Query 008326
Match_columns 570
No_of_seqs 201 out of 493
Neff 3.5
Searched_HMMs 46136
Date Thu Mar 28 22:24:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008326.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008326hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1960 Predicted RNA-binding 100.0 1.1E-37 2.4E-42 322.9 14.3 371 27-429 13-422 (531)
2 KOG0119 Splicing factor 1/bran 100.0 5.4E-28 1.2E-32 255.9 15.0 158 127-294 61-230 (554)
3 cd02395 SF1_like-KH Splicing f 99.9 7.8E-26 1.7E-30 203.3 7.3 95 209-303 1-105 (120)
4 KOG1588 RNA-binding protein Sa 99.9 1.1E-22 2.5E-27 202.8 10.0 127 174-300 55-197 (259)
5 COG5176 MSL5 Splicing factor ( 99.8 2.8E-21 6.1E-26 188.7 10.1 149 142-297 82-243 (269)
6 KOG1960 Predicted RNA-binding 99.2 2.4E-12 5.2E-17 135.5 2.2 150 123-304 233-385 (531)
7 KOG1676 K-homology type RNA bi 99.1 2.3E-09 5E-14 117.4 17.6 166 102-299 137-305 (600)
8 KOG0334 RNA helicase [RNA proc 99.0 2.3E-10 4.9E-15 131.0 3.7 81 103-190 897-978 (997)
9 TIGR03665 arCOG04150 arCOG0415 98.8 1.9E-08 4.1E-13 95.4 9.9 129 122-293 15-150 (172)
10 PRK13763 putative RNA-processi 98.8 3.2E-08 6.9E-13 94.5 10.0 145 104-293 3-156 (180)
11 KOG1676 K-homology type RNA bi 98.7 2.3E-07 5E-12 102.1 16.1 158 107-298 233-393 (600)
12 cd00105 KH-I K homology RNA-bi 98.5 5.1E-07 1.1E-11 70.1 7.4 63 210-289 2-64 (64)
13 cd02393 PNPase_KH Polynucleoti 98.4 5.4E-07 1.2E-11 72.4 6.2 58 210-289 4-61 (61)
14 smart00322 KH K homology RNA-b 98.4 1.9E-06 4.2E-11 65.4 8.0 66 208-292 3-68 (69)
15 PF00013 KH_1: KH domain syndr 98.3 3.6E-07 7.7E-12 71.5 2.8 52 223-288 9-60 (60)
16 cd02394 vigilin_like_KH K homo 98.1 4.8E-06 1E-10 65.5 4.6 53 223-288 9-61 (62)
17 cd02396 PCBP_like_KH K homolog 98.0 2.5E-05 5.4E-10 62.7 6.7 62 211-288 3-64 (65)
18 KOG2191 RNA-binding protein NO 97.9 0.00046 1E-08 72.8 17.3 161 105-300 40-207 (402)
19 KOG0119 Splicing factor 1/bran 97.7 6.6E-05 1.4E-09 82.0 6.8 84 97-190 137-231 (554)
20 PF13014 KH_3: KH domain 97.7 3.8E-05 8.2E-10 57.3 3.2 28 224-251 1-28 (43)
21 PRK13763 putative RNA-processi 97.4 0.0003 6.4E-09 67.6 6.5 63 210-293 5-70 (180)
22 KOG2193 IGF-II mRNA-binding pr 97.4 0.00065 1.4E-08 73.6 9.2 139 123-300 217-355 (584)
23 TIGR03665 arCOG04150 arCOG0415 97.2 0.0004 8.7E-09 66.2 5.1 56 224-294 8-65 (172)
24 cd02395 SF1_like-KH Splicing f 97.1 0.0015 3.3E-08 59.7 7.0 67 117-190 18-96 (120)
25 TIGR02696 pppGpp_PNP guanosine 97.1 0.0025 5.4E-08 73.0 10.0 64 209-294 579-642 (719)
26 COG1094 Predicted RNA-binding 97.0 0.0014 3E-08 64.7 6.0 54 224-295 112-165 (194)
27 TIGR03591 polynuc_phos polyrib 96.9 0.0014 3.1E-08 74.3 6.7 99 210-346 553-651 (684)
28 KOG2193 IGF-II mRNA-binding pr 96.9 0.0054 1.2E-07 66.7 9.9 156 107-300 414-570 (584)
29 KOG2190 PolyC-binding proteins 96.8 0.017 3.6E-07 63.8 12.9 146 118-292 56-206 (485)
30 PLN00207 polyribonucleotide nu 96.6 0.0023 4.9E-08 74.7 5.2 100 210-346 687-787 (891)
31 PRK11824 polynucleotide phosph 95.8 0.011 2.3E-07 67.5 5.0 92 223-346 563-654 (693)
32 KOG2191 RNA-binding protein NO 95.3 0.077 1.7E-06 56.6 9.0 78 208-302 39-116 (402)
33 PRK04163 exosome complex RNA-b 95.3 0.025 5.5E-07 56.5 5.1 53 224-292 155-207 (235)
34 KOG2874 rRNA processing protei 94.7 0.034 7.5E-07 58.1 4.3 57 225-299 160-216 (356)
35 KOG2814 Transcription coactiva 93.7 0.11 2.4E-06 55.2 5.6 63 224-298 67-129 (345)
36 PRK00106 hypothetical protein; 92.6 0.24 5.1E-06 55.6 6.5 60 219-293 231-290 (535)
37 TIGR03319 YmdA_YtgF conserved 92.6 0.22 4.7E-06 55.4 6.1 60 219-293 210-269 (514)
38 KOG1067 Predicted RNA-binding 92.5 0.33 7E-06 55.1 7.3 57 225-298 608-664 (760)
39 PRK12704 phosphodiesterase; Pr 92.4 0.28 6.1E-06 54.6 6.8 59 219-292 216-274 (520)
40 COG1185 Pnp Polyribonucleotide 92.2 0.2 4.3E-06 57.6 5.3 53 225-293 563-615 (692)
41 KOG0336 ATP-dependent RNA heli 91.4 0.33 7.2E-06 53.6 5.7 63 222-300 55-118 (629)
42 KOG1588 RNA-binding protein Sa 91.3 0.71 1.5E-05 47.8 7.7 74 117-192 110-194 (259)
43 KOG2190 PolyC-binding proteins 90.7 1.1 2.4E-05 49.8 9.1 119 117-251 149-293 (485)
44 KOG2192 PolyC-binding hnRNP-K 89.9 0.81 1.8E-05 48.1 6.7 65 224-299 325-389 (390)
45 cd02393 PNPase_KH Polynucleoti 85.7 1.5 3.3E-05 35.3 4.6 56 107-184 5-61 (61)
46 KOG2113 Predicted RNA binding 83.1 2.7 5.9E-05 45.1 6.3 111 118-252 39-153 (394)
47 PF00013 KH_1: KH domain syndr 82.6 3.2 7E-05 32.3 5.1 49 117-183 11-60 (60)
48 PRK12705 hypothetical protein; 82.2 1.3 2.9E-05 49.6 3.8 58 219-291 204-261 (508)
49 COG5176 MSL5 Splicing factor ( 81.9 1.1 2.4E-05 45.7 2.8 83 96-189 146-240 (269)
50 KOG2192 PolyC-binding hnRNP-K 81.6 6.8 0.00015 41.5 8.4 130 120-293 62-192 (390)
51 cd02396 PCBP_like_KH K homolog 79.8 4.7 0.0001 32.4 5.3 52 118-183 12-64 (65)
52 KOG1924 RhoA GTPase effector D 79.5 1.6 3.5E-05 51.3 3.4 10 401-410 440-449 (1102)
53 cd02134 NusA_KH NusA_K homolog 78.2 2.2 4.7E-05 34.5 2.9 27 223-249 34-60 (61)
54 cd00105 KH-I K homology RNA-bi 72.8 9.5 0.0002 29.4 5.1 52 117-183 11-63 (64)
55 COG1097 RRP4 RNA-binding prote 72.1 7.6 0.00017 40.1 5.6 29 223-251 155-183 (239)
56 PF13184 KH_5: NusA-like KH do 69.6 1.9 4.1E-05 36.2 0.6 33 218-250 12-45 (69)
57 KOG2113 Predicted RNA binding 68.9 2.6 5.6E-05 45.3 1.5 64 207-290 25-88 (394)
58 cd02394 vigilin_like_KH K homo 67.0 12 0.00025 29.4 4.6 51 116-183 10-61 (62)
59 PF13014 KH_3: KH domain 64.4 17 0.00037 27.0 4.8 24 117-140 2-26 (43)
60 KOG1924 RhoA GTPase effector D 63.9 7.3 0.00016 46.2 3.9 11 153-163 154-164 (1102)
61 COG1702 PhoH Phosphate starvat 63.0 17 0.00036 39.5 6.1 56 225-298 26-83 (348)
62 smart00322 KH K homology RNA-b 62.5 43 0.00093 25.0 6.8 63 106-187 5-68 (69)
63 PRK15494 era GTPase Era; Provi 62.4 34 0.00073 36.0 8.2 27 224-250 284-318 (339)
64 COG1094 Predicted RNA-binding 62.3 12 0.00026 37.6 4.7 55 225-291 19-74 (194)
65 cd02409 KH-II KH-II (K homolo 54.3 11 0.00025 28.9 2.5 23 225-247 36-58 (68)
66 KOG2208 Vigilin [Lipid transpo 51.0 53 0.0012 38.9 8.1 104 112-252 353-457 (753)
67 KOG1923 Rac1 GTPase effector F 47.4 21 0.00046 42.3 4.1 15 486-500 270-284 (830)
68 KOG0334 RNA helicase [RNA proc 45.2 20 0.00044 43.5 3.7 75 215-294 903-977 (997)
69 COG1159 Era GTPase [General fu 44.8 53 0.0012 35.1 6.3 41 204-249 225-273 (298)
70 TIGR00436 era GTP-binding prot 44.2 22 0.00049 35.6 3.4 27 224-250 232-266 (270)
71 PRK00089 era GTPase Era; Revie 41.0 27 0.00058 35.1 3.3 38 208-250 226-271 (292)
72 KOG1925 Rac1 GTPase effector F 39.3 22 0.00048 40.7 2.6 19 509-527 247-266 (817)
73 PHA01732 proline-rich protein 39.0 29 0.00064 31.3 2.9 12 511-522 17-28 (94)
74 KOG2208 Vigilin [Lipid transpo 38.2 36 0.00078 40.2 4.2 30 225-254 358-387 (753)
75 PRK08406 transcription elongat 38.1 25 0.00053 33.2 2.4 28 224-251 42-69 (140)
76 PF07885 Ion_trans_2: Ion chan 35.7 30 0.00064 28.4 2.3 16 398-414 39-54 (79)
77 PF01371 Trp_repressor: Trp re 34.6 6.5 0.00014 34.7 -1.8 33 109-143 31-70 (87)
78 PRK01064 hypothetical protein; 33.5 30 0.00066 30.0 2.0 20 225-244 41-60 (78)
79 PF14611 SLS: Mitochondrial in 33.1 1E+02 0.0022 30.0 5.8 58 225-298 37-94 (210)
80 PRK01381 Trp operon repressor; 31.8 17 0.00037 33.1 0.3 29 117-145 43-78 (99)
81 PRK02821 hypothetical protein; 30.7 31 0.00067 29.9 1.6 20 225-244 42-61 (77)
82 PF14611 SLS: Mitochondrial in 30.4 5.1E+02 0.011 25.1 11.2 124 117-293 36-164 (210)
83 KOG1423 Ras-like GTPase ERA [C 30.4 6.5 0.00014 42.6 -3.0 40 211-250 325-373 (379)
84 PRK00468 hypothetical protein; 30.1 33 0.00071 29.5 1.7 18 225-242 41-58 (75)
85 cd02414 jag_KH jag_K homology 30.1 32 0.00069 28.8 1.6 21 225-245 35-55 (77)
86 PRK12327 nusA transcription el 28.1 58 0.0013 35.4 3.5 40 210-250 233-273 (362)
87 PF00408 PGM_PMM_IV: Phosphogl 26.8 1.8E+02 0.0039 23.9 5.4 24 269-292 49-72 (73)
88 PTZ00225 60S ribosomal protein 26.2 1.4E+02 0.003 30.2 5.6 59 225-295 117-191 (214)
89 COG4245 TerY Uncharacterized p 25.8 99 0.0021 31.6 4.4 72 156-235 5-80 (207)
90 TIGR01953 NusA transcription t 25.4 76 0.0016 34.2 3.8 39 210-249 231-270 (341)
91 PF09840 DUF2067: Uncharacteri 23.6 2.4E+02 0.0052 28.2 6.6 52 235-300 14-66 (190)
92 PF13083 KH_4: KH domain; PDB: 23.5 19 0.00042 29.5 -0.8 20 225-244 40-59 (73)
93 KOG2675 Adenylate cyclase-asso 23.3 97 0.0021 35.0 4.1 15 175-189 10-24 (480)
94 KOG3273 Predicted RNA-binding 22.7 52 0.0011 33.9 1.8 51 224-292 179-229 (252)
95 KOG2279 Kinase anchor protein 22.2 54 0.0012 37.8 2.0 32 224-255 78-109 (608)
96 COG1837 Predicted RNA-binding 21.6 56 0.0012 28.5 1.6 17 225-241 41-57 (76)
97 TIGR01952 nusA_arch NusA famil 21.3 73 0.0016 30.4 2.4 28 224-251 43-70 (141)
98 PF00639 Rotamase: PPIC-type P 21.2 97 0.0021 26.4 2.9 33 270-302 1-34 (95)
99 PF13711 DUF4160: Domain of un 20.5 2.2E+02 0.0048 23.2 4.8 14 266-279 14-27 (66)
100 KOG3671 Actin regulatory prote 20.3 98 0.0021 35.5 3.5 14 100-113 74-87 (569)
101 COG0195 NusA Transcription elo 20.0 74 0.0016 31.8 2.3 33 219-251 81-113 (190)
102 PF00472 RF-1: RF-1 domain; I 20.0 1.7E+02 0.0036 26.6 4.3 51 227-296 20-74 (113)
No 1
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=100.00 E-value=1.1e-37 Score=322.90 Aligned_cols=371 Identities=18% Similarity=0.142 Sum_probs=255.2
Q ss_pred HhhhccCcchhhhccCcc--ccCCCCCCCCCC-CCCCC--ccccccccCCCcccCCCCCCCccccCCCCCCCCCCCCCCc
Q 008326 27 RKKRKWDQPAESLINFPL--ASFGISLPGVPV-APVVP--APAAAAFFTNPPVASGATVPPVVLQGPLPPKFNQPKVQDE 101 (570)
Q Consensus 27 r~krkwdqpae~~~~~pl--~~~g~~~p~~~~-~~~~~--aa~~~a~~~~~~~~~~~~vpp~~~~~s~~~k~~~~k~~de 101 (570)
-+.|+|||+++.=..+++ .+.|...|+... .+... ++++-++.+|.-+-..-..-+. +-.+.+.+...++..|+
T Consensus 13 ~~~~~WD~~~~~d~~~~~~~~~s~~~~p~eS~~~~~~~h~~~~s~s~~~N~~~~~k~~~~~~-~Na~~~i~~p~N~~K~~ 91 (531)
T KOG1960|consen 13 NYSRDWDSRFTEDSYSRRDSQRSGNEAPRESRYYRKEEHLQERSRSRSPNRDSRWKSSSSGF-ANAHPPIEEPTNNGKEA 91 (531)
T ss_pred CccccccCCCCCccccCchhhhccCCCCCcccccCcchhhhhhhhccCcchhcccccccccc-ccccchhhcccccchhH
Confidence 467899999975444333 222444555332 22222 4555567788755321111111 11122224446777788
Q ss_pred eeEEeEEEcCCCCccccceecchhHHHHHHHHhCCeEeeeccccCCCCC--CCCCCCeEEEEecccccchHHHHHHHHHH
Q 008326 102 LIIAREIVINDSESSVRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAP--PDGEKPLYLHISAGAHVKTAERILAVDHA 179 (570)
Q Consensus 102 ~~f~aEIEINDlPq~~Ry~LTKg~Tq~eIqe~TGA~VtTRGrYyPPg~~--~~gepPLYL~Ieg~telnT~ERikaVD~A 179 (570)
+ ..++.+|||.+++|||.+|||.++++|.+++|+.|.+||+|++++.. .++++||||||.+.+. +++++|
T Consensus 92 ~-~~a~~~iN~~~~~~~~~~TRg~~~d~Ie~~~G~~~~~RGs~~~~El~~vg~~~~pLv~hI~~~T~-------Ei~~~A 163 (531)
T KOG1960|consen 92 A-AAAARRINESLQSTKATSTRGTSYDHIEGITGTTSASRGSAPAPELPPVGSSEGPLVDHIPPSTA-------EITSKA 163 (531)
T ss_pred H-HHHHHHhhcccccccceeccchhHHhhhhhccceeeccCCCCCccCCCCCCCCCcceeecCCccH-------HHHHHH
Confidence 8 48899999999999999999999999999999999999999999974 5789999999999875 699999
Q ss_pred HHHHHHHHHcCCC----------CCCcc--c-------cccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHH
Q 008326 180 AAMVEEMLKQGHA----------GFPTL--Q-------TVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIM 240 (570)
Q Consensus 180 vskIkEiLke~P~----------~~p~~--~-------~p~~~G~k~~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq 240 (570)
+++|+-..+++.. +.+.+ + .++..|+++++ |+||++| +|.||+.+..-|++..||.+|+
T Consensus 164 i~RIkgv~~~~~~~~n~~~V~i~~~~sP~~~i~~~V~~~~f~~G~~Y~~-k~~v~~~-~P~~~~K~~~~~r~d~~La~~~ 241 (531)
T KOG1960|consen 164 IERIKGVFMQDVEINNVRNVYILVRASPLSEIENKVGVQLFSKGRYYPN-KALATDK-DPPLYLKIVSHNRKDLTLALQE 241 (531)
T ss_pred HhhCccceeecccccccceEEEeecCCchhhhccccccccccccccchh-heecccC-CcchhhhhhccCccchhhhhhh
Confidence 9999966655421 11111 1 23577888888 9999999 9999999999999999999999
Q ss_pred HhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhcccccc-----ccccc-cCCC
Q 008326 241 NETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGASRVS-----SCKVY-NAVP 314 (570)
Q Consensus 241 ~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~tV~eE~~a~r~~-----~~k~y-~avp 314 (570)
.||++++.|||||||.+|++.|+|++||||++|+|.+.+.+.+||++|+||+++|+.+|.+|--. .+..| ....
T Consensus 242 ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl~~~v~~~~sr~~~~~~~~~p~~~y~~~~~ 321 (531)
T KOG1960|consen 242 IESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNGNGENGAPRRKWNLEEKVYINLSRGFHRQAIVGPQGAYVKHIQ 321 (531)
T ss_pred hhhhhhhhhccccccccCcccccccCCceeEEeecCCchhhccchhHHHhHHHHHHHHhhhhhhhcccccCCcccccccC
Confidence 99999999999999999999999999999999999999999999999999999999999876211 11222 2222
Q ss_pred CchhhhccccCCC---CccccCccccceeccccccCCCCCCCCCCccceeeecceeecccc--ccccC--CCCCCccCCC
Q 008326 315 PPQQLLTGIQGFG---NEQKLNAGSAVILTSTVNLSSVPLAPSVPGVTTVYSQGMMLQSGG--ILNSV--QPQQNIVGYP 387 (570)
Q Consensus 315 ppqqll~gv~~s~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~--~~~~~--~~~~~~~~~~ 387 (570)
++|.-+-.+..++ +++..|--+- ...++-.++......|.-- .-.++ -+++-.+--.
T Consensus 322 ~~~~~~~~~~g~~s~~i~p~~~~~~~----------------~p~~~~~~~~~~~~~~~~~~~~~~~i~~v~~qy~~~~~ 385 (531)
T KOG1960|consen 322 QETRTRVQIKGQGSAFIEPSTNRESD----------------EPIHLCIMSHDPNAIQRAKVLCEDLIASVHQQYKAWKS 385 (531)
T ss_pred CCCCcceeccCccceeecCCCCCCCC----------------CCcccccccCChhhhhhhhhcccccCCcccccCccccc
Confidence 3343333333332 3333222110 1112222222222223210 00111 1455556667
Q ss_pred CCCCCCCcccccCCCCCcCCChHHHHHHHHhcCCCCCccccc
Q 008326 388 QPVSTGGTSYSGYEGIYPQATPLQQVALALRQSSSPLTSLVA 429 (570)
Q Consensus 388 ~p~~~~g~~y~gy~~iypqatplqqva~~l~~~~s~~~~~v~ 429 (570)
||.+ -+.-+|-||-+|-+-| |+++|+-+.-+-||..+
T Consensus 386 qp~~--~~~~~~~~~~~~p~~~---~~~~~~~~~q~~~qp~~ 422 (531)
T KOG1960|consen 386 QPKD--RDQNQGNRAYNPPNRN---QAFSARDSRQEKTQPTN 422 (531)
T ss_pred CCCc--ccccCCCCCCCCCCcc---ccccCCCCCCCCCCCCC
Confidence 8854 4556788899987776 68888887666665443
No 2
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=99.95 E-value=5.4e-28 Score=255.85 Aligned_cols=158 Identities=23% Similarity=0.323 Sum_probs=128.5
Q ss_pred HHHHHHHhCCeEeeeccccCCC-C-CCCCCCCeEEEEecccccchHH---HHHHHHHHHHHHHHHHHcCCCCCCcccccc
Q 008326 127 QEEIQKCTGAVVITRGKYRLPN-A-PPDGEKPLYLHISAGAHVKTAE---RILAVDHAAAMVEEMLKQGHAGFPTLQTVM 201 (570)
Q Consensus 127 q~eIqe~TGA~VtTRGrYyPPg-~-~~~gepPLYL~Ieg~telnT~E---RikaVD~AvskIkEiLke~P~~~p~~~~p~ 201 (570)
+++|....+.... -+++. + ..++..++|.. .|. ++|||| |.++.++.+..|.++|+.++.|+++.+
T Consensus 61 iee~t~kLrt~d~----~~p~~~e~rSPsp~p~yda-~g~-R~ntRe~R~r~~Le~er~e~I~~~lk~nP~fkpP~D--- 131 (554)
T KOG0119|consen 61 IEEITRKLRTGDV----GVPPPRELRSPSPEPVYDA-KGK-RLNTREQRARKKLEDERHEIIEEILKLNPGFKPPAD--- 131 (554)
T ss_pred HHHhhhhhccccC----CCCCCccccCCCcchhhhh-hcc-chhhHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCcc---
Confidence 4455554444321 14444 3 67888999974 443 478999 578889999999999999999997654
Q ss_pred CCCc-ccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCC------CCCCCCCCCcEEEEE
Q 008326 202 GNGV-QAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEG------LQGEEVHQPLHLFLS 274 (570)
Q Consensus 202 ~~G~-k~~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~------~~g~EsdEPLHV~Is 274 (570)
|.+ ..+++|||||+++||+|||+|+||||||+|+|+||+||||||+||||||++... ......+||||++|+
T Consensus 132 -Yk~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Is 210 (554)
T KOG0119|consen 132 -YKPPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLIS 210 (554)
T ss_pred -cCcccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEe
Confidence 444 378999999999999999999999999999999999999999999999996321 112246899999999
Q ss_pred eCCHHHHHHHHHHHHHHHHH
Q 008326 275 SNNPKSLEEAKRLAENLLDT 294 (570)
Q Consensus 275 a~~~e~l~kAk~LiEnLL~t 294 (570)
+++.|+|++|.++||+||..
T Consensus 211 adt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 211 ADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred cchHHHHHHHHHHHHHHHHh
Confidence 99999999999999999995
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=7.8e-26 Score=203.26 Aligned_cols=95 Identities=22% Similarity=0.404 Sum_probs=86.8
Q ss_pred eeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCC-------CCCCCCCCCcEEEEEeCC--HH
Q 008326 209 STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEG-------LQGEEVHQPLHLFLSSNN--PK 279 (570)
Q Consensus 209 ~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~-------~~g~EsdEPLHV~Isa~~--~e 279 (570)
++|||||++.||+|||+|+||||+|+|+|+|++||||+|.|||+||++.+. ...++.+|||||+|++.+ .+
T Consensus 1 ~~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e 80 (120)
T cd02395 1 TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEE 80 (120)
T ss_pred CCEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHH
Confidence 479999999999999999999999999999999999999999999998654 346678999999999999 99
Q ss_pred HHHHHHHHHHHHHHHHHHH-hcccc
Q 008326 280 SLEEAKRLAENLLDTISAE-CGASR 303 (570)
Q Consensus 280 ~l~kAk~LiEnLL~tV~eE-~~a~r 303 (570)
.+++|+++|++||..+.++ .+.+|
T Consensus 81 ~~~~A~~~I~~ll~~~~~~~~~~~k 105 (120)
T cd02395 81 ALAKAVEAIEELLKPAIEGGNDELK 105 (120)
T ss_pred HHHHHHHHHHHHhccCCCccchHHH
Confidence 9999999999999999877 55554
No 4
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=99.88 E-value=1.1e-22 Score=202.76 Aligned_cols=127 Identities=23% Similarity=0.348 Sum_probs=100.9
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCcccc---ccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEe
Q 008326 174 LAVDHAAAMVEEMLKQGHAGFPTLQT---VMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLR 250 (570)
Q Consensus 174 kaVD~AvskIkEiLke~P~~~p~~~~---p~~~G~k~~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IR 250 (570)
+++++.+.+|.-.+.+.....+.... ........+++|||||++.||+|||+||||||+|+++|+||+||||||+||
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 47888888888777754222222111 111122578999999999999999999999999999999999999999999
Q ss_pred ecCCCCCC-------C-CCCCCCCCCcEEEEEeCCHHH-----HHHHHHHHHHHHHHHHHHhc
Q 008326 251 GRGSGNSE-------G-LQGEEVHQPLHLFLSSNNPKS-----LEEAKRLAENLLDTISAECG 300 (570)
Q Consensus 251 GRGSg~~E-------~-~~g~EsdEPLHV~Isa~~~e~-----l~kAk~LiEnLL~tV~eE~~ 300 (570)
||||++.. + ...++.+|||||+|++..+.. |..|.+.|+.||.++.++..
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 99999852 1 233568999999999988774 77889999999999999886
No 5
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.85 E-value=2.8e-21 Score=188.70 Aligned_cols=149 Identities=14% Similarity=0.119 Sum_probs=124.0
Q ss_pred ccccCCCC--CCCCCCCeEEEEecccccchHH---HHHHHHHHHHHHHHHHHcCCCCCCccccccCCCc-ccceeEEEec
Q 008326 142 GKYRLPNA--PPDGEKPLYLHISAGAHVKTAE---RILAVDHAAAMVEEMLKQGHAGFPTLQTVMGNGV-QAMSTSVFLG 215 (570)
Q Consensus 142 GrYyPPg~--~~~gepPLYL~Ieg~telnT~E---RikaVD~AvskIkEiLke~P~~~p~~~~p~~~G~-k~~~eKI~Ip 215 (570)
+-++|+.. ..+..+|.|..|.. .+||+| ++++.|+.+-++++.++.-+.+.. ++.|-+ ..+++|||||
T Consensus 82 ~d~Vp~~re~Rspsppp~yd~~Gr--Rlntre~ry~kkLeder~~l~era~k~lp~fv~----p~dy~rpsk~q~KiYIP 155 (269)
T COG5176 82 PDGVPSKRELRSPSPPPRYDEIGR--RLNTREARYNKKLEDERLWLKERAQKILPRFVL----PNDYIRPSKYQNKIYIP 155 (269)
T ss_pred CCCCCchhhccCCCCCcchhHHhh--hhhHHHHHHhhhhhHHHHHHHHHHHHhcCcccC----CccccCcccccceEEee
Confidence 33456653 57889999998744 478999 578889999999999999887774 344544 6789999999
Q ss_pred CCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCC-------CCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 008326 216 FDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQ-------GEEVHQPLHLFLSSNNPKSLEEAKRLA 288 (570)
Q Consensus 216 ld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~-------g~EsdEPLHV~Isa~~~e~l~kAk~Li 288 (570)
+++||+.||+|+||||+|.|+|++|..|+|||.|||+||.+ |+.. .....++||++|+++..+++.++.++|
T Consensus 156 V~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvK-egk~ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~ 234 (269)
T COG5176 156 VQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVK-EGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQ 234 (269)
T ss_pred hhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccc-cCcccccCchhhhhhHHhHHHHhhcchhhhHHHHHHHH
Confidence 99999999999999999999999999999999999999986 2211 123568899999999999999999999
Q ss_pred HHHHHHHHH
Q 008326 289 ENLLDTISA 297 (570)
Q Consensus 289 EnLL~tV~e 297 (570)
.|.|.+.+.
T Consensus 235 ~n~I~~a~~ 243 (269)
T COG5176 235 LNAIREARR 243 (269)
T ss_pred HHHHHHHhc
Confidence 999987653
No 6
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=99.24 E-value=2.4e-12 Score=135.55 Aligned_cols=150 Identities=23% Similarity=0.385 Sum_probs=123.3
Q ss_pred chhHHHHHHHHhCCeEeeeccccCCCCC---CCCCCCeEEEEecccccchHHHHHHHHHHHHHHHHHHHcCCCCCCcccc
Q 008326 123 KRHTQEEIQKCTGAVVITRGKYRLPNAP---PDGEKPLYLHISAGAHVKTAERILAVDHAAAMVEEMLKQGHAGFPTLQT 199 (570)
Q Consensus 123 Kg~Tq~eIqe~TGA~VtTRGrYyPPg~~---~~gepPLYL~Ieg~telnT~ERikaVD~AvskIkEiLke~P~~~p~~~~ 199 (570)
+-.++..|+.++++.+..|||+---.++ -++..|.|++|.+.+. +.+..|..+|..++..
T Consensus 233 ~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~-------~g~~~A~r~~~nl~~~---------- 295 (531)
T KOG1960|consen 233 KDLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNG-------NGENGAPRRKWNLEEK---------- 295 (531)
T ss_pred cchhhhhhhhhhhhhhhhccccccccCcccccccCCceeEEeecCCc-------hhhccchhHHHhHHHH----------
Confidence 3467888999999999999998765554 4567999999999987 5566666655554332
Q ss_pred ccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHH
Q 008326 200 VMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPK 279 (570)
Q Consensus 200 p~~~G~k~~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e 279 (570)
++|.+. ..|| +-.|.||-|.|.|||+.+|-.+++|+|.||+|+++.+.+++++|.||||..+++.
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 3357899999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhccccc
Q 008326 280 SLEEAKRLAENLLDTISAECGASRV 304 (570)
Q Consensus 280 ~l~kAk~LiEnLL~tV~eE~~a~r~ 304 (570)
.|+.|+-+|++||..|..+|.+|+.
T Consensus 361 ~~~~~~~~~~~~i~~v~~qy~~~~~ 385 (531)
T KOG1960|consen 361 AIQRAKVLCEDLIASVHQQYKAWKS 385 (531)
T ss_pred hhhhhhhcccccCCcccccCccccc
Confidence 9999999999999999999998863
No 7
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.11 E-value=2.3e-09 Score=117.37 Aligned_cols=166 Identities=20% Similarity=0.287 Sum_probs=120.3
Q ss_pred eeEEeEEEcCCCCccccceecc-hhHHHHHHHHhCCeEee-eccccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHH
Q 008326 102 LIIAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVIT-RGKYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHA 179 (570)
Q Consensus 102 ~~f~aEIEINDlPq~~Ry~LTK-g~Tq~eIqe~TGA~VtT-RGrYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~A 179 (570)
...+.||.|-+- +|-.++-| |+|++.+++++|+.++. +-. ...+...+|| .|+|.-. .|+.|
T Consensus 137 ~~ttqeI~IPa~--k~GlIIGKgGETikqlqe~sg~k~i~iqd~----~~~~~~~Kpl--ritGdp~--------~ve~a 200 (600)
T KOG1676|consen 137 VETTQEILIPAN--KCGLIIGKGGETIKQLQEQSGVKMILVQDG----SIATGADKPL--RITGDPD--------KVEQA 200 (600)
T ss_pred cceeeeeccCcc--ceeeEeccCccHHHHHHhhcCCceEEEecC----CcCCCCCCce--eecCCHH--------HHHHH
Confidence 334678888776 58888877 99999999999998653 221 1233478898 6788763 79999
Q ss_pred HHHHHHHHHcCCCCCCccccccCCCccc-ceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCC
Q 008326 180 AAMVEEMLKQGHAGFPTLQTVMGNGVQA-MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSE 258 (570)
Q Consensus 180 vskIkEiLke~P~~~p~~~~p~~~G~k~-~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E 258 (570)
..+|.++|+++-.-.+.. ...+|... -++++-|. +|.| -||.|||-+|.|||+|+.|||+||+|+=-
T Consensus 201 ~~lV~dil~e~~~~~~g~--~~~~g~~~g~~~~~~V~---VPr~-~VG~IIGkgGE~IKklq~etG~KIQfkpD------ 268 (600)
T KOG1676|consen 201 KQLVADILREEDDEVPGS--GGHAGVRGGGSATREVK---VPRS-KVGIIIGKGGEMIKKLQNETGAKIQFKPD------ 268 (600)
T ss_pred HHHHHHHHHhcccCCCcc--ccccCcCccccceeEEe---cccc-ceeeEEecCchHHHHHhhccCceeEeecC------
Confidence 999999999642211111 12233321 23355444 4565 69999999999999999999999999841
Q ss_pred CCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHh
Q 008326 259 GLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 299 (570)
Q Consensus 259 ~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~tV~eE~ 299 (570)
.+..-|+..+..-.+.+.++.|++||.+||..+.+.-
T Consensus 269 ----d~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~ 305 (600)
T KOG1676|consen 269 ----DDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGA 305 (600)
T ss_pred ----CCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhccC
Confidence 1224557777777889999999999999999998873
No 8
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=98.98 E-value=2.3e-10 Score=131.02 Aligned_cols=81 Identities=32% Similarity=0.514 Sum_probs=76.3
Q ss_pred eEEeEEEcCCCCccccceecchhHHHHHHHHhCCeEeeeccccCCCC-CCCCCCCeEEEEecccccchHHHHHHHHHHHH
Q 008326 103 IIAREIVINDSESSVRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNA-PPDGEKPLYLHISAGAHVKTAERILAVDHAAA 181 (570)
Q Consensus 103 ~f~aEIEINDlPq~~Ry~LTKg~Tq~eIqe~TGA~VtTRGrYyPPg~-~~~gepPLYL~Ieg~telnT~ERikaVD~Avs 181 (570)
+|.++++|||+||.+||.+|..+++..|.+.+++.|+|||.|||+++ +.++|++|||+|+|.++ ..|++|+.
T Consensus 897 ~y~~~~~inD~Pq~~r~~vt~~~~L~~i~e~~~~~it~rg~f~~~gk~p~~gErklyl~ve~~~e-------~~vqra~~ 969 (997)
T KOG0334|consen 897 IYEAELEINDFPQNARWRVTYKEALLRISEPTAAGITTRGKFNPPGKEPKPGERKLYLLVEGPDE-------LSVQRAIE 969 (997)
T ss_pred eeeeeccccccchhcceeeechhhhhhccCccccceeeccccCCCCCCCCCcchhhhhhhhcchh-------HHHHHHHH
Confidence 57999999999999999999999999999999999999999999997 66899999999999988 78999999
Q ss_pred HHHHHHHcC
Q 008326 182 MVEEMLKQG 190 (570)
Q Consensus 182 kIkEiLke~ 190 (570)
+|.+.+++.
T Consensus 970 e~~r~l~e~ 978 (997)
T KOG0334|consen 970 ELERLLEEE 978 (997)
T ss_pred HHHHHHHHH
Confidence 999988875
No 9
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.82 E-value=1.9e-08 Score=95.39 Aligned_cols=129 Identities=20% Similarity=0.193 Sum_probs=87.4
Q ss_pred cchhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEE--ecccccchHHHHHHHHHHHHHHHHHHHcCCCCCCcccc
Q 008326 122 TKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHI--SAGAHVKTAERILAVDHAAAMVEEMLKQGHAGFPTLQT 199 (570)
Q Consensus 122 TKg~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~I--eg~telnT~ERikaVD~AvskIkEiLke~P~~~p~~~~ 199 (570)
..|++++.|+++||+.|...- .+. ...| .+.+. .++++|...|+.+...- .++..+
T Consensus 15 ~gG~~Ik~I~~~tgv~I~Id~----------~~g--~V~I~~~t~d~-------~~i~kA~~~I~~i~~gf---~~e~A~ 72 (172)
T TIGR03665 15 KGGETKKEIEERTGVKLDIDS----------ETG--EVKIEEEDEDP-------LAVMKAREVVKAIGRGF---SPEKAL 72 (172)
T ss_pred CchhHHHHHHHHhCcEEEEEc----------CCc--eEEEecCCCCH-------HHHHHHHHHHHHHHcCC---CHHHHH
Confidence 459999999999999987652 112 2445 33333 58999999999976641 111000
Q ss_pred ccCCCcccceeEEEecCCCC--CCC---ceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEE
Q 008326 200 VMGNGVQAMSTSVFLGFDAD--ASL---NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLS 274 (570)
Q Consensus 200 p~~~G~k~~~eKI~Ipld~~--P~F---NfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Is 274 (570)
- -.|--+.- +| |.+.++ ..- ..+|+|||++|.+++.||..|||+|+|-| =.|+|.
T Consensus 73 ~-l~gd~y~~-~V-i~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~-----------------~~v~i~ 132 (172)
T TIGR03665 73 K-LLDDDYML-EV-IDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG-----------------KTVGII 132 (172)
T ss_pred H-hcCCcceE-EE-EEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC-----------------CEEEEE
Confidence 0 00111111 12 222221 000 25999999999999999999999999975 258899
Q ss_pred eCCHHHHHHHHHHHHHHHH
Q 008326 275 SNNPKSLEEAKRLAENLLD 293 (570)
Q Consensus 275 a~~~e~l~kAk~LiEnLL~ 293 (570)
| ++++++.|++++++||+
T Consensus 133 G-~~~~~~~A~~~i~~li~ 150 (172)
T TIGR03665 133 G-DPEQVQIAREAIEMLIE 150 (172)
T ss_pred C-CHHHHHHHHHHHHHHHc
Confidence 9 99999999999999994
No 10
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.78 E-value=3.2e-08 Score=94.55 Aligned_cols=145 Identities=19% Similarity=0.197 Sum_probs=94.5
Q ss_pred EEeEEEcCCCCccccceec-chhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEe---cccccchHHHHHHHHHH
Q 008326 104 IAREIVINDSESSVRYKLT-KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHIS---AGAHVKTAERILAVDHA 179 (570)
Q Consensus 104 f~aEIEINDlPq~~Ry~LT-Kg~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~Ie---g~telnT~ERikaVD~A 179 (570)
+...+.|..- +.+.++. .|.+++.|+++||+.|...- .+... .|. +.+. ..+++|
T Consensus 3 ~~~~i~IP~~--kig~iIG~gGk~Ik~I~e~tg~~I~i~~----------~~g~V--~I~~~~~~d~-------~~i~kA 61 (180)
T PRK13763 3 MMEYVKIPKD--RIGVLIGKKGETKKEIEERTGVKLEIDS----------ETGEV--IIEPTDGEDP-------LAVLKA 61 (180)
T ss_pred ceEEEEcCHH--HhhhHhccchhHHHHHHHHHCcEEEEEC----------CCCeE--EEEeCCCCCH-------HHHHHH
Confidence 3445666433 3455554 48999999999999997753 12333 444 3443 589999
Q ss_pred HHHHHHHHHcCCCCCCccccccCCCcccceeEEEecCCCC--CCC---ceeeeEeCCCchhHHHHHHhhCcEEEEeecCC
Q 008326 180 AAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDAD--ASL---NIAARIRGPNDQYINHIMNETGATVLLRGRGS 254 (570)
Q Consensus 180 vskIkEiLke~P~~~p~~~~p~~~G~k~~~eKI~Ipld~~--P~F---NfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGS 254 (570)
...|+.+... +.++..+- -.|--+.-+. |.+.++ .+- ..+|+|||++|.+++.||..|||+|+|-|+
T Consensus 62 ~~~I~ai~~g---f~~e~A~~-l~gd~y~~~V--i~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~-- 133 (180)
T PRK13763 62 RDIVKAIGRG---FSPEKALR-LLDDDYVLEV--IDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGK-- 133 (180)
T ss_pred HHHHHHHhcC---CCHHHHHH-HhCCCceEEE--EEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCC--
Confidence 9999998764 11110000 0011111111 111221 000 259999999999999999999999999752
Q ss_pred CCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 008326 255 GNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 293 (570)
Q Consensus 255 g~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~ 293 (570)
.++|.| ++++++.|++.+++|++
T Consensus 134 ---------------~v~i~G-~~~~~~~A~~~I~~li~ 156 (180)
T PRK13763 134 ---------------TVAIIG-DPEQVEIAREAIEMLIE 156 (180)
T ss_pred ---------------EEEEEe-CHHHHHHHHHHHHHHHc
Confidence 277776 99999999999999984
No 11
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.73 E-value=2.3e-07 Score=102.10 Aligned_cols=158 Identities=21% Similarity=0.355 Sum_probs=112.7
Q ss_pred EEEcCCCCccccceecc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHHHHHHHH
Q 008326 107 EIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHAAAMVEE 185 (570)
Q Consensus 107 EIEINDlPq~~Ry~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~AvskIkE 185 (570)
+|.|--+ .+-.++-| |++++.|+.+||+.| .|.|...++.-||+| +|-|... .+++|..+|.+
T Consensus 233 ~V~VPr~--~VG~IIGkgGE~IKklq~etG~KI----QfkpDd~p~speR~~--~IiG~~d--------~ie~Aa~lI~e 296 (600)
T KOG1676|consen 233 EVKVPRS--KVGIIIGKGGEMIKKLQNETGAKI----QFKPDDDPSSPERPA--QIIGTVD--------QIEHAAELINE 296 (600)
T ss_pred EEecccc--ceeeEEecCchHHHHHhhccCcee----EeecCCCCCCcccee--eeecCHH--------HHHHHHHHHHH
Confidence 5555444 47777777 999999999999988 677877776678888 6778653 68899999999
Q ss_pred HHHcCCCCCCccccccCCCcccc--eeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCC
Q 008326 186 MLKQGHAGFPTLQTVMGNGVQAM--STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGE 263 (570)
Q Consensus 186 iLke~P~~~p~~~~p~~~G~k~~--~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~ 263 (570)
||.....-..- .+.-|.-.. +--+-||-+ =.|+|||++|.|||.|..|+||++.|-=- ..
T Consensus 297 ii~~~~~~~~~---~~~~G~P~~~~~fy~~VPa~------KcGLvIGrGGEtIK~in~qSGA~~el~r~---------~p 358 (600)
T KOG1676|consen 297 IIAEAEAGAGG---GMGGGAPGLVAQFYMKVPAD------KCGLVIGRGGETIKQINQQSGARCELSRQ---------PP 358 (600)
T ss_pred HHHHHhccCCC---CcCCCCccceeeEEEecccc------ccccccCCCccchhhhcccCCccccccCC---------CC
Confidence 99864211100 011122111 222224433 27999999999999999999999976421 11
Q ss_pred CCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHH
Q 008326 264 EVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAE 298 (570)
Q Consensus 264 EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~tV~eE 298 (570)
-.+.+..+|+.-.++.+|+-|+.||++-+.-+...
T Consensus 359 ~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~~~n 393 (600)
T KOG1676|consen 359 NGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDIAPN 393 (600)
T ss_pred CCCccceEEEEecCcccchHHHHHHHHHhcccCCC
Confidence 23566889999999999999999999877765544
No 12
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.49 E-value=5.1e-07 Score=70.12 Aligned_cols=63 Identities=27% Similarity=0.393 Sum_probs=50.7
Q ss_pred eEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 008326 210 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 289 (570)
Q Consensus 210 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiE 289 (570)
.+|.||. +++++|||++|.++++|+++|||+|.|...+. ..+...|.|.|. .+++++|+.+++
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 4566764 67999999999999999999999999986433 235567888887 788998888763
No 13
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.42 E-value=5.4e-07 Score=72.36 Aligned_cols=58 Identities=21% Similarity=0.422 Sum_probs=48.2
Q ss_pred eEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 008326 210 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 289 (570)
Q Consensus 210 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiE 289 (570)
+.+.||.+ ++|+|||++|+++|.|+++|||+|.|-- + -.|.|+|.+.+++++|+++++
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------D----------GTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEeChh------heeeeECCCchHHHHHHHHHCCEEEeCC------C----------CEEEEEeCCHHHHHHHHHHhC
Confidence 45556532 5899999999999999999999998742 1 259999999999999999875
No 14
>smart00322 KH K homology RNA-binding domain.
Probab=98.37 E-value=1.9e-06 Score=65.41 Aligned_cols=66 Identities=23% Similarity=0.341 Sum_probs=54.3
Q ss_pred ceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 008326 208 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 287 (570)
Q Consensus 208 ~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~L 287 (570)
...+|+|+. +++|+|||++|.++++|+++|||+|.+.+.++ ....+.|.+. .++++.|+.+
T Consensus 3 ~~~~i~i~~------~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~------------~~~~v~i~g~-~~~v~~a~~~ 63 (69)
T smart00322 3 VTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS------------EERVVEITGP-PENVEKAAEL 63 (69)
T ss_pred eEEEEEEcc------hhcceeECCCchHHHHHHHHHCCEEEECCCCC------------CccEEEEEcC-HHHHHHHHHH
Confidence 345677764 57899999999999999999999999986433 3466888888 8999999999
Q ss_pred HHHHH
Q 008326 288 AENLL 292 (570)
Q Consensus 288 iEnLL 292 (570)
+++++
T Consensus 64 i~~~~ 68 (69)
T smart00322 64 ILEIL 68 (69)
T ss_pred HHHHh
Confidence 98876
No 15
>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=98.31 E-value=3.6e-07 Score=71.47 Aligned_cols=52 Identities=25% Similarity=0.433 Sum_probs=45.9
Q ss_pred ceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 008326 223 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 288 (570)
Q Consensus 223 NfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~Li 288 (570)
+++|+|||++|.++++|+++|||+|.|... ++.-.|.|+| +.+++++|+++|
T Consensus 9 ~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-------------~~~~~v~I~G-~~~~v~~A~~~I 60 (60)
T PF00013_consen 9 SLVGRIIGKKGSNIKEIEEETGVKIQIPDD-------------DERDIVTISG-SPEQVEKAKKMI 60 (60)
T ss_dssp HHHHHHHTGGGHHHHHHHHHHTSEEEEEST-------------TEEEEEEEEE-SHHHHHHHHHHH
T ss_pred HHcCEEECCCCCcHHHhhhhcCeEEEEcCC-------------CCcEEEEEEe-CHHHHHHHHhhC
Confidence 368999999999999999999999999653 1446899999 999999999986
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=98.07 E-value=4.8e-06 Score=65.49 Aligned_cols=53 Identities=23% Similarity=0.337 Sum_probs=45.1
Q ss_pred ceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 008326 223 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 288 (570)
Q Consensus 223 NfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~Li 288 (570)
.++|.|||++|.++++|+++|||+|.|-..+ +..-+|.|+|. .+++.+|++++
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 3689999999999999999999999998642 33457899999 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=97.96 E-value=2.5e-05 Score=62.74 Aligned_cols=62 Identities=21% Similarity=0.219 Sum_probs=45.1
Q ss_pred EEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 008326 211 SVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 288 (570)
Q Consensus 211 KI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~Li 288 (570)
++.||. +.+|+|||.+|.++++|+++|||+|.|--... ......++....+.+++++|+.||
T Consensus 3 r~~ip~------~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----------~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 3 RLLVPS------SQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----------PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred EEEECH------HHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----------CCCCceEEEEEeCHHHHHHHHHhh
Confidence 455653 36899999999999999999999999953211 122233444445699999999886
No 18
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.93 E-value=0.00046 Score=72.77 Aligned_cols=161 Identities=16% Similarity=0.200 Sum_probs=103.2
Q ss_pred EeEEEcCCCCccccceecc-hhHHHHHHHHhCCeEee-ec-cccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHHHH
Q 008326 105 AREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVIT-RG-KYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHAAA 181 (570)
Q Consensus 105 ~aEIEINDlPq~~Ry~LTK-g~Tq~eIqe~TGA~VtT-RG-rYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~Avs 181 (570)
+=.|-|-.+- +--++-| |+|+.++|++|||.|-. |- -|||- ..|| ..+|+|..+ ++..-+.
T Consensus 40 ~ikvLips~A--aGsIIGKGG~ti~~lqk~tgariklSks~dfyPG----TTeR--vcli~Gt~e--------ai~av~e 103 (402)
T KOG2191|consen 40 FLKVLIPSYA--AGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPG----TTER--VCLIQGTVE--------ALNAVHE 103 (402)
T ss_pred EEEEEeeccc--ccceeccchHHHHHHHhccCcEEEeccccccCCC----ccce--EEEEeccHH--------HHHHHHH
Confidence 4466666664 6778888 89999999999999865 22 24441 2333 347888643 5555566
Q ss_pred HHHHHHHcCCCCCCc-cc--cccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEee-cCCCCC
Q 008326 182 MVEEMLKQGHAGFPT-LQ--TVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRG-RGSGNS 257 (570)
Q Consensus 182 kIkEiLke~P~~~p~-~~--~p~~~G~k~~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRG-RGSg~~ 257 (570)
.|.+-|.+.+....- .+ .+.. --+-.+-||.||-. -.|.|||++|.|+|.|+++.||-|+|-- +-.+
T Consensus 104 fI~dKire~p~~~~k~v~~~~pqt-~~r~kqikivvPNs------tag~iigkggAtiK~~~Eqsga~iqisPqkpt~-- 174 (402)
T KOG2191|consen 104 FIADKIREKPQAVAKPVDILQPQT-PDRIKQIKIVVPNS------TAGMIIGKGGATIKAIQEQSGAWIQISPQKPTG-- 174 (402)
T ss_pred HHHHHHHHhHHhhcCCccccCCCC-ccccceeEEeccCC------cccceecCCcchHHHHHHhhCcceEecccCCCC--
Confidence 666666655432211 00 0000 00234577877732 3899999999999999999999999973 2111
Q ss_pred CCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhc
Q 008326 258 EGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECG 300 (570)
Q Consensus 258 E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~tV~eE~~ 300 (570)
. ..+ -.|...+.++|++.+|++|| |.+|.++-+
T Consensus 175 --~---sLq--ervvt~sge~e~~~~A~~~I---L~Ki~eDpq 207 (402)
T KOG2191|consen 175 --I---SLQ--ERVVTVSGEPEQNMKAVSLI---LQKIQEDPQ 207 (402)
T ss_pred --c---cce--eEEEEecCCHHHHHHHHHHH---HHHhhcCCc
Confidence 1 111 25666688899999888775 667777753
No 19
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.69 E-value=6.6e-05 Score=81.95 Aligned_cols=84 Identities=26% Similarity=0.326 Sum_probs=64.8
Q ss_pred CCCCceeEEe--EEEcCCCCccccceecchhHHHHHHHHhCCeEeeeccccCCCC---------CCCCCCCeEEEEeccc
Q 008326 97 KVQDELIIAR--EIVINDSESSVRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNA---------PPDGEKPLYLHISAGA 165 (570)
Q Consensus 97 k~~de~~f~a--EIEINDlPq~~Ry~LTKg~Tq~eIqe~TGA~VtTRGrYyPPg~---------~~~gepPLYL~Ieg~t 165 (570)
+..|++||-- --|||.+- -.+--+|.||+.++++|||.|.+||+---.+. ....+.+||.+|++.+
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvG---LiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt 213 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVG---LIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADT 213 (554)
T ss_pred ccccceecchhhcCCcceeE---EEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecch
Confidence 7778887632 25677763 23347899999999999999999995433321 1235799999999998
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHcC
Q 008326 166 HVKTAERILAVDHAAAMVEEMLKQG 190 (570)
Q Consensus 166 elnT~ERikaVD~AvskIkEiLke~ 190 (570)
+ +.|++|++.|+.+|+..
T Consensus 214 ~-------eki~~Ai~vienli~~a 231 (554)
T KOG0119|consen 214 Q-------EKIKKAIAVIENLIQSA 231 (554)
T ss_pred H-------HHHHHHHHHHHHHHHhh
Confidence 8 78999999999999964
No 20
>PF13014 KH_3: KH domain
Probab=97.67 E-value=3.8e-05 Score=57.28 Aligned_cols=28 Identities=32% Similarity=0.455 Sum_probs=26.3
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEee
Q 008326 224 IAARIRGPNDQYINHIMNETGATVLLRG 251 (570)
Q Consensus 224 fvgrIIGPrGstlK~Iq~ETGaKI~IRG 251 (570)
++|+|||++|.++++|+++|||+|.|--
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC
Confidence 4789999999999999999999999975
No 21
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.42 E-value=0.0003 Score=67.61 Aligned_cols=63 Identities=13% Similarity=0.192 Sum_probs=53.2
Q ss_pred eEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEE---eCCHHHHHHHHH
Q 008326 210 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLS---SNNPKSLEEAKR 286 (570)
Q Consensus 210 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Is---a~~~e~l~kAk~ 286 (570)
..+.||.+ -+|.|||++|.++|.|+++|||+|.|.-. .-.|.|. +.|++.+++|++
T Consensus 5 ~~i~IP~~------kig~iIG~gGk~Ik~I~e~tg~~I~i~~~---------------~g~V~I~~~~~~d~~~i~kA~~ 63 (180)
T PRK13763 5 EYVKIPKD------RIGVLIGKKGETKKEIEERTGVKLEIDSE---------------TGEVIIEPTDGEDPLAVLKARD 63 (180)
T ss_pred EEEEcCHH------HhhhHhccchhHHHHHHHHHCcEEEEECC---------------CCeEEEEeCCCCCHHHHHHHHH
Confidence 45666643 48899999999999999999999999842 1367787 889999999999
Q ss_pred HHHHHHH
Q 008326 287 LAENLLD 293 (570)
Q Consensus 287 LiEnLL~ 293 (570)
+++.|+.
T Consensus 64 ~I~ai~~ 70 (180)
T PRK13763 64 IVKAIGR 70 (180)
T ss_pred HHHHHhc
Confidence 9999987
No 22
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.39 E-value=0.00065 Score=73.57 Aligned_cols=139 Identities=14% Similarity=0.186 Sum_probs=87.4
Q ss_pred chhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHHHHHHHHHHHcCCCCCCccccccC
Q 008326 123 KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHAAAMVEEMLKQGHAGFPTLQTVMG 202 (570)
Q Consensus 123 Kg~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~AvskIkEiLke~P~~~p~~~~p~~ 202 (570)
.|.|+++|-+.|-+.|-+ .-.+.....|+.|-.|-+. +...+|..+|-|+|..+-.-
T Consensus 217 eG~TIknItkqTqsriD~----hrken~Gaaek~itvh~tp----------Eg~s~Ac~~ILeimqkEA~~--------- 273 (584)
T KOG2193|consen 217 EGATIKNITKQTQSRIDV----HRKENAGAAEKIITVHSTP----------EGTSKACKMILEIMQKEAVD--------- 273 (584)
T ss_pred CCccccCcchhhhheeee----eecccCCcccCceEEecCc----------cchHHHHHHHHHHHHHhhhc---------
Confidence 499999999999887643 1122234568988776443 25667888899988764111
Q ss_pred CCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHH
Q 008326 203 NGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLE 282 (570)
Q Consensus 203 ~G~k~~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~ 282 (570)
..+.+ .|||+-.---||+|||||..|.+||+||++||+||.|-- +.| .++ .+-.--+.|-| +-|.+.
T Consensus 274 ---~k~~~--e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~----lqe-ls~--ynpERTItVkG-siEac~ 340 (584)
T KOG2193|consen 274 ---DKVAE--EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISK----LQE-LSL--YNPERTITVKG-SIEACV 340 (584)
T ss_pred ---cchhh--hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeee----hhh-hcc--cCccceEEecc-cHHHHH
Confidence 01111 245553344567999999999999999999999999853 333 111 11123455556 555555
Q ss_pred HHHHHHHHHHHHHHHHhc
Q 008326 283 EAKRLAENLLDTISAECG 300 (570)
Q Consensus 283 kAk~LiEnLL~tV~eE~~ 300 (570)
+|..+ ++.++++-|.
T Consensus 341 ~AE~e---ImkKlre~yE 355 (584)
T KOG2193|consen 341 QAEAE---IMKKLRECYE 355 (584)
T ss_pred HHHHH---HHHHHHHHHh
Confidence 55444 4556666664
No 23
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=97.24 E-value=0.0004 Score=66.19 Aligned_cols=56 Identities=11% Similarity=0.174 Sum_probs=48.7
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEE--EeCCHHHHHHHHHHHHHHHHH
Q 008326 224 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFL--SSNNPKSLEEAKRLAENLLDT 294 (570)
Q Consensus 224 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~I--sa~~~e~l~kAk~LiEnLL~t 294 (570)
.+|.|||++|.++|.|+++|||+|.|--. .=.|.| .+.|++.+++|+++++.|...
T Consensus 8 kig~vIG~gG~~Ik~I~~~tgv~I~Id~~---------------~g~V~I~~~t~d~~~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 8 RIGVLIGKGGETKKEIEERTGVKLDIDSE---------------TGEVKIEEEDEDPLAVMKAREVVKAIGRG 65 (172)
T ss_pred HhhhHhCCchhHHHHHHHHhCcEEEEEcC---------------CceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence 58999999999999999999999999731 125777 789999999999999998873
No 24
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=97.08 E-value=0.0015 Score=59.66 Aligned_cols=67 Identities=27% Similarity=0.306 Sum_probs=53.4
Q ss_pred ccceecchhHHHHHHHHhCCeEeeeccccCCCC----------CCCCCCCeEEEEeccc--ccchHHHHHHHHHHHHHHH
Q 008326 117 VRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNA----------PPDGEKPLYLHISAGA--HVKTAERILAVDHAAAMVE 184 (570)
Q Consensus 117 ~Ry~LTKg~Tq~eIqe~TGA~VtTRGrYyPPg~----------~~~gepPLYL~Ieg~t--elnT~ERikaVD~AvskIk 184 (570)
-|.+=.+|.|+++|+++|||.|.+||+---... ....+.|||++|++.+ . .++++|+.+|+
T Consensus 18 G~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~-------e~~~~A~~~I~ 90 (120)
T cd02395 18 GLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPE-------EALAKAVEAIE 90 (120)
T ss_pred EEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHH-------HHHHHHHHHHH
Confidence 366678999999999999999999997422211 1124788999999988 5 68999999999
Q ss_pred HHHHcC
Q 008326 185 EMLKQG 190 (570)
Q Consensus 185 EiLke~ 190 (570)
+++...
T Consensus 91 ~ll~~~ 96 (120)
T cd02395 91 ELLKPA 96 (120)
T ss_pred HHhccC
Confidence 998853
No 25
>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=97.07 E-value=0.0025 Score=72.98 Aligned_cols=64 Identities=22% Similarity=0.391 Sum_probs=55.2
Q ss_pred eeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 008326 209 STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 288 (570)
Q Consensus 209 ~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~Li 288 (570)
-+.+.|+.+ -+|.||||+|.++|.|+++|||+|-|-- .=+|.|.+.+.+.+++|+++|
T Consensus 579 ~~~~~I~~~------ki~~vIG~gGk~I~~i~~~tg~~Idi~d----------------~G~V~I~a~d~~~~~~A~~~I 636 (719)
T TIGR02696 579 IITVKIPVD------KIGEVIGPKGKMINQIQDETGAEISIED----------------DGTVYIGAADGPSAEAARAMI 636 (719)
T ss_pred eEEEEeChH------HhhheeCCCcHhHHHHHHHHCCEEEEec----------------CcEEEEEeCCHHHHHHHHHHH
Confidence 355666644 4899999999999999999999998852 358999999999999999999
Q ss_pred HHHHHH
Q 008326 289 ENLLDT 294 (570)
Q Consensus 289 EnLL~t 294 (570)
++|+..
T Consensus 637 ~~i~~~ 642 (719)
T TIGR02696 637 NAIANP 642 (719)
T ss_pred HHhhCc
Confidence 999985
No 26
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.97 E-value=0.0014 Score=64.72 Aligned_cols=54 Identities=22% Similarity=0.284 Sum_probs=48.5
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHH
Q 008326 224 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTI 295 (570)
Q Consensus 224 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~tV 295 (570)
.+|||||++|.|.+.||.-|||.|.|.|+ +|.|.| ++++++.|++.||.||+..
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~-----------------tVaiiG-~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK-----------------TVAIIG-GFEQVEIAREAVEMLINGA 165 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc-----------------EEEEec-ChhhhHHHHHHHHHHHcCC
Confidence 48999999999999999999999999994 677776 5789999999999999754
No 27
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=96.94 E-value=0.0014 Score=74.30 Aligned_cols=99 Identities=18% Similarity=0.262 Sum_probs=69.2
Q ss_pred eEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 008326 210 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 289 (570)
Q Consensus 210 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiE 289 (570)
+.+.|+.+ .+|.||||+|.++|.|+++|||+|-|- +.=+|.|.+.+.+.+++|+++|+
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 45556533 489999999999999999999999984 23579999999999999999999
Q ss_pred HHHHHHHHHhccccccccccccCCCCchhhhccccCCCCccccCccccceecccccc
Q 008326 290 NLLDTISAECGASRVSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNL 346 (570)
Q Consensus 290 nLL~tV~eE~~a~r~~~~k~y~avpppqqll~gv~~s~~~~~~~~~~~~~~~~~~~~ 346 (570)
.|.... ...+.|. -.+.++..+|..-.+.. ...|+.|--++
T Consensus 611 ~~~~~~---------~~G~i~~------G~V~~I~~~GafVei~~-g~~GllHiSei 651 (684)
T TIGR03591 611 GITAEP---------EVGKIYE------GKVVRIMDFGAFVEILP-GKDGLVHISEI 651 (684)
T ss_pred hhhccc---------ccCcEEE------EEEEEEeCCEEEEEECC-CcEEEEEHHHc
Confidence 995421 1122221 13566666774443332 25677765544
No 28
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.87 E-value=0.0054 Score=66.74 Aligned_cols=156 Identities=17% Similarity=0.220 Sum_probs=103.4
Q ss_pred EEEcCCCCcccccee-cchhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHHHHHHHH
Q 008326 107 EIVINDSESSVRYKL-TKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHAAAMVEE 185 (570)
Q Consensus 107 EIEINDlPq~~Ry~L-TKg~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~AvskIkE 185 (570)
.+.|-|.- +.-++ .||..+++|.+++||+|-+ -|++-+--++| -..|+|+.+ +.-+|-..|--
T Consensus 414 ~~fiP~~~--vGAiIGkkG~hIKql~RfagASiKI----appE~pdvseR--MViItGppe--------aqfKAQgrifg 477 (584)
T KOG2193|consen 414 RMFIPAQA--VGAIIGKKGQHIKQLSRFAGASIKI----APPEIPDVSER--MVIITGPPE--------AQFKAQGRIFG 477 (584)
T ss_pred eeeccHHH--HHHHHhhcchhHHHHHHhccceeee----cCCCCCCccee--EEEecCChH--------HHHhhhhhhhh
Confidence 34555543 44444 5699999999999999843 23331212233 347888864 66778888888
Q ss_pred HHHcCCCCCCccccccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCC
Q 008326 186 MLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEV 265 (570)
Q Consensus 186 iLke~P~~~p~~~~p~~~G~k~~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~Es 265 (570)
-|++..-+.|-. ..+++.-|-|| .+ .+|||||.+|.|++.+|+-|+|.|.|-- + .++.|
T Consensus 478 KikEenf~~Pke-------evklethirVP-----s~-~aGRvIGKGGktVnELQnlt~AeV~vPr------d-qtpdE- 536 (584)
T KOG2193|consen 478 KIKEENFFLPKE-------EVKLETHIRVP-----SS-AAGRVIGKGGKTVNELQNLTSAEVVVPR------D-QTPDE- 536 (584)
T ss_pred hhhhhccCCchh-------hheeeeeeecc-----ch-hhhhhhccccccHHHHhccccceEEccc------c-CCCCc-
Confidence 888764333211 13555556555 55 7999999999999999999999998852 1 23333
Q ss_pred CCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhc
Q 008326 266 HQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECG 300 (570)
Q Consensus 266 dEPLHV~Isa~~~e~l~kAk~LiEnLL~tV~eE~~ 300 (570)
+|-.-|-|.|. .-....|...+.+|+..|++.-+
T Consensus 537 nd~vivriiGh-fyatq~aQrki~~iv~qvkq~~q 570 (584)
T KOG2193|consen 537 NDQVIVRIIGH-FYATQNAQRKIAHIVNQVKQSGQ 570 (584)
T ss_pred cceeeeeeech-hhcchHHHHHHHHHHHHHHHhhh
Confidence 33344445544 44567788888889988887654
No 29
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.76 E-value=0.017 Score=63.78 Aligned_cols=146 Identities=16% Similarity=0.160 Sum_probs=80.5
Q ss_pred cceecchhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEec-ccccchHHHHHHHHHHHHHHHHHHHcCCCCCCc
Q 008326 118 RYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISA-GAHVKTAERILAVDHAAAMVEEMLKQGHAGFPT 196 (570)
Q Consensus 118 Ry~LTKg~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~Ieg-~telnT~ERikaVD~AvskIkEiLke~P~~~p~ 196 (570)
-|+..+|+++++|..+|++.|-+=- ..++++=--+-|.| ..+++...=..++.+|..+|-..+.++..-
T Consensus 56 ~IIGk~G~~vkkir~~t~s~i~i~~-------~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~~--- 125 (485)
T KOG2190|consen 56 SIIGKKGDIVKKIRKETESKIRVNE-------SLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDEA--- 125 (485)
T ss_pred eEEccCcHHHHHHhhcccccceeec-------CCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcccccccc---
Confidence 5667889999999988877653311 11122111223344 000000000035566555544433322110
Q ss_pred cccccCCC---ccc-ceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEE
Q 008326 197 LQTVMGNG---VQA-MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLF 272 (570)
Q Consensus 197 ~~~p~~~G---~k~-~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~ 272 (570)
. .++| ..+ ...++.|+ .+-+|-|||.+|+.||.|.++|||+|+|-+. .+= ...|.+ |.
T Consensus 126 --~-~d~~~~~~~~~v~~RLlVp------~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~---~lP-----~ster~-V~ 187 (485)
T KOG2190|consen 126 --A-EDNGEDASGPEVTCRLLVP------SSQVGSLIGKGGSLIKEIREETGAKIRVSSD---MLP-----NSTERA-VT 187 (485)
T ss_pred --c-ccCCccccCCceEEEEEec------hhheeeeeccCcHHHHHHHHhcCceEEecCC---CCC-----ccccee-EE
Confidence 0 1111 244 46777787 4469999999999999999999999999985 221 223344 55
Q ss_pred EEeCCHHHHHHHHHHHHHHH
Q 008326 273 LSSNNPKSLEEAKRLAENLL 292 (570)
Q Consensus 273 Isa~~~e~l~kAk~LiEnLL 292 (570)
|+| +++.+.+|-..|-.+|
T Consensus 188 IsG-~~~av~~al~~Is~~L 206 (485)
T KOG2190|consen 188 ISG-EPDAVKKALVQISSRL 206 (485)
T ss_pred EcC-chHHHHHHHHHHHHHH
Confidence 554 5666666644443333
No 30
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.61 E-value=0.0023 Score=74.72 Aligned_cols=100 Identities=17% Similarity=0.221 Sum_probs=71.4
Q ss_pred eEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcE-EEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 008326 210 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGAT-VLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 288 (570)
Q Consensus 210 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaK-I~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~Li 288 (570)
+.+-|+.+ -+|.||||+|.+||.|++|||++ |-|+ |.-+|.|.+.|.+++++|+++|
T Consensus 687 ~~~~i~~~------ki~~vIG~GGktIk~I~eetg~~~Idi~----------------ddg~V~I~a~d~~~i~~A~~~I 744 (891)
T PLN00207 687 HIMKVKPE------KVNMIIGSGGKKVKSIIEETGVEAIDTQ----------------DDGTVKITAKDLSSLEKSKAII 744 (891)
T ss_pred EEEEcCHH------HHHHHhcCCchhHHHHHHHHCCCccCcC----------------CCeeEEEEeCCHHHHHHHHHHH
Confidence 45556533 48999999999999999999998 6654 3489999999999999999999
Q ss_pred HHHHHHHHHHhccccccccccccCCCCchhhhccccCCCCccccCccccceecccccc
Q 008326 289 ENLLDTISAECGASRVSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNL 346 (570)
Q Consensus 289 EnLL~tV~eE~~a~r~~~~k~y~avpppqqll~gv~~s~~~~~~~~~~~~~~~~~~~~ 346 (570)
++|.... ...+.|. .--+.++..+|+.-.+... .-||.|--.+
T Consensus 745 ~~l~~~~---------~vG~iy~-----~g~V~~I~~FGaFVeL~~g-~EGLVHISeL 787 (891)
T PLN00207 745 SSLTMVP---------TVGDIYR-----NCEIKSIAPYGAFVEIAPG-REGLCHISEL 787 (891)
T ss_pred HHHhcCc---------CCCcEEE-----CcEEEEEeccEEEEEeCCC-CEEEEEhhhc
Confidence 9998621 1233331 0125677778855444333 5777775544
No 31
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.78 E-value=0.011 Score=67.50 Aligned_cols=92 Identities=18% Similarity=0.250 Sum_probs=65.5
Q ss_pred ceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhccc
Q 008326 223 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGAS 302 (570)
Q Consensus 223 NfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~tV~eE~~a~ 302 (570)
+-++.+|||+|.++|.|++|||++|-|+ |.-+|.|.+.+.+.+++|+++|+.|....+
T Consensus 563 ~kI~~vIG~gg~~ik~I~~~~~~~idi~----------------d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~------ 620 (693)
T PRK11824 563 DKIRDVIGPGGKTIREITEETGAKIDIE----------------DDGTVKIAATDGEAAEAAKERIEGITAEPE------ 620 (693)
T ss_pred HHHHHHhcCCchhHHHHHHHHCCccccC----------------CCceEEEEcccHHHHHHHHHHHHHhcccCc------
Confidence 3488999999999999999999988763 346799999999999999999999984211
Q ss_pred cccccccccCCCCchhhhccccCCCCccccCccccceecccccc
Q 008326 303 RVSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNL 346 (570)
Q Consensus 303 r~~~~k~y~avpppqqll~gv~~s~~~~~~~~~~~~~~~~~~~~ 346 (570)
..+.|. -.+.++..+|..-.+.. ...|+.|--++
T Consensus 621 ---vG~v~~------G~V~~I~~fGafVei~~-~~~GllhiSel 654 (693)
T PRK11824 621 ---VGEIYE------GKVVRIVDFGAFVEILP-GKDGLVHISEI 654 (693)
T ss_pred ---CCeEEE------EEEEEEECCeEEEEECC-CCEEEEEeeec
Confidence 122221 23566666774444332 35566665444
No 32
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=95.33 E-value=0.077 Score=56.62 Aligned_cols=78 Identities=23% Similarity=0.250 Sum_probs=54.9
Q ss_pred ceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 008326 208 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 287 (570)
Q Consensus 208 ~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~L 287 (570)
+.-||.|| .+ .+|-|||.+|++|..+|+||||+|++- |-+-|.-+.+ -.||+...+-+.|...-+
T Consensus 39 y~ikvLip-----s~-AaGsIIGKGG~ti~~lqk~tgariklS-ks~dfyPGTT-------eRvcli~Gt~eai~av~e- 103 (402)
T KOG2191|consen 39 YFLKVLIP-----SY-AAGSIIGKGGQTIVQLQKETGARIKLS-KSKDFYPGTT-------ERVCLIQGTVEALNAVHE- 103 (402)
T ss_pred eEEEEEee-----cc-cccceeccchHHHHHHHhccCcEEEec-cccccCCCcc-------ceEEEEeccHHHHHHHHH-
Confidence 56788887 33 699999999999999999999999996 4444432222 256776667666665544
Q ss_pred HHHHHHHHHHHhccc
Q 008326 288 AENLLDTISAECGAS 302 (570)
Q Consensus 288 iEnLL~tV~eE~~a~ 302 (570)
-++|+||++.++-
T Consensus 104 --fI~dKire~p~~~ 116 (402)
T KOG2191|consen 104 --FIADKIREKPQAV 116 (402)
T ss_pred --HHHHHHHHhHHhh
Confidence 4556666665543
No 33
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.27 E-value=0.025 Score=56.51 Aligned_cols=53 Identities=19% Similarity=0.345 Sum_probs=46.7
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHH
Q 008326 224 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLL 292 (570)
Q Consensus 224 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL 292 (570)
+++++|||+|.+++.|.++|||+|.| |. .=+|+|.+.+.+.+++|++.|++|-
T Consensus 155 ~i~~lig~~g~~i~~l~~~~~~~I~i-g~---------------NG~VwI~~~~~~~~~~a~~~I~~~e 207 (235)
T PRK04163 155 KVPRVIGKKGSMINMLKEETGCDIIV-GQ---------------NGRIWIKGPDEEDEEIAIEAIKKIE 207 (235)
T ss_pred HHHhhcCCCChhHhhhhhhhCcEEEE-cC---------------CcEEEEeeCCHHHHHHHHHHHHHHH
Confidence 58899999999999999999999988 21 1489999999999999999998754
No 34
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=94.71 E-value=0.034 Score=58.12 Aligned_cols=57 Identities=21% Similarity=0.343 Sum_probs=45.6
Q ss_pred eeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHh
Q 008326 225 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 299 (570)
Q Consensus 225 vgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~tV~eE~ 299 (570)
+.|||||+|+|||.||--|.|-|.+.|. .|++.|+ ..+|+.+++++++-+.+|+-=|
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilVqG~-----------------TVsaiGp-fkGlkevr~IV~DcM~NiHPiY 216 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILVQGN-----------------TVSAIGP-FKGLKEVRKIVEDCMKNIHPIY 216 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEeeCc-----------------EEEeecC-cchHHHHHHHHHHHHhccchHH
Confidence 6799999999999999999999999994 2444443 4578888888888887776444
No 35
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=93.67 E-value=0.11 Score=55.21 Aligned_cols=63 Identities=11% Similarity=0.139 Sum_probs=54.5
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHH
Q 008326 224 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAE 298 (570)
Q Consensus 224 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~tV~eE 298 (570)
|.|.|||-+|.|.|+||+||+|+|.|=-.+. .--|+-|++...+.|.+|.+.|+-||++++..
T Consensus 67 ~~~~lig~~g~trkkle~Etq~~i~lp~p~~------------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~s 129 (345)
T KOG2814|consen 67 FIGWLIGKQGKTRKKLEEETQTNIFLPRPNT------------NKEEIKIIGISRNCVIQALERIAKLIDSDRKS 129 (345)
T ss_pred HhhhhhcccchHHHHHHHhhccceEccCCCC------------CcceEEEeehhHHHHHHHHHHHHHHHHhhhhc
Confidence 6899999999999999999999998853211 22489999999999999999999999999843
No 36
>PRK00106 hypothetical protein; Provisional
Probab=92.63 E-value=0.24 Score=55.64 Aligned_cols=60 Identities=27% Similarity=0.333 Sum_probs=51.1
Q ss_pred CCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 008326 219 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 293 (570)
Q Consensus 219 ~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~ 293 (570)
.|+=.+.|||||-.|.|++.+|.-||+.|.|- |.|--|.|+|-||-.-+-|+.-.|.||.
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 34556899999999999999999999999884 6778899999999988888877666653
No 37
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=92.59 E-value=0.22 Score=55.41 Aligned_cols=60 Identities=23% Similarity=0.326 Sum_probs=50.4
Q ss_pred CCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 008326 219 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 293 (570)
Q Consensus 219 ~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~ 293 (570)
.|+=.+.|||||-.|-|++.+|+-||+.|.|- |.|=-|.|+|-||-.-+-|+.-.|.||.
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 34556899999999999999999999999984 5677899999999988888776666653
No 38
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=92.49 E-value=0.33 Score=55.11 Aligned_cols=57 Identities=21% Similarity=0.286 Sum_probs=48.2
Q ss_pred eeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHH
Q 008326 225 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAE 298 (570)
Q Consensus 225 vgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~tV~eE 298 (570)
+..+|||+|-.+|+|+.|||+.-++ +.=|+-|-+.++..+++||++|+.|+..-+..
T Consensus 608 ~~~lIGp~G~~~kki~~EtGai~~v-----------------De~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~ 664 (760)
T KOG1067|consen 608 RATLIGPGGVLKKKIEVETGAISQV-----------------DEGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQ 664 (760)
T ss_pred hheeecCccceeeeEeeeccceeee-----------------cCceEEEEecCHHHHHHHHHHHHHHhcCcccc
Confidence 6789999999999999999954333 33599999999999999999999998765444
No 39
>PRK12704 phosphodiesterase; Provisional
Probab=92.44 E-value=0.28 Score=54.60 Aligned_cols=59 Identities=24% Similarity=0.316 Sum_probs=49.1
Q ss_pred CCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHH
Q 008326 219 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLL 292 (570)
Q Consensus 219 ~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL 292 (570)
.|+=.+.|||||-.|-|++.+|.-||+.|.|- |.|=-|+|||-|+..-+.|+..++.|+
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 34556899999999999999999999999984 567889999999988777776655554
No 40
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=92.24 E-value=0.2 Score=57.55 Aligned_cols=53 Identities=23% Similarity=0.379 Sum_probs=46.7
Q ss_pred eeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 008326 225 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 293 (570)
Q Consensus 225 vgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~ 293 (570)
++.+|||+|.+++.|..||||+|.|.=.| -|.|.+.+.+...+|+++|+++..
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 56889999999999999999999986433 467888999999999999999983
No 41
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=91.40 E-value=0.33 Score=53.63 Aligned_cols=63 Identities=14% Similarity=0.128 Sum_probs=46.2
Q ss_pred CceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHH-HHHHHHHHHHHHHHHHHHHhc
Q 008326 222 LNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPK-SLEEAKRLAENLLDTISAECG 300 (570)
Q Consensus 222 FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e-~l~kAk~LiEnLL~tV~eE~~ 300 (570)
-+++|++||-+|+.||+||..|.++|+|-- +.+-+.|+-.--. .-.+|+..++++++...+ |+
T Consensus 55 s~mvg~vigrggskik~iq~~tnt~iqii~---------------~~~e~kv~ifg~~~m~~kaka~id~~~~k~e~-yn 118 (629)
T KOG0336|consen 55 SEMVGKVIGRGGSKIKRIQNDTNTRIQIIK---------------CDLEVKVTIFGINHMRKKAKASIDRGQDKDER-YN 118 (629)
T ss_pred hhhhheeeccCcchhhhhhcccceeEEEec---------------cCceeEEEEechHHHHHHHHhhHhhhhhhhhh-cc
Confidence 468999999999999999999999999863 2244444433333 345688888888877554 54
No 42
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=91.30 E-value=0.71 Score=47.83 Aligned_cols=74 Identities=20% Similarity=0.298 Sum_probs=55.4
Q ss_pred ccceecchhHHHHHHHHhCCeEeeeccccCCCC------CC-CC----CCCeEEEEecccccchHHHHHHHHHHHHHHHH
Q 008326 117 VRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNA------PP-DG----EKPLYLHISAGAHVKTAERILAVDHAAAMVEE 185 (570)
Q Consensus 117 ~Ry~LTKg~Tq~eIqe~TGA~VtTRGrYyPPg~------~~-~g----epPLYL~Ieg~telnT~ERikaVD~AvskIkE 185 (570)
-|.+--||.|++.++++|||.|.+||+.-=..+ +. ++ +.|||++|+.... .+|=...+..|+++|++
T Consensus 110 GRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p--~~ea~~rl~~AleeI~k 187 (259)
T KOG1588|consen 110 GRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAP--PAEAYARLAYALEEIKK 187 (259)
T ss_pred cccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCC--HHHHHHHHHHHHHHHHH
Confidence 377789999999999999999999998755432 11 11 6899999988653 23323557889999999
Q ss_pred HHHcCCC
Q 008326 186 MLKQGHA 192 (570)
Q Consensus 186 iLke~P~ 192 (570)
+|.-...
T Consensus 188 lL~P~~e 194 (259)
T KOG1588|consen 188 LLVPDHE 194 (259)
T ss_pred hcCCCCC
Confidence 9876544
No 43
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=90.70 E-value=1.1 Score=49.82 Aligned_cols=119 Identities=20% Similarity=0.200 Sum_probs=74.0
Q ss_pred ccceecc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHHHHHHHHHHHcCCCCCC
Q 008326 117 VRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHAAAMVEEMLKQGHAGFP 195 (570)
Q Consensus 117 ~Ry~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~AvskIkEiLke~P~~~p 195 (570)
+-.+|-| |+.+++|.++|||.|-+-+...|.. .++- +-|.|.- .+|.+|+..|-.+|.+.+.-.+
T Consensus 149 ~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~s----ter~--V~IsG~~--------~av~~al~~Is~~L~~~~~~~~ 214 (485)
T KOG2190|consen 149 VGSLIGKGGSLIKEIREETGAKIRVSSDMLPNS----TERA--VTISGEP--------DAVKKALVQISSRLLENPPRSP 214 (485)
T ss_pred eeeeeccCcHHHHHHHHhcCceEEecCCCCCcc----ccee--EEEcCch--------HHHHHHHHHHHHHHHhcCCcCC
Confidence 4456655 8999999999999998877644432 3333 6788865 4899999999988888531111
Q ss_pred c-----ccc-c--cCCC-----------------cccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEe
Q 008326 196 T-----LQT-V--MGNG-----------------VQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLR 250 (570)
Q Consensus 196 ~-----~~~-p--~~~G-----------------~k~~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IR 250 (570)
+ ..| | ...+ ....+++..+-+ ..|. ..++.|+|.+|..++.|+.++|+-|.+.
T Consensus 215 ~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~-~~p~-~~~~~v~g~~~~~i~~l~~~~~~~i~v~ 292 (485)
T KOG2190|consen 215 PPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKL-ICPS-DKVGSVIGKGGLVIRALRNETGASISVG 292 (485)
T ss_pred CCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhh-cCch-hhceeeecCCCccchhhhhhcCCceEec
Confidence 1 111 1 0001 111111111000 0111 2478999999999999999999888765
Q ss_pred e
Q 008326 251 G 251 (570)
Q Consensus 251 G 251 (570)
=
T Consensus 293 ~ 293 (485)
T KOG2190|consen 293 D 293 (485)
T ss_pred c
Confidence 4
No 44
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=89.94 E-value=0.81 Score=48.13 Aligned_cols=65 Identities=23% Similarity=0.382 Sum_probs=50.8
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHh
Q 008326 224 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 299 (570)
Q Consensus 224 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~tV~eE~ 299 (570)
+-|-|||-+|.-||+|..|+||.|.|- |+.+|.| -.+.+.-.+.++++.|.-|.+|-+..-++.|
T Consensus 325 lggsiigkggqri~~ir~esGA~Ikid-------epleGse----drIitItGTqdQIqnAQYLlQn~Vkq~rerf 389 (390)
T KOG2192|consen 325 LGGSIIGKGGQRIKQIRHESGASIKID-------EPLEGSE----DRIITITGTQDQIQNAQYLLQNSVKQYRERF 389 (390)
T ss_pred cCcceecccchhhhhhhhccCceEEec-------CcCCCCC----ceEEEEeccHHHHhhHHHHHHHHHHhhhccc
Confidence 567899999999999999999999875 3343432 4566667789999999999998777555443
No 45
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=85.69 E-value=1.5 Score=35.33 Aligned_cols=56 Identities=21% Similarity=0.240 Sum_probs=39.8
Q ss_pred EEEcCCCCccccceecc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHHHHHHH
Q 008326 107 EIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHAAAMVE 184 (570)
Q Consensus 107 EIEINDlPq~~Ry~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~AvskIk 184 (570)
.|.|..- ..+.++-+ |+++++|+++|||.|.+- . +. .+.|.|.+. .++++|+.+|+
T Consensus 5 ~i~Ip~~--~ig~iIGkgG~~ik~I~~~tg~~I~i~-----~------~g--~v~I~G~~~-------~~v~~A~~~I~ 61 (61)
T cd02393 5 TMKIPPD--KIRDVIGPGGKTIKKIIEETGVKIDIE-----D------DG--TVYIAASDK-------EAAEKAKKMIE 61 (61)
T ss_pred EEEeChh--heeeeECCCchHHHHHHHHHCCEEEeC-----C------CC--EEEEEeCCH-------HHHHHHHHHhC
Confidence 4455433 45666655 999999999999998642 1 11 478999865 68999988773
No 46
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=83.14 E-value=2.7 Score=45.11 Aligned_cols=111 Identities=16% Similarity=0.173 Sum_probs=69.6
Q ss_pred cceecchhHHHHHHHHhCCeEee--eccccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHHHHHHHHHHHcCCCCCC
Q 008326 118 RYKLTKRHTQEEIQKCTGAVVIT--RGKYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHAAAMVEEMLKQGHAGFP 195 (570)
Q Consensus 118 Ry~LTKg~Tq~eIqe~TGA~VtT--RGrYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~AvskIkEiLke~P~~~p 195 (570)
-..+-+|.+++.|+.+|.+.|.| || +.|.|. ++|.- ..|++|..+|...-..--...-
T Consensus 39 ~ivg~qg~kikalr~KTqtyi~tPsr~-----------eePiF~-vTg~~--------edv~~aRrei~saaeH~~l~~~ 98 (394)
T KOG2113|consen 39 EIVGRQGCKIKALRAKTQTYIKTPSRG-----------EEPIFP-VTGRH--------EDVRRARREIPSAAEHFGLIRA 98 (394)
T ss_pred eecccCccccchhhhhhcceeccCCCC-----------CCCcce-eccCc--------hhHHHHhhcCccccceeeeeee
Confidence 34556799999999999998765 44 447763 45643 5889888777652111100000
Q ss_pred ccccc-cCCCcc-cceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeec
Q 008326 196 TLQTV-MGNGVQ-AMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGR 252 (570)
Q Consensus 196 ~~~~p-~~~G~k-~~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGR 252 (570)
.+... .-.|.. -.+.+.|+-+ | +.++|+++||.|.++|+||+.|..-|.--++
T Consensus 99 s~s~Sgg~~~~s~s~qt~sy~sv---P-~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 99 SRSFSGGTNGASASGQTTSYVSV---P-LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred cccccCCCccccccCCCceeeec---c-ceeeeeccccccCccchheecccceEeeecc
Confidence 00000 001112 2346666553 3 7799999999999999999999988765553
No 47
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=82.56 E-value=3.2 Score=32.35 Aligned_cols=49 Identities=22% Similarity=0.236 Sum_probs=36.1
Q ss_pred cccee-cchhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHHHHHH
Q 008326 117 VRYKL-TKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHAAAMV 183 (570)
Q Consensus 117 ~Ry~L-TKg~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~AvskI 183 (570)
..+++ .+|.++++|++.|||.|..... + ..-.+.|+|. . +.|++|..+|
T Consensus 11 ~~~iIG~~G~~i~~I~~~t~~~I~i~~~---------~-~~~~v~I~G~-~-------~~v~~A~~~I 60 (60)
T PF00013_consen 11 VGRIIGKKGSNIKEIEEETGVKIQIPDD---------D-ERDIVTISGS-P-------EQVEKAKKMI 60 (60)
T ss_dssp HHHHHTGGGHHHHHHHHHHTSEEEEEST---------T-EEEEEEEEES-H-------HHHHHHHHHH
T ss_pred cCEEECCCCCcHHHhhhhcCeEEEEcCC---------C-CcEEEEEEeC-H-------HHHHHHHhhC
Confidence 45555 4599999999999999977443 2 3346788894 3 5788888776
No 48
>PRK12705 hypothetical protein; Provisional
Probab=82.21 E-value=1.3 Score=49.57 Aligned_cols=58 Identities=28% Similarity=0.309 Sum_probs=42.4
Q ss_pred CCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHH
Q 008326 219 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENL 291 (570)
Q Consensus 219 ~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnL 291 (570)
.|+=.+.|||||-.|.|++.+|..||+-|.|- |-|=-|.|++-++..-+.|+...++|
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 44556899999999999999999999998875 23333666777766655555444444
No 49
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=81.89 E-value=1.1 Score=45.72 Aligned_cols=83 Identities=14% Similarity=0.179 Sum_probs=55.5
Q ss_pred CCCCCceeEEeEEEcCCCCccc--ccee-cchhHHHHHHHHhCCeEeeeccccCCCC-C--------CCCCCCeEEEEec
Q 008326 96 PKVQDELIIAREIVINDSESSV--RYKL-TKRHTQEEIQKCTGAVVITRGKYRLPNA-P--------PDGEKPLYLHISA 163 (570)
Q Consensus 96 ~k~~de~~f~aEIEINDlPq~~--Ry~L-TKg~Tq~eIqe~TGA~VtTRGrYyPPg~-~--------~~gepPLYL~Ieg 163 (570)
.|..+++|| .+-++|..| ..+| -+|.||+++++.|+|.|-+||+|--... . ...+-+|+-+|++
T Consensus 146 sk~q~KiYI----PV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~a 221 (269)
T COG5176 146 SKYQNKIYI----PVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEA 221 (269)
T ss_pred ccccceEEe----ehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhc
Confidence 345556654 334444322 2333 7899999999999999999999987652 1 1247889999999
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHc
Q 008326 164 GAHVKTAERILAVDHAAAMVEEMLKQ 189 (570)
Q Consensus 164 ~telnT~ERikaVD~AvskIkEiLke 189 (570)
.++ ....+++..+..+|.+
T Consensus 222 dse-------dki~~~ik~~~n~I~~ 240 (269)
T COG5176 222 DSE-------DKICRLIKSQLNAIRE 240 (269)
T ss_pred chh-------hhHHHHHHHHHHHHHH
Confidence 887 3445555555555544
No 50
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=81.64 E-value=6.8 Score=41.54 Aligned_cols=130 Identities=16% Similarity=0.182 Sum_probs=77.5
Q ss_pred eecc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHHHHHHHHHHHcCCCCCCccc
Q 008326 120 KLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHAAAMVEEMLKQGHAGFPTLQ 198 (570)
Q Consensus 120 ~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~AvskIkEiLke~P~~~p~~~ 198 (570)
++.| |..++.+....+|.|.+--. .-+--.|+|++.-+ -|-+..++|--.|.++....++
T Consensus 62 vigkgg~nik~lr~d~na~v~vpds---------~~peri~tisad~~--------ti~~ilk~iip~lee~f~~~~p-- 122 (390)
T KOG2192|consen 62 VIGKGGKNIKALRTDYNASVSVPDS---------SGPERILTISADIE--------TIGEILKKIIPTLEEGFQLPSP-- 122 (390)
T ss_pred eeccccccHHHHhhhccceeeccCC---------CCCceeEEEeccHH--------HHHHHHHHHhhhhhhCCCCCCc--
Confidence 3444 56777777778887754221 22334567777532 3333333343334444333221
Q ss_pred cccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCH
Q 008326 199 TVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNP 278 (570)
Q Consensus 199 ~p~~~G~k~~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~ 278 (570)
.+-++.|- -.+.|-|||-+|+-+|.+.+.+.|++-| |-|-+.+ --..|+|++..+
T Consensus 123 ---------ce~rllih------qs~ag~iigrngskikelrekcsarlki------ft~c~p~----stdrv~l~~g~~ 177 (390)
T KOG2192|consen 123 ---------CELRLLIH------QSLAGGIIGRNGSKIKELREKCSARLKI------FTECCPH----STDRVVLIGGKP 177 (390)
T ss_pred ---------hhhhhhhh------hhhccceecccchhHHHHHHhhhhhhhh------hhccCCC----CcceEEEecCCc
Confidence 12233331 2368999999999999999999888765 2333322 125789999999
Q ss_pred HHHHHHHHHHHHHHH
Q 008326 279 KSLEEAKRLAENLLD 293 (570)
Q Consensus 279 e~l~kAk~LiEnLL~ 293 (570)
+.|-...+.|-+||.
T Consensus 178 k~v~~~i~~il~~i~ 192 (390)
T KOG2192|consen 178 KRVVECIKIILDLIS 192 (390)
T ss_pred chHHHHHHHHHHHhh
Confidence 888776666666664
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=79.81 E-value=4.7 Score=32.42 Aligned_cols=52 Identities=25% Similarity=0.252 Sum_probs=35.3
Q ss_pred ccee-cchhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHHHHHH
Q 008326 118 RYKL-TKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHAAAMV 183 (570)
Q Consensus 118 Ry~L-TKg~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~AvskI 183 (570)
.+++ .+|.++++|+++|||.|.+.-... ..+.++- +.|+|.. +.+++|..+|
T Consensus 12 g~iIG~~G~~i~~i~~~tga~I~i~~~~~----~~~~~r~--v~I~G~~--------~~v~~A~~~I 64 (65)
T cd02396 12 GSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERV--VTISGKP--------SAVQKALLLI 64 (65)
T ss_pred CeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceE--EEEEeCH--------HHHHHHHHhh
Confidence 3444 568999999999999997732111 1233443 5788875 3788888776
No 52
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=79.48 E-value=1.6 Score=51.28 Aligned_cols=10 Identities=20% Similarity=0.242 Sum_probs=4.9
Q ss_pred CCCCcCCChH
Q 008326 401 EGIYPQATPL 410 (570)
Q Consensus 401 ~~iypqatpl 410 (570)
+|+-|+++--
T Consensus 440 ~~~DPdf~yr 449 (1102)
T KOG1924|consen 440 TGMDPDFKYR 449 (1102)
T ss_pred CCCCCCcchh
Confidence 3455555543
No 53
>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=78.21 E-value=2.2 Score=34.50 Aligned_cols=27 Identities=11% Similarity=0.084 Sum_probs=24.2
Q ss_pred ceeeeEeCCCchhHHHHHHhhCcEEEE
Q 008326 223 NIAARIRGPNDQYINHIMNETGATVLL 249 (570)
Q Consensus 223 NfvgrIIGPrGstlK~Iq~ETGaKI~I 249 (570)
.-+|+.||.+|.+++.++..+|.+|-|
T Consensus 34 ~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 34 DQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred ccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 348999999999999999999988865
No 54
>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=72.76 E-value=9.5 Score=29.44 Aligned_cols=52 Identities=23% Similarity=0.256 Sum_probs=35.0
Q ss_pred cccee-cchhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHHHHHH
Q 008326 117 VRYKL-TKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHAAAMV 183 (570)
Q Consensus 117 ~Ry~L-TKg~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~AvskI 183 (570)
+++++ .+|.++++|++.||+.|...... . ++..--+.|.|.. +.+.+|..+|
T Consensus 11 ~~~vIG~~G~~i~~I~~~s~~~I~i~~~~-----~--~~~~~~v~i~G~~--------~~v~~a~~~i 63 (64)
T cd00105 11 VGRIIGKGGSTIKEIREETGAKIKIPDSG-----S--GSEERIVTITGTP--------EAVEKAKELI 63 (64)
T ss_pred cceeECCCCHHHHHHHHHHCCEEEEcCCC-----C--CCCceEEEEEcCH--------HHHHHHHHHh
Confidence 46666 66999999999999999764311 1 2223335677863 4677777665
No 55
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=72.08 E-value=7.6 Score=40.08 Aligned_cols=29 Identities=17% Similarity=0.409 Sum_probs=25.5
Q ss_pred ceeeeEeCCCchhHHHHHHhhCcEEEEee
Q 008326 223 NIAARIRGPNDQYINHIMNETGATVLLRG 251 (570)
Q Consensus 223 NfvgrIIGPrGstlK~Iq~ETGaKI~IRG 251 (570)
..+-|+||.+|+++|.+.++|+|+|.+==
T Consensus 155 ~kVpRvig~~~sm~~~l~~~~~~~I~VG~ 183 (239)
T COG1097 155 SKVPRVIGKKGSMLNMLKEKTGCEIIVGQ 183 (239)
T ss_pred hhcceEecCCCcHHHHhhhhcCeEEEEec
Confidence 35667999999999999999999998853
No 56
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=69.60 E-value=1.9 Score=36.22 Aligned_cols=33 Identities=18% Similarity=0.264 Sum_probs=25.7
Q ss_pred CCCCCceeeeEeCCCchhHHHHHHhh-CcEEEEe
Q 008326 218 ADASLNIAARIRGPNDQYINHIMNET-GATVLLR 250 (570)
Q Consensus 218 ~~P~FNfvgrIIGPrGstlK~Iq~ET-GaKI~IR 250 (570)
..++++-+|.++|.+|..+|.|++|. |-||.|=
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 35889999999999999999999999 6666543
No 57
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=68.85 E-value=2.6 Score=45.28 Aligned_cols=64 Identities=19% Similarity=0.220 Sum_probs=45.3
Q ss_pred cceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHH
Q 008326 207 AMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKR 286 (570)
Q Consensus 207 ~~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~ 286 (570)
.+.+.+.|| ..|++.|+|++|..+|+|+++|...|.-- ..++ | -+|+.....+.++.||+
T Consensus 25 nvt~sv~vp------s~~v~~ivg~qg~kikalr~KTqtyi~tP---------sr~e---e--PiF~vTg~~edv~~aRr 84 (394)
T KOG2113|consen 25 NVTESVEVP------SEHVAEIVGRQGCKIKALRAKTQTYIKTP---------SRGE---E--PIFPVTGRHEDVRRARR 84 (394)
T ss_pred ccceeeecC------cccceeecccCccccchhhhhhcceeccC---------CCCC---C--CcceeccCchhHHHHhh
Confidence 344555554 56899999999999999999998776421 1111 2 45666667778888888
Q ss_pred HHHH
Q 008326 287 LAEN 290 (570)
Q Consensus 287 LiEn 290 (570)
-|+.
T Consensus 85 ei~s 88 (394)
T KOG2113|consen 85 EIPS 88 (394)
T ss_pred cCcc
Confidence 7765
No 58
>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=66.97 E-value=12 Score=29.41 Aligned_cols=51 Identities=16% Similarity=0.121 Sum_probs=35.2
Q ss_pred cccceecc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHHHHHH
Q 008326 116 SVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHAAAMV 183 (570)
Q Consensus 116 ~~Ry~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~AvskI 183 (570)
..++++-+ |.++++|++.||+.|.+ |+.. ..+ -.+.|.|.. +.|..|+.+|
T Consensus 10 ~~~~iIG~~G~~i~~i~~~~g~~I~i-----~~~~--~~~--~~v~I~G~~--------~~v~~A~~~i 61 (62)
T cd02394 10 LHRFIIGKKGSNIRKIMEETGVKIRF-----PDPG--SKS--DTITITGPK--------ENVEKAKEEI 61 (62)
T ss_pred HhhhccCCCCCcHHHHHHHhCCEEEc-----CCCC--CCC--CEEEEEcCH--------HHHHHHHHHh
Confidence 45666754 89999999999999955 3322 223 335788874 4788887766
No 59
>PF13014 KH_3: KH domain
Probab=64.37 E-value=17 Score=27.02 Aligned_cols=24 Identities=29% Similarity=0.260 Sum_probs=19.3
Q ss_pred cccee-cchhHHHHHHHHhCCeEee
Q 008326 117 VRYKL-TKRHTQEEIQKCTGAVVIT 140 (570)
Q Consensus 117 ~Ry~L-TKg~Tq~eIqe~TGA~VtT 140 (570)
+++++ .+|.++++|+++|||.|.+
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 34555 4599999999999999954
No 60
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=63.87 E-value=7.3 Score=46.24 Aligned_cols=11 Identities=18% Similarity=0.211 Sum_probs=5.9
Q ss_pred CCCCeEEEEec
Q 008326 153 GEKPLYLHISA 163 (570)
Q Consensus 153 gepPLYL~Ieg 163 (570)
...+||-||+.
T Consensus 154 ~t~~l~~Cles 164 (1102)
T KOG1924|consen 154 STKKLLECLES 164 (1102)
T ss_pred ccccHHHHHHH
Confidence 35566655544
No 61
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=63.02 E-value=17 Score=39.53 Aligned_cols=56 Identities=20% Similarity=0.360 Sum_probs=46.1
Q ss_pred eeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH--HHHHHHHHH
Q 008326 225 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE--NLLDTISAE 298 (570)
Q Consensus 225 vgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiE--nLL~tV~eE 298 (570)
.--|.||.|.+++.|++..|+.|.-||. ++.|.+..+ .++.|+.++. .|+..+++.
T Consensus 26 ~~~l~G~~~~~l~l~e~~~gv~i~~rG~-----------------~~~i~g~~~-~v~~A~~~l~~l~~~~~~~~g 83 (348)
T COG1702 26 LVALFGPTDTNLSLLEIALGVSIVARGE-----------------AVRIIGARP-LVDVATRVLLTLELLAEVRRG 83 (348)
T ss_pred hhhhcCCCCccHHHHHHHhCcEEEeCCc-----------------eEEEEechH-HHHHHHHHHhHHHHHHHHhcc
Confidence 4567999999999999999999999993 677777777 7888888888 777666555
No 62
>smart00322 KH K homology RNA-binding domain.
Probab=62.46 E-value=43 Score=25.03 Aligned_cols=63 Identities=21% Similarity=0.240 Sum_probs=41.2
Q ss_pred eEEEcCCCCcccccee-cchhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHHHHHHH
Q 008326 106 REIVINDSESSVRYKL-TKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHAAAMVE 184 (570)
Q Consensus 106 aEIEINDlPq~~Ry~L-TKg~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~AvskIk 184 (570)
.+|.|..-. ..+++ .+|.++++|++.+|+.|...+.-. .---+.|.|.. ..++.|...|.
T Consensus 5 ~~i~i~~~~--~~~liG~~G~~i~~i~~~~~~~i~~~~~~~---------~~~~v~i~g~~--------~~v~~a~~~i~ 65 (69)
T smart00322 5 IEVLIPADK--VGLIIGKGGSTIKKIEEETGVKIDIPEDGS---------EERVVEITGPP--------ENVEKAAELIL 65 (69)
T ss_pred EEEEEcchh--cceeECCCchHHHHHHHHHCCEEEECCCCC---------CccEEEEEcCH--------HHHHHHHHHHH
Confidence 355554432 34444 679999999999999987753111 22336777863 46788878777
Q ss_pred HHH
Q 008326 185 EML 187 (570)
Q Consensus 185 EiL 187 (570)
+.+
T Consensus 66 ~~~ 68 (69)
T smart00322 66 EIL 68 (69)
T ss_pred HHh
Confidence 764
No 63
>PRK15494 era GTPase Era; Provisional
Probab=62.37 E-value=34 Score=36.00 Aligned_cols=27 Identities=30% Similarity=0.187 Sum_probs=22.3
Q ss_pred eeeeEeCCCchhHHHH--------HHhhCcEEEEe
Q 008326 224 IAARIRGPNDQYINHI--------MNETGATVLLR 250 (570)
Q Consensus 224 fvgrIIGPrGstlK~I--------q~ETGaKI~IR 250 (570)
-.+.|||.+|..||+| |+-.||||.|+
T Consensus 284 qk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 284 YKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 4788999999999988 55568888775
No 64
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=62.32 E-value=12 Score=37.58 Aligned_cols=55 Identities=16% Similarity=0.277 Sum_probs=41.7
Q ss_pred eeeEeCCCchhHHHHHHhhCcEEEEeec-CCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHH
Q 008326 225 AARIRGPNDQYINHIMNETGATVLLRGR-GSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENL 291 (570)
Q Consensus 225 vgrIIGPrGstlK~Iq~ETGaKI~IRGR-GSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnL 291 (570)
.+.++|..|.+.+.|+..+||+|.|=.+ ||..++.+ +. ..|+-.+.+|+++++-+
T Consensus 19 ~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~--~~----------t~Dp~~~~ka~d~VkAI 74 (194)
T COG1094 19 IGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTT--RK----------TEDPLALLKARDVVKAI 74 (194)
T ss_pred heeeecccccchHHHHhhcCeEEEEECCCCeEEEEec--CC----------CCChHHHHHHHHHHHHH
Confidence 6889999999999999999999999876 44444322 11 12677888888887655
No 65
>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=54.28 E-value=11 Score=28.87 Aligned_cols=23 Identities=13% Similarity=0.127 Sum_probs=20.2
Q ss_pred eeeEeCCCchhHHHHHHhhCcEE
Q 008326 225 AARIRGPNDQYINHIMNETGATV 247 (570)
Q Consensus 225 vgrIIGPrGstlK~Iq~ETGaKI 247 (570)
.|++||.+|.+++.|+..++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 57899999999999999998554
No 66
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=50.99 E-value=53 Score=38.85 Aligned_cols=104 Identities=16% Similarity=0.169 Sum_probs=71.3
Q ss_pred CCCccccceecc-hhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHHHHHHHHHHHcC
Q 008326 112 DSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHAAAMVEEMLKQG 190 (570)
Q Consensus 112 DlPq~~Ry~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~AvskIkEiLke~ 190 (570)
=+++...|..-| +..+..|.+++++.+..+- ....+++.+++-.. ..+..|.+.|+.+..+.
T Consensus 353 i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~-------~~~~~~~v~~~~~~----------~~~~ka~~~v~~~~~ei 415 (753)
T KOG2208|consen 353 IFPEELKFVIGKKGANIEKIREESQVKIDLPK-------QGSNNKKVVITGVS----------ANDEKAVEDVEKIIAEI 415 (753)
T ss_pred ecHHhhhhhcCCCCccHHHHHHhhhhceeccc-------ccCCCCCeEEeccc----------cchhHHHHHHHHHHHhh
Confidence 345567887766 6669999999999774321 22345667654333 24677777777777765
Q ss_pred CCCCCccccccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeec
Q 008326 191 HAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGR 252 (570)
Q Consensus 191 P~~~p~~~~p~~~G~k~~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGR 252 (570)
++. ...+.++||-+ ..++|||.+|..+..|+.++|| |.|+..
T Consensus 416 ~n~-------------~~~~~~~iP~k------~~~~iig~~g~~i~~I~~k~~~-v~i~f~ 457 (753)
T KOG2208|consen 416 LNS-------------IVKEEVQIPTK------SHKRIIGTKGALINYIMGKHGG-VHIKFQ 457 (753)
T ss_pred hcc-------------cccceeecCcc------chhhhhccccccHHHHHhhcCc-EEEecC
Confidence 543 11234555532 5789999999999999999999 888874
No 67
>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]
Probab=47.45 E-value=21 Score=42.29 Aligned_cols=15 Identities=33% Similarity=0.377 Sum_probs=7.2
Q ss_pred cccceeecccCCCCC
Q 008326 486 SANLDVRNVSNMPPP 500 (570)
Q Consensus 486 ~~~~~v~~~~~~p~p 500 (570)
++...++++-+.|+|
T Consensus 270 sA~~s~~~S~s~ppp 284 (830)
T KOG1923|consen 270 SACDSQPGSGSGPPP 284 (830)
T ss_pred hhcccCCCCCCCCCC
Confidence 444555555555333
No 68
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=45.24 E-value=20 Score=43.46 Aligned_cols=75 Identities=17% Similarity=0.146 Sum_probs=54.4
Q ss_pred cCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHH
Q 008326 215 GFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDT 294 (570)
Q Consensus 215 pld~~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~t 294 (570)
.++.+|.- .+.+|.+--- +.+|...++|.|..||+.=--.... ...++-||++|.+.+...|++|+..++.+|..
T Consensus 903 ~inD~Pq~-~r~~vt~~~~--L~~i~e~~~~~it~rg~f~~~gk~p--~~gErklyl~ve~~~e~~vqra~~e~~r~l~e 977 (997)
T KOG0334|consen 903 EINDFPQN-ARWRVTYKEA--LLRISEPTAAGITTRGKFNPPGKEP--KPGERKLYLLVEGPDELSVQRAIEELERLLEE 977 (997)
T ss_pred cccccchh-cceeeechhh--hhhccCccccceeeccccCCCCCCC--CCcchhhhhhhhcchhHHHHHHHHHHHHHHHH
Confidence 33445543 6777776544 9999999999999999743221111 23456699999999999999999888876543
No 69
>COG1159 Era GTPase [General function prediction only]
Probab=44.75 E-value=53 Score=35.09 Aligned_cols=41 Identities=22% Similarity=0.362 Sum_probs=28.4
Q ss_pred CcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHH--------hhCcEEEE
Q 008326 204 GVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMN--------ETGATVLL 249 (570)
Q Consensus 204 G~k~~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~--------ETGaKI~I 249 (570)
|..+...-|||.=+. -.|-|||.+|..+|.|-. -.||||.|
T Consensus 225 ~~~~I~a~I~Ver~s-----QK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 225 GLLKIHATIYVERES-----QKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred CeEEEEEEEEEecCC-----ccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 334556667776433 467799999999998844 45777754
No 70
>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=44.24 E-value=22 Score=35.59 Aligned_cols=27 Identities=26% Similarity=0.214 Sum_probs=21.6
Q ss_pred eeeeEeCCCchhHHHHH--------HhhCcEEEEe
Q 008326 224 IAARIRGPNDQYINHIM--------NETGATVLLR 250 (570)
Q Consensus 224 fvgrIIGPrGstlK~Iq--------~ETGaKI~IR 250 (570)
-.+.|||.+|..||+|. +-.||+|.|+
T Consensus 232 ~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l~ 266 (270)
T TIGR00436 232 QKKIIIGKNGSMIKAIGIAARKDILELFDCDVFLE 266 (270)
T ss_pred ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 46889999999999984 4457888764
No 71
>PRK00089 era GTPase Era; Reviewed
Probab=41.01 E-value=27 Score=35.09 Aligned_cols=38 Identities=18% Similarity=0.344 Sum_probs=26.9
Q ss_pred ceeEEEecCCCCCCCceeeeEeCCCchhHHHH--------HHhhCcEEEEe
Q 008326 208 MSTSVFLGFDADASLNIAARIRGPNDQYINHI--------MNETGATVLLR 250 (570)
Q Consensus 208 ~~eKI~Ipld~~P~FNfvgrIIGPrGstlK~I--------q~ETGaKI~IR 250 (570)
....|||.-+. -.+.|||.+|.+||+| |+-.||+|.|.
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 44555555332 3788999999999988 45568888765
No 72
>KOG1925 consensus Rac1 GTPase effector FHOS [Signal transduction mechanisms; Cytoskeleton]
Probab=39.32 E-value=22 Score=40.68 Aligned_cols=19 Identities=53% Similarity=1.263 Sum_probs=13.5
Q ss_pred CCCCCCCCCCC-CCCCCCCC
Q 008326 509 NGMPHPPPRNM-PPPPPPKF 527 (570)
Q Consensus 509 ~~mppp~~~~m-ppp~ppkf 527 (570)
.|.|||||+.. ||||||--
T Consensus 247 ~GvPPPPP~G~~PPPPP~~~ 266 (817)
T KOG1925|consen 247 SGVPPPPPKGPFPPPPPLAA 266 (817)
T ss_pred cCCCCCCCCCCCCCCCCCcc
Confidence 57889999987 66655543
No 73
>PHA01732 proline-rich protein
Probab=39.04 E-value=29 Score=31.29 Aligned_cols=12 Identities=42% Similarity=0.808 Sum_probs=4.7
Q ss_pred CCCCCCCCCCCC
Q 008326 511 MPHPPPRNMPPP 522 (570)
Q Consensus 511 mppp~~~~mppp 522 (570)
+|+|+|..||+|
T Consensus 17 pP~P~PpPpPpp 28 (94)
T PHA01732 17 PPAPVPPPPPAP 28 (94)
T ss_pred CCCCCCCCCCCC
Confidence 333444444333
No 74
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=38.20 E-value=36 Score=40.21 Aligned_cols=30 Identities=23% Similarity=0.286 Sum_probs=26.3
Q ss_pred eeeEeCCCchhHHHHHHhhCcEEEEeecCC
Q 008326 225 AARIRGPNDQYINHIMNETGATVLLRGRGS 254 (570)
Q Consensus 225 vgrIIGPrGstlK~Iq~ETGaKI~IRGRGS 254 (570)
...|+|.+|.++.+|+++++|+|.++=.|+
T Consensus 358 ~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~ 387 (753)
T KOG2208|consen 358 LKFVIGKKGANIEKIREESQVKIDLPKQGS 387 (753)
T ss_pred hhhhcCCCCccHHHHHHhhhhceecccccC
Confidence 667999999999999999999999985433
No 75
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=38.07 E-value=25 Score=33.23 Aligned_cols=28 Identities=11% Similarity=0.136 Sum_probs=25.2
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEee
Q 008326 224 IAARIRGPNDQYINHIMNETGATVLLRG 251 (570)
Q Consensus 224 fvgrIIGPrGstlK~Iq~ETGaKI~IRG 251 (570)
-+|..||.+|+.+|.|++..|-||-|=.
T Consensus 42 ~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 42 DMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CccccCCcCchHHHHHHHHhCCceEEEE
Confidence 5799999999999999999998887765
No 76
>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=35.66 E-value=30 Score=28.43 Aligned_cols=16 Identities=44% Similarity=0.752 Sum_probs=10.5
Q ss_pred ccCCCCCcCCChHHHHH
Q 008326 398 SGYEGIYPQATPLQQVA 414 (570)
Q Consensus 398 ~gy~~iypqatplqqva 414 (570)
.|||+++|+ |+.-++.
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 77
>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=34.59 E-value=6.5 Score=34.70 Aligned_cols=33 Identities=21% Similarity=0.322 Sum_probs=25.0
Q ss_pred EcCCCCccccceec-----chhHHHHHHHHhCCeEee--ecc
Q 008326 109 VINDSESSVRYKLT-----KRHTQEEIQKCTGAVVIT--RGK 143 (570)
Q Consensus 109 EINDlPq~~Ry~LT-----Kg~Tq~eIqe~TGA~VtT--RGr 143 (570)
||+++- .||.+- .|.+|.+|.+.||+++.| ||.
T Consensus 31 E~~~l~--~R~~va~~lL~~g~syreIa~~tgvS~aTItRvs 70 (87)
T PF01371_consen 31 ELEALA--QRWQVAKELLDEGKSYREIAEETGVSIATITRVS 70 (87)
T ss_dssp HHHHHH--HHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHH
T ss_pred HHHHHH--HHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHH
Confidence 455553 577554 589999999999999876 664
No 78
>PRK01064 hypothetical protein; Provisional
Probab=33.51 E-value=30 Score=30.00 Aligned_cols=20 Identities=20% Similarity=0.169 Sum_probs=17.2
Q ss_pred eeeEeCCCchhHHHHHHhhC
Q 008326 225 AARIRGPNDQYINHIMNETG 244 (570)
Q Consensus 225 vgrIIGPrGstlK~Iq~ETG 244 (570)
.|++||-+|.+++.|+.-.+
T Consensus 41 ~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred ceEEECCCCccHHHHHHHHH
Confidence 69999999999999987543
No 79
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=33.12 E-value=1e+02 Score=29.96 Aligned_cols=58 Identities=12% Similarity=0.178 Sum_probs=44.5
Q ss_pred eeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHH
Q 008326 225 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAE 298 (570)
Q Consensus 225 vgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~tV~eE 298 (570)
.-.|+.++|..++.|....||+|.+.- +.-.|.|+| +...++.+...+.+++..|+.+
T Consensus 37 ~~LLl~~~~~~L~~l~~~~~~~I~~~~---------------~~~~i~I~g-~k~~~~~i~~~i~~~l~~i~~~ 94 (210)
T PF14611_consen 37 FFLLLTGNGRILENLAARNGAKIEVSR---------------SENRIRITG-TKSTAEYIEASINEILSNIRTE 94 (210)
T ss_pred eeeeecCCchHHHHHHHhcCceEEEec---------------CCcEEEEEc-cHHHHHHHHHHHHHHHhhcEEE
Confidence 448899999999999888899998864 223677777 6666777777777777776655
No 80
>PRK01381 Trp operon repressor; Provisional
Probab=31.84 E-value=17 Score=33.07 Aligned_cols=29 Identities=28% Similarity=0.434 Sum_probs=22.8
Q ss_pred ccceecc-----hhHHHHHHHHhCCeEee--ecccc
Q 008326 117 VRYKLTK-----RHTQEEIQKCTGAVVIT--RGKYR 145 (570)
Q Consensus 117 ~Ry~LTK-----g~Tq~eIqe~TGA~VtT--RGrYy 145 (570)
.||.|-+ +-+|.+|.+++|++|+| ||.-+
T Consensus 43 ~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~ 78 (99)
T PRK01381 43 TRVRIVEELLRGELSQREIKQELGVGIATITRGSNS 78 (99)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHH
Confidence 5786654 47999999999999886 77543
No 81
>PRK02821 hypothetical protein; Provisional
Probab=30.65 E-value=31 Score=29.92 Aligned_cols=20 Identities=5% Similarity=0.129 Sum_probs=17.3
Q ss_pred eeeEeCCCchhHHHHHHhhC
Q 008326 225 AARIRGPNDQYINHIMNETG 244 (570)
Q Consensus 225 vgrIIGPrGstlK~Iq~ETG 244 (570)
+|||||-+|.+++-|..--.
T Consensus 42 ~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 42 LGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CcceeCCCCchHHHHHHHHH
Confidence 89999999999999876543
No 82
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=30.44 E-value=5.1e+02 Score=25.12 Aligned_cols=124 Identities=19% Similarity=0.186 Sum_probs=71.9
Q ss_pred cccee-c-chhHHHHHHHHhCCeEeeeccccCCCCCCCCCCCeEEEEecccccchHHHHHHHHHHHHHHHHHHHcCCCCC
Q 008326 117 VRYKL-T-KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHVKTAERILAVDHAAAMVEEMLKQGHAGF 194 (570)
Q Consensus 117 ~Ry~L-T-Kg~Tq~eIqe~TGA~VtTRGrYyPPg~~~~gepPLYL~Ieg~telnT~ERikaVD~AvskIkEiLke~P~~~ 194 (570)
..++| + ++..+++|....|+.|.+.- ++. .|.|+|.. ..++.+...|+++++.--
T Consensus 36 ~~~LLl~~~~~~L~~l~~~~~~~I~~~~----------~~~--~i~I~g~k--------~~~~~i~~~i~~~l~~i~--- 92 (210)
T PF14611_consen 36 EFFLLLTGNGRILENLAARNGAKIEVSR----------SEN--RIRITGTK--------STAEYIEASINEILSNIR--- 92 (210)
T ss_pred heeeeecCCchHHHHHHHhcCceEEEec----------CCc--EEEEEccH--------HHHHHHHHHHHHHHhhcE---
Confidence 34444 3 46778999888899987633 122 46899965 366777777888776531
Q ss_pred CccccccCCCcccceeEEEecCCCC-CCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEE
Q 008326 195 PTLQTVMGNGVQAMSTSVFLGFDAD-ASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFL 273 (570)
Q Consensus 195 p~~~~p~~~G~k~~~eKI~Ipld~~-P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~I 273 (570)
++.|-++ .+ +.|...+. ---....++.|++.|++-|..-+.+ ..+.++-
T Consensus 93 --------------~~~i~l~--~~~~~~~~~~~-~~~~~~~l~~i~~~t~~~ie~~~~~-------------~~~~i~~ 142 (210)
T PF14611_consen 93 --------------TEEIDLS--PIISKHSEKKN-SQFTPDLLEEIQKLTNVYIEKNPDG-------------NKLKISW 142 (210)
T ss_pred --------------EEEEecc--hhhhhhccccc-ccccHHHHHHHHHHHcEEEEECCCC-------------CeEEEEE
Confidence 1122111 10 11100000 0113457999999999877766532 2233333
Q ss_pred --EeCCHHHHHHHHHHHHHHHH
Q 008326 274 --SSNNPKSLEEAKRLAENLLD 293 (570)
Q Consensus 274 --sa~~~e~l~kAk~LiEnLL~ 293 (570)
.+.+++.++.|++|....+.
T Consensus 143 ~~~~~~~~~~~~a~RlL~~a~~ 164 (210)
T PF14611_consen 143 LASPENEKRADRAKRLLLWALD 164 (210)
T ss_pred EeeccccchHHHHHHHHHHhcc
Confidence 23788888888888766653
No 83
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=30.43 E-value=6.5 Score=42.56 Aligned_cols=40 Identities=18% Similarity=0.249 Sum_probs=29.8
Q ss_pred EEEecCC-CCCCCceeeeEeCCCchhHHHHHHhh--------CcEEEEe
Q 008326 211 SVFLGFD-ADASLNIAARIRGPNDQYINHIMNET--------GATVLLR 250 (570)
Q Consensus 211 KI~Ipld-~~P~FNfvgrIIGPrGstlK~Iq~ET--------GaKI~IR 250 (570)
++||-++ -.|.-....+|||++|.-|++|-.+- +|+|.||
T Consensus 325 ~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~dL~~if~r~V~l~ 373 (379)
T KOG1423|consen 325 VLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRANEDLEDIFQRKVFLR 373 (379)
T ss_pred EEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHHHHHHHHhhceeeEE
Confidence 5666665 35666678899999999999986654 5777665
No 84
>PRK00468 hypothetical protein; Provisional
Probab=30.13 E-value=33 Score=29.52 Aligned_cols=18 Identities=11% Similarity=0.204 Sum_probs=15.9
Q ss_pred eeeEeCCCchhHHHHHHh
Q 008326 225 AARIRGPNDQYINHIMNE 242 (570)
Q Consensus 225 vgrIIGPrGstlK~Iq~E 242 (570)
+|||||-+|.+++-|..-
T Consensus 41 ~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CcceecCCChhHHHHHHH
Confidence 699999999999988653
No 85
>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=30.08 E-value=32 Score=28.79 Aligned_cols=21 Identities=5% Similarity=0.090 Sum_probs=18.1
Q ss_pred eeeEeCCCchhHHHHHHhhCc
Q 008326 225 AARIRGPNDQYINHIMNETGA 245 (570)
Q Consensus 225 vgrIIGPrGstlK~Iq~ETGa 245 (570)
.|+|||.+|.+++-||--+..
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~ 55 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANL 55 (77)
T ss_pred CCeEECCCCccHHHHHHHHHH
Confidence 589999999999999887653
No 86
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=28.08 E-value=58 Score=35.41 Aligned_cols=40 Identities=18% Similarity=0.363 Sum_probs=32.0
Q ss_pred eEEEecCCCCCCCceeeeEeCCCchhHHHHHHhh-CcEEEEe
Q 008326 210 TSVFLGFDADASLNIAARIRGPNDQYINHIMNET-GATVLLR 250 (570)
Q Consensus 210 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ET-GaKI~IR 250 (570)
.||-|= -..++++-+|..||++|+.++.|.+|. |=||-|=
T Consensus 233 tKVAV~-s~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv 273 (362)
T PRK12327 233 TKIAVR-SNNPNVDAKGACVGPKGQRVQNIVSELKGEKIDII 273 (362)
T ss_pred eEEEEE-cCCCCCCchheeECCCChhHHHHHHHhCCCeEEEE
Confidence 566553 246999999999999999999999999 6666443
No 87
>PF00408 PGM_PMM_IV: Phosphoglucomutase/phosphomannomutase, C-terminal domain; InterPro: IPR005843 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1KFQ_B 1KFI_A 3PDK_B 2F7L_A 1TUO_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=26.80 E-value=1.8e+02 Score=23.86 Aligned_cols=24 Identities=13% Similarity=0.347 Sum_probs=19.8
Q ss_pred cEEEEEeCCHHHHHHHHHHHHHHH
Q 008326 269 LHLFLSSNNPKSLEEAKRLAENLL 292 (570)
Q Consensus 269 LHV~Isa~~~e~l~kAk~LiEnLL 292 (570)
+.|++.+.+.+.+++-.+-+.++|
T Consensus 49 iRv~~Ea~~~~~~~~~~~~i~~~i 72 (73)
T PF00408_consen 49 IRVYVEAPDEEELEEIAEEIAEAI 72 (73)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHH
T ss_pred EEEEEEeCCHHHHHHHHHHHHHhh
Confidence 899999999988887777766665
No 88
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=26.18 E-value=1.4e+02 Score=30.20 Aligned_cols=59 Identities=14% Similarity=0.112 Sum_probs=35.1
Q ss_pred eeeEeCCC-------------chhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHH--H-HHHHHHHH
Q 008326 225 AARIRGPN-------------DQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPK--S-LEEAKRLA 288 (570)
Q Consensus 225 vgrIIGPr-------------GstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e--~-l~kAk~Li 288 (570)
+|+++||+ +..+....+|..++|.+|=+-.+ =+|++|=..+.+ + ++++..++
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 58999998 45567777777777777743222 267777654443 2 34444444
Q ss_pred HHHHHHH
Q 008326 289 ENLLDTI 295 (570)
Q Consensus 289 EnLL~tV 295 (570)
+.|....
T Consensus 185 ~~l~~~~ 191 (214)
T PTZ00225 185 NFLVSLL 191 (214)
T ss_pred HHHHHhC
Confidence 4444443
No 89
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=25.78 E-value=99 Score=31.62 Aligned_cols=72 Identities=22% Similarity=0.313 Sum_probs=48.1
Q ss_pred CeEEEEe-cccccchHHHHHHHHHHHHHHHHHHHcCCCCCCcccc---ccCCCcccceeEEEecCCCCCCCceeeeEeCC
Q 008326 156 PLYLHIS-AGAHVKTAERILAVDHAAAMVEEMLKQGHAGFPTLQT---VMGNGVQAMSTSVFLGFDADASLNIAARIRGP 231 (570)
Q Consensus 156 PLYL~Ie-g~telnT~ERikaVD~AvskIkEiLke~P~~~p~~~~---p~~~G~k~~~eKI~Ipld~~P~FNfvgrIIGP 231 (570)
|.||++- ..+. ..|+|++|+..+.++.+-|++++--.-.... -.+. .-++++|+-..-+||+--+-.+
T Consensus 5 P~~lllDtSgSM--~Ge~IealN~Glq~m~~~Lkqdp~Ale~v~lsIVTF~~-----~a~~~~pf~~~~nF~~p~L~a~- 76 (207)
T COG4245 5 PCYLLLDTSGSM--IGEPIEALNAGLQMMIDTLKQDPYALERVELSIVTFGG-----PARVIQPFTDAANFNPPILTAQ- 76 (207)
T ss_pred CEEEEEecCccc--ccccHHHHHHHHHHHHHHHHhChhhhheeEEEEEEecC-----cceEEechhhHhhcCCCceecC-
Confidence 6677762 2222 6889999999999988888887532211110 0111 3578999999999999877766
Q ss_pred Cchh
Q 008326 232 NDQY 235 (570)
Q Consensus 232 rGst 235 (570)
||..
T Consensus 77 GgT~ 80 (207)
T COG4245 77 GGTP 80 (207)
T ss_pred CCCc
Confidence 6543
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=25.40 E-value=76 Score=34.21 Aligned_cols=39 Identities=21% Similarity=0.325 Sum_probs=31.2
Q ss_pred eEEEecCCCCCCCceeeeEeCCCchhHHHHHHhh-CcEEEE
Q 008326 210 TSVFLGFDADASLNIAARIRGPNDQYINHIMNET-GATVLL 249 (570)
Q Consensus 210 eKI~Ipld~~P~FNfvgrIIGPrGstlK~Iq~ET-GaKI~I 249 (570)
.||-|-- ..++.+-+|..||++|+.++.|.+|. |=+|-|
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 5666542 36999999999999999999999998 545543
No 91
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=23.64 E-value=2.4e+02 Score=28.19 Aligned_cols=52 Identities=12% Similarity=0.300 Sum_probs=40.3
Q ss_pred hHHHHHHhhC-cEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhc
Q 008326 235 YINHIMNETG-ATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECG 300 (570)
Q Consensus 235 tlK~Iq~ETG-aKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL~tV~eE~~ 300 (570)
+++.|+.... .-+.+++||.+ |.|.|.|... .++.|...|.+|+..++..|+
T Consensus 14 fle~l~~~~~~~~~~v~~k~n~-------------l~I~i~G~~~-eike~~~~Ik~~~~~vr~k~~ 66 (190)
T PF09840_consen 14 FLERLSKMVKSIYIYVEVKGNS-------------LKIEIQGYEK-EIKEAIRRIKELVRRVRSKYN 66 (190)
T ss_pred HHHHHHhhccCcEEEEEEeCCE-------------EEEEEecChH-HHHHHHHHHHHHHHHHHHHhc
Confidence 4667766643 34557777633 8888888877 899999999999999999765
No 92
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=23.49 E-value=19 Score=29.51 Aligned_cols=20 Identities=20% Similarity=0.313 Sum_probs=17.6
Q ss_pred eeeEeCCCchhHHHHHHhhC
Q 008326 225 AARIRGPNDQYINHIMNETG 244 (570)
Q Consensus 225 vgrIIGPrGstlK~Iq~ETG 244 (570)
.|+|||-+|.|++-||.-++
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHH
T ss_pred cceEECCCCeeHHHHHHHHH
Confidence 79999999999999987554
No 93
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=23.29 E-value=97 Score=35.01 Aligned_cols=15 Identities=13% Similarity=0.202 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHHHHc
Q 008326 175 AVDHAAAMVEEMLKQ 189 (570)
Q Consensus 175 aVD~AvskIkEiLke 189 (570)
.+++|...++.++-.
T Consensus 10 RLE~a~~RLE~Isi~ 24 (480)
T KOG2675|consen 10 RLESATSRLEGISIT 24 (480)
T ss_pred HHHHHHHHhhhhhcC
Confidence 355566666665533
No 94
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=22.75 E-value=52 Score=33.90 Aligned_cols=51 Identities=18% Similarity=0.203 Sum_probs=40.2
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHH
Q 008326 224 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLL 292 (570)
Q Consensus 224 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~l~kAk~LiEnLL 292 (570)
.+|||.|-+|.|--.||+-|.+||.|-+ -.+||.| ...+++-|+.-+-+||
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVlad-----------------~kIHiLG-~~~niriAR~avcsLI 229 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIENVTRTRIVLAD-----------------SKIHILG-AFQNIRIARDAVCSLI 229 (252)
T ss_pred HHHHhhcCCCcceeeeeccceeEEEecC-----------------ceEEEee-cchhhHHHHHhhHhhh
Confidence 4899999999999999999999999976 2344444 3566777877777776
No 95
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=22.17 E-value=54 Score=37.81 Aligned_cols=32 Identities=25% Similarity=0.341 Sum_probs=28.7
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEeecCCC
Q 008326 224 IAARIRGPNDQYINHIMNETGATVLLRGRGSG 255 (570)
Q Consensus 224 fvgrIIGPrGstlK~Iq~ETGaKI~IRGRGSg 255 (570)
+|-+|+|-.|+++|.|...|++||.|+-.-++
T Consensus 78 ~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g 109 (608)
T KOG2279|consen 78 AVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG 109 (608)
T ss_pred ceeeeeccccCCcchhhcccccceecCcccCC
Confidence 68899999999999999999999999975444
No 96
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=21.56 E-value=56 Score=28.49 Aligned_cols=17 Identities=18% Similarity=0.321 Sum_probs=15.6
Q ss_pred eeeEeCCCchhHHHHHH
Q 008326 225 AARIRGPNDQYINHIMN 241 (570)
Q Consensus 225 vgrIIGPrGstlK~Iq~ 241 (570)
+|+|||-+|.+++-|..
T Consensus 41 ~GkvIGk~GRti~AIRT 57 (76)
T COG1837 41 MGKVIGKQGRTIQAIRT 57 (76)
T ss_pred ccceecCCChhHHHHHH
Confidence 79999999999999865
No 97
>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=21.31 E-value=73 Score=30.41 Aligned_cols=28 Identities=11% Similarity=0.141 Sum_probs=24.7
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEee
Q 008326 224 IAARIRGPNDQYINHIMNETGATVLLRG 251 (570)
Q Consensus 224 fvgrIIGPrGstlK~Iq~ETGaKI~IRG 251 (570)
-+|..+|.+|+.+|.|++..|=||-|=.
T Consensus 43 ~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 43 EMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred CccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 5899999999999999988888887665
No 98
>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=21.21 E-value=97 Score=26.36 Aligned_cols=33 Identities=15% Similarity=0.287 Sum_probs=28.1
Q ss_pred EEEEEeCC-HHHHHHHHHHHHHHHHHHHHHhccc
Q 008326 270 HLFLSSNN-PKSLEEAKRLAENLLDTISAECGAS 302 (570)
Q Consensus 270 HV~Isa~~-~e~l~kAk~LiEnLL~tV~eE~~a~ 302 (570)
|++|...+ .+..+++++.++.|+..+......|
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 88998876 7789999999999999999886544
No 99
>PF13711 DUF4160: Domain of unknown function (DUF4160)
Probab=20.48 E-value=2.2e+02 Score=23.24 Aligned_cols=14 Identities=21% Similarity=0.444 Sum_probs=11.2
Q ss_pred CCCcEEEEEeCCHH
Q 008326 266 HQPLHLFLSSNNPK 279 (570)
Q Consensus 266 dEPLHV~Isa~~~e 279 (570)
-+|.||||...+.+
T Consensus 14 H~PpHvHv~~g~~~ 27 (66)
T PF13711_consen 14 HEPPHVHVRYGGFE 27 (66)
T ss_pred CCCCeEEEEcCCcE
Confidence 49999999877744
No 100
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=20.31 E-value=98 Score=35.53 Aligned_cols=14 Identities=14% Similarity=0.128 Sum_probs=10.1
Q ss_pred CceeEEeEEEcCCC
Q 008326 100 DELIIAREIVINDS 113 (570)
Q Consensus 100 de~~f~aEIEINDl 113 (570)
...||.+-++|++=
T Consensus 74 ~rsyFlrl~di~~~ 87 (569)
T KOG3671|consen 74 QRSYFLRLVDIVNN 87 (569)
T ss_pred cceeeeEEeeecCc
Confidence 35678888888765
No 101
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=20.05 E-value=74 Score=31.81 Aligned_cols=33 Identities=9% Similarity=0.142 Sum_probs=27.8
Q ss_pred CCCCceeeeEeCCCchhHHHHHHhhCcEEEEee
Q 008326 219 DASLNIAARIRGPNDQYINHIMNETGATVLLRG 251 (570)
Q Consensus 219 ~P~FNfvgrIIGPrGstlK~Iq~ETGaKI~IRG 251 (570)
..+.+=+|..||++|+.++.|.+|.|=+|-|=-
T Consensus 81 ~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe 113 (190)
T COG0195 81 VVKIDPVGACIGKRGSRVKAVSEELGEKIDVVE 113 (190)
T ss_pred ecCcCchhhhccCCChHHHHHHHHhCCceEEEE
Confidence 346777999999999999999999997775543
No 102
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....
Probab=20.03 E-value=1.7e+02 Score=26.59 Aligned_cols=51 Identities=27% Similarity=0.393 Sum_probs=32.6
Q ss_pred eEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHH----HHHHHHHHHHHHHHHHH
Q 008326 227 RIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPK----SLEEAKRLAENLLDTIS 296 (570)
Q Consensus 227 rIIGPrGstlK~Iq~ETGaKI~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e----~l~kAk~LiEnLL~tV~ 296 (570)
+==||||++++. |..+|.|+=.-++ |.|.+.+.. +.+.|.+....+|..+.
T Consensus 20 RssGpGGQ~VNk----~~s~V~l~h~ptg---------------i~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~~ 74 (113)
T PF00472_consen 20 RSSGPGGQNVNK----TNSKVRLRHIPTG---------------IVVKCQESRSQHQNREDALEKLREKLDEAY 74 (113)
T ss_dssp ESSSSSSCHHHS----SSEEEEEEETTTT---------------EEEEEESSSSHHHHHHHHHHHHHHHHHHHH
T ss_pred ecCCCCCCcccc----cCCEEEEEEeccc---------------EEEEEcccCCHHHHHHHHHHHHHHHHHHHH
Confidence 445999999986 4446666643222 788877554 46666666666666554
Done!