RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 030434
(177 letters)
>gnl|CDD|185498 PTZ00173, PTZ00173, 60S ribosomal protein L10; Provisional.
Length = 213
Score = 345 bits (888), Expect = e-123
Identities = 140/174 (80%), Positives = 151/174 (86%), Gaps = 1/174 (0%)
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 KPQGTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIVSRKWYGF 174
KP GTCARV IGQ+LLS+R K++ A EALRRAK+KFPGRQKI+VS KW GF
Sbjct: 121 KPNGTCARVRIGQILLSIRTKEAYVPQAIEALRRAKYKFPGRQKIVVSNKW-GF 173
>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 = 231 bits (591), Expect = 8e-79
Identities = 101/171 (59%), Positives = 122/171 (71%), Gaps = 3/171 (1%)
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 KPQGTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIVSRKW 171
KP GT ARV IGQ + SV K SN A+EALRRA KFP KI++ + W
Sbjct: 118 KPVGTAARVKIGQKIFSVWTKPSNFDVAKEALRRAAMKFPVPCKIVIEKGW 168
>gnl|CDD|235252 PRK04199, rpl10e, 50S ribosomal protein L10e; Reviewed.
Length = 172
Score = 196 bits (501), Expect = 5e-65
Identities = 82/170 (48%), Positives = 103/170 (60%), Gaps = 3/170 (1%)
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 KPQGTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIVSRK 170
KP GT ARV GQ + +VR + A+EALRRA K P +I+V +
Sbjct: 118 KPVGTAARVEKGQKIFTVRVNPEHLEAAKEALRRAAMKLPTPCRIVVEKG 167
>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 = 136 bits (345), Expect = 3e-42
Identities = 48/126 (38%), Positives = 62/126 (49%), Gaps = 14/126 (11%)
Query: 41 KGVDEFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRIN 100
KG F LV+ E +++E LEAARIA N+Y+ K L +RV P H +
Sbjct: 1 KGNKLFFGEYGLVALEPGRITAEQLEAARIAINRYL----KKKGGKLWIRVFPDHPVTKK 56
Query: 101 KMLSCAGADRLQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKFP 160
L+T M GKP+G ARV GQ+L VR A+EALRRA K P
Sbjct: 57 P---------LETRMGKGKGKPEGWVARVKPGQILFEVRGVPEEE-VAKEALRRAAKKLP 106
Query: 161 GRQKII 166
+ KI+
Sbjct: 107 IKTKIV 112
>gnl|CDD|223275 COG0197, RplP, Ribosomal protein L16/L10E [Translation, ribosomal
structure and biogenesis].
Length = 146
Score = 128 bits (324), Expect = 1e-38
Identities = 49/156 (31%), Positives = 67/156 (42%), Gaps = 21/156 (13%)
Query: 12 IKNKPYPKSRFCRGVPDPKIRIYDVGMKKKGVDEFPFCVHLVSWEKENVSSEALEAARIA 71
+ K R P I I K G F LV+ E +++ +EAARIA
Sbjct: 2 MLQPKRTKYRKQHKGRGPGITIA-----KGGNKVFFGEYGLVALEPGQITARQIEAARIA 56
Query: 72 CNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKPQGTCARVAI 131
N+Y+ + G L +RV P L G DR+ G GKP+G ARV
Sbjct: 57 ANRYLKRGGG-----LWIRVFPDKPLTEKP-----GEDRMGKGK----GKPEGWAARVKP 102
Query: 132 GQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIV 167
G+VL + A+EALRRA K P + K ++
Sbjct: 103 GRVLFEIAGVPEEL--AREALRRAAAKLPVKTKFVI 136
>gnl|CDD|215820 pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e.
Length = 129
Score = 99.1 bits (248), Expect = 3e-27
Identities = 47/162 (29%), Positives = 68/162 (41%), Gaps = 34/162 (20%)
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 GTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKI 165
G ARV GQ+L + + A+EALRRA K P + KI
Sbjct: 90 GWVARVKPGQILFEI--GGVSEEVAKEALRRAASKLPIKTKI 129
>gnl|CDD|211627 TIGR01164, rplP_bact, ribosomal protein L16, bacterial/organelle.
This model describes bacterial and organellar ribosomal
protein L16. The homologous protein of the eukaryotic
cytosol is designated L10 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 126
Score = 34.7 bits (80), Expect = 0.007
Identities = 28/113 (24%), Positives = 47/113 (41%), Gaps = 22/113 (19%)
Query: 52 LVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRL 111
L + E +++ +EAAR+A +Y+ K L +R+ P +K +
Sbjct: 33 LQALEPGWITARQIEAARVAMTRYV-----KRGGKLWIRIFP------DKPYTKKPL--- 78
Query: 112 QTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSLH---AQEALRRAKFKFPG 161
+T M G P+ A V G++L + + A+EA R A K P
Sbjct: 79 ETRMGKGKGNPEYWVAVVKPGKILFEI-----AGVPEEVAREAFRLAASKLPI 126
>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 = 27.9 bits (62), Expect = 2.2
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|236411 PRK09203, rplP, 50S ribosomal protein L16; Reviewed.
Length = 138
Score = 27.0 bits (61), Expect = 4.1
Identities = 31/117 (26%), Positives = 53/117 (45%), Gaps = 18/117 (15%)
Query: 52 LVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRL 111
L + E +++ +EAARIA +++ K GK + +R+ P +K ++
Sbjct: 34 LKALEPGWITARQIEAARIAMTRHI-KRGGK----VWIRIFP------DKPVT---KKPA 79
Query: 112 QTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSLH-AQEALRRAKFKFPGRQKIIV 167
+ M G P+ A V G++L + S A+EALR A K P + K +
Sbjct: 80 EVRMGKGKGSPEYWVAVVKPGRILFEI---AGVSEELAREALRLAAAKLPIKTKFVK 133
>gnl|CDD|218099 pfam04465, DUF499, Protein of unknown function (DUF499). Family of
uncharacterized hypothetical prokaryotic proteins.
Length = 1025
Score = 27.1 bits (60), Expect = 6.6
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 132 GQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIVSRK 170
G+ VR D L +EALRR + +K + +
Sbjct: 720 GKPPAKVREDDV-ILPREEALRRQVCELLKEEKDEIKER 757
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
0.327 0.139 0.442
Gapped
Lambda K H
0.267 0.0623 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,094,806
Number of extensions: 810400
Number of successful extensions: 719
Number of sequences better than 10.0: 1
Number of HSP's gapped: 702
Number of HSP's successfully gapped: 16
Length of query: 177
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 86
Effective length of database: 6,901,388
Effective search space: 593519368
Effective search space used: 593519368
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 56 (25.6 bits)