RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13547
(165 letters)
>gnl|CDD|178621 PLN03072, PLN03072, 60S ribosomal protein L12; Provisional.
Length = 166
Score = 248 bits (634), Expect = 1e-85
Identities = 112/166 (67%), Positives = 142/166 (85%), Gaps = 1/166 (0%)
Query: 1 MPPKFDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATG-DWKGLKIT 59
MPPK DP++V +VY+R GGEVGA SSLAPKIGPLGLSPKK+G+DIAK T DWKGL++T
Sbjct: 1 MPPKLDPSQVVEVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVT 60
Query: 60 VCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPR 119
V LT+QNRQA +SVVPSAA+L+IKALKEP RDRKKVKN+KHNGN+ +D++ I++ MRPR
Sbjct: 61 VKLTVQNRQAKVSVVPSAAALVIKALKEPERDRKKVKNIKHNGNISLDDVIEIAKIMRPR 120
Query: 120 SMARKFVGTVKEVLGTCQSVGATVEGRSARDIIEAIDNGEIEVPEE 165
SMA++ GTVKE+LGTC SVG TV+G+ +D+ + ID+GE+E+PE
Sbjct: 121 SMAKELAGTVKEILGTCVSVGCTVDGKDPKDLQQEIDDGEVEIPEA 166
>gnl|CDD|240269 PTZ00105, PTZ00105, 60S ribosomal protein L12; Provisional.
Length = 140
Score = 229 bits (587), Expect = 8e-79
Identities = 104/140 (74%), Positives = 123/140 (87%)
Query: 26 SSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQAAISVVPSAASLIIKAL 85
SSLAPK+GPLGLSPKKVGDDIAKAT DWKGLK+TV LT+QNRQA + VVP+A+SL+IKAL
Sbjct: 1 SSLAPKVGPLGLSPKKVGDDIAKATKDWKGLKVTVKLTVQNRQATVEVVPTASSLLIKAL 60
Query: 86 KEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEVLGTCQSVGATVEG 145
KEPPRDRKKVKN+KH+GN+ D++ I+RTMRP+SMA+ F GTVKEVLGTC S+G TV+G
Sbjct: 61 KEPPRDRKKVKNIKHSGNLTFDQVIKIARTMRPKSMAKTFKGTVKEVLGTCVSIGCTVDG 120
Query: 146 RSARDIIEAIDNGEIEVPEE 165
S RDI E I+NGEI+VPE
Sbjct: 121 ESPRDIQEKINNGEIKVPES 140
>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 = 148 bits (376), Expect = 8e-47
Identities = 43/133 (32%), Positives = 69/133 (51%), Gaps = 4/133 (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-PSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVK 130
V P A++L+ KA + KK N + GN+ +D++Y I++ P A+ VK
Sbjct: 61 EVKTPPASALLKKA-AGIEKGSKK-PNKEKVGNITLDQVYEIAKIKLPDLNAKTLKSAVK 118
Query: 131 EVLGTCQSVGATV 143
E+LGT +S+G TV
Sbjct: 119 EILGTARSMGITV 131
>gnl|CDD|197819 smart00649, RL11, Ribosomal protein L11/L12.
Length = 132
Score = 141 bits (359), Expect = 3e-44
Identities = 44/134 (32%), Positives = 69/134 (51%), Gaps = 4/134 (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 ISVVPSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVK 130
I P A++L+ KA +K K K GN+ +D++Y I++ RP A+ VK
Sbjct: 61 ILKTPPASALLKKAAGIEKGSKKPGK--KKVGNITLDQVYEIAKIKRPDLNAKDLEAAVK 118
Query: 131 EVLGTCQSVGATVE 144
E+LGT +S+G TVE
Sbjct: 119 EILGTARSMGITVE 132
>gnl|CDD|223158 COG0080, RplK, Ribosomal protein L11 [Translation, ribosomal
structure and biogenesis].
Length = 141
Score = 113 bits (284), Expect = 1e-32
Identities = 43/140 (30%), Positives = 72/140 (51%), Gaps = 4/140 (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-VPSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFV 126
V P A++L+ KA K KN G + + ++ I++T P A+
Sbjct: 64 SFTFIVKTPPASALLKKAAGIEKGSGKPNKN--KVGKLTLAQVREIAKTKMPDLNAKDLE 121
Query: 127 GTVKEVLGTCQSVGATVEGR 146
VKE+LGT +S+G TVEG+
Sbjct: 122 AAVKEILGTARSMGVTVEGK 141
>gnl|CDD|234908 PRK01143, rpl11p, 50S ribosomal protein L11P; Validated.
Length = 163
Score = 86.5 bits (215), Expect = 4e-22
Identities = 43/148 (29%), Positives = 79/148 (53%), Gaps = 9/148 (6%)
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--KEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEVL 133
+LI K L ++ + GN+ +++ I+ + ++ VKEVL
Sbjct: 71 PTTALIKKELGIEKGSGEPGHEVV----GNLSFEQVVKIAIMKKDDLLSYDLKAAVKEVL 126
Query: 134 GTCQSVGATVEGRSARDIIEAIDNGEIE 161
GTC S+G TVEG+ +++ + +D G+ +
Sbjct: 127 GTCVSMGVTVEGKDPKEVQKEVDEGKYD 154
>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 = 69.1 bits (170), Expect = 2e-16
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|189492 pfam00298, Ribosomal_L11, Ribosomal protein L11, RNA binding
domain.
Length = 69
Score = 48.6 bits (117), Expect = 2e-08
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 2/70 (2%)
Query: 74 VPSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEVL 133
P A+ L+ KA + K K G + + ++Y I++ P A VK ++
Sbjct: 2 TPPASYLLKKAAGIE-KGSGKPGKEK-VGKITLKQVYEIAKIKMPDLNANDLEAAVKIII 59
Query: 134 GTCQSVGATV 143
GT +S+G V
Sbjct: 60 GTARSMGIEV 69
>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 = 29.6 bits (67), Expect = 0.67
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 70 AISVVPSAASLIIKALKEPPRDRKKVKNV 98
A + A+ + + L +PP DR V++V
Sbjct: 26 AEQTLSDASRFVWRILYQPPSDRPPVRSV 54
>gnl|CDD|234661 PRK00140, rplK, 50S ribosomal protein L11; Validated.
Length = 141
Score = 28.6 bits (65), Expect = 0.96
Identities = 37/134 (27%), Positives = 62/134 (46%), Gaps = 30/134 (22%)
Query: 29 APKIGPLGLSPKKVGDDIAK-------ATGDWKGLKITVCLTI-QNRQAAISVV---PSA 77
AP +GP L + V +I + T D KGL I V +T+ ++R + + + P A
Sbjct: 21 APPVGP-ALGQRGV--NIMEFCKAFNARTQDQKGLPIPVVITVYEDR--SFTFITKTPPA 75
Query: 78 ASLIIKALK------EPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKE 131
+ L+ KA EP +++KV G + ++ I+ T P A ++
Sbjct: 76 SVLLKKAAGIEKGSGEP--NKEKV------GKITRAQVREIAETKMPDLNAADIEAAMRM 127
Query: 132 VLGTCQSVGATVEG 145
+ GT +S+G VEG
Sbjct: 128 IAGTARSMGIVVEG 141
>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 = 27.3 bits (61), Expect = 3.5
Identities = 20/102 (19%), Positives = 47/102 (46%), Gaps = 7/102 (6%)
Query: 9 EVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQ 68
EV ++ R + GE+ +SL ++ L P ++ ++ + +G + V T++ +
Sbjct: 43 EVSEITERAMRGELDFKASLRERVALLKGLPVELLKEVRENLPLTEGAEELV-KTLKEKG 101
Query: 69 AAISVVPSAASLIIKALKEPPR------DRKKVKNVKHNGNV 104
++V+ L + +K+ +R +V++ K G V
Sbjct: 102 YKVAVISGGFDLFAEHVKDKLGLDAAFANRLEVEDGKLTGLV 143
>gnl|CDD|233274 TIGR01110, mdcA, malonate decarboxylase, alpha subunit. This model
describes malonate decarboxylase alpha subunit, from
both the water-soluble form as found in Klebsiella
pneumoniae and the form couple to sodium ion pumping in
Malonomonas rubra. Malonate decarboxylase Na+ pump is
the paradigm of the family of Na+ transport
decarboxylases. Essentially, it couples the energy
derived from decarboxylation of a carboxylic acid
substrate to move Na+ ion across the bilayer. Functional
malonate decarboylase is a multi subunit protein. The
alpha subunit enzymatically performs the transfer of
malonate (substrate) to an acyl carrier protein subunit
for subsequent decarboxylation, hence the name:
acetyl-S-acyl carrier protein:malonate carrier
protein-SH transferase [Transport and binding proteins,
Cations and iron carrying compounds, Energy metabolism,
Other].
Length = 543
Score = 27.1 bits (60), Expect = 4.7
Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 61 CLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRS 120
C +++ R AI V + + D K+ K ++ G + E I R+ RS
Sbjct: 463 CRSLEERMQAIRGVAGYTEVGLS------ADPKETKTLRQRGIIKTPEDLGIDRSDASRS 516
Query: 121 M 121
+
Sbjct: 517 L 517
>gnl|CDD|227359 COG5026, COG5026, Hexokinase [Carbohydrate transport and
metabolism].
Length = 466
Score = 27.0 bits (60), Expect = 4.8
Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 14/65 (21%)
Query: 60 VCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPR 119
+ I R A ++ VP AA +I K +V +G+V I R R
Sbjct: 376 LVELIGRRAARLAAVPIAAIVIK-------TGAYKAYHVGADGSV-------IERYPGFR 421
Query: 120 SMARK 124
SM R+
Sbjct: 422 SMLRE 426
>gnl|CDD|182273 PRK10157, PRK10157, putative oxidoreductase FixC; Provisional.
Length = 428
Score = 27.2 bits (60), Expect = 4.9
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|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 = 5.0
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|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 26.4 bits (59), Expect = 9.6
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 147 SARDIIEAIDNGEIEV 162
+A +++E I +GEIEV
Sbjct: 807 NAEEVLEKIRDGEIEV 822
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
0.314 0.134 0.383
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: 8,381,274
Number of extensions: 757234
Number of successful extensions: 558
Number of sequences better than 10.0: 1
Number of HSP's gapped: 548
Number of HSP's successfully gapped: 23
Length of query: 165
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 75
Effective length of database: 6,945,742
Effective search space: 520930650
Effective search space used: 520930650
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: 42 (21.9 bits)
S2: 55 (24.8 bits)