RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12461
(294 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 = 0.001
Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 233 HSASVPGILAMDIQVEDTSKILTGGNDCQATVFNKDTEQVVAILKGHRKKVTRVVYHPS 291
H+ V + A D + + +G +D +++ +T + V L GH V+ V + P
Sbjct: 50 HTGPVRDVAASA----DGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPD 104
Score = 38.9 bits (91), Expect = 0.002
Identities = 11/44 (25%), Positives = 21/44 (47%)
Query: 248 EDTSKILTGGNDCQATVFNKDTEQVVAILKGHRKKVTRVVYHPS 291
D K+L+ +D +++ T + + L+GH V V + P
Sbjct: 187 PDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPD 230
Score = 37.7 bits (88), Expect = 0.004
Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 7/75 (9%)
Query: 219 NLRAFRNVSSQAGLHSASVPGILAMDIQVEDTSKILTGG-NDCQATVFNKDTEQVVAILK 277
++ + +++ G H+ V + + D +++ T + VA L
Sbjct: 121 DVETGKCLTTLRG-HTDWV-----NSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLT 174
Query: 278 GHRKKVTRVVYHPSE 292
GH +V V + P
Sbjct: 175 GHTGEVNSVAFSPDG 189
Score = 37.7 bits (88), Expect = 0.005
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 239 GILAMDIQVEDTSKILTGGNDCQATVFNKDTEQVVAILKGHRKKVTRVVYHP 290
G+ + D + TG D V++ +T +++ LKGH V V
Sbjct: 11 GVTCVAF-SPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASA 61
Score = 31.9 bits (73), Expect = 0.34
Identities = 9/39 (23%), Positives = 18/39 (46%)
Query: 253 ILTGGNDCQATVFNKDTEQVVAILKGHRKKVTRVVYHPS 291
+ + D V++ +T + + L+GH V V + P
Sbjct: 108 LSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPD 146
Score = 29.6 bits (67), Expect = 1.7
Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 7/74 (9%)
Query: 219 NLRAFRNVSSQAGLHSASVPGILAMDIQVEDTSKILTGGN-DCQATVFNKDTEQVVAILK 277
+L + + + G H V + +L G+ D V++ T + V L
Sbjct: 205 DLSTGKCLGTLRG-HENGV-----NSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLS 258
Query: 278 GHRKKVTRVVYHPS 291
GH VT + + P
Sbjct: 259 GHTNSVTSLAWSPD 272
>gnl|CDD|182842 PRK10923, glnG, nitrogen regulation protein NR(I); Provisional.
Length = 469
Score = 31.8 bits (72), Expect = 0.49
Identities = 27/82 (32%), Positives = 35/82 (42%), Gaps = 22/82 (26%)
Query: 112 SSSTGPNIGERPALVFSGTQNV--VPGR---------VNGEASNGAGVVGHELHGLRSAH 160
+ T IGE PA+ Q+V + GR +NGE+ G +V H LH H
Sbjct: 134 NGPTTDIIGEAPAM-----QDVFRIIGRLSRSSISVLINGESGTGKELVAHALH----RH 184
Query: 161 VPHANA--IAAEAAGTPNQPVE 180
P A A IA A P +E
Sbjct: 185 SPRAKAPFIALNMAAIPKDLIE 206
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 30.1 bits (66), Expect = 1.5
Identities = 10/45 (22%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 249 DTSKILTGGNDCQATVFN-KDTEQVVAILKGHRKKVTRVVYHPSE 292
D S + +G +D +++ + + ++ L GH V V + P
Sbjct: 252 DGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDG 296
>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 = 26.5 bits (59), Expect = 2.4
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 269 TEQVVAILKGHRKKVTRVVYHPS 291
+ +++ LKGH VT V + P
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPD 23
>gnl|CDD|233585 TIGR01818, ntrC, nitrogen regulation protein NR(I). This model
represents NtrC, a DNA-binding response regulator that
is phosphorylated by NtrB and interacts with sigma-54.
NtrC usually controls the expression of glutamine
synthase, GlnA, and may be called GlnL, GlnG, etc
[Central intermediary metabolism, Nitrogen metabolism,
Regulatory functions, DNA interactions, Signal
transduction, Two-component systems].
Length = 463
Score = 28.9 bits (65), Expect = 3.8
Identities = 26/81 (32%), Positives = 34/81 (41%), Gaps = 16/81 (19%)
Query: 110 GHSSSTGPNIGERPAL--VF------SGTQNVVPGRVNGEASNGAGVVGHELHGLRSAHV 161
G + + IGE PA+ VF S + V +NGE+ G +V LH H
Sbjct: 128 GEAEDSAELIGEAPAMQEVFRAIGRLSRSDITV--LINGESGTGKELVARALH----RHS 181
Query: 162 PHANA--IAAEAAGTPNQPVE 180
P AN IA A P +E
Sbjct: 182 PRANGPFIALNMAAIPKDLIE 202
>gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein. This
model represents a group of paralogous families in
plasmodium species alternately annotated as reticulocyte
binding protein, 235-kDa family protein and rhoptry
protein. Rhoptry protein is localized on the cell surface
and is extremely large (although apparently lacking in
repeat structure) and is important for the process of
invasion of the RBCs by the parasite. These proteins are
found in P. falciparum, P. vivax and P. yoelii.
Length = 2757
Score = 28.9 bits (64), Expect = 4.2
Identities = 17/67 (25%), Positives = 36/67 (53%), Gaps = 10/67 (14%)
Query: 25 DNIVSSAKNYMEDSTELKTKVMELKGELMIDLTEK----------DDDLESCVMSSEHNR 74
++++ + + Y+ED E+K K E++ E+ I++ K DDD + ++S +H+
Sbjct: 1239 EHMIKAMEAYIEDLDEIKEKSPEIENEMGIEMDIKAEMETFNISHDDDKDHHIISKKHDE 1298
Query: 75 PVGDTGE 81
+ D E
Sbjct: 1299 NISDIRE 1305
>gnl|CDD|177853 PLN02202, PLN02202, carbonate dehydratase.
Length = 284
Score = 28.1 bits (62), Expect = 5.2
Identities = 18/68 (26%), Positives = 32/68 (47%)
Query: 151 HELHGLRSAHVPHANAIAAEAAGTPNQPVEQIGISEEVQAKLQDKATILTQERKKRSRAA 210
H LHG++ A H A + + + +IG E ++++DK L +ER K + A
Sbjct: 126 HHLHGVQYAAELHMVHQAKDGSFAVVASLFKIGTEEPFLSQMKDKLVKLKEERFKGNHTA 185
Query: 211 PEDLSTAD 218
++ D
Sbjct: 186 QVEVGKID 193
>gnl|CDD|191258 pfam05337, CSF-1, Macrophage colony stimulating factor-1 (CSF-1).
Colony stimulating factor 1 (CSF-1) is a homodimeric
polypeptide growth factor whose primary function is to
regulate the survival, proliferation, differentiation,
and function of cells of the mononuclear phagocytic
lineage. This lineage includes mononuclear phagocytic
precursors, blood monocytes, tissue macrophages,
osteoclasts, and microglia of the brain, all of which
possess cell surface receptors for CSF-1. The protein
has also been linked with male fertility and mutations
in the Csf-1 gene have been found to cause osteopetrosis
and failure of tooth eruption.
Length = 285
Score = 28.1 bits (62), Expect = 5.5
Identities = 26/98 (26%), Positives = 35/98 (35%), Gaps = 7/98 (7%)
Query: 106 GGSSG-HSSSTGPNIGERPALVFSGTQNVVPGRVNGEASNGAGVVGHELHGLRSAHVPHA 164
G++ S+ G LV N V V+GEAS G G EL S H+
Sbjct: 4 RGAAQPCPSTGWLVPGSEDLLVSLLGSNWVLEEVSGEASEGPLPQGGEL----SPHMIGG 59
Query: 165 NAIAAEAAGTPNQP--VEQIGISEEVQAKLQDKATILT 200
++ AE +Q QI Q +L L
Sbjct: 60 GSLQAEQQLPDSQMEASCQIPFEFVDQEQLDLTKAFLL 97
>gnl|CDD|132240 TIGR03196, pucD, xanthine dehydrogenase D subunit. This gene has
been characterized in B. subtilis as the molybdopterin
binding-subunit of xanthine dehydrogenase (pucD), acting
in conjunction with pucC, the FAD-binding subunit and
pucE, the FeS-binding subunit. The more common XDH
complex (GenProp0640) includes the xdhB gene which is
related to pucD. It appears that most of the relatives
of pucD outside of this narrow clade are involved in
other processes as they are found in unrelated genomic
contexts, contain the more common XDH complex and/or do
not appear to process purines to allantoin.
Length = 768
Score = 28.5 bits (63), Expect = 5.9
Identities = 16/52 (30%), Positives = 21/52 (40%)
Query: 129 GTQNVVPGRVNGEASNGAGVVGHELHGLRSAHVPHANAIAAEAAGTPNQPVE 180
P + AS G + G + G +A A AAE AG P + VE
Sbjct: 517 ADTAKGPKAGSSSASRGTSMSGGAIQGACAAFAAQLKARAAETAGLPAEVVE 568
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 27.9 bits (62), Expect = 8.3
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 276 LKGHRKKVTRVVYHPS 291
L+GH KKV V +HPS
Sbjct: 121 LQGHTKKVGIVSFHPS 136
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
0.312 0.128 0.356
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,112,814
Number of extensions: 1296007
Number of successful extensions: 843
Number of sequences better than 10.0: 1
Number of HSP's gapped: 843
Number of HSP's successfully gapped: 24
Length of query: 294
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 198
Effective length of database: 6,679,618
Effective search space: 1322564364
Effective search space used: 1322564364
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 59 (26.5 bits)