RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031778
(153 letters)
>gnl|CDD|240306 PTZ00178, PTZ00178, 60S ribosomal protein L17; Provisional.
Length = 181
Score = 231 bits (590), Expect = 8e-79
Identities = 94/138 (68%), Positives = 114/138 (82%), Gaps = 1/138 (0%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPF 60
MVKY+++P NP+KS KA+GSDLRVHFKNT ETA AI+ + L +A++YLEDV+A K+ +PF
Sbjct: 1 MVKYARKPQNPSKSAKAKGSDLRVHFKNTYETARAIKGMKLARAQKYLEDVLAKKRCVPF 60
Query: 61 TRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQV 120
RF GGVGRTAQAK + QGRWP KS KF+L LLKNAE+NAE KGLDV+ L ISH+QV
Sbjct: 61 RRFNGGVGRTAQAKE-FGHTQGRWPEKSVKFVLSLLKNAEANAEAKGLDVEKLVISHVQV 119
Query: 121 NQAQKQRRRTYRAHGRIN 138
N+A + RRRTYRAHGRIN
Sbjct: 120 NRAPRGRRRTYRAHGRIN 137
>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 = 185 bits (471), Expect = 3e-61
Identities = 78/147 (53%), Positives = 98/147 (66%), Gaps = 1/147 (0%)
Query: 4 YSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRF 63
YS +P++PTKS KARG +LRV FKN RETA AIR + L KA++YLEDV+ K+A+PF R+
Sbjct: 1 YSYKPEDPTKSAKARGRNLRVSFKNARETARAIRGMELDKARKYLEDVIEMKRAVPFRRY 60
Query: 64 CGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVNQA 123
G VG K GR+PVK+AKFIL +L+NAE+NAE KGLDV+ L I HIQ N+
Sbjct: 61 NGKVGHRRGLKEWGW-TAGRYPVKAAKFILKVLQNAEANAEYKGLDVEKLVIIHIQANKG 119
Query: 124 QKQRRRTYRAHGRINRMFLVLFHLCLI 150
K RR RA GR H+ L+
Sbjct: 120 PKIRRWMPRAFGRATPYNSSPTHIELV 146
>gnl|CDD|179794 PRK04223, rpl22p, 50S ribosomal protein L22P; Reviewed.
Length = 153
Score = 143 bits (364), Expect = 7e-45
Identities = 61/155 (39%), Positives = 85/155 (54%), Gaps = 14/155 (9%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPF 60
+ YS + D P K+ KA G +L + K++ E A IR + L +AK YLEDV+A K+A+PF
Sbjct: 3 RINYSVKAD-PEKTAKAMGRELPISPKHSVEIAREIRGMKLDEAKAYLEDVIALKRAVPF 61
Query: 61 TRFCGGVGRTAQAKNRHPNGQ-----GRWPVKSAKFILDLLKNAESNAEVKGLDVDALYI 115
R VG H G GR+PVK+AK L LL+NAE+NAE KGLD + L I
Sbjct: 62 KRHNKKVG--------HRKGIDGWPAGRYPVKAAKAFLKLLENAEANAEYKGLDTEKLVI 113
Query: 116 SHIQVNQAQKQRRRTYRAHGRINRMFLVLFHLCLI 150
HI ++ + + RA GR ++ +I
Sbjct: 114 VHIAAHKGRVIKGYMPRAFGRATPKNTETVNIEVI 148
>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 = 107 bits (271), Expect = 2e-31
Identities = 48/137 (35%), Positives = 62/137 (45%), Gaps = 34/137 (24%)
Query: 15 CKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAK 74
KA+G LR+ K R A IR + + +A LE V
Sbjct: 1 AKAKGRYLRISPKKARLVARLIRGMSVDEALAQLEFV----------------------- 37
Query: 75 NRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGL-DVDALYISHIQVNQAQKQRRRTYRA 133
P K+AK IL LLK+AE+NAE GL D D LYI HIQVN+ +RR RA
Sbjct: 38 ----------PKKAAKIILKLLKSAEANAENNGLDDPDKLYIKHIQVNKGPTLKRRRPRA 87
Query: 134 HGRINRMFLVLFHLCLI 150
GR N + H+ ++
Sbjct: 88 RGRANPIRKRTCHITVV 104
>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 = 97.9 bits (245), Expect = 2e-27
Identities = 39/126 (30%), Positives = 50/126 (39%), Gaps = 34/126 (26%)
Query: 17 ARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNR 76
A +R+ K R A IR + +A LE V
Sbjct: 1 AVARYIRISPKKARLVADLIRGKSVEEALAILEFV------------------------- 35
Query: 77 HPNGQGRWPVKSAKFILDLLKNAESNAEV-KGLDVDALYISHIQVNQAQKQRRRTYRAHG 135
P K+AK IL LLK+A +NAE KGLD D LYI I V++ +R RA G
Sbjct: 36 --------PKKAAKIILKLLKSAVANAENNKGLDPDNLYIKEIFVDKGPTLKRFRPRARG 87
Query: 136 RINRMF 141
R +
Sbjct: 88 RATPIR 93
>gnl|CDD|223169 COG0091, RplV, Ribosomal protein L22 [Translation, ribosomal
structure and biogenesis].
Length = 120
Score = 95.0 bits (237), Expect = 4e-26
Identities = 41/137 (29%), Positives = 57/137 (41%), Gaps = 35/137 (25%)
Query: 4 YSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRF 63
YS + + P KA+ LR+ K R A IR + +A LE V
Sbjct: 1 YSAKVE-PEMEAKAKARYLRISPKKARLVADLIRGKKVAEALAILEFV------------ 47
Query: 64 CGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAE-VKGLDVDALYISHIQVNQ 122
P K+AK + +L++A +NAE KGLD D L +SHI V++
Sbjct: 48 ---------------------PKKAAKLVKKVLESAIANAENNKGLDPDKLVVSHIAVDK 86
Query: 123 AQKQRRRTYRAHGRINR 139
+R RA GR R
Sbjct: 87 GPVLKRFMPRARGRATR 103
>gnl|CDD|234793 PRK00565, rplV, 50S ribosomal protein L22; Reviewed.
Length = 112
Score = 46.2 bits (111), Expect = 3e-07
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 85 PVKSAKFILDLLKNAESNAEVK-GLDVDALYISHIQVNQAQKQRRRTYRAHGRINR 139
P K+A+ + +LK+A +NAE GLD+D L + V++ +R RA GR +R
Sbjct: 40 PKKAARLVKKVLKSAIANAENNHGLDIDNLVVKEAYVDEGPTLKRFRPRARGRASR 95
>gnl|CDD|138835 PRK12279, PRK12279, 50S ribosomal protein L22/unknown domain fusion
protein; Provisional.
Length = 311
Score = 39.7 bits (92), Expect = 2e-04
Identities = 24/65 (36%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 85 PVKSAKFILDLLKNAESNAEV--KGLDVDALYISHIQVNQAQKQRRRTYRAHGRINRMFL 142
P K A +L LL +A SN + K +D LYI I NQ +R RA G +++F
Sbjct: 40 PKKFAPIVLKLLNSAISNVQHNSKDMDPSKLYIYKIVANQGPTMKRTLPRAKGSADQLFK 99
Query: 143 VLFHL 147
HL
Sbjct: 100 RTTHL 104
>gnl|CDD|214342 CHL00034, rpl22, ribosomal protein L22.
Length = 117
Score = 34.9 bits (81), Expect = 0.004
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 85 PVKSAKFILDLLKNAESNAEV-KGLDVDALYISHIQVNQAQKQRRRTYRAHGR 136
P ++ IL L+ +A +NA GL+ L+IS +V++ +R RA GR
Sbjct: 47 PYRACYPILKLVYSAAANASHNMGLNKANLFISKAEVDEGPTLKRFRPRAQGR 99
>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 = 22/57 (38%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 85 PVKSAKFILDLLKNAESNAEVK-GLDVDALYISHIQVNQAQKQRRRTYRAHGRINRM 140
P K+A I +L +A +NAE GLD D L + I V++ +R RA GR +R+
Sbjct: 36 PKKAAPLIKKVLASAIANAEHNYGLDADNLVVVTIFVDEGPTLKRIRPRAKGRASRI 92
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 77
Score = 26.8 bits (60), Expect = 1.9
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 113 LYISHIQVNQAQKQRRRTYRAHGRINRMFLV 143
L + ++ + +Q R G + R FLV
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLV 32
>gnl|CDD|177862 PLN02214, PLN02214, cinnamoyl-CoA reductase.
Length = 342
Score = 27.8 bits (61), Expect = 2.4
Identities = 30/82 (36%), Positives = 36/82 (43%), Gaps = 11/82 (13%)
Query: 27 KNT--RETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRW 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|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2; Provisional.
Length = 193
Score = 27.4 bits (60), Expect = 2.7
Identities = 11/29 (37%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 125 KQRRRTYRAHGRINRMFLVLFHLCLIFLC 153
+ RRR +A ++R++L F LC +F+C
Sbjct: 163 RSRRRAMQAEESLSRVYL--FLLCFMFMC 189
>gnl|CDD|235159 PRK03784, PRK03784, vtamin B12-transporter permease; Provisional.
Length = 331
Score = 26.1 bits (58), Expect = 8.0
Identities = 9/31 (29%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 123 AQKQRRRTYRAHGRINRMFLVLFHLCLIFLC 153
A++Q+RR R + + ++L L+ LC
Sbjct: 7 ARQQQRRNRR---WLLGLSVLLLLALLLSLC 34
>gnl|CDD|213960 TIGR04347, pseudo_SAM_Halo, pseudo-rSAM protein/SPASM domain
protein. Members of this family all have a C-terminal
SPASM domain (see model TIGR04085), a region usually
found as a C-terminal second 4Fe-4S domain of radical
SAM domain (see pfam04055) proteins. A majority of
rSAM/SPASM proteins modify ribosomally produced
peptides. In a few members of this family, the key Cys
residues of the radical SAM domain have been lost,
making this a pseudo-rSAM family. Members of this
family are restricted so far to Haloarchaea, always
occur next a member of family TIGR04031, and are often
accompanied by another rSAM/SPASM domain protein. The
function of this two or three gene cassette is unknown.
Length = 390
Score = 25.9 bits (57), Expect = 9.1
Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 6/57 (10%)
Query: 10 NPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGG 66
N T+ C H +T A +L +AK L+D+ + +P F GG
Sbjct: 43 NTTRRCNLYCE----HCYAGADTEAAPGELSTAEAKALLDDLADY--GVPVILFSGG 93
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
0.324 0.136 0.413
Gapped
Lambda K H
0.267 0.0736 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,583,663
Number of extensions: 651869
Number of successful extensions: 777
Number of sequences better than 10.0: 1
Number of HSP's gapped: 767
Number of HSP's successfully gapped: 26
Length of query: 153
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 64
Effective length of database: 6,990,096
Effective search space: 447366144
Effective search space used: 447366144
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (24.9 bits)