Query psy14597
Match_columns 191
No_of_seqs 154 out of 1015
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 15:43:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14597.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14597hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3280|consensus 100.0 1.3E-51 2.8E-56 338.4 9.5 148 11-163 2-163 (171)
2 PTZ00076 60S ribosomal protein 100.0 1.6E-42 3.4E-47 299.5 14.8 140 23-170 19-172 (253)
3 COG0203 RplQ Ribosomal protein 100.0 2.9E-41 6.2E-46 263.7 10.6 103 17-126 1-116 (116)
4 TIGR00059 L17 ribosomal protei 100.0 8.2E-41 1.8E-45 260.6 11.2 97 24-127 3-112 (112)
5 PRK05591 rplQ 50S ribosomal pr 100.0 1.1E-40 2.4E-45 260.2 11.2 98 22-126 3-113 (113)
6 PF01196 Ribosomal_L17: Riboso 100.0 1.2E-36 2.6E-41 231.7 8.5 86 36-126 1-97 (97)
7 COG2406 Protein distantly rela 32.2 54 0.0012 27.7 3.2 70 78-166 59-128 (172)
8 PF02762 Cbl_N3: CBL proto-onc 28.7 44 0.00095 25.4 2.0 57 88-157 17-74 (86)
9 PF05848 CtsR: Firmicute trans 28.3 9.8 0.00021 31.6 -1.7 38 87-129 45-92 (152)
10 PF10213 MRP-S28: Mitochondria 19.8 95 0.0021 24.7 2.5 53 77-154 41-93 (127)
No 1
>KOG3280|consensus
Probab=100.00 E-value=1.3e-51 Score=338.42 Aligned_cols=148 Identities=36% Similarity=0.587 Sum_probs=142.3
Q ss_pred hhhcccccccccCCCCCCCcHHHHHHHHHHHHHHHhcCceEechhhHHhhc--------------cCChHHHHHHHHhcc
Q psy14597 11 SRLRIPILAKHRRLRNPEGPQGRVKKLRSIVTALLKYERIEVYHYDGDEAR--------------DTHKETMDMADFWIE 76 (191)
Q Consensus 11 ~~lr~~~~~~~R~~k~~~~~~hR~alLRnlvTsLikhERIeTT~~KAKElR--------------~~~~~t~r~a~~~L~ 76 (191)
+++++.|+|-.+++|+|++++||+++||||||+||+||||||||+||||+| ++|+++|+|+++||.
T Consensus 2 ~~~~~amt~~~~~~Klgr~~~~R~~lLR~lvt~LvkHErIe~t~ara~Ear~~aEklIt~~~k~g~~~~~~~~~a~~~l~ 81 (171)
T KOG3280|consen 2 PRIGVAMTHGRRKLKLGRPPAHRLALLRNLVTQLVKHERIETTWARAKEARRYAEKLITLGKKAGSLHERTARMADGWLR 81 (171)
T ss_pred CceeEEecccchhhhcCCCcHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhcCcHhHHHHHHHhcccc
Confidence 678999999888999999999999999999999999999999999999999 678999999999999
Q ss_pred chhHHHHHHhhhhhhcCCCCCCeeeEEecCCCCCCCCCCCCCceEEEEecCCCCCCCcccCcCchhhHHHHHHHHHHHHH
Q psy14597 77 EKNIVHKLFKVLVPRFQNTTVSYTRAYNAPIPHATPEKSDLSFHSVIELRGNPFPPLVQRAVDSRLHIQNVLLDEAKKEY 156 (191)
Q Consensus 77 ek~lv~KLF~~LaPRy~~R~GGYTRI~kl~~R~~~~~~gD~A~mAiLELvgnp~ppl~~~~~~~~~~l~NvLl~~ar~e~ 156 (191)
++++|+|||+||||||.+|+|||||++|+|+|+ ||+|||||||++|||+|++..+.+++.++||||||.++.++|
T Consensus 82 ekdli~KlF~vl~pRY~dr~ggYTRllrlppr~-----~d~apmavlE~~Gn~~p~~~a~~p~~r~~lh~vll~~l~r~~ 156 (171)
T KOG3280|consen 82 EKDLLHKLFTVLAPRYKDRNGGYTRLLRLPPRR-----GDRAPMAVLELVGNPLPQQAADRPDTRVNLHKVLLFRLLREF 156 (171)
T ss_pred cchHHHHHHHHhchhhccCCCCceehhccCccc-----ccccCceeeeecCCccccccCCCchhhhhhHHHHHHHHHHHh
Confidence 999999999999999999999999999999999 999999999999999999999999999999999999999999
Q ss_pred HHHHHHH
Q psy14597 157 RAQKYAE 163 (191)
Q Consensus 157 ~~~k~~~ 163 (191)
+.++-++
T Consensus 157 ~~~~~e~ 163 (171)
T KOG3280|consen 157 RPPKEEK 163 (171)
T ss_pred ccchhhc
Confidence 9766544
No 2
>PTZ00076 60S ribosomal protein L17; Provisional
Probab=100.00 E-value=1.6e-42 Score=299.50 Aligned_cols=140 Identities=21% Similarity=0.311 Sum_probs=127.4
Q ss_pred CCCCCCCcHHHHHHHHHHHHHHHhcCceEechhhHHhhcc-----------CChHHHHHHHHhccchhHHHHHHhhhhhh
Q psy14597 23 RLRNPEGPQGRVKKLRSIVTALLKYERIEVYHYDGDEARD-----------THKETMDMADFWIEEKNIVHKLFKVLVPR 91 (191)
Q Consensus 23 ~~k~~~~~~hR~alLRnlvTsLikhERIeTT~~KAKElR~-----------~~~~t~r~a~~~L~ek~lv~KLF~~LaPR 91 (191)
..++|++++||++|||||+|+||+||||+||++||||+|. ......+++.+||.++++|+|||++||||
T Consensus 19 ~rKLgR~ssHR~AlLRNLvtsLI~hERIeTTlaKAKELR~~AEKLITlAKk~tl~sRR~a~s~L~d~~av~KLF~eLAPR 98 (253)
T PTZ00076 19 FRRAHGQPHHRWDSIKNQLDELLRYGRLELTLPRAKELQQYAEELIYLAKKDTPESNLKVESMLRTPQGRRKLYEKYVPL 98 (253)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHHcCcEEecHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCHHHHHHHHHHhhhH
Confidence 4456889999999999999999999999999999999992 12223388889999999999999999999
Q ss_pred cCCCCCCeeeEEec-CCCCCCCCCCCCCceEEEEecCCC--CCCCcccCcCchhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy14597 92 FQNTTVSYTRAYNA-PIPHATPEKSDLSFHSVIELRGNP--FPPLVQRAVDSRLHIQNVLLDEAKKEYRAQKYAEIAQDL 168 (191)
Q Consensus 92 y~~R~GGYTRI~kl-~~R~~~~~~gD~A~mAiLELvgnp--~ppl~~~~~~~~~~l~NvLl~~ar~e~~~~k~~~~~~~~ 168 (191)
|++|+||||||+|+ ++|. ||+|+|||||||++| ++|..+++.+..++|+| +++..|++|+ ||.++|.++
T Consensus 99 Y~dR~GGYTRIlK~~g~R~-----GD~ApMAiIELVd~p~e~r~A~pvg~d~~~~i~~-~~~~~r~~~r--~~~~~~~~~ 170 (253)
T PTZ00076 99 YRDRPFFFTRVVNQWRLRL-----RDAAPMAYIEFVDRPGEIRPAKPVGFDKIKYIYE-EMKKTRRNFR--KYFNIAKKF 170 (253)
T ss_pred hcCCCCCeeEEEeCCCCCC-----CCCCCEEEEEeccCcCccccccccchhHHHHHHH-HHHHHHhhHH--HHHHHHHHh
Confidence 99999999999997 6888 999999999999988 88888899999999999 9999999999 999999987
Q ss_pred hh
Q psy14597 169 ES 170 (191)
Q Consensus 169 ~~ 170 (191)
+-
T Consensus 171 ~l 172 (253)
T PTZ00076 171 GL 172 (253)
T ss_pred Cc
Confidence 64
No 3
>COG0203 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-41 Score=263.68 Aligned_cols=103 Identities=26% Similarity=0.359 Sum_probs=97.1
Q ss_pred ccccccCCCCCCCcHHHHHHHHHHHHHHHhcCceEechhhHHhhc-------------cCChHHHHHHHHhccchhHHHH
Q psy14597 17 ILAKHRRLRNPEGPQGRVKKLRSIVTALLKYERIEVYHYDGDEAR-------------DTHKETMDMADFWIEEKNIVHK 83 (191)
Q Consensus 17 ~~~~~R~~k~~~~~~hR~alLRnlvTsLikhERIeTT~~KAKElR-------------~~~~~t~r~a~~~L~ek~lv~K 83 (191)
|+|++...+++++++||.+|||||+++||+||+|+||++||||+| ++|++ |+|..||.|+++|+|
T Consensus 1 Mrh~~~~rkl~rtsshR~amlrnla~sLi~he~I~TT~~KAKelr~~vEkLITlaK~~~l~~R--R~a~~~l~d~~~v~k 78 (116)
T COG0203 1 MRHRKKGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLANR--RLAFARLRDKDAVKK 78 (116)
T ss_pred CCCCccCCCCCCCHHHHHHHHHHHHHHHHHcCceeecHHHHHHHHHHHHHHHHHhhcccHHHH--HHHHHHcccHHHHHH
Confidence 467777888899999999999999999999999999999999999 34555 999999999999999
Q ss_pred HHhhhhhhcCCCCCCeeeEEecCCCCCCCCCCCCCceEEEEec
Q psy14597 84 LFKVLVPRFQNTTVSYTRAYNAPIPHATPEKSDLSFHSVIELR 126 (191)
Q Consensus 84 LF~~LaPRy~~R~GGYTRI~kl~~R~~~~~~gD~A~mAiLELv 126 (191)
||++|+|||.+|+||||||+|+|+|+ ||+|||||||||
T Consensus 79 LF~~iapry~~R~GGYtRIlK~g~R~-----GD~A~maiiElV 116 (116)
T COG0203 79 LFDEIAPRYAERNGGYTRILKLGFRR-----GDNAPMAIIELV 116 (116)
T ss_pred HHHHhChhhcCCCCCeeEEEecCCCC-----CCCCceEEEEeC
Confidence 99999999999999999999999999 999999999997
No 4
>TIGR00059 L17 ribosomal protein L17. Eubacterial and mitochondrial. The mitochondrial form, from yeast, contains an additional 110 amino acids C-terminal to the region found by this model.
Probab=100.00 E-value=8.2e-41 Score=260.60 Aligned_cols=97 Identities=28% Similarity=0.390 Sum_probs=91.8
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHhcCceEechhhHHhhc-------------cCChHHHHHHHHhccchhHHHHHHhhhhh
Q psy14597 24 LRNPEGPQGRVKKLRSIVTALLKYERIEVYHYDGDEAR-------------DTHKETMDMADFWIEEKNIVHKLFKVLVP 90 (191)
Q Consensus 24 ~k~~~~~~hR~alLRnlvTsLikhERIeTT~~KAKElR-------------~~~~~t~r~a~~~L~ek~lv~KLF~~LaP 90 (191)
.++|++++||++|||||+|+||+||||+||++||||+| ++|.+ +++.+||.|+++|+|||++|+|
T Consensus 3 ~klgr~~~hR~allrnl~tsLi~herI~TT~~KAKelr~~aEklIt~AK~~~~~~r--R~~~~~l~~~~~v~KLf~~lap 80 (112)
T TIGR00059 3 RKLGRTSAHRKALLRNLASALIRHEKIKTTLAKAKELRRVVEKLITLAKVDNFNNR--REAKAYIRNKEIVHKLFSEIAP 80 (112)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHCCeEEECHHHHHHHHHHHHHHHHHhcCCChHHH--HHHHHHhCCHHHHHHHHHHHHH
Confidence 46789999999999999999999999999999999999 34555 9999999999999999999999
Q ss_pred hcCCCCCCeeeEEecCCCCCCCCCCCCCceEEEEecC
Q psy14597 91 RFQNTTVSYTRAYNAPIPHATPEKSDLSFHSVIELRG 127 (191)
Q Consensus 91 Ry~~R~GGYTRI~kl~~R~~~~~~gD~A~mAiLELvg 127 (191)
||++|+||||||+|+++|. ||+|||||||||+
T Consensus 81 ry~~R~GGYTRI~kl~~R~-----gD~A~maiiElVd 112 (112)
T TIGR00059 81 RYAQRPGGYTRILKLGPRR-----GDAAEMAIIELVD 112 (112)
T ss_pred HhCCCCCCeEEEEECCCCC-----CCCCCeEEEEecC
Confidence 9999999999999999998 9999999999995
No 5
>PRK05591 rplQ 50S ribosomal protein L17; Validated
Probab=100.00 E-value=1.1e-40 Score=260.19 Aligned_cols=98 Identities=30% Similarity=0.392 Sum_probs=92.2
Q ss_pred cCCCCCCCcHHHHHHHHHHHHHHHhcCceEechhhHHhhc-------------cCChHHHHHHHHhccchhHHHHHHhhh
Q psy14597 22 RRLRNPEGPQGRVKKLRSIVTALLKYERIEVYHYDGDEAR-------------DTHKETMDMADFWIEEKNIVHKLFKVL 88 (191)
Q Consensus 22 R~~k~~~~~~hR~alLRnlvTsLikhERIeTT~~KAKElR-------------~~~~~t~r~a~~~L~ek~lv~KLF~~L 88 (191)
+..++|++++||++|||||+|+||+||||+||++||||+| ++|.+ +++.+||.|+++|+|||++|
T Consensus 3 ~~rkl~r~~~hR~allrnl~tsLi~herI~TT~~KAKelr~~aEklIt~aK~~~~~~r--R~~~~~L~~~~~v~KLf~~l 80 (113)
T PRK05591 3 KGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLHAR--RQAFARLRDKEAVHKLFDEI 80 (113)
T ss_pred CCCCCCCChHHHHHHHHHHHHHHHHcCeEEecHHHHHHHHHHHHHHHHHhhcCChHHH--HHHHHHhCCHHHHHHHHHHH
Confidence 3556799999999999999999999999999999999999 34555 99999999999999999999
Q ss_pred hhhcCCCCCCeeeEEecCCCCCCCCCCCCCceEEEEec
Q psy14597 89 VPRFQNTTVSYTRAYNAPIPHATPEKSDLSFHSVIELR 126 (191)
Q Consensus 89 aPRy~~R~GGYTRI~kl~~R~~~~~~gD~A~mAiLELv 126 (191)
+|||++|+||||||+|+|+|. ||+|+|||||||
T Consensus 81 apry~~R~GGYTRI~k~~~R~-----gD~A~ma~iElV 113 (113)
T PRK05591 81 APRYADRNGGYTRILKLGFRR-----GDNAPMAIIELV 113 (113)
T ss_pred HHHhCcCCCCeEEEEECCCCC-----CCCCCeEEEEeC
Confidence 999999999999999999998 999999999997
No 6
>PF01196 Ribosomal_L17: Ribosomal protein L17; InterPro: IPR000456 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 L17 is one of the proteins from the large ribosomal subunit. Bacterial L17 is a protein of 120 to 130 amino-acid residues while yeast YmL8 is twice as large (238 residues). The N-terminal half of YmL8 is colinear with the sequence of L17 from Escherichia coli.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3F1F_R 1VSP_L 3PYV_N 3PYR_N 3PYO_N 1VSA_L 3MS1_N 3F1H_R 3D5B_R 3MRZ_N ....
Probab=100.00 E-value=1.2e-36 Score=231.69 Aligned_cols=86 Identities=34% Similarity=0.477 Sum_probs=79.9
Q ss_pred HHHHHHHHHHhcCceEechhhHHhhcc-----------CChHHHHHHHHhccchhHHHHHHhhhhhhcCCCCCCeeeEEe
Q psy14597 36 KLRSIVTALLKYERIEVYHYDGDEARD-----------THKETMDMADFWIEEKNIVHKLFKVLVPRFQNTTVSYTRAYN 104 (191)
Q Consensus 36 lLRnlvTsLikhERIeTT~~KAKElR~-----------~~~~t~r~a~~~L~ek~lv~KLF~~LaPRy~~R~GGYTRI~k 104 (191)
|||||+|+||+||||+||++||||+|. .+..+++++.+||.|+++++|||++|+|||++|+||||||+|
T Consensus 1 llrnlvt~Li~herI~TT~~KAke~r~~aErlIt~ak~~~~~~~r~~~~~l~~~~~v~KLf~~l~pRy~~r~GgYTRi~k 80 (97)
T PF01196_consen 1 LLRNLVTSLIRHERIETTLAKAKELRPYAERLITLAKKGDLHARRQALSWLRDKELVKKLFKELAPRYADRNGGYTRIIK 80 (97)
T ss_dssp HHHHHHHHHHHHSEEEEEHHHHHHHHHHHHHHHHHHTSSTHHHHHHHHHCSSSHHHHHHHHTTHHHHTTTSSS-SEEEEE
T ss_pred ChHHHHHHHHhCCeEEecHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHhcchHHHHHHHHHHHHHHccCCCCeEEEEe
Confidence 799999999999999999999999992 244556999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCCCCceEEEEec
Q psy14597 105 APIPHATPEKSDLSFHSVIELR 126 (191)
Q Consensus 105 l~~R~~~~~~gD~A~mAiLELv 126 (191)
+|+|. ||+|+|||||||
T Consensus 81 l~~R~-----gD~A~maiiElV 97 (97)
T PF01196_consen 81 LGPRR-----GDAAPMAIIELV 97 (97)
T ss_dssp EEECS-----SSTCEEEEEEET
T ss_pred CCCCC-----CCCCCEEEEEeC
Confidence 99998 999999999997
No 7
>COG2406 Protein distantly related to bacterial ferritins [General function prediction only]
Probab=32.17 E-value=54 Score=27.72 Aligned_cols=70 Identities=21% Similarity=0.272 Sum_probs=50.9
Q ss_pred hhHHHHHHhhhhhhcCCCCCCeeeEEecCCCCCCCCCCCCCceEEEEecCCCCCCCcccCcCchhhHHHHHHHHHHHHHH
Q psy14597 78 KNIVHKLFKVLVPRFQNTTVSYTRAYNAPIPHATPEKSDLSFHSVIELRGNPFPPLVQRAVDSRLHIQNVLLDEAKKEYR 157 (191)
Q Consensus 78 k~lv~KLF~~LaPRy~~R~GGYTRI~kl~~R~~~~~~gD~A~mAiLELvgnp~ppl~~~~~~~~~~l~NvLl~~ar~e~~ 157 (191)
+.-..|-|+-|+||..+-.|+--|=++ .+ -++-|=|+|+||..+.| -.-++-||+++-+=..+
T Consensus 59 r~E~r~H~e~i~~Ri~elg~~~Prd~~------~l----------~dISgC~~a~LPedp~D-~~~~l~vlv~AE~CAir 121 (172)
T COG2406 59 REEDRKHFELIAPRIYELGGDLPRDMK------KL----------HDISGCKPAYLPEDPYD-IDEILAVLVKAERCAIR 121 (172)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCchhHH------HH----------HhhcCCCCCCCCCCccC-HHHHHHHHHHHHHHHHH
Confidence 344788999999999988776333222 11 14557899999977555 55678889998777777
Q ss_pred HHHHHHHHH
Q psy14597 158 AQKYAEIAQ 166 (191)
Q Consensus 158 ~~k~~~~~~ 166 (191)
-|+||.+
T Consensus 122 --~ykeic~ 128 (172)
T COG2406 122 --AYKEICN 128 (172)
T ss_pred --HHHHHHc
Confidence 8999886
No 8
>PF02762 Cbl_N3: CBL proto-oncogene N-terminus, SH2-like domain; InterPro: IPR014742 Cbl (Casitas B-lineage lymphoma) is an adaptor protein that functions as a negative regulator of many signalling pathways that start from receptors at the cell surface. The N-terminal region of Cbl contains a Cbl-type phosphotyrosine-binding (Cbl-PTB) domain, which is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle (4H) domain, an EF hand-like calcium-binding domain, and a divergent SH2-like domain. The calcium-bound EF-hand wedges between the 4H and SH2 domains, and roughly determines their relative orientation. The Cbl-PTB domain has also been named Cbl N-terminal (Cbl-N) or tyrosine kinase binding (TKB) domain [, ]. The N-terminal 4H domain contains four long alpha-helices. The C and D helices in this domain pack against the adjacent EF-hand-like domain, and a highly conserved loop connecting the A and B helices contacts the SH2-like domain. The EF-hand motif is similar to classical EF-hand proteins. The SH2-like domain retains the general helix-sheet-helix architecture of the SH2 fold, but lacks the secondary beta-sheet, comprising beta-strands D', E and F, and also a prominent BG loop []. This entry represents the SH2-like domain.; PDB: 3PFV_A 3VGO_A 3PLF_B 2Y1M_A 2CBL_A 3BUX_B 3BUN_B 3BUM_B 3OB1_B 3BUW_B ....
Probab=28.72 E-value=44 Score=25.36 Aligned_cols=57 Identities=9% Similarity=0.096 Sum_probs=31.9
Q ss_pred hhhhcCCCCCCeeeEEecC-CCCCCCCCCCCCceEEEEecCCCCCCCcccCcCchhhHHHHHHHHHHHHHH
Q psy14597 88 LVPRFQNTTVSYTRAYNAP-IPHATPEKSDLSFHSVIELRGNPFPPLVQRAVDSRLHIQNVLLDEAKKEYR 157 (191)
Q Consensus 88 LaPRy~~R~GGYTRI~kl~-~R~~~~~~gD~A~mAiLELvgnp~ppl~~~~~~~~~~l~NvLl~~ar~e~~ 157 (191)
-...|.+++|+| |+|+. .|-.+|.+ -+|...---+...+.+ +.|.-.|+++.|+-|.
T Consensus 17 ~L~~~~~kpGsY--iFRlSCTrLGQWAI---------GyV~~dg~I~QTIPqn--k~L~qaLidG~reG~y 74 (86)
T PF02762_consen 17 RLQHYRDKPGSY--IFRLSCTRLGQWAI---------GYVTQDGKILQTIPQN--KSLYQALIDGSREGFY 74 (86)
T ss_dssp HHGGGTTSTTEE--EEEEESSSTTSEEE---------EEEETTSEEEEE--SS--S-HHHHHHHHHHTTSS
T ss_pred HHHHHhCCcccE--EEeeccccccceeE---------EEEcCCCcEEEecCCC--chHHHHHHhccccceE
Confidence 346899999999 45553 45544442 3333222222222222 5677889999887553
No 9
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of Listeria monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [].; PDB: 3H0D_A.
Probab=28.34 E-value=9.8 Score=31.57 Aligned_cols=38 Identities=26% Similarity=0.412 Sum_probs=22.6
Q ss_pred hhhhhcCCC----------CCCeeeEEecCCCCCCCCCCCCCceEEEEecCCC
Q psy14597 87 VLVPRFQNT----------TVSYTRAYNAPIPHATPEKSDLSFHSVIELRGNP 129 (191)
Q Consensus 87 ~LaPRy~~R----------~GGYTRI~kl~~R~~~~~~gD~A~mAiLELvgnp 129 (191)
||.-||.-. .|||-||.|++... .+.--..+++.+|+.
T Consensus 45 Vl~TRFT~e~GY~VESrRGGGGyIRI~rv~~~~-----~~~~~~~l~~~ig~~ 92 (152)
T PF05848_consen 45 VLSTRFTPERGYIVESRRGGGGYIRIVRVPLDD-----EEDLLDHLIESIGDS 92 (152)
T ss_dssp HHHHHSSCCCTEEEEEE-STT-EEEEEEEEEST-----CHHHHHHHHCCS-S-
T ss_pred eeeccccCCCCeEEEeccCCCceEEEEEEccCC-----cHHHHHHHHHHhcCc
Confidence 566688644 78999999997654 122344556666653
No 10
>PF10213 MRP-S28: Mitochondrial ribosomal subunit protein ; InterPro: IPR019349 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 entry represents a conserved region of approx. 125 residues of one of the proteins that makes up the small subunit of the mitochondrial ribosome. In Saccharomyces cerevisiae (Baker's yeast) it is mitochondrial ribosomal protein S24 whereas in humans it is S35.
Probab=19.81 E-value=95 Score=24.74 Aligned_cols=53 Identities=21% Similarity=0.359 Sum_probs=34.2
Q ss_pred chhHHHHHHhhhhhhcCCCCCCeeeEEecCCCCCCCCCCCCCceEEEEecCCCCCCCcccCcCchhhHHHHHHHHHHH
Q psy14597 77 EKNIVHKLFKVLVPRFQNTTVSYTRAYNAPIPHATPEKSDLSFHSVIELRGNPFPPLVQRAVDSRLHIQNVLLDEAKK 154 (191)
Q Consensus 77 ek~lv~KLF~~LaPRy~~R~GGYTRI~kl~~R~~~~~~gD~A~mAiLELvgnp~ppl~~~~~~~~~~l~NvLl~~ar~ 154 (191)
+....+||-.-..+||-.. ..+|-|+.+-||--. .+...-..+++.|+.+|+.
T Consensus 41 ~~~a~~Kl~~LaG~Ryd~~------------------------~d~l~i~sdr~~~~~-qN~~~l~~~l~~L~~EA~~ 93 (127)
T PF10213_consen 41 SEKARHKLKLLAGPRYDPE------------------------TDILKISSDRFPTRA-QNKKYLSDLLTRLIHEAKD 93 (127)
T ss_pred CHHHHHHHHHHhhcccCCC------------------------CCEEEEecccCCCHH-HHHHHHHHHHHHHHHHHhh
Confidence 6777888665555565433 346666666666533 3444556677889999988
Done!