Query 008284
Match_columns 571
No_of_seqs 202 out of 488
Neff 3.5
Searched_HMMs 46136
Date Thu Mar 28 21:51:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008284.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008284hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1960 Predicted RNA-binding 100.0 2.4E-37 5.2E-42 320.5 14.1 371 27-430 13-422 (531)
2 KOG0119 Splicing factor 1/bran 99.9 2.7E-27 5.9E-32 250.6 15.4 147 145-295 75-230 (554)
3 cd02395 SF1_like-KH Splicing f 99.9 1.9E-25 4.1E-30 200.7 9.0 95 210-304 1-105 (120)
4 KOG1588 RNA-binding protein Sa 99.9 3.9E-22 8.4E-27 199.0 10.1 127 175-301 55-197 (259)
5 COG5176 MSL5 Splicing factor ( 99.8 1.1E-20 2.4E-25 184.6 10.1 150 143-297 83-242 (269)
6 KOG1960 Predicted RNA-binding 99.3 2.1E-12 4.6E-17 135.9 4.0 149 123-304 233-384 (531)
7 KOG1676 K-homology type RNA bi 99.2 5.1E-10 1.1E-14 122.4 18.2 165 102-299 137-304 (600)
8 KOG0334 RNA helicase [RNA proc 99.1 7.6E-11 1.7E-15 134.8 3.8 81 103-191 897-978 (997)
9 PRK13763 putative RNA-processi 98.8 2.7E-08 5.8E-13 95.0 9.9 145 104-294 3-156 (180)
10 TIGR03665 arCOG04150 arCOG0415 98.8 2.9E-08 6.2E-13 94.1 9.0 133 118-294 10-150 (172)
11 KOG1676 K-homology type RNA bi 98.7 2.4E-07 5.2E-12 102.0 16.5 160 105-299 231-393 (600)
12 cd00105 KH-I K homology RNA-bi 98.5 5.3E-07 1.2E-11 70.0 7.5 63 211-290 2-64 (64)
13 cd02393 PNPase_KH Polynucleoti 98.4 5E-07 1.1E-11 72.5 6.2 58 211-290 4-61 (61)
14 smart00322 KH K homology RNA-b 98.4 2.2E-06 4.7E-11 65.1 8.1 66 209-293 3-68 (69)
15 PF00013 KH_1: KH domain syndr 98.3 3.4E-07 7.4E-12 71.5 2.8 52 224-289 9-60 (60)
16 KOG2191 RNA-binding protein NO 98.1 0.00013 2.9E-09 76.7 17.4 161 104-300 39-206 (402)
17 cd02394 vigilin_like_KH K homo 98.1 5.1E-06 1.1E-10 65.4 4.8 54 224-290 9-62 (62)
18 cd02396 PCBP_like_KH K homolog 98.0 2.4E-05 5.1E-10 62.9 6.8 62 212-289 3-64 (65)
19 PF13014 KH_3: KH domain 97.6 4.2E-05 9.1E-10 57.0 3.2 28 225-252 1-28 (43)
20 PRK13763 putative RNA-processi 97.4 0.00029 6.2E-09 67.7 6.3 63 211-294 5-70 (180)
21 KOG2193 IGF-II mRNA-binding pr 97.4 0.00087 1.9E-08 72.6 9.8 144 120-303 213-357 (584)
22 TIGR02696 pppGpp_PNP guanosine 97.4 0.0016 3.6E-08 74.4 12.5 63 211-295 580-642 (719)
23 TIGR03665 arCOG04150 arCOG0415 97.2 0.00043 9.3E-09 66.0 5.1 56 225-295 8-65 (172)
24 KOG2193 IGF-II mRNA-binding pr 97.1 0.0025 5.5E-08 69.2 9.9 156 107-301 414-570 (584)
25 KOG0119 Splicing factor 1/bran 97.0 0.00094 2E-08 73.3 6.1 67 117-191 155-231 (554)
26 COG1094 Predicted RNA-binding 97.0 0.0013 2.8E-08 64.9 6.1 146 107-297 11-166 (194)
27 TIGR03591 polynuc_phos polyrib 96.9 0.0017 3.6E-08 73.8 6.8 99 211-347 553-651 (684)
28 cd02395 SF1_like-KH Splicing f 96.8 0.0027 5.9E-08 58.0 6.5 62 122-191 23-96 (120)
29 KOG2190 PolyC-binding proteins 96.7 0.025 5.5E-07 62.4 13.3 138 118-293 56-206 (485)
30 PLN00207 polyribonucleotide nu 96.6 0.0025 5.3E-08 74.4 5.3 100 211-347 687-787 (891)
31 PRK11824 polynucleotide phosph 95.6 0.014 3.1E-07 66.4 5.2 92 224-347 563-654 (693)
32 PRK04163 exosome complex RNA-b 95.5 0.02 4.3E-07 57.3 5.1 54 225-294 155-208 (235)
33 KOG2191 RNA-binding protein NO 95.4 0.07 1.5E-06 56.9 9.1 77 209-302 39-115 (402)
34 KOG2874 rRNA processing protei 95.1 0.023 5E-07 59.4 4.3 58 226-301 160-217 (356)
35 KOG2814 Transcription coactiva 93.8 0.1 2.2E-06 55.5 5.7 64 225-300 67-130 (345)
36 KOG1067 Predicted RNA-binding 93.2 0.22 4.7E-06 56.5 7.2 55 226-297 608-662 (760)
37 COG1185 Pnp Polyribonucleotide 92.9 0.11 2.4E-06 59.5 4.5 53 226-294 563-615 (692)
38 PRK00106 hypothetical protein; 92.8 0.22 4.7E-06 55.9 6.5 60 220-294 231-290 (535)
39 TIGR03319 YmdA_YtgF conserved 92.8 0.2 4.4E-06 55.7 6.2 60 220-294 210-269 (514)
40 PRK12704 phosphodiesterase; Pr 92.5 0.28 6E-06 54.7 6.8 59 220-293 216-274 (520)
41 KOG2190 PolyC-binding proteins 92.5 0.55 1.2E-05 52.2 9.0 120 116-252 148-293 (485)
42 KOG0336 ATP-dependent RNA heli 90.7 0.42 9.1E-06 52.9 5.7 63 223-301 55-118 (629)
43 KOG2192 PolyC-binding hnRNP-K 90.2 0.75 1.6E-05 48.4 6.7 65 225-300 325-389 (390)
44 cd02393 PNPase_KH Polynucleoti 88.1 1.7 3.7E-05 35.0 6.0 57 106-185 4-61 (61)
45 KOG1588 RNA-binding protein Sa 87.9 1.4 3.1E-05 45.6 6.9 73 118-193 111-194 (259)
46 PRK12705 hypothetical protein; 83.3 1.1 2.5E-05 50.1 3.9 58 220-292 204-261 (508)
47 KOG2192 PolyC-binding hnRNP-K 82.9 7.7 0.00017 41.1 9.3 134 117-295 59-193 (390)
48 cd02396 PCBP_like_KH K homolog 82.4 3.8 8.2E-05 33.0 5.5 53 117-184 11-64 (65)
49 PF00013 KH_1: KH domain syndr 80.6 4.4 9.5E-05 31.6 5.2 50 116-184 10-60 (60)
50 KOG1924 RhoA GTPase effector D 80.4 1.5 3.2E-05 51.7 3.4 17 228-244 262-278 (1102)
51 cd02134 NusA_KH NusA_K homolog 78.6 2.1 4.6E-05 34.6 2.9 27 224-250 34-60 (61)
52 KOG2113 Predicted RNA binding 76.0 6 0.00013 42.6 6.1 110 119-253 40-153 (394)
53 cd02394 vigilin_like_KH K homo 74.0 7.2 0.00016 30.6 4.7 58 107-184 3-61 (62)
54 COG1097 RRP4 RNA-binding prote 73.3 6.9 0.00015 40.4 5.6 30 224-253 155-184 (239)
55 smart00322 KH K homology RNA-b 71.9 28 0.00061 26.0 7.5 64 105-188 4-68 (69)
56 cd00105 KH-I K homology RNA-bi 71.9 16 0.00035 28.1 6.2 60 107-184 3-63 (64)
57 PF13184 KH_5: NusA-like KH do 69.4 1.9 4.1E-05 36.2 0.6 33 219-251 12-45 (69)
58 PRK15494 era GTPase Era; Provi 67.4 24 0.00053 37.0 8.3 28 224-251 283-318 (339)
59 TIGR00436 era GTP-binding prot 67.0 24 0.00052 35.4 7.9 27 225-251 232-266 (270)
60 KOG2113 Predicted RNA binding 66.1 3.1 6.7E-05 44.7 1.5 63 209-291 26-88 (394)
61 KOG1924 RhoA GTPase effector D 65.5 6.5 0.00014 46.6 3.9 11 402-412 440-450 (1102)
62 COG1702 PhoH Phosphate starvat 63.1 17 0.00036 39.5 6.2 57 225-299 25-83 (348)
63 COG1094 Predicted RNA-binding 60.9 13 0.00029 37.3 4.7 55 226-292 19-74 (194)
64 COG1159 Era GTPase [General fu 59.9 22 0.00047 37.9 6.3 42 204-250 224-273 (298)
65 COG5176 MSL5 Splicing factor ( 58.7 7.2 0.00016 40.1 2.4 83 97-191 147-241 (269)
66 PF13014 KH_3: KH domain 53.9 14 0.0003 27.5 2.8 24 117-140 2-26 (43)
67 KOG2208 Vigilin [Lipid transpo 53.4 32 0.00069 40.6 6.8 108 108-253 349-457 (753)
68 cd02409 KH-II KH-II (K homolo 53.3 12 0.00026 28.8 2.4 23 226-248 36-58 (68)
69 PRK00089 era GTPase Era; Revie 43.5 24 0.00051 35.5 3.4 38 209-251 226-271 (292)
70 KOG0334 RNA helicase [RNA proc 43.3 21 0.00045 43.4 3.3 74 217-295 904-977 (997)
71 KOG1925 Rac1 GTPase effector F 41.0 20 0.00044 41.0 2.6 19 510-528 247-266 (817)
72 PHA01732 proline-rich protein 40.2 28 0.0006 31.5 2.9 12 512-523 17-28 (94)
73 PRK08406 transcription elongat 38.5 24 0.00053 33.3 2.4 28 225-252 42-69 (140)
74 KOG2208 Vigilin [Lipid transpo 37.3 39 0.00084 39.9 4.3 30 226-255 358-387 (753)
75 KOG1923 Rac1 GTPase effector F 35.5 42 0.00091 40.0 4.1 15 487-501 270-284 (830)
76 PF01371 Trp_repressor: Trp re 35.5 6.3 0.00014 34.8 -1.8 32 110-143 32-70 (87)
77 PRK01064 hypothetical protein; 35.0 27 0.00058 30.3 1.9 19 226-244 41-59 (78)
78 COG2037 Ftr Formylmethanofuran 33.0 5.3E+02 0.011 27.6 11.0 49 117-165 21-80 (297)
79 PRK01381 Trp operon repressor; 32.9 15 0.00032 33.5 0.0 30 117-146 43-79 (99)
80 PRK02821 hypothetical protein; 31.3 30 0.00065 30.0 1.6 20 226-245 42-61 (77)
81 PRK00468 hypothetical protein; 31.1 31 0.00067 29.7 1.7 18 226-243 41-58 (75)
82 PF14611 SLS: Mitochondrial in 29.8 1.3E+02 0.0029 29.1 6.0 58 226-299 37-94 (210)
83 cd02410 archeal_CPSF_KH The ar 29.8 1.4E+02 0.0031 29.0 6.1 94 118-251 19-112 (145)
84 cd02414 jag_KH jag_K homology 28.1 36 0.00079 28.5 1.6 21 226-246 35-55 (77)
85 PRK12327 nusA transcription el 28.0 59 0.0013 35.4 3.5 40 211-251 233-273 (362)
86 PF07885 Ion_trans_2: Ion chan 27.9 48 0.001 27.2 2.3 16 399-415 39-54 (79)
87 PF00408 PGM_PMM_IV: Phosphogl 26.4 1.6E+02 0.0035 24.1 5.1 27 268-294 46-73 (73)
88 COG1855 ATPase (PilT family) [ 25.9 1.3E+02 0.0029 34.6 5.8 70 176-256 458-527 (604)
89 TIGR01953 NusA transcription t 25.5 77 0.0017 34.2 3.8 39 211-250 231-270 (341)
90 KOG2675 Adenylate cyclase-asso 24.6 89 0.0019 35.3 4.1 15 176-190 10-24 (480)
91 KOG3273 Predicted RNA-binding 23.6 48 0.001 34.2 1.8 51 225-293 179-229 (252)
92 KOG2279 Kinase anchor protein 22.8 51 0.0011 38.0 2.0 32 225-256 78-109 (608)
93 PF13083 KH_4: KH domain; PDB: 22.8 21 0.00045 29.4 -0.8 20 226-245 40-59 (73)
94 COG1837 Predicted RNA-binding 22.0 55 0.0012 28.6 1.6 17 226-242 41-57 (76)
95 PRK13764 ATPase; Provisional 21.8 1.1E+02 0.0024 35.5 4.4 69 176-255 453-521 (602)
96 TIGR01952 nusA_arch NusA famil 21.6 73 0.0016 30.4 2.5 28 225-252 43-70 (141)
97 COG0195 NusA Transcription elo 21.4 67 0.0014 32.1 2.3 33 220-252 81-113 (190)
98 KOG3671 Actin regulatory prote 21.2 91 0.002 35.8 3.5 14 100-113 74-87 (569)
99 PF09840 DUF2067: Uncharacteri 20.0 3.1E+02 0.0068 27.4 6.6 52 236-301 14-66 (190)
No 1
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=100.00 E-value=2.4e-37 Score=320.48 Aligned_cols=371 Identities=18% Similarity=0.143 Sum_probs=254.5
Q ss_pred HhhhccCcchhhhccCcc--ccCCCCCCCCCC-CCCCC--ccccccccCCCcccCCCCCCCccccCCCCCCCCCCCCCCc
Q 008284 27 RKKRKWDQPAESLINFPL--ASFGISLPGVPV-APVVP--APAAAAFFTNPPVASGATVPPVVLQGPLPPKFNQPKVQDE 101 (571)
Q Consensus 27 r~krkwdqpae~~~~~pl--~~~g~~~p~~~~-~~~~~--aa~~~a~~~~~~~~~~~~vpp~~~~~~~~~~~~~~k~~de 101 (571)
-+.|+|||+++.=..+++ .+.|...|+... .+... ++++-++.+|.-+-..-..-|.. -.+...+...++.+|+
T Consensus 13 ~~~~~WD~~~~~d~~~~~~~~~s~~~~p~eS~~~~~~~h~~~~s~s~~~N~~~~~k~~~~~~~-Na~~~i~~p~N~~K~~ 91 (531)
T KOG1960|consen 13 NYSRDWDSRFTEDSYSRRDSQRSGNEAPRESRYYRKEEHLQERSRSRSPNRDSRWKSSSSGFA-NAHPPIEEPTNNGKEA 91 (531)
T ss_pred CccccccCCCCCccccCchhhhccCCCCCcccccCcchhhhhhhhccCcchhccccccccccc-cccchhhcccccchhH
Confidence 467899999975444333 222444555332 22222 45555677887553211111111 1111123336777788
Q ss_pred eeEEEEEEcCCCCcccceeecchhHHHHHHhHhCCeEeecccccCCCCC--CCCCCCeEEEEeeccchhhHHHHHHHHHH
Q 008284 102 LIIAREIVINDSESSVRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAP--PDGEKPLYLHISAGAHLKETAERILAVDH 179 (571)
Q Consensus 102 ~~f~aEIEINDlPq~vRy~LTKg~Tq~eIqe~TGA~VtTRGrYyPPgk~--~~~EpPLYL~Ieg~Te~kdt~ERikaVd~ 179 (571)
+. .++++|||.+++|||.+|+|.++++|.+++|+.|.+||+|++++.. .++++||||||.+.|. +.+++
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 5889999999999984 68999
Q ss_pred HHHHHHHHHHccCC----------CCCcc--c-------cccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHH
Q 008284 180 AAAMVEEMLKQGHA----------GFPTL--Q-------TVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHI 240 (571)
Q Consensus 180 AvaeIeEILKE~P~----------~~pp~--~-------~p~~~G~k~~qeKIyIpld~~P~FNfvGrIIGPrGstlK~I 240 (571)
|+++|+-..+++.. +.+.+ + .+...|+++.+ |+||++| +|.||+.+..-|++..||.+|
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 99999977665421 11111 1 23567888888 9999999 999999999999999999999
Q ss_pred HHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhcccccc-----cccccc-CC
Q 008284 241 MNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGASRVS-----SCKVYN-AV 314 (571)
Q Consensus 241 q~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy~a~r~~-----~~~~y~-av 314 (571)
+.||+++++|||||||.+|++.|+|++||||++|+|.+.+.+.+||++|+||+++|+.+|.++-.. .+..|. ..
T Consensus 241 ~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl~~~v~~~~sr~~~~~~~~~p~~~y~~~~ 320 (531)
T KOG1960|consen 241 EIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNGNGENGAPRRKWNLEEKVYINLSRGFHRQAIVGPQGAYVKHI 320 (531)
T ss_pred hhhhhhhhhhccccccccCcccccccCCceeEEeecCCchhhccchhHHHhHHHHHHHHhhhhhhhcccccCCccccccc
Confidence 999999999999999999999999999999999999999999999999999999999999876321 122221 22
Q ss_pred CCchhhhccccCCC---CccccCccccceeccccccCCCCCCCCCCccceeeecceeecccc--ccccCC--CCCCccCC
Q 008284 315 PPPQQLLTGIQGFG---NEQKLNAGSAVILTSTVNLSSVPLAPSVPGVTTVYSQGMMLQSGG--ILNSVQ--PQQNIVGY 387 (571)
Q Consensus 315 pppqqll~gv~~s~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~--~~~~~~--~~~~~~~~ 387 (571)
.++|.-+-.+..++ +++..|--+- ...++-.+.......|.-- .-.+++ +++-.+--
T Consensus 321 ~~~~~~~~~~~g~~s~~i~p~~~~~~~----------------~p~~~~~~~~~~~~~~~~~~~~~~~i~~v~~qy~~~~ 384 (531)
T KOG1960|consen 321 QQETRTRVQIKGQGSAFIEPSTNRESD----------------EPIHLCIMSHDPNAIQRAKVLCEDLIASVHQQYKAWK 384 (531)
T ss_pred CCCCCcceeccCccceeecCCCCCCCC----------------CCcccccccCChhhhhhhhhcccccCCcccccCcccc
Confidence 23333333333222 3333222110 1111222222222222210 111111 34455556
Q ss_pred CCCCCCCCcccccCCCCCcCCChHHHHHHHHhcCCCCCccccc
Q 008284 388 PQPVSTGGTSYSGYEGIYPQATPLQQVALALRQSSSPLTSLVA 430 (571)
Q Consensus 388 ~~p~~~~g~~y~gy~~iypqatplqqva~~l~~~~~~~~~~~~ 430 (571)
.|| .+-+.-+|-||-+|-+-| |+.+|+-+.-+-|+..+
T Consensus 385 ~qp--~~~~~~~~~~~~~~p~~~---~~~~~~~~~q~~~qp~~ 422 (531)
T KOG1960|consen 385 SQP--KDRDQNQGNRAYNPPNRN---QAFSARDSRQEKTQPTN 422 (531)
T ss_pred cCC--CcccccCCCCCCCCCCcc---ccccCCCCCCCCCCCCC
Confidence 688 556667888999987776 67888877666665443
No 2
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=99.95 E-value=2.7e-27 Score=250.58 Aligned_cols=147 Identities=22% Similarity=0.330 Sum_probs=125.0
Q ss_pred cCCC-C-CCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHccCCCCCccccccCCCc-ccceeEEEecCCCCC
Q 008284 145 RLPN-A-PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQTVMGNGV-QAMSTSVFLGFDADA 221 (571)
Q Consensus 145 yPPg-k-~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeIeEILKE~P~~~pp~~~p~~~G~-k~~qeKIyIpld~~P 221 (571)
++++ + ..++..++|..-.-..++++.+.|.++.++....|+++|+..+.|+++.+ |.+ ..+++|||||+++||
T Consensus 75 ~p~~~e~rSPsp~p~yda~g~R~ntRe~R~r~~Le~er~e~I~~~lk~nP~fkpP~D----Yk~p~~~~~Kv~IPvke~P 150 (554)
T KOG0119|consen 75 VPPPRELRSPSPEPVYDAKGKRLNTREQRARKKLEDERHEIIEEILKLNPGFKPPAD----YKPPAKLHDKVYIPVKEFP 150 (554)
T ss_pred CCCCccccCCCcchhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCcc----cCcccccccceecchhhcC
Confidence 4444 3 67888999987555555667778888889999999999999999997764 444 377999999999999
Q ss_pred CCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCC------CCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHH
Q 008284 222 SLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEG------LQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDT 295 (571)
Q Consensus 222 ~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~------~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~t 295 (571)
+|||+|+||||||+|+|+||+||||||+||||||++... ......+||||++|++++.|+|++|.++||+||..
T Consensus 151 d~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 151 DINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred CcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999999996321 11224689999999999999999999999999996
No 3
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.92 E-value=1.9e-25 Score=200.74 Aligned_cols=95 Identities=22% Similarity=0.404 Sum_probs=85.8
Q ss_pred eeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCC-------CCCCCCCCCcEEEEEeCC--HH
Q 008284 210 STSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEG-------LQGEEVHQPLHLFLSSNN--PK 280 (571)
Q Consensus 210 qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~-------~~g~EsdEPLHV~Isa~~--~e 280 (571)
++|||||+|.||+|||+|+||||+|+|+|+|++||||+|.|||+||++.+. ...++.+|||||+|++.+ .+
T Consensus 1 ~~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e 80 (120)
T cd02395 1 TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEE 80 (120)
T ss_pred CCEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHH
Confidence 479999999999999999999999999999999999999999999998653 345678999999999999 99
Q ss_pred HHHHHHHHHHHHHHHHHHH-hcccc
Q 008284 281 SLEEAKRLAENLLDTISAE-CGASR 304 (571)
Q Consensus 281 ~v~kAk~LiEnLL~tV~eE-y~a~r 304 (571)
.+++|+++|++||..+.++ .+.++
T Consensus 81 ~~~~A~~~I~~ll~~~~~~~~~~~k 105 (120)
T cd02395 81 ALAKAVEAIEELLKPAIEGGNDELK 105 (120)
T ss_pred HHHHHHHHHHHHhccCCCccchHHH
Confidence 9999999999999998766 44443
No 4
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=99.87 E-value=3.9e-22 Score=198.99 Aligned_cols=127 Identities=23% Similarity=0.348 Sum_probs=99.1
Q ss_pred HHHHHHHHHHHHHHHccCCCCCcccc---ccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEe
Q 008284 175 LAVDHAAAMVEEMLKQGHAGFPTLQT---VMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLR 251 (571)
Q Consensus 175 kaVd~AvaeIeEILKE~P~~~pp~~~---p~~~G~k~~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IR 251 (571)
+.+++.+.+|.-.+.+.....+.... .........++|||||++.||+|||+||||||+|+++|+||+||||||+||
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 36777777777777654222222111 111122567899999999999999999999999999999999999999999
Q ss_pred ecCCCCCC-------C-CCCCCCCCCcEEEEEeCCHHH-----HHHHHHHHHHHHHHHHHHhc
Q 008284 252 GRGSGNSE-------G-LQGEEVHQPLHLFLSSNNPKS-----LEEAKRLAENLLDTISAECG 301 (571)
Q Consensus 252 GRGSg~~E-------~-~~g~EsdEPLHV~Isa~~~e~-----v~kAk~LiEnLL~tV~eEy~ 301 (571)
||||++.. + ...++.+|||||+|++..+.. |..|.+.|+.||.++.++..
T Consensus 135 GrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~P~~e~~d 197 (259)
T KOG1588|consen 135 GRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLVPDHEDED 197 (259)
T ss_pred cCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcCCCCCCch
Confidence 99999742 1 123458999999999988764 77889999999999998886
No 5
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.83 E-value=1.1e-20 Score=184.57 Aligned_cols=150 Identities=13% Similarity=0.115 Sum_probs=127.8
Q ss_pred cccCCCC--CCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHccCCCCCccccccCCCc-ccceeEEEecCCC
Q 008284 143 KYRLPNA--PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQTVMGNGV-QAMSTSVFLGFDA 219 (571)
Q Consensus 143 rYyPPgk--~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeIeEILKE~P~~~pp~~~p~~~G~-k~~qeKIyIpld~ 219 (571)
-++|+.. ..+..+|.|..|.-..++.+.+.++++.|+..-++++.++.-+.++.+ ++|.+ ..+++|||||+++
T Consensus 83 d~Vp~~re~Rspsppp~yd~~GrRlntre~ry~kkLeder~~l~era~k~lp~fv~p----~dy~rpsk~q~KiYIPV~e 158 (269)
T COG5176 83 DGVPSKRELRSPSPPPRYDEIGRRLNTREARYNKKLEDERLWLKERAQKILPRFVLP----NDYIRPSKYQNKIYIPVQE 158 (269)
T ss_pred CCCCchhhccCCCCCcchhHHhhhhhHHHHHHhhhhhHHHHHHHHHHHHhcCcccCC----ccccCcccccceEEeehhh
Confidence 3466653 578999999999888887777888888999999999999988877744 44544 6789999999999
Q ss_pred CCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCC-------CCCCCCCCcEEEEEeCCHHHHHHHHHHHHHH
Q 008284 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGL-------QGEEVHQPLHLFLSSNNPKSLEEAKRLAENL 292 (571)
Q Consensus 220 ~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~-------~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnL 292 (571)
||+.||+|+||||+|+|+|++|..|+|||.|||+||.+ |+. ......++||++|+++..+++.++..+|.|.
T Consensus 159 yPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvK-egk~ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n~ 237 (269)
T COG5176 159 YPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVK-EGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNA 237 (269)
T ss_pred CcccceeEEEecCCcchHHHHHHHhCCeEEEecccccc-cCcccccCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHHH
Confidence 99999999999999999999999999999999999986 221 1123568899999999999999999999999
Q ss_pred HHHHH
Q 008284 293 LDTIS 297 (571)
Q Consensus 293 L~tV~ 297 (571)
|....
T Consensus 238 I~~a~ 242 (269)
T COG5176 238 IREAR 242 (269)
T ss_pred HHHHh
Confidence 98765
No 6
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=99.27 E-value=2.1e-12 Score=135.92 Aligned_cols=149 Identities=22% Similarity=0.370 Sum_probs=123.5
Q ss_pred chhHHHHHHhHhCCeEeecccccCCCC---CCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHccCCCCCccc
Q 008284 123 KRHTQEEIQKCTGAVVITRGKYRLPNA---PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTLQ 199 (571)
Q Consensus 123 Kg~Tq~eIqe~TGA~VtTRGrYyPPgk---~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeIeEILKE~P~~~pp~~ 199 (571)
+-.++..|+.++++.+..||++----+ .....-|.|+.|.+.+. +.+..|..+|..++..
T Consensus 233 ~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~--------~g~~~A~r~~~nl~~~--------- 295 (531)
T KOG1960|consen 233 KDLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNG--------NGENGAPRRKWNLEEK--------- 295 (531)
T ss_pred cchhhhhhhhhhhhhhhhccccccccCcccccccCCceeEEeecCCc--------hhhccchhHHHhHHHH---------
Confidence 346788899999999999999865444 34678999999999975 4577777777666433
Q ss_pred cccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCH
Q 008284 200 TVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNP 279 (571)
Q Consensus 200 ~p~~~G~k~~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~ 279 (571)
+||-+. ..|| .-.|.||-|.|.|||+.+|-.+++|+|.||+|+++.+.+++++|.||||..+++
T Consensus 296 -------------v~~~~s--r~~~-~~~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i~p~~~~~~~~p~~~~~~~~~~ 359 (531)
T KOG1960|consen 296 -------------VYINLS--RGFH-RQAIVGPQGAYVKHIQQETRTRVQIKGQGSAFIEPSTNRESDEPIHLCIMSHDP 359 (531)
T ss_pred -------------HHHHhh--hhhh-hcccccCCcccccccCCCCCcceeccCccceeecCCCCCCCCCCcccccccCCh
Confidence 222211 1222 335789999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccc
Q 008284 280 KSLEEAKRLAENLLDTISAECGASR 304 (571)
Q Consensus 280 e~v~kAk~LiEnLL~tV~eEy~a~r 304 (571)
..|+.|+-+|++||..|+.+|.+++
T Consensus 360 ~~~~~~~~~~~~~i~~v~~qy~~~~ 384 (531)
T KOG1960|consen 360 NAIQRAKVLCEDLIASVHQQYKAWK 384 (531)
T ss_pred hhhhhhhhcccccCCcccccCcccc
Confidence 9999999999999999999999987
No 7
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.20 E-value=5.1e-10 Score=122.42 Aligned_cols=165 Identities=20% Similarity=0.275 Sum_probs=122.2
Q ss_pred eeEEEEEEcCCCCcccceeecc-hhHHHHHHhHhCCeEee-cccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHH
Q 008284 102 LIIAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVIT-RGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDH 179 (571)
Q Consensus 102 ~~f~aEIEINDlPq~vRy~LTK-g~Tq~eIqe~TGA~VtT-RGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~ 179 (571)
...+.||.|-+-+ |-.++.| |+|++.+++++|+.++. +-.- ..+...||| .|+|+. ..|+.
T Consensus 137 ~~ttqeI~IPa~k--~GlIIGKgGETikqlqe~sg~k~i~iqd~~----~~~~~~Kpl--ritGdp---------~~ve~ 199 (600)
T KOG1676|consen 137 VETTQEILIPANK--CGLIIGKGGETIKQLQEQSGVKMILVQDGS----IATGADKPL--RITGDP---------DKVEQ 199 (600)
T ss_pred cceeeeeccCccc--eeeEeccCccHHHHHHhhcCCceEEEecCC----cCCCCCCce--eecCCH---------HHHHH
Confidence 4456788888874 8999988 99999999999996432 2211 133478998 788886 37999
Q ss_pred HHHHHHHHHHccCCCCCccccccCCCccc-ceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCC
Q 008284 180 AAAMVEEMLKQGHAGFPTLQTVMGNGVQA-MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNS 258 (571)
Q Consensus 180 AvaeIeEILKE~P~~~pp~~~p~~~G~k~-~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~ 258 (571)
|..+|.++|+++-.-.+.. ...+|... -++++-|. +|.| -+|.|||-+|.|||+|+.|||+||+|+=-
T Consensus 200 a~~lV~dil~e~~~~~~g~--~~~~g~~~g~~~~~~V~---VPr~-~VG~IIGkgGE~IKklq~etG~KIQfkpD----- 268 (600)
T KOG1676|consen 200 AKQLVADILREEDDEVPGS--GGHAGVRGGGSATREVK---VPRS-KVGIIIGKGGEMIKKLQNETGAKIQFKPD----- 268 (600)
T ss_pred HHHHHHHHHHhcccCCCcc--ccccCcCccccceeEEe---cccc-ceeeEEecCchHHHHHhhccCceeEeecC-----
Confidence 9999999999753221111 12333322 23455555 4566 69999999999999999999999999851
Q ss_pred CCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHH
Q 008284 259 EGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAE 299 (571)
Q Consensus 259 E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eE 299 (571)
.+..-|+..+..-.+.+.++.|++||.+||..+.+.
T Consensus 269 -----d~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 269 -----DDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred -----CCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence 122456777777789999999999999999998876
No 8
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=99.06 E-value=7.6e-11 Score=134.78 Aligned_cols=81 Identities=32% Similarity=0.514 Sum_probs=76.5
Q ss_pred eEEEEEEcCCCCcccceeecchhHHHHHHhHhCCeEeecccccCCCC-CCCCCCCeEEEEeeccchhhHHHHHHHHHHHH
Q 008284 103 IIAREIVINDSESSVRYKLTKRHTQEEIQKCTGAVVITRGKYRLPNA-PPDGEKPLYLHISAGAHLKETAERILAVDHAA 181 (571)
Q Consensus 103 ~f~aEIEINDlPq~vRy~LTKg~Tq~eIqe~TGA~VtTRGrYyPPgk-~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~Av 181 (571)
+|.++++|||+||.+||++|..+++..|.+.+++.|+|||.|||+++ +.++|++|||+|+|.++ ..|.+|+
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 57999999999999999999999999999999999999999999998 67899999999999886 6899999
Q ss_pred HHHHHHHHcc
Q 008284 182 AMVEEMLKQG 191 (571)
Q Consensus 182 aeIeEILKE~ 191 (571)
.+|+++++++
T Consensus 969 ~e~~r~l~e~ 978 (997)
T KOG0334|consen 969 EELERLLEEE 978 (997)
T ss_pred HHHHHHHHHH
Confidence 9999988876
No 9
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.79 E-value=2.7e-08 Score=95.03 Aligned_cols=145 Identities=19% Similarity=0.194 Sum_probs=96.2
Q ss_pred EEEEEEcCCCCcccceeecc-hhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEe---eccchhhHHHHHHHHHH
Q 008284 104 IAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHIS---AGAHLKETAERILAVDH 179 (571)
Q Consensus 104 f~aEIEINDlPq~vRy~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ie---g~Te~kdt~ERikaVd~ 179 (571)
+...+.|..- +.+..+.+ |.+++.|+++||+.|...- .+... .|. +.+. ..+++
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----------ETGEV--IIEPTDGEDP--------LAVLK 60 (180)
T ss_pred ceEEEEcCHH--HhhhHhccchhHHHHHHHHHCcEEEEEC----------CCCeE--EEEeCCCCCH--------HHHHH
Confidence 4556777554 46777766 8999999999999987643 12333 454 3332 57999
Q ss_pred HHHHHHHHHHccCCCCCccccccCCCcccceeEEEecCCCC-C-CC---ceeeeEeCCCchhHHHHHHhhCcEEEEeecC
Q 008284 180 AAAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDAD-A-SL---NIAARIRGPNDQYINHIMNETGATVLLRGRG 254 (571)
Q Consensus 180 AvaeIeEILKE~P~~~pp~~~p~~~G~k~~qeKIyIpld~~-P-~F---NfvGrIIGPrGstlK~Iq~ETGaKV~IRGRG 254 (571)
|+..|+.++.. +.++..+- -.|-.+.-+.+ .+.++ . +- ..+|+|||++|.+++.||..|||+|+|-|+
T Consensus 61 A~~~I~ai~~g---f~~e~A~~-l~gd~y~~~Vi--~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~- 133 (180)
T PRK13763 61 ARDIVKAIGRG---FSPEKALR-LLDDDYVLEVI--DLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGK- 133 (180)
T ss_pred HHHHHHHHhcC---CCHHHHHH-HhCCCceEEEE--EhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCC-
Confidence 99999998763 11110000 00101111111 11111 0 00 259999999999999999999999999752
Q ss_pred CCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 008284 255 SGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 294 (571)
Q Consensus 255 Sg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~ 294 (571)
.++|.| ++++++.|++.++.|++
T Consensus 134 ----------------~v~i~G-~~~~~~~A~~~I~~li~ 156 (180)
T PRK13763 134 ----------------TVAIIG-DPEQVEIAREAIEMLIE 156 (180)
T ss_pred ----------------EEEEEe-CHHHHHHHHHHHHHHHc
Confidence 277876 99999999999999984
No 10
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.76 E-value=2.9e-08 Score=94.14 Aligned_cols=133 Identities=20% Similarity=0.191 Sum_probs=88.5
Q ss_pred ceeecc-hhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEE--eeccchhhHHHHHHHHHHHHHHHHHHHHccCCC
Q 008284 118 RYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHI--SAGAHLKETAERILAVDHAAAMVEEMLKQGHAG 194 (571)
Q Consensus 118 Ry~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~I--eg~Te~kdt~ERikaVd~AvaeIeEILKE~P~~ 194 (571)
+-.+.+ |++++.|+++||+.|...- .+. .+.| .+.+. .++++|+..|+.+...-
T Consensus 10 g~vIG~gG~~Ik~I~~~tgv~I~Id~----------~~g--~V~I~~~t~d~--------~~i~kA~~~I~~i~~gf--- 66 (172)
T TIGR03665 10 GVLIGKGGETKKEIEERTGVKLDIDS----------ETG--EVKIEEEDEDP--------LAVMKAREVVKAIGRGF--- 66 (172)
T ss_pred hhHhCCchhHHHHHHHHhCcEEEEEc----------CCc--eEEEecCCCCH--------HHHHHHHHHHHHHHcCC---
Confidence 444544 9999999999999987642 122 3455 23322 58999999999976541
Q ss_pred CCccccccCCCcccceeEEEecCCCC--CCC---ceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCC
Q 008284 195 FPTLQTVMGNGVQAMSTSVFLGFDAD--ASL---NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQP 269 (571)
Q Consensus 195 ~pp~~~p~~~G~k~~qeKIyIpld~~--P~F---NfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEP 269 (571)
.++..+- -.|--+.-+ | |.+.++ ..- ..+|+|||++|.+++.||..|||+|+|-|
T Consensus 67 ~~e~A~~-l~gd~y~~~-V-i~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----------------- 126 (172)
T TIGR03665 67 SPEKALK-LLDDDYMLE-V-IDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----------------- 126 (172)
T ss_pred CHHHHHH-hcCCcceEE-E-EEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC-----------------
Confidence 1110000 001011111 2 222221 000 25999999999999999999999999975
Q ss_pred cEEEEEeCCHHHHHHHHHHHHHHHH
Q 008284 270 LHLFLSSNNPKSLEEAKRLAENLLD 294 (571)
Q Consensus 270 LHV~Isa~~~e~v~kAk~LiEnLL~ 294 (571)
-.|+|.| ++++++.|++++++||+
T Consensus 127 ~~v~i~G-~~~~~~~A~~~i~~li~ 150 (172)
T TIGR03665 127 KTVGIIG-DPEQVQIAREAIEMLIE 150 (172)
T ss_pred CEEEEEC-CHHHHHHHHHHHHHHHc
Confidence 2588999 99999999999999994
No 11
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.74 E-value=2.4e-07 Score=101.96 Aligned_cols=160 Identities=21% Similarity=0.354 Sum_probs=117.3
Q ss_pred EEEEEcCCCCcccceeecc-hhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHH
Q 008284 105 AREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAM 183 (571)
Q Consensus 105 ~aEIEINDlPq~vRy~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~Avae 183 (571)
..+|.|.-+ +|..+|.| |++++.|+.+||+.| .|.|...++.-||+| +|-|..+ .+++|..+
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 347777777 48999988 999999999999987 678887777778998 7889753 58899999
Q ss_pred HHHHHHccCCCCCccccccCCCc--ccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCC
Q 008284 184 VEEMLKQGHAGFPTLQTVMGNGV--QAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGL 261 (571)
Q Consensus 184 IeEILKE~P~~~pp~~~p~~~G~--k~~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~ 261 (571)
|.+||.....-..- .++-|. ...+--+-||-+. .|+|||++|.|||.|..|+||++.|-=-
T Consensus 294 I~eii~~~~~~~~~---~~~~G~P~~~~~fy~~VPa~K------cGLvIGrGGEtIK~in~qSGA~~el~r~-------- 356 (600)
T KOG1676|consen 294 INEIIAEAEAGAGG---GMGGGAPGLVAQFYMKVPADK------CGLVIGRGGETIKQINQQSGARCELSRQ-------- 356 (600)
T ss_pred HHHHHHHHhccCCC---CcCCCCccceeeEEEeccccc------cccccCCCccchhhhcccCCccccccCC--------
Confidence 99999875221100 011111 1112222245332 7999999999999999999999976421
Q ss_pred CCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHH
Q 008284 262 QGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAE 299 (571)
Q Consensus 262 ~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eE 299 (571)
....+.+..+++.-.++.+|+-|+.||++-+..+...
T Consensus 357 -~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~~~n 393 (600)
T KOG1676|consen 357 -PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDIAPN 393 (600)
T ss_pred -CCCCCccceEEEEecCcccchHHHHHHHHHhcccCCC
Confidence 1123566889999999999999999999888776544
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=98.48 E-value=5.3e-07 Score=70.01 Aligned_cols=63 Identities=27% Similarity=0.393 Sum_probs=50.7
Q ss_pred eEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 008284 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 290 (571)
Q Consensus 211 eKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiE 290 (571)
.++.||. +++++|||++|.++++|+++|||+|.|...+. ..+...|.|.|. .+.+++|+.+++
T Consensus 2 ~~i~ip~------~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~----------~~~~~~v~i~G~-~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPS------SLVGRIIGKGGSTIKEIREETGAKIKIPDSGS----------GSEERIVTITGT-PEAVEKAKELIL 64 (64)
T ss_pred EEEEEch------hhcceeECCCCHHHHHHHHHHCCEEEEcCCCC----------CCCceEEEEEcC-HHHHHHHHHHhC
Confidence 4566764 67999999999999999999999999986433 234567888887 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=98.43 E-value=5e-07 Score=72.53 Aligned_cols=58 Identities=21% Similarity=0.422 Sum_probs=48.4
Q ss_pred eEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 008284 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 290 (571)
Q Consensus 211 eKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiE 290 (571)
+.+.||-+ ++|+|||++|+++|.|+++|||+|.|-- + -.|.|.|.+.+++++|+++++
T Consensus 4 ~~i~Ip~~------~ig~iIGkgG~~ik~I~~~tg~~I~i~~------------~----g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 4 ETMKIPPD------KIRDVIGPGGKTIKKIIEETGVKIDIED------------D----GTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEeChh------heeeeECCCchHHHHHHHHHCCEEEeCC------------C----CEEEEEeCCHHHHHHHHHHhC
Confidence 45566532 5899999999999999999999998752 1 259999999999999999985
No 14
>smart00322 KH K homology RNA-binding domain.
Probab=98.36 E-value=2.2e-06 Score=65.14 Aligned_cols=66 Identities=23% Similarity=0.341 Sum_probs=54.3
Q ss_pred ceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 008284 209 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 288 (571)
Q Consensus 209 ~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~L 288 (571)
....|+|+. +++|+|||++|.++++|+++|||+|.+.+.++ ....+.|.+. .+.++.|+++
T Consensus 3 ~~~~i~i~~------~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~------------~~~~v~i~g~-~~~v~~a~~~ 63 (69)
T smart00322 3 VTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS------------EERVVEITGP-PENVEKAAEL 63 (69)
T ss_pred eEEEEEEcc------hhcceeECCCchHHHHHHHHHCCEEEECCCCC------------CccEEEEEcC-HHHHHHHHHH
Confidence 345677764 57899999999999999999999999986433 3456888888 8999999999
Q ss_pred HHHHH
Q 008284 289 AENLL 293 (571)
Q Consensus 289 iEnLL 293 (571)
+++++
T Consensus 64 i~~~~ 68 (69)
T smart00322 64 ILEIL 68 (69)
T ss_pred HHHHh
Confidence 98876
No 15
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=98.32 E-value=3.4e-07 Score=71.55 Aligned_cols=52 Identities=25% Similarity=0.433 Sum_probs=45.9
Q ss_pred ceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 008284 224 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 289 (571)
Q Consensus 224 NfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~Li 289 (571)
+++|+|||++|.++++|+++|||+|.|... ++.-.|.|+| +.+++++|+++|
T Consensus 9 ~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-------------~~~~~v~I~G-~~~~v~~A~~~I 60 (60)
T PF00013_consen 9 SLVGRIIGKKGSNIKEIEEETGVKIQIPDD-------------DERDIVTISG-SPEQVEKAKKMI 60 (60)
T ss_dssp HHHHHHHTGGGHHHHHHHHHHTSEEEEEST-------------TEEEEEEEEE-SHHHHHHHHHHH
T ss_pred HHcCEEECCCCCcHHHhhhhcCeEEEEcCC-------------CCcEEEEEEe-CHHHHHHHHhhC
Confidence 369999999999999999999999999653 1446899999 999999999986
No 16
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=98.12 E-value=0.00013 Score=76.75 Aligned_cols=161 Identities=16% Similarity=0.185 Sum_probs=104.8
Q ss_pred EEEEEEcCCCCcccceeecc-hhHHHHHHhHhCCeEee-cc-cccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHH
Q 008284 104 IAREIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVIT-RG-KYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHA 180 (571)
Q Consensus 104 f~aEIEINDlPq~vRy~LTK-g~Tq~eIqe~TGA~VtT-RG-rYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~A 180 (571)
++=+|-|..+- +.-+|.| |+|+.++|.+|||.|-. |- -|||- ..|| -.+|+|..+ ++..-
T Consensus 39 y~ikvLips~A--aGsIIGKGG~ti~~lqk~tgariklSks~dfyPG----TTeR--vcli~Gt~e---------ai~av 101 (402)
T KOG2191|consen 39 YFLKVLIPSYA--AGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPG----TTER--VCLIQGTVE---------ALNAV 101 (402)
T ss_pred eEEEEEeeccc--ccceeccchHHHHHHHhccCcEEEeccccccCCC----ccce--EEEEeccHH---------HHHHH
Confidence 35577887775 7889999 89999999999999864 22 24441 2344 458899753 45555
Q ss_pred HHHHHHHHHccCCCCCc-cc--cccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEee-cCCC
Q 008284 181 AAMVEEMLKQGHAGFPT-LQ--TVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRG-RGSG 256 (571)
Q Consensus 181 vaeIeEILKE~P~~~pp-~~--~p~~~G~k~~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRG-RGSg 256 (571)
+..|.+.|.+.+.-..- .+ .+.... +-.+.||.+|-. -.|.|||++|.|+|.|++|.||-|+|-- +-.+
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 55566666555432211 00 010000 223577877732 4899999999999999999999999973 2111
Q ss_pred CCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHh
Q 008284 257 NSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 300 (571)
Q Consensus 257 ~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy 300 (571)
+ ..+ -.|...+.++|++.+|++|| |++|.++-
T Consensus 175 ~----sLq-----ervvt~sge~e~~~~A~~~I---L~Ki~eDp 206 (402)
T KOG2191|consen 175 I----SLQ-----ERVVTVSGEPEQNMKAVSLI---LQKIQEDP 206 (402)
T ss_pred c----cce-----eEEEEecCCHHHHHHHHHHH---HHHhhcCC
Confidence 1 111 25666788899999998776 56666664
No 17
>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=98.08 E-value=5.1e-06 Score=65.36 Aligned_cols=54 Identities=22% Similarity=0.314 Sum_probs=45.6
Q ss_pred ceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 008284 224 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 290 (571)
Q Consensus 224 NfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiE 290 (571)
.++|.|||++|.++++|+++|||+|.|-..+ +..-+|.|+|. .+++.+|+++++
T Consensus 9 ~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~------------~~~~~v~I~G~-~~~v~~A~~~i~ 62 (62)
T cd02394 9 KLHRFIIGKKGSNIRKIMEETGVKIRFPDPG------------SKSDTITITGP-KENVEKAKEEIL 62 (62)
T ss_pred HHhhhccCCCCCcHHHHHHHhCCEEEcCCCC------------CCCCEEEEEcC-HHHHHHHHHHhC
Confidence 3689999999999999999999999998642 23357899999 789999998763
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=97.97 E-value=2.4e-05 Score=62.89 Aligned_cols=62 Identities=21% Similarity=0.219 Sum_probs=45.4
Q ss_pred EEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 008284 212 SVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 289 (571)
Q Consensus 212 KIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~Li 289 (571)
++.||. +.+|+|||.+|.++++|+++|||+|.|--... ......++....+.+++++|..||
T Consensus 3 r~~ip~------~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----------~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 3 RLLVPS------SQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----------PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred EEEECH------HHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----------CCCCceEEEEEeCHHHHHHHHHhh
Confidence 455653 36899999999999999999999999953211 122233444445699999999987
No 19
>PF13014 KH_3: KH domain
Probab=97.65 E-value=4.2e-05 Score=57.04 Aligned_cols=28 Identities=32% Similarity=0.455 Sum_probs=26.3
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEee
Q 008284 225 IAARIRGPNDQYINHIMNETGATVLLRG 252 (571)
Q Consensus 225 fvGrIIGPrGstlK~Iq~ETGaKV~IRG 252 (571)
++|.|||++|.++++|+++|||+|.|--
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
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.41 E-value=0.00029 Score=67.69 Aligned_cols=63 Identities=13% Similarity=0.192 Sum_probs=53.2
Q ss_pred eEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEE---eCCHHHHHHHHH
Q 008284 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLS---SNNPKSLEEAKR 287 (571)
Q Consensus 211 eKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Is---a~~~e~v~kAk~ 287 (571)
..+.||.+ -+|.|||++|.++|.|+++|||+|.|.-. .-.|.|. +.|++.+++|++
T Consensus 5 ~~i~IP~~------kig~iIG~gGk~Ik~I~e~tg~~I~i~~~---------------~g~V~I~~~~~~d~~~i~kA~~ 63 (180)
T PRK13763 5 EYVKIPKD------RIGVLIGKKGETKKEIEERTGVKLEIDSE---------------TGEVIIEPTDGEDPLAVLKARD 63 (180)
T ss_pred EEEEcCHH------HhhhHhccchhHHHHHHHHHCcEEEEECC---------------CCeEEEEeCCCCCHHHHHHHHH
Confidence 45666643 48999999999999999999999999852 1367787 889999999999
Q ss_pred HHHHHHH
Q 008284 288 LAENLLD 294 (571)
Q Consensus 288 LiEnLL~ 294 (571)
+|+.|+.
T Consensus 64 ~I~ai~~ 70 (180)
T PRK13763 64 IVKAIGR 70 (180)
T ss_pred HHHHHhc
Confidence 9999987
No 21
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.36 E-value=0.00087 Score=72.63 Aligned_cols=144 Identities=15% Similarity=0.188 Sum_probs=89.3
Q ss_pred eecc-hhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHccCCCCCcc
Q 008284 120 KLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPTL 198 (571)
Q Consensus 120 ~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeIeEILKE~P~~~pp~ 198 (571)
++.+ |.|++.|-..|-+.|-+ .--+.....|+.|-+| +..| ...+|.++|-|+|..+-.--
T Consensus 213 IIGkeG~TIknItkqTqsriD~----hrken~Gaaek~itvh--~tpE---------g~s~Ac~~ILeimqkEA~~~--- 274 (584)
T KOG2193|consen 213 IIGKEGATIKNITKQTQSRIDV----HRKENAGAAEKIITVH--STPE---------GTSKACKMILEIMQKEAVDD--- 274 (584)
T ss_pred EecCCCccccCcchhhhheeee----eecccCCcccCceEEe--cCcc---------chHHHHHHHHHHHHHhhhcc---
Confidence 4445 89999999999887643 1112234678999776 4332 45567788888886642110
Q ss_pred ccccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCC
Q 008284 199 QTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNN 278 (571)
Q Consensus 199 ~~p~~~G~k~~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~ 278 (571)
.+.+ .|||+-.---||+||+||..|.++|+|+++||+||.|-- +.| .++ .+-.--+.|-| +
T Consensus 275 ---------k~~~--e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~----lqe-ls~--ynpERTItVkG-s 335 (584)
T KOG2193|consen 275 ---------KVAE--EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISK----LQE-LSL--YNPERTITVKG-S 335 (584)
T ss_pred ---------chhh--hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeee----hhh-hcc--cCccceEEecc-c
Confidence 1111 245553344567999999999999999999999999853 333 111 11123455555 4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhccc
Q 008284 279 PKSLEEAKRLAENLLDTISAECGAS 303 (571)
Q Consensus 279 ~e~v~kAk~LiEnLL~tV~eEy~a~ 303 (571)
-|.+.+|.. .++..+++.|...
T Consensus 336 iEac~~AE~---eImkKlre~yEnD 357 (584)
T KOG2193|consen 336 IEACVQAEA---EIMKKLRECYEND 357 (584)
T ss_pred HHHHHHHHH---HHHHHHHHHHhhh
Confidence 444555444 4456677777653
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=97.36 E-value=0.0016 Score=74.37 Aligned_cols=63 Identities=22% Similarity=0.407 Sum_probs=54.9
Q ss_pred eEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 008284 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 290 (571)
Q Consensus 211 eKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiE 290 (571)
+.+.|+.+ -+|.||||+|.++|.|+++|||+|-|-- .=+|.|.+.+.+.+++|+++|+
T Consensus 580 ~~~~I~~~------ki~~vIG~gGk~I~~i~~~tg~~Idi~d----------------~G~V~I~a~d~~~~~~A~~~I~ 637 (719)
T TIGR02696 580 ITVKIPVD------KIGEVIGPKGKMINQIQDETGAEISIED----------------DGTVYIGAADGPSAEAARAMIN 637 (719)
T ss_pred EEEEeChH------HhhheeCCCcHhHHHHHHHHCCEEEEec----------------CcEEEEEeCCHHHHHHHHHHHH
Confidence 55667644 4899999999999999999999998853 3589999999999999999999
Q ss_pred HHHHH
Q 008284 291 NLLDT 295 (571)
Q Consensus 291 nLL~t 295 (571)
+|+..
T Consensus 638 ~i~~~ 642 (719)
T TIGR02696 638 AIANP 642 (719)
T ss_pred HhhCc
Confidence 99985
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=97.23 E-value=0.00043 Score=65.99 Aligned_cols=56 Identities=11% Similarity=0.174 Sum_probs=48.7
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEE--EeCCHHHHHHHHHHHHHHHHH
Q 008284 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFL--SSNNPKSLEEAKRLAENLLDT 295 (571)
Q Consensus 225 fvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~I--sa~~~e~v~kAk~LiEnLL~t 295 (571)
.+|.|||++|.++|.|+++|||+|.|--. .-.|.| .+.|++.+++|+++|+.|...
T Consensus 8 kig~vIG~gG~~Ik~I~~~tgv~I~Id~~---------------~g~V~I~~~t~d~~~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 8 RIGVLIGKGGETKKEIEERTGVKLDIDSE---------------TGEVKIEEEDEDPLAVMKAREVVKAIGRG 65 (172)
T ss_pred HhhhHhCCchhHHHHHHHHhCcEEEEEcC---------------CceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence 58999999999999999999999999731 125777 789999999999999998873
No 24
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.10 E-value=0.0025 Score=69.17 Aligned_cols=156 Identities=17% Similarity=0.225 Sum_probs=107.8
Q ss_pred EEEcCCCCcccceeecc-hhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHH
Q 008284 107 EIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVE 185 (571)
Q Consensus 107 EIEINDlPq~vRy~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeIe 185 (571)
.+.|.|.- +.-++.+ |..+++|.+++||+|-. -||+-+--++| -..|+|+.+ +.-+|...|-
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 56777764 6666654 99999999999999843 23332222344 447889863 6778899999
Q ss_pred HHHHccCCCCCccccccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCC
Q 008284 186 EMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEE 265 (571)
Q Consensus 186 EILKE~P~~~pp~~~p~~~G~k~~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~E 265 (571)
..|+|+..+.|-.+ ..+++-|-|| .+ .+|||||.+|.|++.+|+-|+|.|.|-- + .++.|
T Consensus 477 gKikEenf~~Pkee-------vklethirVP-----s~-~aGRvIGKGGktVnELQnlt~AeV~vPr------d-qtpdE 536 (584)
T KOG2193|consen 477 GKIKEENFFLPKEE-------VKLETHIRVP-----SS-AAGRVIGKGGKTVNELQNLTSAEVVVPR------D-QTPDE 536 (584)
T ss_pred hhhhhhccCCchhh-------heeeeeeecc-----ch-hhhhhhccccccHHHHhccccceEEccc------c-CCCCc
Confidence 99998855543221 3445555554 55 7999999999999999999999998753 1 23333
Q ss_pred CCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhc
Q 008284 266 VHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECG 301 (571)
Q Consensus 266 sdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy~ 301 (571)
+|-.-|-|.| +.-..+.|...|.+|+..|++.-+
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 3334444444 455667888888889988887654
No 25
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.04 E-value=0.00094 Score=73.27 Aligned_cols=67 Identities=27% Similarity=0.398 Sum_probs=52.6
Q ss_pred cceee-cchhHHHHHHhHhCCeEeecccc-cCCCC--------CCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHH
Q 008284 117 VRYKL-TKRHTQEEIQKCTGAVVITRGKY-RLPNA--------PPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEE 186 (571)
Q Consensus 117 vRy~L-TKg~Tq~eIqe~TGA~VtTRGrY-yPPgk--------~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeIeE 186 (571)
+-.+| -+|.||+.++++|||.|..||+= +-.++ ....+-+||.+|++.|+ +.|++|++.|+.
T Consensus 155 vGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~--------eki~~Ai~vien 226 (554)
T KOG0119|consen 155 VGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQ--------EKIKKAIAVIEN 226 (554)
T ss_pred eEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchH--------HHHHHHHHHHHH
Confidence 45566 46999999999999999999931 11111 12357899999999987 689999999999
Q ss_pred HHHcc
Q 008284 187 MLKQG 191 (571)
Q Consensus 187 ILKE~ 191 (571)
+|++.
T Consensus 227 li~~a 231 (554)
T KOG0119|consen 227 LIQSA 231 (554)
T ss_pred HHHhh
Confidence 99974
No 26
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.00 E-value=0.0013 Score=64.94 Aligned_cols=146 Identities=17% Similarity=0.208 Sum_probs=87.6
Q ss_pred EEEcCCCCcccceeecc-hhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHH
Q 008284 107 EIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVE 185 (571)
Q Consensus 107 EIEINDlPq~vRy~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeIe 185 (571)
-|.|..- +.-+++.+ |++-..|.+.+|+.++... .-.+.-|...-.+.|. ..+.+|...|+
T Consensus 11 ~v~iPk~--R~~~lig~~g~v~k~ie~~~~~~~~iD~------------~~~~V~i~~~~~t~Dp----~~~~ka~d~Vk 72 (194)
T COG1094 11 AVKIPKD--RIGVLIGKWGEVKKAIEEKTGVKLRIDS------------KTGSVTIRTTRKTEDP----LALLKARDVVK 72 (194)
T ss_pred eeecCch--hheeeecccccchHHHHhhcCeEEEEEC------------CCCeEEEEecCCCCCh----HHHHHHHHHHH
Confidence 3555554 34556655 8899999999999876532 1112222222111111 23445555554
Q ss_pred HHHHccCCCCCccccccCCCccccee---EEEecCCCCC---C---CceeeeEeCCCchhHHHHHHhhCcEEEEeecCCC
Q 008284 186 EMLKQGHAGFPTLQTVMGNGVQAMST---SVFLGFDADA---S---LNIAARIRGPNDQYINHIMNETGATVLLRGRGSG 256 (571)
Q Consensus 186 EILKE~P~~~pp~~~p~~~G~k~~qe---KIyIpld~~P---~---FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg 256 (571)
-+ +..|.++..+ +.+++ +.-|.+.++- + -..+|||||++|.|.+.||+-|||.|.|.|+
T Consensus 73 AI---grGF~pe~A~------~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~--- 140 (194)
T COG1094 73 AI---GRGFPPEKAL------KLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK--- 140 (194)
T ss_pred HH---hcCCCHHHHH------HHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc---
Confidence 44 2222221100 11111 1123333221 1 1248999999999999999999999999993
Q ss_pred CCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q 008284 257 NSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTIS 297 (571)
Q Consensus 257 ~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~ 297 (571)
+|.|.| ++++|+.|++.||.||+..+
T Consensus 141 --------------tVaiiG-~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 141 --------------TVAIIG-GFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred --------------EEEEec-ChhhhHHHHHHHHHHHcCCC
Confidence 677776 58899999999999997543
No 27
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=96.90 E-value=0.0017 Score=73.82 Aligned_cols=99 Identities=18% Similarity=0.256 Sum_probs=70.1
Q ss_pred eEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH
Q 008284 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE 290 (571)
Q Consensus 211 eKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiE 290 (571)
+.+.|+.+ .+|.||||+|.++|.|+++|||+|-|-= .=+|.|.+.+.+.+++|+++|+
T Consensus 553 ~~~~I~~~------kI~~vIG~gGk~Ik~I~~~tg~~I~i~d----------------dG~V~i~~~~~~~~~~a~~~I~ 610 (684)
T TIGR03591 553 ETIKINPD------KIRDVIGPGGKVIREITEETGAKIDIED----------------DGTVKIAASDGEAAEAAIKMIE 610 (684)
T ss_pred EEEecCHH------HHHhhcCCCcHHHHHHHHHHCCEEEEec----------------CeEEEEEECcHHHHHHHHHHHH
Confidence 45556533 4899999999999999999999999842 2579999999999999999999
Q ss_pred HHHHHHHHHhccccccccccccCCCCchhhhccccCCCCccccCccccceecccccc
Q 008284 291 NLLDTISAECGASRVSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNL 347 (571)
Q Consensus 291 nLL~tV~eEy~a~r~~~~~~y~avpppqqll~gv~~s~~~~~~~~~~~~~~~~~~~~ 347 (571)
.|.... . ..+.|. -.+.++..+|..-.+.. ...|+.|--++
T Consensus 611 ~~~~~~----~-----~G~i~~------G~V~~I~~~GafVei~~-g~~GllHiSei 651 (684)
T TIGR03591 611 GITAEP----E-----VGKIYE------GKVVRIMDFGAFVEILP-GKDGLVHISEI 651 (684)
T ss_pred hhhccc----c-----cCcEEE------EEEEEEeCCEEEEEECC-CcEEEEEHHHc
Confidence 995421 1 122221 13566667775444433 25677775544
No 28
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=96.85 E-value=0.0027 Score=58.01 Aligned_cols=62 Identities=29% Similarity=0.399 Sum_probs=48.9
Q ss_pred cchhHHHHHHhHhCCeEeecccccCCCC----------CCCCCCCeEEEEeecc--chhhHHHHHHHHHHHHHHHHHHHH
Q 008284 122 TKRHTQEEIQKCTGAVVITRGKYRLPNA----------PPDGEKPLYLHISAGA--HLKETAERILAVDHAAAMVEEMLK 189 (571)
Q Consensus 122 TKg~Tq~eIqe~TGA~VtTRGrYyPPgk----------~~~~EpPLYL~Ieg~T--e~kdt~ERikaVd~AvaeIeEILK 189 (571)
.+|.|+++|+++|||.|.+||+---... ....+-||+++|++.+ . +++++|+.+|++++.
T Consensus 23 PgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~--------e~~~~A~~~I~~ll~ 94 (120)
T cd02395 23 PRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPE--------EALAKAVEAIEELLK 94 (120)
T ss_pred CCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHH--------HHHHHHHHHHHHHhc
Confidence 5699999999999999999996211111 1134678999999998 4 589999999999988
Q ss_pred cc
Q 008284 190 QG 191 (571)
Q Consensus 190 E~ 191 (571)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 53
No 29
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.65 E-value=0.025 Score=62.41 Aligned_cols=138 Identities=17% Similarity=0.171 Sum_probs=79.4
Q ss_pred ceeecchhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEee---------ccchhhHHHHHHHHHHHHHHHHHHH
Q 008284 118 RYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISA---------GAHLKETAERILAVDHAAAMVEEML 188 (571)
Q Consensus 118 Ry~LTKg~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ieg---------~Te~kdt~ERikaVd~AvaeIeEIL 188 (571)
-|+-.+|+++++|..+|++.|-+=- ..++.+=--+-|.| .. .++.+|..+|-..+
T Consensus 56 ~IIGk~G~~vkkir~~t~s~i~i~~-------~~~~c~eRIiti~g~~~~~~~~~~~---------~al~ka~~~iv~~~ 119 (485)
T KOG2190|consen 56 SIIGKKGDIVKKIRKETESKIRVNE-------SLPGCPERIITITGNRVELNLSPAT---------DALFKAFDMIVFKL 119 (485)
T ss_pred eEEccCcHHHHHHhhcccccceeec-------CCCCCCcceEEEecccccccCCchH---------HHHHHHHHHHhhcc
Confidence 4555679999999977777643211 11122222223444 22 25555555544433
Q ss_pred HccCCCCCccccccCCC---ccc-ceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCC
Q 008284 189 KQGHAGFPTLQTVMGNG---VQA-MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGE 264 (571)
Q Consensus 189 KE~P~~~pp~~~p~~~G---~k~-~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~ 264 (571)
.++..- ..+++ ..+ ...++.|| .+-+|-|||.+|+.||.|.++|||+|+|-+. .+=
T Consensus 120 ~~d~~~------~~d~~~~~~~~~v~~RLlVp------~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~---~lP----- 179 (485)
T KOG2190|consen 120 EEDDEA------AEDNGEDASGPEVTCRLLVP------SSQVGSLIGKGGSLIKEIREETGAKIRVSSD---MLP----- 179 (485)
T ss_pred cccccc------cccCCccccCCceEEEEEec------hhheeeeeccCcHHHHHHHHhcCceEEecCC---CCC-----
Confidence 322110 01111 234 45777776 4469999999999999999999999999985 221
Q ss_pred CCCCCcEEEEEeCCHHHHHHHHHHHHHHH
Q 008284 265 EVHQPLHLFLSSNNPKSLEEAKRLAENLL 293 (571)
Q Consensus 265 EsdEPLHV~Isa~~~e~v~kAk~LiEnLL 293 (571)
...|.+ |-|+ .+++.+.+|-..|-.+|
T Consensus 180 ~ster~-V~Is-G~~~av~~al~~Is~~L 206 (485)
T KOG2190|consen 180 NSTERA-VTIS-GEPDAVKKALVQISSRL 206 (485)
T ss_pred ccccee-EEEc-CchHHHHHHHHHHHHHH
Confidence 223334 5554 56666766655444443
No 30
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.59 E-value=0.0025 Score=74.43 Aligned_cols=100 Identities=17% Similarity=0.221 Sum_probs=72.0
Q ss_pred eEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcE-EEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHH
Q 008284 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNETGAT-VLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLA 289 (571)
Q Consensus 211 eKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaK-V~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~Li 289 (571)
+.+-|+.+ -+|.||||+|.+||.|++|||++ |-|+ |.-+|.|.+.+.+.+++|+++|
T Consensus 687 ~~~~i~~~------ki~~vIG~GGktIk~I~eetg~~~Idi~----------------ddg~V~I~a~d~~~i~~A~~~I 744 (891)
T PLN00207 687 HIMKVKPE------KVNMIIGSGGKKVKSIIEETGVEAIDTQ----------------DDGTVKITAKDLSSLEKSKAII 744 (891)
T ss_pred EEEEcCHH------HHHHHhcCCchhHHHHHHHHCCCccCcC----------------CCeeEEEEeCCHHHHHHHHHHH
Confidence 45556533 48999999999999999999998 6554 3479999999999999999999
Q ss_pred HHHHHHHHHHhccccccccccccCCCCchhhhccccCCCCccccCccccceecccccc
Q 008284 290 ENLLDTISAECGASRVSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNL 347 (571)
Q Consensus 290 EnLL~tV~eEy~a~r~~~~~~y~avpppqqll~gv~~s~~~~~~~~~~~~~~~~~~~~ 347 (571)
++|.... ...+.|. .--+.++..+|+.-.+... .-||.|--.+
T Consensus 745 ~~l~~~~---------~vG~iy~-----~g~V~~I~~FGaFVeL~~g-~EGLVHISeL 787 (891)
T PLN00207 745 SSLTMVP---------TVGDIYR-----NCEIKSIAPYGAFVEIAPG-REGLCHISEL 787 (891)
T ss_pred HHHhcCc---------CCCcEEE-----CcEEEEEeccEEEEEeCCC-CEEEEEhhhc
Confidence 9998621 1123431 0125677788855555443 5777775544
No 31
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.61 E-value=0.014 Score=66.45 Aligned_cols=92 Identities=18% Similarity=0.250 Sum_probs=65.9
Q ss_pred ceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhccc
Q 008284 224 NIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECGAS 303 (571)
Q Consensus 224 NfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy~a~ 303 (571)
+-++.+|||+|.++|.|++|||++|-|+ |.-+|.|.+.+.+.+++|+++|+.|....+
T Consensus 563 ~kI~~vIG~gg~~ik~I~~~~~~~idi~----------------d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~------ 620 (693)
T PRK11824 563 DKIRDVIGPGGKTIREITEETGAKIDIE----------------DDGTVKIAATDGEAAEAAKERIEGITAEPE------ 620 (693)
T ss_pred HHHHHHhcCCchhHHHHHHHHCCccccC----------------CCceEEEEcccHHHHHHHHHHHHHhcccCc------
Confidence 3488999999999999999999987763 236799999999999999999999984311
Q ss_pred cccccccccCCCCchhhhccccCCCCccccCccccceecccccc
Q 008284 304 RVSSCKVYNAVPPPQQLLTGIQGFGNEQKLNAGSAVILTSTVNL 347 (571)
Q Consensus 304 r~~~~~~y~avpppqqll~gv~~s~~~~~~~~~~~~~~~~~~~~ 347 (571)
..+.|. -.+.++..+|..-.+.. ...|+.|--++
T Consensus 621 ---vG~v~~------G~V~~I~~fGafVei~~-~~~GllhiSel 654 (693)
T PRK11824 621 ---VGEIYE------GKVVRIVDFGAFVEILP-GKDGLVHISEI 654 (693)
T ss_pred ---CCeEEE------EEEEEEECCeEEEEECC-CCEEEEEeeec
Confidence 122221 23666677775444433 35666665444
No 32
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.49 E-value=0.02 Score=57.26 Aligned_cols=54 Identities=19% Similarity=0.337 Sum_probs=47.4
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 008284 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 294 (571)
Q Consensus 225 fvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~ 294 (571)
+++++|||+|.+++.|.++|||+|.| |. .=+|+|.+.+.+.+++|+++|++|-.
T Consensus 155 ~i~~lig~~g~~i~~l~~~~~~~I~i-g~---------------NG~VwI~~~~~~~~~~a~~~I~~~e~ 208 (235)
T PRK04163 155 KVPRVIGKKGSMINMLKEETGCDIIV-GQ---------------NGRIWIKGPDEEDEEIAIEAIKKIER 208 (235)
T ss_pred HHHhhcCCCChhHhhhhhhhCcEEEE-cC---------------CcEEEEeeCCHHHHHHHHHHHHHHHh
Confidence 58999999999999999999999988 21 14799999999999999999997644
No 33
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=95.44 E-value=0.07 Score=56.93 Aligned_cols=77 Identities=23% Similarity=0.264 Sum_probs=54.3
Q ss_pred ceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 008284 209 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 288 (571)
Q Consensus 209 ~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~L 288 (571)
..-||.|| .+ .+|-|||.+|++|..+|+||||||++- |-+-|.-+.+ -.||+...+-+.|..--++
T Consensus 39 y~ikvLip-----s~-AaGsIIGKGG~ti~~lqk~tgariklS-ks~dfyPGTT-------eRvcli~Gt~eai~av~ef 104 (402)
T KOG2191|consen 39 YFLKVLIP-----SY-AAGSIIGKGGQTIVQLQKETGARIKLS-KSKDFYPGTT-------ERVCLIQGTVEALNAVHEF 104 (402)
T ss_pred eEEEEEee-----cc-cccceeccchHHHHHHHhccCcEEEec-cccccCCCcc-------ceEEEEeccHHHHHHHHHH
Confidence 55788887 33 799999999999999999999999996 4444433322 2577777777777665555
Q ss_pred HHHHHHHHHHHhcc
Q 008284 289 AENLLDTISAECGA 302 (571)
Q Consensus 289 iEnLL~tV~eEy~a 302 (571)
| ++.|+++.+.
T Consensus 105 I---~dKire~p~~ 115 (402)
T KOG2191|consen 105 I---ADKIREKPQA 115 (402)
T ss_pred H---HHHHHHhHHh
Confidence 4 4555555443
No 34
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=95.12 E-value=0.023 Score=59.37 Aligned_cols=58 Identities=21% Similarity=0.340 Sum_probs=47.6
Q ss_pred eeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhc
Q 008284 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECG 301 (571)
Q Consensus 226 vGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy~ 301 (571)
+.|+|||+|+|+|.||--|.|-|.+.|. .|++.|+ ..+|+++++++++.+.+||-=|+
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilVqG~-----------------TVsaiGp-fkGlkevr~IV~DcM~NiHPiY~ 217 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILVQGN-----------------TVSAIGP-FKGLKEVRKIVEDCMKNIHPIYN 217 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEeeCc-----------------EEEeecC-cchHHHHHHHHHHHHhccchHHH
Confidence 6799999999999999999999999993 2444443 46899999999999988875443
No 35
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=93.83 E-value=0.1 Score=55.51 Aligned_cols=64 Identities=11% Similarity=0.132 Sum_probs=55.1
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHh
Q 008284 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 300 (571)
Q Consensus 225 fvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy 300 (571)
|.|.|||-+|.|.|+|++||+|+|.|=-.+. .--|+-|++...+.|.+|.+-|+-||++++..|
T Consensus 67 ~~~~lig~~g~trkkle~Etq~~i~lp~p~~------------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~s~ 130 (345)
T KOG2814|consen 67 FIGWLIGKQGKTRKKLEEETQTNIFLPRPNT------------NKEEIKIIGISRNCVIQALERIAKLIDSDRKSF 130 (345)
T ss_pred HhhhhhcccchHHHHHHHhhccceEccCCCC------------CcceEEEeehhHHHHHHHHHHHHHHHHhhhhcC
Confidence 6899999999999999999999998854321 224899999999999999999999999998443
No 36
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=93.23 E-value=0.22 Score=56.45 Aligned_cols=55 Identities=22% Similarity=0.286 Sum_probs=47.1
Q ss_pred eeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q 008284 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTIS 297 (571)
Q Consensus 226 vGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~ 297 (571)
+..+|||+|-.+|+|+.|||+.-++ +.=|+-|-+.++..+++||++|+.++..-+
T Consensus 608 ~~~lIGp~G~~~kki~~EtGai~~v-----------------De~t~~i~A~~~~am~~Ak~~I~~i~~~~~ 662 (760)
T KOG1067|consen 608 RATLIGPGGVLKKKIEVETGAISQV-----------------DEGTFSIFAPTQAAMEEAKEFIDGIIKDDQ 662 (760)
T ss_pred hheeecCccceeeeEeeeccceeee-----------------cCceEEEEecCHHHHHHHHHHHHHHhcCcc
Confidence 6789999999999999999954333 335999999999999999999999987644
No 37
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=92.91 E-value=0.11 Score=59.50 Aligned_cols=53 Identities=23% Similarity=0.379 Sum_probs=46.9
Q ss_pred eeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 008284 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 294 (571)
Q Consensus 226 vGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~ 294 (571)
++.+|||+|.+++.|..||||+|.|.-.| -|.|.+.+.+...+|+++|+++..
T Consensus 563 I~dvIG~gGk~I~~I~eetg~~IdieddG----------------tv~i~~s~~~~~~~ak~~I~~i~~ 615 (692)
T COG1185 563 IRDVIGPGGKTIKAITEETGVKIDIEDDG----------------TVKIAASDGESAKKAKERIEAITR 615 (692)
T ss_pred HhhccCCcccchhhhhhhhCcEEEecCCC----------------cEEEEecchHHHHHHHHHHHHHHh
Confidence 67899999999999999999999996433 367889999999999999999983
No 38
>PRK00106 hypothetical protein; Provisional
Probab=92.81 E-value=0.22 Score=55.90 Aligned_cols=60 Identities=27% Similarity=0.333 Sum_probs=51.6
Q ss_pred CCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 008284 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 294 (571)
Q Consensus 220 ~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~ 294 (571)
.|+=.+.|||||-.|.|++.+|.-||+.|.|- |.|--|.|+|-||-.-+-|+.-.|.||.
T Consensus 231 lp~demkGriIGreGrNir~~E~~tGvdliid---------------dtp~~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 231 LPDDNMKGRIIGREGRNIRTLESLTGIDVIID---------------DTPEVVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred cCChHhhcceeCCCcchHHHHHHHhCceEEEc---------------CCCCeEEEeCCChHHHHHHHHHHHHHHH
Confidence 34556899999999999999999999999884 6778899999999998888877777664
No 39
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=92.77 E-value=0.2 Score=55.66 Aligned_cols=60 Identities=23% Similarity=0.326 Sum_probs=50.7
Q ss_pred CCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHH
Q 008284 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLD 294 (571)
Q Consensus 220 ~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~ 294 (571)
.|+=.+.|||||-.|-|++.+|.-||+.|.|- |.|=-|.|+|-|+-.-+-|+.-+|.||.
T Consensus 210 lp~d~~kgriigreGrnir~~e~~tgvd~iid---------------dtp~~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 210 LPNDEMKGRIIGREGRNIRALETLTGVDLIID---------------DTPEAVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred cCChhhhccccCCCcchHHHHHHHhCceEEEc---------------CCCCeEEecCCchHHHHHHHHHHHHHHH
Confidence 34556899999999999999999999999984 5677899999999888888777666664
No 40
>PRK12704 phosphodiesterase; Provisional
Probab=92.50 E-value=0.28 Score=54.66 Aligned_cols=59 Identities=24% Similarity=0.316 Sum_probs=49.3
Q ss_pred CCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHH
Q 008284 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLL 293 (571)
Q Consensus 220 ~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL 293 (571)
.|+=.+.|||||-.|-|++.+|.-||+.|.|- |.|=-|+|||-|+..-+.|+.-++.|+
T Consensus 216 lp~d~mkgriigreGrnir~~e~~tgvd~iid---------------dtp~~v~ls~~~~~rre~a~~~l~~l~ 274 (520)
T PRK12704 216 LPNDEMKGRIIGREGRNIRALETLTGVDLIID---------------DTPEAVILSGFDPIRREIARLALEKLV 274 (520)
T ss_pred cCCchhhcceeCCCcchHHHHHHHhCCeEEEc---------------CCCCeEEEecCChhhHHHHHHHHHHHH
Confidence 34556899999999999999999999999984 567889999999988777776665554
No 41
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=92.46 E-value=0.55 Score=52.22 Aligned_cols=120 Identities=20% Similarity=0.199 Sum_probs=76.3
Q ss_pred ccceeecc-hhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHccCCC
Q 008284 116 SVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAG 194 (571)
Q Consensus 116 ~vRy~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeIeEILKE~P~~ 194 (571)
++-.+|.| |+.+++|.++|||.|-+-+...|.. .|+- +-|.|.. .+|.+|...|-..|.+.+.-
T Consensus 148 q~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~s----ter~--V~IsG~~---------~av~~al~~Is~~L~~~~~~ 212 (485)
T KOG2190|consen 148 QVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNS----TERA--VTISGEP---------DAVKKALVQISSRLLENPPR 212 (485)
T ss_pred heeeeeccCcHHHHHHHHhcCceEEecCCCCCcc----ccee--EEEcCch---------HHHHHHHHHHHHHHHhcCCc
Confidence 46677877 8999999999999998876644433 3444 7888875 37888999999888885321
Q ss_pred CCc-----ccc-c--cCCC-----------------cccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEE
Q 008284 195 FPT-----LQT-V--MGNG-----------------VQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVL 249 (571)
Q Consensus 195 ~pp-----~~~-p--~~~G-----------------~k~~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~ 249 (571)
.++ ..| | ...+ .....++..+-+ ..|. ..++.|+|.+|..++.|+.++|+-|.
T Consensus 213 ~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~-~~p~-~~~~~v~g~~~~~i~~l~~~~~~~i~ 290 (485)
T KOG2190|consen 213 SPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKL-ICPS-DKVGSVIGKGGLVIRALRNETGASIS 290 (485)
T ss_pred CCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhh-cCch-hhceeeecCCCccchhhhhhcCCceE
Confidence 111 101 0 0000 011111111000 0111 24789999999999999999998887
Q ss_pred Eee
Q 008284 250 LRG 252 (571)
Q Consensus 250 IRG 252 (571)
+.=
T Consensus 291 v~~ 293 (485)
T KOG2190|consen 291 VGD 293 (485)
T ss_pred ecc
Confidence 654
No 42
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=90.75 E-value=0.42 Score=52.88 Aligned_cols=63 Identities=14% Similarity=0.136 Sum_probs=46.2
Q ss_pred CceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCC-HHHHHHHHHHHHHHHHHHHHHhc
Q 008284 223 LNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNN-PKSLEEAKRLAENLLDTISAECG 301 (571)
Q Consensus 223 FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~-~e~v~kAk~LiEnLL~tV~eEy~ 301 (571)
-+++|++||-+|+.||+||+.|.++|+|-- +.+-+.|+-.- .+.-.+|+.-|+++++...+ |+
T Consensus 55 s~mvg~vigrggskik~iq~~tnt~iqii~---------------~~~e~kv~ifg~~~m~~kaka~id~~~~k~e~-yn 118 (629)
T KOG0336|consen 55 SEMVGKVIGRGGSKIKRIQNDTNTRIQIIK---------------CDLEVKVTIFGINHMRKKAKASIDRGQDKDER-YN 118 (629)
T ss_pred hhhhheeeccCcchhhhhhcccceeEEEec---------------cCceeEEEEechHHHHHHHHhhHhhhhhhhhh-cc
Confidence 468999999999999999999999999863 22334444332 33446788888888877554 54
No 43
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=90.20 E-value=0.75 Score=48.37 Aligned_cols=65 Identities=20% Similarity=0.338 Sum_probs=51.3
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHh
Q 008284 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAEC 300 (571)
Q Consensus 225 fvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy 300 (571)
+-|-|||-+|.-+|+|..|+||.|.|-- +.+|. +-.+.+.-.+.++++.|.-|.+|-+..-++.|
T Consensus 325 lggsiigkggqri~~ir~esGA~Ikide-------pleGs----edrIitItGTqdQIqnAQYLlQn~Vkq~rerf 389 (390)
T KOG2192|consen 325 LGGSIIGKGGQRIKQIRHESGASIKIDE-------PLEGS----EDRIITITGTQDQIQNAQYLLQNSVKQYRERF 389 (390)
T ss_pred cCcceecccchhhhhhhhccCceEEecC-------cCCCC----CceEEEEeccHHHHhhHHHHHHHHHHhhhccc
Confidence 5678999999999999999999998752 33332 24667777899999999999999887555544
No 44
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=88.06 E-value=1.7 Score=35.04 Aligned_cols=57 Identities=21% Similarity=0.238 Sum_probs=42.1
Q ss_pred EEEEcCCCCcccceeecc-hhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHH
Q 008284 106 REIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (571)
Q Consensus 106 aEIEINDlPq~vRy~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeI 184 (571)
..|.|..- .++.++.+ |+++.+|+++|||.|..- . +. .+.|.|.+. .++++|+.+|
T Consensus 4 ~~i~Ip~~--~ig~iIGkgG~~ik~I~~~tg~~I~i~-----~------~g--~v~I~G~~~--------~~v~~A~~~I 60 (61)
T cd02393 4 ETMKIPPD--KIRDVIGPGGKTIKKIIEETGVKIDIE-----D------DG--TVYIAASDK--------EAAEKAKKMI 60 (61)
T ss_pred EEEEeChh--heeeeECCCchHHHHHHHHHCCEEEeC-----C------CC--EEEEEeCCH--------HHHHHHHHHh
Confidence 35666544 47888877 999999999999998642 1 11 478999854 5788888877
Q ss_pred H
Q 008284 185 E 185 (571)
Q Consensus 185 e 185 (571)
+
T Consensus 61 ~ 61 (61)
T cd02393 61 E 61 (61)
T ss_pred C
Confidence 3
No 45
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=87.93 E-value=1.4 Score=45.65 Aligned_cols=73 Identities=18% Similarity=0.241 Sum_probs=52.8
Q ss_pred ceeecchhHHHHHHhHhCCeEeecccccCCCC------CC-C----CCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHH
Q 008284 118 RYKLTKRHTQEEIQKCTGAVVITRGKYRLPNA------PP-D----GEKPLYLHISAGAHLKETAERILAVDHAAAMVEE 186 (571)
Q Consensus 118 Ry~LTKg~Tq~eIqe~TGA~VtTRGrYyPPgk------~~-~----~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeIeE 186 (571)
|.+==||.|+++++++|||.|.+||+--=-.+ +. + =+.||+++|+...- .+.++ ..+..|+++|++
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 55556799999999999999999987643321 11 1 27899999998753 32222 468889999999
Q ss_pred HHHccCC
Q 008284 187 MLKQGHA 193 (571)
Q Consensus 187 ILKE~P~ 193 (571)
+|.-...
T Consensus 188 lL~P~~e 194 (259)
T KOG1588|consen 188 LLVPDHE 194 (259)
T ss_pred hcCCCCC
Confidence 9876543
No 46
>PRK12705 hypothetical protein; Provisional
Probab=83.35 E-value=1.1 Score=50.08 Aligned_cols=58 Identities=28% Similarity=0.307 Sum_probs=42.4
Q ss_pred CCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHH
Q 008284 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENL 292 (571)
Q Consensus 220 ~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnL 292 (571)
.|+=.+.|||||-.|.|++.+|..||+.|.|-- -|=-|.|++-++..-+.|+...++|
T Consensus 204 lp~demkGriIGreGrNir~~E~~tGvdliidd---------------tp~~V~ls~fdp~rreia~~~l~~L 261 (508)
T PRK12705 204 IPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD---------------TPEAVVISSFNPIRREIARLTLEKL 261 (508)
T ss_pred cCChHhhccccCccchhHHHHHHhhCCceEecC---------------CccchhhcccCccchHHHHHHHHHH
Confidence 456668999999999999999999999988752 3333666666666655555444444
No 47
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=82.86 E-value=7.7 Score=41.14 Aligned_cols=134 Identities=16% Similarity=0.168 Sum_probs=81.4
Q ss_pred cceeecc-hhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHccCCCC
Q 008284 117 VRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGF 195 (571)
Q Consensus 117 vRy~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeIeEILKE~P~~~ 195 (571)
+.-.+.| |+.++.+....+|.|.+--. .-+--.|+|+++-+ -|-+..++|---|.++....
T Consensus 59 agavigkgg~nik~lr~d~na~v~vpds---------~~peri~tisad~~---------ti~~ilk~iip~lee~f~~~ 120 (390)
T KOG2192|consen 59 AGAVIGKGGKNIKALRTDYNASVSVPDS---------SGPERILTISADIE---------TIGEILKKIIPTLEEGFQLP 120 (390)
T ss_pred ccceeccccccHHHHhhhccceeeccCC---------CCCceeEEEeccHH---------HHHHHHHHHhhhhhhCCCCC
Confidence 3444555 67788888888888765321 22334567887642 23333333333344544433
Q ss_pred CccccccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEE
Q 008284 196 PTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLS 275 (571)
Q Consensus 196 pp~~~p~~~G~k~~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Is 275 (571)
++ .+-++.|- -.+.|-|||-+|+-+|.+.+.+.||+-|= -|-+.+ --..|+|+
T Consensus 121 ~p-----------ce~rllih------qs~ag~iigrngskikelrekcsarlkif------t~c~p~----stdrv~l~ 173 (390)
T KOG2192|consen 121 SP-----------CELRLLIH------QSLAGGIIGRNGSKIKELREKCSARLKIF------TECCPH----STDRVVLI 173 (390)
T ss_pred Cc-----------hhhhhhhh------hhhccceecccchhHHHHHHhhhhhhhhh------hccCCC----CcceEEEe
Confidence 22 12223221 23689999999999999999998887552 233322 12578999
Q ss_pred eCCHHHHHHHHHHHHHHHHH
Q 008284 276 SNNPKSLEEAKRLAENLLDT 295 (571)
Q Consensus 276 a~~~e~v~kAk~LiEnLL~t 295 (571)
+..++.|-...+.|-+||..
T Consensus 174 ~g~~k~v~~~i~~il~~i~e 193 (390)
T KOG2192|consen 174 GGKPKRVVECIKIILDLISE 193 (390)
T ss_pred cCCcchHHHHHHHHHHHhhc
Confidence 99999887777777666653
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=82.37 E-value=3.8 Score=32.96 Aligned_cols=53 Identities=26% Similarity=0.268 Sum_probs=36.9
Q ss_pred cceeecc-hhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHH
Q 008284 117 VRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (571)
Q Consensus 117 vRy~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeI 184 (571)
+.+.+.+ |.++++|++.|||.|...-... ..+.++- +.|+|.. +.+++|..+|
T Consensus 11 vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----~~~~~r~--v~I~G~~---------~~v~~A~~~I 64 (65)
T cd02396 11 AGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERV--VTISGKP---------SAVQKALLLI 64 (65)
T ss_pred cCeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceE--EEEEeCH---------HHHHHHHHhh
Confidence 5666655 8999999999999987732111 1334453 6788975 3688888776
No 49
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=80.64 E-value=4.4 Score=31.60 Aligned_cols=50 Identities=22% Similarity=0.219 Sum_probs=37.1
Q ss_pred ccceeecc-hhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHH
Q 008284 116 SVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (571)
Q Consensus 116 ~vRy~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeI 184 (571)
.+.+.+.+ |.++++|++.|||.|..... + ..-.+.|+|.. +.|++|.++|
T Consensus 10 ~~~~iIG~~G~~i~~I~~~t~~~I~i~~~---------~-~~~~v~I~G~~---------~~v~~A~~~I 60 (60)
T PF00013_consen 10 LVGRIIGKKGSNIKEIEEETGVKIQIPDD---------D-ERDIVTISGSP---------EQVEKAKKMI 60 (60)
T ss_dssp HHHHHHTGGGHHHHHHHHHHTSEEEEEST---------T-EEEEEEEEESH---------HHHHHHHHHH
T ss_pred HcCEEECCCCCcHHHhhhhcCeEEEEcCC---------C-CcEEEEEEeCH---------HHHHHHHhhC
Confidence 35677765 99999999999999877432 2 34467889943 4788888776
No 50
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=80.43 E-value=1.5 Score=51.67 Aligned_cols=17 Identities=18% Similarity=0.089 Sum_probs=8.4
Q ss_pred eEeCCCchhHHHHHHhh
Q 008284 228 RIRGPNDQYINHIMNET 244 (571)
Q Consensus 228 rIIGPrGstlK~Iq~ET 244 (571)
+|+|....+-|-+++-|
T Consensus 262 ciV~ee~~~ekvl~aiT 278 (1102)
T KOG1924|consen 262 CIVGEENGLEKVLEAIT 278 (1102)
T ss_pred heeehhhHHHHHHHHHH
Confidence 34444444555555544
No 51
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=78.56 E-value=2.1 Score=34.55 Aligned_cols=27 Identities=11% Similarity=0.084 Sum_probs=24.2
Q ss_pred ceeeeEeCCCchhHHHHHHhhCcEEEE
Q 008284 224 NIAARIRGPNDQYINHIMNETGATVLL 250 (571)
Q Consensus 224 NfvGrIIGPrGstlK~Iq~ETGaKV~I 250 (571)
.-+|+.||.+|.+++.++..+|.+|-|
T Consensus 34 ~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 34 DQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred ccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 348999999999999999999988865
No 52
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=75.97 E-value=6 Score=42.61 Aligned_cols=110 Identities=16% Similarity=0.173 Sum_probs=68.4
Q ss_pred eeecchhHHHHHHhHhCCeEee--cccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHccCCCCC
Q 008284 119 YKLTKRHTQEEIQKCTGAVVIT--RGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFP 196 (571)
Q Consensus 119 y~LTKg~Tq~eIqe~TGA~VtT--RGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeIeEILKE~P~~~p 196 (571)
..+-+|.+++.|+.+|.+.|.| || +-|.|. ++|.- ..|++|..+|...-..--...-
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 3455789999999999998765 44 336654 35543 4688888887653211100000
Q ss_pred ccccc-cCCCcc-cceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeec
Q 008284 197 TLQTV-MGNGVQ-AMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGR 253 (571)
Q Consensus 197 p~~~p-~~~G~k-~~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGR 253 (571)
.+... .-++.. ..+.+.|+-+ | +.++|+++||.|.++|+||+.|..-|.--++
T Consensus 99 s~s~Sgg~~~~s~s~qt~sy~sv---P-~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 99 SRSFSGGTNGASASGQTTSYVSV---P-LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred cccccCCCccccccCCCceeeec---c-ceeeeeccccccCccchheecccceEeeecc
Confidence 00011 011112 3356777653 3 7799999999999999999999987765553
No 53
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=73.98 E-value=7.2 Score=30.61 Aligned_cols=58 Identities=17% Similarity=0.194 Sum_probs=39.9
Q ss_pred EEEcCCCCcccceeecc-hhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHH
Q 008284 107 EIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (571)
Q Consensus 107 EIEINDlPq~vRy~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeI 184 (571)
+|.|.. ...++.+.+ |.++.+|++.||+.|..-. .. +.+. .+.|.|.. +.|..|+.+|
T Consensus 3 ~i~Vp~--~~~~~iIG~~G~~i~~i~~~~g~~I~i~~-----~~--~~~~--~v~I~G~~---------~~v~~A~~~i 61 (62)
T cd02394 3 EVEIPK--KLHRFIIGKKGSNIRKIMEETGVKIRFPD-----PG--SKSD--TITITGPK---------ENVEKAKEEI 61 (62)
T ss_pred EEEeCH--HHhhhccCCCCCcHHHHHHHhCCEEEcCC-----CC--CCCC--EEEEEcCH---------HHHHHHHHHh
Confidence 455554 247888876 8999999999999986532 21 2233 45788974 3688887776
No 54
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=73.35 E-value=6.9 Score=40.41 Aligned_cols=30 Identities=17% Similarity=0.399 Sum_probs=26.0
Q ss_pred ceeeeEeCCCchhHHHHHHhhCcEEEEeec
Q 008284 224 NIAARIRGPNDQYINHIMNETGATVLLRGR 253 (571)
Q Consensus 224 NfvGrIIGPrGstlK~Iq~ETGaKV~IRGR 253 (571)
..+-|+||++|+++|.+.++|+|+|.+=--
T Consensus 155 ~kVpRvig~~~sm~~~l~~~~~~~I~VG~N 184 (239)
T COG1097 155 SKVPRVIGKKGSMLNMLKEKTGCEIIVGQN 184 (239)
T ss_pred hhcceEecCCCcHHHHhhhhcCeEEEEecC
Confidence 356689999999999999999999988543
No 55
>smart00322 KH K homology RNA-binding domain.
Probab=71.92 E-value=28 Score=26.02 Aligned_cols=64 Identities=20% Similarity=0.228 Sum_probs=42.4
Q ss_pred EEEEEcCCCCcccceeec-chhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHH
Q 008284 105 AREIVINDSESSVRYKLT-KRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAM 183 (571)
Q Consensus 105 ~aEIEINDlPq~vRy~LT-Kg~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~Avae 183 (571)
..+|.|..- ...+.+. +|.++++|++.+|+.|...+.-. .---+.|.|.. ..+..|...
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 2466664 59999999999999987643111 22336778873 367777777
Q ss_pred HHHHH
Q 008284 184 VEEML 188 (571)
Q Consensus 184 IeEIL 188 (571)
|.+.+
T Consensus 64 i~~~~ 68 (69)
T smart00322 64 ILEIL 68 (69)
T ss_pred HHHHh
Confidence 77764
No 56
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=71.91 E-value=16 Score=28.15 Aligned_cols=60 Identities=23% Similarity=0.268 Sum_probs=39.1
Q ss_pred EEEcCCCCcccceeecc-hhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHH
Q 008284 107 EIVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMV 184 (571)
Q Consensus 107 EIEINDlPq~vRy~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeI 184 (571)
+|.|..- .+++.+.+ |.++.+|++.||+.|...... ....++. +.|.|.. +.+.+|..+|
T Consensus 3 ~i~ip~~--~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~-----~~~~~~~--v~i~G~~---------~~v~~a~~~i 63 (64)
T cd00105 3 RVLVPSS--LVGRIIGKGGSTIKEIREETGAKIKIPDSG-----SGSEERI--VTITGTP---------EAVEKAKELI 63 (64)
T ss_pred EEEEchh--hcceeECCCCHHHHHHHHHHCCEEEEcCCC-----CCCCceE--EEEEcCH---------HHHHHHHHHh
Confidence 4555442 46888855 999999999999998764311 1122333 5777873 3677777665
No 57
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=69.39 E-value=1.9 Score=36.18 Aligned_cols=33 Identities=18% Similarity=0.264 Sum_probs=25.9
Q ss_pred CCCCCceeeeEeCCCchhHHHHHHhh-CcEEEEe
Q 008284 219 ADASLNIAARIRGPNDQYINHIMNET-GATVLLR 251 (571)
Q Consensus 219 ~~P~FNfvGrIIGPrGstlK~Iq~ET-GaKV~IR 251 (571)
..++++.+|.++|.+|..+|.|.+|. |-||.|=
T Consensus 12 ~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 12 GDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp SSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred CCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 35899999999999999999999999 6666554
No 58
>PRK15494 era GTPase Era; Provisional
Probab=67.43 E-value=24 Score=37.03 Aligned_cols=28 Identities=29% Similarity=0.191 Sum_probs=22.7
Q ss_pred ceeeeEeCCCchhHHHH--------HHhhCcEEEEe
Q 008284 224 NIAARIRGPNDQYINHI--------MNETGATVLLR 251 (571)
Q Consensus 224 NfvGrIIGPrGstlK~I--------q~ETGaKV~IR 251 (571)
.-.+.|||.+|..||+| |+-.||||.|+
T Consensus 283 sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 283 SYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred CceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 34788999999999998 55568888765
No 59
>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=67.04 E-value=24 Score=35.36 Aligned_cols=27 Identities=26% Similarity=0.214 Sum_probs=21.7
Q ss_pred eeeeEeCCCchhHHHHH--------HhhCcEEEEe
Q 008284 225 IAARIRGPNDQYINHIM--------NETGATVLLR 251 (571)
Q Consensus 225 fvGrIIGPrGstlK~Iq--------~ETGaKV~IR 251 (571)
-.+.|||.+|.++|+|. +-.||+|.|+
T Consensus 232 ~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l~ 266 (270)
T TIGR00436 232 QKKIIIGKNGSMIKAIGIAARKDILELFDCDVFLE 266 (270)
T ss_pred ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 46889999999999984 4567888764
No 60
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=66.14 E-value=3.1 Score=44.68 Aligned_cols=63 Identities=17% Similarity=0.221 Sum_probs=44.9
Q ss_pred ceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 008284 209 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRL 288 (571)
Q Consensus 209 ~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~L 288 (571)
+.+.+.|| .-|++.|+|++|..+|+|+.+|...|.--- .+ .| -+|+.....+.++.||+-
T Consensus 26 vt~sv~vp------s~~v~~ivg~qg~kikalr~KTqtyi~tPs---------r~---ee--PiF~vTg~~edv~~aRre 85 (394)
T KOG2113|consen 26 VTESVEVP------SEHVAEIVGRQGCKIKALRAKTQTYIKTPS---------RG---EE--PIFPVTGRHEDVRRARRE 85 (394)
T ss_pred cceeeecC------cccceeecccCccccchhhhhhcceeccCC---------CC---CC--CcceeccCchhHHHHhhc
Confidence 34555544 558999999999999999999987663211 11 12 456666677888999887
Q ss_pred HHH
Q 008284 289 AEN 291 (571)
Q Consensus 289 iEn 291 (571)
|+.
T Consensus 86 i~s 88 (394)
T KOG2113|consen 86 IPS 88 (394)
T ss_pred Ccc
Confidence 765
No 61
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=65.46 E-value=6.5 Score=46.62 Aligned_cols=11 Identities=18% Similarity=0.141 Sum_probs=6.3
Q ss_pred CCCCcCCChHH
Q 008284 402 EGIYPQATPLQ 412 (571)
Q Consensus 402 ~~iypqatplq 412 (571)
+|+-|+++--+
T Consensus 440 ~~~DPdf~yr~ 450 (1102)
T KOG1924|consen 440 TGMDPDFKYRF 450 (1102)
T ss_pred CCCCCCcchhh
Confidence 45666666544
No 62
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=63.12 E-value=17 Score=39.49 Aligned_cols=57 Identities=19% Similarity=0.338 Sum_probs=46.4
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH--HHHHHHHHH
Q 008284 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAE--NLLDTISAE 299 (571)
Q Consensus 225 fvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiE--nLL~tV~eE 299 (571)
-.--+.||.|.+++.|++..|+.|.-||. ++.|.+..+ .++.|+.++. .|+..+++.
T Consensus 25 ~~~~l~G~~~~~l~l~e~~~gv~i~~rG~-----------------~~~i~g~~~-~v~~A~~~l~~l~~~~~~~~g 83 (348)
T COG1702 25 ELVALFGPTDTNLSLLEIALGVSIVARGE-----------------AVRIIGARP-LVDVATRVLLTLELLAEVRRG 83 (348)
T ss_pred hhhhhcCCCCccHHHHHHHhCcEEEeCCc-----------------eEEEEechH-HHHHHHHHHhHHHHHHHHhcc
Confidence 34568999999999999999999999993 677777777 8888888887 776666554
No 63
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=60.93 E-value=13 Score=37.35 Aligned_cols=55 Identities=16% Similarity=0.277 Sum_probs=41.6
Q ss_pred eeeEeCCCchhHHHHHHhhCcEEEEeec-CCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHH
Q 008284 226 AARIRGPNDQYINHIMNETGATVLLRGR-GSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENL 292 (571)
Q Consensus 226 vGrIIGPrGstlK~Iq~ETGaKV~IRGR-GSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnL 292 (571)
++.++|..|.+.+.|+..+||+|.|-.+ ||..++.. +. ..|+-.+.+|+++++-+
T Consensus 19 ~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~--~~----------t~Dp~~~~ka~d~VkAI 74 (194)
T COG1094 19 IGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTT--RK----------TEDPLALLKARDVVKAI 74 (194)
T ss_pred heeeecccccchHHHHhhcCeEEEEECCCCeEEEEec--CC----------CCChHHHHHHHHHHHHH
Confidence 7889999999999999999999999876 44444322 11 12677888888887654
No 64
>COG1159 Era GTPase [General function prediction only]
Probab=59.91 E-value=22 Score=37.93 Aligned_cols=42 Identities=21% Similarity=0.361 Sum_probs=28.9
Q ss_pred CCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHH--------HhhCcEEEE
Q 008284 204 NGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIM--------NETGATVLL 250 (571)
Q Consensus 204 ~G~k~~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq--------~ETGaKV~I 250 (571)
.|..+...-|||.=+ .-.|-|||.+|.++|.|- +-.||+|.|
T Consensus 224 ~~~~~I~a~I~Ver~-----sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 224 KGLLKIHATIYVERE-----SQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred CCeEEEEEEEEEecC-----CccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 333455666777633 346789999999999884 445777754
No 65
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=58.70 E-value=7.2 Score=40.08 Aligned_cols=83 Identities=14% Similarity=0.175 Sum_probs=56.6
Q ss_pred CCCCceeEEEEEEcCCCCccc--ceee-cchhHHHHHHhHhCCeEeecccccCCC-CC--------CCCCCCeEEEEeec
Q 008284 97 KVQDELIIAREIVINDSESSV--RYKL-TKRHTQEEIQKCTGAVVITRGKYRLPN-AP--------PDGEKPLYLHISAG 164 (571)
Q Consensus 97 k~~de~~f~aEIEINDlPq~v--Ry~L-TKg~Tq~eIqe~TGA~VtTRGrYyPPg-k~--------~~~EpPLYL~Ieg~ 164 (571)
|..+.+| |.+-++|..+ ..+| -+|.||+++++.|+|.|-.||+|--.. +. ..-+-+|+-+|++.
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 4444554 4556666533 4455 469999999999999999999996653 21 13478899999999
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHcc
Q 008284 165 AHLKETAERILAVDHAAAMVEEMLKQG 191 (571)
Q Consensus 165 Te~kdt~ERikaVd~AvaeIeEILKE~ 191 (571)
++. .+.+++..+..+|.++
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 3455555555555554
No 66
>PF13014 KH_3: KH domain
Probab=53.91 E-value=14 Score=27.47 Aligned_cols=24 Identities=33% Similarity=0.303 Sum_probs=20.1
Q ss_pred cceeecc-hhHHHHHHhHhCCeEee
Q 008284 117 VRYKLTK-RHTQEEIQKCTGAVVIT 140 (571)
Q Consensus 117 vRy~LTK-g~Tq~eIqe~TGA~VtT 140 (571)
+++++-+ |.++++|+++|||.|..
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 4667755 99999999999999865
No 67
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=53.37 E-value=32 Score=40.63 Aligned_cols=108 Identities=17% Similarity=0.176 Sum_probs=73.0
Q ss_pred EEcCCCCcccceeecc-hhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHH
Q 008284 108 IVINDSESSVRYKLTK-RHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEE 186 (571)
Q Consensus 108 IEINDlPq~vRy~LTK-g~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeIeE 186 (571)
|..+=+++..++.+.| +..+..|.+++++.+..+- ....+++.+++-... .+..|++.|+.
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 3344456678888877 6669999999999864321 234567776653332 36666777777
Q ss_pred HHHccCCCCCccccccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeec
Q 008284 187 MLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGR 253 (571)
Q Consensus 187 ILKE~P~~~pp~~~p~~~G~k~~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGR 253 (571)
+..+.++.. ..+.++||-+ ..++|||.+|..++.|+.++|| |.|+..
T Consensus 411 ~~~ei~n~~-------------~~~~~~iP~k------~~~~iig~~g~~i~~I~~k~~~-v~i~f~ 457 (753)
T KOG2208|consen 411 IIAEILNSI-------------VKEEVQIPTK------SHKRIIGTKGALINYIMGKHGG-VHIKFQ 457 (753)
T ss_pred HHHhhhccc-------------ccceeecCcc------chhhhhccccccHHHHHhhcCc-EEEecC
Confidence 776655431 1234556532 5789999999999999999997 666654
No 68
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=53.27 E-value=12 Score=28.75 Aligned_cols=23 Identities=13% Similarity=0.127 Sum_probs=20.2
Q ss_pred eeeEeCCCchhHHHHHHhhCcEE
Q 008284 226 AARIRGPNDQYINHIMNETGATV 248 (571)
Q Consensus 226 vGrIIGPrGstlK~Iq~ETGaKV 248 (571)
.|++||.+|.+++.|+..++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 57899999999999999998544
No 69
>PRK00089 era GTPase Era; Reviewed
Probab=43.48 E-value=24 Score=35.46 Aligned_cols=38 Identities=18% Similarity=0.344 Sum_probs=27.1
Q ss_pred ceeEEEecCCCCCCCceeeeEeCCCchhHHHH--------HHhhCcEEEEe
Q 008284 209 MSTSVFLGFDADASLNIAARIRGPNDQYINHI--------MNETGATVLLR 251 (571)
Q Consensus 209 ~qeKIyIpld~~P~FNfvGrIIGPrGstlK~I--------q~ETGaKV~IR 251 (571)
....|||.-+. -.+.|||.+|.+||+| ++-.||+|.|.
T Consensus 226 i~~~i~v~~~~-----~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 226 IEATIYVERDS-----QKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEccCC-----ceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 44555555332 3788999999999988 55568888765
No 70
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=43.30 E-value=21 Score=43.42 Aligned_cols=74 Identities=18% Similarity=0.152 Sum_probs=54.3
Q ss_pred CCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHH
Q 008284 217 FDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDT 295 (571)
Q Consensus 217 ld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~t 295 (571)
+..+|.- .+.+|.+--- +.+|...++|.|..||+-=-.. ..-...++-||++|.+.+.-.|+.|++.++.+|..
T Consensus 904 inD~Pq~-~r~~vt~~~~--L~~i~e~~~~~it~rg~f~~~g--k~p~~gErklyl~ve~~~e~~vqra~~e~~r~l~e 977 (997)
T KOG0334|consen 904 INDFPQN-ARWRVTYKEA--LLRISEPTAAGITTRGKFNPPG--KEPKPGERKLYLLVEGPDELSVQRAIEELERLLEE 977 (997)
T ss_pred ccccchh-cceeeechhh--hhhccCccccceeeccccCCCC--CCCCCcchhhhhhhhcchhHHHHHHHHHHHHHHHH
Confidence 3445543 7777777554 9999999999999999732211 11122456699999999999999999988886654
No 71
>KOG1925 consensus Rac1 GTPase effector FHOS [Signal transduction mechanisms; Cytoskeleton]
Probab=40.98 E-value=20 Score=40.99 Aligned_cols=19 Identities=53% Similarity=1.263 Sum_probs=13.6
Q ss_pred CCCCCCCCCCC-CCCCCCCC
Q 008284 510 NGMPHPPPRNM-PPPPPPKF 528 (571)
Q Consensus 510 ~~mppp~~~~m-ppp~ppkf 528 (571)
.|.|||||+.. ||||||--
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=40.24 E-value=28 Score=31.48 Aligned_cols=12 Identities=42% Similarity=0.808 Sum_probs=4.7
Q ss_pred CCCCCCCCCCCC
Q 008284 512 MPHPPPRNMPPP 523 (571)
Q Consensus 512 mppp~~~~mppp 523 (571)
+|+|+|..||+|
T Consensus 17 pP~P~PpPpPpp 28 (94)
T PHA01732 17 PPAPVPPPPPAP 28 (94)
T ss_pred CCCCCCCCCCCC
Confidence 333444444333
No 73
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=38.48 E-value=24 Score=33.26 Aligned_cols=28 Identities=11% Similarity=0.136 Sum_probs=25.3
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEee
Q 008284 225 IAARIRGPNDQYINHIMNETGATVLLRG 252 (571)
Q Consensus 225 fvGrIIGPrGstlK~Iq~ETGaKV~IRG 252 (571)
-+|..||.+|+.+|.|++..|-||-|=.
T Consensus 42 ~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 42 DMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CccccCCcCchHHHHHHHHhCCceEEEE
Confidence 5899999999999999999998887765
No 74
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=37.26 E-value=39 Score=39.93 Aligned_cols=30 Identities=23% Similarity=0.286 Sum_probs=26.4
Q ss_pred eeeEeCCCchhHHHHHHhhCcEEEEeecCC
Q 008284 226 AARIRGPNDQYINHIMNETGATVLLRGRGS 255 (571)
Q Consensus 226 vGrIIGPrGstlK~Iq~ETGaKV~IRGRGS 255 (571)
..-|+|.+|.++.+|++++.|+|.++=.|+
T Consensus 358 ~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~ 387 (753)
T KOG2208|consen 358 LKFVIGKKGANIEKIREESQVKIDLPKQGS 387 (753)
T ss_pred hhhhcCCCCccHHHHHHhhhhceecccccC
Confidence 667999999999999999999999985443
No 75
>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]
Probab=35.51 E-value=42 Score=39.97 Aligned_cols=15 Identities=33% Similarity=0.377 Sum_probs=7.2
Q ss_pred cccceeecccCCCCC
Q 008284 487 SANLDVRNVSNMPPP 501 (571)
Q Consensus 487 ~~~~~v~~~~~~p~p 501 (571)
++...++++-+.|+|
T Consensus 270 sA~~s~~~S~s~ppp 284 (830)
T KOG1923|consen 270 SACDSQPGSGSGPPP 284 (830)
T ss_pred hhcccCCCCCCCCCC
Confidence 444555555555333
No 76
>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=35.49 E-value=6.3 Score=34.81 Aligned_cols=32 Identities=22% Similarity=0.351 Sum_probs=24.1
Q ss_pred cCCCCcccceeec-----chhHHHHHHhHhCCeEee--ccc
Q 008284 110 INDSESSVRYKLT-----KRHTQEEIQKCTGAVVIT--RGK 143 (571)
Q Consensus 110 INDlPq~vRy~LT-----Kg~Tq~eIqe~TGA~VtT--RGr 143 (571)
|+++- .||.|- +|.+|.+|.+.+|+++.| ||.
T Consensus 32 ~~~l~--~R~~va~~lL~~g~syreIa~~tgvS~aTItRvs 70 (87)
T PF01371_consen 32 LEALA--QRWQVAKELLDEGKSYREIAEETGVSIATITRVS 70 (87)
T ss_dssp HHHHH--HHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHH
T ss_pred HHHHH--HHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHH
Confidence 44443 577554 489999999999999876 764
No 77
>PRK01064 hypothetical protein; Provisional
Probab=34.98 E-value=27 Score=30.33 Aligned_cols=19 Identities=21% Similarity=0.235 Sum_probs=17.0
Q ss_pred eeeEeCCCchhHHHHHHhh
Q 008284 226 AARIRGPNDQYINHIMNET 244 (571)
Q Consensus 226 vGrIIGPrGstlK~Iq~ET 244 (571)
.|++||-+|.+++.|+.-.
T Consensus 41 ~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred ceEEECCCCccHHHHHHHH
Confidence 6999999999999998754
No 78
>COG2037 Ftr Formylmethanofuran:tetrahydromethanopterin formyltransferase [Energy production and conversion]
Probab=32.98 E-value=5.3e+02 Score=27.62 Aligned_cols=49 Identities=24% Similarity=0.343 Sum_probs=33.0
Q ss_pred cceeecc---hhHHHHHHhHhCCeEeecc--------cccCCCCCCCCCCCeEEEEeecc
Q 008284 117 VRYKLTK---RHTQEEIQKCTGAVVITRG--------KYRLPNAPPDGEKPLYLHISAGA 165 (571)
Q Consensus 117 vRy~LTK---g~Tq~eIqe~TGA~VtTRG--------rYyPPgk~~~~EpPLYL~Ieg~T 165 (571)
+|.++|- +-...--.+.||.--++-| +|.+|.+-+++.+-.|+.|.=..
T Consensus 21 aRvliTAa~~~~a~~AA~eATg~~~sVi~cpaEaGie~~~~peeTPDGRpG~~iqi~~~~ 80 (297)
T COG2037 21 ARVLITAADKKWAKIAATEATGFGTSVIGCPAEAGIEKYLPPEETPDGRPGAIIQICHPK 80 (297)
T ss_pred EEEEEEccchHHHHHHHHhcccCCceeEeeeccccceeecCcccCCCCCCceEEEEEecc
Confidence 5777765 3334445566665444444 49999888889888888887764
No 79
>PRK01381 Trp operon repressor; Provisional
Probab=32.90 E-value=15 Score=33.51 Aligned_cols=30 Identities=30% Similarity=0.464 Sum_probs=23.3
Q ss_pred cceeecc-----hhHHHHHHhHhCCeEee--cccccC
Q 008284 117 VRYKLTK-----RHTQEEIQKCTGAVVIT--RGKYRL 146 (571)
Q Consensus 117 vRy~LTK-----g~Tq~eIqe~TGA~VtT--RGrYyP 146 (571)
.||.|-+ .-+|.+|.+++|++|+| ||.-+-
T Consensus 43 ~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~L 79 (99)
T PRK01381 43 TRVRIVEELLRGELSQREIKQELGVGIATITRGSNSL 79 (99)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHh
Confidence 5787654 47999999999999876 885543
No 80
>PRK02821 hypothetical protein; Provisional
Probab=31.32 E-value=30 Score=30.02 Aligned_cols=20 Identities=5% Similarity=0.129 Sum_probs=17.4
Q ss_pred eeeEeCCCchhHHHHHHhhC
Q 008284 226 AARIRGPNDQYINHIMNETG 245 (571)
Q Consensus 226 vGrIIGPrGstlK~Iq~ETG 245 (571)
+|||||-+|.+++-|..--.
T Consensus 42 ~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 42 LGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CcceeCCCCchHHHHHHHHH
Confidence 89999999999999976543
No 81
>PRK00468 hypothetical protein; Provisional
Probab=31.05 E-value=31 Score=29.65 Aligned_cols=18 Identities=11% Similarity=0.204 Sum_probs=16.0
Q ss_pred eeeEeCCCchhHHHHHHh
Q 008284 226 AARIRGPNDQYINHIMNE 243 (571)
Q Consensus 226 vGrIIGPrGstlK~Iq~E 243 (571)
+|||||-+|.+++-|..-
T Consensus 41 ~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CcceecCCChhHHHHHHH
Confidence 699999999999988653
No 82
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=29.80 E-value=1.3e+02 Score=29.13 Aligned_cols=58 Identities=12% Similarity=0.178 Sum_probs=45.7
Q ss_pred eeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHH
Q 008284 226 AARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAE 299 (571)
Q Consensus 226 vGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eE 299 (571)
.-.|+.++|..++.|....||+|.+.- +.-.|.|+| +...++.+...+.+++..|+.+
T Consensus 37 ~~LLl~~~~~~L~~l~~~~~~~I~~~~---------------~~~~i~I~g-~k~~~~~i~~~i~~~l~~i~~~ 94 (210)
T PF14611_consen 37 FFLLLTGNGRILENLAARNGAKIEVSR---------------SENRIRITG-TKSTAEYIEASINEILSNIRTE 94 (210)
T ss_pred eeeeecCCchHHHHHHHhcCceEEEec---------------CCcEEEEEc-cHHHHHHHHHHHHHHHhhcEEE
Confidence 458899999999999888899998864 123677777 6777888888888888777654
No 83
>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=29.78 E-value=1.4e+02 Score=28.96 Aligned_cols=94 Identities=12% Similarity=0.105 Sum_probs=55.6
Q ss_pred ceeecchhHHHHHHhHhCCeEeecccccCCCCCCCCCCCeEEEEeeccchhhHHHHHHHHHHHHHHHHHHHHccCCCCCc
Q 008284 118 RYKLTKRHTQEEIQKCTGAVVITRGKYRLPNAPPDGEKPLYLHISAGAHLKETAERILAVDHAAAMVEEMLKQGHAGFPT 197 (571)
Q Consensus 118 Ry~LTKg~Tq~eIqe~TGA~VtTRGrYyPPgk~~~~EpPLYL~Ieg~Te~kdt~ERikaVd~AvaeIeEILKE~P~~~pp 197 (571)
++.+-+++-+.+|.....-.|++|. + +.. + .--++|.++|++++=++-....
T Consensus 19 ~~~~~~~dli~~lAk~lrKRIvvR~----------d-ps~---------l-------~~~e~A~~~I~~ivP~ea~i~d- 70 (145)
T cd02410 19 ELFAEDGDLVKDLAKDLRKRIVIRP----------D-PSV---------L-------KPPEEAIKIILEIVPEEAGITD- 70 (145)
T ss_pred HHHhcccHHHHHHHHHHhceEEEcC----------C-hhh---------c-------CCHHHHHHHHHHhCCCccCcee-
Confidence 4445566777788877777777775 1 111 0 1135577888888533211100
Q ss_pred cccccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEe
Q 008284 198 LQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLR 251 (571)
Q Consensus 198 ~~~p~~~G~k~~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IR 251 (571)
..+.... ..|+|=.+. -|+++|.+|.+++.|-.+||=+-.|.
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 0001111 245554332 47899999999999999999776553
No 84
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=28.12 E-value=36 Score=28.45 Aligned_cols=21 Identities=5% Similarity=0.090 Sum_probs=18.2
Q ss_pred eeeEeCCCchhHHHHHHhhCc
Q 008284 226 AARIRGPNDQYINHIMNETGA 246 (571)
Q Consensus 226 vGrIIGPrGstlK~Iq~ETGa 246 (571)
.|+|||.+|.+++-||--+..
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~ 55 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANL 55 (77)
T ss_pred CCeEECCCCccHHHHHHHHHH
Confidence 589999999999999887653
No 85
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=27.98 E-value=59 Score=35.35 Aligned_cols=40 Identities=18% Similarity=0.363 Sum_probs=32.0
Q ss_pred eEEEecCCCCCCCceeeeEeCCCchhHHHHHHhh-CcEEEEe
Q 008284 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNET-GATVLLR 251 (571)
Q Consensus 211 eKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ET-GaKV~IR 251 (571)
.||-|= -..++++-+|..||++|+.++.|.+|. |=+|-|=
T Consensus 233 tKVAV~-s~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv 273 (362)
T PRK12327 233 TKIAVR-SNNPNVDAKGACVGPKGQRVQNIVSELKGEKIDII 273 (362)
T ss_pred eEEEEE-cCCCCCCchheeECCCChhHHHHHHHhCCCeEEEE
Confidence 566553 246999999999999999999999999 6666443
No 86
>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=27.85 E-value=48 Score=27.20 Aligned_cols=16 Identities=44% Similarity=0.752 Sum_probs=10.5
Q ss_pred ccCCCCCcCCChHHHHH
Q 008284 399 SGYEGIYPQATPLQQVA 415 (571)
Q Consensus 399 ~gy~~iypqatplqqva 415 (571)
.|||+++|+ |+.-++.
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 87
>PF00408 PGM_PMM_IV: Phosphoglucomutase/phosphomannomutase, C-terminal domain; InterPro: IPR005843 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1KFQ_B 1KFI_A 3PDK_B 2F7L_A 1TUO_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=26.39 E-value=1.6e+02 Score=24.08 Aligned_cols=27 Identities=15% Similarity=0.430 Sum_probs=21.7
Q ss_pred CC-cEEEEEeCCHHHHHHHHHHHHHHHH
Q 008284 268 QP-LHLFLSSNNPKSLEEAKRLAENLLD 294 (571)
Q Consensus 268 EP-LHV~Isa~~~e~v~kAk~LiEnLL~ 294 (571)
|| +.|++.+.+.+.+++-++-+.++|.
T Consensus 46 EP~iRv~~Ea~~~~~~~~~~~~i~~~ik 73 (73)
T PF00408_consen 46 EPKIRVYVEAPDEEELEEIAEEIAEAIK 73 (73)
T ss_dssp SSEEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred CceEEEEEEeCCHHHHHHHHHHHHHhhC
Confidence 44 8999999999888887777777663
No 88
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=25.90 E-value=1.3e+02 Score=34.60 Aligned_cols=70 Identities=17% Similarity=0.190 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHccCCCCCccccccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCC
Q 008284 176 AVDHAAAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGS 255 (571)
Q Consensus 176 aVd~AvaeIeEILKE~P~~~pp~~~p~~~G~k~~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGS 255 (571)
....|..+|++.++.-.....+-.+. +. -...|+||-+ .++++||-+|..++.|++..|-+|.++-++.
T Consensus 458 ~~~~a~~~i~~~i~r~~p~~~eVe~~-gd----~~avv~vpe~------~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 458 ALKLAEEEIEREIKRYLPGDVEVEVV-GD----GRAVVKVPEK------YIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred hhHHHHHHHHHHHHHhCCCCceEEEe-cC----CeEEEEeCHH------HhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 34556666666666542211111111 00 1235666643 3678999999999999999999999998654
Q ss_pred C
Q 008284 256 G 256 (571)
Q Consensus 256 g 256 (571)
.
T Consensus 527 ~ 527 (604)
T COG1855 527 E 527 (604)
T ss_pred c
Confidence 3
No 89
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=25.48 E-value=77 Score=34.18 Aligned_cols=39 Identities=21% Similarity=0.325 Sum_probs=31.3
Q ss_pred eEEEecCCCCCCCceeeeEeCCCchhHHHHHHhh-CcEEEE
Q 008284 211 TSVFLGFDADASLNIAARIRGPNDQYINHIMNET-GATVLL 250 (571)
Q Consensus 211 eKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ET-GaKV~I 250 (571)
.||-|-- ..++.+-+|..||++|+.++.|.+|. |=+|-|
T Consensus 231 tKvAV~s-~~~~iDpvga~vG~~G~ri~~i~~el~ge~Idi 270 (341)
T TIGR01953 231 TKIAVES-NDENIDPVGACVGPKGSRIQAISKELNGEKIDI 270 (341)
T ss_pred eEEEEEc-CCCCCCcceeeECCCCchHHHHHHHhCCCeEEE
Confidence 5776543 36999999999999999999999998 545433
No 90
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=24.61 E-value=89 Score=35.31 Aligned_cols=15 Identities=13% Similarity=0.202 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHHHc
Q 008284 176 AVDHAAAMVEEMLKQ 190 (571)
Q Consensus 176 aVd~AvaeIeEILKE 190 (571)
.+++|..+++-++-.
T Consensus 10 RLE~a~~RLE~Isi~ 24 (480)
T KOG2675|consen 10 RLESATSRLEGISIT 24 (480)
T ss_pred HHHHHHHHhhhhhcC
Confidence 366667777776543
No 91
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=23.56 E-value=48 Score=34.18 Aligned_cols=51 Identities=18% Similarity=0.203 Sum_probs=40.2
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHH
Q 008284 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLL 293 (571)
Q Consensus 225 fvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL 293 (571)
.+|||.|.+|.|--.||+-|.+||.|-+ -.+||.| ...+++-|+.-+-+||
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVlad-----------------~kIHiLG-~~~niriAR~avcsLI 229 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIENVTRTRIVLAD-----------------SKIHILG-AFQNIRIARDAVCSLI 229 (252)
T ss_pred HHHHhhcCCCcceeeeeccceeEEEecC-----------------ceEEEee-cchhhHHHHHhhHhhh
Confidence 4899999999999999999999999976 2344554 3566777777766666
No 92
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=22.84 E-value=51 Score=38.01 Aligned_cols=32 Identities=25% Similarity=0.341 Sum_probs=28.5
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEeecCCC
Q 008284 225 IAARIRGPNDQYINHIMNETGATVLLRGRGSG 256 (571)
Q Consensus 225 fvGrIIGPrGstlK~Iq~ETGaKV~IRGRGSg 256 (571)
++-+|+|-.|+++|.|...|++||.|+-.-++
T Consensus 78 ~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g 109 (608)
T KOG2279|consen 78 AVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG 109 (608)
T ss_pred ceeeeeccccCCcchhhcccccceecCcccCC
Confidence 68899999999999999999999999875433
No 93
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=22.75 E-value=21 Score=29.37 Aligned_cols=20 Identities=20% Similarity=0.313 Sum_probs=17.6
Q ss_pred eeeEeCCCchhHHHHHHhhC
Q 008284 226 AARIRGPNDQYINHIMNETG 245 (571)
Q Consensus 226 vGrIIGPrGstlK~Iq~ETG 245 (571)
.|+|||-+|.+++-||--.+
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHH
T ss_pred cceEECCCCeeHHHHHHHHH
Confidence 79999999999999987554
No 94
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=21.96 E-value=55 Score=28.55 Aligned_cols=17 Identities=18% Similarity=0.321 Sum_probs=15.7
Q ss_pred eeeEeCCCchhHHHHHH
Q 008284 226 AARIRGPNDQYINHIMN 242 (571)
Q Consensus 226 vGrIIGPrGstlK~Iq~ 242 (571)
+|+|||-+|.+++-|..
T Consensus 41 ~GkvIGk~GRti~AIRT 57 (76)
T COG1837 41 MGKVIGKQGRTIQAIRT 57 (76)
T ss_pred ccceecCCChhHHHHHH
Confidence 89999999999999975
No 95
>PRK13764 ATPase; Provisional
Probab=21.82 E-value=1.1e+02 Score=35.49 Aligned_cols=69 Identities=16% Similarity=0.178 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHHHccCCCCCccccccCCCcccceeEEEecCCCCCCCceeeeEeCCCchhHHHHHHhhCcEEEEeecCC
Q 008284 176 AVDHAAAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGS 255 (571)
Q Consensus 176 aVd~AvaeIeEILKE~P~~~pp~~~p~~~G~k~~qeKIyIpld~~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRGRGS 255 (571)
....|..+|++.++.-.......+...+ -.-.|||+-+. ++.+||.+|..++.|++..|.+|-||-+.-
T Consensus 453 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~v~~~~~~------~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 453 VWRLAEKEIEREIKRYLPGPVEVEVVSD-----NKAVVYVPEKD------IPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred HHHHHHHHHHHHHHHhcCCceEEEEecC-----CeEEEEEChhh------hhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence 4555566666666553311111111111 12457777443 567899999999999999999999998654
No 96
>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=21.56 E-value=73 Score=30.43 Aligned_cols=28 Identities=11% Similarity=0.141 Sum_probs=24.8
Q ss_pred eeeeEeCCCchhHHHHHHhhCcEEEEee
Q 008284 225 IAARIRGPNDQYINHIMNETGATVLLRG 252 (571)
Q Consensus 225 fvGrIIGPrGstlK~Iq~ETGaKV~IRG 252 (571)
-+|..+|.+|+.+|.|++..|=||-|=.
T Consensus 43 ~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 43 EMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred CccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 5899999999999999988888887665
No 97
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=21.43 E-value=67 Score=32.11 Aligned_cols=33 Identities=9% Similarity=0.142 Sum_probs=27.9
Q ss_pred CCCCceeeeEeCCCchhHHHHHHhhCcEEEEee
Q 008284 220 DASLNIAARIRGPNDQYINHIMNETGATVLLRG 252 (571)
Q Consensus 220 ~P~FNfvGrIIGPrGstlK~Iq~ETGaKV~IRG 252 (571)
..+.+=+|..||++|+.++.|.+|.|=+|-|=-
T Consensus 81 ~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe 113 (190)
T COG0195 81 VVKIDPVGACIGKRGSRVKAVSEELGEKIDVVE 113 (190)
T ss_pred ecCcCchhhhccCCChHHHHHHHHhCCceEEEE
Confidence 357777999999999999999999997775544
No 98
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=21.24 E-value=91 Score=35.77 Aligned_cols=14 Identities=14% Similarity=0.128 Sum_probs=10.2
Q ss_pred CceeEEEEEEcCCC
Q 008284 100 DELIIAREIVINDS 113 (571)
Q Consensus 100 de~~f~aEIEINDl 113 (571)
..+||.+-++|++-
T Consensus 74 ~rsyFlrl~di~~~ 87 (569)
T KOG3671|consen 74 QRSYFLRLVDIVNN 87 (569)
T ss_pred cceeeeEEeeecCc
Confidence 35678888888775
No 99
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=20.02 E-value=3.1e+02 Score=27.41 Aligned_cols=52 Identities=12% Similarity=0.300 Sum_probs=40.0
Q ss_pred hHHHHHHhhC-cEEEEeecCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhc
Q 008284 236 YINHIMNETG-ATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDTISAECG 301 (571)
Q Consensus 236 tlK~Iq~ETG-aKV~IRGRGSg~~E~~~g~EsdEPLHV~Isa~~~e~v~kAk~LiEnLL~tV~eEy~ 301 (571)
+++.|++... .-+.+++||.+ |.|.|.|... .+..|...|.+|+..++..|+
T Consensus 14 fle~l~~~~~~~~~~v~~k~n~-------------l~I~i~G~~~-eike~~~~Ik~~~~~vr~k~~ 66 (190)
T PF09840_consen 14 FLERLSKMVKSIYIYVEVKGNS-------------LKIEIQGYEK-EIKEAIRRIKELVRRVRSKYN 66 (190)
T ss_pred HHHHHHhhccCcEEEEEEeCCE-------------EEEEEecChH-HHHHHHHHHHHHHHHHHHHhc
Confidence 4667766643 34457777633 7888888777 999999999999999999775
Done!