RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14230
(110 letters)
>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 = 59.3 bits (144), Expect = 6e-13
Identities = 35/81 (43%), Positives = 55/81 (67%), Gaps = 1/81 (1%)
Query: 9 LENELNLFKQCQKEYQKVLNQRQLLSAQLNENESVQKELDLMK-DGEVYKLIGPILVKQE 67
++ +L +Q Q++ Q + QRQ + AQLNEN+ +EL+ + D EVYKL+G +LVKQE
Sbjct: 1 VQEQLAQLQQLQQQLQAYIVQRQKVEAQLNENKKALEELEKLADDAEVYKLVGNVLVKQE 60
Query: 68 MEEAKQNVKKRIDYISAELKR 88
EEA+ +K+R++ I +KR
Sbjct: 61 KEEARTELKERLETIELRIKR 81
>gnl|CDD|224300 COG1382, GimC, Prefoldin, chaperonin cofactor [Posttranslational
modification, protein turnover, chaperones].
Length = 119
Score = 48.5 bits (116), Expect = 1e-08
Identities = 31/99 (31%), Positives = 57/99 (57%), Gaps = 1/99 (1%)
Query: 2 VEEVQKKLENELNLFKQCQKEYQKVLNQRQLLSAQLNENESVQKELDLM-KDGEVYKLIG 60
+E++ +++ +L +Q Q++ QKV+ Q+Q L AQL E E +EL+ + +D VYK +G
Sbjct: 1 MEQLPPEVQAQLAQLQQLQQQLQKVILQKQQLEAQLKEIEKALEELEKLDEDAPVYKKVG 60
Query: 61 PILVKQEMEEAKQNVKKRIDYISAELKRHDDTIATLDTK 99
+LVK EEA +++R + + +K + L +
Sbjct: 61 NLLVKVSKEEAVDELEERKETLELRIKTLEKQEEKLQER 99
>gnl|CDD|202045 pfam01920, Prefoldin_2, Prefoldin subunit. This family includes
prefoldin subunits that are not detected by pfam02996.
Length = 106
Score = 47.6 bits (114), Expect = 2e-08
Identities = 32/95 (33%), Positives = 57/95 (60%), Gaps = 1/95 (1%)
Query: 10 ENELNLFKQCQKEYQKVLNQRQLLSAQLNENESVQKELDLMKDGE-VYKLIGPILVKQEM 68
+ +N F+Q Q++ Q + Q + L QL E E V +EL+L+ + VYKLIG +LVKQ+
Sbjct: 1 QELINKFQQLQQQLQLLAQQIKQLETQLKEIELVLEELELLDEDTKVYKLIGDVLVKQDK 60
Query: 69 EEAKQNVKKRIDYISAELKRHDDTIATLDTKQDTH 103
EE K+ +++R + + E+K + + L+ + +
Sbjct: 61 EEVKEELEERKETLEKEIKTLEKQLEKLEKELEEL 95
>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 = 36.9 bits (86), Expect = 3e-04
Identities = 30/80 (37%), Positives = 49/80 (61%), Gaps = 1/80 (1%)
Query: 9 LENELNLFKQCQKEYQKVLNQRQLLSAQLNENESVQKELD-LMKDGEVYKLIGPILVKQE 67
++N+L +Q Q++ Q V Q+Q + AQL E E +EL+ L D VYK +G +LVK +
Sbjct: 5 VQNQLAQLQQLQQQLQAVATQKQQVEAQLKEAEKALEELERLPDDTPVYKSVGNLLVKTD 64
Query: 68 MEEAKQNVKKRIDYISAELK 87
EEA Q +K++ + + +K
Sbjct: 65 KEEAIQELKEKKETLELRVK 84
>gnl|CDD|181787 PRK09343, PRK09343, prefoldin subunit beta; Provisional.
Length = 121
Score = 33.9 bits (78), Expect = 0.005
Identities = 20/81 (24%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 1 MVEEVQKKLENELNLFKQCQKEYQKVLNQRQLLSAQLNENESVQKELDLMKDG-EVYKLI 59
M E + +++ +L +Q Q++ +++L Q+ + +L E +EL+ + D +YK++
Sbjct: 1 MAENIPPEVQAQLAQLQQLQQQLERLLQQKSQIDLELREINKALEELEKLPDDTPIYKIV 60
Query: 60 GPILVKQEMEEAKQNVKKRID 80
G +LVK + + ++ +K+R +
Sbjct: 61 GNLLVKVDKTKVEKELKERKE 81
>gnl|CDD|238453 cd00890, Prefoldin, Prefoldin is a hexameric molecular chaperone
complex, found in both eukaryotes and archaea, that
binds and stabilizes newly synthesized polypeptides
allowing them to fold correctly. The complex contains
two alpha and four beta subunits, the two subunits being
evolutionarily related. 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.
The structure of the complex consists of a double beta
barrel assembly with six protruding coiled-coils.
Length = 129
Score = 32.3 bits (74), Expect = 0.018
Identities = 24/113 (21%), Positives = 51/113 (45%), Gaps = 25/113 (22%)
Query: 9 LENELNLFKQCQKEYQKVLNQRQLLSAQLNENESVQKELDLMK----------------- 51
L+ +Q Q++ + + Q Q L AQL E E ++ L+ +K
Sbjct: 1 LQELAAQLQQLQQQLEALQQQLQKLEAQLTEYEKAKETLETLKKAEEEKELLVPLGAGLF 60
Query: 52 -------DGEVYKLIG-PILVKQEMEEAKQNVKKRIDYISAELKRHDDTIATL 96
D +V +G + V++ +EEA + +KKR++ + ++++ + + L
Sbjct: 61 VKAEVKDDDKVLVDLGTGVYVEKSLEEAIEFLKKRLETLEKQIEKLEKQLEKL 113
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 30.1 bits (69), Expect = 0.16
Identities = 20/84 (23%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 2 VEEVQKKLENELNLFKQCQKEYQKVLN-QRQLLS--AQLNENESVQKELDLMKDGEVYKL 58
+E+ +K+LE + ++ ++E ++++ Q Q L + L E+ + L+ ++ E +
Sbjct: 112 LEKKEKELEQKQQELEKKEEELEELIEEQLQELERISGLTAEEAKEILLEKVE--EEARH 169
Query: 59 IGPILVKQEMEEAKQNVKKRIDYI 82
+L+K+ EEAK+ K+ I
Sbjct: 170 EAAVLIKEIEEEAKEEADKKAKEI 193
>gnl|CDD|153124 cd02433, Nodulin-21_like_2, Nodulin-21 and CCC1-related protein
family. Nodulin-21_like_2: This is a family of proteins
closely related to nodulin-21, a plant nodule-specific
protein that may be involved in symbiotic nitrogen
fixation. This family is also related to CCC1, a yeast
vacuole transmembrane protein that functions as an iron
and manganese transporter. .
Length = 234
Score = 28.1 bits (63), Expect = 0.72
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 8/54 (14%)
Query: 22 EYQKVLNQRQLLSAQLNENESVQKELDLMKDGE---VYKLIGPILVKQEMEEAK 72
EY V +QR+LL A + + ++ L + E +Y+ G + EEAK
Sbjct: 70 EYVSVTSQRELLEASIPDERRELRKHPLEEAAELALIYRAKGL-----DEEEAK 118
>gnl|CDD|216038 pfam00639, Rotamase, PPIC-type PPIASE domain. Rotamases increase
the rate of protein folding by catalyzing the
interconversion of cis-proline and trans-proline.
Length = 94
Score = 26.1 bits (58), Expect = 2.0
Identities = 10/35 (28%), Positives = 17/35 (48%)
Query: 62 ILVKQEMEEAKQNVKKRIDYISAELKRHDDTIATL 96
IL+K + K + + I +L+ +DT A L
Sbjct: 2 ILIKPPESADRAAAKAKAEEILEQLQSGEDTFAEL 36
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 239
Score = 26.8 bits (60), Expect = 2.4
Identities = 8/46 (17%), Positives = 19/46 (41%)
Query: 64 VKQEMEEAKQNVKKRIDYISAELKRHDDTIATLDTKQDTHLPITSL 109
+E+E +++ YISA+L +++ + P +
Sbjct: 41 AVEEIEAEANASGQKVSYISADLSDYEEVEQAFAQAVEKGGPPDLV 86
>gnl|CDD|235248 PRK04192, PRK04192, V-type ATP synthase subunit A; Provisional.
Length = 586
Score = 26.3 bits (59), Expect = 3.9
Identities = 7/25 (28%), Positives = 15/25 (60%)
Query: 50 MKDGEVYKLIGPILVKQEMEEAKQN 74
M G++ ++ GP++V + M A+
Sbjct: 2 MTKGKIVRVSGPLVVAEGMGGARMY 26
>gnl|CDD|215414 PLN02772, PLN02772, guanylate kinase.
Length = 398
Score = 26.3 bits (58), Expect = 4.1
Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 21/90 (23%)
Query: 3 EEVQKKLEN---ELNLFK---------------QCQKEYQKVLNQRQLLSAQLNENESVQ 44
E++QK+L N EL K +C K +K+L L + N E+ +
Sbjct: 274 EQIQKRLRNAEAELEQGKSSGIFDHILYNDNLEECYKNLKKLLGLDGLAAV--NGVEAPE 331
Query: 45 KELDLMKDGEVYKLIGPILVKQEMEEAKQN 74
++L K+ V K+ I++++ E+
Sbjct: 332 G-INLPKEHSVSKMDDKIIIQETGEKTSNK 360
>gnl|CDD|235163 PRK03817, PRK03817, galactokinase; Provisional.
Length = 351
Score = 25.7 bits (57), Expect = 6.4
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 2 VEEVQKKLENELNLFKQCQKEYQKVLN--QRQLLSAQLNENESVQKELDLMKDGEVYKLI 59
EE K L K+ +E L R+ L ENE V K D +K+G++ + +
Sbjct: 204 CEEALKILGK--KSSKEVTEEDLSKLPPLLRKRAGYVLRENERVLKVRDALKEGDI-ETL 260
Query: 60 GPILV 64
G +L
Sbjct: 261 GELLT 265
>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 = 25.3 bits (56), Expect = 6.7
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 6/27 (22%)
Query: 16 FKQCQKEYQKVLNQRQLLSAQLNENES 42
+QC++EY + L AQ N NE
Sbjct: 35 IEQCKREY------VEKLKAQKNSNEG 55
>gnl|CDD|182611 PRK10642, PRK10642, proline/glycine betaine transporter;
Provisional.
Length = 490
Score = 25.4 bits (56), Expect = 7.0
Identities = 14/53 (26%), Positives = 24/53 (45%)
Query: 50 MKDGEVYKLIGPILVKQEMEEAKQNVKKRIDYISAELKRHDDTIATLDTKQDT 102
MK+ L G +++EAK+ + + D I ++ D IA L K+
Sbjct: 429 MKETANRPLKGATPAASDIQEAKEILVEHYDNIEQKIDDIDQEIAELQAKRTR 481
>gnl|CDD|117609 pfam09043, Lys-AminoMut_A, D-Lysine 5,6-aminomutase alpha subunit.
Members of his family are involved in the 1,2
rearrangement of the terminal amino group of DL-lysine
and of L-beta-lysine, using adenosylcobalamin (AdoCbl)
and pyridoxal-5'-phosphate as cofactors. The structure
is predominantly a PLP-binding TIM barrel domain, with
several additional alpha-helices and beta-strands at the
N and C termini. These helices and strands form an
intertwined accessory clamp structure that wraps around
the sides of the TIM barrel and extends up toward the
Ado ligand of the Cbl cofactor, providing most of the
interactions observed between the protein and the Ado
ligand of the Cbl, suggesting that its role is mainly in
stabilising AdoCbl in the precatalytic resting state.
Length = 509
Score = 25.5 bits (56), Expect = 8.1
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 44 QKELDL----MKDGEVYKLIGPILVKQEMEEAKQNVKKRIDYI 82
ELDL MKD K + ++ +E+ + N K R DYI
Sbjct: 96 AGELDLTKLPMKDEFEIKAAALAIARETVEKIRGNRKAREDYI 138
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 25.4 bits (56), Expect = 8.3
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 58 LIGPILVKQEMEEAKQNVKKRIDYISAELKR 88
L P+LV E+EE +Q +K+R DY+ L+
Sbjct: 258 LSDPLLVASELEEMRQRIKERRDYLRDGLEA 288
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
0.310 0.128 0.333
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,211,897
Number of extensions: 442956
Number of successful extensions: 848
Number of sequences better than 10.0: 1
Number of HSP's gapped: 824
Number of HSP's successfully gapped: 189
Length of query: 110
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 36
Effective length of database: 7,655,406
Effective search space: 275594616
Effective search space used: 275594616
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (24.3 bits)