RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1332
(103 letters)
>gnl|CDD|220213 pfam09377, SBDS_C, SBDS protein C-terminal domain. This family is
highly conserved in species ranging from archaea to
vertebrates and plants. The family contains several
Shwachman-Bodian-Diamond syndrome (SBDS) proteins from
both mouse and humans. Shwachman-Diamond syndrome is an
autosomal recessive disorder with clinical features that
include pancreatic exocrine insufficiency,
haematological dysfunction and skeletal abnormalities.
Members of this family play a role in RNA metabolism.
Length = 126
Score = 70.4 bits (173), Expect = 3e-17
Identities = 42/77 (54%), Positives = 51/77 (66%), Gaps = 5/77 (6%)
Query: 7 VIPTL--KQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVK-CATSVENEEWSGGGLLLIC 63
VI L KQ + I RA+MRVRV V VK KK+KEKL K VE EE SGGG L+
Sbjct: 52 VIKKLQEKQIIPIARAKMRVRVTVP--VKAAKKVKEKLKKLYEFKVEEEEESGGGWELVV 109
Query: 64 LIDPGKYREIDELVRTE 80
LI+PG +RE+DEL++ E
Sbjct: 110 LIEPGLFRELDELLKKE 126
>gnl|CDD|224417 COG1500, COG1500, Predicted exosome subunit [Translation, ribosomal
structure and biogenesis].
Length = 234
Score = 34.6 bits (80), Expect = 0.004
Identities = 25/92 (27%), Positives = 38/92 (41%), Gaps = 11/92 (11%)
Query: 5 SQVIPTLKQCMSI-----ERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEW-SGGG 58
QV LK I ERA++ V++ V K L K ++ EEW G
Sbjct: 144 EQVQEVLKALRPIIPIRFERAKVAVKIPVEY----AGKAYGLLRKFG-EIKKEEWQEDGS 198
Query: 59 LLLICLIDPGKYREIDELVRTETRGQGTLELL 90
+ + I G E EL+ T+G+ ++L
Sbjct: 199 WICVLEIPAGNQDEFYELLNELTKGEVQTKVL 230
>gnl|CDD|224653 COG1739, COG1739, Uncharacterized conserved protein [Function
unknown].
Length = 203
Score = 33.1 bits (76), Expect = 0.013
Identities = 18/91 (19%), Positives = 34/91 (37%), Gaps = 1/91 (1%)
Query: 1 MYYYSQVIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLL 60
Y + V L+ +IE+ + V + + L+ L + VE +SGG +L
Sbjct: 114 RAYANAVKSALEAAEAIEK-KEAKANHVGCAYRILGLLERLLKQNDDDVEEARYSGGSVL 172
Query: 61 LICLIDPGKYREIDELVRTETRGQGTLELLN 91
L + L++ G + +N
Sbjct: 173 LTVRFRHIVIEAVSRLLKGNHIGPDRFKHIN 203
>gnl|CDD|129392 TIGR00291, RNA_SBDS, rRNA metabolism protein, SBDS family. This
protein family, possibly universal in both archaea and
eukaryotes, appears to be involved in (ribosomal) RNA
metabolism. Mutations in the human ortholog are
associated with Shwachman-Bodian-Diamond syndrome
[Protein synthesis, Other].
Length = 231
Score = 31.3 bits (71), Expect = 0.044
Identities = 19/80 (23%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 6 QVIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSG-GGLLLICL 64
+++ LKQ + I+ +M+V +++ + + E + +V EEW G + +
Sbjct: 148 EIVKALKQIIPIKFEKMKVAIKIPP--ERAGEAIEAISNFG-AVTPEEWQEDGSWICVGE 204
Query: 65 IDPGKYREIDELVRTETRGQ 84
I G YR++ L+ +T+G
Sbjct: 205 IPSGNYRDLMTLLDKKTKGN 224
>gnl|CDD|185627 PTZ00448, PTZ00448, hypothetical protein; Provisional.
Length = 373
Score = 28.8 bits (64), Expect = 0.50
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 17 IERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDEL 76
IERA+M +++ S + + + + +KL + + E + L +P YREID+L
Sbjct: 169 IERAKMMLKL--SVDIVNKQNITKKLNEFNVFPISSEEKHNTYSITFLCEPRYYREIDQL 226
>gnl|CDD|234722 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed.
Length = 232
Score = 27.8 bits (63), Expect = 0.87
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 9/37 (24%)
Query: 17 IERAQMRVRVEVSA---GV------KDVKKLKEKLVK 44
IER RVRV + G+ +++KL+++L K
Sbjct: 57 IERPAKRVRVTIHTARPGIVIGKKGAEIEKLRKELEK 93
>gnl|CDD|237589 PRK14024, PRK14024, phosphoribosyl isomerase A; Provisional.
Length = 241
Score = 26.1 bits (58), Expect = 3.3
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 7/42 (16%)
Query: 20 AQMRVRVEVSAGVKDVKKLKEKLVKCATSV-------ENEEW 54
++ V+VE+S G++D + L+ L V EN EW
Sbjct: 72 GKLDVKVELSGGIRDDESLEAALATGCARVNIGTAALENPEW 113
>gnl|CDD|193508 cd03887, M20_Acy1L2, M20 Peptidase Aminoacylase 1-like protein 2,
amidohydrolase family. Peptidase M20 family,
Aminoacylase 1-like protein 2 (ACY1L2; amidohydrolase)
subfamily. This group contains many uncharacterized
proteins predicted as amidohydrolases, including gene
products of abgA and abgB that catalyze the cleavage of
p-aminobenzoyl-glutamate, a folate catabolite in
Escherichia coli, to p-aminobenzoate and glutamate.
p-Aminobenzoyl-glutamate utilization is catalyzed by the
abg region gene product, AbgT. Aminoacylase 1 (ACY1)
proteins are a class of zinc binding homodimeric enzymes
involved in hydrolysis of N-acetylated proteins.
N-terminal acetylation of proteins is a widespread and
highly conserved process that is involved in the
protection and stability of proteins. Several types of
aminoacylases can be distinguished on the basis of
substrate specificity. ACY1 breaks down cytosolic
aliphatic N-acyl-alpha-amino acids (except L-aspartate),
especially N-acetyl-methionine and acetyl-glutamate into
L-amino acids and an acyl group. However, ACY1 can also
catalyze the reverse reaction, the synthesis of
acetylated amino acids. ACY1 may also play a role in
xenobiotic bioactivation as well as the inter-organ
processing of amino acid-conjugated xenobiotic
derivatives (S-substituted-N-acetyl-L-cysteine).
Length = 358
Score = 25.9 bits (58), Expect = 4.0
Identities = 10/42 (23%), Positives = 21/42 (50%), Gaps = 13/42 (30%)
Query: 7 VIPTLKQCMSIERAQMR--VRVEVSAGVKDVKKLKEKLVKCA 46
V+P + A++ VR + + +++L E++ KCA
Sbjct: 219 VVP--------DYAEVEYYVR---APTREYLEELVERVKKCA 249
>gnl|CDD|236999 PRK11854, aceF, pyruvate dehydrogenase dihydrolipoyltransacetylase;
Validated.
Length = 633
Score = 25.7 bits (57), Expect = 5.4
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 23 RVRVE-VSAGVKD-VKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDE 75
R+ E V A VKD VK+ + A G GLL +D K+ EI+E
Sbjct: 356 RILKEDVQAYVKDAVKRAEAAPAAAAAG-----GGGPGLLPWPKVDFSKFGEIEE 405
>gnl|CDD|238237 cd00405, PRAI, Phosphoribosylanthranilate isomerase (PRAI)
catalyzes the fourth step of the tryptophan
biosynthesis, the conversion of N-(5'-
phosphoribosyl)-anthranilate (PRA) to
1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate
(CdRP). Most PRAIs are monomeric, monofunctional and
thermolabile, but in some thermophile organisms PRAI is
dimeric for reasons of stability and in others it is
fused to other components of the tryptophan biosynthesis
pathway to form multifunctional enzymes.
Length = 203
Score = 25.6 bits (57), Expect = 5.5
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 26 VEVSAGVKDVKKLKE 40
VE S G+KD +K++
Sbjct: 184 VETSPGIKDPEKIRA 198
>gnl|CDD|130875 TIGR01816, sdhA_forward, succinate dehydrogenase, flavoprotein
subunit, E. coli/mitochondrial subgroup. Succinate
dehydrogenase and fumarate reductase are homologous
enzymes reversible in principle but favored under
different circumstances. This model represents a
narrowly defined clade of the succinate dehydrogenase
flavoprotein subunit as found in mitochondria, in
Rickettsia, in E. coli and other Proteobacteria, and in
a few other lineages. However, This model excludes all
known fumarate reductases. It also excludes putative
succinate dehydrogenases that appear to diverged before
the split between E. coli succinate dehydrogenase and
fumarate reductase [Energy metabolism, TCA cycle].
Length = 565
Score = 25.5 bits (56), Expect = 5.5
Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 11 LKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGG---GLLLICLIDP 67
L++ M R + GV+ + LKE+ + +++ W+ L L L++
Sbjct: 436 LQRSMQNHAGVFRTGEVLQKGVEKISALKERYKNVKINDKSKVWNTDLVEALELQNLLEC 495
Query: 68 GKYREIDELVRTETRG 83
+ + R E+RG
Sbjct: 496 AEATAVSAEARKESRG 511
>gnl|CDD|132557 TIGR03518, ABC_perm_GldF, gliding motility-associated ABC
transporter permease protein GldF. Members of this
protein family are exclusive to the Bacteroidetes phylum
(previously Cytophaga-Flavobacteria-Bacteroides). GldF
is believed to be a ABC transporter permease protein
(along with ATP-binding subunit, GldA and a
sunstrate-binding subunit, GldG) and is linked to a type
of rapid surface gliding motility found in certain
Bacteroidetes, such as Flavobacterium johnsoniae and
Cytophaga hutchinsonii. Knockouts of GldF abolish the
gliding phenotype. Gliding motility appears closely
linked to chitin utilization in the model species
Flavobacterium johnsoniae. Bacteroidetes with members of
this protein family appear to have all of the genes
associated with gliding motility.
Length = 240
Score = 25.3 bits (56), Expect = 5.8
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 79 TETRGQGTLELLNLKEVTEGEEVL 102
E R GTLELL + +++ + +L
Sbjct: 74 AEERKLGTLELLLTRPISDWQIIL 97
>gnl|CDD|239095 cd02412, 30S_S3_KH, K homology RNA-binding (KH) domain of the
prokaryotic 30S small ribosomal subunit protein S3. S3
is part of the head region of the 30S ribosomal subunit
and is believed to interact with mRNA as it threads its
way from the latch into the channel. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In general, KH
binds single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional
modifiers of mRNA.
Length = 109
Score = 24.7 bits (55), Expect = 7.5
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 9/37 (24%)
Query: 17 IERAQMRVRVEVSA---GV------KDVKKLKEKLVK 44
IER RV V + G+ ++KL+++L K
Sbjct: 56 IERKADRVEVTIHTARPGIIIGKKGAGIEKLRKELQK 92
>gnl|CDD|153178 cd04906, ACT_ThrD-I_1, First of two tandem C-terminal ACT domains
of threonine dehydratase I (ThrD-I; L-threonine
hydrolyase). This CD includes the first of two tandem
C-terminal ACT domains of threonine dehydratase I
(ThrD-I; L-threonine hydrolyase) which catalyzes the
committed step in branched chain amino acid
biosynthesis in plants and microorganisms, the
pyridoxal 5'-phosphate (PLP)-dependent
dehydration/deamination of L-threonine (or L-serine) to
2-ketobutyrate (or pyruvate). ThrD-I is a cooperative,
feedback-regulated (isoleucine and valine) allosteric
enzyme that forms a tetramer and contains four
pyridoxal phosphate moieties. Members of this CD belong
to the superfamily of ACT regulatory domains.
Length = 85
Score = 24.0 bits (53), Expect = 8.7
Identities = 9/34 (26%), Positives = 17/34 (50%)
Query: 18 ERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVEN 51
+ A + V V V+ G +++ +L E L V +
Sbjct: 38 KDAHIFVGVSVANGAEELAELLEDLKSAGYEVVD 71
>gnl|CDD|225232 COG2357, COG2357, PpGpp synthetase catalytic domain [General
function prediction only].
Length = 231
Score = 25.0 bits (55), Expect = 9.1
Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 1 MYYYSQVIPTLKQCMSIERAQMRVRVE------VSAGVKDVKKLKEKLVK 44
+ Y Q + LK + I R + + V++ VK + + EKL +
Sbjct: 22 LVPYEQALEELKTKLKILRDEYEKLHDYNPIEHVTSRVKSPESILEKLRR 71
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 0.134 0.373
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,189,088
Number of extensions: 431337
Number of successful extensions: 296
Number of sequences better than 10.0: 1
Number of HSP's gapped: 293
Number of HSP's successfully gapped: 27
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: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (24.2 bits)