RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14055
(493 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 = 150 bits (380), Expect = 2e-41
Identities = 64/146 (43%), Positives = 81/146 (55%), Gaps = 29/146 (19%)
Query: 181 ICTRFDFLGHRQQYLCTLNENILNVYLIVCVLIKYQQVDLIRSTRQVYVYLTVVAAGARM 240
IC++ L +Q+ LC N D++ S V GAR+
Sbjct: 1 ICSKLPGLSRKQRRLCRRNP------------------DVMAS----------VGEGARL 32
Query: 241 GIEECQNQFKMSRWNCTTFGNTSQVFGSVLTFKSRETAFVYAISSAGVAYAVTRACSRGE 300
GIEECQ+QF+ RWNC+T + S VFG +L +RETAFVYAISSAGV +AVTRACS G
Sbjct: 33 GIEECQHQFRNRRWNCSTLDS-SSVFGKILKRGTRETAFVYAISSAGVVHAVTRACSEGN 91
Query: 301 LNECSCDNRVRLKKPRTSWQWGGCSE 326
L C CD R + W+WGGCS+
Sbjct: 92 LESCGCDRSRRGRSGPGGWEWGGCSD 117
Score = 123 bits (310), Expect = 1e-31
Identities = 53/139 (38%), Positives = 66/139 (47%), Gaps = 35/139 (25%)
Query: 339 IVVNNQRKRNVKRLRSAVRDAKQPNRTELVYMEESPDYCQRNETRVRLWRDIHFGEKFSR 398
I V + +RL +K P T+LVY+E+SPDYC+RN + G +
Sbjct: 199 IKVEVNNRGKRRRLVRKNPKSKPPTSTDLVYLEDSPDYCERNPSLG------SLGTR--- 249
Query: 399 DFVDSKEDEDSEEALMNLHNNEAGR---RRSLGLDGCKLLCCGRGYMTRIREVEEKCNCK 455
GR + S G DGC LLCCGRGY TR V E+CNCK
Sbjct: 250 -----------------------GRECNKTSSGTDGCDLLCCGRGYNTRTVVVVERCNCK 286
Query: 456 FVWCCNVKCEICRYKREEY 474
F WCC VKC+ CR + E Y
Sbjct: 287 FHWCCYVKCKTCRERVEVY 305
Score = 63.8 bits (156), Expect = 4e-11
Identities = 21/36 (58%), Positives = 28/36 (77%)
Query: 389 DIHFGEKFSRDFVDSKEDEDSEEALMNLHNNEAGRR 424
+I FG +FSR+F+D++E ALMNLHNNEAGR+
Sbjct: 118 NIKFGIRFSREFLDARERGRDARALMNLHNNEAGRK 153
>gnl|CDD|128408 smart00097, WNT1, found in Wnt-1.
Length = 305
Score = 141 bits (357), Expect = 3e-38
Identities = 62/102 (60%), Positives = 73/102 (71%), Gaps = 1/102 (0%)
Query: 230 YLTVVAAGARMGIEECQNQFKMSRWNCTTFGNTSQVFGSVLTFKSRETAFVYAISSAGVA 289
+ VA GA+ GIEECQ+QF+ RWNC+T N S VFG VL +RETAFVYAISSAGVA
Sbjct: 19 VMISVAEGAQEGIEECQHQFRFRRWNCSTLDNAS-VFGKVLRQGTRETAFVYAISSAGVA 77
Query: 290 YAVTRACSRGELNECSCDNRVRLKKPRTSWQWGGCSERFDRG 331
+AVTRACS GEL+ C CD R R + W+WGGCS+ D G
Sbjct: 78 HAVTRACSEGELDSCGCDYRKRGRAGGRGWKWGGCSDNIDFG 119
Score = 108 bits (271), Expect = 2e-26
Identities = 54/153 (35%), Positives = 68/153 (44%), Gaps = 42/153 (27%)
Query: 326 ERFDRGNCNRYGLIVVNNQRKRNVKRLRSAVRDAKQPNRTELVYMEESPDYCQRNETRVR 385
E++D V ++R N K K P T+LVY+E SPD+C++N
Sbjct: 190 EKYDGA------SEVEVDKRGTN-KAPVPKNSTFKPPTETDLVYLESSPDFCEKNPKTGS 242
Query: 386 LWRDIHFGEKFSRDFVDSKEDEDSEEALMNLHNNEAGR---RRSLGLDGCKLLCCGRGYM 442
L GR + S GLDGC LLCCGRGY
Sbjct: 243 L--------------------------------GTQGRQCNKTSKGLDGCDLLCCGRGYN 270
Query: 443 TRIREVEEKCNCKFVWCCNVKCEICRYKREEYL 475
TR EV E+CNCKF WCC VKC+ CR E++
Sbjct: 271 TRTVEVVERCNCKFHWCCYVKCKQCRETVEKHT 303
Score = 55.8 bits (135), Expect = 1e-08
Identities = 22/36 (61%), Positives = 27/36 (75%)
Query: 389 DIHFGEKFSRDFVDSKEDEDSEEALMNLHNNEAGRR 424
+I FG +FSR+FVD++E ALMNLHNNEAGR
Sbjct: 115 NIDFGIRFSREFVDARERGKDARALMNLHNNEAGRL 150
>gnl|CDD|218676 pfam05649, Peptidase_M13_N, Peptidase family M13. M13 peptidases
are well-studied proteases found in a wide range of
organisms including mammals and bacteria. In mammals
they participate in processes such as cardiovascular
development, blood-pressure regulation, nervous control
of respiration, and regulation of the function of
neuropeptides in the central nervous system. In bacteria
they may be used for digestion of milk.
Length = 380
Score = 55.8 bits (135), Expect = 2e-08
Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 8/76 (10%)
Query: 25 ETIESQGVEPLTSILDSLGGWPLISPAWTPAQFDMNRLFAQSIRRWSVHHLFSVFVNVDR 84
+ IE G++PL +L +G ++FD+ A+ R S LF V+ D
Sbjct: 70 DAIEKLGLKPLKPLLKKIGAIK--------SKFDLADALAKLERGGSNGPLFGFGVSPDF 121
Query: 85 SDSSQKNVHFGSGATS 100
+SS+ ++ G
Sbjct: 122 KNSSRNILYLSQGGLG 137
>gnl|CDD|117586 pfam09020, YopE_N, YopE, N terminal. The N terminal YopE domain
targets YopE for secretion from the bacterium and
translocation into eukaryotic cells.
Length = 126
Score = 32.6 bits (73), Expect = 0.13
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 11/71 (15%)
Query: 16 GGRVFNPSQETIESQGVEPLTSILDSLGGW-----------PLISPAWTPAQFDMNRLFA 64
GR +P ++ S+ +E L+S+ S + P+++PA TPAQ F+
Sbjct: 44 AGRTESPQGSSLASRIIEKLSSMAHSAIEFIKRMFSEGSHKPVVTPAPTPAQMPSPTSFS 103
Query: 65 QSIRRWSVHHL 75
SI++ + L
Sbjct: 104 DSIKQLAAETL 114
>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33)
and similar proteins. This subfamily corresponds to the
RRM of Cyp33, also termed peptidyl-prolyl cis-trans
isomerase E (PPIase E), or cyclophilin E, or rotamase E.
Cyp33 is a nuclear RNA-binding cyclophilin with an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal PPIase domain. Cyp33 possesses
RNA-binding activity and preferentially binds to
polyribonucleotide polyA and polyU, but hardly to polyG
and polyC. It binds specifically to mRNA, which can
stimulate its PPIase activity. Moreover, Cyp33 interacts
with the third plant homeodomain (PHD3) zinc finger
cassette of the mixed lineage leukemia (MLL)
proto-oncoprotein and a poly-A RNA sequence through its
RRM domain. It further mediates downregulation of the
expression of MLL target genes HOXC8, HOXA9, CDKN1B, and
C-MYC, in a proline isomerase-dependent manner. Cyp33
also possesses a PPIase activity that catalyzes
cis-trans isomerization of the peptide bond preceding a
proline, which has been implicated in the stimulation of
folding and conformational changes in folded and
unfolded proteins. The PPIase activity can be inhibited
by the immunosuppressive drug cyclosporin A. .
Length = 73
Score = 28.3 bits (64), Expect = 1.5
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 400 FVDSKEDEDSEEALMNLHNNE 420
FV+ +E ED+ A+ N++ +E
Sbjct: 44 FVEFEEPEDAAAAIDNMNESE 64
>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 = 30.6 bits (69), Expect = 2.0
Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 3/71 (4%)
Query: 339 IVVNNQRKRNVKRLRSAVRDAKQPNRTELVYMEESPDYCQRNETRVRLWRDIHF---GEK 395
I+ N +K +KRLR AV +K+P +V E + V + I + G+K
Sbjct: 111 IIKQNWKKWQLKRLREAVEISKRPKTAAVVMEEGIAHVGLVRQYSVEEIQKIEYHMPGKK 170
Query: 396 FSRDFVDSKED 406
+ F + +++
Sbjct: 171 RTLKFGELRKE 181
>gnl|CDD|224317 COG1399, COG1399, Predicted metal-binding, possibly nucleic
acid-binding protein [General function prediction only].
Length = 176
Score = 29.7 bits (67), Expect = 2.4
Identities = 17/82 (20%), Positives = 26/82 (31%), Gaps = 14/82 (17%)
Query: 350 KRLRSAVRDAKQPNR--------TELVYME-----ESPDYCQRNETRVRLWRDIHFGEKF 396
R+ V D +LV ++ E CQR V D+ E F
Sbjct: 32 TRVGEEVIDVDPGVVVGVSAYAEIDLVVLDGQVSAEVTLECQRCLEPVEYPLDVTVTELF 91
Query: 397 SR-DFVDSKEDEDSEEALMNLH 417
R D +E + +E +
Sbjct: 92 VRPDEQADEEPLEDDEVEVIED 113
>gnl|CDD|188093 TIGR00864, PCC, polycystin cation channel protein. The Polycystin
Cation Channel (PCC) Family (TC 1.A.5) Polycystin is a
huge protein of 4303aas. Its repeated leucine-rich (LRR)
segment is found in many proteins. It contains 16
polycystic kidney disease (PKD) domains, one LDL-receptor
class A domain, one C-type lectin family domain, and
16-18 putative TMSs in positions between residues 2200
and 4100. Polycystin-L has been shown to be a cation
(Na+, K+ and Ca2+) channel that is activated by Ca2+. Two
members of the PCC family (polycystin 1 and 2) are
mutated in autosomal dominant polycystic kidney disease,
and polycystin-L is deleted in mice with renal and
retinal defects. Note: this model is restricted to the
amino half for technical reasons.
Length = 2740
Score = 30.4 bits (68), Expect = 2.8
Identities = 20/67 (29%), Positives = 25/67 (37%), Gaps = 10/67 (14%)
Query: 205 VYLIVCVLIKYQQVDLIRSTRQVYVYLTVVAAGARMGIEECQNQFKMSRWNCTTFGNTSQ 264
V L CV K Q + ++ YVYL CQ+ F RW TF N +
Sbjct: 2363 VSL-ECVSCKAQAL--YEVSQNSYVYL-------EGRCLNCQSGFHRGRWAARTFQNDTL 2412
Query: 265 VFGSVLT 271
V T
Sbjct: 2413 VLDESST 2419
>gnl|CDD|143475 cd06567, Peptidase_S41, C-terminal processing peptidase family S41.
Peptidase family S41 (C-terminal processing peptidase
or CTPase family) contains very different subfamilies;
it includes photosystem II D1 C-terminal processing
protease (CTPase), interphotoreceptor retinoid-binding
protein IRBP and tricorn protease (TRI). CTPase and TRI
both contain the PDZ domain while IRBP, although being
very similar to the tail-specific protease domain, lacks
the PDZ insertion domain and hydrolytic activity. These
serine proteases have distinctly different active sites:
in CTPase, the active site consists of a serine/lysine
catalytic dyad while in tricorn core protease, it is a
tetrad (serine, histidine, serine, glutamate). CPases
with different substrate specificities in different
species include processing of D1 protein of the
photosystem II reaction center in higher plants and
cleavage of a peptide of 11 residues from the precursor
form of penicillin-binding protein; and others such as
tricorn protease (TRI) act as a carboxypeptidase,
involved in the degradation of proteasomal products.
CTPase homolog IRBP, secreted by photoreceptors into the
interphotoreceptor matrix, having arisen in the early
evolution of the vertebrate eye, promotes the release of
all-trans retinol from photoreceptors and facilitates
its delivery to the retinal pigment epithelium.
Length = 224
Score = 29.2 bits (66), Expect = 4.0
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 13 WLTGGRVFNPSQETIESQGVEP 34
LT + + PS +IE +GVEP
Sbjct: 198 KLTTAKYYTPSGRSIEGKGVEP 219
>gnl|CDD|235921 PRK07056, PRK07056, amidase; Provisional.
Length = 454
Score = 29.1 bits (66), Expect = 6.0
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 10 ALAWLTGGRVFNPSQETIESQGVEPLTSILDSLG 43
AL LTG F P+ + QG PL++ LDS+G
Sbjct: 190 ALCGLTG---FKPTARRVPLQGAVPLSTTLDSIG 220
>gnl|CDD|179286 PRK01368, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 454
Score = 29.0 bits (65), Expect = 6.6
Identities = 16/36 (44%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 169 CDIIAV--KDILKDICTRFDFLGHRQQYLCTLNENI 202
II V K IL+ I + F L HR QY+ ++N NI
Sbjct: 287 AKIIGVEPKKILESI-SSFQSLPHRMQYIGSIN-NI 320
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 0.135 0.424
Gapped
Lambda K H
0.267 0.0678 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,548,692
Number of extensions: 2325498
Number of successful extensions: 1817
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1813
Number of HSP's successfully gapped: 19
Length of query: 493
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 392
Effective length of database: 6,457,848
Effective search space: 2531476416
Effective search space used: 2531476416
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 (22.0 bits)
S2: 61 (27.4 bits)