RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13347
(339 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 40.1 bits (94), Expect = 3e-05
Identities = 14/28 (50%), Positives = 19/28 (67%), Gaps = 2/28 (7%)
Query: 152 HLRAHLRWHTGERPFVCTWQFCGKRFTR 179
+LR H+R HTGE+P+ C CGK F+
Sbjct: 1 NLRRHMRTHTGEKPYKCP--VCGKSFSS 26
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 36.3 bits (84), Expect = 6e-04
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 210 FQCSECHKKFMRSDHLQKHIKTH 232
++C EC K F L++H++TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 35.8 bits (83), Expect = 9e-04
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 211 QCSECHKKFMRSDHLQKHIKTH 232
+C +C K F R +L++H++TH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 25.8 bits (57), Expect = 3.6
Identities = 9/24 (37%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 137 ICHIEGCNKVYGKTSHLRAHLRWH 160
C C K + + S+L+ HLR H
Sbjct: 1 KCPD--CGKSFSRKSNLKRHLRTH 22
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 33.0 bits (75), Expect = 0.008
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 210 FQCSECHKKFMRSDHLQKHIKTH 232
F+C C K F D L++H++ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 34.7 bits (79), Expect = 0.070
Identities = 21/127 (16%), Positives = 32/127 (25%), Gaps = 23/127 (18%)
Query: 134 KVHICHIEGCNKVYGKTSHLRAHLRWHTGERPFVCTWQFCGKRFTRS------------- 180
K C C K++ + L+ H+ HT P +F+
Sbjct: 320 KPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYK 379
Query: 181 ----DELQVNGGRFGIERTVVRILPMT------WCREKRFQCSECHKKFMRSDHLQKHIK 230
D+ I R + C K F R +L H K
Sbjct: 380 DLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKK 439
Query: 231 THSKTRC 237
H+
Sbjct: 440 IHTNHAP 446
Score = 29.7 bits (66), Expect = 2.3
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 6/65 (9%)
Query: 124 SCSLRTADRKKVHICHIEGCNKVYGKTSHLRAHLRW--HTGE--RPFVCTWQFCGKRFTR 179
S S + CN + ++S L HLR H+GE +PF C + CGK F+R
Sbjct: 278 SDSSSEKGFSLPIKS--KQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSR 335
Query: 180 SDELQ 184
+D L+
Sbjct: 336 NDALK 340
Score = 27.7 bits (61), Expect = 9.9
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 210 FQCSECHKKFMRSDHLQKHIKTHS 233
C C F R +HL +HI++H+
Sbjct: 34 DSCPNCTDSFSRLEHLTRHIRSHT 57
>gnl|CDD|216798 pfam01937, DUF89, Protein of unknown function DUF89. This family
has no known function.
Length = 315
Score = 32.3 bits (74), Expect = 0.30
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 67 EREMFSYMLHGCLWGNTMEYALAA 90
E E+F +L LWGN ++ L A
Sbjct: 102 EEELFKELLKISLWGNIIDLGLLA 125
>gnl|CDD|218820 pfam05943, DUF877, Protein of unknown function (DUF877). This
family consists of a number of uncharacterized bacterial
proteins. The function of this family is unknown.
Length = 423
Score = 31.4 bits (72), Expect = 0.75
Identities = 18/62 (29%), Positives = 21/62 (33%), Gaps = 14/62 (22%)
Query: 44 DSLEEKPRSRRVACTCP------------NCTEG-GEREMFSYMLHGCLWGNTMEYALAA 90
SL E +R + T P N EG E S LWGN YA A
Sbjct: 161 RSLRESEDARYLGLTLPRFLLRLPYGPDTNPVEGFNFEEDVSGDHEDYLWGNA-AYAFAT 219
Query: 91 RV 92
+
Sbjct: 220 NL 221
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 30.8 bits (69), Expect = 1.0
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 21/63 (33%)
Query: 134 KVHICHIEGCNKVYGKTSHLRAHLR-------------------WHTGERPFVCTWQFCG 174
K + C +EGCNK Y + L+ H+ + ++P+ C + C
Sbjct: 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRC--EVCD 405
Query: 175 KRF 177
KR+
Sbjct: 406 KRY 408
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of the
virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA plus-strand.
lambda1 is an Orthoreovirus core protein, VP3 is the
homologous core protein in Aquareoviruses.
Length = 1166
Score = 30.5 bits (69), Expect = 1.6
Identities = 10/41 (24%), Positives = 19/41 (46%)
Query: 212 CSECHKKFMRSDHLQKHIKTHSKTRCTSLVMNFSDNTVVTE 252
C+ C +F D L +H +T +SL+ + + N +
Sbjct: 76 CNVCMAEFSSMDQLAEHQRTTHSIGASSLLTSPAINQAIES 116
>gnl|CDD|218593 pfam05445, Pox_ser-thr_kin, Poxvirus serine/threonine protein
kinase.
Length = 434
Score = 30.1 bits (68), Expect = 1.8
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 95 LKIYKTTAEVNNKIRLSSYFYPALISTLF 123
LKI+ + ++L SYFYP ++ +
Sbjct: 191 LKIFNERKDSEKFVKLFSYFYPKVVKSNI 219
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 26.4 bits (59), Expect = 2.2
Identities = 8/26 (30%), Positives = 9/26 (34%)
Query: 210 FQCSECHKKFMRSDHLQKHIKTHSKT 235
C C K F L H K+H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSHCSL 27
>gnl|CDD|188721 cd09335, LIM5_PINCH, The fifth LIM domain of protein PINCH. The
fifth LIM domain of protein PINCH: PINCH plays pivotal
roles in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 54
Score = 26.9 bits (60), Expect = 2.4
Identities = 13/28 (46%), Positives = 13/28 (46%), Gaps = 1/28 (3%)
Query: 192 IERTVVRILPMTWCREKRFQCSECHKKF 219
IE VV L TWC F CS C K
Sbjct: 8 IEGDVVSALNKTWC-VDHFSCSFCDTKL 34
>gnl|CDD|204557 pfam10843, DUF2578, Protein of unknown function (DUF2578). This is
a Saccharomycete family of proteins with unknown
function. The protein in S. cerevisiae is strongly
induced in response to many stress conditions and is
repressed in drug resistant yeast strains.
Length = 159
Score = 28.6 bits (64), Expect = 3.2
Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 217 KKFMRSDHLQKHIKTH----SKTRCTSLVMNFSDNTVVTEDSKL 256
KKF+R HL +HI+ H K C + F + K+
Sbjct: 80 KKFVR--HLHQHIEKHLLKDIKKCCGYPELKFKKKSKEETFEKI 121
>gnl|CDD|224328 COG1410, MetH, Methionine synthase I, cobalamin-binding domain
[Amino acid transport and metabolism].
Length = 842
Score = 29.2 bits (66), Expect = 3.6
Identities = 8/22 (36%), Positives = 9/22 (40%)
Query: 155 AHLRWHTGERPFVCTWQFCGKR 176
A LR + PF W GK
Sbjct: 599 AELRPYIDWTPFFMQWGLRGKY 620
>gnl|CDD|117765 pfam09212, CBM27, Carbohydrate binding module 27. Members of this
family are carbohydrate binding modules that bind to
beta-1, 4-mannooligosaccharides, carob galactomannan,
and konjac glucomannan, but not to cellulose (insoluble
and soluble) or soluble birchwood xylan. They adopt a
beta sandwich structure comprising 13 beta strands with
a single, small alpha-helix and a single metal atom.
Length = 173
Score = 28.4 bits (63), Expect = 4.2
Identities = 8/24 (33%), Positives = 11/24 (45%), Gaps = 1/24 (4%)
Query: 266 GTPE-SWINTDGNRCFLVNIEAPG 288
G P W GN +N++ PG
Sbjct: 33 GIPAIEWNGEPGNGALQMNVDLPG 56
>gnl|CDD|241529 cd13378, PH_RhoGAP2, Rho GTPase activating protein 2 Pleckstrin
homology (PH) domain. RhoGAP2 (also called RhoGap22 or
ArhGap22) are involved in cell polarity, cell
morphology and cytoskeletal organization. They activate
a GTPase belonging to the RAS superfamily of small
GTP-binding proteins. The encoded protein is
insulin-responsive, is dependent on the kinase Akt, and
requires the Akt-dependent 14-3-3 binding protein which
binds sequentially to two serine residues resulting in
regulation of cell motility. Members here contain an
N-terminal PH domain followed by a RhoGAP domain and
either a BAR or TATA Binding Protein (TBP) Associated
Factor 4 (TAF4) domain. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold,
which is electrostatically polarized. Less than 10% of
PH domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 116
Score = 27.2 bits (60), Expect = 5.2
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 6/32 (18%)
Query: 2 QGQQVQQLQQDPNDPTR--FQILNLCSPGGGG 31
QG QV +L +P +P + F+I PGG G
Sbjct: 49 QGSQVNELPPNPEEPGKHLFEI----LPGGAG 76
>gnl|CDD|214746 smart00614, ZnF_BED, BED zinc finger. DNA-binding domain in
chromatin-boundary-element-binding proteins and
transposases.
Length = 50
Score = 25.5 bits (56), Expect = 6.8
Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 7/41 (17%)
Query: 123 FSCSLRTADRKKVHICHIEGCNKVY-----GKTSHLRAHLR 158
F+ L + K+ C C K G TS+LR HLR
Sbjct: 6 FTLILEKDNGKQRAKCKY--CGKKLSRSSKGGTSNLRRHLR 44
>gnl|CDD|100115 cd05804, StaR_like, StaR_like; a well-conserved protein found in
bacteria, plants, and animals. A family member from
Streptomyces toyocaensis, StaR is part of a gene cluster
involved in the biosynthesis of glycopeptide antibiotics
(GPAs), specifically A47934. It has been speculated that
StaR could be a flavoprotein hydroxylating a tyrosine
sidechain. Some family members have been annotated as
proteins containing tetratricopeptide (TPR) repeats,
which may at least indicate mostly alpha-helical
secondary structure.
Length = 355
Score = 28.0 bits (63), Expect = 7.5
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 140 IEGCNKVYGKTSHLRAHLRWH 160
+E + +S LR H WH
Sbjct: 171 MESWRDTWDCSSMLRGHNWWH 191
>gnl|CDD|227366 COG5033, TFG3, Transcription initiation factor IIF, auxiliary
subunit [Transcription].
Length = 225
Score = 27.8 bits (62), Expect = 8.0
Identities = 10/42 (23%), Positives = 12/42 (28%), Gaps = 8/42 (19%)
Query: 5 QVQQLQQDPNDPTRFQILNLCSPGGGGVTTSIEMVNQEEDSL 46
V QL QDP I I++ D L
Sbjct: 182 FVVQLVQDPIMAVLNLI--------EKGEFKIDLYKLPSDLL 215
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
0.318 0.133 0.417
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,608,495
Number of extensions: 1513735
Number of successful extensions: 1175
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1175
Number of HSP's successfully gapped: 28
Length of query: 339
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 241
Effective length of database: 6,590,910
Effective search space: 1588409310
Effective search space used: 1588409310
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.6 bits)