Query 041023
Match_columns 303
No_of_seqs 243 out of 1421
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 03:03:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041023.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041023hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0571 Rnc dsRNA-specific rib 100.0 1.3E-51 2.7E-56 365.0 20.8 212 67-298 7-232 (235)
2 PRK12371 ribonuclease III; Rev 100.0 3.8E-51 8.2E-56 364.8 21.5 215 63-297 7-231 (235)
3 PRK14718 ribonuclease III; Pro 100.0 3.6E-50 7.9E-55 376.8 21.4 212 68-301 3-226 (467)
4 PRK12372 ribonuclease III; Rev 100.0 2E-49 4.3E-54 370.2 21.6 208 68-297 3-222 (413)
5 PRK00102 rnc ribonuclease III; 100.0 9.7E-47 2.1E-51 336.3 20.9 212 66-297 3-228 (229)
6 TIGR02191 RNaseIII ribonucleas 100.0 3.6E-45 7.8E-50 324.1 20.7 205 71-295 2-220 (220)
7 KOG1817 Ribonuclease [RNA proc 100.0 9.3E-43 2E-47 321.4 16.0 258 8-301 229-507 (533)
8 PF14622 Ribonucleas_3_3: Ribo 100.0 1.3E-31 2.9E-36 218.2 7.2 126 80-225 1-127 (128)
9 smart00535 RIBOc Ribonuclease 100.0 2.6E-29 5.5E-34 204.5 12.0 127 82-227 1-127 (129)
10 cd00593 RIBOc RIBOc. Ribonucle 100.0 2.2E-28 4.8E-33 199.6 11.3 128 82-228 1-130 (133)
11 PF00636 Ribonuclease_3: Ribon 99.9 1.2E-24 2.5E-29 173.4 5.9 108 101-208 1-114 (114)
12 KOG3769 Ribonuclease III domai 99.9 3.8E-22 8.2E-27 177.7 16.2 246 34-301 24-307 (333)
13 KOG0701 dsRNA-specific nucleas 99.6 5.7E-16 1.2E-20 165.1 8.6 254 32-298 1319-1599(1606)
14 KOG0701 dsRNA-specific nucleas 99.6 1.4E-15 3E-20 162.2 11.2 155 67-223 980-1181(1606)
15 KOG1817 Ribonuclease [RNA proc 99.6 2.1E-15 4.5E-20 140.6 9.1 135 67-220 42-233 (533)
16 PHA03103 double-strand RNA-bin 99.3 1.3E-11 2.8E-16 104.9 9.6 84 212-297 84-177 (183)
17 PHA02701 ORF020 dsRNA-binding 99.3 1.4E-11 2.9E-16 104.2 9.1 65 232-297 107-177 (183)
18 PF00035 dsrm: Double-stranded 99.2 4.2E-11 9.2E-16 85.7 8.3 60 235-295 1-67 (67)
19 cd00048 DSRM Double-stranded R 99.2 1.1E-10 2.3E-15 83.4 8.1 61 234-295 1-68 (68)
20 smart00358 DSRM Double-strande 99.2 1.3E-10 2.9E-15 82.9 8.2 60 235-295 1-66 (67)
21 PF14709 DND1_DSRM: double str 98.3 1.4E-06 3.1E-11 64.9 5.6 64 233-296 1-80 (80)
22 KOG3732 Staufen and related do 98.3 1.6E-06 3.6E-11 79.7 6.3 65 232-298 141-212 (339)
23 COG1939 Ribonuclease III famil 97.9 0.00011 2.3E-09 58.8 9.8 113 99-223 14-128 (132)
24 KOG3732 Staufen and related do 97.9 3.4E-05 7.4E-10 71.1 7.1 64 233-298 38-107 (339)
25 KOG4334 Uncharacterized conser 96.7 0.0011 2.4E-08 63.9 3.1 59 236-295 378-441 (650)
26 KOG2777 tRNA-specific adenosin 96.4 0.0064 1.4E-07 60.0 6.0 63 232-298 89-155 (542)
27 PF11469 Ribonucleas_3_2: Ribo 91.0 1.8 3.9E-05 33.6 7.8 87 102-224 2-90 (120)
28 PF03368 Dicer_dimer: Dicer di 88.0 2.9 6.3E-05 31.6 7.1 61 236-298 2-74 (90)
29 PF14954 LIX1: Limb expression 63.8 18 0.00039 31.9 5.5 68 232-301 20-99 (252)
30 PF13820 Nucleic_acid_bd: Puta 63.4 1.2 2.6E-05 37.0 -1.7 90 194-290 3-108 (149)
31 KOG2334 tRNA-dihydrouridine sy 57.9 3.8 8.3E-05 39.6 0.4 66 232-297 374-442 (477)
32 PF00352 TBP: Transcription fa 53.1 50 0.0011 24.4 5.7 43 253-298 43-85 (86)
33 KOG0921 Dosage compensation co 47.6 31 0.00068 36.9 5.0 62 234-297 2-70 (1282)
34 cd00652 TBP_TLF TATA box bindi 43.2 73 0.0016 27.1 5.9 44 252-298 40-83 (174)
35 cd04518 TBP_archaea archaeal T 41.0 79 0.0017 26.9 5.8 44 252-298 40-83 (174)
36 cd04516 TBP_eukaryotes eukaryo 40.3 89 0.0019 26.6 6.0 44 252-298 40-83 (174)
37 PF02169 LPP20: LPP20 lipoprot 39.8 44 0.00095 24.5 3.7 27 268-295 12-38 (92)
38 PF08383 Maf_N: Maf N-terminal 36.3 20 0.00044 22.1 1.0 11 192-202 25-35 (35)
39 PLN00062 TATA-box-binding prot 34.2 1.3E+02 0.0028 25.8 6.0 44 252-298 40-83 (179)
40 PRK00394 transcription factor; 34.0 1.1E+02 0.0025 26.1 5.7 44 252-298 39-82 (179)
41 PF07411 DUF1508: Domain of un 34.0 86 0.0019 20.7 3.9 30 266-300 13-42 (49)
42 cd04517 TLF TBP-like factors ( 32.5 1.3E+02 0.0029 25.5 5.9 43 253-298 41-83 (174)
43 PF13936 HTH_38: Helix-turn-he 32.1 49 0.0011 21.2 2.4 33 123-155 2-34 (44)
44 PF04098 Rad52_Rad22: Rad52/22 29.6 2.4E+02 0.0052 23.3 6.8 18 283-300 111-128 (154)
45 PF01418 HTH_6: Helix-turn-hel 29.1 53 0.0011 23.7 2.5 41 115-157 21-64 (77)
46 PF00333 Ribosomal_S5: Ribosom 28.6 82 0.0018 22.4 3.3 36 259-295 23-62 (67)
47 PRK14741 spoVM stage V sporula 27.4 57 0.0012 18.4 1.8 17 187-203 7-23 (26)
48 PF03672 UPF0154: Uncharacteri 25.0 1.7E+02 0.0037 20.7 4.3 32 103-134 5-40 (64)
49 PF11324 DUF3126: Protein of u 24.8 1.6E+02 0.0035 20.7 4.1 38 237-274 3-42 (63)
50 PF14657 Integrase_AP2: AP2-li 23.3 2E+02 0.0044 18.3 4.2 25 271-297 19-43 (46)
51 cd04518 TBP_archaea archaeal T 22.4 2.7E+02 0.0059 23.6 6.0 43 252-297 131-173 (174)
52 PRK01844 hypothetical protein; 20.6 3E+02 0.0064 20.0 4.9 35 103-137 12-50 (72)
No 1
>COG0571 Rnc dsRNA-specific ribonuclease [Transcription]
Probab=100.00 E-value=1.3e-51 Score=365.00 Aligned_cols=212 Identities=35% Similarity=0.503 Sum_probs=192.6
Q ss_pred CccH-HHhcCCccCCHHHHHHhhcCCCCCCC---CCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcChH
Q 041023 67 NLDE-EEILGYRFNNKNLLEEAFTDPSCPER---FFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTE 142 (303)
Q Consensus 67 ~l~~-e~~lgy~F~~~~LL~~AlTh~S~~~~---~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn~ 142 (303)
.+.. ++.+||+|+|++||.+||||+||.+. ..+|||||||||+||+++|+++||++||+.+||.||.+|+.+||+.
T Consensus 7 ~~~~l~~~lg~~f~~~~lL~~AltH~S~~~e~~~~~~nERLEFLGDavL~l~vae~Lf~~yP~~~EG~Ls~~ra~lV~~~ 86 (235)
T COG0571 7 KLEALEKKLGYTFKDKELLEQALTHRSYANEHKAVENNERLEFLGDAVLGLVVAEYLFKKYPNLPEGELSKLRAALVSEE 86 (235)
T ss_pred HHHHHHHHhCCCcCCHHHHHHHhcCcchhccccCCcchHHHHhhHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Confidence 3556 99999999999999999999999752 4689999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcCchhhhhcCCcchHHHHHHHHHHhhcCCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHhh
Q 041023 143 KLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELL 222 (303)
Q Consensus 143 ~La~~a~~~gL~~~i~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ll 222 (303)
+|+.+|..+||++|++.++++. ..+++..++++||+|||+|||||+|+|+ +.+++|+.+++
T Consensus 87 ~La~ia~~l~l~~~l~lg~ge~-----------------~~gg~~~~silaD~~EAligAiylD~g~--~~~~~~i~~l~ 147 (235)
T COG0571 87 SLAEIARELGLGDYLRLGKGEE-----------------KSGGRRRESILADAFEALIGAIYLDSGL--EAARKFILKLF 147 (235)
T ss_pred HHHHHHHHhCccchhhccCChh-----------------hcCCCCchhHHHHHHHHHHHHHHHhCCh--HHHHHHHHHHH
Confidence 9999999999999999998753 1467788999999999999999999997 89999999999
Q ss_pred cccCCCCc---ccCCCccHHHHHHHhCCCcceEEEee-------cceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHH
Q 041023 223 KPMISPET---LKTHPVTELYEVCQKNKLKVKFVDLW-------KESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDAL 292 (303)
Q Consensus 223 ~~~l~~~~---~~~~Pk~~Lqe~~q~~~~~~~~~~~~-------~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL 292 (303)
.|.+.... ...|||++||||+|.+++..|.|++. ++.|+++|.++|..+|+|.|.|+|+ |||.||++||
T Consensus 148 ~~~~~~~~~~~~~~D~Kt~LQe~~q~~~~~~p~Y~~v~~~g~~h~~~F~v~v~v~~~~~g~G~G~skk~-AEq~AA~~al 226 (235)
T COG0571 148 LPRLEEIDAGDQFKDPKTRLQELLQAQGLVLPEYRLVKEEGPAHDKEFTVEVAVGGKELGTGKGRSKKE-AEQAAAEQAL 226 (235)
T ss_pred HHHHhhccccccccChhHHHHHHHHhcCCCCCeEEEeeccCCCCCceEEEEEEECCeeEEEecccCHHH-HHHHHHHHHH
Confidence 99876432 34799999999999999999988764 3468999999999999999999996 9999999999
Q ss_pred HHHHhh
Q 041023 293 NNIERL 298 (303)
Q Consensus 293 ~~l~~~ 298 (303)
+.+...
T Consensus 227 ~~l~~~ 232 (235)
T COG0571 227 KKLGVK 232 (235)
T ss_pred HHhccc
Confidence 998754
No 2
>PRK12371 ribonuclease III; Reviewed
Probab=100.00 E-value=3.8e-51 Score=364.77 Aligned_cols=215 Identities=25% Similarity=0.276 Sum_probs=187.4
Q ss_pred CCcCCccH-HHhcCCccCCHHHHHHhhcCCCCCC-CCCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcC
Q 041023 63 PNANNLDE-EEILGYRFNNKNLLEEAFTDPSCPE-RFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVN 140 (303)
Q Consensus 63 ~~~~~l~~-e~~lgy~F~~~~LL~~AlTh~S~~~-~~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvs 140 (303)
+....+.. |++|||+|+|++||.+||||+|+.. ...+|||||||||+||+++|+++||.+||++++|.||.+|+.+||
T Consensus 7 ~~~~~~~~le~~lgy~F~~~~Ll~~AlTH~S~~~~~~~~~eRLEFLGDavL~l~vs~~Lf~~~p~~~eG~Lt~~rs~lV~ 86 (235)
T PRK12371 7 LAAATASILEERTGHRFANKERLERALTHSSARASKQGNYERLEFLGDRVLGLCVAEMLFEAFPDASEGELSVRLNQLVN 86 (235)
T ss_pred CCHHHHHHHHHHHCCCCCCHHHHHHHHcCcCcccCCccchHhHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhC
Confidence 34456677 9999999999999999999999974 346899999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHcCchhhhhcCCcchHHHHHHHHHHhhcCCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHH
Q 041023 141 TEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKE 220 (303)
Q Consensus 141 n~~La~~a~~~gL~~~i~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ 220 (303)
|.+|+.+|.++||+++|+.+++.. ..+....++++||+|||+|||||+|+|+ +.+++|+..
T Consensus 87 n~~La~ia~~lgL~~~i~~~~~~~-----------------~~~~~~~~~ilad~~EAliGAiylD~G~--~~a~~~i~~ 147 (235)
T PRK12371 87 AETCAAIADEIGLHDLIRTGSDVK-----------------KLTGKRLLNVRADVVEALIAAIYLDGGL--EAARPFIQR 147 (235)
T ss_pred hHHHHHHHHHCCcHHHhccCcchh-----------------hcCCcccchHHHHHHHHHHHHHHHcCCH--HHHHHHHHH
Confidence 999999999999999999876421 1133455799999999999999999998 899999999
Q ss_pred hhcccCCCC-cccCCCccHHHHHHHhCCCcceEEEee-------cceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHH
Q 041023 221 LLKPMISPE-TLKTHPVTELYEVCQKNKLKVKFVDLW-------KESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDAL 292 (303)
Q Consensus 221 ll~~~l~~~-~~~~~Pk~~Lqe~~q~~~~~~~~~~~~-------~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL 292 (303)
++.|.+... ....|||+.||||||+.+...|.|.+. .+.|+|+|+++|..+|+|.|.|||+ ||++||+.||
T Consensus 148 ~~~~~~~~~~~~~~d~Ks~LqE~~q~~~~~~p~Y~~~~~~Gp~h~~~F~v~v~v~~~~~~~g~G~sKK~-Ae~~AA~~al 226 (235)
T PRK12371 148 YWQKRALETDAARRDAKTELQEWAHAQFGVTPVYRVDSRSGPDHDPRFTVEVEVKGFAPETGEGRSKRA-AEQVAAEKML 226 (235)
T ss_pred HHHHHHhccccccCCHHHHHHHHHHhcCCCCCeEEEEEeecCCCCCeEEEEEEECCEEEEEeeeCCHHH-HHHHHHHHHH
Confidence 998876532 346799999999999987766666543 2468999999999999999999996 9999999999
Q ss_pred HHHHh
Q 041023 293 NNIER 297 (303)
Q Consensus 293 ~~l~~ 297 (303)
++++.
T Consensus 227 ~~~~~ 231 (235)
T PRK12371 227 EREGV 231 (235)
T ss_pred HHhhh
Confidence 99864
No 3
>PRK14718 ribonuclease III; Provisional
Probab=100.00 E-value=3.6e-50 Score=376.80 Aligned_cols=212 Identities=31% Similarity=0.400 Sum_probs=188.1
Q ss_pred ccH-HHhcCCccCCHHHHHHhhcCCCCCCCCCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcChHHHHH
Q 041023 68 LDE-EEILGYRFNNKNLLEEAFTDPSCPERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLAR 146 (303)
Q Consensus 68 l~~-e~~lgy~F~~~~LL~~AlTh~S~~~~~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn~~La~ 146 (303)
+.. |++|||+|+|++||.+||||+||.. .+|||||||||+||+++|+++||++||++++|.||.+|+.+|||.+|+.
T Consensus 3 l~~LEkrLGY~Fkn~~LL~eALTH~Sys~--e~NERLEFLGDAVL~liVse~Lf~~fPdl~EGeLT~LRS~LVSnetLA~ 80 (467)
T PRK14718 3 LSQLESRLRYEFRNAELLRQALTHRSHSA--THNERLEFLGDSVLNCAVAALLFQRFGKLDEGDLSRVRANLVKQQSLYE 80 (467)
T ss_pred HHHHHHHhCCCcCCHHHHHHHHhccCcCc--ccHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHhhhHHHHH
Confidence 455 9999999999999999999999975 4899999999999999999999999999999999999999999999999
Q ss_pred HHHHcCchhhhhcCCcchHHHHHHHHHHhhcCCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHhhcccC
Q 041023 147 VAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMI 226 (303)
Q Consensus 147 ~a~~~gL~~~i~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ll~~~l 226 (303)
+|..+||++||+.+.+.. ..+....+++++|+|||||||||+|+|+ +.++.||..+|.|.+
T Consensus 81 IAr~LGL~d~Lrlg~gE~-----------------~sgG~~~~sILADvFEALIGAIYLDsG~--e~a~~fI~~ll~p~i 141 (467)
T PRK14718 81 IAQALNISDGLRLGEGEL-----------------RSGGFRRPSILADAFEAIIGAVFLDGGF--EAAQGVIKRLYVPIL 141 (467)
T ss_pred HHHHcCchHHHhhCCccc-----------------ccCCCCChhHHHHHHHHHHHHHHHccCH--HHHHHHHHHHHHHHH
Confidence 999999999999887532 1244567899999999999999999998 799999999998876
Q ss_pred CCC---cccCCCccHHHHHHHhCCCcceEEEeec-------ceeEEEEEECCE-EEEEEEeccchHHHHHHHHHHHHHHH
Q 041023 227 SPE---TLKTHPVTELYEVCQKNKLKVKFVDLWK-------ESTAFHIFIEDQ-LLGRGAYAPKKEIAHNRAAKDALNNI 295 (303)
Q Consensus 227 ~~~---~~~~~Pk~~Lqe~~q~~~~~~~~~~~~~-------~~~~v~V~i~~~-~ig~G~g~skk~~Ae~~AA~~AL~~l 295 (303)
+.. ....|||+.||||||+++...|.|.+.. ..|+|.|+++|. ..|+|.|.|||+ |||.||++||++|
T Consensus 142 ~~~d~~~~~kDyKS~LQE~~Qk~~~~~PeY~li~esGPdH~k~F~V~V~v~g~~~~G~G~G~SKKe-AEQ~AAk~AL~kL 220 (467)
T PRK14718 142 DHIDPRTLGKDAKTLLQEYLQGHKIALPTYTVVATHGAAHNQQFEVECTVPKLDIKVSGSGASRRA-AEQAAAKKALDEV 220 (467)
T ss_pred hhhcccccccCHHHHHHHHHHhcCCCCCeeEEeeeecCCCCCeEEEEEEECCeeeEEEEEcCCHHH-HHHHHHHHHHHHh
Confidence 532 2457999999999999999888777642 468999999995 559999999996 9999999999999
Q ss_pred Hhhhcc
Q 041023 296 ERLLNE 301 (303)
Q Consensus 296 ~~~~~~ 301 (303)
+..+|-
T Consensus 221 ~~~~~~ 226 (467)
T PRK14718 221 TAVAPM 226 (467)
T ss_pred cccchh
Confidence 876553
No 4
>PRK12372 ribonuclease III; Reviewed
Probab=100.00 E-value=2e-49 Score=370.18 Aligned_cols=208 Identities=31% Similarity=0.408 Sum_probs=185.0
Q ss_pred ccH-HHhcCCccCCHHHHHHhhcCCCCCCCCCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcChHHHHH
Q 041023 68 LDE-EEILGYRFNNKNLLEEAFTDPSCPERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLAR 146 (303)
Q Consensus 68 l~~-e~~lgy~F~~~~LL~~AlTh~S~~~~~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn~~La~ 146 (303)
+.. |++|||+|+|++||.+||||+||.. .+|||||||||+||+++|+++||++||++++|.||.+|+.+|||.+|+.
T Consensus 3 l~~LEk~LGY~Fkn~~LL~eALTH~Sy~~--~~NERLEFLGDAVL~liVse~Lf~~fP~~~EG~LT~lRS~LVsn~tLA~ 80 (413)
T PRK12372 3 LSQLESRLRYEFRNAELLRQALTHRSHSA--THNERLEFLGDSVLNCAVAALLFQRFGKLDEGDLSRVRANLVKQQSLYE 80 (413)
T ss_pred HHHHHHHhCCCcCCHHHHHHHHhcccccc--ccHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhhHHHHH
Confidence 455 9999999999999999999999865 4899999999999999999999999999999999999999999999999
Q ss_pred HHHHcCchhhhhcCCcchHHHHHHHHHHhhcCCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHhhcccC
Q 041023 147 VAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMI 226 (303)
Q Consensus 147 ~a~~~gL~~~i~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ll~~~l 226 (303)
+|..+||.++|+.+.++. ..+....+++++|+|||+|||||+|+|+ +.++.|+.++|.|.+
T Consensus 81 IA~~LgL~~~Lrlg~ge~-----------------~sgg~~~~kILADvfEALIGAIYLDsG~--e~a~~fV~~ll~p~l 141 (413)
T PRK12372 81 IAQALNISEGLRLGEGEL-----------------RSGGFRRPSILADAFEAIIGAVFLDGGF--EAAQGVIKRLYVPIL 141 (413)
T ss_pred HHHHcCchHhhhcCcchh-----------------hcCCCCCccHHHHHHHHHHHHHHHhCCH--HHHHHHHHHHHHHHH
Confidence 999999999999887532 1244567899999999999999999998 789999999998886
Q ss_pred CCC---cccCCCccHHHHHHHhCCCcceEEEeec-------ceeEEEEEECCE-EEEEEEeccchHHHHHHHHHHHHHHH
Q 041023 227 SPE---TLKTHPVTELYEVCQKNKLKVKFVDLWK-------ESTAFHIFIEDQ-LLGRGAYAPKKEIAHNRAAKDALNNI 295 (303)
Q Consensus 227 ~~~---~~~~~Pk~~Lqe~~q~~~~~~~~~~~~~-------~~~~v~V~i~~~-~ig~G~g~skk~~Ae~~AA~~AL~~l 295 (303)
+.. ....|||+.||||||+++...|.|.+.. ..|+|.|+++|. ..|+|.|.|||+ |||+||+.||++|
T Consensus 142 ~~~~~~~~~~D~KS~LQE~~Q~~~~~~P~Y~lv~e~Gp~h~~~F~V~V~v~g~~~~g~G~G~SKKe-AEQ~AAr~AL~kL 220 (413)
T PRK12372 142 DHIDPRTLGKDAKTLLQEYLQGHKIALPTYTVVATHGAAHNQQFEVECTVPKLDVKVSGSGASRRA-AEQAAAKKALDEV 220 (413)
T ss_pred hhcccccccCCHHHHHHHHHHhcCCCCCeeEEeeeecCCCCceEEEEEEECCeEEEEEEEeCCHHH-HHHHHHHHHHHHH
Confidence 542 2356999999999999999888776532 468999999985 558999999996 9999999999999
Q ss_pred Hh
Q 041023 296 ER 297 (303)
Q Consensus 296 ~~ 297 (303)
..
T Consensus 221 ~~ 222 (413)
T PRK12372 221 MA 222 (413)
T ss_pred hc
Confidence 84
No 5
>PRK00102 rnc ribonuclease III; Reviewed
Probab=100.00 E-value=9.7e-47 Score=336.30 Aligned_cols=212 Identities=34% Similarity=0.500 Sum_probs=186.4
Q ss_pred CCccH-HHhcCCccCCHHHHHHhhcCCCCCC---CCCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcCh
Q 041023 66 NNLDE-EEILGYRFNNKNLLEEAFTDPSCPE---RFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNT 141 (303)
Q Consensus 66 ~~l~~-e~~lgy~F~~~~LL~~AlTh~S~~~---~~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn 141 (303)
..+.. |++|||+|+|++|+.+||||+|+.. ...+|||||||||++|++++++|+|.+||+.++|.|+.+|+.+|||
T Consensus 3 ~~~~~l~~~lg~~f~~~~ll~~Alth~S~~~~~~~~~~nerLefLGDavl~~~v~~~l~~~~p~~~~g~l~~~~~~lvsn 82 (229)
T PRK00102 3 KDLEELQKKLGYTFKDPELLIQALTHRSYANENKGLKHNERLEFLGDAVLELVVSEYLFKRFPDLDEGDLSKLRAALVRE 82 (229)
T ss_pred hhHHHHHHHhCCCCCCHHHHHHHhCccchhccCCCcccchhHHHHHHHHHHHHHHHHHHHHCCCCChhHHHHHHHHHhCH
Confidence 34567 9999999999999999999999953 4679999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHcCchhhhhcCCcchHHHHHHHHHHhhcCCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHh
Q 041023 142 EKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKEL 221 (303)
Q Consensus 142 ~~La~~a~~~gL~~~i~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~l 221 (303)
.+|+.+|.++||+++++++++.. ..+....+++++|+|||+|||||+|+|+ +.+++|+..+
T Consensus 83 ~~la~~a~~lgl~~~i~~~~~~~-----------------~~~~~~~~k~~ad~~EA~iGAiyld~g~--~~~~~~i~~~ 143 (229)
T PRK00102 83 ESLAEIARELGLGEYLLLGKGEE-----------------KSGGRRRPSILADAFEALIGAIYLDQGL--EAARKFILRL 143 (229)
T ss_pred HHHHHHHHHCCcHHHHccCcHHH-----------------HcCCCCCccHHHHHHHHHHHHHHHhCCH--HHHHHHHHHH
Confidence 99999999999999999876421 0123456899999999999999999997 8999999999
Q ss_pred hcccCCCC---cccCCCccHHHHHHHhCCCcceEEEee-------cceeEEEEEECCEEEEEEEeccchHHHHHHHHHHH
Q 041023 222 LKPMISPE---TLKTHPVTELYEVCQKNKLKVKFVDLW-------KESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDA 291 (303)
Q Consensus 222 l~~~l~~~---~~~~~Pk~~Lqe~~q~~~~~~~~~~~~-------~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~A 291 (303)
+.|++... ....|||+.|+|+|++.+...|.|.+. .+.|+|+|+++|+.+|+|.|.|+|+ ||++||+.|
T Consensus 144 ~~~~l~~~~~~~~~~~pk~~L~e~~~~~~~~~p~y~~~~~~g~~~~~~f~~~v~i~~~~~~~g~g~skk~-Ae~~AA~~A 222 (229)
T PRK00102 144 FEPRIEEIDLGDLVKDYKTRLQELLQGRGLPLPEYELVKEEGPAHDKEFTVEVTVNGKELGEGTGSSKKE-AEQAAAKQA 222 (229)
T ss_pred HHHHHHhhccccccCCHHHHHHHHHHHcCCCCCceEEeeccCCCCCceEEEEEEECCEEEEEeeeCCHHH-HHHHHHHHH
Confidence 98876653 346799999999999998876655442 2468999999999999999999996 999999999
Q ss_pred HHHHHh
Q 041023 292 LNNIER 297 (303)
Q Consensus 292 L~~l~~ 297 (303)
|+.|+.
T Consensus 223 l~~l~~ 228 (229)
T PRK00102 223 LKKLKE 228 (229)
T ss_pred HHHHhh
Confidence 999874
No 6
>TIGR02191 RNaseIII ribonuclease III, bacterial. This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family.
Probab=100.00 E-value=3.6e-45 Score=324.13 Aligned_cols=205 Identities=36% Similarity=0.485 Sum_probs=179.3
Q ss_pred HHhcCCccCCHHHHHHhhcCCCCCC----CCCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcChHHHHH
Q 041023 71 EEILGYRFNNKNLLEEAFTDPSCPE----RFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLAR 146 (303)
Q Consensus 71 e~~lgy~F~~~~LL~~AlTh~S~~~----~~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn~~La~ 146 (303)
|++|||+|+|++|+.+||||||+.. ...+|||||||||++|++++++|+|.+||+.++|.|+.+|+.+|||.+|+.
T Consensus 2 e~~lgy~F~~~~ll~~Alth~S~~~~~~~~~~~nerLe~lGd~vl~~~~~~~l~~~~p~~~~~~l~~~~~~lvsn~~la~ 81 (220)
T TIGR02191 2 EKRLGYKFKNKELLEQALTHSSYANEHHKGVKNNERLEFLGDAVLGLVVAEYLFKNFPDLSEGELSKLRAALVSEESLAE 81 (220)
T ss_pred hHHhCCCcCCHHHHHHHhcCcccccccccCccchHHHHHHHHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCHHHHHH
Confidence 6899999999999999999999963 246999999999999999999999999999999999999999999999999
Q ss_pred HHHHcCchhhhhcCCcchHHHHHHHHHHhhcCCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHhhcccC
Q 041023 147 VAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMI 226 (303)
Q Consensus 147 ~a~~~gL~~~i~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ll~~~l 226 (303)
+|.++||+++++++++... ......+++++|+|||+|||||+|+|+ +.+++|+..++.|.+
T Consensus 82 ~a~~~gl~~~i~~~~~~~~-----------------~~~~~~~k~~ad~~eAliGAiyld~g~--~~~~~~i~~~~~~~~ 142 (220)
T TIGR02191 82 VARELGLGKFLLLGKGEEK-----------------SGGRRRESILADAFEALIGAIYLDSGL--EAARKFILKLLIPRI 142 (220)
T ss_pred HHHHCCcHHHhccCchHhh-----------------cCCcccchHHHHHHHHHHHHHHHhCCH--HHHHHHHHHHHHHHH
Confidence 9999999999998864210 123456899999999999999999996 899999999988876
Q ss_pred CC---CcccCCCccHHHHHHHhCCCcceEEEee-------cceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHH
Q 041023 227 SP---ETLKTHPVTELYEVCQKNKLKVKFVDLW-------KESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNI 295 (303)
Q Consensus 227 ~~---~~~~~~Pk~~Lqe~~q~~~~~~~~~~~~-------~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l 295 (303)
.. .....|||+.|+|+|++++...|.|+.. .+.|.|+|+++|+.+|+|.|.|+|+ ||++||++||++|
T Consensus 143 ~~~~~~~~~~~pk~~L~e~~~~~~~~~p~y~~~~~~g~~~~~~f~~~v~~~~~~~~~g~g~skk~-A~~~AA~~Al~~l 220 (220)
T TIGR02191 143 DAIEKEETLKDYKTALQEWAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKE-AEQNAAKAALEKL 220 (220)
T ss_pred HhhhcccccCChHHHHHHHHHHcCCCCceEEEecccCCCCCceEEEEEEECCEEEEEeeeCCHHH-HHHHHHHHHHHhC
Confidence 54 2256799999999999987754544432 2468999999999999999999986 9999999999875
No 7
>KOG1817 consensus Ribonuclease [RNA processing and modification]
Probab=100.00 E-value=9.3e-43 Score=321.42 Aligned_cols=258 Identities=28% Similarity=0.389 Sum_probs=220.1
Q ss_pred hhHHhhhcc-ccchhhhhhHHHHHHHhhhhHHHHhHHHHHhhhhhhcCCCCccCCCCCcCCccH-HHhcCCccCCHHHHH
Q 041023 8 YLLALVVFS-LHSLQIQWSLVVAMEEAHQEEALISHLLQDLFVNEKAGDESESESLPNANNLDE-EEILGYRFNNKNLLE 85 (303)
Q Consensus 8 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-e~~lgy~F~~~~LL~ 85 (303)
.+++.-+|- +.-+.-.|...| -|++|..-|. +++..+...|.+.++.. |+++|..|.+.+++.
T Consensus 229 ~lfs~~~~~~epvlee~w~~~~------------ehelq~~ep~---gDr~~~~~~Ppllp~~~~e~~~g~vF~Hirlla 293 (533)
T KOG1817|consen 229 KLFSRALFVYEPVLEEEWEHEP------------EHELQEQEPA---GDRVLITKYPPLLPLTQFEEIIGIVFIHIRLLA 293 (533)
T ss_pred HHHHHHhhccCchhhccccCCC------------cCcccccCCC---ccccccccCCCCCchhhHHHHHHHHHHHHHHHH
Confidence 345555555 455555677777 7777777554 88888888899999888 999999999999999
Q ss_pred HhhcCCCCCC---CCCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcChHHHHHHHHHcCchhhhhcCCc
Q 041023 86 EAFTDPSCPE---RFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKP 162 (303)
Q Consensus 86 ~AlTh~S~~~---~~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn~~La~~a~~~gL~~~i~~~~~ 162 (303)
+|+|.+|.+. ...+|||||||||+||++++|++||.+||+.+||+||.+|+.+|||++.+.||..+|+++++..+..
T Consensus 294 ~aft~rs~~~n~Lt~gHNqRLEFLGDSilqlv~T~ily~kFPdhhEGhLSlLRssLVsNetqakva~~lgf~e~li~n~~ 373 (533)
T KOG1817|consen 294 RAFTLRSIPFNHLTLGHNQRLEFLGDSILQLVMTEILYRKFPDHHEGHLSLLRSSLVSNETQAKVADDLGFHEYLITNFD 373 (533)
T ss_pred HHhhccCCCchhhhhhhhHHHHHhHHHHHHHHHHHHHHHhCCccccchHHHHHHHHhccHHHHHHHHHhCCchhhhhCcc
Confidence 9999999873 3579999999999999999999999999999999999999999999999999999999999988764
Q ss_pred chHHHHHHHHHHhhcCCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHhhcccCCCCc---ccCCCccHH
Q 041023 163 LLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMISPET---LKTHPVTEL 239 (303)
Q Consensus 163 ~~~~~i~~~~~~~~~~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ll~~~l~~~~---~~~~Pk~~L 239 (303)
. ++ ......|.+||+|||+|||+|+|.|. +.+++|++.++.|.|...+ .+.+|++.|
T Consensus 374 ~-k~-----------------~~~lk~K~~ADlfEAfiGaLyvD~~l--e~~~qf~~~l~~Prl~~fi~nq~wndpkskL 433 (533)
T KOG1817|consen 374 L-KD-----------------FQNLKLKDYADLFEAFIGALYVDKGL--EYCRQFLRVLFFPRLKEFIRNQDWNDPKSKL 433 (533)
T ss_pred h-hh-----------------hhhhhHHHHHHHHHHHHHHHhhcCCc--HHHHHHHHHHhhHHHHHHHHhhhccCcHHHH
Confidence 2 00 11245799999999999999999998 8999999999999876543 467999999
Q ss_pred HHHHHhCCC------cceEEEee-------cceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHhhhcc
Q 041023 240 YEVCQKNKL------KVKFVDLW-------KESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERLLNE 301 (303)
Q Consensus 240 qe~~q~~~~------~~~~~~~~-------~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~~~~ 301 (303)
|++|..... .+|+|.+. ++.|+|.|+++|+.+|+|.|.+.|. |+.+||++||+.++.-|+.
T Consensus 434 qq~cl~~rys~~~epdip~y~V~~~~gpa~~r~y~Vavyf~gkrlat~~G~nik~-Ae~rAA~~ALe~~~~dF~k 507 (533)
T KOG1817|consen 434 QQCCLTLRYSLGGEPDIPLYKVLGAKGPANDRNYKVAVYFKGKRLATGVGSNIKQ-AEMRAAMQALENLKMDFSK 507 (533)
T ss_pred HHHHHHHhcccCCCCCCceEEEecccCCCCCCceEEEEEECCEEEeeccCchHhH-HHHHHHHHHHHHHHhhhHH
Confidence 999987643 36888764 3458999999999999999999996 9999999999999987764
No 8
>PF14622 Ribonucleas_3_3: Ribonuclease-III-like; PDB: 1O0W_A 2A11_A 3N3W_B.
Probab=99.97 E-value=1.3e-31 Score=218.20 Aligned_cols=126 Identities=38% Similarity=0.531 Sum_probs=102.7
Q ss_pred CHHHHHHhhcCCCCC-CCCCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcChHHHHHHHHHcCchhhhh
Q 041023 80 NKNLLEEAFTDPSCP-ERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLR 158 (303)
Q Consensus 80 ~~~LL~~AlTh~S~~-~~~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn~~La~~a~~~gL~~~i~ 158 (303)
|++|+.+||||+||. +...+|||||||||+||++++++|+|+++ +.++|.++.+|+.+|++++|+.+|.++||+++++
T Consensus 1 ~~~Ll~~alTH~S~~~~~~~~nerLefLGd~vL~~~vs~~l~~~~-~~~~g~l~~~~~~lv~~~~La~~a~~lgL~~~i~ 79 (128)
T PF14622_consen 1 DDELLLQALTHKSYAHERKPNNERLEFLGDAVLGLVVSEYLFQRP-PADEGELTRLRSNLVSNETLAEIAKQLGLDKLIR 79 (128)
T ss_dssp SHHHHHHHTB-HHHHHHTCB-SHHHHHHHHHHHHHHHHHHHHHHT-TTSCHHHHHHHHHHHSHHHHHHHHHHTTCGGC-B
T ss_pred CHHHHHHHhcCccccccccCccHHHHHHHHHHHHHHHHHHHHhCc-CccchHHHHHHHHHhChHHHHHHHHHCCHHHHHH
Confidence 689999999999996 34579999999999999999999999995 4589999999999999999999999999999999
Q ss_pred cCCcchHHHHHHHHHHhhcCCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHhhccc
Q 041023 159 HNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPM 225 (303)
Q Consensus 159 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ll~~~ 225 (303)
++++... .+....+++++|+|||+|||||+|+|+ +.+++|+.+.+.|.
T Consensus 80 ~~~~~~~-----------------~~~~~~~~vlad~feAliGAiyld~G~--~~a~~~i~~~i~~~ 127 (128)
T PF14622_consen 80 WGPGEEK-----------------SGGSGSDKVLADVFEALIGAIYLDSGF--EAARKFIQKLILPR 127 (128)
T ss_dssp --HHHHH-----------------TTGGG-HHHHHHHHHHHHHHHHHHH-H--HHHHHHHHHHH---
T ss_pred hCccHhh-----------------cCCCCCccHHHhHHHHHHHHHHHHcCH--HHHHHHHHHHhccc
Confidence 9653210 123456899999999999999999998 89999999887664
No 9
>smart00535 RIBOc Ribonuclease III family.
Probab=99.96 E-value=2.6e-29 Score=204.45 Aligned_cols=127 Identities=39% Similarity=0.633 Sum_probs=113.9
Q ss_pred HHHHHhhcCCCCCCCCCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcChHHHHHHHHHcCchhhhhcCC
Q 041023 82 NLLEEAFTDPSCPERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNK 161 (303)
Q Consensus 82 ~LL~~AlTh~S~~~~~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn~~La~~a~~~gL~~~i~~~~ 161 (303)
.||.+||||||+.....+|||||||||++|+++++.+++.+||+.++|.|+.+++.++||++|+.+|.++||++++++++
T Consensus 1 ~ll~~alth~s~~~~~~~~e~Le~lGd~vl~~~v~~~l~~~~p~~~~~~l~~~~~~lvsn~~la~~a~~~~l~~~i~~~~ 80 (129)
T smart00535 1 SLLLRALTHASYSNEHEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGR 80 (129)
T ss_pred CHHHHHhhcccccccCcchHHHHHHHHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHCHHHHHHHHHHCCcHHHHccCc
Confidence 37899999999987556999999999999999999999999999999999999999999999999999999999999886
Q ss_pred cchHHHHHHHHHHhhcCCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHhhcccCC
Q 041023 162 PLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMIS 227 (303)
Q Consensus 162 ~~~~~~i~~~~~~~~~~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ll~~~l~ 227 (303)
.... ......+++++|+|||+|||||+|+|. +.+++|+.+++.|.++
T Consensus 81 ~~~~-----------------~~~~~~~k~~a~~~eAliGAi~ld~g~--~~~~~~i~~~~~~~~~ 127 (129)
T smart00535 81 GEAI-----------------SGGRDKPSILADVFEALIGAIYLDSGL--EAAREFIRDLLGPRLE 127 (129)
T ss_pred hHhh-----------------cCCcccchHHHHHHHHHHHHHHHhCCH--HHHHHHHHHHHHHHhc
Confidence 5310 122357899999999999999999997 8999999999988665
No 10
>cd00593 RIBOc RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.
Probab=99.95 E-value=2.2e-28 Score=199.64 Aligned_cols=128 Identities=46% Similarity=0.675 Sum_probs=114.6
Q ss_pred HHHHHhhcCCCCCCC--CCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcChHHHHHHHHHcCchhhhhc
Q 041023 82 NLLEEAFTDPSCPER--FFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRH 159 (303)
Q Consensus 82 ~LL~~AlTh~S~~~~--~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn~~La~~a~~~gL~~~i~~ 159 (303)
+|+.+||||+|+... ..+|||||||||++|+++++.+++..+|+.++|.++.+++.++||++|+.++.++||++++++
T Consensus 1 ~ll~~alth~s~~~~~~~~~~e~Le~lGdavl~~~~~~~l~~~~~~~~~~~l~~~~~~~v~n~~l~~~a~~~gl~~~i~~ 80 (133)
T cd00593 1 SLLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRL 80 (133)
T ss_pred CHHHHhhcCccccccCCCcchHHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHCHHHHHHHHHHcCcHHHhcc
Confidence 478999999999864 489999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcchHHHHHHHHHHhhcCCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHhhcccCCC
Q 041023 160 NKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMISP 228 (303)
Q Consensus 160 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ll~~~l~~ 228 (303)
.+.... ......+|+++|+|||+|||||+|+|. +.+++|+..++.|.++.
T Consensus 81 ~~~~~~-----------------~~~~~~~k~~ad~~eAliGAiyld~g~--~~~~~~i~~~~~~~~~~ 130 (133)
T cd00593 81 GKGEEK-----------------SGGRLRPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPLIEE 130 (133)
T ss_pred CchHhh-----------------cCCcccccHHHHHHHHHHHHHHHhCCH--HHHHHHHHHHHHHHHhh
Confidence 875311 112457899999999999999999998 89999999998887654
No 11
>PF00636 Ribonuclease_3: Ribonuclease III domain; InterPro: IPR000999 Prokaryotic ribonuclease III (3.1.26.3 from EC) (gene rnc) [] is an enzyme that digests double-stranded RNA. It is involved in the processing of ribosomal RNA precursors and of some mRNAs. RNase III is evolutionary related to a number of proteins including []: Saccharomyces cerevisiae (Baker's yeast) protein pac1, a ribonuclease that probably inhibits mating and meiosis by degrading a specific mRNA required for sexual development yeast ribonuclease III (gene RNT1), a dsRNA-specific nuclease that cleaves eukaryotic preribosomal RNA at various sites Caenorhabditis elegans hypothetical protein F26E4.13 Paramecium bursaria Chlorella virus 1 (PBCV-1) 1 protein A464R Synechocystis sp. (strain PCC 6803) hypothetical protein slr0346 yeast hypothetical protein SpAC8A4.08c, a protein with a N-terminal helicase domain and a C-terminal RNase III domain C. elegans hypothetical protein K12H4.8, a protein with the same structure as SpAC8A4.08c ; GO: 0003723 RNA binding, 0004525 ribonuclease III activity, 0006396 RNA processing; PDB: 2GSL_A 2NUE_B 1YYO_A 2NUF_A 1YZ9_A 1JFZ_A 1YYW_C 1RC5_B 1YYK_B 1RC7_A ....
Probab=99.90 E-value=1.2e-24 Score=173.44 Aligned_cols=108 Identities=47% Similarity=0.749 Sum_probs=84.7
Q ss_pred hHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcChHHHHHHHHHcCchhhhhcCCcchHHHHHHHHHHhhc---
Q 041023 101 ERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILD--- 177 (303)
Q Consensus 101 erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn~~La~~a~~~gL~~~i~~~~~~~~~~i~~~~~~~~~--- 177 (303)
||||||||+||+++++.++|.+||+.++|.|+.+|+.+|||.+|+.+|.++||+++++..+.....+...+.+....
T Consensus 1 ErLefLGDavL~~~v~~~l~~~~p~~~~~~L~~~r~~~vsn~~L~~~a~~~gl~~~l~~~~~~~~~~~~~~~~~~~~~~~ 80 (114)
T PF00636_consen 1 ERLEFLGDAVLKLLVSEYLFEKYPNLNEGQLTKLRSALVSNKFLARLAVKLGLHKYLRQEPFEIQRWIKPFNEDLNNGDS 80 (114)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTTSSHHHHHHHHHHHHSHHHHHHHHHHTTHGCTCBHHHHHHHHHHHCHHCC------
T ss_pred CcHhHhHHHHHHHHHHHHHHHHCCCCChhHHHHHHHHHhCHHHHHHHHHHhCchHhhhccchhHHHHHHHHHHHHHhccc
Confidence 89999999999999999999999999999999999999999999999999999999997655443332222111100
Q ss_pred ---CCCCCCCCCCCchhHHHHHHHHhhhhcccCC
Q 041023 178 ---YPLHSNGLVDAPKVLADIVESTIGAVFIDCN 208 (303)
Q Consensus 178 ---~~~~~~~~~~~~k~laD~fEAliGAIylD~G 208 (303)
.+.........+|++||+|||+|||||+|+|
T Consensus 81 ~~~~~~~~~~~~~~~k~laD~~EAliGAiyld~G 114 (114)
T PF00636_consen 81 ESSISYDPKNQVLPPKVLADVFEALIGAIYLDSG 114 (114)
T ss_dssp -C-SSS--SSSSHHHHHHHHHHHHHHHHHHHHTT
T ss_pred ccccCCCccccCCccHHHHHHHHHHHHHHHHhcC
Confidence 0000001233689999999999999999998
No 12
>KOG3769 consensus Ribonuclease III domain proteins [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=3.8e-22 Score=177.68 Aligned_cols=246 Identities=22% Similarity=0.248 Sum_probs=193.9
Q ss_pred hhhHHHHhHHHHHhhhhhhcCCCCccCCC-------CCcCCccH-HHhcC-CccCCHHHHHHhhcCCCCCC---------
Q 041023 34 HQEEALISHLLQDLFVNEKAGDESESESL-------PNANNLDE-EEILG-YRFNNKNLLEEAFTDPSCPE--------- 95 (303)
Q Consensus 34 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~l~~-e~~lg-y~F~~~~LL~~AlTh~S~~~--------- 95 (303)
.++-+..+..++++....+..+++.+.-- ...+.+.+ .++|| ..| ..+.+..|||.+|+..
T Consensus 24 ~~~kr~~s~~~r~L~~Rqk~l~~~~~~~krs~~~~W~~~sel~afg~RL~~~~i-s~~~l~ka~t~~s~~~~~kv~~~~l 102 (333)
T KOG3769|consen 24 RQSKRWTSKRLRELIHRQKTLGRPSPPMKRSEYVNWDYNSELSAFGKRLQSEEI-SLSYLLKALTNLSFSYPEKVLRQQL 102 (333)
T ss_pred HHhhhhhhHHHHHHHHHHHhhcCCCccchhhcccCcchhHHHHHHHHHhccccc-cHHHHHHHHhCccccchHHHhhhhh
Confidence 33455567777777766554443222111 11346888 99999 556 7899999999999841
Q ss_pred ---------CCCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcChHHHHHHHHHcCchhhhhcCCcchHH
Q 041023 96 ---------RFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEE 166 (303)
Q Consensus 96 ---------~~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn~~La~~a~~~gL~~~i~~~~~~~~~ 166 (303)
+..+|+.|.-.|..+++++|+.||-.+||++++..+..+-+.+++.+.||.+|..+|++++++......
T Consensus 103 g~~~~~~~~~~~~N~~L~~~Gk~~~~~~v~~~l~~kyPrlP~E~l~ai~n~ll~ee~LahiAt~lGie~l~~seeFp~-- 180 (333)
T KOG3769|consen 103 GAETVAQVNPQYSNEELVEIGKQFLSFYVTEYLKCKYPRLPEEGLHAIVNGLLGEEVLAHIATHLGIEELGLSEEFPK-- 180 (333)
T ss_pred cchhhhhhcCCcchHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHhhhHHHHHHHHHHhhHHHHhhcccCCC--
Confidence 256899999999999999999999999999999999999999999999999999999999988765421
Q ss_pred HHHHHHHHhhcCCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHhh-cccCCC--CcccCCCccHHHHHH
Q 041023 167 QIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELL-KPMISP--ETLKTHPVTELYEVC 243 (303)
Q Consensus 167 ~i~~~~~~~~~~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ll-~~~l~~--~~~~~~Pk~~Lqe~~ 243 (303)
.+.....+...+++-|++|+++...|+ +.+++||.+.+ ...++. .....+|...|.++|
T Consensus 181 ----------------~~eisq~ess~~aI~Al~~~~~~ek~~--~~v~dFI~~qi~~k~L~~~~m~ql~~P~~~L~~lc 242 (333)
T KOG3769|consen 181 ----------------VGEISQDESSRRAIGALLGSVGLEKGF--NFVRDFINDQILSKDLDPREMWQLQWPRRLLSRLC 242 (333)
T ss_pred ----------------chhhhHHHHHHHHHHHHHhcccHHHHH--HHHHHHHHHHhhhhccchHhhccccchHHHHHHHH
Confidence 011223367788888888888888887 67777776544 334542 234679999999999
Q ss_pred HhCCCcceEEEeecc--------eeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHhhhcc
Q 041023 244 QKNKLKVKFVDLWKE--------STAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERLLNE 301 (303)
Q Consensus 244 q~~~~~~~~~~~~~~--------~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~~~~ 301 (303)
++.|++-|++++..+ -|.|++|.|.+.+|+|.|+|-+. |++.||.+||.++-.+.|+
T Consensus 243 kr~~l~epe~Rll~esGr~S~~PvyvVgiYs~kkllGqG~Gesl~~-A~e~AA~dAL~k~y~~tp~ 307 (333)
T KOG3769|consen 243 KRRGLKEPESRLLAESGRNSAEPVYVVGIYSGKKLLGQGQGESLKL-AEEQAARDALIKLYDHTPE 307 (333)
T ss_pred HHcCCCCchhHHHHHhccCccCceEEEEeecCchhhccCcchHHHH-HHHHHHHHHHHHHHcCChh
Confidence 999999998887543 47899999999999999999995 9999999999999887653
No 13
>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]
Probab=99.62 E-value=5.7e-16 Score=165.12 Aligned_cols=254 Identities=29% Similarity=0.328 Sum_probs=176.0
Q ss_pred HhhhhHHHHhHHHHHhhhhhhcCC----CCccCCCCC---c---------CCccH-HHhcCCccCCHHHHHHhhcCCCCC
Q 041023 32 EAHQEEALISHLLQDLFVNEKAGD----ESESESLPN---A---------NNLDE-EEILGYRFNNKNLLEEAFTDPSCP 94 (303)
Q Consensus 32 ~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~---~---------~~l~~-e~~lgy~F~~~~LL~~AlTh~S~~ 94 (303)
.+.++++.+.+++...++...... ...-+..++ + ..+.. |..+||.|.+..++.+|+||-|+.
T Consensus 1319 i~d~v~sli~~~~~~~~~~s~l~~~~~~~~l~~i~es~~~~~~~~~~~~l~~~~~~e~~l~y~f~~~~~l~~a~th~s~~ 1398 (1606)
T KOG0701|consen 1319 IADSVEALIGASLSEGGPSSALLFMDWPPILLDIPESIASPDSIDELRQLLSFGKFEEKLNYRFKLKPYLTQATTHASYI 1398 (1606)
T ss_pred HHHHHHHhhhhhhhccCCCccccccccccccccccccccccchhHHHHHHHHHHhhhcccchhhhhhhcccccccccccc
Confidence 456778888888888777644321 111111111 1 12334 889999999999999999999986
Q ss_pred C--CCCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcChHHHHHHHHHcCchhhhhcCCcchHHHHHHHH
Q 041023 95 E--RFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFS 172 (303)
Q Consensus 95 ~--~~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn~~La~~a~~~gL~~~i~~~~~~~~~~i~~~~ 172 (303)
. ...+|+||||+||+++++.++.|+|...|..++|.++.+|++.|+|...|.+|.+.++++++......+...|.+|+
T Consensus 1399 ~~~~~~C~qrleflgd~vld~~it~hl~~~~~~~sp~~~td~rsa~vnn~~~a~~av~~~~~K~~~~~~~~l~~~I~~~v 1478 (1606)
T KOG0701|consen 1399 YNRITDCYQRLEFLGDAVLDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKADLHKFIIAASPGLIHNIDRFV 1478 (1606)
T ss_pred cCccchhhhhHHHhHHhhhhhhhhhcccccccccCchhhhhhhhHhhccccchhhHHhhcchhHHHhhccccccchHHHH
Confidence 3 46799999999999999999999999999999999999999999999999999999999999988887766777776
Q ss_pred HHhhc----CCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHhhcccCC----CCcccCCCccHHHHHHH
Q 041023 173 EAILD----YPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMIS----PETLKTHPVTELYEVCQ 244 (303)
Q Consensus 173 ~~~~~----~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ll~~~l~----~~~~~~~Pk~~Lqe~~q 244 (303)
..... .+..+.+....||+++|++|++.||||.|+|...+.+ +..+. +... ......||++.+-..+.
T Consensus 1479 ~~~~q~~~~~~~~~~edievpKa~gdi~esiagai~~dsg~~~~~~---~~~~~-a~p~~s~~~E~~~~h~~~~~~~~~~ 1554 (1606)
T KOG0701|consen 1479 SFQLQSNLDSLFGWEEDIEVPKALGDIFESIAGAIKLDSGNMMEPC---IEKFW-ALPPRSPIRELLELHPERALFGKCE 1554 (1606)
T ss_pred HHHHhhccccCCCchhhcccchhhhhhhhcccceeecCcccccchH---hhcCc-CCCCccchhhhccccceeeccchhh
Confidence 54422 1112223457899999999999999999999521111 11221 1111 11224455544433222
Q ss_pred hCCCcceEEEeecceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHhh
Q 041023 245 KNKLKVKFVDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERL 298 (303)
Q Consensus 245 ~~~~~~~~~~~~~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~ 298 (303)
+- .....-.++|.+.++-.+.|.|...+. |+..|++.|++.+...
T Consensus 1555 k~--------~d~~~~~~tv~~~~~~~~~~~g~~~~~-aK~s~~k~A~~ll~~~ 1599 (1606)
T KOG0701|consen 1555 KV--------ADAGKVRVTVDVFNKEVFAGEGRNYRI-AKASAAKAALKLLKKL 1599 (1606)
T ss_pred hh--------hhccceEEEEEecccchhhhcchhhhh-hhhhHHHHHHHHHHHh
Confidence 21 011122455555555556666666664 8888888888887765
No 14
>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]
Probab=99.62 E-value=1.4e-15 Score=162.19 Aligned_cols=155 Identities=42% Similarity=0.681 Sum_probs=127.0
Q ss_pred CccH-HHhcC--CccCCH--------HHHHHhhcCCCCCCCCCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHH
Q 041023 67 NLDE-EEILG--YRFNNK--------NLLEEAFTDPSCPERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLR 135 (303)
Q Consensus 67 ~l~~-e~~lg--y~F~~~--------~LL~~AlTh~S~~~~~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr 135 (303)
+.+. +++++ |.|.+. ++|.+|||+.++.. ..++||||+|||++|++.++.++|.+||+..||+++.+|
T Consensus 980 ~~E~~e~i~n~~~~Fs~~~~~i~~~~s~LLEAlT~~~~~~-s~s~Erle~Lgds~Lk~avsr~l~L~ypd~~Egqls~lr 1058 (1606)
T KOG0701|consen 980 DWEAVEKILNFRYVFSISLASIALSTSLLLEALTTSSCQD-SFSLERLELLGDSLLKLAVSRHLFLTYPDLDEGQLSRLR 1058 (1606)
T ss_pred cccccccccccceeccccccccccchhHHHHHhhcCcccc-chhHHHHHhhHHHHHHHHHHHHHHHhCCcccchhHHHHH
Confidence 4566 88998 999999 99999999999995 789999999999999999999999999999999999999
Q ss_pred HhhcChHHHHHHHHHcCchhhhhcC--Ccc-----------------------------hHHHHHHHHHHhhcCCCCCC-
Q 041023 136 SANVNTEKLARVAIKLGLHKYLRHN--KPL-----------------------------LEEQIREFSEAILDYPLHSN- 183 (303)
Q Consensus 136 ~~lvsn~~La~~a~~~gL~~~i~~~--~~~-----------------------------~~~~i~~~~~~~~~~~~~~~- 183 (303)
+..+++..|+.+|...||..+++.+ .+. ..+.+.+|.+++..+.....
T Consensus 1059 ~~~~~~~nl~~la~~~gl~~~~~~~~fep~~~~~p~~~~~~~~~~k~~~~~~~~~~~~e~~e~~~df~e~~~~~~~~~~~ 1138 (1606)
T KOG0701|consen 1059 DVNVSNDNLARLAVKKGLYSYLRHEGFEPSRWWVPGQLDVNNVDCKDLSGDQNYILYKELDEKIKDFQEAMEKEDGDSRS 1138 (1606)
T ss_pred HhcccccchhhhhhcccchhhcccccccccccccccccccccccccccccccccccccchhhhhhHHHHhhhccCCcccc
Confidence 9999999999999999999999877 211 33456667666654332221
Q ss_pred -C---CCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHhhc
Q 041023 184 -G---LVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLK 223 (303)
Q Consensus 184 -~---~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ll~ 223 (303)
+ ....+|.++|++||++||+|+|+|.+ ....-+...++.
T Consensus 1139 ~~~~~~~~~~ks~adl~eaLlga~~vD~~~~-~~~~~~~~~~lk 1181 (1606)
T KOG0701|consen 1139 KGGDHDWLAPKSPADLLEALLGAIYVDGGLL-ETFETIGDSFLK 1181 (1606)
T ss_pred cccccceecCCCHHHHHHHHHHhhhhhccch-hhhhHHHHHHHh
Confidence 1 34578999999999999999999985 333333444444
No 15
>KOG1817 consensus Ribonuclease [RNA processing and modification]
Probab=99.60 E-value=2.1e-15 Score=140.61 Aligned_cols=135 Identities=33% Similarity=0.519 Sum_probs=112.3
Q ss_pred CccH-HHhcCCccCCHHHHHHhhcCCCCCC--------------------------------------------------
Q 041023 67 NLDE-EEILGYRFNNKNLLEEAFTDPSCPE-------------------------------------------------- 95 (303)
Q Consensus 67 ~l~~-e~~lgy~F~~~~LL~~AlTh~S~~~-------------------------------------------------- 95 (303)
.|+- |+.|||+|+|.-||..||||||+..
T Consensus 42 ~l~~~e~~i~y~f~~r~~~~lal~h~s~~~~~Gt~~dh~kns~tncg~r~~~yg~~~~~~~~kr~~gin~li~imk~l~~ 121 (533)
T KOG1817|consen 42 SLDHLEELIGYTFQDRCLLQLALTHPSHKLNYGTNPDHAKNSLTNCGIRQPKYGDRKEHIMTKRKLGINTLINIMKRLGV 121 (533)
T ss_pred hHHHHHHHhCeeecchHHHHHHhcCchHHhhCCCCchhhhccccccCcCCcccchhHHHHHHHHHhhhhHHHHHHhhccC
Confidence 3666 9999999999999999999999831
Q ss_pred ------CCCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcChHHHHHHHHHcCchhhhhcCCcchHHHHH
Q 041023 96 ------RFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIR 169 (303)
Q Consensus 96 ------~~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn~~La~~a~~~gL~~~i~~~~~~~~~~i~ 169 (303)
...+|||||||||++.+++++.++|..+|..++|.|...|+++|.|..++.+++++.++.++....+..-..
T Consensus 122 ~~~~~s~i~hnErle~lgdavve~~ss~hl~~~~~r~~eggLatyrta~vqnr~la~lakklrkd~fl~yahg~dl~~-- 199 (533)
T KOG1817|consen 122 IQPTHSVIKHNERLEFLGDAVVELLSSNHLYFMFPRLEEGGLATYRTAIVQNRHLAKLAKKLRKDEFLLYAHGYDLCF-- 199 (533)
T ss_pred CCCchhHhHHHHHHHHHhhccHHHHHHHHHHHccccccccchhHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCcchhh--
Confidence 024799999999999999999999999999999999999999999999999999999999998665321000
Q ss_pred HHHHHhhcCCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHH
Q 041023 170 EFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKE 220 (303)
Q Consensus 170 ~~~~~~~~~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ 220 (303)
..+....++++|||++||+|+|+|. ..+...+..
T Consensus 200 ---------------~~E~Kha~an~feavi~a~~l~g~~--~~~e~lfs~ 233 (533)
T KOG1817|consen 200 ---------------ETELKHAMANCFEAVIGAKYLDGGL--VVAEKLFSR 233 (533)
T ss_pred ---------------HHHHHHHHHHHHHHHhHHHHHhcch--HHHHHHHHH
Confidence 0123467999999999999999997 455544443
No 16
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=99.30 E-value=1.3e-11 Score=104.92 Aligned_cols=84 Identities=20% Similarity=0.194 Sum_probs=65.6
Q ss_pred HHHHHHHHHhhcccCCCC----cccCCCccHHHHHHHhCCCcceEEEe------ecceeEEEEEECCEEEEEEEeccchH
Q 041023 212 DIVWKVFKELLKPMISPE----TLKTHPVTELYEVCQKNKLKVKFVDL------WKESTAFHIFIEDQLLGRGAYAPKKE 281 (303)
Q Consensus 212 ~~v~~~i~~ll~~~l~~~----~~~~~Pk~~Lqe~~q~~~~~~~~~~~------~~~~~~v~V~i~~~~ig~G~g~skk~ 281 (303)
+.-..++.+++.+.+... +...|||+.||||||+++... |+.+ +.+.|++.|.|+|+.+|+|.|.|+|+
T Consensus 84 ~~~~~~~~~l~~~~i~~~k~~d~K~kNpKS~LQE~~Qk~~~~~-y~~i~~~Gp~H~p~F~v~V~I~g~~~g~G~G~SKKe 162 (183)
T PHA03103 84 EKSMREDNKSFSDTIPYKKIISWKDKNPCTVINEYCQITSRDW-SINITSSGPSHSPTFTASVIISGIKFKPAIGSTKKE 162 (183)
T ss_pred chhHHHHHHHhhhhcchhhhhccccCChhHHHHHHHHHhCCCe-EEEEEeeCCCCCceEEEEEEECCEEEEEeeeCCHHH
Confidence 445556666666655422 234689999999999988765 4433 23579999999999999999999997
Q ss_pred HHHHHHHHHHHHHHHh
Q 041023 282 IAHNRAAKDALNNIER 297 (303)
Q Consensus 282 ~Ae~~AA~~AL~~l~~ 297 (303)
||++||+.||+.|..
T Consensus 163 -AEQ~AAk~AL~~L~~ 177 (183)
T PHA03103 163 -AKNNAAKLAMDKILN 177 (183)
T ss_pred -HHHHHHHHHHHHHHh
Confidence 999999999999865
No 17
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=99.29 E-value=1.4e-11 Score=104.20 Aligned_cols=65 Identities=20% Similarity=0.310 Sum_probs=55.8
Q ss_pred cCCCccHHHHHHHhCCCcceEEEee------cceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHh
Q 041023 232 KTHPVTELYEVCQKNKLKVKFVDLW------KESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIER 297 (303)
Q Consensus 232 ~~~Pk~~Lqe~~q~~~~~~~~~~~~------~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~ 297 (303)
..|||+.||||||+.+..+.|..+. .+.|++.|+++|..+|+|.|.|||+ ||++||+.||+.|..
T Consensus 107 ~~DpKS~LQE~~Q~~~~~l~Y~li~~~GpdH~~~Ftv~V~V~g~~~g~G~G~SKKe-AEQ~AAk~AL~~L~~ 177 (183)
T PHA02701 107 TLNPVSAVNEFCMRTHRPLEFCETRSGGHDHCPLFTCTIVVSGKVVATASGCSKKL-ARHAACADALTILIN 177 (183)
T ss_pred CCCccHHHHHHHHhcCCCCeEEEEEeECCCCCceEEEEEEECCEEEEEEEeCCHHH-HHHHHHHHHHHHHHh
Confidence 4699999999999998877543332 3569999999999999999999996 999999999998864
No 18
>PF00035 dsrm: Double-stranded RNA binding motif; InterPro: IPR001159 The DsRBD domain is found in a variety of RNA-binding proteins with different structures and exhibiting a diversity of functions []. It is involved in localisation of at least five different mRNAs in the early Drosophila embryo and by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.; GO: 0003725 double-stranded RNA binding, 0005622 intracellular; PDB: 1EKZ_A 1STU_A 1QU6_A 2L2M_A 3ADJ_A 1WHN_A 3LLH_B 2B7V_A 2L3J_A 1UHZ_A ....
Probab=99.24 E-value=4.2e-11 Score=85.71 Aligned_cols=60 Identities=33% Similarity=0.510 Sum_probs=53.3
Q ss_pred CccHHHHHHHhCCCcceEEEeec-------ceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHH
Q 041023 235 PVTELYEVCQKNKLKVKFVDLWK-------ESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNI 295 (303)
Q Consensus 235 Pk~~Lqe~~q~~~~~~~~~~~~~-------~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l 295 (303)
|++.|+|+|++.+..++++.... ..|.|+|+++|..+|.|.|.|||+ |++.||+.||+.|
T Consensus 1 ~~~~L~e~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~i~~~~~~~g~g~sKk~-Ak~~AA~~al~~L 67 (67)
T PF00035_consen 1 PKSRLNEYCQKNKFPPPYYYIEEEGPSHHRPRFICTVYIDGKEYGEGEGSSKKE-AKQQAAKKALQKL 67 (67)
T ss_dssp HHHHHHHHHHHCTSSEEEEEEEEESSSSSSEEEEEEEEETTEEEEEEEESSHHH-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCCCEEEEEEeCCCCCCceEEEEEEECCEEEeEeccCCHHH-HHHHHHHHHHHhC
Confidence 78999999999999888875421 368999999999999999999996 9999999999976
No 19
>cd00048 DSRM Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
Probab=99.19 E-value=1.1e-10 Score=83.40 Aligned_cols=61 Identities=26% Similarity=0.330 Sum_probs=51.0
Q ss_pred CCccHHHHHHHhCCCcceEEEe-e------cceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHH
Q 041023 234 HPVTELYEVCQKNKLKVKFVDL-W------KESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNI 295 (303)
Q Consensus 234 ~Pk~~Lqe~~q~~~~~~~~~~~-~------~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l 295 (303)
||++.|+|+|++++...|.|.. . ...|.|.|+++|..+++|.|.|+|+ |++.||+.||+.|
T Consensus 1 ~p~~~L~e~~~~~~~~~~~y~~~~~~g~~~~~~f~~~v~i~~~~~~~g~g~sKk~-Ak~~AA~~al~~L 68 (68)
T cd00048 1 NPKSLLQELAQKRGKPLPEYELVEEEGPDHAPRFTVEVTVGGKITGEGEGSSKKE-AKQNAAEAALRKL 68 (68)
T ss_pred ChHHHHHHHHHHcCCCCCeEEEeeeeCCCCCCeEEEEEEECCEEEEEeecCCHHH-HHHHHHHHHHHhC
Confidence 7999999999999665444433 2 1468999999999999999999996 9999999999864
No 20
>smart00358 DSRM Double-stranded RNA binding motif.
Probab=99.17 E-value=1.3e-10 Score=82.92 Aligned_cols=60 Identities=28% Similarity=0.354 Sum_probs=51.2
Q ss_pred CccHHHHHHHhCCCcceEEEee------cceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHH
Q 041023 235 PVTELYEVCQKNKLKVKFVDLW------KESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNI 295 (303)
Q Consensus 235 Pk~~Lqe~~q~~~~~~~~~~~~------~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l 295 (303)
|++.|+|+|+++++.+.|.... ...|+|.|+++|+.++.|.|.|+|+ |++.||+.||+.|
T Consensus 1 p~~~L~e~~~~~~~~~~y~~~~~~g~~~~~~f~~~v~i~~~~~~~g~g~sKk~-Ak~~AA~~al~~L 66 (67)
T smart00358 1 PKSLLQELAQKRGLPPEYELVKEEGPDHAPRFTVTVKVGGEYTGEGEGSSKKE-AKQRAAEAALRSL 66 (67)
T ss_pred CchHHHHHHHHCCCCCEEEEEeeeCCCCCCcEEEEEEECCEEEEEeccCCHHH-HHHHHHHHHHHhc
Confidence 8999999999999854554332 2368999999999999999999996 9999999999876
No 21
>PF14709 DND1_DSRM: double strand RNA binding domain from DEAD END PROTEIN 1
Probab=98.30 E-value=1.4e-06 Score=64.88 Aligned_cols=64 Identities=27% Similarity=0.322 Sum_probs=51.2
Q ss_pred CCCccHHHHHHHhCCCcceEEEeec-------ceeEEEEEECCEEE---------EEEEeccchHHHHHHHHHHHHHHHH
Q 041023 233 THPVTELYEVCQKNKLKVKFVDLWK-------ESTAFHIFIEDQLL---------GRGAYAPKKEIAHNRAAKDALNNIE 296 (303)
Q Consensus 233 ~~Pk~~Lqe~~q~~~~~~~~~~~~~-------~~~~v~V~i~~~~i---------g~G~g~skk~~Ae~~AA~~AL~~l~ 296 (303)
.+|++.|+|+|+++++..|.|.+.. ..|.+.|.|.+... +-+.+.+.++.|+..||+.||+.|+
T Consensus 1 k~a~~~L~elC~k~~W~~P~y~l~~~~Gp~~~~~F~ykV~i~~~~~~~~~~~~~~~p~~~~~~~k~Ak~~AA~~~L~~Lg 80 (80)
T PF14709_consen 1 KSAVSLLNELCQKNKWGPPVYELVSESGPDHRKLFLYKVVIPGLEYPFEGSIECFGPTKPSSTKKEAKESAAQQALQALG 80 (80)
T ss_pred CCHHHHHHHHHHhcCCCCCeEEEEeccCCCccEEEEEEEEEcCCCCCCcceEEEccCCCcCccHHHHHHHHHHHHHHhcC
Confidence 4789999999999999999888753 25789999987544 2335666667799999999999874
No 22
>KOG3732 consensus Staufen and related double-stranded-RNA-binding proteins [Intracellular trafficking, secretion, and vesicular transport; Transcription]
Probab=98.26 E-value=1.6e-06 Score=79.69 Aligned_cols=65 Identities=25% Similarity=0.316 Sum_probs=56.7
Q ss_pred cCCCccHHHHHHHhCCCcceEEEeec-------ceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHhh
Q 041023 232 KTHPVTELYEVCQKNKLKVKFVDLWK-------ESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERL 298 (303)
Q Consensus 232 ~~~Pk~~Lqe~~q~~~~~~~~~~~~~-------~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~ 298 (303)
..||++.|+|+||.+++++|.|++.+ +.|++.|.+.+ ...+|.|.||| +|+++||...|+.+.-.
T Consensus 141 ~~NPI~~L~e~~q~k~~k~P~yelv~E~G~~~~rEFv~q~sv~~-~~~~GkG~sKK-iAKRnAAeamLe~l~~~ 212 (339)
T KOG3732|consen 141 VLNPIGRLQELAQAKKWKLPEYELVQESGVPHRREFVIQCSVEN-FTEEGKGPSKK-IAKRNAAEAMLESLGFV 212 (339)
T ss_pred ccChHHHHHHHHHHhCCCCCceEEEeccCCCccceEEEEEEecc-eeeecCCchHH-HHHHHHHHHHHHHhccC
Confidence 56999999999999999999988754 35899999988 57888989998 59999999999998743
No 23
>COG1939 Ribonuclease III family protein [Replication, recombination, and repair]
Probab=97.93 E-value=0.00011 Score=58.76 Aligned_cols=113 Identities=18% Similarity=0.242 Sum_probs=70.4
Q ss_pred ChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcChHHHHHHHHHcCchhhhhcCCcchHHHHHHHHHHhhcC
Q 041023 99 SYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDY 178 (303)
Q Consensus 99 ~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn~~La~~a~~~gL~~~i~~~~~~~~~~i~~~~~~~~~~ 178 (303)
|==-|+|+||||++++|-.|+...+- -.++.|++.-...||.+.-|.+-..+ ..++.- .+..|-+-. ...
T Consensus 14 n~laLAy~GDAV~e~yVR~~~l~~g~-~k~~~lH~~a~~~VsAk~QA~il~~~--~~~Lte----~E~~I~KRg---RNa 83 (132)
T COG1939 14 NGLALAYLGDAVYELYVREYLLLKGK-TKPNDLHKRATAYVSAKAQALILKAL--LEFLTE----EEEEIVKRG---RNA 83 (132)
T ss_pred CHHHHHHhhhHHHHHHHHHHHHhccc-CChHHHHHHHHHHhhHHHHHHHHHHH--HHHhhH----HHHHHHHHh---ccc
Confidence 34569999999999999999987533 36999999999999999988876543 112210 001111100 000
Q ss_pred CCCCC-CCCCC-chhHHHHHHHHhhhhcccCCCCHHHHHHHHHHhhc
Q 041023 179 PLHSN-GLVDA-PKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLK 223 (303)
Q Consensus 179 ~~~~~-~~~~~-~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ll~ 223 (303)
..... ...+. .=-.|.-|||+||.+|+-... +...+++...+.
T Consensus 84 ks~T~~kn~dv~tYr~sTgfEAliGyLyL~~~~--eRL~ell~~~i~ 128 (132)
T COG1939 84 KSGTKPKNTDVETYRMSTGFEALIGYLYLTKQE--ERLEELLNKVIE 128 (132)
T ss_pred ccCCCCCCCChHHHHHhhhHHHHHHHHHHcccH--HHHHHHHHHHHh
Confidence 00000 00011 124678899999999999876 667666665543
No 24
>KOG3732 consensus Staufen and related double-stranded-RNA-binding proteins [Intracellular trafficking, secretion, and vesicular transport; Transcription]
Probab=97.88 E-value=3.4e-05 Score=71.14 Aligned_cols=64 Identities=23% Similarity=0.333 Sum_probs=55.2
Q ss_pred CCCccHHHHHHHhCCCcceEEEe------ecceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHhh
Q 041023 233 THPVTELYEVCQKNKLKVKFVDL------WKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERL 298 (303)
Q Consensus 233 ~~Pk~~Lqe~~q~~~~~~~~~~~------~~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~ 298 (303)
+.|++.|||++.+.+..+.|..+ +.+.|++.|.++ ...+.|.|.|||. |+++||..+|..|+.+
T Consensus 38 KS~IS~l~E~~~r~~~~v~fevl~eeGp~H~~~fv~rvtvg-~~~a~GeG~sKK~-AKh~AA~~~L~~lk~l 107 (339)
T KOG3732|consen 38 KSPISLLQEYGLRRGLTPVYEVLREEGPPHMPNFVFRVTVG-EITATGEGKSKKL-AKHRAAEALLKELKKL 107 (339)
T ss_pred CChHHHHHHHHHHhCCCcceeeeeccCCccCCCeEEEEEEe-eeEEecCCCchhH-HHHHHHHHHHHHHhcC
Confidence 78999999999999987665443 346799999997 6889999999995 9999999999999876
No 25
>KOG4334 consensus Uncharacterized conserved protein, contains double-stranded RNA-binding motif and WW domain [General function prediction only]
Probab=96.72 E-value=0.0011 Score=63.86 Aligned_cols=59 Identities=24% Similarity=0.175 Sum_probs=48.8
Q ss_pred ccHHHHHHHhCCCcceEEEee-----cceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHH
Q 041023 236 VTELYEVCQKNKLKVKFVDLW-----KESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNI 295 (303)
Q Consensus 236 k~~Lqe~~q~~~~~~~~~~~~-----~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l 295 (303)
+-.|.|++|+.....|+|... ...|..+|.+|+-.+|+|.|.|||. |+..||+++|+.|
T Consensus 378 vCiLhEy~q~~lk~~pvyef~e~~n~stpysa~v~~d~~~yGsG~g~sKK~-Ak~~AAR~tLeiL 441 (650)
T KOG4334|consen 378 VCILHEYAQQCLKSLPVYEFAENDNNSTPYSAGVLPDLFPYGSGVGASKKT-AKLVAARDTLEIL 441 (650)
T ss_pred eehHHHHHHHHhhhcceeehhhccCCCCcccccccccccccccccccchHH-HHHHHHHHHHHHh
Confidence 358899998877777777542 2357899999999999999999995 9999999998765
No 26
>KOG2777 consensus tRNA-specific adenosine deaminase 1 [RNA processing and modification]
Probab=96.39 E-value=0.0064 Score=60.04 Aligned_cols=63 Identities=25% Similarity=0.345 Sum_probs=50.1
Q ss_pred cCCCccHHHHHHHhCCCcceEEEe----ecceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHhh
Q 041023 232 KTHPVTELYEVCQKNKLKVKFVDL----WKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERL 298 (303)
Q Consensus 232 ~~~Pk~~Lqe~~q~~~~~~~~~~~----~~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~ 298 (303)
..+|...|.|+.+ +....++.. ....|.|.|.+||..+-.| |.|||+ |++.||+.||+.+..+
T Consensus 89 ~~npv~ll~e~~~--~~~~~~~~~~~~~~~~~F~~~~~vdg~~~~~~-~~sKk~-ak~~aa~~al~~l~~~ 155 (542)
T KOG2777|consen 89 GKNPVSLLHELAN--GLFFDFVNESGPQHAPKFVMSVVVDGRWFEGG-GRSKKE-AKQEAAMAALQVLFKI 155 (542)
T ss_pred cCCchHHHHHHhc--ccceeeeccCCCCCCceEEEEEEECCEEccCC-CcchHH-HHHHHHHHHHHHHHhc
Confidence 5699999999998 333333332 2346899999999988777 999996 9999999999998765
No 27
>PF11469 Ribonucleas_3_2: Ribonuclease III; InterPro: IPR021568 This archaeal family of proteins has no known function. ; PDB: 1ZTD_A.
Probab=91.02 E-value=1.8 Score=33.55 Aligned_cols=87 Identities=24% Similarity=0.276 Sum_probs=58.1
Q ss_pred HHHHhhHHHHHHHHHHHHHH--hCCCCChhchHHHHHhhcChHHHHHHHHHcCchhhhhcCCcchHHHHHHHHHHhhcCC
Q 041023 102 RLEYVGDSVLNLLLTKEQFF--LYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYP 179 (303)
Q Consensus 102 rLEfLGDavL~~~v~~~l~~--~~p~~~~g~Lt~lr~~lvsn~~La~~a~~~gL~~~i~~~~~~~~~~i~~~~~~~~~~~ 179 (303)
-|.-+||++++++++.-|-+ -+|. | .-|-|.+|+---...||.+.+.-..
T Consensus 2 ~Lak~GDSLvNfl~SlALse~lG~Pt---g-------~rVPnaSLaiAl~~a~L~~~~~PR~------------------ 53 (120)
T PF11469_consen 2 GLAKFGDSLVNFLFSLALSEYLGRPT---G-------DRVPNASLAIALELAGLSHLLPPRT------------------ 53 (120)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTS-----------------HHHHHHHHHHTTGGGCS--CG------------------
T ss_pred cHHHHhHHHHHHHHHHHHHHHhCCCC---C-------CCCCChHHHHHHHHHhhhhhCcccc------------------
Confidence 47889999999999987743 3443 2 2377888888888888887664211
Q ss_pred CCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHhhcc
Q 041023 180 LHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKP 224 (303)
Q Consensus 180 ~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ll~~ 224 (303)
...--+|+.||+|+--|+.+-+..+.+-++++.-+.+
T Consensus 54 --------dkh~kGd~aEA~iAyAWLeg~it~eEaveil~~nl~~ 90 (120)
T PF11469_consen 54 --------DKHGKGDIAEALIAYAWLEGKITIEEAVEILKANLTE 90 (120)
T ss_dssp --------GCCGHHHHHHHHHHHHHHTTSS-HHHHHHHHHCT--G
T ss_pred --------cccCccHHHHHHHHHHHHhccccHHHHHHHHHhcCch
Confidence 1235789999999999999988777777777655443
No 28
>PF03368 Dicer_dimer: Dicer dimerisation domain; InterPro: IPR005034 This domain is found in members of the Dicer protein family of dsRNA nucleases. This entry represents a dsRNA-binding domain. RNA interference (RNAi) is an ancient gene-silencing process that plays a fundamental role in diverse eukaryotic functions including viral defence, chromatin remodelling, genome rearrangement, developmental timing, brain morphogenesis, and stem cell maintenance. All RNAi pathways require the multidomain ribonuclease Dicer, which initiates RNAi by cleaving double-stranded RNA (dsRNA) substrates into small fragments ~25 nuleotides in length. A typical eukaryotic Dicer consists of a helicase domain (PDOC51192 from PROSITEDOC), a domain of unknown function, and a PAZ domain (PDOC50821 from PROSITEDOC) at the amino (N)-terminus as well as two ribonuclease III domains (PDOC00448 from PROSITEDOC) and a dsRNA-binding domain (dsRBD) (PDOC50137 from PROSITEDOC) at the carboxy (C)-terminus. The domain of unknown function of ~100 amino acids is predicted to adopt the canonical alpha-beta-beta-beta-alpha-fold found in all dsRBDs [, , , ].; GO: 0016891 endoribonuclease activity, producing 5'-phosphomonoesters; PDB: 2KOU_A.
Probab=88.00 E-value=2.9 Score=31.55 Aligned_cols=61 Identities=15% Similarity=0.169 Sum_probs=36.5
Q ss_pred ccHHHHHHHhCCCc-----ceEEEee--cceeEEEEEECC-----EEEEEEEeccchHHHHHHHHHHHHHHHHhh
Q 041023 236 VTELYEVCQKNKLK-----VKFVDLW--KESTAFHIFIED-----QLLGRGAYAPKKEIAHNRAAKDALNNIERL 298 (303)
Q Consensus 236 k~~Lqe~~q~~~~~-----~~~~~~~--~~~~~v~V~i~~-----~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~ 298 (303)
++.|+++|++.... -|.+.+. ...|.|+|.+-. ...|. ...|++ .|++.||-+|+..|-++
T Consensus 2 i~lL~~yC~~Lp~d~~~~~~P~~~~~~~~~~~~c~v~LP~~~pi~~i~g~-~~~sk~-~AK~sAAf~Ac~~L~~~ 74 (90)
T PF03368_consen 2 ISLLNRYCSTLPSDSFTNLKPEFEIEKIGSGFICTVILPINSPIRSIEGP-PMRSKK-LAKRSAAFEACKKLHEA 74 (90)
T ss_dssp HHHHHHHHTTSSS-TT--SS-EEEEEE--G-EEEEEE--TT-SS--EEEE---SSHH-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCCCCccCCceEEEEEcCCcEEEEEECCCCCCCCeEEcc-ccccHH-HHHHHHHHHHHHHHHHc
Confidence 35678888875321 2444332 335788887642 14555 345666 59999999999999876
No 29
>PF14954 LIX1: Limb expression 1
Probab=63.76 E-value=18 Score=31.90 Aligned_cols=68 Identities=24% Similarity=0.197 Sum_probs=41.4
Q ss_pred cCCCccHHHHHHHhC---CCc-----ceEEEee---cceeEEEEEEC-CEEEEEEEeccchHHHHHHHHHHHHHHHHhhh
Q 041023 232 KTHPVTELYEVCQKN---KLK-----VKFVDLW---KESTAFHIFIE-DQLLGRGAYAPKKEIAHNRAAKDALNNIERLL 299 (303)
Q Consensus 232 ~~~Pk~~Lqe~~q~~---~~~-----~~~~~~~---~~~~~v~V~i~-~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~~ 299 (303)
..|-+..|||+=+.+ |.. +..|+.. .+.|.|-|++- |..+|.-.-...|.+|++.||+.||-+ .+|
T Consensus 20 ~vnvV~~LqeFWq~Kq~r~a~~~~~~lv~YEs~ps~~ppyVcyVTLPGGSCFGnfq~C~tkAEARR~AAKiALmN--Svf 97 (252)
T PF14954_consen 20 DVNVVEALQEFWQMKQSRGADLKSEALVVYESVPSPSPPYVCYVTLPGGSCFGNFQNCPTKAEARRSAAKIALMN--SVF 97 (252)
T ss_pred cchHHHHHHHHHHHHHhccccCCCCCeeeeeccCCCCCCeEEEEeCCCCCccCccccCCcHHHHHhhhHHHHHHH--HHH
Confidence 346678888865432 222 2334332 33577888874 455666555556667999999999853 444
Q ss_pred cc
Q 041023 300 NE 301 (303)
Q Consensus 300 ~~ 301 (303)
.|
T Consensus 98 NE 99 (252)
T PF14954_consen 98 NE 99 (252)
T ss_pred hc
Confidence 44
No 30
>PF13820 Nucleic_acid_bd: Putative nucleic acid-binding region
Probab=63.45 E-value=1.2 Score=37.01 Aligned_cols=90 Identities=22% Similarity=0.340 Sum_probs=56.2
Q ss_pred HHHHHHhhhhcccCCCCHHHHHHHHHHhhcccCCCCc---------------ccCCCccHHHHHHHhCCCcceEEEeecc
Q 041023 194 DIVESTIGAVFIDCNSSIDIVWKVFKELLKPMISPET---------------LKTHPVTELYEVCQKNKLKVKFVDLWKE 258 (303)
Q Consensus 194 D~fEAliGAIylD~G~~~~~v~~~i~~ll~~~l~~~~---------------~~~~Pk~~Lqe~~q~~~~~~~~~~~~~~ 258 (303)
++|-|++|.+- +-+.+++..+.|+..++.+....-. ++....+.|..+++.....+.+--+
T Consensus 3 nifla~~G~l~-~~~~~ld~i~~~l~~L~~~~~~~l~~~~~~~~~sv~V~f~ipreaa~~Lr~LA~~~~~~L~~lgI--- 78 (149)
T PF13820_consen 3 NIFLAYIGGLR-MFQYKLDDIKNWLASLYKPRISDLKVRKVEPWNSVRVTFSIPREAATRLRQLAQHSNPRLRYLGI--- 78 (149)
T ss_pred eEEEEEECChh-hhHHHHHHHHHHHHHHHhcccccceeeccccCceEEEEEechHHHHHHHHHHhhcCCcceeeece---
Confidence 45556777766 5566788999999999988755321 1223346777777766555444322
Q ss_pred eeEEEEEECC-EEEEEEEeccchHHHHHHHHHH
Q 041023 259 STAFHIFIED-QLLGRGAYAPKKEIAHNRAAKD 290 (303)
Q Consensus 259 ~~~v~V~i~~-~~ig~G~g~skk~~Ae~~AA~~ 290 (303)
-.|-|+| ..|+.|.+...-+.|++.|+.+
T Consensus 79 ---~SVQIe~e~~I~l~~~~~~~~~~r~~~~~~ 108 (149)
T PF13820_consen 79 ---LSVQIEGEEPIGLGVSSNSFDEARDRADID 108 (149)
T ss_pred ---EEEEEcCcceeEeccCCCCCcccceecccc
Confidence 2355543 3578887776655577776655
No 31
>KOG2334 consensus tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=57.88 E-value=3.8 Score=39.59 Aligned_cols=66 Identities=20% Similarity=0.161 Sum_probs=53.5
Q ss_pred cCCCccHHHHHHHhCCCcceEEEeec---ceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHh
Q 041023 232 KTHPVTELYEVCQKNKLKVKFVDLWK---ESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIER 297 (303)
Q Consensus 232 ~~~Pk~~Lqe~~q~~~~~~~~~~~~~---~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~ 297 (303)
...|+..|..+|.+.+..-+.|+..+ ..|...++++|+.+-.+.+..+++.|+|.||..+|.+...
T Consensus 374 ~~~~k~~l~~~~~~~~~~~~~ye~~~~~d~lf~si~~~~~~~~~ssi~~~n~k~aeq~aa~~~l~~s~l 442 (477)
T KOG2334|consen 374 WDTPKMVLADLCVKTKANGPVYETVQRTDKLFSSIATARGQKYNSSIWSPNKKSAEQDAAIVALRKSNL 442 (477)
T ss_pred CCCHHHHHHHhhhhhcCCCcchhhhhhhhhhhHHHhhhhhhhhhccccCcchhhHHHHHHHHHHHhcCc
Confidence 46799999999999988777776543 3466677888988888888877778999999999987643
No 32
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=53.09 E-value=50 Score=24.41 Aligned_cols=43 Identities=23% Similarity=0.346 Sum_probs=30.0
Q ss_pred EEeecceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHhh
Q 041023 253 VDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERL 298 (303)
Q Consensus 253 ~~~~~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~ 298 (303)
++..++..++.|+-.|+.+-+|. .|..+ |++ |++..+..|+++
T Consensus 43 ~r~~~p~~t~~IF~sGki~itGa-ks~~~-~~~-a~~~i~~~L~~~ 85 (86)
T PF00352_consen 43 YRLRNPKATVLIFSSGKIVITGA-KSEEE-AKK-AIEKILPILQKL 85 (86)
T ss_dssp EEETTTTEEEEEETTSEEEEEEE-SSHHH-HHH-HHHHHHHHHHHT
T ss_pred EeecCCcEEEEEEcCCEEEEEec-CCHHH-HHH-HHHHHHHHHHHc
Confidence 44455567888999999999985 45553 665 677777766654
No 33
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=47.55 E-value=31 Score=36.91 Aligned_cols=62 Identities=24% Similarity=0.217 Sum_probs=46.7
Q ss_pred CCccHHHHHHHhCCCcceEEEee------cceeEEEEEECCE-EEEEEEeccchHHHHHHHHHHHHHHHHh
Q 041023 234 HPVTELYEVCQKNKLKVKFVDLW------KESTAFHIFIEDQ-LLGRGAYAPKKEIAHNRAAKDALNNIER 297 (303)
Q Consensus 234 ~Pk~~Lqe~~q~~~~~~~~~~~~------~~~~~v~V~i~~~-~ig~G~g~skk~~Ae~~AA~~AL~~l~~ 297 (303)
|-|.-|..||.+.... |.|++. ...|.|.|.+.+. ..+.|....+|+ |+..||++-++.+-.
T Consensus 2 d~k~fly~~~~k~~~~-p~~d~~~~~~~~rqrf~ce~~~~~~~~~~~~~stnkKd-a~knac~dfv~ylvr 70 (1282)
T KOG0921|consen 2 DVKEFLYAWLGKNKYG-PTYDIRSEGRKGRQRFLCEVRVEGFGYTAVGNSTNKKD-AATNAAQDFCQYLVR 70 (1282)
T ss_pred cHHHHHHHHHhhhccC-cceehhhhcccchhheeeeeeccCCcceeeecccccch-hhHHHHHHHHHHhhh
Confidence 4577899999998887 444432 2357899988775 467788888887 999999998887643
No 34
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=43.18 E-value=73 Score=27.09 Aligned_cols=44 Identities=23% Similarity=0.325 Sum_probs=32.0
Q ss_pred EEEeecceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHhh
Q 041023 252 FVDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERL 298 (303)
Q Consensus 252 ~~~~~~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~ 298 (303)
++++.++.-++.|+..|+.+.+|. .|..+ |+. |++..++.|+++
T Consensus 40 i~R~~~P~~t~lIf~sGKivitGa-ks~~~-~~~-a~~~~~~~L~~~ 83 (174)
T cd00652 40 IMRLREPKTTALIFSSGKMVITGA-KSEED-AKL-AARKYARILQKL 83 (174)
T ss_pred EEEcCCCcEEEEEECCCEEEEEec-CCHHH-HHH-HHHHHHHHHHHc
Confidence 344555667899999999999984 45543 665 778787777766
No 35
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=41.01 E-value=79 Score=26.94 Aligned_cols=44 Identities=20% Similarity=0.311 Sum_probs=32.5
Q ss_pred EEEeecceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHhh
Q 041023 252 FVDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERL 298 (303)
Q Consensus 252 ~~~~~~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~ 298 (303)
++++.++.-++.|+..|+.+-+|. .|..+ |+. |++..++.|+++
T Consensus 40 i~Rl~~Pk~t~lIF~SGKiv~tGa-ks~~~-a~~-a~~~~~~~L~~~ 83 (174)
T cd04518 40 VYRLEDPKIAALIFRSGKMVCTGA-KSVED-LHR-AVKEIIKKLKDY 83 (174)
T ss_pred EEEccCCcEEEEEECCCeEEEEcc-CCHHH-HHH-HHHHHHHHHHhc
Confidence 445556667889999999999985 45543 765 778888888776
No 36
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=40.32 E-value=89 Score=26.61 Aligned_cols=44 Identities=20% Similarity=0.329 Sum_probs=31.1
Q ss_pred EEEeecceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHhh
Q 041023 252 FVDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERL 298 (303)
Q Consensus 252 ~~~~~~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~ 298 (303)
++++.++.-++.++..|+.+-+|. .|..+ |+. |++..++.|+++
T Consensus 40 i~Rl~~Pk~t~lIF~SGKiviTGa-ks~e~-a~~-a~~~i~~~L~~~ 83 (174)
T cd04516 40 IMRIREPKTTALIFSSGKMVCTGA-KSEDD-SKL-AARKYARIIQKL 83 (174)
T ss_pred EEEeCCCcEEEEEECCCeEEEEec-CCHHH-HHH-HHHHHHHHHHHc
Confidence 344556666889999999999984 45543 665 667777777765
No 37
>PF02169 LPP20: LPP20 lipoprotein; InterPro: IPR002217 A major antigen has been recognised in Helicobacter pylori, a protein with an apparent molecular weight of 20,000 and mass 18,283 kDa []. DNA sequence analysis revealed a 525 bp gene, encoding a 175-amino acid residue product with a typical 21-residue lipoprotein signal peptide and consensus prolipoprotein processing site []. Results of experimental work with Lpp20 are consistent with it being a nonessential lipoprotein []. Prokaryotic membrane lipoproteins are synthesised with precursor signal peptides that are cleaved by specific peptidases (signal peptidase II). The enzyme recognises a conserved sequence, cutting upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached [].; GO: 0009279 cell outer membrane
Probab=39.78 E-value=44 Score=24.54 Aligned_cols=27 Identities=19% Similarity=0.275 Sum_probs=20.0
Q ss_pred CEEEEEEEeccchHHHHHHHHHHHHHHH
Q 041023 268 DQLLGRGAYAPKKEIAHNRAAKDALNNI 295 (303)
Q Consensus 268 ~~~ig~G~g~skk~~Ae~~AA~~AL~~l 295 (303)
..+.|.|.|.+... |++.|-.+..+.+
T Consensus 12 ~~l~a~G~~~~~~~-A~~~A~~~la~~i 38 (92)
T PF02169_consen 12 QYLYAVGSGSSREQ-AKQDALANLAEQI 38 (92)
T ss_pred cEEEEEEcccChHH-HHHHHHHHHHHhe
Confidence 34789999988864 8887777666644
No 38
>PF08383 Maf_N: Maf N-terminal region; InterPro: IPR013592 This region is found in various leucine zipper transcription factors of the Maf family. These are implicated in the regulation of insulin gene expression [], in erythroid differentiation [], and in differentiation of the neuroretina [].
Probab=36.27 E-value=20 Score=22.06 Aligned_cols=11 Identities=45% Similarity=0.567 Sum_probs=9.1
Q ss_pred HHHHHHHHhhh
Q 041023 192 LADIVESTIGA 202 (303)
Q Consensus 192 laD~fEAliGA 202 (303)
-.|++||+||+
T Consensus 25 pEDAvEaLi~~ 35 (35)
T PF08383_consen 25 PEDAVEALIGN 35 (35)
T ss_pred HHHHHHHHhcC
Confidence 36999999984
No 39
>PLN00062 TATA-box-binding protein; Provisional
Probab=34.18 E-value=1.3e+02 Score=25.79 Aligned_cols=44 Identities=20% Similarity=0.288 Sum_probs=30.3
Q ss_pred EEEeecceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHhh
Q 041023 252 FVDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERL 298 (303)
Q Consensus 252 ~~~~~~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~ 298 (303)
++++.++.-++.|+..|+.+-+|. .|.. .|+. |++..++.|+++
T Consensus 40 i~Rl~~Pk~t~lIF~SGKiviTGa-ks~e-~a~~-a~~~~~~~L~~l 83 (179)
T PLN00062 40 IMRIREPKTTALIFASGKMVCTGA-KSEH-DSKL-AARKYARIIQKL 83 (179)
T ss_pred EEEeCCCcEEEEEECCCeEEEEec-CCHH-HHHH-HHHHHHHHHHHc
Confidence 345556666889999999999984 4444 3654 667666777665
No 40
>PRK00394 transcription factor; Reviewed
Probab=34.04 E-value=1.1e+02 Score=26.05 Aligned_cols=44 Identities=23% Similarity=0.295 Sum_probs=32.2
Q ss_pred EEEeecceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHhh
Q 041023 252 FVDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERL 298 (303)
Q Consensus 252 ~~~~~~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~ 298 (303)
++++.++.-++.|+-.|+.+-+|. .|..+ |+. |++..++.|+++
T Consensus 39 i~Rl~~Pk~t~lIf~sGKiv~tGa-~S~~~-a~~-a~~~~~~~l~~~ 82 (179)
T PRK00394 39 VYRLEDPKIAALIFRSGKVVCTGA-KSVED-LHE-AVKIIIKKLKEL 82 (179)
T ss_pred EEEecCCceEEEEEcCCcEEEEcc-CCHHH-HHH-HHHHHHHHHHHc
Confidence 344555667889999999999984 45543 775 778888888776
No 41
>PF07411 DUF1508: Domain of unknown function (DUF1508); InterPro: IPR010879 This domain is found in a family of proteins, which have no known function. Members of this family are often found as tandem repeats and in some cases represent the whole protein.; PDB: 3BID_H 2K49_A 2K8E_A 2K7I_A.
Probab=34.04 E-value=86 Score=20.67 Aligned_cols=30 Identities=7% Similarity=0.133 Sum_probs=20.5
Q ss_pred ECCEEEEEEEeccchHHHHHHHHHHHHHHHHhhhc
Q 041023 266 IEDQLLGRGAYAPKKEIAHNRAAKDALNNIERLLN 300 (303)
Q Consensus 266 i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~~~ 300 (303)
-||+.++.+.+.+.+. +|+.+++.++.--|
T Consensus 13 ~ng~viasse~Y~sk~-----~a~~~I~~Vk~~a~ 42 (49)
T PF07411_consen 13 GNGEVIASSEGYSSKA-----DAEKGIESVKKNAP 42 (49)
T ss_dssp TTS-EEEEBEEBSSHH-----HHHHHHHHHHHHTT
T ss_pred CCCCEEEecCCcCCHH-----HHHHHHHHHHHhCC
Confidence 3688999998888774 66667766665433
No 42
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=32.54 E-value=1.3e+02 Score=25.51 Aligned_cols=43 Identities=19% Similarity=0.286 Sum_probs=30.0
Q ss_pred EEeecceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHhh
Q 041023 253 VDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERL 298 (303)
Q Consensus 253 ~~~~~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~~ 298 (303)
++..++.-++.++-+|+.+.+|. .|.. .|+. |++..++.++++
T Consensus 41 ~R~~~Pk~t~lIF~sGKiviTGa-ks~~-~~~~-a~~~~~~~l~~~ 83 (174)
T cd04517 41 MRLREPRATASVWSSGKITITGA-TSEE-EAKQ-AARRAARLLQKL 83 (174)
T ss_pred EEecCCcEEEEEECCCeEEEEcc-CCHH-HHHH-HHHHHHHHHHHc
Confidence 34445556788999999999984 4554 3665 677777777665
No 43
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=32.12 E-value=49 Score=21.17 Aligned_cols=33 Identities=18% Similarity=0.353 Sum_probs=15.9
Q ss_pred CCCCChhchHHHHHhhcChHHHHHHHHHcCchh
Q 041023 123 YPNLPPGSLTRLRSANVNTEKLARVAIKLGLHK 155 (303)
Q Consensus 123 ~p~~~~g~Lt~lr~~lvsn~~La~~a~~~gL~~ 155 (303)
|+.+++.+-..+...+-.+.+...+|..+|.+.
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~s~~~IA~~lg~s~ 34 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGMSIREIAKRLGRSR 34 (44)
T ss_dssp ----------HHHHHHCS---HHHHHHHTT--H
T ss_pred ccchhhhHHHHHHHHHHcCCCHHHHHHHHCcCc
Confidence 567788887788888889999999999999775
No 44
>PF04098 Rad52_Rad22: Rad52/22 family double-strand break repair protein; InterPro: IPR007232 The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to Rad52. These proteins contain two helix-hairpin-helix motifs [].; GO: 0006281 DNA repair, 0006310 DNA recombination; PDB: 1KN0_I 1H2I_U.
Probab=29.61 E-value=2.4e+02 Score=23.26 Aligned_cols=18 Identities=33% Similarity=0.353 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHHhhhc
Q 041023 283 AHNRAAKDALNNIERLLN 300 (303)
Q Consensus 283 Ae~~AA~~AL~~l~~~~~ 300 (303)
|++.|.-+|+++--..|+
T Consensus 111 akK~AvtdAlKRA~~~fG 128 (154)
T PF04098_consen 111 AKKGAVTDALKRALRSFG 128 (154)
T ss_dssp HHHHHHHHHHHHHHHTT-
T ss_pred hHHHHHHHHHHHHHHHHH
Confidence 566666666666555554
No 45
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=29.12 E-value=53 Score=23.67 Aligned_cols=41 Identities=17% Similarity=0.232 Sum_probs=26.1
Q ss_pred HHHHHHHh---CCCCChhchHHHHHhhcChHHHHHHHHHcCchhhh
Q 041023 115 LTKEQFFL---YPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYL 157 (303)
Q Consensus 115 v~~~l~~~---~p~~~~g~Lt~lr~~lvsn~~La~~a~~~gL~~~i 157 (303)
+++|+..+ .+..+..++. +..-||..++.+.|+++|+..|-
T Consensus 21 Ia~yil~~~~~~~~~si~elA--~~~~vS~sti~Rf~kkLG~~gf~ 64 (77)
T PF01418_consen 21 IADYILENPDEIAFMSISELA--EKAGVSPSTIVRFCKKLGFSGFK 64 (77)
T ss_dssp HHHHHHH-HHHHCT--HHHHH--HHCTS-HHHHHHHHHHCTTTCHH
T ss_pred HHHHHHhCHHHHHHccHHHHH--HHcCCCHHHHHHHHHHhCCCCHH
Confidence 44444443 2344555444 56889999999999999998874
No 46
>PF00333 Ribosomal_S5: Ribosomal protein S5, N-terminal domain; InterPro: IPR013810 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S5 is one of the proteins from the small ribosomal subunit, and is a protein of 166 to 254 amino-acid residues. In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational error frequencies. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacterial, cyanelle, red algal chloroplast, archaeal and fungal mitochondrial S5; mammalian, Caenorhabditis elegans, Drosophila and plant S2; and yeast S4 (SUP44). This entry represents the N-terminal domain of ribosomal protein S5, which has an alpha-beta(3)-alpha structure that folds into two layers, alpha/beta.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZKQ_e 2XZN_E 2XZM_E 3O30_B 1S1H_E 3IZB_E 3U5C_C 3U5G_C 3O2Z_B 3BBN_E ....
Probab=28.57 E-value=82 Score=22.39 Aligned_cols=36 Identities=22% Similarity=0.299 Sum_probs=23.9
Q ss_pred eeEEEEEECCE--E--EEEEEeccchHHHHHHHHHHHHHHH
Q 041023 259 STAFHIFIEDQ--L--LGRGAYAPKKEIAHNRAAKDALNNI 295 (303)
Q Consensus 259 ~~~v~V~i~~~--~--ig~G~g~skk~~Ae~~AA~~AL~~l 295 (303)
+|.+-|.+++. . +|.|.+..... |-+.|-++|.++|
T Consensus 23 ~~~alvvvGn~~G~vG~G~gKa~~~~~-Ai~kA~~~A~knl 62 (67)
T PF00333_consen 23 SFRALVVVGNGNGLVGFGVGKAKEVPD-AIRKAKRKAKKNL 62 (67)
T ss_dssp EEEEEEEEECSSSEEEEEEEEESSHHH-HHHHHHHHHHCSE
T ss_pred EEEEEEEEecCCCcEecCcccchhHHH-HHHHHHHHHHhCC
Confidence 45666777543 3 55666666664 8888888887655
No 47
>PRK14741 spoVM stage V sporulation protein M; Provisional
Probab=27.38 E-value=57 Score=18.43 Aligned_cols=17 Identities=35% Similarity=0.661 Sum_probs=14.9
Q ss_pred CCchhHHHHHHHHhhhh
Q 041023 187 DAPKVLADIVESTIGAV 203 (303)
Q Consensus 187 ~~~k~laD~fEAliGAI 203 (303)
..||.++.++.|++||.
T Consensus 7 klpkflgg~vra~l~~f 23 (26)
T PRK14741 7 KLPKFLGGIVRAMLGSF 23 (26)
T ss_pred eccHHHHHHHHHHHHHh
Confidence 45899999999999985
No 48
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=25.04 E-value=1.7e+02 Score=20.72 Aligned_cols=32 Identities=9% Similarity=0.267 Sum_probs=23.5
Q ss_pred HHHhhHHHHHHHHHHHHHHhC----CCCChhchHHH
Q 041023 103 LEYVGDSVLNLLLTKEQFFLY----PNLPPGSLTRL 134 (303)
Q Consensus 103 LEfLGDavL~~~v~~~l~~~~----p~~~~g~Lt~l 134 (303)
+.+++-.++.++++...++++ |..+|..+..+
T Consensus 5 lali~G~~~Gff~ar~~~~k~l~~NPpine~mir~M 40 (64)
T PF03672_consen 5 LALIVGAVIGFFIARKYMEKQLKENPPINEKMIRAM 40 (64)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
Confidence 678899999999999888765 55555554443
No 49
>PF11324 DUF3126: Protein of unknown function (DUF3126); InterPro: IPR021473 This family of proteins with unknown function appear to be restricted to Alphaproteobacteria.
Probab=24.83 E-value=1.6e+02 Score=20.74 Aligned_cols=38 Identities=13% Similarity=0.175 Sum_probs=21.5
Q ss_pred cHHHHHHHhCCCc--ceEEEeecceeEEEEEECCEEEEEE
Q 041023 237 TELYEVCQKNKLK--VKFVDLWKESTAFHIFIEDQLLGRG 274 (303)
Q Consensus 237 ~~Lqe~~q~~~~~--~~~~~~~~~~~~v~V~i~~~~ig~G 274 (303)
.+||.+.++.-.. +.+..-.+..-.++|++++.++|.=
T Consensus 3 ~klq~yLr~~f~n~~i~v~~rpk~~dsaEV~~g~EfiGvi 42 (63)
T PF11324_consen 3 KKLQAYLRRTFGNPGITVKARPKKDDSAEVYIGDEFIGVI 42 (63)
T ss_pred HHHHHHHHHHhCCCceEEEcCCCCCCceEEEeCCEEEEEE
Confidence 4566666654322 2222112223479999999999873
No 50
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=23.26 E-value=2e+02 Score=18.33 Aligned_cols=25 Identities=24% Similarity=0.300 Sum_probs=13.6
Q ss_pred EEEEEeccchHHHHHHHHHHHHHHHHh
Q 041023 271 LGRGAYAPKKEIAHNRAAKDALNNIER 297 (303)
Q Consensus 271 ig~G~g~skk~~Ae~~AA~~AL~~l~~ 297 (303)
.-.+...++++ |+. |+..++..+.+
T Consensus 19 ~~k~GF~Tkke-A~~-~~~~~~~~~~~ 43 (46)
T PF14657_consen 19 KTKRGFKTKKE-AEK-ALAKIEAELEN 43 (46)
T ss_pred EEcCCCCcHHH-HHH-HHHHHHHHHHc
Confidence 34443456664 887 44446555543
No 51
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=22.42 E-value=2.7e+02 Score=23.65 Aligned_cols=43 Identities=16% Similarity=0.298 Sum_probs=27.7
Q ss_pred EEEeecceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHHHHHHh
Q 041023 252 FVDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIER 297 (303)
Q Consensus 252 ~~~~~~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL~~l~~ 297 (303)
+|++.++.-++-|+..|+.+-+|. .|..+ ++. |.+.-+..|++
T Consensus 131 vyR~~~pk~~~lIF~SGKvvitGa-ks~~~-~~~-a~~~i~~~l~~ 173 (174)
T cd04518 131 VYRLDEPKVVLLLFSSGKMVITGA-KSEED-AKR-AVEKLLSRLKE 173 (174)
T ss_pred EEEecCCcEEEEEeCCCEEEEEec-CCHHH-HHH-HHHHHHHHHhh
Confidence 345555667888999999999994 44443 554 45555555543
No 52
>PRK01844 hypothetical protein; Provisional
Probab=20.63 E-value=3e+02 Score=19.98 Aligned_cols=35 Identities=14% Similarity=0.330 Sum_probs=25.6
Q ss_pred HHHhhHHHHHHHHHHHHHHhC----CCCChhchHHHHHh
Q 041023 103 LEYVGDSVLNLLLTKEQFFLY----PNLPPGSLTRLRSA 137 (303)
Q Consensus 103 LEfLGDavL~~~v~~~l~~~~----p~~~~g~Lt~lr~~ 137 (303)
+.+|+-.++.++++...+++| |..+|..+..+-..
T Consensus 12 ~~li~G~~~Gff~ark~~~k~lk~NPpine~mir~Mm~Q 50 (72)
T PRK01844 12 VALVAGVALGFFIARKYMMNYLQKNPPINEQMLKMMMMQ 50 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence 568889999999998887765 67777665544433
Done!