RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3289
(189 letters)
>gnl|CDD|220415 pfam09809, MRP-L27, Mitochondrial ribosomal protein L27. Members
of this family of proteins are components of the
mitochondrial ribosome large subunit. They are also
involved in apoptosis and cell cycle regulation.
Length = 113
Score = 89.8 bits (223), Expect = 1e-23
Identities = 47/125 (37%), Positives = 63/125 (50%), Gaps = 19/125 (15%)
Query: 37 KKNFRKFNWIN-RGTQQHREEQKLNPDPRFTPTYGVRKV-LQTSDGRPVV--ETIPELIV 92
K R+F + RG + + + G + TS GR V+ E +P +V
Sbjct: 1 KGGNRRFPLTSKRGNKTFYKGR------------GASGIGRHTSSGRYVIIWEKVPTFVV 48
Query: 93 PNLEGFNLKPYVSYRTNEIQTPEFTAKDLFIEVYAEKINKDFEANKLDEDG---NPLQPS 149
P+L GF LKPYVSY+ E+ EFTAKDLF VYA KI KDF+ LD D +P+
Sbjct: 49 PDLTGFKLKPYVSYKAPEVIQSEFTAKDLFNAVYAPKIFKDFKEGTLDPDLLEKKGKEPT 108
Query: 150 DNELL 154
+ L
Sbjct: 109 EEGKL 113
>gnl|CDD|240552 cd13147, MATE_MJ0709_like, Uncharacterized subfamily of the
multidrug and toxic compound extrusion (MATE) proteins,
similar to Methanocaldococcus jannaschii MJ0709. The
integral membrane proteins from the MATE family are
involved in exporting metabolites across the cell
membrane and are responsible for multidrug resistance
(MDR) in many bacteria and animals. A number of family
members are involved in the synthesis of peptidoglycan
components in bacteria.
Length = 441
Score = 29.8 bits (68), Expect = 0.86
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 5/31 (16%)
Query: 14 PIIDRGGALVSGSGYGSTGASYGKKNFRKFN 44
P+I A+ S TGA+YG +N+ K
Sbjct: 282 PLIGIATAVTS-----VTGAAYGARNYEKLK 307
>gnl|CDD|130271 TIGR01204, bioW, 6-carboxyhexanoate--CoA ligase. Alternate name:
pimeloyl-CoA synthase [Biosynthesis of cofactors,
prosthetic groups, and carriers, Biotin].
Length = 232
Score = 29.5 bits (66), Expect = 0.92
Identities = 20/44 (45%), Positives = 26/44 (59%), Gaps = 5/44 (11%)
Query: 122 FIEVYAEKINKDFEANKLDEDGNPLQPSDNELLTPEEAEKRARK 165
F+++ EK+ KDFE K NPL+ S +PEEA K ARK
Sbjct: 40 FMQIKVEKV-KDFEIVKF----NPLKISTYSFSSPEEARKFARK 78
>gnl|CDD|99972 cd03799, GT1_amsK_like, This is a family of GT1
glycosyltransferases found specifically in certain
bacteria. amsK in Erwinia amylovora, has been reported
to be involved in the biosynthesis of amylovoran, a
exopolysaccharide acting as a virulence factor.
Length = 355
Score = 29.1 bits (66), Expect = 1.6
Identities = 9/23 (39%), Positives = 11/23 (47%), Gaps = 4/23 (17%)
Query: 80 GRPVVET----IPELIVPNLEGF 98
G PV+ T IPEL+ G
Sbjct: 285 GLPVISTDVSGIPELVEDGETGL 307
>gnl|CDD|216439 pfam01333, Apocytochr_F_C, Apocytochrome F, C-terminal. This is
a sub-family of cytochrome C. See pfam00034.
Length = 118
Score = 27.9 bits (63), Expect = 1.6
Identities = 18/47 (38%), Positives = 22/47 (46%), Gaps = 18/47 (38%)
Query: 70 GVRKVLQTSDGRPVVETIP---ELIV---------------PNLEGF 98
G ++T+DG VVETIP ELIV PN+ GF
Sbjct: 23 GYEVTIETADGETVVETIPAGPELIVSEGQTVKADQPLTNNPNVGGF 69
>gnl|CDD|150162 pfam09398, FOP_dimer, FOP N terminal dimerisation domain.
Fibroblast growth factor receptor 1 (FGFR1) oncogene
partner (FOP) is a centrosomal protein that is involved
in anchoring microtubules to subcellular structures.
This domain includes a Lis-homology motif. It forms an
alpha helical bundle and is involved in dimerisation.
Length = 81
Score = 27.1 bits (60), Expect = 2.0
Identities = 20/58 (34%), Positives = 25/58 (43%), Gaps = 10/58 (17%)
Query: 72 RKVLQTSDGRPVVETIPELIVPNLEGFNLKPYVSYRTNEIQTPE------FTAKDLFI 123
+K L T DGR V E I E L+ FNL ++ E E AK+L I
Sbjct: 10 KKFLNTKDGRLVAELIREF----LQFFNLDFTLAVFQPEASLLEGLDGRENLAKELGI 63
>gnl|CDD|197323 cd09089, INPP5c_Synj, Catalytic inositol polyphosphate
5-phosphatase (INPP5c) domain of synaptojanins. This
subfamily contains the INPP5c domains of two human
synaptojanins, synaptojanin 1 (Synj1) and synaptojanin 2
(Synj2), and related proteins. It belongs to a family of
Mg2+-dependent inositol polyphosphate 5-phosphatases,
which hydrolyze the 5-phosphate from the inositol ring
of various 5-position phosphorylated phosphoinositides
(PIs) and inositol phosphates (IPs). They belong to the
large EEP (exonuclease/endonuclease/phosphatase)
superfamily that contains functionally diverse enzymes
that share a common catalytic mechanism of cleaving
phosphodiester bonds. Synj1 occurs as two main isoforms:
a brain enriched 145 KDa protein (Synj1-145) and a
ubiquitously expressed 170KDa protein (Synj1-170).
Synj1-145 participates in clathrin-mediated endocytosis.
The primary substrate of the Synj1-145 INPP5c domain is
PI(4,5)P2, which it converts to PI4P. Synj1-145 may work
with membrane curvature sensors/generators (such as
endophilin) to remove PI(4,5)P2 from curved membranes.
The recruitment of the INPP5c domain of Synj1-145 to
endophilin-induced membranes leads to a fragmentation
and condensation of these structures. The PI(4,5)P2 to
PI4P conversion may cooperate with dynamin to produce
membrane fission. In addition to this INPP5c domain,
Synjs contain an N-terminal Sac1-like domain; the Sac1
domain can dephosphorylate a variety of
phosphoinositides in vitro. Synj2 can hydrolyze
phosphatidylinositol diphosphate (PIP2) to
phosphatidylinositol phosphate (PIP). Synj2 occurs as
multiple alternative splice variants in various tissues.
These variants share the INPP5c domain and the Sac1
domain. Synj2A is recruited to the mitochondria via its
interaction with OMP25 (a mitochondrial outer membrane
protein). Synj2B is found at nerve terminals in the
brain and at the spermatid manchette in testis. Synj2B
undergoes further alternative splicing to give 2B1 and
2B2. In clathrin-mediated endocytosis, Synj2
participates in the formation of clathrin-coated pits,
and perhaps also in vesicle decoating. Rac1 GTPase
regulates the intracellular localization of Synj2 forms,
but not Synj1. Synj2 may contribute to the role of Rac1
in cell migration and invasion, and is a potential
target for therapeutic intervention in malignant tumors.
Length = 328
Score = 28.5 bits (64), Expect = 2.0
Identities = 16/37 (43%), Positives = 18/37 (48%), Gaps = 5/37 (13%)
Query: 55 EEQKLNPDPRFTPT----YGVRKVLQTSDGRPVVETI 87
E DP + P YG R L+TSD RPVV I
Sbjct: 291 ESLVETNDPTWNPGTLLYYG-RAELKTSDHRPVVAII 326
>gnl|CDD|183437 PRK12322, PRK12322, NADH dehydrogenase subunit D; Provisional.
Length = 366
Score = 28.5 bits (64), Expect = 2.2
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 53 HREEQKLNPDPRFTPTYGVRKVLQTSDGRPVVETIP 88
EE LN P+ T+GV +++ DG +VE P
Sbjct: 3 RTEEMLLNVGPQHPSTHGVFRLVLKIDGEIIVEATP 38
>gnl|CDD|179234 PRK01151, rps17E, 30S ribosomal protein S17e; Validated.
Length = 58
Score = 26.0 bits (58), Expect = 2.8
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 117 TAKDLFIEVYAEKINKDFEANK 138
TA++L +E Y + DFE NK
Sbjct: 11 TAEEL-LEKYPDLFTTDFETNK 31
>gnl|CDD|223344 COG0266, Nei, Formamidopyrimidine-DNA glycosylase [DNA replication,
recombination, and repair].
Length = 273
Score = 27.2 bits (61), Expect = 5.0
Identities = 12/45 (26%), Positives = 16/45 (35%), Gaps = 4/45 (8%)
Query: 40 FRKFNWINRGTQQHREEQKLNPDP---RFTPTYGVRKVLQTSDGR 81
F I + H KL P+P F P Y + + L R
Sbjct: 114 FGTMLLIEDLEEVHPVLAKLGPEPLSDDFDPEY-LAEKLAKKKRR 157
>gnl|CDD|219660 pfam07952, Toxin_trans, Clostridium neurotoxin, Translocation
domain. The Clostridium neurotoxin family is composed
of tetanus neurotoxin and seven serotypes of botulinum
neurotoxin. The structure of the botulinum neurotoxin
reveals a four domain protein. The N-terminal catalytic
domain (pfam01742), the central translocation domains
and two receptor binding domains. Subsequent to cell
surface binding and receptor mediated endocytosis of the
neurotoxin, an acid induced conformational change in the
neurotoxin translocation domain is believed to allow the
domain to penetrate the endosome and from a pore,
thereby facilitating the passage of the catalytic domain
across the membrane into the cytosol. The structure of
the translocation reveals a pair of helices that are 105
Angstroms long and is structurally distinct from other
pore forming toxins.
Length = 320
Score = 27.4 bits (61), Expect = 5.3
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 85 ETIPELIVPNLEGFNLKPYVSYRTNEIQT 113
E IPEL +P + F +K Y+ + I+T
Sbjct: 118 EFIPELTIPVIGAFTIKSYIGNKNKIIKT 146
>gnl|CDD|133872 PHA00380, PHA00380, tail protein.
Length = 599
Score = 27.6 bits (61), Expect = 5.4
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 62 DPRFTPTYGVRK--VLQTSDGRPVVETIPE 89
D +F P+Y VR+ S+G+PVV TI E
Sbjct: 120 DIKFQPSYIVREHQTEWQSNGKPVVNTIDE 149
>gnl|CDD|176978 CHL00037, petA, cytochrome f.
Length = 320
Score = 27.2 bits (61), Expect = 6.2
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 18/43 (41%)
Query: 74 VLQTSDGRPVVETIP---ELIV---------------PNLEGF 98
++ TSDGR VV+ IP EL+V PN+ GF
Sbjct: 229 IVDTSDGRQVVDIIPPGPELLVSEGESIKLDQPLTNNPNVGGF 271
>gnl|CDD|212130 cd11665, LamB_like, Aspergillus nidulans lactam utilization protein
LamB and similar proteins. This eukaryotic and
bacterial subfamily of the LamB/YbgL family, includes
Aspergillus nidulans protein LamB. The lamb gene locates
at the lam locus of Aspergillus nidulans, consisting of
two divergently transcribed genes, lamA and lamB, needed
for the utilization of lactams such as 2-pyrrolidinone.
Both genes are under the control of the positive
regulatory gene amdR and are subject to carbon and
nitrogen metabolite repression. Although the exact
molecular function of lamb encoding protein LamB is
unknown, it might be required for conversion of
exogenous 2-pyrrolidinone to endogenous GABA.
Length = 238
Score = 26.9 bits (60), Expect = 7.0
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 14/70 (20%)
Query: 115 EFTAKDL---FI-EVYAEKINKDFEANKLDEDGNPLQPSDNELLTPEEAEKRARKTGSDL 170
E AK+L FI E YA D + D DG + +++ + PEE +R R+ +D
Sbjct: 146 EKVAKELGIPFIPEFYA-----DLD---YDPDGKLVITREHKAIDPEEIAERVRRALTD- 196
Query: 171 FDQEVDVGDR 180
VG +
Sbjct: 197 -GSVTSVGGK 205
>gnl|CDD|220670 pfam10274, ParcG, Parkin co-regulated protein. This family of
proteins is transcribed anti-sense along the DNA to the
Parkin gene product and the two appear to be
transcribed under the same promoter. The protein has
predicted alpha-helical and beta-sheet domains which
suggest its function is in the ubiquitin/proteasome
system. Mutations in parkin are the genetic cause of
early-onset and autosomal recessive juvenile
parkinsonism.
Length = 183
Score = 26.5 bits (59), Expect = 7.0
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 64 RFTPTYGVRKVLQTSDGRPVVETIPELIVP 93
RF G+ +L+ G ++ +P+LI+P
Sbjct: 55 RFVARNGIIDLLEAGGGEKILPVLPQLILP 84
>gnl|CDD|206641 cd00157, Rho, Ras homology family (Rho) of small guanosine
triphosphatases (GTPases). Members of the Rho (Ras
homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1,
RhoBTB, and Rop. There are 22 human Rho family members
identified currently. These proteins are all involved in
the reorganization of the actin cytoskeleton in response
to external stimuli. They also have roles in cell
transformation by Ras in cytokinesis, in focal adhesion
formation and in the stimulation of stress-activated
kinase. These various functions are controlled through
distinct effector proteins and mediated through a
GTP-binding/GTPase cycle involving three classes of
regulating proteins: GAPs (GTPase-activating proteins),
GEFs (guanine nucleotide exchange factors), and GDIs
(guanine nucleotide dissociation inhibitors). Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Since crystal structures
often lack C-terminal residues, this feature is not
available for annotation in many of the CDs in the
hierarchy.
Length = 171
Score = 26.4 bits (59), Expect = 7.7
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 136 ANKLD--EDGNPLQP--SDNELLTPEEAEKRARKTGSDLF 171
K+D +DGN L+ + +TPEE EK A++ G+ +
Sbjct: 111 GTKIDLRDDGNTLKKLEKKQKPITPEEGEKLAKEIGAVKY 150
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
0.313 0.136 0.393
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,033,565
Number of extensions: 948247
Number of successful extensions: 684
Number of sequences better than 10.0: 1
Number of HSP's gapped: 684
Number of HSP's successfully gapped: 27
Length of query: 189
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 98
Effective length of database: 6,901,388
Effective search space: 676336024
Effective search space used: 676336024
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 (21.9 bits)
S2: 56 (25.3 bits)