Query 027581
Match_columns 221
No_of_seqs 150 out of 1070
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 12:03:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027581.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027581hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00147 rpl4 ribosomal protei 100.0 2E-42 4.3E-47 300.7 9.5 111 98-209 6-123 (215)
2 PRK05319 rplD 50S ribosomal pr 100.0 1.8E-41 3.8E-46 292.0 9.3 112 99-210 1-118 (205)
3 PRK14547 rplD 50S ribosomal pr 100.0 1.4E-41 3E-46 307.7 9.0 112 98-209 1-118 (298)
4 KOG1624 Mitochondrial/chloropl 100.0 9.3E-40 2E-44 293.2 10.1 154 56-213 13-175 (290)
5 COG0088 RplD Ribosomal protein 100.0 1.6E-39 3.5E-44 282.5 8.8 116 98-213 1-123 (214)
6 PF00573 Ribosomal_L4: Ribosom 100.0 1.5E-38 3.2E-43 271.1 7.3 99 114-212 1-106 (192)
7 PRK14907 rplD 50S ribosomal pr 100.0 2.6E-38 5.6E-43 286.1 7.6 98 112-209 102-207 (295)
8 PRK04042 rpl4lp 50S ribosomal 100.0 1.8E-34 4E-39 256.7 9.1 108 99-211 1-123 (254)
9 TIGR03672 rpl4p_arch 50S ribos 100.0 1.7E-33 3.7E-38 250.1 8.8 108 99-211 1-123 (251)
10 PLN00185 60S ribosomal protein 99.9 1.3E-27 2.9E-32 223.8 9.4 108 100-210 8-137 (405)
11 PTZ00428 60S ribosomal protein 99.9 1.1E-25 2.4E-30 209.8 9.3 106 99-210 5-132 (381)
12 KOG1475 Ribosomal protein RPL1 98.8 4.4E-09 9.4E-14 97.1 5.4 111 100-211 6-133 (363)
13 PTZ00428 60S ribosomal protein 89.9 0.18 4E-06 48.3 1.9 46 130-175 41-91 (381)
14 PHA02324 hypothetical protein 25.4 49 0.0011 23.2 1.6 27 140-166 19-46 (47)
No 1
>CHL00147 rpl4 ribosomal protein L4; Validated
Probab=100.00 E-value=2e-42 Score=300.69 Aligned_cols=111 Identities=33% Similarity=0.432 Sum_probs=105.0
Q ss_pred ceeeEEeccCCCe-eeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCC
Q 027581 98 DLVIPVTNFFNED-KGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLR 176 (221)
Q Consensus 98 ~m~ipV~~~~Ge~-~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~R 176 (221)
.++++|+|++|+. +|+++|+++|| .+++.||||++|+||++++|||||+||||+||+|||||||+||||||||||++|
T Consensus 6 ~~~~~v~~~~g~~~~~~~~l~~~vf-~~~~~~ll~~~v~~~~a~~R~gt~~tKtR~eV~G~grKp~~QKGTGrAR~Gs~r 84 (215)
T CHL00147 6 FLNYPVIDLTGKEKSETIKLKLNVL-EKSGNYLLHRALVRQNNNQRQGTASTKTRSEVRGGGRKPWKQKGTGRARAGSNR 84 (215)
T ss_pred eeeEEEEccCCCeecceEEeCHHHh-CCchHhHHHHHHHHHHHHHhhcccccCccccccCCCCCCcccCCCCccCCCCCc
Confidence 3589999999999 89999999999 557799999999999999999999999999999999999999999999999999
Q ss_pred CCCc--c---c-cCCCcccccCCHHHHHHHHHHHHhhcc
Q 027581 177 GPQG--W---Y-YNARSKAQKPCYKVEQEGAAAWVEDCS 209 (221)
Q Consensus 177 sP~~--G---~-PkPRdy~~kLNKKvRrlALrsALSa~~ 209 (221)
||+| | | |+||||+++||||+|++||++|||+.+
T Consensus 85 sP~~rgGG~afgP~pR~y~~klnKKvrrlAl~sALS~k~ 123 (215)
T CHL00147 85 SPLWKGGGVIFGPKPKTYSNKLNKKERRLALRTLLYNKS 123 (215)
T ss_pred CCcccCCEeecCCCCcchhhhcCHHHHHHHHHHHHHHhh
Confidence 9999 3 3 999999999999999999999999753
No 2
>PRK05319 rplD 50S ribosomal protein L4; Provisional
Probab=100.00 E-value=1.8e-41 Score=292.00 Aligned_cols=112 Identities=43% Similarity=0.591 Sum_probs=108.2
Q ss_pred eeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCCC
Q 027581 99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178 (221)
Q Consensus 99 m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~RsP 178 (221)
|+++|+|++|+..|+|+||++||+.|+|.||||++|+||++|+||||++||+|+||+|+|+|||+||||||||+|++++|
T Consensus 1 ~~~~v~~~~g~~~~~i~l~~~vF~~~~r~dll~~~v~~~~~~~Rqgta~tk~r~ev~GsgrK~~~QKGTGrAR~Gs~rsP 80 (205)
T PRK05319 1 MELKVLNLDGKEAGEVELSDAVFGVEPNEALLHQVVVAQLANARQGTHATKTRSEVSGGGKKPWRQKGTGRARQGSIRSP 80 (205)
T ss_pred CeeEEEcCCCCCcceEEcCHHHhCCCccHHHHHHHHHHHHHhcccCcccCCcccccCCCCCCCCCCCCCCccCcCcccCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Cc--c---c-cCCCcccccCCHHHHHHHHHHHHhhccc
Q 027581 179 QG--W---Y-YNARSKAQKPCYKVEQEGAAAWVEDCSI 210 (221)
Q Consensus 179 ~~--G---~-PkPRdy~~kLNKKvRrlALrsALSa~~~ 210 (221)
+| | | |+|++|+++||||+|++|+++||++++.
T Consensus 81 ~~rGGg~afgpkpr~~~~klnkK~~~lAl~~aLs~k~~ 118 (205)
T PRK05319 81 QWRGGGVVFGPKPRDYSQKLNKKVRRLALRSALSEKAR 118 (205)
T ss_pred cccCCeeeCCCCccchhhhcCHHHHHHHHHHHHHHHHh
Confidence 99 3 3 9999999999999999999999997765
No 3
>PRK14547 rplD 50S ribosomal protein L4; Provisional
Probab=100.00 E-value=1.4e-41 Score=307.73 Aligned_cols=112 Identities=41% Similarity=0.526 Sum_probs=108.2
Q ss_pred ceeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCC
Q 027581 98 DLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRG 177 (221)
Q Consensus 98 ~m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~Rs 177 (221)
||+++|||++|+.+|+|+||++||+.++|.||||++|+||++++||||++||+|+||+|+|||||+||||||||+|++|+
T Consensus 1 M~~~~v~~~~g~~~g~ieL~~~vF~~~~r~dllh~vv~~q~a~~Rqgt~~tKtRaEV~G~GkKP~rQKGTGrAR~Gs~rs 80 (298)
T PRK14547 1 MATCDVLDWQGKKVGSAELPLKVFDVETNIPLIHQVVVAQMAAARQGTHHTKTRAEVRGGGKKPWRQKGTGRARQGSIRA 80 (298)
T ss_pred CceeEEeccCCCCcceEECCHHHhCCCccHHHHHHHHHHHHHhhhcCCCCCCceeeccCCCCCccCCCCCcccCcCCccC
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCc--c---c-cCCCcccccCCHHHHHHHHHHHHhhcc
Q 027581 178 PQG--W---Y-YNARSKAQKPCYKVEQEGAAAWVEDCS 209 (221)
Q Consensus 178 P~~--G---~-PkPRdy~~kLNKKvRrlALrsALSa~~ 209 (221)
|+| | | |+||+|++|||||+|++||++||++..
T Consensus 81 P~wrGGGvafGPkpR~y~~klNKK~rrlAlrsALS~k~ 118 (298)
T PRK14547 81 PQWRGGGTVHGPRPREYNQRTPKKMRQAALRGALSDRA 118 (298)
T ss_pred CceeCCeeecCCCCchhhhhcCHHHHHHHHHHHHHHHH
Confidence 999 3 3 999999999999999999999999655
No 4
>KOG1624 consensus Mitochondrial/chloroplast ribosomal protein L4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.3e-40 Score=293.24 Aligned_cols=154 Identities=39% Similarity=0.565 Sum_probs=134.4
Q ss_pred hhhhhhccccccCCCCCCCCCCcccccccccCCCCcccCCc--cceeeEEeccCCCeeeeEEcCccccCCCCchhHHHHH
Q 027581 56 FLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLH--QDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRV 133 (221)
Q Consensus 56 ~~~~r~~~~~~~~~~~~e~~~P~~ll~~~~~~~~~~~~~~~--~~m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhra 133 (221)
++..|.++++..++.. .+++. |-+..+.+|+.....+ |.+.+++..+++|++|.++||+++|.+++|.||||+|
T Consensus 13 ~ss~~~l~ss~~~~~~---~~~s~-l~~~~~~~p~~p~~~~p~qa~v~~~~~~e~E~~gl~~l~~dvf~~~~RrDIlhra 88 (290)
T KOG1624|consen 13 FSSKRNLVSSTQSPPE---QITSA-LHKESTLKPELPVSIPPKQAWVEPLDFFELEKVGLVDLHPDVFAEPPRRDILHRA 88 (290)
T ss_pred HHHHHHHHhhccCCcc---ccccc-cccccccCcCCCCCcChhhheeeeccccccccceeeecChhhhccchHHHHHHHH
Confidence 3455667888765543 66776 5666677777765555 9999999999999999999999999999999999999
Q ss_pred HHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCCCCc--c---c-cC-CCcccccCCHHHHHHHHHHHHh
Q 027581 134 VRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQG--W---Y-YN-ARSKAQKPCYKVEQEGAAAWVE 206 (221)
Q Consensus 134 V~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~RsP~~--G---~-Pk-PRdy~~kLNKKvRrlALrsALS 206 (221)
|+||.+|+|+||++||||+||.|+|+|||+||||||||||+.|+|++ | + |+ ||||++|||+|||.|||++||+
T Consensus 89 v~wq~~nrrvgtastktRaEv~ggGrKp~~QKgtGrAr~Gs~rsP~r~gGg~~~gpr~P~d~~~~Lp~kvr~lgl~~ALS 168 (290)
T KOG1624|consen 89 VVWQLDNRRVGTASTKTRAEVRGGGRKPWPQKGTGRARVGSLRSPQRRGGGVAHGPRGPRDYSYKLPSKVRSLGLKIALS 168 (290)
T ss_pred HHHhhcccccccccCCccccccCCCCCcCcccCCCcccccCccCcccCCCccccCCCCCcchhhhccHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999 3 2 77 9999999999999999999999
Q ss_pred hcccccc
Q 027581 207 DCSICSS 213 (221)
Q Consensus 207 a~~~~~~ 213 (221)
+.+.-|+
T Consensus 169 ~~~a~~~ 175 (290)
T KOG1624|consen 169 AKLAQDD 175 (290)
T ss_pred HHHhCCc
Confidence 6554443
No 5
>COG0088 RplD Ribosomal protein L4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-39 Score=282.55 Aligned_cols=116 Identities=41% Similarity=0.514 Sum_probs=111.2
Q ss_pred ceeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCC
Q 027581 98 DLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRG 177 (221)
Q Consensus 98 ~m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~Rs 177 (221)
||+++|+|++|+.+|++++++.||+.+++.||||+||+||++++|||||++|+|+||+|+|+|||+|||||+||+|++++
T Consensus 1 m~k~~v~~~~G~~~g~~~~~~~vf~~~~~~dli~~av~a~~a~~RQgt~~~k~rgevs~~g~Kp~~QkgtgraR~gs~rs 80 (214)
T COG0088 1 MMKLKVYDLDGEEVGEVELLPEVFGPERNEDLIHRAVLAQLANRRQGTHSTKTRGEVSGGGKKPWGQKGTGRARQGSIRS 80 (214)
T ss_pred CCcceEeCCCCCCccccccChhhccCCchHHHHHHHHHHHHHhhhccCCCCCCcccccccCcCCCCCCcCCcCCCCCCCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCc--c---c-cCC-CcccccCCHHHHHHHHHHHHhhcccccc
Q 027581 178 PQG--W---Y-YNA-RSKAQKPCYKVEQEGAAAWVEDCSICSS 213 (221)
Q Consensus 178 P~~--G---~-PkP-Rdy~~kLNKKvRrlALrsALSa~~~~~~ 213 (221)
|+| | | |+| |||+++||||||++||++|||+++..++
T Consensus 81 P~~rGGg~a~gPkp~r~~~~klnkK~rrlAl~sAls~ka~~~~ 123 (214)
T COG0088 81 PQWRGGGVAHGPKPERDYSQKLNKKERRLALRSALSAKARAGK 123 (214)
T ss_pred CeeecCccccCCCCccchhhhcCHHHHHHHHHHHHHHhccCCC
Confidence 999 3 3 999 9999999999999999999999987643
No 6
>PF00573 Ribosomal_L4: Ribosomal protein L4/L1 family; InterPro: IPR002136 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 ribosomal L4/L1 from eukaryotes and plants and L4 from bacteria. L4 from yeast has been shown to bind rRNA []. These proteins have 246 (plant) to 427 (human) amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_D 1VSA_D 3D5D_F 3MS1_E 3F1F_F 3PYO_E 3MRZ_E 3F1H_F 3PYR_E 1VSP_D ....
Probab=100.00 E-value=1.5e-38 Score=271.06 Aligned_cols=99 Identities=48% Similarity=0.735 Sum_probs=91.7
Q ss_pred EEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCCCCc--c---c-cCC-C
Q 027581 114 MVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQG--W---Y-YNA-R 186 (221)
Q Consensus 114 IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~RsP~~--G---~-PkP-R 186 (221)
||||++||++|+|.||||+||+||++++||||++||+|+||+|+|||||+|||||+||+|++++|+| | | |+| |
T Consensus 1 i~L~~~vF~~~~r~~llh~~v~~~~~~~Rqgt~~tktr~ev~g~grKp~~QKGTGrAR~Gs~rsP~~rgGg~afgPkp~r 80 (192)
T PF00573_consen 1 IELSPDVFNVPVRPDLLHRAVVWQLANRRQGTASTKTRSEVSGSGRKPWPQKGTGRARQGSIRSPQWRGGGVAFGPKPPR 80 (192)
T ss_dssp -ES-CGGGGSSTSHHHHHHHHHHHHHHTSSBT-SSSTSTTSSSSSSSSSSSSSSSSSSSSSCTSTTSTTSSBSSSSSSTS
T ss_pred CCCCHHHhCCCCcHHHHHHHHHHHHHhccCCccCCccceEEecccCcccCCCCCcccccCccccceeeccEEecCCcccc
Confidence 7999999999999999999999999999999999999999999999999999999999999999999 3 3 999 9
Q ss_pred cccccCCHHHHHHHHHHHHhhccccc
Q 027581 187 SKAQKPCYKVEQEGAAAWVEDCSICS 212 (221)
Q Consensus 187 dy~~kLNKKvRrlALrsALSa~~~~~ 212 (221)
||+++||||+|++||++||++.+..+
T Consensus 81 ~~~~klnkK~r~lAl~~aLs~k~~~~ 106 (192)
T PF00573_consen 81 DYSYKLNKKVRRLALRSALSAKAAEG 106 (192)
T ss_dssp BCSHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred cceecCChHHHHHHHHHHHHHhhccc
Confidence 99999999999999999999876543
No 7
>PRK14907 rplD 50S ribosomal protein L4; Provisional
Probab=100.00 E-value=2.6e-38 Score=286.11 Aligned_cols=98 Identities=39% Similarity=0.473 Sum_probs=93.7
Q ss_pred eeEEcCccccCCC-CchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCCCCc--c---c-cC
Q 027581 112 GFMVLAGDVFDVP-IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQG--W---Y-YN 184 (221)
Q Consensus 112 g~IeLp~~VF~~p-~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~RsP~~--G---~-Pk 184 (221)
..|+|+++||+.+ ++.+|||++|+||++++|||||+||+|+||+|||+|||+||||||||||++|||+| | | |+
T Consensus 102 ~~ieL~~~vF~~e~~~~~llh~~V~~q~A~~RqGT~~TKtRsEVsGggkKPwrQKGTGRAR~GS~RSP~wrGGGvaFGPk 181 (295)
T PRK14907 102 NTSKLPKKLFASEKIYSQAIFDTILSERASRRQGTHKVKTRAEVSGTGKKPWRQKGTGRARAGSTRSPIFVGGGRAFGPT 181 (295)
T ss_pred ceEEeCHHHhCCCccchhHHHHHHHHHHHHhccccccccchhhccCCCCCCcccCCCCccCCCCCcCCcccCCeeecCCC
Confidence 4599999999999 89999999999999999999999999999999999999999999999999999999 3 2 99
Q ss_pred C-CcccccCCHHHHHHHHHHHHhhcc
Q 027581 185 A-RSKAQKPCYKVEQEGAAAWVEDCS 209 (221)
Q Consensus 185 P-Rdy~~kLNKKvRrlALrsALSa~~ 209 (221)
| |+|+++||+|+|++||++||++.+
T Consensus 182 P~RdY~~KLNKKvRrLALrsALS~ka 207 (295)
T PRK14907 182 PERNYKLKVNKKVRFNAFVSALTLLA 207 (295)
T ss_pred CccchhhhcCHHHHHHHHHHHHHHhc
Confidence 9 999999999999999999999765
No 8
>PRK04042 rpl4lp 50S ribosomal protein L4P; Provisional
Probab=100.00 E-value=1.8e-34 Score=256.67 Aligned_cols=108 Identities=25% Similarity=0.237 Sum_probs=102.0
Q ss_pred eeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCC-----CCCceeccccCCcc---CcccccCccee
Q 027581 99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGT-----HSTKTISEVSGTGK---KPWRQKGTGRA 170 (221)
Q Consensus 99 m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGt-----a~TKtRsEVsGsgk---KpwrQKGTGRA 170 (221)
|+++|||++|+..|+++||+ ||+.++|.||||++|+||++|+|||| |+||||+||+|+|| |||+|||||||
T Consensus 1 ~~v~v~~~~g~~~g~i~L~~-vF~~~~~~~lv~~vv~~~~an~Rqgt~~~~ta~tKtraev~G~Gr~~~Kp~rQKGTGrA 79 (254)
T PRK04042 1 MKAKVYDLDGEVVGEIELPA-VFEEPVRPDLIRRAVLAAQTARLQPKGRDPLAGKRTSAESWGSGRGIARVPRLKGGSRA 79 (254)
T ss_pred CeeEEEcCCCCCcceEehhH-hhCCCCcHHHHHHHHHHHHHhccCCCCCCccccCccceeEcCCCCCcCcCCccCCCCCc
Confidence 68999999999999999995 99999999999999999999999994 89999999999999 99999999999
Q ss_pred ccCCCCCCCc--c---c-cCC-CcccccCCHHHHHHHHHHHHhhcccc
Q 027581 171 RHGTLRGPQG--W---Y-YNA-RSKAQKPCYKVEQEGAAAWVEDCSIC 211 (221)
Q Consensus 171 R~Gs~RsP~~--G---~-PkP-Rdy~~kLNKKvRrlALrsALSa~~~~ 211 (221)
| |+|+| | + |+| |+|+++||||+|++||++||++.+..
T Consensus 80 r----rsP~~rGGgv~fgPkp~R~y~~klnkK~rrlAlrsALs~k~~~ 123 (254)
T PRK04042 80 A----FVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATANP 123 (254)
T ss_pred c----ccCccCcCCeeCCCCCCcccccccCHHHHHHHHHHHHHHhhhh
Confidence 7 99999 3 2 999 99999999999999999999987654
No 9
>TIGR03672 rpl4p_arch 50S ribosomal protein L4P. One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.
Probab=100.00 E-value=1.7e-33 Score=250.14 Aligned_cols=108 Identities=26% Similarity=0.250 Sum_probs=102.0
Q ss_pred eeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCC-----CCCceeccccCCcc---CcccccCccee
Q 027581 99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGT-----HSTKTISEVSGTGK---KPWRQKGTGRA 170 (221)
Q Consensus 99 m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGt-----a~TKtRsEVsGsgk---KpwrQKGTGRA 170 (221)
|+++|+|++|+..|+++|| +||+.++|.||||++|+||++|+|||| ++||||+||+|+|| |||+|||||||
T Consensus 1 m~~~v~~~~g~~~~~i~l~-~vF~~~~~~~lv~~vv~~~~an~Rqgt~~~~~a~tKtraev~G~Grg~aKp~rQKGTGrA 79 (251)
T TIGR03672 1 MKAKVYDLDGEVVGEIELP-AVFEEPVRPDLIKRAVLAAQTNRLQPYGADPYAGKRTSAESWGSGRGIARVPRIKGGSRA 79 (251)
T ss_pred CceEEEccCCCCcceEehH-HhhCCCccHHHHHHHHHHHHHhccCCCCCCcccCcccceeEccCCCCcCCCCccCCCCcc
Confidence 6899999999999999999 599999999999999999999999999 57999999999999 99999999999
Q ss_pred ccCCCCCCCc--c---c-cCC-CcccccCCHHHHHHHHHHHHhhcccc
Q 027581 171 RHGTLRGPQG--W---Y-YNA-RSKAQKPCYKVEQEGAAAWVEDCSIC 211 (221)
Q Consensus 171 R~Gs~RsP~~--G---~-PkP-Rdy~~kLNKKvRrlALrsALSa~~~~ 211 (221)
+|+|+| | + |+| |+|+++||||+|++||++||++.+..
T Consensus 80 ----~rsP~~rGGGv~fgPkp~R~y~~klNkK~rrlAl~sALs~k~~~ 123 (251)
T TIGR03672 80 ----ARVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATADP 123 (251)
T ss_pred ----eecCccCcCCeeCCCCCCcccceecCHHHHHHHHHHHHHHhcch
Confidence 999999 3 2 999 99999999999999999999986653
No 10
>PLN00185 60S ribosomal protein L4-1; Provisional
Probab=99.94 E-value=1.3e-27 Score=223.82 Aligned_cols=108 Identities=22% Similarity=0.240 Sum_probs=102.6
Q ss_pred eeEEeccCC----CeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCC-----ceeccccCCccCcc---ccc--
Q 027581 100 VIPVTNFFN----EDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHST-----KTISEVSGTGKKPW---RQK-- 165 (221)
Q Consensus 100 ~ipV~~~~G----e~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~T-----KtRsEVsGsgkKpw---rQK-- 165 (221)
.++|||++| +.+|+|+|| +||+.|+|+||||+|++++++|+||+|+.+ +|++|++|+|+++| +||
T Consensus 8 ~v~V~~~~g~~~~~~~~~v~Lp-~VF~~piR~dlv~~v~~~~~~n~RQp~~~~~~AG~qtsAeswGtGR~vaRiPR~kgg 86 (405)
T PLN00185 8 LVSVQSLDGDMATDKSATVALP-DVMTAPIRPDIVNFVHTNISKNSRQPYAVSKKAGHQTSAESWGTGRAVSRIPRVPGG 86 (405)
T ss_pred eeEEEcCCCCccccccceeehH-HHhCCCCCHHHHHHHHHHHHHhccCCCCCCcccCCcceeeecCCCCCceecccccCC
Confidence 589999999 778999999 999999999999999999999999999999 99999999999999 999
Q ss_pred CcceeccCCCCCCCc---cc---cCC--CcccccCCHHHHHHHHHHHHhhccc
Q 027581 166 GTGRARHGTLRGPQG---WY---YNA--RSKAQKPCYKVEQEGAAAWVEDCSI 210 (221)
Q Consensus 166 GTGRAR~Gs~RsP~~---G~---PkP--Rdy~~kLNKKvRrlALrsALSa~~~ 210 (221)
||||||+|.. |.| |+ |+| |+|+++||+|+|++|+++||++++.
T Consensus 87 GT~RAgqGa~--~~~~rGGr~FgP~p~~R~~~~KvNkK~rRlAl~SALAa~a~ 137 (405)
T PLN00185 87 GTHRAGQGAF--GNMCRGGRMFAPTKTWRRWHRKVNVNQKRYAVVSALAASAV 137 (405)
T ss_pred CCCcCCccCc--CCcCCCCeeCCCCCCccccccccCHHHHHHHHHHHHHhhcc
Confidence 9999999999 888 32 999 9999999999999999999999984
No 11
>PTZ00428 60S ribosomal protein L4; Provisional
Probab=99.92 E-value=1.1e-25 Score=209.76 Aligned_cols=106 Identities=25% Similarity=0.290 Sum_probs=98.1
Q ss_pred eeeEEeccCC-CeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceecc-----
Q 027581 99 LVIPVTNFFN-EDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARH----- 172 (221)
Q Consensus 99 m~ipV~~~~G-e~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~----- 172 (221)
++++|||.+| +..|+|+|| +||+.|+|.||||+||+++++|+||||+.++++++ ++++|+| ||||||+
T Consensus 5 ~~v~V~~~~g~~~~~~v~Lp-~VF~~pir~dlV~~vv~~~~aN~RQgta~s~~ag~--~tsaksw---GTGRA~aripR~ 78 (381)
T PTZ00428 5 PVVSVYSASDKSVVGTVPLP-AVFTAPIRPDLVQFVHTNMAKNRRQAYAVKPLAGM--QHSAESW---GTGRAVARIPRV 78 (381)
T ss_pred CeeEEEcCCCCcccceEehH-HhhCCCCcHHHHHHHHHHHHHhccCCCCcCCCCCC--CCCceec---CCCCCccccccc
Confidence 6899999998 778999999 89999999999999999999999999999988888 7888999 8888888
Q ss_pred ---CCCCCCC-----c--c---c-cCC--CcccccCCHHHHHHHHHHHHhhccc
Q 027581 173 ---GTLRGPQ-----G--W---Y-YNA--RSKAQKPCYKVEQEGAAAWVEDCSI 210 (221)
Q Consensus 173 ---Gs~RsP~-----~--G---~-PkP--Rdy~~kLNKKvRrlALrsALSa~~~ 210 (221)
|+.|||+ | | + |+| |+|+++||+|+|++|+++||+++++
T Consensus 79 kg~GT~Rs~qGa~~n~~rGG~~FgP~~~~R~~~~KvNkK~rR~Al~SALaa~a~ 132 (381)
T PTZ00428 79 SGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRKVNLNQKRHAVASALAASGV 132 (381)
T ss_pred cCCCCCcCcccccCCcCCCceEcCCCCCccccccccCHHHHHHHHHHHHHhhcc
Confidence 8889888 7 3 2 999 9999999999999999999999974
No 12
>KOG1475 consensus Ribosomal protein RPL1/RPL2/RL4L4 [RNA processing and modification]
Probab=98.82 E-value=4.4e-09 Score=97.13 Aligned_cols=111 Identities=22% Similarity=0.209 Sum_probs=86.9
Q ss_pred eeEEeccCCCee-eeEEcCccccCCCCchhHHHHHHHHHHHHcccCCC-----CCceeccccCCccCcc-----cccCcc
Q 027581 100 VIPVTNFFNEDK-GFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTH-----STKTISEVSGTGKKPW-----RQKGTG 168 (221)
Q Consensus 100 ~ipV~~~~Ge~~-g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta-----~TKtRsEVsGsgkKpw-----rQKGTG 168 (221)
.+.||+.+|+.. +.+.|| +||.+|+|+||++-+......|+||.|+ ...+.+|-+|+|+-.- ++-||+
T Consensus 6 ~vtvy~~~g~~s~~~l~lp-~vf~aPiRpdlv~~v~~~~~~n~rQpyAVs~kAG~QtSAESWGTGRAvaRiPRV~GGGT~ 84 (363)
T KOG1475|consen 6 LVTVYSLDGEASKKTLTLP-AVFSAPIRPDLVNFVHTQVRKNRRQPYAVSEKAGHQTSAESWGTGRAVARIPRVGGGGTH 84 (363)
T ss_pred eeeEEeccccccccccccc-ceeccCCcHHHHHHHHHHHhhccccchhhhhhhccccchhhcccccceecccccCCCCcc
Confidence 578999999875 459999 9999999999999999999999999998 3367889888877432 445555
Q ss_pred eeccCCCCCCCc-c---ccC-C-CcccccCCHHHHHHHHHHHHhhcccc
Q 027581 169 RARHGTLRGPQG-W---YYN-A-RSKAQKPCYKVEQEGAAAWVEDCSIC 211 (221)
Q Consensus 169 RAR~Gs~RsP~~-G---~Pk-P-Rdy~~kLNKKvRrlALrsALSa~~~~ 211 (221)
||=+|-...=-. | +|. . |.|..++|..+++.|+.+|++++++.
T Consensus 85 RsGQgAFgNmCR~GrMfaPtKt~RrW~rkVn~n~Kr~A~asaiaasavp 133 (363)
T KOG1475|consen 85 RSGQGAFGNMCRGGRMFAPTKTWRRWHRKVNENEKRYAIASAIAASAVP 133 (363)
T ss_pred cccchhhhhhcccccccCchhhHHHHhhhhhhhhhhhHHHhhhhhhhhh
Confidence 555444322222 2 264 3 89999999999999999999998864
No 13
>PTZ00428 60S ribosomal protein L4; Provisional
Probab=89.86 E-value=0.18 Score=48.32 Aligned_cols=46 Identities=22% Similarity=0.221 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHcccCCCCCceeccccCCccCcc---ccc--CcceeccCCC
Q 027581 130 IHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPW---RQK--GTGRARHGTL 175 (221)
Q Consensus 130 IhraV~~q~anrRqGta~TKtRsEVsGsgkKpw---rQK--GTGRAR~Gs~ 175 (221)
....-..-+.+....++..++.+|++|+|+.++ +|| ||+||++|..
T Consensus 41 ~~~~aN~RQgta~s~~ag~~tsakswGTGRA~aripR~kg~GT~Rs~qGa~ 91 (381)
T PTZ00428 41 TNMAKNRRQAYAVKPLAGMQHSAESWGTGRAVARIPRVSGGGTHRSGQGAF 91 (381)
T ss_pred HHHHHhccCCCCcCCCCCCCCCceecCCCCCccccccccCCCCCcCccccc
Confidence 333334444555566666689999999999999 999 8889999655
No 14
>PHA02324 hypothetical protein
Probab=25.37 E-value=49 Score=23.16 Aligned_cols=27 Identities=37% Similarity=0.573 Sum_probs=21.0
Q ss_pred HcccCCC-CCceeccccCCccCcccccC
Q 027581 140 KRQQGTH-STKTISEVSGTGKKPWRQKG 166 (221)
Q Consensus 140 nrRqGta-~TKtRsEVsGsgkKpwrQKG 166 (221)
+-|||.. +||-.+..+-+-+|||+..|
T Consensus 19 ~TRQG~G~~TKysATsRN~akK~YRGQG 46 (47)
T PHA02324 19 KTRQGQGKNTKYSATSRNNAKKPYRGQG 46 (47)
T ss_pred cccccCCccceeeeeccccccCcccCCC
Confidence 4577765 78888888888999997655
Done!