RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1750
(214 letters)
>gnl|CDD|215821 pfam00254, FKBP_C, FKBP-type peptidyl-prolyl cis-trans isomerase.
Length = 94
Score = 55.3 bits (134), Expect = 2e-10
Identities = 26/93 (27%), Positives = 46/93 (49%), Gaps = 4/93 (4%)
Query: 62 DTRPQRGDLCVISGFGKLEDDTLVET----FDNLEICVGDLELVHGMDYVLPLMEMGEEC 117
+ ++GD + GKLED T+ ++ E +G +++ G D L M++GE+
Sbjct: 2 PEKAKKGDTVTVHYTGKLEDGTVFDSSKDRGKPFEFTLGSGQVIPGWDEGLLGMKVGEKR 61
Query: 118 QIEITARFGYGDKGEPSKSIPPGAKLYYSLTLH 150
++ I YG++G IPP A L + + L
Sbjct: 62 KLTIPPELAYGEEGLAGGVIPPNATLVFEVELL 94
>gnl|CDD|223619 COG0545, FkpA, FKBP-type peptidyl-prolyl cis-trans isomerases 1
[Posttranslational modification, protein turnover,
chaperones].
Length = 205
Score = 36.2 bits (84), Expect = 0.005
Identities = 34/118 (28%), Positives = 56/118 (47%), Gaps = 15/118 (12%)
Query: 43 VDILGSGHIKKKITKHGEPDTRPQRGDLCVISGFGKLEDDTLVETFDN-------LEICV 95
V L SG ++ K+ K G+ P++GD + G L D T+ FD+ E +
Sbjct: 96 VKTLPSG-LQYKVLKAGDGAA-PKKGDTVTVHYTGTLIDGTV---FDSSYDRGQPAEFPL 150
Query: 96 GDLELVHGMDYVLPLMEMGEECQIEITARFGYGDKGEPSKSIPPGAKLYYSLTLHSVL 153
G ++ G D L M++G + ++ I YG++G P IPP + L + + L V
Sbjct: 151 G--GVIPGWDEGLQGMKVGGKRKLTIPPELAYGERGVPG-VIPPNSTLVFEVELLDVK 205
>gnl|CDD|222112 pfam13414, TPR_11, TPR repeat.
Length = 69
Score = 30.0 bits (68), Expect = 0.18
Identities = 11/33 (33%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 174 KHRGNWFYSRGDNSFAVQCYRRSLDFLDSSNMD 206
K+ GN + GD A++ Y ++L+ LD N +
Sbjct: 7 KNLGNALFKLGDYDEAIEAYEKALE-LDPDNAE 38
>gnl|CDD|212520 cd09994, HDAC_AcuC_like, Class I histone deacetylase AcuC (Acetoin
utilization protein)-like enzymes. AcuC (Acetoin
utilization protein) is a class I deacetylase found only
in bacteria and is involved in post-translational
control of the acetyl-coenzyme A synthetase (AcsA).
Deacetylase AcuC works in coordination with deacetylase
SrtN (class III), possibly to maintain AcsA in active
(deacetylated) form and let the cell grow under low
concentration of acetate. B. subtilis AcuC is a member
of operon acuABC; this operon is repressed by the
presence of glucose and does not show induction by
acetoin; acetoin is a bacterial fermentation product
that can be converted to acetate via the butanediol
cycle in absence of other carbon sources. Inactivation
of AcuC leads to slower growth and lower cell yield
under low-acetate conditions in Bacillus subtilis. In
general, Class I histone deacetylases (HDACs) are
Zn-dependent enzymes that catalyze hydrolysis of
N(6)-acetyl-lysine residues in histone amino termini to
yield a deacetylated histone (EC 3.5.1.98). Enzymes
belonging to this group participate in regulation of a
number of processes through protein (mostly different
histones) modification (deacetylation). Class I histone
deacetylases in general act via the formation of large
multiprotein complexes. Members of this class are
involved in cell cycle regulation, DNA damage response,
embryonic development, cytokine signaling important for
immune response and in posttranslational control of the
acetyl coenzyme A synthetase.
Length = 313
Score = 31.4 bits (72), Expect = 0.28
Identities = 11/37 (29%), Positives = 16/37 (43%)
Query: 97 DLELVHGMDYVLPLMEMGEECQIEITARFGYGDKGEP 133
+L L H DY+ + E + E R G G + P
Sbjct: 52 ELLLFHTPDYIEAVKEASRGQEPEGRGRLGLGTEDNP 88
>gnl|CDD|183207 PRK11570, PRK11570, peptidyl-prolyl cis-trans isomerase;
Provisional.
Length = 206
Score = 30.9 bits (70), Expect = 0.34
Identities = 35/123 (28%), Positives = 56/123 (45%), Gaps = 9/123 (7%)
Query: 35 EEEVEDEWVDILGSGHIKKKITKHGEPDTRPQRGDLCVISGFGKLED----DTLVETFDN 90
EE + E V+ SG ++ ++ GE P R D + GKL D D+ V +
Sbjct: 89 EENAKKEGVNSTESG-LQFRVLTQGEGAI-PARTDRVRVHYTGKLIDGTVFDSSVARGEP 146
Query: 91 LEICVGDLELVHGMDYVLPLMEMGEECQIEITARFGYGDKGEPSKSIPPGAKLYYSLTLH 150
E V + + G L LM +G + ++ I YG++G SIPP + L + + L
Sbjct: 147 AEFPVNGV--IPGWIEALTLMPVGSKWELTIPHELAYGERG-AGASIPPFSTLVFEVELL 203
Query: 151 SVL 153
+L
Sbjct: 204 EIL 206
>gnl|CDD|235523 PRK05592, rplO, 50S ribosomal protein L15; Reviewed.
Length = 146
Score = 28.9 bits (66), Expect = 1.1
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 9/54 (16%)
Query: 9 NNGDLNSFE---IVDKADVEENPVIPDKPEEEVEDEWVDILGSGHIKKKITKHG 59
N GDLN FE V ++ +I + V +LG+G + KK+T
Sbjct: 78 NLGDLNKFEEGTEVTLEALKAAGLIRKN------IKGVKVLGNGELTKKLTVKA 125
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to as
the Sar1-N-terminal activation recruitment (STAR) motif.
The STAR motif mediates the recruitment of Sar1 to ER
membranes and facilitates its interaction with mammalian
Sec12 GEF leading to activation.
Length = 191
Score = 28.8 bits (65), Expect = 1.6
Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 3/49 (6%)
Query: 32 DKPEEEVEDEWVDILGSGHI--KKKITKHGEPDTRPQRGDLC-VISGFG 77
DKP E+E + LG K + RP +C V+ G
Sbjct: 131 DKPGAVSEEELREALGLYGTTTGKGGVSLKVSNIRPVEVFMCSVVKRQG 179
>gnl|CDD|223976 COG1047, SlpA, FKBP-type peptidyl-prolyl cis-trans isomerases 2
[Posttranslational modification, protein turnover,
chaperones].
Length = 174
Score = 28.4 bits (64), Expect = 2.2
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 10/60 (16%)
Query: 77 GKLEDDTLVETFDNLEICVGDLELVHGMDYVLPL-------MEMGEECQIEITARFGYGD 129
K+ED +V+T D G L + G ++P E+GEE +EI +G+
Sbjct: 15 LKVEDGEVVDTTDENY---GPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGE 71
>gnl|CDD|185771 cd09248, BRO1_Rhophilin_1, Protein-interacting Bro1-like domain of
RhoA-binding protein Rhophilin-1. This subfamily
contains the Bro1-like domain of the RhoA-binding
protein, Rhophilin-1. It belongs to the BRO1_Alix_like
superfamily which also includes the Bro1-like domains of
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), RhoA-binding
protein Rhophilin-2, Brox, Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, Ustilago maydis
Rim23 (also known as PalC), and related domains.
Rhophilin-1 binds both GDP- and GTP-bound RhoA.
Bro1-like domains are boomerang-shaped, and part of the
domain is a tetratricopeptide repeat (TPR)-like
structure. In addition to this Bro1-like domain,
Rhophilin-1 contains an N-terminal Rho-binding domain
and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1)
domain. The Drosophila knockout of the Rhophilin-1 is
embryonic lethal, suggesting an essential role in
embryonic development. The isolated Bro1-like domain of
Rhophilin-1 binds human immunodeficiency virus type 1
(HIV-1) nucleocapsid. Rhophilin-1 lacks the V-shaped (V)
domain found in many members of the BRO1_Alix_ like
superfamily.
Length = 384
Score = 28.7 bits (64), Expect = 2.3
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 6/35 (17%)
Query: 26 ENPVIPDKPEEEVEDEWVDILGSGHIKKKITKHGE 60
E P +P +PEE + LG H+K+ I E
Sbjct: 282 EGPSLPQEPEERRK------LGKAHLKRAILGQEE 310
>gnl|CDD|238112 cd00189, TPR, Tetratricopeptide repeat domain; typically contains
34 amino acids
[WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-
X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found
in a variety of organisms including bacteria,
cyanobacteria, yeast, fungi, plants, and humans in
various subcellular locations; involved in a variety of
functions including protein-protein interactions, but
common features in the interaction partners have not
been defined; involved in chaperone, cell-cycle,
transciption, and protein transport complexes; the
number of TPR motifs varies among proteins (1,3-11,13
15,16,19); 5-6 tandem repeats generate a right-handed
helical structure with an amphipathic channel that is
thought to accomodate an alpha-helix of a target
protein; it has been proposed that TPR proteins
preferably interact with WD-40 repeat proteins, but in
many instances several TPR-proteins seem to aggregate to
multi-protein complexes; examples of TPR-proteins
include, Cdc16p, Cdc23p and Cdc27p components of the
cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal
targeting signals, the Tom70p co-receptor for
mitochondrial targeting signals, Ser/Thr phosphatase 5C
and the p110 subunit of O-GlcNAc transferase; three
copies of the repeat are present here.
Length = 100
Score = 26.6 bits (59), Expect = 4.5
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 174 KHRGNWFYSRGDNSFAVQCYRRSLDFLDSSNMDT 207
+ GN +Y GD A++ Y ++L+ LD N D
Sbjct: 4 LNLGNLYYKLGDYDEALEYYEKALE-LDPDNADA 36
>gnl|CDD|226966 COG4607, CeuA, ABC-type enterochelin transport system, periplasmic
component [Inorganic ion transport and metabolism].
Length = 320
Score = 26.9 bits (60), Expect = 7.3
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 4/27 (14%)
Query: 2 DESISNGNNGDLNSFEIVDKADVEENP 28
DE+I N N+G SFE + E+NP
Sbjct: 229 DENIKNSNHGQPVSFEYI----KEKNP 251
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
0.315 0.137 0.409
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,200,652
Number of extensions: 1077520
Number of successful extensions: 610
Number of sequences better than 10.0: 1
Number of HSP's gapped: 610
Number of HSP's successfully gapped: 14
Length of query: 214
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 121
Effective length of database: 6,812,680
Effective search space: 824334280
Effective search space used: 824334280
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: 42 (21.9 bits)
S2: 57 (25.7 bits)