RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16185
(263 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 = 61.2 bits (149), Expect = 7e-13
Identities = 21/57 (36%), Positives = 26/57 (45%), Gaps = 8/57 (14%)
Query: 13 YCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCN 69
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 = 54.3 bits (131), Expect = 3e-10
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 8/55 (14%)
Query: 14 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQC 68
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 = 40.9 bits (96), Expect = 1e-04
Identities = 21/71 (29%), Positives = 29/71 (40%), Gaps = 11/71 (15%)
Query: 12 KYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTK 71
K CW+C ++ N C C+ +K VH+ CL WI N +C CN
Sbjct: 9 KCCWICKDEYDVVTNY-----CNCKNENKIVHKECLEEWI------NTSKNKSCKICNGP 57
Query: 72 YFIVYPYRGLL 82
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 = 39.9 bits (93), Expect = 0.001
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 7 ISSDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACP 66
++ D + C +C ED R+ PC C G+ K++H+ CL W++ C
Sbjct: 8 MNEDKRSCRICRT--EDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGT------KKCD 59
Query: 67 QCNTKY 72
C+ +Y
Sbjct: 60 ICHYEY 65
>gnl|CDD|165197 PHA02862, PHA02862, 5L protein; Provisional.
Length = 156
Score = 38.4 bits (89), Expect = 0.001
Identities = 22/65 (33%), Positives = 27/65 (41%), Gaps = 11/65 (16%)
Query: 14 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 73
CW+C D+RN C C K VH C+ WI+ +K C C TKY
Sbjct: 5 CWICNDVC-DERNNF----CGCNEEYKVVHIKCMQLWINYSKK------KECNLCKTKYN 53
Query: 74 IVYPY 78
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 = 0.44
Identities = 15/61 (24%), Positives = 21/61 (34%), Gaps = 4/61 (6%)
Query: 14 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVA---CPQCNT 70
C +C+A D + C H ACL W+ + V+ CP C
Sbjct: 5 CGICYAYR-LDGGEIPDISCDNPKCGLPFHIACLYEWLRTLRDSRQSFNVSFGTCPYCKA 63
Query: 71 K 71
K
Sbjct: 64 K 64
>gnl|CDD|218772 pfam05840, Phage_GPA, Bacteriophage replication gene A protein
(GPA). This family consists of a group of bacteriophage
replication gene A protein (GPA) like sequences from
both viruses and bacteria. The members of this family
are likely to be endonucleases.
Length = 374
Score = 31.3 bits (71), Expect = 0.48
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 131 LGALSLRFCLVHPLVNINRQYRFQLDN----ILR-ICDKGLLRRLRARQVIGRENGLQVM 185
L L++ F + HP R+ + + I R C+K LR+L+ + RE+ L +
Sbjct: 44 LAQLAISFTIDHPHYKKERKKKITAEELESAIARLTCEKWWLRQLKRIRKRWREHLLIAV 103
Query: 186 REV 188
V
Sbjct: 104 GLV 106
>gnl|CDD|226226 COG3703, ChaC, Uncharacterized protein involved in cation transport
[Inorganic ion transport and metabolism].
Length = 190
Score = 30.0 bits (68), Expect = 0.85
Identities = 15/62 (24%), Positives = 22/62 (35%), Gaps = 22/62 (35%)
Query: 208 WCHIHRHQG-------------HPQ-----DLPQAAEVRHAEETTSVGLRGPATQYVADL 249
W + G HPQ D Q A + A VGL GP +Y+ +
Sbjct: 103 WLPVELEGGRRVNALVFVGDRKHPQYAGDLDAEQIAAIIAAA----VGLSGPNAEYLFNT 158
Query: 250 VK 251
++
Sbjct: 159 LQ 160
>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 = 1.2
Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 8/56 (14%)
Query: 13 YCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQC 68
YC VC +D + C G +W H ACL + + + CP+C
Sbjct: 1 YCAVCGKVDDDGE---LLL---CDGCDRWFHLACLG--PPLEPEEIPEGEWYCPEC 48
>gnl|CDD|218099 pfam04465, DUF499, Protein of unknown function (DUF499). Family of
uncharacterized hypothetical prokaryotic proteins.
Length = 1025
Score = 29.4 bits (66), Expect = 2.0
Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 14/63 (22%)
Query: 81 LLVSLLDTIDTAVYKLCPFVAAGVVLGSMYWCAVTYGAVTV-----------MVVSPLHT 129
LVS+ +D + P V GV++GS+ V +V + S +
Sbjct: 924 KLVSIKSVVDLDSLERIPEVFEGVIVGSL---EVEKPLWSVSFDTTDPKVFEYIWSEIEE 980
Query: 130 YLG 132
+LG
Sbjct: 981 FLG 983
>gnl|CDD|132172 TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase. Members of
this protein family are 3-hexulose-6-phosphate synthase
(HPS), or the HPS domain of a fusion protein. This
enzyme is part of the ribulose monophosphate (RuMP)
pathway, which in one direction removes the toxic
metabolite formaldehyde by assimilation into
fructose-6-phosphate. In the other direction, in species
lacking a complete pentose phosphate pathway, the RuMP
pathway yields ribulose-5-phosphate, necessary for
nucleotide biosynthesis, at the cost of also yielding
formaldehyde. These latter species tend usually have a
formaldehyde-activating enzyme to attach formaldehyde to
the C1 carrier tetrahydromethanopterin. In these
species, the enzyme is viewed as a lyase rather than a
synthase and is called D-arabino 3-hexulose 6-phosphate
formaldehyde lyase. Note that there is some overlap in
specificity with the Escherichia coli enzyme
3-keto-L-gulonate 6-phosphate decarboxylase.
Length = 206
Score = 28.9 bits (65), Expect = 2.4
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 12/41 (29%)
Query: 220 DLPQAAEVRHAEETTSVGLRGPATQYVADLVKLGTPCIKRE 260
D+ +A E+ AE+ YV D++++GTP IK E
Sbjct: 10 DIEEALEL--AEKVA---------DYV-DIIEIGTPLIKNE 38
>gnl|CDD|235356 PRK05170, PRK05170, hypothetical protein; Provisional.
Length = 147
Score = 27.6 bits (62), Expect = 4.2
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 34 LCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTK 71
LC G K CL++ DE +T VAC + K
Sbjct: 23 LCDGCGK----CCLHKLEDEDTGEIYYTNVACRLLDIK 56
>gnl|CDD|227470 COG5141, COG5141, PHD zinc finger-containing protein [General
function prediction only].
Length = 669
Score = 28.4 bits (63), Expect = 4.8
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 14 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQAC 46
C C +TH ++ NA+ C G VHQ+C
Sbjct: 196 CTKCTSTHNENSNAIVF----CDGCEICVHQSC 224
>gnl|CDD|225530 COG2983, COG2983, Uncharacterized conserved protein [Function
unknown].
Length = 153
Score = 27.0 bits (60), Expect = 8.0
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 6/48 (12%)
Query: 34 LCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCN--TKYFIVYPYR 79
LC G CL++ DE +T+VAC + T Y R
Sbjct: 28 LCDGCG----LCCLHKLEDEDTDEIYYTRVACELLDPETCRCKDYENR 71
>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 = 8.6
Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 96 LCPFVAAGVVLGSMYWCAVTYGA-VTVM 122
L P +A G ++W + + V V
Sbjct: 258 LTPLMATVSAFGLLFWFGFPFNSIVCVT 285
>gnl|CDD|215512 PLN02950, PLN02950, 4-alpha-glucanotransferase.
Length = 909
Score = 27.4 bits (61), Expect = 9.9
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 15/75 (20%)
Query: 82 LVSLLDTIDTAVYKLCPFVAAGVVLGSMYWCAVTYGAVTVMVVSPLHTYLGALSLRFCLV 141
LV LL DT+V+ M+W + Y +++V + PL+ + ALS R L
Sbjct: 299 LVQLLPVNDTSVHG-------------MWWDSYPYSSLSVFALHPLYLRVQALSER--LP 343
Query: 142 HPLVNINRQYRFQLD 156
L ++ R QLD
Sbjct: 344 EDLKAEIQKARKQLD 358
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
0.328 0.141 0.464
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: 13,228,396
Number of extensions: 1251638
Number of successful extensions: 1536
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1534
Number of HSP's successfully gapped: 31
Length of query: 263
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 168
Effective length of database: 6,723,972
Effective search space: 1129627296
Effective search space used: 1129627296
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 (21.8 bits)
S2: 58 (26.1 bits)