RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031274
(162 letters)
>gnl|CDD|185498 PTZ00173, PTZ00173, 60S ribosomal protein L10; Provisional.
Length = 213
Score = 268 bits (687), Expect = 5e-93
Identities = 104/126 (82%), Positives = 109/126 (86%)
Query: 1 MGRRPARCYRQIKNKPYPKSRFCRGVPDPKIRIYDVGMKKKGVDEFPFCVHLVSWEKENV 60
MGRRPARCYR KNKPYPKSRFCRGVPDPKIRIYD+G KK VDEFP CVH+VS E E +
Sbjct: 1 MGRRPARCYRYCKNKPYPKSRFCRGVPDPKIRIYDIGRKKATVDEFPVCVHIVSDEYEQI 60
Query: 61 SSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFG 120
SSEALEAARI+ NKYM K AGKD FHLR+RVHPFHVLRINKMLSCAGADRLQTGMRGAFG
Sbjct: 61 SSEALEAARISANKYMVKRAGKDGFHLRIRVHPFHVLRINKMLSCAGADRLQTGMRGAFG 120
Query: 121 KPQAIV 126
KP
Sbjct: 121 KPNGTC 126
>gnl|CDD|129380 TIGR00279, L10e, ribosomal protein L10.e. This model finds the
archaeal and eukaryotic forms of ribosomal protein L10.
The protein is encoded by multiple loci in some
eukaryotes and has been assigned a number of
extra-ribosomal functions, some of which will require
re-evaluation in the context of identification as a
ribosomal protein. L10.e is distantly related to
eubacterial ribosomal protein L16 [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 172
Score = 180 bits (459), Expect = 6e-59
Identities = 84/152 (55%), Positives = 107/152 (70%), Gaps = 8/152 (5%)
Query: 1 MGRRPARCYRQIKNKPYPKSRFCRGVPDPKIRIYDVGMKKKGVDEFPFCVHLVSWEKENV 60
M RRPARCYR KN+PY +S + +GVP KIRIYD+G K EFP CVHLV+ E E +
Sbjct: 1 MARRPARCYRYQKNRPYTRSEYIKGVPGSKIRIYDMGNK---SAEFPVCVHLVAKEPEQI 57
Query: 61 SSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFG 120
ALEAARIA NKYM + AG+ +HL++RV+P H+LR NKM + AGADR+Q GMRGAFG
Sbjct: 58 RHNALEAARIAANKYMTRRAGRMGYHLKIRVYPHHILRENKMATGAGADRIQQGMRGAFG 117
Query: 121 KPQAIVFMLK---RLFVVQS--SSFLVAKKSL 147
KP +K ++F V + S+F VAK++L
Sbjct: 118 KPVGTAARVKIGQKIFSVWTKPSNFDVAKEAL 149
>gnl|CDD|235252 PRK04199, rpl10e, 50S ribosomal protein L10e; Reviewed.
Length = 172
Score = 151 bits (385), Expect = 1e-47
Identities = 62/122 (50%), Positives = 76/122 (62%), Gaps = 3/122 (2%)
Query: 1 MGRRPARCYRQIKNKPYPKSRFCRGVPDPKIRIYDVGMKKKGVDEFPFCVHLVSWEKENV 60
M RPARCYR I Y + + GVP PKI +D+G +FP V LV E +
Sbjct: 1 MPLRPARCYRHISKPAYTRREYIGGVPGPKIVKFDMGNLS---GDFPVEVSLVVEEPCQI 57
Query: 61 SSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFG 120
ALEAARIA NKY+ K G+ +HL++RV+P HVLR NKM + AGADR+ GMR AFG
Sbjct: 58 RHNALEAARIAANKYLTKTVGRSNYHLKIRVYPHHVLRENKMATGAGADRVSDGMRLAFG 117
Query: 121 KP 122
KP
Sbjct: 118 KP 119
>gnl|CDD|238714 cd01433, Ribosomal_L16_L10e, Ribosomal_L16_L10e: L16 is an
essential protein in the large ribosomal subunit of
bacteria, mitochondria, and chloroplasts. Large subunits
that lack L16 are defective in peptidyl transferase
activity, peptidyl-tRNA hydrolysis activity, association
with the 30S subunit, binding of aminoacyl-tRNA and
interaction with antibiotics. L16 is required for the
function of elongation factor P (EF-P), a protein
involved in peptide bond synthesis through the
stimulation of peptidyl transferase activity by the
ribosome. Mutations in L16 and the adjoining bases of
23S rRNA confer antibiotic resistance in bacteria,
suggesting a role for L16 in the formation of the
antibiotic binding site. The GTPase RbgA (YlqF) is
essential for the assembly of the large subunit, and it
is believed to regulate the incorporation of L16. L10e
is the archaeal and eukaryotic cytosolic homolog of
bacterial L16. L16 and L10e exhibit structural
differences at the N-terminus.
Length = 112
Score = 89.5 bits (223), Expect = 8e-24
Identities = 37/111 (33%), Positives = 50/111 (45%), Gaps = 17/111 (15%)
Query: 41 KGVDEFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRIN 100
KG F LV+ E +++E LEAARIA N+Y+ K L +RV P H +
Sbjct: 1 KGNKLFFGEYGLVALEPGRITAEQLEAARIAINRYL----KKKGGKLWIRVFPDHPVTKK 56
Query: 101 KMLSCAGADRLQTGMRGAFGKPQAIVFMLKR---LF-VVQSSSFLVAKKSL 147
L+T M GKP+ V +K LF V VAK++L
Sbjct: 57 P---------LETRMGKGKGKPEGWVARVKPGQILFEVRGVPEEEVAKEAL 98
>gnl|CDD|223275 COG0197, RplP, Ribosomal protein L16/L10E [Translation, ribosomal
structure and biogenesis].
Length = 146
Score = 88.8 bits (221), Expect = 3e-23
Identities = 32/111 (28%), Positives = 43/111 (38%), Gaps = 19/111 (17%)
Query: 12 IKNKPYPKSRFCRGVPDPKIRIYDVGMKKKGVDEFPFCVHLVSWEKENVSSEALEAARIA 71
+ K R P I I K G F LV+ E +++ +EAARIA
Sbjct: 2 MLQPKRTKYRKQHKGRGPGITIA-----KGGNKVFFGEYGLVALEPGQITARQIEAARIA 56
Query: 72 CNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKP 122
N+Y+ + G L +RV P L G DR+ G GKP
Sbjct: 57 ANRYLKRGGG-----LWIRVFPDKPLTEKP-----GEDRMGKGK----GKP 93
>gnl|CDD|215820 pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e.
Length = 129
Score = 67.1 bits (165), Expect = 5e-15
Identities = 38/147 (25%), Positives = 58/147 (39%), Gaps = 35/147 (23%)
Query: 5 PARC-YRQIKNKPYPKSRFCRGVPDPKIRIYDVGMKKKGVDEFPFCVHLVSWEKENVSSE 63
P R YR K + + + VP K+ D G L + E +++
Sbjct: 1 PKRTKYR--KYQK-GRLEYGGAVPGNKLAFGDYG--------------LKALEPGRITAR 43
Query: 64 ALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKPQ 123
+EAARIA N+Y+ K L +RV P + + G + GKP+
Sbjct: 44 QIEAARIAINRYL-----KRGGKLWIRVFPDKPVTKKPAETRMGKGK---------GKPE 89
Query: 124 ---AIVFMLKRLFVVQSSSFLVAKKSL 147
A V + LF + S VAK++L
Sbjct: 90 GWVARVKPGQILFEIGGVSEEVAKEAL 116
>gnl|CDD|239572 cd03490, Topoisomer_IB_N_1, Topoisomer_IB_N_1: A subgroup of the
N-terminal DNA binding fragment found in eukaryotic DNA
topoisomerase (topo) IB. Topo IB proteins include the
monomeric yeast and human topo I and heterodimeric topo
I from Leishmania donvanni. Topo I enzymes are divided
into: topo type IA (bacterial) and type IB
(eukaryotic). Topo I relaxes superhelical tension in
duplex DNA by creating a single-strand nick, the broken
strand can then rotate around the unbroken strand to
remove DNA supercoils and, the nick is religated,
liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit religation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topos I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topos I have putative roles
in organizing the kinetoplast DNA network unique to
these parasites. This family may represent more than
one structural domain.
Length = 217
Score = 28.3 bits (63), Expect = 1.5
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 34 YDVGMKKKGVDEFPFCVHLVSWEKENVSSEALE 66
+ K++ E+PF LV W +E VSS LE
Sbjct: 108 KEAKKKERAKREYPFNYALVDWIREKVSSNKLE 140
>gnl|CDD|185157 PRK15245, PRK15245, type III effector phosphothreonine lyase;
Provisional.
Length = 241
Score = 26.0 bits (57), Expect = 8.5
Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 42 GVDEFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRV 89
G+ + F ++ N + AR + FAG D FH+ V
Sbjct: 63 GMRQSGFFAMSQGFQLVNHGYDVFIHARRESPQSKGDFAG-DKFHISV 109
>gnl|CDD|216820 pfam01974, tRNA_int_endo, tRNA intron endonuclease, catalytic
C-terminal domain. Members of this family cleave pre
tRNA at the 5' and 3' splice sites to release the
intron EC:3.1.27.9.
Length = 85
Score = 24.9 bits (55), Expect = 9.5
Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 7/66 (10%)
Query: 7 RCYRQIKNKPY-PKSRFCRGVPDPKIRIYDVGMKKKGVDEFPFCVHLVSWEKENVSSEAL 65
YR ++ + Y +S G R+Y+ + G + V ++S ++E + L
Sbjct: 6 VVYRDLRERGYVVRSGLKFGA---DFRVYE---RGPGKGHSEYLVRVLSEDEEISWLDLL 59
Query: 66 EAARIA 71
A R+A
Sbjct: 60 RAVRLA 65
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.326 0.137 0.417
Gapped
Lambda K H
0.267 0.0758 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,298,606
Number of extensions: 753579
Number of successful extensions: 608
Number of sequences better than 10.0: 1
Number of HSP's gapped: 599
Number of HSP's successfully gapped: 19
Length of query: 162
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 73
Effective length of database: 6,990,096
Effective search space: 510277008
Effective search space used: 510277008
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 55 (24.9 bits)