RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5287
(65 letters)
>gnl|CDD|239904 cd04457, S1_S28E, S1_S28E: S28E, S1-like RNA-binding domain.
S1-like RNA-binding domains are found in a wide variety
of RNA-associated proteins. S28E protein is a component
of the 30S ribosomal subunit. S28E is highly conserved
among archaea and eukaryotes. S28E may control
precursor RNA splicing and turnover in mRNA maturation
process but its function in the ribosome is largely
unknown. The structure contains an OB-fold found in
many oligosaccharide and nucleic acid binding proteins.
This implies that S28E might be involved in protein
synthesis.
Length = 60
Score = 97.3 bits (243), Expect = 4e-29
Identities = 46/59 (77%), Positives = 53/59 (89%)
Query: 7 LARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARRLR 65
LA VIK LGRTGS+G+ TQV+VEF+ D+ R+IIRNVKGPVREGDIL LLE+EREARRLR
Sbjct: 2 LAEVIKVLGRTGSRGEVTQVRVEFMDDKGRSIIRNVKGPVREGDILMLLETEREARRLR 60
>gnl|CDD|240261 PTZ00085, PTZ00085, 40S ribosomal protein S28; Provisional.
Length = 73
Score = 88.7 bits (220), Expect = 2e-25
Identities = 44/68 (64%), Positives = 56/68 (82%), Gaps = 3/68 (4%)
Query: 1 MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQ---NRTIIRNVKGPVREGDILTLLES 57
+Q LA+VIK LGRTGS+G TQV+V+ +G++ RT+IRNVKGPVREGDIL+L+E+
Sbjct: 6 DTEQPKLAKVIKVLGRTGSRGGVTQVRVQLMGEEGDAGRTLIRNVKGPVREGDILSLMET 65
Query: 58 EREARRLR 65
EREARRLR
Sbjct: 66 EREARRLR 73
>gnl|CDD|216359 pfam01200, Ribosomal_S28e, Ribosomal protein S28e.
Length = 69
Score = 87.4 bits (217), Expect = 4e-25
Identities = 41/66 (62%), Positives = 51/66 (77%), Gaps = 2/66 (3%)
Query: 2 DKQVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESER 59
+++ LA VI+ LGRTGS+G+ TQV+V + D+ R I RNVKGPVR GDIL LLE+ER
Sbjct: 4 EQEAKLAEVIEVLGRTGSRGEVTQVRVRILEGRDKGRIITRNVKGPVRVGDILMLLETER 63
Query: 60 EARRLR 65
EARRLR
Sbjct: 64 EARRLR 69
>gnl|CDD|224964 COG2053, RPS28A, Ribosomal protein S28E/S33 [Translation,
ribosomal structure and biogenesis].
Length = 69
Score = 72.1 bits (177), Expect = 5e-19
Identities = 41/67 (61%), Positives = 48/67 (71%), Gaps = 2/67 (2%)
Query: 1 MDKQVVLARVIKTLGRTGSQGQCTQVKVEFI--GDQNRTIIRNVKGPVREGDILTLLESE 58
M ++ A VI+ LGRTG G+ TQVKV + D+ R I RNVKGPVR GDIL LLE+E
Sbjct: 1 MMEEATPAEVIEVLGRTGMTGEVTQVKVRILEGRDKGRIITRNVKGPVRVGDILMLLETE 60
Query: 59 REARRLR 65
REARRLR
Sbjct: 61 REARRLR 67
>gnl|CDD|235197 PRK04007, rps28e, 30S ribosomal protein S28e; Validated.
Length = 70
Score = 67.3 bits (165), Expect = 3e-17
Identities = 35/67 (52%), Positives = 45/67 (67%), Gaps = 2/67 (2%)
Query: 1 MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESE 58
+++ A VI+ +GRTG G+ TQVK + D+ R I RNVKGPVR GDIL L E+E
Sbjct: 2 AEEEGTPAEVIEIIGRTGMTGEVTQVKCRILEGRDKGRIITRNVKGPVRVGDILMLRETE 61
Query: 59 REARRLR 65
REAR+L
Sbjct: 62 REARKLG 68
>gnl|CDD|233826 TIGR02346, chap_CCT_theta, T-complex protein 1, theta subunit.
Members of this family, all eukaryotic, are part of the
group II chaperonin complex called CCT (chaperonin
containing TCP-1) or TRiC. The archaeal equivalent group
II chaperonin is often called the thermosome. Both are
somewhat related to the group I chaperonin of bacterial,
GroEL/GroES. This family consists exclusively of the CCT
alpha chain (part of a paralogous family) from animals,
plants, fungi, and other eukaryotes.
Length = 531
Score = 28.9 bits (65), Expect = 0.11
Identities = 15/56 (26%), Positives = 20/56 (35%), Gaps = 10/56 (17%)
Query: 7 LARVIKTLGRTG----------SQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDIL 52
L R+ KT+G T G V V IG T+ + G R I+
Sbjct: 313 LRRLCKTVGATPLPRLGAPTPEELGYVDSVYVSEIGGDKVTVFKQENGDSRISTII 368
>gnl|CDD|112770 pfam03971, IDH, Monomeric isocitrate dehydrogenase.
NADP(+)-dependent isocitrate dehydrogenase (ICD) is an
important enzyme of the intermediary metabolism, as it
controls the carbon flux within the citric acid cycle
and supplies the cell with 2-oxoglutarate EC:1.1.1.42
and NADPH for biosynthetic purposes.
Length = 735
Score = 27.5 bits (61), Expect = 0.39
Identities = 6/31 (19%), Positives = 15/31 (48%)
Query: 22 QCTQVKVEFIGDQNRTIIRNVKGPVREGDIL 52
Q V++EF+ + + ++ G+I+
Sbjct: 188 QAGMVRIEFVAKDGKVKVLKDPVALQAGEII 218
>gnl|CDD|239457 cd03341, TCP1_theta, TCP-1 (CTT or eukaryotic type II) chaperonin
family, theta subunit. Chaperonins are involved in
productive folding of proteins. They share a common
general morphology, a double toroid of 2 stacked rings.
In contrast to bacterial group I chaperonins (GroEL),
each ring of the eukaryotic cytosolic chaperonin (CTT)
consists of eight different, but homologous subunits.
Their common function is to sequester nonnative proteins
inside their central cavity and promote folding by using
energy derived from ATP hydrolysis. The best studied in
vivo substrates of CTT are actin and tubulin.
Length = 472
Score = 26.8 bits (60), Expect = 0.66
Identities = 16/56 (28%), Positives = 22/56 (39%), Gaps = 10/56 (17%)
Query: 7 LARVIKTLGRT----------GSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDIL 52
L R+ +T+G T G C V VE IGD + R K + I+
Sbjct: 265 LRRLCRTVGATPLPRLGAPTPEEIGYCDSVYVEEIGDTKVVVFRQNKEDSKIATIV 320
>gnl|CDD|225394 COG2838, Icd, Monomeric isocitrate dehydrogenase [Energy production
and conversion].
Length = 744
Score = 25.9 bits (57), Expect = 1.6
Identities = 7/31 (22%), Positives = 16/31 (51%)
Query: 22 QCTQVKVEFIGDQNRTIIRNVKGPVREGDIL 52
Q T V++EF + + +++G+I+
Sbjct: 194 QATDVRIEFTAKDGKKKVLKPPVALQDGEII 224
>gnl|CDD|183511 PRK12411, PRK12411, cytidine deaminase; Provisional.
Length = 132
Score = 25.3 bits (55), Expect = 2.2
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 21 GQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLL 55
G C QV VE + + N+ G V+E + LL
Sbjct: 87 GACRQVMVELCKQDTKVYLSNLHGDVQETTVGELL 121
>gnl|CDD|237968 PRK15447, PRK15447, putative protease; Provisional.
Length = 301
Score = 24.8 bits (55), Expect = 3.0
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 52 LTLLESEREARRLR 65
L L+E+ E + LR
Sbjct: 69 LALVEAPSELKELR 82
>gnl|CDD|225802 COG3263, COG3263, NhaP-type Na+/H+ and K+/H+ antiporters with a
unique C-terminal domain [Inorganic ion transport and
metabolism].
Length = 574
Score = 25.1 bits (55), Expect = 3.0
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 35 NRTIIRNVKGPVREGDILTLLESEREARRL 64
+ I +REGD+L ++ SER+ R L
Sbjct: 448 GQLIHPQGSTRLREGDVLCVIGSERDLRAL 477
>gnl|CDD|224000 COG1074, RecB, ATP-dependent exoDNAse (exonuclease V) beta subunit
(contains helicase and exonuclease domains) [DNA
replication, recombination, and repair].
Length = 1139
Score = 25.1 bits (55), Expect = 3.1
Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 34 QNRTIIRNVKGPVREGDILTLLESEREARRLR 65
+ ++ + P+R GDI L+ S EA +
Sbjct: 541 EGEAVLDGER-PIRAGDIAVLVRSRNEAAAIE 571
>gnl|CDD|238189 cd00309, chaperonin_type_I_II, chaperonin families, type I and type
II. Chaperonins are involved in productive folding of
proteins. They share a common general morphology, a
double toroid of 2 stacked rings, each composed of 7-9
subunits. There are 2 main chaperonin groups. The
symmetry of type I is seven-fold and they are found in
eubacteria (GroEL) and in organelles of eubacterial
descent (hsp60 and RBP). The symmetry of type II is
eight- or nine-fold and they are found in archea
(thermosome), thermophilic bacteria (TF55) and in the
eukaryotic cytosol (CTT). Their common function is to
sequester nonnative proteins inside their central cavity
and promote folding by using energy derived from ATP
hydrolysis.
Length = 464
Score = 24.7 bits (55), Expect = 3.6
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 21 GQCTQVKVEFIGDQNRTIIRNVKGP 45
G V+ IGD+ T I KG
Sbjct: 286 GTAGLVEETKIGDEKYTFIEGCKGG 310
>gnl|CDD|132113 TIGR03069, PS_II_S4, photosystem II S4 domain protein. Members of
this protein family are about 265 residues long and each
contains an S4 RNA-binding domain of about 48 residues.
The member from the Cyanobacterium, Synechocystis sp.
PCC 6803, was detected as a novel polypeptide in a
highly purified preparation of active photosystem II
(Kashino, et al., 2002). The phylogenetic distribution,
including Cyanobacteria and Arabidopsis, supports a role
in photosystem II, although the high bit score cutoffs
for this model reflect similar sequences in
non-photosynthetic organisms such as Carboxydothermus
hydrogenoformans, a Gram-positive bacterium [Energy
metabolism, Photosynthesis].
Length = 257
Score = 24.6 bits (54), Expect = 4.2
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 11 IKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTL-LESEREARRL 64
I LG G+Q CT EF+ + +R+V+ + + L + + R + L
Sbjct: 124 IWVLGDRGAQALCTPELAEFL-QEKLGQVRDVEVKCKAIPLEELQIPAPRTPKEL 177
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
0.320 0.138 0.373
Gapped
Lambda K H
0.267 0.0802 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,140,789
Number of extensions: 221725
Number of successful extensions: 276
Number of sequences better than 10.0: 1
Number of HSP's gapped: 272
Number of HSP's successfully gapped: 20
Length of query: 65
Length of database: 10,937,602
Length adjustment: 36
Effective length of query: 29
Effective length of database: 9,340,858
Effective search space: 270884882
Effective search space used: 270884882
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 (21.8 bits)
S2: 53 (24.1 bits)