RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy952
(573 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 = 52.6 bits (127), Expect = 2e-09
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 171 HEDDIAWPNALTLDYFTERLYWADAHLDYIASVDLDGKH 209
+ PN L +D+ RLYW D LD I +LDG +
Sbjct: 4 LSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTN 42
Score = 49.9 bits (120), Expect = 2e-08
Identities = 18/43 (41%), Positives = 24/43 (55%)
Query: 80 ERVIRHDSHGLEGLAVDWVGRKLYWLDRHSKQLDVAELDGTNR 122
++ GLAVDW+ +LYW D ++VA LDGTNR
Sbjct: 1 RTLLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 42.2 bits (100), Expect = 1e-05
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 210 KHIVISGQKVPHVFALTLFEDHIYWTDWNTKSINRADKFNGRD 252
+ ++ SG P+ A+ E +YWTDW I A+ +G +
Sbjct: 1 RTLLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVAN-LDGTN 42
Score = 32.6 bits (75), Expect = 0.027
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 122 RKTLKTAIQDPRGITLHPGIGYVYFSSWNLQAYIGKIGMDGSN 164
R L + + P G+ + G +Y++ W L I +DG+N
Sbjct: 1 RTLLSSGLGHPNGLAVDWIEGRLYWTDWGL-DVIEVANLDGTN 42
Score = 30.3 bits (69), Expect = 0.18
Identities = 7/37 (18%), Positives = 14/37 (37%)
Query: 37 YSLVHQDLLNVVAMDFHYKENRFYFADVAAKTIYRSR 73
+L+ L + + + E R Y+ D I +
Sbjct: 1 RTLLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVAN 37
>gnl|CDD|238060 cd00112, LDLa, Low Density Lipoprotein Receptor Class A domain, a
cysteine-rich repeat that plays a central role in
mammalian cholesterol metabolism; the receptor protein
binds LDL and transports it into cells by endocytosis; 7
successive cysteine-rich repeats of about 40 amino acids
are present in the N-terminal of this multidomain
membrane protein; other homologous domains occur in
related receptors, including the very low-density
lipoprotein receptor and the LDL receptor-related
protein/alpha 2-macroglobulin receptor, and in proteins
which are functionally unrelated, such as the C9
component of complement; the binding of calcium is
required for in vitro formation of the native disulfide
isomer and is necessary in establishing and maintaining
the modular structure.
Length = 35
Score = 51.1 bits (123), Expect = 7e-09
Identities = 19/30 (63%), Positives = 21/30 (70%)
Query: 413 DTEFACRNGHCIPKLWVCDFDNDCGDDSDE 442
EF C NG CIP WVCD ++DCGD SDE
Sbjct: 3 PNEFRCANGRCIPSSWVCDGEDDCGDGSDE 32
Score = 48.7 bits (117), Expect = 4e-08
Identities = 17/32 (53%), Positives = 21/32 (65%)
Query: 309 CSSSQFRCNNGKCIDYHLVCNKESDCEDDSDE 340
C ++FRC NG+CI VC+ E DC D SDE
Sbjct: 1 CPPNEFRCANGRCIPSSWVCDGEDDCGDGSDE 32
Score = 46.0 bits (110), Expect = 5e-07
Identities = 18/34 (52%), Positives = 25/34 (73%), Gaps = 1/34 (2%)
Query: 525 CPPHHLKCANTNICVEPYWLCDGDNDCGDMSDED 558
CPP+ +CAN C+ W+CDG++DCGD SDE+
Sbjct: 1 CPPNEFRCAN-GRCIPSSWVCDGEDDCGDGSDEE 33
Score = 43.7 bits (104), Expect = 3e-06
Identities = 21/40 (52%), Positives = 23/40 (57%), Gaps = 5/40 (12%)
Query: 452 CTKGWERCPGKTNYRCIPKWLFCDGKDDCRDGSDELPQNC 491
C RC N RCIP CDG+DDC DGSDE +NC
Sbjct: 1 CPPNEFRC---ANGRCIPSSWVCDGEDDCGDGSDE--ENC 35
>gnl|CDD|200964 pfam00057, Ldl_recept_a, Low-density lipoprotein receptor domain
class A.
Length = 37
Score = 50.4 bits (121), Expect = 1e-08
Identities = 17/34 (50%), Positives = 23/34 (67%)
Query: 307 STCSSSQFRCNNGKCIDYHLVCNKESDCEDDSDE 340
STC +F+C +G+CI VC+ + DCED SDE
Sbjct: 1 STCGPDEFQCGSGECIPMSWVCDGDPDCEDGSDE 34
Score = 47.3 bits (113), Expect = 2e-07
Identities = 18/28 (64%), Positives = 19/28 (67%)
Query: 415 EFACRNGHCIPKLWVCDFDNDCGDDSDE 442
EF C +G CIP WVCD D DC D SDE
Sbjct: 7 EFQCGSGECIPMSWVCDGDPDCEDGSDE 34
Score = 41.5 bits (98), Expect = 2e-05
Identities = 16/35 (45%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 524 TCPPHHLKCANTNICVEPYWLCDGDNDCGDMSDED 558
TC P +C + C+ W+CDGD DC D SDE
Sbjct: 2 TCGPDEFQCGS-GECIPMSWVCDGDPDCEDGSDEK 35
Score = 39.2 bits (92), Expect = 1e-04
Identities = 15/28 (53%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 464 NYRCIPKWLFCDGKDDCRDGSDELPQNC 491
+ CIP CDG DC DGSDE +NC
Sbjct: 12 SGECIPMSWVCDGDPDCEDGSDE--KNC 37
>gnl|CDD|197566 smart00192, LDLa, Low-density lipoprotein receptor domain class A.
Cysteine-rich repeat in the low-density lipoprotein
(LDL) receptor that plays a central role in mammalian
cholesterol metabolism. The N-terminal type A repeats in
LDL receptor bind the lipoproteins. Other homologous
domains occur in related receptors, including the very
low-density lipoprotein receptor and the LDL
receptor-related protein/alpha 2-macroglobulin receptor,
and in proteins which are functionally unrelated, such
as the C9 component of complement. Mutations in the LDL
receptor gene cause familial hypercholesterolemia.
Length = 33
Score = 49.6 bits (119), Expect = 2e-08
Identities = 19/29 (65%), Positives = 20/29 (68%)
Query: 414 TEFACRNGHCIPKLWVCDFDNDCGDDSDE 442
EF C NG CIP WVCD +DCGD SDE
Sbjct: 5 GEFQCDNGRCIPSSWVCDGVDDCGDGSDE 33
Score = 47.2 bits (113), Expect = 1e-07
Identities = 16/33 (48%), Positives = 21/33 (63%)
Query: 308 TCSSSQFRCNNGKCIDYHLVCNKESDCEDDSDE 340
TC +F+C+NG+CI VC+ DC D SDE
Sbjct: 1 TCPPGEFQCDNGRCIPSSWVCDGVDDCGDGSDE 33
Score = 43.8 bits (104), Expect = 3e-06
Identities = 18/34 (52%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 524 TCPPHHLKCANTNICVEPYWLCDGDNDCGDMSDE 557
TCPP +C N C+ W+CDG +DCGD SDE
Sbjct: 1 TCPPGEFQCDN-GRCIPSSWVCDGVDDCGDGSDE 33
Score = 41.9 bits (99), Expect = 1e-05
Identities = 19/35 (54%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 452 CTKGWERCPGKTNYRCIPKWLFCDGKDDCRDGSDE 486
C G +C N RCIP CDG DDC DGSDE
Sbjct: 2 CPPGEFQCD---NGRCIPSSWVCDGVDDCGDGSDE 33
>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 = 45.6 bits (109), Expect = 6e-07
Identities = 12/44 (27%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 142 GYVYFSSWNLQAYIGKIGMDGSNFTRILTHEDDIAWPNALTLDY 185
G +Y++ +L+A I ++GS+ + + +D+ WPN + +D
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLFS--EDLQWPNGIAVDP 42
Score = 37.9 bits (89), Expect = 4e-04
Identities = 18/44 (40%), Positives = 27/44 (61%), Gaps = 6/44 (13%)
Query: 100 RKLYWLD---RHSKQLDVAELDGTNRKTL-KTAIQDPRGITLHP 139
+LYW D R S + VA+L+G++R+TL +Q P GI + P
Sbjct: 1 GRLYWTDSSLRAS--ISVADLNGSDRRTLFSEDLQWPNGIAVDP 42
Score = 35.2 bits (82), Expect = 0.003
Identities = 11/42 (26%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 230 DHIYWTDWNTKSINRADKFNGRDYR-VLRNTTHRPYDIHVYH 270
+YWTD + ++ NG D R + P I V
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIAVDP 42
Score = 32.1 bits (74), Expect = 0.041
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 188 ERLYWADAHLD-YIASVDLDGKHKHIVISGQKVPHVFALTLFE 229
RLYW D+ L I+ DL+G + + S + + +
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLFSED-LQWPNGIAVDP 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 = 43.6 bits (104), Expect = 2e-06
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 367 GYYCECNTGYKLLEDGKACTDIDE 390
Y C C GY+L DG+ C DIDE
Sbjct: 1 SYTCSCPPGYQLSGDGRTCEDIDE 24
>gnl|CDD|214542 smart00179, EGF_CA, Calcium-binding EGF-like domain.
Length = 39
Score = 37.6 bits (88), Expect = 4e-04
Identities = 18/42 (42%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 345 NVDECAKVETNQCGHKCVDTLTGYYCECNTGYKLLEDGKACT 386
++DECA Q G CV+T+ Y CEC GY DG+ C
Sbjct: 1 DIDECASGNPCQNGGTCVNTVGSYRCECPPGY---TDGRNCE 39
>gnl|CDD|238011 cd00054, EGF_CA, Calcium-binding EGF-like domain, present in a
large number of membrane-bound and extracellular (mostly
animal) proteins. Many of these proteins require calcium
for their biological function and calcium-binding sites
have been found to be located at the N-terminus of
particular EGF-like domains; calcium-binding may be
crucial for numerous protein-protein interactions. Six
conserved core cysteines form three disulfide bridges as
in non calcium-binding EGF domains, whose structures are
very similar. EGF_CA can be found in tandem repeat
arrangements.
Length = 38
Score = 36.1 bits (84), Expect = 0.002
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 345 NVDECAKVETNQCGHKCVDTLTGYYCECNTGYKL 378
++DECA Q G CV+T+ Y C C GY
Sbjct: 1 DIDECASGNPCQNGGTCVNTVGSYRCSCPPGYTG 34
>gnl|CDD|225926 COG3391, COG3391, Uncharacterized conserved protein [Function
unknown].
Length = 381
Score = 39.9 bits (93), Expect = 0.003
Identities = 27/128 (21%), Positives = 47/128 (36%), Gaps = 15/128 (11%)
Query: 47 VVAMDFHYKENRFYFADVAAKTIYRSRVGSTEKERVIRHDSHGLEGLAVDWVGRKLYWLD 106
V + +N D + ++ R VGS V G+AVD G ++Y +
Sbjct: 174 VYVTNSD--DNTVSVIDTSGNSVVRGSVGS----LVGVGTGPA--GIAVDPDGNRVYVAN 225
Query: 107 RHSKQLDVAELDGTNRKTLKT----AIQDPRGITLHPGIGYVYFSSWNLQAYIGKIGMDG 162
S +V ++D T PRG+ + P Y ++ + + I DG
Sbjct: 226 DGSGSNNVLKIDTATGNVTATDLPVGSGAPRGVAVDPAGKAAYVAN-SQGGTVSVI--DG 282
Query: 163 SNFTRILT 170
+ + T
Sbjct: 283 ATDRVVKT 290
Score = 31.4 bits (71), Expect = 1.5
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 92 GLAVDWVGRKLYWLDRHSKQLDVAELDGTNRKTLKT--AIQDPRGITLHPGIGYVY 145
GLAVD G+ +Y + + V+ +D K T P G+ + P VY
Sbjct: 120 GLAVDPDGKYVYVANAGNGNNTVSVIDAATNKVTATIPVGNTPTGVAVDPDGNKVY 175
>gnl|CDD|238752 cd01475, vWA_Matrilin, VWA_Matrilin: In cartilaginous plate,
extracellular matrix molecules mediate cell-matrix and
matrix-matrix interactions thereby providing tissue
integrity. Some members of the matrilin family are
expressed specifically in developing cartilage
rudiments. The matrilin family consists of at least four
members. All the members of the matrilin family contain
VWA domains, EGF-like domains and a heptad repeat
coiled-coiled domain at the carboxy terminus which is
responsible for the oligomerization of the matrilins.
The VWA domains have been shown to be essential for
matrilin network formation by interacting with matrix
ligands.
Length = 224
Score = 39.3 bits (92), Expect = 0.003
Identities = 15/41 (36%), Positives = 19/41 (46%)
Query: 344 CNVDECAKVETNQCGHKCVDTLTGYYCECNTGYKLLEDGKA 384
C V + ++ C C+ T Y C C GY LLED K
Sbjct: 184 CVVPDLCATLSHVCQQVCISTPGSYLCACTEGYALLEDNKT 224
>gnl|CDD|219496 pfam07645, EGF_CA, Calcium-binding EGF domain.
Length = 42
Score = 31.9 bits (73), Expect = 0.044
Identities = 18/42 (42%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 346 VDECAKVETNQC--GHKCVDTLTGYYCECNTGYKLLEDGKAC 385
VDECA T+ C CV+T+ + C C GY+ EDG C
Sbjct: 2 VDECA-DGTHNCPANTVCVNTIGSFECVCPDGYENNEDGTNC 42
>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 = 30.5 bits (69), Expect = 0.16
Identities = 14/33 (42%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 348 ECAKVETNQC--GHKCVDTLTGYYCECNTGYKL 378
ECA +N C G CV+T Y C C GY
Sbjct: 1 ECA--ASNPCSNGGTCVNTPGSYRCVCPPGYTG 31
>gnl|CDD|216201 pfam00930, DPPIV_N, Dipeptidyl peptidase IV (DPP IV) N-terminal
region. This family is an alignment of the region to
the N-terminal side of the active site. The Prosite
motif does not correspond to this Pfam entry.
Length = 348
Score = 33.1 bits (76), Expect = 0.43
Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 11/65 (16%)
Query: 95 VDWVGRK---LYWLDRHSKQLDVAELDG-TNRKTLKTAIQDPRGITLH-------PGIGY 143
V W + + WL+R LD+ +D T R + + LH G G+
Sbjct: 187 VKWTPDEKLLVQWLNRDQNVLDLVLVDTETGRTVVLLEETSDGWVELHQDPVFLRDGSGF 246
Query: 144 VYFSS 148
++ S
Sbjct: 247 LWISE 251
>gnl|CDD|214544 smart00181, EGF, Epidermal growth factor-like domain.
Length = 35
Score = 28.6 bits (64), Expect = 0.58
Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 3/32 (9%)
Query: 348 ECAKVETNQCGH-KCVDTLTGYYCECNTGYKL 378
ECA C + C++T Y C C GY
Sbjct: 1 ECA--SGGPCSNGTCINTPGSYTCSCPPGYTG 30
>gnl|CDD|225921 COG3386, COG3386, Gluconolactonase [Carbohydrate transport and
metabolism].
Length = 307
Score = 31.6 bits (72), Expect = 1.2
Identities = 25/127 (19%), Positives = 41/127 (32%), Gaps = 30/127 (23%)
Query: 50 MDFHYKENRFYFADVAAKTIYRS-------RVGSTEKERVIRHDSHGLEGLAVD------ 96
+ F Y AD A I+R +G + +G+AVD
Sbjct: 168 LAFSPDGKTLYVADTPANRIHRYDLDPATGPIGGRRGFVDFDEEPGLPDGMAVDADGNLW 227
Query: 97 ----WVGRKLYWLDRHSKQLDVAELD----------GTNRKTLK-TAIQD--PRGITLHP 139
W G ++ + K L +L G + TL T+ + R +T P
Sbjct: 228 VAAVWGGGRVVRFNPDGKLLGEIKLPVKRPTNPAFGGPDLNTLYITSARSGMSRMLTADP 287
Query: 140 GIGYVYF 146
G ++
Sbjct: 288 LGGGLFS 294
>gnl|CDD|188693 cd08739, RGS_RGS9, Regulator of G protein signaling (RGS) domain
found in the RGS9 protein. The RGS (Regulator of
G-protein Signaling) domain is an essential part of the
RGS9 protein, a member of R7 subfamily of the RGS
protein family. RGS is a diverse group of
multifunctional proteins that regulate cellular
signaling events downstream of G-protein coupled
receptors (GPCRs). As a major G-protein regulator, RGS
domain containing proteins are involved in many crucial
cellular processes such as regulation of intracellular
trafficking, glial differentiation, embryonic axis
formation, skeletal and muscle development, and cell
migration during early embryogenesis. Other members of
the R7 subfamily (Neuronal RGS) include: RGS6, RGS7, and
RGS11, all of which are expressed predominantly in the
nervous system, form an obligatory complex with
G-beta-5, and play important roles in the regulation of
crucial neuronal processes such as vision and motor
control. Additionally they have been implicated in many
neurological conditions such as anxiety, schizophrenia,
and drug dependence. RGS9 forms constitutive complexes
with G-beta-5 subunit and controls such fundamental
functions as vision and behavior. RGS9 exists in two
splice isoforms: RGS9-1 which regulates
phototransduction in rods and cones and RGS9-2 which
regulates dopamine and opioid signaling in the basal
ganglia. In addition, RGS9 was found to bind many other
proteins outside of G protein signaling pathways
including: mu-opioid receptor, beta-arrestin,
alpha-actinin-2, NMDAR, polycystin, spinophilin, and
guanylyl cyclase, among others.
Length = 121
Score = 29.2 bits (65), Expect = 2.3
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 203 VDLDGKHKHIVISGQKVPHVFALTLFEDHIY 233
+++DGK I + G K PH + L + HIY
Sbjct: 72 INIDGKTMDITVKGLKHPHRYVLDAAQTHIY 102
>gnl|CDD|214865 smart00861, Transket_pyr, Transketolase, pyrimidine binding
domain. Transketolase (TK) catalyzes the reversible
transfer of a two-carbon ketol unit from xylulose
5-phosphate to an aldose receptor, such as ribose
5-phosphate, to form sedoheptulose 7-phosphate and
glyceraldehyde 3- phosphate. This enzyme, together with
transaldolase, provides a link between the glycolytic
and pentose-phosphate pathways. TK requires thiamine
pyrophosphate as a cofactor. In most sources where TK
has been purified, it is a homodimer of approximately
70 Kd subunits. TK sequences from a variety of
eukaryotic and prokaryotic sources show that the enzyme
has been evolutionarily conserved. In the peroxisomes
of methylotrophic yeast Hansenula polymorpha, there is
a highly related enzyme, dihydroxy-acetone synthase
(DHAS) (also known as formaldehyde transketolase),
which exhibits a very unusual specificity by including
formaldehyde amongst its substrates.
Length = 136
Score = 29.4 bits (67), Expect = 2.8
Identities = 12/35 (34%), Positives = 13/35 (37%), Gaps = 1/35 (2%)
Query: 59 FYFADVA-AKTIYRSRVGSTEKERVIRHDSHGLEG 92
+F AK RS S V RHD G G
Sbjct: 45 IFFTFFDRAKDQIRSAGASGNVPVVFRHDGGGGVG 79
>gnl|CDD|193472 pfam12999, PRKCSH-like, Glucosidase II beta subunit-like. The
sequences found in this family are similar to a region
found in the beta-subunit of glucosidase II, which is
also known as protein kinase C substrate 80K-H (PRKCSH).
The enzyme catalyzes the sequential removal of two
alpha-1,3-linked glucose residues in the second step of
N-linked oligosaccharide processing. The beta subunit is
required for the solubility and stability of the
heterodimeric enzyme, and is involved in retaining the
enzyme within the endoplasmic reticulum.
Length = 176
Score = 29.4 bits (66), Expect = 3.7
Identities = 24/64 (37%), Positives = 27/64 (42%), Gaps = 12/64 (18%)
Query: 435 DCGDDSDEPAYMCRQRNCTKGWERCPGK---TNYRCIPKWLFCDG---KDDCRDGSDELP 488
DC D SDEP C+ G C + Y IP + DG D C DGSDE
Sbjct: 59 DCPDGSDEPG----TNACSNGKFYCANEGFIPGY--IPSFKVDDGVCDYDICCDGSDEAL 112
Query: 489 QNCP 492
CP
Sbjct: 113 GKCP 116
>gnl|CDD|215652 pfam00008, EGF, EGF-like domain. There is no clear separation
between noise and signal. pfam00053 is very similar, but
has 8 instead of 6 conserved cysteines. Includes some
cytokine receptors. The EGF domain misses the N-terminus
regions of the Ca2+ binding EGF domains (this is the
main reason of discrepancy between swiss-prot domain
start/end and Pfam). The family is hard to model due to
many similar but different sub-types of EGF domains.
Pfam certainly misses a number of EGF domains.
Length = 32
Score = 26.6 bits (59), Expect = 3.7
Identities = 13/27 (48%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 353 ETNQCGH--KCVDTLTGYYCECNTGYK 377
N C + CVDT GY CEC GY
Sbjct: 3 PNNPCSNGGTCVDTPGGYTCECPEGYT 29
>gnl|CDD|234493 TIGR04189, surface_SprA, cell surface protein SprA. SprA is a cell
surface protein widely distributed in the Bacteroidetes
lineage. In Flavobacterium johnsoniae, a species that
shows gliding motility, mutation disrupts gliding.
Length = 2315
Score = 30.0 bits (68), Expect = 4.2
Identities = 11/54 (20%), Positives = 22/54 (40%), Gaps = 3/54 (5%)
Query: 213 VISGQKVPHVFALTLFEDHIYWTDWN-TKSINRADKFNGRDYRVLRNTTHRPYD 265
G P ++ + +Y +WN TKS+ R + FN ++ + +
Sbjct: 1669 SGPGTGEPVLYQKNFTFNRLYNLNWNLTKSL-RLN-FNANTNAIIDEPGNGDVN 1720
>gnl|CDD|234542 TIGR04321, spiroSPASM, spiro-SPASM protein. This three-domain
protein is restricted to the spirochetes and widely
distributed (excepting Borrelia). It has a conserved
C-terminal SPASM domain, a 4Fe-4S binding domain shared
by a number of peptide-modifying and heme-modifying
radical SAM proteins. It has a central radical SAM
domain, although half the members have lost the
signature 4Fe-4S-binding Cys residues, fail to register
with the radical SAM domain definition of pfam04055, and
must be considered pseudo-SAM proteins. PSI-BLAST shows
a relationship between the N-terminal domain and various
predicted glycosyltransferases (e.g. Bacillus subtilis
SpsF) and cytidyltransferases. In some Treponema
species, this protein appears to split into two tandem
genes.
Length = 507
Score = 29.6 bits (67), Expect = 5.6
Identities = 21/102 (20%), Positives = 33/102 (32%), Gaps = 18/102 (17%)
Query: 104 WLDRHSKQLDVAELDGTNRKTLKTAIQDPRGITLHPGIGYVYF---SSWNLQAYIGKIGM 160
+L+V +D T G+ V W A + KI
Sbjct: 31 KAASLPPELNVFLN-------TSAPSKDEVSATSSEGLDPVKVVSRDDWTEIALLEKISS 83
Query: 161 DGSNFTRILTHEDDIAWPNALTLDY-FTERLYWADAHLDYIA 201
+ + L +A LD TE+L + HL+Y+A
Sbjct: 84 ELWDADCFL-----YFPGDAPFLDPDLTEKLL--ERHLEYLA 118
>gnl|CDD|198352 cd07774, FGGY_1, uncharacterized subgroup; belongs to the FGGY
family of carbohydrate kinases. This subfamily is
composed of uncharacterized carbohydrate kinases. They
are sequence homologous to bacterial glycerol kinase and
have been classified as members of the FGGY family of
carbohydrate kinases. The monomers of FGGY proteins
contain two large domains, which are separated by a deep
cleft that forms the active site. This model includes
both the N-terminal domain, which adopts a ribonuclease
H-like fold, and the structurally related C-terminal
domain.
Length = 430
Score = 28.9 bits (65), Expect = 8.1
Identities = 10/62 (16%), Positives = 15/62 (24%), Gaps = 7/62 (11%)
Query: 247 KFNGRDYRVLRNTTHR-------PYDIHVYHPLKGTTRHAWLTAHRGSTTVADMIRSVYL 299
G PY P++ +T+ D+ RSV
Sbjct: 307 ILGGEASSKRAQEKLLDSAALFYPYSRGSGSPIRSEIAGGAFYGLTDTTSQEDITRSVLE 366
Query: 300 GS 301
G
Sbjct: 367 GL 368
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 0.137 0.465
Gapped
Lambda K H
0.267 0.0843 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,226,330
Number of extensions: 2628867
Number of successful extensions: 1758
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1751
Number of HSP's successfully gapped: 52
Length of query: 573
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 471
Effective length of database: 6,413,494
Effective search space: 3020755674
Effective search space used: 3020755674
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 (21.8 bits)
S2: 62 (27.5 bits)