RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5792
(377 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 = 46.4 bits (111), Expect = 2e-07
Identities = 16/30 (53%), Positives = 20/30 (66%)
Query: 240 IAVDWIAQNIYWSDPKENVIEVARLTGQYR 269
+AVDWI +YW+D +VIEVA L G R
Sbjct: 14 LAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 43.7 bits (104), Expect = 2e-06
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 270 YVLISGGVDQPSALAVDPESGYLFWSESGKIPLIARAGLDGK 311
L+S G+ P+ LAVD G L+W++ G +I A LDG
Sbjct: 1 RTLLSSGLGHPNGLAVDWIEGRLYWTDWGL-DVIEVANLDGT 41
Score = 35.7 bits (83), Expect = 0.001
Identities = 10/38 (26%), Positives = 14/38 (36%)
Query: 182 SKVSLAAKVDFHAAEDYIYWVDIDHGTISRTHRDGTGR 219
S + + E +YW D I + DGT R
Sbjct: 6 SGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 28.0 bits (63), Expect = 0.94
Identities = 11/44 (25%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 313 QTILAQEIIMPIKDITLDRKNKRVYWCYSVGSNVLESMDYSGGS 356
+T+L+ + P + +D R+YW G +V+E + G +
Sbjct: 1 RTLLSSGLGHP-NGLAVDWIEGRLYWT-DWGLDVIEVANLDGTN 42
Score = 26.0 bits (58), Expect = 3.9
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 66 FYKGRIIYSDANDGNIRSINLDGSN 90
+ +GR+ ++D I NLDG+N
Sbjct: 18 WIEGRLYWTDWGLDVIEVANLDGTN 42
>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 = 39.5 bits (93), Expect = 7e-05
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 247 QNIYWSDPK-ENVIEVARLTGQYRYVLISGGVDQPSALAVDP 287
+YW+D I VA L G R L S + P+ +AVDP
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIAVDP 42
Score = 28.7 bits (65), Expect = 0.46
Identities = 12/42 (28%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 290 GYLFWSESGKIPLIARAGLDGKKQ-TILAQEIIMPIKDITLD 330
G L+W++S I+ A L+G + T+ ++++ P I +D
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLFSEDLQWP-NGIAVD 41
>gnl|CDD|219847 pfam08450, SGL, SMP-30/Gluconolaconase/LRE-like region. This
family describes a region that is found in proteins
expressed by a variety of eukaryotic and prokaryotic
species. These proteins include various enzymes, such as
senescence marker protein 30 (SMP-30), gluconolactonase
and luciferin-regenerating enzyme (LRE). SMP-30 is known
to hydrolyse diisopropyl phosphorofluoridate in the
liver, and has been noted as having sequence similarity,
in the region described in this family, with PON1 and
LRE.
Length = 245
Score = 31.4 bits (72), Expect = 0.61
Identities = 9/24 (37%), Positives = 10/24 (41%)
Query: 193 HAAEDYIYWVDIDHGTISRTHRDG 216
E +YWVDI G I R
Sbjct: 8 DEEEGALYWVDILGGRIHRLDPAT 31
>gnl|CDD|237999 cd00038, CAP_ED, effector domain of the CAP family of transcription
factors; members include CAP (or cAMP receptor protein
(CRP)), which binds cAMP, FNR (fumarate and nitrate
reduction), which uses an iron-sulfur cluster to sense
oxygen) and CooA, a heme containing CO sensor. In all
cases binding of the effector leads to conformational
changes and the ability to activate transcription.
Cyclic nucleotide-binding domain similar to CAP are also
present in cAMP- and cGMP-dependent protein kinases
(cAPK and cGPK) and vertebrate cyclic nucleotide-gated
ion-channels. Cyclic nucleotide-monophosphate binding
domain; proteins that bind cyclic nucleotides (cAMP or
cGMP) share a structural domain of about 120 residues;
the best studied is the prokaryotic catabolite gene
activator, CAP, where such a domain is known to be
composed of three alpha-helices and a distinctive
eight-stranded, antiparallel beta-barrel structure;
three conserved glycine residues are thought to be
essential for maintenance of the structural integrity of
the beta-barrel; CooA is a homodimeric transcription
factor that belongs to CAP family; cAMP- and
cGMP-dependent protein kinases (cAPK and cGPK) contain
two tandem copies of the cyclic nucleotide-binding
domain; cAPK's are composed of two different subunits, a
catalytic chain and a regulatory chain, which contains
both copies of the domain; cGPK's are single chain
enzymes that include the two copies of the domain in
their N-terminal section; also found in vertebrate
cyclic nucleotide-gated ion-channels.
Length = 115
Score = 28.8 bits (65), Expect = 1.8
Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 8/58 (13%)
Query: 181 LSKVSLAAKVDFHAAEDYIYW----VD----IDHGTISRTHRDGTGRENIIEYVETGD 230
L +++ A + A + I D + G++ D GRE I+ ++ GD
Sbjct: 10 LEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGD 67
>gnl|CDD|225921 COG3386, COG3386, Gluconolactonase [Carbohydrate transport and
metabolism].
Length = 307
Score = 28.9 bits (65), Expect = 4.8
Identities = 9/34 (26%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 192 FHAAEDYIYWVDIDHGTISRTHRDGTGRENIIEY 225
+ + WVDI G I R TG++ +
Sbjct: 32 WDPDRGALLWVDILGGRIHRLD-PETGKKRVFPS 64
>gnl|CDD|172990 PRK14524, rpsP, 30S ribosomal protein S16; Provisional.
Length = 94
Score = 27.1 bits (60), Expect = 5.5
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 3/62 (4%)
Query: 210 SRTHRDGTGRENIIEYVETGDPTPVDQFTDIAVDWIAQNIYWSDPKENVIEVARLTGQYR 269
SR RDG E++ Y +P + + AV+WI + + P + V ++ R G +
Sbjct: 24 SRKRRDGAYIESLGYYNPLKEPYEIKVDVERAVEWILKG---AQPSDTVRDILRKFGVMK 80
Query: 270 YV 271
V
Sbjct: 81 KV 82
>gnl|CDD|236594 PRK09618, flgD, flagellar basal body rod modification protein;
Provisional.
Length = 142
Score = 27.7 bits (62), Expect = 6.0
Identities = 8/40 (20%), Positives = 15/40 (37%), Gaps = 5/40 (12%)
Query: 241 AVDWIAQNIYWSDPKENVIE-----VARLTGQYRYVLISG 275
+ I + + W ++ V + G Y VL +G
Sbjct: 87 YSELIGKEVEWEGEDGEIVSGTVTSVKQKDGDYPLVLDNG 126
>gnl|CDD|223736 COG0664, Crp, cAMP-binding proteins - catabolite gene activator and
regulatory subunit of cAMP-dependent protein kinases
[Signal transduction mechanisms].
Length = 214
Score = 27.9 bits (62), Expect = 7.7
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 4/41 (9%)
Query: 192 FHAAE--DYIYWVDIDHGTISRTHRDGTGRENIIEYVETGD 230
F E D +Y + G + GRE I+ ++ GD
Sbjct: 35 FTEGEEADSLYIIL--SGIVKLYANTEDGREIILGFLGPGD 73
>gnl|CDD|225241 COG2366, COG2366, Protein related to penicillin acylase [General
function prediction only].
Length = 768
Score = 28.2 bits (63), Expect = 9.3
Identities = 15/121 (12%), Positives = 30/121 (24%), Gaps = 20/121 (16%)
Query: 201 WVDIDHGTISRTHRDGTGRENIIEYVETGDPTPVDQ---FTDIAVDWIAQN-------IY 250
W+ + + + + + + G PV + IA+ W
Sbjct: 346 WLPFEQRNETIKVKGANPIQLEVPWTNHG---PVVEDGGGLYIALSWTGLVPTDEILACL 402
Query: 251 WSDPKENVIEVARLTGQYRYVLISGGVDQPSALAVDPESGYLFWSESGKIPLIARAGLDG 310
+ E +Y P +G + + G P+ R G
Sbjct: 403 LLNLAATSFEDFGNAAEY-------FAIPPQNWVYADAAGNIGYLPPGLYPIRERGDPVG 455
Query: 311 K 311
Sbjct: 456 P 456
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 0.135 0.390
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,240,521
Number of extensions: 1889559
Number of successful extensions: 1522
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1520
Number of HSP's successfully gapped: 22
Length of query: 377
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 279
Effective length of database: 6,590,910
Effective search space: 1838863890
Effective search space used: 1838863890
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: 60 (26.8 bits)