RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12868
(302 letters)
>gnl|CDD|219619 pfam07885, Ion_trans_2, Ion channel. This family includes the two
membrane helix type ion channels found in bacteria.
Length = 74
Score = 58.0 bits (141), Expect = 3e-11
Identities = 23/52 (44%), Positives = 33/52 (63%)
Query: 95 WSFPAALMFSLSIFTMIGYGNMVPRTLLGKATTVVYAVFGIPLYVLYFRNMG 146
W F AL FS T IGYG++VP T G+ T++Y + GIPL++L+ +G
Sbjct: 23 WDFLDALYFSFVTLTTIGYGDIVPLTDAGRLFTIIYILIGIPLFLLFLAVLG 74
Score = 38.7 bits (91), Expect = 2e-04
Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 12/81 (14%)
Query: 188 VLGGYVATGTVMFAEWEN---WPILDSCYFCVTSLCKIGIGDFVPGANILDSKSGHHIKL 244
+L + GTV ++ E W LD+ YF +L IG GD VP +
Sbjct: 2 LLLLVLIFGTVYYSLEEEGWGWDFLDALYFSFVTLTTIGYGDIVPLTDAGR--------- 52
Query: 245 IINFIYLLLGMGLIAMCFDLM 265
+ IY+L+G+ L + ++
Sbjct: 53 LFTIIYILIGIPLFLLFLAVL 73
>gnl|CDD|180643 PRK06645, PRK06645, DNA polymerase III subunits gamma and tau;
Validated.
Length = 507
Score = 31.0 bits (70), Expect = 0.91
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 50 EITVYYNIMNKTSWQNACDETLLIYQKNLTHQVK 83
EI +YY ++N T +N D L +T ++K
Sbjct: 413 EIDIYYFLLNHTELKNLSDNRLEFVSLEVTSKIK 446
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 30.4 bits (69), Expect = 1.2
Identities = 15/68 (22%), Positives = 22/68 (32%), Gaps = 1/68 (1%)
Query: 96 SFPAALMFSLSIFTMIGYGNMVPRTLLGKATTVVYAVFGIP-LYVLYFRNMGKVLAQSFR 154
PA + L IG L ++ + IP L+ R G LAQ
Sbjct: 136 IAPAVVALVLIAVVTIGLSFFSIPLALLLGLILLLLLLIIPTLFYRAGRKFGAHLAQGRA 195
Query: 155 WLYTWLYE 162
L + +
Sbjct: 196 ALRSQFTD 203
>gnl|CDD|198235 cd10372, SH2_STAT1, Src homology 2 (SH2) domain found in signal
transducer and activator of transcription (STAT) 1
proteins. STAT1 is a member of the STAT family of
transcription factors. STAT1 is involved in
upregulating genes due to a signal by interferons.
STAT1 forms homodimers or heterodimers with STAT3 that
bind to the Interferon-Gamma Activated Sequence (GAS)
promoter element in response to IFN-gamma stimulation.
STAT1 forms a heterodimer with STAT2 that can bind
Interferon Stimulated Response Element (ISRE) promoter
element in response to either IFN-alpha or IFN-beta
stimulation. Binding in both cases leads to an
increased expression of ISG (Interferon Stimulated
Genes). STAT1 has been shown to interact with protein
kinase R, Src, IRF1, STAT3, MCM5, STAT2, CD117, Fanconi
anemia, complementation group C, CREB-binding protein,
Interleukin 27 receptor, alpha subunit, PIAS1, BRCA1,
Epidermal growth factor receptor, PTK2, Mammalian
target of rapamycin, IFNAR2, PRKCD, TRADD, C-jun,
Calcitriol receptor, ISGF3G, and GNB2L1. STAT proteins
mediate the signaling of cytokines and a number of
growth factors from the receptors of these
extracellular signaling molecules to the cell nucleus.
STATs are specifically phosphorylated by
receptor-associated Janus kinases, receptor tyrosine
kinases, or cytoplasmic tyrosine kinases. The
phosphorylated STAT molecules dimerize by reciprocal
binding of their SH2 domains to the phosphotyrosine
residues. These dimeric STATs translocate into the
nucleus, bind to specific DNA sequences, and regulate
the transcription of their target genes. However there
are a number of unphosphorylated STATs that travel
between the cytoplasm and nucleus and some STATs that
exist as dimers in unstimulated cells that can exert
biological functions independent of being activated.
There are seven mammalian STAT family members which
have been identified: STAT1, STAT2, STAT3, STAT4, STAT5
(STAT5A and STAT5B), and STAT6. There are 6 conserved
domains in STAT: N-terminal domain (NTD), coiled-coil
domain (CCD), DNA-binding domain (DBD), alpha-helical
linker domain (LD), SH2 domain, and transactivation
domain (TAD). NTD is involved in dimerization of
unphosphorylated STATs monomers and for the
tetramerization between STAT1, STAT3, STAT4 and STAT5
on promoters with two or more tandem STAT binding
sites. It also plays a role in promoting interactions
with transcriptional co-activators such as CREB binding
protein (CBP)/p300, as well as being important for
nuclear import and deactivation of STATs involving
tyrosine de-phosphorylation. CCD interacts with other
proteins, such as IFN regulatory protein 9 (IRF-9/p48)
with STAT1 and c-JUN with STAT3 and is also thought to
participate in the negative regulation of these
proteins. Distinct genes are bound to STATs via their
DBD domain. This domain is also involved in nuclear
translocation of activated STAT1 and STAT3
phosphorylated dimers upon cytokine stimulation. LD
links the DNA-binding and SH2 domains and is important
for the transcriptional activation of STAT1 in response
to IFN-gamma. It also plays a role in protein-protein
interactions and has also been implicated in the
constitutive nucleocytoplasmic shuttling of
unphosphorylated STATs in resting cells. The SH2
domain is necessary for receptor association and
tyrosine phosphodimer formation. Residues within this
domain may be particularly important for some cellular
functions mediated by the STATs as well as residues
adjacent to this domain. The TAD interacts with
several proteins, namely minichromosome maintenance
complex component 5 (MCM5), breast cancer 1 (BRCA1) and
CBP/p300. TAD also contains a modulatory
phosphorylation site that regulates STAT activity and
is necessary for maximal transcription of a number of
target genes. The conserved tyrosine residue present in
the C-terminus is crucial for dimerization via
interaction with the SH2 domain upon the interaction of
the ligand with the receptor. STAT activation by
tyrosine phosphorylation also determines nuclear import
and retention, DNA binding to specific DNA elements in
the promoters of responsive genes, and transcriptional
activation of STAT dimers. In addition to the SH2
domain there is a coiled-coil domain, a DNA binding
domain, and a transactivation domain in the STAT
proteins. In general SH2 domains are involved in signal
transduction. They typically bind pTyr-containing
ligands via two surface pockets, a pTyr and hydrophobic
binding pocket, allowing proteins with SH2 domains to
localize to tyrosine phosphorylated sites.
Length = 151
Score = 28.7 bits (64), Expect = 2.1
Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 4/45 (8%)
Query: 18 GAFSFSWIE--TKEERPQIARVEDLTNK--TVLKLWEITVYYNIM 58
GA +F+W+E P VE T K + + +I Y +M
Sbjct: 54 GAITFTWVERSQNGGEPDFHAVEPYTKKELSAVTFPDIIRNYKVM 98
>gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab GTPase family 33 includes Rab33A and
Rab33B. Rab33B/Rab33A subfamily. Rab33B is ubiquitously
expressed in mouse tissues and cells, where it is
localized to the medial Golgi cisternae. It colocalizes
with alpha-mannose II. Together with the other cisternal
Rabs, Rab6A and Rab6A', it is believed to regulate the
Golgi response to stress and is likely a molecular
target in stress-activated signaling pathways. Rab33A
(previously known as S10) is expressed primarily in the
brain and immune system cells. In humans, it is located
on the X chromosome at Xq26 and its expression is
down-regulated in tuberculosis patients. Experimental
evidence suggests that Rab33A is a novel CD8+ T cell
factor that likely plays a role in tuberculosis disease
processes. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 28.6 bits (64), Expect = 2.8
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 10/48 (20%)
Query: 141 YFRNMGKVL-------AQSFRWLYTWLYECTMEDRRSEGEVSPRIIVP 181
Y+RN+ V+ SF L +W+ EC ++ S PRI+V
Sbjct: 72 YYRNVHAVVFVYDVTNMASFHSLPSWIEEC---EQHSLPNEVPRILVG 116
>gnl|CDD|236711 PRK10537, PRK10537, voltage-gated potassium channel; Provisional.
Length = 393
Score = 28.8 bits (65), Expect = 3.3
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 94 IWSFPAALMFSLSIFTMIGYGNMVPRTLLGKATTVVYAVFGI 135
I S A FS+ + +GYG++VP + + T+ + GI
Sbjct: 166 IESLSTAFYFSIVTMSTVGYGDIVPVSESARLFTISVIILGI 207
>gnl|CDD|240386 PTZ00370, PTZ00370, STEVOR; Provisional.
Length = 296
Score = 28.8 bits (65), Expect = 3.7
Identities = 20/71 (28%), Positives = 28/71 (39%), Gaps = 19/71 (26%)
Query: 104 SLSIFTMIGYGNMVPRT----------LLGKATTVVYAVF---GIPLYVLYFRNMGKVLA 150
S+SIF M+ +++ L G A + + F GI VL +LA
Sbjct: 215 SISIFNMLSEESIISALKAGGVTCVSGLAGTAASAASSAFYPYGIAALVLL------ILA 268
Query: 151 QSFRWLYTWLY 161
LY WLY
Sbjct: 269 VVLIILYIWLY 279
>gnl|CDD|216239 pfam01007, IRK, Inward rectifier potassium channel.
Length = 336
Score = 28.4 bits (64), Expect = 4.2
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 91 VHEIWSFPAALMFSLSIFTMIGYG 114
V + SF +A +FS+ T IGYG
Sbjct: 78 VMNVHSFTSAFLFSIETQTTIGYG 101
>gnl|CDD|177807 PLN00414, PLN00414, glycosyltransferase family protein.
Length = 446
Score = 28.4 bits (63), Expect = 4.5
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 258 IAMCFDLMREDVRVKVRNLKTDI 280
I DL+R+ + KVR LK D+
Sbjct: 88 IFDAMDLLRDQIEAKVRALKPDL 110
>gnl|CDD|220773 pfam10476, DUF2448, Protein of unknown function C-terminus
(DUF2448). The family DUF2349 is the N-terminal part of
this family. This protein is found in eukaryotes but its
function is not known.
Length = 204
Score = 28.0 bits (62), Expect = 4.9
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 172 GEVSPRIIVPSTACLW--VLGGYVATGTVMFAEWENWPILDSCYFCVTSLC 220
G + R I + LW +L Y+A + A +W LD+ FC TSLC
Sbjct: 128 GPIRLRRIDAFASVLWALILCLYLAEHYLQTAAP-SW--LDTAKFCTTSLC 175
>gnl|CDD|129308 TIGR00204, dxs, 1-deoxy-D-xylulose-5-phosphate synthase. DXP
synthase is a thiamine diphosphate-dependent enzyme
related to transketolase and the pyruvate dehydrogenase
E1-beta subunit. By an acyloin condensation of pyruvate
with glyceraldehyde 3-phosphate, it produces
1-deoxy-D-xylulose 5-phosphate, a precursor of thiamine
diphosphate (TPP), pyridoxal phosphate, and the
isoprenoid building block isopentenyl diphosphate (IPP)
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other, Biosynthesis of cofactors, prosthetic
groups, and carriers, Pyridoxine, Biosynthesis of
cofactors, prosthetic groups, and carriers, Thiamine].
Length = 617
Score = 27.8 bits (62), Expect = 7.9
Identities = 17/57 (29%), Positives = 23/57 (40%), Gaps = 12/57 (21%)
Query: 110 MIGYGNMVPRTLL--------GKATTVVYAVFGIPLYVLYFRNMGKVLAQSFRWLYT 158
++G+G +VP L G TVV A F PL + +A S L T
Sbjct: 500 ILGFGTLVPEALEVAESLNEKGIEATVVDARFVKPLDE----ELILEIAASHEKLVT 552
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 27.9 bits (62), Expect = 8.1
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 8/72 (11%)
Query: 99 AALMFSLSIFTMIGYGNMVPRTLLGKATTVVYAVFGIPLYVLYFRNMGKVLAQSFRWLYT 158
+A+ +S++ T +GYG++ + + Y +F + L NM ++ + R
Sbjct: 253 SAIYWSITTMTTVGYGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVVEGTRR--- 309
Query: 159 WLYECTMEDRRS 170
TME R S
Sbjct: 310 -----TMEFRNS 316
>gnl|CDD|204622 pfam11297, DUF3098, Protein of unknown function (DUF3098). This
bacterial family of proteins has no known function.
Length = 64
Score = 25.3 bits (56), Expect = 9.6
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 246 INFIYLLLGMGLIAMCFDLM 265
IN+I L +G+ +IA+ F LM
Sbjct: 6 INYILLAIGIAVIALGFILM 25
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
0.327 0.141 0.454
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,651,866
Number of extensions: 1486387
Number of successful extensions: 1709
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1705
Number of HSP's successfully gapped: 33
Length of query: 302
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 206
Effective length of database: 6,679,618
Effective search space: 1376001308
Effective search space used: 1376001308
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 (21.7 bits)
S2: 59 (26.4 bits)