RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11104
(70 letters)
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 35.8 bits (83), Expect = 5e-05
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 17 VNCLAWHQNQGWIAVGGDDGLLKV 40
V +A+ + +A G DDG ++V
Sbjct: 14 VTSVAFSPDGNLLASGSDDGTVRV 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 = 34.6 bits (80), Expect = 2e-04
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 17 VNCLAWHQNQGWIAVGGDDGLLKV 40
V +A+ + ++A G DDG +K+
Sbjct: 15 VTSVAFSPDGKYLASGSDDGTIKL 38
>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 = 35.4 bits (82), Expect = 6e-04
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 16 KVNCLAWHQNQGWIAVGGDDGLLKVLKLDTVSL 48
V C+A+ + +A G DG +KV L+T L
Sbjct: 11 GVTCVAFSPDGKLLATGSGDGTIKVWDLETGEL 43
Score = 32.7 bits (75), Expect = 0.007
Identities = 10/36 (27%), Positives = 18/36 (50%)
Query: 17 VNCLAWHQNQGWIAVGGDDGLLKVLKLDTVSLTIMI 52
VN +A+ + +A G +DG ++V L T +
Sbjct: 222 VNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTL 257
Score = 31.2 bits (71), Expect = 0.023
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 17 VNCLAWHQNQGWIAVGGDDGLLKV 40
V LAW + +A G DG +++
Sbjct: 264 VTSLAWSPDGKRLASGSADGTIRI 287
Score = 30.0 bits (68), Expect = 0.050
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 17 VNCLAWHQNQGWIAVGGDDGLLKVLKLDT 45
VN +A+ + + DG +K+ L T
Sbjct: 180 VNSVAFSPDGEKLLSSSSDGTIKLWDLST 208
Score = 29.2 bits (66), Expect = 0.12
Identities = 6/29 (20%), Positives = 15/29 (51%)
Query: 17 VNCLAWHQNQGWIAVGGDDGLLKVLKLDT 45
V+ +A+ + ++ D +KV ++T
Sbjct: 96 VSSVAFSPDGRILSSSSRDKTIKVWDVET 124
Score = 26.9 bits (60), Expect = 0.61
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 17 VNCLAWHQNQGWIAVGGDDGLLKV 40
VN +A+ + ++A DG +K+
Sbjct: 138 VNSVAFSPDGTFVASSSQDGTIKL 161
Score = 26.9 bits (60), Expect = 0.73
Identities = 7/33 (21%), Positives = 15/33 (45%)
Query: 17 VNCLAWHQNQGWIAVGGDDGLLKVLKLDTVSLT 49
V +A + ++A G D +++ L+T
Sbjct: 54 VRDVAASADGTYLASGSSDKTIRLWDLETGECV 86
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 27.7 bits (60), Expect = 0.41
Identities = 8/38 (21%), Positives = 20/38 (52%)
Query: 8 KIAIPNNTKVNCLAWHQNQGWIAVGGDDGLLKVLKLDT 45
+ +++ V +A+ + +A G DG +++ L+T
Sbjct: 278 RTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLET 315
Score = 25.8 bits (55), Expect = 2.2
Identities = 9/42 (21%), Positives = 18/42 (42%)
Query: 4 YLSKKIAIPNNTKVNCLAWHQNQGWIAVGGDDGLLKVLKLDT 45
LS + + + +A+ + + G DG +K+ LD
Sbjct: 55 DLSSLLLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDN 96
Score = 24.7 bits (52), Expect = 5.6
Identities = 6/47 (12%), Positives = 20/47 (42%)
Query: 7 KKIAIPNNTKVNCLAWHQNQGWIAVGGDDGLLKVLKLDTVSLTIMII 53
+ + ++ ++ + +A G DG +++ L + S + +
Sbjct: 234 LRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTL 280
>gnl|CDD|177282 PHA00447, PHA00447, lysozyme.
Length = 142
Score = 25.9 bits (57), Expect = 1.6
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 22 WHQNQGWIAVG 32
WH+ QGW+ VG
Sbjct: 34 WHKEQGWLDVG 44
>gnl|CDD|218359 pfam04981, NMD3, NMD3 family. The NMD3 protein is involved in
nonsense mediated mRNA decay. This amino terminal
region contains four conserved CXXC motifs that could
be metal binding. NMD3 is involved in export of the 60S
ribosomal subunit is mediated by the adapter protein
Nmd3p in a Crm1p-dependent pathway.
Length = 238
Score = 25.0 bits (55), Expect = 3.4
Identities = 9/61 (14%), Positives = 16/61 (26%), Gaps = 15/61 (24%)
Query: 11 IPNNTKVN----CLAWHQNQGWIAVGGDDGLLKVLKLDTVSLTIMIILFQERNLQDKLPP 66
IP V C + W+ LL++ + + + L
Sbjct: 29 IPEELTVLVCRNCGRYLIPNRWVDAEESRELLEIC--------LKKL---YKGLNKVKKV 77
Query: 67 L 67
L
Sbjct: 78 L 78
>gnl|CDD|132123 TIGR03079, CH4_NH3mon_ox_B, methane monooxygenase/ammonia
monooxygenase, subunit B. Both ammonia oxidizers such
as Nitrosomonas europaea and methanotrophs (obligate
methane oxidizers) such as Methylococcus capsulatus each
can grow only on their own characteristic substrate.
However, both groups have the ability to oxidize both
substrates, and so the relevant enzymes must be named
here according to their ability to oxidze both. The
protein family represented here reflects subunit B of
both the particulate methane monooxygenase of
methylotrophs and the ammonia monooxygenase of
nitrifying bacteria.
Length = 399
Score = 24.9 bits (54), Expect = 3.7
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 4/41 (9%)
Query: 29 IAVGGDDGLL----KVLKLDTVSLTIMIILFQERNLQDKLP 65
+ GD+ LL K L + LT+ I+ R +DK P
Sbjct: 206 LLAYGDNLLLDPMDKKLTIGVAILTLAIVWGGYRYTEDKHP 246
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
0.324 0.141 0.432
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: 3,444,458
Number of extensions: 245704
Number of successful extensions: 219
Number of sequences better than 10.0: 1
Number of HSP's gapped: 219
Number of HSP's successfully gapped: 18
Length of query: 70
Length of database: 10,937,602
Length adjustment: 40
Effective length of query: 30
Effective length of database: 9,163,442
Effective search space: 274903260
Effective search space used: 274903260
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 (21.5 bits)
S2: 53 (24.2 bits)