RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13667
(144 letters)
>gnl|CDD|202045 pfam01920, Prefoldin_2, Prefoldin subunit. This family includes
prefoldin subunits that are not detected by pfam02996.
Length = 106
Score = 74.6 bits (184), Expect = 2e-18
Identities = 33/106 (31%), Positives = 60/106 (56%)
Query: 14 EEVYNGFQNLRAEQRQIATKLSELEQELTEHKIVLDTLKDLDGDRRCFRLIGGVLCEKTV 73
+E+ N FQ L+ + + +A ++ +LE +L E ++VL+ L+ LD D + ++LIG VL ++
Sbjct: 1 QELINKFQQLQQQLQLLAQQIKQLETQLKEIELVLEELELLDEDTKVYKLIGDVLVKQDK 60
Query: 74 KEVIPTLTTNRDQLNTLINSLNEQLTKKGIEINEYKDKFDIQLQGN 119
+EV L ++ L I +L +QL K E+ E K++
Sbjct: 61 EEVKEELEERKETLEKEIKTLEKQLEKLEKELEELKEELYKLFGQQ 106
>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 = 45.1 bits (107), Expect = 4e-07
Identities = 22/98 (22%), Positives = 45/98 (45%)
Query: 14 EEVYNGFQNLRAEQRQIATKLSELEQELTEHKIVLDTLKDLDGDRRCFRLIGGVLCEKTV 73
+E Q L+ + + + ++E +L E+K L+ L+ L D ++L+G VL ++
Sbjct: 2 QEQLAQLQQLQQQLQAYIVQRQKVEAQLNENKKALEELEKLADDAEVYKLVGNVLVKQEK 61
Query: 74 KEVIPTLTTNRDQLNTLINSLNEQLTKKGIEINEYKDK 111
+E L + + I L Q ++ E ++K
Sbjct: 62 EEARTELKERLETIELRIKRLERQEEDLQEKLKELQEK 99
>gnl|CDD|224300 COG1382, GimC, Prefoldin, chaperonin cofactor [Posttranslational
modification, protein turnover, chaperones].
Length = 119
Score = 40.4 bits (95), Expect = 3e-05
Identities = 21/99 (21%), Positives = 48/99 (48%)
Query: 13 DEEVYNGFQNLRAEQRQIATKLSELEQELTEHKIVLDTLKDLDGDRRCFRLIGGVLCEKT 72
+ Q L+ + +++ + +LE +L E + L+ L+ LD D ++ +G +L + +
Sbjct: 8 VQAQLAQLQQLQQQLQKVILQKQQLEAQLKEIEKALEELEKLDEDAPVYKKVGNLLVKVS 67
Query: 73 VKEVIPTLTTNRDQLNTLINSLNEQLTKKGIEINEYKDK 111
+E + L ++ L I +L +Q K + E + +
Sbjct: 68 KEEAVDELEERKETLELRIKTLEKQEEKLQERLEELQSE 106
>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 = 34.2 bits (79), Expect = 0.007
Identities = 29/122 (23%), Positives = 52/122 (42%), Gaps = 24/122 (19%)
Query: 14 EEVYNGFQNLRAEQRQIATKLSELEQELTEHKIVLDTLKDLD------------------ 55
+E+ Q L+ + + +L +LE +LTE++ +TL+ L
Sbjct: 2 QELAAQLQQLQQQLEALQQQLQKLEAQLTEYEKAKETLETLKKAEEEKELLVPLGAGLFV 61
Query: 56 -----GDRRCFRLIG-GVLCEKTVKEVIPTLTTNRDQLNTLINSLNEQLTKKGIEINEYK 109
D + +G GV EK+++E I L + L I L +QL K +I E +
Sbjct: 62 KAEVKDDDKVLVDLGTGVYVEKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQ 121
Query: 110 DK 111
++
Sbjct: 122 EE 123
>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 = 32.7 bits (75), Expect = 0.018
Identities = 19/78 (24%), Positives = 40/78 (51%)
Query: 20 FQNLRAEQRQIATKLSELEQELTEHKIVLDTLKDLDGDRRCFRLIGGVLCEKTVKEVIPT 79
Q L+ + + +AT+ ++E +L E + L+ L+ L D ++ +G +L + +E I
Sbjct: 12 LQQLQQQLQAVATQKQQVEAQLKEAEKALEELERLPDDTPVYKSVGNLLVKTDKEEAIQE 71
Query: 80 LTTNRDQLNTLINSLNEQ 97
L ++ L + +L Q
Sbjct: 72 LKEKKETLELRVKTLQRQ 89
>gnl|CDD|181787 PRK09343, PRK09343, prefoldin subunit beta; Provisional.
Length = 121
Score = 32.0 bits (73), Expect = 0.047
Identities = 23/96 (23%), Positives = 43/96 (44%), Gaps = 7/96 (7%)
Query: 20 FQNLRAEQRQIATKLSELEQELTEHKIVLDTLKDLDGDRRCFRLIGGVLC----EKTVKE 75
Q L+ + ++ + S+++ EL E L+ L+ L D ++++G +L K KE
Sbjct: 16 LQQLQQQLERLLQQKSQIDLELREINKALEELEKLPDDTPIYKIVGNLLVKVDKTKVEKE 75
Query: 76 VIPTLTTNRDQLNTLIN---SLNEQLTKKGIEINEY 108
+ + TL L E+L + +INE
Sbjct: 76 LKERKELLELRSRTLEKQEKKLREKLKELQAKINEM 111
>gnl|CDD|178487 PLN02899, PLN02899, alpha-galactosidase.
Length = 633
Score = 32.1 bits (73), Expect = 0.079
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 13 DEEVYNGFQNLRAEQRQIATKLSELEQELTEHK 45
E+Y F NL E+ +I+ K+S+L + L K
Sbjct: 559 KGEIYVAFFNLNQEKTKISAKISDLAKALPGSK 591
>gnl|CDD|235179 PRK03947, PRK03947, prefoldin subunit alpha; Reviewed.
Length = 140
Score = 28.7 bits (65), Expect = 0.68
Identities = 26/122 (21%), Positives = 44/122 (36%), Gaps = 24/122 (19%)
Query: 14 EEVYNGFQNLRAEQRQIATKLSELEQELTEHKIVLDTLKDLDG-----------DRRCFR 62
EE+ Q L+A+ + +L EL+ + E +TL++L F
Sbjct: 9 EELAAQLQALQAQIEALQQQLEELQASINELDTAKETLEELKSKGEGKETLVPIGAGSFV 68
Query: 63 L------------IG-GVLCEKTVKEVIPTLTTNRDQLNTLINSLNEQLTKKGIEINEYK 109
+G G EK + E I L +++L + L E L K I +
Sbjct: 69 KAKVKDKDKVIVSLGAGYSAEKDLDEAIEILDKRKEELEKALEKLEEALQKLASRIAQLA 128
Query: 110 DK 111
+
Sbjct: 129 QE 130
>gnl|CDD|181721 PRK09242, PRK09242, tropinone reductase; Provisional.
Length = 257
Score = 28.9 bits (65), Expect = 0.87
Identities = 22/104 (21%), Positives = 41/104 (39%), Gaps = 9/104 (8%)
Query: 20 FQNLRAEQRQIATKLSELEQELTEHKIVLDTLKDLDGDRRCFRLIGGVLCEKTVKEVIPT 79
F L A+ +A L Q E L + +R L V ++ + ++
Sbjct: 29 FLGLGADVLIVARDADALAQARDE-------LAEEFPEREVHGLAADVSDDEDRRAILDW 81
Query: 80 LTTNRDQLNTLINSLNEQLTKKGIEINEYKDKFDIQLQGNKTSA 123
+ + D L+ L+N+ + K I+ E D++ + N SA
Sbjct: 82 VEDHWDGLHILVNNAGGNIRKAAIDYTE--DEWRGIFETNLFSA 123
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 28.9 bits (65), Expect = 1.2
Identities = 23/90 (25%), Positives = 41/90 (45%), Gaps = 5/90 (5%)
Query: 13 DEEVYNGFQNLRAEQRQIATKLSELEQELTEHKIVLDTLKDLDGDRRCFRLIGGVLCEK- 71
EE+ F+ LR E ++ +L+E+ EL E K ++ L+ L E+
Sbjct: 371 LEELEELFEALREELAELEAELAEIRNELEELK---REIESLEERLERLSERLEDLKEEL 427
Query: 72 -TVKEVIPTLTTNRDQLNTLINSLNEQLTK 100
++ + L T ++LN + L EQL +
Sbjct: 428 KELEAELEELQTELEELNEELEELEEQLEE 457
>gnl|CDD|238327 cd00584, Prefoldin_alpha, Prefoldin alpha subunit; 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 = 28.0 bits (63), Expect = 1.2
Identities = 25/112 (22%), Positives = 44/112 (39%), Gaps = 24/112 (21%)
Query: 21 QNLRAEQRQIATKLSELEQELTEHKIVLDTLKDL------------------------DG 56
Q L+ E ++ +L+ L + + E++ +TL+ L D
Sbjct: 9 QVLQQEIEELQQELARLNEAIAEYEQAKETLETLKKADEGKETLVPLGAGVFVKAKVKDT 68
Query: 57 DRRCFRLIGGVLCEKTVKEVIPTLTTNRDQLNTLINSLNEQLTKKGIEINEY 108
D+ L G EK ++E I L ++L I L ++L K +IN
Sbjct: 69 DKVLVDLGTGYYVEKDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTL 120
>gnl|CDD|227042 COG4698, COG4698, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 197
Score = 28.2 bits (63), Expect = 1.3
Identities = 14/49 (28%), Positives = 20/49 (40%)
Query: 71 KTVKEVIPTLTTNRDQLNTLINSLNEQLTKKGIEINEYKDKFDIQLQGN 119
E +TT R QLN LINS E + + Y ++ + N
Sbjct: 47 SEKSEKSFQITTTRSQLNELINSYLEDYQTEEMPYKVYITDEHVEFEAN 95
>gnl|CDD|129394 TIGR00293, TIGR00293, prefoldin, archaeal alpha subunit/eukaryotic
subunit 5. Members of this protein family, rich in
coiled coil regions, are molecular chaperones in the
class of the prefoldin (GimC) alpha subunit. Prefoldin
is a hexamer of two alpha and four beta subunits. This
protein appears universal in the archaea but is
restricted to Aquifex aeolicus among bacteria so far.
Eukaryotes have several related proteins; only prefoldin
subunit 5, which appeared the most similar to archaeal
prefoldin alpha, is included in this model. This model
finds a set of small proteins from the Archaea and from
Aquifex aeolicus that may represent two orthologous
groups. The proteins are predicted to be mostly coiled
coil [Protein fate, Protein folding and stabilization].
Length = 126
Score = 26.9 bits (60), Expect = 2.3
Identities = 21/115 (18%), Positives = 40/115 (34%), Gaps = 23/115 (20%)
Query: 21 QNLRAEQRQIATKLSELEQELTEHKIVLDTLKDLDGDRRCFRLI---------------- 64
Q L+ + + +++ L + E + ++TL+DL G L+
Sbjct: 9 QILQQQVESLQAQIAALRALIAELETAIETLEDLKGAEGKETLVPVGAGSFVKAKVKDTD 68
Query: 65 -------GGVLCEKTVKEVIPTLTTNRDQLNTLINSLNEQLTKKGIEINEYKDKF 112
G EK +E I L ++L I L E L + + + +
Sbjct: 69 KVLVSIGSGYYVEKDAEEAIEFLKKRIEELEKAIEKLQEALAELASRAQQLEQEA 123
>gnl|CDD|222878 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 27.7 bits (62), Expect = 2.8
Identities = 18/53 (33%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 3 DAKKKTTKLTDEEVYNG--FQNLRAEQRQIATKLSELEQELTEHKIVLDTLKD 53
K +L E V N L+ E +I SEL +E IV D LKD
Sbjct: 362 KVKAAIEELQAEFVDNAEELAKLQDELDKIVKTKSELVKEKYHRGIVTDLLKD 414
>gnl|CDD|234780 PRK00488, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Validated.
Length = 339
Score = 27.0 bits (61), Expect = 3.5
Identities = 19/102 (18%), Positives = 33/102 (32%), Gaps = 27/102 (26%)
Query: 29 QIATKLSELEQ----------ELTEHKIVLDTLKDLDGDRRCFRLIGGVLCEKTVKEVIP 78
A+ L LE ELTE +L L L + R + G + E+
Sbjct: 17 AAASDLEALEALRVKYLGKKGELTE---LLKGLGKLPPEER--KEAG-----ALINEL-- 64
Query: 79 TLTTNRDQLNTLINSLNEQLTKKGIEINEYKDKFDIQLQGNK 120
+ + + E+L + + D+ L G +
Sbjct: 65 -----KQAIEAALEERKEELEAAALNARLAAETIDVTLPGRR 101
>gnl|CDD|220467 pfam09911, DUF2140, Uncharacterized protein conserved in bacteria
(DUF2140). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 187
Score = 26.8 bits (60), Expect = 3.7
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 79 TLTTNRDQLNTLINSLNEQLTKKG 102
T+TTN+ QLN LI S + K
Sbjct: 47 TITTNKKQLNALIASYLKDYQKGS 70
>gnl|CDD|204544 pfam10712, NAD-GH, NAD-specific glutamate dehydrogenase. The
members of this are annotated as being NAD-specific
glutamate dehydrogenase encoded in antisense gene pair
with DnaK-J. However, this could not be confirmed.
Length = 574
Score = 26.9 bits (60), Expect = 4.0
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 4/34 (11%)
Query: 37 LEQELTEHKIVLD----TLKDLDGDRRCFRLIGG 66
L+ EL E +V L+ D R L GG
Sbjct: 120 LQVELAERLVVRRHFALALEHADRHGRLVVLRGG 153
>gnl|CDD|149875 pfam08941, USP8_interact, USP8 interacting. This domain
interacts with the UBP deubiquitinating enzyme USP8.
Length = 179
Score = 26.7 bits (59), Expect = 4.6
Identities = 9/30 (30%), Positives = 19/30 (63%)
Query: 23 LRAEQRQIATKLSELEQELTEHKIVLDTLK 52
LR+ + AT+++EL+ +H+I ++ K
Sbjct: 2 LRSIVQDQATEIAELKHTQVDHEIQINEQK 31
>gnl|CDD|172745 PRK14257, PRK14257, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 329
Score = 26.6 bits (58), Expect = 6.1
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 6/67 (8%)
Query: 3 DAKKKTTKLTDEEVYNGFQNLRAEQRQIA------TKLSELEQELTEHKIVLDTLKDLDG 56
+ K +L + +Y+ FQ L QR A K +EL+Q L + K +D LK+
Sbjct: 17 NQKTNLNELDAKAIYDEFQKLNKYQRAFAWLKLPKQKKAELKQFLNKKKTQVDLLKEDFN 76
Query: 57 DRRCFRL 63
F +
Sbjct: 77 HANVFEI 83
>gnl|CDD|232988 TIGR00468, pheS, phenylalanyl-tRNA synthetase, alpha subunit. Most
phenylalanyl-tRNA synthetases are heterodimeric, with 2
alpha (pheS) and 2 beta (pheT) subunits. This model
describes the alpha subunit, which shows some similarity
to class II aminoacyl-tRNA ligases. Mitochondrial
phenylalanyl-tRNA synthetase is a single polypeptide
chain, active as a monomer, and similar to this chain
rather than to the beta chain, but excluded from this
model. An interesting feature of the alignment of all
sequences captured by this model is a deep split between
non-spirochete bacterial examples and all other
examples; supporting this split is a relative deletion
of about 50 residues in the former set between two
motifs well conserved throughout the alignment [Protein
synthesis, tRNA aminoacylation].
Length = 293
Score = 26.1 bits (58), Expect = 6.5
Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 13/78 (16%)
Query: 45 KIVLDTLKDLDGDRRCFRLIGGVLCEKTVKEVIPTLTTNRDQLNTLINSLNEQLTKKGIE 104
K +L L L + L + EV + +L + L +L G+
Sbjct: 3 KDLLKQLGKLTKEETKPALG------ALINEV-------KIELQDELTKLKPELESAGLW 49
Query: 105 INEYKDKFDIQLQGNKTS 122
+ +D+ L G K
Sbjct: 50 SKLKFETYDVSLPGTKIY 67
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 26.2 bits (58), Expect = 7.6
Identities = 21/92 (22%), Positives = 35/92 (38%), Gaps = 9/92 (9%)
Query: 23 LRAEQRQIATKLSELEQELTEHKIVLDTL----KDLDGDRRCFRLIGGVLCEKTVKEVIP 78
+ E + K ELE+EL E + L L DL +R L + I
Sbjct: 852 IEKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLREL-----ERKIE 906
Query: 79 TLTTNRDQLNTLINSLNEQLTKKGIEINEYKD 110
L ++ ++ L +L E++E +D
Sbjct: 907 ELEAQIEKKRKRLSELKAKLEALEEELSEIED 938
>gnl|CDD|151980 pfam11544, Spc42p, Spindle pole body component Spc42p. Spc42p is a
42-kD component of the S.cerevisiae spindle body that
localises to the electron dense central region of the
SPB.Spc42p is a phosphoprotein which forms a polymeric
layer at the periphery of the SPB central plaque. This
functions during SPB duplication and also facilitates
the attachment of the SPB to the nuclear membrane.
Length = 74
Score = 24.8 bits (54), Expect = 9.3
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 74 KEVIPTLTTNRDQLNTLINSLNEQLTKKGIEINEYKDKFDIQLQGNKTSAPPPKQENESA 133
KE+ L ++++ L N L L K I+ E K + QLQ + S K+ ++
Sbjct: 6 KELNFKLREKQEEIERL-NVLIGSLRAKLIKYTELNKKLEDQLQNLQISNDLNKKLSDDR 64
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
0.311 0.130 0.353
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,972,810
Number of extensions: 612684
Number of successful extensions: 1041
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1022
Number of HSP's successfully gapped: 116
Length of query: 144
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 56
Effective length of database: 7,034,450
Effective search space: 393929200
Effective search space used: 393929200
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: 54 (24.6 bits)