Score = 175 (66.7 bits), Expect = 2.1e-13, P = 2.1e-13
Identities = 40/87 (45%), Positives = 53/87 (60%)
Query: 1 MGNMLIDF---PMKLLMPSSFENIKEIAFKTMHAASK---------LYGLEIEKVRTLNK 48
+G ++ F P+KLLMP+ NI E A KT+ +ASK LYG ++EKV TLN
Sbjct: 5 LGGRVVHFANLPIKLLMPAKLTNIHEFALKTIPSASKIEIKRVLESLYGFDVEKVNTLNM 64
Query: 49 QGMKKRREGCLVTGPNYKKAYRTLKKP 75
G KK+R G L+ +YKKAY TL+ P
Sbjct: 65 DGKKKKRGGLLIAKADYKKAYVTLRSP 91
Parameters:
V=100
filter=SEG
E=0.001
ctxfactor=1.00
Query ----- As Used ----- ----- Computed ----
Frame MatID Matrix name Lambda K H Lambda K H
+0 0 BLOSUM62 0.320 0.135 0.386 same same same
Q=9,R=2 0.244 0.0300 0.180 n/a n/a n/a
Query
Frame MatID Length Eff.Length E S W T X E2 S2
+0 0 75 75 0.00091 102 3 11 22 0.36 29
29 0.47 29
Statistics:
Database: /share/blast/go-seqdb.fasta
Title: go_20130330-seqdb.fasta
Posted: 5:47:42 AM PDT Apr 1, 2013
Created: 5:47:42 AM PDT Apr 1, 2013
Format: XDF-1
# of letters in database: 169,044,731
# of sequences in database: 368,745
# of database sequences satisfying E: 1
No. of states in DFA: 468 (50 KB)
Total size of DFA: 83 KB (2065 KB)
Time to generate neighborhood: 0.00u 0.00s 0.00t Elapsed: 00:00:00
No. of threads or processors used: 24
Search cpu time: 8.21u 0.15s 8.36t Elapsed: 00:00:00
Total cpu time: 8.21u 0.15s 8.36t Elapsed: 00:00:00
Start: Fri May 10 07:51:28 2013 End: Fri May 10 07:51:28 2013
Probab=99.90 E-value=2.4e-24 Score=137.97 Aligned_cols=69 Identities=16% Similarity=0.182 Sum_probs=62.4
Q ss_pred CcceeeecC---ccccCCCeEEEEEcCCCCc---------eeccEEceEEEEeeCCceeeecceeeeCCCeeEEEEEecC
Q 048067 7 DFPMKLLMP---SSFENIKEIAFKTMHAASK---------LYGLEIEKVRTLNKQGMKKRREGCLVTGPNYKKAYRTLKK 74 (75)
Q Consensus 7 n~~~klv~~---~~~~~~n~y~F~V~~~anK---------~f~VkV~~VnT~~~~gK~Kr~~~~~g~~~~~KKA~VtL~~ 74 (75)
|++.+|+++ ..+.+.|+|+|+|+++||| +|||+|.+|||++++||.||.|+..|++++||||||||++
T Consensus 2 ~iI~~PivTEKs~~l~e~n~y~F~V~~~anK~eIK~avE~lf~VkV~~VNt~~~~~k~kr~~~~~G~~~~~KKAiVtL~~ 81 (93)
T CHL00030 2 DGIKYPVFTDKSIRLLEKNQYTFDVDSGSTKTEIKHWIELFFGVKVIAVNSHRLPRKKRRMGPIMGHKMHYKRMIITLQP 81 (93)
T ss_pred ceeccceeCHHHHHhhHCCEEEEEECCCCCHHHHHHHHHHHhCCeEEEEEEEEcCCCccccCCcccccCCcEEEEEEcCC
Confidence 577888887 2344579999999999999 9999999999999999999999999999999999999987
Q ss_pred C
Q 048067 75 P 75 (75)
Q Consensus 75 p 75 (75)
+
T Consensus 82 g 82 (93)
T CHL00030 82 G 82 (93)
T ss_pred c
Confidence 4
>PF00276 Ribosomal_L23: Ribosomal protein L23; InterPro: IPR013025 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms
Probab=99.88 E-value=2.8e-23 Score=131.58 Aligned_cols=69 Identities=35% Similarity=0.492 Sum_probs=60.6
Q ss_pred CcceeeecCc----cccCCCeEEEEEcCCCCc---------eeccEEceEEEEeeCCceeeecceeeeCCCeeEEEEEec
Q 048067 7 DFPMKLLMPS----SFENIKEIAFKTMHAASK---------LYGLEIEKVRTLNKQGMKKRREGCLVTGPNYKKAYRTLK 73 (75)
Q Consensus 7 n~~~klv~~~----~~~~~n~y~F~V~~~anK---------~f~VkV~~VnT~~~~gK~Kr~~~~~g~~~~~KKA~VtL~ 73 (75)
|++..|+++. ..++.|+|+|+|+++||| +|||+|.+|||++++||.+|.|...|++++||||||+|+
T Consensus 2 ~ii~~p~iTeKs~~~~~~~n~~tF~V~~~atK~~Ik~aie~iy~V~V~~Vnt~~~~gk~kR~g~~~g~~~~~KKaiVtL~ 81 (91)
T PF00276_consen 2 DIIKKPVITEKSMKLLENPNQYTFEVDPRATKTEIKEAIEKIYGVKVKKVNTMNYPGKKKRKGKFVGKTKDYKKAIVTLK 81 (91)
T ss_dssp TTEEEE--SHHHHHHHHHSSEEEEEETTTSTHHHHHHHHHHHHTSEEEEEEEEEETSEEEESSSCEEEE-EEEEEEEEES
T ss_pred CEeecceecHhHHHhhhcCCEEEEEEeCCCCHHHHHHHHHhhcCCCeeEEEEeEeCCCceEeCCccccCCCcEEEEEEeC
Confidence 7888999982 345569999999999999 999999999999999999999999999999999999999
Q ss_pred CC
Q 048067 74 KP 75 (75)
Q Consensus 74 ~p 75 (75)
++
T Consensus 82 ~~ 83 (91)
T PF00276_consen 82 EG 83 (91)
T ss_dssp TT
T ss_pred CC
Confidence 86
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 domain is found in both eukaryotic L25 and prokaryotic and eukaryotic L23 proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3DF4_T 3DF2_T 4A1E_R 4A1A_R 4A1C_R 4A17_R 2HGU_W 2HGQ_W 1N88_A 2HGJ_W ....
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts.
