Query psy8679
Match_columns 221
No_of_seqs 209 out of 290
Neff 4.1
Searched_HMMs 46136
Date Sat Aug 17 00:57:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8679.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8679hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3492|consensus 100.0 1.1E-90 2.4E-95 580.1 11.2 169 53-221 12-180 (180)
2 PF03657 UPF0113: Uncharacteri 100.0 3.1E-58 6.8E-63 385.3 3.9 147 54-216 15-162 (162)
3 COG1374 NIP7 Protein involved 100.0 1.4E-44 3E-49 306.6 5.5 157 56-218 15-176 (176)
4 KOG3492|consensus 99.9 5.4E-25 1.2E-29 185.0 4.0 77 3-90 15-91 (180)
5 PF03657 UPF0113: Uncharacteri 99.1 4.5E-11 9.7E-16 100.8 2.5 56 3-64 17-72 (162)
6 smart00359 PUA Putative RNA-bi 98.8 2E-08 4.4E-13 71.7 6.0 73 136-208 1-74 (77)
7 TIGR00451 unchar_dom_2 unchara 98.4 1.3E-06 2.8E-11 67.8 6.9 90 114-205 10-100 (107)
8 COG1374 NIP7 Protein involved 98.3 2.8E-07 6.1E-12 79.2 1.6 58 2-59 14-76 (176)
9 PRK14560 putative RNA-binding 98.2 5.1E-06 1.1E-10 69.0 6.6 88 116-205 58-146 (160)
10 TIGR03684 arCOG00985 arCOG0415 98.0 1.5E-05 3.2E-10 65.5 6.5 91 114-206 49-140 (150)
11 PF01472 PUA: PUA domain; Int 97.9 2.5E-05 5.3E-10 57.2 5.2 67 137-204 2-68 (74)
12 PRK13794 hypothetical protein; 97.8 0.0001 2.2E-09 71.1 9.5 108 102-209 85-199 (479)
13 PRK13534 7-cyano-7-deazaguanin 97.7 0.00014 3.1E-09 72.7 9.5 103 103-206 527-633 (639)
14 PRK13795 hypothetical protein; 97.4 0.00051 1.1E-08 68.4 8.3 101 103-204 88-194 (636)
15 COG5270 PUA domain (predicted 96.8 0.002 4.4E-08 56.5 4.8 97 102-198 90-191 (202)
16 COG1370 Prefoldin, molecular c 96.7 0.0057 1.2E-07 52.0 6.6 90 116-206 58-150 (155)
17 TIGR00432 arcsn_tRNA_tgt tRNA- 96.6 0.0045 9.7E-08 61.2 6.7 89 116-205 444-535 (540)
18 PF13636 Nol1_Nop2_Fmu_2: pre- 96.5 0.0062 1.3E-07 47.4 5.3 81 98-188 9-90 (102)
19 COG2016 Predicted RNA-binding 95.9 0.046 1E-06 46.8 8.3 85 114-199 56-141 (161)
20 PRK04270 H/ACA RNA-protein com 95.3 0.027 5.9E-07 51.6 4.9 70 136-206 226-295 (300)
21 PRK11933 yebU rRNA (cytosine-C 94.3 0.092 2E-06 51.1 6.1 102 76-189 351-453 (470)
22 PRK05429 gamma-glutamyl kinase 93.7 0.091 2E-06 49.3 4.6 71 129-199 272-345 (372)
23 TIGR00425 CBF5 rRNA pseudourid 93.5 0.11 2.3E-06 48.5 4.7 79 136-215 238-319 (322)
24 COG3270 Uncharacterized conser 93.5 0.12 2.6E-06 42.8 4.4 81 97-187 30-111 (127)
25 TIGR01027 proB glutamate 5-kin 91.7 0.26 5.6E-06 46.1 4.7 71 128-198 263-336 (363)
26 COG1549 Queuine tRNA-ribosyltr 90.3 0.79 1.7E-05 45.6 6.7 92 103-204 421-512 (519)
27 PRK08557 hypothetical protein; 86.6 1.1 2.4E-05 43.1 4.9 106 101-214 42-152 (417)
28 PRK13402 gamma-glutamyl kinase 70.2 6.5 0.00014 37.2 4.4 70 129-198 268-340 (368)
29 PRK15128 23S rRNA m(5)C1962 me 60.2 16 0.00034 34.8 4.9 49 137-190 4-58 (396)
30 PF09157 TruB-C_2: Pseudouridi 55.8 11 0.00023 26.0 2.2 45 138-188 3-47 (58)
31 COG0263 ProB Glutamate 5-kinas 46.4 26 0.00056 33.9 3.9 70 129-199 271-343 (369)
32 PRK14124 tRNA pseudouridine sy 42.0 27 0.00059 32.7 3.3 62 136-198 229-290 (308)
33 TIGR02624 rhamnu_1P_ald rhamnu 36.5 46 0.001 30.2 3.9 59 136-206 67-139 (270)
34 COG2092 EFB1 Translation elong 34.6 23 0.0005 27.8 1.4 19 170-188 32-50 (88)
35 PF02393 US22: US22 like; Int 32.6 1.5E+02 0.0032 22.7 5.6 76 21-96 28-114 (125)
36 PF12894 Apc4_WD40: Anaphase-p 32.1 31 0.00068 23.5 1.6 31 42-86 16-46 (47)
37 KOG2523|consensus 29.6 1.4E+02 0.0029 26.4 5.3 105 100-207 57-170 (181)
38 PRK11558 putative ssRNA endonu 27.0 51 0.0011 26.2 2.1 43 161-204 46-88 (97)
No 1
>KOG3492|consensus
Probab=100.00 E-value=1.1e-90 Score=580.11 Aligned_cols=169 Identities=64% Similarity=1.099 Sum_probs=165.7
Q ss_pred ecceecccccccccccccCCCCeeEEEeeCcEEEEEcHHHHhhhcccCCCCeeeeeeeeeeeeecceEEEEeeehhhhcc
Q psy8679 53 ALGTCFGNIGSNVKLLIDRPDGTYCFREMRDRVFYVSEKILTLAENFGPDHLLALGTCFGKFTKSGKFRLHITALSYLAP 132 (221)
Q Consensus 53 slGtc~GyiG~ni~~li~~~d~~y~frlhk~rVyYvs~~l~k~a~~i~r~~L~S~Gtc~GkFtKs~kFrl~ItaL~~La~ 132 (221)
-+-++.+|||+|+..||||||++||||+||||||||||.++++|++|+|+||+|+||||||||||+|||||||||+||||
T Consensus 12 vfekla~yIG~Nv~~lidr~D~~~cfrlhkdRVyyvsEr~~k~a~~isr~~L~s~Gtc~GKFTKt~kfrlhitaL~~La~ 91 (180)
T KOG3492|consen 12 VFEKLAKYIGDNVSHLIDRPDGTYCFRLHKDRVYYVSERIMKLAACISRKNLVSLGTCFGKFTKTGKFRLHITALDYLAP 91 (180)
T ss_pred HHHHHHHHHhhhhheeecCCCCceeeEeeCceEEeehHHHHHHHhhhcccceeEEeEEEeeeeccceEEEeeeehhhhhh
Confidence 35578899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcceEEEccCccceeecccccccccceeecccCCCcceEEEEecCCCeeeEEeeeechhHhhhcCCCcEEEEeccccee
Q psy8679 133 YAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGFNQSDIGE 212 (221)
Q Consensus 133 ~ak~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~akst~~~~~~dp~~ivv~~qaD~Ge 212 (221)
||+|||||||+|||+|||||||+|||++||||++|+|+|||||||+|+|||||++||||++||++||+++||+||||+||
T Consensus 92 ~Ak~KvWiKp~~Em~flYGNhvlKs~vgRitd~~p~~~GVvVysm~DvPLGFGv~Akst~d~r~~dp~aiv~~hQaDiGE 171 (180)
T KOG3492|consen 92 YAKYKVWIKPNAEMQFLYGNHVLKSGVGRITDGIPQHQGVVVYSMNDVPLGFGVTAKSTQDCRKADPTAIVVLHQADIGE 171 (180)
T ss_pred hhheeEEeccCcccceeecccchhcccceecCCCCCcceEEEEeccCCccccceeecCcccccccCCcEEEEEEecchHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeccccccC
Q psy8679 213 YIRCEDELC 221 (221)
Q Consensus 213 YLR~E~~l~ 221 (221)
|||+||+|.
T Consensus 172 YlR~E~~l~ 180 (180)
T KOG3492|consen 172 YLRNEDTLF 180 (180)
T ss_pred HhhcccccC
Confidence 999999973
No 2
>PF03657 UPF0113: Uncharacterised protein family (UPF0113); InterPro: IPR005155 This entry represents PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain containing proteins such as the ribosomal biogenesis factor NIP7 [, ]. PUA domains are predicted to bind RNA molecules with complex folded structures []. NIP7 is required for efficient 60S ribosome subunit biogenesis and has been shown to interact with another essential nucleolar protein, Nop8p, and the exosome subunit Rrp43p. These three proteins are required for 60S subunit synthesis and may be part of a dynamic complex involved in this process.; PDB: 1T5Y_A 1SQW_A 2P38_A.
Probab=100.00 E-value=3.1e-58 Score=385.26 Aligned_cols=147 Identities=60% Similarity=0.988 Sum_probs=126.8
Q ss_pred cceecccccccccccccCCCCeeEEEeeCcEEEEEcHHHHhhhcccCCCCeeeeeeeeeeeeecc-eEEEEeeehhhhcc
Q psy8679 54 LGTCFGNIGSNVKLLIDRPDGTYCFREMRDRVFYVSEKILTLAENFGPDHLLALGTCFGKFTKSG-KFRLHITALSYLAP 132 (221)
Q Consensus 54 lGtc~GyiG~ni~~li~~~d~~y~frlhk~rVyYvs~~l~k~a~~i~r~~L~S~Gtc~GkFtKs~-kFrl~ItaL~~La~ 132 (221)
+..+.+|.+++ ++++. ..+|||+|++||||||+++++.|++ +++++|+|||+|+|||++ ||+|||||+++||+
T Consensus 15 ~~kL~~yg~~~---~l~~~-~~~~~~~~~~~Vyyvs~~l~~~~~~--~~~~~s~G~~~G~f~k~~~kf~l~i~~l~~la~ 88 (162)
T PF03657_consen 15 FEKLSKYGGNN---LLDHF-DFYVFRLHKDRVYYVSEELMKLASN--RPNLYSLGTCLGKFTKKGKKFRLHITALDYLAP 88 (162)
T ss_dssp HHHHHCCCCGH---CCEET-EEEEEECCTCEEEEEEHHHHCCCTT--CHHHHCCSEEEEEE-TTTSEEEEEGHHHHCCCC
T ss_pred HHHHHHhcchh---hcccc-cceeeeeecceEEEECHHHHHHHhC--CCccceeceEEEEEecCCccceeeHHHHHHhhh
Confidence 34566774444 66655 5799999999999999999999998 899999999999999854 99999999999999
Q ss_pred cCcceEEEccCccceeecccccccccceeecccCCCcceEEEEecCCCeeeEEeeeechhHhhhcCCCcEEEEeccccee
Q psy8679 133 YAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGFNQSDIGE 212 (221)
Q Consensus 133 ~ak~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~akst~~~~~~dp~~ivv~~qaD~Ge 212 (221)
||++||||||+|||+|||||||+||||+||||++|+| ||||||||+||||| +++.+|++++|+||+|+||
T Consensus 89 ~~~~kvwvk~~~e~~FLYGndV~ks~i~~i~e~~~~~--VvV~n~~d~~LGfG--------~~~~~~~~~vv~~~~DiGe 158 (162)
T PF03657_consen 89 YAKNKVWVKPKAEMLFLYGNDVLKSSIGRITEDTPQN--VVVYNMNDVPLGFG--------CRKSDPDGKVVKNQADIGE 158 (162)
T ss_dssp C-SSEEEE-HHHHHHHCTT--EEGGGEEEEETTS-TC--EEEEETTS-EEEEE--------ECSTCHCCCCCECCEEGGG
T ss_pred ccceeEEECCCceEEeeecCCchHhhcEEecCCCCce--EEEEeCCCCeEEEE--------EeccCCCCEEEEEcCccee
Confidence 9999999999999999999999999999999999999 99999999999999 6688999999999999999
Q ss_pred eecc
Q psy8679 213 YIRC 216 (221)
Q Consensus 213 YLR~ 216 (221)
|||+
T Consensus 159 YLR~ 162 (162)
T PF03657_consen 159 YLRE 162 (162)
T ss_dssp T-S-
T ss_pred eecC
Confidence 9995
No 3
>COG1374 NIP7 Protein involved in ribosomal biogenesis, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-44 Score=306.61 Aligned_cols=157 Identities=38% Similarity=0.519 Sum_probs=149.2
Q ss_pred eecccccccccccccCC-CCeeEEE--ee-CcE-EEEEcHHHHhhhcccCCCCeeeeeeeeeeeeecceEEEEeeehhhh
Q psy8679 56 TCFGNIGSNVKLLIDRP-DGTYCFR--EM-RDR-VFYVSEKILTLAENFGPDHLLALGTCFGKFTKSGKFRLHITALSYL 130 (221)
Q Consensus 56 tc~GyiG~ni~~li~~~-d~~y~fr--lh-k~r-VyYvs~~l~k~a~~i~r~~L~S~Gtc~GkFtKs~kFrl~ItaL~~L 130 (221)
.+..|++++|..+++.. +..++|+ ++ ++| ||+|++...+.|+.++|+|++|+|||||+||++++||+|+++|++|
T Consensus 15 kl~~~e~~lI~~~l~~~g~~~~~f~~~~~~~~r~v~~V~~~~~~l~~~i~r~np~~~G~~~g~~~~~~~fR~~~~~l~~l 94 (176)
T COG1374 15 KLSSWEGDLIRKELSKYGELDHLFFHLLKVKDRDVYEVNEVVWKLAESIERKNPYSLGTFFGKRVKGGLFRKHVESLEEL 94 (176)
T ss_pred cchhHHHHHHHHHHHhccccchhhhhheeeccccEEEEeeehhhhhhcccccCcceeceeecccccCCeeeeehhhhHHH
Confidence 45678999999999877 5567777 66 888 9999999999999999999999999999999999999999999999
Q ss_pred cccCcceEEEccCccceeecccccccccceeecccCCCcceEEEEecCCCeeeEEeeeechhHhhhcCCCcEEEEecccc
Q psy8679 131 APYAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGFNQSDI 210 (221)
Q Consensus 131 a~~ak~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~akst~~~~~~dp~~ivv~~qaD~ 210 (221)
|+++.+|+||+|+|||+|||||| +|+|+.++++.+|++++|+||||||+|||||+++.|+++-+++-|++ |+|+
T Consensus 95 a~~~~~k~~v~~~~e~~FLYg~~-lkd~~~e~~~~~~~~~~v~V~~~nd~~lgiGvg~~s~~ed~~~i~~~-----l~D~ 168 (176)
T COG1374 95 ARIAIIKNYVKERGEMLFLYGND-LKDHVKEIIDEIPENGGVFVFNMNDVPLGIGVGALSPSEDGRLIKNA-----LKDV 168 (176)
T ss_pred HHHhheeeeeccCceeEEEeccc-cchhhhhhccccCCcceEEEEEcCCCceEEEecccCchhhccccccc-----cchh
Confidence 99999999999999999999999 99999999999999999999999999999999999999999999987 9999
Q ss_pred eeeecccc
Q psy8679 211 GEYIRCED 218 (221)
Q Consensus 211 GeYLR~E~ 218 (221)
|||||+|+
T Consensus 169 GeYLRr~~ 176 (176)
T COG1374 169 GEYLRRGG 176 (176)
T ss_pred hhhhhcCC
Confidence 99999985
No 4
>KOG3492|consensus
Probab=99.90 E-value=5.4e-25 Score=185.01 Aligned_cols=77 Identities=47% Similarity=0.820 Sum_probs=68.8
Q ss_pred cccccccccccccccCCCCceeEEEeCCeEEEEcHHHHhhhcccCcccceecceecccccccccccccCCCCeeEEEeeC
Q psy8679 3 QVIHNIGSNVKLLIDRPDGTYCFREMRDRVFYVSEKILTLAENFGPDHLLALGTCFGNIGSNVKLLIDRPDGTYCFREMR 82 (221)
Q Consensus 3 ~~~~yiG~n~~~li~r~d~~y~FRlhk~RVyYvse~i~k~At~i~r~~L~slGtc~GyiG~ni~~li~~~d~~y~frlhk 82 (221)
.+|.|||+|+++||||||++|||||||||||||||.+||+|++|+|+||+|+|||+|-.-+. .-||||=
T Consensus 15 kla~yIG~Nv~~lidr~D~~~cfrlhkdRVyyvsEr~~k~a~~isr~~L~s~Gtc~GKFTKt-----------~kfrlhi 83 (180)
T KOG3492|consen 15 KLAKYIGDNVSHLIDRPDGTYCFRLHKDRVYYVSERIMKLAACISRKNLVSLGTCFGKFTKT-----------GKFRLHI 83 (180)
T ss_pred HHHHHHhhhhheeecCCCCceeeEeeCceEEeehHHHHHHHhhhcccceeEEeEEEeeeecc-----------ceEEEee
Confidence 47899999999999999999999999999999999999999999999999999999866433 4799997
Q ss_pred cEEEEEcH
Q psy8679 83 DRVFYVSE 90 (221)
Q Consensus 83 ~rVyYvs~ 90 (221)
.-..|++.
T Consensus 84 taL~~La~ 91 (180)
T KOG3492|consen 84 TALDYLAP 91 (180)
T ss_pred eehhhhhh
Confidence 77666543
No 5
>PF03657 UPF0113: Uncharacterised protein family (UPF0113); InterPro: IPR005155 This entry represents PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain containing proteins such as the ribosomal biogenesis factor NIP7 [, ]. PUA domains are predicted to bind RNA molecules with complex folded structures []. NIP7 is required for efficient 60S ribosome subunit biogenesis and has been shown to interact with another essential nucleolar protein, Nop8p, and the exosome subunit Rrp43p. These three proteins are required for 60S subunit synthesis and may be part of a dynamic complex involved in this process.; PDB: 1T5Y_A 1SQW_A 2P38_A.
Probab=99.08 E-value=4.5e-11 Score=100.79 Aligned_cols=56 Identities=43% Similarity=0.773 Sum_probs=46.4
Q ss_pred cccccccccccccccCCCCceeEEEeCCeEEEEcHHHHhhhcccCcccceecceeccccccc
Q psy8679 3 QVIHNIGSNVKLLIDRPDGTYCFREMRDRVFYVSEKILTLAENFGPDHLLALGTCFGNIGSN 64 (221)
Q Consensus 3 ~~~~yiG~n~~~li~r~d~~y~FRlhk~RVyYvse~i~k~At~i~r~~L~slGtc~GyiG~n 64 (221)
.+++| |.|. ++++.+ .+|||+|++|||||||++++.|++ +++++|+|||+|-+|++
T Consensus 17 kL~~y-g~~~--~l~~~~-~~~~~~~~~~Vyyvs~~l~~~~~~--~~~~~s~G~~~G~f~k~ 72 (162)
T PF03657_consen 17 KLSKY-GGNN--LLDHFD-FYVFRLHKDRVYYVSEELMKLASN--RPNLYSLGTCLGKFTKK 72 (162)
T ss_dssp HHHCC-CCGH--CCEETE-EEEEECCTCEEEEEEHHHHCCCTT--CHHHHCCSEEEEEE-TT
T ss_pred HHHHh-cchh--hccccc-ceeeeeecceEEEECHHHHHHHhC--CCccceeceEEEEEecC
Confidence 35667 4444 666554 699999999999999999999999 99999999999999875
No 6
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=98.76 E-value=2e-08 Score=71.68 Aligned_cols=73 Identities=23% Similarity=0.299 Sum_probs=66.9
Q ss_pred ceEEEccCccceeecccccccccceeecccCCCcceEEEEecCCCeeeEEeeeechhHhhhcC-CCcEEEEecc
Q psy8679 136 FKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLAD-PLAIVGFNQS 208 (221)
Q Consensus 136 ~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~akst~~~~~~d-p~~ivv~~qa 208 (221)
.+++|++++++.+++|..|+.++|.+++.++...+-|.|++.++.|||.|.+..++.++.++. +.++++..+.
T Consensus 1 ~~i~v~~~~~~~i~~g~~v~~~~v~~~~~~~~~g~~V~v~~~~g~~vg~G~~~~~s~~~~~~~~~~g~~v~~~~ 74 (77)
T smart00359 1 GKVVVDDGAVKAILNGASLLAPGVVRVDGGIKEGDVVVIVDEKGEPLGIGLANMSSEEMARIKGEKGLAVKVRR 74 (77)
T ss_pred CEEEEchhHHHHHHcCCCcccceeEEEeCCcCCCCEEEEEcCCCCEEEEEEEeCCHHHHHHHhccCceEEEEEE
Confidence 379999999999999999999999999999999999999999999999999999999999987 6677776554
No 7
>TIGR00451 unchar_dom_2 uncharacterized domain 2. This uncharacterized domain is found a number of enzymes and uncharacterized proteins, often at the C-terminus. It is found in some but not all members of a family of related tRNA-guanine transglycosylases (tgt), which exchange a guanine base for some modified base without breaking the phosphodiester backbone of the tRNA. It is also found in rRNA pseudouridine synthase, another enzyme of RNA base modification not otherwise homologous to tgt. It is found, again at the C-terminus, in two putative glutamate 5-kinases. It is also found in a family of small, uncharacterized archaeal proteins consisting mostly of this domain.
Probab=98.36 E-value=1.3e-06 Score=67.82 Aligned_cols=90 Identities=23% Similarity=0.249 Sum_probs=76.7
Q ss_pred eeecceEEEEeeehhhhcccCcceEEEccCccceeecccccccccceeecccCCCcceEEEEecC-CCeeeEEeeeechh
Q psy8679 114 FTKSGKFRLHITALSYLAPYAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMN-DVPLGFGVAAKSTA 192 (221)
Q Consensus 114 FtKs~kFrl~ItaL~~La~~ak~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~n-d~pLGFGv~akst~ 192 (221)
|...++|.+++.++..+-. ...+|+|++++...-+.|.+++..+|...++++.+++-|.|++.+ +.|+|.|++..|+.
T Consensus 10 ~~~~~~~~ptl~~~~~~~~-~~~~v~vd~~a~~~l~~Ga~L~~pGV~~~~~~~~~gd~V~I~~~~~~~~iavG~a~~~s~ 88 (107)
T TIGR00451 10 FIYDDKVIPSLKGALKLME-DKKIVVVDNGAVKFLKNGADVMRPGIVDADEDIKEGDDVVVVDENKDRPLAVGIALMSGE 88 (107)
T ss_pred EEECCeEcccHHHHHhChh-hCCEEEEChhHHHHHHCCccccCCeeEeCCCCcCCCCEEEEEECCCCeEEEEEEEecCHH
Confidence 3345689999988865544 368999999988766799999999999999999999999999987 89999999999999
Q ss_pred HhhhcCCCcEEEE
Q psy8679 193 ECKLADPLAIVGF 205 (221)
Q Consensus 193 ~~~~~dp~~ivv~ 205 (221)
|++..+ .+++|.
T Consensus 89 e~~~~~-~G~~v~ 100 (107)
T TIGR00451 89 EMKEMD-KGKAVK 100 (107)
T ss_pred HHHhcC-CCeEEE
Confidence 999884 466654
No 8
>COG1374 NIP7 Protein involved in ribosomal biogenesis, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=98.27 E-value=2.8e-07 Score=79.19 Aligned_cols=58 Identities=26% Similarity=0.350 Sum_probs=53.7
Q ss_pred ccccccccccccccccCC-CCceeEE--Ee-CCe-EEEEcHHHHhhhcccCcccceecceecc
Q psy8679 2 NQVIHNIGSNVKLLIDRP-DGTYCFR--EM-RDR-VFYVSEKILTLAENFGPDHLLALGTCFG 59 (221)
Q Consensus 2 ~~~~~yiG~n~~~li~r~-d~~y~FR--lh-k~R-VyYvse~i~k~At~i~r~~L~slGtc~G 59 (221)
.+.++++|++|..+++.. +..++|+ ++ ++| ||+|++...++|++|+|.|+.|+|||+|
T Consensus 14 rkl~~~e~~lI~~~l~~~g~~~~~f~~~~~~~~r~v~~V~~~~~~l~~~i~r~np~~~G~~~g 76 (176)
T COG1374 14 RKLSSWEGDLIRKELSKYGELDHLFFHLLKVKDRDVYEVNEVVWKLAESIERKNPYSLGTFFG 76 (176)
T ss_pred ccchhHHHHHHHHHHHhccccchhhhhheeeccccEEEEeeehhhhhhcccccCcceeceeec
Confidence 467899999999999988 6678998 77 999 9999999999999999999999999998
No 9
>PRK14560 putative RNA-binding protein; Provisional
Probab=98.16 E-value=5.1e-06 Score=69.02 Aligned_cols=88 Identities=16% Similarity=0.109 Sum_probs=77.7
Q ss_pred ecceEEEEeeehhhhcccCcceEEEccCccceeecccccccccceeecccCCCcceEEEEecC-CCeeeEEeeeechhHh
Q psy8679 116 KSGKFRLHITALSYLAPYAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMN-DVPLGFGVAAKSTAEC 194 (221)
Q Consensus 116 Ks~kFrl~ItaL~~La~~ak~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~n-d~pLGFGv~akst~~~ 194 (221)
.++.|.+++.++..+ |....+|.|.+.+....+.|.+++..||..+++++.+++-|+|++.+ +.|+|.|.+.-|+.++
T Consensus 58 ~d~~~~Ptl~~~~~~-~~~~~~v~Vd~~a~~~i~~Ga~lm~pGV~~~~~~~~~Gd~V~I~~~~~~~~vavG~~~~s~~ei 136 (160)
T PRK14560 58 VDDELFPTLRGALKL-KPEKRRVVVDAGAVKFVSNGADVMAPGIVEADEDIKEGDIVFVVEETHGKPLAVGRALMDGDEM 136 (160)
T ss_pred eCCcccccHHHHHhC-CccCCEEEEeccHHHHHHCCCceecCeeeeCCCCCCCCCEEEEEECCCCeEEEEEEEeeCHHHH
Confidence 367899999998877 66678999999988888899999999999999999999999999987 9999999999999999
Q ss_pred hhcCCCcEEEE
Q psy8679 195 KLADPLAIVGF 205 (221)
Q Consensus 195 ~~~dp~~ivv~ 205 (221)
+..+ .|++|.
T Consensus 137 ~~~~-kG~~v~ 146 (160)
T PRK14560 137 VEEK-KGKAVK 146 (160)
T ss_pred hhcC-CceEEE
Confidence 8644 466654
No 10
>TIGR03684 arCOG00985 arCOG04150 universal archaeal PUA-domain protein. This universal archaeal protein contains a domain possibly associated with RNA binding (pfam01472, TIGR00451).
Probab=98.01 E-value=1.5e-05 Score=65.48 Aligned_cols=91 Identities=22% Similarity=0.277 Sum_probs=78.8
Q ss_pred eeecceEEEEeeehhhhcccCcceEEEccCccceeecccccccccceeecccCCCcceEEEEecC-CCeeeEEeeeechh
Q psy8679 114 FTKSGKFRLHITALSYLAPYAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMN-DVPLGFGVAAKSTA 192 (221)
Q Consensus 114 FtKs~kFrl~ItaL~~La~~ak~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~n-d~pLGFGv~akst~ 192 (221)
|..++.|.+++.++..+.+ ...+|.|++.+...-+-|.|++..+|..+++++..++-|+|++.+ +.|+|.|.+.-|++
T Consensus 49 ~~~~~~~~Ptl~~~~~~~~-~~~~v~Vd~~a~~~l~~Ga~lm~pGV~~~~~~~~~Gd~V~I~~~~~~~~vavG~a~~ss~ 127 (150)
T TIGR03684 49 FEKDGRLIPTLYLLLELNP-DKNRVVVDEGAVKFIINGADIMAPGIVSADPSIKEGDIVFVVDETHRKPLAVGIALMDAE 127 (150)
T ss_pred EEeCCcccccHHHHHhCCc-cCCEEEECccHHHHHhcCcccccCceecCCCCCCCCCEEEEEECCCCeEEEEEEEeeCHH
Confidence 5557899999988876643 578999999988877899999999999999999999999999988 99999999999999
Q ss_pred HhhhcCCCcEEEEe
Q psy8679 193 ECKLADPLAIVGFN 206 (221)
Q Consensus 193 ~~~~~dp~~ivv~~ 206 (221)
+++... .|++|.+
T Consensus 128 ei~~~~-kG~av~~ 140 (150)
T TIGR03684 128 EMEEEK-KGKAVKN 140 (150)
T ss_pred HHhhcC-CCeEEEE
Confidence 998654 4666543
No 11
>PF01472 PUA: PUA domain; InterPro: IPR002478 The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found []. PUA is a highly conserved RNA-binding motif found in a wide range of archaeal, bacterial and eukaryotic proteins, including enzymes that catalyse tRNA and rRNA post-transcriptional modifications, proteins involved in ribosome biogenesis and translation, as well as in enzymes involved in proline biosynthesis [, ]. The structures of several PUA-RNA complexes reveal a common RNA recognition surface, but also some versatility in the way in which the motif binds to RNA []. PUA motifs are involved in dyskeratosis congenita and cancer, pointing to links between RNA metabolism and human diseases [].; GO: 0003723 RNA binding; PDB: 1ZE2_A 1ZE1_A 1R3E_A 2AB4_A 3R90_D 2J5T_A 2J5V_B 1Q7H_A 2APO_A 2RFK_A ....
Probab=97.89 E-value=2.5e-05 Score=57.17 Aligned_cols=67 Identities=19% Similarity=0.246 Sum_probs=59.8
Q ss_pred eEEEccCccceeecccccccccceeecccCCCcceEEEEecCCCeeeEEeeeechhHhhhcCCCcEEE
Q psy8679 137 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVG 204 (221)
Q Consensus 137 Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~akst~~~~~~dp~~ivv 204 (221)
+|||+.++....+.|.+++-.||.++.+++++.+-|.|++.++.++|.|.+..|..++.++.. +..+
T Consensus 2 ~vvVd~~a~~~i~~Ga~L~~~GV~~~~~~f~~gd~V~i~~~~g~~ia~G~a~~ss~ei~~~~~-g~~~ 68 (74)
T PF01472_consen 2 RVVVDDGAVEAILNGASLFAPGVVEVDGDFRKGDEVAIVDEDGEVIAVGRANMSSEEIKKMKK-GKAV 68 (74)
T ss_dssp EEEE-HHHHHHHHTTSEEEGGGEEEEETT--TTSEEEEEETTSSEEEEEEESSTHHHHHHHSS-SEEE
T ss_pred EEEECccHHHHHHcCCCcchHHhEECCCCcCCCCEEEEEcCCCeEEEEEEEecCHHHHHHHcC-CcEe
Confidence 689999999999999999999999999999999999999999999999999999999999984 4544
No 12
>PRK13794 hypothetical protein; Provisional
Probab=97.81 E-value=0.0001 Score=71.12 Aligned_cols=108 Identities=22% Similarity=0.273 Sum_probs=83.5
Q ss_pred CCeeeeeeeeeeee---ecce--EEEEeeehhhhcccC-cceEEEccCccceee-cccccccccceeecccCCCcceEEE
Q psy8679 102 DHLLALGTCFGKFT---KSGK--FRLHITALSYLAPYA-QFKVWVKPQAEQQFL-YGHNILKSGLARITENTPKYQGVIV 174 (221)
Q Consensus 102 ~~L~S~Gtc~GkFt---Ks~k--Frl~ItaL~~La~~a-k~Kvwvk~~gE~~FL-YGn~V~Ks~l~rite~~~~~~GVvV 174 (221)
++++.=|..+|-+. ..++ |.|++.+...|-+.+ +.+|.|++.+...-+ .|.+|+..||..+++++..++-|+|
T Consensus 85 ~eVi~dg~~l~~l~~~~~~~~w~~~l~~~ga~~l~~~~~~~~V~Vd~ga~~~v~~~G~~v~~~GV~~~~~~i~~gd~V~I 164 (479)
T PRK13794 85 EEIIVDGAVVGIIRYNEKKHRWKIIPRPEGARRLIPTAKKKFIVVKDDVPKFIRNKGASVLRPGVAEASEDIEEGDDVII 164 (479)
T ss_pred eEEEECCEEEEEEEeccccceeEEecCHHHHHHhhhccCCcEEEECccHHHHHHhCCCeecCCceEEecCCcCCCCEEEE
Confidence 45566688888732 3455 555666666665543 578999976666555 8999999999999999999999999
Q ss_pred EecCCCeeeEEeeeechhHhhhcCCCcEEEEeccc
Q psy8679 175 LNMNDVPLGFGVAAKSTAECKLADPLAIVGFNQSD 209 (221)
Q Consensus 175 ~n~nd~pLGFGv~akst~~~~~~dp~~ivv~~qaD 209 (221)
.+.+|.++|.|++.-|+.+++..+..-+|=.+.++
T Consensus 165 v~~~g~~iavG~a~~s~~ei~~~~~G~~Vkvr~~~ 199 (479)
T PRK13794 165 LDENGDVVGVGRARMSYEEIVNMEKGMVVKVRKSE 199 (479)
T ss_pred EcCCCcEEEEEEeecCHHHHHhccCceEEEEEecc
Confidence 99999999999999999999998775443333434
No 13
>PRK13534 7-cyano-7-deazaguanine tRNA-ribosyltransferase; Provisional
Probab=97.74 E-value=0.00014 Score=72.71 Aligned_cols=103 Identities=19% Similarity=0.259 Sum_probs=87.6
Q ss_pred Ceeeeeeeeeeee-ecceEEEEeeehhhhc---ccCcceEEEccCccceeecccccccccceeecccCCCcceEEEEecC
Q psy8679 103 HLLALGTCFGKFT-KSGKFRLHITALSYLA---PYAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMN 178 (221)
Q Consensus 103 ~L~S~Gtc~GkFt-Ks~kFrl~ItaL~~La---~~ak~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~n 178 (221)
+++.=|..++-+. ..|.|.|++.|...|- ++.+++|.|++.++..-.=|.+|+..||...++++..++-|+|.+.+
T Consensus 527 ~I~vdg~~l~~l~~~dg~~~pt~~GA~~l~~~~~~~~~~V~Vd~~a~~~v~~G~~v~apgVv~~d~~ir~gDeV~Vv~e~ 606 (639)
T PRK13534 527 QVLDKGEILATMRANDGFLILSKEGAKRLHEKLPFPKYRVVVDKESEPFARKGKSVFAKFVIDCDEEIRPYDEVLVVNED 606 (639)
T ss_pred EEEECCEEEEEEEecCCEEEEcHHHHHHHHhccCCCCcEEEECCcchhhhhCCCcccCCcceecCCCCCCCCEEEEEecC
Confidence 3444488888776 6789999999988884 34468999998888877789999999999999999999999999999
Q ss_pred CCeeeEEeeeechhHhhhcCCCcEEEEe
Q psy8679 179 DVPLGFGVAAKSTAECKLADPLAIVGFN 206 (221)
Q Consensus 179 d~pLGFGv~akst~~~~~~dp~~ivv~~ 206 (221)
|.|||.|++.-|..|+...+. |++|..
T Consensus 607 ~~~lavG~A~~~~~em~~~~~-G~avkv 633 (639)
T PRK13534 607 DELLAYGKALLNGRELMEFNY-GLAVKV 633 (639)
T ss_pred CcEEEEEEEecCHHHHhhcCC-ceEEEE
Confidence 999999999999999998755 566643
No 14
>PRK13795 hypothetical protein; Provisional
Probab=97.41 E-value=0.00051 Score=68.39 Aligned_cols=101 Identities=18% Similarity=0.165 Sum_probs=81.7
Q ss_pred Ceeeeeeeeee--ee---ecceEEEEeeehhhhc-ccCcceEEEccCccceeecccccccccceeecccCCCcceEEEEe
Q psy8679 103 HLLALGTCFGK--FT---KSGKFRLHITALSYLA-PYAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLN 176 (221)
Q Consensus 103 ~L~S~Gtc~Gk--Ft---Ks~kFrl~ItaL~~La-~~ak~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n 176 (221)
.++.=|..+|- |. ...+|.|++.|...|. +..+.+|.|+..+...-.-|.+|+..||..+++++..++-|+|.+
T Consensus 88 ~vivdg~~~~~l~fd~~~~~~~~~p~l~ga~~l~~~~~~~~VvVd~ga~~~v~~Ga~l~~~GI~~~~~~i~~gd~V~I~~ 167 (636)
T PRK13795 88 EIIVDGRVIGHLRFDLLELRWRFEPRLEGAKRLLKKRLKKWVIVDKGALEPIKNGKNVLAPGVVEADLDIKKGDEVVVVT 167 (636)
T ss_pred EEEECCEEEEEEEeecccccceEecCHHHHHHHhhccCCcEEEEcccHHHHHHcCCcccCCceEEEeCCCCCCCEEEEEe
Confidence 34445677773 32 2336778887666664 466799999988877777999999999999999999999999999
Q ss_pred cCCCeeeEEeeeechhHhhhcCCCcEEE
Q psy8679 177 MNDVPLGFGVAAKSTAECKLADPLAIVG 204 (221)
Q Consensus 177 ~nd~pLGFGv~akst~~~~~~dp~~ivv 204 (221)
.++.++|.|++.-|+.+++..+.. ++|
T Consensus 168 e~g~~vavG~a~~s~~e~~~~~kG-~~V 194 (636)
T PRK13795 168 EDGEVVGVGRAKMDGDDMIKRFRG-RAV 194 (636)
T ss_pred CCCCEEEEEEeccCHHHHhhccCC-eEE
Confidence 999999999999999999988664 444
No 15
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=96.77 E-value=0.002 Score=56.49 Aligned_cols=97 Identities=24% Similarity=0.315 Sum_probs=85.4
Q ss_pred CCeeeeeeeeeee--e--ecc-eEEEEeeehhhhcccCcceEEEccCccceeecccccccccceeecccCCCcceEEEEe
Q psy8679 102 DHLLALGTCFGKF--T--KSG-KFRLHITALSYLAPYAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLN 176 (221)
Q Consensus 102 ~~L~S~Gtc~GkF--t--Ks~-kFrl~ItaL~~La~~ak~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n 176 (221)
+.++--|-.||-. . |-+ +|+|..++.-.|-.--+.=+||+-+++..-.-|.||+.-+|...++++++++-|+|.+
T Consensus 90 dEIvvdG~i~g~i~fd~~k~rW~~~lk~eGAk~L~e~~~k~~~i~~~~~E~~~Ng~nV~~~gV~e~~~~i~~~d~viVv~ 169 (202)
T COG5270 90 DEIVVDGFIFGIIRFDLRKLRWRFGLKLEGAKLLLEKGKKGRKIDRGAVEPVKNGKNVLPPGVIEAEDSIERGDEVIVVS 169 (202)
T ss_pred ceEEecceEEEEEEecchhcccccccChHHHHHHHHhcCccEEEEcccchhhhccCcccCCceeeccCCcccCCeEEEEe
Confidence 5788888888843 2 222 8999999988887766778999999999999999999999999999999999999999
Q ss_pred cCCCeeeEEeeeechhHhhhcC
Q psy8679 177 MNDVPLGFGVAAKSTAECKLAD 198 (221)
Q Consensus 177 ~nd~pLGFGv~akst~~~~~~d 198 (221)
.|+.+.|+|.+.+|..+..+-.
T Consensus 170 ~ng~~vGVg~a~~~~~~~in~~ 191 (202)
T COG5270 170 ENGRVVGVGIAKKSYEELINPE 191 (202)
T ss_pred cCCEEEEEEEEecCHHHhcCcc
Confidence 9999999999999999887765
No 16
>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones]
Probab=96.67 E-value=0.0057 Score=51.96 Aligned_cols=90 Identities=23% Similarity=0.266 Sum_probs=79.0
Q ss_pred ecceEEEEeeehhhhcc---cCcceEEEccCccceeecccccccccceeecccCCCcceEEEEecCCCeeeEEeeeechh
Q psy8679 116 KSGKFRLHITALSYLAP---YAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTA 192 (221)
Q Consensus 116 Ks~kFrl~ItaL~~La~---~ak~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~akst~ 192 (221)
.+|-|.|++++-..|-. +.+++|.|...+|---=-|++||-.++....|++-.++=|+|.|.+|..|+-|.+.-|..
T Consensus 58 ~DG~~tL~~~Ga~~L~~~l~~P~~RVvV~~E~e~f~r~Gk~VFaKfVi~~D~~iR~~dEvlVVne~d~LlAvGra~ls~~ 137 (155)
T COG1370 58 NDGLFTLTIEGARRLHRALPFPRMRVVVSDEAEEFVRKGKSVFAKFVIDVDEEIRAGDEVLVVNEDDELLAVGRALLSGA 137 (155)
T ss_pred CCceEEechhhhHHHHhcCCCCceEEEeccccHHHHHhccchhhhheeccCcccCCCCeEEEECCCCcEEEeeeEeecHH
Confidence 46778889988777754 777999999888876679999999999999999999999999999999999999999999
Q ss_pred HhhhcCCCcEEEEe
Q psy8679 193 ECKLADPLAIVGFN 206 (221)
Q Consensus 193 ~~~~~dp~~ivv~~ 206 (221)
|++.++- |+.|.-
T Consensus 138 E~~~~~~-G~AVkV 150 (155)
T COG1370 138 EMREFER-GMAVKV 150 (155)
T ss_pred HHhhccc-cEEEEE
Confidence 9999886 555543
No 17
>TIGR00432 arcsn_tRNA_tgt tRNA-guanine transglycosylase, archaeosine-15-forming. This tRNA-guanine transglycosylase (tgt) differs from the tgt of E. coli and other Bacteria in the site of action and the modification that results. It exchanges 7-cyano-7-deazaguanine (preQ0) with guanine at position 15 of archaeal tRNA; this nucleotide is subsequently converted to archaeosine, found exclusively in the Archaea. This enzyme from Haloferax volcanii has been purified, characterized, and partially sequenced and is the basis for identifying this family. In contrast, bacterial tgt catalyzes the exchange of preQ0 or preQ1 for the guanine base at position 34; this nucleotide is subsequently modified to queuosine. Archeoglobus fulgidus has both enzymes, while some other Archaea have just this one.
Probab=96.63 E-value=0.0045 Score=61.19 Aligned_cols=89 Identities=18% Similarity=0.165 Sum_probs=78.9
Q ss_pred ecceEEEEeeehhhhcc---cCcceEEEccCccceeecccccccccceeecccCCCcceEEEEecCCCeeeEEeeeechh
Q psy8679 116 KSGKFRLHITALSYLAP---YAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTA 192 (221)
Q Consensus 116 Ks~kFrl~ItaL~~La~---~ak~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~akst~ 192 (221)
..|-|.|++.+-..|.. +.+++|+|++..+.-|.=|++||-.||....+++-.++=|+|.+.+|..||.|.+.-|..
T Consensus 444 ~dg~l~lt~~Ga~~l~~~~~~p~~rV~v~~~~~~f~~~g~~vfak~V~~ad~~IR~~dEV~vv~~~~~llavGra~lsg~ 523 (540)
T TIGR00432 444 SDGLLVLGAEGAVRLHKGTDYPAWRVAVNEESEPFARKGKSVFAKFIIDCDNNIRANDEVLIVNADDELLATGKALLCAE 523 (540)
T ss_pred CCCeEEeCHHHHHHHHhcCCCCceEEEECCcchhhccCCCcccCCccccCCCCCCCCCeEEEEcCCCcEEEEEehhcCHH
Confidence 46788888888877744 446999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhcCCCcEEEE
Q psy8679 193 ECKLADPLAIVGF 205 (221)
Q Consensus 193 ~~~~~dp~~ivv~ 205 (221)
|+...+. |+.|.
T Consensus 524 em~~~~~-G~AVk 535 (540)
T TIGR00432 524 EMMDLNH-GQAVK 535 (540)
T ss_pred HHHhhcC-ceEEE
Confidence 9998876 45543
No 18
>PF13636 Nol1_Nop2_Fmu_2: pre-rRNA processing and ribosome biogenesis; PDB: 3M4X_A 3M6U_B 3M6V_B 3M6W_A 3M6X_A.
Probab=96.48 E-value=0.0062 Score=47.35 Aligned_cols=81 Identities=20% Similarity=0.327 Sum_probs=58.3
Q ss_pred ccCCCCeeeeeeeeeeeeecceEEEEeeehhhhcccCc-ceEEEccCccceeecccccccccceeecccCCCcceEEEEe
Q psy8679 98 NFGPDHLLALGTCFGKFTKSGKFRLHITALSYLAPYAQ-FKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLN 176 (221)
Q Consensus 98 ~i~r~~L~S~Gtc~GkFtKs~kFrl~ItaL~~La~~ak-~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n 176 (221)
.+++-++...|+-+|++.| +.|+++-...-.+.+.+. +.|=++..--..||-|.++--+. ...|-++..
T Consensus 9 ~~~~l~v~r~Gl~lg~~~k-~~f~Ps~~la~~~~~~~~~~~iel~~e~a~~yl~Ge~i~~~~---------~~~G~vlv~ 78 (102)
T PF13636_consen 9 DLPGLKVLRAGLYLGEIKK-NRFEPSHALAMALGPEATKNVIELDDEQALRYLRGEDIELDP---------PDKGWVLVT 78 (102)
T ss_dssp --TTSEECECSEEEEEEET-TEEEEBHHHHHCB--GCCS-EEEETCHHHHHHHCT--EE-SS-----------EEEEEEE
T ss_pred ccCCCeEEecCcEeeeEeC-CcEEECHHHHHhhCccccceEEECCHHHHHHHHcCCcccCCC---------CCCcEEEEE
Confidence 3455589999999999976 899999988888877764 66777766667899999983332 367777777
Q ss_pred cCCCeeeEEeee
Q psy8679 177 MNDVPLGFGVAA 188 (221)
Q Consensus 177 ~nd~pLGFGv~a 188 (221)
-.+.|||||...
T Consensus 79 ~~g~~LG~gk~~ 90 (102)
T PF13636_consen 79 YEGFPLGWGKYV 90 (102)
T ss_dssp ECCCEEEEEEEE
T ss_pred ECCEeeEEEEee
Confidence 789999999984
No 19
>COG2016 Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis]
Probab=95.95 E-value=0.046 Score=46.80 Aligned_cols=85 Identities=21% Similarity=0.325 Sum_probs=74.7
Q ss_pred eeecceEEEEeeehhhhcccCcceEEEccCccceeecccccccccceeecccCCCcceEEEEecC-CCeeeEEeeeechh
Q psy8679 114 FTKSGKFRLHITALSYLAPYAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMN-DVPLGFGVAAKSTA 192 (221)
Q Consensus 114 FtKs~kFrl~ItaL~~La~~ak~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~n-d~pLGFGv~akst~ 192 (221)
|...++.-+++-+|..+-+ +++.|-|...|...-+-|-||+.-||-...+++++.+.|||-... +-||..|++--|..
T Consensus 56 f~~~~~~iPTl~~l~~~~~-~~~~V~VD~GAvk~v~nGADvM~PGIv~~~~~ik~Gd~VvV~~e~~~~plAVG~alm~~~ 134 (161)
T COG2016 56 FQRDDRLIPTLRLLLKLPP-GKYVVVVDEGAVKFVLNGADVMAPGIVSADGEIKEGDIVVVVDEKKGRPLAVGIALMSGK 134 (161)
T ss_pred EEeCCeechhhHHHHhCCC-CccEEEEcCccHhhhcCCCceeccceeecCCCccCCCEEEEEEcCCCCeeEEEeeccCHH
Confidence 6666677777777776655 346999999999999999999999999999999999999999998 99999999999999
Q ss_pred HhhhcCC
Q psy8679 193 ECKLADP 199 (221)
Q Consensus 193 ~~~~~dp 199 (221)
|+...+.
T Consensus 135 em~~~~k 141 (161)
T COG2016 135 EMEEKKK 141 (161)
T ss_pred HHhhhcC
Confidence 9987665
No 20
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=95.29 E-value=0.027 Score=51.59 Aligned_cols=70 Identities=21% Similarity=0.193 Sum_probs=60.3
Q ss_pred ceEEEccCccceeecccccccccceeecccCCCcceEEEEecCCCeeeEEeeeechhHhhhcCCCcEEEEe
Q psy8679 136 FKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGFN 206 (221)
Q Consensus 136 ~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~akst~~~~~~dp~~ivv~~ 206 (221)
-++.|.+.+...+..|+++...++.++.++....+-|+|++.++.++|.|.+..|++++++. +.|++|..
T Consensus 226 P~V~Lde~aa~~I~nG~~L~~~gi~~~~~~~~~gd~V~I~~~~G~~LAIG~~~~ss~el~~~-~kG~~vk~ 295 (300)
T PRK04270 226 PKIIIKDSAVDAIAHGAPLYAPGIAKLEKGIKKGDLVAVFTLKGELVALGKALMDSDEILKA-EKGIVVDL 295 (300)
T ss_pred CceEECHHHHHHHHcCCccccCCceecccccCCCCEEEEEeCCCcEEEEEEEccCHHHHHhc-CCceEEEE
Confidence 47888888888889999999888888877776777799999999999999999999999998 66787753
No 21
>PRK11933 yebU rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
Probab=94.33 E-value=0.092 Score=51.09 Aligned_cols=102 Identities=16% Similarity=0.252 Sum_probs=72.3
Q ss_pred eEEEeeCcEEEEEcHHHHhhhcccCCCCeeeeeeeeeeeeecceEEEEeeehhhhcc-cCcceEEEccCccceeeccccc
Q psy8679 76 YCFREMRDRVFYVSEKILTLAENFGPDHLLALGTCFGKFTKSGKFRLHITALSYLAP-YAQFKVWVKPQAEQQFLYGHNI 154 (221)
Q Consensus 76 y~frlhk~rVyYvs~~l~k~a~~i~r~~L~S~Gtc~GkFtKs~kFrl~ItaL~~La~-~ak~Kvwvk~~gE~~FLYGn~V 154 (221)
..+..++++||++.+.+.. .+..-.++..|+.+|++.| +.|..+-...-.|.+ -.+..+=+...--..||-|..+
T Consensus 351 ~~~~~~~~~l~~~p~~~~~---~~~~l~v~r~Gl~lg~~kk-~rfePs~ala~~l~~~~~~~~~~l~~~~~~~Yl~ge~l 426 (470)
T PRK11933 351 LRLWQRDKEVWLFPAGIEP---LIGKVRFSRIGIKLAETHK-KGYRWQHEAVIALASPDNANAFELTPQEAEEWYMGRDI 426 (470)
T ss_pred CcEEEECCEEEEeccccch---hhcCCeEeeeceeEeeeec-CCeeEcHHHHHHhCcccccceEecCHHHHHHHHCCCCc
Confidence 4577889999999997533 2444569999999999987 899998543333333 3345566665556679999987
Q ss_pred ccccceeecccCCCcceEEEEecCCCeeeEEeeee
Q psy8679 155 LKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAK 189 (221)
Q Consensus 155 ~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~ak 189 (221)
--+ +++ ..|-++..-++.|||||....
T Consensus 427 ~~~------~~~--~~G~~lv~~~g~~lG~gK~~~ 453 (470)
T PRK11933 427 YPQ------TAP--PAGEVIVTYQGQPIGLAKRVG 453 (470)
T ss_pred cCC------CCC--CCCEEEEEECCEeeEEEEeeC
Confidence 422 222 257777777999999999964
No 22
>PRK05429 gamma-glutamyl kinase; Provisional
Probab=93.74 E-value=0.091 Score=49.26 Aligned_cols=71 Identities=14% Similarity=0.200 Sum_probs=62.7
Q ss_pred hhccc--CcceEEEccCcccee-ecccccccccceeecccCCCcceEEEEecCCCeeeEEeeeechhHhhhcCC
Q psy8679 129 YLAPY--AQFKVWVKPQAEQQF-LYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADP 199 (221)
Q Consensus 129 ~La~~--ak~Kvwvk~~gE~~F-LYGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~akst~~~~~~dp 199 (221)
||+-. .+-+|+|+..|...- --|..++-.+|..++.++...+-|.|++.++.++|.|.+..|+.|+++...
T Consensus 272 wi~~~~~~~g~i~vd~gA~~al~~~g~sLl~~Gi~~v~g~f~~gd~V~i~~~~g~~va~G~~~~~s~e~~~~~g 345 (372)
T PRK05429 272 WIAGALQPAGEIVVDAGAVKALLERGKSLLPAGVTAVEGDFSRGDVVRIVDPDGREIARGLVNYSSDELRRIAG 345 (372)
T ss_pred HHhcCCCCCCeEEECccHHHHHHhcCCccCccchhheECcccCCCEEEEECCCCCEEEEEEecCCHHHHHHHcC
Confidence 45433 457999998888777 689999999999999999999999999999999999999999999987743
No 23
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=93.53 E-value=0.11 Score=48.45 Aligned_cols=79 Identities=27% Similarity=0.340 Sum_probs=62.5
Q ss_pred ceEEEccCccceeecccccccccceeecccCCCcceEEEEecCCCeeeEEeeeechhHhhhcCCCcEEEE---eccccee
Q psy8679 136 FKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGF---NQSDIGE 212 (221)
Q Consensus 136 ~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~akst~~~~~~dp~~ivv~---~qaD~Ge 212 (221)
-++-|.+.....+..|.++.-.++.+++++++..+-|+|++.++.+||.|.+.-|++++...+ .|++|- ...|.|-
T Consensus 238 P~V~Vd~~~a~~I~NG~~I~~pgv~~~d~~i~~gd~V~V~~~~G~~LAIGea~~s~~ei~~~~-kG~vV~~~~~~~~~~~ 316 (322)
T TIGR00425 238 KRVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVAVITLKGEAVAVGIALMSTKDIANAD-KGVVADVKRVIMERGT 316 (322)
T ss_pred CceEeCHHHHHHHHCCCccccccccccccccCCCCEEEEEECCCEEEEEEEEecCHHHHhhcC-CcEEEEEEEEeeCCCC
Confidence 366677777777889999988888877766666677999998999999999999999999877 567664 4567776
Q ss_pred eec
Q psy8679 213 YIR 215 (221)
Q Consensus 213 YLR 215 (221)
|=+
T Consensus 317 ~~~ 319 (322)
T TIGR00425 317 YPR 319 (322)
T ss_pred CCC
Confidence 643
No 24
>COG3270 Uncharacterized conserved protein [Function unknown]
Probab=93.48 E-value=0.12 Score=42.79 Aligned_cols=81 Identities=15% Similarity=0.244 Sum_probs=67.4
Q ss_pred cccCCCCeeeeeeeeeeeeecceEEEEeeehhhhcccCc-ceEEEccCccceeecccccccccceeecccCCCcceEEEE
Q psy8679 97 ENFGPDHLLALGTCFGKFTKSGKFRLHITALSYLAPYAQ-FKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVL 175 (221)
Q Consensus 97 ~~i~r~~L~S~Gtc~GkFtKs~kFrl~ItaL~~La~~ak-~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~ 175 (221)
.++.+.+. ..|+-+|.|.| +.||+++++-..|+|-+. +=|=+.+..--.+.=|+|| .-+.+.++|=|+.
T Consensus 30 p~l~k~~~-r~GI~lg~~~k-kg~r~s~e~~~al~p~~~~nsiELd~e~a~~w~rG~dV--------~~~~~~~~g~viv 99 (127)
T COG3270 30 PCLFKEKI-HNGIKLGEIHK-KGYRWSHEGGFALAPPAVRNSIELDEEEAREWMRGRDV--------EPQESGPAGWVIV 99 (127)
T ss_pred cchhhhhh-hcceEEEEEec-cCeeEEeeEEEEeCChhhcceEEeCHHHHHhhhcCCcc--------ccCCCCCCceEEE
Confidence 34555666 89999999988 679999999999999885 8899998888888899985 4455677778888
Q ss_pred ecCCCeeeEEee
Q psy8679 176 NMNDVPLGFGVA 187 (221)
Q Consensus 176 n~nd~pLGFGv~ 187 (221)
--++.+||||.-
T Consensus 100 ~~~~~~lG~aK~ 111 (127)
T COG3270 100 KFQGNGLGLAKV 111 (127)
T ss_pred EECCcccceeee
Confidence 888999999987
No 25
>TIGR01027 proB glutamate 5-kinase. Bacterial ProB proteins hit the full length of this model, but the ProB-like domain of delta 1-pyrroline-5-carboxylate synthetase does not hit the C-terminal 100 residues of this model. The noise cutoff is set low enough to hit delta 1-pyrroline-5-carboxylate synthetase and other partial matches to this family.
Probab=91.68 E-value=0.26 Score=46.15 Aligned_cols=71 Identities=23% Similarity=0.283 Sum_probs=62.9
Q ss_pred hhhccc--CcceEEEccCccceeec-ccccccccceeecccCCCcceEEEEecCCCeeeEEeeeechhHhhhcC
Q psy8679 128 SYLAPY--AQFKVWVKPQAEQQFLY-GHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLAD 198 (221)
Q Consensus 128 ~~La~~--ak~Kvwvk~~gE~~FLY-Gn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~akst~~~~~~d 198 (221)
.|||-. .+-.|+|.+.++..-+- |..++-++|..+..++...+-|-|.+.++.|||-|.+..|..|+++..
T Consensus 263 ~wi~~~~~~~G~i~vD~gA~~al~~~g~sLl~~Gi~~v~g~F~~gd~v~i~~~~~~~ia~g~~~y~s~~~~~i~ 336 (363)
T TIGR01027 263 FWIAFASEPAGEITVDAGAEEALLERGKSLLPAGIVGVEGNFSRGEVVEILNPEGQDIGRGLVNYSSDELEKIK 336 (363)
T ss_pred HHHhCCCCcCCeEEEChhHHHHHHhcCCccCCccceeeECcccCCCEEEEECCCCCEEEEEEecCCHHHHHHHc
Confidence 455543 45699999998888876 899999999999999999999999999999999999999999998764
No 26
>COG1549 Queuine tRNA-ribosyltransferases, contain PUA domain [Translation, ribosomal structure and biogenesis]
Probab=90.31 E-value=0.79 Score=45.58 Aligned_cols=92 Identities=23% Similarity=0.276 Sum_probs=69.7
Q ss_pred CeeeeeeeeeeeeecceEEEEeeehhhhcccCcceEEEccCccceeecccccccccceeecccCCCcceEEEEecCCCee
Q psy8679 103 HLLALGTCFGKFTKSGKFRLHITALSYLAPYAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPL 182 (221)
Q Consensus 103 ~L~S~Gtc~GkFtKs~kFrl~ItaL~~La~~ak~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pL 182 (221)
.++. |.-+|+|+-+ .-.++..+..+|- . .+.||.=. -|.=-.+|++.++.+.+|++-.|+-|+|.- ++..+
T Consensus 421 ~~~~-n~ql~~~~~~-~ls~t~~g~~~~~--~-~~~~VEId---~f~~~g~v~a~GV~da~edIrpnDeV~vv~-~~~v~ 491 (519)
T COG1549 421 FLLI-NEQLGTFTPN-LLSLTPFGAELLY--G-GIYWVEID---DFIPRGSVFAPGVVDADEDIRPNDEVVVVH-GGEVR 491 (519)
T ss_pred EEec-cceeeccccc-ceeccHhHhhhhh--c-CeeEEEcC---CccccccccccccccCCCCCCcCCEEEEEe-CCeEE
Confidence 4444 8899999975 3333333444443 2 67777522 277788999999999999999999997765 88999
Q ss_pred eEEeeeechhHhhhcCCCcEEE
Q psy8679 183 GFGVAAKSTAECKLADPLAIVG 204 (221)
Q Consensus 183 GFGv~akst~~~~~~dp~~ivv 204 (221)
|.|+++-|..++..+.. |++|
T Consensus 492 gVGrA~msg~eM~~akk-GiaV 512 (519)
T COG1549 492 GVGRAVMSGREMVEAKK-GIAV 512 (519)
T ss_pred EEeeeecChHHhcccCC-ceEE
Confidence 99999999999998876 4554
No 27
>PRK08557 hypothetical protein; Provisional
Probab=86.59 E-value=1.1 Score=43.15 Aligned_cols=106 Identities=19% Similarity=0.188 Sum_probs=74.2
Q ss_pred CCCeeeeeeeeeeee---ecceEEEEeeehhhhcccCcceEEEccCccceeecccccccccceeecc--cCCCcceEEEE
Q psy8679 101 PDHLLALGTCFGKFT---KSGKFRLHITALSYLAPYAQFKVWVKPQAEQQFLYGHNILKSGLARITE--NTPKYQGVIVL 175 (221)
Q Consensus 101 r~~L~S~Gtc~GkFt---Ks~kFrl~ItaL~~La~~ak~Kvwvk~~gE~~FLYGn~V~Ks~l~rite--~~~~~~GVvV~ 175 (221)
.+.++.=|-+||-+. ...+++++.++..++-. +.+|-|+| -..+|=|.+|....+..+.+ ++..++=|+|-
T Consensus 42 ~~ev~~~g~~~g~~~~~~~~~~w~~~p~~~~~~~~--~~~~~~~~--~~~~~~g~~v~~~~~~~~~~~~~~~~~~~v~~~ 117 (417)
T PRK08557 42 RKRVYISEDQIGILEFDLLDLDWKFHPSPSYYLIE--EPKIKLKP--TKRRLKGKYIKEELIENPEELNEILENDYVGVE 117 (417)
T ss_pred hhheeECCeEEEEEEEccccceeEEccchhhhhcc--Cceeeecc--cccccCCccccccccccccccccCCCCCEEEEe
Confidence 367888899999654 34577887777765533 56777776 45588999999998888777 77667734443
Q ss_pred ecCCCeeeEEeeeechhHhhhcCCCcEEEEecccceeee
Q psy8679 176 NMNDVPLGFGVAAKSTAECKLADPLAIVGFNQSDIGEYI 214 (221)
Q Consensus 176 n~nd~pLGFGv~akst~~~~~~dp~~ivv~~qaD~GeYL 214 (221)
+ +..+|.|++..++...+++.+.. ....+|+-.++
T Consensus 118 ~--~~~~gvg~~~~~~~k~~~~~~~~--~~~~~~~~~~i 152 (417)
T PRK08557 118 I--GNFLGVGVKKEDRIKIKDLSLKK--ELDFEKIEDYL 152 (417)
T ss_pred c--CCEEEEEEeecceEEEEecccCC--CCCcccHHHHH
Confidence 3 78999999988887777777644 23334444443
No 28
>PRK13402 gamma-glutamyl kinase; Provisional
Probab=70.20 E-value=6.5 Score=37.25 Aligned_cols=70 Identities=11% Similarity=0.125 Sum_probs=61.3
Q ss_pred hhccc--CcceEEEccCccceeec-ccccccccceeecccCCCcceEEEEecCCCeeeEEeeeechhHhhhcC
Q psy8679 129 YLAPY--AQFKVWVKPQAEQQFLY-GHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLAD 198 (221)
Q Consensus 129 ~La~~--ak~Kvwvk~~gE~~FLY-Gn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~akst~~~~~~d 198 (221)
|||-. .+=.++|.+.|+.--+- |..+|-++|.++.-++...+-|-|++.++..+|-|.+..|..|+++..
T Consensus 268 Wi~~~~~~~G~i~vd~ga~~al~~~~~sLl~~gi~~v~g~F~~gd~v~i~~~~g~~~~rg~~~y~s~~~~~i~ 340 (368)
T PRK13402 268 WMAHTSGPQGEIVVENDFDRALDNHSEQLTSDDVVEIKGDFSVGDTILVRKGDGTKLAKGKSNYSSCLLNFIK 340 (368)
T ss_pred HHhCCCCCCeeEEECccHHHHHHhcCCcccccceEEEeCEecCCCEEEEECCCCCEEEEEEccCCHHHHHHHc
Confidence 45432 34589999998888875 699999999999999999999999999999999999999999998763
No 29
>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional
Probab=60.17 E-value=16 Score=34.84 Aligned_cols=49 Identities=10% Similarity=0.208 Sum_probs=35.8
Q ss_pred eEEEccCccce------eecccccccccceeecccCCCcceEEEEecCCCeeeEEeeeec
Q psy8679 137 KVWVKPQAEQQ------FLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKS 190 (221)
Q Consensus 137 Kvwvk~~gE~~------FLYGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~aks 190 (221)
+|.+|+.++.. ++|.+.| .++..+.+..+-|.|++.++.+||.|.....
T Consensus 4 ~v~l~~~~~~~~~~ghpwv~~~~i-----~~~~~~~~~G~~v~v~~~~g~~lg~g~~n~~ 58 (396)
T PRK15128 4 RLVLAKGREKSLLRRHPWVFSGAV-----ARMEGKASLGETIDIVDHQGKWLARGAYSPA 58 (396)
T ss_pred EEEECcchHhHHhcCCCeEEhHHh-----ccccCCCCCCCEEEEEcCCCCEEEEEEECCC
Confidence 57788776654 6676666 4444345567789999999999999998543
No 30
>PF09157 TruB-C_2: Pseudouridine synthase II TruB, C-terminal; InterPro: IPR015240 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. The C-terminal domain adopts a secondary structure consisting of a four-stranded beta sheet and one alpha helix, similar to that found in PUA domains. It is predominantly involved in RNA-binding, being mostly found in tRNA pseudouridine synthase B (TruB) []. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1ZL3_A 1K8W_A 1R3F_A.
Probab=55.77 E-value=11 Score=25.98 Aligned_cols=45 Identities=22% Similarity=0.321 Sum_probs=29.4
Q ss_pred EEEccCccceeecccccccccceeecccCCCcceEEEEecCCCeeeEEeee
Q psy8679 138 VWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAA 188 (221)
Q Consensus 138 vwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~a 188 (221)
|-+++.....|+-|+-|-- .+..+..+-|-||+.++..||.|...
T Consensus 3 v~L~~~~~~~~~~Gq~v~~------~~~~~~~~~vrvy~~~~~FlGig~~~ 47 (58)
T PF09157_consen 3 VVLDEEQAKRFLHGQRVRL------RDDAPPDGLVRVYDEDGRFLGIGEID 47 (58)
T ss_dssp EEE-HHHHHHHTTT--B---------SS--SSSEEEEETTTTEEEEEEEE-
T ss_pred EEeCHHHHHHHHCcCcccc------cCCCCCCceEEEECCCCEEEEEEEEc
Confidence 4455666677888888832 55666777899999999999999984
No 31
>COG0263 ProB Glutamate 5-kinase [Amino acid transport and metabolism]
Probab=46.45 E-value=26 Score=33.87 Aligned_cols=70 Identities=17% Similarity=0.192 Sum_probs=61.4
Q ss_pred hhcccC--cceEEEccCccceee-cccccccccceeecccCCCcceEEEEecCCCeeeEEeeeechhHhhhcCC
Q psy8679 129 YLAPYA--QFKVWVKPQAEQQFL-YGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADP 199 (221)
Q Consensus 129 ~La~~a--k~Kvwvk~~gE~~FL-YGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~akst~~~~~~dp 199 (221)
+|+-+. .=++||...++.--+ .|+.++=++|..+.-++...+-|-|. .++.++|=|....|..|.++...
T Consensus 271 Wi~~~~~~~G~i~iD~GA~~Al~~~gkSLLpaGV~~V~G~F~rGdvV~i~-~~g~~iarG~v~Y~s~el~~i~G 343 (369)
T COG0263 271 WIAGALPPAGEITVDAGAVEALLEQGKSLLPAGVTSVEGNFSRGDVVRIR-PQGGEIARGLVNYSSDELRKIAG 343 (369)
T ss_pred HhhcCCCCCceEEECccHHHHHHhcCCccccccceEeeeeecCCCEEEEe-cCCceeEeeeccCCHHHHHHHhC
Confidence 444443 368999999999999 99999999999999999999999999 77779999999999999987654
No 32
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=42.05 E-value=27 Score=32.68 Aligned_cols=62 Identities=18% Similarity=0.165 Sum_probs=45.0
Q ss_pred ceEEEccCccceeecccccccccceeecccCCCcceEEEEecCCCeeeEEeeeechhHhhhcC
Q psy8679 136 FKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLAD 198 (221)
Q Consensus 136 ~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pLGFGv~akst~~~~~~d 198 (221)
-++-|+++....+.+|+.+--+.+.++ .+.+..+-|+|++.++.+||.|..-.+...++...
T Consensus 229 p~v~l~~~~~~~i~~G~~i~~~~~~~~-~~~~~~~~v~v~~~~g~~lai~~~~~~~~~~~~~~ 290 (308)
T PRK14124 229 PKVVIHQESTEKILNGSQIYLEMVKEW-DNFKKDDVVRVFDEEGRLLAIARAERNSSFLETLK 290 (308)
T ss_pred ceEEeCHHHHHHHHCCCcccccccccc-cccCCCCEEEEEcCCCeEEEEEEEecCCceeeeee
Confidence 578899998899999998854433333 22334555899998899999999877776666543
No 33
>TIGR02624 rhamnu_1P_ald rhamnulose-1-phosphate aldolase. Members of this family are the enzyme RhaD, rhamnulose-1-phosphate aldolase.
Probab=36.53 E-value=46 Score=30.22 Aligned_cols=59 Identities=17% Similarity=0.193 Sum_probs=39.2
Q ss_pred ceEEEccCccceeecccccccccceeecccCCCcceEEEEecCCCee----eEEeeeechhHhh----------hcCCCc
Q psy8679 136 FKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPL----GFGVAAKSTAECK----------LADPLA 201 (221)
Q Consensus 136 ~Kvwvk~~gE~~FLYGn~V~Ks~l~rite~~~~~~GVvV~n~nd~pL----GFGv~akst~~~~----------~~dp~~ 201 (221)
..+||+|+| ++.++++++.+++-+|++.++++..+ ||.-..|.|+|.. +..|+.
T Consensus 67 ~~~lITpSG------------~~~~~l~~~~~~d~~iv~vd~~G~~~~~~~~~~~g~kPSsE~~mH~~v~~~iy~~rpd~ 134 (270)
T TIGR02624 67 KYFLVTGSG------------KFFRNVEENPAENLGILRVSEDGASVHLLWGLTDGGVPTSELPAHFMSHIARLKVDPEN 134 (270)
T ss_pred CEEEEeCCC------------CCHHhcccCchhceeEEEECCCCCEEEeeccccCCCCcChHHHHHHHHHHHHHHhCCCC
Confidence 469999997 35567877756666788999999877 3422336666643 345665
Q ss_pred EEEEe
Q psy8679 202 IVGFN 206 (221)
Q Consensus 202 ivv~~ 206 (221)
-.|.|
T Consensus 135 ~AVvH 139 (270)
T TIGR02624 135 RVIMH 139 (270)
T ss_pred CEEEc
Confidence 55555
No 34
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=34.56 E-value=23 Score=27.80 Aligned_cols=19 Identities=26% Similarity=0.744 Sum_probs=15.6
Q ss_pred ceEEEEecCCCeeeEEeee
Q psy8679 170 QGVIVLNMNDVPLGFGVAA 188 (221)
Q Consensus 170 ~GVvV~n~nd~pLGFGv~a 188 (221)
.|+.+-.+..+|+|||..|
T Consensus 32 ~g~~~~~~~~epIaFGLka 50 (88)
T COG2092 32 EGYELIKIEEEPIAFGLKA 50 (88)
T ss_pred ccceeccceeEeeeeeeee
Confidence 4566559999999999986
No 35
>PF02393 US22: US22 like; InterPro: IPR003360 Herpesviruses are large and complex DNA viruses, widely found in nature. Human cytomegalovirus (HCMV), an important human pathogen, defines the betaherpesvirus family. Mouse cytomegalovirus (MCMV) and rat cytomegalovirus serve as biological model systems for HCMV. HCMV, MCMV, and rat CMV display the largest genomes among the herpesviruses and are essentially co-linear over the central 180 kb of the 230-kb genomes. Betaherpesviruses, which include the CMVs as well as human herpesviruses 6 and 7, differ from alpha- and gammaherpesviruses by the presence of additional gene families such as the US22 gene family, which are mainly clustered at the ends of the genome. The US22 family was first described in HCMV. This gene family comprises 12 members in both HCMV and MCMV and 11 in rat CMV []. Members of the US22 gene family are characterised by stretches of hydrophobic and charged residues as well as up to four conserved sequence motifs which are specific for betaherpesviruses. Motif I differs between the HCMV US and UL family members []. Motifs I and II have consensus sequences, while motifs III and IV are less well defined but have stretches of non-polar residues [, ]. Members of this gene family are widely divergent in function and their involvement in viral replication []. This entry contains US22 family members from the Cytomegalovirus, Muromegalovirus and the Roseolovirus taxonomic groups. The name sake of this family US22 is an early nuclear protein that is secreted from cells []. The US22 family may have a role in virus replication and pathogenesis [].
Probab=32.58 E-value=1.5e+02 Score=22.65 Aligned_cols=76 Identities=12% Similarity=0.207 Sum_probs=50.8
Q ss_pred CceeEEEeCCeEEE--EcH-HHHhhhccc--Ccccceecceecccccc------cccccccCCCCeeEEEeeCcEEEEEc
Q psy8679 21 GTYCFREMRDRVFY--VSE-KILTLAENF--GPDHLLALGTCFGNIGS------NVKLLIDRPDGTYCFREMRDRVFYVS 89 (221)
Q Consensus 21 ~~y~FRlhk~RVyY--vse-~i~k~At~i--~r~~L~slGtc~GyiG~------ni~~li~~~d~~y~frlhk~rVyYvs 89 (221)
+.+++++....=.- .+. .+....... -.+.|.-+|++-.+.+. .+.-+++....-|++-...+++|++.
T Consensus 28 ~~~~l~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lG~v~~~~~~~~~~~~~~vvl~~~~G~Vy~yd~~~~~l~~lA 107 (125)
T PF02393_consen 28 GGWYLRLCGREDLPYMGTAELLRCWRRSYLCCCERLEVLGVVGHYSPEGCVFRDRLVVLVGESGRVYAYDPEDDRLYRLA 107 (125)
T ss_pred CCeeEEEechhhccccccHHHHHHHHHHcCCCCcEEEEEEEEEEEcCCCCCccceEEEEEeCCCeEEEEEcCCCEEEEEe
Confidence 35888887554433 232 233333333 45899999999998653 55566675555688998889999999
Q ss_pred HHHHhhh
Q psy8679 90 EKILTLA 96 (221)
Q Consensus 90 ~~l~k~a 96 (221)
.++...+
T Consensus 108 ~~l~~F~ 114 (125)
T PF02393_consen 108 DSLEEFF 114 (125)
T ss_pred CCHHHHH
Confidence 8885543
No 36
>PF12894 Apc4_WD40: Anaphase-promoting complex subunit 4 WD40 domain
Probab=32.12 E-value=31 Score=23.48 Aligned_cols=31 Identities=26% Similarity=0.277 Sum_probs=22.7
Q ss_pred hhcccCcccceecceecccccccccccccCCCCeeEEEeeCcEEE
Q psy8679 42 LAENFGPDHLLALGTCFGNIGSNVKLLIDRPDGTYCFREMRDRVF 86 (221)
Q Consensus 42 ~At~i~r~~L~slGtc~GyiG~ni~~li~~~d~~y~frlhk~rVy 86 (221)
.++--|+-.|+.+|+--| .-+++|++++|||
T Consensus 16 ~~~w~P~mdLiA~~t~~g--------------~v~v~Rl~~qriw 46 (47)
T PF12894_consen 16 CMSWCPTMDLIALGTEDG--------------EVLVYRLNWQRIW 46 (47)
T ss_pred EEEECCCCCEEEEEECCC--------------eEEEEECCCcCcc
Confidence 555667778888887432 2489999999986
No 37
>KOG2523|consensus
Probab=29.57 E-value=1.4e+02 Score=26.39 Aligned_cols=105 Identities=24% Similarity=0.297 Sum_probs=79.3
Q ss_pred CCCCeeeeeeeeeeeee-cceEEEEeeehhhhcccC--cceEEEccCccceeecccccccccce----eecccCCCcceE
Q psy8679 100 GPDHLLALGTCFGKFTK-SGKFRLHITALSYLAPYA--QFKVWVKPQAEQQFLYGHNILKSGLA----RITENTPKYQGV 172 (221)
Q Consensus 100 ~r~~L~S~Gtc~GkFtK-s~kFrl~ItaL~~La~~a--k~Kvwvk~~gE~~FLYGn~V~Ks~l~----rite~~~~~~GV 172 (221)
.+-.|+|+|--.==|-+ .|+| +..|.+|-+|. -+.+-|...|=..-|=|-||+=-++. .++...+..+-|
T Consensus 57 d~i~L~s~~G~~~fF~~~dg~~---~PTLRllhk~p~~~~~~qvD~GAIkfvlsGAnIMcPGlts~g~~l~~~~ekd~~V 133 (181)
T KOG2523|consen 57 DHIELLSVNGEVLFFCHRDGPY---IPTLRLLHKYPFIFPHVQVDRGAIKFVLSGANIMCPGLTSPGAKLPPGVEKDTIV 133 (181)
T ss_pred CeeEEEEeCCEEEEEEecCCCc---cchhHHHhhCCCccceEEecCcceeeeecCCceEcccCCCCcccCCCCccCCCEE
Confidence 34468888843333332 3355 44577887755 48999999999999999999877764 577777888999
Q ss_pred EEEecCCC-eeeEEeeeechhHhhhcCC-CcEEEEec
Q psy8679 173 IVLNMNDV-PLGFGVAAKSTAECKLADP-LAIVGFNQ 207 (221)
Q Consensus 173 vV~n~nd~-pLGFGv~akst~~~~~~dp-~~ivv~~q 207 (221)
+|+-.... +|-.|.+.-|++|++.... .||=.+|-
T Consensus 134 ~i~aeGK~~alAiG~~~ms~kei~s~nKGiGIE~~H~ 170 (181)
T KOG2523|consen 134 AIMAEGKEHALAIGLTKMSAKEIKSVNKGIGIENYHY 170 (181)
T ss_pred EEEecCchhhhhhhhhhhcHHHHHhhccCCceEEEEe
Confidence 99999888 9999999999999998765 45555553
No 38
>PRK11558 putative ssRNA endonuclease; Provisional
Probab=27.04 E-value=51 Score=26.21 Aligned_cols=43 Identities=14% Similarity=0.052 Sum_probs=31.9
Q ss_pred eecccCCCcceEEEEecCCCeeeEEeeeechhHhhhcCCCcEEE
Q psy8679 161 RITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVG 204 (221)
Q Consensus 161 rite~~~~~~GVvV~n~nd~pLGFGv~akst~~~~~~dp~~ivv 204 (221)
++++.++....|.+++-+.++ ||..-......-.-.|=+|+.+
T Consensus 46 ~v~~~~~~G~avmv~~~~~eq-G~~~~t~G~~rr~~vD~DGl~L 88 (97)
T PRK11558 46 QVTQLAEEGNVVMAWATNTES-GFEFQTFGENRRIPVDLDGLRL 88 (97)
T ss_pred HHHHhCCCCcEEEEEcCCCCC-CcEEEecCCCCccEEecCCCEE
Confidence 477888899999999999888 9999877666444444444433
Done!