Query 011603
Match_columns 481
No_of_seqs 209 out of 484
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 03:12:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011603.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011603hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1960 Predicted RNA-binding 100.0 1.1E-39 2.5E-44 332.7 13.3 266 26-303 12-303 (531)
2 KOG0119 Splicing factor 1/bran 100.0 5.3E-28 1.2E-32 252.2 15.5 161 127-295 61-230 (554)
3 cd02395 SF1_like-KH Splicing f 99.9 4.8E-26 1E-30 201.6 8.1 101 210-310 1-111 (120)
4 KOG1588 RNA-binding protein Sa 99.9 1.9E-22 4.2E-27 198.1 10.2 127 175-301 55-197 (259)
5 COG5176 MSL5 Splicing factor ( 99.8 1.2E-20 2.7E-25 181.2 10.1 152 142-298 82-243 (269)
6 KOG1960 Predicted RNA-binding 99.2 4.2E-12 9.2E-17 131.6 4.3 149 123-304 233-384 (531)
7 KOG1676 K-homology type RNA bi 99.2 5.4E-10 1.2E-14 120.4 18.0 166 101-299 136-304 (600)
8 KOG0334 RNA helicase [RNA proc 99.1 6.5E-11 1.4E-15 133.5 3.8 83 102-192 896-979 (997)
9 PRK13763 putative RNA-processi 98.8 2.6E-08 5.7E-13 93.7 9.5 145 104-294 3-156 (180)
10 TIGR03665 arCOG04150 arCOG0415 98.8 3.4E-08 7.3E-13 92.3 10.0 133 118-294 10-150 (172)
11 KOG1676 K-homology type RNA bi 98.6 1.9E-06 4.2E-11 93.5 16.8 160 105-299 231-393 (600)
12 cd00105 KH-I K homology RNA-bi 98.5 5E-07 1.1E-11 69.2 7.5 63 211-290 2-64 (64)
13 cd02393 PNPase_KH Polynucleoti 98.5 4.5E-07 9.7E-12 71.6 7.1 58 211-290 4-61 (61)
14 PF00013 KH_1: KH domain syndr 98.4 1.9E-07 4E-12 71.9 3.0 52 224-289 9-60 (60)
15 smart00322 KH K homology RNA-b 98.4 2.1E-06 4.7E-11 64.3 8.1 66 209-293 3-68 (69)
16 cd02394 vigilin_like_KH K homo 98.2 3.4E-06 7.4E-11 65.3 5.3 53 224-289 9-61 (62)
17 KOG2191 RNA-binding protein NO 98.1 0.00016 3.4E-09 74.9 17.8 164 104-300 39-206 (402)
18 cd02396 PCBP_like_KH K homolog 98.0 2.1E-05 4.6E-10 62.1 6.7 62 212-289 3-64 (65)
19 KOG2193 IGF-II mRNA-binding pr 97.7 0.00015 3.2E-09 77.0 9.7 141 120-302 213-356 (584)
20 PF13014 KH_3: KH domain 97.7 3.8E-05 8.3E-10 56.2 3.2 28 225-252 1-28 (43)
21 PRK13763 putative RNA-processi 97.5 0.00025 5.5E-09 67.0 6.5 63 211-294 5-70 (180)
22 TIGR02696 pppGpp_PNP guanosine 97.3 0.0018 3.9E-08 72.9 12.2 91 178-295 552-642 (719)
23 TIGR03665 arCOG04150 arCOG0415 97.3 0.00036 7.8E-09 65.5 5.0 56 225-295 8-65 (172)
24 cd02395 SF1_like-KH Splicing f 97.1 0.0011 2.4E-08 59.5 6.3 64 122-191 23-96 (120)
25 COG1094 Predicted RNA-binding 97.0 0.0011 2.4E-08 64.2 6.1 143 107-296 11-165 (194)
26 KOG0119 Splicing factor 1/bran 97.0 0.00097 2.1E-08 72.0 6.1 67 117-191 155-231 (554)
27 TIGR03591 polynuc_phos polyrib 97.0 0.0012 2.6E-08 73.9 6.6 100 210-347 552-651 (684)
28 KOG2193 IGF-II mRNA-binding pr 96.8 0.0068 1.5E-07 64.9 10.1 156 107-301 414-570 (584)
29 KOG2190 PolyC-binding proteins 96.8 0.022 4.9E-07 61.8 13.6 141 118-293 56-206 (485)
30 PLN00207 polyribonucleotide nu 96.7 0.0015 3.3E-08 74.9 4.9 101 210-348 686-788 (891)
31 PRK11824 polynucleotide phosph 96.1 0.0082 1.8E-07 67.4 5.7 93 224-348 563-655 (693)
32 KOG2190 PolyC-binding proteins 95.8 0.21 4.5E-06 54.5 14.5 60 117-191 149-209 (485)
33 PRK04163 exosome complex RNA-b 95.4 0.021 4.5E-07 56.2 5.0 53 225-293 155-207 (235)
34 KOG2191 RNA-binding protein NO 95.4 0.068 1.5E-06 56.0 8.7 76 209-301 39-114 (402)
35 KOG2874 rRNA processing protei 95.2 0.022 4.7E-07 58.5 4.3 57 226-300 160-216 (356)
36 KOG1067 Predicted RNA-binding 95.0 0.04 8.7E-07 61.0 5.9 81 226-323 608-698 (760)
37 KOG2814 Transcription coactiva 94.1 0.085 1.8E-06 55.1 5.6 64 225-300 67-130 (345)
38 PRK00106 hypothetical protein; 93.9 0.12 2.5E-06 57.1 6.5 60 220-294 231-290 (535)
39 TIGR03319 YmdA_YtgF conserved 93.8 0.12 2.5E-06 56.7 6.2 60 220-294 210-269 (514)
40 PRK12704 phosphodiesterase; Pr 93.7 0.15 3.2E-06 55.9 6.8 59 220-293 216-274 (520)
41 COG1185 Pnp Polyribonucleotide 92.8 0.16 3.4E-06 57.4 5.3 53 226-294 563-615 (692)
42 KOG0336 ATP-dependent RNA heli 91.9 0.28 6.1E-06 53.2 5.7 63 223-301 55-118 (629)
43 cd02393 PNPase_KH Polynucleoti 90.2 0.97 2.1E-05 35.7 6.0 57 106-185 4-61 (61)
44 KOG2192 PolyC-binding hnRNP-K 89.2 1 2.2E-05 46.5 6.7 65 225-300 325-389 (390)
45 KOG1588 RNA-binding protein Sa 87.8 1.5 3.3E-05 44.7 6.8 90 101-193 89-194 (259)
46 PRK12705 hypothetical protein; 86.5 0.67 1.4E-05 51.0 3.8 58 220-292 204-261 (508)
47 KOG2113 Predicted RNA binding 85.7 1.7 3.8E-05 45.6 6.1 110 120-253 41-153 (394)
48 cd02396 PCBP_like_KH K homolog 85.4 3.3 7.2E-05 32.6 6.3 53 117-184 11-64 (65)
49 KOG2192 PolyC-binding hnRNP-K 83.4 7.5 0.00016 40.4 9.4 133 118-295 60-193 (390)
50 PF00013 KH_1: KH domain syndr 82.4 3.6 7.9E-05 31.4 5.3 49 117-184 11-60 (60)
51 smart00322 KH K homology RNA-b 79.7 15 0.00031 27.1 7.6 64 105-188 4-68 (69)
52 cd02134 NusA_KH NusA_K homolog 79.6 1.9 4.1E-05 34.1 2.9 26 225-250 35-60 (61)
53 cd00105 KH-I K homology RNA-bi 76.4 12 0.00026 28.3 6.4 60 107-184 3-63 (64)
54 COG1097 RRP4 RNA-binding prote 74.5 6.4 0.00014 39.9 5.6 28 225-252 156-183 (239)
55 cd02394 vigilin_like_KH K homo 74.2 8.2 0.00018 29.7 5.1 58 107-184 3-61 (62)
56 PRK15494 era GTPase Era; Provi 73.1 16 0.00035 37.7 8.4 28 224-251 283-318 (339)
57 PF13184 KH_5: NusA-like KH do 71.0 1.6 3.4E-05 35.9 0.4 33 219-251 12-45 (69)
58 TIGR00436 era GTP-binding prot 70.2 20 0.00043 35.3 8.0 27 225-251 232-266 (270)
59 COG1702 PhoH Phosphate starvat 68.4 12 0.00025 39.9 6.2 57 225-299 25-83 (348)
60 KOG2113 Predicted RNA binding 68.0 3.3 7.1E-05 43.7 2.1 63 209-291 26-88 (394)
61 KOG2208 Vigilin [Lipid transpo 63.0 26 0.00057 40.6 8.2 108 108-253 349-457 (753)
62 COG5176 MSL5 Splicing factor ( 60.3 6.6 0.00014 39.5 2.5 76 108-191 154-241 (269)
63 PF13014 KH_3: KH domain 57.9 11 0.00024 27.4 2.7 25 117-141 2-27 (43)
64 COG1159 Era GTPase [General fu 54.7 31 0.00067 36.1 6.3 42 204-250 224-273 (298)
65 COG1094 Predicted RNA-binding 54.0 29 0.00064 34.2 5.7 68 100-191 89-165 (194)
66 cd02409 KH-II KH-II (K homolo 53.1 12 0.00027 28.1 2.5 23 226-248 36-58 (68)
67 KOG0334 RNA helicase [RNA proc 45.9 20 0.00042 42.8 3.6 76 215-295 902-977 (997)
68 PF01371 Trp_repressor: Trp re 44.9 1.1 2.3E-05 38.7 -5.0 27 117-143 37-70 (87)
69 PRK00089 era GTPase Era; Revie 40.0 29 0.00062 34.3 3.4 38 209-251 226-271 (292)
70 PRK08406 transcription elongat 39.8 22 0.00049 32.8 2.4 28 225-252 42-69 (140)
71 KOG2208 Vigilin [Lipid transpo 38.8 36 0.00077 39.6 4.3 30 226-255 358-387 (753)
72 PF07885 Ion_trans_2: Ion chan 38.1 26 0.00056 28.2 2.2 16 399-415 39-54 (79)
73 PRK01381 Trp operon repressor; 36.6 11 0.00024 33.5 -0.1 29 117-145 43-78 (99)
74 PRK01064 hypothetical protein; 33.4 30 0.00064 29.4 1.9 20 226-245 41-60 (78)
75 PF14611 SLS: Mitochondrial in 31.2 1.2E+02 0.0027 28.8 6.0 59 226-300 37-95 (210)
76 PRK12327 nusA transcription el 29.6 54 0.0012 35.0 3.5 39 211-250 233-272 (362)
77 PRK02821 hypothetical protein; 29.1 34 0.00074 29.0 1.6 20 226-245 42-61 (77)
78 KOG2279 Kinase anchor protein 28.9 49 0.0011 37.4 3.2 90 225-337 78-167 (608)
79 PRK00468 hypothetical protein; 28.8 36 0.00077 28.6 1.7 18 226-243 41-58 (75)
80 PF14611 SLS: Mitochondrial in 28.0 5.3E+02 0.012 24.5 11.2 125 117-294 36-164 (210)
81 cd02414 jag_KH jag_K homology 27.1 39 0.00085 27.7 1.6 22 226-247 35-56 (77)
82 PTZ00225 60S ribosomal protein 27.0 1.3E+02 0.0029 29.7 5.5 58 226-295 117-190 (214)
83 TIGR01953 NusA transcription t 26.9 70 0.0015 33.8 3.8 39 211-250 231-270 (341)
84 PF00408 PGM_PMM_IV: Phosphogl 26.2 1.8E+02 0.0039 23.3 5.3 26 268-293 46-72 (73)
85 COG1855 ATPase (PilT family) [ 25.1 1.4E+02 0.0029 33.8 5.6 70 176-256 458-527 (604)
86 PF00639 Rotamase: PPIC-type P 24.2 86 0.0019 26.1 3.2 33 271-303 1-34 (95)
87 PF13711 DUF4160: Domain of un 24.2 1.7E+02 0.0037 23.4 4.8 14 267-280 14-27 (66)
88 TIGR01952 nusA_arch NusA famil 23.5 62 0.0014 30.2 2.4 28 225-252 43-70 (141)
89 COG1185 Pnp Polyribonucleotide 22.5 1.3E+02 0.0028 35.0 5.0 62 106-190 552-616 (692)
90 COG0195 NusA Transcription elo 22.3 62 0.0013 31.7 2.2 33 220-252 81-113 (190)
91 PF09840 DUF2067: Uncharacteri 22.2 2.7E+02 0.0059 27.2 6.6 52 236-301 14-66 (190)
92 PRK06418 transcription elongat 21.8 69 0.0015 30.9 2.4 26 227-252 72-97 (166)
93 PF00472 RF-1: RF-1 domain; I 21.6 2.8E+02 0.0061 24.6 6.0 51 228-297 20-74 (113)
94 KOG3273 Predicted RNA-binding 20.5 61 0.0013 32.7 1.8 51 225-293 179-229 (252)
95 TIGR02696 pppGpp_PNP guanosine 20.5 1.4E+02 0.0031 34.8 4.9 62 106-190 580-642 (719)
96 COG1837 Predicted RNA-binding 20.4 62 0.0013 27.6 1.6 18 226-243 41-58 (76)
97 TIGR03591 polynuc_phos polyrib 20.3 1.5E+02 0.0032 34.1 5.0 53 116-189 561-614 (684)
98 PF13083 KH_4: KH domain; PDB: 20.1 23 0.0005 28.5 -1.0 20 226-245 40-59 (73)
No 1
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=100.00 E-value=1.1e-39 Score=332.75 Aligned_cols=266 Identities=18% Similarity=0.158 Sum_probs=203.3
Q ss_pred HHhhhcCCccccccccCCCccc--CCCCCCCCC-CCCCC--ccccccccCCCcccCCCCCCCccccCCCCCCCCCCCCCC
Q 011603 26 QRKKRKWDQPAESLINFPLASF--GISLPGVPV-APVVP--APAAAAFFTNPPVASGATVPPVVLQGPLPPKFNQPKVQD 100 (481)
Q Consensus 26 ~r~~~kwdqpa~~~~~~p~~~~--g~~~pg~~~-~~~~~--aa~~~a~~~~~~~~~~~~~pp~~~~~~~~~~~~~~k~~d 100 (481)
--++|||||+++..-.+++... +.-.|+..- ..... ++++-++.+|+-+-..-..-+-.- .+..-+...++.+|
T Consensus 12 ~~~~~~WD~~~~~d~~~~~~~~~s~~~~p~eS~~~~~~~h~~~~s~s~~~N~~~~~k~~~~~~~N-a~~~i~~p~N~~K~ 90 (531)
T KOG1960|consen 12 DNYSRDWDSRFTEDSYSRRDSQRSGNEAPRESRYYRKEEHLQERSRSRSPNRDSRWKSSSSGFAN-AHPPIEEPTNNGKE 90 (531)
T ss_pred CCccccccCCCCCccccCchhhhccCCCCCcccccCcchhhhhhhhccCcchhcccccccccccc-ccchhhcccccchh
Confidence 3578999999997765544332 333444221 11000 222333444442210000000000 01111223455556
Q ss_pred ceeEEEEEEcCCCCcccceeeechhhHHHHHhhhCCeEeeecceeCCCCC--CCCCCCeEEEEeeccchhhHHHHHHHHH
Q 011603 101 ELIIAREIVINDSESSVRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAP--PDGEKPLYLHISAGAHLKETAERILAVD 178 (481)
Q Consensus 101 e~~~~aEIeINDlpq~~R~~LTk~~Tq~eI~e~TGA~VtTRGrY~PP~~~--~~gepPLYL~Ieg~tq~kdt~ERi~aVd 178 (481)
++ ..++++|||.+++|||.+|+|.++++|.+++|+.|.+||+|++++.. .++++||||||.+.| . +.++
T Consensus 91 ~~-~~a~~~iN~~~~~~~~~~TRg~~~d~Ie~~~G~~~~~RGs~~~~El~~vg~~~~pLv~hI~~~T--~------Ei~~ 161 (531)
T KOG1960|consen 91 AA-AAAARRINESLQSTKATSTRGTSYDHIEGITGTTSASRGSAPAPELPPVGSSEGPLVDHIPPST--A------EITS 161 (531)
T ss_pred HH-HHHHHHhhcccccccceeccchhHHhhhhhccceeeccCCCCCccCCCCCCCCCcceeecCCcc--H------HHHH
Confidence 66 88999999999999999999999999999999999999999999974 578999999999977 2 5999
Q ss_pred HHHHHHHHHHHcCC--CC--------CCCc---------cccCCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHH
Q 011603 179 HAAAMVEEMLKQGH--AG--------FPTL---------QTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINH 239 (481)
Q Consensus 179 ~AvaeIkEILKe~p--~~--------~pp~---------~~p~~~G~k~~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~ 239 (481)
+|+++|+-.++.+. +. .+.+ .++..+|++|++ |.||++| +|.||+.++.-|++..||.+
T Consensus 162 ~Ai~RIkgv~~~~~~~~n~~~V~i~~~~sP~~~i~~~V~~~~f~~G~~Y~~-k~~v~~~-~P~~~~K~~~~~r~d~~La~ 239 (531)
T KOG1960|consen 162 KAIERIKGVFMQDVEINNVRNVYILVRASPLSEIENKVGVQLFSKGRYYPN-KALATDK-DPPLYLKIVSHNRKDLTLAL 239 (531)
T ss_pred HHHhhCccceeecccccccceEEEeecCCchhhhccccccccccccccchh-heecccC-CcchhhhhhccCccchhhhh
Confidence 99999997766652 11 1111 123578899999 9999999 99999999999999999999
Q ss_pred HHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhhhcc
Q 011603 240 IMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGAS 303 (481)
Q Consensus 240 Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~eE~~~~ 303 (481)
|+.||++++.|||||||.+|++.|+|++|||||+|+|.+.+.+.+||++|+||+++|+.+|.+|
T Consensus 240 ~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl~~~v~~~~sr~ 303 (531)
T KOG1960|consen 240 QEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNGNGENGAPRRKWNLEEKVYINLSRG 303 (531)
T ss_pred hhhhhhhhhhhccccccccCcccccccCCceeEEeecCCchhhccchhHHHhHHHHHHHHhhhh
Confidence 9999999999999999999999999999999999999999999999999999999999999765
No 2
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=99.95 E-value=5.3e-28 Score=252.24 Aligned_cols=161 Identities=22% Similarity=0.323 Sum_probs=135.0
Q ss_pred HHHHHhhhCCeEeeecce-eCCC-C-CCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCCccccCC
Q 011603 127 QEEIQKCTGAVVITRGKY-RLPN-A-PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQTVMG 203 (481)
Q Consensus 127 q~eI~e~TGA~VtTRGrY-~PP~-~-~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeIkEILKe~p~~~pp~~~p~~ 203 (481)
+++|.+..+. |.+ +|+. + +.++..|+|..-.-..++++.|.|+++-++..+.|+++||..+.+.++.+|...
T Consensus 61 iee~t~kLrt-----~d~~~p~~~e~rSPsp~p~yda~g~R~ntRe~R~r~~Le~er~e~I~~~lk~nP~fkpP~DYk~p 135 (554)
T KOG0119|consen 61 IEEITRKLRT-----GDVGVPPPRELRSPSPEPVYDAKGKRLNTREQRARKKLEDERHEIIEEILKLNPGFKPPADYKPP 135 (554)
T ss_pred HHHhhhhhcc-----ccCCCCCCccccCCCcchhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCcccCcc
Confidence 5566665554 333 4554 3 678999999887666667788889999999999999999999999988765322
Q ss_pred CCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCC------CCCCCCCCCcEEEEEeC
Q 011603 204 NGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEG------LQGEEVHQPLHLFLSSN 277 (481)
Q Consensus 204 ~G~k~~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~------~~g~Es~EPLHV~Isa~ 277 (481)
..+++|||||+|+||+|||+|+||||+|+|+|+||+||||||+||||||++... ......+||||++|+++
T Consensus 136 ---~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isad 212 (554)
T KOG0119|consen 136 ---AKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISAD 212 (554)
T ss_pred ---cccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecc
Confidence 267899999999999999999999999999999999999999999999997422 11234789999999999
Q ss_pred CHHHHHHHHHHHHHHHHH
Q 011603 278 NPKSLEEAKRLAENLLDT 295 (481)
Q Consensus 278 ~~e~v~~Ak~LiE~LL~t 295 (481)
+.|+|++|.++||+||..
T Consensus 213 t~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 213 TQEKIKKAIAVIENLIQS 230 (554)
T ss_pred hHHHHHHHHHHHHHHHHh
Confidence 999999999999999995
No 3
>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=99.93 E-value=4.8e-26 Score=201.58 Aligned_cols=101 Identities=21% Similarity=0.373 Sum_probs=89.0
Q ss_pred eeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCC-------CCCCCCCCCcEEEEEeCC--HH
Q 011603 210 STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEG-------LQGEEVHQPLHLFLSSNN--PK 280 (481)
Q Consensus 210 eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~-------~~g~Es~EPLHV~Isa~~--~e 280 (481)
++|||||+|.||+|||+|+||||+|+|+|+|++||||+|.|||+||++.+. ...++.+|||||+|++++ .+
T Consensus 1 ~~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e 80 (120)
T cd02395 1 TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEE 80 (120)
T ss_pred CCEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHH
Confidence 479999999999999999999999999999999999999999999998654 345678999999999999 99
Q ss_pred HHHHHHHHHHHHHHHHHHh-hhccccccccc
Q 011603 281 SLEEAKRLAENLLDTISAE-CGASRVSSCKV 310 (481)
Q Consensus 281 ~v~~Ak~LiE~LL~tV~eE-~~~~r~~~~~~ 310 (481)
.+++|+++|++||..+.++ .+.++-.....
T Consensus 81 ~~~~A~~~I~~ll~~~~~~~~~~~k~~ql~~ 111 (120)
T cd02395 81 ALAKAVEAIEELLKPAIEGGNDELKREQLRE 111 (120)
T ss_pred HHHHHHHHHHHHhccCCCccchHHHHHHHHH
Confidence 9999999999999999877 55554433333
No 4
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=99.87 E-value=1.9e-22 Score=198.14 Aligned_cols=127 Identities=23% Similarity=0.343 Sum_probs=100.5
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCccc---cCCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEe
Q 011603 175 LAVDHAAAMVEEMLKQGHAGFPTLQT---VMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLR 251 (481)
Q Consensus 175 ~aVd~AvaeIkEILKe~p~~~pp~~~---p~~~G~k~~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IR 251 (481)
+.+++.+.+|.-.+.+..+..+...+ ..........+||+||++.||+|||+||||||+|+++|+||+||||||+||
T Consensus 55 rLL~~Ei~rv~~~~~~~~~~~~~~~~~~~~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 55 RLLDEEIERVQTSGRQHGSKEPEELPYADVYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred HHHHHHHHHHHhhhhhccCCCchhcccccCccCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 57888888888777754322222211 111222567899999999999999999999999999999999999999999
Q ss_pred ecCCCCCC-------CC-CCCCCCCCcEEEEEeCCHHH-----HHHHHHHHHHHHHHHHHhhh
Q 011603 252 GRGSGNSE-------GL-QGEEVHQPLHLFLSSNNPKS-----LEEAKRLAENLLDTISAECG 301 (481)
Q Consensus 252 GRGSg~~E-------~~-~g~Es~EPLHV~Isa~~~e~-----v~~Ak~LiE~LL~tV~eE~~ 301 (481)
||||++.. +. ..++.+|||||+|++..+.. |..|.+.|+.||.++.+++.
T Consensus 135 GrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~P~~e~~d 197 (259)
T KOG1588|consen 135 GRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLVPDHEDED 197 (259)
T ss_pred cCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcCCCCCCch
Confidence 99999842 21 23458999999999988764 66889999999999999887
No 5
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.83 E-value=1.2e-20 Score=181.21 Aligned_cols=152 Identities=13% Similarity=0.096 Sum_probs=129.4
Q ss_pred cceeCCCC--CCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCCccccCCCCc-ccceeEEEecCC
Q 011603 142 GKYRLPNA--PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQTVMGNGV-QAMSTSVFLGFD 218 (481)
Q Consensus 142 GrY~PP~~--~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeIkEILKe~p~~~pp~~~p~~~G~-k~~eeKI~Iple 218 (481)
+.++|+.. +.+..+|.|..|....++.+.+.++++-|+...++++.++.-+-++.+.++ .+ ...++|||||++
T Consensus 82 ~d~Vp~~re~Rspsppp~yd~~GrRlntre~ry~kkLeder~~l~era~k~lp~fv~p~dy----~rpsk~q~KiYIPV~ 157 (269)
T COG5176 82 PDGVPSKRELRSPSPPPRYDEIGRRLNTREARYNKKLEDERLWLKERAQKILPRFVLPNDY----IRPSKYQNKIYIPVQ 157 (269)
T ss_pred CCCCCchhhccCCCCCcchhHHhhhhhHHHHHHhhhhhHHHHHHHHHHHHhcCcccCCccc----cCcccccceEEeehh
Confidence 44567653 678999999999999888888889999999999999999988887765443 33 567899999999
Q ss_pred CCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCC-------CCCCCCCcEEEEEeCCHHHHHHHHHHHHH
Q 011603 219 ADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQ-------GEEVHQPLHLFLSSNNPKSLEEAKRLAEN 291 (481)
Q Consensus 219 ~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~-------g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~ 291 (481)
+||+.||+|+||||+|.|+|++|..|+|||.|||+||.+. +.. -....++||++|+++..+++.++.++|.+
T Consensus 158 eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKe-gk~ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n 236 (269)
T COG5176 158 EYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKE-GKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLN 236 (269)
T ss_pred hCcccceeEEEecCCcchHHHHHHHhCCeEEEeccccccc-CcccccCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHH
Confidence 9999999999999999999999999999999999999862 221 11256789999999999999999999999
Q ss_pred HHHHHHH
Q 011603 292 LLDTISA 298 (481)
Q Consensus 292 LL~tV~e 298 (481)
.|.+...
T Consensus 237 ~I~~a~~ 243 (269)
T COG5176 237 AIREARR 243 (269)
T ss_pred HHHHHhc
Confidence 9987653
No 6
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=99.24 E-value=4.2e-12 Score=131.63 Aligned_cols=149 Identities=23% Similarity=0.390 Sum_probs=124.4
Q ss_pred chhhHHHHHhhhCCeEeeecceeCCCCC---CCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCCcc
Q 011603 123 KRHTQEEIQKCTGAVVITRGKYRLPNAP---PDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQ 199 (481)
Q Consensus 123 k~~Tq~eI~e~TGA~VtTRGrY~PP~~~---~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeIkEILKe~p~~~pp~~ 199 (481)
+-.++..|+.++++.+..||++---.++ .+..-|.|+.|.+.+- +.+..|..+|..++..
T Consensus 233 ~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~--------~g~~~A~r~~~nl~~~--------- 295 (531)
T KOG1960|consen 233 KDLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNG--------NGENGAPRRKWNLEEK--------- 295 (531)
T ss_pred cchhhhhhhhhhhhhhhhccccccccCcccccccCCceeEEeecCCc--------hhhccchhHHHhHHHH---------
Confidence 4567889999999999999998654453 3667899999999883 4678888777777542
Q ss_pred ccCCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCH
Q 011603 200 TVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNP 279 (481)
Q Consensus 200 ~p~~~G~k~~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~ 279 (481)
++|.+. ..|| .-.|.||-|.|.|||+.+|-.+++|+|.||+|+++.+++++++|.||||..+++
T Consensus 296 -------------v~~~~s--r~~~-~~~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i~p~~~~~~~~p~~~~~~~~~~ 359 (531)
T KOG1960|consen 296 -------------VYINLS--RGFH-RQAIVGPQGAYVKHIQQETRTRVQIKGQGSAFIEPSTNRESDEPIHLCIMSHDP 359 (531)
T ss_pred -------------HHHHhh--hhhh-hcccccCCcccccccCCCCCcceeccCccceeecCCCCCCCCCCcccccccCCh
Confidence 222211 1222 335789999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhccc
Q 011603 280 KSLEEAKRLAENLLDTISAECGASR 304 (481)
Q Consensus 280 e~v~~Ak~LiE~LL~tV~eE~~~~r 304 (481)
..|+.|+-||++||..|+.+|..|+
T Consensus 360 ~~~~~~~~~~~~~i~~v~~qy~~~~ 384 (531)
T KOG1960|consen 360 NAIQRAKVLCEDLIASVHQQYKAWK 384 (531)
T ss_pred hhhhhhhhcccccCCcccccCcccc
Confidence 9999999999999999999998876
No 7
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.20 E-value=5.4e-10 Score=120.41 Aligned_cols=166 Identities=20% Similarity=0.277 Sum_probs=122.8
Q ss_pred ceeEEEEEEcCCCCcccceeeec-hhhHHHHHhhhCCeEeeecceeCCCC-CCCCCCCeEEEEeeccchhhHHHHHHHHH
Q 011603 101 ELIIAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNA-PPDGEKPLYLHISAGAHLKETAERILAVD 178 (481)
Q Consensus 101 e~~~~aEIeINDlpq~~R~~LTk-~~Tq~eI~e~TGA~VtTRGrY~PP~~-~~~gepPLYL~Ieg~tq~kdt~ERi~aVd 178 (481)
....+.||.|-+-. |-.++.| |+|++.+++.+||.+.. +=++. .+...||| .|+|+. ..|+
T Consensus 136 ~~~ttqeI~IPa~k--~GlIIGKgGETikqlqe~sg~k~i~----iqd~~~~~~~~Kpl--ritGdp---------~~ve 198 (600)
T KOG1676|consen 136 SVETTQEILIPANK--CGLIIGKGGETIKQLQEQSGVKMIL----VQDGSIATGADKPL--RITGDP---------DKVE 198 (600)
T ss_pred ccceeeeeccCccc--eeeEeccCccHHHHHHhhcCCceEE----EecCCcCCCCCCce--eecCCH---------HHHH
Confidence 44467899998887 8999998 99999999999987544 11222 33478888 788876 4799
Q ss_pred HHHHHHHHHHHcCCCCCCCccccCCCCcc-cceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCC
Q 011603 179 HAAAMVEEMLKQGHAGFPTLQTVMGNGVQ-AMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGN 257 (481)
Q Consensus 179 ~AvaeIkEILKe~p~~~pp~~~p~~~G~k-~~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~ 257 (481)
.|..+|.++|+++-.-.+... ..+|.. --++++-|. +|+| -||.|||-+|.|||+|+.|||+||+|+=-
T Consensus 199 ~a~~lV~dil~e~~~~~~g~~--~~~g~~~g~~~~~~V~---VPr~-~VG~IIGkgGE~IKklq~etG~KIQfkpD---- 268 (600)
T KOG1676|consen 199 QAKQLVADILREEDDEVPGSG--GHAGVRGGGSATREVK---VPRS-KVGIIIGKGGEMIKKLQNETGAKIQFKPD---- 268 (600)
T ss_pred HHHHHHHHHHHhcccCCCccc--cccCcCccccceeEEe---cccc-ceeeEEecCchHHHHHhhccCceeEeecC----
Confidence 999999999997532221111 122221 123455555 4566 69999999999999999999999999841
Q ss_pred CCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHh
Q 011603 258 SEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAE 299 (481)
Q Consensus 258 ~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~eE 299 (481)
.+..-|+..+..-.+.+.++.|++||.+||..+.+.
T Consensus 269 ------d~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 269 ------DDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred ------CCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence 122446677777778999999999999999998877
No 8
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=99.07 E-value=6.5e-11 Score=133.47 Aligned_cols=83 Identities=31% Similarity=0.502 Sum_probs=77.1
Q ss_pred eeEEEEEEcCCCCcccceeeechhhHHHHHhhhCCeEeeecceeCCCC-CCCCCCCeEEEEeeccchhhHHHHHHHHHHH
Q 011603 102 LIIAREIVINDSESSVRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNA-PPDGEKPLYLHISAGAHLKETAERILAVDHA 180 (481)
Q Consensus 102 ~~~~aEIeINDlpq~~R~~LTk~~Tq~eI~e~TGA~VtTRGrY~PP~~-~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~A 180 (481)
..|.++++|||+||.+||++|..+++..|.+.+++.|+|||.|||+++ +.++|++|||+|++.++ ..|.+|
T Consensus 896 ~~y~~~~~inD~Pq~~r~~vt~~~~L~~i~e~~~~~it~rg~f~~~gk~p~~gErklyl~ve~~~e--------~~vqra 967 (997)
T KOG0334|consen 896 FIYEAELEINDFPQNARWRVTYKEALLRISEPTAAGITTRGKFNPPGKEPKPGERKLYLLVEGPDE--------LSVQRA 967 (997)
T ss_pred ceeeeeccccccchhcceeeechhhhhhccCccccceeeccccCCCCCCCCCcchhhhhhhhcchh--------HHHHHH
Confidence 368999999999999999999999999999999999999999999997 67899999999999874 589999
Q ss_pred HHHHHHHHHcCC
Q 011603 181 AAMVEEMLKQGH 192 (481)
Q Consensus 181 vaeIkEILKe~p 192 (481)
+.++++.+++..
T Consensus 968 ~~e~~r~l~e~~ 979 (997)
T KOG0334|consen 968 IEELERLLEEEV 979 (997)
T ss_pred HHHHHHHHHHHH
Confidence 999999888763
No 9
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.78 E-value=2.6e-08 Score=93.71 Aligned_cols=145 Identities=19% Similarity=0.204 Sum_probs=96.3
Q ss_pred EEEEEEcCCCCcccceeeec-hhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEe---eccchhhHHHHHHHHHH
Q 011603 104 IAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHIS---AGAHLKETAERILAVDH 179 (481)
Q Consensus 104 ~~aEIeINDlpq~~R~~LTk-~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ie---g~tq~kdt~ERi~aVd~ 179 (481)
+...+.|..-. .+..+.+ |.+++.|+++||+.|...-. +... .|. +.+ + ..+++
T Consensus 3 ~~~~i~IP~~k--ig~iIG~gGk~Ik~I~e~tg~~I~i~~~----------~g~V--~I~~~~~~d--~------~~i~k 60 (180)
T PRK13763 3 MMEYVKIPKDR--IGVLIGKKGETKKEIEERTGVKLEIDSE----------TGEV--IIEPTDGED--P------LAVLK 60 (180)
T ss_pred ceEEEEcCHHH--hhhHhccchhHHHHHHHHHCcEEEEECC----------CCeE--EEEeCCCCC--H------HHHHH
Confidence 45566675444 6777776 79999999999999887531 1233 454 333 2 58999
Q ss_pred HHHHHHHHHHcCCCCCCCccccCCCCcccceeEEEecCCCC--CCC---ceeeEEeCCCchhHHHHHHhhCcEEEEeecC
Q 011603 180 AAAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDAD--ASL---NIAARIRGPNDQYINHIMNETGATVLLRGRG 254 (481)
Q Consensus 180 AvaeIkEILKe~p~~~pp~~~p~~~G~k~~eeKI~Iple~~--P~F---N~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRG 254 (481)
|++.|+.++..- .++.-+- -.|--+.-+.+ .+.++ .+- ..+|+|||++|.++|.||..|||+|.|-++
T Consensus 61 A~~~I~ai~~gf---~~e~A~~-l~gd~y~~~Vi--~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~- 133 (180)
T PRK13763 61 ARDIVKAIGRGF---SPEKALR-LLDDDYVLEVI--DLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGK- 133 (180)
T ss_pred HHHHHHHHhcCC---CHHHHHH-HhCCCceEEEE--EhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCC-
Confidence 999999987631 1110000 00001111111 11111 011 259999999999999999999999999642
Q ss_pred CCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 011603 255 SGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 294 (481)
Q Consensus 255 Sg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~ 294 (481)
.|+|.| ++++++.|++.++.|++
T Consensus 134 ----------------~v~i~G-~~~~~~~A~~~I~~li~ 156 (180)
T PRK13763 134 ----------------TVAIIG-DPEQVEIAREAIEMLIE 156 (180)
T ss_pred ----------------EEEEEe-CHHHHHHHHHHHHHHHc
Confidence 277776 99999999999999984
No 10
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.78 E-value=3.4e-08 Score=92.31 Aligned_cols=133 Identities=20% Similarity=0.199 Sum_probs=88.6
Q ss_pred ceeeec-hhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEE--eeccchhhHHHHHHHHHHHHHHHHHHHHcCCCC
Q 011603 118 RYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHI--SAGAHLKETAERILAVDHAAAMVEEMLKQGHAG 194 (481)
Q Consensus 118 R~~LTk-~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~I--eg~tq~kdt~ERi~aVd~AvaeIkEILKe~p~~ 194 (481)
+-.+.+ |++++.|+++||+.|...- ++. .+.| .+.+ + ..+++|++.|+.+...-.
T Consensus 10 g~vIG~gG~~Ik~I~~~tgv~I~Id~----------~~g--~V~I~~~t~d--~------~~i~kA~~~I~~i~~gf~-- 67 (172)
T TIGR03665 10 GVLIGKGGETKKEIEERTGVKLDIDS----------ETG--EVKIEEEDED--P------LAVMKAREVVKAIGRGFS-- 67 (172)
T ss_pred hhHhCCchhHHHHHHHHhCcEEEEEc----------CCc--eEEEecCCCC--H------HHHHHHHHHHHHHHcCCC--
Confidence 344544 8999999999999988752 112 2345 2322 2 589999999999765311
Q ss_pred CCCccccCCCCcccceeEEEecCCCC--CCC---ceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCC
Q 011603 195 FPTLQTVMGNGVQAMSTSVFLGFDAD--ASL---NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQP 269 (481)
Q Consensus 195 ~pp~~~p~~~G~k~~eeKI~Iple~~--P~F---N~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EP 269 (481)
++..+- -.|--+.-+ | |.+.++ ..- ..+|+|||++|.+++.||..|||+|.|-|
T Consensus 68 -~e~A~~-l~gd~y~~~-V-i~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----------------- 126 (172)
T TIGR03665 68 -PEKALK-LLDDDYMLE-V-IDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----------------- 126 (172)
T ss_pred -HHHHHH-hcCCcceEE-E-EEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC-----------------
Confidence 110000 000011111 2 222221 000 25999999999999999999999999974
Q ss_pred cEEEEEeCCHHHHHHHHHHHHHHHH
Q 011603 270 LHLFLSSNNPKSLEEAKRLAENLLD 294 (481)
Q Consensus 270 LHV~Isa~~~e~v~~Ak~LiE~LL~ 294 (481)
=.|+|.| ++++++.|++++++||+
T Consensus 127 ~~v~i~G-~~~~~~~A~~~i~~li~ 150 (172)
T TIGR03665 127 KTVGIIG-DPEQVQIAREAIEMLIE 150 (172)
T ss_pred CEEEEEC-CHHHHHHHHHHHHHHHc
Confidence 2588999 99999999999999994
No 11
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.56 E-value=1.9e-06 Score=93.54 Aligned_cols=160 Identities=21% Similarity=0.353 Sum_probs=116.6
Q ss_pred EEEEEcCCCCcccceeeec-hhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHH
Q 011603 105 AREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAM 183 (481)
Q Consensus 105 ~aEIeINDlpq~~R~~LTk-~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~Avae 183 (481)
..+|.|--+. |-.+|.| |++++.|+.+||+.| .|+|+..++.-||+| .|-|.. ..+++|..+
T Consensus 231 ~~~V~VPr~~--VG~IIGkgGE~IKklq~etG~KI----QfkpDd~p~speR~~--~IiG~~---------d~ie~Aa~l 293 (600)
T KOG1676|consen 231 TREVKVPRSK--VGIIIGKGGEMIKKLQNETGAKI----QFKPDDDPSSPERPA--QIIGTV---------DQIEHAAEL 293 (600)
T ss_pred eeEEeccccc--eeeEEecCchHHHHHhhccCcee----EeecCCCCCCcccee--eeecCH---------HHHHHHHHH
Confidence 3567666665 8889998 999999999999865 677888777778988 788865 378999999
Q ss_pred HHHHHHcCCCCCCCccccCCCCcccc--eeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCC
Q 011603 184 VEEMLKQGHAGFPTLQTVMGNGVQAM--STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGL 261 (481)
Q Consensus 184 IkEILKe~p~~~pp~~~p~~~G~k~~--eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~ 261 (481)
|++||........-. +.-|.-.. +--+-||-+ =.|+|||++|.|+|.|..|+||++.|-=-
T Consensus 294 I~eii~~~~~~~~~~---~~~G~P~~~~~fy~~VPa~------KcGLvIGrGGEtIK~in~qSGA~~el~r~-------- 356 (600)
T KOG1676|consen 294 INEIIAEAEAGAGGG---MGGGAPGLVAQFYMKVPAD------KCGLVIGRGGETIKQINQQSGARCELSRQ-------- 356 (600)
T ss_pred HHHHHHHHhccCCCC---cCCCCccceeeEEEecccc------ccccccCCCccchhhhcccCCccccccCC--------
Confidence 999998762211000 11111111 222335533 27999999999999999999999976421
Q ss_pred CCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHh
Q 011603 262 QGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAE 299 (481)
Q Consensus 262 ~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~eE 299 (481)
..-.+.+..+++.-.++..|+-|+.||++-+.-+...
T Consensus 357 -~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~~~n 393 (600)
T KOG1676|consen 357 -PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDIAPN 393 (600)
T ss_pred -CCCCCccceEEEEecCcccchHHHHHHHHHhcccCCC
Confidence 1123566888999999999999999999877765544
No 12
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.49 E-value=5e-07 Score=69.19 Aligned_cols=63 Identities=27% Similarity=0.393 Sum_probs=50.7
Q ss_pred eEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 011603 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 290 (481)
Q Consensus 211 eKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE 290 (481)
.+|.||. +++++|||++|.++++|+++|||+|.|...+. ..+...|.|.|. .+.++.|+.+++
T Consensus 2 ~~i~ip~------~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~----------~~~~~~v~i~G~-~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPS------SLVGRIIGKGGSTIKEIREETGAKIKIPDSGS----------GSEERIVTITGT-PEAVEKAKELIL 64 (64)
T ss_pred EEEEEch------hhcceeECCCCHHHHHHHHHHCCEEEEcCCCC----------CCCceEEEEEcC-HHHHHHHHHHhC
Confidence 4567764 67999999999999999999999999986432 235567888887 788999988763
No 13
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.48 E-value=4.5e-07 Score=71.57 Aligned_cols=58 Identities=21% Similarity=0.403 Sum_probs=48.5
Q ss_pred eEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 011603 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 290 (481)
Q Consensus 211 eKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE 290 (481)
+.+.||.+ ++|+|||++|+++|.|+++|||+|.|-- .-.|.|.|.+.+++++|+++++
T Consensus 4 ~~i~Ip~~------~ig~iIGkgG~~ik~I~~~tg~~I~i~~----------------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 4 ETMKIPPD------KIRDVIGPGGKTIKKIIEETGVKIDIED----------------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEeChh------heeeeECCCchHHHHHHHHHCCEEEeCC----------------CCEEEEEeCCHHHHHHHHHHhC
Confidence 45666533 5899999999999999999999998742 1259999999999999999985
No 14
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=98.40 E-value=1.9e-07 Score=71.94 Aligned_cols=52 Identities=25% Similarity=0.433 Sum_probs=45.9
Q ss_pred ceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 011603 224 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 289 (481)
Q Consensus 224 N~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~Li 289 (481)
+++|+|||++|.++|+|+++|||+|.|... ++.-.|.|+| +++++++|+++|
T Consensus 9 ~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-------------~~~~~v~I~G-~~~~v~~A~~~I 60 (60)
T PF00013_consen 9 SLVGRIIGKKGSNIKEIEEETGVKIQIPDD-------------DERDIVTISG-SPEQVEKAKKMI 60 (60)
T ss_dssp HHHHHHHTGGGHHHHHHHHHHTSEEEEEST-------------TEEEEEEEEE-SHHHHHHHHHHH
T ss_pred HHcCEEECCCCCcHHHhhhhcCeEEEEcCC-------------CCcEEEEEEe-CHHHHHHHHhhC
Confidence 368999999999999999999999999653 1456899999 999999999986
No 15
>smart00322 KH K homology RNA-binding domain.
Probab=98.37 E-value=2.1e-06 Score=64.35 Aligned_cols=66 Identities=23% Similarity=0.341 Sum_probs=54.2
Q ss_pred ceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 011603 209 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 288 (481)
Q Consensus 209 ~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~L 288 (481)
...+|.|+. +++|+|||++|.++++|+++|||+|.+.+.++ ....+.|.++ .+.+..|+.+
T Consensus 3 ~~~~i~i~~------~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~------------~~~~v~i~g~-~~~v~~a~~~ 63 (69)
T smart00322 3 VTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS------------EERVVEITGP-PENVEKAAEL 63 (69)
T ss_pred eEEEEEEcc------hhcceeECCCchHHHHHHHHHCCEEEECCCCC------------CccEEEEEcC-HHHHHHHHHH
Confidence 345677764 57899999999999999999999999986433 3466888888 8999999999
Q ss_pred HHHHH
Q 011603 289 AENLL 293 (481)
Q Consensus 289 iE~LL 293 (481)
+++++
T Consensus 64 i~~~~ 68 (69)
T smart00322 64 ILEIL 68 (69)
T ss_pred HHHHh
Confidence 98876
No 16
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.17 E-value=3.4e-06 Score=65.32 Aligned_cols=53 Identities=23% Similarity=0.337 Sum_probs=45.1
Q ss_pred ceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 011603 224 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 289 (481)
Q Consensus 224 N~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~Li 289 (481)
.+++.|||++|.++++|+++|||+|.|-..+ +..-.|.|+|. .+++.+|++++
T Consensus 9 ~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~------------~~~~~v~I~G~-~~~v~~A~~~i 61 (62)
T cd02394 9 KLHRFIIGKKGSNIRKIMEETGVKIRFPDPG------------SKSDTITITGP-KENVEKAKEEI 61 (62)
T ss_pred HHhhhccCCCCCcHHHHHHHhCCEEEcCCCC------------CCCCEEEEEcC-HHHHHHHHHHh
Confidence 3689999999999999999999999997642 33467899999 78999999876
No 17
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=98.12 E-value=0.00016 Score=74.92 Aligned_cols=164 Identities=17% Similarity=0.151 Sum_probs=103.9
Q ss_pred EEEEEEcCCCCcccceeeec-hhhHHHHHhhhCCeEee-e-cceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHH
Q 011603 104 IAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVIT-R-GKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHA 180 (481)
Q Consensus 104 ~~aEIeINDlpq~~R~~LTk-~~Tq~eI~e~TGA~VtT-R-GrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~A 180 (481)
++-+|-|..+- +--+|.| |+|+.+++++|||.|-. | =.||| -..|| ..+|+|..+ ++- ..++-.
T Consensus 39 y~ikvLips~A--aGsIIGKGG~ti~~lqk~tgariklSks~dfyP----GTTeR--vcli~Gt~e--ai~---av~efI 105 (402)
T KOG2191|consen 39 YFLKVLIPSYA--AGSIIGKGGQTIVQLQKETGARIKLSKSKDFYP----GTTER--VCLIQGTVE--ALN---AVHEFI 105 (402)
T ss_pred eEEEEEeeccc--ccceeccchHHHHHHHhccCcEEEeccccccCC----Cccce--EEEEeccHH--HHH---HHHHHH
Confidence 66778888777 7889999 89999999999999866 2 23442 13344 458888762 111 122333
Q ss_pred HHHHHHHHHcCCCCCCCccccCCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEee-cCCCCCC
Q 011603 181 AAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRG-RGSGNSE 259 (481)
Q Consensus 181 vaeIkEILKe~p~~~pp~~~p~~~G~k~~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRG-RGSg~~E 259 (481)
.++|+|+....-......+.-... +-.+-||.||-. -.|.|||++|.|+|.|++|.||-|+|-- +-.+.
T Consensus 106 ~dKire~p~~~~k~v~~~~pqt~~--r~kqikivvPNs------tag~iigkggAtiK~~~Eqsga~iqisPqkpt~~-- 175 (402)
T KOG2191|consen 106 ADKIREKPQAVAKPVDILQPQTPD--RIKQIKIVVPNS------TAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGI-- 175 (402)
T ss_pred HHHHHHhHHhhcCCccccCCCCcc--ccceeEEeccCC------cccceecCCcchHHHHHHhhCcceEecccCCCCc--
Confidence 445555544332211111100111 234678888732 3899999999999999999999999973 21111
Q ss_pred CCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhh
Q 011603 260 GLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 300 (481)
Q Consensus 260 ~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~eE~ 300 (481)
.-.-.|...+.+++++.+|++|| |.+|.++-
T Consensus 176 -------sLqervvt~sge~e~~~~A~~~I---L~Ki~eDp 206 (402)
T KOG2191|consen 176 -------SLQERVVTVSGEPEQNMKAVSLI---LQKIQEDP 206 (402)
T ss_pred -------cceeEEEEecCCHHHHHHHHHHH---HHHhhcCC
Confidence 11124666688899999988775 66777664
No 18
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=97.99 E-value=2.1e-05 Score=62.13 Aligned_cols=62 Identities=21% Similarity=0.215 Sum_probs=45.0
Q ss_pred EEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 011603 212 SVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 289 (481)
Q Consensus 212 KI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~Li 289 (481)
++.||. +.+|+|||.+|.++++|+++|||+|.|--.. +...+.-++....+++++++|+.||
T Consensus 3 r~~ip~------~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~----------~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 3 RLLVPS------SQAGSIIGKGGSTIKEIREETGAKIRVSKSV----------LPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred EEEECH------HHcCeeECCCcHHHHHHHHHHCCEEEEcCCC----------CCCCCceEEEEEeCHHHHHHHHHhh
Confidence 556663 3689999999999999999999999995311 1122233444445599999999986
No 19
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.72 E-value=0.00015 Score=77.04 Aligned_cols=141 Identities=16% Similarity=0.188 Sum_probs=90.7
Q ss_pred eeec-hhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCCc
Q 011603 120 KLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTL 198 (481)
Q Consensus 120 ~LTk-~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeIkEILKe~p~~~pp~ 198 (481)
+|.+ |.|++.|...|-+.|-+ .--......|+.|-+|-+. +...+|+++|-++|..+-.
T Consensus 213 IIGkeG~TIknItkqTqsriD~----hrken~Gaaek~itvh~tp-----------Eg~s~Ac~~ILeimqkEA~----- 272 (584)
T KOG2193|consen 213 IIGKEGATIKNITKQTQSRIDV----HRKENAGAAEKIITVHSTP-----------EGTSKACKMILEIMQKEAV----- 272 (584)
T ss_pred EecCCCccccCcchhhhheeee----eecccCCcccCceEEecCc-----------cchHHHHHHHHHHHHHhhh-----
Confidence 3454 89999999999887644 2122234679998766443 2566788889888865411
Q ss_pred cccCCCCcccceeEE--EecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEe
Q 011603 199 QTVMGNGVQAMSTSV--FLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSS 276 (481)
Q Consensus 199 ~~p~~~G~k~~eeKI--~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa 276 (481)
.+|+ .|||+-.---||+|||||..|.++|.|+++||+||.|-- +.| .++ .+-.--+.|-|
T Consensus 273 -----------~~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~----lqe-ls~--ynpERTItVkG 334 (584)
T KOG2193|consen 273 -----------DDKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISK----LQE-LSL--YNPERTITVKG 334 (584)
T ss_pred -----------ccchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeee----hhh-hcc--cCccceEEecc
Confidence 1122 255554445678999999999999999999999999853 332 111 11224466666
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHhhhc
Q 011603 277 NNPKSLEEAKRLAENLLDTISAECGA 302 (481)
Q Consensus 277 ~~~e~v~~Ak~LiE~LL~tV~eE~~~ 302 (481)
+-|.+.+|..+ ++..+++.|+.
T Consensus 335 -siEac~~AE~e---ImkKlre~yEn 356 (584)
T KOG2193|consen 335 -SIEACVQAEAE---IMKKLRECYEN 356 (584)
T ss_pred -cHHHHHHHHHH---HHHHHHHHHhh
Confidence 55555555544 45566666643
No 20
>PF13014 KH_3: KH domain
Probab=97.67 E-value=3.8e-05 Score=56.23 Aligned_cols=28 Identities=32% Similarity=0.455 Sum_probs=26.2
Q ss_pred eeeEEeCCCchhHHHHHHhhCcEEEEee
Q 011603 225 IAARIRGPNDQYINHIMNETGATVLLRG 252 (481)
Q Consensus 225 ~vgrIIGP~Gs~lK~Iq~ETGaKI~IRG 252 (481)
++|.|||++|+++++|+++|||+|.|--
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC
Confidence 4789999999999999999999999975
No 21
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.46 E-value=0.00025 Score=67.01 Aligned_cols=63 Identities=13% Similarity=0.192 Sum_probs=53.2
Q ss_pred eEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEE---eCCHHHHHHHHH
Q 011603 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLS---SNNPKSLEEAKR 287 (481)
Q Consensus 211 eKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Is---a~~~e~v~~Ak~ 287 (481)
..+.||.+ -+|.|||++|.++|.|+++|||+|.|.-. .-.|.|. +.|++.+++|++
T Consensus 5 ~~i~IP~~------kig~iIG~gGk~Ik~I~e~tg~~I~i~~~---------------~g~V~I~~~~~~d~~~i~kA~~ 63 (180)
T PRK13763 5 EYVKIPKD------RIGVLIGKKGETKKEIEERTGVKLEIDSE---------------TGEVIIEPTDGEDPLAVLKARD 63 (180)
T ss_pred EEEEcCHH------HhhhHhccchhHHHHHHHHHCcEEEEECC---------------CCeEEEEeCCCCCHHHHHHHHH
Confidence 45666643 48899999999999999999999999842 1367787 889999999999
Q ss_pred HHHHHHH
Q 011603 288 LAENLLD 294 (481)
Q Consensus 288 LiE~LL~ 294 (481)
+++.|+.
T Consensus 64 ~I~ai~~ 70 (180)
T PRK13763 64 IVKAIGR 70 (180)
T ss_pred HHHHHhc
Confidence 9999987
No 22
>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=97.33 E-value=0.0018 Score=72.90 Aligned_cols=91 Identities=16% Similarity=0.248 Sum_probs=66.2
Q ss_pred HHHHHHHHHHHHcCCCCCCCccccCCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCC
Q 011603 178 DHAAAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGN 257 (481)
Q Consensus 178 d~AvaeIkEILKe~p~~~pp~~~p~~~G~k~~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~ 257 (481)
.++...|-++|++..... .+. ..+.+ .-+++.|+.+ -+|.||||+|.++|.|+++|||+|-|-
T Consensus 552 ~~g~~~Il~~m~~al~~p--~~~-s~~aP--~~~~~~I~~~------ki~~vIG~gGk~I~~i~~~tg~~Idi~------ 614 (719)
T TIGR02696 552 RDARLAILDVMAEAIDTP--DEM-SPYAP--RIITVKIPVD------KIGEVIGPKGKMINQIQDETGAEISIE------ 614 (719)
T ss_pred HHHHHHHHHHHHHHHhCc--ccc-ccCCC--eeEEEEeChH------HhhheeCCCcHhHHHHHHHHCCEEEEe------
Confidence 334445666666653321 111 12222 2456667644 489999999999999999999999875
Q ss_pred CCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHH
Q 011603 258 SEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDT 295 (481)
Q Consensus 258 ~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~t 295 (481)
|.=+|.|.+.+.+.+++|+++|++|+..
T Consensus 615 ----------d~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 615 ----------DDGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred ----------cCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 2368999999999999999999999985
No 23
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=97.27 E-value=0.00036 Score=65.48 Aligned_cols=56 Identities=11% Similarity=0.174 Sum_probs=48.7
Q ss_pred eeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEE--EeCCHHHHHHHHHHHHHHHHH
Q 011603 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFL--SSNNPKSLEEAKRLAENLLDT 295 (481)
Q Consensus 225 ~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~I--sa~~~e~v~~Ak~LiE~LL~t 295 (481)
.+|.|||++|.++|.|+++|||+|.|--. .=.|.| .+.|++.+++|+++|+.|...
T Consensus 8 kig~vIG~gG~~Ik~I~~~tgv~I~Id~~---------------~g~V~I~~~t~d~~~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 8 RIGVLIGKGGETKKEIEERTGVKLDIDSE---------------TGEVKIEEEDEDPLAVMKAREVVKAIGRG 65 (172)
T ss_pred HhhhHhCCchhHHHHHHHHhCcEEEEEcC---------------CceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence 58899999999999999999999999731 125777 789999999999999998773
No 24
>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=97.12 E-value=0.0011 Score=59.53 Aligned_cols=64 Identities=30% Similarity=0.399 Sum_probs=48.6
Q ss_pred echhhHHHHHhhhCCeEeeecceeCCCC----------CCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcC
Q 011603 122 TKRHTQEEIQKCTGAVVITRGKYRLPNA----------PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQG 191 (481)
Q Consensus 122 Tk~~Tq~eI~e~TGA~VtTRGrY~PP~~----------~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeIkEILKe~ 191 (481)
.+|.|+++|+++|||.|.+||+---... ....+-||+++|++.+. .+ +++++|+.+|+++++..
T Consensus 23 PgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~----~~--e~~~~A~~~I~~ll~~~ 96 (120)
T cd02395 23 PRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETP----PE--EALAKAVEAIEELLKPA 96 (120)
T ss_pred CCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCc----HH--HHHHHHHHHHHHHhccC
Confidence 3699999999999999999996321111 11346789999999871 11 58999999999999843
No 25
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.05 E-value=0.0011 Score=64.20 Aligned_cols=143 Identities=17% Similarity=0.212 Sum_probs=87.0
Q ss_pred EEEcCCCCcccceeeec-hhhHHHHHhhhCCeEee--ecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHH
Q 011603 107 EIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVIT--RGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAM 183 (481)
Q Consensus 107 EIeINDlpq~~R~~LTk-~~Tq~eI~e~TGA~VtT--RGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~Avae 183 (481)
-|.|..-. .-+++.+ |++-..|.+.+|+.++. +..++ -|...-.+.|. -.+-+|.+.
T Consensus 11 ~v~iPk~R--~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V--------------~i~~~~~t~Dp----~~~~ka~d~ 70 (194)
T COG1094 11 AVKIPKDR--IGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSV--------------TIRTTRKTEDP----LALLKARDV 70 (194)
T ss_pred eeecCchh--heeeecccccchHHHHhhcCeEEEEECCCCeE--------------EEEecCCCCCh----HHHHHHHHH
Confidence 35565554 5666665 88999999999998776 32222 22222101121 134444444
Q ss_pred HHHHHHcCCCCCCCccccCCCCccccee---EEEecCCCC---CCC---ceeeEEeCCCchhHHHHHHhhCcEEEEeecC
Q 011603 184 VEEMLKQGHAGFPTLQTVMGNGVQAMST---SVFLGFDAD---ASL---NIAARIRGPNDQYINHIMNETGATVLLRGRG 254 (481)
Q Consensus 184 IkEILKe~p~~~pp~~~p~~~G~k~~ee---KI~Iple~~---P~F---N~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRG 254 (481)
|+-+ +..+.++.. .+.+++ +--|.+.++ ++- -.+|||||++|.|.+.||+-|||.|.|.|+
T Consensus 71 VkAI---grGF~pe~A------~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~- 140 (194)
T COG1094 71 VKAI---GRGFPPEKA------LKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK- 140 (194)
T ss_pred HHHH---hcCCCHHHH------HHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc-
Confidence 4433 112221110 011111 112333332 111 248999999999999999999999999993
Q ss_pred CCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHH
Q 011603 255 SGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTI 296 (481)
Q Consensus 255 Sg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~tV 296 (481)
+|.|.| ++++|+.|++-+|.||+-.
T Consensus 141 ----------------tVaiiG-~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 141 ----------------TVAIIG-GFEQVEIAREAVEMLINGA 165 (194)
T ss_pred ----------------EEEEec-ChhhhHHHHHHHHHHHcCC
Confidence 777876 6889999999999999753
No 26
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.04 E-value=0.00097 Score=71.98 Aligned_cols=67 Identities=27% Similarity=0.401 Sum_probs=52.2
Q ss_pred cceeee-chhhHHHHHhhhCCeEeeeccee-CCCC--------CCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHH
Q 011603 117 VRYKLT-KRHTQEEIQKCTGAVVITRGKYR-LPNA--------PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEE 186 (481)
Q Consensus 117 ~R~~LT-k~~Tq~eI~e~TGA~VtTRGrY~-PP~~--------~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeIkE 186 (481)
+-.+|. +|.||+.++++|||.|..||+=- -.++ ....+-+||.+|++.|+ +.|++|++.|+.
T Consensus 155 vGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~--------eki~~Ai~vien 226 (554)
T KOG0119|consen 155 VGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQ--------EKIKKAIAVIEN 226 (554)
T ss_pred eEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchH--------HHHHHHHHHHHH
Confidence 345565 69999999999999999999321 1111 22457899999999885 589999999999
Q ss_pred HHHcC
Q 011603 187 MLKQG 191 (481)
Q Consensus 187 ILKe~ 191 (481)
+|+..
T Consensus 227 li~~a 231 (554)
T KOG0119|consen 227 LIQSA 231 (554)
T ss_pred HHHhh
Confidence 99874
No 27
>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=97.00 E-value=0.0012 Score=73.85 Aligned_cols=100 Identities=18% Similarity=0.251 Sum_probs=72.4
Q ss_pred eeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 011603 210 STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 289 (481)
Q Consensus 210 eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~Li 289 (481)
-+.+.|+.+ .+|.||||+|.++|.|+++|||+|-|- +.=+|.|.+.+.+.+++|+++|
T Consensus 552 ~~~~~I~~~------kI~~vIG~gGk~Ik~I~~~tg~~I~i~----------------ddG~V~i~~~~~~~~~~a~~~I 609 (684)
T TIGR03591 552 IETIKINPD------KIRDVIGPGGKVIREITEETGAKIDIE----------------DDGTVKIAASDGEAAEAAIKMI 609 (684)
T ss_pred EEEEecCHH------HHHhhcCCCcHHHHHHHHHHCCEEEEe----------------cCeEEEEEECcHHHHHHHHHHH
Confidence 355666543 489999999999999999999999984 2357999999999999999999
Q ss_pred HHHHHHHHHhhhccccccccccccCCCchhhccCcccccccccCCcccchhhcccccc
Q 011603 290 ENLLDTISAECGASRVSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNL 347 (481)
Q Consensus 290 E~LL~tV~eE~~~~r~~~~~~y~~~pppq~~l~g~~~~~~~~~~~~~~~~~~~~~~~~ 347 (481)
+.|... + ..++.|- -.+.++..+|..-.+.. ...|+.|--++
T Consensus 610 ~~~~~~----~-----~~G~i~~------G~V~~I~~~GafVei~~-g~~GllHiSei 651 (684)
T TIGR03591 610 EGITAE----P-----EVGKIYE------GKVVRIMDFGAFVEILP-GKDGLVHISEI 651 (684)
T ss_pred Hhhhcc----c-----ccCcEEE------EEEEEEeCCEEEEEECC-CcEEEEEHHHc
Confidence 999542 1 1233332 35777777785544433 25677775544
No 28
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.83 E-value=0.0068 Score=64.85 Aligned_cols=156 Identities=17% Similarity=0.205 Sum_probs=106.7
Q ss_pred EEEcCCCCcccceeee-chhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHH
Q 011603 107 EIVINDSESSVRYKLT-KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVE 185 (481)
Q Consensus 107 EIeINDlpq~~R~~LT-k~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeIk 185 (481)
.+.|.|.- +.-+|. ||..+++|.+++||+|-.- ||+-+--++| -..|+|+. ++.-+|-..|-
T Consensus 414 ~~fiP~~~--vGAiIGkkG~hIKql~RfagASiKIa----ppE~pdvseR--MViItGpp---------eaqfKAQgrif 476 (584)
T KOG2193|consen 414 RMFIPAQA--VGAIIGKKGQHIKQLSRFAGASIKIA----PPEIPDVSER--MVIITGPP---------EAQFKAQGRIF 476 (584)
T ss_pred eeeccHHH--HHHHHhhcchhHHHHHHhccceeeec----CCCCCCccee--EEEecCCh---------HHHHhhhhhhh
Confidence 45566654 555666 5999999999999997642 3332222344 45789987 47788899999
Q ss_pred HHHHcCCCCCCCccccCCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCC
Q 011603 186 EMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEE 265 (481)
Q Consensus 186 EILKe~p~~~pp~~~p~~~G~k~~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~E 265 (481)
..|+++-.+.|-. ...+++-|-|| .+ .+|||||.+|.|++-||+-|+|.|.|-- ..++.|
T Consensus 477 gKikEenf~~Pke-------evklethirVP-----s~-~aGRvIGKGGktVnELQnlt~AeV~vPr-------dqtpdE 536 (584)
T KOG2193|consen 477 GKIKEENFFLPKE-------EVKLETHIRVP-----SS-AAGRVIGKGGKTVNELQNLTSAEVVVPR-------DQTPDE 536 (584)
T ss_pred hhhhhhccCCchh-------hheeeeeeecc-----ch-hhhhhhccccccHHHHhccccceEEccc-------cCCCCc
Confidence 9998874433221 13455666555 55 7999999999999999999999998752 123333
Q ss_pred CCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011603 266 VHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECG 301 (481)
Q Consensus 266 s~EPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~eE~~ 301 (481)
+|-.-|-|.| +.-....|...|.+|+..|++..+
T Consensus 537 -nd~vivriiG-hfyatq~aQrki~~iv~qvkq~~q 570 (584)
T KOG2193|consen 537 -NDQVIVRIIG-HFYATQNAQRKIAHIVNQVKQSGQ 570 (584)
T ss_pred -cceeeeeeec-hhhcchHHHHHHHHHHHHHHHhhh
Confidence 3333444444 455567788888899988887654
No 29
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.75 E-value=0.022 Score=61.82 Aligned_cols=141 Identities=16% Similarity=0.177 Sum_probs=80.3
Q ss_pred ceeeechhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEee---------ccchhhHHHHHHHHHHHHHHHHHHH
Q 011603 118 RYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISA---------GAHLKETAERILAVDHAAAMVEEML 188 (481)
Q Consensus 118 R~~LTk~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg---------~tq~kdt~ERi~aVd~AvaeIkEIL 188 (481)
-|+-.+|+++++|..+|++.|-+--. .++ +.|| -+-|.| .. .++.+|.++|-..+
T Consensus 56 ~IIGk~G~~vkkir~~t~s~i~i~~~--~~~---c~eR--Iiti~g~~~~~~~~~~~---------~al~ka~~~iv~~~ 119 (485)
T KOG2190|consen 56 SIIGKKGDIVKKIRKETESKIRVNES--LPG---CPER--IITITGNRVELNLSPAT---------DALFKAFDMIVFKL 119 (485)
T ss_pred eEEccCcHHHHHHhhcccccceeecC--CCC---CCcc--eEEEecccccccCCchH---------HHHHHHHHHHhhcc
Confidence 45556799999999888876443111 011 1222 223344 22 35666655554443
Q ss_pred HcCCCCCCCccccCCCCccc-ceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCC
Q 011603 189 KQGHAGFPTLQTVMGNGVQA-MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVH 267 (481)
Q Consensus 189 Ke~p~~~pp~~~p~~~G~k~-~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~ 267 (481)
.++..-.. +. ...+..+ ...++.|| .+-+|-|||.+|+.||.|.++|||+|+|-+. .+= -+.
T Consensus 120 ~~d~~~~~--d~-~~~~~~~~v~~RLlVp------~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~---~lP-----~st 182 (485)
T KOG2190|consen 120 EEDDEAAE--DN-GEDASGPEVTCRLLVP------SSQVGSLIGKGGSLIKEIREETGAKIRVSSD---MLP-----NST 182 (485)
T ss_pred cccccccc--cC-CccccCCceEEEEEec------hhheeeeeccCcHHHHHHHHhcCceEEecCC---CCC-----ccc
Confidence 32211110 00 0111234 45677787 4469999999999999999999999999985 221 123
Q ss_pred CCcEEEEEeCCHHHHHHHHHHHHHHH
Q 011603 268 QPLHLFLSSNNPKSLEEAKRLAENLL 293 (481)
Q Consensus 268 EPLHV~Isa~~~e~v~~Ak~LiE~LL 293 (481)
|.+ |.|+ .+++.+.+|-..|-.+|
T Consensus 183 er~-V~Is-G~~~av~~al~~Is~~L 206 (485)
T KOG2190|consen 183 ERA-VTIS-GEPDAVKKALVQISSRL 206 (485)
T ss_pred cee-EEEc-CchHHHHHHHHHHHHHH
Confidence 334 5554 46666777655544433
No 30
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.73 E-value=0.0015 Score=74.94 Aligned_cols=101 Identities=19% Similarity=0.230 Sum_probs=74.5
Q ss_pred eeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcE-EEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 011603 210 STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGAT-VLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 288 (481)
Q Consensus 210 eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaK-I~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~L 288 (481)
-+++-|+.+ -+|.||||+|.++|.|++|||++ |-|+ |.-+|.|.+.|.+.+++|+++
T Consensus 686 i~~~~i~~~------ki~~vIG~GGktIk~I~eetg~~~Idi~----------------ddg~V~I~a~d~~~i~~A~~~ 743 (891)
T PLN00207 686 IHIMKVKPE------KVNMIIGSGGKKVKSIIEETGVEAIDTQ----------------DDGTVKITAKDLSSLEKSKAI 743 (891)
T ss_pred eEEEEcCHH------HHHHHhcCCchhHHHHHHHHCCCccCcC----------------CCeeEEEEeCCHHHHHHHHHH
Confidence 355656533 48999999999999999999998 6554 358999999999999999999
Q ss_pred HHHHHHHHHHhhhcccccccccc-ccCCCchhhccCcccccccccCCcccchhhccccccc
Q 011603 289 AENLLDTISAECGASRVSSCKVY-NAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNLS 348 (481)
Q Consensus 289 iE~LL~tV~eE~~~~r~~~~~~y-~~~pppq~~l~g~~~~~~~~~~~~~~~~~~~~~~~~~ 348 (481)
|++|.... .-.+.| + .-+.+|..+|+.-.+... .-||.|--.++
T Consensus 744 I~~l~~~~---------~vG~iy~~------g~V~~I~~FGaFVeL~~g-~EGLVHISeLs 788 (891)
T PLN00207 744 ISSLTMVP---------TVGDIYRN------CEIKSIAPYGAFVEIAPG-REGLCHISELS 788 (891)
T ss_pred HHHHhcCc---------CCCcEEEC------cEEEEEeccEEEEEeCCC-CEEEEEhhhcC
Confidence 99998621 134555 2 246778888855444433 57887755443
No 31
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.08 E-value=0.0082 Score=67.41 Aligned_cols=93 Identities=18% Similarity=0.251 Sum_probs=68.3
Q ss_pred ceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhhhcc
Q 011603 224 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGAS 303 (481)
Q Consensus 224 N~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~eE~~~~ 303 (481)
+-++.+|||+|.++|.|++|||++|-|+ |.-+|.|.+.+.+.+++|+++|+.|....
T Consensus 563 ~kI~~vIG~gg~~ik~I~~~~~~~idi~----------------d~G~v~i~~~~~~~~~~a~~~I~~~~~~~------- 619 (693)
T PRK11824 563 DKIRDVIGPGGKTIREITEETGAKIDIE----------------DDGTVKIAATDGEAAEAAKERIEGITAEP------- 619 (693)
T ss_pred HHHHHHhcCCchhHHHHHHHHCCccccC----------------CCceEEEEcccHHHHHHHHHHHHHhcccC-------
Confidence 3478999999999999999999987763 34789999999999999999999998421
Q ss_pred ccccccccccCCCchhhccCcccccccccCCcccchhhccccccc
Q 011603 304 RVSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNLS 348 (481)
Q Consensus 304 r~~~~~~y~~~pppq~~l~g~~~~~~~~~~~~~~~~~~~~~~~~~ 348 (481)
...+.|. -.+.++..+|..-.+.. ...|+.|--+++
T Consensus 620 --~vG~v~~------G~V~~I~~fGafVei~~-~~~GllhiSels 655 (693)
T PRK11824 620 --EVGEIYE------GKVVRIVDFGAFVEILP-GKDGLVHISEIA 655 (693)
T ss_pred --cCCeEEE------EEEEEEECCeEEEEECC-CCEEEEEeeecc
Confidence 1233332 35777777885544433 356666655443
No 32
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=95.77 E-value=0.21 Score=54.51 Aligned_cols=60 Identities=28% Similarity=0.307 Sum_probs=46.5
Q ss_pred cceeeec-hhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcC
Q 011603 117 VRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQG 191 (481)
Q Consensus 117 ~R~~LTk-~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeIkEILKe~ 191 (481)
+-.+|.| |+.+++|.++|||.|-+-+. +.|. ..++- +-|.|.. .+|.+|+..|-..|.+.
T Consensus 149 ~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~--V~IsG~~---------~av~~al~~Is~~L~~~ 209 (485)
T KOG2190|consen 149 VGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN---STERA--VTISGEP---------DAVKKALVQISSRLLEN 209 (485)
T ss_pred eeeeeccCcHHHHHHHHhcCceEEecCC-CCCc---cccee--EEEcCch---------HHHHHHHHHHHHHHHhc
Confidence 6677887 99999999999999998777 4343 23333 7888865 48889988888888774
No 33
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.44 E-value=0.021 Score=56.23 Aligned_cols=53 Identities=21% Similarity=0.353 Sum_probs=46.7
Q ss_pred eeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHH
Q 011603 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLL 293 (481)
Q Consensus 225 ~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL 293 (481)
+++++|||+|.+++.|.++|||+|.| | +.=+|+|.+.+.+.+++|+++|++|-
T Consensus 155 ~i~~lig~~g~~i~~l~~~~~~~I~i-g---------------~NG~VwI~~~~~~~~~~a~~~I~~~e 207 (235)
T PRK04163 155 KVPRVIGKKGSMINMLKEETGCDIIV-G---------------QNGRIWIKGPDEEDEEIAIEAIKKIE 207 (235)
T ss_pred HHHhhcCCCChhHhhhhhhhCcEEEE-c---------------CCcEEEEeeCCHHHHHHHHHHHHHHH
Confidence 58899999999999999999999988 2 12479999999999999999998754
No 34
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=95.40 E-value=0.068 Score=56.00 Aligned_cols=76 Identities=22% Similarity=0.272 Sum_probs=53.8
Q ss_pred ceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 011603 209 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 288 (481)
Q Consensus 209 ~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~L 288 (481)
..-||.|| .+ .+|-|||.+|++|-.+|+||||+|++- |-+-|.-+.+ -.||+...+-+.|...-++
T Consensus 39 y~ikvLip-----s~-AaGsIIGKGG~ti~~lqk~tgariklS-ks~dfyPGTT-------eRvcli~Gt~eai~av~ef 104 (402)
T KOG2191|consen 39 YFLKVLIP-----SY-AAGSIIGKGGQTIVQLQKETGARIKLS-KSKDFYPGTT-------ERVCLIQGTVEALNAVHEF 104 (402)
T ss_pred eEEEEEee-----cc-cccceeccchHHHHHHHhccCcEEEec-cccccCCCcc-------ceEEEEeccHHHHHHHHHH
Confidence 55688887 33 699999999999999999999999986 4444432222 2577777777766665544
Q ss_pred HHHHHHHHHHhhh
Q 011603 289 AENLLDTISAECG 301 (481)
Q Consensus 289 iE~LL~tV~eE~~ 301 (481)
++|+|+++.+
T Consensus 105 ---I~dKire~p~ 114 (402)
T KOG2191|consen 105 ---IADKIREKPQ 114 (402)
T ss_pred ---HHHHHHHhHH
Confidence 4556666653
No 35
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=95.19 E-value=0.022 Score=58.46 Aligned_cols=57 Identities=21% Similarity=0.343 Sum_probs=46.7
Q ss_pred eeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhh
Q 011603 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 300 (481)
Q Consensus 226 vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~eE~ 300 (481)
+.|||||+|+|+|.||--|.|-|.+.|. -|++.|+ ..+|.++++++++.+.+|+.=|
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilVqG~-----------------TVsaiGp-fkGlkevr~IV~DcM~NiHPiY 216 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILVQGN-----------------TVSAIGP-FKGLKEVRKIVEDCMKNIHPIY 216 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEeeCc-----------------EEEeecC-cchHHHHHHHHHHHHhccchHH
Confidence 6799999999999999999999999994 2444443 4678899999999888877544
No 36
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=94.97 E-value=0.04 Score=60.99 Aligned_cols=81 Identities=20% Similarity=0.251 Sum_probs=59.3
Q ss_pred eeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhhhc---
Q 011603 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGA--- 302 (481)
Q Consensus 226 vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~eE~~~--- 302 (481)
+..+|||+|-.+|+|+.|||+.-++ +.=|+-|-++++..+++||++|+.++..-+...-.
T Consensus 608 ~~~lIGp~G~~~kki~~EtGai~~v-----------------De~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~l~~g~ 670 (760)
T KOG1067|consen 608 RATLIGPGGVLKKKIEVETGAISQV-----------------DEGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQDLEFGG 670 (760)
T ss_pred hheeecCccceeeeEeeeccceeee-----------------cCceEEEEecCHHHHHHHHHHHHHHhcCccccceEeee
Confidence 6789999999999999999954332 44699999999999999999999998764443222
Q ss_pred ---cccccccccccC----CCchhhccC
Q 011603 303 ---SRVSSCKVYNAV----PPPQQLLTG 323 (481)
Q Consensus 303 ---~r~~~~~~y~~~----pppq~~l~g 323 (481)
..+...+.||++ |.+|-||.-
T Consensus 671 vy~~tIt~~rd~G~~V~l~p~~~~Llh~ 698 (760)
T KOG1067|consen 671 VYTATITEIRDTGVMVELYPMQQGLLHN 698 (760)
T ss_pred EEEEEEeeecccceEEEecCCchhhccc
Confidence 244555666643 445545443
No 37
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=94.11 E-value=0.085 Score=55.10 Aligned_cols=64 Identities=11% Similarity=0.132 Sum_probs=55.0
Q ss_pred eeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhh
Q 011603 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 300 (481)
Q Consensus 225 ~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~eE~ 300 (481)
|.|.|+|-+|.+.|+|++||+|+|.|==.+. ..-|+-|++...+.|.+|.+-|+-||++++..|
T Consensus 67 ~~~~lig~~g~trkkle~Etq~~i~lp~p~~------------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~s~ 130 (345)
T KOG2814|consen 67 FIGWLIGKQGKTRKKLEEETQTNIFLPRPNT------------NKEEIKIIGISRNCVIQALERIAKLIDSDRKSF 130 (345)
T ss_pred HhhhhhcccchHHHHHHHhhccceEccCCCC------------CcceEEEeehhHHHHHHHHHHHHHHHHhhhhcC
Confidence 6899999999999999999999998853211 225899999999999999999999999998443
No 38
>PRK00106 hypothetical protein; Provisional
Probab=93.89 E-value=0.12 Score=57.08 Aligned_cols=60 Identities=27% Similarity=0.333 Sum_probs=51.9
Q ss_pred CCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 011603 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 294 (481)
Q Consensus 220 ~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~ 294 (481)
.|+=.+.|||||..|.|++.+|.-||+.|.|- |.|--|.|||-||-.-+-|+.-++.||.
T Consensus 231 lp~demkGriIGreGrNir~~E~~tGvdliid---------------dtp~~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 231 LPDDNMKGRIIGREGRNIRTLESLTGIDVIID---------------DTPEVVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred cCChHhhcceeCCCcchHHHHHHHhCceEEEc---------------CCCCeEEEeCCChHHHHHHHHHHHHHHH
Confidence 45667899999999999999999999999884 6788899999999998888877766654
No 39
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=93.80 E-value=0.12 Score=56.65 Aligned_cols=60 Identities=23% Similarity=0.326 Sum_probs=51.3
Q ss_pred CCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 011603 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 294 (481)
Q Consensus 220 ~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~ 294 (481)
.|+=.+.|||||-.|-|++.+|.-||+.|.|- |.|=-|.|||-||-.-+-|+.-++.||.
T Consensus 210 lp~d~~kgriigreGrnir~~e~~tgvd~iid---------------dtp~~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 210 LPNDEMKGRIIGREGRNIRALETLTGVDLIID---------------DTPEAVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred cCChhhhccccCCCcchHHHHHHHhCceEEEc---------------CCCCeEEecCCchHHHHHHHHHHHHHHH
Confidence 45667899999999999999999999999984 5677899999999988888877666653
No 40
>PRK12704 phosphodiesterase; Provisional
Probab=93.69 E-value=0.15 Score=55.94 Aligned_cols=59 Identities=24% Similarity=0.316 Sum_probs=49.8
Q ss_pred CCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHH
Q 011603 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLL 293 (481)
Q Consensus 220 ~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL 293 (481)
.|+=.+.|||||-.|-|++.+|.-||+.|.|- |.|=-|+|||-|+-.-+.|+..++.|+
T Consensus 216 lp~d~mkgriigreGrnir~~e~~tgvd~iid---------------dtp~~v~ls~~~~~rre~a~~~l~~l~ 274 (520)
T PRK12704 216 LPNDEMKGRIIGREGRNIRALETLTGVDLIID---------------DTPEAVILSGFDPIRREIARLALEKLV 274 (520)
T ss_pred cCCchhhcceeCCCcchHHHHHHHhCCeEEEc---------------CCCCeEEEecCChhhHHHHHHHHHHHH
Confidence 45667899999999999999999999999984 568889999999998777776655554
No 41
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=92.76 E-value=0.16 Score=57.38 Aligned_cols=53 Identities=21% Similarity=0.310 Sum_probs=46.7
Q ss_pred eeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 011603 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 294 (481)
Q Consensus 226 vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~ 294 (481)
++.+|||+|.++|.|..||||+|.|.=. =-|.|.+.+.+...+|++.|+++..
T Consensus 563 I~dvIG~gGk~I~~I~eetg~~Idiedd----------------Gtv~i~~s~~~~~~~ak~~I~~i~~ 615 (692)
T COG1185 563 IRDVIGPGGKTIKAITEETGVKIDIEDD----------------GTVKIAASDGESAKKAKERIEAITR 615 (692)
T ss_pred HhhccCCcccchhhhhhhhCcEEEecCC----------------CcEEEEecchHHHHHHHHHHHHHHh
Confidence 5678999999999999999999998633 3467889999999999999999983
No 42
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=91.85 E-value=0.28 Score=53.20 Aligned_cols=63 Identities=14% Similarity=0.128 Sum_probs=46.3
Q ss_pred CceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHH-HHHHHHHHHHHHHHHHHHhhh
Q 011603 223 LNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPK-SLEEAKRLAENLLDTISAECG 301 (481)
Q Consensus 223 FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e-~v~~Ak~LiE~LL~tV~eE~~ 301 (481)
-+++|++||-+|+.+|+||..|+++|+|-- +.+-+.|+-.--. .-.+|+.-++++++...+ |+
T Consensus 55 s~mvg~vigrggskik~iq~~tnt~iqii~---------------~~~e~kv~ifg~~~m~~kaka~id~~~~k~e~-yn 118 (629)
T KOG0336|consen 55 SEMVGKVIGRGGSKIKRIQNDTNTRIQIIK---------------CDLEVKVTIFGINHMRKKAKASIDRGQDKDER-YN 118 (629)
T ss_pred hhhhheeeccCcchhhhhhcccceeEEEec---------------cCceeEEEEechHHHHHHHHhhHhhhhhhhhh-cc
Confidence 368999999999999999999999999862 2344444433333 345688888888877654 53
No 43
>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=90.22 E-value=0.97 Score=35.73 Aligned_cols=57 Identities=21% Similarity=0.238 Sum_probs=41.6
Q ss_pred EEEEcCCCCcccceeeec-hhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHH
Q 011603 106 REIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (481)
Q Consensus 106 aEIeINDlpq~~R~~LTk-~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeI 184 (481)
..|.|..- .++..+.+ |+++.+|+++|||.|..- . +. .+.|.|.+. +++++|+++|
T Consensus 4 ~~i~Ip~~--~ig~iIGkgG~~ik~I~~~tg~~I~i~-----~------~g--~v~I~G~~~--------~~v~~A~~~I 60 (61)
T cd02393 4 ETMKIPPD--KIRDVIGPGGKTIKKIIEETGVKIDIE-----D------DG--TVYIAASDK--------EAAEKAKKMI 60 (61)
T ss_pred EEEEeChh--heeeeECCCchHHHHHHHHHCCEEEeC-----C------CC--EEEEEeCCH--------HHHHHHHHHh
Confidence 34555433 37888887 999999999999998752 1 11 478999762 5789888877
Q ss_pred H
Q 011603 185 E 185 (481)
Q Consensus 185 k 185 (481)
+
T Consensus 61 ~ 61 (61)
T cd02393 61 E 61 (61)
T ss_pred C
Confidence 3
No 44
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=89.17 E-value=1 Score=46.48 Aligned_cols=65 Identities=22% Similarity=0.361 Sum_probs=50.7
Q ss_pred eeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhh
Q 011603 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 300 (481)
Q Consensus 225 ~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~eE~ 300 (481)
+-|-|||.+|.-+|+|..|+||.|.|- |+.++. +-.+.+.-.+.++++.|.-|.++-+..-++.|
T Consensus 325 lggsiigkggqri~~ir~esGA~Ikid-------epleGs----edrIitItGTqdQIqnAQYLlQn~Vkq~rerf 389 (390)
T KOG2192|consen 325 LGGSIIGKGGQRIKQIRHESGASIKID-------EPLEGS----EDRIITITGTQDQIQNAQYLLQNSVKQYRERF 389 (390)
T ss_pred cCcceecccchhhhhhhhccCceEEec-------CcCCCC----CceEEEEeccHHHHhhHHHHHHHHHHhhhccc
Confidence 567899999999999999999999875 233332 24566667789999999999998877555443
No 45
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=87.83 E-value=1.5 Score=44.68 Aligned_cols=90 Identities=14% Similarity=0.223 Sum_probs=59.4
Q ss_pred ceeEEEEEE--cCCCCcc---cceeeechhhHHHHHhhhCCeEeeecceeCCCC------CC-C----CCCCeEEEEeec
Q 011603 101 ELIIAREIV--INDSESS---VRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNA------PP-D----GEKPLYLHISAG 164 (481)
Q Consensus 101 e~~~~aEIe--INDlpq~---~R~~LTk~~Tq~eI~e~TGA~VtTRGrY~PP~~------~~-~----gepPLYL~Ieg~ 164 (481)
.+.....|. |+-+|.- -|.+==||.|++.++++|||.|.+||+--=-++ +. + =+.||+++|+..
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~ 168 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETE 168 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEe
Confidence 344444444 4444531 233334899999999999999999997644331 11 1 167899999986
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHcCCC
Q 011603 165 AHLKETAERILAVDHAAAMVEEMLKQGHA 193 (481)
Q Consensus 165 tq~kdt~ERi~aVd~AvaeIkEILKe~p~ 193 (481)
.- ++-++ ..+..|+++|+++|.-..+
T Consensus 169 ~p-~~ea~--~rl~~AleeI~klL~P~~e 194 (259)
T KOG1588|consen 169 AP-PAEAY--ARLAYALEEIKKLLVPDHE 194 (259)
T ss_pred CC-HHHHH--HHHHHHHHHHHHhcCCCCC
Confidence 52 22233 5688899999999875544
No 46
>PRK12705 hypothetical protein; Provisional
Probab=86.51 E-value=0.67 Score=51.01 Aligned_cols=58 Identities=28% Similarity=0.309 Sum_probs=44.1
Q ss_pred CCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHH
Q 011603 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENL 292 (481)
Q Consensus 220 ~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~L 292 (481)
.|+-.+.|||||-.|.|++.+|..||+.|.|- |.|=-|.|++-|+..-+.|+..+++|
T Consensus 204 lp~demkGriIGreGrNir~~E~~tGvdliid---------------dtp~~V~ls~fdp~rreia~~~l~~L 261 (508)
T PRK12705 204 IPSDAMKGRIIGREGRNIRAFEGLTGVDLIID---------------DTPEAVVISSFNPIRREIARLTLEKL 261 (508)
T ss_pred cCChHhhccccCccchhHHHHHHhhCCceEec---------------CCccchhhcccCccchHHHHHHHHHH
Confidence 45667899999999999999999999998875 33434777777777666665554444
No 47
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=85.73 E-value=1.7 Score=45.63 Aligned_cols=110 Identities=15% Similarity=0.183 Sum_probs=66.9
Q ss_pred eeechhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCC-CCc
Q 011603 120 KLTKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGF-PTL 198 (481)
Q Consensus 120 ~LTk~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeIkEILKe~p~~~-pp~ 198 (481)
.+-+|.+++.|+.+|...|.|- .-++-|.| -++|.- +.|++|..+|...-. ..... -.+
T Consensus 41 vg~qg~kikalr~KTqtyi~tP---------sr~eePiF-~vTg~~---------edv~~aRrei~saae-H~~l~~~s~ 100 (394)
T KOG2113|consen 41 VGRQGCKIKALRAKTQTYIKTP---------SRGEEPIF-PVTGRH---------EDVRRARREIPSAAE-HFGLIRASR 100 (394)
T ss_pred cccCccccchhhhhhcceeccC---------CCCCCCcc-eeccCc---------hhHHHHhhcCccccc-eeeeeeecc
Confidence 3456888999999998776651 12234666 345532 578888877765211 10000 000
Q ss_pred ccc-CCCCcc-cceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeec
Q 011603 199 QTV-MGNGVQ-AMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGR 253 (481)
Q Consensus 199 ~~p-~~~G~k-~~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGR 253 (481)
... .-++.. -.+.+.|+- .| +.++|+++||.|.++|+||+.+..-|.--++
T Consensus 101 s~Sgg~~~~s~s~qt~sy~s---vP-~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 101 SFSGGTNGASASGQTTSYVS---VP-LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred cccCCCccccccCCCceeee---cc-ceeeeeccccccCccchheecccceEeeecc
Confidence 000 011222 235666655 33 7799999999999999999999988865554
No 48
>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=85.43 E-value=3.3 Score=32.63 Aligned_cols=53 Identities=26% Similarity=0.267 Sum_probs=37.2
Q ss_pred cceeeec-hhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHH
Q 011603 117 VRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (481)
Q Consensus 117 ~R~~LTk-~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeI 184 (481)
+.+.+.+ |.++++|+++|||.|.+.-. ....+.++- +.|+|.. +.+++|..+|
T Consensus 11 vg~iIG~~G~~i~~i~~~tga~I~i~~~----~~~~~~~r~--v~I~G~~---------~~v~~A~~~I 64 (65)
T cd02396 11 AGSIIGKGGSTIKEIREETGAKIRVSKS----VLPGSTERV--VTISGKP---------SAVQKALLLI 64 (65)
T ss_pred cCeeECCCcHHHHHHHHHHCCEEEEcCC----CCCCCCceE--EEEEeCH---------HHHHHHHHhh
Confidence 4566665 89999999999999887321 112344453 6788965 4788888776
No 49
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=83.43 E-value=7.5 Score=40.41 Aligned_cols=133 Identities=16% Similarity=0.161 Sum_probs=81.2
Q ss_pred ceeeec-hhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCC
Q 011603 118 RYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFP 196 (481)
Q Consensus 118 R~~LTk-~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeIkEILKe~p~~~p 196 (481)
--.+.| |+.++.+....+|.|++--. +-+--.|+|+++. +-|-+..++|---|.++.....
T Consensus 60 gavigkgg~nik~lr~d~na~v~vpds---------~~peri~tisad~---------~ti~~ilk~iip~lee~f~~~~ 121 (390)
T KOG2192|consen 60 GAVIGKGGKNIKALRTDYNASVSVPDS---------SGPERILTISADI---------ETIGEILKKIIPTLEEGFQLPS 121 (390)
T ss_pred cceeccccccHHHHhhhccceeeccCC---------CCCceeEEEeccH---------HHHHHHHHHHhhhhhhCCCCCC
Confidence 334445 56777777788887776321 2233456788754 2344444444444555544332
Q ss_pred CccccCCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEe
Q 011603 197 TLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSS 276 (481)
Q Consensus 197 p~~~p~~~G~k~~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa 276 (481)
+ .+-++.|- -.+.|-|||-+|+-+|.+.+.+.|++-|- -|-+.+ --..|+|++
T Consensus 122 p-----------ce~rllih------qs~ag~iigrngskikelrekcsarlkif------t~c~p~----stdrv~l~~ 174 (390)
T KOG2192|consen 122 P-----------CELRLLIH------QSLAGGIIGRNGSKIKELREKCSARLKIF------TECCPH----STDRVVLIG 174 (390)
T ss_pred c-----------hhhhhhhh------hhhccceecccchhHHHHHHhhhhhhhhh------hccCCC----CcceEEEec
Confidence 2 12223221 23689999999999999999998887652 233322 125789999
Q ss_pred CCHHHHHHHHHHHHHHHHH
Q 011603 277 NNPKSLEEAKRLAENLLDT 295 (481)
Q Consensus 277 ~~~e~v~~Ak~LiE~LL~t 295 (481)
..++.|-...+.|-+||..
T Consensus 175 g~~k~v~~~i~~il~~i~e 193 (390)
T KOG2192|consen 175 GKPKRVVECIKIILDLISE 193 (390)
T ss_pred CCcchHHHHHHHHHHHhhc
Confidence 9999888777776666653
No 50
>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=82.42 E-value=3.6 Score=31.44 Aligned_cols=49 Identities=22% Similarity=0.237 Sum_probs=37.3
Q ss_pred cceeeec-hhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHH
Q 011603 117 VRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (481)
Q Consensus 117 ~R~~LTk-~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeI 184 (481)
..+.+.+ |.++++|++.|||.|..... + ..-.+.|.|.. +.|++|.++|
T Consensus 11 ~~~iIG~~G~~i~~I~~~t~~~I~i~~~---------~-~~~~v~I~G~~---------~~v~~A~~~I 60 (60)
T PF00013_consen 11 VGRIIGKKGSNIKEIEEETGVKIQIPDD---------D-ERDIVTISGSP---------EQVEKAKKMI 60 (60)
T ss_dssp HHHHHTGGGHHHHHHHHHHTSEEEEEST---------T-EEEEEEEEESH---------HHHHHHHHHH
T ss_pred cCEEECCCCCcHHHhhhhcCeEEEEcCC---------C-CcEEEEEEeCH---------HHHHHHHhhC
Confidence 5677775 99999999999999988543 2 33467899943 4788888776
No 51
>smart00322 KH K homology RNA-binding domain.
Probab=79.73 E-value=15 Score=27.12 Aligned_cols=64 Identities=20% Similarity=0.234 Sum_probs=42.9
Q ss_pred EEEEEcCCCCcccceeee-chhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHH
Q 011603 105 AREIVINDSESSVRYKLT-KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAM 183 (481)
Q Consensus 105 ~aEIeINDlpq~~R~~LT-k~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~Avae 183 (481)
..+|.|..-. ..+.+. +|.++++|++.+|+.|...+.-. .---+.|.|.. ..+..|...
T Consensus 4 ~~~i~i~~~~--~~~liG~~G~~i~~i~~~~~~~i~~~~~~~---------~~~~v~i~g~~---------~~v~~a~~~ 63 (69)
T smart00322 4 TIEVLIPADK--VGLIIGKGGSTIKKIEEETGVKIDIPEDGS---------EERVVEITGPP---------ENVEKAAEL 63 (69)
T ss_pred EEEEEEcchh--cceeECCCchHHHHHHHHHCCEEEECCCCC---------CccEEEEEcCH---------HHHHHHHHH
Confidence 4456665533 466665 59999999999999988754111 22336788864 467778887
Q ss_pred HHHHH
Q 011603 184 VEEML 188 (481)
Q Consensus 184 IkEIL 188 (481)
|.+.+
T Consensus 64 i~~~~ 68 (69)
T smart00322 64 ILEIL 68 (69)
T ss_pred HHHHh
Confidence 77765
No 52
>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=79.65 E-value=1.9 Score=34.13 Aligned_cols=26 Identities=12% Similarity=0.059 Sum_probs=23.8
Q ss_pred eeeEEeCCCchhHHHHHHhhCcEEEE
Q 011603 225 IAARIRGPNDQYINHIMNETGATVLL 250 (481)
Q Consensus 225 ~vgrIIGP~Gs~lK~Iq~ETGaKI~I 250 (481)
-+|+.||.+|.+++.++..+|-+|-|
T Consensus 35 ~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 35 QLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cceeeECCCCHHHHHHHHHHCCCeEE
Confidence 48999999999999999999988865
No 53
>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=76.44 E-value=12 Score=28.34 Aligned_cols=60 Identities=23% Similarity=0.277 Sum_probs=39.1
Q ss_pred EEEcCCCCcccceeeec-hhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHH
Q 011603 107 EIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (481)
Q Consensus 107 EIeINDlpq~~R~~LTk-~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeI 184 (481)
+|.|..- .+++.+.+ |.++.+|++.||+.|..... .....+ --+.|.|.. +.+.+|..+|
T Consensus 3 ~i~ip~~--~~~~vIG~~G~~i~~I~~~s~~~I~i~~~-----~~~~~~--~~v~i~G~~---------~~v~~a~~~i 63 (64)
T cd00105 3 RVLVPSS--LVGRIIGKGGSTIKEIREETGAKIKIPDS-----GSGSEE--RIVTITGTP---------EAVEKAKELI 63 (64)
T ss_pred EEEEchh--hcceeECCCCHHHHHHHHHHCCEEEEcCC-----CCCCCc--eEEEEEcCH---------HHHHHHHHHh
Confidence 3444442 36788875 99999999999999886531 111223 335777863 4677777665
No 54
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=74.46 E-value=6.4 Score=39.86 Aligned_cols=28 Identities=18% Similarity=0.413 Sum_probs=25.1
Q ss_pred eeeEEeCCCchhHHHHHHhhCcEEEEee
Q 011603 225 IAARIRGPNDQYINHIMNETGATVLLRG 252 (481)
Q Consensus 225 ~vgrIIGP~Gs~lK~Iq~ETGaKI~IRG 252 (481)
.+-|+||++|+++|.+.++|+|+|.|==
T Consensus 156 kVpRvig~~~sm~~~l~~~~~~~I~VG~ 183 (239)
T COG1097 156 KVPRVIGKKGSMLNMLKEKTGCEIIVGQ 183 (239)
T ss_pred hcceEecCCCcHHHHhhhhcCeEEEEec
Confidence 4667999999999999999999999853
No 55
>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=74.24 E-value=8.2 Score=29.69 Aligned_cols=58 Identities=17% Similarity=0.168 Sum_probs=40.1
Q ss_pred EEEcCCCCcccceeeec-hhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHH
Q 011603 107 EIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (481)
Q Consensus 107 EIeINDlpq~~R~~LTk-~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeI 184 (481)
+|.|.. ...++.+.+ |.++.+|++.|||.|..-. .. +.+ -.+.|.|.. +.|.+|+.+|
T Consensus 3 ~i~Vp~--~~~~~iIG~~G~~i~~i~~~~g~~I~i~~-----~~--~~~--~~v~I~G~~---------~~v~~A~~~i 61 (62)
T cd02394 3 EVEIPK--KLHRFIIGKKGSNIRKIMEETGVKIRFPD-----PG--SKS--DTITITGPK---------ENVEKAKEEI 61 (62)
T ss_pred EEEeCH--HHhhhccCCCCCcHHHHHHHhCCEEEcCC-----CC--CCC--CEEEEEcCH---------HHHHHHHHHh
Confidence 345544 347888886 8999999999999987643 21 223 345788864 4788887776
No 56
>PRK15494 era GTPase Era; Provisional
Probab=73.09 E-value=16 Score=37.67 Aligned_cols=28 Identities=29% Similarity=0.191 Sum_probs=22.7
Q ss_pred ceeeEEeCCCchhHHHH--------HHhhCcEEEEe
Q 011603 224 NIAARIRGPNDQYINHI--------MNETGATVLLR 251 (481)
Q Consensus 224 N~vgrIIGP~Gs~lK~I--------q~ETGaKI~IR 251 (481)
.-.+.|||.+|.++|+| ++-.||||.|+
T Consensus 283 sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 283 SYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred CceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 34788999999999988 55568888775
No 57
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=71.00 E-value=1.6 Score=35.93 Aligned_cols=33 Identities=18% Similarity=0.264 Sum_probs=25.7
Q ss_pred CCCCCceeeEEeCCCchhHHHHHHhh-CcEEEEe
Q 011603 219 ADASLNIAARIRGPNDQYINHIMNET-GATVLLR 251 (481)
Q Consensus 219 ~~P~FN~vgrIIGP~Gs~lK~Iq~ET-GaKI~IR 251 (481)
..++++-+|..+|.+|..+|.|.+|. |-||.|=
T Consensus 12 ~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 12 GDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp SSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred CCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 35899999999999999999999999 6666543
No 58
>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=70.15 E-value=20 Score=35.35 Aligned_cols=27 Identities=26% Similarity=0.214 Sum_probs=21.6
Q ss_pred eeeEEeCCCchhHHHHH--------HhhCcEEEEe
Q 011603 225 IAARIRGPNDQYINHIM--------NETGATVLLR 251 (481)
Q Consensus 225 ~vgrIIGP~Gs~lK~Iq--------~ETGaKI~IR 251 (481)
-.+.|||.+|..+|+|. +-.||||.|+
T Consensus 232 ~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l~ 266 (270)
T TIGR00436 232 QKKIIIGKNGSMIKAIGIAARKDILELFDCDVFLE 266 (270)
T ss_pred ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 46889999999999984 4557888764
No 59
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=68.38 E-value=12 Score=39.87 Aligned_cols=57 Identities=19% Similarity=0.338 Sum_probs=46.5
Q ss_pred eeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH--HHHHHHHHh
Q 011603 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE--NLLDTISAE 299 (481)
Q Consensus 225 ~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE--~LL~tV~eE 299 (481)
-.--|.||.|.+++.|++..|+.|.-||. ++.|.+..+ .++.|+.++. .|+..++..
T Consensus 25 ~~~~l~G~~~~~l~l~e~~~gv~i~~rG~-----------------~~~i~g~~~-~v~~A~~~l~~l~~~~~~~~g 83 (348)
T COG1702 25 ELVALFGPTDTNLSLLEIALGVSIVARGE-----------------AVRIIGARP-LVDVATRVLLTLELLAEVRRG 83 (348)
T ss_pred hhhhhcCCCCccHHHHHHHhCcEEEeCCc-----------------eEEEEechH-HHHHHHHHHhHHHHHHHHhcc
Confidence 34567999999999999999999999993 677788777 8888888888 777665554
No 60
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=68.02 E-value=3.3 Score=43.66 Aligned_cols=63 Identities=19% Similarity=0.238 Sum_probs=45.2
Q ss_pred ceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 011603 209 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 288 (481)
Q Consensus 209 ~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~L 288 (481)
+.+.+.|| .-|++.|+|++|..+|+|+.+|...|.--- .++ | -+|+.....+.|+.||+-
T Consensus 26 vt~sv~vp------s~~v~~ivg~qg~kikalr~KTqtyi~tPs---------r~e---e--PiF~vTg~~edv~~aRre 85 (394)
T KOG2113|consen 26 VTESVEVP------SEHVAEIVGRQGCKIKALRAKTQTYIKTPS---------RGE---E--PIFPVTGRHEDVRRARRE 85 (394)
T ss_pred cceeeecC------cccceeecccCccccchhhhhhcceeccCC---------CCC---C--CcceeccCchhHHHHhhc
Confidence 34555554 558999999999999999999987764211 111 2 456666677888999888
Q ss_pred HHH
Q 011603 289 AEN 291 (481)
Q Consensus 289 iE~ 291 (481)
|+-
T Consensus 86 i~s 88 (394)
T KOG2113|consen 86 IPS 88 (394)
T ss_pred Ccc
Confidence 765
No 61
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=63.04 E-value=26 Score=40.57 Aligned_cols=108 Identities=17% Similarity=0.171 Sum_probs=74.8
Q ss_pred EEcCCCCcccceeeec-hhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHH
Q 011603 108 IVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEE 186 (481)
Q Consensus 108 IeINDlpq~~R~~LTk-~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeIkE 186 (481)
+..+=+|+..+|.+.| +..+..|.+++++.+..+= ....+++.+++-... .+.+|++.|+.
T Consensus 349 i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~-------~~~~~~~v~~~~~~~-----------~~~ka~~~v~~ 410 (753)
T KOG2208|consen 349 IKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK-------QGSNNKKVVITGVSA-----------NDEKAVEDVEK 410 (753)
T ss_pred eEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc-------ccCCCCCeEEecccc-----------chhHHHHHHHH
Confidence 3333456668888887 5569999999998765421 225567776654443 46677777777
Q ss_pred HHHcCCCCCCCccccCCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeec
Q 011603 187 MLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGR 253 (481)
Q Consensus 187 ILKe~p~~~pp~~~p~~~G~k~~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGR 253 (481)
+..+-++. -..+.++||-+ ...+|+|.+|..+..|+.++|| |.|+..
T Consensus 411 ~~~ei~n~-------------~~~~~~~iP~k------~~~~iig~~g~~i~~I~~k~~~-v~i~f~ 457 (753)
T KOG2208|consen 411 IIAEILNS-------------IVKEEVQIPTK------SHKRIIGTKGALINYIMGKHGG-VHIKFQ 457 (753)
T ss_pred HHHhhhcc-------------cccceeecCcc------chhhhhccccccHHHHHhhcCc-EEEecC
Confidence 77766553 11234556533 5779999999999999999999 888864
No 62
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=60.27 E-value=6.6 Score=39.50 Aligned_cols=76 Identities=13% Similarity=0.154 Sum_probs=54.4
Q ss_pred EEcCCCCccc--ceeee-chhhHHHHHhhhCCeEeeecceeCCC-C-C-------CCCCCCeEEEEeeccchhhHHHHHH
Q 011603 108 IVINDSESSV--RYKLT-KRHTQEEIQKCTGAVVITRGKYRLPN-A-P-------PDGEKPLYLHISAGAHLKETAERIL 175 (481)
Q Consensus 108 IeINDlpq~~--R~~LT-k~~Tq~eI~e~TGA~VtTRGrY~PP~-~-~-------~~gepPLYL~Ieg~tq~kdt~ERi~ 175 (481)
|.+-++|..+ ..+|. +|.||+++++.|+|.|-.||+|--.. + . ..-+-+|+-+|++.++ .
T Consensus 154 IPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adse--------d 225 (269)
T COG5176 154 IPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSE--------D 225 (269)
T ss_pred eehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchh--------h
Confidence 4556777533 44555 79999999999999999999997553 2 1 1347789999999885 2
Q ss_pred HHHHHHHHHHHHHHcC
Q 011603 176 AVDHAAAMVEEMLKQG 191 (481)
Q Consensus 176 aVd~AvaeIkEILKe~ 191 (481)
.+.+++..+..+|.++
T Consensus 226 ki~~~ik~~~n~I~~a 241 (269)
T COG5176 226 KICRLIKSQLNAIREA 241 (269)
T ss_pred hHHHHHHHHHHHHHHH
Confidence 4556666666666655
No 63
>PF13014 KH_3: KH domain
Probab=57.89 E-value=11 Score=27.41 Aligned_cols=25 Identities=32% Similarity=0.279 Sum_probs=20.7
Q ss_pred cceeeec-hhhHHHHHhhhCCeEeee
Q 011603 117 VRYKLTK-RHTQEEIQKCTGAVVITR 141 (481)
Q Consensus 117 ~R~~LTk-~~Tq~eI~e~TGA~VtTR 141 (481)
+++.+-+ |.++++|+++|||.|..-
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 4567775 999999999999998763
No 64
>COG1159 Era GTPase [General function prediction only]
Probab=54.67 E-value=31 Score=36.11 Aligned_cols=42 Identities=21% Similarity=0.362 Sum_probs=29.1
Q ss_pred CCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHH--------HhhCcEEEE
Q 011603 204 NGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIM--------NETGATVLL 250 (481)
Q Consensus 204 ~G~k~~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq--------~ETGaKI~I 250 (481)
.|..+....|+|.=+. =.|-|||.+|.++|.|- +-.||||.|
T Consensus 224 ~~~~~I~a~I~Ver~s-----QK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 224 KGLLKIHATIYVERES-----QKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred CCeEEEEEEEEEecCC-----ccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 3334556678877443 46779999999999884 445677654
No 65
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=53.98 E-value=29 Score=34.25 Aligned_cols=68 Identities=24% Similarity=0.243 Sum_probs=51.8
Q ss_pred CceeEEEEEEcCCCCc---------ccceeeechhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhH
Q 011603 100 DELIIAREIVINDSES---------SVRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKET 170 (481)
Q Consensus 100 de~~~~aEIeINDlpq---------~~R~~LTk~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt 170 (481)
|++ +-.-|+|-|+-. .-|..=+.|-|..-|+++|||.|++-|.++ +|-|.-
T Consensus 89 d~~-~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~tV--------------aiiG~~----- 148 (194)
T COG1094 89 DDY-YLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGKTV--------------AIIGGF----- 148 (194)
T ss_pred CCc-EEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCcEE--------------EEecCh-----
Confidence 444 777788877653 235555679999999999999999999888 888865
Q ss_pred HHHHHHHHHHHHHHHHHHHcC
Q 011603 171 AERILAVDHAAAMVEEMLKQG 191 (481)
Q Consensus 171 ~ERi~aVd~AvaeIkEILKe~ 191 (481)
+.|+.|..-|+.+|...
T Consensus 149 ----~~v~iAr~AVemli~G~ 165 (194)
T COG1094 149 ----EQVEIAREAVEMLINGA 165 (194)
T ss_pred ----hhhHHHHHHHHHHHcCC
Confidence 36777777777777544
No 66
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=53.09 E-value=12 Score=28.14 Aligned_cols=23 Identities=13% Similarity=0.127 Sum_probs=20.2
Q ss_pred eeEEeCCCchhHHHHHHhhCcEE
Q 011603 226 AARIRGPNDQYINHIMNETGATV 248 (481)
Q Consensus 226 vgrIIGP~Gs~lK~Iq~ETGaKI 248 (481)
.|++||.+|.+++.|+..++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 57899999999999999998554
No 67
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=45.87 E-value=20 Score=42.83 Aligned_cols=76 Identities=18% Similarity=0.162 Sum_probs=55.4
Q ss_pred ecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 011603 215 LGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 294 (481)
Q Consensus 215 Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~ 294 (481)
..++.+|-- .+.+|.+--- +.+|...++|.|..||+.=-.. ..-...++-||++|.+.+.-.|++|+..++.+|.
T Consensus 902 ~~inD~Pq~-~r~~vt~~~~--L~~i~e~~~~~it~rg~f~~~g--k~p~~gErklyl~ve~~~e~~vqra~~e~~r~l~ 976 (997)
T KOG0334|consen 902 LEINDFPQN-ARWRVTYKEA--LLRISEPTAAGITTRGKFNPPG--KEPKPGERKLYLLVEGPDELSVQRAIEELERLLE 976 (997)
T ss_pred ccccccchh-cceeeechhh--hhhccCccccceeeccccCCCC--CCCCCcchhhhhhhhcchhHHHHHHHHHHHHHHH
Confidence 344555544 7777777654 9999999999999999743321 1112234669999999999999999998887554
Q ss_pred H
Q 011603 295 T 295 (481)
Q Consensus 295 t 295 (481)
.
T Consensus 977 e 977 (997)
T KOG0334|consen 977 E 977 (997)
T ss_pred H
Confidence 3
No 68
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=44.87 E-value=1.1 Score=38.73 Aligned_cols=27 Identities=26% Similarity=0.400 Sum_probs=21.7
Q ss_pred cceeee-----chhhHHHHHhhhCCeEee--ecc
Q 011603 117 VRYKLT-----KRHTQEEIQKCTGAVVIT--RGK 143 (481)
Q Consensus 117 ~R~~LT-----k~~Tq~eI~e~TGA~VtT--RGr 143 (481)
.||.|- .|.++.+|.+.||+++.| ||.
T Consensus 37 ~R~~va~~lL~~g~syreIa~~tgvS~aTItRvs 70 (87)
T PF01371_consen 37 QRWQVAKELLDEGKSYREIAEETGVSIATITRVS 70 (87)
T ss_dssp HHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHH
T ss_pred HHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHH
Confidence 477554 489999999999999877 664
No 69
>PRK00089 era GTPase Era; Reviewed
Probab=40.04 E-value=29 Score=34.29 Aligned_cols=38 Identities=18% Similarity=0.344 Sum_probs=27.1
Q ss_pred ceeEEEecCCCCCCCceeeEEeCCCchhHHHH--------HHhhCcEEEEe
Q 011603 209 MSTSVFLGFDADASLNIAARIRGPNDQYINHI--------MNETGATVLLR 251 (481)
Q Consensus 209 ~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~I--------q~ETGaKI~IR 251 (481)
....|+|.-+. -.+.|||.+|.++|+| ++-.||||.|.
T Consensus 226 i~~~i~v~~~~-----~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 226 IEATIYVERDS-----QKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEccCC-----ceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 44555555333 3788999999999988 45568888765
No 70
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=39.75 E-value=22 Score=32.83 Aligned_cols=28 Identities=11% Similarity=0.136 Sum_probs=25.2
Q ss_pred eeeEEeCCCchhHHHHHHhhCcEEEEee
Q 011603 225 IAARIRGPNDQYINHIMNETGATVLLRG 252 (481)
Q Consensus 225 ~vgrIIGP~Gs~lK~Iq~ETGaKI~IRG 252 (481)
-+|..+|.+|+.+|.|++..|-||-|=.
T Consensus 42 ~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 42 DMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CccccCCcCchHHHHHHHHhCCceEEEE
Confidence 4799999999999999999998887765
No 71
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=38.84 E-value=36 Score=39.56 Aligned_cols=30 Identities=23% Similarity=0.286 Sum_probs=26.1
Q ss_pred eeEEeCCCchhHHHHHHhhCcEEEEeecCC
Q 011603 226 AARIRGPNDQYINHIMNETGATVLLRGRGS 255 (481)
Q Consensus 226 vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGS 255 (481)
...|+|.+|.++.+|++++.|+|.++=.|+
T Consensus 358 ~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~ 387 (753)
T KOG2208|consen 358 LKFVIGKKGANIEKIREESQVKIDLPKQGS 387 (753)
T ss_pred hhhhcCCCCccHHHHHHhhhhceecccccC
Confidence 667999999999999999999999985433
No 72
>PF07885 Ion_trans_2: Ion channel; InterPro: IPR013099 This entry includes the two membrane helix type ion channels found in bacteria []. ; PDB: 1KKD_A 2A0L_A 1ORQ_C 3UKM_C 1LNQ_E 3OUS_A 3LDC_A 3LDD_A 3RBZ_A 3LDE_A ....
Probab=38.12 E-value=26 Score=28.21 Aligned_cols=16 Identities=44% Similarity=0.752 Sum_probs=10.5
Q ss_pred ccCCCCCcCCChHHHHH
Q 011603 399 SGYEGIYPQATPLQQVA 415 (481)
Q Consensus 399 ~gy~~iypqatplqq~a 415 (481)
-|||+++|+ |+.-++.
T Consensus 39 vGyGDi~p~-t~~gr~~ 54 (79)
T PF07885_consen 39 VGYGDIVPQ-TPAGRIF 54 (79)
T ss_dssp ---SSSSTS-SHHHHHH
T ss_pred ccCCCccCC-ccchHHH
Confidence 599999999 8885543
No 73
>PRK01381 Trp operon repressor; Provisional
Probab=36.56 E-value=11 Score=33.49 Aligned_cols=29 Identities=28% Similarity=0.434 Sum_probs=23.0
Q ss_pred cceeeec-----hhhHHHHHhhhCCeEee--eccee
Q 011603 117 VRYKLTK-----RHTQEEIQKCTGAVVIT--RGKYR 145 (481)
Q Consensus 117 ~R~~LTk-----~~Tq~eI~e~TGA~VtT--RGrY~ 145 (481)
.||.|-+ .-+|.||.+++|++|+| ||.-+
T Consensus 43 ~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~ 78 (99)
T PRK01381 43 TRVRIVEELLRGELSQREIKQELGVGIATITRGSNS 78 (99)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHH
Confidence 5776664 47999999999999887 77544
No 74
>PRK01064 hypothetical protein; Provisional
Probab=33.39 E-value=30 Score=29.38 Aligned_cols=20 Identities=20% Similarity=0.169 Sum_probs=17.3
Q ss_pred eeEEeCCCchhHHHHHHhhC
Q 011603 226 AARIRGPNDQYINHIMNETG 245 (481)
Q Consensus 226 vgrIIGP~Gs~lK~Iq~ETG 245 (481)
.|++||-+|.+++.|+.-..
T Consensus 41 ~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred ceEEECCCCccHHHHHHHHH
Confidence 69999999999999987543
No 75
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=31.22 E-value=1.2e+02 Score=28.79 Aligned_cols=59 Identities=12% Similarity=0.158 Sum_probs=45.8
Q ss_pred eeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhh
Q 011603 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 300 (481)
Q Consensus 226 vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~eE~ 300 (481)
.-.|+.++|..++.|...-||+|.+.- +.-.|.|+| +...++.+...+.+++..|+.+.
T Consensus 37 ~~LLl~~~~~~L~~l~~~~~~~I~~~~---------------~~~~i~I~g-~k~~~~~i~~~i~~~l~~i~~~~ 95 (210)
T PF14611_consen 37 FFLLLTGNGRILENLAARNGAKIEVSR---------------SENRIRITG-TKSTAEYIEASINEILSNIRTEE 95 (210)
T ss_pred eeeeecCCchHHHHHHHhcCceEEEec---------------CCcEEEEEc-cHHHHHHHHHHHHHHHhhcEEEE
Confidence 458899999999999888899998863 224677777 66667777778888887776664
No 76
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=29.62 E-value=54 Score=35.01 Aligned_cols=39 Identities=18% Similarity=0.393 Sum_probs=31.7
Q ss_pred eEEEecCCCCCCCceeeEEeCCCchhHHHHHHhh-CcEEEE
Q 011603 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNET-GATVLL 250 (481)
Q Consensus 211 eKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ET-GaKI~I 250 (481)
.||-|= -..|+++-+|..||++|+.++.|.+|. |=||-|
T Consensus 233 tKVAV~-s~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdi 272 (362)
T PRK12327 233 TKIAVR-SNNPNVDAKGACVGPKGQRVQNIVSELKGEKIDI 272 (362)
T ss_pred eEEEEE-cCCCCCCchheeECCCChhHHHHHHHhCCCeEEE
Confidence 577653 246999999999999999999999999 655544
No 77
>PRK02821 hypothetical protein; Provisional
Probab=29.14 E-value=34 Score=28.99 Aligned_cols=20 Identities=5% Similarity=0.129 Sum_probs=17.4
Q ss_pred eeEEeCCCchhHHHHHHhhC
Q 011603 226 AARIRGPNDQYINHIMNETG 245 (481)
Q Consensus 226 vgrIIGP~Gs~lK~Iq~ETG 245 (481)
+|||||-+|.+++-|..--.
T Consensus 42 ~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 42 LGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CcceeCCCCchHHHHHHHHH
Confidence 89999999999999876544
No 78
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=28.92 E-value=49 Score=37.44 Aligned_cols=90 Identities=23% Similarity=0.276 Sum_probs=54.1
Q ss_pred eeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhhhccc
Q 011603 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGASR 304 (481)
Q Consensus 225 ~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~eE~~~~r 304 (481)
++-+|+|-.|+++|.|...|++||.|+-.-++ +=.+.+.+.-+..+..|+.++-..+.
T Consensus 78 ~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g------------~e~~~~~~~~p~~v~~a~a~~~~~~~---------- 135 (608)
T KOG2279|consen 78 AVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG------------DERVLLISGFPVQVCKAKAAIHQILT---------- 135 (608)
T ss_pred ceeeeeccccCCcchhhcccccceecCcccCC------------cccchhhccCCCCCChHHHHHHHHHh----------
Confidence 68899999999999999999999999864333 22233333344555555544332221
Q ss_pred cccccccccCCCchhhccCcccccccccCCccc
Q 011603 305 VSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGS 337 (481)
Q Consensus 305 ~~~~~~y~~~pppq~~l~g~~~~~~~~~~~~~~ 337 (481)
....+--..+-||.+.--+..-|.|+..+...
T Consensus 136 -~~~pvk~~lsvpqr~~~~i~grgget~~si~~ 167 (608)
T KOG2279|consen 136 -ENTPVSEQLSVPQRSVGRIIGRGGETIRSICK 167 (608)
T ss_pred -cCCcccccccchhhhcccccccchhhhcchhc
Confidence 01223333556666666566556555544433
No 79
>PRK00468 hypothetical protein; Provisional
Probab=28.81 E-value=36 Score=28.63 Aligned_cols=18 Identities=11% Similarity=0.204 Sum_probs=15.9
Q ss_pred eeEEeCCCchhHHHHHHh
Q 011603 226 AARIRGPNDQYINHIMNE 243 (481)
Q Consensus 226 vgrIIGP~Gs~lK~Iq~E 243 (481)
+|||||-+|.+++-|..-
T Consensus 41 ~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CcceecCCChhHHHHHHH
Confidence 699999999999988653
No 80
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=27.96 E-value=5.3e+02 Score=24.51 Aligned_cols=125 Identities=18% Similarity=0.144 Sum_probs=73.0
Q ss_pred cceeee--chhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcCCCC
Q 011603 117 VRYKLT--KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAG 194 (481)
Q Consensus 117 ~R~~LT--k~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeIkEILKe~p~~ 194 (481)
..+.|. .+..+.+|....|+.|.+.-. + --|.|+|.. ..++-+...|+++++.-
T Consensus 36 ~~~LLl~~~~~~L~~l~~~~~~~I~~~~~----------~--~~i~I~g~k---------~~~~~i~~~i~~~l~~i--- 91 (210)
T PF14611_consen 36 EFFLLLTGNGRILENLAARNGAKIEVSRS----------E--NRIRITGTK---------STAEYIEASINEILSNI--- 91 (210)
T ss_pred heeeeecCCchHHHHHHHhcCceEEEecC----------C--cEEEEEccH---------HHHHHHHHHHHHHHhhc---
Confidence 344444 367788887888999887431 1 246899954 36666777788887543
Q ss_pred CCCccccCCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEE
Q 011603 195 FPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFL 274 (481)
Q Consensus 195 ~pp~~~p~~~G~k~~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~I 274 (481)
.++.|-++. -.+.|...+. ---....++.|++.|++-|..-+.+ ..+.++-
T Consensus 92 --------------~~~~i~l~~-~~~~~~~~~~-~~~~~~~l~~i~~~t~~~ie~~~~~-------------~~~~i~~ 142 (210)
T PF14611_consen 92 --------------RTEEIDLSP-IISKHSEKKN-SQFTPDLLEEIQKLTNVYIEKNPDG-------------NKLKISW 142 (210)
T ss_pred --------------EEEEEecch-hhhhhccccc-ccccHHHHHHHHHHHcEEEEECCCC-------------CeEEEEE
Confidence 122232220 0011100000 0113457999999999888776532 2233333
Q ss_pred --EeCCHHHHHHHHHHHHHHHH
Q 011603 275 --SSNNPKSLEEAKRLAENLLD 294 (481)
Q Consensus 275 --sa~~~e~v~~Ak~LiE~LL~ 294 (481)
...+++..+.|++|....+.
T Consensus 143 ~~~~~~~~~~~~a~RlL~~a~~ 164 (210)
T PF14611_consen 143 LASPENEKRADRAKRLLLWALD 164 (210)
T ss_pred EeeccccchHHHHHHHHHHhcc
Confidence 23888889999998876664
No 81
>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=27.10 E-value=39 Score=27.67 Aligned_cols=22 Identities=5% Similarity=0.086 Sum_probs=18.7
Q ss_pred eeEEeCCCchhHHHHHHhhCcE
Q 011603 226 AARIRGPNDQYINHIMNETGAT 247 (481)
Q Consensus 226 vgrIIGP~Gs~lK~Iq~ETGaK 247 (481)
.|+|||.+|.+++-||--+..-
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~~ 56 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANLV 56 (77)
T ss_pred CCeEECCCCccHHHHHHHHHHH
Confidence 5899999999999999877633
No 82
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=26.97 E-value=1.3e+02 Score=29.72 Aligned_cols=58 Identities=14% Similarity=0.098 Sum_probs=34.4
Q ss_pred eeEEeCCC-------------chhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHH--H-HHHHHHHH
Q 011603 226 AARIRGPN-------------DQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPK--S-LEEAKRLA 289 (481)
Q Consensus 226 vgrIIGP~-------------Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e--~-v~~Ak~Li 289 (481)
+|+++||+ +..+....+|...+|.+|=+-.+ =+|++|=..+.+ + ++.+..++
T Consensus 117 lgk~LGp~~~p~gK~P~~~~~~~dl~~~i~~~k~~v~~r~~k~~------------~~~~~VGk~~m~~e~i~eNi~a~l 184 (214)
T PTZ00225 117 VPRLVGPHMHRMGKFPTVCSPSESLPDKVVELRSTVKFQLKKVL------------CLGTCVGHVEMTEEQLRQNVVMAI 184 (214)
T ss_pred hhhhcCCCCCcCCCCCcccCCccCHHHHHHHHhheeEEEecCcc------------EEEeEEccCCCCHHHHHHHHHHHH
Confidence 58888887 45577777788777777753222 377777654443 2 33344444
Q ss_pred HHHHHH
Q 011603 290 ENLLDT 295 (481)
Q Consensus 290 E~LL~t 295 (481)
+.|...
T Consensus 185 ~~l~~~ 190 (214)
T PTZ00225 185 NFLVSL 190 (214)
T ss_pred HHHHHh
Confidence 444443
No 83
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=26.88 E-value=70 Score=33.81 Aligned_cols=39 Identities=21% Similarity=0.325 Sum_probs=31.3
Q ss_pred eEEEecCCCCCCCceeeEEeCCCchhHHHHHHhh-CcEEEE
Q 011603 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNET-GATVLL 250 (481)
Q Consensus 211 eKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ET-GaKI~I 250 (481)
.||-|-- ..|+.+-+|..||++|+.++.|.+|. |=||-|
T Consensus 231 tKvAV~s-~~~~iDpvga~vG~~G~ri~~i~~el~ge~Idi 270 (341)
T TIGR01953 231 TKIAVES-NDENIDPVGACVGPKGSRIQAISKELNGEKIDI 270 (341)
T ss_pred eEEEEEc-CCCCCCcceeeECCCCchHHHHHHHhCCCeEEE
Confidence 5776543 36999999999999999999999998 544433
No 84
>PF00408 PGM_PMM_IV: Phosphoglucomutase/phosphomannomutase, C-terminal domain; InterPro: IPR005843 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1KFQ_B 1KFI_A 3PDK_B 2F7L_A 1TUO_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=26.22 E-value=1.8e+02 Score=23.27 Aligned_cols=26 Identities=15% Similarity=0.440 Sum_probs=20.7
Q ss_pred CC-cEEEEEeCCHHHHHHHHHHHHHHH
Q 011603 268 QP-LHLFLSSNNPKSLEEAKRLAENLL 293 (481)
Q Consensus 268 EP-LHV~Isa~~~e~v~~Ak~LiE~LL 293 (481)
|| +.|++.+.+.+.+++-.+-+.++|
T Consensus 46 EP~iRv~~Ea~~~~~~~~~~~~i~~~i 72 (73)
T PF00408_consen 46 EPKIRVYVEAPDEEELEEIAEEIAEAI 72 (73)
T ss_dssp SSEEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred CceEEEEEEeCCHHHHHHHHHHHHHhh
Confidence 45 999999999988887777666665
No 85
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=25.07 E-value=1.4e+02 Score=33.84 Aligned_cols=70 Identities=16% Similarity=0.130 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCccccCCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHHhhCcEEEEeecCC
Q 011603 176 AVDHAAAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGS 255 (481)
Q Consensus 176 aVd~AvaeIkEILKe~p~~~pp~~~p~~~G~k~~eeKI~Iple~~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGS 255 (481)
....|..+|.+.++.-.....+-++.. --...|+||-+ .++++||-+|..++.|++..|-+|.++-++.
T Consensus 458 ~~~~a~~~i~~~i~r~~p~~~eVe~~g-----d~~avv~vpe~------~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 458 ALKLAEEEIEREIKRYLPGDVEVEVVG-----DGRAVVKVPEK------YIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred hhHHHHHHHHHHHHHhCCCCceEEEec-----CCeEEEEeCHH------HhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 355566666666654422111111110 01245666644 3678999999999999999999999998654
Q ss_pred C
Q 011603 256 G 256 (481)
Q Consensus 256 g 256 (481)
.
T Consensus 527 ~ 527 (604)
T COG1855 527 E 527 (604)
T ss_pred c
Confidence 3
No 86
>PF00639 Rotamase: PPIC-type PPIASE domain; InterPro: IPR000297 Peptidylprolyl isomerase (5.2.1.8 from EC) is an enzyme that accelerates protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides []. It has been reported in bacteria and eukayotes. Synonyms for proteins with this domain are: Peptidylprolyl isomerase, Peptidyl-prolyl cis-trans isomerase, PPIase, rotamase, cyclophilin, FKBP65.; GO: 0016853 isomerase activity; PDB: 2JZV_A 2PV3_B 1M5Y_A 2PV2_B 2PV1_A 1JNS_A 1JNT_A 3KAB_A 2ZR6_A 2XPB_A ....
Probab=24.21 E-value=86 Score=26.14 Aligned_cols=33 Identities=15% Similarity=0.287 Sum_probs=27.7
Q ss_pred EEEEEeCC-HHHHHHHHHHHHHHHHHHHHhhhcc
Q 011603 271 HLFLSSNN-PKSLEEAKRLAENLLDTISAECGAS 303 (481)
Q Consensus 271 HV~Isa~~-~e~v~~Ak~LiE~LL~tV~eE~~~~ 303 (481)
|++|..++ .+..+++++.++.|+..+......|
T Consensus 1 HIl~~~~~~~~~~~~~~~~a~~i~~~l~~g~~~F 34 (95)
T PF00639_consen 1 HILVKPPPSDEEKDAAKKKAEEIYEQLKKGEDSF 34 (95)
T ss_dssp EEEEESTTSCCHHHHHHHHHHHHHHHHHTTSSSH
T ss_pred CEEEECCCchhhHHHHHHHHHHHHHHHHhCchhH
Confidence 88898776 7789999999999999999886533
No 87
>PF13711 DUF4160: Domain of unknown function (DUF4160)
Probab=24.18 E-value=1.7e+02 Score=23.36 Aligned_cols=14 Identities=21% Similarity=0.444 Sum_probs=11.1
Q ss_pred CCCcEEEEEeCCHH
Q 011603 267 HQPLHLFLSSNNPK 280 (481)
Q Consensus 267 ~EPLHV~Isa~~~e 280 (481)
-+|.||||...+.+
T Consensus 14 H~PpHvHv~~g~~~ 27 (66)
T PF13711_consen 14 HEPPHVHVRYGGFE 27 (66)
T ss_pred CCCCeEEEEcCCcE
Confidence 59999999877643
No 88
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=23.48 E-value=62 Score=30.22 Aligned_cols=28 Identities=11% Similarity=0.141 Sum_probs=24.8
Q ss_pred eeeEEeCCCchhHHHHHHhhCcEEEEee
Q 011603 225 IAARIRGPNDQYINHIMNETGATVLLRG 252 (481)
Q Consensus 225 ~vgrIIGP~Gs~lK~Iq~ETGaKI~IRG 252 (481)
-+|..+|++|+.+|.|++..|=||-|=.
T Consensus 43 ~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 43 EMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred CccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 5899999999999999988888887665
No 89
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=22.47 E-value=1.3e+02 Score=35.01 Aligned_cols=62 Identities=19% Similarity=0.224 Sum_probs=47.9
Q ss_pred EEEEcCCCCcccceeeec-hhhHHHHHhhhCCeEee--ecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHH
Q 011603 106 REIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVIT--RGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAA 182 (481)
Q Consensus 106 aEIeINDlpq~~R~~LTk-~~Tq~eI~e~TGA~VtT--RGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~Ava 182 (481)
....++..+.+.|-.+.+ |.++++|.++||+.|.+ .|... |.+.+. +..++|+.
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~IdieddGtv~---------------i~~s~~--------~~~~~ak~ 608 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDGTVK---------------IAASDG--------ESAKKAKE 608 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCCCcEE---------------EEecch--------HHHHHHHH
Confidence 456778888888888887 89999999999999877 44433 555543 47888999
Q ss_pred HHHHHHHc
Q 011603 183 MVEEMLKQ 190 (481)
Q Consensus 183 eIkEILKe 190 (481)
.|+.+..+
T Consensus 609 ~I~~i~~e 616 (692)
T COG1185 609 RIEAITRE 616 (692)
T ss_pred HHHHHHhh
Confidence 99998854
No 90
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=22.28 E-value=62 Score=31.68 Aligned_cols=33 Identities=9% Similarity=0.142 Sum_probs=27.8
Q ss_pred CCCCceeeEEeCCCchhHHHHHHhhCcEEEEee
Q 011603 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRG 252 (481)
Q Consensus 220 ~P~FN~vgrIIGP~Gs~lK~Iq~ETGaKI~IRG 252 (481)
.++.+=+|..||++|+.+|.|.+|.|=||-|=-
T Consensus 81 ~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe 113 (190)
T COG0195 81 VVKIDPVGACIGKRGSRVKAVSEELGEKIDVVE 113 (190)
T ss_pred ecCcCchhhhccCCChHHHHHHHHhCCceEEEE
Confidence 356777999999999999999999997775543
No 91
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=22.16 E-value=2.7e+02 Score=27.25 Aligned_cols=52 Identities=12% Similarity=0.300 Sum_probs=39.8
Q ss_pred hHHHHHHhhC-cEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011603 236 YINHIMNETG-ATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECG 301 (481)
Q Consensus 236 ~lK~Iq~ETG-aKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~eE~~ 301 (481)
+++.|++... .-+.+++||.+ |.|.|-|... .++.+...|.+|+..++..|+
T Consensus 14 fle~l~~~~~~~~~~v~~k~n~-------------l~I~i~G~~~-eike~~~~Ik~~~~~vr~k~~ 66 (190)
T PF09840_consen 14 FLERLSKMVKSIYIYVEVKGNS-------------LKIEIQGYEK-EIKEAIRRIKELVRRVRSKYN 66 (190)
T ss_pred HHHHHHhhccCcEEEEEEeCCE-------------EEEEEecChH-HHHHHHHHHHHHHHHHHHHhc
Confidence 4666766633 34457776633 8888888887 899999999999999999764
No 92
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=21.81 E-value=69 Score=30.87 Aligned_cols=26 Identities=12% Similarity=0.087 Sum_probs=24.1
Q ss_pred eEEeCCCchhHHHHHHhhCcEEEEee
Q 011603 227 ARIRGPNDQYINHIMNETGATVLLRG 252 (481)
Q Consensus 227 grIIGP~Gs~lK~Iq~ETGaKI~IRG 252 (481)
|.-||++|.+++++++..|=+|.|=.
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEEE
Confidence 88999999999999999999887766
No 93
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....
Probab=21.57 E-value=2.8e+02 Score=24.62 Aligned_cols=51 Identities=27% Similarity=0.393 Sum_probs=32.8
Q ss_pred EEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHH----HHHHHHHHHHHHHHHHH
Q 011603 228 RIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPK----SLEEAKRLAENLLDTIS 297 (481)
Q Consensus 228 rIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e----~v~~Ak~LiE~LL~tV~ 297 (481)
+==||||.+++. |..+|.|+=.-++ |.|.+.+.- +.+.|.+....+|....
T Consensus 20 RssGpGGQ~VNk----~~s~V~l~h~ptg---------------i~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~~ 74 (113)
T PF00472_consen 20 RSSGPGGQNVNK----TNSKVRLRHIPTG---------------IVVKCQESRSQHQNREDALEKLREKLDEAY 74 (113)
T ss_dssp ESSSSSSCHHHS----SSEEEEEEETTTT---------------EEEEEESSSSHHHHHHHHHHHHHHHHHHHH
T ss_pred ecCCCCCCcccc----cCCEEEEEEeccc---------------EEEEEcccCCHHHHHHHHHHHHHHHHHHHH
Confidence 345999999976 4556777644222 778877543 56667666666666655
No 94
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=20.53 E-value=61 Score=32.72 Aligned_cols=51 Identities=18% Similarity=0.203 Sum_probs=40.0
Q ss_pred eeeEEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHH
Q 011603 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLL 293 (481)
Q Consensus 225 ~vgrIIGP~Gs~lK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es~EPLHV~Isa~~~e~v~~Ak~LiE~LL 293 (481)
.+|||.|.+|.|---||+-|.+||.|-+ -.+||.| ..++++-|+.-+-+||
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVlad-----------------~kIHiLG-~~~niriAR~avcsLI 229 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIENVTRTRIVLAD-----------------SKIHILG-AFQNIRIARDAVCSLI 229 (252)
T ss_pred HHHHhhcCCCcceeeeeccceeEEEecC-----------------ceEEEee-cchhhHHHHHhhHhhh
Confidence 3899999999999999999999999976 2344444 4566777877766666
No 95
>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=20.46 E-value=1.4e+02 Score=34.82 Aligned_cols=62 Identities=18% Similarity=0.186 Sum_probs=45.0
Q ss_pred EEEEcCCCCcccceeeec-hhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHH
Q 011603 106 REIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (481)
Q Consensus 106 aEIeINDlpq~~R~~LTk-~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeI 184 (481)
..+.|+ |.+.|-.|.. |.++++|.++||+.|...- +- .+.|.+.+. +.+++|+++|
T Consensus 580 ~~~~I~--~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-----------~G--~V~I~a~d~--------~~~~~A~~~I 636 (719)
T TIGR02696 580 ITVKIP--VDKIGEVIGPKGKMINQIQDETGAEISIED-----------DG--TVYIGAADG--------PSAEAARAMI 636 (719)
T ss_pred EEEEeC--hHHhhheeCCCcHhHHHHHHHHCCEEEEec-----------Cc--EEEEEeCCH--------HHHHHHHHHH
Confidence 344453 3346777775 9999999999999987732 22 245777763 5799999999
Q ss_pred HHHHHc
Q 011603 185 EEMLKQ 190 (481)
Q Consensus 185 kEILKe 190 (481)
+.++..
T Consensus 637 ~~i~~~ 642 (719)
T TIGR02696 637 NAIANP 642 (719)
T ss_pred HHhhCc
Confidence 999874
No 96
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=20.44 E-value=62 Score=27.58 Aligned_cols=18 Identities=17% Similarity=0.252 Sum_probs=16.1
Q ss_pred eeEEeCCCchhHHHHHHh
Q 011603 226 AARIRGPNDQYINHIMNE 243 (481)
Q Consensus 226 vgrIIGP~Gs~lK~Iq~E 243 (481)
+|+|||-+|.+++-|..-
T Consensus 41 ~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 41 MGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred ccceecCCChhHHHHHHH
Confidence 899999999999998653
No 97
>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=20.32 E-value=1.5e+02 Score=34.13 Aligned_cols=53 Identities=23% Similarity=0.250 Sum_probs=39.4
Q ss_pred ccceeeec-hhhHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHH
Q 011603 116 SVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLK 189 (481)
Q Consensus 116 ~~R~~LTk-~~Tq~eI~e~TGA~VtTRGrY~PP~~~~~gepPLYL~Ieg~tq~kdt~ERi~aVd~AvaeIkEILK 189 (481)
+.|-.|.+ |.++++|+++||+.|.+.- +- .+.|.+.++ ..+++|+.+|+.+..
T Consensus 561 kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------dG--~V~i~~~~~--------~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 561 KIRDVIGPGGKVIREITEETGAKIDIED-----------DG--TVKIAASDG--------EAAEAAIKMIEGITA 614 (684)
T ss_pred HHHhhcCCCcHHHHHHHHHHCCEEEEec-----------Ce--EEEEEECcH--------HHHHHHHHHHHhhhc
Confidence 35666765 9999999999999988732 11 235666653 589999999998854
No 98
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=20.13 E-value=23 Score=28.47 Aligned_cols=20 Identities=20% Similarity=0.313 Sum_probs=17.6
Q ss_pred eeEEeCCCchhHHHHHHhhC
Q 011603 226 AARIRGPNDQYINHIMNETG 245 (481)
Q Consensus 226 vgrIIGP~Gs~lK~Iq~ETG 245 (481)
.|+|||-+|.+++-||.-.+
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHH
T ss_pred cceEECCCCeeHHHHHHHHH
Confidence 79999999999999987654
Done!