Query 010778
Match_columns 501
No_of_seqs 216 out of 482
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 04:27:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010778.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010778hhsearch_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 8.7E-38 1.9E-42 320.2 12.9 268 26-305 12-305 (531)
2 KOG0119 Splicing factor 1/bran 100.0 1E-28 2.2E-33 258.4 15.6 161 127-295 61-230 (554)
3 cd02395 SF1_like-KH Splicing f 99.9 2.4E-26 5.1E-31 204.2 8.2 96 210-305 1-106 (120)
4 KOG1588 RNA-binding protein Sa 99.9 1E-22 2.2E-27 200.8 10.2 127 175-301 55-197 (259)
5 COG5176 MSL5 Splicing factor ( 99.9 1.5E-21 3.2E-26 188.3 10.2 183 110-298 47-243 (269)
6 KOG1676 K-homology type RNA bi 99.2 5E-10 1.1E-14 121.1 18.5 166 101-299 136-304 (600)
7 KOG1960 Predicted RNA-binding 99.2 7.2E-12 1.6E-16 130.4 3.9 148 124-304 234-384 (531)
8 KOG0334 RNA helicase [RNA proc 99.1 2E-11 4.4E-16 137.9 3.5 83 102-192 896-979 (997)
9 TIGR03665 arCOG04150 arCOG0415 98.8 2.1E-08 4.6E-13 94.0 9.9 133 118-294 10-150 (172)
10 PRK13763 putative RNA-processi 98.8 3E-08 6.4E-13 93.7 10.7 145 104-294 3-156 (180)
11 cd00105 KH-I K homology RNA-bi 98.5 3.2E-07 6.9E-12 70.5 7.6 63 211-290 2-64 (64)
12 KOG1676 K-homology type RNA bi 98.5 2.7E-06 5.9E-11 92.8 17.2 156 105-295 231-389 (600)
13 cd02393 PNPase_KH Polynucleoti 98.5 3.8E-07 8.2E-12 72.3 7.5 58 211-290 4-61 (61)
14 PF00013 KH_1: KH domain syndr 98.4 1.3E-07 2.8E-12 73.0 2.6 59 211-289 2-60 (60)
15 smart00322 KH K homology RNA-b 98.4 1.4E-06 3.1E-11 65.4 8.2 66 209-293 3-68 (69)
16 cd02394 vigilin_like_KH K homo 98.2 2.5E-06 5.3E-11 66.3 5.4 53 224-289 9-61 (62)
17 KOG2191 RNA-binding protein NO 98.2 8.6E-05 1.9E-09 77.1 17.8 163 104-301 39-207 (402)
18 cd02396 PCBP_like_KH K homolog 98.0 1.5E-05 3.3E-10 63.2 6.7 61 212-289 3-64 (65)
19 PF13014 KH_3: KH domain 97.7 2.7E-05 5.7E-10 57.3 3.2 28 225-252 1-28 (43)
20 KOG2193 IGF-II mRNA-binding pr 97.7 8.1E-05 1.7E-09 79.3 7.6 142 121-302 214-356 (584)
21 PRK13763 putative RNA-processi 97.5 0.00017 3.7E-09 68.4 6.5 64 210-294 4-70 (180)
22 TIGR03665 arCOG04150 arCOG0415 97.3 0.00025 5.5E-09 66.7 4.9 56 225-295 8-65 (172)
23 TIGR02696 pppGpp_PNP guanosine 97.3 0.0011 2.4E-08 74.9 10.6 64 210-295 579-642 (719)
24 COG1094 Predicted RNA-binding 97.2 0.0007 1.5E-08 65.9 6.1 54 225-296 112-165 (194)
25 cd02395 SF1_like-KH Splicing f 97.1 0.0012 2.7E-08 59.4 6.3 66 120-191 21-96 (120)
26 TIGR03591 polynuc_phos polyrib 97.1 0.00089 1.9E-08 75.1 6.5 100 210-347 552-651 (684)
27 KOG2193 IGF-II mRNA-binding pr 96.8 0.0076 1.7E-07 64.8 10.7 157 107-302 414-571 (584)
28 KOG0119 Splicing factor 1/bran 96.8 0.0022 4.8E-08 69.6 6.6 66 118-191 156-231 (554)
29 PLN00207 polyribonucleotide nu 96.8 0.0012 2.6E-08 76.0 4.6 101 210-348 686-788 (891)
30 KOG2190 PolyC-binding proteins 96.8 0.021 4.5E-07 62.3 13.6 141 118-293 56-206 (485)
31 PRK11824 polynucleotide phosph 96.1 0.007 1.5E-07 68.1 5.4 93 224-348 563-655 (693)
32 PRK04163 exosome complex RNA-b 95.7 0.015 3.2E-07 57.4 4.8 54 225-294 155-208 (235)
33 KOG2190 PolyC-binding proteins 95.4 0.32 6.9E-06 53.3 14.2 60 117-191 149-209 (485)
34 KOG2191 RNA-binding protein NO 95.2 0.082 1.8E-06 55.7 8.7 77 209-302 39-115 (402)
35 KOG1067 Predicted RNA-binding 95.2 0.029 6.3E-07 62.3 5.7 71 226-313 608-684 (760)
36 KOG2874 rRNA processing protei 95.0 0.025 5.4E-07 58.4 4.1 57 226-300 160-216 (356)
37 KOG2814 Transcription coactiva 94.1 0.082 1.8E-06 55.4 5.5 62 225-298 67-128 (345)
38 PRK00106 hypothetical protein; 93.9 0.12 2.6E-06 57.2 6.5 60 220-294 231-290 (535)
39 TIGR03319 YmdA_YtgF conserved 93.8 0.12 2.6E-06 56.7 6.3 60 220-294 210-269 (514)
40 PRK12704 phosphodiesterase; Pr 93.7 0.15 3.2E-06 56.1 6.8 59 220-293 216-274 (520)
41 COG1185 Pnp Polyribonucleotide 93.1 0.13 2.8E-06 58.3 5.3 54 226-295 563-616 (692)
42 KOG0336 ATP-dependent RNA heli 91.8 0.28 6E-06 53.5 5.6 63 223-301 55-118 (629)
43 KOG2192 PolyC-binding hnRNP-K 88.8 1.1 2.4E-05 46.6 6.6 65 225-300 325-389 (390)
44 KOG1588 RNA-binding protein Sa 88.5 1.3 2.7E-05 45.4 6.8 74 118-194 111-195 (259)
45 cd02393 PNPase_KH Polynucleoti 88.2 2 4.4E-05 34.1 6.5 57 106-185 4-61 (61)
46 PRK12705 hypothetical protein; 86.4 0.68 1.5E-05 51.2 3.8 58 220-292 204-261 (508)
47 KOG2192 PolyC-binding hnRNP-K 84.0 6.7 0.00014 41.0 9.3 133 118-295 60-193 (390)
48 cd02396 PCBP_like_KH K homolog 83.5 4.4 9.4E-05 32.1 6.2 53 117-184 11-64 (65)
49 PF00013 KH_1: KH domain syndr 81.1 4.3 9.4E-05 31.2 5.3 49 117-184 11-60 (60)
50 KOG2113 Predicted RNA binding 80.9 3.8 8.3E-05 43.4 6.3 110 120-253 41-153 (394)
51 cd02134 NusA_KH NusA_K homolog 80.8 1.7 3.7E-05 34.5 3.0 26 225-250 35-60 (61)
52 smart00322 KH K homology RNA-b 77.1 18 0.0004 26.7 7.5 64 105-188 4-68 (69)
53 cd02394 vigilin_like_KH K homo 74.7 8.8 0.00019 29.6 5.4 58 107-184 3-61 (62)
54 COG1097 RRP4 RNA-binding prote 72.9 7.2 0.00016 39.7 5.6 29 224-252 155-183 (239)
55 PRK15494 era GTPase Era; Provi 72.3 18 0.0004 37.4 8.5 28 224-251 283-318 (339)
56 cd00105 KH-I K homology RNA-bi 70.8 19 0.0004 27.4 6.3 60 107-184 3-63 (64)
57 PF13184 KH_5: NusA-like KH do 70.5 1.4 2.9E-05 36.5 -0.1 33 219-251 12-45 (69)
58 TIGR00436 era GTP-binding prot 69.6 22 0.00047 35.2 8.1 27 225-251 232-266 (270)
59 COG1094 Predicted RNA-binding 67.6 8.5 0.00018 38.1 4.7 55 226-292 19-74 (194)
60 KOG2113 Predicted RNA binding 66.6 3.7 8.1E-05 43.5 2.1 63 209-291 26-88 (394)
61 COG1702 PhoH Phosphate starvat 66.6 14 0.00029 39.6 6.3 57 225-299 25-83 (348)
62 KOG2208 Vigilin [Lipid transpo 64.3 25 0.00055 40.9 8.3 108 108-253 349-457 (753)
63 cd02409 KH-II KH-II (K homolo 57.1 9.9 0.00021 28.8 2.5 23 226-248 36-58 (68)
64 COG5176 MSL5 Splicing factor ( 52.5 10 0.00022 38.5 2.3 76 108-191 154-241 (269)
65 PF01371 Trp_repressor: Trp re 51.3 0.85 1.8E-05 39.5 -4.7 32 110-143 32-70 (87)
66 PF13014 KH_3: KH domain 50.8 16 0.00035 26.7 2.6 24 117-140 2-26 (43)
67 KOG0334 RNA helicase [RNA proc 47.0 18 0.00039 43.3 3.6 76 216-296 903-978 (997)
68 COG1159 Era GTPase [General fu 44.1 59 0.0013 34.2 6.4 41 205-250 225-273 (298)
69 PRK08406 transcription elongat 42.6 19 0.00041 33.5 2.4 28 225-252 42-69 (140)
70 PRK01381 Trp operon repressor; 41.2 11 0.00023 33.9 0.4 29 117-145 43-78 (99)
71 PRK00089 era GTPase Era; Revie 40.1 30 0.00066 34.3 3.5 38 209-251 226-271 (292)
72 KOG2208 Vigilin [Lipid transpo 39.2 35 0.00076 39.8 4.3 29 226-254 358-386 (753)
73 PF07885 Ion_trans_2: Ion chan 38.2 26 0.00056 28.4 2.2 16 399-415 39-54 (79)
74 PRK01064 hypothetical protein; 35.7 27 0.00058 29.8 2.0 20 226-245 41-60 (78)
75 KOG2279 Kinase anchor protein 32.8 42 0.00091 38.1 3.4 93 225-340 78-170 (608)
76 PRK02821 hypothetical protein; 31.5 29 0.00063 29.6 1.6 20 226-245 42-61 (77)
77 PRK12327 nusA transcription el 31.4 49 0.0011 35.4 3.6 40 211-251 233-273 (362)
78 cd02414 jag_KH jag_K homology 31.4 30 0.00066 28.5 1.7 22 226-247 35-56 (77)
79 PRK00468 hypothetical protein; 31.1 30 0.00066 29.2 1.6 19 226-244 41-59 (75)
80 PF14611 SLS: Mitochondrial in 30.2 1.3E+02 0.0027 28.9 5.8 58 226-299 37-94 (210)
81 TIGR01953 NusA transcription t 28.9 64 0.0014 34.3 3.9 40 211-251 231-271 (341)
82 COG1855 ATPase (PilT family) [ 26.0 1.2E+02 0.0027 34.3 5.5 70 176-256 458-527 (604)
83 PF09840 DUF2067: Uncharacteri 25.7 1.4E+02 0.0031 29.3 5.4 52 236-301 14-66 (190)
84 TIGR01952 nusA_arch NusA famil 25.5 54 0.0012 30.8 2.4 28 225-252 43-70 (141)
85 COG0195 NusA Transcription elo 24.7 52 0.0011 32.3 2.2 33 220-252 81-113 (190)
86 PF13711 DUF4160: Domain of un 24.1 1.7E+02 0.0037 23.5 4.8 14 267-280 14-27 (66)
87 PF00408 PGM_PMM_IV: Phosphogl 23.9 1.9E+02 0.0042 23.2 5.1 26 268-293 46-72 (73)
88 PRK06418 transcription elongat 23.7 60 0.0013 31.4 2.4 26 227-252 72-97 (166)
89 COG1837 Predicted RNA-binding 22.6 52 0.0011 28.2 1.5 18 226-243 41-58 (76)
90 PF00639 Rotamase: PPIC-type P 22.2 91 0.002 26.1 3.0 31 271-301 1-32 (95)
91 TIGR01321 TrpR trp operon repr 21.8 24 0.00052 31.3 -0.6 26 117-142 43-75 (94)
92 COG1185 Pnp Polyribonucleotide 20.9 1.5E+02 0.0033 34.6 5.2 64 106-190 552-616 (692)
93 PRK12329 nusA transcription el 20.9 78 0.0017 35.1 2.8 42 210-252 264-306 (449)
94 PF13083 KH_4: KH domain; PDB: 20.1 19 0.00041 29.1 -1.5 20 226-245 40-59 (73)
95 PF00472 RF-1: RF-1 domain; I 20.0 2.8E+02 0.006 24.8 5.7 51 228-297 20-74 (113)
No 1
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=100.00 E-value=8.7e-38 Score=320.19 Aligned_cols=268 Identities=18% Similarity=0.148 Sum_probs=203.7
Q ss_pred HHhhhccCCcccccccCCCccC--CCCCCCCCC-C-CC-CCccccccccCCccccCCCCCCCcccCCCCCCCCCCCCCCC
Q 010778 26 QRKKRKWDQPAESLINFPLASF--GISLPGVPV-A-PV-VPAPAAAAFFTNPPVASGATVPPVVLQGPLPPKFNQPKVQD 100 (501)
Q Consensus 26 ~r~~~kwdqpa~~~~~~p~~~~--g~~~pg~~~-~-~~-~~aa~~~a~~~~~~~~~~~~~pp~~~~~s~~~~~~~~k~~d 100 (501)
--++|||||+++....+++... |...|+..- . ++ --+++|-++.+|+-+-..-..-+-.- .+..-+...++..|
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 3578999999998876554332 344444322 0 00 01222333444442210000000000 01111222455556
Q ss_pred ceeEEEEEEcCCCCccccceecchhHHHHHHhhhCCeEeeecceeCCCCC--CCCCCCeEEEEEeccchhhHHHHHHHHH
Q 010778 101 ELIIAREIVINDSESSVRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAP--PDGEKPLYLHISAGAHLKETAERILAVD 178 (501)
Q Consensus 101 e~~f~aEIeINDlPq~vR~~LTK~~Tq~eI~e~TGAsItTRG~Y~PPgk~--~~~EpPLYL~Ieg~Tq~kdtaEri~aVd 178 (501)
+. ..++++|||.+++||+.+|+|.++++|.+++|+.|.+||+|++++.+ .++++||||||.+.| + +.++
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 578999999999987 2 4899
Q ss_pred HHHHHHHHHHHcCC--CC--------CCCc---------cccCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHH
Q 010778 179 HAAAMVEEMLKQGH--AG--------FPTL---------QTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINH 239 (501)
Q Consensus 179 ~AvalIkEILKE~P--~~--------~pp~---------~~p~~~g~k~~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~ 239 (501)
+|++.|+-.++.+. +. .+-+ .++..+|+++.+ |.+|++| +|.||+.++.-|++..+|.+
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 99999997766542 11 1110 123467888888 9999999 99999999999999999999
Q ss_pred HHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhccccc
Q 010778 240 IMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGASRV 305 (501)
Q Consensus 240 Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~~E~~~~r~ 305 (501)
|+.|+++++.|||||||.+|++.|+|++|||||+|+|.+.+.+.+||++|+||+++|+.+|.+|-.
T Consensus 240 ~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl~~~v~~~~sr~~~ 305 (531)
T KOG1960|consen 240 QEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNGNGENGAPRRKWNLEEKVYINLSRGFH 305 (531)
T ss_pred hhhhhhhhhhhccccccccCcccccccCCceeEEeecCCchhhccchhHHHhHHHHHHHHhhhhhh
Confidence 999999999999999999999999999999999999999999999999999999999999987643
No 2
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=99.96 E-value=1e-28 Score=258.45 Aligned_cols=161 Identities=22% Similarity=0.303 Sum_probs=134.9
Q ss_pred HHHHHhhhCCeEeeecce-eCCC-C-CCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCCccccCC
Q 010778 127 QEEIQKCTGAVVITRGKY-RLPN-A-PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQTVMG 203 (501)
Q Consensus 127 q~eI~e~TGAsItTRG~Y-~PPg-k-~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalIkEILKE~P~~~pp~~~p~~ 203 (501)
+++|....+.. .+ +|++ + +.++..++|..-.-..++++.+.|+++-++..++|+++|+..+.++++.+|...
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 IEEITRKLRTG-----DVGVPPPRELRSPSPEPVYDAKGKRLNTREQRARKKLEDERHEIIEEILKLNPGFKPPADYKPP 135 (554)
T ss_pred HHHhhhhhccc-----cCCCCCCccccCCCcchhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCcccCcc
Confidence 55666655533 33 4555 3 678899999876666667888999999999999999999999999988776332
Q ss_pred CCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCC------CCCCCCCCCcEEEEEeC
Q 010778 204 NGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEG------LQGEEVHQPLHLFLSSN 277 (501)
Q Consensus 204 ~g~k~~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~------~~g~EsdEPLHV~Isa~ 277 (501)
..+++|||||+|+||+|||+|+||||||+|+|+||+||||||+||||||++... ......+||||++|+++
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 267999999999999999999999999999999999999999999999996422 11234789999999999
Q ss_pred CHHHHHHHHHHHHHHHHH
Q 010778 278 NPKSLEEAKRLAENLLDT 295 (501)
Q Consensus 278 ~~e~v~~Ak~LiE~LL~t 295 (501)
++|+|++|+++||+||..
T Consensus 213 t~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 213 TQEKIKKAIAVIENLIQS 230 (554)
T ss_pred hHHHHHHHHHHHHHHHHh
Confidence 999999999999999996
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=2.4e-26 Score=204.21 Aligned_cols=96 Identities=22% Similarity=0.393 Sum_probs=86.7
Q ss_pred eeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCC-------CCCCCCCCCcEEEEEeCC--HH
Q 010778 210 STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEG-------LQGEEVHQPLHLFLSSNN--PK 280 (501)
Q Consensus 210 eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~-------~~g~EsdEPLHV~Isa~~--~e 280 (501)
++|||||+|.||+|||+|+||||+|+|+|+|++||||||.|||+||++.+. ...++.+|||||+|++++ .+
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-hccccc
Q 010778 281 SLEEAKRLAENLLDTISAE-CGASRV 305 (501)
Q Consensus 281 ~v~~Ak~LiE~LL~tV~~E-~~~~r~ 305 (501)
++++|+++|++||..+.++ .+.++.
T Consensus 81 ~~~~A~~~I~~ll~~~~~~~~~~~k~ 106 (120)
T cd02395 81 ALAKAVEAIEELLKPAIEGGNDELKR 106 (120)
T ss_pred HHHHHHHHHHHHhccCCCccchHHHH
Confidence 9999999999999999876 454443
No 4
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=99.88 E-value=1e-22 Score=200.77 Aligned_cols=127 Identities=23% Similarity=0.340 Sum_probs=99.3
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCccc---cCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEe
Q 010778 175 LAVDHAAAMVEEMLKQGHAGFPTLQT---VMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLR 251 (501)
Q Consensus 175 ~aVd~AvalIkEILKE~P~~~pp~~~---p~~~g~k~~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IR 251 (501)
+.+++.+.+|.-.+.+..+..+...+ .........++|||||++.||+|||+||||||+|+++|+||+||||||+||
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 46777777777777654222222211 111122567899999999999999999999999999999999999999999
Q ss_pred ecCCCCCC-------CC-CCCCCCCCcEEEEEeCCHH-----HHHHHHHHHHHHHHHHHHHhc
Q 010778 252 GRGSGNSE-------GL-QGEEVHQPLHLFLSSNNPK-----SLEEAKRLAENLLDTISAECG 301 (501)
Q Consensus 252 GRGSg~~E-------~~-~g~EsdEPLHV~Isa~~~e-----~v~~Ak~LiE~LL~tV~~E~~ 301 (501)
||||++.. +. ..++.+|||||+|++..+. .|..|.+.|+.||.++.++..
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 99999742 11 2345899999999998876 467889999999999998886
No 5
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.85 E-value=1.5e-21 Score=188.32 Aligned_cols=183 Identities=13% Similarity=0.105 Sum_probs=142.6
Q ss_pred cCCCCccccceecchhH-----HHHHHhhhCCeEeeecceeCCCC--CCCCCCCeEEEEEeccchhhHHHHHHHHHHHHH
Q 010778 110 INDSESSVRYKLTKRHT-----QEEIQKCTGAVVITRGKYRLPNA--PPDGEKPLYLHISAGAHLKETAERILAVDHAAA 182 (501)
Q Consensus 110 INDlPq~vR~~LTK~~T-----q~eI~e~TGAsItTRG~Y~PPgk--~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~Ava 182 (501)
.|.||..+--.||.-.. ...+.|.|-..- -+.++|+.. ..+..+|-|..|.-..++++.+.+++..|+..-
T Consensus 47 ~~~l~s~i~~~lt~eqi~~y~~~~r~~eit~Klr--t~d~Vp~~re~Rspsppp~yd~~GrRlntre~ry~kkLeder~~ 124 (269)
T COG5176 47 FNSLPSKISGALTREQIYSYQVMMRPFEITEKLR--TPDGVPSKRELRSPSPPPRYDEIGRRLNTREARYNKKLEDERLW 124 (269)
T ss_pred hhcchhHhhhhhhHHHHHHHHHhccHhhhhhhhc--CCCCCCchhhccCCCCCcchhHHhhhhhHHHHHHhhhhhHHHHH
Confidence 56777665555654321 112223332221 244567764 678999999999988888888999999999999
Q ss_pred HHHHHHHcCCCCCCCccccCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCC
Q 010778 183 MVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQ 262 (501)
Q Consensus 183 lIkEILKE~P~~~pp~~~p~~~g~k~~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~ 262 (501)
++++.++.-+-++.+.++. ++...++|||||+++||+.||+|+||||+|+|+|++|..|+|||.|||+||.+. +..
T Consensus 125 l~era~k~lp~fv~p~dy~---rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKe-gk~ 200 (269)
T COG5176 125 LKERAQKILPRFVLPNDYI---RPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKE-GKI 200 (269)
T ss_pred HHHHHHHhcCcccCCcccc---CcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccccccc-Ccc
Confidence 9999999888887654432 125678999999999999999999999999999999999999999999999862 211
Q ss_pred -------CCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHH
Q 010778 263 -------GEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISA 298 (501)
Q Consensus 263 -------g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~~ 298 (501)
.....++||++|+++..+++.++.++|.+.|.+...
T Consensus 201 ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n~I~~a~~ 243 (269)
T COG5176 201 SSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARR 243 (269)
T ss_pred cccCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHHHHHHHhc
Confidence 123567899999999999999999999999987753
No 6
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.21 E-value=5e-10 Score=121.12 Aligned_cols=166 Identities=20% Similarity=0.278 Sum_probs=122.5
Q ss_pred ceeEEEEEEcCCCCccccceecc-hhHHHHHHhhhCCeEeeecceeCCCC-CCCCCCCeEEEEEeccchhhHHHHHHHHH
Q 010778 101 ELIIAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNA-PPDGEKPLYLHISAGAHLKETAERILAVD 178 (501)
Q Consensus 101 e~~f~aEIeINDlPq~vR~~LTK-~~Tq~eI~e~TGAsItTRG~Y~PPgk-~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd 178 (501)
....+.||.|-+-. |-..+.| |+|++.++|.+||.+.. +=++. .+...||| .|+|+. ..|+
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 44467888898877 8999988 99999999999987544 11222 33478888 788876 4789
Q ss_pred HHHHHHHHHHHcCCCCCCCccccCCCCcc-cceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCC
Q 010778 179 HAAAMVEEMLKQGHAGFPTLQTVMGNGVQ-AMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGN 257 (501)
Q Consensus 179 ~AvalIkEILKE~P~~~pp~~~p~~~g~k-~~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~ 257 (501)
.|..+|.++|+++-.-.+... ..+|.. --++++-|. +|+| -||.|||-+|.|||+|+.|||+||+|+=
T Consensus 199 ~a~~lV~dil~e~~~~~~g~~--~~~g~~~g~~~~~~V~---VPr~-~VG~IIGkgGE~IKklq~etG~KIQfkp----- 267 (600)
T KOG1676|consen 199 QAKQLVADILREEDDEVPGSG--GHAGVRGGGSATREVK---VPRS-KVGIIIGKGGEMIKKLQNETGAKIQFKP----- 267 (600)
T ss_pred HHHHHHHHHHHhcccCCCccc--cccCcCccccceeEEe---cccc-ceeeEEecCchHHHHHhhccCceeEeec-----
Confidence 999999999997532221111 122221 123355555 4566 6999999999999999999999999984
Q ss_pred CCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHH
Q 010778 258 SEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAE 299 (501)
Q Consensus 258 ~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~~E 299 (501)
..+..-|+..+..-.+.++++.|++||.+||..+.+.
T Consensus 268 -----Dd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 268 -----DDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred -----CCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence 1122445666666778999999999999999998877
No 7
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=99.21 E-value=7.2e-12 Score=130.45 Aligned_cols=148 Identities=22% Similarity=0.386 Sum_probs=122.7
Q ss_pred hhHHHHHHhhhCCeEeeecceeCCCCC---CCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCCccc
Q 010778 124 RHTQEEIQKCTGAVVITRGKYRLPNAP---PDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQT 200 (501)
Q Consensus 124 ~~Tq~eI~e~TGAsItTRG~Y~PPgk~---~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalIkEILKE~P~~~pp~~~ 200 (501)
-.++..|+.++++.+..||++----++ -+..-|.|+.|.+.+- +.+..|..+|..++..
T Consensus 234 d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~--------~g~~~A~r~~~nl~~~---------- 295 (531)
T KOG1960|consen 234 DLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNG--------NGENGAPRRKWNLEEK---------- 295 (531)
T ss_pred chhhhhhhhhhhhhhhhccccccccCcccccccCCceeEEeecCCc--------hhhccchhHHHhHHHH----------
Confidence 467889999999999999998654443 4667899999999873 4677777777766542
Q ss_pred cCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHH
Q 010778 201 VMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPK 280 (501)
Q Consensus 201 p~~~g~k~~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e 280 (501)
+||.+. ..|| .-.|.||-|.|.|||+.+|-.+++|+|.||+|+++.+++++++|.||||..+++.
T Consensus 296 ------------v~~~~s--r~~~-~~~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i~p~~~~~~~~p~~~~~~~~~~~ 360 (531)
T KOG1960|consen 296 ------------VYINLS--RGFH-RQAIVGPQGAYVKHIQQETRTRVQIKGQGSAFIEPSTNRESDEPIHLCIMSHDPN 360 (531)
T ss_pred ------------HHHHhh--hhhh-hcccccCCcccccccCCCCCcceeccCccceeecCCCCCCCCCCcccccccCChh
Confidence 332211 1222 2257899999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhcccc
Q 010778 281 SLEEAKRLAENLLDTISAECGASR 304 (501)
Q Consensus 281 ~v~~Ak~LiE~LL~tV~~E~~~~r 304 (501)
.|+.|+-||++||-.|..+|..|+
T Consensus 361 ~~~~~~~~~~~~i~~v~~qy~~~~ 384 (531)
T KOG1960|consen 361 AIQRAKVLCEDLIASVHQQYKAWK 384 (531)
T ss_pred hhhhhhhcccccCCcccccCcccc
Confidence 999999999999999999999875
No 8
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=99.13 E-value=2e-11 Score=137.87 Aligned_cols=83 Identities=31% Similarity=0.502 Sum_probs=77.2
Q ss_pred eeEEEEEEcCCCCccccceecchhHHHHHHhhhCCeEeeecceeCCCC-CCCCCCCeEEEEEeccchhhHHHHHHHHHHH
Q 010778 102 LIIAREIVINDSESSVRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNA-PPDGEKPLYLHISAGAHLKETAERILAVDHA 180 (501)
Q Consensus 102 ~~f~aEIeINDlPq~vR~~LTK~~Tq~eI~e~TGAsItTRG~Y~PPgk-~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~A 180 (501)
..|.++++|||+||.+||++|..+++..|.|.+++.|+|||.|||+++ +.++|++|||+|++.++ ..|++|
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 468999999999999999999999999999999999999999999997 67899999999999874 689999
Q ss_pred HHHHHHHHHcCC
Q 010778 181 AAMVEEMLKQGH 192 (501)
Q Consensus 181 valIkEILKE~P 192 (501)
+.++++.+++..
T Consensus 968 ~~e~~r~l~e~~ 979 (997)
T KOG0334|consen 968 IEELERLLEEEV 979 (997)
T ss_pred HHHHHHHHHHHH
Confidence 999999888763
No 9
>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=98.82 E-value=2.1e-08 Score=93.95 Aligned_cols=133 Identities=21% Similarity=0.222 Sum_probs=88.6
Q ss_pred cceecc-hhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEE--EeccchhhHHHHHHHHHHHHHHHHHHHHcCCCC
Q 010778 118 RYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHI--SAGAHLKETAERILAVDHAAAMVEEMLKQGHAG 194 (501)
Q Consensus 118 R~~LTK-~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~I--eg~Tq~kdtaEri~aVd~AvalIkEILKE~P~~ 194 (501)
+-.+.+ |++++.|+++||+.|...- ++.. +.| .+.+ + .++++|++.|+.+...-.
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----------ETGE--VKIEEEDED--P------LAVMKAREVVKAIGRGFS-- 67 (172)
T ss_pred hhHhCCchhHHHHHHHHhCcEEEEEc----------CCce--EEEecCCCC--H------HHHHHHHHHHHHHHcCCC--
Confidence 334444 9999999999999988752 1223 345 2322 2 489999999999765411
Q ss_pred CCCccccCCCCcccceeEEEecCCCC---C-CC-ceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCC
Q 010778 195 FPTLQTVMGNGVQAMSTSVFLGFDAD---A-SL-NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQP 269 (501)
Q Consensus 195 ~pp~~~p~~~g~k~~eeKI~Ipve~~---P-~F-NfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEP 269 (501)
++..+- -.+--+.- +| |.+.++ + .| ..+|+|||++|.+++.||..|||+|+|-|
T Consensus 68 -~e~A~~-l~gd~y~~-~V-i~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----------------- 126 (172)
T TIGR03665 68 -PEKALK-LLDDDYML-EV-IDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----------------- 126 (172)
T ss_pred -HHHHHH-hcCCcceE-EE-EEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC-----------------
Confidence 110000 00001111 12 222221 0 01 26999999999999999999999999974
Q ss_pred cEEEEEeCCHHHHHHHHHHHHHHHH
Q 010778 270 LHLFLSSNNPKSLEEAKRLAENLLD 294 (501)
Q Consensus 270 LHV~Isa~~~e~v~~Ak~LiE~LL~ 294 (501)
-.|+|.| ++++++.|++++++||+
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 10
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.81 E-value=3e-08 Score=93.67 Aligned_cols=145 Identities=19% Similarity=0.214 Sum_probs=96.0
Q ss_pred EEEEEEcCCCCccccceecc-hhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEE---eccchhhHHHHHHHHHH
Q 010778 104 IAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHIS---AGAHLKETAERILAVDH 179 (501)
Q Consensus 104 f~aEIeINDlPq~vR~~LTK-~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ie---g~Tq~kdtaEri~aVd~ 179 (501)
+...+.|..-. .+..+.+ |++++.|+++||+.|...- ++... .|. +.+ + ..+++
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--IGVLIGKKGETKKEIEERTGVKLEIDS----------ETGEV--IIEPTDGED--P------LAVLK 60 (180)
T ss_pred ceEEEEcCHHH--hhhHhccchhHHHHHHHHHCcEEEEEC----------CCCeE--EEEeCCCCC--H------HHHHH
Confidence 45566675443 6667766 8999999999999988753 12334 454 333 2 48999
Q ss_pred HHHHHHHHHHcCCCCCCCccccCCCCcccceeEEEecCCCC-C---CC-ceeEEEeCCCchhHHHHHHhhCCEEEEeecC
Q 010778 180 AAAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDAD-A---SL-NIAARIRGPNDQYINHIMNETGATVLLRGRG 254 (501)
Q Consensus 180 AvalIkEILKE~P~~~pp~~~p~~~g~k~~eeKI~Ipve~~-P---~F-NfvgrIIGP~GstlK~Iq~ETGaKI~IRGRG 254 (501)
|+++|+.+...- .++.-+- -.|--+.-+.+ .+.++ + .| ..+|+|||++|.++|.||..|||+|+|-++
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 0 01 269999999999999999999999999742
Q ss_pred CCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 010778 255 SGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 294 (501)
Q Consensus 255 Sg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~ 294 (501)
.++|.| ++++++.|++.+++|++
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 11
>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=98.54 E-value=3.2e-07 Score=70.46 Aligned_cols=63 Identities=27% Similarity=0.393 Sum_probs=50.9
Q ss_pred eEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 010778 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 290 (501)
Q Consensus 211 eKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE 290 (501)
.+|.||. +++++|||++|.++++|+++|||+|.|...+. ..++..|.|.|. .+++++|+.+++
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 4667774 68999999999999999999999999986432 235567888887 788999988763
No 12
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.54 E-value=2.7e-06 Score=92.80 Aligned_cols=156 Identities=21% Similarity=0.351 Sum_probs=112.6
Q ss_pred EEEEEcCCCCccccceecc-hhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHH
Q 010778 105 AREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAM 183 (501)
Q Consensus 105 ~aEIeINDlPq~vR~~LTK-~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~Aval 183 (501)
..+|.|--+. |-.+|-| |++++.|+.+||+.| +|.|+..++.-||+| .|-|.. ..+++|.++
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 3466666665 8888888 999999999999766 677888877779988 788875 378899999
Q ss_pred HHHHHHcCCCCCCCccccCCCCcccc--eeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCC
Q 010778 184 VEEMLKQGHAGFPTLQTVMGNGVQAM--STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGL 261 (501)
Q Consensus 184 IkEILKE~P~~~pp~~~p~~~g~k~~--eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~ 261 (501)
|++||.+......- .+.-|.-.. +--+-||-+ =.|+|||++|.|+|.|..|+||++.|-=-
T Consensus 294 I~eii~~~~~~~~~---~~~~G~P~~~~~fy~~VPa~------KcGLvIGrGGEtIK~in~qSGA~~el~r~-------- 356 (600)
T KOG1676|consen 294 INEIIAEAEAGAGG---GMGGGAPGLVAQFYMKVPAD------KCGLVIGRGGETIKQINQQSGARCELSRQ-------- 356 (600)
T ss_pred HHHHHHHHhccCCC---CcCCCCccceeeEEEecccc------ccccccCCCccchhhhcccCCccccccCC--------
Confidence 99999875221100 011111111 222224533 27999999999999999999999976421
Q ss_pred CCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHH
Q 010778 262 QGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDT 295 (501)
Q Consensus 262 ~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~t 295 (501)
..-.+.+..+++.-.++.+|+.|+.||++-+.-
T Consensus 357 -~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~ 389 (600)
T KOG1676|consen 357 -PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGD 389 (600)
T ss_pred -CCCCCccceEEEEecCcccchHHHHHHHHHhcc
Confidence 112356688888899999999999999876543
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=98.52 E-value=3.8e-07 Score=72.27 Aligned_cols=58 Identities=21% Similarity=0.403 Sum_probs=48.6
Q ss_pred eEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 010778 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 290 (501)
Q Consensus 211 eKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE 290 (501)
+.+.||-+ ++|+|||++|+++|.|+++|||+|.|-- .-.|.|.|++.+++++|+++++
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 6899999999999999999999998742 1259999999999999999975
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=98.42 E-value=1.3e-07 Score=73.01 Aligned_cols=59 Identities=22% Similarity=0.361 Sum_probs=49.4
Q ss_pred eEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 010778 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 289 (501)
Q Consensus 211 eKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~Li 289 (501)
++|.||- +++|+|||++|.++|+|+++|||+|.|... ++.-.|.|+| +++++++|+++|
T Consensus 2 ~~i~vp~------~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-------------~~~~~v~I~G-~~~~v~~A~~~I 60 (60)
T PF00013_consen 2 ERIEVPS------SLVGRIIGKKGSNIKEIEEETGVKIQIPDD-------------DERDIVTISG-SPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEH------HHHHHHHTGGGHHHHHHHHHHTSEEEEEST-------------TEEEEEEEEE-SHHHHHHHHHHH
T ss_pred EEEEECH------HHcCEEECCCCCcHHHhhhhcCeEEEEcCC-------------CCcEEEEEEe-CHHHHHHHHhhC
Confidence 4556652 378999999999999999999999999653 1456899999 999999999986
No 15
>smart00322 KH K homology RNA-binding domain.
Probab=98.42 E-value=1.4e-06 Score=65.44 Aligned_cols=66 Identities=23% Similarity=0.341 Sum_probs=54.4
Q ss_pred ceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 010778 209 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 288 (501)
Q Consensus 209 ~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~L 288 (501)
...+|.|+. +++|+|||++|.++++|+++|||+|.+.+.++ ....+.|.++ .++++.|+.+
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 010778 289 AENLL 293 (501)
Q Consensus 289 iE~LL 293 (501)
+++++
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=98.21 E-value=2.5e-06 Score=66.33 Aligned_cols=53 Identities=23% Similarity=0.337 Sum_probs=45.2
Q ss_pred ceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 010778 224 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 289 (501)
Q Consensus 224 NfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~Li 289 (501)
.++|.|||++|.++++|+++|||+|.|-..+ +..-.|.|+|. .+++.+|++++
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 34467899998 78999999876
No 17
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=98.20 E-value=8.6e-05 Score=77.11 Aligned_cols=163 Identities=15% Similarity=0.175 Sum_probs=106.1
Q ss_pred EEEEEEcCCCCccccceecc-hhHHHHHHhhhCCeEee-e-cceeCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHH
Q 010778 104 IAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVIT-R-GKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHA 180 (501)
Q Consensus 104 f~aEIeINDlPq~vR~~LTK-~~Tq~eI~e~TGAsItT-R-G~Y~PPgk~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~A 180 (501)
++-.|-|..+- +--.|.| |+|+.+++++|||.|-. | =.||| -..|| -.+|+|.. +++..-
T Consensus 39 y~ikvLips~A--aGsIIGKGG~ti~~lqk~tgariklSks~dfyP----GTTeR--vcli~Gt~---------eai~av 101 (402)
T KOG2191|consen 39 YFLKVLIPSYA--AGSIIGKGGQTIVQLQKETGARIKLSKSKDFYP----GTTER--VCLIQGTV---------EALNAV 101 (402)
T ss_pred eEEEEEeeccc--ccceeccchHHHHHHHhccCcEEEeccccccCC----Cccce--EEEEeccH---------HHHHHH
Confidence 67778888877 7889999 89999999999999876 2 23442 13454 45789976 244444
Q ss_pred HHHHHHHHHcCCCCCCC-ccccCCCCc-ccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEee-cCCCC
Q 010778 181 AAMVEEMLKQGHAGFPT-LQTVMGNGV-QAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRG-RGSGN 257 (501)
Q Consensus 181 valIkEILKE~P~~~pp-~~~p~~~g~-k~~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRG-RGSg~ 257 (501)
++.|.+.|.+.+....- .+.-.+..+ +-.+-||.+|-. -.|.|||++|.|+|.|++|.||-|+|-- +-.+.
T Consensus 102 ~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNs------tag~iigkggAtiK~~~Eqsga~iqisPqkpt~~ 175 (402)
T KOG2191|consen 102 HEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNS------TAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGI 175 (402)
T ss_pred HHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCC------cccceecCCcchHHHHHHhhCcceEecccCCCCc
Confidence 44555555544332211 000000001 234678888733 5799999999999999999999999973 21111
Q ss_pred CCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhc
Q 010778 258 SEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECG 301 (501)
Q Consensus 258 ~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~~E~~ 301 (501)
.-.-.|...+.+++++.+|++|| |.+|.+|-+
T Consensus 176 ---------sLqervvt~sge~e~~~~A~~~I---L~Ki~eDpq 207 (402)
T KOG2191|consen 176 ---------SLQERVVTVSGEPEQNMKAVSLI---LQKIQEDPQ 207 (402)
T ss_pred ---------cceeEEEEecCCHHHHHHHHHHH---HHHhhcCCc
Confidence 11124666688899999998775 667777643
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=98.03 E-value=1.5e-05 Score=63.20 Aligned_cols=61 Identities=21% Similarity=0.238 Sum_probs=45.0
Q ss_pred EEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcE-EEEEeCCHHHHHHHHHHH
Q 010778 212 SVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLH-LFLSSNNPKSLEEAKRLA 289 (501)
Q Consensus 212 KI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLH-V~Isa~~~e~v~~Ak~Li 289 (501)
++.||. +.+|+|||.+|.++++|+++|||+|.|--.. +...+.- |.|+ .+++++++|+.|+
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----------LPGSTERVVTIS-GKPSAVQKALLLI 64 (65)
T ss_pred EEEECH------HHcCeeECCCcHHHHHHHHHHCCEEEEcCCC----------CCCCCceEEEEE-eCHHHHHHHHHhh
Confidence 556663 3689999999999999999999999995311 1112223 4555 5699999999886
No 19
>PF13014 KH_3: KH domain
Probab=97.74 E-value=2.7e-05 Score=57.32 Aligned_cols=28 Identities=32% Similarity=0.455 Sum_probs=26.3
Q ss_pred eeEEEeCCCchhHHHHHHhhCCEEEEee
Q 010778 225 IAARIRGPNDQYINHIMNETGATVLLRG 252 (501)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGaKI~IRG 252 (501)
++|.|||++|.++|+|+++|||+|.|--
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 20
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.71 E-value=8.1e-05 Score=79.32 Aligned_cols=142 Identities=15% Similarity=0.182 Sum_probs=87.2
Q ss_pred ecc-hhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCCcc
Q 010778 121 LTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQ 199 (501)
Q Consensus 121 LTK-~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalIkEILKE~P~~~pp~~ 199 (501)
|.+ |.|++.|-..|.+.|-+ .--......|+.|-+|-+. +...+|.++|-|+|..+-..-
T Consensus 214 IGkeG~TIknItkqTqsriD~----hrken~Gaaek~itvh~tp-----------Eg~s~Ac~~ILeimqkEA~~~---- 274 (584)
T KOG2193|consen 214 IGKEGATIKNITKQTQSRIDV----HRKENAGAAEKIITVHSTP-----------EGTSKACKMILEIMQKEAVDD---- 274 (584)
T ss_pred ecCCCccccCcchhhhheeee----eecccCCcccCceEEecCc-----------cchHHHHHHHHHHHHHhhhcc----
Confidence 444 89999999999887644 1111234678998766433 144567777888886541110
Q ss_pred ccCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCH
Q 010778 200 TVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNP 279 (501)
Q Consensus 200 ~p~~~g~k~~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~ 279 (501)
+ +.+ .||++-.---||+|||||..|.++|+||++||+||.|-- +.| .++ .+-.--+.|-| +-
T Consensus 275 -------k-~~~--e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~----lqe-ls~--ynpERTItVkG-si 336 (584)
T KOG2193|consen 275 -------K-VAE--EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISK----LQE-LSL--YNPERTITVKG-SI 336 (584)
T ss_pred -------c-hhh--hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeee----hhh-hcc--cCccceEEecc-cH
Confidence 0 111 245554444568999999999999999999999999853 232 111 11123456666 55
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcc
Q 010778 280 KSLEEAKRLAENLLDTISAECGA 302 (501)
Q Consensus 280 e~v~~Ak~LiE~LL~tV~~E~~~ 302 (501)
|.+.+|..+ ++..+++.|+.
T Consensus 337 Eac~~AE~e---ImkKlre~yEn 356 (584)
T KOG2193|consen 337 EACVQAEAE---IMKKLRECYEN 356 (584)
T ss_pred HHHHHHHHH---HHHHHHHHHhh
Confidence 555555544 45566666654
No 21
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.54 E-value=0.00017 Score=68.38 Aligned_cols=64 Identities=13% Similarity=0.182 Sum_probs=53.7
Q ss_pred eeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEE---eCCHHHHHHHH
Q 010778 210 STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLS---SNNPKSLEEAK 286 (501)
Q Consensus 210 eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Is---a~~~e~v~~Ak 286 (501)
...+.||.+ -+|.|||++|.++|.|+++|||+|.|.-. .-.|.|. +.|++.+++|+
T Consensus 4 ~~~i~IP~~------kig~iIG~gGk~Ik~I~e~tg~~I~i~~~---------------~g~V~I~~~~~~d~~~i~kA~ 62 (180)
T PRK13763 4 MEYVKIPKD------RIGVLIGKKGETKKEIEERTGVKLEIDSE---------------TGEVIIEPTDGEDPLAVLKAR 62 (180)
T ss_pred eEEEEcCHH------HhhhHhccchhHHHHHHHHHCcEEEEECC---------------CCeEEEEeCCCCCHHHHHHHH
Confidence 345666644 48899999999999999999999999742 1367787 88999999999
Q ss_pred HHHHHHHH
Q 010778 287 RLAENLLD 294 (501)
Q Consensus 287 ~LiE~LL~ 294 (501)
++++.|+.
T Consensus 63 ~~I~ai~~ 70 (180)
T PRK13763 63 DIVKAIGR 70 (180)
T ss_pred HHHHHHhc
Confidence 99999987
No 22
>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=97.34 E-value=0.00025 Score=66.72 Aligned_cols=56 Identities=11% Similarity=0.174 Sum_probs=48.6
Q ss_pred eeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEE--EeCCHHHHHHHHHHHHHHHHH
Q 010778 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFL--SSNNPKSLEEAKRLAENLLDT 295 (501)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~I--sa~~~e~v~~Ak~LiE~LL~t 295 (501)
.+|.|||++|.++|.|+++|||+|.|--. .=.|.| .+.|++.+++|+++++.|...
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 125778 789999999999999998773
No 23
>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=97.34 E-value=0.0011 Score=74.89 Aligned_cols=64 Identities=22% Similarity=0.395 Sum_probs=55.7
Q ss_pred eeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 010778 210 STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 289 (501)
Q Consensus 210 eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~Li 289 (501)
-+++.|+.+ -+|.||||+|.++|.|++||||+|-|- |.=+|.|.+.|.+++++|+++|
T Consensus 579 ~~~~~I~~~------ki~~vIG~gGk~I~~i~~~tg~~Idi~----------------d~G~V~I~a~d~~~~~~A~~~I 636 (719)
T TIGR02696 579 IITVKIPVD------KIGEVIGPKGKMINQIQDETGAEISIE----------------DDGTVYIGAADGPSAEAARAMI 636 (719)
T ss_pred eEEEEeChH------HhhheeCCCcHhHHHHHHHHCCEEEEe----------------cCcEEEEEeCCHHHHHHHHHHH
Confidence 456667644 489999999999999999999999875 2468999999999999999999
Q ss_pred HHHHHH
Q 010778 290 ENLLDT 295 (501)
Q Consensus 290 E~LL~t 295 (501)
++|+..
T Consensus 637 ~~i~~~ 642 (719)
T TIGR02696 637 NAIANP 642 (719)
T ss_pred HHhhCc
Confidence 999885
No 24
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.18 E-value=0.0007 Score=65.86 Aligned_cols=54 Identities=22% Similarity=0.284 Sum_probs=49.1
Q ss_pred eeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHH
Q 010778 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTI 296 (501)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~tV 296 (501)
.+|||||++|.|.+.||+-|||.|.|.|+ +|+|.| ++++++.|++-+|.||+-.
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~-----------------tVaiiG-~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK-----------------TVAIIG-GFEQVEIAREAVEMLINGA 165 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc-----------------EEEEec-ChhhhHHHHHHHHHHHcCC
Confidence 68999999999999999999999999993 788887 6899999999999999743
No 25
>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=97.08 E-value=0.0012 Score=59.42 Aligned_cols=66 Identities=29% Similarity=0.354 Sum_probs=49.2
Q ss_pred eecchhHHHHHHhhhCCeEeeecceeCCCC----------CCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHHHHH
Q 010778 120 KLTKRHTQEEIQKCTGAVVITRGKYRLPNA----------PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLK 189 (501)
Q Consensus 120 ~LTK~~Tq~eI~e~TGAsItTRG~Y~PPgk----------~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalIkEILK 189 (501)
+=.+|.|+++|+++|||.|.+||+---... ....+-||+++|++.+. ++ +++++|+.+|++++.
T Consensus 21 IGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~----~~--e~~~~A~~~I~~ll~ 94 (120)
T cd02395 21 LGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETP----PE--EALAKAVEAIEELLK 94 (120)
T ss_pred ECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCc----HH--HHHHHHHHHHHHHhc
Confidence 336799999999999999999996211111 01346779999999871 11 589999999999998
Q ss_pred cC
Q 010778 190 QG 191 (501)
Q Consensus 190 E~ 191 (501)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 43
No 26
>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=97.07 E-value=0.00089 Score=75.08 Aligned_cols=100 Identities=16% Similarity=0.178 Sum_probs=72.6
Q ss_pred eeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 010778 210 STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 289 (501)
Q Consensus 210 eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~Li 289 (501)
-+.+.|+.+ .+|.||||+|.++|.|++||||+|-|- +.=+|.|.+.+.+.+++|+++|
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 355666644 489999999999999999999999984 2357999999999999999999
Q ss_pred HHHHHHHHHHhccccccccccccCCCCchhhhcccccccccccCCcccchhhcccccc
Q 010778 290 ENLLDTISAECGASRVSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNL 347 (501)
Q Consensus 290 E~LL~tV~~E~~~~r~~~~k~y~~~pppqq~~~gv~~~~~~~~~~~~~~~~~~~~~~~ 347 (501)
+.|... + ..+..++| .+.+|..+|..-.+.. ...|+.|--++
T Consensus 610 ~~~~~~----~----~~G~i~~G-------~V~~I~~~GafVei~~-g~~GllHiSei 651 (684)
T TIGR03591 610 EGITAE----P----EVGKIYEG-------KVVRIMDFGAFVEILP-GKDGLVHISEI 651 (684)
T ss_pred Hhhhcc----c----ccCcEEEE-------EEEEEeCCEEEEEECC-CcEEEEEHHHc
Confidence 999542 1 11333443 5777777775444433 25677775544
No 27
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.84 E-value=0.0076 Score=64.79 Aligned_cols=157 Identities=17% Similarity=0.210 Sum_probs=107.4
Q ss_pred EEEcCCCCccccceec-chhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHH
Q 010778 107 EIVINDSESSVRYKLT-KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVE 185 (501)
Q Consensus 107 EIeINDlPq~vR~~LT-K~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalIk 185 (501)
.+.|.|.- +.-+|. ||..+++|.+.+||+|-.- ||+-+--++| -..|+|+. ++.-+|...|-
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 555664 5999999999999998642 3332223444 44789986 47788889999
Q ss_pred HHHHcCCCCCCCccccCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCC
Q 010778 186 EMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEE 265 (501)
Q Consensus 186 EILKE~P~~~pp~~~p~~~g~k~~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~E 265 (501)
..|+|+..+.|-.+ ..+++-|-|| .+ .+|||||.+|.|++-||+-|+|.|.|-- ..++.|
T Consensus 477 gKikEenf~~Pkee-------vklethirVP-----s~-~aGRvIGKGGktVnELQnlt~AeV~vPr-------dqtpdE 536 (584)
T KOG2193|consen 477 GKIKEENFFLPKEE-------VKLETHIRVP-----SS-AAGRVIGKGGKTVNELQNLTSAEVVVPR-------DQTPDE 536 (584)
T ss_pred hhhhhhccCCchhh-------heeeeeeecc-----ch-hhhhhhccccccHHHHhccccceEEccc-------cCCCCc
Confidence 99998744433221 3455556555 55 7999999999999999999999998752 223333
Q ss_pred CCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhcc
Q 010778 266 VHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGA 302 (501)
Q Consensus 266 sdEPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~~E~~~ 302 (501)
+|-.-|-|.| +.-....|...+.+|+..|++..+.
T Consensus 537 -nd~vivriiG-hfyatq~aQrki~~iv~qvkq~~q~ 571 (584)
T KOG2193|consen 537 -NDQVIVRIIG-HFYATQNAQRKIAHIVNQVKQSGQH 571 (584)
T ss_pred -cceeeeeeec-hhhcchHHHHHHHHHHHHHHHhhhh
Confidence 3334444544 4455677888888899888876543
No 28
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.82 E-value=0.0022 Score=69.58 Aligned_cols=66 Identities=26% Similarity=0.387 Sum_probs=51.2
Q ss_pred ccee-cchhHHHHHHhhhCCeEeeecce-eCCCC--------CCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHHH
Q 010778 118 RYKL-TKRHTQEEIQKCTGAVVITRGKY-RLPNA--------PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEM 187 (501)
Q Consensus 118 R~~L-TK~~Tq~eI~e~TGAsItTRG~Y-~PPgk--------~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalIkEI 187 (501)
-.+| -+|.||+.++++|||.|..||+= +-.++ ....+-+||.+|++.|+ +.|++|++.|+.+
T Consensus 156 GLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~--------eki~~Ai~vienl 227 (554)
T KOG0119|consen 156 GLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQ--------EKIKKAIAVIENL 227 (554)
T ss_pred EEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchH--------HHHHHHHHHHHHH
Confidence 3444 56999999999999999999932 11111 22347789999999885 5899999999999
Q ss_pred HHcC
Q 010778 188 LKQG 191 (501)
Q Consensus 188 LKE~ 191 (501)
|++.
T Consensus 228 i~~a 231 (554)
T KOG0119|consen 228 IQSA 231 (554)
T ss_pred HHhh
Confidence 9974
No 29
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.79 E-value=0.0012 Score=76.01 Aligned_cols=101 Identities=19% Similarity=0.232 Sum_probs=74.4
Q ss_pred eeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCE-EEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 010778 210 STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGAT-VLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 288 (501)
Q Consensus 210 eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaK-I~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~L 288 (501)
-+++-|+.+ -+|.||||+|.++|.|++|||++ |-|+ |.-+|.|.+.|.+++++|+++
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 355666543 58999999999999999999998 7654 458999999999999999999
Q ss_pred HHHHHHHHHHHhccccccccccc-cCCCCchhhhcccccccccccCCcccchhhccccccc
Q 010778 289 AENLLDTISAECGASRVSSCKVY-NAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNLS 348 (501)
Q Consensus 289 iE~LL~tV~~E~~~~r~~~~k~y-~~~pppqq~~~gv~~~~~~~~~~~~~~~~~~~~~~~~ 348 (501)
|++|... ..-.+.| + .-+.+|..+|+.-.+... .-||.|--.++
T Consensus 744 I~~l~~~---------~~vG~iy~~------g~V~~I~~FGaFVeL~~g-~EGLVHISeLs 788 (891)
T PLN00207 744 ISSLTMV---------PTVGDIYRN------CEIKSIAPYGAFVEIAPG-REGLCHISELS 788 (891)
T ss_pred HHHHhcC---------cCCCcEEEC------cEEEEEeccEEEEEeCCC-CEEEEEhhhcC
Confidence 9999862 1224455 2 246778888855444433 57777755443
No 30
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.78 E-value=0.021 Score=62.32 Aligned_cols=141 Identities=16% Similarity=0.151 Sum_probs=81.6
Q ss_pred cceecchhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEEe---------ccchhhHHHHHHHHHHHHHHHHHHH
Q 010778 118 RYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISA---------GAHLKETAERILAVDHAAAMVEEML 188 (501)
Q Consensus 118 R~~LTK~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ieg---------~Tq~kdtaEri~aVd~AvalIkEIL 188 (501)
-|+-.+|+++++|..+|++.|-+-=. . + .+.||= +-|.| .. .++.+|.++|-..+
T Consensus 56 ~IIGk~G~~vkkir~~t~s~i~i~~~-~-~---~c~eRI--iti~g~~~~~~~~~~~---------~al~ka~~~iv~~~ 119 (485)
T KOG2190|consen 56 SIIGKKGDIVKKIRKETESKIRVNES-L-P---GCPERI--ITITGNRVELNLSPAT---------DALFKAFDMIVFKL 119 (485)
T ss_pred eEEccCcHHHHHHhhcccccceeecC-C-C---CCCcce--EEEecccccccCCchH---------HHHHHHHHHHhhcc
Confidence 45667799999999888876543111 0 1 122222 23444 22 35566555554443
Q ss_pred HcCCCCCCCccccCCCCccc-ceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCC
Q 010778 189 KQGHAGFPTLQTVMGNGVQA-MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVH 267 (501)
Q Consensus 189 KE~P~~~pp~~~p~~~g~k~-~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~Esd 267 (501)
.++..-.. +. ...+..+ ...++.|| .+-+|-|||.+|+.||.|.++|||+|+|-+. .+ + -..
T Consensus 120 ~~d~~~~~--d~-~~~~~~~~v~~RLlVp------~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~---~l-P----~st 182 (485)
T KOG2190|consen 120 EEDDEAAE--DN-GEDASGPEVTCRLLVP------SSQVGSLIGKGGSLIKEIREETGAKIRVSSD---ML-P----NST 182 (485)
T ss_pred cccccccc--cC-CccccCCceEEEEEec------hhheeeeeccCcHHHHHHHHhcCceEEecCC---CC-C----ccc
Confidence 32211110 00 0111234 45777787 4579999999999999999999999999985 22 1 123
Q ss_pred CCcEEEEEeCCHHHHHHHHHHHHHHH
Q 010778 268 QPLHLFLSSNNPKSLEEAKRLAENLL 293 (501)
Q Consensus 268 EPLHV~Isa~~~e~v~~Ak~LiE~LL 293 (501)
|.+ |.|+| +++.+.+|-..|-.+|
T Consensus 183 er~-V~IsG-~~~av~~al~~Is~~L 206 (485)
T KOG2190|consen 183 ERA-VTISG-EPDAVKKALVQISSRL 206 (485)
T ss_pred cee-EEEcC-chHHHHHHHHHHHHHH
Confidence 334 55554 6677777755554444
No 31
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.13 E-value=0.007 Score=68.14 Aligned_cols=93 Identities=17% Similarity=0.186 Sum_probs=68.0
Q ss_pred ceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhccc
Q 010778 224 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGAS 303 (501)
Q Consensus 224 NfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~~E~~~~ 303 (501)
+-++.+|||+|.++|.|++|||++|-|+ |.-+|.|.+.+.+.+++|+++|+.|.....
T Consensus 563 ~kI~~vIG~gg~~ik~I~~~~~~~idi~----------------d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~------ 620 (693)
T PRK11824 563 DKIRDVIGPGGKTIREITEETGAKIDIE----------------DDGTVKIAATDGEAAEAAKERIEGITAEPE------ 620 (693)
T ss_pred HHHHHHhcCCchhHHHHHHHHCCccccC----------------CCceEEEEcccHHHHHHHHHHHHHhcccCc------
Confidence 3478999999999999999999988763 347899999999999999999999884211
Q ss_pred cccccccccCCCCchhhhcccccccccccCCcccchhhccccccc
Q 010778 304 RVSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNLS 348 (501)
Q Consensus 304 r~~~~k~y~~~pppqq~~~gv~~~~~~~~~~~~~~~~~~~~~~~~ 348 (501)
-+..++| .+.+|..+|..-.+.. ...|+.|--+++
T Consensus 621 --vG~v~~G-------~V~~I~~fGafVei~~-~~~GllhiSels 655 (693)
T PRK11824 621 --VGEIYEG-------KVVRIVDFGAFVEILP-GKDGLVHISEIA 655 (693)
T ss_pred --CCeEEEE-------EEEEEECCeEEEEECC-CCEEEEEeeecc
Confidence 1233333 5777777885544433 356666654443
No 32
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.66 E-value=0.015 Score=57.44 Aligned_cols=54 Identities=20% Similarity=0.345 Sum_probs=47.3
Q ss_pred eeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 010778 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 294 (501)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~ 294 (501)
+++++|||+|.+++.|.++|||+|.| | +.=+|+|.+.+.+.+++|+++|++|-.
T Consensus 155 ~i~~lig~~g~~i~~l~~~~~~~I~i-g---------------~NG~VwI~~~~~~~~~~a~~~I~~~e~ 208 (235)
T PRK04163 155 KVPRVIGKKGSMINMLKEETGCDIIV-G---------------QNGRIWIKGPDEEDEEIAIEAIKKIER 208 (235)
T ss_pred HHHhhcCCCChhHhhhhhhhCcEEEE-c---------------CCcEEEEeeCCHHHHHHHHHHHHHHHh
Confidence 58899999999999999999999988 2 124799999999999999999987543
No 33
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=95.39 E-value=0.32 Score=53.34 Aligned_cols=60 Identities=27% Similarity=0.281 Sum_probs=46.0
Q ss_pred ccceecc-hhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHHHHHcC
Q 010778 117 VRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQG 191 (501)
Q Consensus 117 vR~~LTK-~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalIkEILKE~ 191 (501)
+-.+|.| |+.+++|.|+|||.|-+-+... |. ..++- +-|.|.. .+|.+|...|-..|.+.
T Consensus 149 ~GslIGK~G~~Ik~Ire~TgA~I~v~~~~l-P~---ster~--V~IsG~~---------~av~~al~~Is~~L~~~ 209 (485)
T KOG2190|consen 149 VGSLIGKGGSLIKEIREETGAKIRVSSDML-PN---STERA--VTISGEP---------DAVKKALVQISSRLLEN 209 (485)
T ss_pred eeeeeccCcHHHHHHHHhcCceEEecCCCC-Cc---cccee--EEEcCch---------HHHHHHHHHHHHHHHhc
Confidence 5667777 9999999999999999877733 33 23333 7888865 48889988888888874
No 34
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=95.23 E-value=0.082 Score=55.66 Aligned_cols=77 Identities=23% Similarity=0.273 Sum_probs=53.4
Q ss_pred ceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 010778 209 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 288 (501)
Q Consensus 209 ~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~L 288 (501)
..-||.|| . +.+|-|||.+|++|-.+|+||||+|++- |-+-|.-+.+ -.||+...+-+.|..--++
T Consensus 39 y~ikvLip-----s-~AaGsIIGKGG~ti~~lqk~tgariklS-ks~dfyPGTT-------eRvcli~Gt~eai~av~ef 104 (402)
T KOG2191|consen 39 YFLKVLIP-----S-YAAGSIIGKGGQTIVQLQKETGARIKLS-KSKDFYPGTT-------ERVCLIQGTVEALNAVHEF 104 (402)
T ss_pred eEEEEEee-----c-ccccceeccchHHHHHHHhccCcEEEec-cccccCCCcc-------ceEEEEeccHHHHHHHHHH
Confidence 56788887 3 3789999999999999999999999986 4333332222 2466666666666655444
Q ss_pred HHHHHHHHHHHhcc
Q 010778 289 AENLLDTISAECGA 302 (501)
Q Consensus 289 iE~LL~tV~~E~~~ 302 (501)
++|+++++.+.
T Consensus 105 ---I~dKire~p~~ 115 (402)
T KOG2191|consen 105 ---IADKIREKPQA 115 (402)
T ss_pred ---HHHHHHHhHHh
Confidence 45566665543
No 35
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=95.22 E-value=0.029 Score=62.29 Aligned_cols=71 Identities=17% Similarity=0.209 Sum_probs=54.9
Q ss_pred eEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhcc---
Q 010778 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGA--- 302 (501)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~~E~~~--- 302 (501)
+..+|||+|-.+|+|+.|||+.-++ +.=|+-|-++++..+++||++|+.++..-+...-.
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 6789999999999999999954333 44699999999999999999999998764443222
Q ss_pred ---ccccccccccC
Q 010778 303 ---SRVSSCKVYNA 313 (501)
Q Consensus 303 ---~r~~~~k~y~~ 313 (501)
..+.+.+.||+
T Consensus 671 vy~~tIt~~rd~G~ 684 (760)
T KOG1067|consen 671 VYTATITEIRDTGV 684 (760)
T ss_pred EEEEEEeeecccce
Confidence 24455566664
No 36
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=95.01 E-value=0.025 Score=58.36 Aligned_cols=57 Identities=21% Similarity=0.343 Sum_probs=46.8
Q ss_pred eEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHh
Q 010778 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 300 (501)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~~E~ 300 (501)
+.|||||+|+|+|.||--|.|-|.+.|. .|++.|+ ..+|++++++++|.+.+++.=|
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 5689999999999999999999999993 3444443 5688999999999888876544
No 37
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=94.10 E-value=0.082 Score=55.44 Aligned_cols=62 Identities=11% Similarity=0.140 Sum_probs=54.2
Q ss_pred eeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHH
Q 010778 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISA 298 (501)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~~ 298 (501)
|.|.|||-+|.|.|+||+||+|+|.+==.+. ..-|+-|++-..+.|.+|.+.|+-||++++.
T Consensus 67 ~~~~lig~~g~trkkle~Etq~~i~lp~p~~------------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~ 128 (345)
T KOG2814|consen 67 FIGWLIGKQGKTRKKLEEETQTNIFLPRPNT------------NKEEIKIIGISRNCVIQALERIAKLIDSDRK 128 (345)
T ss_pred HhhhhhcccchHHHHHHHhhccceEccCCCC------------CcceEEEeehhHHHHHHHHHHHHHHHHhhhh
Confidence 6899999999999999999999998853211 2258999999999999999999999999883
No 38
>PRK00106 hypothetical protein; Provisional
Probab=93.87 E-value=0.12 Score=57.23 Aligned_cols=60 Identities=27% Similarity=0.333 Sum_probs=51.7
Q ss_pred CCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 010778 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 294 (501)
Q Consensus 220 ~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~ 294 (501)
.|+=.+.|||||..|.|++.+|.-||+.|.|- |.|--|.|||-||-.-+-|+.-.|.||.
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 45666899999999999999999999999983 6778899999999998888877666654
No 39
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=93.76 E-value=0.12 Score=56.74 Aligned_cols=60 Identities=23% Similarity=0.326 Sum_probs=50.9
Q ss_pred CCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 010778 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 294 (501)
Q Consensus 220 ~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~ 294 (501)
.|+=.+.|||||-.|.|++.+|.-||+.|.|- |.|=-|.|||-||-.-+-|+.-.+.||.
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 5677899999999988888776666653
No 40
>PRK12704 phosphodiesterase; Provisional
Probab=93.68 E-value=0.15 Score=56.07 Aligned_cols=59 Identities=24% Similarity=0.316 Sum_probs=49.6
Q ss_pred CCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHH
Q 010778 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLL 293 (501)
Q Consensus 220 ~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL 293 (501)
.|+=.+.|||||-.|.|++.+|.-||+.|.|- |.|=-|+|||-|+-.-+.|+.-++.|+
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 45666899999999999999999999999984 568889999999988777776655554
No 41
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=93.13 E-value=0.13 Score=58.29 Aligned_cols=54 Identities=22% Similarity=0.371 Sum_probs=47.0
Q ss_pred eEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHH
Q 010778 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDT 295 (501)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~t 295 (501)
++.+|||+|.++|.|..||||+|.|.=.| -|.|.+.+.+...+|+++|+++...
T Consensus 563 I~dvIG~gGk~I~~I~eetg~~IdieddG----------------tv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 563 IRDVIGPGGKTIKAITEETGVKIDIEDDG----------------TVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred HhhccCCcccchhhhhhhhCcEEEecCCC----------------cEEEEecchHHHHHHHHHHHHHHhh
Confidence 56789999999999999999999986333 4678899999999999999999843
No 42
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=91.84 E-value=0.28 Score=53.52 Aligned_cols=63 Identities=14% Similarity=0.127 Sum_probs=46.1
Q ss_pred CceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCH-HHHHHHHHHHHHHHHHHHHHhc
Q 010778 223 LNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNP-KSLEEAKRLAENLLDTISAECG 301 (501)
Q Consensus 223 FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~-e~v~~Ak~LiE~LL~tV~~E~~ 301 (501)
-+++|++||-+|+.+|+||..|+++|+|-- +.+-+.|.-.-- +.-.+|+.-++.+++...+ |+
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 224444443322 3445688888888877654 54
No 43
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=88.81 E-value=1.1 Score=46.55 Aligned_cols=65 Identities=22% Similarity=0.361 Sum_probs=50.1
Q ss_pred eeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHh
Q 010778 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 300 (501)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~~E~ 300 (501)
+-|-|||-+|.-+|+|..|+||.|.|- |+.++. +-.+.+.-.+.++++.|.-|.++-+..-++.|
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 24566666789999999999998877544443
No 44
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=88.53 E-value=1.3 Score=45.42 Aligned_cols=74 Identities=18% Similarity=0.238 Sum_probs=53.1
Q ss_pred cceecchhHHHHHHhhhCCeEeeecceeCCCC------CC-C----CCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHH
Q 010778 118 RYKLTKRHTQEEIQKCTGAVVITRGKYRLPNA------PP-D----GEKPLYLHISAGAHLKETAERILAVDHAAAMVEE 186 (501)
Q Consensus 118 R~~LTK~~Tq~eI~e~TGAsItTRG~Y~PPgk------~~-~----~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalIkE 186 (501)
|.+==||.|+++++++|||.|.+||+--=-++ +. + =+.||+++|+...- ++.++ ..+..|+++|++
T Consensus 111 RILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p-~~ea~--~rl~~AleeI~k 187 (259)
T KOG1588|consen 111 RILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAP-PAEAY--ARLAYALEEIKK 187 (259)
T ss_pred ccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCC-HHHHH--HHHHHHHHHHHH
Confidence 44446799999999999999999997643331 11 1 16789999998652 33333 567889999999
Q ss_pred HHHcCCCC
Q 010778 187 MLKQGHAG 194 (501)
Q Consensus 187 ILKE~P~~ 194 (501)
+|....+.
T Consensus 188 lL~P~~e~ 195 (259)
T KOG1588|consen 188 LLVPDHED 195 (259)
T ss_pred hcCCCCCC
Confidence 99765443
No 45
>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=88.17 E-value=2 Score=34.05 Aligned_cols=57 Identities=21% Similarity=0.238 Sum_probs=41.1
Q ss_pred EEEEcCCCCccccceecc-hhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHH
Q 010778 106 REIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (501)
Q Consensus 106 aEIeINDlPq~vR~~LTK-~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalI 184 (501)
..|.|..- .++..+-+ |+++.+|+++|||.|..- . +. .+.|.|.+. .++++|+++|
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 37788876 999999999999998752 1 12 478999753 4788888887
Q ss_pred H
Q 010778 185 E 185 (501)
Q Consensus 185 k 185 (501)
+
T Consensus 61 ~ 61 (61)
T cd02393 61 E 61 (61)
T ss_pred C
Confidence 3
No 46
>PRK12705 hypothetical protein; Provisional
Probab=86.43 E-value=0.68 Score=51.17 Aligned_cols=58 Identities=28% Similarity=0.309 Sum_probs=43.9
Q ss_pred CCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHH
Q 010778 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENL 292 (501)
Q Consensus 220 ~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~L 292 (501)
.|+-.+.|||||-.|.|++.+|..||+.|.|- |.|=-|.|++-|+..-+.|+...++|
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 45667899999999999999999999999875 23334677777777666665544444
No 47
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=84.00 E-value=6.7 Score=40.99 Aligned_cols=133 Identities=16% Similarity=0.162 Sum_probs=81.1
Q ss_pred cceecc-hhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCC
Q 010778 118 RYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFP 196 (501)
Q Consensus 118 R~~LTK-~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalIkEILKE~P~~~p 196 (501)
--.+.| |+.++.+....+|+|.+-- .+-|---|+|+++. +-|-+..++|---|.++....+
T Consensus 60 gavigkgg~nik~lr~d~na~v~vpd---------s~~peri~tisad~---------~ti~~ilk~iip~lee~f~~~~ 121 (390)
T KOG2192|consen 60 GAVIGKGGKNIKALRTDYNASVSVPD---------SSGPERILTISADI---------ETIGEILKKIIPTLEEGFQLPS 121 (390)
T ss_pred cceeccccccHHHHhhhccceeeccC---------CCCCceeEEEeccH---------HHHHHHHHHHhhhhhhCCCCCC
Confidence 334444 5677777777888776522 12233456888864 2333333344444455544432
Q ss_pred CccccCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEe
Q 010778 197 TLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSS 276 (501)
Q Consensus 197 p~~~p~~~g~k~~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa 276 (501)
+ .+-++.|- -.+.|-|||-+|+-+|.|.+...|++-|- -|-+.+ --..|+|.+
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 333322 124788999
Q ss_pred CCHHHHHHHHHHHHHHHHH
Q 010778 277 NNPKSLEEAKRLAENLLDT 295 (501)
Q Consensus 277 ~~~e~v~~Ak~LiE~LL~t 295 (501)
..++.|-...+.+-+||..
T Consensus 175 g~~k~v~~~i~~il~~i~e 193 (390)
T KOG2192|consen 175 GKPKRVVECIKIILDLISE 193 (390)
T ss_pred CCcchHHHHHHHHHHHhhc
Confidence 9999888777777666653
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=83.46 E-value=4.4 Score=32.11 Aligned_cols=53 Identities=26% Similarity=0.267 Sum_probs=36.6
Q ss_pred ccceecc-hhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHH
Q 010778 117 VRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (501)
Q Consensus 117 vR~~LTK-~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalI 184 (501)
+.+.+-+ |.++++|+++|||.|...-. ....+.++- +.|+|.. +.+++|..+|
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 4455554 89999999999999888321 112344553 5788975 3788888776
No 49
>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=81.09 E-value=4.3 Score=31.16 Aligned_cols=49 Identities=22% Similarity=0.237 Sum_probs=36.9
Q ss_pred ccceecc-hhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHH
Q 010778 117 VRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (501)
Q Consensus 117 vR~~LTK-~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalI 184 (501)
+.+.+.+ |.++++|++.|||.|..... + ..-.+.|.|.. +.|++|.++|
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 5677755 99999999999999988543 2 33467899943 4788888776
No 50
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=80.94 E-value=3.8 Score=43.42 Aligned_cols=110 Identities=15% Similarity=0.183 Sum_probs=66.3
Q ss_pred eecchhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCC-CCc
Q 010778 120 KLTKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGF-PTL 198 (501)
Q Consensus 120 ~LTK~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalIkEILKE~P~~~-pp~ 198 (501)
..-+|.+++.|+.+|.+-|.|- ..++-|.| -++|.- ..|++|..+|...-. ..... -.+
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 3456888889999998776651 12244776 345642 478888877765211 00000 000
Q ss_pred ccc-CCCCcc-cceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeec
Q 010778 199 QTV-MGNGVQ-AMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGR 253 (501)
Q Consensus 199 ~~p-~~~g~k-~~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGR 253 (501)
... .-++.. .-+.+.|+- .| +.++|+++||.|.++|+||+.+..-|.--++
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 011112 234566654 23 7799999999999999999999988865554
No 51
>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=80.77 E-value=1.7 Score=34.53 Aligned_cols=26 Identities=12% Similarity=0.059 Sum_probs=23.9
Q ss_pred eeEEEeCCCchhHHHHHHhhCCEEEE
Q 010778 225 IAARIRGPNDQYINHIMNETGATVLL 250 (501)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGaKI~I 250 (501)
-+|+.||.+|.+++.++..+|-+|-|
T Consensus 35 ~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 35 QLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cceeeECCCCHHHHHHHHHHCCCeEE
Confidence 48999999999999999999988865
No 52
>smart00322 KH K homology RNA-binding domain.
Probab=77.14 E-value=18 Score=26.66 Aligned_cols=64 Identities=20% Similarity=0.240 Sum_probs=42.3
Q ss_pred EEEEEcCCCCcccccee-cchhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHH
Q 010778 105 AREIVINDSESSVRYKL-TKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAM 183 (501)
Q Consensus 105 ~aEIeINDlPq~vR~~L-TK~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~Aval 183 (501)
..+|.|..-. ..+.+ .+|.++++|++.+|+.|...+.-. .---+.|.|.. ..+..|...
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 3455665533 45566 459999999999999988753111 22336788864 467777777
Q ss_pred HHHHH
Q 010778 184 VEEML 188 (501)
Q Consensus 184 IkEIL 188 (501)
|.+.+
T Consensus 64 i~~~~ 68 (69)
T smart00322 64 ILEIL 68 (69)
T ss_pred HHHHh
Confidence 77765
No 53
>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=74.73 E-value=8.8 Score=29.64 Aligned_cols=58 Identities=17% Similarity=0.194 Sum_probs=39.6
Q ss_pred EEEcCCCCccccceecc-hhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHH
Q 010778 107 EIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (501)
Q Consensus 107 EIeINDlPq~vR~~LTK-~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalI 184 (501)
+|.|.. ...+..+-+ |.++.+|++.|||.|..-. .. +.+. .+.|.|.. +.|..|+.+|
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--SKSD--TITITGPK---------ENVEKAKEEI 61 (62)
T ss_pred EEEeCH--HHhhhccCCCCCcHHHHHHHhCCEEEcCC-----CC--CCCC--EEEEEcCH---------HHHHHHHHHh
Confidence 345544 346778866 8999999999999986633 22 2233 45788974 4788887776
No 54
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=72.91 E-value=7.2 Score=39.69 Aligned_cols=29 Identities=17% Similarity=0.409 Sum_probs=25.5
Q ss_pred ceeEEEeCCCchhHHHHHHhhCCEEEEee
Q 010778 224 NIAARIRGPNDQYINHIMNETGATVLLRG 252 (501)
Q Consensus 224 NfvgrIIGP~GstlK~Iq~ETGaKI~IRG 252 (501)
..+-|+||++|+++|.+.++|+|+|.+==
T Consensus 155 ~kVpRvig~~~sm~~~l~~~~~~~I~VG~ 183 (239)
T COG1097 155 SKVPRVIGKKGSMLNMLKEKTGCEIIVGQ 183 (239)
T ss_pred hhcceEecCCCcHHHHhhhhcCeEEEEec
Confidence 35667999999999999999999998853
No 55
>PRK15494 era GTPase Era; Provisional
Probab=72.29 E-value=18 Score=37.45 Aligned_cols=28 Identities=29% Similarity=0.191 Sum_probs=22.9
Q ss_pred ceeEEEeCCCchhHHHH--------HHhhCCEEEEe
Q 010778 224 NIAARIRGPNDQYINHI--------MNETGATVLLR 251 (501)
Q Consensus 224 NfvgrIIGP~GstlK~I--------q~ETGaKI~IR 251 (501)
.-.+.|||.+|.++|+| |+-.||||.|+
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 35788999999999987 55568888775
No 56
>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=70.82 E-value=19 Score=27.37 Aligned_cols=60 Identities=22% Similarity=0.284 Sum_probs=38.5
Q ss_pred EEEcCCCCccccceec-chhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHH
Q 010778 107 EIVINDSESSVRYKLT-KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (501)
Q Consensus 107 EIeINDlPq~vR~~LT-K~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalI 184 (501)
+|.|.. ..+++.+. +|.++.+|++.||+.|.... ......+. -+.|.|.. +.+.+|..+|
T Consensus 3 ~i~ip~--~~~~~vIG~~G~~i~~I~~~s~~~I~i~~-----~~~~~~~~--~v~i~G~~---------~~v~~a~~~i 63 (64)
T cd00105 3 RVLVPS--SLVGRIIGKGGSTIKEIREETGAKIKIPD-----SGSGSEER--IVTITGTP---------EAVEKAKELI 63 (64)
T ss_pred EEEEch--hhcceeECCCCHHHHHHHHHHCCEEEEcC-----CCCCCCce--EEEEEcCH---------HHHHHHHHHh
Confidence 344444 23677774 59999999999999988653 11122233 35778863 3677777665
No 57
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=70.46 E-value=1.4 Score=36.47 Aligned_cols=33 Identities=18% Similarity=0.264 Sum_probs=25.8
Q ss_pred CCCCCceeEEEeCCCchhHHHHHHhh-CCEEEEe
Q 010778 219 ADASLNIAARIRGPNDQYINHIMNET-GATVLLR 251 (501)
Q Consensus 219 ~~P~FNfvgrIIGP~GstlK~Iq~ET-GaKI~IR 251 (501)
..++++-+|..+|.+|..+|.|++|. |-||.|=
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 6666544
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=69.59 E-value=22 Score=35.20 Aligned_cols=27 Identities=26% Similarity=0.214 Sum_probs=21.8
Q ss_pred eeEEEeCCCchhHHHHH--------HhhCCEEEEe
Q 010778 225 IAARIRGPNDQYINHIM--------NETGATVLLR 251 (501)
Q Consensus 225 fvgrIIGP~GstlK~Iq--------~ETGaKI~IR 251 (501)
-.+.|||.+|.++|+|. +-.||||.|+
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 47889999999999984 4558888764
No 59
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=67.55 E-value=8.5 Score=38.08 Aligned_cols=55 Identities=16% Similarity=0.284 Sum_probs=41.9
Q ss_pred eEEEeCCCchhHHHHHHhhCCEEEEeec-CCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHH
Q 010778 226 AARIRGPNDQYINHIMNETGATVLLRGR-GSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENL 292 (501)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETGaKI~IRGR-GSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~L 292 (501)
++.++|+.|.+.+.|++.+||+|.|=.+ ||..++... . ..||-.+.+|+++++-+
T Consensus 19 ~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~--~----------t~Dp~~~~ka~d~VkAI 74 (194)
T COG1094 19 IGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTR--K----------TEDPLALLKARDVVKAI 74 (194)
T ss_pred heeeecccccchHHHHhhcCeEEEEECCCCeEEEEecC--C----------CCChHHHHHHHHHHHHH
Confidence 6899999999999999999999999876 444433221 1 13778888998887654
No 60
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=66.64 E-value=3.7 Score=43.49 Aligned_cols=63 Identities=19% Similarity=0.225 Sum_probs=45.5
Q ss_pred ceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 010778 209 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 288 (501)
Q Consensus 209 ~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~L 288 (501)
..+.+.|| .-|++.|+|++|..+|+|+.+|...|.-- ..++ | -+++.....+.++.||+-
T Consensus 26 vt~sv~vp------s~~v~~ivg~qg~kikalr~KTqtyi~tP---------sr~e---e--PiF~vTg~~edv~~aRre 85 (394)
T KOG2113|consen 26 VTESVEVP------SEHVAEIVGRQGCKIKALRAKTQTYIKTP---------SRGE---E--PIFPVTGRHEDVRRARRE 85 (394)
T ss_pred cceeeecC------cccceeecccCccccchhhhhhcceeccC---------CCCC---C--CcceeccCchhHHHHhhc
Confidence 44555554 55899999999999999999998776421 1111 2 456666677889999988
Q ss_pred HHH
Q 010778 289 AEN 291 (501)
Q Consensus 289 iE~ 291 (501)
|+.
T Consensus 86 i~s 88 (394)
T KOG2113|consen 86 IPS 88 (394)
T ss_pred Ccc
Confidence 765
No 61
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=66.62 E-value=14 Score=39.59 Aligned_cols=57 Identities=19% Similarity=0.338 Sum_probs=45.7
Q ss_pred eeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH--HHHHHHHHH
Q 010778 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE--NLLDTISAE 299 (501)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE--~LL~tV~~E 299 (501)
-.--|.||.|.+++.|++..|+.|.-||. ++.|.+..+ .++.|+.+.. .|+..+++.
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 34568899999999999999999999993 677777776 8888888877 666665544
No 62
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=64.25 E-value=25 Score=40.89 Aligned_cols=108 Identities=17% Similarity=0.176 Sum_probs=74.2
Q ss_pred EEcCCCCccccceecc-hhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHH
Q 010778 108 IVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEE 186 (501)
Q Consensus 108 IeINDlPq~vR~~LTK-~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalIkE 186 (501)
+..+=+|+..++.+.| +..+..|.+++++.+..+= ....+++.+++-... .+..|++.|+.
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 3344456668888877 5569999999998865421 225567777654433 35666777777
Q ss_pred HHHcCCCCCCCccccCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeec
Q 010778 187 MLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGR 253 (501)
Q Consensus 187 ILKE~P~~~pp~~~p~~~g~k~~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGR 253 (501)
+..+-++.. ..+.++||-+ ...+|||.+|..+..|+.++|| |.|+..
T Consensus 411 ~~~ei~n~~-------------~~~~~~iP~k------~~~~iig~~g~~i~~I~~k~~~-v~i~f~ 457 (753)
T KOG2208|consen 411 IIAEILNSI-------------VKEEVQIPTK------SHKRIIGTKGALINYIMGKHGG-VHIKFQ 457 (753)
T ss_pred HHHhhhccc-------------ccceeecCcc------chhhhhccccccHHHHHhhcCc-EEEecC
Confidence 776665431 1234556533 5779999999999999999999 888874
No 63
>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=57.05 E-value=9.9 Score=28.81 Aligned_cols=23 Identities=13% Similarity=0.127 Sum_probs=20.2
Q ss_pred eEEEeCCCchhHHHHHHhhCCEE
Q 010778 226 AARIRGPNDQYINHIMNETGATV 248 (501)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETGaKI 248 (501)
.|++||.+|.+++.|+..++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 57899999999999999998554
No 64
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=52.46 E-value=10 Score=38.49 Aligned_cols=76 Identities=13% Similarity=0.146 Sum_probs=52.7
Q ss_pred EEcCCCCccc--ccee-cchhHHHHHHhhhCCeEeeecceeCCC-CC--------CCCCCCeEEEEEeccchhhHHHHHH
Q 010778 108 IVINDSESSV--RYKL-TKRHTQEEIQKCTGAVVITRGKYRLPN-AP--------PDGEKPLYLHISAGAHLKETAERIL 175 (501)
Q Consensus 108 IeINDlPq~v--R~~L-TK~~Tq~eI~e~TGAsItTRG~Y~PPg-k~--------~~~EpPLYL~Ieg~Tq~kdtaEri~ 175 (501)
|.+.|+|..+ ..+| -+|.||+++++.|+|.|-.||+|---. +. ..-+-+|+-+|++.++ .
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 4556777544 3344 469999999999999999999996543 21 1347789999999875 2
Q ss_pred HHHHHHHHHHHHHHcC
Q 010778 176 AVDHAAAMVEEMLKQG 191 (501)
Q Consensus 176 aVd~AvalIkEILKE~ 191 (501)
.+.+++..+..++.++
T Consensus 226 ki~~~ik~~~n~I~~a 241 (269)
T COG5176 226 KICRLIKSQLNAIREA 241 (269)
T ss_pred hHHHHHHHHHHHHHHH
Confidence 3455555566666554
No 65
>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=51.30 E-value=0.85 Score=39.55 Aligned_cols=32 Identities=22% Similarity=0.351 Sum_probs=24.1
Q ss_pred cCCCCccccceec-----chhHHHHHHhhhCCeEee--ecc
Q 010778 110 INDSESSVRYKLT-----KRHTQEEIQKCTGAVVIT--RGK 143 (501)
Q Consensus 110 INDlPq~vR~~LT-----K~~Tq~eI~e~TGAsItT--RG~ 143 (501)
|+++- .||.|- +|.++.+|.+.||+++.| ||.
T Consensus 32 ~~~l~--~R~~va~~lL~~g~syreIa~~tgvS~aTItRvs 70 (87)
T PF01371_consen 32 LEALA--QRWQVAKELLDEGKSYREIAEETGVSIATITRVS 70 (87)
T ss_dssp HHHHH--HHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHH
T ss_pred HHHHH--HHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHH
Confidence 34444 577655 489999999999999877 653
No 66
>PF13014 KH_3: KH domain
Probab=50.77 E-value=16 Score=26.68 Aligned_cols=24 Identities=33% Similarity=0.303 Sum_probs=19.8
Q ss_pred ccceecc-hhHHHHHHhhhCCeEee
Q 010778 117 VRYKLTK-RHTQEEIQKCTGAVVIT 140 (501)
Q Consensus 117 vR~~LTK-~~Tq~eI~e~TGAsItT 140 (501)
+++.+-+ |.++++|+++|||.|..
T Consensus 2 vg~iIG~~G~~I~~I~~~tg~~I~i 26 (43)
T PF13014_consen 2 VGRIIGKGGSTIKEIREETGAKIQI 26 (43)
T ss_pred cCeEECCCChHHHHHHHHhCcEEEE
Confidence 4556654 99999999999999876
No 67
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=46.97 E-value=18 Score=43.29 Aligned_cols=76 Identities=17% Similarity=0.133 Sum_probs=55.9
Q ss_pred cCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHH
Q 010778 216 GFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDT 295 (501)
Q Consensus 216 pve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~t 295 (501)
.++++|.- .+.++.+--- +.+|...++|.|..||+-=-....+ ...++-||++|.+.+.-.|++|+..++.+|..
T Consensus 903 ~inD~Pq~-~r~~vt~~~~--L~~i~e~~~~~it~rg~f~~~gk~p--~~gErklyl~ve~~~e~~vqra~~e~~r~l~e 977 (997)
T KOG0334|consen 903 EINDFPQN-ARWRVTYKEA--LLRISEPTAAGITTRGKFNPPGKEP--KPGERKLYLLVEGPDELSVQRAIEELERLLEE 977 (997)
T ss_pred cccccchh-cceeeechhh--hhhccCccccceeeccccCCCCCCC--CCcchhhhhhhhcchhHHHHHHHHHHHHHHHH
Confidence 44455544 7888877654 9999999999999999743221111 22456699999999999999999988876554
Q ss_pred H
Q 010778 296 I 296 (501)
Q Consensus 296 V 296 (501)
.
T Consensus 978 ~ 978 (997)
T KOG0334|consen 978 E 978 (997)
T ss_pred H
Confidence 3
No 68
>COG1159 Era GTPase [General function prediction only]
Probab=44.05 E-value=59 Score=34.24 Aligned_cols=41 Identities=22% Similarity=0.363 Sum_probs=28.9
Q ss_pred CcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHH--------HhhCCEEEE
Q 010778 205 GVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIM--------NETGATVLL 250 (501)
Q Consensus 205 g~k~~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq--------~ETGaKI~I 250 (501)
+..+...-|||.=+ .=.|-|||.+|.++|.|- +-.||||.|
T Consensus 225 ~~~~I~a~I~Ver~-----sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 225 GLLKIHATIYVERE-----SQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred CeEEEEEEEEEecC-----CccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 33455667777644 346789999999999884 445777755
No 69
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=42.55 E-value=19 Score=33.46 Aligned_cols=28 Identities=11% Similarity=0.136 Sum_probs=25.4
Q ss_pred eeEEEeCCCchhHHHHHHhhCCEEEEee
Q 010778 225 IAARIRGPNDQYINHIMNETGATVLLRG 252 (501)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGaKI~IRG 252 (501)
-+|..||.+|+.+|.|++..|-||-|=.
T Consensus 42 ~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 42 DMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CccccCCcCchHHHHHHHHhCCceEEEE
Confidence 5799999999999999999999997765
No 70
>PRK01381 Trp operon repressor; Provisional
Probab=41.15 E-value=11 Score=33.87 Aligned_cols=29 Identities=28% Similarity=0.434 Sum_probs=23.0
Q ss_pred ccceecc-----hhHHHHHHhhhCCeEee--eccee
Q 010778 117 VRYKLTK-----RHTQEEIQKCTGAVVIT--RGKYR 145 (501)
Q Consensus 117 vR~~LTK-----~~Tq~eI~e~TGAsItT--RG~Y~ 145 (501)
.||.|-+ .-+|.||.+++|++|+| ||.-+
T Consensus 43 ~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~ 78 (99)
T PRK01381 43 TRVRIVEELLRGELSQREIKQELGVGIATITRGSNS 78 (99)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHH
Confidence 5887765 47999999999999887 77433
No 71
>PRK00089 era GTPase Era; Reviewed
Probab=40.06 E-value=30 Score=34.25 Aligned_cols=38 Identities=18% Similarity=0.344 Sum_probs=27.5
Q ss_pred ceeEEEecCCCCCCCceeEEEeCCCchhHHHH--------HHhhCCEEEEe
Q 010778 209 MSTSVFLGFDADASLNIAARIRGPNDQYINHI--------MNETGATVLLR 251 (501)
Q Consensus 209 ~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~I--------q~ETGaKI~IR 251 (501)
....|+|.-+. -.+.|||.+|.++|+| |+-.||||.|.
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 45556665333 3788999999999988 45568888765
No 72
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=39.15 E-value=35 Score=39.78 Aligned_cols=29 Identities=21% Similarity=0.271 Sum_probs=25.8
Q ss_pred eEEEeCCCchhHHHHHHhhCCEEEEeecC
Q 010778 226 AARIRGPNDQYINHIMNETGATVLLRGRG 254 (501)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETGaKI~IRGRG 254 (501)
..-|+|.+|.++.+|++++.|+|.++=.|
T Consensus 358 ~~~v~GK~~~ni~ki~e~~~~~i~~~~~~ 386 (753)
T KOG2208|consen 358 LKFVIGKKGANIEKIREESQVKIDLPKQG 386 (753)
T ss_pred hhhhcCCCCccHHHHHHhhhhceeccccc
Confidence 66799999999999999999999998533
No 73
>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=38.19 E-value=26 Score=28.36 Aligned_cols=16 Identities=44% Similarity=0.752 Sum_probs=10.5
Q ss_pred ccCCCCCcCCChHHHHH
Q 010778 399 SGYEGIYPQATPLQQVA 415 (501)
Q Consensus 399 ~gy~~iypqatplqqva 415 (501)
-|||+++|+ |+.-++.
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 74
>PRK01064 hypothetical protein; Provisional
Probab=35.73 E-value=27 Score=29.83 Aligned_cols=20 Identities=20% Similarity=0.169 Sum_probs=17.3
Q ss_pred eEEEeCCCchhHHHHHHhhC
Q 010778 226 AARIRGPNDQYINHIMNETG 245 (501)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETG 245 (501)
+|++||-+|.+++.|+.-.+
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
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=32.76 E-value=42 Score=38.14 Aligned_cols=93 Identities=23% Similarity=0.252 Sum_probs=58.8
Q ss_pred eeEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhcccc
Q 010778 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGASR 304 (501)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~~E~~~~r 304 (501)
++-+|+|-.|+++|.|...|++||.|+-.-++ +=.+.+.+.-+..+..|+.++-..+.
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 22333444355555566554332221
Q ss_pred ccccccccCCCCchhhhcccccccccccCCcccchh
Q 010778 305 VSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVI 340 (501)
Q Consensus 305 ~~~~k~y~~~pppqq~~~gv~~~~~~~~~~~~~~~~ 340 (501)
....+--.++-||.+.--+..-|.|+..+...+.+
T Consensus 136 -~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~ 170 (608)
T KOG2279|consen 136 -ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSG 170 (608)
T ss_pred -cCCcccccccchhhhcccccccchhhhcchhcccc
Confidence 01233444677777777777777666555544333
No 76
>PRK02821 hypothetical protein; Provisional
Probab=31.53 E-value=29 Score=29.58 Aligned_cols=20 Identities=5% Similarity=0.129 Sum_probs=17.4
Q ss_pred eEEEeCCCchhHHHHHHhhC
Q 010778 226 AARIRGPNDQYINHIMNETG 245 (501)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETG 245 (501)
+|||||-+|.+++-|..--.
T Consensus 42 ~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 42 LGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CcceeCCCCchHHHHHHHHH
Confidence 89999999999999876554
No 77
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=31.38 E-value=49 Score=35.42 Aligned_cols=40 Identities=18% Similarity=0.363 Sum_probs=32.3
Q ss_pred eEEEecCCCCCCCceeEEEeCCCchhHHHHHHhh-CCEEEEe
Q 010778 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNET-GATVLLR 251 (501)
Q Consensus 211 eKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ET-GaKI~IR 251 (501)
.||-|= -..|+++-+|..||++|+.++.|.+|. |=||-|=
T Consensus 233 tKVAV~-s~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv 273 (362)
T PRK12327 233 TKIAVR-SNNPNVDAKGACVGPKGQRVQNIVSELKGEKIDII 273 (362)
T ss_pred eEEEEE-cCCCCCCchheeECCCChhHHHHHHHhCCCeEEEE
Confidence 566553 246999999999999999999999999 6666544
No 78
>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=31.37 E-value=30 Score=28.47 Aligned_cols=22 Identities=5% Similarity=0.086 Sum_probs=18.8
Q ss_pred eEEEeCCCchhHHHHHHhhCCE
Q 010778 226 AARIRGPNDQYINHIMNETGAT 247 (501)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETGaK 247 (501)
.|+|||.+|.+++-||--+..-
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~~ 56 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANLV 56 (77)
T ss_pred CCeEECCCCccHHHHHHHHHHH
Confidence 4899999999999999877633
No 79
>PRK00468 hypothetical protein; Provisional
Probab=31.12 E-value=30 Score=29.20 Aligned_cols=19 Identities=11% Similarity=0.193 Sum_probs=16.2
Q ss_pred eEEEeCCCchhHHHHHHhh
Q 010778 226 AARIRGPNDQYINHIMNET 244 (501)
Q Consensus 226 vgrIIGP~GstlK~Iq~ET 244 (501)
+|||||-+|.+++-|..--
T Consensus 41 ~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CcceecCCChhHHHHHHHH
Confidence 6999999999999886543
No 80
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=30.16 E-value=1.3e+02 Score=28.88 Aligned_cols=58 Identities=12% Similarity=0.178 Sum_probs=45.5
Q ss_pred eEEEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHH
Q 010778 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAE 299 (501)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~~E 299 (501)
.-.|+.++|..++.|....||+|.+.- +.-.|.|+| +...++.+...+.+++..++.+
T Consensus 37 ~~LLl~~~~~~L~~l~~~~~~~I~~~~---------------~~~~i~I~g-~k~~~~~i~~~i~~~l~~i~~~ 94 (210)
T PF14611_consen 37 FFLLLTGNGRILENLAARNGAKIEVSR---------------SENRIRITG-TKSTAEYIEASINEILSNIRTE 94 (210)
T ss_pred eeeeecCCchHHHHHHHhcCceEEEec---------------CCcEEEEEc-cHHHHHHHHHHHHHHHhhcEEE
Confidence 458999999999999888899998864 224677777 6667777788888888777655
No 81
>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=28.92 E-value=64 Score=34.25 Aligned_cols=40 Identities=20% Similarity=0.297 Sum_probs=31.9
Q ss_pred eEEEecCCCCCCCceeEEEeCCCchhHHHHHHhh-CCEEEEe
Q 010778 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNET-GATVLLR 251 (501)
Q Consensus 211 eKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ET-GaKI~IR 251 (501)
.||-|=- ..|+.+-+|..||++|+.++.|.+|. |=||-|=
T Consensus 231 tKvAV~s-~~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv 271 (341)
T TIGR01953 231 TKIAVES-NDENIDPVGACVGPKGSRIQAISKELNGEKIDII 271 (341)
T ss_pred eEEEEEc-CCCCCCcceeeECCCCchHHHHHHHhCCCeEEEE
Confidence 5666543 36999999999999999999999999 5555443
No 82
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=25.96 E-value=1.2e+02 Score=34.30 Aligned_cols=70 Identities=16% Similarity=0.142 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCccccCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCCEEEEeecCC
Q 010778 176 AVDHAAAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGS 255 (501)
Q Consensus 176 aVd~AvalIkEILKE~P~~~pp~~~p~~~g~k~~eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRGRGS 255 (501)
....|..+|++.++.-.....+-++.. . -...|+||-+ .++++||-+|..+++|++..|-+|.++-++.
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-D----GRAVVKVPEK------YIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred hhHHHHHHHHHHHHHhCCCCceEEEec-C----CeEEEEeCHH------HhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 345566666666665422111111110 0 1245667644 3678999999999999999999999998755
Q ss_pred C
Q 010778 256 G 256 (501)
Q Consensus 256 g 256 (501)
-
T Consensus 527 ~ 527 (604)
T COG1855 527 E 527 (604)
T ss_pred c
Confidence 3
No 83
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=25.73 E-value=1.4e+02 Score=29.27 Aligned_cols=52 Identities=12% Similarity=0.300 Sum_probs=40.0
Q ss_pred hHHHHHHhhC-CEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhc
Q 010778 236 YINHIMNETG-ATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECG 301 (501)
Q Consensus 236 tlK~Iq~ETG-aKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE~LL~tV~~E~~ 301 (501)
+++.|++... .-+.+++||.+ |.|.|-|... .++.|...|.+|+..++..|+
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 4667766643 34457777633 8888888777 999999999999999999765
No 84
>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=25.49 E-value=54 Score=30.79 Aligned_cols=28 Identities=11% Similarity=0.141 Sum_probs=25.1
Q ss_pred eeEEEeCCCchhHHHHHHhhCCEEEEee
Q 010778 225 IAARIRGPNDQYINHIMNETGATVLLRG 252 (501)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGaKI~IRG 252 (501)
-+|..+|++|+.+|.|++..|=||-|=.
T Consensus 43 ~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 43 EMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred CccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 5899999999999999988898887765
No 85
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=24.65 E-value=52 Score=32.33 Aligned_cols=33 Identities=9% Similarity=0.142 Sum_probs=28.3
Q ss_pred CCCCceeEEEeCCCchhHHHHHHhhCCEEEEee
Q 010778 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRG 252 (501)
Q Consensus 220 ~P~FNfvgrIIGP~GstlK~Iq~ETGaKI~IRG 252 (501)
.++.+=+|..||++|+.+|.|.+|.|=||-|=-
T Consensus 81 ~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe 113 (190)
T COG0195 81 VVKIDPVGACIGKRGSRVKAVSEELGEKIDVVE 113 (190)
T ss_pred ecCcCchhhhccCCChHHHHHHHHhCCceEEEE
Confidence 457778999999999999999999997776654
No 86
>PF13711 DUF4160: Domain of unknown function (DUF4160)
Probab=24.09 E-value=1.7e+02 Score=23.48 Aligned_cols=14 Identities=21% Similarity=0.444 Sum_probs=11.1
Q ss_pred CCCcEEEEEeCCHH
Q 010778 267 HQPLHLFLSSNNPK 280 (501)
Q Consensus 267 dEPLHV~Isa~~~e 280 (501)
-+|.||||...+.+
T Consensus 14 H~PpHvHv~~g~~~ 27 (66)
T PF13711_consen 14 HEPPHVHVRYGGFE 27 (66)
T ss_pred CCCCeEEEEcCCcE
Confidence 48999999977743
No 87
>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=23.91 E-value=1.9e+02 Score=23.24 Aligned_cols=26 Identities=15% Similarity=0.440 Sum_probs=20.8
Q ss_pred CC-cEEEEEeCCHHHHHHHHHHHHHHH
Q 010778 268 QP-LHLFLSSNNPKSLEEAKRLAENLL 293 (501)
Q Consensus 268 EP-LHV~Isa~~~e~v~~Ak~LiE~LL 293 (501)
|| +.|++++.+.+.+++-.+-+.++|
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 55 999999999888887777666665
No 88
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=23.72 E-value=60 Score=31.42 Aligned_cols=26 Identities=12% Similarity=0.087 Sum_probs=24.3
Q ss_pred EEEeCCCchhHHHHHHhhCCEEEEee
Q 010778 227 ARIRGPNDQYINHIMNETGATVLLRG 252 (501)
Q Consensus 227 grIIGP~GstlK~Iq~ETGaKI~IRG 252 (501)
|.-||++|.++|++++..|=+|.|=.
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEEE
Confidence 88999999999999999999998776
No 89
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=22.62 E-value=52 Score=28.21 Aligned_cols=18 Identities=17% Similarity=0.252 Sum_probs=16.0
Q ss_pred eEEEeCCCchhHHHHHHh
Q 010778 226 AARIRGPNDQYINHIMNE 243 (501)
Q Consensus 226 vgrIIGP~GstlK~Iq~E 243 (501)
+|+|||-+|.+++-|..-
T Consensus 41 ~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 41 MGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred ccceecCCChhHHHHHHH
Confidence 899999999999998653
No 90
>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=22.22 E-value=91 Score=26.10 Aligned_cols=31 Identities=16% Similarity=0.324 Sum_probs=26.8
Q ss_pred EEEEEeCC-HHHHHHHHHHHHHHHHHHHHHhc
Q 010778 271 HLFLSSNN-PKSLEEAKRLAENLLDTISAECG 301 (501)
Q Consensus 271 HV~Isa~~-~e~v~~Ak~LiE~LL~tV~~E~~ 301 (501)
||+|..++ .+..+++++.++.|...+.....
T Consensus 1 HIl~~~~~~~~~~~~~~~~a~~i~~~l~~g~~ 32 (95)
T PF00639_consen 1 HILVKPPPSDEEKDAAKKKAEEIYEQLKKGED 32 (95)
T ss_dssp EEEEESTTSCCHHHHHHHHHHHHHHHHHTTSS
T ss_pred CEEEECCCchhhHHHHHHHHHHHHHHHHhCch
Confidence 88998776 77899999999999999988755
No 91
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=21.84 E-value=24 Score=31.31 Aligned_cols=26 Identities=31% Similarity=0.465 Sum_probs=21.3
Q ss_pred ccceecc-----hhHHHHHHhhhCCeEee--ec
Q 010778 117 VRYKLTK-----RHTQEEIQKCTGAVVIT--RG 142 (501)
Q Consensus 117 vR~~LTK-----~~Tq~eI~e~TGAsItT--RG 142 (501)
.||.|-. +-||.||.+.+|++++| ||
T Consensus 43 ~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~ 75 (94)
T TIGR01321 43 DRIRIVNELLNGNMSQREIASKLGVSIATITRG 75 (94)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH
Confidence 5777654 67999999999999876 55
No 92
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=20.94 E-value=1.5e+02 Score=34.63 Aligned_cols=64 Identities=17% Similarity=0.186 Sum_probs=47.6
Q ss_pred EEEEcCCCCccccceecc-hhHHHHHHhhhCCeEeeecceeCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHH
Q 010778 106 REIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (501)
Q Consensus 106 aEIeINDlPq~vR~~LTK-~~Tq~eI~e~TGAsItTRG~Y~PPgk~~~~EpPLYL~Ieg~Tq~kdtaEri~aVd~AvalI 184 (501)
....++..+.+-|-.+.+ |.++.+|.++||+.|-+. ++.-.+ |.+.+. ..+++|+..|
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------ddGtv~--i~~s~~--------~~~~~ak~~I 610 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DDGTVK--IAASDG--------ESAKKAKERI 610 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CCCcEE--EEecch--------HHHHHHHHHH
Confidence 456788888888888877 899999999999998762 122232 555543 4678899999
Q ss_pred HHHHHc
Q 010778 185 EEMLKQ 190 (501)
Q Consensus 185 kEILKE 190 (501)
+.+..+
T Consensus 611 ~~i~~e 616 (692)
T COG1185 611 EAITRE 616 (692)
T ss_pred HHHHhh
Confidence 998854
No 93
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=20.86 E-value=78 Score=35.13 Aligned_cols=42 Identities=14% Similarity=0.215 Sum_probs=33.9
Q ss_pred eeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhh-CCEEEEee
Q 010778 210 STSVFLGFDADASLNIAARIRGPNDQYINHIMNET-GATVLLRG 252 (501)
Q Consensus 210 eeKI~Ipve~~P~FNfvgrIIGP~GstlK~Iq~ET-GaKI~IRG 252 (501)
-.||-|-- ..|+++-+|..||++|+.++.|.+|. |=||-|=-
T Consensus 264 RtKVAV~S-~d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~ 306 (449)
T PRK12329 264 RTKIAVDT-LERDVDPVGACIGARGSRIQAVVNELRGEKIDVIR 306 (449)
T ss_pred eeEEEEEc-CCCCCChhhccCCCCcchHHHHHHHhCCCeEEEEE
Confidence 36776532 46899999999999999999999999 77775543
No 94
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=20.14 E-value=19 Score=29.14 Aligned_cols=20 Identities=20% Similarity=0.313 Sum_probs=17.5
Q ss_pred eEEEeCCCchhHHHHHHhhC
Q 010778 226 AARIRGPNDQYINHIMNETG 245 (501)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETG 245 (501)
.|+|||-+|.+++-||.-.+
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 78999999999999987554
No 95
>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=20.05 E-value=2.8e+02 Score=24.79 Aligned_cols=51 Identities=27% Similarity=0.393 Sum_probs=32.9
Q ss_pred EEeCCCchhHHHHHHhhCCEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHH----HHHHHHHHHHHHHHHHH
Q 010778 228 RIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPK----SLEEAKRLAENLLDTIS 297 (501)
Q Consensus 228 rIIGP~GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e----~v~~Ak~LiE~LL~tV~ 297 (501)
+==||||++++. |..+|.|+=.-++ |.|.+.+.- +.+.|.+....+|....
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 345999999875 5566777654222 788877543 56666666666666555
Done!