RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031693
(155 letters)
>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 = 192 bits (489), Expect = 4e-64
Identities = 69/142 (48%), Positives = 92/142 (64%), Gaps = 2/142 (1%)
Query: 11 RPVAATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAF 70
+ + I+L VPAG A PAPPVGPALGQ +N+M FCK FNART Y+P P+ V IT +
Sbjct: 1 KKIVGIIKLQVPAGQANPAPPVGPALGQRGVNIMEFCKQFNARTADYEPGLPVPVVITVY 60
Query: 71 KDNTFEFTVKSPSVTWYLKKAAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYM 130
+D +F F VK+P V++ LKKAAG+E GS P +T K + EIA++K SD
Sbjct: 61 EDKSFTFIVKTPPVSYLLKKAAGVEKGSKNPKKEKVGKITRKQVREIAEIKMSD--LNTK 118
Query: 131 PLESICKSIIGTAATMGIKVVK 152
+E+ K I GTA +MGI++V
Sbjct: 119 DIEAAMKIIAGTAKSMGIEIVG 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 = 183 bits (468), Expect = 6e-61
Identities = 70/134 (52%), Positives = 88/134 (65%), Gaps = 3/134 (2%)
Query: 17 IRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTFE 76
I+L VPAG A PAPP+GPALGQ +N+M FCK+FNART+ YK P+ V IT + D +F
Sbjct: 1 IKLQVPAGKASPAPPLGPALGQLGVNIMKFCKEFNARTKDYK-GLPVPVKITVYNDRSFT 59
Query: 77 FTVKSPSVTWYLKKAAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPLESIC 136
F VK+P + LKKAAGIE GS +P +TL +YEIAK+K D L+S
Sbjct: 60 FEVKTPPASALLKKAAGIEKGSKKPNKEKVGNITLDQVYEIAKIKLPD--LNAKTLKSAV 117
Query: 137 KSIIGTAATMGIKV 150
K I+GTA +MGI V
Sbjct: 118 KEILGTARSMGITV 131
>gnl|CDD|197819 smart00649, RL11, Ribosomal protein L11/L12.
Length = 132
Score = 179 bits (456), Expect = 4e-59
Identities = 68/135 (50%), Positives = 89/135 (65%), Gaps = 3/135 (2%)
Query: 17 IRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTFE 76
I+L +PAG A PAPP+GPALGQ +N+M FCK+FNART+ K P+ V IT + D +F
Sbjct: 1 IKLQIPAGKANPAPPLGPALGQLGINIMEFCKEFNARTKD-KKGLPIPVKITVYNDKSFT 59
Query: 77 FTVKSPSVTWYLKKAAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPLESIC 136
F +K+P + LKKAAGIE GS +PG +TL +YEIAK+K+ D LE+
Sbjct: 60 FILKTPPASALLKKAAGIEKGSKKPGKKKVGNITLDQVYEIAKIKRPD--LNAKDLEAAV 117
Query: 137 KSIIGTAATMGIKVV 151
K I+GTA +MGI V
Sbjct: 118 KEILGTARSMGITVE 132
>gnl|CDD|234661 PRK00140, rplK, 50S ribosomal protein L11; Validated.
Length = 141
Score = 156 bits (398), Expect = 4e-50
Identities = 64/139 (46%), Positives = 82/139 (58%), Gaps = 3/139 (2%)
Query: 13 VAATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKD 72
V I+L +PAG A PAPPVGPALGQ +N+M FCK FNARTQ + P+ V IT ++D
Sbjct: 5 VVGYIKLQIPAGKANPAPPVGPALGQRGVNIMEFCKAFNARTQD-QKGLPIPVVITVYED 63
Query: 73 NTFEFTVKSPSVTWYLKKAAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPL 132
+F F K+P + LKKAAGIE GS P +T + EIA+ K D +
Sbjct: 64 RSFTFITKTPPASVLLKKAAGIEKGSGEPNKEKVGKITRAQVREIAETKMPDLNAA--DI 121
Query: 133 ESICKSIIGTAATMGIKVV 151
E+ + I GTA +MGI V
Sbjct: 122 EAAMRMIAGTARSMGIVVE 140
>gnl|CDD|223158 COG0080, RplK, Ribosomal protein L11 [Translation, ribosomal
structure and biogenesis].
Length = 141
Score = 153 bits (388), Expect = 1e-48
Identities = 67/139 (48%), Positives = 87/139 (62%), Gaps = 3/139 (2%)
Query: 13 VAATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKD 72
V I+L VPAG A P+PPVGPALGQ +N+M FCK+FNA T+ K P+ V IT ++D
Sbjct: 4 VVKIIKLQVPAGKANPSPPVGPALGQLGVNIMEFCKEFNAATKDEK-GLPVPVVITVYED 62
Query: 73 NTFEFTVKSPSVTWYLKKAAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPL 132
+F F VK+P + LKKAAGIE GS +P +TL + EIAK K D + L
Sbjct: 63 RSFTFIVKTPPASALLKKAAGIEKGSGKPNKNKVGKLTLAQVREIAKTKMPDLNAK--DL 120
Query: 133 ESICKSIIGTAATMGIKVV 151
E+ K I+GTA +MG+ V
Sbjct: 121 EAAVKEILGTARSMGVTVE 139
>gnl|CDD|177049 CHL00127, rpl11, ribosomal protein L11; Validated.
Length = 140
Score = 112 bits (282), Expect = 1e-32
Identities = 57/139 (41%), Positives = 82/139 (58%), Gaps = 3/139 (2%)
Query: 13 VAATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKD 72
A I+L +PAG A PAPPVGPALGQ+ +N+ FCK++NART+ + V I+ ++D
Sbjct: 5 KLAIIKLALPAGKATPAPPVGPALGQHGVNINLFCKEYNARTKDKI-GLIIPVEISVYED 63
Query: 73 NTFEFTVKSPSVTWYLKKAAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPL 132
++ F +K+P + L KAAGI+ GS P ++T+K + EIA++K D L
Sbjct: 64 KSYTFILKTPPASVLLAKAAGIKKGSGEPNKKKVGSITIKQLEEIAQIKLPDLNTI--SL 121
Query: 133 ESICKSIIGTAATMGIKVV 151
K I GTA MGI +
Sbjct: 122 SKAIKIIEGTAKNMGISIK 140
>gnl|CDD|189492 pfam00298, Ribosomal_L11, Ribosomal protein L11, RNA binding
domain.
Length = 69
Score = 100 bits (253), Expect = 4e-29
Identities = 36/71 (50%), Positives = 46/71 (64%), Gaps = 2/71 (2%)
Query: 80 KSPSVTWYLKKAAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPLESICKSI 139
K+P ++ LKKAAGIE GS +PG +TLK +YEIAK+K D LE+ K I
Sbjct: 1 KTPPASYLLKKAAGIEKGSGKPGKEKVGKITLKQVYEIAKIKMPDLNA--NDLEAAVKII 58
Query: 140 IGTAATMGIKV 150
IGTA +MGI+V
Sbjct: 59 IGTARSMGIEV 69
>gnl|CDD|234908 PRK01143, rpl11p, 50S ribosomal protein L11P; Validated.
Length = 163
Score = 88.8 bits (221), Expect = 3e-23
Identities = 43/141 (30%), Positives = 69/141 (48%), Gaps = 10/141 (7%)
Query: 14 AATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITA-FKD 72
+ + V G A P PP+GPALG LN+ ++ N +T+ +K + V +
Sbjct: 2 KKVVEVLVEGGKATPGPPLGPALGPLGLNVKQVVQEINEKTKDFK-GMQVPVKVIVDTDT 60
Query: 73 NTFEFTVKSPSVTWYLKKAAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYM-- 130
FE V P T +KK GIE GS PGH ++ + + +IA +K+ D +
Sbjct: 61 KKFEIEVGIPPTTALIKKELGIEKGSGEPGHEVVGNLSFEQVVKIAIMKKDD-----LLS 115
Query: 131 -PLESICKSIIGTAATMGIKV 150
L++ K ++GT +MG+ V
Sbjct: 116 YDLKAAVKEVLGTCVSMGVTV 136
>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 = 84.9 bits (211), Expect = 8e-23
Identities = 34/60 (56%), Positives = 43/60 (71%), Gaps = 1/60 (1%)
Query: 16 TIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTF 75
I+L VPAG A PAPP+GPALGQ +N+M FCK+FNA T+ YK P+ V IT + D +F
Sbjct: 1 VIKLQVPAGKANPAPPLGPALGQLGVNIMEFCKEFNAATKDYK-GLPVPVKITVYNDRSF 59
>gnl|CDD|184732 PRK14539, PRK14539, 50S ribosomal protein L11/unknown domain fusion
protein; Provisional.
Length = 196
Score = 72.3 bits (177), Expect = 2e-16
Identities = 48/143 (33%), Positives = 74/143 (51%), Gaps = 7/143 (4%)
Query: 8 LTRRPVAATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTI 67
+ ++ V +L AG A+P GP+L +N+ F K FN T+ E P+ V I
Sbjct: 1 MAKKEVVKVAKLQFNAGQAKP----GPSLAGVGINMPEFTKQFNDATRDRGGE-PVPVQI 55
Query: 68 TAFKDNTFEFTVKSPSVTWYLKKAAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYC 127
T +KD +F+F + + ++ +K+AA I+SGS+ T+TL + EIAK K D
Sbjct: 56 TVYKDKSFDFKLFTAPASFKIKQAAKIKSGSANSKTTIVGTITLSQLEEIAKYKLPD--L 113
Query: 128 QYMPLESICKSIIGTAATMGIKV 150
+E +I GTA MG+ V
Sbjct: 114 NTDDVEEAMHTIAGTAKNMGVLV 136
>gnl|CDD|240358 PTZ00321, PTZ00321, ribosomal protein L11; Provisional.
Length = 342
Score = 72.7 bits (178), Expect = 6e-16
Identities = 44/140 (31%), Positives = 71/140 (50%), Gaps = 7/140 (5%)
Query: 18 RLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQ-KYKPETPMSVTITAFKDNTFE 76
R + AG A PPVG + L M F K FN RT+ +K + + V I + D ++
Sbjct: 54 RFFIKAGKAATGPPVGQEFSKLGLKAMDFAKSFNDRTKPHFKDDVELIVRIQVYFDKSYL 113
Query: 77 FTVKSPSVTWYLKKAAGIESGSSRP----GHVTASTVTLKHIYEIAKVKQ-SDPYCQYMP 131
FT++ P W++ +A + + P GH A +TL+ YEIAK+K S +Y
Sbjct: 114 FTIEPPPTAWFILRALRKKRRETGPVPLRGHYCA-LMTLEMAYEIAKMKPRSWGRPEYPL 172
Query: 132 LESICKSIIGTAATMGIKVV 151
+E+ + ++G A MG+ +
Sbjct: 173 IETRVRRVVGQARRMGVCFI 192
>gnl|CDD|178621 PLN03072, PLN03072, 60S ribosomal protein L12; Provisional.
Length = 166
Score = 29.8 bits (67), Expect = 0.38
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 107 STVTLKHIYEIAKVKQSDPYCQYMPLESICKSIIGTAATMGIKV 150
++L + EIAK+ + + L K I+GT ++G V
Sbjct: 103 GNISLDDVIEIAKIMRPRSMAK--ELAGTVKEILGTCVSVGCTV 144
>gnl|CDD|216846 pfam02014, Reeler, Reeler domain.
Length = 127
Score = 28.8 bits (65), Expect = 0.65
Identities = 15/66 (22%), Positives = 22/66 (33%), Gaps = 14/66 (21%)
Query: 15 ATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNT 74
A + GGA P P Y + + Y P +VTI+ +T
Sbjct: 1 ACSDMLPGHGGASPQTTDSP----YTIT---------VSPESYVPGQTYTVTISKSSGDT 47
Query: 75 FE-FTV 79
F F +
Sbjct: 48 FRGFLL 53
>gnl|CDD|217595 pfam03514, GRAS, GRAS family transcription factor. Sequence
analysis of the products of the GRAS (GAI, RGA, SCR)
gene family indicates that they share a variable
amino-terminus and a highly conserved carboxyl-terminus
that contains five recognisable motifs. Proteins in the
GRAS family are transcription factors that seem to be
involved in development and other processes. Mutation of
the SCARECROW (SCR) gene results in a radial pattern
defect, loss of a ground tissue layer, in the root. The
PAT1 protein is involved in phytochrome A signal
transduction.
Length = 372
Score = 28.4 bits (64), Expect = 1.8
Identities = 11/51 (21%), Positives = 16/51 (31%), Gaps = 4/51 (7%)
Query: 2 ATLKEILTRRPVAA-TIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFN 51
+L + L RP +R+T G P L + L F
Sbjct: 126 PSLIQALASRPGGPPHLRIT---GIGSPQFSSAEELEETGDRLAQFADSLG 173
>gnl|CDD|200381 TIGR04130, FnlA, UDP-N-acetylglucosamine
4,6-dehydratase/5-epimerase. The FnlA enzyme is the
first step in the biosynthesis of UDP-FucNAc from
UDP-GlcNAc in E. coli (along with FnlB and FnlC). The
proteins identified by this model include FnlA homologs
in the O-antigen clusters of O4, O25, O26, O29 (Shigella
D11), O118, O145 and O172 serotype strains, all of which
produce O-antigens containing FucNAc (or the further
modified FucNAm). A homolog from Pseudomonas aerugiosa
serotype O11, WbjB, also involved in the biosynthesis of
UDP-FucNAc has been characterized and is now believed to
carry out both the initial 4,6-dehydratase reaction and
the subsequent epimerization of the resulting methyl
group at C-5. A phylogenetic tree of related sequences
shows a distinct clade of enzymes involved in the
biosynthesis of UDP-QuiNAc (Qui=qinovosamine). This
clade appears to be descendant from the common ancestor
of the Pseudomonas and E. coli fucose-biosynthesis
enzymes. It has been hypothesized that the first step in
the biosynthesis of these two compounds may be the same,
and thus that these enzymes all have the same function.
At present, lacking sufficient confirmation of this, the
current model trusted cutoff only covers the tree
segment surrounding the E. coli genes. The clades
containing the Pseudomonas and QuiNAc biosynthesis
enzymes score above the noise cutoff. Immediately below
the noise cutoff are enzymes involved in the
biosynthesis of UDP-RhaNAc (Rha=rhamnose), which again
may or may not produce the same product.
Length = 337
Score = 28.4 bits (63), Expect = 1.8
Identities = 11/29 (37%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 114 IYEIAKVKQSDPYCQYMPLESICKSIIGT 142
IY A +KQ P C++ P+E++ +++GT
Sbjct: 77 IYHAAALKQV-PSCEFHPMEAVKTNVLGT 104
>gnl|CDD|220299 pfam09586, YfhO, Bacterial membrane protein YfhO. This protein is
a conserved membrane protein. The yfhO gene is
transcribed in Difco sporulation medium and the
transcription is affected by the YvrGHb two-component
system. Some members of this family have been annotated
as glycosyl transferases of the PMT family.
Length = 835
Score = 26.8 bits (60), Expect = 5.3
Identities = 8/48 (16%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 37 GQYRLNLMAF-CKDFNARTQKYKPETPMSVTITAFKDNTFEFTVKSPS 83
GQ L+ + ++ + K + +T + DN T+ +
Sbjct: 727 GQLSLDDLQLYGLNYTTLKKAIKKLKEQQLKVTKYSDNKLSGTINTKK 774
>gnl|CDD|204259 pfam09517, RE_Eco29kI, Eco29kI restriction endonuclease. This
family includes the Eco29kI (recognises and cleaves
CCGC^GG) restriction endonuclease.
Length = 170
Score = 26.3 bits (58), Expect = 5.8
Identities = 12/59 (20%), Positives = 19/59 (32%), Gaps = 7/59 (11%)
Query: 103 HVTASTVTLKHIYE----IAKVKQSDP---YCQYMPLESICKSIIGTAATMGIKVVKEL 154
+ + E IA+V D C+++ E I IK+ K L
Sbjct: 54 NAPPGNELFNRLREHARSIAQVSDLDLEDFMCRFVIFELHGSDWIPLIEAALIKLFKPL 112
>gnl|CDD|145055 pfam01701, PSI_PsaJ, Photosystem I reaction centre subunit IX /
PsaJ. This family consists of the photosystem I
reaction centre subunit IX or PsaJ from various
organisms including Synechocystis sp. (strain pcc
6803), Pinus thunbergii (green pine) and Zea mays
(maize). PsaJ is a small 4.4kDa, chloroplastal encoded,
hydrophobic subunit of the photosystem I reaction
complex its function is not yet fully understood. PsaJ
can be cross-linked to PsaF and has a single predicted
transmembrane domain it has a proposed role in
maintaining PsaF in the correct orientation to allow
for fast electron transfer from soluble donor proteins
to P700+.
Length = 37
Score = 24.2 bits (53), Expect = 6.6
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 1 MATLKEILTRRPVAATIRLTVPAG 24
M K+ L+ PV AT+ LT AG
Sbjct: 1 MQDFKKYLSTAPVLATLWLTFTAG 24
>gnl|CDD|219636 pfam07911, DUF1677, Protein of unknown function (DUF1677). The
sequences found in this family are all derived from
hypothetical plant proteins of unknown function. The
region features a number of highly conserved cysteine
residues.
Length = 91
Score = 25.0 bits (55), Expect = 8.5
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 4/35 (11%)
Query: 23 AGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKY 57
PA V AL ++ MAFC+ FN+ ++
Sbjct: 45 LRRGSPAIGVEEALARH----MAFCRRFNSTSRPN 75
>gnl|CDD|227848 COG5561, COG5561, Predicted metal-binding protein [Function
unknown].
Length = 101
Score = 25.3 bits (55), Expect = 9.4
Identities = 13/28 (46%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 124 DPYCQYMPLESICKSIIGTAATMGIKVV 151
P C Y E I K I MGIKVV
Sbjct: 70 KPKCPYASAEEIAKKEI---EKMGIKVV 94
>gnl|CDD|236205 PRK08259, PRK08259, enoyl-CoA hydratase; Provisional.
Length = 254
Score = 26.0 bits (58), Expect = 9.7
Identities = 15/30 (50%), Positives = 15/30 (50%), Gaps = 7/30 (23%)
Query: 7 ILTRRPVAAT----IRLT---VPAGGARPA 29
ILT RPV A I L VP G AR A
Sbjct: 158 ILTGRPVDADEALAIGLANRVVPKGQARAA 187
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
0.318 0.131 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: 7,636,443
Number of extensions: 646141
Number of successful extensions: 666
Number of sequences better than 10.0: 1
Number of HSP's gapped: 647
Number of HSP's successfully gapped: 27
Length of query: 155
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 66
Effective length of database: 6,990,096
Effective search space: 461346336
Effective search space used: 461346336
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 (21.7 bits)
S2: 55 (24.8 bits)