Query 023961
Match_columns 274
No_of_seqs 214 out of 866
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 07:53:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023961.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023961hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00069 60S ribosomal protein 100.0 4E-119 8E-124 831.0 25.4 273 1-273 1-277 (300)
2 KOG0875 60S ribosomal protein 100.0 6.3E-92 1.4E-96 636.7 16.2 244 1-273 1-245 (264)
3 PRK08569 rpl18p 50S ribosomal 100.0 3.2E-79 7E-84 539.7 17.1 191 11-250 2-192 (193)
4 COG0256 RplR Ribosomal protein 100.0 1.3E-39 2.8E-44 271.1 7.8 123 14-172 1-125 (125)
5 PF00861 Ribosomal_L18p: Ribos 100.0 5.3E-32 1.1E-36 222.8 8.2 118 20-172 2-119 (119)
6 PF14204 Ribosomal_L18_c: Ribo 100.0 1.7E-32 3.7E-37 218.7 1.0 83 191-273 1-84 (94)
7 CHL00139 rpl18 ribosomal prote 100.0 5.7E-31 1.2E-35 214.8 6.5 106 33-172 4-109 (109)
8 PRK05593 rplR 50S ribosomal pr 100.0 2.9E-30 6.3E-35 212.9 9.1 108 29-172 9-117 (117)
9 TIGR00060 L18_bact ribosomal p 100.0 4.8E-29 1E-33 205.1 9.6 107 30-172 8-114 (114)
10 cd00432 Ribosomal_L18_L5e Ribo 100.0 1.5E-28 3.3E-33 196.5 9.0 95 46-170 9-103 (103)
11 PTZ00032 60S ribosomal protein 99.9 8.1E-25 1.7E-29 194.9 7.8 101 37-172 99-211 (211)
12 PTZ00090 40S ribosomal protein 96.3 0.019 4.2E-07 52.9 8.0 92 46-172 116-208 (233)
13 KOG3333 Mitochondrial/chloropl 96.1 0.014 3.1E-07 51.5 6.0 66 48-124 60-125 (188)
14 PF00411 Ribosomal_S11: Riboso 95.1 0.17 3.7E-06 41.4 8.6 96 51-181 3-107 (110)
15 TIGR03632 bact_S11 30S ribosom 93.8 0.38 8.2E-06 39.3 7.9 95 51-180 3-106 (108)
16 PRK05309 30S ribosomal protein 93.5 0.52 1.1E-05 39.8 8.4 101 46-181 15-124 (128)
17 PRK09607 rps11p 30S ribosomal 93.5 0.62 1.3E-05 39.9 8.9 102 50-181 11-125 (132)
18 CHL00041 rps11 ribosomal prote 93.0 0.67 1.4E-05 38.5 8.2 97 41-172 6-102 (116)
19 PTZ00129 40S ribosomal protein 90.8 2.1 4.6E-05 37.4 9.1 102 50-181 30-144 (149)
20 TIGR03628 arch_S11P archaeal r 88.1 3.2 6.9E-05 34.7 7.9 93 51-172 5-100 (114)
21 KOG0408 Mitochondrial/chloropl 75.0 14 0.00029 33.3 7.2 89 48-172 79-168 (190)
22 PF14821 Thr_synth_N: Threonin 67.6 8.7 0.00019 29.5 3.9 61 160-242 17-78 (79)
23 COG0100 RpsK Ribosomal protein 65.8 26 0.00057 30.0 6.8 96 51-181 21-125 (129)
24 PRK05337 beta-hexosaminidase; 42.7 32 0.0007 33.2 4.1 65 95-184 96-172 (337)
25 PF13069 DUF3933: Protein of u 40.4 7.8 0.00017 28.0 -0.4 15 58-76 3-17 (53)
26 PRK10251 phosphopantetheinyltr 35.4 73 0.0016 29.0 4.9 62 96-172 50-111 (207)
27 PF08673 RsbU_N: Phosphoserine 30.3 96 0.0021 24.1 4.2 41 209-249 11-54 (77)
28 PRK14083 HSP90 family protein; 29.7 32 0.00069 36.1 1.8 48 197-246 319-369 (601)
29 PRK05218 heat shock protein 90 29.2 51 0.0011 34.5 3.2 48 197-246 339-389 (613)
30 PRK10713 2Fe-2S ferredoxin Yfa 27.1 34 0.00073 26.2 1.2 17 160-176 21-37 (84)
31 PF06518 DUF1104: Protein of u 26.4 83 0.0018 25.4 3.3 42 207-248 34-78 (93)
32 cd04518 TBP_archaea archaeal T 25.0 4.2E+02 0.0091 23.4 7.8 54 42-112 29-83 (174)
33 PF00452 Bcl-2: Apoptosis regu 24.2 1.4E+02 0.0029 23.0 4.1 40 210-249 4-45 (101)
34 PF06292 DUF1041: Domain of Un 24.2 34 0.00073 28.3 0.7 40 201-240 53-96 (106)
35 PF14412 AHH: A nuclease famil 22.7 1.4E+02 0.0029 23.5 3.9 43 199-248 65-107 (109)
36 PF06648 DUF1160: Protein of u 22.6 1.1E+02 0.0024 26.0 3.5 43 199-242 18-63 (122)
37 TIGR01795 CM_mono_cladeE monof 22.3 1.2E+02 0.0027 24.1 3.6 52 194-245 23-81 (94)
38 PRK14102 nifW nitrogenase stab 21.8 1E+02 0.0022 25.6 3.1 30 220-249 39-74 (105)
39 COG2977 EntD Phosphopantethein 21.5 1.6E+02 0.0036 27.5 4.7 67 94-174 50-121 (228)
40 PF04282 DUF438: Family of unk 20.8 1.6E+02 0.0034 22.8 3.7 24 204-227 3-27 (71)
41 PRK00771 signal recognition pa 20.4 2E+02 0.0043 29.0 5.4 53 187-239 275-329 (437)
No 1
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=100.00 E-value=3.7e-119 Score=831.05 Aligned_cols=273 Identities=64% Similarity=1.023 Sum_probs=265.4
Q ss_pred CcceeeecCccccccccccccccccCchhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEec
Q 023961 1 MAFAKAQKSKAYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYA 80 (274)
Q Consensus 1 m~fvk~~kn~ay~~ryqvk~RRRRegKTdY~~R~rli~qdknky~s~KpRLvVrrTNk~IiaQIi~~~~~GD~tLasAsS 80 (274)
|+||||+||+|||+||||||||||||||||++|++||.||||||||||||||||+||++|||||+.+.++||+|||||+|
T Consensus 1 M~fvKv~KnkaY~~ryqvkfRRRREGKTdY~~R~rLi~q~knKynspK~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S 80 (300)
T PTZ00069 1 MAFVKVVKNKAYFKRFQVKYRRRREGKTDYYARRRLILQDKNKYNSPKYRLVVRITNKDIICQIVYATIVGDKVLAAAYS 80 (300)
T ss_pred CCceeeeecccccccccchhhhhhcccccHHHHHHHHHccccccCCCCceEEEEEECCcEEEEEEEeecCCCEEEEEeeh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccccccccCCCcHHHHHHHHHHHHHHHHHhhcccccccCcccccCccccc-ccCC-CCCCceEEEeecCcccccCCce
Q 023961 81 HELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDYSV-EPTE-NRRPFRALLDVGLVKTTTGNRV 158 (274)
Q Consensus 81 ~eL~k~g~k~g~tN~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~~g~~~~v-e~~~-~~~~f~~vLD~Gl~r~t~g~RV 158 (274)
+||++|||++|++|++||||||+|+|+|+|++||||+.|+|++++||++|+| |+.+ +++||+|||||||+|+|+|+||
T Consensus 81 ~eL~kyG~k~gl~N~~AAY~TGlL~arR~L~kl~ld~~y~G~~e~~g~~y~v~e~~~~~~rpf~a~LDiGL~rtt~G~RV 160 (300)
T PTZ00069 81 HELPRFGIPVGLTNYAAAYATGLLLARRLLKKLGLDKQFEGVKEADGEYYHVDEEDDEERRPFKAILDVGLARTTTGNRV 160 (300)
T ss_pred hhHhhcCcCCCCccHHHHHHHHHHHHHHHHHhhcccccccCcccccCcccccccccccCCCCceEEEeeccccCCCCcee
Confidence 9999999999999999999999999999999999999999999999999999 7766 7999999999999999999999
Q ss_pred eeeecccccCCccccCCccccCCCCCCccCCCHHhhhhhcccccHHHHHHHhcccChHHHHhhHHHHHHcCCCcchHHHH
Q 023961 159 FGALKGALDGGLDIPHSEKRFAGFSKDSKQLDAEVHRKYIYCGHVAAYMRTLMEDEPEKYQSHFCEYIKRGIEADNLEEL 238 (274)
Q Consensus 159 faalKGA~DgGL~iPh~~~~fp~~~~~~k~~~ae~~~~ri~G~hva~Y~~~L~eed~e~yk~qFS~yik~~~~p~~~e~~ 238 (274)
|||||||+||||+||||+++|||||.++++||||+|++||+|+|||+||+.|+|||||+|++|||+||++||+||+||+|
T Consensus 161 FaalKGa~DgGl~IPhs~~rfpg~d~e~~~~dAe~hR~rI~G~HVa~Ym~~Lkeedee~yk~qFS~yik~gl~~d~le~~ 240 (300)
T PTZ00069 161 FGALKGAVDGGLHIPHSPNRFPGYSKEKDSYDAEVHRDRIFGKHVAEYMKQLKEEDPDKYKKQFSKYIKAGVGPDSLEDM 240 (300)
T ss_pred eeehhcccccCcccCCCCCcCCCCCccccccChHHHHhhhcchhHHHHHHHhhhhChHHHHHHHHHHHHcCCChhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCCCCCCCCC--cccccCCCCCCCC
Q 023961 239 YKKVHAAIRADPNQKKSEKKPP--AEHKRYGQCIMWL 273 (274)
Q Consensus 239 y~~~~~~I~~~p~~~~~~k~~~--~~~k~~~~~kms~ 273 (274)
|++||++|++||.+++++++.+ ..+|+|+.+|||+
T Consensus 241 y~~ah~~Ir~~P~~~~~~kk~~~~~~~Kr~~~~Klt~ 277 (300)
T PTZ00069 241 YKKAHAAIRANPSKVKKKKKKKKKVVHKKYKTKKLTG 277 (300)
T ss_pred HHHHHHHHHhCcCccCccccccccccccccccccCCH
Confidence 9999999999998876666543 3678999999996
No 2
>KOG0875 consensus 60S ribosomal protein L5 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.3e-92 Score=636.75 Aligned_cols=244 Identities=64% Similarity=1.030 Sum_probs=238.8
Q ss_pred CcceeeecCccccccccccccccccCchhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEec
Q 023961 1 MAFAKAQKSKAYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYA 80 (274)
Q Consensus 1 m~fvk~~kn~ay~~ryqvk~RRRRegKTdY~~R~rli~qdknky~s~KpRLvVrrTNk~IiaQIi~~~~~GD~tLasAsS 80 (274)
|+|||++|+++||+||||+|||||||||||++|++|+.||+||||+|++||+||+||++|+|||+++.++||.++|+|+|
T Consensus 1 m~fvk~~k~~~y~kryqvk~rrrreGkTdy~arkrl~~qdknk~nt~kyR~ivr~~n~~iicqi~~~~i~gd~v~~~a~s 80 (264)
T KOG0875|consen 1 MGFVKVVKSKAYFKRYQVKFRRRREGKTDYYARKRLVVQDKNKYNTPKYRMIVRVINKDIICQIAYATIEGDVIVRAAYA 80 (264)
T ss_pred CcchheeccccccccccceEEEecCCCccHHHHHHHHhhcccccCCCceEEEEEEechhhHHHHHhheecceEEEEeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccccccccCCCcHHHHHHHHHHHHHHHHHhhcccccccCcccccCcccccccCC-CCCCceEEEeecCcccccCCcee
Q 023961 81 HELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDYSVEPTE-NRRPFRALLDVGLVKTTTGNRVF 159 (274)
Q Consensus 81 ~eL~k~g~k~g~tN~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~~g~~~~ve~~~-~~~~f~~vLD~Gl~r~t~g~RVf 159 (274)
+||++||++.|++|++||||||+|||+|+|+.||||++|+|+++++|++|+||++| +|+||+|+||+||+|+|+|+|||
T Consensus 81 ~elpkyg~~~GLtNyaAay~TglLLarR~l~~~gmD~~yeg~~e~~gde~~~e~idgq~~aFt~~Ld~GLaRtttg~kvF 160 (264)
T KOG0875|consen 81 HELPKYGVKVGLTNYAAAYCTGLLLACRLLKRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVF 160 (264)
T ss_pred ccccccccccccchhHHHHhhHHHHHHHHHHHhCcccccccceeecCcccccccccCCCCCeEEEecccccccCCCceee
Confidence 99999999999999999999999999999999999999999999999999999988 79999999999999999999999
Q ss_pred eeecccccCCccccCCccccCCCCCCccCCCHHhhhhhcccccHHHHHHHhcccChHHHHhhHHHHHHcCCCcchHHHHH
Q 023961 160 GALKGALDGGLDIPHSEKRFAGFSKDSKQLDAEVHRKYIYCGHVAAYMRTLMEDEPEKYQSHFCEYIKRGIEADNLEELY 239 (274)
Q Consensus 160 aalKGA~DgGL~iPh~~~~fp~~~~~~k~~~ae~~~~ri~G~hva~Y~~~L~eed~e~yk~qFS~yik~~~~p~~~e~~y 239 (274)
||||||+||||.||||+++||| |.|+|||+|++|||.||+.|++||+|++||
T Consensus 161 GAlkga~dGGL~IPHs~krFpG----------------------------l~e~d~e~y~~~fs~~i~~g~~ad~i~~~y 212 (264)
T KOG0875|consen 161 GALKGAVDGGLSIPHSTKRFPG----------------------------LTEESEEKYKKEFSGYIAKGVEADSIEGMY 212 (264)
T ss_pred eeeehhcccceecCCccccCCC----------------------------ccccchhhhhHHHhhhhhccccHHHHHHHH
Confidence 9999999999999999999999 789999999999999999999999999999
Q ss_pred HHHHHHHhcCCCCCCCCCCCCcccccCCCCCCCC
Q 023961 240 KKVHAAIRADPNQKKSEKKPPAEHKRYGQCIMWL 273 (274)
Q Consensus 240 ~~~~~~I~~~p~~~~~~k~~~~~~k~~~~~kms~ 273 (274)
++||++|+++|.++|++| ..+++|+|+.+|||+
T Consensus 213 ~~ahaaIra~p~~~k~~k-~~k~~k~~~~~klt~ 245 (264)
T KOG0875|consen 213 KKAHAAIRADPSPKKTEK-AAKESKRYNAKKLTY 245 (264)
T ss_pred HHHHHHhhcccCcccccc-ccccchhhccccCCH
Confidence 999999999999999877 445789999999986
No 3
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=100.00 E-value=3.2e-79 Score=539.73 Aligned_cols=191 Identities=45% Similarity=0.722 Sum_probs=185.0
Q ss_pred cccccccccccccccCchhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecCCcccccccc
Q 023961 11 AYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEV 90 (274)
Q Consensus 11 ay~~ryqvk~RRRRegKTdY~~R~rli~qdknky~s~KpRLvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~ 90 (274)
|.++||||||||||||||||++|++|+.++ +||||||+||+|||||||+++++||+|||||||+||+.+||.+
T Consensus 2 a~g~ry~v~~rRrRegkTdY~~R~rl~~~~-------kpRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~g~~~ 74 (193)
T PRK08569 2 ATGPRYKVPFRRRREGKTDYRKRLKLLLSG-------KPRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKYGWKG 74 (193)
T ss_pred CCCCccccceeccccccccHHHHHHHHhcC-------CCEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhccccC
Confidence 678999999999999999999999999998 7999999999999999997777899999999999999999999
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhhcccccccCcccccCcccccccCCCCCCceEEEeecCcccccCCceeeeecccccCCc
Q 023961 91 GLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGL 170 (274)
Q Consensus 91 g~tN~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~~g~~~~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL 170 (274)
+++|++|||+||+|||+|||++ ||++ ||||+||++||+||||||+||||+|+||
T Consensus 75 ~~~N~~AAy~vG~llA~ral~k--------Gi~~------------------vvfDrGg~~yh~gGRV~A~akgArd~GL 128 (193)
T PRK08569 75 DTGNTPAAYLTGLLAGKKALKA--------GVEE------------------AVLDIGLHRPTKGSRVFAALKGAIDAGL 128 (193)
T ss_pred CCCCHHHHHHHHHHHHHHHHHC--------CCCE------------------EEEecCCccccCCccHHHHHHHHHHcCC
Confidence 9999999999999999999999 9998 9999999999999999999999999999
Q ss_pred cccCCccccCCCCCCccCCCHHhhhhhcccccHHHHHHHhcccChHHHHhhHHHHHHcCCCcchHHHHHHHHHHHHhcCC
Q 023961 171 DIPHSEKRFAGFSKDSKQLDAEVHRKYIYCGHVAAYMRTLMEDEPEKYQSHFCEYIKRGIEADNLEELYKKVHAAIRADP 250 (274)
Q Consensus 171 ~iPh~~~~fp~~~~~~k~~~ae~~~~ri~G~hva~Y~~~L~eed~e~yk~qFS~yik~~~~p~~~e~~y~~~~~~I~~~p 250 (274)
+||||+++|||+ +||+|+|||+||+.|+||| |++|||+||++||+|++||+||++||++|++..
T Consensus 129 ~fPh~~~~~p~~-------------~ri~G~Hia~y~~~l~~e~---y~~~Fs~y~~~g~~~~~l~~~~~~~~~~i~~~~ 192 (193)
T PRK08569 129 EIPHGEEVLPDE-------------DRIRGEHIAEYAESLKEEN---YKKQFSKYLERGLDPEDLPEHFEEVKEKILEEY 192 (193)
T ss_pred cCCCCCCcCCCc-------------cccccchHHHHHHHHhhhH---HHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhc
Confidence 999999999995 7999999999999999988 999999999999999999999999999999753
No 4
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-39 Score=271.10 Aligned_cols=123 Identities=43% Similarity=0.610 Sum_probs=111.5
Q ss_pred ccccccccccccCchhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecC--CccccccccC
Q 023961 14 KRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAH--ELPRYGLEVG 91 (274)
Q Consensus 14 ~ryqvk~RRRRegKTdY~~R~rli~qdknky~s~KpRLvVrrTNk~IiaQIi~~~~~GD~tLasAsS~--eL~k~g~k~g 91 (274)
++|++++||++++||+|+.|.+|. + ++++||||||+||+|||||||++...+ ||++|||+ ||.++||+.+
T Consensus 1 ~~~~~~~rr~~~~kr~~r~R~kl~--g----~~~rpRL~V~rSnkhi~aQiId~~~~~--tla~aSt~~~~l~~~g~~~~ 72 (125)
T COG0256 1 PRYKVKFRRRRRGKRAYRIRKKLL--G----TSGRPRLVVRRSNRHIYAQIIDDVKGG--TLASASTLSKELRKYGKKGG 72 (125)
T ss_pred CccchhhHHHHHHhHHHHHHHhhc--c----CCCCcEEEEEEeCCcEEEEEEEcCCCc--eEEEEEcchHHHHhhcccCC
Confidence 589999999999999999999999 4 488999999999999999999997555 55555555 5667999999
Q ss_pred CCcHHHHHHHHHHHHHHHHHhhcccccccCcccccCcccccccCCCCCCceEEEeecCcccccCCceeeeecccccCCcc
Q 023961 92 LTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGLD 171 (274)
Q Consensus 92 ~tN~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~~g~~~~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL~ 171 (274)
++|++|||+||+|+|+||+++ ||++ ||||+|.+.|| |||||+++||+|+||+
T Consensus 73 ~~N~~aA~~vG~lia~ra~~k--------gi~~------------------vVfdr~g~~yh--gRV~Ala~~AreaGL~ 124 (125)
T COG0256 73 GGNTEAAYLVGKLIAERALAK--------GIEE------------------VVFDRGGYKYH--GRVAALADGAREAGLE 124 (125)
T ss_pred CCCHHHHHHHHHHHHHHHHHc--------CCcE------------------EEEcCCCCCcc--hHHHHHHHHHHHcCcC
Confidence 999999999999999999999 9998 99999999995 7999999999999998
Q ss_pred c
Q 023961 172 I 172 (274)
Q Consensus 172 i 172 (274)
+
T Consensus 125 f 125 (125)
T COG0256 125 F 125 (125)
T ss_pred C
Confidence 6
No 5
>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....
Probab=99.97 E-value=5.3e-32 Score=222.80 Aligned_cols=118 Identities=37% Similarity=0.445 Sum_probs=98.9
Q ss_pred ccccccCchhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecCCccccccccCCCcHHHHH
Q 023961 20 YKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAY 99 (274)
Q Consensus 20 ~RRRRegKTdY~~R~rli~qdknky~s~KpRLvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~g~tN~~AAy 99 (274)
++++|+.|++|.+|+.+.. +++|||+|++||+|||||||++...++.++||+.+.+|+.+||+.+++|++|||
T Consensus 2 k~~~~~~r~~~~r~~~~~~-------~~~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~~l~~~~~~~~~~n~~aa~ 74 (119)
T PF00861_consen 2 KKRRRRRRKLRIRRKIKGT-------AERPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSKELKKYGWKGSTKNVEAAY 74 (119)
T ss_dssp SCHHHHHHHHHHHHHHHHT-------TSSEEEEEEEESSEEEEEEEECTTTEEEEEEEEETTTGGGTT-SSTTSSHHHHH
T ss_pred hhHHHHHHHHHHHHHHhcC-------CCCCEEEEEeccCeEEEEEEeeCCCCeEEEEEecchhhhhhhhccCCCCEehHH
Confidence 4566666666666666555 558999999999999999999976555555566666777889999999999999
Q ss_pred HHHHHHHHHHHHhhcccccccCcccccCcccccccCCCCCCceEEEeecCcccccCCceeeeecccccCCccc
Q 023961 100 CTGLLLARRVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGLDI 172 (274)
Q Consensus 100 ~tGlLlA~Ral~k~~~~~~y~Gi~e~~g~~~~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL~i 172 (274)
+||+|||+||+++ ||.. ++||+|.++|| |||+|+++||+|+||+|
T Consensus 75 ~vG~lla~ra~~~--------gi~~------------------v~fdr~~~~y~--grv~a~~~~~re~Gl~f 119 (119)
T PF00861_consen 75 LVGELLAKRALEK--------GIAK------------------VVFDRGGYKYH--GRVKALADGAREGGLEF 119 (119)
T ss_dssp HHHHHHHHHHHHT--------TSSE------------------EEECTSTSSSS--SHHHHHHHHHHHTTCB-
T ss_pred HHHHHHHHHHHHc--------CCcE------------------EEEcCCCCccc--HHHHHHHHHHHHcCCCC
Confidence 9999999999999 9987 99999999995 69999999999999986
No 6
>PF14204 Ribosomal_L18_c: Ribosomal L18 C-terminal region; PDB: 2ZKR_n 4A1E_M 4A1C_M 4A1A_M 4A17_M 3O58_E 1S1I_E 3IZS_Q 3O5H_E 3IZR_Q.
Probab=99.97 E-value=1.7e-32 Score=218.72 Aligned_cols=83 Identities=59% Similarity=0.926 Sum_probs=76.9
Q ss_pred HHhhhhhcccccHHHHHHHhcccChHHHHhhHHHHHHcCCCcchHHHHHHHHHHHHhcCCCCCCCCCCCCc-ccccCCCC
Q 023961 191 AEVHRKYIYCGHVAAYMRTLMEDEPEKYQSHFCEYIKRGIEADNLEELYKKVHAAIRADPNQKKSEKKPPA-EHKRYGQC 269 (274)
Q Consensus 191 ae~~~~ri~G~hva~Y~~~L~eed~e~yk~qFS~yik~~~~p~~~e~~y~~~~~~I~~~p~~~~~~k~~~~-~~k~~~~~ 269 (274)
||+|++||+|+|||+||+.|+|||||+|++|||+||++||+||+||+||++||++||+||++.+++++.+. .+|+|+.+
T Consensus 1 Ae~hr~rI~G~HVaeYm~~L~eed~e~yk~qFs~yik~gi~p~~le~~y~~~h~~Ir~dP~~~~k~~k~~~~~~k~~~~~ 80 (94)
T PF14204_consen 1 AEVHRDRIFGGHVAEYMEELKEEDPEKYKRQFSKYIKKGIEPDDLEEMYKKAHAAIREDPSPKKKEKKEYKAEKKRYKPK 80 (94)
T ss_dssp -HCHHHCSSSSHCHHHHHSCSSCSSSTCSHHHHHHHHHHCSSSHHHHHHHHHHHCCCHSCCCCCCSTSSS-CHHHHHSCC
T ss_pred ChHHHhCcCchhHHHHHHHHHhhCHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHHhCcccccccccccchhhcccCcc
Confidence 79999999999999999999999999999999999999999999999999999999999999888765443 56999999
Q ss_pred CCCC
Q 023961 270 IMWL 273 (274)
Q Consensus 270 kms~ 273 (274)
|||+
T Consensus 81 Klt~ 84 (94)
T PF14204_consen 81 KLTL 84 (94)
T ss_dssp CCCH
T ss_pred cCCH
Confidence 9996
No 7
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=99.97 E-value=5.7e-31 Score=214.84 Aligned_cols=106 Identities=25% Similarity=0.234 Sum_probs=95.2
Q ss_pred HHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecCCccccccccCCCcHHHHHHHHHHHHHHHHHh
Q 023961 33 RIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKM 112 (274)
Q Consensus 33 R~rli~qdknky~s~KpRLvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~g~tN~~AAy~tGlLlA~Ral~k 112 (274)
|.|..+.|+ +.+|||+|++||+|||||||++ . .++|||||||.|+..++|..+++|++||+++|++||+|++++
T Consensus 4 r~r~ki~g~----~~rpRL~V~rSnkhiyaQvidd-~-~g~tlasaST~ek~~~~~~~~~~n~~aA~~vG~lla~ra~~~ 77 (109)
T CHL00139 4 RVRKKIKGT----AERPRLSVFRSNKHIYAQIIDD-T-NGKTLVACSTLEPDVKSSLSSTSTCDASKLVGQKLAKKSLKK 77 (109)
T ss_pred eeeeeecCC----CCCCEEEEEEeCCeEEEEEEEC-C-CCCEEEEEecCchhhhccccCCCCHHHHHHHHHHHHHHHHHC
Confidence 344445564 6699999999999999999996 3 459999999999999999888999999999999999999999
Q ss_pred hcccccccCcccccCcccccccCCCCCCceEEEeecCcccccCCceeeeecccccCCccc
Q 023961 113 LEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGLDI 172 (274)
Q Consensus 113 ~~~~~~y~Gi~e~~g~~~~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL~i 172 (274)
||++ |+||+|+++|| |||+|+++||+|+||+.
T Consensus 78 --------gi~~------------------vvfDrgg~~yh--GrV~a~a~~are~GL~f 109 (109)
T CHL00139 78 --------GITK------------------VVFDRGGKLYH--GRIKALAEAAREAGLQF 109 (109)
T ss_pred --------CCCE------------------EEEcCCCCccc--hHHHHHHHHHHHhCCCC
Confidence 9998 99999999996 79999999999999973
No 8
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=99.96 E-value=2.9e-30 Score=212.93 Aligned_cols=108 Identities=31% Similarity=0.289 Sum_probs=97.7
Q ss_pred hHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecCCcc-ccccccCCCcHHHHHHHHHHHHH
Q 023961 29 DYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELP-RYGLEVGLTNYAAAYCTGLLLAR 107 (274)
Q Consensus 29 dY~~R~rli~qdknky~s~KpRLvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~-k~g~k~g~tN~~AAy~tGlLlA~ 107 (274)
..+.|.|..++++ +.+|||+|++||+||||||||+ ++|+|||||||.|+. +++|+ ++|++|||+||++||+
T Consensus 9 ~r~~r~r~ki~g~----~~rpRL~V~~SnkhiyAQvidd--~~~~tl~saST~e~~~k~~~~--~~n~~aa~~vG~~la~ 80 (117)
T PRK05593 9 RRHRRVRKKISGT----AERPRLSVFRSNRHIYAQVIDD--VKGKTLASASTLEKDVRAGLK--GGNKEAAKKVGKLIAE 80 (117)
T ss_pred HHHHHHHHHhcCC----CCCCEEEEEEeCCeEEEEEEEC--CCCEEEEEEecCcHhHhcccc--CCCHHHHHHHHHHHHH
Confidence 4556777777775 7799999999999999999987 599999999999998 57776 7899999999999999
Q ss_pred HHHHhhcccccccCcccccCcccccccCCCCCCceEEEeecCcccccCCceeeeecccccCCccc
Q 023961 108 RVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGLDI 172 (274)
Q Consensus 108 Ral~k~~~~~~y~Gi~e~~g~~~~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL~i 172 (274)
|++++ ||++ +|||+|+++|| |||+|+++||+|+||+.
T Consensus 81 ra~~~--------gi~~------------------vvfDrg~~~yh--GrV~a~a~~are~Gl~f 117 (117)
T PRK05593 81 RAKAK--------GIKQ------------------VVFDRGGYKYH--GRVKALADAAREAGLKF 117 (117)
T ss_pred HHHHC--------CCCE------------------EEEcCCCCccc--HHHHHHHHHHHHhCCCC
Confidence 99999 9998 99999999994 69999999999999974
No 9
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=99.96 E-value=4.8e-29 Score=205.09 Aligned_cols=107 Identities=31% Similarity=0.298 Sum_probs=93.2
Q ss_pred HHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecCCccccccccCCCcHHHHHHHHHHHHHHH
Q 023961 30 YRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRV 109 (274)
Q Consensus 30 Y~~R~rli~qdknky~s~KpRLvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~g~tN~~AAy~tGlLlA~Ra 109 (274)
.+.|.|..+.++..| .+|||+|++||+||||||||+ ++|+|||||||.|+. ++ +++|++|||+||++||++|
T Consensus 8 r~~r~r~ki~gt~~~--~rpRL~V~rSnk~iyaQiIdd--~~~~tlasaST~ek~-~~---~~~n~~aA~~vG~~la~ra 79 (114)
T TIGR00060 8 RHKRIRRKLRETGEA--NRPRLVVFRSNRHIYAQVIDD--SKSEVLASASTLEKK-LK---YTGNKDAAKKVGKLVAERL 79 (114)
T ss_pred HHHHHHHHhcCCCCC--CCcEEEEEEeCCeEEEEEEEC--CCCEEEEEEecchhh-hc---CCCCHHHHHHHHHHHHHHH
Confidence 345666666664111 489999999999999999987 599999999999986 32 6789999999999999999
Q ss_pred HHhhcccccccCcccccCcccccccCCCCCCceEEEeecCcccccCCceeeeecccccCCccc
Q 023961 110 LKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGLDI 172 (274)
Q Consensus 110 l~k~~~~~~y~Gi~e~~g~~~~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL~i 172 (274)
+++ ||++ |+||+|+++|| |||.|+++||+|+||+.
T Consensus 80 ~~~--------gi~~------------------vvfDrgg~~Yh--Grv~A~a~~aRe~Gl~F 114 (114)
T TIGR00060 80 KEK--------GIKD------------------VVFDRGGYKYH--GRVAALAEAAREAGLNF 114 (114)
T ss_pred HHC--------CCCE------------------EEEeCCCCcch--HHHHHHHHHHHHhCCCC
Confidence 999 9998 99999999996 69999999999999974
No 10
>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.
Probab=99.95 E-value=1.5e-28 Score=196.49 Aligned_cols=95 Identities=43% Similarity=0.497 Sum_probs=90.4
Q ss_pred CCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecCCccccccccCCCcHHHHHHHHHHHHHHHHHhhcccccccCcccc
Q 023961 46 TPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEA 125 (274)
Q Consensus 46 s~KpRLvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~g~tN~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~ 125 (274)
.++|||+|++||+|||||||++. +|+|||+|||+|++.+++..+++|++|||++|.+||+|++++ |+++
T Consensus 9 ~~~~RL~v~~Sn~~i~aqvi~~~--~~~vl~sast~e~~~~~~~~~~~n~~aA~~vG~~la~r~~~~--------gi~~- 77 (103)
T cd00432 9 QERPRLVVRKSNKHIYAQIIDDS--GDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEK--------GIKK- 77 (103)
T ss_pred CCCCEEEEEEeCCEEEEEEEEeC--cCeEEEEEecCchhhcccccCCCcHHHHHHHHHHHHHHHHHC--------CCCE-
Confidence 45899999999999999999984 899999999999998888888999999999999999999999 9998
Q ss_pred cCcccccccCCCCCCceEEEeecCcccccCCceeeeecccccCCc
Q 023961 126 TGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGL 170 (274)
Q Consensus 126 ~g~~~~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL 170 (274)
++||+|++++ ||||+|+++|++|+||
T Consensus 78 -----------------vv~D~~~~~~--~grv~a~~~~~r~~Gl 103 (103)
T cd00432 78 -----------------VVFDRGGYRY--HGRVKALAKGAREGGL 103 (103)
T ss_pred -----------------EEEeCCCccc--ccHHHHHHHHHHHcCC
Confidence 9999999999 6899999999999997
No 11
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=99.91 E-value=8.1e-25 Score=194.87 Aligned_cols=101 Identities=24% Similarity=0.209 Sum_probs=88.6
Q ss_pred HHhCCCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecCCcccccccc------------CCCcHHHHHHHHHH
Q 023961 37 INQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEV------------GLTNYAAAYCTGLL 104 (274)
Q Consensus 37 i~qdknky~s~KpRLvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~------------g~tN~~AAy~tGlL 104 (274)
|+||| -+|||+|++||+|||||||||. .+.|||||||.+....+... .++|++||+.+|.+
T Consensus 99 i~~gk-----rrPRLsV~RSnkHIYAQIIDD~--~~~TLasaSTlek~l~~~~~~~~~~~~n~~~~~g~nieaA~~VGk~ 171 (211)
T PTZ00032 99 IIKGK-----RRPRLTLKNTNNQMYATIVDDY--TRHVLCFSCTNFKYLSHIFGTYPTKTTNRVRNNGGTIKAAYELGKL 171 (211)
T ss_pred HHcCC-----CcceEEEEecCCeEEEEEEECC--CCCEEEEecCCCHHHHhhhcccccccccccccCCCcHHHHHHHHHH
Confidence 56664 4799999999999999999984 66999999999876433211 46799999999999
Q ss_pred HHHHHHHhhcccccccCcccccCcccccccCCCCCCceEEEeecCcccccCCceeeeecccccCCccc
Q 023961 105 LARRVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGLDI 172 (274)
Q Consensus 105 lA~Ral~k~~~~~~y~Gi~e~~g~~~~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL~i 172 (274)
||++|+++ ||++ |+||+|+++|| |||.|+++|||++||..
T Consensus 172 IAerAl~k--------GI~k------------------VvFDRgGy~YH--GRVkALAdaARe~GLkF 211 (211)
T PTZ00032 172 IGRKALSK--------GISK------------------VRFDRAHYKYA--GKVEALAEGARAVGLQF 211 (211)
T ss_pred HHHHHHHC--------CCCE------------------EEEeCCCCeeh--hHHHHHHHHHHHcCCCC
Confidence 99999999 9998 99999999997 69999999999999963
No 12
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=96.26 E-value=0.019 Score=52.88 Aligned_cols=92 Identities=16% Similarity=0.288 Sum_probs=70.9
Q ss_pred CCcceEEEEecCCcEEEEEEeeecCCCE-EEEEEecCCccccccccCCCcHHHHHHHHHHHHHHHHHhhcccccccCccc
Q 023961 46 TPKYRFVVRFTNKDITAQIISASIAGDI-VLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVE 124 (274)
Q Consensus 46 s~KpRLvVrrTNk~IiaQIi~~~~~GD~-tLasAsS~eL~k~g~k~g~tN~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e 124 (274)
+.+.++||.-|-+++++||.|. .|+. ||+-+|+-.....|-+.+ ---||+.++.-+|+++.+. |+..
T Consensus 116 ~~~f~~vI~aSfNNTIVTlTD~--~GNv~tl~WSSAG~~GFKGsKKs--TpfAAQ~aae~aakka~~~--------GIk~ 183 (233)
T PTZ00090 116 TDRFMLVITTSKNNVHAQVVNK--SKNYKTVFGSFAGNVGFRKKLQQ--SERCAYRIGENIAKKCRRL--------GIFA 183 (233)
T ss_pred CCcEEEEEEeccCcEEEEEEeC--CCCEEEEEEEcccccCcccCccC--CHHHHHHHHHHHHHHHHHc--------CCeE
Confidence 5578999999999999999996 5875 788888877654454322 3458899999999999998 9886
Q ss_pred ccCcccccccCCCCCCceEEEeecCcccccCCceeeeecccccCCccc
Q 023961 125 ATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGLDI 172 (274)
Q Consensus 125 ~~g~~~~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL~i 172 (274)
+|+=+... |+ .-+|+++....||.|
T Consensus 184 --------------------V~V~vKGp--Gg-REtALRaL~~~GLkI 208 (233)
T PTZ00090 184 --------------------VDIKFRRI--MR-VETVLQAFYANGLQV 208 (233)
T ss_pred --------------------EEEEEeCC--Ch-HHHHHHHHHHCCCEE
Confidence 34444444 33 688999999999873
No 13
>KOG3333 consensus Mitochondrial/chloroplast ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=96.08 E-value=0.014 Score=51.47 Aligned_cols=66 Identities=21% Similarity=0.104 Sum_probs=55.2
Q ss_pred cceEEEEecCCcEEEEEEeeecCCCEEEEEEecCCccccccccCCCcHHHHHHHHHHHHHHHHHhhcccccccCccc
Q 023961 48 KYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVE 124 (274)
Q Consensus 48 KpRLvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~g~tN~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e 124 (274)
=+||-|-+|..|+-.-+.... |.|+.||||.|.....---+++|+.|+--+|..||.|.|+. ||..
T Consensus 60 wh~lev~~~~~hveg~v~H~~---~gvvvSAST~EwaIk~qLYst~dtsA~~niGRVLAqRCLqs--------GI~f 125 (188)
T KOG3333|consen 60 WHRLEVIRTQHHVEGLVEHQN---GGVVVSASTREWAIKKQLYSTRDTSACENIGRVLAQRCLQS--------GINF 125 (188)
T ss_pred eeEEEEeecccceeeeeeEec---CCEEEEecccchHHHHHHhhccchHHHHHHHHHHHHHHHHh--------Ccce
Confidence 368999999999999999873 45888999999863322236789999999999999999999 9885
No 14
>PF00411 Ribosomal_S11: Ribosomal protein S11; InterPro: IPR001971 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S11 [] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. On the basis of sequence similarities, S11 belongs to a family of bacterial, archaeal and eukaryotic ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_K 3U5C_O 3O2Z_H 3IZB_K 3U5G_O 3O30_H 1S1H_K 3BBN_K 2XZN_K 2XZM_K ....
Probab=95.13 E-value=0.17 Score=41.37 Aligned_cols=96 Identities=23% Similarity=0.208 Sum_probs=66.5
Q ss_pred EEEEecCCcEEEEEEeeecCCCEEEEEEecCCccccccccCCCcHHHHHHHHHHHHHHHHHhhcccccccCcccccCccc
Q 023961 51 FVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDY 130 (274)
Q Consensus 51 LvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~g~tN~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~~g~~~ 130 (274)
+-|+-|.+++++.+.|. .| .++++.|+-.+...|-. -....||+.++.-+++++.+. |++.+
T Consensus 3 ihI~~s~NNt~vtlTd~--~G-~~~~~~S~G~~gfK~~r--k~t~~Aa~~~a~~~~~~~~~~--------gi~~v----- 64 (110)
T PF00411_consen 3 IHIKSSFNNTIVTLTDL--KG-NVLFWSSAGSLGFKGAR--KSTPYAAQQAAEKIAKKAKEL--------GIKTV----- 64 (110)
T ss_dssp EEEEEESSEEEEEEEET--TS-EEEEEEETTTSSTTTTC--GSSHHHHHHHHHHHHHHHHCT--------TEEEE-----
T ss_pred EEEEecCCCEEEEEECC--CC-CEEEEEecccccccccc--ccCHHHHHHHHHHHHHHHHHc--------CCeEE-----
Confidence 46888999999999996 35 78888888766544433 346788999999999999998 88751
Q ss_pred ccccCCCCCCceEEEeecCcccccCCceeeeecccccCCcc---------ccCCccccCC
Q 023961 131 SVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGLD---------IPHSEKRFAG 181 (274)
Q Consensus 131 ~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL~---------iPh~~~~fp~ 181 (274)
.++| .| .+-|| .+++++....||. |||+-.|-|.
T Consensus 65 -----------~v~i-kG----~g~gr-~~~lk~l~~~gl~I~~I~D~T~iphnGcR~kK 107 (110)
T PF00411_consen 65 -----------RVKI-KG----FGPGR-EAALKALKKSGLKIVSITDVTPIPHNGCRPKK 107 (110)
T ss_dssp -----------EEEE-ES----SSTTH-HHHHHHHHHTTSEEEEEEEETT--SSSS--TT
T ss_pred -----------EEEE-cC----CCccH-HHHHHHHHhcCCEEEEEEeecCCCCCCCCCCC
Confidence 1333 34 22234 4677888889986 5888777664
No 15
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=93.82 E-value=0.38 Score=39.34 Aligned_cols=95 Identities=22% Similarity=0.207 Sum_probs=67.8
Q ss_pred EEEEecCCcEEEEEEeeecCCCEEEEEEecCCccccccccCCCcHHHHHHHHHHHHHHHHHhhcccccccCcccccCccc
Q 023961 51 FVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDY 130 (274)
Q Consensus 51 LvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~g~tN~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~~g~~~ 130 (274)
+-|.-|.+++++-+.|. .|+ +++.+|+-.+...|-. -...-||+.++..+++++++. |+..+.
T Consensus 3 ~hI~~s~NNT~itlTd~--~g~-~~~~~S~G~~gfkg~r--k~t~~Aa~~~a~~~~~~~~~~--------gi~~v~---- 65 (108)
T TIGR03632 3 AHIHATFNNTIVTITDP--QGN-VLSWASAGAVGFKGSK--KSTPYAAQLAAEDAAKKAKEF--------GMKTVD---- 65 (108)
T ss_pred EEEEccCCCEEEEEEcC--CCC-EEEEEecCceeeCCCc--cCCHHHHHHHHHHHHHHHHHc--------CCcEEE----
Confidence 45788999999999996 464 8888887766544433 234667999999999999998 887621
Q ss_pred ccccCCCCCCceEEEeecCcccccCCceeeeecccccCCcc---------ccCCccccC
Q 023961 131 SVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGLD---------IPHSEKRFA 180 (274)
Q Consensus 131 ~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL~---------iPh~~~~fp 180 (274)
++| .|+- -|| -+++++....||. |||+-.|.|
T Consensus 66 ------------v~~-kG~G----~gr-~~~ir~l~~~glkI~~I~D~T~iphNGcR~~ 106 (108)
T TIGR03632 66 ------------VYV-KGPG----AGR-ESAIRALQAAGLEVTSIKDVTPIPHNGCRPP 106 (108)
T ss_pred ------------EEE-ECCC----CcH-HHHHHHHHHCCCEEEEEEEcCCCCCCCcCCC
Confidence 333 4532 134 5688888888986 588777766
No 16
>PRK05309 30S ribosomal protein S11; Validated
Probab=93.50 E-value=0.52 Score=39.83 Aligned_cols=101 Identities=22% Similarity=0.175 Sum_probs=72.2
Q ss_pred CCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecCCccccccccCCCcHHHHHHHHHHHHHHHHHhhcccccccCcccc
Q 023961 46 TPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEA 125 (274)
Q Consensus 46 s~KpRLvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~g~tN~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~ 125 (274)
-+.--+-|+.|.+++++-+.|. .| .+|+.+|+-.+...|-. -...-||+.++.-+++.+++. |+..+
T Consensus 15 ~~~gi~hI~~t~NNTiitlTd~--~G-~~~~~~S~G~~gfKg~r--K~T~~Aa~~aa~~~~~~~~~~--------gi~~v 81 (128)
T PRK05309 15 IPSGVAHIHATFNNTIVTITDR--QG-NVISWASAGGLGFKGSR--KSTPYAAQVAAEDAAKKAKEH--------GMKTV 81 (128)
T ss_pred cceeEEEEEccCCCEEEEEEcC--CC-CEEEEEecCccEeCCCc--cCCHHHHHHHHHHHHHHHHHc--------CCcEE
Confidence 3446788999999999999995 46 57888877665444433 234558999999999999998 88752
Q ss_pred cCcccccccCCCCCCceEEEeecCcccccCCceeeeecccccCCcc---------ccCCccccCC
Q 023961 126 TGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGLD---------IPHSEKRFAG 181 (274)
Q Consensus 126 ~g~~~~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL~---------iPh~~~~fp~ 181 (274)
. ++| .|+- -|| -+++++....||. |||+-.|-|.
T Consensus 82 ~----------------v~i-kG~G----~Gr-~~air~L~~~glkI~~I~D~TpiphNGcR~~K 124 (128)
T PRK05309 82 E----------------VFV-KGPG----SGR-ESAIRALQAAGLEVTSIKDVTPIPHNGCRPPK 124 (128)
T ss_pred E----------------EEE-ECCC----CcH-HHHHHHHHHCCCEEEEEEEcCCCCCCCcCcCC
Confidence 1 333 4532 234 5778888888986 5888888775
No 17
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=93.49 E-value=0.62 Score=39.86 Aligned_cols=102 Identities=15% Similarity=0.089 Sum_probs=71.3
Q ss_pred eEEEEecCCcEEEEEEeeecCCCEEEEEEecCCccccccccCCCcHHHHHHHHHHHHHHHHHhhcccccccCcccccCcc
Q 023961 50 RFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGED 129 (274)
Q Consensus 50 RLvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~g~tN~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~~g~~ 129 (274)
=+-|+-|-++.+..|.|. .|..||+.+|+-.....|-+. ..--||..++.-+++++++. |+..+.
T Consensus 11 i~hI~as~NNTivtvTD~--~G~~~~~~~S~G~~g~kg~kK--~TpyAAq~aae~~~~~~~~~--------Gi~~v~--- 75 (132)
T PRK09607 11 IAHIYASFNNTIITITDL--TGAETIAKSSGGMVVKADRDE--SSPYAAMQAAEKAAEDAKEK--------GITGVH--- 75 (132)
T ss_pred EEEEEcccCCeEEEEEcC--CCCEEEEEecCcceeeCCCcc--CCHHHHHHHHHHHHHHHHHc--------CCcEEE---
Confidence 456778889999999996 587799988887665555432 23347899999999999998 988621
Q ss_pred cccccCCCCCCceEEEeec--Cccccc--CCceeeeecccccCCcc---------ccCCccccCC
Q 023961 130 YSVEPTENRRPFRALLDVG--LVKTTT--GNRVFGALKGALDGGLD---------IPHSEKRFAG 181 (274)
Q Consensus 130 ~~ve~~~~~~~f~~vLD~G--l~r~t~--g~RVfaalKGA~DgGL~---------iPh~~~~fp~ 181 (274)
+.+ .| +..+.+ -|| -+++++...+||. |||+--|-|+
T Consensus 76 -------------v~v-kG~Ggn~~~~~G~Gr-~~airal~~~glkI~~I~DvTpiPhNGCRp~K 125 (132)
T PRK09607 76 -------------IKV-RAPGGNGQKSPGPGA-QAAIRALARAGLRIGRIEDVTPIPHDGTRPPG 125 (132)
T ss_pred -------------EEE-EecCCCCCcCCCCcH-HHHHHHHHHCCCEEEEEEEcCCCCCCCCCCCC
Confidence 222 22 222222 233 4578888888986 6999988887
No 18
>CHL00041 rps11 ribosomal protein S11
Probab=93.01 E-value=0.67 Score=38.46 Aligned_cols=97 Identities=21% Similarity=0.158 Sum_probs=70.3
Q ss_pred CCCCCCCcceEEEEecCCcEEEEEEeeecCCCEEEEEEecCCccccccccCCCcHHHHHHHHHHHHHHHHHhhccccccc
Q 023961 41 KNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYE 120 (274)
Q Consensus 41 knky~s~KpRLvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~g~tN~~AAy~tGlLlA~Ral~k~~~~~~y~ 120 (274)
++|.+.+.--+-|+.|.+++++-+.|. .| .+|+.+|+-.+...|-. -...-||+.++.-+++++++.
T Consensus 6 ~~~~~~~~gi~hI~~t~NNTiiTlTd~--~G-~~l~~~S~G~~gfKg~r--K~T~~Aa~~~a~~~~~~~~~~-------- 72 (116)
T CHL00041 6 KSKRKIPKGVIHIQASFNNTIVTVTDV--RG-RVISWSSAGACGFKGAR--KGTPFAAQTAAENAIRTVIDQ-------- 72 (116)
T ss_pred cccccceeEEEEEEcccCCEEEEEEcC--CC-CEEEEEecCceeeCCCc--cCCHHHHHHHHHHHHHHHHHc--------
Confidence 445556666788999999999999996 46 68999988766544433 234568899999999999998
Q ss_pred CcccccCcccccccCCCCCCceEEEeecCcccccCCceeeeecccccCCccc
Q 023961 121 GHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGLDI 172 (274)
Q Consensus 121 Gi~e~~g~~~~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL~i 172 (274)
|+..+. ++| .|.- -|| -+++++....||.|
T Consensus 73 gi~~v~----------------I~i-kG~G----~Gr-~~~ir~l~~~glkI 102 (116)
T CHL00041 73 GMKRAE----------------VMI-KGPG----LGR-DTALRAIRRSGLKL 102 (116)
T ss_pred CCcEEE----------------EEE-ECCC----CcH-HHHHHHHHHCCCEE
Confidence 887622 444 5532 244 56788888999875
No 19
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=90.77 E-value=2.1 Score=37.38 Aligned_cols=102 Identities=20% Similarity=0.125 Sum_probs=67.5
Q ss_pred eEEEEecCCcEEEEEEeeecCCCEEEEEEecCCccccccccCCCc-HHHHHHHHHHHHHHHHHhhcccccccCcccccCc
Q 023961 50 RFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTN-YAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGE 128 (274)
Q Consensus 50 RLvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~g~tN-~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~~g~ 128 (274)
=+-|+-|-++.+..|.|. .| .+++.+||-.+...|-.- .+ --||..+..-+|+++++. ||..+.
T Consensus 30 i~hI~as~NNTiItiTD~--~G-~~~~w~SsG~~gfKg~r~--KsTpyAAq~aa~~~a~k~~~~--------Gi~~v~-- 94 (149)
T PTZ00129 30 VAHIFASFNDTFIHVTDL--SG-RETLVRVTGGMKVKADRD--ESSPYAAMMAAQDVAARCKEL--------GINALH-- 94 (149)
T ss_pred EEEEEcccCCeEEEEEcc--cC-CEEEEEecCcceeccccc--CCCHHHHHHHHHHHHHHHHHc--------CCeEEE--
Confidence 355777888999999996 46 566666665554333221 23 337888899999999999 988711
Q ss_pred ccccccCCCCCCceEEE-eecCccccc--CCceeeeecccccCCcc---------ccCCccccCC
Q 023961 129 DYSVEPTENRRPFRALL-DVGLVKTTT--GNRVFGALKGALDGGLD---------IPHSEKRFAG 181 (274)
Q Consensus 129 ~~~ve~~~~~~~f~~vL-D~Gl~r~t~--g~RVfaalKGA~DgGL~---------iPh~~~~fp~ 181 (274)
+.| =.|+..+.+ -|| -+++++...+||. |||+-.|-|+
T Consensus 95 --------------V~vr~~gg~~~kg~GpGr-~~airaL~~~glkI~~I~DvTPiPhNGcRppk 144 (149)
T PTZ00129 95 --------------IKLRATGGVRTKTPGPGA-QAALRALARAGLKIGRIEDVTPIPTDSTRRKG 144 (149)
T ss_pred --------------EEEEecCCCCCCCCCCCH-HHHHHHHHHCCCEEEEEEecCCCCCCCCCCCC
Confidence 222 123333332 223 4578888999986 6999888886
No 20
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=88.11 E-value=3.2 Score=34.71 Aligned_cols=93 Identities=13% Similarity=0.049 Sum_probs=63.9
Q ss_pred EEEEecCCcEEEEEEeeecCCCEEEEEEecCCccccccccCCCcHHHHHHHHHHHHHHHHHhhcccccccCcccccCccc
Q 023961 51 FVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDY 130 (274)
Q Consensus 51 LvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~g~tN~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~~g~~~ 130 (274)
+-|+-|-++.+..|.|. .|..||+-+|+-.....|-+. ..--||..+..-+++++++. |+..+.
T Consensus 5 ~hI~as~NNTiitvTD~--~G~~~~~~~S~G~~g~kg~kk--~TpyAAq~aa~~~~~~~~~~--------Gi~~v~---- 68 (114)
T TIGR03628 5 AHIYSSFNNTIITITDI--TGAETIARSSGGMVVKADRDE--SSPYAAMQAAGRAAEKAKER--------GITGLH---- 68 (114)
T ss_pred EEEEccCCCeEEEEEcC--CCCEEEEEecCcceEeCCCcc--CCHHHHHHHHHHHHHHHHHc--------CCcEEE----
Confidence 35777888999999985 587899988887776655432 23347888999999999998 988621
Q ss_pred ccccCCCCCCceEEEe-ecCccccc--CCceeeeecccccCCccc
Q 023961 131 SVEPTENRRPFRALLD-VGLVKTTT--GNRVFGALKGALDGGLDI 172 (274)
Q Consensus 131 ~ve~~~~~~~f~~vLD-~Gl~r~t~--g~RVfaalKGA~DgGL~i 172 (274)
+.|= .|+.++++ -|| -+++++...+||.|
T Consensus 69 ------------v~ikG~gg~~~~~~G~Gr-~~air~l~~~glkI 100 (114)
T TIGR03628 69 ------------IKVRAPGGNGQKSPGPGA-QAAIRALARAGLRI 100 (114)
T ss_pred ------------EEEEecCCCCCCCCCCcH-HHHHHHHHHCCCEE
Confidence 2221 12333332 233 45788888899875
No 21
>KOG0408 consensus Mitochondrial/chloroplast ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=75.04 E-value=14 Score=33.35 Aligned_cols=89 Identities=21% Similarity=0.182 Sum_probs=57.8
Q ss_pred cceEEEEecCCcEEEEEEeeecCCCEEEEEEecCCccc-cccccCCCcHHHHHHHHHHHHHHHHHhhcccccccCccccc
Q 023961 48 KYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPR-YGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEAT 126 (274)
Q Consensus 48 KpRLvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k-~g~k~g~tN~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~~ 126 (274)
-|=.-|+-|-++.++|+.|.. | .++..+|- -++- .+-. -+|++ ||..+|--++.++..+ |+..+-
T Consensus 79 iPi~hIraS~NNTivtVtd~k--g-~vi~~~Sc-gteGFrntr-kgT~i-AaQtaavaa~~r~v~~--------G~~~vr 144 (190)
T KOG0408|consen 79 IPIIHIRASFNNTIVTVTDVK--G-EVISWSSC-GTEGFRNTR-KGTPI-AAQTAAVAAIRRAVDQ--------GMQTVR 144 (190)
T ss_pred cceEEEEecCCCeEEEEEccC--C-cEEEEeec-ccccccccc-cCCch-hHHHHHHHHHHHHHHh--------cceEEE
Confidence 355668899999999999963 5 56655443 3332 2222 23454 6678888999999999 987511
Q ss_pred CcccccccCCCCCCceEEEeecCcccccCCceeeeecccccCCccc
Q 023961 127 GEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGLDI 172 (274)
Q Consensus 127 g~~~~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL~i 172 (274)
|-=.||- -|| -++|+|.+-+||.|
T Consensus 145 -----------------V~VkGlG----pGR-msa~kgl~m~Gl~v 168 (190)
T KOG0408|consen 145 -----------------VRVKGLG----PGR-MSALKGLRMGGLLV 168 (190)
T ss_pred -----------------EEEecCC----ccH-HHHHhhhhhcceEE
Confidence 1222332 134 46899999999974
No 22
>PF14821 Thr_synth_N: Threonine synthase N terminus; PDB: 3V7N_A 1VB3_A 1KL7_A.
Probab=67.59 E-value=8.7 Score=29.54 Aligned_cols=61 Identities=25% Similarity=0.349 Sum_probs=31.7
Q ss_pred eeecc-cccCCccccCCccccCCCCCCccCCCHHhhhhhcccccHHHHHHHhcccChHHHHhhHHHHHHcCCCcchHHHH
Q 023961 160 GALKG-ALDGGLDIPHSEKRFAGFSKDSKQLDAEVHRKYIYCGHVAAYMRTLMEDEPEKYQSHFCEYIKRGIEADNLEEL 238 (274)
Q Consensus 160 aalKG-A~DgGL~iPh~~~~fp~~~~~~k~~~ae~~~~ri~G~hva~Y~~~L~eed~e~yk~qFS~yik~~~~p~~~e~~ 238 (274)
|+++| |-||||.||. .+|-.+ .+.+ +.+.+..- +|.=..-++.|+...|++++|.++
T Consensus 17 Ail~GlA~DGGLyvP~---~iP~l~-------~~~l-~~l~~~sy-----------~elA~~il~~f~~~di~~~~L~~i 74 (79)
T PF14821_consen 17 AILQGLAPDGGLYVPE---EIPKLS-------KEEL-EELKNLSY-----------AELAFEILSPFLGDDIPEEELKEI 74 (79)
T ss_dssp HHHH-SBTTSB-EEES---S------------HHHH-HHHTTS-H-----------HHHHHHHHHHHCCCCS-HHHHHHH
T ss_pred HHHhCCCCCCeeEecC---cCCCCC-------HHHH-HHHHCCCH-----------HHHHHHHHHHHHccCCCHHHHHHH
Confidence 35555 6799999998 477643 2211 12222222 223344677788778889999888
Q ss_pred HHHH
Q 023961 239 YKKV 242 (274)
Q Consensus 239 y~~~ 242 (274)
-++|
T Consensus 75 i~~A 78 (79)
T PF14821_consen 75 IEKA 78 (79)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 7765
No 23
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=65.84 E-value=26 Score=30.03 Aligned_cols=96 Identities=18% Similarity=0.117 Sum_probs=61.4
Q ss_pred EEEEecCCcEEEEEEeeecCCCEEEEEEecCCccccccccCCCcHHHHHHHHHHHHHHHHHhhcccccccCcccccCccc
Q 023961 51 FVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDY 130 (274)
Q Consensus 51 LvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~g~tN~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~~g~~~ 130 (274)
.=|+-|-++.+.-|.|. .| .+++.++|-.+-..|-. .+.--||-..+..+|+.+++. |++++.
T Consensus 21 ahI~asfNNTivtitD~--~G-n~i~wassG~~gfk~~r--k~tpyAA~~aa~~aa~~a~e~--------Gi~~v~---- 83 (129)
T COG0100 21 AHIHASFNNTIVTITDL--TG-NVIIWASSGGMGFKGSR--KSTPYAAQLAAEDAAKKAKEH--------GIKSVE---- 83 (129)
T ss_pred EEEEcccCCcEEEecCC--CC-CEEEEEecCCceEcCCC--CCCHHHHHHHHHHHHHHHHHh--------CccEEE----
Confidence 45666777777778775 46 78888888777554433 234556677788888999998 887621
Q ss_pred ccccCCCCCCceEEEeecCcccccCCceeeeecccccCCcc---------ccCCccccCC
Q 023961 131 SVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGLD---------IPHSEKRFAG 181 (274)
Q Consensus 131 ~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL~---------iPh~~~~fp~ 181 (274)
++++- .+-|| -||+....-+||. |||+-.|=|+
T Consensus 84 ------------v~vkg-----pG~Gr-eaAiraL~~ag~~i~~I~DvTPiphnG~Rppk 125 (129)
T COG0100 84 ------------VKVKG-----PGPGR-EAAIRALAAAGLKITRIEDVTPIPHNGCRPPK 125 (129)
T ss_pred ------------EEEEC-----CCCcH-HHHHHHHHHccceEEEEEEcCCCCCCCCCCCC
Confidence 33332 11122 2344444456664 6999888886
No 24
>PRK05337 beta-hexosaminidase; Provisional
Probab=42.72 E-value=32 Score=33.21 Aligned_cols=65 Identities=25% Similarity=0.407 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccccCcccccCcccccccCCCCCCceEEEeecCcccccCCcee------------eee
Q 023961 95 YAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVF------------GAL 162 (274)
Q Consensus 95 ~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~~g~~~~ve~~~~~~~f~~vLD~Gl~r~t~g~RVf------------aal 162 (274)
.+.|+..|..+|+.+... ||.- -|--++|+.-...-.|+|-| |++
T Consensus 96 ~~la~~~g~~~a~Elra~--------Gin~---------------~~aPvlDv~~~~~~ig~RsfgeDp~lv~~~a~a~i 152 (337)
T PRK05337 96 LKLAEEAGWLMAAELRAC--------GIDL---------------SFAPVLDLDGISAVIGDRAFHRDPQVVAALASAFI 152 (337)
T ss_pred HHHHHHHHHHHHHHHHHh--------CCCc---------------cccCccCCCCCCCeeeccCCCCCHHHHHHHHHHHH
Confidence 788999999999999887 6642 01135666411111234444 478
Q ss_pred cccccCCccccCCccccCCCCC
Q 023961 163 KGALDGGLDIPHSEKRFAGFSK 184 (274)
Q Consensus 163 KGA~DgGL~iPh~~~~fp~~~~ 184 (274)
+|..++| |-..-|-|||++.
T Consensus 153 ~Glq~~g--v~~~~KHFpG~G~ 172 (337)
T PRK05337 153 DGMHAAG--MAATGKHFPGHGA 172 (337)
T ss_pred HHHHHCC--CEEEecccCCCCC
Confidence 9999888 4567789999864
No 25
>PF13069 DUF3933: Protein of unknown function (DUF3933)
Probab=40.44 E-value=7.8 Score=28.02 Aligned_cols=15 Identities=40% Similarity=0.505 Sum_probs=10.2
Q ss_pred CcEEEEEEeeecCCCEEEE
Q 023961 58 KDITAQIISASIAGDIVLA 76 (274)
Q Consensus 58 k~IiaQIi~~~~~GD~tLa 76 (274)
..+|||||+ |++-|+
T Consensus 3 qyvicqii~----g~kyla 17 (53)
T PF13069_consen 3 QYVICQIID----GTKYLA 17 (53)
T ss_pred eEEEEEEec----CccHHH
Confidence 468999987 544443
No 26
>PRK10251 phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex; Provisional
Probab=35.38 E-value=73 Score=29.02 Aligned_cols=62 Identities=16% Similarity=0.066 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHHhhcccccccCcccccCcccccccCCCCCCceEEEeecCcccccCCceeeeecccccCCccc
Q 023961 96 AAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGALDGGLDI 172 (274)
Q Consensus 96 ~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~~g~~~~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA~DgGL~i 172 (274)
-+-++.|.++|+.||..+|.... .++.+ +|.-++.+ ++=+..+|+++.+.+++- ...-||+|
T Consensus 50 r~EflAgR~~A~~aL~~lg~~~~-~~~g~-~r~P~wP~------------gi~gSISHS~~~a~aav~-~~~VGIDI 111 (207)
T PRK10251 50 KAEHLAGRIAAVYALREYGYKCV-PAIGE-LRQPVWPA------------GVYGSISHCGTTALAVVS-RQPIGIDI 111 (207)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCC-CCcCC-CCCccCCC------------CceeCcccccCeEEEEEe-CCCcEEEe
Confidence 35688999999999999876642 23221 22222211 233567888888777764 33456666
No 27
>PF08673 RsbU_N: Phosphoserine phosphatase RsbU, N-terminal domain; InterPro: IPR014787 The phosphoserine phosphatase RsbU acts as a positive regulator of the general stress-response factor of Gram-positive organisms, sigma-B. RsbU dephosphorylates rsbV in response to environmental stress conveyed from the rsbXST module. The phosphatase activity of RsbU is stimulated during the stress response by associating with the RsbT kinase. This association leads to the induction of sigmaB activity. The N-terminal domain forms a helix-swapped dimer that is otherwise similar to the KaiA domain dimer. Deletions in the N-terminal domain are deleterious to the activity of RsbU. The C-terminal domain of RsbU is similar to the catalytic domains of PP2C-type phosphatases [].; PDB: 2J6Y_D 2J6Z_A 2J70_A 1W53_A.
Probab=30.34 E-value=96 Score=24.09 Aligned_cols=41 Identities=20% Similarity=0.363 Sum_probs=26.1
Q ss_pred HhcccChHH-HH-hhHHHH-HHcCCCcchHHHHHHHHHHHHhcC
Q 023961 209 TLMEDEPEK-YQ-SHFCEY-IKRGIEADNLEELYKKVHAAIRAD 249 (274)
Q Consensus 209 ~L~eed~e~-yk-~qFS~y-ik~~~~p~~~e~~y~~~~~~I~~~ 249 (274)
+|...||.. |+ .+||+. |+.+|.|++|-++.+++...+-.+
T Consensus 11 yl~~~~E~~L~~~~~~~r~~i~~~I~PEeIv~iH~~~v~~l~~~ 54 (77)
T PF08673_consen 11 YLETQDEQSLYQAQEFGRELIEKDISPEEIVEIHKSAVQELSPS 54 (77)
T ss_dssp HHHH--HHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHH-TT
T ss_pred HHhCCCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHccc
Confidence 344455543 32 267774 688999999999999999988655
No 28
>PRK14083 HSP90 family protein; Provisional
Probab=29.67 E-value=32 Score=36.06 Aligned_cols=48 Identities=15% Similarity=0.166 Sum_probs=36.2
Q ss_pred hcccccHHHHHHHhcccChHHHHh---hHHHHHHcCCCcchHHHHHHHHHHHH
Q 023961 197 YIYCGHVAAYMRTLMEDEPEKYQS---HFCEYIKRGIEADNLEELYKKVHAAI 246 (274)
Q Consensus 197 ri~G~hva~Y~~~L~eed~e~yk~---qFS~yik~~~~p~~~e~~y~~~~~~I 246 (274)
+..|+-|.++.+.|.++|+++|.+ +|+.+||.|+--| .+.+++...-+
T Consensus 319 ~~i~kki~~~L~~la~~d~e~y~~f~~~~g~~lK~g~~~D--~~~~~~l~~lL 369 (601)
T PRK14083 319 EELGEAIRKWLIGLATTDPERLRRLLAVHHLGVKALASHD--DELLRLILPWL 369 (601)
T ss_pred HHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHHHHhcC--HHHHHHHHHhc
Confidence 457889999999999999998886 8888999998643 22444444433
No 29
>PRK05218 heat shock protein 90; Provisional
Probab=29.24 E-value=51 Score=34.49 Aligned_cols=48 Identities=21% Similarity=0.295 Sum_probs=36.8
Q ss_pred hcccccHHHHHHHhcccChHHHHh---hHHHHHHcCCCcchHHHHHHHHHHHH
Q 023961 197 YIYCGHVAAYMRTLMEDEPEKYQS---HFCEYIKRGIEADNLEELYKKVHAAI 246 (274)
Q Consensus 197 ri~G~hva~Y~~~L~eed~e~yk~---qFS~yik~~~~p~~~e~~y~~~~~~I 246 (274)
...|+-|.++.+.|.++|+++|.+ +|+.+||.|+--| .+++++...-+
T Consensus 339 ~~l~~kv~~~l~~la~~d~~~y~~f~~~~~~~lK~g~~~D--~~~~~~~~~lL 389 (613)
T PRK05218 339 KAITKKVLDELEKLAKNDREKYEKFWKEFGPVLKEGLYED--FANREKLAKLL 389 (613)
T ss_pred HHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHhhhhcc--HHHHHHHHhhc
Confidence 457889999999999999998876 7888999998755 23555544444
No 30
>PRK10713 2Fe-2S ferredoxin YfaE; Provisional
Probab=27.08 E-value=34 Score=26.22 Aligned_cols=17 Identities=6% Similarity=-0.039 Sum_probs=14.7
Q ss_pred eeecccccCCccccCCc
Q 023961 160 GALKGALDGGLDIPHSE 176 (274)
Q Consensus 160 aalKGA~DgGL~iPh~~ 176 (274)
-+|..|.+.|+.||||-
T Consensus 21 tlL~a~~~~gi~~p~~C 37 (84)
T PRK10713 21 SLLAALESHNVAVEYQC 37 (84)
T ss_pred cHHHHHHHcCCCCCCCC
Confidence 37788999999999985
No 31
>PF06518 DUF1104: Protein of unknown function (DUF1104); InterPro: IPR009488 This family consists of several hypothetical proteins of unknown function which appear to be found exclusively in Helicobacter pylori.; PDB: 2XRH_A.
Probab=26.44 E-value=83 Score=25.41 Aligned_cols=42 Identities=14% Similarity=0.378 Sum_probs=33.0
Q ss_pred HHHhcccChHHHHhhHHHHHHc---CCCcchHHHHHHHHHHHHhc
Q 023961 207 MRTLMEDEPEKYQSHFCEYIKR---GIEADNLEELYKKVHAAIRA 248 (274)
Q Consensus 207 ~~~L~eed~e~yk~qFS~yik~---~~~p~~~e~~y~~~~~~I~~ 248 (274)
|..|..++--.|++||.+++.. .+++++..++=++++.++.+
T Consensus 34 ~~~m~~~~~k~f~~~~~~~~~kn~~~ms~~e~~k~~~ev~k~~~~ 78 (93)
T PF06518_consen 34 LKKMKEKEAKDFKKQFKEAARKNLSKMSVEERKKRREEVRKALEK 78 (93)
T ss_dssp HHHS-HHHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHH
T ss_pred HHhCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Confidence 5667777788999999999886 46788988888888888864
No 32
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=24.98 E-value=4.2e+02 Score=23.38 Aligned_cols=54 Identities=17% Similarity=0.265 Sum_probs=33.5
Q ss_pred CCCCCCc-ceEEEEecCCcEEEEEEeeecCCCEEEEEEecCCccccccccCCCcHHHHHHHHHHHHHHHHHh
Q 023961 42 NKYNTPK-YRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKM 112 (274)
Q Consensus 42 nky~s~K-pRLvVrrTNk~IiaQIi~~~~~GD~tLasAsS~eL~k~g~k~g~tN~~AAy~tGlLlA~Ral~k 112 (274)
..||..+ |=|++|..+-...+-|..+ | +++|+ |.++.+.|......+++.+.+.
T Consensus 29 ~eY~P~~fpgli~Rl~~Pk~t~lIF~S---G-Kiv~t-------------Gaks~~~a~~a~~~~~~~L~~~ 83 (174)
T cd04518 29 AEYNPDQFPGLVYRLEDPKIAALIFRS---G-KMVCT-------------GAKSVEDLHRAVKEIIKKLKDY 83 (174)
T ss_pred cEECCCcCcEEEEEccCCcEEEEEECC---C-eEEEE-------------ccCCHHHHHHHHHHHHHHHHhc
Confidence 4788777 5577777666676766653 5 66664 2345556666666666665444
No 33
>PF00452 Bcl-2: Apoptosis regulator proteins, Bcl-2 family; InterPro: IPR000712 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 2WH6_A 1K3K_A 1AF3_A 3PK1_B 2K7W_A 1F16_A 3PL7_C 2VM6_A 3I1H_A 3MQP_A ....
Probab=24.24 E-value=1.4e+02 Score=23.03 Aligned_cols=40 Identities=23% Similarity=0.443 Sum_probs=31.8
Q ss_pred hcccChHHHHhhHHHHHHc-CC-CcchHHHHHHHHHHHHhcC
Q 023961 210 LMEDEPEKYQSHFCEYIKR-GI-EADNLEELYKKVHAAIRAD 249 (274)
Q Consensus 210 L~eed~e~yk~qFS~yik~-~~-~p~~~e~~y~~~~~~I~~~ 249 (274)
+-+|=+..|...|++.+.. .+ +|++..+.|.++-+.|-+|
T Consensus 4 i~~~~e~~~~~~f~~~~~~l~~~~~~~~~~~f~~v~~~lf~d 45 (101)
T PF00452_consen 4 IADELERKYEDFFENMLNQLNINTPDNAYETFNEVAEELFED 45 (101)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCSSSTTTHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhcc
Confidence 3344467788889998885 45 7888999999999999887
No 34
>PF06292 DUF1041: Domain of Unknown Function (DUF1041); InterPro: IPR010439 This entry represents Calcium-dependent secretion activators that are involved in the exocytosis of vesicles filled with neurotransmitters and neuropeptides. They also may specifically mediate the Ca2+-dependent exocytosis of large dense-core vesicles (DCVs) and other dense-core vesicles by acting as a PtdIns(4,5)P2-binding protein that acts at prefusion step following ATP-dependent priming and participates in DCVs-membrane fusion []. However, it probably also participates in small clear synaptic vesicles (SVs) exocytosis and it is unclear whether its function is related to Ca2+ triggering []. This protein is often found in tandem repeats and co-occur with C2 domains IPR000008 from INTERPRO, Protein kinase C, phorbol ester/diacylglycerol binding regions IPR002219 from INTERPRO and PH domains IPR001849 from INTERPRO.
Probab=24.23 E-value=34 Score=28.27 Aligned_cols=40 Identities=20% Similarity=0.358 Sum_probs=32.4
Q ss_pred ccHHHHHHHhcccChHHHH---hhHHHHHHcCCC-cchHHHHHH
Q 023961 201 GHVAAYMRTLMEDEPEKYQ---SHFCEYIKRGIE-ADNLEELYK 240 (274)
Q Consensus 201 ~hva~Y~~~L~eed~e~yk---~qFS~yik~~~~-p~~~e~~y~ 240 (274)
-|+++.+-.+.+||++-|. .||+.++.-|.. ++.+=.+|.
T Consensus 53 ~~L~eL~v~vleed~e~y~~vln~F~~~~~l~~~hAE~fWsLfa 96 (106)
T PF06292_consen 53 IRLIELCVSVLEEDKEHYAPVLNQFPWELDLGVEHAEIFWSLFA 96 (106)
T ss_pred HHHHHHHHHHHHhhhhhhhhHhhhchhhhhHHHHHHHHHHHHHH
Confidence 4789999999999999999 999999887644 666655554
No 35
>PF14412 AHH: A nuclease family of the HNH/ENDO VII superfamily with conserved AHH
Probab=22.71 E-value=1.4e+02 Score=23.55 Aligned_cols=43 Identities=12% Similarity=0.169 Sum_probs=26.0
Q ss_pred ccccHHHHHHHhcccChHHHHhhHHHHHHcCCCcchHHHHHHHHHHHHhc
Q 023961 199 YCGHVAAYMRTLMEDEPEKYQSHFCEYIKRGIEADNLEELYKKVHAAIRA 248 (274)
Q Consensus 199 ~G~hva~Y~~~L~eed~e~yk~qFS~yik~~~~p~~~e~~y~~~~~~I~~ 248 (274)
.|.|-.+|.+.+.++=...-. ..+.+++.+.+..+++...|+.
T Consensus 65 ~g~H~~~Y~~~V~~~L~~~~~-------~~~~~~~~~~~~l~~i~~~l~~ 107 (109)
T PF14412_consen 65 RGRHPNEYNKYVRERLDKIEN-------SKKENREEFRKELQKIKNELRN 107 (109)
T ss_pred CCCCcHHHHHHHHHHHHHHHH-------HhhcCHHHHHHHHHHHHHHHHc
Confidence 399999998887643221111 2344566666666776666654
No 36
>PF06648 DUF1160: Protein of unknown function (DUF1160); InterPro: IPR010594 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf75; it is a family of uncharacterised viral proteins.
Probab=22.63 E-value=1.1e+02 Score=26.00 Aligned_cols=43 Identities=16% Similarity=0.393 Sum_probs=35.1
Q ss_pred ccccHHHHHHHhcccCh---HHHHhhHHHHHHcCCCcchHHHHHHHH
Q 023961 199 YCGHVAAYMRTLMEDEP---EKYQSHFCEYIKRGIEADNLEELYKKV 242 (274)
Q Consensus 199 ~G~hva~Y~~~L~eed~---e~yk~qFS~yik~~~~p~~~e~~y~~~ 242 (274)
.-.|+.+|++.|. .|+ +++.+-|..+|.+.|++|.|=.++..+
T Consensus 18 v~~~l~~ylkel~-~d~tf~~Kl~~Il~mFl~~eid~e~~y~l~~~~ 63 (122)
T PF06648_consen 18 VNTHLKKYLKELE-RDETFLDKLIKILKMFLNDEIDVEDMYNLFGAV 63 (122)
T ss_pred HHHHHHHHHHHhc-cCchHHHHHHHHHHHHHhCCCCHHHHHHHHhcc
Confidence 4468899999998 444 577778889999999999998888765
No 37
>TIGR01795 CM_mono_cladeE monofunctional chorismate mutase, alpha proteobacterial type. The alpha proteobacterial members are trusted because the pathways of CM are evident and there is only one plausible CM in the genome. In S. coelicolor, however, there is another aparrent monofunctional CM.
Probab=22.31 E-value=1.2e+02 Score=24.06 Aligned_cols=52 Identities=10% Similarity=0.209 Sum_probs=34.4
Q ss_pred hhhhc-ccccHHHHHHH--hcccChHHHHhhHHHHHH----cCCCcchHHHHHHHHHHH
Q 023961 194 HRKYI-YCGHVAAYMRT--LMEDEPEKYQSHFCEYIK----RGIEADNLEELYKKVHAA 245 (274)
Q Consensus 194 ~~~ri-~G~hva~Y~~~--L~eed~e~yk~qFS~yik----~~~~p~~~e~~y~~~~~~ 245 (274)
+.+|. +...|+.|-.. +.=-||+.-+..+..+.. .|++|+-++.+|+.+|+.
T Consensus 23 L~~R~~~~~~ia~~K~~~~~~v~dp~Re~~vl~~~~~~a~~~gl~p~~~e~i~~~i~~e 81 (94)
T TIGR01795 23 LAERFKCTSQVGVLKANAGLAPADPAREDYQIARLRRLAIDAGLDPEFAEKFLNFIVTE 81 (94)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
Confidence 33443 34445555332 222467777777777755 499999999999998864
No 38
>PRK14102 nifW nitrogenase stabilizing/protective protein; Provisional
Probab=21.77 E-value=1e+02 Score=25.62 Aligned_cols=30 Identities=13% Similarity=0.192 Sum_probs=19.9
Q ss_pred hhHHHHHHc------CCCcchHHHHHHHHHHHHhcC
Q 023961 220 SHFCEYIKR------GIEADNLEELYKKVHAAIRAD 249 (274)
Q Consensus 220 ~qFS~yik~------~~~p~~~e~~y~~~~~~I~~~ 249 (274)
++|++||.. +++++.+-..|..+.+.-=++
T Consensus 39 krf~qyl~~~~~~~~~~~e~~~~~~yr~~L~~AY~d 74 (105)
T PRK14102 39 KQFSQLIAEIDANFPDLSEEEKLEKYQLALEEAYQV 74 (105)
T ss_pred HHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHH
Confidence 599999984 456666666666666554433
No 39
>COG2977 EntD Phosphopantetheinyl transferase component of siderophore synthetase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=21.49 E-value=1.6e+02 Score=27.55 Aligned_cols=67 Identities=21% Similarity=0.172 Sum_probs=39.1
Q ss_pred cHHHHHHHHHHHHHHHHHhhcccccccCcccccCcccccccCCCCCCceEEEeecCcccccCCceeeeeccc----ccCC
Q 023961 94 NYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKGA----LDGG 169 (274)
Q Consensus 94 N~~AAy~tGlLlA~Ral~k~~~~~~y~Gi~e~~g~~~~ve~~~~~~~f~~vLD~Gl~r~t~g~RVfaalKGA----~DgG 169 (274)
.--|.++.|..+|+.||..+| ...+-+..-.+|+--+-+. +=+..+|.++.-. |+=+. +--|
T Consensus 50 KRkaEflAgR~cA~~AL~~lg-~~~~Pi~~G~~raPlWP~g------------vvGSIsH~~~~A~-Avv~~~~~~~~iG 115 (228)
T COG2977 50 KRKAEFLAGRICARQALRELG-VADVPILRGEDRAPLWPAG------------VVGSISHCDGTAL-AVVARRGRVRSIG 115 (228)
T ss_pred HHHHHHHHHHHHHHHHHHHhC-CCCCCcccCCCCCCCCCCc------------ceEEeeccCCeee-Eeeecccccccce
Confidence 345678999999999999998 5555455332333222222 1245566655433 33334 4448
Q ss_pred ccc-cC
Q 023961 170 LDI-PH 174 (274)
Q Consensus 170 L~i-Ph 174 (274)
|+| ||
T Consensus 116 IDiE~~ 121 (228)
T COG2977 116 IDIEPH 121 (228)
T ss_pred eecccc
Confidence 888 55
No 40
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=20.81 E-value=1.6e+02 Score=22.78 Aligned_cols=24 Identities=17% Similarity=0.423 Sum_probs=16.7
Q ss_pred HHHHHHh-cccChHHHHhhHHHHHH
Q 023961 204 AAYMRTL-MEDEPEKYQSHFCEYIK 227 (274)
Q Consensus 204 a~Y~~~L-~eed~e~yk~qFS~yik 227 (274)
.+|+..| .-+|+|.-+++|.+.+.
T Consensus 3 K~ii~~Lh~G~~~e~vk~~F~~~~~ 27 (71)
T PF04282_consen 3 KEIIKRLHEGEDPEEVKEEFKKLFS 27 (71)
T ss_pred HHHHHHHhCCCCHHHHHHHHHHHHC
Confidence 3555666 55788888888887644
No 41
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=20.37 E-value=2e+02 Score=29.04 Aligned_cols=53 Identities=9% Similarity=0.213 Sum_probs=33.2
Q ss_pred cCCCHHhhhhhccc-ccHHHHHHHhccc-ChHHHHhhHHHHHHcCCCcchHHHHH
Q 023961 187 KQLDAEVHRKYIYC-GHVAAYMRTLMED-EPEKYQSHFCEYIKRGIEADNLEELY 239 (274)
Q Consensus 187 k~~~ae~~~~ri~G-~hva~Y~~~L~ee-d~e~yk~qFS~yik~~~~p~~~e~~y 239 (274)
..|+|+.+-+||+| ++|..-++..++. |++.-++-..+..+..+|-+++-+-+
T Consensus 275 e~f~~~~~~~~ilgmgd~~~l~e~~~~~~~~~~~~~~~~~~~~~~f~l~d~~~q~ 329 (437)
T PRK00771 275 ERFDPDRFISRLLGMGDLESLLEKVEEALDEEEEEKDVEKMMKGKFTLKDMYKQL 329 (437)
T ss_pred CcCCHHHHHHHHhCCCChHHHHHHHHHhhhHHHHHHHHHHHHcCCcCHHHHHHHH
Confidence 57999999999999 8888888777665 44444333333333334444443333
Done!