RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10347
(67 letters)
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 41.1 bits (97), Expect = 6e-07
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 1 MTAYITELSDMVPTCSALARKPDKLTILRMAVAHMKALR 39
+ EL ++PT +K K ILR+A+ ++K+L+
Sbjct: 11 INEAFDELRSLLPTLPK-NKKLSKAEILRLAIEYIKSLQ 48
>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA-
binding proteins that act as transcription factors;
60-100 amino acids long. A DNA-binding basic region is
followed by two alpha-helices separated by a variable
loop region; HLH forms homo- and heterodimers,
dimerization creates a parallel, left-handed, four
helix bundle; the basic region N-terminal to the first
amphipathic helix mediates high-affinity DNA-binding;
there are several groups of HLH proteins: those
(E12/E47) which bind specific hexanucleotide sequences
such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3),
those lacking the basic domain (Emc, Id) function as
negative regulators since they fail to bind DNA, those
(hairy, E(spl), deadpan) which repress transcription
although they can bind specific hexanucleotide
sequences such as N-box (5-CACGc/aG-3), those which
have a COE domain (Collier/Olf-1/EBF) which is involved
in both in dimerization and in DNA binding, and those
which bind pentanucleotides ACGTG or GCGTG and have a
PAS domain which allows the dimerization between PAS
proteins, the binding of small molecules (e.g.,
dioxin), and interactions with non-PAS proteins.
Length = 60
Score = 37.2 bits (87), Expect = 2e-05
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 1 MTAYITELSDMVPTCSALARKPDKLTILRMAVAHMKALR 39
+ EL ++PT ++K K ILR AV ++K+L+
Sbjct: 19 INDAFDELRSLLPT-LPPSKKLSKAEILRKAVDYIKSLQ 56
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 37.1 bits (87), Expect = 2e-05
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 1 MTAYITELSDMVPTCSALARKPDKLTILRMAVAHMKALR 39
+ EL +++PT +K K ILR+A+ ++K L+
Sbjct: 16 INDAFEELRELLPTPPN--KKLSKAEILRLAIEYIKHLQ 52
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 26.8 bits (60), Expect = 0.74
Identities = 11/30 (36%), Positives = 14/30 (46%)
Query: 4 YITELSDMVPTCSALARKPDKLTILRMAVA 33
YI E S M+P + A +L MA A
Sbjct: 94 YIQEASSMLPVAALFADDNAPQRVLDMAAA 123
>gnl|CDD|227670 COG5379, BtaA, S-adenosylmethionine:diacylglycerol
3-amino-3-carboxypropyl transferase [Lipid metabolism].
Length = 414
Score = 26.8 bits (59), Expect = 0.84
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 18 LARKPDKLTILRMAVAH--MKALRVTAVNTFRH-HSQPWLFVHFGQNIDS 64
L+R P ++ ++ + AH + L++ A FRH S L F
Sbjct: 81 LSRAPARIDVVDLNPAHIALNRLKLAA---FRHLPSHEDLVRFFALAGTR 127
>gnl|CDD|219836 pfam08429, PLU-1, PLU-1-like protein. Sequences in this family
bear similarity to the central region of PLU-1. This is
a nuclear protein that may have a role in DNA-binding
and transcription, and is closely associated with the
malignant phenotype of breast cancer. This region is
found in various other Jumonji/ARID domain-containing
proteins (see pfam02373, pfam01388).
Length = 335
Score = 26.1 bits (58), Expect = 1.1
Identities = 13/44 (29%), Positives = 20/44 (45%)
Query: 3 AYITELSDMVPTCSALARKPDKLTILRMAVAHMKALRVTAVNTF 46
+ EL ++V L KP++L L VA +A + A F
Sbjct: 281 PKLDELEELVAESEPLPVKPEELRQLEKEVARAEAWKEKAKKLF 324
>gnl|CDD|163630 cd07387, MPP_PolD2_C, PolD2 (DNA polymerase delta, subunit 2),
C-terminal domain. PolD2 (DNA polymerase delta, subunit
2) is an auxiliary subunit of the eukaryotic DNA
polymerase delta (PolD) complex thought to play a
regulatory role and to serve as a scaffold for PolD
assembly by interacting simultaneously with all of the
other three subunits. PolD2 is catalytically inactive
and lacks the active site residues required for
phosphoesterase activity in other members of this
superfamily. PolD2 is also involved in the recruitment
of several proteins regulating DNA metabolism, including
p21, PDIP1, PDIP38, PDIP46, and WRN. Human PolD consists
of four subunits: p125 (PolD1), p50 (PolD2), p66(PolD3),
and p12(PolD4). PolD is one of three major replicases
in eukaryotes. PolD also plays an essential role in
translesion DNA synthesis, homologous recombination, and
DNA repair. Within the PolD complex, PolD2 tightly
associates with PolD3. PolD2 belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but share a conserved domain with
an active site consisting of two metal ions (usually
manganese, iron, or zinc) coordinated with octahedral
geometry by a cage of histidine, aspartate, and
asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 257
Score = 26.0 bits (58), Expect = 1.2
Identities = 9/32 (28%), Positives = 14/32 (43%), Gaps = 8/32 (25%)
Query: 44 NTFRHHSQPWLF----VHF----GQNIDSIFR 67
+T + P+ F V GQN+D I +
Sbjct: 128 STLNLVTNPYEFSIDGVRVLGTSGQNVDDILK 159
>gnl|CDD|148140 pfam06348, DUF1059, Protein of unknown function (DUF1059). This
family consists of several short hypothetical archaeal
proteins of unknown function.
Length = 57
Score = 25.0 bits (55), Expect = 1.4
Identities = 7/29 (24%), Positives = 11/29 (37%)
Query: 9 SDMVPTCSALARKPDKLTILRMAVAHMKA 37
D+ C AR + +LR H +
Sbjct: 7 GDVGMDCGFEARADSEDELLRAVKEHARV 35
>gnl|CDD|227753 COG5466, COG5466, Predicted small metal-binding protein [Function
unknown].
Length = 59
Score = 24.0 bits (52), Expect = 3.9
Identities = 9/36 (25%), Positives = 15/36 (41%)
Query: 1 MTAYITELSDMVPTCSALARKPDKLTILRMAVAHMK 36
M Y+ + + C AR + ++R V H K
Sbjct: 1 MAMYLFKCGSLGMGCGFEARADSEAEVMRRIVEHAK 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
0.329 0.134 0.414
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,308,698
Number of extensions: 230183
Number of successful extensions: 275
Number of sequences better than 10.0: 1
Number of HSP's gapped: 274
Number of HSP's successfully gapped: 10
Length of query: 67
Length of database: 10,937,602
Length adjustment: 38
Effective length of query: 29
Effective length of database: 9,252,150
Effective search space: 268312350
Effective search space used: 268312350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 53 (24.1 bits)