RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1964
(531 letters)
>gnl|CDD|202161 pfam02214, K_tetra, K+ channel tetramerisation domain. The
N-terminal, cytoplasmic tetramerisation domain (T1) of
voltage-gated K+ channels encodes molecular determinants
for subfamily-specific assembly of alpha-subunits into
functional tetrameric channels. It is distantly related
to the BTB/POZ domain pfam00651.
Length = 92
Score = 84.1 bits (209), Expect = 6e-20
Identities = 34/94 (36%), Positives = 45/94 (47%), Gaps = 5/94 (5%)
Query: 15 VKLNVGGSLHYTTIGTLTK-HDTMLRAMFSGRMEILTDSEGWVLIDRCGKHFGIILNFLR 73
V+LNVGG T+ TLT+ DT+L + R + D DR KHF ILNF R
Sbjct: 1 VRLNVGGKRFETSKSTLTRFPDTLLGRLLK-RCDFYDDDTNEYFFDRSPKHFETILNFYR 59
Query: 74 DGQVSLPENP-KDVAELLAEAKYYCITELT-DLC 105
G L + L E ++Y + EL +LC
Sbjct: 60 TG-GKLHRPEEVCLDSFLEELEFYGLGELAIELC 92
Score = 49.5 bits (119), Expect = 1e-07
Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 320 RCQRFGRMEGWVLIDRCGKHFGIILNFLRDGQVSLPENP-KDVAELLAEAKYYCITALCL 378
RC + DR KHF ILNF R G L + L E ++Y + L +
Sbjct: 31 RCDFYDDDTNEYFFDRSPKHFETILNFYRTG-GKLHRPEEVCLDSFLEELEFYGLGELAI 89
>gnl|CDD|197585 smart00225, BTB, Broad-Complex, Tramtrack and Bric a brac. Domain
in Broad-Complex, Tramtrack and Bric a brac. Also known
as POZ (poxvirus and zinc finger) domain. Known to be a
protein-protein interaction motif found at the N-termini
of several C2H2-type transcription factors as well as
Shaw-type potassium channels. Known structure reveals a
tightly intertwined dimer formed via interactions
between N-terminal strand and helix structures. However
in a subset of BTB/POZ domains, these two secondary
structures appear to be missing. Be aware SMART predicts
BTB/POZ domains without the beta1- and alpha1-secondary
structures.
Length = 97
Score = 80.0 bits (198), Expect = 2e-18
Identities = 34/99 (34%), Positives = 47/99 (47%), Gaps = 3/99 (3%)
Query: 14 YVKLNVGGSLHYTTIGTLTKHDTMLRAMFSGRMEILTDSEGWVLIDRCGKHFGIILNFLR 73
V L VGG + L H +A+FS + SE L D + F +LNFL
Sbjct: 1 DVTLVVGGKKFHAHKAVLAAHSPYFKALFSSDFKESDKSE-IYLDDVSPEDFRALLNFLY 59
Query: 74 DGQVSLPENPKDVAELLAEAKYYCITELTDLCEQTIKRK 112
G++ LPE +V ELL A Y I L +LCE+ + +
Sbjct: 60 TGKLDLPEE--NVEELLELADYLQIPGLVELCEEFLLKL 96
Score = 46.9 bits (112), Expect = 9e-07
Identities = 22/54 (40%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 332 LIDRCGKHFGIILNFLRDGQVSLPENPKDVAELLAEAKYYCITALCLNFSYFLL 385
L D + F +LNFL G++ LPE +V ELL A Y I L FLL
Sbjct: 43 LDDVSPEDFRALLNFLYTGKLDLPEE--NVEELLELADYLQIPGLVELCEEFLL 94
>gnl|CDD|216043 pfam00651, BTB, BTB/POZ domain. The BTB (for BR-C, ttk and bab) or
POZ (for Pox virus and Zinc finger) domain is present
near the N-terminus of a fraction of zinc finger
(pfam00096) proteins and in proteins that contain the
pfam01344 motif such as Kelch and a family of pox virus
proteins. The BTB/POZ domain mediates homomeric
dimerisation and in some instances heteromeric
dimerisation. The structure of the dimerised PLZF
BTB/POZ domain has been solved and consists of a tightly
intertwined homodimer. The central scaffolding of the
protein is made up of a cluster of alpha-helices flanked
by short beta-sheets at both the top and bottom of the
molecule. POZ domains from several zinc finger proteins
have been shown to mediate transcriptional repression
and to interact with components of histone deacetylase
co-repressor complexes including N-CoR and SMRT. The POZ
or BTB domain is also known as BR-C/Ttk or ZiN.
Length = 101
Score = 35.7 bits (83), Expect = 0.008
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 65 FGIILNFLRDGQVSLPENPKDVAELLAEAKYYCITELTDLCEQTIK 110
F +L F+ G++ + E ++V +LLA A I L D CE+ +
Sbjct: 58 FEALLEFIYTGKLEITE--ENVDDLLALADKLQIPALIDKCEEFLI 101
Score = 28.4 bits (64), Expect = 3.4
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 5/44 (11%)
Query: 340 FGIILNFLRDGQVSLPENPKDVAELLAEAKYYCITAL---CLNF 380
F +L F+ G++ + E ++V +LLA A I AL C F
Sbjct: 58 FEALLEFIYTGKLEITE--ENVDDLLALADKLQIPALIDKCEEF 99
>gnl|CDD|227611 COG5291, COG5291, Predicted membrane protein [Function unknown].
Length = 313
Score = 31.1 bits (70), Expect = 1.2
Identities = 28/86 (32%), Positives = 39/86 (45%), Gaps = 4/86 (4%)
Query: 370 YYCITALCLNFSYFLLGIWHSKSTYWIKILQFLGLELYFSGTSHDVLPLGVSYRFSGRLL 429
Y I+AL +FS + IW ++ I+QF G + G + LG S+ S R +
Sbjct: 121 YGGISALGTSFSATITYIWSKRNPR--AIIQFFGF-ISVPGKYLPFILLGFSF-LSRRGI 176
Query: 430 FIKDVIGSRTSHDVLPFGVSYRFSGR 455
I DV+G H FG Y GR
Sbjct: 177 SIDDVLGFVVGHLFHYFGDIYPMIGR 202
>gnl|CDD|146952 pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, domain 7. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Rpb2 is the
second largest subunit of the RNA polymerase. This
domain comprised of the structural domains anchor and
clamp. The clamp region (C-terminal) contains a
zinc-binding motif. The clamp region is named due to its
interaction with the clamp domain found in Rpb1. The
domain also contains a region termed "switch 4". The
switches within the polymerase are thought to signal
different stages of transcription.
Length = 78
Score = 27.4 bits (62), Expect = 4.5
Identities = 8/12 (66%), Positives = 8/12 (66%)
Query: 322 QRFGRMEGWVLI 333
QRFG ME W L
Sbjct: 3 QRFGEMEVWALE 14
>gnl|CDD|214898 smart00901, FRG, This domain contains a conserved N-terminal
(F/Y)RG motif. It is functionally uncharacterised.
Length = 103
Score = 28.1 bits (63), Expect = 4.5
Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 4/68 (5%)
Query: 306 GILWRGQSRRINALR--CQRFGRMEGWVLIDRCGKHFGIILNFLRDGQVSLPENPKDVAE 363
+L+RGQS L R +L + ++ NF R L ++P D E
Sbjct: 4 RLLFRGQSDAYWPLVPSLFRKKGFYPDLLSSDDERR--LLRNFKRQAPNRLDKSPSDDLE 61
Query: 364 LLAEAKYY 371
LA A++Y
Sbjct: 62 WLALAQHY 69
>gnl|CDD|220322 pfam09626, DHC, Dihaem cytochrome c. Dihaem cytochrome c (DHC) is
a soluble c-type cytochrome that folds into two distinct
domains, each binding a single haem group and connected
by a small linker region. Despite little sequence
similarity, the N-terminal domain (residues 12-75) is a
class I type cytochrome c, that binds one of the haems,
but the domain surrounding the other haem is
structurally unique. DHC binds electrostatically to an
oxygen-binding protein, sphaeroides haem protein (SHP),
as a component of a conserved electron transfer pathway.
DHC acts as the physiological electron donor for SHP
during phototrophic growth. In certain species DHC is
found upstream of pfam01292.
Length = 118
Score = 28.1 bits (63), Expect = 5.2
Identities = 13/76 (17%), Positives = 23/76 (30%), Gaps = 17/76 (22%)
Query: 52 SEGW-VLIDRCGKHFG-----------IILNFLRDGQVSLPENPKDVAELLAEAKYYCIT 99
+ W ++ HFG +I +LR L + + + + E IT
Sbjct: 19 AASWRKIMADLDDHFGTDASLDPPTRALIWAYLRANAADLSGSRRKILRSVPEPVPLRIT 78
Query: 100 ELTDLCEQTIKRKQRE 115
E + E
Sbjct: 79 ES-----PYFRALHPE 89
>gnl|CDD|240067 cd04716, BAH_plantDCM_I, BAH, or Bromo Adjacent Homology domain,
first copy present in DNA
(Cytosine-5)-methyltransferases (DCM) from plants. DNA
methylation, or the covalent addition of a methyl group
to cytosine within the context of the CpG dinucleotide,
has profound effects on the genome. These effects
include transcriptional repression via inhibition of
transcription factor binding, the recruitment of
methyl-binding proteins and their associated chromatin
remodeling factors, X chromosome inactivation,
imprinting, and the suppression of parasitic DNA
sequences. DNA methylation is also essential for proper
embryonic development and is an important player in both
DNA repair and genome stability. BAH domains are found
in a variety of proteins playing roles in
transcriptional silencing and the remodeling of
chromatin. It is assumed that in most or all of these
instances the BAH domain mediates protein-protein
interactions.
Length = 122
Score = 28.2 bits (63), Expect = 5.5
Identities = 8/43 (18%), Positives = 16/43 (37%)
Query: 341 GIILNFLRDGQVSLPENPKDVAELLAEAKYYCITALCLNFSYF 383
+++ ++ QV K + YY C+ +S F
Sbjct: 75 DCLISKVKILQVPPNVGTKRKKPNSEKCDYYYDMEYCVPYSTF 117
>gnl|CDD|232843 TIGR00133, gatB, aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase,
B subunit. The heterotrimer GatABC is responsible for
transferring the NH2 group that converts Glu to Gln, or
Asp to Asn after the Glu or Asp has been ligated to the
tRNA for Gln or Asn, respectively. In Lactobacillus,
GatABC is responsible only for tRNA(Gln). In the
Archaea, GatABC is responsible only for tRNA(Asn), while
GatDE is responsible for tRNA(Gln). In lineages that
include Thermus, Chlamydia, or Acidithiobacillus, the
GatABC complex catalyzes both [Protein synthesis, tRNA
aminoacylation].
Length = 478
Score = 28.9 bits (65), Expect = 6.9
Identities = 15/67 (22%), Positives = 30/67 (44%), Gaps = 13/67 (19%)
Query: 64 HFGIILNFLRDGQVS----------LPENPKDVAELLAEAKYYCIT---ELTDLCEQTIK 110
++ +++G++S + EN D ++L+ E I+ EL + E+ IK
Sbjct: 373 DLAELIKLIKEGKISGKSAKQLIEEMLENGGDPSKLIEELGLEQISDEKELIKIIEEVIK 432
Query: 111 RKQRETE 117
+E E
Sbjct: 433 ENPKEVE 439
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 0.140 0.434
Gapped
Lambda K H
0.267 0.0721 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,661,678
Number of extensions: 2757490
Number of successful extensions: 2786
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2780
Number of HSP's successfully gapped: 16
Length of query: 531
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 430
Effective length of database: 6,457,848
Effective search space: 2776874640
Effective search space used: 2776874640
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: 61 (27.3 bits)