Query psy4063
Match_columns 205
No_of_seqs 113 out of 763
Neff 3.6
Searched_HMMs 46136
Date Sat Aug 17 00:22:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4063.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4063hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0093 RplN Ribosomal protein 100.0 1.9E-42 4.1E-47 276.2 9.2 107 34-158 1-122 (122)
2 CHL00057 rpl14 ribosomal prote 100.0 2.6E-42 5.7E-47 275.3 10.0 107 34-158 1-122 (122)
3 PRK05483 rplN 50S ribosomal pr 100.0 3.2E-42 6.9E-47 274.6 10.1 107 34-158 1-122 (122)
4 TIGR01067 rplN_bact ribosomal 100.0 5.3E-42 1.1E-46 273.2 10.4 107 34-158 1-122 (122)
5 TIGR03673 rpl14p_arch 50S ribo 100.0 1.8E-41 3.9E-46 273.7 10.6 110 30-158 6-131 (131)
6 PTZ00054 60S ribosomal protein 100.0 3.6E-41 7.7E-46 274.4 10.5 110 30-158 14-139 (139)
7 PRK08571 rpl14p 50S ribosomal 100.0 4.4E-41 9.5E-46 271.7 10.8 109 31-158 8-132 (132)
8 PF00238 Ribosomal_L14: Riboso 100.0 4.7E-41 1E-45 266.8 5.4 106 34-157 1-121 (122)
9 PTZ00320 ribosomal protein L14 100.0 1.6E-37 3.5E-42 262.5 9.4 104 36-157 61-187 (188)
10 KOG3441|consensus 100.0 3E-36 6.4E-41 244.3 9.3 143 10-158 6-149 (149)
11 KOG0901|consensus 99.9 6.9E-27 1.5E-31 191.9 8.5 112 27-157 12-144 (145)
12 smart00333 TUDOR Tudor domain. 49.6 36 0.00079 22.3 4.0 34 73-107 4-38 (57)
13 PF13811 DUF4186: Domain of un 38.6 17 0.00038 29.4 1.3 43 144-194 29-77 (111)
14 KOG0171|consensus 32.1 66 0.0014 28.1 3.9 31 103-133 116-147 (176)
15 PF02721 DUF223: Domain of unk 31.6 40 0.00087 25.0 2.2 22 110-135 2-23 (95)
16 cd04508 TUDOR Tudor domains ar 29.7 1.4E+02 0.0031 18.7 4.3 32 75-107 1-34 (48)
17 PRK13149 H/ACA RNA-protein com 28.0 78 0.0017 23.1 3.2 27 101-130 22-50 (73)
18 COG1465 Predicted alternative 27.4 2.4E+02 0.0053 27.1 6.9 60 61-120 266-343 (376)
19 PF08940 DUF1918: Domain of un 24.4 82 0.0018 22.9 2.6 37 71-108 2-44 (58)
20 KOG0936|consensus 24.4 1.2E+02 0.0026 26.4 4.1 27 109-135 4-30 (182)
21 CHL00084 rpl19 ribosomal prote 22.5 1.6E+02 0.0034 23.9 4.2 26 72-97 23-56 (117)
22 TIGR03170 flgA_cterm flagella 22.3 2.9E+02 0.0062 21.0 5.5 51 32-93 63-116 (122)
23 TIGR01024 rplS_bact ribosomal 22.0 1.6E+02 0.0035 23.7 4.1 26 72-97 19-52 (113)
24 PF01245 Ribosomal_L19: Riboso 21.6 2.1E+02 0.0044 22.9 4.7 27 71-97 18-52 (113)
25 PF08696 Dna2: DNA replication 20.5 5.5E+02 0.012 22.0 7.6 48 70-129 23-70 (209)
26 COG4959 TraF Type IV secretory 20.2 2.8E+02 0.006 24.2 5.4 60 72-131 90-159 (173)
27 PRK05338 rplS 50S ribosomal pr 20.2 1.8E+02 0.004 23.5 4.2 26 72-97 19-52 (116)
28 COG0824 FcbC Predicted thioest 20.1 4.2E+02 0.0091 20.9 6.2 62 68-136 66-131 (137)
No 1
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-42 Score=276.17 Aligned_cols=107 Identities=30% Similarity=0.462 Sum_probs=101.6
Q ss_pred cccccCeEEEEeCChhcccccccCCCcEEEEEcc--CCcccccCCEEEEEEc----------CeeeeEEEEeEEec---c
Q psy4063 34 HIKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYN--QTHIGTIGDKVLVAIK----------GEKKKGIIVGVKKH---Q 98 (205)
Q Consensus 34 MIqk~T~L~VaDNSGagk~~~~~~K~v~CI~V~~--k~r~A~IGD~IvVSVK----------GeV~kAVIVRtKk~---~ 98 (205)
|||.+|+|+|+||||| |.++||+|++ ++++|++||+|++||| |++++|||||||++ .
T Consensus 1 miq~~t~l~vADNSGA--------k~v~~I~V~gg~~r~~A~vGD~ivvsVKka~P~~~vKkg~V~~AViVRtkk~~rR~ 72 (122)
T COG0093 1 MIQVQTRLNVADNSGA--------KEVMCIKVLGGSRRRYAGVGDIIVVSVKKAIPRGMVKKGDVVKAVVVRTKKEVRRP 72 (122)
T ss_pred CcccccEEEEccCCCC--------cEEEEEEEeccccccccCCCCEEEEEEeeccCCcceeccceEEEEEEEeCCceEcC
Confidence 8999999999999998 7889999998 5669999999999998 78999999999998 4
Q ss_pred CCCeeeeCCceEEEECCCCCccceEEecchhHHHHhhhhhhcccCCCCchhhhhhhHHHH
Q psy4063 99 KPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKEKTLSKGADYTNTLNSINNIS 158 (205)
Q Consensus 99 dG~~ikFddNavVLLn~kg~PlGTRI~GPVp~ELR~k~~~~~~~~~~~~~KIlSlA~~ii 158 (205)
||++++|||||+||+|++|+|+||||||||++|+|++ +|+||+|||+.++
T Consensus 73 DGs~i~FddNA~Viin~~g~P~GtrI~GPVaRElr~~----------~~~kI~SlA~eVv 122 (122)
T COG0093 73 DGSYIKFDDNAAVIINPDGEPRGTRIFGPVARELRER----------GFMKIASLAPEVV 122 (122)
T ss_pred CCCEEEeCCceEEEECCCCCcccceEecchhHHHHhc----------CCceeeecceecC
Confidence 8999999999999999999999999999999999999 9999999999764
No 2
>CHL00057 rpl14 ribosomal protein L14
Probab=100.00 E-value=2.6e-42 Score=275.27 Aligned_cols=107 Identities=29% Similarity=0.433 Sum_probs=101.2
Q ss_pred cccccCeEEEEeCChhcccccccCCCcEEEEEcc--CCcccccCCEEEEEEc----------CeeeeEEEEeEEec---c
Q psy4063 34 HIKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYN--QTHIGTIGDKVLVAIK----------GEKKKGIIVGVKKH---Q 98 (205)
Q Consensus 34 MIqk~T~L~VaDNSGagk~~~~~~K~v~CI~V~~--k~r~A~IGD~IvVSVK----------GeV~kAVIVRtKk~---~ 98 (205)
|||.+|+|+|+||||| |.++||++|+ ++++|++||+|+|+|| |++++|||||||++ .
T Consensus 1 MIq~~t~l~v~DNSGa--------k~v~cI~v~~~~~~~~a~vGD~IvvsVk~~~~~~k~kkg~v~kAvIVrtk~~~~r~ 72 (122)
T CHL00057 1 MIQPQTYLNVADNSGA--------RKLMCIRVLGASNRKYAHIGDVIIAVVKEAVPNMPLKRSEVVRAVIVRTCKELKRD 72 (122)
T ss_pred CCCcCCEEEEeECCCC--------cEEEEEEEeCCCCCccccCCCEEEEEEEeccCCCceecCCEEEEEEEEeccccCcC
Confidence 9999999999999998 8899999997 5678999999999997 69999999999997 4
Q ss_pred CCCeeeeCCceEEEECCCCCccceEEecchhHHHHhhhhhhcccCCCCchhhhhhhHHHH
Q psy4063 99 KPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKEKTLSKGADYTNTLNSINNIS 158 (205)
Q Consensus 99 dG~~ikFddNavVLLn~kg~PlGTRI~GPVp~ELR~k~~~~~~~~~~~~~KIlSlA~~ii 158 (205)
||++++|||||+||+|++++|+||||+||||+|||++ +|+||+|||+.++
T Consensus 73 dG~~i~F~~Na~VLin~~~~p~GTrI~Gpv~~elr~k----------~~~Ki~sla~~vi 122 (122)
T CHL00057 73 NGMIIRFDDNAAVVIDQEGNPKGTRVFGPIARELREK----------NFTKIVSLAPEVL 122 (122)
T ss_pred CCcEEEcCCceEEEECCCCCEeEeEEEccchHHHhhc----------CCeEEEecccccC
Confidence 8999999999999999999999999999999999998 9999999999764
No 3
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=100.00 E-value=3.2e-42 Score=274.64 Aligned_cols=107 Identities=30% Similarity=0.470 Sum_probs=101.3
Q ss_pred cccccCeEEEEeCChhcccccccCCCcEEEEEcc--CCcccccCCEEEEEEc----------CeeeeEEEEeEEec---c
Q psy4063 34 HIKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYN--QTHIGTIGDKVLVAIK----------GEKKKGIIVGVKKH---Q 98 (205)
Q Consensus 34 MIqk~T~L~VaDNSGagk~~~~~~K~v~CI~V~~--k~r~A~IGD~IvVSVK----------GeV~kAVIVRtKk~---~ 98 (205)
|||.+|+|+|+||||| +.++||++|+ ++++|++||+|+|+|| |++++|||||||++ .
T Consensus 1 MIq~~t~l~v~DNSGa--------k~v~cI~v~g~~~~~~a~iGD~I~vsVkk~~~~~~~kkg~v~~AvIVrtkk~~~r~ 72 (122)
T PRK05483 1 MIQQETRLNVADNSGA--------KEVMCIKVLGGSKRRYASIGDVIVVSVKEAIPRGKVKKGDVVKAVVVRTKKGVRRP 72 (122)
T ss_pred CCCCCCEEEEeECCCC--------CEEEEEEEeCCCCCCccccCCEEEEEEEEcCCCCcccCCCEeeEEEEEeccceecC
Confidence 9999999999999998 8899999997 5678999999999997 89999999999998 5
Q ss_pred CCCeeeeCCceEEEECCCCCccceEEecchhHHHHhhhhhhcccCCCCchhhhhhhHHHH
Q psy4063 99 KPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKEKTLSKGADYTNTLNSINNIS 158 (205)
Q Consensus 99 dG~~ikFddNavVLLn~kg~PlGTRI~GPVp~ELR~k~~~~~~~~~~~~~KIlSlA~~ii 158 (205)
||++++|||||+||||++++|+||||+||||+|||++ +|+||+|||+.++
T Consensus 73 dG~~i~F~dNavVLin~~~~p~GTrI~Gpv~~elr~~----------~~~Ki~sla~~v~ 122 (122)
T PRK05483 73 DGSYIRFDDNAAVLLNNDGEPRGTRIFGPVARELRDK----------KFMKIVSLAPEVL 122 (122)
T ss_pred CCCEEEcCCCEEEEECCCCCEeEeEEeccchHHHhhc----------CCcEEEecccccC
Confidence 8999999999999999999999999999999999987 8999999999764
No 4
>TIGR01067 rplN_bact ribosomal protein L14, bacterial/organelle. This model distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms.
Probab=100.00 E-value=5.3e-42 Score=273.22 Aligned_cols=107 Identities=30% Similarity=0.461 Sum_probs=101.4
Q ss_pred cccccCeEEEEeCChhcccccccCCCcEEEEEcc--CCcccccCCEEEEEEc----------CeeeeEEEEeEEec---c
Q psy4063 34 HIKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYN--QTHIGTIGDKVLVAIK----------GEKKKGIIVGVKKH---Q 98 (205)
Q Consensus 34 MIqk~T~L~VaDNSGagk~~~~~~K~v~CI~V~~--k~r~A~IGD~IvVSVK----------GeV~kAVIVRtKk~---~ 98 (205)
|||.+|+|+|+||||| +.++||++|+ ++++|.+||+|+|+|| ||+++|||||||++ .
T Consensus 1 MIq~~t~l~v~DNSGa--------k~v~cI~v~~~~~~~~a~iGD~I~vsVk~~~~~~~~kkg~v~~AvIVrtkk~~~r~ 72 (122)
T TIGR01067 1 MIQQQSRLNVADNSGA--------KKVQCIKVLGGSRRRYATVGDVIVVVVKDAIPNGKVKKGDVVKAVIVRTKKGVRRK 72 (122)
T ss_pred CCCcCCEEEEeECCCC--------cEEEEEEEeCCCCCCccccCCEEEEEEEEcCCCCccccccEEEEEEEEeecceEeC
Confidence 9999999999999998 8899999997 4578999999999998 89999999999998 4
Q ss_pred CCCeeeeCCceEEEECCCCCccceEEecchhHHHHhhhhhhcccCCCCchhhhhhhHHHH
Q psy4063 99 KPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKEKTLSKGADYTNTLNSINNIS 158 (205)
Q Consensus 99 dG~~ikFddNavVLLn~kg~PlGTRI~GPVp~ELR~k~~~~~~~~~~~~~KIlSlA~~ii 158 (205)
||++++|||||+||+|++++|+||||+||||+|||++ +|+||+|||+.|+
T Consensus 73 dG~~i~F~~Na~VLin~~~~p~GTrI~Gpv~~elr~~----------~~~Ki~sla~~i~ 122 (122)
T TIGR01067 73 DGSYIRFDDNACVLINKNKEPRGTRIFGPVARELRDK----------GFMKIVSLAPEVI 122 (122)
T ss_pred CCCEEECCCceEEEECCCCCEeeeEEEccchHHHhhc----------CCceeeeccchhC
Confidence 8999999999999999999999999999999999998 8999999999864
No 5
>TIGR03673 rpl14p_arch 50S ribosomal protein L14P. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Probab=100.00 E-value=1.8e-41 Score=273.71 Aligned_cols=110 Identities=23% Similarity=0.302 Sum_probs=100.7
Q ss_pred cccccccccCeEEEEeCChhcccccccCCCcEEEEEcc-----CC-cccccCCEEEEEEc-------CeeeeEEEEeEEe
Q psy4063 30 PCLHHIKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYN-----QT-HIGTIGDKVLVAIK-------GEKKKGIIVGVKK 96 (205)
Q Consensus 30 ~~~~MIqk~T~L~VaDNSGagk~~~~~~K~v~CI~V~~-----k~-r~A~IGD~IvVSVK-------GeV~kAVIVRtKk 96 (205)
....|||.+|+|+|+||||| |.++||+|++ ++ ++|++||+|+|+|| ||+++|||||||+
T Consensus 6 ~~~~mIq~~t~L~VaDNSGa--------k~v~cI~vl~~~g~~~r~~~a~iGD~IvvsVK~~~p~~kg~v~kAVIVRtkk 77 (131)
T TIGR03673 6 GITRALPVGSLLVCADNTGA--------KEVEVISVKGYKGVKRRLPCAGVGDMVVVSVKKGTPEMRKQVFKAVVVRQRK 77 (131)
T ss_pred ccceeeccCCEEEEeeCCCC--------ceEEEEEEeeeCCCcccCCccccCCEEEEEEEECCccccCCEeEEEEEEeCc
Confidence 35679999999999999998 8899999993 23 56999999999998 8999999999999
Q ss_pred c---cCCCeeeeCCceEEEECCCCCccceEEecchhHHHHhhhhhhcccCCCCchhhhhhhHHHH
Q psy4063 97 H---QKPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKEKTLSKGADYTNTLNSINNIS 158 (205)
Q Consensus 97 ~---~dG~~ikFddNavVLLn~kg~PlGTRI~GPVp~ELR~k~~~~~~~~~~~~~KIlSlA~~ii 158 (205)
+ .||++++|||||+||||++++|+||||+||||+|| ++ +|+||+|||+.++
T Consensus 78 ~~~R~dGs~i~FddNa~VLin~~~~P~GTRI~GpV~rEl-~~----------~~~Ki~SlA~~vi 131 (131)
T TIGR03673 78 EYRRPDGTRVKFEDNAVVIVTPDGEPKGTEIKGPVAREA-AE----------RWPKIASIASIIV 131 (131)
T ss_pred ceecCCCcEEEeCCcEEEEECCCCCEeeeEEEccchHHH-Hh----------CccHheeccchhC
Confidence 8 48999999999999999999999999999999999 45 6999999999874
No 6
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=100.00 E-value=3.6e-41 Score=274.39 Aligned_cols=110 Identities=17% Similarity=0.209 Sum_probs=100.8
Q ss_pred cccccccccCeEEEEeCChhcccccccCCCcEEEEEcc----CC--cccccCCEEEEEEc-------CeeeeEEEEeEEe
Q psy4063 30 PCLHHIKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYN----QT--HIGTIGDKVLVAIK-------GEKKKGIIVGVKK 96 (205)
Q Consensus 30 ~~~~MIqk~T~L~VaDNSGagk~~~~~~K~v~CI~V~~----k~--r~A~IGD~IvVSVK-------GeV~kAVIVRtKk 96 (205)
....|||.+|+|+|+||||| |.++||+|++ ++ ++|++||+|+|||| |++++|||||||+
T Consensus 14 ~~~~mIq~~t~L~vaDNSGA--------k~v~cI~vlg~~g~~~r~~~a~iGD~IvvsVKk~~p~~kg~V~kAVIVRtKk 85 (139)
T PTZ00054 14 RVTLGLPVGAVVNCADNSGA--------KNLYIIAVKGIHGRLNRLPSASLGDMVLATVKKGKPELRKKVLNAVIIRQRK 85 (139)
T ss_pred ccceeecCCCEEEEeeCCCc--------cEEEEEEEeccCcCCccCcccccCCEEEEEEEECCCcccCCEeeEEEEEECc
Confidence 34669999999999999998 8899999996 23 46999999999997 8999999999999
Q ss_pred c---cCCCeeeeCCceEEEECCCCCccceEEecchhHHHHhhhhhhcccCCCCchhhhhhhHHHH
Q psy4063 97 H---QKPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKEKTLSKGADYTNTLNSINNIS 158 (205)
Q Consensus 97 ~---~dG~~ikFddNavVLLn~kg~PlGTRI~GPVp~ELR~k~~~~~~~~~~~~~KIlSlA~~ii 158 (205)
+ .||++++|||||+||||++++|+||||+||||+|| ++ +|+||+|||+.++
T Consensus 86 ~~rR~dGs~i~F~dNA~VLin~~~~p~GTRI~GpV~rEl-~~----------~~~KI~SLA~~vi 139 (139)
T PTZ00054 86 AWRRKDGVFIYFEDNAGVIVNPKGEMKGSAITGPVAKEC-AD----------LWPKISSAAPAIV 139 (139)
T ss_pred ceEcCCCcEEEeCCcEEEEECCCCCEeeeEEeCchhHHH-Hh----------CccHhhccccccC
Confidence 8 58999999999999999999999999999999999 44 5999999999864
No 7
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=100.00 E-value=4.4e-41 Score=271.75 Aligned_cols=109 Identities=22% Similarity=0.324 Sum_probs=99.9
Q ss_pred ccccccccCeEEEEeCChhcccccccCCCcEEEEEcc----CC--cccccCCEEEEEEc-------CeeeeEEEEeEEec
Q psy4063 31 CLHHIKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYN----QT--HIGTIGDKVLVAIK-------GEKKKGIIVGVKKH 97 (205)
Q Consensus 31 ~~~MIqk~T~L~VaDNSGagk~~~~~~K~v~CI~V~~----k~--r~A~IGD~IvVSVK-------GeV~kAVIVRtKk~ 97 (205)
...|||.+|+|+|+||||| |.++||+|++ .+ ++|.+||+|+|+|| |++++|||||||++
T Consensus 8 ~~~mIq~~T~L~VaDNSGA--------k~v~cI~vlg~~g~~~r~~~a~iGD~IvvsVK~~~p~~kg~v~kAVIVRtkk~ 79 (132)
T PRK08571 8 VTRGLPVGARLVCADNTGA--------KEVEIISVKGYKGVKRRLPKAGVGDMVVVSVKKGTPEMRKQVLRAVVVRQRKE 79 (132)
T ss_pred ccceecCCCEEEEeeCCCC--------CeEEEEEEeccCCCCccCCccccCCEEEEEEEECCCcccCCEeEEEEEEeccc
Confidence 4569999999999999998 8899999985 23 45999999999998 79999999999998
Q ss_pred ---cCCCeeeeCCceEEEECCCCCccceEEecchhHHHHhhhhhhcccCCCCchhhhhhhHHHH
Q psy4063 98 ---QKPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKEKTLSKGADYTNTLNSINNIS 158 (205)
Q Consensus 98 ---~dG~~ikFddNavVLLn~kg~PlGTRI~GPVp~ELR~k~~~~~~~~~~~~~KIlSlA~~ii 158 (205)
.||++++|||||+||||++++|+||||+||||+|| ++ +|+||+|||+.++
T Consensus 80 ~~R~dGs~i~F~dNa~VLin~~~~p~GTRI~GpV~~El-~~----------~~~Ki~sLA~~vi 132 (132)
T PRK08571 80 YRRPDGTRVKFEDNAAVIVTPEGTPKGTEIKGPVAREA-AE----------RWPKIASIASIIV 132 (132)
T ss_pred eEcCCCcEEEeCCcEEEEECCCCCEeeeEEeccchHHH-hh----------CCchheeccchhC
Confidence 58999999999999999999999999999999999 44 5999999999864
No 8
>PF00238 Ribosomal_L14: Ribosomal protein L14p/L23e; InterPro: IPR000218 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 L14 is one of the proteins from the large ribosomal subunit. In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities []. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins []. L14 is a protein of 119 to 137 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_M 4A1C_J 4A1E_J 4A1A_J 4A17_J 1VSP_I 3D5D_O 1VSA_I 3MRZ_K 3F1F_O ....
Probab=100.00 E-value=4.7e-41 Score=266.76 Aligned_cols=106 Identities=35% Similarity=0.545 Sum_probs=98.7
Q ss_pred cccccCeEEEEeCChhcccccccCCCcEEEEEcc--CCcccccCCEEEEEEc----------CeeeeEEEEeEEec---c
Q psy4063 34 HIKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYN--QTHIGTIGDKVLVAIK----------GEKKKGIIVGVKKH---Q 98 (205)
Q Consensus 34 MIqk~T~L~VaDNSGagk~~~~~~K~v~CI~V~~--k~r~A~IGD~IvVSVK----------GeV~kAVIVRtKk~---~ 98 (205)
|||.+|+|+|+||||| +.++||++|+ ++++|++||+|+|||| |++++|||||||++ .
T Consensus 1 MIq~~t~L~v~DNSGa--------k~v~cI~v~~~~~~~~a~vGD~I~vsVkk~~~~~~vkkg~v~~avIVrtk~~~~r~ 72 (122)
T PF00238_consen 1 MIQKGTILKVADNSGA--------KKVKCIKVLGGKRRKYASVGDIIVVSVKKGRPKSKVKKGQVYKAVIVRTKKPIRRK 72 (122)
T ss_dssp -BETTEEEEESBSSSE--------EEEEEEEETSSTTTSEE-TTSEEEEEEEEE-SSSSSTTTEEEEEEEEECSSEEETT
T ss_pred CCCCCCEEEEeeCCCC--------cEEEEEEEeCCcCccccccceEEEEEEeecccCccccccceEEEEEEEEeEEEEEe
Confidence 9999999999999998 7889999997 5678999999999993 89999999999998 6
Q ss_pred CCCeeeeCCceEEEECCCCCccceEEecchhHHHHhhhhhhcccCCCCchhhhhhhHHH
Q psy4063 99 KPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKEKTLSKGADYTNTLNSINNI 157 (205)
Q Consensus 99 dG~~ikFddNavVLLn~kg~PlGTRI~GPVp~ELR~k~~~~~~~~~~~~~KIlSlA~~i 157 (205)
||++++|||||+||+|++++|+||||+||||+|+|++ +|+||+|||+.|
T Consensus 73 dg~~i~F~~Na~VLln~~~~p~GtrI~Gpv~~elr~~----------~~~ki~sla~~i 121 (122)
T PF00238_consen 73 DGSFIKFDDNAVVLLNKKGNPLGTRIFGPVPRELRKK----------KFPKILSLASRI 121 (122)
T ss_dssp TSEEEEESSEEEEEEETTSSBSSSSBCSEEEHHHHHT----------TSHHHHHHSSCE
T ss_pred CCcEEEeCCccEEEEcCCCCEeeeEEEeeehHHhhHc----------CCchHHhhcccc
Confidence 9999999999999999999999999999999999988 899999999865
No 9
>PTZ00320 ribosomal protein L14; Provisional
Probab=100.00 E-value=1.6e-37 Score=262.50 Aligned_cols=104 Identities=18% Similarity=0.164 Sum_probs=98.4
Q ss_pred cccCeEEEEeCChhcccccccCCCcEEEEEccCCcccccCCE----EEEEEc----------------CeeeeEEEEeEE
Q psy4063 36 KLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQTHIGTIGDK----VLVAIK----------------GEKKKGIIVGVK 95 (205)
Q Consensus 36 qk~T~L~VaDNSGagk~~~~~~K~v~CI~V~~k~r~A~IGD~----IvVSVK----------------GeV~kAVIVRtK 95 (205)
.-+|+|+|+||||| |.++||+|+.++++|.+||+ |+|||| |+|++|||||||
T Consensus 61 ~~qT~L~VaDNSGA--------K~V~CIkVl~~rr~A~IGDi~~~~IvVsVKka~P~~~~~~~~kVKKG~V~kAVIVRTK 132 (188)
T PTZ00320 61 SDQVKLHCVDNTNC--------KHVRLISKATAERFAHCRVFPAVAHRVSVQRFKSGRGEVSRHRVKPGNIYWVCLLSRR 132 (188)
T ss_pred CCCcEEEEEeCCCC--------cEEEEEEEecCCCceeeccccCceEEEEEeecccCccccccCceecCCEEEEEEEEEC
Confidence 36899999999998 88999999988899999999 999997 699999999999
Q ss_pred ec---cCCCeeeeCCceEEEECCCCCccceEEecchhHHHHhhhhhhcccCCCCchhhhhhhHHH
Q psy4063 96 KH---QKPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKEKTLSKGADYTNTLNSINNI 157 (205)
Q Consensus 96 k~---~dG~~ikFddNavVLLn~kg~PlGTRI~GPVp~ELR~k~~~~~~~~~~~~~KIlSlA~~i 157 (205)
++ .||++++|||||+||||++++|+||||+|||++|||++ +|+||+|||+-+
T Consensus 133 K~irR~DGs~IrFDdNAaVLIN~qgePlGTRIfGPVaRELR~k----------~f~KIvSLAp~~ 187 (188)
T PTZ00320 133 QTNTRMSGLQTNFDRNTCILMNDQRVPLGTRVMYCAGRHVNHK----------YHLKAVVLANFF 187 (188)
T ss_pred cccCCCCCCEEEeCCcEEEEECCCCCEeeeEEecchhHHHhhc----------CCceeeeccccc
Confidence 98 48999999999999999999999999999999999999 999999999864
No 10
>KOG3441|consensus
Probab=100.00 E-value=3e-36 Score=244.34 Aligned_cols=143 Identities=42% Similarity=0.664 Sum_probs=133.4
Q ss_pred CCcccCcchhc-ccccccccccccccccccCeEEEEeCChhcccccccCCCcEEEEEccCCcccccCCEEEEEEcCeeee
Q psy4063 10 PSYQTTPSALK-LCSDLYHTTPCLHHIKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQTHIGTIGDKVLVAIKGEKKK 88 (205)
Q Consensus 10 ~~~~~~~~~~~-~~~~~~st~~~~~MIqk~T~L~VaDNSGagk~~~~~~K~v~CI~V~~k~r~A~IGD~IvVSVKGeV~k 88 (205)
++++||--.+. +...++.|+..+..|++.|+|+|+|||..|++++.+++.++||+||+++..+.+||.|+|+||||+.+
T Consensus 6 ~l~~p~t~~~~~~s~~~lhtt~s~~~I~k~tRlrVVDNSaLGk~a~~~gr~PrCIHVYkkrgvg~~GDkiLvAIkGQmkK 85 (149)
T KOG3441|consen 6 GLWGPFTCVSRVLSHHCLHTTGSLMGIHKRTRLRVVDNSALGKEADTTGRLPRCIHVYKKRGVGELGDKILVAIKGQMKK 85 (149)
T ss_pred hcccceeeehhhhhhhHhhcchHHHhhhhhheEEEecchhhcccccccCCCCceEEEEecccccccccEEEEEEecceee
Confidence 56777765555 67778999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeEEeccCCCeeeeCCceEEEECCCCCccceEEecchhHHHHhhhhhhcccCCCCchhhhhhhHHHH
Q psy4063 89 GIIVGVKKHQKPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKEKTLSKGADYTNTLNSINNIS 158 (205)
Q Consensus 89 AVIVRtKk~~dG~~ikFddNavVLLn~kg~PlGTRI~GPVp~ELR~k~~~~~~~~~~~~~KIlSlA~~ii 158 (205)
|+||+.......+.++||+|++||||++|+|+||||..|||..||.. +++++|+|++++|++++
T Consensus 86 a~vVGh~~~~k~~~P~fDsNniVLiddnGnPlGtRI~~PIPT~Lr~~------~~~~~ysKVLAiA~~fv 149 (149)
T KOG3441|consen 86 AYVVGHVHYRKHGVPVFDSNNIVLIDDNGNPLGTRITAPIPTKLRAN------RGNVQYSKVLAIANKFV 149 (149)
T ss_pred eEEEEeeccCCCCCcccCCCcEEEECCCCCcccceEeccCcHHHHhc------cCCcchhhHHHHHhhcC
Confidence 99999998888999999999999999999999999999999999976 78999999999999864
No 11
>KOG0901|consensus
Probab=99.94 E-value=6.9e-27 Score=191.90 Aligned_cols=112 Identities=20% Similarity=0.278 Sum_probs=101.4
Q ss_pred ccccccccccccCeEEEEeCChhcccccccCCCcEEEEEccC-C-----cccccCCEEEEEEc------------Ceeee
Q psy4063 27 HTTPCLHHIKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQ-T-----HIGTIGDKVLVAIK------------GEKKK 88 (205)
Q Consensus 27 st~~~~~MIqk~T~L~VaDNSGagk~~~~~~K~v~CI~V~~k-~-----r~A~IGD~IvVSVK------------GeV~k 88 (205)
...+.+.||+.||.++|+||||| |.++||+|.+. + ..|.+||+|+++|| |+++.
T Consensus 12 ~k~r~s~~~~~g~~incaDNSgA--------knL~~isv~g~~Grlnrl~~A~~GD~vva~vKka~~~Pe~r~k~g~~~~ 83 (145)
T KOG0901|consen 12 VKFRISLGLPVGAVINCADNSGA--------KNLYCISVKGIKGRLNRLPAAGVGDMVVATVKKAHGKPELRKKVGEVLP 83 (145)
T ss_pred hhhhhhhccccceEEEecCCCCc--------ceEEEEEEeccccccccccCCCcCCEEEEEEecccCCCccCcEecccce
Confidence 34456899999999999999998 77899999983 2 37999999999998 46799
Q ss_pred EEEEeEEecc---CCCeeeeCCceEEEECCCCCccceEEecchhHHHHhhhhhhcccCCCCchhhhhhhHHH
Q psy4063 89 GIIVGVKKHQ---KPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKEKTLSKGADYTNTLNSINNI 157 (205)
Q Consensus 89 AVIVRtKk~~---dG~~ikFddNavVLLn~kg~PlGTRI~GPVp~ELR~k~~~~~~~~~~~~~KIlSlA~~i 157 (205)
|+|||+++.. ||++++|+|||+|++|++++|.||||+|||++|++.. |+||+|+|..+
T Consensus 84 avvVr~~k~~~r~dgs~~~f~dnA~v~~~~~~e~~gs~i~G~v~~e~~~~-----------~~kias~A~~i 144 (145)
T KOG0901|consen 84 AVVVRQKKSKRRKDGSIAYFEDNAGVIVNNKGEPKGSAITGPVGKELADL-----------WPKIASLAGLV 144 (145)
T ss_pred eeEEeeccccccCCCcEEEEcCceEEEEcccCccccceeccccChhHhhh-----------hHHHHhhcccc
Confidence 9999999984 7999999999999999999999999999999999998 99999999865
No 12
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=49.57 E-value=36 Score=22.29 Aligned_cols=34 Identities=24% Similarity=0.158 Sum_probs=27.0
Q ss_pred ccCCEEEEEE-cCeeeeEEEEeEEeccCCCeeeeCC
Q psy4063 73 TIGDKVLVAI-KGEKKKGIIVGVKKHQKPHIPKTDT 107 (205)
Q Consensus 73 ~IGD~IvVSV-KGeV~kAVIVRtKk~~dG~~ikFdd 107 (205)
.+|+.+++-- .|..++|.|+..... +...+.|.|
T Consensus 4 ~~G~~~~a~~~d~~wyra~I~~~~~~-~~~~V~f~D 38 (57)
T smart00333 4 KVGDKVAARWEDGEWYRARIIKVDGE-QLYEVFFID 38 (57)
T ss_pred CCCCEEEEEeCCCCEEEEEEEEECCC-CEEEEEEEC
Confidence 5788888887 799999999998765 445677776
No 13
>PF13811 DUF4186: Domain of unknown function (DUF4186)
Probab=38.56 E-value=17 Score=29.45 Aligned_cols=43 Identities=23% Similarity=0.304 Sum_probs=29.1
Q ss_pred CCCchhhhhhhHHHHHHHHHHhccccccccc------cCCCCcCcceEEeeccCCCC
Q psy4063 144 GADYTNTLNSINNISMNVAKLLKFSRCSPLH------FSPSYSHSSFRLQHATGTSS 194 (205)
Q Consensus 144 ~~~~~KIlSlA~~ii~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~ 194 (205)
..+...|..-|..+|.. -| .|-. =.|--.|.-|.-||||||-.
T Consensus 29 ~kG~~~I~~Ha~dfi~~---RL-----apA~p~nDGkQTPmrGHPVFiAQHATatCC 77 (111)
T PF13811_consen 29 DKGLDTIREHARDFIAK---RL-----APAQPPNDGKQTPMRGHPVFIAQHATATCC 77 (111)
T ss_pred HhCHHHHHHHHHHHHHH---Hh-----CccCCCCCCCCCCCCCCCeeeecCCCccch
Confidence 34778888877776543 22 2222 24666899999999999853
No 14
>KOG0171|consensus
Probab=32.12 E-value=66 Score=28.05 Aligned_cols=31 Identities=23% Similarity=0.305 Sum_probs=21.3
Q ss_pred eeeCCceEEEE-CCCCCccceEEecchhHHHH
Q psy4063 103 PKTDTNNVVLI-DDSGTPLGTRIHVPIPSMLR 133 (205)
Q Consensus 103 ikFddNavVLL-n~kg~PlGTRI~GPVp~ELR 133 (205)
++--++-|-+. |+.++-.-+|-+||+|-.|-
T Consensus 116 i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI 147 (176)
T KOG0171|consen 116 IRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLI 147 (176)
T ss_pred eeccCceEEEecCCCCCcccccccCCCchhhe
Confidence 33334444444 45567999999999998774
No 15
>PF02721 DUF223: Domain of unknown function DUF223; InterPro: IPR003871 The function of this domain has not been characterised, but may be involved in nucleic acid or nucleotide binding.
Probab=31.64 E-value=40 Score=24.97 Aligned_cols=22 Identities=36% Similarity=0.665 Sum_probs=19.0
Q ss_pred EEEECCCCCccceEEecchhHHHHhh
Q psy4063 110 VVLIDDSGTPLGTRIHVPIPSMLRTI 135 (205)
Q Consensus 110 vVLLn~kg~PlGTRI~GPVp~ELR~k 135 (205)
.||+|++| ++|.+-||+++-.+
T Consensus 2 mvL~De~G----~~I~A~I~~~~~~~ 23 (95)
T PF02721_consen 2 MVLVDEKG----DKIQATIPKELVDK 23 (95)
T ss_pred EEEEecCC----CEEEEEECHHHHHH
Confidence 58898875 99999999999877
No 16
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=29.72 E-value=1.4e+02 Score=18.75 Aligned_cols=32 Identities=16% Similarity=0.059 Sum_probs=22.9
Q ss_pred CCEEEEEEc--CeeeeEEEEeEEeccCCCeeeeCC
Q psy4063 75 GDKVLVAIK--GEKKKGIIVGVKKHQKPHIPKTDT 107 (205)
Q Consensus 75 GD~IvVSVK--GeV~kAVIVRtKk~~dG~~ikFdd 107 (205)
|+.+.+-.. |.-++|.|+.... .+...+.|.|
T Consensus 1 G~~c~a~~~~d~~wyra~V~~~~~-~~~~~V~f~D 34 (48)
T cd04508 1 GDLCLAKYSDDGKWYRAKITSILS-DGKVEVFFVD 34 (48)
T ss_pred CCEEEEEECCCCeEEEEEEEEECC-CCcEEEEEEc
Confidence 667777776 8999999998875 2334566665
No 17
>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed
Probab=28.03 E-value=78 Score=23.15 Aligned_cols=27 Identities=19% Similarity=0.378 Sum_probs=19.8
Q ss_pred CeeeeCCceEEEECCCCCccce--EEecchhH
Q psy4063 101 HIPKTDTNNVVLIDDSGTPLGT--RIHVPIPS 130 (205)
Q Consensus 101 ~~ikFddNavVLLn~kg~PlGT--RI~GPVp~ 130 (205)
..++| |+ .+.|++++.+|. .|||||-.
T Consensus 22 ~~P~~--n~-~V~~~~~~~IGkV~dIfGPV~~ 50 (73)
T PRK13149 22 KQPPI--GS-VVYDKKLKKIGKVVDVFGPVKE 50 (73)
T ss_pred CCCCC--CC-EeECCCCCEeEEEEEEECCCCC
Confidence 35666 33 448888899997 69999954
No 18
>COG1465 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]
Probab=27.36 E-value=2.4e+02 Score=27.06 Aligned_cols=60 Identities=22% Similarity=0.320 Sum_probs=43.0
Q ss_pred EEEEEcc-CCcc---cccCCEEEEEEc-CeeeeEEEEeEEecc----------CCCe---eeeCCceEEEECCCCCcc
Q psy4063 61 RVIAIYN-QTHI---GTIGDKVLVAIK-GEKKKGIIVGVKKHQ----------KPHI---PKTDTNNVVLIDDSGTPL 120 (205)
Q Consensus 61 ~CI~V~~-k~r~---A~IGD~IvVSVK-GeV~kAVIVRtKk~~----------dG~~---ikFddNavVLLn~kg~Pl 120 (205)
..|.+.+ +.+| -+.||.|.++=. |....|+|=|.|-+. +|.. +-=+-..+=|++++|+|+
T Consensus 266 aYi~vPg~kTkYLaEL~aGDeV~iVD~dGr~R~aiVGRvKIErRPl~lIeAey~g~~i~tiLQNAETIkLv~~dG~pv 343 (376)
T COG1465 266 AYIRVPGGKTKYLAELKAGDEVLIVDFDGRTRSAIVGRVKIERRPLMLIEAEYEGVEISTILQNAETIKLVNPDGEPV 343 (376)
T ss_pred EEEEcCCCceEEhhhhcCCCeEEEEecCCceeEEEEEEEEeecCceEEEEEEecCcEEEEEeccceeEEEEcCCCcEe
Confidence 4577766 5566 478999988765 999999999998762 3442 333444567889999876
No 19
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=24.40 E-value=82 Score=22.94 Aligned_cols=37 Identities=24% Similarity=0.431 Sum_probs=22.9
Q ss_pred ccccCCEEEEEEc--C-eeeeEEEEeEEeccCC---CeeeeCCc
Q psy4063 71 IGTIGDKVLVAIK--G-EKKKGIIVGVKKHQKP---HIPKTDTN 108 (205)
Q Consensus 71 ~A~IGD~IvVSVK--G-eV~kAVIVRtKk~~dG---~~ikFddN 108 (205)
.|.+||.++|--. | --..|.||..+-+ +| -.++|+|+
T Consensus 2 ~A~vGD~lvv~g~~vg~~~r~GeIveV~g~-dG~PPY~VRw~D~ 44 (58)
T PF08940_consen 2 HASVGDRLVVHGRTVGQPDRHGEIVEVRGP-DGSPPYLVRWDDT 44 (58)
T ss_dssp ---TTEEEEES-TTTS--EEEEEEEE-S-S-SS-S-EEEEETTT
T ss_pred CCCCCCEEEEcCCcCCCCCcEeEEEEEECC-CCCCCEEEEecCC
Confidence 4789999987665 3 5678899988774 44 47999983
No 20
>KOG0936|consensus
Probab=24.38 E-value=1.2e+02 Score=26.39 Aligned_cols=27 Identities=15% Similarity=0.348 Sum_probs=24.7
Q ss_pred eEEEECCCCCccceEEecchhHHHHhh
Q psy4063 109 NVVLIDDSGTPLGTRIHVPIPSMLRTI 135 (205)
Q Consensus 109 avVLLn~kg~PlGTRI~GPVp~ELR~k 135 (205)
|+.+.|++|.|.=++..-|+|.|....
T Consensus 4 AvlifNn~gkPRL~KFY~p~~~~~Qq~ 30 (182)
T KOG0936|consen 4 AVLIFNNKGKPRLVKFYTPVDEEKQQQ 30 (182)
T ss_pred EEEEecCCCCcceeeecCcCChHHHHH
Confidence 678899999999999999999988776
No 21
>CHL00084 rpl19 ribosomal protein L19
Probab=22.54 E-value=1.6e+02 Score=23.95 Aligned_cols=26 Identities=27% Similarity=0.448 Sum_probs=21.3
Q ss_pred cccCCEEEEEEc---C-----eeeeEEEEeEEec
Q psy4063 72 GTIGDKVLVAIK---G-----EKKKGIIVGVKKH 97 (205)
Q Consensus 72 A~IGD~IvVSVK---G-----eV~kAVIVRtKk~ 97 (205)
-.+||+|.|.++ | |.+.|+|+..+..
T Consensus 23 f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~ 56 (117)
T CHL00084 23 IRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNS 56 (117)
T ss_pred cCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCC
Confidence 579999999995 4 4899999997754
No 22
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=22.34 E-value=2.9e+02 Score=20.96 Aligned_cols=51 Identities=20% Similarity=0.238 Sum_probs=34.8
Q ss_pred cccccccCeEEEEeCChhcccccccCCCcEEEEEcc-CCcccccCCEEEEEE-c-CeeeeEEEEe
Q psy4063 32 LHHIKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYN-QTHIGTIGDKVLVAI-K-GEKKKGIIVG 93 (205)
Q Consensus 32 ~~MIqk~T~L~VaDNSGagk~~~~~~K~v~CI~V~~-k~r~A~IGD~IvVSV-K-GeV~kAVIVR 93 (205)
...+.+|..+.+.=.+|. .-|...+ --..|.+||.|.|-= . |++..|.|+.
T Consensus 63 ~~~V~~G~~V~i~~~~~~-----------~~i~~~g~Al~~g~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 63 PWLVKRGDTVTVIARGGG-----------LSVTTEGKALEDGAVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred ccEEcCCCEEEEEEecCC-----------EEEEEEEEEccccCCCCEEEEEECCCCCEEEEEEeC
Confidence 456777777777777774 2333333 234689999999884 3 8899988874
No 23
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=21.99 E-value=1.6e+02 Score=23.74 Aligned_cols=26 Identities=27% Similarity=0.492 Sum_probs=21.6
Q ss_pred cccCCEEEEEEc---C-----eeeeEEEEeEEec
Q psy4063 72 GTIGDKVLVAIK---G-----EKKKGIIVGVKKH 97 (205)
Q Consensus 72 A~IGD~IvVSVK---G-----eV~kAVIVRtKk~ 97 (205)
-.+||+|.|.++ | |.+.|+|+..+..
T Consensus 19 f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~ 52 (113)
T TIGR01024 19 FRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGG 52 (113)
T ss_pred cCCCCEEEEEEEEccCCceEcccEEEEEEEEeCC
Confidence 479999999886 2 5799999998865
No 24
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 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 L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=21.62 E-value=2.1e+02 Score=22.91 Aligned_cols=27 Identities=26% Similarity=0.482 Sum_probs=22.9
Q ss_pred ccccCCEEEEEEc---C-----eeeeEEEEeEEec
Q psy4063 71 IGTIGDKVLVAIK---G-----EKKKGIIVGVKKH 97 (205)
Q Consensus 71 ~A~IGD~IvVSVK---G-----eV~kAVIVRtKk~ 97 (205)
.-.+||+|.|.++ | +.+.|+|+.-+..
T Consensus 18 ~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~ 52 (113)
T PF01245_consen 18 EFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRR 52 (113)
T ss_dssp SSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBS
T ss_pred CcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECC
Confidence 3579999999997 3 7999999998885
No 25
>PF08696 Dna2: DNA replication factor Dna2; InterPro: IPR014808 Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways []. ; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication
Probab=20.53 E-value=5.5e+02 Score=21.99 Aligned_cols=48 Identities=8% Similarity=0.009 Sum_probs=33.6
Q ss_pred cccccCCEEEEEEcCeeeeEEEEeEEeccCCCeeeeCCceEEEECCCCCccceEEecchh
Q psy4063 70 HIGTIGDKVLVAIKGEKKKGIIVGVKKHQKPHIPKTDTNNVVLIDDSGTPLGTRIHVPIP 129 (205)
Q Consensus 70 r~A~IGD~IvVSVKGeV~kAVIVRtKk~~dG~~ikFddNavVLLn~kg~PlGTRI~GPVp 129 (205)
-.-.+||.|-+.- ....++..+-=++++.++++++--.-||+|-+-+.
T Consensus 23 t~v~~Gd~I~ii~------------~~~~~~~~~v~~~~~~lIl~PD~LiS~T~Va~s~~ 70 (209)
T PF08696_consen 23 TPVSPGDIIHIIG------------EFDDDDPCIVDNDSNLLILHPDILISATSVASSFF 70 (209)
T ss_pred CCCcCCCEEEEEE------------EeCCCCCEEEeCCCCEEEEcCCceecceeeecccc
Confidence 3478999985543 22234455555666799999999899999977664
No 26
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=20.22 E-value=2.8e+02 Score=24.23 Aligned_cols=60 Identities=22% Similarity=0.238 Sum_probs=33.6
Q ss_pred cccCCEEEEEEcCeeeeEEEEeEEeccC----------CCeeeeCCceEEEECCCCCccceEEecchhHH
Q psy4063 72 GTIGDKVLVAIKGEKKKGIIVGVKKHQK----------PHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSM 131 (205)
Q Consensus 72 A~IGD~IvVSVKGeV~kAVIVRtKk~~d----------G~~ikFddNavVLLn~kg~PlGTRI~GPVp~E 131 (205)
|-.||.|-+.=++-...|..|-...+.| |.+.--.+.-.+|-+.+..-.-+|-|||||.|
T Consensus 90 Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR~lp~~~gcR~l~~~el~lL~~~~~~SfDsRYfGpipas 159 (173)
T COG4959 90 ALPGQHVCITSQGIAIDGKPVAASLPVDRVGRALPRWQGCRYLAPSELLLLTDRSSTSFDSRYFGPIPAS 159 (173)
T ss_pred cCCCCcEEEecceEEECCEEeeeeccccccCCcCCcccCCceecCCeEEEEeccCCcccccceecccCHH
Confidence 5556666544444444444444444433 33332222233444456678999999999986
No 27
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=20.20 E-value=1.8e+02 Score=23.49 Aligned_cols=26 Identities=27% Similarity=0.461 Sum_probs=21.8
Q ss_pred cccCCEEEEEEc---C-----eeeeEEEEeEEec
Q psy4063 72 GTIGDKVLVAIK---G-----EKKKGIIVGVKKH 97 (205)
Q Consensus 72 A~IGD~IvVSVK---G-----eV~kAVIVRtKk~ 97 (205)
-.+||+|.|.++ | +.+.|+|+..+..
T Consensus 19 f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~ 52 (116)
T PRK05338 19 FRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGR 52 (116)
T ss_pred cCCCCEEEEEEEEccCCceEeccEEEEEEEEeCC
Confidence 479999999886 4 5899999998865
No 28
>COG0824 FcbC Predicted thioesterase [General function prediction only]
Probab=20.10 E-value=4.2e+02 Score=20.86 Aligned_cols=62 Identities=23% Similarity=0.385 Sum_probs=34.1
Q ss_pred CCcccccCCEEEEEEc-Ceeee-EEEEeEEeccCCCeeeeCCc-eEEEEC-CCCCccceEEecchhHHHHhhh
Q psy4063 68 QTHIGTIGDKVLVAIK-GEKKK-GIIVGVKKHQKPHIPKTDTN-NVVLID-DSGTPLGTRIHVPIPSMLRTIL 136 (205)
Q Consensus 68 k~r~A~IGD~IvVSVK-GeV~k-AVIVRtKk~~dG~~ikFddN-avVLLn-~kg~PlGTRI~GPVp~ELR~k~ 136 (205)
-++.+..||.+.|... .++-. .++....-...+ .+.+... -.|-+| +.+.|. |+|.+++++|
T Consensus 66 y~~p~~~~d~l~v~~~v~~~~~~s~~~~~~i~~~~-~l~a~~~~~~V~v~~~~~kp~------~~P~~~~~~l 131 (137)
T COG0824 66 YLRPARLGDVLTVRTRVEELGGKSLTLGYEIVNED-ELLATGETTLVCVDLKTGKPV------PLPPELREAL 131 (137)
T ss_pred ECCCccCCCEEEEEEEEEeecCeEEEEEEEEEeCC-EEEEEEEEEEEEEECCCCCcc------cCCHHHHHHH
Confidence 3567899999888876 22111 233333332222 3333322 234455 344454 8999999873
Done!