Query 020116
Match_columns 331
No_of_seqs 129 out of 284
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 07:08:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020116.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020116hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3943 THUMP domain-containin 100.0 6.6E-45 1.4E-49 330.8 13.8 243 31-327 36-281 (291)
2 PF02926 THUMP: THUMP domain; 99.6 5.3E-15 1.2E-19 125.5 10.7 109 159-307 35-144 (144)
3 COG1818 Predicted RNA-binding 99.6 3.8E-14 8.2E-19 126.4 13.7 109 176-317 55-163 (175)
4 PRK01565 thiamine biosynthesis 98.5 8.3E-07 1.8E-11 88.7 11.6 84 182-290 71-155 (394)
5 PRK01269 tRNA s(4)U8 sulfurtra 98.3 5.3E-06 1.2E-10 85.0 12.1 85 181-290 72-156 (482)
6 PRK08384 thiamine biosynthesis 98.2 1.9E-05 4.1E-10 78.8 12.6 88 182-290 72-159 (381)
7 TIGR00342 thiazole biosynthesi 98.0 4.9E-05 1.1E-09 75.5 11.3 81 184-290 71-151 (371)
8 COG0301 ThiI Thiamine biosynth 97.8 0.00019 4.2E-09 71.5 10.9 101 182-306 70-182 (383)
9 COG0116 Predicted N6-adenine-s 94.5 0.14 3E-06 51.4 7.8 104 179-314 53-163 (381)
10 TIGR01177 conserved hypothetic 94.2 0.28 6.1E-06 47.7 9.2 81 191-306 61-141 (329)
11 PRK11783 rlmL 23S rRNA m(2)G24 90.4 1.5 3.3E-05 47.3 9.6 100 180-307 52-154 (702)
12 PF06331 Tbf5: Transcription f 56.1 11 0.00024 28.9 2.5 22 38-64 5-26 (68)
13 TIGR01213 conserved hypothetic 51.4 34 0.00073 34.7 5.8 92 190-290 57-149 (388)
14 KOG2671 Putative RNA methylase 42.2 34 0.00073 34.5 4.1 53 220-291 97-150 (421)
15 PF13590 DUF4136: Domain of un 23.3 2.1E+02 0.0044 23.8 5.4 56 219-290 15-70 (151)
16 COG1258 Predicted pseudouridyl 23.2 1.4E+02 0.0031 30.3 5.0 30 260-290 126-155 (398)
17 PF01910 DUF77: Domain of unkn 20.8 4.4E+02 0.0095 21.0 7.0 67 157-232 12-78 (92)
18 KOG2715 Uncharacterized conser 20.6 1.1E+02 0.0023 27.9 3.2 34 138-171 21-54 (210)
No 1
>KOG3943 consensus THUMP domain-containing proteins [General function prediction only]
Probab=100.00 E-value=6.6e-45 Score=330.84 Aligned_cols=243 Identities=19% Similarity=0.311 Sum_probs=186.0
Q ss_pred CcccCCCCceEEEEeCCChhhhHHHHHHHHHHHhh-hcccCcccccccCCCccCCccccccccCCCCCCcCCCcccCccc
Q 020116 31 SSLLQRSHSGFLLTCTIKREKSATKEAISILHKYV-GHNNIENSQRLESSNTAGDSKRRKVCTDDMGGKCADGAEINSIE 109 (331)
Q Consensus 31 ~~~L~~G~~GilvTC~~grEk~A~~E~~~LLne~a-d~ly~~~~~~~e~~~~~~~~~~~k~~~~~~~~e~~d~~~~e~e~ 109 (331)
...|+||.+|||+||+ ++||||++|+|.||+|.. |..||++. .+.++. . +.|.|..++ ..|.|.
T Consensus 36 ~~~lepG~~Gi~~tC~-~HErQA~QEaysl~~ElygD~~~G~~~--~~~~E~-a----------p~gsE~~~~-~aeaEl 100 (291)
T KOG3943|consen 36 PRQLEPGLQGILITCN-MHERQAVQEAYSLLNELYGDDMYGPEK--FTDKEQ-A----------PSGSEGEDD-DAEAEL 100 (291)
T ss_pred ccccCCCcceEEEEcc-chHHHHHHHHHHHHHHHhcCcccCchh--ccCccc-C----------CCCCcCCCC-hHHHhh
Confidence 3579999999999999 599999999999999975 45665431 001111 1 111111000 111110
Q ss_pred cccccccccccccCCCcCCCCCCccccccceeccccceEEEEeccCCCCCHHHHHHHHHHhhcc--CCcCCceeEEEeee
Q 020116 110 EDSAGGLQKNECHSSVKTDTNTETDFDMSLVKLTRNGLLLLTFPREHSPNTINIVSNIFQSLGS--GSLKSPVWCHRIFP 187 (331)
Q Consensus 110 ~die~~~ke~e~~k~~krf~~~~~~~~f~~vkl~~~Gv~fi~f~~~~~~dP~~lv~~I~~dv~~--~~~~~tRfi~Rl~P 187 (331)
.|.+.+ .++++.- -+....|.+|+++|+|+.||.... ++.|.++|+.|++|+.+ ++.+++||+|||+|
T Consensus 101 kdEe~g----ddLk~~~----~~~~~P~~Fv~~~~~Cv~f~~t~K--niVpe~~v~~i~~dm~elk~k~kRtR~~Qr~~P 170 (291)
T KOG3943|consen 101 KDEEVG----DDLKAST----EMRLRPFQFVESGANCVVFIRTLK--NIVPEKLVHHILQDMYELKTKKKRTRVIQRMLP 170 (291)
T ss_pred hhhhhH----HHHhhhh----hhhcCchhhhhccCceEEeecccC--ccCchHHHHHHHHHHHhhhccchhhhhhhhhcc
Confidence 011111 1122100 001124789999999999999865 57999999999999987 56789999999999
Q ss_pred eeeEeecCHHHHHHHHHHHHHhhcccccccCCCCceeEEEEcccCccccccCCCCCCCCccccccCChhHHHHHHHHHhh
Q 020116 188 IQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVK 267 (331)
Q Consensus 188 I~~tc~A~~~~i~~~~~~l~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~~vI~~VA~~V~ 267 (331)
|++||.|.+++|.+++..+|.+||+.... .+-.||+|+|++|| | +++.|++||+.|+.+|.
T Consensus 171 i~~tc~a~le~m~k~a~~VI~p~fkap~t--gK~~tf~VE~k~RN-----------n------~~v~r~~vi~~V~~~Vc 231 (291)
T KOG3943|consen 171 ISGTCKAFLEDMKKYAETVIEPWFKAPNT--GKKGTFQVEYKSRN-----------N------SHVNREEVIREVAGIVC 231 (291)
T ss_pred ccchHHhhHHHHHHHHHHhhcccccCCCC--CcCceEEEEEEecc-----------c------cchhHHHHHHHHHHHHH
Confidence 99999999999999999999999975531 35579999999999 6 99999999999999999
Q ss_pred hcCCCCeeeCCCCCeEEEEEEeeCCCCCCCccEEEEEeecCCccccccceeeeeccCCCC
Q 020116 268 EVVSDSAVDLKSPELSVLVELLPISGLPSELLVVGVSILPQKLVTTKPRLSIRALVSGTN 327 (331)
Q Consensus 268 ~~~~~hkVdLknPd~~IlVEV~k~~~~~~~~~v~giSVv~~y~~~~K~~l~~~~l~~~~~ 327 (331)
..++..+|||+|||++|+|||++ . ++||||+.+|+-++|||| ++++.-+.
T Consensus 232 ~l~se~~VdL~n~D~t~~Ve~~k--s------~I~~~Vv~dy~~~RKYnl--q~~~~s~~ 281 (291)
T KOG3943|consen 232 TLNSENKVDLTNPDYTVVVEIIK--A------VICLSVVKDYMLFRKYNL--QEVVKSPK 281 (291)
T ss_pred hcCccceeeccCCCeEEEEEeee--c------eeeeeehHHHHHHHHhhH--HHhhcccC
Confidence 99999999999999999999999 7 999999999999999998 66665443
No 2
>PF02926 THUMP: THUMP domain; InterPro: IPR004114 The THUMP domain is shared by 4-thiouridine, pseudouridine synthases and RNA methylases[] and is probably an RNA-binding domain that adopts an alpha/beta fold similar to that found in the C-terminal domain of translation initiation factor 3 and ribosomal protein S8. The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets []. This domain is found in the thiamine biosynthesis proteins (ThiI) (see IPR003720 from INTERPRO).; PDB: 3TLJ_A 3TM5_B 3TM4_A 2DIR_A 3TMA_A 1VBK_B 3K0B_A 2C5S_A 3LDU_A 3V8V_B ....
Probab=99.60 E-value=5.3e-15 Score=125.49 Aligned_cols=109 Identities=24% Similarity=0.268 Sum_probs=92.6
Q ss_pred CHHHHHHHHHHhhccCCcCCceeEEEeeeeeeEeecCHHHHHHHHHHHHHhhcccccccCCCCceeEEEEcccCcccccc
Q 020116 159 NTINIVSNIFQSLGSGSLKSPVWCHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQN 238 (331)
Q Consensus 159 dP~~lv~~I~~dv~~~~~~~tRfi~Rl~PI~~tc~A~~~~i~~~~~~l~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~ 238 (331)
...+.+.+.+.. +++++|++|++..|.+++++|.+.+..++..++.. ...||+|++++|+
T Consensus 35 ~~~~~~~~~~~~--------~~~~~ri~p~~~~~~~~~~~i~~~~~~~~~~~~~~------~~~tF~V~~~r~~------ 94 (144)
T PF02926_consen 35 GDSEEIYRALEK--------LRGISRIIPICRFCEADLEEIKEKAKELLWEKFIK------EDKTFAVRCRRRG------ 94 (144)
T ss_dssp EHHHHHHHHHHH--------SSSESEEEEEEEEEESSHHHHHHHHHCSHGGGHSH------TTSEEEEEEEEES------
T ss_pred CCHHHHHHHHhc--------ccceeEEEEEEEEcCCCHHHHHHHHHHHHHHHhCC------CCCEEEEEEEEcC------
Confidence 355555555554 35999999999999999999999999999988842 2239999999999
Q ss_pred CCCCCCCCccccc-cCChhHHHHHHHHHhhhcCCCCeeeCCCCCeEEEEEEeeCCCCCCCccEEEEEeec
Q 020116 239 KIPKDTKDSDVSA-LLDRNKCFTIVAAAVKEVVSDSAVDLKSPELSVLVELLPISGLPSELLVVGVSILP 307 (331)
Q Consensus 239 ~~~~~n~~~~~~~-~l~R~~vI~~VA~~V~~~~~~hkVdLknPd~~IlVEV~k~~~~~~~~~v~giSVv~ 307 (331)
+ . .++++++.+.|+++|....+ ++|||+|||++|.||+++ + .|+|||.+
T Consensus 95 -----~------~~~~~s~ei~~~vg~~i~~~~~-~~Vdl~~Pd~~i~Vev~~--~------~~~i~i~~ 144 (144)
T PF02926_consen 95 -----K------HFPFTSMEIEREVGDAIKEKGG-PKVDLKNPDVVIHVEVRK--D------KCYISIDT 144 (144)
T ss_dssp -----S------SSSSCHHHHHHHHHHHHHHHHH-TEE-SSSSSEEEEEEEET--T------EEEEEEES
T ss_pred -----C------ccccCHHHHHHHHHHHHHHHhC-CCccCcCcCEEEEEEEEC--C------EEEEEEeC
Confidence 4 4 89999999999999998655 899999999999999999 9 99999975
No 3
>COG1818 Predicted RNA-binding protein, contains THUMP domain [General function prediction only]
Probab=99.57 E-value=3.8e-14 Score=126.38 Aligned_cols=109 Identities=28% Similarity=0.400 Sum_probs=89.4
Q ss_pred cCCceeEEEeeeeeeEeecCHHHHHHHHHHHHHhhcccccccCCCCceeEEEEcccCccccccCCCCCCCCccccccCCh
Q 020116 176 LKSPVWCHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDR 255 (331)
Q Consensus 176 ~~~tRfi~Rl~PI~~tc~A~~~~i~~~~~~l~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R 255 (331)
....-++.|++|+...|.+++++|...+..+++.+. .++.||||+.++|+ + -.++-
T Consensus 55 ~~~~~~~~rv~pv~~~~~~dldeI~~~~~~l~~~~i-------~~~~tFaVr~~rRG-----------~------~~f~s 110 (175)
T COG1818 55 LKEVPEVERVIPVEIEVETDLDEIEEAAAELAEEKI-------KEGKTFAVRTKRRG-----------K------HDFTS 110 (175)
T ss_pred hcCCCceeeEEEEEeeccCCHHHHHHHHHHHHhccc-------CCCCeEEEEEeecC-----------C------CCccc
Confidence 345678999999999999999999999999999877 47789999999999 2 23333
Q ss_pred hHHHHHHHHHhhhcCCCCeeeCCCCCeEEEEEEeeCCCCCCCccEEEEEeecCCccccccce
Q 020116 256 NKCFTIVAAAVKEVVSDSAVDLKSPELSVLVELLPISGLPSELLVVGVSILPQKLVTTKPRL 317 (331)
Q Consensus 256 ~~vI~~VA~~V~~~~~~hkVdLknPd~~IlVEV~k~~~~~~~~~v~giSVv~~y~~~~K~~l 317 (331)
.++--.++++|..+ .+..|||++||++|.|||++ . .+||||+++....+|+.+
T Consensus 111 ~~~~v~vg~~v~~~-tg~~VdL~~Pd~vv~Vevl~--~------~a~Isv~~~~~e~~k~~~ 163 (175)
T COG1818 111 RDVEVVVGEAVKKA-TGAEVDLEDPDKVVWVEVLG--D------RAGISVLPGEKEEKKIKL 163 (175)
T ss_pred cceeehhHHHHHHH-hCCcccCCCCCEEEEEEEec--C------cceEEEeCchhhhhhccc
Confidence 34434555666653 68999999999999999999 8 899999998877777644
No 4
>PRK01565 thiamine biosynthesis protein ThiI; Provisional
Probab=98.51 E-value=8.3e-07 Score=88.71 Aligned_cols=84 Identities=18% Similarity=0.226 Sum_probs=72.1
Q ss_pred EEEeeeeeeEeecCHHHHHHHHHHHHHhhcccccccCCCCceeEEEEcccCccccccCCCCCCCCccccc-cCChhHHHH
Q 020116 182 CHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSA-LLDRNKCFT 260 (331)
Q Consensus 182 i~Rl~PI~~tc~A~~~~i~~~~~~l~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~-~l~R~~vI~ 260 (331)
|+.+.|+.. |..++++|.+.+..++..+. ....||+|+.++++ + . .++..++-.
T Consensus 71 I~~~s~~~~-~~~~~e~I~~~~~~~~~~~~-------~~~~tF~Vr~rR~~-----------k------~f~~tS~ei~r 125 (394)
T PRK01565 71 IQSFSPVYK-VEKDLEAIKEAALELLKEVY-------KEGKTFKVEARRSD-----------K------SFPLDSMELNR 125 (394)
T ss_pred cceEEEEEE-ECCCHHHHHHHHHHHHHhhc-------cCCCcEEEEEEECC-----------C------CCCCChHHHHH
Confidence 667778874 78999999999999988764 24569999999998 3 4 789999999
Q ss_pred HHHHHhhhcCCCCeeeCCCCCeEEEEEEee
Q 020116 261 IVAAAVKEVVSDSAVDLKSPELSVLVELLP 290 (331)
Q Consensus 261 ~VA~~V~~~~~~hkVdLknPd~~IlVEV~k 290 (331)
.|++.|....++.+|||+|||++|.|||.+
T Consensus 126 ~vG~~I~~~~~~~~VdL~nPd~~i~vei~~ 155 (394)
T PRK01565 126 ELGAYILENFPNLKVDVKNPDVTLRVEVRK 155 (394)
T ss_pred HHHHHHHhhCCCCcccccCCCeEEEEEEEc
Confidence 999999876556899999999999999987
No 5
>PRK01269 tRNA s(4)U8 sulfurtransferase; Provisional
Probab=98.31 E-value=5.3e-06 Score=84.99 Aligned_cols=85 Identities=18% Similarity=0.259 Sum_probs=73.2
Q ss_pred eEEEeeeeeeEeecCHHHHHHHHHHHHHhhcccccccCCCCceeEEEEcccCccccccCCCCCCCCccccccCChhHHHH
Q 020116 181 WCHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFT 260 (331)
Q Consensus 181 fi~Rl~PI~~tc~A~~~~i~~~~~~l~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~~vI~ 260 (331)
=++++.|+..++..++++|...+..++..++. ..||+|+.++++ + ..++..++-.
T Consensus 72 Gi~~~~~v~~~~~~~~e~I~~~a~~~~~~~~~--------~~tF~VrarR~~-----------k------~~~~S~ei~r 126 (482)
T PRK01269 72 GIHHFLEVEEYPFTDLHDIFEKALALYREQLE--------GKTFCVRVKRRG-----------K------HDFTSIDVER 126 (482)
T ss_pred CceEEEEEEEECCCCHHHHHHHHHHHHHHhcC--------CCeEEEEEEeCC-----------C------CCCChHHHHH
Confidence 36788999999889999999999999888762 359999999988 4 4788889999
Q ss_pred HHHHHhhhcCCCCeeeCCCCCeEEEEEEee
Q 020116 261 IVAAAVKEVVSDSAVDLKSPELSVLVELLP 290 (331)
Q Consensus 261 ~VA~~V~~~~~~hkVdLknPd~~IlVEV~k 290 (331)
.|++.|.....+.+|||+|||++|.|||.+
T Consensus 127 ~vG~~I~~~~~~~~VdL~nPD~~i~VeI~~ 156 (482)
T PRK01269 127 YVGGGLNQHIESAGVDLKNPDVTVHLEIRD 156 (482)
T ss_pred HHHHHHHHhCCCCceeCCCCCEEEEEEEEC
Confidence 999999754456899999999999999988
No 6
>PRK08384 thiamine biosynthesis protein ThiI; Provisional
Probab=98.19 E-value=1.9e-05 Score=78.81 Aligned_cols=88 Identities=20% Similarity=0.170 Sum_probs=69.2
Q ss_pred EEEeeeeeeEeecCHHHHHHHHHHHHHhhcccccccCCCCceeEEEEcccCccccccCCCCCCCCccccccCChhHHHHH
Q 020116 182 CHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTI 261 (331)
Q Consensus 182 i~Rl~PI~~tc~A~~~~i~~~~~~l~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~~vI~~ 261 (331)
|..+.|+.. |..++++|...+..++..++.... ....||+|+.++.+ . .-.++..++=..
T Consensus 72 I~~~s~~~~-~~~~~~~i~~~~~~~~~~~~~~~~---~~~~tF~V~~rR~~-----------k-----~f~~tS~ei~~~ 131 (381)
T PRK08384 72 IVSLSPAME-IDAELEKINRTALKLFRRKKRELE---LEKPRFRVTARRIT-----------K-----EFPLKSPEIQAK 131 (381)
T ss_pred ceeEEEEEE-eCCCHHHHHHHHHHHHHHhhhccc---ccCCeEEEEEEeCC-----------C-----CCCCChHHHHHH
Confidence 455666654 557899999999999988763110 12359999999998 2 136888999999
Q ss_pred HHHHhhhcCCCCeeeCCCCCeEEEEEEee
Q 020116 262 VAAAVKEVVSDSAVDLKSPELSVLVELLP 290 (331)
Q Consensus 262 VA~~V~~~~~~hkVdLknPd~~IlVEV~k 290 (331)
|++.|... ++.+|||+|||+.|.|||-+
T Consensus 132 vG~~i~~~-~~~~Vdl~~Pd~~i~vEir~ 159 (381)
T PRK08384 132 VGEYILEN-EESEVDLHNYDIEVGVELME 159 (381)
T ss_pred HHHHHHhc-CCCCccCcCCCEEEEEEEEe
Confidence 99999765 46899999999999999977
No 7
>TIGR00342 thiazole biosynthesis/tRNA modification protein ThiI. The protein product of the thiI gene is required for the synthesis of the thiazole moiety in thiamine biosynthesis. It also acts in the generation of 4-thiouridine in tRNA, and may occur in species (such as Mycoplasma genitalium) that lack de novo thiamine biosynthesis.
Probab=98.00 E-value=4.9e-05 Score=75.50 Aligned_cols=81 Identities=25% Similarity=0.336 Sum_probs=63.5
Q ss_pred EeeeeeeEeecCHHHHHHHHHHHHHhhcccccccCCCCceeEEEEcccCccccccCCCCCCCCccccccCChhHHHHHHH
Q 020116 184 RIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVA 263 (331)
Q Consensus 184 Rl~PI~~tc~A~~~~i~~~~~~l~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~~vI~~VA 263 (331)
.+-|+. .|..++++|. .+..++..+.. ...||+|+.++++ . .=.++..++-..|+
T Consensus 71 ~~s~~~-~~~~~~~~i~-~~~~~~~~~~~-------~~~tF~Vr~kR~~-----------k-----~f~~~S~ei~r~~G 125 (371)
T TIGR00342 71 SFSPAF-KCDLPFDEIH-ILLKALKQLRK-------EGKTFKVRTKRRG-----------K-----DFPLNSVEVNKYVG 125 (371)
T ss_pred EEEEEE-EECCCHHHHH-HHHHHHHHhhc-------cCCcEEEEEEECC-----------C-----CCCCChHHHHHHHH
Confidence 333443 5677899999 78788877652 3459999999998 1 13466999999999
Q ss_pred HHhhhcCCCCeeeCCCCCeEEEEEEee
Q 020116 264 AAVKEVVSDSAVDLKSPELSVLVELLP 290 (331)
Q Consensus 264 ~~V~~~~~~hkVdLknPd~~IlVEV~k 290 (331)
+.|... .+.+|||+|||++|.|||.+
T Consensus 126 ~~i~~~-~~~~VdL~nPd~~i~vei~~ 151 (371)
T TIGR00342 126 GGIVEK-IGLKVDLTNPDITVHIEIRE 151 (371)
T ss_pred HHHHHH-cCCcccccCCCEEEEEEEEC
Confidence 999865 34899999999999999987
No 8
>COG0301 ThiI Thiamine biosynthesis ATP pyrophosphatase [Coenzyme metabolism]
Probab=97.76 E-value=0.00019 Score=71.49 Aligned_cols=101 Identities=19% Similarity=0.185 Sum_probs=71.3
Q ss_pred EEEeeeeeeEeecCHHHHHHHHHHHHHhhcccccccCCCCceeEEEEcccCccccccCCCCCCCCccccccCChhHHHHH
Q 020116 182 CHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTI 261 (331)
Q Consensus 182 i~Rl~PI~~tc~A~~~~i~~~~~~l~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~~vI~~ 261 (331)
|+-+.|+.. |..+++++...+..++...+ .+..||+|+.++++. | -.++..+|=..
T Consensus 70 I~s~sp~~~-v~~~~~~i~~~~~~~~~~~~-------~~g~tF~V~arR~~k----------~------f~~~S~ev~~~ 125 (383)
T COG0301 70 IVSFSPAME-VEASLEEIIKAALLALRRKY-------KEGKTFKVRARRAGK----------E------FPFTSLEVNRY 125 (383)
T ss_pred cceeceeEE-ecCCcHHHHHHHHHHHHHhh-------hcCCeEEEEEEeCCC----------C------CCCCHHHHHHH
Confidence 444555543 45566666666666665554 244599999999992 2 46788899999
Q ss_pred HHHHhhhcCCCCeeeCCCCCeEEEEEEee------------CCCCCCCccEEEEEee
Q 020116 262 VAAAVKEVVSDSAVDLKSPELSVLVELLP------------ISGLPSELLVVGVSIL 306 (331)
Q Consensus 262 VA~~V~~~~~~hkVdLknPd~~IlVEV~k------------~~~~~~~~~v~giSVv 306 (331)
|++.|.....+.+|||+|||++|.|||-. ..|+|.|++==+|+.|
T Consensus 126 vG~~i~~~~~~~~Vdl~~Pdv~i~iEIr~~~ayi~~~~~~G~GGLPvGt~Gk~l~Ll 182 (383)
T COG0301 126 VGEAILENIESAGVDLKNPDVEIHIEIREDKAYIYTERIKGPGGLPVGTQGKVLLLL 182 (383)
T ss_pred HHHHHHhhcccceeecCCCCeEEEEEEecCeEEEEEeeeccCCCCccccCCcEEEEE
Confidence 99998876568899999999999999984 1256666554444444
No 9
>COG0116 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]
Probab=94.47 E-value=0.14 Score=51.38 Aligned_cols=104 Identities=20% Similarity=0.212 Sum_probs=68.6
Q ss_pred ceeEEEeeeeeeEeec-CHHHHHHHHHHH-HHhhcccccccCCCCceeEEEEcccCccccccCCCCCCCCccccccCChh
Q 020116 179 PVWCHRIFPIQATCVL-KEKELQATVSKL-VLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRN 256 (331)
Q Consensus 179 tRfi~Rl~PI~~tc~A-~~~~i~~~~~~l-~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~ 256 (331)
+|-.+|+.=+-..|.+ +.++|-..+..+ +..||+ +..||+|.++.=+ . ...+..
T Consensus 53 sRta~Ri~i~l~~fk~~~~~dly~~v~~i~w~~~~~-------~~~tf~V~~~~~~-----------~------~~~~s~ 108 (381)
T COG0116 53 SRTASRILLPLGEFKAETLDDLYEAVKAINWEEYFP-------EGATFAVRFRGVG-----------S------HLFTSP 108 (381)
T ss_pred HHHHHhhheeeeeeeeCCHHHHHHHhhcCCHHHhCC-------CCCEEEEEEEecc-----------C------CccccH
Confidence 4667777777777766 799998888777 788884 5569999966444 1 222223
Q ss_pred HHHHHHHHHhhhc-----CCCCeeeCCCCCeEEEEEEeeCCCCCCCccEEEEEeecCCccccc
Q 020116 257 KCFTIVAAAVKEV-----VSDSAVDLKSPELSVLVELLPISGLPSELLVVGVSILPQKLVTTK 314 (331)
Q Consensus 257 ~vI~~VA~~V~~~-----~~~hkVdLknPd~~IlVEV~k~~~~~~~~~v~giSVv~~y~~~~K 314 (331)
++=..|-++|-+. ...-.||+..||+.|-|++.+ + .|-|+|=--=.-+.|
T Consensus 109 ~~a~~vkdAIvd~~~~~~~~r~~v~~~~Pdv~i~v~l~~--~------~~~l~iDttG~sLhk 163 (381)
T COG0116 109 DIARIVKDAIVDRFRRKYGRRPSVDLDGPDVRINVELDK--D------TATLGIDTTGDSLHK 163 (381)
T ss_pred HHHHHHHHHHHHHHhhccCCCCCccccCCCeEEEEEEEc--C------EEEEEEeCCCcchhh
Confidence 3333333333322 222389999999999999999 8 788887532224444
No 10
>TIGR01177 conserved hypothetical protein TIGR01177. This family is found exclusively in the Archaea.
Probab=94.18 E-value=0.28 Score=47.73 Aligned_cols=81 Identities=20% Similarity=0.182 Sum_probs=56.6
Q ss_pred EeecCHHHHHHHHHHHHHhhcccccccCCCCceeEEEEcccCccccccCCCCCCCCccccccCChhHHHHHHHHHhhhcC
Q 020116 191 TCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKEVV 270 (331)
Q Consensus 191 tc~A~~~~i~~~~~~l~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~~vI~~VA~~V~~~~ 270 (331)
.|..+.+++...+..+--..+ .. .+|+|..+..+ + +..++..+-+.+++.+...
T Consensus 61 ~~~~~~~~l~~~~~~~~~~~~-------~~-~sf~v~~~~~~-----------~------~~~~~~~~~~~ig~~i~~~- 114 (329)
T TIGR01177 61 YDTCAAKDLYDFVAGLEASDL-------DR-KSFAVRVRDLR-----------G------YSVDKARLERKIGAILKKK- 114 (329)
T ss_pred hcCCCHHHHHHHHhhcchhhc-------cC-CeEEEEEEecC-----------C------CCCCHHHHHHHHHHHHHhc-
Confidence 444567778777665422222 12 59999998877 3 3566655556687777653
Q ss_pred CCCeeeCCCCCeEEEEEEeeCCCCCCCccEEEEEee
Q 020116 271 SDSAVDLKSPELSVLVELLPISGLPSELLVVGVSIL 306 (331)
Q Consensus 271 ~~hkVdLknPd~~IlVEV~k~~~~~~~~~v~giSVv 306 (331)
+.+|||+|||+.|.|.+.+ + .|-+|+.
T Consensus 115 -g~~v~l~~Pd~~i~v~~~~--~------~~~~g~~ 141 (329)
T TIGR01177 115 -GFKVSLRRPDIVVRVVITE--D------IFYLGRV 141 (329)
T ss_pred -CCccccCCCCeEEEEEEEC--C------eEEEEEE
Confidence 3599999999999999988 7 6777764
No 11
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=90.35 E-value=1.5 Score=47.32 Aligned_cols=100 Identities=15% Similarity=0.159 Sum_probs=60.6
Q ss_pred eeEEEeeeeeeEeec-CHHHHHHHHHHH-HHhhcccccccCCCCceeEEEEcccCccccccCCCCCCCCccccccCChhH
Q 020116 180 VWCHRIFPIQATCVL-KEKELQATVSKL-VLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNK 257 (331)
Q Consensus 180 Rfi~Rl~PI~~tc~A-~~~~i~~~~~~l-~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~~ 257 (331)
|...|++=.-....+ +.++|...+..+ +..||+ ...||+|....++ + +-.++.+--..
T Consensus 52 R~A~RVll~l~~f~a~~~~~Ly~~v~~i~W~~~l~-------~~~tf~V~~~~~~-----------s--~l~~~~~~~~~ 111 (702)
T PRK11783 52 RLASRILLPLAEFKVYSDLDLYLGVQAIDWTEHFS-------PDKTFAVDFSGTN-----------D--EIRNTQFGALK 111 (702)
T ss_pred cchhheEEEeeeeecCCHHHHHHHHHcCCHHHhCC-------CCCeEEEEEEEec-----------C--CccCcHHHHHH
Confidence 444444333334433 788888877765 444553 3459999988776 1 00012222233
Q ss_pred HHHHHHHHhhhcCC-CCeeeCCCCCeEEEEEEeeCCCCCCCccEEEEEeec
Q 020116 258 CFTIVAAAVKEVVS-DSAVDLKSPELSVLVELLPISGLPSELLVVGVSILP 307 (331)
Q Consensus 258 vI~~VA~~V~~~~~-~hkVdLknPd~~IlVEV~k~~~~~~~~~v~giSVv~ 307 (331)
|-++|.+.+..... .-.||+++||+.|.|.+.+ + .|.|||=-
T Consensus 112 vKdAI~d~~~~~~~~rp~vd~~~pdv~i~~~~~~--~------~~~l~ld~ 154 (702)
T PRK11783 112 VKDAIVDRFRRKGGPRPSVDKEQPDIRINARLNK--G------EATISLDL 154 (702)
T ss_pred HHHHHHHHHHHhcCCCCCCCCCCCCEEEEEEEeC--C------EEEEEEEC
Confidence 44445555543321 2379999999999999999 8 78888753
No 12
>PF06331 Tbf5: Transcription factor TFIIH complex subunit Tfb5; InterPro: IPR009400 This entry represents nucleotide excision repair (NER) proteins, such as TTDA subunit of TFIIH basal transcription factor complex (also known as subunit 5 of RNA polymerase II transcription factor B), and Rex1. These proteins have a structural motif consisting of a 2-layer sandwich structure with an alpha/beta plait topology. Nucleotide excision repair is a major pathway for repairing UV light-induced DNA damage in most organisms. Transcription/repair factor IIH (TFIIH) is essential for RNA polymerase II transcription and nucleotide excision repair. The TFIIH complex consists of ten subunits: ERCC2, ERCC3, GTF2H1, GTF2H2, GTF2H3, GTF2H4, GTF2H5, MNAT1, CDK7 and CCNH. Defects in GTF2H5 cause the disease trichothiodystrophy (TTD), therefore GTF2H5 (general transcription factor 2H subunit 5) is also known as the TTD group A (TTDA) subunit (and as Tfb5) []. The TTDA subunit is responsible for the DNA repair function of the complex. TTDA is present both bound to TFIIH, and as a free fraction that shuffles between the cytoplasm and nucleus; induction of NER-type DNA lesions shifts the balance towards TTDA's more stable association with TFIIH []. TTDA is also required for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell. REX1 (required for excision 1) is required for DNA repair in the single-celled, photosynthetic algae Chlamydomonas reinhardtii [], and has homologues in other eukaryotes.; GO: 0003677 DNA binding, 0006289 nucleotide-excision repair; PDB: 2JNJ_B 1YDL_A 3DGP_B 3DOM_B.
Probab=56.06 E-value=11 Score=28.86 Aligned_cols=22 Identities=32% Similarity=0.410 Sum_probs=18.7
Q ss_pred CceEEEEeCCChhhhHHHHHHHHHHHh
Q 020116 38 HSGFLLTCTIKREKSATKEAISILHKY 64 (331)
Q Consensus 38 ~~GilvTC~~grEk~A~~E~~~LLne~ 64 (331)
.+|+||+|+. |+++++--||+.
T Consensus 5 ~kGvLv~CDp-----a~Kq~il~ld~~ 26 (68)
T PF06331_consen 5 IKGVLVECDP-----AIKQFILHLDES 26 (68)
T ss_dssp EEEEEEES-H-----HHHHHHHHHHHH
T ss_pred eeeEEEEcCH-----HHHHHHHHHhcC
Confidence 5799999997 899999999984
No 13
>TIGR01213 conserved hypothetical protein TIGR01213. Members of this family show twilight-zone similarity to several predicted RNA pseudouridine synthases. All trusted members of this family are archaeal. Several eukaryotic homologs lack N-terminal homology including two CXXC motifs.
Probab=51.35 E-value=34 Score=34.70 Aligned_cols=92 Identities=17% Similarity=0.168 Sum_probs=48.6
Q ss_pred eEeecCHHHHHHHHHHHHHhhcccccccCCCCceeEEEEcccC-ccccccCCCCCCCCccccccCChhHHHHHHHHHhhh
Q 020116 190 ATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRG-FEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKE 268 (331)
Q Consensus 190 ~tc~A~~~~i~~~~~~l~~~~F~~~~~~~~~p~tfaI~~~~Rn-~~~~e~~~~~~n~~~~~~~~l~R~~vI~~VA~~V~~ 268 (331)
..|..-.+.+...++.++...=. -+=.||.|..+--. ..|.|.++|... +-....+|++ ++=..|+..|..
T Consensus 57 ~iC~g~f~~~~~~a~~~~~~l~~------~ef~tf~VGt~~p~~i~e~E~~i~~~~-gl~~~E~iK~-E~nRevGk~~~~ 128 (388)
T TIGR01213 57 DVCGGIFDRFDEAADLVAEKVGD------YDFSTFLVGTRFPPDVIELEEEIRKEF-GSGGGESIKR-EFNREVGKLFVK 128 (388)
T ss_pred ccccChHhHHHHHHHHHHHHhhc------CccceEEEeeeCCHHHHHHHHHHHHHh-CCCcchhHHH-HHhHHHHHHHHH
Confidence 45655555555555555443211 12257888655422 233333332111 0000123433 444455555544
Q ss_pred cCCCCeeeCCCCCeEEEEEEee
Q 020116 269 VVSDSAVDLKSPELSVLVELLP 290 (331)
Q Consensus 269 ~~~~hkVdLknPd~~IlVEV~k 290 (331)
. .+-.||..|||++|+|+...
T Consensus 129 ~-~gk~~d~~~Pdv~i~vd~~~ 149 (388)
T TIGR01213 129 R-TGKEVDFERPDLVIMVEFEY 149 (388)
T ss_pred H-hCCCccCCCCCEEEEEEcCC
Confidence 3 47899999999999998766
No 14
>KOG2671 consensus Putative RNA methylase [Replication, recombination and repair]
Probab=42.16 E-value=34 Score=34.48 Aligned_cols=53 Identities=17% Similarity=0.332 Sum_probs=36.2
Q ss_pred CCceeEEEEcccCccccccCCCCCCCCccccccCChhHHHHHHHHHhhhcCCCCeeeCCCCCeEE-EEEEeeC
Q 020116 220 RPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKEVVSDSAVDLKSPELSV-LVELLPI 291 (331)
Q Consensus 220 ~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~~vI~~VA~~V~~~~~~hkVdLknPd~~I-lVEV~k~ 291 (331)
...||+|.+..=| ..++.++.++.|+.+ .-++=.-+|||+||+.+. ++|-+.+
T Consensus 97 ~dssfki~fetfg------------------k~~t~~e~~~~I~~f-~ylpfeG~Vnlk~Pq~~f~viE~y~~ 150 (421)
T KOG2671|consen 97 SDSSFKIRFETFG------------------KKLTQDEQVEIIESF-DYLPFEGPVNLKNPQHVFFVIEEYEL 150 (421)
T ss_pred cCceeEEEEEEec------------------ccccHHHHHHHhhhh-eeccccceeccCCCceEEEEEEeecc
Confidence 3458999888766 455666777766643 333346799999999776 4566663
No 15
>PF13590 DUF4136: Domain of unknown function (DUF4136)
Probab=23.26 E-value=2.1e+02 Score=23.76 Aligned_cols=56 Identities=14% Similarity=0.027 Sum_probs=41.0
Q ss_pred CCCceeEEEEcccCccccccCCCCCCCCccccccCChhHHHHHHHHHhhhcCCCCeeeCCCCCeEEEEEEee
Q 020116 219 SRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKEVVSDSAVDLKSPELSVLVELLP 290 (331)
Q Consensus 219 ~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~~vI~~VA~~V~~~~~~hkVdLknPd~~IlVEV~k 290 (331)
..-.||++.....+ .. ..+.+....|..+|...+.. .|.+.+..+||++|-+.+.-
T Consensus 15 ~~ykTy~~~~~~~~--~~------------~~~~~~~~~i~~~v~~~L~~--~G~~~~~~~aDl~V~~~~~~ 70 (151)
T PF13590_consen 15 SQYKTYAFVPSSSD--PA------------QSNPLDDQRIQDAVEQELAA--KGYRRVPENADLLVSYHYSV 70 (151)
T ss_pred CCCCeEEEecCCcC--cc------------ccCcHHHHHHHHHHHHHHHH--CCCeecccCCCEEEEEEEEE
Confidence 34578999887432 00 02677777888889988875 47777799999999988876
No 16
>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=23.16 E-value=1.4e+02 Score=30.27 Aligned_cols=30 Identities=17% Similarity=0.360 Sum_probs=22.6
Q ss_pred HHHHHHhhhcCCCCeeeCCCCCeEEEEEEee
Q 020116 260 TIVAAAVKEVVSDSAVDLKSPELSVLVELLP 290 (331)
Q Consensus 260 ~~VA~~V~~~~~~hkVdLknPd~~IlVEV~k 290 (331)
..++.++... .|..+|..|||++|+|++.-
T Consensus 126 REvGK~~~~~-~G~~~d~~~Pdi~i~vd~~~ 155 (398)
T COG1258 126 REVGKRLASK-TGKEPDFDNPDIVIVVDLET 155 (398)
T ss_pred HHHHHHHHHh-cCCCCCCCCCCEEEEEecCC
Confidence 3455544433 57899999999999999966
No 17
>PF01910 DUF77: Domain of unknown function DUF77; InterPro: IPR002767 This entry contains several hypothetical proteins of unknown function found in archaebacteria, eukaryotes and eubacteria. The structures of YBL001c from Saccharomyces cerevisiae and its homologue MTH1187 from the archaea Methanobacterium thermoautotrophicum have been determined []. These proteins have a ferredoxin-like alpha/beta sandwich structure with anti-parallel beta-sheets. Generally, they have two domains that form a single beta-sheet dimer, where two dimers pack sheet-to-sheet into a tetramer, some proteins having an extra C-terminal helix. ; PDB: 1LXJ_A 1YQH_A 2EKY_G 2EPI_A 1VK8_D 2IBO_C 1LXN_B.
Probab=20.80 E-value=4.4e+02 Score=20.97 Aligned_cols=67 Identities=10% Similarity=0.087 Sum_probs=51.0
Q ss_pred CCCHHHHHHHHHHhhccCCcCCceeEEEeeeeeeEeecCHHHHHHHHHHHHHhhcccccccCCCCceeEEEEcccC
Q 020116 157 SPNTINIVSNIFQSLGSGSLKSPVWCHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRG 232 (331)
Q Consensus 157 ~~dP~~lv~~I~~dv~~~~~~~tRfi~Rl~PI~~tc~A~~~~i~~~~~~l~~~~F~~~~~~~~~p~tfaI~~~~Rn 232 (331)
..++..+|.++++-+++.+ .=.++.|...+-.++.+++.++++.+.+.-|.... .-...-|.+..|-
T Consensus 12 ~~s~~~~V~~~i~~i~~sg-----l~y~v~pm~T~iEGe~dev~~~i~~~~e~~~~~G~----~Rv~t~ikId~R~ 78 (92)
T PF01910_consen 12 GESVSAYVAEAIEVIKESG-----LKYEVGPMGTTIEGELDEVMALIKEAHEALFEAGA----KRVVTVIKIDDRR 78 (92)
T ss_dssp SSHHHHHHHHHHHHHHTSS-----SEEEEETTEEEEEEEHHHHHHHHHHHHHHHHCTTS----SEEEEEEEEEEES
T ss_pred CCCHHHHHHHHHHHHHHcC-----CceEEcCCccEEEecHHHHHHHHHHHHHHHHHcCC----CeEEEEEEEEEcC
Confidence 4688899999999886653 45789999999999999999999999998885321 2244455555555
No 18
>KOG2715 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=20.59 E-value=1.1e+02 Score=27.93 Aligned_cols=34 Identities=18% Similarity=0.201 Sum_probs=30.7
Q ss_pred cceeccccceEEEEeccCCCCCHHHHHHHHHHhh
Q 020116 138 SLVKLTRNGLLLLTFPREHSPNTINIVSNIFQSL 171 (331)
Q Consensus 138 ~~vkl~~~Gv~fi~f~~~~~~dP~~lv~~I~~dv 171 (331)
.+|++++.|.+|..+..+-+.||-.|..++|++-
T Consensus 21 ~wVRlNVGGt~f~TtktTl~rdp~sFl~rl~q~~ 54 (210)
T KOG2715|consen 21 LWVRLNVGGTVFLTTKTTLPRDPKSFLYRLCQRE 54 (210)
T ss_pred EEEEEecCCEEEEeeeeccccCcHHHHHHHHhcc
Confidence 5789999999999999888999999999999874
Done!