Query 025560
Match_columns 251
No_of_seqs 191 out of 890
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 07:04:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025560.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025560hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01310 L7 60S ribosomal pro 100.0 2.8E-85 6E-90 582.6 23.8 233 15-251 1-235 (235)
2 KOG3184 60S ribosomal protein 100.0 9.3E-67 2E-71 463.6 16.6 234 13-251 1-235 (235)
3 cd01657 Ribosomal_L7_archeal_e 100.0 3.4E-63 7.3E-68 419.5 16.0 159 92-251 1-159 (159)
4 PRK06049 rpl30p 50S ribosomal 100.0 1.5E-61 3.3E-66 407.0 16.2 154 91-251 1-154 (154)
5 TIGR01309 L30P_arch 50S riboso 100.0 6.9E-60 1.5E-64 396.2 15.1 151 93-251 1-152 (152)
6 COG1841 RpmD Ribosomal protein 99.8 2.7E-19 5.9E-24 126.7 6.0 55 93-147 1-55 (55)
7 cd00355 Ribosomal_L30_like Rib 99.7 4.5E-18 9.6E-23 119.5 6.5 53 94-146 1-53 (53)
8 PF00327 Ribosomal_L30: Riboso 99.7 1E-16 2.2E-21 112.1 7.2 52 92-143 1-52 (52)
9 PF08079 Ribosomal_L30_N: Ribo 99.7 1.4E-17 3E-22 123.8 3.0 71 16-90 1-71 (71)
10 PRK05611 rpmD 50S ribosomal pr 99.6 5.4E-16 1.2E-20 111.4 6.9 55 93-147 4-58 (59)
11 TIGR01308 rpmD_bact ribosomal 99.6 4.1E-15 8.8E-20 105.5 6.5 54 94-147 2-55 (55)
12 cd01658 Ribosomal_L30 Ribosoma 99.6 8.7E-15 1.9E-19 103.3 6.3 53 93-145 1-53 (54)
13 KOG4799 Mitochondrial ribosoma 97.1 0.0012 2.5E-08 56.3 6.4 73 87-159 53-134 (182)
14 PF00571 CBS: CBS domain CBS d 33.3 63 0.0014 21.1 3.3 45 143-198 11-56 (57)
15 KOG1097 Adenine deaminase/aden 26.9 1.1E+02 0.0024 30.1 4.8 54 97-150 245-299 (399)
16 TIGR03757 conj_TIGR03757 integ 26.2 98 0.0021 25.1 3.7 33 113-158 78-110 (113)
17 PF11372 DUF3173: Domain of un 20.4 96 0.0021 22.4 2.3 30 154-183 27-56 (59)
18 PF07511 DUF1525: Protein of u 20.0 1.5E+02 0.0032 24.1 3.6 33 114-159 78-110 (114)
No 1
>TIGR01310 L7 60S ribosomal protein L7, eukaryotic. Members of this family average ~ 250 residues in length, somewhat longer than the archaeal L30P/L7E homolog (~ 155 residues) and much longer than the related bacterial/organellar form (~ 60 residues).
Probab=100.00 E-value=2.8e-85 Score=582.56 Aligned_cols=233 Identities=52% Similarity=0.874 Sum_probs=227.4
Q ss_pred hHHHHhhhhHHHHHHHHHHHHHhcccCcccccccccchhhcCcHHHHHHHHHHHHHHHHHHHhhhcCCCccCCCCCceEE
Q 025560 15 ETVLKKRKSTEALALTRKAQLELGKYGHGQKNKKSKVEDIKRPEQFIKQFRDQELDLIRMKQRGKRSKKVIGKPKSKLLF 94 (251)
Q Consensus 15 E~~lkkrk~~~~~~~~~~~~~~~~k~~~~~~~k~~rk~~~krae~~v~ey~~~e~~~~r~kr~ak~~~~~~~~~e~kl~~ 94 (251)
|++|||||++++++.++++++.+.+ ++++.+++.+|+|||+|+++|+++++|.+|++|+++++|++|+|+|++++|
T Consensus 1 e~llkkrk~~~~~~~~~~~~~~~~k----~~~~~~k~~~fkr~e~~~~~y~~~e~d~~r~~r~~k~~~~~~~~~e~kl~f 76 (235)
T TIGR01310 1 ELLLKKRKARQELAVVRAKQAKAKK----KRNKKKKKHYFKRAESFVHEYRKAERERIRLKRLAKKPGKFYVPAEHKLLF 76 (235)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHhhcccCcCCCCCCeEEE
Confidence 7899999999999999999888877 777788899999999999999999999999999999999999999999999
Q ss_pred EEeecCCCCCChHHHHHHHHhCCCCcCcEEEEeCChhHHHHHHhccCeEEEecCChHHHHHHHHHhcccccCCceecCCC
Q 025560 95 IIRIQGTSDMHRRTKKILYNLRLRRIFSGVFVRATDGMLEVLQKVEPYVTYGYPNLVNVKELIYKKGYATVDRQRIPLTD 174 (251)
Q Consensus 95 ViRirg~~~~~p~~~k~L~~LrL~ki~~~vfv~~n~~~~~mL~~V~pyV~~G~p~~~tvr~Li~KRG~~k~~~~~~~ltd 174 (251)
||||||++++||++++||++|||+++||||||++|+++.+||++|+|||||||||++||++||||||+++++++++||||
T Consensus 77 VIRirG~~~v~p~v~k~L~lLRL~~in~~Vfvk~~~~~~~ML~~VepYVt~G~p~l~tvr~Li~KRG~~k~~~~~v~Ltd 156 (235)
T TIGR01310 77 VIRIKGINGIPPKPRKVLRLLRLKQVHNGVFVKVNKATLQMLRIVEPYVAYGYPNLKSVRELIYKRGFAKINGQRVPLTD 156 (235)
T ss_pred EEEeCCCCCCCHHHHHHHHHhCCCccceEEEEECCHHHHHHHHhcCCeEEEecCCHHHHHHHHHHhCceeeCCCeeeCCh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHhhhcccCCcccHHHHHHHHHhcCCchhhhhcccCccccCCCCCCcCC--cccccccCCCCCCChHHHHHHHHhhC
Q 025560 175 NNIIEQTLGKYGIICIEDIVHEIANVGPHFKEVVNFLGPLTLNKPEGGLLG--KKQPFKDGGEAGNREEEINELISKMN 251 (251)
Q Consensus 175 n~lie~~lg~~gi~ciEDlv~eI~~~g~~f~~~~~fl~pFkL~~P~~G~~~--~k~~~~~gG~~G~r~~~In~Li~rM~ 251 (251)
|+|||++||++||+|+|||||||+|+|+||+++++|||||+||||+|||+. +++||.+||++||||++||+||++|+
T Consensus 157 n~iiE~~lg~~gi~ciEDliheI~t~g~~fk~i~~~L~PFrL~~Pr~G~~~~~~~~~~~egG~~G~r~~~IN~Li~rM~ 235 (235)
T TIGR01310 157 NTIIEQHLGKYGIICIEDLIHEIYTVGPHFKEVNNFLWPFKLSSPVKGFGKRKKVKHFKEGGDFGNREDAINELIRKMN 235 (235)
T ss_pred hHHHHHhhccCCcccHHHHHHHHHhCCCCHHHHhcCccCccCCCCcccccccCcccCcccCCCCCccHHHHHHHHHHhC
Confidence 999999999999999999999999999999999999999999999999974 88999999999999999999999997
No 2
>KOG3184 consensus 60S ribosomal protein L7 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.3e-67 Score=463.60 Aligned_cols=234 Identities=44% Similarity=0.760 Sum_probs=229.3
Q ss_pred chhHHHHhhhhHHHHHHHHHHHHHhcccCcccccccccchhhcCcHHHHHHHHHHHHHHHHHHHhhhcCCCccCCCCCce
Q 025560 13 VAETVLKKRKSTEALALTRKAQLELGKYGHGQKNKKSKVEDIKRPEQFIKQFRDQELDLIRMKQRGKRSKKVIGKPKSKL 92 (251)
Q Consensus 13 vpE~~lkkrk~~~~~~~~~~~~~~~~k~~~~~~~k~~rk~~~krae~~v~ey~~~e~~~~r~kr~ak~~~~~~~~~e~kl 92 (251)
+||++|| ||+++++++++++++.+.+ ..++.++...++++++|+++|++++++.++++|.+++.+++|+|+++++
T Consensus 1 vPE~llk-rk~~~~~~~~~~~~~~~~k----~~~k~~~~~~~~~~e~~~~~~~~~~r~~i~~~r~~~~~~~~~~~~e~~l 75 (235)
T KOG3184|consen 1 VPENLLK-RKAQAELATQALRKLLAKK----EIRKKKRKLFLKKAKHYHKEYRQKYRTEIRMARIARKAGNFYVPAEPKL 75 (235)
T ss_pred Cchhhhh-hhhHHHHHHHHHHHHHHHH----HHHhccchhHHHHHHHHHHHHHhhhhHHHHHHHHHhccccCcCcccccc
Confidence 6999999 9999999999999999988 7778889999999999999999999999999999999999999999999
Q ss_pred EEEEeecCCCCCChHHHHHHHHhCCCCcCcEEEEeCChhHHHHHHhccCeEEEecCChHHHHHHHHHhccc-ccCCceec
Q 025560 93 LFIIRIQGTSDMHRRTKKILYNLRLRRIFSGVFVRATDGMLEVLQKVEPYVTYGYPNLVNVKELIYKKGYA-TVDRQRIP 171 (251)
Q Consensus 93 ~~ViRirg~~~~~p~~~k~L~~LrL~ki~~~vfv~~n~~~~~mL~~V~pyV~~G~p~~~tvr~Li~KRG~~-k~~~~~~~ 171 (251)
+||||++|+++++|+++++|++|+|.+||+||||++|+++.+||++|+||||||+||+++|++||||||++ ++++++++
T Consensus 76 ~fvvri~gin~v~pk~~k~l~lLrL~~If~g~fVKlnk~~~~mLriVepYVa~G~pnlksv~elI~krG~~k~~~~k~i~ 155 (235)
T KOG3184|consen 76 AFVIRIRGVNGVEPKSRKVLQLLRLKQIFNGTFVKLNKATVNMLRIVEPYIAWGYPNLKSVSELIYKRGYGKKIEKKRIP 155 (235)
T ss_pred ceeeecccccccCchHHHHHHHHHhhccccceeEEechhhhhhHhhcccceeeccCcHHHHHHHHhhcccccccCCceec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999 49999999
Q ss_pred CCChhhHhhhcccCCcccHHHHHHHHHhcCCchhhhhcccCccccCCCCCCcCCcccccccCCCCCCChHHHHHHHHhhC
Q 025560 172 LTDNNIIEQTLGKYGIICIEDIVHEIANVGPHFKEVVNFLGPLTLNKPEGGLLGKKQPFKDGGEAGNREEEINELISKMN 251 (251)
Q Consensus 172 ltdn~lie~~lg~~gi~ciEDlv~eI~~~g~~f~~~~~fl~pFkL~~P~~G~~~~k~~~~~gG~~G~r~~~In~Li~rM~ 251 (251)
||||.++++++|++|++|+||++|+|+++|++|+++++|||||+|++|.+||..+..||.|||++||||+.||+|+++|+
T Consensus 156 ltdn~ii~~~lgk~~~i~~edl~hei~~vg~~fk~~n~fL~pf~l~~~~~~~~~k~~h~~e~g~~g~~~~~in~L~~~~~ 235 (235)
T KOG3184|consen 156 LTDNFLIERKLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPVAGHKTKFGHFKEGGTAGNRGEHINDLIRQLN 235 (235)
T ss_pred cccchHHHHhcCCcceeechhhhccccccchhHHHHhhccCceeccCcccchhhhccccccCCCCCchHHHHHHHHHhcC
Confidence 99999999999999999999999999999999999999999999999999999988999999999999999999999996
No 3
>cd01657 Ribosomal_L7_archeal_euk Ribosomal protein L7, which is found in archaea and eukaryotes but not in prokaryotes, binds domain II of the 23S rRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. The eukaryotic L7 members have an N-terminal extension not found in the archeal L7 orthologs. L7 is closely related to the ribosomal L30 protein found in eukaryotes and prokaryotes.
Probab=100.00 E-value=3.4e-63 Score=419.45 Aligned_cols=159 Identities=54% Similarity=0.887 Sum_probs=156.9
Q ss_pred eEEEEeecCCCCCChHHHHHHHHhCCCCcCcEEEEeCChhHHHHHHhccCeEEEecCChHHHHHHHHHhcccccCCceec
Q 025560 92 LLFIIRIQGTSDMHRRTKKILYNLRLRRIFSGVFVRATDGMLEVLQKVEPYVTYGYPNLVNVKELIYKKGYATVDRQRIP 171 (251)
Q Consensus 92 l~~ViRirg~~~~~p~~~k~L~~LrL~ki~~~vfv~~n~~~~~mL~~V~pyV~~G~p~~~tvr~Li~KRG~~k~~~~~~~ 171 (251)
++||||+||.++++|++++||++|||+++|+|||+++||+++|||++|+|||+||+||++||++||+|||+++++++++|
T Consensus 1 l~~Virirg~~g~~~~~r~tL~~LgL~k~~~~v~~~~t~~~~gmL~kV~~~V~~ge~~~~tv~~Li~kRG~~~~~~~~~~ 80 (159)
T cd01657 1 LYAVVRIRGIVGVPPKIRKTLQLLRLRRINNAVFVKLTKATIGMLKKVEPYVTWGEPNLETLRELIYKRGRLKGNGQRIP 80 (159)
T ss_pred CEEEEEecCcCCCCHHHHHHHHHcCCCcCCCEEEEeCCHHHHHHHHHhhhheEeccCcHHHHHHHHHHhCeecCCCeeee
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCChhhHhhhcccCCcccHHHHHHHHHhcCCchhhhhcccCccccCCCCCCcCCcccccccCCCCCCChHHHHHHHHhhC
Q 025560 172 LTDNNIIEQTLGKYGIICIEDIVHEIANVGPHFKEVVNFLGPLTLNKPEGGLLGKKQPFKDGGEAGNREEEINELISKMN 251 (251)
Q Consensus 172 ltdn~lie~~lg~~gi~ciEDlv~eI~~~g~~f~~~~~fl~pFkL~~P~~G~~~~k~~~~~gG~~G~r~~~In~Li~rM~ 251 (251)
||||+++|++| ++||+|+|||||||+++|++|+++++|+|||+||||++||++++++|++||++||||++||+||++|+
T Consensus 81 ltdn~iie~~l-~~gi~ciedlv~~i~~~~~~f~~~~~~l~pF~L~~P~~g~~~~~~~~~~gG~~G~r~~~In~Li~~m~ 159 (159)
T cd01657 81 LTDNYLVEKTL-KKGIICIEDLAHEIYTGGPNFKEVNNFLPPFRLHPPRGGFKGKKRHFSEGGELGYRGEDINELIRRMI 159 (159)
T ss_pred CChHHHHHHHc-ccCcccHHHHHHHHHhCccCHHHhhccCCCeECCCcccchhccccccccCCCCCccHHHHHHHHHHhC
Confidence 99999999999 99999999999999999999999999999999999999999888999999999999999999999997
No 4
>PRK06049 rpl30p 50S ribosomal protein L30P; Reviewed
Probab=100.00 E-value=1.5e-61 Score=407.03 Aligned_cols=154 Identities=34% Similarity=0.538 Sum_probs=147.4
Q ss_pred ceEEEEeecCCCCCChHHHHHHHHhCCCCcCcEEEEeCChhHHHHHHhccCeEEEecCChHHHHHHHHHhcccccCCcee
Q 025560 91 KLLFIIRIQGTSDMHRRTKKILYNLRLRRIFSGVFVRATDGMLEVLQKVEPYVTYGYPNLVNVKELIYKKGYATVDRQRI 170 (251)
Q Consensus 91 kl~~ViRirg~~~~~p~~~k~L~~LrL~ki~~~vfv~~n~~~~~mL~~V~pyV~~G~p~~~tvr~Li~KRG~~k~~~~~~ 170 (251)
.++||+|+||.++++|++++||++|||+++|+|||+++||+++|||++|+|||+|||||++||++||||||++ .|+ +
T Consensus 1 ~~~~ViriRg~ig~~~~~r~tL~~LgL~ki~~~V~v~~tp~~~GML~kV~~~V~~ge~~~~tv~~Li~kRG~~-~g~-~- 77 (154)
T PRK06049 1 EMYAVIRIRGRVNVPRDIADTLKMLRLHRVNHCVLVPETPSYKGMLQKVKDYVTWGEIDADTLAELLRKRGRL-EGN-K- 77 (154)
T ss_pred CcEEEEEecCCCCCCHHHHHHHHHcCCCcCCCEEEEeCCHHHHHHHHhhhceeEEeeCchHHHHHHHHHhCcc-cCC-C-
Confidence 3799999999999999999999999999999999999999999999999999999999999999999999994 444 4
Q ss_pred cCCChhhHhhhcccCCcccHHHHHHHHHhcCCchhhhhcccCccccCCCCCCcCCcccccccCCCCCCChHHHHHHHHhh
Q 025560 171 PLTDNNIIEQTLGKYGIICIEDIVHEIANVGPHFKEVVNFLGPLTLNKPEGGLLGKKQPFKDGGEAGNREEEINELISKM 250 (251)
Q Consensus 171 ~ltdn~lie~~lg~~gi~ciEDlv~eI~~~g~~f~~~~~fl~pFkL~~P~~G~~~~k~~~~~gG~~G~r~~~In~Li~rM 250 (251)
|||||+|+| + +||+|+|||||||+++|++|+++++|+|||+||||+|||++++++|.+||++||||++||+||++|
T Consensus 78 ~ltd~~i~e-~---~g~~~iedl~~~i~~~~~~fk~~~~~~~~FrL~pPr~G~~~~k~~~~~gG~~G~r~~~In~Li~rM 153 (154)
T PRK06049 78 KLTDEYVKE-N---TGYDSIEELAEALVEGEIKLKDLPGLKPVFRLHPPRGGFGGIKRPFKEGGELGYRGEKINELLRRM 153 (154)
T ss_pred CCCHHHHHH-h---cCCccHHHHHHHHHhCCCCHHHhhcccCceecCCcchhhhhcccccccCCCCCccHHHHHHHHHHh
Confidence 999999977 3 499999999999999999999999999999999999999999999999999999999999999999
Q ss_pred C
Q 025560 251 N 251 (251)
Q Consensus 251 ~ 251 (251)
+
T Consensus 154 ~ 154 (154)
T PRK06049 154 R 154 (154)
T ss_pred C
Confidence 6
No 5
>TIGR01309 L30P_arch 50S ribosomal protein L30P, archaeal. This model represents the archaeal ribosomal protein similar to longer (~ 250 residue) eukaryotic 60S ribosomal protein L7 and to the much shorter (~ 60 residue) bacterial 50S ribosomal protein L30. Protein naming follows the SwissProt designation as L30P, while the gene symbol rpmD follows TIGR usage.
Probab=100.00 E-value=6.9e-60 Score=396.20 Aligned_cols=151 Identities=33% Similarity=0.503 Sum_probs=143.9
Q ss_pred EEEEeecCCCCCChHHHHHHHHhCCCCcCcEEEEeCChhHHHHHHhccCeEEEecCChHHHHHHHHHhcccccCCceecC
Q 025560 93 LFIIRIQGTSDMHRRTKKILYNLRLRRIFSGVFVRATDGMLEVLQKVEPYVTYGYPNLVNVKELIYKKGYATVDRQRIPL 172 (251)
Q Consensus 93 ~~ViRirg~~~~~p~~~k~L~~LrL~ki~~~vfv~~n~~~~~mL~~V~pyV~~G~p~~~tvr~Li~KRG~~k~~~~~~~l 172 (251)
++|+||||.++++|++++||++|||+++|+|||+++||+++|||++|+|||+|||||++||++||||||++. |+ .||
T Consensus 1 ~~ViriRg~ig~~~~~r~tL~~LrL~ri~~~V~v~~tp~~~gML~kV~~yV~~ge~~~~tv~~Li~kRG~~~-g~--~~l 77 (152)
T TIGR01309 1 LAVIRIRGTVDVPRDIADTLEMLRLHRVNHCVLYPETPTYLGMLQKVKDYVTWGEIDEDTLELLIRKRGRLV-GG--DKV 77 (152)
T ss_pred CeEEEecCcCCCCHHHHHHHHHcCCCcCCCEEEEeCCHHHHHHHHHhHhheeEecCCHHHHHHHHHHhcccc-CC--CcC
Confidence 589999999999999999999999999999999999999999999999999999999999999999999975 55 399
Q ss_pred CChhhHhhhcccCCcccHHHHHHHHHhcCCchhhhhcccCccccCCCCCCcC-CcccccccCCCCCCChHHHHHHHHhhC
Q 025560 173 TDNNIIEQTLGKYGIICIEDIVHEIANVGPHFKEVVNFLGPLTLNKPEGGLL-GKKQPFKDGGEAGNREEEINELISKMN 251 (251)
Q Consensus 173 tdn~lie~~lg~~gi~ciEDlv~eI~~~g~~f~~~~~fl~pFkL~~P~~G~~-~~k~~~~~gG~~G~r~~~In~Li~rM~ 251 (251)
|||+ ||++| ||+|+|||||||+++|++|++++ |+|||+||||++||+ +++++|.+||++||||++||+||++|+
T Consensus 78 td~~-i~e~~---g~~~iedl~~~i~~~~~~f~~~~-~~~~FrL~pPr~G~~~~~k~~~~~gG~~G~r~~~In~Li~rMi 152 (152)
T TIGR01309 78 TDEY-VKEVT---GYESVDELAKALVEGEIKLSEAG-LKPVFRLHPPRKGFKGGIKTPYRDGGELGYRGEKINELLRRMR 152 (152)
T ss_pred CHHH-HHHHc---CCccHHHHHHHHHcCCCCccccC-ccCceeCCCCCcccccccccccccCCCCcccHHHHHHHHHHhC
Confidence 9986 57777 79999999999999999999996 999999999999998 789999999999999999999999996
No 6
>COG1841 RpmD Ribosomal protein L30/L7E [Translation, ribosomal structure and biogenesis]
Probab=99.78 E-value=2.7e-19 Score=126.66 Aligned_cols=55 Identities=31% Similarity=0.321 Sum_probs=53.7
Q ss_pred EEEEeecCCCCCChHHHHHHHHhCCCCcCcEEEEeCChhHHHHHHhccCeEEEec
Q 025560 93 LFIIRIQGTSDMHRRTKKILYNLRLRRIFSGVFVRATDGMLEVLQKVEPYVTYGY 147 (251)
Q Consensus 93 ~~ViRirg~~~~~p~~~k~L~~LrL~ki~~~vfv~~n~~~~~mL~~V~pyV~~G~ 147 (251)
++|+|+||.+|++|++++||++|||+++|++|++++||+++|||++|+|||+||+
T Consensus 1 ~~V~~iRs~ig~~~~~r~tl~~LgL~kin~~v~~~dtp~irGMi~kV~~lV~v~e 55 (55)
T COG1841 1 LKVTLIRSPIGRPPKIRKTLRLLGLRKINHTVIVEDTPAVRGMLNKVKHLVTVGE 55 (55)
T ss_pred CeEEEEeccCCCChHHHHHHHHhCCCccCCEEEEcCCHHHHHHHHHHHhheEecC
Confidence 4799999999999999999999999999999999999999999999999999996
No 7
>cd00355 Ribosomal_L30_like Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. The eukaryotic L30 members have N- and/or C-terminal extensions not found in their prokaryotic orthologs. L30 is closely related to the ribosomal L7 protein found in eukaryotes and archaea.
Probab=99.74 E-value=4.5e-18 Score=119.46 Aligned_cols=53 Identities=32% Similarity=0.437 Sum_probs=52.1
Q ss_pred EEEeecCCCCCChHHHHHHHHhCCCCcCcEEEEeCChhHHHHHHhccCeEEEe
Q 025560 94 FIIRIQGTSDMHRRTKKILYNLRLRRIFSGVFVRATDGMLEVLQKVEPYVTYG 146 (251)
Q Consensus 94 ~ViRirg~~~~~p~~~k~L~~LrL~ki~~~vfv~~n~~~~~mL~~V~pyV~~G 146 (251)
+|+|+||.++++|++++||++|||+++|++||+++||+++|||++|+|||+||
T Consensus 1 ~V~~irs~ig~~~~~~~tl~~LgL~k~~~~v~~~~tp~~~gml~kV~~lV~~~ 53 (53)
T cd00355 1 KVTRVRSLIGRPPKQRKTLKALGLRKINQTVFVKDTPSIRGMLRKVKHLVTVG 53 (53)
T ss_pred CEEEecCCCCCCHHHHHHHHHcCCCcCCCEEEEeCCHHHHHHHHhccceEEEC
Confidence 58999999999999999999999999999999999999999999999999998
No 8
>PF00327 Ribosomal_L30: Ribosomal protein L30p/L7e; InterPro: IPR016082 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 L30 is one of the proteins from the large ribosomal subunit. L30 belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups bacteria and archaea L30, yeast mitochondrial L33, and Drosophila melanogaster, Dictyostelium discoideum (Slime mold), fungal and mammalian L7 ribosomal proteins. L30 from bacteria are small proteins of about 60 residues, those from archaea are proteins of about 150 residues, and eukaryotic L7 are proteins of about 250 to 270 residues. This entry represents a domain with a ferredoxin-like fold, with a core structure consisting of core: beta-alpha-beta-alpha-beta. This domain is found in prokaryotic ribosomal protein L30 (short-chain member of the family), as well as in archaeal L30 (L30a) (long-chain member of the family), the later containing an additional C-terminal (sub)domain).; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3DF2_Y 3DF4_Y 3O5H_G 3O58_G 1S1I_F 3IZS_e 1M1K_X 1M90_X 1QVG_V 1YIT_W ....
Probab=99.68 E-value=1e-16 Score=112.11 Aligned_cols=52 Identities=37% Similarity=0.542 Sum_probs=49.0
Q ss_pred eEEEEeecCCCCCChHHHHHHHHhCCCCcCcEEEEeCChhHHHHHHhccCeE
Q 025560 92 LLFIIRIQGTSDMHRRTKKILYNLRLRRIFSGVFVRATDGMLEVLQKVEPYV 143 (251)
Q Consensus 92 l~~ViRirg~~~~~p~~~k~L~~LrL~ki~~~vfv~~n~~~~~mL~~V~pyV 143 (251)
++||+||||.++++|++++||++|||+++|++||+++||+++|||++|+|||
T Consensus 1 ~l~V~~irs~~g~~~~~~~tl~~LgL~k~~~~v~~~~t~~~~gml~kV~~lV 52 (52)
T PF00327_consen 1 LLFVTRIRSPIGAPPKVRKTLKALGLRKINQAVFVKNTPSIRGMLKKVKHLV 52 (52)
T ss_dssp EEEEEESS-STTSSHHHHHHHHHTT-SSTTEEEEEESSHHHHHHHHHTGCGE
T ss_pred CEEEEEeCCCCCCCHHHHHHHHHcCCCcCCCEEEEECCHHHHHHHHHHHhhC
Confidence 5899999999999999999999999999999999999999999999999998
No 9
>PF08079 Ribosomal_L30_N: Ribosomal L30 N-terminal domain; InterPro: IPR012988 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 [, ]. This presumed domain is found at the N terminus of Ribosomal L30 proteins and has been termed RL30NT or NUC018 [].; PDB: 3IZR_e 3O5H_G 3O58_G 3IZS_e 4A1A_V 4A17_V 4A1E_V 4A1C_V.
Probab=99.68 E-value=1.4e-17 Score=123.75 Aligned_cols=71 Identities=34% Similarity=0.513 Sum_probs=63.1
Q ss_pred HHHHhhhhHHHHHHHHHHHHHhcccCcccccccccchhhcCcHHHHHHHHHHHHHHHHHHHhhhcCCCccCCCCC
Q 025560 16 TVLKKRKSTEALALTRKAQLELGKYGHGQKNKKSKVEDIKRPEQFIKQFRDQELDLIRMKQRGKRSKKVIGKPKS 90 (251)
Q Consensus 16 ~~lkkrk~~~~~~~~~~~~~~~~k~~~~~~~k~~rk~~~krae~~v~ey~~~e~~~~r~kr~ak~~~~~~~~~e~ 90 (251)
||||||+++++++...+++..+.+ +..+.+++.+|+|||+|++||+++++|+++|+|+|++.|+||||+||
T Consensus 1 s~LKKrK~~~~~~~~~~~~~~~~k----~~~~~~r~~~~kRAekY~kEYr~~erd~Irl~R~Ak~~G~fyvpaEp 71 (71)
T PF08079_consen 1 SLLKKRKRNEKLKAKRAKKAAARK----KKRKKKRKEIFKRAEKYVKEYRQKERDEIRLKREAKKAGNFYVPAEP 71 (71)
T ss_dssp CCCHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCS-SEE----
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHccCccCCCCC
Confidence 589999999999999999988888 77888999999999999999999999999999999999999999997
No 10
>PRK05611 rpmD 50S ribosomal protein L30; Reviewed
Probab=99.64 E-value=5.4e-16 Score=111.41 Aligned_cols=55 Identities=24% Similarity=0.233 Sum_probs=54.0
Q ss_pred EEEEeecCCCCCChHHHHHHHHhCCCCcCcEEEEeCChhHHHHHHhccCeEEEec
Q 025560 93 LFIIRIQGTSDMHRRTKKILYNLRLRRIFSGVFVRATDGMLEVLQKVEPYVTYGY 147 (251)
Q Consensus 93 ~~ViRirg~~~~~p~~~k~L~~LrL~ki~~~vfv~~n~~~~~mL~~V~pyV~~G~ 147 (251)
++|+++||.+|.+|++++||++|||+++|++|++++||+++|||++|+|||+|.+
T Consensus 4 ~~I~~vRs~ig~~~~~r~tl~~LgL~k~~~~v~~~dtp~~rGmi~kV~~lV~vee 58 (59)
T PRK05611 4 LKITLVKSLIGRKPKQRATLRGLGLRKINSTVELEDTPAIRGMINKVSHLVKVEE 58 (59)
T ss_pred EEEEEeecCCCCCHHHHHHHHHcCCCcCCCEEEecCCHHHHHHHHHhHhhEEEEe
Confidence 8999999999999999999999999999999999999999999999999999986
No 11
>TIGR01308 rpmD_bact ribosomal protein L30, bacterial/organelle. This model describes bacterial (and organellar) 50S ribosomal protein L30. Homologous ribosomal proteins of the eukaryotic cytosol and of the archaea differ substantially in architecture, from bacterial L30 and also from each other, and are described by separate models.
Probab=99.58 E-value=4.1e-15 Score=105.46 Aligned_cols=54 Identities=19% Similarity=0.220 Sum_probs=52.2
Q ss_pred EEEeecCCCCCChHHHHHHHHhCCCCcCcEEEEeCChhHHHHHHhccCeEEEec
Q 025560 94 FIIRIQGTSDMHRRTKKILYNLRLRRIFSGVFVRATDGMLEVLQKVEPYVTYGY 147 (251)
Q Consensus 94 ~ViRirg~~~~~p~~~k~L~~LrL~ki~~~vfv~~n~~~~~mL~~V~pyV~~G~ 147 (251)
.|+++||.+|.+|++++||++|||+++|++|++++||+++|||++|+|||.+.+
T Consensus 2 kItlvrs~ig~~~~~r~tl~~LgL~k~~~~v~~~dtp~irGMi~kV~~lV~vee 55 (55)
T TIGR01308 2 KVTLVRSLIGRPKKQRKTLKALGLRKIGRQVVLEDNPAIRGMVNKVKHLVKVEE 55 (55)
T ss_pred EEEEEeCCCCCCHHHHHHHHHcCCCcCCCEEEecCCHHHHHHHHHhHheEEEeC
Confidence 589999999999999999999999999999999999999999999999999864
No 12
>cd01658 Ribosomal_L30 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. The eukaryotic L30 members have N- and/or C-terminal extensions not found in their prokaryotic orthologs. L30 is closely related to the ribosomal L7 protein found in eukaryotes and archaea.
Probab=99.55 E-value=8.7e-15 Score=103.34 Aligned_cols=53 Identities=21% Similarity=0.266 Sum_probs=51.3
Q ss_pred EEEEeecCCCCCChHHHHHHHHhCCCCcCcEEEEeCChhHHHHHHhccCeEEE
Q 025560 93 LFIIRIQGTSDMHRRTKKILYNLRLRRIFSGVFVRATDGMLEVLQKVEPYVTY 145 (251)
Q Consensus 93 ~~ViRirg~~~~~p~~~k~L~~LrL~ki~~~vfv~~n~~~~~mL~~V~pyV~~ 145 (251)
+.|+++||.+|.+|++++||++|||+++|++|++++||+++|||++|+|||.+
T Consensus 1 ~~i~~iRs~ig~~~~~r~tl~~LgL~k~~~~v~~~~tp~~~Gml~kV~~lV~v 53 (54)
T cd01658 1 LKITLVKSLIGRPKKQRATLKALGLKKINQTVVHKDTPSIRGMINKVKHLVKV 53 (54)
T ss_pred CEEEEEeCCCCCCHHHHHHHHHcCCCcCCCEEEecCCHHHHHHHHHHhheEEe
Confidence 36899999999999999999999999999999999999999999999999987
No 13
>KOG4799 consensus Mitochondrial ribosomal protein L30 [Translation, ribosomal structure and biogenesis]
Probab=97.15 E-value=0.0012 Score=56.35 Aligned_cols=73 Identities=19% Similarity=0.193 Sum_probs=65.9
Q ss_pred CCC-CceEEEEeecCCCCCChHHHHHHHHhCCCCcCc-EEEEeCChhHHHHHHhccCeEE-------EecCChHHHHHHH
Q 025560 87 KPK-SKLLFIIRIQGTSDMHRRTKKILYNLRLRRIFS-GVFVRATDGMLEVLQKVEPYVT-------YGYPNLVNVKELI 157 (251)
Q Consensus 87 ~~e-~kl~~ViRirg~~~~~p~~~k~L~~LrL~ki~~-~vfv~~n~~~~~mL~~V~pyV~-------~G~p~~~tvr~Li 157 (251)
|.+ +||..|.|||+..+.|..-.+++++|||....+ -..+++.|++-.-|.+|+|+|. +|+|..+-|+..+
T Consensus 53 P~~p~KL~~v~rik~t~~~PyWek~iik~lGld~k~t~~qV~kNip~vNakLwkIKHLI~~~pv~fp~gePte~di~~t~ 132 (182)
T KOG4799|consen 53 PQNPHKLHIVTRIKSTRRRPYWEKDIIKMLGLDKKHTRPQVHKNIPSVNAKLWKIKHLIRLRPVEFPGGEPTEDDISSTS 132 (182)
T ss_pred CCCccceEEEEEeccccCCcchHHHHHHHhCcccccCCceEeecccchhhHHHHhhheeEEEeeccCCCCCchhhhhhhh
Confidence 444 589999999999999999999999999999998 7888999999999999999985 6999999999887
Q ss_pred HH
Q 025560 158 YK 159 (251)
Q Consensus 158 ~K 159 (251)
.|
T Consensus 133 Lk 134 (182)
T KOG4799|consen 133 LK 134 (182)
T ss_pred hc
Confidence 64
No 14
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=33.26 E-value=63 Score=21.11 Aligned_cols=45 Identities=29% Similarity=0.524 Sum_probs=30.1
Q ss_pred EEEecCChHHHHHHHHHhcccccCCceecCCChhhHhhhcccC-CcccHHHHHHHHH
Q 025560 143 VTYGYPNLVNVKELIYKKGYATVDRQRIPLTDNNIIEQTLGKY-GIICIEDIVHEIA 198 (251)
Q Consensus 143 V~~G~p~~~tvr~Li~KRG~~k~~~~~~~ltdn~lie~~lg~~-gi~ciEDlv~eI~ 198 (251)
+.-..-++..+-+++.+.+. ..+|+.|+. |+. |+++..||++.+.
T Consensus 11 ~v~~~~~l~~~~~~~~~~~~-----~~~~V~d~~------~~~~G~is~~dl~~~l~ 56 (57)
T PF00571_consen 11 TVSPDDSLEEALEIMRKNGI-----SRLPVVDED------GKLVGIISRSDLLKALL 56 (57)
T ss_dssp EEETTSBHHHHHHHHHHHTS-----SEEEEESTT------SBEEEEEEHHHHHHHHH
T ss_pred EEcCcCcHHHHHHHHHHcCC-----cEEEEEecC------CEEEEEEEHHHHHhhhh
Confidence 33444556667777776664 346777644 333 9999999999875
No 15
>KOG1097 consensus Adenine deaminase/adenosine deaminase [Nucleotide transport and metabolism]
Probab=26.89 E-value=1.1e+02 Score=30.08 Aligned_cols=54 Identities=17% Similarity=0.090 Sum_probs=44.3
Q ss_pred eecCCC-CCChHHHHHHHHhCCCCcCcEEEEeCChhHHHHHHhccCeEEEecCCh
Q 025560 97 RIQGTS-DMHRRTKKILYNLRLRRIFSGVFVRATDGMLEVLQKVEPYVTYGYPNL 150 (251)
Q Consensus 97 Rirg~~-~~~p~~~k~L~~LrL~ki~~~vfv~~n~~~~~mL~~V~pyV~~G~p~~ 150 (251)
-+-|-. +-+..++..|.+|+..+|.||.++...|...++++.-.=.++..-.|-
T Consensus 245 ~HaGE~~~~~~~v~~~LD~l~~~RIGHG~~l~~dp~L~~~~k~~nI~lEiCP~SN 299 (399)
T KOG1097|consen 245 FHAGETNGGASVVKNALDLLGTERIGHGYFLTKDPELINLLKSRNIALEICPISN 299 (399)
T ss_pred EEccccCCChHHHHHHHHhhCCccccCceeccCCHHHHHHHHhcCceEEEccchh
Confidence 344655 688899999999999999999999999999999988776666655443
No 16
>TIGR03757 conj_TIGR03757 integrating conjugative element protein, PFL_4709 family. Members of this protein belong to extended genomic regions that appear to be spread by conjugative transfer.
Probab=26.17 E-value=98 Score=25.12 Aligned_cols=33 Identities=27% Similarity=0.450 Sum_probs=24.4
Q ss_pred HHhCCCCcCcEEEEeCChhHHHHHHhccCeEEEecCChHHHHHHHH
Q 025560 113 YNLRLRRIFSGVFVRATDGMLEVLQKVEPYVTYGYPNLVNVKELIY 158 (251)
Q Consensus 113 ~~LrL~ki~~~vfv~~n~~~~~mL~~V~pyV~~G~p~~~tvr~Li~ 158 (251)
..||++++=--|| . ..||.||++|..--..++.
T Consensus 78 w~lGi~k~PAVV~-D------------~~~VVYG~~DV~~A~~~~~ 110 (113)
T TIGR03757 78 WQLGVTKIPAVVV-D------------RRYVVYGETDVARALALIQ 110 (113)
T ss_pred HHcCCccCCEEEE-c------------CCeEEecCccHHHHHHHHH
Confidence 3678877654444 3 5699999999988777764
No 17
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=20.45 E-value=96 Score=22.39 Aligned_cols=30 Identities=27% Similarity=0.537 Sum_probs=23.8
Q ss_pred HHHHHHhcccccCCceecCCChhhHhhhcc
Q 025560 154 KELIYKKGYATVDRQRIPLTDNNIIEQTLG 183 (251)
Q Consensus 154 r~Li~KRG~~k~~~~~~~ltdn~lie~~lg 183 (251)
++++-++|+-..+++++-.-.-.+||+.||
T Consensus 27 K~~lV~~G~~~Y~nkRlg~VP~~~VEeiLG 56 (59)
T PF11372_consen 27 KALLVQKGFSFYNNKRLGRVPASAVEEILG 56 (59)
T ss_pred HHHHHHcCCCcccCCccCcccHHHHHHHHC
Confidence 456778999888988877777788898885
No 18
>PF07511 DUF1525: Protein of unknown function (DUF1525); InterPro: IPR011090 This family of proteins is restricted to the Gammaproteobacteria. Members belong to extended genomic regions that appear to be spread by conjugative transfer.
Probab=20.02 E-value=1.5e+02 Score=24.07 Aligned_cols=33 Identities=24% Similarity=0.383 Sum_probs=25.5
Q ss_pred HhCCCCcCcEEEEeCChhHHHHHHhccCeEEEecCChHHHHHHHHH
Q 025560 114 NLRLRRIFSGVFVRATDGMLEVLQKVEPYVTYGYPNLVNVKELIYK 159 (251)
Q Consensus 114 ~LrL~ki~~~vfv~~n~~~~~mL~~V~pyV~~G~p~~~tvr~Li~K 159 (251)
.||+.++=-.||= .-||.||++|..-...++..
T Consensus 78 ~lgi~k~PAVVfD-------------~~~VVYG~tDV~~A~~~~~~ 110 (114)
T PF07511_consen 78 SLGITKYPAVVFD-------------DRYVVYGETDVARALARIEQ 110 (114)
T ss_pred HhCccccCEEEEc-------------CCeEEecccHHHHHHHHHHH
Confidence 6788776555543 67999999999988887764
Done!