Query 029802
Match_columns 187
No_of_seqs 105 out of 184
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 03:53:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029802.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029802hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3492 Ribosome biogenesis pr 100.0 6E-100 1E-104 620.6 15.2 179 1-187 1-179 (180)
2 PF03657 UPF0113: Uncharacteri 100.0 4.3E-68 9.3E-73 434.2 3.0 159 1-183 3-162 (162)
3 COG1374 NIP7 Protein involved 100.0 4.3E-50 9.3E-55 331.9 5.9 172 1-185 1-176 (176)
4 smart00359 PUA Putative RNA-bi 98.8 1.2E-08 2.5E-13 71.2 5.8 73 103-175 1-74 (77)
5 PRK14560 putative RNA-binding 98.7 1E-07 2.2E-12 77.2 8.5 138 3-172 8-146 (160)
6 TIGR03684 arCOG00985 arCOG0415 98.6 7.2E-07 1.6E-11 71.4 12.3 137 1-172 1-139 (150)
7 TIGR00451 unchar_dom_2 unchara 98.5 6.1E-07 1.3E-11 67.9 7.0 90 81-172 10-100 (107)
8 PRK13534 7-cyano-7-deazaguanin 98.1 7.6E-05 1.7E-09 72.7 14.3 101 71-172 528-632 (639)
9 PRK13795 hypothetical protein; 98.0 7E-05 1.5E-09 72.5 11.1 143 1-170 45-194 (636)
10 PRK13794 hypothetical protein; 97.9 4.9E-05 1.1E-09 71.5 9.5 109 69-177 85-200 (479)
11 PF01472 PUA: PUA domain; Int 97.9 1.3E-05 2.8E-10 57.2 4.2 67 104-171 2-68 (74)
12 COG2016 Predicted RNA-binding 97.5 0.00089 1.9E-08 55.7 9.3 131 3-166 8-141 (161)
13 COG1370 Prefoldin, molecular c 97.3 0.0013 2.8E-08 54.4 7.4 89 83-172 58-149 (155)
14 COG5270 PUA domain (predicted 97.1 0.00093 2E-08 57.1 5.3 97 69-165 90-191 (202)
15 PF13636 Nol1_Nop2_Fmu_2: pre- 97.0 0.0011 2.3E-08 50.3 4.4 81 65-155 9-90 (102)
16 TIGR00432 arcsn_tRNA_tgt tRNA- 96.9 0.0028 6.1E-08 61.0 7.4 88 83-171 444-534 (540)
17 PRK04270 H/ACA RNA-protein com 95.7 0.016 3.5E-07 51.7 4.9 69 103-172 226-294 (300)
18 PRK11933 yebU rRNA (cytosine-C 95.7 0.029 6.2E-07 53.1 6.6 102 43-156 351-453 (470)
19 COG3270 Uncharacterized conser 94.8 0.043 9.3E-07 44.2 4.1 80 65-154 31-111 (127)
20 TIGR00425 CBF5 rRNA pseudourid 94.4 0.059 1.3E-06 48.8 4.7 78 104-182 239-319 (322)
21 PRK05429 gamma-glutamyl kinase 94.4 0.061 1.3E-06 49.1 4.7 71 96-166 272-345 (372)
22 TIGR01027 proB glutamate 5-kin 92.7 0.19 4.1E-06 45.8 4.9 71 95-165 263-336 (363)
23 PRK08557 hypothetical protein; 92.5 0.76 1.6E-05 43.1 8.7 131 1-168 6-141 (417)
24 COG1549 Queuine tRNA-ribosyltr 91.0 0.75 1.6E-05 44.6 7.0 88 75-171 425-512 (519)
25 PRK13402 gamma-glutamyl kinase 72.6 5.2 0.00011 36.9 4.2 64 103-166 277-341 (368)
26 PF09157 TruB-C_2: Pseudouridi 70.0 4.1 8.8E-05 27.3 2.2 45 105-155 3-47 (58)
27 PRK15128 23S rRNA m(5)C1962 me 68.7 10 0.00023 35.1 5.3 49 104-157 4-58 (396)
28 PRK14124 tRNA pseudouridine sy 55.7 14 0.00031 33.6 3.6 62 103-165 229-290 (308)
29 COG0263 ProB Glutamate 5-kinas 48.1 23 0.0005 33.3 3.8 70 96-166 271-343 (369)
30 COG2092 EFB1 Translation elong 37.2 20 0.00043 27.4 1.3 19 137-155 32-50 (88)
31 KOG2523 Predicted RNA-binding 33.7 1.1E+02 0.0024 26.1 5.4 108 65-175 55-171 (181)
32 COG0130 TruB Pseudouridine syn 33.7 33 0.00071 30.7 2.4 66 82-154 175-258 (271)
33 TIGR02624 rhamnu_1P_ald rhamnu 33.4 58 0.0013 28.8 3.9 54 96-161 59-117 (270)
34 PF02762 Cbl_N3: CBL proto-onc 33.1 60 0.0013 24.6 3.3 30 2-51 7-36 (86)
35 PRK11558 putative ssRNA endonu 32.3 48 0.001 25.6 2.8 43 128-171 46-88 (97)
36 PF08366 LLGL: LLGL2; InterPr 30.1 2.3E+02 0.0049 22.1 6.2 76 102-177 16-94 (105)
37 TIGR01639 P_fal_TIGR01639 Plas 28.7 30 0.00066 24.0 1.1 22 2-23 8-29 (61)
38 PF08920 SF3b1: Splicing facto 27.8 22 0.00049 29.0 0.3 13 2-14 85-97 (144)
39 PF09707 Cas_Cas2CT1978: CRISP 24.1 65 0.0014 24.2 2.2 32 127-159 43-74 (86)
40 PF11829 DUF3349: Protein of u 22.9 75 0.0016 24.4 2.4 17 2-18 34-50 (96)
41 PF09183 DUF1947: Domain of un 22.5 1.7E+02 0.0037 21.1 4.0 43 4-59 5-47 (65)
42 TIGR00523 eIF-1A eukaryotic/ar 21.5 1.1E+02 0.0023 23.5 3.0 36 75-110 19-61 (99)
43 smart00652 eIF1a eukaryotic tr 21.4 1.1E+02 0.0024 22.5 2.9 36 75-110 5-47 (83)
44 PRK10681 DNA-binding transcrip 21.4 2.4E+02 0.0052 24.2 5.5 93 7-112 77-176 (252)
45 PF12594 DUF3764: Protein of u 20.9 60 0.0013 24.5 1.5 16 163-178 44-59 (86)
46 PF07430 PP1: Phloem filament 20.8 72 0.0016 27.8 2.0 44 67-110 142-191 (202)
47 COG3512 CRISPR-associated prot 20.1 27 0.00058 27.7 -0.6 27 115-141 49-75 (116)
No 1
>KOG3492 consensus Ribosome biogenesis protein NIP7 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.1e-100 Score=620.57 Aligned_cols=179 Identities=67% Similarity=1.118 Sum_probs=178.1
Q ss_pred CCCCCHHHHHHHHHHHhhhhcccccccccCCCCCCCCCCCCceEEEeeCceEEEEcHHHHHhhccCCCCCeeeeeeeEEE
Q 029802 1 MRPLDEAETTAVFEKLFKFTGNNLKNIVENPSHEGPDPNPGRYCFRLHKNRVYYVSESLVKRATNIARPKLVSLGTCIGK 80 (187)
Q Consensus 1 MR~LteeE~~~vf~KL~kyiG~nl~~li~~~~~~~~~~~d~~y~frl~k~rVyyvs~~l~~~a~~i~r~~L~S~Gtc~Gk 80 (187)
|||||+||++.+||||++|||+|+..||+|| |++||||+||+|||||||.++++|++|+|+||+|+||||||
T Consensus 1 MR~Lt~Eetk~vfekla~yIG~Nv~~lidr~--------D~~~cfrlhkdRVyyvsEr~~k~a~~isr~~L~s~Gtc~GK 72 (180)
T KOG3492|consen 1 MRPLTEEETKVVFEKLAKYIGDNVSHLIDRP--------DGTYCFRLHKDRVYYVSERIMKLAACISRKNLVSLGTCFGK 72 (180)
T ss_pred CCCCcHHHHHHHHHHHHHHHhhhhheeecCC--------CCceeeEeeCceEEeehHHHHHHHhhhcccceeEEeEEEee
Confidence 9999999999999999999999999999999 99999999999999999999999999999999999999999
Q ss_pred eeecceEEEEeeehHhHhhcccceEEeCCCCccccccccccccccccccccccCCCCeEEEEecCCCceeEEeeeechhh
Q 029802 81 FTHGGKFHLTIQALSLVAANARHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQD 160 (187)
Q Consensus 81 FtKs~kFrl~itaL~~La~~a~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~akst~~ 160 (187)
||||||||||||||+||||||+|||||||+|||+|||||||+||||+||||++|+|+|||||||||+||||||+||||++
T Consensus 73 FTKt~kfrlhitaL~~La~~Ak~KvWiKp~~Em~flYGNhvlKs~vgRitd~~p~~~GVvVysm~DvPLGFGv~Akst~d 152 (180)
T KOG3492|consen 73 FTKTGKFRLHITALDYLAPYAKYKVWIKPNAEMQFLYGNHVLKSGVGRITDGIPQHQGVVVYSMNDVPLGFGVTAKSTQD 152 (180)
T ss_pred eeccceEEEeeeehhhhhhhhheeEEeccCcccceeecccchhcccceecCCCCCcceEEEEeccCCccccceeecCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCCeeEEEecccceeeeccccCC
Q 029802 161 CRKLDPNGIVVLHQSDIGEYLRMEDEL 187 (187)
Q Consensus 161 ~~~~dp~~ivv~~qaD~GeYLR~E~~l 187 (187)
||++||++|||+||||+|||||+||+|
T Consensus 153 ~r~~dp~aiv~~hQaDiGEYlR~E~~l 179 (180)
T KOG3492|consen 153 CRKADPTAIVVLHQADIGEYLRNEDTL 179 (180)
T ss_pred ccccCCcEEEEEEecchHHHhhccccc
Confidence 999999999999999999999999986
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=4.3e-68 Score=434.22 Aligned_cols=159 Identities=64% Similarity=1.066 Sum_probs=139.3
Q ss_pred CCCCCHHHHHHHHHHHhhhhcccccccccCCCCCCCCCCCCceEEEeeCceEEEEcHHHHHhhccCCCCCeeeeeeeEEE
Q 029802 1 MRPLDEAETTAVFEKLFKFTGNNLKNIVENPSHEGPDPNPGRYCFRLHKNRVYYVSESLVKRATNIARPKLVSLGTCIGK 80 (187)
Q Consensus 1 MR~LteeE~~~vf~KL~kyiG~nl~~li~~~~~~~~~~~d~~y~frl~k~rVyyvs~~l~~~a~~i~r~~L~S~Gtc~Gk 80 (187)
|||||+||+++||+||++|++.+ +++. +..+|||+|++||||||+++++.|++ +++++|+|||+|+
T Consensus 3 mR~Lt~eE~~~v~~kL~~yg~~~---~l~~---------~~~~~~~~~~~~Vyyvs~~l~~~~~~--~~~~~s~G~~~G~ 68 (162)
T PF03657_consen 3 MRPLTEEETKIVFEKLSKYGGNN---LLDH---------FDFYVFRLHKDRVYYVSEELMKLASN--RPNLYSLGTCLGK 68 (162)
T ss_dssp EEE--HHHHHHHHHHHHCCCCGH---CCEE---------TEEEEEECCTCEEEEEEHHHHCCCTT--CHHHHCCSEEEEE
T ss_pred CCCCCHHHHHHHHHHHHHhcchh---hccc---------ccceeeeeecceEEEECHHHHHHHhC--CCccceeceEEEE
Confidence 89999999999999999996666 5554 35799999999999999999998888 8999999999999
Q ss_pred eeecc-eEEEEeeehHhHhhcccceEEeCCCCccccccccccccccccccccccCCCCeEEEEecCCCceeEEeeeechh
Q 029802 81 FTHGG-KFHLTIQALSLVAANARHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQ 159 (187)
Q Consensus 81 FtKs~-kFrl~itaL~~La~~a~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~akst~ 159 (187)
|||++ ||+||||||++||+||++||||||+|||+|||||||+||||+||||++|+| ||||||||+|||||
T Consensus 69 f~k~~~kf~l~i~~l~~la~~~~~kvwvk~~~e~~FLYGndV~ks~i~~i~e~~~~~--VvV~n~~d~~LGfG------- 139 (162)
T PF03657_consen 69 FTKKGKKFRLHITALDYLAPYAKNKVWVKPKAEMLFLYGNDVLKSSIGRITEDTPQN--VVVYNMNDVPLGFG------- 139 (162)
T ss_dssp E-TTTSEEEEEGHHHHCCCCC-SSEEEE-HHHHHHHCTT--EEGGGEEEEETTS-TC--EEEEETTS-EEEEE-------
T ss_pred EecCCccceeeHHHHHHhhhccceeEEECCCceEEeeecCCchHhhcEEecCCCCce--EEEEeCCCCeEEEE-------
Confidence 99854 999999999999999999999999999999999999999999999999999 99999999999999
Q ss_pred hhhccCCCeeEEEecccceeeecc
Q 029802 160 DCRKLDPNGIVVLHQSDIGEYLRM 183 (187)
Q Consensus 160 ~~~~~dp~~ivv~~qaD~GeYLR~ 183 (187)
|++.+|++++|+||+|+|||||+
T Consensus 140 -~~~~~~~~~vv~~~~DiGeYLR~ 162 (162)
T PF03657_consen 140 -CRKSDPDGKVVKNQADIGEYLRE 162 (162)
T ss_dssp -ECSTCHCCCCCECCEEGGGT-S-
T ss_pred -EeccCCCCEEEEEcCcceeeecC
Confidence 67888999999999999999995
No 3
>COG1374 NIP7 Protein involved in ribosomal biogenesis, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.3e-50 Score=331.93 Aligned_cols=172 Identities=38% Similarity=0.529 Sum_probs=163.5
Q ss_pred CCCCCHHHHHHHHHHHhhhhcccccccccCCCCCCCCCCCCceEEE--ee-Cce-EEEEcHHHHHhhccCCCCCeeeeee
Q 029802 1 MRPLDEAETTAVFEKLFKFTGNNLKNIVENPSHEGPDPNPGRYCFR--LH-KNR-VYYVSESLVKRATNIARPKLVSLGT 76 (187)
Q Consensus 1 MR~LteeE~~~vf~KL~kyiG~nl~~li~~~~~~~~~~~d~~y~fr--l~-k~r-Vyyvs~~l~~~a~~i~r~~L~S~Gt 76 (187)
||+|+++|++..|+||+.|+++++..+++.. ++..++|+ ++ ++| ||+|++...+.|+.++|+|++|+||
T Consensus 1 mr~~~~e~~~~~~rkl~~~e~~lI~~~l~~~-------g~~~~~f~~~~~~~~r~v~~V~~~~~~l~~~i~r~np~~~G~ 73 (176)
T COG1374 1 MRGLKPEEGKMRVRKLSSWEGDLIRKELSKY-------GELDHLFFHLLKVKDRDVYEVNEVVWKLAESIERKNPYSLGT 73 (176)
T ss_pred CCCCCccccceeeccchhHHHHHHHHHHHhc-------cccchhhhhheeeccccEEEEeeehhhhhhcccccCcceece
Confidence 9999999999999999999999999999865 14457777 66 888 9999999999999999999999999
Q ss_pred eEEEeeecceEEEEeeehHhHhhcccceEEeCCCCccccccccccccccccccccccCCCCeEEEEecCCCceeEEeeee
Q 029802 77 CIGKFTHGGKFHLTIQALSLVAANARHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAK 156 (187)
Q Consensus 77 c~GkFtKs~kFrl~itaL~~La~~a~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~ak 156 (187)
|||+|++++.||+|+++|++||+++.+|+||+|+|||+|||||| +|+|+.++++.+|++++|+||||||.|||||+++.
T Consensus 74 ~~g~~~~~~~fR~~~~~l~~la~~~~~k~~v~~~~e~~FLYg~~-lkd~~~e~~~~~~~~~~v~V~~~nd~~lgiGvg~~ 152 (176)
T COG1374 74 FFGKRVKGGLFRKHVESLEELARIAIIKNYVKERGEMLFLYGND-LKDHVKEIIDEIPENGGVFVFNMNDVPLGIGVGAL 152 (176)
T ss_pred eecccccCCeeeeehhhhHHHHHHhheeeeeccCceeEEEeccc-cchhhhhhccccCCcceEEEEEcCCCceEEEeccc
Confidence 99999999999999999999999999999999999999999999 99999999999999999999999999999999999
Q ss_pred chhhhhccCCCeeEEEecccceeeecccc
Q 029802 157 SMQDCRKLDPNGIVVLHQSDIGEYLRMED 185 (187)
Q Consensus 157 st~~~~~~dp~~ivv~~qaD~GeYLR~E~ 185 (187)
|+++.+++-+++ |+|+|||||+|+
T Consensus 153 s~~ed~~~i~~~-----l~D~GeYLRr~~ 176 (176)
T COG1374 153 SPSEDGRLIKNA-----LKDVGEYLRRGG 176 (176)
T ss_pred Cchhhccccccc-----cchhhhhhhcCC
Confidence 999988888876 999999999985
No 4
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=98.80 E-value=1.2e-08 Score=71.21 Aligned_cols=73 Identities=27% Similarity=0.436 Sum_probs=66.8
Q ss_pred ceEEeCCCCccccccccccccccccccccccCCCCeEEEEecCCCceeEEeeeechhhhhccC-CCeeEEEecc
Q 029802 103 HKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQDCRKLD-PNGIVVLHQS 175 (187)
Q Consensus 103 ~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~akst~~~~~~d-p~~ivv~~qa 175 (187)
.+++|++++++.+++|.+|+.++|.+++.+....+-|.|++.++.|||.|.+..++.++.+.. +.++++..+.
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 6677776654
No 5
>PRK14560 putative RNA-binding protein; Provisional
Probab=98.68 E-value=1e-07 Score=77.20 Aligned_cols=138 Identities=18% Similarity=0.222 Sum_probs=103.6
Q ss_pred CCCHHHHHHHHHHHhhhhcccccccccCCCCCCCCCCCCceEEEeeCceEEEEcHHHHHhhccCCCCCeeeeeeeEEEee
Q 029802 3 PLDEAETTAVFEKLFKFTGNNLKNIVENPSHEGPDPNPGRYCFRLHKNRVYYVSESLVKRATNIARPKLVSLGTCIGKFT 82 (187)
Q Consensus 3 ~LteeE~~~vf~KL~kyiG~nl~~li~~~~~~~~~~~d~~y~frl~k~rVyyvs~~l~~~a~~i~r~~L~S~Gtc~GkFt 82 (187)
+|+..|.|.++++|..-.|..... +. .-..+..-.+-++|++....+ + |.
T Consensus 8 ~l~~s~~k~L~~~l~~~~~~~~~~--~~---------~~~~~~~~~~~~~~~~~~~p~-----------~--------f~ 57 (160)
T PRK14560 8 HLSKKEVKEIKEELKEKFGVDIDG--KD---------AVEEVETDKKEEIYLVDGEPL-----------F--------FK 57 (160)
T ss_pred ccCHHHHHHHHHHHHHHcCCCccc--cc---------cEEEEEcCCcEEEEEECCEEE-----------E--------EE
Confidence 688999999999998755633221 10 111222223556666653221 1 33
Q ss_pred ecceEEEEeeehHhHhhcccceEEeCCCCccccccccccccccccccccccCCCCeEEEEecC-CCceeEEeeeechhhh
Q 029802 83 HGGKFHLTIQALSLVAANARHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMS-DVPLGFGVAAKSMQDC 161 (187)
Q Consensus 83 Ks~kFrl~itaL~~La~~a~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~n-d~pLGfGv~akst~~~ 161 (187)
.++.|.+++.++..+ |....+|.|.+.+....+.|.+++..||..+++++..++-|+|++.+ +.|+|.|++.-|+.++
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 367899999888877 66678999999998888899999999999999999999999999987 9999999999999999
Q ss_pred hccCCCeeEEE
Q 029802 162 RKLDPNGIVVL 172 (187)
Q Consensus 162 ~~~dp~~ivv~ 172 (187)
.... .|++|.
T Consensus 137 ~~~~-kG~~v~ 146 (160)
T PRK14560 137 VEEK-KGKAVK 146 (160)
T ss_pred hhcC-CceEEE
Confidence 8543 455554
No 6
>TIGR03684 arCOG00985 arCOG04150 universal archaeal PUA-domain protein. This universal archaeal protein contains a domain possibly associated with RNA binding (pfam01472, TIGR00451).
Probab=98.64 E-value=7.2e-07 Score=71.45 Aligned_cols=137 Identities=20% Similarity=0.291 Sum_probs=102.8
Q ss_pred CCCCCHHHHHHHHHHHhhhhcccccccccCCCCCCCCCCCCc-eEEEeeCceEEEEcHHHHHhhccCCCCCeeeeeeeEE
Q 029802 1 MRPLDEAETTAVFEKLFKFTGNNLKNIVENPSHEGPDPNPGR-YCFRLHKNRVYYVSESLVKRATNIARPKLVSLGTCIG 79 (187)
Q Consensus 1 MR~LteeE~~~vf~KL~kyiG~nl~~li~~~~~~~~~~~d~~-y~frl~k~rVyyvs~~l~~~a~~i~r~~L~S~Gtc~G 79 (187)
..+|+..|.+.++++|.+..|- ... +.. -+...++.++|++. |.-++
T Consensus 1 r~~l~~~d~k~l~~~l~~~~g~------~~~--------~~~v~~~~~~~~~~~~~d------------------g~p~~ 48 (150)
T TIGR03684 1 RHFLSKKELKELLEELKEYYGI------DIE--------KAKLEVAETDKFEIYLVD------------------GKPLL 48 (150)
T ss_pred CccCcHHHHHHHHHHHHHHcCC------CCC--------CCeEEEEEcCCeEEEEEC------------------CEEEE
Confidence 3689999999999999888882 111 111 11111222333332 22333
Q ss_pred EeeecceEEEEeeehHhHhhcccceEEeCCCCccccccccccccccccccccccCCCCeEEEEecC-CCceeEEeeeech
Q 029802 80 KFTHGGKFHLTIQALSLVAANARHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMS-DVPLGFGVAAKSM 158 (187)
Q Consensus 80 kFtKs~kFrl~itaL~~La~~a~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~n-d~pLGfGv~akst 158 (187)
|..++.|.+++.++..+. ....+|.|.+.+...-+-|.|++..+|..+++++..++-|+|++.+ +.|+|.|++.-|+
T Consensus 49 -~~~~~~~~Ptl~~~~~~~-~~~~~v~Vd~~a~~~l~~Ga~lm~pGV~~~~~~~~~Gd~V~I~~~~~~~~vavG~a~~ss 126 (150)
T TIGR03684 49 -FEKDGRLIPTLYLLLELN-PDKNRVVVDEGAVKFIINGADIMAPGIVSADPSIKEGDIVFVVDETHRKPLAVGIALMDA 126 (150)
T ss_pred -EEeCCcccccHHHHHhCC-ccCCEEEECccHHHHHhcCcccccCceecCCCCCCCCCEEEEEECCCCeEEEEEEEeeCH
Confidence 555789999998887654 3578999999998888899999999999999999999999999988 9999999999999
Q ss_pred hhhhccCCCeeEEE
Q 029802 159 QDCRKLDPNGIVVL 172 (187)
Q Consensus 159 ~~~~~~dp~~ivv~ 172 (187)
.+++... .+++|.
T Consensus 127 ~ei~~~~-kG~av~ 139 (150)
T TIGR03684 127 EEMEEEK-KGKAVK 139 (150)
T ss_pred HHHhhcC-CCeEEE
Confidence 9998654 455554
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=98.45 E-value=6.1e-07 Score=67.92 Aligned_cols=90 Identities=23% Similarity=0.342 Sum_probs=76.4
Q ss_pred eeecceEEEEeeehHhHhhcccceEEeCCCCccccccccccccccccccccccCCCCeEEEEecC-CCceeEEeeeechh
Q 029802 81 FTHGGKFHLTIQALSLVAANARHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMS-DVPLGFGVAAKSMQ 159 (187)
Q Consensus 81 FtKs~kFrl~itaL~~La~~a~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~n-d~pLGfGv~akst~ 159 (187)
|...++|.+++.++..+-. ...+|+|++++...-+.|.+++..+|...++++.+++-|.|++.+ +.|+|.|++..|+.
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 368999999988877799999999999999999999999999987 89999999999999
Q ss_pred hhhccCCCeeEEE
Q 029802 160 DCRKLDPNGIVVL 172 (187)
Q Consensus 160 ~~~~~dp~~ivv~ 172 (187)
+++..+ .+++|.
T Consensus 89 e~~~~~-~G~~v~ 100 (107)
T TIGR00451 89 EMKEMD-KGKAVK 100 (107)
T ss_pred HHHhcC-CCeEEE
Confidence 999874 456553
No 8
>PRK13534 7-cyano-7-deazaguanine tRNA-ribosyltransferase; Provisional
Probab=98.10 E-value=7.6e-05 Score=72.75 Aligned_cols=101 Identities=19% Similarity=0.220 Sum_probs=86.4
Q ss_pred eeeeeeeEEEee-ecceEEEEeeehHhHhh---cccceEEeCCCCccccccccccccccccccccccCCCCeEEEEecCC
Q 029802 71 LVSLGTCIGKFT-HGGKFHLTIQALSLVAA---NARHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMSD 146 (187)
Q Consensus 71 L~S~Gtc~GkFt-Ks~kFrl~itaL~~La~---~a~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd 146 (187)
++.=|..++-+. ..|.|.|++.|...|-. +.+++|.|...++..-+=|.+|+..||...++++..++-|+|.+.+|
T Consensus 528 I~vdg~~l~~l~~~dg~~~pt~~GA~~l~~~~~~~~~~V~Vd~~a~~~v~~G~~v~apgVv~~d~~ir~gDeV~Vv~e~~ 607 (639)
T PRK13534 528 VLDKGEILATMRANDGFLILSKEGAKRLHEKLPFPKYRVVVDKESEPFARKGKSVFAKFVIDCDEEIRPYDEVLVVNEDD 607 (639)
T ss_pred EEECCEEEEEEEecCCEEEEcHHHHHHHHhccCCCCcEEEECCcchhhhhCCCcccCCcceecCCCCCCCCEEEEEecCC
Confidence 444478888776 67899999999888853 34689999988888777899999999999999999999999999999
Q ss_pred CceeEEeeeechhhhhccCCCeeEEE
Q 029802 147 VPLGFGVAAKSMQDCRKLDPNGIVVL 172 (187)
Q Consensus 147 ~pLGfGv~akst~~~~~~dp~~ivv~ 172 (187)
.|||.|++.-|..++...+. |++|.
T Consensus 608 ~~lavG~A~~~~~em~~~~~-G~avk 632 (639)
T PRK13534 608 ELLAYGKALLNGRELMEFNY-GLAVK 632 (639)
T ss_pred cEEEEEEEecCHHHHhhcCC-ceEEE
Confidence 99999999999999987755 55554
No 9
>PRK13795 hypothetical protein; Provisional
Probab=97.96 E-value=7e-05 Score=72.54 Aligned_cols=143 Identities=22% Similarity=0.195 Sum_probs=105.0
Q ss_pred CCCCCHHHHHHHHHHHhhhhcccccccccCCCCCCCCCCCCceEEEeeCceEEEEcHHHHHhhccCCC-CCeeeeeeeEE
Q 029802 1 MRPLDEAETTAVFEKLFKFTGNNLKNIVENPSHEGPDPNPGRYCFRLHKNRVYYVSESLVKRATNIAR-PKLVSLGTCIG 79 (187)
Q Consensus 1 MR~LteeE~~~vf~KL~kyiG~nl~~li~~~~~~~~~~~d~~y~frl~k~rVyyvs~~l~~~a~~i~r-~~L~S~Gtc~G 79 (187)
.||-.+.|.+.+.+.|....|.++ +. ++ ....|+|-. .-.| +.++.=|..+|
T Consensus 45 ~r~a~~~d~~~i~~~l~~~fG~~~--~~-----------~~-~~vllnK~~-------------~~d~~~~vivdg~~~~ 97 (636)
T PRK13795 45 VRPAFPYDIEFIRRVLEEEFGCDL--IP-----------ED-KLVLLNKIP-------------GEDRADEIIVDGRVIG 97 (636)
T ss_pred CCcCCHHHHHHHHHHHHHHcCCCC--CC-----------CC-cEEEEecCC-------------CCCcceEEEECCEEEE
Confidence 489999999999999988778653 11 11 223322210 0001 23344466777
Q ss_pred E--ee---ecceEEEEeeehHhHh-hcccceEEeCCCCccccccccccccccccccccccCCCCeEEEEecCCCceeEEe
Q 029802 80 K--FT---HGGKFHLTIQALSLVA-ANARHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGV 153 (187)
Q Consensus 80 k--Ft---Ks~kFrl~itaL~~La-~~a~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv 153 (187)
- |. ....|.|++.|+..|. +..+.+|.|+..+...-+-|.+|+..||..+++++..++-|+|.+.++.++|.|+
T Consensus 98 ~l~fd~~~~~~~~~p~l~ga~~l~~~~~~~~VvVd~ga~~~v~~Ga~l~~~GI~~~~~~i~~gd~V~I~~e~g~~vavG~ 177 (636)
T PRK13795 98 HLRFDLLELRWRFEPRLEGAKRLLKKRLKKWVIVDKGALEPIKNGKNVLAPGVVEADLDIKKGDEVVVVTEDGEVVGVGR 177 (636)
T ss_pred EEEeecccccceEecCHHHHHHHhhccCCcEEEEcccHHHHHHcCCcccCCceEEEeCCCCCCCEEEEEeCCCCEEEEEE
Confidence 3 32 2347888888776664 4567899999888877779999999999999999999999999999999999999
Q ss_pred eeechhhhhccCCCeeE
Q 029802 154 AAKSMQDCRKLDPNGIV 170 (187)
Q Consensus 154 ~akst~~~~~~dp~~iv 170 (187)
+..|+.++........|
T Consensus 178 a~~s~~e~~~~~kG~~V 194 (636)
T PRK13795 178 AKMDGDDMIKRFRGRAV 194 (636)
T ss_pred eccCHHHHhhccCCeEE
Confidence 99999999887664333
No 10
>PRK13794 hypothetical protein; Provisional
Probab=97.94 E-value=4.9e-05 Score=71.51 Aligned_cols=109 Identities=17% Similarity=0.274 Sum_probs=84.2
Q ss_pred CCeeeeeeeEEEee---ecce--EEEEeeehHhHhhcc-cceEEeCCCCccccc-cccccccccccccccccCCCCeEEE
Q 029802 69 PKLVSLGTCIGKFT---HGGK--FHLTIQALSLVAANA-RHKVWIKPTSEMSFL-YGNHVLKGGLGRITDSIAPGDGVVV 141 (187)
Q Consensus 69 ~~L~S~Gtc~GkFt---Ks~k--Frl~itaL~~La~~a-~~Kvwvk~~~E~~FL-YGn~V~Ks~l~rite~~~~~~gVvV 141 (187)
.+++.=|..+|-+. ..++ |.|++.+...|-+.+ +++|.|++.+...-+ .|.+|+..||..+++++..++-|+|
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 44556677888732 3355 555666666665554 568999976666666 8999999999999999999999999
Q ss_pred EecCCCceeEEeeeechhhhhccCCCeeEEEecccc
Q 029802 142 YSMSDVPLGFGVAAKSMQDCRKLDPNGIVVLHQSDI 177 (187)
Q Consensus 142 ~n~nd~pLGfGv~akst~~~~~~dp~~ivv~~qaD~ 177 (187)
++.+|.++|.|++..|+.+++..+...+|=.+.++.
T Consensus 165 v~~~g~~iavG~a~~s~~ei~~~~~G~~Vkvr~~~~ 200 (479)
T PRK13794 165 LDENGDVVGVGRARMSYEEIVNMEKGMVVKVRKSEE 200 (479)
T ss_pred EcCCCcEEEEEEeecCHHHHHhccCceEEEEEeccC
Confidence 999999999999999999999987754444444443
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=97.93 E-value=1.3e-05 Score=57.17 Aligned_cols=67 Identities=19% Similarity=0.324 Sum_probs=59.5
Q ss_pred eEEeCCCCccccccccccccccccccccccCCCCeEEEEecCCCceeEEeeeechhhhhccCCCeeEE
Q 029802 104 KVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQDCRKLDPNGIVV 171 (187)
Q Consensus 104 Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~akst~~~~~~dp~~ivv 171 (187)
+|||+..+....+.|.+++-.||.++..+++..+-|.|++.++.++|.|++..|..++.++.. +..+
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 4443
No 12
>COG2016 Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis]
Probab=97.49 E-value=0.00089 Score=55.67 Aligned_cols=131 Identities=21% Similarity=0.256 Sum_probs=99.6
Q ss_pred CCCHHHHHHHHHHHhhhhcccccccccCCCCCCCCCCCCceEEEe--eCceEEEEcHHHHHhhccCCCCCeeeeeeeEEE
Q 029802 3 PLDEAETTAVFEKLFKFTGNNLKNIVENPSHEGPDPNPGRYCFRL--HKNRVYYVSESLVKRATNIARPKLVSLGTCIGK 80 (187)
Q Consensus 3 ~LteeE~~~vf~KL~kyiG~nl~~li~~~~~~~~~~~d~~y~frl--~k~rVyyvs~~l~~~a~~i~r~~L~S~Gtc~Gk 80 (187)
+|...|.+.++++|..|-|.- |.. ....-... .+-.+||+.-+.+ =
T Consensus 8 ~lskke~k~l~~~~~~~~~~~----l~~---------k~~v~v~~~~~~~~ii~vdG~pl-------------------~ 55 (161)
T COG2016 8 FLSKKEVKKLVEKLEEYSGEE----LPG---------KAEVEVAKCDDKFEIILVDGEPL-------------------L 55 (161)
T ss_pred ccCHHHHHHHHHHHHHhcccc----cCC---------cceEEEEecCCcEEEEEECCEEE-------------------E
Confidence 589999999999999999822 211 11111111 2445666655444 2
Q ss_pred eeecceEEEEeeehHhHhhcccceEEeCCCCccccccccccccccccccccccCCCCeEEEEecC-CCceeEEeeeechh
Q 029802 81 FTHGGKFHLTIQALSLVAANARHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMS-DVPLGFGVAAKSMQ 159 (187)
Q Consensus 81 FtKs~kFrl~itaL~~La~~a~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~n-d~pLGfGv~akst~ 159 (187)
|-..++.-+++-+|..+-+ +++.|-|...|...-+-|-||+.=+|-...+++++.+.|||-... +-||..|++--|..
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 5555666666666655544 456999999999999999999999999999999999999999998 99999999999999
Q ss_pred hhhccCC
Q 029802 160 DCRKLDP 166 (187)
Q Consensus 160 ~~~~~dp 166 (187)
++...+.
T Consensus 135 em~~~~k 141 (161)
T COG2016 135 EMEEKKK 141 (161)
T ss_pred HHhhhcC
Confidence 9976554
No 13
>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones]
Probab=97.25 E-value=0.0013 Score=54.41 Aligned_cols=89 Identities=26% Similarity=0.314 Sum_probs=78.0
Q ss_pred ecceEEEEeeehHhHhh---cccceEEeCCCCccccccccccccccccccccccCCCCeEEEEecCCCceeEEeeeechh
Q 029802 83 HGGKFHLTIQALSLVAA---NARHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQ 159 (187)
Q Consensus 83 Ks~kFrl~itaL~~La~---~a~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~akst~ 159 (187)
.+|-|.|++.+-..|-. +.+++|.|+..+|---=-|++||-.++....|++..++=|+|.|.+|..|+-|.+.-|..
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 46788899998877765 667799999888776679999999999999999999999999999999999999999999
Q ss_pred hhhccCCCeeEEE
Q 029802 160 DCRKLDPNGIVVL 172 (187)
Q Consensus 160 ~~~~~dp~~ivv~ 172 (187)
|++..+- ++.|.
T Consensus 138 E~~~~~~-G~AVk 149 (155)
T COG1370 138 EMREFER-GMAVK 149 (155)
T ss_pred HHhhccc-cEEEE
Confidence 9998886 44443
No 14
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=97.10 E-value=0.00093 Score=57.07 Aligned_cols=97 Identities=25% Similarity=0.312 Sum_probs=84.8
Q ss_pred CCeeeeeeeEEEe--e--ec-ceEEEEeeehHhHhhcccceEEeCCCCccccccccccccccccccccccCCCCeEEEEe
Q 029802 69 PKLVSLGTCIGKF--T--HG-GKFHLTIQALSLVAANARHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYS 143 (187)
Q Consensus 69 ~~L~S~Gtc~GkF--t--Ks-~kFrl~itaL~~La~~a~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n 143 (187)
+.++--|-.||-. . |- =+|+|..++.-.|-.--+.=+||+-+++..-.-|.||+.-+|...+++++.++-|+|.+
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 5677777777743 2 22 28999999998887776788999999999999999999999999999999999999999
Q ss_pred cCCCceeEEeeeechhhhhccC
Q 029802 144 MSDVPLGFGVAAKSMQDCRKLD 165 (187)
Q Consensus 144 ~nd~pLGfGv~akst~~~~~~d 165 (187)
.|+.+.|+|.+.+|..+..+-.
T Consensus 170 ~ng~~vGVg~a~~~~~~~in~~ 191 (202)
T COG5270 170 ENGRVVGVGIAKKSYEELINPE 191 (202)
T ss_pred cCCEEEEEEEEecCHHHhcCcc
Confidence 9999999999999999987765
No 15
>PF13636 Nol1_Nop2_Fmu_2: pre-rRNA processing and ribosome biogenesis; PDB: 3M4X_A 3M6U_B 3M6V_B 3M6W_A 3M6X_A.
Probab=97.00 E-value=0.0011 Score=50.31 Aligned_cols=81 Identities=17% Similarity=0.386 Sum_probs=59.3
Q ss_pred cCCCCCeeeeeeeEEEeeecceEEEEeeehHhHhhcc-cceEEeCCCCccccccccccccccccccccccCCCCeEEEEe
Q 029802 65 NIARPKLVSLGTCIGKFTHGGKFHLTIQALSLVAANA-RHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYS 143 (187)
Q Consensus 65 ~i~r~~L~S~Gtc~GkFtKs~kFrl~itaL~~La~~a-~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n 143 (187)
.+++-+++..|+.+|++.| +.|+++-.+.-.+.+.+ ++.|=++..--..||-|.++--+. ...|-++..
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 3455689999999999987 89999998888887776 446777776777899999984332 377888888
Q ss_pred cCCCceeEEeee
Q 029802 144 MSDVPLGFGVAA 155 (187)
Q Consensus 144 ~nd~pLGfGv~a 155 (187)
-.+.|||||...
T Consensus 79 ~~g~~LG~gk~~ 90 (102)
T PF13636_consen 79 YEGFPLGWGKYV 90 (102)
T ss_dssp ECCCEEEEEEEE
T ss_pred ECCEeeEEEEee
Confidence 899999999984
No 16
>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=96.90 E-value=0.0028 Score=60.98 Aligned_cols=88 Identities=19% Similarity=0.182 Sum_probs=78.5
Q ss_pred ecceEEEEeeehHhHhhc---ccceEEeCCCCccccccccccccccccccccccCCCCeEEEEecCCCceeEEeeeechh
Q 029802 83 HGGKFHLTIQALSLVAAN---ARHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQ 159 (187)
Q Consensus 83 Ks~kFrl~itaL~~La~~---a~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~akst~ 159 (187)
..|-|.|++.+-..|... ..++|+|++..+.=|.=|++||-.||....+++..++=|+|.|.+|..||.|.|.-|..
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 468899999988888543 46899999999999999999999999999999999999999999999999999999999
Q ss_pred hhhccCCCeeEE
Q 029802 160 DCRKLDPNGIVV 171 (187)
Q Consensus 160 ~~~~~dp~~ivv 171 (187)
|+...+. |+.|
T Consensus 524 em~~~~~-G~AV 534 (540)
T TIGR00432 524 EMMDLNH-GQAV 534 (540)
T ss_pred HHHhhcC-ceEE
Confidence 9988876 4444
No 17
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=95.70 E-value=0.016 Score=51.68 Aligned_cols=69 Identities=25% Similarity=0.358 Sum_probs=59.6
Q ss_pred ceEEeCCCCccccccccccccccccccccccCCCCeEEEEecCCCceeEEeeeechhhhhccCCCeeEEE
Q 029802 103 HKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQDCRKLDPNGIVVL 172 (187)
Q Consensus 103 ~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~akst~~~~~~dp~~ivv~ 172 (187)
.+|.|.+.+...+..|+++.-.++.++.++....+-|+|++.++.++|.|.+..|+.++++. +.+++|.
T Consensus 226 P~V~Lde~aa~~I~nG~~L~~~gi~~~~~~~~~gd~V~I~~~~G~~LAIG~~~~ss~el~~~-~kG~~vk 294 (300)
T PRK04270 226 PKIIIKDSAVDAIAHGAPLYAPGIAKLEKGIKKGDLVAVFTLKGELVALGKALMDSDEILKA-EKGIVVD 294 (300)
T ss_pred CceEECHHHHHHHHcCCccccCCceecccccCCCCEEEEEeCCCcEEEEEEEccCHHHHHhc-CCceEEE
Confidence 37888888888899999999888888777766777799999999999999999999999987 6677764
No 18
>PRK11933 yebU rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
Probab=95.67 E-value=0.029 Score=53.14 Aligned_cols=102 Identities=12% Similarity=0.263 Sum_probs=73.2
Q ss_pred eEEEeeCceEEEEcHHHHHhhccCCCCCeeeeeeeEEEeeecceEEEEeeehHhHhhc-ccceEEeCCCCcccccccccc
Q 029802 43 YCFRLHKNRVYYVSESLVKRATNIARPKLVSLGTCIGKFTHGGKFHLTIQALSLVAAN-ARHKVWIKPTSEMSFLYGNHV 121 (187)
Q Consensus 43 y~frl~k~rVyyvs~~l~~~a~~i~r~~L~S~Gtc~GkFtKs~kFrl~itaL~~La~~-a~~Kvwvk~~~E~~FLYGn~V 121 (187)
+.+..++++||++.+.+.. .+..-+++..|+++|++.| +.|..+-...-.|.+. ++..+=+....-..||-|..+
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 4577789999999997533 3445679999999999987 8999985433333333 344566666666679999997
Q ss_pred ccccccccccccCCCCeEEEEecCCCceeEEeeee
Q 029802 122 LKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAK 156 (187)
Q Consensus 122 ~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~ak 156 (187)
--+ +. +..|-++..-++.|||||....
T Consensus 427 ~~~------~~--~~~G~~lv~~~g~~lG~gK~~~ 453 (470)
T PRK11933 427 YPQ------TA--PPAGEVIVTYQGQPIGLAKRVG 453 (470)
T ss_pred cCC------CC--CCCCEEEEEECCEeeEEEEeeC
Confidence 422 21 1358777777999999999964
No 19
>COG3270 Uncharacterized conserved protein [Function unknown]
Probab=94.77 E-value=0.043 Score=44.23 Aligned_cols=80 Identities=15% Similarity=0.233 Sum_probs=67.3
Q ss_pred cCCCCCeeeeeeeEEEeeecceEEEEeeehHhHhhcc-cceEEeCCCCccccccccccccccccccccccCCCCeEEEEe
Q 029802 65 NIARPKLVSLGTCIGKFTHGGKFHLTIQALSLVAANA-RHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYS 143 (187)
Q Consensus 65 ~i~r~~L~S~Gtc~GkFtKs~kFrl~itaL~~La~~a-~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n 143 (187)
++.+.+. ..|+.||.|.| .-||+++++-..|+|-+ ++=|=+.+..-..+.=|+|| .-+.+.++|=|+.-
T Consensus 31 ~l~k~~~-r~GI~lg~~~k-kg~r~s~e~~~al~p~~~~nsiELd~e~a~~w~rG~dV--------~~~~~~~~g~viv~ 100 (127)
T COG3270 31 CLFKEKI-HNGIKLGEIHK-KGYRWSHEGGFALAPPAVRNSIELDEEEAREWMRGRDV--------EPQESGPAGWVIVK 100 (127)
T ss_pred chhhhhh-hcceEEEEEec-cCeeEEeeEEEEeCChhhcceEEeCHHHHHhhhcCCcc--------ccCCCCCCceEEEE
Confidence 4555667 99999999988 67999999999999997 56888888888888999986 34556777788888
Q ss_pred cCCCceeEEee
Q 029802 144 MSDVPLGFGVA 154 (187)
Q Consensus 144 ~nd~pLGfGv~ 154 (187)
-++.+||+|.-
T Consensus 101 ~~~~~lG~aK~ 111 (127)
T COG3270 101 FQGNGLGLAKV 111 (127)
T ss_pred ECCcccceeee
Confidence 89999999987
No 20
>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=94.44 E-value=0.059 Score=48.81 Aligned_cols=78 Identities=26% Similarity=0.423 Sum_probs=62.5
Q ss_pred eEEeCCCCccccccccccccccccccccccCCCCeEEEEecCCCceeEEeeeechhhhhccCCCeeEEE---ecccceee
Q 029802 104 KVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQDCRKLDPNGIVVL---HQSDIGEY 180 (187)
Q Consensus 104 Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~akst~~~~~~dp~~ivv~---~qaD~GeY 180 (187)
+|-|.+.....+..|+++.-.++.+++++....+-|+|++.++.+||+|.+.-|++++...+ .+++|- ...|.|-|
T Consensus 239 ~V~Vd~~~a~~I~NG~~I~~pgv~~~d~~i~~gd~V~V~~~~G~~LAIGea~~s~~ei~~~~-kG~vV~~~~~~~~~~~~ 317 (322)
T TIGR00425 239 RVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVAVITLKGEAVAVGIALMSTKDIANAD-KGVVADVKRVIMERGTY 317 (322)
T ss_pred ceEeCHHHHHHHHCCCccccccccccccccCCCCEEEEEECCCEEEEEEEEecCHHHHhhcC-CcEEEEEEEEeeCCCCC
Confidence 67777777777889999988888877766666677999998999999999999999999877 466654 45677776
Q ss_pred ec
Q 029802 181 LR 182 (187)
Q Consensus 181 LR 182 (187)
=+
T Consensus 318 ~~ 319 (322)
T TIGR00425 318 PR 319 (322)
T ss_pred CC
Confidence 43
No 21
>PRK05429 gamma-glutamyl kinase; Provisional
Probab=94.37 E-value=0.061 Score=49.11 Aligned_cols=71 Identities=14% Similarity=0.253 Sum_probs=62.3
Q ss_pred hHhhc--ccceEEeCCCCcccc-ccccccccccccccccccCCCCeEEEEecCCCceeEEeeeechhhhhccCC
Q 029802 96 LVAAN--ARHKVWIKPTSEMSF-LYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQDCRKLDP 166 (187)
Q Consensus 96 ~La~~--a~~Kvwvk~~~E~~F-LYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~akst~~~~~~dp 166 (187)
+|+-. .+-+|+|+..|...- --|.+++-.+|..++.++...+-|.|++.++.++|.|.+..|+.++.+...
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 355999998888777 689999999999999999999999999999999999999999999987744
No 22
>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=92.66 E-value=0.19 Score=45.85 Aligned_cols=71 Identities=17% Similarity=0.288 Sum_probs=62.4
Q ss_pred HhHhhc--ccceEEeCCCCcccccc-ccccccccccccccccCCCCeEEEEecCCCceeEEeeeechhhhhccC
Q 029802 95 SLVAAN--ARHKVWIKPTSEMSFLY-GNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQDCRKLD 165 (187)
Q Consensus 95 ~~La~~--a~~Kvwvk~~~E~~FLY-Gn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~akst~~~~~~d 165 (187)
.+||-. .+-.|+|...|...-+- |.+++-++|..+..++...+-|-|.+.++.+||-|.+..|..++++..
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 355543 34599999888888876 899999999999999999999999999999999999999999998764
No 23
>PRK08557 hypothetical protein; Provisional
Probab=92.47 E-value=0.76 Score=43.12 Aligned_cols=131 Identities=17% Similarity=0.094 Sum_probs=91.5
Q ss_pred CCCCCHHHHHHHHHHHhhhhcccccccccCCCCCCCCCCCCceEEEeeCceEEEEcHHHHHhhccCCCCCeeeeeeeEEE
Q 029802 1 MRPLDEAETTAVFEKLFKFTGNNLKNIVENPSHEGPDPNPGRYCFRLHKNRVYYVSESLVKRATNIARPKLVSLGTCIGK 80 (187)
Q Consensus 1 MR~LteeE~~~vf~KL~kyiG~nl~~li~~~~~~~~~~~d~~y~frl~k~rVyyvs~~l~~~a~~i~r~~L~S~Gtc~Gk 80 (187)
.||--+.|++.+-+-+.+--|.+..-|++.. .| -| -.+.++.=|-+||-
T Consensus 6 ~r~a~~~d~~~~~~~~~~~f~~~~~vllnk~--------p~-------~d----------------~~~ev~~~g~~~g~ 54 (417)
T PRK08557 6 TKFASPYEIKILNKLTNKNFQYDDAIILEKL--------SG-------LD----------------YRKRVYISEDQIGI 54 (417)
T ss_pred cCcCCHHHHHHHHHHHHHHcCCCeEEEEeCC--------CC-------cc----------------chhheeECCeEEEE
Confidence 4788888999888888777777765666654 11 00 01556777889996
Q ss_pred ee---ecceEEEEeeehHhHhhcccceEEeCCCCcccccccccccccccccccc--ccCCCCeEEEEecCCCceeEEeee
Q 029802 81 FT---HGGKFHLTIQALSLVAANARHKVWIKPTSEMSFLYGNHVLKGGLGRITD--SIAPGDGVVVYSMSDVPLGFGVAA 155 (187)
Q Consensus 81 Ft---Ks~kFrl~itaL~~La~~a~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite--~~~~~~gVvV~n~nd~pLGfGv~a 155 (187)
+. ...+++++.++..++-. +++|-|+| -..+|=|.+|....+.-+.+ ++..++-|+|-+ +.++|.|++.
T Consensus 55 ~~~~~~~~~w~~~p~~~~~~~~--~~~~~~~~--~~~~~~g~~v~~~~~~~~~~~~~~~~~~~v~~~~--~~~~gvg~~~ 128 (417)
T PRK08557 55 LEFDLLDLDWKFHPSPSYYLIE--EPKIKLKP--TKRRLKGKYIKEELIENPEELNEILENDYVGVEI--GNFLGVGVKK 128 (417)
T ss_pred EEEccccceeEEccchhhhhcc--Cceeeecc--cccccCCccccccccccccccccCCCCCEEEEec--CCEEEEEEee
Confidence 63 34577777777765533 56777776 55588999999998888777 676677444433 7899999998
Q ss_pred echhhhhccCCCe
Q 029802 156 KSMQDCRKLDPNG 168 (187)
Q Consensus 156 kst~~~~~~dp~~ 168 (187)
.++...+++.+..
T Consensus 129 ~~~~k~~~~~~~~ 141 (417)
T PRK08557 129 EDRIKIKDLSLKK 141 (417)
T ss_pred cceEEEEecccCC
Confidence 8777777776643
No 24
>COG1549 Queuine tRNA-ribosyltransferases, contain PUA domain [Translation, ribosomal structure and biogenesis]
Probab=91.01 E-value=0.75 Score=44.56 Aligned_cols=88 Identities=25% Similarity=0.335 Sum_probs=65.6
Q ss_pred eeeEEEeeecceEEEEeeehHhHhhcccceEEeCCCCccccccccccccccccccccccCCCCeEEEEecCCCceeEEee
Q 029802 75 GTCIGKFTHGGKFHLTIQALSLVAANARHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVA 154 (187)
Q Consensus 75 Gtc~GkFtKs~kFrl~itaL~~La~~a~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~ 154 (187)
|.-+|+|+-+ .-.++..+..+|- . .+.||.=. -|.=-.+|++.++.+.+|++.+|+-|+|.- ++..+|.|+|
T Consensus 425 n~ql~~~~~~-~ls~t~~g~~~~~--~-~~~~VEId---~f~~~g~v~a~GV~da~edIrpnDeV~vv~-~~~v~gVGrA 496 (519)
T COG1549 425 NEQLGTFTPN-LLSLTPFGAELLY--G-GIYWVEID---DFIPRGSVFAPGVVDADEDIRPNDEVVVVH-GGEVRGVGRA 496 (519)
T ss_pred cceeeccccc-ceeccHhHhhhhh--c-CeeEEEcC---CccccccccccccccCCCCCCcCCEEEEEe-CCeEEEEeee
Confidence 7777777764 3333333444333 2 57777422 277788999999999999999999997765 8899999999
Q ss_pred eechhhhhccCCCeeEE
Q 029802 155 AKSMQDCRKLDPNGIVV 171 (187)
Q Consensus 155 akst~~~~~~dp~~ivv 171 (187)
+-|..++..+... +.|
T Consensus 497 ~msg~eM~~akkG-iaV 512 (519)
T COG1549 497 VMSGREMVEAKKG-IAV 512 (519)
T ss_pred ecChHHhcccCCc-eEE
Confidence 9999999888764 444
No 25
>PRK13402 gamma-glutamyl kinase; Provisional
Probab=72.55 E-value=5.2 Score=36.90 Aligned_cols=64 Identities=11% Similarity=0.093 Sum_probs=58.4
Q ss_pred ceEEeCCCCcccccc-ccccccccccccccccCCCCeEEEEecCCCceeEEeeeechhhhhccCC
Q 029802 103 HKVWIKPTSEMSFLY-GNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQDCRKLDP 166 (187)
Q Consensus 103 ~Kvwvk~~~E~~FLY-Gn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~akst~~~~~~dp 166 (187)
=.++|.+.|..--+. |..+|-++|.++.-++...+.|-|++.++..+|-|.+..|..|+++...
T Consensus 277 G~i~vd~ga~~al~~~~~sLl~~gi~~v~g~F~~gd~v~i~~~~g~~~~rg~~~y~s~~~~~i~g 341 (368)
T PRK13402 277 GEIVVENDFDRALDNHSEQLTSDDVVEIKGDFSVGDTILVRKGDGTKLAKGKSNYSSCLLNFIKD 341 (368)
T ss_pred eeEEECccHHHHHHhcCCcccccceEEEeCEecCCCEEEEECCCCCEEEEEEccCCHHHHHHHcC
Confidence 388999888888875 6999999999999999999999999999999999999999999987633
No 26
>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=70.04 E-value=4.1 Score=27.29 Aligned_cols=45 Identities=29% Similarity=0.349 Sum_probs=29.6
Q ss_pred EEeCCCCccccccccccccccccccccccCCCCeEEEEecCCCceeEEeee
Q 029802 105 VWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAA 155 (187)
Q Consensus 105 vwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~a 155 (187)
|-+++.....|+-|+.|-- .+..+..+-|-||+.++.+||.|...
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 4455566677888998832 55566777999999999999999984
No 27
>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional
Probab=68.74 E-value=10 Score=35.11 Aligned_cols=49 Identities=14% Similarity=0.254 Sum_probs=35.8
Q ss_pred eEEeCCCCccc------cccccccccccccccccccCCCCeEEEEecCCCceeEEeeeec
Q 029802 104 KVWIKPTSEMS------FLYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAKS 157 (187)
Q Consensus 104 Kvwvk~~~E~~------FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~aks 157 (187)
+|.+|+.++.. ++|.+.| .++..+.+..+-|.|++.++.+||.|.....
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 57778876654 5666666 4444345567789999999999999998543
No 28
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=55.65 E-value=14 Score=33.61 Aligned_cols=62 Identities=21% Similarity=0.190 Sum_probs=45.5
Q ss_pred ceEEeCCCCccccccccccccccccccccccCCCCeEEEEecCCCceeEEeeeechhhhhccC
Q 029802 103 HKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQDCRKLD 165 (187)
Q Consensus 103 ~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~akst~~~~~~d 165 (187)
-+|-|+++....+.+|+.+--+.+..+ .+....+-|+|++.++.+||+|..-.+...++...
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 488899999999999998854433333 22334456899998899999999877777666544
No 29
>COG0263 ProB Glutamate 5-kinase [Amino acid transport and metabolism]
Probab=48.13 E-value=23 Score=33.26 Aligned_cols=70 Identities=17% Similarity=0.268 Sum_probs=61.0
Q ss_pred hHhhcc--cceEEeCCCCccccc-cccccccccccccccccCCCCeEEEEecCCCceeEEeeeechhhhhccCC
Q 029802 96 LVAANA--RHKVWIKPTSEMSFL-YGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQDCRKLDP 166 (187)
Q Consensus 96 ~La~~a--~~Kvwvk~~~E~~FL-YGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLGfGv~akst~~~~~~dp 166 (187)
+|+-++ .=+|+|...++.--+ .|+.++=++|..+.-++...+-|-|+ .++..+|=|....|..|.++...
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 348999999999999 99999999999999999999999999 77779999999999999987654
No 30
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=37.20 E-value=20 Score=27.39 Aligned_cols=19 Identities=26% Similarity=0.690 Sum_probs=15.7
Q ss_pred CeEEEEecCCCceeEEeee
Q 029802 137 DGVVVYSMSDVPLGFGVAA 155 (187)
Q Consensus 137 ~gVvV~n~nd~pLGfGv~a 155 (187)
.|+.+-.+..+|+|||..|
T Consensus 32 ~g~~~~~~~~epIaFGLka 50 (88)
T COG2092 32 EGYELIKIEEEPIAFGLKA 50 (88)
T ss_pred ccceeccceeEeeeeeeee
Confidence 4566669999999999986
No 31
>KOG2523 consensus Predicted RNA-binding protein with PUA domain [Translation, ribosomal structure and biogenesis]
Probab=33.74 E-value=1.1e+02 Score=26.12 Aligned_cols=108 Identities=19% Similarity=0.254 Sum_probs=82.2
Q ss_pred cCCCCCeeeeeeeEEEeee-cceEEEEeeehHhHhhc--ccceEEeCCCCcccccccccccccccc----ccccccCCCC
Q 029802 65 NIARPKLVSLGTCIGKFTH-GGKFHLTIQALSLVAAN--ARHKVWIKPTSEMSFLYGNHVLKGGLG----RITDSIAPGD 137 (187)
Q Consensus 65 ~i~r~~L~S~Gtc~GkFtK-s~kFrl~itaL~~La~~--a~~Kvwvk~~~E~~FLYGn~V~Ks~l~----rite~~~~~~ 137 (187)
|=.+-.|+|+|.-.==|-+ .|+| +..|.+|-+| +-+.+-|...|=...|=|-||+=-++. .++...+..+
T Consensus 55 C~d~i~L~s~~G~~~fF~~~dg~~---~PTLRllhk~p~~~~~~qvD~GAIkfvlsGAnIMcPGlts~g~~l~~~~ekd~ 131 (181)
T KOG2523|consen 55 CKDHIELLSVNGEVLFFCHRDGPY---IPTLRLLHKYPFIFPHVQVDRGAIKFVLSGANIMCPGLTSPGAKLPPGVEKDT 131 (181)
T ss_pred ccCeeEEEEeCCEEEEEEecCCCc---cchhHHHhhCCCccceEEecCcceeeeecCCceEcccCCCCcccCCCCccCCC
Confidence 4455668899844443432 3355 4567888877 567999999999999999999877764 5677777889
Q ss_pred eEEEEecCCC-ceeEEeeeechhhhhccCC-CeeEEEecc
Q 029802 138 GVVVYSMSDV-PLGFGVAAKSMQDCRKLDP-NGIVVLHQS 175 (187)
Q Consensus 138 gVvV~n~nd~-pLGfGv~akst~~~~~~dp-~~ivv~~qa 175 (187)
-|+|+-.... +|-+|.+.-|+.|++..+. .+|=.+|--
T Consensus 132 ~V~i~aeGK~~alAiG~~~ms~kei~s~nKGiGIE~~H~l 171 (181)
T KOG2523|consen 132 IVAIMAEGKEHALAIGLTKMSAKEIKSVNKGIGIENYHYL 171 (181)
T ss_pred EEEEEecCchhhhhhhhhhhcHHHHHhhccCCceEEEEec
Confidence 9999999888 9999999999999987765 566666543
No 32
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=33.66 E-value=33 Score=30.74 Aligned_cols=66 Identities=24% Similarity=0.366 Sum_probs=47.5
Q ss_pred eecceEEE----EeeehHhHh-----------hc--ccc-eEEeCCCCccccccccccccccccccccccCCCCeEEEEe
Q 029802 82 THGGKFHL----TIQALSLVA-----------AN--ARH-KVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYS 143 (187)
Q Consensus 82 tKs~kFrl----~itaL~~La-----------~~--a~~-Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n 143 (187)
|++|.|.+ .++.|+.+. .+ .-+ |++++++....+.+|+. -++.. .+..+.|.|++
T Consensus 175 t~~g~f~~~~~~~l~~l~~~~~~~~~~~~~p~e~~l~~lpk~~i~~~~~~~i~~G~~---~~~~~----~~~~~~v~v~~ 247 (271)
T COG0130 175 TRVGPFSEEDAVTLELLDELDAESLLRLLLPLESALSDLPRLVLKDSAANAIKYGAK---PGLLD----IELGGLVRVYT 247 (271)
T ss_pred ccccccccccccchhhHHHHHhhhhhccccchhHHhccCCcEecCHHHHHHHHcCCc---hhccc----cccCCcEEEEc
Confidence 56788877 566666653 12 233 99999999999999998 22111 78999999999
Q ss_pred cCCCceeEEee
Q 029802 144 MSDVPLGFGVA 154 (187)
Q Consensus 144 ~nd~pLGfGv~ 154 (187)
..+..++.|..
T Consensus 248 ~~~~~~al~~~ 258 (271)
T COG0130 248 AKGLGIALGEI 258 (271)
T ss_pred cCCeEEEEeeh
Confidence 99855555544
No 33
>TIGR02624 rhamnu_1P_ald rhamnulose-1-phosphate aldolase. Members of this family are the enzyme RhaD, rhamnulose-1-phosphate aldolase.
Probab=33.42 E-value=58 Score=28.77 Aligned_cols=54 Identities=7% Similarity=0.079 Sum_probs=34.8
Q ss_pred hHhhcc-cceEEeCCCCccccccccccccccccccccccCCCCeEEEEecCCCcee----EEeeeechhhh
Q 029802 96 LVAANA-RHKVWIKPTSEMSFLYGNHVLKGGLGRITDSIAPGDGVVVYSMSDVPLG----FGVAAKSMQDC 161 (187)
Q Consensus 96 ~La~~a-~~Kvwvk~~~E~~FLYGn~V~Ks~l~rite~~~~~~gVvV~n~nd~pLG----fGv~akst~~~ 161 (187)
+-+|+- ...+||+|+|- +..+++++.+++-+|++.++++..+- |.-..|.|+|.
T Consensus 59 ~~~~~~~~~~~lITpSG~------------~~~~l~~~~~~d~~iv~vd~~G~~~~~~~~~~~g~kPSsE~ 117 (270)
T TIGR02624 59 FPAPELANKYFLVTGSGK------------FFRNVEENPAENLGILRVSEDGASVHLLWGLTDGGVPTSEL 117 (270)
T ss_pred cccccccCCEEEEeCCCC------------CHHhcccCchhceeEEEECCCCCEEEeeccccCCCCcChHH
Confidence 334443 34799999973 45678766556667888999998773 32223666654
No 34
>PF02762 Cbl_N3: CBL proto-oncogene N-terminus, SH2-like domain; InterPro: IPR014742 Cbl (Casitas B-lineage lymphoma) is an adaptor protein that functions as a negative regulator of many signalling pathways that start from receptors at the cell surface. The N-terminal region of Cbl contains a Cbl-type phosphotyrosine-binding (Cbl-PTB) domain, which is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle (4H) domain, an EF hand-like calcium-binding domain, and a divergent SH2-like domain. The calcium-bound EF-hand wedges between the 4H and SH2 domains, and roughly determines their relative orientation. The Cbl-PTB domain has also been named Cbl N-terminal (Cbl-N) or tyrosine kinase binding (TKB) domain [, ]. The N-terminal 4H domain contains four long alpha-helices. The C and D helices in this domain pack against the adjacent EF-hand-like domain, and a highly conserved loop connecting the A and B helices contacts the SH2-like domain. The EF-hand motif is similar to classical EF-hand proteins. The SH2-like domain retains the general helix-sheet-helix architecture of the SH2 fold, but lacks the secondary beta-sheet, comprising beta-strands D', E and F, and also a prominent BG loop []. This entry represents the SH2-like domain.; PDB: 3PFV_A 3VGO_A 3PLF_B 2Y1M_A 2CBL_A 3BUX_B 3BUN_B 3BUM_B 3OB1_B 3BUW_B ....
Probab=33.12 E-value=60 Score=24.61 Aligned_cols=30 Identities=37% Similarity=0.605 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHHHHHhhhhcccccccccCCCCCCCCCCCCceEEEeeCce
Q 029802 2 RPLDEAETTAVFEKLFKFTGNNLKNIVENPSHEGPDPNPGRYCFRLHKNR 51 (187)
Q Consensus 2 R~LteeE~~~vf~KL~kyiG~nl~~li~~~~~~~~~~~d~~y~frl~k~r 51 (187)
-=||-+|.+. .|..|+ ++ .|+|+|||.-.|
T Consensus 7 AFlTYdevk~---~L~~~~--------~k---------pGsYiFRlSCTr 36 (86)
T PF02762_consen 7 AFLTYDEVKA---RLQHYR--------DK---------PGSYIFRLSCTR 36 (86)
T ss_dssp TT--HHHHHH---HHGGGT--------TS---------TTEEEEEEESSS
T ss_pred EEEeHHHHHH---HHHHHh--------CC---------cccEEEeecccc
Confidence 3467777665 444444 44 389999997544
No 35
>PRK11558 putative ssRNA endonuclease; Provisional
Probab=32.27 E-value=48 Score=25.58 Aligned_cols=43 Identities=16% Similarity=0.299 Sum_probs=31.6
Q ss_pred ccccccCCCCeEEEEecCCCceeEEeeeechhhhhccCCCeeEE
Q 029802 128 RITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQDCRKLDPNGIVV 171 (187)
Q Consensus 128 rite~~~~~~gVvV~n~nd~pLGfGv~akst~~~~~~dp~~ivv 171 (187)
++++.++....|.|++-+.++ ||..-......-.-.|=+|+.+
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 9999877766433344444433
No 36
>PF08366 LLGL: LLGL2; InterPro: IPR013577 This domain is found in lethal giant larvae homologue 2 (LLGL2) proteins and syntaxin-binding proteins like tomosyn []. It has been identified in eukaryotes and tends to be found together with WD repeats (IPR001680 from INTERPRO).
Probab=30.08 E-value=2.3e+02 Score=22.06 Aligned_cols=76 Identities=20% Similarity=0.329 Sum_probs=52.0
Q ss_pred cceE-EeCC-CCcccccccccccccccc-ccccccCCCCeEEEEecCCCceeEEeeeechhhhhccCCCeeEEEecccc
Q 029802 102 RHKV-WIKP-TSEMSFLYGNHVLKGGLG-RITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQDCRKLDPNGIVVLHQSDI 177 (187)
Q Consensus 102 ~~Kv-wvk~-~~E~~FLYGn~V~Ks~l~-rite~~~~~~gVvV~n~nd~pLGfGv~akst~~~~~~dp~~ivv~~qaD~ 177 (187)
-.|| |..- ++|...+|..=.-+++-+ |=+=.+-+....+|+.|..-.+.|=....+...+-.-+|.+++|.-+-|.
T Consensus 16 I~Ki~w~~~~~~~~~iiFsGGmp~~~ygdr~~vTV~~g~~~~~ldf~s~VIDF~~i~~~~~~~e~~~P~alvVL~e~eL 94 (105)
T PF08366_consen 16 INKILWRTSRNGEPFIIFSGGMPRASYGDRHCVTVMQGKTHVVLDFTSRVIDFFTICESPWPNEFQDPYALVVLLEEEL 94 (105)
T ss_pred eeEEEEEecCCCCcEEEEeCCccccccCCCceEEEEeCCEEEEEEcCCceEEEEEEcCCCCccccCCCcEEEEEEcCcE
Confidence 4577 6643 466555655544443211 11111336788999999999999999988877888889999999887764
No 37
>TIGR01639 P_fal_TIGR01639 Plasmodium falciparum uncharacterized domain TIGR01639. This model represents a conserved sequence region of about 60 amino acids found in over 40 predicted proteins of Plasmodium falciparum. It is not found elsewhere, including closely related species such as Plasmodium yoelii. No member of this family is characterized.
Probab=28.70 E-value=30 Score=23.98 Aligned_cols=22 Identities=18% Similarity=0.315 Sum_probs=18.9
Q ss_pred CCCCHHHHHHHHHHHhhhhccc
Q 029802 2 RPLDEAETTAVFEKLFKFTGNN 23 (187)
Q Consensus 2 R~LteeE~~~vf~KL~kyiG~n 23 (187)
++||+||+..+...|...+..+
T Consensus 8 ~~lTeEEl~~~i~~L~~~~~~~ 29 (61)
T TIGR01639 8 KKLSKEELNELINSLDEIPNRN 29 (61)
T ss_pred HHccHHHHHHHHHhhcCCCCHH
Confidence 5799999999999998887654
No 38
>PF08920 SF3b1: Splicing factor 3B subunit 1; InterPro: IPR015016 This group of proteins consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly []. ; PDB: 2FHO_A 3LQV_P 2PEH_D 2F9J_P 2F9D_Q.
Probab=27.83 E-value=22 Score=29.05 Aligned_cols=13 Identities=38% Similarity=0.687 Sum_probs=9.4
Q ss_pred CCCCHHHHHHHHH
Q 029802 2 RPLDEAETTAVFE 14 (187)
Q Consensus 2 R~LteeE~~~vf~ 14 (187)
|||||||+..+|-
T Consensus 85 rpLTDEELD~mLP 97 (144)
T PF08920_consen 85 RPLTDEELDAMLP 97 (144)
T ss_dssp S-S-HHHHHHTS-
T ss_pred CcCCHHHHHHhCC
Confidence 8999999999884
No 39
>PF09707 Cas_Cas2CT1978: CRISPR-associated protein (Cas_Cas2CT1978); InterPro: IPR010152 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a minor branch of the Cas2 family of CRISPR-associated protein which are found in IPR003799 from INTERPRO. Cas2 is one of four protein families (Cas1 to Cas4) that are associated with CRISPR elements and always occur near a repeat cluster, usually in the order cas3-cas4-cas1-cas2. The function of Cas2 (and Cas1) is unknown. Cas3 proteins appear to be helicases while Cas4 proteins resemble RecB-type exonucleases, suggesting that these genes are involved in DNA metabolism or gene expression [].
Probab=24.09 E-value=65 Score=24.20 Aligned_cols=32 Identities=28% Similarity=0.437 Sum_probs=26.3
Q ss_pred cccccccCCCCeEEEEecCCCceeEEeeeechh
Q 029802 127 GRITDSIAPGDGVVVYSMSDVPLGFGVAAKSMQ 159 (187)
Q Consensus 127 ~rite~~~~~~gVvV~n~nd~pLGfGv~akst~ 159 (187)
.++++.+++...+.+++.++ +-||..-.....
T Consensus 43 ~~v~~~~~~G~a~m~~~~~n-eqG~~~~t~G~~ 74 (86)
T PF09707_consen 43 ERVTEWIGDGSAVMVWSDNN-EQGFDFRTLGDP 74 (86)
T ss_pred HHHHhhCCCccEEEEEccCC-CCCEEEEEeCCC
Confidence 35788899999999999988 999998765443
No 40
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=22.86 E-value=75 Score=24.44 Aligned_cols=17 Identities=29% Similarity=0.354 Sum_probs=14.6
Q ss_pred CCCCHHHHHHHHHHHhh
Q 029802 2 RPLDEAETTAVFEKLFK 18 (187)
Q Consensus 2 R~LteeE~~~vf~KL~k 18 (187)
|.||++|++.|-..|..
T Consensus 34 r~Ltd~ev~~Va~~L~~ 50 (96)
T PF11829_consen 34 RRLTDDEVAEVAAELAA 50 (96)
T ss_dssp TTS-HHHHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHHh
Confidence 78999999999999976
No 41
>PF09183 DUF1947: Domain of unknown function (DUF1947); InterPro: IPR015266 Members of this entry are a set of hypothetical archaeal proteins. Their exact function has not, as yet, been defined. ; PDB: 1Q7H_A.
Probab=22.51 E-value=1.7e+02 Score=21.14 Aligned_cols=43 Identities=19% Similarity=0.202 Sum_probs=23.9
Q ss_pred CCHHHHHHHHHHHhhhhcccccccccCCCCCCCCCCCCceEEEeeCceEEEEcHHH
Q 029802 4 LDEAETTAVFEKLFKFTGNNLKNIVENPSHEGPDPNPGRYCFRLHKNRVYYVSESL 59 (187)
Q Consensus 4 LteeE~~~vf~KL~kyiG~nl~~li~~~~~~~~~~~d~~y~frl~k~rVyyvs~~l 59 (187)
|++.|.+.+++++....|-+|.. +.-=+...++.-.||++..+
T Consensus 5 LSkKe~k~~~~k~~~~ygIdi~~-------------~~vEI~~~kk~~~yyi~~~p 47 (65)
T PF09183_consen 5 LSKKEIKEIKEKIKEKYGIDISG-------------EKVEIGKEKKFSIYYIDGVP 47 (65)
T ss_dssp --HHHHHHHHHHHHT-TT---TT----------------EEEE-SS-EEEEETTEE
T ss_pred ccHHHHHHHHHHHHHHhCcCCCc-------------cceeeeeccceEEEEECCch
Confidence 78999999999999977777643 12234444666677776644
No 42
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=21.51 E-value=1.1e+02 Score=23.47 Aligned_cols=36 Identities=14% Similarity=0.449 Sum_probs=22.8
Q ss_pred eeeEEEeee---cceEEEEee-ehHhHhhc---ccceEEeCCC
Q 029802 75 GTCIGKFTH---GGKFHLTIQ-ALSLVAAN---ARHKVWIKPT 110 (187)
Q Consensus 75 Gtc~GkFtK---s~kFrl~it-aL~~La~~---a~~Kvwvk~~ 110 (187)
|..+|++++ ++.|+.... +...||.- -+++|||++.
T Consensus 19 ~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~iwI~~G 61 (99)
T TIGR00523 19 GEILGVIEQMLGAGRVKVRCLDGKTRLGRIPGKLKKRIWIREG 61 (99)
T ss_pred CEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCC
Confidence 667787776 467776532 44455544 3569999953
No 43
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=21.45 E-value=1.1e+02 Score=22.52 Aligned_cols=36 Identities=25% Similarity=0.469 Sum_probs=22.4
Q ss_pred eeeEEEeee---cceEEEEee-ehHhHhhcc---cceEEeCCC
Q 029802 75 GTCIGKFTH---GGKFHLTIQ-ALSLVAANA---RHKVWIKPT 110 (187)
Q Consensus 75 Gtc~GkFtK---s~kFrl~it-aL~~La~~a---~~Kvwvk~~ 110 (187)
|..+|++++ ++.|+...+ +-..||.-+ +++|||++.
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~dG~~~la~ipgK~Rk~iwI~~G 47 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCADGKERLARIPGKMRKKVWIRRG 47 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCC
Confidence 455677765 567776643 445555443 569999954
No 44
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=21.37 E-value=2.4e+02 Score=24.15 Aligned_cols=93 Identities=8% Similarity=0.021 Sum_probs=56.8
Q ss_pred HHHHHHHHHHhhhhcccccccccCCCCCCCCCCCCceEEE----e-eCc--eEEEEcHHHHHhhccCCCCCeeeeeeeEE
Q 029802 7 AETTAVFEKLFKFTGNNLKNIVENPSHEGPDPNPGRYCFR----L-HKN--RVYYVSESLVKRATNIARPKLVSLGTCIG 79 (187)
Q Consensus 7 eE~~~vf~KL~kyiG~nl~~li~~~~~~~~~~~d~~y~fr----l-~k~--rVyyvs~~l~~~a~~i~r~~L~S~Gtc~G 79 (187)
+|.+.+=++-+.+|.++=.-+|| .|+=|+. | +.. .|+--|..++..+..-+.-+++.+| |
T Consensus 77 ~~K~~IA~~Aa~lI~~g~tIflD----------~GtT~~~la~~L~~~~~ltvvTnsl~i~~~l~~~~~~~villG---G 143 (252)
T PRK10681 77 EEKRRAAQLAATLVEPNQTLFFD----------CGTTTPWIIEAIDNELPFTAVCYSLNTFLALQEKPHCRAILCG---G 143 (252)
T ss_pred HHHHHHHHHHHhhcCCCCEEEEE----------CCccHHHHHHhcCCCCCeEEEECCHHHHHHHhhCCCCEEEEEC---c
Confidence 45555555556666555444554 2332222 1 112 3444456566554444445688888 6
Q ss_pred EeeecceEEEEeeehHhHhhcccceEEeCCCCc
Q 029802 80 KFTHGGKFHLTIQALSLVAANARHKVWIKPTSE 112 (187)
Q Consensus 80 kFtKs~kFrl~itaL~~La~~a~~Kvwvk~~~E 112 (187)
++.+....-.-..+++.|.+|.-.+..+-.+|=
T Consensus 144 ~~~~~~~~~~G~~~~~~l~~~~~D~afig~~gi 176 (252)
T PRK10681 144 EFHASNAIFKPLDFQQTLDNICPDIAFYSAAGV 176 (252)
T ss_pred EEecCcceeeCHHHHHHHHhhCCCEEEEeCcee
Confidence 776655666677788999999888999988764
No 45
>PF12594 DUF3764: Protein of unknown function (DUF3764); InterPro: IPR022240 This family of proteins is found in bacteria. Proteins in this family are typically between 89 and 101 amino acids in length.
Probab=20.92 E-value=60 Score=24.55 Aligned_cols=16 Identities=44% Similarity=0.760 Sum_probs=13.8
Q ss_pred ccCCCeeEEEecccce
Q 029802 163 KLDPNGIVVLHQSDIG 178 (187)
Q Consensus 163 ~~dp~~ivv~~qaD~G 178 (187)
+-||+.++|.+|++-|
T Consensus 44 kdDp~kv~vI~Qa~eg 59 (86)
T PF12594_consen 44 KDDPQKVIVIHQAPEG 59 (86)
T ss_pred cCCCceEEEEEecCHH
Confidence 4789999999999865
No 46
>PF07430 PP1: Phloem filament protein PP1; InterPro: IPR009994 This domain represents a conserved region approximately 200 residues long, four copies of which are found within the plant phloem filament protein PP1. This is one of the constituents of the proteinaceous filaments found in the sieve elements of Cucurbita phloem [].
Probab=20.78 E-value=72 Score=27.77 Aligned_cols=44 Identities=27% Similarity=0.228 Sum_probs=32.6
Q ss_pred CCCCeeeeeeeEEEeee----cceEEEEeeehHhHhhcccc--eEEeCCC
Q 029802 67 ARPKLVSLGTCIGKFTH----GGKFHLTIQALSLVAANARH--KVWIKPT 110 (187)
Q Consensus 67 ~r~~L~S~Gtc~GkFtK----s~kFrl~itaL~~La~~a~~--Kvwvk~~ 110 (187)
+.++|--..+--|..-+ ..||||||-|.|-...-.+| -||+|+.
T Consensus 142 ~gd~LkF~KV~eGw~q~l~~d~ikYrLhI~AkDg~G~~~~YeAvV~~k~~ 191 (202)
T PF07430_consen 142 AGDKLKFEKVYEGWYQDLGNDGIKYRLHIVAKDGLGRLGNYEAVVWEKQF 191 (202)
T ss_pred cCCceEEEEEeeEEEEeccCCCceEEEEEEeecCCCCcCceEEEEEEecc
Confidence 34667777777776533 25899999999998888888 6888764
No 47
>COG3512 CRISPR-associated protein, Cas2 homolog [Defense mechanisms]
Probab=20.09 E-value=27 Score=27.70 Aligned_cols=27 Identities=15% Similarity=0.340 Sum_probs=23.3
Q ss_pred cccccccccccccccccccCCCCeEEE
Q 029802 115 FLYGNHVLKGGLGRITDSIAPGDGVVV 141 (187)
Q Consensus 115 FLYGn~V~Ks~l~rite~~~~~~gVvV 141 (187)
-+-|++-.++|++|+.|..|+.+.|=.
T Consensus 49 i~kg~~s~~~~i~rl~e~lP~~Gnir~ 75 (116)
T COG3512 49 ILKGRDSNQKHIGRLREHLPNEGNIRC 75 (116)
T ss_pred HHhCchhHHHHHHHHHHhCCCCCceEE
Confidence 356999999999999999999987744
Done!