RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1800
(81 letters)
>gnl|CDD|177670 PLN00036, PLN00036, 40S ribosomal protein S4; Provisional.
Length = 261
Score = 104 bits (262), Expect = 1e-29
Identities = 44/63 (69%), Positives = 51/63 (80%)
Query: 4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
GNL M+TGGRN GRVG + NRE+H GSF+I+HVKD GH FATRL NVF+IGKGTK + S
Sbjct: 178 GNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWIS 237
Query: 64 KPK 66
PK
Sbjct: 238 LPK 240
>gnl|CDD|240511 cd06087, KOW_RPS4, KOW motif of Ribosomal Protein S4 (RPS4).
RPS4 plays a critical role in the core assembly of the
small ribosomal subunit with a KOW motif at its
C-terminal. RPS4 also acts as a general transcription
antiterminator factor and regulates ribosomal RNA
expression level. KOW domain is known as an RNA-binding
motif that is shared so far among some families of
ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. RPS4 deficiency in human has
been associated with Turner syndrome. Archeae RPS4
(RPS4e) showed substantial identity to the eukaryotic
equivalents RPS4, but the archaeal proteins formed a
different complex from the eukaryotic proteins.
Length = 55
Score = 94.5 bits (236), Expect = 8e-28
Identities = 37/53 (69%), Positives = 43/53 (81%)
Query: 3 PGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIG 55
GNL M+TGGRN+GRVG + ERH GSFDIVHVKD G+ FATRL+NVF+IG
Sbjct: 3 EGNLAMVTGGRNVGRVGVIKEIERHKGSFDIVHVKDAAGNEFATRLSNVFVIG 55
>gnl|CDD|240277 PTZ00118, PTZ00118, 40S ribosomal protein S4; Provisional.
Length = 262
Score = 98.4 bits (245), Expect = 5e-27
Identities = 42/64 (65%), Positives = 53/64 (82%)
Query: 3 PGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFC 62
GNL MITGG N+GRVGT+V++E+HPGSFD++HVKD G FATRL+NVF+IG GTK +
Sbjct: 177 VGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYV 236
Query: 63 SKPK 66
S P+
Sbjct: 237 SLPR 240
>gnl|CDD|140250 PTZ00223, PTZ00223, 40S ribosomal protein S4; Provisional.
Length = 273
Score = 75.8 bits (186), Expect = 2e-18
Identities = 31/53 (58%), Positives = 41/53 (77%)
Query: 4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGK 56
G + M+TGG N GR+G +V+ ERHPG+FDI +KD +GH FATR N+F+IGK
Sbjct: 175 GKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGK 227
>gnl|CDD|224388 COG1471, RPS4A, Ribosomal protein S4E [Translation, ribosomal
structure and biogenesis].
Length = 241
Score = 72.3 bits (178), Expect = 3e-17
Identities = 24/56 (42%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 3 PGNLCMITGGRNLGRVGTVVNRERHPGS-FDIVHVKDGNGHVFATRLNNVFIIGKG 57
G L +TGGR++GRVGT+V E S ++V V+D G+ F T + VF+IG+
Sbjct: 176 EGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFVIGED 231
>gnl|CDD|179820 PRK04313, PRK04313, 30S ribosomal protein S4e; Validated.
Length = 237
Score = 58.7 bits (143), Expect = 3e-12
Identities = 23/56 (41%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 3 PGNLCMITGGRNLGRVGTVVNRERHPGSF-DIVHVKDGNGHVFATRLNNVFIIGKG 57
GNL +ITGG+++G +G + E S +IV ++D +G F T L+ VF+IGK
Sbjct: 174 EGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGKE 229
>gnl|CDD|144165 pfam00467, KOW, KOW motif. This family has been extended to
coincide with ref. The KOW (Kyprides, Ouzounis, Woese)
motif is found in a variety of ribosomal proteins and
NusG.
Length = 32
Score = 32.0 bits (74), Expect = 0.003
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 3 PGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVK 37
G++ + G G+ G VV + VHV+
Sbjct: 1 KGDVVRVISGPFKGKKGKVVEVDDSKA---RVHVE 32
>gnl|CDD|232837 TIGR00125, cyt_tran_rel, cytidyltransferase-like domain. Protein
families that contain at least one copy of this domain
include citrate lyase ligase, pantoate-beta-alanine
ligase, glycerol-3-phosphate cytidyltransferase,
ADP-heptose synthase, phosphocholine
cytidylyltransferase, lipopolysaccharide core
biosynthesis protein KdtB, the bifunctional protein
NadR, and a number whose function is unknown. Many of
these proteins are known to use CTP or ATP and release
pyrophosphate.
Length = 66
Score = 28.4 bits (64), Expect = 0.12
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 8/51 (15%)
Query: 28 PGSFDIVHVKDGNGHVF----ATRLNNVFIIGKGTKAFCSKPKRNFVSPRQ 74
G+FD H GH+ A L + I+G G+ F + K V +
Sbjct: 5 VGTFDPFH----LGHLDLLERAKELFDELIVGVGSDQFVNPLKGEPVFSLE 51
>gnl|CDD|128978 smart00739, KOW, KOW (Kyprides, Ouzounis, Woese) motif. Motif in
ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Length = 28
Score = 26.9 bits (61), Expect = 0.19
Identities = 6/25 (24%), Positives = 11/25 (44%)
Query: 3 PGNLCMITGGRNLGRVGTVVNRERH 27
G+ + G G+VG V+ +
Sbjct: 4 VGDTVRVIAGPFKGKVGKVLEVDGE 28
>gnl|CDD|240504 cd00380, KOW, KOW: an acronym for the authors' surnames
(Kyrpides, Ouzounis and Woese). KOW domain is known as
an RNA-binding motif that is shared so far among some
families of ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. The KOW motif contains an
invariants glycine residue and comprises alternating
blocks of hydrophilic and hydrophobic residues.
Length = 49
Score = 26.4 bits (59), Expect = 0.56
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 6/52 (11%)
Query: 4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVK---DGNGHVFATRLNNVF 52
G++ + G GR G VV+ + F IV VK G R ++V
Sbjct: 1 GDVVRVLRGPYKGREGVVVDIDPR---FGIVTVKGATGSKGAELKVRFDDVD 49
>gnl|CDD|216589 pfam01588, tRNA_bind, Putative tRNA binding domain. This domain
is found in prokaryotic methionyl-tRNA synthetases,
prokaryotic phenylalanyl tRNA synthetases the yeast GU4
nucleic-binding protein (G4p1 or p42, ARC1), human
tyrosyl-tRNA synthetase, and endothelial-monocyte
activating polypeptide II. G4p1 binds specifically to
tRNA form a complex with methionyl-tRNA synthetases. In
human tyrosyl-tRNA synthetase this domain may direct
tRNA to the active site of the enzyme. This domain may
perform a common function in tRNA aminoacylation.
Length = 95
Score = 26.8 bits (60), Expect = 0.65
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 17 RVGTVVNRERHPGS 30
RVG V+ E+HP +
Sbjct: 2 RVGKVLEAEKHPNA 15
>gnl|CDD|239066 cd02153, tRNA_bindingDomain, The tRNA binding domain is also
known as the Myf domain in literature. This domain is
found in a diverse collection of tRNA binding proteins,
including prokaryotic phenylalanyl tRNA synthetases
(PheRS), methionyl-tRNA synthetases (MetRS), human
tyrosyl-tRNA synthetase(hTyrRS), Saccharomyces
cerevisiae Arc1p, Thermus thermophilus CsaA, Aquifex
aeolicus Trbp111, human p43 and human EMAP-II. PheRS,
MetRS and hTyrRS aminoacylate their cognate tRNAs.
Arc1p is a transactivator of yeast methionyl-tRNA and
glutamyl-tRNA synthetases. The molecular chaperones
Trbp111 and CsaA also contain this domain. CsaA has
export related activities; Trbp111 is
structure-specific recognizing the L-shape of the tRNA
fold. This domain has general tRNA binding properties.
In a subset of this family this domain has the added
capability of a cytokine. For example the p43 component
of the Human aminoacyl-tRNA synthetase complex is
cleaved to release EMAP-II cytokine. EMAP-II has
multiple activities during apoptosis, angiogenesis and
inflammation and participates in malignant
transformation. An EMAP-II-like cytokine is released
from hTyrRS upon cleavage. The active cytokine
heptapeptide locates to this domain. For homodimeric
members of this group which include CsaA, Trbp111 and
Escherichia coli MetRS this domain acts as a
dimerization domain.
Length = 99
Score = 26.7 bits (60), Expect = 0.79
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 4/28 (14%)
Query: 17 RVGTVVNRERHPGSFD---IVHVKDGNG 41
RVG +V E HP + D ++ V G
Sbjct: 2 RVGKIVEAEPHPNA-DKLYVLKVDIGEE 28
>gnl|CDD|176916 cd08907, START_STARD8-like, C-terminal lipid-binding START domain
of mammalian STARD8 and related proteins, which also
have an N-terminal Rho GTPase-activating protein
(RhoGAP) domain. This subgroup includes the
steroidogenic acute regulatory protein (StAR)-related
lipid transfer (START) domains of STARD8 (also known as
deleted in liver cancer 3/DLC3, and Arhgap38) and
related proteins. It belongs to the START domain family,
and in turn to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. Proteins belonging to this subfamily also have a
RhoGAP domain. The precise function of the START domain
in this subgroup is unclear.
Length = 205
Score = 26.4 bits (58), Expect = 1.3
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 5/55 (9%)
Query: 22 VNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTC 76
V RERH D++H + V NN + T + P+R+FV R
Sbjct: 71 VLRERHLWDEDLLHSQ-----VIEALENNTEVYHYVTDSMAPHPRRDFVVLRMWR 120
>gnl|CDD|150114 pfam09338, Gly_reductase, Glycine/sarcosine/betaine reductase
component B subunits. This is a family of glycine
reductase, sarcosine reductase and betaine reductases.
These enzymes catalyze the following reactions.
sarcosine reductase: Acetyl phosphate + methylamine +
thioredoxin disulphide = N-methylglycine + phosphate +
thioredoxin Acetyl phosphate + NH(3) + thioredoxin
disulphide = glycine + phosphate + thioredoxin. betaine
reductase: Acetyl phosphate + trimethylamine +
thioredoxin disulphide = N,N,N-trimethylglycine +
phosphate + thioredoxin.
Length = 428
Score = 26.1 bits (58), Expect = 2.3
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 10/41 (24%)
Query: 27 HPG-SFDIVHVKD---------GNGHVFATRLNNVFIIGKG 57
PG S I+ VKD G G +F ++ V +G+G
Sbjct: 52 RPGESVRIIPVKDVIEPRVKVEGEGGIFPGFISKVETVGEG 92
>gnl|CDD|182844 PRK10926, PRK10926, ferredoxin-NADP reductase; Provisional.
Length = 248
Score = 25.8 bits (57), Expect = 2.3
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 17 RVGTVVNRERHPGS 30
R+ TVV+RE PGS
Sbjct: 167 RIQTVVSRETAPGS 180
>gnl|CDD|216901 pfam02145, Rap_GAP, Rap/ran-GAP.
Length = 187
Score = 25.6 bits (57), Expect = 2.5
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 7/56 (12%)
Query: 22 VNRERHPGSFDIVHV------KDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVS 71
+ ++RH G+ DIV++ N + ++ N+VFI+ K SK VS
Sbjct: 73 LEKKRHIGN-DIVNIIFNESGLPFNPNTIKSQFNHVFIVIYPLKNDDSKSTLYKVS 127
>gnl|CDD|173906 cd00812, LeuRS_core, catalytic core domain of leucyl-tRNA
synthetases. Leucyl tRNA synthetase (LeuRS) catalytic
core domain. This class I enzyme is a monomer which
aminoacylates the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding. In Aquifex
aeolicus, the gene encoding LeuRS is split in two, just
before the KMSKS motif. Consequently, LeuRS is a
heterodimer, which likely superimposes with the LeuRS
monomer found in most other organisms. LeuRS has an
insertion in the core domain, which is subject to both
deletions and rearrangements and thus differs between
prokaryotic LeuRS and archaeal/eukaryotic LeuRS. This
editing region hydrolyzes mischarged cognate tRNAs and
thus prevents the incorporation of chemically similar
amino acids.
Length = 314
Score = 25.7 bits (57), Expect = 3.0
Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 48 LNNVFIIGKGTKAFCSKPKRNFVSPRQT 75
+ ++ +G K SK K N V+P +
Sbjct: 264 IVQGMVLLEGEKM--SKSKGNVVTPDEA 289
>gnl|CDD|173921 cd02170, cytidylyltransferase, cytidylyltransferase. The
cytidylyltransferase family includes cholinephosphate
cytidylyltransferase (CCT), glycerol-3-phosphate
cytidylyltransferase, RafE and phosphoethanolamine
cytidylyltransferase (ECT). All enzymes catalyze the
transfer of a cytidylyl group from CTP to various
substrates.
Length = 136
Score = 25.3 bits (56), Expect = 3.0
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 8/43 (18%)
Query: 29 GSFDIVHVKDGNGHV----FATRLNNVFIIGKGTKAFCSKPKR 67
G+FDI+H GH+ A +L + I+G +K KR
Sbjct: 8 GTFDIIHP----GHIRFLEEAKKLGDYLIVGVARDETVAKIKR 46
>gnl|CDD|187684 cd09626, DOMON_glucodextranase_like, DOMON-like domain of various
glycoside hydrolases. This DOMON-like domain is found
at the C-terminus of various bacterial proteins that
play roles in metabolizing carbohydrates, such as
glucodextranase (hydrolyzes alpha-1,6-glucosidic
linkages of dextran from the non-reducing end), glucan
alpha-1,4-glucosidase, pullulanase (degrades pullulan,
a polysaccharide built from maltotriose units),
arabinogalactan endo-1,4-beta-galactosidase, and
others. Consequently, the DOMON-like domains in this
family co-occur with catalytic domains from various
glycosyl hydrolase families. The precise function of
the DOMON domains in these proteins is not clear, they
may be involved in interactions with carbohydrates.
Length = 220
Score = 25.4 bits (56), Expect = 3.6
Identities = 7/28 (25%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 27 HPGSFDIVHVK---DGNGHVFATRLNNV 51
PG+FD+ G+ + F +L +
Sbjct: 26 KPGAFDLTGFTVYEAGDKYRFRVKLALL 53
>gnl|CDD|234655 PRK00133, metG, methionyl-tRNA synthetase; Reviewed.
Length = 673
Score = 25.5 bits (57), Expect = 3.7
Identities = 5/14 (35%), Positives = 8/14 (57%)
Query: 17 RVGTVVNRERHPGS 30
RV +V E+ G+
Sbjct: 579 RVAKIVEAEKVEGA 592
>gnl|CDD|234191 TIGR03377, glycerol3P_GlpA, glycerol-3-phosphate dehydrogenase,
anaerobic, A subunit. Members of this protein family
are the A subunit, product of the glpA gene, of a
three-subunit, membrane-anchored, FAD-dependent
anaerobic glycerol-3-phosphate dehydrogenase [Energy
metabolism, Anaerobic].
Length = 516
Score = 25.0 bits (55), Expect = 4.5
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIV 34
MFP ++ + TV+NR R P DI+
Sbjct: 203 MFPAKGALLIMNHRI--NNTVINRCRKPSDADIL 234
>gnl|CDD|223151 COG0073, ARC1, EMAP domain [General function prediction only].
Length = 123
Score = 24.6 bits (54), Expect = 5.3
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 17 RVGTVVNRERHPGS 30
RVG VV E HP +
Sbjct: 22 RVGKVVEAEPHPNA 35
>gnl|CDD|237028 PRK12267, PRK12267, methionyl-tRNA synthetase; Reviewed.
Length = 648
Score = 24.8 bits (55), Expect = 6.4
Identities = 5/14 (35%), Positives = 7/14 (50%)
Query: 17 RVGTVVNRERHPGS 30
RV V+ E+ S
Sbjct: 554 RVAEVLEAEKVEKS 567
>gnl|CDD|216440 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain. This
family contains OB-fold domains that bind to nucleic
acids. The family includes the anti-codon binding
domain of lysyl, aspartyl, and asparaginyl -tRNA
synthetases (See pfam00152). Aminoacyl-tRNA synthetases
catalyze the addition of an amino acid to the
appropriate tRNA molecule EC:6.1.1.-. This family also
includes part of RecG helicase involved in DNA repair.
Replication factor A is a heterotrimeric complex, that
contains a subunit in this family. This domain is also
found at the C-terminus of bacterial DNA polymerase III
alpha chain.
Length = 75
Score = 23.8 bits (52), Expect = 7.5
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 18 VGTVVNRERHPGSFDIVHVKDGNGHV 43
G V + R G + ++DG G +
Sbjct: 4 AGRVTSVRRSGGKVAFLTLRDGTGSI 29
>gnl|CDD|178509 PLN02921, PLN02921, naphthoate synthase.
Length = 327
Score = 24.4 bits (53), Expect = 8.0
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 51 VFIIGKGTKAFCS 63
+ + GKGTKAFCS
Sbjct: 115 IILTGKGTKAFCS 127
>gnl|CDD|147785 pfam05822, UMPH-1, Pyrimidine 5'-nucleotidase (UMPH-1). This
family consists of several eukaryotic pyrimidine
5'-nucleotidase proteins. P5'N-1, also known as uridine
monophosphate hydrolase-1 (UMPH-1), is a member of a
large functional group of enzymes, characterized by the
ability to dephosphorylate nucleic acids. P5'N-1
catalyzes the dephosphorylation of pyrimidine nucleoside
monophosphates to the corresponding nucleosides.
Deficiencies in this proteins function can lead to
several different disorders in humans.
Length = 246
Score = 24.2 bits (53), Expect = 8.1
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 23 NRERHPGSFDIVHVKDG 39
N +++ S+DIV V D
Sbjct: 217 NLDKYMDSYDIVLVDDE 233
>gnl|CDD|235350 PRK05134, PRK05134, bifunctional 3-demethylubiquinone-9
3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol
methylase; Provisional.
Length = 233
Score = 24.3 bits (54), Expect = 8.2
Identities = 14/45 (31%), Positives = 16/45 (35%), Gaps = 20/45 (44%)
Query: 25 ERHPGSFDIV-------HVKD-------------GNGHVFATRLN 49
HPG FD+V HV D G VF + LN
Sbjct: 109 AEHPGQFDVVTCMEMLEHVPDPASFVRACAKLVKPGGLVFFSTLN 153
>gnl|CDD|216517 pfam01467, CTP_transf_2, Cytidylyltransferase. This family
includes: Cholinephosphate cytidylyltransferase.
Glycerol-3-phosphate cytidylyltransferase.
Length = 148
Score = 23.9 bits (52), Expect = 9.1
Identities = 11/49 (22%), Positives = 18/49 (36%), Gaps = 9/49 (18%)
Query: 28 PGSFDIVHVKDGNGHVFATR-----LNNVFIIGKGTKAFCSKPKRNFVS 71
G+FD +H GH+ + I+G + K +N S
Sbjct: 3 GGTFDPIH----LGHLRLLEQAKELFDLDKIVGVPSDESPHKDTKNLFS 47
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
0.325 0.142 0.454
Gapped
Lambda K H
0.267 0.0941 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,118,352
Number of extensions: 322003
Number of successful extensions: 342
Number of sequences better than 10.0: 1
Number of HSP's gapped: 340
Number of HSP's successfully gapped: 32
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (23.8 bits)