RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13546
(109 letters)
>gnl|CDD|178621 PLN03072, PLN03072, 60S ribosomal protein L12; Provisional.
Length = 166
Score = 161 bits (410), Expect = 2e-52
Identities = 75/98 (76%), Positives = 87/98 (88%), Gaps = 1/98 (1%)
Query: 1 MPPKFDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATG-DWKGLKIT 59
MPPK DP++V +VY+R GGEVGA SSLAPKIGPLGLSPKK+G+DIAK T DWKGL++T
Sbjct: 1 MPPKLDPSQVVEVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVT 60
Query: 60 VCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKN 97
V LT+QNRQA +SVVPSAA+L+IKALKEP RDRKKVKN
Sbjct: 61 VKLTVQNRQAKVSVVPSAAALVIKALKEPERDRKKVKN 98
>gnl|CDD|240269 PTZ00105, PTZ00105, 60S ribosomal protein L12; Provisional.
Length = 140
Score = 130 bits (328), Expect = 3e-40
Identities = 61/72 (84%), Positives = 68/72 (94%)
Query: 26 SSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQAAISVVPSAASLIIKAL 85
SSLAPK+GPLGLSPKKVGDDIAKAT DWKGLK+TV LT+QNRQA + VVP+A+SL+IKAL
Sbjct: 1 SSLAPKVGPLGLSPKKVGDDIAKATKDWKGLKVTVKLTVQNRQATVEVVPTASSLLIKAL 60
Query: 86 KEPPRDRKKVKN 97
KEPPRDRKKVKN
Sbjct: 61 KEPPRDRKKVKN 72
>gnl|CDD|197819 smart00649, RL11, Ribosomal protein L11/L12.
Length = 132
Score = 100 bits (251), Expect = 9e-29
Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 2/87 (2%)
Query: 13 VYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQ--AA 70
+ L+ G+ L P +G LG++ + + T D KGL I V +T+ N +
Sbjct: 1 IKLQIPAGKANPAPPLGPALGQLGINIMEFCKEFNARTKDKKGLPIPVKITVYNDKSFTF 60
Query: 71 ISVVPSAASLIIKALKEPPRDRKKVKN 97
I P A++L+ KA +K K
Sbjct: 61 ILKTPPASALLKKAAGIEKGSKKPGKK 87
>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 = 95.2 bits (238), Expect = 9e-27
Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 3/90 (3%)
Query: 13 VYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQN-RQAAI 71
+ L+ G+ L P +G LG++ K + T D+KGL + V +T+ N R
Sbjct: 1 IKLQVPAGKASPAPPLGPALGQLGVNIMKFCKEFNARTKDYKGLPVPVKITVYNDRSFTF 60
Query: 72 SVV-PSAASLIIKALKEPPRDRKKVKNDWS 100
V P A++L+ KA + KK +
Sbjct: 61 EVKTPPASALLKKA-AGIEKGSKKPNKEKV 89
>gnl|CDD|223158 COG0080, RplK, Ribosomal protein L11 [Translation, ribosomal
structure and biogenesis].
Length = 141
Score = 77.6 bits (192), Expect = 1e-19
Identities = 26/91 (28%), Positives = 44/91 (48%), Gaps = 2/91 (2%)
Query: 9 EVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTI-QNR 67
VK + L+ G+ + + P +G LG++ + + AT D KGL + V +T+ ++R
Sbjct: 4 VVKIIKLQVPAGKANPSPPVGPALGQLGVNIMEFCKEFNAATKDEKGLPVPVVITVYEDR 63
Query: 68 QAAISV-VPSAASLIIKALKEPPRDRKKVKN 97
V P A++L+ KA K KN
Sbjct: 64 SFTFIVKTPPASALLKKAAGIEKGSGKPNKN 94
>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 = 70.2 bits (173), Expect = 1e-17
Identities = 16/58 (27%), Positives = 30/58 (51%)
Query: 12 KVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQA 69
+ L+ G+ L P +G LG++ + + AT D+KGL + V +T+ N ++
Sbjct: 1 VIKLQVPAGKANPAPPLGPALGQLGVNIMEFCKEFNAATKDYKGLPVPVKITVYNDRS 58
>gnl|CDD|234908 PRK01143, rpl11p, 50S ribosomal protein L11P; Validated.
Length = 163
Score = 44.5 bits (106), Expect = 8e-07
Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 3/70 (4%)
Query: 19 GGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQN--RQAAISV-VP 75
GG+ L P +GPLGL+ K+V +I + T D+KG+++ V + + ++ I V +P
Sbjct: 11 GGKATPGPPLGPALGPLGLNVKQVVQEINEKTKDFKGMQVPVKVIVDTDTKKFEIEVGIP 70
Query: 76 SAASLIIKAL 85
+LI K L
Sbjct: 71 PTTALIKKEL 80
>gnl|CDD|182273 PRK10157, PRK10157, putative oxidoreductase FixC; Provisional.
Length = 428
Score = 28.0 bits (62), Expect = 0.94
Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 19 GGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQAAISVVPSAA 78
G V ++ + P+ G + + P+ VGD + A GD G+ + + TI+ AI+ +AA
Sbjct: 271 GKLVEYSAHVVPEAG-INMLPELVGDGVLIA-GDAAGMCMNLGFTIRGMDLAIAAGEAAA 328
Query: 79 SLIIKALKEPPRDRKKV 95
++ A+K ++K+
Sbjct: 329 KTVLSAMKSDDFSKQKL 345
>gnl|CDD|237938 PRK15306, PRK15306, putative fimbrial protein StkD; Provisional.
Length = 190
Score = 27.3 bits (60), Expect = 1.3
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 22 VGATSSLAPKIGPLGLSPKKVG-DDI--AKATGDWKGLKITVC-LTIQNRQAAISVVPSA 77
VG T S + +G S +V DD+ AT D+K L I C ++Q+ + +I+ PS
Sbjct: 48 VGGTGSDTVQELIIGNSSGEVRIDDVRAGTATADFK-LVIVECPASLQSLKTSINGTPSG 106
Query: 78 ASLIIK 83
S I
Sbjct: 107 YSTKIL 112
>gnl|CDD|218090 pfam04450, BSP, Peptidase of plants and bacteria. These basic
secretory proteins (BSPs) are believed to be part of
the plants defence mechanism against pathogens.
Length = 203
Score = 27.3 bits (61), Expect = 1.5
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 70 AISVVPSAASLIIKALKEPPRDRKKVK 96
A + A+ + + L +PP DR V+
Sbjct: 26 AEQTLSDASRFVWRILYQPPSDRPPVR 52
>gnl|CDD|232927 TIGR00338, serB, phosphoserine phosphatase SerB. Phosphoserine
phosphatase catalyzes the reaction 3-phospho-serine +
H2O = L-serine + phosphate. It catalyzes the last of
three steps in the biosynthesis of serine from
D-3-phosphoglycerate. Note that this enzyme acts on free
phosphoserine, not on phosphoserine residues of
phosphoproteins [Amino acid biosynthesis, Serine
family].
Length = 219
Score = 26.9 bits (60), Expect = 2.1
Identities = 15/79 (18%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 9 EVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQ 68
EV ++ R + GE+ +SL ++ L P ++ ++ + +G + V T++ +
Sbjct: 43 EVSEITERAMRGELDFKASLRERVALLKGLPVELLKEVRENLPLTEGAEELV-KTLKEKG 101
Query: 69 AAISVVPSAASLIIKALKE 87
++V+ L + +K+
Sbjct: 102 YKVAVISGGFDLFAEHVKD 120
>gnl|CDD|114410 pfam05684, DUF819, Protein of unknown function (DUF819). This
family contains proteins of unknown function from
archaeal, bacterial and plant species.
Length = 379
Score = 27.0 bits (60), Expect = 2.4
Identities = 13/59 (22%), Positives = 19/59 (32%)
Query: 22 VGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQAAISVVPSAASL 80
V K K G+D AKA K ++ I + ++V A L
Sbjct: 168 VSLKRFQDHKTKADTSKLKADGNDAAKAVAYEKRNPSSLVDIIFLIGVSFAIVAVAMKL 226
>gnl|CDD|129165 TIGR00055, uppS, undecaprenyl diphosphate synthase. This enzyme
builds undecaprenyl diphosphate, a molecule that in
bacteria is used a carrier in synthesizing cell wall
components. Alternate name: undecaprenyl pyrophosphate
synthetase. Activity has been demonstrated
experimentally for members of this family from
Micrococcus luteus, E. coli, Haemophilus influenzae, and
Streptococcus pneumoniae [Cell envelope, Biosynthesis
and degradation of surface polysaccharides and
lipopolysaccharides].
Length = 226
Score = 26.6 bits (59), Expect = 2.5
Identities = 15/70 (21%), Positives = 24/70 (34%), Gaps = 14/70 (20%)
Query: 32 IGPLGLSPKKVGDDIAKA---TGDWKGLKITVCLTIQNRQAAISVVPSAASLIIKALKEP 88
IG L L K++ + I KA T + + + R I+ A+K+
Sbjct: 92 IGDLSLLSKELQEKIKKAEEDTKNNTDFTLNIAFNYGGRNE-----------ILHAVKQI 140
Query: 89 PRDRKKVKND 98
K K
Sbjct: 141 AEKVKSGKLL 150
>gnl|CDD|107374 cd06379, PBP1_iGluR_NMDA_NR1, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NR1, an essential channel-forming subunit
of the NMDA receptor. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NR1, an essential channel-forming subunit
of the NMDA receptor. The ionotropic N-methyl-d-asparate
(NMDA) subtype of glutamate receptor serves critical
functions in neuronal development, functioning, and
degeneration in the mammalian central nervous system.
The functional NMDA receptor is a heterotetramer
ccomposed of two NR1 and two NR2 (A, B, C, and D) or of
NR3 (A and B) subunits. The receptor controls a cation
channel that is highly permeable to monovalent ions and
calcium and exhibits voltage-dependent inhibition by
magnesium. Dual agonists, glutamate and glycine, are
required for efficient activation of the NMDA receptor.
When co-expressed with NR1, the NR3 subunits form
receptors that are activated by glycine alone and
therefore can be classified as excitatory glycine
receptors. NR1/NR3 receptors are calcium-impermeable and
unaffected by ligands acting at the NR2
glutamate-binding site.
Length = 377
Score = 25.9 bits (57), Expect = 4.6
Identities = 9/34 (26%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 70 AISVVPSAASLII--KALKEPPRDRKKVKNDWSW 101
A++V+ SA + + + EPPR+ W
Sbjct: 279 AVAVLASAIQELFEKENITEPPRECVGNTVIWET 312
>gnl|CDD|221583 pfam12449, DUF3684, Protein of unknown function (DUF3684). This
domain family is found in eukaryotes, and is typically
between 1072 and 1090 amino acids in length.
Length = 1084
Score = 25.4 bits (56), Expect = 7.8
Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 4/73 (5%)
Query: 23 GATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGL-KITVCLTIQNRQAAISVVPSAASLI 81
T S +P P +P+ + D + +V L I SV S A+ +
Sbjct: 95 RLTGSSSP---PKPKTPEPAKVEENLDAEDLTEISTSSVFLHIFTANIQTSVSQSFAAEL 151
Query: 82 IKALKEPPRDRKK 94
+A K+PP K
Sbjct: 152 ERATKKPPPKTTK 164
>gnl|CDD|214352 CHL00068, rpl20, ribosomal protein L20.
Length = 115
Score = 24.8 bits (55), Expect = 9.0
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 81 IIKALKEPPRDRKKVKNDW 99
+KAL RDRKK K D+
Sbjct: 39 KMKALVSSYRDRKKKKRDF 57
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
0.316 0.135 0.423
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: 5,403,827
Number of extensions: 435387
Number of successful extensions: 378
Number of sequences better than 10.0: 1
Number of HSP's gapped: 373
Number of HSP's successfully gapped: 22
Length of query: 109
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 35
Effective length of database: 7,655,406
Effective search space: 267939210
Effective search space used: 267939210
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.0 bits)