Query 003062
Match_columns 852
No_of_seqs 391 out of 2513
Neff 8.1
Searched_HMMs 46136
Date Thu Mar 28 16:16:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003062.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003062hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0701 dsRNA-specific nucleas 100.0 5.6E-57 1.2E-61 547.5 13.7 793 1-849 378-1600(1606)
2 KOG1817 Ribonuclease [RNA proc 100.0 7.9E-51 1.7E-55 424.4 25.3 403 387-847 15-503 (533)
3 PRK12371 ribonuclease III; Rev 100.0 7E-44 1.5E-48 368.6 22.4 220 605-849 10-233 (235)
4 COG0571 Rnc dsRNA-specific rib 100.0 2.5E-43 5.4E-48 359.3 21.5 222 605-850 6-234 (235)
5 PRK12372 ribonuclease III; Rev 100.0 2.8E-43 6E-48 377.1 21.3 217 607-850 3-225 (413)
6 PRK14718 ribonuclease III; Pro 100.0 4.3E-43 9.4E-48 376.3 20.6 216 607-849 3-224 (467)
7 PRK00102 rnc ribonuclease III; 100.0 5.3E-40 1.2E-44 343.4 21.6 218 606-847 4-228 (229)
8 TIGR02191 RNaseIII ribonucleas 100.0 1.6E-38 3.4E-43 330.5 20.6 212 610-845 1-220 (220)
9 PRK12371 ribonuclease III; Rev 99.9 6.3E-27 1.4E-31 242.3 11.6 134 416-582 13-148 (235)
10 COG0571 Rnc dsRNA-specific rib 99.9 1.3E-26 2.9E-31 236.7 11.3 134 416-582 9-146 (235)
11 PF14622 Ribonucleas_3_3: Ribo 99.9 6.3E-27 1.4E-31 220.8 6.1 126 620-770 1-126 (128)
12 PRK14718 ribonuclease III; Pro 99.9 2.5E-26 5.5E-31 247.4 11.5 132 417-582 5-136 (467)
13 PRK12372 ribonuclease III; Rev 99.9 4.1E-26 9E-31 245.2 11.4 132 417-582 5-136 (413)
14 smart00535 RIBOc Ribonuclease 99.9 2.3E-24 5.1E-29 204.6 10.9 127 622-773 1-127 (129)
15 cd00593 RIBOc RIBOc. Ribonucle 99.9 1.9E-24 4.1E-29 206.4 10.0 130 622-774 1-130 (133)
16 PF14622 Ribonucleas_3_3: Ribo 99.9 3.5E-24 7.7E-29 202.1 5.8 120 434-582 2-123 (128)
17 PRK00102 rnc ribonuclease III; 99.9 2.2E-23 4.8E-28 218.0 11.0 134 416-582 6-143 (229)
18 smart00535 RIBOc Ribonuclease 99.9 6.8E-23 1.5E-27 194.5 9.6 119 436-582 2-121 (129)
19 TIGR02191 RNaseIII ribonucleas 99.9 7E-23 1.5E-27 213.0 10.3 132 418-582 1-137 (220)
20 cd00593 RIBOc RIBOc. Ribonucle 99.9 7.1E-23 1.5E-27 195.5 9.0 119 436-582 2-123 (133)
21 PF00636 Ribonuclease_3: Ribon 99.9 2E-22 4.3E-27 187.0 5.8 112 643-754 1-114 (114)
22 PF00636 Ribonuclease_3: Ribon 99.9 1.3E-22 2.8E-27 188.2 3.6 113 453-571 1-114 (114)
23 KOG1817 Ribonuclease [RNA proc 99.8 8.2E-21 1.8E-25 200.0 9.7 120 435-583 290-413 (533)
24 cd02844 PAZ_CAF_like PAZ domai 99.8 4E-20 8.7E-25 173.6 8.3 115 275-392 16-135 (135)
25 PF03368 Dicer_dimer: Dicer di 99.8 9E-19 2E-23 153.6 6.1 68 32-99 17-88 (90)
26 cd02843 PAZ_dicer_like PAZ dom 99.7 2.2E-18 4.7E-23 155.1 6.9 110 246-366 6-119 (122)
27 KOG3769 Ribonuclease III domai 99.7 5.7E-16 1.2E-20 157.1 14.6 222 601-849 59-305 (333)
28 cd02845 PAZ_piwi_like PAZ doma 99.5 3.8E-14 8.3E-19 130.5 7.9 89 287-386 25-113 (117)
29 KOG0701 dsRNA-specific nucleas 99.4 3.3E-13 7.1E-18 166.9 8.9 161 605-770 979-1182(1606)
30 PF02170 PAZ: PAZ domain; Int 99.2 4.1E-12 8.9E-17 121.4 2.2 107 286-411 25-133 (135)
31 KOG1042 Germ-line stem cell di 99.2 3.2E-11 6.9E-16 133.9 7.5 102 287-402 281-382 (845)
32 PF00035 dsrm: Double-stranded 98.9 2.2E-08 4.7E-13 83.1 10.4 64 781-845 1-67 (67)
33 PHA02701 ORF020 dsRNA-binding 98.8 1.7E-08 3.7E-13 97.7 9.8 69 778-847 107-177 (183)
34 cd02825 PAZ PAZ domain, named 98.8 5.9E-09 1.3E-13 96.5 5.8 83 287-386 30-114 (115)
35 smart00358 DSRM Double-strande 98.8 3E-08 6.4E-13 82.2 8.9 65 781-846 1-67 (67)
36 cd00048 DSRM Double-stranded R 98.8 4.5E-08 9.8E-13 81.2 9.4 65 780-845 1-68 (68)
37 PHA03103 double-strand RNA-bin 98.8 4.8E-08 1E-12 95.4 10.6 88 758-847 84-177 (183)
38 KOG3769 Ribonuclease III domai 98.2 5.3E-06 1.2E-10 85.4 8.5 162 432-627 77-258 (333)
39 cd02846 PAZ_argonaute_like PAZ 98.0 5.7E-06 1.2E-10 76.6 5.3 80 288-386 30-113 (114)
40 KOG3732 Staufen and related do 97.9 3.2E-05 7E-10 81.7 8.1 71 777-850 140-214 (339)
41 PF14709 DND1_DSRM: double str 97.7 9.9E-05 2.1E-09 63.3 7.0 68 779-846 1-80 (80)
42 PLN03202 protein argonaute; Pr 97.6 6.2E-05 1.3E-09 93.2 5.3 81 287-386 292-382 (900)
43 KOG3732 Staufen and related do 97.5 0.00025 5.5E-09 75.1 7.8 70 779-850 38-109 (339)
44 COG1939 Ribonuclease III famil 97.4 0.00058 1.2E-08 62.1 7.5 110 643-767 16-126 (132)
45 KOG2777 tRNA-specific adenosin 95.6 0.022 4.8E-07 65.0 6.8 67 778-848 89-155 (542)
46 COG1939 Ribonuclease III famil 95.5 0.025 5.5E-07 51.7 5.4 113 451-582 14-126 (132)
47 KOG0354 DEAD-box like helicase 95.3 0.0082 1.8E-07 70.9 2.2 30 1-30 498-527 (746)
48 KOG4334 Uncharacterized conser 94.4 0.028 6E-07 62.0 3.1 64 782-846 378-442 (650)
49 cd00048 DSRM Double-stranded R 89.7 0.72 1.6E-05 37.5 5.3 34 45-82 33-68 (68)
50 PF14709 DND1_DSRM: double str 87.4 1.7 3.7E-05 37.2 6.1 48 35-82 17-79 (80)
51 PF00035 dsrm: Double-stranded 86.2 1.8 3.9E-05 35.2 5.5 36 45-82 32-67 (67)
52 smart00358 DSRM Double-strande 85.9 1.7 3.7E-05 35.2 5.2 36 45-82 31-66 (67)
53 KOG1041 Translation initiation 84.3 1.3 2.8E-05 55.3 5.3 82 286-386 276-361 (876)
54 PF11469 Ribonucleas_3_2: Ribo 81.3 8.9 0.00019 33.9 7.7 80 454-580 2-85 (120)
55 PF03368 Dicer_dimer: Dicer di 80.0 9.7 0.00021 33.4 7.8 64 782-849 2-75 (90)
56 PF14954 LIX1: Limb expression 77.9 3.5 7.5E-05 41.4 4.7 36 45-80 58-93 (252)
57 PHA03103 double-strand RNA-bin 74.9 11 0.00023 37.6 7.3 63 6-84 113-177 (183)
58 PF14954 LIX1: Limb expression 70.4 9.6 0.00021 38.4 5.7 63 779-843 21-93 (252)
59 PHA02701 ORF020 dsRNA-binding 70.0 23 0.00049 35.2 8.2 68 2-83 108-176 (183)
60 PRK13766 Hef nuclease; Provisi 62.1 5.3 0.00012 49.7 2.8 28 2-29 448-476 (773)
61 PLN00206 DEAD-box ATP-dependen 52.0 9.5 0.00021 45.1 2.5 20 2-21 443-462 (518)
62 PRK01297 ATP-dependent RNA hel 51.2 8.1 0.00017 45.1 1.7 23 2-24 410-432 (475)
63 PF08383 Maf_N: Maf N-terminal 50.3 6.7 0.00015 27.4 0.5 12 554-565 24-35 (35)
64 PRK04837 ATP-dependent RNA hel 50.1 7.1 0.00015 44.8 1.0 21 1-21 329-349 (423)
65 KOG0921 Dosage compensation co 46.8 25 0.00055 42.9 4.8 67 780-847 2-70 (1282)
66 PF11469 Ribonucleas_3_2: Ribo 46.1 68 0.0015 28.6 6.0 85 645-769 3-89 (120)
67 PRK11664 ATP-dependent RNA hel 45.4 18 0.00038 45.1 3.5 22 9-30 315-337 (812)
68 PRK05298 excinuclease ABC subu 42.3 18 0.00039 44.0 2.9 29 2-30 526-555 (652)
69 PRK02287 hypothetical protein; 38.1 25 0.00053 34.7 2.5 33 556-588 107-139 (171)
70 PTZ00110 helicase; Provisional 37.7 18 0.00038 43.1 1.8 22 2-23 452-473 (545)
71 PRK11192 ATP-dependent RNA hel 37.5 16 0.00036 41.9 1.4 29 2-30 320-350 (434)
72 PRK11776 ATP-dependent RNA hel 37.1 16 0.00035 42.3 1.3 22 2-23 317-338 (460)
73 KOG0346 RNA helicase [RNA proc 34.8 22 0.00047 40.0 1.7 21 1-21 377-397 (569)
74 PRK14741 spoVM stage V sporula 33.6 29 0.00062 22.3 1.4 18 732-749 6-23 (26)
75 COG1111 MPH1 ERCC4-like helica 32.6 31 0.00068 39.6 2.5 28 1-28 449-476 (542)
76 PRK10590 ATP-dependent RNA hel 32.6 19 0.00042 41.7 1.0 20 2-21 320-339 (456)
77 PRK11057 ATP-dependent DNA hel 30.9 33 0.00072 41.4 2.6 28 2-29 311-340 (607)
78 PF04034 DUF367: Domain of unk 30.5 42 0.00091 31.3 2.6 33 556-588 66-98 (127)
79 PTZ00424 helicase 45; Provisio 29.6 19 0.00041 40.8 0.2 21 2-22 342-362 (401)
80 TIGR00614 recQ_fam ATP-depende 25.9 31 0.00068 40.2 1.2 27 2-28 301-329 (470)
81 COG2042 Uncharacterized conser 24.6 65 0.0014 31.5 2.8 30 556-585 115-144 (179)
82 PF00333 Ribosomal_S5: Ribosom 22.6 1.7E+02 0.0038 24.1 4.6 39 807-846 21-63 (67)
83 PRK12898 secA preprotein trans 22.0 42 0.0009 40.5 1.2 21 2-22 554-574 (656)
84 PRK04537 ATP-dependent RNA hel 21.2 43 0.00093 40.1 1.1 20 2-21 332-351 (572)
85 PRK11634 ATP-dependent RNA hel 20.9 44 0.00096 40.4 1.2 29 2-30 320-350 (629)
86 PLN03137 ATP-dependent DNA hel 20.7 70 0.0015 41.0 2.8 28 2-29 755-784 (1195)
87 PRK09200 preprotein translocas 20.3 47 0.001 41.1 1.2 17 2-18 509-525 (790)
88 KOG4334 Uncharacterized conser 20.3 3.2E+02 0.007 31.4 7.4 67 779-847 490-558 (650)
No 1
>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]
Probab=100.00 E-value=5.6e-57 Score=547.47 Aligned_cols=793 Identities=29% Similarity=0.373 Sum_probs=559.5
Q ss_pred CCCcchhhHHHHHhhcccccCCCcEEEEEec-----ccc---------CCCeEEEcC----------------CeEEEEE
Q 003062 1 MFDPSHTVCSFIQSRGRARMQNSDYLLMLKR-----YFK---------PTPKFDINK----------------EMGICTL 50 (852)
Q Consensus 1 rFD~p~t~~syIQSRGRAR~~~S~yi~m~e~-----~~~---------~~P~~~~~~----------------~~~~~~v 50 (852)
+||.|.++++|||+.||||...+.|+++.+. +.+ ++|.+...+ ..+.-+|
T Consensus 378 ~~~~~~~~~~~vq~~~r~~~~~~~~~i~~~t~~~~~~~~~s~~~~~~i~~~~l~~~~~~~v~~~~~~~e~~~~~~~~~~v 457 (1606)
T KOG0701|consen 378 LFDAPTYYRSYVQKKGRARAADSYLVILGETLSAVSLKNPSYAYTEQIPRPQLFLRLDANVNKYCARAELLKHVPFLSTV 457 (1606)
T ss_pred eccCcchHHHHHHhhcccccchhhHHHHHhhhhhhhhcChhHhHHhhcccchhhcccccchHHHHHHHHhccCCCcceeE
Confidence 6899999999999999999999999998875 332 234443200 2345556
Q ss_pred EcCCCCCCccccccCcHHHHHHHHHHHHHHHHHhcCCCCCCCCCccccchhcc----------------ccCCCCCCCCC
Q 003062 51 YLPNNCPIQTVIAQGNIKTLKQTACLEACKKLHQIGALTDNLLPDVVVEEHDA----------------QKHGNEPYDAE 114 (852)
Q Consensus 51 ~LP~~~p~~~~~~~~s~~~Ak~~aAf~Ac~~L~~~G~ldd~LlP~~~~~~~~~----------------~~~~~~~~~~~ 114 (852)
.||.++|.+ .-+.-+|.+||++|++||+++|.+++..... .-.++++....
T Consensus 458 ~~~~~~p~~-------------~~~~~~~~~l~~~~~~d~~~~~~gk~~~~~~~~~~~~~~ee~~~~~~~~~~~s~~~~~ 524 (1606)
T KOG0701|consen 458 VLPVNSPLK-------------MCIVGLCLKLHKIGELDDCLHPKGKEPKACLEEVDTEEEEEVLQGFEPRPGSSKRRQQ 524 (1606)
T ss_pred EEecCchHH-------------HHHHHhHHHHHHhhhhhhhhcccccchHHhhhhhccccchhhccccCCCCCccccccc
Confidence 666665544 2223399999999999999999988543211 01123444455
Q ss_pred CCccCCccccCCCCCCCcceEEEEEEeecCCC----cC----------CCCCceEEEEecCcCccccccccceeeeeCCe
Q 003062 115 HPIYFPPELVNQCPQDTKITYHCYLIELKQNF----NY----------DIPAHDIVLAVRTELESEIKKVNFDLEVDRGR 180 (852)
Q Consensus 115 ~~~~~~~~~~~~w~~~~~~~~~~~~i~l~~~~----~~----------~~~~~~~~llt~~~LP~~~~~~~~~Lf~~~~~ 180 (852)
|....+.++.+..+..+. +||.|++.+.-.. .. ......|++++-+++|.. +.|+.+..+|+
T Consensus 525 ~~k~~~~~~~~~~~~~~~-~c~~~~~~~~~~~~~~e~~n~~~r~~~~~~~~~~~~~~l~~~~i~~~---~~~~~a~~sG~ 600 (1606)
T KOG0701|consen 525 YLKHIARERNDSVPKADQ-PCYLYVIGLELTMPLPEERNFERRKLYPPEDLTYCFGILTAKLIPKI---PHFPVATRSGE 600 (1606)
T ss_pred ccchhHHHhcccccCCCC-ceeeeeeccceecCCchhcccccccccCchhhhhhhcccchhhhccc---ccccceeccCc
Confidence 666666776665554333 4677777653111 00 112457999999999985 58999999998
Q ss_pred EEEEEeeCc-ccccCHHHHHHHHHHHHHHHHHHhccccchhhHHhhhccccCCCCccEEEecCCCC------ccCccccc
Q 003062 181 LTVNLKHLG-KIQLTPDKVLLCRRFQIALFRVIMDHNLDKLNEILKGLWLRDNLEIDYLLLPASEQ------SIDWEPVA 253 (852)
Q Consensus 181 ~~v~l~~~~-~i~l~~e~l~~l~~Ft~~lf~~v~~~~~~~~~~~~~~~~~~~~~~~~yl~~Pl~~~------~iDw~~v~ 253 (852)
+++++.... ...+.+++++....|+..+|..+.+.-. +..-+.+......+.++|.+.. .|+|..++
T Consensus 601 ~~~~~l~~~~~~~~~~~~~~~~~~f~~~~~~~v~~~~~------~~~~~~~~~~~l~~~llp~~~~~~~~~~~i~~k~l~ 674 (1606)
T KOG0701|consen 601 VKVSLLLAFSEALVKSEQLDEIQEFLNYIFTEVLRLAK------INLEFDPKTAELIETLLPLNVLADKRAIIIVRKFLE 674 (1606)
T ss_pred hhHHHHHhhhhhhcchhhccCcchhcccchhhhhhhhc------cccccCCchhhHHHHhcccccccccchhhhHHHHHH
Confidence 888875432 2357788888889999999999988521 1112233556677888996521 78999888
Q ss_pred cccccccccCCCCCCCCcccccchhhccCCCcccccccCcEEEcCcCC---ceEEEEeecCCCCCCCCCCCCCCCcchHH
Q 003062 254 SLSFPCDIGLKHHKNCSTMSNARVVQTKSGPLCTCMIYNSVVCTPHSG---QIYYITGVLGHLNANSLFTRNDGGAITYK 330 (852)
Q Consensus 254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~~~~---~~Y~v~~i~~dl~p~S~f~~~~~~~~ty~ 330 (852)
.+..+.......+.+ . -+...++..+++.+++++ |.| ..|++..|.....|+|.||. -.+-++.
T Consensus 675 ~iv~~~~~~~~~~~~-~--------~~~~~~f~~~~~~~~~~~--~rn~~~~~~~~~~v~~~~~pss~~~g--~~~~~~~ 741 (1606)
T KOG0701|consen 675 AIVAPSDLMPIPSKD-E--------VRKAKYFDGEDSQDAVGM--YRNDDQPQFYVAEVLPLLAPSSLFPG--LDYETFN 741 (1606)
T ss_pred HHhCcccccCCCChh-h--------hhhhhhcccccchhhhhh--hhcccccceeeeeeeeeccchhcCCC--cchheee
Confidence 876544321111111 0 123446777888999888 433 25688999999999999983 3456888
Q ss_pred HHHHHHhCcccccCCceeEEEeeccccccccchhhhhccC-------CCCcc--eeecCcchhhhhcccCcHHHHHHhhh
Q 003062 331 KHYEERYGIQLCFDQELLLNGRRIFHAQNYLSKCRQEKQR-------EPSKI--SFELPPELCRIIMGPMSLSTFYSFTF 401 (852)
Q Consensus 331 ~yy~~k~~~~i~~~~QPlL~~~~~~~r~N~L~~~~~~~~~-------~~~~~--~~~L~PElC~~~~~p~~~~~~~~~~~ 401 (852)
.||..+|+..+++..||++.++....+.|++.++...... ..++. ..-+--++ ..+|.+++.|+.+-+
T Consensus 742 ~v~~~~~~~~i~~~~q~~~~~~~~~s~l~~~~~r~~~~~~~~l~~~s~~~e~~~~es~~~~~---~~h~~~~s~~~~~~~ 818 (1606)
T KOG0701|consen 742 EVYRFKYALTITSLNQSLLDVDHTSSRLNLLVPRGDNQKGSALPNSSSETERLKDESLEHSL---IIHPALASLWRRAVC 818 (1606)
T ss_pred eeeeccccchhhhccccccccccchhhhcccCchhhccccceeecccchhhhhhHHHhhccC---CCCcCcchhhhhhcc
Confidence 9999999999999999999999999999999888532110 00000 01122222 357888999999999
Q ss_pred hhhHHHHHHHHHHHHHHHH------------HHhh-cc------------------------------------------
Q 003062 402 VPSIMHRLQSLLLAVNLKN------------MLLD-HC------------------------------------------ 426 (852)
Q Consensus 402 lPsi~~rle~~l~a~~l~~------------~l~~-~~------------------------------------------ 426 (852)
+|.+++|++. .+...+. .+.. .|
T Consensus 819 ~p~~v~~v~~--tg~~~s~~ta~~li~~~~~~i~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~ 896 (1606)
T KOG0701|consen 819 LPEILYRVLL--TGALVSLSTAVDLIPHDFSSILSKSFEKEASKSDKNKDEYSCDLALPKENPVKQVLGKANQLDKVNQQ 896 (1606)
T ss_pred Ccchheeecc--ccceeeeecccchhhhhhhhccchhhccccccCCCCccccceeecccCCCchhhhhchhhhhhHHHhh
Confidence 9999998753 1111100 0000 00
Q ss_pred ------------------------------------------c----c--------------------C-----------
Q 003062 427 ------------------------------------------M----Q--------------------N----------- 429 (852)
Q Consensus 427 ------------------------------------------~----~--------------------~----------- 429 (852)
+ . .
T Consensus 897 av~l~~~~~~~~~~~~~d~~~~n~~~~~~~~~~~~~i~~a~~p~~~~~~~~~~~~~s~~~~n~l~~~~~~~~~~~s~~~~ 976 (1606)
T KOG0701|consen 897 AVELQECIQLHEVGALDDHLVFNKGVADQVLAKRESISLATRPELVSPFIPEPPTTSHLISNRLSPSSPSNSDLNSLLPN 976 (1606)
T ss_pred hhhhhhhhhhhcccccccccccCccccchhhhhccccccccCcccccccccCCchhhhhhhhhcCccCCCCCCccccccc
Confidence 0 0 0
Q ss_pred ---------CCCC---------------HHHHHHHhccCCCCCCCCchhhhhhhhhHHhHHHHHHHHHhcCCCCcchhhH
Q 003062 430 ---------VTIP---------------TSKVLEAITTKKCQEGFHLESLETLGDSFLKYAASQQLFKTYQNHHEGLLSV 485 (852)
Q Consensus 430 ---------~~~~---------------~~lll~AlT~~s~~~~~nyeRLE~LGDs~Lk~~~s~~l~~~~p~~~eg~Ls~ 485 (852)
..++ ..+|+||||++++.+.+++||||+|||++||++++.++|.+||+.+||+|+.
T Consensus 977 ~~~~~E~~e~i~n~~~~Fs~~~~~i~~~~s~LLEAlT~~~~~~s~s~Erle~Lgds~Lk~avsr~l~L~ypd~~Egqls~ 1056 (1606)
T KOG0701|consen 977 KRSDWEAVEKILNFRYVFSISLASIALSTSLLLEALTTSSCQDSFSLERLELLGDSLLKLAVSRHLFLTYPDLDEGQLSR 1056 (1606)
T ss_pred ccccccccccccccceeccccccccccchhHHHHHhhcCccccchhHHHHHhhHHHHHHHHHHHHHHHhCCcccchhHHH
Confidence 0011 2689999999999999999999999999999999999999999999999999
Q ss_pred HHhhccccHHHHHHHHhCCccccccccccCCCCcccCCCCC--CCcccCc--c-------cccc---------cc---cc
Q 003062 486 KKDRIISNAALCKLGCDHKLPGFIRTEPFDPKMWMIPGDNS--GSYELND--H-------SLFN---------ER---KI 542 (852)
Q Consensus 486 ~r~~~vsN~~L~~~a~~~gL~~~i~~~~f~~~~w~~~~~~~--~~~~~~~--~-------~~~~---------~~---~~ 542 (852)
+|+.+++|.+|++.|...||++|++.+.|.|..|-.|+... +..|... + ++.. +. ..
T Consensus 1057 lr~~~~~~~nl~~la~~~gl~~~~~~~~fep~~~~~p~~~~~~~~~~k~~~~~~~~~~~~e~~e~~~df~e~~~~~~~~~ 1136 (1606)
T KOG0701|consen 1057 LRDVNVSNDNLARLAVKKGLYSYLRHEGFEPSRWWVPGQLDVNNVDCKDLSGDQNYILYKELDEKIKDFQEAMEKEDGDS 1136 (1606)
T ss_pred HHHhcccccchhhhhhcccchhhcccccccccccccccccccccccccccccccccccccchhhhhhHHHHhhhccCCcc
Confidence 99999999999999999999999999999997655554311 1112110 0 0000 00 01
Q ss_pred cccc--ccccccchhHHHHHHHHHHHhhcCChHHHH-----HhhhhcCccccCCCc------------------------
Q 003062 543 YVTG--RKKVKSKTVADVVEALIGAFLSTGGENVGL-----IFLDRIGIKVDFVNV------------------------ 591 (852)
Q Consensus 543 ~~~~--~~~~~~K~lADv~EAliGA~yl~~G~~~a~-----~~~~~l~~~~~~~~~------------------------ 591 (852)
...+ .++...|++||++|||+||+|+|+|...+. .+++|.++..++...
T Consensus 1137 ~~~~~~~~~~~~ks~adl~eaLlga~~vD~~~~~~~~~~~~~~lk~~~~~~dy~~~e~~~~~~~~~~~s~~~~~~~~~~l 1216 (1606)
T KOG0701|consen 1137 RSKGGDHDWLAPKSPADLLEALLGAIYVDGGLLETFETIGDSFLKWSITNYDYDTLEPKHAGKLSFRRSKIVKKKNLDRL 1216 (1606)
T ss_pred cccccccceecCCCHHHHHHHHHHhhhhhccchhhhhHHHHHHHhhhhhhhhhhcccccchhhhhhhhhhHhhhhhHHHH
Confidence 1111 357889999999999999999999998888 888888766442100
Q ss_pred ----c---------------------------cch-------------------------------------h--cc---
Q 003062 592 ----P---------------------------YER-------------------------------------Q--FQ--- 598 (852)
Q Consensus 592 ----~---------------------------~~~-------------------------------------~--~~--- 598 (852)
. +++ + ..
T Consensus 1217 er~l~~~~~~~~~~l~~~~~~~~s~~~~~ld~~erl~~~~d~vld~l~~~~~~~~~~~~~~~~lt~~~~~~v~~l~e~~~ 1296 (1606)
T KOG0701|consen 1217 ERELGLKFKFLEAALLVQAFIHCSLRAEGLDATERLEFLGDAVLDKLSDKHPFEVFIRLDGGELTDLREAGVNTLNENDL 1296 (1606)
T ss_pred HHhhcccchhhhhhcchhhcccccccccccchHHHHHhhHHHHHHHHHHhhhHhhhhcccCcchhhhhhhhhhhhhhccc
Confidence 0 000 0 00
Q ss_pred ----------------------------------------------c----------------Ch----hhHHhHHHHHH
Q 003062 599 ----------------------------------------------V----------------QA----ERLVNVRHLES 612 (852)
Q Consensus 599 ----------------------------------------------~----------------~~----~~~~~~~~le~ 612 (852)
+ +. .....+..+|.
T Consensus 1297 ~~~v~~~l~~~l~~~s~~~~K~i~d~v~sli~~~~~~~~~~s~l~~~~~~~~l~~i~es~~~~~~~~~~~~l~~~~~~e~ 1376 (1606)
T KOG0701|consen 1297 NVKVPKSLPYNLLDQSSVLEKSIADSVEALIGASLSEGGPSSALLFMDWPPILLDIPESIASPDSIDELRQLLSFGKFEE 1376 (1606)
T ss_pred ccccCCcceeeehhhccCccchHHHHHHHhhhhhhhccCCCccccccccccccccccccccccchhHHHHHHHHHHhhhc
Confidence 0 00 01123567889
Q ss_pred HcCcccCCHHHHHHHhccCCCCCCCCCCcchhhhHhhHHHHHHHHHHHHHHhCCCCCcchHHHHHHHhcChHHHHHHHHH
Q 003062 613 LLNYSFRDPSLLVEALTHGSYMLPEIPRCYQRLEFLGDAVLDYLITVYLYNKYPTLSPGDLTDMRSASVNNDCYALSSVK 692 (852)
Q Consensus 613 ~lgy~F~~~~LL~~AlTH~S~~~~~~~~~yeRLEfLGDavLd~~v~~~l~~~~p~~~~~~Lt~~r~~lv~n~~La~~a~~ 692 (852)
.+||.|.++.++.+|+||.||..+....||||||||||+|+++.|++|+|...+..+||.++++|+++|+|...|.+|++
T Consensus 1377 ~l~y~f~~~~~l~~a~th~s~~~~~~~~C~qrleflgd~vld~~it~hl~~~~~~~sp~~~td~rsa~vnn~~~a~~av~ 1456 (1606)
T KOG0701|consen 1377 KLNYRFKLKPYLTQATTHASYIYNRITDCYQRLEFLGDAVLDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVK 1456 (1606)
T ss_pred ccchhhhhhhcccccccccccccCccchhhhhHHHhHHhhhhhhhhhcccccccccCchhhhhhhhHhhccccchhhHHh
Confidence 99999999999999999999988889999999999999999999999999999999999999999999999999999999
Q ss_pred cCCchhhhccChhHHHHHHHHHhhhhhhccccccCccccCCCChhhHHHHHHHhheeeeeCCCCHHHHHHHHHHhhcccC
Q 003062 693 HGLHKHILHASQELYKWINITVDSFERLSLESTFGWESETSFPKALGDIIESLSGAIFVDSGCNKEVVFESIRPLLEPMI 772 (852)
Q Consensus 693 ~gL~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~laD~~EAliGAi~~DsG~~~~~v~~~~~~~l~~~~ 772 (852)
.++|+|+.+.+..+...|..++....+.......+|.+....||+++|++|++.||||+|+|...+.+.. .+.+.
T Consensus 1457 ~~~~K~~~~~~~~l~~~I~~~v~~~~q~~~~~~~~~~edievpKa~gdi~esiagai~~dsg~~~~~~~~----~~~a~- 1531 (1606)
T KOG0701|consen 1457 ADLHKFIIAASPGLIHNIDRFVSFQLQSNLDSLFGWEEDIEVPKALGDIFESIAGAIKLDSGNMMEPCIE----KFWAL- 1531 (1606)
T ss_pred hcchhHHHhhccccccchHHHHHHHHhhccccCCCchhhcccchhhhhhhhcccceeecCcccccchHhh----cCcCC-
Confidence 9999999999999999999999988776665667999999999999999999999999999954332221 11111
Q ss_pred CcccccCChhhHHHHHHHhCCCceeeEEee--ecCCceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHHHHHHhhhhC
Q 003062 773 TPETMRLQPARELNEYCQKHHFSMKKTVAP--RINGKAAVTVEVHANGTLFKHTHADADKETAKKVASKEVLKSLKASF 849 (852)
Q Consensus 773 ~~~~~~~~P~~~L~e~~~~~~~~~~~~~~~--~~~g~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~AL~~L~~~~ 849 (852)
....|++++.+...+. ..|.+.. ...+..+.+|.|..+|. . .|.|.+...||..|++.|++.|+...
T Consensus 1532 ----p~~s~~~E~~~~h~~~---~~~~~~~k~~d~~~~~~tv~~~~~~~--~-~~~g~~~~~aK~s~~k~A~~ll~~~~ 1600 (1606)
T KOG0701|consen 1532 ----PPRSPIRELLELHPER---ALFGKCEKVADAGKVRVTVDVFNKEV--F-AGEGRNYRIAKASAAKAALKLLKKLG 1600 (1606)
T ss_pred ----CCccchhhhcccccee---eccchhhhhhhccceEEEEEecccch--h-hhcchhhhhhhhhHHHHHHHHHHHhh
Confidence 1233334333322211 1111111 11233334444444443 3 68899999999999999998887653
No 2
>KOG1817 consensus Ribonuclease [RNA processing and modification]
Probab=100.00 E-value=7.9e-51 Score=424.43 Aligned_cols=403 Identities=23% Similarity=0.296 Sum_probs=325.5
Q ss_pred hcccCcHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHhhccccCCCCCHHHHHHHhccCCCCCC-----------------
Q 003062 387 IMGPMSLSTFYSFTFVPSIMHRLQSLLLAVNLKNMLLDHCMQNVTIPTSKVLEAITTKKCQEG----------------- 449 (852)
Q Consensus 387 ~~~p~~~~~~~~~~~lPsi~~rle~~l~a~~l~~~l~~~~~~~~~~~~~lll~AlT~~s~~~~----------------- 449 (852)
....+..++...++++|.+.|+|.....-..|.+.|+|.|++. .++.-||||||....
T Consensus 15 ~~tg~~~dv~~h~~m~~~~~~hir~~~~l~~~e~~i~y~f~~r-----~~~~lal~h~s~~~~~Gt~~dh~kns~tncg~ 89 (533)
T KOG1817|consen 15 WKTGIRSDVCQHAMMLPVLTHHIRYHQSLDHLEELIGYTFQDR-----CLLQLALTHPSHKLNYGTNPDHAKNSLTNCGI 89 (533)
T ss_pred HHhCcchHHHHHHHHHHHHhhhhhHHHhHHHHHHHhCeeecch-----HHHHHHhcCchHHhhCCCCchhhhccccccCc
Confidence 3456778888899999999999998888889999999999987 778889999996310
Q ss_pred ----------------------------------------CCchhhhhhhhhHHhHHHHHHHHHhcCCCCcchhhHHHhh
Q 003062 450 ----------------------------------------FHLESLETLGDSFLKYAASQQLFKTYQNHHEGLLSVKKDR 489 (852)
Q Consensus 450 ----------------------------------------~nyeRLE~LGDs~Lk~~~s~~l~~~~p~~~eg~Ls~~r~~ 489 (852)
..+||||||||++-.+++|.++|..+|...||.|...|..
T Consensus 90 r~~~yg~~~~~~~~kr~~gin~li~imk~l~~~~~~~s~i~hnErle~lgdavve~~ss~hl~~~~~r~~eggLatyrta 169 (533)
T KOG1817|consen 90 RQPKYGDRKEHIMTKRKLGINTLINIMKRLGVIQPTHSVIKHNERLEFLGDAVVELLSSNHLYFMFPRLEEGGLATYRTA 169 (533)
T ss_pred CCcccchhHHHHHHHHHhhhhHHHHHHhhccCCCCchhHhHHHHHHHHHhhccHHHHHHHHHHHccccccccchhHHHHH
Confidence 1799999999999999999999999999999999999999
Q ss_pred ccccHHHHHHHHhCCccccccccccCCCCcccCCCCCCCcccCccccccccccccccccccccchhHHHHHHHHHHHhhc
Q 003062 490 IISNAALCKLGCDHKLPGFIRTEPFDPKMWMIPGDNSGSYELNDHSLFNERKIYVTGRKKVKSKTVADVVEALIGAFLST 569 (852)
Q Consensus 490 ~vsN~~L~~~a~~~gL~~~i~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~K~lADv~EAliGA~yl~ 569 (852)
+|.|++|+.+|+++.++.|+... -|.. .|+.. --...+|++|||+|||.|++
T Consensus 170 ~vqnr~la~lakklrkd~fl~ya---------hg~d---l~~~~----------------E~Kha~an~feavi~a~~l~ 221 (533)
T KOG1817|consen 170 IVQNRHLAKLAKKLRKDEFLLYA---------HGYD---LCFET----------------ELKHAMANCFEAVIGAKYLD 221 (533)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHh---------cCcc---hhhHH----------------HHHHHHHHHHHHHhHHHHHh
Confidence 99999999999999999998752 2220 11111 13568999999999999999
Q ss_pred CChHHHHHhhhhc--Ccc----ccCCCcccc---hhccc-------ChhhHHhHHHHHHHcCcccCCHHHHHHHhccCCC
Q 003062 570 GGENVGLIFLDRI--GIK----VDFVNVPYE---RQFQV-------QAERLVNVRHLESLLNYSFRDPSLLVEALTHGSY 633 (852)
Q Consensus 570 ~G~~~a~~~~~~l--~~~----~~~~~~~~~---~~~~~-------~~~~~~~~~~le~~lgy~F~~~~LL~~AlTH~S~ 633 (852)
+|...+....... +.+ -.|...+.+ .+-+. ..+....+-++|+++|-.|.++.+|.+|+|-.|.
T Consensus 222 g~~~~~e~lfs~~~~~~epvlee~w~~~~ehelq~~ep~gDr~~~~~~Ppllp~~~~e~~~g~vF~Hirlla~aft~rs~ 301 (533)
T KOG1817|consen 222 GGLVVAEKLFSRALFVYEPVLEEEWEHEPEHELQEQEPAGDRVLITKYPPLLPLTQFEEIIGIVFIHIRLLARAFTLRSI 301 (533)
T ss_pred cchHHHHHHHHHHhhccCchhhccccCCCcCcccccCCCccccccccCCCCCchhhHHHHHHHHHHHHHHHHHHhhccCC
Confidence 9998877664432 211 223332222 11110 0011234568999999999999999999999997
Q ss_pred CCCC-CCCcchhhhHhhHHHHHHHHHHHHHHhCCCCCcchHHHHHHHhcChHHHHHHHHHcCCchhhhccChhHHHHHHH
Q 003062 634 MLPE-IPRCYQRLEFLGDAVLDYLITVYLYNKYPTLSPGDLTDMRSASVNNDCYALSSVKHGLHKHILHASQELYKWINI 712 (852)
Q Consensus 634 ~~~~-~~~~yeRLEfLGDavLd~~v~~~l~~~~p~~~~~~Lt~~r~~lv~n~~La~~a~~~gL~~~l~~~~~~~~~~i~~ 712 (852)
..++ ...+|||||||||+||+++++++||.+||+.++|+|+.+|+.+|||++-+.+|..+|+++++..+...-.
T Consensus 302 ~~n~Lt~gHNqRLEFLGDSilqlv~T~ily~kFPdhhEGhLSlLRssLVsNetqakva~~lgf~e~li~n~~~k~----- 376 (533)
T KOG1817|consen 302 PFNHLTLGHNQRLEFLGDSILQLVMTEILYRKFPDHHEGHLSLLRSSLVSNETQAKVADDLGFHEYLITNFDLKD----- 376 (533)
T ss_pred CchhhhhhhhHHHHHhHHHHHHHHHHHHHHHhCCccccchHHHHHHHHhccHHHHHHHHHhCCchhhhhCcchhh-----
Confidence 6433 4579999999999999999999999999999999999999999999999999999999999987753211
Q ss_pred HHhhhhhhccccccCccccCCCChhhHHHHHHHhheeeeeCCCCHHHHHHHHHHhhcccCCc---ccccCChhhHHHHHH
Q 003062 713 TVDSFERLSLESTFGWESETSFPKALGDIIESLSGAIFVDSGCNKEVVFESIRPLLEPMITP---ETMRLQPARELNEYC 789 (852)
Q Consensus 713 ~~~~~~~~~~~~~~~~~~~~~~~k~laD~~EAliGAi~~DsG~~~~~v~~~~~~~l~~~~~~---~~~~~~P~~~L~e~~ 789 (852)
+. ....|.+||+|||+|||+|+|.|. +.|++|+..++.|.+.. .....+|+..|+++|
T Consensus 377 ~~-----------------~lk~K~~ADlfEAfiGaLyvD~~l--e~~~qf~~~l~~Prl~~fi~nq~wndpkskLqq~c 437 (533)
T KOG1817|consen 377 FQ-----------------NLKLKDYADLFEAFIGALYVDKGL--EYCRQFLRVLFFPRLKEFIRNQDWNDPKSKLQQCC 437 (533)
T ss_pred hh-----------------hhhHHHHHHHHHHHHHHHhhcCCc--HHHHHHHHHHhhHHHHHHHHhhhccCcHHHHHHHH
Confidence 00 234589999999999999999665 78999999999998754 334579999999999
Q ss_pred HhCCCc------eeeEEeeecCC---ceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHHHHHHhhh
Q 003062 790 QKHHFS------MKKTVAPRING---KAAVTVEVHANGTLFKHTHADADKETAKKVASKEVLKSLKA 847 (852)
Q Consensus 790 ~~~~~~------~~~~~~~~~~g---~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~AL~~L~~ 847 (852)
-...++ +++-.+....| .+.|+|.|+++|+.++ +|.|+|.+.|+.+||+.||+.++.
T Consensus 438 l~~rys~~~epdip~y~V~~~~gpa~~r~y~Vavyf~gkrla-t~~G~nik~Ae~rAA~~ALe~~~~ 503 (533)
T KOG1817|consen 438 LTLRYSLGGEPDIPLYKVLGAKGPANDRNYKVAVYFKGKRLA-TGVGSNIKQAEMRAAMQALENLKM 503 (533)
T ss_pred HHHhcccCCCCCCceEEEecccCCCCCCceEEEEEECCEEEe-eccCchHhHHHHHHHHHHHHHHHh
Confidence 876553 34222333333 4679999999999998 899999999999999999999884
No 3
>PRK12371 ribonuclease III; Reviewed
Probab=100.00 E-value=7e-44 Score=368.61 Aligned_cols=220 Identities=26% Similarity=0.316 Sum_probs=188.7
Q ss_pred HhHHHHHHHcCcccCCHHHHHHHhccCCCCCCCCCCcchhhhHhhHHHHHHHHHHHHHHhCCCCCcchHHHHHHHhcChH
Q 003062 605 VNVRHLESLLNYSFRDPSLLVEALTHGSYMLPEIPRCYQRLEFLGDAVLDYLITVYLYNKYPTLSPGDLTDMRSASVNND 684 (852)
Q Consensus 605 ~~~~~le~~lgy~F~~~~LL~~AlTH~S~~~~~~~~~yeRLEfLGDavLd~~v~~~l~~~~p~~~~~~Lt~~r~~lv~n~ 684 (852)
..++.||++|||+|+|+.||.+||||+|+. +....+||||||||||||+++|+++||.+||+.++|+||.+|+.+|||+
T Consensus 10 ~~~~~le~~lgy~F~~~~Ll~~AlTH~S~~-~~~~~~~eRLEFLGDavL~l~vs~~Lf~~~p~~~eG~Lt~~rs~lV~n~ 88 (235)
T PRK12371 10 ATASILEERTGHRFANKERLERALTHSSAR-ASKQGNYERLEFLGDRVLGLCVAEMLFEAFPDASEGELSVRLNQLVNAE 88 (235)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHcCcCcc-cCCccchHhHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhChH
Confidence 457889999999999999999999999997 3344699999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcCCchhhhccChhHHHHHHHHHhhhhhhccccccCccccCCCChhhHHHHHHHhheeeeeCCCCHHHHHHHH
Q 003062 685 CYALSSVKHGLHKHILHASQELYKWINITVDSFERLSLESTFGWESETSFPKALGDIIESLSGAIFVDSGCNKEVVFESI 764 (852)
Q Consensus 685 ~La~~a~~~gL~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~laD~~EAliGAi~~DsG~~~~~v~~~~ 764 (852)
+||.+|.++||++||+.++..... .....+|++||+|||+|||||+|+|+ +.|++|+
T Consensus 89 ~La~ia~~lgL~~~i~~~~~~~~~---------------------~~~~~~~ilad~~EAliGAiylD~G~--~~a~~~i 145 (235)
T PRK12371 89 TCAAIADEIGLHDLIRTGSDVKKL---------------------TGKRLLNVRADVVEALIAAIYLDGGL--EAARPFI 145 (235)
T ss_pred HHHHHHHHCCcHHHhccCcchhhc---------------------CCcccchHHHHHHHHHHHHHHHcCCH--HHHHHHH
Confidence 999999999999999987643210 01345699999999999999999987 6899999
Q ss_pred HHhhcccCCc-ccccCChhhHHHHHHHhCCC-ceeeEEeeec--CCceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHH
Q 003062 765 RPLLEPMITP-ETMRLQPARELNEYCQKHHF-SMKKTVAPRI--NGKAAVTVEVHANGTLFKHTHADADKETAKKVASKE 840 (852)
Q Consensus 765 ~~~l~~~~~~-~~~~~~P~~~L~e~~~~~~~-~~~~~~~~~~--~g~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~ 840 (852)
.+++.|.+.. .....|||++|+||||+.+. .+.|..+... ++...|+|+|+++|..++ +|.|.|||+|++.||++
T Consensus 146 ~~~~~~~~~~~~~~~~d~Ks~LqE~~q~~~~~~p~Y~~~~~~Gp~h~~~F~v~v~v~~~~~~-~g~G~sKK~Ae~~AA~~ 224 (235)
T PRK12371 146 QRYWQKRALETDAARRDAKTELQEWAHAQFGVTPVYRVDSRSGPDHDPRFTVEVEVKGFAPE-TGEGRSKRAAEQVAAEK 224 (235)
T ss_pred HHHHHHHHhccccccCCHHHHHHHHHHhcCCCCCeEEEEEeecCCCCCeEEEEEEECCEEEE-EeeeCCHHHHHHHHHHH
Confidence 9999887643 23457999999999997754 4558744333 235789999999999887 89999999999999999
Q ss_pred HHHHhhhhC
Q 003062 841 VLKSLKASF 849 (852)
Q Consensus 841 AL~~L~~~~ 849 (852)
||++|+...
T Consensus 225 al~~~~~~~ 233 (235)
T PRK12371 225 MLEREGVWK 233 (235)
T ss_pred HHHHhhhhc
Confidence 999997643
No 4
>COG0571 Rnc dsRNA-specific ribonuclease [Transcription]
Probab=100.00 E-value=2.5e-43 Score=359.32 Aligned_cols=222 Identities=32% Similarity=0.432 Sum_probs=195.7
Q ss_pred HhHHHHHHHcCcccCCHHHHHHHhccCCCCCCC-CCCcchhhhHhhHHHHHHHHHHHHHHhCCCCCcchHHHHHHHhcCh
Q 003062 605 VNVRHLESLLNYSFRDPSLLVEALTHGSYMLPE-IPRCYQRLEFLGDAVLDYLITVYLYNKYPTLSPGDLTDMRSASVNN 683 (852)
Q Consensus 605 ~~~~~le~~lgy~F~~~~LL~~AlTH~S~~~~~-~~~~yeRLEfLGDavLd~~v~~~l~~~~p~~~~~~Lt~~r~~lv~n 683 (852)
..+..+++.+||+|+|+.||.+||||+||.... ...+||||||||||||+++|++|||++||+.++|+||.+|+.+||+
T Consensus 6 ~~~~~l~~~lg~~f~~~~lL~~AltH~S~~~e~~~~~~nERLEFLGDavL~l~vae~Lf~~yP~~~EG~Ls~~ra~lV~~ 85 (235)
T COG0571 6 KKLEALEKKLGYTFKDKELLEQALTHRSYANEHKAVENNERLEFLGDAVLGLVVAEYLFKKYPNLPEGELSKLRAALVSE 85 (235)
T ss_pred HHHHHHHHHhCCCcCCHHHHHHHhcCcchhccccCCcchHHHHhhHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Confidence 357889999999999999999999999997422 5679999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHcCCchhhhccChhHHHHHHHHHhhhhhhccccccCccccCCCChhhHHHHHHHhheeeeeCCCCHHHHHHH
Q 003062 684 DCYALSSVKHGLHKHILHASQELYKWINITVDSFERLSLESTFGWESETSFPKALGDIIESLSGAIFVDSGCNKEVVFES 763 (852)
Q Consensus 684 ~~La~~a~~~gL~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~laD~~EAliGAi~~DsG~~~~~v~~~ 763 (852)
++|+.+|..+||.+||+.++++.... ....+++++|+|||+|||||+|+|. +.+++|
T Consensus 86 ~~La~ia~~l~l~~~l~lg~ge~~~g---------------------g~~~~silaD~~EAligAiylD~g~--~~~~~~ 142 (235)
T COG0571 86 ESLAEIARELGLGDYLRLGKGEEKSG---------------------GRRRESILADAFEALIGAIYLDSGL--EAARKF 142 (235)
T ss_pred HHHHHHHHHhCccchhhccCChhhcC---------------------CCCchhHHHHHHHHHHHHHHHhCCh--HHHHHH
Confidence 99999999999999999998875431 2457899999999999999999994 699999
Q ss_pred HHHhhcccCCc---ccccCChhhHHHHHHHhCCCcee-eEEeeecC--CceEEEEEEEECCEEEEeEEeeCCHHHHHHHH
Q 003062 764 IRPLLEPMITP---ETMRLQPARELNEYCQKHHFSMK-KTVAPRIN--GKAAVTVEVHANGTLFKHTHADADKETAKKVA 837 (852)
Q Consensus 764 ~~~~l~~~~~~---~~~~~~P~~~L~e~~~~~~~~~~-~~~~~~~~--g~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~A 837 (852)
+.+++.|.+.. .....||+++|++|+|.++...+ |..+..++ +...|++.|.++|..++ .|.|+|+|+|++.|
T Consensus 143 i~~l~~~~~~~~~~~~~~~D~Kt~LQe~~q~~~~~~p~Y~~v~~~g~~h~~~F~v~v~v~~~~~g-~G~G~skk~AEq~A 221 (235)
T COG0571 143 ILKLFLPRLEEIDAGDQFKDPKTRLQELLQAQGLVLPEYRLVKEEGPAHDKEFTVEVAVGGKELG-TGKGRSKKEAEQAA 221 (235)
T ss_pred HHHHHHHHHhhccccccccChhHHHHHHHHhcCCCCCeEEEeeccCCCCCceEEEEEEECCeeEE-EecccCHHHHHHHH
Confidence 99999998763 22338999999999998887554 87554442 46899999999999888 89999999999999
Q ss_pred HHHHHHHhhhhCC
Q 003062 838 SKEVLKSLKASFP 850 (852)
Q Consensus 838 A~~AL~~L~~~~~ 850 (852)
|+.||+.|....+
T Consensus 222 A~~al~~l~~~~~ 234 (235)
T COG0571 222 AEQALKKLGVKEP 234 (235)
T ss_pred HHHHHHHhccccC
Confidence 9999999987654
No 5
>PRK12372 ribonuclease III; Reviewed
Probab=100.00 E-value=2.8e-43 Score=377.11 Aligned_cols=217 Identities=29% Similarity=0.432 Sum_probs=187.2
Q ss_pred HHHHHHHcCcccCCHHHHHHHhccCCCCCCCCCCcchhhhHhhHHHHHHHHHHHHHHhCCCCCcchHHHHHHHhcChHHH
Q 003062 607 VRHLESLLNYSFRDPSLLVEALTHGSYMLPEIPRCYQRLEFLGDAVLDYLITVYLYNKYPTLSPGDLTDMRSASVNNDCY 686 (852)
Q Consensus 607 ~~~le~~lgy~F~~~~LL~~AlTH~S~~~~~~~~~yeRLEfLGDavLd~~v~~~l~~~~p~~~~~~Lt~~r~~lv~n~~L 686 (852)
+..||++|||+|+|+.||.+||||+||. ..+|||||||||+||+++|++|||.+||++++|+||.+|+.+|||++|
T Consensus 3 l~~LEk~LGY~Fkn~~LL~eALTH~Sy~----~~~NERLEFLGDAVL~liVse~Lf~~fP~~~EG~LT~lRS~LVsn~tL 78 (413)
T PRK12372 3 LSQLESRLRYEFRNAELLRQALTHRSHS----ATHNERLEFLGDSVLNCAVAALLFQRFGKLDEGDLSRVRANLVKQQSL 78 (413)
T ss_pred HHHHHHHhCCCcCCHHHHHHHHhccccc----cccHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhhHHH
Confidence 5679999999999999999999999986 248999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCchhhhccChhHHHHHHHHHhhhhhhccccccCccccCCCChhhHHHHHHHhheeeeeCCCCHHHHHHHHHH
Q 003062 687 ALSSVKHGLHKHILHASQELYKWINITVDSFERLSLESTFGWESETSFPKALGDIIESLSGAIFVDSGCNKEVVFESIRP 766 (852)
Q Consensus 687 a~~a~~~gL~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~laD~~EAliGAi~~DsG~~~~~v~~~~~~ 766 (852)
+.+|.++||.+||+.+..+... .....+++|+|+|||+|||||+|+|+ +.++.|+.+
T Consensus 79 A~IA~~LgL~~~Lrlg~ge~~s---------------------gg~~~~kILADvfEALIGAIYLDsG~--e~a~~fV~~ 135 (413)
T PRK12372 79 YEIAQALNISEGLRLGEGELRS---------------------GGFRRPSILADAFEAIIGAVFLDGGF--EAAQGVIKR 135 (413)
T ss_pred HHHHHHcCchHhhhcCcchhhc---------------------CCCCCccHHHHHHHHHHHHHHHhCCH--HHHHHHHHH
Confidence 9999999999999988754321 11357899999999999999999986 589999999
Q ss_pred hhcccCCc---ccccCChhhHHHHHHHhCCCce-eeEEeeec--CCceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHH
Q 003062 767 LLEPMITP---ETMRLQPARELNEYCQKHHFSM-KKTVAPRI--NGKAAVTVEVHANGTLFKHTHADADKETAKKVASKE 840 (852)
Q Consensus 767 ~l~~~~~~---~~~~~~P~~~L~e~~~~~~~~~-~~~~~~~~--~g~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~ 840 (852)
++.|++.. .....||++.|+||+|+++... .|..+... +....|+|.|+++|..+..+|.|.|||+|++.||+.
T Consensus 136 ll~p~l~~~~~~~~~~D~KS~LQE~~Q~~~~~~P~Y~lv~e~Gp~h~~~F~V~V~v~g~~~~g~G~G~SKKeAEQ~AAr~ 215 (413)
T PRK12372 136 LYVPILDHIDPRTLGKDAKTLLQEYLQGHKIALPTYTVVATHGAAHNQQFEVECTVPKLDVKVSGSGASRRAAEQAAAKK 215 (413)
T ss_pred HHHHHHhhcccccccCCHHHHHHHHHHhcCCCCCeeEEeeeecCCCCceEEEEEEECCeEEEEEEEeCCHHHHHHHHHHH
Confidence 99887653 2335799999999999988764 47644333 235789999999996554489999999999999999
Q ss_pred HHHHhhhhCC
Q 003062 841 VLKSLKASFP 850 (852)
Q Consensus 841 AL~~L~~~~~ 850 (852)
||++|+...|
T Consensus 216 AL~kL~~~~~ 225 (413)
T PRK12372 216 ALDEVMAAAP 225 (413)
T ss_pred HHHHHhcccc
Confidence 9999996554
No 6
>PRK14718 ribonuclease III; Provisional
Probab=100.00 E-value=4.3e-43 Score=376.32 Aligned_cols=216 Identities=29% Similarity=0.421 Sum_probs=186.8
Q ss_pred HHHHHHHcCcccCCHHHHHHHhccCCCCCCCCCCcchhhhHhhHHHHHHHHHHHHHHhCCCCCcchHHHHHHHhcChHHH
Q 003062 607 VRHLESLLNYSFRDPSLLVEALTHGSYMLPEIPRCYQRLEFLGDAVLDYLITVYLYNKYPTLSPGDLTDMRSASVNNDCY 686 (852)
Q Consensus 607 ~~~le~~lgy~F~~~~LL~~AlTH~S~~~~~~~~~yeRLEfLGDavLd~~v~~~l~~~~p~~~~~~Lt~~r~~lv~n~~L 686 (852)
+..||++|||+|+|+.||.+||||+||. ..+|||||||||+||+++|++|||.+||++++|.||.+|+.+|||++|
T Consensus 3 l~~LEkrLGY~Fkn~~LL~eALTH~Sys----~e~NERLEFLGDAVL~liVse~Lf~~fPdl~EGeLT~LRS~LVSnetL 78 (467)
T PRK14718 3 LSQLESRLRYEFRNAELLRQALTHRSHS----ATHNERLEFLGDSVLNCAVAALLFQRFGKLDEGDLSRVRANLVKQQSL 78 (467)
T ss_pred HHHHHHHhCCCcCCHHHHHHHHhccCcC----cccHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHhhhHHH
Confidence 5679999999999999999999999996 248999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCchhhhccChhHHHHHHHHHhhhhhhccccccCccccCCCChhhHHHHHHHhheeeeeCCCCHHHHHHHHHH
Q 003062 687 ALSSVKHGLHKHILHASQELYKWINITVDSFERLSLESTFGWESETSFPKALGDIIESLSGAIFVDSGCNKEVVFESIRP 766 (852)
Q Consensus 687 a~~a~~~gL~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~laD~~EAliGAi~~DsG~~~~~v~~~~~~ 766 (852)
+.+|.++||++||+.+..+... .....+++|+|+|||||||||+|+|+ +.+++||.+
T Consensus 79 A~IAr~LGL~d~Lrlg~gE~~s---------------------gG~~~~sILADvFEALIGAIYLDsG~--e~a~~fI~~ 135 (467)
T PRK14718 79 YEIAQALNISDGLRLGEGELRS---------------------GGFRRPSILADAFEAIIGAVFLDGGF--EAAQGVIKR 135 (467)
T ss_pred HHHHHHcCchHHHhhCCccccc---------------------CCCCChhHHHHHHHHHHHHHHHccCH--HHHHHHHHH
Confidence 9999999999999987654321 11347899999999999999999997 589999999
Q ss_pred hhcccCCc---ccccCChhhHHHHHHHhCCCce-eeEEeeec--CCceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHH
Q 003062 767 LLEPMITP---ETMRLQPARELNEYCQKHHFSM-KKTVAPRI--NGKAAVTVEVHANGTLFKHTHADADKETAKKVASKE 840 (852)
Q Consensus 767 ~l~~~~~~---~~~~~~P~~~L~e~~~~~~~~~-~~~~~~~~--~g~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~ 840 (852)
+|.|++.. .....||++.|+||||+++... .|..+... ++...|+|.|+++|..+.+.|.|.|||+|++.||+.
T Consensus 136 ll~p~i~~~d~~~~~kDyKS~LQE~~Qk~~~~~PeY~li~esGPdH~k~F~V~V~v~g~~~~G~G~G~SKKeAEQ~AAk~ 215 (467)
T PRK14718 136 LYVPILDHIDPRTLGKDAKTLLQEYLQGHKIALPTYTVVATHGAAHNQQFEVECTVPKLDIKVSGSGASRRAAEQAAAKK 215 (467)
T ss_pred HHHHHHhhhcccccccCHHHHHHHHHHhcCCCCCeeEEeeeecCCCCCeEEEEEEECCeeeEEEEEcCCHHHHHHHHHHH
Confidence 99887643 2345799999999999998764 48744333 346789999999996553489999999999999999
Q ss_pred HHHHhhhhC
Q 003062 841 VLKSLKASF 849 (852)
Q Consensus 841 AL~~L~~~~ 849 (852)
||++|+...
T Consensus 216 AL~kL~~~~ 224 (467)
T PRK14718 216 ALDEVTAVA 224 (467)
T ss_pred HHHHhcccc
Confidence 999998443
No 7
>PRK00102 rnc ribonuclease III; Reviewed
Probab=100.00 E-value=5.3e-40 Score=343.40 Aligned_cols=218 Identities=33% Similarity=0.498 Sum_probs=188.1
Q ss_pred hHHHHHHHcCcccCCHHHHHHHhccCCCCC-CCCCCcchhhhHhhHHHHHHHHHHHHHHhCCCCCcchHHHHHHHhcChH
Q 003062 606 NVRHLESLLNYSFRDPSLLVEALTHGSYML-PEIPRCYQRLEFLGDAVLDYLITVYLYNKYPTLSPGDLTDMRSASVNND 684 (852)
Q Consensus 606 ~~~~le~~lgy~F~~~~LL~~AlTH~S~~~-~~~~~~yeRLEfLGDavLd~~v~~~l~~~~p~~~~~~Lt~~r~~lv~n~ 684 (852)
+++.||++|||+|+|+.|+.+||||+||.. .....+|||||||||+||++++++|||.+||+.++|.|+.+|+.+|||+
T Consensus 4 ~~~~l~~~lg~~f~~~~ll~~Alth~S~~~~~~~~~~nerLefLGDavl~~~v~~~l~~~~p~~~~g~l~~~~~~lvsn~ 83 (229)
T PRK00102 4 DLEELQKKLGYTFKDPELLIQALTHRSYANENKGLKHNERLEFLGDAVLELVVSEYLFKRFPDLDEGDLSKLRAALVREE 83 (229)
T ss_pred hHHHHHHHhCCCCCCHHHHHHHhCccchhccCCCcccchhHHHHHHHHHHHHHHHHHHHHCCCCChhHHHHHHHHHhCHH
Confidence 578899999999999999999999999963 2356799999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcCCchhhhccChhHHHHHHHHHhhhhhhccccccCccccCCCChhhHHHHHHHhheeeeeCCCCHHHHHHHH
Q 003062 685 CYALSSVKHGLHKHILHASQELYKWINITVDSFERLSLESTFGWESETSFPKALGDIIESLSGAIFVDSGCNKEVVFESI 764 (852)
Q Consensus 685 ~La~~a~~~gL~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~laD~~EAliGAi~~DsG~~~~~v~~~~ 764 (852)
+|+.+|.++||+++|+.++..... .....+|+++|+|||+|||||+|+|. +.+++|+
T Consensus 84 ~la~~a~~lgl~~~i~~~~~~~~~---------------------~~~~~~k~~ad~~EA~iGAiyld~g~--~~~~~~i 140 (229)
T PRK00102 84 SLAEIARELGLGEYLLLGKGEEKS---------------------GGRRRPSILADAFEALIGAIYLDQGL--EAARKFI 140 (229)
T ss_pred HHHHHHHHCCcHHHHccCcHHHHc---------------------CCCCCccHHHHHHHHHHHHHHHhCCH--HHHHHHH
Confidence 999999999999999987643210 01346799999999999999999986 5899999
Q ss_pred HHhhcccCCc---ccccCChhhHHHHHHHhCCCc-eeeEEeeecC--CceEEEEEEEECCEEEEeEEeeCCHHHHHHHHH
Q 003062 765 RPLLEPMITP---ETMRLQPARELNEYCQKHHFS-MKKTVAPRIN--GKAAVTVEVHANGTLFKHTHADADKETAKKVAS 838 (852)
Q Consensus 765 ~~~l~~~~~~---~~~~~~P~~~L~e~~~~~~~~-~~~~~~~~~~--g~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA 838 (852)
.+++.|++.. .....||++.|+++|++.+.. +.|+.+...+ ..+.|+|+|+++|+.++ +|.|.|+++||+.||
T Consensus 141 ~~~~~~~l~~~~~~~~~~~pk~~L~e~~~~~~~~~p~y~~~~~~g~~~~~~f~~~v~i~~~~~~-~g~g~skk~Ae~~AA 219 (229)
T PRK00102 141 LRLFEPRIEEIDLGDLVKDYKTRLQELLQGRGLPLPEYELVKEEGPAHDKEFTVEVTVNGKELG-EGTGSSKKEAEQAAA 219 (229)
T ss_pred HHHHHHHHHhhccccccCCHHHHHHHHHHHcCCCCCceEEeeccCCCCCceEEEEEEECCEEEE-EeeeCCHHHHHHHHH
Confidence 9998887654 234579999999999988775 4576333332 24789999999999887 899999999999999
Q ss_pred HHHHHHhhh
Q 003062 839 KEVLKSLKA 847 (852)
Q Consensus 839 ~~AL~~L~~ 847 (852)
++||+.|+.
T Consensus 220 ~~Al~~l~~ 228 (229)
T PRK00102 220 KQALKKLKE 228 (229)
T ss_pred HHHHHHHhh
Confidence 999999975
No 8
>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=1.6e-38 Score=330.50 Aligned_cols=212 Identities=33% Similarity=0.455 Sum_probs=182.0
Q ss_pred HHHHcCcccCCHHHHHHHhccCCCCCC--CCCCcchhhhHhhHHHHHHHHHHHHHHhCCCCCcchHHHHHHHhcChHHHH
Q 003062 610 LESLLNYSFRDPSLLVEALTHGSYMLP--EIPRCYQRLEFLGDAVLDYLITVYLYNKYPTLSPGDLTDMRSASVNNDCYA 687 (852)
Q Consensus 610 le~~lgy~F~~~~LL~~AlTH~S~~~~--~~~~~yeRLEfLGDavLd~~v~~~l~~~~p~~~~~~Lt~~r~~lv~n~~La 687 (852)
||++|||+|+|++||.+|||||||... ....+|||||||||+||++++++|+|.+||+.++|.|+.+|+.+|||.+|+
T Consensus 1 ~e~~lgy~F~~~~ll~~Alth~S~~~~~~~~~~~nerLe~lGd~vl~~~~~~~l~~~~p~~~~~~l~~~~~~lvsn~~la 80 (220)
T TIGR02191 1 LEKRLGYKFKNKELLEQALTHSSYANEHHKGVKNNERLEFLGDAVLGLVVAEYLFKNFPDLSEGELSKLRAALVSEESLA 80 (220)
T ss_pred ChHHhCCCcCCHHHHHHHhcCcccccccccCccchHHHHHHHHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCHHHHH
Confidence 589999999999999999999999732 245799999999999999999999999999999999999999999999999
Q ss_pred HHHHHcCCchhhhccChhHHHHHHHHHhhhhhhccccccCccccCCCChhhHHHHHHHhheeeeeCCCCHHHHHHHHHHh
Q 003062 688 LSSVKHGLHKHILHASQELYKWINITVDSFERLSLESTFGWESETSFPKALGDIIESLSGAIFVDSGCNKEVVFESIRPL 767 (852)
Q Consensus 688 ~~a~~~gL~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~laD~~EAliGAi~~DsG~~~~~v~~~~~~~ 767 (852)
.+|.++||+++|+.++..... .....+|+++|+|||+|||||+|+| ++.+++|+..+
T Consensus 81 ~~a~~~gl~~~i~~~~~~~~~---------------------~~~~~~k~~ad~~eAliGAiyld~g--~~~~~~~i~~~ 137 (220)
T TIGR02191 81 EVARELGLGKFLLLGKGEEKS---------------------GGRRRESILADAFEALIGAIYLDSG--LEAARKFILKL 137 (220)
T ss_pred HHHHHCCcHHHhccCchHhhc---------------------CCcccchHHHHHHHHHHHHHHHhCC--HHHHHHHHHHH
Confidence 999999999999987643210 0134689999999999999999999 57899999999
Q ss_pred hcccCCc---ccccCChhhHHHHHHHhCCC-ceeeEEeeec--CCceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHHH
Q 003062 768 LEPMITP---ETMRLQPARELNEYCQKHHF-SMKKTVAPRI--NGKAAVTVEVHANGTLFKHTHADADKETAKKVASKEV 841 (852)
Q Consensus 768 l~~~~~~---~~~~~~P~~~L~e~~~~~~~-~~~~~~~~~~--~g~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~A 841 (852)
+.|.+.. .....||++.|+++|++.+. .+.|+.+... .+.+.|+|+|+++|+.++ +|.|.|+++||+.||+.|
T Consensus 138 ~~~~~~~~~~~~~~~~pk~~L~e~~~~~~~~~p~y~~~~~~g~~~~~~f~~~v~~~~~~~~-~g~g~skk~A~~~AA~~A 216 (220)
T TIGR02191 138 LIPRIDAIEKEETLKDYKTALQEWAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYG-EGKGKSKKEAEQNAAKAA 216 (220)
T ss_pred HHHHHHhhhcccccCChHHHHHHHHHHcCCCCceEEEecccCCCCCceEEEEEEECCEEEE-EeeeCCHHHHHHHHHHHH
Confidence 8887653 23457999999999998765 4567633222 225689999999999988 899999999999999999
Q ss_pred HHHh
Q 003062 842 LKSL 845 (852)
Q Consensus 842 L~~L 845 (852)
|++|
T Consensus 217 l~~l 220 (220)
T TIGR02191 217 LEKL 220 (220)
T ss_pred HHhC
Confidence 9875
No 9
>PRK12371 ribonuclease III; Reviewed
Probab=99.94 E-value=6.3e-27 Score=242.33 Aligned_cols=134 Identities=28% Similarity=0.373 Sum_probs=116.7
Q ss_pred HHHHHHHhhccccCCCCCHHHHHHHhccCCCCC--CCCchhhhhhhhhHHhHHHHHHHHHhcCCCCcchhhHHHhhcccc
Q 003062 416 VNLKNMLLDHCMQNVTIPTSKVLEAITTKKCQE--GFHLESLETLGDSFLKYAASQQLFKTYQNHHEGLLSVKKDRIISN 493 (852)
Q Consensus 416 ~~l~~~l~~~~~~~~~~~~~lll~AlT~~s~~~--~~nyeRLE~LGDs~Lk~~~s~~l~~~~p~~~eg~Ls~~r~~~vsN 493 (852)
.+|++.|+|.|++. .++.+||||+|+.. ..||||||||||+||+++++.+||.+||+++||.||.+|+.+|||
T Consensus 13 ~~le~~lgy~F~~~-----~Ll~~AlTH~S~~~~~~~~~eRLEFLGDavL~l~vs~~Lf~~~p~~~eG~Lt~~rs~lV~n 87 (235)
T PRK12371 13 SILEERTGHRFANK-----ERLERALTHSSARASKQGNYERLEFLGDRVLGLCVAEMLFEAFPDASEGELSVRLNQLVNA 87 (235)
T ss_pred HHHHHHHCCCCCCH-----HHHHHHHcCcCcccCCccchHhHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCh
Confidence 45788899999876 89999999999865 359999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhCCccccccccccCCCCcccCCCCCCCcccCccccccccccccccccccccchhHHHHHHHHHHHhhcCChH
Q 003062 494 AALCKLGCDHKLPGFIRTEPFDPKMWMIPGDNSGSYELNDHSLFNERKIYVTGRKKVKSKTVADVVEALIGAFLSTGGEN 573 (852)
Q Consensus 494 ~~L~~~a~~~gL~~~i~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~K~lADv~EAliGA~yl~~G~~ 573 (852)
++|+++|.++||++||+.. ++... ..+ ...+|++||+|||+|||+|+|+|.+
T Consensus 88 ~~La~ia~~lgL~~~i~~~---------~~~~~-----------------~~~--~~~~~ilad~~EAliGAiylD~G~~ 139 (235)
T PRK12371 88 ETCAAIADEIGLHDLIRTG---------SDVKK-----------------LTG--KRLLNVRADVVEALIAAIYLDGGLE 139 (235)
T ss_pred HHHHHHHHHCCcHHHhccC---------cchhh-----------------cCC--cccchHHHHHHHHHHHHHHHcCCHH
Confidence 9999999999999999863 22200 001 1246899999999999999999999
Q ss_pred HHHHhhhhc
Q 003062 574 VGLIFLDRI 582 (852)
Q Consensus 574 ~a~~~~~~l 582 (852)
.|.+|+..+
T Consensus 140 ~a~~~i~~~ 148 (235)
T PRK12371 140 AARPFIQRY 148 (235)
T ss_pred HHHHHHHHH
Confidence 999998765
No 10
>COG0571 Rnc dsRNA-specific ribonuclease [Transcription]
Probab=99.94 E-value=1.3e-26 Score=236.68 Aligned_cols=134 Identities=28% Similarity=0.378 Sum_probs=117.6
Q ss_pred HHHHHHHhhccccCCCCCHHHHHHHhccCCCCCC----CCchhhhhhhhhHHhHHHHHHHHHhcCCCCcchhhHHHhhcc
Q 003062 416 VNLKNMLLDHCMQNVTIPTSKVLEAITTKKCQEG----FHLESLETLGDSFLKYAASQQLFKTYQNHHEGLLSVKKDRII 491 (852)
Q Consensus 416 ~~l~~~l~~~~~~~~~~~~~lll~AlT~~s~~~~----~nyeRLE~LGDs~Lk~~~s~~l~~~~p~~~eg~Ls~~r~~~v 491 (852)
..|.+.+++.|++. .++.+||||+|+... .||||||||||+||.++++.+||.+||+.+||.||.+|+.+|
T Consensus 9 ~~l~~~lg~~f~~~-----~lL~~AltH~S~~~e~~~~~~nERLEFLGDavL~l~vae~Lf~~yP~~~EG~Ls~~ra~lV 83 (235)
T COG0571 9 EALEKKLGYTFKDK-----ELLEQALTHRSYANEHKAVENNERLEFLGDAVLGLVVAEYLFKKYPNLPEGELSKLRAALV 83 (235)
T ss_pred HHHHHHhCCCcCCH-----HHHHHHhcCcchhccccCCcchHHHHhhHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Confidence 56788899998876 899999999999764 489999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHHhCCccccccccccCCCCcccCCCCCCCcccCccccccccccccccccccccchhHHHHHHHHHHHhhcCC
Q 003062 492 SNAALCKLGCDHKLPGFIRTEPFDPKMWMIPGDNSGSYELNDHSLFNERKIYVTGRKKVKSKTVADVVEALIGAFLSTGG 571 (852)
Q Consensus 492 sN~~L~~~a~~~gL~~~i~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~K~lADv~EAliGA~yl~~G 571 (852)
|+..|+++|..+||.+||+. ..|.. . ..+. -.++++||+|||+|||+|+|+|
T Consensus 84 ~~~~La~ia~~l~l~~~l~l---------g~ge~----------~-------~gg~--~~~silaD~~EAligAiylD~g 135 (235)
T COG0571 84 SEESLAEIARELGLGDYLRL---------GKGEE----------K-------SGGR--RRESILADAFEALIGAIYLDSG 135 (235)
T ss_pred HHHHHHHHHHHhCccchhhc---------cCChh----------h-------cCCC--CchhHHHHHHHHHHHHHHHhCC
Confidence 99999999999999999987 34431 1 0111 3688999999999999999999
Q ss_pred hHHHHHhhhhc
Q 003062 572 ENVGLIFLDRI 582 (852)
Q Consensus 572 ~~~a~~~~~~l 582 (852)
++.+++|+..+
T Consensus 136 ~~~~~~~i~~l 146 (235)
T COG0571 136 LEAARKFILKL 146 (235)
T ss_pred hHHHHHHHHHH
Confidence 99999997543
No 11
>PF14622 Ribonucleas_3_3: Ribonuclease-III-like; PDB: 1O0W_A 2A11_A 3N3W_B.
Probab=99.93 E-value=6.3e-27 Score=220.85 Aligned_cols=126 Identities=40% Similarity=0.583 Sum_probs=102.1
Q ss_pred CHHHHHHHhccCCCCCCCCCCcchhhhHhhHHHHHHHHHHHHHHhCCCCCcchHHHHHHHhcChHHHHHHHHHcCCchhh
Q 003062 620 DPSLLVEALTHGSYMLPEIPRCYQRLEFLGDAVLDYLITVYLYNKYPTLSPGDLTDMRSASVNNDCYALSSVKHGLHKHI 699 (852)
Q Consensus 620 ~~~LL~~AlTH~S~~~~~~~~~yeRLEfLGDavLd~~v~~~l~~~~p~~~~~~Lt~~r~~lv~n~~La~~a~~~gL~~~l 699 (852)
|++||.+||||+||. ++...+|||||||||+||++++++|+|+++| .++|.++.+|+.+|++++|+.+|.++||++++
T Consensus 1 ~~~Ll~~alTH~S~~-~~~~~~nerLefLGd~vL~~~vs~~l~~~~~-~~~g~l~~~~~~lv~~~~La~~a~~lgL~~~i 78 (128)
T PF14622_consen 1 DDELLLQALTHKSYA-HERKPNNERLEFLGDAVLGLVVSEYLFQRPP-ADEGELTRLRSNLVSNETLAEIAKQLGLDKLI 78 (128)
T ss_dssp SHHHHHHHTB-HHHH-HHTCB-SHHHHHHHHHHHHHHHHHHHHHHTT-TSCHHHHHHHHHHHSHHHHHHHHHHTTCGGC-
T ss_pred CHHHHHHHhcCcccc-ccccCccHHHHHHHHHHHHHHHHHHHHhCcC-ccchHHHHHHHHHhChHHHHHHHHHCCHHHHH
Confidence 689999999999997 4446899999999999999999999999955 48999999999999999999999999999999
Q ss_pred hccChhHHHHHHHHHhhhhhhccccccCccccCCCChhhHHHHHHHhheeeeeCCCCHHHHHHHHHHhhcc
Q 003062 700 LHASQELYKWINITVDSFERLSLESTFGWESETSFPKALGDIIESLSGAIFVDSGCNKEVVFESIRPLLEP 770 (852)
Q Consensus 700 ~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~laD~~EAliGAi~~DsG~~~~~v~~~~~~~l~~ 770 (852)
+.+.+.... .....+|+++|+|||+|||||+|+|+ +++.+|+.+++-|
T Consensus 79 ~~~~~~~~~---------------------~~~~~~~vlad~feAliGAiyld~G~--~~a~~~i~~~i~~ 126 (128)
T PF14622_consen 79 RWGPGEEKS---------------------GGSGSDKVLADVFEALIGAIYLDSGF--EAARKFIQKLILP 126 (128)
T ss_dssp B--HHHHHT---------------------TGGG-HHHHHHHHHHHHHHHHHHH-H--HHHHHHHHHHH--
T ss_pred HhCccHhhc---------------------CCCCCccHHHhHHHHHHHHHHHHcCH--HHHHHHHHHHhcc
Confidence 985432211 01346799999999999999999998 4899999887655
No 12
>PRK14718 ribonuclease III; Provisional
Probab=99.93 E-value=2.5e-26 Score=247.42 Aligned_cols=132 Identities=26% Similarity=0.351 Sum_probs=116.3
Q ss_pred HHHHHHhhccccCCCCCHHHHHHHhccCCCCCCCCchhhhhhhhhHHhHHHHHHHHHhcCCCCcchhhHHHhhccccHHH
Q 003062 417 NLKNMLLDHCMQNVTIPTSKVLEAITTKKCQEGFHLESLETLGDSFLKYAASQQLFKTYQNHHEGLLSVKKDRIISNAAL 496 (852)
Q Consensus 417 ~l~~~l~~~~~~~~~~~~~lll~AlT~~s~~~~~nyeRLE~LGDs~Lk~~~s~~l~~~~p~~~eg~Ls~~r~~~vsN~~L 496 (852)
+|+++|+|.|++. .+|.+||||+|+.. .||||||||||+||+++++.+||.+||+++||.||.+|+.+|||.+|
T Consensus 5 ~LEkrLGY~Fkn~-----~LL~eALTH~Sys~-e~NERLEFLGDAVL~liVse~Lf~~fPdl~EGeLT~LRS~LVSnetL 78 (467)
T PRK14718 5 QLESRLRYEFRNA-----ELLRQALTHRSHSA-THNERLEFLGDSVLNCAVAALLFQRFGKLDEGDLSRVRANLVKQQSL 78 (467)
T ss_pred HHHHHhCCCcCCH-----HHHHHHHhccCcCc-ccHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHhhhHHH
Confidence 5788999999876 89999999999865 49999999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCccccccccccCCCCcccCCCCCCCcccCccccccccccccccccccccchhHHHHHHHHHHHhhcCChHHHH
Q 003062 497 CKLGCDHKLPGFIRTEPFDPKMWMIPGDNSGSYELNDHSLFNERKIYVTGRKKVKSKTVADVVEALIGAFLSTGGENVGL 576 (852)
Q Consensus 497 ~~~a~~~gL~~~i~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~K~lADv~EAliGA~yl~~G~~~a~ 576 (852)
+++|+++||.+||+.. .+.. . ..+ ..+++++||+|||||||+|+|+|++.+.
T Consensus 79 A~IAr~LGL~d~Lrlg---------~gE~----------~-------sgG--~~~~sILADvFEALIGAIYLDsG~e~a~ 130 (467)
T PRK14718 79 YEIAQALNISDGLRLG---------EGEL----------R-------SGG--FRRPSILADAFEAIIGAVFLDGGFEAAQ 130 (467)
T ss_pred HHHHHHcCchHHHhhC---------Cccc----------c-------cCC--CCChhHHHHHHHHHHHHHHHccCHHHHH
Confidence 9999999999999862 2220 0 011 1368999999999999999999999999
Q ss_pred Hhhhhc
Q 003062 577 IFLDRI 582 (852)
Q Consensus 577 ~~~~~l 582 (852)
.|+..+
T Consensus 131 ~fI~~l 136 (467)
T PRK14718 131 GVIKRL 136 (467)
T ss_pred HHHHHH
Confidence 998765
No 13
>PRK12372 ribonuclease III; Reviewed
Probab=99.93 E-value=4.1e-26 Score=245.22 Aligned_cols=132 Identities=26% Similarity=0.352 Sum_probs=116.1
Q ss_pred HHHHHHhhccccCCCCCHHHHHHHhccCCCCCCCCchhhhhhhhhHHhHHHHHHHHHhcCCCCcchhhHHHhhccccHHH
Q 003062 417 NLKNMLLDHCMQNVTIPTSKVLEAITTKKCQEGFHLESLETLGDSFLKYAASQQLFKTYQNHHEGLLSVKKDRIISNAAL 496 (852)
Q Consensus 417 ~l~~~l~~~~~~~~~~~~~lll~AlT~~s~~~~~nyeRLE~LGDs~Lk~~~s~~l~~~~p~~~eg~Ls~~r~~~vsN~~L 496 (852)
+|+++|+|.|++. .||.+||||+|+... ||||||||||+||+++++.+||.+||+++||.||.+|+.+|||.+|
T Consensus 5 ~LEk~LGY~Fkn~-----~LL~eALTH~Sy~~~-~NERLEFLGDAVL~liVse~Lf~~fP~~~EG~LT~lRS~LVsn~tL 78 (413)
T PRK12372 5 QLESRLRYEFRNA-----ELLRQALTHRSHSAT-HNERLEFLGDSVLNCAVAALLFQRFGKLDEGDLSRVRANLVKQQSL 78 (413)
T ss_pred HHHHHhCCCcCCH-----HHHHHHHhccccccc-cHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhhHHH
Confidence 5788999999876 999999999998654 8999999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCccccccccccCCCCcccCCCCCCCcccCccccccccccccccccccccchhHHHHHHHHHHHhhcCChHHHH
Q 003062 497 CKLGCDHKLPGFIRTEPFDPKMWMIPGDNSGSYELNDHSLFNERKIYVTGRKKVKSKTVADVVEALIGAFLSTGGENVGL 576 (852)
Q Consensus 497 ~~~a~~~gL~~~i~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~K~lADv~EAliGA~yl~~G~~~a~ 576 (852)
+++|.++||.+||+.. .+.. . ..+ ...+|++||+|||||||+|+|+|++.+.
T Consensus 79 A~IA~~LgL~~~Lrlg---------~ge~----------~-------sgg--~~~~kILADvfEALIGAIYLDsG~e~a~ 130 (413)
T PRK12372 79 YEIAQALNISEGLRLG---------EGEL----------R-------SGG--FRRPSILADAFEAIIGAVFLDGGFEAAQ 130 (413)
T ss_pred HHHHHHcCchHhhhcC---------cchh----------h-------cCC--CCCccHHHHHHHHHHHHHHHhCCHHHHH
Confidence 9999999999999862 2220 0 011 1368999999999999999999999999
Q ss_pred Hhhhhc
Q 003062 577 IFLDRI 582 (852)
Q Consensus 577 ~~~~~l 582 (852)
.|+..+
T Consensus 131 ~fV~~l 136 (413)
T PRK12372 131 GVIKRL 136 (413)
T ss_pred HHHHHH
Confidence 998766
No 14
>smart00535 RIBOc Ribonuclease III family.
Probab=99.91 E-value=2.3e-24 Score=204.62 Aligned_cols=127 Identities=48% Similarity=0.680 Sum_probs=111.5
Q ss_pred HHHHHHhccCCCCCCCCCCcchhhhHhhHHHHHHHHHHHHHHhCCCCCcchHHHHHHHhcChHHHHHHHHHcCCchhhhc
Q 003062 622 SLLVEALTHGSYMLPEIPRCYQRLEFLGDAVLDYLITVYLYNKYPTLSPGDLTDMRSASVNNDCYALSSVKHGLHKHILH 701 (852)
Q Consensus 622 ~LL~~AlTH~S~~~~~~~~~yeRLEfLGDavLd~~v~~~l~~~~p~~~~~~Lt~~r~~lv~n~~La~~a~~~gL~~~l~~ 701 (852)
.||.+|||||||..+ ..+|||||||||+||+++++.|++.++|+.+++.|+.+++.+|||++|+.+|.++||+++++.
T Consensus 1 ~ll~~alth~s~~~~--~~~~e~Le~lGd~vl~~~v~~~l~~~~p~~~~~~l~~~~~~lvsn~~la~~a~~~~l~~~i~~ 78 (129)
T smart00535 1 SLLLRALTHASYSNE--HEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRL 78 (129)
T ss_pred CHHHHHhhccccccc--CcchHHHHHHHHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHCHHHHHHHHHHCCcHHHHcc
Confidence 378999999999732 269999999999999999999999999999999999999999999999999999999999998
Q ss_pred cChhHHHHHHHHHhhhhhhccccccCccccCCCChhhHHHHHHHhheeeeeCCCCHHHHHHHHHHhhcccCC
Q 003062 702 ASQELYKWINITVDSFERLSLESTFGWESETSFPKALGDIIESLSGAIFVDSGCNKEVVFESIRPLLEPMIT 773 (852)
Q Consensus 702 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~laD~~EAliGAi~~DsG~~~~~v~~~~~~~l~~~~~ 773 (852)
++..... .| ...+|+++|+|||+|||||+|+|. +.+++|+..++.|.++
T Consensus 79 ~~~~~~~------------------~~---~~~~k~~a~~~eAliGAi~ld~g~--~~~~~~i~~~~~~~~~ 127 (129)
T smart00535 79 GRGEAIS------------------GG---RDKPSILADVFEALIGAIYLDSGL--EAAREFIRDLLGPRLE 127 (129)
T ss_pred CchHhhc------------------CC---cccchHHHHHHHHHHHHHHHhCCH--HHHHHHHHHHHHHHhc
Confidence 7654221 01 357899999999999999999985 6899999998887653
No 15
>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=99.91 E-value=1.9e-24 Score=206.39 Aligned_cols=130 Identities=44% Similarity=0.599 Sum_probs=114.8
Q ss_pred HHHHHHhccCCCCCCCCCCcchhhhHhhHHHHHHHHHHHHHHhCCCCCcchHHHHHHHhcChHHHHHHHHHcCCchhhhc
Q 003062 622 SLLVEALTHGSYMLPEIPRCYQRLEFLGDAVLDYLITVYLYNKYPTLSPGDLTDMRSASVNNDCYALSSVKHGLHKHILH 701 (852)
Q Consensus 622 ~LL~~AlTH~S~~~~~~~~~yeRLEfLGDavLd~~v~~~l~~~~p~~~~~~Lt~~r~~lv~n~~La~~a~~~gL~~~l~~ 701 (852)
.|+.+||||+|+.......+|||||||||+||+++++.|++.++|+.+++.++.+++.+|||++|+.+|.++||+++++.
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 37899999999974333579999999999999999999999999999999999999999999999999999999999998
Q ss_pred cChhHHHHHHHHHhhhhhhccccccCccccCCCChhhHHHHHHHhheeeeeCCCCHHHHHHHHHHhhcccCCc
Q 003062 702 ASQELYKWINITVDSFERLSLESTFGWESETSFPKALGDIIESLSGAIFVDSGCNKEVVFESIRPLLEPMITP 774 (852)
Q Consensus 702 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~laD~~EAliGAi~~DsG~~~~~v~~~~~~~l~~~~~~ 774 (852)
.+..... .....+|++||+|||+|||||+|+|. +.+++|+..++.|.+..
T Consensus 81 ~~~~~~~---------------------~~~~~~k~~ad~~eAliGAiyld~g~--~~~~~~i~~~~~~~~~~ 130 (133)
T cd00593 81 GKGEEKS---------------------GGRLRPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPLIEE 130 (133)
T ss_pred CchHhhc---------------------CCcccccHHHHHHHHHHHHHHHhCCH--HHHHHHHHHHHHHHHhh
Confidence 8764321 12467899999999999999999997 68999999988876543
No 16
>PF14622 Ribonucleas_3_3: Ribonuclease-III-like; PDB: 1O0W_A 2A11_A 3N3W_B.
Probab=99.89 E-value=3.5e-24 Score=202.13 Aligned_cols=120 Identities=31% Similarity=0.428 Sum_probs=97.3
Q ss_pred HHHHHHHhccCCCCC--CCCchhhhhhhhhHHhHHHHHHHHHhcCCCCcchhhHHHhhccccHHHHHHHHhCCccccccc
Q 003062 434 TSKVLEAITTKKCQE--GFHLESLETLGDSFLKYAASQQLFKTYQNHHEGLLSVKKDRIISNAALCKLGCDHKLPGFIRT 511 (852)
Q Consensus 434 ~~lll~AlT~~s~~~--~~nyeRLE~LGDs~Lk~~~s~~l~~~~p~~~eg~Ls~~r~~~vsN~~L~~~a~~~gL~~~i~~ 511 (852)
..++++||||+|+.. ..||||||||||+||+++++.++|..+| .++|.++..|+.+|+|.+|+++|.++||+++|+.
T Consensus 2 ~~Ll~~alTH~S~~~~~~~~nerLefLGd~vL~~~vs~~l~~~~~-~~~g~l~~~~~~lv~~~~La~~a~~lgL~~~i~~ 80 (128)
T PF14622_consen 2 DELLLQALTHKSYAHERKPNNERLEFLGDAVLGLVVSEYLFQRPP-ADEGELTRLRSNLVSNETLAEIAKQLGLDKLIRW 80 (128)
T ss_dssp HHHHHHHTB-HHHHHHTCB-SHHHHHHHHHHHHHHHHHHHHHHTT-TSCHHHHHHHHHHHSHHHHHHHHHHTTCGGC-B-
T ss_pred HHHHHHHhcCccccccccCccHHHHHHHHHHHHHHHHHHHHhCcC-ccchHHHHHHHHHhChHHHHHHHHHCCHHHHHHh
Confidence 478999999999863 4699999999999999999999999854 4899999999999999999999999999999987
Q ss_pred cccCCCCcccCCCCCCCcccCccccccccccccccccccccchhHHHHHHHHHHHhhcCChHHHHHhhhhc
Q 003062 512 EPFDPKMWMIPGDNSGSYELNDHSLFNERKIYVTGRKKVKSKTVADVVEALIGAFLSTGGENVGLIFLDRI 582 (852)
Q Consensus 512 ~~f~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~K~lADv~EAliGA~yl~~G~~~a~~~~~~l 582 (852)
. ++.. .......+|++||+|||+|||+|+|+|.+.|.+|+...
T Consensus 81 ~---------~~~~-------------------~~~~~~~~~vlad~feAliGAiyld~G~~~a~~~i~~~ 123 (128)
T PF14622_consen 81 G---------PGEE-------------------KSGGSGSDKVLADVFEALIGAIYLDSGFEAARKFIQKL 123 (128)
T ss_dssp ----------HHHH-------------------HTTGGG-HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH
T ss_pred C---------ccHh-------------------hcCCCCCccHHHhHHHHHHHHHHHHcCHHHHHHHHHHH
Confidence 2 2110 00112468899999999999999999999999998654
No 17
>PRK00102 rnc ribonuclease III; Reviewed
Probab=99.89 E-value=2.2e-23 Score=217.96 Aligned_cols=134 Identities=26% Similarity=0.375 Sum_probs=116.9
Q ss_pred HHHHHHHhhccccCCCCCHHHHHHHhccCCCCC----CCCchhhhhhhhhHHhHHHHHHHHHhcCCCCcchhhHHHhhcc
Q 003062 416 VNLKNMLLDHCMQNVTIPTSKVLEAITTKKCQE----GFHLESLETLGDSFLKYAASQQLFKTYQNHHEGLLSVKKDRII 491 (852)
Q Consensus 416 ~~l~~~l~~~~~~~~~~~~~lll~AlT~~s~~~----~~nyeRLE~LGDs~Lk~~~s~~l~~~~p~~~eg~Ls~~r~~~v 491 (852)
..++++|+|.|++. .++++||||+|+.. ..||||||||||++|+++++.+||.+||+.++|.|+.+|+.+|
T Consensus 6 ~~l~~~lg~~f~~~-----~ll~~Alth~S~~~~~~~~~~nerLefLGDavl~~~v~~~l~~~~p~~~~g~l~~~~~~lv 80 (229)
T PRK00102 6 EELQKKLGYTFKDP-----ELLIQALTHRSYANENKGLKHNERLEFLGDAVLELVVSEYLFKRFPDLDEGDLSKLRAALV 80 (229)
T ss_pred HHHHHHhCCCCCCH-----HHHHHHhCccchhccCCCcccchhHHHHHHHHHHHHHHHHHHHHCCCCChhHHHHHHHHHh
Confidence 46889999999876 89999999999853 4699999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHHhCCccccccccccCCCCcccCCCCCCCcccCccccccccccccccccccccchhHHHHHHHHHHHhhcCC
Q 003062 492 SNAALCKLGCDHKLPGFIRTEPFDPKMWMIPGDNSGSYELNDHSLFNERKIYVTGRKKVKSKTVADVVEALIGAFLSTGG 571 (852)
Q Consensus 492 sN~~L~~~a~~~gL~~~i~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~K~lADv~EAliGA~yl~~G 571 (852)
||++|+++|.++||++||+.. ++.. . ..+ ..++|++||+|||+|||+|+|+|
T Consensus 81 sn~~la~~a~~lgl~~~i~~~---------~~~~----------~-------~~~--~~~~k~~ad~~EA~iGAiyld~g 132 (229)
T PRK00102 81 REESLAEIARELGLGEYLLLG---------KGEE----------K-------SGG--RRRPSILADAFEALIGAIYLDQG 132 (229)
T ss_pred CHHHHHHHHHHCCcHHHHccC---------cHHH----------H-------cCC--CCCccHHHHHHHHHHHHHHHhCC
Confidence 999999999999999999863 2210 0 000 13578999999999999999999
Q ss_pred hHHHHHhhhhc
Q 003062 572 ENVGLIFLDRI 582 (852)
Q Consensus 572 ~~~a~~~~~~l 582 (852)
.+.+.+|+..+
T Consensus 133 ~~~~~~~i~~~ 143 (229)
T PRK00102 133 LEAARKFILRL 143 (229)
T ss_pred HHHHHHHHHHH
Confidence 99999998776
No 18
>smart00535 RIBOc Ribonuclease III family.
Probab=99.88 E-value=6.8e-23 Score=194.54 Aligned_cols=119 Identities=32% Similarity=0.436 Sum_probs=104.8
Q ss_pred HHHHHhccCCCCCCC-CchhhhhhhhhHHhHHHHHHHHHhcCCCCcchhhHHHhhccccHHHHHHHHhCCcccccccccc
Q 003062 436 KVLEAITTKKCQEGF-HLESLETLGDSFLKYAASQQLFKTYQNHHEGLLSVKKDRIISNAALCKLGCDHKLPGFIRTEPF 514 (852)
Q Consensus 436 lll~AlT~~s~~~~~-nyeRLE~LGDs~Lk~~~s~~l~~~~p~~~eg~Ls~~r~~~vsN~~L~~~a~~~gL~~~i~~~~f 514 (852)
++++||||+|+.... ||||||||||+||+++++.++|.++|+.++|.|+..|+.+|||++|+++|.++||+++++..+.
T Consensus 2 ll~~alth~s~~~~~~~~e~Le~lGd~vl~~~v~~~l~~~~p~~~~~~l~~~~~~lvsn~~la~~a~~~~l~~~i~~~~~ 81 (129)
T smart00535 2 LLLRALTHASYSNEHEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81 (129)
T ss_pred HHHHHhhcccccccCcchHHHHHHHHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHCHHHHHHHHHHCCcHHHHccCch
Confidence 689999999998876 9999999999999999999999999999999999999999999999999999999999987421
Q ss_pred CCCCcccCCCCCCCcccCccccccccccccccccccccchhHHHHHHHHHHHhhcCChHHHHHhhhhc
Q 003062 515 DPKMWMIPGDNSGSYELNDHSLFNERKIYVTGRKKVKSKTVADVVEALIGAFLSTGGENVGLIFLDRI 582 (852)
Q Consensus 515 ~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~K~lADv~EAliGA~yl~~G~~~a~~~~~~l 582 (852)
. . ......++|++||+|||+|||+|+++|.+.+.+|+..+
T Consensus 82 ~--------~--------------------~~~~~~~~k~~a~~~eAliGAi~ld~g~~~~~~~i~~~ 121 (129)
T smart00535 82 E--------A--------------------ISGGRDKPSILADVFEALIGAIYLDSGLEAAREFIRDL 121 (129)
T ss_pred H--------h--------------------hcCCcccchHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 1 0 00011478999999999999999999999999997543
No 19
>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=99.88 E-value=7e-23 Score=213.00 Aligned_cols=132 Identities=25% Similarity=0.354 Sum_probs=114.8
Q ss_pred HHHHHhhccccCCCCCHHHHHHHhccCCCCCC-----CCchhhhhhhhhHHhHHHHHHHHHhcCCCCcchhhHHHhhccc
Q 003062 418 LKNMLLDHCMQNVTIPTSKVLEAITTKKCQEG-----FHLESLETLGDSFLKYAASQQLFKTYQNHHEGLLSVKKDRIIS 492 (852)
Q Consensus 418 l~~~l~~~~~~~~~~~~~lll~AlT~~s~~~~-----~nyeRLE~LGDs~Lk~~~s~~l~~~~p~~~eg~Ls~~r~~~vs 492 (852)
|+++|+|.|++. +++.+||||+|+... .||||||||||++|+++++.++|..||+.++|.|+.+|+.+||
T Consensus 1 ~e~~lgy~F~~~-----~ll~~Alth~S~~~~~~~~~~~nerLe~lGd~vl~~~~~~~l~~~~p~~~~~~l~~~~~~lvs 75 (220)
T TIGR02191 1 LEKRLGYKFKNK-----ELLEQALTHSSYANEHHKGVKNNERLEFLGDAVLGLVVAEYLFKNFPDLSEGELSKLRAALVS 75 (220)
T ss_pred ChHHhCCCcCCH-----HHHHHHhcCcccccccccCccchHHHHHHHHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHhC
Confidence 467889999886 899999999998643 4999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHhCCccccccccccCCCCcccCCCCCCCcccCccccccccccccccccccccchhHHHHHHHHHHHhhcCCh
Q 003062 493 NAALCKLGCDHKLPGFIRTEPFDPKMWMIPGDNSGSYELNDHSLFNERKIYVTGRKKVKSKTVADVVEALIGAFLSTGGE 572 (852)
Q Consensus 493 N~~L~~~a~~~gL~~~i~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~K~lADv~EAliGA~yl~~G~ 572 (852)
|++|+++|.++||++||+.. ++.. .......+|++||+|||+|||+|+|+|.
T Consensus 76 n~~la~~a~~~gl~~~i~~~---------~~~~-------------------~~~~~~~~k~~ad~~eAliGAiyld~g~ 127 (220)
T TIGR02191 76 EESLAEVARELGLGKFLLLG---------KGEE-------------------KSGGRRRESILADAFEALIGAIYLDSGL 127 (220)
T ss_pred HHHHHHHHHHCCcHHHhccC---------chHh-------------------hcCCcccchHHHHHHHHHHHHHHHhCCH
Confidence 99999999999999999863 2210 0001135789999999999999999999
Q ss_pred HHHHHhhhhc
Q 003062 573 NVGLIFLDRI 582 (852)
Q Consensus 573 ~~a~~~~~~l 582 (852)
+.|.+|+..+
T Consensus 128 ~~~~~~i~~~ 137 (220)
T TIGR02191 128 EAARKFILKL 137 (220)
T ss_pred HHHHHHHHHH
Confidence 9999998766
No 20
>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=99.88 E-value=7.1e-23 Score=195.54 Aligned_cols=119 Identities=34% Similarity=0.498 Sum_probs=106.9
Q ss_pred HHHHHhccCCCCCC---CCchhhhhhhhhHHhHHHHHHHHHhcCCCCcchhhHHHhhccccHHHHHHHHhCCcccccccc
Q 003062 436 KVLEAITTKKCQEG---FHLESLETLGDSFLKYAASQQLFKTYQNHHEGLLSVKKDRIISNAALCKLGCDHKLPGFIRTE 512 (852)
Q Consensus 436 lll~AlT~~s~~~~---~nyeRLE~LGDs~Lk~~~s~~l~~~~p~~~eg~Ls~~r~~~vsN~~L~~~a~~~gL~~~i~~~ 512 (852)
++++||||+|+... .||||||||||+||+++++.++|..+|+.++|.++.+|+.+|||++|+++|.++||+++|+..
T Consensus 2 ll~~alth~s~~~~~~~~~~e~Le~lGdavl~~~~~~~l~~~~~~~~~~~l~~~~~~~v~n~~l~~~a~~~gl~~~i~~~ 81 (133)
T cd00593 2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81 (133)
T ss_pred HHHHhhcCccccccCCCcchHHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHCHHHHHHHHHHcCcHHHhccC
Confidence 68899999999875 899999999999999999999999999999999999999999999999999999999999875
Q ss_pred ccCCCCcccCCCCCCCcccCccccccccccccccccccccchhHHHHHHHHHHHhhcCChHHHHHhhhhc
Q 003062 513 PFDPKMWMIPGDNSGSYELNDHSLFNERKIYVTGRKKVKSKTVADVVEALIGAFLSTGGENVGLIFLDRI 582 (852)
Q Consensus 513 ~f~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~K~lADv~EAliGA~yl~~G~~~a~~~~~~l 582 (852)
+.... ......+|.+||+|||+|||+|+++|.+.+.+|+.++
T Consensus 82 ~~~~~----------------------------~~~~~~~k~~ad~~eAliGAiyld~g~~~~~~~i~~~ 123 (133)
T cd00593 82 KGEEK----------------------------SGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRL 123 (133)
T ss_pred chHhh----------------------------cCCcccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 32110 0123579999999999999999999999999999885
No 21
>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=99.86 E-value=2e-22 Score=186.99 Aligned_cols=112 Identities=42% Similarity=0.686 Sum_probs=89.0
Q ss_pred hhhhHhhHHHHHHHHHHHHHHhCCCCCcchHHHHHHHhcChHHHHHHHHHcCCchhhhccChhHHHHHHHHHhhhhhhcc
Q 003062 643 QRLEFLGDAVLDYLITVYLYNKYPTLSPGDLTDMRSASVNNDCYALSSVKHGLHKHILHASQELYKWINITVDSFERLSL 722 (852)
Q Consensus 643 eRLEfLGDavLd~~v~~~l~~~~p~~~~~~Lt~~r~~lv~n~~La~~a~~~gL~~~l~~~~~~~~~~i~~~~~~~~~~~~ 722 (852)
|||||||||||+++|+.|||.+||+.+++.||.+|+.+|||++|+.+|+++||++|++..+.....++..+.+.......
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 89999999999999999999999999999999999999999999999999999999998877766655443222111110
Q ss_pred --ccccCccccCCCChhhHHHHHHHhheeeeeCC
Q 003062 723 --ESTFGWESETSFPKALGDIIESLSGAIFVDSG 754 (852)
Q Consensus 723 --~~~~~~~~~~~~~k~laD~~EAliGAi~~DsG 754 (852)
............+|++||+|||+|||||+|+|
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 00111113455789999999999999999998
No 22
>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=99.86 E-value=1.3e-22 Score=188.23 Aligned_cols=113 Identities=35% Similarity=0.546 Sum_probs=90.1
Q ss_pred hhhhhhhhhHHhHHHHHHHHHhcCCCCcchhhHHHhhccccHHHHHHHHhCCccccccccccCCCCcccCC-CCCCCccc
Q 003062 453 ESLETLGDSFLKYAASQQLFKTYQNHHEGLLSVKKDRIISNAALCKLGCDHKLPGFIRTEPFDPKMWMIPG-DNSGSYEL 531 (852)
Q Consensus 453 eRLE~LGDs~Lk~~~s~~l~~~~p~~~eg~Ls~~r~~~vsN~~L~~~a~~~gL~~~i~~~~f~~~~w~~~~-~~~~~~~~ 531 (852)
||||||||+||+++++.++|.+||++++|.||.+|+.+|||++|+.+|.++||++||+..+++...|..+. .......
T Consensus 1 ErLefLGDavL~~~v~~~l~~~~p~~~~~~L~~~r~~~vsn~~L~~~a~~~gl~~~l~~~~~~~~~~~~~~~~~~~~~~- 79 (114)
T PF00636_consen 1 ERLEFLGDAVLKLLVSEYLFEKYPNLNEGQLTKLRSALVSNKFLARLAVKLGLHKYLRQEPFEIQRWIKPFNEDLNNGD- 79 (114)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTTSSHHHHHHHHHHHHSHHHHHHHHHHTTHGCTCBHHHHHHHHHHHCHHCC------
T ss_pred CcHhHhHHHHHHHHHHHHHHHHCCCCChhHHHHHHHHHhCHHHHHHHHHHhCchHhhhccchhHHHHHHHHHHHHHhcc-
Confidence 89999999999999999999999999999999999999999999999999999999999888877766651 1000000
Q ss_pred CccccccccccccccccccccchhHHHHHHHHHHHhhcCC
Q 003062 532 NDHSLFNERKIYVTGRKKVKSKTVADVVEALIGAFLSTGG 571 (852)
Q Consensus 532 ~~~~~~~~~~~~~~~~~~~~~K~lADv~EAliGA~yl~~G 571 (852)
+. . ...+....+...+|++||+|||+|||+|+|+|
T Consensus 80 -~~-~---~~~~~~~~~~~~~k~laD~~EAliGAiyld~G 114 (114)
T PF00636_consen 80 -SE-S---SISYDPKNQVLPPKVLADVFEALIGAIYLDSG 114 (114)
T ss_dssp ----C----SSS--SSSSHHHHHHHHHHHHHHHHHHHHTT
T ss_pred -cc-c---ccCCCccccCCccHHHHHHHHHHHHHHHHhcC
Confidence 00 0 00001113457899999999999999999998
No 23
>KOG1817 consensus Ribonuclease [RNA processing and modification]
Probab=99.83 E-value=8.2e-21 Score=199.96 Aligned_cols=120 Identities=31% Similarity=0.415 Sum_probs=106.8
Q ss_pred HHHHHHhccCCCCC----CCCchhhhhhhhhHHhHHHHHHHHHhcCCCCcchhhHHHhhccccHHHHHHHHhCCcccccc
Q 003062 435 SKVLEAITTKKCQE----GFHLESLETLGDSFLKYAASQQLFKTYQNHHEGLLSVKKDRIISNAALCKLGCDHKLPGFIR 510 (852)
Q Consensus 435 ~lll~AlT~~s~~~----~~nyeRLE~LGDs~Lk~~~s~~l~~~~p~~~eg~Ls~~r~~~vsN~~L~~~a~~~gL~~~i~ 510 (852)
.++.+|+|..+... ..+||||||||||||.+++|.++|.+||+.+||.||.+|+.+|+|++-+++|..+|+++|+.
T Consensus 290 rlla~aft~rs~~~n~Lt~gHNqRLEFLGDSilqlv~T~ily~kFPdhhEGhLSlLRssLVsNetqakva~~lgf~e~li 369 (533)
T KOG1817|consen 290 RLLARAFTLRSIPFNHLTLGHNQRLEFLGDSILQLVMTEILYRKFPDHHEGHLSLLRSSLVSNETQAKVADDLGFHEYLI 369 (533)
T ss_pred HHHHHHhhccCCCchhhhhhhhHHHHHhHHHHHHHHHHHHHHHhCCccccchHHHHHHHHhccHHHHHHHHHhCCchhhh
Confidence 78889999998763 35999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccCCCCcccCCCCCCCcccCccccccccccccccccccccchhHHHHHHHHHHHhhcCChHHHHHhhhhcC
Q 003062 511 TEPFDPKMWMIPGDNSGSYELNDHSLFNERKIYVTGRKKVKSKTVADVVEALIGAFLSTGGENVGLIFLDRIG 583 (852)
Q Consensus 511 ~~~f~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~K~lADv~EAliGA~yl~~G~~~a~~~~~~l~ 583 (852)
.. |+.+ ..+..+.|.+||+|||+|||.|+|+|.+.+.+|++.+-
T Consensus 370 ~n-~~~k----------------------------~~~~lk~K~~ADlfEAfiGaLyvD~~le~~~qf~~~l~ 413 (533)
T KOG1817|consen 370 TN-FDLK----------------------------DFQNLKLKDYADLFEAFIGALYVDKGLEYCRQFLRVLF 413 (533)
T ss_pred hC-cchh----------------------------hhhhhhHHHHHHHHHHHHHHHhhcCCcHHHHHHHHHHh
Confidence 73 1111 12336899999999999999999999999999998764
No 24
>cd02844 PAZ_CAF_like PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has been implicated in flower morphogenesis and in early Arabidopsis development and might function through posttranscriptional regulation of specific mRNA molecules. PAZ domains are named after the proteins Piwi, Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.
Probab=99.81 E-value=4e-20 Score=173.56 Aligned_cols=115 Identities=39% Similarity=0.743 Sum_probs=99.9
Q ss_pred cchhhccCCCcccccccCcEEEcCcCCceEEEEeecCCCCCCCCCCCCCC-CcchHHHHHHHHhCcccccCCceeEEEee
Q 003062 275 ARVVQTKSGPLCTCMIYNSVVCTPHSGQIYYITGVLGHLNANSLFTRNDG-GAITYKKHYEERYGIQLCFDQELLLNGRR 353 (852)
Q Consensus 275 ~~~~~~~~~~~~~~~~~~~~V~~~~~~~~Y~v~~i~~dl~p~S~f~~~~~-~~~ty~~yy~~k~~~~i~~~~QPlL~~~~ 353 (852)
..++++++|.+..++++|.+|+++|++++|+|++|. +++|.|+|+..++ ..+||.+||+++||+.|.+++||||+++.
T Consensus 16 ~~~l~~~~~~~~~~~l~g~~V~t~hn~r~Y~I~~i~-~~~p~s~F~~~~~~~~~Sy~eYy~~kY~i~L~~~~QPLL~~~~ 94 (135)
T cd02844 16 SDLLHLADGSFCACDLKGSVVTAPHNGRFYVISGIL-DLNANSSFPGKEGLGYATYAEYFKEKYGIVLNHPNQPLLKGKQ 94 (135)
T ss_pred cceeeeccCcccHHHhcCCEEEEcCCCcEEEEEEEc-CCCccCcccCCCCCceeeHHHHHHHHhCceeccCCcceEEEec
Confidence 456889999999999999999999999999999999 9999999986554 56899999999999999999999999999
Q ss_pred ccccccccchhhhhccC----CCCcceeecCcchhhhhcccCc
Q 003062 354 IFHAQNYLSKCRQEKQR----EPSKISFELPPELCRIIMGPMS 392 (852)
Q Consensus 354 ~~~r~N~L~~~~~~~~~----~~~~~~~~L~PElC~~~~~p~~ 392 (852)
+++++|+|+++.+.++. +.....++||||||.+ +++|
T Consensus 95 ~~~~~NlL~~~~~~~~~~~~~~~~~~~v~L~PELC~~--~~~p 135 (135)
T cd02844 95 IFNLHNLLHNRFEEKGESEEKEKDRYFVELPPELCSV--IDLP 135 (135)
T ss_pred ccccceecccccccccccccccccceEEEeChHHhcc--ccCC
Confidence 99999999999765432 3344458999999965 5543
No 25
>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=99.75 E-value=9e-19 Score=153.59 Aligned_cols=68 Identities=40% Similarity=0.619 Sum_probs=46.9
Q ss_pred cccCCCeEEE--cCCeEEEEEEcCCCCCCccc--cccCcHHHHHHHHHHHHHHHHHhcCCCCCCCCCccccc
Q 003062 32 YFKPTPKFDI--NKEMGICTLYLPNNCPIQTV--IAQGNIKTLKQTACLEACKKLHQIGALTDNLLPDVVVE 99 (852)
Q Consensus 32 ~~~~~P~~~~--~~~~~~~~v~LP~~~p~~~~--~~~~s~~~Ak~~aAf~Ac~~L~~~G~ldd~LlP~~~~~ 99 (852)
|++++|+|++ .+++|+|+|+||.++|++.+ .+|+||+.|||+|||+||++||++|+|||||+|..+++
T Consensus 17 ~~~~~P~~~~~~~~~~~~c~v~LP~~~pi~~i~g~~~~sk~~AK~sAAf~Ac~~L~~~g~ldd~L~P~~~~~ 88 (90)
T PF03368_consen 17 FTNLKPEFEIEKIGSGFICTVILPINSPIRSIEGPPMRSKKLAKRSAAFEACKKLHEAGELDDHLLPISKER 88 (90)
T ss_dssp T--SS-EEEEEE--G-EEEEEE--TT-SS--EEEE--SSHHHHHHHHHHHHHHHHHHH-S-TTTS--HHHH-
T ss_pred CccCCceEEEEEcCCcEEEEEECCCCCCCCeEEccccccHHHHHHHHHHHHHHHHHHcCCCccccCCCCCCc
Confidence 6778999998 45689999999999999987 89999999999999999999999999999999986543
No 26
>cd02843 PAZ_dicer_like PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA interference pathway. It generates dsRNAs which are approximately 20 bp long (siRNAs), which in turn target hydrolysis of homologous RNAs. PAZ domains are named after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.
Probab=99.74 E-value=2.2e-18 Score=155.10 Aligned_cols=110 Identities=17% Similarity=0.172 Sum_probs=89.3
Q ss_pred ccCccccccccccccccCCCCCCCCcccccchhhccCCCcccccccCcEEEcCcCC----ceEEEEeecCCCCCCCCCCC
Q 003062 246 SIDWEPVASLSFPCDIGLKHHKNCSTMSNARVVQTKSGPLCTCMIYNSVVCTPHSG----QIYYITGVLGHLNANSLFTR 321 (852)
Q Consensus 246 ~iDw~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~~~~----~~Y~v~~i~~dl~p~S~f~~ 321 (852)
.|||.+|+.+...... .+.... -.......++++++.|++|+++|+| ++|+|++|++|++|.|+|+.
T Consensus 6 ~iDw~~~~~i~~~~~~-~p~~~~--------~~~r~~~~f~~~~~~g~vV~t~YnN~d~pK~Y~V~dI~~dltP~S~F~~ 76 (122)
T cd02843 6 DIDWEFMEKIEANARI-GPRATP--------DEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPG 76 (122)
T ss_pred eechhHHHHHhhhccc-CCCCCh--------hHHhhcCCCCHHHhCCCEEeecccCCCCCeEEEEEEEcCCCCCCCCCCC
Confidence 6999999986433221 000000 0113445789999999999999998 79999999999999999985
Q ss_pred CCCCcchHHHHHHHHhCcccccCCceeEEEeeccccccccchhhh
Q 003062 322 NDGGAITYKKHYEERYGIQLCFDQELLLNGRRIFHAQNYLSKCRQ 366 (852)
Q Consensus 322 ~~~~~~ty~~yy~~k~~~~i~~~~QPlL~~~~~~~r~N~L~~~~~ 366 (852)
. .++||.+||++|||+.|.+.+||||+++.++.++|||+|+..
T Consensus 77 ~--~~~Ty~eYyk~KY~I~I~~~~QPLL~v~~~s~~lNll~pr~~ 119 (122)
T cd02843 77 P--EYETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYV 119 (122)
T ss_pred C--CCccHHHHHHHhcCeEeccCCCCcEeecCccccccccCcccc
Confidence 4 379999999999999999999999999999999999999753
No 27
>KOG3769 consensus Ribonuclease III domain proteins [Translation, ribosomal structure and biogenesis]
Probab=99.67 E-value=5.7e-16 Score=157.07 Aligned_cols=222 Identities=19% Similarity=0.238 Sum_probs=175.7
Q ss_pred hhhHHhHHHHHHHcC-cccCCHHHHHHHhccCCCCCC----------------CCCCcchhhhHhhHHHHHHHHHHHHHH
Q 003062 601 AERLVNVRHLESLLN-YSFRDPSLLVEALTHGSYMLP----------------EIPRCYQRLEFLGDAVLDYLITVYLYN 663 (852)
Q Consensus 601 ~~~~~~~~~le~~lg-y~F~~~~LL~~AlTH~S~~~~----------------~~~~~yeRLEfLGDavLd~~v~~~l~~ 663 (852)
......+..++++|| -.| ..+.|..|||.+||... ....+|+-|--.|..++++.|++||-.
T Consensus 59 W~~~sel~afg~RL~~~~i-s~~~l~ka~t~~s~~~~~kv~~~~lg~~~~~~~~~~~~N~~L~~~Gk~~~~~~v~~~l~~ 137 (333)
T KOG3769|consen 59 WDYNSELSAFGKRLQSEEI-SLSYLLKALTNLSFSYPEKVLRQQLGAETVAQVNPQYSNEELVEIGKQFLSFYVTEYLKC 137 (333)
T ss_pred cchhHHHHHHHHHhccccc-cHHHHHHHHhCccccchHHHhhhhhcchhhhhhcCCcchHHHHHHHHHHHHHHHHHHHHH
Confidence 334456899999999 455 67889999999999642 235789999999999999999999999
Q ss_pred hCCCCCcchHHHHHHHhcChHHHHHHHHHcCCchhhhccChhHHHHHHHHHhhhhhhccccccCccccCCCChhhHHHHH
Q 003062 664 KYPTLSPGDLTDMRSASVNNDCYALSSVKHGLHKHILHASQELYKWINITVDSFERLSLESTFGWESETSFPKALGDIIE 743 (852)
Q Consensus 664 ~~p~~~~~~Lt~~r~~lv~n~~La~~a~~~gL~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~laD~~E 743 (852)
+||.++...++.+-+.+.+.+.||.+|..+|+.++++..+.....+ ....+...+++=
T Consensus 138 kyPrlP~E~l~ai~n~ll~ee~LahiAt~lGie~l~~seeFp~~~e----------------------isq~ess~~aI~ 195 (333)
T KOG3769|consen 138 KYPRLPEEGLHAIVNGLLGEEVLAHIATHLGIEELGLSEEFPKVGE----------------------ISQDESSRRAIG 195 (333)
T ss_pred hccCCcHHHHHHHHHHhhhHHHHHHHHHHhhHHHHhhcccCCCchh----------------------hhHHHHHHHHHH
Confidence 9999999999999999999999999999999998887654321111 112257788899
Q ss_pred HHhheeeeeCCCCHHHHHHHHHHhh-cccCCcccc--cCChhhHHHHHHHhCCCcee-eEEeeecCC----ceEEEEEEE
Q 003062 744 SLSGAIFVDSGCNKEVVFESIRPLL-EPMITPETM--RLQPARELNEYCQKHHFSMK-KTVAPRING----KAAVTVEVH 815 (852)
Q Consensus 744 AliGAi~~DsG~~~~~v~~~~~~~l-~~~~~~~~~--~~~P~~~L~e~~~~~~~~~~-~~~~~~~~g----~~~~~~~v~ 815 (852)
|++|+++...|++ .|.+||.+.| ..-+.+..+ ..+|.++|.++|++.|.+-+ ++ +..+.| .+.|.|+||
T Consensus 196 Al~~~~~~ek~~~--~v~dFI~~qi~~k~L~~~~m~ql~~P~~~L~~lckr~~l~epe~R-ll~esGr~S~~PvyvVgiY 272 (333)
T KOG3769|consen 196 ALLGSVGLEKGFN--FVRDFINDQILSKDLDPREMWQLQWPRRLLSRLCKRRGLKEPESR-LLAESGRNSAEPVYVVGIY 272 (333)
T ss_pred HHHhcccHHHHHH--HHHHHHHHHhhhhccchHhhccccchHHHHHHHHHHcCCCCchhH-HHHHhccCccCceEEEEee
Confidence 9999999888774 5666665433 333333222 37999999999999998543 44 334444 578999999
Q ss_pred ECCEEEEeEEeeCCHHHHHHHHHHHHHHHhhhhC
Q 003062 816 ANGTLFKHTHADADKETAKKVASKEVLKSLKASF 849 (852)
Q Consensus 816 v~~~~i~~~g~g~s~k~Ak~~AA~~AL~~L~~~~ 849 (852)
.|.+.+| .|.|.|.+.|+..||..||.+|-...
T Consensus 273 s~kkllG-qG~Gesl~~A~e~AA~dAL~k~y~~t 305 (333)
T KOG3769|consen 273 SGKKLLG-QGQGESLKLAEEQAARDALIKLYDHT 305 (333)
T ss_pred cCchhhc-cCcchHHHHHHHHHHHHHHHHHHcCC
Confidence 9999998 89999999999999999999986554
No 28
>cd02845 PAZ_piwi_like PAZ domain, Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be essential for the maintenance of germline stem cells. In the Drosophila male germline, Piwi was shown to be involved in the silencing of retrotransposons in the male gametes. The Piwi proteins share their domain architecture with other members of the argonaute family. The PAZ domain has been named after the proteins Piwi, Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might
Probab=99.50 E-value=3.8e-14 Score=130.54 Aligned_cols=89 Identities=27% Similarity=0.331 Sum_probs=73.7
Q ss_pred cccccCcEEEcCcCCceEEEEeecCCCCCCCCCCCCCCCcchHHHHHHHHhCcccccCCceeEEEeeccccccccchhhh
Q 003062 287 TCMIYNSVVCTPHSGQIYYITGVLGHLNANSLFTRNDGGAITYKKHYEERYGIQLCFDQELLLNGRRIFHAQNYLSKCRQ 366 (852)
Q Consensus 287 ~~~~~~~~V~~~~~~~~Y~v~~i~~dl~p~S~f~~~~~~~~ty~~yy~~k~~~~i~~~~QPlL~~~~~~~r~N~L~~~~~ 366 (852)
..+++|.+|++.|+++.|.|.+|+++++|.|+|+..++...||.+||+++||+.|.+++||||++....+. .
T Consensus 25 ~~~l~g~~V~t~yn~k~Y~I~~I~~~~~p~s~F~~~~~~~~S~~~Yy~~kY~i~I~~~~qPLL~~~~k~~~--~------ 96 (117)
T cd02845 25 EKELIGSIVLTRYNNKTYRIDDIDFDKTPLSTFKKSDGTEITFVEYYKKQYNIEITDLNQPLLVSRPKRRD--P------ 96 (117)
T ss_pred HHHcCCCEEEEeeCCeEEEEeEecCCCCccccCcCCCCCeeeHHHHHHHHcCCccccCCCCcEEeeccccc--c------
Confidence 35688999999999999999999999999999987655678999999999999999999999999744321 0
Q ss_pred hccCCCCcceeecCcchhhh
Q 003062 367 EKQREPSKISFELPPELCRI 386 (852)
Q Consensus 367 ~~~~~~~~~~~~L~PElC~~ 386 (852)
.......++||||+|.+
T Consensus 97 ---~~~~~~~iyL~pElC~l 113 (117)
T cd02845 97 ---RGGEKEPIYLIPELCFL 113 (117)
T ss_pred ---CCCCCcEEEEchHHhhh
Confidence 11233458999999965
No 29
>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]
Probab=99.41 E-value=3.3e-13 Score=166.95 Aligned_cols=161 Identities=33% Similarity=0.432 Sum_probs=125.0
Q ss_pred HhHHHHHHHcC--cccCCH--------HHHHHHhccCCCCCCCCCCcchhhhHhhHHHHHHHHHHHHHHhCCCCCcchHH
Q 003062 605 VNVRHLESLLN--YSFRDP--------SLLVEALTHGSYMLPEIPRCYQRLEFLGDAVLDYLITVYLYNKYPTLSPGDLT 674 (852)
Q Consensus 605 ~~~~~le~~lg--y~F~~~--------~LL~~AlTH~S~~~~~~~~~yeRLEfLGDavLd~~v~~~l~~~~p~~~~~~Lt 674 (852)
.+.+.+|.++. |.|.++ .+|+|||||+++. ...+|||||+|||++|++.++.|||.+||+..+|+++
T Consensus 979 ~~~E~~e~i~n~~~~Fs~~~~~i~~~~s~LLEAlT~~~~~---~s~s~Erle~Lgds~Lk~avsr~l~L~ypd~~Egqls 1055 (1606)
T KOG0701|consen 979 SDWEAVEKILNFRYVFSISLASIALSTSLLLEALTTSSCQ---DSFSLERLELLGDSLLKLAVSRHLFLTYPDLDEGQLS 1055 (1606)
T ss_pred ccccccccccccceeccccccccccchhHHHHHhhcCccc---cchhHHHHHhhHHHHHHHHHHHHHHHhCCcccchhHH
Confidence 45778999998 999999 9999999999997 5789999999999999999999999999999999999
Q ss_pred HHHHHhcChHHHHHHHHHcCCchhhhccChhHH-------------------------------HHHHHHHhhhhhhccc
Q 003062 675 DMRSASVNNDCYALSSVKHGLHKHILHASQELY-------------------------------KWINITVDSFERLSLE 723 (852)
Q Consensus 675 ~~r~~lv~n~~La~~a~~~gL~~~l~~~~~~~~-------------------------------~~i~~~~~~~~~~~~~ 723 (852)
.+|+.+++|+.++.+|+..||..++++...+.. ..+.++...-.. ..+
T Consensus 1056 ~lr~~~~~~~nl~~la~~~gl~~~~~~~~fep~~~~~p~~~~~~~~~~k~~~~~~~~~~~~e~~e~~~df~e~~~~-~~~ 1134 (1606)
T KOG0701|consen 1056 RLRDVNVSNDNLARLAVKKGLYSYLRHEGFEPSRWWVPGQLDVNNVDCKDLSGDQNYILYKELDEKIKDFQEAMEK-EDG 1134 (1606)
T ss_pred HHHHhcccccchhhhhhcccchhhcccccccccccccccccccccccccccccccccccccchhhhhhHHHHhhhc-cCC
Confidence 999999999999999999999999998832221 222222221110 011
Q ss_pred ccc--CccccCCCChhhHHHHHHHhheeeeeCCCCHHHHHHHHHHhhcc
Q 003062 724 STF--GWESETSFPKALGDIIESLSGAIFVDSGCNKEVVFESIRPLLEP 770 (852)
Q Consensus 724 ~~~--~~~~~~~~~k~laD~~EAliGAi~~DsG~~~~~v~~~~~~~l~~ 770 (852)
... +-......||.++|++||++||+|+|+|.+ +...-+...+|+.
T Consensus 1135 ~~~~~~~~~~~~~~ks~adl~eaLlga~~vD~~~~-~~~~~~~~~~lk~ 1182 (1606)
T KOG0701|consen 1135 DSRSKGGDHDWLAPKSPADLLEALLGAIYVDGGLL-ETFETIGDSFLKW 1182 (1606)
T ss_pred cccccccccceecCCCHHHHHHHHHHhhhhhccch-hhhhHHHHHHHhh
Confidence 111 001245689999999999999999999886 3333344555553
No 30
>PF02170 PAZ: PAZ domain; InterPro: IPR003100 This domain is named after the proteins Piwi Argonaut and Zwille. It is also found in the CAF protein from Arabidopsis thaliana. The function of the domain is unknown but has been found in the middle region of a number of members of the Argonaute protein family, which also contain the Piwi domain (IPR003165 from INTERPRO) in their C-terminal region []. Several members of this family have been implicated in the development and maintenance of stem cells through the RNA-mediated gene-quelling mechanisms associated with the protein DICER. ; GO: 0005515 protein binding; PDB: 1R6Z_P 1T2R_A 1T2S_A 3MJ0_A 1VYN_A 3O3I_X 2L5C_A 3O6E_X 3O7V_X 2L5D_A ....
Probab=99.21 E-value=4.1e-12 Score=121.39 Aligned_cols=107 Identities=32% Similarity=0.387 Sum_probs=88.1
Q ss_pred ccccccCcEEEcCcCC--ceEEEEeecCCCCCCCCCCCCCCCcchHHHHHHHHhCcccccCCceeEEEeeccccccccch
Q 003062 286 CTCMIYNSVVCTPHSG--QIYYITGVLGHLNANSLFTRNDGGAITYKKHYEERYGIQLCFDQELLLNGRRIFHAQNYLSK 363 (852)
Q Consensus 286 ~~~~~~~~~V~~~~~~--~~Y~v~~i~~dl~p~S~f~~~~~~~~ty~~yy~~k~~~~i~~~~QPlL~~~~~~~r~N~L~~ 363 (852)
....++|..|.+.|++ +.|.|.+|.++.+|.++|+..++..+||.+||+++||++|.+++||+|.++...+.
T Consensus 25 ~~~~lkg~~V~~~~~~~~r~~~I~~i~~~~~~~~~F~~~~g~~itv~eYf~~~Y~i~L~~p~~Pll~~~~~~~~------ 98 (135)
T PF02170_consen 25 LERALKGLKVTTTYNNNKRTYKIKGISFDPAPESTFPDNDGKEITVAEYFKEKYNIRLKYPDLPLLNVKSKKKK------ 98 (135)
T ss_dssp HHHHHTTEEEEETTTTCCEEEEEEEEEEEETTTSEEEETTSEEEEHHHHHHHTCT---SSTTSEEEEECSTTTT------
T ss_pred HHHHcCCcEEEEecCCCceEEEEeEEECCCCcceeeecCCCceEEhHHHHHhhhhcccccCCCCeEEeccCCCC------
Confidence 3567999999999998 89999999999999999987657889999999999999999999999998854321
Q ss_pred hhhhccCCCCcceeecCcchhhhhcccCcHHHHHHhhhhhhHHHHHHH
Q 003062 364 CRQEKQREPSKISFELPPELCRIIMGPMSLSTFYSFTFVPSIMHRLQS 411 (852)
Q Consensus 364 ~~~~~~~~~~~~~~~L~PElC~~~~~p~~~~~~~~~~~lPsi~~rle~ 411 (852)
..+++|||+|.+ .|.+...+......|++++|.++
T Consensus 99 -----------~~~~lP~Elc~i--~~~q~~~~~~~~~~~s~m~r~~~ 133 (135)
T PF02170_consen 99 -----------QPIYLPPELCFI--VPGQRYKKKLFTCQPSIMIRFAC 133 (135)
T ss_dssp -----------TCEEEECCGEEE--ETTTBB-SS--HHHHHHHHHHHS
T ss_pred -----------ceEEEChhHhcc--cCCcHHHHhccHHHHHHHHHHHh
Confidence 246899999964 79999999999999999999874
No 31
>KOG1042 consensus Germ-line stem cell division protein Hiwi/Piwi; negative developmental regulator [Cell cycle control, cell division, chromosome partitioning]
Probab=99.18 E-value=3.2e-11 Score=133.88 Aligned_cols=102 Identities=21% Similarity=0.253 Sum_probs=80.8
Q ss_pred cccccCcEEEcCcCCceEEEEeecCCCCCCCCCCCCCCCcchHHHHHHHHhCcccccCCceeEEEeeccccccccchhhh
Q 003062 287 TCMIYNSVVCTPHSGQIYYITGVLGHLNANSLFTRNDGGAITYKKHYEERYGIQLCFDQELLLNGRRIFHAQNYLSKCRQ 366 (852)
Q Consensus 287 ~~~~~~~~V~~~~~~~~Y~v~~i~~dl~p~S~f~~~~~~~~ty~~yy~~k~~~~i~~~~QPlL~~~~~~~r~N~L~~~~~ 366 (852)
...+.|.+|+|+|||++|+|++|+|+.+|.|+|.+.++ .+||.|||+++|+++|.+.+||+|..+...++.
T Consensus 281 ~~~~~glivLT~YNNktyriddvD~~~tP~stF~k~dg-eIs~veYyk~qYni~I~dl~QPlliS~~k~K~~-------- 351 (845)
T KOG1042|consen 281 NKNVIGLIVLTRYNNKTYRIDDVDFSQTPLSTFKKDDG-EISFVEYYKKQYNIEITDLNQPLLISEPKDKRP-------- 351 (845)
T ss_pred HHHhcceEEEEecCCceeeeeccccCcCccceeeecCc-eeeHhHHHHHhcCeEEeeCCcceEeccCcccCC--------
Confidence 34588999999999999999999999999999987655 899999999999999999999999887655421
Q ss_pred hccCCCCcceeecCcchhhhhcccCcHHHHHHhhhh
Q 003062 367 EKQREPSKISFELPPELCRIIMGPMSLSTFYSFTFV 402 (852)
Q Consensus 367 ~~~~~~~~~~~~L~PElC~~~~~p~~~~~~~~~~~l 402 (852)
+.......+|+||||.+ ..+...+-.-+.++
T Consensus 352 ---~g~~~q~~~lIPELc~~--TGLtd~mr~dF~~M 382 (845)
T KOG1042|consen 352 ---KGEPPQLAMLIPELCFL--TGLTDEMRSDFQLM 382 (845)
T ss_pred ---CCCCccceeeehhhhhc--cCCcHHHHhhHHHH
Confidence 12233457899999965 56655554333333
No 32
>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=98.86 E-value=2.2e-08 Score=83.14 Aligned_cols=64 Identities=28% Similarity=0.419 Sum_probs=54.8
Q ss_pred hhhHHHHHHHhCCCceeeEEeeecCC---ceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHHHHHHh
Q 003062 781 PARELNEYCQKHHFSMKKTVAPRING---KAAVTVEVHANGTLFKHTHADADKETAKKVASKEVLKSL 845 (852)
Q Consensus 781 P~~~L~e~~~~~~~~~~~~~~~~~~g---~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~AL~~L 845 (852)
|++.|+|+|++.++.++|......++ ...|.|+|+++|..++ .|.|.||++||+.||+.||+.|
T Consensus 1 ~~~~L~e~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~i~~~~~~-~g~g~sKk~Ak~~AA~~al~~L 67 (67)
T PF00035_consen 1 PKSRLNEYCQKNKFPPPYYYIEEEGPSHHRPRFICTVYIDGKEYG-EGEGSSKKEAKQQAAKKALQKL 67 (67)
T ss_dssp HHHHHHHHHHHCTSSEEEEEEEEESSSSSSEEEEEEEEETTEEEE-EEEESSHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCCCEEEEEEeCCCCCCceEEEEEEECCEEEe-EeccCCHHHHHHHHHHHHHHhC
Confidence 78999999999998887653433333 2589999999999998 8999999999999999999986
No 33
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=98.82 E-value=1.7e-08 Score=97.67 Aligned_cols=69 Identities=20% Similarity=0.326 Sum_probs=58.8
Q ss_pred cCChhhHHHHHHHhCCCceeeEEeeec--CCceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHHHHHHhhh
Q 003062 778 RLQPARELNEYCQKHHFSMKKTVAPRI--NGKAAVTVEVHANGTLFKHTHADADKETAKKVASKEVLKSLKA 847 (852)
Q Consensus 778 ~~~P~~~L~e~~~~~~~~~~~~~~~~~--~g~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~AL~~L~~ 847 (852)
..||++.||||+|+.+....|..+... ++.+.|+|.|+++|..++ +|.|.|||+||+.||+.||++|..
T Consensus 107 ~~DpKS~LQE~~Q~~~~~l~Y~li~~~GpdH~~~Ftv~V~V~g~~~g-~G~G~SKKeAEQ~AAk~AL~~L~~ 177 (183)
T PHA02701 107 TLNPVSAVNEFCMRTHRPLEFCETRSGGHDHCPLFTCTIVVSGKVVA-TASGCSKKLARHAACADALTILIN 177 (183)
T ss_pred CCCccHHHHHHHHhcCCCCeEEEEEeECCCCCceEEEEEEECCEEEE-EEEeCCHHHHHHHHHHHHHHHHHh
Confidence 369999999999998765678644433 336889999999999998 899999999999999999999864
No 34
>cd02825 PAZ PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. This parent model also contains structures of an archaeal PAZ domain.
Probab=98.80 E-value=5.9e-09 Score=96.46 Aligned_cols=83 Identities=28% Similarity=0.370 Sum_probs=66.9
Q ss_pred cccccCcEEEcCcC--CceEEEEeecCCCCCCCCCCCCCCCcchHHHHHHHHhCcccccCCceeEEEeeccccccccchh
Q 003062 287 TCMIYNSVVCTPHS--GQIYYITGVLGHLNANSLFTRNDGGAITYKKHYEERYGIQLCFDQELLLNGRRIFHAQNYLSKC 364 (852)
Q Consensus 287 ~~~~~~~~V~~~~~--~~~Y~v~~i~~dl~p~S~f~~~~~~~~ty~~yy~~k~~~~i~~~~QPlL~~~~~~~r~N~L~~~ 364 (852)
...++|..|.+.|+ ++.|.|.++.+..++.+ |...++..+||.+||++|||+.+.+++||+|++....+
T Consensus 30 ~~~lkg~~V~~~h~~~~r~y~i~~i~~~~a~~~-f~~~~~~~isv~dYf~~kY~~~l~~p~~Pll~~~~~~~-------- 100 (115)
T cd02825 30 TKELKGLKVEDTHNPLNRVYRPDGETRLKAPSQ-LKHSDGKEITFADYFKERYNLTLTDLNQPLLIVKFSSK-------- 100 (115)
T ss_pred HHHcCCCEEEEecCCCceEEEEeeEECCCChhh-eecCCCCEEEHHHHHHHHcCCcccCCCCCEEEecCccc--------
Confidence 45678899999998 67999999998666655 76556778899999999999999999999999885432
Q ss_pred hhhccCCCCcceeecCcchhhh
Q 003062 365 RQEKQREPSKISFELPPELCRI 386 (852)
Q Consensus 365 ~~~~~~~~~~~~~~L~PElC~~ 386 (852)
....++||||+|.+
T Consensus 101 --------~~~~~~lp~Elc~i 114 (115)
T cd02825 101 --------KSYSILLPPELCVI 114 (115)
T ss_pred --------CCCceEEchheEEe
Confidence 11235799999964
No 35
>smart00358 DSRM Double-stranded RNA binding motif.
Probab=98.78 E-value=3e-08 Score=82.22 Aligned_cols=65 Identities=26% Similarity=0.311 Sum_probs=54.5
Q ss_pred hhhHHHHHHHhCCCceeeEEeeec--CCceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHHHHHHhh
Q 003062 781 PARELNEYCQKHHFSMKKTVAPRI--NGKAAVTVEVHANGTLFKHTHADADKETAKKVASKEVLKSLK 846 (852)
Q Consensus 781 P~~~L~e~~~~~~~~~~~~~~~~~--~g~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~AL~~L~ 846 (852)
|++.|+|+|+++++.+.|...... ++...|+|.|.++|+.++ +|.|.|+++||+.||+.||+.|.
T Consensus 1 p~~~L~e~~~~~~~~~~y~~~~~~g~~~~~~f~~~v~i~~~~~~-~g~g~sKk~Ak~~AA~~al~~L~ 67 (67)
T smart00358 1 PKSLLQELAQKRGLPPEYELVKEEGPDHAPRFTVTVKVGGEYTG-EGEGSSKKEAKQRAAEAALRSLK 67 (67)
T ss_pred CchHHHHHHHHCCCCCEEEEEeeeCCCCCCcEEEEEEECCEEEE-EeccCCHHHHHHHHHHHHHHhcC
Confidence 789999999999887677643322 234689999999998887 89999999999999999999873
No 36
>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=98.76 E-value=4.5e-08 Score=81.24 Aligned_cols=65 Identities=25% Similarity=0.266 Sum_probs=53.3
Q ss_pred ChhhHHHHHHHhCCC-ceeeEEeeecCC--ceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHHHHHHh
Q 003062 780 QPARELNEYCQKHHF-SMKKTVAPRING--KAAVTVEVHANGTLFKHTHADADKETAKKVASKEVLKSL 845 (852)
Q Consensus 780 ~P~~~L~e~~~~~~~-~~~~~~~~~~~g--~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~AL~~L 845 (852)
||++.|+|+|+++++ .+.|......++ ...|+|.|.++|...+ +|.|.|+++||+.||+.||+.|
T Consensus 1 ~p~~~L~e~~~~~~~~~~~y~~~~~~g~~~~~~f~~~v~i~~~~~~-~g~g~sKk~Ak~~AA~~al~~L 68 (68)
T cd00048 1 NPKSLLQELAQKRGKPLPEYELVEEEGPDHAPRFTVEVTVGGKITG-EGEGSSKKEAKQNAAEAALRKL 68 (68)
T ss_pred ChHHHHHHHHHHcCCCCCeEEEeeeeCCCCCCeEEEEEEECCEEEE-EeecCCHHHHHHHHHHHHHHhC
Confidence 699999999999854 555763333332 4789999999997776 8999999999999999999875
No 37
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=98.76 E-value=4.8e-08 Score=95.43 Aligned_cols=88 Identities=20% Similarity=0.220 Sum_probs=66.4
Q ss_pred HHHHHHHHHhhcccCCccc----ccCChhhHHHHHHHhCCCceeeEEeee--cCCceEEEEEEEECCEEEEeEEeeCCHH
Q 003062 758 EVVFESIRPLLEPMITPET----MRLQPARELNEYCQKHHFSMKKTVAPR--INGKAAVTVEVHANGTLFKHTHADADKE 831 (852)
Q Consensus 758 ~~v~~~~~~~l~~~~~~~~----~~~~P~~~L~e~~~~~~~~~~~~~~~~--~~g~~~~~~~v~v~~~~i~~~g~g~s~k 831 (852)
+....++.+++.+.+.... -..||++.|+||+|+++... |..+.. .++.+.|+|.|.++|+.++ +|.|.|||
T Consensus 84 ~~~~~~~~~l~~~~i~~~k~~d~K~kNpKS~LQE~~Qk~~~~~-y~~i~~~Gp~H~p~F~v~V~I~g~~~g-~G~G~SKK 161 (183)
T PHA03103 84 EKSMREDNKSFSDTIPYKKIISWKDKNPCTVINEYCQITSRDW-SINITSSGPSHSPTFTASVIISGIKFK-PAIGSTKK 161 (183)
T ss_pred chhHHHHHHHhhhhcchhhhhccccCChhHHHHHHHHHhCCCe-EEEEEeeCCCCCceEEEEEEECCEEEE-EeeeCCHH
Confidence 3445566666666654321 23689999999999877654 332322 2346889999999999988 89999999
Q ss_pred HHHHHHHHHHHHHhhh
Q 003062 832 TAKKVASKEVLKSLKA 847 (852)
Q Consensus 832 ~Ak~~AA~~AL~~L~~ 847 (852)
+||+.||+.||+.|..
T Consensus 162 eAEQ~AAk~AL~~L~~ 177 (183)
T PHA03103 162 EAKNNAAKLAMDKILN 177 (183)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999999999999864
No 38
>KOG3769 consensus Ribonuclease III domain proteins [Translation, ribosomal structure and biogenesis]
Probab=98.17 E-value=5.3e-06 Score=85.39 Aligned_cols=162 Identities=19% Similarity=0.198 Sum_probs=119.3
Q ss_pred CCHHHHHHHhccCCCCC-------------------CCCchhhhhhhhhHHhHHHHHHHHHhcCCCCcchhhHHHhhccc
Q 003062 432 IPTSKVLEAITTKKCQE-------------------GFHLESLETLGDSFLKYAASQQLFKTYQNHHEGLLSVKKDRIIS 492 (852)
Q Consensus 432 ~~~~lll~AlT~~s~~~-------------------~~nyeRLE~LGDs~Lk~~~s~~l~~~~p~~~eg~Ls~~r~~~vs 492 (852)
+..+.++.|||.+|+.. ..+|+-|--.|-.++.+.++.++-++||..++..++.+-+.+++
T Consensus 77 is~~~l~ka~t~~s~~~~~kv~~~~lg~~~~~~~~~~~~N~~L~~~Gk~~~~~~v~~~l~~kyPrlP~E~l~ai~n~ll~ 156 (333)
T KOG3769|consen 77 ISLSYLLKALTNLSFSYPEKVLRQQLGAETVAQVNPQYSNEELVEIGKQFLSFYVTEYLKCKYPRLPEEGLHAIVNGLLG 156 (333)
T ss_pred ccHHHHHHHHhCccccchHHHhhhhhcchhhhhhcCCcchHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHhhh
Confidence 55577778888877642 24899999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHhCCccccccccccCCCCcccCCCCCCCcccCccccccccccccccccccccchhHHHHHHHHHHHhhcCCh
Q 003062 493 NAALCKLGCDHKLPGFIRTEPFDPKMWMIPGDNSGSYELNDHSLFNERKIYVTGRKKVKSKTVADVVEALIGAFLSTGGE 572 (852)
Q Consensus 493 N~~L~~~a~~~gL~~~i~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~K~lADv~EAliGA~yl~~G~ 572 (852)
.+.|+.+|..+|++++++++.|.+ ++. . ..+++.++++-||+|+++...|.
T Consensus 157 ee~LahiAt~lGie~l~~seeFp~-----~~e----------------------i--sq~ess~~aI~Al~~~~~~ek~~ 207 (333)
T KOG3769|consen 157 EEVLAHIATHLGIEELGLSEEFPK-----VGE----------------------I--SQDESSRRAIGALLGSVGLEKGF 207 (333)
T ss_pred HHHHHHHHHHhhHHHHhhcccCCC-----chh----------------------h--hHHHHHHHHHHHHHhcccHHHHH
Confidence 999999999999999999988742 111 0 13588899999999999999999
Q ss_pred HHHHHhhhhcCccccCCC-cccchhcccChhhHHhHHHHHHHcCcccCCHHHHHHH
Q 003062 573 NVGLIFLDRIGIKVDFVN-VPYERQFQVQAERLVNVRHLESLLNYSFRDPSLLVEA 627 (852)
Q Consensus 573 ~~a~~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~le~~lgy~F~~~~LL~~A 627 (852)
..+.+|+..=-...++.. ..|+-+ +| ...+..+-+..|.+=--+.|+.++
T Consensus 208 ~~v~dFI~~qi~~k~L~~~~m~ql~---~P--~~~L~~lckr~~l~epe~Rll~es 258 (333)
T KOG3769|consen 208 NFVRDFINDQILSKDLDPREMWQLQ---WP--RRLLSRLCKRRGLKEPESRLLAES 258 (333)
T ss_pred HHHHHHHHHHhhhhccchHhhcccc---ch--HHHHHHHHHHcCCCCchhHHHHHh
Confidence 999998754222222210 111110 11 123555556666655555566654
No 39
>cd02846 PAZ_argonaute_like PAZ domain, argonaute_like subfamily. Argonaute is part of the RNA-induced silencing complex (RISC), and is an endonuclease that plays a key role in the RNA interference pathway. The PAZ domain has been named after the proteins Piwi,Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.
Probab=98.04 E-value=5.7e-06 Score=76.55 Aligned_cols=80 Identities=26% Similarity=0.360 Sum_probs=63.6
Q ss_pred ccccCcEEEcCcC---CceEEEEeecCCCCCCCCCCCCCC-CcchHHHHHHHHhCcccccCCceeEEEeeccccccccch
Q 003062 288 CMIYNSVVCTPHS---GQIYYITGVLGHLNANSLFTRNDG-GAITYKKHYEERYGIQLCFDQELLLNGRRIFHAQNYLSK 363 (852)
Q Consensus 288 ~~~~~~~V~~~~~---~~~Y~v~~i~~dl~p~S~f~~~~~-~~~ty~~yy~~k~~~~i~~~~QPlL~~~~~~~r~N~L~~ 363 (852)
..++|.-|.+.|. ++.|.|.++..+..+...|+..++ ..+|+.+||+++|++.+.++++|+|.+..-
T Consensus 30 ~~lkgl~v~~~~~~~~~r~~~i~~l~~~~~~~~~F~~~~~~~~isV~dYf~~~y~~~l~~p~lP~v~~g~~--------- 100 (114)
T cd02846 30 KALKGLKVEVTHRGNTNRKYKIKGLSAEPASQQTFELKDGEKEISVADYFKEKYNIRLKYPNLPCLQVGRK--------- 100 (114)
T ss_pred HHhCCCEEEEEcCCCCCceEEEeeccCCCccceEEEcCCCCcEEEHHHHHHHHcCCcccCCCCCEEEeCCC---------
Confidence 4467777888886 689999999888777788876544 478999999999999999999999987621
Q ss_pred hhhhccCCCCcceeecCcchhhh
Q 003062 364 CRQEKQREPSKISFELPPELCRI 386 (852)
Q Consensus 364 ~~~~~~~~~~~~~~~L~PElC~~ 386 (852)
....++|+|+|.+
T Consensus 101 ----------~~~~~~P~Elc~i 113 (114)
T cd02846 101 ----------GKPNYLPMELCNI 113 (114)
T ss_pred ----------CCCcEecceeEEe
Confidence 1125799999964
No 40
>KOG3732 consensus Staufen and related double-stranded-RNA-binding proteins [Intracellular trafficking, secretion, and vesicular transport; Transcription]
Probab=97.89 E-value=3.2e-05 Score=81.70 Aligned_cols=71 Identities=20% Similarity=0.278 Sum_probs=60.1
Q ss_pred ccCChhhHHHHHHHhCCCcee-eEEeeecCC---ceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHHHHHHhhhhCC
Q 003062 777 MRLQPARELNEYCQKHHFSMK-KTVAPRING---KAAVTVEVHANGTLFKHTHADADKETAKKVASKEVLKSLKASFP 850 (852)
Q Consensus 777 ~~~~P~~~L~e~~~~~~~~~~-~~~~~~~~g---~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~AL~~L~~~~~ 850 (852)
...||+.+|+|+||.++++.+ |. +..+.| ...|++.|.+++.+ .+|+|.|||.||+.||++.|+.|....|
T Consensus 140 ~~~NPI~~L~e~~q~k~~k~P~ye-lv~E~G~~~~rEFv~q~sv~~~~--~~GkG~sKKiAKRnAAeamLe~l~~~~~ 214 (339)
T KOG3732|consen 140 QVLNPIGRLQELAQAKKWKLPEYE-LVQESGVPHRREFVIQCSVENFT--EEGKGPSKKIAKRNAAEAMLESLGFVKP 214 (339)
T ss_pred cccChHHHHHHHHHHhCCCCCceE-EEeccCCCccceEEEEEEeccee--eecCCchHHHHHHHHHHHHHHHhccCCC
Confidence 357999999999999999776 77 445555 56899999999986 4899999999999999999999985544
No 41
>PF14709 DND1_DSRM: double strand RNA binding domain from DEAD END PROTEIN 1
Probab=97.72 E-value=9.9e-05 Score=63.26 Aligned_cols=68 Identities=22% Similarity=0.313 Sum_probs=52.1
Q ss_pred CChhhHHHHHHHhCCCcee-eEEeeec--CCceEEEEEEEECCEEEE---------eEEeeCCHHHHHHHHHHHHHHHhh
Q 003062 779 LQPARELNEYCQKHHFSMK-KTVAPRI--NGKAAVTVEVHANGTLFK---------HTHADADKETAKKVASKEVLKSLK 846 (852)
Q Consensus 779 ~~P~~~L~e~~~~~~~~~~-~~~~~~~--~g~~~~~~~v~v~~~~i~---------~~g~g~s~k~Ak~~AA~~AL~~L~ 846 (852)
.||+..|+++|++++|..+ |...... +|...|++.|.|.+.... ..-...++++||..||+.||+.|+
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 4899999999999999766 7643222 235689999999886541 123458999999999999999874
No 42
>PLN03202 protein argonaute; Provisional
Probab=97.58 E-value=6.2e-05 Score=93.21 Aligned_cols=81 Identities=26% Similarity=0.296 Sum_probs=65.0
Q ss_pred cccccCcEEEcCcCCceEEEEeecCCCCCCCCCCCCC---------CCcchHHHHHHHHhCcccccC-CceeEEEeeccc
Q 003062 287 TCMIYNSVVCTPHSGQIYYITGVLGHLNANSLFTRND---------GGAITYKKHYEERYGIQLCFD-QELLLNGRRIFH 356 (852)
Q Consensus 287 ~~~~~~~~V~~~~~~~~Y~v~~i~~dl~p~S~f~~~~---------~~~~ty~~yy~~k~~~~i~~~-~QPlL~~~~~~~ 356 (852)
...++|..|.+.|+++.|.|.+|.++.++..+|...+ +..+|+.+||+++|++.|.++ ++|+|.+..
T Consensus 292 ~~~lkGl~V~t~~~~k~yrI~~i~~~~a~~~~F~~~~~~~~~~~~~~~~iSv~dYfk~~Yni~l~~p~~lPlv~~g~--- 368 (900)
T PLN03202 292 KRMLKNLRVKVSPSNQEYKITGLSEKPCKEQTFSLKQRNGNGNEVETVEITVYDYFVKHRGIELRYSGDLPCINVGK--- 368 (900)
T ss_pred HHHhcCCEEEEecCCceEEEeeccCCCCcceEEEcccCCcccccCCcceEEHHHHHHHHcCccccCCCCCCEEEcCC---
Confidence 3567899999999999999999999999999996431 236899999999999999986 789885331
Q ss_pred cccccchhhhhccCCCCcceeecCcchhhh
Q 003062 357 AQNYLSKCRQEKQREPSKISFELPPELCRI 386 (852)
Q Consensus 357 r~N~L~~~~~~~~~~~~~~~~~L~PElC~~ 386 (852)
....++||||+|.+
T Consensus 369 ----------------~~~~~ylP~ElC~i 382 (900)
T PLN03202 369 ----------------PKRPTYFPIELCSL 382 (900)
T ss_pred ----------------CCCCeEEcceeeEc
Confidence 11135799999965
No 43
>KOG3732 consensus Staufen and related double-stranded-RNA-binding proteins [Intracellular trafficking, secretion, and vesicular transport; Transcription]
Probab=97.50 E-value=0.00025 Score=75.06 Aligned_cols=70 Identities=23% Similarity=0.201 Sum_probs=58.0
Q ss_pred CChhhHHHHHHHhCCCceeeEEeeecC--CceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHHHHHHhhhhCC
Q 003062 779 LQPARELNEYCQKHHFSMKKTVAPRIN--GKAAVTVEVHANGTLFKHTHADADKETAKKVASKEVLKSLKASFP 850 (852)
Q Consensus 779 ~~P~~~L~e~~~~~~~~~~~~~~~~~~--g~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~AL~~L~~~~~ 850 (852)
..|++.|+|++.+.+..+.|++...++ +.+.|++.|.|+... ++|.|.|||.||++||..+|+.|+.-.|
T Consensus 38 KS~IS~l~E~~~r~~~~v~fevl~eeGp~H~~~fv~rvtvg~~~--a~GeG~sKK~AKh~AA~~~L~~lk~l~~ 109 (339)
T KOG3732|consen 38 KSPISLLQEYGLRRGLTPVYEVLREEGPPHMPNFVFRVTVGEIT--ATGEGKSKKLAKHRAAEALLKELKKLPP 109 (339)
T ss_pred CChHHHHHHHHHHhCCCcceeeeeccCCccCCCeEEEEEEeeeE--EecCCCchhHHHHHHHHHHHHHHhcCCC
Confidence 789999999999999888888444333 257899999999543 5899999999999999999999986443
No 44
>COG1939 Ribonuclease III family protein [Replication, recombination, and repair]
Probab=97.39 E-value=0.00058 Score=62.12 Aligned_cols=110 Identities=23% Similarity=0.204 Sum_probs=66.6
Q ss_pred hhhhHhhHHHHHHHHHHHHHHhCCCCCcchHHHHHHHhcChHHHHHHHHHcCCchhhhccChhHHHHHHHHHhhhhhhcc
Q 003062 643 QRLEFLGDAVLDYLITVYLYNKYPTLSPGDLTDMRSASVNNDCYALSSVKHGLHKHILHASQELYKWINITVDSFERLSL 722 (852)
Q Consensus 643 eRLEfLGDavLd~~v~~~l~~~~p~~~~~~Lt~~r~~lv~n~~La~~a~~~gL~~~l~~~~~~~~~~i~~~~~~~~~~~~ 722 (852)
=-|+|+||||+++.|-.|+....-. .|..||..-.+.||...=|.+-..+ ..++. +.-.+.+++-.....
T Consensus 16 laLAy~GDAV~e~yVR~~~l~~g~~-k~~~lH~~a~~~VsAk~QA~il~~~--~~~Lt-------e~E~~I~KRgRNaks 85 (132)
T COG1939 16 LALAYLGDAVYELYVREYLLLKGKT-KPNDLHKRATAYVSAKAQALILKAL--LEFLT-------EEEEEIVKRGRNAKS 85 (132)
T ss_pred HHHHHhhhHHHHHHHHHHHHhcccC-ChHHHHHHHHHHhhHHHHHHHHHHH--HHHhh-------HHHHHHHHHhccccc
Confidence 4589999999999999999876433 6999999999999999877765442 22221 111111111000000
Q ss_pred ccccCccccCCC-ChhhHHHHHHHhheeeeeCCCCHHHHHHHHHHh
Q 003062 723 ESTFGWESETSF-PKALGDIIESLSGAIFVDSGCNKEVVFESIRPL 767 (852)
Q Consensus 723 ~~~~~~~~~~~~-~k~laD~~EAliGAi~~DsG~~~~~v~~~~~~~ 767 (852)
.+.+-+ .++ .=-.|.-|||+||.+|+-... +...+++...
T Consensus 86 -~T~~kn--~dv~tYr~sTgfEAliGyLyL~~~~--eRL~ell~~~ 126 (132)
T COG1939 86 -GTKPKN--TDVETYRMSTGFEALIGYLYLTKQE--ERLEELLNKV 126 (132)
T ss_pred -CCCCCC--CChHHHHHhhhHHHHHHHHHHcccH--HHHHHHHHHH
Confidence 011100 011 115788999999999998654 3444444443
No 45
>KOG2777 consensus tRNA-specific adenosine deaminase 1 [RNA processing and modification]
Probab=95.65 E-value=0.022 Score=65.00 Aligned_cols=67 Identities=18% Similarity=0.179 Sum_probs=51.1
Q ss_pred cCChhhHHHHHHHhCCCceeeEEeeecCCceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHHHHHHhhhh
Q 003062 778 RLQPARELNEYCQKHHFSMKKTVAPRINGKAAVTVEVHANGTLFKHTHADADKETAKKVASKEVLKSLKAS 848 (852)
Q Consensus 778 ~~~P~~~L~e~~~~~~~~~~~~~~~~~~g~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~AL~~L~~~ 848 (852)
..+|+..|+|+.+ +..+.+.......+...|.|.|.|+|+..- |.|.|||+||..||+.||+.|-..
T Consensus 89 ~~npv~ll~e~~~--~~~~~~~~~~~~~~~~~F~~~~~vdg~~~~--~~~~sKk~ak~~aa~~al~~l~~~ 155 (542)
T KOG2777|consen 89 GKNPVSLLHELAN--GLFFDFVNESGPQHAPKFVMSVVVDGRWFE--GGGRSKKEAKQEAAMAALQVLFKI 155 (542)
T ss_pred cCCchHHHHHHhc--ccceeeeccCCCCCCceEEEEEEECCEEcc--CCCcchHHHHHHHHHHHHHHHHhc
Confidence 5799999999988 322332212233346789999999999864 459999999999999999988644
No 46
>COG1939 Ribonuclease III family protein [Replication, recombination, and repair]
Probab=95.52 E-value=0.025 Score=51.69 Aligned_cols=113 Identities=20% Similarity=0.162 Sum_probs=68.7
Q ss_pred CchhhhhhhhhHHhHHHHHHHHHhcCCCCcchhhHHHhhccccHHHHHHHHhCCccccccccccCCCCcccCCCCCCCcc
Q 003062 451 HLESLETLGDSFLKYAASQQLFKTYQNHHEGLLSVKKDRIISNAALCKLGCDHKLPGFIRTEPFDPKMWMIPGDNSGSYE 530 (852)
Q Consensus 451 nyeRLE~LGDs~Lk~~~s~~l~~~~p~~~eg~Ls~~r~~~vsN~~L~~~a~~~gL~~~i~~~~f~~~~w~~~~~~~~~~~ 530 (852)
|-=-|.|+||||+.+.+-.|+....-. ..+.||..-.+.||-+.=+.+-.. +..++..+ . ..|.-.|...+...
T Consensus 14 n~laLAy~GDAV~e~yVR~~~l~~g~~-k~~~lH~~a~~~VsAk~QA~il~~--~~~~Lte~-E--~~I~KRgRNaks~T 87 (132)
T COG1939 14 NGLALAYLGDAVYELYVREYLLLKGKT-KPNDLHKRATAYVSAKAQALILKA--LLEFLTEE-E--EEIVKRGRNAKSGT 87 (132)
T ss_pred CHHHHHHhhhHHHHHHHHHHHHhcccC-ChHHHHHHHHHHhhHHHHHHHHHH--HHHHhhHH-H--HHHHHHhcccccCC
Confidence 444789999999999999988876433 688999999999987765554332 11122110 0 11222222111000
Q ss_pred cCccccccccccccccccccccchhHHHHHHHHHHHhhcCChHHHHHhhhhc
Q 003062 531 LNDHSLFNERKIYVTGRKKVKSKTVADVVEALIGAFLSTGGENVGLIFLDRI 582 (852)
Q Consensus 531 ~~~~~~~~~~~~~~~~~~~~~~K~lADv~EAliGA~yl~~G~~~a~~~~~~l 582 (852)
....-....=-.|..+|||||..|+..-.+.-..++.|.
T Consensus 88 -------------~~kn~dv~tYr~sTgfEAliGyLyL~~~~eRL~ell~~~ 126 (132)
T COG1939 88 -------------KPKNTDVETYRMSTGFEALIGYLYLTKQEERLEELLNKV 126 (132)
T ss_pred -------------CCCCCChHHHHHhhhHHHHHHHHHHcccHHHHHHHHHHH
Confidence 000001122245889999999999999888777777664
No 47
>KOG0354 consensus DEAD-box like helicase [General function prediction only]
Probab=95.35 E-value=0.0082 Score=70.93 Aligned_cols=30 Identities=33% Similarity=0.532 Sum_probs=28.2
Q ss_pred CCCcchhhHHHHHhhcccccCCCcEEEEEe
Q 003062 1 MFDPSHTVCSFIQSRGRARMQNSDYLLMLK 30 (852)
Q Consensus 1 rFD~p~t~~syIQSRGRAR~~~S~yi~m~e 30 (852)
|||...|.+..||||||||+++|++++++.
T Consensus 498 cYd~~snpIrmIQrrGRgRa~ns~~vll~t 527 (746)
T KOG0354|consen 498 CYDYSSNPIRMVQRRGRGRARNSKCVLLTT 527 (746)
T ss_pred EecCCccHHHHHHHhccccccCCeEEEEEc
Confidence 799999999999999999999999999953
No 48
>KOG4334 consensus Uncharacterized conserved protein, contains double-stranded RNA-binding motif and WW domain [General function prediction only]
Probab=94.44 E-value=0.028 Score=62.01 Aligned_cols=64 Identities=25% Similarity=0.186 Sum_probs=49.2
Q ss_pred hhHHHHHHHhCCC-ceeeEEeeecCCceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHHHHHHhh
Q 003062 782 ARELNEYCQKHHF-SMKKTVAPRINGKAAVTVEVHANGTLFKHTHADADKETAKKVASKEVLKSLK 846 (852)
Q Consensus 782 ~~~L~e~~~~~~~-~~~~~~~~~~~g~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~AL~~L~ 846 (852)
+-.|+|++|.... .+.|.-...++....|..+|.+++-.+| +|.|.|||.||..||+.+|++|-
T Consensus 378 vCiLhEy~q~~lk~~pvyef~e~~n~stpysa~v~~d~~~yG-sG~g~sKK~Ak~~AAR~tLeiLI 442 (650)
T KOG4334|consen 378 VCILHEYAQQCLKSLPVYEFAENDNNSTPYSAGVLPDLFPYG-SGVGASKKTAKLVAARDTLEILI 442 (650)
T ss_pred eehHHHHHHHHhhhcceeehhhccCCCCcccccccccccccc-cccccchHHHHHHHHHHHHHHhc
Confidence 4578888886433 3335422333345679999999999998 89999999999999999999884
No 49
>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=89.73 E-value=0.72 Score=37.46 Aligned_cols=34 Identities=21% Similarity=0.068 Sum_probs=26.9
Q ss_pred eEEEEEEcCCCCCCccc--cccCcHHHHHHHHHHHHHHHH
Q 003062 45 MGICTLYLPNNCPIQTV--IAQGNIKTLKQTACLEACKKL 82 (852)
Q Consensus 45 ~~~~~v~LP~~~p~~~~--~~~~s~~~Ak~~aAf~Ac~~L 82 (852)
.|+|+|.+.. ... ...+||+.||+.||..|+..|
T Consensus 33 ~f~~~v~i~~----~~~~~g~g~sKk~Ak~~AA~~al~~L 68 (68)
T cd00048 33 RFTVEVTVGG----KITGEGEGSSKKEAKQNAAEAALRKL 68 (68)
T ss_pred eEEEEEEECC----EEEEEeecCCHHHHHHHHHHHHHHhC
Confidence 6999999965 222 344699999999999999875
No 50
>PF14709 DND1_DSRM: double strand RNA binding domain from DEAD END PROTEIN 1
Probab=87.39 E-value=1.7 Score=37.22 Aligned_cols=48 Identities=15% Similarity=0.212 Sum_probs=36.7
Q ss_pred CCCeEEE--cC---C--eEEEEEEcCCCCCC-ccc-------cccCcHHHHHHHHHHHHHHHH
Q 003062 35 PTPKFDI--NK---E--MGICTLYLPNNCPI-QTV-------IAQGNIKTLKQTACLEACKKL 82 (852)
Q Consensus 35 ~~P~~~~--~~---~--~~~~~v~LP~~~p~-~~~-------~~~~s~~~Ak~~aAf~Ac~~L 82 (852)
..|.|.+ .. + .|.++|++|.-.-. ... .++.+++.||.+||-.|...|
T Consensus 17 ~~P~y~l~~~~Gp~~~~~F~ykV~i~~~~~~~~~~~~~~~p~~~~~~~k~Ak~~AA~~~L~~L 79 (80)
T PF14709_consen 17 GPPVYELVSESGPDHRKLFLYKVVIPGLEYPFEGSIECFGPTKPSSTKKEAKESAAQQALQAL 79 (80)
T ss_pred CCCeEEEEeccCCCccEEEEEEEEEcCCCCCCcceEEEccCCCcCccHHHHHHHHHHHHHHhc
Confidence 3699987 11 2 79999999987653 211 678899999999999887665
No 51
>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=86.24 E-value=1.8 Score=35.16 Aligned_cols=36 Identities=31% Similarity=0.229 Sum_probs=26.4
Q ss_pred eEEEEEEcCCCCCCccccccCcHHHHHHHHHHHHHHHH
Q 003062 45 MGICTLYLPNNCPIQTVIAQGNIKTLKQTACLEACKKL 82 (852)
Q Consensus 45 ~~~~~v~LP~~~p~~~~~~~~s~~~Ak~~aAf~Ac~~L 82 (852)
.|.|+|.+....-- .....||+.||+.||-.|++.|
T Consensus 32 ~f~~~~~i~~~~~~--~g~g~sKk~Ak~~AA~~al~~L 67 (67)
T PF00035_consen 32 RFICTVYIDGKEYG--EGEGSSKKEAKQQAAKKALQKL 67 (67)
T ss_dssp EEEEEEEETTEEEE--EEEESSHHHHHHHHHHHHHHHH
T ss_pred eEEEEEEECCEEEe--EeccCCHHHHHHHHHHHHHHhC
Confidence 58899988432110 1334699999999999999987
No 52
>smart00358 DSRM Double-stranded RNA binding motif.
Probab=85.91 E-value=1.7 Score=35.23 Aligned_cols=36 Identities=19% Similarity=0.017 Sum_probs=27.4
Q ss_pred eEEEEEEcCCCCCCccccccCcHHHHHHHHHHHHHHHH
Q 003062 45 MGICTLYLPNNCPIQTVIAQGNIKTLKQTACLEACKKL 82 (852)
Q Consensus 45 ~~~~~v~LP~~~p~~~~~~~~s~~~Ak~~aAf~Ac~~L 82 (852)
.|+|+|.+... .-......||+.||+.||-+|+..|
T Consensus 31 ~f~~~v~i~~~--~~~~g~g~sKk~Ak~~AA~~al~~L 66 (67)
T smart00358 31 RFTVTVKVGGE--YTGEGEGSSKKEAKQRAAEAALRSL 66 (67)
T ss_pred cEEEEEEECCE--EEEEeccCCHHHHHHHHHHHHHHhc
Confidence 68999988542 0112446899999999999999887
No 53
>KOG1041 consensus Translation initiation factor 2C (eIF-2C) and related proteins [Translation, ribosomal structure and biogenesis]
Probab=84.27 E-value=1.3 Score=55.30 Aligned_cols=82 Identities=24% Similarity=0.275 Sum_probs=62.0
Q ss_pred ccccccCcEEEcCc--CCceEEEEeecCCCCCCCCCCCCC--CCcchHHHHHHHHhCcccccCCceeEEEeecccccccc
Q 003062 286 CTCMIYNSVVCTPH--SGQIYYITGVLGHLNANSLFTRND--GGAITYKKHYEERYGIQLCFDQELLLNGRRIFHAQNYL 361 (852)
Q Consensus 286 ~~~~~~~~~V~~~~--~~~~Y~v~~i~~dl~p~S~f~~~~--~~~~ty~~yy~~k~~~~i~~~~QPlL~~~~~~~r~N~L 361 (852)
....++|--|...| .++.|.|.++...-.-...|+..+ +...|-.+||+.+|++.+.+++-|.|++.+-.+
T Consensus 276 ~~~~lkgL~v~~~h~~~~r~~~i~~l~~~~a~~~~F~l~~~~~~~~tV~~Yf~~ky~~~Lkyp~LPcv~v~~~~~----- 350 (876)
T KOG1041|consen 276 IKKALKGLKVYVTHGKRKRKIKIMGLSKKPAKNTTFELKDKKGREITVADYFLEKYNITLKYPDLPCVVVKRPKR----- 350 (876)
T ss_pred HHHHhhCcEEEEecccCcceEEEecccCCcccCceeeccCCCceEEeHHHHHHHhcCccccCCCCccEeecCCCC-----
Confidence 34557777777777 346899999987666677787544 466899999999999999999999998873211
Q ss_pred chhhhhccCCCCcceeecCcchhhh
Q 003062 362 SKCRQEKQREPSKISFELPPELCRI 386 (852)
Q Consensus 362 ~~~~~~~~~~~~~~~~~L~PElC~~ 386 (852)
..++|.|+|.+
T Consensus 351 --------------~~~~PmElc~i 361 (876)
T KOG1041|consen 351 --------------ENFYPMELCNI 361 (876)
T ss_pred --------------Ccccchhheec
Confidence 13689999964
No 54
>PF11469 Ribonucleas_3_2: Ribonuclease III; InterPro: IPR021568 This archaeal family of proteins has no known function. ; PDB: 1ZTD_A.
Probab=81.28 E-value=8.9 Score=33.90 Aligned_cols=80 Identities=24% Similarity=0.265 Sum_probs=53.7
Q ss_pred hhhhhhhhHHhHHHHHHHHH--hcCCCCcchhhHHHhhccccHHHHHHHHhCCccccccccccCCCCcccCCCCCCCccc
Q 003062 454 SLETLGDSFLKYAASQQLFK--TYQNHHEGLLSVKKDRIISNAALCKLGCDHKLPGFIRTEPFDPKMWMIPGDNSGSYEL 531 (852)
Q Consensus 454 RLE~LGDs~Lk~~~s~~l~~--~~p~~~eg~Ls~~r~~~vsN~~L~~~a~~~gL~~~i~~~~f~~~~w~~~~~~~~~~~~ 531 (852)
-|.-+|||...|+.|..|-. .+|. | .-|-|..|+..-...||.+.+. |-
T Consensus 2 ~Lak~GDSLvNfl~SlALse~lG~Pt---g-------~rVPnaSLaiAl~~a~L~~~~~-----------PR-------- 52 (120)
T PF11469_consen 2 GLAKFGDSLVNFLFSLALSEYLGRPT---G-------DRVPNASLAIALELAGLSHLLP-----------PR-------- 52 (120)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTS-----------------HHHHHHHHHHTTGGGCS-------------C--------
T ss_pred cHHHHhHHHHHHHHHHHHHHHhCCCC---C-------CCCCChHHHHHHHHHhhhhhCc-----------cc--------
Confidence 36789999999999998753 3443 3 3478999998877788877663 21
Q ss_pred CccccccccccccccccccccchhHHHHHHHHHHHhhcCCh--HHHHHhhh
Q 003062 532 NDHSLFNERKIYVTGRKKVKSKTVADVVEALIGAFLSTGGE--NVGLIFLD 580 (852)
Q Consensus 532 ~~~~~~~~~~~~~~~~~~~~~K~lADv~EAliGA~yl~~G~--~~a~~~~~ 580 (852)
+....-.|..||+|.-+++.|-+ +.|..+++
T Consensus 53 ------------------~dkh~kGd~aEA~iAyAWLeg~it~eEaveil~ 85 (120)
T PF11469_consen 53 ------------------TDKHGKGDIAEALIAYAWLEGKITIEEAVEILK 85 (120)
T ss_dssp ------------------GGCCGHHHHHHHHHHHHHHTTSS-HHHHHHHHH
T ss_pred ------------------ccccCccHHHHHHHHHHHHhccccHHHHHHHHH
Confidence 12335579999999999999864 45666654
No 55
>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=79.96 E-value=9.7 Score=33.40 Aligned_cols=64 Identities=20% Similarity=0.141 Sum_probs=36.8
Q ss_pred hhHHHHHHHhCCC------ceeeEEeeecCCceEEEEEEEECC----EEEEeEEeeCCHHHHHHHHHHHHHHHhhhhC
Q 003062 782 ARELNEYCQKHHF------SMKKTVAPRINGKAAVTVEVHANG----TLFKHTHADADKETAKKVASKEVLKSLKASF 849 (852)
Q Consensus 782 ~~~L~e~~~~~~~------~~~~~~~~~~~g~~~~~~~v~v~~----~~i~~~g~g~s~k~Ak~~AA~~AL~~L~~~~ 849 (852)
+..|+++|++... .+.|. ....+ ..|.|+|..=. +.+. .....|++.||+.||-+|++.|.+.+
T Consensus 2 i~lL~~yC~~Lp~d~~~~~~P~~~-~~~~~--~~~~c~v~LP~~~pi~~i~-g~~~~sk~~AK~sAAf~Ac~~L~~~g 75 (90)
T PF03368_consen 2 ISLLNRYCSTLPSDSFTNLKPEFE-IEKIG--SGFICTVILPINSPIRSIE-GPPMRSKKLAKRSAAFEACKKLHEAG 75 (90)
T ss_dssp HHHHHHHHTTSSS-TT--SS-EEE-EEE----G-EEEEEE--TT-SS--EE-EE--SSHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHhcCCCCCCccCCceEE-EEEcC--CcEEEEEECCCCCCCCeEE-ccccccHHHHHHHHHHHHHHHHHHcC
Confidence 4567888876422 23354 22222 25888887632 2222 23578999999999999999998653
No 56
>PF14954 LIX1: Limb expression 1
Probab=77.91 E-value=3.5 Score=41.38 Aligned_cols=36 Identities=14% Similarity=0.095 Sum_probs=32.0
Q ss_pred eEEEEEEcCCCCCCccccccCcHHHHHHHHHHHHHH
Q 003062 45 MGICTLYLPNNCPIQTVIAQGNIKTLKQTACLEACK 80 (852)
Q Consensus 45 ~~~~~v~LP~~~p~~~~~~~~s~~~Ak~~aAf~Ac~ 80 (852)
-|.|-|+||..+.+-.+..++||..|||+||=-|..
T Consensus 58 pyVcyVTLPGGSCFGnfq~C~tkAEARR~AAKiALm 93 (252)
T PF14954_consen 58 PYVCYVTLPGGSCFGNFQNCPTKAEARRSAAKIALM 93 (252)
T ss_pred CeEEEEeCCCCCccCccccCCcHHHHHhhhHHHHHH
Confidence 478999999999999998899999999999976643
No 57
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=74.90 E-value=11 Score=37.61 Aligned_cols=63 Identities=13% Similarity=0.082 Sum_probs=41.2
Q ss_pred hhhHHHHHhhcccccCCCcEEEEEeccccCCCeEEEcCCeEEEEEEcCCCCCCccc--cccCcHHHHHHHHHHHHHHHHH
Q 003062 6 HTVCSFIQSRGRARMQNSDYLLMLKRYFKPTPKFDINKEMGICTLYLPNNCPIQTV--IAQGNIKTLKQTACLEACKKLH 83 (852)
Q Consensus 6 ~t~~syIQSRGRAR~~~S~yi~m~e~~~~~~P~~~~~~~~~~~~v~LP~~~p~~~~--~~~~s~~~Ak~~aAf~Ac~~L~ 83 (852)
.-+..|.|++||.. |.++.+.=-+..|. |.|+|.+.. +.. ..-.|||.|++.||-.|+.+|-
T Consensus 113 S~LQE~~Qk~~~~~-----y~~i~~~Gp~H~p~-------F~v~V~I~g----~~~g~G~G~SKKeAEQ~AAk~AL~~L~ 176 (183)
T PHA03103 113 TVINEYCQITSRDW-----SINITSSGPSHSPT-------FTASVIISG----IKFKPAIGSTKKEAKNNAAKLAMDKIL 176 (183)
T ss_pred HHHHHHHHHhCCCe-----EEEEEeeCCCCCce-------EEEEEEECC----EEEEEeeeCCHHHHHHHHHHHHHHHHH
Confidence 45677889888772 65542210111244 667887765 222 3346999999999999999985
Q ss_pred h
Q 003062 84 Q 84 (852)
Q Consensus 84 ~ 84 (852)
.
T Consensus 177 ~ 177 (183)
T PHA03103 177 N 177 (183)
T ss_pred h
Confidence 3
No 58
>PF14954 LIX1: Limb expression 1
Probab=70.38 E-value=9.6 Score=38.38 Aligned_cols=63 Identities=21% Similarity=0.222 Sum_probs=41.6
Q ss_pred CChhhHHHHHHH-hC--CCcee------eEEeeecCCceEEEEEEEE-CCEEEEeEEeeCCHHHHHHHHHHHHHH
Q 003062 779 LQPARELNEYCQ-KH--HFSMK------KTVAPRINGKAAVTVEVHA-NGTLFKHTHADADKETAKKVASKEVLK 843 (852)
Q Consensus 779 ~~P~~~L~e~~~-~~--~~~~~------~~~~~~~~g~~~~~~~v~v-~~~~i~~~g~g~s~k~Ak~~AA~~AL~ 843 (852)
.|-+..|+|+=+ |+ |-.++ |+ ...+..+.|.|-|.+ ||-..|.--...|+.+|++.||+.||-
T Consensus 21 vnvV~~LqeFWq~Kq~r~a~~~~~~lv~YE--s~ps~~ppyVcyVTLPGGSCFGnfq~C~tkAEARR~AAKiALm 93 (252)
T PF14954_consen 21 VNVVEALQEFWQMKQSRGADLKSEALVVYE--SVPSPSPPYVCYVTLPGGSCFGNFQNCPTKAEARRSAAKIALM 93 (252)
T ss_pred chHHHHHHHHHHHHHhccccCCCCCeeeee--ccCCCCCCeEEEEeCCCCCccCccccCCcHHHHHhhhHHHHHH
Confidence 577788888433 43 22221 33 222334668888887 556665556679999999999999994
No 59
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=69.97 E-value=23 Score=35.24 Aligned_cols=68 Identities=18% Similarity=0.238 Sum_probs=42.8
Q ss_pred CCcchhhHHHHHhhcccccCCCcEEEEEeccccCCCeEEEcCCeEEEEEEcCCCCCCcc-ccccCcHHHHHHHHHHHHHH
Q 003062 2 FDPSHTVCSFIQSRGRARMQNSDYLLMLKRYFKPTPKFDINKEMGICTLYLPNNCPIQT-VIAQGNIKTLKQTACLEACK 80 (852)
Q Consensus 2 FD~p~t~~syIQSRGRAR~~~S~yi~m~e~~~~~~P~~~~~~~~~~~~v~LP~~~p~~~-~~~~~s~~~Ak~~aAf~Ac~ 80 (852)
.|.-..+..|+|.+||-- .|.+.-+.--+..|. |+++|.+-.. .. ...-+|||.|++.||-.|+.
T Consensus 108 ~DpKS~LQE~~Q~~~~~l----~Y~li~~~GpdH~~~-------Ftv~V~V~g~---~~g~G~G~SKKeAEQ~AAk~AL~ 173 (183)
T PHA02701 108 LNPVSAVNEFCMRTHRPL----EFCETRSGGHDHCPL-------FTCTIVVSGK---VVATASGCSKKLARHAACADALT 173 (183)
T ss_pred CCccHHHHHHHHhcCCCC----eEEEEEeECCCCCce-------EEEEEEECCE---EEEEEEeCCHHHHHHHHHHHHHH
Confidence 355566788999988654 475553321112344 5566666321 11 13347999999999999999
Q ss_pred HHH
Q 003062 81 KLH 83 (852)
Q Consensus 81 ~L~ 83 (852)
.|-
T Consensus 174 ~L~ 176 (183)
T PHA02701 174 ILI 176 (183)
T ss_pred HHH
Confidence 884
No 60
>PRK13766 Hef nuclease; Provisional
Probab=62.09 E-value=5.3 Score=49.71 Aligned_cols=28 Identities=21% Similarity=0.529 Sum_probs=24.3
Q ss_pred CCcchhhHHHHHhhccc-ccCCCcEEEEE
Q 003062 2 FDPSHTVCSFIQSRGRA-RMQNSDYLLML 29 (852)
Q Consensus 2 FD~p~t~~syIQSRGRA-R~~~S~yi~m~ 29 (852)
||+|.+...||||.||+ |....+.++|+
T Consensus 448 yd~~~s~~r~iQR~GR~gR~~~~~v~~l~ 476 (773)
T PRK13766 448 YEPVPSEIRSIQRKGRTGRQEEGRVVVLI 476 (773)
T ss_pred eCCCCCHHHHHHHhcccCcCCCCEEEEEE
Confidence 89999999999999998 76677777775
No 61
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=51.97 E-value=9.5 Score=45.06 Aligned_cols=20 Identities=35% Similarity=0.547 Sum_probs=18.1
Q ss_pred CCcchhhHHHHHhhcccccC
Q 003062 2 FDPSHTVCSFIQSRGRARMQ 21 (852)
Q Consensus 2 FD~p~t~~syIQSRGRAR~~ 21 (852)
||+|.+..+||||.|||-+.
T Consensus 443 ~d~P~s~~~yihRiGRaGR~ 462 (518)
T PLN00206 443 FDMPNTIKEYIHQIGRASRM 462 (518)
T ss_pred eCCCCCHHHHHHhccccccC
Confidence 89999999999999999554
No 62
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=51.25 E-value=8.1 Score=45.09 Aligned_cols=23 Identities=13% Similarity=0.274 Sum_probs=20.4
Q ss_pred CCcchhhHHHHHhhcccccCCCc
Q 003062 2 FDPSHTVCSFIQSRGRARMQNSD 24 (852)
Q Consensus 2 FD~p~t~~syIQSRGRAR~~~S~ 24 (852)
||+|.|..+|+|+.|||-+.+..
T Consensus 410 ~~~P~s~~~y~Qr~GRaGR~g~~ 432 (475)
T PRK01297 410 FTLPEDPDDYVHRIGRTGRAGAS 432 (475)
T ss_pred eCCCCCHHHHHHhhCccCCCCCC
Confidence 79999999999999999887543
No 63
>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=50.34 E-value=6.7 Score=27.45 Aligned_cols=12 Identities=67% Similarity=0.811 Sum_probs=9.7
Q ss_pred hhHHHHHHHHHH
Q 003062 554 TVADVVEALIGA 565 (852)
Q Consensus 554 ~lADv~EAliGA 565 (852)
+--|+||||||+
T Consensus 24 tpEDAvEaLi~~ 35 (35)
T PF08383_consen 24 TPEDAVEALIGN 35 (35)
T ss_pred CHHHHHHHHhcC
Confidence 347999999984
No 64
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=50.06 E-value=7.1 Score=44.76 Aligned_cols=21 Identities=14% Similarity=0.309 Sum_probs=18.2
Q ss_pred CCCcchhhHHHHHhhcccccC
Q 003062 1 MFDPSHTVCSFIQSRGRARMQ 21 (852)
Q Consensus 1 rFD~p~t~~syIQSRGRAR~~ 21 (852)
.||+|.+..+|+||.|||-+.
T Consensus 329 ~~d~P~s~~~yiqR~GR~gR~ 349 (423)
T PRK04837 329 NYDLPDDCEDYVHRIGRTGRA 349 (423)
T ss_pred EeCCCCchhheEeccccccCC
Confidence 389999999999999996554
No 65
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=46.76 E-value=25 Score=42.92 Aligned_cols=67 Identities=15% Similarity=0.177 Sum_probs=53.4
Q ss_pred ChhhHHHHHHHhCCCceeeEEeeecC--CceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHHHHHHhhh
Q 003062 780 QPARELNEYCQKHHFSMKKTVAPRIN--GKAAVTVEVHANGTLFKHTHADADKETAKKVASKEVLKSLKA 847 (852)
Q Consensus 780 ~P~~~L~e~~~~~~~~~~~~~~~~~~--g~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~AL~~L~~ 847 (852)
+-+.-|+.||.+..+.+.|. +..+. +...|.|.|.+.+.....+|...++|.|++.||+.-++-|-.
T Consensus 2 d~k~fly~~~~k~~~~p~~d-~~~~~~~~rqrf~ce~~~~~~~~~~~~~stnkKda~knac~dfv~ylvr 70 (1282)
T KOG0921|consen 2 DVKEFLYAWLGKNKYGPTYD-IRSEGRKGRQRFLCEVRVEGFGYTAVGNSTNKKDAATNAAQDFCQYLVR 70 (1282)
T ss_pred cHHHHHHHHHhhhccCccee-hhhhcccchhheeeeeeccCCcceeeecccccchhhHHHHHHHHHHhhh
Confidence 44677899999999987776 44443 356799999998876666899999999999999998887753
No 66
>PF11469 Ribonucleas_3_2: Ribonuclease III; InterPro: IPR021568 This archaeal family of proteins has no known function. ; PDB: 1ZTD_A.
Probab=46.09 E-value=68 Score=28.59 Aligned_cols=85 Identities=24% Similarity=0.316 Sum_probs=54.0
Q ss_pred hhHhhHHHHHHHHHHHHHH--hCCCCCcchHHHHHHHhcChHHHHHHHHHcCCchhhhccChhHHHHHHHHHhhhhhhcc
Q 003062 645 LEFLGDAVLDYLITVYLYN--KYPTLSPGDLTDMRSASVNNDCYALSSVKHGLHKHILHASQELYKWINITVDSFERLSL 722 (852)
Q Consensus 645 LEfLGDavLd~~v~~~l~~--~~p~~~~~~Lt~~r~~lv~n~~La~~a~~~gL~~~l~~~~~~~~~~i~~~~~~~~~~~~ 722 (852)
|.-+||++++++++--|-+ -+|.- .-|-|..||..-..-||.+.+.--
T Consensus 3 Lak~GDSLvNfl~SlALse~lG~Ptg----------~rVPnaSLaiAl~~a~L~~~~~PR-------------------- 52 (120)
T PF11469_consen 3 LAKFGDSLVNFLFSLALSEYLGRPTG----------DRVPNASLAIALELAGLSHLLPPR-------------------- 52 (120)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTS-----------------HHHHHHHHHHTTGGGCS--C--------------------
T ss_pred HHHHhHHHHHHHHHHHHHHHhCCCCC----------CCCCChHHHHHHHHHhhhhhCccc--------------------
Confidence 6779999999998887754 23332 236677787666667777665411
Q ss_pred ccccCccccCCCChhhHHHHHHHhheeeeeCCCCHHHHHHHHHHhhc
Q 003062 723 ESTFGWESETSFPKALGDIIESLSGAIFVDSGCNKEVVFESIRPLLE 769 (852)
Q Consensus 723 ~~~~~~~~~~~~~k~laD~~EAliGAi~~DsG~~~~~v~~~~~~~l~ 769 (852)
.-...-+|+.||+++=-|+..-...+.+.+++..-+.
T Consensus 53 ----------~dkh~kGd~aEA~iAyAWLeg~it~eEaveil~~nl~ 89 (120)
T PF11469_consen 53 ----------TDKHGKGDIAEALIAYAWLEGKITIEEAVEILKANLT 89 (120)
T ss_dssp ----------GGCCGHHHHHHHHHHHHHHTTSS-HHHHHHHHHCT--
T ss_pred ----------ccccCccHHHHHHHHHHHHhccccHHHHHHHHHhcCc
Confidence 0113579999999999999988877777766665443
No 67
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=45.40 E-value=18 Score=45.13 Aligned_cols=22 Identities=27% Similarity=0.282 Sum_probs=16.8
Q ss_pred HHHHHhhccccc-CCCcEEEEEe
Q 003062 9 CSFIQSRGRARM-QNSDYLLMLK 30 (852)
Q Consensus 9 ~syIQSRGRAR~-~~S~yi~m~e 30 (852)
.||+||+|||-. ..-+.+.|..
T Consensus 315 asa~QR~GRaGR~~~G~cyrL~t 337 (812)
T PRK11664 315 ASMTQRAGRAGRLEPGICLHLYS 337 (812)
T ss_pred hhhhhhccccCCCCCcEEEEecC
Confidence 489999999955 5667777764
No 68
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=42.29 E-value=18 Score=43.98 Aligned_cols=29 Identities=31% Similarity=0.260 Sum_probs=21.3
Q ss_pred CCcchhhHHHHHhhccc-ccCCCcEEEEEe
Q 003062 2 FDPSHTVCSFIQSRGRA-RMQNSDYLLMLK 30 (852)
Q Consensus 2 FD~p~t~~syIQSRGRA-R~~~S~yi~m~e 30 (852)
|..|.+..+|||+.||| |.+..+.|+++.
T Consensus 526 fG~~~~~~~yiqr~GR~gR~~~G~~i~~~~ 555 (652)
T PRK05298 526 EGFLRSERSLIQTIGRAARNVNGKVILYAD 555 (652)
T ss_pred cccCCCHHHHHHHhccccCCCCCEEEEEec
Confidence 44688999999999995 665555555544
No 69
>PRK02287 hypothetical protein; Provisional
Probab=38.09 E-value=25 Score=34.70 Aligned_cols=33 Identities=24% Similarity=0.205 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHhhcCChHHHHHhhhhcCccccC
Q 003062 556 ADVVEALIGAFLSTGGENVGLIFLDRIGIKVDF 588 (852)
Q Consensus 556 ADv~EAliGA~yl~~G~~~a~~~~~~l~~~~~~ 588 (852)
=.++||+.+|+|+.|..+.|.+++..|.-...|
T Consensus 107 Ls~vEAlAaaLyI~G~~~~A~~ll~~F~WG~~F 139 (171)
T PRK02287 107 LSSVEALAAALYILGFKEEAEKILSKFKWGHTF 139 (171)
T ss_pred ccHHHHHHHHHHHcCCHHHHHHHHhhCCChHHH
Confidence 358999999999999999999999887644444
No 70
>PTZ00110 helicase; Provisional
Probab=37.74 E-value=18 Score=43.10 Aligned_cols=22 Identities=18% Similarity=0.416 Sum_probs=19.4
Q ss_pred CCcchhhHHHHHhhcccccCCC
Q 003062 2 FDPSHTVCSFIQSRGRARMQNS 23 (852)
Q Consensus 2 FD~p~t~~syIQSRGRAR~~~S 23 (852)
||+|.+..+||||.|||-+.+.
T Consensus 452 ~d~P~s~~~yvqRiGRtGR~G~ 473 (545)
T PTZ00110 452 FDFPNQIEDYVHRIGRTGRAGA 473 (545)
T ss_pred eCCCCCHHHHHHHhcccccCCC
Confidence 8999999999999999876543
No 71
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=37.51 E-value=16 Score=41.91 Aligned_cols=29 Identities=14% Similarity=0.348 Sum_probs=21.8
Q ss_pred CCcchhhHHHHHhhcccccCCC--cEEEEEe
Q 003062 2 FDPSHTVCSFIQSRGRARMQNS--DYLLMLK 30 (852)
Q Consensus 2 FD~p~t~~syIQSRGRAR~~~S--~yi~m~e 30 (852)
||+|.+...|||+-|||-+.++ .-+.+++
T Consensus 320 ~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~~ 350 (434)
T PRK11192 320 FDMPRSADTYLHRIGRTGRAGRKGTAISLVE 350 (434)
T ss_pred ECCCCCHHHHhhcccccccCCCCceEEEEec
Confidence 8999999999999999855433 3344443
No 72
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=37.12 E-value=16 Score=42.34 Aligned_cols=22 Identities=14% Similarity=0.223 Sum_probs=19.2
Q ss_pred CCcchhhHHHHHhhcccccCCC
Q 003062 2 FDPSHTVCSFIQSRGRARMQNS 23 (852)
Q Consensus 2 FD~p~t~~syIQSRGRAR~~~S 23 (852)
||+|.+..+||||-|||-+.+.
T Consensus 317 ~d~p~~~~~yiqR~GRtGR~g~ 338 (460)
T PRK11776 317 YELARDPEVHVHRIGRTGRAGS 338 (460)
T ss_pred ecCCCCHhHhhhhcccccCCCC
Confidence 8999999999999999876543
No 73
>KOG0346 consensus RNA helicase [RNA processing and modification]
Probab=34.77 E-value=22 Score=40.04 Aligned_cols=21 Identities=38% Similarity=0.490 Sum_probs=17.7
Q ss_pred CCCcchhhHHHHHhhcccccC
Q 003062 1 MFDPSHTVCSFIQSRGRARMQ 21 (852)
Q Consensus 1 rFD~p~t~~syIQSRGRAR~~ 21 (852)
-||+|.|..|||.|=||--+-
T Consensus 377 NFD~P~t~~sYIHRvGRTaRg 397 (569)
T KOG0346|consen 377 NFDFPETVTSYIHRVGRTARG 397 (569)
T ss_pred ecCCCCchHHHHHhccccccC
Confidence 399999999999999984433
No 74
>PRK14741 spoVM stage V sporulation protein M; Provisional
Probab=33.60 E-value=29 Score=22.28 Aligned_cols=18 Identities=33% Similarity=0.717 Sum_probs=15.7
Q ss_pred CCCChhhHHHHHHHhhee
Q 003062 732 TSFPKALGDIIESLSGAI 749 (852)
Q Consensus 732 ~~~~k~laD~~EAliGAi 749 (852)
...||+++.++.|++||.
T Consensus 6 iklpkflgg~vra~l~~f 23 (26)
T PRK14741 6 IKLPKFLGGIVRAMLGSF 23 (26)
T ss_pred EeccHHHHHHHHHHHHHh
Confidence 467999999999999974
No 75
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=32.61 E-value=31 Score=39.58 Aligned_cols=28 Identities=18% Similarity=0.408 Sum_probs=20.7
Q ss_pred CCCcchhhHHHHHhhcccccCCCcEEEE
Q 003062 1 MFDPSHTVCSFIQSRGRARMQNSDYLLM 28 (852)
Q Consensus 1 rFD~p~t~~syIQSRGRAR~~~S~yi~m 28 (852)
+||.-.+-+-+||||||.=++.+=.|++
T Consensus 449 fYEpvpSeIR~IQR~GRTGR~r~Grv~v 476 (542)
T COG1111 449 FYEPVPSEIRSIQRKGRTGRKRKGRVVV 476 (542)
T ss_pred EecCCcHHHHHHHhhCccccCCCCeEEE
Confidence 5888899999999999975554433333
No 76
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=32.58 E-value=19 Score=41.72 Aligned_cols=20 Identities=10% Similarity=0.311 Sum_probs=18.0
Q ss_pred CCcchhhHHHHHhhcccccC
Q 003062 2 FDPSHTVCSFIQSRGRARMQ 21 (852)
Q Consensus 2 FD~p~t~~syIQSRGRAR~~ 21 (852)
||+|.+..+|||+-|||=+.
T Consensus 320 ~~~P~~~~~yvqR~GRaGR~ 339 (456)
T PRK10590 320 YELPNVPEDYVHRIGRTGRA 339 (456)
T ss_pred eCCCCCHHHhhhhccccccC
Confidence 89999999999999998654
No 77
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=30.85 E-value=33 Score=41.39 Aligned_cols=28 Identities=29% Similarity=0.489 Sum_probs=22.5
Q ss_pred CCcchhhHHHHHhhcccccC--CCcEEEEE
Q 003062 2 FDPSHTVCSFIQSRGRARMQ--NSDYLLML 29 (852)
Q Consensus 2 FD~p~t~~syIQSRGRAR~~--~S~yi~m~ 29 (852)
||+|.+..+|+|+-|||-+. .+.-++++
T Consensus 311 ~d~P~s~~~y~Qr~GRaGR~G~~~~~ill~ 340 (607)
T PRK11057 311 FDIPRNIESYYQETGRAGRDGLPAEAMLFY 340 (607)
T ss_pred eCCCCCHHHHHHHhhhccCCCCCceEEEEe
Confidence 79999999999999999665 35555553
No 78
>PF04034 DUF367: Domain of unknown function (DUF367); InterPro: IPR007177 This domain is found in a family of proteins of unknown function. It appears to be found in eukaryotes and archaebacteria, and occurs associated with a potential metal-binding region in RNase L inhibitor, RLI (IPR007209 from INTERPRO).
Probab=30.47 E-value=42 Score=31.34 Aligned_cols=33 Identities=24% Similarity=0.223 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHhhcCChHHHHHhhhhcCccccC
Q 003062 556 ADVVEALIGAFLSTGGENVGLIFLDRIGIKVDF 588 (852)
Q Consensus 556 ADv~EAliGA~yl~~G~~~a~~~~~~l~~~~~~ 588 (852)
=.|+||+.+|.|+.|=.+.|.+++..|.-...|
T Consensus 66 LscvEAlAAaLyI~G~~~~A~~lL~~FkWG~~F 98 (127)
T PF04034_consen 66 LSCVEALAAALYILGFKEQAEELLSKFKWGHTF 98 (127)
T ss_pred ccHHHHHHHHHHHcCCHHHHHHHHhcCCCcHHH
Confidence 358999999999999999999999888654444
No 79
>PTZ00424 helicase 45; Provisional
Probab=29.57 E-value=19 Score=40.79 Aligned_cols=21 Identities=19% Similarity=0.317 Sum_probs=18.8
Q ss_pred CCcchhhHHHHHhhcccccCC
Q 003062 2 FDPSHTVCSFIQSRGRARMQN 22 (852)
Q Consensus 2 FD~p~t~~syIQSRGRAR~~~ 22 (852)
||+|.+..+|+|+.|||.+.+
T Consensus 342 ~~~p~s~~~y~qr~GRagR~g 362 (401)
T PTZ00424 342 YDLPASPENYIHRIGRSGRFG 362 (401)
T ss_pred ECCCCCHHHEeecccccccCC
Confidence 799999999999999997654
No 80
>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.85 E-value=31 Score=40.15 Aligned_cols=27 Identities=26% Similarity=0.406 Sum_probs=21.6
Q ss_pred CCcchhhHHHHHhhcccccC--CCcEEEE
Q 003062 2 FDPSHTVCSFIQSRGRARMQ--NSDYLLM 28 (852)
Q Consensus 2 FD~p~t~~syIQSRGRAR~~--~S~yi~m 28 (852)
||+|+++.+|+|+-|||=+. .+..+++
T Consensus 301 ~~~P~s~~~y~Qr~GRaGR~G~~~~~~~~ 329 (470)
T TIGR00614 301 YSLPKSMESYYQESGRAGRDGLPSECHLF 329 (470)
T ss_pred eCCCCCHHHHHhhhcCcCCCCCCceEEEE
Confidence 79999999999999999765 3444444
No 81
>COG2042 Uncharacterized conserved protein [Function unknown]
Probab=24.57 E-value=65 Score=31.46 Aligned_cols=30 Identities=20% Similarity=0.174 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHhhcCChHHHHHhhhhcCcc
Q 003062 556 ADVVEALIGAFLSTGGENVGLIFLDRIGIK 585 (852)
Q Consensus 556 ADv~EAliGA~yl~~G~~~a~~~~~~l~~~ 585 (852)
=.++||+++|.|+-|-.+.|.+++..|.-.
T Consensus 115 Lss~EAlaAaLYI~G~~deA~~lls~F~WG 144 (179)
T COG2042 115 LSSAEALAAALYIVGFKDEASELLSKFKWG 144 (179)
T ss_pred hchHHHHHHHHHHhCcHHHHHHHHhhCccc
Confidence 357999999999999999999999877543
No 82
>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=22.61 E-value=1.7e+02 Score=24.12 Aligned_cols=39 Identities=15% Similarity=0.066 Sum_probs=29.4
Q ss_pred ceEEEEEEEECC----EEEEeEEeeCCHHHHHHHHHHHHHHHhh
Q 003062 807 KAAVTVEVHANG----TLFKHTHADADKETAKKVASKEVLKSLK 846 (852)
Q Consensus 807 ~~~~~~~v~v~~----~~i~~~g~g~s~k~Ak~~AA~~AL~~L~ 846 (852)
...|.+-|.+++ .-++ .|.+.+...|-++|-.+|.++|.
T Consensus 21 ~~~~~alvvvGn~~G~vG~G-~gKa~~~~~Ai~kA~~~A~knl~ 63 (67)
T PF00333_consen 21 IFSFRALVVVGNGNGLVGFG-VGKAKEVPDAIRKAKRKAKKNLI 63 (67)
T ss_dssp EEEEEEEEEEECSSSEEEEE-EEEESSHHHHHHHHHHHHHCSEE
T ss_pred eeEEEEEEEEecCCCcEecC-cccchhHHHHHHHHHHHHHhCCE
Confidence 356777777755 2233 78889999999999999987764
No 83
>PRK12898 secA preprotein translocase subunit SecA; Reviewed
Probab=21.98 E-value=42 Score=40.54 Aligned_cols=21 Identities=19% Similarity=0.045 Sum_probs=18.7
Q ss_pred CCcchhhHHHHHhhcccccCC
Q 003062 2 FDPSHTVCSFIQSRGRARMQN 22 (852)
Q Consensus 2 FD~p~t~~syIQSRGRAR~~~ 22 (852)
||+|.+.+.|+|++||+=+.+
T Consensus 554 ~d~P~s~r~y~hr~GRTGRqG 574 (656)
T PRK12898 554 TERHDSARIDRQLAGRCGRQG 574 (656)
T ss_pred cCCCCCHHHHHHhcccccCCC
Confidence 799999999999999986654
No 84
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=21.23 E-value=43 Score=40.11 Aligned_cols=20 Identities=15% Similarity=0.338 Sum_probs=17.9
Q ss_pred CCcchhhHHHHHhhcccccC
Q 003062 2 FDPSHTVCSFIQSRGRARMQ 21 (852)
Q Consensus 2 FD~p~t~~syIQSRGRAR~~ 21 (852)
||+|.+..+|||+-|||-+.
T Consensus 332 yd~P~s~~~yvqRiGRaGR~ 351 (572)
T PRK04537 332 YDLPFDAEDYVHRIGRTARL 351 (572)
T ss_pred cCCCCCHHHHhhhhcccccC
Confidence 89999999999999998553
No 85
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=20.93 E-value=44 Score=40.44 Aligned_cols=29 Identities=21% Similarity=0.360 Sum_probs=22.0
Q ss_pred CCcchhhHHHHHhhcccccCC--CcEEEEEe
Q 003062 2 FDPSHTVCSFIQSRGRARMQN--SDYLLMLK 30 (852)
Q Consensus 2 FD~p~t~~syIQSRGRAR~~~--S~yi~m~e 30 (852)
||+|.+..+|||+-|||=..+ ..-++++.
T Consensus 320 ~d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~ 350 (629)
T PRK11634 320 YDIPMDSESYVHRIGRTGRAGRAGRALLFVE 350 (629)
T ss_pred eCCCCCHHHHHHHhccccCCCCcceEEEEec
Confidence 799999999999999985443 34455543
No 86
>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional
Probab=20.66 E-value=70 Score=40.97 Aligned_cols=28 Identities=21% Similarity=0.296 Sum_probs=22.9
Q ss_pred CCcchhhHHHHHhhcccccC--CCcEEEEE
Q 003062 2 FDPSHTVCSFIQSRGRARMQ--NSDYLLML 29 (852)
Q Consensus 2 FD~p~t~~syIQSRGRAR~~--~S~yi~m~ 29 (852)
||+|+++.+|+|+-|||-+. .|.-|+++
T Consensus 755 ydlPkSiEsYyQriGRAGRDG~~g~cILly 784 (1195)
T PLN03137 755 HSLPKSIEGYHQECGRAGRDGQRSSCVLYY 784 (1195)
T ss_pred cCCCCCHHHHHhhhcccCCCCCCceEEEEe
Confidence 79999999999999999875 35555553
No 87
>PRK09200 preprotein translocase subunit SecA; Reviewed
Probab=20.33 E-value=47 Score=41.06 Aligned_cols=17 Identities=24% Similarity=0.216 Sum_probs=7.8
Q ss_pred CCcchhhHHHHHhhccc
Q 003062 2 FDPSHTVCSFIQSRGRA 18 (852)
Q Consensus 2 FD~p~t~~syIQSRGRA 18 (852)
||+|.+.+.|+|++||+
T Consensus 509 ~d~p~s~r~y~qr~GRt 525 (790)
T PRK09200 509 TERMESRRVDLQLRGRS 525 (790)
T ss_pred ccCCCCHHHHHHhhccc
Confidence 34444444444444444
No 88
>KOG4334 consensus Uncharacterized conserved protein, contains double-stranded RNA-binding motif and WW domain [General function prediction only]
Probab=20.30 E-value=3.2e+02 Score=31.36 Aligned_cols=67 Identities=16% Similarity=0.155 Sum_probs=40.4
Q ss_pred CChhhHHHHHHH-hCCC-ceeeEEeeecCCceEEEEEEEECCEEEEeEEeeCCHHHHHHHHHHHHHHHhhh
Q 003062 779 LQPARELNEYCQ-KHHF-SMKKTVAPRINGKAAVTVEVHANGTLFKHTHADADKETAKKVASKEVLKSLKA 847 (852)
Q Consensus 779 ~~P~~~L~e~~~-~~~~-~~~~~~~~~~~g~~~~~~~v~v~~~~i~~~g~g~s~k~Ak~~AA~~AL~~L~~ 847 (852)
..|-..|.+..+ .+|+ ....+..-..++...-.+...+|... ..+.+.+++++|+.|+++-|++|.-
T Consensus 490 psPy~iL~~cl~Rn~g~~d~~ik~E~i~~~nqkse~im~~Gkht--~~~~cknkr~gkQlASQ~ilq~lHP 558 (650)
T KOG4334|consen 490 PSPYNILRDCLSRNLGWNDLVIKKEMIGNGNQKSEVIMILGKHT--EEAECKNKRQGKQLASQRILQKLHP 558 (650)
T ss_pred CCHHHHHHHHHHhhcCCcceeeeeeccCCCCccceeEeeeccce--eeeeeechhHHHHHHHHHHHHHhCH
Confidence 466677777555 3455 22211111112222223334456654 3689999999999999999999864
Done!