RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3866
(70 letters)
>gnl|CDD|233864 TIGR02432, lysidine_TilS_N, tRNA(Ile)-lysidine synthetase,
N-terminal domain. The only examples in which the
wobble position of a tRNA must discriminate between G
and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA
(stop) vs. UGG (Trp). In all bacteria, the wobble
position of the tRNA(Ile) recognizing AUA is lysidine,
a lysine derivative of cytidine. This family describes
a protein domain found, apparently, in all bacteria in
a single copy. Eukaryotic sequences appear to be
organellar. The domain archictecture of this protein
family is variable; some, including characterized
proteins of E. coli and B. subtilis known to be
tRNA(Ile)-lysidine synthetase, include a conserved
50-residue domain that many other members lack. This
protein belongs to the ATP-binding PP-loop family (
pfam01171). It appears in the literature and protein
databases as TilS, YacA, and putative cell cycle
protein MesJ (a misnomer) [Protein synthesis, tRNA and
rRNA base modification].
Length = 189
Score = 40.3 bits (95), Expect = 1e-05
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 7 KVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYID 47
++LVA SG SMALLHLL L ++ + A ++D
Sbjct: 1 RILVAVSGGVDSMALLHLL-----LKLQPKLKIRLIAAHVD 36
>gnl|CDD|223115 COG0037, MesJ, tRNA(Ile)-lysidine synthase MesJ [Cell cycle
control, cell division, chromosome partitioning].
Length = 298
Score = 39.8 bits (93), Expect = 2e-05
Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 7/44 (15%)
Query: 6 DKVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYIDDG 49
K+LVA SG S+ALLHLL+E V A+++D G
Sbjct: 22 YKILVAVSGGKDSLALLHLLKE-------LGRRIEVEAVHVDHG 58
>gnl|CDD|238950 cd01992, PP-ATPase, N-terminal domain of predicted ATPase of the
PP-loop faimly implicated in cell cycle control [Cell
division and chromosome partitioning]. This is a
subfamily of Adenine nucleotide alpha hydrolases
superfamily.Adeninosine nucleotide alpha hydrolases
superfamily includes N type ATP PPases and ATP
sulphurylases. It forms a apha/beta/apha fold which
binds to Adenosine group. This domain has a strongly
conserved motif SGGXD at the N terminus.
Length = 185
Score = 39.5 bits (93), Expect = 2e-05
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 5/41 (12%)
Query: 7 KVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYID 47
K+LVA SG SMALLHLL E R+ + A+++D
Sbjct: 1 KILVAVSGGPDSMALLHLLSE-----LKPRLGLRLVAVHVD 36
>gnl|CDD|216343 pfam01171, ATP_bind_3, PP-loop family. This family of proteins
belongs to the PP-loop superfamily.
Length = 182
Score = 36.4 bits (85), Expect = 3e-04
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 7 KVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYIDDG 49
K+LVA SG SMALL+LL + + A ++D G
Sbjct: 1 KILVAVSGGPDSMALLYLL-----KKLKPKFGIDLTAAHVDHG 38
>gnl|CDD|236737 PRK10696, PRK10696, tRNA 2-thiocytidine biosynthesis protein
TtcA; Provisional.
Length = 258
Score = 36.0 bits (84), Expect = 4e-04
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 1 MMRPQDKVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYIDDG 49
M+ D+V+V SG S LL +L + L I F + A+ +D
Sbjct: 25 MIEEGDRVMVCLSGGKDSYTLLDIL---LNLQKRAPINFELVAVNLDQK 70
>gnl|CDD|238951 cd01993, Alpha_ANH_like_II, This is a subfamily of Adenine
nucleotide alpha hydrolases superfamily.Adeninosine
nucleotide alpha hydrolases superfamily includes N
type ATP PPases and ATP sulphurylases. It forms a
apha/beta/apha fold which binds to Adenosine group.
This subfamily of proteins is predicted to bind ATP.
This domainhas a strongly conserved motif SGGKD at the
N terminus.
Length = 185
Score = 35.7 bits (83), Expect = 5e-04
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 7 KVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYIDDG 49
++LVA SG S+ LLH+L++ L F + A+ +D+G
Sbjct: 1 RILVALSGGKDSLVLLHVLKK---LQRRYPYGFELEALTVDEG 40
>gnl|CDD|182626 PRK10660, tilS, tRNA(Ile)-lysidine synthetase; Provisional.
Length = 436
Score = 34.2 bits (79), Expect = 0.002
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 13/59 (22%)
Query: 4 PQDKVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYIDDGSISQVSKSKLNPN 62
++LVAFSG S LLHLL +Q + + ++ AI++ G L+PN
Sbjct: 14 TSRQILVAFSGGLDSTVLLHLL---VQWRTENPGV-TLRAIHVHHG---------LSPN 59
>gnl|CDD|238846 cd01713, PAPS_reductase, This domain is found in phosphoadenosine
phosphosulphate (PAPS) reductase enzymes or PAPS
sulphotransferase. PAPS reductase is part of the
adenine nucleotide alpha hydrolases superfamily also
including N type ATP PPases and ATP sulphurylases. A
highly modified version of the P loop, the fingerprint
peptide of mononucleotide-binding proteins, is present
in the active site of the protein, which appears to be
a positively charged cleft containing a number of
conserved arginine and lysine residues. Although PAPS
reductase has no ATPase activity, it shows a striking
similarity to the structure of the ATP pyrophosphatase
(ATP PPase) domain of GMP synthetase, indicating that
both enzyme families have evolved from a common
ancestral nucleotide-binding fold. The enzyme uses
thioredoxin as an electron donor for the reduction of
PAPS to phospho-adenosine-phosphate (PAP) . It is also
found in NodP nodulation protein P from Rhizobium
meliloti which has ATP sulphurylase activity (sulphate
adenylate transferase) .
Length = 173
Score = 29.7 bits (67), Expect = 0.065
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 6/41 (14%)
Query: 7 KVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYID 47
V+V+FSG S LLHL + L V I++D
Sbjct: 1 NVVVSFSGGKDSTVLLHLALK------ALPELKPVPVIFLD 35
>gnl|CDD|238944 cd01986, Alpha_ANH_like, Adenine nucleotide alpha hydrolases
superfamily including N type ATP PPases and ATP
sulphurylases. The domain forms a apha/beta/apha fold
which binds to Adenosine group..
Length = 103
Score = 27.9 bits (62), Expect = 0.22
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 9/42 (21%)
Query: 8 VLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYIDDG 49
VLVAFSG S LL K++ + V A+ +D G
Sbjct: 1 VLVAFSGGKDSSVAAALL---------KKLGYQVIAVTVDHG 33
>gnl|CDD|217816 pfam03959, FSH1, Serine hydrolase (FSH1). This is a family of
serine hydrolases.
Length = 209
Score = 27.2 bits (61), Expect = 0.61
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 9 LVAFS-GSHSSMALLHLLQEGMQLSSHKRILFSVCA 43
++ FS G+ + L LL+EG+ L SH + F++
Sbjct: 104 ILGFSQGAALAAILASLLEEGLPLESHPPLKFAILI 139
>gnl|CDD|226478 COG3969, COG3969, Predicted phosphoadenosine phosphosulfate
sulfotransferase [General function prediction only].
Length = 407
Score = 27.0 bits (60), Expect = 0.64
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 6 DKVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYID 47
+V V+FSG S +LHL+ E + + +I ++ID
Sbjct: 28 PRVCVSFSGGKDSGLMLHLVAEVARENGRDKI----SVLFID 65
>gnl|CDD|223558 COG0482, TrmU, Predicted
tRNA(5-methylaminomethyl-2-thiouridylate)
methyltransferase, contains the PP-loop ATPase domain
[Translation, ribosomal structure and biogenesis].
Length = 356
Score = 25.7 bits (57), Expect = 1.8
Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 12/41 (29%)
Query: 5 QDKVLVAFSG---SHSSMALLHLLQEG-------MQLSSHK 35
+ KVLV SG S + LL ++G M+
Sbjct: 3 KKKVLVGMSGGVDSSVAAYLLK--EQGYEVIGLFMKNWDED 41
>gnl|CDD|224522 COG1606, COG1606, ATP-utilizing enzymes of the PP-loop
superfamily [General function prediction only].
Length = 269
Score = 25.4 bits (56), Expect = 2.2
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 2 MRPQDKVLVAFSGSHSSMALLHLLQE 27
++ + KV+VAFSG S L L +E
Sbjct: 14 IKEKKKVVVAFSGGVDSSLLAKLAKE 39
>gnl|CDD|213221 cd03254, ABCC_Glucan_exporter_like, ATP-binding cassette domain
of glucan transporter and related proteins, subfamily
C. Glucan exporter ATP-binding protein. In A.
tumefaciens cyclic beta-1, 2-glucan must be transported
into the periplasmic space to exert its action as a
virulence factor. This subfamily belongs to the
MRP-like family and is involved in drug, peptide, and
lipid export. The MRP-like family, similar to all ABC
proteins, have a common four-domain core structure
constituted by two membrane-spanning domains each
composed of six transmembrane (TM) helices and two
nucleotide-binding domains (NBD). ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 229
Score = 25.3 bits (56), Expect = 2.8
Identities = 8/23 (34%), Positives = 10/23 (43%)
Query: 44 IYIDDGSISQVSKSKLNPNFGSV 66
I ID I +S+ L G V
Sbjct: 60 ILIDGIDIRDISRKSLRSMIGVV 82
>gnl|CDD|173128 PRK14665, mnmA, tRNA-specific 2-thiouridylase MnmA; Provisional.
Length = 360
Score = 25.3 bits (55), Expect = 3.2
Identities = 12/33 (36%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 1 MMRPQDKVLVAFS-GSHSSMALLHLLQEGMQLS 32
MM +VL+ S G+ SS+A + LL+ G +++
Sbjct: 1 MMEKNKRVLLGMSGGTDSSVAAMLLLEAGYEVT 33
>gnl|CDD|238917 cd01942, ribokinase_group_A, Ribokinase-like subgroup A. Found in
bacteria and archaea, this subgroup is part of the
ribokinase/pfkB superfamily. Its oligomerization state
is unknown at this time.
Length = 279
Score = 25.0 bits (55), Expect = 3.2
Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 2/49 (4%)
Query: 16 HSSMALLHLLQEGMQLSSHKRIL--FSVCAIYIDDGSISQVSKSKLNPN 62
H + L L +EG+ S + + + A + DG +Q++
Sbjct: 64 HGRLYLEELREEGVDTSHVRVVDEDSTGVAFILTDGDDNQIAYFYPGAM 112
>gnl|CDD|240886 cd12440, RRM_SYNJ, RNA recognition motif in synaptojanin-1,
synaptojanin-2 and similar proteins. This subfamily
corresponds to the RRM of two active
phosphatidylinositol phosphate phosphatases,
synaptojanin-1 and synaptojanin-2. They have different
interaction partners and are likely to have different
biological functions. Synaptojanin-1 was originally
identified as one of the major Grb2-binding proteins
that may participate in synaptic vesicle endocytosis.
It also acts as a Src homology 3 (SH3) domain-binding
brain-specific inositol 5-phosphatase with a putative
role in clathrin-mediated endocytosis. Synaptojanin-2
is a ubiquitously expressed homolog of synaptojanin-1.
It is a novel Rac1 effector regulating the early step
of clathrin-mediated endocytosis. Synaptojanin-2
directly and specifically interacts with Rac1 in a
GTP-dependent manner. It mediates the inhibitory effect
of Rac1 on endocytosis and plays an important role in
the Rac1-mediated control of cell growth. Both,
synaptojanin-1 and synaptojanin-2, have two
tissue-specific alternative splicing isoforms, a
shorter isoform expressed in brain and a longer isoform
in peripheral tissues. Synaptojanin-1 contains an
N-terminal domain homologous to the cytoplasmic portion
of the yeast protein Sac1p, a central inositol
5-phosphatase domain followed by a putative RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal proline-rich region mediating the binding of
synaptojanin-1 to various SH3 domain-containing
proteins including amphiphysin, SH3p4, SH3p8, SH3p13,
and Grb2. Synaptojanin-2 shows high sequence homology
to the N-terminal Sac1p homology domain, the central
inositol 5-phosphatase domain, the putative RNA
recognition motif (RRM) of synaptojanin-1, but differs
in the proline-rich region. .
Length = 78
Score = 24.4 bits (53), Expect = 3.8
Identities = 11/33 (33%), Positives = 21/33 (63%), Gaps = 3/33 (9%)
Query: 5 QDKVLVAFSGSHSSMALLHLLQEGMQLSSHKRI 37
+ +LV F S++A+L L G+Q+ +H+R+
Sbjct: 44 HEGMLVTFRDGVSALAVLAL--SGLQI-NHRRL 73
>gnl|CDD|200016 TIGR00454, TIGR00454, TIGR00454 family protein. At this time
this gene appears to be present only in Archea
[Hypothetical proteins, Conserved].
Length = 175
Score = 24.9 bits (54), Expect = 4.1
Identities = 14/51 (27%), Positives = 25/51 (49%)
Query: 19 MALLHLLQEGMQLSSHKRILFSVCAIYIDDGSISQVSKSKLNPNFGSVCPY 69
AL+ +G +L ++ L VC + D +S + KSK+N + P+
Sbjct: 1 DALIMAGGKGTRLGGVEKPLIEVCGRCLIDHVLSPLLKSKVNNIIIATSPH 51
>gnl|CDD|213592 TIGR01179, galE, UDP-glucose-4-epimerase GalE. Alternate name:
UDPgalactose 4-epimerase This enzyme interconverts
UDP-glucose and UDP-galactose. A set of related
proteins, some of which are tentatively identified as
UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus
halodurans, and several archaea, but deeply branched
from this set and lacking experimental evidence, are
excluded from This model and described by a separate
model [Energy metabolism, Sugars].
Length = 328
Score = 24.6 bits (54), Expect = 4.4
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 25 LQEGMQLSSHKRILFS-VCAIYIDDGSISQVSKSKLNP 61
L E MQ + K+ +FS A+Y + SI S L P
Sbjct: 104 LLEAMQQAGVKKFIFSSSAAVYGEPSSIPISEDSPLGP 141
>gnl|CDD|107367 cd06372, PBP1_GC_G_like, Ligand-binding domain of membrane
guanylyl cyclase G. This group includes the
ligand-binding domain of membrane guanylyl cyclase G
(GC-G) which is a sperm surface receptor and might
function, similar to its sea urchin counterpart, in the
early signaling event that regulates the Ca2+
influx/efflux and subsequent motility response in
sperm. GC-G appears to be a pseudogene in human.
Furthermore, in contrast to the other orphan receptor
GCs, GC-G has a broad tissue distribution in rat,
including lung, intestine, kidney, and skeletal muscle.
Length = 391
Score = 24.4 bits (53), Expect = 6.0
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 48 DGSISQVSKSKLNPNFGSVCPYA 70
G I QV K ++ FG CP A
Sbjct: 58 AGFIDQVQKEHISALFGPACPEA 80
>gnl|CDD|219472 pfam07575, Nucleopor_Nup85, Nup85 Nucleoporin. A family of
nucleoporins conserved from yeast to human. THe nuclear
pore complex is a large assembly composed of two
essential complexes: the heptameric Nup84 complex and
the heteromeric Nic96-containing complex. The Nup84
complex is composed of one copy each of Nup84, Nup85,
Nup120, Nup133, Nup145C, Sec13, and Seh1. The structure
of a complex of Nup85 and Seh1 was solved. The
N-terminus of Nup85 is inserted and forms a
three-stranded blade that completes the Seh1 6-bladed
beta-propeller in trans. Following its N-terminal
insertion blade, Nup85 forms a compact cuboid structure
composed of 20 helices, with two distinct modules,
referred to as crown and trunk.
Length = 564
Score = 23.8 bits (52), Expect = 8.6
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 17 SSMALLHLLQEGMQLSSHKRILFSVCAIYID 47
+M LL+ L SHK L+ V Y+D
Sbjct: 352 INMREFLLLEYASVLMSHKS-LWQVAIDYLD 381
>gnl|CDD|217035 pfam02441, Flavoprotein, Flavoprotein. This family contains
diverse flavoprotein enzymes. This family includes
epidermin biosynthesis protein, EpiD, which has been
shown to be a flavoprotein that binds FMN. This enzyme
catalyzes the removal of two reducing equivalents from
the cysteine residue of the C-terminal meso-lanthionine
of epidermin to form a --C==C-- double bond. This
family also includes the B chain of dipicolinate
synthase a small polar molecule that accumulates to
high concentrations in bacterial endospores, and is
thought to play a role in spore heat resistance, or the
maintenance of heat resistance. dipicolinate synthase
catalyzes the formation of dipicolinic acid from
dihydroxydipicolinic acid. This family also includes
phenyl-acrylic acid decarboxylase (EC:4.1.1.-).
Length = 132
Score = 23.7 bits (52), Expect = 9.0
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 7 KVLVAFSGSHSSMALLHLLQE 27
K+L+ +GS +++ L LL+E
Sbjct: 2 KILLGITGSSAAIKALRLLRE 22
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
0.322 0.132 0.383
Gapped
Lambda K H
0.267 0.0717 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,304,447
Number of extensions: 230186
Number of successful extensions: 243
Number of sequences better than 10.0: 1
Number of HSP's gapped: 242
Number of HSP's successfully gapped: 23
Length of query: 70
Length of database: 10,937,602
Length adjustment: 40
Effective length of query: 30
Effective length of database: 9,163,442
Effective search space: 274903260
Effective search space used: 274903260
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.2 bits)