Query 008337
Match_columns 569
No_of_seqs 201 out of 477
Neff 3.6
Searched_HMMs 46136
Date Thu Mar 28 22:32:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008337.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008337hhsearch_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 2.6E-38 5.6E-43 327.7 13.2 370 26-428 12-422 (531)
2 KOG0119 Splicing factor 1/bran 99.9 1.4E-27 3E-32 252.9 15.4 163 123-293 59-230 (554)
3 cd02395 SF1_like-KH Splicing f 99.9 1.3E-25 2.8E-30 202.0 8.1 96 208-303 1-106 (120)
4 KOG1588 RNA-binding protein Sa 99.9 6.3E-22 1.4E-26 197.6 10.1 127 173-299 55-197 (259)
5 COG5176 MSL5 Splicing factor ( 99.8 9.2E-21 2E-25 185.1 10.1 182 108-296 47-243 (269)
6 KOG1960 Predicted RNA-binding 99.1 2.5E-11 5.5E-16 128.0 4.8 178 122-343 234-414 (531)
7 KOG1676 K-homology type RNA bi 99.1 1.8E-09 3.9E-14 118.3 17.7 166 98-297 135-304 (600)
8 KOG0334 RNA helicase [RNA proc 99.1 3.6E-11 7.9E-16 137.5 3.0 82 100-189 896-978 (997)
9 PRK13763 putative RNA-processi 98.8 1.9E-08 4E-13 96.3 9.0 145 102-292 3-156 (180)
10 TIGR03665 arCOG04150 arCOG0415 98.8 1.5E-08 3.3E-13 96.2 8.3 133 116-292 10-150 (172)
11 KOG1676 K-homology type RNA bi 98.6 2.3E-06 4.9E-11 94.6 17.5 155 104-293 232-389 (600)
12 cd02393 PNPase_KH Polynucleoti 98.5 4E-07 8.7E-12 73.1 7.1 58 209-288 4-61 (61)
13 cd00105 KH-I K homology RNA-bi 98.5 5.6E-07 1.2E-11 70.0 7.4 63 209-288 2-64 (64)
14 PF00013 KH_1: KH domain syndr 98.4 1.7E-07 3.7E-12 73.4 2.5 59 209-287 2-60 (60)
15 smart00322 KH K homology RNA-b 98.4 2.1E-06 4.6E-11 65.4 8.0 66 207-291 3-68 (69)
16 cd02394 vigilin_like_KH K homo 98.2 3.1E-06 6.6E-11 66.7 5.3 53 222-287 9-61 (62)
17 cd02396 PCBP_like_KH K homolog 98.1 1.4E-05 3E-10 64.3 7.3 62 210-287 3-64 (65)
18 KOG2191 RNA-binding protein NO 97.9 0.00069 1.5E-08 71.5 17.5 162 102-298 39-206 (402)
19 PF13014 KH_3: KH domain 97.6 4.1E-05 8.8E-10 57.2 3.1 28 223-250 1-28 (43)
20 KOG2193 IGF-II mRNA-binding pr 97.4 0.00049 1.1E-08 74.5 8.9 137 121-299 217-355 (584)
21 PRK13763 putative RNA-processi 97.4 0.00031 6.7E-09 67.6 6.4 63 209-292 5-70 (180)
22 TIGR03665 arCOG04150 arCOG0415 97.2 0.00048 1.1E-08 65.7 4.9 55 223-292 8-64 (172)
23 TIGR02696 pppGpp_PNP guanosine 97.2 0.0012 2.6E-08 75.5 8.8 63 209-293 580-642 (719)
24 COG1094 Predicted RNA-binding 97.1 0.00083 1.8E-08 66.3 6.0 145 106-295 12-166 (194)
25 TIGR03591 polynuc_phos polyrib 97.0 0.0021 4.6E-08 73.1 8.7 99 209-345 553-651 (684)
26 KOG2193 IGF-II mRNA-binding pr 97.0 0.0044 9.5E-08 67.4 10.0 155 106-299 415-570 (584)
27 cd02395 SF1_like-KH Splicing f 96.9 0.0021 4.6E-08 58.7 6.5 64 118-189 21-96 (120)
28 KOG0119 Splicing factor 1/bran 96.9 0.0014 3.1E-08 71.9 6.1 64 118-189 158-231 (554)
29 KOG2190 PolyC-binding proteins 96.8 0.014 3.1E-07 64.4 12.7 138 116-291 56-206 (485)
30 PLN00207 polyribonucleotide nu 96.7 0.0016 3.4E-08 76.1 4.7 131 173-345 652-787 (891)
31 PRK11824 polynucleotide phosph 95.7 0.011 2.3E-07 67.6 4.7 92 222-345 563-654 (693)
32 PRK04163 exosome complex RNA-b 95.5 0.018 4E-07 57.6 4.9 54 223-292 155-208 (235)
33 KOG2190 PolyC-binding proteins 95.4 0.28 6E-06 54.5 14.1 60 115-189 149-209 (485)
34 KOG2874 rRNA processing protei 94.9 0.027 6E-07 58.8 4.1 57 224-298 160-216 (356)
35 KOG2191 RNA-binding protein NO 94.6 0.14 3.1E-06 54.6 8.6 77 207-300 39-115 (402)
36 KOG2814 Transcription coactiva 93.6 0.11 2.5E-06 55.2 5.5 64 223-298 67-130 (345)
37 COG1185 Pnp Polyribonucleotide 93.6 0.074 1.6E-06 60.9 4.4 53 224-292 563-615 (692)
38 KOG1067 Predicted RNA-binding 93.0 0.19 4.2E-06 56.8 6.4 58 223-297 607-664 (760)
39 PRK00106 hypothetical protein; 92.9 0.2 4.3E-06 56.2 6.5 60 218-292 231-290 (535)
40 TIGR03319 YmdA_YtgF conserved 92.8 0.2 4.3E-06 55.8 6.2 60 218-292 210-269 (514)
41 PRK12704 phosphodiesterase; Pr 92.7 0.25 5.5E-06 55.1 6.8 59 218-291 216-274 (520)
42 KOG0336 ATP-dependent RNA heli 91.2 0.36 7.7E-06 53.4 5.7 63 221-299 55-118 (629)
43 cd02393 PNPase_KH Polynucleoti 89.0 1 2.3E-05 36.3 5.4 57 104-183 4-61 (61)
44 KOG2192 PolyC-binding hnRNP-K 88.8 1.1 2.3E-05 47.2 6.7 65 223-298 325-389 (390)
45 KOG2192 PolyC-binding hnRNP-K 87.1 3.4 7.5E-05 43.6 9.1 130 119-293 63-193 (390)
46 KOG1588 RNA-binding protein Sa 87.0 1.7 3.8E-05 45.1 6.8 73 116-191 111-194 (259)
47 PRK12705 hypothetical protein; 82.8 1.2 2.6E-05 50.0 3.8 58 218-290 204-261 (508)
48 KOG1924 RhoA GTPase effector D 82.1 1.2 2.5E-05 52.4 3.4 15 175-189 209-223 (1102)
49 KOG2113 Predicted RNA binding 80.9 2.8 6E-05 45.0 5.4 108 119-251 42-153 (394)
50 PF00013 KH_1: KH domain syndr 80.4 4.5 9.8E-05 31.6 5.2 49 115-182 11-60 (60)
51 cd02396 PCBP_like_KH K homolog 79.7 6 0.00013 31.8 5.9 52 115-182 11-64 (65)
52 cd02134 NusA_KH NusA_K homolog 78.8 2 4.4E-05 34.7 2.9 27 222-248 34-60 (61)
53 smart00322 KH K homology RNA-b 75.8 19 0.00041 27.0 7.4 64 103-186 4-68 (69)
54 cd02394 vigilin_like_KH K homo 73.6 9.8 0.00021 29.9 5.4 58 105-182 3-61 (62)
55 KOG2208 Vigilin [Lipid transpo 73.0 13 0.00028 43.8 8.5 108 106-251 349-457 (753)
56 COG1097 RRP4 RNA-binding prote 71.8 7 0.00015 40.3 5.3 28 222-249 155-182 (239)
57 COG1702 PhoH Phosphate starvat 70.4 9.9 0.00022 41.2 6.2 57 223-297 25-83 (348)
58 PRK15494 era GTPase Era; Provi 69.6 21 0.00046 37.6 8.4 28 222-249 283-318 (339)
59 KOG1923 Rac1 GTPase effector F 68.6 5.6 0.00012 46.8 4.2 17 484-500 269-285 (830)
60 KOG1924 RhoA GTPase effector D 68.4 5.7 0.00012 47.1 4.2 11 400-410 440-450 (1102)
61 PF13184 KH_5: NusA-like KH do 67.4 1.9 4E-05 36.3 0.1 33 217-249 12-45 (69)
62 cd00105 KH-I K homology RNA-bi 67.3 23 0.00049 27.3 6.2 52 115-182 11-63 (64)
63 KOG2113 Predicted RNA binding 67.3 3.5 7.6E-05 44.3 2.1 63 207-289 26-88 (394)
64 TIGR00436 era GTP-binding prot 65.5 27 0.00059 35.0 8.0 27 223-249 232-266 (270)
65 KOG4307 RNA binding protein RB 59.8 91 0.002 37.2 11.5 30 454-483 171-200 (944)
66 PF13014 KH_3: KH domain 58.8 20 0.00043 26.6 4.3 24 115-138 2-26 (43)
67 COG5176 MSL5 Splicing factor ( 57.9 7.4 0.00016 40.0 2.4 76 106-189 154-241 (269)
68 COG1094 Predicted RNA-binding 56.2 18 0.00038 36.5 4.6 56 223-290 18-74 (194)
69 cd02409 KH-II KH-II (K homolo 53.6 12 0.00025 28.9 2.4 23 224-246 36-58 (68)
70 KOG0334 RNA helicase [RNA proc 48.0 17 0.00037 44.1 3.6 76 213-293 902-977 (997)
71 PF01371 Trp_repressor: Trp re 46.5 4.2 9.2E-05 35.9 -1.2 32 108-141 32-70 (87)
72 KOG2208 Vigilin [Lipid transpo 41.7 30 0.00065 40.9 4.3 31 223-253 357-387 (753)
73 PRK01381 Trp operon repressor; 39.9 12 0.00027 34.0 0.7 29 115-143 43-78 (99)
74 PRK00089 era GTPase Era; Revie 39.9 29 0.00063 34.9 3.4 38 207-249 226-271 (292)
75 PHA01732 proline-rich protein 38.9 30 0.00064 31.2 2.9 13 508-520 15-27 (94)
76 PRK08406 transcription elongat 38.7 23 0.0005 33.4 2.3 28 223-250 42-69 (140)
77 COG1159 Era GTPase [General fu 37.0 85 0.0019 33.6 6.4 42 203-249 225-274 (298)
78 PF07885 Ion_trans_2: Ion chan 35.9 29 0.00063 28.5 2.2 16 397-413 39-54 (79)
79 KOG2279 Kinase anchor protein 35.0 47 0.001 38.3 4.3 93 223-338 78-170 (608)
80 PRK01064 hypothetical protein; 33.8 31 0.00066 30.0 2.1 20 224-243 41-60 (78)
81 PF14611 SLS: Mitochondrial in 32.9 1.1E+02 0.0024 29.7 6.1 60 223-298 36-95 (210)
82 KOG1925 Rac1 GTPase effector F 32.6 32 0.00069 39.5 2.5 21 508-528 247-268 (817)
83 COG4245 TerY Uncharacterized p 30.6 1.8E+02 0.0038 29.9 7.0 73 153-233 4-79 (207)
84 cd02414 jag_KH jag_K homology 27.9 37 0.0008 28.4 1.6 21 224-244 35-55 (77)
85 COG1855 ATPase (PilT family) [ 27.8 1.1E+02 0.0023 35.3 5.5 69 174-253 458-526 (604)
86 PRK02821 hypothetical protein; 27.7 36 0.00078 29.5 1.5 22 223-244 41-62 (77)
87 PRK12327 nusA transcription el 27.7 59 0.0013 35.4 3.5 40 209-249 233-273 (362)
88 PRK00468 hypothetical protein; 27.1 38 0.00083 29.1 1.6 18 224-241 41-58 (75)
89 KOG2675 Adenylate cyclase-asso 27.1 75 0.0016 35.9 4.2 15 174-188 10-24 (480)
90 TIGR01953 NusA transcription t 25.4 77 0.0017 34.2 3.8 39 209-248 231-270 (341)
91 COG5178 PRP8 U5 snRNP spliceos 24.8 69 0.0015 40.3 3.6 9 519-527 25-33 (2365)
92 PTZ00225 60S ribosomal protein 24.4 1.5E+02 0.0033 29.9 5.5 58 224-293 117-190 (214)
93 PF00639 Rotamase: PPIC-type P 24.0 86 0.0019 26.7 3.2 33 269-301 1-34 (95)
94 TIGR01952 nusA_arch NusA famil 23.0 63 0.0014 30.9 2.3 28 223-250 43-70 (141)
95 TIGR02696 pppGpp_PNP guanosine 22.6 1.1E+02 0.0024 36.4 4.6 62 104-188 580-642 (719)
96 COG1185 Pnp Polyribonucleotide 22.5 1.2E+02 0.0027 35.8 4.9 64 104-188 552-616 (692)
97 PF13711 DUF4160: Domain of un 22.5 3.1E+02 0.0067 22.4 6.0 13 265-277 14-26 (66)
98 PF09840 DUF2067: Uncharacteri 21.8 2.7E+02 0.0058 27.9 6.5 52 234-299 14-66 (190)
99 PRK06418 transcription elongat 21.7 68 0.0015 31.6 2.3 73 225-297 72-159 (166)
100 TIGR01321 TrpR trp operon repr 21.4 29 0.00063 31.3 -0.2 26 115-140 43-75 (94)
101 PF00472 RF-1: RF-1 domain; I 21.2 2.9E+02 0.0062 25.1 6.1 51 227-296 21-75 (113)
102 COG0195 NusA Transcription elo 21.1 66 0.0014 32.2 2.2 33 218-250 81-113 (190)
103 PRK13764 ATPase; Provisional 20.8 1.1E+02 0.0024 35.6 4.1 39 209-253 483-521 (602)
104 TIGR03591 polynuc_phos polyrib 20.0 1.2E+02 0.0027 35.5 4.3 61 104-187 553-614 (684)
No 1
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=100.00 E-value=2.6e-38 Score=327.75 Aligned_cols=370 Identities=18% Similarity=0.153 Sum_probs=255.1
Q ss_pred HHhhhccCccccccccCcc--ccCCCCCCCCC-CCCCCC--cccccccccCccccCCCCCCCcccCCC-CCCCCcCCCCc
Q 008337 26 QRKKRKWDQPAESLINFPL--ASFGISLPGVP-VAPVVP--APAAAAFFTNPPVASGATVPPVVLQGP-LPPKFNQVQDE 99 (569)
Q Consensus 26 ~r~krkwd~~a~~~~~~p~--~~~g~~~~~~~-~~~~~~--aa~~~a~~~~~q~~a~~~~pp~~~~~s-~~~~~~k~~de 99 (569)
--++|+|||+++.=..+++ .+.|.-.|+.. +.+... ++++-++.+|..+-+--..-+..-+.- +-...|+.+|+
T Consensus 12 ~~~~~~WD~~~~~d~~~~~~~~~s~~~~p~eS~~~~~~~h~~~~s~s~~~N~~~~~k~~~~~~~Na~~~i~~p~N~~K~~ 91 (531)
T KOG1960|consen 12 DNYSRDWDSRFTEDSYSRRDSQRSGNEAPRESRYYRKEEHLQERSRSRSPNRDSRWKSSSSGFANAHPPIEEPTNNGKEA 91 (531)
T ss_pred CCccccccCCCCCccccCchhhhccCCCCCcccccCcchhhhhhhhccCcchhccccccccccccccchhhcccccchhH
Confidence 3578999999975333332 22234444433 222212 455556899988755211111111111 11126778888
Q ss_pred ccEEEEEEeCCCCcccchhccchhHHHHHHHHhCCeEeeeccccCCCCC--CCCCCCeEEEEEeccchhhHHHHHHHHHH
Q 008337 100 LIIAREIVINDSESSVRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAP--PDGEKPLYLHISAGAHLKETAERILAVDH 177 (569)
Q Consensus 100 ~~f~aEIEINDlPq~~R~~LTKg~Tq~eIqe~TGA~VtTRGrY~PPgk~--~~gEpPLYL~Ieg~te~kdTaERi~aVdr 177 (569)
+ .+++++|||.+++|||.+|+|.++++|.+++|+.|.+||+|++++.+ .++++||||||.+.|- +.+++
T Consensus 92 ~-~~a~~~iN~~~~~~~~~~TRg~~~d~Ie~~~G~~~~~RGs~~~~El~~vg~~~~pLv~hI~~~T~--------Ei~~~ 162 (531)
T KOG1960|consen 92 A-AAAARRINESLQSTKATSTRGTSYDHIEGITGTTSASRGSAPAPELPPVGSSEGPLVDHIPPSTA--------EITSK 162 (531)
T ss_pred H-HHHHHHhhcccccccceeccchhHHhhhhhccceeeccCCCCCccCCCCCCCCCcceeecCCccH--------HHHHH
Confidence 8 89999999999999999999999999999999999999999999975 4789999999999862 58999
Q ss_pred HHHHHHHHHHcCCC----------CCCCc--c-------ccCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHH
Q 008337 178 AAAMVEEMLKQGHA----------GFPTL--Q-------TVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHI 238 (569)
Q Consensus 178 A~alIeEIIKE~p~----------~~pp~--~-------~p~~~G~k~~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~I 238 (569)
|+++|+-.++.+.. +.+.+ + .+..+|++|++ |+||++| +|.||+.+..-|++..+|.+|
T Consensus 163 Ai~RIkgv~~~~~~~~n~~~V~i~~~~sP~~~i~~~V~~~~f~~G~~Y~~-k~~v~~~-~P~~~~K~~~~~r~d~~La~~ 240 (531)
T KOG1960|consen 163 AIERIKGVFMQDVEINNVRNVYILVRASPLSEIENKVGVQLFSKGRYYPN-KALATDK-DPPLYLKIVSHNRKDLTLALQ 240 (531)
T ss_pred HHhhCccceeecccccccceEEEeecCCchhhhccccccccccccccchh-heecccC-CcchhhhhhccCccchhhhhh
Confidence 99999977766421 11111 1 23467889998 9999998 999999999999999999999
Q ss_pred HHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhhcccccccc-----cccc-cC
Q 008337 239 MNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGASRVSSC-----KVYN-AV 312 (569)
Q Consensus 239 q~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~tV~eE~~~fr~~~~-----k~y~-av 312 (569)
+.||++++.|||||||.+|++.|+|++|||||+|+|.+.+.+.+|+++|+||+++|+.+|.+|-.... ..|- -+
T Consensus 241 ~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl~~~v~~~~sr~~~~~~~~~p~~~y~~~~ 320 (531)
T KOG1960|consen 241 EIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNGNGENGAPRRKWNLEEKVYINLSRGFHRQAIVGPQGAYVKHI 320 (531)
T ss_pred hhhhhhhhhhccccccccCcccccccCCceeEEeecCCchhhccchhHHHhHHHHHHHHhhhhhhhcccccCCccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999987744211 2221 00
Q ss_pred CCchhh---cccccCcCcccccCcccchhhcccccccCCCCCCCCCccceeeecceeeccc-----cccccCCCCCCccc
Q 008337 313 PPPQQL---LTGIQGFGNEQKLNAGSAVILTSTVNLSSVPLAPSVPGVTTVYSQGMMLQSG-----GILNSVQPQQNIVG 384 (569)
Q Consensus 313 Pppq~~---l~Gv~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~-----~~~~~~~~~~~~~~ 384 (569)
-+||.- ..|-++--|++..|--+- ...++-.++.....+|.- -..-++ +++-.+.
T Consensus 321 ~~~~~~~~~~~g~~s~~i~p~~~~~~~----------------~p~~~~~~~~~~~~~~~~~~~~~~~i~~v-~~qy~~~ 383 (531)
T KOG1960|consen 321 QQETRTRVQIKGQGSAFIEPSTNRESD----------------EPIHLCIMSHDPNAIQRAKVLCEDLIASV-HQQYKAW 383 (531)
T ss_pred CCCCCcceeccCccceeecCCCCCCCC----------------CCcccccccCChhhhhhhhhcccccCCcc-cccCccc
Confidence 122222 222222224444332111 111111222222222220 011122 5555666
Q ss_pred CCCCCCCCCcccccCCCCCcCCChHHHHHHHhhcCCCCCccccc
Q 008337 385 YPQPVSTGGTSYSGYEGIYPQATPLQQVALALRQSSSPLTSLVA 428 (569)
Q Consensus 385 ~~~p~~~ggt~y~gy~~iypqatplqqva~~l~~~~s~~~~~v~ 428 (569)
-.||.+. +--+|-||-+|-+-| |+++|+-+.-+-||..+
T Consensus 384 ~~qp~~~--~~~~~~~~~~~p~~~---~~~~~~~~~q~~~qp~~ 422 (531)
T KOG1960|consen 384 KSQPKDR--DQNQGNRAYNPPNRN---QAFSARDSRQEKTQPTN 422 (531)
T ss_pred ccCCCcc--cccCCCCCCCCCCcc---ccccCCCCCCCCCCCCC
Confidence 6788444 445788888887776 68888887666666443
No 2
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=99.95 E-value=1.4e-27 Score=252.89 Aligned_cols=163 Identities=21% Similarity=0.300 Sum_probs=131.5
Q ss_pred hHHHHHHHHhCCeEeeeccccCCC-C-CCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCCccccC
Q 008337 123 HTQEEIQKCTGAVVITRGKYRLPN-A-PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQTVM 200 (569)
Q Consensus 123 ~Tq~eIqe~TGA~VtTRGrY~PPg-k-~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alIeEIIKE~p~~~pp~~~p~ 200 (569)
..+++|.+..+....- +|++ + ..++..++|..-.-..++++.|.|.++-++..+.|+++|+..+.|.++.+|
T Consensus 59 ~~iee~t~kLrt~d~~----~p~~~e~rSPsp~p~yda~g~R~ntRe~R~r~~Le~er~e~I~~~lk~nP~fkpP~DY-- 132 (554)
T KOG0119|consen 59 LRIEEITRKLRTGDVG----VPPPRELRSPSPEPVYDAKGKRLNTREQRARKKLEDERHEIIEEILKLNPGFKPPADY-- 132 (554)
T ss_pred HHHHHhhhhhccccCC----CCCCccccCCCcchhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCccc--
Confidence 3455555554444211 3444 3 678888898766555555677778888899999999999999999977654
Q ss_pred CCCc-ccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCC------CCCCCCCCCcEEEEE
Q 008337 201 GNGV-QAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEG------LQGEEVHQPLHLFLS 273 (569)
Q Consensus 201 ~~G~-k~~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~------~~g~EsdEPLHV~Is 273 (569)
.+ ..+++|||||+++||+|||+|+||||||+|+|+||+||||||+||||||++... .....++|||||+|+
T Consensus 133 --k~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Is 210 (554)
T KOG0119|consen 133 --KPPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLIS 210 (554)
T ss_pred --CcccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEe
Confidence 43 268899999999999999999999999999999999999999999999997422 112237899999999
Q ss_pred eCCHHHHHHHHHHHHHHHHH
Q 008337 274 SNNPKSLEEAKRLAENLLDT 293 (569)
Q Consensus 274 a~~~e~v~~Ak~LiEnLL~t 293 (569)
++++|+|++|+++||+||..
T Consensus 211 adt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 211 ADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred cchHHHHHHHHHHHHHHHHh
Confidence 99999999999999999996
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=99.92 E-value=1.3e-25 Score=202.05 Aligned_cols=96 Identities=22% Similarity=0.393 Sum_probs=86.6
Q ss_pred eeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCC-------CCCCCCCCCcEEEEEeCC--HH
Q 008337 208 STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEG-------LQGEEVHQPLHLFLSSNN--PK 278 (569)
Q Consensus 208 qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~-------~~g~EsdEPLHV~Isa~~--~e 278 (569)
++|||||++.||+|||+|+||||+|+|+|+|++||||+|.|||+||++.+. ...++.+|||||+|++++ .+
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 479999999999999999999999999999999999999999999998653 345678999999999999 99
Q ss_pred HHHHHHHHHHHHHHHHHHh-hccccc
Q 008337 279 SLEEAKRLAENLLDTISAE-CGASRV 303 (569)
Q Consensus 279 ~v~~Ak~LiEnLL~tV~eE-~~~fr~ 303 (569)
.+++|+++|++||..+.++ .+.++.
T Consensus 81 ~~~~A~~~I~~ll~~~~~~~~~~~k~ 106 (120)
T cd02395 81 ALAKAVEAIEELLKPAIEGGNDELKR 106 (120)
T ss_pred HHHHHHHHHHHHhccCCCccchHHHH
Confidence 9999999999999999877 444443
No 4
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=99.86 E-value=6.3e-22 Score=197.65 Aligned_cols=127 Identities=23% Similarity=0.345 Sum_probs=98.1
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCccc---cCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEe
Q 008337 173 LAVDHAAAMVEEMLKQGHAGFPTLQT---VMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLR 249 (569)
Q Consensus 173 ~aVdrA~alIeEIIKE~p~~~pp~~~---p~~~G~k~~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IR 249 (569)
+.++..+.+|.-.+.+.....+...+ .........++|||||++.||+|||+||||||+|+++|+||+||||||+||
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 46777777777777653222222111 111122468899999999999999999999999999999999999999999
Q ss_pred eccCCCCC-------CCC-CCCCCCCcEEEEEeCCHHH-----HHHHHHHHHHHHHHHHHhhc
Q 008337 250 GRGSGNSE-------GLQ-GEEVHQPLHLFLSSNNPKS-----LEEAKRLAENLLDTISAECG 299 (569)
Q Consensus 250 GRGSg~~E-------~~~-g~EsdEPLHV~Isa~~~e~-----v~~Ak~LiEnLL~tV~eE~~ 299 (569)
||||++.. +.. .+..+|||||+|++..+.. |..|.+.|+.||.++.++..
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 99999731 222 2348899999999888764 66889999999999999887
No 5
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.83 E-value=9.2e-21 Score=185.13 Aligned_cols=182 Identities=13% Similarity=0.095 Sum_probs=140.5
Q ss_pred eCCCCcccchhccchh-----HHHHHHHHhCCeEeeeccccCCCC--CCCCCCCeEEEEEeccchhhHHHHHHHHHHHHH
Q 008337 108 INDSESSVRYKLTKRH-----TQEEIQKCTGAVVITRGKYRLPNA--PPDGEKPLYLHISAGAHLKETAERILAVDHAAA 180 (569)
Q Consensus 108 INDlPq~~R~~LTKg~-----Tq~eIqe~TGA~VtTRGrY~PPgk--~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~a 180 (569)
.|.||..+--.||.-+ ....+.|.|-..-+ +-++|+.. ..+..+|-|..|.-..++.+.+.++++.|+..-
T Consensus 47 ~~~l~s~i~~~lt~eqi~~y~~~~r~~eit~Klrt--~d~Vp~~re~Rspsppp~yd~~GrRlntre~ry~kkLeder~~ 124 (269)
T COG5176 47 FNSLPSKISGALTREQIYSYQVMMRPFEITEKLRT--PDGVPSKRELRSPSPPPRYDEIGRRLNTREARYNKKLEDERLW 124 (269)
T ss_pred hhcchhHhhhhhhHHHHHHHHHhccHhhhhhhhcC--CCCCCchhhccCCCCCcchhHHhhhhhHHHHHHhhhhhHHHHH
Confidence 4667766655665432 12223333332222 23356653 568899999999988887788888899999999
Q ss_pred HHHHHHHcCCCCCCCccccCCCCc-ccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCC
Q 008337 181 MVEEMLKQGHAGFPTLQTVMGNGV-QAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGL 259 (569)
Q Consensus 181 lIeEIIKE~p~~~pp~~~p~~~G~-k~~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~ 259 (569)
++++.++.-+.++.+ ++|.+ ..+++|||||+++||+.||+|+||||+|+|+|++|..|+|||.|||+||.+. +.
T Consensus 125 l~era~k~lp~fv~p----~dy~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKe-gk 199 (269)
T COG5176 125 LKERAQKILPRFVLP----NDYIRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKE-GK 199 (269)
T ss_pred HHHHHHHhcCcccCC----ccccCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccccccc-Cc
Confidence 999999988777744 34433 5688999999999999999999999999999999999999999999999873 21
Q ss_pred C-------CCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHH
Q 008337 260 Q-------GEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISA 296 (569)
Q Consensus 260 ~-------g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~tV~e 296 (569)
. .....++||++|+++.++++.+++++|.+.|.+.+.
T Consensus 200 ~ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n~I~~a~~ 243 (269)
T COG5176 200 ISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARR 243 (269)
T ss_pred ccccCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHHHHHHHhc
Confidence 1 112557899999999999999999999999988754
No 6
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=99.15 E-value=2.5e-11 Score=127.96 Aligned_cols=178 Identities=21% Similarity=0.328 Sum_probs=133.9
Q ss_pred hhHHHHHHHHhCCeEeeeccccCCCCC---CCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCCccc
Q 008337 122 RHTQEEIQKCTGAVVITRGKYRLPNAP---PDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQT 198 (569)
Q Consensus 122 g~Tq~eIqe~TGA~VtTRGrY~PPgk~---~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alIeEIIKE~p~~~pp~~~ 198 (569)
-.++..|+-++++.+..||++----++ .+..-|.|++|.+.+- +.+..|..+|..++..
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 457888999999999999998655453 3556899999999974 4566777666665442
Q ss_pred cCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHH
Q 008337 199 VMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPK 278 (569)
Q Consensus 199 p~~~G~k~~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e 278 (569)
+||-+. ..|| .-.|.||-|.|.|||+.+|-.+++|+|.||+|+++.+++++++|.||||...++.
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 222211 1222 2257899999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccccccccccccCCCchhhcccccCcCcccccCcccchhhcccc
Q 008337 279 SLEEAKRLAENLLDTISAECGASRVSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTV 343 (569)
Q Consensus 279 ~v~~Ak~LiEnLL~tV~eE~~~fr~~~~k~y~avPppq~~l~Gv~~s~~~~~~~~~~~~~~~~~~ 343 (569)
.|+.|+-||++||..|..+|..|+. .||. .+|-+.-+---.+|..+.+.|-.+-
T Consensus 361 ~~~~~~~~~~~~i~~v~~qy~~~~~---------qp~~--~~~~~~~~~~~~p~~~~~~~~~~~~ 414 (531)
T KOG1960|consen 361 AIQRAKVLCEDLIASVHQQYKAWKS---------QPKD--RDQNQGNRAYNPPNRNQAFSARDSR 414 (531)
T ss_pred hhhhhhhcccccCCcccccCccccc---------CCCc--ccccCCCCCCCCCCccccccCCCCC
Confidence 9999999999999999999988763 2222 2333333444445555555444443
No 7
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.12 E-value=1.8e-09 Score=118.28 Aligned_cols=166 Identities=20% Similarity=0.292 Sum_probs=121.3
Q ss_pred CcccEEEEEEeCCCCcccchhccc-hhHHHHHHHHhCCeEee--eccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHH
Q 008337 98 DELIIAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVIT--RGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILA 174 (569)
Q Consensus 98 de~~f~aEIEINDlPq~~R~~LTK-g~Tq~eIqe~TGA~VtT--RGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~a 174 (569)
+....+.||.|-+-. |-..+.| |+|++.++|++|+.+.. .| .......||| .|+|.. ..
T Consensus 135 ~~~~ttqeI~IPa~k--~GlIIGKgGETikqlqe~sg~k~i~iqd~-----~~~~~~~Kpl--ritGdp---------~~ 196 (600)
T KOG1676|consen 135 GSVETTQEILIPANK--CGLIIGKGGETIKQLQEQSGVKMILVQDG-----SIATGADKPL--RITGDP---------DK 196 (600)
T ss_pred CccceeeeeccCccc--eeeEeccCccHHHHHHhhcCCceEEEecC-----CcCCCCCCce--eecCCH---------HH
Confidence 344467788887776 8888887 99999999999988653 22 1233468888 788875 47
Q ss_pred HHHHHHHHHHHHHcCCCCCCCccccCCCCcc-cceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccC
Q 008337 175 VDHAAAMVEEMLKQGHAGFPTLQTVMGNGVQ-AMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGS 253 (569)
Q Consensus 175 VdrA~alIeEIIKE~p~~~pp~~~p~~~G~k-~~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGS 253 (569)
|+.|..+|.++|+++-.-.+... ..+|.. --++.+-|. +|.+ -||.|||-+|.|||+|+.|||+||+|+=.
T Consensus 197 ve~a~~lV~dil~e~~~~~~g~~--~~~g~~~g~~~~~~V~---VPr~-~VG~IIGkgGE~IKklq~etG~KIQfkpD-- 268 (600)
T KOG1676|consen 197 VEQAKQLVADILREEDDEVPGSG--GHAGVRGGGSATREVK---VPRS-KVGIIIGKGGEMIKKLQNETGAKIQFKPD-- 268 (600)
T ss_pred HHHHHHHHHHHHHhcccCCCccc--cccCcCccccceeEEe---cccc-ceeeEEecCchHHHHHhhccCceeEeecC--
Confidence 99999999999997532221111 222221 122345444 4676 79999999999999999999999999822
Q ss_pred CCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHh
Q 008337 254 GNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAE 297 (569)
Q Consensus 254 g~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~tV~eE 297 (569)
. +..-|+..+..-.+.+.++.|.+||.+||..+.+.
T Consensus 269 ------d--~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 269 ------D--DPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred ------C--CCCCccceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence 1 11345677777788999999999999999999877
No 8
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=99.09 E-value=3.6e-11 Score=137.50 Aligned_cols=82 Identities=32% Similarity=0.516 Sum_probs=76.9
Q ss_pred ccEEEEEEeCCCCcccchhccchhHHHHHHHHhCCeEeeeccccCCCC-CCCCCCCeEEEEEeccchhhHHHHHHHHHHH
Q 008337 100 LIIAREIVINDSESSVRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNA-PPDGEKPLYLHISAGAHLKETAERILAVDHA 178 (569)
Q Consensus 100 ~~f~aEIEINDlPq~~R~~LTKg~Tq~eIqe~TGA~VtTRGrY~PPgk-~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA 178 (569)
..|.++++||||||++||++|..+++..|.+.+++.|+|||.|||+++ +.++|++|||+|+|.++ ..|.+|
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 358999999999999999999999999999999999999999999998 67899999999999875 689999
Q ss_pred HHHHHHHHHcC
Q 008337 179 AAMVEEMLKQG 189 (569)
Q Consensus 179 ~alIeEIIKE~ 189 (569)
+..++++++++
T Consensus 968 ~~e~~r~l~e~ 978 (997)
T KOG0334|consen 968 IEELERLLEEE 978 (997)
T ss_pred HHHHHHHHHHH
Confidence 99999988876
No 9
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.80 E-value=1.9e-08 Score=96.28 Aligned_cols=145 Identities=19% Similarity=0.214 Sum_probs=96.1
Q ss_pred EEEEEEeCCCCcccchhccc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEE---eccchhhHHHHHHHHHH
Q 008337 102 IAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHIS---AGAHLKETAERILAVDH 177 (569)
Q Consensus 102 f~aEIEINDlPq~~R~~LTK-g~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ie---g~te~kdTaERi~aVdr 177 (569)
+...+.|..-. .+..+.+ |+++..|+++||+.|...- .+... .|. +.+ + .++++
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 45566665444 5667775 8999999999999987643 12333 455 333 2 58999
Q ss_pred HHHHHHHHHHcCCCCCCCccccCCCCcccceeEEEecCCCC-C---CC-ceeEEEeCCCchhHHHHHHhhCcEEEEeecc
Q 008337 178 AAAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDAD-A---SL-NIAARIRGPNDQYINHIMNETGATVLLRGRG 252 (569)
Q Consensus 178 A~alIeEIIKE~p~~~pp~~~p~~~G~k~~qeKI~Ipld~~-P---~F-NfvgrIIGPrGstlK~Iq~ETGaKI~IRGRG 252 (569)
|+++|+.++.. +.++..+- -.|--+.-+.+ .+.++ . .| ..+|+|||++|.++|.||..|||+|+|-|+
T Consensus 61 A~~~I~ai~~g---f~~e~A~~-l~gd~y~~~Vi--~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~- 133 (180)
T PRK13763 61 ARDIVKAIGRG---FSPEKALR-LLDDDYVLEVI--DLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGK- 133 (180)
T ss_pred HHHHHHHHhcC---CCHHHHHH-HhCCCceEEEE--EhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCC-
Confidence 99999998773 11110000 00001111111 11222 0 01 279999999999999999999999999643
Q ss_pred CCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 008337 253 SGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 292 (569)
Q Consensus 253 Sg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~ 292 (569)
.++|.| ++++++.|++.++.|++
T Consensus 134 ----------------~v~i~G-~~~~~~~A~~~I~~li~ 156 (180)
T PRK13763 134 ----------------TVAIIG-DPEQVEIAREAIEMLIE 156 (180)
T ss_pred ----------------EEEEEe-CHHHHHHHHHHHHHHHc
Confidence 277776 99999999999999984
No 10
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.79 E-value=1.5e-08 Score=96.17 Aligned_cols=133 Identities=20% Similarity=0.207 Sum_probs=88.7
Q ss_pred chhcc-chhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEE--EeccchhhHHHHHHHHHHHHHHHHHHHHcCCCC
Q 008337 116 RYKLT-KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHI--SAGAHLKETAERILAVDHAAAMVEEMLKQGHAG 192 (569)
Q Consensus 116 R~~LT-Kg~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~I--eg~te~kdTaERi~aVdrA~alIeEIIKE~p~~ 192 (569)
+-.+. .|+++..|+++||+.|...- ++. .+.| .+.+ + .++++|+++|+.+...-.
T Consensus 10 g~vIG~gG~~Ik~I~~~tgv~I~Id~----------~~g--~V~I~~~t~d--~------~~i~kA~~~I~~i~~gf~-- 67 (172)
T TIGR03665 10 GVLIGKGGETKKEIEERTGVKLDIDS----------ETG--EVKIEEEDED--P------LAVMKAREVVKAIGRGFS-- 67 (172)
T ss_pred hhHhCCchhHHHHHHHHhCcEEEEEc----------CCc--eEEEecCCCC--H------HHHHHHHHHHHHHHcCCC--
Confidence 33444 49999999999999987652 112 3455 2332 2 589999999999766411
Q ss_pred CCCccccCCCCcccceeEEEecCCCC--C--CC-ceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCC
Q 008337 193 FPTLQTVMGNGVQAMSTSVFLGFDAD--A--SL-NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQP 267 (569)
Q Consensus 193 ~pp~~~p~~~G~k~~qeKI~Ipld~~--P--~F-NfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEP 267 (569)
++..+- -.+--+.-+ | |.+.++ . .| ..+|+|||++|.+++.||..|||+|+|-|
T Consensus 68 -~e~A~~-l~gd~y~~~-V-i~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----------------- 126 (172)
T TIGR03665 68 -PEKALK-LLDDDYMLE-V-IDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----------------- 126 (172)
T ss_pred -HHHHHH-hcCCcceEE-E-EEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC-----------------
Confidence 110000 000011111 2 222221 0 01 27999999999999999999999999974
Q ss_pred cEEEEEeCCHHHHHHHHHHHHHHHH
Q 008337 268 LHLFLSSNNPKSLEEAKRLAENLLD 292 (569)
Q Consensus 268 LHV~Isa~~~e~v~~Ak~LiEnLL~ 292 (569)
=.|+|.| ++++++.|++++++||+
T Consensus 127 ~~v~i~G-~~~~~~~A~~~i~~li~ 150 (172)
T TIGR03665 127 KTVGIIG-DPEQVQIAREAIEMLIE 150 (172)
T ss_pred CEEEEEC-CHHHHHHHHHHHHHHHc
Confidence 2588999 99999999999999994
No 11
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.56 E-value=2.3e-06 Score=94.57 Aligned_cols=155 Identities=21% Similarity=0.347 Sum_probs=110.3
Q ss_pred EEEEeCCCCcccchhccc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHH
Q 008337 104 REIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 182 (569)
Q Consensus 104 aEIEINDlPq~~R~~LTK-g~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alI 182 (569)
.+|.|--+ +|-.+|.| |++++.|+.+||+.| +|+|+..++.-||+| +|-|.. ..|++|.++|
T Consensus 232 ~~V~VPr~--~VG~IIGkgGE~IKklq~etG~KI----QfkpDd~p~speR~~--~IiG~~---------d~ie~Aa~lI 294 (600)
T KOG1676|consen 232 REVKVPRS--KVGIIIGKGGEMIKKLQNETGAKI----QFKPDDDPSSPERPA--QIIGTV---------DQIEHAAELI 294 (600)
T ss_pred eEEecccc--ceeeEEecCchHHHHHhhccCcee----EeecCCCCCCcccee--eeecCH---------HHHHHHHHHH
Confidence 34444433 36777777 999999999999999 778888877778988 788875 3688999999
Q ss_pred HHHHHcCCCCCCCccccCCCCcccc--eeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCC
Q 008337 183 EEMLKQGHAGFPTLQTVMGNGVQAM--STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQ 260 (569)
Q Consensus 183 eEIIKE~p~~~pp~~~p~~~G~k~~--qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~ 260 (569)
.+||.+......-. +..|.-.. +--+-||-+ =.|+|||++|.|||.|..|+||++.|-=.
T Consensus 295 ~eii~~~~~~~~~~---~~~G~P~~~~~fy~~VPa~------KcGLvIGrGGEtIK~in~qSGA~~el~r~--------- 356 (600)
T KOG1676|consen 295 NEIIAEAEAGAGGG---MGGGAPGLVAQFYMKVPAD------KCGLVIGRGGETIKQINQQSGARCELSRQ--------- 356 (600)
T ss_pred HHHHHHHhccCCCC---cCCCCccceeeEEEecccc------ccccccCCCccchhhhcccCCccccccCC---------
Confidence 99998752211000 11121111 222224433 47899999999999999999999866311
Q ss_pred CCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHH
Q 008337 261 GEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDT 293 (569)
Q Consensus 261 g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~t 293 (569)
..-.+.+..+++.-.++.+|+.|+.||++-+..
T Consensus 357 ~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~ 389 (600)
T KOG1676|consen 357 PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGD 389 (600)
T ss_pred CCCCCccceEEEEecCcccchHHHHHHHHHhcc
Confidence 122456688899999999999999999875543
No 12
>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=98.49 E-value=4e-07 Score=73.14 Aligned_cols=58 Identities=21% Similarity=0.403 Sum_probs=48.9
Q ss_pred eEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 008337 209 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 288 (569)
Q Consensus 209 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE 288 (569)
+.+.||.+ ++|+|||++|+++|.|+++|||+|.|-- .-.|.|+|.+.+++++|+++++
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 45666643 7899999999999999999999998742 1259999999999999999875
No 13
>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=98.47 E-value=5.6e-07 Score=70.04 Aligned_cols=63 Identities=27% Similarity=0.393 Sum_probs=50.6
Q ss_pred eEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 008337 209 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 288 (569)
Q Consensus 209 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE 288 (569)
.+|.||. +++++|||++|.++++|+++|||+|.|...+. ..+...|.|.|. .+++.+|+.+++
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 4567774 58999999999999999999999999986533 234566888887 788888888763
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=98.38 E-value=1.7e-07 Score=73.36 Aligned_cols=59 Identities=22% Similarity=0.361 Sum_probs=49.2
Q ss_pred eEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 008337 209 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 287 (569)
Q Consensus 209 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~Li 287 (569)
.+|.||- +++|+|||++|.++++|+++|||+|.|... ++.-.|.|+| +.+++++|+++|
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 3555652 388999999999999999999999999644 1446899999 999999999986
No 15
>smart00322 KH K homology RNA-binding domain.
Probab=98.36 E-value=2.1e-06 Score=65.36 Aligned_cols=66 Identities=23% Similarity=0.341 Sum_probs=54.3
Q ss_pred ceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 008337 207 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 286 (569)
Q Consensus 207 ~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~L 286 (569)
....|+|+. +++|+|||++|.++++|+++|||+|.+.+.++ ....+.|.|. .+.+..|+.+
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 58899999999999999999999999986533 3356888888 8999999999
Q ss_pred HHHHH
Q 008337 287 AENLL 291 (569)
Q Consensus 287 iEnLL 291 (569)
+++++
T Consensus 64 i~~~~ 68 (69)
T smart00322 64 ILEIL 68 (69)
T ss_pred HHHHh
Confidence 98876
No 16
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.17 E-value=3.1e-06 Score=66.72 Aligned_cols=53 Identities=23% Similarity=0.337 Sum_probs=45.1
Q ss_pred ceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 008337 222 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 287 (569)
Q Consensus 222 NfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~Li 287 (569)
.++|.|||++|.++++|+++|||+|.|-..+ +..-+|.|+|. .+++.+|++++
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 3789999999999999999999999997552 23457899999 78999998876
No 17
>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=98.07 E-value=1.4e-05 Score=64.32 Aligned_cols=62 Identities=21% Similarity=0.217 Sum_probs=45.1
Q ss_pred EEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 008337 210 SVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 287 (569)
Q Consensus 210 KI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~Li 287 (569)
++.||.+ .+|+|||.+|.++++|+++|||+|.|--... .....-++....+.+++++|++||
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 RLLVPSS------QAGSIIGKGGSTIKEIREETGAKIRVSKSVL----------PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred EEEECHH------HcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----------CCCCceEEEEEeCHHHHHHHHHhh
Confidence 5566633 8899999999999999999999999953211 112233444445599999999886
No 18
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.88 E-value=0.00069 Score=71.53 Aligned_cols=162 Identities=16% Similarity=0.187 Sum_probs=102.8
Q ss_pred EEEEEEeCCCCcccchhccc-hhHHHHHHHHhCCeEee-ecc-ccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHH
Q 008337 102 IAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVIT-RGK-YRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHA 178 (569)
Q Consensus 102 f~aEIEINDlPq~~R~~LTK-g~Tq~eIqe~TGA~VtT-RGr-Y~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA 178 (569)
++-.|-|-.+- +--.|.| |+|+.++|.+|||.|-. |-+ ||| + ..|| ..+|+|..+ +|..-
T Consensus 39 y~ikvLips~A--aGsIIGKGG~ti~~lqk~tgariklSks~dfyP-G---TTeR--vcli~Gt~e---------ai~av 101 (402)
T KOG2191|consen 39 YFLKVLIPSYA--AGSIIGKGGQTIVQLQKETGARIKLSKSKDFYP-G---TTER--VCLIQGTVE---------ALNAV 101 (402)
T ss_pred eEEEEEeeccc--ccceeccchHHHHHHHhccCcEEEeccccccCC-C---ccce--EEEEeccHH---------HHHHH
Confidence 66677777776 6778888 89999999999999865 322 331 1 3454 458999752 44444
Q ss_pred HHHHHHHHHcCCCCCCC-ccc-cCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEe-eccCCC
Q 008337 179 AAMVEEMLKQGHAGFPT-LQT-VMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLR-GRGSGN 255 (569)
Q Consensus 179 ~alIeEIIKE~p~~~pp-~~~-p~~~G~k~~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IR-GRGSg~ 255 (569)
++.|.+.|.+.+....- .+. ....--+-.+-||.||-. -.|.|||++|.|+|.|++|+||-|+|- =+-.+.
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 44455544444322111 000 000000234577878732 678999999999999999999999997 221111
Q ss_pred CCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhh
Q 008337 256 SEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 298 (569)
Q Consensus 256 ~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~tV~eE~ 298 (569)
. ---.|...+.+++++.+|++|| |++|.++-
T Consensus 176 ----s-----Lqervvt~sge~e~~~~A~~~I---L~Ki~eDp 206 (402)
T KOG2191|consen 176 ----S-----LQERVVTVSGEPEQNMKAVSLI---LQKIQEDP 206 (402)
T ss_pred ----c-----ceeEEEEecCCHHHHHHHHHHH---HHHhhcCC
Confidence 1 1124666688889998887765 66777764
No 19
>PF13014 KH_3: KH domain
Probab=97.65 E-value=4.1e-05 Score=57.16 Aligned_cols=28 Identities=32% Similarity=0.455 Sum_probs=26.2
Q ss_pred eeEEEeCCCchhHHHHHHhhCcEEEEee
Q 008337 223 IAARIRGPNDQYINHIMNETGATVLLRG 250 (569)
Q Consensus 223 fvgrIIGPrGstlK~Iq~ETGaKI~IRG 250 (569)
++|.|||++|.++++|+++|||+|.|--
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 5789999999999999999999999975
No 20
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.43 E-value=0.00049 Score=74.45 Aligned_cols=137 Identities=15% Similarity=0.182 Sum_probs=85.5
Q ss_pred chhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCCccccC
Q 008337 121 KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQTVM 200 (569)
Q Consensus 121 Kg~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alIeEIIKE~p~~~pp~~~p~ 200 (569)
.|.|+++|...|-+.|-+-- -......|+.|-+|-+.. ...+|..+|-|+|..+-.
T Consensus 217 eG~TIknItkqTqsriD~hr----ken~Gaaek~itvh~tpE-----------g~s~Ac~~ILeimqkEA~--------- 272 (584)
T KOG2193|consen 217 EGATIKNITKQTQSRIDVHR----KENAGAAEKIITVHSTPE-----------GTSKACKMILEIMQKEAV--------- 272 (584)
T ss_pred CCccccCcchhhhheeeeee----cccCCcccCceEEecCcc-----------chHHHHHHHHHHHHHhhh---------
Confidence 38999999999888874311 111236689887665442 355677778888865411
Q ss_pred CCCcccceeEE--EecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHH
Q 008337 201 GNGVQAMSTSV--FLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPK 278 (569)
Q Consensus 201 ~~G~k~~qeKI--~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e 278 (569)
.+|+ .||++-.---||+|||||..|.+||+|+++||+||.|-- +.|-. + .+-.--+.|.| +-|
T Consensus 273 -------~~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~----lqels-~--ynpERTItVkG-siE 337 (584)
T KOG2193|consen 273 -------DDKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISK----LQELS-L--YNPERTITVKG-SIE 337 (584)
T ss_pred -------ccchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeee----hhhhc-c--cCccceEEecc-cHH
Confidence 1122 245553444569999999999999999999999999852 22210 0 11123456666 555
Q ss_pred HHHHHHHHHHHHHHHHHHhhc
Q 008337 279 SLEEAKRLAENLLDTISAECG 299 (569)
Q Consensus 279 ~v~~Ak~LiEnLL~tV~eE~~ 299 (569)
.+.+|.. +++..+++-|.
T Consensus 338 ac~~AE~---eImkKlre~yE 355 (584)
T KOG2193|consen 338 ACVQAEA---EIMKKLRECYE 355 (584)
T ss_pred HHHHHHH---HHHHHHHHHHh
Confidence 5555544 44556666664
No 21
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.40 E-value=0.00031 Score=67.58 Aligned_cols=63 Identities=13% Similarity=0.192 Sum_probs=53.3
Q ss_pred eEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEE---eCCHHHHHHHHH
Q 008337 209 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLS---SNNPKSLEEAKR 285 (569)
Q Consensus 209 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Is---a~~~e~v~~Ak~ 285 (569)
..+.||.+ -+|.|||++|.++|.|+++|||+|.|.-. .-.|.|. +.|++.+++|++
T Consensus 5 ~~i~IP~~------kig~iIG~gGk~Ik~I~e~tg~~I~i~~~---------------~g~V~I~~~~~~d~~~i~kA~~ 63 (180)
T PRK13763 5 EYVKIPKD------RIGVLIGKKGETKKEIEERTGVKLEIDSE---------------TGEVIIEPTDGEDPLAVLKARD 63 (180)
T ss_pred EEEEcCHH------HhhhHhccchhHHHHHHHHHCcEEEEECC---------------CCeEEEEeCCCCCHHHHHHHHH
Confidence 45666643 68899999999999999999999999743 1367787 889999999999
Q ss_pred HHHHHHH
Q 008337 286 LAENLLD 292 (569)
Q Consensus 286 LiEnLL~ 292 (569)
+++.|+.
T Consensus 64 ~I~ai~~ 70 (180)
T PRK13763 64 IVKAIGR 70 (180)
T ss_pred HHHHHhc
Confidence 9999987
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=97.17 E-value=0.00048 Score=65.74 Aligned_cols=55 Identities=11% Similarity=0.184 Sum_probs=48.3
Q ss_pred eeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEE--EeCCHHHHHHHHHHHHHHHH
Q 008337 223 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFL--SSNNPKSLEEAKRLAENLLD 292 (569)
Q Consensus 223 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~I--sa~~~e~v~~Ak~LiEnLL~ 292 (569)
.+|.|||++|.++|.|+++|||+|.|--. .=.|.| .+.|++.+.+|+++++.|..
T Consensus 8 kig~vIG~gG~~Ik~I~~~tgv~I~Id~~---------------~g~V~I~~~t~d~~~i~kA~~~I~~i~~ 64 (172)
T TIGR03665 8 RIGVLIGKGGETKKEIEERTGVKLDIDSE---------------TGEVKIEEEDEDPLAVMKAREVVKAIGR 64 (172)
T ss_pred HhhhHhCCchhHHHHHHHHhCcEEEEEcC---------------CceEEEecCCCCHHHHHHHHHHHHHHHc
Confidence 68899999999999999999999999722 125777 78999999999999999877
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=97.17 E-value=0.0012 Score=75.51 Aligned_cols=63 Identities=22% Similarity=0.411 Sum_probs=55.0
Q ss_pred eEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 008337 209 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 288 (569)
Q Consensus 209 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE 288 (569)
+.+.|+.+ -+|.||||+|.++|.|+++|||+|-|- +.=+|.|.+.+.+++++|+++|+
T Consensus 580 ~~~~I~~~------ki~~vIG~gGk~I~~i~~~tg~~Idi~----------------d~G~V~I~a~d~~~~~~A~~~I~ 637 (719)
T TIGR02696 580 ITVKIPVD------KIGEVIGPKGKMINQIQDETGAEISIE----------------DDGTVYIGAADGPSAEAARAMIN 637 (719)
T ss_pred EEEEeChH------HhhheeCCCcHhHHHHHHHHCCEEEEe----------------cCcEEEEEeCCHHHHHHHHHHHH
Confidence 55667644 688999999999999999999999885 23579999999999999999999
Q ss_pred HHHHH
Q 008337 289 NLLDT 293 (569)
Q Consensus 289 nLL~t 293 (569)
+|+..
T Consensus 638 ~i~~~ 642 (719)
T TIGR02696 638 AIANP 642 (719)
T ss_pred HhhCc
Confidence 99985
No 24
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.12 E-value=0.00083 Score=66.26 Aligned_cols=145 Identities=17% Similarity=0.217 Sum_probs=87.5
Q ss_pred EEeCCCCcccchhccc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHH
Q 008337 106 IVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEE 184 (569)
Q Consensus 106 IEINDlPq~~R~~LTK-g~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alIeE 184 (569)
|.|-..+ .-+++.+ |++-..|.+.+|+.++.-. .-.+.-|...-.+.|. .++.+|.+.|+-
T Consensus 12 v~iPk~R--~~~lig~~g~v~k~ie~~~~~~~~iD~------------~~~~V~i~~~~~t~Dp----~~~~ka~d~VkA 73 (194)
T COG1094 12 VKIPKDR--IGVLIGKWGEVKKAIEEKTGVKLRIDS------------KTGSVTIRTTRKTEDP----LALLKARDVVKA 73 (194)
T ss_pred eecCchh--heeeecccccchHHHHhhcCeEEEEEC------------CCCeEEEEecCCCCCh----HHHHHHHHHHHH
Confidence 4444433 3344443 8899999999999987532 1122233332111121 245555555554
Q ss_pred HHHcCCCCCCCccccCCCCccccee---EEEecCCCCCC-----Cc-eeEEEeCCCchhHHHHHHhhCcEEEEeeccCCC
Q 008337 185 MLKQGHAGFPTLQTVMGNGVQAMST---SVFLGFDADAS-----LN-IAARIRGPNDQYINHIMNETGATVLLRGRGSGN 255 (569)
Q Consensus 185 IIKE~p~~~pp~~~p~~~G~k~~qe---KI~Ipld~~P~-----FN-fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~ 255 (569)
+ . ..+.++.. .+.+++ +.-|.+.++-+ |- .+|||||++|.|.+.||.-|||.|.|.|+
T Consensus 74 I-g--rGF~pe~A------~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~---- 140 (194)
T COG1094 74 I-G--RGFPPEKA------LKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK---- 140 (194)
T ss_pred H-h--cCCCHHHH------HHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc----
Confidence 3 1 11221110 011111 12233333211 22 78999999999999999999999999987
Q ss_pred CCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q 008337 256 SEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTIS 295 (569)
Q Consensus 256 ~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~tV~ 295 (569)
+|.|.| ++++++.|++.||.||+...
T Consensus 141 -------------tVaiiG-~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 141 -------------TVAIIG-GFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred -------------EEEEec-ChhhhHHHHHHHHHHHcCCC
Confidence 677776 58899999999999997543
No 25
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.00 E-value=0.0021 Score=73.09 Aligned_cols=99 Identities=18% Similarity=0.260 Sum_probs=71.8
Q ss_pred eEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 008337 209 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 288 (569)
Q Consensus 209 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE 288 (569)
+.+.|+.+ .+|.||||+|.++|.|++||||+|-|- +.=+|.|.+.+.+.+++|+++|+
T Consensus 553 ~~~~I~~~------kI~~vIG~gGk~Ik~I~~~tg~~I~i~----------------ddG~V~i~~~~~~~~~~a~~~I~ 610 (684)
T TIGR03591 553 ETIKINPD------KIRDVIGPGGKVIREITEETGAKIDIE----------------DDGTVKIAASDGEAAEAAIKMIE 610 (684)
T ss_pred EEEecCHH------HHHhhcCCCcHHHHHHHHHHCCEEEEe----------------cCeEEEEEECcHHHHHHHHHHHH
Confidence 45556543 788999999999999999999999984 23578899999999999999999
Q ss_pred HHHHHHHHhhcccccccccccccCCCchhhcccccCcCcccccCcccchhhcccccc
Q 008337 289 NLLDTISAECGASRVSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNL 345 (569)
Q Consensus 289 nLL~tV~eE~~~fr~~~~k~y~avPppq~~l~Gv~~s~~~~~~~~~~~~~~~~~~~~ 345 (569)
.|... + ..++.|. -.+.+|..+|..-.... ...|+.|--++
T Consensus 611 ~~~~~----~-----~~G~i~~------G~V~~I~~~GafVei~~-g~~GllHiSei 651 (684)
T TIGR03591 611 GITAE----P-----EVGKIYE------GKVVRIMDFGAFVEILP-GKDGLVHISEI 651 (684)
T ss_pred hhhcc----c-----ccCcEEE------EEEEEEeCCEEEEEECC-CcEEEEEHHHc
Confidence 99542 1 1233443 35777777774444332 25677775544
No 26
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.95 E-value=0.0044 Score=67.41 Aligned_cols=155 Identities=17% Similarity=0.212 Sum_probs=104.9
Q ss_pred EEeCCCCcccchhcc-chhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHH
Q 008337 106 IVINDSESSVRYKLT-KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEE 184 (569)
Q Consensus 106 IEINDlPq~~R~~LT-Kg~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alIeE 184 (569)
+.|-|.- +--++. ||..+++|.+++||+|-. -||+.+--.+| -..|+|+. ++.-+|...|-.
T Consensus 415 ~fiP~~~--vGAiIGkkG~hIKql~RfagASiKI----appE~pdvseR--MViItGpp---------eaqfKAQgrifg 477 (584)
T KOG2193|consen 415 MFIPAQA--VGAIIGKKGQHIKQLSRFAGASIKI----APPEIPDVSER--MVIITGPP---------EAQFKAQGRIFG 477 (584)
T ss_pred eeccHHH--HHHHHhhcchhHHHHHHhccceeee----cCCCCCCccee--EEEecCCh---------HHHHhhhhhhhh
Confidence 4454444 455565 599999999999999843 23332223344 45799986 477888899999
Q ss_pred HHHcCCCCCCCccccCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCC
Q 008337 185 MLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEV 264 (569)
Q Consensus 185 IIKE~p~~~pp~~~p~~~G~k~~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es 264 (569)
.|+|+.-+.|..+ ..+++-|-|| .+ .+|||||.+|.|++-+|+-|+|.|.|--. .++.|
T Consensus 478 KikEenf~~Pkee-------vklethirVP-----s~-~aGRvIGKGGktVnELQnlt~AeV~vPrd-------qtpdE- 536 (584)
T KOG2193|consen 478 KIKEENFFLPKEE-------VKLETHIRVP-----SS-AAGRVIGKGGKTVNELQNLTSAEVVVPRD-------QTPDE- 536 (584)
T ss_pred hhhhhccCCchhh-------heeeeeeecc-----ch-hhhhhhccccccHHHHhccccceEEcccc-------CCCCc-
Confidence 9998744443322 2455556555 55 89999999999999999999999987522 22223
Q ss_pred CCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhhc
Q 008337 265 HQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECG 299 (569)
Q Consensus 265 dEPLHV~Isa~~~e~v~~Ak~LiEnLL~tV~eE~~ 299 (569)
+|-.-|-|.| +.-....|..-+.+|+..|++..+
T Consensus 537 nd~vivriiG-hfyatq~aQrki~~iv~qvkq~~q 570 (584)
T KOG2193|consen 537 NDQVIVRIIG-HFYATQNAQRKIAHIVNQVKQSGQ 570 (584)
T ss_pred cceeeeeeec-hhhcchHHHHHHHHHHHHHHHhhh
Confidence 3333344444 445567788888889888887653
No 27
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=96.93 E-value=0.0021 Score=58.74 Aligned_cols=64 Identities=28% Similarity=0.353 Sum_probs=49.2
Q ss_pred hccchhHHHHHHHHhCCeEeeeccccCCCC----------CCCCCCCeEEEEEecc--chhhHHHHHHHHHHHHHHHHHH
Q 008337 118 KLTKRHTQEEIQKCTGAVVITRGKYRLPNA----------PPDGEKPLYLHISAGA--HLKETAERILAVDHAAAMVEEM 185 (569)
Q Consensus 118 ~LTKg~Tq~eIqe~TGA~VtTRGrY~PPgk----------~~~gEpPLYL~Ieg~t--e~kdTaERi~aVdrA~alIeEI 185 (569)
+=.+|.|+++|+++|||.|.+||+----.. ....+-||+++|++.+ + .++++|+.+|+++
T Consensus 21 IGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~--------e~~~~A~~~I~~l 92 (120)
T cd02395 21 LGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPE--------EALAKAVEAIEEL 92 (120)
T ss_pred ECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHH--------HHHHHHHHHHHHH
Confidence 334799999999999999999996311111 0124678999999987 4 5899999999999
Q ss_pred HHcC
Q 008337 186 LKQG 189 (569)
Q Consensus 186 IKE~ 189 (569)
+...
T Consensus 93 l~~~ 96 (120)
T cd02395 93 LKPA 96 (120)
T ss_pred hccC
Confidence 9843
No 28
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.91 E-value=0.0014 Score=71.94 Aligned_cols=64 Identities=27% Similarity=0.398 Sum_probs=50.2
Q ss_pred hcc-chhHHHHHHHHhCCeEeeeccc-cCCCC--------CCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHHHHH
Q 008337 118 KLT-KRHTQEEIQKCTGAVVITRGKY-RLPNA--------PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLK 187 (569)
Q Consensus 118 ~LT-Kg~Tq~eIqe~TGA~VtTRGrY-~PPgk--------~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alIeEIIK 187 (569)
+|. +|.||+.++++|||.|..||+= +-+++ ....+-+||.+|++.|+ +.|++|++.|+.+|+
T Consensus 158 iiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~--------eki~~Ai~vienli~ 229 (554)
T KOG0119|consen 158 IIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQ--------EKIKKAIAVIENLIQ 229 (554)
T ss_pred EecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchH--------HHHHHHHHHHHHHHH
Confidence 444 7999999999999999999932 11111 12346889999999986 589999999999999
Q ss_pred cC
Q 008337 188 QG 189 (569)
Q Consensus 188 E~ 189 (569)
+.
T Consensus 230 ~a 231 (554)
T KOG0119|consen 230 SA 231 (554)
T ss_pred hh
Confidence 64
No 29
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.80 E-value=0.014 Score=64.41 Aligned_cols=138 Identities=17% Similarity=0.166 Sum_probs=81.1
Q ss_pred chhccchhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEe---------ccchhhHHHHHHHHHHHHHHHHHHH
Q 008337 116 RYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISA---------GAHLKETAERILAVDHAAAMVEEML 186 (569)
Q Consensus 116 R~~LTKg~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg---------~te~kdTaERi~aVdrA~alIeEII 186 (569)
=|...||+++++|..+|++.|-+= +...+.+=--+-|.| .. .++.+|..+|-..+
T Consensus 56 ~IIGk~G~~vkkir~~t~s~i~i~-------~~~~~c~eRIiti~g~~~~~~~~~~~---------~al~ka~~~iv~~~ 119 (485)
T KOG2190|consen 56 SIIGKKGDIVKKIRKETESKIRVN-------ESLPGCPERIITITGNRVELNLSPAT---------DALFKAFDMIVFKL 119 (485)
T ss_pred eEEccCcHHHHHHhhcccccceee-------cCCCCCCcceEEEecccccccCCchH---------HHHHHHHHHHhhcc
Confidence 456667999999998777775321 111122212223555 32 35666555554443
Q ss_pred HcCCCCCCCccccCCCC---ccc-ceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCC
Q 008337 187 KQGHAGFPTLQTVMGNG---VQA-MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGE 262 (569)
Q Consensus 187 KE~p~~~pp~~~p~~~G---~k~-~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~ 262 (569)
.++..-. .+++ -++ ...++.|| .+-+|-|||.+|+.||.|.++|||+|+|-+. .+=.
T Consensus 120 ~~d~~~~------~d~~~~~~~~~v~~RLlVp------~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~---~lP~---- 180 (485)
T KOG2190|consen 120 EEDDEAA------EDNGEDASGPEVTCRLLVP------SSQVGSLIGKGGSLIKEIREETGAKIRVSSD---MLPN---- 180 (485)
T ss_pred ccccccc------ccCCccccCCceEEEEEec------hhheeeeeccCcHHHHHHHHhcCceEEecCC---CCCc----
Confidence 3221111 1111 134 45777787 4589999999999999999999999999877 2211
Q ss_pred CCCCCcEEEEEeCCHHHHHHHHHHHHHHH
Q 008337 263 EVHQPLHLFLSSNNPKSLEEAKRLAENLL 291 (569)
Q Consensus 263 EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL 291 (569)
+.|.+ |.|+ .+++.+.+|-..|-.+|
T Consensus 181 -ster~-V~Is-G~~~av~~al~~Is~~L 206 (485)
T KOG2190|consen 181 -STERA-VTIS-GEPDAVKKALVQISSRL 206 (485)
T ss_pred -cccee-EEEc-CchHHHHHHHHHHHHHH
Confidence 22334 5444 56666666655444443
No 30
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.70 E-value=0.0016 Score=76.05 Aligned_cols=131 Identities=15% Similarity=0.148 Sum_probs=85.7
Q ss_pred HHHHHHHHHHHHHH---HcC-CCCCCCccccCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcE-EE
Q 008337 173 LAVDHAAAMVEEML---KQG-HAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGAT-VL 247 (569)
Q Consensus 173 ~aVdrA~alIeEII---KE~-p~~~pp~~~p~~~G~k~~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaK-I~ 247 (569)
++++.|.+-+..++ ++. +.+... . ..+.+ .-+.+-|+.+ -+|.||||+|.+||.|++|||++ |-
T Consensus 652 eAL~~A~~g~~~Il~~M~~~i~~pr~~--~-s~~aP--~i~~~~i~~~------ki~~vIG~GGktIk~I~eetg~~~Id 720 (891)
T PLN00207 652 RALLQAKDGRKHILAEMSKCSPPPSKR--L-SKYAP--LIHIMKVKPE------KVNMIIGSGGKKVKSIIEETGVEAID 720 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhh--h-cccCC--eeEEEEcCHH------HHHHHhcCCchhHHHHHHHHCCCccC
Confidence 56777766555554 332 222211 1 12222 2245556533 78899999999999999999998 66
Q ss_pred EeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhhcccccccccccccCCCchhhcccccCcCc
Q 008337 248 LRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGASRVSSCKVYNAVPPPQQLLTGIQGFGN 327 (569)
Q Consensus 248 IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~tV~eE~~~fr~~~~k~y~avPppq~~l~Gv~~s~~ 327 (569)
|+ |.-+|.|.+.|.+++++|+++|++|.... ...+.|. ..-+.+|..+|+
T Consensus 721 i~----------------ddg~V~I~a~d~~~i~~A~~~I~~l~~~~---------~vG~iy~-----~g~V~~I~~FGa 770 (891)
T PLN00207 721 TQ----------------DDGTVKITAKDLSSLEKSKAIISSLTMVP---------TVGDIYR-----NCEIKSIAPYGA 770 (891)
T ss_pred cC----------------CCeeEEEEeCCHHHHHHHHHHHHHHhcCc---------CCCcEEE-----CcEEEEEeccEE
Confidence 55 45889999999999999999999998621 1345662 024677888884
Q ss_pred ccccCcccchhhcccccc
Q 008337 328 EQKLNAGSAVILTSTVNL 345 (569)
Q Consensus 328 ~~~~~~~~~~~~~~~~~~ 345 (569)
.-..... .-||.|--.+
T Consensus 771 FVeL~~g-~EGLVHISeL 787 (891)
T PLN00207 771 FVEIAPG-REGLCHISEL 787 (891)
T ss_pred EEEeCCC-CEEEEEhhhc
Confidence 4444332 5677775544
No 31
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.74 E-value=0.011 Score=67.64 Aligned_cols=92 Identities=18% Similarity=0.250 Sum_probs=67.7
Q ss_pred ceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhhccc
Q 008337 222 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGAS 301 (569)
Q Consensus 222 NfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~tV~eE~~~f 301 (569)
+-++.+|||+|.++|.|++|||++|-|+ +.-+|.|.+.+.+.+++|+++|+.|....
T Consensus 563 ~kI~~vIG~gg~~ik~I~~~~~~~idi~----------------d~G~v~i~~~~~~~~~~a~~~I~~~~~~~------- 619 (693)
T PRK11824 563 DKIRDVIGPGGKTIREITEETGAKIDIE----------------DDGTVKIAATDGEAAEAAKERIEGITAEP------- 619 (693)
T ss_pred HHHHHHhcCCchhHHHHHHHHCCccccC----------------CCceEEEEcccHHHHHHHHHHHHHhcccC-------
Confidence 3578999999999999999999988764 34679999999999999999999998421
Q ss_pred ccccccccccCCCchhhcccccCcCcccccCcccchhhcccccc
Q 008337 302 RVSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNL 345 (569)
Q Consensus 302 r~~~~k~y~avPppq~~l~Gv~~s~~~~~~~~~~~~~~~~~~~~ 345 (569)
..++.|. -.+.+|..+|..-.... ...|+.|--++
T Consensus 620 --~vG~v~~------G~V~~I~~fGafVei~~-~~~GllhiSel 654 (693)
T PRK11824 620 --EVGEIYE------GKVVRIVDFGAFVEILP-GKDGLVHISEI 654 (693)
T ss_pred --cCCeEEE------EEEEEEECCeEEEEECC-CCEEEEEeeec
Confidence 1233443 35777777774444332 25666665444
No 32
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.49 E-value=0.018 Score=57.57 Aligned_cols=54 Identities=17% Similarity=0.290 Sum_probs=47.1
Q ss_pred eeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 008337 223 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 292 (569)
Q Consensus 223 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~ 292 (569)
++++||||+|.+++.|.++|||+|.|- . .=+|+|.+.+.+.+++|+++|++|-.
T Consensus 155 ~i~~lig~~g~~i~~l~~~~~~~I~ig-~---------------NG~VwI~~~~~~~~~~a~~~I~~~e~ 208 (235)
T PRK04163 155 KVPRVIGKKGSMINMLKEETGCDIIVG-Q---------------NGRIWIKGPDEEDEEIAIEAIKKIER 208 (235)
T ss_pred HHHhhcCCCChhHhhhhhhhCcEEEEc-C---------------CcEEEEeeCCHHHHHHHHHHHHHHHh
Confidence 788999999999999999999999883 1 14799999999999999999987543
No 33
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=95.43 E-value=0.28 Score=54.52 Aligned_cols=60 Identities=28% Similarity=0.307 Sum_probs=44.9
Q ss_pred cchhccc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHHHHHcC
Q 008337 115 VRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQG 189 (569)
Q Consensus 115 ~R~~LTK-g~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alIeEIIKE~ 189 (569)
+=.+|.| |+.+++|.+.|||.|-+-+. +.|. ..||- +.|.|.. .+|.+|+..|-.+|.+.
T Consensus 149 ~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~--V~IsG~~---------~av~~al~~Is~~L~~~ 209 (485)
T KOG2190|consen 149 VGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN---STERA--VTISGEP---------DAVKKALVQISSRLLEN 209 (485)
T ss_pred eeeeeccCcHHHHHHHHhcCceEEecCC-CCCc---cccee--EEEcCch---------HHHHHHHHHHHHHHHhc
Confidence 4456676 99999999999999987666 3333 33443 7899975 48888988888888774
No 34
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=94.87 E-value=0.027 Score=58.81 Aligned_cols=57 Identities=21% Similarity=0.339 Sum_probs=45.8
Q ss_pred eEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhh
Q 008337 224 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 298 (569)
Q Consensus 224 vgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~tV~eE~ 298 (569)
+.|||||+|+|||.||--|.|-|.+.|.- |++.|+ ..+|.++++++++.+.+|+-=|
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilVqG~T-----------------VsaiGp-fkGlkevr~IV~DcM~NiHPiY 216 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILVQGNT-----------------VSAIGP-FKGLKEVRKIVEDCMKNIHPIY 216 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEeeCcE-----------------EEeecC-cchHHHHHHHHHHHHhccchHH
Confidence 56899999999999999999999999872 333333 4678889999998888776544
No 35
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=94.60 E-value=0.14 Score=54.63 Aligned_cols=77 Identities=25% Similarity=0.265 Sum_probs=53.2
Q ss_pred ceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 008337 207 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 286 (569)
Q Consensus 207 ~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~L 286 (569)
..-||.|| . +.+|-|||.+|++|-.+|+||||+|++- |-+-|.-+.+ -.||+...+-+.|...-
T Consensus 39 y~ikvLip-----s-~AaGsIIGKGG~ti~~lqk~tgariklS-ks~dfyPGTT-------eRvcli~Gt~eai~av~-- 102 (402)
T KOG2191|consen 39 YFLKVLIP-----S-YAAGSIIGKGGQTIVQLQKETGARIKLS-KSKDFYPGTT-------ERVCLIQGTVEALNAVH-- 102 (402)
T ss_pred eEEEEEee-----c-ccccceeccchHHHHHHHhccCcEEEec-cccccCCCcc-------ceEEEEeccHHHHHHHH--
Confidence 55788887 3 3889999999999999999999999986 4333332222 24666666666666554
Q ss_pred HHHHHHHHHHhhcc
Q 008337 287 AENLLDTISAECGA 300 (569)
Q Consensus 287 iEnLL~tV~eE~~~ 300 (569)
|-++|+|+++.++
T Consensus 103 -efI~dKire~p~~ 115 (402)
T KOG2191|consen 103 -EFIADKIREKPQA 115 (402)
T ss_pred -HHHHHHHHHhHHh
Confidence 4455666666543
No 36
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=93.59 E-value=0.11 Score=55.18 Aligned_cols=64 Identities=11% Similarity=0.132 Sum_probs=55.3
Q ss_pred eeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhh
Q 008337 223 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 298 (569)
Q Consensus 223 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~tV~eE~ 298 (569)
|.|.|||-+|.+.|+|++||+|+|.|==.+. .--|+-|++...+.|.+|.+-|+-||++++..|
T Consensus 67 ~~~~lig~~g~trkkle~Etq~~i~lp~p~~------------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~s~ 130 (345)
T KOG2814|consen 67 FIGWLIGKQGKTRKKLEEETQTNIFLPRPNT------------NKEEIKIIGISRNCVIQALERIAKLIDSDRKSF 130 (345)
T ss_pred HhhhhhcccchHHHHHHHhhccceEccCCCC------------CcceEEEeehhHHHHHHHHHHHHHHHHhhhhcC
Confidence 7899999999999999999999998853311 225899999999999999999999999998444
No 37
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=93.56 E-value=0.074 Score=60.89 Aligned_cols=53 Identities=23% Similarity=0.379 Sum_probs=46.5
Q ss_pred eEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 008337 224 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 292 (569)
Q Consensus 224 vgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~ 292 (569)
++.+|||+|.+++.|..||||+|.|.-.| -|.|.+.+.+...+|+++|+++..
T Consensus 563 I~dvIG~gGk~I~~I~eetg~~IdieddG----------------tv~i~~s~~~~~~~ak~~I~~i~~ 615 (692)
T COG1185 563 IRDVIGPGGKTIKAITEETGVKIDIEDDG----------------TVKIAASDGESAKKAKERIEAITR 615 (692)
T ss_pred HhhccCCcccchhhhhhhhCcEEEecCCC----------------cEEEEecchHHHHHHHHHHHHHHh
Confidence 45789999999999999999999997443 366889999999999999999983
No 38
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=92.97 E-value=0.19 Score=56.84 Aligned_cols=58 Identities=21% Similarity=0.269 Sum_probs=48.4
Q ss_pred eeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHh
Q 008337 223 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAE 297 (569)
Q Consensus 223 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~tV~eE 297 (569)
=+..+|||+|-.+|+|+.|||+.-++ +.=|+-|-+.++..+++|+++|+.++..-+..
T Consensus 607 k~~~lIGp~G~~~kki~~EtGai~~v-----------------De~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~ 664 (760)
T KOG1067|consen 607 KRATLIGPGGVLKKKIEVETGAISQV-----------------DEGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQ 664 (760)
T ss_pred hhheeecCccceeeeEeeeccceeee-----------------cCceEEEEecCHHHHHHHHHHHHHHhcCcccc
Confidence 46689999999999999999954332 44689999999999999999999998764443
No 39
>PRK00106 hypothetical protein; Provisional
Probab=92.92 E-value=0.2 Score=56.25 Aligned_cols=60 Identities=27% Similarity=0.333 Sum_probs=51.4
Q ss_pred CCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 008337 218 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 292 (569)
Q Consensus 218 ~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~ 292 (569)
.|+=.+.|||||-.|.|++.+|.-||+.|.|= |.|--|.|||-|+-.-+-|+...|.||.
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 35667899999999999999999999999873 5778899999999998888887766653
No 40
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=92.81 E-value=0.2 Score=55.81 Aligned_cols=60 Identities=23% Similarity=0.326 Sum_probs=50.8
Q ss_pred CCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 008337 218 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 292 (569)
Q Consensus 218 ~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~ 292 (569)
.|+=.+.|||||-.|-|++.+|+-||+.|.|= |.|=-|.|||-|+-.-+-|+..+|.||.
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 45667899999999999999999999999884 5677899999999988888877666653
No 41
>PRK12704 phosphodiesterase; Provisional
Probab=92.65 E-value=0.25 Score=55.08 Aligned_cols=59 Identities=24% Similarity=0.316 Sum_probs=49.4
Q ss_pred CCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHH
Q 008337 218 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLL 291 (569)
Q Consensus 218 ~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL 291 (569)
.|+=.+.|||||-.|-|++.+|.-||+.|.|= |.|=-|+|||-|+..-+.|+..++.|+
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 45667899999999999999999999999884 567889999999988777777665554
No 42
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=91.17 E-value=0.36 Score=53.40 Aligned_cols=63 Identities=14% Similarity=0.137 Sum_probs=45.4
Q ss_pred CceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHH-HHHHHHHHHHHHHHHHHHhhc
Q 008337 221 LNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPK-SLEEAKRLAENLLDTISAECG 299 (569)
Q Consensus 221 FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e-~v~~Ak~LiEnLL~tV~eE~~ 299 (569)
-+++|++||-+|+.||+||..|+++|+|- .+.+-+.|+-.--. .-.+|+.-++++++...+ |+
T Consensus 55 s~mvg~vigrggskik~iq~~tnt~iqii---------------~~~~e~kv~ifg~~~m~~kaka~id~~~~k~e~-yn 118 (629)
T KOG0336|consen 55 SEMVGKVIGRGGSKIKRIQNDTNTRIQII---------------KCDLEVKVTIFGINHMRKKAKASIDRGQDKDER-YN 118 (629)
T ss_pred hhhhheeeccCcchhhhhhcccceeEEEe---------------ccCceeEEEEechHHHHHHHHhhHhhhhhhhhh-cc
Confidence 36999999999999999999999999985 12244444433333 345688888888876544 53
No 43
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=89.03 E-value=1 Score=36.29 Aligned_cols=57 Identities=21% Similarity=0.244 Sum_probs=41.5
Q ss_pred EEEEeCCCCcccchhccc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHH
Q 008337 104 REIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 182 (569)
Q Consensus 104 aEIEINDlPq~~R~~LTK-g~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alI 182 (569)
..|.|..-. ++..+.+ |+++.+|+++|||.|..- . +. .+.|.|.+. .++++|+++|
T Consensus 4 ~~i~Ip~~~--ig~iIGkgG~~ik~I~~~tg~~I~i~-----~------~g--~v~I~G~~~--------~~v~~A~~~I 60 (61)
T cd02393 4 ETMKIPPDK--IRDVIGPGGKTIKKIIEETGVKIDIE-----D------DG--TVYIAASDK--------EAAEKAKKMI 60 (61)
T ss_pred EEEEeChhh--eeeeECCCchHHHHHHHHHCCEEEeC-----C------CC--EEEEEeCCH--------HHHHHHHHHh
Confidence 345554433 6778886 999999999999998642 1 11 478999753 5789998887
Q ss_pred H
Q 008337 183 E 183 (569)
Q Consensus 183 e 183 (569)
+
T Consensus 61 ~ 61 (61)
T cd02393 61 E 61 (61)
T ss_pred C
Confidence 3
No 44
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=88.85 E-value=1.1 Score=47.25 Aligned_cols=65 Identities=22% Similarity=0.361 Sum_probs=50.4
Q ss_pred eeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhh
Q 008337 223 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 298 (569)
Q Consensus 223 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~tV~eE~ 298 (569)
+-|-|||-+|.-+|+|..|+||.|.|- |+..+. +-.+.+.-.++++++.|.-|.++-+..-++.|
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 667899999999999999999988774 223232 24566667799999999999998877555544
No 45
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=87.11 E-value=3.4 Score=43.62 Aligned_cols=130 Identities=16% Similarity=0.178 Sum_probs=81.3
Q ss_pred ccc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCCcc
Q 008337 119 LTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQ 197 (569)
Q Consensus 119 LTK-g~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alIeEIIKE~p~~~pp~~ 197 (569)
+.| |+.++.+....+|.|.+-- ..-+--.|+|++.- +-|-+..++|--.|.++.....+
T Consensus 63 igkgg~nik~lr~d~na~v~vpd---------s~~peri~tisad~---------~ti~~ilk~iip~lee~f~~~~p-- 122 (390)
T KOG2192|consen 63 IGKGGKNIKALRTDYNASVSVPD---------SSGPERILTISADI---------ETIGEILKKIIPTLEEGFQLPSP-- 122 (390)
T ss_pred eccccccHHHHhhhccceeeccC---------CCCCceeEEEeccH---------HHHHHHHHHHhhhhhhCCCCCCc--
Confidence 344 6777888888888876522 12233456888863 23444444444445555443322
Q ss_pred ccCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCH
Q 008337 198 TVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNP 277 (569)
Q Consensus 198 ~p~~~G~k~~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~ 277 (569)
.+-++.|- -.++|-|||-+|+-+|.+.+.+.|++-|= .|-+.+ --..|+|++..+
T Consensus 123 ---------ce~rllih------qs~ag~iigrngskikelrekcsarlkif------t~c~p~----stdrv~l~~g~~ 177 (390)
T KOG2192|consen 123 ---------CELRLLIH------QSLAGGIIGRNGSKIKELREKCSARLKIF------TECCPH----STDRVVLIGGKP 177 (390)
T ss_pred ---------hhhhhhhh------hhhccceecccchhHHHHHHhhhhhhhhh------hccCCC----CcceEEEecCCc
Confidence 12223231 12789999999999999999998877552 333322 125789999999
Q ss_pred HHHHHHHHHHHHHHHH
Q 008337 278 KSLEEAKRLAENLLDT 293 (569)
Q Consensus 278 e~v~~Ak~LiEnLL~t 293 (569)
+.|-...+.|-+||..
T Consensus 178 k~v~~~i~~il~~i~e 193 (390)
T KOG2192|consen 178 KRVVECIKIILDLISE 193 (390)
T ss_pred chHHHHHHHHHHHhhc
Confidence 9988877777777654
No 46
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=86.96 E-value=1.7 Score=45.09 Aligned_cols=73 Identities=18% Similarity=0.241 Sum_probs=52.5
Q ss_pred chhccchhHHHHHHHHhCCeEeeeccccCCCC------CC-C----CCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHH
Q 008337 116 RYKLTKRHTQEEIQKCTGAVVITRGKYRLPNA------PP-D----GEKPLYLHISAGAHLKETAERILAVDHAAAMVEE 184 (569)
Q Consensus 116 R~~LTKg~Tq~eIqe~TGA~VtTRGrY~PPgk------~~-~----gEpPLYL~Ieg~te~kdTaERi~aVdrA~alIeE 184 (569)
|.+==+|.|+++++++|||.|.+||+--=-++ +. + =+.+|+++|+...- ++-++ ..+..|+++|++
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 44445899999999999999999997643331 11 1 16789999998752 22222 568889999999
Q ss_pred HHHcCCC
Q 008337 185 MLKQGHA 191 (569)
Q Consensus 185 IIKE~p~ 191 (569)
+|.....
T Consensus 188 lL~P~~e 194 (259)
T KOG1588|consen 188 LLVPDHE 194 (259)
T ss_pred hcCCCCC
Confidence 9976544
No 47
>PRK12705 hypothetical protein; Provisional
Probab=82.81 E-value=1.2 Score=49.96 Aligned_cols=58 Identities=28% Similarity=0.309 Sum_probs=42.6
Q ss_pred CCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHH
Q 008337 218 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENL 290 (569)
Q Consensus 218 ~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnL 290 (569)
.|+=.+.|||||-.|.|++.+|..||+.|.|- |-|=-|.|++-++..-+.|+...++|
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 45667899999999999999999999988875 23333666666666655555544444
No 48
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=82.15 E-value=1.2 Score=52.42 Aligned_cols=15 Identities=0% Similarity=0.175 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHHHcC
Q 008337 175 VDHAAAMVEEMLKQG 189 (569)
Q Consensus 175 VdrA~alIeEIIKE~ 189 (569)
..+++.+++.+|...
T Consensus 209 ~~eiIrClka~mNn~ 223 (1102)
T KOG1924|consen 209 LQEIIRCLKAFMNNK 223 (1102)
T ss_pred HHHHHHHHHHHhccc
Confidence 444555555665543
No 49
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=80.87 E-value=2.8 Score=45.02 Aligned_cols=108 Identities=17% Similarity=0.187 Sum_probs=66.4
Q ss_pred ccchhHHHHHHHHhCCeEee--eccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCCc
Q 008337 119 LTKRHTQEEIQKCTGAVVIT--RGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTL 196 (569)
Q Consensus 119 LTKg~Tq~eIqe~TGA~VtT--RGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alIeEIIKE~p~~~pp~ 196 (569)
+-+|-+++.|+.+|.+-|.| || +-|.| -++|.- ..|++|..+|...-..--...-.+
T Consensus 42 g~qg~kikalr~KTqtyi~tPsr~-----------eePiF-~vTg~~---------edv~~aRrei~saaeH~~l~~~s~ 100 (394)
T KOG2113|consen 42 GRQGCKIKALRAKTQTYIKTPSRG-----------EEPIF-PVTGRH---------EDVRRARREIPSAAEHFGLIRASR 100 (394)
T ss_pred ccCccccchhhhhhcceeccCCCC-----------CCCcc-eeccCc---------hhHHHHhhcCccccceeeeeeecc
Confidence 44577889999999988865 44 44776 455642 468888777765211100000000
Q ss_pred ccc-CCCCcc-cceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeec
Q 008337 197 QTV-MGNGVQ-AMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGR 251 (569)
Q Consensus 197 ~~p-~~~G~k-~~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGR 251 (569)
... .-++.. -.+.+.|+-+ | +.++|+++||.|.++|+||+-+..-|.--++
T Consensus 101 s~Sgg~~~~s~s~qt~sy~sv---P-~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 101 SFSGGTNGASASGQTTSYVSV---P-LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred cccCCCccccccCCCceeeec---c-ceeeeeccccccCccchheecccceEeeecc
Confidence 010 001111 3345666542 3 6799999999999999999999987765555
No 50
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=80.44 E-value=4.5 Score=31.58 Aligned_cols=49 Identities=22% Similarity=0.237 Sum_probs=37.3
Q ss_pred cchhccc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHH
Q 008337 115 VRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 182 (569)
Q Consensus 115 ~R~~LTK-g~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alI 182 (569)
+.+.+.+ |.++.+|++.|||.|..... + ..-.+.|+|.. +.|++|+++|
T Consensus 11 ~~~iIG~~G~~i~~I~~~t~~~I~i~~~---------~-~~~~v~I~G~~---------~~v~~A~~~I 60 (60)
T PF00013_consen 11 VGRIIGKKGSNIKEIEEETGVKIQIPDD---------D-ERDIVTISGSP---------EQVEKAKKMI 60 (60)
T ss_dssp HHHHHTGGGHHHHHHHHHHTSEEEEEST---------T-EEEEEEEEESH---------HHHHHHHHHH
T ss_pred cCEEECCCCCcHHHhhhhcCeEEEEcCC---------C-CcEEEEEEeCH---------HHHHHHHhhC
Confidence 5677775 99999999999999987442 2 33467899943 4788888776
No 51
>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=79.73 E-value=6 Score=31.83 Aligned_cols=52 Identities=25% Similarity=0.275 Sum_probs=36.5
Q ss_pred cchhcc-chhHHHHHHHHhCCeEeeeccccCCCC-CCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHH
Q 008337 115 VRYKLT-KRHTQEEIQKCTGAVVITRGKYRLPNA-PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 182 (569)
Q Consensus 115 ~R~~LT-Kg~Tq~eIqe~TGA~VtTRGrY~PPgk-~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alI 182 (569)
+.+.+. +|.++++|++.|||.|... +.. ..+.++- +.|+|.. +.+++|+.+|
T Consensus 11 vg~iIG~~G~~i~~i~~~tga~I~i~-----~~~~~~~~~r~--v~I~G~~---------~~v~~A~~~I 64 (65)
T cd02396 11 AGSIIGKGGSTIKEIREETGAKIRVS-----KSVLPGSTERV--VTISGKP---------SAVQKALLLI 64 (65)
T ss_pred cCeeECCCcHHHHHHHHHHCCEEEEc-----CCCCCCCCceE--EEEEeCH---------HHHHHHHHhh
Confidence 344555 4899999999999999773 222 2344453 6899975 4688888877
No 52
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=78.83 E-value=2 Score=34.67 Aligned_cols=27 Identities=11% Similarity=0.084 Sum_probs=24.3
Q ss_pred ceeEEEeCCCchhHHHHHHhhCcEEEE
Q 008337 222 NIAARIRGPNDQYINHIMNETGATVLL 248 (569)
Q Consensus 222 NfvgrIIGPrGstlK~Iq~ETGaKI~I 248 (569)
.-+|+.||.+|.+++.++..+|.+|-|
T Consensus 34 ~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 34 DQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred ccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 367899999999999999999988865
No 53
>smart00322 KH K homology RNA-binding domain.
Probab=75.76 E-value=19 Score=27.03 Aligned_cols=64 Identities=20% Similarity=0.234 Sum_probs=42.6
Q ss_pred EEEEEeCCCCcccchhcc-chhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHH
Q 008337 103 AREIVINDSESSVRYKLT-KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAM 181 (569)
Q Consensus 103 ~aEIEINDlPq~~R~~LT-Kg~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~al 181 (569)
..+|.|..-. ..+.+. +|.++++|++.||+.|...+.-. .---+.|.|.. ..+..|...
T Consensus 4 ~~~i~i~~~~--~~~liG~~G~~i~~i~~~~~~~i~~~~~~~---------~~~~v~i~g~~---------~~v~~a~~~ 63 (69)
T smart00322 4 TIEVLIPADK--VGLIIGKGGSTIKKIEEETGVKIDIPEDGS---------EERVVEITGPP---------ENVEKAAEL 63 (69)
T ss_pred EEEEEEcchh--cceeECCCchHHHHHHHHHCCEEEECCCCC---------CccEEEEEcCH---------HHHHHHHHH
Confidence 4456665533 455555 59999999999999987653111 22346788873 467778887
Q ss_pred HHHHH
Q 008337 182 VEEML 186 (569)
Q Consensus 182 IeEII 186 (569)
|.+.+
T Consensus 64 i~~~~ 68 (69)
T smart00322 64 ILEIL 68 (69)
T ss_pred HHHHh
Confidence 87765
No 54
>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=73.61 E-value=9.8 Score=29.88 Aligned_cols=58 Identities=17% Similarity=0.164 Sum_probs=39.9
Q ss_pred EEEeCCCCcccchhccc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHH
Q 008337 105 EIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 182 (569)
Q Consensus 105 EIEINDlPq~~R~~LTK-g~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alI 182 (569)
+|.|.. ...++.+.+ |.++.+|++.|||.|..- +.. +.+ -.+.|.|.. +.|..|+.+|
T Consensus 3 ~i~Vp~--~~~~~iIG~~G~~i~~i~~~~g~~I~i~-----~~~--~~~--~~v~I~G~~---------~~v~~A~~~i 61 (62)
T cd02394 3 EVEIPK--KLHRFIIGKKGSNIRKIMEETGVKIRFP-----DPG--SKS--DTITITGPK---------ENVEKAKEEI 61 (62)
T ss_pred EEEeCH--HHhhhccCCCCCcHHHHHHHhCCEEEcC-----CCC--CCC--CEEEEEcCH---------HHHHHHHHHh
Confidence 445544 346778885 899999999999999553 222 223 345799974 4788888776
No 55
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=72.97 E-value=13 Score=43.75 Aligned_cols=108 Identities=17% Similarity=0.176 Sum_probs=74.9
Q ss_pred EEeCCCCcccchhccc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHHHH
Q 008337 106 IVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEE 184 (569)
Q Consensus 106 IEINDlPq~~R~~LTK-g~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alIeE 184 (569)
|..+=+++...+.+.| +..+..|.+++++.+..+= ....+++.+++-... .+..|+++|+.
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 3333456667888776 5669999999999974311 224567776554443 36677777887
Q ss_pred HHHcCCCCCCCccccCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeec
Q 008337 185 MLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGR 251 (569)
Q Consensus 185 IIKE~p~~~pp~~~p~~~G~k~~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGR 251 (569)
++.+.++.. ..+.++||-+ +.++|||.+|..+..|+.++|| |.|+..
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 777765531 2244566633 6779999999999999999998 888765
No 56
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=71.76 E-value=7 Score=40.34 Aligned_cols=28 Identities=18% Similarity=0.436 Sum_probs=25.2
Q ss_pred ceeEEEeCCCchhHHHHHHhhCcEEEEe
Q 008337 222 NIAARIRGPNDQYINHIMNETGATVLLR 249 (569)
Q Consensus 222 NfvgrIIGPrGstlK~Iq~ETGaKI~IR 249 (569)
..+-|+||++|+++|.+.++|+|+|.+=
T Consensus 155 ~kVpRvig~~~sm~~~l~~~~~~~I~VG 182 (239)
T COG1097 155 SKVPRVIGKKGSMLNMLKEKTGCEIIVG 182 (239)
T ss_pred hhcceEecCCCcHHHHhhhhcCeEEEEe
Confidence 3566799999999999999999999985
No 57
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=70.36 E-value=9.9 Score=41.18 Aligned_cols=57 Identities=19% Similarity=0.338 Sum_probs=46.3
Q ss_pred eeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH--HHHHHHHHh
Q 008337 223 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE--NLLDTISAE 297 (569)
Q Consensus 223 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiE--nLL~tV~eE 297 (569)
-.--|.||.|.+++.|++..|+.|.-||. ++.|.+..+ .++.|+.++. .|+..+++.
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 34467999999999999999999999987 567777777 7888888887 777666555
No 58
>PRK15494 era GTPase Era; Provisional
Probab=69.61 E-value=21 Score=37.56 Aligned_cols=28 Identities=29% Similarity=0.191 Sum_probs=22.9
Q ss_pred ceeEEEeCCCchhHHHH--------HHhhCcEEEEe
Q 008337 222 NIAARIRGPNDQYINHI--------MNETGATVLLR 249 (569)
Q Consensus 222 NfvgrIIGPrGstlK~I--------q~ETGaKI~IR 249 (569)
.-.+.|||.+|..||+| |+-.||||.|+
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 35678999999999988 55568888776
No 59
>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]
Probab=68.59 E-value=5.6 Score=46.77 Aligned_cols=17 Identities=29% Similarity=0.317 Sum_probs=10.7
Q ss_pred cccccceecccCCCCCC
Q 008337 484 LSANLDVRNVSNMPPPS 500 (569)
Q Consensus 484 ~~~~~~v~~~~~~p~p~ 500 (569)
.+.++.++++-+.|+|.
T Consensus 269 asA~~s~~~S~s~pppp 285 (830)
T KOG1923|consen 269 ASACDSQPGSGSGPPPP 285 (830)
T ss_pred hhhcccCCCCCCCCCCC
Confidence 56677777766665543
No 60
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=68.38 E-value=5.7 Score=47.09 Aligned_cols=11 Identities=18% Similarity=0.141 Sum_probs=7.3
Q ss_pred CCCCcCCChHH
Q 008337 400 EGIYPQATPLQ 410 (569)
Q Consensus 400 ~~iypqatplq 410 (569)
+|+-|+++--+
T Consensus 440 ~~~DPdf~yr~ 450 (1102)
T KOG1924|consen 440 TGMDPDFKYRF 450 (1102)
T ss_pred CCCCCCcchhh
Confidence 56777777554
No 61
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=67.42 E-value=1.9 Score=36.26 Aligned_cols=33 Identities=18% Similarity=0.264 Sum_probs=25.7
Q ss_pred CCCCCceeEEEeCCCchhHHHHHHhh-CcEEEEe
Q 008337 217 ADASLNIAARIRGPNDQYINHIMNET-GATVLLR 249 (569)
Q Consensus 217 ~~P~FNfvgrIIGPrGstlK~Iq~ET-GaKI~IR 249 (569)
..++++-+|..||.+|..+|.|.+|. |-||.|=
T Consensus 12 ~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 12 GDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp SSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred CCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 35899999999999999999999999 6666543
No 62
>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=67.33 E-value=23 Score=27.34 Aligned_cols=52 Identities=23% Similarity=0.282 Sum_probs=35.6
Q ss_pred cchhcc-chhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHH
Q 008337 115 VRYKLT-KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 182 (569)
Q Consensus 115 ~R~~LT-Kg~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alI 182 (569)
+++.+. +|.++.+|++.||+.|.... ... ++..--+.|.|.. +.+.+|..+|
T Consensus 11 ~~~vIG~~G~~i~~I~~~s~~~I~i~~-----~~~--~~~~~~v~i~G~~---------~~v~~a~~~i 63 (64)
T cd00105 11 VGRIIGKGGSTIKEIREETGAKIKIPD-----SGS--GSEERIVTITGTP---------EAVEKAKELI 63 (64)
T ss_pred cceeECCCCHHHHHHHHHHCCEEEEcC-----CCC--CCCceEEEEEcCH---------HHHHHHHHHh
Confidence 567776 59999999999999997643 111 2223335788873 3677777765
No 63
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=67.32 E-value=3.5 Score=44.29 Aligned_cols=63 Identities=21% Similarity=0.255 Sum_probs=44.3
Q ss_pred ceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 008337 207 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 286 (569)
Q Consensus 207 ~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~L 286 (569)
+.+.+.|| .-|++.|+|++|..+|+|+++|...|.---| ++ | -+++...-.+.++.||+-
T Consensus 26 vt~sv~vp------s~~v~~ivg~qg~kikalr~KTqtyi~tPsr---------~e---e--PiF~vTg~~edv~~aRre 85 (394)
T KOG2113|consen 26 VTESVEVP------SEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---------GE---E--PIFPVTGRHEDVRRARRE 85 (394)
T ss_pred cceeeecC------cccceeecccCccccchhhhhhcceeccCCC---------CC---C--CcceeccCchhHHHHhhc
Confidence 44555554 5599999999999999999999987642111 11 2 345566666778888887
Q ss_pred HHH
Q 008337 287 AEN 289 (569)
Q Consensus 287 iEn 289 (569)
|+.
T Consensus 86 i~s 88 (394)
T KOG2113|consen 86 IPS 88 (394)
T ss_pred Ccc
Confidence 764
No 64
>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=65.52 E-value=27 Score=35.03 Aligned_cols=27 Identities=26% Similarity=0.214 Sum_probs=21.8
Q ss_pred eeEEEeCCCchhHHHHH--------HhhCcEEEEe
Q 008337 223 IAARIRGPNDQYINHIM--------NETGATVLLR 249 (569)
Q Consensus 223 fvgrIIGPrGstlK~Iq--------~ETGaKI~IR 249 (569)
-.+.|||.+|..+|+|. +-.||||.|+
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 56789999999999984 4558888765
No 65
>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]
Probab=59.80 E-value=91 Score=37.20 Aligned_cols=30 Identities=23% Similarity=0.307 Sum_probs=18.8
Q ss_pred ccccccccccCCCCCCCccCCCCCCCCccc
Q 008337 454 PQKRKFQELPVGSKGPAKHNQGSEIPNRSE 483 (569)
Q Consensus 454 ~qrrkfqelpv~~k~~~~~~q~~~~~~~~~ 483 (569)
.++|||...=-+--++-+-+|.-.+.--|+
T Consensus 171 ~~~~~lk~~~gg~a~p~~~~qpPplPavgl 200 (944)
T KOG4307|consen 171 ENSVKLKDPFGGDAGPYKFQQPPPLPAVGL 200 (944)
T ss_pred CCceeecccCCCCCCCCccCCCCCCCCccc
Confidence 578888765555556667777665443333
No 66
>PF13014 KH_3: KH domain
Probab=58.80 E-value=20 Score=26.63 Aligned_cols=24 Identities=29% Similarity=0.243 Sum_probs=19.3
Q ss_pred cchhcc-chhHHHHHHHHhCCeEee
Q 008337 115 VRYKLT-KRHTQEEIQKCTGAVVIT 138 (569)
Q Consensus 115 ~R~~LT-Kg~Tq~eIqe~TGA~VtT 138 (569)
+++.+. +|.++++|+++|||.|..
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 345555 499999999999999954
No 67
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=57.85 E-value=7.4 Score=39.97 Aligned_cols=76 Identities=13% Similarity=0.132 Sum_probs=53.1
Q ss_pred EEeCCCCcccc--hhcc-chhHHHHHHHHhCCeEeeeccccCCC-CC--------CCCCCCeEEEEEeccchhhHHHHHH
Q 008337 106 IVINDSESSVR--YKLT-KRHTQEEIQKCTGAVVITRGKYRLPN-AP--------PDGEKPLYLHISAGAHLKETAERIL 173 (569)
Q Consensus 106 IEINDlPq~~R--~~LT-Kg~Tq~eIqe~TGA~VtTRGrY~PPg-k~--------~~gEpPLYL~Ieg~te~kdTaERi~ 173 (569)
|-+-+||..+= .+|. +|.||+++++.|+|.|-.||+|---. +. ..-+-+|+-+|++.++.
T Consensus 154 IPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsed-------- 225 (269)
T COG5176 154 IPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSED-------- 225 (269)
T ss_pred eehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhh--------
Confidence 44567775442 2343 79999999999999999999996543 21 13477899999999863
Q ss_pred HHHHHHHHHHHHHHcC
Q 008337 174 AVDHAAAMVEEMLKQG 189 (569)
Q Consensus 174 aVdrA~alIeEIIKE~ 189 (569)
.+.+++..+..+|.++
T Consensus 226 ki~~~ik~~~n~I~~a 241 (269)
T COG5176 226 KICRLIKSQLNAIREA 241 (269)
T ss_pred hHHHHHHHHHHHHHHH
Confidence 4555556566666554
No 68
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=56.17 E-value=18 Score=36.50 Aligned_cols=56 Identities=16% Similarity=0.265 Sum_probs=41.5
Q ss_pred eeEEEeCCCchhHHHHHHhhCcEEEEeec-cCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHH
Q 008337 223 IAARIRGPNDQYINHIMNETGATVLLRGR-GSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENL 290 (569)
Q Consensus 223 fvgrIIGPrGstlK~Iq~ETGaKI~IRGR-GSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnL 290 (569)
=.+.|+|..|.+.+.|+..+||+|.|=.+ ||..++.+. . ..|+-.+.+|+++++-+
T Consensus 18 R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~--~----------t~Dp~~~~ka~d~VkAI 74 (194)
T COG1094 18 RIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTR--K----------TEDPLALLKARDVVKAI 74 (194)
T ss_pred hheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecC--C----------CCChHHHHHHHHHHHHH
Confidence 46789999999999999999999999866 444433221 1 12777888888877643
No 69
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=53.57 E-value=12 Score=28.86 Aligned_cols=23 Identities=13% Similarity=0.127 Sum_probs=20.1
Q ss_pred eEEEeCCCchhHHHHHHhhCcEE
Q 008337 224 AARIRGPNDQYINHIMNETGATV 246 (569)
Q Consensus 224 vgrIIGPrGstlK~Iq~ETGaKI 246 (569)
.|++||.+|.+++.|+..++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 47899999999999999998554
No 70
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=48.00 E-value=17 Score=44.08 Aligned_cols=76 Identities=18% Similarity=0.162 Sum_probs=55.1
Q ss_pred ecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 008337 213 LGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 292 (569)
Q Consensus 213 Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~ 292 (569)
..++++|-- .+.++.+--- +.+|...++|.|..||+-=-....+ ...++-||++|.+.+.-.|+.|+..++.+|.
T Consensus 902 ~~inD~Pq~-~r~~vt~~~~--L~~i~e~~~~~it~rg~f~~~gk~p--~~gErklyl~ve~~~e~~vqra~~e~~r~l~ 976 (997)
T KOG0334|consen 902 LEINDFPQN-ARWRVTYKEA--LLRISEPTAAGITTRGKFNPPGKEP--KPGERKLYLLVEGPDELSVQRAIEELERLLE 976 (997)
T ss_pred ccccccchh-cceeeechhh--hhhccCccccceeeccccCCCCCCC--CCcchhhhhhhhcchhHHHHHHHHHHHHHHH
Confidence 344455543 7778776544 9999999999999999833211111 2234669999999999999999998887654
Q ss_pred H
Q 008337 293 T 293 (569)
Q Consensus 293 t 293 (569)
.
T Consensus 977 e 977 (997)
T KOG0334|consen 977 E 977 (997)
T ss_pred H
Confidence 3
No 71
>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=46.48 E-value=4.2 Score=35.86 Aligned_cols=32 Identities=22% Similarity=0.351 Sum_probs=24.3
Q ss_pred eCCCCcccchhcc-----chhHHHHHHHHhCCeEee--ecc
Q 008337 108 INDSESSVRYKLT-----KRHTQEEIQKCTGAVVIT--RGK 141 (569)
Q Consensus 108 INDlPq~~R~~LT-----Kg~Tq~eIqe~TGA~VtT--RGr 141 (569)
|+++- .||.|- +|.+|.+|.+.||++++| ||.
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 489999999999999886 764
No 72
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=41.69 E-value=30 Score=40.88 Aligned_cols=31 Identities=23% Similarity=0.248 Sum_probs=26.5
Q ss_pred eeEEEeCCCchhHHHHHHhhCcEEEEeeccC
Q 008337 223 IAARIRGPNDQYINHIMNETGATVLLRGRGS 253 (569)
Q Consensus 223 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGS 253 (569)
+...|+|.+|.++.+|+++++|+|.++=.|+
T Consensus 357 ~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~ 387 (753)
T KOG2208|consen 357 ELKFVIGKKGANIEKIREESQVKIDLPKQGS 387 (753)
T ss_pred hhhhhcCCCCccHHHHHHhhhhceecccccC
Confidence 4567899999999999999999999985433
No 73
>PRK01381 Trp operon repressor; Provisional
Probab=39.94 E-value=12 Score=34.00 Aligned_cols=29 Identities=28% Similarity=0.434 Sum_probs=23.2
Q ss_pred cchhccc-----hhHHHHHHHHhCCeEee--ecccc
Q 008337 115 VRYKLTK-----RHTQEEIQKCTGAVVIT--RGKYR 143 (569)
Q Consensus 115 ~R~~LTK-----g~Tq~eIqe~TGA~VtT--RGrY~ 143 (569)
.||.|-+ +-+|.||.+.+|++|+| ||.-+
T Consensus 43 ~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~ 78 (99)
T PRK01381 43 TRVRIVEELLRGELSQREIKQELGVGIATITRGSNS 78 (99)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHH
Confidence 5887765 47999999999999886 87543
No 74
>PRK00089 era GTPase Era; Reviewed
Probab=39.90 E-value=29 Score=34.90 Aligned_cols=38 Identities=18% Similarity=0.344 Sum_probs=27.0
Q ss_pred ceeEEEecCCCCCCCceeEEEeCCCchhHHHH--------HHhhCcEEEEe
Q 008337 207 MSTSVFLGFDADASLNIAARIRGPNDQYINHI--------MNETGATVLLR 249 (569)
Q Consensus 207 ~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~I--------q~ETGaKI~IR 249 (569)
....|||.-+. -.+.|||.+|.+||+| ++-.||+|.|.
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 44455554332 3678999999999988 45568888775
No 75
>PHA01732 proline-rich protein
Probab=38.95 E-value=30 Score=31.24 Aligned_cols=13 Identities=31% Similarity=0.416 Sum_probs=5.5
Q ss_pred CCCCCCCCCCCCC
Q 008337 508 NGMPHPPPRNMPP 520 (569)
Q Consensus 508 ~~mpppp~~~mpp 520 (569)
..+|+|+|..||+
T Consensus 15 pPpP~P~PpPpPp 27 (94)
T PHA01732 15 PLPPAPVPPPPPA 27 (94)
T ss_pred CCCCCCCCCCCCC
Confidence 3334444444444
No 76
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=38.75 E-value=23 Score=33.44 Aligned_cols=28 Identities=11% Similarity=0.136 Sum_probs=25.2
Q ss_pred eeEEEeCCCchhHHHHHHhhCcEEEEee
Q 008337 223 IAARIRGPNDQYINHIMNETGATVLLRG 250 (569)
Q Consensus 223 fvgrIIGPrGstlK~Iq~ETGaKI~IRG 250 (569)
-+|..||.+|+.+|.|++..|-||-|=.
T Consensus 42 ~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 42 DMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CccccCCcCchHHHHHHHHhCCceEEEE
Confidence 6799999999999999999998887664
No 77
>COG1159 Era GTPase [General function prediction only]
Probab=37.01 E-value=85 Score=33.62 Aligned_cols=42 Identities=21% Similarity=0.358 Sum_probs=28.6
Q ss_pred CcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHH--------HhhCcEEEEe
Q 008337 203 GVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIM--------NETGATVLLR 249 (569)
Q Consensus 203 G~k~~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq--------~ETGaKI~IR 249 (569)
|.-+...-|||.=+ .-.|.|||.+|..+|.|- .-.||||.|-
T Consensus 225 ~~~~I~a~I~Ver~-----sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L~ 274 (298)
T COG1159 225 GLLKIHATIYVERE-----SQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYLE 274 (298)
T ss_pred CeEEEEEEEEEecC-----CccceEECCCcHHHHHHHHHHHHHHHHHhCCceEEE
Confidence 33445566777644 345679999999999884 4457777653
No 78
>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=35.87 E-value=29 Score=28.50 Aligned_cols=16 Identities=44% Similarity=0.752 Sum_probs=10.5
Q ss_pred ccCCCCCcCCChHHHHH
Q 008337 397 SGYEGIYPQATPLQQVA 413 (569)
Q Consensus 397 ~gy~~iypqatplqqva 413 (569)
-|||+++|+ |+.-++.
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 79
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=35.02 E-value=47 Score=38.28 Aligned_cols=93 Identities=24% Similarity=0.274 Sum_probs=57.6
Q ss_pred eeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhhcccc
Q 008337 223 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGASR 302 (569)
Q Consensus 223 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~tV~eE~~~fr 302 (569)
++-+|+|-.|+++|.|...|++||.|+-.-++- =.+.+.+.-+..+-.|+.++-..+. +
T Consensus 78 ~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~------------e~~~~~~~~p~~v~~a~a~~~~~~~----~----- 136 (608)
T KOG2279|consen 78 AVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGD------------ERVLLISGFPVQVCKAKAAIHQILT----E----- 136 (608)
T ss_pred ceeeeeccccCCcchhhcccccceecCcccCCc------------ccchhhccCCCCCChHHHHHHHHHh----c-----
Confidence 888999999999999999999999998654431 2233333344455555443322221 0
Q ss_pred cccccccccCCCchhhcccccCcCcccccCcccchh
Q 008337 303 VSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVI 338 (569)
Q Consensus 303 ~~~~k~y~avPppq~~l~Gv~~s~~~~~~~~~~~~~ 338 (569)
...+-...+-||.+.--+..-|.|+.++...+.+
T Consensus 137 --~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~ 170 (608)
T KOG2279|consen 137 --NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSG 170 (608)
T ss_pred --CCcccccccchhhhcccccccchhhhcchhcccc
Confidence 1123334566677666677777666666644444
No 80
>PRK01064 hypothetical protein; Provisional
Probab=33.76 E-value=31 Score=29.96 Aligned_cols=20 Identities=20% Similarity=0.169 Sum_probs=17.2
Q ss_pred eEEEeCCCchhHHHHHHhhC
Q 008337 224 AARIRGPNDQYINHIMNETG 243 (569)
Q Consensus 224 vgrIIGPrGstlK~Iq~ETG 243 (569)
.|++||-+|.+++.|+.-..
T Consensus 41 ~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred ceEEECCCCccHHHHHHHHH
Confidence 59999999999999987543
No 81
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=32.85 E-value=1.1e+02 Score=29.68 Aligned_cols=60 Identities=12% Similarity=0.141 Sum_probs=45.1
Q ss_pred eeEEEeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhh
Q 008337 223 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 298 (569)
Q Consensus 223 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~tV~eE~ 298 (569)
..-+|+.++|..++.|....||+|.+.- +.-.|.|+| +...++.+...+.+++..|+.+.
T Consensus 36 ~~~LLl~~~~~~L~~l~~~~~~~I~~~~---------------~~~~i~I~g-~k~~~~~i~~~i~~~l~~i~~~~ 95 (210)
T PF14611_consen 36 EFFLLLTGNGRILENLAARNGAKIEVSR---------------SENRIRITG-TKSTAEYIEASINEILSNIRTEE 95 (210)
T ss_pred heeeeecCCchHHHHHHHhcCceEEEec---------------CCcEEEEEc-cHHHHHHHHHHHHHHHhhcEEEE
Confidence 3448899999999999888899998862 223577777 66667777777777777776653
No 82
>KOG1925 consensus Rac1 GTPase effector FHOS [Signal transduction mechanisms; Cytoskeleton]
Probab=32.65 E-value=32 Score=39.48 Aligned_cols=21 Identities=52% Similarity=1.208 Sum_probs=14.3
Q ss_pred CCCCCCCCCCC-CCCCCCCCCC
Q 008337 508 NGMPHPPPRNM-PPPPPPKFTL 528 (569)
Q Consensus 508 ~~mpppp~~~m-pp~pppkf~~ 528 (569)
.|.|||||+.. ||||||--+.
T Consensus 247 ~GvPPPPP~G~~PPPPP~~~~L 268 (817)
T KOG1925|consen 247 SGVPPPPPKGPFPPPPPLAAPL 268 (817)
T ss_pred cCCCCCCCCCCCCCCCCCcccC
Confidence 57888888886 6656655443
No 83
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=30.55 E-value=1.8e+02 Score=29.86 Aligned_cols=73 Identities=21% Similarity=0.258 Sum_probs=47.0
Q ss_pred CCeEEEEEeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCCcc---ccCCCCcccceeEEEecCCCCCCCceeEEEeC
Q 008337 153 KPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQ---TVMGNGVQAMSTSVFLGFDADASLNIAARIRG 229 (569)
Q Consensus 153 pPLYL~Ieg~te~kdTaERi~aVdrA~alIeEIIKE~p~~~pp~~---~p~~~G~k~~qeKI~Ipld~~P~FNfvgrIIG 229 (569)
-|-||++-= ..-=+.|+|++++..+.++.+-|++++--.-... ...+. ..++++|+-+.-+||+--+-.+
T Consensus 4 lP~~lllDt--SgSM~Ge~IealN~Glq~m~~~Lkqdp~Ale~v~lsIVTF~~-----~a~~~~pf~~~~nF~~p~L~a~ 76 (207)
T COG4245 4 LPCYLLLDT--SGSMIGEPIEALNAGLQMMIDTLKQDPYALERVELSIVTFGG-----PARVIQPFTDAANFNPPILTAQ 76 (207)
T ss_pred CCEEEEEec--CcccccccHHHHHHHHHHHHHHHHhChhhhheeEEEEEEecC-----cceEEechhhHhhcCCCceecC
Confidence 367877732 1123578899999999988888887753221111 00111 3578999998999998877665
Q ss_pred CCch
Q 008337 230 PNDQ 233 (569)
Q Consensus 230 PrGs 233 (569)
+|.
T Consensus 77 -GgT 79 (207)
T COG4245 77 -GGT 79 (207)
T ss_pred -CCC
Confidence 553
No 84
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=27.88 E-value=37 Score=28.43 Aligned_cols=21 Identities=5% Similarity=0.090 Sum_probs=18.2
Q ss_pred eEEEeCCCchhHHHHHHhhCc
Q 008337 224 AARIRGPNDQYINHIMNETGA 244 (569)
Q Consensus 224 vgrIIGPrGstlK~Iq~ETGa 244 (569)
.|+|||.+|.+++-||--+..
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~ 55 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANL 55 (77)
T ss_pred CCeEECCCCccHHHHHHHHHH
Confidence 489999999999999887764
No 85
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=27.83 E-value=1.1e+02 Score=35.34 Aligned_cols=69 Identities=16% Similarity=0.148 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCccccCCCCcccceeEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccC
Q 008337 174 AVDHAAAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGS 253 (569)
Q Consensus 174 aVdrA~alIeEIIKE~p~~~pp~~~p~~~G~k~~qeKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGS 253 (569)
+...|..+|++.|+.-......-++.. . -...|+||-+ .++++||-+|..+++|++..|-+|.++-.+.
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 345566666666665322111111110 0 1245666644 4668999999999999999999999996644
No 86
>PRK02821 hypothetical protein; Provisional
Probab=27.74 E-value=36 Score=29.51 Aligned_cols=22 Identities=9% Similarity=0.096 Sum_probs=18.0
Q ss_pred eeEEEeCCCchhHHHHHHhhCc
Q 008337 223 IAARIRGPNDQYINHIMNETGA 244 (569)
Q Consensus 223 fvgrIIGPrGstlK~Iq~ETGa 244 (569)
=+|||||-+|.+++-|..--.+
T Consensus 41 D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 41 DLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred hCcceeCCCCchHHHHHHHHHH
Confidence 4799999999999998765443
No 87
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=27.72 E-value=59 Score=35.36 Aligned_cols=40 Identities=18% Similarity=0.363 Sum_probs=32.2
Q ss_pred eEEEecCCCCCCCceeEEEeCCCchhHHHHHHhh-CcEEEEe
Q 008337 209 TSVFLGFDADASLNIAARIRGPNDQYINHIMNET-GATVLLR 249 (569)
Q Consensus 209 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ET-GaKI~IR 249 (569)
.||-|= -..++++-+|..||++|+.++.|.+|. |=||-|=
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 577653 246999999999999999999999999 6666443
No 88
>PRK00468 hypothetical protein; Provisional
Probab=27.11 E-value=38 Score=29.09 Aligned_cols=18 Identities=11% Similarity=0.204 Sum_probs=15.7
Q ss_pred eEEEeCCCchhHHHHHHh
Q 008337 224 AARIRGPNDQYINHIMNE 241 (569)
Q Consensus 224 vgrIIGPrGstlK~Iq~E 241 (569)
+|||||-+|.+++-|..-
T Consensus 41 ~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CcceecCCChhHHHHHHH
Confidence 599999999999988654
No 89
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=27.11 E-value=75 Score=35.85 Aligned_cols=15 Identities=13% Similarity=0.202 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHHHc
Q 008337 174 AVDHAAAMVEEMLKQ 188 (569)
Q Consensus 174 aVdrA~alIeEIIKE 188 (569)
.+++|..+++.++-.
T Consensus 10 RLE~a~~RLE~Isi~ 24 (480)
T KOG2675|consen 10 RLESATSRLEGISIT 24 (480)
T ss_pred HHHHHHHHhhhhhcC
Confidence 356666677776643
No 90
>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=25.41 E-value=77 Score=34.18 Aligned_cols=39 Identities=21% Similarity=0.325 Sum_probs=31.6
Q ss_pred eEEEecCCCCCCCceeEEEeCCCchhHHHHHHhh-CcEEEE
Q 008337 209 TSVFLGFDADASLNIAARIRGPNDQYINHIMNET-GATVLL 248 (569)
Q Consensus 209 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ET-GaKI~I 248 (569)
.||-|=- ..++++-+|..||++|+.++.|.+|. |=||-|
T Consensus 231 tKvAV~s-~~~~iDpvga~vG~~G~ri~~i~~el~ge~Idi 270 (341)
T TIGR01953 231 TKIAVES-NDENIDPVGACVGPKGSRIQAISKELNGEKIDI 270 (341)
T ss_pred eEEEEEc-CCCCCCcceeeECCCCchHHHHHHHhCCCeEEE
Confidence 6776543 36999999999999999999999998 555543
No 91
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=24.84 E-value=69 Score=40.27 Aligned_cols=9 Identities=67% Similarity=1.667 Sum_probs=5.5
Q ss_pred CCCCCCCCC
Q 008337 519 PPPPPPKFT 527 (569)
Q Consensus 519 pp~pppkf~ 527 (569)
||||||...
T Consensus 25 ppPppPg~~ 33 (2365)
T COG5178 25 PPPPPPGVN 33 (2365)
T ss_pred CCccCCCcc
Confidence 445677775
No 92
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=24.43 E-value=1.5e+02 Score=29.91 Aligned_cols=58 Identities=14% Similarity=0.098 Sum_probs=33.9
Q ss_pred eEEEeCCC-------------chhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHH--H-HHHHHHHH
Q 008337 224 AARIRGPN-------------DQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPK--S-LEEAKRLA 287 (569)
Q Consensus 224 vgrIIGPr-------------GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e--~-v~~Ak~Li 287 (569)
+|+++||+ +..+....+|..++|.+|=+-.+ =+|++|=..+.+ + ++.+..++
T Consensus 117 lgk~LGp~~~p~gK~P~~~~~~~dl~~~i~~~k~~v~~r~~k~~------------~~~~~VGk~~m~~e~i~eNi~a~l 184 (214)
T PTZ00225 117 VPRLVGPHMHRMGKFPTVCSPSESLPDKVVELRSTVKFQLKKVL------------CLGTCVGHVEMTEEQLRQNVVMAI 184 (214)
T ss_pred hhhhcCCCCCcCCCCCcccCCccCHHHHHHHHhheeEEEecCcc------------EEEeEEccCCCCHHHHHHHHHHHH
Confidence 58888887 45577777788777877743211 277777644443 2 33344444
Q ss_pred HHHHHH
Q 008337 288 ENLLDT 293 (569)
Q Consensus 288 EnLL~t 293 (569)
+.|...
T Consensus 185 ~~l~~~ 190 (214)
T PTZ00225 185 NFLVSL 190 (214)
T ss_pred HHHHHh
Confidence 444433
No 93
>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=23.98 E-value=86 Score=26.68 Aligned_cols=33 Identities=15% Similarity=0.287 Sum_probs=28.1
Q ss_pred EEEEEeCC-HHHHHHHHHHHHHHHHHHHHhhccc
Q 008337 269 HLFLSSNN-PKSLEEAKRLAENLLDTISAECGAS 301 (569)
Q Consensus 269 HV~Isa~~-~e~v~~Ak~LiEnLL~tV~eE~~~f 301 (569)
|++|..++ .+..+++++.++.|...+......|
T Consensus 1 HIl~~~~~~~~~~~~~~~~a~~i~~~l~~g~~~F 34 (95)
T PF00639_consen 1 HILVKPPPSDEEKDAAKKKAEEIYEQLKKGEDSF 34 (95)
T ss_dssp EEEEESTTSCCHHHHHHHHHHHHHHHHHTTSSSH
T ss_pred CEEEECCCchhhHHHHHHHHHHHHHHHHhCchhH
Confidence 88998765 7889999999999999999886544
No 94
>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=22.99 E-value=63 Score=30.85 Aligned_cols=28 Identities=11% Similarity=0.141 Sum_probs=24.8
Q ss_pred eeEEEeCCCchhHHHHHHhhCcEEEEee
Q 008337 223 IAARIRGPNDQYINHIMNETGATVLLRG 250 (569)
Q Consensus 223 fvgrIIGPrGstlK~Iq~ETGaKI~IRG 250 (569)
-+|..||.+|+.+|.|++..|=||-|=.
T Consensus 43 ~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 43 EMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred CccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 6889999999999999988898887665
No 95
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=22.65 E-value=1.1e+02 Score=36.41 Aligned_cols=62 Identities=18% Similarity=0.186 Sum_probs=45.3
Q ss_pred EEEEeCCCCcccchhccc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHH
Q 008337 104 REIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 182 (569)
Q Consensus 104 aEIEINDlPq~~R~~LTK-g~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alI 182 (569)
..|.|+ |.+.|-.+.. |.++.+|+++||+.|...- +- .+.|.+.+. ..+++|+++|
T Consensus 580 ~~~~I~--~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-----------~G--~V~I~a~d~--------~~~~~A~~~I 636 (719)
T TIGR02696 580 ITVKIP--VDKIGEVIGPKGKMINQIQDETGAEISIED-----------DG--TVYIGAADG--------PSAEAARAMI 636 (719)
T ss_pred EEEEeC--hHHhhheeCCCcHhHHHHHHHHCCEEEEec-----------Cc--EEEEEeCCH--------HHHHHHHHHH
Confidence 455554 3346667775 9999999999999985422 22 346888764 5789999999
Q ss_pred HHHHHc
Q 008337 183 EEMLKQ 188 (569)
Q Consensus 183 eEIIKE 188 (569)
+.++..
T Consensus 637 ~~i~~~ 642 (719)
T TIGR02696 637 NAIANP 642 (719)
T ss_pred HHhhCc
Confidence 999884
No 96
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=22.51 E-value=1.2e+02 Score=35.81 Aligned_cols=64 Identities=17% Similarity=0.200 Sum_probs=47.7
Q ss_pred EEEEeCCCCcccchhccc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHH
Q 008337 104 REIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 182 (569)
Q Consensus 104 aEIEINDlPq~~R~~LTK-g~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alI 182 (569)
+...++.-+.+.|-.+.+ |.++.+|.++||+.|-+. ++.-. .|.+.+. ..+++|+..|
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------ddGtv--~i~~s~~--------~~~~~ak~~I 610 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DDGTV--KIAASDG--------ESAKKAKERI 610 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CCCcE--EEEecch--------HHHHHHHHHH
Confidence 456788888888988886 899999999999998652 12223 3555543 4688899999
Q ss_pred HHHHHc
Q 008337 183 EEMLKQ 188 (569)
Q Consensus 183 eEIIKE 188 (569)
+.+..+
T Consensus 611 ~~i~~e 616 (692)
T COG1185 611 EAITRE 616 (692)
T ss_pred HHHHhh
Confidence 998854
No 97
>PF13711 DUF4160: Domain of unknown function (DUF4160)
Probab=22.47 E-value=3.1e+02 Score=22.42 Aligned_cols=13 Identities=23% Similarity=0.447 Sum_probs=10.4
Q ss_pred CCCcEEEEEeCCH
Q 008337 265 HQPLHLFLSSNNP 277 (569)
Q Consensus 265 dEPLHV~Isa~~~ 277 (569)
-+|.||||...+.
T Consensus 14 H~PpHvHv~~g~~ 26 (66)
T PF13711_consen 14 HEPPHVHVRYGGF 26 (66)
T ss_pred CCCCeEEEEcCCc
Confidence 4899999987763
No 98
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=21.82 E-value=2.7e+02 Score=27.91 Aligned_cols=52 Identities=12% Similarity=0.300 Sum_probs=40.1
Q ss_pred hHHHHHHhhC-cEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHhhc
Q 008337 234 YINHIMNETG-ATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECG 299 (569)
Q Consensus 234 tlK~Iq~ETG-aKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~~Ak~LiEnLL~tV~eE~~ 299 (569)
+++.|++... .-+.+++||.+ |.|.|.|... .+..|...|.+|+..++..|+
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 4666766643 34557777633 8888888877 999999999999999999764
No 99
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=21.68 E-value=68 Score=31.58 Aligned_cols=73 Identities=12% Similarity=0.070 Sum_probs=43.6
Q ss_pred EEEeCCCchhHHHHHHhhCcEEEEeeccCC---CCC----CC-------CCCCCCCCcE-EEEEeCCHHHHHHHHHHHHH
Q 008337 225 ARIRGPNDQYINHIMNETGATVLLRGRGSG---NSE----GL-------QGEEVHQPLH-LFLSSNNPKSLEEAKRLAEN 289 (569)
Q Consensus 225 grIIGPrGstlK~Iq~ETGaKI~IRGRGSg---~~E----~~-------~g~EsdEPLH-V~Isa~~~e~v~~Ak~LiEn 289 (569)
|.-||++|.+++++++..|=+|.|=.-..- +++ +. .......-++ +.|...+...+..-.+..+.
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevVE~s~d~~~fl~Nl~~PA~V~gV~i~~~~dG~~~~kV~Vd~~Dk~~l~~k~e~~~~ 151 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVVEKTNDIKKLAVQLLSPARVLGVNTVWLPDGTVQYVIRVSRRDRRRLPAKPELLES 151 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEEEcCCCHHHHHHhcCCCcEEEEEEEEEeCCCcEEEEEEECHHHhhcccccHHHHHH
Confidence 889999999999999999999877753221 000 00 0001112233 66655555556655566666
Q ss_pred HHHHHHHh
Q 008337 290 LLDTISAE 297 (569)
Q Consensus 290 LL~tV~eE 297 (569)
++..+...
T Consensus 152 v~~kltgk 159 (166)
T PRK06418 152 ILSKITGT 159 (166)
T ss_pred HHHHHHCC
Confidence 66555544
No 100
>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=21.39 E-value=29 Score=31.31 Aligned_cols=26 Identities=31% Similarity=0.465 Sum_probs=21.5
Q ss_pred cchhccc-----hhHHHHHHHHhCCeEee--ec
Q 008337 115 VRYKLTK-----RHTQEEIQKCTGAVVIT--RG 140 (569)
Q Consensus 115 ~R~~LTK-----g~Tq~eIqe~TGA~VtT--RG 140 (569)
.||.|-. +-||.||.+.+|++++| ||
T Consensus 43 ~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~ 75 (94)
T TIGR01321 43 DRIRIVNELLNGNMSQREIASKLGVSIATITRG 75 (94)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH
Confidence 5876664 67999999999999876 66
No 101
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....
Probab=21.17 E-value=2.9e+02 Score=25.12 Aligned_cols=51 Identities=25% Similarity=0.359 Sum_probs=33.1
Q ss_pred EeCCCchhHHHHHHhhCcEEEEeeccCCCCCCCCCCCCCCCcEEEEEeCCHH----HHHHHHHHHHHHHHHHHH
Q 008337 227 IRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPK----SLEEAKRLAENLLDTISA 296 (569)
Q Consensus 227 IIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e----~v~~Ak~LiEnLL~tV~e 296 (569)
==||||+++++ |..+|.|+=.-+| |.|.+.+.- +.+.|.+....+|..+..
T Consensus 21 ssGpGGQ~VNk----~~s~V~l~h~ptg---------------i~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~~~ 75 (113)
T PF00472_consen 21 SSGPGGQNVNK----TNSKVRLRHIPTG---------------IVVKCQESRSQHQNREDALEKLREKLDEAYR 75 (113)
T ss_dssp SSSSSSCHHHS----SSEEEEEEETTTT---------------EEEEEESSSSHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCCCCCcccc----cCCEEEEEEeccc---------------EEEEEcccCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34999999965 4557777744333 778877543 456676666666666653
No 102
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=21.13 E-value=66 Score=32.18 Aligned_cols=33 Identities=9% Similarity=0.142 Sum_probs=28.1
Q ss_pred CCCCceeEEEeCCCchhHHHHHHhhCcEEEEee
Q 008337 218 DASLNIAARIRGPNDQYINHIMNETGATVLLRG 250 (569)
Q Consensus 218 ~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRG 250 (569)
..+.+=+|..||++|..++.|.+|.|=||-|=-
T Consensus 81 ~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe 113 (190)
T COG0195 81 VVKIDPVGACIGKRGSRVKAVSEELGEKIDVVE 113 (190)
T ss_pred ecCcCchhhhccCCChHHHHHHHHhCCceEEEE
Confidence 357778999999999999999999997776553
No 103
>PRK13764 ATPase; Provisional
Probab=20.84 E-value=1.1e+02 Score=35.57 Aligned_cols=39 Identities=15% Similarity=0.226 Sum_probs=31.9
Q ss_pred eEEEecCCCCCCCceeEEEeCCCchhHHHHHHhhCcEEEEeeccC
Q 008337 209 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGS 253 (569)
Q Consensus 209 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGS 253 (569)
-.|||+-+ .++.+||.+|..+++|++..|.+|-||-+.-
T Consensus 483 ~~v~~~~~------~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 483 AVVYVPEK------DIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred EEEEEChh------hhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence 46777755 4457899999999999999999999996643
No 104
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=20.05 E-value=1.2e+02 Score=35.45 Aligned_cols=61 Identities=25% Similarity=0.256 Sum_probs=43.5
Q ss_pred EEEEeCCCCcccchhccc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEEeccchhhHHHHHHHHHHHHHHH
Q 008337 104 REIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 182 (569)
Q Consensus 104 aEIEINDlPq~~R~~LTK-g~Tq~eIqe~TGA~VtTRGrY~PPgk~~~gEpPLYL~Ieg~te~kdTaERi~aVdrA~alI 182 (569)
..+.|+ |.+.|-.+.+ |.++++|+++||+.|.+.- + =.+.|.+.++ ..+++|+.+|
T Consensus 553 ~~~~I~--~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------d--G~V~i~~~~~--------~~~~~a~~~I 609 (684)
T TIGR03591 553 ETIKIN--PDKIRDVIGPGGKVIREITEETGAKIDIED-----------D--GTVKIAASDG--------EAAEAAIKMI 609 (684)
T ss_pred EEEecC--HHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------C--eEEEEEECcH--------HHHHHHHHHH
Confidence 345554 2336677775 9999999999999997621 2 2345777663 5799999999
Q ss_pred HHHHH
Q 008337 183 EEMLK 187 (569)
Q Consensus 183 eEIIK 187 (569)
+.+..
T Consensus 610 ~~~~~ 614 (684)
T TIGR03591 610 EGITA 614 (684)
T ss_pred Hhhhc
Confidence 98855
Done!