RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12788
(254 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 = 34.2 bits (79), Expect = 0.044
Identities = 24/120 (20%), Positives = 55/120 (45%), Gaps = 16/120 (13%)
Query: 11 YALSW-PAGY-ILAAGSDRIVTIYE-SDGRVHRIFDYTAPHYKEREFTVACSSPSGQAVV 67
++++ P G +L++ SD + +++ S G+ E SP G +
Sbjct: 181 NSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTL-----RGHENGVNSVAFSPDGYLLA 235
Query: 68 VGSYDN-IKLFAWSPSKSVWEEQPNKTIPNL-YTISALSWKRDGSRIACGGLCGSVELFE 125
GS D I+++ + + +T+ ++++L+W DG R+A G G++ +++
Sbjct: 236 SGSEDGTIRVW------DLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 31.9 bits (73), Expect = 0.23
Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 6 HPVPPYALSW-PAGYILAAGS-DRIVTIYESDGRVHRIFDYTAPHYKEREFTVACSSPSG 63
H ++++ P GY+LA+GS D + +++ T + ++A S P G
Sbjct: 218 HENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGEC---VQTLSGHTNSVTSLAWS-PDG 273
Query: 64 QAVVVGSYDN-IKLFA 78
+ + GS D I+++
Sbjct: 274 KRLASGSADGTIRIWD 289
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 32.8 bits (73), Expect = 0.18
Identities = 24/114 (21%), Positives = 45/114 (39%), Gaps = 6/114 (5%)
Query: 12 ALSWPAGYILAAGSDRIVTIYESDGRVHRIFDYTAPHYKEREFTVACSSPSGQAVVVGSY 71
A S + + SD V ++ D ++ E + SP G +V G
Sbjct: 291 AFSPDGKLLASGSSDGTVRLW--DLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGS 348
Query: 72 DNIKLFAWSPSKSVWEEQPNKTIPNLYTISALSWKRDGSRIACGGLCGSVELFE 125
D+ + W +P KT+ + ++S+ DG ++ G G+V L++
Sbjct: 349 DDGTIRLWDLRTG----KPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWD 398
>gnl|CDD|182098 PRK09828, PRK09828, putative fimbrial outer membrane usher protein;
Provisional.
Length = 865
Score = 31.3 bits (71), Expect = 0.50
Identities = 23/58 (39%), Positives = 27/58 (46%), Gaps = 23/58 (39%)
Query: 8 VPPYA-----LSWPAGYILAAGSDRIVTIYESDGRVHRIFDYTAPHYKEREFTVACSS 60
VPP A LS P+GY GSD IVTI E+DG +R F+ SS
Sbjct: 311 VPPGAFVIDDLS-PSGY----GSDLIVTIEEADG-------------SKRTFSQPFSS 350
>gnl|CDD|216001 pfam00577, Usher, Type VII secretion system (T7SS), usher protein.
The chaperone-usher (CU) pathway or Type VII secretion
system (T7SS) in Gram-negative (diderm) bacteria is
responsible for the secretion and assembly of prepilins
for fimbriae biogenesis, the prototypical Type 1 pili.
Following the prepilins export to the periplasm by the
Sec translocon, the biogenesis of fimbriae requires a
two-component assembly and transport system which is
composed of a periplasmic chaperone and an outer
membrane protein, which has been termed a molecular
'usher'. The usher protein is rather large (from 86 to
100 Kd) and seems to be mainly composed of
membrane-spanning beta-sheets, a structure reminiscent
of porins. Although the degree of sequence similarity of
these proteins is not very high they share a number of
characteristics. One of these is the presence of two
pairs of cysteines, the first one located in the
N-terminal part and the second at the C-terminal
extremity that are probably involved in disulphide
bonds. The best conserved region is located in the
central part of these proteins.
Length = 552
Score = 30.3 bits (69), Expect = 0.97
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 10/59 (16%)
Query: 1 GRVV-QHPVP--PYALS--WPAGYILAAGSDRIVTIYESDGRVHR-IFDYTAPHYKERE 53
G V+ Q VP P+ ++ +P+G G D VT+ ESDG V Y++ R
Sbjct: 107 GYVIYQTTVPPGPFEITDLYPSGS----GGDLDVTVTESDGSVQTFTVPYSSVPNLLRP 161
>gnl|CDD|234144 TIGR03197, MnmC_Cterm, tRNA U-34 5-methylaminomethyl-2-thiouridine
biosynthesis protein MnmC, C-terminal domain. In
Escherichia coli, the protein previously designated YfcK
is now identified as the bifunctional enzyme MnmC. It
acts, following the action of the heterotetramer of GidA
and MnmE, in the modification of U-34 of certain tRNA to
5-methylaminomethyl-2-thiouridine (mnm5s2U). In other
bacterial, the corresponding proteins are usually but
always found as a single polypeptide chain, but
occasionally as the product of tandem genes. This model
represents the C-terminal region of the multifunctional
protein [Protein synthesis, tRNA and rRNA base
modification].
Length = 381
Score = 29.2 bits (66), Expect = 2.3
Identities = 11/42 (26%), Positives = 15/42 (35%), Gaps = 9/42 (21%)
Query: 77 FAWSPSKSVWEEQPNKTIPNLYTISALSWKRDGSRIACGGLC 118
+ K+ +P P LY + L GSR GL
Sbjct: 314 AELAKDKNRPIAEPAPYYPGLYVLGGL-----GSR----GLT 346
>gnl|CDD|139075 PRK12568, PRK12568, glycogen branching enzyme; Provisional.
Length = 730
Score = 28.8 bits (64), Expect = 3.3
Identities = 27/89 (30%), Positives = 36/89 (40%), Gaps = 14/89 (15%)
Query: 23 AGSDRIVTIYESDGRVHRIFDYTAPHYKEREFTVACSSPSGQAVVVGSYDNIKLFAWSPS 82
AG+ I +DGRV D P ++ E P A VV S FAW+ +
Sbjct: 185 AGARYKYAITAADGRVLLKAD---PVARQTEL------PPATASVVPSAAA---FAWTDA 232
Query: 83 KSVWEEQPNKTIPNL--YTISALSWKRDG 109
+ P L Y + A SW+RDG
Sbjct: 233 AWMARRDPAAVPAPLSIYEVHAASWRRDG 261
>gnl|CDD|224951 COG2040, MHT1, Homocysteine/selenocysteine methylase
(S-methylmethionine-dependent) [Amino acid transport and
metabolism].
Length = 300
Score = 28.1 bits (63), Expect = 4.2
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 78 AWSPSKSVWEEQPNKTIPNLYTISALSWKRDGSRIACGGLCGS 120
+ P+ W + Y+ A SW G+RI GG C +
Sbjct: 245 QYDPAGKTW--HGPALSADSYSTLAKSWVEAGARII-GGCCRT 284
>gnl|CDD|223689 COG0616, SppA, Periplasmic serine proteases (ClpP class)
[Posttranslational modification, protein turnover,
chaperones / Intracellular trafficking and secretion].
Length = 317
Score = 27.8 bits (62), Expect = 5.5
Identities = 10/22 (45%), Positives = 13/22 (59%), Gaps = 2/22 (9%)
Query: 8 VPPYALSWPAGYILAAGSDRIV 29
V YA S GY +A +D+IV
Sbjct: 135 VGGYAAS--GGYYIALAADKIV 154
>gnl|CDD|234500 TIGR04206, near_ArtA, TIGR04206 family protein. Members of this
integral membrane protein family are found exclusively
in halophilic archaea. In at least three species
(Haloarcula marismortui, Haloquadratum walsbyi, and
Haloferax volcanii), members are found in the gene
neighborhood of archaeosortase A, suggesting a role in
protein sorting.
Length = 139
Score = 27.0 bits (60), Expect = 6.2
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 8 VPPYALSWPAG---YILAAGSDRIVTIYESDGRV 38
+PPY L+WP G Y+ A GS D RV
Sbjct: 57 LPPYILAWPLGVALYLFAVGSAVAGVFGREDVRV 90
>gnl|CDD|221076 pfam11316, Rhamno_transf, Putative rhamnosyl transferase. Most
members of this family are uncharacterized, but one is a
putative side-chain-rhamnosyl transferase.
Length = 235
Score = 27.2 bits (61), Expect = 7.7
Identities = 12/59 (20%), Positives = 19/59 (32%), Gaps = 15/59 (25%)
Query: 5 QHPVPPYALSWPAGYILAAGSDRIV-------------TIYESDGRVHRIFDYTAPHYK 50
A+ + GY+L D IV +Y G I ++ H+K
Sbjct: 146 WAANRRVAIDFNRGYVLRLEGDGIVALPLRTPFWNAGLAVYVRPGDRRTIMNF--GHHK 202
>gnl|CDD|173055 PRK14591, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 169
Score = 26.5 bits (58), Expect = 9.8
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 9/48 (18%)
Query: 212 NEKFYFDNVTVCLVFNAGE------LSIIEYGNNEILTCVRIPTDSSE 253
++ YF ++ C V N + IIE G NE+L C D+SE
Sbjct: 97 EDEVYFKDLIGCSVKNINNDSFGVVVDIIETGANEVLVCKE---DNSE 141
>gnl|CDD|179541 PRK03114, PRK03114, NTPase; Reviewed.
Length = 169
Score = 26.5 bits (59), Expect = 9.8
Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 7/57 (12%)
Query: 121 VELFESVLKRTIWKGKFEMIYVS-PSQVLVKPLSGESKGRGVILKSQYGYEITDVAI 176
V E V K VS PS V +P S E +G I +++ E + I
Sbjct: 13 VGAVEKVWKDAEI------TSVSVPSGVAAQPFSDEETMQGAINRAKRALEEGEADI 63
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
0.319 0.137 0.421
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,136,537
Number of extensions: 1236480
Number of successful extensions: 963
Number of sequences better than 10.0: 1
Number of HSP's gapped: 961
Number of HSP's successfully gapped: 21
Length of query: 254
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 159
Effective length of database: 6,723,972
Effective search space: 1069111548
Effective search space used: 1069111548
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 (21.7 bits)
S2: 58 (26.1 bits)