RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11515
(117 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 = 81.1 bits (201), Expect = 2e-21
Identities = 31/82 (37%), Positives = 38/82 (46%), Gaps = 5/82 (6%)
Query: 13 RFSTSIQTLMWVPDSFFTALLSGRISSLKDETGAIFIDRDPKVFAIILNYLRTRDIDLKS 72
RF TS TL PD+ LL R D+T F DR PK F ILN+ RT L
Sbjct: 9 RFETSKSTLTRFPDTLLGRLLK-RCDFYDDDTNEYFFDRSPKHFETILNFYRT-GGKLHR 66
Query: 73 TD---LRTLRHEAEYYGIAPLV 91
+ L + E E+YG+ L
Sbjct: 67 PEEVCLDSFLEELEFYGLGELA 88
>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 = 57.3 bits (139), Expect = 4e-12
Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 5/87 (5%)
Query: 13 RFSTSIQTLMWVPDSFFTALLSGRISSLKDETGAIFIDRDPKVFAIILNYLRTRDIDLKS 72
+F L +F AL S D++ D P+ F +LN+L T +DL
Sbjct: 10 KFHAHKAVLAAHSP-YFKALFSSDFKE-SDKSEIYLDDVSPEDFRALLNFLYTGKLDLPE 67
Query: 73 TDLRTLRHEAEYYGIAPLVKRLVLCED 99
++ L A+Y I LV+ LCE+
Sbjct: 68 ENVEELLELADYLQIPGLVE---LCEE 91
>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 = 27.6 bits (62), Expect = 0.71
Identities = 10/48 (20%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 52 DPKVFAIILNYLRTRDIDLKSTDLRTLRHEAEYYGIAPLVKRLVLCED 99
P+ F +L ++ T +++ ++ L A+ I L+ CE+
Sbjct: 54 SPEDFEALLEFIYTGKLEITEENVDDLLALADKLQIPALID---KCEE 98
>gnl|CDD|237876 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA polymerase;
Provisional.
Length = 553
Score = 28.4 bits (64), Expect = 0.86
Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 9/65 (13%)
Query: 33 LSGRISSLKDETGAIFIDR--DPKVFAIILNYLRTRDIDLKST---DLRTLRHEAEYYGI 87
R++ L E +P +L LR I+L ST +LR + H A +
Sbjct: 202 RPARLAELAAEIREALGRPRLNPDSPQQVLRALRRAGIELPSTRKWELREIDHPA----V 257
Query: 88 APLVK 92
PL++
Sbjct: 258 EPLLE 262
>gnl|CDD|236290 PRK08564, PRK08564, 5'-methylthioadenosine phosphorylase II;
Reviewed.
Length = 267
Score = 28.1 bits (63), Expect = 0.98
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 6 YLLIEIPRFSTSIQTLMW 23
Y+ IE PRFST ++ MW
Sbjct: 162 YICIEGPRFSTRAESRMW 179
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 26.8 bits (59), Expect = 2.9
Identities = 22/78 (28%), Positives = 33/78 (42%), Gaps = 18/78 (23%)
Query: 2 KLEPYLLIEIPRFSTSIQTLMWVPDSFFTALLSGRISSLKD----ETGAIFIDRDPKVFA 57
K E IEIP T IQ SGR S L + ++ I DP++F
Sbjct: 484 KEEGKYYIEIPDVRTYIQA-------------SGRTSRLFAGGITKGASVLIVDDPEIFN 530
Query: 58 IILNYLRTR-DIDLKSTD 74
++ +R R + + KS +
Sbjct: 531 ALIRQMRFRFEFEFKSFE 548
>gnl|CDD|237037 PRK12285, PRK12285, tryptophanyl-tRNA synthetase; Reviewed.
Length = 368
Score = 26.8 bits (60), Expect = 3.2
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 28 FFTALLSGRISSLKDETGAIFIDRDPKVFA 57
F L G++SS K E+ AI++ DP+
Sbjct: 243 FMPGLTGGKMSSSKPES-AIYLTDDPETVK 271
>gnl|CDD|173585 PTZ00394, PTZ00394, glucosamine-fructose-6-phosphate
aminotransferase; Provisional.
Length = 670
Score = 26.8 bits (59), Expect = 3.7
Identities = 18/54 (33%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 40 LKDETGAIFIDRDPKVFAIILNYLRTRDIDLKSTDLRTLRHEAEYYG-IAPLVK 92
LK+E D D +V +++ YL TR DL L G A LVK
Sbjct: 145 LKEEGYHFSSDTDTEVISVLSEYLYTRKGIHNFADL-ALEVSRMVEGSYALLVK 197
>gnl|CDD|183108 PRK11377, PRK11377, dihydroxyacetone kinase subunit M; Provisional.
Length = 473
Score = 26.3 bits (58), Expect = 4.9
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 62 YLRTRDIDLKSTDLRTLRH 80
YL+ R ID+ RTL H
Sbjct: 365 YLQARYIDVDDLLHRTLVH 383
>gnl|CDD|237858 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
Length = 445
Score = 26.2 bits (58), Expect = 5.6
Identities = 10/43 (23%), Positives = 16/43 (37%)
Query: 10 EIPRFSTSIQTLMWVPDSFFTALLSGRISSLKDETGAIFIDRD 52
+ P F I L P+ F A ++ K F+ +D
Sbjct: 177 QAPLFGFRINRLKTTPEKFLAAPADASVTFEKSGLPNFFLSKD 219
>gnl|CDD|220412 pfam09804, DUF2347, Uncharacterized conserved protein (DUF2347).
Members of this family of hypothetical proteins have no
known function.
Length = 496
Score = 25.8 bits (57), Expect = 6.5
Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 15/63 (23%)
Query: 46 AIF-IDRDPKVFAIILNYLRTRDIDLKSTDLRTL--------------RHEAEYYGIAPL 90
A+F I D K I+ DIDL+ + ++L HE EYYG++
Sbjct: 3 ALFLIQFDVKAGYTIVWSRSLPDIDLEGIEYKSLPSGIHEVSEDLVYFVHEKEYYGLSAF 62
Query: 91 VKR 93
+
Sbjct: 63 RQN 65
>gnl|CDD|220547 pfam10065, DUF2303, Uncharacterized conserved protein (DUF2303).
Members of this family of hypothetical bacterial
proteins have no known function.
Length = 272
Score = 25.4 bits (56), Expect = 8.1
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 37 ISSLKDETGAIFIDRDPKVFAIILNY 62
++ K E IFID DP + +
Sbjct: 72 VNRHKTEGTQIFIDADPMSATAVFDL 97
>gnl|CDD|153351 cd07667, BAR_SNX30, The Bin/Amphiphysin/Rvs (BAR) domain of
Sorting Nexin 30. BAR domains are dimerization, lipid
binding and curvature sensing modules found in many
different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs
also contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs. The
specific function of SNX30 is still unknown. BAR
domains form dimers that bind to membranes, induce
membrane bending and curvature, and may also be
involved in protein-protein interactions.
Length = 240
Score = 25.3 bits (55), Expect = 9.3
Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 31 ALLSGRISSLKDETGAIFIDRDPKVFAIILNYLRTRDIDLKSTD---LRTLRHEAEY 84
ALLS S+K TG + P FA I +YL T + L + D R ++ E EY
Sbjct: 28 ALLSKMGESVKYVTGGYKLRSRPLEFAAIGDYLDTFALKLGTIDRIAQRIIKEEIEY 84
>gnl|CDD|213329 cd05127, RasGAP_IQGAP_like, Ras-GTPase Activating Domain of IQ
motif containing GTPase activating proteins. This
family represents IQ motif containing GTPase activating
protein (IQGAP) which associated with the Ras
GTP-binding protein. A primary function of IQGAP
proteins is to modulate cytoskeletal architecture. There
are three known IQGAP family members: IQGAP1, IQGAP2 and
IQGAP3. Human IQGAP1 and IQGAP2 share 62% identity.
IQGAPs are multi-domain molecules having a
calponin-homology (CH) domain which binds F-actin,
IQGAP-specific repeats, a single WW domain, four IQ
motifs that mediate interactions with calmodulin, and a
RasGAP related domain that binds active Rho family
GTPases. IQGAP is an essential regulator of cytoskeletal
function. IQGAP1 negatively regulates Ras family GTPases
by stimulating their intrinsic GTPase activity, the
protein actually lacks GAP activity. Both IQGAP1 and
IQGAP2 specifically bind to Cdc42 and Rac1, but not to
RhoA. Despite of their similarities to part of the
sequence of RasGAP, neither IQGAP1 nor IQGAP2 interacts
with Ras. IQGAP3, only present in mammals, regulates the
organization of the cytoskeleton under the regulation of
Rac1 and Cdc42 in neuronal cells. The depletion of
IQGAP3 is shown to impair neurite or axon outgrowth in
neuronal cells with disorganized cytoskeleton.
Length = 331
Score = 25.2 bits (56), Expect = 9.4
Identities = 6/23 (26%), Positives = 10/23 (43%)
Query: 12 PRFSTSIQTLMWVPDSFFTALLS 34
R ++ L + D F TA+
Sbjct: 117 KRLIEHLEKLRAITDKFLTAITE 139
>gnl|CDD|224625 COG1711, COG1711, DNA replication initiation complex subunit,
GINS family [Replication, recombination, and
repair].
Length = 223
Score = 25.2 bits (55), Expect = 9.8
Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 7/62 (11%)
Query: 17 SIQTLMWVPDSFFTALLSGRISSLKDETGAIFIDRDPKVFAIILNYLRTRDIDLKSTDLR 76
S L + + F+ + S I L+DE G RD + YL T I+ +D R
Sbjct: 15 SQDGLTEIDEDFYRDVRS-FIKELEDEAGRAEEARDIE------KYLLTDRIETAKSDAR 67
Query: 77 TL 78
++
Sbjct: 68 SI 69
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
0.325 0.143 0.430
Gapped
Lambda K H
0.267 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,236,352
Number of extensions: 555880
Number of successful extensions: 597
Number of sequences better than 10.0: 1
Number of HSP's gapped: 594
Number of HSP's successfully gapped: 23
Length of query: 117
Length of database: 10,937,602
Length adjustment: 80
Effective length of query: 37
Effective length of database: 7,389,282
Effective search space: 273403434
Effective search space used: 273403434
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)