RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4164
(147 letters)
>gnl|CDD|215109 PLN00410, PLN00410, U5 snRNP protein, DIM1 family; Provisional.
Length = 142
Score = 53.7 bits (129), Expect = 7e-10
Identities = 19/27 (70%), Positives = 25/27 (92%)
Query: 1 MSYMLGHLHNGWQVDQAILSEEDRVVI 27
MSY+L HLH+GW VDQAIL+EE+R+V+
Sbjct: 1 MSYLLPHLHSGWAVDQAILAEEERLVV 27
>gnl|CDD|190488 pfam02966, DIM1, Mitosis protein DIM1.
Length = 133
Score = 46.5 bits (111), Expect = 2e-07
Identities = 17/24 (70%), Positives = 20/24 (83%)
Query: 4 MLGHLHNGWQVDQAILSEEDRVVI 27
+L HL GW VDQAILSEEDR+V+
Sbjct: 1 LLPHLRTGWHVDQAILSEEDRLVV 24
>gnl|CDD|239252 cd02954, DIM1, Dim1 family; Dim1 is also referred to as U5 small
nuclear ribonucleoprotein particle (snRNP)-specific
15kD protein. It is a component of U5 snRNP, which
pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5]
tri-snRNP complex required for pre-mRNA splicing. Dim1
interacts with multiple splicing-associated proteins,
suggesting that it functions at multiple control points
in the splicing of pre-mRNA as part of a large
spliceosomal complex involving many protein-protein
interactions. U5 snRNP contains seven core proteins
(common to all snRNPs) and nine U5-specific proteins,
one of which is Dim1. Dim1 adopts a thioredoxin fold
but does not contain the redox active CXXC motif. It is
essential for G2/M phase transition, as a consequence
to its role in pre-mRNA splicing.
Length = 114
Score = 37.7 bits (88), Expect = 3e-04
Identities = 13/18 (72%), Positives = 17/18 (94%)
Query: 10 NGWQVDQAILSEEDRVVI 27
+GW VDQAILSEE++VV+
Sbjct: 1 SGWAVDQAILSEEEKVVV 18
>gnl|CDD|205079 pfam12799, LRR_4, Leucine Rich repeats (2 copies). Leucine rich
repeats are short sequence motifs present in a number
of proteins with diverse functions and cellular
locations. These repeats are usually involved in
protein-protein interactions. Each Leucine Rich Repeat
is composed of a beta-alpha unit. These units form
elongated non-globular structures. Leucine Rich Repeats
are often flanked by cysteine rich domains.
Length = 43
Score = 29.8 bits (68), Expect = 0.079
Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 41 SLRTLSLYGNPIEKIREYRAVVSTMIPQLVTLDSVLYGNPIEKIRE 86
+L TL L N I + +S + P L TLD L GN I +
Sbjct: 2 NLETLDLSNNQITDLPP----LSNL-PNLETLD--LSGNKITDLSP 40
>gnl|CDD|143169 cd04968, Ig3_Contactin_like, Third Ig domain of contactin.
Ig3_Contactin_like: Third Ig domain of contactins.
Contactins are neural cell adhesion molecules and are
comprised of six Ig domains followed by four fibronectin
type III(FnIII) domains anchored to the membrane by
glycosylphosphatidylinositol. The first four Ig domains
form the intermolecular binding fragment, which arranges
as a compact U-shaped module via contacts between Ig
domains 1 and 4, and between Ig domains 2 and 3.
Contactin-2 (TAG-1, axonin-1) may play a part in the
neuronal processes of neurite outgrowth, axon guidance
and fasciculation, and neuronal migration. This group
also includes contactin-1 and contactin-5. The different
contactins show different expression patterns in the
central nervous system. During development and in
adulthood, contactin-2 is transiently expressed in
subsets of central and peripheral neurons. Contactin-5
is expressed specifically in the rat postnatal nervous
system, peaking at about 3 weeks postnatal, and a lack
of contactin-5 (NB-2) results in an impairment of
neuronal act ivity in the rat auditory system.
Contactin-5 is highly expressed in the adult human brain
in the occipital lobe and in the amygdala. Contactin-1
is differentially expressed in tumor tissues and may,
through a RhoA mechanism, facilitate invasion and
metastasis of human lung adenocarcinoma.
Length = 88
Score = 27.1 bits (60), Expect = 1.5
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 68 QLVTLDSVLYGNPIEKIREYRAVVSTMIPQLVTLDS--VFILPSEKQE 113
Q VTL+ GNP+ +I+ +R V +M S V +P+ + E
Sbjct: 17 QNVTLECFALGNPVPQIK-WRKVDGSMPSSAEISMSGAVLKIPNIQFE 63
>gnl|CDD|234856 PRK00885, PRK00885, phosphoribosylamine--glycine ligase;
Provisional.
Length = 420
Score = 28.1 bits (64), Expect = 1.8
Identities = 9/19 (47%), Positives = 10/19 (52%), Gaps = 5/19 (26%)
Query: 23 DRVVIEEYL-----SVFVL 36
RVVIEE+L S F
Sbjct: 180 ARVVIEEFLDGEEASFFAF 198
>gnl|CDD|238421 cd00825, decarbox_cond_enzymes, decarboxylating condensing enzymes;
Family of enzymes that catalyze the formation of a new
carbon-carbon bond by a decarboxylating Claisen-like
condensation reaction. Members are involved in the
synthesis of fatty acids and polyketides, a diverse
group of natural products. Both pathways are an
iterative series of additions of small carbon units,
usually acetate, to a nascent acyl group. There are 2
classes of decarboxylating condensing enzymes, which can
be distinguished by sequence similarity, type of active
site residues and type of primer units (acetyl CoA or
acyl carrier protein (ACP) linked units).
Length = 332
Score = 28.0 bits (62), Expect = 2.0
Identities = 6/39 (15%), Positives = 11/39 (28%)
Query: 12 WQVDQAILSEEDRVVIEEYLSVFVLRRVNSLRTLSLYGN 50
D ++ S F + T ++ GN
Sbjct: 228 LVAHGTGTPIGDVKELKLLRSEFGDKSPAVSATKAMTGN 266
>gnl|CDD|237678 PRK14335, PRK14335, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 455
Score = 27.6 bits (61), Expect = 2.6
Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 14/95 (14%)
Query: 17 AILSEEDRVVIEEYLSV-----FVLRRVNSLRTLSLYGNPIEKIREYRAVVSTMIPQLVT 71
A +++E R+ +L V VL+R+N T Y + + K++ IP +
Sbjct: 259 ATIAQESRLCRLVHLPVQHGSNGVLKRMNRSYTREHYLSLVGKLKA-------SIPNVAL 311
Query: 72 LDSVLYGNPIEKIREYRAVVSTMIPQLVTLDSVFI 106
+L G P E ++ + M + V DS F+
Sbjct: 312 STDILIGFPGETEEDFEQTLDLM--REVEFDSAFM 344
>gnl|CDD|223645 COG0572, Udk, Uridine kinase [Nucleotide transport and metabolism].
Length = 218
Score = 26.5 bits (59), Expect = 5.1
Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 8/86 (9%)
Query: 9 HNGWQVDQAILSEEDRVVIEEYLSVFVLRRVNSLRTLSLYGNPIEKIREYRAVVSTMIPQ 68
+ + I E + VVI E + + R+ L L ++ + +R R + + +
Sbjct: 94 KTHTREPETIKVEPNDVVIVEGILLLYDERLRDLMDLKIFVDTDADVRLIRRIKRDVQER 153
Query: 69 LVTLDSVLYGNPIEKIREYRAVVSTM 94
L+SV I +Y V M
Sbjct: 154 GRDLESV--------IEQYVKTVRPM 171
>gnl|CDD|232890 TIGR00235, udk, uridine kinase. Model contains a number of longer
eukaryotic proteins and starts bringing in
phosphoribulokinase hits at scores of 160 and below
[Purines, pyrimidines, nucleosides, and nucleotides,
Salvage of nucleosides and nucleotides].
Length = 207
Score = 26.6 bits (59), Expect = 5.2
Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 8/85 (9%)
Query: 15 DQAILSEEDRVVIEEYLSVFVLRRVNSLRTLSLYGNPIEKIREYRAVVSTMIPQLVTLDS 74
+ + E VVI E + R+ L L ++ + IR R + + + +LDS
Sbjct: 98 KETVHIEPKDVVILEGIMPLFDERLRDLMDLKIFVDTPLDIRLIRRIERDINERGRSLDS 157
Query: 75 VLYGNPIEKIREYRAVVSTMIPQLV 99
V I +YR V M Q V
Sbjct: 158 V--------IDQYRKTVRPMYEQFV 174
>gnl|CDD|212106 cd10794, GH57N_PfGalA_like, N-terminal catalytic domain of
alpha-galactosidase; glycoside hydrolase family 57
(GH57). Alpha-galactosidases (GalA, EC 3.2.1.22)
catalyze the hydrolysis of alpha-1,6-linked galactose
residues from oligosaccharides and polymeric
galactomannans. Based on sequence similarity, the
majority of eukaryotic and bacterial GalAs have been
classified into glycoside hydrolase family GH27, GH36,
and GH4, respectively. This subfamily is represented by
a novel type of GalA from Pyrococcus furiosus (PfGalA),
which belongs to the GH57 family. PfGalA is an extremely
thermo-active and thermostable GalA that functions as a
bacterial-like GalA, however, without the capacity to
hydrolyze polysaccharides. It specifically catalyzes the
hydrolysis of para-nitrophenyl-alpha-galactopyranoside,
and to some extent that of melibiose and raffinose.
PfGalA has a pH optimum between 5.0-5.5.
Length = 305
Score = 25.8 bits (57), Expect = 8.7
Identities = 13/46 (28%), Positives = 17/46 (36%), Gaps = 1/46 (2%)
Query: 10 NGWQVDQAILSEEDRVVIEEYLSVFVLRRVNSLRTLSLYGNPIEKI 55
N Q D + ++EYLS R + LYGN E
Sbjct: 175 NDSIAFQKFYVHGD-LGLDEYLSYLARWLATDQRAIMLYGNDAEIF 219
>gnl|CDD|168377 PRK06072, PRK06072, enoyl-CoA hydratase; Provisional.
Length = 248
Score = 25.9 bits (57), Expect = 9.1
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 115 NALNAEIRSYLLPKYEKLEAATFKRTAV 142
NALN E+R+ + K +++ A R +
Sbjct: 22 NALNLEMRNEFISKLKQINADPKIRVVI 49
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
0.318 0.133 0.361
Gapped
Lambda K H
0.267 0.0977 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,534,960
Number of extensions: 683750
Number of successful extensions: 514
Number of sequences better than 10.0: 1
Number of HSP's gapped: 514
Number of HSP's successfully gapped: 23
Length of query: 147
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 59
Effective length of database: 7,034,450
Effective search space: 415032550
Effective search space used: 415032550
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 (21.7 bits)
S2: 54 (24.2 bits)