Query 019435
Match_columns 341
No_of_seqs 245 out of 465
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 09:26:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019435.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019435hhsearch_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 1E-108 2E-113 780.7 18.5 298 11-312 18-354 (356)
2 COG1094 Predicted RNA-binding 100.0 5.6E-44 1.2E-48 324.2 10.4 134 45-178 3-138 (194)
3 KOG3273 Predicted RNA-binding 100.0 7.5E-34 1.6E-38 260.8 8.2 130 49-178 73-205 (252)
4 PRK13763 putative RNA-processi 100.0 1.5E-28 3.2E-33 219.5 11.1 125 53-178 6-131 (180)
5 TIGR03665 arCOG04150 arCOG0415 99.9 1.9E-27 4.2E-32 210.8 10.6 123 54-178 2-125 (172)
6 cd02395 SF1_like-KH Splicing f 96.8 0.00036 7.9E-09 59.8 0.7 27 152-178 16-42 (120)
7 PF13014 KH_3: KH domain 96.4 0.0012 2.6E-08 46.2 0.7 26 153-178 2-27 (43)
8 cd02393 PNPase_KH Polynucleoti 96.0 0.0024 5.1E-08 48.2 0.7 27 152-178 12-38 (61)
9 KOG1588 RNA-binding protein Sa 95.7 0.0038 8.2E-08 60.3 0.7 26 153-178 109-134 (259)
10 cd00105 KH-I K homology RNA-bi 95.6 0.0046 1E-07 44.9 0.7 27 152-178 10-36 (64)
11 TIGR03319 YmdA_YtgF conserved 95.5 0.0049 1.1E-07 64.0 0.9 27 152-178 215-241 (514)
12 smart00322 KH K homology RNA-b 95.4 0.0058 1.3E-07 43.4 0.8 28 151-178 12-39 (69)
13 PF00013 KH_1: KH domain syndr 95.4 0.0032 6.9E-08 46.1 -0.6 26 152-177 10-35 (60)
14 cd02394 vigilin_like_KH K homo 95.1 0.009 1.9E-07 44.0 1.1 28 151-178 9-36 (62)
15 KOG2193 IGF-II mRNA-binding pr 94.9 0.037 7.9E-07 57.3 5.0 108 51-178 412-529 (584)
16 PRK12704 phosphodiesterase; Pr 94.9 0.0099 2.1E-07 61.9 0.9 27 152-178 221-247 (520)
17 PRK00106 hypothetical protein; 94.5 0.014 3E-07 61.3 0.9 27 152-178 236-262 (535)
18 PRK13763 putative RNA-processi 94.3 0.093 2E-06 47.5 5.6 66 60-132 105-171 (180)
19 PF13083 KH_4: KH domain; PDB: 94.2 0.013 2.7E-07 45.2 -0.1 23 153-175 40-62 (73)
20 cd02396 PCBP_like_KH K homolog 93.6 0.025 5.4E-07 42.6 0.6 27 152-178 10-36 (65)
21 KOG1676 K-homology type RNA bi 93.6 0.061 1.3E-06 57.1 3.6 116 52-178 141-266 (600)
22 PRK12705 hypothetical protein; 92.8 0.041 8.8E-07 57.6 0.9 27 152-178 209-235 (508)
23 cd02414 jag_KH jag_K homology 92.6 0.065 1.4E-06 41.9 1.6 23 153-175 35-57 (77)
24 KOG2193 IGF-II mRNA-binding pr 92.2 0.077 1.7E-06 55.0 1.9 82 79-178 227-316 (584)
25 COG5176 MSL5 Splicing factor ( 92.0 0.077 1.7E-06 50.8 1.5 48 152-200 164-254 (269)
26 COG1847 Jag Predicted RNA-bind 88.4 0.22 4.8E-06 47.0 1.3 23 153-175 102-124 (208)
27 PRK01064 hypothetical protein; 87.7 0.29 6.2E-06 39.6 1.4 21 153-173 41-61 (78)
28 cd02134 NusA_KH NusA_K homolog 87.5 0.25 5.5E-06 37.3 0.9 26 152-177 35-60 (61)
29 PRK02821 hypothetical protein; 87.4 0.28 6.1E-06 39.6 1.2 55 109-170 3-59 (77)
30 PRK00468 hypothetical protein; 87.4 0.31 6.7E-06 39.0 1.4 18 153-170 41-58 (75)
31 TIGR03665 arCOG04150 arCOG0415 87.4 0.19 4.2E-06 45.1 0.2 27 152-178 8-34 (172)
32 cd02393 PNPase_KH Polynucleoti 87.2 1 2.2E-05 34.0 4.0 55 53-112 5-60 (61)
33 cd02409 KH-II KH-II (K homolo 86.4 0.4 8.8E-06 34.6 1.5 23 153-175 36-58 (68)
34 COG1837 Predicted RNA-binding 85.2 0.42 9.2E-06 38.7 1.2 18 153-170 41-58 (76)
35 TIGR03591 polynuc_phos polyrib 80.8 0.58 1.3E-05 50.5 0.4 27 152-178 561-587 (684)
36 PF00013 KH_1: KH domain syndr 80.1 8.4 0.00018 28.0 6.3 55 53-112 3-60 (60)
37 KOG0119 Splicing factor 1/bran 79.1 0.68 1.5E-05 48.8 0.3 26 153-178 155-180 (554)
38 TIGR02696 pppGpp_PNP guanosine 74.7 8 0.00017 42.6 6.8 82 51-142 579-661 (719)
39 cd00105 KH-I K homology RNA-bi 74.2 5.5 0.00012 28.6 3.9 56 52-112 2-63 (64)
40 cd02394 vigilin_like_KH K homo 68.2 11 0.00023 27.6 4.3 55 53-112 3-61 (62)
41 TIGR02696 pppGpp_PNP guanosine 67.0 2.2 4.7E-05 46.8 0.6 27 152-178 588-614 (719)
42 KOG2191 RNA-binding protein NO 61.9 27 0.00059 35.8 7.1 135 50-194 39-210 (402)
43 cd02396 PCBP_like_KH K homolog 60.2 13 0.00028 27.8 3.6 57 51-112 1-64 (65)
44 PRK08406 transcription elongat 59.5 5.1 0.00011 35.3 1.4 25 153-177 110-134 (140)
45 PRK04163 exosome complex RNA-b 58.6 3.4 7.5E-05 38.9 0.2 26 153-178 156-181 (235)
46 TIGR00112 proC pyrroline-5-car 57.8 8.5 0.00018 35.9 2.6 99 68-172 124-225 (245)
47 KOG2814 Transcription coactiva 57.6 4.5 9.7E-05 41.0 0.8 27 152-178 67-93 (345)
48 PF05598 DUF772: Transposase d 57.6 13 0.00028 28.2 3.2 61 97-160 2-67 (77)
49 KOG1676 K-homology type RNA bi 56.5 10 0.00022 40.9 3.3 111 56-178 60-175 (600)
50 TIGR03591 polynuc_phos polyrib 48.0 69 0.0015 35.0 7.9 78 53-142 554-632 (684)
51 smart00322 KH K homology RNA-b 45.5 58 0.0013 22.5 4.8 60 51-115 4-67 (69)
52 PRK07680 late competence prote 45.0 23 0.0005 33.1 3.4 97 69-172 142-243 (273)
53 cd01104 HTH_MlrA-CarA Helix-Tu 43.5 45 0.00097 24.4 4.1 32 98-129 37-68 (68)
54 KOG2190 PolyC-binding proteins 42.2 35 0.00076 36.0 4.5 125 49-178 137-292 (485)
55 COG1097 RRP4 RNA-binding prote 40.3 11 0.00023 36.7 0.4 72 104-178 90-182 (239)
56 PF00403 HMA: Heavy-metal-asso 40.2 1E+02 0.0023 22.1 5.6 31 67-97 12-44 (62)
57 PF07650 KH_2: KH domain syndr 39.6 11 0.00023 29.1 0.2 24 152-175 35-58 (78)
58 PRK04163 exosome complex RNA-b 38.7 82 0.0018 29.7 6.0 67 45-117 141-208 (235)
59 PLN00207 polyribonucleotide nu 38.7 13 0.00029 41.9 0.8 27 152-178 695-722 (891)
60 COG1185 Pnp Polyribonucleotide 38.0 44 0.00094 37.0 4.5 64 54-122 556-620 (692)
61 PF14748 P5CR_dimer: Pyrroline 37.6 9.1 0.0002 31.8 -0.5 56 114-173 31-87 (107)
62 PF15232 DUF4585: Domain of un 36.7 12 0.00026 30.6 0.1 24 226-249 2-25 (75)
63 PRK06928 pyrroline-5-carboxyla 36.6 55 0.0012 31.0 4.5 96 70-171 146-245 (277)
64 cd02410 archeal_CPSF_KH The ar 35.8 1.3E+02 0.0028 27.3 6.5 91 84-178 4-112 (145)
65 COG1159 Era GTPase [General fu 35.3 29 0.00062 34.7 2.5 53 122-177 198-273 (298)
66 cd04764 HTH_MlrA-like_sg1 Heli 34.9 66 0.0014 23.8 3.9 32 98-129 36-67 (67)
67 PRK08406 transcription elongat 34.8 27 0.00059 30.8 2.0 26 153-178 43-68 (140)
68 PRK11824 polynucleotide phosph 34.8 18 0.00038 39.5 1.0 26 153-178 565-590 (693)
69 PRK15494 era GTPase Era; Provi 33.1 30 0.00065 34.0 2.2 27 152-178 284-318 (339)
70 cd02395 SF1_like-KH Splicing f 29.9 1.9E+02 0.0042 24.9 6.4 52 67-122 23-99 (120)
71 cd04763 HTH_MlrA-like Helix-Tu 28.6 1.2E+02 0.0026 22.6 4.3 34 96-129 35-68 (68)
72 COG1782 Predicted metal-depend 28.2 1.8E+02 0.004 31.8 7.0 113 62-178 5-135 (637)
73 KOG2190 PolyC-binding proteins 28.1 23 0.00051 37.3 0.5 118 48-178 254-374 (485)
74 TIGR00436 era GTP-binding prot 26.9 27 0.00058 32.7 0.7 25 152-176 232-264 (270)
75 KOG4656 Copper chaperone for s 25.5 73 0.0016 31.0 3.3 72 49-129 8-83 (247)
76 COG1094 Predicted RNA-binding 25.3 27 0.00058 33.0 0.4 27 152-178 18-44 (194)
77 PRK14634 hypothetical protein; 25.0 3.2E+02 0.007 24.5 7.1 89 64-156 6-102 (155)
78 PRK00089 era GTPase Era; Revie 23.5 32 0.0007 32.2 0.6 26 153-178 238-271 (292)
79 smart00422 HTH_MERR helix_turn 23.3 1.4E+02 0.003 21.8 3.8 31 99-129 38-68 (70)
80 PRK07634 pyrroline-5-carboxyla 23.1 78 0.0017 28.7 2.9 95 68-170 146-244 (245)
81 TIGR03675 arCOG00543 arCOG0054 23.1 1.8E+02 0.0039 31.6 6.0 92 83-178 20-129 (630)
82 PF13812 PPR_3: Pentatricopept 23.0 73 0.0016 19.6 2.0 21 110-130 6-26 (34)
83 COG0134 TrpC Indole-3-glycerol 22.9 55 0.0012 32.0 2.0 69 98-170 115-193 (254)
84 PRK10076 pyruvate formate lyas 22.6 1.7E+02 0.0037 27.2 5.1 84 85-177 36-130 (213)
85 PTZ00431 pyrroline carboxylate 22.3 1.3E+02 0.0028 28.2 4.3 97 70-172 139-238 (260)
86 cd01105 HTH_GlnR-like Helix-Tu 21.7 1.3E+02 0.0029 23.9 3.7 33 98-130 38-70 (88)
87 cd02412 30S_S3_KH K homology R 20.6 58 0.0013 27.2 1.4 19 153-171 72-90 (109)
88 KOG1560 Translation initiation 20.2 15 0.00032 36.9 -2.5 86 130-243 211-310 (339)
No 1
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=9.7e-109 Score=780.72 Aligned_cols=298 Identities=66% Similarity=1.028 Sum_probs=279.0
Q ss_pred cccCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCcceeeeeeeecCchhHHHHHHhhhhHHHHHhhcccEEEEEcccCe
Q 019435 11 KKHKGKHDKPKPWDEDPNIDHWKVEKFDPFWNEGGMLEVSSFSTLFPQYREKYLQEAWPMVKGALKEYGVSCELNLVEGS 90 (341)
Q Consensus 11 ~~~~~~~~~~kpwd~~~~id~wk~~~f~~edn~~g~~eessF~vlfPkyRe~yLKe~W~~Ikk~Le~~~l~i~LDl~eGs 90 (341)
.+++.+|..++|||++++||+|+++.|+.+|||+||+|+|||+||||+||++||+++|+.|.++|++|+|.|.|||.+|+
T Consensus 18 ~~~k~~~e~~k~~~~~~~~d~wki~~Fs~edn~~g~~EeSSfatlFPKYREkYlke~wp~v~raL~e~~i~c~lDL~egs 97 (356)
T KOG2874|consen 18 ENKKPKPETDKPWDPDDNIDMWKIEKFSKEDNPHGFLEESSFATLFPKYREKYLKECWPLVERALDEHHIKCVLDLVEGS 97 (356)
T ss_pred hhcccccccCCCCCCCCcchhhcccccCcccCccchhhhhhHHhhhHHHHHHHHHHHHHHHHHHHHhcCcceEEeeccce
Confidence 35677899999999998899999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHHhhcccceeEEEeecccccCchhhhhhhccccCCCCchhHHHHHh
Q 019435 91 MTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEMQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEIL 170 (341)
Q Consensus 91 V~VrTt~kT~DP~~IiKArD~IkAIaRGF~~EqAlkLLeDD~~~DIIdI~~lv~nke~f~RrrgRIIG~~GkTkkaIE~L 170 (341)
|+|+||++|||||+|++|||||++++||||++||++||+||++||||+|+++|+|+++|++||+||||+||.|++|||+|
T Consensus 98 m~V~TtRkT~DPyIiikArdlIKLlaRsVp~eqAvkiLqDev~CdiIkIgn~V~nkerFvKRRqRLiGpng~TLKAlelL 177 (356)
T KOG2874|consen 98 MTVKTTRKTRDPYIIIKARDLIKLLARSVPFEQAVKILQDEVACDIIKIGNLVRNKERFVKRRQRLIGPNGSTLKALELL 177 (356)
T ss_pred eEEeecccccCceeeeeHHHHHHHHHcCCCHHHHHHHHhhccceeeeehhhhhccHHHHHHHHHHhcCCCchhHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcchhhHH----------------------------------HHHHHhhhhcCccccccCcccccccccccccccccccc
Q 019435 171 TGCYILVQ----------------------------------ILMVKKELEKDPALANENWDRFLPKFKKKNVKQKKVKS 216 (341)
Q Consensus 171 T~~yI~Vq----------------------------------~LmiKreL~kd~~l~~e~W~rflP~fkkk~~~~~k~~~ 216 (341)
|+|||+|| +|||||||++||+|+|||||||||+|+++|++++|+++
T Consensus 178 T~CYilVqG~TVsaiGpfkGlkevr~IV~DcM~NiHPiY~IK~LmiKRel~kd~~l~ne~W~rfLP~fkkknv~k~K~~K 257 (356)
T KOG2874|consen 178 TNCYILVQGNTVSAIGPFKGLKEVRKIVEDCMKNIHPIYNIKTLMIKRELAKDPELANEDWSRFLPQFKKKNVKKRKPKK 257 (356)
T ss_pred hhcEEEeeCcEEEeecCcchHHHHHHHHHHHHhccchHHHHHHHHHHHHhhcChhhccccHHHHhHHhhhhhhhhccccc
Confidence 99999999 99999999999999999999999999999999999866
Q ss_pred -ccCCCCCCCCCCCCCchhhhhhhccccccChhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCC----Cchh
Q 019435 217 -KEKKPYTPFPPPPQPSKIDKLLESGEYFLSERKKESKKWQEKQEKQAEKTAENKRKRDAAFIPPEEPSRQN----SCEA 291 (341)
Q Consensus 217 -~~kk~ytpfpp~~~~~k~D~~lesGeyFl~~~~k~~~~~~~~~~kq~~~~~~~~~~r~~~~~~p~e~~~~~----~~~~ 291 (341)
+.||+||||||+|++||||+|||||||||+++++++++++|+.++|+++..+++++|+++|+||+|.+... ...+
T Consensus 258 ~~~kk~ytpfPp~q~~sKiD~eleSGEYFl~~~~k~~kK~~e~~Ekq~e~~~er~~~r~k~fi~peE~~~~~~~~~~~~~ 337 (356)
T KOG2874|consen 258 VKGKKEYTPFPPAQPPSKIDKELESGEYFLRDEEKSRKKMQEKKEKQAEKRKERQEERMKAFIPPEEESRKPSNKKKEAS 337 (356)
T ss_pred ccCCCCCCCCCCCcCcchhhhhhhcchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCccccccccccCCCCC
Confidence 45899999999999999999999999999999999999999999999999999999999999999987644 3334
Q ss_pred hcccchHHHHHHHHHHHHHHH
Q 019435 292 EDKTNDVAAMAKSLKEKAKKL 312 (341)
Q Consensus 292 ~~~~~~~~~~~~~~k~k~~~~ 312 (341)
+..++|+.. ++.|++++
T Consensus 338 ~~~~i~~~~----~k~k~~ka 354 (356)
T KOG2874|consen 338 TETKIDVLS----IKAKLKKA 354 (356)
T ss_pred CcchHHHHH----HHHhhhhc
Confidence 444444433 45665554
No 2
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=100.00 E-value=5.6e-44 Score=324.17 Aligned_cols=134 Identities=33% Similarity=0.550 Sum_probs=128.7
Q ss_pred CcceeeeeeeecCchhHHHHHHhhhhHHHHHh-hcccEEEEEcccCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHH
Q 019435 45 GMLEVSSFSTLFPQYREKYLQEAWPMVKGALK-EYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQ 123 (341)
Q Consensus 45 g~~eessF~vlfPkyRe~yLKe~W~~Ikk~Le-~~~l~i~LDl~eGsV~VrTt~kT~DP~~IiKArD~IkAIaRGF~~Eq 123 (341)
++.+.++++|.||+||++||+..|+.|+++|+ .++++|+||+.+|+|+|+||++|.||+++++|+|||+||+|||+||+
T Consensus 3 ~~~~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~ 82 (194)
T COG1094 3 EFAEKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEK 82 (194)
T ss_pred cccccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHH
Confidence 46788899999999999999999999999995 57799999999999999999999999999999999999999999999
Q ss_pred HHHhhcccceeEEEeeccccc-CchhhhhhhccccCCCCchhHHHHHhhcchhhHH
Q 019435 124 AIKILDDEMQCDIIKIGNLVR-NKERFVKRRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 124 AlkLLeDD~~~DIIdI~~lv~-nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
|++||+||++||||||+++++ +++||.|++|||||++|+|+++||+||||||+||
T Consensus 83 A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~ 138 (194)
T COG1094 83 ALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY 138 (194)
T ss_pred HHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe
Confidence 999999999999999999997 5567999999999999999999999999999999
No 3
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.5e-34 Score=260.83 Aligned_cols=130 Identities=19% Similarity=0.319 Sum_probs=122.8
Q ss_pred eeeeeeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEcccCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHHh
Q 019435 49 VSSFSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKI 127 (341)
Q Consensus 49 essF~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~eGsV~VrTt~kT~DP~~IiKArD~IkAIaRGF~~EqAlkL 127 (341)
..+.+|++|+||+++|+++|+.||.+| ++++++|+||+...+|+++||..|.||..++|+.|||+||..||+++||++|
T Consensus 73 ~e~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmNlK~r~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DAiAL 152 (252)
T KOG3273|consen 73 IETRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMNLKARSVELRTCKDTEDPSALQKGADFVRAFILGFDIDDAIAL 152 (252)
T ss_pred cceeeccCCcccCChHHHhhHhhhhHHHHhhhheeEeecccceeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhHHHH
Confidence 334589999999999999999999999 8999999999999999999999999999999999999999999999999999
Q ss_pred hc-ccceeEEEeeccccc-CchhhhhhhccccCCCCchhHHHHHhhcchhhHH
Q 019435 128 LD-DEMQCDIIKIGNLVR-NKERFVKRRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 128 Le-DD~~~DIIdI~~lv~-nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
|+ ||+|+|.+.|+++.. .++|++|++|||+|++|+|++|||+.|.|+|+|+
T Consensus 153 lrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla 205 (252)
T KOG3273|consen 153 LRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA 205 (252)
T ss_pred HhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEec
Confidence 98 999977777777653 6799999999999999999999999999999998
No 4
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.95 E-value=1.5e-28 Score=219.50 Aligned_cols=125 Identities=23% Similarity=0.395 Sum_probs=121.5
Q ss_pred eeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEcccCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHHhhccc
Q 019435 53 STLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDE 131 (341)
Q Consensus 53 ~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~eGsV~VrTt~kT~DP~~IiKArD~IkAIaRGF~~EqAlkLLeDD 131 (341)
.+.||++|..+|...|+.+.+.| +++|++|.+|..+|.|.|.||. |.||+++++|++||.||++||+|++|++++.|+
T Consensus 6 ~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~~-~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~gd~ 84 (180)
T PRK13763 6 YVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTD-GEDPLAVLKARDIVKAIGRGFSPEKALRLLDDD 84 (180)
T ss_pred EEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeCC-CCCHHHHHHHHHHHHHHhcCCCHHHHHHHhCCC
Confidence 57899999999999999999999 6899999999999999999998 999999999999999999999999999999999
Q ss_pred ceeEEEeecccccCchhhhhhhccccCCCCchhHHHHHhhcchhhHH
Q 019435 132 MQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 132 ~~~DIIdI~~lv~nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
|+++||+|.++..+++||.|++|||||++|+|+++||++|||+|.|+
T Consensus 85 y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~ 131 (180)
T PRK13763 85 YVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY 131 (180)
T ss_pred ceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc
Confidence 99999999999888999999999999999999999999999999998
No 5
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=99.94 E-value=1.9e-27 Score=210.80 Aligned_cols=123 Identities=22% Similarity=0.403 Sum_probs=118.7
Q ss_pred eecCchhHHHHHHhhhhHHHHH-hhcccEEEEEcccCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHHhhcccc
Q 019435 54 TLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEM 132 (341)
Q Consensus 54 vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~eGsV~VrTt~kT~DP~~IiKArD~IkAIaRGF~~EqAlkLLeDD~ 132 (341)
+.||++|...|...|+.+.+.| ++++++|+||..+|.|.|+ ..|.||+++++|++||.||++||+|++|++||.|++
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~V~I~--~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~gd~y 79 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIE--EEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDY 79 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEe--cCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcCCcc
Confidence 5689999999999999999999 6899999999999999997 568999999999999999999999999999999999
Q ss_pred eeEEEeecccccCchhhhhhhccccCCCCchhHHHHHhhcchhhHH
Q 019435 133 QCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 133 ~~DIIdI~~lv~nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
+|+||+|.++.++++||.+++|||||++|+|+++||.+|||+|+|+
T Consensus 80 ~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~ 125 (172)
T TIGR03665 80 MLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY 125 (172)
T ss_pred eEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc
Confidence 9999999999889999999999999999999999999999999998
No 6
>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=96.83 E-value=0.00036 Score=59.79 Aligned_cols=27 Identities=37% Similarity=0.476 Sum_probs=25.6
Q ss_pred hhccccCCCCchhHHHHHhhcchhhHH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
.+||||||+|+|.+.||.-|||.|.|.
T Consensus 16 ~IG~IIGPgG~tiK~i~~eTg~kI~Ir 42 (120)
T cd02395 16 FVGLILGPRGNTLKQLEKETGAKISIR 42 (120)
T ss_pred eeEEEECCCChHHHHHHHHHCCEEEEe
Confidence 579999999999999999999999986
No 7
>PF13014 KH_3: KH domain
Probab=96.38 E-value=0.0012 Score=46.18 Aligned_cols=26 Identities=27% Similarity=0.405 Sum_probs=24.0
Q ss_pred hccccCCCCchhHHHHHhhcchhhHH
Q 019435 153 RQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
-|+|||++|.|.+.|+..|+|+|.|.
T Consensus 2 vg~iIG~~G~~I~~I~~~tg~~I~i~ 27 (43)
T PF13014_consen 2 VGRIIGKGGSTIKEIREETGAKIQIP 27 (43)
T ss_pred cCeEECCCChHHHHHHHHhCcEEEEC
Confidence 37999999999999999999999875
No 8
>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=96.01 E-value=0.0024 Score=48.24 Aligned_cols=27 Identities=26% Similarity=0.454 Sum_probs=24.9
Q ss_pred hhccccCCCCchhHHHHHhhcchhhHH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
.+|+|||++|+|.+.|+.-|||.|.|.
T Consensus 12 ~ig~iIGkgG~~ik~I~~~tg~~I~i~ 38 (61)
T cd02393 12 KIRDVIGPGGKTIKKIIEETGVKIDIE 38 (61)
T ss_pred heeeeECCCchHHHHHHHHHCCEEEeC
Confidence 569999999999999999999998775
No 9
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=95.66 E-value=0.0038 Score=60.28 Aligned_cols=26 Identities=38% Similarity=0.745 Sum_probs=25.1
Q ss_pred hccccCCCCchhHHHHHhhcchhhHH
Q 019435 153 RQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
.|||+||.|.|++.||.-|||+|+|-
T Consensus 109 VGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 109 VGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred ccccccCCcchHHHHHHHHCCeEEEe
Confidence 59999999999999999999999997
No 10
>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=95.57 E-value=0.0046 Score=44.95 Aligned_cols=27 Identities=26% Similarity=0.357 Sum_probs=24.9
Q ss_pred hhccccCCCCchhHHHHHhhcchhhHH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
..++|||++|++.+.|+..|||.|.|.
T Consensus 10 ~~~~vIG~~G~~i~~I~~~s~~~I~i~ 36 (64)
T cd00105 10 LVGRIIGKGGSTIKEIREETGAKIKIP 36 (64)
T ss_pred hcceeECCCCHHHHHHHHHHCCEEEEc
Confidence 469999999999999999999999875
No 11
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.49 E-value=0.0049 Score=64.04 Aligned_cols=27 Identities=26% Similarity=0.601 Sum_probs=25.9
Q ss_pred hhccccCCCCchhHHHHHhhcchhhHH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
.+|||||++|+..+++|.+|||.|.|-
T Consensus 215 ~kgriigreGrnir~~e~~tgvd~iid 241 (514)
T TIGR03319 215 MKGRIIGREGRNIRALETLTGVDLIID 241 (514)
T ss_pred hhccccCCCcchHHHHHHHhCceEEEc
Confidence 579999999999999999999999998
No 12
>smart00322 KH K homology RNA-binding domain.
Probab=95.41 E-value=0.0058 Score=43.36 Aligned_cols=28 Identities=29% Similarity=0.383 Sum_probs=25.0
Q ss_pred hhhccccCCCCchhHHHHHhhcchhhHH
Q 019435 151 KRRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 151 RrrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
...|+|||++|.+.+.|+..|||.|.+.
T Consensus 12 ~~~~~liG~~G~~i~~i~~~~~~~i~~~ 39 (69)
T smart00322 12 DKVGLIIGKGGSTIKKIEEETGVKIDIP 39 (69)
T ss_pred hhcceeECCCchHHHHHHHHHCCEEEEC
Confidence 3569999999999999999999998764
No 13
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=95.39 E-value=0.0032 Score=46.13 Aligned_cols=26 Identities=27% Similarity=0.394 Sum_probs=24.5
Q ss_pred hhccccCCCCchhHHHHHhhcchhhH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILV 177 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~V 177 (341)
..|+|||++|++.+.||..|||.|.|
T Consensus 10 ~~~~iIG~~G~~i~~I~~~t~~~I~i 35 (60)
T PF00013_consen 10 LVGRIIGKKGSNIKEIEEETGVKIQI 35 (60)
T ss_dssp HHHHHHTGGGHHHHHHHHHHTSEEEE
T ss_pred HcCEEECCCCCcHHHhhhhcCeEEEE
Confidence 57999999999999999999999877
No 14
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=95.13 E-value=0.009 Score=44.02 Aligned_cols=28 Identities=21% Similarity=0.334 Sum_probs=25.5
Q ss_pred hhhccccCCCCchhHHHHHhhcchhhHH
Q 019435 151 KRRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 151 RrrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
...|+|||++|.+.+.|+.-|||.|.|.
T Consensus 9 ~~~~~iIG~~G~~i~~i~~~~g~~I~i~ 36 (62)
T cd02394 9 KLHRFIIGKKGSNIRKIMEETGVKIRFP 36 (62)
T ss_pred HHhhhccCCCCCcHHHHHHHhCCEEEcC
Confidence 3569999999999999999999999875
No 15
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=94.91 E-value=0.037 Score=57.31 Aligned_cols=108 Identities=17% Similarity=0.149 Sum_probs=75.3
Q ss_pred eeeeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEc------ccCeEEEEcCCCCCChHHHHhHHHHHH--HHHc-CCC
Q 019435 51 SFSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNL------VEGSMTVSTTRKTRDPYIIVKARDLIR--LLSR-SVP 120 (341)
Q Consensus 51 sF~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl------~eGsV~VrTt~kT~DP~~IiKArD~Ik--AIaR-GF~ 120 (341)
...++||..=...|...-+.--+.| ...|..|.|.. .++.|+| |.||.+.+||.--|- .--- .|.
T Consensus 412 ~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViI-----tGppeaqfKAQgrifgKikEenf~~ 486 (584)
T KOG2193|consen 412 QVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVII-----TGPPEAQFKAQGRIFGKIKEENFFL 486 (584)
T ss_pred heeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEe-----cCChHHHHhhhhhhhhhhhhhccCC
Confidence 3457788888888988888777777 56888888754 3555555 589999999985442 1111 222
Q ss_pred hHHHHHhhcccceeEEEeecccccCchhhhhhhccccCCCCchhHHHHHhhcchhhHH
Q 019435 121 APQAIKILDDEMQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 121 ~EqAlkLLeDD~~~DIIdI~~lv~nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
|.. -++|...++ .=+++.|||||++|+|..-|.+||++-|+|-
T Consensus 487 Pke------------evklethir---VPs~~aGRvIGKGGktVnELQnlt~AeV~vP 529 (584)
T KOG2193|consen 487 PKE------------EVKLETHIR---VPSSAAGRVIGKGGKTVNELQNLTSAEVVVP 529 (584)
T ss_pred chh------------hheeeeeee---ccchhhhhhhccccccHHHHhccccceEEcc
Confidence 222 233333333 3356789999999999999999999998886
No 16
>PRK12704 phosphodiesterase; Provisional
Probab=94.85 E-value=0.0099 Score=61.90 Aligned_cols=27 Identities=26% Similarity=0.601 Sum_probs=25.9
Q ss_pred hhccccCCCCchhHHHHHhhcchhhHH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
.+|||||++|+..+++|.+|||.|.|-
T Consensus 221 mkgriigreGrnir~~e~~tgvd~iid 247 (520)
T PRK12704 221 MKGRIIGREGRNIRALETLTGVDLIID 247 (520)
T ss_pred hhcceeCCCcchHHHHHHHhCCeEEEc
Confidence 579999999999999999999999998
No 17
>PRK00106 hypothetical protein; Provisional
Probab=94.47 E-value=0.014 Score=61.32 Aligned_cols=27 Identities=22% Similarity=0.554 Sum_probs=25.9
Q ss_pred hhccccCCCCchhHHHHHhhcchhhHH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
.+|||||++|+..+|+|.+|||.|.|-
T Consensus 236 mkGriIGreGrNir~~E~~tGvdliid 262 (535)
T PRK00106 236 MKGRIIGREGRNIRTLESLTGIDVIID 262 (535)
T ss_pred hhcceeCCCcchHHHHHHHhCceEEEc
Confidence 579999999999999999999999998
No 18
>PRK13763 putative RNA-processing protein; Provisional
Probab=94.26 E-value=0.093 Score=47.53 Aligned_cols=66 Identities=17% Similarity=0.196 Sum_probs=56.7
Q ss_pred hHHHHHHhhhhHHHHHh-hcccEEEEEcccCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHHhhcccc
Q 019435 60 REKYLQEAWPMVKGALK-EYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEM 132 (341)
Q Consensus 60 Re~yLKe~W~~Ikk~Le-~~~l~i~LDl~eGsV~VrTt~kT~DP~~IiKArD~IkAIaRGF~~EqAlkLLeDD~ 132 (341)
+...|-.--+.+.+.|+ .+++.+.++- ..|.|. .||..+..|++.|.+|.+|++++.|+++|+++.
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~--~~v~i~-----G~~~~~~~A~~~I~~li~g~~~~~~~~~l~~~~ 171 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYG--KTVAII-----GDPEQVEIAREAIEMLIEGAPHGTVYKFLERKK 171 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcC--CEEEEE-----eCHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHH
Confidence 56777888889999995 6999988874 557764 699999999999999999999999999999763
No 19
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=94.21 E-value=0.013 Score=45.17 Aligned_cols=23 Identities=30% Similarity=0.442 Sum_probs=20.8
Q ss_pred hccccCCCCchhHHHHHhhcchh
Q 019435 153 RQHLVGPNSSTLKALEILTGCYI 175 (341)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~yI 175 (341)
-|||||++|+|+.||+.|++.++
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~~~~ 62 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVNAAA 62 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHHHHH
T ss_pred cceEECCCCeeHHHHHHHHHHHH
Confidence 49999999999999999987765
No 20
>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=93.65 E-value=0.025 Score=42.60 Aligned_cols=27 Identities=30% Similarity=0.417 Sum_probs=25.0
Q ss_pred hhccccCCCCchhHHHHHhhcchhhHH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
..|+|||++|.+.+.|+..|||.|.|.
T Consensus 10 ~vg~iIG~~G~~i~~i~~~tga~I~i~ 36 (65)
T cd02396 10 QAGSIIGKGGSTIKEIREETGAKIRVS 36 (65)
T ss_pred HcCeeECCCcHHHHHHHHHHCCEEEEc
Confidence 479999999999999999999999874
No 21
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=93.61 E-value=0.061 Score=57.14 Aligned_cols=116 Identities=19% Similarity=0.172 Sum_probs=82.1
Q ss_pred eeeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEcccCeE--EEEcCCCCCChHHHHhHHHHHHHHHcC----CChHHH
Q 019435 52 FSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSM--TVSTTRKTRDPYIIVKARDLIRLLSRS----VPAPQA 124 (341)
Q Consensus 52 F~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~eGsV--~VrTt~kT~DP~~IiKArD~IkAIaRG----F~~EqA 124 (341)
-.++||..|...|...-+..-+-| +..++.|.|.-+.... .+++-+.|.||+.+..|+.||.=|.+- .+.+.
T Consensus 141 qeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~g~~- 219 (600)
T KOG1676|consen 141 QEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEVPGSG- 219 (600)
T ss_pred eeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCCCccc-
Confidence 478999999999999999999999 7788888877654433 356667799999999999998876661 11110
Q ss_pred HHhhc-ccceeEE--EeecccccCchhhhhhhccccCCCCchhHHHHHhhcchhhHH
Q 019435 125 IKILD-DEMQCDI--IKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 125 lkLLe-DD~~~DI--IdI~~lv~nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
--.. +...-.- |+|-.+ .-|=|||++|.|.|-|.+-||++|-+-
T Consensus 220 -~~~g~~~g~~~~~~V~VPr~---------~VG~IIGkgGE~IKklq~etG~KIQfk 266 (600)
T KOG1676|consen 220 -GHAGVRGGGSATREVKVPRS---------KVGIIIGKGGEMIKKLQNETGAKIQFK 266 (600)
T ss_pred -cccCcCccccceeEEecccc---------ceeeEEecCchHHHHHhhccCceeEee
Confidence 0000 1111111 112111 248899999999999999999998776
No 22
>PRK12705 hypothetical protein; Provisional
Probab=92.81 E-value=0.041 Score=57.59 Aligned_cols=27 Identities=22% Similarity=0.528 Sum_probs=25.8
Q ss_pred hhccccCCCCchhHHHHHhhcchhhHH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
.+|||||++|+..+++|.+||+.|.|-
T Consensus 209 mkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 209 MKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred hhccccCccchhHHHHHHhhCCceEec
Confidence 689999999999999999999999887
No 23
>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=92.65 E-value=0.065 Score=41.93 Aligned_cols=23 Identities=30% Similarity=0.410 Sum_probs=20.1
Q ss_pred hccccCCCCchhHHHHHhhcchh
Q 019435 153 RQHLVGPNSSTLKALEILTGCYI 175 (341)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~yI 175 (341)
-|+|||++|+|+.||+-|++..+
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~~~ 57 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANLVL 57 (77)
T ss_pred CCeEECCCCccHHHHHHHHHHHH
Confidence 39999999999999999987543
No 24
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=92.17 E-value=0.077 Score=55.02 Aligned_cols=82 Identities=26% Similarity=0.342 Sum_probs=49.7
Q ss_pred ccEEEEEcc--------cCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHHhhcccceeEEEeecccccCchhhh
Q 019435 79 GVSCELNLV--------EGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEMQCDIIKIGNLVRNKERFV 150 (341)
Q Consensus 79 ~l~i~LDl~--------eGsV~VrTt~kT~DP~~IiKArD~IkAIaRGF~~EqAlkLLeDD~~~DIIdI~~lv~nke~f~ 150 (341)
.++|++|.. +..|+|-.|.+. .-+|..+|--|.-. +|. +|++. +=|-|+-+.-| .
T Consensus 227 qTqsriD~hrken~Gaaek~itvh~tpEg-----~s~Ac~~ILeimqk----EA~---~~k~~-~e~pLk~lAHN--~-- 289 (584)
T KOG2193|consen 227 QTQSRIDVHRKENAGAAEKIITVHSTPEG-----TSKACKMILEIMQK----EAV---DDKVA-EEIPLKILAHN--N-- 289 (584)
T ss_pred hhhheeeeeecccCCcccCceEEecCccc-----hHHHHHHHHHHHHH----hhh---ccchh-hhcchhhhhhc--c--
Confidence 345555554 677899876653 23444443322221 111 12222 33445544333 2
Q ss_pred hhhccccCCCCchhHHHHHhhcchhhHH
Q 019435 151 KRRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 151 RrrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
.-|||||+.|+.++-||--|||.|.|.
T Consensus 290 -lvGRLIGKeGrnlKkIeq~TgTkITis 316 (584)
T KOG2193|consen 290 -LVGRLIGKEGRNLKKIEQDTGTKITIS 316 (584)
T ss_pred -hhhhhhhhccccHHHHHhhcCCceeee
Confidence 359999999999999999999999887
No 25
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=91.99 E-value=0.077 Score=50.76 Aligned_cols=48 Identities=31% Similarity=0.464 Sum_probs=41.8
Q ss_pred hhccccCCCCchhHHHHHhhcchhhHH-------------------------------------------HHHHHhhhhc
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILVQ-------------------------------------------ILMVKKELEK 188 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~Vq-------------------------------------------~LmiKreL~k 188 (341)
-.|=||||-|+|++.+|..|+|+|.|- .|-+-||...
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 359999999999999999999999887 5556789999
Q ss_pred CccccccCcccc
Q 019435 189 DPALANENWDRF 200 (341)
Q Consensus 189 d~~l~~e~W~rf 200 (341)
+|+= --||.||
T Consensus 244 ~PeG-qnDlkR~ 254 (269)
T COG5176 244 NPEG-QNDLKRF 254 (269)
T ss_pred CCcc-cchHHHH
Confidence 9997 5689987
No 26
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=88.40 E-value=0.22 Score=47.00 Aligned_cols=23 Identities=35% Similarity=0.613 Sum_probs=21.3
Q ss_pred hccccCCCCchhHHHHHhhcchh
Q 019435 153 RQHLVGPNSSTLKALEILTGCYI 175 (341)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~yI 175 (341)
-|||||.+|+|+.||+.|++.++
T Consensus 102 ~~~LIG~~Gk~LdALQ~L~n~~l 124 (208)
T COG1847 102 AGRLIGKHGKTLDALQYLANLYL 124 (208)
T ss_pred hhhhhccCCcchHHHHHHHHHHh
Confidence 69999999999999999998774
No 27
>PRK01064 hypothetical protein; Provisional
Probab=87.73 E-value=0.29 Score=39.56 Aligned_cols=21 Identities=24% Similarity=0.370 Sum_probs=18.3
Q ss_pred hccccCCCCchhHHHHHhhcc
Q 019435 153 RQHLVGPNSSTLKALEILTGC 173 (341)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~ 173 (341)
.||+||++|+|..+|-.+.++
T Consensus 41 ~g~vIGk~G~~i~air~l~~~ 61 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLVS 61 (78)
T ss_pred ceEEECCCCccHHHHHHHHHH
Confidence 599999999999999887543
No 28
>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=87.52 E-value=0.25 Score=37.30 Aligned_cols=26 Identities=15% Similarity=0.172 Sum_probs=23.5
Q ss_pred hhccccCCCCchhHHHHHhhcchhhH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILV 177 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~V 177 (341)
-.|+.||++|++-+.++.++|.+|-|
T Consensus 35 ~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 35 QLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cceeeECCCCHHHHHHHHHHCCCeEE
Confidence 46999999999999999999988865
No 29
>PRK02821 hypothetical protein; Provisional
Probab=87.41 E-value=0.28 Score=39.56 Aligned_cols=55 Identities=15% Similarity=0.306 Sum_probs=31.1
Q ss_pred HHHHHHHHcCCC-hHHHHHhhcc-cceeEEEeecccccCchhhhhhhccccCCCCchhHHHHHh
Q 019435 109 RDLIRLLSRSVP-APQAIKILDD-EMQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEIL 170 (341)
Q Consensus 109 rD~IkAIaRGF~-~EqAlkLLeD-D~~~DIIdI~~lv~nke~f~RrrgRIIG~~GkTkkaIE~L 170 (341)
.+||..|++++= -.+++.+-.. +-...+|.|.- +++ -.|||||++|+|-+||=.+
T Consensus 3 ~~lv~~ivk~LVd~Pe~V~V~~~~~~~~~~i~l~v---~~~----D~GrVIGk~Gr~i~AIRtl 59 (77)
T PRK02821 3 ADAVEHLVRGIVDNPDDVRVDSHTNRRGRTLEVRV---HPD----DLGKVIGRGGRTATALRTV 59 (77)
T ss_pred HHHHHHHHHHhCCCCCeEEEEEEECCCcEEEEEEE---Chh----hCcceeCCCCchHHHHHHH
Confidence 467777766642 3344444321 10112333331 222 3699999999999999654
No 30
>PRK00468 hypothetical protein; Provisional
Probab=87.41 E-value=0.31 Score=38.99 Aligned_cols=18 Identities=17% Similarity=0.333 Sum_probs=16.3
Q ss_pred hccccCCCCchhHHHHHh
Q 019435 153 RQHLVGPNSSTLKALEIL 170 (341)
Q Consensus 153 rgRIIG~~GkTkkaIE~L 170 (341)
.|||||++|+|-.||-.+
T Consensus 41 ~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CcceecCCChhHHHHHHH
Confidence 599999999999999765
No 31
>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=87.35 E-value=0.19 Score=45.12 Aligned_cols=27 Identities=30% Similarity=0.351 Sum_probs=25.0
Q ss_pred hhccccCCCCchhHHHHHhhcchhhHH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
++|.|||++|+|.+.|+..|||.|.|.
T Consensus 8 kig~vIG~gG~~Ik~I~~~tgv~I~Id 34 (172)
T TIGR03665 8 RIGVLIGKGGETKKEIEERTGVKLDID 34 (172)
T ss_pred HhhhHhCCchhHHHHHHHHhCcEEEEE
Confidence 578999999999999999999998776
No 32
>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=87.16 E-value=1 Score=33.96 Aligned_cols=55 Identities=16% Similarity=0.237 Sum_probs=48.0
Q ss_pred eeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEcccCeEEEEcCCCCCChHHHHhHHHHH
Q 019435 53 STLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLI 112 (341)
Q Consensus 53 ~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~eGsV~VrTt~kT~DP~~IiKArD~I 112 (341)
.+.+|+.+...|-.--+...+.| +++++.+.++- +|.|.|.. .|+..+..|.++|
T Consensus 5 ~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-~g~v~I~G----~~~~~v~~A~~~I 60 (61)
T cd02393 5 TMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-DGTVYIAA----SDKEAAEKAKKMI 60 (61)
T ss_pred EEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-CCEEEEEe----CCHHHHHHHHHHh
Confidence 57789999999999999999999 67999999987 79999985 5678899888876
No 33
>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=86.38 E-value=0.4 Score=34.56 Aligned_cols=23 Identities=17% Similarity=0.323 Sum_probs=20.4
Q ss_pred hccccCCCCchhHHHHHhhcchh
Q 019435 153 RQHLVGPNSSTLKALEILTGCYI 175 (341)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~yI 175 (341)
-|++||++|+++.+|+.+++-++
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 59999999999999999988553
No 34
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=85.22 E-value=0.42 Score=38.65 Aligned_cols=18 Identities=22% Similarity=0.473 Sum_probs=15.9
Q ss_pred hccccCCCCchhHHHHHh
Q 019435 153 RQHLVGPNSSTLKALEIL 170 (341)
Q Consensus 153 rgRIIG~~GkTkkaIE~L 170 (341)
.||+||++|+|.+||=-+
T Consensus 41 ~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 41 MGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred ccceecCCChhHHHHHHH
Confidence 699999999999999643
No 35
>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=80.76 E-value=0.58 Score=50.52 Aligned_cols=27 Identities=19% Similarity=0.460 Sum_probs=25.5
Q ss_pred hhccccCCCCchhHHHHHhhcchhhHH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
.+|+|||++|+|.+.|+.-|||.|.|.
T Consensus 561 kI~~vIG~gGk~Ik~I~~~tg~~I~i~ 587 (684)
T TIGR03591 561 KIRDVIGPGGKVIREITEETGAKIDIE 587 (684)
T ss_pred HHHhhcCCCcHHHHHHHHHHCCEEEEe
Confidence 389999999999999999999999988
No 36
>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=80.13 E-value=8.4 Score=27.97 Aligned_cols=55 Identities=18% Similarity=0.135 Sum_probs=46.0
Q ss_pred eeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEcc--cCeEEEEcCCCCCChHHHHhHHHHH
Q 019435 53 STLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLV--EGSMTVSTTRKTRDPYIIVKARDLI 112 (341)
Q Consensus 53 ~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~--eGsV~VrTt~kT~DP~~IiKArD~I 112 (341)
.+++|.....+|-.--+..-+.| +.+++.|.++-. ...|+|. .++-.+..|.++|
T Consensus 3 ~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~-----G~~~~v~~A~~~I 60 (60)
T PF00013_consen 3 RIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTIS-----GSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEE-----ESHHHHHHHHHHH
T ss_pred EEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEE-----eCHHHHHHHHhhC
Confidence 57899999999999999999999 579999999765 3466775 4777899998876
No 37
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=79.13 E-value=0.68 Score=48.82 Aligned_cols=26 Identities=35% Similarity=0.483 Sum_probs=24.3
Q ss_pred hccccCCCCchhHHHHHhhcchhhHH
Q 019435 153 RQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
.|=|||+-|.|++-||.-|||+|.|-
T Consensus 155 vGLiiGPRG~TqK~lE~etgAKI~IR 180 (554)
T KOG0119|consen 155 VGLIIGPRGNTQKRLERETGAKIAIR 180 (554)
T ss_pred eEEEecCCccHHHHHHHHhCCeEEEe
Confidence 48999999999999999999999884
No 38
>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=74.70 E-value=8 Score=42.62 Aligned_cols=82 Identities=11% Similarity=0.159 Sum_probs=65.8
Q ss_pred eeeeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEcccCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHHhhc
Q 019435 51 SFSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILD 129 (341)
Q Consensus 51 sF~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~eGsV~VrTt~kT~DP~~IiKArD~IkAIaRGF~~EqAlkLLe 129 (341)
.+.+-||+++..-|..--+.+-+.| +++|++|.++- +|.|.|.. .|.-.+.+|.++|..|...|.++ ..
T Consensus 579 ~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-~G~V~I~a----~d~~~~~~A~~~I~~i~~~~~~~-----vG 648 (719)
T TIGR02696 579 IITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-DGTVYIGA----ADGPSAEAARAMINAIANPTMPE-----VG 648 (719)
T ss_pred eEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-CcEEEEEe----CCHHHHHHHHHHHHHhhCcCcCC-----CC
Confidence 3467799999999999999999999 78999999985 79999986 78889999999999999975433 22
Q ss_pred ccceeEEEeeccc
Q 019435 130 DEMQCDIIKIGNL 142 (341)
Q Consensus 130 DD~~~DIIdI~~l 142 (341)
+-+...|.+|.+|
T Consensus 649 ~i~~GkV~~I~df 661 (719)
T TIGR02696 649 ERFLGTVVKTTAF 661 (719)
T ss_pred CEEEEEEEEEECc
Confidence 3344666666654
No 39
>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=74.24 E-value=5.5 Score=28.64 Aligned_cols=56 Identities=21% Similarity=0.199 Sum_probs=45.2
Q ss_pred eeeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEcc-----cCeEEEEcCCCCCChHHHHhHHHHH
Q 019435 52 FSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLV-----EGSMTVSTTRKTRDPYIIVKARDLI 112 (341)
Q Consensus 52 F~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~-----eGsV~VrTt~kT~DP~~IiKArD~I 112 (341)
..+.+|.....+|-.--+..-+.| +.+++.|.++.. ...|+|..+ +..+..|..+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~-----~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT-----PEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcC-----HHHHHHHHHHh
Confidence 468899999999999999999999 479999999875 456677653 66888887765
No 40
>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=68.21 E-value=11 Score=27.60 Aligned_cols=55 Identities=15% Similarity=0.166 Sum_probs=45.4
Q ss_pred eeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEcc---cCeEEEEcCCCCCChHHHHhHHHHH
Q 019435 53 STLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLV---EGSMTVSTTRKTRDPYIIVKARDLI 112 (341)
Q Consensus 53 ~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~---eGsV~VrTt~kT~DP~~IiKArD~I 112 (341)
.+.+|.....+|-.--+...+.| +.+++.|.+... ++.|+|..+ +..+..|.++|
T Consensus 3 ~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-----~~~v~~A~~~i 61 (62)
T cd02394 3 EVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP-----KENVEKAKEEI 61 (62)
T ss_pred EEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC-----HHHHHHHHHHh
Confidence 57789999999999998888888 679999999875 689999863 56788887765
No 41
>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=67.04 E-value=2.2 Score=46.85 Aligned_cols=27 Identities=19% Similarity=0.426 Sum_probs=25.4
Q ss_pred hhccccCCCCchhHHHHHhhcchhhHH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
.+|.|||++|+|.+.|..-|||.|-|.
T Consensus 588 ki~~vIG~gGk~I~~i~~~tg~~Idi~ 614 (719)
T TIGR02696 588 KIGEVIGPKGKMINQIQDETGAEISIE 614 (719)
T ss_pred HhhheeCCCcHhHHHHHHHHCCEEEEe
Confidence 579999999999999999999999887
No 42
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=61.89 E-value=27 Score=35.84 Aligned_cols=135 Identities=21% Similarity=0.281 Sum_probs=80.9
Q ss_pred eeeeeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEcc-------cCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCCh
Q 019435 50 SSFSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLV-------EGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPA 121 (341)
Q Consensus 50 ssF~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~-------eGsV~VrTt~kT~DP~~IiKArD~IkAIaRGF~~ 121 (341)
...+||||.|--..|...-+..-.-| .+.+..|.|--. +-.|.+-+ ..--+|+-...||.==.|.-+-
T Consensus 39 y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~----Gt~eai~av~efI~dKire~p~ 114 (402)
T KOG2191|consen 39 YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQ----GTVEALNAVHEFIADKIREKPQ 114 (402)
T ss_pred eEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEe----ccHHHHHHHHHHHHHHHHHhHH
Confidence 56699999999999999999988888 578888877532 11222221 1222455445555433332222
Q ss_pred HHHH--HhhcccceeEEEe-ecccccCchhhhhhhccccCCCCchhHHHHHhhcchhhHH--------------------
Q 019435 122 PQAI--KILDDEMQCDIIK-IGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQ-------------------- 178 (341)
Q Consensus 122 EqAl--kLLeDD~~~DIId-I~~lv~nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~Vq-------------------- 178 (341)
.++- .+|+--. -|-+. |+-++.|. --|=|||++|.|.++|-+-++|+|.|+
T Consensus 115 ~~~k~v~~~~pqt-~~r~kqikivvPNs-----tag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~ 188 (402)
T KOG2191|consen 115 AVAKPVDILQPQT-PDRIKQIKIVVPNS-----TAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEP 188 (402)
T ss_pred hhcCCccccCCCC-ccccceeEEeccCC-----cccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCH
Confidence 2111 1111000 11111 22222221 137899999999999999999999988
Q ss_pred ------HHHHHhhhhcCccccc
Q 019435 179 ------ILMVKKELEKDPALAN 194 (341)
Q Consensus 179 ------~LmiKreL~kd~~l~~ 194 (341)
.=||=..+..||.-..
T Consensus 189 e~~~~A~~~IL~Ki~eDpqs~s 210 (402)
T KOG2191|consen 189 EQNMKAVSLILQKIQEDPQSGS 210 (402)
T ss_pred HHHHHHHHHHHHHhhcCCcccc
Confidence 3467778888987543
No 43
>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=60.22 E-value=13 Score=27.82 Aligned_cols=57 Identities=19% Similarity=0.179 Sum_probs=45.5
Q ss_pred eeeeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEccc------CeEEEEcCCCCCChHHHHhHHHHH
Q 019435 51 SFSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVE------GSMTVSTTRKTRDPYIIVKARDLI 112 (341)
Q Consensus 51 sF~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~e------GsV~VrTt~kT~DP~~IiKArD~I 112 (341)
++.+++|..-..+|-...+..-+.| +++|+.+.+.... ..|+|. .+|-.+..|..+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~-----G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTIS-----GKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEE-----eCHHHHHHHHHhh
Confidence 4678999999999999999999999 5799999987654 456665 4566788887765
No 44
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=59.50 E-value=5.1 Score=35.27 Aligned_cols=25 Identities=12% Similarity=0.149 Sum_probs=22.6
Q ss_pred hccccCCCCchhHHHHHhhcchhhH
Q 019435 153 RQHLVGPNSSTLKALEILTGCYILV 177 (341)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~yI~V 177 (341)
.|+.||++|++.+++..|++-++=|
T Consensus 110 ~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 110 KGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred cchhhCCCCHHHHHHHHHhCCccCC
Confidence 5999999999999999999988754
No 45
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=58.56 E-value=3.4 Score=38.90 Aligned_cols=26 Identities=31% Similarity=0.535 Sum_probs=24.5
Q ss_pred hccccCCCCchhHHHHHhhcchhhHH
Q 019435 153 RQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
++||||++|.+.+.|...|+|.|.|.
T Consensus 156 i~~lig~~g~~i~~l~~~~~~~I~ig 181 (235)
T PRK04163 156 VPRVIGKKGSMINMLKEETGCDIIVG 181 (235)
T ss_pred HHhhcCCCChhHhhhhhhhCcEEEEc
Confidence 68999999999999999999999988
No 46
>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=57.78 E-value=8.5 Score=35.90 Aligned_cols=99 Identities=18% Similarity=0.270 Sum_probs=67.0
Q ss_pred hhhHHHHHhhcccEEEEEcccCeEEEEcCCCCCChHH-HHhHHHHH-HHHHcCCChHHHHHhhcccceeEEEeecccc-c
Q 019435 68 WPMVKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYI-IVKARDLI-RLLSRSVPAPQAIKILDDEMQCDIIKIGNLV-R 144 (341)
Q Consensus 68 W~~Ikk~Le~~~l~i~LDl~eGsV~VrTt~kT~DP~~-IiKArD~I-kAIaRGF~~EqAlkLLeDD~~~DIIdI~~lv-~ 144 (341)
-..|...++..|..+.++ +..+.+-|.--.--|.. ..=+..|+ .++..|++.++|.+|...-+. -...+. .
T Consensus 124 ~~~v~~lf~~~G~~~~v~--E~~~~~~talsgsgPA~~~~~~~al~~~~v~~Gl~~~~A~~lv~~~~~----G~a~l~~~ 197 (245)
T TIGR00112 124 RALVLALFKAVGEVVELP--EALMDAVTALSGSGPAYVFLFIEALADAGVKQGLPRELALELAAQTVK----GAAKLLEE 197 (245)
T ss_pred HHHHHHHHHhCCCEEEEC--HHHcchHHhhccCcHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH----HHHHHHHh
Confidence 356666668899998887 56666554433344433 22233343 467899999999999864321 011222 3
Q ss_pred CchhhhhhhccccCCCCchhHHHHHhhc
Q 019435 145 NKERFVKRRQHLVGPNSSTLKALEILTG 172 (341)
Q Consensus 145 nke~f~RrrgRIIG~~GkTkkaIE~LT~ 172 (341)
++.++.-.+.++.-|+|.|-.+|+.|-.
T Consensus 198 ~~~~~~~l~~~v~spgGtT~~gl~~Le~ 225 (245)
T TIGR00112 198 SGEHPALLKDQVTSPGGTTIAGLAVLEE 225 (245)
T ss_pred cCCCHHHHHHcCCCCcHHHHHHHHHHHH
Confidence 5579999999999999999999988754
No 47
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=57.65 E-value=4.5 Score=40.98 Aligned_cols=27 Identities=30% Similarity=0.240 Sum_probs=25.1
Q ss_pred hhccccCCCCchhHHHHHhhcchhhHH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
-.|=|||.+|+|++-||+-|+|.|.+-
T Consensus 67 ~~~~lig~~g~trkkle~Etq~~i~lp 93 (345)
T KOG2814|consen 67 FIGWLIGKQGKTRKKLEEETQTNIFLP 93 (345)
T ss_pred HhhhhhcccchHHHHHHHhhccceEcc
Confidence 378999999999999999999999886
No 48
>PF05598 DUF772: Transposase domain (DUF772); InterPro: IPR008490 This presumed domain is found at the N terminus of transposase insH and other related transposases.
Probab=57.58 E-value=13 Score=28.23 Aligned_cols=61 Identities=18% Similarity=0.319 Sum_probs=47.0
Q ss_pred CCCCChHHHHhHHHHHHHHHcCC-ChHHHHHhhcccc----eeEEEeecccccCchhhhhhhccccCCC
Q 019435 97 RKTRDPYIIVKARDLIRLLSRSV-PAPQAIKILDDEM----QCDIIKIGNLVRNKERFVKRRQHLVGPN 160 (341)
Q Consensus 97 ~kT~DP~~IiKArD~IkAIaRGF-~~EqAlkLLeDD~----~~DIIdI~~lv~nke~f~RrrgRIIG~~ 160 (341)
+.+.+|..++++ +|=+...|+ +..+....+.+++ +|. +++.+-+-+...|.|-|.|++..+
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 347899888887 555667798 9999999998873 387 777766666678999998887654
No 49
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=56.47 E-value=10 Score=40.94 Aligned_cols=111 Identities=16% Similarity=0.180 Sum_probs=72.4
Q ss_pred cCchhHHHHHHhhhh-HHHHHhhcccEEEEEcccCeEEEEcCCCCCChHHHHhHHHHHHHH-HcCC---ChHHHHHhhcc
Q 019435 56 FPQYREKYLQEAWPM-VKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLL-SRSV---PAPQAIKILDD 130 (341)
Q Consensus 56 fPkyRe~yLKe~W~~-Ikk~Le~~~l~i~LDl~eGsV~VrTt~kT~DP~~IiKArD~IkAI-aRGF---~~EqAlkLLeD 130 (341)
+|.-=-..+...-+. |...+-+.||.+.+....+.+-.+.+..+..|..+..|+.||-=+ +||- +++++.- .
T Consensus 60 VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~~~~~~~~~q~---~ 136 (600)
T KOG1676|consen 60 VPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAKQLIGEVVSRGRPPGGFPDNQG---S 136 (600)
T ss_pred CCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHHHHHhhhhhhhccCCCCCccccCC---c
Confidence 444433442333333 444445788888888888888888888899999999999988765 5553 2221111 0
Q ss_pred cceeEEEeecccccCchhhhhhhccccCCCCchhHHHHHhhcchhhHH
Q 019435 131 EMQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 131 D~~~DIIdI~~lv~nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
......|.|-. + +-|-|||++|-|.+.|.+-|||.+.|-
T Consensus 137 ~~ttqeI~IPa---~------k~GlIIGKgGETikqlqe~sg~k~i~i 175 (600)
T KOG1676|consen 137 VETTQEILIPA---N------KCGLIIGKGGETIKQLQEQSGVKMILV 175 (600)
T ss_pred cceeeeeccCc---c------ceeeEeccCccHHHHHHhhcCCceEEE
Confidence 11122233332 2 348899999999999999999997665
No 50
>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=47.96 E-value=69 Score=35.03 Aligned_cols=78 Identities=10% Similarity=0.148 Sum_probs=61.3
Q ss_pred eeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEcccCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHHhhccc
Q 019435 53 STLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDE 131 (341)
Q Consensus 53 ~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~eGsV~VrTt~kT~DP~~IiKArD~IkAIaRGF~~EqAlkLLeDD 131 (341)
.+-||+.+..-|..--+.+.+.| +++|+.|.++- +|.|.|.. .|...+.+|..+|..+..... ..+-
T Consensus 554 ~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-dG~V~i~~----~~~~~~~~a~~~I~~~~~~~~-------~G~i 621 (684)
T TIGR03591 554 TIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-DGTVKIAA----SDGEAAEAAIKMIEGITAEPE-------VGKI 621 (684)
T ss_pred EEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-CeEEEEEE----CcHHHHHHHHHHHHhhhcccc-------cCcE
Confidence 57799999999999999999999 78999999986 79999986 677899999999998844211 1233
Q ss_pred ceeEEEeeccc
Q 019435 132 MQCDIIKIGNL 142 (341)
Q Consensus 132 ~~~DIIdI~~l 142 (341)
+...|..|.++
T Consensus 622 ~~G~V~~I~~~ 632 (684)
T TIGR03591 622 YEGKVVRIMDF 632 (684)
T ss_pred EEEEEEEEeCC
Confidence 44666666654
No 51
>smart00322 KH K homology RNA-binding domain.
Probab=45.47 E-value=58 Score=22.54 Aligned_cols=60 Identities=17% Similarity=0.185 Sum_probs=45.5
Q ss_pred eeeeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEccc---CeEEEEcCCCCCChHHHHhHHHHHHHH
Q 019435 51 SFSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVE---GSMTVSTTRKTRDPYIIVKARDLIRLL 115 (341)
Q Consensus 51 sF~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~e---GsV~VrTt~kT~DP~~IiKArD~IkAI 115 (341)
+..+.+|.....+|-..-+..-+.| ..+++.+.+.... ..++|.. ++..+..|+++|...
T Consensus 4 ~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g-----~~~~v~~a~~~i~~~ 67 (69)
T smart00322 4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITG-----PPENVEKAAELILEI 67 (69)
T ss_pred EEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEc-----CHHHHHHHHHHHHHH
Confidence 3467889999999988888888888 4688888776643 6677764 367888888887643
No 52
>PRK07680 late competence protein ComER; Validated
Probab=45.04 E-value=23 Score=33.13 Aligned_cols=97 Identities=9% Similarity=0.119 Sum_probs=60.3
Q ss_pred hhHHHHHhhcccEEEEEcccCeEEEEcCCCCCChHHHHhHH-HHHHH-HH-cCCChHHHHHhhcccce--eEEEeecccc
Q 019435 69 PMVKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKAR-DLIRL-LS-RSVPAPQAIKILDDEMQ--CDIIKIGNLV 143 (341)
Q Consensus 69 ~~Ikk~Le~~~l~i~LDl~eGsV~VrTt~kT~DP~~IiKAr-D~IkA-Ia-RGF~~EqAlkLLeDD~~--~DIIdI~~lv 143 (341)
..+...++..|..+.++ +..+.+-+.--.--|..+.-.- -|+.+ +. .||+.++|..++-+=+. ... +.
T Consensus 142 ~~~~~ll~~~G~~~~i~--e~~~~~~~~l~gs~pa~~~~~~~al~~~~~~~~Gl~~~~a~~~~~~~~~G~~~l-----~~ 214 (273)
T PRK07680 142 QKLERLFSNISTPLVIE--EDITRVSSDIVSCGPAFFSYLLQRFIDAAVEETNISKEEATTLASEMLIGMGKL-----LE 214 (273)
T ss_pred HHHHHHHHcCCCEEEEC--hHhcchhhhhccchHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHH-----HH
Confidence 45566667788777776 3333333222122333333322 24433 44 59999999999864321 111 12
Q ss_pred cCchhhhhhhccccCCCCchhHHHHHhhc
Q 019435 144 RNKERFVKRRQHLVGPNSSTLKALEILTG 172 (341)
Q Consensus 144 ~nke~f~RrrgRIIG~~GkTkkaIE~LT~ 172 (341)
.++.|+.-.+.++.-|+|.|-.+|+.|-.
T Consensus 215 ~~~~~~~~l~~~v~spgG~T~~gl~~le~ 243 (273)
T PRK07680 215 KGLYTLPTLQEKVCVKGGITGEGIKVLEE 243 (273)
T ss_pred hcCCCHHHHHHhCCCCChhHHHHHHHHHH
Confidence 35579999999999999999999988755
No 53
>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=43.46 E-value=45 Score=24.43 Aligned_cols=32 Identities=22% Similarity=0.142 Sum_probs=28.1
Q ss_pred CCCChHHHHhHHHHHHHHHcCCChHHHHHhhc
Q 019435 98 KTRDPYIIVKARDLIRLLSRSVPAPQAIKILD 129 (341)
Q Consensus 98 kT~DP~~IiKArD~IkAIaRGF~~EqAlkLLe 129 (341)
..+++-.+...+.+..+...||+++++.++|+
T Consensus 37 r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~~ 68 (68)
T cd01104 37 RLYSEADVARLRLIRRLTSEGVRISQAAALAL 68 (68)
T ss_pred eecCHHHHHHHHHHHHHHHCCCCHHHHHHHhC
Confidence 35778899999999999999999999999874
No 54
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=42.20 E-value=35 Score=36.03 Aligned_cols=125 Identities=18% Similarity=0.129 Sum_probs=84.0
Q ss_pred eeeeeeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEcc------cCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCC-
Q 019435 49 VSSFSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLV------EGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVP- 120 (341)
Q Consensus 49 essF~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~------eGsV~VrTt~kT~DP~~IiKArD~IkAIaRGF~- 120 (341)
+-++..|+|.....+|...-+.+-+-| +.++.+|++=.. +..|+|. ..|.++.+|--.|-++.+-+.
T Consensus 137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~Is-----G~~~av~~al~~Is~~L~~~~~ 211 (485)
T KOG2190|consen 137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTIS-----GEPDAVKKALVQISSRLLENPP 211 (485)
T ss_pred ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEc-----CchHHHHHHHHHHHHHHHhcCC
Confidence 446899999999999999999988888 789999988554 6667775 567789999887777777632
Q ss_pred ----hHHHHHhhcc-c-ceeE-EEeecc-------c---ccCchhh------hhhhccccCCCCchhHHHHHhhcchhhH
Q 019435 121 ----APQAIKILDD-E-MQCD-IIKIGN-------L---VRNKERF------VKRRQHLVGPNSSTLKALEILTGCYILV 177 (341)
Q Consensus 121 ----~EqAlkLLeD-D-~~~D-IIdI~~-------l---v~nke~f------~RrrgRIIG~~GkTkkaIE~LT~~yI~V 177 (341)
+-.+..-..- - ..-. +..... . +...+.+ .-..++|||++|..-.+|++-|+.-|+|
T Consensus 212 ~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v 291 (485)
T KOG2190|consen 212 RSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISV 291 (485)
T ss_pred cCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEe
Confidence 1222211111 0 0000 011110 0 0001111 2257999999999999999999999999
Q ss_pred H
Q 019435 178 Q 178 (341)
Q Consensus 178 q 178 (341)
+
T Consensus 292 ~ 292 (485)
T KOG2190|consen 292 G 292 (485)
T ss_pred c
Confidence 8
No 55
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=40.34 E-value=11 Score=36.66 Aligned_cols=72 Identities=21% Similarity=0.373 Sum_probs=45.1
Q ss_pred HHHhHHHHHHHHHcCCC--hHHHHHhhc-cc-ceeEEEeeccc-----ccCchhhhhhh------------ccccCCCCc
Q 019435 104 IIVKARDLIRLLSRSVP--APQAIKILD-DE-MQCDIIKIGNL-----VRNKERFVKRR------------QHLVGPNSS 162 (341)
Q Consensus 104 ~IiKArD~IkAIaRGF~--~EqAlkLLe-DD-~~~DIIdI~~l-----v~nke~f~Rrr------------gRIIG~~Gk 162 (341)
+++-+.++ +.|-|+ -.+--..|+ .| +++.|.++..- ......+-+.+ =|+||++|+
T Consensus 90 A~L~ls~~---~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p~kVpRvig~~~s 166 (239)
T COG1097 90 ALLSLSDF---LRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPPSKVPRVIGKKGS 166 (239)
T ss_pred eEeehhhh---hcccccccccccccccccCCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEchhhcceEecCCCc
Confidence 34455555 456555 223334555 33 55777666531 11223333333 369999999
Q ss_pred hhHHHHHhhcchhhHH
Q 019435 163 TLKALEILTGCYILVQ 178 (341)
Q Consensus 163 TkkaIE~LT~~yI~Vq 178 (341)
-.+.|...|+|.|+|.
T Consensus 167 m~~~l~~~~~~~I~VG 182 (239)
T COG1097 167 MLNMLKEKTGCEIIVG 182 (239)
T ss_pred HHHHhhhhcCeEEEEe
Confidence 9999999999999998
No 56
>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=40.21 E-value=1e+02 Score=22.10 Aligned_cols=31 Identities=29% Similarity=0.270 Sum_probs=23.9
Q ss_pred hhhhHHHHHh-hccc-EEEEEcccCeEEEEcCC
Q 019435 67 AWPMVKGALK-EYGV-SCELNLVEGSMTVSTTR 97 (341)
Q Consensus 67 ~W~~Ikk~Le-~~~l-~i~LDl~eGsV~VrTt~ 97 (341)
|=..|.++|. .-|+ .+.+|+.++.|+|....
T Consensus 12 C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~ 44 (62)
T PF00403_consen 12 CAKKVEKALSKLPGVKSVKVDLETKTVTVTYDP 44 (62)
T ss_dssp HHHHHHHHHHTSTTEEEEEEETTTTEEEEEEST
T ss_pred HHHHHHHHHhcCCCCcEEEEECCCCEEEEEEec
Confidence 3456788884 4676 59999999999998743
No 57
>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=39.60 E-value=11 Score=29.11 Aligned_cols=24 Identities=13% Similarity=0.148 Sum_probs=19.3
Q ss_pred hhccccCCCCchhHHHHHhhcchh
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYI 175 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI 175 (341)
..|.|||.+|++.+.|....+-.+
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 469999999999999977655443
No 58
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=38.74 E-value=82 Score=29.74 Aligned_cols=67 Identities=15% Similarity=0.072 Sum_probs=53.5
Q ss_pred CcceeeeeeeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEcccCeEEEEcCCCCCChHHHHhHHHHHHHHHc
Q 019435 45 GMLEVSSFSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSR 117 (341)
Q Consensus 45 g~~eessF~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~eGsV~VrTt~kT~DP~~IiKArD~IkAIaR 117 (341)
|.++. -|.+-+|++...-|...-+.+-+.| +.+++.|-+.. +|.|.|.. .|+-.+..|..+|+.+.+
T Consensus 141 G~L~~-G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-NG~VwI~~----~~~~~~~~a~~~I~~~e~ 208 (235)
T PRK04163 141 GKIEG-GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-NGRIWIKG----PDEEDEEIAIEAIKKIER 208 (235)
T ss_pred CccCC-CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-CcEEEEee----CCHHHHHHHHHHHHHHHh
Confidence 44443 3677889998888877777888888 67888887776 69999986 778899999999998776
No 59
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=38.74 E-value=13 Score=41.93 Aligned_cols=27 Identities=22% Similarity=0.295 Sum_probs=24.7
Q ss_pred hhccccCCCCchhHHHHHhhcch-hhHH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCY-ILVQ 178 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~y-I~Vq 178 (341)
.+|.|||++|+|.+.|..-||+. |-+.
T Consensus 695 ki~~vIG~GGktIk~I~eetg~~~Idi~ 722 (891)
T PLN00207 695 KVNMIIGSGGKKVKSIIEETGVEAIDTQ 722 (891)
T ss_pred HHHHHhcCCchhHHHHHHHHCCCccCcC
Confidence 47899999999999999999999 7776
No 60
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=38.01 E-value=44 Score=36.99 Aligned_cols=64 Identities=17% Similarity=0.211 Sum_probs=53.3
Q ss_pred eecCchhHHHHHHhhhhHHHHH-hhcccEEEEEcccCeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChH
Q 019435 54 TLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAP 122 (341)
Q Consensus 54 vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~eGsV~VrTt~kT~DP~~IiKArD~IkAIaRGF~~E 122 (341)
+-+|+-...-+...-+.+.+.| +++|++|.++ .+|+|.|-+ .|.-.+.+|++.|..|.+-|.+-
T Consensus 556 ~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-ddGtv~i~~----s~~~~~~~ak~~I~~i~~e~evg 620 (692)
T COG1185 556 IKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-DDGTVKIAA----SDGESAKKAKERIEAITREVEVG 620 (692)
T ss_pred EccCHHHHhhccCCcccchhhhhhhhCcEEEec-CCCcEEEEe----cchHHHHHHHHHHHHHHhhcccc
Confidence 4467777777777777778877 8999999999 899999987 67779999999999999766654
No 61
>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=37.65 E-value=9.1 Score=31.82 Aligned_cols=56 Identities=18% Similarity=0.335 Sum_probs=38.5
Q ss_pred HHHcCCChHHHHHhhcccceeEEEeecccc-cCchhhhhhhccccCCCCchhHHHHHhhcc
Q 019435 114 LLSRSVPAPQAIKILDDEMQCDIIKIGNLV-RNKERFVKRRQHLVGPNSSTLKALEILTGC 173 (341)
Q Consensus 114 AIaRGF~~EqAlkLLeDD~~~DIIdI~~lv-~nke~f~RrrgRIIG~~GkTkkaIE~LT~~ 173 (341)
++..|++.++|.+|.-.-+. -...+. .++.++...+.++.-|+|.|-.+|+.|-.-
T Consensus 31 ~v~~Gl~~~~A~~lv~~t~~----G~a~ll~~~~~~~~~l~~~v~tPgG~T~~gl~~L~~~ 87 (107)
T PF14748_consen 31 AVAQGLPREEARKLVAQTFI----GAAKLLEESGRSPAELRDEVTTPGGTTIAGLEVLEKG 87 (107)
T ss_dssp HHHTT--HHHHHHHHHHHHH----HHHHHHHHCSS-HHHHHHHHS-TTSHHHHHHHHHHHT
T ss_pred HHHcCCCHHHHHHHHHHHHH----HHHHHHHccCCCHHHHhhhccCCCCcHHHHHHHHHHC
Confidence 57899999999999854321 111222 245699999999999999999999987654
No 62
>PF15232 DUF4585: Domain of unknown function (DUF4585)
Probab=36.71 E-value=12 Score=30.57 Aligned_cols=24 Identities=29% Similarity=0.540 Sum_probs=18.9
Q ss_pred CCCCCCchhhhhhhccccccChhH
Q 019435 226 PPPPQPSKIDKLLESGEYFLSERK 249 (341)
Q Consensus 226 pp~~~~~k~D~~lesGeyFl~~~~ 249 (341)
|.++..+|+=+--+||+||+-+--
T Consensus 2 ~~~~tqrKvL~DP~SG~Yy~vd~P 25 (75)
T PF15232_consen 2 PYPATQRKVLQDPESGQYYVVDAP 25 (75)
T ss_pred CCCccCccEeecCCCCCEEEEecC
Confidence 346777888888999999996643
No 63
>PRK06928 pyrroline-5-carboxylate reductase; Reviewed
Probab=36.64 E-value=55 Score=31.03 Aligned_cols=96 Identities=14% Similarity=0.261 Sum_probs=62.1
Q ss_pred hHHHHHhhcccEEEEEcccCeEEEEcCCCCCChHHHH-hHHHHHH-HHHc-CCChHHHHHhhcccceeEEEeecccc-cC
Q 019435 70 MVKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIV-KARDLIR-LLSR-SVPAPQAIKILDDEMQCDIIKIGNLV-RN 145 (341)
Q Consensus 70 ~Ikk~Le~~~l~i~LDl~eGsV~VrTt~kT~DP~~Ii-KArD~Ik-AIaR-GF~~EqAlkLLeDD~~~DIIdI~~lv-~n 145 (341)
.|...++..|....++ +..+.+-|.--.--|..+. =+.-|+. ++.. |++.++|.+|.-.=+. --..+. .+
T Consensus 146 ~v~~l~~~~G~~~~v~--E~~~d~~tal~gsgPA~~~~~~~al~~a~~~~ggl~~~~a~~l~~~~~~----G~a~l~~~~ 219 (277)
T PRK06928 146 RLEETLSHFSHVMTIR--EENMDIASNLTSSSPGFIAAIFEEFAEAAVRNSSLSDEEAFQFLNFALA----GTGKLLVEE 219 (277)
T ss_pred HHHHHHHhCCCEEEEc--hhhCceeeeeecCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH----HHHHHHHcc
Confidence 4566668889988887 3555554433334454433 2333444 3343 6999999999864321 000111 35
Q ss_pred chhhhhhhccccCCCCchhHHHHHhh
Q 019435 146 KERFVKRRQHLVGPNSSTLKALEILT 171 (341)
Q Consensus 146 ke~f~RrrgRIIG~~GkTkkaIE~LT 171 (341)
+.|+.-.|.++.-|+|.|-.+|+.|-
T Consensus 220 ~~~p~~l~~~v~spgGtT~~gl~~le 245 (277)
T PRK06928 220 DYTFSGTIERVATKGGITAEGAEVIQ 245 (277)
T ss_pred CCCHHHHHHhCCCCChHHHHHHHHHH
Confidence 57999999999999999999998774
No 64
>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=35.80 E-value=1.3e+02 Score=27.32 Aligned_cols=91 Identities=23% Similarity=0.288 Sum_probs=55.4
Q ss_pred EEcccCeEEEEcCCCCCChHHHHhHHHHHHHHHc--------------CCChHHHHHhhcccce--eEEEeecccccCch
Q 019435 84 LNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSR--------------SVPAPQAIKILDDEMQ--CDIIKIGNLVRNKE 147 (341)
Q Consensus 84 LDl~eGsV~VrTt~kT~DP~~IiKArD~IkAIaR--------------GF~~EqAlkLLeDD~~--~DIIdI~~lv~nke 147 (341)
++...=.+.|-| .||-.+..--|+|+-||. =.++++|.+++.+=+- -.|-||.=-...++
T Consensus 4 vefEGPelviYt----k~P~~~~~~~dli~~lAk~lrKRIvvR~dps~l~~~e~A~~~I~~ivP~ea~i~di~Fd~~tGE 79 (145)
T cd02410 4 VEFEGPELVVYT----KNPELFAEDGDLVKDLAKDLRKRIVIRPDPSVLKPPEEAIKIILEIVPEEAGITDIYFDDDTGE 79 (145)
T ss_pred eEeeCCeEEEEE----CCHHHHhcccHHHHHHHHHHhceEEEcCChhhcCCHHHHHHHHHHhCCCccCceeeEecCCCcE
Confidence 444455667775 888888776778777763 2467888877743110 11222220011233
Q ss_pred hhhhh--hccccCCCCchhHHHHHhhcchhhHH
Q 019435 148 RFVKR--RQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 148 ~f~Rr--rgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
-...+ =|++||.+|.|+.-|=.-||-.-.|.
T Consensus 80 V~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 80 VIIEAEKPGLVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred EEEEEcCCeEEEecCchhHHHHHHHhCCeeEEE
Confidence 33333 49999999999888888888665553
No 65
>COG1159 Era GTPase [General function prediction only]
Probab=35.35 E-value=29 Score=34.74 Aligned_cols=53 Identities=21% Similarity=0.493 Sum_probs=35.0
Q ss_pred HHHHHhhccc----ceeEEEeecccccCchhhhh-----------hhccccCCCCchhHHH--------HHhhcchhhH
Q 019435 122 PQAIKILDDE----MQCDIIKIGNLVRNKERFVK-----------RRQHLVGPNSSTLKAL--------EILTGCYILV 177 (341)
Q Consensus 122 EqAlkLLeDD----~~~DIIdI~~lv~nke~f~R-----------rrgRIIG~~GkTkkaI--------E~LT~~yI~V 177 (341)
|+++..|.|| +..+|.+...- .+...+ .+|=|||.||.+++.| |.+-+|.|.+
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 33666655542 112211 3678999999987776 6666666543
No 66
>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=34.91 E-value=66 Score=23.79 Aligned_cols=32 Identities=16% Similarity=0.175 Sum_probs=28.6
Q ss_pred CCCChHHHHhHHHHHHHHHcCCChHHHHHhhc
Q 019435 98 KTRDPYIIVKARDLIRLLSRSVPAPQAIKILD 129 (341)
Q Consensus 98 kT~DP~~IiKArD~IkAIaRGF~~EqAlkLLe 129 (341)
...++..|...+.+..+...|||+++...+|+
T Consensus 36 R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l~ 67 (67)
T cd04764 36 RYYTDEDIELLKKIKTLLEKGLSIKEIKEILN 67 (67)
T ss_pred eeeCHHHHHHHHHHHHHHHCCCCHHHHHHHhC
Confidence 35888899999999999999999999988874
No 67
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=34.83 E-value=27 Score=30.78 Aligned_cols=26 Identities=23% Similarity=0.171 Sum_probs=23.3
Q ss_pred hccccCCCCchhHHHHHhhcchhhHH
Q 019435 153 RQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
.|..||++|+.-++|+++.|-+|-|-
T Consensus 43 vG~~IG~~G~rI~~i~e~lgekIdVv 68 (140)
T PRK08406 43 MGLAIGKGGENVKRLEEKLGKDIELV 68 (140)
T ss_pred ccccCCcCchHHHHHHHHhCCceEEE
Confidence 49999999999999999999887665
No 68
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=34.81 E-value=18 Score=39.46 Aligned_cols=26 Identities=23% Similarity=0.475 Sum_probs=24.3
Q ss_pred hccccCCCCchhHHHHHhhcchhhHH
Q 019435 153 RQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
++.+||++|+|.+.|..-||+.|-+.
T Consensus 565 I~~vIG~gg~~ik~I~~~~~~~idi~ 590 (693)
T PRK11824 565 IRDVIGPGGKTIREITEETGAKIDIE 590 (693)
T ss_pred HHHHhcCCchhHHHHHHHHCCccccC
Confidence 68999999999999999999988877
No 69
>PRK15494 era GTPase Era; Provisional
Probab=33.13 E-value=30 Score=34.02 Aligned_cols=27 Identities=22% Similarity=0.356 Sum_probs=21.1
Q ss_pred hhccccCCCCchhHHH--------HHhhcchhhHH
Q 019435 152 RRQHLVGPNSSTLKAL--------EILTGCYILVQ 178 (341)
Q Consensus 152 rrgRIIG~~GkTkkaI--------E~LT~~yI~Vq 178 (341)
.++=|||.+|++.+.| |.+.||.|.+.
T Consensus 284 qk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 284 YKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 4788999999987765 77888876554
No 70
>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=29.86 E-value=1.9e+02 Score=24.91 Aligned_cols=52 Identities=15% Similarity=0.068 Sum_probs=38.1
Q ss_pred hhhhHHHHH-hhcccEEEEEccc----------------------CeEEEEcCCCCCC--hHHHHhHHHHHHHHHcCCCh
Q 019435 67 AWPMVKGAL-KEYGVSCELNLVE----------------------GSMTVSTTRKTRD--PYIIVKARDLIRLLSRSVPA 121 (341)
Q Consensus 67 ~W~~Ikk~L-e~~~l~i~LDl~e----------------------GsV~VrTt~kT~D--P~~IiKArD~IkAIaRGF~~ 121 (341)
--+..-+.| +++|+.|.|.-.. +.|.|.+ .| .-.+.+|..+|..|...+.+
T Consensus 23 PgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a----~~~~~e~~~~A~~~I~~ll~~~~~ 98 (120)
T cd02395 23 PRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITA----ETPPEEALAKAVEAIEELLKPAIE 98 (120)
T ss_pred CCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEe----CCcHHHHHHHHHHHHHHHhccCCC
Confidence 345566677 6799998887542 7788875 55 57899999999988876555
Q ss_pred H
Q 019435 122 P 122 (341)
Q Consensus 122 E 122 (341)
+
T Consensus 99 ~ 99 (120)
T cd02395 99 G 99 (120)
T ss_pred c
Confidence 4
No 71
>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=28.62 E-value=1.2e+02 Score=22.57 Aligned_cols=34 Identities=15% Similarity=0.189 Sum_probs=28.7
Q ss_pred CCCCCChHHHHhHHHHHHHHHcCCChHHHHHhhc
Q 019435 96 TRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILD 129 (341)
Q Consensus 96 t~kT~DP~~IiKArD~IkAIaRGF~~EqAlkLLe 129 (341)
.....+...|...+.+..+...||+++++..+|+
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 3345777889999999999999999999998874
No 72
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=28.23 E-value=1.8e+02 Score=31.77 Aligned_cols=113 Identities=21% Similarity=0.253 Sum_probs=71.3
Q ss_pred HHHHHhhhhHHHHHhhcccEEEEEcccCeEEEEcCCCCCChHHHHhHHHHHHHHHcC--------------CChHHHHHh
Q 019435 62 KYLQEAWPMVKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRS--------------VPAPQAIKI 127 (341)
Q Consensus 62 ~yLKe~W~~Ikk~Le~~~l~i~LDl~eGsV~VrTt~kT~DP~~IiKArD~IkAIaRG--------------F~~EqAlkL 127 (341)
.+|.+.-..|...+-.----..++...=.+.|-| .+|-.+.+--|+|+-||.- .++++|.++
T Consensus 5 ~~l~ei~~~i~~~~p~~~~It~vefEGPelvvY~----k~P~~~~~~~dlik~lAk~lrKRI~iR~dPsvl~~~e~A~~~ 80 (637)
T COG1782 5 EVLEEIRNKINEILPSDVKITDVEFEGPELVVYT----KNPELFAKDGDLIKDLAKDLRKRIIIRPDPSVLKPPEEARKI 80 (637)
T ss_pred HHHHHHHHHHHHhCCCcCceEEEEecCCeEEEEe----cCHHHhccchhHHHHHHHHHhhceEeccCchhcCCHHHHHHH
Confidence 4677777777777732222245777777888885 8898888766888777642 478999988
Q ss_pred hcccce--eEEEeecccccCchhhhh--hhccccCCCCchhHHHHHhhcchhhHH
Q 019435 128 LDDEMQ--CDIIKIGNLVRNKERFVK--RRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 128 LeDD~~--~DIIdI~~lv~nke~f~R--rrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
..+-+= .+|-||.=--.+++.+.- -=|=+||++|+|+.-|-.-||-.--|.
T Consensus 81 I~eivP~ea~i~~i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~iv 135 (637)
T COG1782 81 ILEIVPEEAGITDIYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIV 135 (637)
T ss_pred HHHhCccccCceeEEecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceee
Confidence 753221 222222100012343332 348899999999999988777654444
No 73
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=28.07 E-value=23 Score=37.29 Aligned_cols=118 Identities=19% Similarity=0.189 Sum_probs=70.2
Q ss_pred eeeeeeeecCchhHHHHHHhhhhHHHHH-hhcccEEEEEcc-cC-eEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHH
Q 019435 48 EVSSFSTLFPQYREKYLQEAWPMVKGAL-KEYGVSCELNLV-EG-SMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQA 124 (341)
Q Consensus 48 eessF~vlfPkyRe~yLKe~W~~Ikk~L-e~~~l~i~LDl~-eG-sV~VrTt~kT~DP~~IiKArD~IkAIaRGF~~EqA 124 (341)
++-.|.++.|.-...-+...-+.+...| .+++..+.++.. .. .|++.....+.|.|... +.|+.+.++.--.
T Consensus 254 ~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a-----~~a~~~~~~~~~~ 328 (485)
T KOG2190|consen 254 EELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTDRIVTISARENPEDRYSMA-----QEALLLVQPRISE 328 (485)
T ss_pred hhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCcceeeeccccCcccccccc-----hhhhhhccccccc
Confidence 4445677888878777888888888888 467777777655 32 35555544455544321 2222222221100
Q ss_pred HHhhcccceeEEEeecccccCchhhhhhhccccCCCCchhHHHHHhhcchhhHH
Q 019435 125 IKILDDEMQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 125 lkLLeDD~~~DIIdI~~lv~nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
..- ++- --.+.-.-++. ....|.|||++|...-.|..+||+.|.|+
T Consensus 329 ~~~--~~~-~~~v~~~l~vp-----s~~igciiGk~G~~iseir~~tgA~I~I~ 374 (485)
T KOG2190|consen 329 NAG--DDL-TQTVTQRLLVP-----SDLIGCIIGKGGAKISEIRQRTGASISIL 374 (485)
T ss_pred ccc--ccc-cceeeeeeccC-----ccccceeecccccchHHHHHhcCCceEEc
Confidence 000 110 11111111222 23689999999999999999999999998
No 74
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=26.85 E-value=27 Score=32.73 Aligned_cols=25 Identities=28% Similarity=0.569 Sum_probs=19.2
Q ss_pred hhccccCCCCchhHHH--------HHhhcchhh
Q 019435 152 RRQHLVGPNSSTLKAL--------EILTGCYIL 176 (341)
Q Consensus 152 rrgRIIG~~GkTkkaI--------E~LT~~yI~ 176 (341)
.++-|||.+|++.+.| |.+.||.|.
T Consensus 232 ~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~ 264 (270)
T TIGR00436 232 QKKIIIGKNGSMIKAIGIAARKDILELFDCDVF 264 (270)
T ss_pred ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEE
Confidence 3688999999988776 666676654
No 75
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=25.49 E-value=73 Score=30.97 Aligned_cols=72 Identities=25% Similarity=0.288 Sum_probs=50.3
Q ss_pred eeeeeeecCchhHHHHHHhhhhHHHHHh-hccc-EEEEEcccCeEEEEcCCCCCChHHHHhHHH--HHHHHHcCCChHHH
Q 019435 49 VSSFSTLFPQYREKYLQEAWPMVKGALK-EYGV-SCELNLVEGSMTVSTTRKTRDPYIIVKARD--LIRLLSRSVPAPQA 124 (341)
Q Consensus 49 essF~vlfPkyRe~yLKe~W~~Ikk~Le-~~~l-~i~LDl~eGsV~VrTt~kT~DP~~IiKArD--~IkAIaRGF~~EqA 124 (341)
+..|+| |-+=+. |=..|+..|+ --|| ++++|+.++.|.|.|+ .-|..|+.+-+ =.+|+.+|+-..+|
T Consensus 8 ~~efaV--~M~ces----cvnavk~~L~~V~Gi~~vevdle~q~v~v~ts---~p~s~i~~~le~tGr~Avl~G~G~psa 78 (247)
T KOG4656|consen 8 EAEFAV--QMTCES----CVNAVKACLKGVPGINSVEVDLEQQIVSVETS---VPPSEIQNTLENTGRDAVLRGAGKPSA 78 (247)
T ss_pred eEEEEE--echhHH----HHHHHHHHhccCCCcceEEEEhhhcEEEEEcc---CChHHHHHHHHhhChheEEecCCchhH
Confidence 344554 444444 4466788885 3444 6899999999999984 45556655432 35788899999999
Q ss_pred HHhhc
Q 019435 125 IKILD 129 (341)
Q Consensus 125 lkLLe 129 (341)
+.|+.
T Consensus 79 val~a 83 (247)
T KOG4656|consen 79 VALLA 83 (247)
T ss_pred HHHHH
Confidence 99986
No 76
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=25.34 E-value=27 Score=33.01 Aligned_cols=27 Identities=30% Similarity=0.324 Sum_probs=24.7
Q ss_pred hhccccCCCCchhHHHHHhhcchhhHH
Q 019435 152 RRQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 152 rrgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
|.+=|||+.|.+++.||..|+|.|.|-
T Consensus 18 R~~~lig~~g~v~k~ie~~~~~~~~iD 44 (194)
T COG1094 18 RIGVLIGKWGEVKKAIEEKTGVKLRID 44 (194)
T ss_pred hheeeecccccchHHHHhhcCeEEEEE
Confidence 568899999999999999999998876
No 77
>PRK14634 hypothetical protein; Provisional
Probab=24.98 E-value=3.2e+02 Score=24.47 Aligned_cols=89 Identities=12% Similarity=0.180 Sum_probs=54.3
Q ss_pred HHHhhhhHHHHHhhcccEEEEEcc---c---CeEEEEcCCCCCChHHHHhHHHHHHHHHcCCChHHHHHhhcccceeEEE
Q 019435 64 LQEAWPMVKGALKEYGVSCELNLV---E---GSMTVSTTRKTRDPYIIVKARDLIRLLSRSVPAPQAIKILDDEMQCDII 137 (341)
Q Consensus 64 LKe~W~~Ikk~Le~~~l~i~LDl~---e---GsV~VrTt~kT~DP~~IiKArD~IkAIaRGF~~EqAlkLLeDD~~~DII 137 (341)
....|..+...++.+|+.+ +|+. + ..+.|.-.....++..|--+..+=++|+-=+..++ ++.+.|+|||=
T Consensus 6 ~~~i~~l~~~~~~~~G~el-vdve~~~~~~~~~lrV~ID~~~g~~v~lddC~~vSr~is~~LD~~d---~i~~~Y~LEVS 81 (155)
T PRK14634 6 LPDLETLASATAADKGFEL-CGIQVLTHLQPMTLQVQIRRSSGSDVSLDDCAGFSGPMGEALEASQ---LLTEAYVLEIS 81 (155)
T ss_pred HHHHHHHHHHHHHHcCCEE-EEEEEEeCCCCcEEEEEEECCCCCcccHHHHHHHHHHHHHHhcccc---cCCCCeEEEEe
Confidence 4567778888787777664 3332 1 22444433233444677777777777765555444 34566888776
Q ss_pred eec--ccccCchhhhhhhccc
Q 019435 138 KIG--NLVRNKERFVKRRQHL 156 (341)
Q Consensus 138 dI~--~lv~nke~f~RrrgRI 156 (341)
.=+ .-..+..||.|.+||.
T Consensus 82 SPGldRpL~~~~~f~r~~G~~ 102 (155)
T PRK14634 82 SPGIGDQLSSDRDFQTFRGFP 102 (155)
T ss_pred CCCCCCcCCCHHHHHHhCCCe
Confidence 544 2234678999999984
No 78
>PRK00089 era GTPase Era; Reviewed
Probab=23.54 E-value=32 Score=32.20 Aligned_cols=26 Identities=23% Similarity=0.473 Sum_probs=20.3
Q ss_pred hccccCCCCchhHHH--------HHhhcchhhHH
Q 019435 153 RQHLVGPNSSTLKAL--------EILTGCYILVQ 178 (341)
Q Consensus 153 rgRIIG~~GkTkkaI--------E~LT~~yI~Vq 178 (341)
++=|||.+|++.+.| |.+.||.|.+.
T Consensus 238 k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 238 KGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred eeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 788999999998776 66777776543
No 79
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=23.27 E-value=1.4e+02 Score=21.75 Aligned_cols=31 Identities=13% Similarity=0.075 Sum_probs=27.3
Q ss_pred CCChHHHHhHHHHHHHHHcCCChHHHHHhhc
Q 019435 99 TRDPYIIVKARDLIRLLSRSVPAPQAIKILD 129 (341)
Q Consensus 99 T~DP~~IiKArD~IkAIaRGF~~EqAlkLLe 129 (341)
.+++..+...+.+..+...||+++++-.+|+
T Consensus 38 ~y~~~dl~~l~~i~~lr~~g~~~~~i~~~l~ 68 (70)
T smart00422 38 LYSDEDLERLRFIKRLKELGFSLEEIKELLE 68 (70)
T ss_pred ecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 4778899999999999999999999888875
No 80
>PRK07634 pyrroline-5-carboxylate reductase; Reviewed
Probab=23.08 E-value=78 Score=28.67 Aligned_cols=95 Identities=19% Similarity=0.176 Sum_probs=58.5
Q ss_pred hhhHHHHHhhcccEEEEEcccCeEEEEcCCCCCChHHHHh-HHHHHH-HHHcCCChHHHHHhhcccce--eEEEeecccc
Q 019435 68 WPMVKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVK-ARDLIR-LLSRSVPAPQAIKILDDEMQ--CDIIKIGNLV 143 (341)
Q Consensus 68 W~~Ikk~Le~~~l~i~LDl~eGsV~VrTt~kT~DP~~IiK-ArD~Ik-AIaRGF~~EqAlkLLeDD~~--~DIIdI~~lv 143 (341)
...+...++..|..+.++. ..+..-|.--+--|..+.. +..++. +...||+.++|.+++-.=+. .+ +.
T Consensus 146 ~~~v~~lf~~~G~~~~~~e--~~~~~~~a~~gs~pa~~~~~~~a~~~~~~~~Gl~~~~a~~~~~~~~~g~~~------~~ 217 (245)
T PRK07634 146 KETLQLILKGIGTSQLCTE--EEVHQLTAVTGSAPAFLYYFAESLIEATKSYGVDEETAKHLVIQMISGSAS------ML 217 (245)
T ss_pred HHHHHHHHHhCCCEEEECH--HHcchHHhhhcchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH------HH
Confidence 3455665677888887763 3344433322344433222 222333 45679999999999863211 11 11
Q ss_pred cCchhhhhhhccccCCCCchhHHHHHh
Q 019435 144 RNKERFVKRRQHLVGPNSSTLKALEIL 170 (341)
Q Consensus 144 ~nke~f~RrrgRIIG~~GkTkkaIE~L 170 (341)
.+..|+.-.+.++.=|+|.|..+|..|
T Consensus 218 ~~~~~~~~l~~~v~spgG~T~~gl~~l 244 (245)
T PRK07634 218 EQTQDPANLREQVTTPGGSTAEGLKAL 244 (245)
T ss_pred hCCCCHHHHHHhCCCCChHHHHHHHHh
Confidence 223578889999999999999998765
No 81
>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=23.06 E-value=1.8e+02 Score=31.63 Aligned_cols=92 Identities=21% Similarity=0.316 Sum_probs=61.1
Q ss_pred EEEcccCeEEEEcCCCCCChHHHHhHHHHHHHHHcC--------------CChHHHHHhhcccce--eEEEeecccccCc
Q 019435 83 ELNLVEGSMTVSTTRKTRDPYIIVKARDLIRLLSRS--------------VPAPQAIKILDDEMQ--CDIIKIGNLVRNK 146 (341)
Q Consensus 83 ~LDl~eGsV~VrTt~kT~DP~~IiKArD~IkAIaRG--------------F~~EqAlkLLeDD~~--~DIIdI~~lv~nk 146 (341)
.++...=.|.|-| .||-.+..--|+|+-||.- .++++|.+++.+=+- -.|-||.=-...+
T Consensus 20 ~~~~egp~~~~~~----~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~f~~~~~ 95 (630)
T TIGR03675 20 DVEFEGPELVIYT----KNPELFAKDDDLVKELAKKLRKRIVIRPDPSVLLPPEEAIEKIKEIVPEEAGITDIYFDDVTG 95 (630)
T ss_pred EEEEeCCeEEEEe----CCHHHhccchHHHHHHHHHhhceEEEecChhhcCCHHHHHHHHHHhCCCcCCceeEEecCCCc
Confidence 4666677788875 8998888877888888742 467888887753110 2222332111133
Q ss_pred hhhhhh--hccccCCCCchhHHHHHhhcchhhHH
Q 019435 147 ERFVKR--RQHLVGPNSSTLKALEILTGCYILVQ 178 (341)
Q Consensus 147 e~f~Rr--rgRIIG~~GkTkkaIE~LT~~yI~Vq 178 (341)
|.+..+ =|.+||++|.|+.-|=.-||-.-.|.
T Consensus 96 ~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~ 129 (630)
T TIGR03675 96 EVIIEAEKPGLVIGKGGSTLREITAETGWTPKVV 129 (630)
T ss_pred eEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEE
Confidence 444433 49999999999999988888766664
No 82
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=23.03 E-value=73 Score=19.62 Aligned_cols=21 Identities=19% Similarity=0.441 Sum_probs=18.2
Q ss_pred HHHHHHHcCCChHHHHHhhcc
Q 019435 110 DLIRLLSRSVPAPQAIKILDD 130 (341)
Q Consensus 110 D~IkAIaRGF~~EqAlkLLeD 130 (341)
-+|.|+++.=.++.|+.+|++
T Consensus 6 ~ll~a~~~~g~~~~a~~~~~~ 26 (34)
T PF13812_consen 6 ALLRACAKAGDPDAALQLFDE 26 (34)
T ss_pred HHHHHHHHCCCHHHHHHHHHH
Confidence 478899999999999999863
No 83
>COG0134 TrpC Indole-3-glycerol phosphate synthase [Amino acid transport and metabolism]
Probab=22.90 E-value=55 Score=31.99 Aligned_cols=69 Identities=29% Similarity=0.422 Sum_probs=52.7
Q ss_pred CCCChHHHHhHH----HHHHHHHcCCChHHHHHhhc--cc----ceeEEEeecccccCchhhhhhhccccCCCCchhHHH
Q 019435 98 KTRDPYIIVKAR----DLIRLLSRSVPAPQAIKILD--DE----MQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKAL 167 (341)
Q Consensus 98 kT~DP~~IiKAr----D~IkAIaRGF~~EqAlkLLe--DD----~~~DIIdI~~lv~nke~f~RrrgRIIG~~GkTkkaI 167 (341)
...|||.|..|| |.|-+|..-++-++.-.|++ -+ ...||-+..++ ++..+.-.+|||=|.+-+.++
T Consensus 115 FiiD~yQI~~Ar~~GADavLLI~~~L~~~~l~el~~~A~~LGm~~LVEVh~~eEl----~rAl~~ga~iIGINnRdL~tf 190 (254)
T COG0134 115 FIIDPYQIYEARAAGADAVLLIVAALDDEQLEELVDRAHELGMEVLVEVHNEEEL----ERALKLGAKIIGINNRDLTTL 190 (254)
T ss_pred CCCCHHHHHHHHHcCcccHHHHHHhcCHHHHHHHHHHHHHcCCeeEEEECCHHHH----HHHHhCCCCEEEEeCCCcchh
Confidence 368999999985 88999999999998888886 23 33444444444 345556889999999999988
Q ss_pred HHh
Q 019435 168 EIL 170 (341)
Q Consensus 168 E~L 170 (341)
|--
T Consensus 191 ~vd 193 (254)
T COG0134 191 EVD 193 (254)
T ss_pred eec
Confidence 753
No 84
>PRK10076 pyruvate formate lyase II activase; Provisional
Probab=22.60 E-value=1.7e+02 Score=27.24 Aligned_cols=84 Identities=10% Similarity=0.040 Sum_probs=44.1
Q ss_pred EcccCeEEEEcCCCCCChHHHHhHHHHHHHH-Hc---------CCChHHHHH-hhcccceeEEEeecccccCchhhhhhh
Q 019435 85 NLVEGSMTVSTTRKTRDPYIIVKARDLIRLL-SR---------SVPAPQAIK-ILDDEMQCDIIKIGNLVRNKERFVKRR 153 (341)
Q Consensus 85 Dl~eGsV~VrTt~kT~DP~~IiKArD~IkAI-aR---------GF~~EqAlk-LLeDD~~~DIIdI~~lv~nke~f~Rrr 153 (341)
+...|.|++..+..+--|-.+ .++++++ .+ |+-+..++. |+. -+.+-.+||+.+ +.+...+.=
T Consensus 36 ~~sggGVt~SGGEPllq~~fl---~~l~~~~k~~gi~~~leTnG~~~~~~~~~l~~-~~D~~l~DiK~~--d~~~~~~~t 109 (213)
T PRK10076 36 RTSGGGVTLSGGEVLMQAEFA---TRFLQRLRLWGVSCAIETAGDAPASKLLPLAK-LCDEVLFDLKIM--DATQARDVV 109 (213)
T ss_pred cCCCCEEEEeCchHHcCHHHH---HHHHHHHHHcCCCEEEECCCCCCHHHHHHHHH-hcCEEEEeeccC--CHHHHHHHH
Confidence 334689999875444333222 3444443 23 333444444 443 333556777765 223222233
Q ss_pred ccccCCCCchhHHHHHhhcchhhH
Q 019435 154 QHLVGPNSSTLKALEILTGCYILV 177 (341)
Q Consensus 154 gRIIG~~GkTkkaIE~LT~~yI~V 177 (341)
| +.++.++.+|+.+...-+-|
T Consensus 110 G---~~~~~il~nl~~l~~~g~~v 130 (213)
T PRK10076 110 K---MNLPRVLENLRLLVSEGVNV 130 (213)
T ss_pred C---CCHHHHHHHHHHHHhCCCcE
Confidence 3 45677888888777664433
No 85
>PTZ00431 pyrroline carboxylate reductase; Provisional
Probab=22.34 E-value=1.3e+02 Score=28.18 Aligned_cols=97 Identities=14% Similarity=0.192 Sum_probs=64.3
Q ss_pred hHHHHHhhcccEEEEEcccCeEEEEcCCCCCChHHHHh-HHHHH-HHHHcCCChHHHHHhhcccceeEEEeecccc-cCc
Q 019435 70 MVKGALKEYGVSCELNLVEGSMTVSTTRKTRDPYIIVK-ARDLI-RLLSRSVPAPQAIKILDDEMQCDIIKIGNLV-RNK 146 (341)
Q Consensus 70 ~Ikk~Le~~~l~i~LDl~eGsV~VrTt~kT~DP~~IiK-ArD~I-kAIaRGF~~EqAlkLLeDD~~~DIIdI~~lv-~nk 146 (341)
.|...++..|..+.++ +..+.+-|.--.--|..+.- +..++ -++..|++.++|.+|.-.=+. =-..++ .+.
T Consensus 139 ~v~~l~~~~G~~~~v~--E~~~d~~ta~~gsgPA~~~~~~~al~~~~v~~Gl~~~~a~~l~~~~~~----G~a~ll~~~~ 212 (260)
T PTZ00431 139 KVIDIFSACGIIQEIK--EKDMDIATAISGCGPAYVFLFIESLIDAGVKNGLNRDVSKNLVLQTIL----GSVHMVKASD 212 (260)
T ss_pred HHHHHHHhCCcEEEEC--hHHcchhhhhcCCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH----HHHHHHHhcC
Confidence 4556567889888887 44666655433343543332 23333 467899999999999865321 000111 345
Q ss_pred hhhhhhhccccCCCCchhHHHHHhhc
Q 019435 147 ERFVKRRQHLVGPNSSTLKALEILTG 172 (341)
Q Consensus 147 e~f~RrrgRIIG~~GkTkkaIE~LT~ 172 (341)
.|+.-.|.++.=|+|.|-.+|..|-.
T Consensus 213 ~~~~~l~~~v~spgG~T~~gl~~le~ 238 (260)
T PTZ00431 213 QPVQQLKDDVCSPGGITIVGLYTLEK 238 (260)
T ss_pred CCHHHHHHhCCCCChHHHHHHHHHHH
Confidence 68999999999999999999987743
No 86
>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=21.66 E-value=1.3e+02 Score=23.90 Aligned_cols=33 Identities=12% Similarity=0.076 Sum_probs=29.7
Q ss_pred CCCChHHHHhHHHHHHHHHcCCChHHHHHhhcc
Q 019435 98 KTRDPYIIVKARDLIRLLSRSVPAPQAIKILDD 130 (341)
Q Consensus 98 kT~DP~~IiKArD~IkAIaRGF~~EqAlkLLeD 130 (341)
...++..|...+.+..+...||+++++..+|..
T Consensus 38 R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~~ 70 (88)
T cd01105 38 RKYSLADVDRLLVIKELLDEGFTLAAAVEKLRR 70 (88)
T ss_pred eecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 357888999999999999999999999999973
No 87
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=20.56 E-value=58 Score=27.24 Aligned_cols=19 Identities=11% Similarity=0.191 Sum_probs=16.1
Q ss_pred hccccCCCCchhHHHHHhh
Q 019435 153 RQHLVGPNSSTLKALEILT 171 (341)
Q Consensus 153 rgRIIG~~GkTkkaIE~LT 171 (341)
=|+|||..|++...|..+.
T Consensus 72 Pg~vIG~~G~~i~~L~~~l 90 (109)
T cd02412 72 PGIIIGKKGAGIEKLRKEL 90 (109)
T ss_pred CCcccCCchHHHHHHHHHH
Confidence 4999999999999887653
No 88
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=20.21 E-value=15 Score=36.92 Aligned_cols=86 Identities=23% Similarity=0.433 Sum_probs=48.9
Q ss_pred ccceeEEEeecccccCchhhhhhhccccCCCCchhHHHHHhhcchhhHH-------HHHHHhhh-------hcCcccccc
Q 019435 130 DEMQCDIIKIGNLVRNKERFVKRRQHLVGPNSSTLKALEILTGCYILVQ-------ILMVKKEL-------EKDPALANE 195 (341)
Q Consensus 130 DD~~~DIIdI~~lv~nke~f~RrrgRIIG~~GkTkkaIE~LT~~yI~Vq-------~LmiKreL-------~kd~~l~~e 195 (341)
|...+.-+|++.- .++.+-..=++-.=----.-|-+++.--+.++ .+.-||.- ..+|.|-.+
T Consensus 211 dk~~~~~fdlgs~----t~leknir~lme~vDEl~qe~~~l~kyqr~~~rqq~~~~q~~aKrqaENa~R~argep~lP~d 286 (339)
T KOG1560|consen 211 DKPLHSNFDLGSG----TRLEKNIRLLMERVDELHQEIVNLNKYQRQLARQQAKKHQWIAKRQAENANRAARGEPPLPED 286 (339)
T ss_pred cccccccccccch----hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCCCChH
Confidence 4444666777643 33333322222111112223334444444444 55555543 357888888
Q ss_pred CccccccccccccccccccccccCCCCCCCCCCCCCchhhhhhhcccc
Q 019435 196 NWDRFLPKFKKKNVKQKKVKSKEKKPYTPFPPPPQPSKIDKLLESGEY 243 (341)
Q Consensus 196 ~W~rflP~fkkk~~~~~k~~~~~kk~ytpfpp~~~~~k~D~~lesGey 243 (341)
+|.|. |-|||+|+.+|-.|.||.-
T Consensus 287 d~kr~------------------------fk~pq~p~rLdslLiS~qi 310 (339)
T KOG1560|consen 287 DWKRI------------------------FKPPQEPRRLDSLLISGQI 310 (339)
T ss_pred HHHHH------------------------hcCCCchhHHHHHHHhhhH
Confidence 88763 3478999999999999964
Done!