Query 045484
Match_columns 179
No_of_seqs 155 out of 883
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 02:33:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045484.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045484hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01171 rplB_bact ribosomal 100.0 2.6E-53 5.6E-58 369.0 9.0 142 18-175 101-269 (273)
2 PRK09374 rplB 50S ribosomal pr 100.0 3.6E-53 7.7E-58 368.6 9.3 142 18-175 103-271 (276)
3 PTZ00031 ribosomal protein L2; 100.0 4.2E-53 9.1E-58 373.6 8.2 139 18-169 134-299 (317)
4 CHL00052 rpl2 ribosomal protei 100.0 1.1E-52 2.4E-57 365.1 9.2 142 18-175 101-270 (273)
5 COG0090 RplB Ribosomal protein 100.0 1.8E-52 3.9E-57 362.7 8.5 138 19-169 104-269 (275)
6 PF03947 Ribosomal_L2_C: Ribos 100.0 7.9E-44 1.7E-48 280.6 4.9 102 39-153 1-130 (130)
7 PRK09612 rpl2p 50S ribosomal p 100.0 1.3E-41 2.8E-46 291.2 7.0 110 18-136 68-209 (238)
8 PTZ00180 60S ribosomal protein 100.0 6.6E-40 1.4E-44 283.7 6.8 110 18-136 75-218 (260)
9 KOG2309 60s ribosomal protein 100.0 2.9E-32 6.3E-37 233.1 7.0 117 12-137 63-213 (248)
10 KOG0438 Mitochondrial/chloropl 100.0 2.9E-32 6.2E-37 240.0 4.8 141 21-169 133-301 (312)
11 PF03991 Prion_octapep: Copper 77.5 1.4 2.9E-05 20.2 0.9 7 128-134 1-7 (8)
12 KOG0438 Mitochondrial/chloropl 61.0 2.7 5.8E-05 38.4 -0.1 19 48-66 160-178 (312)
13 PF10371 EKR: Domain of unknow 51.2 5.4 0.00012 28.1 0.2 22 39-60 28-50 (59)
14 TIGR02899 spore_safA spore coa 38.2 30 0.00065 20.4 2.1 26 8-33 17-42 (44)
15 PF01476 LysM: LysM domain; I 37.9 14 0.00031 22.5 0.6 26 7-33 18-43 (44)
16 PF00181 Ribosomal_L2: Ribosom 32.2 22 0.00047 25.5 0.8 16 18-33 62-77 (77)
17 PRK10871 nlpD lipoprotein NlpD 24.2 55 0.0012 29.9 2.1 25 10-35 83-107 (319)
18 cd05694 S1_Rrp5_repeat_hs2_sc2 23.9 66 0.0014 22.6 2.1 25 4-35 30-54 (74)
19 PF09962 DUF2196: Uncharacteri 20.6 59 0.0013 23.4 1.3 17 114-130 30-46 (62)
20 KOG1489 Predicted GTP-binding 20.1 97 0.0021 29.1 2.9 45 26-70 97-142 (366)
No 1
>TIGR01171 rplB_bact ribosomal protein L2, bacterial/organellar. This model distinguishes bacterial and organellar ribosomal protein L2 from its counterparts in the archaea nad in the eukaryotic cytosol. Plant mitochondrial examples tend to have long, variable inserts.
Probab=100.00 E-value=2.6e-53 Score=368.95 Aligned_cols=142 Identities=35% Similarity=0.575 Sum_probs=128.5
Q ss_pred cCCCCCccccCcEEEeecCCccCCCCeeccCCCCcccccccceEeeccc-----hhhhh---------------------
Q 045484 18 NLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKL-----NQLVM--------------------- 71 (179)
Q Consensus 18 ~~~~~~~~~~Gq~I~~G~~A~i~~GN~LPlsalPlg~IP~Gt~I~nIE~-----Gql~r--------------------- 71 (179)
-+=++|.+++||+|++|++|++++||+| ||.+||+||.|||||+ |||+|
T Consensus 101 YIlap~gl~~Gd~I~~g~~~~i~~Gn~l-----pL~~IP~Gt~I~NIE~~pg~Ggkl~RsAGt~A~ii~k~~~~~~vkLP 175 (273)
T TIGR01171 101 YILAPKGLKVGDTVISGPEAPIKPGNAL-----PLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQILAKEGGYVTLRLP 175 (273)
T ss_pred EEEccCCCCCCCEEEECCCCCCCCcCCc-----ccccCCCCCEEEEEEecCCCCceEEEecCCeEEEEEecCCEEEEECC
Confidence 4568999999999999999999999999 5789999999999998 88886
Q ss_pred -hhhheEeccceEeEeeeecCCCchhhhhhhhhhhhhcccCCCCCeeeeeeCCCCcCCCCCCCCCCCCCCCCCCCCCCCC
Q 045484 72 -TLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPW 150 (179)
Q Consensus 72 -~~ik~v~~~CrAtIG~Va~ggsN~~h~~k~lgKAGr~r~lg~RP~VRGvaMNpvdHPhGGG~gk~~~~~~~g~~~~tpW 150 (179)
+++++|+++|+||||+| ||.+|.+++++|||++||+++||+||||||||||||||||||+++ +|++|+|||
T Consensus 176 SGe~r~i~~~c~AtiG~V----sn~~~~~~~~gKAG~~r~lg~rP~VRGvAMNpvDHPHGGGegk~~----~g~~~~spw 247 (273)
T TIGR01171 176 SGEMRMVLKECRATIGEV----GNEDHNNIVLGKAGRSRWLGIRPTVRGVAMNPVDHPHGGGEGRTP----GGRHPVTPW 247 (273)
T ss_pred CCCeEEECCcCeEEEEEc----cCCchhccEeccchhheeCCCCCccccEecCcccCCCCCCCCcCC----CCCCCCCCC
Confidence 56789999999999999 899999999999999999999999999999999999999999997 568999999
Q ss_pred CccccceecCccccCccccceeeee
Q 045484 151 GKPCKWCKTASRKKKRKFSCLIILS 175 (179)
Q Consensus 151 G~~~kg~kTr~~kk~~k~~~~~i~~ 175 (179)
|+++||+|||++ +|+++.+|++
T Consensus 248 G~~~kg~kTr~~---~k~~~~~i~~ 269 (273)
T TIGR01171 248 GKPTKGYKTRKK---KKYSDKFIVR 269 (273)
T ss_pred eeeccccccCCC---CCCCCceEEE
Confidence 999999999976 4444445543
No 2
>PRK09374 rplB 50S ribosomal protein L2; Validated
Probab=100.00 E-value=3.6e-53 Score=368.60 Aligned_cols=142 Identities=35% Similarity=0.556 Sum_probs=128.8
Q ss_pred cCCCCCccccCcEEEeecCCccCCCCeeccCCCCcccccccceEeeccc-----hhhhh---------------------
Q 045484 18 NLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKL-----NQLVM--------------------- 71 (179)
Q Consensus 18 ~~~~~~~~~~Gq~I~~G~~A~i~~GN~LPlsalPlg~IP~Gt~I~nIE~-----Gql~r--------------------- 71 (179)
-+=++|.+++||+|++|.++++++||+| ||.+||+||.|||||+ |||+|
T Consensus 103 YIlAp~gl~~Gd~I~~g~~~~i~~Gn~l-----pL~~IP~Gt~I~NIE~~pG~Ggkl~RsAGt~A~ii~k~~~~~~vkLP 177 (276)
T PRK09374 103 YILAPKGLKVGDTVVSGPDADIKPGNAL-----PLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQLVAKEGKYATLRLP 177 (276)
T ss_pred EEEecCCCCCCCEEEeCCCCCCCccCcc-----ccccCCCCCEEEEEEecCCCCceeEeecCCeEEEEEecCCEEEEECC
Confidence 4558999999999999999999999999 5789999999999998 88886
Q ss_pred -hhhheEeccceEeEeeeecCCCchhhhhhhhhhhhhcccCCCCCeeeeeeCCCCcCCCCCCCCCCCCCCCCCCCCCCCC
Q 045484 72 -TLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPW 150 (179)
Q Consensus 72 -~~ik~v~~~CrAtIG~Va~ggsN~~h~~k~lgKAGr~r~lg~RP~VRGvaMNpvdHPhGGG~gk~~~~~~~g~~~~tpW 150 (179)
+++++|+++|+||||+| ||.+|.+++++|||++||+++||+||||||||||||||||||+++ +|++|+|||
T Consensus 178 SGe~r~i~~~c~AtIG~V----sn~~~~~~~lgKAG~~r~lg~rP~VRGVAMNpvDHPHGGGegkt~----~g~~~~spw 249 (276)
T PRK09374 178 SGEVRKVLAECRATIGEV----GNEEHSNISLGKAGRSRWLGIRPTVRGVAMNPVDHPHGGGEGRTS----GGRHPVTPW 249 (276)
T ss_pred CCCeEEEcccccEEEEee----cCcchhhcchhhhhhheeCCCCCccccEecCcccCCCCCCCCcCC----CCCCCCCCC
Confidence 56789999999999999 899999999999999999999999999999999999999999997 568999999
Q ss_pred CccccceecCccccCccccceeeee
Q 045484 151 GKPCKWCKTASRKKKRKFSCLIILS 175 (179)
Q Consensus 151 G~~~kg~kTr~~kk~~k~~~~~i~~ 175 (179)
|+++||+|||++ +|++|.+|++
T Consensus 250 G~~~kg~kTr~~---~k~~~~~i~~ 271 (276)
T PRK09374 250 GKPTKGYKTRKK---NKRSDKFIVR 271 (276)
T ss_pred eeecccccccCC---CCCCCceEEE
Confidence 999999999975 4445555554
No 3
>PTZ00031 ribosomal protein L2; Provisional
Probab=100.00 E-value=4.2e-53 Score=373.62 Aligned_cols=139 Identities=32% Similarity=0.528 Sum_probs=127.7
Q ss_pred cCCCCCccccCcEEEeecCCccCCCCeeccCCCCcccccccceEeeccc-----hhhhh---------------------
Q 045484 18 NLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKL-----NQLVM--------------------- 71 (179)
Q Consensus 18 ~~~~~~~~~~Gq~I~~G~~A~i~~GN~LPlsalPlg~IP~Gt~I~nIE~-----Gql~r--------------------- 71 (179)
-+=+++.+++||+|++|.+|++++||+| ||.+||+||.|||||+ |||+|
T Consensus 134 YIlApeGl~vGd~I~sg~~a~i~~GN~l-----PL~~IP~GT~IhNIE~~pG~Ggkl~RSAGt~A~Ii~k~~~~~~VkLP 208 (317)
T PTZ00031 134 YILAPLLLRPGDKIIASKYANINPGNSL-----PLRNIPVGSIVHNVEMRPGAGGQIIRAGGTYATVVSKDEQFATLKLK 208 (317)
T ss_pred EEEccCCCCCCCEEEeCCCCCCCccCcc-----ccccCCCCCEEEEEEecCCCCceEEEecCCeEEEEEccCCEEEEECC
Confidence 4558999999999999999999999999 5789999999999998 88886
Q ss_pred -hhhheEeccceEeEeeeecCCCchhhhhhhhhhhhhcccCCCCCeeeeeeCCCCcCCCCCCCCCCCCCCCCCCCCCCCC
Q 045484 72 -TLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPW 150 (179)
Q Consensus 72 -~~ik~v~~~CrAtIG~Va~ggsN~~h~~k~lgKAGr~r~lg~RP~VRGvaMNpvdHPhGGG~gk~~~~~~~g~~~~tpW 150 (179)
+++++|+++|+||||+| ||.+|.+++++|||++||+++||+||||||||||||||||||+++ +|++|+|||
T Consensus 209 SGe~r~i~~~C~ATIG~V----sn~~~~~k~lgKAG~~Rwlg~RP~VRGVAMNPVDHPHGGGeGkt~----~gr~p~spW 280 (317)
T PTZ00031 209 STEIRKFPLDCWATIGQV----SNLEHHMRILGKAGVNRWLGKRPVVRGVAMNPSKHPHGGGTSKKG----TKRPKCSLW 280 (317)
T ss_pred CCCEEEECccCeEEEEEc----cCCccccceeccchhhhcCCCCCCcccCccCCccCCCCCCCCCCC----CCCCCCCCC
Confidence 46788999999999999 899999999999999999999999999999999999999999997 568999999
Q ss_pred CccccceecCccccCcccc
Q 045484 151 GKPCKWCKTASRKKKRKFS 169 (179)
Q Consensus 151 G~~~kg~kTr~~kk~~k~~ 169 (179)
|+++||+|||++|++++||
T Consensus 281 G~~tkG~kTrk~k~~~~~i 299 (317)
T PTZ00031 281 GICRDGYKTRSKKKPLGLI 299 (317)
T ss_pred ccccCCcccCCCCCCCceE
Confidence 9999999999865555543
No 4
>CHL00052 rpl2 ribosomal protein L2
Probab=100.00 E-value=1.1e-52 Score=365.07 Aligned_cols=142 Identities=35% Similarity=0.575 Sum_probs=127.2
Q ss_pred cCCCCCccccCcEEEeecCCccCCCCeeccCCCCcccccccceEeeccc-----hhhhh---------------------
Q 045484 18 NLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKL-----NQLVM--------------------- 71 (179)
Q Consensus 18 ~~~~~~~~~~Gq~I~~G~~A~i~~GN~LPlsalPlg~IP~Gt~I~nIE~-----Gql~r--------------------- 71 (179)
-+=++|.+++||+|++|.+|++++||+| ||.+||+||.|||||+ |||+|
T Consensus 101 YIlAp~gl~~Gd~I~~g~~~~i~~Gn~l-----pL~~IP~Gt~I~NIE~~pg~Ggk~~RsAGt~A~ii~k~~~~~~vkLP 175 (273)
T CHL00052 101 YILHPRGLKIGDTIVSGTEAPIKIGNAL-----PLTNIPLGTAIHNIEITPGKGGQLARAAGAVAKLIAKEGKSATLKLP 175 (273)
T ss_pred EEEccCCCCCCCEEEeCCCCCCCccccc-----ccccCCCCCEEEEEEecCCCCceEEEecCCeEEEEEecCCEEEEECC
Confidence 3458999999999999999999999999 5789999999999998 88886
Q ss_pred -hhhheEeccceEeEeeeecCCCchhhhhhhhhhhhhcccCCCCCeeeeeeCCCCcCCCCCCCCCCCCCCCCCC-CCCCC
Q 045484 72 -TLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGR-CSLTP 149 (179)
Q Consensus 72 -~~ik~v~~~CrAtIG~Va~ggsN~~h~~k~lgKAGr~r~lg~RP~VRGvaMNpvdHPhGGG~gk~~~~~~~g~-~~~tp 149 (179)
+++++|+++|+||||+| ||.+|.+++++|||++||+++||+||||||||||||||||||+++ +|+ +|+||
T Consensus 176 SGe~r~v~~~c~AtIG~V----sn~~~~~~~lgKAG~~r~lg~rP~VRGvAMNpvDHPHGGGegkt~----~Gr~~~vsp 247 (273)
T CHL00052 176 SGEVRLISKNCSATIGQV----GNVDVNNKSLGKAGSKRWLGKRPKVRGVVMNPVDHPHGGGEGRAP----IGRKKPVTP 247 (273)
T ss_pred CCCeEEECCcCeEEEEEc----cCCchhhcEecchhhhhcCCCCCcCCeEecCCccCCCCCCCccCC----CCCcCCCCc
Confidence 46788999999999999 899999999999999999999999999999999999999999986 564 68999
Q ss_pred CCccccceecCccccCccccceeeee
Q 045484 150 WGKPCKWCKTASRKKKRKFSCLIILS 175 (179)
Q Consensus 150 WG~~~kg~kTr~~kk~~k~~~~~i~~ 175 (179)
||+++||+|||++ +|+++.+|++
T Consensus 248 wG~~~kg~kTr~~---~k~~~~~i~~ 270 (273)
T CHL00052 248 WGKPALGRKTRKR---KKYSDNLILR 270 (273)
T ss_pred CcccccccCccCC---CCCCCCeEEe
Confidence 9999999999975 3444444443
No 5
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-52 Score=362.69 Aligned_cols=138 Identities=32% Similarity=0.476 Sum_probs=127.4
Q ss_pred CCCCCccccCcEEEeecCCccCCCCeeccCCCCcccccccceEeeccc-----hhhhh----------------------
Q 045484 19 LGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKL-----NQLVM---------------------- 71 (179)
Q Consensus 19 ~~~~~~~~~Gq~I~~G~~A~i~~GN~LPlsalPlg~IP~Gt~I~nIE~-----Gql~r---------------------- 71 (179)
+=+++-|++||+|++|++|+|++||+| ||++||+||.|||||+ |||+|
T Consensus 104 ilAp~Gl~vGd~I~sG~~a~ik~GN~l-----pL~~IP~Gt~VhNVE~~pG~GGq~aRSaGtyA~vv~~~~~y~~vrLpS 178 (275)
T COG0090 104 ILAPEGLKVGDVIESGKDADIKPGNAL-----PLGNIPEGTIVHNVELKPGDGGQLARSAGTYAQVVGKEGNYVIVRLPS 178 (275)
T ss_pred EEccCccccCCEEEeCCCCCcCCccee-----eeccCCCCceEEeeeeccCCCceEEEeCCceEEEEEccCCEEEEECCC
Confidence 458999999999999999999999999 5799999999999999 99987
Q ss_pred hhhheEeccceEeEeeeecCCCchhhhhhhhhhhhhcccCCCCCeeeeeeCCCCcCCCCCCCCCCCCCCCCCCCCCCCCC
Q 045484 72 TLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWG 151 (179)
Q Consensus 72 ~~ik~v~~~CrAtIG~Va~ggsN~~h~~k~lgKAGr~r~lg~RP~VRGvaMNpvdHPhGGG~gk~~~~~~~g~~~~tpWG 151 (179)
++++.|+++||||||+| +|.+|.+++|+|||++||+++||+|||||||||||||||||||++ ++++|+||||
T Consensus 179 Ge~r~v~~~CrATIGvV----~n~~~~~~~lgKAGr~r~~g~rPtVRGvAMNpvDHPHGGGeg~~~----ggk~p~~pwg 250 (275)
T COG0090 179 GEMRKVLSECRATIGVV----ANGGHILKPLGKAGRARHKGKRPTVRGVAMNPVDHPHGGGEGQHP----GGKPPTVPWG 250 (275)
T ss_pred CCeEeecccccEEEEEe----cCCccccceecccchhcCCccCCccceeecCCCcCCCCCCCCCCC----CCCCCCCCCC
Confidence 46789999999999999 788999999999999999999999999999999999999999987 4689999999
Q ss_pred ccccceecCcccc-Ccccc
Q 045484 152 KPCKWCKTASRKK-KRKFS 169 (179)
Q Consensus 152 ~~~kg~kTr~~kk-~~k~~ 169 (179)
++++|++||..+| +++||
T Consensus 251 ~~~~Gkktr~~~krt~~~i 269 (275)
T COG0090 251 KPTPGKKTRIAAKRTGKFI 269 (275)
T ss_pred CCCCcccccccccccCcee
Confidence 9999999999533 66654
No 6
>PF03947 Ribosomal_L2_C: Ribosomal Proteins L2, C-terminal domain; InterPro: IPR022669 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 L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3MRZ_C 3F1H_D 3PYO_C 3F1F_D 3PYV_C 3PYR_C 1VSA_B 3D5B_D 3PYT_C 3MS1_C ....
Probab=100.00 E-value=7.9e-44 Score=280.58 Aligned_cols=102 Identities=40% Similarity=0.765 Sum_probs=92.2
Q ss_pred cCCCCeeccCCCCcccccccceEeeccc-----hhhhh----------------------hhhheEeccceEeEeeeecC
Q 045484 39 LHRHSSLGFSALPFSTITLLNAISPVKL-----NQLVM----------------------TLILKLEVACHLLVCMLGPS 91 (179)
Q Consensus 39 i~~GN~LPlsalPlg~IP~Gt~I~nIE~-----Gql~r----------------------~~ik~v~~~CrAtIG~Va~g 91 (179)
|++||+| ||.+||+||.|||||. ++|+| +++++|+++|+||||+|
T Consensus 1 i~~Gn~~-----pL~~ip~Gt~I~nIE~~pg~g~~~~RaAGt~a~ii~k~~~~~~ikLPSG~~k~v~~~c~AtiG~v--- 72 (130)
T PF03947_consen 1 IKIGNSL-----PLGNIPIGTIIHNIELKPGDGGKLARAAGTYAQIISKEGNYVVIKLPSGEIKLVSSNCRATIGRV--- 72 (130)
T ss_dssp SSTTSEE-----EGGGSSTTEEEESBESSTTSSEEBSSSTTBBEEEEEEESSEEEEEETTSEEEEEETTSEEEESCB---
T ss_pred CCCccch-----hHhhCCCCCEEEEEecCCCCCceEEeeCCCEEEEEEeccceeEEEecCCCeEeecccceEEEEEe---
Confidence 6899999 5789999999999998 78876 46678999999999999
Q ss_pred CCchhhhhhhhhhhhhcccCCCCCeeeeeeCCCCcCCCCCCCCCCCCCCCCCC-CCCCCCCcc
Q 045484 92 STTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGR-CSLTPWGKP 153 (179)
Q Consensus 92 gsN~~h~~k~lgKAGr~r~lg~RP~VRGvaMNpvdHPhGGG~gk~~~~~~~g~-~~~tpWG~~ 153 (179)
+|.+|.+++++|||++||+++||+||||||||||||||||+|+++ +|| +|+||||++
T Consensus 73 -sn~~~~~~~~~KAG~~r~~g~rP~VRGvamNpvdHPhGGG~g~~~----~gr~~~~s~wg~p 130 (130)
T PF03947_consen 73 -SNGGHKEKKLGKAGRNRWLGKRPKVRGVAMNPVDHPHGGGEGKTS----GGRPPPVSPWGKP 130 (130)
T ss_dssp -SSTTGGGSB-SSHHHHHHTCCSSS-SGTCSTTTTSSTCTSSSSSS----TSSSSEBTTTSSS
T ss_pred -cCccccchhhhhhhhccccccCccccceeeccccCcCCCCCCcCC----CCCCCCCCCCCCC
Confidence 899999999999999999999999999999999999999999987 467 899999986
No 7
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated
Probab=100.00 E-value=1.3e-41 Score=291.23 Aligned_cols=110 Identities=22% Similarity=0.289 Sum_probs=103.6
Q ss_pred cCCCCCccccCcEEEeecCCccCCCCeeccCCCCcccccccceEeeccc-----hhhhh---------------------
Q 045484 18 NLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKL-----NQLVM--------------------- 71 (179)
Q Consensus 18 ~~~~~~~~~~Gq~I~~G~~A~i~~GN~LPlsalPlg~IP~Gt~I~nIE~-----Gql~r--------------------- 71 (179)
-+=+++.+++||+|++|.++++++||+| ||.+||+||.|||||+ |||+|
T Consensus 68 YIiAp~gl~~Gd~I~sg~~~~i~~Gn~l-----pL~~IP~Gt~I~NIE~~pG~Ggkl~RSAGt~A~Ii~k~~~~~~vkLP 142 (238)
T PRK09612 68 LILAPEGLYVGQEIEIGPSAEIKPGNTL-----PLGEIPEGTPVCNIESRPGDGGKFARSSGTYALVVGHEGDKVIVQLP 142 (238)
T ss_pred EEEccCCCCCCCEEEeCCCCCCCCcccc-----CHhhCCCCCEEEEEEecCCCCcceEEcCCCeEEEEEecCCEEEEECC
Confidence 4568999999999999999999999999 6789999999999999 88886
Q ss_pred -hhhheEeccceEeEeeeecCCCchhhhhhhhhhhhhcccC-----CCCCeeeeeeCCCCcCCCCCCCCCC
Q 045484 72 -TLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWL-----GQRPVIRGVPMNPVDHPRGRGEGRG 136 (179)
Q Consensus 72 -~~ik~v~~~CrAtIG~Va~ggsN~~h~~k~lgKAGr~r~l-----g~RP~VRGvaMNpvdHPhGGG~gk~ 136 (179)
+++++|+++|+||||+| +|.+|.+++++|||++||+ ++||+||||||||||||||||||++
T Consensus 143 SGe~r~i~~~c~AtiG~V----sn~~~~~~~lgKAG~~r~~~k~~~g~rP~VRGvAMNpvDHPHGGGeg~~ 209 (238)
T PRK09612 143 SGKIKELNPRCRATIGVV----AGGGRKEKPFLKAGKKYHKMKAKAKKWPRVRGVAMNAVDHPHGGGNHQH 209 (238)
T ss_pred CCCeEEECCcCeEEEEEc----cCCccccceeeechhhhhhhhccCCCCCccCeEeeCCccCCcCCCCCCC
Confidence 46788999999999999 8999999999999999999 9999999999999999999999987
No 8
>PTZ00180 60S ribosomal protein L8; Provisional
Probab=100.00 E-value=6.6e-40 Score=283.65 Aligned_cols=110 Identities=22% Similarity=0.243 Sum_probs=101.4
Q ss_pred cCCCCCccccCcEEEeecCCccCCCCeeccCCCCcccccccceEeeccc-----hhhhh---------------------
Q 045484 18 NLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKL-----NQLVM--------------------- 71 (179)
Q Consensus 18 ~~~~~~~~~~Gq~I~~G~~A~i~~GN~LPlsalPlg~IP~Gt~I~nIE~-----Gql~r--------------------- 71 (179)
-+=++|.+++||+|++|++|++++||+| ||.+||+||.|||||+ |||+|
T Consensus 75 YIlAp~gl~vGd~I~~g~~a~i~~GN~l-----pL~~IP~GT~IhNIE~~pG~GgklaRSAGt~A~ii~k~k~~~~~~vk 149 (260)
T PTZ00180 75 LMVAPEGMYTGQYVYCGAKAPLAIGNVL-----PLGQIPEGTIVCNVEEKPGDRGTLARASGCYATIIGHSDDGGKTRIR 149 (260)
T ss_pred EEEeeCCCCCCCEEEeCCCCCCCCcCcc-----CHhhCCCCCeEEEEeccCCCCceEEEecCCeEEEEEEcccCCEEEEE
Confidence 4568999999999999999999999999 5789999999999999 88886
Q ss_pred ---hhhheEeccceEeEeeeecCCCchhhhhhhhhhhhhcccC-----CCCCeeeeeeCCCCcCCCCCCCCCC
Q 045484 72 ---TLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWL-----GQRPVIRGVPMNPVDHPRGRGEGRG 136 (179)
Q Consensus 72 ---~~ik~v~~~CrAtIG~Va~ggsN~~h~~k~lgKAGr~r~l-----g~RP~VRGvaMNpvdHPhGGG~gk~ 136 (179)
+++++|+++|+||||+| +|.+|.+++|+|||++||+ .+||+||||||||||||||||||++
T Consensus 150 LPSGe~r~v~~~c~ATIG~V----sn~~~~~k~l~KAG~~~~~~~a~~~rwP~VRGVAMNPvDHPHGGGegk~ 218 (260)
T PTZ00180 150 LPSGQKKTVSSLSRAMIGIV----AGGGRIDKPVLKAGNAFHKYRGKRNCWPKVRGVAMNPVEHPHGGGNHQH 218 (260)
T ss_pred CCCCCeEeECCCCeEEEEEc----cCCcchheeeccccchhhhhhCcCCCCCccccEeeCCccCCcCCCCCCC
Confidence 45678999999999999 8999999999999999997 4579999999999999999999983
No 9
>KOG2309 consensus 60s ribosomal protein L2/L8 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2.9e-32 Score=233.13 Aligned_cols=117 Identities=25% Similarity=0.326 Sum_probs=101.7
Q ss_pred hhhhhccCCCCCccccCcEEEeecCCccCCCCeeccCCCCcccccccceEeeccc-----hhhhh---------------
Q 045484 12 IDRRNQNLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKL-----NQLVM--------------- 71 (179)
Q Consensus 12 ~~~~~~~~~~~~~~~~Gq~I~~G~~A~i~~GN~LPlsalPlg~IP~Gt~I~nIE~-----Gql~r--------------- 71 (179)
.+.+-+-+-+.|..|+||+++||.+|++.+||+| |++++|+|+.|||+|. |.|+|
T Consensus 63 ~~~~~~~F~a~eg~~tgq~~~~g~ka~~~ignv~-----~~~s~peg~~v~~ve~~~gdrg~lar~sGnya~vIaHn~dt 137 (248)
T KOG2309|consen 63 YKKDKELFIAAEGMYTGQFVYCGKKAQLNIGNVL-----PVGSMPEGTIVCNVEEKPGDRGALARASGNYAIVIAHNPDT 137 (248)
T ss_pred ccceeEEEeccccceecceecCCcccccccccee-----eccccccceEEEEeeccCchhhhHHhhcCceeEEEecCccc
Confidence 3444556677888999999999999999999999 5799999999999999 77776
Q ss_pred --hhh-------heEeccceEeEeeeecCCCchhhhhhhhhhhhhcccC-----CCCCeeeeeeCCCCcCCCCCCCCCCC
Q 045484 72 --TLI-------LKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWL-----GQRPVIRGVPMNPVDHPRGRGEGRGK 137 (179)
Q Consensus 72 --~~i-------k~v~~~CrAtIG~Va~ggsN~~h~~k~lgKAGr~r~l-----g~RP~VRGvaMNpvdHPhGGG~gk~~ 137 (179)
|.| +.|++.|||+||+|| ||+ +.++|++|||+.|++ +.||+||||||||||||||||+++..
T Consensus 138 ~kTrIkLPsgaKKvV~S~~RamIG~vA-ggG---~~dKp~lKag~a~~K~~~Krn~wPrvRGVAMnPVeHphGGgnhqhi 213 (248)
T KOG2309|consen 138 KKTRIKLPSGAKKVVQSACRAMIGVVA-GGG---RTDKPLLKAGRAYHKYKAKRNCWPRVRGVAMNPVEHPHGGGNHQHI 213 (248)
T ss_pred cceEEecCCCccceeccccceEEEEec-CCc---cccchhhhhhhHHHHhhhhcCCchhhcceecccccCCCCCCccccc
Confidence 222 469999999999997 444 889999999999986 45999999999999999999999974
No 10
>KOG0438 consensus Mitochondrial/chloroplast ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2.9e-32 Score=239.97 Aligned_cols=141 Identities=30% Similarity=0.494 Sum_probs=118.4
Q ss_pred CCCccccCcEEEeecCCc-----cCCCCeeccCCCCcccccccceEeeccchhhhh----------------------hh
Q 045484 21 NRDTERDRQKWLGAEYAQ-----LHRHSSLGFSALPFSTITLLNAISPVKLNQLVM----------------------TL 73 (179)
Q Consensus 21 ~~~~~~~Gq~I~~G~~A~-----i~~GN~LPlsalPlg~IP~Gt~I~nIE~Gql~r----------------------~~ 73 (179)
+.|.+.+||.|..+.+.+ .+.||++||++||++++.+..++.+...+||+| ++
T Consensus 133 a~egm~aGD~i~ss~~i~~~av~~~~Gna~Pl~~lp~GT~ih~~e~~p~~~~~f~raAGt~a~ilak~~~~aiv~Lps~r 212 (312)
T KOG0438|consen 133 ATEGLKAGDTILSSRKIPFMAVKGKEGNALPLGDLPVGTLIHNVEITPGRSAQFARAAGTSATILAKAGKFAIVQLPSKR 212 (312)
T ss_pred EecCCCCCCccccccccccccccccCCCceeecccchhhhhhhhccCCCcchhhhhhcCchhhhhhcCCCceeEEccccc
Confidence 567788999999888877 799999976666655555555555555588886 23
Q ss_pred hheEeccceEeEeeeecCCCchhhhhhhhhhhhhcccCCCCCeeeeeeCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 045484 74 ILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGKP 153 (179)
Q Consensus 74 ik~v~~~CrAtIG~Va~ggsN~~h~~k~lgKAGr~r~lg~RP~VRGvaMNpvdHPhGGG~gk~~~~~~~g~~~~tpWG~~ 153 (179)
.+.|+.+|+||||+| ||++|+.+.+||||++||+|+||.||||+||++|||||||.|+.- ....|++|||++
T Consensus 213 ~~~~~~tC~ATvGrv----sni~~~~r~~GkAgr~rwlG~Rp~vrg~~~s~~~H~kgg~~gr~i----~~~~P~~~~~~~ 284 (312)
T KOG0438|consen 213 ERSVLRTCVATVGRV----SNIDHNHRILGKAGRSRWLGKRPQVRGVLMSGLDHPKGGGKGRKI----GRKKPVTPWGKP 284 (312)
T ss_pred hhhhhhhhheeeccc----cccccccceecccchhhhcccCcccccccccCccCCCCCCccccc----cCCCCCCccccc
Confidence 356999999999999 999999999999999999999999999999999999999999872 346899999999
Q ss_pred ccc-eecCccccCcccc
Q 045484 154 CKW-CKTASRKKKRKFS 169 (179)
Q Consensus 154 ~kg-~kTr~~kk~~k~~ 169 (179)
+|+ ++||+++..+|.-
T Consensus 285 ak~~~~~r~~~~a~k~~ 301 (312)
T KOG0438|consen 285 AKGLRPTRRKKGANKVL 301 (312)
T ss_pred cccCCCccccccccccc
Confidence 999 9999887776654
No 11
>PF03991 Prion_octapep: Copper binding octapeptide repeat; InterPro: IPR020949 Prion protein (PrP-c) [, , ] is a small glycoprotein found in high quantity in the brain of animals infected with certain degenerative neurological diseases, such as sheep scrapie and bovine spongiform encephalopathy (BSE), and the human dementias Creutzfeldt-Jacob disease (CJD) and Gerstmann-Straussler syndrome (GSS). PrP-c is encoded in the host genome and is expressed both in normal and infected cells. During infection, however, the PrP-c molecule become altered (conformationally rather than at the amino acid level) to an abnormal isoform, PrP-sc. In detergent-treated brain extracts from infected individuals, fibrils composed of polymers of PrP-sc, namely scrapie-associated fibrils or prion rods, can be evidenced by electron microscopy. The precise function of the normal PrP isoform in healthy individuals remains unknown. Several results, mainly obtained in transgenic animals, indicate that PrP-c might play a role in long-term potentiation, in sleep physiology, in oxidative burst compensation (PrP can fix four Cu2+ through its octarepeat domain), in interactions with the extracellular matrix (PrP-c can bind to the precursor of the laminin receptor, LRP), in apoptosis and in signal transduction (costimulation of PrP-c induces a modulation of Fyn kinase phosphorylation) []. The normal isoform, PrP-c, is anchored at the cell membrane, in rafts, through a glycosyl phosphatidyl inositol (GPI); its half-life at the cell surface is 5 h, after which the protein is internalised through a caveolae-dependent mechanism and degraded in the endolysosome compartment. Conversion between PrP-c and PrP-sc occurs likely during the internalisation process. This repeat is found at the amino terminus of mammalian prion proteins. It has been shown to bind to copper [].
Probab=77.49 E-value=1.4 Score=20.23 Aligned_cols=7 Identities=57% Similarity=1.080 Sum_probs=5.3
Q ss_pred CCCCCCC
Q 045484 128 PRGRGEG 134 (179)
Q Consensus 128 PhGGG~g 134 (179)
|||||-|
T Consensus 1 phgG~Wg 7 (8)
T PF03991_consen 1 PHGGGWG 7 (8)
T ss_pred CCCCcCC
Confidence 7888755
No 12
>KOG0438 consensus Mitochondrial/chloroplast ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=61.02 E-value=2.7 Score=38.39 Aligned_cols=19 Identities=26% Similarity=0.478 Sum_probs=18.0
Q ss_pred CCCCcccccccceEeeccc
Q 045484 48 SALPFSTITLLNAISPVKL 66 (179)
Q Consensus 48 salPlg~IP~Gt~I~nIE~ 66 (179)
.|+||+.||.||.|||+|.
T Consensus 160 na~Pl~~lp~GT~ih~~e~ 178 (312)
T KOG0438|consen 160 NALPLGDLPVGTLIHNVEI 178 (312)
T ss_pred Cceeecccchhhhhhhhcc
Confidence 3899999999999999999
No 13
>PF10371 EKR: Domain of unknown function; InterPro: IPR019456 EKR is a short, 33 residue, domain found in bacterial and some lower eukaryotic species which lies between a POR (pyruvate ferredoxin/flavodoxin oxidoreductase) domain (IPR019752 from INTERPRO) and the 4Fe-4S binding domain (IPR017896 from INTERPRO). It contains a characteristic EKR sequence motif. The exact function of this domain is not known. ; GO: 0016903 oxidoreductase activity, acting on the aldehyde or oxo group of donors, 0055114 oxidation-reduction process; PDB: 2PDA_B 2C3Y_A 2C3P_B 2UZA_A 2C3U_B 2C42_A 1B0P_B 2C3M_A 2C3O_B 1KEK_B ....
Probab=51.18 E-value=5.4 Score=28.11 Aligned_cols=22 Identities=27% Similarity=0.215 Sum_probs=13.1
Q ss_pred cCCCCeeccCCCCc-ccccccce
Q 045484 39 LHRHSSLGFSALPF-STITLLNA 60 (179)
Q Consensus 39 i~~GN~LPlsalPl-g~IP~Gt~ 60 (179)
...||-||+|+++. |++|.||.
T Consensus 28 ~~~Gd~LPVSaf~~dGt~p~GTa 50 (59)
T PF10371_consen 28 AQEGDDLPVSAFPPDGTFPTGTA 50 (59)
T ss_dssp TTTGGGS-GGGS-TT--B-TTGG
T ss_pred HccCCCCCceecCCCCCccCchh
Confidence 46799999998886 67777764
No 14
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=38.25 E-value=30 Score=20.35 Aligned_cols=26 Identities=19% Similarity=0.018 Sum_probs=18.9
Q ss_pred eehhhhhhhccCCCCCccccCcEEEe
Q 045484 8 RQSEIDRRNQNLGNRDTERDRQKWLG 33 (179)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~Gq~I~~ 33 (179)
.-.+|-+.|..+.++++++.||.+.+
T Consensus 17 ~~~~l~~~N~~~~~~~~~~~g~~l~i 42 (44)
T TIGR02899 17 DFDELIQANPQLSNPNLIYPGMKIKI 42 (44)
T ss_pred CHHHHHHHhhcCCCCCCcCCCCEEec
Confidence 34566666766667788999998764
No 15
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=37.87 E-value=14 Score=22.50 Aligned_cols=26 Identities=19% Similarity=0.166 Sum_probs=20.0
Q ss_pred eeehhhhhhhccCCCCCccccCcEEEe
Q 045484 7 VRQSEIDRRNQNLGNRDTERDRQKWLG 33 (179)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~Gq~I~~ 33 (179)
+..++|-+-|.++...+ |++||+|..
T Consensus 18 ~~~~~l~~~N~~~~~~~-l~~G~~l~i 43 (44)
T PF01476_consen 18 ISVDELMELNPNIDSDN-LQPGQKLCI 43 (44)
T ss_dssp S-HHHHHHHCCTTHGGC-GGTTEEEEE
T ss_pred hhHhHHHHhcCCCCccc-CCCCCEEEe
Confidence 45678888887887777 999999864
No 16
>PF00181 Ribosomal_L2: Ribosomal Proteins L2, RNA binding domain; InterPro: IPR022666 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 L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YIT_A 1Q7Y_C 1YJN_A 3CPW_A 3I56_A 1VQ9_A 1M1K_C 3CC7_A 1YIJ_A 1K9M_C ....
Probab=32.22 E-value=22 Score=25.53 Aligned_cols=16 Identities=0% Similarity=-0.232 Sum_probs=13.3
Q ss_pred cCCCCCccccCcEEEe
Q 045484 18 NLGNRDTERDRQKWLG 33 (179)
Q Consensus 18 ~~~~~~~~~~Gq~I~~ 33 (179)
-+=++|.+++||+|+|
T Consensus 62 yiiA~eg~~vGd~I~s 77 (77)
T PF00181_consen 62 YIIAPEGMKVGDIIES 77 (77)
T ss_dssp EEEEBTTEBTTEEEEE
T ss_pred EEEeECCCcCCCEEEC
Confidence 3457899999999986
No 17
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=24.24 E-value=55 Score=29.90 Aligned_cols=25 Identities=16% Similarity=0.140 Sum_probs=20.8
Q ss_pred hhhhhhhccCCCCCccccCcEEEeec
Q 045484 10 SEIDRRNQNLGNRDTERDRQKWLGAE 35 (179)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~Gq~I~~G~ 35 (179)
.||-+.| ||.+++++|+||++....
T Consensus 83 ~~La~~N-~l~~p~~I~~GQ~L~i~~ 107 (319)
T PRK10871 83 RDLAQRN-NIQAPYSLNVGQTLQVGN 107 (319)
T ss_pred HHHHHhc-CCCCCccccCCCEEEeCC
Confidence 4666677 889999999999999843
No 18
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=23.92 E-value=66 Score=22.56 Aligned_cols=25 Identities=12% Similarity=0.054 Sum_probs=19.1
Q ss_pred eeeeeehhhhhhhccCCCCCccccCcEEEeec
Q 045484 4 TCYVRQSEIDRRNQNLGNRDTERDRQKWLGAE 35 (179)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~Gq~I~~G~ 35 (179)
+.++..+|++.. +.+++||.+.|--
T Consensus 30 ~Gfl~~~~~~~~-------~~~~~Gq~v~~~V 54 (74)
T cd05694 30 TGFLPKKDAGNF-------SKLKVGQLLLCVV 54 (74)
T ss_pred EEEEEHHHCCcc-------cccCCCCEEEEEE
Confidence 567788888754 7889999988764
No 19
>PF09962 DUF2196: Uncharacterized conserved protein (DUF2196); InterPro: IPR019240 A pair of adjacent genes, ablAB (acetyl-beta-lysine biosynthesis) encodes lysine 2,3-aminomutase and beta-lysine acetyltransferase in methanogenic archaea. Homologous pairs, possibly with identical function, occur in a wide range of species, including Bacillus subtilis. This model describes a conserved hypothetical protein, small in size, with a phylogenetic distribution moderately well correlated to that of the acetyltransferase family. This protein family is also described as DUF2196 and COG4895 from COG. The function is unknown.
Probab=20.61 E-value=59 Score=23.36 Aligned_cols=17 Identities=24% Similarity=0.612 Sum_probs=14.2
Q ss_pred CCeeeeeeCCCCcCCCC
Q 045484 114 RPVIRGVPMNPVDHPRG 130 (179)
Q Consensus 114 RP~VRGvaMNpvdHPhG 130 (179)
+..|.-+--|..+||||
T Consensus 30 ~GiV~~iLT~s~~HP~G 46 (62)
T PF09962_consen 30 EGIVKDILTNSPTHPHG 46 (62)
T ss_pred cEEhheeecCCCCCCCC
Confidence 56777777899999998
No 20
>KOG1489 consensus Predicted GTP-binding protein (ODN superfamily) [General function prediction only]
Probab=20.11 E-value=97 Score=29.12 Aligned_cols=45 Identities=7% Similarity=-0.028 Sum_probs=31.4
Q ss_pred ccCcEEEeecCCccCCCCeeccC-CCCcccccccceEeeccchhhh
Q 045484 26 RDRQKWLGAEYAQLHRHSSLGFS-ALPFSTITLLNAISPVKLNQLV 70 (179)
Q Consensus 26 ~~Gq~I~~G~~A~i~~GN~LPls-alPlg~IP~Gt~I~nIE~Gql~ 70 (179)
++++.|+...-..-+..++.--+ ..-+-.+|.||.+..+|.|+++
T Consensus 97 ~~~s~~~a~~Ge~~~s~~~~g~~ak~~~i~VP~Gt~v~d~~~~~~v 142 (366)
T KOG1489|consen 97 HVGSLIQAPNGENGKSKMCHGSNAKHSEIRVPVGTVVKDIEQGKLV 142 (366)
T ss_pred cCCceEEccCCCcCccccccCCCcceEEEecCCccEEeecccchhH
Confidence 67777777666666666665433 2234458999999999887776
Done!