RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6056
(153 letters)
>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain,
a specialized type of Zn-finger of 40 to 60 residues
that binds two atoms of zinc; defined by the
'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)-
H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved
in mediating protein-protein interactions; identified
in a proteins with a wide range of functions such as
viral replication, signal transduction, and
development; has two variants, the C3HC4-type and a
C3H2C3-type (RING-H2 finger), which have different
cysteine/histidine pattern; a subset of RINGs are
associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
Length = 45
Score = 37.4 bits (87), Expect = 1e-04
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 48 CPICLLVLNNRSYTDTCLHEFCFLCIKQWSQISSESSPALCK 89
CPICL C H FC CI +W + + P LC+
Sbjct: 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCP-LCR 42
>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger). The
C3HC4 type zinc-finger (RING finger) is a cysteine-rich
domain of 40 to 60 residues that coordinates two zinc
ions, and has the consensus sequence:
C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C
where X is any amino acid. Many proteins containing a
RING finger play a key role in the ubiquitination
pathway.
Length = 40
Score = 37.1 bits (86), Expect = 1e-04
Identities = 12/29 (41%), Positives = 13/29 (44%)
Query: 48 CPICLLVLNNRSYTDTCLHEFCFLCIKQW 76
CPICL + C H FC CI W
Sbjct: 1 CPICLEEPKDPVTILPCGHLFCSKCILSW 29
>gnl|CDD|214546 smart00184, RING, Ring finger. E3 ubiquitin-protein ligase
activity is intrinsic to the RING domain of c-Cbl and
is likely to be a general function of this domain;
Various RING fingers exhibit binding activity towards
E2 ubiquitin-conjugating enzymes (Ubc' s).
Length = 40
Score = 35.6 bits (82), Expect = 5e-04
Identities = 13/38 (34%), Positives = 18/38 (47%)
Query: 48 CPICLLVLNNRSYTDTCLHEFCFLCIKQWSQISSESSP 85
CPICL C H FC CI++W + + + P
Sbjct: 1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCP 38
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 32.9 bits (75), Expect = 0.006
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 48 CPICLLVLNNRSYTDTCLHEFCFLCIKQWSQISSE 82
CPICL +L + C H FC CI ++ + S+
Sbjct: 5 CPICLDLLRDPVVLTPCGHVFCRECILRYLKKKSK 39
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 30.8 bits (70), Expect = 0.037
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 2/36 (5%)
Query: 48 CPICL--LVLNNRSYTDTCLHEFCFLCIKQWSQISS 81
CPICL C H F C+ +W + S+
Sbjct: 3 CPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSN 38
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 32.9 bits (75), Expect = 0.041
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 1/43 (2%)
Query: 47 RCPICLLVLNNRSYTDTCLHEFCFLCIKQWSQISSESSPALCK 89
+C +CL S T C H FC C+ LC+
Sbjct: 217 KCFLCLEEPEVPSCT-PCGHLFCLSCLLISWTKKKYEFCPLCR 258
>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18. All proteins in this
family for which functions are known are involved in
nucleotide excision repair.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 397
Score = 31.1 bits (70), Expect = 0.20
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 47 RCPICLLVLNNRSYTDTCLHEFCFLCIKQWSQISSESSPALCKMSKQRLLL 97
RC IC + T +C H FC LCI++ +S++ LC+ Q L
Sbjct: 28 RCHICKDFFDVPVLT-SCSHTFCSLCIRRC--LSNQPKCPLCRAEDQESKL 75
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 30.8 bits (69), Expect = 0.31
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 6/50 (12%)
Query: 48 CPICLLVLN--NRSYTD----TCLHEFCFLCIKQWSQISSESSPALCKMS 91
C IC VL+ +RS TC ++F C+ +W S+ S+ LC+
Sbjct: 1472 CAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSE 1521
>gnl|CDD|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation
motif. This zinc-finger is the dimerisation motif for
LisH proteins, and is also a typical RING-type of plant
ubiquitin ligases.
Length = 55
Score = 28.1 bits (63), Expect = 0.44
Identities = 6/38 (15%), Positives = 15/38 (39%), Gaps = 3/38 (7%)
Query: 48 CPICLLVLNNRS---YTDTCLHEFCFLCIKQWSQISSE 82
CPI V+ + C H + +++ ++ +
Sbjct: 13 CPISKEVMTDEENPPVMLPCGHVYSRKALEKLAKNGGK 50
>gnl|CDD|221473 pfam12230, PRP21_like_P, Pre-mRNA splicing factor PRP21 like
protein. This domain family is found in eukaryotes, and
is typically between 212 and 238 amino acids in length.
The family is found in association with pfam01805. There
are two completely conserved residues (W and H) that may
be functionally important. PRP21 is required for
assembly of the prespliceosome and it interacts with U2
snRNP and/or pre-mRNA in the prespliceosome. This family
also contains proteins similar to PRP21, such as the
mammalian SF3a. SF3a also interacts with U2 snRNP from
the prespliceosome, converting it to its active form.
Length = 230
Score = 29.7 bits (67), Expect = 0.47
Identities = 8/28 (28%), Positives = 14/28 (50%)
Query: 24 KKQKNDNPSEDDSDGDRPTSPTSRCPIC 51
K +K+ PS + ++P +CPI
Sbjct: 148 KIRKDYVPSGNKPRAEKPKKKMIKCPIT 175
>gnl|CDD|165237 PHA02926, PHA02926, zinc finger-like protein; Provisional.
Length = 242
Score = 28.5 bits (63), Expect = 1.3
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 9/62 (14%)
Query: 43 SPTSRCPICLLVL------NNRSY--TDTCLHEFCFLCIKQWSQISSESSPA-LCKMSKQ 93
S C IC V+ N+R + D+C H FC CI W + E+ + C + +
Sbjct: 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRT 227
Query: 94 RL 95
R
Sbjct: 228 RF 229
>gnl|CDD|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2;
Provisional.
Length = 193
Score = 28.1 bits (62), Expect = 1.5
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 25 KQKNDNPSEDDSDGDRPTSPTSRCPICLLVLNNRSYTDTCLHEFCFLCIKQWSQISSES 83
++ D+ + DS GD C ICL + + T C H FC+ CI +W+ S+ S
Sbjct: 4 EKDEDDTTLVDSGGD------FDCNICLDQVRDPVVT-LCGHLFCWPCIHKWTYASNNS 55
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase
[Signal transduction mechanisms].
Length = 391
Score = 28.5 bits (63), Expect = 1.7
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 47 RCPICLLVLNNRSYTDTCLHEFCFLCIK 74
RC IC ++ T TC H FC LCI+
Sbjct: 27 RCRICDCRISIPCET-TCGHTFCSLCIR 53
>gnl|CDD|185622 PTZ00443, PTZ00443, Thioredoxin domain-containing protein;
Provisional.
Length = 224
Score = 28.1 bits (62), Expect = 1.8
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 110 VYDIMILQ-VNTSTFKGLFGVNIGRIDRLHLFTFGHFQSRKTRVP 153
+YD S+F LFG+ +G + L F+ G+ + + P
Sbjct: 171 IYDAAFAGFFTISSFAFLFGILMGLMIALFAFSKGNSTAHANKKP 215
>gnl|CDD|222981 PHA03096, PHA03096, p28-like protein; Provisional.
Length = 284
Score = 27.8 bits (62), Expect = 2.5
Identities = 19/80 (23%), Positives = 26/80 (32%), Gaps = 13/80 (16%)
Query: 11 KRRLELPEIQQASKKQKNDNPSEDDSDGDRPTSPTSRCPICLLV-----LNNRSYTD--T 63
K L +I+Q +QK + + C ICL + + Y
Sbjct: 150 KYLLHPTDIKQRYNEQKTCLSYQLR------LLLSKICGICLENIKAKYIIKKYYGILSE 203
Query: 64 CLHEFCFLCIKQWSQISSES 83
HEF CIK W S
Sbjct: 204 IKHEFNIFCIKIWMTESLYK 223
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 27.8 bits (61), Expect = 3.0
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 17 PEIQQASK-KQKNDNPSE--DDSDGDRPTSPTSRCPICLLVLNNRSYTDTCLHEFCFLCI 73
P++Q K +Q+ +E D +P + + +CP+C +L N T C H FC CI
Sbjct: 243 PDVQSWEKYQQRTKAVAEIPDQVYKMQPPNISLKCPLCHCLLRNPMKTPCCGHTFCDECI 302
>gnl|CDD|177189 MTH00131, CYTB, cytochrome b; Provisional.
Length = 380
Score = 26.2 bits (58), Expect = 8.2
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 91 SKQRLLLFASATECLQYINVYDIMIL 116
SKQR L F T+ L + V D++IL
Sbjct: 310 SKQRGLTFRPLTQFLFWTLVADVLIL 335
>gnl|CDD|188805 cd09421, LIM3_LIMPETin, The third LIM domain of protein LIMPETin.
The third LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is
a transcription regulator. 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 = 59
Score = 24.5 bits (53), Expect = 9.1
Identities = 10/16 (62%), Positives = 10/16 (62%)
Query: 59 SYTDTCLHEFCFLCIK 74
SY D HE CFLC K
Sbjct: 20 SYKDKHWHEACFLCSK 35
>gnl|CDD|177162 MTH00100, CYTB, cytochrome b; Provisional.
Length = 379
Score = 26.1 bits (58), Expect = 9.7
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 90 MSKQRLLLFASATECLQYINVYDIMIL 116
SKQR ++F ++CL ++ V D++ L
Sbjct: 309 TSKQRSMMFRPLSQCLFWLLVADLLTL 335
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 0.134 0.406
Gapped
Lambda K H
0.267 0.0678 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,207,571
Number of extensions: 577682
Number of successful extensions: 484
Number of sequences better than 10.0: 1
Number of HSP's gapped: 482
Number of HSP's successfully gapped: 26
Length of query: 153
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 64
Effective length of database: 6,990,096
Effective search space: 447366144
Effective search space used: 447366144
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: 55 (25.1 bits)