RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy951
(428 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 = 44.9 bits (107), Expect = 1e-06
Identities = 20/44 (45%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 23 RSLVMTGVRHPTGLSVDAAMDHTLYWVDSKLNTIESVRHDGRNR 66
R+L+ +G+ HP GL+VD ++ LYW D L+ IE DG NR
Sbjct: 1 RTLLSSGLGHPNGLAVDW-IEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 37.6 bits (88), Expect = 4e-04
Identities = 7/35 (20%), Positives = 14/35 (40%)
Query: 319 VISDERRIEALDIDPVDEIIYWVDSYDRNIRRSFM 353
+ S L +D ++ +YW D I + +
Sbjct: 4 LSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANL 38
Score = 37.6 bits (88), Expect = 4e-04
Identities = 7/35 (20%), Positives = 14/35 (40%)
Query: 364 VISDERRIEALDIDPVDEIIYWVDSYDRNIRRSFM 398
+ S L +D ++ +YW D I + +
Sbjct: 4 LSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANL 38
Score = 28.3 bits (64), Expect = 0.69
Identities = 8/21 (38%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 73 SDKLQHP--ISLDVFENNIYW 91
S L HP +++D E +YW
Sbjct: 5 SSGLGHPNGLAVDWIEGRLYW 25
Score = 28.3 bits (64), Expect = 0.84
Identities = 8/22 (36%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 1 MFWAETGASPRIESAWMDGSHR 22
++W + G IE A +DG++R
Sbjct: 23 LYWTDWG-LDVIEVANLDGTNR 43
>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 = 36.4 bits (85), Expect = 0.001
Identities = 12/39 (30%), Positives = 23/39 (58%)
Query: 1 MFWAETGASPRIESAWMDGSHRRSLVMTGVRHPTGLSVD 39
++W ++ I A ++GS RR+L ++ P G++VD
Sbjct: 3 LYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIAVD 41
Score = 33.3 bits (77), Expect = 0.011
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 46 LYWVDSKL-NTIESVRHDGRNRQTILSGSDKLQHPISLDVFE 86
LYW DS L +I +G +R+T+ S+ LQ P + V
Sbjct: 3 LYWTDSSLRASISVADLNGSDRRTLF--SEDLQWPNGIAVDP 42
>gnl|CDD|214544 smart00181, EGF, Epidermal growth factor-like domain.
Length = 35
Score = 33.3 bits (76), Expect = 0.010
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 138 PCSQ-SPCSH-LCLVIPGGYQCACPE 161
C+ PCS+ C+ PG Y C+CP
Sbjct: 1 ECASGGPCSNGTCINTPGSYTCSCPP 26
>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 = 32.8 bits (75), Expect = 0.017
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 138 PCSQS-PCSH--LCLVIPGGYQCACPE 161
C+ S PCS+ C+ PG Y+C CP
Sbjct: 1 ECAASNPCSNGGTCVNTPGSYRCVCPP 27
>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 = 32.4 bits (74), Expect = 0.023
Identities = 12/24 (50%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 140 SQSPCSH--LCLVIPGGYQCACPE 161
+PCS+ C+ PGGY C CPE
Sbjct: 3 PNNPCSNGGTCVDTPGGYTCECPE 26
>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 = 30.7 bits (70), Expect = 0.087
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 3/28 (10%)
Query: 137 NPC-SQSPCSH--LCLVIPGGYQCACPE 161
+ C S +PC + C+ G Y+C+CP
Sbjct: 3 DECASGNPCQNGGTCVNTVGSYRCSCPP 30
Score = 29.9 bits (68), Expect = 0.18
Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 191 CQNGGMCAESETGDLTCNCRQDFAGTFCE 219
CQNGG C + G C+C + G CE
Sbjct: 11 CQNGGTCVNTV-GSYRCSCPPGYTGRNCE 38
>gnl|CDD|223494 COG0417, PolB, DNA polymerase elongation subunit (family B) [DNA
replication, recombination, and repair].
Length = 792
Score = 34.7 bits (80), Expect = 0.096
Identities = 22/105 (20%), Positives = 37/105 (35%), Gaps = 22/105 (20%)
Query: 307 RAYETHKRRFRDVISDERRIEALDI--------------DPVDEIIYWVDSYDRNIRRSF 352
+ DV R + A DI DP+ I Y +++ I
Sbjct: 138 SIHSLFLEHREDVRPPLRVL-AFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLIEVFI 196
Query: 353 MLEAQKGQVQAVISDERRIEAL-----DIDPVDEIIYW-VDSYDR 391
+ V+ VIS+ +E + DP D I+ + D++D
Sbjct: 197 YTSGEGFSVEVVISEAELLERFVELIREYDP-DVIVGYNGDNFDW 240
>gnl|CDD|214542 smart00179, EGF_CA, Calcium-binding EGF-like domain.
Length = 39
Score = 28.8 bits (65), Expect = 0.46
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 3/28 (10%)
Query: 137 NPC-SQSPCSH--LCLVIPGGYQCACPE 161
+ C S +PC + C+ G Y+C CP
Sbjct: 3 DECASGNPCQNGGTCVNTVGSYRCECPP 30
Score = 26.4 bits (59), Expect = 3.7
Identities = 12/30 (40%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 191 CQNGGMCAESETGDLTCNCRQDF-AGTFCE 219
CQNGG C + G C C + G CE
Sbjct: 11 CQNGGTC-VNTVGSYRCECPPGYTDGRNCE 39
>gnl|CDD|173248 PRK14787, PRK14787, lipoprotein signal peptidase; Provisional.
Length = 159
Score = 30.4 bits (69), Expect = 0.99
Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 16/66 (24%)
Query: 213 FAGTFCENYTGIGQGLTLGRSLLYIPTLLLLL--ALVSATVYYVWRKR--------PFGK 262
F T+ EN GI GL P +LLLL A+ + ++YV R + FG
Sbjct: 40 FKLTYAEN-RGIAFGLEFAP-----PEVLLLLTGAISAGVLWYVLRSKNRTPLFLLAFGL 93
Query: 263 TMGSAL 268
+G +
Sbjct: 94 ILGGGI 99
>gnl|CDD|222628 pfam14256, YwiC, YwiC-like protein. The YwiC-like protein family
includes the B. subtilis YwiC protein, which is
functionally uncharacterized. This domain family is
found in bacteria, and is approximately 130 amino acids
in length. There is a single completely conserved
residue G that may be functionally important.
Length = 129
Score = 29.9 bits (68), Expect = 1.1
Identities = 9/27 (33%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 233 SLLYIPTLLLLLALVSATVYYVWRKRP 259
LL+ +L L V+ +Y+ RKR
Sbjct: 82 GLLWFALAMLPLFAVN--IYFAKRKRE 106
>gnl|CDD|119321 cd06579, TM_PBP1_transp_AraH_like, Transmembrane subunit (TM) of
Escherichia coli AraH and related proteins. E. coli AraH
is the TM of a Periplasmic Binding Protein
(PBP)-dependent ATP-Binding Cassette (ABC) transporter
involved in the uptake of the monosaccharide arabinose.
This group also contains E. coli RbsC, AlsC, and MglC,
which are TMs of other monosaccharide transporters, the
ribose transporter, the D-allose transporter and the
galactose transporter, respectively. The D-allose
transporter may also be involved in low affinity ribose
transport. These transporters generally bind type 1
PBPs. PBP-dependent ABC transporters consist of a PBP,
two TMs, and two cytoplasmic ABCs, and are mainly
involved in importing solutes from the environment. The
solute is captured by the PBP, which delivers it to a
gated translocation pathway formed by the two TMs. The
two ABCs bind and hydrolyze ATP and drive the transport
reaction. Proteins in this subgroup have a single TM
which homodimerizes to generate the transmembrane pore.
Length = 263
Score = 30.1 bits (69), Expect = 1.7
Identities = 9/34 (26%), Positives = 19/34 (55%)
Query: 231 GRSLLYIPTLLLLLALVSATVYYVWRKRPFGKTM 264
G +L IP +L+ V+ +++ R+ FG+ +
Sbjct: 112 GGLILGIPVPVLIALAVALVAWFLLRRTRFGRYL 145
>gnl|CDD|219496 pfam07645, EGF_CA, Calcium-binding EGF domain.
Length = 42
Score = 27.3 bits (61), Expect = 1.8
Identities = 7/36 (19%), Positives = 14/36 (38%), Gaps = 3/36 (8%)
Query: 134 SAPNPCSQSPCSHLCLVIPGGYQCACPENATPKLPG 169
+ C + +C+ G ++C CP+ G
Sbjct: 7 DGTHNCPANT---VCVNTIGSFECVCPDGYENNEDG 39
>gnl|CDD|220248 pfam09455, Cas_DxTHG, CRISPR-associated (Cas) DxTHG family. CRISPR
is a term for Clustered Regularly Interspaced Short
Palidromic Repeats. A number of protein families appear
only in association with these repeats and are
designated Cas (CRISPR associated) proteins. The family
describes Cas proteins of about 400 residues that
include the motif [VIL]-D-x-[ST]-H-[GS]. The CRISPR and
associated proteins are thought to be involved in the
evolution of host resistance. The exact molecular
function of this family is currently unknown.
Length = 370
Score = 30.5 bits (69), Expect = 1.8
Identities = 19/104 (18%), Positives = 38/104 (36%), Gaps = 16/104 (15%)
Query: 294 LGLTIVYSNGPEIRAYETHKRRFRDVISDERRIEALDIDPVDEIIYW---VDSYDRNIRR 350
L +V G AY S+ +D+ P+ EI+ W V S+
Sbjct: 135 RSLKLVTLKGVYYGAYN----------SEPGIAPVIDLTPLVEILDWIIAVRSFLEYGDA 184
Query: 351 SFMLEAQKGQVQAVISDERRIEALDIDPVDEIIYWVDSYDRNIR 394
F+ E K + + I + R+ + +++I + + +
Sbjct: 185 KFLAELLKNEKKRKIKESRKK---LPENLEKIAKLLKALSNGLP 225
>gnl|CDD|181892 PRK09478, mglC, beta-methylgalactoside transporter inner membrane
component; Provisional.
Length = 336
Score = 29.7 bits (67), Expect = 2.7
Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 1/50 (2%)
Query: 215 GTFCENYTGIGQGLTLGRSLLYIPTLLLLLALVSATVYYVWRKRPFGKTM 264
F ++ QG S + + + A V+ +W K FGK +
Sbjct: 162 SGFDSGFSTFAQGFVALGSFR-LSYITFYALIAVAFVWVLWNKTRFGKNI 210
>gnl|CDD|224213 COG1294, AppB, Cytochrome bd-type quinol oxidase, subunit 2 [Energy
production and conversion].
Length = 346
Score = 29.1 bits (66), Expect = 4.1
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 233 SLLYIPTLLLLLALVSATVYYVWRK 257
S LY+P +L+L L+ V + +R
Sbjct: 86 SGLYLPMILVLFGLIFRGVAFEFRS 110
>gnl|CDD|223469 COG0392, COG0392, Predicted integral membrane protein [Function
unknown].
Length = 322
Score = 28.9 bits (65), Expect = 5.7
Identities = 17/67 (25%), Positives = 25/67 (37%), Gaps = 4/67 (5%)
Query: 232 RSLLYIPTLLLLLALVSATVYYVWRKRPFGKTMGSALSTQSVSFRQGTNVEFGAPAFNN- 290
+L I LLLA + + Y +T +L +S + F A NN
Sbjct: 45 AALKGINLTWLLLAFLLYLLSYALLTLYD-RTALKSLG-VKLSLWKVALASFIAYFLNNI 102
Query: 291 -GASLGL 296
A+LG
Sbjct: 103 TPAALGS 109
>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 = 28.5 bits (64), Expect = 5.8
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 135 APNPCSQSP--CSHLCLVIPGGYQCACPE 161
P+ C+ C +C+ PG Y CAC E
Sbjct: 186 VPDLCATLSHVCQQVCISTPGSYLCACTE 214
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 28.8 bits (64), Expect = 5.9
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 279 TNVEFGAPAFNNGASLGLTIVYSNGPEIRAYETHKRRFRDVISDERRIEALDI---DPVD 335
T+ F + GA L ++ + S+ P++ +E+ K R R V DE I + I DP +
Sbjct: 21 TDRPFRTLCYEMGAGLTVSEMMSSNPQV--WESDKSRLRMVHIDEPGIRTVQIAGSDPKE 78
>gnl|CDD|177189 MTH00131, CYTB, cytochrome b; Provisional.
Length = 380
Score = 28.5 bits (64), Expect = 7.9
Identities = 18/39 (46%), Positives = 23/39 (58%), Gaps = 6/39 (15%)
Query: 221 YTGIGQGLTLGRSLLYIPT-----LLLLLALVSATVYYV 254
Y IG+GL G S LY T +LLLL +++A V YV
Sbjct: 95 YLHIGRGLYYG-SYLYKETWNIGVVLLLLVMMTAFVGYV 132
>gnl|CDD|234052 TIGR02900, spore_V_B, stage V sporulation protein B. SpoVB is the
stage V sporulation protein B of the bacterial endopore
formation program in Bacillus subtilis and various other
Firmcutes. It is nearly universal among
endospore-formers. Paralogs with rather high sequence
similarity to SpoVB exist, including YkvU in B. subtilis
and a number of proteins in the genus Clostridium.
Member sequences for the seed alignment were chosen to
select those proteins, no more than one to a genome,
closest to B. subtilis SpoVB in a neighbor joining tree
[Cellular processes, Sporulation and germination].
Length = 488
Score = 28.4 bits (64), Expect = 8.8
Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 3/48 (6%)
Query: 222 TGIGQGLTLGRSLLYIPTLLLLLALVSATVYYVWRKRPFGKTMGSALS 269
I QGL + L L+ A+V + +V P G A++
Sbjct: 371 QSILQGLGKQKVALRN---SLIGAIVKIILLFVLTSIPSINIYGYAIT 415
>gnl|CDD|184798 PRK14704, PRK14704, anaerobic ribonucleoside triphosphate
reductase; Provisional.
Length = 618
Score = 28.2 bits (63), Expect = 9.4
Identities = 17/82 (20%), Positives = 31/82 (37%), Gaps = 14/82 (17%)
Query: 262 KTMGSALSTQSVSFRQGTNVEFGA---PAFNNGASLGLTIVYSNGPEIR-AYETHKRRFR 317
+ + SAL+ S+ F+ N++ G F+ P +R E HK+R +
Sbjct: 111 QDIKSALALSSIIFQANQNMQHGGQSFALFD----------VDLAPYVRKTVERHKKRLQ 160
Query: 318 DVISDERRIEALDIDPVDEIIY 339
+ +IE + Y
Sbjct: 161 SYPLTKEQIEEFAWKETENDTY 182
>gnl|CDD|217631 pfam03595, C4dic_mal_tran, C4-dicarboxylate transporter/malic acid
transport protein. This family of transporters have ten
alpha helical transmembrane segments. The structure of a
bacterial homologue of SLAC1 shows it to have a trimeric
arrangement. The pore is composed of five helices with a
conserved phe residue involved in gating. One homologue,
Mae1 from the yeast Schizosaccharomyces pombe, functions
as a malate uptake transporter; another, Ssu1 from
Saccharomyces cerevisiae and other fungi including
Aspergillus fumigatus, is characterized as a sulphite
efflux pump; and TehA from Escherichia coli is
identified as a tellurite resistance protein by virtue
of its association in the tehA/tehB operon. Many
homologues are incorrectly annotated as tellurite
resistance/dicarboxylate transporter (TDT) proteins.
Length = 314
Score = 27.9 bits (63), Expect = 9.7
Identities = 19/87 (21%), Positives = 29/87 (33%), Gaps = 17/87 (19%)
Query: 221 YTGIGQGLTLGRSLLYIPTLLLLLALVSATVYYVWRKRPFGKT-------MG-SALSTQS 272
G G L + LAL+ + + R RPF + +G AL+T
Sbjct: 223 QILGGLGDLFALLLWGLGLFWFFLALLL--LLRLLRLRPFSLSWWAFTFPLGAYALATLL 280
Query: 273 VSFRQGTNVEFGAPAFNNGASLGLTIV 299
G+PAF L ++
Sbjct: 281 ------LAKALGSPAF-RVLGTILLVI 300
>gnl|CDD|203331 pfam05830, NodZ, Nodulation protein Z (NodZ). The nodulation genes
of Rhizobia are regulated by the nodD gene product in
response to host-produced flavonoids and appear to
encode enzymes involved in the production of a
lipo-chitose signal molecule required for infection and
nodule formation. NodZ is required for the addition of a
2-O-methylfucose residue to the terminal reducing
N-acetylglucosamine of the nodulation signal. This
substitution is essential for the biological activity of
this molecule. Mutations in nodZ result in defective
nodulation. nodZ represents a unique nodulation gene
that is not under the control of NodD and yet is
essential for the synthesis of an active nodulation
signal.
Length = 322
Score = 27.9 bits (62), Expect = 9.9
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 11 RIESAWMDGSHRRSLVMTGVRHPTGLSVDAAMDHTLYWVDSKL 53
RI++ + + S++ VRH G + MDH YW D +L
Sbjct: 156 RIDAIYQEHFLGYSIIGVHVRHGNGEDI---MDHAPYWADPEL 195
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
0.320 0.135 0.415
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: 21,854,063
Number of extensions: 2114298
Number of successful extensions: 1904
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1901
Number of HSP's successfully gapped: 39
Length of query: 428
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 328
Effective length of database: 6,502,202
Effective search space: 2132722256
Effective search space used: 2132722256
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: 60 (27.1 bits)