RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15190
(117 letters)
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 39.6 bits (93), Expect = 1e-04
Identities = 23/114 (20%), Positives = 43/114 (37%), Gaps = 13/114 (11%)
Query: 3 VW---AQQPCVTVGGHFGPVRDIQWEPSGQFIISVSEDQTTRLHAPFVGKNTWYEMARPQ 59
+W + T+ GH V + + P G+ + S S D+T ++ GK +
Sbjct: 77 LWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCL----TTLR 132
Query: 60 VHGYDLTCLALI--STFVFASGADEKV----VRAFRTTQNFVDNIQRLCGLDFS 107
H + +A TFV +S D + +R + + + + FS
Sbjct: 133 GHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFS 186
Score = 38.9 bits (91), Expect = 2e-04
Identities = 12/40 (30%), Positives = 19/40 (47%)
Query: 3 VWAQQPCVTVGGHFGPVRDIQWEPSGQFIISVSEDQTTRL 42
+ + T+ GH V + W P G+ + S S D T R+
Sbjct: 248 LRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRI 287
Score = 34.6 bits (80), Expect = 0.005
Identities = 17/105 (16%), Positives = 40/105 (38%), Gaps = 10/105 (9%)
Query: 11 TVGGHFGPVRDIQWEPSGQFIISVSEDQTTRLHAPFVGKNTWYEMARPQVHGYDLTCLAL 70
T+ GH G V + + P G+ + + S D T ++ T + + H + +A
Sbjct: 4 TLKGHTGGVTCVAFSPDGKLLATGSGDGTIKV----WDLETGELLRTLKGHTGPVRDVAA 59
Query: 71 I--STFVFASGADEKV----VRAFRTTQNFVDNIQRLCGLDFSQH 109
T++ + +D+ + + + + + + FS
Sbjct: 60 SADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPD 104
Score = 34.2 bits (79), Expect = 0.007
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 6 QQPCVTVGGHFGPVRDIQWEPSGQFIISVSEDQTTRL 42
+ T+ GH GPVRD+ G ++ S S D+T RL
Sbjct: 41 GELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRL 77
Score = 30.0 bits (68), Expect = 0.23
Identities = 22/88 (25%), Positives = 34/88 (38%), Gaps = 8/88 (9%)
Query: 3 VW---AQQPCVTVGGHFGPVRDIQWEPSGQFIISVSEDQTTRLHAPFVGKNTWYEMARPQ 59
+W + T+ GH V + + P G + S SED T R+ T +
Sbjct: 203 LWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWD----LRTGECVQTLS 258
Query: 60 VHGYDLTCLALI-STFVFASGADEKVVR 86
H +T LA ASG+ + +R
Sbjct: 259 GHTNSVTSLAWSPDGKRLASGSADGTIR 286
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 35.8 bits (83), Expect = 2e-04
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 7 QPCVTVGGHFGPVRDIQWEPSGQFIISVSEDQTTRL 42
+ T+ GH GPV + + P G + S S+D T R+
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRV 37
>gnl|CDD|197651 smart00320, WD40, WD40 repeats. Note that these repeats are
permuted with respect to the structural repeats
(blades) of the beta propeller domain.
Length = 40
Score = 35.8 bits (83), Expect = 3e-04
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 7 QPCVTVGGHFGPVRDIQWEPSGQFIISVSEDQTTRLH 43
+ T+ GH GPV + + P G+++ S S+D T +L
Sbjct: 3 ELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 33.1 bits (74), Expect = 0.023
Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 4/87 (4%)
Query: 6 QQPCVTVGGHFGPVRDIQWEPSGQFIISVSEDQTTRLHAPFVGKNTWYEMARPQVHGYDL 65
T+ GH V + + P G+ + S S D T RL + + H +
Sbjct: 274 SSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRL--WDLETGKLLSSLTLKGHEGPV 331
Query: 66 TCLALIS--TFVFASGADEKVVRAFRT 90
+ L+ + + + G+D+ +R +
Sbjct: 332 SSLSFSPDGSLLVSGGSDDGTIRLWDL 358
Score = 30.4 bits (67), Expect = 0.19
Identities = 19/114 (16%), Positives = 38/114 (33%), Gaps = 8/114 (7%)
Query: 9 CVTVGGHFGPVRDIQWEPSGQFIISVSEDQTTRL---HAPFVGKNTWYEMARPQVHGYDL 65
+ + GH + I + P G+ ++S S D T +L + + V L
Sbjct: 58 SLLLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLAL 117
Query: 66 TCLALISTFVFASGADEKVV-----RAFRTTQNFVDNIQRLCGLDFSQHPTNIL 114
+ S + +S D V + + + + + L FS +
Sbjct: 118 SSPDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLA 171
Score = 28.1 bits (61), Expect = 1.0
Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 4/64 (6%)
Query: 24 WEPSGQFIISVSEDQTTRLHAPFVGKNTWYEMARPQVHGYDLTCLALIS-TFVFASGADE 82
+ P G + S S D T RL + ++ H + +A + ASG+ +
Sbjct: 249 FSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSG---HSSSVLSVAFSPDGKLLASGSSD 305
Query: 83 KVVR 86
VR
Sbjct: 306 GTVR 309
Score = 25.4 bits (54), Expect = 8.9
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 10 VTVGGHFGPVRDIQWEPSGQFIISVSEDQTTRL 42
+ GH V + + P G+ + S S D T RL
Sbjct: 406 RNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRL 438
>gnl|CDD|213918 TIGR04305, fol_rel_CADD, putative folate metabolism protein, CADD
family. This protein family, related to but outside the
family of PqqC proteins involved in PQQ biosynthesis,
includes the well-studied Chlamydia protein CADD
(Chlamydia protein Associating with Death Domains),
which can induce apoptosis in a host cell. Other members
of this family occur in Rickettsia and Wolbachia,
unrelated in terms of phylogeny (both are
alphaproteobacteria) but similar in living
intracellularly. Local gene context in these species,
although not in Trichodesmium or Nitrosomonas eutropha,
suggests a role in folate metabolism, and some species
with this protein lack FolE but have other folate
synthesis proteins.
Length = 212
Score = 28.1 bits (63), Expect = 0.98
Identities = 14/32 (43%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 74 FVFASGADEKVVR---AFRTTQNFVDNIQRLC 102
F G D+K VR A +TQ VD RLC
Sbjct: 88 FAEGLGLDDKEVRNAPALPSTQKLVDTFFRLC 119
>gnl|CDD|235976 PRK07232, PRK07232, bifunctional malic enzyme
oxidoreductase/phosphotransacetylase; Reviewed.
Length = 752
Score = 27.8 bits (63), Expect = 1.4
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 3/22 (13%)
Query: 75 VFASGADEKVVRAFRTTQNFVD 96
VFA G +E+V+RA Q VD
Sbjct: 443 VFAEGEEERVLRA---AQEVVD 461
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 27.6 bits (61), Expect = 1.4
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 8 PCVTVGGHFGPVRDIQWEPS-GQFIISVSEDQTTRL 42
P + + GH + D+Q+ P + + S SED T R+
Sbjct: 66 PVIKLKGHTSSILDLQFNPCFSEILASGSEDLTIRV 101
>gnl|CDD|183799 PRK12862, PRK12862, malic enzyme; Reviewed.
Length = 763
Score = 26.4 bits (59), Expect = 4.2
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 3/22 (13%)
Query: 75 VFASGADEKVVRAFRTTQNFVD 96
VFA G DE+V+RA Q VD
Sbjct: 451 VFAEGEDERVLRA---AQVVVD 469
>gnl|CDD|236100 PRK07798, PRK07798, acyl-CoA synthetase; Validated.
Length = 533
Score = 26.0 bits (58), Expect = 5.5
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 10/32 (31%)
Query: 55 MARPQV------HGYDLTCLALISTFVFASGA 80
MARP + YDL+ L I++ GA
Sbjct: 279 MARPLLDALEARGPYDLSSLFAIAS----GGA 306
>gnl|CDD|238911 cd01936, Ntn_CA, Cephalosporin acylase (CA) belongs to a family of
beta-lactam acylases that includes penicillin G acylase
(PGA) and aculeacin A acylase. PGA and CA are crucial
for the production of backbone chemicals like
6-aminopenicillanic acid and 7-aminocephalosporanic acid
(7-ACA), which can be used to synthesize semi-synthetic
penicillins and cephalosporins, respectively. While
both PGA and CA have a conserved Ntn (N-terminal
nucleophile) hydrolase fold and the structural
similarity at their active sites is very high, their
sequence similarity to other Ntn's is low.
Length = 469
Score = 25.7 bits (57), Expect = 6.6
Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 10/57 (17%)
Query: 35 SEDQTTRL----HAPFVGKNTWYEMARPQVH---GYDLTCLALISTFVFASGADEKV 84
+ + L H P+ G +YE + G D+ +L + V G +E +
Sbjct: 72 TANGNGMLLINPHFPWTGGVRFYEA---HLTSPGGLDVYGASLPGSPVINIGFNEHL 125
>gnl|CDD|213291 cd05924, FACL_like_5, Uncharacterized subfamily of fatty acid CoA
ligase (FACL). Fatty acyl-CoA ligases catalyze the
ATP-dependent activation of fatty acids in a two-step
reaction. The carboxylate substrate first reacts with
ATP to form an acyl-adenylate intermediate, which then
reacts with CoA to produce an acyl-CoA ester. This is a
required step before free fatty acids can participate in
most catabolic and anabolic reactions.
Length = 365
Score = 25.7 bits (57), Expect = 7.3
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 10/32 (31%)
Query: 55 MARPQVH------GYDLTCLALISTFVFASGA 80
ARP + YDL+ L IS+ SGA
Sbjct: 118 FARPLLEALEAAGRYDLSSLRAISS----SGA 145
>gnl|CDD|214889 smart00892, Endonuclease_NS, DNA/RNA non-specific endonuclease. A
family of bacterial and eukaryotic endonucleases share
the following characteristics: they act on both DNA and
RNA, cleave double-stranded and single-stranded nucleic
acids and require a divalent ion such as magnesium for
their activity. An histidine has been shown to be
essential for the activity of the Serratia marcescens
nuclease. This residue is located in a conserved region
which also contains an aspartic acid residue that could
be implicated in the binding of the divalent ion.
Length = 198
Score = 25.4 bits (56), Expect = 7.9
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 88 FRTTQNFVDNIQRLCGLDF 106
Q VDNI+RL GLDF
Sbjct: 174 LCEFQVPVDNIERLTGLDF 192
>gnl|CDD|235534 PRK05618, PRK05618, 50S ribosomal protein L25/general stress
protein Ctc; Reviewed.
Length = 197
Score = 25.2 bits (56), Expect = 8.3
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 7/38 (18%)
Query: 19 VRDIQWEPSGQFII-----SVSEDQTTRLHAP--FVGK 49
V+D+Q P FI+ V + ++ P FVG+
Sbjct: 76 VKDVQRHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGE 113
>gnl|CDD|216713 pfam01804, Penicil_amidase, Penicillin amidase. Penicillin amidase
or penicillin acylase EC:3.5.1.11 catalyzes the
hydrolysis of benzylpenicillin to phenylacetic acid and
6-aminopenicillanic acid (6-APA) a key intermediate in
the the synthesis of penicillins. Also in the family are
cephalosporin acylase and aculeacin A acylase, which are
involved in the synthesis of related peptide
antibiotics.
Length = 668
Score = 25.4 bits (56), Expect = 9.9
Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 7/58 (12%)
Query: 43 HAPFVGKNTWYEMARPQVH--GYDLTCLALISTFVFASGADEKVVRAFRTTQNFVDNI 98
H P+ + WYE Q+ G+D+ G ++ V A+ T + D +
Sbjct: 162 HLPWSAPSVWYEA---QLVAPGFDVYGATFPGLPGILIGHNQTV--AWGATVSGADVV 214
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
0.326 0.138 0.449
Gapped
Lambda K H
0.267 0.0682 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,892,333
Number of extensions: 480239
Number of successful extensions: 438
Number of sequences better than 10.0: 1
Number of HSP's gapped: 437
Number of HSP's successfully gapped: 29
Length of query: 117
Length of database: 10,937,602
Length adjustment: 80
Effective length of query: 37
Effective length of database: 7,389,282
Effective search space: 273403434
Effective search space used: 273403434
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.3 bits)