Query psy5246
Match_columns 119
No_of_seqs 131 out of 1146
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 21:27:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5246.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5246hhsearch_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 8E-30 1.7E-34 183.5 9.9 89 27-119 2-91 (117)
2 CHL00139 rpl18 ribosomal prote 100.0 1.1E-29 2.3E-34 181.0 9.2 81 36-119 2-83 (109)
3 TIGR00060 L18_bact ribosomal p 100.0 1.9E-29 4.2E-34 181.1 9.4 84 29-119 2-88 (114)
4 COG0256 RplR Ribosomal protein 99.9 9.2E-28 2E-32 174.7 10.0 90 27-119 7-99 (125)
5 KOG3333|consensus 99.9 5.7E-27 1.2E-31 176.8 9.0 104 16-119 24-127 (188)
6 PF00861 Ribosomal_L18p: Ribos 99.9 9.8E-26 2.1E-30 161.9 9.1 87 29-118 3-92 (119)
7 cd00432 Ribosomal_L18_L5e Ribo 99.9 5.3E-24 1.2E-28 148.6 9.4 68 52-119 11-79 (103)
8 PTZ00032 60S ribosomal protein 99.9 1.3E-23 2.9E-28 163.3 8.6 67 53-119 106-185 (211)
9 PRK08569 rpl18p 50S ribosomal 99.9 1.7E-21 3.7E-26 150.7 9.1 70 47-119 30-102 (193)
10 PTZ00069 60S ribosomal protein 99.0 2.3E-09 5E-14 87.7 9.0 61 53-113 49-112 (300)
11 PF00411 Ribosomal_S11: Riboso 97.0 0.0037 7.9E-08 44.3 7.0 62 55-118 3-64 (110)
12 TIGR03632 bact_S11 30S ribosom 96.8 0.01 2.2E-07 42.0 7.8 62 55-118 3-64 (108)
13 PTZ00090 40S ribosomal protein 96.6 0.02 4.3E-07 45.8 8.8 64 53-118 119-184 (233)
14 CHL00041 rps11 ribosomal prote 96.5 0.022 4.7E-07 40.9 7.8 64 53-118 14-77 (116)
15 PRK05309 30S ribosomal protein 96.4 0.033 7.1E-07 40.7 8.3 64 53-118 18-81 (128)
16 KOG0875|consensus 95.0 0.031 6.8E-07 45.4 3.9 65 53-117 49-117 (264)
17 PTZ00129 40S ribosomal protein 94.9 0.19 4.1E-06 37.9 7.7 65 53-118 29-93 (149)
18 PRK09607 rps11p 30S ribosomal 94.8 0.2 4.2E-06 37.1 7.4 64 53-118 10-74 (132)
19 TIGR03628 arch_S11P archaeal r 94.8 0.22 4.7E-06 35.9 7.4 63 54-118 4-67 (114)
20 COG0100 RpsK Ribosomal protein 91.2 1.3 2.7E-05 32.8 6.8 63 54-118 20-82 (129)
21 KOG0408|consensus 81.3 10 0.00022 29.5 7.3 65 52-118 79-143 (190)
22 KOG0407|consensus 70.8 21 0.00045 26.2 6.1 64 53-118 17-81 (139)
23 TIGR01917 gly_red_sel_B glycin 37.0 46 0.001 29.2 3.7 27 92-118 314-340 (431)
24 PF03646 FlaG: FlaG protein; 36.1 69 0.0015 21.8 3.8 23 53-75 57-79 (107)
25 PF03900 Porphobil_deamC: Porp 31.5 18 0.00039 23.3 0.3 47 55-112 25-74 (74)
26 TIGR01918 various_sel_PB selen 31.2 64 0.0014 28.3 3.6 27 92-118 314-340 (431)
27 TIGR00212 hemC porphobilinogen 31.1 1.8E+02 0.0038 24.2 6.0 40 63-114 253-292 (292)
28 PF07355 GRDB: Glycine/sarcosi 30.4 59 0.0013 27.7 3.2 27 92-118 318-344 (349)
29 PF02961 BAF: Barrier to autoi 27.8 45 0.00098 23.2 1.8 24 94-117 19-42 (89)
30 PF11798 IMS_HHH: IMS family H 27.2 33 0.00071 18.9 0.8 15 101-115 18-32 (32)
31 PRK07738 flagellar protein Fla 26.5 1.3E+02 0.0027 21.8 4.0 24 53-76 66-89 (117)
32 PRK13690 hypothetical protein; 25.2 1.6E+02 0.0034 23.1 4.5 43 73-116 26-69 (184)
33 PF04260 DUF436: Protein of un 24.6 1.7E+02 0.0036 22.7 4.5 43 73-116 19-62 (172)
34 PLN02691 porphobilinogen deami 20.9 3.5E+02 0.0075 23.1 6.1 43 63-114 301-343 (351)
35 PF05589 DUF768: Protein of un 20.2 1.7E+02 0.0036 19.0 3.2 24 93-116 22-45 (64)
36 PRK08452 flagellar protein Fla 20.0 1.7E+02 0.0038 21.2 3.7 24 53-76 73-96 (124)
No 1
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=99.96 E-value=8e-30 Score=183.55 Aligned_cols=89 Identities=22% Similarity=0.278 Sum_probs=82.2
Q ss_pred chhHHHHHHhccccccccccCCCcceeEEEEEecCCcEEEEEEECCCCe-EEEEEcchHHhhhcccCCCCHHHHHHHHHH
Q psy5246 27 PRNLERLRIARKPQGYHLDRLGREYWHTLYFTTTKKHITGQIVHNNGNV-VVSASTNEWALKKHLYNTNDICAYSNLARV 105 (119)
Q Consensus 27 ~r~~~R~rr~~rir~k~~~~~~r~~~pRL~V~rSnkhiyAQlIdd~~g~-L~sAST~e~~ik~~l~~~~n~~aA~~vG~~ 105 (119)
.+++.|.+|+.|+|+++.|++++ |||+||+||+|||||||||++++ |+||||+|++++..+. ++|++||+.||++
T Consensus 2 ~~~~~r~~r~~r~r~ki~g~~~r---pRL~V~~SnkhiyAQvidd~~~~tl~saST~e~~~k~~~~-~~n~~aa~~vG~~ 77 (117)
T PRK05593 2 DKKEARLRRHRRVRKKISGTAER---PRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDVRAGLK-GGNKEAAKKVGKL 77 (117)
T ss_pred chHHHHHHHHHHHHHHhcCCCCC---CEEEEEEeCCeEEEEEEECCCCEEEEEEecCcHhHhcccc-CCCHHHHHHHHHH
Confidence 46677889999999999999999 99999999999999999999997 9999999999965544 8999999999999
Q ss_pred HHHHHHhcCCceeC
Q psy5246 106 LAQRCLETGISEIT 119 (119)
Q Consensus 106 lAera~~~GI~~V~ 119 (119)
||++|+++||++|+
T Consensus 78 la~ra~~~gi~~vv 91 (117)
T PRK05593 78 IAERAKAKGIKQVV 91 (117)
T ss_pred HHHHHHHCCCCEEE
Confidence 99999999999874
No 2
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=99.96 E-value=1.1e-29 Score=180.99 Aligned_cols=81 Identities=25% Similarity=0.281 Sum_probs=77.2
Q ss_pred hccccccccccCCCcceeEEEEEecCCcEEEEEEECCCCe-EEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcC
Q psy5246 36 ARKPQGYHLDRLGREYWHTLYFTTTKKHITGQIVHNNGNV-VVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETG 114 (119)
Q Consensus 36 ~~rir~k~~~~~~r~~~pRL~V~rSnkhiyAQlIdd~~g~-L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~G 114 (119)
+.|+|+++.|++++ |||+||+||+|||||||||.+|+ |+||||+|+++++++.+++|+++|+.||++||+||+++|
T Consensus 2 ~~r~r~ki~g~~~r---pRL~V~rSnkhiyaQvidd~~g~tlasaST~ek~~~~~~~~~~n~~aA~~vG~lla~ra~~~g 78 (109)
T CHL00139 2 RERVRKKIKGTAER---PRLSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVKSSLSSTSTCDASKLVGQKLAKKSLKKG 78 (109)
T ss_pred CeeeeeeecCCCCC---CEEEEEEeCCeEEEEEEECCCCCEEEEEecCchhhhccccCCCCHHHHHHHHHHHHHHHHHCC
Confidence 67899999999999 99999999999999999999997 999999999999988889999999999999999999999
Q ss_pred CceeC
Q psy5246 115 ISEIT 119 (119)
Q Consensus 115 I~~V~ 119 (119)
|++|+
T Consensus 79 i~~vv 83 (109)
T CHL00139 79 ITKVV 83 (109)
T ss_pred CCEEE
Confidence 99874
No 3
>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=1.9e-29 Score=181.08 Aligned_cols=84 Identities=25% Similarity=0.318 Sum_probs=77.7
Q ss_pred hHHHHHHhccccccccccC--CCcceeEEEEEecCCcEEEEEEECCCCe-EEEEEcchHHhhhcccCCCCHHHHHHHHHH
Q psy5246 29 NLERLRIARKPQGYHLDRL--GREYWHTLYFTTTKKHITGQIVHNNGNV-VVSASTNEWALKKHLYNTNDICAYSNLARV 105 (119)
Q Consensus 29 ~~~R~rr~~rir~k~~~~~--~r~~~pRL~V~rSnkhiyAQlIdd~~g~-L~sAST~e~~ik~~l~~~~n~~aA~~vG~~ 105 (119)
++.|++|+.|+|+++.|++ ++ |||+||+||+|||||||||++++ |+||||+|++++ +++|+++|+.||++
T Consensus 2 ~~~r~~r~~r~r~ki~gt~~~~r---pRL~V~rSnk~iyaQiIdd~~~~tlasaST~ek~~~----~~~n~~aA~~vG~~ 74 (114)
T TIGR00060 2 KSARIRRHKRIRRKLRETGEANR---PRLVVFRSNRHIYAQVIDDSKSEVLASASTLEKKLK----YTGNKDAAKKVGKL 74 (114)
T ss_pred cHHHHHHHHHHHHHhcCCCCCCC---cEEEEEEeCCeEEEEEEECCCCEEEEEEecchhhhc----CCCCHHHHHHHHHH
Confidence 3557788999999999998 88 99999999999999999999997 999999999875 57899999999999
Q ss_pred HHHHHHhcCCceeC
Q psy5246 106 LAQRCLETGISEIT 119 (119)
Q Consensus 106 lAera~~~GI~~V~ 119 (119)
||++|+++||++|+
T Consensus 75 la~ra~~~gi~~vv 88 (114)
T TIGR00060 75 VAERLKEKGIKDVV 88 (114)
T ss_pred HHHHHHHCCCCEEE
Confidence 99999999999874
No 4
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=9.2e-28 Score=174.75 Aligned_cols=90 Identities=27% Similarity=0.278 Sum_probs=82.1
Q ss_pred chhHHHHHHhccccccccccCCCcceeEEEEEecCCcEEEEEEECCCCe-EEEEEcchHHhhh--cccCCCCHHHHHHHH
Q psy5246 27 PRNLERLRIARKPQGYHLDRLGREYWHTLYFTTTKKHITGQIVHNNGNV-VVSASTNEWALKK--HLYNTNDICAYSNLA 103 (119)
Q Consensus 27 ~r~~~R~rr~~rir~k~~~~~~r~~~pRL~V~rSnkhiyAQlIdd~~g~-L~sAST~e~~ik~--~l~~~~n~~aA~~vG 103 (119)
.|+..+.+++.|+|.++.+++++ |||+||+||+|||||||||..+. |++|||.++++++ +...++|+++|++||
T Consensus 7 ~rr~~~~kr~~r~R~kl~g~~~r---pRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~~~~~N~~aA~~vG 83 (125)
T COG0256 7 FRRRRRGKRAYRIRKKLLGTSGR---PRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGGGGNTEAAYLVG 83 (125)
T ss_pred hHHHHHHhHHHHHHHhhccCCCC---cEEEEEEeCCcEEEEEEEcCCCceEEEEEcchHHHHhhcccCCCCCHHHHHHHH
Confidence 36678889999999999999999 99999999999999999999987 9999999999965 344568999999999
Q ss_pred HHHHHHHHhcCCceeC
Q psy5246 104 RVLAQRCLETGISEIT 119 (119)
Q Consensus 104 ~~lAera~~~GI~~V~ 119 (119)
+++|++|+++||++|+
T Consensus 84 ~lia~ra~~kgi~~vV 99 (125)
T COG0256 84 KLIAERALAKGIEEVV 99 (125)
T ss_pred HHHHHHHHHcCCcEEE
Confidence 9999999999999985
No 5
>KOG3333|consensus
Probab=99.94 E-value=5.7e-27 Score=176.83 Aligned_cols=104 Identities=51% Similarity=0.853 Sum_probs=100.9
Q ss_pred ccccceeeccCchhHHHHHHhccccccccccCCCcceeEEEEEecCCcEEEEEEECCCCeEEEEEcchHHhhhcccCCCC
Q psy5246 16 GAAGKCVHNKNPRNLERLRIARKPQGYHLDRLGREYWHTLYFTTTKKHITGQIVHNNGNVVVSASTNEWALKKHLYNTND 95 (119)
Q Consensus 16 ~~~~~~~~nrn~r~~~R~rr~~rir~k~~~~~~r~~~pRL~V~rSnkhiyAQlIdd~~g~L~sAST~e~~ik~~l~~~~n 95 (119)
-++.|.|+||||||.|+++++.+.+||....|.|+|||+|.|.++.+|+.+-|.|.++|+++||||.||+|+.+|+++.|
T Consensus 24 ~a~a~~f~NRNPRNlEll~~a~k~~Gy~~ekp~Rsywh~lev~~~~~hveg~v~H~~~gvvvSAST~EwaIk~qLYst~d 103 (188)
T KOG3333|consen 24 EAVAPEFTNRNPRNLELLSVARKERGYRTEKPSRSYWHRLEVIRTQHHVEGLVEHQNGGVVVSASTREWAIKKQLYSTRD 103 (188)
T ss_pred hhhchhhhcCCcchHHHHhhhccCccceecccchhheeEEEEeecccceeeeeeEecCCEEEEecccchHHHHHHhhccc
Confidence 46889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcCCceeC
Q psy5246 96 ICAYSNLARVLAQRCLETGISEIT 119 (119)
Q Consensus 96 ~~aA~~vG~~lAera~~~GI~~V~ 119 (119)
+.||..||++||+||++.||.+++
T Consensus 104 tsA~~niGRVLAqRCLqsGI~fm~ 127 (188)
T KOG3333|consen 104 TSACENIGRVLAQRCLQSGINFMV 127 (188)
T ss_pred hHHHHHHHHHHHHHHHHhCcceec
Confidence 999999999999999999999764
No 6
>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....
Probab=99.93 E-value=9.8e-26 Score=161.93 Aligned_cols=87 Identities=29% Similarity=0.264 Sum_probs=77.8
Q ss_pred hHHHHHHhccccccccccCCCcceeEEEEEecCCcEEEEEEECCCCe-EEEEEcchHHhhhcc--cCCCCHHHHHHHHHH
Q psy5246 29 NLERLRIARKPQGYHLDRLGREYWHTLYFTTTKKHITGQIVHNNGNV-VVSASTNEWALKKHL--YNTNDICAYSNLARV 105 (119)
Q Consensus 29 ~~~R~rr~~rir~k~~~~~~r~~~pRL~V~rSnkhiyAQlIdd~~g~-L~sAST~e~~ik~~l--~~~~n~~aA~~vG~~ 105 (119)
+..+.+++.+++.+..+++++ |||+||+||+|||||||||..+. |++|||.+++++..+ .+++|+++|+.||++
T Consensus 3 ~~~~~~r~~~~r~~~~~~~~~---~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~~l~~~~~~~~~~n~~aa~~vG~l 79 (119)
T PF00861_consen 3 KRRRRRRKLRIRRKIKGTAER---PRLVVFRSNKHIYAQIIDDSKGGTLASASTLSKELKKYGWKGSTKNVEAAYLVGEL 79 (119)
T ss_dssp CHHHHHHHHHHHHHHHHTTSS---EEEEEEEESSEEEEEEEECTTTEEEEEEEEETTTGGGTT-SSTTSSHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHhcCCCC---CEEEEEeccCeEEEEEEeeCCCCeEEEEEecchhhhhhhhccCCCCEehHHHHHHH
Confidence 445667777778888888888 99999999999999999999997 999999999998754 567899999999999
Q ss_pred HHHHHHhcCCcee
Q psy5246 106 LAQRCLETGISEI 118 (119)
Q Consensus 106 lAera~~~GI~~V 118 (119)
||++|+++||..|
T Consensus 80 la~ra~~~gi~~v 92 (119)
T PF00861_consen 80 LAKRALEKGIAKV 92 (119)
T ss_dssp HHHHHHHTTSSEE
T ss_pred HHHHHHHcCCcEE
Confidence 9999999999876
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=99.91 E-value=5.3e-24 Score=148.62 Aligned_cols=68 Identities=38% Similarity=0.491 Sum_probs=64.6
Q ss_pred eeEEEEEecCCcEEEEEEECCCCe-EEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcCCceeC
Q psy5246 52 WHTLYFTTTKKHITGQIVHNNGNV-VVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGISEIT 119 (119)
Q Consensus 52 ~pRL~V~rSnkhiyAQlIdd~~g~-L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~GI~~V~ 119 (119)
+|||+|++||+|||||||||.+++ |++|||.|+++++++++++|+++|+.||++||+||+++||++|+
T Consensus 11 ~~RL~v~~Sn~~i~aqvi~~~~~~vl~sast~e~~~~~~~~~~~n~~aA~~vG~~la~r~~~~gi~~vv 79 (103)
T cd00432 11 RPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVV 79 (103)
T ss_pred CCEEEEEEeCCEEEEEEEEeCcCeEEEEEecCchhhcccccCCCcHHHHHHHHHHHHHHHHHCCCCEEE
Confidence 399999999999999999999886 99999999999998889999999999999999999999999874
No 8
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=99.90 E-value=1.3e-23 Score=163.35 Aligned_cols=67 Identities=22% Similarity=0.274 Sum_probs=62.9
Q ss_pred eEEEEEecCCcEEEEEEECCCCe-EEEEEcchHHhhhccc------------CCCCHHHHHHHHHHHHHHHHhcCCceeC
Q psy5246 53 HTLYFTTTKKHITGQIVHNNGNV-VVSASTNEWALKKHLY------------NTNDICAYSNLARVLAQRCLETGISEIT 119 (119)
Q Consensus 53 pRL~V~rSnkhiyAQlIdd~~g~-L~sAST~e~~ik~~l~------------~~~n~~aA~~vG~~lAera~~~GI~~V~ 119 (119)
|||+|||||+|||||||||.+|+ ||||||+++++++.+. .++|+++|+.||++||++|+++||++|+
T Consensus 106 PRLsV~RSnkHIYAQIIDD~~~~TLasaSTlek~l~~~~~~~~~~~~n~~~~~g~nieaA~~VGk~IAerAl~kGI~kVv 185 (211)
T PTZ00032 106 PRLTLKNTNNQMYATIVDDYTRHVLCFSCTNFKYLSHIFGTYPTKTTNRVRNNGGTIKAAYELGKLIGRKALSKGISKVR 185 (211)
T ss_pred ceEEEEecCCeEEEEEEECCCCCEEEEecCCCHHHHhhhcccccccccccccCCCcHHHHHHHHHHHHHHHHHCCCCEEE
Confidence 99999999999999999999997 9999999999977554 5789999999999999999999999985
No 9
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=99.86 E-value=1.7e-21 Score=150.66 Aligned_cols=70 Identities=26% Similarity=0.301 Sum_probs=65.2
Q ss_pred CCCcceeEEEEEecCCcEEEEEE--ECCCCe-EEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcCCceeC
Q psy5246 47 LGREYWHTLYFTTTKKHITGQIV--HNNGNV-VVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGISEIT 119 (119)
Q Consensus 47 ~~r~~~pRL~V~rSnkhiyAQlI--dd~~g~-L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~GI~~V~ 119 (119)
.++ |||+|++||+||||||| ||++++ |+||||+|++.+++..+++|++||+.||.+||+||+++||++|+
T Consensus 30 ~~k---pRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~g~~~~~~N~~AAy~vG~llA~ral~kGi~~vv 102 (193)
T PRK08569 30 SGK---PRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKYGWKGDTGNTPAAYLTGLLAGKKALKAGVEEAV 102 (193)
T ss_pred cCC---CEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhccccCCCCCHHHHHHHHHHHHHHHHHCCCCEEE
Confidence 456 99999999999999999 888887 99999999999888778899999999999999999999999874
No 10
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=98.99 E-value=2.3e-09 Score=87.72 Aligned_cols=61 Identities=25% Similarity=0.184 Sum_probs=54.7
Q ss_pred eEEEEEecCCcEEEEEEE-C-CCCe-EEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhc
Q psy5246 53 HTLYFTTTKKHITGQIVH-N-NGNV-VVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLET 113 (119)
Q Consensus 53 pRL~V~rSnkhiyAQlId-d-~~g~-L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~ 113 (119)
|||+|..||++|.|||+. . ++.+ |++|+|.|+.-.++..+.+|.+||+..|.++|.|++++
T Consensus 49 ~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S~eL~kyG~k~gl~N~~AAY~TGlL~arR~L~k 112 (300)
T PTZ00069 49 YRLVVRITNKDIICQIVYATIVGDKVLAAAYSHELPRFGIPVGLTNYAAAYATGLLLARRLLKK 112 (300)
T ss_pred ceEEEEEECCcEEEEEEEeecCCCEEEEEeehhhHhhcCcCCCCccHHHHHHHHHHHHHHHHHh
Confidence 999999999999999998 3 3445 99999999876777677899999999999999999998
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=97.02 E-value=0.0037 Score=44.27 Aligned_cols=62 Identities=18% Similarity=0.232 Sum_probs=53.4
Q ss_pred EEEEecCCcEEEEEEECCCCeEEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcCCcee
Q psy5246 55 LYFTTTKKHITGQIVHNNGNVVVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGISEI 118 (119)
Q Consensus 55 L~V~rSnkhiyAQlIdd~~g~L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~GI~~V 118 (119)
+.|+-|.+++.+.|.|..+.++.+.|+-...+++. ......||..+++.++++|++.||..|
T Consensus 3 ihI~~s~NNt~vtlTd~~G~~~~~~S~G~~gfK~~--rk~t~~Aa~~~a~~~~~~~~~~gi~~v 64 (110)
T PF00411_consen 3 IHIKSSFNNTIVTLTDLKGNVLFWSSAGSLGFKGA--RKSTPYAAQQAAEKIAKKAKELGIKTV 64 (110)
T ss_dssp EEEEEESSEEEEEEEETTSEEEEEEETTTSSTTTT--CGSSHHHHHHHHHHHHHHHHCTTEEEE
T ss_pred EEEEecCCCEEEEEECCCCCEEEEEeccccccccc--cccCHHHHHHHHHHHHHHHHHcCCeEE
Confidence 67899999999999998877888888877777654 356889999999999999999999876
No 12
>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=96.80 E-value=0.01 Score=42.04 Aligned_cols=62 Identities=21% Similarity=0.162 Sum_probs=51.9
Q ss_pred EEEEecCCcEEEEEEECCCCeEEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcCCcee
Q psy5246 55 LYFTTTKKHITGQIVHNNGNVVVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGISEI 118 (119)
Q Consensus 55 L~V~rSnkhiyAQlIdd~~g~L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~GI~~V 118 (119)
+.|+-|.+++...|.|..+.+++.+|+-...+++. .....-||..+++.++++|++.||..|
T Consensus 3 ~hI~~s~NNT~itlTd~~g~~~~~~S~G~~gfkg~--rk~t~~Aa~~~a~~~~~~~~~~gi~~v 64 (108)
T TIGR03632 3 AHIHATFNNTIVTITDPQGNVLSWASAGAVGFKGS--KKSTPYAAQLAAEDAAKKAKEFGMKTV 64 (108)
T ss_pred EEEEccCCCEEEEEEcCCCCEEEEEecCceeeCCC--ccCCHHHHHHHHHHHHHHHHHcCCcEE
Confidence 67899999999999999777777777766666653 356788999999999999999999876
No 13
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=96.58 E-value=0.02 Score=45.80 Aligned_cols=64 Identities=20% Similarity=0.327 Sum_probs=52.6
Q ss_pred eEEEEEecCCcEEEEEEECCCCe--EEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcCCcee
Q psy5246 53 HTLYFTTTKKHITGQIVHNNGNV--VVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGISEI 118 (119)
Q Consensus 53 pRL~V~rSnkhiyAQlIdd~~g~--L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~GI~~V 118 (119)
-+|+|.-|-+++.++|.|..+.+ |+-+|+-...+++. ..+.-=||+.+++.+|+.|++.||.+|
T Consensus 119 f~~vI~aSfNNTIVTlTD~~GNv~tl~WSSAG~~GFKGs--KKsTpfAAQ~aae~aakka~~~GIk~V 184 (233)
T PTZ00090 119 FMLVITTSKNNVHAQVVNKSKNYKTVFGSFAGNVGFRKK--LQQSERCAYRIGENIAKKCRRLGIFAV 184 (233)
T ss_pred EEEEEEeccCcEEEEEEeCCCCEEEEEEEcccccCcccC--ccCCHHHHHHHHHHHHHHHHHcCCeEE
Confidence 57999999999999999999995 66656555556543 245678999999999999999999876
No 14
>CHL00041 rps11 ribosomal protein S11
Probab=96.49 E-value=0.022 Score=40.90 Aligned_cols=64 Identities=11% Similarity=0.135 Sum_probs=54.1
Q ss_pred eEEEEEecCCcEEEEEEECCCCeEEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcCCcee
Q psy5246 53 HTLYFTTTKKHITGQIVHNNGNVVVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGISEI 118 (119)
Q Consensus 53 pRL~V~rSnkhiyAQlIdd~~g~L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~GI~~V 118 (119)
=-+.|+-|.+++...|.|..+.+|+.+|.-...+++. .....-||..+++.+++.|++.||..|
T Consensus 14 gi~hI~~t~NNTiiTlTd~~G~~l~~~S~G~~gfKg~--rK~T~~Aa~~~a~~~~~~~~~~gi~~v 77 (116)
T CHL00041 14 GVIHIQASFNNTIVTVTDVRGRVISWSSAGACGFKGA--RKGTPFAAQTAAENAIRTVIDQGMKRA 77 (116)
T ss_pred EEEEEEcccCCEEEEEEcCCCCEEEEEecCceeeCCC--ccCCHHHHHHHHHHHHHHHHHcCCcEE
Confidence 3789999999999999998876788888776667654 346778999999999999999999876
No 15
>PRK05309 30S ribosomal protein S11; Validated
Probab=96.38 E-value=0.033 Score=40.68 Aligned_cols=64 Identities=20% Similarity=0.180 Sum_probs=53.5
Q ss_pred eEEEEEecCCcEEEEEEECCCCeEEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcCCcee
Q psy5246 53 HTLYFTTTKKHITGQIVHNNGNVVVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGISEI 118 (119)
Q Consensus 53 pRL~V~rSnkhiyAQlIdd~~g~L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~GI~~V 118 (119)
..+.|+-|.++....|.|..+.+++.+|.-...+++. ..+...||..+++.+++.|++.||..|
T Consensus 18 gi~hI~~t~NNTiitlTd~~G~~~~~~S~G~~gfKg~--rK~T~~Aa~~aa~~~~~~~~~~gi~~v 81 (128)
T PRK05309 18 GVAHIHATFNNTIVTITDRQGNVISWASAGGLGFKGS--RKSTPYAAQVAAEDAAKKAKEHGMKTV 81 (128)
T ss_pred eEEEEEccCCCEEEEEEcCCCCEEEEEecCccEeCCC--ccCCHHHHHHHHHHHHHHHHHcCCcEE
Confidence 4899999999999999998777777777665566553 356788999999999999999999876
No 16
>KOG0875|consensus
Probab=94.99 E-value=0.031 Score=45.41 Aligned_cols=65 Identities=22% Similarity=0.133 Sum_probs=52.1
Q ss_pred eEEEEEecCCcEEEEEEE-CCCC-e-EEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHh-cCCce
Q psy5246 53 HTLYFTTTKKHITGQIVH-NNGN-V-VVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLE-TGISE 117 (119)
Q Consensus 53 pRL~V~rSnkhiyAQlId-d~~g-~-L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~-~GI~~ 117 (119)
+||.|..+|+.|.+||+- .-+| + +++|.+.|..-.+......|-.||+..|.+||.|+++ .|.++
T Consensus 49 yR~ivr~~n~~iicqi~~~~i~gd~v~~~a~s~elpkyg~~~GLtNyaAay~TglLLarR~l~~~gmD~ 117 (264)
T KOG0875|consen 49 YRMIVRVINKDIICQIAYATIEGDVIVRAAYAHELPKYGVKVGLTNYAAAYCTGLLLACRLLKRFGMDK 117 (264)
T ss_pred eEEEEEEechhhHHHHHhheecceEEEEeeccccccccccccccchhHHHHhhHHHHHHHHHHHhCccc
Confidence 899999999999999998 3344 5 8888888766554444568999999999999999986 55443
No 17
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=94.94 E-value=0.19 Score=37.92 Aligned_cols=65 Identities=17% Similarity=0.148 Sum_probs=51.8
Q ss_pred eEEEEEecCCcEEEEEEECCCCeEEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcCCcee
Q psy5246 53 HTLYFTTTKKHITGQIVHNNGNVVVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGISEI 118 (119)
Q Consensus 53 pRL~V~rSnkhiyAQlIdd~~g~L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~GI~~V 118 (119)
--+.|+-|-++....|.|..+.+++.+|+-...+++.. ..+.-=||...++.+|++|++.||..|
T Consensus 29 Gi~hI~as~NNTiItiTD~~G~~~~w~SsG~~gfKg~r-~KsTpyAAq~aa~~~a~k~~~~Gi~~v 93 (149)
T PTZ00129 29 GVAHIFASFNDTFIHVTDLSGRETLVRVTGGMKVKADR-DESSPYAAMMAAQDVAARCKELGINAL 93 (149)
T ss_pred EEEEEEcccCCeEEEEEcccCCEEEEEecCcceecccc-cCCCHHHHHHHHHHHHHHHHHcCCeEE
Confidence 57899999999999999988888777776665665431 123456899999999999999999876
No 18
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=94.83 E-value=0.2 Score=37.08 Aligned_cols=64 Identities=14% Similarity=0.085 Sum_probs=49.8
Q ss_pred eEEEEEecCCcEEEEEEECCCC-eEEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcCCcee
Q psy5246 53 HTLYFTTTKKHITGQIVHNNGN-VVVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGISEI 118 (119)
Q Consensus 53 pRL~V~rSnkhiyAQlIdd~~g-~L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~GI~~V 118 (119)
--+.|+-|-++....|.|..+. +|+.+|.-...+++. ..+.-=||...++.++++|++.||..|
T Consensus 10 gi~hI~as~NNTivtvTD~~G~~~~~~~S~G~~g~kg~--kK~TpyAAq~aae~~~~~~~~~Gi~~v 74 (132)
T PRK09607 10 GIAHIYASFNNTIITITDLTGAETIAKSSGGMVVKADR--DESSPYAAMQAAEKAAEDAKEKGITGV 74 (132)
T ss_pred eEEEEEcccCCeEEEEEcCCCCEEEEEecCcceeeCCC--ccCCHHHHHHHHHHHHHHHHHcCCcEE
Confidence 5789999999999999998876 466666554444321 234556899999999999999999876
No 19
>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=94.78 E-value=0.22 Score=35.93 Aligned_cols=63 Identities=14% Similarity=0.092 Sum_probs=48.9
Q ss_pred EEEEEecCCcEEEEEEECCCCe-EEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcCCcee
Q psy5246 54 TLYFTTTKKHITGQIVHNNGNV-VVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGISEI 118 (119)
Q Consensus 54 RL~V~rSnkhiyAQlIdd~~g~-L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~GI~~V 118 (119)
-+.|+-|-++....|.|..+.. |+-+|+-...+++. ..+.-=||...++.++++|++.||..|
T Consensus 4 i~hI~as~NNTiitvTD~~G~~~~~~~S~G~~g~kg~--kk~TpyAAq~aa~~~~~~~~~~Gi~~v 67 (114)
T TIGR03628 4 IAHIYSSFNNTIITITDITGAETIARSSGGMVVKADR--DESSPYAAMQAAGRAAEKAKERGITGL 67 (114)
T ss_pred EEEEEccCCCeEEEEEcCCCCEEEEEecCcceEeCCC--ccCCHHHHHHHHHHHHHHHHHcCCcEE
Confidence 4678889999999999888765 77766655544432 234567899999999999999999876
No 20
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=91.15 E-value=1.3 Score=32.80 Aligned_cols=63 Identities=21% Similarity=0.183 Sum_probs=48.6
Q ss_pred EEEEEecCCcEEEEEEECCCCeEEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcCCcee
Q psy5246 54 TLYFTTTKKHITGQIVHNNGNVVVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGISEI 118 (119)
Q Consensus 54 RL~V~rSnkhiyAQlIdd~~g~L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~GI~~V 118 (119)
-..|+.|-++....+-|..+..+..+|+=...+++.- .+.--||...++..|+.+++.||..|
T Consensus 20 vahI~asfNNTivtitD~~Gn~i~wassG~~gfk~~r--k~tpyAA~~aa~~aa~~a~e~Gi~~v 82 (129)
T COG0100 20 VAHIHASFNNTIVTITDLTGNVIIWASSGGMGFKGSR--KSTPYAAQLAAEDAAKKAKEHGIKSV 82 (129)
T ss_pred eEEEEcccCCcEEEecCCCCCEEEEEecCCceEcCCC--CCCHHHHHHHHHHHHHHHHHhCccEE
Confidence 3566677777666666666667889898877776542 46777889999999999999999876
No 21
>KOG0408|consensus
Probab=81.29 E-value=10 Score=29.49 Aligned_cols=65 Identities=11% Similarity=0.152 Sum_probs=50.0
Q ss_pred eeEEEEEecCCcEEEEEEECCCCeEEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcCCcee
Q psy5246 52 WHTLYFTTTKKHITGQIVHNNGNVVVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGISEI 118 (119)
Q Consensus 52 ~pRL~V~rSnkhiyAQlIdd~~g~L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~GI~~V 118 (119)
+|-+.|.-|-++...||.|..+-++.++|----.+++. ..+.--||...|-..+.++.+.|+..|
T Consensus 79 iPi~hIraS~NNTivtVtd~kg~vi~~~ScgteGFrnt--rkgT~iAaQtaavaa~~r~v~~G~~~v 143 (190)
T KOG0408|consen 79 IPIIHIRASFNNTIVTVTDVKGEVISWSSCGTEGFRNT--RKGTPIAAQTAAVAAIRRAVDQGMQTV 143 (190)
T ss_pred cceEEEEecCCCeEEEEEccCCcEEEEeeccccccccc--ccCCchhHHHHHHHHHHHHHHhcceEE
Confidence 48899999999999999988777666655544456653 234566788888889999999998765
No 22
>KOG0407|consensus
Probab=70.85 E-value=21 Score=26.22 Aligned_cols=64 Identities=16% Similarity=0.159 Sum_probs=43.3
Q ss_pred eEEEEEecCCcEEEEEEECCCCe-EEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcCCcee
Q psy5246 53 HTLYFTTTKKHITGQIVHNNGNV-VVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGISEI 118 (119)
Q Consensus 53 pRL~V~rSnkhiyAQlIdd~~g~-L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~GI~~V 118 (119)
--..||-|-+..++.|-|-.+.. |+-...--+ ++.. ...+.--||-+.++.+|.+|++.||+.+
T Consensus 17 gvahi~asfndtfvhitdlsg~eti~rvtggmk-vkad-rdesspyaamlaaqdva~kck~~gi~al 81 (139)
T KOG0407|consen 17 GVAHIFASFNDTFVHVTDLSGKETIVRVTGGMK-VKAD-RDESSPYAAMLAAQDVAAKCKELGITAL 81 (139)
T ss_pred eEEEEEeecccceEEEeccCCceEEEEecCCeE-Eecc-cccCChHHHHHHHHHHHHHHHhcCeeEE
Confidence 34567888888888887766665 766543221 1111 1124567888999999999999999854
No 23
>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=37.03 E-value=46 Score=29.16 Aligned_cols=27 Identities=15% Similarity=0.393 Sum_probs=24.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcCCcee
Q psy5246 92 NTNDICAYSNLARVLAQRCLETGISEI 118 (119)
Q Consensus 92 ~~~n~~aA~~vG~~lAera~~~GI~~V 118 (119)
.+++++.++..|..||+++++.|++-|
T Consensus 314 ~gt~~~~a~~~g~eIa~~Lk~dgVDAv 340 (431)
T TIGR01917 314 NGTAVANSKQFAKEFSKELLAAGVDAV 340 (431)
T ss_pred CCccHHHHHHHHHHHHHHHHHcCCCEE
Confidence 467888999999999999999999976
No 24
>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=36.11 E-value=69 Score=21.76 Aligned_cols=23 Identities=0% Similarity=0.068 Sum_probs=20.3
Q ss_pred eEEEEEecCCcEEEEEEECCCCe
Q psy5246 53 HTLYFTTTKKHITGQIVHNNGNV 75 (119)
Q Consensus 53 pRL~V~rSnkhiyAQlIdd~~g~ 75 (119)
-++.|......++++|||.++|.
T Consensus 57 l~F~vde~~~~~vVkViD~~T~e 79 (107)
T PF03646_consen 57 LRFSVDEESGRVVVKVIDKETGE 79 (107)
T ss_dssp EEEEEEEETTEEEEEEEETTT-S
T ss_pred eEEEEecCCCcEEEEEEECCCCc
Confidence 68999999999999999999985
No 25
>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=31.50 E-value=18 Score=23.26 Aligned_cols=47 Identities=15% Similarity=0.197 Sum_probs=26.6
Q ss_pred EEEEecCC--cEEEEEEECCCCe-EEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHh
Q psy5246 55 LYFTTTKK--HITGQIVHNNGNV-VVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLE 112 (119)
Q Consensus 55 L~V~rSnk--hiyAQlIdd~~g~-L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~ 112 (119)
.+.+..+. ++.+.+.+.++.. +..++- .++.+.+..+|+.+|+..++
T Consensus 25 ~a~~~~~~~l~l~~~v~~~dG~~~~~~~~~-----------~~~~~~a~~lg~~la~~l~~ 74 (74)
T PF03900_consen 25 YAKIEGDERLRLRAMVGSPDGSRIIIRVEI-----------TGPIEDAEELGKKLAEELLA 74 (74)
T ss_dssp EEEEETTE-EEEEEEEE-TTSSSEEEEEEE-----------EE-GGGHCCHHHHHHHHHHH
T ss_pred EEEEcCCCEEEEEEEEECCCCCEEEEEEEE-----------EcCHHHHHHHHHHHHHHHhC
Confidence 34444555 5556666655544 443331 12556778899999988764
No 26
>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=31.21 E-value=64 Score=28.31 Aligned_cols=27 Identities=11% Similarity=0.276 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcCCcee
Q psy5246 92 NTNDICAYSNLARVLAQRCLETGISEI 118 (119)
Q Consensus 92 ~~~n~~aA~~vG~~lAera~~~GI~~V 118 (119)
.+++...++..|..||+++++.|++.|
T Consensus 314 ~gt~~~~a~~~g~eIa~~Lk~dgVDAV 340 (431)
T TIGR01918 314 NGTTVAESKQFAKEFVVELKQGGVDAV 340 (431)
T ss_pred CCchHHHHHHHHHHHHHHHHHcCCCEE
Confidence 456888999999999999999999976
No 27
>TIGR00212 hemC porphobilinogen deaminase. Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin
Probab=31.05 E-value=1.8e+02 Score=24.16 Aligned_cols=40 Identities=18% Similarity=0.310 Sum_probs=26.8
Q ss_pred cEEEEEEECCCCeEEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcC
Q psy5246 63 HITGQIVHNNGNVVVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETG 114 (119)
Q Consensus 63 hiyAQlIdd~~g~L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~G 114 (119)
++++.+.++++..++.++. .++.+.| .+|..+|+..++.|
T Consensus 253 ~l~~~v~~~dG~~~~~~~~-----------~g~~~~a-~lG~~la~~l~~~g 292 (292)
T TIGR00212 253 TLIAMVADLDGKEVIREEK-----------EGNIEDA-ELGTEVAEELLKRG 292 (292)
T ss_pred EEEEEEECCCCCEEEEEEE-----------ecCHHHH-HHHHHHHHHHHhcC
Confidence 5666666665555444332 1345667 99999999998876
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=30.36 E-value=59 Score=27.72 Aligned_cols=27 Identities=15% Similarity=0.304 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcCCcee
Q psy5246 92 NTNDICAYSNLARVLAQRCLETGISEI 118 (119)
Q Consensus 92 ~~~n~~aA~~vG~~lAera~~~GI~~V 118 (119)
.+.+++.++..|..||+.+++.|++-|
T Consensus 318 ~gt~~~~~~~~g~eIa~~Lk~dgVDAV 344 (349)
T PF07355_consen 318 NGTAVANAKRFGPEIAKELKEDGVDAV 344 (349)
T ss_pred CCccHHHHHHHHHHHHHHHHHcCCCEE
Confidence 456888899999999999999999976
No 29
>PF02961 BAF: Barrier to autointegration factor; InterPro: IPR004122 Barrier-to-autointegration factor (BAF) is an essential protein that is highly conserved in metazoan evolution, and which may act as a DNA-bridging protein []. BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filament proteins that anchor nuclear-pore complexes in place, and nuclear LEM-domain proteins that bind to laminins filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organisation, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans []. BAF can be exploited by retroviruses to act as a host component of pre-integration complexes, which promote the integration of the retroviral DNA into the host chromosome by preventing autointegration of retroviral DNA []. BAF might contribute to the assembly or activity of retroviral pre-integration complexes through direct binding to the retroviral proteins p55 Gag and matrix, as well as to DNA.; GO: 0003677 DNA binding; PDB: 2ODG_A 2BZF_A 2EZX_B 2EZY_B 1QCK_B 1CI4_B 2EZZ_B.
Probab=27.76 E-value=45 Score=23.19 Aligned_cols=24 Identities=21% Similarity=0.410 Sum_probs=15.6
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCce
Q psy5246 94 NDICAYSNLARVLAQRCLETGISE 117 (119)
Q Consensus 94 ~n~~aA~~vG~~lAera~~~GI~~ 117 (119)
..+..-.=||.+++.++.++|+++
T Consensus 19 K~V~~laGIG~~lg~~L~~~GfdK 42 (89)
T PF02961_consen 19 KPVTELAGIGPVLGKRLEEKGFDK 42 (89)
T ss_dssp -BGGGSTT--HHHHHHHHHTT--B
T ss_pred CCccccCCcCHHHHHHHHHCCCcH
Confidence 345555679999999999999986
No 30
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=27.23 E-value=33 Score=18.93 Aligned_cols=15 Identities=20% Similarity=0.357 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHhcCC
Q psy5246 101 NLARVLAQRCLETGI 115 (119)
Q Consensus 101 ~vG~~lAera~~~GI 115 (119)
=||+.++++..+.||
T Consensus 18 GIG~kt~~kL~~~GI 32 (32)
T PF11798_consen 18 GIGKKTAKKLNKLGI 32 (32)
T ss_dssp TS-HHHHHHHHCTT-
T ss_pred CccHHHHHHHHHccC
Confidence 378999999988887
No 31
>PRK07738 flagellar protein FlaG; Provisional
Probab=26.48 E-value=1.3e+02 Score=21.76 Aligned_cols=24 Identities=17% Similarity=0.105 Sum_probs=21.6
Q ss_pred eEEEEEecCCcEEEEEEECCCCeE
Q psy5246 53 HTLYFTTTKKHITGQIVHNNGNVV 76 (119)
Q Consensus 53 pRL~V~rSnkhiyAQlIdd~~g~L 76 (119)
-+..|+.....++++|||.++|.+
T Consensus 66 L~F~vdeet~~~vVkVvD~~T~EV 89 (117)
T PRK07738 66 LKFELHEKLNEYYVQVVDERTNEV 89 (117)
T ss_pred eEEEEecCCCcEEEEEEECCCCee
Confidence 689999999999999999998863
No 32
>PRK13690 hypothetical protein; Provisional
Probab=25.23 E-value=1.6e+02 Score=23.11 Aligned_cols=43 Identities=23% Similarity=0.310 Sum_probs=33.3
Q ss_pred CCe-EEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcCCc
Q psy5246 73 GNV-VVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGIS 116 (119)
Q Consensus 73 ~g~-L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~GI~ 116 (119)
+.. ++.+||.|-. -+.+++.++.+.|..|=..|-+-+.+.||.
T Consensus 26 g~i~VvGcSTSEV~-G~~IGt~ss~eva~~i~~~l~~~~~~~gi~ 69 (184)
T PRK13690 26 GQIFVLGCSTSEVL-GERIGTAGSLEVAEAIVEALLEVLKETGIH 69 (184)
T ss_pred CCEEEEecchHhhC-CcccCCcChHHHHHHHHHHHHHHhhhcCcE
Confidence 346 8899999853 334556688899999999888888899885
No 33
>PF04260 DUF436: Protein of unknown function (DUF436) ; InterPro: IPR006340 Members of this family are uncharacterised proteins of about 180 amino acids from the Bacillus/Clostridium group of Gram-positive bacteria, found in no more than one copy per genome. ; PDB: 1V8D_C.
Probab=24.63 E-value=1.7e+02 Score=22.72 Aligned_cols=43 Identities=26% Similarity=0.276 Sum_probs=26.9
Q ss_pred CCe-EEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcCCc
Q psy5246 73 GNV-VVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGIS 116 (119)
Q Consensus 73 ~g~-L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~GI~ 116 (119)
+.. ++.+||.|-.= ..+.+.++.+.|..|=+.|-+-+.+.||.
T Consensus 19 g~i~VvGcSTSEV~G-~~IGt~~s~eva~ai~~~l~~~~~~~gi~ 62 (172)
T PF04260_consen 19 GQIFVVGCSTSEVAG-ERIGTASSLEVAEAIFEALLEVLKERGIY 62 (172)
T ss_dssp T-EEEEEE-HHHHHT-T-------HHHHHHHHHHHHHHHHTTT-E
T ss_pred CCEEEEeeeHHHcCC-cccCCCCcHHHHHHHHHHHHHHHHHcCcE
Confidence 346 88999998542 33456688899999999999999999885
No 34
>PLN02691 porphobilinogen deaminase
Probab=20.86 E-value=3.5e+02 Score=23.13 Aligned_cols=43 Identities=12% Similarity=0.147 Sum_probs=27.9
Q ss_pred cEEEEEEECCCCeEEEEEcchHHhhhcccCCCCHHHHHHHHHHHHHHHHhcC
Q psy5246 63 HITGQIVHNNGNVVVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETG 114 (119)
Q Consensus 63 hiyAQlIdd~~g~L~sAST~e~~ik~~l~~~~n~~aA~~vG~~lAera~~~G 114 (119)
++.+.+.+++++.++.++... ..+.+.|..+|+.+|+..++.|
T Consensus 301 ~l~~~v~s~dG~~~~~~~~~g---------~~~~~~a~~lG~~la~~ll~~g 343 (351)
T PLN02691 301 DFRGLVASPDGKQVLETSRKG---------PYVIDDAVAMGKDAGKELKSKA 343 (351)
T ss_pred EEEEEEECCCCCEEEEEEEec---------CCCHHHHHHHHHHHHHHHHHhh
Confidence 455566666555555443211 0146678999999999998876
No 35
>PF05589 DUF768: Protein of unknown function (DUF768); InterPro: IPR008486 This family consists of several uncharacterised hypothetical proteins from Rhizobium loti (Mesorhizobium loti).
Probab=20.15 E-value=1.7e+02 Score=19.02 Aligned_cols=24 Identities=29% Similarity=0.333 Sum_probs=20.4
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCCc
Q psy5246 93 TNDICAYSNLARVLAQRCLETGIS 116 (119)
Q Consensus 93 ~~n~~aA~~vG~~lAera~~~GI~ 116 (119)
..++-++..+.+.+..-|+++||.
T Consensus 22 ~~d~is~~~La~kl~adA~a~Gi~ 45 (64)
T PF05589_consen 22 KADIISAAELAEKLFADAEAAGIP 45 (64)
T ss_pred ccchhhHHHHHHHHHHHHHHcCCC
Confidence 356778888999999999999986
No 36
>PRK08452 flagellar protein FlaG; Provisional
Probab=20.04 E-value=1.7e+02 Score=21.20 Aligned_cols=24 Identities=17% Similarity=0.206 Sum_probs=20.9
Q ss_pred eEEEEEecCCcEEEEEEECCCCeE
Q psy5246 53 HTLYFTTTKKHITGQIVHNNGNVV 76 (119)
Q Consensus 53 pRL~V~rSnkhiyAQlIdd~~g~L 76 (119)
-+.+++....-+|++|+|.++|.|
T Consensus 73 L~F~~de~~~~~vVkVvD~~T~eV 96 (124)
T PRK08452 73 IRFGYNDKIKGLVVSVKEANGGKV 96 (124)
T ss_pred eEEEEcCCCCcEEEEEEECCCCce
Confidence 578888888899999999998863
Done!