Query 023905
Match_columns 275
No_of_seqs 152 out of 1285
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 07:30:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023905.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023905hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00143 rpl3 ribosomal protei 100.0 1.2E-90 2.5E-95 618.8 25.6 207 58-266 1-207 (207)
2 PRK00001 rplC 50S ribosomal pr 100.0 1.8E-87 4E-92 599.2 24.9 208 58-269 1-209 (210)
3 TIGR03625 L3_bact 50S ribosoma 100.0 4.6E-87 9.9E-92 593.5 23.8 201 61-263 1-202 (202)
4 KOG3141 Mitochondrial/chloropl 100.0 5.1E-86 1.1E-90 608.0 20.7 238 35-275 37-278 (310)
5 COG0087 RplC Ribosomal protein 100.0 1.9E-81 4.2E-86 562.2 21.3 210 59-270 1-214 (218)
6 PF00297 Ribosomal_L3: Ribosom 100.0 5.4E-71 1.2E-75 507.8 16.1 196 66-263 1-263 (263)
7 PRK04231 rpl3p 50S ribosomal p 100.0 1.8E-51 4E-56 387.6 20.5 212 56-269 36-318 (337)
8 TIGR03626 L3_arch archaeal rib 100.0 2.7E-51 5.8E-56 385.4 20.9 211 56-268 32-312 (330)
9 PTZ00103 60S ribosomal protein 100.0 1.9E-47 4.2E-52 364.7 19.4 208 57-268 41-343 (390)
10 KOG0746 60S ribosomal protein 99.9 7.6E-25 1.6E-29 205.6 6.9 206 58-267 29-333 (384)
11 smart00739 KOW KOW (Kyprides, 61.9 12 0.00026 22.3 3.0 25 161-186 2-26 (28)
12 PF13629 T2SS-T3SS_pil_N: Pilu 51.4 42 0.00091 25.0 5.1 35 47-81 29-65 (72)
13 cd05702 S1_Rrp5_repeat_hs11_sc 39.4 1.4E+02 0.0031 21.4 6.7 19 77-95 1-19 (70)
14 KOG2500 Uncharacterized conser 33.9 58 0.0013 30.7 4.1 80 91-180 90-173 (253)
15 PF07629 DUF1590: Protein of u 28.7 29 0.00064 22.8 0.9 19 10-28 5-24 (32)
16 PF11205 DUF2987: Protein of u 27.0 24 0.00051 30.6 0.3 51 95-148 16-66 (148)
17 PF06003 SMN: Survival motor n 25.1 1.5E+02 0.0033 27.8 5.3 32 64-95 68-104 (264)
18 PRK06788 flagellar motor switc 24.3 65 0.0014 27.1 2.4 65 120-184 24-90 (119)
19 PRK15095 FKBP-type peptidyl-pr 21.7 1.7E+02 0.0036 25.2 4.5 31 65-95 93-124 (156)
No 1
>CHL00143 rpl3 ribosomal protein L3; Validated
Probab=100.00 E-value=1.2e-90 Score=618.80 Aligned_cols=207 Identities=57% Similarity=0.987 Sum_probs=201.8
Q ss_pred ceeeeeEEEeeeeeEECCCCcEEEEEEEEeCCCeEEEEeeccCCCCeeEEEEeeeeeccccCChhhcchhhhcCCCCCce
Q 023905 58 AGIGVMGTKLGMMSYFEPDGTVVPVTVVGFREGNIVTQVKTEATDGYDAVQIGYRRVRDKKLTKPELGHLQKSGLIPMRH 137 (275)
Q Consensus 58 ~r~Glig~KiGMt~if~~~G~~vpvTVl~~~~~~vV~~vkt~e~dGY~AvqvG~g~~~~k~~~Kp~~G~f~kagv~pkr~ 137 (275)
|++||||+|+||||+|||+|+++||||||++ +|+|+|+||.|+|||+|+||||++.++++++||++|||+|+|++|+++
T Consensus 1 m~~glig~KiGMt~~f~~~G~~vpvTvl~~~-~~~V~~~kt~e~dGY~avqvg~~~~~~k~~~K~~~G~f~ka~v~p~r~ 79 (207)
T CHL00143 1 MSIGLLGTKIGMTQIFDETGNAIPVTILKVG-PCVITQIKTLTTDGYNAIQIGYKQVSTKKLTKPQLGHLQKSNVPPLKY 79 (207)
T ss_pred CcceEEEEEccceEEECCCCCEEEEEEEEEC-CeEEEEEecCCCCCcEEEEEeeeecccccCChhhcchhHHcCCCcceE
Confidence 4789999999999999999999999999996 699999999999999999999999999999999999999999999999
Q ss_pred EEEEEecCCCCcCCCcEEeccccccCCCEEEEEEEeeccceeeeeeeeccCCCCCCCCCCCCCCCCCCCCCCCCCcccCC
Q 023905 138 LQEFRLQSIDGFEAGQKLAFEEIFNEGDLVDVSGTTIGKGFQGGIKRHNFRRGAMTHGSKSHRQLGSIGAGTTPGRVYKG 217 (275)
Q Consensus 138 l~Efrv~~~~~~~~G~~l~~~~~F~~Gq~VDV~g~SKGKGF~GvmKR~gF~g~pasHGSk~HR~~GSiG~~~~PgRV~kG 217 (275)
|+|||++++++|++|++|++ ++|++||+|||+|+|||||||||||||||+++|+||||++||++||||++++|||||||
T Consensus 80 l~Efrv~~~~~~~vG~~l~v-~~F~~Gq~VDV~g~sKGKGF~GvmKR~gF~g~pasHGs~~HR~~GSiG~~~~PgRV~kG 158 (207)
T CHL00143 80 LKEFRVKSSEEFEVGQPLTV-DAFSVGQLVNVSGKSIGKGFAGLQKRHNFSRGPMTHGSKNHRAPGSIGAGTTPGRVYPG 158 (207)
T ss_pred EEEEEcCCcccCCCCCEEEh-hhccCCCEEEEEEEecCCcceeeeEeeccCCCCCccCCCCCCCCcccCCCCCCCeEcCC
Confidence 99999988778999999998 69999999999999999999999999999999999998899999999999999999999
Q ss_pred CCCCCCCCCeeEEEEceEEEEEeCCCCEEEEeccCCCCCCCeEEEEece
Q 023905 218 KKMPGRMGGTTRKIRKLKIVKIDNDLRVVMIKGAVPGKPGNLLRVAPAK 266 (275)
Q Consensus 218 kkMaG~mG~~~~Tv~Nl~V~kId~e~nli~VKGsVPG~k~~~V~I~~a~ 266 (275)
||||||||++++|++||+|++||+|+|||||||||||+++++|.|+|++
T Consensus 159 kKMpG~mG~~~~Tv~nl~Vv~vd~e~nli~VkGsVPG~~g~~v~i~~~~ 207 (207)
T CHL00143 159 KKMAGRLGNKKVTIKNLKILKVDSENNLLVLKGSVPGKPGNLLSISPSK 207 (207)
T ss_pred CccCCCCCCeeEEEeccEEEEEeCCCCEEEEEecCcCCCCCEEEEEECC
Confidence 9999999999999999999999999999999999999999999999974
No 2
>PRK00001 rplC 50S ribosomal protein L3; Validated
Probab=100.00 E-value=1.8e-87 Score=599.17 Aligned_cols=208 Identities=49% Similarity=0.881 Sum_probs=201.5
Q ss_pred ceeeeeEEEeeeeeEECCCCcEEEEEEEEeCCCeEEEEeeccCCCCeeEEEEeeeeeccccCChhhcchhhhcCCCCCce
Q 023905 58 AGIGVMGTKLGMMSYFEPDGTVVPVTVVGFREGNIVTQVKTEATDGYDAVQIGYRRVRDKKLTKPELGHLQKSGLIPMRH 137 (275)
Q Consensus 58 ~r~Glig~KiGMt~if~~~G~~vpvTVl~~~~~~vV~~vkt~e~dGY~AvqvG~g~~~~k~~~Kp~~G~f~kagv~pkr~ 137 (275)
||+||||+|+||||+|||+|+++||||||++ +|+|+|+||.|+|||+|+||||++.++++++||++|||+|+|++|+++
T Consensus 1 m~~Glig~KiGMt~ifd~~G~~vpvTvl~v~-~~~V~~~kt~e~dGY~avqvG~~~~~~~~~~Kp~~G~f~kag~~pkr~ 79 (210)
T PRK00001 1 MMKGILGKKVGMTQIFTEDGESIPVTVIEAG-PNVVTQVKTVEKDGYNAVQLGFGDKKEKRVNKPEAGHFAKAGVEPKRH 79 (210)
T ss_pred CccEEEEEEecceEEECCCCCEEEEEEEEec-CcEEEEEeCCCCCCcEEEEEeccccCcccCCHHHhHHHHHcCCCcceE
Confidence 5899999999999999999999999999996 699999999999999999999999999999999999999999999999
Q ss_pred EEEEEecCCCCcCCCcEEeccccccCCCEEEEEEEeeccceeeeeeeeccCCCCCCCC-CCCCCCCCCCCCCCCCCcccC
Q 023905 138 LQEFRLQSIDGFEAGQKLAFEEIFNEGDLVDVSGTTIGKGFQGGIKRHNFRRGAMTHG-SKSHRQLGSIGAGTTPGRVYK 216 (275)
Q Consensus 138 l~Efrv~~~~~~~~G~~l~~~~~F~~Gq~VDV~g~SKGKGF~GvmKR~gF~g~pasHG-Sk~HR~~GSiG~~~~PgRV~k 216 (275)
|+|||. ++.+++|++|++ ++|++||+|||+|+|||||||||||||||+++|+||| |++||++||||++++|+||||
T Consensus 80 l~Efr~--~~~~~~G~~l~v-~~F~~G~~VDV~g~tKGKGFqGvmKR~gf~g~p~sHG~s~~hR~~GSiG~~~~PgrV~k 156 (210)
T PRK00001 80 LREFRV--VEEYEVGQEITV-DIFEAGQKVDVTGTSKGKGFAGVIKRHNFSGGPASHGNSRSHRRPGSIGARQTPGRVFK 156 (210)
T ss_pred EEEEcc--CCCCCCCCEEee-hhccCCCEEEEEEEEcCCcceeceEecccCCCCCcCCcCcCCcCCcccCCCCCCCeECC
Confidence 999993 457999999998 7999999999999999999999999999999999999 899999999999999999999
Q ss_pred CCCCCCCCCCeeEEEEceEEEEEeCCCCEEEEeccCCCCCCCeEEEEeceecC
Q 023905 217 GKKMPGRMGGTTRKIRKLKIVKIDNDLRVVMIKGAVPGKPGNLLRVAPAKIVG 269 (275)
Q Consensus 217 GkkMaG~mG~~~~Tv~Nl~V~kId~e~nli~VKGsVPG~k~~~V~I~~a~~~~ 269 (275)
|+|||||||++++|++||+|++||+|+|||||||||||+++++|+|+||++..
T Consensus 157 gkkmaG~mG~~~~T~~nl~V~~i~~~~nli~vkGsVPG~~~~~v~ir~a~k~~ 209 (210)
T PRK00001 157 GKKMAGHMGNERVTVQNLEVVKVDAERNLLLVKGAVPGAKGGLVIIKPAVKAK 209 (210)
T ss_pred CcccCCCCCCeEEEEeCCEEEEEcCCCCEEEEEecCcCCCCCEEEEEeeeecC
Confidence 99999999999999999999999999999999999999999999999998753
No 3
>TIGR03625 L3_bact 50S ribosomal protein L3, bacterial. This model describes bacterial (and mitochondrial and chloroplast) class of ribosomal protein L3. A separate model describes the archaeal form, where both belong to Pfam family pfam00297. The name is phrased to meet the needs of bacterial genome annotation. Organellar forms typically will have transit peptides, N-terminal to the region modeled here.
Probab=100.00 E-value=4.6e-87 Score=593.50 Aligned_cols=201 Identities=50% Similarity=0.920 Sum_probs=196.8
Q ss_pred eeeEEEeeeeeEECCCCcEEEEEEEEeCCCeEEEEeeccCCCCeeEEEEeeeeeccccCChhhcchhhhcCCCCCceEEE
Q 023905 61 GVMGTKLGMMSYFEPDGTVVPVTVVGFREGNIVTQVKTEATDGYDAVQIGYRRVRDKKLTKPELGHLQKSGLIPMRHLQE 140 (275)
Q Consensus 61 Glig~KiGMt~if~~~G~~vpvTVl~~~~~~vV~~vkt~e~dGY~AvqvG~g~~~~k~~~Kp~~G~f~kagv~pkr~l~E 140 (275)
||||+|+||||+|||+|+++||||||++ +|+|+|+||.|+|||+||||||++.++++++||++|||+|+|++|+++|+|
T Consensus 1 Glig~KiGMt~if~~~G~~ipvTVl~v~-~~~V~q~kt~e~dGY~AvqvG~~~~~~~~~~Kp~~G~f~Kag~~pkr~l~E 79 (202)
T TIGR03625 1 GLLGKKVGMTQIFTEDGKAVPVTVIEVG-PNVVTQVKTVEKDGYSAVQLGFGEKKEKRVNKPEAGHFAKAGVEPKRHLRE 79 (202)
T ss_pred CccEEecceeEEECCCCcEEEEEEEEeC-CcEEEEEeCCCCCCcEEEEEeccccccccCChhhhhHHHHcCCCcCcEEEE
Confidence 7999999999999999999999999996 589999999999999999999999999999999999999999999999999
Q ss_pred EEecCCCCcCCCcEEeccccccCCCEEEEEEEeeccceeeeeeeeccCCCCCCCC-CCCCCCCCCCCCCCCCCcccCCCC
Q 023905 141 FRLQSIDGFEAGQKLAFEEIFNEGDLVDVSGTTIGKGFQGGIKRHNFRRGAMTHG-SKSHRQLGSIGAGTTPGRVYKGKK 219 (275)
Q Consensus 141 frv~~~~~~~~G~~l~~~~~F~~Gq~VDV~g~SKGKGF~GvmKR~gF~g~pasHG-Sk~HR~~GSiG~~~~PgRV~kGkk 219 (275)
||+++++++++|++|++ |+|++||+|||+|+|||||||||||||||+++|+||| |++||++||||+++||+|||||+|
T Consensus 80 frv~~~~~~~~G~~l~v-~~F~~G~~VDV~g~skGKGFqGvmKR~gf~g~~~sHG~s~~hR~~GSiG~~~~PgrV~kgkk 158 (202)
T TIGR03625 80 FRVDDLEGYEVGDEITV-DIFEAGQKVDVTGTSKGKGFAGVMKRHNFSGGPASHGNSKSHRAPGSIGQRQTPGRVFKGKK 158 (202)
T ss_pred EEcCCcccCCCCCEEEe-eeecCCCEEEEEEEEcCCcceeceEecccCCCCcccCCCCCCCCCCccCCCCCCCeEcCCCc
Confidence 99988778999999998 7999999999999999999999999999999999999 899999999999999999999999
Q ss_pred CCCCCCCeeEEEEceEEEEEeCCCCEEEEeccCCCCCCCeEEEE
Q 023905 220 MPGRMGGTTRKIRKLKIVKIDNDLRVVMIKGAVPGKPGNLLRVA 263 (275)
Q Consensus 220 MaG~mG~~~~Tv~Nl~V~kId~e~nli~VKGsVPG~k~~~V~I~ 263 (275)
||||||++++|++||+|++||+|+|||||||||||+++++|+|+
T Consensus 159 m~G~mG~~~~T~~Nl~V~~id~e~n~i~vkGsVPG~~~~~v~ir 202 (202)
T TIGR03625 159 MAGHMGNERVTVQNLEVVKVDAERNLLLVKGAVPGAKGSLVLIK 202 (202)
T ss_pred cCCCcCCeeEEEeccEEEEEcCCCCEEEEEecCcCCCCCEEEeC
Confidence 99999999999999999999999999999999999999999985
No 4
>KOG3141 consensus Mitochondrial/chloroplast ribosomal protein L3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.1e-86 Score=608.04 Aligned_cols=238 Identities=45% Similarity=0.790 Sum_probs=219.6
Q ss_pred CCCCCccccccCcccccccc-ccc--ceeeeeEEEeeeeeEECCCCcEEEEEEEEeCCCeEEEEeeccCCCCeeEEEEee
Q 023905 35 SPKQPLIFTTKRTTTHIVSM-SYE--AGIGVMGTKLGMMSYFEPDGTVVPVTVVGFREGNIVTQVKTEATDGYDAVQIGY 111 (275)
Q Consensus 35 ~p~~p~~~~~~~~~~~~~~~-~~~--~r~Glig~KiGMt~if~~~G~~vpvTVl~~~~~~vV~~vkt~e~dGY~AvqvG~ 111 (275)
.|..+.+..+ ++....+. |.+ +|+|+|+.|+|||++||+||+++||||||+++++||.++.+++++||.||||||
T Consensus 37 ~~~~~~l~~~--~~~~~~~~v~~p~s~R~GvI~~K~GMmp~w~k~G~ri~~TiL~v~d~~Vi~~~t~E~~~g~~avqVG~ 114 (310)
T KOG3141|consen 37 APAKSILLLL--KEEPNARKVWIPSSRRVGVIARKLGMMPLWDKDGERIPVTILQVDDNHVIKYITPEAKGGYFAVQVGY 114 (310)
T ss_pred CcchhhhccC--cCcccccccccCCcccceeEEEeccCchhhccCCCEEEEEEEEEecceEEEEechhhcCCeEEEEecc
Confidence 3434556664 33444443 555 999999999999999999999999999999998988886666699999999999
Q ss_pred eeeccccCChhhcchhhhcCCCCCceEEEEEecCCCCcCCCcEEeccccccCCCEEEEEEEeeccceeeeeeeeccCCCC
Q 023905 112 RRVRDKKLTKPELGHLQKSGLIPMRHLQEFRLQSIDGFEAGQKLAFEEIFNEGDLVDVSGTTIGKGFQGGIKRHNFRRGA 191 (275)
Q Consensus 112 g~~~~k~~~Kp~~G~f~kagv~pkr~l~Efrv~~~~~~~~G~~l~~~~~F~~Gq~VDV~g~SKGKGF~GvmKR~gF~g~p 191 (275)
|..++++++|+++|||+++|++||++|+||+|++++.+.+|+.|.+ +||++||||||+|+|+|||||||||||||+|+|
T Consensus 115 g~~~p~kltk~~~g~f~~~gv~pK~~l~eF~Vt~~al~~pGt~l~~-~hFk~GqyVDV~g~TigkGFqGvmKR~GFkG~p 193 (310)
T KOG3141|consen 115 GTVKPKKLTKAELGHFRSAGVPPKRHLREFRVTEEALLPPGTPLFA-RHFKPGQYVDVTGKTIGKGFQGVMKRHGFKGGP 193 (310)
T ss_pred ccCChHHhhHHHHHHHHHcCCChhhhhheEeechhccCCCCcccch-hhcCCCceEEEEeeEeccccccceeeccccCCc
Confidence 9999999999999999999999999999999997666778999976 799999999999999999999999999999999
Q ss_pred CCCC-CCCCCCCCCCCCCCCCCcccCCCCCCCCCCCeeEEEEceEEEEEeCCCCEEEEeccCCCCCCCeEEEEeceecCC
Q 023905 192 MTHG-SKSHRQLGSIGAGTTPGRVYKGKKMPGRMGGTTRKIRKLKIVKIDNDLRVVMIKGAVPGKPGNLLRVAPAKIVGK 270 (275)
Q Consensus 192 asHG-Sk~HR~~GSiG~~~~PgRV~kGkkMaG~mG~~~~Tv~Nl~V~kId~e~nli~VKGsVPG~k~~~V~I~~a~~~~~ 270 (275)
|||| |++||++||+|++++|||||||+||||||||+++|++||+||+||.|+|+|||||||||++|++|+|+||++...
T Consensus 194 asHG~sksHR~~GS~G~~~~pgRV~pGrKMpGhMG~~~rtik~LkV~kId~~~nvi~VkGsVpG~~g~~V~I~Da~~~~~ 273 (310)
T KOG3141|consen 194 ASHGTSKSHRRPGSIGQGTTPGRVWPGRKMPGHMGNEWRTIKGLKVWKIDTELNVIWVKGSVPGPKGNLVKIKDAILPTV 273 (310)
T ss_pred cccCccccccCCccccCCCCCcccccCCcCCcccCcceEEEeeeEEEEEcCCceEEEEecccCCCCCCEEEEEecccccC
Confidence 9999 899999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred CCCCC
Q 023905 271 NIPKN 275 (275)
Q Consensus 271 ~~p~~ 275 (275)
.+|||
T Consensus 274 ~i~k~ 278 (310)
T KOG3141|consen 274 DIPKN 278 (310)
T ss_pred CcccC
Confidence 88886
No 5
>COG0087 RplC Ribosomal protein L3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-81 Score=562.16 Aligned_cols=210 Identities=49% Similarity=0.821 Sum_probs=201.8
Q ss_pred eeeeeEEEeeeeeEECCCCcEEEEEEEEeCCCeEEEEeeccCCCCeeEEEEeeeeeccccCChhhcchhhhcCCCCCceE
Q 023905 59 GIGVMGTKLGMMSYFEPDGTVVPVTVVGFREGNIVTQVKTEATDGYDAVQIGYRRVRDKKLTKPELGHLQKSGLIPMRHL 138 (275)
Q Consensus 59 r~Glig~KiGMt~if~~~G~~vpvTVl~~~~~~vV~~vkt~e~dGY~AvqvG~g~~~~k~~~Kp~~G~f~kagv~pkr~l 138 (275)
+.|+||+|+||||+||++|..+||||||++ ||+|.|+||.|+|||+|+||+|++.+.++++||++|||+|+++.|+++|
T Consensus 1 ~~G~~G~KvGMT~vf~~~g~~vPVTVie~~-p~~V~~vkt~e~dGy~a~qv~~~~~k~~~~~k~~~g~~~k~~~~~k~~l 79 (218)
T COG0087 1 MLGFLGYKVGMTHVFDERGISVPVTVIEVP-PNVVVQVKTYETDGYRAVQVGAGDRKAKRVNKPLVGHFAKAGVKPKRHL 79 (218)
T ss_pred CcccceEeccceEEEccCCcEEEEEEEEcC-CcEEEEEEecccCCcEEEEEeecceeeehhccceeeeecccCCCCCCeE
Confidence 479999999999999999999999999996 7999999999999999999999999999999999999999999999999
Q ss_pred EEEEecCCC---CcCCCcEEeccccccCCCEEEEEEEeeccceeeeeeeeccCCCCCCCC-CCCCCCCCCCCCCCCCCcc
Q 023905 139 QEFRLQSID---GFEAGQKLAFEEIFNEGDLVDVSGTTIGKGFQGGIKRHNFRRGAMTHG-SKSHRQLGSIGAGTTPGRV 214 (275)
Q Consensus 139 ~Efrv~~~~---~~~~G~~l~~~~~F~~Gq~VDV~g~SKGKGF~GvmKR~gF~g~pasHG-Sk~HR~~GSiG~~~~PgRV 214 (275)
+|||+.+.+ .|++|+++++ |+|++||+|||+|+||||||||+||||||+++|+||| +.+||++||||++|||+||
T Consensus 80 ~E~rv~~~~~~~~~e~g~ei~~-dvF~~g~~VDV~gvTKGKGF~G~~KR~gf~~~p~sHg~~~~hR~~GSiG~~~~P~rV 158 (218)
T COG0087 80 AEFRVGGGDVAEKFEVGQEITV-DVFKEGELVDVTGVTKGKGFQGVMKRWGFKGGPASHGSSLSHRRPGSIGQRQTPGRV 158 (218)
T ss_pred EEEEecCccccceechhhhhch-hhccCCCEEEEEEEecccccceeeeecccccCCcccCCCccccCCcccCCCCCCCce
Confidence 999997654 4899999986 8999999999999999999999999999999999999 6699999999999999999
Q ss_pred cCCCCCCCCCCCeeEEEEceEEEEEeCCCCEEEEeccCCCCCCCeEEEEeceecCC
Q 023905 215 YKGKKMPGRMGGTTRKIRKLKIVKIDNDLRVVMIKGAVPGKPGNLLRVAPAKIVGK 270 (275)
Q Consensus 215 ~kGkkMaG~mG~~~~Tv~Nl~V~kId~e~nli~VKGsVPG~k~~~V~I~~a~~~~~ 270 (275)
|||++||||||++++|+|||+|++||.|+|||||||||||+++++|.||+|++...
T Consensus 159 ~~g~kmaG~mG~~~vTvqNl~Vv~id~e~~~ilVkGaVPG~~k~~v~vr~a~k~~~ 214 (218)
T COG0087 159 FKGKKMAGHMGNERVTVQNLEVVKVDVENNLILVKGAVPGAKKRLVVVRPAVKAKK 214 (218)
T ss_pred eCCCccCccCCCceEEEEeeEEEEEcCCCCEEEEecccCCCCCceEEEehhhccCC
Confidence 99999999999999999999999999999999999999999999999999998654
No 6
>PF00297 Ribosomal_L3: Ribosomal protein L3; InterPro: IPR000597 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L3 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L3 is known to bind to the 23S rRNA and may participate in the formation of the peptidyltransferase centre of the ribosome. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities includes bacterial, red algal, cyanelle, mammalian, yeast and Arabidopsis thaliana L3 proteins; archaeal Haloarcula marismortui HmaL3 (HL1), and yeast mitochondrial YmL9 [, , , ].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3UZ8_E 2X9U_E 3UZ1_E 3KNM_E 4ABS_E 2WDI_E 3UYG_E 4DHC_E 2J01_E 2Y11_E ....
Probab=100.00 E-value=5.4e-71 Score=507.79 Aligned_cols=196 Identities=44% Similarity=0.787 Sum_probs=181.4
Q ss_pred EeeeeeEE---------CCC-CcEEEEEEEEeCCCeEEEEeeccC----------------------------CCCeeEE
Q 023905 66 KLGMMSYF---------EPD-GTVVPVTVVGFREGNIVTQVKTEA----------------------------TDGYDAV 107 (275)
Q Consensus 66 KiGMt~if---------~~~-G~~vpvTVl~~~~~~vV~~vkt~e----------------------------~dGY~Av 107 (275)
|+||||+| +++ |..+||||||++ ||+|+++||.| +|||+|+
T Consensus 1 K~GMT~v~~~~~~~~s~~~~~g~~~pVTVle~~-p~~V~~ir~~~~~~~G~~~~~~~~~~~~~~~~~r~~~~~~~g~~a~ 79 (263)
T PF00297_consen 1 KVGMTHVFMIDDRPGSPTEGKGVFVPVTVLEVP-PCVVVGIRTYEDTNDGLKAVQEVWAEHISDDLKRRIYKNKDGYKAV 79 (263)
T ss_dssp EEEEEEEEEEB-STTSTTTTSEEEEEEEEEEE---EEEEEEEEEEEETTEEEEEEEEESS--STHHHGTCTSTTSSCHCC
T ss_pred CCcceEEEEecCcCCCccCCCCEEEEEEEEEEC-CeEEEEEEeEecCCCcceeeEEEeccccccccceeeecccccchhh
Confidence 89999999 776 999999999996 79999999999 9999999
Q ss_pred EEeeeeeccccCChhhcchhhhcCCC---CCceEEEEEecCC----------CCcCCCcEEeccccccCCCEEEEEEEee
Q 023905 108 QIGYRRVRDKKLTKPELGHLQKSGLI---PMRHLQEFRLQSI----------DGFEAGQKLAFEEIFNEGDLVDVSGTTI 174 (275)
Q Consensus 108 qvG~g~~~~k~~~Kp~~G~f~kagv~---pkr~l~Efrv~~~----------~~~~~G~~l~~~~~F~~Gq~VDV~g~SK 174 (275)
|++|++.+++..+++++|||++++++ ++++|+||++.+. +.+.+|++|+++|+|++||+|||+|+||
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~k~~i~E~~v~~~~~~~~~~~a~~~l~~G~~i~v~dvF~~Gq~VDV~gvTK 159 (263)
T PF00297_consen 80 QLGFGEKKEKRVSKRLLGHFQKAGVPIPKKKPHIMEFRVSGGDVEEKLEYAKELLGVGKEIKVNDVFKEGQYVDVIGVTK 159 (263)
T ss_dssp EECCCHHCCSTSCCECCEEHHGGGSSSS-CSSEEEEEECESSSHHHHHHHHHHHCSCSSEBSCCTTSSTTSEEEEEEEE-
T ss_pred hhhhhhccccccchhhhhcccccccchhhccceeEEecccccChhHhhhhhhhhcCccceeehhheecccceEEEEEeec
Confidence 99999999999999999999999999 9999999999877 5688999999989999999999999999
Q ss_pred ccceeeeeeeeccCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCeeEEEEceEEEEEeC-------------
Q 023905 175 GKGFQGGIKRHNFRRGAMTHGSKSHRQLGSIGAGTTPGRVYKGKKMPGRMGGTTRKIRKLKIVKIDN------------- 241 (275)
Q Consensus 175 GKGF~GvmKR~gF~g~pasHGSk~HR~~GSiG~~~~PgRV~kGkkMaG~mG~~~~Tv~Nl~V~kId~------------- 241 (275)
|||||||||||||+++|+|||+..||++||||+ ++|+|||+|++||||||++++|++||+|++||+
T Consensus 160 GKGFqGv~KR~gf~~~p~sHg~~~hR~~GsiG~-~~PgrV~~g~kmaGqmG~~~rT~~Nl~I~~i~~~~~i~p~ggf~~y 238 (263)
T PF00297_consen 160 GKGFQGVMKRWGFKGGPASHGSSKHRKPGSIGA-WTPGRVFKGKKMAGQMGNHRRTEQNLRIVKIDDDKEINPKGGFKHY 238 (263)
T ss_dssp EEEEETHHHHCSS--S-SSSSSTTSSSSS-SSC-SSSSSCGTTSTSSEEESSSEEEEEEEEEEEEETSSSSSSTT-BTTT
T ss_pred CccccccccccCCCccCCCCCCcccCCCCcccc-cccceeecccccCccccceEEEecCcEEEEeCCCccccCCCCceeE
Confidence 999999999999999999999433999999999 999999999999999999999999999999999
Q ss_pred ---CCCEEEEeccCCCCCCCeEEEE
Q 023905 242 ---DLRVVMIKGAVPGKPGNLLRVA 263 (275)
Q Consensus 242 ---e~nli~VKGsVPG~k~~~V~I~ 263 (275)
|+||||||||||||++++|+||
T Consensus 239 G~v~~n~ilvKGsVPG~~~~~V~iR 263 (263)
T PF00297_consen 239 GLVENNLILVKGSVPGPKKRLVKIR 263 (263)
T ss_dssp B--TTTEEEEES-TSSSTTEEEEEE
T ss_pred eeecCCEEEEeccccCCCCceEEeC
Confidence 9999999999999999999997
No 7
>PRK04231 rpl3p 50S ribosomal protein L3P; Reviewed
Probab=100.00 E-value=1.8e-51 Score=387.64 Aligned_cols=212 Identities=29% Similarity=0.452 Sum_probs=169.4
Q ss_pred ccceeeeeEEEeeeeeEECCCCc----------EEEEEEEEeCCCeEEEEeeccCCCCee--EEE-Eeeeeec---cccC
Q 023905 56 YEAGIGVMGTKLGMMSYFEPDGT----------VVPVTVVGFREGNIVTQVKTEATDGYD--AVQ-IGYRRVR---DKKL 119 (275)
Q Consensus 56 ~~~r~Glig~KiGMt~if~~~G~----------~vpvTVl~~~~~~vV~~vkt~e~dGY~--Avq-vG~g~~~---~k~~ 119 (275)
-+...|++|+|.|||+++..|-+ ..||||||++ |.+|..++--..+-|. ++- +=+.+.+ .+++
T Consensus 36 ~p~l~~F~GyKaGMTHv~~~ddrp~S~~~gkEi~~~VTviEtP-Pm~V~gir~Y~~~~~Gl~~~~evwa~~l~~~~~Rr~ 114 (337)
T PRK04231 36 EPKLLGFAGYKAGMTHVIMIDDRPNSPTEGKEIFVPVTVLETP-PMRVAAIRAYEKDPYGLKVLTEVWAEDLDKELERRI 114 (337)
T ss_pred CcceeEeeeeccCCeEEEEecCCCCCccCCCeEEEeEEEEeCC-CeEEEEEEEEeECCCCcEEEEEEecccchHHHhhhc
Confidence 56789999999999998875432 8999999995 7888888665555442 211 1111111 1222
Q ss_pred Chhh----------------cchh-----------hh-cCCCCCc-eEEEEEecCCC-----C---cCCCcEEecccccc
Q 023905 120 TKPE----------------LGHL-----------QK-SGLIPMR-HLQEFRLQSID-----G---FEAGQKLAFEEIFN 162 (275)
Q Consensus 120 ~Kp~----------------~G~f-----------~k-agv~pkr-~l~Efrv~~~~-----~---~~~G~~l~~~~~F~ 162 (275)
+++. .+.+ ++ .+++-|. +|.|++|...+ + -.+|++|+++|+|+
T Consensus 115 ~~~~~~~~~~~~~~~~~~~~~~~~~~vR~i~~Tqp~~~~~l~kKkp~i~Ei~v~Gg~i~~k~~~a~~llG~~i~v~dvF~ 194 (337)
T PRK04231 115 TLPKKDEKKKAFEKLLKLLEEGKIVDVRVIVHTQPKLVTGVPKKKPEIMEIRIGGGSVEERLEYAKELLGKEISISDVFK 194 (337)
T ss_pred cccccchhhHHHHHHHHHhhcCCeeEEEEEEEechhhccCCCCCCCCEEEEeecCCCHHHHHHHHHHhcCCccchhhhcc
Confidence 2221 0111 12 2566665 89999997532 1 15799999988999
Q ss_pred CCCEEEEEEEeeccceeeeeeeeccCCCCCCCC-CCCCCCCCCCCCCCCCCcccCCCCCCCCCCCeeEEEEceEEEEEeC
Q 023905 163 EGDLVDVSGTTIGKGFQGGIKRHNFRRGAMTHG-SKSHRQLGSIGAGTTPGRVYKGKKMPGRMGGTTRKIRKLKIVKIDN 241 (275)
Q Consensus 163 ~Gq~VDV~g~SKGKGF~GvmKR~gF~g~pasHG-Sk~HR~~GSiG~~~~PgRV~kGkkMaG~mG~~~~Tv~Nl~V~kId~ 241 (275)
+||+|||+|+|||||||||||||||+++|++|| ++.||++||||+ |+|+|||+|++||||||++++|++||+|++||.
T Consensus 195 ~Ge~VDV~gvTKGKGfqGvvKRwg~~~~p~~Hg~~~~~R~~GsiG~-~~P~rV~~~~~maGqmG~~~rT~~N~~I~kI~~ 273 (337)
T PRK04231 195 EGQLVDVIAVTKGKGFQGVVKRWGVKLLPRKHKRRGGSRHIGTLGP-WNPSRVMWTVPQAGQMGFHQRTEYNKRILKIGD 273 (337)
T ss_pred CCCEEEEEEEEeCCccccCeeccCcCCCCCccCCCCCCCCCcccCC-CCCCcccCCCccCCCCCCceEEEecCEEEEEcC
Confidence 999999999999999999999999999999999 679999999997 899999999999999999999999999999998
Q ss_pred -----------------CCCEEEEeccCCCCCCCeEEEEeceecC
Q 023905 242 -----------------DLRVVMIKGAVPGKPGNLLRVAPAKIVG 269 (275)
Q Consensus 242 -----------------e~nli~VKGsVPG~k~~~V~I~~a~~~~ 269 (275)
++||||||||||||++++|+|++|++..
T Consensus 274 ~~~~ItP~GGF~hYG~V~~~~ilvKGsVPG~~kr~v~lr~air~~ 318 (337)
T PRK04231 274 DGDEITPKGGFLHYGLVRNDYVLIKGSVPGPAKRLIRLRPAIRPP 318 (337)
T ss_pred CccccccCCCccccccccCCEEEEEecccCCCCceEEEehhhccC
Confidence 5999999999999999999999998643
No 8
>TIGR03626 L3_arch archaeal ribosomal protein L3. This model describes exclusively the archaeal class of ribosomal protein L3. A separate model (TIGR03625) describes the bacterial/organelle form, and both belong to Pfam family pfam00297. Eukaryotic proteins are excluded from this model.
Probab=100.00 E-value=2.7e-51 Score=385.40 Aligned_cols=211 Identities=31% Similarity=0.435 Sum_probs=168.7
Q ss_pred ccceeeeeEEEeeeeeEECCCC----------cEEEEEEEEeCCCeEEEEeeccCCC--CeeEEEEeee-eec---cccC
Q 023905 56 YEAGIGVMGTKLGMMSYFEPDG----------TVVPVTVVGFREGNIVTQVKTEATD--GYDAVQIGYR-RVR---DKKL 119 (275)
Q Consensus 56 ~~~r~Glig~KiGMt~if~~~G----------~~vpvTVl~~~~~~vV~~vkt~e~d--GY~AvqvG~g-~~~---~k~~ 119 (275)
-+...|++|+|.|||+++-.+- ...||||||++ |.+|..++--..+ |..++-=-+. +.+ .+++
T Consensus 32 ~~~l~~F~GyKaGMTHvv~~~drp~S~~~gkEv~~~VTviEtP-Pm~v~gir~Y~~t~~Gl~~l~~vwa~~l~~e~~r~~ 110 (330)
T TIGR03626 32 EPKLQGFAGYKAGMTHVIMVDDRKNSPTEGKEISVPVTVLEAP-PLRVAAIRAYGKDPYGLKVLTEVWANNLDKELSRKI 110 (330)
T ss_pred CceeeeeeeeccCCeEEEEecCCCCCCcCCCeEEeeeEEEecC-CeEEEEEEEEEECCCCcEEEEEEeeccCcHHHhhcc
Confidence 5688999999999999886432 47899999995 6888877544333 4333321121 111 1122
Q ss_pred Chhh-----------cchhh---------------h-cCCCCCc-eEEEEEecCCC-----C---cCCCcEEeccccccC
Q 023905 120 TKPE-----------LGHLQ---------------K-SGLIPMR-HLQEFRLQSID-----G---FEAGQKLAFEEIFNE 163 (275)
Q Consensus 120 ~Kp~-----------~G~f~---------------k-agv~pkr-~l~Efrv~~~~-----~---~~~G~~l~~~~~F~~ 163 (275)
.++. ...++ + .+++-|. +|+|++|...+ + -.+|++|+++|+|++
T Consensus 111 ~~~k~~~~~~~~~~~~~~l~~~~~~iRvi~~Tqp~~~~~~~kKkp~imEi~v~Gg~i~~k~~~a~~~lG~~i~v~dvF~~ 190 (330)
T TIGR03626 111 TLPKNYDVEEKLEKIEELLENDADDVRLIVHTQPKLVTGVPKKKPEIMEIRIGGGSVEERFEYALSILGKEISVSDVFKE 190 (330)
T ss_pred ccccccchhhHHHHHHHHHhcCceEEEEEEEeccccccCcccCCccEEEEeecCCCHHHHhHhhHhcCCcEEehhheecC
Confidence 2211 11111 2 2566665 89999997543 1 257999999889999
Q ss_pred CCEEEEEEEeeccceeeeeeeeccCCCCCCCC-CCCCCCCCCCCCCCCCCcccCCCCCCCCCCCeeEEEEceEEEEEeCC
Q 023905 164 GDLVDVSGTTIGKGFQGGIKRHNFRRGAMTHG-SKSHRQLGSIGAGTTPGRVYKGKKMPGRMGGTTRKIRKLKIVKIDND 242 (275)
Q Consensus 164 Gq~VDV~g~SKGKGF~GvmKR~gF~g~pasHG-Sk~HR~~GSiG~~~~PgRV~kGkkMaG~mG~~~~Tv~Nl~V~kId~e 242 (275)
||+|||+|+|||||||||||||||+++|++|| ++.||++||||+ |+|+|||+|++||||||++++|++||+|++||+|
T Consensus 191 Ge~VDV~gvTKGKGfqGvvKRwg~~~~p~~hg~~~~~R~~GsiG~-~~P~rV~~~~~maGqmG~~~rT~~N~~I~kI~~e 269 (330)
T TIGR03626 191 GQLVDVIAVTKGKGFQGVVKRWGVKLLPRKHKRRKGGRHIGTLGP-WTPSRVRWTVPQAGQMGYHQRTEYNKRILKIGED 269 (330)
T ss_pred CCEEEEEEEEcCCccccCeeccccCCCCCccCCCCCCCCCcccCC-CCCCcccCCcccCCCCCCceEEEecCEEEEEcCc
Confidence 99999999999999999999999999999999 679999999997 8999999999999999999999999999999999
Q ss_pred -----------------CCEEEEeccCCCCCCCeEEEEeceec
Q 023905 243 -----------------LRVVMIKGAVPGKPGNLLRVAPAKIV 268 (275)
Q Consensus 243 -----------------~nli~VKGsVPG~k~~~V~I~~a~~~ 268 (275)
+||||||||||||++++|+|++|++.
T Consensus 270 ~~~ItP~GGF~~YG~Vk~~~ilvKGsVPG~~~r~v~lr~a~~~ 312 (330)
T TIGR03626 270 GDEITPKGGFVNYGLVRNDYVLIKGSVPGPSKRLIRLRDAIRP 312 (330)
T ss_pred cccccccCCccccccccCCEEEEEecCcCCCCceEEEehhhcc
Confidence 99999999999999999999999864
No 9
>PTZ00103 60S ribosomal protein L3; Provisional
Probab=100.00 E-value=1.9e-47 Score=364.69 Aligned_cols=208 Identities=24% Similarity=0.359 Sum_probs=162.3
Q ss_pred cceeeeeEEEeeeeeEECCCC----------cEEEEEEEEeCCCeEEEEeeccCCC--CeeEEEEee-eeecc---ccC-
Q 023905 57 EAGIGVMGTKLGMMSYFEPDG----------TVVPVTVVGFREGNIVTQVKTEATD--GYDAVQIGY-RRVRD---KKL- 119 (275)
Q Consensus 57 ~~r~Glig~KiGMt~if~~~G----------~~vpvTVl~~~~~~vV~~vkt~e~d--GY~AvqvG~-g~~~~---k~~- 119 (275)
+...|++|+|.|||+|+-++- ...||||||++ |.+|+.++--..+ |..++-=-+ ...++ +++
T Consensus 41 p~L~aF~GyKAGMTHvv~~~drp~S~~~~kEv~~~VTIiEtP-Pm~V~GirgY~~tp~Gl~~l~~vwA~~l~~e~~rr~y 119 (390)
T PTZ00103 41 PHLTAFMGYKAGMTHIVRDVDRPGSKLHKKEVVEAVTIIEAP-PMVVVGIVGYRETPRGLRALTTVWAHHLSDEFRRRFY 119 (390)
T ss_pred ceEeeeeeeccCCeEEEEecCCCCCCcCCCeEEeeeEEEeCC-CeEEEEEEEEEECCCCcEEeEEEeeccCcHHHhhhhc
Confidence 578999999999999886532 47899999995 6888876433333 322221111 11110 111
Q ss_pred -C----------------------hhhcchhh---------------hcCCCCCc-eEEEEEecCCC-----Cc---CCC
Q 023905 120 -T----------------------KPELGHLQ---------------KSGLIPMR-HLQEFRLQSID-----GF---EAG 152 (275)
Q Consensus 120 -~----------------------Kp~~G~f~---------------kagv~pkr-~l~Efrv~~~~-----~~---~~G 152 (275)
+ +.++..++ +..++-|. +|+|++|...+ +| .+|
T Consensus 120 k~~~~s~k~af~k~~~~~~~~~~~~~~~~~l~k~~~~IRvi~hTqp~~~~l~kKkp~imEiqv~GGsv~~k~d~a~~llg 199 (390)
T PTZ00103 120 KNWYKSKKKAFTKYKKFAATKKAEERTLKRIKKYCSVIRVIAHTQPSKLPLGQKKAHVMEIQVNGGSVAEKVDFAKSLLE 199 (390)
T ss_pred cccchhhhhhhhhhhhhhcchhhHHHHHHHHhhcccEEEEEEEcchhhcCcCCcCccEEEEeecCCCHHHHHHHHHHHhc
Confidence 0 01111112 12244454 89999997643 12 579
Q ss_pred cEEeccccccCCCEEEEEEEeeccceeeeeeeeccCCCCC-CCCCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCeeEEE
Q 023905 153 QKLAFEEIFNEGDLVDVSGTTIGKGFQGGIKRHNFRRGAM-THGSKSHRQLGSIGAGTTPGRVYKGKKMPGRMGGTTRKI 231 (275)
Q Consensus 153 ~~l~~~~~F~~Gq~VDV~g~SKGKGF~GvmKR~gF~g~pa-sHGSk~HR~~GSiG~~~~PgRV~kGkkMaG~mG~~~~Tv 231 (275)
++|+++|+|++||+|||+|+|||||||||||||||+++|+ ||| .||++||||+ |+|+||++|++||||||++++|+
T Consensus 200 k~i~v~dvF~~ge~VDVigvTKGKGfqGvvKRwg~~~~p~ktH~--~~RkvGsiG~-w~P~RV~~~v~~aGQmG~h~rTe 276 (390)
T PTZ00103 200 KEVPVDSVFQQNEMIDVIGVTKGHGFEGVVKRWGVTRLPRKTHR--GLRKVACIGA-WHPARVQYTVPRAGQHGYHHRTE 276 (390)
T ss_pred CeechhhhccCCCEeeeEEEEcCCccccCeeccccCCCCccccC--CCCCCCccCC-CCCCcccCCCccCcCCCCceEEE
Confidence 9999989999999999999999999999999999999995 999 5999999999 69999999999999999999999
Q ss_pred EceEEEEEeC------------------------------CCCEEEEeccCCCCCCCeEEEEeceec
Q 023905 232 RKLKIVKIDN------------------------------DLRVVMIKGAVPGKPGNLLRVAPAKIV 268 (275)
Q Consensus 232 ~Nl~V~kId~------------------------------e~nli~VKGsVPG~k~~~V~I~~a~~~ 268 (275)
+|++|++||. ++||||||||||||++++|+||+|++.
T Consensus 277 ~Nk~I~rI~~~~~~~~~~t~~~~~~~~ItP~GGF~hYG~V~~d~imiKGsVpGp~kr~v~lR~ai~~ 343 (390)
T PTZ00103 277 LNKKIYRIGVAEDPNNATTEADLTEKTITPMGGFPHYGTVRNDFLMLKGCVVGPKKRVITLRKSLVP 343 (390)
T ss_pred eccEEEEEcCCCCcccccccccccccccccCCCccccceecCCEEEEeccccCCCCceEEEehhhcc
Confidence 9999999998 789999999999999999999999764
No 10
>KOG0746 consensus 60S ribosomal protein L3 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=7.6e-25 Score=205.63 Aligned_cols=206 Identities=23% Similarity=0.302 Sum_probs=154.9
Q ss_pred ceeeeeEEEeeeeeEECC---CC-------cEEEEEEEEeCCCeEEEEe----ecc----------------------CC
Q 023905 58 AGIGVMGTKLGMMSYFEP---DG-------TVVPVTVVGFREGNIVTQV----KTE----------------------AT 101 (275)
Q Consensus 58 ~r~Glig~KiGMt~if~~---~G-------~~vpvTVl~~~~~~vV~~v----kt~----------------------e~ 101 (275)
..+++||+|.|||.|..| .| .+.+|||||.+ |.||+.+ +|. .+
T Consensus 29 hlT~FlgYKAGMThivRe~drpgsK~~kkEv~eAVTi~etP-pmvVvgvvgyv~Tp~Glr~l~tv~A~hlSde~~Rrfyk 107 (384)
T KOG0746|consen 29 HLTAFLGYKAGMTHIVREVDRPGSKVNKKEVVEAVTIVETP-PMVVVGIVGYVETPRGLRTLKTVWAEHLSDECKRRFYK 107 (384)
T ss_pred eEeeeecccccceeeehhhcCcccccchhhheeeEEEeccC-CEEEEEEeeeeecCchHHHHHHHHHHHhhHHHHHHHHH
Confidence 567999999999999976 24 36799999995 7888875 221 12
Q ss_pred CCeeEEEEeeeeecccc---CC-hhhcchhhhc---C---------------C-CCCceEEEEEecCCC--------CcC
Q 023905 102 DGYDAVQIGYRRVRDKK---LT-KPELGHLQKS---G---------------L-IPMRHLQEFRLQSID--------GFE 150 (275)
Q Consensus 102 dGY~AvqvG~g~~~~k~---~~-Kp~~G~f~ka---g---------------v-~pkr~l~Efrv~~~~--------~~~ 150 (275)
|.|.+-.-+|-....++ .. +.+.-.|++. - + .-|.||+|.+++... .-.
T Consensus 108 nw~kskkkaft~~~k~~~~~~gk~~~~~~~~~~kky~~virv~ahtq~~~~~l~qkkahlmeiqvngGtia~KvdwA~~~ 187 (384)
T KOG0746|consen 108 NWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKVDWARER 187 (384)
T ss_pred hhhhhhhHHHHHHhhhhhhhhcchhhHHHHHHHHhhhheeeeeeechhhhhhhhhhhhhheeeeecCCcHHHHhHHHHhh
Confidence 22211111110000000 00 0011111111 0 0 257899999997543 123
Q ss_pred CCcEEeccccccCCCEEEEEEEeeccceeeeeeeeccCCCC-CCCCCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCeeE
Q 023905 151 AGQKLAFEEIFNEGDLVDVSGTTIGKGFQGGIKRHNFRRGA-MTHGSKSHRQLGSIGAGTTPGRVYKGKKMPGRMGGTTR 229 (275)
Q Consensus 151 ~G~~l~~~~~F~~Gq~VDV~g~SKGKGF~GvmKR~gF~g~p-asHGSk~HR~~GSiG~~~~PgRV~kGkkMaG~mG~~~~ 229 (275)
..+++.++++|+..|.+|++|+|||+||.||..|||.+.+| .||- ..|...|||+ |+|.||.....+|||+|++++
T Consensus 188 lEkqv~v~~vF~qdemId~IgvtkGkGykGvt~rw~tkklprkthr--glrkvaciga-whpa~V~~sVaRaGqkgyHhr 264 (384)
T KOG0746|consen 188 LEKQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHR--GLRKVACIGA-WHPARVAFSVARAGQKGYHHR 264 (384)
T ss_pred hhccCchhhccccccccceeeeeecccccccccccccccCcchhcc--cchheeeccc-ccccceeeeeeccccccchhh
Confidence 56888888999999999999999999999999999999999 7776 5799999999 999999999999999999999
Q ss_pred EEEceEEEEEeCC-------------------------------CCEEEEeccCCCCCCCeEEEEecee
Q 023905 230 KIRKLKIVKIDND-------------------------------LRVVMIKGAVPGKPGNLLRVAPAKI 267 (275)
Q Consensus 230 Tv~Nl~V~kId~e-------------------------------~nli~VKGsVPG~k~~~V~I~~a~~ 267 (275)
|..|.+|++|... |+++|+||||+|++.+++.++.++.
T Consensus 265 TeiNkkiY~ig~g~~~~~nastdyDlt~k~itpmggf~hYG~V~ndfvM~kgcvvg~kKrv~TLrksll 333 (384)
T KOG0746|consen 265 TEINKKIYRIGQGKLIKNNASTDYDLTEKSITPMGGFPHYGEVINDFVMLKGCVVGPKKRVVTLRKSLL 333 (384)
T ss_pred hhhhhheeecccccccccccccCccccccccccCCCcceeeeeechheeecccccCccccccchhhhhh
Confidence 9999999999652 6899999999999999999998854
No 11
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=61.95 E-value=12 Score=22.28 Aligned_cols=25 Identities=32% Similarity=0.327 Sum_probs=21.1
Q ss_pred ccCCCEEEEEEEeeccceeeeeeeec
Q 023905 161 FNEGDLVDVSGTTIGKGFQGGIKRHN 186 (275)
Q Consensus 161 F~~Gq~VDV~g~SKGKGF~GvmKR~g 186 (275)
|++|+.|.|++ -.-+|+.|.+.++.
T Consensus 2 ~~~G~~V~I~~-G~~~g~~g~i~~i~ 26 (28)
T smart00739 2 FEVGDTVRVIA-GPFKGKVGKVLEVD 26 (28)
T ss_pred CCCCCEEEEeE-CCCCCcEEEEEEEc
Confidence 78899999988 55889999998764
No 12
>PF13629 T2SS-T3SS_pil_N: Pilus formation protein N terminal region
Probab=51.45 E-value=42 Score=25.00 Aligned_cols=35 Identities=20% Similarity=0.323 Sum_probs=26.3
Q ss_pred cccccccccccceeeeeEEEeeeee--EECCCCcEEE
Q 023905 47 TTTHIVSMSYEAGIGVMGTKLGMMS--YFEPDGTVVP 81 (275)
Q Consensus 47 ~~~~~~~~~~~~r~Glig~KiGMt~--if~~~G~~vp 81 (275)
|+-+......++..=++|++.|.|. +||++|...-
T Consensus 29 p~Iadv~~~~~~~v~i~gk~~G~T~l~vw~~~~~~~~ 65 (72)
T PF13629_consen 29 PEIADVTVLSPNEVYITGKKPGTTTLIVWDKDGRVIQ 65 (72)
T ss_pred CCEEEEEEeCCCEEEEEEeCceeEEEEEECCCCCEEE
Confidence 3444444446678899999999998 8999998533
No 13
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=39.39 E-value=1.4e+02 Score=21.41 Aligned_cols=19 Identities=21% Similarity=0.330 Sum_probs=13.3
Q ss_pred CcEEEEEEEEeCCCeEEEE
Q 023905 77 GTVVPVTVVGFREGNIVTQ 95 (275)
Q Consensus 77 G~~vpvTVl~~~~~~vV~~ 95 (275)
|..++++|+++.+..+.+.
T Consensus 1 G~iV~g~V~~i~~~gi~v~ 19 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQ 19 (70)
T ss_pred CCEEEEEEEEEECCcEEEE
Confidence 6788899999865444444
No 14
>KOG2500 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.88 E-value=58 Score=30.74 Aligned_cols=80 Identities=23% Similarity=0.327 Sum_probs=51.1
Q ss_pred eEEEEeeccCCCCeeE-EEEeeeeecc-ccCChhhcchhhhcCCCCCceEEEEEecCCCCcCCCcEEeccccccCCCEEE
Q 023905 91 NIVTQVKTEATDGYDA-VQIGYRRVRD-KKLTKPELGHLQKSGLIPMRHLQEFRLQSIDGFEAGQKLAFEEIFNEGDLVD 168 (275)
Q Consensus 91 ~vV~~vkt~e~dGY~A-vqvG~g~~~~-k~~~Kp~~G~f~kagv~pkr~l~Efrv~~~~~~~~G~~l~~~~~F~~Gq~VD 168 (275)
..|..| ++-+|-.| +-+||++..+ .-+|-.+.-||+=..- -+|+.- .+..+..+..|++ -|++||.+.
T Consensus 90 YFViRv--~dgngr~AFiGlGF~eR~dafDfnvaLqDHfkyv~~-----~~e~ek-~eq~~d~~pslDl--gFKEGeTIk 159 (253)
T KOG2500|consen 90 YFVIRV--EDGNGRHAFIGLGFGERGDAFDFNVALQDHFKYVKR-----QKEAEK-QEQHYDAGPSLDL--GFKEGETIK 159 (253)
T ss_pred EEEEEE--eCCCccEEEEeecccccccccchhhhHHHHHHHHHH-----HHHHHh-hhcccCCCccccc--cccCCcEEE
Confidence 455443 45666444 5699998865 4577788888863321 123332 2346788888876 699999987
Q ss_pred EEEE--eeccceee
Q 023905 169 VSGT--TIGKGFQG 180 (275)
Q Consensus 169 V~g~--SKGKGF~G 180 (275)
+.=. ||++|=.+
T Consensus 160 inikn~tkk~g~~s 173 (253)
T KOG2500|consen 160 INIKNITKKKGAAS 173 (253)
T ss_pred EEeecccccccccc
Confidence 7544 67777433
No 15
>PF07629 DUF1590: Protein of unknown function (DUF1590); InterPro: IPR011481 These hypothetical proteins in Rhodopirellula baltica have a conserved C-terminal region.
Probab=28.75 E-value=29 Score=22.78 Aligned_cols=19 Identities=42% Similarity=1.008 Sum_probs=15.1
Q ss_pred ccCC-CCcccccccCCCCCc
Q 023905 10 GHCP-PSLSLKCNFPFRPTR 28 (275)
Q Consensus 10 ~~~~-~~~~~~~~~~~~~~~ 28 (275)
.||| +.+|+-+.||-.|.-
T Consensus 5 a~~pppeislna~fptppaa 24 (32)
T PF07629_consen 5 ADCPPPEISLNARFPTPPAA 24 (32)
T ss_pred CCCCCCcceeccccCCChhh
Confidence 3677 999999999977643
No 16
>PF11205 DUF2987: Protein of unknown function (DUF2987); InterPro: IPR021370 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=26.97 E-value=24 Score=30.61 Aligned_cols=51 Identities=10% Similarity=0.212 Sum_probs=35.7
Q ss_pred EeeccCCCCeeEEEEeeeeeccccCChhhcchhhhcCCCCCceEEEEEecCCCC
Q 023905 95 QVKTEATDGYDAVQIGYRRVRDKKLTKPELGHLQKSGLIPMRHLQEFRLQSIDG 148 (275)
Q Consensus 95 ~vkt~e~dGY~AvqvG~g~~~~k~~~Kp~~G~f~kagv~pkr~l~Efrv~~~~~ 148 (275)
+.|+.++.+|..|+|||.=.+ .....+++.+++-+.-..+-.++.+++...
T Consensus 16 ~lK~~~k~~~~~v~~af~~~~---~~~~~~C~I~~a~i~te~~~~pL~i~~~~e 66 (148)
T PF11205_consen 16 RLKQVNKEDYSDVKVAFFLPD---AQTGQACQIKKAWIETEKHYEPLTITADGE 66 (148)
T ss_pred HHhhhccCCCccEEEEEEEEc---CCCCccceEEEEEEEEcCceEEeccCCCCe
Confidence 358888999999999998554 333455777777776666666666655443
No 17
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=25.10 E-value=1.5e+02 Score=27.79 Aligned_cols=32 Identities=28% Similarity=0.435 Sum_probs=22.1
Q ss_pred EEEee--eeeEECCCCcEEEEEEEEeCCC---eEEEE
Q 023905 64 GTKLG--MMSYFEPDGTVVPVTVVGFREG---NIVTQ 95 (275)
Q Consensus 64 g~KiG--Mt~if~~~G~~vpvTVl~~~~~---~vV~~ 95 (275)
--|+| +..+|.+||..-++||..|+.. |+|+.
T Consensus 68 ~WkvGd~C~A~~s~Dg~~Y~A~I~~i~~~~~~~~V~f 104 (264)
T PF06003_consen 68 KWKVGDKCMAVYSEDGQYYPATIESIDEEDGTCVVVF 104 (264)
T ss_dssp ---TT-EEEEE-TTTSSEEEEEEEEEETTTTEEEEEE
T ss_pred CCCCCCEEEEEECCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 44555 4578999999999999999752 66664
No 18
>PRK06788 flagellar motor switch protein; Validated
Probab=24.28 E-value=65 Score=27.15 Aligned_cols=65 Identities=14% Similarity=0.142 Sum_probs=46.6
Q ss_pred ChhhcchhhhcCCCCCceEEEEEecC--CCCcCCCcEEeccccccCCCEEEEEEEeeccceeeeeee
Q 023905 120 TKPELGHLQKSGLIPMRHLQEFRLQS--IDGFEAGQKLAFEEIFNEGDLVDVSGTTIGKGFQGGIKR 184 (275)
Q Consensus 120 ~Kp~~G~f~kagv~pkr~l~Efrv~~--~~~~~~G~~l~~~~~F~~Gq~VDV~g~SKGKGF~GvmKR 184 (275)
++..+..+....++..-.|.+.+++- --.+.+|+.|.++..+..==.|-|-+..+++|..|++..
T Consensus 24 ~~~~l~~L~~v~V~v~aeLG~t~ltl~DlL~L~vGDVI~Ldk~~~dpv~v~Vng~~~f~G~~Gv~~~ 90 (119)
T PRK06788 24 SKAHIDTVSDISIELGVKLGKASITLGDVKQLKVGDVLEVEKNLGHKVDVYLSNMKVGIGEAIVMDE 90 (119)
T ss_pred chhhhHHhhcCceEEEEEEecceecHHHHhCCCCCCEEEeCCcCCCCEEEEECCEEEEEEEEEEECC
Confidence 45677788888888888888777653 336789999999544333333445688999999998864
No 19
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=21.68 E-value=1.7e+02 Score=25.23 Aligned_cols=31 Identities=16% Similarity=0.371 Sum_probs=22.8
Q ss_pred EEeeee-eEECCCCcEEEEEEEEeCCCeEEEE
Q 023905 65 TKLGMM-SYFEPDGTVVPVTVVGFREGNIVTQ 95 (275)
Q Consensus 65 ~KiGMt-~if~~~G~~vpvTVl~~~~~~vV~~ 95 (275)
.++||. .+-+++|..++++|+++++..|...
T Consensus 93 ~~~G~~~~~~~~~G~~~~~~V~~i~~~~v~vD 124 (156)
T PRK15095 93 PEIGAIMLFTAMDGSEMPGVIREINGDSITVD 124 (156)
T ss_pred CCCCCEEEEECCCCCEEEEEEEEEcCCEEEEE
Confidence 356666 3445689999999999987666655
Done!