Query psy13118
Match_columns 286
No_of_seqs 168 out of 1128
Neff 3.5
Searched_HMMs 46136
Date Fri Aug 16 20:01:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13118.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13118hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1475|consensus 100.0 1.9E-56 4.1E-61 418.4 8.6 188 17-286 1-188 (363)
2 PLN00185 60S ribosomal protein 100.0 4.7E-55 1E-59 420.7 16.0 188 16-286 2-193 (405)
3 PTZ00428 60S ribosomal protein 100.0 1E-52 2.2E-57 402.4 15.9 187 17-286 1-188 (381)
4 PRK04042 rpl4lp 50S ribosomal 100.0 4E-46 8.6E-51 341.8 15.2 178 21-286 1-178 (254)
5 TIGR03672 rpl4p_arch 50S ribos 100.0 1.5E-44 3.2E-49 331.0 14.9 177 21-286 1-177 (251)
6 PRK05319 rplD 50S ribosomal pr 100.0 1.7E-35 3.7E-40 262.9 13.4 145 21-273 1-147 (205)
7 COG0088 RplD Ribosomal protein 100.0 1.9E-35 4.2E-40 265.3 10.6 157 20-283 1-158 (214)
8 PRK14547 rplD 50S ribosomal pr 100.0 9.2E-35 2E-39 271.8 13.3 145 20-272 1-148 (298)
9 CHL00147 rpl4 ribosomal protei 100.0 1.5E-32 3.3E-37 246.5 12.5 143 21-274 7-154 (215)
10 PRK14907 rplD 50S ribosomal pr 100.0 3.8E-31 8.2E-36 247.3 10.8 142 26-274 93-237 (295)
11 PF00573 Ribosomal_L4: Ribosom 100.0 3.5E-31 7.6E-36 232.9 7.3 131 37-273 1-134 (192)
12 PLN00185 60S ribosomal protein 99.9 8.9E-25 1.9E-29 211.5 5.1 118 47-169 41-170 (405)
13 KOG1475|consensus 99.9 7E-25 1.5E-29 206.5 4.0 96 63-169 58-165 (363)
14 KOG1624|consensus 99.9 1.3E-22 2.7E-27 189.0 9.7 148 24-278 57-206 (290)
15 PTZ00428 60S ribosomal protein 99.9 2.8E-22 6E-27 193.2 5.5 118 47-169 36-165 (381)
16 COG0088 RplD Ribosomal protein 99.6 7.5E-16 1.6E-20 139.0 4.0 109 44-169 30-140 (214)
17 PRK04042 rpl4lp 50S ribosomal 99.5 3.9E-14 8.4E-19 131.0 4.5 97 46-161 30-135 (254)
18 TIGR03672 rpl4p_arch 50S ribos 99.4 5.7E-14 1.2E-18 129.7 4.4 97 46-161 30-135 (251)
19 PF00573 Ribosomal_L4: Ribosom 98.9 1.9E-09 4.1E-14 95.5 4.6 110 47-172 17-127 (192)
20 PRK05319 rplD 50S ribosomal pr 98.5 5.8E-08 1.3E-12 87.1 3.2 103 46-171 31-139 (205)
21 PRK14547 rplD 50S ribosomal pr 98.4 2.8E-07 6.1E-12 87.5 4.8 107 46-172 32-142 (298)
22 PRK14907 rplD 50S ribosomal pr 98.2 1.6E-06 3.4E-11 82.5 4.7 108 45-172 119-229 (295)
23 CHL00147 rpl4 ribosomal protei 97.9 1.6E-05 3.4E-10 72.4 5.0 107 44-172 35-146 (215)
24 KOG1624|consensus 93.0 0.13 2.9E-06 49.4 4.5 98 47-163 85-183 (290)
25 PRK11595 DNA utilization prote 21.1 1.8E+02 0.0039 26.2 4.8 52 210-274 164-216 (227)
26 PF13514 AAA_27: AAA domain 20.2 1.1E+02 0.0025 33.8 3.9 48 214-272 1031-1080(1111)
No 1
>KOG1475|consensus
Probab=100.00 E-value=1.9e-56 Score=418.43 Aligned_cols=188 Identities=70% Similarity=1.177 Sum_probs=179.2
Q ss_pred hhcCceeEEecCCCCcccceeeccccccccCchhHHHHHHHHHHhcCCCCCCCCCCCccceeeeeeCCCcceeccccccC
Q psy13118 17 GVARPLITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARIPRVRG 96 (286)
Q Consensus 17 ~~~m~~i~v~~~~~~~~g~~v~lp~vf~~~ir~~lI~~~v~~~q~~gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~rq 96 (286)
++++|+|+||+++|+.+.++++||.||.+|||+|++++++..+..|.|||||.+..+|+++++||||+||+++|+|+
T Consensus 1 ~~arp~vtvy~~~g~~s~~~l~lp~vf~aPiRpdlv~~v~~~~~~n~rQpyAVs~kAG~QtSAESWGTGRAvaRiPR--- 77 (363)
T KOG1475|consen 1 AAARPLVTVYSLDGEASKKTLTLPAVFSAPIRPDLVNFVHTQVRKNRRQPYAVSEKAGHQTSAESWGTGRAVARIPR--- 77 (363)
T ss_pred CCccceeeEEecccccccccccccceeccCCcHHHHHHHHHHHhhccccchhhhhhhccccchhhcccccceecccc---
Confidence 57899999999999999999999999999999999999999999999999999999999999999999998876554
Q ss_pred CCcccCCCCccccccccccccCCCchhhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccccccccccccccccc
Q psy13118 97 GGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRV 176 (286)
Q Consensus 97 kGTgrArqGa~~~~~rgGr~ahpp~~~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s~~~~~~~~r~p~~ 176 (286)
.
T Consensus 78 -------------------------------------------------------------------------------V 78 (363)
T KOG1475|consen 78 -------------------------------------------------------------------------------V 78 (363)
T ss_pred -------------------------------------------------------------------------------c
Confidence 5
Q ss_pred cCCCccccCccccCcccccceeeCCCCCCcccccccCHHHHHHHHHHHHHhccCchhhhccCccccCCCCcCEEEecCCC
Q psy13118 177 RGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQ 256 (286)
Q Consensus 177 ~ggGt~rAgqgA~aP~~rGG~~~~p~~~~r~~~~kvn~k~rr~A~~saia~~~~~~lV~~RGH~i~~v~~~~lvV~d~~~ 256 (286)
.||||+|+|||||.++||||+||+|+++||+||++||.+++|||+.||||+++.+.||++|||+|++++|.||||+|+++
T Consensus 79 ~GGGT~RsGQgAFgNmCR~GrMfaPtKt~RrW~rkVn~n~Kr~A~asaiaasavpaLv~arGHrIe~VpelPlVVsd~ve 158 (363)
T KOG1475|consen 79 GGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRKVNENEKRYAIASAIAASAVPALVMARGHRIEEVPELPLVVSDKVE 158 (363)
T ss_pred CCCCcccccchhhhhhcccccccCchhhHHHHhhhhhhhhhhhHHHhhhhhhhhhHHHHhcCccccccccCceEeehhhH
Confidence 78888888888889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccHHHHHHHHHHCCCcchhHhhhccCCC
Q psy13118 257 EYKKTKQATIFLHRIKAWNDVLKVQSSGTF 286 (286)
Q Consensus 257 ~~~KTKe~~~~Lk~l~~~~Dv~r~~~~r~~ 286 (286)
++.||||++.+|+++++|+|++++..|+.+
T Consensus 159 ~~~KTkeAV~~Lk~~~a~~di~kv~~S~~~ 188 (363)
T KOG1475|consen 159 SFRKTKEAVALLKKLKAWNDIKKVYNSRRL 188 (363)
T ss_pred HHHhHHHHHHHHHHhccHHHHHHHHhhccc
Confidence 999999999999999999999999998764
No 2
>PLN00185 60S ribosomal protein L4-1; Provisional
Probab=100.00 E-value=4.7e-55 Score=420.73 Aligned_cols=188 Identities=67% Similarity=1.087 Sum_probs=176.4
Q ss_pred hhhcCceeEEecCCC----CcccceeeccccccccCchhHHHHHHHHHHhcCCCCCCCCCCCccceeeeeeCCCcceecc
Q psy13118 16 VGVARPLITVYSEKN----EPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARI 91 (286)
Q Consensus 16 ~~~~m~~i~v~~~~~----~~~g~~v~lp~vf~~~ir~~lI~~~v~~~q~~gRqp~Ag~~~~g~kt~ae~~G~GRkv~Rv 91 (286)
|++++|.++|||.+| +.++ +|+||+||.+|||+|+|++++.+++.|.||||+.++.+|++|++||||+||+++|+
T Consensus 2 ~~~~rp~v~V~~~~g~~~~~~~~-~v~Lp~VF~~piR~dlv~~v~~~~~~n~RQp~~~~~~AG~qtsAeswGtGR~vaRi 80 (405)
T PLN00185 2 AAAARPLVSVQSLDGDMATDKSA-TVALPDVMTAPIRPDIVNFVHTNISKNSRQPYAVSKKAGHQTSAESWGTGRAVSRI 80 (405)
T ss_pred CcccCCeeEEEcCCCCccccccc-eeehHHHhCCCCCHHHHHHHHHHHHHhccCCCCCCcccCCcceeeecCCCCCceec
Confidence 688999999999999 5566 69999999999999999999999999999999999999999999999999998876
Q ss_pred ccccCCCcccCCCCccccccccccccCCCchhhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCcccccccccccccc
Q psy13118 92 PRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVA 171 (286)
Q Consensus 92 P~~rqkGTgrArqGa~~~~~rgGr~ahpp~~~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s~~~~~~~~ 171 (286)
|+.
T Consensus 81 PR~----------------------------------------------------------------------------- 83 (405)
T PLN00185 81 PRV----------------------------------------------------------------------------- 83 (405)
T ss_pred ccc-----------------------------------------------------------------------------
Confidence 654
Q ss_pred ccccccCCCccccCccccCcccccceeeCCCCCCcccccccCHHHHHHHHHHHHHhccCchhhhccCccccCCCCcCEEE
Q psy13118 172 RIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVV 251 (286)
Q Consensus 172 r~p~~~ggGt~rAgqgA~aP~~rGG~~~~p~~~~r~~~~kvn~k~rr~A~~saia~~~~~~lV~~RGH~i~~v~~~~lvV 251 (286)
+||||+|||||+|.++|+||+||+|+++||+|++|||+||||+|++||||+++.++||++|||+|++++|+||||
T Consensus 84 -----kggGT~RAgqGa~~~~~rGGr~FgP~p~~R~~~~KvNkK~rRlAl~SALAa~a~~~lV~arGH~i~~v~e~pLVV 158 (405)
T PLN00185 84 -----PGGGTHRAGQGAFGNMCRGGRMFAPTKTWRRWHRKVNVNQKRYAVVSALAASAVPSLVMARGHKIENVPEVPLVV 158 (405)
T ss_pred -----cCCCCCcCCccCcCCcCCCCeeCCCCCCccccccccCHHHHHHHHHHHHHhhccchhhhcccccccccccCCEEE
Confidence 677777777777788999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCCCcccHHHHHHHHHHCCCcchhHhhhccCCC
Q psy13118 252 SDKIQEYKKTKQATIFLHRIKAWNDVLKVQSSGTF 286 (286)
Q Consensus 252 ~d~~~~~~KTKe~~~~Lk~l~~~~Dv~r~~~~r~~ 286 (286)
+|++++++|||+++++|++||+++|++|++++++|
T Consensus 159 ~d~~e~~~KTK~av~~Lk~lg~~~d~~k~~~s~~i 193 (405)
T PLN00185 159 SDSAESIEKTSAAIKILKQIGAYADVEKAKDSKGI 193 (405)
T ss_pred EeCccCCcCHHHHHHHHHHcCCcccchhhhccccc
Confidence 99999999999999999999999999999988765
No 3
>PTZ00428 60S ribosomal protein L4; Provisional
Probab=100.00 E-value=1e-52 Score=402.42 Aligned_cols=187 Identities=66% Similarity=1.084 Sum_probs=176.4
Q ss_pred hhcCceeEEecCCC-CcccceeeccccccccCchhHHHHHHHHHHhcCCCCCCCCCCCccceeeeeeCCCcceecccccc
Q psy13118 17 GVARPLITVYSEKN-EPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARIPRVR 95 (286)
Q Consensus 17 ~~~m~~i~v~~~~~-~~~g~~v~lp~vf~~~ir~~lI~~~v~~~q~~gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~r 95 (286)
|+++|+++|||.+| +..+ +|+||+||.+|||+|+|++++.+++.|.||||+.+.++|+++++++||+||+++|+|
T Consensus 1 ~~~r~~v~V~~~~g~~~~~-~v~Lp~VF~~pir~dlV~~vv~~~~aN~RQgta~s~~ag~~tsakswGTGRA~arip--- 76 (381)
T PTZ00428 1 MTARPVVSVYSASDKSVVG-TVPLPAVFTAPIRPDLVQFVHTNMAKNRRQAYAVKPLAGMQHSAESWGTGRAVARIP--- 76 (381)
T ss_pred CCCCCeeEEEcCCCCcccc-eEehHHhhCCCCcHHHHHHHHHHHHHhccCCCCcCCCCCCCCCceecCCCCCccccc---
Confidence 57899999999999 5566 799999999999999999999999999999999999999999999999999877555
Q ss_pred CCCcccCCCCccccccccccccCCCchhhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCcccccccccccccccccc
Q psy13118 96 GGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPR 175 (286)
Q Consensus 96 qkGTgrArqGa~~~~~rgGr~ahpp~~~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s~~~~~~~~r~p~ 175 (286)
+
T Consensus 77 -------------------------------------------------------------------------------R 77 (381)
T PTZ00428 77 -------------------------------------------------------------------------------R 77 (381)
T ss_pred -------------------------------------------------------------------------------c
Confidence 4
Q ss_pred ccCCCccccCccccCcccccceeeCCCCCCcccccccCHHHHHHHHHHHHHhccCchhhhccCccccCCCCcCEEEecCC
Q psy13118 176 VRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKI 255 (286)
Q Consensus 176 ~~ggGt~rAgqgA~aP~~rGG~~~~p~~~~r~~~~kvn~k~rr~A~~saia~~~~~~lV~~RGH~i~~v~~~~lvV~d~~ 255 (286)
.+||||+|++||+|+|+|+||+||+|+++||+|++|||+||||+|++||||+++.++||++|||+|++++|+||||+|++
T Consensus 78 ~kg~GT~Rs~qGa~~n~~rGG~~FgP~~~~R~~~~KvNkK~rR~Al~SALaa~a~~~lv~argh~i~~v~e~plVV~d~~ 157 (381)
T PTZ00428 78 VSGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRKVNLNQKRHAVASALAASGVPALVMARGHRISNVPEVPLVVSDSV 157 (381)
T ss_pred ccCCCCCcCcccccCCcCCCceEcCCCCCccccccccCHHHHHHHHHHHHHhhccchhhhcccccccccccCCEEEEcCc
Confidence 57888889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccHHHHHHHHHHCCCcchhHhhhccCCC
Q psy13118 256 QEYKKTKQATIFLHRIKAWNDVLKVQSSGTF 286 (286)
Q Consensus 256 ~~~~KTKe~~~~Lk~l~~~~Dv~r~~~~r~~ 286 (286)
++++|||+++++|++||+++|+++++++++|
T Consensus 158 e~~~KTK~av~~Lk~lg~~~d~~k~~~s~~~ 188 (381)
T PTZ00428 158 ESYEKTKEAVAFLKALGAFDDVNRVNDSKKI 188 (381)
T ss_pred CCCCCHHHHHHHHHHcCCcccchhhhccccc
Confidence 8889999999999999999999999998765
No 4
>PRK04042 rpl4lp 50S ribosomal protein L4P; Provisional
Probab=100.00 E-value=4e-46 Score=341.78 Aligned_cols=178 Identities=37% Similarity=0.620 Sum_probs=164.0
Q ss_pred ceeEEecCCCCcccceeeccccccccCchhHHHHHHHHHHhcCCCCCCCCCCCccceeeeeeCCCcceeccccccCCCcc
Q psy13118 21 PLITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARIPRVRGGGTH 100 (286)
Q Consensus 21 ~~i~v~~~~~~~~g~~v~lp~vf~~~ir~~lI~~~v~~~q~~gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~rqkGTg 100 (286)
|+++|||.+|+.++ +++||+||+.|+|+++|++++.++++|.|||++.++++++++++|+||+||++.+.| ||||||
T Consensus 1 ~~v~v~~~~g~~~g-~i~L~~vF~~~~~~~lv~~vv~~~~an~Rqgt~~~~ta~tKtraev~G~Gr~~~Kp~--rQKGTG 77 (254)
T PRK04042 1 MKAKVYDLDGEVVG-EIELPAVFEEPVRPDLIRRAVLAAQTARLQPKGRDPLAGKRTSAESWGSGRGIARVP--RLKGGS 77 (254)
T ss_pred CeeEEEcCCCCCcc-eEehhHhhCCCCcHHHHHHHHHHHHHhccCCCCCCccccCccceeEcCCCCCcCcCC--ccCCCC
Confidence 57999999999998 699999999999999999999999999999998888899999999999999666533 688886
Q ss_pred cCCCCccccccccccccCCCchhhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccccccccccccccccccCCC
Q psy13118 101 RSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRVRGGG 180 (286)
Q Consensus 101 rArqGa~~~~~rgGr~ahpp~~~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s~~~~~~~~r~p~~~ggG 180 (286)
|||
T Consensus 78 rAr----------------------------------------------------------------------------- 80 (254)
T PRK04042 78 RAA----------------------------------------------------------------------------- 80 (254)
T ss_pred Ccc-----------------------------------------------------------------------------
Confidence 664
Q ss_pred ccccCccccCcccccceeeCCCCCCcccccccCHHHHHHHHHHHHHhccCchhhhccCccccCCCCcCEEEecCCCCccc
Q psy13118 181 THRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKK 260 (286)
Q Consensus 181 t~rAgqgA~aP~~rGG~~~~p~~~~r~~~~kvn~k~rr~A~~saia~~~~~~lV~~RGH~i~~v~~~~lvV~d~~~~~~K 260 (286)
++|+||||++||||+|||+|++|+|+|+|++||+|||++++...||++|||+|++++|+||||+|+|++.+|
T Consensus 81 --------rsP~~rGGgv~fgPkp~R~y~~klnkK~rrlAlrsALs~k~~~~lv~~~~~~~~~~~e~~lvvvd~~~~~~K 152 (254)
T PRK04042 81 --------FVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATANPELVKARGHVFEGVPELPLVVVDDFESLKK 152 (254)
T ss_pred --------ccCccCcCCeeCCCCCCcccccccCHHHHHHHHHHHHHHhhhhhhhhhcCccccCCCccCEEEEcccccccC
Confidence 367888888999999999999999999999999999999999999999999999999999999999998899
Q ss_pred HHHHHHHHHHCCCcchhHhhhccCCC
Q psy13118 261 TKQATIFLHRIKAWNDVLKVQSSGTF 286 (286)
Q Consensus 261 TKe~~~~Lk~l~~~~Dv~r~~~~r~~ 286 (286)
||+++++|++||+++|+++++++++|
T Consensus 153 TK~~~~~Lk~lg~~~~~~~~~~~~~~ 178 (254)
T PRK04042 153 TKEVRELLEKLGLYDDVERAKEGKKI 178 (254)
T ss_pred HHHHHHHHHHcCCcccchhhhcccee
Confidence 99999999999999999998887543
No 5
>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=1.5e-44 Score=331.05 Aligned_cols=177 Identities=36% Similarity=0.598 Sum_probs=162.1
Q ss_pred ceeEEecCCCCcccceeeccccccccCchhHHHHHHHHHHhcCCCCCCCCCCCccceeeeeeCCCcceeccccccCCCcc
Q psy13118 21 PLITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARIPRVRGGGTH 100 (286)
Q Consensus 21 ~~i~v~~~~~~~~g~~v~lp~vf~~~ir~~lI~~~v~~~q~~gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~rqkGTg 100 (286)
|+++|||.+|+.++ +++||+||+.|+++++|++++.++++|.||+++.++.++++|++|+||+||++++.| ||||||
T Consensus 1 m~~~v~~~~g~~~~-~i~l~~vF~~~~~~~lv~~vv~~~~an~Rqgt~~~~~a~tKtraev~G~Grg~aKp~--rQKGTG 77 (251)
T TIGR03672 1 MKAKVYDLDGEVVG-EIELPAVFEEPVRPDLIKRAVLAAQTNRLQPYGADPYAGKRTSAESWGSGRGIARVP--RIKGGS 77 (251)
T ss_pred CceEEEccCCCCcc-eEehHHhhCCCccHHHHHHHHHHHHHhccCCCCCCcccCcccceeEccCCCCcCCCC--ccCCCC
Confidence 56899999999988 699999999999999999999999999999998777889999999999999776644 589887
Q ss_pred cCCCCccccccccccccCCCchhhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccccccccccccccccccCCC
Q psy13118 101 RSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRVRGGG 180 (286)
Q Consensus 101 rArqGa~~~~~rgGr~ahpp~~~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s~~~~~~~~r~p~~~ggG 180 (286)
|| .
T Consensus 78 rA----~------------------------------------------------------------------------- 80 (251)
T TIGR03672 78 RA----A------------------------------------------------------------------------- 80 (251)
T ss_pred cc----e-------------------------------------------------------------------------
Confidence 66 2
Q ss_pred ccccCccccCcccccceeeCCCCCCcccccccCHHHHHHHHHHHHHhccCchhhhccCccccCCCCcCEEEecCCCCccc
Q psy13118 181 THRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKK 260 (286)
Q Consensus 181 t~rAgqgA~aP~~rGG~~~~p~~~~r~~~~kvn~k~rr~A~~saia~~~~~~lV~~RGH~i~~v~~~~lvV~d~~~~~~K 260 (286)
++|+||||+++|||+|||+|++|||+|+|++|++|||++++...||++|||+|+++ |+||||+|+|++.+|
T Consensus 81 --------rsP~~rGGGv~fgPkp~R~y~~klNkK~rrlAl~sALs~k~~~~lv~~~~~~~~~~-e~~lvVvd~~~~~~K 151 (251)
T TIGR03672 81 --------RVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATADPELVKARGHVFEGD-ELPIVVVDDFESLKK 151 (251)
T ss_pred --------ecCccCcCCeeCCCCCCcccceecCHHHHHHHHHHHHHHhcchhhhhhcccccccc-cccEEEEeCCCCCCC
Confidence 36777778899999999999999999999999999999999999999999999999 999999999998899
Q ss_pred HHHHHHHHHHCCCcchhHhhhccCCC
Q psy13118 261 TKQATIFLHRIKAWNDVLKVQSSGTF 286 (286)
Q Consensus 261 TKe~~~~Lk~l~~~~Dv~r~~~~r~~ 286 (286)
||+++++|++|++++|+++++.|++|
T Consensus 152 TK~~~~~Lk~l~~~~~~~~~~~~~~~ 177 (251)
T TIGR03672 152 TKEVRELLEALGVYDDIERAKEGKKI 177 (251)
T ss_pred HHHHHHHHHHcCCccccchhhcccee
Confidence 99999999999999999988887653
No 6
>PRK05319 rplD 50S ribosomal protein L4; Provisional
Probab=100.00 E-value=1.7e-35 Score=262.89 Aligned_cols=145 Identities=29% Similarity=0.342 Sum_probs=129.6
Q ss_pred ceeEEecCCCCcccceeecc-ccccccCchhHHHHHHHHHHhcCCCCCCCCCCCccceeeeeeCCCcceeccccccCCCc
Q psy13118 21 PLITVYSEKNEPTGQTVTLP-SVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARIPRVRGGGT 99 (286)
Q Consensus 21 ~~i~v~~~~~~~~g~~v~lp-~vf~~~ir~~lI~~~v~~~q~~gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~rqkGT 99 (286)
|+++|||.+|+.+| +|+|| ++|+.|+|+|+||+++.+++.+.|||+|. +++++|++|+|+|++ +||||
T Consensus 1 ~~~~v~~~~g~~~~-~i~l~~~vF~~~~r~dll~~~v~~~~~~~Rqgta~-----tk~r~ev~GsgrK~~-----~QKGT 69 (205)
T PRK05319 1 MELKVLNLDGKEAG-EVELSDAVFGVEPNEALLHQVVVAQLANARQGTHA-----TKTRSEVSGGGKKPW-----RQKGT 69 (205)
T ss_pred CeeEEEcCCCCCcc-eEEcCHHHhCCCccHHHHHHHHHHHHHhcccCccc-----CCcccccCCCCCCCC-----CCCCC
Confidence 57899999999998 59998 89999999999999999999999999764 689999999999864 69999
Q ss_pred ccCCCCccccccccccccCCCchhhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccccccccccccccccccCC
Q psy13118 100 HRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRVRGG 179 (286)
Q Consensus 100 grArqGa~~~~~rgGr~ahpp~~~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s~~~~~~~~r~p~~~gg 179 (286)
||||+|+. ++|+|
T Consensus 70 GrAR~Gs~----------------------------------------------------------------rsP~~--- 82 (205)
T PRK05319 70 GRARQGSI----------------------------------------------------------------RSPQW--- 82 (205)
T ss_pred CccCcCcc----------------------------------------------------------------cCCcc---
Confidence 99999998 65555
Q ss_pred CccccCccccCcccccceeeCCCCCCcccccccCHHHHHHHHHHHHHhccCchhhhccCccccCCCCcCEEEecCCC-Cc
Q psy13118 180 GTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQ-EY 258 (286)
Q Consensus 180 Gt~rAgqgA~aP~~rGG~~~~p~~~~r~~~~kvn~k~rr~A~~saia~~~~~~lV~~RGH~i~~v~~~~lvV~d~~~-~~ 258 (286)
|||+++|||+| |+|++|+|+|+|++|+++||++++. +.+|+|+|+++ +.
T Consensus 83 --------------rGGg~afgpkp-r~~~~klnkK~~~lAl~~aLs~k~~---------------~~~l~Vvd~~~~~~ 132 (205)
T PRK05319 83 --------------RGGGVVFGPKP-RDYSQKLNKKVRRLALRSALSEKAR---------------EGRLVVVDDLSLEA 132 (205)
T ss_pred --------------cCCeeeCCCCc-cchhhhcCHHHHHHHHHHHHHHHHh---------------cCCeEEEeccccCC
Confidence 55567777787 7999999999999999999999963 57788999986 68
Q ss_pred ccHHHHHHHHHHCCC
Q psy13118 259 KKTKQATIFLHRIKA 273 (286)
Q Consensus 259 ~KTKe~~~~Lk~l~~ 273 (286)
+|||++.++|+.+|+
T Consensus 133 ~KTk~~~~~l~~lg~ 147 (205)
T PRK05319 133 PKTKELAAKLKNLGL 147 (205)
T ss_pred CCHHHHHHHHHHcCC
Confidence 999999999999996
No 7
>COG0088 RplD Ribosomal protein L4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-35 Score=265.31 Aligned_cols=157 Identities=29% Similarity=0.354 Sum_probs=131.3
Q ss_pred CceeEEecCCCCcccceeeccccccccCchhHHHHHHHHHHhcCCCCCCCCCCCccceeeeeeCCCcceeccccccCCCc
Q psy13118 20 RPLITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARIPRVRGGGT 99 (286)
Q Consensus 20 m~~i~v~~~~~~~~g~~v~lp~vf~~~ir~~lI~~~v~~~q~~gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~rqkGT 99 (286)
||+++|||.+|+.+|+...+|++|..+.+.|+|++++.+++++.||||+. .++++|++|+|++++ +||||
T Consensus 1 m~k~~v~~~~G~~~g~~~~~~~vf~~~~~~dli~~av~a~~a~~RQgt~~-----~k~rgevs~~g~Kp~-----~Qkgt 70 (214)
T COG0088 1 MMKLKVYDLDGEEVGEVELLPEVFGPERNEDLIHRAVLAQLANRRQGTHS-----TKTRGEVSGGGKKPW-----GQKGT 70 (214)
T ss_pred CCcceEeCCCCCCccccccChhhccCCchHHHHHHHHHHHHHhhhccCCC-----CCCcccccccCcCCC-----CCCcC
Confidence 78999999999999963444689887777899999999999999999886 588899999999865 69999
Q ss_pred ccCCCCccccccccccccCCCchhhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccccccccccccccccccCC
Q psy13118 100 HRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRVRGG 179 (286)
Q Consensus 100 grArqGa~~~~~rgGr~ahpp~~~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s~~~~~~~~r~p~~~gg 179 (286)
||||+|++ +.
T Consensus 71 graR~gs~----------------------------------------------------------------rs------ 80 (214)
T COG0088 71 GRARQGSI----------------------------------------------------------------RS------ 80 (214)
T ss_pred CcCCCCCC----------------------------------------------------------------CC------
Confidence 99999999 43
Q ss_pred CccccCccccCcccccceeeCCCCCCcccccccCHHHHHHHHHHHHHhccCc-hhhhccCccccCCCCcCEEEecCCCCc
Q psy13118 180 GTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVP-ALVMSKGHMIQDVPEFPLVVSDKIQEY 258 (286)
Q Consensus 180 Gt~rAgqgA~aP~~rGG~~~~p~~~~r~~~~kvn~k~rr~A~~saia~~~~~-~lV~~RGH~i~~v~~~~lvV~d~~~~~ 258 (286)
|+||||+++|||+|+|+|++|||+|+|++||+||||+++.. +||..+||.|++ .
T Consensus 81 -----------P~~rGGg~a~gPkp~r~~~~klnkK~rrlAl~sAls~ka~~~~lv~~~~~~~~~--------------~ 135 (214)
T COG0088 81 -----------PQWRGGGVAHGPKPERDYSQKLNKKERRLALRSALSAKARAGKLVVVRGHVFED--------------A 135 (214)
T ss_pred -----------CeeecCccccCCCCccchhhhcCHHHHHHHHHHHHHHhccCCCEEEEecccccC--------------C
Confidence 55666778888899999999999999999999999999865 454444444432 5
Q ss_pred ccHHHHHHHHHHCCCcchhHhhhcc
Q psy13118 259 KKTKQATIFLHRIKAWNDVLKVQSS 283 (286)
Q Consensus 259 ~KTKe~~~~Lk~l~~~~Dv~r~~~~ 283 (286)
+|||+++++|++ ++.|.+++...
T Consensus 136 ~kTK~~~~~lk~--l~~~~~~~l~~ 158 (214)
T COG0088 136 PKTKELVEFLKK--LGLDVKRLLIV 158 (214)
T ss_pred ccHHHHHHHHHH--hhhhhceeEEe
Confidence 779999999999 56777666544
No 8
>PRK14547 rplD 50S ribosomal protein L4; Provisional
Probab=100.00 E-value=9.2e-35 Score=271.84 Aligned_cols=145 Identities=25% Similarity=0.330 Sum_probs=129.3
Q ss_pred CceeEEecCCCCcccceeecc-ccccccCchhHHHHHHHHHHhcCCCCCCCCCCCccceeeeeeCCCcceeccccccCCC
Q psy13118 20 RPLITVYSEKNEPTGQTVTLP-SVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARIPRVRGGG 98 (286)
Q Consensus 20 m~~i~v~~~~~~~~g~~v~lp-~vf~~~ir~~lI~~~v~~~q~~gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~rqkG 98 (286)
|++++|||.+|+.+| +|+|| +||+.|+|.||||+++.+++.+.||+++ ++++++||+|+|||++ +|||
T Consensus 1 M~~~~v~~~~g~~~g-~ieL~~~vF~~~~r~dllh~vv~~q~a~~Rqgt~-----~tKtRaEV~G~GkKP~-----rQKG 69 (298)
T PRK14547 1 MATCDVLDWQGKKVG-SAELPLKVFDVETNIPLIHQVVVAQMAAARQGTH-----HTKTRAEVRGGGKKPW-----RQKG 69 (298)
T ss_pred CceeEEeccCCCCcc-eEECCHHHhCCCccHHHHHHHHHHHHHhhhcCCC-----CCCceeeccCCCCCcc-----CCCC
Confidence 679999999999998 69998 7999999999999999999999999987 5799999999999754 6999
Q ss_pred cccCCCCccccccccccccCCCchhhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccccccccccccccccccC
Q psy13118 99 THRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRVRG 178 (286)
Q Consensus 99 TgrArqGa~~~~~rgGr~ahpp~~~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s~~~~~~~~r~p~~~g 178 (286)
|||||+|++ |+|+|+|
T Consensus 70 TGrAR~Gs~----------------------------------------------------------------rsP~wrG 85 (298)
T PRK14547 70 TGRARQGSI----------------------------------------------------------------RAPQWRG 85 (298)
T ss_pred CcccCcCCc----------------------------------------------------------------cCCceeC
Confidence 999999999 7677666
Q ss_pred CCccccCccccCcccccceeeCCCCCCcccccccCHHHHHHHHHHHHHhccCchhhhccCccccCCCCcCEEEecCCC--
Q psy13118 179 GGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQ-- 256 (286)
Q Consensus 179 gGt~rAgqgA~aP~~rGG~~~~p~~~~r~~~~kvn~k~rr~A~~saia~~~~~~lV~~RGH~i~~v~~~~lvV~d~~~-- 256 (286)
| +++|||+| |+|++|||+|+|++||+|||+++. .+.+|+|+|+|.
T Consensus 86 G-----------------GvafGPkp-R~y~~klNKK~rrlAlrsALS~k~---------------~~~~liVVd~~~~~ 132 (298)
T PRK14547 86 G-----------------GTVHGPRP-REYNQRTPKKMRQAALRGALSDRA---------------RDNRLIVVESLQDG 132 (298)
T ss_pred C-----------------eeecCCCC-chhhhhcCHHHHHHHHHHHHHHHH---------------hcCCEEEEeCcccc
Confidence 4 45555566 999999999999999999999985 357789999994
Q ss_pred CcccHHHHHHHHHHCC
Q psy13118 257 EYKKTKQATIFLHRIK 272 (286)
Q Consensus 257 ~~~KTKe~~~~Lk~l~ 272 (286)
+.+|||+++++|+.|+
T Consensus 133 ~~~KTK~~~~~L~~l~ 148 (298)
T PRK14547 133 DPPSTKAVAQALSVME 148 (298)
T ss_pred CCcCHHHHHHHHHhcc
Confidence 6899999999999987
No 9
>CHL00147 rpl4 ribosomal protein L4; Validated
Probab=99.98 E-value=1.5e-32 Score=246.48 Aligned_cols=143 Identities=24% Similarity=0.331 Sum_probs=125.1
Q ss_pred ceeEEecCCCCc-ccceeecc-ccccccCchhHHHHHHHHHHhcCCCCCCCCCCCccceeeeeeCCCcceeccccccCCC
Q psy13118 21 PLITVYSEKNEP-TGQTVTLP-SVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARIPRVRGGG 98 (286)
Q Consensus 21 ~~i~v~~~~~~~-~g~~v~lp-~vf~~~ir~~lI~~~v~~~q~~gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~rqkG 98 (286)
++++|+|.+|+. +| +++|+ ++| .+.+.++||+++.+++++.||+++. +++++|++|+|||++ +|||
T Consensus 7 ~~~~v~~~~g~~~~~-~~~l~~~vf-~~~~~~ll~~~v~~~~a~~R~gt~~-----tKtR~eV~G~grKp~-----~QKG 74 (215)
T CHL00147 7 LNYPVIDLTGKEKSE-TIKLKLNVL-EKSGNYLLHRALVRQNNNQRQGTAS-----TKTRSEVRGGGRKPW-----KQKG 74 (215)
T ss_pred eeEEEEccCCCeecc-eEEeCHHHh-CCchHhHHHHHHHHHHHHHhhcccc-----cCccccccCCCCCCc-----ccCC
Confidence 479999999999 78 69998 699 5567999999999999999999774 799999999999865 6999
Q ss_pred cccCCCCccccccccccccCCCchhhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccccccccccccccccccC
Q psy13118 99 THRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRVRG 178 (286)
Q Consensus 99 TgrArqGa~~~~~rgGr~ahpp~~~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s~~~~~~~~r~p~~~g 178 (286)
|||||+|++ |+|+|+|
T Consensus 75 TGrAR~Gs~----------------------------------------------------------------rsP~~rg 90 (215)
T CHL00147 75 TGRARAGSN----------------------------------------------------------------RSPLWKG 90 (215)
T ss_pred CCccCCCCC----------------------------------------------------------------cCCcccC
Confidence 999999999 8888887
Q ss_pred CCccccCccccCcccccceeeCCCCCCcccccccCHHHHHHHHHHHHHhccCchhhhccCccccCCCCcCEEEecCCC--
Q psy13118 179 GGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQ-- 256 (286)
Q Consensus 179 gGt~rAgqgA~aP~~rGG~~~~p~~~~r~~~~kvn~k~rr~A~~saia~~~~~~lV~~RGH~i~~v~~~~lvV~d~~~-- 256 (286)
| |+.|+| +| |+|++|+|+|+|++||++||+++.. .|+|+|+++
T Consensus 91 G----------------G~afgP-~p-R~y~~klnKKvrrlAl~sALS~k~~-----------------~l~VVd~~~~~ 135 (215)
T CHL00147 91 G----------------GVIFGP-KP-KTYSNKLNKKERRLALRTLLYNKSN-----------------NITVVENFESS 135 (215)
T ss_pred C----------------EeecCC-CC-cchhhhcCHHHHHHHHHHHHHHhhC-----------------CeEEEcccccc
Confidence 6 566777 56 9999999999999999999999841 367777775
Q ss_pred -CcccHHHHHHHHHHCCCc
Q psy13118 257 -EYKKTKQATIFLHRIKAW 274 (286)
Q Consensus 257 -~~~KTKe~~~~Lk~l~~~ 274 (286)
+.+|||++.++|++++++
T Consensus 136 ~~~~KTK~~~~~L~~l~~~ 154 (215)
T CHL00147 136 ITNPKTKAFINLLKKLNIN 154 (215)
T ss_pred cCCCCHHHHHHHHHHcCCC
Confidence 359999999999999985
No 10
>PRK14907 rplD 50S ribosomal protein L4; Provisional
Probab=99.97 E-value=3.8e-31 Score=247.34 Aligned_cols=142 Identities=30% Similarity=0.334 Sum_probs=122.0
Q ss_pred ecCCCCcccceeecc-cccccc-CchhHHHHHHHHHHhcCCCCCCCCCCCccceeeeeeCCCcceeccccccCCCcccCC
Q psy13118 26 YSEKNEPTGQTVTLP-SVFKAP-IRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARIPRVRGGGTHRSG 103 (286)
Q Consensus 26 ~~~~~~~~g~~v~lp-~vf~~~-ir~~lI~~~v~~~q~~gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~rqkGTgrAr 103 (286)
+..++...-.+++|+ +||+.+ ++.++||+++.+++++.||+++. .++++|+.|+|+++| +||||||||
T Consensus 93 ~~~~~~~~~~~ieL~~~vF~~e~~~~~llh~~V~~q~A~~RqGT~~-----TKtRsEVsGggkKPw-----rQKGTGRAR 162 (295)
T PRK14907 93 FEASNKLFKNTSKLPKKLFASEKIYSQAIFDTILSERASRRQGTHK-----VKTRAEVSGTGKKPW-----RQKGTGRAR 162 (295)
T ss_pred hhhhcccccceEEeCHHHhCCCccchhHHHHHHHHHHHHhcccccc-----ccchhhccCCCCCCc-----ccCCCCccC
Confidence 334444444579997 699998 89999999999999999999874 799999999999865 699999999
Q ss_pred CCccccccccccccCCCchhhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccccccccccccccccccCCCccc
Q psy13118 104 QGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRVRGGGTHR 183 (286)
Q Consensus 104 qGa~~~~~rgGr~ahpp~~~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s~~~~~~~~r~p~~~ggGt~r 183 (286)
||++ |+|+|+||
T Consensus 163 ~GS~----------------------------------------------------------------RSP~wrGG---- 174 (295)
T PRK14907 163 AGST----------------------------------------------------------------RSPIFVGG---- 174 (295)
T ss_pred CCCC----------------------------------------------------------------cCCcccCC----
Confidence 9999 98888886
Q ss_pred cCccccCcccccceeeCCCCCCcccccccCHHHHHHHHHHHHHhccCchhhhccCccccCCCCcCEEEecCCC-CcccHH
Q psy13118 184 SGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQ-EYKKTK 262 (286)
Q Consensus 184 AgqgA~aP~~rGG~~~~p~~~~r~~~~kvn~k~rr~A~~saia~~~~~~lV~~RGH~i~~v~~~~lvV~d~~~-~~~KTK 262 (286)
|++|+| +|+|+|+++||+|+|++||+|||++++. + .|+|+|+|. +.+|||
T Consensus 175 ------------GvaFGP-kP~RdY~~KLNKKvRrLALrsALS~ka~---------------~-~LvVVd~~~le~~KTK 225 (295)
T PRK14907 175 ------------GRAFGP-TPERNYKLKVNKKVRFNAFVSALTLLAN---------------S-KAVLVDDFKLEKISTK 225 (295)
T ss_pred ------------eeecCC-CCccchhhhcCHHHHHHHHHHHHHHhcc---------------C-CEEEEecccCCCCCHH
Confidence 577777 6779999999999999999999999863 3 377888875 468999
Q ss_pred HHHHHHHHCCCc
Q psy13118 263 QATIFLHRIKAW 274 (286)
Q Consensus 263 e~~~~Lk~l~~~ 274 (286)
+++++|++||++
T Consensus 226 ~l~~~L~~lgl~ 237 (295)
T PRK14907 226 DLIKKLTKLKIN 237 (295)
T ss_pred HHHHHHHHcCcc
Confidence 999999999985
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=99.97 E-value=3.5e-31 Score=232.92 Aligned_cols=131 Identities=34% Similarity=0.437 Sum_probs=113.6
Q ss_pred eec-cccccccCchhHHHHHHHHHHhcCCCCCCCCCCCccceeeeeeCCCcceeccccccCCCcccCCCCcccccccccc
Q psy13118 37 VTL-PSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGR 115 (286)
Q Consensus 37 v~l-p~vf~~~ir~~lI~~~v~~~q~~gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~rqkGTgrArqGa~~~~~rgGr 115 (286)
|+| |+||+.|+|+|+||+++.+++.+.||+++. +++++|++|+|+|++ +||||||||+|+.
T Consensus 1 i~L~~~vF~~~~r~~llh~~v~~~~~~~Rqgt~~-----tktr~ev~g~grKp~-----~QKGTGrAR~Gs~-------- 62 (192)
T PF00573_consen 1 IELSPDVFNVPVRPDLLHRAVVWQLANRRQGTAS-----TKTRSEVSGSGRKPW-----PQKGTGRARQGSI-------- 62 (192)
T ss_dssp -ES-CGGGGSSTSHHHHHHHHHHHHHHTSSBT-S-----SSTSTTSSSSSSSSS-----SSSSSSSSSSSSC--------
T ss_pred CCCCHHHhCCCCcHHHHHHHHHHHHHhccCCccC-----CccceEEecccCccc-----CCCCCcccccCcc--------
Confidence 689 689999999999999999999999999875 578999999999854 6999999999999
Q ss_pred ccCCCchhhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccccccccccccccccccCCCccccCccccCccccc
Q psy13118 116 MFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRA 195 (286)
Q Consensus 116 ~ahpp~~~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s~~~~~~~~r~p~~~ggGt~rAgqgA~aP~~rG 195 (286)
++|+| +|
T Consensus 63 --------------------------------------------------------rsP~~-----------------rg 69 (192)
T PF00573_consen 63 --------------------------------------------------------RSPQW-----------------RG 69 (192)
T ss_dssp --------------------------------------------------------TSTTS-----------------TT
T ss_pred --------------------------------------------------------cccee-----------------ec
Confidence 65555 55
Q ss_pred ceeeCCCCCCcccccccCHHHHHHHHHHHHHhccCchhhhccCccccCCCCcCEEEecCCC--CcccHHHHHHHHHHCCC
Q psy13118 196 GRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQ--EYKKTKQATIFLHRIKA 273 (286)
Q Consensus 196 G~~~~p~~~~r~~~~kvn~k~rr~A~~saia~~~~~~lV~~RGH~i~~v~~~~lvV~d~~~--~~~KTKe~~~~Lk~l~~ 273 (286)
|+++|||+|||+|+++||+|+|++||++||++++. +..|+|+|+|+ +.+|||++.++|+++++
T Consensus 70 Gg~afgPkp~r~~~~klnkK~r~lAl~~aLs~k~~---------------~~~l~vvd~~~~~~~~kTk~~~~~L~~~~~ 134 (192)
T PF00573_consen 70 GGVAFGPKPPRDYSYKLNKKVRRLALRSALSAKAA---------------EGNLIVVDNFSPLEEPKTKDLVKLLKKLGL 134 (192)
T ss_dssp SSBSSSSSSTSBCSHHHHHHHHHHHHHHHHHHHHH---------------TTHHHHCTSCSSSSSSSHHHHHHHHHHTTT
T ss_pred cEEecCCcccccceecCChHHHHHHHHHHHHHhhc---------------ccceEEeeccccccccCHHHHHHHHHHhhh
Confidence 56777778899999999999999999999999974 34467778886 47999999999999998
No 12
>PLN00185 60S ribosomal protein L4-1; Provisional
Probab=99.90 E-value=8.9e-25 Score=211.54 Aligned_cols=118 Identities=47% Similarity=0.767 Sum_probs=107.5
Q ss_pred CchhHHHHHHHHHHhcCCCCCCCCCCCccceeeeeeCCCcceeccccccCCCcccCCCCccccccccccccCCCchhhhh
Q psy13118 47 IRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRW 126 (286)
Q Consensus 47 ir~~lI~~~v~~~q~~gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~rqkGTgrArqGa~~~~~rgGr~ahpp~~~k~~ 126 (286)
|+..+....-..+|+++.+|+||..+.+.. |+-+.+..| +||+++. ||||||||++.+||+||++++|+.+||+|
T Consensus 41 v~~v~~~~~~n~RQp~~~~~~AG~qtsAes-wGtGR~vaR-iPR~kgg---GT~RAgqGa~~~~~rGGr~FgP~p~~R~~ 115 (405)
T PLN00185 41 VNFVHTNISKNSRQPYAVSKKAGHQTSAES-WGTGRAVSR-IPRVPGG---GTHRAGQGAFGNMCRGGRMFAPTKTWRRW 115 (405)
T ss_pred HHHHHHHHHHhccCCCCCCcccCCcceeee-cCCCCCcee-cccccCC---CCCcCCccCcCCcCCCCeeCCCCCCcccc
Confidence 588999999999999999999996666643 666677778 9999988 99999999999999999999999999999
Q ss_pred hhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccc------------ccccccc
Q psy13118 127 HRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAE------------SWGTGRA 169 (286)
Q Consensus 127 ~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~------------s~~~~~~ 169 (286)
|+|||+|||++|++|||||++.|+||++|||+|++- +..+||+
T Consensus 116 ~~KvNkK~rRlAl~SALAa~a~~~lV~arGH~i~~v~e~pLVV~d~~e~~~KTK~ 170 (405)
T PLN00185 116 HRKVNVNQKRYAVVSALAASAVPSLVMARGHKIENVPEVPLVVSDSAESIEKTSA 170 (405)
T ss_pred ccccCHHHHHHHHHHHHHhhccchhhhcccccccccccCCEEEEeCccCCcCHHH
Confidence 999999999999999999999999999999999442 6778888
No 13
>KOG1475|consensus
Probab=99.90 E-value=7e-25 Score=206.48 Aligned_cols=96 Identities=58% Similarity=0.974 Sum_probs=86.8
Q ss_pred CCCCCCCCCCCccceeeeeeCCCcceeccccccCCCcccCCCCccccccccccccCCCchhhhhhhhhhhhhHHHHHHHH
Q psy13118 63 HRQPYAVSKDAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSA 142 (286)
Q Consensus 63 gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~rqkGTgrArqGa~~~~~rgGr~ahpp~~~k~~~~kiN~ker~~A~~sA 142 (286)
|.|-.|-||++|+-.. | +|||++- ||+|++||+|.||||||||+||+++|++||+++|.+||+||+.||
T Consensus 58 G~QtSAESWGTGRAva-------R-iPRV~GG---GT~RsGQgAFgNmCR~GrMfaPtKt~RrW~rkVn~n~Kr~A~asa 126 (363)
T KOG1475|consen 58 GHQTSAESWGTGRAVA-------R-IPRVGGG---GTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRKVNENEKRYAIASA 126 (363)
T ss_pred ccccchhhccccccee-------c-ccccCCC---CcccccchhhhhhcccccccCchhhHHHHhhhhhhhhhhhHHHhh
Confidence 4555555777776544 7 9999994 899999999999999999999999999999999999999999999
Q ss_pred HhhccChhHHhhcCCccccc------------ccccccc
Q psy13118 143 IAASSVPALVMSKGHQTSAE------------SWGTGRA 169 (286)
Q Consensus 143 iAata~~~lV~~RGH~~~~~------------s~~~~~~ 169 (286)
||||+.|.||++|||+|++- |+.+||+
T Consensus 127 iaasavpaLv~arGHrIe~VpelPlVVsd~ve~~~KTke 165 (363)
T KOG1475|consen 127 IAASAVPALVMARGHRIEEVPELPLVVSDKVESFRKTKE 165 (363)
T ss_pred hhhhhhhHHHHhcCccccccccCceEeehhhHHHHhHHH
Confidence 99999999999999999985 7888887
No 14
>KOG1624|consensus
Probab=99.88 E-value=1.3e-22 Score=189.01 Aligned_cols=148 Identities=28% Similarity=0.293 Sum_probs=126.2
Q ss_pred EEecCCCCcccceeecc-ccccccCchhHHHHHHHHHHhcCCCCCCCCCCCccceeeeeeCCCcceeccccccCCCcccC
Q psy13118 24 TVYSEKNEPTGQTVTLP-SVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARIPRVRGGGTHRS 102 (286)
Q Consensus 24 ~v~~~~~~~~g~~v~lp-~vf~~~ir~~lI~~~v~~~q~~gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~rqkGTgrA 102 (286)
.+-+.++|++| -+.|| ++|.+++|.|+||+++.++..|+|+++|. +++++|+.|+|||++ +|||||||
T Consensus 57 ~~~~~e~E~~g-l~~l~~dvf~~~~RrDIlhrav~wq~~nrrvgtas-----tktRaEv~ggGrKp~-----~QKgtGrA 125 (290)
T KOG1624|consen 57 PLDFFELEKVG-LVDLHPDVFAEPPRRDILHRAVVWQLDNRRVGTAS-----TKTRAEVRGGGRKPW-----PQKGTGRA 125 (290)
T ss_pred eccccccccce-eeecChhhhccchHHHHHHHHHHHhhccccccccc-----CCccccccCCCCCcC-----cccCCCcc
Confidence 34457899999 59996 89999999999999999999999999875 699999999999865 69999999
Q ss_pred CCCccccccccccccCCCchhhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccccccccccccccccccCCCcc
Q psy13118 103 GQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRVRGGGTH 182 (286)
Q Consensus 103 rqGa~~~~~rgGr~ahpp~~~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s~~~~~~~~r~p~~~ggGt~ 182 (286)
|+|+. |+|+++||
T Consensus 126 r~Gs~----------------------------------------------------------------rsP~r~gG--- 138 (290)
T KOG1624|consen 126 RVGSL----------------------------------------------------------------RSPQRRGG--- 138 (290)
T ss_pred cccCc----------------------------------------------------------------cCcccCCC---
Confidence 99999 88888876
Q ss_pred ccCccccCcccccceeeCCCCCCcccccccCHHHHHHHHHHHHHhccCchhhhccCccccCCCCcCEEEecCCC-CcccH
Q psy13118 183 RSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQ-EYKKT 261 (286)
Q Consensus 183 rAgqgA~aP~~rGG~~~~p~~~~r~~~~kvn~k~rr~A~~saia~~~~~~lV~~RGH~i~~v~~~~lvV~d~~~-~~~KT 261 (286)
|++++|+-| |+|..++|.|+|.+||+.||+++.. +..|+|.|++. ..+||
T Consensus 139 -------------g~~~gpr~P-~d~~~~Lp~kvr~lgl~~ALS~~~a---------------~~~l~I~d~~~L~t~~p 189 (290)
T KOG1624|consen 139 -------------GVAHGPRGP-RDYSYKLPSKVRSLGLKIALSAKLA---------------QDDLHIVDELGLPTGKP 189 (290)
T ss_pred -------------ccccCCCCC-cchhhhccHHHHHHHHHHHHHHHHh---------------CCceEEecccCCCCCCc
Confidence 678888545 9999999999999999999998853 45578888886 46899
Q ss_pred HHHHHHHHHCCCcchhH
Q psy13118 262 KQATIFLHRIKAWNDVL 278 (286)
Q Consensus 262 Ke~~~~Lk~l~~~~Dv~ 278 (286)
|-.+++++.-+...++.
T Consensus 190 k~~~~l~~~~~~g~~vl 206 (290)
T KOG1624|consen 190 KYLLNLLAQRNWGTSVL 206 (290)
T ss_pred HHHHHHHHHHhcCCeeE
Confidence 99999998765544443
No 15
>PTZ00428 60S ribosomal protein L4; Provisional
Probab=99.86 E-value=2.8e-22 Score=193.22 Aligned_cols=118 Identities=47% Similarity=0.797 Sum_probs=104.8
Q ss_pred CchhHHHHHHHHHHhcCCCCCCCCCCCccceeeeeeCCCcceeccccccCCCcccCCCCccccccccccccCCCchhhhh
Q psy13118 47 IRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRW 126 (286)
Q Consensus 47 ir~~lI~~~v~~~q~~gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~rqkGTgrArqGa~~~~~rgGr~ahpp~~~k~~ 126 (286)
++..+.+..-..+|++...+++|.. .+.+.|+-+.+..| +||+++ +||+||+||+|.|+|+||++++|+.+|++|
T Consensus 36 V~~vv~~~~aN~RQgta~s~~ag~~-tsakswGTGRA~ar-ipR~kg---~GT~Rs~qGa~~n~~rGG~~FgP~~~~R~~ 110 (381)
T PTZ00428 36 VQFVHTNMAKNRRQAYAVKPLAGMQ-HSAESWGTGRAVAR-IPRVSG---GGTHRSGQGAFGNMCRGGRMFAPTKTWRRW 110 (381)
T ss_pred HHHHHHHHHHhccCCCCcCCCCCCC-CCceecCCCCCccc-cccccC---CCCCcCcccccCCcCCCceEcCCCCCcccc
Confidence 5788889999999999999999863 44455666677778 999994 599999999999999999999999999999
Q ss_pred hhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccc------------ccccccc
Q psy13118 127 HRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAE------------SWGTGRA 169 (286)
Q Consensus 127 ~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~------------s~~~~~~ 169 (286)
|+|||+|||++|++||||+++.|+||++|||+|++. ++.+||+
T Consensus 111 ~~KvNkK~rR~Al~SALaa~a~~~lv~argh~i~~v~e~plVV~d~~e~~~KTK~ 165 (381)
T PTZ00428 111 HRKVNLNQKRHAVASALAASGVPALVMARGHRISNVPEVPLVVSDSVESYEKTKE 165 (381)
T ss_pred ccccCHHHHHHHHHHHHHhhccchhhhcccccccccccCCEEEEcCcCCCCCHHH
Confidence 999999999999999999999999999999999442 5578888
No 16
>COG0088 RplD Ribosomal protein L4 [Translation, ribosomal structure and biogenesis]
Probab=99.58 E-value=7.5e-16 Score=139.00 Aligned_cols=109 Identities=21% Similarity=0.225 Sum_probs=92.8
Q ss_pred cccCchhHHHHHHHHHHhcCCCCCCCCCCCccceeeeeeCCCcceeccccccCCCcccCCCCccccccccccccCCCchh
Q psy13118 44 KAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIW 123 (286)
Q Consensus 44 ~~~ir~~lI~~~v~~~q~~gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~rqkGTgrArqGa~~~~~rgGr~ahpp~~~ 123 (286)
..-|+..++.+....+|+++.++++| +-+.++.++.++|..+.|| +++ .|+ - +||||+++|||+++
T Consensus 30 ~dli~~av~a~~a~~RQgt~~~k~rg-----evs~~g~Kp~~QkgtgraR--~gs-~rs----P--~~rGGg~a~gPkp~ 95 (214)
T COG0088 30 EDLIHRAVLAQLANRRQGTHSTKTRG-----EVSGGGKKPWGQKGTGRAR--QGS-IRS----P--QWRGGGVAHGPKPE 95 (214)
T ss_pred HHHHHHHHHHHHHhhhccCCCCCCcc-----cccccCcCCCCCCcCCcCC--CCC-CCC----C--eeecCccccCCCCc
Confidence 36789999999999999999999986 4556667777777777674 433 333 2 47999999999999
Q ss_pred hhhhhhhhhhhHHHHHHHHHhhccCh-hHHhhcCCcccc-cccccccc
Q psy13118 124 RRWHRKVNVNQRRYAMVSAIAASSVP-ALVMSKGHQTSA-ESWGTGRA 169 (286)
Q Consensus 124 k~~~~kiN~ker~~A~~sAiAata~~-~lV~~RGH~~~~-~s~~~~~~ 169 (286)
+.|+.|||+|||++|+.||||++++. +||..+||.|++ .. ||+
T Consensus 96 r~~~~klnkK~rrlAl~sAls~ka~~~~lv~~~~~~~~~~~k---TK~ 140 (214)
T COG0088 96 RDYSQKLNKKERRLALRSALSAKARAGKLVVVRGHVFEDAPK---TKE 140 (214)
T ss_pred cchhhhcCHHHHHHHHHHHHHHhccCCCEEEEecccccCCcc---HHH
Confidence 99999999999999999999999999 999999999994 33 776
No 17
>PRK04042 rpl4lp 50S ribosomal protein L4P; Provisional
Probab=99.46 E-value=3.9e-14 Score=131.00 Aligned_cols=97 Identities=33% Similarity=0.451 Sum_probs=81.6
Q ss_pred cCchhHHHHHHHHHHhcCCCCCCCC------CCCcc---ceeeeeeCCCcceeccccccCCCcccCCCCccccccccccc
Q psy13118 46 PIRPDVVNFVHQNLSKNHRQPYAVS------KDAGH---QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRM 116 (286)
Q Consensus 46 ~ir~~lI~~~v~~~q~~gRqp~Ag~------~~~g~---kt~ae~~G~GRkv~RvP~~rqkGTgrArqGa~~~~~rgGr~ 116 (286)
-++..++++....+|..+-.|+|+. ++.|. +.+. ..|+|++ .|-| +||||++
T Consensus 30 lv~~vv~~~~an~Rqgt~~~~ta~tKtraev~G~Gr~~~Kp~r-QKGTGrA-rrsP-----------------~~rGGgv 90 (254)
T PRK04042 30 LIRRAVLAAQTARLQPKGRDPLAGKRTSAESWGSGRGIARVPR-LKGGSRA-AFVP-----------------QAVGGRR 90 (254)
T ss_pred HHHHHHHHHHHhccCCCCCCccccCccceeEcCCCCCcCcCCc-cCCCCCc-cccC-----------------ccCcCCe
Confidence 3688999999999999888888874 34444 3332 2478885 3555 4699999
Q ss_pred cCCCchhhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCcccc
Q psy13118 117 FAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSA 161 (286)
Q Consensus 117 ahpp~~~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~ 161 (286)
+|||++|++|+.|||+|||++|+.||||+++..+||++|||++++
T Consensus 91 ~fgPkp~R~y~~klnkK~rrlAlrsALs~k~~~~lv~~~~~~~~~ 135 (254)
T PRK04042 91 AHPPKVEKDLHEKINKKERRLAIRSAIAATANPELVKARGHVFEG 135 (254)
T ss_pred eCCCCCCcccccccCHHHHHHHHHHHHHHhhhhhhhhhcCccccC
Confidence 999999999999999999999999999999999999999999999
No 18
>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=99.44 E-value=5.7e-14 Score=129.74 Aligned_cols=97 Identities=33% Similarity=0.482 Sum_probs=82.4
Q ss_pred cCchhHHHHHHHHHHhcCCCCCCCC------CCCcc---ceeeeeeCCCcceeccccccCCCcccCCCCccccccccccc
Q psy13118 46 PIRPDVVNFVHQNLSKNHRQPYAVS------KDAGH---QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRM 116 (286)
Q Consensus 46 ~ir~~lI~~~v~~~q~~gRqp~Ag~------~~~g~---kt~ae~~G~GRkv~RvP~~rqkGTgrArqGa~~~~~rgGr~ 116 (286)
-++..++.+....+|.....|.|++ ++.|. +.+. ..|+|++ .|-|. ||||++
T Consensus 30 lv~~vv~~~~an~Rqgt~~~~~a~tKtraev~G~Grg~aKp~r-QKGTGrA-~rsP~-----------------~rGGGv 90 (251)
T TIGR03672 30 LIKRAVLAAQTNRLQPYGADPYAGKRTSAESWGSGRGIARVPR-IKGGSRA-ARVPQ-----------------AVGGRR 90 (251)
T ss_pred HHHHHHHHHHHhccCCCCCCcccCcccceeEccCCCCcCCCCc-cCCCCcc-eecCc-----------------cCcCCe
Confidence 4688899999999999988887773 44445 3222 3488886 66664 599999
Q ss_pred cCCCchhhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCcccc
Q psy13118 117 FAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSA 161 (286)
Q Consensus 117 ahpp~~~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~ 161 (286)
+|||++|++|+.|||+|||++|+.|||++++..+||.+|||+|+.
T Consensus 91 ~fgPkp~R~y~~klNkK~rrlAl~sALs~k~~~~lv~~~~~~~~~ 135 (251)
T TIGR03672 91 AHPPKVEKDLHEKINKKERRLAIRSAIAATADPELVKARGHVFEG 135 (251)
T ss_pred eCCCCCCcccceecCHHHHHHHHHHHHHHhcchhhhhhccccccc
Confidence 999999999999999999999999999999999999999999998
No 19
>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=98.87 E-value=1.9e-09 Score=95.54 Aligned_cols=110 Identities=20% Similarity=0.191 Sum_probs=82.1
Q ss_pred CchhHHHHHHHHHHhcCCCCCCC-CCCCccceeeeeeCCCcceeccccccCCCcccCCCCccccccccccccCCCchhhh
Q psy13118 47 IRPDVVNFVHQNLSKNHRQPYAV-SKDAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRR 125 (286)
Q Consensus 47 ir~~lI~~~v~~~q~~gRqp~Ag-~~~~g~kt~ae~~G~GRkv~RvP~~rqkGTgrArqGa~~~~~rgGr~ahpp~~~k~ 125 (286)
|+..++++.....|.....++-+ ..+.|.| .-.-.|+|++ |.++.+ +- +++||.++|||++++.
T Consensus 17 lh~~v~~~~~~~Rqgt~~tktr~ev~g~grK-p~~QKGTGrA--R~Gs~r----------sP--~~rgGg~afgPkp~r~ 81 (192)
T PF00573_consen 17 LHRAVVWQLANRRQGTASTKTRSEVSGSGRK-PWPQKGTGRA--RQGSIR----------SP--QWRGGGVAFGPKPPRD 81 (192)
T ss_dssp HHHHHHHHHHHTSSBT-SSSTSTTSSSSSSS-SSSSSSSSSS--SSSSCT----------ST--TSTTSSBSSSSSSTSB
T ss_pred HHHHHHHHHHhccCCccCCccceEEecccCc-ccCCCCCccc--ccCccc----------cc--eeeccEEecCCccccc
Confidence 68899999999999999888655 2222333 2233477774 544422 11 4699999999999999
Q ss_pred hhhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccccccccccccc
Q psy13118 126 WHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVAR 172 (286)
Q Consensus 126 ~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s~~~~~~~~r 172 (286)
|+.+||+|++++|++|||++.+..+.|.-.+ .|++..-.+||++..
T Consensus 82 ~~~klnkK~r~lAl~~aLs~k~~~~~l~vvd-~~~~~~~~kTk~~~~ 127 (192)
T PF00573_consen 82 YSYKLNKKVRRLALRSALSAKAAEGNLIVVD-NFSPLEEPKTKDLVK 127 (192)
T ss_dssp CSHHHHHHHHHHHHHHHHHHHHHTTHHHHCT-SCSSSSSSSHHHHHH
T ss_pred ceecCChHHHHHHHHHHHHHhhcccceEEee-ccccccccCHHHHHH
Confidence 9999999999999999999999999999998 444355667777433
No 20
>PRK05319 rplD 50S ribosomal protein L4; Provisional
Probab=98.52 E-value=5.8e-08 Score=87.11 Aligned_cols=103 Identities=20% Similarity=0.217 Sum_probs=71.6
Q ss_pred cCchhHHHHHHHHHHhc----CCCCCCCCCCCccceeeeeeCCCcceeccccccCCCcccCCCCccccccccccccCCCc
Q psy13118 46 PIRPDVVNFVHQNLSKN----HRQPYAVSKDAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTR 121 (286)
Q Consensus 46 ~ir~~lI~~~v~~~q~~----gRqp~Ag~~~~g~kt~ae~~G~GRkv~RvP~~rqkGTgrArqGa~~~~~rgGr~ahpp~ 121 (286)
-++..++++....+|.. .|...+| .|.|-+ .-.|+||+ | + |. .+.- ++|||.++|||+
T Consensus 31 ll~~~v~~~~~~~Rqgta~tk~r~ev~G---sgrK~~-~QKGTGrA--R-----~-Gs--~rsP----~~rGGg~afgpk 92 (205)
T PRK05319 31 LLHQVVVAQLANARQGTHATKTRSEVSG---GGKKPW-RQKGTGRA--R-----Q-GS--IRSP----QWRGGGVVFGPK 92 (205)
T ss_pred HHHHHHHHHHHhcccCcccCCcccccCC---CCCCCC-CCCCCCcc--C-----c-Cc--ccCC----cccCCeeeCCCC
Confidence 46888888888888877 4666554 354432 22367763 3 2 11 1222 259999999999
Q ss_pred hhhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccc--ccccccccc
Q psy13118 122 IWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAE--SWGTGRAVA 171 (286)
Q Consensus 122 ~~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~--s~~~~~~~~ 171 (286)
++ .|+.|||+|||++|++|||+++++..-| ..+++. +..+||++.
T Consensus 93 pr-~~~~klnkK~~~lAl~~aLs~k~~~~~l----~Vvd~~~~~~~KTk~~~ 139 (205)
T PRK05319 93 PR-DYSQKLNKKVRRLALRSALSEKAREGRL----VVVDDLSLEAPKTKELA 139 (205)
T ss_pred cc-chhhhcCHHHHHHHHHHHHHHHHhcCCe----EEEeccccCCCCHHHHH
Confidence 87 9999999999999999999999986433 344443 556777743
No 21
>PRK14547 rplD 50S ribosomal protein L4; Provisional
Probab=98.40 E-value=2.8e-07 Score=87.45 Aligned_cols=107 Identities=21% Similarity=0.243 Sum_probs=75.3
Q ss_pred cCchhHHHHHHHHHHhcCCCCCCC-CCCCccceeeeeeCCCcceeccccccCCCcccCCCCccccccccccccCCCchhh
Q psy13118 46 PIRPDVVNFVHQNLSKNHRQPYAV-SKDAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWR 124 (286)
Q Consensus 46 ~ir~~lI~~~v~~~q~~gRqp~Ag-~~~~g~kt~ae~~G~GRkv~RvP~~rqkGTgrArqGa~~~~~rgGr~ahpp~~~k 124 (286)
=|+..++.+.-..+|......+-+ .++.|+|-+. -.|+||+ |+ |+-|+ - ++|||.++|||++ |
T Consensus 32 llh~vv~~q~a~~Rqgt~~tKtRaEV~G~GkKP~r-QKGTGrA-------R~-Gs~rs--P----~wrGGGvafGPkp-R 95 (298)
T PRK14547 32 LIHQVVVAQMAAARQGTHHTKTRAEVRGGGKKPWR-QKGTGRA-------RQ-GSIRA--P----QWRGGGTVHGPRP-R 95 (298)
T ss_pred HHHHHHHHHHHhhhcCCCCCCceeeccCCCCCccC-CCCCccc-------Cc-CCccC--C----ceeCCeeecCCCC-c
Confidence 367889999999999888776655 6667777664 5677774 23 22221 1 2599999999997 9
Q ss_pred hhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccc---cccccccccc
Q psy13118 125 RWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAE---SWGTGRAVAR 172 (286)
Q Consensus 125 ~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~---s~~~~~~~~r 172 (286)
.|+.|||+|+|++|++|||++...-.-+ ..+++. +..+||++..
T Consensus 96 ~y~~klNKK~rrlAlrsALS~k~~~~~l----iVVd~~~~~~~~KTK~~~~ 142 (298)
T PRK14547 96 EYNQRTPKKMRQAALRGALSDRARDNRL----IVVESLQDGDPPSTKAVAQ 142 (298)
T ss_pred hhhhhcCHHHHHHHHHHHHHHHHhcCCE----EEEeCccccCCcCHHHHHH
Confidence 9999999999999999999987632111 223332 4567777443
No 22
>PRK14907 rplD 50S ribosomal protein L4; Provisional
Probab=98.19 E-value=1.6e-06 Score=82.50 Aligned_cols=108 Identities=21% Similarity=0.176 Sum_probs=74.3
Q ss_pred ccCchhHHHHHHHHHHhcCCCCCCC-CCCCccceeeeeeCCCcceeccccccCCCcccCCCCccccccccccccCCCchh
Q psy13118 45 APIRPDVVNFVHQNLSKNHRQPYAV-SKDAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIW 123 (286)
Q Consensus 45 ~~ir~~lI~~~v~~~q~~gRqp~Ag-~~~~g~kt~ae~~G~GRkv~RvP~~rqkGTgrArqGa~~~~~rgGr~ahpp~~~ 123 (286)
.-+...++++.-.++|-.....+-+ ..+.|.+-+ .--|+||+ |+ |+-|+-+ .|||.++|+|+++
T Consensus 119 ~llh~~V~~q~A~~RqGT~~TKtRsEVsGggkKPw-rQKGTGRA-------R~-GS~RSP~------wrGGGvaFGPkP~ 183 (295)
T PRK14907 119 QAIFDTILSERASRRQGTHKVKTRAEVSGTGKKPW-RQKGTGRA-------RA-GSTRSPI------FVGGGRAFGPTPE 183 (295)
T ss_pred hHHHHHHHHHHHHhccccccccchhhccCCCCCCc-ccCCCCcc-------CC-CCCcCCc------ccCCeeecCCCCc
Confidence 3467788888877777666555443 334455533 23588884 23 3333332 3999999999999
Q ss_pred hhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCccccccc--cccccccc
Q psy13118 124 RRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESW--GTGRAVAR 172 (286)
Q Consensus 124 k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s~--~~~~~~~r 172 (286)
+.|+.+||+|+|++|++|||++.+.-+|| .+++..+ .+||++..
T Consensus 184 RdY~~KLNKKvRrLALrsALS~ka~~~Lv-----VVd~~~le~~KTK~l~~ 229 (295)
T PRK14907 184 RNYKLKVNKKVRFNAFVSALTLLANSKAV-----LVDDFKLEKISTKDLIK 229 (295)
T ss_pred cchhhhcCHHHHHHHHHHHHHHhccCCEE-----EEecccCCCCCHHHHHH
Confidence 99999999999999999999998876666 5554322 25666443
No 23
>CHL00147 rpl4 ribosomal protein L4; Validated
Probab=97.89 E-value=1.6e-05 Score=72.40 Aligned_cols=107 Identities=18% Similarity=0.211 Sum_probs=73.8
Q ss_pred cccCchhHHHHHHHHHHhcCCCCCCC-CCCCccceeeeeeCCCcceeccccccCCCcccCCCCccccccccccccCCCch
Q psy13118 44 KAPIRPDVVNFVHQNLSKNHRQPYAV-SKDAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRI 122 (286)
Q Consensus 44 ~~~ir~~lI~~~v~~~q~~gRqp~Ag-~~~~g~kt~ae~~G~GRkv~RvP~~rqkGTgrArqGa~~~~~rgGr~ahpp~~ 122 (286)
..-+...++++.-..+|-.....+-+ ..+.|.|-+ .--|+||+ | + |+-|+-+ .|||..+|+|++
T Consensus 35 ~~ll~~~v~~~~a~~R~gt~~tKtR~eV~G~grKp~-~QKGTGrA--R-----~-Gs~rsP~------~rgGG~afgP~p 99 (215)
T CHL00147 35 NYLLHRALVRQNNNQRQGTASTKTRSEVRGGGRKPW-KQKGTGRA--R-----A-GSNRSPL------WKGGGVIFGPKP 99 (215)
T ss_pred HhHHHHHHHHHHHHHhhcccccCccccccCCCCCCc-ccCCCCcc--C-----C-CCCcCCc------ccCCEeecCCCC
Confidence 44567888888888887766555544 334455533 33588884 2 2 2222222 399999999997
Q ss_pred hhhhhhhhhhhhHHHHHHHHHhhccChhHHhhcCCcccccc--c--cccccccc
Q psy13118 123 WRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAES--W--GTGRAVAR 172 (286)
Q Consensus 123 ~k~~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s--~--~~~~~~~r 172 (286)
+.|+.+||+|+|++|++|||++.+. + =+.+++.+ + .+||++..
T Consensus 100 -R~y~~klnKKvrrlAl~sALS~k~~-~-----l~VVd~~~~~~~~~KTK~~~~ 146 (215)
T CHL00147 100 -KTYSNKLNKKERRLALRTLLYNKSN-N-----ITVVENFESSITNPKTKAFIN 146 (215)
T ss_pred -cchhhhcCHHHHHHHHHHHHHHhhC-C-----eEEEcccccccCCCCHHHHHH
Confidence 9999999999999999999999865 2 25666655 5 56676443
No 24
>KOG1624|consensus
Probab=93.00 E-value=0.13 Score=49.35 Aligned_cols=98 Identities=22% Similarity=0.240 Sum_probs=65.2
Q ss_pred CchhHHHHHHHHHHhcCCCCCCC-CCCCccceeeeeeCCCcceeccccccCCCcccCCCCccccccccccccCCCchhhh
Q psy13118 47 IRPDVVNFVHQNLSKNHRQPYAV-SKDAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRR 125 (286)
Q Consensus 47 ir~~lI~~~v~~~q~~gRqp~Ag-~~~~g~kt~ae~~G~GRkv~RvP~~rqkGTgrArqGa~~~~~rgGr~ahpp~~~k~ 125 (286)
+.+.++++.-..++...-.++-+ .++.|.|-+.. .|+||+ |+ |+-|+ =-+ +||..+|.|+.-+.
T Consensus 85 lhrav~wq~~nrrvgtastktRaEv~ggGrKp~~Q-KgtGrA--r~------Gs~rs--P~r----~gGg~~~gpr~P~d 149 (290)
T KOG1624|consen 85 LHRAVVWQLDNRRVGTASTKTRAEVRGGGRKPWPQ-KGTGRA--RV------GSLRS--PQR----RGGGVAHGPRGPRD 149 (290)
T ss_pred HHHHHHHhhcccccccccCCccccccCCCCCcCcc-cCCCcc--cc------cCccC--ccc----CCCccccCCCCCcc
Confidence 47888888887777665544433 44455554432 377773 22 22122 123 78999999999999
Q ss_pred hhhhhhhhhHHHHHHHHHhhccChhHHhhcCCcccccc
Q psy13118 126 WHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAES 163 (286)
Q Consensus 126 ~~~kiN~ker~~A~~sAiAata~~~lV~~RGH~~~~~s 163 (286)
|.=++|.|+|.+|++.|+.+- +-+.-=|.+++.-
T Consensus 150 ~~~~Lp~kvr~lgl~~ALS~~----~a~~~l~I~d~~~ 183 (290)
T KOG1624|consen 150 YSYKLPSKVRSLGLKIALSAK----LAQDDLHIVDELG 183 (290)
T ss_pred hhhhccHHHHHHHHHHHHHHH----HhCCceEEecccC
Confidence 999999999999999999843 2233335565553
No 25
>PRK11595 DNA utilization protein GntX; Provisional
Probab=21.14 E-value=1.8e+02 Score=26.23 Aligned_cols=52 Identities=13% Similarity=0.096 Sum_probs=35.2
Q ss_pred cccCHHHHHHHHHHHHHhccCchhhhccCccccCCCCcCEEEecCCCC-cccHHHHHHHHHHCCCc
Q psy13118 210 RKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQE-YKKTKQATIFLHRIKAW 274 (286)
Q Consensus 210 ~kvn~k~rr~A~~saia~~~~~~lV~~RGH~i~~v~~~~lvV~d~~~~-~~KTKe~~~~Lk~l~~~ 274 (286)
..+++++|+.-+..++.... ++....++|+||+-. -....++.+.|++.|+.
T Consensus 164 ~~l~~~~R~~n~~~~f~~~~-------------~~~~~~vllvDDv~tTG~Tl~~~~~~L~~~g~~ 216 (227)
T PRK11595 164 HFLSARLRKRNLKNAFRLEL-------------PVQGQHMAIVDDVVTTGSTVAEIAQLLLRNGAA 216 (227)
T ss_pred ccCCHHHHhhhhhhhhccCC-------------CCCCCEEEEEeeeecchHHHHHHHHHHHHcCCc
Confidence 45688999888887775432 122345677777754 46667888888888754
No 26
>PF13514 AAA_27: AAA domain
Probab=20.16 E-value=1.1e+02 Score=33.84 Aligned_cols=48 Identities=17% Similarity=0.243 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHhccCchhhhccCccccCCCCcCEEEecCCC--CcccHHHHHHHHHHCC
Q psy13118 214 VNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQ--EYKKTKQATIFLHRIK 272 (286)
Q Consensus 214 ~k~rr~A~~saia~~~~~~lV~~RGH~i~~v~~~~lvV~d~~~--~~~KTKe~~~~Lk~l~ 272 (286)
+-|--+||+-|++.... .....+|||++|-|. +...++.++++|..|.
T Consensus 1031 ~dQLYLALRLA~~e~~~-----------~~~~~lP~IlDD~fvnfDd~R~~~~l~~L~~ls 1080 (1111)
T PF13514_consen 1031 RDQLYLALRLALAELLA-----------EQGEPLPFILDDIFVNFDDERARAALELLAELS 1080 (1111)
T ss_pred HHHHHHHHHHHHHHHHH-----------hCCCCCcEEeeCCccccCHHHHHHHHHHHHHhc
Confidence 35666888888877641 223479999988885 3589999999999875
Done!