Query 025111
Match_columns 257
No_of_seqs 234 out of 925
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 02:46:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025111.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025111hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00069 60S ribosomal protein 100.0 2E-104 5E-109 725.6 24.8 255 1-255 1-298 (300)
2 KOG0875 60S ribosomal protein 100.0 3.4E-77 7.4E-82 535.4 15.5 223 1-252 1-263 (264)
3 PRK08569 rpl18p 50S ribosomal 100.0 1.8E-70 3.9E-75 479.6 16.1 177 11-211 2-192 (193)
4 PF14204 Ribosomal_L18_c: Ribo 100.0 7.9E-38 1.7E-42 246.8 -0.5 93 152-244 1-94 (94)
5 COG0256 RplR Ribosomal protein 100.0 9.3E-35 2E-39 239.7 7.7 113 14-133 1-125 (125)
6 PF00861 Ribosomal_L18p: Ribos 99.9 3.5E-28 7.6E-33 198.4 7.1 106 20-133 2-119 (119)
7 PRK05593 rplR 50S ribosomal pr 99.9 5.7E-26 1.2E-30 185.7 8.6 97 28-133 8-117 (117)
8 CHL00139 rpl18 ribosomal prote 99.9 1.9E-26 4.1E-31 186.5 5.7 94 32-132 3-108 (109)
9 TIGR00060 L18_bact ribosomal p 99.9 2.1E-25 4.5E-30 181.8 8.8 94 29-133 7-114 (114)
10 cd00432 Ribosomal_L18_L5e Ribo 99.9 5E-23 1.1E-27 163.3 7.9 83 46-131 9-103 (103)
11 PTZ00032 60S ribosomal protein 99.9 6.1E-22 1.3E-26 174.7 6.9 88 37-132 99-210 (211)
12 KOG3333 Mitochondrial/chloropl 96.7 0.0044 9.5E-08 54.0 6.0 81 49-133 61-154 (188)
13 PTZ00090 40S ribosomal protein 96.0 0.027 5.8E-07 51.4 7.6 83 46-133 116-208 (233)
14 PRK05309 30S ribosomal protein 94.4 0.24 5.3E-06 41.3 8.1 90 47-142 16-124 (128)
15 TIGR03632 bact_S11 30S ribosom 94.4 0.19 4.2E-06 40.6 7.2 85 51-141 3-106 (108)
16 PF00411 Ribosomal_S11: Riboso 94.2 0.17 3.7E-06 40.9 6.6 86 51-142 3-107 (110)
17 CHL00041 rps11 ribosomal prote 94.0 0.23 5E-06 40.7 6.9 87 41-133 6-102 (116)
18 PRK09607 rps11p 30S ribosomal 93.3 0.45 9.8E-06 40.2 7.7 88 50-142 11-125 (132)
19 PTZ00129 40S ribosomal protein 92.3 0.51 1.1E-05 40.7 6.8 86 50-142 30-144 (149)
20 TIGR03628 arch_S11P archaeal r 86.5 2.7 5.8E-05 34.7 6.4 62 51-117 5-66 (114)
21 COG0100 RpsK Ribosomal protein 81.6 5.4 0.00012 33.7 6.4 86 51-142 21-125 (129)
22 KOG0408 Mitochondrial/chloropl 72.5 14 0.00031 32.8 6.6 80 48-133 79-168 (190)
23 PF14821 Thr_synth_N: Threonin 44.2 28 0.0006 26.4 3.1 56 126-203 23-78 (79)
24 PF08673 RsbU_N: Phosphoserine 35.3 70 0.0015 24.5 4.1 41 170-210 11-54 (77)
25 cd04518 TBP_archaea archaeal T 34.4 2.1E+02 0.0046 25.0 7.5 58 42-117 29-87 (174)
26 COG2101 SPT15 TATA-box binding 33.2 2E+02 0.0043 25.9 7.1 84 42-143 35-138 (185)
27 PF13069 DUF3933: Protein of u 32.4 12 0.00026 26.7 -0.5 15 58-76 3-17 (53)
28 PF13907 DUF4208: Domain of un 31.5 50 0.0011 26.1 2.9 44 159-202 54-99 (100)
29 PRK14083 HSP90 family protein; 29.2 27 0.00059 36.2 1.3 49 158-208 319-370 (601)
30 PF08218 Citrate_ly_lig: Citra 28.9 1.2E+02 0.0027 27.1 5.1 72 30-122 43-115 (182)
31 PF06292 DUF1041: Domain of Un 27.1 25 0.00055 28.6 0.5 40 162-201 53-96 (106)
32 PRK05218 heat shock protein 90 26.6 51 0.0011 34.1 2.7 48 158-207 339-389 (613)
33 PF00452 Bcl-2: Apoptosis regu 24.2 1.2E+02 0.0027 23.0 3.9 37 175-211 8-46 (101)
34 TIGR01795 CM_mono_cladeE monof 21.1 1.4E+02 0.003 23.5 3.6 33 174-206 45-81 (94)
35 PRK14102 nifW nitrogenase stab 20.4 1.1E+02 0.0025 25.0 3.1 30 181-210 39-74 (105)
No 1
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=100.00 E-value=2.4e-104 Score=725.59 Aligned_cols=255 Identities=62% Similarity=0.983 Sum_probs=244.8
Q ss_pred CcceeeecCccccccccccchhhccCchhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEec
Q 025111 1 MAFVKAQKSKAYFKRFQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDIIAQIVSANIVGDSVLAAAYA 80 (257)
Q Consensus 1 m~fvk~~kn~ay~~ryqvk~rRRregkTdY~~R~rli~~~knkyns~kpRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS 80 (257)
|+||||+||+|||+||||||||||||||||++|++||.||+||||||+||||||+||++||||||.+.++||+|||||+|
T Consensus 1 M~fvKv~KnkaY~~ryqvkfRRRREGKTdY~~R~rLi~q~knKynspK~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S 80 (300)
T PTZ00069 1 MAFVKVVKNKAYFKRFQVKYRRRREGKTDYYARRRLILQDKNKYNSPKYRLVVRITNKDIICQIVYATIVGDKVLAAAYS 80 (300)
T ss_pred CCceeeeecccccccccchhhhhhcccccHHHHHHHHHccccccCCCCceEEEEEECCcEEEEEEEeecCCCEEEEEeeh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccccCCccHHHHHHHHHHHHHHHHHhcCCCccccccc-------------------------------------
Q 025111 81 HELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYEGNV------------------------------------- 123 (257)
Q Consensus 81 ~el~k~g~k~~~~N~~AAy~tG~LlA~ral~k~Gl~~~YhG~v------------------------------------- 123 (257)
+||++|||++|++|++||||||+|+|+|+|+++||++.|.|..
T Consensus 81 ~eL~kyG~k~gl~N~~AAY~TGlL~arR~L~kl~ld~~y~G~~e~~g~~y~v~e~~~~~~rpf~a~LDiGL~rtt~G~RV 160 (300)
T PTZ00069 81 HELPRFGIPVGLTNYAAAYATGLLLARRLLKKLGLDKQFEGVKEADGEYYHVDEEDDEERRPFKAILDVGLARTTTGNRV 160 (300)
T ss_pred hhHhhcCcCCCCccHHHHHHHHHHHHHHHHHhhcccccccCcccccCcccccccccccCCCCceEEEeeccccCCCCcee
Confidence 9999999999999999999999999999999999999999872
Q ss_pred ----cccccccccccCCCCccCCcCCCCCCCCHHhhhcccccccHHHHHHhhcccChHHHHhhHHHHHHcCCCcchHHHH
Q 025111 124 ----EGALDGGLDIPHSDKRFAGFSKDGKQLDAEVHRKYIYGGHVAAYMSTLMEDEPEKYQSHFTEYIKKGIDADGLEAL 199 (257)
Q Consensus 124 ----kGArD~GL~IPhs~~~fp~~~~~~k~~~ae~~~~rI~G~hVa~Ym~~L~eed~e~ykkqFS~yik~gi~p~~~e~~ 199 (257)
+||+||||+||||+++|||||.++++||||+|++||+|+|||+||+.|+|||||+|++|||+||++||+||+||+|
T Consensus 161 FaalKGa~DgGl~IPhs~~rfpg~d~e~~~~dAe~hR~rI~G~HVa~Ym~~Lkeedee~yk~qFS~yik~gl~~d~le~~ 240 (300)
T PTZ00069 161 FGALKGAVDGGLHIPHSPNRFPGYSKEKDSYDAEVHRDRIFGKHVAEYMKQLKEEDPDKYKKQFSKYIKAGVGPDSLEDM 240 (300)
T ss_pred eeehhcccccCcccCCCCCcCCCCCccccccChHHHHhhhcchhHHHHHHHhhhhChHHHHHHHHHHHHcCCChhHHHHH
Confidence 1999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCCCCCCCCc--ccccccCCCCCCHHHHHHHHHHHHHHHhhhhccc
Q 025111 200 YKKVHAAIRADPTMKKSEKPAP--KEHKRYNLKKLTYEERKAKLVERLNALNSAVDEE 255 (257)
Q Consensus 200 y~~~~~~I~~~P~~~k~~k~~~--~~~k~~~~~Klt~~qrk~rv~~K~~~~~~~~~~~ 255 (257)
|++||++|++||++++++++.+ ..+|+|+.+|||++||++||++|++++++.++++
T Consensus 241 y~~ah~~Ir~~P~~~~~~kk~~~~~~~Kr~~~~Klt~~qrk~rv~~k~a~~~~~~q~~ 298 (300)
T PTZ00069 241 YKKAHAAIRANPSKVKKKKKKKKKVVHKKYKTKKLTGKQRKARVKAKKAQRRERLQKK 298 (300)
T ss_pred HHHHHHHHHhCcCccCccccccccccccccccccCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999998876665542 4678999999999999999999999999877654
No 2
>KOG0875 consensus 60S ribosomal protein L5 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.4e-77 Score=535.42 Aligned_cols=223 Identities=68% Similarity=1.060 Sum_probs=215.3
Q ss_pred CcceeeecCccccccccccchhhccCchhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEec
Q 025111 1 MAFVKAQKSKAYFKRFQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDIIAQIVSANIVGDSVLAAAYA 80 (257)
Q Consensus 1 m~fvk~~kn~ay~~ryqvk~rRRregkTdY~~R~rli~~~knkyns~kpRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS 80 (257)
|+|||++|+++||+||||+|||||||||||++|++|+.||+||||+|++||+|++||++|+|||+++.++||+++|+|+|
T Consensus 1 m~fvk~~k~~~y~kryqvk~rrrreGkTdy~arkrl~~qdknk~nt~kyR~ivr~~n~~iicqi~~~~i~gd~v~~~a~s 80 (264)
T KOG0875|consen 1 MGFVKVVKSKAYFKRYQVKFRRRREGKTDYYARKRLVVQDKNKYNTPKYRMIVRVINKDIICQIAYATIEGDVIVRAAYA 80 (264)
T ss_pred CcchheeccccccccccceEEEecCCCccHHHHHHHHhhcccccCCCceEEEEEEechhhHHHHHhheecceEEEEeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccccCCccHHHHHHHHHHHHHHHHHhcCCCcccccccc------------------------------------
Q 025111 81 HELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYEGNVE------------------------------------ 124 (257)
Q Consensus 81 ~el~k~g~k~~~~N~~AAy~tG~LlA~ral~k~Gl~~~YhG~vk------------------------------------ 124 (257)
+||++||++.|++|++||||||+|||+|+|+.+|||..|.|.++
T Consensus 81 ~elpkyg~~~GLtNyaAay~TglLLarR~l~~~gmD~~yeg~~e~~gde~~~e~idgq~~aFt~~Ld~GLaRtttg~kvF 160 (264)
T KOG0875|consen 81 HELPKYGVKVGLTNYAAAYCTGLLLACRLLKRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVF 160 (264)
T ss_pred ccccccccccccchhHHHHhhHHHHHHHHHHHhCcccccccceeecCcccccccccCCCCCeEEEecccccccCCCceee
Confidence 99999999999999999999999999999999999999998654
Q ss_pred ----ccccccccccCCCCccCCcCCCCCCCCHHhhhcccccccHHHHHHhhcccChHHHHhhHHHHHHcCCCcchHHHHH
Q 025111 125 ----GALDGGLDIPHSDKRFAGFSKDGKQLDAEVHRKYIYGGHVAAYMSTLMEDEPEKYQSHFTEYIKKGIDADGLEALY 200 (257)
Q Consensus 125 ----GArD~GL~IPhs~~~fp~~~~~~k~~~ae~~~~rI~G~hVa~Ym~~L~eed~e~ykkqFS~yik~gi~p~~~e~~y 200 (257)
||+||||.||||+++||| |.|+|||.|++|||.||+.|++||+|++||
T Consensus 161 GAlkga~dGGL~IPHs~krFpG----------------------------l~e~d~e~y~~~fs~~i~~g~~ad~i~~~y 212 (264)
T KOG0875|consen 161 GALKGAVDGGLSIPHSTKRFPG----------------------------LTEESEEKYKKEFSGYIAKGVEADSIEGMY 212 (264)
T ss_pred eeeehhcccceecCCccccCCC----------------------------ccccchhhhhHHHhhhhhccccHHHHHHHH
Confidence 899999999999999999 889999999999999999999999999999
Q ss_pred HHHHHHHhcCCCCCCCCCCCcccccccCCCCCCHHHHHHHHHHHHHHHhhhh
Q 025111 201 KKVHAAIRADPTMKKSEKPAPKEHKRYNLKKLTYEERKAKLVERLNALNSAV 252 (257)
Q Consensus 201 ~~~~~~I~~~P~~~k~~k~~~~~~k~~~~~Klt~~qrk~rv~~K~~~~~~~~ 252 (257)
++||++|++||+++++++ ..+.+|+|+.++||+|||++||+||+++|+.+.
T Consensus 213 ~~ahaaIra~p~~~k~~k-~~k~~k~~~~~klt~eerk~rv~~k~~~~~~~~ 263 (264)
T KOG0875|consen 213 KKAHAAIRADPSPKKTEK-AAKESKRYNAKKLTYEERKDQVAQKVAALLGAQ 263 (264)
T ss_pred HHHHHHhhcccCcccccc-ccccchhhccccCCHHHHHHHHHHHHHHhhccC
Confidence 999999999999998877 445789999999999999999999999988654
No 3
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=100.00 E-value=1.8e-70 Score=479.59 Aligned_cols=177 Identities=40% Similarity=0.669 Sum_probs=169.4
Q ss_pred cccccccccchhhccCchhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEeccccccccccc
Q 025111 11 AYFKRFQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEV 90 (257)
Q Consensus 11 ay~~ryqvk~rRRregkTdY~~R~rli~~~knkyns~kpRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~ 90 (257)
|.++||||||||||||||||++|++|+.++ +||||||+||+|||||||+++++||+|||||||+||+.+||.+
T Consensus 2 a~g~ry~v~~rRrRegkTdY~~R~rl~~~~-------kpRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~g~~~ 74 (193)
T PRK08569 2 ATGPRYKVPFRRRREGKTDYRKRLKLLLSG-------KPRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKYGWKG 74 (193)
T ss_pred CCCCccccceeccccccccHHHHHHHHhcC-------CCEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhccccC
Confidence 678999999999999999999999999988 6999999999999999997777899999999999999999999
Q ss_pred CCccHHHHHHHHHHHHHHHHHhcCCCc--------ccc--cccc----ccccccccccCCCCccCCcCCCCCCCCHHhhh
Q 025111 91 GLTNYAAAYCTGLLLARRVLKMLEMDD--------EYE--GNVE----GALDGGLDIPHSDKRFAGFSKDGKQLDAEVHR 156 (257)
Q Consensus 91 ~~~N~~AAy~tG~LlA~ral~k~Gl~~--------~Yh--G~vk----GArD~GL~IPhs~~~fp~~~~~~k~~~ae~~~ 156 (257)
+++|++|||+||+|||+|||++ ||.. .|| |+|+ ||||+||+||||+++|||+
T Consensus 75 ~~~N~~AAy~vG~llA~ral~k-Gi~~vvfDrGg~~yh~gGRV~A~akgArd~GL~fPh~~~~~p~~------------- 140 (193)
T PRK08569 75 DTGNTPAAYLTGLLAGKKALKA-GVEEAVLDIGLHRPTKGSRVFAALKGAIDAGLEIPHGEEVLPDE------------- 140 (193)
T ss_pred CCCCHHHHHHHHHHHHHHHHHC-CCCEEEEecCCccccCCccHHHHHHHHHHcCCcCCCCCCcCCCc-------------
Confidence 9999999999999999999997 9977 888 9995 9999999999999999996
Q ss_pred cccccccHHHHHHhhcccChHHHHhhHHHHHHcCCCcchHHHHHHHHHHHHhcCC
Q 025111 157 KYIYGGHVAAYMSTLMEDEPEKYQSHFTEYIKKGIDADGLEALYKKVHAAIRADP 211 (257)
Q Consensus 157 ~rI~G~hVa~Ym~~L~eed~e~ykkqFS~yik~gi~p~~~e~~y~~~~~~I~~~P 211 (257)
+||+|+|||+||+.|+||| |++|||+||++||+|++||+||++||++|++..
T Consensus 141 ~ri~G~Hia~y~~~l~~e~---y~~~Fs~y~~~g~~~~~l~~~~~~~~~~i~~~~ 192 (193)
T PRK08569 141 DRIRGEHIAEYAESLKEEN---YKKQFSKYLERGLDPEDLPEHFEEVKEKILEEY 192 (193)
T ss_pred cccccchHHHHHHHHhhhH---HHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhc
Confidence 7999999999999999988 999999999999999999999999999999763
No 4
>PF14204 Ribosomal_L18_c: Ribosomal L18 C-terminal region; PDB: 2ZKR_n 4A1E_M 4A1C_M 4A1A_M 4A17_M 3O58_E 1S1I_E 3IZS_Q 3O5H_E 3IZR_Q.
Probab=100.00 E-value=7.9e-38 Score=246.77 Aligned_cols=93 Identities=60% Similarity=0.963 Sum_probs=86.2
Q ss_pred HHhhhcccccccHHHHHHhhcccChHHHHhhHHHHHHcCCCcchHHHHHHHHHHHHhcCCCCCCCCCC-CcccccccCCC
Q 025111 152 AEVHRKYIYGGHVAAYMSTLMEDEPEKYQSHFTEYIKKGIDADGLEALYKKVHAAIRADPTMKKSEKP-APKEHKRYNLK 230 (257)
Q Consensus 152 ae~~~~rI~G~hVa~Ym~~L~eed~e~ykkqFS~yik~gi~p~~~e~~y~~~~~~I~~~P~~~k~~k~-~~~~~k~~~~~ 230 (257)
||+|++||+|+|||+||+.|+|||||+|++|||+||++||+||+||+||++||++||+||++.+++++ ++..+++|+.+
T Consensus 1 Ae~hr~rI~G~HVaeYm~~L~eed~e~yk~qFs~yik~gi~p~~le~~y~~~h~~Ir~dP~~~~k~~k~~~~~~k~~~~~ 80 (94)
T PF14204_consen 1 AEVHRDRIFGGHVAEYMEELKEEDPEKYKRQFSKYIKKGIEPDDLEEMYKKAHAAIREDPSPKKKEKKEYKAEKKRYKPK 80 (94)
T ss_dssp -HCHHHCSSSSHCHHHHHSCSSCSSSTCSHHHHHHHHHHCSSSHHHHHHHHHHHCCCHSCCCCCCSTSSS-CHHHHHSCC
T ss_pred ChHHHhCcCchhHHHHHHHHHhhCHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHHhCcccccccccccchhhcccCcc
Confidence 79999999999999999999999999999999999999999999999999999999999999888754 44467999999
Q ss_pred CCCHHHHHHHHHHH
Q 025111 231 KLTYEERKAKLVER 244 (257)
Q Consensus 231 Klt~~qrk~rv~~K 244 (257)
|||++||++||+||
T Consensus 81 Klt~~eRk~rv~~K 94 (94)
T PF14204_consen 81 KLTLEERKARVKQK 94 (94)
T ss_dssp CCCHHHHCCHSCCC
T ss_pred cCCHHHHHHHHhcC
Confidence 99999999999875
No 5
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.3e-35 Score=239.67 Aligned_cols=113 Identities=39% Similarity=0.644 Sum_probs=101.2
Q ss_pred ccccccchhhccCchhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCc
Q 025111 14 KRFQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLT 93 (257)
Q Consensus 14 ~ryqvk~rRRregkTdY~~R~rli~~~knkyns~kpRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~ 93 (257)
++|++++||++++||+|+.|.+|. ++ +++||||||+||+|||||||+|...||.+++|+.+.+|.++||+.+++
T Consensus 1 ~~~~~~~rr~~~~kr~~r~R~kl~--g~----~~rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~~~~~ 74 (125)
T COG0256 1 PRYKVKFRRRRRGKRAYRIRKKLL--GT----SGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGGGG 74 (125)
T ss_pred CccchhhHHHHHHhHHHHHHHhhc--cC----CCCcEEEEEEeCCcEEEEEEEcCCCceEEEEEcchHHHHhhcccCCCC
Confidence 589999999999999999999999 43 889999999999999999999987665555555555677799999999
Q ss_pred cHHHHHHHHHHHHHHHHHhcCCCc--------ccccccc----ccccccccc
Q 025111 94 NYAAAYCTGLLLARRVLKMLEMDD--------EYEGNVE----GALDGGLDI 133 (257)
Q Consensus 94 N~~AAy~tG~LlA~ral~k~Gl~~--------~YhG~vk----GArD~GL~I 133 (257)
|++|||+||+|+|+||+++ ||++ .|||+|. ||+|+||++
T Consensus 75 N~~aA~~vG~lia~ra~~k-gi~~vVfdr~g~~yhgRV~Ala~~AreaGL~f 125 (125)
T COG0256 75 NTEAAYLVGKLIAERALAK-GIEEVVFDRGGYKYHGRVAALADGAREAGLEF 125 (125)
T ss_pred CHHHHHHHHHHHHHHHHHc-CCcEEEEcCCCCCcchHHHHHHHHHHHcCcCC
Confidence 9999999999999999997 9977 9999994 999999985
No 6
>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 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 L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....
Probab=99.95 E-value=3.5e-28 Score=198.41 Aligned_cols=106 Identities=36% Similarity=0.475 Sum_probs=89.0
Q ss_pred chhhccCchhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCccHHHHH
Q 025111 20 YKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAY 99 (257)
Q Consensus 20 ~rRRregkTdY~~R~rli~~~knkyns~kpRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~N~~AAy 99 (257)
++++|+.|++|..|+.+.. +++|||+|++||+|||||||++...||.+.||+.+.+|+.+||+.+++|++|||
T Consensus 2 k~~~~~~r~~~~r~~~~~~-------~~~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~~l~~~~~~~~~~n~~aa~ 74 (119)
T PF00861_consen 2 KKRRRRRRKLRIRRKIKGT-------AERPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSKELKKYGWKGSTKNVEAAY 74 (119)
T ss_dssp SCHHHHHHHHHHHHHHHHT-------TSSEEEEEEEESSEEEEEEEECTTTEEEEEEEEETTTGGGTT-SSTTSSHHHHH
T ss_pred hhHHHHHHHHHHHHHHhcC-------CCCCEEEEEeccCeEEEEEEeeCCCCeEEEEEecchhhhhhhhccCCCCEehHH
Confidence 4566777777777776655 558999999999999999999987666666666677788899999999999999
Q ss_pred HHHHHHHHHHHHhcCCCc--------ccccccc----ccccccccc
Q 025111 100 CTGLLLARRVLKMLEMDD--------EYEGNVE----GALDGGLDI 133 (257)
Q Consensus 100 ~tG~LlA~ral~k~Gl~~--------~YhG~vk----GArD~GL~I 133 (257)
+||++||+||+++ ||.. .|||+|+ ||+|+||+|
T Consensus 75 ~vG~lla~ra~~~-gi~~v~fdr~~~~y~grv~a~~~~~re~Gl~f 119 (119)
T PF00861_consen 75 LVGELLAKRALEK-GIAKVVFDRGGYKYHGRVKALADGAREGGLEF 119 (119)
T ss_dssp HHHHHHHHHHHHT-TSSEEEECTSTSSSSSHHHHHHHHHHHTTCB-
T ss_pred HHHHHHHHHHHHc-CCcEEEEcCCCCcccHHHHHHHHHHHHcCCCC
Confidence 9999999999997 8865 9999985 999999986
No 7
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=99.93 E-value=5.7e-26 Score=185.70 Aligned_cols=97 Identities=30% Similarity=0.357 Sum_probs=86.6
Q ss_pred hhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEeccccc-ccccccCCccHHHHHHHHHHHH
Q 025111 28 TDYRARIRLINQDKNKYNTPKYRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELP-RYGLEVGLTNYAAAYCTGLLLA 106 (257)
Q Consensus 28 TdY~~R~rli~~~knkyns~kpRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~-k~g~k~~~~N~~AAy~tG~LlA 106 (257)
..++.|.|..+.|+ +.+|||+|++||+||||||||| +||.|||||||.|+. +++|+ ++|++|||+||.+||
T Consensus 8 ~~r~~r~r~ki~g~----~~rpRL~V~~SnkhiyAQvidd--~~~~tl~saST~e~~~k~~~~--~~n~~aa~~vG~~la 79 (117)
T PRK05593 8 LRRHRRVRKKISGT----AERPRLSVFRSNRHIYAQVIDD--VKGKTLASASTLEKDVRAGLK--GGNKEAAKKVGKLIA 79 (117)
T ss_pred HHHHHHHHHHhcCC----CCCCEEEEEEeCCeEEEEEEEC--CCCEEEEEEecCcHhHhcccc--CCCHHHHHHHHHHHH
Confidence 35667888888886 7899999999999999999988 488999999999998 57886 789999999999999
Q ss_pred HHHHHhcCCCc--------ccccccc----ccccccccc
Q 025111 107 RRVLKMLEMDD--------EYEGNVE----GALDGGLDI 133 (257)
Q Consensus 107 ~ral~k~Gl~~--------~YhG~vk----GArD~GL~I 133 (257)
+||+++ ||.. .|||+|+ ||||+||+.
T Consensus 80 ~ra~~~-gi~~vvfDrg~~~yhGrV~a~a~~are~Gl~f 117 (117)
T PRK05593 80 ERAKAK-GIKQVVFDRGGYKYHGRVKALADAAREAGLKF 117 (117)
T ss_pred HHHHHC-CCCEEEEcCCCCcccHHHHHHHHHHHHhCCCC
Confidence 999997 9976 9999985 999999973
No 8
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=99.93 E-value=1.9e-26 Score=186.48 Aligned_cols=94 Identities=27% Similarity=0.313 Sum_probs=83.7
Q ss_pred HHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCccHHHHHHHHHHHHHHHHH
Q 025111 32 ARIRLINQDKNKYNTPKYRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLK 111 (257)
Q Consensus 32 ~R~rli~~~knkyns~kpRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~N~~AAy~tG~LlA~ral~ 111 (257)
.|.|..+.|+ +.+|||+|++||+|||||||||. .| .|||||||.|+..++|..+++|++||++||.+||+||++
T Consensus 3 ~r~r~ki~g~----~~rpRL~V~rSnkhiyaQvidd~-~g-~tlasaST~ek~~~~~~~~~~n~~aA~~vG~lla~ra~~ 76 (109)
T CHL00139 3 ERVRKKIKGT----AERPRLSVFRSNKHIYAQIIDDT-NG-KTLVACSTLEPDVKSSLSSTSTCDASKLVGQKLAKKSLK 76 (109)
T ss_pred eeeeeeecCC----CCCCEEEEEEeCCeEEEEEEECC-CC-CEEEEEecCchhhhccccCCCCHHHHHHHHHHHHHHHHH
Confidence 3455556675 77999999999999999999964 45 999999999999999988899999999999999999999
Q ss_pred hcCCCc--------ccccccc----cccccccc
Q 025111 112 MLEMDD--------EYEGNVE----GALDGGLD 132 (257)
Q Consensus 112 k~Gl~~--------~YhG~vk----GArD~GL~ 132 (257)
+ ||+. .|||+|+ ||||+||+
T Consensus 77 ~-gi~~vvfDrgg~~yhGrV~a~a~~are~GL~ 108 (109)
T CHL00139 77 K-GITKVVFDRGGKLYHGRIKALAEAAREAGLQ 108 (109)
T ss_pred C-CCCEEEEcCCCCccchHHHHHHHHHHHhCCC
Confidence 7 9976 8999985 99999996
No 9
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=99.92 E-value=2.1e-25 Score=181.78 Aligned_cols=94 Identities=31% Similarity=0.361 Sum_probs=82.4
Q ss_pred hHHHHHHHHHhCCCCCCC--CcceEEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCccHHHHHHHHHHHH
Q 025111 29 DYRARIRLINQDKNKYNT--PKYRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLA 106 (257)
Q Consensus 29 dY~~R~rli~~~knkyns--~kpRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~N~~AAy~tG~LlA 106 (257)
..+.|.|..+.|+ + .+|||+||+||+||||||||| ++|.|||||||.++. ++ +++|++|||+||++||
T Consensus 7 ~r~~r~r~ki~gt----~~~~rpRL~V~rSnk~iyaQiIdd--~~~~tlasaST~ek~-~~---~~~n~~aA~~vG~~la 76 (114)
T TIGR00060 7 RRHKRIRRKLRET----GEANRPRLVVFRSNRHIYAQVIDD--SKSEVLASASTLEKK-LK---YTGNKDAAKKVGKLVA 76 (114)
T ss_pred HHHHHHHHHhcCC----CCCCCcEEEEEEeCCeEEEEEEEC--CCCEEEEEEecchhh-hc---CCCCHHHHHHHHHHHH
Confidence 4567778888886 4 599999999999999999998 488999999999986 32 6789999999999999
Q ss_pred HHHHHhcCCCc--------ccccccc----ccccccccc
Q 025111 107 RRVLKMLEMDD--------EYEGNVE----GALDGGLDI 133 (257)
Q Consensus 107 ~ral~k~Gl~~--------~YhG~vk----GArD~GL~I 133 (257)
++|+++ ||.. .|||+|+ ||||+||+.
T Consensus 77 ~ra~~~-gi~~vvfDrgg~~YhGrv~A~a~~aRe~Gl~F 114 (114)
T TIGR00060 77 ERLKEK-GIKDVVFDRGGYKYHGRVAALAEAAREAGLNF 114 (114)
T ss_pred HHHHHC-CCCEEEEeCCCCcchHHHHHHHHHHHHhCCCC
Confidence 999997 9976 9999995 999999963
No 10
>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.
Probab=99.88 E-value=5e-23 Score=163.30 Aligned_cols=83 Identities=42% Similarity=0.590 Sum_probs=77.0
Q ss_pred CCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCccHHHHHHHHHHHHHHHHHhcCCCc--------
Q 025111 46 TPKYRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDD-------- 117 (257)
Q Consensus 46 s~kpRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~N~~AAy~tG~LlA~ral~k~Gl~~-------- 117 (257)
.++|||+|++||+|||||||++. +|.|||||||.|++.+++..+++|++|||+||.+||+|++++ |+..
T Consensus 9 ~~~~RL~v~~Sn~~i~aqvi~~~--~~~vl~sast~e~~~~~~~~~~~n~~aA~~vG~~la~r~~~~-gi~~vv~D~~~~ 85 (103)
T cd00432 9 QERPRLVVRKSNKHIYAQIIDDS--GDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEK-GIKKVVFDRGGY 85 (103)
T ss_pred CCCCEEEEEEeCCEEEEEEEEeC--cCeEEEEEecCchhhcccccCCCcHHHHHHHHHHHHHHHHHC-CCCEEEEeCCCc
Confidence 45899999999999999999995 889999999999999888888999999999999999999997 9876
Q ss_pred ccccccc----ccccccc
Q 025111 118 EYEGNVE----GALDGGL 131 (257)
Q Consensus 118 ~YhG~vk----GArD~GL 131 (257)
.|||+|+ |++|+||
T Consensus 86 ~~~grv~a~~~~~r~~Gl 103 (103)
T cd00432 86 RYHGRVKALAKGAREGGL 103 (103)
T ss_pred ccccHHHHHHHHHHHcCC
Confidence 8899985 9999997
No 11
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=99.85 E-value=6.1e-22 Score=174.72 Aligned_cols=88 Identities=28% Similarity=0.320 Sum_probs=75.8
Q ss_pred HHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEeccccccccccc------------CCccHHHHHHHHHH
Q 025111 37 INQDKNKYNTPKYRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEV------------GLTNYAAAYCTGLL 104 (257)
Q Consensus 37 i~~~knkyns~kpRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~------------~~~N~~AAy~tG~L 104 (257)
|++|| .+|||+|++||+|||||||||. ...|||||||.+....+..+ +++|++||+.+|.+
T Consensus 99 i~~gk-----rrPRLsV~RSnkHIYAQIIDD~--~~~TLasaSTlek~l~~~~~~~~~~~~n~~~~~g~nieaA~~VGk~ 171 (211)
T PTZ00032 99 IIKGK-----RRPRLTLKNTNNQMYATIVDDY--TRHVLCFSCTNFKYLSHIFGTYPTKTTNRVRNNGGTIKAAYELGKL 171 (211)
T ss_pred HHcCC-----CcceEEEEecCCeEEEEEEECC--CCCEEEEecCCCHHHHhhhcccccccccccccCCCcHHHHHHHHHH
Confidence 56775 5799999999999999999996 44999999999876433211 46899999999999
Q ss_pred HHHHHHHhcCCCc--------ccccccc----cccccccc
Q 025111 105 LARRVLKMLEMDD--------EYEGNVE----GALDGGLD 132 (257)
Q Consensus 105 lA~ral~k~Gl~~--------~YhG~vk----GArD~GL~ 132 (257)
||++|+++ ||.. .|||+|+ |||++||+
T Consensus 172 IAerAl~k-GI~kVvFDRgGy~YHGRVkALAdaARe~GLk 210 (211)
T PTZ00032 172 IGRKALSK-GISKVRFDRAHYKYAGKVEALAEGARAVGLQ 210 (211)
T ss_pred HHHHHHHC-CCCEEEEeCCCCeehhHHHHHHHHHHHcCCC
Confidence 99999997 9976 9999996 99999996
No 12
>KOG3333 consensus Mitochondrial/chloroplast ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=96.66 E-value=0.0044 Score=53.99 Aligned_cols=81 Identities=20% Similarity=0.179 Sum_probs=64.5
Q ss_pred ceEEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCccHHHHHHHHHHHHHHHHHhcCCCcccccc-c----
Q 025111 49 YRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYEGN-V---- 123 (257)
Q Consensus 49 pRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~N~~AAy~tG~LlA~ral~k~Gl~~~YhG~-v---- 123 (257)
+||-|-+|..|+-+-+.... | -|++||||.|.....---+++|+.|+--+|..||.|+|.. ||.-..-|- +
T Consensus 61 h~lev~~~~~hveg~v~H~~--~-gvvvSAST~EwaIk~qLYst~dtsA~~niGRVLAqRCLqs-GI~fm~~~~t~ea~~ 136 (188)
T KOG3333|consen 61 HRLEVIRTQHHVEGLVEHQN--G-GVVVSASTREWAIKKQLYSTRDTSACENIGRVLAQRCLQS-GINFMVYQPTPEAAA 136 (188)
T ss_pred eEEEEeecccceeeeeeEec--C-CEEEEecccchHHHHHHhhccchHHHHHHHHHHHHHHHHh-CcceeccCCChhhcc
Confidence 58889999999999998874 4 6788999999874333346789999999999999999997 998744442 2
Q ss_pred --------cccccccccc
Q 025111 124 --------EGALDGGLDI 133 (257)
Q Consensus 124 --------kGArD~GL~I 133 (257)
++.-|+||..
T Consensus 137 ~s~~q~l~~a~~e~Gv~l 154 (188)
T KOG3333|consen 137 SSSMQRLQSAMTEGGVVL 154 (188)
T ss_pred chHHHHHHHHHHhCCeee
Confidence 1677888865
No 13
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=96.02 E-value=0.027 Score=51.38 Aligned_cols=83 Identities=16% Similarity=0.272 Sum_probs=61.9
Q ss_pred CCcceEEEEecCCcEEEEEEeeecCCCE-EEEEEecccccccccccCCccHHHHHHHHHHHHHHHHHhcCCCc---cccc
Q 025111 46 TPKYRFVVRFTNKDIIAQIVSANIVGDS-VLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDD---EYEG 121 (257)
Q Consensus 46 s~kpRLvVr~Snr~I~aQIi~~~~~GD~-tlasAsS~el~k~g~k~~~~N~~AAy~tG~LlA~ral~k~Gl~~---~YhG 121 (257)
+.+.++||.-|-+++++||+|. .|.. ||+-+|+-.....|-+. +.--||+.++.-+|++|.+. ||.. ..+|
T Consensus 116 ~~~f~~vI~aSfNNTIVTlTD~--~GNv~tl~WSSAG~~GFKGsKK--sTpfAAQ~aae~aakka~~~-GIk~V~V~vKG 190 (233)
T PTZ00090 116 TDRFMLVITTSKNNVHAQVVNK--SKNYKTVFGSFAGNVGFRKKLQ--QSERCAYRIGENIAKKCRRL-GIFAVDIKFRR 190 (233)
T ss_pred CCcEEEEEEeccCcEEEEEEeC--CCCEEEEEEEcccccCcccCcc--CCHHHHHHHHHHHHHHHHHc-CCeEEEEEEeC
Confidence 4689999999999999999997 5875 78888887765444332 23558899999999999994 9976 3444
Q ss_pred --cc----cccccccccc
Q 025111 122 --NV----EGALDGGLDI 133 (257)
Q Consensus 122 --~v----kGArD~GL~I 133 (257)
.. ++...+||.|
T Consensus 191 pGgREtALRaL~~~GLkI 208 (233)
T PTZ00090 191 IMRVETVLQAFYANGLQV 208 (233)
T ss_pred CChHHHHHHHHHHCCCEE
Confidence 22 3666677763
No 14
>PRK05309 30S ribosomal protein S11; Validated
Probab=94.45 E-value=0.24 Score=41.34 Aligned_cols=90 Identities=23% Similarity=0.204 Sum_probs=64.5
Q ss_pred CcceEEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCccHHHHHHHHHHHHHHHHHhcCCCc---cccc--
Q 025111 47 PKYRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDD---EYEG-- 121 (257)
Q Consensus 47 ~kpRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~N~~AAy~tG~LlA~ral~k~Gl~~---~YhG-- 121 (257)
+.--+-|+-|.+++++-+.|. .| .+|+.+|+-.+...|-. -...-||+.++.-+++.+++. |+.. ...|
T Consensus 16 ~~gi~hI~~t~NNTiitlTd~--~G-~~~~~~S~G~~gfKg~r--K~T~~Aa~~aa~~~~~~~~~~-gi~~v~v~ikG~G 89 (128)
T PRK05309 16 PSGVAHIHATFNNTIVTITDR--QG-NVISWASAGGLGFKGSR--KSTPYAAQVAAEDAAKKAKEH-GMKTVEVFVKGPG 89 (128)
T ss_pred ceeEEEEEccCCCEEEEEEcC--CC-CEEEEEecCccEeCCCc--cCCHHHHHHHHHHHHHHHHHc-CCcEEEEEEECCC
Confidence 346788999999999999996 47 57887777665444432 234569999999999999984 9865 3333
Q ss_pred -----ccccccccccc---------ccCCCCccCC
Q 025111 122 -----NVEGALDGGLD---------IPHSDKRFAG 142 (257)
Q Consensus 122 -----~vkGArD~GL~---------IPhs~~~fp~ 142 (257)
.+++....||. |||+-.|-|.
T Consensus 90 ~Gr~~air~L~~~glkI~~I~D~TpiphNGcR~~K 124 (128)
T PRK05309 90 SGRESAIRALQAAGLEVTSIKDVTPIPHNGCRPPK 124 (128)
T ss_pred CcHHHHHHHHHHCCCEEEEEEEcCCCCCCCcCcCC
Confidence 12355566765 5888888775
No 15
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=94.40 E-value=0.19 Score=40.63 Aligned_cols=85 Identities=24% Similarity=0.231 Sum_probs=61.1
Q ss_pred EEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCccHHHHHHHHHHHHHHHHHhcCCCc---cccc------
Q 025111 51 FVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDD---EYEG------ 121 (257)
Q Consensus 51 LvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~N~~AAy~tG~LlA~ral~k~Gl~~---~YhG------ 121 (257)
+-|+-|.+++++-+.|. .| .+++.+|+-.+...|-. ....-||..++..+++++++ +|+.. ...|
T Consensus 3 ~hI~~s~NNT~itlTd~--~g-~~~~~~S~G~~gfkg~r--k~t~~Aa~~~a~~~~~~~~~-~gi~~v~v~~kG~G~gr~ 76 (108)
T TIGR03632 3 AHIHATFNNTIVTITDP--QG-NVLSWASAGAVGFKGSK--KSTPYAAQLAAEDAAKKAKE-FGMKTVDVYVKGPGAGRE 76 (108)
T ss_pred EEEEccCCCEEEEEEcC--CC-CEEEEEecCceeeCCCc--cCCHHHHHHHHHHHHHHHHH-cCCcEEEEEEECCCCcHH
Confidence 45788999999999997 47 47888887766544433 23466799999999999999 49876 3333
Q ss_pred -ccccccccccc---------ccCCCCccC
Q 025111 122 -NVEGALDGGLD---------IPHSDKRFA 141 (257)
Q Consensus 122 -~vkGArD~GL~---------IPhs~~~fp 141 (257)
.+++....||. |||+--|.|
T Consensus 77 ~~ir~l~~~glkI~~I~D~T~iphNGcR~~ 106 (108)
T TIGR03632 77 SAIRALQAAGLEVTSIKDVTPIPHNGCRPP 106 (108)
T ss_pred HHHHHHHHCCCEEEEEEEcCCCCCCCcCCC
Confidence 22466667775 588777766
No 16
>PF00411 Ribosomal_S11: Ribosomal protein S11; InterPro: IPR001971 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 S11 [] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. On the basis of sequence similarities, S11 belongs to a family of bacterial, archaeal and eukaryotic ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_K 3U5C_O 3O2Z_H 3IZB_K 3U5G_O 3O30_H 1S1H_K 3BBN_K 2XZN_K 2XZM_K ....
Probab=94.24 E-value=0.17 Score=40.91 Aligned_cols=86 Identities=20% Similarity=0.242 Sum_probs=59.6
Q ss_pred EEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCccHHHHHHHHHHHHHHHHHhcCCCc---cccc----c-
Q 025111 51 FVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDD---EYEG----N- 122 (257)
Q Consensus 51 LvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~N~~AAy~tG~LlA~ral~k~Gl~~---~YhG----~- 122 (257)
+-|+-|.+++++.+.|. .| .++++.|+-.+...|-. .....||+.++.-+++++.+. |+.. ...| +
T Consensus 3 ihI~~s~NNt~vtlTd~--~G-~~~~~~S~G~~gfK~~r--k~t~~Aa~~~a~~~~~~~~~~-gi~~v~v~ikG~g~gr~ 76 (110)
T PF00411_consen 3 IHIKSSFNNTIVTLTDL--KG-NVLFWSSAGSLGFKGAR--KSTPYAAQQAAEKIAKKAKEL-GIKTVRVKIKGFGPGRE 76 (110)
T ss_dssp EEEEEESSEEEEEEEET--TS-EEEEEEETTTSSTTTTC--GSSHHHHHHHHHHHHHHHHCT-TEEEEEEEEESSSTTHH
T ss_pred EEEEecCCCEEEEEECC--CC-CEEEEEecccccccccc--ccCHHHHHHHHHHHHHHHHHc-CCeEEEEEEcCCCccHH
Confidence 45888999999999997 47 78888888766544432 346789999999999999995 8865 3334 2
Q ss_pred --cccccccccc---------ccCCCCccCC
Q 025111 123 --VEGALDGGLD---------IPHSDKRFAG 142 (257)
Q Consensus 123 --vkGArD~GL~---------IPhs~~~fp~ 142 (257)
+++....||. |||+--|-|.
T Consensus 77 ~~lk~l~~~gl~I~~I~D~T~iphnGcR~kK 107 (110)
T PF00411_consen 77 AALKALKKSGLKIVSITDVTPIPHNGCRPKK 107 (110)
T ss_dssp HHHHHHHHTTSEEEEEEEETT--SSSS--TT
T ss_pred HHHHHHHhcCCEEEEEEeecCCCCCCCCCCC
Confidence 2456667775 5888777664
No 17
>CHL00041 rps11 ribosomal protein S11
Probab=93.97 E-value=0.23 Score=40.75 Aligned_cols=87 Identities=20% Similarity=0.179 Sum_probs=63.2
Q ss_pred CCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCccHHHHHHHHHHHHHHHHHhcCCCc---
Q 025111 41 KNKYNTPKYRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDD--- 117 (257)
Q Consensus 41 knkyns~kpRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~N~~AAy~tG~LlA~ral~k~Gl~~--- 117 (257)
++|.+.+.--+-|+-|.+++++-+.|. .| .+|+.+|+-.+...|-. ....-||+.++.-+++++++. |+..
T Consensus 6 ~~~~~~~~gi~hI~~t~NNTiiTlTd~--~G-~~l~~~S~G~~gfKg~r--K~T~~Aa~~~a~~~~~~~~~~-gi~~v~I 79 (116)
T CHL00041 6 KSKRKIPKGVIHIQASFNNTIVTVTDV--RG-RVISWSSAGACGFKGAR--KGTPFAAQTAAENAIRTVIDQ-GMKRAEV 79 (116)
T ss_pred cccccceeEEEEEEcccCCEEEEEEcC--CC-CEEEEEecCceeeCCCc--cCCHHHHHHHHHHHHHHHHHc-CCcEEEE
Confidence 445566666788999999999999997 47 68998888766544432 234668999999999999995 9876
Q ss_pred cccc-------cccccccccccc
Q 025111 118 EYEG-------NVEGALDGGLDI 133 (257)
Q Consensus 118 ~YhG-------~vkGArD~GL~I 133 (257)
...| .+++....||.|
T Consensus 80 ~ikG~G~Gr~~~ir~l~~~glkI 102 (116)
T CHL00041 80 MIKGPGLGRDTALRAIRRSGLKL 102 (116)
T ss_pred EEECCCCcHHHHHHHHHHCCCEE
Confidence 3333 234666777764
No 18
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=93.32 E-value=0.45 Score=40.24 Aligned_cols=88 Identities=16% Similarity=0.160 Sum_probs=64.7
Q ss_pred eEEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCccHHHHHHHHHHHHHHHHHhcCCCc---cccc-----
Q 025111 50 RFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDD---EYEG----- 121 (257)
Q Consensus 50 RLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~N~~AAy~tG~LlA~ral~k~Gl~~---~YhG----- 121 (257)
-+-|+-|-++.++-|.|. .|..||+.+|+-...+.|-+. +.--||..++.-+++++++. ||.. ...|
T Consensus 11 i~hI~as~NNTivtvTD~--~G~~~~~~~S~G~~g~kg~kK--~TpyAAq~aae~~~~~~~~~-Gi~~v~v~vkG~Ggn~ 85 (132)
T PRK09607 11 IAHIYASFNNTIITITDL--TGAETIAKSSGGMVVKADRDE--SSPYAAMQAAEKAAEDAKEK-GITGVHIKVRAPGGNG 85 (132)
T ss_pred EEEEEcccCCeEEEEEcC--CCCEEEEEecCcceeeCCCcc--CCHHHHHHHHHHHHHHHHHc-CCcEEEEEEEecCCCC
Confidence 456788899999999997 487799888887665555332 23448899999999999994 9976 4444
Q ss_pred ----------ccccccccccc---------ccCCCCccCC
Q 025111 122 ----------NVEGALDGGLD---------IPHSDKRFAG 142 (257)
Q Consensus 122 ----------~vkGArD~GL~---------IPhs~~~fp~ 142 (257)
.+.+...+||. |||+--|-|.
T Consensus 86 ~~~~G~Gr~~airal~~~glkI~~I~DvTpiPhNGCRp~K 125 (132)
T PRK09607 86 QKSPGPGAQAAIRALARAGLRIGRIEDVTPIPHDGTRPPG 125 (132)
T ss_pred CcCCCCcHHHHHHHHHHCCCEEEEEEEcCCCCCCCCCCCC
Confidence 22356677775 5999888886
No 19
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=92.35 E-value=0.51 Score=40.72 Aligned_cols=86 Identities=14% Similarity=0.133 Sum_probs=59.8
Q ss_pred eEEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCC-cc-HHHHHHHHHHHHHHHHHhcCCCc---cc-----
Q 025111 50 RFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGL-TN-YAAAYCTGLLLARRVLKMLEMDD---EY----- 119 (257)
Q Consensus 50 RLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~-~N-~~AAy~tG~LlA~ral~k~Gl~~---~Y----- 119 (257)
=+-|+-|-++.++.|.|. .| .+++.+||-.+...| .. .+ --||..+.+-+++++++. ||.. ..
T Consensus 30 i~hI~as~NNTiItiTD~--~G-~~~~w~SsG~~gfKg---~r~KsTpyAAq~aa~~~a~k~~~~-Gi~~v~V~vr~~gg 102 (149)
T PTZ00129 30 VAHIFASFNDTFIHVTDL--SG-RETLVRVTGGMKVKA---DRDESSPYAAMMAAQDVAARCKEL-GINALHIKLRATGG 102 (149)
T ss_pred EEEEEcccCCeEEEEEcc--cC-CEEEEEecCcceecc---cccCCCHHHHHHHHHHHHHHHHHc-CCeEEEEEEEecCC
Confidence 345778889999999997 47 556666665554333 33 33 347889999999999995 9976 33
Q ss_pred ---cc-------ccccccccccc---------ccCCCCccCC
Q 025111 120 ---EG-------NVEGALDGGLD---------IPHSDKRFAG 142 (257)
Q Consensus 120 ---hG-------~vkGArD~GL~---------IPhs~~~fp~ 142 (257)
+| .+++...+||. |||+-.|-|+
T Consensus 103 ~~~kg~GpGr~~airaL~~~glkI~~I~DvTPiPhNGcRppk 144 (149)
T PTZ00129 103 VRTKTPGPGAQAALRALARAGLKIGRIEDVTPIPTDSTRRKG 144 (149)
T ss_pred CCCCCCCCCHHHHHHHHHHCCCEEEEEEecCCCCCCCCCCCC
Confidence 22 12366677775 6999888886
No 20
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=86.47 E-value=2.7 Score=34.75 Aligned_cols=62 Identities=11% Similarity=0.031 Sum_probs=48.1
Q ss_pred EEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCccHHHHHHHHHHHHHHHHHhcCCCc
Q 025111 51 FVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDD 117 (257)
Q Consensus 51 LvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~N~~AAy~tG~LlA~ral~k~Gl~~ 117 (257)
+-|+-|-++.++-|.|. .|..||+-+|+-...+.|-+. +.--||..+..-+++++++ +||..
T Consensus 5 ~hI~as~NNTiitvTD~--~G~~~~~~~S~G~~g~kg~kk--~TpyAAq~aa~~~~~~~~~-~Gi~~ 66 (114)
T TIGR03628 5 AHIYSSFNNTIITITDI--TGAETIARSSGGMVVKADRDE--SSPYAAMQAAGRAAEKAKE-RGITG 66 (114)
T ss_pred EEEEccCCCeEEEEEcC--CCCEEEEEecCcceEeCCCcc--CCHHHHHHHHHHHHHHHHH-cCCcE
Confidence 34778889999999997 487889988887776555432 2344788999999999999 49976
No 21
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=81.61 E-value=5.4 Score=33.75 Aligned_cols=86 Identities=19% Similarity=0.194 Sum_probs=58.4
Q ss_pred EEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCccHHHHHHHHHHHHHHHHHhcCCCc---cccc----c-
Q 025111 51 FVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDD---EYEG----N- 122 (257)
Q Consensus 51 LvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~N~~AAy~tG~LlA~ral~k~Gl~~---~YhG----~- 122 (257)
.=|+-|-++.++-|.|. .| .+|+.+||-.+...|-. .+.--||-+.+..+|+.+++. ||.. ..+| +
T Consensus 21 ahI~asfNNTivtitD~--~G-n~i~wassG~~gfk~~r--k~tpyAA~~aa~~aa~~a~e~-Gi~~v~v~vkgpG~Gre 94 (129)
T COG0100 21 AHIHASFNNTIVTITDL--TG-NVIIWASSGGMGFKGSR--KSTPYAAQLAAEDAAKKAKEH-GIKSVEVKVKGPGPGRE 94 (129)
T ss_pred EEEEcccCCcEEEecCC--CC-CEEEEEecCCceEcCCC--CCCHHHHHHHHHHHHHHHHHh-CccEEEEEEECCCCcHH
Confidence 44667778888888886 47 77888888877554433 234556677788888999995 9876 3344 1
Q ss_pred --cccccccccc---------ccCCCCccCC
Q 025111 123 --VEGALDGGLD---------IPHSDKRFAG 142 (257)
Q Consensus 123 --vkGArD~GL~---------IPhs~~~fp~ 142 (257)
+.+..-+||. |||+-.|=|+
T Consensus 95 aAiraL~~ag~~i~~I~DvTPiphnG~Rppk 125 (129)
T COG0100 95 AAIRALAAAGLKITRIEDVTPIPHNGCRPPK 125 (129)
T ss_pred HHHHHHHHccceEEEEEEcCCCCCCCCCCCC
Confidence 1233455654 6999888876
No 22
>KOG0408 consensus Mitochondrial/chloroplast ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=72.46 E-value=14 Score=32.81 Aligned_cols=80 Identities=19% Similarity=0.189 Sum_probs=53.2
Q ss_pred cceEEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCccHHHHHHHHHHHHHHHHHhcCCCc---ccc----
Q 025111 48 KYRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDD---EYE---- 120 (257)
Q Consensus 48 kpRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~N~~AAy~tG~LlA~ral~k~Gl~~---~Yh---- 120 (257)
-|=.-|+-|-++.++|+.|.. | .++..+|--.-...+-. .++++ ||..+|--++.++..+ |+.. ...
T Consensus 79 iPi~hIraS~NNTivtVtd~k--g-~vi~~~ScgteGFrntr-kgT~i-AaQtaavaa~~r~v~~-G~~~vrV~VkGlGp 152 (190)
T KOG0408|consen 79 IPIIHIRASFNNTIVTVTDVK--G-EVISWSSCGTEGFRNTR-KGTPI-AAQTAAVAAIRRAVDQ-GMQTVRVRVKGLGP 152 (190)
T ss_pred cceEEEEecCCCeEEEEEccC--C-cEEEEeecccccccccc-cCCch-hHHHHHHHHHHHHHHh-cceEEEEEEecCCc
Confidence 455568999999999999974 6 66655443322222222 23444 6778888999999996 8865 222
Q ss_pred cc---ccccccccccc
Q 025111 121 GN---VEGALDGGLDI 133 (257)
Q Consensus 121 G~---vkGArD~GL~I 133 (257)
|+ ++|.+-+||.|
T Consensus 153 GRmsa~kgl~m~Gl~v 168 (190)
T KOG0408|consen 153 GRMSALKGLRMGGLLV 168 (190)
T ss_pred cHHHHHhhhhhcceEE
Confidence 33 46999999874
No 23
>PF14821 Thr_synth_N: Threonine synthase N terminus; PDB: 3V7N_A 1VB3_A 1KL7_A.
Probab=44.18 E-value=28 Score=26.41 Aligned_cols=56 Identities=21% Similarity=0.306 Sum_probs=30.6
Q ss_pred cccccccccCCCCccCCcCCCCCCCCHHhhhcccccccHHHHHHhhcccChHHHHhhHHHHHHcCCCcchHHHHHHHH
Q 025111 126 ALDGGLDIPHSDKRFAGFSKDGKQLDAEVHRKYIYGGHVAAYMSTLMEDEPEKYQSHFTEYIKKGIDADGLEALYKKV 203 (257)
Q Consensus 126 ArD~GL~IPhs~~~fp~~~~~~k~~~ae~~~~rI~G~hVa~Ym~~L~eed~e~ykkqFS~yik~gi~p~~~e~~y~~~ 203 (257)
|-||||-||. .||.. +.+.+ +.+.+..-. |.=..-++.|+...|++++|.++-++|
T Consensus 23 A~DGGLyvP~---~iP~l-------~~~~l-~~l~~~sy~-----------elA~~il~~f~~~di~~~~L~~ii~~A 78 (79)
T PF14821_consen 23 APDGGLYVPE---EIPKL-------SKEEL-EELKNLSYA-----------ELAFEILSPFLGDDIPEEELKEIIEKA 78 (79)
T ss_dssp BTTSB-EEES---S------------HHHH-HHHTTS-HH-----------HHHHHHHHHHCCCCS-HHHHHHHHHHH
T ss_pred CCCCeeEecC---cCCCC-------CHHHH-HHHHCCCHH-----------HHHHHHHHHHHccCCCHHHHHHHHHHH
Confidence 7899999997 47774 22222 122333222 233456778887788899998887665
No 24
>PF08673 RsbU_N: Phosphoserine phosphatase RsbU, N-terminal domain; InterPro: IPR014787 The phosphoserine phosphatase RsbU acts as a positive regulator of the general stress-response factor of Gram-positive organisms, sigma-B. RsbU dephosphorylates rsbV in response to environmental stress conveyed from the rsbXST module. The phosphatase activity of RsbU is stimulated during the stress response by associating with the RsbT kinase. This association leads to the induction of sigmaB activity. The N-terminal domain forms a helix-swapped dimer that is otherwise similar to the KaiA domain dimer. Deletions in the N-terminal domain are deleterious to the activity of RsbU. The C-terminal domain of RsbU is similar to the catalytic domains of PP2C-type phosphatases [].; PDB: 2J6Y_D 2J6Z_A 2J70_A 1W53_A.
Probab=35.31 E-value=70 Score=24.52 Aligned_cols=41 Identities=15% Similarity=0.235 Sum_probs=26.0
Q ss_pred hhcccChHHHH--hhHHHH-HHcCCCcchHHHHHHHHHHHHhcC
Q 025111 170 TLMEDEPEKYQ--SHFTEY-IKKGIDADGLEALYKKVHAAIRAD 210 (257)
Q Consensus 170 ~L~eed~e~yk--kqFS~y-ik~gi~p~~~e~~y~~~~~~I~~~ 210 (257)
+|...||...- .+||+. |+.+|.|++|-++.+++-..+-.+
T Consensus 11 yl~~~~E~~L~~~~~~~r~~i~~~I~PEeIv~iH~~~v~~l~~~ 54 (77)
T PF08673_consen 11 YLETQDEQSLYQAQEFGRELIEKDISPEEIVEIHKSAVQELSPS 54 (77)
T ss_dssp HHHH--HHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHH-TT
T ss_pred HHhCCCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHccc
Confidence 34455554332 267754 688999999999999999888655
No 25
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=34.38 E-value=2.1e+02 Score=24.96 Aligned_cols=58 Identities=16% Similarity=0.238 Sum_probs=35.5
Q ss_pred CCCCCCc-ceEEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCccHHHHHHHHHHHHHHHHHhcCCCc
Q 025111 42 NKYNTPK-YRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDD 117 (257)
Q Consensus 42 nkyns~k-pRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~N~~AAy~tG~LlA~ral~k~Gl~~ 117 (257)
.-||..+ |=|++|..+-...+-|... | +++|+ |.++.+.|......+++.+.+ +|++.
T Consensus 29 ~eY~P~~fpgli~Rl~~Pk~t~lIF~S---G-Kiv~t-------------Gaks~~~a~~a~~~~~~~L~~-~g~~~ 87 (174)
T cd04518 29 AEYNPDQFPGLVYRLEDPKIAALIFRS---G-KMVCT-------------GAKSVEDLHRAVKEIIKKLKD-YGIKV 87 (174)
T ss_pred cEECCCcCcEEEEEccCCcEEEEEECC---C-eEEEE-------------ccCCHHHHHHHHHHHHHHHHh-cCCCc
Confidence 4788887 5566666665666666553 6 55553 223555666666666666544 68765
No 26
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=33.19 E-value=2e+02 Score=25.88 Aligned_cols=84 Identities=23% Similarity=0.345 Sum_probs=56.4
Q ss_pred CCCCCCc-ceEEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCCccHHHHHHHHHHHHHHHHHhcCCCcccc
Q 025111 42 NKYNTPK-YRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYE 120 (257)
Q Consensus 42 nkyns~k-pRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~~N~~AAy~tG~LlA~ral~k~Gl~~~Yh 120 (257)
..||... |=||.|...-..-+=|..+ | +++|+ |.+|.+.+..+-..+++.+.. .|++-...
T Consensus 35 aeYnP~qFpGlv~Rl~ePk~a~LIF~S---G-K~VcT-------------GaKs~ed~~~av~~~~~~L~~-~g~~~~~~ 96 (185)
T COG2101 35 AEYNPEQFPGLVYRLEEPKTAALIFRS---G-KVVCT-------------GAKSVEDVHRAVKKLAKKLKD-GGIDIDFE 96 (185)
T ss_pred CccCHhHCCeeEEEecCCcceEEEEec---C-cEEEe-------------ccCcHHHHHHHHHHHHHHHHh-cCcCcCCC
Confidence 3788886 6677766666665555543 6 55653 456888888888888888777 57765433
Q ss_pred cccc------------------cccccccc-ccCCCCccCCc
Q 025111 121 GNVE------------------GALDGGLD-IPHSDKRFAGF 143 (257)
Q Consensus 121 G~vk------------------GArD~GL~-IPhs~~~fp~~ 143 (257)
-.++ -|.--|++ +-.-++.|||.
T Consensus 97 p~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGL 138 (185)
T COG2101 97 PEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGL 138 (185)
T ss_pred CceEEEEEEEEeccCccccHHHHHHhccccccccccccCCee
Confidence 2221 56666776 67788999994
No 27
>PF13069 DUF3933: Protein of unknown function (DUF3933)
Probab=32.43 E-value=12 Score=26.68 Aligned_cols=15 Identities=40% Similarity=0.636 Sum_probs=10.2
Q ss_pred CcEEEEEEeeecCCCEEEE
Q 025111 58 KDIIAQIVSANIVGDSVLA 76 (257)
Q Consensus 58 r~I~aQIi~~~~~GD~tla 76 (257)
..+|||||+ |++-|+
T Consensus 3 qyvicqii~----g~kyla 17 (53)
T PF13069_consen 3 QYVICQIID----GTKYLA 17 (53)
T ss_pred eEEEEEEec----CccHHH
Confidence 458999998 555443
No 28
>PF13907 DUF4208: Domain of unknown function (DUF4208)
Probab=31.49 E-value=50 Score=26.10 Aligned_cols=44 Identities=27% Similarity=0.520 Sum_probs=34.3
Q ss_pred cccccHHHHHHhhcccChHHHHhhHHHHHHc--CCCcchHHHHHHH
Q 025111 159 IYGGHVAAYMSTLMEDEPEKYQSHFTEYIKK--GIDADGLEALYKK 202 (257)
Q Consensus 159 I~G~hVa~Ym~~L~eed~e~ykkqFS~yik~--gi~p~~~e~~y~~ 202 (257)
..|.||-.-.....+.+++....+|-.|... -.+++.|.+||.+
T Consensus 54 ~IG~~I~~~l~~~~~~~~~~l~~~LW~fvs~fwp~~~~kL~~mY~k 99 (100)
T PF13907_consen 54 KIGDFIDSILKEYKDDEPEKLRKHLWSFVSKFWPNKGKKLHKMYKK 99 (100)
T ss_pred HHHHHHHHHHHhcccchHHHHHHHHHHHHHHcCCCCHHHHHHHHHc
Confidence 4788888887777766778999999999984 2336788888875
No 29
>PRK14083 HSP90 family protein; Provisional
Probab=29.23 E-value=27 Score=36.15 Aligned_cols=49 Identities=14% Similarity=0.187 Sum_probs=37.3
Q ss_pred ccccccHHHHHHhhcccChHHHHh---hHHHHHHcCCCcchHHHHHHHHHHHHh
Q 025111 158 YIYGGHVAAYMSTLMEDEPEKYQS---HFTEYIKKGIDADGLEALYKKVHAAIR 208 (257)
Q Consensus 158 rI~G~hVa~Ym~~L~eed~e~ykk---qFS~yik~gi~p~~~e~~y~~~~~~I~ 208 (257)
...|+-|.++.+.|.++|+++|.+ +|+.+||.|+--|. +.+++...-++
T Consensus 319 ~~i~kki~~~L~~la~~d~e~y~~f~~~~g~~lK~g~~~D~--~~~~~l~~lL~ 370 (601)
T PRK14083 319 EELGEAIRKWLIGLATTDPERLRRLLAVHHLGVKALASHDD--ELLRLILPWLP 370 (601)
T ss_pred HHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHHHHhcCH--HHHHHHHHhce
Confidence 456888999999999999998886 88999999987442 34555444443
No 30
>PF08218 Citrate_ly_lig: Citrate lyase ligase C-terminal domain; InterPro: IPR013166 [Citrate (pro-3S)-lyase] ligase (6.2.1.22 from EC), also known as citrate lyase ligase, is responsible for acetylation of the prosthetic group (2-(5''-phosphoribosyl)-3'-dephosphocoenzyme-A) of the gamma subunit of citrate lyase. It converts the inactive thiol form of the enzyme to the active form. In Clostridium sphenoides, citrate lyase ligase actively degrades citrate. In Clostridium sporosphaeroides and Lactococcus lactis, however, the enzyme is under stringent regulatory control. The enzyme's activity in anaerobic bacteria is modulated by phosphorylation and dephosphorylation []. The proteins in this entry represent the C-terminal domain of citrate lyase ligase.; GO: 0008771 [citrate (pro-3S)-lyase] ligase activity
Probab=28.94 E-value=1.2e+02 Score=27.10 Aligned_cols=72 Identities=17% Similarity=0.217 Sum_probs=47.2
Q ss_pred HHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecccccccccccCC-ccHHHHHHHHHHHHHH
Q 025111 30 YRARIRLINQDKNKYNTPKYRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELPRYGLEVGL-TNYAAAYCTGLLLARR 108 (257)
Q Consensus 30 Y~~R~rli~~~knkyns~kpRLvVr~Snr~I~aQIi~~~~~GD~tlasAsS~el~k~g~k~~~-~N~~AAy~tG~LlA~r 108 (257)
+.-|..|+.+|+ +.-+.++|+-|+..|+-+.. .|-|=++... -...-|.+-..++++.
T Consensus 43 f~~R~~LVk~G~----~~L~NV~V~~~g~YiIS~aT-----------------FPsYFlK~~~~~~~~~~~lD~~iF~~~ 101 (182)
T PF08218_consen 43 FADRYELVKEGT----ADLPNVTVHPGGDYIISSAT-----------------FPSYFLKDEDDVIKAQAELDATIFKKY 101 (182)
T ss_pred HHHHHHHHHHHh----CcCCCEEEEcCCCeeeeccc-----------------ChhhhccchhHHHHHHHHHHHHHHHHH
Confidence 678999999997 66788888766555543333 3334333221 1234455666777887
Q ss_pred HHHhcCCCcccccc
Q 025111 109 VLKMLEMDDEYEGN 122 (257)
Q Consensus 109 al~k~Gl~~~YhG~ 122 (257)
.-..+||...|-|.
T Consensus 102 IAp~L~It~RfVG~ 115 (182)
T PF08218_consen 102 IAPALGITKRFVGE 115 (182)
T ss_pred hhHhcCcccceeCC
Confidence 77779999999883
No 31
>PF06292 DUF1041: Domain of Unknown Function (DUF1041); InterPro: IPR010439 This entry represents Calcium-dependent secretion activators that are involved in the exocytosis of vesicles filled with neurotransmitters and neuropeptides. They also may specifically mediate the Ca2+-dependent exocytosis of large dense-core vesicles (DCVs) and other dense-core vesicles by acting as a PtdIns(4,5)P2-binding protein that acts at prefusion step following ATP-dependent priming and participates in DCVs-membrane fusion []. However, it probably also participates in small clear synaptic vesicles (SVs) exocytosis and it is unclear whether its function is related to Ca2+ triggering []. This protein is often found in tandem repeats and co-occur with C2 domains IPR000008 from INTERPRO, Protein kinase C, phorbol ester/diacylglycerol binding regions IPR002219 from INTERPRO and PH domains IPR001849 from INTERPRO.
Probab=27.11 E-value=25 Score=28.64 Aligned_cols=40 Identities=18% Similarity=0.380 Sum_probs=32.0
Q ss_pred ccHHHHHHhhcccChHHHH---hhHHHHHHcCCC-cchHHHHHH
Q 025111 162 GHVAAYMSTLMEDEPEKYQ---SHFTEYIKKGID-ADGLEALYK 201 (257)
Q Consensus 162 ~hVa~Ym~~L~eed~e~yk---kqFS~yik~gi~-p~~~e~~y~ 201 (257)
.|.++.+-.+.+||++-|- .||+.++.-|.. ++.+=.+|.
T Consensus 53 ~~L~eL~v~vleed~e~y~~vln~F~~~~~l~~~hAE~fWsLfa 96 (106)
T PF06292_consen 53 IRLIELCVSVLEEDKEHYAPVLNQFPWELDLGVEHAEIFWSLFA 96 (106)
T ss_pred HHHHHHHHHHHHhhhhhhhhHhhhchhhhhHHHHHHHHHHHHHH
Confidence 5788999999999999999 999999877644 555555554
No 32
>PRK05218 heat shock protein 90; Provisional
Probab=26.62 E-value=51 Score=34.14 Aligned_cols=48 Identities=23% Similarity=0.308 Sum_probs=36.7
Q ss_pred ccccccHHHHHHhhcccChHHHHh---hHHHHHHcCCCcchHHHHHHHHHHHH
Q 025111 158 YIYGGHVAAYMSTLMEDEPEKYQS---HFTEYIKKGIDADGLEALYKKVHAAI 207 (257)
Q Consensus 158 rI~G~hVa~Ym~~L~eed~e~ykk---qFS~yik~gi~p~~~e~~y~~~~~~I 207 (257)
...|.-|.++...|.++|+++|.+ .|+.+||.|+--|. +++++.-.-+
T Consensus 339 ~~l~~kv~~~l~~la~~d~~~y~~f~~~~~~~lK~g~~~D~--~~~~~~~~lL 389 (613)
T PRK05218 339 KAITKKVLDELEKLAKNDREKYEKFWKEFGPVLKEGLYEDF--ANREKLAKLL 389 (613)
T ss_pred HHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHhhhhccH--HHHHHHHhhc
Confidence 446788999999999999998877 78899999987552 3555544444
No 33
>PF00452 Bcl-2: Apoptosis regulator proteins, Bcl-2 family; InterPro: IPR000712 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 2WH6_A 1K3K_A 1AF3_A 3PK1_B 2K7W_A 1F16_A 3PL7_C 2VM6_A 3I1H_A 3MQP_A ....
Probab=24.24 E-value=1.2e+02 Score=23.01 Aligned_cols=37 Identities=19% Similarity=0.361 Sum_probs=30.6
Q ss_pred ChHHHHhhHHHHHHc-CC-CcchHHHHHHHHHHHHhcCC
Q 025111 175 EPEKYQSHFTEYIKK-GI-DADGLEALYKKVHAAIRADP 211 (257)
Q Consensus 175 d~e~ykkqFS~yik~-gi-~p~~~e~~y~~~~~~I~~~P 211 (257)
=+..|...|++.+.. .+ +|++..+.|.++-+.|-+|+
T Consensus 8 ~e~~~~~~f~~~~~~l~~~~~~~~~~~f~~v~~~lf~d~ 46 (101)
T PF00452_consen 8 LERKYEDFFENMLNQLNINTPDNAYETFNEVAEELFEDG 46 (101)
T ss_dssp HHHHHHHHHHHHHHHHCSSSTTTHHHHHHHHHHHHTTTS
T ss_pred HHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhccC
Confidence 356788889998875 45 78889999999999999983
No 34
>TIGR01795 CM_mono_cladeE monofunctional chorismate mutase, alpha proteobacterial type. The alpha proteobacterial members are trusted because the pathways of CM are evident and there is only one plausible CM in the genome. In S. coelicolor, however, there is another aparrent monofunctional CM.
Probab=21.13 E-value=1.4e+02 Score=23.49 Aligned_cols=33 Identities=12% Similarity=0.276 Sum_probs=25.2
Q ss_pred cChHHHHhhHHHHHH----cCCCcchHHHHHHHHHHH
Q 025111 174 DEPEKYQSHFTEYIK----KGIDADGLEALYKKVHAA 206 (257)
Q Consensus 174 ed~e~ykkqFS~yik----~gi~p~~~e~~y~~~~~~ 206 (257)
-||+.-...+..+.. .|++|+-++.+|+-+|+.
T Consensus 45 ~dp~Re~~vl~~~~~~a~~~gl~p~~~e~i~~~i~~e 81 (94)
T TIGR01795 45 ADPAREDYQIARLRRLAIDAGLDPEFAEKFLNFIVTE 81 (94)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
Confidence 356666666666644 499999999999998864
No 35
>PRK14102 nifW nitrogenase stabilizing/protective protein; Provisional
Probab=20.44 E-value=1.1e+02 Score=24.97 Aligned_cols=30 Identities=10% Similarity=0.161 Sum_probs=19.3
Q ss_pred hhHHHHHHc------CCCcchHHHHHHHHHHHHhcC
Q 025111 181 SHFTEYIKK------GIDADGLEALYKKVHAAIRAD 210 (257)
Q Consensus 181 kqFS~yik~------gi~p~~~e~~y~~~~~~I~~~ 210 (257)
++|++||.. +++++.+-..|..+.+.-=+|
T Consensus 39 krf~qyl~~~~~~~~~~~e~~~~~~yr~~L~~AY~d 74 (105)
T PRK14102 39 KQFSQLIAEIDANFPDLSEEEKLEKYQLALEEAYQV 74 (105)
T ss_pred HHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHH
Confidence 589999984 455666666666665554333
Done!