccCceeEEEEcCccc-cChhhHhhhhccccCCCCchHHHHHHHhC
Q 021811 44 RLLSRSVPAPQAIKILDDEMQCDIIKIGNLV-RNKERFVKRRQHLVGPNSSTLKALEILTG 103 (307)
Q Consensus 44 kAIaRGF~~E~AlkLLeDd~~~dIIdI~~~~-~nke~f~RrrgRIIG~~GkTkkaIE~LT~ 103 (307)
.++..|++.++|.+|.-.-+. --..+. .++.++...+.++.-|+|.|..+|+.|-.
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 357899999999998764321 111222 24569999999999999999999998753
No 70
>PF15232 DUF4585: Domain of unknown function (DUF4585)
Probab=41.37 E-value=8.8 Score=30.82 Aligned_cols=24 Identities=29% Similarity=0.540 Sum_probs=19.1
Q ss_pred CCCCCCchhhhhhhccccccCchH
Q 021811 192 PPPPQPSKIDKLLESGEYFLSERK 215 (307)
Q Consensus 192 pp~~~~~k~d~~~esgeyfl~~~~ 215 (307)
|.+++.+|+=.--+||+||+-+--
T Consensus 2 ~~~~tqrKvL~DP~SG~Yy~vd~P 25 (75)
T PF15232_consen 2 PYPATQRKVLQDPESGQYYVVDAP 25 (75)
T ss_pred CCCccCccEeecCCCCCEEEEecC
Confidence 456777898888999999997654
No 71
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=39.31 E-value=26 Score=32.23 Aligned_cols=31 Identities=16% Similarity=0.214 Sum_probs=27.3
Q ss_pred hhhccccCCCCchHHHHHHHhCceEEEeCce
Q 021811 82 KRRQHLVGPNSSTLKALEILTGCYILVQGNT 112 (307)
Q Consensus 82 RrrgRIIG~~GkTkkaIE~LT~~yI~V~G~T 112 (307)
.-+++.||++|++.+.+-.|||-+|-|..-.
T Consensus 151 ~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~~ 181 (190)
T COG0195 151 DQLSLAIGKGGQNVRLASQLTGWEIDIETIS 181 (190)
T ss_pred HHHhhccCcccHHHHHHHHHhCCEEEEEehh
Confidence 4588999999999999999999999887543
No 72
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=38.08 E-value=50 Score=36.02 Aligned_cols=46 Identities=24% Similarity=0.418 Sum_probs=39.8
Q ss_pred HHHHHhhhccEEEEEcCCCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCCh
Q 021811 2 VKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPA 52 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~ilKArD~IkAIaRGF~~ 52 (307)
|..+.+++|+.+.++ ..|+|.|.+ .|...+.+|++.|..|.+-|.+
T Consensus 574 I~~I~eetg~~Idie-ddGtv~i~~----s~~~~~~~ak~~I~~i~~e~ev 619 (692)
T COG1185 574 IKAITEETGVKIDIE-DDGTVKIAA----SDGESAKKAKERIEAITREVEV 619 (692)
T ss_pred hhhhhhhhCcEEEec-CCCcEEEEe----cchHHHHHHHHHHHHHHhhccc
Confidence 567889999999999 899999997 6678999999999999965544
No 73
>PRK04056 Maf-like protein; Reviewed
Probab=36.14 E-value=56 Score=29.50 Aligned_cols=40 Identities=18% Similarity=0.190 Sum_probs=29.9
Q ss_pred EEEeCceEE-----EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 106 ILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 106 I~V~G~TVs-----IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
|+|...||. |+|.+.+...|++-+..| .|+.|-||.=..+
T Consensus 63 ~vI~aDTvV~~~g~ilgKP~~~~eA~~~L~~l-sg~~h~V~T~v~l 107 (180)
T PRK04056 63 NLLVADSVVSCGNKILRKAKDKEEAREMLKLQ-SGNEISVLTCMIL 107 (180)
T ss_pred EEEEeCEEEEECCEEecCCCCHHHHHHHHHHH-CCCcEEEEEEEEE
Confidence 566655644 789999999999988766 7779977765444
No 74
>COG0424 Maf Nucleotide-binding protein implicated in inhibition of septum formation [Cell division and chromosome partitioning]
Probab=35.59 E-value=56 Score=30.25 Aligned_cols=55 Identities=16% Similarity=0.247 Sum_probs=43.2
Q ss_pred CCchHHHHHHHh-CceEEEeCceEE----EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 91 NSSTLKALEILT-GCYILVQGNTVA----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 91 ~GkTkkaIE~LT-~~yI~V~G~TVs----IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
..+.....+.+. +|-|+-.|..|+ |+|.+...+.|+.-+..+ .|+.|-||.=..+
T Consensus 51 ~~KA~~va~~~~~~~~VigaDtvv~ldgrilgKP~~~~eA~~~L~~l-SG~~h~v~T~v~l 110 (193)
T COG0424 51 EEKARAVAARLPPDALVIGADTVVVLDGRILGKPKDEEEAREMLRKL-SGRTHQVYTGVAL 110 (193)
T ss_pred HHHHHHHHHhCCCCCEEEecCeEEEECCEEecCCCCHHHHHHHHHHh-cCCeEEEEEEEEE
Confidence 367888888887 888888888877 488889999888777665 8989988865544
No 75
>TIGR02494 PFLE_PFLC glycyl-radical enzyme activating protein family. This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA, ), benzylsuccinate synthase (BssD, ), gycerol dehydratase (DhaB2, ) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0
Probab=35.49 E-value=3.2e+02 Score=25.33 Aligned_cols=107 Identities=17% Similarity=0.096 Sum_probs=52.3
Q ss_pred CCeEEEEcCCCCCChHHHHhHHHHHHHHH-------cCCCh-HHHHhhhccCceeEEEEcCccccChhhHhhhhccccCC
Q 021811 19 EGSMTVSTTRKTRDPYIIVKARDLIRLLS-------RSVPA-PQAIKILDDEMQCDIIKIGNLVRNKERFVKRRQHLVGP 90 (307)
Q Consensus 19 egsV~V~tt~kT~DP~~ilKArD~IkAIa-------RGF~~-E~AlkLLeDd~~~dIIdI~~~~~nke~f~RrrgRIIG~ 90 (307)
.+.|++.....+-.|-.+...-+.++..+ -|+-+ +..-++++ .+..-.|+|..+ +.+.+.+.+| +.
T Consensus 126 ~~~V~~sGGEPll~~~~l~~l~~~~k~~g~~~~i~TnG~~~~~~~~~ll~-~~d~~~isl~~~--~~~~~~~~~g---~~ 199 (295)
T TIGR02494 126 GGGVTLSGGEPLLQPEFALALLQACHERGIHTAVETSGFTPWETIEKVLP-YVDLFLFDIKHL--DDERHKEVTG---VD 199 (295)
T ss_pred CCcEEeeCcchhchHHHHHHHHHHHHHcCCcEeeeCCCCCCHHHHHHHHh-hCCEEEEeeccC--ChHHHHHHhC---CC
Confidence 46688776444444433222222222221 34433 34444553 222223566554 4455555555 24
Q ss_pred CCchHHHHHHHhCceEEEeCceEEEecCCCcHHHHHHHHHH
Q 021811 91 NSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVED 131 (307)
Q Consensus 91 ~GkTkkaIE~LT~~yI~V~G~TVsIIG~~~~IkiAR~aIed 131 (307)
...++++|+.|....+.+.=.++.+-|-.++.......+.-
T Consensus 200 ~~~vl~~i~~l~~~~~~~~i~~~~v~~~n~~~~ei~~l~~~ 240 (295)
T TIGR02494 200 NEPILENLEALAAAGKNVVIRIPVIPGFNDSEENIEAIAAF 240 (295)
T ss_pred hHHHHHHHHHHHhCCCcEEEEeceeCCcCCCHHHHHHHHHH
Confidence 56788888888776654433344343444555555554433
No 76
>PRK11145 pflA pyruvate formate lyase-activating enzyme 1; Provisional
Probab=34.29 E-value=2.7e+02 Score=25.12 Aligned_cols=107 Identities=14% Similarity=0.017 Sum_probs=56.5
Q ss_pred CeEEEEcCCCCCChHHHHhHHHHHHHHH-------cCCCh---HHHHhhhccCceeEEEEcCccccChhhHhhhhccccC
Q 021811 20 GSMTVSTTRKTRDPYIIVKARDLIRLLS-------RSVPA---PQAIKILDDEMQCDIIKIGNLVRNKERFVKRRQHLVG 89 (307)
Q Consensus 20 gsV~V~tt~kT~DP~~ilKArD~IkAIa-------RGF~~---E~AlkLLeDd~~~dIIdI~~~~~nke~f~RrrgRIIG 89 (307)
+.|++.....+-+|..+......++..+ -|+.+ +.+-.++. .+.+-.|+|..+. .+.+.+.+|.
T Consensus 72 ~~V~~sGGEPll~~~~~~~l~~~~k~~g~~i~l~TNG~~~~~~~~~~~ll~-~~d~v~islk~~~--~e~~~~~~g~--- 145 (246)
T PRK11145 72 GGVTASGGEAILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLD-VTDLVMLDLKQMN--DEIHQNLVGV--- 145 (246)
T ss_pred CeEEEeCccHhcCHHHHHHHHHHHHHcCCCEEEECCCCCCcchHHHHHHHH-hCCEEEECCCcCC--hhhcccccCC---
Confidence 4677765444444443433333333211 25432 44444443 2223346676653 3333344442
Q ss_pred CCCchHHHHHHHhCceEEEeCceEEEecCCCcHHHHHHHHHHH
Q 021811 90 PNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDC 132 (307)
Q Consensus 90 ~~GkTkkaIE~LT~~yI~V~G~TVsIIG~~~~IkiAR~aIedl 132 (307)
.+..++.+|+.+...-+-|.-.++.+=|-.+..+.++..+.-|
T Consensus 146 ~~~~~l~~i~~l~~~g~~v~i~~~li~g~nd~~~ei~~l~~~l 188 (246)
T PRK11145 146 SNHRTLEFARYLAKRNQKTWIRYVVVPGWTDDDDSAHRLGEFI 188 (246)
T ss_pred ChHHHHHHHHHHHhCCCcEEEEEEEECCCCCCHHHHHHHHHHH
Confidence 4466777778877665666667777777777666666655444
No 77
>PRK06476 pyrroline-5-carboxylate reductase; Reviewed
Probab=33.48 E-value=1.1e+02 Score=27.99 Aligned_cols=98 Identities=9% Similarity=0.044 Sum_probs=57.8
Q ss_pred HHHHHhhhccEEEEEcCCCeEEEEcCCCCCChHHHHhH-HHHHH-HHHcCCChHHHHhhhccCceeEEEEcCccccChhh
Q 021811 2 VKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKA-RDLIR-LLSRSVPAPQAIKILDDEMQCDIIKIGNLVRNKER 79 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~ilKA-rD~Ik-AIaRGF~~E~AlkLLeDd~~~dIIdI~~~~~nke~ 79 (307)
++.+++..|-.+.+... ..+..-|.-- .-|..++-. ..++. +...||+.++|..++..=+. -...+ -+...+.+
T Consensus 136 ~~~l~~~lG~~~~~~~e-~~~d~~~a~~-s~~a~~~~~~~~~~~~~~~~Gl~~~~a~~~~~~~~~-G~~~l-~~~~~~~~ 211 (258)
T PRK06476 136 VAALFDALGTAVECDSE-EEYDLLAAAS-ALMATYFGILETATGWLEEQGLKRQKARAYLAPLFA-SLAQD-AVRSTKTD 211 (258)
T ss_pred HHHHHHhcCCcEEECCh-Hhccceeehh-ccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH-HHHHH-HHhcCCCC
Confidence 56677777776665422 2222222211 123333322 23332 35679999999999874321 00000 01134578
Q ss_pred HhhhhccccCCCCchHHHHHHHhC
Q 021811 80 FVKRRQHLVGPNSSTLKALEILTG 103 (307)
Q Consensus 80 f~RrrgRIIG~~GkTkkaIE~LT~ 103 (307)
+.-.|.++.-|+|.|...|+.|-.
T Consensus 212 ~~~l~~~v~spgGtT~~gl~~le~ 235 (258)
T PRK06476 212 FSALSREFSTKGGLNEQVLNDFSR 235 (258)
T ss_pred HHHHHHhCCCCCchHHHHHHHHHH
Confidence 889999999999999999998854
No 78
>PRK12491 pyrroline-5-carboxylate reductase; Reviewed
Probab=33.41 E-value=67 Score=30.24 Aligned_cols=95 Identities=17% Similarity=0.218 Sum_probs=66.0
Q ss_pred HHHHHhhhccEEEEEcCCCeEEEEcCCCCCChHHH-HhHHHHH-HHHHcCCChHHHHhhhccCce--eEEEEcCccccCh
Q 021811 2 VKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYII-VKARDLI-RLLSRSVPAPQAIKILDDEMQ--CDIIKIGNLVRNK 77 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~egsV~V~tt~kT~DP~~i-lKArD~I-kAIaRGF~~E~AlkLLeDd~~--~dIIdI~~~~~nk 77 (307)
|+.+++..|....++ |..|.+-|.--.--|..+ .=...++ -++..|+|.++|.++...=+. .. -+..+.
T Consensus 147 v~~lf~~~G~~~~~~--E~~~d~~talsgsgPAf~~~~~eal~~a~v~~Gl~~~~A~~l~~~t~~G~a~-----ll~~~~ 219 (272)
T PRK12491 147 VLNIFNIFGQTEVVN--EKLMDVVTSISGSSPAYVYMFIEAMADAAVLGGMPRKQAYKFAAQAVLGSAK-----MVLETG 219 (272)
T ss_pred HHHHHHcCCCEEEEc--HHHhhhHHHhccCcHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH-----HHHhcC
Confidence 677888888887776 667777765545555432 2223344 356789999999999875421 00 011355
Q ss_pred hhHhhhhccccCCCCchHHHHHHHhC
Q 021811 78 ERFVKRRQHLVGPNSSTLKALEILTG 103 (307)
Q Consensus 78 e~f~RrrgRIIG~~GkTkkaIE~LT~ 103 (307)
.++.-.|.++.=|+|.|...|+.|-.
T Consensus 220 ~~p~~l~~~V~sPGGtT~~gl~~le~ 245 (272)
T PRK12491 220 IHPGELKDMVCSPGGTTIEAVATLEE 245 (272)
T ss_pred CCHHHHHHhCCCCchHHHHHHHHHHH
Confidence 78889999999999999999998754
No 79
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=33.25 E-value=36 Score=29.54 Aligned_cols=24 Identities=25% Similarity=0.216 Sum_probs=20.0
Q ss_pred hhccccCCCCchHHHHHHHhCceE
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYI 106 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI 106 (307)
.-|..||++|+..++|+++.|-.|
T Consensus 42 ~vG~~IG~~G~rI~~i~e~lgekI 65 (140)
T PRK08406 42 DMGLAIGKGGENVKRLEEKLGKDI 65 (140)
T ss_pred CccccCCcCchHHHHHHHHhCCce
Confidence 358999999999999999886444
No 80
>PRK00148 Maf-like protein; Reviewed
Probab=32.56 E-value=83 Score=28.68 Aligned_cols=31 Identities=10% Similarity=0.097 Sum_probs=24.5
Q ss_pred EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 115 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 115 IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
|+|.+.+.+.|++-+..+ .|+.|-||.=..+
T Consensus 77 Il~KP~~~eeA~~~L~~l-sG~~h~v~T~v~l 107 (194)
T PRK00148 77 LLGKPHTPEEAIERWQQM-SGRTGELYTGHAL 107 (194)
T ss_pred EecCCCCHHHHHHHHHHh-CCCCcEEEEEEEE
Confidence 689999999999977666 6889988764433
No 81
>PRK01526 Maf-like protein; Reviewed
Probab=32.39 E-value=69 Score=29.54 Aligned_cols=52 Identities=17% Similarity=0.266 Sum_probs=34.2
Q ss_pred hHHHHHHHhCceEEEeCceEE-----EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 94 TLKALEILTGCYILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 94 TkkaIE~LT~~yI~V~G~TVs-----IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
.....+.+..-.++|...||. |+|.+.+.+.|++-+..| .|+.|-||.-..+
T Consensus 60 A~~v~~~~~~~~~VI~aDTvV~~~g~IlgKP~~~~eA~~mL~~l-sG~~h~V~Tgv~l 116 (205)
T PRK01526 60 AIKIASQIEESAIIIAADTVAAVGRRILPKATTYEEVKNCIKML-SGRRHRVYTGLCI 116 (205)
T ss_pred HHHHHhhcCCCCEEEEeCeEEEECCEEecCCCCHHHHHHHHHHh-CCCCeEEEEEEEE
Confidence 333334333233556655644 789999999999988777 6879987754444
No 82
>TIGR02493 PFLA pyruvate formate-lyase 1-activating enzyme. An iron-sulfur protein with a radical-SAM domain (pfam04055). A single glycine residue in EC 2.3.1.54, formate C-acetyltransferase (formate-pyruvate lyase), is oxidized to the corresponding radical by transfer of H from its CH2 to AdoMet with concomitant cleavage of the latter. The reaction requires Fe2+. The first stage is reduction of the AdoMet to give methionine and the 5'-deoxyadenosin-5-yl radical, which then abstracts a hydrogen radical from the glycine residue.
Probab=32.34 E-value=3.6e+02 Score=23.94 Aligned_cols=108 Identities=16% Similarity=0.117 Sum_probs=60.6
Q ss_pred CeEEEEcCCCCCChHHHHhHHHHHHHHH-------cCC-C--hHHHHhhhccCceeEEEEcCccccChhhHhhhhccccC
Q 021811 20 GSMTVSTTRKTRDPYIIVKARDLIRLLS-------RSV-P--APQAIKILDDEMQCDIIKIGNLVRNKERFVKRRQHLVG 89 (307)
Q Consensus 20 gsV~V~tt~kT~DP~~ilKArD~IkAIa-------RGF-~--~E~AlkLLeDd~~~dIIdI~~~~~nke~f~RrrgRIIG 89 (307)
+.|++.....+-+|..+...-..++..+ -|+ . .+.+.++++. +..-.|+|..+ +.+.+.+.+|.
T Consensus 67 ~~I~~~GGEPll~~~~~~~li~~~~~~g~~~~i~TNG~~~~~~~~~~~ll~~-~d~v~isl~~~--~~~~~~~~~g~--- 140 (235)
T TIGR02493 67 GGVTFSGGEPLLQPEFLSELFKACKELGIHTCLDTSGFLGGCTEAADELLEY-TDLVLLDIKHF--NPEKYKKLTGV--- 140 (235)
T ss_pred CeEEEeCcccccCHHHHHHHHHHHHHCCCCEEEEcCCCCCccHHHHHHHHHh-CCEEEEeCCCC--CHHHHHHHHCC---
Confidence 4677776555555544333333333322 122 1 3555566652 22234555543 44454444443
Q ss_pred CCCchHHHHHHHhCceEEEeCceEEEecCCCcHHHHHHHHHHHh
Q 021811 90 PNSSTLKALEILTGCYILVQGNTVAAMGSFKGLKQVRRIVEDCM 133 (307)
Q Consensus 90 ~~GkTkkaIE~LT~~yI~V~G~TVsIIG~~~~IkiAR~aIedlI 133 (307)
..-+++++|+.+....+-+.-++|.+-|..++...+.+.+..+.
T Consensus 141 ~~~~v~~~i~~l~~~g~~~~v~~vv~~~~~~n~~ei~~l~~~~~ 184 (235)
T TIGR02493 141 SLQPTLDFAKYLAKRNKPIWIRYVLVPGYTDSEEDIEALAEFVK 184 (235)
T ss_pred CcHHHHHHHHHHHhCCCcEEEEEeeeCCcCCCHHHHHHHHHHHH
Confidence 44678999999887666665566655566678888877776665
No 83
>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=32.12 E-value=1.4e+02 Score=27.58 Aligned_cols=80 Identities=21% Similarity=0.375 Sum_probs=51.4
Q ss_pred HHHHHhhh----ccEEEEEcC-----CCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHhhhccCceeEEEEcCc
Q 021811 2 VKGALKEY----GVSCELNLV-----EGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEMQCDIIKIGN 72 (307)
Q Consensus 2 v~~~le~~----~i~i~lDl~-----egsV~V~tt~kT~DP~~ilKArD~IkAIaRGF~~E~AlkLLeDd~~~dIIdI~~ 72 (307)
++.+++.. ++.+++-.. .++|+|.. ++-++|+|.+|..+-. . |.+=|-+
T Consensus 112 l~~~~~~l~~~~~~~v~V~~V~N~fFG~~ItVaG---------LLTg~Dii~~L~~~~~--------~-----d~lllP~ 169 (204)
T PF04459_consen 112 LKPLVEKLNRIPGLEVEVVPVKNRFFGGTITVAG---------LLTGQDIIEQLKGKEL--------G-----DLLLLPD 169 (204)
T ss_pred HHHHHHHHhccCCCeEEEEEeecCCCCCCeEEee---------CccHHHHHHHhCcCCC--------C-----CEEEECH
Confidence 34555555 666666544 67788875 9999999998876111 1 2222222
Q ss_pred cccChhhHhhh-hccccCCCCchHHHHHHHhCceEEEeCc
Q 021811 73 LVRNKERFVKR-RQHLVGPNSSTLKALEILTGCYILVQGN 111 (307)
Q Consensus 73 ~~~nke~f~Rr-rgRIIG~~GkTkkaIE~LT~~yI~V~G~ 111 (307)
.+.+- .++.+ +|.|..-|+.--|+.|.|-..
T Consensus 170 ------~ml~~~~~~fL--DD~t~~el~~~lg~~v~vv~~ 201 (204)
T PF04459_consen 170 ------VMLRHGEGVFL--DDMTLEELEERLGVPVIVVRG 201 (204)
T ss_pred ------HHhcCCCCccC--CCCcHHHHHHHhCCcEEEeCC
Confidence 22233 55556 788999999998998887653
No 84
>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=32.00 E-value=1.1e+02 Score=21.68 Aligned_cols=37 Identities=27% Similarity=0.343 Sum_probs=28.3
Q ss_pred HHHHHhhhccEEEEEcC--CCeEEEEcCCCCCChHHHHhHHHHH
Q 021811 2 VKGALKEYGVSCELNLV--EGSMTVSTTRKTRDPYIIVKARDLI 43 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~--egsV~V~tt~kT~DP~~ilKArD~I 43 (307)
|..+-+++++.+.++.. ...|+|. .++..+..|+++|
T Consensus 22 i~~I~~~t~~~I~i~~~~~~~~v~I~-----G~~~~v~~A~~~I 60 (60)
T PF00013_consen 22 IKEIEEETGVKIQIPDDDERDIVTIS-----GSPEQVEKAKKMI 60 (60)
T ss_dssp HHHHHHHHTSEEEEESTTEEEEEEEE-----ESHHHHHHHHHHH
T ss_pred HHHhhhhcCeEEEEcCCCCcEEEEEE-----eCHHHHHHHHhhC
Confidence 56777899999999765 3466665 4778899998876
No 85
>PRK10629 EnvZ/OmpR regulon moderator; Provisional
Probab=31.81 E-value=95 Score=26.74 Aligned_cols=40 Identities=15% Similarity=0.224 Sum_probs=34.9
Q ss_pred HHHHHhhhccEE-EEEcCCCeEEEEcCCCCCChHHHHhHHHHHHH
Q 021811 2 VKGALKEYGVSC-ELNLVEGSMTVSTTRKTRDPYIIVKARDLIRL 45 (307)
Q Consensus 2 v~~~le~~~i~i-~lDl~egsV~V~tt~kT~DP~~ilKArD~IkA 45 (307)
|..+|++.||.+ .+...++++.|+- .||..=++|+|+++.
T Consensus 55 v~~~L~~~gI~~ksi~~~~~~~~irf----~~~~~Ql~Ak~vL~~ 95 (127)
T PRK10629 55 VYQHLDANGIHIKSITPENDSLLIRF----DSPEQSAAAKEVLDR 95 (127)
T ss_pred HHHHHHHCCCCcceEEeeCCEEEEEE----CCHHHHHHHHHHHHH
Confidence 678899999988 6788899999996 788889999999974
No 86
>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=31.69 E-value=1.2e+02 Score=21.70 Aligned_cols=37 Identities=19% Similarity=0.290 Sum_probs=29.2
Q ss_pred HHHHHhhhccEEEEEcC---CCeEEEEcCCCCCChHHHHhHHHHH
Q 021811 2 VKGALKEYGVSCELNLV---EGSMTVSTTRKTRDPYIIVKARDLI 43 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~---egsV~V~tt~kT~DP~~ilKArD~I 43 (307)
|+++-+++|+.+.+... ++.|+|..+ +..+..|.++|
T Consensus 22 i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-----~~~v~~A~~~i 61 (62)
T cd02394 22 IRKIMEETGVKIRFPDPGSKSDTITITGP-----KENVEKAKEEI 61 (62)
T ss_pred HHHHHHHhCCEEEcCCCCCCCCEEEEEcC-----HHHHHHHHHHh
Confidence 56778899999999875 689999863 66788887765
No 87
>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=31.52 E-value=81 Score=22.97 Aligned_cols=33 Identities=18% Similarity=0.217 Sum_probs=28.7
Q ss_pred CCCCChHHHHhHHHHHHHHHcCCChHHHHhhhc
Q 021811 28 RKTRDPYIIVKARDLIRLLSRSVPAPQAIKILD 60 (307)
Q Consensus 28 ~kT~DP~~ilKArD~IkAIaRGF~~E~AlkLLe 60 (307)
....++..+...+.+..+...|||+++...+|+
T Consensus 35 ~R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l~ 67 (67)
T cd04764 35 RRYYTDEDIELLKKIKTLLEKGLSIKEIKEILN 67 (67)
T ss_pred ceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHhC
Confidence 344788899999999999999999999988875
No 88
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=31.08 E-value=48 Score=34.91 Aligned_cols=51 Identities=16% Similarity=0.170 Sum_probs=38.9
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeC-ce---EEEecCCCcHHHHHHHHHHHh
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQG-NT---VAAMGSFKGLKQVRRIVEDCM 133 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G-~T---VsIIG~~~~IkiAR~aIedlI 133 (307)
--|-+||.+|+..+-|.+-|+|.|-+.- .- |-|-|.-.--+.|..+|+..+
T Consensus 57 mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~~~m~~kaka~id~~~ 111 (629)
T KOG0336|consen 57 MVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGINHMRKKAKASIDRGQ 111 (629)
T ss_pred hhheeeccCcchhhhhhcccceeEEEeccCceeEEEEechHHHHHHHHhhHhhhh
Confidence 3578999999999999999999997753 33 556665555566777777666
No 89
>PRK07679 pyrroline-5-carboxylate reductase; Reviewed
Probab=30.86 E-value=64 Score=29.94 Aligned_cols=95 Identities=16% Similarity=0.220 Sum_probs=57.6
Q ss_pred HHHHHhhhccEEEEEcCCCeEEEEcCCCCCCh-HHHHhHHHHH-HHHHcCCChHHHHhhhccCce--eEEEEcCccccCh
Q 021811 2 VKGALKEYGVSCELNLVEGSMTVSTTRKTRDP-YIIVKARDLI-RLLSRSVPAPQAIKILDDEMQ--CDIIKIGNLVRNK 77 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~egsV~V~tt~kT~DP-~~ilKArD~I-kAIaRGF~~E~AlkLLeDd~~--~dIIdI~~~~~nk 77 (307)
|+.+++..|-.+.++. ..+..-|..-.--| |...=+.-+. -+...|++.++|..++.+-+. ... +....
T Consensus 149 v~~l~~~~G~~~~v~e--~~~~~~~a~~Gsgpa~~~~~~eal~e~~~~~Gl~~~~a~~~~~~~~~gsa~~-----~~~~~ 221 (279)
T PRK07679 149 AKALFETIGLVSVVEE--EDMHAVTALSGSGPAYIYYVVEAMEKAAKKIGLKEDVAKSLILQTMIGAAEM-----LKASE 221 (279)
T ss_pred HHHHHHhCCcEEEeCH--HHhhhHHHhhcCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH-----HHhcC
Confidence 5667788887776662 23432232212222 2222233344 368899999999999987311 000 11123
Q ss_pred hhHhhhhccccCCCCchHHHHHHHhC
Q 021811 78 ERFVKRRQHLVGPNSSTLKALEILTG 103 (307)
Q Consensus 78 e~f~RrrgRIIG~~GkTkkaIE~LT~ 103 (307)
.++.-.+.++.-|+|.|..+|+.|-.
T Consensus 222 ~~~~~l~~~v~spgg~t~~gl~~l~~ 247 (279)
T PRK07679 222 KHPSILRKEITSPGGTTEAGIEVLQE 247 (279)
T ss_pred CCHHHHHHhcCCCchHHHHHHHHHHH
Confidence 45666788898999999999988754
No 90
>PF13721 SecD-TM1: SecD export protein N-terminal TM region
Probab=30.45 E-value=1e+02 Score=25.32 Aligned_cols=40 Identities=23% Similarity=0.316 Sum_probs=34.8
Q ss_pred HHHHHhhhccEEE-EEcCCCeEEEEcCCCCCChHHHHhHHHHHHH
Q 021811 2 VKGALKEYGVSCE-LNLVEGSMTVSTTRKTRDPYIIVKARDLIRL 45 (307)
Q Consensus 2 v~~~le~~~i~i~-lDl~egsV~V~tt~kT~DP~~ilKArD~IkA 45 (307)
|+.+|++.||... +...++++.|+- .|+..=++|+|+++.
T Consensus 51 v~~~L~~~~I~~k~i~~~~~~llirf----~~~~~Ql~Ak~~L~~ 91 (101)
T PF13721_consen 51 VEQALKAAGIAVKSIEQEGDSLLIRF----DSTDQQLKAKDVLSK 91 (101)
T ss_pred HHHHHHHCCCCcceEEeeCCEEEEEE----CCHHHHHHHHHHHHH
Confidence 6788999999884 888899999996 788899999999874
No 91
>PRK14361 Maf-like protein; Provisional
Probab=29.85 E-value=97 Score=28.13 Aligned_cols=31 Identities=10% Similarity=0.080 Sum_probs=24.6
Q ss_pred EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 115 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 115 IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
|+|.+.+.+.|++-+..| .|+.|-||.=..+
T Consensus 74 ilgKP~~~eeA~~~L~~l-sG~~h~V~T~v~l 104 (187)
T PRK14361 74 LLAKPADEAENEAFLRVL-SGRTHQVYTGVAV 104 (187)
T ss_pred EecCCCCHHHHHHHHHHh-CCCceEEEEEEEE
Confidence 689999999999988877 6778976654443
No 92
>PRK00234 Maf-like protein; Reviewed
Probab=29.56 E-value=89 Score=28.38 Aligned_cols=32 Identities=9% Similarity=0.071 Sum_probs=25.0
Q ss_pred EEecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 114 AAMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 114 sIIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
-|+|.+.+.+.|++-+..+ .|+.|-||.-..+
T Consensus 77 ~Il~KP~~~~eA~~mL~~l-sG~~h~V~T~v~l 108 (192)
T PRK00234 77 QILGKPHTFERAREQLLAA-SGQSVTFLTGLAL 108 (192)
T ss_pred EECCCCCCHHHHHHHHHHH-CCCcEEEEEEEEE
Confidence 3789999999999987776 7879987655444
No 93
>PRK14365 Maf-like protein; Provisional
Probab=29.24 E-value=86 Score=28.69 Aligned_cols=46 Identities=11% Similarity=0.172 Sum_probs=31.6
Q ss_pred HHHhCceEEEeCceEE-----EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 99 EILTGCYILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 99 E~LT~~yI~V~G~TVs-----IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
+.+.++ ++|...||. |+|.+.+.+.|++-+..+ .|+.|-||.=..+
T Consensus 59 ~~~~~~-~vI~aDTvV~~~g~Il~KP~~~~eA~~~L~~l-sg~~h~v~T~v~l 109 (197)
T PRK14365 59 KHFDSG-IIISADTSVFCNGEVLGKPASPENAEEMLEKL-SGRKFLVITGLTV 109 (197)
T ss_pred HhCCCC-EEEEeCeEEEECCEEecCCCCHHHHHHHHHHH-CCCceEEEEEEEE
Confidence 333443 555555543 789999999999977766 6879987765443
No 94
>PRK00884 Maf-like protein; Reviewed
Probab=28.61 E-value=1e+02 Score=28.18 Aligned_cols=40 Identities=13% Similarity=0.196 Sum_probs=28.9
Q ss_pred EEEeCceEE-----EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 106 ILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 106 I~V~G~TVs-----IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
|+|...||. |+|.+.+.+.|++-+..| .|+.|-||.=..+
T Consensus 64 ~VI~aDTvV~~~g~ilgKP~~~eeA~~~L~~l-sG~~h~V~Tgv~l 108 (194)
T PRK00884 64 LIIGSDQVCVLDGEITGKPLTEENARAQLRKA-SGNIVTFYTGLAL 108 (194)
T ss_pred EEEEeCeEEEECCEEecCCCCHHHHHHHHHHH-CCCceEEEEEEEE
Confidence 444444433 789999999999988876 7879987754444
No 95
>PRK00648 Maf-like protein; Reviewed
Probab=28.43 E-value=98 Score=28.11 Aligned_cols=40 Identities=18% Similarity=0.300 Sum_probs=29.3
Q ss_pred EEEeCceEE-----EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 106 ILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 106 I~V~G~TVs-----IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
|+|...||. |+|.+.+...|++-+..+ .|+.|-||.=..+
T Consensus 67 ~VI~aDTvV~~~g~ilgKP~~~~eA~~~L~~l-sG~~h~v~T~v~l 111 (191)
T PRK00648 67 LIITADTIVWYDGKVLGKPKDEEEAVEMLRTL-SGKTHEVITGVCL 111 (191)
T ss_pred EEEEeCeEEEECCEEeCCCCCHHHHHHHHHHh-CCCCeEEEEEEEE
Confidence 555555543 689999999999988777 6779987765444
No 96
>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=27.91 E-value=31 Score=30.24 Aligned_cols=27 Identities=7% Similarity=0.083 Sum_probs=0.0
Q ss_pred hccccCCCCchHHHHHHHhCceEEEeC
Q 021811 84 RQHLVGPNSSTLKALEILTGCYILVQG 110 (307)
Q Consensus 84 rgRIIG~~GkTkkaIE~LT~~yI~V~G 110 (307)
+++.||++|++.+-.-.|||-++=|.+
T Consensus 111 ~~~AIGk~G~Ni~la~~l~~~~~dI~~ 137 (141)
T TIGR01952 111 KGIAIGKGGKNIERAKELAKRHHDIDD 137 (141)
T ss_pred hhhhhCCCchhHHHHHHHhcCccCCeE
No 97
>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=27.90 E-value=1.2e+02 Score=22.13 Aligned_cols=34 Identities=15% Similarity=0.189 Sum_probs=28.6
Q ss_pred CCCCCChHHHHhHHHHHHHHHcCCChHHHHhhhc
Q 021811 27 TRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILD 60 (307)
Q Consensus 27 t~kT~DP~~ilKArD~IkAIaRGF~~E~AlkLLe 60 (307)
.....+...|...+.+..+...||+++++..+|+
T Consensus 35 g~R~yt~~di~~l~~i~~l~~~g~~l~~i~~~l~ 68 (68)
T cd04763 35 GHRLFNDADIDRILEIKRWIDNGVQVSKVKKLLS 68 (68)
T ss_pred CCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHhC
Confidence 3445777889999999999999999999998874
No 98
>PRK00078 Maf-like protein; Reviewed
Probab=26.15 E-value=1.1e+02 Score=27.89 Aligned_cols=40 Identities=18% Similarity=0.289 Sum_probs=29.1
Q ss_pred EEEeCceEE-----EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 106 ILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 106 I~V~G~TVs-----IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
++|...||. |+|.+.+.+.|++-+..| .|+.|-||.=..+
T Consensus 66 lvI~aDTvV~~~g~ilgKP~~~eeA~~~L~~l-sG~~h~V~Tgv~l 110 (192)
T PRK00078 66 IVIGCDTIVAFNGKVLGKPKDEEDAFEMLKAL-SGNEHEVYSGIAI 110 (192)
T ss_pred EEEEeCeEEEECCEEeCCCCCHHHHHHHHHHH-CCCcEEEEEEEEE
Confidence 555555543 689999999999988877 6779987764433
No 99
>PRK14368 Maf-like protein; Provisional
Probab=25.53 E-value=1.3e+02 Score=27.45 Aligned_cols=52 Identities=19% Similarity=0.202 Sum_probs=33.0
Q ss_pred chHHHHHHHhCceEEEeCce-EE----EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 93 STLKALEILTGCYILVQGNT-VA----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 93 kTkkaIE~LT~~yI~V~G~T-Vs----IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
++....+...++ ++|...| |. |+|.+.+...|++-+..| .|+.|-||.=.-+
T Consensus 55 KA~~v~~~~~~~-~vI~aDTvV~~~g~ilgKP~~~~eA~~~L~~l-sG~~h~v~Tgv~l 111 (193)
T PRK14368 55 KARAAAALAEGR-FFIGADTIVVCDGEIMGKPKDEADAVRMLKKL-SGVPHEVITGFAV 111 (193)
T ss_pred HHHHHHHhCCCC-EEEEeCcEEEECCEEecCCCCHHHHHHHHHHh-CCCCcEEEEEEEE
Confidence 333333433444 4444444 32 689999999999987776 6779987654443
No 100
>PRK14363 Maf-like protein; Provisional
Probab=24.81 E-value=1.1e+02 Score=28.20 Aligned_cols=41 Identities=17% Similarity=0.381 Sum_probs=30.1
Q ss_pred eEEEeCceEE-----EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 105 YILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 105 yI~V~G~TVs-----IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
.++|...||. |+|.+.+...|++-+..| .|+.|.||.-..+
T Consensus 62 ~lvI~aDTVV~~~g~IlgKP~~~eeA~~~L~~l-sG~~H~V~T~v~l 107 (204)
T PRK14363 62 ILVIGSDTVVVLDGNILGKPESLEEAKGMLKKL-SGRWHVVYTGVAF 107 (204)
T ss_pred CEEEEeCeEEEECCEEcCCCCCHHHHHHHHHHH-CCCCcEEEEEEEE
Confidence 3555555543 789999999999988877 6778987765544
No 101
>COG1159 Era GTPase [General function prediction only]
Probab=24.78 E-value=70 Score=31.60 Aligned_cols=53 Identities=21% Similarity=0.493 Sum_probs=34.5
Q ss_pred HHHHhhhccC----ceeEEEEcCccccChhhHhh-----------hhccccCCCCchHHHH--------HHHhCceEEE
Q 021811 53 PQAIKILDDE----MQCDIIKIGNLVRNKERFVK-----------RRQHLVGPNSSTLKAL--------EILTGCYILV 108 (307)
Q Consensus 53 E~AlkLLeDd----~~~dIIdI~~~~~nke~f~R-----------rrgRIIG~~GkTkkaI--------E~LT~~yI~V 108 (307)
|+++..|.|+ +..+|-+...- .+...+ .+|=|||.||.+++.| |.+-+|.|.+
T Consensus 198 Ek~~~~l~eElPhsv~VeIe~~~~~---~~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 198 EKLLLLLREELPHSVAVEIEEFEER---EKGLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred HHHHHhcccccCceEEEEEEEEEec---CCCeEEEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 8999999998 34566555542 122222 3677999999887654 6666666544
No 102
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=24.53 E-value=1.1e+02 Score=23.69 Aligned_cols=35 Identities=14% Similarity=0.159 Sum_probs=25.1
Q ss_pred hhhccccCCCCchHHHHHHHhCceEEEeCceEEEecCCCcH
Q 021811 82 KRRQHLVGPNSSTLKALEILTGCYILVQGNTVAAMGSFKGL 122 (307)
Q Consensus 82 RrrgRIIG~~GkTkkaIE~LT~~yI~V~G~TVsIIG~~~~I 122 (307)
-..|..||.+|...++|....+ |..|-++...+.+
T Consensus 17 d~vG~~iG~~G~rik~i~~~L~------gekIdvV~~s~d~ 51 (69)
T PF13184_consen 17 DPVGACIGKKGSRIKAISEELN------GEKIDVVEYSDDP 51 (69)
T ss_dssp -HHHHHH-CCCCCHHHHHHHTT------T-EEEEEE--SSH
T ss_pred CcceecCccccHHHHHHHHHhC------CCeEEEEEcCCCH
Confidence 3578999999999999999886 6777777766664
No 103
>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=24.22 E-value=3e+02 Score=23.32 Aligned_cols=48 Identities=17% Similarity=0.105 Sum_probs=35.7
Q ss_pred HHHHHhhhccEEEEEcCC----------------------CeEEEEcCCCCCC--hHHHHhHHHHHHHHHcCCChH
Q 021811 2 VKGALKEYGVSCELNLVE----------------------GSMTVSTTRKTRD--PYIIVKARDLIRLLSRSVPAP 53 (307)
Q Consensus 2 v~~~le~~~i~i~lDl~e----------------------gsV~V~tt~kT~D--P~~ilKArD~IkAIaRGF~~E 53 (307)
++.+-+++|+.|.|.-.. +.|.|.+ .| .-.+.+|..+|..|...+.++
T Consensus 28 iK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a----~~~~~e~~~~A~~~I~~ll~~~~~~ 99 (120)
T cd02395 28 LKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITA----ETPPEEALAKAVEAIEELLKPAIEG 99 (120)
T ss_pred HHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEe----CCcHHHHHHHHHHHHHHHhccCCCc
Confidence 455568889888887642 7788876 56 577899999999888765554
No 104
>PRK02478 Maf-like protein; Reviewed
Probab=24.07 E-value=1.5e+02 Score=27.18 Aligned_cols=31 Identities=19% Similarity=0.315 Sum_probs=24.4
Q ss_pred EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 115 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 115 IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
|+|.+.+-+.|++-+..| .|+.|-||.-..+
T Consensus 85 ilgKP~~~~eA~~~L~~l-sG~~h~V~T~v~l 115 (199)
T PRK02478 85 VFHKPKDMEEARRHLQKL-SGKTHQLNSAVVL 115 (199)
T ss_pred EecCCCCHHHHHHHHHHh-cCCCcEEEEEEEE
Confidence 789999999999887776 7779987755443
No 105
>PRK14364 Maf-like protein; Provisional
Probab=23.92 E-value=1.5e+02 Score=26.82 Aligned_cols=31 Identities=13% Similarity=0.171 Sum_probs=24.6
Q ss_pred EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 115 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 115 IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
|+|.+.+.+.|++-+.++ .|+.|-||.-..+
T Consensus 73 ilgKP~~~eeA~~~L~~l-sG~~h~V~Tgv~l 103 (181)
T PRK14364 73 IIGKPDSKQHAFDIWKQL-SGRWHDVFSGICI 103 (181)
T ss_pred EecCCCCHHHHHHHHHHh-CCCCeEEEEEEEE
Confidence 689999999999988777 6778977665444
No 106
>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=23.91 E-value=62 Score=29.88 Aligned_cols=26 Identities=27% Similarity=0.570 Sum_probs=20.0
Q ss_pred hhccccCCCCchHHH--------HHHHhCceEEE
Q 021811 83 RRQHLVGPNSSTLKA--------LEILTGCYILV 108 (307)
Q Consensus 83 rrgRIIG~~GkTkka--------IE~LT~~yI~V 108 (307)
.++-|||.+|++++. ||.+.||.|.+
T Consensus 232 ~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l 265 (270)
T TIGR00436 232 QKKIIIGKNGSMIKAIGIAARKDILELFDCDVFL 265 (270)
T ss_pred ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 478899999998765 56677777654
No 107
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=23.72 E-value=49 Score=27.23 Aligned_cols=23 Identities=13% Similarity=0.172 Sum_probs=18.3
Q ss_pred hhccccCCCCchHHHHHHHhCce
Q 021811 83 RRQHLVGPNSSTLKALEILTGCY 105 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~y 105 (307)
+=|.|||++|+++..|..+....
T Consensus 71 rPg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 71 RPGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred CCCcccCCchHHHHHHHHHHHHH
Confidence 46899999999999887754443
No 108
>PF04365 DUF497: Protein of unknown function (DUF497); InterPro: IPR007460 This entry is represented by Burkholderia phage Bups phi1, Orf7.3. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 3U97_A.
Probab=23.49 E-value=34 Score=26.72 Aligned_cols=32 Identities=9% Similarity=0.079 Sum_probs=16.3
Q ss_pred HHHHHHHcCCChHHHHhhhccCceeEEEEcCc
Q 021811 41 DLIRLLSRSVPAPQAIKILDDEMQCDIIKIGN 72 (307)
Q Consensus 41 D~IkAIaRGF~~E~AlkLLeDd~~~dIIdI~~ 72 (307)
+....--+|+++++|..+|.|+..+.+.|...
T Consensus 6 ~~~N~~KHgi~f~~a~~vf~d~~~l~~~d~~~ 37 (80)
T PF04365_consen 6 NEKNIRKHGISFEEAEEVFFDPPRLEIPDRRH 37 (80)
T ss_dssp HHHHHHHHS--GGG--HHH----HHTSEE--E
T ss_pred HHHHHHHhCcCHHHHHHHHhhccceeeccccc
Confidence 34445569999999999999998877777664
No 109
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=23.33 E-value=2e+02 Score=21.71 Aligned_cols=38 Identities=32% Similarity=0.410 Sum_probs=27.6
Q ss_pred HHHHHhhhc--cEEEEEcCCCeEEEEcCCCCCChHHHHhH
Q 021811 2 VKGALKEYG--VSCELNLVEGSMTVSTTRKTRDPYIIVKA 39 (307)
Q Consensus 2 v~~~le~~~--i~i~lDl~egsV~V~tt~kT~DP~~ilKA 39 (307)
|+++|+... ..+.+|+..|+++|.......+.-.|..|
T Consensus 20 V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~a 59 (71)
T COG2608 20 VEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEA 59 (71)
T ss_pred HHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHH
Confidence 677888777 78889999988888765544555555555
No 110
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=22.98 E-value=1.4e+02 Score=21.33 Aligned_cols=31 Identities=13% Similarity=0.075 Sum_probs=27.3
Q ss_pred CCChHHHHhHHHHHHHHHcCCChHHHHhhhc
Q 021811 30 TRDPYIIVKARDLIRLLSRSVPAPQAIKILD 60 (307)
Q Consensus 30 T~DP~~ilKArD~IkAIaRGF~~E~AlkLLe 60 (307)
-+++..+...+.+..+...|||++++-.+|+
T Consensus 38 ~y~~~dl~~l~~i~~lr~~g~~~~~i~~~l~ 68 (70)
T smart00422 38 LYSDEDLERLRFIKRLKELGFSLEEIKELLE 68 (70)
T ss_pred ecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 4678889999999999999999999988875
No 111
>COG0134 TrpC Indole-3-glycerol phosphate synthase [Amino acid transport and metabolism]
Probab=22.78 E-value=52 Score=31.71 Aligned_cols=72 Identities=28% Similarity=0.394 Sum_probs=53.4
Q ss_pred CCCCChHHHHhHH----HHHHHHHcCCChHHHHhhhc--cC----ceeEEEEcCccccChhhHhhhhccccCCCCchHHH
Q 021811 28 RKTRDPYIIVKAR----DLIRLLSRSVPAPQAIKILD--DE----MQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKA 97 (307)
Q Consensus 28 ~kT~DP~~ilKAr----D~IkAIaRGF~~E~AlkLLe--Dd----~~~dIIdI~~~~~nke~f~RrrgRIIG~~GkTkka 97 (307)
+-.-|||.|..|| |.|-+|..-++.++.-.|++ -+ ...||-|..++ ++..+.-.+|||=|-+.+..
T Consensus 114 DFiiD~yQI~~Ar~~GADavLLI~~~L~~~~l~el~~~A~~LGm~~LVEVh~~eEl----~rAl~~ga~iIGINnRdL~t 189 (254)
T COG0134 114 DFIIDPYQIYEARAAGADAVLLIVAALDDEQLEELVDRAHELGMEVLVEVHNEEEL----ERALKLGAKIIGINNRDLTT 189 (254)
T ss_pred cCCCCHHHHHHHHHcCcccHHHHHHhcCHHHHHHHHHHHHHcCCeeEEEECCHHHH----HHHHhCCCCEEEEeCCCcch
Confidence 3457999999996 88999999999998888887 22 33444444443 34455688999999999999
Q ss_pred HHHHhC
Q 021811 98 LEILTG 103 (307)
Q Consensus 98 IE~LT~ 103 (307)
+|.--+
T Consensus 190 f~vdl~ 195 (254)
T COG0134 190 LEVDLE 195 (254)
T ss_pred heecHH
Confidence 885333
No 112
>PRK00032 Maf-like protein; Reviewed
Probab=22.56 E-value=1.4e+02 Score=27.14 Aligned_cols=31 Identities=10% Similarity=0.157 Sum_probs=24.5
Q ss_pred EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 115 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 115 IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
|+|.+.+.+.|++-+..| .|+.|-||.=..+
T Consensus 79 IlgKP~~~eeA~~~L~~l-sG~~h~v~T~v~l 109 (190)
T PRK00032 79 VLEKPRDAADAAAMLRAL-SGRTHQVMTAVAL 109 (190)
T ss_pred EecCCCCHHHHHHHHHHh-CCCCcEEEEEEEE
Confidence 789999999999988776 6779987765444
No 113
>cd00555 Maf Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or nucleic acid-binding protein with structural similarity to the hypoxanthine/xanthine NTP pyrophosphatase Ham1 from Methanococcus jannaschii, RNase H from Escherichia coli, and some other nucleotide or RNA-binding proteins.
Probab=22.51 E-value=1.6e+02 Score=26.32 Aligned_cols=31 Identities=23% Similarity=0.366 Sum_probs=24.1
Q ss_pred EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 115 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 115 IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
|+|.+.+.+.|++-+.++ .|+.|-||.=.-+
T Consensus 76 il~KP~~~~eA~~~L~~l-sg~~h~v~T~v~l 106 (180)
T cd00555 76 ILGKPKDREEAREMLKRL-SGRTHEVYTGVAL 106 (180)
T ss_pred EEcCCCCHHHHHHHHHHH-cCCCcEEEEEEEE
Confidence 689999999999987776 6668987654443
No 114
>KOG3088 consensus Secretory carrier membrane protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.44 E-value=1.6e+02 Score=29.44 Aligned_cols=22 Identities=41% Similarity=0.824 Sum_probs=15.7
Q ss_pred CCCCCCCCCCC----CCchhhhhhhc
Q 021811 185 KKPYTPFPPPP----QPSKIDKLLES 206 (307)
Q Consensus 185 kk~~tpfpp~~----~~~k~d~~~es 206 (307)
.-...|+||++ ++.-+|+-+++
T Consensus 29 ~~~~~p~~~~~~~~~~~~tv~~P~~~ 54 (313)
T KOG3088|consen 29 TPPLSPLPPEPAPSDQGPTVDIPLDS 54 (313)
T ss_pred CCCCCCCCCCCCCCCCCCccccCCCC
Confidence 34567788888 55678887777
No 115
>PRK14362 Maf-like protein; Provisional
Probab=22.25 E-value=1.3e+02 Score=27.75 Aligned_cols=53 Identities=11% Similarity=0.154 Sum_probs=34.3
Q ss_pred CchHHHHHHHhCceEEEeCceEE-----EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 92 SSTLKALEILTGCYILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 92 GkTkkaIE~LT~~yI~V~G~TVs-----IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
++.....+.+.++ ++|...||. |+|.+.+...|++-+..| .|+.|-||.-..+
T Consensus 62 ~KA~~v~~~~~~~-~VI~ADTvV~~~g~ilgKP~~~eeA~~~L~~l-sG~~H~V~Tgv~l 119 (207)
T PRK14362 62 AKARAVAADHAGR-LVIAADTVVALDGMILGKPADRADALSMLRRL-AGRTHEVVSACCV 119 (207)
T ss_pred HHHHHHHHhCCCC-EEEEeCeEEEeCCEEcCCCCCHHHHHHHHHHh-CCCceEEEEEEEE
Confidence 3333334444444 455555543 689999999999987776 6779987765544
No 116
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=21.81 E-value=1.3e+02 Score=23.60 Aligned_cols=34 Identities=12% Similarity=0.078 Sum_probs=30.1
Q ss_pred CCCChHHHHhHHHHHHHHHcCCChHHHHhhhccC
Q 021811 29 KTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDE 62 (307)
Q Consensus 29 kT~DP~~ilKArD~IkAIaRGF~~E~AlkLLeDd 62 (307)
..+++..+...+.+..+...|||++++.++|+.+
T Consensus 38 R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~~~ 71 (88)
T cd01105 38 RKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRR 71 (88)
T ss_pred eecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHc
Confidence 3478889999999999999999999999999844
No 117
>TIGR00172 maf MAF protein. This nonessential gene causes inhibition of septation when overexpressed. A member of the family is found in the Archaeon Pyrococcus horikoshii and another in the round worm Caenorhabditis elegans.
Probab=21.62 E-value=1.8e+02 Score=26.30 Aligned_cols=31 Identities=19% Similarity=0.274 Sum_probs=24.1
Q ss_pred EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 115 AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 115 IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
|+|.+.+.+.|++-+..+ .|+.|-||.=..+
T Consensus 79 ilgKP~~~~eA~~~L~~l-sG~~h~V~Tgv~l 109 (183)
T TIGR00172 79 IYGKPKDKEEAAEFLRKL-SGQEHEVYTAVAL 109 (183)
T ss_pred EecCCCCHHHHHHHHHHh-CCCCcEEEEEEEE
Confidence 689999999999987776 6778987765443
No 118
>PRK04425 Maf-like protein; Reviewed
Probab=21.26 E-value=1.7e+02 Score=26.85 Aligned_cols=40 Identities=18% Similarity=0.314 Sum_probs=29.4
Q ss_pred EEEeCceEE-----EecCCCcHHHHHHHHHHHhcCCCchhHHHHHH
Q 021811 106 ILVQGNTVA-----AMGSFKGLKQVRRIVEDCMQNKMHPVYHIKIL 146 (307)
Q Consensus 106 I~V~G~TVs-----IIG~~~~IkiAR~aIedlI~g~iHpVY~ikel 146 (307)
|+|...||. |+|.+.+.+.|+.-+.++ .|+.|-||.-..+
T Consensus 67 lvI~aDTvV~~~g~ilgKP~~~eeA~~~L~~l-sg~~h~v~T~v~l 111 (196)
T PRK04425 67 LIVGADQVAWCDGRQWGKPMNLANAQKMLMHL-SGREIEFYSALVL 111 (196)
T ss_pred EEEEeCeEEEECCEEecCCCCHHHHHHHHHHh-CCCcEEEEEEEEE
Confidence 444444433 699999999999988875 6779987765554
No 119
>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=21.13 E-value=2.6e+02 Score=29.98 Aligned_cols=93 Identities=20% Similarity=0.311 Sum_probs=62.1
Q ss_pred EEEEcCCCeEEEEcCCCCCChHHHHhHHHHHHHHHcC--------------CChHHHHhhhccCce--eEEEEcCccccC
Q 021811 13 CELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRS--------------VPAPQAIKILDDEMQ--CDIIKIGNLVRN 76 (307)
Q Consensus 13 i~lDl~egsV~V~tt~kT~DP~~ilKArD~IkAIaRG--------------F~~E~AlkLLeDd~~--~dIIdI~~~~~n 76 (307)
..++.+.=.+.|.| .||-.+..--|+|+-||+- .++++|.++..+=+- -.|-||.=-...
T Consensus 19 ~~~~~egp~~~~~~----~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~f~~~~ 94 (630)
T TIGR03675 19 TDVEFEGPELVIYT----KNPELFAKDDDLVKELAKKLRKRIVIRPDPSVLLPPEEAIEKIKEIVPEEAGITDIYFDDVT 94 (630)
T ss_pred EEEEEeCCeEEEEe----CCHHHhccchHHHHHHHHHhhceEEEecChhhcCCHHHHHHHHHHhCCCcCCceeEEecCCC
Confidence 35667677888886 8999988877888888742 468888887763210 122222100112
Q ss_pred hhhHhhh--hccccCCCCchHHHHHHHhCceEEEe
Q 021811 77 KERFVKR--RQHLVGPNSSTLKALEILTGCYILVQ 109 (307)
Q Consensus 77 ke~f~Rr--rgRIIG~~GkTkkaIE~LT~~yI~V~ 109 (307)
+|..... =|.+||++|.|++-|=.-||-.-.|.
T Consensus 95 ~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~ 129 (630)
T TIGR03675 95 GEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVV 129 (630)
T ss_pred ceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEE
Confidence 3443333 58999999999999988898777663
No 120
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=20.94 E-value=80 Score=31.69 Aligned_cols=30 Identities=17% Similarity=0.242 Sum_probs=26.2
Q ss_pred hhccccCCCCchHHHHHHHhCceEEEeCce
Q 021811 83 RRQHLVGPNSSTLKALEILTGCYILVQGNT 112 (307)
Q Consensus 83 rrgRIIG~~GkTkkaIE~LT~~yI~V~G~T 112 (307)
-.+.-||++|++.+-.-.|||++|-|...+
T Consensus 313 ~~~~AIGk~G~Nv~la~~L~~~~idi~s~~ 342 (362)
T PRK12327 313 QLSLAIGKEGQNARLAARLTGWKIDIKSES 342 (362)
T ss_pred hcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence 467889999999999999999999887644
No 121
>PRK00089 era GTPase Era; Reviewed
Probab=20.80 E-value=75 Score=29.34 Aligned_cols=27 Identities=22% Similarity=0.474 Sum_probs=20.9
Q ss_pred hhccccCCCCchHHH--------HHHHhCceEEEe
Q 021811 83 RRQHLVGPNSSTLKA--------LEILTGCYILVQ 109 (307)
Q Consensus 83 rrgRIIG~~GkTkka--------IE~LT~~yI~V~ 109 (307)
-++=|||.+|++++. ||.+.||.|.+.
T Consensus 237 ~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 237 QKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred ceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 378899999998765 577888877653
No 122
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=20.49 E-value=1.3e+02 Score=28.90 Aligned_cols=46 Identities=24% Similarity=0.293 Sum_probs=33.8
Q ss_pred EEEEEcCCCeEEEEcCCCCCChHHHHhHHH--HHHHHHcCCChHHHHhhhc
Q 021811 12 SCELNLVEGSMTVSTTRKTRDPYIIVKARD--LIRLLSRSVPAPQAIKILD 60 (307)
Q Consensus 12 ~i~lDl~egsV~V~tt~kT~DP~~ilKArD--~IkAIaRGF~~E~AlkLLe 60 (307)
++++|+.++.|.|.|+ .-|-.|+.+-+ =.+|+-||+...+|+.|+.
T Consensus 36 ~vevdle~q~v~v~ts---~p~s~i~~~le~tGr~Avl~G~G~psaval~a 83 (247)
T KOG4656|consen 36 SVEVDLEQQIVSVETS---VPPSEIQNTLENTGRDAVLRGAGKPSAVALLA 83 (247)
T ss_pred eEEEEhhhcEEEEEcc---CChHHHHHHHHhhChheEEecCCchhHHHHHH
Confidence 6899999999999984 33444444332 2467888888888888876
No 123
>PRK11901 hypothetical protein; Reviewed
Probab=20.08 E-value=1.1e+02 Score=30.70 Aligned_cols=26 Identities=15% Similarity=0.322 Sum_probs=21.9
Q ss_pred EeCce--EEEecCCCcHHHHHHHHHHHh
Q 021811 108 VQGNT--VAAMGSFKGLKQVRRIVEDCM 133 (307)
Q Consensus 108 V~G~T--VsIIG~~~~IkiAR~aIedlI 133 (307)
.+|+. |.+.|.|.....|+.||..|=
T Consensus 278 RnGkpWYVVvyG~Y~Sr~eAk~Ai~sLP 305 (327)
T PRK11901 278 RDGKPWYVLVSGNYASSAEAKRAIATLP 305 (327)
T ss_pred ECCceEEEEEecCcCCHHHHHHHHHhCC
Confidence 34554 899999999999999999773
No 124
>PLN02688 pyrroline-5-carboxylate reductase
Probab=20.03 E-value=31 Score=31.36 Aligned_cols=55 Identities=9% Similarity=0.191 Sum_probs=41.2
Q ss_pred HHHcCCChHHHHhhhccCceeEEEEcCc-cccChhhHhhhhccccCCCCchHHHHHHHhC
Q 021811 45 LLSRSVPAPQAIKILDDEMQCDIIKIGN-LVRNKERFVKRRQHLVGPNSSTLKALEILTG 103 (307)
Q Consensus 45 AIaRGF~~E~AlkLLeDd~~~dIIdI~~-~~~nke~f~RrrgRIIG~~GkTkkaIE~LT~ 103 (307)
+...|+++++|..++.+-.. .-.. +..++.++...+.++.-|+|.|...|+.|-.
T Consensus 187 ~~~~Gl~~~~a~~~~~~~~~----gs~~l~~~~~~~~~~l~~~v~spgG~t~~~l~~l~~ 242 (266)
T PLN02688 187 GVAAGLPRDVALSLAAQTVL----GAAKMVLETGKHPGQLKDMVTSPGGTTIAGVHELEK 242 (266)
T ss_pred HHHcCCCHHHHHHHHHHHHH----HHHHHHHhcCCCHHHHHHhCCCCchHHHHHHHHHHH
Confidence 56689999999999976421 0001 1124578888999999999999999998753
Done!