Query 036252
Match_columns 318
No_of_seqs 276 out of 1504
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 10:54:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036252.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036252hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00135 60S acidic ribosomal 100.0 1.3E-94 2.8E-99 682.3 26.9 310 1-318 1-310 (310)
2 PTZ00240 60S ribosomal protein 100.0 2E-93 4.2E-98 673.5 27.4 311 5-317 2-323 (323)
3 PRK04019 rplP0 acidic ribosoma 100.0 2.3E-73 5.1E-78 543.9 22.3 266 5-276 2-268 (330)
4 KOG0815 60S acidic ribosomal p 100.0 2.3E-69 5E-74 473.5 21.3 245 1-248 1-245 (245)
5 cd05795 Ribosomal_P0_L10e Ribo 100.0 4E-57 8.6E-62 396.6 18.4 175 9-185 1-175 (175)
6 cd05796 Ribosomal_P0_like Ribo 100.0 3.4E-51 7.3E-56 355.2 17.2 162 9-171 1-163 (163)
7 KOG0816 Protein involved in mR 100.0 7.1E-51 1.5E-55 352.7 14.6 195 5-200 17-212 (223)
8 COG0244 RplJ Ribosomal protein 100.0 2.2E-32 4.8E-37 239.5 7.0 173 4-200 1-174 (175)
9 cd00379 Ribosomal_L10_P0 Ribos 99.9 1.2E-23 2.6E-28 180.4 6.8 122 9-138 1-126 (155)
10 PF00466 Ribosomal_L10: Riboso 99.9 2E-22 4.3E-27 160.9 10.4 96 7-109 2-99 (100)
11 PRK00099 rplJ 50S ribosomal pr 99.8 7.4E-21 1.6E-25 166.5 10.8 97 7-110 2-99 (172)
12 PRK04019 rplP0 acidic ribosoma 99.8 2.4E-21 5.3E-26 185.6 8.2 240 12-274 35-290 (330)
13 cd05797 Ribosomal_L10 Ribosoma 99.8 1.2E-20 2.7E-25 162.6 10.6 97 7-110 1-98 (157)
14 KOG1762 60s acidic ribosomal p 99.6 4.4E-16 9.6E-21 124.5 3.5 94 199-318 13-114 (114)
15 cd05833 Ribosomal_P2 Ribosomal 99.5 3.2E-15 6.9E-20 121.0 4.3 85 208-318 17-109 (109)
16 PTZ00373 60S Acidic ribosomal 99.5 1.2E-14 2.5E-19 117.8 4.6 85 208-318 19-112 (112)
17 PF00428 Ribosomal_60s: 60s Ac 99.5 4.2E-15 9.2E-20 116.3 -0.3 84 234-317 1-88 (88)
18 cd05831 Ribosomal_P1 Ribosomal 99.5 4.1E-14 8.9E-19 113.6 4.5 86 206-317 15-103 (103)
19 PLN00138 large subunit ribosom 99.4 7.8E-14 1.7E-18 113.5 4.6 85 208-318 17-113 (113)
20 cd04411 Ribosomal_P1_P2_L12p R 99.4 8.6E-14 1.9E-18 112.0 3.7 84 208-317 16-105 (105)
21 PTZ00240 60S ribosomal protein 99.2 9E-11 1.9E-15 111.8 13.0 216 12-247 35-277 (323)
22 KOG3449 60S acidic ribosomal p 99.1 3E-11 6.5E-16 96.2 3.4 77 227-318 25-112 (112)
23 COG2058 RPP1A Ribosomal protei 99.0 2.3E-10 4.9E-15 91.2 3.4 85 208-318 16-109 (109)
24 PRK06402 rpl12p 50S ribosomal 98.7 5.6E-09 1.2E-13 83.9 2.4 85 208-318 16-106 (106)
25 PTZ00135 60S acidic ribosomal 98.7 2.2E-07 4.8E-12 88.6 11.5 217 12-248 37-271 (310)
26 TIGR03685 L21P_arch 50S riboso 98.1 1.9E-06 4.1E-11 69.5 2.1 45 208-278 16-60 (105)
27 cd05832 Ribosomal_L12p Ribosom 98.0 2.8E-06 6E-11 68.4 1.5 46 208-279 16-61 (106)
28 KOG4241 Mitochondrial ribosoma 97.0 0.0024 5.2E-08 57.0 6.9 88 15-110 79-167 (245)
29 PF00428 Ribosomal_60s: 60s Ac 93.9 0.032 7E-07 43.4 1.7 30 208-248 1-30 (88)
30 cd05795 Ribosomal_P0_L10e Ribo 92.5 1 2.2E-05 39.6 9.1 128 12-148 30-175 (175)
31 PF07697 7TMR-HDED: 7TM-HD ext 79.5 1 2.2E-05 40.0 1.6 26 158-183 194-219 (222)
32 COG2058 RPP1A Ribosomal protei 77.6 1.1 2.5E-05 36.1 1.1 15 304-318 92-106 (109)
33 KOG3414 Component of the U4/U6 63.5 13 0.00029 31.1 4.4 86 12-118 42-127 (142)
34 KOG3449 60S acidic ribosomal p 61.8 4.8 0.0001 32.6 1.5 19 239-257 50-68 (112)
35 cd05833 Ribosomal_P2 Ribosomal 60.1 4 8.7E-05 33.2 0.8 14 294-308 89-102 (109)
36 PF08800 VirE_N: VirE N-termin 53.7 21 0.00045 29.9 4.2 33 19-51 24-56 (136)
37 PF12953 DUF3842: Domain of un 53.5 20 0.00044 30.0 3.9 76 28-103 2-86 (131)
38 TIGR03685 L21P_arch 50S riboso 50.6 7.1 0.00015 31.5 0.8 21 228-248 9-30 (105)
39 cd05832 Ribosomal_L12p Ribosom 49.3 4.6 0.0001 32.7 -0.5 22 227-248 8-30 (106)
40 cd04411 Ribosomal_P1_P2_L12p R 48.6 8.1 0.00018 31.2 0.8 8 301-308 92-99 (105)
41 PTZ00373 60S Acidic ribosomal 47.7 8.4 0.00018 31.5 0.8 10 241-250 54-63 (112)
42 COG2117 Predicted subunit of t 45.4 44 0.00095 29.4 4.8 69 161-237 3-79 (198)
43 COG1480 Predicted membrane-ass 42.2 17 0.00037 38.4 2.3 49 133-189 220-273 (700)
44 KOG1762 60s acidic ribosomal p 40.9 8.7 0.00019 31.4 -0.1 8 304-311 97-104 (114)
45 TIGR00762 DegV EDD domain prot 37.5 2.1E+02 0.0046 26.5 8.7 120 12-186 65-186 (275)
46 PF08496 Peptidase_S49_N: Pept 34.7 82 0.0018 27.2 4.9 26 24-49 96-122 (155)
47 PLN00138 large subunit ribosom 33.6 21 0.00046 29.2 1.1 12 240-251 51-62 (113)
48 cd05796 Ribosomal_P0_like Ribo 33.4 2.7E+02 0.0058 23.8 8.1 112 12-131 30-161 (163)
49 COG0303 MoeA Molybdopterin bio 31.0 85 0.0019 31.3 5.1 30 119-149 142-171 (404)
50 PTZ00329 eukaryotic translatio 30.9 44 0.00095 28.9 2.6 29 169-197 94-122 (155)
51 PF14226 DIOX_N: non-haem diox 29.9 1.1E+02 0.0024 23.9 4.8 42 7-49 9-50 (116)
52 PLN00208 translation initiatio 29.2 50 0.0011 28.2 2.6 25 170-194 95-119 (145)
53 cd03067 PDI_b_PDIR_N PDIb fami 27.7 1.7E+02 0.0036 23.8 5.2 66 38-111 6-73 (112)
54 PRK01777 hypothetical protein; 26.4 55 0.0012 25.8 2.3 32 113-149 10-41 (95)
55 KOG4300 Predicted methyltransf 25.7 72 0.0016 29.3 3.1 40 29-69 154-198 (252)
56 TIGR00253 RNA_bind_YhbY putati 24.6 3.5E+02 0.0076 21.3 7.4 77 15-95 6-85 (95)
57 smart00460 TGc Transglutaminas 24.5 48 0.001 23.2 1.5 17 138-154 17-33 (68)
58 PF03993 DUF349: Domain of Unk 21.0 52 0.0011 24.0 1.2 38 6-50 31-68 (77)
59 COG3473 Maleate cis-trans isom 20.1 75 0.0016 29.1 2.1 132 122-276 8-143 (238)
60 PF01985 CRS1_YhbY: CRS1 / Yhb 20.1 3.1E+02 0.0068 20.7 5.4 47 15-61 6-54 (84)
No 1
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=100.00 E-value=1.3e-94 Score=682.30 Aligned_cols=310 Identities=52% Similarity=0.833 Sum_probs=289.7
Q ss_pred CCcccccHHHHHHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccCCcEEEEEehHHHHHHHHhhhhhhCCccccc
Q 036252 1 MATRLSKAEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSIRLHAERTGNRDLLN 80 (318)
Q Consensus 1 ~~~~~~~~e~K~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~~~~~~vgKNtL~~~Al~~~~~~~~~~~~~~ 80 (318)
|+ +..+|+||+++|++|+++|++|++++|++|+||+++|||+||+.||++++++||||||||+||+++.++ .++++.
T Consensus 1 ~~-~~~~re~K~~~v~~l~e~l~~y~~v~vv~~~nv~s~ql~~iR~~LR~~a~~~vgKNTL~r~AL~~~~~~--~~~l~~ 77 (310)
T PTZ00135 1 MA-KPEKKAKKKAYFEKLYELLEKYKKILIVSVDNVGSKQMQDIRRSLRGKAELLMGKNTLIRKALKQRLEE--LPELEK 77 (310)
T ss_pred CC-cchhHHHHHHHHHHHHHHHHhCCEEEEEEcCCCCHHHHHHHHHHHhcCCEEEEEehHHHHHHHhhCccc--ccChHH
Confidence 45 778999999999999999999999999999999999999999999998999999999999999998655 345999
Q ss_pred ccccccCceEEEEecCChhhHHHHHHhccccccccCCCccCceEEeCCCCCCCCCCchhhhhhcCCceEEecceeEeecC
Q 036252 81 LIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVVPPGNTGLDPSQTSFFQVLNIPTKINKGTVEIITP 160 (318)
Q Consensus 81 L~~~l~G~~gliFt~~dp~~v~k~l~~~k~~~~ar~G~iA~~dVvi~~G~t~~~p~~~~~fq~LgIptki~~G~I~i~~d 160 (318)
|.++|+||+||+|||+||.+++++|.+|++++|||+|.|||+||+||+|||+|+|+++++||+|||||+|++|+|+|.+|
T Consensus 78 L~~~LkG~~gliFTn~dp~ev~k~l~~~k~~~~AKaG~iAp~dv~ip~G~t~~~P~~~~~fq~LgipTkI~kG~I~I~~d 157 (310)
T PTZ00135 78 LLPHVKGNVGFVFTKDDLFEVKPVILENKVPAPARAGVIAPIDVVIPAGPTGMDPSQTSFFQALGIATKIVKGQIEITNE 157 (310)
T ss_pred HHhhccCCEEEEEECCCHHHHHHHHHHcCCccccccCCCCCceEEEcCCCCCCCcchhhHHHHcCCceEecCCeEEEecC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEeecCcccCcchHHHHhhcCCCccccccceeeeeeCCcccCCccccCChHHHHHHHHHHHHHHHHHhhhcCcccCCCC
Q 036252 161 VELIKKGDRVGSSESALLSKLAIKPFSYGLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAA 240 (318)
Q Consensus 161 ~~v~~~G~~v~~~~A~lL~~L~i~p~~~~l~l~~~~~~g~~~~~~~l~it~e~~~~~~~~a~~~~~~lsl~ag~pt~~s~ 240 (318)
++||++||+||++||+||++|||+|++|+|.+.++||+|.+|++++|+||+|+|..+|++|++++++||+++||||+++|
T Consensus 158 ~~v~k~Ge~v~~~~A~LL~~L~I~p~~~~l~~~~~yd~g~~~~~~vL~i~~e~~~~~~~~~~~~i~als~aag~pt~~s~ 237 (310)
T PTZ00135 158 VHLIKEGQKVGASQAVLLQKLNIKPFSYGLEVLSIYDNGSIYDAKVLDITDEDIVAKFQEGVQNVAAISLAAGYPTEASA 237 (310)
T ss_pred eEEecCCCCcCHHHHHHHHHcCCCeEEEEEEEEEEEECCeEeCHHHcCCCHHHHHHHHHHHHHHHHHHHHHhCCCcHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHhhhhhhhhccccccchhcHHHHhcCcchhhhhccchhhhccCChhhhhhhhccCCccccccccCCCCCC
Q 036252 241 PHFFINGYKNVLSFAVATEYSFSQADKVKEYLKDPSKFAAAAAPAAAARAAPVAAAKEEKKEEPAEESDDDMGLSLFD 318 (318)
Q Consensus 241 p~~i~~a~~~~~al~~~~~~~~~~~~~ik~ll~~~~a~~~aa~~aa~~~~~~~~~~~~~~~~~~~ee~d~dmgfglFd 318 (318)
||+|+|||+++++|+++++|+||+.++++++++||+++++ | |++++ ++++ +++++ ++||||||||||||||||
T Consensus 238 p~~ia~a~k~~~a~a~~~~~~~~~~~~~~~~~a~~~~~~~-~-~~~~~-~~~~-~~~~~-~~~~~ee~~~~~g~~lf~ 310 (310)
T PTZ00135 238 PHSILNAFKNLAAIGLESGFTFPLAEKIKEALANPSAAAA-A-AAAAA-AAAA-AAAAA-PAEEEEEEEDDMGFGLFD 310 (310)
T ss_pred HHHHHHHHHHHHHHHhhcCCCChhhHHHHHhhcCchhhcc-C-ccccC-cccc-ccccc-ccccccCcchhccccCCC
Confidence 9999999999999999999999999999999999999886 3 33222 2222 22232 356778889999999998
No 2
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=100.00 E-value=2e-93 Score=673.46 Aligned_cols=311 Identities=40% Similarity=0.646 Sum_probs=285.2
Q ss_pred cccHHHHHHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccCCcEEEEEehHHHHHHHHhhhhhhCCcccccc---
Q 036252 5 LSKAEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSIRLHAERTGNRDLLNL--- 81 (318)
Q Consensus 5 ~~~~e~K~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~~~~~~vgKNtL~~~Al~~~~~~~~~~~~~~L--- 81 (318)
.+.++||.+++++|++++++|++||||+++|||++|||+||+.||++++|+||||||||+||++..++++.+++++|
T Consensus 2 ~~~~~~K~~~v~~l~~~l~~y~~v~Iv~~~nv~s~qlq~IR~~lrg~a~~~~GKNtlm~~AL~~~~~~~~~~~~~~ll~~ 81 (323)
T PTZ00240 2 PSITTAKREYEERLVDCLTKYSCVLFVGMDNVRSQQVHDVRRALRGKAEFVMGKKTLQAKIVEKRAQAKKASAEAKLFND 81 (323)
T ss_pred CchhHHHHHHHHHHHHHHHhCCEEEEEEecCCCcHHHHHHHHHhhCCcEEEEecHHHHHHHHhhccccccchhHHHHhhh
Confidence 35689999999999999999999999999999999999999999999999999999999999998776665557776
Q ss_pred ----cccccCceEEEEecCChhhHHHHHHhccccccccCCCccCceEEeCCCCCCCCCCchhhhhhcCCceEEecceeEe
Q 036252 82 ----IPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVVPPGNTGLDPSQTSFFQVLNIPTKINKGTVEI 157 (318)
Q Consensus 82 ----~~~l~G~~gliFt~~dp~~v~k~l~~~k~~~~ar~G~iA~~dVvi~~G~t~~~p~~~~~fq~LgIptki~~G~I~i 157 (318)
.++|+||+||+|||.||++|+++|++|++++|||+|+|||+||+||+|||+|+|+++++||+|||||+|++|+|+|
T Consensus 82 ~~~~~~~l~GnvgliFTn~~p~ev~~~l~~~k~~a~AraG~IAp~dVvvpaG~T~~~P~~~s~fq~LGIpTkI~kGkIeI 161 (323)
T PTZ00240 82 QCEEKNLLSGNTGLIFTNNEVQEITSVLDSHRVKAPARVGAIAPCDVIVPAGSTGMEPTQTSFFQALNIATKIAKGMVEI 161 (323)
T ss_pred hccccccccCCEEEEEeCCCHHHHHHHHHHcCCcccccCCCCCCceEEECCCCCCCCCcchHHHHHcCCCeEecCcEEEE
Confidence 4999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCcEEeecCcccCcchHHHHhhcCCCccccccceeeeeeCCcccCCccccCChHHHHHHHHHHHHHHHHHhhhcCcccC
Q 036252 158 ITPVELIKKGDRVGSSESALLSKLAIKPFSYGLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTI 237 (318)
Q Consensus 158 ~~d~~v~~~G~~v~~~~A~lL~~L~i~p~~~~l~l~~~~~~g~~~~~~~l~it~e~~~~~~~~a~~~~~~lsl~ag~pt~ 237 (318)
.+|++||++||+||++||+||++|||+|++|+++++++||+|.+|++++|+||+|+|.++|++|++++++||+++||||+
T Consensus 162 ~~d~~v~k~Ge~V~~~~A~LL~~L~IkP~~~gl~l~~vyd~g~i~~~~vL~i~~e~~~~~~~~a~~~~~~lsl~~~~pt~ 241 (323)
T PTZ00240 162 VTEKKVLSVGDKVDNSTATLLQKLNISPFYYQVEVLSVWDRGVLFTREDLSMTEDVVEKMLMEGLSNVAAMSLGAGIPTA 241 (323)
T ss_pred ecCeEEecCCCCcCHHHHHHHHHcCCCeEEEEEEEEEEEeCCeecCHHHcCCCHHHHHHHHHHHHHHHHHHHHhhCCCcH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCChhHHHHHHHhhhhhhhhccccccchhcHHHHhcCcchhhhh---ccchhhhccCChhhhhhhhccCCccccccccCC
Q 036252 238 AAAPHFFINGYKNVLSFAVATEYSFSQADKVKEYLKDPSKFAAA---AAPAAAARAAPVAAAKEEKKEEPAEESDDDMGL 314 (318)
Q Consensus 238 ~s~p~~i~~a~~~~~al~~~~~~~~~~~~~ik~ll~~~~a~~~a---a~~aa~~~~~~~~~~~~~~~~~~~ee~d~dmgf 314 (318)
+++||+|+|||+++++|+++++|+||+..+++..++||+++++. |+|+|++ +++++++++ +++|++||+||||||
T Consensus 242 ~si~~~i~~a~~~~~alav~~~~~~~~~~~~~~~~A~~~~~~~~~~~a~~~a~~-~~~~~~~~~-~~~~~~e~~~~d~~~ 319 (323)
T PTZ00240 242 ATIGPMLVDAFKNLLAVSVATSYEFEEHNGKELREAALEGLLGGGGSAAAEAAA-AAPAAASAA-AKEEEEESDEDDFGM 319 (323)
T ss_pred HHHHHHHHHHHHHHHHHhhhcCcCChhhHHHHHhhhCHHhhhcccccccccccc-ccccccccc-cccCCccCcccccCc
Confidence 99999999999999999999999999999999999999988742 2122221 112222222 245667788899999
Q ss_pred C-CC
Q 036252 315 S-LF 317 (318)
Q Consensus 315 g-lF 317 (318)
| ||
T Consensus 320 ~~~~ 323 (323)
T PTZ00240 320 GALF 323 (323)
T ss_pred cccC
Confidence 7 66
No 3
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=100.00 E-value=2.3e-73 Score=543.92 Aligned_cols=266 Identities=31% Similarity=0.481 Sum_probs=255.5
Q ss_pred cccHHHHHHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccCCcEEEEEehHHHHHHHHhhhhhhCCccccccccc
Q 036252 5 LSKAEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSIRLHAERTGNRDLLNLIPL 84 (318)
Q Consensus 5 ~~~~e~K~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~~~~~~vgKNtL~~~Al~~~~~~~~~~~~~~L~~~ 84 (318)
...++||.++|++|+++|++|++++|++|+|++++|+|+||+.||+.++|+|||||||++||+++.+ ++++.|.++
T Consensus 2 ~~~~e~K~~~v~el~~~l~~~~~v~iv~~~gl~~~ql~~lR~~lr~~~~~~v~KNtL~~~Al~~~~~----~~~~~L~~~ 77 (330)
T PRK04019 2 EHVPEWKKEEVEELKELIKSYPVVGIVDLEGIPARQLQEIRRKLRGKAELKVSKNTLIKRALEEAGE----EDLEKLEDY 77 (330)
T ss_pred CchHHHHHHHHHHHHHHHHhCCEEEEEEcCCCCHHHHHHHHHHHHcCCEEEEEehHHHHHHHHhcCc----ccHHHHHhh
Confidence 3458999999999999999999999999999999999999999998899999999999999998753 349999999
Q ss_pred ccCceEEEEecCChhhHHHHHHhccccccccCCCccCceEEeCCCCCCCCCCc-hhhhhhcCCceEEecceeEeecCcEE
Q 036252 85 LQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVVPPGNTGLDPSQ-TSFFQVLNIPTKINKGTVEIITPVEL 163 (318)
Q Consensus 85 l~G~~gliFt~~dp~~v~k~l~~~k~~~~ar~G~iA~~dVvi~~G~t~~~p~~-~~~fq~LgIptki~~G~I~i~~d~~v 163 (318)
|+|+|||+|||+||++++++|.+|++++|||+|+|||+||+||+|||+++|++ .++||+|||||+|++|+|+|.+|++|
T Consensus 78 l~G~~alift~~dp~~v~k~l~~~~~~~~ak~G~iA~~divip~G~t~~~P~~~~~~l~~lgipt~i~~G~I~i~~~~~v 157 (330)
T PRK04019 78 LEGQVALIFTNMNPFKLYKLLEKSKTPAPAKPGDIAPEDIVVPAGPTGFPPGPILSELQKLGIPARIQKGKIVIKKDTVV 157 (330)
T ss_pred ccCCEEEEEECCCHHHHHHHHHHcCCcccCCCCCCCCCeEEEcCCCCCCCCcccHHHHHHcCCCeEecCCEEEEecCeEE
Confidence 99999999999999999999999999999999999999999999999999998 59999999999999999999999999
Q ss_pred eecCcccCcchHHHHhhcCCCccccccceeeeeeCCcccCCccccCChHHHHHHHHHHHHHHHHHhhhcCcccCCCChhH
Q 036252 164 IKKGDRVGSSESALLSKLAIKPFSYGLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHF 243 (318)
Q Consensus 164 ~~~G~~v~~~~A~lL~~L~i~p~~~~l~l~~~~~~g~~~~~~~l~it~e~~~~~~~~a~~~~~~lsl~ag~pt~~s~p~~ 243 (318)
|++|++|+++||.+|++|||+|++|++++.++|++|.+|++++|+||++++..+|.+|++++.+||++++|||++++||+
T Consensus 158 ~~~G~~v~~~~a~lL~~LgI~p~~~~~~i~a~~~~G~~~~~~~l~i~~e~~~~~i~~A~~~a~~Ls~~~~~pt~~tl~~~ 237 (330)
T PRK04019 158 AKAGEVISPELANVLQKLGIKPIEVGLDLKAAYEDGVIYTPEVLAIDEEKYRSDIQEAAQNAFNLAVNAAYPTPETLETL 237 (330)
T ss_pred ecCCCCcCHHHHHHHHHcCCCHHHhhhHHHHHHhcCCccCHHHccCCHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhhhhhccccccchhcHHHHhcCcc
Q 036252 244 FINGYKNVLSFAVATEYSFSQADKVKEYLKDPS 276 (318)
Q Consensus 244 i~~a~~~~~al~~~~~~~~~~~~~ik~ll~~~~ 276 (318)
|++||+++++|+++++|.++ +.++.+|....
T Consensus 238 i~kA~~~a~aLa~~~~~~t~--e~~~~il~kA~ 268 (330)
T PRK04019 238 IQKAFREAKALAVEAGIVTP--ETADDILSKAV 268 (330)
T ss_pred HHHHHHHHHHHHHHcCCCCh--hhHHHHHHHHH
Confidence 99999999999999999777 66888886543
No 4
>KOG0815 consensus 60S acidic ribosomal protein P0 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-69 Score=473.46 Aligned_cols=245 Identities=60% Similarity=0.972 Sum_probs=239.9
Q ss_pred CCcccccHHHHHHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccCCcEEEEEehHHHHHHHHhhhhhhCCccccc
Q 036252 1 MATRLSKAEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSIRLHAERTGNRDLLN 80 (318)
Q Consensus 1 ~~~~~~~~e~K~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~~~~~~vgKNtL~~~Al~~~~~~~~~~~~~~ 80 (318)
|. +...++||..++.++++++++|+.++++..+|+.+.|||+||+.||+.+++.||||||||+|++...++.+. ++.
T Consensus 1 m~-~~~~~e~k~~y~~K~~~L~~~y~~~~~v~~dnv~s~ql~~ir~~lrg~a~vlmgkntm~rrair~~~~~~~~--~~~ 77 (245)
T KOG0815|consen 1 MV-RADKAEKKAVYFTKLRQLFEEYPKCFVVGADNVGSTQLQNIRKQLRGDAVVLMGKNTMMRRAIRGHLENNPA--LEK 77 (245)
T ss_pred Cc-chhhhHHHHHHHHHHHHHHHhcCceEEEeecchhhHHHHHHHHHhcCceeeeechhHHHHHHHHhccCCcHH--HHh
Confidence 55 788999999999999999999999999999999999999999999999999999999999999998877666 999
Q ss_pred ccccccCceEEEEecCChhhHHHHHHhccccccccCCCccCceEEeCCCCCCCCCCchhhhhhcCCceEEecceeEeecC
Q 036252 81 LIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVVPPGNTGLDPSQTSFFQVLNIPTKINKGTVEIITP 160 (318)
Q Consensus 81 L~~~l~G~~gliFt~~dp~~v~k~l~~~k~~~~ar~G~iA~~dVvi~~G~t~~~p~~~~~fq~LgIptki~~G~I~i~~d 160 (318)
|.++++|++||+||++|..++++.|.++++.++||+|.|||+||+||+++||+.|+++||||+|||||||.+|+|||.+|
T Consensus 78 llp~~~g~vgfvftk~~L~ei~~~i~~n~~~apar~GaiAp~dV~V~~~nTg~~P~ktsfFQaLgIpTKIsrGtiEIlsd 157 (245)
T KOG0815|consen 78 LLPVVKGNVGFVFTKGDLKEIRKEIIENKVGAPARVGAIAPIDVTVPAQNTGLGPEKTSFFQALGIPTKISRGTIEILSD 157 (245)
T ss_pred hccceeeceeEEEEeccHHHHHHHHHhcccccccccCCcCCceEEeccccCCCCcchhhhhhhcCCceeeecceEEeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEeecCcccCcchHHHHhhcCCCccccccceeeeeeCCcccCCccccCChHHHHHHHHHHHHHHHHHhhhcCcccCCCC
Q 036252 161 VELIKKGDRVGSSESALLSKLAIKPFSYGLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAA 240 (318)
Q Consensus 161 ~~v~~~G~~v~~~~A~lL~~L~i~p~~~~l~l~~~~~~g~~~~~~~l~it~e~~~~~~~~a~~~~~~lsl~ag~pt~~s~ 240 (318)
+.++++||||+++||.||.+|||+||.|||.+..+||||++|+|++||||+|++..+|.+|+++++++|+++||||-+++
T Consensus 158 V~lik~GDKVGaSEAtLLnmL~IsPFsyGLvv~qVyDnGsiy~pevLDiteE~l~~~f~~~vs~va~~sL~~~ypt~asv 237 (245)
T KOG0815|consen 158 VQLIKTGDKVGASEATLLNMLNISPFSYGLVVQQVYDNGSIYNPEVLDITEEDLFSKFLSGVSNVASVSLAAGYPTLASV 237 (245)
T ss_pred ceeeccCCccChhHHHHHhhhCCCccccceEEEEEecCCcccChhhcCCcHHHHHHHHHHHHHHHHHHHHhcCCCccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHH
Q 036252 241 PHFFINGY 248 (318)
Q Consensus 241 p~~i~~a~ 248 (318)
||+|.|+|
T Consensus 238 ~h~~~n~~ 245 (245)
T KOG0815|consen 238 PHSFINAY 245 (245)
T ss_pred chhhhhcC
Confidence 99999975
No 5
>cd05795 Ribosomal_P0_L10e Ribosomal protein L10 family, P0 and L10e subfamily; composed of eukaryotic 60S ribosomal protein P0 and the archaeal P0 homolog, L10e. P0 or L10e forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). These eukaryotic and archaeal P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.
Probab=100.00 E-value=4e-57 Score=396.58 Aligned_cols=175 Identities=54% Similarity=0.865 Sum_probs=169.7
Q ss_pred HHHHHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccCCcEEEEEehHHHHHHHHhhhhhhCCcccccccccccCc
Q 036252 9 EKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSIRLHAERTGNRDLLNLIPLLQGN 88 (318)
Q Consensus 9 e~K~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~~~~~~vgKNtL~~~Al~~~~~~~~~~~~~~L~~~l~G~ 88 (318)
+||+++|++|++++++|++++|++|+|++++|+++||+.||++++|+|||||||++||+++.+ ..++++.|.++|+|+
T Consensus 1 ~~K~~~v~el~e~l~~~~~v~v~~~~gl~~~ql~~lR~~lr~~~~~~v~KNtL~~~Al~~~~~--~~~~~~~L~~~l~G~ 78 (175)
T cd05795 1 EWKKEYVEKLTELLKSYPKVLIVDADNVGSKQLQKIRRSLRGKAEILMGKNTLIRRALRNLGD--ENPELEKLLPYLKGN 78 (175)
T ss_pred ChHHHHHHHHHHHHHhCCEEEEEEecCCChHHHHHHHHHhhCCCEEEEechHHHHHHHHhccc--ccccHHHHHHHhcCC
Confidence 699999999999999999999999999999999999999998899999999999999999863 334599999999999
Q ss_pred eEEEEecCChhhHHHHHHhccccccccCCCccCceEEeCCCCCCCCCCchhhhhhcCCceEEecceeEeecCcEEeecCc
Q 036252 89 VGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVVPPGNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELIKKGD 168 (318)
Q Consensus 89 ~gliFt~~dp~~v~k~l~~~k~~~~ar~G~iA~~dVvi~~G~t~~~p~~~~~fq~LgIptki~~G~I~i~~d~~v~~~G~ 168 (318)
+||+|||+||++++++|++|++++|||+|+|||+||+||+|+|+|+|+|+++||+|||||+|++|+|+|.+|++||++||
T Consensus 79 ~~liFt~~dp~~v~k~l~~~~~~~~ar~G~iA~~dvvi~~G~t~~~p~~~~~~~~lgiptki~~G~i~i~~d~~v~k~G~ 158 (175)
T cd05795 79 VGFIFTNGDPFEIRKILEENKVPAPAKPGAIAPCDVVVPAGPTGMPPGPTSFFQALGIPTKIEKGKIEIISDVVVVKKGE 158 (175)
T ss_pred EEEEEECCCHHHHHHHHHHcCCcccccCCCccCceEEEcCCCcCCCCCchHHHHHcCCceEEecCEEEEecCeEEecCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCcchHHHHhhcCCCc
Q 036252 169 RVGSSESALLSKLAIKP 185 (318)
Q Consensus 169 ~v~~~~A~lL~~L~i~p 185 (318)
+||++||.||++|||+|
T Consensus 159 ~v~~~~A~lL~~l~i~P 175 (175)
T cd05795 159 KVGASEATLLNKLNIKP 175 (175)
T ss_pred CcCHHHHHHHHHcCCCC
Confidence 99999999999999998
No 6
>cd05796 Ribosomal_P0_like Ribosomal protein L10 family, P0-like protein subfamily; composed of uncharacterized eukaryotic proteins with similarity to the 60S ribosomal protein P0, including the Saccharomyces cerevisiae protein called mRNA turnover protein 4 (MRT4). MRT4 may be involved in mRNA decay. P0 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. It occupies the L7/L12 stalk of the ribosome. The stalk is known to contain the binding site for elongation factors EF-G and EF-Tu; however, there is disagreement as to whether or not P0 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, P0 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WAS
Probab=100.00 E-value=3.4e-51 Score=355.20 Aligned_cols=162 Identities=25% Similarity=0.395 Sum_probs=156.0
Q ss_pred HHHHHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccCCcEEEEEehHHHHHHHHhhhhhhCCcccccccccccCc
Q 036252 9 EKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSIRLHAERTGNRDLLNLIPLLQGN 88 (318)
Q Consensus 9 e~K~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~~~~~~vgKNtL~~~Al~~~~~~~~~~~~~~L~~~l~G~ 88 (318)
+||.+++++|+++|++|++++|++|+|++++|+|+||+.||+. +|+|||||||++||+++.+++..++++.|.++|+|+
T Consensus 1 e~K~~~v~~l~e~l~~y~~v~iv~~~gl~~~ql~~iR~~lr~~-~~~v~KNtl~~~Al~~~~~~~~~~~~~~L~~~l~G~ 79 (163)
T cd05796 1 ELKQKLVENIREAVDKYKYIYVFSVDNMRNNKLKDIRQEWKDS-RFFFGKNKVMQVALGRTPEDEYKPNLHKLSKYLKGQ 79 (163)
T ss_pred ChHHHHHHHHHHHHHhCCEEEEEEecCCCHHHHHHHHHHhcCC-EEEEEchHHHHHHHhhCccccccccHHHHHHHhCCC
Confidence 6999999999999999999999999999999999999999986 999999999999999987776777899999999999
Q ss_pred eEEEEecCChhhHHHHHHhccccccccCCCccCceEEeCCCCCCCCCCc-hhhhhhcCCceEEecceeEeecCcEEeecC
Q 036252 89 VGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVVPPGNTGLDPSQ-TSFFQVLNIPTKINKGTVEIITPVELIKKG 167 (318)
Q Consensus 89 ~gliFt~~dp~~v~k~l~~~k~~~~ar~G~iA~~dVvi~~G~t~~~p~~-~~~fq~LgIptki~~G~I~i~~d~~v~~~G 167 (318)
+||+|||+||++++++|.+|++++|||+|+|||+||+||+|+|++.|++ .++||+|||||+|++|+|+|.+|++||++|
T Consensus 80 ~~lift~~dp~~v~k~l~~~~~~~~ar~G~iA~~dvvi~~G~~~~~p~~~~~~~~~lgiptki~~G~I~i~~d~~v~k~G 159 (163)
T cd05796 80 VGLLFTNEPPEEVIEYFDSYSEPDFARAGSIATETVTLPEGPLEQFPHSMEPQLRKLGLPTKLKKGVITLEADYVVCEEG 159 (163)
T ss_pred EEEEEECCCHHHHHHHHHHcCCcccccCCCCCCceEEEeCCCCCCCCCCcchHHHHcCCCeEEeCCEEEEecCcEEECCC
Confidence 9999999999999999999999999999999999999999999987765 899999999999999999999999999999
Q ss_pred cccC
Q 036252 168 DRVG 171 (318)
Q Consensus 168 ~~v~ 171 (318)
|+||
T Consensus 160 ~~v~ 163 (163)
T cd05796 160 KVLT 163 (163)
T ss_pred CCCc
Confidence 9986
No 7
>KOG0816 consensus Protein involved in mRNA turnover [RNA processing and modification]
Probab=100.00 E-value=7.1e-51 Score=352.67 Aligned_cols=195 Identities=26% Similarity=0.400 Sum_probs=189.7
Q ss_pred cccHHHHHHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccCCcEEEEEehHHHHHHHHhhhhhhCCccccccccc
Q 036252 5 LSKAEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSIRLHAERTGNRDLLNLIPL 84 (318)
Q Consensus 5 ~~~~e~K~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~~~~~~vgKNtL~~~Al~~~~~~~~~~~~~~L~~~ 84 (318)
++.+++|+.+|++|++++++|+++||+++.|||+..+++||.+|+ +++|+||||++|.+||+...++++.+++++++..
T Consensus 17 KKg~e~K~~i~~~ir~~vd~Y~~v~Vf~~~nMRn~~lk~iR~~~k-~sr~f~GknKVm~vaLG~~~~dE~~~~l~klskl 95 (223)
T KOG0816|consen 17 KKGKEKKEAIVEEIREAVDKYPYVFVFEVPNMRNTTLKEIRQDFK-NSRFFFGKNKVMQVALGRSREDEYKENLYKLSKL 95 (223)
T ss_pred hhhHHHHHHHHHHHHHHHhhCCeEEEEEcCCcchHHHHHHHHHhh-ccceecchhhHHHHHhcCCchhhHHHHHHHhhhh
Confidence 457899999999999999999999999999999999999999999 7999999999999999999999999999999999
Q ss_pred ccCceEEEEecCChhhHHHHHHhccccccccCCCccCceEEeCCCCC-CCCCCchhhhhhcCCceEEecceeEeecCcEE
Q 036252 85 LQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVVPPGNT-GLDPSQTSFFQVLNIPTKINKGTVEIITPVEL 163 (318)
Q Consensus 85 l~G~~gliFt~~dp~~v~k~l~~~k~~~~ar~G~iA~~dVvi~~G~t-~~~p~~~~~fq~LgIptki~~G~I~i~~d~~v 163 (318)
|+|.+||+|||.++.++..+|.+|...+|||+|++||.+|+||+||. .+++++.+++|+|||||++.+|+|+|.+|++|
T Consensus 96 l~G~~GLlFTd~~keeV~e~f~sy~~~DyaR~g~vA~~Tv~ip~Gpl~~f~hsmEP~lRklglPt~lk~G~vtL~sdy~V 175 (223)
T KOG0816|consen 96 LKGSVGLLFTDMSKEEVIEWFRSYVEEDYARAGDVAPETVTIPEGPLEQFAHSMEPQLRKLGLPTKLKKGVVTLLSDYTV 175 (223)
T ss_pred ccCceEEEecCCCHHHHHHHHHHHHHHhhhccCCcCcceEeecCcchhhcccccchhhHhhcCceeecCCeEEEecCcee
Confidence 99999999999999999999999999999999999999999999997 58899999999999999999999999999999
Q ss_pred eecCcccCcchHHHHhhcCCCccccccceeeeeeCCc
Q 036252 164 IKKGDRVGSSESALLSKLAIKPFSYGLIVMSVYENGS 200 (318)
Q Consensus 164 ~~~G~~v~~~~A~lL~~L~i~p~~~~l~l~~~~~~g~ 200 (318)
|++|++++++||.||++||+++++|++.+.++|+..+
T Consensus 176 CeEG~~Ld~rqA~ILKlfg~kma~Fkl~~~~~w~~s~ 212 (223)
T KOG0816|consen 176 CEEGDVLDPRQAKILKLFGKKMAKFKLAVKAYWSKSS 212 (223)
T ss_pred ecCCcccCHHHHHHHHHHhHhhHhheEEEEEEEcCcc
Confidence 9999999999999999999999999999999998543
No 8
>COG0244 RplJ Ribosomal protein L10 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2.2e-32 Score=239.55 Aligned_cols=173 Identities=26% Similarity=0.320 Sum_probs=164.7
Q ss_pred ccccHHHHHHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccC-CcEEEEEehHHHHHHHHhhhhhhCCccccccc
Q 036252 4 RLSKAEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRD-HSIVLMGKNTMMKRSIRLHAERTGNRDLLNLI 82 (318)
Q Consensus 4 ~~~~~e~K~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~-~~~~~vgKNtL~~~Al~~~~~~~~~~~~~~L~ 82 (318)
|...++||.++|++++++|++|++++|+||+|+++.|+++||++||+ +++++|+||||+++||+++. .+.|.
T Consensus 1 ~~~~~e~K~~~v~el~e~~~~s~~~~i~dy~Gl~~~ql~~lR~~lr~~g~~lkV~KNtL~~rAl~~~~-------~e~l~ 73 (175)
T COG0244 1 MALAREWKKELVAELKELIKESPSVVIVDYRGLTVAQLTELRKKLREAGAKLKVVKNTLLRRALEEAG-------LEGLD 73 (175)
T ss_pred CCccHHHHHHHHHHHHHHHhhCCEEEEEEeCCCcHHHHHHHHHHHHhCCcEEEEEhhHHHHHHHHhcc-------hhhHH
Confidence 34678999999999999999999999999999999999999999997 59999999999999999986 67799
Q ss_pred ccccCceEEEEecCChhhHHHHHHhccccccccCCCccCceEEeCCCCCCCCCCchhhhhhcCCceEEecceeEeecCcE
Q 036252 83 PLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVVPPGNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVE 162 (318)
Q Consensus 83 ~~l~G~~gliFt~~dp~~v~k~l~~~k~~~~ar~G~iA~~dVvi~~G~t~~~p~~~~~fq~LgIptki~~G~I~i~~d~~ 162 (318)
++|+|+++++||++||++++|+|.+|..+. |++++.++.+++|. .|++|+.+..|+|.+.+|..
T Consensus 74 ~~l~Gp~ai~fs~~dp~~~~K~~~~f~k~~----~~~~~~~~~~~eg~------------~l~~~~v~~~aklp~~~el~ 137 (175)
T COG0244 74 DLLKGPTAIAFSNEDPVAAAKLLKDFAKEA----GDKAPIKGGVPEGK------------VLGAAEVIALAKLPSKEELV 137 (175)
T ss_pred HhccCCeEEEEecCCHHHHHHHHHHHhhhh----cccceEEEEEecCc------------ccCHHHHHHHhcCCcHHHHH
Confidence 999999999999999999999999998766 99999999999998 48899999999999999999
Q ss_pred EeecCcccCcchHHHHhhcCCCccccccceeeeeeCCc
Q 036252 163 LIKKGDRVGSSESALLSKLAIKPFSYGLIVMSVYENGS 200 (318)
Q Consensus 163 v~~~G~~v~~~~A~lL~~L~i~p~~~~l~l~~~~~~g~ 200 (318)
+...|..+.|.. .++..|++.|.++++.+.++|++|.
T Consensus 138 ~~l~g~~~ap~~-~~~~~L~a~~~~~~~~~~a~~~~g~ 174 (175)
T COG0244 138 VMLLGVLQAPAT-KLLRALKAVPDKVGLKLLAAYEKGV 174 (175)
T ss_pred HHHHHhhHhhHH-HHHHHHhccHHHHhhHHHHhhccCC
Confidence 999999999999 9999999999999999999999885
No 9
>cd00379 Ribosomal_L10_P0 Ribosomal protein L10 family; composed of the large subunit ribosomal protein called L10 in bacteria, P0 in eukaryotes, and L10e in archaea, as well as uncharacterized P0-like eukaryotic proteins. In all three kingdoms, L10 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been sho
Probab=99.89 E-value=1.2e-23 Score=180.42 Aligned_cols=122 Identities=31% Similarity=0.447 Sum_probs=115.2
Q ss_pred HHHHHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccCC-cEEEEEehHHHHHHHHhhhhhhCCcccccccccccC
Q 036252 9 EKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDH-SIVLMGKNTMMKRSIRLHAERTGNRDLLNLIPLLQG 87 (318)
Q Consensus 9 e~K~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~~-~~~~vgKNtL~~~Al~~~~~~~~~~~~~~L~~~l~G 87 (318)
++|.+++++++++|++|+.+++++|+|++++++++||+.||+. ++++|+|||||++||+++. ++.+.++|+|
T Consensus 1 ~~K~~~v~~l~~~l~~~~~v~v~~~~~l~~~~~~~lR~~l~~~~~~~~v~KNtl~~~Al~~t~-------~~~~~~~l~G 73 (155)
T cd00379 1 EKKEELVEELKELLKKYKSVVVVDYRGLTVAQLTELRKELRESGAKLKVGKNTLMRRALKGTG-------FEELKPLLKG 73 (155)
T ss_pred CchHHHHHHHHHHHHhCCEEEEEecCCCcHHHHHHHHHHHHHcCCEEEEEehHHHHHHHcCCC-------ccchhhhCcC
Confidence 5899999999999999999999999999999999999999975 8999999999999999985 7888899999
Q ss_pred ceEEEEecCChhhHHHHHHhcccc---ccccCCCccCceEEeCCCCCCCCCCch
Q 036252 88 NVGMIFTKGDLKEVSDEVSKHKVA---APARVGLVAPIDVVVPPGNTGLDPSQT 138 (318)
Q Consensus 88 ~~gliFt~~dp~~v~k~l~~~k~~---~~ar~G~iA~~dVvi~~G~t~~~p~~~ 138 (318)
+++++||++||.++.++|.+|+.. .++|+|.++ .+|+.|.+.+.+++.|.
T Consensus 74 ~~~~~f~~~~~~~~~k~~~~~~k~~~~~~~k~g~~~-~~v~~~~~~~~l~~lp~ 126 (155)
T cd00379 74 PTALAFTNEDPVEVAKVLKDFAKENKKLFAKGGVVA-GKVLDPAGVTALAKLPS 126 (155)
T ss_pred CEEEEEeCCChHHHHHHHHHHHHhCCCceEEEEEEc-CEecCHHHHHHHhcCCC
Confidence 999999999999999999999888 899999999 99999999988777663
No 10
>PF00466 Ribosomal_L10: Ribosomal protein L10; InterPro: IPR001790 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 [, ]. On the basis of sequence similarities the following prokaryotic and eukaryotic ribosomal proteins can be grouped: Bacterial 50S ribosomal protein L10; Archaebacterial acidic ribosomal protein P0 homologue (L10E); Eukaryotic 60S ribosomal protein P0 (L10E). This entry represents the ribosomal protein L10P family, with includes the above mentioned ribosomal proteins.; GO: 0042254 ribosome biogenesis, 0005622 intracellular; PDB: 3A1Y_G 3D5D_J 3PYT_I 3PYV_I 3D5B_J 3PYO_I 3PYR_I 3MS1_I 3MRZ_I 1VQ9_G ....
Probab=99.88 E-value=2e-22 Score=160.93 Aligned_cols=96 Identities=30% Similarity=0.447 Sum_probs=91.2
Q ss_pred cHHHHHHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccCC-cEEEEEehHHHHHHHHhhhhhhCCcccc-ccccc
Q 036252 7 KAEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDH-SIVLMGKNTMMKRSIRLHAERTGNRDLL-NLIPL 84 (318)
Q Consensus 7 ~~e~K~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~~-~~~~vgKNtL~~~Al~~~~~~~~~~~~~-~L~~~ 84 (318)
+|++|++++++++++|++|+.+++++|+|+++.|+++||++||+. ++++|+|||||++||+++. .+ .|.++
T Consensus 2 ~~~~K~~~v~~~~~~l~~~~~v~v~~~~~l~~~~~~~lR~~l~~~~~~~~v~KN~l~~~Al~~~~-------~~~~l~~~ 74 (100)
T PF00466_consen 2 TKEKKEEIVEELKELLKKSKYVIVVDYNGLSANQLQELRKELRKKGGKFKVVKNTLMKKALKNTG-------FEEALSPL 74 (100)
T ss_dssp SCHHHHHHHHHHHHHHHCSSEEEEEECTTSCHHHHHHHHHHHHHHTEEEEECSHHHHHHHHHHHH-------TSSSSSCC
T ss_pred cHHHHHHHHHHHHHHHHhCCEEEEEEeCCCCHHHHHHHHHHHHhcCcEEEEecHHHHHHHHhcCc-------cccCcccc
Confidence 689999999999999999999999999999999999999999985 9999999999999999986 44 68999
Q ss_pred ccCceEEEEecCChhhHHHHHHhcc
Q 036252 85 LQGNVGMIFTKGDLKEVSDEVSKHK 109 (318)
Q Consensus 85 l~G~~gliFt~~dp~~v~k~l~~~k 109 (318)
|+|++|++||++||.+++++|.+|.
T Consensus 75 l~G~~~~if~~~d~~~~~k~l~~~~ 99 (100)
T PF00466_consen 75 LKGPTALIFSNEDPFEIAKILKKFA 99 (100)
T ss_dssp TSSSEEEEEESSSHHHHHHHHHHST
T ss_pred ccCCEEEEEECCCHHHHHHHHHHhc
Confidence 9999999999999999999999874
No 11
>PRK00099 rplJ 50S ribosomal protein L10; Reviewed
Probab=99.84 E-value=7.4e-21 Score=166.47 Aligned_cols=97 Identities=20% Similarity=0.242 Sum_probs=92.5
Q ss_pred cHHHHHHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccC-CcEEEEEehHHHHHHHHhhhhhhCCcccccccccc
Q 036252 7 KAEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRD-HSIVLMGKNTMMKRSIRLHAERTGNRDLLNLIPLL 85 (318)
Q Consensus 7 ~~e~K~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~-~~~~~vgKNtL~~~Al~~~~~~~~~~~~~~L~~~l 85 (318)
+|++|.++++++++++++|+.+++++|+|++++|+++||+.||+ +++++|+|||||++|++++. ++.|.++|
T Consensus 2 ~r~~K~~~v~~l~~~l~~~~~v~v~~~~gl~~~~~~~lR~~lr~~~~~~~V~KNtL~~~Al~~~~-------~~~l~~~l 74 (172)
T PRK00099 2 NREEKKEIVAELAEKLKKAQSAVVADYRGLTVAQMTELRKKLREAGVEYKVVKNTLARRALEGTG-------FEGLDDLL 74 (172)
T ss_pred CHHHHHHHHHHHHHHHHhCCEEEEEecCCCcHHHHHHHHHHHHHcCCEEEEehhHHHHHHHhcCC-------chhhhhhC
Confidence 68999999999999999999999999999999999999999997 58999999999999999874 89999999
Q ss_pred cCceEEEEecCChhhHHHHHHhccc
Q 036252 86 QGNVGMIFTKGDLKEVSDEVSKHKV 110 (318)
Q Consensus 86 ~G~~gliFt~~dp~~v~k~l~~~k~ 110 (318)
+|++|++||++||.++++++.+|..
T Consensus 75 ~G~~al~fs~~d~~~~~k~l~~f~K 99 (172)
T PRK00099 75 KGPTAIAFSYEDPVAAAKVLKDFAK 99 (172)
T ss_pred cCCeEEEEeCCChHHHHHHHHHHHh
Confidence 9999999999999999999999854
No 12
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=99.84 E-value=2.4e-21 Score=185.61 Aligned_cols=240 Identities=15% Similarity=0.134 Sum_probs=192.1
Q ss_pred HHHHHHHHHHHhccCeEEEEEec-------CCCchHHHHHHHHccCCcEEEEEehHH--HHHHHHhhhhhhCC-cc----
Q 036252 12 IAYDARLCKLLEEYSQILIVAAD-------NVGSNQLQHIRAGLRDHSIVLMGKNTM--MKRSIRLHAERTGN-RD---- 77 (318)
Q Consensus 12 ~~~v~~l~e~l~~y~~v~iv~~~-------~v~s~ql~~iR~~lr~~~~~~vgKNtL--~~~Al~~~~~~~~~-~~---- 77 (318)
...+++||..|+....+.++.-+ +.....+.+|-..|+|..-+.+.+... +.+.+.+.....+. .|
T Consensus 35 ~~ql~~lR~~lr~~~~~~v~KNtL~~~Al~~~~~~~~~~L~~~l~G~~alift~~dp~~v~k~l~~~~~~~~ak~G~iA~ 114 (330)
T PRK04019 35 ARQLQEIRRKLRGKAELKVSKNTLIKRALEEAGEEDLEKLEDYLEGQVALIFTNMNPFKLYKLLEKSKTPAPAKPGDIAP 114 (330)
T ss_pred HHHHHHHHHHHHcCCEEEEEehHHHHHHHHhcCcccHHHHHhhccCCEEEEEECCCHHHHHHHHHHcCCcccCCCCCCCC
Confidence 45688899999987555554322 221133788999999887777775443 33445443322211 00
Q ss_pred cccccccccCceEEEEecCChhhHHHHHHhccccccccCCC--ccCceEEeCCCCCCCCCCchhhhhhcCCceEEeccee
Q 036252 78 LLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGL--VAPIDVVVPPGNTGLDPSQTSFFQVLNIPTKINKGTV 155 (318)
Q Consensus 78 ~~~L~~~l~G~~gliFt~~dp~~v~k~l~~~k~~~~ar~G~--iA~~dVvi~~G~t~~~p~~~~~fq~LgIptki~~G~I 155 (318)
.+...+ .|+| +.+|+.+...|.+.+.+++++.|. |+++++++++|+| ++|++.+.||+|||++...+++|
T Consensus 115 ~divip--~G~t-----~~~P~~~~~~l~~lgipt~i~~G~I~i~~~~~v~~~G~~-v~~~~a~lL~~LgI~p~~~~~~i 186 (330)
T PRK04019 115 EDIVVP--AGPT-----GFPPGPILSELQKLGIPARIQKGKIVIKKDTVVAKAGEV-ISPELANVLQKLGIKPIEVGLDL 186 (330)
T ss_pred CeEEEc--CCCC-----CCCCcccHHHHHHcCCCeEecCCEEEEecCeEEecCCCC-cCHHHHHHHHHcCCCHHHhhhHH
Confidence 122222 4555 789999999999999999999999 9999999999999 99999999999999999999996
Q ss_pred EeecCcEEeecCcccCcchHHHHhhcCCCccccccceeeeeeCCcccCCccccCChHHHHHHHHHHHHHHHHHhhhcCcc
Q 036252 156 EIITPVELIKKGDRVGSSESALLSKLAIKPFSYGLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYP 235 (318)
Q Consensus 156 ~i~~d~~v~~~G~~v~~~~A~lL~~L~i~p~~~~l~l~~~~~~g~~~~~~~l~it~e~~~~~~~~a~~~~~~lsl~ag~p 235 (318)
..++..|..++++.+ +|.|.+|...+..+|.++..++.+...+|++.+...|.+|++++.+|+.+++||
T Consensus 187 -----~a~~~~G~~~~~~~l------~i~~e~~~~~i~~A~~~a~~Ls~~~~~pt~~tl~~~i~kA~~~a~aLa~~~~~~ 255 (330)
T PRK04019 187 -----KAAYEDGVIYTPEVL------AIDEEKYRSDIQEAAQNAFNLAVNAAYPTPETLETLIQKAFREAKALAVEAGIV 255 (330)
T ss_pred -----HHHHhcCCccCHHHc------cCCHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 567788999999887 699999999999999999989999999999999999999999999999999999
Q ss_pred cCCCChhHHHHHHHhhhhhhhhccccccchhcHHHHhcC
Q 036252 236 TIAAAPHFFINGYKNVLSFAVATEYSFSQADKVKEYLKD 274 (318)
Q Consensus 236 t~~s~p~~i~~a~~~~~al~~~~~~~~~~~~~ik~ll~~ 274 (318)
|++++++++.+|+.++.+|+.+++=. ..+.+-|.+
T Consensus 256 t~e~~~~il~kA~~~~~ala~~~~~~----~~~~~~~~~ 290 (330)
T PRK04019 256 TPETADDILSKAVAQALALAAALADK----DALDEELKE 290 (330)
T ss_pred ChhhHHHHHHHHHHHHHHHHHHhcCc----ccccHHHHh
Confidence 99999999999999999999887532 345454543
No 13
>cd05797 Ribosomal_L10 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-in
Probab=99.84 E-value=1.2e-20 Score=162.63 Aligned_cols=97 Identities=24% Similarity=0.295 Sum_probs=92.5
Q ss_pred cHHHHHHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccCC-cEEEEEehHHHHHHHHhhhhhhCCcccccccccc
Q 036252 7 KAEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDH-SIVLMGKNTMMKRSIRLHAERTGNRDLLNLIPLL 85 (318)
Q Consensus 7 ~~e~K~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~~-~~~~vgKNtL~~~Al~~~~~~~~~~~~~~L~~~l 85 (318)
.|++|.++++++++++++|+.+++++|+|++++|+++||+.||+. ++++|+||||+++|++++. ++.|.++|
T Consensus 1 ~~~~K~~~v~~l~~~l~~~~~v~v~~~~gl~~~~~~~lR~~lr~~~~~~~V~KNtL~~~Al~~t~-------~~~l~~~l 73 (157)
T cd05797 1 NREKKEEIVAELKEKLKEAKSVVVADYRGLTVAQLTELRKELREAGVKLKVVKNTLAKRALEGTG-------FEDLDDLL 73 (157)
T ss_pred ChHHHHHHHHHHHHHHHhCCEEEEEecCCCcHHHHHHHHHHHHHcCCEEEEehhHHHHHHHhcCC-------chhhHhhC
Confidence 479999999999999999999999999999999999999999974 8999999999999999875 88999999
Q ss_pred cCceEEEEecCChhhHHHHHHhccc
Q 036252 86 QGNVGMIFTKGDLKEVSDEVSKHKV 110 (318)
Q Consensus 86 ~G~~gliFt~~dp~~v~k~l~~~k~ 110 (318)
+|+++++||++||.++.++|.+|..
T Consensus 74 ~G~~al~f~~~d~~~~~k~l~~f~k 98 (157)
T cd05797 74 KGPTAIAFSEEDPVAAAKVLKDFAK 98 (157)
T ss_pred cCCEEEEEeCCChHHHHHHHHHHHH
Confidence 9999999999999999999999866
No 14
>KOG1762 consensus 60s acidic ribosomal protein P1 [Translation, ribosomal structure and biogenesis]
Probab=99.60 E-value=4.4e-16 Score=124.54 Aligned_cols=94 Identities=33% Similarity=0.423 Sum_probs=68.2
Q ss_pred CcccCCccccCChHHHHHHHHHHHHHHHHHhhhcCcccCCCChhHHHHHHHhhhhhhhhccccccchhcHHHHhcCcchh
Q 036252 199 GSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGYKNVLSFAVATEYSFSQADKVKEYLKDPSKF 278 (318)
Q Consensus 199 g~~~~~~~l~it~e~~~~~~~~a~~~~~~lsl~ag~pt~~s~p~~i~~a~~~~~al~~~~~~~~~~~~~ik~ll~~~~a~ 278 (318)
+.++--+.+.||.+.+. .|.+++|..++.+||.+|++++.+ .+++++|.|.+++
T Consensus 13 alIL~d~~i~it~dki~-----------tl~kaa~v~ve~~Wp~lfakale~---------------vni~~li~n~gag 66 (114)
T KOG1762|consen 13 ALILHDDEIEVTADKIN-----------TLTKAAGVNVEPYWPGLFAKALEG---------------VNIKELICNVGAG 66 (114)
T ss_pred hhhccccceeeehhhhh-----------hHHHhccCcccccchhHHHHHhcc---------------CChHHHHHhcccC
Confidence 34444555578888765 899999999999999999999988 5799999999974
Q ss_pred hhhc-cch------hh-hccCChhhhhhhhccCCccccccccCCCCCC
Q 036252 279 AAAA-APA------AA-ARAAPVAAAKEEKKEEPAEESDDDMGLSLFD 318 (318)
Q Consensus 279 ~~aa-~~a------a~-~~~~~~~~~~~~~~~~~~ee~d~dmgfglFd 318 (318)
+++. +++ ++ +++++++++++++++|+.|||||||||||||
T Consensus 67 ~~a~a~~~~~~~~aa~~~~aA~~~Ekk~eak~EeseesddDmgfGLfd 114 (114)
T KOG1762|consen 67 GGALAAGAAAAGGAAAAGGAAAAEEKKEEAKKEESEESDDDMGFGLFD 114 (114)
T ss_pred CccCCCccccccccccccccccchHHHHHhhhhhhcccccccccCCCC
Confidence 4322 111 11 1123334445555677889999999999998
No 15
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=99.55 E-value=3.2e-15 Score=121.04 Aligned_cols=85 Identities=41% Similarity=0.482 Sum_probs=58.9
Q ss_pred cCChHHHHHHHHHHHHHHHHHhhhcCcccCCCChhHHHHHHHhhhhhhhhccccccchhcHHHHhcCcchh-------hh
Q 036252 208 DLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGYKNVLSFAVATEYSFSQADKVKEYLKDPSKF-------AA 280 (318)
Q Consensus 208 ~it~e~~~~~~~~a~~~~~~lsl~ag~pt~~s~p~~i~~a~~~~~al~~~~~~~~~~~~~ik~ll~~~~a~-------~~ 280 (318)
.||.++|. +|..++|+.+++.||.+|.+++++ ++|.++|++...- ++
T Consensus 17 ~pTa~dI~-----------~IL~AaGveVe~~~~~lf~~~L~G---------------Kdi~eLIa~g~~kl~s~~~~~~ 70 (109)
T cd05833 17 SPSAADVK-----------KILGSVGVEVDDEKLNKVISELEG---------------KDVEELIAAGKEKLASVPAGAG 70 (109)
T ss_pred CCCHHHHH-----------HHHHHcCCCccHHHHHHHHHHHcC---------------CCHHHHHHHhHhhhcCCCcccc
Confidence 57788776 999999999999999999999988 7899999875441 11
Q ss_pred hccchhhhccC-ChhhhhhhhccCCccccccccCCCCCC
Q 036252 281 AAAPAAAARAA-PVAAAKEEKKEEPAEESDDDMGLSLFD 318 (318)
Q Consensus 281 aa~~aa~~~~~-~~~~~~~~~~~~~~ee~d~dmgfglFd 318 (318)
+++|+++++++ +.+++++++++|++|||||||||||||
T Consensus 71 ~aa~a~~~~a~aa~~~~~e~kkee~eee~ddDmGf~LFd 109 (109)
T cd05833 71 GAAPAAAAAAAAAAAAKKEEKKEESEEESDDDMGFGLFD 109 (109)
T ss_pred ccccccccccccccchhhhhhccCCccccccccCCCCCC
Confidence 12122222111 112233444556666679999999998
No 16
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=99.51 E-value=1.2e-14 Score=117.78 Aligned_cols=85 Identities=31% Similarity=0.410 Sum_probs=57.1
Q ss_pred cCChHHHHHHHHHHHHHHHHHhhhcCcccCCCChhHHHHHHHhhhhhhhhccccccchhcHHHHhc-------Ccchhhh
Q 036252 208 DLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGYKNVLSFAVATEYSFSQADKVKEYLK-------DPSKFAA 280 (318)
Q Consensus 208 ~it~e~~~~~~~~a~~~~~~lsl~ag~pt~~s~p~~i~~a~~~~~al~~~~~~~~~~~~~ik~ll~-------~~~a~~~ 280 (318)
.||.++|. +|..++|+.+...|+.+|.++++. ++|.++|+ ..+.+++
T Consensus 19 ~pTaddI~-----------kIL~AaGveVd~~~~~l~~~~L~G---------------KdI~ELIa~G~~kl~svgg~~~ 72 (112)
T PTZ00373 19 NPTKKEVK-----------NVLSAVNADVEDDVLDNFFKSLEG---------------KTPHELIAAGMKKLQNIGGGVA 72 (112)
T ss_pred CCCHHHHH-----------HHHHHcCCCccHHHHHHHHHHHcC---------------CCHHHHHHHhHHHHhcccCccc
Confidence 47777766 999999999999999999999988 78999887 3432211
Q ss_pred hc-cchhhh-ccCChhhhhhhhccCCccccccccCCCCCC
Q 036252 281 AA-APAAAA-RAAPVAAAKEEKKEEPAEESDDDMGLSLFD 318 (318)
Q Consensus 281 aa-~~aa~~-~~~~~~~~~~~~~~~~~ee~d~dmgfglFd 318 (318)
++ ++++++ ++++++++++++++|++|||||||||||||
T Consensus 73 aa~a~a~~~~~~~~~~~~~~e~k~ee~ee~ddDmgf~LFd 112 (112)
T PTZ00373 73 AAAAPAAGAATAGAKAEAKKEEKKEEEEEEEDDLGFSLFG 112 (112)
T ss_pred ccccccccccccccchhhhhhhcccccccccccccccccC
Confidence 11 111111 122222233333456667889999999998
No 17
>PF00428 Ribosomal_60s: 60s Acidic ribosomal protein; InterPro: IPR001813 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 [, ]. The 60S acidic ribosomal protein plays an important role in the elongation step of protein synthesis. This family includes archaebacterial L12, eukaryotic P0, P1 and P2 []. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Alt a 6, Alt a 12, Cla h 3, Cla h 4 and Cla h 12.; GO: 0003735 structural constituent of ribosome, 0006414 translational elongation, 0005622 intracellular, 0005840 ribosome; PDB: 3A1Y_C 3N2D_B 2LBF_A 3IZS_t 3IZR_t 1S4J_A 2JDL_C 2W1O_B 1S4H_A 2ZKR_g.
Probab=99.48 E-value=4.2e-15 Score=116.32 Aligned_cols=84 Identities=40% Similarity=0.401 Sum_probs=58.6
Q ss_pred cccCCCChhHHHHHHHhhhhhhhhccccccchhcHHHHhcCcchhh--hhccchhhhc-cCChhhhhhhhccCC-ccccc
Q 036252 234 YPTIAAAPHFFINGYKNVLSFAVATEYSFSQADKVKEYLKDPSKFA--AAAAPAAAAR-AAPVAAAKEEKKEEP-AEESD 309 (318)
Q Consensus 234 ~pt~~s~p~~i~~a~~~~~al~~~~~~~~~~~~~ik~ll~~~~a~~--~aa~~aa~~~-~~~~~~~~~~~~~~~-~ee~d 309 (318)
|||.+.++++|..++.++.+..+.+.+.+.+.++|+++|++++++. ++++++++++ .++++++++++++++ +||+|
T Consensus 1 ~pT~~~i~~vl~aag~~v~~~~~~~~~~~l~~~~i~~li~~~~~~~~~~aaa~aaa~aa~~~a~a~~e~kkEeeeeEEed 80 (88)
T PF00428_consen 1 EPTAENIKKVLKAAGVEVEAIWLELFAKALEGKDIKELIANGSAGMAAAAAAAAAAAAAAAAAAAAEEEKKEEEEEEEED 80 (88)
T ss_dssp S-SCCCHHHHHHHHTHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHHHSTTHHHHT--SS-S
T ss_pred CCCHHHHHHHHHHhCCchhHHHHHHHHHHHcCCcHHHHHhcccccccccccccccccccccccccchhcccccccccccc
Confidence 6899999999999999999999999999999999999999999773 2221222211 222222223223333 36889
Q ss_pred cccCCCCC
Q 036252 310 DDMGLSLF 317 (318)
Q Consensus 310 ~dmgfglF 317 (318)
+|||||||
T Consensus 81 ~dmGf~LF 88 (88)
T PF00428_consen 81 DDMGFGLF 88 (88)
T ss_dssp SSSSTTTT
T ss_pred cccCcCCC
Confidence 99999999
No 18
>cd05831 Ribosomal_P1 Ribosomal protein P1. This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers) and bacteria may have four or six copies (two or three homodimers), depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and
Probab=99.46 E-value=4.1e-14 Score=113.62 Aligned_cols=86 Identities=41% Similarity=0.529 Sum_probs=62.5
Q ss_pred cccCChHHHHHHHHHHHHHHHHHhhhcCcccCCCChhHHHHHHHhhhhhhhhccccccchhcHHHHhcCcchhhhhccch
Q 036252 206 VLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGYKNVLSFAVATEYSFSQADKVKEYLKDPSKFAAAAAPA 285 (318)
Q Consensus 206 ~l~it~e~~~~~~~~a~~~~~~lsl~ag~pt~~s~p~~i~~a~~~~~al~~~~~~~~~~~~~ik~ll~~~~a~~~aa~~a 285 (318)
-+.||.++|. ++...+|+.+...||.+|.+++++ ++|.++|+++++++++++|+
T Consensus 15 ~~~~Tae~I~-----------~ilkAaGveve~~~~~~f~~~L~g---------------k~i~elIa~~~~~~~~aap~ 68 (103)
T cd05831 15 GIEITADNIN-----------ALLKAAGVNVEPYWPGLFAKALEG---------------KDIKDLLSNVGGGGGGAAPA 68 (103)
T ss_pred CCCCCHHHHH-----------HHHHHcCCcccHHHHHHHHHHHcC---------------CCHHHHhhcccccccccccc
Confidence 3478898877 999999999999999999999988 78999999987544332232
Q ss_pred hhhc--cCC-hhhhhhhhccCCccccccccCCCCC
Q 036252 286 AAAR--AAP-VAAAKEEKKEEPAEESDDDMGLSLF 317 (318)
Q Consensus 286 a~~~--~~~-~~~~~~~~~~~~~ee~d~dmgfglF 317 (318)
++++ +++ +++++++++++++||+|||||||||
T Consensus 69 a~~a~~~~~~~~~~~~~kk~e~eee~d~dmgfglF 103 (103)
T cd05831 69 AAAAAAAAAAAEAKKEEKKEEEEEESDDDMGFGLF 103 (103)
T ss_pred ccccccccccccchhhhcccccccccccccccccC
Confidence 2211 111 1223344456667788999999999
No 19
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=99.44 E-value=7.8e-14 Score=113.52 Aligned_cols=85 Identities=35% Similarity=0.429 Sum_probs=57.5
Q ss_pred cCChHHHHHHHHHHHHHHHHHhhhcCcccCCCChhHHHHHHHhhhhhhhhccccccchhcHHHHhcC-------cchhhh
Q 036252 208 DLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGYKNVLSFAVATEYSFSQADKVKEYLKD-------PSKFAA 280 (318)
Q Consensus 208 ~it~e~~~~~~~~a~~~~~~lsl~ag~pt~~s~p~~i~~a~~~~~al~~~~~~~~~~~~~ik~ll~~-------~~a~~~ 280 (318)
.||.++|. +|...+|+.+.+.|+.+|.++++. ++|.++|++ ++++++
T Consensus 17 ~pta~dI~-----------~IL~AaGvevd~~~~~~f~~~L~g---------------K~i~eLIa~G~~kl~sv~~gg~ 70 (113)
T PLN00138 17 CPSAEDLK-----------DILGSVGADADDDRIELLLSEVKG---------------KDITELIASGREKLASVPSGGG 70 (113)
T ss_pred CCCHHHHH-----------HHHHHcCCcccHHHHHHHHHHHcC---------------CCHHHHHHhchhccccCCCCCc
Confidence 57888776 999999999999999999999988 789999954 544332
Q ss_pred hcc-chhh--hc-cC-ChhhhhhhhccCCccccccccCCCCCC
Q 036252 281 AAA-PAAA--AR-AA-PVAAAKEEKKEEPAEESDDDMGLSLFD 318 (318)
Q Consensus 281 aa~-~aa~--~~-~~-~~~~~~~~~~~~~~ee~d~dmgfglFd 318 (318)
+++ ++++ ++ ++ +++++++++++|++|||||||||||||
T Consensus 71 aa~a~a~a~~~~~~~~~~~~~~~e~k~e~eeE~ddDmGfgLFd 113 (113)
T PLN00138 71 VAVAAAAAPAAGGAAAPAAEAKKEEKVEEKEESDDDMGFSLFD 113 (113)
T ss_pred cccccccccccccccccccchhhhhhccccccccccccccccC
Confidence 211 1111 10 11 111222333445667889999999998
No 20
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=99.42 E-value=8.6e-14 Score=112.04 Aligned_cols=84 Identities=35% Similarity=0.472 Sum_probs=58.0
Q ss_pred cCChHHHHHHHHHHHHHHHHHhhhcCcccCCCChhHHHHHHHhhhhhhhhccccccchhcHHHHhcCcchh------hhh
Q 036252 208 DLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGYKNVLSFAVATEYSFSQADKVKEYLKDPSKF------AAA 281 (318)
Q Consensus 208 ~it~e~~~~~~~~a~~~~~~lsl~ag~pt~~s~p~~i~~a~~~~~al~~~~~~~~~~~~~ik~ll~~~~a~------~~a 281 (318)
.||.++|. +|...+|..+.+.|+..+.+++.+ .+|.++|++..+- +++
T Consensus 16 ~~ta~~I~-----------~IL~aaGveVe~~~~~~~~~aLaG---------------k~V~eli~~g~~kl~~~~~~~~ 69 (105)
T cd04411 16 ELTEDKIK-----------ELLSAAGAEIEPERVKLFLSALNG---------------KNIDEVISKGKELMSSQAAAAA 69 (105)
T ss_pred CCCHHHHH-----------HHHHHcCCCcCHHHHHHHHHHHcC---------------CCHHHHHHHHHhhccCCCCccc
Confidence 48888877 999999999999999999999988 6799999876541 111
Q ss_pred ccchhhhccCChhhhhhhhccCCccccccccCCCCC
Q 036252 282 AAPAAAARAAPVAAAKEEKKEEPAEESDDDMGLSLF 317 (318)
Q Consensus 282 a~~aa~~~~~~~~~~~~~~~~~~~ee~d~dmgfglF 317 (318)
+++++++++++++++++++++|++||||||||||||
T Consensus 70 a~~~a~~~~~~~~~~~~e~k~ee~eE~dddmgf~LF 105 (105)
T cd04411 70 APAATAAATAEPAEKAEEAKEEEEEEEDEDFGFGLF 105 (105)
T ss_pred cccccccccccchhhhhhhhcccccccccccCcccC
Confidence 101111112222233344455667888999999999
No 21
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=99.24 E-value=9e-11 Score=111.78 Aligned_cols=216 Identities=12% Similarity=0.109 Sum_probs=160.7
Q ss_pred HHHHHHHHHHHhccCeEEEEEecCC-----------CchHHHHHH-------HHccCCcEEEEEehHHHHH--HHHhhhh
Q 036252 12 IAYDARLCKLLEEYSQILIVAADNV-----------GSNQLQHIR-------AGLRDHSIVLMGKNTMMKR--SIRLHAE 71 (318)
Q Consensus 12 ~~~v~~l~e~l~~y~~v~iv~~~~v-----------~s~ql~~iR-------~~lr~~~~~~vgKNtL~~~--Al~~~~~ 71 (318)
...+++||..|+....+++-.-+=| ....++++- ..++|+.-+++-+-..... -+.....
T Consensus 35 s~qlq~IR~~lrg~a~~~~GKNtlm~~AL~~~~~~~~~~~~~~ll~~~~~~~~~l~GnvgliFTn~~p~ev~~~l~~~k~ 114 (323)
T PTZ00240 35 SQQVHDVRRALRGKAEFVMGKKTLQAKIVEKRAQAKKASAEAKLFNDQCEEKNLLSGNTGLIFTNNEVQEITSVLDSHRV 114 (323)
T ss_pred cHHHHHHHHHhhCCcEEEEecHHHHHHHHhhccccccchhHHHHhhhhccccccccCCEEEEEeCCCHHHHHHHHHHcCC
Confidence 3568889999987766665432211 112366663 6788887777776655433 2333221
Q ss_pred hhCC-cc----cccccccccCceEEEEecCChhhHHHHHHhccccccccCCC--ccCceEEeCCCCCCCCCCchhhhhhc
Q 036252 72 RTGN-RD----LLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGL--VAPIDVVVPPGNTGLDPSQTSFFQVL 144 (318)
Q Consensus 72 ~~~~-~~----~~~L~~~l~G~~gliFt~~dp~~v~k~l~~~k~~~~ar~G~--iA~~dVvi~~G~t~~~p~~~~~fq~L 144 (318)
..+. .| .+-..+ .|+| +.+|. ....|.+...|+....|. |..+.+++++|.. ++|++...|++|
T Consensus 115 ~a~AraG~IAp~dVvvp--aG~T-----~~~P~-~~s~fq~LGIpTkI~kGkIeI~~d~~v~k~Ge~-V~~~~A~LL~~L 185 (323)
T PTZ00240 115 KAPARVGAIAPCDVIVP--AGST-----GMEPT-QTSFFQALNIATKIAKGMVEIVTEKKVLSVGDK-VDNSTATLLQKL 185 (323)
T ss_pred cccccCCCCCCceEEEC--CCCC-----CCCCc-chHHHHHcCCCeEecCcEEEEecCeEEecCCCC-cCHHHHHHHHHc
Confidence 1111 00 122223 4665 57887 488999999999999998 7788889999999 999999999999
Q ss_pred CCceEEecceeEeecCcEEeecCcccCcchHHHHhhcCCCccccccceeeeeeCCcccCCccccCChHHHHHHHHHHHHH
Q 036252 145 NIPTKINKGTVEIITPVELIKKGDRVGSSESALLSKLAIKPFSYGLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSR 224 (318)
Q Consensus 145 gIptki~~G~I~i~~d~~v~~~G~~v~~~~A~lL~~L~i~p~~~~l~l~~~~~~g~~~~~~~l~it~e~~~~~~~~a~~~ 224 (318)
||..---+-+|. .++..|...+++. |+|....|.-++...+.+-..++.+.-++|.+.+.-.+.+|+.+
T Consensus 186 ~IkP~~~gl~l~-----~vyd~g~i~~~~v------L~i~~e~~~~~~~~a~~~~~~lsl~~~~pt~~si~~~i~~a~~~ 254 (323)
T PTZ00240 186 NISPFYYQVEVL-----SVWDRGVLFTRED------LSMTEDVVEKMLMEGLSNVAAMSLGAGIPTAATIGPMLVDAFKN 254 (323)
T ss_pred CCCeEEEEEEEE-----EEEeCCeecCHHH------cCCCHHHHHHHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHH
Confidence 999976665533 4556777777765 55888888888888888877788888999999999999999999
Q ss_pred HHHHhhhcCcccCCCChhHHHHH
Q 036252 225 VASLALSIRYPTIAAAPHFFING 247 (318)
Q Consensus 225 ~~~lsl~ag~pt~~s~p~~i~~a 247 (318)
+.+|+++++|+++++.+..+.+|
T Consensus 255 ~~alav~~~~~~~~~~~~~~~~A 277 (323)
T PTZ00240 255 LLAVSVATSYEFEEHNGKELREA 277 (323)
T ss_pred HHHHhhhcCcCChhhHHHHHhhh
Confidence 99999999999999999888777
No 22
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=99.13 E-value=3e-11 Score=96.19 Aligned_cols=77 Identities=43% Similarity=0.531 Sum_probs=43.0
Q ss_pred HHhhhcCcccCCCChhHHHHHHHhhhhhhhhccccccchhcHHHHhc-------C-cchhhhhc--cchhhh-ccCChhh
Q 036252 227 SLALSIRYPTIAAAPHFFINGYKNVLSFAVATEYSFSQADKVKEYLK-------D-PSKFAAAA--APAAAA-RAAPVAA 295 (318)
Q Consensus 227 ~lsl~ag~pt~~s~p~~i~~a~~~~~al~~~~~~~~~~~~~ik~ll~-------~-~~a~~~aa--~~aa~~-~~~~~~~ 295 (318)
.+.-..|..+...+-.++...++. ++|.++|+ + |+++++++ ++++++ +++++..
T Consensus 25 kIl~sVG~E~d~e~i~~visel~G---------------K~i~ElIA~G~eklAsvpsGGa~~aaa~~aaggaa~aa~~a 89 (112)
T KOG3449|consen 25 KILESVGAEIDDERINLVLSELKG---------------KDIEELIAAGREKLASVPSGGAVAAAAAPAAGGAAGAAPAA 89 (112)
T ss_pred HHHHHhCcccCHHHHHHHHHHhcC---------------CCHHHHHHHhHHHHhcCCCCCccccccCcCCCCCccCCccc
Confidence 666667777666666666666655 56666654 3 33333221 111111 1222222
Q ss_pred hhhhhccCCccccccccCCCCCC
Q 036252 296 AKEEKKEEPAEESDDDMGLSLFD 318 (318)
Q Consensus 296 ~~~~~~~~~~ee~d~dmgfglFd 318 (318)
.++++|+|++|||||||||+|||
T Consensus 90 ~~~e~keEe~eesddDmgf~lFd 112 (112)
T KOG3449|consen 90 AKEEEKEEEKEESDDDMGFGLFD 112 (112)
T ss_pred hhhhhhhhhcccccccccccccC
Confidence 23334555668999999999998
No 23
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=99.00 E-value=2.3e-10 Score=91.22 Aligned_cols=85 Identities=38% Similarity=0.458 Sum_probs=58.3
Q ss_pred cCChHHHHHHHHHHHHHHHHHhhhcCcccCCCChhHHHHHHHhhhhhhhhccccccchhcHHHHhcCcchhhhhc--cch
Q 036252 208 DLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGYKNVLSFAVATEYSFSQADKVKEYLKDPSKFAAAA--APA 285 (318)
Q Consensus 208 ~it~e~~~~~~~~a~~~~~~lsl~ag~pt~~s~p~~i~~a~~~~~al~~~~~~~~~~~~~ik~ll~~~~a~~~aa--~~a 285 (318)
.||.+.|. ++..++|+.+.+.|-..+..++.. .+|+++|.+.....+++ +++
T Consensus 16 ei~e~~l~-----------~vl~aaGveve~~r~k~lvaaLeg---------------~~idE~i~~~~~~~~a~a~a~a 69 (109)
T COG2058 16 EITEDNLK-----------SVLEAAGVEVEEARAKALVAALEG---------------VDIDEVIKNAAEAPAAAAAAGA 69 (109)
T ss_pred cCCHHHHH-----------HHHHHcCCCccHHHHHHHHHHhcC---------------CCHHHHHHHhcccccccCCccc
Confidence 68888877 888999999999999999999988 68999998866532211 111
Q ss_pred hh---h--ccCCh--hhhhhhhccCCccccccccCCCCCC
Q 036252 286 AA---A--RAAPV--AAAKEEKKEEPAEESDDDMGLSLFD 318 (318)
Q Consensus 286 a~---~--~~~~~--~~~~~~~~~~~~ee~d~dmgfglFd 318 (318)
++ + .++++ .+++++++++.+||||+||||||||
T Consensus 70 aaa~~A~~~~a~~~~ea~eEe~eEe~~EE~~~~~lf~LF~ 109 (109)
T COG2058 70 AAAAAAGAEAAAEADEAEEEEKEEEAEEESDDDMLFGLFG 109 (109)
T ss_pred ccccccccccccchhhHHHHHhhhchhhcccccchhhccC
Confidence 11 1 11111 1222333455678889999999998
No 24
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=98.72 E-value=5.6e-09 Score=83.95 Aligned_cols=85 Identities=27% Similarity=0.366 Sum_probs=56.4
Q ss_pred cCChHHHHHHHHHHHHHHHHHhhhcCcccCCCChhHHHHHHHhhhhhhhhccccccchhcHHHHhcCcchhhhhccchhh
Q 036252 208 DLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGYKNVLSFAVATEYSFSQADKVKEYLKDPSKFAAAAAPAAA 287 (318)
Q Consensus 208 ~it~e~~~~~~~~a~~~~~~lsl~ag~pt~~s~p~~i~~a~~~~~al~~~~~~~~~~~~~ik~ll~~~~a~~~aa~~aa~ 287 (318)
.||.+.|. +|..++|..+.+.|+.+|.+++.+ .+|.++|.+.++..++++++++
T Consensus 16 ~it~e~I~-----------~IL~AAGveVee~~~k~~v~aL~G---------------kdIeElI~~a~~~~~a~~~a~~ 69 (106)
T PRK06402 16 EINEDNLK-----------KVLEAAGVEVDEARVKALVAALED---------------VNIEEAIKKAAAAPVAAAAAAA 69 (106)
T ss_pred CCCHHHHH-----------HHHHHcCCCccHHHHHHHHHHHcC---------------CCHHHHHHhccccccccccccc
Confidence 68888877 999999999999999999999988 6899999988764433322211
Q ss_pred --hccCChhh-hhhhhccCCccccccccCCC---CCC
Q 036252 288 --ARAAPVAA-AKEEKKEEPAEESDDDMGLS---LFD 318 (318)
Q Consensus 288 --~~~~~~~~-~~~~~~~~~~ee~d~dmgfg---lFd 318 (318)
+++++.++ +++++++++++++|++++.| ||+
T Consensus 70 ~~~~~~~~~~~~~~~~~ee~~~~~ee~~~~gl~~lfg 106 (106)
T PRK06402 70 AAAAAAAAEEKKEEEEEEEEKEESEEEAAAGLGALFG 106 (106)
T ss_pred ccccccccchhhhhhhhhhhccccHHHHHhhHHHhcC
Confidence 11122222 22222344455666666555 675
No 25
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=98.65 E-value=2.2e-07 Score=88.56 Aligned_cols=217 Identities=15% Similarity=0.076 Sum_probs=152.0
Q ss_pred HHHHHHHHHHHhccCeEEEEEec-------CCC--chHHHHHHHHccCCcEEEEEehHHH--HHHHHhhhhhhC-Ccc--
Q 036252 12 IAYDARLCKLLEEYSQILIVAAD-------NVG--SNQLQHIRAGLRDHSIVLMGKNTMM--KRSIRLHAERTG-NRD-- 77 (318)
Q Consensus 12 ~~~v~~l~e~l~~y~~v~iv~~~-------~v~--s~ql~~iR~~lr~~~~~~vgKNtL~--~~Al~~~~~~~~-~~~-- 77 (318)
...+.+||..|+....+++..-+ +.. ...+..|-..|+|+.-+.+.+.... ++.+.+.....+ +.|
T Consensus 37 s~ql~~iR~~LR~~a~~~vgKNTL~r~AL~~~~~~~~~l~~L~~~LkG~~gliFTn~dp~ev~k~l~~~k~~~~AKaG~i 116 (310)
T PTZ00135 37 SKQMQDIRRSLRGKAELLMGKNTLIRKALKQRLEELPELEKLLPHVKGNVGFVFTKDDLFEVKPVILENKVPAPARAGVI 116 (310)
T ss_pred HHHHHHHHHHHhcCCEEEEEehHHHHHHHhhCcccccChHHHHhhccCCEEEEEECCCHHHHHHHHHHcCCccccccCCC
Confidence 45688899999876555554222 111 1247888899999887877765443 233433221111 100
Q ss_pred --cccccccccCceEEEEecCChhhHHHHHHhccccccccCCC--ccCceEEeCCCCCCCCCCchhhhhhcCCceEEecc
Q 036252 78 --LLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGL--VAPIDVVVPPGNTGLDPSQTSFFQVLNIPTKINKG 153 (318)
Q Consensus 78 --~~~L~~~l~G~~gliFt~~dp~~v~k~l~~~k~~~~ar~G~--iA~~dVvi~~G~t~~~p~~~~~fq~LgIptki~~G 153 (318)
.+-..+ .|+| ..+|.. ...|.+...|+....|. |..+.+++.+|.. ++|++...|+.|||..---+-
T Consensus 117 Ap~dv~ip--~G~t-----~~~P~~-~~~fq~LgipTkI~kG~I~I~~d~~v~k~Ge~-v~~~~A~LL~~L~I~p~~~~l 187 (310)
T PTZ00135 117 APIDVVIP--AGPT-----GMDPSQ-TSFFQALGIATKIVKGQIEITNEVHLIKEGQK-VGASQAVLLQKLNIKPFSYGL 187 (310)
T ss_pred CCceEEEc--CCCC-----CCCcch-hhHHHHcCCceEecCCeEEEecCeEEecCCCC-cCHHHHHHHHHcCCCeEEEEE
Confidence 111222 3554 678875 88999999999999998 7788889999999 999999999999999976666
Q ss_pred eeEeecCcEEeecCcccCcchHHHHhhcCCCccccccceeeeeeCCcccCCccccCChHHHHHHHHHHHHHHHHHhhhcC
Q 036252 154 TVEIITPVELIKKGDRVGSSESALLSKLAIKPFSYGLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIR 233 (318)
Q Consensus 154 ~I~i~~d~~v~~~G~~v~~~~A~lL~~L~i~p~~~~l~l~~~~~~g~~~~~~~l~it~e~~~~~~~~a~~~~~~lsl~ag 233 (318)
++. .+...|...+++. |+|....+.-++...+.+-..++...-.+|+..+...|.+|+.++.+|+++++
T Consensus 188 ~~~-----~~yd~g~~~~~~v------L~i~~e~~~~~~~~~~~~i~als~aag~pt~~s~p~~ia~a~k~~~a~a~~~~ 256 (310)
T PTZ00135 188 EVL-----SIYDNGSIYDAKV------LDITDEDIVAKFQEGVQNVAAISLAAGYPTEASAPHSILNAFKNLAAIGLESG 256 (310)
T ss_pred EEE-----EEEECCeEeCHHH------cCCCHHHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHhhcC
Confidence 643 3455566666654 44776666666666665555566666678999999999999999999999999
Q ss_pred cccCCCChhHHHHHH
Q 036252 234 YPTIAAAPHFFINGY 248 (318)
Q Consensus 234 ~pt~~s~p~~i~~a~ 248 (318)
|+.++..+.....|.
T Consensus 257 ~~~~~~~~~~~~~a~ 271 (310)
T PTZ00135 257 FTFPLAEKIKEALAN 271 (310)
T ss_pred CCChhhHHHHHhhcC
Confidence 998877766554443
No 26
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=98.06 E-value=1.9e-06 Score=69.54 Aligned_cols=45 Identities=9% Similarity=0.178 Sum_probs=39.6
Q ss_pred cCChHHHHHHHHHHHHHHHHHhhhcCcccCCCChhHHHHHHHhhhhhhhhccccccchhcHHHHhcCcchh
Q 036252 208 DLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGYKNVLSFAVATEYSFSQADKVKEYLKDPSKF 278 (318)
Q Consensus 208 ~it~e~~~~~~~~a~~~~~~lsl~ag~pt~~s~p~~i~~a~~~~~al~~~~~~~~~~~~~ik~ll~~~~a~ 278 (318)
.||.+.+. +|...+|+.+...|+..|++++.+ +++.++|.++.+.
T Consensus 16 ~iT~e~I~-----------~IL~AAGv~ve~~~~~~la~~L~g---------------k~i~eli~~~~~a 60 (105)
T TIGR03685 16 EINEENLK-----------AVLEAAGVEVDEARVKALVAALEG---------------VNIEEAIKKAAAA 60 (105)
T ss_pred CCCHHHHH-----------HHHHHhCCcccHHHHHHHHHHHcC---------------CCHHHHHHhhhcc
Confidence 68888877 899999999999999999999988 6899999887643
No 27
>cd05832 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera
Probab=97.97 E-value=2.8e-06 Score=68.45 Aligned_cols=46 Identities=11% Similarity=0.176 Sum_probs=40.7
Q ss_pred cCChHHHHHHHHHHHHHHHHHhhhcCcccCCCChhHHHHHHHhhhhhhhhccccccchhcHHHHhcCcchhh
Q 036252 208 DLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGYKNVLSFAVATEYSFSQADKVKEYLKDPSKFA 279 (318)
Q Consensus 208 ~it~e~~~~~~~~a~~~~~~lsl~ag~pt~~s~p~~i~~a~~~~~al~~~~~~~~~~~~~ik~ll~~~~a~~ 279 (318)
.||.+.+. +|...+|+.+.+.|+..|++++.+ .+|.++|++.++.+
T Consensus 16 eITae~I~-----------~IL~AAGveVd~~~~~ala~aL~g---------------kdIeElIa~~~~~~ 61 (106)
T cd05832 16 EINEENLK-----------KVLEAAGIEVDEARVKALVAALEE---------------VNIDEAIKKAAVAA 61 (106)
T ss_pred CCCHHHHH-----------HHHHHhCCcccHHHHHHHHHHHcC---------------CCHHHHHHhccccc
Confidence 68888877 899999999999999999999988 68999999888633
No 28
>KOG4241 consensus Mitochondrial ribosomal protein L10 [Translation, ribosomal structure and biogenesis]
Probab=96.97 E-value=0.0024 Score=57.00 Aligned_cols=88 Identities=17% Similarity=0.197 Sum_probs=78.1
Q ss_pred HHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccC-CcEEEEEehHHHHHHHHhhhhhhCCcccccccccccCceEEEE
Q 036252 15 DARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRD-HSIVLMGKNTMMKRSIRLHAERTGNRDLLNLIPLLQGNVGMIF 93 (318)
Q Consensus 15 v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~-~~~~~vgKNtL~~~Al~~~~~~~~~~~~~~L~~~l~G~~gliF 93 (318)
..++...++++..+.++.+--++..++--.|.+||. +..|+..-|++++.+++++. ++.|.+++.||.+++|
T Consensus 79 ~re~~~v~~~~R~~Avcq~~~v~a~d~~~~r~QLrk~ni~~ksygnkIlk~~~~~t~-------y~~l~plfvgnh~ill 151 (245)
T KOG4241|consen 79 LREDWMVREEFRVMAVCQFLPVPARDLWFARNQLRKKNIEFKSYGNKILKKIFDKTP-------YSSLNPLFVGNHAILL 151 (245)
T ss_pred HHHHHHHHhhhhheeeeecccCcHHHHHHHHHHHHhccchhhhchHHHHHHHHhcCc-------hhhhhhheeccceEEE
Confidence 345677889999999999999999999999999997 58999999999999999886 8999999999999999
Q ss_pred ecCChhhHHHHHHhccc
Q 036252 94 TKGDLKEVSDEVSKHKV 110 (318)
Q Consensus 94 t~~dp~~v~k~l~~~k~ 110 (318)
. .|+.+++.++...+.
T Consensus 152 ~-~d~~kik~~lri~r~ 167 (245)
T KOG4241|consen 152 A-KDISKIKSILRITRK 167 (245)
T ss_pred c-CChHHHHHHHHHHhh
Confidence 7 577788888876643
No 29
>PF00428 Ribosomal_60s: 60s Acidic ribosomal protein; InterPro: IPR001813 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 [, ]. The 60S acidic ribosomal protein plays an important role in the elongation step of protein synthesis. This family includes archaebacterial L12, eukaryotic P0, P1 and P2 []. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Alt a 6, Alt a 12, Cla h 3, Cla h 4 and Cla h 12.; GO: 0003735 structural constituent of ribosome, 0006414 translational elongation, 0005622 intracellular, 0005840 ribosome; PDB: 3A1Y_C 3N2D_B 2LBF_A 3IZS_t 3IZR_t 1S4J_A 2JDL_C 2W1O_B 1S4H_A 2ZKR_g.
Probab=93.91 E-value=0.032 Score=43.43 Aligned_cols=30 Identities=13% Similarity=0.117 Sum_probs=15.7
Q ss_pred cCChHHHHHHHHHHHHHHHHHhhhcCcccCCCChhHHHHHH
Q 036252 208 DLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGY 248 (318)
Q Consensus 208 ~it~e~~~~~~~~a~~~~~~lsl~ag~pt~~s~p~~i~~a~ 248 (318)
+||.+.|...+. .+|..+.+.|+.++.+++
T Consensus 1 ~pT~~~i~~vl~-----------aag~~v~~~~~~~~~~~l 30 (88)
T PF00428_consen 1 EPTAENIKKVLK-----------AAGVEVEAIWLELFAKAL 30 (88)
T ss_dssp S-SCCCHHHHHH-----------HHTHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHH-----------HhCCchhHHHHHHHHHHH
Confidence 467777774444 444444445555555554
No 30
>cd05795 Ribosomal_P0_L10e Ribosomal protein L10 family, P0 and L10e subfamily; composed of eukaryotic 60S ribosomal protein P0 and the archaeal P0 homolog, L10e. P0 or L10e forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). These eukaryotic and archaeal P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.
Probab=92.46 E-value=1 Score=39.55 Aligned_cols=128 Identities=16% Similarity=0.196 Sum_probs=85.0
Q ss_pred HHHHHHHHHHHhccCeEEEEEe-------cCCC--chHHHHHHHHccCCcEEEEEehHHH--HHHHHhhhhhhCC-cc--
Q 036252 12 IAYDARLCKLLEEYSQILIVAA-------DNVG--SNQLQHIRAGLRDHSIVLMGKNTMM--KRSIRLHAERTGN-RD-- 77 (318)
Q Consensus 12 ~~~v~~l~e~l~~y~~v~iv~~-------~~v~--s~ql~~iR~~lr~~~~~~vgKNtL~--~~Al~~~~~~~~~-~~-- 77 (318)
...+.+||..+.....+.+..- .+.. ...+..|...|+|..-+.+.+.... .+.+.+.....+. .|
T Consensus 30 ~~ql~~lR~~lr~~~~~~v~KNtL~~~Al~~~~~~~~~~~~L~~~l~G~~~liFt~~dp~~v~k~l~~~~~~~~ar~G~i 109 (175)
T cd05795 30 SKQLQKIRRSLRGKAEILMGKNTLIRRALRNLGDENPELEKLLPYLKGNVGFIFTNGDPFEIRKILEENKVPAPAKPGAI 109 (175)
T ss_pred hHHHHHHHHHhhCCCEEEEechHHHHHHHHhcccccccHHHHHHHhcCCEEEEEECCCHHHHHHHHHHcCCcccccCCCc
Confidence 4567889999987655544421 1221 1137788889998887878765443 3344443222111 01
Q ss_pred --cccccccccCceEEEEecCChhhHHHHHHhccccccccCCC--ccCceEEeCCCCCCCCCCchhhhhhcCCce
Q 036252 78 --LLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGL--VAPIDVVVPPGNTGLDPSQTSFFQVLNIPT 148 (318)
Q Consensus 78 --~~~L~~~l~G~~gliFt~~dp~~v~k~l~~~k~~~~ar~G~--iA~~dVvi~~G~t~~~p~~~~~fq~LgIpt 148 (318)
.+-..+ .|+|+ .+|...- .|.+...|+....|. |..+.+++.+|.. ++|++...|+.|||..
T Consensus 110 A~~dvvi~--~G~t~-----~~p~~~~-~~~~lgiptki~~G~i~i~~d~~v~k~G~~-v~~~~A~lL~~l~i~P 175 (175)
T cd05795 110 APCDVVVP--AGPTG-----MPPGPTS-FFQALGIPTKIEKGKIEIISDVVVVKKGEK-VGASEATLLNKLNIKP 175 (175)
T ss_pred cCceEEEc--CCCcC-----CCCCchH-HHHHcCCceEEecCEEEEecCeEEecCCCC-cCHHHHHHHHHcCCCC
Confidence 111222 46663 4555544 899999999999998 7888899999999 9999999999999963
No 31
>PF07697 7TMR-HDED: 7TM-HD extracellular; InterPro: IPR011624 This entry represents the extracellular domain of the 7TM-HD (7TM Receptors with HD hydrolase) protein family []. These proteins are known or predicted, to posses metal-dependent phospohydrolase activity.
Probab=79.54 E-value=1 Score=40.04 Aligned_cols=26 Identities=19% Similarity=0.300 Sum_probs=22.5
Q ss_pred ecCcEEeecCcccCcchHHHHhhcCC
Q 036252 158 ITPVELIKKGDRVGSSESALLSKLAI 183 (318)
Q Consensus 158 ~~d~~v~~~G~~v~~~~A~lL~~L~i 183 (318)
.+.-.++++|++||+++..+|+.||+
T Consensus 194 ~~Ge~IV~kGe~VT~e~~~~L~~l~~ 219 (222)
T PF07697_consen 194 KKGEVIVRKGEIVTEEQYEKLESLGL 219 (222)
T ss_pred cCCCEEecCCcEeCHHHHHHHHHcCC
Confidence 33347999999999999999999986
No 32
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=77.57 E-value=1.1 Score=36.15 Aligned_cols=15 Identities=20% Similarity=0.268 Sum_probs=11.1
Q ss_pred CccccccccCCCCCC
Q 036252 304 PAEESDDDMGLSLFD 318 (318)
Q Consensus 304 ~~ee~d~dmgfglFd 318 (318)
+++.++++..++||+
T Consensus 92 eEe~~EE~~~~~lf~ 106 (109)
T COG2058 92 EEEAEEESDDDMLFG 106 (109)
T ss_pred hhchhhcccccchhh
Confidence 345567889988995
No 33
>KOG3414 consensus Component of the U4/U6.U5 snRNP/mitosis protein DIM1 [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=63.54 E-value=13 Score=31.09 Aligned_cols=86 Identities=17% Similarity=0.179 Sum_probs=59.0
Q ss_pred HHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccCCcEEEEEehHHHHHHHHhhhhhhCCcccccccccccCceEE
Q 036252 12 IAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSIRLHAERTGNRDLLNLIPLLQGNVGM 91 (318)
Q Consensus 12 ~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~~~~~~vgKNtL~~~Al~~~~~~~~~~~~~~L~~~l~G~~gl 91 (318)
.++++++.+.++++-.+|++|.+.+ ..+.+.=.--...+.+++-+|+=|+.=++.. .|+=+
T Consensus 42 D~~L~~i~~~vsnfa~IylvdideV--~~~~~~~~l~~p~tvmfFfn~kHmkiD~gtg-----------------dn~Ki 102 (142)
T KOG3414|consen 42 DELLSSIAEDVSNFAVIYLVDIDEV--PDFVKMYELYDPPTVMFFFNNKHMKIDLGTG-----------------DNNKI 102 (142)
T ss_pred HHHHHHHHHHHhhceEEEEEecchh--hhhhhhhcccCCceEEEEEcCceEEEeeCCC-----------------CCceE
Confidence 4578899999999999999999944 3333332222234799999998887766532 34456
Q ss_pred EEecCChhhHHHHHHhccccccccCCC
Q 036252 92 IFTKGDLKEVSDEVSKHKVAAPARVGL 118 (318)
Q Consensus 92 iFt~~dp~~v~k~l~~~k~~~~ar~G~ 118 (318)
.|.-+|-.+..++++.- -.-||.|.
T Consensus 103 n~~~~~kq~~Idiie~i--yRga~KGK 127 (142)
T KOG3414|consen 103 NFAFEDKQEFIDIIETI--YRGARKGK 127 (142)
T ss_pred EEEeccHHHHHHHHHHH--HHhhhcCC
Confidence 67778888888888764 22355554
No 34
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=61.81 E-value=4.8 Score=32.64 Aligned_cols=19 Identities=11% Similarity=0.181 Sum_probs=12.2
Q ss_pred CChhHHHHHHHhhhhhhhh
Q 036252 239 AAPHFFINGYKNVLSFAVA 257 (318)
Q Consensus 239 s~p~~i~~a~~~~~al~~~ 257 (318)
++-.+|+..-..+.++...
T Consensus 50 ~i~ElIA~G~eklAsvpsG 68 (112)
T KOG3449|consen 50 DIEELIAAGREKLASVPSG 68 (112)
T ss_pred CHHHHHHHhHHHHhcCCCC
Confidence 5677777777766555443
No 35
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=60.12 E-value=4 Score=33.16 Aligned_cols=14 Identities=36% Similarity=0.567 Sum_probs=6.1
Q ss_pred hhhhhhhccCCcccc
Q 036252 294 AAAKEEKKEEPAEES 308 (318)
Q Consensus 294 ~~~~~~~~~~~~ee~ 308 (318)
+++++| ++||++++
T Consensus 89 e~kkee-~eee~ddD 102 (109)
T cd05833 89 EEKKEE-SEEESDDD 102 (109)
T ss_pred hhhccC-Cccccccc
Confidence 334443 44444443
No 36
>PF08800 VirE_N: VirE N-terminal domain; InterPro: IPR014907 This domain is associated with the N terminus of Virulence E proteins. The function of the domain is unknown.
Probab=53.73 E-value=21 Score=29.89 Aligned_cols=33 Identities=18% Similarity=0.396 Sum_probs=29.0
Q ss_pred HHHHhccCeEEEEEecCCCchHHHHHHHHccCC
Q 036252 19 CKLLEEYSQILIVAADNVGSNQLQHIRAGLRDH 51 (318)
Q Consensus 19 ~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~~ 51 (318)
...+..|+.++++|++++...++.++|+.++..
T Consensus 24 ~~~l~~~sglv~lDiD~l~~ee~~~~r~~l~~~ 56 (136)
T PF08800_consen 24 ADNLKAYSGLVVLDIDHLDPEEAEELRQLLFED 56 (136)
T ss_pred hhhhhhCCCcEEEEeCCCCHHHHHHHHHHHhcC
Confidence 356778999999999999999999999999853
No 37
>PF12953 DUF3842: Domain of unknown function (DUF3842); InterPro: IPR024208 This family of proteins has no known function.
Probab=53.46 E-value=20 Score=29.99 Aligned_cols=76 Identities=16% Similarity=0.405 Sum_probs=52.6
Q ss_pred EEEEEecC--CCchHHHHHHHHccCCc-EEEEEehHHHHHHHHhhhhhhCCcccccc------cccccCceEEEEecCCh
Q 036252 28 ILIVAADN--VGSNQLQHIRAGLRDHS-IVLMGKNTMMKRSIRLHAERTGNRDLLNL------IPLLQGNVGMIFTKGDL 98 (318)
Q Consensus 28 v~iv~~~~--v~s~ql~~iR~~lr~~~-~~~vgKNtL~~~Al~~~~~~~~~~~~~~L------~~~l~G~~gliFt~~dp 98 (318)
+.|+|=+| +...-+++||+.+.+.. .+-+|=|.+..-++-+...++..+|-..+ .+.+-|+.|+++.|.=.
T Consensus 2 I~VIDGQGGGiG~~iv~~lr~~~~~~~eI~AlGTNa~AT~~MlKaGA~~gATGENaIv~n~~~aDiIvGpigIv~a~sml 81 (131)
T PF12953_consen 2 IAVIDGQGGGIGKQIVEKLRKELPEEVEIIALGTNAIATSAMLKAGANEGATGENAIVVNARKADIIVGPIGIVIANSML 81 (131)
T ss_pred EEEEeCCCChhHHHHHHHHHHhCCCCcEEEEEehhHHHHHHHHHcCCCCcccccchheeccCCCCEEECcHHHhccCccc
Confidence 56666664 77888899999999755 55589999999998887666544332221 45677777777777655
Q ss_pred hhHHH
Q 036252 99 KEVSD 103 (318)
Q Consensus 99 ~~v~k 103 (318)
.|+-.
T Consensus 82 GEiTp 86 (131)
T PF12953_consen 82 GEITP 86 (131)
T ss_pred ccccH
Confidence 44443
No 38
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=50.56 E-value=7.1 Score=31.52 Aligned_cols=21 Identities=10% Similarity=-0.202 Sum_probs=11.2
Q ss_pred HhhhcCc-ccCCCChhHHHHHH
Q 036252 228 LALSIRY-PTIAAAPHFFINGY 248 (318)
Q Consensus 228 lsl~ag~-pt~~s~p~~i~~a~ 248 (318)
|+...|. ||.+.+..++..+-
T Consensus 9 ll~~~g~~iT~e~I~~IL~AAG 30 (105)
T TIGR03685 9 LLHSAGKEINEENLKAVLEAAG 30 (105)
T ss_pred HHHhcCCCCCHHHHHHHHHHhC
Confidence 3333333 66666666665554
No 39
>cd05832 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera
Probab=49.26 E-value=4.6 Score=32.67 Aligned_cols=22 Identities=5% Similarity=-0.265 Sum_probs=11.4
Q ss_pred HHhhhcCc-ccCCCChhHHHHHH
Q 036252 227 SLALSIRY-PTIAAAPHFFINGY 248 (318)
Q Consensus 227 ~lsl~ag~-pt~~s~p~~i~~a~ 248 (318)
-|+...|. ||.+.+..++..+-
T Consensus 8 LLL~~~G~eITae~I~~IL~AAG 30 (106)
T cd05832 8 LLLHYAGKEINEENLKKVLEAAG 30 (106)
T ss_pred HHHHhcCCCCCHHHHHHHHHHhC
Confidence 34444443 56666655555554
No 40
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=48.64 E-value=8.1 Score=31.16 Aligned_cols=8 Identities=38% Similarity=0.613 Sum_probs=3.4
Q ss_pred ccCCcccc
Q 036252 301 KEEPAEES 308 (318)
Q Consensus 301 ~~~~~ee~ 308 (318)
++||++++
T Consensus 92 e~eE~ddd 99 (105)
T cd04411 92 EEEEEDED 99 (105)
T ss_pred cccccccc
Confidence 44444443
No 41
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=47.72 E-value=8.4 Score=31.48 Aligned_cols=10 Identities=20% Similarity=0.388 Sum_probs=4.3
Q ss_pred hhHHHHHHHh
Q 036252 241 PHFFINGYKN 250 (318)
Q Consensus 241 p~~i~~a~~~ 250 (318)
..+|......
T Consensus 54 ~ELIa~G~~k 63 (112)
T PTZ00373 54 HELIAAGMKK 63 (112)
T ss_pred HHHHHHhHHH
Confidence 3444444444
No 42
>COG2117 Predicted subunit of tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]
Probab=45.39 E-value=44 Score=29.38 Aligned_cols=69 Identities=19% Similarity=0.236 Sum_probs=48.3
Q ss_pred cEEeecCcccCcchHHHHhhcCCCccccccc--eeeeeeC------CcccCCccccCChHHHHHHHHHHHHHHHHHhhhc
Q 036252 161 VELIKKGDRVGSSESALLSKLAIKPFSYGLI--VMSVYEN------GSVYSPEVLDLTEDDIATKFLEAVSRVASLALSI 232 (318)
Q Consensus 161 ~~v~~~G~~v~~~~A~lL~~L~i~p~~~~l~--l~~~~~~------g~~~~~~~l~it~e~~~~~~~~a~~~~~~lsl~a 232 (318)
+.++--|-|=|+=.|-+|++||+.+--..+. +..-|.- -.-|+-+||.++.+-+ .+|..++++-
T Consensus 3 v~vLfSGGKDSSLaA~iL~klgyev~LVTvnFGv~d~~k~A~~tA~~lgF~h~vl~Ldr~il--------e~A~em~ied 74 (198)
T COG2117 3 VYVLFSGGKDSSLAALILDKLGYEVELVTVNFGVLDSWKYARETAAILGFPHEVLQLDREIL--------EDAVEMIIED 74 (198)
T ss_pred eEEEecCCCchhHHHHHHHHhCCCcEEEEEEeccccchhhHHHHHHHhCCCcceeccCHHHH--------HHHHHHHHhc
Confidence 4556667777888899999999988643332 3333321 1237788888887754 4788999999
Q ss_pred CcccC
Q 036252 233 RYPTI 237 (318)
Q Consensus 233 g~pt~ 237 (318)
|||..
T Consensus 75 g~P~~ 79 (198)
T COG2117 75 GYPRN 79 (198)
T ss_pred CCCch
Confidence 99974
No 43
>COG1480 Predicted membrane-associated HD superfamily hydrolase [General function prediction only]
Probab=42.24 E-value=17 Score=38.36 Aligned_cols=49 Identities=27% Similarity=0.462 Sum_probs=35.0
Q ss_pred CCCCchhhh-----hhcCCceEEecceeEeecCcEEeecCcccCcchHHHHhhcCCCccccc
Q 036252 133 LDPSQTSFF-----QVLNIPTKINKGTVEIITPVELIKKGDRVGSSESALLSKLAIKPFSYG 189 (318)
Q Consensus 133 ~~p~~~~~f-----q~LgIptki~~G~I~i~~d~~v~~~G~~v~~~~A~lL~~L~i~p~~~~ 189 (318)
++|.++... ++.. |++|.+|+ .++++|+.|+.++..+|++||+.--+..
T Consensus 220 ~D~e~T~~~~~ea~~~v~-~V~I~~gq-------iIv~~ge~It~~~~~~L~~lgl~~~s~~ 273 (700)
T COG1480 220 YDEEQTENLRQEALSKVE-PVKISKGQ-------IIVKEGEIITDEDYVILDLLGLLSLSVN 273 (700)
T ss_pred cCHHHHHHHHHHHHhccC-ceEEecCc-------eEeecCceecHHHHHHHHHhhHHhcccc
Confidence 566665433 2232 56666655 7899999999999999999988665544
No 44
>KOG1762 consensus 60s acidic ribosomal protein P1 [Translation, ribosomal structure and biogenesis]
Probab=40.87 E-value=8.7 Score=31.37 Aligned_cols=8 Identities=38% Similarity=0.596 Sum_probs=3.9
Q ss_pred Cccccccc
Q 036252 304 PAEESDDD 311 (318)
Q Consensus 304 ~~ee~d~d 311 (318)
.+||+++.
T Consensus 97 k~Eesees 104 (114)
T KOG1762|consen 97 KKEESEES 104 (114)
T ss_pred hhhhhccc
Confidence 34555554
No 45
>TIGR00762 DegV EDD domain protein, DegV family. This family of proteins is related to DegV of Bacillus subtilis and includes paralogous sets in several species (B. subtilis, Deinococcus radiodurans, Mycoplasma pneumoniae) that are closer in percent identity to each than to most homologs from other species. This suggests both recent paralogy and diversity of function. DegV itself is encoded immediately downstream of DegU, a transcriptional regulator of degradation, but is itself uncharacterized. Crystallography suggested a lipid-binding site, while comparison of the crystal structure to dihydroxyacetone kinase and to a mannose transporter EIIA domain suggests a conserved domain, EDD, with phosphotransferase activity.
Probab=37.54 E-value=2.1e+02 Score=26.52 Aligned_cols=120 Identities=19% Similarity=0.193 Sum_probs=77.1
Q ss_pred HHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccC--CcEEEEEehHHHHHHHHhhhhhhCCcccccccccccCce
Q 036252 12 IAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRD--HSIVLMGKNTMMKRSIRLHAERTGNRDLLNLIPLLQGNV 89 (318)
Q Consensus 12 ~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~--~~~~~vgKNtL~~~Al~~~~~~~~~~~~~~L~~~l~G~~ 89 (318)
.++.+.+++++++|..|+++.+..--|...+..|..-.. .-.+.|.=...+-.+.+-.... ..++.+ .
T Consensus 65 ~~~~~~~~~l~~~~~~vi~i~iSs~lSgty~~a~~aa~~~~~~~i~ViDS~~~s~~~g~~v~~-----a~~~~~--~--- 134 (275)
T TIGR00762 65 GEFLELYEKLLEEGDEVLSIHLSSGLSGTYQSARQAAEMVDEAKVTVIDSKSASMGLGLLVLE-----AAKLAE--E--- 134 (275)
T ss_pred HHHHHHHHHHHhCCCeEEEEEcCCchhHHHHHHHHHHhhCCCCCEEEECChHHHHHHHHHHHH-----HHHHHH--c---
Confidence 456666778888998999999987667777766655443 2367777777666666554311 111111 1
Q ss_pred EEEEecCChhhHHHHHHhccccccccCCCccCceEEeCCCCCCCCCCchhhhhhcCCceEEecceeEeecCcEEeecCcc
Q 036252 90 GMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVVPPGNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELIKKGDR 169 (318)
Q Consensus 90 gliFt~~dp~~v~k~l~~~k~~~~ar~G~iA~~dVvi~~G~t~~~p~~~~~fq~LgIptki~~G~I~i~~d~~v~~~G~~ 169 (318)
+.++.++.+.+++++... ..++ +..+..-+.+|-+
T Consensus 135 -----G~s~~eI~~~l~~~~~~~---------~~~f-------------------------------~v~~L~~L~~gGR 169 (275)
T TIGR00762 135 -----GKSLEEILAKLEELRERT---------KLYF-------------------------------VVDTLEYLVKGGR 169 (275)
T ss_pred -----CCCHHHHHHHHHHHHhhc---------EEEE-------------------------------EECcHHHHHhcCC
Confidence 357889999988876522 1122 1222233345666
Q ss_pred cCcchHHHHhhcCCCcc
Q 036252 170 VGSSESALLSKLAIKPF 186 (318)
Q Consensus 170 v~~~~A~lL~~L~i~p~ 186 (318)
|+.-++.+-++|+|+|.
T Consensus 170 is~~~~~~g~lL~ikPI 186 (275)
T TIGR00762 170 ISKAAALIGSLLNIKPI 186 (275)
T ss_pred ccHHHHHHHHhhcceeE
Confidence 88999999999999996
No 46
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=34.69 E-value=82 Score=27.17 Aligned_cols=26 Identities=4% Similarity=0.330 Sum_probs=23.8
Q ss_pred ccCeEEEEEecC-CCchHHHHHHHHcc
Q 036252 24 EYSQILIVAADN-VGSNQLQHIRAGLR 49 (318)
Q Consensus 24 ~y~~v~iv~~~~-v~s~ql~~iR~~lr 49 (318)
.-+++||+||+| ++.++...||.+..
T Consensus 96 ~~~r~~VldF~Gdi~A~~v~~LReeis 122 (155)
T PF08496_consen 96 PKPRLFVLDFKGDIKASEVESLREEIS 122 (155)
T ss_pred CCCeEEEEecCCCccHHHHHHHHHHHH
Confidence 468999999997 99999999999986
No 47
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=33.62 E-value=21 Score=29.16 Aligned_cols=12 Identities=8% Similarity=0.318 Sum_probs=5.3
Q ss_pred ChhHHHHHHHhh
Q 036252 240 APHFFINGYKNV 251 (318)
Q Consensus 240 ~p~~i~~a~~~~ 251 (318)
+..+|.+...++
T Consensus 51 i~eLIa~G~~kl 62 (113)
T PLN00138 51 ITELIASGREKL 62 (113)
T ss_pred HHHHHHhchhcc
Confidence 344444444443
No 48
>cd05796 Ribosomal_P0_like Ribosomal protein L10 family, P0-like protein subfamily; composed of uncharacterized eukaryotic proteins with similarity to the 60S ribosomal protein P0, including the Saccharomyces cerevisiae protein called mRNA turnover protein 4 (MRT4). MRT4 may be involved in mRNA decay. P0 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. It occupies the L7/L12 stalk of the ribosome. The stalk is known to contain the binding site for elongation factors EF-G and EF-Tu; however, there is disagreement as to whether or not P0 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, P0 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WAS
Probab=33.45 E-value=2.7e+02 Score=23.85 Aligned_cols=112 Identities=10% Similarity=0.068 Sum_probs=69.7
Q ss_pred HHHHHHHHHHHhccCeEEEEEec-------CCCc----hHHHHHHHHccCCcEEEEEehHHH--HHHHHhhhhhhCC-cc
Q 036252 12 IAYDARLCKLLEEYSQILIVAAD-------NVGS----NQLQHIRAGLRDHSIVLMGKNTMM--KRSIRLHAERTGN-RD 77 (318)
Q Consensus 12 ~~~v~~l~e~l~~y~~v~iv~~~-------~v~s----~ql~~iR~~lr~~~~~~vgKNtL~--~~Al~~~~~~~~~-~~ 77 (318)
...+.+||..|+.. .+++..-. +... ..+..|-..|+|+.-+.+.+.... ++.|.+.....+. .|
T Consensus 30 ~~ql~~iR~~lr~~-~~~v~KNtl~~~Al~~~~~~~~~~~~~~L~~~l~G~~~lift~~dp~~v~k~l~~~~~~~~ar~G 108 (163)
T cd05796 30 NNKLKDIRQEWKDS-RFFFGKNKVMQVALGRTPEDEYKPNLHKLSKYLKGQVGLLFTNEPPEEVIEYFDSYSEPDFARAG 108 (163)
T ss_pred HHHHHHHHHHhcCC-EEEEEchHHHHHHHhhCccccccccHHHHHHHhCCCEEEEEECCCHHHHHHHHHHcCCcccccCC
Confidence 45788999999886 55554221 2211 127788889998888888765333 3334443221111 00
Q ss_pred ----cccccccccCceEEEEecCChhhHHHHHHhccccccccCCC--ccCceEEeCCCCC
Q 036252 78 ----LLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGL--VAPIDVVVPPGNT 131 (318)
Q Consensus 78 ----~~~L~~~l~G~~gliFt~~dp~~v~k~l~~~k~~~~ar~G~--iA~~dVvi~~G~t 131 (318)
.+-..+ .|++ ...|..+...|.+...|+....|. |..+.+++.+|..
T Consensus 109 ~iA~~dvvi~--~G~~-----~~~p~~~~~~~~~lgiptki~~G~I~i~~d~~v~k~G~~ 161 (163)
T cd05796 109 SIATETVTLP--EGPL-----EQFPHSMEPQLRKLGLPTKLKKGVITLEADYVVCEEGKV 161 (163)
T ss_pred CCCCceEEEe--CCCC-----CCCCCCcchHHHHcCCCeEEeCCEEEEecCcEEECCCCC
Confidence 011111 2433 345667777999999999999996 7888899999975
No 49
>COG0303 MoeA Molybdopterin biosynthesis enzyme [Coenzyme metabolism]
Probab=31.00 E-value=85 Score=31.31 Aligned_cols=30 Identities=33% Similarity=0.510 Sum_probs=24.4
Q ss_pred ccCceEEeCCCCCCCCCCchhhhhhcCCceE
Q 036252 119 VAPIDVVVPPGNTGLDPSQTSFFQVLNIPTK 149 (318)
Q Consensus 119 iA~~dVvi~~G~t~~~p~~~~~fq~LgIptk 149 (318)
+++-+|++++| |-+.|...+.|-.+||..-
T Consensus 142 i~~G~vil~~G-~~L~p~~i~llas~Gi~~V 171 (404)
T COG0303 142 VAKGDVILRAG-TRLTPAEIALLASLGIAEV 171 (404)
T ss_pred ccCCCEeecCC-CCcCHHHHHHHHhCCCceE
Confidence 88888899999 6688888888888888643
No 50
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=30.93 E-value=44 Score=28.90 Aligned_cols=29 Identities=10% Similarity=0.169 Sum_probs=24.9
Q ss_pred ccCcchHHHHhhcCCCccccccceeeeee
Q 036252 169 RVGSSESALLSKLAIKPFSYGLIVMSVYE 197 (318)
Q Consensus 169 ~v~~~~A~lL~~L~i~p~~~~l~l~~~~~ 197 (318)
+.+++|+.-|+..|.=|..|++.=...+.
T Consensus 94 Ry~~devr~Lk~~g~~P~~~~~~~~~~~~ 122 (155)
T PTZ00329 94 KYTPDEARALKQHGELPETAKINETDIFD 122 (155)
T ss_pred EcCHHHHHHHHHcCCCCcceeeccccccC
Confidence 47899999999999999999887777663
No 51
>PF14226 DIOX_N: non-haem dioxygenase in morphine synthesis N-terminal; PDB: 3OOX_A 1BK0_A 1IPS_B 1QIQ_A 1OC1_A 2Y86_A 2Y60_A 1W03_A 2VE1_A 1QJF_A ....
Probab=29.87 E-value=1.1e+02 Score=23.88 Aligned_cols=42 Identities=14% Similarity=0.226 Sum_probs=34.2
Q ss_pred cHHHHHHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHcc
Q 036252 7 KAEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLR 49 (318)
Q Consensus 7 ~~e~K~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr 49 (318)
..+.+.+++++|.+.++++-.++|++. |++...++++.+..+
T Consensus 9 ~~~~~~~~~~~l~~A~~~~GFf~l~nh-Gi~~~l~~~~~~~~~ 50 (116)
T PF14226_consen 9 DPADREEVAEQLRDACEEWGFFYLVNH-GIPQELIDRVFAAAR 50 (116)
T ss_dssp CHHHHHHHHHHHHHHHHHTSEEEEESS-SSSHHHHHHHHHHHH
T ss_pred CCccHHHHHHHHHHHHHhCCEEEEecc-cccchhhHHHHHHHH
Confidence 457789999999999999888777665 898877777777665
No 52
>PLN00208 translation initiation factor (eIF); Provisional
Probab=29.19 E-value=50 Score=28.24 Aligned_cols=25 Identities=20% Similarity=-0.004 Sum_probs=20.9
Q ss_pred cCcchHHHHhhcCCCccccccceee
Q 036252 170 VGSSESALLSKLAIKPFSYGLIVMS 194 (318)
Q Consensus 170 v~~~~A~lL~~L~i~p~~~~l~l~~ 194 (318)
.+++|+.-|+..|.=|..|.+.=..
T Consensus 95 y~~dqvr~Lkk~G~~P~~f~~~~~~ 119 (145)
T PLN00208 95 YMPDEARLLKAYGELPENTRLNEGI 119 (145)
T ss_pred cCHHHHHHHHHcCCCCcceeecccc
Confidence 6899999999999999988774433
No 53
>cd03067 PDI_b_PDIR_N PDIb family, PDIR subfamily, N-terminal TRX-like b domain; composed of proteins similar to human PDIR (for Protein Disulfide Isomerase Related). PDIR is composed of three redox active TRX (a) domains and an N-terminal redox inactive TRX-like (b) domain. Similar to PDI, it is involved in oxidative protein folding in the endoplasmic reticulum (ER) through its isomerase and chaperone activities. These activities are lower compared to PDI, probably due to PDIR acting only on a subset of proteins. PDIR is preferentially expressed in cells actively secreting proteins and its expression is induced by stress. Similar to PDI, the isomerase and chaperone activities of PDIR are independent; CXXC mutants lacking isomerase activity retain chaperone activity. The TRX-like b domain of PDIR is critical for its chaperone activity.
Probab=27.69 E-value=1.7e+02 Score=23.77 Aligned_cols=66 Identities=17% Similarity=0.178 Sum_probs=46.0
Q ss_pred chHHHHHHHHccC--CcEEEEEehHHHHHHHHhhhhhhCCcccccccccccCceEEEEecCChhhHHHHHHhcccc
Q 036252 38 SNQLQHIRAGLRD--HSIVLMGKNTMMKRSIRLHAERTGNRDLLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVA 111 (318)
Q Consensus 38 s~ql~~iR~~lr~--~~~~~vgKNtL~~~Al~~~~~~~~~~~~~~L~~~l~G~~gliFt~~dp~~v~k~l~~~k~~ 111 (318)
..+.+++.+.||- +.-+++.|..--.-+.-.. +....+.++|+--++|-+-.-.+-+|++++.++.
T Consensus 6 i~d~KdfKKLLRTr~NVLvLy~ks~k~a~~~Lk~--------~~~~A~~vkG~gT~~~vdCgd~e~kKLCKKlKv~ 73 (112)
T cd03067 6 ISDHKDFKKLLRTRNNVLVLYSKSAKSAEALLKL--------LSDVAQAVKGQGTIAWIDCGDSESRKLCKKLKVD 73 (112)
T ss_pred ccchHHHHHHHhhcCcEEEEEecchhhHHHHHHH--------HHHHHHHhcCceeEEEEecCChHHHHHHHHHccC
Confidence 4567888888885 3455566654433222221 4556667889988999888888999999999884
No 54
>PRK01777 hypothetical protein; Validated
Probab=26.36 E-value=55 Score=25.81 Aligned_cols=32 Identities=9% Similarity=-0.088 Sum_probs=21.4
Q ss_pred cccCCCccCceEEeCCCCCCCCCCchhhhhhcCCceE
Q 036252 113 PARVGLVAPIDVVVPPGNTGLDPSQTSFFQVLNIPTK 149 (318)
Q Consensus 113 ~ar~G~iA~~dVvi~~G~t~~~p~~~~~fq~LgIptk 149 (318)
||.+....+..+.+|+|-| ...-++++||+..
T Consensus 10 ya~~~~~~~~~l~vp~GtT-----v~dal~~sgi~~~ 41 (95)
T PRK01777 10 YALPERQYLQRLTLQEGAT-----VEEAIRASGLLEL 41 (95)
T ss_pred EECCCceEEEEEEcCCCCc-----HHHHHHHcCCCcc
Confidence 4555556668888999887 2234677777655
No 55
>KOG4300 consensus Predicted methyltransferase [General function prediction only]
Probab=25.72 E-value=72 Score=29.31 Aligned_cols=40 Identities=18% Similarity=0.349 Sum_probs=26.1
Q ss_pred EEEEecCCCchHHHHHHHHccCCcEEEE-----EehHHHHHHHHhh
Q 036252 29 LIVAADNVGSNQLQHIRAGLRDHSIVLM-----GKNTMMKRSIRLH 69 (318)
Q Consensus 29 ~iv~~~~v~s~ql~~iR~~lr~~~~~~v-----gKNtL~~~Al~~~ 69 (318)
++++.++. +++|+++|+-||.++++++ |+-...-+-+++.
T Consensus 154 vLCSve~~-~k~L~e~~rlLRpgG~iifiEHva~~y~~~n~i~q~v 198 (252)
T KOG4300|consen 154 VLCSVEDP-VKQLNEVRRLLRPGGRIIFIEHVAGEYGFWNRILQQV 198 (252)
T ss_pred EEeccCCH-HHHHHHHHHhcCCCcEEEEEecccccchHHHHHHHHH
Confidence 34444444 7999999999998877764 4444444444443
No 56
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=24.58 E-value=3.5e+02 Score=21.28 Aligned_cols=77 Identities=9% Similarity=0.119 Sum_probs=52.1
Q ss_pred HHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccCC--cEEEEEehHHHHH-HHHhhhhhhCCcccccccccccCceEE
Q 036252 15 DARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDH--SIVLMGKNTMMKR-SIRLHAERTGNRDLLNLIPLLQGNVGM 91 (318)
Q Consensus 15 v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~~--~~~~vgKNtL~~~-Al~~~~~~~~~~~~~~L~~~l~G~~gl 91 (318)
-..|+..-..-+-++.+.=+|++-+-+.+++..|..+ .++++.+|.--.+ .+-..-.+.. -..+... -|++++
T Consensus 6 r~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~---~a~~Vq~-iG~~~v 81 (95)
T TIGR00253 6 KRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKET---GACNVQV-IGKTIV 81 (95)
T ss_pred HHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHH---CCEEEEE-EccEEE
Confidence 3457777788888999999999999999999999864 7888888853322 1211111111 1233333 499998
Q ss_pred EEec
Q 036252 92 IFTK 95 (318)
Q Consensus 92 iFt~ 95 (318)
+|-.
T Consensus 82 lYR~ 85 (95)
T TIGR00253 82 LYRP 85 (95)
T ss_pred EEec
Confidence 8863
No 57
>smart00460 TGc Transglutaminase/protease-like homologues. Transglutaminases are enzymes that establish covalent links between proteins. A subset of transglutaminase homologues appear to catalyse the reverse reaction, the hydrolysis of peptide bonds. Proteins with this domain are both extracellular and intracellular, and it is likely that the eukaryotic intracellular proteins are involved in signalling events.
Probab=24.48 E-value=48 Score=23.21 Aligned_cols=17 Identities=24% Similarity=0.600 Sum_probs=14.9
Q ss_pred hhhhhhcCCceEEecce
Q 036252 138 TSFFQVLNIPTKINKGT 154 (318)
Q Consensus 138 ~~~fq~LgIptki~~G~ 154 (318)
...+|.+|||+++..|-
T Consensus 17 ~~llr~~GIpar~v~g~ 33 (68)
T smart00460 17 VALLRSLGIPARVVSGY 33 (68)
T ss_pred HHHHHHCCCCeEEEeee
Confidence 46799999999999885
No 58
>PF03993 DUF349: Domain of Unknown Function (DUF349); InterPro: IPR007139 This motif is found singly or as up to five tandem repeats in a small set of bacterial proteins. There are two or three alpha-helices, and possibly a beta-strand.
Probab=21.03 E-value=52 Score=23.99 Aligned_cols=38 Identities=16% Similarity=0.147 Sum_probs=29.8
Q ss_pred ccHHHHHHHHHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccC
Q 036252 6 SKAEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRD 50 (318)
Q Consensus 6 ~~~e~K~~~v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~ 50 (318)
...+.|..++++++.+...-+ -+-....+++|++.|+.
T Consensus 31 ~n~~~K~~Li~~~~~l~~~~d-------~~~~~~~~k~l~~~Wk~ 68 (77)
T PF03993_consen 31 ENLEKKEALIEEAEALAESED-------WKEAAEEIKELQQEWKE 68 (77)
T ss_pred HHHHHHHHHHHHHHHhccccc-------HHHHHHHHHHHHHHHHH
Confidence 346789999999988887655 33448889999999985
No 59
>COG3473 Maleate cis-trans isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.14 E-value=75 Score=29.06 Aligned_cols=132 Identities=17% Similarity=0.272 Sum_probs=78.0
Q ss_pred ceEEeCCCCCCCCCCchhhhhhcCCceEEecceeEeecCcEE--eecCcccCcchHHHHhhcCCCccccccceeeeeeCC
Q 036252 122 IDVVVPPGNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVEL--IKKGDRVGSSESALLSKLAIKPFSYGLIVMSVYENG 199 (318)
Q Consensus 122 ~dVvi~~G~t~~~p~~~~~fq~LgIptki~~G~I~i~~d~~v--~~~G~~v~~~~A~lL~~L~i~p~~~~l~l~~~~~~g 199 (318)
.-.+||.-+|.|+|+...+|.+-||..-..+-. +.+ ++. +.+=+..+...|.+|.--+.+..-|+...-.+. .|
T Consensus 8 IGlIVpSSntTmE~ef~~m~~~ervs~H~sRmp--l~~-VT~EeL~~M~~~t~~aAl~Lada~vdvI~Y~CtsgS~i-~G 83 (238)
T COG3473 8 IGLIVPSSNTTMEPEFWRMLPSERVSVHTSRMP--LKN-VTPEELLKMESYTERAALELADAGVDVIVYGCTSGSLI-GG 83 (238)
T ss_pred eeEEEecCCCccchHHHHhhhhccceeeecccc--ccc-CCHHHHHHHHHHHHHHHHhcCccccCEEEEeccceeee-cC
Confidence 346899999999999888888766655544333 211 000 011123444555555555555555554432222 33
Q ss_pred cccCCccccCChHHHHHHHHHHHHHHHHHhhhcCcccCCCChhHHHHHHHh--hhhhhhhccccccchhcHHHHhcCcc
Q 036252 200 SVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGYKN--VLSFAVATEYSFSQADKVKEYLKDPS 276 (318)
Q Consensus 200 ~~~~~~~l~it~e~~~~~~~~a~~~~~~lsl~ag~pt~~s~p~~i~~a~~~--~~al~~~~~~~~~~~~~ik~ll~~~~ 276 (318)
.-| +.++. .++..+.+.|+-. -+....+|++. +..+++-+-|+-+-.+..++|+++-|
T Consensus 84 ~~~--------d~ei~----------~~ie~~~~v~vvT-ts~Avv~aL~al~a~ri~vlTPY~~evn~~e~ef~~~~G 143 (238)
T COG3473 84 PGY--------DKEIA----------QRIEEAKGVPVVT-TSTAVVEALNALGAQRISVLTPYIDEVNQREIEFLEANG 143 (238)
T ss_pred Cch--------hHHHH----------HHHHhccCCceee-chHHHHHHHHhhCcceEEEeccchhhhhhHHHHHHHhCC
Confidence 333 33343 2444455666533 35667777754 34678889999999999999998766
No 60
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=20.10 E-value=3.1e+02 Score=20.71 Aligned_cols=47 Identities=17% Similarity=0.208 Sum_probs=30.4
Q ss_pred HHHHHHHHhccCeEEEEEecCCCchHHHHHHHHccCC--cEEEEEehHH
Q 036252 15 DARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDH--SIVLMGKNTM 61 (318)
Q Consensus 15 v~~l~e~l~~y~~v~iv~~~~v~s~ql~~iR~~lr~~--~~~~vgKNtL 61 (318)
...|+..-..-+-++.+.=+|++-+-+++|+..|..+ .++++.+|..
T Consensus 6 ~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~ 54 (84)
T PF01985_consen 6 RKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCR 54 (84)
T ss_dssp HHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--H
T ss_pred HHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCH
Confidence 3456666666677788888899999999999999753 6777776533
Done!