Query 030128
Match_columns 182
No_of_seqs 119 out of 923
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 08:58:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030128.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030128hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00156 60S ribosomal protein 100.0 6.9E-71 1.5E-75 448.5 15.7 170 6-175 3-172 (172)
2 PRK04219 rpl5p 50S ribosomal p 100.0 4E-68 8.6E-73 434.9 15.5 171 4-174 5-176 (177)
3 COG0094 RplE Ribosomal protein 100.0 5.8E-61 1.3E-65 390.8 11.4 152 3-155 18-180 (180)
4 KOG0397 60S ribosomal protein 100.0 7.2E-55 1.6E-59 345.4 10.0 175 3-177 2-176 (176)
5 PRK00010 rplE 50S ribosomal pr 100.0 9.3E-53 2E-57 345.1 12.0 135 4-138 19-163 (179)
6 CHL00078 rpl5 ribosomal protei 100.0 1.9E-52 4.2E-57 343.8 11.8 135 4-138 20-164 (181)
7 KOG0398 Mitochondrial/chloropl 100.0 1.3E-40 2.8E-45 280.8 9.4 141 3-143 110-264 (278)
8 PF00673 Ribosomal_L5_C: ribos 100.0 2.8E-29 6E-34 187.2 6.4 74 66-139 1-81 (95)
9 PF00281 Ribosomal_L5: Ribosom 99.8 9.6E-21 2.1E-25 129.1 5.3 54 9-62 1-56 (56)
10 COG1504 Uncharacterized conser 65.7 9.4 0.0002 29.9 3.7 33 146-178 39-71 (121)
11 cd01803 Ubiquitin Ubiquitin. U 26.7 1.8E+02 0.0039 19.2 4.7 45 31-75 22-75 (76)
12 PF01807 zf-CHC2: CHC2 zinc fi 26.6 39 0.00085 24.8 1.4 23 154-176 74-96 (97)
13 PF08261 Carcinustatin: Carcin 26.1 22 0.00048 15.3 -0.0 7 102-108 2-8 (8)
14 TIGR01589 A_thal_3526 uncharac 22.1 56 0.0012 22.5 1.4 17 156-172 16-32 (57)
15 PF09456 RcsC: RcsC Alpha-Beta 20.4 81 0.0018 23.5 2.1 24 69-92 2-25 (92)
No 1
>PTZ00156 60S ribosomal protein L11; Provisional
Probab=100.00 E-value=6.9e-71 Score=448.45 Aligned_cols=170 Identities=79% Similarity=1.270 Sum_probs=167.2
Q ss_pred ccCCCCCceeeeEEEEEccCCchhHHHHHHHHHHHHHhCCCceeeeeeccccCceeeeCceEEEEEEEcCchHHHHHHHh
Q 030128 6 KLSNPMREIKVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVFSKARYTVRSFGIRRNEKIACYVTVRGDKAMQLLESG 85 (182)
Q Consensus 6 ~~~n~m~iP~I~KIvin~gvg~~~~~L~~a~~~L~~ITGQkp~~t~AKksia~FkiRkG~piG~kVTLRg~~my~FL~kl 85 (182)
..+|+|++|+|+|||||+|+|++++.|+.|..+|+.||||+|++|+||+||++||||+||||||+|||||++||+||+||
T Consensus 3 ~~~n~m~~PkI~KIvvN~gvGe~~~~L~~a~~~L~~ITGQkPv~tkAKksia~FkiRkG~pIG~kVTLRg~~m~eFLdrl 82 (172)
T PTZ00156 3 KKENPMRKIRIEKLVLNICVGESGDRLTRAAKVLEQLTGQKPVFSKARYTVRSFGIRRNEKIACHVTVRGDKAEEILERG 82 (172)
T ss_pred ccCCCccCceeEEEEEEcCcCchHHHHHHHHHHHHHHcCCceEEEEhhcccccccccCCCEEEEEEEEchHHHHHHHHHH
Confidence 34899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcccccccccCCCCCceeEEecccccccccccccCCCCccccEEEEEeecccceeeeeccccCCCCCCcccChHHHHHHh
Q 030128 86 LKVKEYELLRRNFSDTGCFGFGIQEHIDLGIKYDPSTGIYGMDFFVVLERPGYRVGRRRRCKSRVGIQHRVTKEDAMKWF 165 (182)
Q Consensus 86 irirdf~l~~~sfD~~GN~sfGi~e~~~FEi~yd~~~~i~GmdItivt~a~g~r~a~r~~~~~~i~~~h~v~~~e~~~~~ 165 (182)
++++||+|+.++||++|||+|||+||++||++|||..+++||||+|++++||||+++|++++++||.+|||++|||++||
T Consensus 83 irirDf~l~~~sFD~~GN~sfGI~e~i~fei~yD~~~~i~GmdI~ivl~rpG~rv~~R~~~~~~i~~~hrv~~eea~~~~ 162 (172)
T PTZ00156 83 LKVKEFELKKRNFSDTGNFGFGIQEHIDLGIKYDPSTGIYGMDFYVVLGRPGFRVARRKRKQSKVGKSHRVTKEEAMKWF 162 (172)
T ss_pred HhhhcccccCcccCCCcccccCCchheeeceecCcccCcccCceEEEEeCCcceeeecccccccCCCCceeCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhccEEEec
Q 030128 166 QVKYEGVILN 175 (182)
Q Consensus 166 ~~~~~~~~~~ 175 (182)
+++|||+|++
T Consensus 163 ~~~~~v~v~~ 172 (172)
T PTZ00156 163 KTTFDGIILN 172 (172)
T ss_pred HhhcCEEEcC
Confidence 9999999974
No 2
>PRK04219 rpl5p 50S ribosomal protein L5P; Reviewed
Probab=100.00 E-value=4e-68 Score=434.89 Aligned_cols=171 Identities=49% Similarity=0.847 Sum_probs=167.6
Q ss_pred CcccCCCCCceeeeEEEEEccCCchhHHHHHHHHHHHHHhCCCceeeeeeccccCceeeeCceEEEEEEEcCchHHHHHH
Q 030128 4 EKKLSNPMREIKVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVFSKARYTVRSFGIRRNEKIACYVTVRGDKAMQLLE 83 (182)
Q Consensus 4 ~~~~~n~m~iP~I~KIvin~gvg~~~~~L~~a~~~L~~ITGQkp~~t~AKksia~FkiRkG~piG~kVTLRg~~my~FL~ 83 (182)
...-+|+|++|+|+||+||+|+|++++.|..|..+|++||||+|++++||++|++||||+|+|+||+|||||++||+||+
T Consensus 5 ~~~~~N~m~iPkI~KIvin~gvgea~~~L~~a~~~L~~ITGQkP~~tkAKksIa~FkiRkG~pIG~kVTLRg~~m~~FL~ 84 (177)
T PRK04219 5 EDWEMNPMRKPRIEKVVVNIGVGESGERLTKAEKLLEELTGQKPVRTRAKKTIPDFGIRKGEPIGVKVTLRGEKAEEFLK 84 (177)
T ss_pred ccccCCCccCceeeEEEEEcCcHHHHHHHHHHHHHHHHHhCCCceeeeccccccccCccCCCEEEEEEEEccHHHHHHHH
Confidence 44568999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcccccccccCCCCCceeEEecccccccc-cccccCCCCccccEEEEEeecccceeeeeccccCCCCCCcccChHHHH
Q 030128 84 SGLKVKEYELLRRNFSDTGCFGFGIQEHIDL-GIKYDPSTGIYGMDFFVVLERPGYRVGRRRRCKSRVGIQHRVTKEDAM 162 (182)
Q Consensus 84 klirirdf~l~~~sfD~~GN~sfGi~e~~~F-Ei~yd~~~~i~GmdItivt~a~g~r~a~r~~~~~~i~~~h~v~~~e~~ 162 (182)
+|+.+.||.|+.++||++|||+|||+||++| |++|||..+++||||+|+|++||||+++|++++++||++|||++|||+
T Consensus 85 rli~ivd~~l~~~sfD~~GN~sfGI~e~~~fpei~yd~~~~i~GmdI~ivt~rpg~rv~~r~~~~~~i~~~~~~~~~e~~ 164 (177)
T PRK04219 85 TALEAVGNRLKASSFDETGNVSFGIEEHIDFPGVKYDPEIGIFGMDVCVTLERPGYRVARRRRKRRKIPSRHRVTKEEAI 164 (177)
T ss_pred HHHHhhcCCCCCcccCCCceEeeCchhhhccCccccCcccccccccEEEEEcCCccchhhhhhccccCCCCceeCHHHHH
Confidence 9999999999999999999999999999999 999999999999999999999999999999999999999999999999
Q ss_pred HHhHhhccEEEe
Q 030128 163 KWFQVKYEGVIL 174 (182)
Q Consensus 163 ~~~~~~~~~~~~ 174 (182)
+||+++|||+|+
T Consensus 165 ~~~~~~~~~~~~ 176 (177)
T PRK04219 165 EFLEENFGVEVV 176 (177)
T ss_pred HHHHHhcCeEEe
Confidence 999999999996
No 3
>COG0094 RplE Ribosomal protein L5 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.8e-61 Score=390.78 Aligned_cols=152 Identities=38% Similarity=0.649 Sum_probs=145.0
Q ss_pred CCcccCCCCCceeeeEEEEEccCCch---hHHHHHHHHHHHHHhCCCceeeeeeccccCceeeeCceEEEEEEEcCchHH
Q 030128 3 SEKKLSNPMREIKVQKLVLNISVGES---GDRLTRAAKVLEQLSGQTPVFSKARYTVRSFGIRRNEKIACYVTVRGDKAM 79 (182)
Q Consensus 3 ~~~~~~n~m~iP~I~KIvin~gvg~~---~~~L~~a~~~L~~ITGQkp~~t~AKksia~FkiRkG~piG~kVTLRg~~my 79 (182)
.+.+|.|||++|+|+|||||+|+||| ++.|+.|..+|++||||||++|+||+||++||||+|+||||||||||++||
T Consensus 18 ~~~~y~n~M~~P~i~KVvvNmGvGEa~~d~~~l~~A~~~L~~ItGQKPv~tkAkksia~FkiR~g~pIG~KVTLRg~rm~ 97 (180)
T COG0094 18 KKFGYSNPMQVPRIEKVVVNMGVGEAAADGKRLEKAAKDLELITGQKPVITKAKKSIAGFKIREGMPIGVKVTLRGERMY 97 (180)
T ss_pred HhhccCCccccceeEEEEEEccchhhhhchHHHHHHHHHHHHHhCCCceeeehhcccccccccCCCeeeEEEEEchHHHH
Confidence 46899999999999999999999999 689999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhh-----cccccc-cccCCCCCceeEEecccccccc-cccccCCCCccccEEEEEeecccceeeeecc-ccCCCC
Q 030128 80 QLLESGL-----KVKEYE-LLRRNFSDTGCFGFGIQEHIDL-GIKYDPSTGIYGMDFFVVLERPGYRVGRRRR-CKSRVG 151 (182)
Q Consensus 80 ~FL~kli-----rirdf~-l~~~sfD~~GN~sfGi~e~~~F-Ei~yd~~~~i~GmdItivt~a~g~r~a~r~~-~~~~i~ 151 (182)
+||++|+ |+|||+ |+.+|||+.|||+|||+||++| |++|||.++++||||+|+|+|+| ++.+|++ +...+|
T Consensus 98 eFL~rl~~i~lPrvrdfrGls~~sFDg~GN~sfGI~E~i~FPei~yD~~~~i~GMdi~ivtta~~-d~e~R~ll~~~~~P 176 (180)
T COG0094 98 EFLDRLLNIALPRVRDFRGLSPKSFDGRGNYSFGIKEQIIFPEIDYDPIIGIRGMDITIVTTAKG-DVEARALLSAFGIP 176 (180)
T ss_pred HHHHHHHHhhccccccccCCCccccCCCCceEecchheeecCccccCccCCccCceEEEEecCCC-hHHHHHHHHhcCCC
Confidence 9999999 889999 9999999999999999999999 99999999999999999999999 5555555 888999
Q ss_pred CCcc
Q 030128 152 IQHR 155 (182)
Q Consensus 152 ~~h~ 155 (182)
-.|+
T Consensus 177 f~~~ 180 (180)
T COG0094 177 FRKR 180 (180)
T ss_pred CCCC
Confidence 9885
No 4
>KOG0397 consensus 60S ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.2e-55 Score=345.37 Aligned_cols=175 Identities=83% Similarity=1.272 Sum_probs=171.9
Q ss_pred CCcccCCCCCceeeeEEEEEccCCchhHHHHHHHHHHHHHhCCCceeeeeeccccCceeeeCceEEEEEEEcCchHHHHH
Q 030128 3 SEKKLSNPMREIKVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVFSKARYTVRSFGIRRNEKIACYVTVRGDKAMQLL 82 (182)
Q Consensus 3 ~~~~~~n~m~iP~I~KIvin~gvg~~~~~L~~a~~~L~~ITGQkp~~t~AKksia~FkiRkG~piG~kVTLRg~~my~FL 82 (182)
.+..-.|||+..+|.|++||++++||++.|..|.++||++|||+|++++|+.+|.+|+||.++.|+|.||.||+++++.|
T Consensus 2 ~~~~~~npMrel~i~KL~lnIcvgESGdrLtRAaKvLEQLtGQ~pvfskaryTvR~fGirRNEKIAvh~tVrG~KAeeiL 81 (176)
T KOG0397|consen 2 MEKKAQNPMRELKIQKLVLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGIRRNEKIAVHVTVRGPKAEEIL 81 (176)
T ss_pred ccccccCchHhhhhheeeEEEeecccchHHHHHHHHHHHhcCCCccchhhhhhHHhhccccCceEEEEEEeeCccHHHHH
Confidence 56778899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcccccccccCCCCCceeEEecccccccccccccCCCCccccEEEEEeecccceeeeeccccCCCCCCcccChHHHH
Q 030128 83 ESGLKVKEYELLRRNFSDTGCFGFGIQEHIDLGIKYDPSTGIYGMDFFVVLERPGYRVGRRRRCKSRVGIQHRVTKEDAM 162 (182)
Q Consensus 83 ~klirirdf~l~~~sfD~~GN~sfGi~e~~~FEi~yd~~~~i~GmdItivt~a~g~r~a~r~~~~~~i~~~h~v~~~e~~ 162 (182)
++.|++++|+|..++|+.+|||.|||+||++++|.|||.++|||||..+|+.+||+|+++|+||++++|.+||+++||||
T Consensus 82 e~gLkVkeYeL~~~nFS~tgnFGFGiqEHIDLGikYDPsiGIyGmDFyVvl~RpG~rv~~rkr~~g~vG~~hr~~ked~~ 161 (176)
T KOG0397|consen 82 ERGLKVKEYELRKRNFSDTGNFGFGIQEHIDLGIKYDPSIGIYGMDFYVVLGRPGYRVARRKRCKGRVGNKHRVTKEDAM 161 (176)
T ss_pred HhccchhhhhhhhhcccccCCcccchhhheeccceeCCCcceeeeeEEEEecCCcchhhhhccCcCccCccccccHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHhhccEEEecCc
Q 030128 163 KWFQVKYEGVILNKS 177 (182)
Q Consensus 163 ~~~~~~~~~~~~~~~ 177 (182)
.|||++|+..|+|.|
T Consensus 162 kwFq~kydgvil~~k 176 (176)
T KOG0397|consen 162 KWFQQKYDGVILPKK 176 (176)
T ss_pred HHHHHhCceeecCCC
Confidence 999999999999875
No 5
>PRK00010 rplE 50S ribosomal protein L5; Validated
Probab=100.00 E-value=9.3e-53 Score=345.14 Aligned_cols=135 Identities=33% Similarity=0.564 Sum_probs=130.3
Q ss_pred CcccCCCCCceeeeEEEEEccCCchhH---HHHHHHHHHHHHhCCCceeeeeeccccCceeeeCceEEEEEEEcCchHHH
Q 030128 4 EKKLSNPMREIKVQKLVLNISVGESGD---RLTRAAKVLEQLSGQTPVFSKARYTVRSFGIRRNEKIACYVTVRGDKAMQ 80 (182)
Q Consensus 4 ~~~~~n~m~iP~I~KIvin~gvg~~~~---~L~~a~~~L~~ITGQkp~~t~AKksia~FkiRkG~piG~kVTLRg~~my~ 80 (182)
..+|+|+|++|+|+||+||+|+|++.+ .|..|..+|++||||+|++|+||+||++||||+|+|+||||||||++||+
T Consensus 19 ~~~y~n~m~iPki~KIvin~gvg~~~~~~~~l~~a~~~L~~ITGQkP~~t~aKksi~~fkiRkg~piG~kVTLRg~~my~ 98 (179)
T PRK00010 19 EFGYKNVMQVPKLEKIVLNMGVGEAVADKKLLENAVEDLTLITGQKPVVTKAKKSIAGFKLREGMPIGCKVTLRGERMYE 98 (179)
T ss_pred HhCCCCcccCCceeEEEEEccCcchhhchHHHHHHHHHHHHHhCCceEEEeccccccccCCCCCCEEEEEEEECcHHHHH
Confidence 468999999999999999999999853 79999999999999999999999999999999999999999999999999
Q ss_pred HHHHhh-----cccccc-cccCCCCCceeEEecccccccc-cccccCCCCccccEEEEEeecccc
Q 030128 81 LLESGL-----KVKEYE-LLRRNFSDTGCFGFGIQEHIDL-GIKYDPSTGIYGMDFFVVLERPGY 138 (182)
Q Consensus 81 FL~kli-----rirdf~-l~~~sfD~~GN~sfGi~e~~~F-Ei~yd~~~~i~GmdItivt~a~g~ 138 (182)
||+||+ |+|||+ ++.++||++|||+|||+||++| |++||++++++||||+|||+|+++
T Consensus 99 FL~kli~~vlPrirdf~Gi~~~sfD~~Gn~sfGi~e~~~FPei~yd~~~~i~G~~Itivtta~t~ 163 (179)
T PRK00010 99 FLDRLINIALPRVRDFRGLSPKSFDGRGNYTLGIKEQIIFPEIDYDKIDKIRGMDITIVTTAKTD 163 (179)
T ss_pred HHHHHHHHhcccccccccccccccCCCceEEECcchhhcCCCcccCccCCcCCceEEEEeccCCH
Confidence 999999 799999 9999999999999999999999 999999999999999999998864
No 6
>CHL00078 rpl5 ribosomal protein L5
Probab=100.00 E-value=1.9e-52 Score=343.81 Aligned_cols=135 Identities=27% Similarity=0.505 Sum_probs=130.0
Q ss_pred CcccCCCCCceeeeEEEEEccCCchh---HHHHHHHHHHHHHhCCCceeeeeeccccCceeeeCceEEEEEEEcCchHHH
Q 030128 4 EKKLSNPMREIKVQKLVLNISVGESG---DRLTRAAKVLEQLSGQTPVFSKARYTVRSFGIRRNEKIACYVTVRGDKAMQ 80 (182)
Q Consensus 4 ~~~~~n~m~iP~I~KIvin~gvg~~~---~~L~~a~~~L~~ITGQkp~~t~AKksia~FkiRkG~piG~kVTLRg~~my~ 80 (182)
..+|+|+|++|+|+||+||+|+|++. +.|+.|..+|+.||||+|++++||+||++||||+|+|+||||||||++||+
T Consensus 20 ~~~~~n~m~iP~i~KIvin~gvg~~~~~~k~l~~a~~~L~~ITGQkP~~t~AKksia~FkiRkg~piG~kVTLRg~~my~ 99 (181)
T CHL00078 20 KFLYKNIHQVPKLKKIVINRGLGEASQNSKILESSIKELTIITGQKPIITRAKKAIAGFKIREKMPVGVSVTLRGDKMYA 99 (181)
T ss_pred HhCCCCcccCCceeEEEEecCchhhhhchHHHHHHHHHHHHHhCCceEEEeecccchhcCccCCCEEEEEEEECcHhHHH
Confidence 46899999999999999999999975 469999999999999999999999999999999999999999999999999
Q ss_pred HHHHhh-----cccccc-cccCCCCCceeEEecccccccc-cccccCCCCccccEEEEEeecccc
Q 030128 81 LLESGL-----KVKEYE-LLRRNFSDTGCFGFGIQEHIDL-GIKYDPSTGIYGMDFFVVLERPGY 138 (182)
Q Consensus 81 FL~kli-----rirdf~-l~~~sfD~~GN~sfGi~e~~~F-Ei~yd~~~~i~GmdItivt~a~g~ 138 (182)
||+||+ |+|||+ ++.++||++|||+|||+||++| |++||++.+++||||+|||+|+++
T Consensus 100 FL~kli~~vlPrirdf~Gi~~~sfd~~Gn~sfGi~e~~~FPEi~~d~~~~i~G~~Itivtta~t~ 164 (181)
T CHL00078 100 FLDRLINLALPRIRDFQGLSPKSFDGHGNYNLGLKEQLMFPEIDYDKIDQIRGMDISIVTTAKTD 164 (181)
T ss_pred HHHHHHHHhcccccccccccccccCCCceEEECcchhccCCCcccCccCCcCCCeEEEEEeeCCH
Confidence 999999 799999 9999999999999999999999 999999999999999999998864
No 7
>KOG0398 consensus Mitochondrial/chloroplast ribosomal protein L5/L7 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-40 Score=280.83 Aligned_cols=141 Identities=26% Similarity=0.416 Sum_probs=132.3
Q ss_pred CCcccCCCCCceeeeEEEEEccCCchh---HHHHHHHHHHHHHhCCCceeeeeeccccCceeeeCceEEEEEEEcCchHH
Q 030128 3 SEKKLSNPMREIKVQKLVLNISVGESG---DRLTRAAKVLEQLSGQTPVFSKARYTVRSFGIRRNEKIACYVTVRGDKAM 79 (182)
Q Consensus 3 ~~~~~~n~m~iP~I~KIvin~gvg~~~---~~L~~a~~~L~~ITGQkp~~t~AKksia~FkiRkG~piG~kVTLRg~~my 79 (182)
.+..|-|+.++|+|+||||||+++|+. ..|+.|.+++++||||+|..++||+.|++||||+|+|+|+||||||+.||
T Consensus 110 p~~~~vn~~nvP~v~kVVvnc~~~eA~~n~~~l~~am~~~~~ITG~kP~~~~ar~dV~twKlR~g~p~G~kVtL~G~~My 189 (278)
T KOG0398|consen 110 PEFKYVNIHNVPKVQKVVVNCGIGEAAQNDKGLEAAMKDIALITGQKPIKTRARADVATWKLREGQPLGIKVTLRGDVMY 189 (278)
T ss_pred ccccccChhhCCceeeeeeecccHHhhhhHHHHHHHHHHHHHHhCCCcceeeecccCCceeeccCCcceeEEEEechHHH
Confidence 356788999999999999999999984 37999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhh-----cccccc-cccCCCCCceeEEeccc--ccccc-ccc--ccCCCCccccEEEEEeecccceeeee
Q 030128 80 QLLESGL-----KVKEYE-LLRRNFSDTGCFGFGIQ--EHIDL-GIK--YDPSTGIYGMDFFVVLERPGYRVGRR 143 (182)
Q Consensus 80 ~FL~kli-----rirdf~-l~~~sfD~~GN~sfGi~--e~~~F-Ei~--yd~~~~i~GmdItivt~a~g~r~a~r 143 (182)
.||++|+ |++||+ ++.+|+|++||+|||++ ++-.| ||+ ||.++..+||||+|.|+++.++.||+
T Consensus 190 ~FLs~L~elvLPr~rdfkGvSp~Sgd~~GniSfGl~aEd~~~FPeI~An~d~~pkt~Gm~vnI~T~ak~d~~ar~ 264 (278)
T KOG0398|consen 190 SFLSRLIELVLPRTRDFKGVSPSSGDGNGNISFGLKAEDQGVFPEIRANFDAVPKTRGMDVNISTTAKSDQEARK 264 (278)
T ss_pred HHHHHHHHHhccccccccCcCCCCcCCCCCEEeccchhhcccCchhhhhhhccccccceeEeecccccchHHHHH
Confidence 9999999 999999 99999999999999999 34457 885 99999999999999999999998875
No 8
>PF00673 Ribosomal_L5_C: ribosomal L5P family C-terminus; InterPro: IPR002132 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 L5, ~180 amino acids in length, is one of the proteins from the large ribosomal subunit. In Escherichia coli, L5 is known to be involved in binding 5S RNA to the large ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , , ], groups: Eubacterial L5. Algal chloroplast L5. Cyanelle L5. Archaebacterial L5. Mammalian L11. Tetrahymena thermophila L21. Dictyostelium discoideum (Slime mold) L5 Saccharomyces cerevisiae (Baker's yeast) L16 (39A). Plant mitochondrial L5. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1IQ4_B 2ZJR_D 2ZJP_D 3PIO_D 3CF5_D 2ZJQ_D 3DLL_D 3PIP_D 2WDL_G 3UZN_G ....
Probab=99.96 E-value=2.8e-29 Score=187.23 Aligned_cols=74 Identities=39% Similarity=0.776 Sum_probs=70.6
Q ss_pred eEEEEEEEcCchHHHHHHHhh-----cccccc-cccCCCCCceeEEecccccccc-cccccCCCCccccEEEEEeecccc
Q 030128 66 KIACYVTVRGDKAMQLLESGL-----KVKEYE-LLRRNFSDTGCFGFGIQEHIDL-GIKYDPSTGIYGMDFFVVLERPGY 138 (182)
Q Consensus 66 piG~kVTLRg~~my~FL~kli-----rirdf~-l~~~sfD~~GN~sfGi~e~~~F-Ei~yd~~~~i~GmdItivt~a~g~ 138 (182)
||||||||||++||+||+||+ |+|||+ ++.++||.+|||+|||+|+++| |++||++++++||||+|+|+++..
T Consensus 1 PiG~kvTLRg~~m~~FL~kli~~vlPrik~f~g~~~~~fd~~Gn~sfGi~e~~~Fpei~yd~~~~i~G~~i~i~t~ak~~ 80 (95)
T PF00673_consen 1 PIGCKVTLRGKKMYEFLDKLITIVLPRIKDFKGLKASSFDNSGNFSFGIKEHILFPEIEYDPFPGIFGMDITIVTTAKTP 80 (95)
T ss_dssp EEEEEEEEEHHHHHHHHHHHHHTTTTTSSSTSSBSSTTBSSSSEEEEEESSSSSSSSSSSTSSSSSSCEEEEEEESCSSH
T ss_pred CeEEEEEEccHHHHHHHHHHHHHhhhhcccccccCccccCCCceEEEEeeeeeecCCccccCCCCccceEEEEEEecCCc
Confidence 899999999999999999999 889999 9999999999999999999999 999999999999999999877655
Q ss_pred e
Q 030128 139 R 139 (182)
Q Consensus 139 r 139 (182)
.
T Consensus 81 ~ 81 (95)
T PF00673_consen 81 K 81 (95)
T ss_dssp H
T ss_pred H
Confidence 4
No 9
>PF00281 Ribosomal_L5: Ribosomal protein L5; InterPro: IPR002132 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 L5, ~180 amino acids in length, is one of the proteins from the large ribosomal subunit. In Escherichia coli, L5 is known to be involved in binding 5S RNA to the large ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , , ], groups: Eubacterial L5. Algal chloroplast L5. Cyanelle L5. Archaebacterial L5. Mammalian L11. Tetrahymena thermophila L21. Dictyostelium discoideum (Slime mold) L5 Saccharomyces cerevisiae (Baker's yeast) L16 (39A). Plant mitochondrial L5. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1IQ4_B 4A1A_D 4A1C_D 4A17_D 4A1E_D 3BBO_H 3O5H_K 1S1I_J 3O58_K 3IZS_E ....
Probab=99.82 E-value=9.6e-21 Score=129.09 Aligned_cols=54 Identities=50% Similarity=0.805 Sum_probs=49.8
Q ss_pred CCCCceeeeEEEEEccCCchhHH--HHHHHHHHHHHhCCCceeeeeeccccCceee
Q 030128 9 NPMREIKVQKLVLNISVGESGDR--LTRAAKVLEQLSGQTPVFSKARYTVRSFGIR 62 (182)
Q Consensus 9 n~m~iP~I~KIvin~gvg~~~~~--L~~a~~~L~~ITGQkp~~t~AKksia~FkiR 62 (182)
|+|++|+|+||+||+|+|++.+. |+.|..+|+.||||+|++|+||+++++||||
T Consensus 1 N~m~vPki~KIvin~gvg~~~~~k~l~~a~~~L~~ItGQkp~~t~aKksia~FkiR 56 (56)
T PF00281_consen 1 NVMQVPKIEKIVINIGVGEAGDDKVLEKAKKELEQITGQKPVITKAKKSIANFKIR 56 (56)
T ss_dssp STTTSSEEEEEEEEEESSTTSSTHHHHHHHHHHHHHHSS--EEEEESSSBSSSTBS
T ss_pred CCccccEEEEEEEECCCCccccchHHHHHHHHHHHHhCCceeEEEeeccccccccC
Confidence 89999999999999999998654 9999999999999999999999999999997
No 10
>COG1504 Uncharacterized conserved protein [Function unknown]
Probab=65.67 E-value=9.4 Score=29.88 Aligned_cols=33 Identities=18% Similarity=0.335 Sum_probs=28.1
Q ss_pred ccCCCCCCcccChHHHHHHhHhhccEEEecCcc
Q 030128 146 CKSRVGIQHRVTKEDAMKWFQVKYEGVILNKSQ 178 (182)
Q Consensus 146 ~~~~i~~~h~v~~~e~~~~~~~~~~~~~~~~~~ 178 (182)
-+++-|-+|+++.||+.++|.+.+++.|+-.-|
T Consensus 39 skrK~GTSHkl~~eEle~~lee~~E~ivvGTG~ 71 (121)
T COG1504 39 SKRKYGTSHKLALEELEELLEEGPEVIVVGTGQ 71 (121)
T ss_pred hhhhcCcccccCHHHHHHHHhcCCcEEEEecCc
Confidence 355889999999999999999999998876543
No 11
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=26.67 E-value=1.8e+02 Score=19.20 Aligned_cols=45 Identities=13% Similarity=0.344 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHhCCCc---eee------eeeccccCceeeeCceEEEEEEEcC
Q 030128 31 RLTRAAKVLEQLSGQTP---VFS------KARYTVRSFGIRRNEKIACYVTVRG 75 (182)
Q Consensus 31 ~L~~a~~~L~~ITGQkp---~~t------~AKksia~FkiRkG~piG~kVTLRg 75 (182)
.+......++..+|-.| .+. .-.++++.+++..|.-+-+.+.|+|
T Consensus 22 tV~~lK~~i~~~~g~~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i~l~~~~~g 75 (76)
T cd01803 22 TIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 75 (76)
T ss_pred cHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCcHHHcCCCCCCEEEEEEEccC
Confidence 44555566666776543 222 2356789999999999999999887
No 12
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=26.59 E-value=39 Score=24.75 Aligned_cols=23 Identities=22% Similarity=0.416 Sum_probs=15.2
Q ss_pred cccChHHHHHHhHhhccEEEecC
Q 030128 154 HRVTKEDAMKWFQVKYEGVILNK 176 (182)
Q Consensus 154 h~v~~~e~~~~~~~~~~~~~~~~ 176 (182)
+.++-.||.+||.+.||+++...
T Consensus 74 ~~~~f~eAv~~l~~~~~i~i~~~ 96 (97)
T PF01807_consen 74 EGCSFKEAVKWLAEEFGIEIPNE 96 (97)
T ss_dssp HT--HHHHHHHHHHHHT---GTT
T ss_pred hCCCHHHHHHHHHHHhCCCCCCC
Confidence 45688999999999999998653
No 13
>PF08261 Carcinustatin: Carcinustatin peptide
Probab=26.14 E-value=22 Score=15.33 Aligned_cols=7 Identities=43% Similarity=1.208 Sum_probs=4.6
Q ss_pred eeEEecc
Q 030128 102 GCFGFGI 108 (182)
Q Consensus 102 GN~sfGi 108 (182)
|-|+||+
T Consensus 2 gpy~fgl 8 (8)
T PF08261_consen 2 GPYSFGL 8 (8)
T ss_pred CcccccC
Confidence 5577775
No 14
>TIGR01589 A_thal_3526 uncharacterized plant-specific domain TIGR01589. This model represents an uncharacterized plant-specific domain 57 residues in length. It is found toward the N-terminus of most proteins that contain it. Examples include at least 10 proteins from Arabidopsis thaliana and at least one from Oryza sativa.
Probab=22.11 E-value=56 Score=22.45 Aligned_cols=17 Identities=12% Similarity=0.165 Sum_probs=15.0
Q ss_pred cChHHHHHHhHhhccEE
Q 030128 156 VTKEDAMKWFQVKYEGV 172 (182)
Q Consensus 156 v~~~e~~~~~~~~~~~~ 172 (182)
.|++|.+++|.++.|++
T Consensus 16 Msk~E~v~~L~~~a~I~ 32 (57)
T TIGR01589 16 MSKEETVSFLFENAGIS 32 (57)
T ss_pred CCHHHHHHHHHHHcCCC
Confidence 68999999999998865
No 15
>PF09456 RcsC: RcsC Alpha-Beta-Loop (ABL); InterPro: IPR019017 This domain is found in the C terminus of the signal transduction response regulator (phospho-relay) kinase RcsC, between the ATP-binding region (IPR003594 from INTERPRO) and the receiver region (IPR001789 from INTERPRO). This domain forms a discrete alpha/beta/loop structure []. The Rcs signalling pathway controls a variety of physiological functions like capsule synthesis, cell division or motility in prokaryotes. The Rcs regulation cascade, involving a multi-step phosphorelay between the two membrane-bound hybrid sensor kinases RcsC and RcsD and the global regulator RcsB, is, up to now, one of the most complicated regulatory systems in bacteria []. ; GO: 0004673 protein histidine kinase activity, 0004871 signal transducer activity, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent, 0018106 peptidyl-histidine phosphorylation, 0005886 plasma membrane, 0016021 integral to membrane; PDB: 2AYY_A 2AYX_A.
Probab=20.43 E-value=81 Score=23.51 Aligned_cols=24 Identities=17% Similarity=0.439 Sum_probs=17.0
Q ss_pred EEEEEcCchHHHHHHHhhcccccc
Q 030128 69 CYVTVRGDKAMQLLESGLKVKEYE 92 (182)
Q Consensus 69 ~kVTLRg~~my~FL~klirirdf~ 92 (182)
|=+.+|+..|..||.+|++--.+.
T Consensus 2 cwL~irNa~Le~yL~~lL~~~G~~ 25 (92)
T PF09456_consen 2 CWLAIRNAYLESYLQRLLSYHGFQ 25 (92)
T ss_dssp EEEE---HHHHHHHHHHHCTTTEE
T ss_pred EEEEehhHHHHHHHHHHHHHCCcE
Confidence 667899999999999999555555
Done!