RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3895
(185 letters)
>gnl|CDD|128983 smart00744, RINGv, The RING-variant domain is a C4HC3 zinc-finger
like motif found in a number of cellular and viral
proteins. Some of these proteins have been shown both
in vivo and in vitro to have ubiquitin E3 ligase
activity. The RING-variant domain is reminiscent of both
the RING and the PHD domains and may represent an
evolutionary intermediate. To describe this domain the
term PHD/LAP domain has been used in the past. Extended
description: The RING-variant (RINGv) domain contains a
C4HC3 zinc-finger-like motif similar to the PHD domain,
while some of the spacing between the Cys/His residues
follow a pattern somewhat closer to that found in the
RING domain. The RINGv domain, similar to the RING, PHD
and LIM domains, is thought to bind two zinc ions
co-ordinated by the highly conserved Cys and His
residues. RING variant domain: C-x (2) -C-x(10-45)-C-x
(1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a
PHD: C-x(1-2) -C-x
(7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C
Classical RING domain: C-x (2) -C-x
(9-39)-C-x(1-3)-H-x(2-3)-C-x(2)-C-x(4-48) -C-x(2)-C.
Length = 49
Score = 61.5 bits (150), Expect = 2e-13
Identities = 21/57 (36%), Positives = 26/57 (45%), Gaps = 8/57 (14%)
Query: 70 YCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCN 126
C +C E D V PC C+G+ K+VHQ CL RWI+E C C
Sbjct: 1 ICRICHD--EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGN------KTCEICK 49
>gnl|CDD|221845 pfam12906, RINGv, RING-variant domain.
Length = 47
Score = 55.1 bits (133), Expect = 4e-11
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 8/55 (14%)
Query: 71 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQC 125
C +C E+D ++PC CRG+ K+VHQ+CL RW+ C C
Sbjct: 1 CRICLEGEEEDEP--LIRPCRCRGSLKYVHQSCLERWLKTSGN------TTCEIC 47
>gnl|CDD|177491 PHA02825, PHA02825, LAP/PHD finger-like protein; Provisional.
Length = 162
Score = 41.3 bits (97), Expect = 5e-05
Identities = 21/71 (29%), Positives = 29/71 (40%), Gaps = 11/71 (15%)
Query: 69 KYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTK 128
K CW+C ++ N C C+ +K VH+ CL WI N +C CN
Sbjct: 9 KCCWICKDEYDVVTNY-----CNCKNENKIVHKECLEEWI------NTSKNKSCKICNGP 57
Query: 129 YFIVYPYRGLL 139
Y I Y+
Sbjct: 58 YNIKKNYKKCT 68
>gnl|CDD|227510 COG5183, SSM4, Protein involved in mRNA turnover and stability [RNA
processing and modification].
Length = 1175
Score = 41.1 bits (96), Expect = 2e-04
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 67 DLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCN 126
D + C +C ED R+ PC C G+ K++H+ CL W++ C C+
Sbjct: 11 DKRSCRICRT--EDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGT------KKCDICH 62
Query: 127 TKY 129
+Y
Sbjct: 63 YEY 65
>gnl|CDD|165197 PHA02862, PHA02862, 5L protein; Provisional.
Length = 156
Score = 38.4 bits (89), Expect = 6e-04
Identities = 22/65 (33%), Positives = 27/65 (41%), Gaps = 11/65 (16%)
Query: 71 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130
CW+C D+RN C C K VH C+ WI+ +K C C TKY
Sbjct: 5 CWICNDVC-DERNNF----CGCNEEYKVVHIKCMQLWINYSKK------KECNLCKTKYN 53
Query: 131 IVYPY 135
I Y
Sbjct: 54 IKKTY 58
>gnl|CDD|204746 pfam11793, FANCL_C, FANCL C-terminal domain. This domain is found
at the C-terminus of the Fancl protein in humans which
is the putative E3 ubiquitin ligase subunit of the FA
complex (Fanconi anaemia). Eight subunits of the Fanconi
anaemia gene products form a multisubunit nuclear
complex which is required for mono-ubiquitination of a
downstream FA protein, FANCD2.
Length = 70
Score = 28.9 bits (65), Expect = 0.37
Identities = 15/61 (24%), Positives = 21/61 (34%), Gaps = 4/61 (6%)
Query: 71 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVA---CPQCNT 127
C +C+A D + C H ACL W+ + V+ CP C
Sbjct: 5 CGICYAYR-LDGGEIPDISCDNPKCGLPFHIACLYEWLRTLRDSRQSFNVSFGTCPYCKA 63
Query: 128 K 128
K
Sbjct: 64 K 64
>gnl|CDD|201356 pfam00628, PHD, PHD-finger. PHD folds into an interleaved type of
Zn-finger chelating 2 Zn ions in a similar manner to
that of the RING and FYVE domains. Several PHD fingers
have been identified as binding modules of methylated
histone H3.
Length = 51
Score = 27.5 bits (61), Expect = 0.71
Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 8/56 (14%)
Query: 70 YCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQC 125
YC VC +D + C G +W H ACL + + + CP+C
Sbjct: 1 YCAVCGKVDDDGE---LLL---CDGCDRWFHLACLG--PPLEPEEIPEGEWYCPEC 48
>gnl|CDD|119255 pfam10735, DUF2526, Protein of unknown function (DUF2526). This
family of proteins with unknown function is restricted
to Enterobacteriaceae. The family has a highly
conserved sequence.
Length = 77
Score = 28.0 bits (62), Expect = 0.87
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 4 QRERNERSLVNEAVLMAIQRHGLQHQQDEDQ 34
Q R ER + + AI HG QH++D +
Sbjct: 35 QLSREERYDQQQRLRTAIAHHGRQHKEDREA 65
>gnl|CDD|215915 pfam00429, TLV_coat, ENV polyprotein (coat polyprotein).
Length = 560
Score = 28.2 bits (63), Expect = 2.5
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 5/52 (9%)
Query: 18 LMAIQR-HGLQHQQDEDQDETSSSVQSPPGVIQSKSDSAGVVVLEIERSVDL 68
L++ Q+ LQH D SS+ ++ S VVL+ R +DL
Sbjct: 419 LVSTQQFTSLQHALISDIQALESSIND----LEDSLTSLAEVVLQNRRGLDL 466
>gnl|CDD|235356 PRK05170, PRK05170, hypothetical protein; Provisional.
Length = 147
Score = 27.6 bits (62), Expect = 2.5
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 91 LCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTK 128
LC G K CL++ DE +T VAC + K
Sbjct: 23 LCDGCGK----CCLHKLEDEDTGEIYYTNVACRLLDIK 56
>gnl|CDD|213361 cd12827, EcCorA_ZntB-like_u2, uncharacterized bacterial subfamily
of the Escherichia coli CorA-Salmonella typhimurium ZntB
family. A uncharacterized subfamily of the Escherichia
coli CorA-Salmonella typhimurium ZntB (EcCorA-ZntB_like)
family of the MIT superfamily of essential membrane
proteins involved in transporting divalent cations
(uptake or efflux) across membranes.The EcCorA-ZntB-like
family includes the Mg2+ transporters Escherichia coli
and Salmonella typhimurium CorAs, which can also
transport Co2+, and Ni2+. Structures of the
intracellular domain of EcCorA-ZntB-like family members,
Vibrio parahaemolyticus and Salmonella typhimurium ZntB,
form funnel-shaped homopentamers, the tip of the funnel
is formed from two C-terminal transmembrane (TM) helices
from each monomer, and the large opening of the funnel
from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport through Salmonella typhimurium CorA. Natural
variants such as GVN and GIN, such as occur in some ZntB
family proteins, may be associated with the transport of
different divalent cations, such as zinc and cadmium.
The functional diversity of MIT transporters may also be
due to minor structural differences regulating gating,
substrate selection, and transport.
Length = 289
Score = 28.2 bits (64), Expect = 2.6
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 8/35 (22%)
Query: 9 ERSLV--------NEAVLMAIQRHGLQHQQDEDQD 35
E+SLV NE VL ++R +ED++
Sbjct: 154 EKSLVYFSTSLKSNEIVLEKLKRSRSLKLDEEDKE 188
>gnl|CDD|215494 PLN02915, PLN02915, cellulose synthase A [UDP-forming], catalytic
subunit.
Length = 1044
Score = 28.0 bits (62), Expect = 3.5
Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 21/73 (28%)
Query: 63 ERSVDLKYCWVC---FATHEDDRNALWVQPC---LCRGTSKWVHQACLNRWIDEKQKGNA 116
+S D K C VC ED + + C +C+ ++ E+ +GN
Sbjct: 10 RQSADAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEY-----------ERSEGNQ 58
Query: 117 FTQVACPQCNTKY 129
CPQCNT+Y
Sbjct: 59 ----CCPQCNTRY 67
>gnl|CDD|217050 pfam02460, Patched, Patched family. The transmembrane protein
Patched is a receptor for the morphogene Sonic Hedgehog.
This protein associates with the smoothened protein to
transduce hedgehog signals.
Length = 801
Score = 27.7 bits (62), Expect = 3.7
Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 153 LCPFVAAGVVLGSMYWCAVTYGA-VTVM 179
L P +A G ++W + + V V
Sbjct: 258 LTPLMATVSAFGLLFWFGFPFNSIVCVT 285
>gnl|CDD|227470 COG5141, COG5141, PHD zinc finger-containing protein [General
function prediction only].
Length = 669
Score = 28.0 bits (62), Expect = 3.9
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 71 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQAC 103
C C +TH ++ NA+ C G VHQ+C
Sbjct: 196 CTKCTSTHNENSNAIVF----CDGCEICVHQSC 224
>gnl|CDD|215358 PLN02666, PLN02666, 5-oxoprolinase.
Length = 1275
Score = 27.4 bits (61), Expect = 5.4
Identities = 20/65 (30%), Positives = 22/65 (33%), Gaps = 24/65 (36%)
Query: 44 PPGVIQSKSDSAGVV---VLEIERSVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVH 100
PPG S SD A VV VL +R D V Q C C
Sbjct: 1079 PPGSFLSPSDKAAVVGGNVLTSQRVTD-----VVLTA---------FQACACS------- 1117
Query: 101 QACLN 105
Q C+N
Sbjct: 1118 QGCMN 1122
>gnl|CDD|225530 COG2983, COG2983, Uncharacterized conserved protein [Function
unknown].
Length = 153
Score = 26.6 bits (59), Expect = 5.7
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 6/48 (12%)
Query: 91 LCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCN--TKYFIVYPYR 136
LC G CL++ DE +T+VAC + T Y R
Sbjct: 28 LCDGCG----LCCLHKLEDEDTDEIYYTRVACELLDPETCRCKDYENR 71
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and
similar proteins. This subfamily corresponds to the
RRM1 in tRNA selenocysteine-associated protein 1
(SECp43), yeast negative growth regulatory protein NGR1
(RBP1), yeast protein NAM8, and similar proteins.
SECp43 is an RNA-binding protein associated
specifically with eukaryotic selenocysteine tRNA
[tRNA(Sec)]. It may play an adaptor role in the
mechanism of selenocysteine insertion. SECp43 is
located primarily in the nucleus and contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal polar/acidic region. Yeast
proteins, NGR1 and NAM8, show high sequence similarity
with SECp43. NGR1 is a putative glucose-repressible
protein that binds both RNA and single-stranded DNA
(ssDNA). It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains three RRMs, two of which
are followed by a glutamine-rich stretch that may be
involved in transcriptional activity. In addition, NGR1
has an asparagine-rich region near the C-terminus which
also harbors a methionine-rich region. NAM8 is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. NAM8
also contains three RRMs. .
Length = 81
Score = 25.3 bits (56), Expect = 7.6
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 70 YCWVCFATHEDDRNAL 85
Y +V FATHE AL
Sbjct: 43 YGFVEFATHEAAEQAL 58
>gnl|CDD|215239 PLN02436, PLN02436, cellulose synthase A.
Length = 1094
Score = 26.8 bits (59), Expect = 9.8
Identities = 10/20 (50%), Positives = 14/20 (70%), Gaps = 4/20 (20%)
Query: 110 EKQKGNAFTQVACPQCNTKY 129
E+++GN ACPQC T+Y
Sbjct: 73 ERREGNQ----ACPQCKTRY 88
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
0.322 0.133 0.429
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,826,531
Number of extensions: 749384
Number of successful extensions: 675
Number of sequences better than 10.0: 1
Number of HSP's gapped: 674
Number of HSP's successfully gapped: 28
Length of query: 185
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 94
Effective length of database: 6,901,388
Effective search space: 648730472
Effective search space used: 648730472
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (25.3 bits)