Query 020866
Match_columns 320
No_of_seqs 127 out of 269
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 05:47:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020866.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020866hhsearch_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 8.5E-47 1.8E-51 340.6 15.0 239 32-315 37-280 (291)
2 PF02926 THUMP: THUMP domain; 99.6 1E-14 2.3E-19 123.0 10.5 123 135-296 22-144 (144)
3 COG1818 Predicted RNA-binding 99.5 5.2E-13 1.1E-17 118.3 14.2 107 166-305 56-162 (175)
4 PRK01565 thiamine biosynthesis 98.5 1.3E-06 2.7E-11 86.9 11.7 110 134-279 46-155 (394)
5 PRK01269 tRNA s(4)U8 sulfurtra 98.2 1E-05 2.2E-10 82.4 11.7 85 170-279 72-156 (482)
6 PRK08384 thiamine biosynthesis 98.2 2.1E-05 4.5E-10 78.0 12.5 88 171-279 72-159 (381)
7 COG0301 ThiI Thiamine biosynth 97.9 9.5E-05 2.1E-09 73.2 11.3 101 171-295 70-182 (383)
8 TIGR00342 thiazole biosynthesi 97.8 0.00016 3.4E-09 71.4 11.0 81 173-279 71-151 (371)
9 TIGR01177 conserved hypothetic 93.3 0.48 1E-05 45.8 9.1 81 180-295 61-141 (329)
10 COG0116 Predicted N6-adenine-s 90.1 1.5 3.2E-05 43.8 8.5 96 169-296 54-156 (381)
11 PRK11783 rlmL 23S rRNA m(2)G24 87.7 13 0.00028 40.0 14.3 99 167-296 54-154 (702)
12 TIGR01213 conserved hypothetic 46.8 60 0.0013 32.7 6.7 91 180-279 58-149 (388)
13 PF06331 Tbf5: Transcription f 45.8 20 0.00043 27.2 2.5 21 38-63 5-25 (68)
14 COG1258 Predicted pseudouridyl 36.2 54 0.0012 32.9 4.5 34 245-279 122-155 (398)
15 PF15408 PH_7: Pleckstrin homo 31.4 51 0.0011 26.5 2.8 68 1-68 26-93 (104)
16 PF13590 DUF4136: Domain of un 24.3 2E+02 0.0044 23.6 5.6 56 208-279 15-70 (151)
17 PRK14835 undecaprenyl pyrophos 21.8 2.2E+02 0.0047 27.3 5.8 33 185-221 143-175 (275)
18 KOG2671 Putative RNA methylase 21.5 1.5E+02 0.0033 29.8 4.7 52 209-279 97-149 (421)
19 TIGR00055 uppS undecaprenyl di 21.2 1.3E+02 0.0028 28.1 4.0 33 185-221 99-131 (226)
20 PRK14828 undecaprenyl pyrophos 20.1 2.1E+02 0.0046 27.0 5.3 33 185-221 124-156 (256)
No 1
>KOG3943 consensus THUMP domain-containing proteins [General function prediction only]
Probab=100.00 E-value=8.5e-47 Score=340.65 Aligned_cols=239 Identities=20% Similarity=0.311 Sum_probs=187.0
Q ss_pred CCCCCCCceEEEEcCCChhhHHHHHHHHHHHHhhhcc--CCCCCcccccccccCCCCCCCCCCcccChhhhhhhHHhhh-
Q 020866 32 SLLQRSHSGFLLTCTIKREKSATKEAISILHKRLESS--NTAGDSKRRKVCTDDMGGKCADGAEINSIEEDSAGGLQKN- 108 (320)
Q Consensus 32 ~~l~~g~~G~lvTC~~~rEk~A~~E~~~lL~e~~d~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~ie~~~~i~kEl~- 108 (320)
..|+||.+|||+||+ ++||||++|||.||+|..... +++....+++. +.|.|+.+.+ .|.+ +-..|+.
T Consensus 37 ~~lepG~~Gi~~tC~-~HErQA~QEaysl~~ElygD~~~G~~~~~~~E~a---p~gsE~~~~~----aeaE-lkdEe~gd 107 (291)
T KOG3943|consen 37 RQLEPGLQGILITCN-MHERQAVQEAYSLLNELYGDDMYGPEKFTDKEQA---PSGSEGEDDD----AEAE-LKDEEVGD 107 (291)
T ss_pred cccCCCcceEEEEcc-chHHHHHHHHHHHHHHHhcCcccCchhccCcccC---CCCCcCCCCh----HHHh-hhhhhhHH
Confidence 379999999999999 599999999999999986554 33321111100 1111111111 1111 0001111
Q ss_pred hcccCCCCCCCCCCccccceeecCCcceEEEEccCCCCCCHHHHHHHHHHHHcC--CCCCCCceEEeeeeeeeeeecCHH
Q 020866 109 ECHSSVKTDTNTETDFDMSLVKLTRNGLLLLTFPREHSPNTINIVSNIFQSLGS--GSLKSPVWCHRIFPIQATCVLKEK 186 (320)
Q Consensus 109 elk~~~kr~~~~~~~~~f~~v~~~~~gv~fi~f~~~~~~dP~~lv~~I~~d~~~--~~~~~tR~i~RliPI~~tc~a~~~ 186 (320)
+|++.. .++...|++|+++|+|+.||+ +..++-|.++|+.|++++.+ ++.++|||+|||+||+.||.|.++
T Consensus 108 dLk~~~-----~~~~~P~~Fv~~~~~Cv~f~~--t~KniVpe~~v~~i~~dm~elk~k~kRtR~~Qr~~Pi~~tc~a~le 180 (291)
T KOG3943|consen 108 DLKAST-----EMRLRPFQFVESGANCVVFIR--TLKNIVPEKLVHHILQDMYELKTKKKRTRVIQRMLPISGTCKAFLE 180 (291)
T ss_pred HHhhhh-----hhhcCchhhhhccCceEEeec--ccCccCchHHHHHHHHHHHhhhccchhhhhhhhhccccchHHhhHH
Confidence 233222 111222999999999999999 88899999999999999965 557899999999999999999999
Q ss_pred HHHHHHHHHHHhhcccccccCCCCceEEEEEcccCccccccCCCCCCCCcccccCCChhHHHHHHHHhhhhcCCCceeeC
Q 020866 187 ELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKEVVSDSAVDL 266 (320)
Q Consensus 187 ~i~~~~~~ll~~~F~~~~~~~~~~~tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~vI~~VA~~V~~~~~~hkVdL 266 (320)
.|.+++..+|.+||+.. ...+..||+|+|++||++ ++.|++||++|+.+|.-.++..+|||
T Consensus 181 ~m~k~a~~VI~p~fkap--~tgK~~tf~VE~k~RNn~-----------------~v~r~~vi~~V~~~Vc~l~se~~VdL 241 (291)
T KOG3943|consen 181 DMKKYAETVIEPWFKAP--NTGKKGTFQVEYKSRNNS-----------------HVNREEVIREVAGIVCTLNSENKVDL 241 (291)
T ss_pred HHHHHHHHhhcccccCC--CCCcCceEEEEEEecccc-----------------chhHHHHHHHHHHHHHhcCccceeec
Confidence 99999999999999863 335888999999999987 99999999999999998888999999
Q ss_pred CCCCeEEEEEEeeCCCCCCCceEEEEEeeCCCccccccceeeeeccCCC
Q 020866 267 KSPELSVLVELLPISGLPSELLVVGVSILPQKLVTTKPRLSIRALVSGT 315 (320)
Q Consensus 267 knPd~vIlVEV~k~~~~~~~~~vcgiSVv~~y~~~~K~~l~~~~l~~~~ 315 (320)
+|||++|+|||++ . +.|||||++|+-++|||| ++++.-+
T Consensus 242 ~n~D~t~~Ve~~k--s------~I~~~Vv~dy~~~RKYnl--q~~~~s~ 280 (291)
T KOG3943|consen 242 TNPDYTVVVEIIK--A------VICLSVVKDYMLFRKYNL--QEVVKSP 280 (291)
T ss_pred cCCCeEEEEEeee--c------eeeeeehHHHHHHHHhhH--HHhhccc
Confidence 9999999999999 7 899999999999999997 6665433
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=99.58 E-value=1e-14 Score=123.03 Aligned_cols=123 Identities=24% Similarity=0.284 Sum_probs=97.6
Q ss_pred ceEEEEccCCCCCCHHHHHHHHHHHHcCCCCCCCceEEeeeeeeeeeecCHHHHHHHHHHHHHhhcccccccCCCCceEE
Q 020866 135 GLLLLTFPREHSPNTINIVSNIFQSLGSGSLKSPVWCHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFA 214 (320)
Q Consensus 135 gv~fi~f~~~~~~dP~~lv~~I~~d~~~~~~~~tR~i~RliPI~~tc~a~~~~i~~~~~~ll~~~F~~~~~~~~~~~tfa 214 (320)
+.+++......+....+.+...+..+ ++++|++|++..|.+++++|.+.+..++..++.. ...||+
T Consensus 22 ~~i~i~~~~~~~~~~~~~~~~~~~~~--------~~~~ri~p~~~~~~~~~~~i~~~~~~~~~~~~~~------~~~tF~ 87 (144)
T PF02926_consen 22 GRILIDVGGEDPEGDSEEIYRALEKL--------RGISRIIPICRFCEADLEEIKEKAKELLWEKFIK------EDKTFA 87 (144)
T ss_dssp CEEEEETTEEEEEEHHHHHHHHHHHS--------SSESEEEEEEEEEESSHHHHHHHHHCSHGGGHSH------TTSEEE
T ss_pred CEEEEEeCCccccCCHHHHHHHHhcc--------cceeEEEEEEEEcCCCHHHHHHHHHHHHHHHhCC------CCCEEE
Confidence 44555522222333555555555543 5999999999999999999999999999999863 233999
Q ss_pred EEEcccCccccccCCCCCCCCcccccCCChhHHHHHHHHhhhhcCCCceeeCCCCCeEEEEEEeeCCCCCCCceEEEEEe
Q 020866 215 VGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKEVVSDSAVDLKSPELSVLVELLPISGLPSELLVVGVSI 294 (320)
Q Consensus 215 I~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~vI~~VA~~V~~~~~~hkVdLknPd~vIlVEV~k~~~~~~~~~vcgiSV 294 (320)
|.+++|++. ..++++++.+.|+++|.+..+ ++|||+|||++|.||+++ + .|+|||
T Consensus 88 V~~~r~~~~----------------~~~~s~ei~~~vg~~i~~~~~-~~Vdl~~Pd~~i~Vev~~--~------~~~i~i 142 (144)
T PF02926_consen 88 VRCRRRGKH----------------FPFTSMEIEREVGDAIKEKGG-PKVDLKNPDVVIHVEVRK--D------KCYISI 142 (144)
T ss_dssp EEEEEESSS----------------SSSCHHHHHHHHHHHHHHHHH-TEE-SSSSSEEEEEEEET--T------EEEEEE
T ss_pred EEEEEcCCc----------------cccCHHHHHHHHHHHHHHHhC-CCccCcCcCEEEEEEEEC--C------EEEEEE
Confidence 999999953 269999999999999986533 899999999999999999 8 999999
Q ss_pred eC
Q 020866 295 LP 296 (320)
Q Consensus 295 v~ 296 (320)
++
T Consensus 143 ~~ 144 (144)
T PF02926_consen 143 DT 144 (144)
T ss_dssp ES
T ss_pred eC
Confidence 75
No 3
>COG1818 Predicted RNA-binding protein, contains THUMP domain [General function prediction only]
Probab=99.49 E-value=5.2e-13 Score=118.29 Aligned_cols=107 Identities=26% Similarity=0.375 Sum_probs=90.7
Q ss_pred CCCceEEeeeeeeeeeecCHHHHHHHHHHHHHhhcccccccCCCCceEEEEEcccCccccccCCCCCCCCcccccCCChh
Q 020866 166 KSPVWCHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRN 245 (320)
Q Consensus 166 ~~tR~i~RliPI~~tc~a~~~~i~~~~~~ll~~~F~~~~~~~~~~~tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~ 245 (320)
...-++.|++|+...|.+++++|.+.+..++..+. .+..||||..++|+.- .++..
T Consensus 56 ~~~~~~~rv~pv~~~~~~dldeI~~~~~~l~~~~i-------~~~~tFaVr~~rRG~~-----------------~f~s~ 111 (175)
T COG1818 56 KEVPEVERVIPVEIEVETDLDEIEEAAAELAEEKI-------KEGKTFAVRTKRRGKH-----------------DFTSR 111 (175)
T ss_pred cCCCceeeEEEEEeeccCCHHHHHHHHHHHHhccc-------CCCCeEEEEEeecCCC-----------------Ccccc
Confidence 34578999999999999999999999999999865 3778999999999932 56666
Q ss_pred HHHHHHHHhhhhcCCCceeeCCCCCeEEEEEEeeCCCCCCCceEEEEEeeCCCccccccc
Q 020866 246 KCFTIVAAAVKEVVSDSAVDLKSPELSVLVELLPISGLPSELLVVGVSILPQKLVTTKPR 305 (320)
Q Consensus 246 ~vI~~VA~~V~~~~~~hkVdLknPd~vIlVEV~k~~~~~~~~~vcgiSVv~~y~~~~K~~ 305 (320)
++--.+...|.. ..+..|||++||++|-|||++ . .+||||+++-...+|+.
T Consensus 112 ~~~v~vg~~v~~-~tg~~VdL~~Pd~vv~Vevl~--~------~a~Isv~~~~~e~~k~~ 162 (175)
T COG1818 112 DVEVVVGEAVKK-ATGAEVDLEDPDKVVWVEVLG--D------RAGISVLPGEKEEKKIK 162 (175)
T ss_pred ceeehhHHHHHH-HhCCcccCCCCCEEEEEEEec--C------cceEEEeCchhhhhhcc
Confidence 666666666654 258999999999999999999 8 89999999987777754
No 4
>PRK01565 thiamine biosynthesis protein ThiI; Provisional
Probab=98.47 E-value=1.3e-06 Score=86.89 Aligned_cols=110 Identities=14% Similarity=0.185 Sum_probs=82.2
Q ss_pred cceEEEEccCCCCCCHHHHHHHHHHHHcCCCCCCCceEEeeeeeeeeeecCHHHHHHHHHHHHHhhcccccccCCCCceE
Q 020866 134 NGLLLLTFPREHSPNTINIVSNIFQSLGSGSLKSPVWCHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKF 213 (320)
Q Consensus 134 ~gv~fi~f~~~~~~dP~~lv~~I~~d~~~~~~~~tR~i~RliPI~~tc~a~~~~i~~~~~~ll~~~F~~~~~~~~~~~tf 213 (320)
.|-+||.. ...++.++.+. +.. .==|..+.|+.. |..++++|.+.+..++..+.. +..||
T Consensus 46 ~~r~~v~~---~~~~~~~~~~~-l~~--------vfGI~~~s~~~~-~~~~~e~I~~~~~~~~~~~~~-------~~~tF 105 (394)
T PRK01565 46 RDRMYIEL---NGEDYEEVIER-LKK--------VFGIQSFSPVYK-VEKDLEAIKEAALELLKEVYK-------EGKTF 105 (394)
T ss_pred CCEEEEEe---CCcCHHHHHHH-Hhh--------CCCcceEEEEEE-ECCCHHHHHHHHHHHHHhhcc-------CCCcE
Confidence 46777773 22355554432 222 223566778874 789999999999999887642 45699
Q ss_pred EEEEcccCccccccCCCCCCCCcccccCCChhHHHHHHHHhhhhcCCCceeeCCCCCeEEEEEEee
Q 020866 214 AVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKEVVSDSAVDLKSPELSVLVELLP 279 (320)
Q Consensus 214 aI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~vI~~VA~~V~~~~~~hkVdLknPd~vIlVEV~k 279 (320)
+|..++++.. =.++..++-..|++.|.+..++.+|||+|||++|.|||.+
T Consensus 106 ~Vr~rR~~k~----------------f~~tS~ei~r~vG~~I~~~~~~~~VdL~nPd~~i~vei~~ 155 (394)
T PRK01565 106 KVEARRSDKS----------------FPLDSMELNRELGAYILENFPNLKVDVKNPDVTLRVEVRK 155 (394)
T ss_pred EEEEEECCCC----------------CCCChHHHHHHHHHHHHhhCCCCcccccCCCeEEEEEEEc
Confidence 9999998731 1589999999999999865445899999999999999986
No 5
>PRK01269 tRNA s(4)U8 sulfurtransferase; Provisional
Probab=98.22 E-value=1e-05 Score=82.40 Aligned_cols=85 Identities=18% Similarity=0.250 Sum_probs=73.0
Q ss_pred eEEeeeeeeeeeecCHHHHHHHHHHHHHhhcccccccCCCCceEEEEEcccCccccccCCCCCCCCcccccCCChhHHHH
Q 020866 170 WCHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFT 249 (320)
Q Consensus 170 ~i~RliPI~~tc~a~~~~i~~~~~~ll~~~F~~~~~~~~~~~tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~vI~ 249 (320)
=++++.|+..++..++++|.+.+..++..++. ..||+|..++++.. .++..++-.
T Consensus 72 Gi~~~~~v~~~~~~~~e~I~~~a~~~~~~~~~--------~~tF~VrarR~~k~-----------------~~~S~ei~r 126 (482)
T PRK01269 72 GIHHFLEVEEYPFTDLHDIFEKALALYREQLE--------GKTFCVRVKRRGKH-----------------DFTSIDVER 126 (482)
T ss_pred CceEEEEEEEECCCCHHHHHHHHHHHHHHhcC--------CCeEEEEEEeCCCC-----------------CCChHHHHH
Confidence 46788999998889999999999999888762 34999999998754 789999999
Q ss_pred HHHHhhhhcCCCceeeCCCCCeEEEEEEee
Q 020866 250 IVAAAVKEVVSDSAVDLKSPELSVLVELLP 279 (320)
Q Consensus 250 ~VA~~V~~~~~~hkVdLknPd~vIlVEV~k 279 (320)
.|++.+.+...+.+|||+|||++|.|||.+
T Consensus 127 ~vG~~I~~~~~~~~VdL~nPD~~i~VeI~~ 156 (482)
T PRK01269 127 YVGGGLNQHIESAGVDLKNPDVTVHLEIRD 156 (482)
T ss_pred HHHHHHHHhCCCCceeCCCCCEEEEEEEEC
Confidence 999999644346799999999999999987
No 6
>PRK08384 thiamine biosynthesis protein ThiI; Provisional
Probab=98.18 E-value=2.1e-05 Score=78.05 Aligned_cols=88 Identities=22% Similarity=0.170 Sum_probs=69.6
Q ss_pred EEeeeeeeeeeecCHHHHHHHHHHHHHhhcccccccCCCCceEEEEEcccCccccccCCCCCCCCcccccCCChhHHHHH
Q 020866 171 CHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTI 250 (320)
Q Consensus 171 i~RliPI~~tc~a~~~~i~~~~~~ll~~~F~~~~~~~~~~~tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~vI~~ 250 (320)
|..+.|+.. |..++++|.+.+..++..+..... ....||+|..++.+.+ -.++..|+-..
T Consensus 72 I~~~s~~~~-~~~~~~~i~~~~~~~~~~~~~~~~---~~~~tF~V~~rR~~k~----------------f~~tS~ei~~~ 131 (381)
T PRK08384 72 IVSLSPAME-IDAELEKINRTALKLFRRKKRELE---LEKPRFRVTARRITKE----------------FPLKSPEIQAK 131 (381)
T ss_pred ceeEEEEEE-eCCCHHHHHHHHHHHHHHhhhccc---ccCCeEEEEEEeCCCC----------------CCCChHHHHHH
Confidence 455666654 557899999999999998864210 1346999999998731 17999999999
Q ss_pred HHHhhhhcCCCceeeCCCCCeEEEEEEee
Q 020866 251 VAAAVKEVVSDSAVDLKSPELSVLVELLP 279 (320)
Q Consensus 251 VA~~V~~~~~~hkVdLknPd~vIlVEV~k 279 (320)
|++.|... ++.+|||+|||++|.|||-+
T Consensus 132 vG~~i~~~-~~~~Vdl~~Pd~~i~vEir~ 159 (381)
T PRK08384 132 VGEYILEN-EESEVDLHNYDIEVGVELME 159 (381)
T ss_pred HHHHHHhc-CCCCccCcCCCEEEEEEEEe
Confidence 99999754 46899999999999999976
No 7
>COG0301 ThiI Thiamine biosynthesis ATP pyrophosphatase [Coenzyme metabolism]
Probab=97.91 E-value=9.5e-05 Score=73.16 Aligned_cols=101 Identities=20% Similarity=0.199 Sum_probs=75.2
Q ss_pred EEeeeeeeeeeecCHHHHHHHHHHHHHhhcccccccCCCCceEEEEEcccCccccccCCCCCCCCcccccCCChhHHHHH
Q 020866 171 CHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTI 250 (320)
Q Consensus 171 i~RliPI~~tc~a~~~~i~~~~~~ll~~~F~~~~~~~~~~~tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~vI~~ 250 (320)
|+-+.|+.. |..+++++..++..++..... +..||+|..++++.+ =.++..+|-..
T Consensus 70 I~s~sp~~~-v~~~~~~i~~~~~~~~~~~~~-------~g~tF~V~arR~~k~----------------f~~~S~ev~~~ 125 (383)
T COG0301 70 IVSFSPAME-VEASLEEIIKAALLALRRKYK-------EGKTFKVRARRAGKE----------------FPFTSLEVNRY 125 (383)
T ss_pred cceeceeEE-ecCCcHHHHHHHHHHHHHhhh-------cCCeEEEEEEeCCCC----------------CCCCHHHHHHH
Confidence 445556654 677777887777777776653 455999999999862 17999999999
Q ss_pred HHHhhhhcCCCceeeCCCCCeEEEEEEee------------CCCCCCCceEEEEEee
Q 020866 251 VAAAVKEVVSDSAVDLKSPELSVLVELLP------------ISGLPSELLVVGVSIL 295 (320)
Q Consensus 251 VA~~V~~~~~~hkVdLknPd~vIlVEV~k------------~~~~~~~~~vcgiSVv 295 (320)
|++.|-......+|||+|||++|.|||-. ..|+|.|++-=+|+.|
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 99999765467899999999999999984 1456666444444444
No 8
>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=97.80 E-value=0.00016 Score=71.41 Aligned_cols=81 Identities=25% Similarity=0.331 Sum_probs=64.0
Q ss_pred eeeeeeeeeecCHHHHHHHHHHHHHhhcccccccCCCCceEEEEEcccCccccccCCCCCCCCcccccCCChhHHHHHHH
Q 020866 173 RIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVA 252 (320)
Q Consensus 173 RliPI~~tc~a~~~~i~~~~~~ll~~~F~~~~~~~~~~~tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~vI~~VA 252 (320)
.+-|+. .|..++++|. .+..++..+.. ...||+|+.++++.+ -+++..++-..|+
T Consensus 71 ~~s~~~-~~~~~~~~i~-~~~~~~~~~~~-------~~~tF~Vr~kR~~k~----------------f~~~S~ei~r~~G 125 (371)
T TIGR00342 71 SFSPAF-KCDLPFDEIH-ILLKALKQLRK-------EGKTFKVRTKRRGKD----------------FPLNSVEVNKYVG 125 (371)
T ss_pred EEEEEE-EECCCHHHHH-HHHHHHHHhhc-------cCCcEEEEEEECCCC----------------CCCChHHHHHHHH
Confidence 344444 4678899999 88888887653 345999999998731 2577999999999
Q ss_pred HhhhhcCCCceeeCCCCCeEEEEEEee
Q 020866 253 AAVKEVVSDSAVDLKSPELSVLVELLP 279 (320)
Q Consensus 253 ~~V~~~~~~hkVdLknPd~vIlVEV~k 279 (320)
+.|... .+.+|||+|||++|.|||.+
T Consensus 126 ~~i~~~-~~~~VdL~nPd~~i~vei~~ 151 (371)
T TIGR00342 126 GGIVEK-IGLKVDLTNPDITVHIEIRE 151 (371)
T ss_pred HHHHHH-cCCcccccCCCEEEEEEEEC
Confidence 999754 34899999999999999987
No 9
>TIGR01177 conserved hypothetical protein TIGR01177. This family is found exclusively in the Archaea.
Probab=93.34 E-value=0.48 Score=45.84 Aligned_cols=81 Identities=19% Similarity=0.137 Sum_probs=56.2
Q ss_pred eeecCHHHHHHHHHHHHHhhcccccccCCCCceEEEEEcccCccccccCCCCCCCCcccccCCChhHHHHHHHHhhhhcC
Q 020866 180 TCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKEVV 259 (320)
Q Consensus 180 tc~a~~~~i~~~~~~ll~~~F~~~~~~~~~~~tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~vI~~VA~~V~~~~ 259 (320)
.|..+.+++.+.+..+--..+ ...+|+|..+..+.. ..++..+-+.+++.+...
T Consensus 61 ~~~~~~~~l~~~~~~~~~~~~--------~~~sf~v~~~~~~~~-----------------~~~~~~~~~~ig~~i~~~- 114 (329)
T TIGR01177 61 YDTCAAKDLYDFVAGLEASDL--------DRKSFAVRVRDLRGY-----------------SVDKARLERKIGAILKKK- 114 (329)
T ss_pred hcCCCHHHHHHHHhhcchhhc--------cCCeEEEEEEecCCC-----------------CCCHHHHHHHHHHHHHhc-
Confidence 344566777777665432222 125999999887743 466666667788888642
Q ss_pred CCceeeCCCCCeEEEEEEeeCCCCCCCceEEEEEee
Q 020866 260 SDSAVDLKSPELSVLVELLPISGLPSELLVVGVSIL 295 (320)
Q Consensus 260 ~~hkVdLknPd~vIlVEV~k~~~~~~~~~vcgiSVv 295 (320)
+.+|||++||+.|.|.+.+ + .|-+|..
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 6 6666664
No 10
>COG0116 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]
Probab=90.11 E-value=1.5 Score=43.82 Aligned_cols=96 Identities=21% Similarity=0.240 Sum_probs=63.2
Q ss_pred ceEEeeeeeeeeeecC-HHHHHHHHHHH-HHhhcccccccCCCCceEEEEEcccCccccccCCCCCCCCcccccCCChhH
Q 020866 169 VWCHRIFPIQATCVLK-EKELQATVSKL-VLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNK 246 (320)
Q Consensus 169 R~i~RliPI~~tc~a~-~~~i~~~~~~l-l~~~F~~~~~~~~~~~tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~ 246 (320)
|-..|+.=+-..|++. .++|-..+..+ ...||+ +..||+|.++.-+.. ..+..+
T Consensus 54 Rta~Ri~i~l~~fk~~~~~dly~~v~~i~w~~~~~-------~~~tf~V~~~~~~~~-----------------~~~s~~ 109 (381)
T COG0116 54 RTASRILLPLGEFKAETLDDLYEAVKAINWEEYFP-------EGATFAVRFRGVGSH-----------------LFTSPD 109 (381)
T ss_pred HHHHhhheeeeeeeeCCHHHHHHHhhcCCHHHhCC-------CCCEEEEEEEeccCC-----------------ccccHH
Confidence 5555655444555544 88887777665 777885 567999996644422 344445
Q ss_pred HHHHHHHhhhh-----cCCCceeeCCCCCeEEEEEEeeCCCCCCCceEEEEEeeC
Q 020866 247 CFTIVAAAVKE-----VVSDSAVDLKSPELSVLVELLPISGLPSELLVVGVSILP 296 (320)
Q Consensus 247 vI~~VA~~V~~-----~~~~hkVdLknPd~vIlVEV~k~~~~~~~~~vcgiSVv~ 296 (320)
+=..|-++|-+ ....-.||+..||+.|-|++.+ + .|-|+|--
T Consensus 110 ~a~~vkdAIvd~~~~~~~~r~~v~~~~Pdv~i~v~l~~--~------~~~l~iDt 156 (381)
T COG0116 110 IARIVKDAIVDRFRRKYGRRPSVDLDGPDVRINVELDK--D------TATLGIDT 156 (381)
T ss_pred HHHHHHHHHHHHHhhccCCCCCccccCCCeEEEEEEEc--C------EEEEEEeC
Confidence 55445445432 1122389999999999999999 8 78777753
No 11
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=87.74 E-value=13 Score=40.05 Aligned_cols=99 Identities=13% Similarity=0.136 Sum_probs=57.9
Q ss_pred CCceEEeeeeeeeeeecCHHHHHHHHHHH-HHhhcccccccCCCCceEEEEEcccCccccccCCCCCCCCcccccCCChh
Q 020866 167 SPVWCHRIFPIQATCVLKEKELQATVSKL-VLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRN 245 (320)
Q Consensus 167 ~tR~i~RliPI~~tc~a~~~~i~~~~~~l-l~~~F~~~~~~~~~~~tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~ 245 (320)
.+|-+.+|-.... .+.++|...+..+ ...||+ ...+|+|....++..- ..+.+.-.
T Consensus 54 A~RVll~l~~f~a---~~~~~Ly~~v~~i~W~~~l~-------~~~tf~V~~~~~~s~l-------------~~~~~~~~ 110 (702)
T PRK11783 54 ASRILLPLAEFKV---YSDLDLYLGVQAIDWTEHFS-------PDKTFAVDFSGTNDEI-------------RNTQFGAL 110 (702)
T ss_pred hhheEEEeeeeec---CCHHHHHHHHHcCCHHHhCC-------CCCeEEEEEEEecCCc-------------cCcHHHHH
Confidence 4566666544332 2678888777664 333443 4459999988766310 00011112
Q ss_pred HHHHHHHHhhhhcC-CCceeeCCCCCeEEEEEEeeCCCCCCCceEEEEEeeC
Q 020866 246 KCFTIVAAAVKEVV-SDSAVDLKSPELSVLVELLPISGLPSELLVVGVSILP 296 (320)
Q Consensus 246 ~vI~~VA~~V~~~~-~~hkVdLknPd~vIlVEV~k~~~~~~~~~vcgiSVv~ 296 (320)
.|-++|.+.+.... ..-+||+++||+.|.|.+.+ + -|.||+=-
T Consensus 111 ~vKdAI~d~~~~~~~~rp~vd~~~pdv~i~~~~~~--~------~~~l~ld~ 154 (702)
T PRK11783 111 KVKDAIVDRFRRKGGPRPSVDKEQPDIRINARLNK--G------EATISLDL 154 (702)
T ss_pred HHHHHHHHHHHHhcCCCCCCCCCCCCEEEEEEEeC--C------EEEEEEEC
Confidence 33334444443211 12369999999999999999 8 78887753
No 12
>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=46.79 E-value=60 Score=32.70 Aligned_cols=91 Identities=16% Similarity=0.142 Sum_probs=49.2
Q ss_pred eeecCHHHHHHHHHHHHHhhcccccccCCCCceEEEEEcccCc-cccccCCCCCCCCcccccCCChhHHHHHHHHhhhhc
Q 020866 180 TCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGF-EEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKEV 258 (320)
Q Consensus 180 tc~a~~~~i~~~~~~ll~~~F~~~~~~~~~~~tfaI~~~~Rn~-~e~~~~~~~~~~~~~~~~~l~R~~vI~~VA~~V~~~ 258 (320)
+|.--.+.|.+.+..++..-=. -+-.||.|..+.-.. .|.|.+...... -....+| |.++-..|++.|...
T Consensus 58 iC~g~f~~~~~~a~~~~~~l~~------~ef~tf~VGt~~p~~i~e~E~~i~~~~g-l~~~E~i-K~E~nRevGk~~~~~ 129 (388)
T TIGR01213 58 VCGGIFDRFDEAADLVAEKVGD------YDFSTFLVGTRFPPDVIELEEEIRKEFG-SGGGESI-KREFNREVGKLFVKR 129 (388)
T ss_pred cccChHhHHHHHHHHHHHHhhc------CccceEEEeeeCCHHHHHHHHHHHHHhC-CCcchhH-HHHHhHHHHHHHHHH
Confidence 4555555566666655554311 355688886654221 111111000000 0000133 456666677777543
Q ss_pred CCCceeeCCCCCeEEEEEEee
Q 020866 259 VSDSAVDLKSPELSVLVELLP 279 (320)
Q Consensus 259 ~~~hkVdLknPd~vIlVEV~k 279 (320)
.+-.||..+||++|+|+...
T Consensus 130 -~gk~~d~~~Pdv~i~vd~~~ 149 (388)
T TIGR01213 130 -TGKEVDFERPDLVIMVEFEY 149 (388)
T ss_pred -hCCCccCCCCCEEEEEEcCC
Confidence 37899999999999999876
No 13
>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=45.84 E-value=20 Score=27.21 Aligned_cols=21 Identities=33% Similarity=0.460 Sum_probs=18.2
Q ss_pred CceEEEEcCCChhhHHHHHHHHHHHH
Q 020866 38 HSGFLLTCTIKREKSATKEAISILHK 63 (320)
Q Consensus 38 ~~G~lvTC~~~rEk~A~~E~~~lL~e 63 (320)
.+|+||+|+. |+++++--||+
T Consensus 5 ~kGvLv~CDp-----a~Kq~il~ld~ 25 (68)
T PF06331_consen 5 IKGVLVECDP-----AIKQFILHLDE 25 (68)
T ss_dssp EEEEEEES-H-----HHHHHHHHHHH
T ss_pred eeeEEEEcCH-----HHHHHHHHHhc
Confidence 5799999997 99999999998
No 14
>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=36.15 E-value=54 Score=32.93 Aligned_cols=34 Identities=15% Similarity=0.304 Sum_probs=26.1
Q ss_pred hHHHHHHHHhhhhcCCCceeeCCCCCeEEEEEEee
Q 020866 245 NKCFTIVAAAVKEVVSDSAVDLKSPELSVLVELLP 279 (320)
Q Consensus 245 ~~vI~~VA~~V~~~~~~hkVdLknPd~vIlVEV~k 279 (320)
.++-..|++.+.+. .+..+|..|||++|+|++.-
T Consensus 122 ~E~nREvGK~~~~~-~G~~~d~~~Pdi~i~vd~~~ 155 (398)
T COG1258 122 HEFNREVGKRLASK-TGKEPDFDNPDIVIVVDLET 155 (398)
T ss_pred HHHHHHHHHHHHHh-cCCCCCCCCCCEEEEEecCC
Confidence 45566666666543 47899999999999999965
No 15
>PF15408 PH_7: Pleckstrin homology domain
Probab=31.43 E-value=51 Score=26.46 Aligned_cols=68 Identities=19% Similarity=0.275 Sum_probs=54.3
Q ss_pred CChHHHhhcCCCccccccccccCCcccCCCCCCCCCCCceEEEEcCCChhhHHHHHHHHHHHHhhhcc
Q 020866 1 MTEEKEEEELKPWEQHSRVISIPRFDYNSPSSLLQRSHSGFLLTCTIKREKSATKEAISILHKRLESS 68 (320)
Q Consensus 1 ~~~~~~~~~~~~w~~~~~~~~~~r~~y~~~~~~l~~g~~G~lvTC~~~rEk~A~~E~~~lL~e~~d~~ 68 (320)
|.++|--+.|-.++-.+-|..+|=-.++..+..|....-|||.|-.-++--+|-..--......++-+
T Consensus 26 ~~~~KGG~~L~sF~L~~s~~s~Pm~~~~~A~~N~Gi~A~G~L~~~~~~~~~~~FA~S~~~~~~Wi~~m 93 (104)
T PF15408_consen 26 MYEDKGGQYLCSFQLSSSVVSHPMVNFSQAVPNLGINAFGFLMYSPSRRHVQCFASSKKVCQSWIQVM 93 (104)
T ss_pred EecccCCceeeeeehhhhhhhcccccccccCCCCCeeEEEEEEecCCcchhhhhhhHHHHHHHHHHHh
Confidence 45667777777888889999999888888877777777899999998877788777777777766665
No 16
>PF13590 DUF4136: Domain of unknown function (DUF4136)
Probab=24.29 E-value=2e+02 Score=23.60 Aligned_cols=56 Identities=14% Similarity=0.010 Sum_probs=41.1
Q ss_pred CCCceEEEEEcccCccccccCCCCCCCCcccccCCChhHHHHHHHHhhhhcCCCceeeCCCCCeEEEEEEee
Q 020866 208 SRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKEVVSDSAVDLKSPELSVLVELLP 279 (320)
Q Consensus 208 ~~~~tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~vI~~VA~~V~~~~~~hkVdLknPd~vIlVEV~k 279 (320)
....||++.....+.. ....+....|.+.|...+.. .+++.+..+||++|-+.+.-
T Consensus 15 ~~ykTy~~~~~~~~~~--------------~~~~~~~~~i~~~v~~~L~~--~G~~~~~~~aDl~V~~~~~~ 70 (151)
T PF13590_consen 15 SQYKTYAFVPSSSDPA--------------QSNPLDDQRIQDAVEQELAA--KGYRRVPENADLLVSYHYSV 70 (151)
T ss_pred CCCCeEEEecCCcCcc--------------ccCcHHHHHHHHHHHHHHHH--CCCeecccCCCEEEEEEEEE
Confidence 3567899888843110 01267778889999998874 47877799999999988876
No 17
>PRK14835 undecaprenyl pyrophosphate synthase; Provisional
Probab=21.84 E-value=2.2e+02 Score=27.35 Aligned_cols=33 Identities=18% Similarity=0.227 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHhhcccccccCCCCceEEEEEcccC
Q 020866 185 EKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRG 221 (320)
Q Consensus 185 ~~~i~~~~~~ll~~~F~~~~~~~~~~~tfaI~~~~Rn 221 (320)
.+++.+.+..+....-+. ..-....||.|..|+
T Consensus 143 p~~l~~~i~~~e~~T~~~----~~~~Lnia~~Yggr~ 175 (275)
T PRK14835 143 PPKVLEALEELEERTEGH----EGMLLNIAVGYGGRE 175 (275)
T ss_pred CHHHHHHHHHHHHHhcCC----CCeEEEEEeccCCHH
Confidence 456666666665554322 134578999999887
No 18
>KOG2671 consensus Putative RNA methylase [Replication, recombination and repair]
Probab=21.49 E-value=1.5e+02 Score=29.75 Aligned_cols=52 Identities=17% Similarity=0.286 Sum_probs=35.2
Q ss_pred CCceEEEEEcccCccccccCCCCCCCCcccccCCChhHHHHHHHHhhhhcCCCceeeCCCCCeEEE-EEEee
Q 020866 209 RPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKEVVSDSAVDLKSPELSVL-VELLP 279 (320)
Q Consensus 209 ~~~tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~vI~~VA~~V~~~~~~hkVdLknPd~vIl-VEV~k 279 (320)
...||+|.+..=|. .++.++.++.|+..=- .+=.-+|||+||+.+.. +|-+.
T Consensus 97 ~dssfki~fetfgk------------------~~t~~e~~~~I~~f~y-lpfeG~Vnlk~Pq~~f~viE~y~ 149 (421)
T KOG2671|consen 97 SDSSFKIRFETFGK------------------KLTQDEQVEIIESFDY-LPFEGPVNLKNPQHVFFVIEEYE 149 (421)
T ss_pred cCceeEEEEEEecc------------------cccHHHHHHHhhhhee-ccccceeccCCCceEEEEEEeec
Confidence 45688888877652 5667777777665421 11257999999998765 46665
No 19
>TIGR00055 uppS undecaprenyl diphosphate synthase. Alternate name: undecaprenyl pyrophosphate synthetase. Activity has been demonstrated experimentally for members of this family from Micrococcus luteus, E. coli, Haemophilus influenzae, and Streptococcus pneumoniae.
Probab=21.16 E-value=1.3e+02 Score=28.05 Aligned_cols=33 Identities=27% Similarity=0.327 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHhhcccccccCCCCceEEEEEcccC
Q 020866 185 EKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRG 221 (320)
Q Consensus 185 ~~~i~~~~~~ll~~~F~~~~~~~~~~~tfaI~~~~Rn 221 (320)
.+++.+.+..+....-+. ..-....|+.|..|.
T Consensus 99 p~~~~~~i~~~e~~T~~n----~~~~lnia~~Yggr~ 131 (226)
T TIGR00055 99 SKELQEKIKKAEEDTKNN----TDFTLNIAFNYGGRN 131 (226)
T ss_pred CHHHHHHHHHHHHHhcCC----CceEEEEEecCCCHH
Confidence 456666666666665332 134567888888886
No 20
>PRK14828 undecaprenyl pyrophosphate synthase; Provisional
Probab=20.08 E-value=2.1e+02 Score=27.03 Aligned_cols=33 Identities=21% Similarity=0.180 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHhhcccccccCCCCceEEEEEcccC
Q 020866 185 EKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRG 221 (320)
Q Consensus 185 ~~~i~~~~~~ll~~~F~~~~~~~~~~~tfaI~~~~Rn 221 (320)
.+++.+.+..+-....+. ..-...+|+.|..|+
T Consensus 124 p~~~~~~~~~~e~~T~~~----~~~~Lnia~~Yggr~ 156 (256)
T PRK14828 124 PAPSANRLKEAEEATVGN----DGIKVNVAVGYGGRQ 156 (256)
T ss_pred CHHHHHHHHHHHHhhcCC----CCcEEEEEecCCCHH
Confidence 456666666655554332 124567888888886
Done!