RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5756
(360 letters)
>gnl|CDD|240254 PTZ00069, PTZ00069, 60S ribosomal protein L5; Provisional.
Length = 300
Score = 400 bits (1030), Expect = e-140
Identities = 149/225 (66%), Positives = 181/225 (80%), Gaps = 1/225 (0%)
Query: 45 MGFVKVVKNKQYFKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDI 104
M FVKVVKNK YFKR+QVK++RRREGKTDYYAR+RLI+QDKNKYN+PKYRL+VR +NKDI
Sbjct: 1 MAFVKVVKNKAYFKRFQVKYRRRREGKTDYYARRRLILQDKNKYNSPKYRLVVRITNKDI 60
Query: 105 TCQVAYSRIEGDHIICSAYSHELPKYGIKVGLTNYAAAYATGLLLARRLLKNLNLDRLYV 164
CQ+ Y+ I GD ++ +AYSHELP++GI VGLTNYAAAYATGLLLARRLLK L LD+ +
Sbjct: 61 ICQIVYATIVGDKVLAAAYSHELPRFGIPVGLTNYAAAYATGLLLARRLLKKLGLDKQFE 120
Query: 165 GCTEVTGEEFSV-ESVDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVKR 223
G E GE + V E D+ F+ LDVGL +T+TG +VFGA+KGAVDGGL+IPHS R
Sbjct: 121 GVKEADGEYYHVDEEDDEERRPFKAILDVGLARTTTGNRVFGALKGAVDGGLHIPHSPNR 180
Query: 224 FPGYDNESKDFNAEIHRKHIFGLHVAEYMRQLSEEDDEAFKRQFS 268
FPGY E ++AE+HR IFG HVAEYM+QL EED + +K+QFS
Sbjct: 181 FPGYSKEKDSYDAEVHRDRIFGKHVAEYMKQLKEEDPDKYKKQFS 225
>gnl|CDD|236294 PRK08569, rpl18p, 50S ribosomal protein L18P; Reviewed.
Length = 193
Score = 158 bits (401), Expect = 4e-47
Identities = 79/210 (37%), Positives = 106/210 (50%), Gaps = 50/210 (23%)
Query: 59 RYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAYSRIEGDHI 118
RY+V F+RRREGKTDY R +L++ K RL+VR +NK + Q+ +GD
Sbjct: 6 RYKVPFRRRREGKTDYRKRLKLLLSGKP-------RLVVRKTNKHVIAQIVKYDPKGDRT 58
Query: 119 ICSAYSHELPKYGIKVGLTNYAAAYATGLLLARRLLKNLNLDRLYVGCTEVTGEEFSVES 178
+ SA+S EL KYG K N AAY TGLL ++ LK G E +V
Sbjct: 59 LASAHSRELAKYGWKGDTGNTPAAYLTGLLAGKKALKA--------------GVEEAV-- 102
Query: 179 VDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVKRFPGYDNESKDFNAEI 238
LD+GL + + G++VF A+KGA+D GL IPH + P D
Sbjct: 103 -----------LDIGLHRPTKGSRVFAALKGAIDAGLEIPHGEEVLPDED---------- 141
Query: 239 HRKHIFGLHVAEYMRQLSEEDDEAFKRQFS 268
I G H+AEY L EE+ +K+QFS
Sbjct: 142 ---RIRGEHIAEYAESLKEEN---YKKQFS 165
>gnl|CDD|216159 pfam00861, Ribosomal_L18p, Ribosomal L18p/L5e family. This family
includes ribosomal proteins from the large subunit. This
family includes L18 from bacteria and L5 from
eukaryotes. It has been shown that the amino terminal 93
amino acids of rat Rpl5 are necessary and sufficient to
bind 5S rRNA in vitro. Suggesting that the entire family
has a function in rRNA binding.
Length = 119
Score = 145 bits (369), Expect = 2e-43
Identities = 51/148 (34%), Positives = 62/148 (41%), Gaps = 29/148 (19%)
Query: 70 GKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAYSRIEGDHIICSAYSHELPK 129
GK RKRL V+ K K + RL+VR SNK I Q+ G + S S EL K
Sbjct: 1 GKRRRRRRKRLRVRRKLKGTAERPRLVVRRSNKHIYAQIIDDTKGGTLVSASTLSKELKK 60
Query: 130 YGIKVGLTNYAAAYATGLLLARRLLKNLNLDRLYVGCTEVTGEEFSVESVDKGPGAFRCY 189
YG+K G N AAAY GLLLA+R LK KG
Sbjct: 61 YGLKGGGNNTAAAYLVGLLLAKRALK-------------------------KG----IAV 91
Query: 190 LDVGLMKTSTGAKVFGAMKGAVDGGLNI 217
+ + +VF KGA + GLN
Sbjct: 92 VVFDRGGYTYHGRVFALAKGAREAGLNF 119
>gnl|CDD|238246 cd00432, Ribosomal_L18_L5e, Ribosomal L18/L5e: L18 (L5e) is a
ribosomal protein found in the central protuberance (CP)
of the large subunit. L18 binds 5S rRNA and induces a
conformational change that stimulates the binding of L5
to 5S rRNA. Association of 5S rRNA with 23S rRNA depends
on the binding of L18 and L5 to 5S rRNA. L18/L5e is
generally described as L18 in prokaryotes and archaea,
and as L5e (or L5) in eukaryotes. In bacteria, the CP
proteins L5, L18, and L25 are required for the ribosome
to incorporate 5S rRNA into the large subunit, one of
the last steps in ribosome assembly. In archaea, both
L18 and L5 bind 5S rRNA; in eukaryotes, only the L18
homolog (L5e) binds 5S rRNA but a homolog to L5 is also
identified.
Length = 103
Score = 113 bits (284), Expect = 5e-31
Identities = 41/141 (29%), Positives = 53/141 (37%), Gaps = 38/141 (26%)
Query: 75 YARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAYSRIEGDHIICSAYSHELPKYGIKV 134
RKRL Q + RL+VR SNK I Q+ GD + SA + EL G+
Sbjct: 1 RRRKRLGTQ-------ERPRLVVRKSNKHIYAQIIDD--SGDKTLVSASTLELAIKGVLG 51
Query: 135 GLTNYAAAYATGLLLARRLLKNLNLDRLYVGCTEVTGEEFSVESVDKGPGAFRCYLDVGL 194
N AAY G LLA+R L+ G + D G
Sbjct: 52 SGNNVEAAYLVGRLLAKRALEK---------------------------GIKKVVFDRGG 84
Query: 195 MKTSTGAKVFGAMKGAVDGGL 215
+ +V KGA +GGL
Sbjct: 85 YR--YHGRVKALAKGAREGGL 103
>gnl|CDD|223334 COG0256, RplR, Ribosomal protein L18 [Translation, ribosomal
structure and biogenesis].
Length = 125
Score = 112 bits (282), Expect = 2e-30
Identities = 49/159 (30%), Positives = 60/159 (37%), Gaps = 35/159 (22%)
Query: 59 RYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAYSRIEGDHI 118
RY+VKF+RRR GK Y RK+L + + RL+VR SN+ I Q+ G
Sbjct: 2 RYKVKFRRRRRGKRAYRIRKKL------LGTSGRPRLVVRRSNRHIYAQIIDDVKGGTLA 55
Query: 119 ICSAYSHELPKYGIKVGLTNYAAAYATGLLLARRLLKNLNLDRLYVGCTEVTGEEFSVES 178
S S EL KYG K G N AAY G L+A R L G EV
Sbjct: 56 SASTLSKELRKYGKKGGGGNTEAAYLVGKLIAERALAK--------GIEEVV-------- 99
Query: 179 VDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNI 217
+V GA + GL
Sbjct: 100 -------------FDRGGYKYHGRVAALADGAREAGLEF 125
>gnl|CDD|222592 pfam14204, Ribosomal_L18_c, Ribosomal L18 C-terminal region. This
domain is the C-terminal end of ribosomal L18/L5
proteins.
Length = 93
Score = 72.2 bits (178), Expect = 6e-16
Identities = 23/33 (69%), Positives = 27/33 (81%)
Query: 237 EIHRKHIFGLHVAEYMRQLSEEDDEAFKRQFSE 269
E+HRK+IFG HVAEYM L EED+E +KRQFS
Sbjct: 1 EVHRKYIFGGHVAEYMETLKEEDEERYKRQFSR 33
>gnl|CDD|161774 TIGR00224, pckA, phosphoenolpyruvate carboxykinase (ATP). Involved
in the gluconeogenesis pathway. It converts oxaloacetic
acid to phosphoenolpyruvate using ATP. Enzyme is a
monomer. The reaction is also catalysed by
phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32)
using GTP instead of ATP, described in PROSITE:PDOC00421
[Energy metabolism, Glycolysis/gluconeogenesis].
Length = 532
Score = 31.4 bits (71), Expect = 0.72
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 64 FKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAY 110
++ + T +RKRL V D PKYRL VR +VA+
Sbjct: 94 WQHLKGLVTRQLSRKRLFVVDAFCGADPKYRLSVRV-----VTEVAW 135
>gnl|CDD|178715 PLN03171, PLN03171, chalcone synthase-like protein; Provisional.
Length = 399
Score = 31.1 bits (70), Expect = 0.80
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 8/73 (10%)
Query: 142 AYATGLLLARRLLKNLNLDRLYVGCTEVTGEEFSVESVDKGP--GAFRCYLDVGLMKTST 199
A A L LA+ L +N R+ V E+T F+ GP G F+ L+ GL
Sbjct: 172 AGAAALRLAKDLAENNRGARVLVVAAEITLLLFN------GPDEGCFQTLLNQGLFGDGA 225
Query: 200 GAKVFGAMKGAVD 212
A + GA A +
Sbjct: 226 AAVIVGADADAAE 238
>gnl|CDD|236264 PRK08432, PRK08432, flagellar motor switch protein FliY; Validated.
Length = 283
Score = 30.7 bits (70), Expect = 0.95
Identities = 21/120 (17%), Positives = 42/120 (35%), Gaps = 21/120 (17%)
Query: 255 LSEEDDEAFKRQFSERVGGWGT-LSEQLGMTKSSFKCEKLWIVYFCVGIGENL-----AC 308
+ ++D +A K S G T L Q + K +F E + EN A
Sbjct: 86 MDDDDLDAAKEIASNIFGAISTSLGAQKLLPKLNFTIEN------VEFVDENPDLSDYAK 139
Query: 309 LHDISCRLYKLRKKIK---NSNF-----PPTLHAKSPTMSYDGPVHNHGLRAEMSSDDVR 360
L S ++ ++ +I + F T + +A +S+++++
Sbjct: 140 LFLFSFKIEDIKSQIILLMDEAFENIFEKKPKEEGEET-TDSASEEIKTHKASLSNEEIK 198
>gnl|CDD|241169 cd12725, RRM2_CPEB1, RNA recognition motif 2 in cytoplasmic
polyadenylation element-binding protein 1 (CPEB-1) and
similar proteins. This subgroup corresponds to the
RRM2 of CPEB-1 (also termed CPE-BP1 or CEBP), an
RNA-binding protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bound to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. CPEB-1
contains an N-terminal unstructured region, two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a Zn-finger motif. Both of the RRMs and the Zn
finger are required for CPEB-1 to bind CPE. The
N-terminal regulatory region may be responsible for
CPEB-1 interacting with other proteins. .
Length = 86
Score = 28.1 bits (63), Expect = 1.7
Identities = 10/33 (30%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 31 RV-FRSLKSFFKPLEMGFVKVVKNKQYFKRYQV 62
RV F + +S+ K ++ FV+ +K ++ K+ Q+
Sbjct: 49 RVTFNNQRSYMKAVKAAFVE-IKTPKFTKKVQI 80
>gnl|CDD|182432 PRK10404, PRK10404, hypothetical protein; Provisional.
Length = 101
Score = 28.7 bits (64), Expect = 1.8
Identities = 16/30 (53%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 123 YSHELPKYGIKVGLTNYAAAYATGLLLARR 152
Y HE P GI VG A GLLLARR
Sbjct: 75 YVHEKPWQGIGVGA---AVGLVLGLLLARR 101
>gnl|CDD|181762 PRK09291, PRK09291, short chain dehydrogenase; Provisional.
Length = 257
Score = 29.2 bits (66), Expect = 3.0
Identities = 11/28 (39%), Positives = 13/28 (46%), Gaps = 1/28 (3%)
Query: 119 ICSAYSHELPKYGIKVGLTNYAAAYATG 146
I A EL +GI+V N Y TG
Sbjct: 155 IAEAMHAELKPFGIQVATVN-PGPYLTG 181
>gnl|CDD|235524 PRK05593, rplR, 50S ribosomal protein L18; Reviewed.
Length = 117
Score = 27.8 bits (63), Expect = 3.9
Identities = 22/82 (26%), Positives = 30/82 (36%), Gaps = 7/82 (8%)
Query: 76 ARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAYSRI--EGDHIICSAYSHELPKYGIK 133
R+ V+ K + RL V SN+ I QV I + SA + E
Sbjct: 8 LRRHRRVRKKISGTAERPRLSVFRSNRHIYAQV----IDDVKGKTLASASTLE-KDVRAG 62
Query: 134 VGLTNYAAAYATGLLLARRLLK 155
+ N AA G L+A R
Sbjct: 63 LKGGNKEAAKKVGKLIAERAKA 84
>gnl|CDD|224779 COG1866, PckA, Phosphoenolpyruvate carboxykinase (ATP) [Energy
production and conversion].
Length = 529
Score = 28.9 bits (65), Expect = 4.7
Identities = 15/40 (37%), Positives = 18/40 (45%)
Query: 63 KFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNK 102
F R + TDY + K L V D P YRL VR +
Sbjct: 88 TFDRLKGDVTDYLSGKDLFVVDGFAGADPDYRLPVRVVTE 127
>gnl|CDD|218076 pfam04417, DUF501, Protein of unknown function (DUF501). Family of
uncharacterized bacterial proteins.
Length = 128
Score = 27.2 bits (61), Expect = 7.0
Identities = 21/91 (23%), Positives = 31/91 (34%), Gaps = 28/91 (30%)
Query: 235 NAEIHRKHIFGLHVAEYMRQLSEE--DDEAFKRQF--------SERVGGWGTLSEQL--- 281
A I R L A M++L E +DE + + + R W LS++
Sbjct: 36 VAAISR-----LEAAGVMKELQERLDEDEELRAAYVAAHERYLARR---WELLSDEFVPE 87
Query: 282 -------GMTKSSFKCEKLWIVYFCVGIGEN 305
GM KC + + G G N
Sbjct: 88 LAGVGAGGMPDFRVKCLHALVAHHLAGPGVN 118
>gnl|CDD|236471 PRK09344, PRK09344, phosphoenolpyruvate carboxykinase; Provisional.
Length = 526
Score = 27.9 bits (63), Expect = 9.5
Identities = 13/37 (35%), Positives = 17/37 (45%)
Query: 63 KFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRF 99
KF ++ Y + K L V D P+YRL VR
Sbjct: 86 KFDALKQKVLAYLSGKDLFVVDGFAGADPEYRLPVRV 122
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
0.322 0.138 0.419
Gapped
Lambda K H
0.267 0.0805 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,357,641
Number of extensions: 1772660
Number of successful extensions: 1416
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1409
Number of HSP's successfully gapped: 22
Length of query: 360
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 262
Effective length of database: 6,590,910
Effective search space: 1726818420
Effective search space used: 1726818420
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 60 (26.7 bits)