RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13634
(242 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 = 36.0 bits (84), Expect = 8e-04
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 206 NVKNIKALDYDPVARQIYWIDSKLQAIKRAS 236
+ + L D + ++YW D L I+ A+
Sbjct: 7 GLGHPNGLAVDWIEGRLYWTDWGLDVIEVAN 37
Score = 29.1 bits (66), Expect = 0.23
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 34 NSLTVNYDEKRVYYVNLLSSSIESIDIEGRN 64
N L V++ E R+Y+ + IE +++G N
Sbjct: 12 NGLAVDWIEGRLYWTDWGLDVIEVANLDGTN 42
Score = 26.8 bits (60), Expect = 1.6
Identities = 11/22 (50%), Positives = 13/22 (59%), Gaps = 3/22 (13%)
Query: 3 WSDWGAGNGGTIERSALDGTQR 24
W+DWG IE + LDGT R
Sbjct: 25 WTDWGLD---VIEVANLDGTNR 43
>gnl|CDD|201923 pfam01683, EB, EB module. This domain has no known function. It is
found in several C. elegans proteins. The domain
contains 8 conserved cysteines that probably form four
disulphide bridges. This domain is found associated with
kunitz domains pfam00014.
Length = 52
Score = 27.0 bits (60), Expect = 1.4
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 158 KCECPTHYTMVNGTC 172
C+CP +T+V G C
Sbjct: 38 TCQCPEGFTLVGGRC 52
>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 = 25.5 bits (56), Expect = 3.7
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 8/35 (22%)
Query: 134 CAVANNECDY--LCLATPGRGGGLNYKCECPTHYT 166
CA A+N C C+ TPG +Y+C CP YT
Sbjct: 2 CA-ASNPCSNGGTCVNTPG-----SYRCVCPPGYT 30
>gnl|CDD|215330 PLN02612, PLN02612, phytoene desaturase.
Length = 567
Score = 28.3 bits (63), Expect = 4.6
Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 6/68 (8%)
Query: 164 HYTMVNGTCMAPSSFLIYAQRNILSRLITDPTQCPDSPYEIPNVKNIKALDYDPVARQIY 223
H+ + NG+ + ++ +IL L+ PD EIP K + L PV
Sbjct: 344 HFLLTNGSVVEGDVYVSATPVDILKLLL------PDQWKEIPYFKKLDKLVGVPVINVHI 397
Query: 224 WIDSKLQA 231
W D KL+
Sbjct: 398 WFDRKLKN 405
>gnl|CDD|224370 COG1453, COG1453, Predicted oxidoreductases of the aldo/keto
reductase family [General function prediction only].
Length = 391
Score = 27.7 bits (62), Expect = 6.6
Identities = 10/32 (31%), Positives = 14/32 (43%)
Query: 210 IKALDYDPVARQIYWIDSKLQAIKRASENATR 241
+ A +D V Q +ID K QA + A
Sbjct: 163 VDAYPWDFVQLQYNYIDQKNQAGTEGLKYAAS 194
>gnl|CDD|236356 PRK08944, motB, flagellar motor protein MotB; Reviewed.
Length = 302
Score = 27.3 bits (61), Expect = 6.9
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 7/34 (20%)
Query: 59 DIEGRNKITIVANIEDKPVTLTLYKSEIFYSNWD 92
D+ G IT+ + ++ P+ SE++ SNWD
Sbjct: 207 DVPG--IITVSGHTDNVPI-----SSELYRSNWD 233
>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 = 24.7 bits (54), Expect = 7.0
Identities = 14/32 (43%), Positives = 15/32 (46%), Gaps = 7/32 (21%)
Query: 138 NNECDY--LCLATPGRGGGLNYKCECPTHYTM 167
NN C C+ TPG Y CECP YT
Sbjct: 4 NNPCSNGGTCVDTPGG-----YTCECPEGYTG 30
>gnl|CDD|218955 pfam06247, Plasmod_Pvs28, Plasmodium ookinete surface protein
Pvs28. This family consists of several ookinete surface
protein (Pvs28) from several species of Plasmodium.
Pvs25 and Pvs28 are expressed on the surface of
ookinetes. These proteins are potential candidates for
vaccine and induce antibodies that block the infectivity
of Plasmodium vivax in immunised animals.
Length = 196
Score = 27.0 bits (60), Expect = 7.8
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 138 NNEC-DY-LCLATPGRGGGLNYKCECPTHYTMVNGTC 172
N C +Y C+ + KC C YT+ G C
Sbjct: 49 NKVCGEYATCINQANKAEEKALKCGCINGYTLSQGVC 85
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
0.316 0.132 0.402
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: 11,836,983
Number of extensions: 1050859
Number of successful extensions: 823
Number of sequences better than 10.0: 1
Number of HSP's gapped: 823
Number of HSP's successfully gapped: 12
Length of query: 242
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 148
Effective length of database: 6,768,326
Effective search space: 1001712248
Effective search space used: 1001712248
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 (21.6 bits)
S2: 58 (26.3 bits)