Query 048058
Match_columns 157
No_of_seqs 121 out of 1045
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 05:52:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048058.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048058hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00185 60S ribosomal protein 100.0 3.5E-52 7.5E-57 367.2 11.9 152 1-157 1-157 (405)
2 PRK04042 rpl4lp 50S ribosomal 100.0 2.7E-50 5.9E-55 338.5 11.0 142 7-157 1-142 (254)
3 TIGR03672 rpl4p_arch 50S ribos 100.0 1.3E-48 2.8E-53 327.8 10.7 141 7-157 1-141 (251)
4 PTZ00428 60S ribosomal protein 100.0 2.4E-47 5.3E-52 334.8 11.5 150 3-157 1-152 (381)
5 COG0088 RplD Ribosomal protein 100.0 2.9E-44 6.3E-49 295.7 8.9 131 6-150 1-134 (214)
6 PRK14547 rplD 50S ribosomal pr 100.0 4.5E-42 9.7E-47 294.3 8.8 117 7-138 2-120 (298)
7 CHL00147 rpl4 ribosomal protei 100.0 7.2E-42 1.6E-46 281.5 8.3 117 6-138 6-125 (215)
8 PRK05319 rplD 50S ribosomal pr 100.0 9.6E-42 2.1E-46 278.6 8.5 120 7-141 1-122 (205)
9 KOG1475 Ribosomal protein RPL1 100.0 1E-41 2.2E-46 291.8 7.0 152 3-157 1-152 (363)
10 PRK14907 rplD 50S ribosomal pr 100.0 2.9E-39 6.4E-44 276.2 6.8 107 25-141 103-212 (295)
11 PF00573 Ribosomal_L4: Ribosom 100.0 1.1E-38 2.4E-43 258.0 8.6 110 26-145 1-112 (192)
12 KOG1624 Mitochondrial/chloropl 100.0 7.9E-32 1.7E-36 228.4 6.8 127 9-155 56-185 (290)
13 PTZ00428 60S ribosomal protein 64.3 8.2 0.00018 35.0 3.6 84 42-138 33-129 (381)
14 COG3880 Modulator of heat shoc 32.2 39 0.00085 27.7 2.4 47 96-142 106-155 (176)
15 KOG0377 Protein serine/threoni 26.4 22 0.00049 33.5 0.1 29 90-118 343-371 (631)
No 1
>PLN00185 60S ribosomal protein L4-1; Provisional
Probab=100.00 E-value=3.5e-52 Score=367.20 Aligned_cols=152 Identities=80% Similarity=1.207 Sum_probs=146.3
Q ss_pred CcccCCCccEEeccCC----CccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccc
Q 048058 1 MAAAARPLITVQSLEG----DMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRA 76 (157)
Q Consensus 1 ~~~~~~~~v~V~n~~G----~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k 76 (157)
|||++||.++|||++| +.+ ++|+||+||+.|+|+||||+||+++++|+||||+.++.||+++++||||+|++
T Consensus 1 ~~~~~rp~v~V~~~~g~~~~~~~----~~v~Lp~VF~~piR~dlv~~v~~~~~~n~RQp~~~~~~AG~qtsAeswGtGR~ 76 (405)
T PLN00185 1 AAAAARPLVSVQSLDGDMATDKS----ATVALPDVMTAPIRPDIVNFVHTNISKNSRQPYAVSKKAGHQTSAESWGTGRA 76 (405)
T ss_pred CCcccCCeeEEEcCCCCcccccc----ceeehHHHhCCCCCHHHHHHHHHHHHHhccCCCCCCcccCCcceeeecCCCCC
Confidence 7999999999999999 555 89999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCCCcccCCCCCCCccccccccccCCcc-CcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCC
Q 048058 77 VSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKI-WRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMP 155 (157)
Q Consensus 77 ~~r~prqkg~GtgRar~g~rsP~~rGGg~afgPkp-~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~P 155 (157)
++|+|||||.||+|||||++ |+|++||++|||+| ||+|++|||+|+|++|++||||+++.++||.+|||+|++++++|
T Consensus 77 vaRiPR~kggGT~RAgqGa~-~~~~rGGr~FgP~p~~R~~~~KvNkK~rRlAl~SALAa~a~~~lV~arGH~i~~v~e~p 155 (405)
T PLN00185 77 VSRIPRVPGGGTHRAGQGAF-GNMCRGGRMFAPTKTWRRWHRKVNVNQKRYAVVSALAASAVPSLVMARGHKIENVPEVP 155 (405)
T ss_pred ceecccccCCCCCcCCccCc-CCcCCCCeeCCCCCCccccccccCHHHHHHHHHHHHHhhccchhhhcccccccccccCC
Confidence 99999999999999999988 88888888888887 69999999999999999999999999999999999999999999
Q ss_pred CC
Q 048058 156 LV 157 (157)
Q Consensus 156 iv 157 (157)
||
T Consensus 156 LV 157 (405)
T PLN00185 156 LV 157 (405)
T ss_pred EE
Confidence 86
No 2
>PRK04042 rpl4lp 50S ribosomal protein L4P; Provisional
Probab=100.00 E-value=2.7e-50 Score=338.54 Aligned_cols=142 Identities=43% Similarity=0.677 Sum_probs=133.9
Q ss_pred CccEEeccCCCccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCC
Q 048058 7 PLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGG 86 (157)
Q Consensus 7 ~~v~V~n~~G~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~ 86 (157)
|+++|||++|+.+ +++|||+||+.++|+||||++|++|++|+||||+.+|+|+||+|+||||+|++.+|+||||
T Consensus 1 ~~v~v~~~~g~~~----g~i~L~~vF~~~~~~~lv~~vv~~~~an~Rqgt~~~~ta~tKtraev~G~Gr~~~Kp~rQK-- 74 (254)
T PRK04042 1 MKAKVYDLDGEVV----GEIELPAVFEEPVRPDLIRRAVLAAQTARLQPKGRDPLAGKRTSAESWGSGRGIARVPRLK-- 74 (254)
T ss_pred CeeEEEcCCCCCc----ceEehhHhhCCCCcHHHHHHHHHHHHHhccCCCCCCccccCccceeEcCCCCCcCcCCccC--
Confidence 4799999999999 8999999999999999999999999999999999999999999999999999887778855
Q ss_pred CcccCCCCCCCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCCCC
Q 048058 87 GTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157 (157)
Q Consensus 87 GtgRar~g~rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~Piv 157 (157)
|||||+ +||+|||||++|||+|+|+|++|||||+|++||+||||+++.++||++|||.|++++|||||
T Consensus 75 GTGrAr---rsP~~rGGgv~fgPkp~R~y~~klnkK~rrlAlrsALs~k~~~~lv~~~~~~~~~~~e~~lv 142 (254)
T PRK04042 75 GGSRAA---FVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATANPELVKARGHVFEGVPELPLV 142 (254)
T ss_pred CCCCcc---ccCccCcCCeeCCCCCCcccccccCHHHHHHHHHHHHHHhhhhhhhhhcCccccCCCccCEE
Confidence 555554 89999999999999999999999999999999999999999999999999999999999985
No 3
>TIGR03672 rpl4p_arch 50S ribosomal protein L4P. One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.
Probab=100.00 E-value=1.3e-48 Score=327.85 Aligned_cols=141 Identities=43% Similarity=0.665 Sum_probs=132.8
Q ss_pred CccEEeccCCCccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCC
Q 048058 7 PLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGG 86 (157)
Q Consensus 7 ~~v~V~n~~G~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~ 86 (157)
|+++|||++|+.+ ++++||+||+.|++++|||++|++|++|+||||+++|.|+||+|+||||+|++++|+|||||
T Consensus 1 m~~~v~~~~g~~~----~~i~l~~vF~~~~~~~lv~~vv~~~~an~Rqgt~~~~~a~tKtraev~G~Grg~aKp~rQKG- 75 (251)
T TIGR03672 1 MKAKVYDLDGEVV----GEIELPAVFEEPVRPDLIKRAVLAAQTNRLQPYGADPYAGKRTSAESWGSGRGIARVPRIKG- 75 (251)
T ss_pred CceEEEccCCCCc----ceEehHHhhCCCccHHHHHHHHHHHHHhccCCCCCCcccCcccceeEccCCCCcCCCCccCC-
Confidence 4789999999998 89999999999999999999999999999999999899999999999999998888888555
Q ss_pred CcccCCCCCCCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCCCC
Q 048058 87 GTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157 (157)
Q Consensus 87 GtgRar~g~rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~Piv 157 (157)
|||| .+||+|||||++|||+|||+|++|||||+|++|++||||+++.++||.+|||.|+++ ++|||
T Consensus 76 -TGrA---~rsP~~rGGGv~fgPkp~R~y~~klNkK~rrlAl~sALs~k~~~~lv~~~~~~~~~~-e~~lv 141 (251)
T TIGR03672 76 -GSRA---ARVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATADPELVKARGHVFEGD-ELPIV 141 (251)
T ss_pred -CCcc---eecCccCcCCeeCCCCCCcccceecCHHHHHHHHHHHHHHhcchhhhhhcccccccc-cccEE
Confidence 5555 689999999999999999999999999999999999999999999999999999999 88875
No 4
>PTZ00428 60S ribosomal protein L4; Provisional
Probab=100.00 E-value=2.4e-47 Score=334.80 Aligned_cols=150 Identities=67% Similarity=1.119 Sum_probs=143.6
Q ss_pred ccCCCccEEeccCC-CccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeecccccccccc
Q 048058 3 AAARPLITVQSLEG-DMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIP 81 (157)
Q Consensus 3 ~~~~~~v~V~n~~G-~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~p 81 (157)
|++||+++|||++| +.+ ++|+||+||+.|+|+||||+||+++++|+||||++++++++++++|+||||++.+|+|
T Consensus 1 ~~~r~~v~V~~~~g~~~~----~~v~Lp~VF~~pir~dlV~~vv~~~~aN~RQgta~s~~ag~~tsakswGTGRA~arip 76 (381)
T PTZ00428 1 MTARPVVSVYSASDKSVV----GTVPLPAVFTAPIRPDLVQFVHTNMAKNRRQAYAVKPLAGMQHSAESWGTGRAVARIP 76 (381)
T ss_pred CCCCCeeEEEcCCCCccc----ceEehHHhhCCCCcHHHHHHHHHHHHHhccCCCCcCCCCCCCCCceecCCCCCccccc
Confidence 67899999999999 556 8999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCcccCCCCCCCccccccccccCCcc-CcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCCCC
Q 048058 82 RVPGGGTHRAGQGAFGNMCRGGRMFAPTKI-WRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157 (157)
Q Consensus 82 rqkg~GtgRar~g~rsP~~rGGg~afgPkp-~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~Piv 157 (157)
||+|.||+|+++|+++|+|+||+ +|||+| ||+|++|||+|+|++|++||||+++.+.||++|||+||+++|+|||
T Consensus 77 R~kg~GT~Rs~qGa~~n~~rGG~-~FgP~~~~R~~~~KvNkK~rR~Al~SALaa~a~~~lv~argh~i~~v~e~plV 152 (381)
T PTZ00428 77 RVSGGGTHRSGQGAFGNMCRGGR-MFAPTKTWRRWHRKVNLNQKRHAVASALAASGVPALVMARGHRISNVPEVPLV 152 (381)
T ss_pred cccCCCCCcCcccccCCcCCCce-EcCCCCCccccccccCHHHHHHHHHHHHHhhccchhhhcccccccccccCCEE
Confidence 99999999999999999999888 666666 7999999999999999999999999999999999999999999986
No 5
>COG0088 RplD Ribosomal protein L4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-44 Score=295.69 Aligned_cols=131 Identities=31% Similarity=0.373 Sum_probs=120.8
Q ss_pred CCccEEeccCCCccccCCcccccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccC
Q 048058 6 RPLITVQSLEGDMATDASSTVPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVP 84 (157)
Q Consensus 6 ~~~v~V~n~~G~~~~~~gg~ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqk 84 (157)
||+++|||++|+.+ ++++++ +||..+.+.||||++|++|++|+|||||+ +++++|++|+|+| || +
T Consensus 1 m~k~~v~~~~G~~~----g~~~~~~~vf~~~~~~dli~~av~a~~a~~RQgt~~-----~k~rgevs~~g~K----p~-~ 66 (214)
T COG0088 1 MMKLKVYDLDGEEV----GEVELLPEVFGPERNEDLIHRAVLAQLANRRQGTHS-----TKTRGEVSGGGKK----PW-G 66 (214)
T ss_pred CCcceEeCCCCCCc----cccccChhhccCCchHHHHHHHHHHHHHhhhccCCC-----CCCcccccccCcC----CC-C
Confidence 45999999999999 997775 79998888999999999999999999876 4789999999997 54 6
Q ss_pred CCCcccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccCh-hhHhhcCcccCC
Q 048058 85 GGGTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVP-SLVMARGHKIET 150 (157)
Q Consensus 85 g~GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~-~~v~~rgh~~~~ 150 (157)
|+||||||+|+ ++|+|||||++|||+|+|||++|||||||+|||+||||+++++ +||..+||.|++
T Consensus 67 QkgtgraR~gs~rsP~~rGGg~a~gPkp~r~~~~klnkK~rrlAl~sAls~ka~~~~lv~~~~~~~~~ 134 (214)
T COG0088 67 QKGTGRARQGSIRSPQWRGGGVAHGPKPERDYSQKLNKKERRLALRSALSAKARAGKLVVVRGHVFED 134 (214)
T ss_pred CCcCCcCCCCCCCCCeeecCccccCCCCccchhhhcCHHHHHHHHHHHHHHhccCCCEEEEecccccC
Confidence 77888888886 9999999999999999999999999999999999999999999 999999999994
No 6
>PRK14547 rplD 50S ribosomal protein L4; Provisional
Probab=100.00 E-value=4.5e-42 Score=294.28 Aligned_cols=117 Identities=23% Similarity=0.295 Sum_probs=109.7
Q ss_pred CccEEeccCCCccccCCcccccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCC
Q 048058 7 PLITVQSLEGDMATDASSTVPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPG 85 (157)
Q Consensus 7 ~~v~V~n~~G~~~~~~gg~ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg 85 (157)
++++|||++|+.+ ++|+|| +||+.++|.||||++|++|++|+||||+ +||+|+||+|+|+| || +|
T Consensus 2 ~~~~v~~~~g~~~----g~ieL~~~vF~~~~r~dllh~vv~~q~a~~Rqgt~-----~tKtRaEV~G~GkK----P~-rQ 67 (298)
T PRK14547 2 ATCDVLDWQGKKV----GSAELPLKVFDVETNIPLIHQVVVAQMAAARQGTH-----HTKTRAEVRGGGKK----PW-RQ 67 (298)
T ss_pred ceeEEeccCCCCc----ceEECCHHHhCCCccHHHHHHHHHHHHHhhhcCCC-----CCCceeeccCCCCC----cc-CC
Confidence 4999999999999 999998 7999999999999999999999999975 67999999999997 55 68
Q ss_pred CCcccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccCh
Q 048058 86 GGTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVP 138 (157)
Q Consensus 86 ~GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~ 138 (157)
|||||||+|+ +||+|||||++|||+| |+|++|||||+|+|||+||||+++..
T Consensus 68 KGTGrAR~Gs~rsP~wrGGGvafGPkp-R~y~~klNKK~rrlAlrsALS~k~~~ 120 (298)
T PRK14547 68 KGTGRARQGSIRAPQWRGGGTVHGPRP-REYNQRTPKKMRQAALRGALSDRARD 120 (298)
T ss_pred CCCcccCcCCccCCceeCCeeecCCCC-chhhhhcCHHHHHHHHHHHHHHHHhc
Confidence 8888899887 8999999999999999 99999999999999999999999865
No 7
>CHL00147 rpl4 ribosomal protein L4; Validated
Probab=100.00 E-value=7.2e-42 Score=281.54 Aligned_cols=117 Identities=24% Similarity=0.307 Sum_probs=106.6
Q ss_pred CCccEEeccCCCc-cccCCcccccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeecccccccccccc
Q 048058 6 RPLITVQSLEGDM-ATDASSTVPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRV 83 (157)
Q Consensus 6 ~~~v~V~n~~G~~-~~~~gg~ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prq 83 (157)
-++++|+|++|+. + +++||+ +|| .++++||||++|+||++|+||||+ .||+|+||+|+|+| ||
T Consensus 6 ~~~~~v~~~~g~~~~----~~~~l~~~vf-~~~~~~ll~~~v~~~~a~~R~gt~-----~tKtR~eV~G~grK----p~- 70 (215)
T CHL00147 6 FLNYPVIDLTGKEKS----ETIKLKLNVL-EKSGNYLLHRALVRQNNNQRQGTA-----STKTRSEVRGGGRK----PW- 70 (215)
T ss_pred eeeEEEEccCCCeec----ceEEeCHHHh-CCchHhHHHHHHHHHHHHHhhccc-----ccCccccccCCCCC----Cc-
Confidence 3579999999999 8 899998 599 567799999999999999999975 57999999999997 55
Q ss_pred CCCCcccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccCh
Q 048058 84 PGGGTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVP 138 (157)
Q Consensus 84 kg~GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~ 138 (157)
+||||||||+|+ +||+|||||++|||+| |+|+++||||+|++|+++|||+++..
T Consensus 71 ~QKGTGrAR~Gs~rsP~~rgGG~afgP~p-R~y~~klnKKvrrlAl~sALS~k~~~ 125 (215)
T CHL00147 71 KQKGTGRARAGSNRSPLWKGGGVIFGPKP-KTYSNKLNKKERRLALRTLLYNKSNN 125 (215)
T ss_pred ccCCCCccCCCCCcCCcccCCEeecCCCC-cchhhhcCHHHHHHHHHHHHHHhhCC
Confidence 688888888887 9999999999999999 99999999999999999999999764
No 8
>PRK05319 rplD 50S ribosomal protein L4; Provisional
Probab=100.00 E-value=9.6e-42 Score=278.56 Aligned_cols=120 Identities=28% Similarity=0.333 Sum_probs=110.0
Q ss_pred CccEEeccCCCccccCCcccccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCC
Q 048058 7 PLITVQSLEGDMATDASSTVPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPG 85 (157)
Q Consensus 7 ~~v~V~n~~G~~~~~~gg~ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg 85 (157)
|+++|||++|+.+ ++|+|| +||+.|+|.||||++|++|++|+||||+ +||+|+||+|+|+| || +|
T Consensus 1 ~~~~v~~~~g~~~----~~i~l~~~vF~~~~r~dll~~~v~~~~~~~Rqgta-----~tk~r~ev~GsgrK----~~-~Q 66 (205)
T PRK05319 1 MELKVLNLDGKEA----GEVELSDAVFGVEPNEALLHQVVVAQLANARQGTH-----ATKTRSEVSGGGKK----PW-RQ 66 (205)
T ss_pred CeeEEEcCCCCCc----ceEEcCHHHhCCCccHHHHHHHHHHHHHhcccCcc-----cCCcccccCCCCCC----CC-CC
Confidence 4789999999998 899998 7999999999999999999999999964 67999999999987 44 57
Q ss_pred CCcccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhH
Q 048058 86 GGTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLV 141 (157)
Q Consensus 86 ~GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v 141 (157)
|||||||+|+ +||+|||||++|||+| |+|++|||||+|+||+++|||+++.+.-+
T Consensus 67 KGTGrAR~Gs~rsP~~rGGg~afgpkp-r~~~~klnkK~~~lAl~~aLs~k~~~~~l 122 (205)
T PRK05319 67 KGTGRARQGSIRSPQWRGGGVVFGPKP-RDYSQKLNKKVRRLALRSALSEKAREGRL 122 (205)
T ss_pred CCCCccCcCcccCCcccCCeeeCCCCc-cchhhhcCHHHHHHHHHHHHHHHHhcCCe
Confidence 7888888887 9999999999999999 89999999999999999999999987433
No 9
>KOG1475 consensus Ribosomal protein RPL1/RPL2/RL4L4 [RNA processing and modification]
Probab=100.00 E-value=1e-41 Score=291.82 Aligned_cols=152 Identities=78% Similarity=1.273 Sum_probs=148.8
Q ss_pred ccCCCccEEeccCCCccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccc
Q 048058 3 AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPR 82 (157)
Q Consensus 3 ~~~~~~v~V~n~~G~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~pr 82 (157)
|++|+.++||+.||+.++ +++.||+||..|+|+||++.++..+..|+||+|+.++.||+++++|+||+|+.++|+||
T Consensus 1 ~~arp~vtvy~~~g~~s~---~~l~lp~vf~aPiRpdlv~~v~~~~~~n~rQpyAVs~kAG~QtSAESWGTGRAvaRiPR 77 (363)
T KOG1475|consen 1 AAARPLVTVYSLDGEASK---KTLTLPAVFSAPIRPDLVNFVHTQVRKNRRQPYAVSEKAGHQTSAESWGTGRAVARIPR 77 (363)
T ss_pred CCccceeeEEeccccccc---ccccccceeccCCcHHHHHHHHHHHhhccccchhhhhhhccccchhhcccccceecccc
Confidence 578999999999999984 68999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCcccCCCCCCCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCCCC
Q 048058 83 VPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157 (157)
Q Consensus 83 qkg~GtgRar~g~rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~Piv 157 (157)
.+|.||+|+|||.+.++||||++++|.+.||.|+.++|-.++++|+.||+++++.+.||++|||+||+++|||||
T Consensus 78 V~GGGT~RsGQgAFgNmCR~GrMfaPtKt~RrW~rkVn~n~Kr~A~asaiaasavpaLv~arGHrIe~VpelPlV 152 (363)
T KOG1475|consen 78 VGGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRKVNENEKRYAIASAIAASAVPALVMARGHRIEEVPELPLV 152 (363)
T ss_pred cCCCCcccccchhhhhhcccccccCchhhHHHHhhhhhhhhhhhHHHhhhhhhhhhHHHHhcCccccccccCceE
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999997
No 10
>PRK14907 rplD 50S ribosomal protein L4; Provisional
Probab=100.00 E-value=2.9e-39 Score=276.24 Aligned_cols=107 Identities=27% Similarity=0.240 Sum_probs=98.1
Q ss_pred ccccc-cccccc-CChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCCCcccCCCCC-CCcccc
Q 048058 25 TVPLP-DVMKAS-IRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGA-FGNMCR 101 (157)
Q Consensus 25 ~ieLp-~vF~~~-~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~GtgRar~g~-rsP~~r 101 (157)
.|+|+ +||+.+ ++++|||++|+||++|+||||+ .+|+|+||+|+|+| || +|+||||||+|+ +||+||
T Consensus 103 ~ieL~~~vF~~e~~~~~llh~~V~~q~A~~RqGT~-----~TKtRsEVsGggkK----Pw-rQKGTGRAR~GS~RSP~wr 172 (295)
T PRK14907 103 TSKLPKKLFASEKIYSQAIFDTILSERASRRQGTH-----KVKTRAEVSGTGKK----PW-RQKGTGRARAGSTRSPIFV 172 (295)
T ss_pred eEEeCHHHhCCCccchhHHHHHHHHHHHHhccccc-----cccchhhccCCCCC----Cc-ccCCCCccCCCCCcCCccc
Confidence 48997 699999 7999999999999999999976 57999999999997 55 688888888887 999999
Q ss_pred ccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhH
Q 048058 102 GGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLV 141 (157)
Q Consensus 102 GGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v 141 (157)
|||++|||+|+|+|+++||||+|+|||++|||+++..+||
T Consensus 173 GGGvaFGPkP~RdY~~KLNKKvRrLALrsALS~ka~~~Lv 212 (295)
T PRK14907 173 GGGRAFGPTPERNYKLKVNKKVRFNAFVSALTLLANSKAV 212 (295)
T ss_pred CCeeecCCCCccchhhhcCHHHHHHHHHHHHHHhccCCEE
Confidence 9999999999999999999999999999999999987655
No 11
>PF00573 Ribosomal_L4: Ribosomal protein L4/L1 family; InterPro: IPR002136 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 family includes ribosomal L4/L1 from eukaryotes and plants and L4 from bacteria. L4 from yeast has been shown to bind rRNA []. These proteins have 246 (plant) to 427 (human) amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_D 1VSA_D 3D5D_F 3MS1_E 3F1F_F 3PYO_E 3MRZ_E 3F1H_F 3PYR_E 1VSP_D ....
Probab=100.00 E-value=1.1e-38 Score=258.04 Aligned_cols=110 Identities=33% Similarity=0.408 Sum_probs=100.8
Q ss_pred cccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCCCcccCCCCC-CCcccccc
Q 048058 26 VPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGA-FGNMCRGG 103 (157)
Q Consensus 26 ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~GtgRar~g~-rsP~~rGG 103 (157)
|||+ +||+.|+|+||||++|++|++|+||||++ +|+|+||+|+|+| || +||||||||+|+ +||+||||
T Consensus 1 i~L~~~vF~~~~r~~llh~~v~~~~~~~Rqgt~~-----tktr~ev~g~grK----p~-~QKGTGrAR~Gs~rsP~~rgG 70 (192)
T PF00573_consen 1 IELSPDVFNVPVRPDLLHRAVVWQLANRRQGTAS-----TKTRSEVSGSGRK----PW-PQKGTGRARQGSIRSPQWRGG 70 (192)
T ss_dssp -ES-CGGGGSSTSHHHHHHHHHHHHHHTSSBT-S-----SSTSTTSSSSSSS----SS-SSSSSSSSSSSSCTSTTSTTS
T ss_pred CCCCHHHhCCCCcHHHHHHHHHHHHHhccCCccC-----CccceEEecccCc----cc-CCCCCcccccCccccceeecc
Confidence 6894 79999999999999999999999999764 6899999999987 65 788888888887 99999999
Q ss_pred ccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhHhhcC
Q 048058 104 RMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARG 145 (157)
Q Consensus 104 g~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rg 145 (157)
|++|||+|+|+|+++||||+|++||++|||+++.++.+.-.+
T Consensus 71 g~afgPkp~r~~~~klnkK~r~lAl~~aLs~k~~~~~l~vvd 112 (192)
T PF00573_consen 71 GVAFGPKPPRDYSYKLNKKVRRLALRSALSAKAAEGNLIVVD 112 (192)
T ss_dssp SBSSSSSSTSBCSHHHHHHHHHHHHHHHHHHHHHTTHHHHCT
T ss_pred EEecCCcccccceecCChHHHHHHHHHHHHHhhcccceEEee
Confidence 999999999999999999999999999999999999998876
No 12
>KOG1624 consensus Mitochondrial/chloroplast ribosomal protein L4 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=7.9e-32 Score=228.45 Aligned_cols=127 Identities=26% Similarity=0.310 Sum_probs=112.0
Q ss_pred cEEeccCCCccccCCcccccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCCC
Q 048058 9 ITVQSLEGDMATDASSTVPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGG 87 (157)
Q Consensus 9 v~V~n~~G~~~~~~gg~ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~G 87 (157)
+++.+.++|++ |.++|+ ++|.+++|-||||++|+|++.|+|+|+ |++|+|+|+.|+|+| || .|||
T Consensus 56 ~~~~~~e~E~~----gl~~l~~dvf~~~~RrDIlhrav~wq~~nrrvgt-----astktRaEv~ggGrK----p~-~QKg 121 (290)
T KOG1624|consen 56 EPLDFFELEKV----GLVDLHPDVFAEPPRRDILHRAVVWQLDNRRVGT-----ASTKTRAEVRGGGRK----PW-PQKG 121 (290)
T ss_pred eeccccccccc----eeeecChhhhccchHHHHHHHHHHHhhccccccc-----ccCCccccccCCCCC----cC-cccC
Confidence 35567899999 999997 899999999999999999999999996 567999999999997 54 6778
Q ss_pred cccCCCCC-CCccccccccccCCc-cCcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCC
Q 048058 88 THRAGQGA-FGNMCRGGRMFAPTK-IWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMP 155 (157)
Q Consensus 88 tgRar~g~-rsP~~rGGg~afgPk-p~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~P 155 (157)
|||||.|+ +||+++|||++|||+ | |+|+++||.|+|.|||+.|||++..++.. |.+|+.. ||
T Consensus 122 tGrAr~Gs~rsP~r~gGg~~~gpr~P-~d~~~~Lp~kvr~lgl~~ALS~~~a~~~l----~I~d~~~-L~ 185 (290)
T KOG1624|consen 122 TGRARVGSLRSPQRRGGGVAHGPRGP-RDYSYKLPSKVRSLGLKIALSAKLAQDDL----HIVDELG-LP 185 (290)
T ss_pred CCcccccCccCcccCCCccccCCCCC-cchhhhccHHHHHHHHHHHHHHHHhCCce----EEecccC-CC
Confidence 88899897 999999999999999 7 99999999999999999999988877653 6666653 44
No 13
>PTZ00428 60S ribosomal protein L4; Provisional
Probab=64.29 E-value=8.2 Score=35.02 Aligned_cols=84 Identities=13% Similarity=-0.010 Sum_probs=51.5
Q ss_pred HHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCCCcccCCCCCCCccccccccccCCc------c----
Q 048058 42 GFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTK------I---- 111 (157)
Q Consensus 42 ~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~GtgRar~g~rsP~~rGGg~afgPk------p---- 111 (157)
.++|.....+.+.. .+.+++.++++++ +++.+ +| |||||++ |.|=..|||....|. -
T Consensus 33 ~dlV~~vv~~~~aN-~RQgta~s~~ag~--~tsak----sw----GTGRA~a--ripR~kg~GT~Rs~qGa~~n~~rGG~ 99 (381)
T PTZ00428 33 PDLVQFVHTNMAKN-RRQAYAVKPLAGM--QHSAE----SW----GTGRAVA--RIPRVSGGGTHRSGQGAFGNMCRGGR 99 (381)
T ss_pred HHHHHHHHHHHHHh-ccCCCCcCCCCCC--CCCce----ec----CCCCCcc--ccccccCCCCCcCcccccCCcCCCce
Confidence 45666666666665 4667888877777 56654 67 5666654 457677777544443 1
Q ss_pred ---CcceeeccCHHHHHHHHHHHHHhccCh
Q 048058 112 ---WRRWHRKINVNQKRYAIVSAIAASAVP 138 (157)
Q Consensus 112 ---~r~~~~kiNkK~rrlAl~sALs~ka~~ 138 (157)
+....++..+|+-+---+.||..-+..
T Consensus 100 ~FgP~~~~R~~~~KvNkK~rR~Al~SALaa 129 (381)
T PTZ00428 100 MFAPTKTWRRWHRKVNLNQKRHAVASALAA 129 (381)
T ss_pred EcCCCCCccccccccCHHHHHHHHHHHHHh
Confidence 112225677777777777777654433
No 14
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=32.23 E-value=39 Score=27.69 Aligned_cols=47 Identities=23% Similarity=0.194 Sum_probs=38.3
Q ss_pred CCcccc---ccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhHh
Q 048058 96 FGNMCR---GGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVM 142 (157)
Q Consensus 96 rsP~~r---GGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~ 142 (157)
-+|+++ ||++.|-=+.+.+...+||-+.+-.||+-+|...+..+...
T Consensus 106 i~pi~~rvq~g~~~H~GK~P~~~~~~i~~~~~I~~L~e~Lq~~i~~EefE 155 (176)
T COG3880 106 ISPIITRVQGGYVEHVGKVPKRIGRKINPKRKIIALKEALQDLIEREEFE 155 (176)
T ss_pred hhHHHHHhhCCceeecCcCcccccccccHHHHHHHHHHHHHHHHHHHHHH
Confidence 478665 77798876666889999999999999999999888776544
No 15
>KOG0377 consensus Protein serine/threonine phosphatase RDGC/PPEF, contains STphosphatase and EF-hand domains [Signal transduction mechanisms]
Probab=26.45 E-value=22 Score=33.53 Aligned_cols=29 Identities=24% Similarity=0.379 Sum_probs=21.9
Q ss_pred cCCCCCCCccccccccccCCccCcceeec
Q 048058 90 RAGQGAFGNMCRGGRMFAPTKIWRRWHRK 118 (157)
Q Consensus 90 Rar~g~rsP~~rGGg~afgPkp~r~~~~k 118 (157)
++-.|...+.+||||.-|||-..-++.+|
T Consensus 343 ~~~~GC~pNt~RGgG~yFGpDvT~~~Lqk 371 (631)
T KOG0377|consen 343 QATMGCVPNTLRGGGCYFGPDVTDNFLQK 371 (631)
T ss_pred ccccCCCcccccCCcceeCchHHHHHHHH
Confidence 34457889999999999999875445443
Done!