RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18101
(126 letters)
>gnl|CDD|215821 pfam00254, FKBP_C, FKBP-type peptidyl-prolyl cis-trans isomerase.
Length = 94
Score = 39.5 bits (93), Expect = 3e-05
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 51 DTRPQRGDLCVISGFGKLEDDTLVET----FDNLEICVGDLELVHGMDYVLPLMEMGEEC 106
+ ++GD + GKLED T+ ++ E +G +++ G D L M++GE+
Sbjct: 2 PEKAKKGDTVTVHYTGKLEDGTVFDSSKDRGKPFEFTLGSGQVIPGWDEGLLGMKVGEKR 61
Query: 107 QIEITARFGYGDKGEP 122
++ I YG++G
Sbjct: 62 KLTIPPELAYGEEGLA 77
>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 = 36.4 bits (85), Expect = 0.002
Identities = 12/40 (30%), Positives = 18/40 (45%)
Query: 86 DLELVHGMDYVLPLMEMGEECQIEITARFGYGDKGEPIFK 125
+L L H DY+ + E + E R G G + P+F
Sbjct: 52 ELLLFHTPDYIEAVKEASRGQEPEGRGRLGLGTEDNPVFP 91
>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 = 0.62
Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 3/49 (6%)
Query: 21 DKPEEEVEDEWVDILGSGHI--KKKITKHGEPDTRPQRGDLC-VISGFG 66
DKP E+E + LG K + RP +C V+ G
Sbjct: 131 DKPGAVSEEELREALGLYGTTTGKGGVSLKVSNIRPVEVFMCSVVKRQG 179
>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 = 28.3 bits (63), Expect = 1.0
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 6/35 (17%)
Query: 15 ENPVIPDKPEEEVEDEWVDILGSGHIKKKITKHGE 49
E P +P +PEE + LG H+K+ I E
Sbjct: 282 EGPSLPQEPEERRK------LGKAHLKRAILGQEE 310
>gnl|CDD|223619 COG0545, FkpA, FKBP-type peptidyl-prolyl cis-trans isomerases 1
[Posttranslational modification, protein turnover,
chaperones].
Length = 205
Score = 27.4 bits (61), Expect = 1.7
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 12/77 (15%)
Query: 54 PQRGDLCVISGFGKLEDDTLVETFDN-------LEICVGDLELVHGMDYVLPLMEMGEEC 106
P++GD + G L D T+ FD+ E +G ++ G D L M++G +
Sbjct: 116 PKKGDTVTVHYTGTLIDGTV---FDSSYDRGQPAEFPLG--GVIPGWDEGLQGMKVGGKR 170
Query: 107 QIEITARFGYGDKGEPI 123
++ I YG++G P
Sbjct: 171 KLTIPPELAYGERGVPG 187
>gnl|CDD|222188 pfam13512, TPR_18, Tetratricopeptide repeat.
Length = 142
Score = 25.7 bits (57), Expect = 5.6
Identities = 14/39 (35%), Positives = 18/39 (46%)
Query: 15 ENPVIPDKPEEEVEDEWVDILGSGHIKKKITKHGEPDTR 53
V+PDKP E+ E L SG+ I + DTR
Sbjct: 1 NKEVVPDKPPSELYQEAQKALQSGNYTTAIEQLEALDTR 39
>gnl|CDD|238113 cd00190, Tryp_SPc, Trypsin-like serine protease; Many of these are
synthesized as inactive precursor zymogens that are
cleaved during limited proteolysis to generate their
active forms. Alignment contains also inactive enzymes
that have substitutions of the catalytic triad residues.
Length = 232
Score = 26.1 bits (58), Expect = 5.7
Identities = 5/23 (21%), Positives = 9/23 (39%)
Query: 49 EPDTRPQRGDLCVISGFGKLEDD 71
G C +SG+G+ +
Sbjct: 113 SSGYNLPAGTTCTVSGWGRTSEG 135
>gnl|CDD|233534 TIGR01693, UTase_glnD, [Protein-PII] uridylyltransferase. This
model describes GlnD, the
uridylyltransferase/uridylyl-removing enzyme for the
nitrogen regulatory protein PII. Not all homologs of PII
share the property of uridylyltransferase modification
on the characteristic Tyr residue (see Prosite pattern
PS00496 and document PDOC00439), but the modification
site is preserved in the PII homolog of all species with
a member of this family [Central intermediary
metabolism, Nitrogen metabolism, Regulatory functions,
Protein interactions].
Length = 850
Score = 25.8 bits (57), Expect = 8.1
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 107 QIEITARFGYGDKGEP 122
Q EI A GYGD+G P
Sbjct: 250 QDEIAAALGYGDEGNP 265
>gnl|CDD|223501 COG0424, Maf, Nucleotide-binding protein implicated in inhibition
of septum formation [Cell division and chromosome
partitioning].
Length = 193
Score = 25.2 bits (56), Expect = 9.9
Identities = 8/26 (30%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 4 PFEIVDKADVEENPVIPDKPEEEVED 29
PFE++ +D++E + ++P E V
Sbjct: 24 PFEVI-PSDIDEPLLKAEEPREYVLR 48
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
0.317 0.143 0.433
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,844,994
Number of extensions: 617304
Number of successful extensions: 530
Number of sequences better than 10.0: 1
Number of HSP's gapped: 530
Number of HSP's successfully gapped: 24
Length of query: 126
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 41
Effective length of database: 7,167,512
Effective search space: 293867992
Effective search space used: 293867992
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 (24.2 bits)