Query 029135
Match_columns 198
No_of_seqs 149 out of 1045
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 08:03:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029135.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029135hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05593 rplR 50S ribosomal pr 100.0 7.9E-35 1.7E-39 229.1 9.2 106 50-158 2-112 (117)
2 TIGR00060 L18_bact ribosomal p 100.0 7.2E-35 1.6E-39 229.2 8.7 102 52-159 2-110 (114)
3 CHL00139 rpl18 ribosomal prote 100.0 1.6E-34 3.5E-39 225.1 4.9 99 59-159 2-105 (109)
4 COG0256 RplR Ribosomal protein 100.0 1.7E-33 3.6E-38 225.0 8.6 109 48-158 5-120 (125)
5 PF00861 Ribosomal_L18p: Ribos 100.0 3.4E-30 7.3E-35 201.5 7.5 107 51-159 2-115 (119)
6 PTZ00032 60S ribosomal protein 99.9 5.8E-28 1.3E-32 206.7 6.2 89 70-159 103-207 (211)
7 cd00432 Ribosomal_L18_L5e Ribo 99.9 2.3E-27 5E-32 179.7 6.3 95 63-159 2-101 (103)
8 PRK08569 rpl18p 50S ribosomal 99.9 1.7E-26 3.8E-31 195.8 7.5 105 50-159 13-126 (193)
9 PTZ00069 60S ribosomal protein 99.2 7E-11 1.5E-15 106.4 9.3 85 50-136 22-112 (300)
10 KOG3333 Mitochondrial/chloropl 98.3 9.7E-07 2.1E-11 74.8 5.0 67 73-142 61-127 (188)
11 PF00411 Ribosomal_S11: Riboso 96.3 0.027 5.9E-07 43.8 7.8 63 75-142 3-65 (110)
12 PTZ00090 40S ribosomal protein 95.8 0.029 6.3E-07 49.8 6.7 73 71-147 117-190 (233)
13 TIGR03632 bact_S11 30S ribosom 95.6 0.064 1.4E-06 41.8 7.2 63 75-142 3-65 (108)
14 CHL00041 rps11 ribosomal prote 94.9 0.14 3E-06 40.5 7.2 65 73-142 14-78 (116)
15 PRK05309 30S ribosomal protein 94.5 0.21 4.5E-06 40.3 7.4 65 72-141 17-81 (128)
16 KOG0875 60S ribosomal protein 94.4 0.075 1.6E-06 48.0 5.1 76 71-151 47-125 (264)
17 PRK09607 rps11p 30S ribosomal 94.1 0.16 3.5E-06 41.6 6.2 70 74-147 11-80 (132)
18 TIGR03628 arch_S11P archaeal r 93.8 0.22 4.7E-06 39.8 6.1 69 75-147 5-73 (114)
19 PTZ00129 40S ribosomal protein 90.3 1.3 2.9E-05 37.0 7.1 67 72-142 28-94 (149)
20 COG0100 RpsK Ribosomal protein 82.2 3.1 6.8E-05 34.2 5.0 63 75-142 21-83 (129)
21 KOG0408 Mitochondrial/chloropl 62.6 38 0.00082 29.6 7.1 66 71-141 78-143 (190)
22 KOG0407 40S ribosomal protein 62.3 30 0.00065 28.6 6.2 63 75-141 19-81 (139)
23 PF03646 FlaG: FlaG protein; 59.5 44 0.00095 25.1 6.3 40 59-98 43-82 (107)
24 PRK07738 flagellar protein Fla 43.2 1E+02 0.0022 24.9 6.2 38 60-97 53-90 (117)
25 cd07367 CarBb CarBb is the B s 38.9 30 0.00065 30.4 2.9 86 60-150 32-121 (268)
26 TIGR01917 gly_red_sel_B glycin 31.4 23 0.00049 34.4 1.0 29 113-142 313-341 (431)
27 PF03900 Porphobil_deamC: Porp 30.4 1.4E+02 0.0031 21.1 4.8 59 64-135 12-74 (74)
28 PF07355 GRDB: Glycine/sarcosi 30.1 27 0.00059 32.9 1.3 29 113-142 317-345 (349)
29 COG3894 Uncharacterized metal- 29.4 68 0.0015 32.4 3.9 36 74-109 166-201 (614)
30 PF05374 Mu-conotoxin: Mu-Cono 27.7 27 0.00059 21.0 0.6 9 155-163 11-19 (22)
31 PRK08868 flagellar protein Fla 26.5 2.6E+02 0.0056 23.5 6.3 38 60-97 78-115 (144)
32 TIGR01918 various_sel_PB selen 25.9 32 0.00069 33.4 1.0 29 113-142 313-341 (431)
33 PRK08452 flagellar protein Fla 25.8 2.4E+02 0.0052 22.9 5.9 32 66-97 66-97 (124)
34 cd07359 PCA_45_Doxase_B_like S 24.5 72 0.0016 27.5 2.8 92 60-154 34-129 (271)
35 PF03263 Cucumo_2B: Cucumoviru 23.6 65 0.0014 25.8 2.2 22 46-68 12-33 (103)
36 smart00259 ZnF_A20 A20-like zi 22.1 39 0.00085 20.6 0.5 10 13-22 7-16 (26)
No 1
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=100.00 E-value=7.9e-35 Score=229.12 Aligned_cols=106 Identities=28% Similarity=0.400 Sum_probs=99.4
Q ss_pred chHHHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHH
Q 029135 50 ARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVL 129 (198)
Q Consensus 50 ~K~e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklL 129 (198)
++++.|.+|++|+|+||.||+++|||+||+||+|||||||||++++||+|+||+|++++..+ . ++|++||+ .||++|
T Consensus 2 ~~~~~r~~r~~r~r~ki~g~~~rpRL~V~~SnkhiyAQvidd~~~~tl~saST~e~~~k~~~-~-~~n~~aa~-~vG~~l 78 (117)
T PRK05593 2 DKKEARLRRHRRVRKKISGTAERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDVRAGL-K-GGNKEAAK-KVGKLI 78 (117)
T ss_pred chHHHHHHHHHHHHHHhcCCCCCCEEEEEEeCCeEEEEEEECCCCEEEEEEecCcHhHhccc-c-CCCHHHHH-HHHHHH
Confidence 56778899999999999999999999999999999999999999999999999999986533 2 79999999 999999
Q ss_pred HHHHHhcChhHHH-----Hhhhheeehhhhhhhc
Q 029135 130 VKSLSRLVLHLTL-----RKFHLMIVMAPVVVRE 158 (198)
Q Consensus 130 AerAkeaGI~~~v-----~kyHg~i~~~~~~~~~ 158 (198)
|++|+++||++++ ++|||+|..+++-+|+
T Consensus 79 a~ra~~~gi~~vvfDrg~~~yhGrV~a~a~~are 112 (117)
T PRK05593 79 AERAKAKGIKQVVFDRGGYKYHGRVKALADAARE 112 (117)
T ss_pred HHHHHHCCCCEEEEcCCCCcccHHHHHHHHHHHH
Confidence 9999999999998 8999999999999887
No 2
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=100.00 E-value=7.2e-35 Score=229.23 Aligned_cols=102 Identities=25% Similarity=0.376 Sum_probs=95.7
Q ss_pred HHHHHHHHHHHHhhhcCCC--CCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHH
Q 029135 52 TESAKIRNRRIQKKFNGTP--TKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVL 129 (198)
Q Consensus 52 ~e~R~rR~rRiRkKI~GTa--~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklL 129 (198)
++.|.+|+.|+|+||.||+ ++|||+||+||+|||||||||++++||+|+||+|++++ +++|+++|+ +||++|
T Consensus 2 ~~~r~~r~~r~r~ki~gt~~~~rpRL~V~rSnk~iyaQiIdd~~~~tlasaST~ek~~~-----~~~n~~aA~-~vG~~l 75 (114)
T TIGR00060 2 KSARIRRHKRIRRKLRETGEANRPRLVVFRSNRHIYAQVIDDSKSEVLASASTLEKKLK-----YTGNKDAAK-KVGKLV 75 (114)
T ss_pred cHHHHHHHHHHHHHhcCCCCCCCcEEEEEEeCCeEEEEEEECCCCEEEEEEecchhhhc-----CCCCHHHHH-HHHHHH
Confidence 3567789999999999999 89999999999999999999999999999999999975 348999999 999999
Q ss_pred HHHHHhcChhHHH-----Hhhhheeehhhhhhhcc
Q 029135 130 VKSLSRLVLHLTL-----RKFHLMIVMAPVVVREC 159 (198)
Q Consensus 130 AerAkeaGI~~~v-----~kyHg~i~~~~~~~~~~ 159 (198)
||+|+++||+.++ ++|||+|..+++-+||-
T Consensus 76 a~ra~~~gi~~vvfDrgg~~YhGrv~A~a~~aRe~ 110 (114)
T TIGR00060 76 AERLKEKGIKDVVFDRGGYKYHGRVAALAEAAREA 110 (114)
T ss_pred HHHHHHCCCCEEEEeCCCCcchHHHHHHHHHHHHh
Confidence 9999999999999 89999999999999974
No 3
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=100.00 E-value=1.6e-34 Score=225.13 Aligned_cols=99 Identities=31% Similarity=0.403 Sum_probs=94.7
Q ss_pred HHHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcCh
Q 029135 59 NRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVL 138 (198)
Q Consensus 59 ~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI 138 (198)
++|+|+||.||+++|||+||+||+|||||||||.+|+||+|+||+|+++++|+ ++++|+++|+ .||++|||+|+++||
T Consensus 2 ~~r~r~ki~g~~~rpRL~V~rSnkhiyaQvidd~~g~tlasaST~ek~~~~~~-~~~~n~~aA~-~vG~lla~ra~~~gi 79 (109)
T CHL00139 2 RERVRKKIKGTAERPRLSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVKSSL-SSTSTCDASK-LVGQKLAKKSLKKGI 79 (109)
T ss_pred CeeeeeeecCCCCCCEEEEEEeCCeEEEEEEECCCCCEEEEEecCchhhhccc-cCCCCHHHHH-HHHHHHHHHHHHCCC
Confidence 57899999999999999999999999999999999999999999999999987 6789999999 999999999999999
Q ss_pred hHHH-----Hhhhheeehhhhhhhcc
Q 029135 139 HLTL-----RKFHLMIVMAPVVVREC 159 (198)
Q Consensus 139 ~~~v-----~kyHg~i~~~~~~~~~~ 159 (198)
++++ ++|||+|..+++-.|+-
T Consensus 80 ~~vvfDrgg~~yhGrV~a~a~~are~ 105 (109)
T CHL00139 80 TKVVFDRGGKLYHGRIKALAEAAREA 105 (109)
T ss_pred CEEEEcCCCCccchHHHHHHHHHHHh
Confidence 9999 89999999999999873
No 4
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-33 Score=225.04 Aligned_cols=109 Identities=24% Similarity=0.255 Sum_probs=101.4
Q ss_pred hcchHHHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcC--CCCCCCCCHHHHHHHH
Q 029135 48 ANARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRG--NGNPPCSTIFPLSRKL 125 (198)
Q Consensus 48 ~~~K~e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~--~l~~~~~NieAA~~~V 125 (198)
+..|++++.+|+.|+|+||.|++++|||+|||||+|||||||||..+.||+++||++++++. |. ..++|+++|+ +|
T Consensus 5 ~~~rr~~~~kr~~r~R~kl~g~~~rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~-~~~~N~~aA~-~v 82 (125)
T COG0256 5 VKFRRRRRGKRAYRIRKKLLGTSGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKK-GGGGNTEAAY-LV 82 (125)
T ss_pred hhhHHHHHHhHHHHHHHhhccCCCCcEEEEEEeCCcEEEEEEEcCCCceEEEEEcchHHHHhhccc-CCCCCHHHHH-HH
Confidence 34677888999999999999999999999999999999999999999999999999999954 54 4578999999 99
Q ss_pred HHHHHHHHHhcChhHHH-----Hhhhheeehhhhhhhc
Q 029135 126 LSVLVKSLSRLVLHLTL-----RKFHLMIVMAPVVVRE 158 (198)
Q Consensus 126 GklLAerAkeaGI~~~v-----~kyHg~i~~~~~~~~~ 158 (198)
|++||++|+++||+++| ++|||||..+++-.||
T Consensus 83 G~lia~ra~~kgi~~vVfdr~g~~yhgRV~Ala~~Are 120 (125)
T COG0256 83 GKLIAERALAKGIEEVVFDRGGYKYHGRVAALADGARE 120 (125)
T ss_pred HHHHHHHHHHcCCcEEEEcCCCCCcchHHHHHHHHHHH
Confidence 99999999999999999 9999999999998876
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=99.96 E-value=3.4e-30 Score=201.51 Aligned_cols=107 Identities=25% Similarity=0.322 Sum_probs=98.6
Q ss_pred hHHHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcC--CCCCCCCCHHHHHHHHHHH
Q 029135 51 RTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRG--NGNPPCSTIFPLSRKLLSV 128 (198)
Q Consensus 51 K~e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~--~l~~~~~NieAA~~~VGkl 128 (198)
|++.+.+|+.++|+++.+++++|||+||+||+|||||||||..+.||+++||++++++. |. .+++|+++|+ .||++
T Consensus 2 k~~~~~~r~~~~r~~~~~~~~~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~~l~~~~~~-~~~~n~~aa~-~vG~l 79 (119)
T PF00861_consen 2 KKRRRRRRKLRIRRKIKGTAERPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSKELKKYGWK-GSTKNVEAAY-LVGEL 79 (119)
T ss_dssp SCHHHHHHHHHHHHHHHHTTSSEEEEEEEESSEEEEEEEECTTTEEEEEEEEETTTGGGTT-S-STTSSHHHHH-HHHHH
T ss_pred hhHHHHHHHHHHHHHHhcCCCCCEEEEEeccCeEEEEEEeeCCCCeEEEEEecchhhhhhhhc-cCCCCEehHH-HHHHH
Confidence 45677889999999999999999999999999999999999999999999999999985 33 5678999999 99999
Q ss_pred HHHHHHhcChhHHH-----Hhhhheeehhhhhhhcc
Q 029135 129 LVKSLSRLVLHLTL-----RKFHLMIVMAPVVVREC 159 (198)
Q Consensus 129 LAerAkeaGI~~~v-----~kyHg~i~~~~~~~~~~ 159 (198)
||++|+++||..++ ++|||+|..+++-+|+.
T Consensus 80 la~ra~~~gi~~v~fdr~~~~y~grv~a~~~~~re~ 115 (119)
T PF00861_consen 80 LAKRALEKGIAKVVFDRGGYKYHGRVKALADGAREG 115 (119)
T ss_dssp HHHHHHHTTSSEEEECTSTSSSSSHHHHHHHHHHHT
T ss_pred HHHHHHHcCCcEEEEcCCCCcccHHHHHHHHHHHHc
Confidence 99999999998888 89999999999998875
No 6
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=99.94 E-value=5.8e-28 Score=206.74 Aligned_cols=89 Identities=19% Similarity=0.170 Sum_probs=82.1
Q ss_pred CCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCC-----------CCCCCHHHHHHHHHHHHHHHHHhcCh
Q 029135 70 PTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGN-----------PPCSTIFPLSRKLLSVLVKSLSRLVL 138 (198)
Q Consensus 70 a~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~-----------~~~~NieAA~~~VGklLAerAkeaGI 138 (198)
..||||+|||||+|||||||||.+|+||+|+||+++++++.++ ..++|+++|+ .||++|||+|+++||
T Consensus 103 krrPRLsV~RSnkHIYAQIIDD~~~~TLasaSTlek~l~~~~~~~~~~~~n~~~~~g~nieaA~-~VGk~IAerAl~kGI 181 (211)
T PTZ00032 103 KRRPRLTLKNTNNQMYATIVDDYTRHVLCFSCTNFKYLSHIFGTYPTKTTNRVRNNGGTIKAAY-ELGKLIGRKALSKGI 181 (211)
T ss_pred CCcceEEEEecCCeEEEEEEECCCCCEEEEecCCCHHHHhhhcccccccccccccCCCcHHHHH-HHHHHHHHHHHHCCC
Confidence 3699999999999999999999999999999999999976431 1478999999 999999999999999
Q ss_pred hHHH-----Hhhhheeehhhhhhhcc
Q 029135 139 HLTL-----RKFHLMIVMAPVVVREC 159 (198)
Q Consensus 139 ~~~v-----~kyHg~i~~~~~~~~~~ 159 (198)
++++ ++|||||..++|-.||-
T Consensus 182 ~kVvFDRgGy~YHGRVkALAdaARe~ 207 (211)
T PTZ00032 182 SKVRFDRAHYKYAGKVEALAEGARAV 207 (211)
T ss_pred CEEEEeCCCCeehhHHHHHHHHHHHc
Confidence 9999 99999999999999984
No 7
>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=99.94 E-value=2.3e-27 Score=179.70 Aligned_cols=95 Identities=26% Similarity=0.297 Sum_probs=88.0
Q ss_pred HhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135 63 QKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL 142 (198)
Q Consensus 63 RkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v 142 (198)
++++.|+..+|||+|++||+|||||||||.+++||+++||+|+++++++ ++++|++||+ .||++||++|+++||++++
T Consensus 2 ~~~~~~~~~~~RL~v~~Sn~~i~aqvi~~~~~~vl~sast~e~~~~~~~-~~~~n~~aA~-~vG~~la~r~~~~gi~~vv 79 (103)
T cd00432 2 RRKRLGTQERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVL-GSGNNVEAAY-LVGRLLAKRALEKGIKKVV 79 (103)
T ss_pred ceEecCcCCCCEEEEEEeCCEEEEEEEEeCcCeEEEEEecCchhhcccc-cCCCcHHHHH-HHHHHHHHHHHHCCCCEEE
Confidence 3455677789999999999999999999999999999999999999877 6789999999 9999999999999999998
Q ss_pred -----Hhhhheeehhhhhhhcc
Q 029135 143 -----RKFHLMIVMAPVVVREC 159 (198)
Q Consensus 143 -----~kyHg~i~~~~~~~~~~ 159 (198)
++|||+|..+.+-+|+.
T Consensus 80 ~D~~~~~~~grv~a~~~~~r~~ 101 (103)
T cd00432 80 FDRGGYRYHGRVKALAKGAREG 101 (103)
T ss_pred EeCCCcccccHHHHHHHHHHHc
Confidence 99999999999988874
No 8
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=99.93 E-value=1.7e-26 Score=195.79 Aligned_cols=105 Identities=15% Similarity=0.075 Sum_probs=97.1
Q ss_pred chHHHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEE--ecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHH
Q 029135 50 ARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLV--DDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLS 127 (198)
Q Consensus 50 ~K~e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQII--DD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGk 127 (198)
.|.|.++.+++|.|.... ++|||+||+||+||||||| ||++|+||+||||+|++.++|. .+++|++||+ +||.
T Consensus 13 RrRegkTdY~~R~rl~~~---~kpRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~g~~-~~~~N~~AAy-~vG~ 87 (193)
T PRK08569 13 RRREGKTDYRKRLKLLLS---GKPRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKYGWK-GDTGNTPAAY-LTGL 87 (193)
T ss_pred ccccccccHHHHHHHHhc---CCCEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhcccc-CCCCCHHHHH-HHHH
Confidence 467888899999887654 7999999999999999999 9999999999999999999987 5789999999 9999
Q ss_pred HHHHHHHhcChhHHH-----Hhhh--heeehhhhhhhcc
Q 029135 128 VLVKSLSRLVLHLTL-----RKFH--LMIVMAPVVVREC 159 (198)
Q Consensus 128 lLAerAkeaGI~~~v-----~kyH--g~i~~~~~~~~~~ 159 (198)
+||++|+++||+++| ++|| |||.-+++-.|+.
T Consensus 88 llA~ral~kGi~~vvfDrGg~~yh~gGRV~A~akgArd~ 126 (193)
T PRK08569 88 LAGKKALKAGVEEAVLDIGLHRPTKGSRVFAALKGAIDA 126 (193)
T ss_pred HHHHHHHHCCCCEEEEecCCccccCCccHHHHHHHHHHc
Confidence 999999999999998 9999 9999999999975
No 9
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=99.20 E-value=7e-11 Score=106.40 Aligned_cols=85 Identities=16% Similarity=0.053 Sum_probs=74.4
Q ss_pred chHHHHHHHHHHHHhhhcCC----CCCCeEEEEeccceEEEEEE--ecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHH
Q 029135 50 ARTESAKIRNRRIQKKFNGT----PTKPRLSVFCSDKQLYAMLV--DDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSR 123 (198)
Q Consensus 50 ~K~e~R~rR~rRiRkKI~GT----a~RPRLsVfRSNKHIYAQII--DD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~ 123 (198)
-|.|.++.+++|.|.-+.+. +-+|||+|..||++|.|||+ +.+++++|++|.|.|+.-+||. .+.+|.+||+
T Consensus 22 RRREGKTdY~~R~rLi~q~knKynspK~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S~eL~kyG~k-~gl~N~~AAY- 99 (300)
T PTZ00069 22 RRREGKTDYYARRRLILQDKNKYNSPKYRLVVRITNKDIICQIVYATIVGDKVLAAAYSHELPRFGIP-VGLTNYAAAY- 99 (300)
T ss_pred hhhcccccHHHHHHHHHccccccCCCCceEEEEEECCcEEEEEEEeecCCCEEEEEeehhhHhhcCcC-CCCccHHHHH-
Confidence 36677788888888777652 24899999999999999999 5789999999999999878887 6789999999
Q ss_pred HHHHHHHHHHHhc
Q 029135 124 KLLSVLVKSLSRL 136 (198)
Q Consensus 124 ~VGklLAerAkea 136 (198)
++|.++|.|++++
T Consensus 100 ~TGlL~arR~L~k 112 (300)
T PTZ00069 100 ATGLLLARRLLKK 112 (300)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999999987
No 10
>KOG3333 consensus Mitochondrial/chloroplast ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=98.29 E-value=9.7e-07 Score=74.77 Aligned_cols=67 Identities=15% Similarity=0.126 Sum_probs=61.5
Q ss_pred CeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135 73 PRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL 142 (198)
Q Consensus 73 PRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v 142 (198)
.||.|-++..|+-+-|.. .+|.+++||||.|+.|+..+ .++.|+.|+. .+|.+||+||++.||+..+
T Consensus 61 h~lev~~~~~hveg~v~H-~~~gvvvSAST~EwaIk~qL-Yst~dtsA~~-niGRVLAqRCLqsGI~fm~ 127 (188)
T KOG3333|consen 61 HRLEVIRTQHHVEGLVEH-QNGGVVVSASTREWAIKKQL-YSTRDTSACE-NIGRVLAQRCLQSGINFMV 127 (188)
T ss_pred eEEEEeecccceeeeeeE-ecCCEEEEecccchHHHHHH-hhccchHHHH-HHHHHHHHHHHHhCcceec
Confidence 489999999999999886 66778899999999999877 7889999999 9999999999999999877
No 11
>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=96.26 E-value=0.027 Score=43.79 Aligned_cols=63 Identities=17% Similarity=0.191 Sum_probs=53.0
Q ss_pred EEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135 75 LSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL 142 (198)
Q Consensus 75 LsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v 142 (198)
+-|+-|.+++.+.+.| ..|+++.+.|+-...+++. ..++..||+ .+++.++++|++.||..+.
T Consensus 3 ihI~~s~NNt~vtlTd-~~G~~~~~~S~G~~gfK~~---rk~t~~Aa~-~~a~~~~~~~~~~gi~~v~ 65 (110)
T PF00411_consen 3 IHIKSSFNNTIVTLTD-LKGNVLFWSSAGSLGFKGA---RKSTPYAAQ-QAAEKIAKKAKELGIKTVR 65 (110)
T ss_dssp EEEEEESSEEEEEEEE-TTSEEEEEEETTTSSTTTT---CGSSHHHHH-HHHHHHHHHHHCTTEEEEE
T ss_pred EEEEecCCCEEEEEEC-CCCCEEEEEeccccccccc---cccCHHHHH-HHHHHHHHHHHHcCCeEEE
Confidence 6788999999999987 6688999999987777763 347889999 9999999999999987544
No 12
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=95.82 E-value=0.029 Score=49.81 Aligned_cols=73 Identities=15% Similarity=0.052 Sum_probs=57.5
Q ss_pred CCCeEEEEeccceEEEEEEecCCCe-EEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHHHhhhh
Q 029135 71 TKPRLSVFCSDKQLYAMLVDDQNKK-CLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTLRKFHL 147 (198)
Q Consensus 71 ~RPRLsVfRSNKHIYAQIIDD~~gk-TLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v~kyHg 147 (198)
++-+++|.-|-+++.++|.|..+.. ||+-+|+-...+++.. .++--||+ .+++.+|++|++.||..+-=.++|
T Consensus 117 ~~f~~vI~aSfNNTIVTlTD~~GNv~tl~WSSAG~~GFKGsK---KsTpfAAQ-~aae~aakka~~~GIk~V~V~vKG 190 (233)
T PTZ00090 117 DRFMLVITTSKNNVHAQVVNKSKNYKTVFGSFAGNVGFRKKL---QQSERCAY-RIGENIAKKCRRLGIFAVDIKFRR 190 (233)
T ss_pred CcEEEEEEeccCcEEEEEEeCCCCEEEEEEEcccccCcccCc---cCCHHHHH-HHHHHHHHHHHHcCCeEEEEEEeC
Confidence 4668999999999999999866664 6888888777777643 35667777 999999999999998766533443
No 13
>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=95.59 E-value=0.064 Score=41.79 Aligned_cols=63 Identities=11% Similarity=0.072 Sum_probs=51.6
Q ss_pred EEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135 75 LSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL 142 (198)
Q Consensus 75 LsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v 142 (198)
+-|+.|.+++.+.+.|. .|++++.+|+-...+++. ..++.-||. .+++.+++++++.||..+.
T Consensus 3 ~hI~~s~NNT~itlTd~-~g~~~~~~S~G~~gfkg~---rk~t~~Aa~-~~a~~~~~~~~~~gi~~v~ 65 (108)
T TIGR03632 3 AHIHATFNNTIVTITDP-QGNVLSWASAGAVGFKGS---KKSTPYAAQ-LAAEDAAKKAKEFGMKTVD 65 (108)
T ss_pred EEEEccCCCEEEEEEcC-CCCEEEEEecCceeeCCC---ccCCHHHHH-HHHHHHHHHHHHcCCcEEE
Confidence 56899999999999986 566888888877777763 346778888 9999999999999987654
No 14
>CHL00041 rps11 ribosomal protein S11
Probab=94.87 E-value=0.14 Score=40.52 Aligned_cols=65 Identities=9% Similarity=0.058 Sum_probs=54.1
Q ss_pred CeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135 73 PRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL 142 (198)
Q Consensus 73 PRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v 142 (198)
=-+-|+.|-+++.+.+-|. .|++|+.+|.-...+++. ..++..||. .+++.++++|++.|+..+-
T Consensus 14 gi~hI~~t~NNTiiTlTd~-~G~~l~~~S~G~~gfKg~---rK~T~~Aa~-~~a~~~~~~~~~~gi~~v~ 78 (116)
T CHL00041 14 GVIHIQASFNNTIVTVTDV-RGRVISWSSAGACGFKGA---RKGTPFAAQ-TAAENAIRTVIDQGMKRAE 78 (116)
T ss_pred EEEEEEcccCCEEEEEEcC-CCCEEEEEecCceeeCCC---ccCCHHHHH-HHHHHHHHHHHHcCCcEEE
Confidence 3788999999999999985 578999999877777763 246778888 9999999999999987754
No 15
>PRK05309 30S ribosomal protein S11; Validated
Probab=94.49 E-value=0.21 Score=40.27 Aligned_cols=65 Identities=9% Similarity=0.053 Sum_probs=53.6
Q ss_pred CCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHH
Q 029135 72 KPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLT 141 (198)
Q Consensus 72 RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~ 141 (198)
.-.+-|+-|.+++.+.+-| ..|++++..|.-...+++. ..++..||. .+++.+++.|++.||..+
T Consensus 17 ~gi~hI~~t~NNTiitlTd-~~G~~~~~~S~G~~gfKg~---rK~T~~Aa~-~aa~~~~~~~~~~gi~~v 81 (128)
T PRK05309 17 SGVAHIHATFNNTIVTITD-RQGNVISWASAGGLGFKGS---RKSTPYAAQ-VAAEDAAKKAKEHGMKTV 81 (128)
T ss_pred eeEEEEEccCCCEEEEEEc-CCCCEEEEEecCccEeCCC---ccCCHHHHH-HHHHHHHHHHHHcCCcEE
Confidence 4589999999999999998 5678898888866667663 346778888 999999999999998643
No 16
>KOG0875 consensus 60S ribosomal protein L5 [Translation, ribosomal structure and biogenesis]
Probab=94.38 E-value=0.075 Score=47.97 Aligned_cols=76 Identities=9% Similarity=-0.039 Sum_probs=58.1
Q ss_pred CCCeEEEEeccceEEEEEEe--cCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHh-cChhHHHHhhhh
Q 029135 71 TKPRLSVFCSDKQLYAMLVD--DQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSR-LVLHLTLRKFHL 147 (198)
Q Consensus 71 ~RPRLsVfRSNKHIYAQIID--D~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAke-aGI~~~v~kyHg 147 (198)
.+.|+.|..+|+.|.+||+- -+++.+++++-+-|..-++.. ..-.|-.||+ ..|-+||.|+++ .|.+. .|-|
T Consensus 47 ~kyR~ivr~~n~~iicqi~~~~i~gd~v~~~a~s~elpkyg~~-~GLtNyaAay-~TglLLarR~l~~~gmD~---~yeg 121 (264)
T KOG0875|consen 47 PKYRMIVRVINKDIICQIAYATIEGDVIVRAAYAHELPKYGVK-VGLTNYAAAY-CTGLLLACRLLKRFGMDK---IYEG 121 (264)
T ss_pred CceEEEEEEechhhHHHHHhheecceEEEEeeccccccccccc-cccchhHHHH-hhHHHHHHHHHHHhCccc---cccc
Confidence 58899999999999999994 356677888888888766643 3346889999 999999999874 45554 3554
Q ss_pred eeeh
Q 029135 148 MIVM 151 (198)
Q Consensus 148 ~i~~ 151 (198)
-..+
T Consensus 122 ~~e~ 125 (264)
T KOG0875|consen 122 QVEV 125 (264)
T ss_pred ceee
Confidence 4433
No 17
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=94.14 E-value=0.16 Score=41.57 Aligned_cols=70 Identities=7% Similarity=-0.082 Sum_probs=55.4
Q ss_pred eEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHHHhhhh
Q 029135 74 RLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTLRKFHL 147 (198)
Q Consensus 74 RLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v~kyHg 147 (198)
-+-|+-|-++.++.|-|..+.+||+.+|.-...+++. ..++--||. ..++.++++|++.||..+-=+.+|
T Consensus 11 i~hI~as~NNTivtvTD~~G~~~~~~~S~G~~g~kg~---kK~TpyAAq-~aae~~~~~~~~~Gi~~v~v~vkG 80 (132)
T PRK09607 11 IAHIYASFNNTIITITDLTGAETIAKSSGGMVVKADR---DESSPYAAM-QAAEKAAEDAKEKGITGVHIKVRA 80 (132)
T ss_pred EEEEEcccCCeEEEEEcCCCCEEEEEecCcceeeCCC---ccCCHHHHH-HHHHHHHHHHHHcCCcEEEEEEEe
Confidence 6789999999999999866667998888876666552 235666888 999999999999999877655544
No 18
>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=93.76 E-value=0.22 Score=39.84 Aligned_cols=69 Identities=7% Similarity=-0.077 Sum_probs=53.6
Q ss_pred EEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHHHhhhh
Q 029135 75 LSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTLRKFHL 147 (198)
Q Consensus 75 LsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v~kyHg 147 (198)
+-|+-|-++..+.|-|..+..+|+.+|+-...+++.. .++--||. ...+.++++|++.||..+-=+.+|
T Consensus 5 ~hI~as~NNTiitvTD~~G~~~~~~~S~G~~g~kg~k---k~TpyAAq-~aa~~~~~~~~~~Gi~~v~v~ikG 73 (114)
T TIGR03628 5 AHIYSSFNNTIITITDITGAETIARSSGGMVVKADRD---ESSPYAAM-QAAGRAAEKAKERGITGLHIKVRA 73 (114)
T ss_pred EEEEccCCCeEEEEEcCCCCEEEEEecCcceEeCCCc---cCCHHHHH-HHHHHHHHHHHHcCCcEEEEEEEe
Confidence 4578888999999998777788999888777776532 35667788 999999999999999866544443
No 19
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=90.31 E-value=1.3 Score=37.03 Aligned_cols=67 Identities=9% Similarity=0.025 Sum_probs=51.2
Q ss_pred CCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135 72 KPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL 142 (198)
Q Consensus 72 RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v 142 (198)
.--+-|+-|-++....|-| ..|.+++..|+-...+++.. ..++--||. ...+.++++|++.||..+-
T Consensus 28 ~Gi~hI~as~NNTiItiTD-~~G~~~~w~SsG~~gfKg~r--~KsTpyAAq-~aa~~~a~k~~~~Gi~~v~ 94 (149)
T PTZ00129 28 FGVAHIFASFNDTFIHVTD-LSGRETLVRVTGGMKVKADR--DESSPYAAM-MAAQDVAARCKELGINALH 94 (149)
T ss_pred EEEEEEEcccCCeEEEEEc-ccCCEEEEEecCcceecccc--cCCCHHHHH-HHHHHHHHHHHHcCCeEEE
Confidence 3478899999999999987 55677777787666676522 135556788 9999999999999987653
No 20
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=82.18 E-value=3.1 Score=34.19 Aligned_cols=63 Identities=11% Similarity=0.066 Sum_probs=45.7
Q ss_pred EEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135 75 LSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL 142 (198)
Q Consensus 75 LsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v 142 (198)
.-|+.|-++....|- |..|+.+..+||=-..+++.- .++--||. ..++..++.+++.||..+=
T Consensus 21 ahI~asfNNTivtit-D~~Gn~i~wassG~~gfk~~r---k~tpyAA~-~aa~~aa~~a~e~Gi~~v~ 83 (129)
T COG0100 21 AHIHASFNNTIVTIT-DLTGNVIIWASSGGMGFKGSR---KSTPYAAQ-LAAEDAAKKAKEHGIKSVE 83 (129)
T ss_pred EEEEcccCCcEEEec-CCCCCEEEEEecCCceEcCCC---CCCHHHHH-HHHHHHHHHHHHhCccEEE
Confidence 445556555555554 588899999999877777622 35556666 9999999999999987653
No 21
>KOG0408 consensus Mitochondrial/chloroplast ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=62.61 E-value=38 Score=29.57 Aligned_cols=66 Identities=9% Similarity=0.062 Sum_probs=52.0
Q ss_pred CCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHH
Q 029135 71 TKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLT 141 (198)
Q Consensus 71 ~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~ 141 (198)
+-|-.-|.-|-++...||.| ..|.++.++|---..|++.- .++--||. -.|-..+.++++.|+..+
T Consensus 78 eiPi~hIraS~NNTivtVtd-~kg~vi~~~ScgteGFrntr---kgT~iAaQ-taavaa~~r~v~~G~~~v 143 (190)
T KOG0408|consen 78 EIPIIHIRASFNNTIVTVTD-VKGEVISWSSCGTEGFRNTR---KGTPIAAQ-TAAVAAIRRAVDQGMQTV 143 (190)
T ss_pred ccceEEEEecCCCeEEEEEc-cCCcEEEEeecccccccccc---cCCchhHH-HHHHHHHHHHHHhcceEE
Confidence 67888899999999999986 77888888777666677632 34556777 788899999999997654
No 22
>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=62.33 E-value=30 Score=28.56 Aligned_cols=63 Identities=10% Similarity=0.071 Sum_probs=45.5
Q ss_pred EEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHH
Q 029135 75 LSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLT 141 (198)
Q Consensus 75 LsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~ 141 (198)
.-||-|-+..++.|-|-.+..||+-..---+ ++.. ...+.--||- +..+..|.+|++.||..+
T Consensus 19 ahi~asfndtfvhitdlsg~eti~rvtggmk-vkad--rdesspyaam-laaqdva~kck~~gi~al 81 (139)
T KOG0407|consen 19 AHIFASFNDTFVHVTDLSGKETIVRVTGGMK-VKAD--RDESSPYAAM-LAAQDVAAKCKELGITAL 81 (139)
T ss_pred EEEEeecccceEEEeccCCceEEEEecCCeE-Eecc--cccCChHHHH-HHHHHHHHHHHhcCeeEE
Confidence 4577788888888999999999987654322 2221 2235556777 888999999999998753
No 23
>PF03646 FlaG: FlaG protein; InterPro: IPR005186 Although these proteins are known to be important for flagellar their exact function is unknown.; PDB: 2HC5_A.
Probab=59.51 E-value=44 Score=25.15 Aligned_cols=40 Identities=13% Similarity=0.176 Sum_probs=29.1
Q ss_pred HHHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEE
Q 029135 59 NRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLF 98 (198)
Q Consensus 59 ~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLa 98 (198)
-.++...+......-+..|......++++|||.++|++|=
T Consensus 43 v~~ln~~~~~~~~~l~F~vde~~~~~vVkViD~~T~eVIR 82 (107)
T PF03646_consen 43 VEKLNEFLQALNTSLRFSVDEESGRVVVKVIDKETGEVIR 82 (107)
T ss_dssp HHHHHHHHTTSS--EEEEEEEETTEEEEEEEETTT-SEEE
T ss_pred HHHHHHHHHhcCCceEEEEecCCCcEEEEEEECCCCcEEE
Confidence 3445555554445669999999999999999999999983
No 24
>PRK07738 flagellar protein FlaG; Provisional
Probab=43.15 E-value=1e+02 Score=24.90 Aligned_cols=38 Identities=11% Similarity=0.286 Sum_probs=30.5
Q ss_pred HHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEE
Q 029135 60 RRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCL 97 (198)
Q Consensus 60 rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTL 97 (198)
.++...+......-+..|......++++|||..+|++|
T Consensus 53 eklN~~l~~~~~~L~F~vdeet~~~vVkVvD~~T~EVI 90 (117)
T PRK07738 53 DGMNELLEPSQTSLKFELHEKLNEYYVQVVDERTNEVI 90 (117)
T ss_pred HHHHHHHHhcCCceEEEEecCCCcEEEEEEECCCCeee
Confidence 34455555544577999999999999999999999988
No 25
>cd07367 CarBb CarBb is the B subunit of the Class III Extradiol ring-cleavage dioxygenase, 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBb is the B subunit of 2-aminophenol 1,6-dioxygenase (CarB), which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. It is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, it has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=38.92 E-value=30 Score=30.44 Aligned_cols=86 Identities=13% Similarity=0.137 Sum_probs=47.0
Q ss_pred HHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChh
Q 029135 60 RRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLH 139 (198)
Q Consensus 60 rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~ 139 (198)
++++.++.. .+|...|--|+.|...+-.|....-++....+.. ++... +-+....+... .+...|++.+.+.||+
T Consensus 32 ~~~~~~l~~--~~Pd~ivvis~dH~~~~~~~~~p~~~i~~~~~~~-~~~~~-g~p~~~~~gd~-~LA~~i~~~l~~~g~~ 106 (268)
T cd07367 32 AEIGRRVRE--SRPDVLVVISSDHLFNINLSLQPPFVVGTADSYT-PFGDM-DIPRELFPGHR-EFARAFVRQAAEDGFD 106 (268)
T ss_pred HHHHHHHHH--cCCCEEEEEeCchhhhcccccCCceEEeeccccc-cCCcC-CCCcccCCCCH-HHHHHHHHHHHHcCCC
Confidence 446666753 5899999999988544433333333333322222 22211 11111222233 4555888999999997
Q ss_pred HHHH----hhhheee
Q 029135 140 LTLR----KFHLMIV 150 (198)
Q Consensus 140 ~~v~----kyHg~i~ 150 (198)
.+.. .=||-.+
T Consensus 107 ~~~~~~~~lDHG~~v 121 (268)
T cd07367 107 LAQAEELRPDHGVMV 121 (268)
T ss_pred eeeecCccCCcchhc
Confidence 7652 2377665
No 26
>TIGR01917 gly_red_sel_B glycine reductase, selenoprotein B. Glycine reductase is a complex with two selenoprotein subunits, A and B. This model represents the glycine reductase selenoprotein B. Closely related to it, but excluded from this model, are selenoprotein B subunits of betaine reductase and sarcosine reductase. All contain selenocysteine incorporated during translation at a specific UGA codon.
Probab=31.44 E-value=23 Score=34.40 Aligned_cols=29 Identities=7% Similarity=0.014 Sum_probs=26.0
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135 113 PPCSTIFPLSRKLLSVLVKSLSRLVLHLTL 142 (198)
Q Consensus 113 ~~~~NieAA~~~VGklLAerAkeaGI~~~v 142 (198)
+.+.+.+.++ ..|+.||+++++.|||.+|
T Consensus 313 G~gt~~~~a~-~~g~eIa~~Lk~dgVDAvI 341 (431)
T TIGR01917 313 GNGTAVANSK-QFAKEFSKELLAAGVDAVI 341 (431)
T ss_pred CCCccHHHHH-HHHHHHHHHHHHcCCCEEE
Confidence 3567888999 8999999999999999987
No 27
>PF03900 Porphobil_deamC: Porphobilinogen deaminase, C-terminal domain; InterPro: IPR022418 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. Porphobilinogen deaminase (also known as hydroxymethylbilane synthase, 2.5.1.61 from EC) functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the polymerisation of four PBG molecules into the tetrapyrrole structure, preuroporphyrinogen, with the concomitant release of four molecules of ammonia. This enzyme uses a unique dipyrro-methane cofactor made from two molecules of PBG, which is covalently attached to a cysteine side chain. The tetrapyrrole product is synthesized in an ordered, sequential fashion, by initial attachment of the first pyrrole unit (ring A) to the cofactor, followed by subsequent additions of the remaining pyrrole units (rings B, C, D) to the growing pyrrole chain []. The link between the pyrrole ring and the cofactor is broken once all the pyrroles have been added. This enzyme is folded into three distinct domains that enclose a single, large active site that makes use of an aspartic acid as its one essential catalytic residue, acting as a general acid/base during catalysis [, ]. A deficiency of hydroxymethylbilane synthase is implicated in the neuropathic disease, Acute Intermittent Porphyria (AIP) []. This entry represents the C-terminal domain of porphobilinogen deaminase, an enzyme involved in tetrapyrrole biosynthesis. The structure of this alpha/beta domain consists of alpha-beta(3)-alpha in two layers []. Porphobilinogen deaminase has a three-domain structure. Domains 1 (N-terminal) and 2 are duplications with the same structure, resembling the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 (C-terminal), but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins []. The enzyme has a single catalytic site, and the flexibility between domains is thought to aid elongation of the polypyrrole product in the active-site cleft of the enzyme.; GO: 0033014 tetrapyrrole biosynthetic process; PDB: 3EQ1_B 3ECR_A 1GTK_A 1AH5_A 2YPN_A 1PDA_A 1YPN_A.
Probab=30.37 E-value=1.4e+02 Score=21.10 Aligned_cols=59 Identities=19% Similarity=0.187 Sum_probs=32.5
Q ss_pred hhhcCCCCCC--eEEEEeccc--eEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHh
Q 029135 64 KKFNGTPTKP--RLSVFCSDK--QLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSR 135 (198)
Q Consensus 64 kKI~GTa~RP--RLsVfRSNK--HIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAke 135 (198)
+.+.|.=.-| -.+.+..++ ++.+.+.|+++.+.+...+- .++.+.+. .+|+.+|+..++
T Consensus 12 ~~l~ggC~~Piga~a~~~~~~~l~l~~~v~~~dG~~~~~~~~~------------~~~~~~a~-~lg~~la~~l~~ 74 (74)
T PF03900_consen 12 KELGGGCHSPIGAYAKIEGDERLRLRAMVGSPDGSRIIIRVEI------------TGPIEDAE-ELGKKLAEELLA 74 (74)
T ss_dssp HHCT--TTSSEEEEEEEETTE-EEEEEEEE-TTSSSEEEEEEE------------EE-GGGHC-CHHHHHHHHHHH
T ss_pred HHhCCCCCCceeeEEEEcCCCEEEEEEEEECCCCCEEEEEEEE------------EcCHHHHH-HHHHHHHHHHhC
Confidence 3445433456 455555666 66666667666652333221 12557777 889999888764
No 28
>PF07355 GRDB: Glycine/sarcosine/betaine reductase selenoprotein B (GRDB); InterPro: IPR022787 This entry represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. All members are expected to contain an internal UGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon. ; GO: 0030699 glycine reductase activity, 0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor, 0055114 oxidation-reduction process, 0030700 glycine reductase complex
Probab=30.09 E-value=27 Score=32.95 Aligned_cols=29 Identities=7% Similarity=0.031 Sum_probs=24.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135 113 PPCSTIFPLSRKLLSVLVKSLSRLVLHLTL 142 (198)
Q Consensus 113 ~~~~NieAA~~~VGklLAerAkeaGI~~~v 142 (198)
+.+.+++.++ ..|..||+.+++.|||.||
T Consensus 317 G~gt~~~~~~-~~g~eIa~~Lk~dgVDAVI 345 (349)
T PF07355_consen 317 GNGTAVANAK-RFGPEIAKELKEDGVDAVI 345 (349)
T ss_pred CCCccHHHHH-HHHHHHHHHHHHcCCCEEE
Confidence 3556788888 9999999999999999764
No 29
>COG3894 Uncharacterized metal-binding protein [General function prediction only]
Probab=29.40 E-value=68 Score=32.40 Aligned_cols=36 Identities=19% Similarity=0.128 Sum_probs=29.2
Q ss_pred eEEEEeccceEEEEEEecCCCeEEEEEechhhhhcC
Q 029135 74 RLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRG 109 (198)
Q Consensus 74 RLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~ 109 (198)
=+.|=--..-|-||+||-.+|++++++.|....+.+
T Consensus 166 GvAvDlGTS~i~aqlVDL~sgevv~t~~T~n~ql~~ 201 (614)
T COG3894 166 GVAVDLGTSGIRAQLVDLKSGEVVATVITSNPQLPG 201 (614)
T ss_pred eeEEecccceeeeEEEeccCCcEEEeeeccCCCCCC
Confidence 344444556789999999999999999999888764
No 30
>PF05374 Mu-conotoxin: Mu-Conotoxin; InterPro: IPR008036 This entry represents Mu-type conotoxins. Cone snail toxins, conotoxins, are small peptides with disulphide connectivity, that target ion-channels or G-protein coupled receptors. Based on the number and pattern of disulphide bonds and biological activities, conotoxins can be classified into several families []. Omega, delta and kappa families of conotoxins have a knottin or inhibitor cystine knot scaffold. The knottin scaffold is a very special disulphide through disulphide knot, in which the III-VI disulphide bond crosses the macrocycle formed by two other disulphide bonds (I-IV and II-V) and the interconnecting backbone segments, where I-VI indicates the six cysteine residues starting from the N terminus. The disulphide bonding network as well as specific amino acids in inter-cysteine loops provide specificity of conotoxin []. The cysteine arrangement is the same for omega, delta and kappa families, but omega conotoxins are calcium channel blockers, whereas delta conotoxins delay the inactivation of sodium channels and kappa conotoxins are potassium channel blockers []. Mu conotoxins have two types of cysteine arrangement, but the knottin scaffold is not observed. Conotoxin gm9a, a putative 27-residue polypeptide encoded by Conus gloriamaris, has been shown to adopt an inhibitory cystine knot motif constrained by three disulphide bonds [, ].Mu conotoxins target the voltage-gated sodium channels, preferential skeletal muscle [], and are useful probes for investigating voltage-dependent sodium channels of excitable tissues []. Alpha conotoxins have two types of cysteine arrangement [] and are competitive nicotinic acetylcholine receptor antagonists. ; GO: 0019871 sodium channel inhibitor activity, 0009405 pathogenesis, 0005576 extracellular region; PDB: 1R9I_A 1GIB_A 1TCJ_A 1TCG_A 1TCK_A 1TCH_A.
Probab=27.72 E-value=27 Score=20.96 Aligned_cols=9 Identities=56% Similarity=1.077 Sum_probs=7.0
Q ss_pred hhhcccccc
Q 029135 155 VVRECKPLR 163 (198)
Q Consensus 155 ~~~~~~~~~ 163 (198)
+-|+|||.+
T Consensus 11 ksR~CkP~~ 19 (22)
T PF05374_consen 11 KSRQCKPQR 19 (22)
T ss_dssp CSGGGTSST
T ss_pred ccccccccc
Confidence 458999976
No 31
>PRK08868 flagellar protein FlaG; Provisional
Probab=26.51 E-value=2.6e+02 Score=23.48 Aligned_cols=38 Identities=3% Similarity=-0.011 Sum_probs=29.6
Q ss_pred HHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEE
Q 029135 60 RRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCL 97 (198)
Q Consensus 60 rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTL 97 (198)
.++.+.+......-+..|.....-++++|||.++|.+|
T Consensus 78 eklNe~~~~~n~~L~F~vdeetgr~VVkViD~~T~EVI 115 (144)
T PRK08868 78 EQMNEFVKSINKGLSFRVDEESGRDVVTIYEASTGDII 115 (144)
T ss_pred HHHHHHHHhhcCceEEEEecCCCCEEEEEEECCCCcee
Confidence 34444444444567999999999999999999999988
No 32
>TIGR01918 various_sel_PB selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family. This model represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. This model is built in fragment mode to assist in recognizing fragmentary translations. All members are expected to contain an internal TGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon.
Probab=25.92 E-value=32 Score=33.41 Aligned_cols=29 Identities=10% Similarity=0.047 Sum_probs=25.9
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135 113 PPCSTIFPLSRKLLSVLVKSLSRLVLHLTL 142 (198)
Q Consensus 113 ~~~~NieAA~~~VGklLAerAkeaGI~~~v 142 (198)
+.+.+.+.++ ..|..||+++++.|+|.+|
T Consensus 313 G~gt~~~~a~-~~g~eIa~~Lk~dgVDAVI 341 (431)
T TIGR01918 313 GNGTTVAESK-QFAKEFVVELKQGGVDAVI 341 (431)
T ss_pred CCCchHHHHH-HHHHHHHHHHHHcCCCEEE
Confidence 3567788889 9999999999999999987
No 33
>PRK08452 flagellar protein FlaG; Provisional
Probab=25.76 E-value=2.4e+02 Score=22.87 Aligned_cols=32 Identities=16% Similarity=0.090 Sum_probs=26.2
Q ss_pred hcCCCCCCeEEEEeccceEEEEEEecCCCeEE
Q 029135 66 FNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCL 97 (198)
Q Consensus 66 I~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTL 97 (198)
+......-+..+......+|++|+|..+|++|
T Consensus 66 ~~~~~~~L~F~~de~~~~~vVkVvD~~T~eVI 97 (124)
T PRK08452 66 MKRLDTNIRFGYNDKIKGLVVSVKEANGGKVI 97 (124)
T ss_pred HHhhCCceEEEEcCCCCcEEEEEEECCCCcee
Confidence 33334567889999989999999999999988
No 34
>cd07359 PCA_45_Doxase_B_like Subunit B of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and simlar enzymes. This subfamily of class III extradiol dioxygenases consists of a number of proteins with known enzymatic activities: Protocatechuate (PCA) 4,5-dioxygenase (LigAB), 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), 3-O-Methylgallate Dioxygenase, 2-aminophenol 1,6-dioxygenase, as well as proteins without any known enzymatic activity. These proteins play essential roles in the degradation of aromatic compounds by catalyzing the incorporation of both atoms of molecular oxygen into their preferred substrates. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model repres
Probab=24.49 E-value=72 Score=27.55 Aligned_cols=92 Identities=13% Similarity=0.162 Sum_probs=50.7
Q ss_pred HHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChh
Q 029135 60 RRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLH 139 (198)
Q Consensus 60 rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~ 139 (198)
++++..+.. .+|...|--|+.|....-.|....-++...-+..-....+........+... .+...|.+.+.+.|++
T Consensus 34 ~~~~~~l~~--~~Pd~ivvis~~h~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~d~-elA~~i~~~~~~~g~~ 110 (271)
T cd07359 34 ARIRDRLEA--ARPDVVVVVGNDHFTNFFLDNMPAFAIGIADSYEGPDEGWLGIPRAPVPGDA-DLARHLLAGLVEDGFD 110 (271)
T ss_pred HHHHHHHHH--hCCCEEEEEeCcHHhhcCcccCCceEEeecccccCCccccccCcCCCCCCCH-HHHHHHHHHHHHcCCC
Confidence 345666653 5999999999988776544433333443322221111110011123333444 4555778888899997
Q ss_pred HHHH----hhhheeehhhh
Q 029135 140 LTLR----KFHLMIVMAPV 154 (198)
Q Consensus 140 ~~v~----kyHg~i~~~~~ 154 (198)
.+.. .=||-.+-.+-
T Consensus 111 ~a~~~~~~lDHg~~vpL~~ 129 (271)
T cd07359 111 VAFSYELRLDHGITVPLHF 129 (271)
T ss_pred eeccCCCCCCcchhhHHHH
Confidence 6664 55888664443
No 35
>PF03263 Cucumo_2B: Cucumovirus protein 2B; InterPro: IPR004946 This family of cucumovirus proteins may be long-distance movement proteins. ; PDB: 2ZI0_B 3CZ3_C.
Probab=23.59 E-value=65 Score=25.80 Aligned_cols=22 Identities=18% Similarity=0.295 Sum_probs=15.3
Q ss_pred hhhcchHHHHHHHHHHHHhhhcC
Q 029135 46 ARANARTESAKIRNRRIQKKFNG 68 (198)
Q Consensus 46 a~~~~K~e~R~rR~rRiRkKI~G 68 (198)
|+++.++..|.++|++.| |-+|
T Consensus 12 arm~Ekkk~rR~~Hk~NR-keRG 33 (103)
T PF03263_consen 12 ARMVEKKKQRRRSHKKNR-KERG 33 (103)
T ss_dssp HHHHHHHHHHHHHHHHHH-HHHT
T ss_pred HHHHHHHHHHHHHHHHhH-HhcC
Confidence 667777777778887776 4444
No 36
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=22.10 E-value=39 Score=20.58 Aligned_cols=10 Identities=50% Similarity=1.135 Sum_probs=8.3
Q ss_pred ccccccCCCC
Q 029135 13 NACDFFGTKA 22 (198)
Q Consensus 13 ~~~~~~g~~~ 22 (198)
++|+|||+..
T Consensus 7 ~~CgF~G~~~ 16 (26)
T smart00259 7 PGCGFFGNPA 16 (26)
T ss_pred CCCCCcCChh
Confidence 6899999874
Done!