RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 030568
(175 letters)
>gnl|CDD|240306 PTZ00178, PTZ00178, 60S ribosomal protein L17; Provisional.
Length = 181
Score = 261 bits (668), Expect = 2e-90
Identities = 109/175 (62%), Positives = 134/175 (76%), Gaps = 1/175 (0%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTREAAHALRKLSLTKAKRYLEDVMAHKQAIPF 60
MVKY+++P NP+KS KA+GSDLRVHFKNT E A A++ + L +A++YLEDV+A K+ +PF
Sbjct: 1 MVKYARKPQNPSKSAKAKGSDLRVHFKNTYETARAIKGMKLARAQKYLEDVLAKKRCVPF 60
Query: 61 TRFCRGVGRTAQAKNRNPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQV 120
RF GVGRTAQAK + QGRWP KS KF+L LLKNAE+NAE KGLDV+ L ISH+QV
Sbjct: 61 RRFNGGVGRTAQAKEFG-HTQGRWPEKSVKFVLSLLKNAEANAEAKGLDVEKLVISHVQV 119
Query: 121 NQAQKQRRRTYRAHGRINPYMSSPCHIELTLSEKEEPVKKEPETQLASRKPRTAT 175
N+A + RRRTYRAHGRINP+MSSPCHIEL +EK+E V K E K + A
Sbjct: 120 NRAPRGRRRTYRAHGRINPFMSSPCHIELIATEKDETVPKPKEAPKKQTKKQLAR 174
>gnl|CDD|211620 TIGR01038, L22_arch, ribosomal protein
L22(archaeal)/L17(eukaryotic/archaeal). This model
describes the ribosomal protein of the eukaryotic
cytosol and of the Archaea, variously designated as L17,
L22, and L23. The corresponding bacterial homolog,
described by a separate model, is designated L22
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 150
Score = 197 bits (502), Expect = 1e-65
Identities = 84/151 (55%), Positives = 104/151 (68%), Gaps = 1/151 (0%)
Query: 4 YSKEPDNPTKSCKARGSDLRVHFKNTREAAHALRKLSLTKAKRYLEDVMAHKQAIPFTRF 63
YS +P++PTKS KARG +LRV FKN RE A A+R + L KA++YLEDV+ K+A+PF R+
Sbjct: 1 YSYKPEDPTKSAKARGRNLRVSFKNARETARAIRGMELDKARKYLEDVIEMKRAVPFRRY 60
Query: 64 CRGVGRTAQAKNRNPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVNQA 123
VG K GR+PVK+AKFIL +L+NAE+NAE KGLDV+ L I HIQ N+
Sbjct: 61 NGKVGHRRGLK-EWGWTAGRYPVKAAKFILKVLQNAEANAEYKGLDVEKLVIIHIQANKG 119
Query: 124 QKQRRRTYRAHGRINPYMSSPCHIELTLSEK 154
K RR RA GR PY SSP HIEL + EK
Sbjct: 120 PKIRRWMPRAFGRATPYNSSPTHIELVVEEK 150
>gnl|CDD|179794 PRK04223, rpl22p, 50S ribosomal protein L22P; Reviewed.
Length = 153
Score = 144 bits (366), Expect = 7e-45
Identities = 63/155 (40%), Positives = 91/155 (58%), Gaps = 8/155 (5%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTREAAHALRKLSLTKAKRYLEDVMAHKQAIPF 60
+ YS + D P K+ KA G +L + K++ E A +R + L +AK YLEDV+A K+A+PF
Sbjct: 3 RINYSVKAD-PEKTAKAMGRELPISPKHSVEIAREIRGMKLDEAKAYLEDVIALKRAVPF 61
Query: 61 TRFCRGVGRTAQAKNRNPNG--QGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHI 118
R + VG + +G GR+PVK+AK L LL+NAE+NAE KGLD + L I HI
Sbjct: 62 KRHNKKVGH-----RKGIDGWPAGRYPVKAAKAFLKLLENAEANAEYKGLDTEKLVIVHI 116
Query: 119 QVNQAQKQRRRTYRAHGRINPYMSSPCHIELTLSE 153
++ + + RA GR P + +IE+ L E
Sbjct: 117 AAHKGRVIKGYMPRAFGRATPKNTETVNIEVILEE 151
>gnl|CDD|238205 cd00336, Ribosomal_L22, Ribosomal protein L22/L17e. L22 (L17 in
eukaryotes) is a core protein of the large ribosomal
subunit. It is the only ribosomal protein that
interacts with all six domains of 23S rRNA, and is one
of the proteins important for directing the proper
folding and stabilizing the conformation of 23S rRNA.
L22 is the largest protein contributor to the surface of
the polypeptide exit channel, the tunnel through which
the polypeptide product passes. L22 is also one of six
proteins located at the putative translocon binding site
on the exterior surface of the ribosome.
Length = 105
Score = 121 bits (307), Expect = 2e-36
Identities = 52/138 (37%), Positives = 64/138 (46%), Gaps = 34/138 (24%)
Query: 15 CKARGSDLRVHFKNTREAAHALRKLSLTKAKRYLEDVMAHKQAIPFTRFCRGVGRTAQAK 74
KA+G LR+ K R A +R +S+ +A LE V
Sbjct: 1 AKAKGRYLRISPKKARLVARLIRGMSVDEALAQLEFV----------------------- 37
Query: 75 NRNPNGQGRWPVKSAKFILDLLKNAESNAEVKGL-DVDALYISHIQVNQAQKQRRRTYRA 133
P K+AK IL LLK+AE+NAE GL D D LYI HIQVN+ +RR RA
Sbjct: 38 ----------PKKAAKIILKLLKSAEANAENNGLDDPDKLYIKHIQVNKGPTLKRRRPRA 87
Query: 134 HGRINPYMSSPCHIELTL 151
GR NP CHI + L
Sbjct: 88 RGRANPIRKRTCHITVVL 105
>gnl|CDD|143988 pfam00237, Ribosomal_L22, Ribosomal protein L22p/L17e. This family
includes L22 from prokaryotes and chloroplasts and L17
from eukaryotes.
Length = 105
Score = 109 bits (275), Expect = 1e-31
Identities = 45/138 (32%), Positives = 57/138 (41%), Gaps = 34/138 (24%)
Query: 17 ARGSDLRVHFKNTREAAHALRKLSLTKAKRYLEDVMAHKQAIPFTRFCRGVGRTAQAKNR 76
A +R+ K R A +R S+ +A LE V
Sbjct: 1 AVARYIRISPKKARLVADLIRGKSVEEALAILEFV------------------------- 35
Query: 77 NPNGQGRWPVKSAKFILDLLKNAESNAEV-KGLDVDALYISHIQVNQAQKQRRRTYRAHG 135
P K+AK IL LLK+A +NAE KGLD D LYI I V++ +R RA G
Sbjct: 36 --------PKKAAKIILKLLKSAVANAENNKGLDPDNLYIKEIFVDKGPTLKRFRPRARG 87
Query: 136 RINPYMSSPCHIELTLSE 153
R P HI + LSE
Sbjct: 88 RATPIRKRTSHITIVLSE 105
>gnl|CDD|223169 COG0091, RplV, Ribosomal protein L22 [Translation, ribosomal
structure and biogenesis].
Length = 120
Score = 106 bits (268), Expect = 2e-30
Identities = 44/154 (28%), Positives = 64/154 (41%), Gaps = 35/154 (22%)
Query: 4 YSKEPDNPTKSCKARGSDLRVHFKNTREAAHALRKLSLTKAKRYLEDVMAHKQAIPFTRF 63
YS + + P KA+ LR+ K R A +R + +A LE V
Sbjct: 1 YSAKVE-PEMEAKAKARYLRISPKKARLVADLIRGKKVAEALAILEFV------------ 47
Query: 64 CRGVGRTAQAKNRNPNGQGRWPVKSAKFILDLLKNAESNAE-VKGLDVDALYISHIQVNQ 122
P K+AK + +L++A +NAE KGLD D L +SHI V++
Sbjct: 48 ---------------------PKKAAKLVKKVLESAIANAENNKGLDPDKLVVSHIAVDK 86
Query: 123 AQKQRRRTYRAHGRINPYMSSPCHIELTLSEKEE 156
+R RA GR HI + + EKE+
Sbjct: 87 GPVLKRFMPRARGRATRINKRTSHITVVVREKEK 120
>gnl|CDD|234793 PRK00565, rplV, 50S ribosomal protein L22; Reviewed.
Length = 112
Score = 53.9 bits (131), Expect = 5e-10
Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 85 PVKSAKFILDLLKNAESNAEVK-GLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSS 143
P K+A+ + +LK+A +NAE GLD+D L + V++ +R RA GR +
Sbjct: 40 PKKAARLVKKVLKSAIANAENNHGLDIDNLVVKEAYVDEGPTLKRFRPRARGRASRIRKR 99
Query: 144 PCHIELTLSEKEE 156
HI + ++EKEE
Sbjct: 100 TSHITVVVAEKEE 112
>gnl|CDD|214342 CHL00034, rpl22, ribosomal protein L22.
Length = 117
Score = 42.6 bits (101), Expect = 8e-06
Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 85 PVKSAKFILDLLKNAESNAEV-KGLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSS 143
P ++ IL L+ +A +NA GL+ L+IS +V++ +R RA GR P
Sbjct: 47 PYRACYPILKLVYSAAANASHNMGLNKANLFISKAEVDEGPTLKRFRPRAQGRSYPIKKP 106
Query: 144 PCHIELTLSEK 154
CHI + L +
Sbjct: 107 TCHITIVLKDI 117
>gnl|CDD|138835 PRK12279, PRK12279, 50S ribosomal protein L22/unknown domain fusion
protein; Provisional.
Length = 311
Score = 42.4 bits (99), Expect = 5e-05
Identities = 28/92 (30%), Positives = 42/92 (45%), Gaps = 3/92 (3%)
Query: 85 PVKSAKFILDLLKNAESNAEV--KGLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMS 142
P K A +L LL +A SN + K +D LYI I NQ +R RA G +
Sbjct: 40 PKKFAPIVLKLLNSAISNVQHNSKDMDPSKLYIYKIVANQGPTMKRTLPRAKGSADQLFK 99
Query: 143 SPCHIELTLSEKEEPVKKEPETQLASRKPRTA 174
H+E+ LS+ +KE + ++K +
Sbjct: 100 RTTHLEIVLSDDVNEREKELAA-IKAKKSKKP 130
>gnl|CDD|130116 TIGR01044, rplV_bact, ribosomal protein L22, bacterial type. This
model decribes bacterial and chloroplast ribosomal
protein L22 [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 103
Score = 33.6 bits (77), Expect = 0.011
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 85 PVKSAKFILDLLKNAESNAEVK-GLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSS 143
P K+A I +L +A +NAE GLD D L + I V++ +R RA GR +
Sbjct: 36 PKKAAPLIKKVLASAIANAEHNYGLDADNLVVVTIFVDEGPTLKRIRPRAKGRASRIRKR 95
Query: 144 PCHIELTL 151
HI + +
Sbjct: 96 TSHITVVV 103
>gnl|CDD|227510 COG5183, SSM4, Protein involved in mRNA turnover and stability [RNA
processing and modification].
Length = 1175
Score = 30.3 bits (68), Expect = 0.54
Identities = 21/84 (25%), Positives = 30/84 (35%), Gaps = 5/84 (5%)
Query: 8 PDNPT-KSCKARGSDLRVHFKNTRE--AAHALRKLSLTKAKRYLEDVMAHK--QAIPFTR 62
D+P CK GS +H + E +K + + +D+ Q IPF+
Sbjct: 24 RDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDIYKEDMPQIIPFSI 83
Query: 63 FCRGVGRTAQAKNRNPNGQGRWPV 86
R V T R G W V
Sbjct: 84 LIRKVADTGWKATRVLLTIGLWCV 107
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP
2H9), which represent a group of nuclear RNA binding
proteins that are involved in pre-mRNA processing.
GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein
which interacts with RNA in a G-rich element-dependent
manner. It may function in RNA packaging, stabilization
of RNA secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2
(also termed RBM35B) are epithelial-specific RNA
binding proteins that promote splicing of the
epithelial variant of fibroblast growth factor receptor
2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1
(also termed p120-Catenin) transcripts. Fusilli shows
high sequence homology to ESRPs. It can regulate
endogenous FGFR2 splicing and functions as a splicing
factor. The biological roles of both, RBM12 and RBM12B,
remain unclear. RBM19 is a nucleolar protein conserved
in eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 26.0 bits (58), Expect = 3.3
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 24 VHFKNTREAAHALRKLSLTKAKRYLE 49
V F + +A ALRK + RY+E
Sbjct: 46 VEFASPEDARRALRKHNNKMGGRYIE 71
>gnl|CDD|218763 pfam05817, Ribophorin_II, Oligosaccharyltransferase subunit
Ribophorin II. This family contains eukaryotic
Ribophorin II (RPN2) proteins. The mammalian
oligosaccharyltransferase (OST) is a protein complex
that effects the cotranslational N-glycosylation of
newly synthesised polypeptides, and is composed of the
following proteins: ribophorins I and II (RI and RII),
OST48, and Dadl, N33/IAP, OST4, STT3. The family also
includes the SWP1 protein from yeast. In yeast the
oligosaccharyltransferase complex is composed 7 or 8
subunits, SWP1, being one of them.
Length = 636
Score = 27.8 bits (62), Expect = 3.5
Identities = 7/35 (20%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 138 NPYMSSPCHIELTLSEKEEPVKKEPETQLASRKPR 172
N ++ + +EL E+ P E ++ P+
Sbjct: 500 NSFLWNVADVELKFPEEPAPSTVEAKS---LFGPK 531
>gnl|CDD|148521 pfam06950, DUF1293, Protein of unknown function (DUF1293). This
family consists of several bacterial and phage proteins
of around 115 residues in length. The function of this
family is unknown.
Length = 115
Score = 26.0 bits (57), Expect = 6.6
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 123 AQKQRRRTYRAHGRINPYMSSPCHIELTLSEKEE 156
++K +RRT G +NP P I+ T + K E
Sbjct: 35 SEKFKRRTLGESGDVNPQWDQPLMIDHTYALKLE 68
>gnl|CDD|177862 PLN02214, PLN02214, cinnamoyl-CoA reductase.
Length = 342
Score = 26.6 bits (58), Expect = 7.3
Identities = 30/82 (36%), Positives = 37/82 (45%), Gaps = 11/82 (13%)
Query: 27 KNT--REAAHALRKLSLTKAKRYLEDVMAHKQAIPFTRFCRGVGRTAQAKNRNPNGQGRW 84
KNT RE +L L KA L+D A K AI C GV TA +P
Sbjct: 48 KNTHLRELEGGKERLILCKAD--LQDYEALKAAIDG---CDGVFHTASPVTDDPEQMVEP 102
Query: 85 PVKSAKFILDLLKNAESNAEVK 106
V AKF++ NA + A+VK
Sbjct: 103 AVNGAKFVI----NAAAEAKVK 120
>gnl|CDD|99796 cd06199, SiR, Cytochrome p450- like alpha subunits of E. coli
sulfite reductase (SiR) multimerize with beta subunits
to catalyze the NADPH dependent reduction of sulfite to
sulfide. Beta subunits have an Fe4S4 cluster and a
siroheme, while the alpha subunits (cysJ gene) are of
the cytochrome p450 (CyPor) family having FAD and FMN as
prosthetic groups and utilizing NADPH. Cypor (including
cyt -450 reductase, nitric oxide synthase, and
methionine synthase reductase) are ferredoxin reductase
(FNR)-like proteins with an additional N-terminal FMN
domain and a connecting sub-domain inserted within the
flavin binding portion of the FNR-like domain. The
connecting domain orients the N-terminal FMN domain with
the C-terminal FNR domain.
Length = 360
Score = 26.4 bits (59), Expect = 7.9
Identities = 11/23 (47%), Positives = 11/23 (47%), Gaps = 1/23 (4%)
Query: 29 TREAAHALRKLSLTKAKRYLEDV 51
E A A K L K KRY DV
Sbjct: 338 DEEEAEAYLK-ELKKEKRYQRDV 359
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
0.315 0.128 0.372
Gapped
Lambda K H
0.267 0.0598 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,460,078
Number of extensions: 737232
Number of successful extensions: 685
Number of sequences better than 10.0: 1
Number of HSP's gapped: 674
Number of HSP's successfully gapped: 22
Length of query: 175
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 85
Effective length of database: 6,945,742
Effective search space: 590388070
Effective search space used: 590388070
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: 56 (25.6 bits)