RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17326
(264 letters)
>gnl|CDD|214531 smart00135, LY, Low-density lipoprotein-receptor YWTD domain.
Type "B" repeats in low-density lipoprotein (LDL)
receptor that plays a central role in mammalian
cholesterol metabolism. Also present in a variety of
molecules similar to gp300/megalin.
Length = 43
Score = 53.4 bits (129), Expect = 5e-10
Identities = 17/42 (40%), Positives = 27/42 (64%)
Query: 8 TIISTKIYWPNGLTLDIATRRVYFAESKLDFIDFCNYDGTSR 49
T++S+ + PNGL +D R+Y+ + LD I+ N DGT+R
Sbjct: 2 TLLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 28.7 bits (65), Expect = 0.38
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 73 HPHSLTI--FEDTLYWTDRQLNRVLSAHKFRGKN 104
HP+ L + E LYWTD L+ + A G N
Sbjct: 10 HPNGLAVDWIEGRLYWTDWGLDVIEVA-NLDGTN 42
>gnl|CDD|163639 cd07396, MPP_Nbla03831, Homo sapiens Nbla03831 and related
proteins, metallophosphatase domain. Nbla03831 (also
known as LOC56985) is an uncharacterized Homo sapiens
protein with a domain that belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 267
Score = 33.0 bits (76), Expect = 0.10
Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 13/69 (18%)
Query: 37 DFIDFCNYDGTSRQQDTLYWTDRQLN-------RVVAGSHYLLHPHSLTIFEDTLYWTDR 89
F+D+ G +Q L W +L +V+ SH+ LHP S L W
Sbjct: 152 RFVDWNG--GIGEEQ--LQWLRNELQEADANGEKVIIFSHFPLHPES--TSPHGLLWNHE 205
Query: 90 QLNRVLSAH 98
++ +L A+
Sbjct: 206 EVLSILRAY 214
>gnl|CDD|215683 pfam00058, Ldl_recept_b, Low-density lipoprotein receptor repeat
class B. This domain is also known as the YWTD motif
after the most conserved region of the repeat. The YWTD
repeat is found in multiple tandem repeats and has been
predicted to form a beta-propeller structure.
Length = 42
Score = 29.8 bits (68), Expect = 0.12
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 82 DTLYWTDRQLNRVLSAHKFRGKNQ-TVVSHLISQPLSIHVHH 122
LYWTD L +S G ++ T+ S + P I V
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIAVDP 42
Score = 29.4 bits (67), Expect = 0.16
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 1 MDESSRSTIISTKIYWPNGLTLDI 24
++ S R T+ S + WPNG+ +D
Sbjct: 19 LNGSDRRTLFSEDLQWPNGIAVDP 42
>gnl|CDD|221695 pfam12662, cEGF, Complement Clr-like EGF-like. cEGF, or complement
Clr-like EGF, domains have six conserved cysteine
residues disulfide-bonded into the characteristic
pattern 'ababcc'. They are found in blood coagulation
proteins such as fibrillin, Clr and Cls, thrombomodulin,
and the LDL receptor. The core fold of the EGF domain
consists of two small beta-hairpins packed against each
other. Two major structural variants have been
identified based on the structural context of the
C-terminal cysteine residue of disulfide 'c' in the
C-terminal hairpin: hEGFs and cEGFs. In cEGFs the
C-terminal thiol resides on the C-terminal beta-sheet,
resulting in long loop-lengths between the cysteine
residues of disulfide 'c', typically C[10+]XC. These
longer loop-lengths may have arisen by selective
cysteine loss from a four-disulfide EGF template such as
laminin or integrin. Tandem cEGF domains have five
linking residues between terminal cysteines of adjacent
domains. cEGF domains may or may not bind calcium in the
linker region. cEGF domains with the consensus motif
CXN4X[F,Y]XCXC are hydroxylated exclusively on the
asparagine residue.
Length = 24
Score = 29.0 bits (66), Expect = 0.17
Identities = 9/20 (45%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 151 GYTCKCIAGFRVTKDGR-CV 169
YTC C G++++ DGR C
Sbjct: 1 SYTCSCPPGYQLSGDGRTCE 20
>gnl|CDD|238247 cd00433, Peptidase_M17, Cytosol aminopeptidase family, N-terminal
and catalytic domains. Family M17 contains zinc- and
manganese-dependent exopeptidases ( EC 3.4.11.1),
including leucine aminopeptidase. They catalyze removal
of amino acids from the N-terminus of a protein and play
a key role in protein degradation and in the metabolism
of biologically active peptides. They do not contain
HEXXH motif (which is used as one of the signature
patterns to group the peptidase families) in the
metal-binding site. The two associated zinc ions and the
active site are entirely enclosed within the C-terminal
catalytic domain in leucine aminopeptidase. The enzyme
is a hexamer, with the catalytic domains clustered
around the three-fold axis, and the two trimers related
to one another by a two-fold rotation. The N-terminal
domain is structurally similar to the ADP-ribose binding
Macro domain. This family includes proteins from
bacteria, archaea, animals and plants.
Length = 468
Score = 31.0 bits (71), Expect = 0.65
Identities = 26/99 (26%), Positives = 38/99 (38%), Gaps = 18/99 (18%)
Query: 132 DCVNAPCQQLCLLSPSS----STGYTCKCIAGFRVTKDGRCVEEETPVLL-VMKGS---- 182
D VN P L+P+ + + V + E LL V KGS
Sbjct: 162 DLVNTPA---NDLTPTYLAEEAKELAKELGVKVEVLDEKELEELGMGALLAVGKGSEEPP 218
Query: 183 QIVDVSLKPGDKKETPVLLVMKGSQIV-D---VSLKPGD 217
+++ + K + P+ LV KG I D +SLKP
Sbjct: 219 RLIVLEYKGKGASKKPIALVGKG--ITFDTGGLSLKPAA 255
>gnl|CDD|214544 smart00181, EGF, Epidermal growth factor-like domain.
Length = 35
Score = 27.1 bits (60), Expect = 1.2
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 6/36 (16%)
Query: 135 NAPCQQ-LCLLSPSSSTGYTCKCIAGFRVTKDGRCV 169
PC C+ +P S YTC C G+ T D RC
Sbjct: 5 GGPCSNGTCINTPGS---YTCSCPPGY--TGDKRCE 35
>gnl|CDD|235777 PRK06302, PRK06302, acetyl-CoA carboxylase biotin carboxyl carrier
protein subunit; Validated.
Length = 155
Score = 29.0 bits (66), Expect = 1.4
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 13/56 (23%)
Query: 190 KPGD--KKETPVLLV--MKG-SQIVDVSLKPGDKSSGIITPVVGVENGLQVEFDKK 240
+ GD K+ + ++ MK ++I DKS G++T ++ VENG VEF +
Sbjct: 103 EVGDTVKEGQTLCIIEAMKVMNEI------EADKS-GVVTEIL-VENGQPVEFGQP 150
>gnl|CDD|238010 cd00053, EGF, Epidermal growth factor domain, found in epidermal
growth factor (EGF) presents in a large number of
proteins, mostly animal; the list of proteins currently
known to contain one or more copies of an EGF-like
pattern is large and varied; the functional significance
of EGF-like domains in what appear to be unrelated
proteins is not yet clear; a common feature is that
these repeats are found in the extracellular domain of
membrane-bound proteins or in proteins known to be
secreted (exception: prostaglandin G/H synthase); the
domain includes six cysteine residues which have been
shown to be involved in disulfide bonds; the main
structure is a two-stranded beta-sheet followed by a
loop to a C-terminal short two-stranded sheet;
Subdomains between the conserved cysteines vary in
length; the region between the 5th and 6th cysteine
contains two conserved glycines of which at least one
is present in most EGF-like domains; a subset of
these bind calcium.
Length = 36
Score = 26.3 bits (58), Expect = 2.5
Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 7/35 (20%)
Query: 137 PCQ--QLCLLSPSSSTGYTCKCIAGFRVTKDGRCV 169
PC C+ +P S Y C C G+ T D C
Sbjct: 7 PCSNGGTCVNTPGS---YRCVCPPGY--TGDRSCE 36
>gnl|CDD|220699 pfam10336, DUF2420, Protein of unknown function (DUF2420). This is
a family of proteins conserved in fungi. The function is
not known.
Length = 112
Score = 27.7 bits (62), Expect = 2.8
Identities = 22/62 (35%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 76 SLTIFEDTLYWTDRQLNRVLSAHKFRGKNQTVVSHLISQPLSIHVHHPSLQP--ITR-ND 132
L I ED +Y D LN +LS + +N+ I + L I + S +P ITR ND
Sbjct: 47 DLKITEDNVYSKDITLNDILSLFEILRENEDGEE-DIPESLDIVL---SSRPRFITRYND 102
Query: 133 CV 134
V
Sbjct: 103 LV 104
>gnl|CDD|131135 TIGR02080, O_succ_thio_ly, O-succinylhomoserine (thiol)-lyase.
This family consists of O-succinylhomoserine
(thiol)-lyase, one of three different enzymes designated
cystathionine gamma-synthase and involved in methionine
biosynthesis. In all three cases, sulfur is added by
transsulfuration from Cys to yield cystathionine rather
than by a sulfhydrylation step that uses H2S directly
and bypasses cystathionine [Amino acid biosynthesis,
Aspartate family].
Length = 382
Score = 28.6 bits (64), Expect = 3.2
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 105 QTVVSHLISQPLSIHVHHPSL 125
Q +V +L +QPL +++P L
Sbjct: 259 QAIVEYLQTQPLVKKIYYPGL 279
>gnl|CDD|236522 PRK09450, cyaA, adenylate cyclase; Provisional.
Length = 830
Score = 28.7 bits (65), Expect = 3.4
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 5/35 (14%)
Query: 91 LNRVLSAHKFRGKNQTVVSHLISQPLSIHVHHPSL 125
L R L+A V L+ PL +HV+HP L
Sbjct: 20 LARALAALSPA---FQQVLSLL--PLLLHVNHPLL 49
>gnl|CDD|216552 pfam01526, DDE_Tnp_Tn3, Tn3 transposase DDE domain. This family
includes transposases of Tn3, Tn21, Tn1721, Tn2501,
Tn3926 transposons from E-coli. The specific binding of
the Tn3 transposase to DNA has been demonstrated.
Sequence analysis has suggested that the invariant triad
of Asp689, Asp765, Glu895 (numbering as in Tn3) may
correspond to the D-D-35-E motif previously implicated
in the catalysis of numerous transposases.
Length = 388
Score = 28.3 bits (64), Expect = 4.7
Identities = 12/64 (18%), Positives = 22/64 (34%), Gaps = 20/64 (31%)
Query: 46 GTSRQQDTLYWTDRQLNRVVAGSHYLLHPHSLTIFEDTLYWTD--------RQLNRVLSA 97
+ +Q+ LY R+L R+ + +LL Y D LN+ +
Sbjct: 260 SSYARQNPLYKALRELGRIEK-TLFLLD-----------YIDDPELRREIQAGLNKGEAR 307
Query: 98 HKFR 101
+
Sbjct: 308 NSLA 311
>gnl|CDD|218404 pfam05056, DUF674, Protein of unknown function (DUF674). This
family is found in Arabidopsis thaliana and contains
several uncharacterized proteins.
Length = 462
Score = 27.9 bits (62), Expect = 5.9
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 6/40 (15%)
Query: 1 MDESSRSTIISTKIYWPNGLTLDIATRRVYFAESKLDFID 40
M +SS IS + L +D +V AE+ DF+D
Sbjct: 1 MAQSSEEPKISLR------LLIDEEKNKVVLAEAGKDFVD 34
>gnl|CDD|215193 PLN02337, PLN02337, lipoxygenase.
Length = 866
Score = 28.1 bits (63), Expect = 6.2
Identities = 14/29 (48%), Positives = 18/29 (62%), Gaps = 5/29 (17%)
Query: 57 TDRQLNRVVAGSHYLLHPHSLTIFEDTLY 85
T+RQL+ V+ H LLHPH F DT+
Sbjct: 537 TNRQLS-VLHPIHKLLHPH----FRDTMN 560
>gnl|CDD|224382 COG1465, COG1465, Predicted alternative 3-dehydroquinate synthase
[Amino acid transport and metabolism].
Length = 376
Score = 27.9 bits (62), Expect = 6.3
Identities = 26/102 (25%), Positives = 37/102 (36%), Gaps = 24/102 (23%)
Query: 134 VNAPCQQLCLLSPSSSTGYTCKCIAGFRVT---KDGRCVE--------EETPVLLV---- 178
VNA + P T Y + AG V DGR E P++L+
Sbjct: 259 VNAGAVHAYIRVPGGKTKYLAELKAGDEVLIVDFDGRTRSAIVGRVKIERRPLMLIEAEY 318
Query: 179 --MKGSQIVDVSLKPGDKKETPVLLVMKGSQIVDVSLKPGDK 218
++ S I+ ET L+ G + LKPGD+
Sbjct: 319 EGVEISTILQ-------NAETIKLVNPDGEPVSVAELKPGDE 353
>gnl|CDD|237052 PRK12313, PRK12313, glycogen branching enzyme; Provisional.
Length = 633
Score = 27.9 bits (63), Expect = 6.9
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 4/29 (13%)
Query: 59 RQLNRVVAGSHYLLHPHSLTIFEDTLYWT 87
++LN VV YL HP L I E++ W
Sbjct: 343 QKLNEVV----YLEHPDVLMIAEESTAWP 367
>gnl|CDD|152824 pfam12389, Peptidase_M73, Camelysin metallo-endopeptidase.
Length = 199
Score = 27.3 bits (60), Expect = 7.2
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 177 LVMKGSQIVDVS-LKPGDKKETPVLLVMKGS-QIVDVSLK 214
L + +VD+ LKPGD E L KGS I DV L
Sbjct: 48 LALDPKTLVDIKDLKPGDSVEKEFKLENKGSLDIKDVKLA 87
>gnl|CDD|240432 PTZ00477, PTZ00477, rhoptry-associated protein; Provisional.
Length = 524
Score = 27.4 bits (61), Expect = 9.5
Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 4/55 (7%)
Query: 30 YFAESKLDFIDFCNYDGTSRQQDTLYWTDRQLNRVVAGSHYLLHPHSLTIFEDTL 84
Y +++K D FC D + +R + R AG Y L + D L
Sbjct: 66 YLSKNKYDPSMFCEGDLET----CHTLVNRYVERCKAGDCYTLDNVKVFESGDRL 116
>gnl|CDD|240621 cd01620, Ala_dh_like, Alanine dehydrogenase and related
dehydrogenases. Alanine dehydrogenase/Transhydrogenase,
such as the hexameric L-alanine dehydrogenase of
Phormidium lapideum, contain 2 Rossmann fold-like
domains linked by an alpha helical region. Related
proteins include Saccharopine Dehydrogenase (SDH),
bifunctional lysine ketoglutarate reductase
/saccharopine dehydrogenase enzyme,
N(5)-(carboxyethyl)ornithine synthase, and Rubrum
transdehydrogenase. Alanine dehydrogenase (L-AlaDH)
catalyzes the NAD-dependent conversion of pyrucate to
L-alanine via reductive amination. Transhydrogenases
found in bacterial and inner mitochondrial membranes
link NAD(P)(H)-dependent redox reactions to proton
translocation. The energy of the proton electrochemical
gradient (delta-p), generated by the respiratory
electron transport chain, is consumed by
transhydrogenase in NAD(P)+ reduction. Transhydrogenase
is likely involved in the regulation of the citric acid
cycle. Rubrum transhydrogenase has 3 components, dI,
dII, and dIII. dII spans the membrane while dI and dIII
protrude on the cytoplasmic/matirx side. DI contains 2
domains with Rossmann folds, linked by a long alpha
helix, and contains a NAD binding site. Two dI
polypeptides (represented in this sub-family)
spontaneously form a heterotrimer with one dIII in the
absence of dII. In the heterotrimer, both dI chains may
bind NAD, but only one is well-ordered. dIII also binds
a well-ordered NADP, but in a different orientation than
classical Rossmann domains.
Length = 317
Score = 27.0 bits (60), Expect = 9.8
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 9/53 (16%)
Query: 184 IVDVSLKPGDKKETPVLLV------MK-GSQIVDVSLKPGDKSSGIITPVVGV 229
+++ L G P+L++ MK G+ IVD++ G I GV
Sbjct: 227 LINAILVDG--PRAPILIMEELVGPMKRGAVIVDLAADQGGNDETSIPTTEGV 277
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
0.317 0.134 0.404
Gapped
Lambda K H
0.267 0.0632 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,823,266
Number of extensions: 1164337
Number of successful extensions: 830
Number of sequences better than 10.0: 1
Number of HSP's gapped: 829
Number of HSP's successfully gapped: 24
Length of query: 264
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 169
Effective length of database: 6,723,972
Effective search space: 1136351268
Effective search space used: 1136351268
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: 41 (21.7 bits)
S2: 58 (26.3 bits)