RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031086
(166 letters)
>gnl|CDD|178621 PLN03072, PLN03072, 60S ribosomal protein L12; Provisional.
Length = 166
Score = 301 bits (772), Expect = e-106
Identities = 153/164 (93%), Positives = 161/164 (98%)
Query: 1 MPPKFDPSQVVDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVT 60
MPPK DPSQVV+VYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVT
Sbjct: 1 MPPKLDPSQVVEVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVT 60
Query: 61 VKLTVQNRQAKVAVVPSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKVMRPR 120
VKLTVQNRQAKV+VVPSAAALVIKALKEPERDRKK KNIKHNGNI+LDDVIEIAK+MRPR
Sbjct: 61 VKLTVQNRQAKVSVVPSAAALVIKALKEPERDRKKVKNIKHNGNISLDDVIEIAKIMRPR 120
Query: 121 SMAKDLSGTVKEILGTCVSVGCTVDGKDPRDLQQEITDGDVEIP 164
SMAK+L+GTVKEILGTCVSVGCTVDGKDP+DLQQEI DG+VEIP
Sbjct: 121 SMAKELAGTVKEILGTCVSVGCTVDGKDPKDLQQEIDDGEVEIP 164
>gnl|CDD|240269 PTZ00105, PTZ00105, 60S ribosomal protein L12; Provisional.
Length = 140
Score = 230 bits (588), Expect = 6e-79
Identities = 101/139 (72%), Positives = 125/139 (89%), Gaps = 1/139 (0%)
Query: 26 SSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQAKVAVVPSAAALVIKA 85
SSLAPK+GPLGLSPKK+G+DIAK T KDWKGL+VTVKLTVQNRQA V VVP+A++L+IKA
Sbjct: 1 SSLAPKVGPLGLSPKKVGDDIAKAT-KDWKGLKVTVKLTVQNRQATVEVVPTASSLLIKA 59
Query: 86 LKEPERDRKKTKNIKHNGNITLDDVIEIAKVMRPRSMAKDLSGTVKEILGTCVSVGCTVD 145
LKEP RDRKK KNIKH+GN+T D VI+IA+ MRP+SMAK GTVKE+LGTCVS+GCTVD
Sbjct: 60 LKEPPRDRKKVKNIKHSGNLTFDQVIKIARTMRPKSMAKTFKGTVKEVLGTCVSIGCTVD 119
Query: 146 GKDPRDLQQEITDGDVEIP 164
G+ PRD+Q++I +G++++P
Sbjct: 120 GESPRDIQEKINNGEIKVP 138
>gnl|CDD|100101 cd00349, Ribosomal_L11, Ribosomal protein L11. Ribosomal protein
L11, together with proteins L10 and L7/L12, and 23S
rRNA, form the L7/L12 stalk on the surface of the large
subunit of the ribosome. The homologous eukaryotic
cytoplasmic protein is also called 60S ribosomal protein
L12, which is distinct from the L12 involved in the
formation of the L7/L12 stalk. The C-terminal domain
(CTD) of L11 is essential for binding 23S rRNA, while
the N-terminal domain (NTD) contains the binding site
for the antibiotics thiostrepton and micrococcin. L11
and 23S rRNA form an essential part of the
GTPase-associated region (GAR). Based on differences in
the relative positions of the L11 NTD and CTD during the
translational cycle, L11 is proposed to play a
significant role in the binding of initiation factors,
elongation factors, and release factors to the ribosome.
Several factors, including the class I release factors
RF1 and RF2, are known to interact directly with L11. In
eukaryotes, L11 has been implicated in regulating the
levels of ubiquinated p53 and MDM2 in the MDM2-p53
feedback loop, which is responsible for apoptosis in
response to DNA damage. In bacteria, the "stringent
response" to harsh conditions allows bacteria to
survive, and ribosomes that lack L11 are deficient in
stringent factor stimulation.
Length = 131
Score = 160 bits (407), Expect = 2e-51
Identities = 59/134 (44%), Positives = 76/134 (56%), Gaps = 5/134 (3%)
Query: 13 VYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQN-RQAK 71
+ ++V G+ A L P +G LG++ K ++ T KD+KGL V VK+TV N R
Sbjct: 1 IKLQVPAGKASPAPPLGPALGQLGVNIMKFCKEFNART-KDYKGLPVPVKITVYNDRSFT 59
Query: 72 VAVV-PSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKVMRPRSMAKDLSGTV 130
V P A+AL+ KA E+ KK N + GNITLD V EIAK+ P AK L V
Sbjct: 60 FEVKTPPASALLKKA-AGIEKGSKK-PNKEKVGNITLDQVYEIAKIKLPDLNAKTLKSAV 117
Query: 131 KEILGTCVSVGCTV 144
KEILGT S+G TV
Sbjct: 118 KEILGTARSMGITV 131
>gnl|CDD|197819 smart00649, RL11, Ribosomal protein L11/L12.
Length = 132
Score = 153 bits (388), Expect = 2e-48
Identities = 55/135 (40%), Positives = 77/135 (57%), Gaps = 5/135 (3%)
Query: 13 VYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQ--A 70
+ +++ G+ A L P +G LG++ + ++ T KD KGL + VK+TV N +
Sbjct: 1 IKLQIPAGKANPAPPLGPALGQLGINIMEFCKEFNART-KDKKGLPIPVKITVYNDKSFT 59
Query: 71 KVAVVPSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKVMRPRSMAKDLSGTV 130
+ P A+AL+ KA + +K K K GNITLD V EIAK+ RP AKDL V
Sbjct: 60 FILKTPPASALLKKAAGIEKGSKKPGK--KKVGNITLDQVYEIAKIKRPDLNAKDLEAAV 117
Query: 131 KEILGTCVSVGCTVD 145
KEILGT S+G TV+
Sbjct: 118 KEILGTARSMGITVE 132
>gnl|CDD|223158 COG0080, RplK, Ribosomal protein L11 [Translation, ribosomal
structure and biogenesis].
Length = 141
Score = 123 bits (312), Expect = 6e-37
Identities = 53/137 (38%), Positives = 74/137 (54%), Gaps = 5/137 (3%)
Query: 13 VYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTV-QNRQAK 71
+ ++V G+ + + P +G LG++ + ++ T KD KGL V V +TV ++R
Sbjct: 8 IKLQVPAGKANPSPPVGPALGQLGVNIMEFCKEFNAAT-KDEKGLPVPVVITVYEDRSFT 66
Query: 72 VAV-VPSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKVMRPRSMAKDLSGTV 130
V P A+AL+ KA + K KN G +TL V EIAK P AKDL V
Sbjct: 67 FIVKTPPASALLKKAAGIEKGSGKPNKN--KVGKLTLAQVREIAKTKMPDLNAKDLEAAV 124
Query: 131 KEILGTCVSVGCTVDGK 147
KEILGT S+G TV+GK
Sbjct: 125 KEILGTARSMGVTVEGK 141
>gnl|CDD|234908 PRK01143, rpl11p, 50S ribosomal protein L11P; Validated.
Length = 163
Score = 106 bits (267), Expect = 6e-30
Identities = 55/153 (35%), Positives = 92/153 (60%), Gaps = 10/153 (6%)
Query: 13 VYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQAKV 72
V V V GG+ L P +GPLGL+ K++ ++I ++T KD+KG++V VK+ V K
Sbjct: 5 VEVLVEGGKATPGPPLGPALGPLGLNVKQVVQEINEKT-KDFKGMQVPVKVIVDTDTKKF 63
Query: 73 AV---VPSAAALVIKAL--KEPERDRKKTKNIKHNGNITLDDVIEIAKVMRPRSMAKDLS 127
+ +P AL+ K L ++ + GN++ + V++IA + + ++ DL
Sbjct: 64 EIEVGIPPTTALIKKELGIEKGSGEPGHEVV----GNLSFEQVVKIAIMKKDDLLSYDLK 119
Query: 128 GTVKEILGTCVSVGCTVDGKDPRDLQQEITDGD 160
VKE+LGTCVS+G TV+GKDP+++Q+E+ +G
Sbjct: 120 AAVKEVLGTCVSMGVTVEGKDPKEVQKEVDEGK 152
>gnl|CDD|217808 pfam03946, Ribosomal_L11_N, Ribosomal protein L11, N-terminal
domain. The N-terminal domain of Ribosomal protein L11
adopts an alpha/beta fold and is followed by the RNA
binding C-terminal domain.
Length = 59
Score = 67.1 bits (165), Expect = 1e-15
Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 13 VYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQAK 71
+ ++V G+ A L P +G LG++ + ++ T KD+KGL V VK+TV N ++
Sbjct: 2 IKLQVPAGKANPAPPLGPALGQLGVNIMEFCKEFNAAT-KDYKGLPVPVKITVYNDRSF 59
>gnl|CDD|189492 pfam00298, Ribosomal_L11, Ribosomal protein L11, RNA binding
domain.
Length = 69
Score = 65.9 bits (162), Expect = 4e-15
Identities = 29/70 (41%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 75 VPSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKVMRPRSMAKDLSGTVKEIL 134
P A+ L+ KA E+ K K G ITL V EIAK+ P A DL VK I+
Sbjct: 2 TPPASYLLKKAAGI-EKGSGKPGKEK-VGKITLKQVYEIAKIKMPDLNANDLEAAVKIII 59
Query: 135 GTCVSVGCTV 144
GT S+G V
Sbjct: 60 GTARSMGIEV 69
>gnl|CDD|233500 TIGR01632, L11_bact, 50S ribosomal protein L11. This model
represents bacterial, chloroplast, and most
mitochondrial forms of 50S ribosomal protein L11
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 140
Score = 38.5 bits (90), Expect = 3e-04
Identities = 41/132 (31%), Positives = 57/132 (43%), Gaps = 12/132 (9%)
Query: 23 GAASSLAPKIGP-LGLSPKKIGE---DIAKETAKDWKGLRVTVKLTVQNRQAKVAVV--P 76
++ AP +GP LG I E TA GL V V +TV ++ +V P
Sbjct: 13 AGQANPAPPVGPALGQRGVNIMEFCKQFNARTADYEPGLPVPVVITVYEDKSFTFIVKTP 72
Query: 77 SAAALVIKALKEPERDRKKTKNIKHN--GNITLDDVIEIAKVMRPRSMAKDLSGTVKEIL 134
+ L+ KA K +KN K G IT V EIA++ KD+ +K I
Sbjct: 73 PVSYLLKKAAGV----EKGSKNPKKEKVGKITRKQVREIAEIKMSDLNTKDIEAAMKIIA 128
Query: 135 GTCVSVGCTVDG 146
GT S+G + G
Sbjct: 129 GTAKSMGIEIVG 140
>gnl|CDD|177049 CHL00127, rpl11, ribosomal protein L11; Validated.
Length = 140
Score = 34.7 bits (80), Expect = 0.007
Identities = 32/122 (26%), Positives = 59/122 (48%), Gaps = 5/122 (4%)
Query: 25 ASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQAKVAVV--PSAAALV 82
A + P +G G++ ++ T KD GL + V+++V ++ ++ P A+ L+
Sbjct: 21 APPVGPALGQHGVNINLFCKEYNART-KDKIGLIIPVEISVYEDKSYTFILKTPPASVLL 79
Query: 83 IKALKEPERDRKKTKNIKHNGNITLDDVIEIAKVMRPRSMAKDLSGTVKEILGTCVSVGC 142
KA + N K G+IT+ + EIA++ P LS +K I GT ++G
Sbjct: 80 AKAAGI--KKGSGEPNKKKVGSITIKQLEEIAQIKLPDLNTISLSKAIKIIEGTAKNMGI 137
Query: 143 TV 144
++
Sbjct: 138 SI 139
>gnl|CDD|234661 PRK00140, rplK, 50S ribosomal protein L11; Validated.
Length = 141
Score = 31.6 bits (73), Expect = 0.091
Identities = 39/132 (29%), Positives = 58/132 (43%), Gaps = 25/132 (18%)
Query: 29 APKIGPLGLSPKKIGEDIAK------ETAKDWKGLRVTVKLTVQNRQAKVAVV--PSAAA 80
AP +GP L + + +I + +D KGL + V +TV ++ + P A+
Sbjct: 21 APPVGP-ALGQRGV--NIMEFCKAFNARTQDQKGLPIPVVITVYEDRSFTFITKTPPASV 77
Query: 81 LVIKALK------EPERDRKKTKNIKHNGNITLDDVIEIAKVMRPRSMAKDLSGTVKEIL 134
L+ KA EP K K G IT V EIA+ P A D+ ++ I
Sbjct: 78 LLKKAAGIEKGSGEP----NKEKV----GKITRAQVREIAETKMPDLNAADIEAAMRMIA 129
Query: 135 GTCVSVGCTVDG 146
GT S+G V+G
Sbjct: 130 GTARSMGIVVEG 141
>gnl|CDD|240302 PTZ00169, PTZ00169, ADP/ATP transporter on adenylate translocase;
Provisional.
Length = 300
Score = 27.8 bits (62), Expect = 2.8
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 18 TGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGL 57
+GG GA+S L + PL + ++ DI K +++ GL
Sbjct: 119 SGGLAGASSLLI--VYPLDFARTRLASDIGKGGDREFTGL 156
>gnl|CDD|131935 TIGR02889, spore_YpeB, germination protein YpeB. Members of this
family are YpeB, a protein usually encoded with the
putative spore-cortex-lytic enzyme SleB and required,
together with SleB, for normal germination. This family
is retricted to endospore-forming species in the
Firmicutes lineage of bacteria, and found in all such
species to date except Clostridium perfringens. The
matching phenotypes of mutants in SleB (called a lytic
transglycosylase) and YpeB suggests that YpeB is
necessary to allow SleB to function [Cellular processes,
Sporulation and germination].
Length = 435
Score = 27.7 bits (62), Expect = 3.6
Identities = 26/112 (23%), Positives = 43/112 (38%), Gaps = 28/112 (25%)
Query: 23 GAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQAKVAVVPSAAALV 82
G S + P GL K+I ++ AK+ A+D+ G N ++ VV S
Sbjct: 197 GPFSDSVINLTPKGLKGKEISKEEAKQIARDFLG---------DNAATRIEVVDSGKNGG 247
Query: 83 IKA----LKEPERDRKKTKNIKHNG---------------NITLDDVIEIAK 115
I +K+P R + N+ G I+L++ + AK
Sbjct: 248 IPTYSFEVKDPGRKARIYMNVSKKGGHPLWFLDNRPVSKPKISLNEAVNKAK 299
>gnl|CDD|220185 pfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This
family includes methionyl tRNA synthetases.
Length = 388
Score = 27.2 bits (61), Expect = 4.2
Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 14/61 (22%)
Query: 12 DVYVR-----------VTGG-EVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRV 59
DVY R VTG E G LA + G++P+++ + +E + +K +
Sbjct: 26 DVYARYLRLRGYDVLFVTGTDEHGTKIELAAEK--EGVTPQELVDRYHEEFKELFKKFNI 83
Query: 60 T 60
+
Sbjct: 84 S 84
>gnl|CDD|236893 PRK11282, glcE, glycolate oxidase FAD binding subunit; Provisional.
Length = 352
Score = 26.7 bits (60), Expect = 6.3
Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 10/47 (21%)
Query: 12 DVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLR 58
+Y+R++G E GA + ++G GE++ A W+ LR
Sbjct: 208 TLYLRLSGAE-GAVKAARERLG---------GEELDDAEAAFWQQLR 244
>gnl|CDD|234816 PRK00702, PRK00702, ribose-5-phosphate isomerase A; Provisional.
Length = 220
Score = 26.6 bits (60), Expect = 6.5
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 72 VAVVPSAAALVIKALKEPERD---RKKTKNIKHNGNITLDDVIEIAKVMRPRSMAKDLSG 128
V V+P A + V + L++ R + NGN LD + ++ P ++ K+L+
Sbjct: 135 VEVIPFARSAVARELEKLGGQPELRMDEPVVTDNGNYILD--VHFGRIPDPEALEKELNN 192
Query: 129 TV 130
Sbjct: 193 IP 194
>gnl|CDD|180921 PRK07306, PRK07306, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 720
Score = 26.6 bits (59), Expect = 8.4
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 40 KKIGEDIAKETAKDWKGLRVTVK---LTVQNRQA 70
K++ + I TA DW LR V L QNR A
Sbjct: 544 KELFKGIFIPTAADWAALRDAVMKDGLYHQNRLA 577
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
0.313 0.133 0.375
Gapped
Lambda K H
0.267 0.0820 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,441,657
Number of extensions: 765713
Number of successful extensions: 751
Number of sequences better than 10.0: 1
Number of HSP's gapped: 736
Number of HSP's successfully gapped: 34
Length of query: 166
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 76
Effective length of database: 6,945,742
Effective search space: 527876392
Effective search space used: 527876392
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (24.8 bits)