RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5902
(103 letters)
>gnl|CDD|238607 cd01276, PKCI_related, Protein Kinase C Interacting protein related
(PKCI): PKCI and related proteins belong to the
ubiquitous HIT family of hydrolases that act on
alpha-phosphates of ribonucleotides. The members of this
subgroup have a conserved HxHxHxx motif (x is a
hydrophobic residue) that is a signature for this
family. No enzymatic activity has been reported however,
for PKCI and its related members.
Length = 104
Score = 56.0 bits (136), Expect = 8e-12
Identities = 23/48 (47%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 50 HILGHLMIVAKKVAAKKLIRN--YRVVVNNGWEAVQFSGHLHLHVLGG 95
+LGHL+ A KVA I YR+V+N G + Q HLHLH+LGG
Sbjct: 57 ELLGHLLSAAAKVAKDLGIAEDGYRLVINCGKDGGQEVFHLHLHLLGG 104
>gnl|CDD|216377 pfam01230, HIT, HIT domain.
Length = 97
Score = 47.3 bits (113), Expect = 2e-08
Identities = 24/51 (47%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 51 ILGHLMIVAKKVAA---KKLIRNYRVVVNNGWEAVQFSGHLHLHVLGGRPL 98
LG LM AKKVA K YR+V+NNG A Q HLH+HV+ R
Sbjct: 47 ELGDLMSEAKKVARALGKAKADGYRIVINNGAAAGQSVPHLHIHVIPRREG 97
>gnl|CDD|221348 pfam11969, DcpS_C, Scavenger mRNA decapping enzyme C-term binding.
This family consists of several scavenger mRNA decapping
enzymes (DcpS) and is the C-terminal region. DcpS is a
scavenger pyrophosphatase that hydrolyses the residual
cap structure following 3' to 5' decay of an mRNA. The
association of DcpS with 3' to 5' exonuclease exosome
components suggests that these two activities are linked
and there is a coupled exonucleolytic decay-dependent
decapping pathway. The C-terminal domain contains a
histidine triad (HIT) sequence with three histidines
separated by hydrophobic residues. The central histidine
within the DcpS HIT motif is critical for decapping
activity and defines the HIT motif as a new mRNA
decapping domain, making DcpS the first member of the
HIT family of proteins with a defined biological
function.
Length = 113
Score = 46.0 bits (110), Expect = 8e-08
Identities = 19/44 (43%), Positives = 26/44 (59%)
Query: 51 ILGHLMIVAKKVAAKKLIRNYRVVVNNGWEAVQFSGHLHLHVLG 94
+LGH+ VAKK+A +K YR V+ G+ HLHLHV+
Sbjct: 58 LLGHMREVAKKIAKEKYNEGYRDVLRLGFHYGPSVYHLHLHVIA 101
>gnl|CDD|182648 PRK10687, PRK10687, purine nucleoside phosphoramidase; Provisional.
Length = 119
Score = 42.6 bits (100), Expect = 2e-06
Identities = 20/49 (40%), Positives = 31/49 (63%), Gaps = 2/49 (4%)
Query: 52 LGHLMIVAKKVAAKKLIRN--YRVVVNNGWEAVQFSGHLHLHVLGGRPL 98
LG ++ VA K+A ++ I YR+++N Q H+H+H+LGGRPL
Sbjct: 62 LGRMITVAAKIAEQEGIAEDGYRLIMNTNRHGGQEVYHIHMHLLGGRPL 110
>gnl|CDD|223611 COG0537, Hit, Diadenosine tetraphosphate (Ap4A) hydrolase and other
HIT family hydrolases [Nucleotide transport and
metabolism / Carbohydrate transport and metabolism /
General function prediction only].
Length = 138
Score = 41.6 bits (98), Expect = 7e-06
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 51 ILGHLMIVAKKVAAKKLIRN-----YRVVVNNGWEAVQFSGHLHLHVLGGRPLHWPPG 103
L L ++A+K+A K L Y + +NNG A Q HLH+H++
Sbjct: 56 ELAELFLLAQKIA-KALKEAFGADGYNIGINNGKAAGQEVFHLHIHIIPRYKGDDNFP 112
>gnl|CDD|238608 cd01277, HINT_subgroup, HINT (histidine triad nucleotide-binding
protein) subgroup: Members of this CD belong to the
superfamily of histidine triad hydrolases that act on
alpha-phosphate of ribonucleotides. This subgroup
includes members from all three forms of cellular life.
Although the biochemical function has not been
characterised for many of the members of this subgroup,
the proteins from Yeast have been shown to be involved
in secretion, peroxisome formation and gene expression.
Length = 103
Score = 37.6 bits (88), Expect = 1e-04
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 8/57 (14%)
Query: 45 CERLFHI----LGHLMIVAKKVA----AKKLIRNYRVVVNNGWEAVQFSGHLHLHVL 93
E L + L L++ AKKVA ++ NNG A Q H+H+HV+
Sbjct: 45 YENLLDLDPEELAELILAAKKVARALKKALKADGLNILQNNGRAAGQVVFHVHVHVI 101
>gnl|CDD|238263 cd00468, HIT_like, HIT family: HIT (Histidine triad) proteins,
named for a motif related to the sequence HxHxH/Qxx (x,
a hydrophobic amino acid), are a superfamily of
nucleotide hydrolases and transferases, which act on
the alpha-phosphate of ribonucleotides. On the basis of
sequence, substrate specificity, structure, evolution
and mechanism, HIT proteins are classified in the
literacture into three major branches: the Hint branch,
which consists of adenosine 5' -monophosphoramide
hydrolases, the Fhit branch, that consists of
diadenosine polyphosphate hydrolases, and the GalT
branch consisting of specific nucloside monophosphate
transferases. Further sequence analysis reveals several
new closely related, yet uncharacterized subgroups.
Length = 86
Score = 35.9 bits (83), Expect = 4e-04
Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 4/47 (8%)
Query: 52 LGHLMIVAKKVAAK----KLIRNYRVVVNNGWEAVQFSGHLHLHVLG 94
L L+I A++VAA+ + + V VN+G A Q H+HLHVL
Sbjct: 40 LADLVITAQRVAAELEKHGNVPSLTVFVNDGAAAGQSVPHVHLHVLP 86
>gnl|CDD|236232 PRK08309, PRK08309, short chain dehydrogenase; Provisional.
Length = 177
Score = 31.6 bits (72), Expect = 0.033
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 3/39 (7%)
Query: 15 TVALCWVHGTPPQGNVFVANRVSKLQQTIDCERLFHILG 53
+A+ W+H + V + +T RLFH+LG
Sbjct: 77 DLAVAWIHSSAKDALSVVCRELDGSSETY---RLFHVLG 112
>gnl|CDD|238970 cd02012, TPP_TK, Thiamine pyrophosphate (TPP) family, Transketolase
(TK) subfamily, TPP-binding module; TK catalyzes the
transfer of a two-carbon unit from ketose phosphates to
aldose phosphates. In heterotrophic organisms, TK
provides a link between glycolysis and the pentose
phosphate pathway and provides precursors for
nucleotide, aromatic amino acid and vitamin
biosynthesis. In addition, the enzyme plays a central
role in the Calvin cycle in plants. Typically, TKs are
homodimers. They require TPP and divalent cations, such
as magnesium ions, for activity.
Length = 255
Score = 31.3 bits (72), Expect = 0.049
Identities = 15/37 (40%), Positives = 17/37 (45%), Gaps = 9/37 (24%)
Query: 63 AAKKLIRNYRVVV-------NNG--WEAVQFSGHLHL 90
A K L +YRV V G WEA F+GH L
Sbjct: 120 AEKLLGFDYRVYVLLGDGELQEGSVWEAASFAGHYKL 156
>gnl|CDD|223531 COG0455, flhG, Antiactivator of flagellar biosynthesis FleN, an
ATPase [Cell motility].
Length = 262
Score = 29.9 bits (68), Expect = 0.18
Identities = 15/75 (20%), Positives = 24/75 (32%), Gaps = 12/75 (16%)
Query: 10 CFTDSTVALCWV--HGTPPQGNVFVANRVS----------KLQQTIDCERLFHILGHLMI 57
TD+ + + G G V NRV L Q + + ++
Sbjct: 148 SITDAYKTIKILSKLGLDLLGRRVVLNRVRSTKEGVDVAALLIQVVKQVPVLQVIPFDPE 207
Query: 58 VAKKVAAKKLIRNYR 72
V + +A K I Y
Sbjct: 208 VRRALAEGKPIVLYS 222
>gnl|CDD|227458 COG5129, MAK16, Nuclear protein with HMG-like acidic region
[General function prediction only].
Length = 303
Score = 29.6 bits (66), Expect = 0.21
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 35 RVSKLQQTIDCER---LFHILGHLMIVAKKVAAKKLIRNYRVVV 75
R++KL Q + R LF G M+ K+ ++ +R + +
Sbjct: 110 RLTKLTQYLLKARRLALFKEHGEYMVRKPKMNRREKLRERKALN 153
>gnl|CDD|235793 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed.
Length = 146
Score = 27.9 bits (63), Expect = 0.66
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 50 HILGHLMIVAKKVAAKKLIRNYRVVVNNGWEAV 82
ILG L A VA K+L+ VV+ N +AV
Sbjct: 12 QILGRL---ASYVA-KRLLEGEEVVIVNAEKAV 40
>gnl|CDD|214638 smart00363, S4, S4 RNA-binding domain.
Length = 60
Score = 26.0 bits (58), Expect = 1.3
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 47 RLFHILGHLMIVAKKVAAKKLIRNYRVVVNN 77
RL L L + + A++LI RV VN
Sbjct: 2 RLDKFLARLGLAPSRSQARRLIEQGRVKVNG 32
>gnl|CDD|225798 COG3259, FrhA, Coenzyme F420-reducing hydrogenase, alpha subunit
[Energy production and conversion].
Length = 441
Score = 26.2 bits (58), Expect = 4.0
Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 63 AAKKLIRNYRVVVNNGWEAVQFSGHLHLHVLGGRPLH 99
A +I Y + + G + VLGG+ +H
Sbjct: 123 ADPGMIDEYPELAKEAIRLRKI-GQTIVEVLGGKAIH 158
>gnl|CDD|201819 pfam01479, S4, S4 domain. The S4 domain is a small domain
consisting of 60-65 amino acid residues that was
detected in the bacterial ribosomal protein S4,
eukaryotic ribosomal S9, two families of pseudouridine
synthases, a novel family of predicted RNA methylases,
a yeast protein containing a pseudouridine synthetase
and a deaminase domain, bacterial tyrosyl-tRNA
synthetases, and a number of uncharacterized, small
proteins that may be involved in translation
regulation. The S4 domain probably mediates binding to
RNA.
Length = 48
Score = 24.4 bits (54), Expect = 4.3
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 46 ERLFHILGHLMIVAKKVAAKKLIRNYRVVVNN 77
RL +L L + + + A++LIR+ V VN
Sbjct: 1 MRLDKVLARLGLASSRSEARQLIRHGHVRVNG 32
>gnl|CDD|162192 TIGR01077, L13_A_E, ribosomal protein L13, archaeal/eukaryotic.
This model represents ribosomal protein of L13 from the
Archaea and from the eukaryotic cytosol. Bacterial and
organellar forms are represented by model TIGR01066
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 142
Score = 24.7 bits (54), Expect = 7.8
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 50 HILGHLMIVAKKVAAKKLIRNYRVVVNNGWEAV 82
HILG L A VA K+L+ +VVV N + V
Sbjct: 8 HILGRL---ASVVA-KQLLNGEKVVVVNAEKIV 36
>gnl|CDD|241372 cd13218, PH-GRAM2_TCB1D8_TCB1D9_family, TCB1D8 and TCB1D9 family
Pleckstrin Homology-Glucosyltransferases, Rab-like
GTPase activators and Myotubularins (PH-GRAM) domain,
repeat 2. TBC1D8, TBC1D8B, TBC1D9 and TBC1D9B may act
as a GTPase-activating proteins for Rab family
protein(s). They all contain an N-terminal PH-GRAM
domain and a C-terminal Rab-GTPase-TBC (Tre-2, BUB2p,
and Cdc16p) domain. This cd contains the second repeat
of the PH-GRAM domain. The GRAM domain is found in
glucosyltransferases, myotubularins and other putative
membrane-associated proteins. The GRAM domain is part
of a larger motif with a pleckstrin homology (PH)
domain fold.
Length = 96
Score = 24.5 bits (53), Expect = 8.6
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 1 KLFKVENYVCFTDSTVALCWV 21
K+F ENY+CF LC V
Sbjct: 24 KMFISENYICFASKEGNLCSV 44
>gnl|CDD|236499 PRK09404, sucA, 2-oxoglutarate dehydrogenase E1 component;
Reviewed.
Length = 924
Score = 25.1 bits (56), Expect = 8.8
Identities = 9/32 (28%), Positives = 11/32 (34%), Gaps = 11/32 (34%)
Query: 58 VAKKVAAKKLIRNYRVVVNNGWEAVQFSGHLH 89
+V +LI YR F GHL
Sbjct: 77 SDPQVKVLQLINAYR-----------FRGHLA 97
>gnl|CDD|241508 cd13354, PH-GRAM2_TCB1D9_TCB1D9B, TBC1 domain family members 9
and 9B (TBC1D9 and TBC1D9B) Pleckstrin
Homology-Glucosyltransferases, Rab-like GTPase
activators and Myotubularins (PH-GRAM) domain, repeat
2. TBC1D9 and TCB1D9B may act as a GTPase-activating
proteins for Rab family protein(s). TBC1D9 and TCB1D9B
contain two N-terminal PH-GRAM domain and a C-terminal
Rab-GTPase-TBC (Tre-2, BUB2p, and Cdc16p) domain. This
cd contains the second repeat of the PH-GRAM domain.
The GRAM domain is found in glucosyltransferases,
myotubularins and other putative membrane-associated
proteins. The GRAM domain is part of a larger motif
with a pleckstrin homology (PH) domain fold.
Length = 114
Score = 24.5 bits (54), Expect = 8.9
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 1 KLFKVENYVCFTDSTVALCWV 21
+L+ +NY+CFT L +
Sbjct: 30 QLYLSQNYICFTSKVEDLVSL 50
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
0.326 0.141 0.469
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,225,377
Number of extensions: 426211
Number of successful extensions: 460
Number of sequences better than 10.0: 1
Number of HSP's gapped: 454
Number of HSP's successfully gapped: 21
Length of query: 103
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 34
Effective length of database: 7,877,176
Effective search space: 267823984
Effective search space used: 267823984
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.1 bits)