RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12031
(128 letters)
>gnl|CDD|214708 smart00523, DWA, Domain A in dwarfin family proteins.
Length = 109
Score = 90.1 bits (224), Expect = 1e-24
Identities = 28/117 (23%), Positives = 49/117 (41%), Gaps = 16/117 (13%)
Query: 9 VKQKWASRLLGKLRKDITQECREDFVLSIT--GKKPAMCVLSNPDQKGKMRRIDCLRQAD 66
V++KWA + L K + ++ E+ + ++ G P CVL G+++ A
Sbjct: 1 VEEKWAKKATESLLKKLKKKQLEELLQAVESKGGPPTRCVLIPRSLDGRLQV------AH 54
Query: 67 KVWRLDLVMVILFKAIPLESTDGERLEKAPECAHP------SLCVNPYHINVSVREL 117
+ ++ LF+ L+S L+ P C H +C NPYH + R
Sbjct: 55 RKGLPHVLYCRLFRWPDLQS--PHELKALPTCEHAFESKSDEVCCNPYHYSRVERPE 109
>gnl|CDD|217397 pfam03165, MH1, MH1 domain. The MH1 (MAD homology 1) domain is
found at the amino terminus of MAD related proteins such
as Smads. This domain is separated from the MH2 domain
by a non-conserved linker region. The crystal structure
of the MH1 domain shows that a highly conserved 11
residue beta hairpin is used to bind the DNA consensus
sequence GNCN in the major groove, shown to be vital for
the transcriptional activation of target genes. Not all
examples of MH1 can bind to DNA however. Smad2 cannot
bind DNA and has a large insertion within the hairpin
that presumably abolishes DNA binding. A basic helix
(H2) in MH1 with the nuclear localisation signal KKLKK
has been shown to be essential for Smad3 nuclear import.
Smads also use the MH1 domain to interact with
transcription factors such as Jun, TFE3, Sp1, and Runx.
Length = 103
Score = 72.4 bits (178), Expect = 7e-18
Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 26/117 (22%)
Query: 10 KQKWASRLLGKLRKDITQECREDFVLSIT--GKKPAMCV---------LSNPDQKGKMRR 58
+K LL KL+K + E+ L++ G P CV L +KG
Sbjct: 1 AKKAVESLLKKLKKKK--QQLEELELAVESRGGPPTKCVTIPRSLDGRLQVAGRKGLPHV 58
Query: 59 IDCLRQADKVWRL-DLVMVILFKAIPLESTDGERLEKAPECAHPSLCVNPYHINVSV 114
I C ++WR DL KAIP R +K +C+NPYH +
Sbjct: 59 IYC-----RLWRWPDLQSQHELKAIPTCEYAF-RSKK------DEVCINPYHYSRVE 103
>gnl|CDD|129965 TIGR00887, 2A0109, phosphate:H+ symporter. This model represents
the phosphate uptake symporter subfamily of the major
facilitator superfamily (pfam00083) [Transport and
binding proteins, Anions].
Length = 502
Score = 27.8 bits (62), Expect = 1.6
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 5/47 (10%)
Query: 60 DCLRQADKVWRLDLVMVILFKAIPLESTDGERLEKAPECAHPSLCVN 106
C+ D +WR+ +I F A+P RL PE + V
Sbjct: 194 SCVPAVDYMWRI----LIGFGAVPALLALYFRL-TIPETPRYTADVA 235
>gnl|CDD|212674 cd10232, ScSsz1p_like_NBD, Nucleotide-binding domain of
Saccharmomyces cerevisiae Ssz1pp and similar proteins.
Saccharomyces cerevisiae Ssz1p (also known as
/Pdr13p/YHR064C) belongs to the heat shock protein 70
(HSP70) family of chaperones that assist in protein
folding and assembly and can direct incompetent "client"
proteins towards degradation. Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. HSP70 chaperone
activity is regulated by various co-chaperones: J-domain
proteins and nucleotide exchange factors (NEFs). Some
family members are not chaperones but rather, function
as NEFs for their Hsp70 partners, while other family
members function as both chaperones and NEFs. Ssz1 does
not function as a chaperone; it facilitates the
interaction between the HSP70 Ssb protein and its
partner J-domain protein Zuo1 (also known as zuotin) on
the ribosome. Ssz1 is found in a stable heterodimer
(called RAC, ribosome associated complex) with Zuo1.
Zuo1 can only stimulate the ATPase activity of Ssb, when
it is in complex with Ssz1. Ssz1 binds ATP but neither
nucleotide-binding, hydrolysis, or its SBD, is needed
for its in vivo function.
Length = 386
Score = 27.7 bits (62), Expect = 1.7
Identities = 15/37 (40%), Positives = 17/37 (45%), Gaps = 9/37 (24%)
Query: 14 ASRLLGKLRKDITQECREDFVLSITGKKPAMCVLSNP 50
R L +L +E EDF GKK A VLS P
Sbjct: 118 TVRFLRRL-----KEAAEDF----LGKKVAGAVLSVP 145
>gnl|CDD|237794 PRK14705, PRK14705, glycogen branching enzyme; Provisional.
Length = 1224
Score = 26.5 bits (58), Expect = 5.0
Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 10/66 (15%)
Query: 58 RIDCLRQADKVWRLDLVMVILFKAIPLES--TDGERLEKAPECAHPSLCVNPYHINVSVR 115
R+ +A VW L PL++ RLE + A P +PYH +V
Sbjct: 553 RVPMTHEAHGVWAAVLE--------PLQAGHVPDYRLEVTYDGAEPVTIDDPYHYLPTVG 604
Query: 116 ELDLYL 121
E+DL+L
Sbjct: 605 EVDLHL 610
>gnl|CDD|236158 PRK08132, PRK08132, FAD-dependent oxidoreductase; Provisional.
Length = 547
Score = 26.4 bits (59), Expect = 5.5
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 63 RQADKVWRLDL 73
RQ D VWR+D
Sbjct: 237 RQPDNVWRIDF 247
>gnl|CDD|182018 PRK09651, PRK09651, RNA polymerase sigma factor FecI; Provisional.
Length = 172
Score = 25.9 bits (57), Expect = 6.1
Identities = 13/29 (44%), Positives = 14/29 (48%)
Query: 74 VMVILFKAIPLESTDGERLEKAPECAHPS 102
VMV LF+ LE E L PE PS
Sbjct: 71 VMVDLFRRNALEKAYLEMLALMPEGGAPS 99
>gnl|CDD|226535 COG4049, COG4049, Uncharacterized protein containing
archaeal-type C2H2 Zn-finger [General function
prediction only].
Length = 65
Score = 25.0 bits (54), Expect = 6.2
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 79 FKAIPLESTDGERLEKAPEC 98
KAI + DGE + P C
Sbjct: 4 LKAIKVRDRDGEEFLRCPRC 23
>gnl|CDD|227260 COG4923, COG4923, Predicted nuclease (RNAse H fold) [General
function prediction only].
Length = 245
Score = 26.1 bits (57), Expect = 6.7
Identities = 7/40 (17%), Positives = 15/40 (37%)
Query: 87 TDGERLEKAPECAHPSLCVNPYHINVSVRELDLYLANYIN 126
G E + + + + I +RE+D +L +
Sbjct: 101 IYGRASEVNRATSGKGVSIQAWGIVSKIREVDAFLIARPD 140
>gnl|CDD|221366 pfam11996, DUF3491, Protein of unknown function (DUF3491). This
family of proteins is functionally uncharacterized. This
protein is found in bacteria. Proteins in this family
are typically between 286 to 3225 amino acids in length.
This protein is found associated with pfam04488. This
protein is found associated with pfam04488.
Length = 934
Score = 26.2 bits (58), Expect = 6.9
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 8/54 (14%)
Query: 75 MVILFKAIPLESTDG---ERLEKAPECAHPSLCVNPYH-INVSVRE-LDLYLAN 123
+ ++FK +ES D + LEK A P L +P+ IN S R L+L+L
Sbjct: 634 IRLVFKNFFIESMDTISEKTLEKE---AKPILASDPHRFINPSYRNHLELFLGE 684
>gnl|CDD|119405 cd00219, ToxGAP, GTPase-activating protein (GAP) domain found in
bacterial cytotoxins, ExoS, SptP, and YopE. Part of
protein secretion system; stimulates Rac1- dependent
cytoskeletal changes that promote bacterial
internalization.
Length = 120
Score = 25.1 bits (55), Expect = 8.1
Identities = 13/35 (37%), Positives = 15/35 (42%), Gaps = 4/35 (11%)
Query: 71 LDLVMVILFKAIPLESTDGERLEKAPECAHPSLCV 105
L + L KA LES D E+L K H L
Sbjct: 6 LPSALKGLDKASELESLDAEQLRK----NHDRLAT 36
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
0.321 0.136 0.413
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,499,333
Number of extensions: 551349
Number of successful extensions: 339
Number of sequences better than 10.0: 1
Number of HSP's gapped: 333
Number of HSP's successfully gapped: 16
Length of query: 128
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 42
Effective length of database: 7,123,158
Effective search space: 299172636
Effective search space used: 299172636
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 (21.9 bits)
S2: 53 (24.3 bits)