Query 008318
Match_columns 570
No_of_seqs 198 out of 459
Neff 3.5
Searched_HMMs 46136
Date Thu Mar 28 22:17:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008318.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008318hhsearch_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 3E-37 6.5E-42 319.7 14.1 367 27-429 13-422 (531)
2 KOG0119 Splicing factor 1/bran 99.9 2.3E-27 5E-32 251.1 15.1 159 127-294 61-230 (554)
3 cd02395 SF1_like-KH Splicing f 99.9 7.9E-25 1.7E-29 196.7 8.8 89 210-298 1-99 (120)
4 KOG1588 RNA-binding protein Sa 99.9 6.9E-22 1.5E-26 197.2 10.0 126 175-300 55-197 (259)
5 COG5176 MSL5 Splicing factor ( 99.8 1.4E-20 3.1E-25 183.8 9.7 180 110-296 47-242 (269)
6 KOG1960 Predicted RNA-binding 99.2 2.8E-12 6.2E-17 135.0 1.1 147 124-303 234-384 (531)
7 KOG1676 K-homology type RNA bi 99.1 2.7E-09 5.9E-14 116.8 17.3 184 102-317 137-328 (600)
8 KOG0334 RNA helicase [RNA proc 99.1 5.4E-11 1.2E-15 136.0 3.8 82 103-192 897-979 (997)
9 TIGR03665 arCOG04150 arCOG0415 98.8 2.7E-08 5.9E-13 94.2 9.8 129 122-293 15-150 (172)
10 PRK13763 putative RNA-processi 98.8 3.3E-08 7.1E-13 94.4 9.2 145 104-293 3-156 (180)
11 KOG1676 K-homology type RNA bi 98.7 2.1E-07 4.6E-12 102.3 16.4 160 105-298 231-393 (600)
12 cd00105 KH-I K homology RNA-bi 98.4 8.6E-07 1.9E-11 68.8 7.5 63 211-289 2-64 (64)
13 cd02393 PNPase_KH Polynucleoti 98.4 9.2E-07 2E-11 71.0 6.1 50 225-289 12-61 (61)
14 smart00322 KH K homology RNA-b 98.3 3.5E-06 7.6E-11 64.0 8.0 66 209-292 3-68 (69)
15 PF00013 KH_1: KH domain syndr 98.2 5.4E-07 1.2E-11 70.4 2.3 52 224-288 9-60 (60)
16 cd02394 vigilin_like_KH K homo 98.0 6.9E-06 1.5E-10 64.6 4.6 53 224-288 9-61 (62)
17 KOG2191 RNA-binding protein NO 97.9 0.00046 9.9E-09 72.8 17.4 162 104-300 39-207 (402)
18 cd02396 PCBP_like_KH K homolog 97.9 3.2E-05 6.8E-10 62.2 6.1 56 224-288 9-64 (65)
19 PF13014 KH_3: KH domain 97.6 4.1E-05 9E-10 57.1 3.1 28 225-252 1-28 (43)
20 KOG2193 IGF-II mRNA-binding pr 97.5 0.00045 9.8E-09 74.7 9.6 140 123-301 217-356 (584)
21 PRK13763 putative RNA-processi 97.3 0.00038 8.3E-09 66.8 6.3 64 211-294 5-71 (180)
22 TIGR02696 pppGpp_PNP guanosine 97.3 0.0017 3.7E-08 74.3 11.9 131 176-346 550-680 (719)
23 TIGR03665 arCOG04150 arCOG0415 97.2 0.00043 9.4E-09 65.9 4.7 56 225-294 8-65 (172)
24 cd02395 SF1_like-KH Splicing f 97.1 0.0011 2.3E-08 60.6 6.3 64 120-191 21-96 (120)
25 COG1094 Predicted RNA-binding 97.1 0.00095 2.1E-08 65.8 6.0 54 225-295 112-165 (194)
26 KOG0119 Splicing factor 1/bran 97.0 0.0011 2.3E-08 72.9 6.2 66 118-191 156-231 (554)
27 KOG2193 IGF-II mRNA-binding pr 96.8 0.0061 1.3E-07 66.3 9.5 156 107-300 414-570 (584)
28 TIGR03591 polynuc_phos polyrib 96.7 0.0027 5.8E-08 72.2 6.8 99 211-346 553-651 (684)
29 KOG2190 PolyC-binding proteins 96.6 0.028 6.1E-07 62.0 13.1 139 117-292 55-206 (485)
30 PLN00207 polyribonucleotide nu 96.4 0.0048 1E-07 72.1 6.4 100 210-346 686-787 (891)
31 PRK04163 exosome complex RNA-b 95.7 0.012 2.6E-07 58.8 4.3 55 224-293 154-208 (235)
32 PRK11824 polynucleotide phosph 95.7 0.015 3.1E-07 66.4 5.6 93 224-347 563-655 (693)
33 KOG1067 Predicted RNA-binding 95.1 0.036 7.9E-07 62.4 6.1 72 226-313 608-685 (760)
34 KOG2190 PolyC-binding proteins 95.0 0.47 1E-05 52.7 14.2 61 116-191 148-209 (485)
35 KOG2191 RNA-binding protein NO 95.0 0.099 2.1E-06 55.8 8.6 77 209-301 39-115 (402)
36 KOG2874 rRNA processing protei 94.7 0.034 7.4E-07 58.2 4.2 55 226-297 160-214 (356)
37 COG1185 Pnp Polyribonucleotide 94.2 0.13 2.8E-06 58.9 7.9 53 226-293 563-615 (692)
38 KOG2814 Transcription coactiva 93.4 0.13 2.8E-06 54.8 5.4 63 225-298 67-129 (345)
39 PRK00106 hypothetical protein; 92.3 0.28 6E-06 55.1 6.5 60 220-293 231-290 (535)
40 TIGR03319 YmdA_YtgF conserved 92.2 0.26 5.7E-06 54.8 6.2 61 219-293 209-269 (514)
41 PRK12704 phosphodiesterase; Pr 92.1 0.32 7E-06 54.1 6.8 59 220-292 216-274 (520)
42 KOG0336 ATP-dependent RNA heli 91.0 0.36 7.8E-06 53.4 5.5 64 222-300 54-118 (629)
43 cd02393 PNPase_KH Polynucleoti 89.3 1.3 2.8E-05 35.8 6.1 56 107-185 5-61 (61)
44 KOG2192 PolyC-binding hnRNP-K 88.6 2.3 5E-05 44.9 8.9 133 118-294 60-193 (390)
45 KOG1588 RNA-binding protein Sa 87.5 1.4 2.9E-05 45.8 6.4 73 118-193 111-194 (259)
46 KOG2113 Predicted RNA binding 85.7 1.8 3.8E-05 46.5 6.2 110 119-253 40-153 (394)
47 KOG2192 PolyC-binding hnRNP-K 84.8 2.3 4.9E-05 44.9 6.4 65 225-299 325-389 (390)
48 cd02396 PCBP_like_KH K homolog 80.4 5.8 0.00013 31.9 6.0 52 117-184 11-64 (65)
49 PRK12705 hypothetical protein; 80.0 1.8 3.8E-05 48.6 3.9 34 219-252 203-236 (508)
50 PF00013 KH_1: KH domain syndr 79.7 4.9 0.00011 31.3 5.2 49 117-184 11-60 (60)
51 KOG1924 RhoA GTPase effector D 79.7 1.6 3.5E-05 51.3 3.4 11 401-411 440-450 (1102)
52 cd02134 NusA_KH NusA_K homolog 78.0 2.2 4.9E-05 34.4 2.9 27 224-250 34-60 (61)
53 KOG2113 Predicted RNA binding 72.3 2.3 5E-05 45.6 2.0 53 223-290 34-88 (394)
54 cd00105 KH-I K homology RNA-bi 71.3 17 0.00036 28.0 6.2 60 107-184 3-63 (64)
55 COG1702 PhoH Phosphate starvat 69.1 10 0.00022 41.0 6.0 56 226-298 26-83 (348)
56 COG1097 RRP4 RNA-binding prote 69.0 14 0.00031 38.1 6.8 32 223-254 154-185 (239)
57 cd02394 vigilin_like_KH K homo 68.8 12 0.00027 29.3 5.0 58 107-184 3-61 (62)
58 PF13184 KH_5: NusA-like KH do 68.6 2 4.3E-05 36.1 0.5 32 219-250 12-44 (69)
59 smart00322 KH K homology RNA-b 67.4 40 0.00087 25.2 7.4 64 105-188 4-68 (69)
60 KOG1924 RhoA GTPase effector D 64.2 7.1 0.00015 46.3 3.9 7 106-112 97-103 (1102)
61 COG5176 MSL5 Splicing factor ( 59.2 7.1 0.00015 40.1 2.5 83 97-191 147-241 (269)
62 PF13014 KH_3: KH domain 56.6 34 0.00073 25.4 5.2 24 117-140 2-26 (43)
63 PRK15494 era GTPase Era; Provi 55.6 55 0.0012 34.4 8.4 27 225-251 284-318 (339)
64 COG1094 Predicted RNA-binding 54.9 34 0.00074 34.5 6.4 67 102-191 90-165 (194)
65 KOG2208 Vigilin [Lipid transpo 54.2 43 0.00093 39.6 8.0 108 108-253 349-457 (753)
66 cd02409 KH-II KH-II (K homolo 52.9 12 0.00026 28.8 2.4 23 226-248 36-58 (68)
67 KOG0334 RNA helicase [RNA proc 51.4 14 0.0003 44.8 3.5 71 218-294 905-977 (997)
68 KOG1923 Rac1 GTPase effector F 48.3 20 0.00043 42.5 4.1 15 486-500 270-284 (830)
69 PF01371 Trp_repressor: Trp re 45.7 1.2 2.5E-05 39.3 -4.7 33 109-143 31-70 (87)
70 TIGR00436 era GTP-binding prot 42.1 26 0.00056 35.2 3.4 27 225-251 232-266 (270)
71 KOG1925 Rac1 GTPase effector F 39.8 22 0.00047 40.8 2.6 19 509-527 247-266 (817)
72 PHA01732 proline-rich protein 39.4 29 0.00063 31.3 2.9 12 511-522 17-28 (94)
73 PRK00089 era GTPase Era; Revie 38.4 31 0.00068 34.6 3.4 38 209-251 226-271 (292)
74 PRK08406 transcription elongat 37.3 25 0.00055 33.2 2.3 28 225-252 42-69 (140)
75 PF07885 Ion_trans_2: Ion chan 35.2 30 0.00066 28.4 2.3 16 398-414 39-54 (79)
76 PRK01064 hypothetical protein; 35.0 28 0.0006 30.2 2.1 19 226-244 41-59 (78)
77 PF00408 PGM_PMM_IV: Phosphogl 34.1 1.1E+02 0.0025 25.0 5.4 38 244-292 34-72 (73)
78 COG2037 Ftr Formylmethanofuran 32.5 5.2E+02 0.011 27.6 10.9 50 117-166 21-81 (297)
79 COG1159 Era GTPase [General fu 30.7 1.3E+02 0.0029 32.2 6.6 41 205-250 225-273 (298)
80 PRK02821 hypothetical protein; 30.2 31 0.00067 29.9 1.5 21 225-245 41-61 (77)
81 PRK00468 hypothetical protein; 29.9 32 0.0007 29.5 1.6 18 226-243 41-58 (75)
82 PRK01381 Trp operon repressor; 29.5 17 0.00037 33.1 -0.1 30 116-145 42-78 (99)
83 PF14611 SLS: Mitochondrial in 29.3 1.3E+02 0.0027 29.3 5.7 59 226-299 37-95 (210)
84 PF09981 DUF2218: Uncharacteri 29.0 81 0.0018 27.6 3.9 62 234-295 11-78 (89)
85 KOG2208 Vigilin [Lipid transpo 28.9 58 0.0013 38.6 3.9 30 226-255 358-387 (753)
86 cd02414 jag_KH jag_K homology 28.7 35 0.00075 28.6 1.6 34 211-248 24-57 (77)
87 PF14611 SLS: Mitochondrial in 28.4 5.6E+02 0.012 24.9 10.9 124 117-293 36-164 (210)
88 PRK12327 nusA transcription el 27.6 60 0.0013 35.3 3.5 40 211-251 233-273 (362)
89 KOG1423 Ras-like GTPase ERA [C 27.4 7.9 0.00017 41.9 -3.0 41 211-251 324-373 (379)
90 cd02410 archeal_CPSF_KH The ar 25.8 1.9E+02 0.0041 28.1 6.1 94 118-251 19-112 (145)
91 TIGR01953 NusA transcription t 24.7 80 0.0017 34.0 3.8 39 211-250 231-270 (341)
92 COG1855 ATPase (PilT family) [ 24.5 1.4E+02 0.0031 34.4 5.7 69 176-255 458-526 (604)
93 KOG2675 Adenylate cyclase-asso 23.7 95 0.0021 35.1 4.1 12 177-188 11-22 (480)
94 PF09840 DUF2067: Uncharacteri 22.4 2.7E+02 0.0059 27.8 6.7 52 236-300 14-66 (190)
95 TIGR01952 nusA_arch NusA famil 21.9 68 0.0015 30.6 2.4 28 225-252 43-70 (141)
96 PRK06418 transcription elongat 21.3 70 0.0015 31.5 2.3 72 227-298 72-159 (166)
97 PF00639 Rotamase: PPIC-type P 21.2 97 0.0021 26.3 3.0 33 270-302 1-34 (95)
98 PF13083 KH_4: KH domain; PDB: 21.1 20 0.00043 29.4 -1.2 20 226-245 40-59 (73)
99 COG1837 Predicted RNA-binding 21.0 61 0.0013 28.3 1.7 18 226-243 41-58 (76)
100 KOG3671 Actin regulatory prote 20.6 96 0.0021 35.6 3.5 14 552-565 531-544 (569)
No 1
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=100.00 E-value=3e-37 Score=319.70 Aligned_cols=367 Identities=17% Similarity=0.122 Sum_probs=253.0
Q ss_pred HhhhccCcchhhhccCcc--ccCCCCCCCCC-CCCCCC--ccccccccCCccccCCCCCCCccccCCCCCCCCCCCCCCc
Q 008318 27 RKKRKWDQPAESLINFPL--ASFGISLPGVP-VAPVVP--APAAAAFFTNPPVASGATVPPVVLQGPLPPKFNQPKVQDE 101 (570)
Q Consensus 27 r~krkwdqpae~~~~~pl--~~~g~~~p~~~-~~~~~~--aa~~~a~~~~~~~~~~~~vpp~~~~~~~~~~~~~~k~~de 101 (570)
-+.|+|||+++.=..+++ .+.|...|+.. ..+... ++++-++.+|+++-..-..-+..- ....-+...++..|+
T Consensus 13 ~~~~~WD~~~~~d~~~~~~~~~s~~~~p~eS~~~~~~~h~~~~s~s~~~N~~~~~k~~~~~~~N-a~~~i~~p~N~~K~~ 91 (531)
T KOG1960|consen 13 NYSRDWDSRFTEDSYSRRDSQRSGNEAPRESRYYRKEEHLQERSRSRSPNRDSRWKSSSSGFAN-AHPPIEEPTNNGKEA 91 (531)
T ss_pred CccccccCCCCCccccCchhhhccCCCCCcccccCcchhhhhhhhccCcchhcccccccccccc-ccchhhcccccchhH
Confidence 467899999975444333 22244455533 222222 566666899987742211212111 111123336778888
Q ss_pred eeEEEEEEeCCCCcccceeeechhhHHHHHhHhCCeEeeecceeCCCCC--CCCCCCeEEEEeeccchhhHHHHHHHHHH
Q 008318 102 LIIAREIVINDSESSVRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAP--PDGEKPLYLHISAGAHLKETAERILAVDH 179 (570)
Q Consensus 102 ~~f~~EIEINDlPq~~Ry~LTKg~TQ~eIqe~TGA~VtTRGrYyPPgk~--~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~ 179 (570)
+. .++++|||.+++|||++|+|.++++|.+++|+.|.+||+|++++.+ .++++||||||.+.|- +++++
T Consensus 92 ~~-~a~~~iN~~~~~~~~~~TRg~~~d~Ie~~~G~~~~~RGs~~~~El~~vg~~~~pLv~hI~~~T~--------Ei~~~ 162 (531)
T KOG1960|consen 92 AA-AAARRINESLQSTKATSTRGTSYDHIEGITGTTSASRGSAPAPELPPVGSSEGPLVDHIPPSTA--------EITSK 162 (531)
T ss_pred HH-HHHHHhhcccccccceeccchhHHhhhhhccceeeccCCCCCccCCCCCCCCCcceeecCCccH--------HHHHH
Confidence 84 8899999999999999999999999999999999999999999874 5789999999999984 68999
Q ss_pred HHHHHHHHHHcCCC----------CCCc--cc-------cccCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHH
Q 008318 180 AAAMVEEMLKQGHA----------GFPT--LQ-------TVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHI 240 (570)
Q Consensus 180 AiaeIeEILKE~P~----------~~p~--~~-------~p~~~G~k~~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~I 240 (570)
|+++|+-..+++.. ..+. .+ ++...|+++.+ |++|++| +|.||+.+..-|++..||.+|
T Consensus 163 Ai~RIkgv~~~~~~~~n~~~V~i~~~~sP~~~i~~~V~~~~f~~G~~Y~~-k~~v~~~-~P~~~~K~~~~~r~d~~La~~ 240 (531)
T KOG1960|consen 163 AIERIKGVFMQDVEINNVRNVYILVRASPLSEIENKVGVQLFSKGRYYPN-KALATDK-DPPLYLKIVSHNRKDLTLALQ 240 (531)
T ss_pred HHhhCccceeecccccccceEEEeecCCchhhhccccccccccccccchh-heecccC-CcchhhhhhccCccchhhhhh
Confidence 99999966665421 1111 01 22467888888 9999999 999999999999999999999
Q ss_pred HhhhCcEEEEeeccCcCCCCCCC-CCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHHHHHhhcccccccccccCCCCc---
Q 008318 241 MNETGATVLLRGRGSGNSEGLQG-EVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGASRVSSCKVYNAVPPP--- 316 (570)
Q Consensus 241 q~ETGAKI~IRGRGSg~~E~~~g-EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy~a~r~~~~k~y~avppp--- 316 (570)
+.||++++.|||||||.+|++.| |++||||++|+|.+.+.+.+||++|+||+++|+.+|.+|- ....-++|.+
T Consensus 241 ~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl~~~v~~~~sr~~---~~~~~~~p~~~y~ 317 (531)
T KOG1960|consen 241 EIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNGNGENGAPRRKWNLEEKVYINLSRGF---HRQAIVGPQGAYV 317 (531)
T ss_pred hhhhhhhhhhccccccccCcccccccCCceeEEeecCCchhhccchhHHHhHHHHHHHHhhhhh---hhcccccCCcccc
Confidence 99999999999999999999999 9999999999999999999999999999999999998753 1122222221
Q ss_pred ------cc---cccccccccccccCCccccceeccccccCCCCCCCCCCccceeeecceeecccc--ccccC--CCCCCc
Q 008318 317 ------QQ---LLTGIQGFGNEQKLNAGSAVILTSTVNLSSVPLAPSVPGVTTVYSQGMMLQSGG--ILNSV--QPQQNI 383 (570)
Q Consensus 317 ------qQ---~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~--~~~~~--~~~~~~ 383 (570)
|- +..|++.-=+++..|--+- .-.++-.++......|.-- .-.++ -+++-.
T Consensus 318 ~~~~~~~~~~~~~~g~~s~~i~p~~~~~~~----------------~p~~~~~~~~~~~~~~~~~~~~~~~i~~v~~qy~ 381 (531)
T KOG1960|consen 318 KHIQQETRTRVQIKGQGSAFIEPSTNRESD----------------EPIHLCIMSHDPNAIQRAKVLCEDLIASVHQQYK 381 (531)
T ss_pred cccCCCCCcceeccCccceeecCCCCCCCC----------------CCcccccccCChhhhhhhhhcccccCCcccccCc
Confidence 11 1222221113333222110 1112222222222223210 00111 145555
Q ss_pred cCCCCCCCCCCcccccCCCCCcCCChHHHHHHHHhcCCCCCccccc
Q 008318 384 VGYPQPVSTGGTSYSGYEGIYPQATPLQQVALALRQSSSPLTSLVA 429 (570)
Q Consensus 384 ~~~~~p~~~~g~~y~gy~~iypqatplqqva~~l~~~~s~~~~~v~ 429 (570)
+--.||.+ -+.-+|-||-+|-+-| |+++|+-+.-+-||..+
T Consensus 382 ~~~~qp~~--~~~~~~~~~~~~p~~~---~~~~~~~~~q~~~qp~~ 422 (531)
T KOG1960|consen 382 AWKSQPKD--RDQNQGNRAYNPPNRN---QAFSARDSRQEKTQPTN 422 (531)
T ss_pred ccccCCCc--ccccCCCCCCCCCCcc---ccccCCCCCCCCCCCCC
Confidence 66678854 4556788899987776 68888887666665443
No 2
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=99.95 E-value=2.3e-27 Score=251.06 Aligned_cols=159 Identities=23% Similarity=0.342 Sum_probs=132.1
Q ss_pred HHHHHhHhCCeEeeecceeCCC-C-CCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCccccccCC
Q 008318 127 QEEIQKCTGAVVITRGKYRLPN-A-PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQTVMGN 204 (570)
Q Consensus 127 Q~eIqe~TGA~VtTRGrYyPPg-k-~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeIeEILKE~P~~~p~~~~p~~~ 204 (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~----DY 132 (554)
T KOG0119|consen 61 IEEITRKLRTGDV----GVPPPRELRSPSPEPVYDAKGKRLNTREQRARKKLEDERHEIIEEILKLNPGFKPPA----DY 132 (554)
T ss_pred HHHhhhhhccccC----CCCCCccccCCCcchhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCc----cc
Confidence 3455554444321 13444 3 6788999999877777677778888889999999999999999999765 45
Q ss_pred Cc-ccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCC-----C---CCCCCcEEEEEc
Q 008318 205 GV-QAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQ-----G---EVHQPLHLFLSS 275 (570)
Q Consensus 205 G~-k~~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~-----g---EsdEPLHV~Isa 275 (570)
.+ ..+++|||||+++||+|||+|+||||||+|+|+||+||||||+||||||+. |+.. . .++||||++|++
T Consensus 133 k~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvk-Egk~~~~d~~~~~~~~epLH~~Isa 211 (554)
T KOG0119|consen 133 KPPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVK-EGKGRSDDLSYIPKENEPLHCLISA 211 (554)
T ss_pred CcccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEecccccc-ccccCCcccccccccccceeEEEec
Confidence 55 378999999999999999999999999999999999999999999999984 4431 1 478999999999
Q ss_pred CCHHHHHHHHHHHHHHHHH
Q 008318 276 NNPKSLEEAKRLAENLLDT 294 (570)
Q Consensus 276 ~~~e~v~kAk~LiEnLL~t 294 (570)
++.|+|++|.++||+||..
T Consensus 212 dt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 212 DTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred chHHHHHHHHHHHHHHHHh
Confidence 9999999999999999995
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=99.91 E-value=7.9e-25 Score=196.72 Aligned_cols=89 Identities=24% Similarity=0.436 Sum_probs=81.9
Q ss_pred eeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCC-------CC-CCCCCcEEEEEcCC--HH
Q 008318 210 STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGL-------QG-EVHQPLHLFLSSNN--PK 279 (570)
Q Consensus 210 eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~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 4799999999999999999999999999999999999999999999875532 23 78999999999999 99
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 008318 280 SLEEAKRLAENLLDTISAE 298 (570)
Q Consensus 280 ~v~kAk~LiEnLL~tV~eE 298 (570)
++++|+++|++||..+.++
T Consensus 81 ~~~~A~~~I~~ll~~~~~~ 99 (120)
T cd02395 81 ALAKAVEAIEELLKPAIEG 99 (120)
T ss_pred HHHHHHHHHHHHhccCCCc
Confidence 9999999999999988765
No 4
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=99.86 E-value=6.9e-22 Score=197.18 Aligned_cols=126 Identities=23% Similarity=0.364 Sum_probs=97.9
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCcccc---ccCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEe
Q 008318 175 LAVDHAAAMVEEMLKQGHAGFPTLQT---VMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLR 251 (570)
Q Consensus 175 ~aVd~AiaeIeEILKE~P~~~p~~~~---p~~~G~k~~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IR 251 (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 36777777777776653222222211 111122578899999999999999999999999999999999999999999
Q ss_pred eccCcCC-------CCCCC--CCCCCcEEEEEcCCHHH-----HHHHHHHHHHHHHHHHHHhh
Q 008318 252 GRGSGNS-------EGLQG--EVHQPLHLFLSSNNPKS-----LEEAKRLAENLLDTISAECG 300 (570)
Q Consensus 252 GRGSg~~-------E~~~g--EsdEPLHV~Isa~~~e~-----v~kAk~LiEnLL~tV~eEy~ 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 9999852 22223 48899999999888764 66889999999999988876
No 5
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.83 E-value=1.4e-20 Score=183.81 Aligned_cols=180 Identities=14% Similarity=0.106 Sum_probs=140.0
Q ss_pred eCCCCcccceeeechhh-----HHHHHhHhCCeEeeecceeCCCC--CCCCCCCeEEEEeeccchhhHHHHHHHHHHHHH
Q 008318 110 INDSESSVRYKLTKRHT-----QEEIQKCTGAVVITRGKYRLPNA--PPDGEKPLYLHISAGAHLKETAERILAVDHAAA 182 (570)
Q Consensus 110 INDlPq~~Ry~LTKg~T-----Q~eIqe~TGA~VtTRGrYyPPgk--~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~Aia 182 (570)
.|.||...--.||+-+. .-.+.|.|-..- -+-++|+.. +.+..+|.|..|....++.+.+.++++.|+..-
T Consensus 47 ~~~l~s~i~~~lt~eqi~~y~~~~r~~eit~Klr--t~d~Vp~~re~Rspsppp~yd~~GrRlntre~ry~kkLeder~~ 124 (269)
T COG5176 47 FNSLPSKISGALTREQIYSYQVMMRPFEITEKLR--TPDGVPSKRELRSPSPPPRYDEIGRRLNTREARYNKKLEDERLW 124 (269)
T ss_pred hhcchhHhhhhhhHHHHHHHHHhccHhhhhhhhc--CCCCCCchhhccCCCCCcchhHHhhhhhHHHHHHhhhhhHHHHH
Confidence 46666655555554321 112222222211 133466653 678999999999999988888888889999999
Q ss_pred HHHHHHHcCCCCCCccccccCCCc-ccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCC
Q 008318 183 MVEEMLKQGHAGFPTLQTVMGNGV-QAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGL 261 (570)
Q Consensus 183 eIeEILKE~P~~~p~~~~p~~~G~-k~~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~ 261 (570)
++++.++.-+-++. +++|.+ ...++|||||+++||+.||+|+||||+|+|+|.+|..|+|||.|||+||.. |+.
T Consensus 125 l~era~k~lp~fv~----p~dy~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvK-egk 199 (269)
T COG5176 125 LKERAQKILPRFVL----PNDYIRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVK-EGK 199 (269)
T ss_pred HHHHHHHhcCcccC----CccccCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccc-cCc
Confidence 99999998887774 345544 678999999999999999999999999999999999999999999999974 332
Q ss_pred C------C--CCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHHH
Q 008318 262 Q------G--EVHQPLHLFLSSNNPKSLEEAKRLAENLLDTIS 296 (570)
Q Consensus 262 ~------g--EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~ 296 (570)
. + ...++||++|+++..+++.++.++|.+.|.+..
T Consensus 200 ~ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n~I~~a~ 242 (269)
T COG5176 200 ISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREAR 242 (269)
T ss_pred ccccCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHHHHHHHh
Confidence 1 1 356889999999999999999999999998765
No 6
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=99.21 E-value=2.8e-12 Score=134.96 Aligned_cols=147 Identities=22% Similarity=0.387 Sum_probs=121.3
Q ss_pred hhhHHHHHhHhCCeEeeecceeCCCCC---CCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCcccc
Q 008318 124 RHTQEEIQKCTGAVVITRGKYRLPNAP---PDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQT 200 (570)
Q Consensus 124 g~TQ~eIqe~TGA~VtTRGrYyPPgk~---~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeIeEILKE~P~~~p~~~~ 200 (570)
-.++..|+.++++.+..||++---.++ -+..-|.|+.|.+.+. +.+..|..+|..++..
T Consensus 234 d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~--------~g~~~A~r~~~nl~~~---------- 295 (531)
T KOG1960|consen 234 DLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNG--------NGENGAPRRKWNLEEK---------- 295 (531)
T ss_pred chhhhhhhhhhhhhhhhccccccccCcccccccCCceeEEeecCCc--------hhhccchhHHHhHHHH----------
Confidence 457788999999999999998654443 4678999999999985 4677777777666432
Q ss_pred ccCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCC-CCCCCcEEEEEcCCHH
Q 008318 201 VMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQG-EVHQPLHLFLSSNNPK 279 (570)
Q Consensus 201 p~~~G~k~~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~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 333111 1222 23578999999999999999999999999999999999 9999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccc
Q 008318 280 SLEEAKRLAENLLDTISAECGASR 303 (570)
Q Consensus 280 ~v~kAk~LiEnLL~tV~eEy~a~r 303 (570)
.|+.|+-||++||..|..+|.++.
T Consensus 361 ~~~~~~~~~~~~i~~v~~qy~~~~ 384 (531)
T KOG1960|consen 361 AIQRAKVLCEDLIASVHQQYKAWK 384 (531)
T ss_pred hhhhhhhcccccCCcccccCcccc
Confidence 999999999999999999998865
No 7
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.09 E-value=2.7e-09 Score=116.84 Aligned_cols=184 Identities=20% Similarity=0.278 Sum_probs=127.6
Q ss_pred eeEEEEEEeCCCCcccceeeec-hhhHHHHHhHhCCeEeeecceeCCCC-CCCCCCCeEEEEeeccchhhHHHHHHHHHH
Q 008318 102 LIIAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNA-PPDGEKPLYLHISAGAHLKETAERILAVDH 179 (570)
Q Consensus 102 ~~f~~EIEINDlPq~~Ry~LTK-g~TQ~eIqe~TGA~VtTRGrYyPPgk-~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~ 179 (570)
...+.||.|-+- +|-.++-| |+|++.+++++|+.+.. +=++. .....||| .|+|.. ..|+.
T Consensus 137 ~~ttqeI~IPa~--k~GlIIGKgGETikqlqe~sg~k~i~----iqd~~~~~~~~Kpl--ritGdp---------~~ve~ 199 (600)
T KOG1676|consen 137 VETTQEILIPAN--KCGLIIGKGGETIKQLQEQSGVKMIL----VQDGSIATGADKPL--RITGDP---------DKVEQ 199 (600)
T ss_pred cceeeeeccCcc--ceeeEeccCccHHHHHHhhcCCceEE----EecCCcCCCCCCce--eecCCH---------HHHHH
Confidence 334678888777 58889987 99999999999986432 11222 33478898 778875 37999
Q ss_pred HHHHHHHHHHcCCCCCCccccccCCCccc-ceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCC
Q 008318 180 AAAMVEEMLKQGHAGFPTLQTVMGNGVQA-MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNS 258 (570)
Q Consensus 180 AiaeIeEILKE~P~~~p~~~~p~~~G~k~-~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~ 258 (570)
|..+|.++|+++-.-.+.. ...+|... -++++.| .+|.| -+|.|||-+|.|||+|+.|||+||+|+=.
T Consensus 200 a~~lV~dil~e~~~~~~g~--~~~~g~~~g~~~~~~V---~VPr~-~VG~IIGkgGE~IKklq~etG~KIQfkpD----- 268 (600)
T KOG1676|consen 200 AKQLVADILREEDDEVPGS--GGHAGVRGGGSATREV---KVPRS-KVGIIIGKGGEMIKKLQNETGAKIQFKPD----- 268 (600)
T ss_pred HHHHHHHHHHhcccCCCcc--ccccCcCccccceeEE---ecccc-ceeeEEecCchHHHHHhhccCceeEeecC-----
Confidence 9999999999753222111 02233322 2335555 34566 69999999999999999999999999832
Q ss_pred CCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHHHHHhhc-----ccccccccccCCCCcc
Q 008318 259 EGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGA-----SRVSSCKVYNAVPPPQ 317 (570)
Q Consensus 259 E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy~a-----~r~~~~k~y~avpppq 317 (570)
.+..-++..+..-.+.+.+++|++||.+||..+.+.-.. .-......|..||.-.
T Consensus 269 ----d~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~~~~~~~G~P~~~~~fy~~VPa~K 328 (600)
T KOG1676|consen 269 ----DDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGAGGGMGGGAPGLVAQFYMKVPADK 328 (600)
T ss_pred ----CCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhccCCCCcCCCCccceeeEEEeccccc
Confidence 012345666777788999999999999999998877311 1111125677777544
No 8
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=99.08 E-value=5.4e-11 Score=135.98 Aligned_cols=82 Identities=32% Similarity=0.500 Sum_probs=77.1
Q ss_pred eEEEEEEeCCCCcccceeeechhhHHHHHhHhCCeEeeecceeCCCC-CCCCCCCeEEEEeeccchhhHHHHHHHHHHHH
Q 008318 103 IIAREIVINDSESSVRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNA-PPDGEKPLYLHISAGAHLKETAERILAVDHAA 181 (570)
Q Consensus 103 ~f~~EIEINDlPq~~Ry~LTKg~TQ~eIqe~TGA~VtTRGrYyPPgk-~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~Ai 181 (570)
+|.++++|||+||.+||.+|..+++..|.+.+++.|+|||.|||+++ +.++|++|||+|++.++ ..|.+|+
T Consensus 897 ~y~~~~~inD~Pq~~r~~vt~~~~L~~i~e~~~~~it~rg~f~~~gk~p~~gErklyl~ve~~~e--------~~vqra~ 968 (997)
T KOG0334|consen 897 IYEAELEINDFPQNARWRVTYKEALLRISEPTAAGITTRGKFNPPGKEPKPGERKLYLLVEGPDE--------LSVQRAI 968 (997)
T ss_pred eeeeeccccccchhcceeeechhhhhhccCccccceeeccccCCCCCCCCCcchhhhhhhhcchh--------HHHHHHH
Confidence 57999999999999999999999999999999999999999999997 77899999999999886 6899999
Q ss_pred HHHHHHHHcCC
Q 008318 182 AMVEEMLKQGH 192 (570)
Q Consensus 182 aeIeEILKE~P 192 (570)
.+++++|+++.
T Consensus 969 ~e~~r~l~e~~ 979 (997)
T KOG0334|consen 969 EELERLLEEEV 979 (997)
T ss_pred HHHHHHHHHHH
Confidence 99999988863
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=98.79 E-value=2.7e-08 Score=94.24 Aligned_cols=129 Identities=20% Similarity=0.211 Sum_probs=86.7
Q ss_pred echhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEE--eeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCccc
Q 008318 122 TKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHI--SAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQ 199 (570)
Q Consensus 122 TKg~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~I--eg~Te~kdt~ERi~aVd~AiaeIeEILKE~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 71 (172)
T TIGR03665 15 KGGETKKEIEERTGVKLDIDS----------ETG--EVKIEEEDEDP--------LAVMKAREVVKAIGRGF---SPEKA 71 (172)
T ss_pred CchhHHHHHHHHhCcEEEEEc----------CCc--eEEEecCCCCH--------HHHHHHHHHHHHHHcCC---CHHHH
Confidence 349999999999999987642 112 3455 23332 58999999999976541 11100
Q ss_pred cccCCCcccceeEEEecCCCC---C-CC-ceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEE
Q 008318 200 TVMGNGVQAMSTSVFLGFDAD---A-SL-NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLS 274 (570)
Q Consensus 200 ~p~~~G~k~~eeKI~Ipvd~~---P-~F-NfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Is 274 (570)
+- -.|--+..+- |.+.++ + .| ..+|+|||++|.+++.||..|||+|+|-|+ .|+|.
T Consensus 72 ~~-l~gd~y~~~V--i~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~~----------------~v~i~ 132 (172)
T TIGR03665 72 LK-LLDDDYMLEV--IDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYGK----------------TVGII 132 (172)
T ss_pred HH-hcCCcceEEE--EEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcCC----------------EEEEE
Confidence 00 0010111122 222221 0 01 269999999999999999999999999752 58899
Q ss_pred cCCHHHHHHHHHHHHHHHH
Q 008318 275 SNNPKSLEEAKRLAENLLD 293 (570)
Q Consensus 275 a~~~e~v~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=98.75 E-value=3.3e-08 Score=94.41 Aligned_cols=145 Identities=20% Similarity=0.206 Sum_probs=95.4
Q ss_pred EEEEEEeCCCCcccceeeec-hhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEe---eccchhhHHHHHHHHHH
Q 008318 104 IAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHIS---AGAHLKETAERILAVDH 179 (570)
Q Consensus 104 f~~EIEINDlPq~~Ry~LTK-g~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ie---g~Te~kdt~ERi~aVd~ 179 (570)
+...+.|..- +.+.++.+ |.+++.|+++||+.|...- .+.. +.|. +.+. ..+++
T Consensus 3 ~~~~i~IP~~--kig~iIG~gGk~Ik~I~e~tg~~I~i~~----------~~g~--V~I~~~~~~d~--------~~i~k 60 (180)
T PRK13763 3 MMEYVKIPKD--RIGVLIGKKGETKKEIEERTGVKLEIDS----------ETGE--VIIEPTDGEDP--------LAVLK 60 (180)
T ss_pred ceEEEEcCHH--HhhhHhccchhHHHHHHHHHCcEEEEEC----------CCCe--EEEEeCCCCCH--------HHHHH
Confidence 4456666544 35666655 8999999999999987643 1233 3454 3332 58999
Q ss_pred HHHHHHHHHHcCCCCCCccccccCCCcccceeEEEecCCCC-C---CC-ceeeEEeCCCchhHHHHHhhhCcEEEEeecc
Q 008318 180 AAAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDAD-A---SL-NIAARIRGPNDQYINHIMNETGATVLLRGRG 254 (570)
Q Consensus 180 AiaeIeEILKE~P~~~p~~~~p~~~G~k~~eeKI~Ipvd~~-P---~F-NfvgrIIGP~GstlK~Iq~ETGAKI~IRGRG 254 (570)
|...|+.++.. +.++..+- -.|-.+.-+.+.| .++ . .| ..+|+|||++|.++|.||..|||+|+|-|+
T Consensus 61 A~~~I~ai~~g---f~~e~A~~-l~gd~y~~~Vi~i--~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~- 133 (180)
T PRK13763 61 ARDIVKAIGRG---FSPEKALR-LLDDDYVLEVIDL--SDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGK- 133 (180)
T ss_pred HHHHHHHHhcC---CCHHHHHH-HhCCCceEEEEEh--hhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCC-
Confidence 99999998763 11110000 0010111122222 121 0 01 269999999999999999999999999753
Q ss_pred CcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHH
Q 008318 255 SGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 293 (570)
Q Consensus 255 Sg~~E~~~gEsdEPLHV~Isa~~~e~v~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=98.75 E-value=2.1e-07 Score=102.32 Aligned_cols=160 Identities=21% Similarity=0.367 Sum_probs=115.8
Q ss_pred EEEEEeCCCCcccceeeec-hhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHH
Q 008318 105 AREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAM 183 (570)
Q Consensus 105 ~~EIEINDlPq~~Ry~LTK-g~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~Aiae 183 (570)
..+|.|--+ ++-.+|-| |++++.|+.+||+.| +|.|+..++.-||+| +|-|..+ .+++|..+
T Consensus 231 ~~~V~VPr~--~VG~IIGkgGE~IKklq~etG~KI----QfkpDd~p~speR~~--~IiG~~d---------~ie~Aa~l 293 (600)
T KOG1676|consen 231 TREVKVPRS--KVGIIIGKGGEMIKKLQNETGAKI----QFKPDDDPSSPERPA--QIIGTVD---------QIEHAAEL 293 (600)
T ss_pred eeEEecccc--ceeeEEecCchHHHHHhhccCcee----EeecCCCCCCcccee--eeecCHH---------HHHHHHHH
Confidence 346666665 57888877 999999999999977 788888877789998 7788753 68899999
Q ss_pred HHHHHHcCCCCCCccccccCCCcccc--eeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCC
Q 008318 184 VEEMLKQGHAGFPTLQTVMGNGVQAM--STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGL 261 (570)
Q Consensus 184 IeEILKE~P~~~p~~~~p~~~G~k~~--eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~ 261 (570)
|.+||.+......- .++-|.-.. +--+-||-+. .|+|||++|.|+|.|..|+||++.|-=- +
T Consensus 294 I~eii~~~~~~~~~---~~~~G~P~~~~~fy~~VPa~K------cGLvIGrGGEtIK~in~qSGA~~el~r~-~------ 357 (600)
T KOG1676|consen 294 INEIIAEAEAGAGG---GMGGGAPGLVAQFYMKVPADK------CGLVIGRGGETIKQINQQSGARCELSRQ-P------ 357 (600)
T ss_pred HHHHHHHHhccCCC---CcCCCCccceeeEEEeccccc------cccccCCCccchhhhcccCCccccccCC-C------
Confidence 99999875322110 011121111 2223344333 7999999999999999999999865321 1
Q ss_pred CCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHHHHH
Q 008318 262 QGEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAE 298 (570)
Q Consensus 262 ~gEsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eE 298 (570)
-..+.+..+++.-.++.+|+.|+.||++-+.-+...
T Consensus 358 -p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~~~n 393 (600)
T KOG1676|consen 358 -PNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDIAPN 393 (600)
T ss_pred -CCCCccceEEEEecCcccchHHHHHHHHHhcccCCC
Confidence 024556788899999999999999999887765543
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=98.43 E-value=8.6e-07 Score=68.83 Aligned_cols=63 Identities=27% Similarity=0.393 Sum_probs=50.5
Q ss_pred eEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHH
Q 008318 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAE 289 (570)
Q Consensus 211 eKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~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 4666754 68999999999999999999999999986533 234566888887 788999988763
No 13
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.36 E-value=9.2e-07 Score=71.00 Aligned_cols=50 Identities=22% Similarity=0.455 Sum_probs=44.2
Q ss_pred eeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHH
Q 008318 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAE 289 (570)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiE 289 (570)
++|+|||++|+++|.|+++|||+|.|-- .-.|.|.|.+.+++++|+++++
T Consensus 12 ~ig~iIGkgG~~ik~I~~~tg~~I~i~~---------------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 12 KIRDVIGPGGKTIKKIIEETGVKIDIED---------------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred heeeeECCCchHHHHHHHHHCCEEEeCC---------------CCEEEEEeCCHHHHHHHHHHhC
Confidence 6899999999999999999999998742 1259999999999999999875
No 14
>smart00322 KH K homology RNA-binding domain.
Probab=98.30 E-value=3.5e-06 Score=63.97 Aligned_cols=66 Identities=23% Similarity=0.341 Sum_probs=54.0
Q ss_pred ceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHH
Q 008318 209 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLA 288 (570)
Q Consensus 209 ~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~Li 288 (570)
...+|.|+. ++.|+|||++|.++++|+++|||+|.+.+.++ ....+.|.+. .+++..|+.++
T Consensus 3 ~~~~i~i~~------~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~-----------~~~~v~i~g~-~~~v~~a~~~i 64 (69)
T smart00322 3 VTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS-----------EERVVEITGP-PENVEKAAELI 64 (69)
T ss_pred eEEEEEEcc------hhcceeECCCchHHHHHHHHHCCEEEECCCCC-----------CccEEEEEcC-HHHHHHHHHHH
Confidence 345667753 57899999999999999999999999986533 3466888888 89999999998
Q ss_pred HHHH
Q 008318 289 ENLL 292 (570)
Q Consensus 289 EnLL 292 (570)
++++
T Consensus 65 ~~~~ 68 (69)
T smart00322 65 LEIL 68 (69)
T ss_pred HHHh
Confidence 8876
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=98.24 E-value=5.4e-07 Score=70.44 Aligned_cols=52 Identities=25% Similarity=0.411 Sum_probs=46.0
Q ss_pred ceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHH
Q 008318 224 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLA 288 (570)
Q Consensus 224 NfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~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-----------D-ERDIVTISG-SPEQVEKAKKMI 60 (60)
T ss_dssp HHHHHHHTGGGHHHHHHHHHHTSEEEEEST-----------T-EEEEEEEEE-SHHHHHHHHHHH
T ss_pred HHcCEEECCCCCcHHHhhhhcCeEEEEcCC-----------C-CcEEEEEEe-CHHHHHHHHhhC
Confidence 478999999999999999999999999654 1 446899999 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=98.02 E-value=6.9e-06 Score=64.59 Aligned_cols=53 Identities=23% Similarity=0.337 Sum_probs=45.3
Q ss_pred ceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHH
Q 008318 224 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLA 288 (570)
Q Consensus 224 NfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~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 4689999999999999999999999998653 23467899999 78999998876
No 17
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.94 E-value=0.00046 Score=72.83 Aligned_cols=162 Identities=16% Similarity=0.211 Sum_probs=104.0
Q ss_pred EEEEEEeCCCCcccceeeec-hhhHHHHHhHhCCeEee-ecc-eeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHH
Q 008318 104 IAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVIT-RGK-YRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHA 180 (570)
Q Consensus 104 f~~EIEINDlPq~~Ry~LTK-g~TQ~eIqe~TGA~VtT-RGr-YyPPgk~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~A 180 (570)
++=+|-|-.+- +--+|-| |+|+.++|++|||.|-. |-+ || ++.----.+|+|..+ ++..-
T Consensus 39 y~ikvLips~A--aGsIIGKGG~ti~~lqk~tgariklSks~dfy------PGTTeRvcli~Gt~e---------ai~av 101 (402)
T KOG2191|consen 39 YFLKVLIPSYA--AGSIIGKGGQTIVQLQKETGARIKLSKSKDFY------PGTTERVCLIQGTVE---------ALNAV 101 (402)
T ss_pred eEEEEEeeccc--ccceeccchHHHHHHHhccCcEEEeccccccC------CCccceEEEEeccHH---------HHHHH
Confidence 34467776663 7888888 89999999999998854 221 33 332233458889763 45555
Q ss_pred HHHHHHHHHcCCCCCCc---cccccCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEe-eccCc
Q 008318 181 AAMVEEMLKQGHAGFPT---LQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLR-GRGSG 256 (570)
Q Consensus 181 iaeIeEILKE~P~~~p~---~~~p~~~G~k~~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IR-GRGSg 256 (570)
+..|.+.|.|.+....- ...+.... +-.+-||.+|-. -.|.|||++|.|+|.|++|+||-|+|- -+-.+
T Consensus 102 ~efI~dKire~p~~~~k~v~~~~pqt~~-r~kqikivvPNs------tag~iigkggAtiK~~~Eqsga~iqisPqkpt~ 174 (402)
T KOG2191|consen 102 HEFIADKIREKPQAVAKPVDILQPQTPD-RIKQIKIVVPNS------TAGMIIGKGGATIKAIQEQSGAWIQISPQKPTG 174 (402)
T ss_pred HHHHHHHHHHhHHhhcCCccccCCCCcc-ccceeEEeccCC------cccceecCCcchHHHHHHhhCcceEecccCCCC
Confidence 55666666655432211 00010000 234567777632 479999999999999999999999997 33111
Q ss_pred CCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHHHHHhh
Q 008318 257 NSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECG 300 (570)
Q Consensus 257 ~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy~ 300 (570)
. ..+| .|...+.+++++.+|++|| |+.|.|+-+
T Consensus 175 ~------sLqe--rvvt~sge~e~~~~A~~~I---L~Ki~eDpq 207 (402)
T KOG2191|consen 175 I------SLQE--RVVTVSGEPEQNMKAVSLI---LQKIQEDPQ 207 (402)
T ss_pred c------ccee--EEEEecCCHHHHHHHHHHH---HHHhhcCCc
Confidence 1 1222 4666688899999996664 667776643
No 18
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=97.88 E-value=3.2e-05 Score=62.15 Aligned_cols=56 Identities=23% Similarity=0.236 Sum_probs=42.1
Q ss_pred ceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHH
Q 008318 224 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLA 288 (570)
Q Consensus 224 NfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~Li 288 (570)
+.+|+|||.+|.++++|+++|||+|.|--... ......++....+.+++++|+.|+
T Consensus 9 ~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~---------~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 9 SQAGSIIGKGGSTIKEIREETGAKIRVSKSVL---------PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred HHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC---------CCCCceEEEEEeCHHHHHHHHHhh
Confidence 36899999999999999999999999953211 122233444445699999999886
No 19
>PF13014 KH_3: KH domain
Probab=97.65 E-value=4.1e-05 Score=57.06 Aligned_cols=28 Identities=32% Similarity=0.455 Sum_probs=26.3
Q ss_pred eeeEEeCCCchhHHHHHhhhCcEEEEee
Q 008318 225 IAARIRGPNDQYINHIMNETGATVLLRG 252 (570)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGAKI~IRG 252 (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 4789999999999999999999999976
No 20
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.50 E-value=0.00045 Score=74.73 Aligned_cols=140 Identities=14% Similarity=0.188 Sum_probs=86.8
Q ss_pred chhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCcccccc
Q 008318 123 KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQTVM 202 (570)
Q Consensus 123 Kg~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeIeEILKE~P~~~p~~~~p~ 202 (570)
.|.|++.|-..|-+.|-+ .--+.....|+.|-+|-+. | ...+|..+|-|+|..+-.--
T Consensus 217 eG~TIknItkqTqsriD~----hrken~Gaaek~itvh~tp--E---------g~s~Ac~~ILeimqkEA~~~------- 274 (584)
T KOG2193|consen 217 EGATIKNITKQTQSRIDV----HRKENAGAAEKIITVHSTP--E---------GTSKACKMILEIMQKEAVDD------- 274 (584)
T ss_pred CCccccCcchhhhheeee----eecccCCcccCceEEecCc--c---------chHHHHHHHHHHHHHhhhcc-------
Confidence 389999999999887643 1112234678999777443 2 45667788999886642110
Q ss_pred CCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHH
Q 008318 203 GNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLE 282 (570)
Q Consensus 203 ~~G~k~~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~ 282 (570)
.+.+ .||++-.---||+|||||..|.+||+||++||+||.|-- +.| -++ .+-.--+.|-| +-|.+.
T Consensus 275 -----k~~~--e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~----lqe-ls~-ynpERTItVkG-siEac~ 340 (584)
T KOG2193|consen 275 -----KVAE--EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISK----LQE-LSL-YNPERTITVKG-SIEACV 340 (584)
T ss_pred -----chhh--hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeee----hhh-hcc-cCccceEEecc-cHHHHH
Confidence 1111 244443334568999999999999999999999999853 222 011 11223455555 555555
Q ss_pred HHHHHHHHHHHHHHHHhhc
Q 008318 283 EAKRLAENLLDTISAECGA 301 (570)
Q Consensus 283 kAk~LiEnLL~tV~eEy~a 301 (570)
+|.. +++..+++-|..
T Consensus 341 ~AE~---eImkKlre~yEn 356 (584)
T KOG2193|consen 341 QAEA---EIMKKLRECYEN 356 (584)
T ss_pred HHHH---HHHHHHHHHHhh
Confidence 5544 445566666654
No 21
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.35 E-value=0.00038 Score=66.82 Aligned_cols=64 Identities=13% Similarity=0.184 Sum_probs=53.1
Q ss_pred eEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEE---cCCHHHHHHHHHH
Q 008318 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLS---SNNPKSLEEAKRL 287 (570)
Q Consensus 211 eKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Is---a~~~e~v~kAk~L 287 (570)
..+.||.+ -+|.|||++|.++|.|+++|||+|.|.-. .-.|.|. +.|++.+++|+++
T Consensus 5 ~~i~IP~~------kig~iIG~gGk~Ik~I~e~tg~~I~i~~~--------------~g~V~I~~~~~~d~~~i~kA~~~ 64 (180)
T PRK13763 5 EYVKIPKD------RIGVLIGKKGETKKEIEERTGVKLEIDSE--------------TGEVIIEPTDGEDPLAVLKARDI 64 (180)
T ss_pred EEEEcCHH------HhhhHhccchhHHHHHHHHHCcEEEEECC--------------CCeEEEEeCCCCCHHHHHHHHHH
Confidence 45566543 48899999999999999999999999753 1356777 8899999999999
Q ss_pred HHHHHHH
Q 008318 288 AENLLDT 294 (570)
Q Consensus 288 iEnLL~t 294 (570)
++.|+..
T Consensus 65 I~ai~~g 71 (180)
T PRK13763 65 VKAIGRG 71 (180)
T ss_pred HHHHhcC
Confidence 9999873
No 22
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.32 E-value=0.0017 Score=74.26 Aligned_cols=131 Identities=15% Similarity=0.180 Sum_probs=84.0
Q ss_pred HHHHHHHHHHHHHHcCCCCCCccccccCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccC
Q 008318 176 AVDHAAAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGS 255 (570)
Q Consensus 176 aVd~AiaeIeEILKE~P~~~p~~~~p~~~G~k~~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGS 255 (570)
...+|...|-++|++...... +. ..+.+ .-+.+.|+.+ -+|.||||+|.++|.|+.+|||+|-|--
T Consensus 550 ~A~~g~~~Il~~m~~al~~p~--~~-s~~aP--~~~~~~I~~~------ki~~vIG~gGk~I~~i~~~tg~~Idi~d--- 615 (719)
T TIGR02696 550 QARDARLAILDVMAEAIDTPD--EM-SPYAP--RIITVKIPVD------KIGEVIGPKGKMINQIQDETGAEISIED--- 615 (719)
T ss_pred HHHHHHHHHHHHHHHHHhCcc--cc-ccCCC--eeEEEEeChH------HhhheeCCCcHhHHHHHHHHCCEEEEec---
Confidence 334445556666666532111 11 12222 2356667544 4889999999999999999999998753
Q ss_pred cCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHHHHHhhcccccccccccCCCCccccccccccccccccCCcc
Q 008318 256 GNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGASRVSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAG 335 (570)
Q Consensus 256 g~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy~a~r~~~~k~y~avpppqQ~~~g~~~~~~~~~~~~~ 335 (570)
.=+|.|.+.+.+++++|+++|++|+..- + +..+..|-. -+..+..+|..-.+..
T Consensus 616 ------------~G~V~I~a~d~~~~~~A~~~I~~i~~~~--~-----~~vG~i~~G------kV~~I~dfGaFVel~~- 669 (719)
T TIGR02696 616 ------------DGTVYIGAADGPSAEAARAMINAIANPT--M-----PEVGERFLG------TVVKTTAFGAFVSLLP- 669 (719)
T ss_pred ------------CcEEEEEeCCHHHHHHHHHHHHHhhCcC--c-----CCCCCEEEE------EEEEEECceEEEEecC-
Confidence 3579999999999999999999998850 0 111222211 3556777885444432
Q ss_pred ccceecccccc
Q 008318 336 SAVILTSTVNL 346 (570)
Q Consensus 336 ~~~~~~~~~~~ 346 (570)
..-||.|.-.+
T Consensus 670 G~eGLvHISei 680 (719)
T TIGR02696 670 GKDGLLHISQI 680 (719)
T ss_pred CceEEEEhhhc
Confidence 35778775544
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=97.18 E-value=0.00043 Score=65.94 Aligned_cols=56 Identities=11% Similarity=0.174 Sum_probs=48.6
Q ss_pred eeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEE--EcCCHHHHHHHHHHHHHHHHH
Q 008318 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFL--SSNNPKSLEEAKRLAENLLDT 294 (570)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~I--sa~~~e~v~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 58899999999999999999999998742 124777 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=97.12 E-value=0.0011 Score=60.65 Aligned_cols=64 Identities=28% Similarity=0.353 Sum_probs=49.9
Q ss_pred eeechhhHHHHHhHhCCeEeeecceeCCCC----------CCCCCCCeEEEEeecc--chhhHHHHHHHHHHHHHHHHHH
Q 008318 120 KLTKRHTQEEIQKCTGAVVITRGKYRLPNA----------PPDGEKPLYLHISAGA--HLKETAERILAVDHAAAMVEEM 187 (570)
Q Consensus 120 ~LTKg~TQ~eIqe~TGA~VtTRGrYyPPgk----------~~~gEpPLYL~Ieg~T--e~kdt~ERi~aVd~AiaeIeEI 187 (570)
+=.+|.|+++|+++|||.|.+||+---... ....+-||+++|++.+ . .++++|+.+|+++
T Consensus 21 IGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~--------e~~~~A~~~I~~l 92 (120)
T cd02395 21 LGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPE--------EALAKAVEAIEEL 92 (120)
T ss_pred ECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHH--------HHHHHHHHHHHHH
Confidence 336799999999999999999996211111 1134678999999998 4 5899999999999
Q ss_pred HHcC
Q 008318 188 LKQG 191 (570)
Q Consensus 188 LKE~ 191 (570)
+...
T Consensus 93 l~~~ 96 (120)
T cd02395 93 LKPA 96 (120)
T ss_pred hccC
Confidence 8853
No 25
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.08 E-value=0.00095 Score=65.83 Aligned_cols=54 Identities=22% Similarity=0.284 Sum_probs=49.2
Q ss_pred eeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHH
Q 008318 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTI 295 (570)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~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 78999999999999999999999999996 677776 6899999999999999753
No 26
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.01 E-value=0.0011 Score=72.87 Aligned_cols=66 Identities=26% Similarity=0.387 Sum_probs=52.1
Q ss_pred ceee-echhhHHHHHhHhCCeEeeecce-eCCCC--------CCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHH
Q 008318 118 RYKL-TKRHTQEEIQKCTGAVVITRGKY-RLPNA--------PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEM 187 (570)
Q Consensus 118 Ry~L-TKg~TQ~eIqe~TGA~VtTRGrY-yPPgk--------~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeIeEI 187 (570)
-.+| -+|.||+.++++|||.|..||+= +-.|+ ....+-+||.+|++.|+ +.|++|++.|+.+
T Consensus 156 GLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~--------eki~~Ai~vienl 227 (554)
T KOG0119|consen 156 GLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQ--------EKIKKAIAVIENL 227 (554)
T ss_pred EEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchH--------HHHHHHHHHHHHH
Confidence 4455 57999999999999999999932 11111 12357899999999987 6899999999999
Q ss_pred HHcC
Q 008318 188 LKQG 191 (570)
Q Consensus 188 LKE~ 191 (570)
|++.
T Consensus 228 i~~a 231 (554)
T KOG0119|consen 228 IQSA 231 (554)
T ss_pred HHhh
Confidence 9974
No 27
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.79 E-value=0.0061 Score=66.31 Aligned_cols=156 Identities=16% Similarity=0.214 Sum_probs=105.5
Q ss_pred EEEeCCCCcccceee-echhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHH
Q 008318 107 EIVINDSESSVRYKL-TKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVE 185 (570)
Q Consensus 107 EIEINDlPq~~Ry~L-TKg~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeIe 185 (570)
.+.|-|.- +.-++ .||..+++|.+++||+|-. -||+-+--++| -..|+|+.+ +.-+|-..|-
T Consensus 414 ~~fiP~~~--vGAiIGkkG~hIKql~RfagASiKI----appE~pdvseR--MViItGppe---------aqfKAQgrif 476 (584)
T KOG2193|consen 414 RMFIPAQA--VGAIIGKKGQHIKQLSRFAGASIKI----APPEIPDVSER--MVIITGPPE---------AQFKAQGRIF 476 (584)
T ss_pred eeeccHHH--HHHHHhhcchhHHHHHHhccceeee----cCCCCCCccee--EEEecCChH---------HHHhhhhhhh
Confidence 45566653 45555 4699999999999999843 23332222333 457888864 6778888899
Q ss_pred HHHHcCCCCCCccccccCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCC
Q 008318 186 EMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEV 265 (570)
Q Consensus 186 EILKE~P~~~p~~~~p~~~G~k~~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEs 265 (570)
--|+|+..+.|-.. .+++.-|-| |.+ .+|||||.+|.|++.+|+-|+|.|.|--. .++++
T Consensus 477 gKikEenf~~Pkee-------vklethirV-----Ps~-~aGRvIGKGGktVnELQnlt~AeV~vPrd-------qtpdE 536 (584)
T KOG2193|consen 477 GKIKEENFFLPKEE-------VKLETHIRV-----PSS-AAGRVIGKGGKTVNELQNLTSAEVVVPRD-------QTPDE 536 (584)
T ss_pred hhhhhhccCCchhh-------heeeeeeec-----cch-hhhhhhccccccHHHHhccccceEEcccc-------CCCCc
Confidence 99998865553221 345555544 455 89999999999999999999999987432 23333
Q ss_pred CCCcEEEEEcCCHHHHHHHHHHHHHHHHHHHHHhh
Q 008318 266 HQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECG 300 (570)
Q Consensus 266 dEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy~ 300 (570)
+|-.-|-|.| +.-....|..-+.+|+..|++.-+
T Consensus 537 nd~vivriiG-hfyatq~aQrki~~iv~qvkq~~q 570 (584)
T KOG2193|consen 537 NDQVIVRIIG-HFYATQNAQRKIAHIVNQVKQSGQ 570 (584)
T ss_pred cceeeeeeec-hhhcchHHHHHHHHHHHHHHHhhh
Confidence 4434444444 455667777888888888876543
No 28
>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=96.74 E-value=0.0027 Score=72.16 Aligned_cols=99 Identities=18% Similarity=0.259 Sum_probs=70.3
Q ss_pred eEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHH
Q 008318 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAEN 290 (570)
Q Consensus 211 eKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEn 290 (570)
+.+.|+.+ .+|.||||+|.++|.|++||||+|-|-- .=+|.|.+.+.+.+++|+++++.
T Consensus 553 ~~~~I~~~------kI~~vIG~gGk~Ik~I~~~tg~~I~i~d---------------dG~V~i~~~~~~~~~~a~~~I~~ 611 (684)
T TIGR03591 553 ETIKINPD------KIRDVIGPGGKVIREITEETGAKIDIED---------------DGTVKIAASDGEAAEAAIKMIEG 611 (684)
T ss_pred EEEecCHH------HHHhhcCCCcHHHHHHHHHHCCEEEEec---------------CeEEEEEECcHHHHHHHHHHHHh
Confidence 45556433 4889999999999999999999998843 24789999999999999999999
Q ss_pred HHHHHHHHhhcccccccccccCCCCccccccccccccccccCCccccceecccccc
Q 008318 291 LLDTISAECGASRVSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNL 346 (570)
Q Consensus 291 LL~tV~eEy~a~r~~~~k~y~avpppqQ~~~g~~~~~~~~~~~~~~~~~~~~~~~~ 346 (570)
|... +. ..+.|-. .+.++..+|..-.+.. ...|+.|--++
T Consensus 612 ~~~~----~~-----~G~i~~G------~V~~I~~~GafVei~~-g~~GllHiSei 651 (684)
T TIGR03591 612 ITAE----PE-----VGKIYEG------KVVRIMDFGAFVEILP-GKDGLVHISEI 651 (684)
T ss_pred hhcc----cc-----cCcEEEE------EEEEEeCCEEEEEECC-CcEEEEEHHHc
Confidence 9542 11 1222211 3667777775544433 25677775544
No 29
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.58 E-value=0.028 Score=62.03 Aligned_cols=139 Identities=17% Similarity=0.159 Sum_probs=81.0
Q ss_pred cceeeechhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEee---------ccchhhHHHHHHHHHHHHHHHHHH
Q 008318 117 VRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISA---------GAHLKETAERILAVDHAAAMVEEM 187 (570)
Q Consensus 117 ~Ry~LTKg~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ieg---------~Te~kdt~ERi~aVd~AiaeIeEI 187 (570)
--|+-.+|+++++|..+|++.|-+=- ..++.+=--+-|.| .. .++.+|..+|-..
T Consensus 55 G~IIGk~G~~vkkir~~t~s~i~i~~-------~~~~c~eRIiti~g~~~~~~~~~~~---------~al~ka~~~iv~~ 118 (485)
T KOG2190|consen 55 GSIIGKKGDIVKKIRKETESKIRVNE-------SLPGCPERIITITGNRVELNLSPAT---------DALFKAFDMIVFK 118 (485)
T ss_pred eeEEccCcHHHHHHhhcccccceeec-------CCCCCCcceEEEecccccccCCchH---------HHHHHHHHHHhhc
Confidence 34666789999999988877653211 11122222223344 22 3566655555443
Q ss_pred HHcCCCCCCccccccCCC---ccc-ceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCC
Q 008318 188 LKQGHAGFPTLQTVMGNG---VQA-MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQG 263 (570)
Q Consensus 188 LKE~P~~~p~~~~p~~~G---~k~-~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~g 263 (570)
+.++..- ..+++ ..+ ...++.|+ .+-+|-|||-+|+.||.|.++|||+|+|-+. .+ +
T Consensus 119 ~~~d~~~------~~d~~~~~~~~~v~~RLlVp------~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~---~l-P--- 179 (485)
T KOG2190|consen 119 LEEDDEA------AEDNGEDASGPEVTCRLLVP------SSQVGSLIGKGGSLIKEIREETGAKIRVSSD---ML-P--- 179 (485)
T ss_pred ccccccc------cccCCccccCCceEEEEEec------hhheeeeeccCcHHHHHHHHhcCceEEecCC---CC-C---
Confidence 3322110 01112 134 46788885 4579999999999999999999999999987 11 1
Q ss_pred CCCCCcEEEEEcCCHHHHHHHHHHHHHHH
Q 008318 264 EVHQPLHLFLSSNNPKSLEEAKRLAENLL 292 (570)
Q Consensus 264 EsdEPLHV~Isa~~~e~v~kAk~LiEnLL 292 (570)
-..|.+ |.| +.+++.+.+|-..|-.+|
T Consensus 180 ~ster~-V~I-sG~~~av~~al~~Is~~L 206 (485)
T KOG2190|consen 180 NSTERA-VTI-SGEPDAVKKALVQISSRL 206 (485)
T ss_pred ccccee-EEE-cCchHHHHHHHHHHHHHH
Confidence 123444 444 456666766644444333
No 30
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.44 E-value=0.0048 Score=72.06 Aligned_cols=100 Identities=18% Similarity=0.228 Sum_probs=73.3
Q ss_pred eeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcE-EEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHH
Q 008318 210 STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGAT-VLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLA 288 (570)
Q Consensus 210 eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAK-I~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~Li 288 (570)
-+.+.|+. +-+|.||||+|.++|.|+.|||++ |-|+ |.-+|.|.+.|.+++++|+++|
T Consensus 686 i~~~~i~~------~ki~~vIG~GGktIk~I~eetg~~~Idi~---------------ddg~V~I~a~d~~~i~~A~~~I 744 (891)
T PLN00207 686 IHIMKVKP------EKVNMIIGSGGKKVKSIIEETGVEAIDTQ---------------DDGTVKITAKDLSSLEKSKAII 744 (891)
T ss_pred eEEEEcCH------HHHHHHhcCCchhHHHHHHHHCCCccCcC---------------CCeeEEEEeCCHHHHHHHHHHH
Confidence 34565643 358899999999999999999998 6554 3478999999999999999999
Q ss_pred HHHHHHHHHHhhcccccccccc-cCCCCccccccccccccccccCCccccceecccccc
Q 008318 289 ENLLDTISAECGASRVSSCKVY-NAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNL 346 (570)
Q Consensus 289 EnLL~tV~eEy~a~r~~~~k~y-~avpppqQ~~~g~~~~~~~~~~~~~~~~~~~~~~~~ 346 (570)
++|.... -..+.| +. -+.++..+|+.-.+... .-||.|--.+
T Consensus 745 ~~l~~~~---------~vG~iy~~g------~V~~I~~FGaFVeL~~g-~EGLVHISeL 787 (891)
T PLN00207 745 SSLTMVP---------TVGDIYRNC------EIKSIAPYGAFVEIAPG-REGLCHISEL 787 (891)
T ss_pred HHHhcCc---------CCCcEEECc------EEEEEeccEEEEEeCCC-CEEEEEhhhc
Confidence 9998621 124455 21 36678888855444433 5788775544
No 31
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.68 E-value=0.012 Score=58.81 Aligned_cols=55 Identities=20% Similarity=0.325 Sum_probs=47.5
Q ss_pred ceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHH
Q 008318 224 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 293 (570)
Q Consensus 224 NfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEnLL~ 293 (570)
++++++|||+|.+++.|.++|||+|.| | +.=+|+|.+.+.+.+++|+++|++|-.
T Consensus 154 ~~i~~lig~~g~~i~~l~~~~~~~I~i-g--------------~NG~VwI~~~~~~~~~~a~~~I~~~e~ 208 (235)
T PRK04163 154 VKVPRVIGKKGSMINMLKEETGCDIIV-G--------------QNGRIWIKGPDEEDEEIAIEAIKKIER 208 (235)
T ss_pred HHHHhhcCCCChhHhhhhhhhCcEEEE-c--------------CCcEEEEeeCCHHHHHHHHHHHHHHHh
Confidence 358899999999999999999999988 2 124799999999999999999987543
No 32
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.68 E-value=0.015 Score=66.41 Aligned_cols=93 Identities=18% Similarity=0.251 Sum_probs=66.8
Q ss_pred ceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHHHHHhhccc
Q 008318 224 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGASR 303 (570)
Q Consensus 224 NfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy~a~r 303 (570)
+-++.+|||+|.++|.|++|||++|-|+ +.-+|.|.+.+.+.+++|+++++.|... +.
T Consensus 563 ~kI~~vIG~gg~~ik~I~~~~~~~idi~---------------d~G~v~i~~~~~~~~~~a~~~I~~~~~~----~~--- 620 (693)
T PRK11824 563 DKIRDVIGPGGKTIREITEETGAKIDIE---------------DDGTVKIAATDGEAAEAAKERIEGITAE----PE--- 620 (693)
T ss_pred HHHHHHhcCCchhHHHHHHHHCCccccC---------------CCceEEEEcccHHHHHHHHHHHHHhccc----Cc---
Confidence 4578999999999999999999987763 3467999999999999999999999842 11
Q ss_pred ccccccccCCCCccccccccccccccccCCccccceeccccccC
Q 008318 304 VSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNLS 347 (570)
Q Consensus 304 ~~~~k~y~avpppqQ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~ 347 (570)
..+.|-. .+.++..+|..-.+.. ...|+.|--+++
T Consensus 621 --vG~v~~G------~V~~I~~fGafVei~~-~~~GllhiSels 655 (693)
T PRK11824 621 --VGEIYEG------KVVRIVDFGAFVEILP-GKDGLVHISEIA 655 (693)
T ss_pred --CCeEEEE------EEEEEECCeEEEEECC-CCEEEEEeeecc
Confidence 1223321 3667777774444433 356776655443
No 33
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=95.10 E-value=0.036 Score=62.36 Aligned_cols=72 Identities=17% Similarity=0.178 Sum_probs=55.3
Q ss_pred eeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHHHHHhhcc---
Q 008318 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGAS--- 302 (570)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy~a~--- 302 (570)
+..+|||+|-.+|+|+.|||+.-+ .+.=|+-|-++++..+++||++|+.++..-++.--.|
T Consensus 608 ~~~lIGp~G~~~kki~~EtGai~~----------------vDe~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~l~~g~v 671 (760)
T KOG1067|consen 608 RATLIGPGGVLKKKIEVETGAISQ----------------VDEGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQDLEFGGV 671 (760)
T ss_pred hheeecCccceeeeEeeeccceee----------------ecCceEEEEecCHHHHHHHHHHHHHHhcCccccceEeeeE
Confidence 678999999999999999995533 2557999999999999999999999987644332222
Q ss_pred ---cccccccccCC
Q 008318 303 ---RVSSCKVYNAV 313 (570)
Q Consensus 303 ---r~~~~k~y~av 313 (570)
.+.+-+.||++
T Consensus 672 y~~tIt~~rd~G~~ 685 (760)
T KOG1067|consen 672 YTATITEIRDTGVM 685 (760)
T ss_pred EEEEEeeecccceE
Confidence 34455667664
No 34
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=95.00 E-value=0.47 Score=52.72 Aligned_cols=61 Identities=28% Similarity=0.303 Sum_probs=45.7
Q ss_pred ccceeeec-hhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcC
Q 008318 116 SVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQG 191 (570)
Q Consensus 116 ~~Ry~LTK-g~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeIeEILKE~ 191 (570)
++-.+|-| |+.+++|.++|||.|-+-+. +.|. ..++- +-|.|.. .+|.+|+..|-..|.+.
T Consensus 148 q~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~--V~IsG~~---------~av~~al~~Is~~L~~~ 209 (485)
T KOG2190|consen 148 QVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN---STERA--VTISGEP---------DAVKKALVQISSRLLEN 209 (485)
T ss_pred heeeeeccCcHHHHHHHHhcCceEEecCC-CCCc---cccee--EEEcCch---------HHHHHHHHHHHHHHHhc
Confidence 35667766 89999999999999987666 3333 23333 7888875 47889999898888874
No 35
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=94.99 E-value=0.099 Score=55.84 Aligned_cols=77 Identities=25% Similarity=0.278 Sum_probs=53.5
Q ss_pred ceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHH
Q 008318 209 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLA 288 (570)
Q Consensus 209 ~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~Li 288 (570)
..-||.|| .+ .+|-|||.+|++|-.+|+||||+|++- |-+-|. .| - --.||+...+-+.|..--
T Consensus 39 y~ikvLip-----s~-AaGsIIGKGG~ti~~lqk~tgariklS-ks~dfy---PG-T--TeRvcli~Gt~eai~av~--- 102 (402)
T KOG2191|consen 39 YFLKVLIP-----SY-AAGSIIGKGGQTIVQLQKETGARIKLS-KSKDFY---PG-T--TERVCLIQGTVEALNAVH--- 102 (402)
T ss_pred eEEEEEee-----cc-cccceeccchHHHHHHHhccCcEEEec-cccccC---CC-c--cceEEEEeccHHHHHHHH---
Confidence 55688885 33 789999999999999999999999986 322221 12 1 135777777777776654
Q ss_pred HHHHHHHHHHhhc
Q 008318 289 ENLLDTISAECGA 301 (570)
Q Consensus 289 EnLL~tV~eEy~a 301 (570)
|-++|.|+|+.++
T Consensus 103 efI~dKire~p~~ 115 (402)
T KOG2191|consen 103 EFIADKIREKPQA 115 (402)
T ss_pred HHHHHHHHHhHHh
Confidence 4455666766654
No 36
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=94.69 E-value=0.034 Score=58.15 Aligned_cols=55 Identities=22% Similarity=0.375 Sum_probs=44.1
Q ss_pred eeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHHHH
Q 008318 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISA 297 (570)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~e 297 (570)
+.|||||+|+|||.||--|.|-|.+.|. .|++.|+ ..+|..+++++++-+.+|+-
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilVqG~----------------TVsaiGp-fkGlkevr~IV~DcM~NiHP 214 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILVQGN----------------TVSAIGP-FKGLKEVRKIVEDCMKNIHP 214 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEeeCc----------------EEEeecC-cchHHHHHHHHHHHHhccch
Confidence 5689999999999999999999999996 2444433 46788888888887777653
No 37
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=94.24 E-value=0.13 Score=58.94 Aligned_cols=53 Identities=23% Similarity=0.390 Sum_probs=47.1
Q ss_pred eeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHH
Q 008318 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 293 (570)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEnLL~ 293 (570)
++.+|||+|.+++.|..||||+|.|.-.|+ |.|.+.+.+...+|+++|+++..
T Consensus 563 I~dvIG~gGk~I~~I~eetg~~IdieddGt---------------v~i~~s~~~~~~~ak~~I~~i~~ 615 (692)
T COG1185 563 IRDVIGPGGKTIKAITEETGVKIDIEDDGT---------------VKIAASDGESAKKAKERIEAITR 615 (692)
T ss_pred HhhccCCcccchhhhhhhhCcEEEecCCCc---------------EEEEecchHHHHHHHHHHHHHHh
Confidence 457899999999999999999999975544 67889999999999999999983
No 38
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=93.36 E-value=0.13 Score=54.80 Aligned_cols=63 Identities=11% Similarity=0.139 Sum_probs=54.9
Q ss_pred eeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHHHHH
Q 008318 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAE 298 (570)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~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 6899999999999999999999998854421 23589999999999999999999999998843
No 39
>PRK00106 hypothetical protein; Provisional
Probab=92.26 E-value=0.28 Score=55.09 Aligned_cols=60 Identities=27% Similarity=0.319 Sum_probs=50.8
Q ss_pred CCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHH
Q 008318 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 293 (570)
Q Consensus 220 ~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEnLL~ 293 (570)
.|+=.+.|||||-.|.|++.+|.-||+.|.| .|.|=-|.|+|-||---+-|+.-.|.||.
T Consensus 231 lp~demkGriIGreGrNir~~E~~tGvdlii--------------ddtp~~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 231 LPDDNMKGRIIGREGRNIRTLESLTGIDVII--------------DDTPEVVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred cCChHhhcceeCCCcchHHHHHHHhCceEEE--------------cCCCCeEEEeCCChHHHHHHHHHHHHHHH
Confidence 3455689999999999999999999999988 45677899999999988888877666654
No 40
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=92.22 E-value=0.26 Score=54.78 Aligned_cols=61 Identities=23% Similarity=0.305 Sum_probs=49.7
Q ss_pred CCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHH
Q 008318 219 ADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 293 (570)
Q Consensus 219 ~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEnLL~ 293 (570)
..|+=.+.|||||-.|.|++.+|.-||+.|.| .|.|=-|.|+|-||---+-|+.-.+.||.
T Consensus 209 ~lp~d~~kgriigreGrnir~~e~~tgvd~ii--------------ddtp~~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 209 NLPNDEMKGRIIGREGRNIRALETLTGVDLII--------------DDTPEAVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred EcCChhhhccccCCCcchHHHHHHHhCceEEE--------------cCCCCeEEecCCchHHHHHHHHHHHHHHH
Confidence 34555689999999999999999999999988 34567788999999887777776666653
No 41
>PRK12704 phosphodiesterase; Provisional
Probab=92.11 E-value=0.32 Score=54.13 Aligned_cols=59 Identities=24% Similarity=0.302 Sum_probs=48.1
Q ss_pred CCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHH
Q 008318 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLL 292 (570)
Q Consensus 220 ~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEnLL 292 (570)
.|+=.+.|||||-.|.|++.+|.-||+.|.| .|.|=-|+|||-|+..-+.|+...+.|+
T Consensus 216 lp~d~mkgriigreGrnir~~e~~tgvd~ii--------------ddtp~~v~ls~~~~~rre~a~~~l~~l~ 274 (520)
T PRK12704 216 LPNDEMKGRIIGREGRNIRALETLTGVDLII--------------DDTPEAVILSGFDPIRREIARLALEKLV 274 (520)
T ss_pred cCCchhhcceeCCCcchHHHHHHHhCCeEEE--------------cCCCCeEEEecCChhhHHHHHHHHHHHH
Confidence 4455689999999999999999999999988 4567789999988887666766555553
No 42
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=91.03 E-value=0.36 Score=53.37 Aligned_cols=64 Identities=14% Similarity=0.127 Sum_probs=46.3
Q ss_pred CCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHH-HHHHHHHHHHHHHHHHHHHhh
Q 008318 222 SLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPK-SLEEAKRLAENLLDTISAECG 300 (570)
Q Consensus 222 ~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e-~v~kAk~LiEnLL~tV~eEy~ 300 (570)
.-+++|++||-+|+.+|+||..|+++|+|-- +.+-+.|+-.--. .-.+|+.-++++++...+ |+
T Consensus 54 ks~mvg~vigrggskik~iq~~tnt~iqii~--------------~~~e~kv~ifg~~~m~~kaka~id~~~~k~e~-yn 118 (629)
T KOG0336|consen 54 KSEMVGKVIGRGGSKIKRIQNDTNTRIQIIK--------------CDLEVKVTIFGINHMRKKAKASIDRGQDKDER-YN 118 (629)
T ss_pred hhhhhheeeccCcchhhhhhcccceeEEEec--------------cCceeEEEEechHHHHHHHHhhHhhhhhhhhh-cc
Confidence 3468999999999999999999999999853 2244444433333 345788888888876544 65
No 43
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=89.31 E-value=1.3 Score=35.76 Aligned_cols=56 Identities=21% Similarity=0.240 Sum_probs=41.0
Q ss_pred EEEeCCCCcccceeeec-hhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHH
Q 008318 107 EIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVE 185 (570)
Q Consensus 107 EIEINDlPq~~Ry~LTK-g~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeIe 185 (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 4556443 46788866 999999999999998642 1 11 478999764 57888888773
No 44
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=88.62 E-value=2.3 Score=44.87 Aligned_cols=133 Identities=16% Similarity=0.174 Sum_probs=83.1
Q ss_pred ceeeec-hhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCC
Q 008318 118 RYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFP 196 (570)
Q Consensus 118 Ry~LTK-g~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeIeEILKE~P~~~p 196 (570)
--++.| |.+++.+....+|.|++-- ..-+--.|+|++..+ -|-+..++|---|.++....+
T Consensus 60 gavigkgg~nik~lr~d~na~v~vpd---------s~~peri~tisad~~---------ti~~ilk~iip~lee~f~~~~ 121 (390)
T KOG2192|consen 60 GAVIGKGGKNIKALRTDYNASVSVPD---------SSGPERILTISADIE---------TIGEILKKIIPTLEEGFQLPS 121 (390)
T ss_pred cceeccccccHHHHhhhccceeeccC---------CCCCceeEEEeccHH---------HHHHHHHHHhhhhhhCCCCCC
Confidence 334444 6677888888888876522 122334567888643 222223333333444443332
Q ss_pred ccccccCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcC
Q 008318 197 TLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSN 276 (570)
Q Consensus 197 ~~~~p~~~G~k~~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~ 276 (570)
.++-++.| --.++|-|||-||+-+|.+.+...|++-| |.|++.+ ---.|+|++.
T Consensus 122 -----------pce~rlli------hqs~ag~iigrngskikelrekcsarlki------ft~c~p~---stdrv~l~~g 175 (390)
T KOG2192|consen 122 -----------PCELRLLI------HQSLAGGIIGRNGSKIKELREKCSARLKI------FTECCPH---STDRVVLIGG 175 (390)
T ss_pred -----------chhhhhhh------hhhhccceecccchhHHHHHHhhhhhhhh------hhccCCC---CcceEEEecC
Confidence 23334444 23478999999999999999988887754 3444433 2247899999
Q ss_pred CHHHHHHHHHHHHHHHHH
Q 008318 277 NPKSLEEAKRLAENLLDT 294 (570)
Q Consensus 277 ~~e~v~kAk~LiEnLL~t 294 (570)
.++.|-...+.+-+||..
T Consensus 176 ~~k~v~~~i~~il~~i~e 193 (390)
T KOG2192|consen 176 KPKRVVECIKIILDLISE 193 (390)
T ss_pred CcchHHHHHHHHHHHhhc
Confidence 999998887777777754
No 45
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=87.54 E-value=1.4 Score=45.82 Aligned_cols=73 Identities=18% Similarity=0.241 Sum_probs=53.1
Q ss_pred ceeeechhhHHHHHhHhCCeEeeecceeCCCC------CC-C----CCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHH
Q 008318 118 RYKLTKRHTQEEIQKCTGAVVITRGKYRLPNA------PP-D----GEKPLYLHISAGAHLKETAERILAVDHAAAMVEE 186 (570)
Q Consensus 118 Ry~LTKg~TQ~eIqe~TGA~VtTRGrYyPPgk------~~-~----gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeIeE 186 (570)
|.+==||.|+++++++|||.|.+||+--=-.+ +. + =+.||+++|+...- .+.++ ..+..|+++|++
T Consensus 111 RILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p-~~ea~--~rl~~AleeI~k 187 (259)
T KOG1588|consen 111 RILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAP-PAEAY--ARLAYALEEIKK 187 (259)
T ss_pred ccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCC-HHHHH--HHHHHHHHHHHH
Confidence 55557899999999999999999997633321 11 1 26899999998763 32222 468889999999
Q ss_pred HHHcCCC
Q 008318 187 MLKQGHA 193 (570)
Q Consensus 187 ILKE~P~ 193 (570)
+|.-...
T Consensus 188 lL~P~~e 194 (259)
T KOG1588|consen 188 LLVPDHE 194 (259)
T ss_pred hcCCCCC
Confidence 9876543
No 46
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=85.69 E-value=1.8 Score=46.48 Aligned_cols=110 Identities=16% Similarity=0.164 Sum_probs=67.6
Q ss_pred eeeechhhHHHHHhHhCCeEee--ecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCC
Q 008318 119 YKLTKRHTQEEIQKCTGAVVIT--RGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFP 196 (570)
Q Consensus 119 y~LTKg~TQ~eIqe~TGA~VtT--RGrYyPPgk~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeIeEILKE~P~~~p 196 (570)
..+-+|.+++.|+.+|.+.|.| || +-|.|. ++|.- ..|++|..+|.-.-..--...-
T Consensus 40 ivg~qg~kikalr~KTqtyi~tPsr~-----------eePiF~-vTg~~---------edv~~aRrei~saaeH~~l~~~ 98 (394)
T KOG2113|consen 40 IVGRQGCKIKALRAKTQTYIKTPSRG-----------EEPIFP-VTGRH---------EDVRRARREIPSAAEHFGLIRA 98 (394)
T ss_pred ecccCccccchhhhhhcceeccCCCC-----------CCCcce-eccCc---------hhHHHHhhcCccccceeeeeee
Confidence 3456789999999999988765 33 336654 45543 4688887777653111000000
Q ss_pred ccccc-cCCCcc-cceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeec
Q 008318 197 TLQTV-MGNGVQ-AMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGR 253 (570)
Q Consensus 197 ~~~~p-~~~G~k-~~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGR 253 (570)
.+... .-.|.. --+.+.|+- .| +.++|+++||.|.++|+||+.+..-|.--++
T Consensus 99 s~s~Sgg~~~~s~s~qt~sy~s---vP-~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 99 SRSFSGGTNGASASGQTTSYVS---VP-LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred cccccCCCccccccCCCceeee---cc-ceeeeeccccccCccchheecccceEeeecc
Confidence 00000 011112 234566653 34 7899999999999999999999988866565
No 47
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=84.80 E-value=2.3 Score=44.95 Aligned_cols=65 Identities=20% Similarity=0.310 Sum_probs=49.1
Q ss_pred eeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHHHHHh
Q 008318 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 299 (570)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy 299 (570)
+-|-|||-+|.-+|+|..|+||.|.|--- . |..| -.+.+...+.++++.|.-|.++-+..-++.|
T Consensus 325 lggsiigkggqri~~ir~esGA~Ikidep-------l--eGse-drIitItGTqdQIqnAQYLlQn~Vkq~rerf 389 (390)
T KOG2192|consen 325 LGGSIIGKGGQRIKQIRHESGASIKIDEP-------L--EGSE-DRIITITGTQDQIQNAQYLLQNSVKQYRERF 389 (390)
T ss_pred cCcceecccchhhhhhhhccCceEEecCc-------C--CCCC-ceEEEEeccHHHHhhHHHHHHHHHHhhhccc
Confidence 56789999999999999999999987531 1 1222 3566666789999999999888776544443
No 48
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=80.44 E-value=5.8 Score=31.89 Aligned_cols=52 Identities=25% Similarity=0.275 Sum_probs=36.1
Q ss_pred cceeee-chhhHHHHHhHhCCeEeeecceeCCCC-CCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHH
Q 008318 117 VRYKLT-KRHTQEEIQKCTGAVVITRGKYRLPNA-PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (570)
Q Consensus 117 ~Ry~LT-Kg~TQ~eIqe~TGA~VtTRGrYyPPgk-~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeI 184 (570)
+.+++- +|.++++|++.|||.|.+. +.. ..+.++- +.|+|.. ..+++|..+|
T Consensus 11 vg~iIG~~G~~i~~i~~~tga~I~i~-----~~~~~~~~~r~--v~I~G~~---------~~v~~A~~~I 64 (65)
T cd02396 11 AGSIIGKGGSTIKEIREETGAKIRVS-----KSVLPGSTERV--VTISGKP---------SAVQKALLLI 64 (65)
T ss_pred cCeeECCCcHHHHHHHHHHCCEEEEc-----CCCCCCCCceE--EEEEeCH---------HHHHHHHHhh
Confidence 455664 5899999999999998763 222 2334443 6788975 3688888776
No 49
>PRK12705 hypothetical protein; Provisional
Probab=79.99 E-value=1.8 Score=48.60 Aligned_cols=34 Identities=21% Similarity=0.265 Sum_probs=29.2
Q ss_pred CCCCCceeeEEeCCCchhHHHHHhhhCcEEEEee
Q 008318 219 ADASLNIAARIRGPNDQYINHIMNETGATVLLRG 252 (570)
Q Consensus 219 ~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRG 252 (570)
+.|+=.+.|||||-.|.|++.+|..||+-|.|--
T Consensus 203 ~lp~demkGriIGreGrNir~~E~~tGvdliidd 236 (508)
T PRK12705 203 PIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD 236 (508)
T ss_pred ecCChHhhccccCccchhHHHHHHhhCCceEecC
Confidence 3455568999999999999999999999988853
No 50
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=79.72 E-value=4.9 Score=31.34 Aligned_cols=49 Identities=22% Similarity=0.237 Sum_probs=36.2
Q ss_pred cceeee-chhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHH
Q 008318 117 VRYKLT-KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (570)
Q Consensus 117 ~Ry~LT-Kg~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeI 184 (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-ERDIVTISGSP---------EQVEKAKKMI 60 (60)
T ss_dssp HHHHHTGGGHHHHHHHHHHTSEEEEEST---------T-EEEEEEEEESH---------HHHHHHHHHH
T ss_pred cCEEECCCCCcHHHhhhhcCeEEEEcCC---------C-CcEEEEEEeCH---------HHHHHHHhhC
Confidence 566674 499999999999999977442 2 33467889943 4788887766
No 51
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=79.66 E-value=1.6 Score=51.35 Aligned_cols=11 Identities=18% Similarity=0.141 Sum_probs=5.4
Q ss_pred CCCCcCCChHH
Q 008318 401 EGIYPQATPLQ 411 (570)
Q Consensus 401 ~~iypqatplq 411 (570)
+|+-|+++--+
T Consensus 440 ~~~DPdf~yr~ 450 (1102)
T KOG1924|consen 440 TGMDPDFKYRF 450 (1102)
T ss_pred CCCCCCcchhh
Confidence 34555555433
No 52
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=78.03 E-value=2.2 Score=34.43 Aligned_cols=27 Identities=11% Similarity=0.084 Sum_probs=24.2
Q ss_pred ceeeEEeCCCchhHHHHHhhhCcEEEE
Q 008318 224 NIAARIRGPNDQYINHIMNETGATVLL 250 (570)
Q Consensus 224 NfvgrIIGP~GstlK~Iq~ETGAKI~I 250 (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 53
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=72.29 E-value=2.3 Score=45.65 Aligned_cols=53 Identities=19% Similarity=0.255 Sum_probs=42.0
Q ss_pred CceeeEEeCCCchhHHHHHhhhCcEEEE--eeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHH
Q 008318 223 LNIAARIRGPNDQYINHIMNETGATVLL--RGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAEN 290 (570)
Q Consensus 223 FNfvgrIIGP~GstlK~Iq~ETGAKI~I--RGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEn 290 (570)
..|++.|+|++|..+|+|+.+|...|.- ||| | -+|+.....+.++.||+-|+-
T Consensus 34 s~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e-------------e--PiF~vTg~~edv~~aRrei~s 88 (394)
T KOG2113|consen 34 SEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE-------------E--PIFPVTGRHEDVRRARREIPS 88 (394)
T ss_pred cccceeecccCccccchhhhhhcceeccCCCCC-------------C--CcceeccCchhHHHHhhcCcc
Confidence 6689999999999999999999988642 232 2 456677777888999887765
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=71.27 E-value=17 Score=28.04 Aligned_cols=60 Identities=22% Similarity=0.296 Sum_probs=38.6
Q ss_pred EEEeCCCCcccceee-echhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHH
Q 008318 107 EIVINDSESSVRYKL-TKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (570)
Q Consensus 107 EIEINDlPq~~Ry~L-TKg~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeI 184 (570)
+|.|..- .+++++ .+|.++.+|++.||+.|.... ... ++..--+.|.|.. ..+.+|..+|
T Consensus 3 ~i~ip~~--~~~~vIG~~G~~i~~I~~~s~~~I~i~~-----~~~--~~~~~~v~i~G~~---------~~v~~a~~~i 63 (64)
T cd00105 3 RVLVPSS--LVGRIIGKGGSTIKEIREETGAKIKIPD-----SGS--GSEERIVTITGTP---------EAVEKAKELI 63 (64)
T ss_pred EEEEchh--hcceeECCCCHHHHHHHHHHCCEEEEcC-----CCC--CCCceEEEEEcCH---------HHHHHHHHHh
Confidence 3444442 367778 559999999999999987543 111 2233335777873 3577776665
No 55
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=69.06 E-value=10 Score=41.03 Aligned_cols=56 Identities=20% Similarity=0.360 Sum_probs=45.5
Q ss_pred eeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHH--HHHHHHHHH
Q 008318 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAE--NLLDTISAE 298 (570)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~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 4468899999999999999999999995 667777766 8888888877 666665554
No 56
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=68.97 E-value=14 Score=38.13 Aligned_cols=32 Identities=19% Similarity=0.419 Sum_probs=27.0
Q ss_pred CceeeEEeCCCchhHHHHHhhhCcEEEEeecc
Q 008318 223 LNIAARIRGPNDQYINHIMNETGATVLLRGRG 254 (570)
Q Consensus 223 FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRG 254 (570)
...+-|+||++|+++|-+.++|+|+|.+==-|
T Consensus 154 p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG 185 (239)
T COG1097 154 PSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG 185 (239)
T ss_pred hhhcceEecCCCcHHHHhhhhcCeEEEEecCC
Confidence 34567899999999999999999999885433
No 57
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=68.82 E-value=12 Score=29.27 Aligned_cols=58 Identities=19% Similarity=0.188 Sum_probs=39.3
Q ss_pred EEEeCCCCcccceeeec-hhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHH
Q 008318 107 EIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (570)
Q Consensus 107 EIEINDlPq~~Ry~LTK-g~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeI 184 (570)
+|.|.. ...++++-+ |.++.+|++.||+.|..- +.. +..-.+.|.|.. +.|.+|+.+|
T Consensus 3 ~i~Vp~--~~~~~iIG~~G~~i~~i~~~~g~~I~i~-----~~~----~~~~~v~I~G~~---------~~v~~A~~~i 61 (62)
T cd02394 3 EVEIPK--KLHRFIIGKKGSNIRKIMEETGVKIRFP-----DPG----SKSDTITITGPK---------ENVEKAKEEI 61 (62)
T ss_pred EEEeCH--HHhhhccCCCCCcHHHHHHHhCCEEEcC-----CCC----CCCCEEEEEcCH---------HHHHHHHHHh
Confidence 455544 246788855 899999999999998553 221 223345788874 3688887766
No 58
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=68.59 E-value=2 Score=36.09 Aligned_cols=32 Identities=19% Similarity=0.293 Sum_probs=25.2
Q ss_pred CCCCCceeeEEeCCCchhHHHHHhhh-CcEEEE
Q 008318 219 ADASLNIAARIRGPNDQYINHIMNET-GATVLL 250 (570)
Q Consensus 219 ~~P~FNfvgrIIGP~GstlK~Iq~ET-GAKI~I 250 (570)
..++++-+|.++|.+|..+|.|++|. |-||.|
T Consensus 12 ~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdv 44 (69)
T PF13184_consen 12 GDPNIDPVGACIGKKGSRIKAISEELNGEKIDV 44 (69)
T ss_dssp SSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEE
T ss_pred CCCCcCcceecCccccHHHHHHHHHhCCCeEEE
Confidence 45899999999999999999999999 655544
No 59
>smart00322 KH K homology RNA-binding domain.
Probab=67.35 E-value=40 Score=25.16 Aligned_cols=64 Identities=20% Similarity=0.234 Sum_probs=42.3
Q ss_pred EEEEEeCCCCcccceee-echhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHH
Q 008318 105 AREIVINDSESSVRYKL-TKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAM 183 (570)
Q Consensus 105 ~~EIEINDlPq~~Ry~L-TKg~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~Aiae 183 (570)
..+|.|..- ...+++ .+|.++++|++.+|+.|...+.-. .---+.|.|.. ..+..|...
T Consensus 4 ~~~i~i~~~--~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~---------~~~~v~i~g~~---------~~v~~a~~~ 63 (69)
T smart00322 4 TIEVLIPAD--KVGLIIGKGGSTIKKIEEETGVKIDIPEDGS---------EERVVEITGPP---------ENVEKAAEL 63 (69)
T ss_pred EEEEEEcch--hcceeECCCchHHHHHHHHHCCEEEECCCCC---------CccEEEEEcCH---------HHHHHHHHH
Confidence 345666553 245666 569999999999999987653111 22336778873 367777777
Q ss_pred HHHHH
Q 008318 184 VEEML 188 (570)
Q Consensus 184 IeEIL 188 (570)
|.+.+
T Consensus 64 i~~~~ 68 (69)
T smart00322 64 ILEIL 68 (69)
T ss_pred HHHHh
Confidence 77764
No 60
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=64.16 E-value=7.1 Score=46.31 Aligned_cols=7 Identities=29% Similarity=0.662 Sum_probs=3.9
Q ss_pred EEEEeCC
Q 008318 106 REIVIND 112 (570)
Q Consensus 106 ~EIEIND 112 (570)
.+.+||.
T Consensus 97 ~dmni~e 103 (1102)
T KOG1924|consen 97 EDMNINE 103 (1102)
T ss_pred hhccccH
Confidence 3556664
No 61
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=59.19 E-value=7.1 Score=40.12 Aligned_cols=83 Identities=14% Similarity=0.187 Sum_probs=56.9
Q ss_pred CCCCceeEEEEEEeCCCCccc--ceee-echhhHHHHHhHhCCeEeeecceeCCC-C-C-------CCCCCCeEEEEeec
Q 008318 97 KVQDELIIAREIVINDSESSV--RYKL-TKRHTQEEIQKCTGAVVITRGKYRLPN-A-P-------PDGEKPLYLHISAG 164 (570)
Q Consensus 97 k~~de~~f~~EIEINDlPq~~--Ry~L-TKg~TQ~eIqe~TGA~VtTRGrYyPPg-k-~-------~~gEpPLYL~Ieg~ 164 (570)
|..+..| |-+-+||..| ..+| -+|.||+++++.|+|.|-.||+|--.. + . ..-+-+|+-+|++.
T Consensus 147 k~q~KiY----IPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~ad 222 (269)
T COG5176 147 KYQNKIY----IPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEAD 222 (269)
T ss_pred cccceEE----eehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcc
Confidence 4444454 4566777533 3344 579999999999999999999996543 2 1 13478899999999
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHcC
Q 008318 165 AHLKETAERILAVDHAAAMVEEMLKQG 191 (570)
Q Consensus 165 Te~kdt~ERi~aVd~AiaeIeEILKE~ 191 (570)
++. ...+++..+..+|.++
T Consensus 223 sed--------ki~~~ik~~~n~I~~a 241 (269)
T COG5176 223 SED--------KICRLIKSQLNAIREA 241 (269)
T ss_pred hhh--------hHHHHHHHHHHHHHHH
Confidence 873 3455555566666554
No 62
>PF13014 KH_3: KH domain
Probab=56.56 E-value=34 Score=25.42 Aligned_cols=24 Identities=29% Similarity=0.243 Sum_probs=19.6
Q ss_pred cceeee-chhhHHHHHhHhCCeEee
Q 008318 117 VRYKLT-KRHTQEEIQKCTGAVVIT 140 (570)
Q Consensus 117 ~Ry~LT-Kg~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 456674 499999999999999854
No 63
>PRK15494 era GTPase Era; Provisional
Probab=55.58 E-value=55 Score=34.43 Aligned_cols=27 Identities=30% Similarity=0.168 Sum_probs=22.0
Q ss_pred eeeEEeCCCchhHHHHH--------hhhCcEEEEe
Q 008318 225 IAARIRGPNDQYINHIM--------NETGATVLLR 251 (570)
Q Consensus 225 fvgrIIGP~GstlK~Iq--------~ETGAKI~IR 251 (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 47889999999999984 4478888765
No 64
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=54.87 E-value=34 Score=34.50 Aligned_cols=67 Identities=22% Similarity=0.203 Sum_probs=51.1
Q ss_pred eeEEEEEEeCCCCc---------ccceeeechhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHH
Q 008318 102 LIIAREIVINDSES---------SVRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAE 172 (570)
Q Consensus 102 ~~f~~EIEINDlPq---------~~Ry~LTKg~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ieg~Te~kdt~E 172 (570)
.++-.-|+|-|+-. +.|.+=++|-|-.-|+++||+.|++-|.++ +|=|.-+
T Consensus 90 ~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~tV--------------aiiG~~~------ 149 (194)
T COG1094 90 DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGKTV--------------AIIGGFE------ 149 (194)
T ss_pred CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCcEE--------------EEecChh------
Confidence 44677888877754 345556889999999999999999999988 8888752
Q ss_pred HHHHHHHHHHHHHHHHHcC
Q 008318 173 RILAVDHAAAMVEEMLKQG 191 (570)
Q Consensus 173 Ri~aVd~AiaeIeEILKE~ 191 (570)
.|+.|..-|+-+|...
T Consensus 150 ---~v~iAr~AVemli~G~ 165 (194)
T COG1094 150 ---QVEIAREAVEMLINGA 165 (194)
T ss_pred ---hhHHHHHHHHHHHcCC
Confidence 5666766677776554
No 65
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=54.19 E-value=43 Score=39.57 Aligned_cols=108 Identities=17% Similarity=0.168 Sum_probs=74.2
Q ss_pred EEeCCCCcccceeeec-hhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHH
Q 008318 108 IVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEE 186 (570)
Q Consensus 108 IEINDlPq~~Ry~LTK-g~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeIeE 186 (570)
|..+=+++..+|.+-| +..+..|.+++++.+..+- ....+++.+++-... .+.+|++.|+.
T Consensus 349 i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~-------~~~~~~~v~~~~~~~-----------~~~ka~~~v~~ 410 (753)
T KOG2208|consen 349 IKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK-------QGSNNKKVVITGVSA-----------NDEKAVEDVEK 410 (753)
T ss_pred eEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc-------ccCCCCCeEEecccc-----------chhHHHHHHHH
Confidence 3334456678888866 6669999999999864321 225677777764443 36667777777
Q ss_pred HHHcCCCCCCccccccCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeec
Q 008318 187 MLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGR 253 (570)
Q Consensus 187 ILKE~P~~~p~~~~p~~~G~k~~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGR 253 (570)
+..+.++.. ..+.++||- + +.++|||.+|..+..|+.++|| |.|+..
T Consensus 411 ~~~ei~n~~-------------~~~~~~iP~-----k-~~~~iig~~g~~i~~I~~k~~~-v~i~f~ 457 (753)
T KOG2208|consen 411 IIAEILNSI-------------VKEEVQIPT-----K-SHKRIIGTKGALINYIMGKHGG-VHIKFQ 457 (753)
T ss_pred HHHhhhccc-------------ccceeecCc-----c-chhhhhccccccHHHHHhhcCc-EEEecC
Confidence 777665431 113455542 2 5779999999999999999998 888775
No 66
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=52.91 E-value=12 Score=28.76 Aligned_cols=23 Identities=13% Similarity=0.127 Sum_probs=20.2
Q ss_pred eeEEeCCCchhHHHHHhhhCcEE
Q 008318 226 AARIRGPNDQYINHIMNETGATV 248 (570)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETGAKI 248 (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 67
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=51.38 E-value=14 Score=44.81 Aligned_cols=71 Identities=18% Similarity=0.140 Sum_probs=53.8
Q ss_pred CCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCC--CCCCCcEEEEEcCCHHHHHHHHHHHHHHHHH
Q 008318 218 DADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQG--EVHQPLHLFLSSNNPKSLEEAKRLAENLLDT 294 (570)
Q Consensus 218 d~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~g--EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~t 294 (570)
+.+|-- .+.+|.+--- +.+|...++|.|..||+-= ..... ..++-||++|.+.+.-.|++|+..++.+|..
T Consensus 905 nD~Pq~-~r~~vt~~~~--L~~i~e~~~~~it~rg~f~---~~gk~p~~gErklyl~ve~~~e~~vqra~~e~~r~l~e 977 (997)
T KOG0334|consen 905 NDFPQN-ARWRVTYKEA--LLRISEPTAAGITTRGKFN---PPGKEPKPGERKLYLLVEGPDELSVQRAIEELERLLEE 977 (997)
T ss_pred cccchh-cceeeechhh--hhhccCccccceeeccccC---CCCCCCCCcchhhhhhhhcchhHHHHHHHHHHHHHHHH
Confidence 455543 7788876544 9999999999999999832 11111 3556699999999999999999888886543
No 68
>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]
Probab=48.26 E-value=20 Score=42.45 Aligned_cols=15 Identities=33% Similarity=0.377 Sum_probs=7.4
Q ss_pred cccceeecccCCCCC
Q 008318 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 444555555555433
No 69
>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=45.75 E-value=1.2 Score=39.31 Aligned_cols=33 Identities=21% Similarity=0.333 Sum_probs=24.6
Q ss_pred EeCCCCcccceeee-----chhhHHHHHhHhCCeEee--ecc
Q 008318 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 ELEAL--AQRWQVAKELLDEGKSYREIAEETGVSIATITRVS 70 (87)
T ss_dssp HHHHH--HHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHH
T ss_pred HHHHH--HHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHH
Confidence 34455 3577554 589999999999999876 764
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=42.12 E-value=26 Score=35.17 Aligned_cols=27 Identities=26% Similarity=0.203 Sum_probs=22.0
Q ss_pred eeeEEeCCCchhHHHHHhh--------hCcEEEEe
Q 008318 225 IAARIRGPNDQYINHIMNE--------TGATVLLR 251 (570)
Q Consensus 225 fvgrIIGP~GstlK~Iq~E--------TGAKI~IR 251 (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 4688999999999998554 68888764
No 71
>KOG1925 consensus Rac1 GTPase effector FHOS [Signal transduction mechanisms; Cytoskeleton]
Probab=39.76 E-value=22 Score=40.76 Aligned_cols=19 Identities=53% Similarity=1.263 Sum_probs=13.5
Q ss_pred CCCCCCCCCCC-CCCCCCCC
Q 008318 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 72
>PHA01732 proline-rich protein
Probab=39.37 E-value=29 Score=31.34 Aligned_cols=12 Identities=42% Similarity=0.808 Sum_probs=4.7
Q ss_pred CCCCCCCCCCCC
Q 008318 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 73
>PRK00089 era GTPase Era; Reviewed
Probab=38.41 E-value=31 Score=34.57 Aligned_cols=38 Identities=18% Similarity=0.329 Sum_probs=26.8
Q ss_pred ceeEEEecCCCCCCCceeeEEeCCCchhHHHHHh--------hhCcEEEEe
Q 008318 209 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMN--------ETGATVLLR 251 (570)
Q Consensus 209 ~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~--------ETGAKI~IR 251 (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 44555554332 378899999999999854 468888664
No 74
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=37.27 E-value=25 Score=33.15 Aligned_cols=28 Identities=11% Similarity=0.136 Sum_probs=25.2
Q ss_pred eeeEEeCCCchhHHHHHhhhCcEEEEee
Q 008318 225 IAARIRGPNDQYINHIMNETGATVLLRG 252 (570)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGAKI~IRG 252 (570)
-+|..||.+|+.+|.|++..|-||-|=.
T Consensus 42 ~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 42 DMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CccccCCcCchHHHHHHHHhCCceEEEE
Confidence 5799999999999999999999987665
No 75
>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=35.20 E-value=30 Score=28.36 Aligned_cols=16 Identities=44% Similarity=0.752 Sum_probs=10.5
Q ss_pred ccCCCCCcCCChHHHHH
Q 008318 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 76
>PRK01064 hypothetical protein; Provisional
Probab=35.04 E-value=28 Score=30.22 Aligned_cols=19 Identities=21% Similarity=0.235 Sum_probs=16.8
Q ss_pred eeEEeCCCchhHHHHHhhh
Q 008318 226 AARIRGPNDQYINHIMNET 244 (570)
Q Consensus 226 vgrIIGP~GstlK~Iq~ET 244 (570)
.|++||-+|.+++.|+.-.
T Consensus 41 ~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred ceEEECCCCccHHHHHHHH
Confidence 6999999999999998753
No 77
>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=34.12 E-value=1.1e+02 Score=25.00 Aligned_cols=38 Identities=21% Similarity=0.489 Sum_probs=26.9
Q ss_pred hCcEEEEeeccCcCCCCCCCCCCCC-cEEEEEcCCHHHHHHHHHHHHHHH
Q 008318 244 TGATVLLRGRGSGNSEGLQGEVHQP-LHLFLSSNNPKSLEEAKRLAENLL 292 (570)
Q Consensus 244 TGAKI~IRGRGSg~~E~~~gEsdEP-LHV~Isa~~~e~v~kAk~LiEnLL 292 (570)
-|..+.||=-|+ || +.|++++.+.+.+++-.+-+.++|
T Consensus 34 dG~~l~vR~SgT-----------EP~iRv~~Ea~~~~~~~~~~~~i~~~i 72 (73)
T PF00408_consen 34 DGWRLLVRPSGT-----------EPKIRVYVEAPDEEELEEIAEEIAEAI 72 (73)
T ss_dssp TEEEEEEEEESS-----------SSEEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred CceEEEEECCCC-----------CceEEEEEEeCCHHHHHHHHHHHHHhh
Confidence 455555665443 55 999999998888887766666665
No 78
>COG2037 Ftr Formylmethanofuran:tetrahydromethanopterin formyltransferase [Energy production and conversion]
Probab=32.48 E-value=5.2e+02 Score=27.63 Aligned_cols=50 Identities=24% Similarity=0.340 Sum_probs=34.4
Q ss_pred cceeeec---hhhHHHHHhHhCCeEeeec--------ceeCCCCCCCCCCCeEEEEeeccc
Q 008318 117 VRYKLTK---RHTQEEIQKCTGAVVITRG--------KYRLPNAPPDGEKPLYLHISAGAH 166 (570)
Q Consensus 117 ~Ry~LTK---g~TQ~eIqe~TGA~VtTRG--------rYyPPgk~~~gEpPLYL~Ieg~Te 166 (570)
+|.++|- +-...--.+.||.--++-| +|.+|.+-+++.+-.|+.|.=...
T Consensus 21 aRvliTAa~~~~a~~AA~eATg~~~sVi~cpaEaGie~~~~peeTPDGRpG~~iqi~~~~~ 81 (297)
T COG2037 21 ARVLITAADKKWAKIAATEATGFGTSVIGCPAEAGIEKYLPPEETPDGRPGAIIQICHPKK 81 (297)
T ss_pred EEEEEEccchHHHHHHHHhcccCCceeEeeeccccceeecCcccCCCCCCceEEEEEecch
Confidence 5777765 3344445566665444444 499999999999999998887653
No 79
>COG1159 Era GTPase [General function prediction only]
Probab=30.71 E-value=1.3e+02 Score=32.20 Aligned_cols=41 Identities=22% Similarity=0.385 Sum_probs=28.6
Q ss_pred CcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhh--------hCcEEEE
Q 008318 205 GVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNE--------TGATVLL 250 (570)
Q Consensus 205 G~k~~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~E--------TGAKI~I 250 (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 334556667775443 4677999999999998544 5777754
No 80
>PRK02821 hypothetical protein; Provisional
Probab=30.20 E-value=31 Score=29.92 Aligned_cols=21 Identities=5% Similarity=0.063 Sum_probs=17.5
Q ss_pred eeeEEeCCCchhHHHHHhhhC
Q 008318 225 IAARIRGPNDQYINHIMNETG 245 (570)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETG 245 (570)
=+|||||-+|.+++-|..--.
T Consensus 41 D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 41 DLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred hCcceeCCCCchHHHHHHHHH
Confidence 379999999999999876543
No 81
>PRK00468 hypothetical protein; Provisional
Probab=29.92 E-value=32 Score=29.54 Aligned_cols=18 Identities=11% Similarity=0.204 Sum_probs=15.8
Q ss_pred eeEEeCCCchhHHHHHhh
Q 008318 226 AARIRGPNDQYINHIMNE 243 (570)
Q Consensus 226 vgrIIGP~GstlK~Iq~E 243 (570)
+|||||-+|.+++-|..=
T Consensus 41 ~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CcceecCCChhHHHHHHH
Confidence 699999999999988653
No 82
>PRK01381 Trp operon repressor; Provisional
Probab=29.47 E-value=17 Score=33.11 Aligned_cols=30 Identities=27% Similarity=0.424 Sum_probs=23.1
Q ss_pred ccceeeec-----hhhHHHHHhHhCCeEee--eccee
Q 008318 116 SVRYKLTK-----RHTQEEIQKCTGAVVIT--RGKYR 145 (570)
Q Consensus 116 ~~Ry~LTK-----g~TQ~eIqe~TGA~VtT--RGrYy 145 (570)
..||.|-+ .-+|.||.+++|++|+| ||.-+
T Consensus 42 ~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~ 78 (99)
T PRK01381 42 GTRVRIVEELLRGELSQREIKQELGVGIATITRGSNS 78 (99)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHH
Confidence 36786654 47999999999999875 87544
No 83
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=29.27 E-value=1.3e+02 Score=29.28 Aligned_cols=59 Identities=12% Similarity=0.156 Sum_probs=44.0
Q ss_pred eeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHHHHHh
Q 008318 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 299 (570)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy 299 (570)
.-+|+.++|..++.|...-||+|.+.-. .-.|.|+| +...++.+...+.+++..|+.+.
T Consensus 37 ~~LLl~~~~~~L~~l~~~~~~~I~~~~~--------------~~~i~I~g-~k~~~~~i~~~i~~~l~~i~~~~ 95 (210)
T PF14611_consen 37 FFLLLTGNGRILENLAARNGAKIEVSRS--------------ENRIRITG-TKSTAEYIEASINEILSNIRTEE 95 (210)
T ss_pred eeeeecCCchHHHHHHHhcCceEEEecC--------------CcEEEEEc-cHHHHHHHHHHHHHHHhhcEEEE
Confidence 4489999999999998888999987642 23677777 66667777777777777766443
No 84
>PF09981 DUF2218: Uncharacterized protein conserved in bacteria (DUF2218); InterPro: IPR014543 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 2JPI_A.
Probab=28.96 E-value=81 Score=27.64 Aligned_cols=62 Identities=11% Similarity=0.181 Sum_probs=42.2
Q ss_pred chhHHHHHhhhCcEEEEeeccC-cCCCCCCC-----CCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHH
Q 008318 234 DQYINHIMNETGATVLLRGRGS-GNSEGLQG-----EVHQPLHLFLSSNNPKSLEEAKRLAENLLDTI 295 (570)
Q Consensus 234 GstlK~Iq~ETGAKI~IRGRGS-g~~E~~~g-----EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV 295 (570)
..|+|+|.+-.+=|+-+.--+. |.+.-..| ..++-|+|.|++++.+.|++.+..+.+-|..+
T Consensus 11 ~ryl~qLc~Hf~hk~~v~~d~~~g~i~f~~G~~~l~a~~~~L~l~vea~~~~~L~~~~~vv~~HL~rF 78 (89)
T PF09981_consen 11 SRYLKQLCKHFAHKFEVEWDEDSGRITFPFGTCTLSAEPDALTLRVEAPDAEALARLEDVVARHLERF 78 (89)
T ss_dssp HHHHHHHHHHTTTSSEEEE-SSEEEEE-SSS-EEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHhcCCCceEEcCCceEEEeCCEEEEEEeCCCeEEEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence 3577888777776766663332 22222233 35677999999999999999998888777654
No 85
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=28.92 E-value=58 Score=38.55 Aligned_cols=30 Identities=23% Similarity=0.286 Sum_probs=26.7
Q ss_pred eeEEeCCCchhHHHHHhhhCcEEEEeeccC
Q 008318 226 AARIRGPNDQYINHIMNETGATVLLRGRGS 255 (570)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETGAKI~IRGRGS 255 (570)
..-|+|.+|.++.+|+++++|++.++=.|+
T Consensus 358 ~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~ 387 (753)
T KOG2208|consen 358 LKFVIGKKGANIEKIREESQVKIDLPKQGS 387 (753)
T ss_pred hhhhcCCCCccHHHHHHhhhhceecccccC
Confidence 667999999999999999999999887554
No 86
>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=28.75 E-value=35 Score=28.59 Aligned_cols=34 Identities=9% Similarity=0.133 Sum_probs=23.5
Q ss_pred eEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEE
Q 008318 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATV 248 (570)
Q Consensus 211 eKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI 248 (570)
+.+.|-++.. =.|+|||.+|.+++-||-=+..-+
T Consensus 24 ~~i~i~i~~~----~~g~LIGk~G~tL~AlQ~L~~~~~ 57 (77)
T cd02414 24 DTVEVNISGD----DIGLLIGKRGKTLDALQYLANLVL 57 (77)
T ss_pred CEEEEEEecC----CCCeEECCCCccHHHHHHHHHHHH
Confidence 3455555431 248999999999999987766433
No 87
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=28.36 E-value=5.6e+02 Score=24.87 Aligned_cols=124 Identities=19% Similarity=0.165 Sum_probs=72.8
Q ss_pred cceee-ec-hhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcCCCC
Q 008318 117 VRYKL-TK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAG 194 (570)
Q Consensus 117 ~Ry~L-TK-g~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeIeEILKE~P~~ 194 (570)
..++| +. +..+.+|....|+.|.+.- ++ -.|.|+|.. ..++.+...|+++++.-
T Consensus 36 ~~~LLl~~~~~~L~~l~~~~~~~I~~~~----------~~--~~i~I~g~k---------~~~~~i~~~i~~~l~~i--- 91 (210)
T PF14611_consen 36 EFFLLLTGNGRILENLAARNGAKIEVSR----------SE--NRIRITGTK---------STAEYIEASINEILSNI--- 91 (210)
T ss_pred heeeeecCCchHHHHHHHhcCceEEEec----------CC--cEEEEEccH---------HHHHHHHHHHHHHHhhc---
Confidence 44555 33 6778888778899887632 11 146899964 35666667777776652
Q ss_pred CCccccccCCCcccceeEEEecCCCC-CCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccCcCCCCCCCCCCCCcEEEE
Q 008318 195 FPTLQTVMGNGVQAMSTSVFLGFDAD-ASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEVHQPLHLFL 273 (570)
Q Consensus 195 ~p~~~~p~~~G~k~~eeKI~Ipvd~~-P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGSg~~E~~~gEsdEPLHV~I 273 (570)
.++.|.+ ..+ +.|...+. ---....++.|++.|++-|..-+.+. .+.++-
T Consensus 92 --------------~~~~i~l--~~~~~~~~~~~~-~~~~~~~l~~i~~~t~~~ie~~~~~~------------~~~i~~ 142 (210)
T PF14611_consen 92 --------------RTEEIDL--SPIISKHSEKKN-SQFTPDLLEEIQKLTNVYIEKNPDGN------------KLKISW 142 (210)
T ss_pred --------------EEEEEec--chhhhhhccccc-ccccHHHHHHHHHHHcEEEEECCCCC------------eEEEEE
Confidence 1223322 111 11100000 01245678999999998887766532 233333
Q ss_pred --EcCCHHHHHHHHHHHHHHHH
Q 008318 274 --SSNNPKSLEEAKRLAENLLD 293 (570)
Q Consensus 274 --sa~~~e~v~kAk~LiEnLL~ 293 (570)
.+.+++..+.|++|....+.
T Consensus 143 ~~~~~~~~~~~~a~RlL~~a~~ 164 (210)
T PF14611_consen 143 LASPENEKRADRAKRLLLWALD 164 (210)
T ss_pred EeeccccchHHHHHHHHHHhcc
Confidence 23888888899888766553
No 88
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=27.61 E-value=60 Score=35.30 Aligned_cols=40 Identities=18% Similarity=0.363 Sum_probs=32.3
Q ss_pred eEEEecCCCCCCCceeeEEeCCCchhHHHHHhhh-CcEEEEe
Q 008318 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNET-GATVLLR 251 (570)
Q Consensus 211 eKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ET-GAKI~IR 251 (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 566652 246999999999999999999999998 6666443
No 89
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=27.36 E-value=7.9 Score=41.94 Aligned_cols=41 Identities=17% Similarity=0.211 Sum_probs=31.8
Q ss_pred eEEEecCC-CCCCCceeeEEeCCCchhHHHHHhh--------hCcEEEEe
Q 008318 211 TSVFLGFD-ADASLNIAARIRGPNDQYINHIMNE--------TGATVLLR 251 (570)
Q Consensus 211 eKI~Ipvd-~~P~FNfvgrIIGP~GstlK~Iq~E--------TGAKI~IR 251 (570)
.++||-++ -.|.-....+|||++|.-|++|-.+ .+++|.||
T Consensus 324 g~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~dL~~if~r~V~l~ 373 (379)
T KOG1423|consen 324 GVLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRANEDLEDIFQRKVFLR 373 (379)
T ss_pred cEEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHHHHHHHHhhceeeEE
Confidence 36677666 4677778999999999999999766 46777665
No 90
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=25.84 E-value=1.9e+02 Score=28.15 Aligned_cols=94 Identities=12% Similarity=0.115 Sum_probs=55.2
Q ss_pred ceeeechhhHHHHHhHhCCeEeeecceeCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHcCCCCCCc
Q 008318 118 RYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPT 197 (570)
Q Consensus 118 Ry~LTKg~TQ~eIqe~TGA~VtTRGrYyPPgk~~~gEpPLYL~Ieg~Te~kdt~ERi~aVd~AiaeIeEILKE~P~~~p~ 197 (570)
++.+-+++-+.+|.+...-.|++|. ++.. + .--++|.+.|.+++=++-....
T Consensus 19 ~~~~~~~dli~~lAk~lrKRIvvR~-----------dps~---------l-------~~~e~A~~~I~~ivP~ea~i~d- 70 (145)
T cd02410 19 ELFAEDGDLVKDLAKDLRKRIVIRP-----------DPSV---------L-------KPPEEAIKIILEIVPEEAGITD- 70 (145)
T ss_pred HHHhcccHHHHHHHHHHhceEEEcC-----------Chhh---------c-------CCHHHHHHHHHHhCCCccCcee-
Confidence 4455566777777777777777665 1111 0 1135577788888533211110
Q ss_pred cccccCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEe
Q 008318 198 LQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLR 251 (570)
Q Consensus 198 ~~~p~~~G~k~~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IR 251 (570)
..+.... ..|+|=.+. -|+++|.+|.+++.|-.+||=+-.|.
T Consensus 71 i~Fd~~t------GEV~IeaeK------PG~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 71 IYFDDDT------GEVIIEAEK------PGLVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred eEecCCC------cEEEEEEcC------CeEEEecCchhHHHHHHHhCCeeEEE
Confidence 0011112 245553332 47899999999999999999776553
No 91
>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=24.72 E-value=80 Score=34.04 Aligned_cols=39 Identities=21% Similarity=0.325 Sum_probs=31.5
Q ss_pred eEEEecCCCCCCCceeeEEeCCCchhHHHHHhhh-CcEEEE
Q 008318 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNET-GATVLL 250 (570)
Q Consensus 211 eKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ET-GAKI~I 250 (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 5776532 47999999999999999999999998 555543
No 92
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=24.53 E-value=1.4e+02 Score=34.36 Aligned_cols=69 Identities=17% Similarity=0.185 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHHcCCCCCCccccccCCCcccceeEEEecCCCCCCCceeeEEeCCCchhHHHHHhhhCcEEEEeeccC
Q 008318 176 AVDHAAAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGS 255 (570)
Q Consensus 176 aVd~AiaeIeEILKE~P~~~p~~~~p~~~G~k~~eeKI~Ipvd~~P~FNfvgrIIGP~GstlK~Iq~ETGAKI~IRGRGS 255 (570)
....|..+|++.|+.-.....+-.+. + --...|+||-+ .++++||-+|..+++|++..|-+|.++-++.
T Consensus 458 ~~~~a~~~i~~~i~r~~p~~~eVe~~-g----d~~avv~vpe~------~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 458 ALKLAEEEIEREIKRYLPGDVEVEVV-G----DGRAVVKVPEK------YIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred hhHHHHHHHHHHHHHhCCCCceEEEe-c----CCeEEEEeCHH------HhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 35556666776666542211111111 0 01134566533 3678899999999999999999999997655
No 93
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=23.69 E-value=95 Score=35.09 Aligned_cols=12 Identities=17% Similarity=0.326 Sum_probs=6.6
Q ss_pred HHHHHHHHHHHH
Q 008318 177 VDHAAAMVEEML 188 (570)
Q Consensus 177 Vd~AiaeIeEIL 188 (570)
+++|..+++.++
T Consensus 11 LE~a~~RLE~Is 22 (480)
T KOG2675|consen 11 LESATSRLEGIS 22 (480)
T ss_pred HHHHHHHhhhhh
Confidence 455555555554
No 94
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=22.39 E-value=2.7e+02 Score=27.83 Aligned_cols=52 Identities=12% Similarity=0.300 Sum_probs=40.5
Q ss_pred hHHHHHhhhC-cEEEEeeccCcCCCCCCCCCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHHHHHhh
Q 008318 236 YINHIMNETG-ATVLLRGRGSGNSEGLQGEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECG 300 (570)
Q Consensus 236 tlK~Iq~ETG-AKI~IRGRGSg~~E~~~gEsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy~ 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 4566766643 34557888654 8888888877 999999999999999999764
No 95
>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=21.90 E-value=68 Score=30.60 Aligned_cols=28 Identities=11% Similarity=0.141 Sum_probs=24.8
Q ss_pred eeeEEeCCCchhHHHHHhhhCcEEEEee
Q 008318 225 IAARIRGPNDQYINHIMNETGATVLLRG 252 (570)
Q Consensus 225 fvgrIIGP~GstlK~Iq~ETGAKI~IRG 252 (570)
-+|..+|.+|+.+|.|++..|=||-|=.
T Consensus 43 ~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 43 EMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred CccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 5899999999999999888898887665
No 96
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=21.34 E-value=70 Score=31.49 Aligned_cols=72 Identities=15% Similarity=0.162 Sum_probs=44.4
Q ss_pred eEEeCCCchhHHHHHhhhCcEEEEeeccCc---CCCCCC------C-----CCC-CCcE-EEEEcCCHHHHHHHHHHHHH
Q 008318 227 ARIRGPNDQYINHIMNETGATVLLRGRGSG---NSEGLQ------G-----EVH-QPLH-LFLSSNNPKSLEEAKRLAEN 290 (570)
Q Consensus 227 grIIGP~GstlK~Iq~ETGAKI~IRGRGSg---~~E~~~------g-----Esd-EPLH-V~Isa~~~e~v~kAk~LiEn 290 (570)
|.-||++|.+++++++..|=+|.|=.-..- +++... + ..+ .-++ |.|...|-..+..-.+..+.
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevVE~s~d~~~fl~Nl~~PA~V~gV~i~~~~dG~~~~kV~Vd~~Dk~~l~~k~e~~~~ 151 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVVEKTNDIKKLAVQLLSPARVLGVNTVWLPDGTVQYVIRVSRRDRRRLPAKPELLES 151 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEEEcCCCHHHHHHhcCCCcEEEEEEEEEeCCCcEEEEEEECHHHhhcccccHHHHHH
Confidence 889999999999999999999977764221 111100 0 011 2233 66666666666666666666
Q ss_pred HHHHHHHH
Q 008318 291 LLDTISAE 298 (570)
Q Consensus 291 LL~tV~eE 298 (570)
++..+...
T Consensus 152 v~~kltgk 159 (166)
T PRK06418 152 ILSKITGT 159 (166)
T ss_pred HHHHHHCC
Confidence 66555443
No 97
>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=21.19 E-value=97 Score=26.34 Aligned_cols=33 Identities=15% Similarity=0.287 Sum_probs=27.6
Q ss_pred EEEEEcCC-HHHHHHHHHHHHHHHHHHHHHhhcc
Q 008318 270 HLFLSSNN-PKSLEEAKRLAENLLDTISAECGAS 302 (570)
Q Consensus 270 HV~Isa~~-~e~v~kAk~LiEnLL~tV~eEy~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 89998776 7789999999999999998876533
No 98
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=21.13 E-value=20 Score=29.43 Aligned_cols=20 Identities=20% Similarity=0.313 Sum_probs=17.3
Q ss_pred eeEEeCCCchhHHHHHhhhC
Q 008318 226 AARIRGPNDQYINHIMNETG 245 (570)
Q Consensus 226 vgrIIGP~GstlK~Iq~ETG 245 (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 78999999999999986544
No 99
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=20.98 E-value=61 Score=28.29 Aligned_cols=18 Identities=17% Similarity=0.252 Sum_probs=16.0
Q ss_pred eeEEeCCCchhHHHHHhh
Q 008318 226 AARIRGPNDQYINHIMNE 243 (570)
Q Consensus 226 vgrIIGP~GstlK~Iq~E 243 (570)
+|+|||-+|.+++-|..-
T Consensus 41 ~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 41 MGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred ccceecCCChhHHHHHHH
Confidence 799999999999999653
No 100
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=20.56 E-value=96 Score=35.59 Aligned_cols=14 Identities=21% Similarity=0.273 Sum_probs=10.0
Q ss_pred CCchhhHHHHhhcc
Q 008318 552 PVVSDTLVKLMEYG 565 (570)
Q Consensus 552 ~~~~dtl~klm~yg 565 (570)
.+..+-|.+|||-=
T Consensus 531 ~~lagal~~~m~ar 544 (569)
T KOG3671|consen 531 GGLAGALANLMDAR 544 (569)
T ss_pred CccccHHHHHHHHH
Confidence 34568899999753
Done!