RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14232
(112 letters)
>gnl|CDD|224300 COG1382, GimC, Prefoldin, chaperonin cofactor [Posttranslational
modification, protein turnover, chaperones].
Length = 119
Score = 30.7 bits (70), Expect = 0.055
Identities = 15/47 (31%), Positives = 28/47 (59%)
Query: 2 VEEVQKKLENELNLFKQCQKEYQKVLNQRQLLSAQLNENESVQKYCN 48
+E++ +++ +L +Q Q++ QKV+ Q+Q L AQL E E +
Sbjct: 1 MEQLPPEVQAQLAQLQQLQQQLQKVILQKQQLEAQLKEIEKALEELE 47
>gnl|CDD|238345 cd00632, Prefoldin_beta, Prefoldin beta; Prefoldin is a hexameric
molecular chaperone complex, composed of two
evolutionarily related subunits (alpha and beta), which
are found in both eukaryotes and archaea. Prefoldin
binds and stabilizes newly synthesized polypeptides
allowing them to fold correctly. The hexameric
structure consists of a double beta barrel assembly
with six protruding coiled-coils. The alpha prefoldin
subunits have two beta hairpin structures while the
beta prefoldin subunits (this CD) have only one hairpin
that is most similar to the second hairpin of the alpha
subunit. The prefoldin hexamer consists of two alpha
and four beta subunits and is assembled from the beta
hairpins of all six subunits. The alpha subunits
initially dimerize providing a structural nucleus for
the assembly of the beta subunits. In archaea, there is
usually only one gene for each subunit while in
eukaryotes there two or more paralogous genes encoding
each subunit adding heterogeneity to the structure of
the hexamer.
Length = 105
Score = 30.4 bits (69), Expect = 0.061
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 9 LENELNLFKQCQKEYQKVLNQRQLLSAQLNENESV 43
++ +L +Q Q++ Q + QRQ + AQLNEN+
Sbjct: 1 VQEQLAQLQQLQQQLQAYIVQRQKVEAQLNENKKA 35
>gnl|CDD|233980 TIGR02712, urea_carbox, urea carboxylase. Members of this family
are ATP-dependent urea carboxylase, including
characterized members from Oleomonas sagaranensis (alpha
class Proteobacterium) and yeasts such as Saccharomyces
cerevisiae. The allophanate hydrolase domain of the
yeast enzyme is not included in this model and is
represented by an adjacent gene in Oleomonas
sagaranensis. The fusion of urea carboxylase and
allophanate hydrolase is designated urea amidolyase. The
enzyme from Oleomonas sagaranensis was shown to be
highly active on acetamide and formamide as well as urea
[Central intermediary metabolism, Nitrogen metabolism].
Length = 1201
Score = 29.6 bits (67), Expect = 0.26
Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 7/47 (14%)
Query: 20 QKEYQ-KVLNQRQLLSA------QLNENESVQKYCNIVHLDLGWESS 59
Q Y +V++Q +LL QL E +Q IVHL L WE
Sbjct: 856 QIHYDPRVISQSELLEVLVAIEEQLPAAEDLQVPSRIVHLPLSWEDP 902
>gnl|CDD|131391 TIGR02338, gimC_beta, prefoldin, beta subunit, archaeal.
Chaperonins are cytosolic, ATP-dependent molecular
chaperones, with a conserved toroidal architecture,
that assist in the folding of nascent and/or denatured
polypeptide chains. The group I chaperonin system
consists of GroEL and GroES, and is found (usually) in
bacteria and organelles of bacterial origin. The group
II chaperonin system, called the thermosome in Archaea
and TRiC or CCT in the Eukaryota, is structurally
similar but only distantly related. Prefoldin, also
called GimC, is a complex in Archaea and Eukaryota,
that works with group II chaperonins. Members of this
protein family are the archaeal clade of the beta class
of prefoldin subunit. Closely related, but outside the
scope of this family are the eukaryotic beta-class
prefoldin subunits, Gim-1,3,4 and 6. The alpha class
prefoldin subunits are more distantly related.
Length = 110
Score = 27.3 bits (61), Expect = 1.1
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 9 LENELNLFKQCQKEYQKVLNQRQLLSAQLNENE 41
++N+L +Q Q++ Q V Q+Q + AQL E E
Sbjct: 5 VQNQLAQLQQLQQQLQAVATQKQQVEAQLKEAE 37
>gnl|CDD|173785 cd03365, TOPRIM_TopoIIA, TOPRIM_TopoIIA: topoisomerase-primase
(TOPRIM) nucleotidyl transferase/hydrolase domain of
the type found in proteins of the type IIA family of
DNA topoisomerases similar to Saccharomyces cerevisiae
Topoisomerase II. TopoIIA enzymes cut both strands of
the duplex DNA to remove (relax) both positive and
negative supercoils in DNA. These enzymes covalently
attach to the 5' ends of the cut DNA, separate the free
ends of the cleaved strands, pass another region of the
duplex through this gap, then rejoin the ends. These
proteins also catenate/ decatenate duplex rings. The
TOPRIM domain has two conserved motifs, one of which
centers at a conserved glutamate and the other one at
two conserved aspartates (DxD). This glutamate and two
aspartates, cluster together to form a highly acid
surface patch. The conserved glutamate may act as a
general base in strand joining and as a general acid in
strand cleavage by topisomerases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full
catalytic function.
Length = 120
Score = 26.9 bits (60), Expect = 1.4
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 25 KVLNQRQLLSAQLNENESVQKYCNIVHLDLGWESSRDGLKFCTARMGRLL 74
K+LN R+ Q+ EN +Q I+ L G +S + K + R GRL+
Sbjct: 35 KLLNVREASHKQIMENAEIQNIKKILGLQHG-KSDYESTK--SLRYGRLM 81
>gnl|CDD|219673 pfam07970, COPIIcoated_ERV, Endoplasmic reticulum vesicle
transporter. This family is conserved from plants and
fungi to humans. Erv46 works in close conjunction with
Erv41 and together they form a complex which cycles
between the endoplasmic reticulum and Golgi complex.
Erv46-41 interacts strongly with the endoplasmic
reticulum glucosidase II. Mammalian glucosidase II
comprises a catalytic alpha-subunit and a 58 kDa beta
subunit, which is required for ER localisation. All
proteins identified biochemically as Erv41p-Erv46p
interactors are localised to the early secretory
pathway and are involved in protein maturation and
processing in the ER and/or sorting into COPII vesicles
for transport to the Golgi.
Length = 222
Score = 27.3 bits (61), Expect = 1.5
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 10/34 (29%)
Query: 16 FKQCQKEYQKVLNQRQLLSAQLNENESVQKYCNI 49
+QC++EY + L AQ N NE C +
Sbjct: 35 IEQCKREY------VEKLKAQKNSNEG----CRV 58
>gnl|CDD|202045 pfam01920, Prefoldin_2, Prefoldin subunit. This family includes
prefoldin subunits that are not detected by pfam02996.
Length = 106
Score = 26.4 bits (59), Expect = 2.2
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 10 ENELNLFKQCQKEYQKVLNQRQLLSAQLNENESVQK 45
+ +N F+Q Q++ Q + Q + L QL E E V +
Sbjct: 1 QELINKFQQLQQQLQLLAQQIKQLETQLKEIELVLE 36
>gnl|CDD|214591 smart00264, BAG, BAG domains, present in regulator of Hsp70
proteins. BAG domains, present in Bcl-2-associated
athanogene 1 and silencer of death domains.
Length = 79
Score = 26.1 bits (58), Expect = 2.2
Identities = 11/43 (25%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 1 MVEEVQKKLENELNLFKQCQKEYQKVLNQRQLLSAQLNENESV 43
+++EVQKK+E E+ + + + + + +L+ L + +SV
Sbjct: 8 VLDEVQKKIEKEVQVADGKKDDKEYLRLSEELM-KLLLKLDSV 49
>gnl|CDD|165114 PHA02747, PHA02747, protein tyrosine phosphatase; Provisional.
Length = 312
Score = 25.7 bits (56), Expect = 5.7
Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 10/83 (12%)
Query: 8 KLENELNLFKQCQKEYQKVLNQ---RQLLSAQLNENESVQKYCNIVHLDLGWESSRDGLK 64
K N+LN F + E+ +++ + + + + EN+ +Y +I W+ +R L
Sbjct: 16 KRRNQLNCFGIIRDEHHQIILKPFDGLIANFEKPENQPKNRYWDIP----CWDHNRVILD 71
Query: 65 FCTARMGRLLDKMSASAFDLFHD 87
+ G D + A+ D F D
Sbjct: 72 ---SGGGSTSDYIHANWIDGFED 91
>gnl|CDD|215593 PLN03128, PLN03128, DNA topoisomerase 2; Provisional.
Length = 1135
Score = 25.8 bits (57), Expect = 6.2
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 25 KVLNQRQLLSAQLNENESVQKYCNIVHLDLGWESSRDGLKFCTARMGRLL 74
K+LN R+ Q+ +N + I+ L G + K + R G L+
Sbjct: 460 KLLNVREASHKQIMKNAEITNIKQILGLQFGKTYDEENTK--SLRYGHLM 507
>gnl|CDD|214617 smart00323, RasGAP, GTPase-activator protein for Ras-like GTPases.
All alpha-helical domain that accelerates the GTPase
activity of Ras, thereby "switching" it into an "off"
position. Improved domain limits from structure.
Length = 344
Score = 25.7 bits (57), Expect = 6.7
Identities = 15/66 (22%), Positives = 25/66 (37%), Gaps = 3/66 (4%)
Query: 22 EYQKVLNQRQL---LSAQLNENESVQKYCNIVHLDLGWESSRDGLKFCTARMGRLLDKMS 78
Y K++ + L L L + +K C + L E L+ + RL D +
Sbjct: 105 VYMKLVGNQYLHTTLKPVLKKIVESKKSCEVDPAKLEGEDLETNLENLLQYVERLFDAII 164
Query: 79 ASAFDL 84
S+ L
Sbjct: 165 NSSDRL 170
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 25.6 bits (57), Expect = 7.3
Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 7 KKLENELNLFKQCQKEYQKVLNQRQLLSAQLNENESV 43
K+ EL ++ ++E + + LL QL E E +
Sbjct: 167 KQARRELEDLQEKERERAQ---RADLLQFQLEELEEL 200
>gnl|CDD|185184 PRK15284, PRK15284, putative fimbrial outer membrane usher protein
StfC; Provisional.
Length = 881
Score = 25.6 bits (56), Expect = 7.4
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 70 MGRLLDKMSASAFDLFHDRQERERGSLSWYSKKSLD 105
+GR L A AFD+ H + ++ S Y K SLD
Sbjct: 422 VGRDLALFGAVAFDVTHSHTKLDKDSA--YGKGSLD 455
>gnl|CDD|222858 PHA02533, 17, large terminase protein; Provisional.
Length = 534
Score = 25.4 bits (56), Expect = 8.8
Identities = 16/54 (29%), Positives = 21/54 (38%), Gaps = 12/54 (22%)
Query: 45 KYCNIVHLDLG------WESSRDGLK------FCTARMGRLLDKMSASAFDLFH 86
YC I H+D G + +D LK F + R L K + A L H
Sbjct: 44 NYCAITHIDYGTIKVQMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLH 97
>gnl|CDD|119427 cd05167, PI4Kc_III_alpha, Phosphoinositide 4-kinase (PI4K), Type
III, alpha isoform, catalytic domain; The PI4K catalytic
domain family is part of a larger superfamily that
includes the catalytic domains of other kinases such as
the typical serine/threonine/tyrosine protein kinases
(PKs), aminoglycoside phosphotransferase, choline
kinase, and RIO kinases. PI4Ks catalyze the transfer of
the gamma-phosphoryl group from ATP to the 4-hydroxyl of
the inositol ring of D-myo-phosphatidylinositol (PtdIns)
to generate PtdIns(4)P, the major precursor in the
synthesis of other phosphoinositides including
PtdIns(4,5)P2, PtdIns(3,4)P2, and PtdIns(3,4,5)P3. Two
isoforms of type III PI4K, alpha and beta, exist in most
eukaryotes. PI4KIIIalpha is a 220 kDa protein found in
the plasma membrane and the endoplasmic reticulum (ER).
The role of PI4KIIIalpha in the ER remains unclear. In
the plasma membrane, it provides PtdIns(4)P, which is
then converted by PI5Ks to PtdIns(4,5)P2, an important
signaling molecule. Vertebrate PI4KIIIalpha is also part
of a signaling complex associated with P2X7 ion
channels. The yeast homolog, Stt4p, is also important in
regulating the conversion of phosphatidylserine to
phosphatidylethanolamine at the ER and Golgi interface.
Mammalian PI4KIIIalpha is highly expressed in the
nervous system.
Length = 311
Score = 25.3 bits (56), Expect = 9.2
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 10/58 (17%)
Query: 38 NENESVQKYCNIVHLDLGW--ESSRDG-LKF------CTARMGRLLD-KMSASAFDLF 85
N N + +I+H+D G+ E S G LKF T M +++ M A+ F F
Sbjct: 169 NGNIMIDDDGHIIHIDFGFIFEISPGGNLKFESAPFKLTKEMVQIMGGSMEATPFKWF 226
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
0.316 0.130 0.374
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,201,522
Number of extensions: 412613
Number of successful extensions: 619
Number of sequences better than 10.0: 1
Number of HSP's gapped: 617
Number of HSP's successfully gapped: 69
Length of query: 112
Length of database: 10,937,602
Length adjustment: 76
Effective length of query: 36
Effective length of database: 7,566,698
Effective search space: 272401128
Effective search space used: 272401128
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: 53 (24.1 bits)