RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2958
(129 letters)
>gnl|CDD|215724 pfam00110, wnt, wnt family. Wnt genes have been identified in
vertebrates and invertebrates but not in plants,
unicellular eukaryotes or prokaryotes. In humans, 19 WNT
proteins are known. Because of their insolubility little
is known about Wnt protein structure, but all have 23 or
24 Cys residues whose spacing is highly conserved.
Signal transduction by Wnt proteins (including the
Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity
pathway) is mediated by receptors of the Frizzled and
LDL-receptor-related protein (LRP) families.
Length = 308
Score = 110 bits (278), Expect = 1e-30
Identities = 44/113 (38%), Positives = 62/113 (54%), Gaps = 25/113 (22%)
Query: 1 MQRVCKCHGMSGSCSVKVCWKRLPSFQQVGDILASRYEGAYFVKQVGDILASRYEGAYFV 60
M+ CKCHG+SGSC++K CWK+LP F++VGD+L +Y+GA
Sbjct: 159 MKTECKCHGVSGSCTLKTCWKQLPDFREVGDLLKEKYDGA-------------------- 198
Query: 61 KVVNNQRKRNVKRLRSAVRDAKQPNRTELVYMEESPDYCQRNETG-----RGR 108
V + +RL +K P T+LVY+E+SPDYC+RN + RGR
Sbjct: 199 IKVEVNNRGKRRRLVRKNPKSKPPTSTDLVYLEDSPDYCERNPSLGSLGTRGR 251
>gnl|CDD|128408 smart00097, WNT1, found in Wnt-1.
Length = 305
Score = 98.2 bits (245), Expect = 8e-26
Identities = 41/104 (39%), Positives = 57/104 (54%), Gaps = 20/104 (19%)
Query: 1 MQRVCKCHGMSGSCSVKVCWKRLPSFQQVGDILASRYEGAYFVKQVGDILASRYEGAYFV 60
M+R CKCHG+SGSC+VK CW +LP F++VGD L +Y+GA
Sbjct: 156 MKRECKCHGVSGSCTVKTCWLQLPDFRKVGDYLKEKYDGA-------------------S 196
Query: 61 KVVNNQRKRNVKRLRSAVRDAKQPNRTELVYMEESPDYCQRNET 104
+V ++R N K K P T+LVY+E SPD+C++N
Sbjct: 197 EVEVDKRGTN-KAPVPKNSTFKPPTETDLVYLESSPDFCEKNPK 239
>gnl|CDD|198395 cd10448, GIY-YIG_unchar_3, GIY-YIG domain of uncharacterized
hypothetical protein found in bacteria. The family
includes a group of uncharacterized bacterial proteins
with a GIY-YIG domain that shows statistically
significant similarity to the N-terminal catalytic
domains of GIY-YIG family of intron-encoded homing
endonuclease I-TevI and catalytic GIY-YIG domain of
nucleotide excision repair endonuclease UvrC.
Length = 87
Score = 27.5 bits (62), Expect = 0.90
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 49 ILASRYEGAYFVKVVNNQRKRNVKRLRSAVRD--AKQPNRTELVYMEESPD 97
ILA++ G ++ V ++ +R + + + + N T LVY EE D
Sbjct: 5 ILANKRNGTLYIGVTSDLIRR-IYEHKEGLGSGFTSKYNVTRLVYYEEFED 54
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 28.4 bits (64), Expect = 1.1
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 24 PSFQQVGDILASRYEGAYFV 43
P F+ V + EGAYFV
Sbjct: 69 PLFEDVAPEIVELLEGAYFV 88
>gnl|CDD|218984 pfam06314, ADC, Acetoacetate decarboxylase (ADC). This family
consists of several acetoacetate decarboxylase (ADC)
proteins (EC:4.1.1.4).
Length = 240
Score = 27.7 bits (62), Expect = 1.5
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 70 NVKRLRSAVRDAKQPNRTELVYMEESPDYCQRNETGRGRSDLFPEP 115
N+K + S D P+ ELV + S + TG +LFP
Sbjct: 163 NLKIIPS--VDGGGPDVCELVRYQLSDVGVKEAWTGPASLELFPSA 206
>gnl|CDD|223081 COG0002, ArgC, Acetylglutamate semialdehyde dehydrogenase [Amino
acid transport and metabolism].
Length = 349
Score = 27.6 bits (62), Expect = 1.9
Identities = 8/36 (22%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 9 GMSGSCSVKVCWKRLPSFQQVGDILASRYEGAYFVK 44
G+ + +K+ K L + +++ Y G FV+
Sbjct: 244 GILATIYLKL--KDLVTLEELHAAYEEFYAGEPFVR 277
>gnl|CDD|117729 pfam09175, DUF1944, Domain of unknown function (DUF1944). Members
of this family adopt a structure consisting of several
large open beta-sheets. Their exact function has not, as
yet, been determined.
Length = 165
Score = 27.2 bits (61), Expect = 2.0
Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 16/67 (23%)
Query: 7 CHGMSGSCSVKVCWKRLPSFQQVGDILASRYEGAYFVKQVGDILASRYEGAYFVKVVNNQ 66
G + +KV W+RLPS +K+ ++ GA F+ + +
Sbjct: 82 LVGSKPAARLKVAWERLPS----------------SLKRYAKRVSEYIPGAAFLLGFSQK 125
Query: 67 RKRNVKR 73
+++N +R
Sbjct: 126 KEKNPER 132
>gnl|CDD|165863 PLN02219, PLN02219, probable galactinol--sucrose
galactosyltransferase 2.
Length = 775
Score = 27.7 bits (61), Expect = 2.0
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 38 EGAYFVKQVGDILASRYEGAYFVKVVNNQRKRNVKRLRSAVRDAKQPNRTELVYM 92
EGA F ++ I E A F K N+Q+ V L+ V DAKQ + + VY+
Sbjct: 257 EGAQFATRLTGI----KENAKFQK--NDQKNEQVSGLKHVVDDAKQRHNVKQVYV 305
>gnl|CDD|99950 cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfamily, specific to
fungi. SNF2 is a yeast protein involved in
transcriptional activation, it is the catalytic
component of the SWI/SNF ATP-dependent chromatin
remodeling complex. The protein is essential for the
regulation of gene expression (both positive and
negative) of a large number of genes. The SWI/SNF
complex changes chromatin structure by altering
DNA-histone contacts within the nucleosome, which
results in a re-positioning of the nucleosome and
facilitates or represses the binding of gene-specific
transcription factors. Bromodomains are 110 amino acid
long domains, that are found in many chromatin
associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 103
Score = 26.5 bits (59), Expect = 2.4
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 101 RNETGRGRSDLFPEPSSSNRPPNFLLCI 128
+ETGR S+LF E S P++ + I
Sbjct: 16 EDETGRKLSELFLEKPSKKLYPDYYVII 43
>gnl|CDD|188840 cd09456, LIM2_Enigma, The second LIM domain of Enigma. The second
LIM domain of Enigma: Enigma was initially characterized
in humans as a protein containing three LIM domains at
the C-terminus and a PDZ domain at N-terminus. The
third LIM domain specifically interacts with the insulin
receptor and the second LIM domain interacts with the
receptor tyrosine kinase Ret and the adaptor protein
APS. Thus Enigma is implicated in signal transduction
processes, such as mitogenic activity, insulin related
actin organization, and glucose metabolism. Enigma is
expressed in multiple tissues, such as skeletal muscle,
heart, bone and brain. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 25.7 bits (56), Expect = 2.5
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 82 KQPNRTELVYMEESPDYCQRN 102
K P R YMEE YC+R+
Sbjct: 31 KTPIRNRAFYMEEGAPYCERD 51
>gnl|CDD|222689 pfam14335, DUF4391, Domain of unknown function (DUF4391). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and archaea.
Proteins in this family are typically between 220 and
257 amino acids in length.
Length = 221
Score = 26.8 bits (60), Expect = 3.0
Identities = 18/83 (21%), Positives = 30/83 (36%), Gaps = 14/83 (16%)
Query: 16 VKVCWKR---LPSFQQVGDILASRYEGAYFVKQVGDILASRYEGAYFVKVVNNQRKR--- 69
W L G L + YE V Q+ + AS G Y + + + +R
Sbjct: 126 FATPWAFLDSLSLSLFSGLNLDALYES--IVNQIIKLNASSNTGVYEKEDLKERVERLEQ 183
Query: 70 ------NVKRLRSAVRDAKQPNR 86
+ +L+ ++ KQ NR
Sbjct: 184 IEELEKEIAKLKKKLKKEKQFNR 206
>gnl|CDD|129217 TIGR00111, pelota, mRNA surveillance protein pelota. This model
describes the Drosophila protein Pelota, the budding
yeast protein DOM34 which it can replace, and a set of
closely related archaeal proteins. Members contain a
proposed RNA binding motif. The meiotic defect in pelota
mutants may be a complex result of a protein translation
defect, as suggested in yeast by ribosomal protein
RPS30A being a multicopy suppressor and by an altered
polyribosome profile in DOM34 mutants rescued by RPS30A.
This family is homologous to a family of peptide chain
release factors. Pelota is proposed to act in protein
translation [Protein synthesis, Translation factors].
Length = 351
Score = 27.1 bits (60), Expect = 3.3
Identities = 12/36 (33%), Positives = 17/36 (47%)
Query: 64 NNQRKRNVKRLRSAVRDAKQPNRTELVYMEESPDYC 99
N +K +KRLR AV +K+P +V E
Sbjct: 114 QNWKKWQLKRLREAVEISKRPKTAAVVMEEGIAHVG 149
>gnl|CDD|212510 cd11724, TP_methylase_like, Uncharacterized subfamily of S-AdoMet
dependent tetrapyrrole methylases. TP-methylases use
S-AdoMet (S-adenosyl-L-methionine or SAM) in the
methylation of diverse substrates. Most members catalyze
various methylation steps in cobalamin (vitamin B12)
biosynthesis, other members like Diphthine synthase and
Ribosomal RNA small subunit methyltransferase I (RsmI)
act on other substrates. The function of this subfamily
is not known.
Length = 255
Score = 26.1 bits (58), Expect = 5.1
Identities = 11/43 (25%), Positives = 18/43 (41%)
Query: 41 YFVKQVGDILASRYEGAYFVKVVNNQRKRNVKRLRSAVRDAKQ 83
Y K ++ A + F + QR+ VK +R A+ K
Sbjct: 60 YGGKPWENLEAEKSPREAFEEEKKRQREEFVKVIREALAQGKN 102
>gnl|CDD|226288 COG3765, WzzB, Chain length determinant protein [Cell envelope
biogenesis, outer membrane].
Length = 347
Score = 26.3 bits (58), Expect = 5.8
Identities = 13/68 (19%), Positives = 25/68 (36%), Gaps = 12/68 (17%)
Query: 65 NQRKRNVKRLRSAVRDAKQPNRTELVYME-----ESPDYC-------QRNETGRGRSDLF 112
Q+ +++L+ A++ A + V + PD+ R E + D+F
Sbjct: 213 AQKDVRIQQLKEALKIANAAGIKKPVTSNGQDVTDDPDFLLGSDALEARLENEKAVPDVF 272
Query: 113 PEPSSSNR 120
NR
Sbjct: 273 ELNYLQNR 280
>gnl|CDD|225063 COG2152, COG2152, Predicted glycosylase [Carbohydrate transport and
metabolism].
Length = 314
Score = 26.2 bits (58), Expect = 6.4
Identities = 6/48 (12%), Positives = 13/48 (27%)
Query: 77 AVRDAKQPNRTELVYMEESPDYCQRNETGRGRSDLFPEPSSSNRPPNF 124
+D R ++ ++ D + G+ L P
Sbjct: 125 VTKDFLNWERIGAIFPPDNKDAALFPKKINGKYALLHRPVLGEYGMKG 172
>gnl|CDD|215134 PLN02242, PLN02242, methionine gamma-lyase.
Length = 418
Score = 25.9 bits (57), Expect = 6.7
Identities = 23/98 (23%), Positives = 39/98 (39%), Gaps = 32/98 (32%)
Query: 5 CKCHGMSGSCSV--KVCWKRLPSFQQVGDILASR--YEGAY-----FVKQVGDILASRYE 55
C GMS SV ++C G ++AS Y G + F+ + +I +
Sbjct: 96 CTASGMSAISSVLLQLC-------SSGGHVVASNTLYGGTHALLAHFLPRKCNITTT--- 145
Query: 56 GAYFVKVVNNQRKRNVKRLRSAVRDAKQPNRTELVYME 93
FV + + AV+ A P +T+++Y E
Sbjct: 146 ---FVDITDL----------EAVKKAVVPGKTKVLYFE 170
>gnl|CDD|131827 TIGR02780, TrbJ_Ti, P-type conjugative transfer protein TrbJ. The
TrbJ protein is found in the trb locus of Agrobacterium
Ti plasmids where it is involved in the type IV
secretion system for plasmid conjugative transfer. TrbJ
is a homolog of the F-type TraE protein (which is
believed to be an inner membrane pore-forming protein,
TIGR02761) as well as the vir system VirB5 protein.
Length = 246
Score = 25.9 bits (57), Expect = 7.5
Identities = 15/69 (21%), Positives = 27/69 (39%), Gaps = 4/69 (5%)
Query: 20 WKRLPS-FQQVGDILASRYEGAYFVKQVGDILASRYEGAYFVKVVNNQRKRNVKRLRSAV 78
W RL S Q++ +I++ AY + + DI + Y+G + + + A
Sbjct: 77 WNRLESSLQKLTNIISQAQALAYDIANLDDIFSQLYQGYDSYA---ASSGSDRQNMSDAY 133
Query: 79 RDAKQPNRT 87
Q R
Sbjct: 134 ARWAQTTRD 142
>gnl|CDD|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like
family. The second LIM domain of Enigma-like family:
The Enigma LIM domain family is comprised of three
members: Enigma, ENH, and Cypher (mouse)/ZASP (human).
These subfamily members contain a single PDZ domain at
the N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone and brain. The third LIM domain specifically
interacts with the insulin receptor and the second LIM
domain interacts with the receptor tyrosine kinase Ret
and the adaptor protein APS. Thus Enigma is implicated
in signal transduction processes, such as mitogenic
activity, insulin related actin organization, and
glucose metabolism. The second member, ENH protein, was
first identified in rat brain. It has been shown that
ENH interacts with protein kinase D1 (PKD1) via its LIM
domains and forms a complex with PKD1 and the alpha1C
subunit of cardiac L-type voltage-gated calcium channel
in rat neonatal cardiomyocytes. The N-terminal PDZ
domain interacts with alpha-actinin at the Z-line.
ZASP/Cypher is required for maintenance of Z-line
structure during muscle contraction, but not required
for Z-line assembly. In heart, Cypher/ZASP plays a
structural role through its interaction with
cytoskeletal Z-line proteins. In addition, there is
increasing evidence that Cypher/ZASP also performs
signaling functions. Studies reveal that Cypher/ZASP
interacts with and directs PKC to the Z-line, where PKC
phosphorylates downstream signaling targets. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 24.4 bits (53), Expect = 7.5
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 82 KQPNRTELVYMEESPDYCQRN 102
KQP L +ME+ YC+++
Sbjct: 31 KQPIGNSLFHMEDGEPYCEKD 51
>gnl|CDD|223098 COG0019, LysA, Diaminopimelate decarboxylase [Amino acid transport
and metabolism].
Length = 394
Score = 25.7 bits (57), Expect = 7.7
Identities = 13/43 (30%), Positives = 16/43 (37%), Gaps = 7/43 (16%)
Query: 22 RLPSFQQVGDILASRYEGAY-FVKQVGDILASRYEGAYFVKVV 63
LP +VGD+L GAY +S Y G V
Sbjct: 356 ALPEPLKVGDLLVILDAGAYGASM------SSNYNGRPRPAEV 392
>gnl|CDD|172862 PRK14386, PRK14386, hypothetical protein; Provisional.
Length = 106
Score = 25.0 bits (54), Expect = 9.2
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 2 QRVCKCH--GMSGSCSVKVCWKRLPSFQQV 29
+R+C+CH G SG V R SF Q+
Sbjct: 52 KRICRCHPWGGSGYDPVPPKAIRFISFHQI 81
>gnl|CDD|233597 TIGR01850, argC, N-acetyl-gamma-glutamyl-phosphate reductase,
common form. This model represents the more common of
two related families of
N-acetyl-gamma-glutamyl-phosphate reductase, an enzyme
catalyzing the third step or Arg biosynthesis from Glu.
The two families differ by phylogeny, similarity
clustering, and the gap architecture in a multiple
sequence alignment. Bacterial members of this family
tend to be found within Arg biosynthesis operons [Amino
acid biosynthesis, Glutamate family].
Length = 346
Score = 25.6 bits (57), Expect = 9.2
Identities = 4/24 (16%), Positives = 9/24 (37%)
Query: 44 KQVGDILASRYEGAYFVKVVNNQR 67
+ + + Y FV+V+
Sbjct: 257 EDLRALYEEFYADEPFVRVLPEGG 280
>gnl|CDD|233695 TIGR02037, degP_htrA_DO, periplasmic serine protease, Do/DeqQ
family. This family consists of a set proteins various
designated DegP, heat shock protein HtrA, and protease
DO. The ortholog in Pseudomonas aeruginosa is designated
MucD and is found in an operon that controls mucoid
phenotype. This family also includes the DegQ (HhoA)
paralog in E. coli which can rescue a DegP mutant, but
not the smaller DegS paralog, which cannot. Members of
this family are located in the periplasm and have
separable functions as both protease and chaperone.
Members have a trypsin domain and two copies of a PDZ
domain. This protein protects bacteria from thermal and
other stresses and may be important for the survival of
bacterial pathogens.// The chaperone function is
dominant at low temperatures, whereas the proteolytic
activity is turned on at elevated temperatures [Protein
fate, Protein folding and stabilization, Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 428
Score = 25.6 bits (57), Expect = 9.5
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 10/45 (22%)
Query: 45 QVGDILASRYEGAYFVKVVNNQRKRNVKRLRSAVRDAKQPNRTEL 89
Q GD++ S VN Q +V LR + AK+ R L
Sbjct: 381 QPGDVILS----------VNQQPVSSVAELRKVLARAKKGGRVAL 415
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
0.321 0.135 0.417
Gapped
Lambda K H
0.267 0.0725 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,294,867
Number of extensions: 529931
Number of successful extensions: 448
Number of sequences better than 10.0: 1
Number of HSP's gapped: 443
Number of HSP's successfully gapped: 29
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
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)