RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2479
(156 letters)
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 47.0 bits (112), Expect = 3e-08
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 70 FDCILCRSTI---WKPVTTPCGHSYCWMCLDRCLDYSSSCPLCKTS 112
+C +C + V PCGH + CLD+ L S++CPLC+
Sbjct: 1 DECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRAP 46
>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 = 45.5 bits (108), Expect = 1e-07
Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 71 DCILCRSTIWKPV-TTPCGHSYCWMCLDRCLDY-SSSCPLCKTSL 113
+C +C +PV PCGH +C C+D+ L ++CPLC+T +
Sbjct: 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 48.0 bits (114), Expect = 3e-07
Identities = 21/55 (38%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 69 DFDCILCRSTIWKPVTTPCGHSYCWMCL--DRCLDYSSSCPLC--KTSLADVGIL 119
D+ C LC P TPCGH +C CL CPLC K V IL
Sbjct: 215 DYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKVIIL 269
>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 = 48.1 bits (114), Expect = 4e-07
Identities = 16/45 (35%), Positives = 24/45 (53%)
Query: 68 SDFDCILCRSTIWKPVTTPCGHSYCWMCLDRCLDYSSSCPLCKTS 112
+ C +C+ PV T C H++C +C+ RCL CPLC+
Sbjct: 25 TSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAE 69
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 43.6 bits (103), Expect = 5e-07
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 68 SDFDCILCRSTIWKPVT-TPCGHSYCWMCLDRCLDYSSSCPLCKT 111
+ +C +C + PV TPCGH +C C+ R L S CP+C+T
Sbjct: 1 EELECPICLDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45
>gnl|CDD|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2; Provisional.
Length = 193
Score = 45.1 bits (106), Expect = 3e-06
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 19/77 (24%)
Query: 61 DLTRADSS-DFDCILCRSTIWKPVTTPCGHSYCWMCLDRCLDYSSS-------------- 105
D T DS DFDC +C + PV T CGH +CW C+ + Y+S+
Sbjct: 9 DTTLVDSGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHK-WTYASNNSRQRVDQYDHKRE 67
Query: 106 ---CPLCKTSLADVGIL 119
CP+CK+ +++ ++
Sbjct: 68 PPKCPVCKSDVSEATLV 84
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal
transduction mechanisms].
Length = 391
Score = 43.2 bits (101), Expect = 2e-05
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 62 LTRADSSDFDCILCRSTIWKPVTTPCGHSYCWMCLDRCLDYSSSCPLCK 110
L DS C +C I P T CGH++C +C+ R L CP+C+
Sbjct: 19 LKGLDSMLR-CRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCR 66
>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 = 39.0 bits (91), Expect = 3e-05
Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 72 CILCRSTIWK-PVTTPCGHSYCWMCLDRCLDYSS-SCPLC 109
C +C K PV PCGH++C C+ + L+ + +CP+C
Sbjct: 1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 374
Score = 40.4 bits (94), Expect = 1e-04
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 6/68 (8%)
Query: 50 NTEFQPSSLKIDLTRADSSDFDCILCRSTIWKP---VTTPCGHSYCWMCLDR-CLDYSSS 105
+P S I+ +C +C S K PC H + C+D+ L YS+
Sbjct: 306 KGSLKPLS--IERAVEADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNK 363
Query: 106 CPLCKTSL 113
CP+C+T++
Sbjct: 364 CPVCRTAI 371
>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 = 36.3 bits (84), Expect = 3e-04
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 72 CILCRSTIWKPV-TTPCGHSYCWMCLDRCLDYSS-SCPLC 109
C +C PV PCGH +C C+ L+ + +CPLC
Sbjct: 1 CPICLEEPKDPVTILPCGHLFCSKCILSWLESGNVTCPLC 40
>gnl|CDD|227481 COG5152, COG5152, Uncharacterized conserved protein, contains RING
and CCCH-type Zn-fingers [General function prediction
only].
Length = 259
Score = 37.0 bits (85), Expect = 0.002
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 70 FDCILCRSTIWKPVTTPCGHSYCWMCLDRCLDYSSSCPLC 109
F C +C+ PV T CGHS+C +C R C +C
Sbjct: 197 FLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVC 236
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 35.3 bits (81), Expect = 0.007
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 13/61 (21%)
Query: 67 SSDFDCILCRSTIW-------------KPVTTPCGHSYCWMCLDRCLDYSSSCPLCKTSL 113
+SD C +C ++ P PCGH CL L+ +CP+C+ +
Sbjct: 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPV 344
Query: 114 A 114
Sbjct: 345 I 345
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 35.0 bits (80), Expect = 0.009
Identities = 20/72 (27%), Positives = 27/72 (37%), Gaps = 2/72 (2%)
Query: 47 KLKNTEFQPSSLKIDLTRADSSDFDCILCRSTIWKPVTTPCGHSYCWMCL--DRCLDYSS 104
K N +P+ D + +C +C + PCGH C C R L
Sbjct: 39 KKNNLSAEPNLTTSSADDTDEENMNCQICAGSTTYSARYPCGHQICHACAVRLRALYMQK 98
Query: 105 SCPLCKTSLADV 116
CPLC+T V
Sbjct: 99 GCPLCRTETEAV 110
>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 = 30.4 bits (69), Expect = 0.059
Identities = 13/46 (28%), Positives = 17/46 (36%), Gaps = 6/46 (13%)
Query: 68 SDFDCILCR----STIWKPVTTPCGHSYCWMCLDRCLDYSSS--CP 107
S F C + + PV PCGH Y L++ CP
Sbjct: 9 SIFVCPISKEVMTDEENPPVMLPCGHVYSRKALEKLAKNGGKFKCP 54
>gnl|CDD|206613 pfam14447, Prok-RING_4, Prokaryotic RING finger family 4. RING
finger family domain found sporadically in bacteria. The
finger is fused to an N-terminal alpha-helical domain,
ROT/Trove-like repeats and a C-terminal TerD domain. The
architecture suggests a possible role in an
RNA-processing complex.
Length = 55
Score = 29.2 bits (66), Expect = 0.17
Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 2/47 (4%)
Query: 69 DFDCILCRSTIWKPVTTPCGHSYCWMCLDRCLDYSSSCPLCKTSLAD 115
+ C+ C + K V PCGH D + + CP C T
Sbjct: 7 EQPCLFCGTVGTKGVLLPCGHLIPDGTFD--GERYNGCPFCGTPFEP 51
>gnl|CDD|221556 pfam12392, DUF3656, Collagenase. This domain family is found in
bacteria, archaea and eukaryotes, and is approximately
120 amino acids in length. The family is found in
association with pfam01136.
Length = 122
Score = 30.2 bits (69), Expect = 0.19
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 30 EARKIPVLLTRILTEVDKLKNTEFQPSSLKIDL 62
A+K P+ R+ ++ KL NT F+ L+IDL
Sbjct: 60 PAKKRPLTEERLREQLGKLGNTPFELEELEIDL 92
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are components
of TFIIH, a complex that is involved in nucleotide
excision repair and transcription initiation. Also known
as MAT1 (menage a trois 1). 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 = 309
Score = 30.9 bits (70), Expect = 0.23
Identities = 27/85 (31%), Positives = 35/85 (41%), Gaps = 17/85 (20%)
Query: 69 DFDCILCRSTIW-----KPVTTPCGHSYCWMCLDRC-LDYSSSCPLCKTSL--------- 113
D C C++T + K + CGH+ C C+D + S SCP C T L
Sbjct: 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFRVQL 62
Query: 114 -ADVGILATTCIEKR-LKAINKTFE 136
D + I KR LK NK E
Sbjct: 63 FEDPTVEKEVDIRKRVLKIYNKREE 87
>gnl|CDD|188400 TIGR03885, flavin_revert, probable non-F420 flavinoid
oxidoreductase. This model represents a clade of
proteins within the larger subfamily TIGR03557. The
parent model includes the F420-dependent
glucose-6-phosphate dehydrogenase (TIGR03554) and many
other proteins. Excepting the members of this family,
all members of TIGR03557 occur in species capable of
synthesizing coenzyme F420. All members of the seed
alignment for this model are from species that lack
F420 biosynthesis. It is suggested that members of this
family bind FMN, or FO, or a novel flavinoid cofactor,
but not F420 per se [Unknown function, Enzymes of
unknown specificity].
Length = 315
Score = 29.3 bits (66), Expect = 0.85
Identities = 10/45 (22%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 52 EFQPSSLKIDLTRADSSDFDCILCRSTI--WKPVTTPCGHSYCWM 94
+F PS L + A+ + FD ++ W G ++ W+
Sbjct: 9 QFAPSDLLQYVQAAEQAGFDAVMSSDHFHPWSERQGQSGFAWSWL 53
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 29.0 bits (65), Expect = 0.91
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 8/54 (14%)
Query: 66 DSSDFDCILCRSTIW-KP-------VTTPCGHSYCWMCLDRCLDYSSSCPLCKT 111
S D +C +C ++ K + + C H +C C+D ++CP+C+T
Sbjct: 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRT 224
>gnl|CDD|147470 pfam05290, Baculo_IE-1, Baculovirus immediate-early protein (IE-0).
The Autographa californica multinucleocapsid nuclear
polyhedrosis virus (AcMNPV) ie-1 gene product (IE-1) is
thought to play a central role in stimulating early
viral transcription. IE-1 has been demonstrated to
activate several early viral gene promoters and to
negatively regulate the promoters of two other AcMNPV
regulatory genes, ie-0 and ie-2. It is thought that that
IE-1 negatively regulates the expression of certain
genes by binding directly, or as part of a complex, to
promoter regions containing a specific IE-1-binding
motif (5'-ACBYGTAA-3') near their mRNA start sites.
Length = 141
Score = 28.1 bits (63), Expect = 1.3
Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 3/29 (10%)
Query: 87 CGHSYCWMCLDRCLDYSS---SCPLCKTS 112
CG+ C +C + + CP+CKTS
Sbjct: 102 CGYKICNLCYANLWKFCTVYPVCPVCKTS 130
>gnl|CDD|213835 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members commonly
are called EngB based on homology to EngA, one of
several other GTPases of ribosome biogenesis. Cutoffs as
set find essentially all bacterial members, but also
identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about 80
percent of bacterial genomes [Protein synthesis, Other].
Length = 178
Score = 27.0 bits (61), Expect = 3.3
Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 30 EARKIPVLLTRILTEVDKLKNTEFQPSSLKIDLTRADSSDFDCIL 74
R IPVL+ +LT+ DKLK +E KI +D L
Sbjct: 126 RERGIPVLI--VLTKADKLKKSELNKQLKKIKKALKKDADDSVQL 168
>gnl|CDD|221705 pfam12678, zf-rbx1, RING-H2 zinc finger. There are 8 cysteine/
histidine residues which are proposed to be the
conserved residues involved in zinc binding. The
protein, of which this domain is the conserved region,
participates in diverse functions relevant to chromosome
metabolism and cell cycle control.
Length = 73
Score = 25.9 bits (57), Expect = 3.8
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 69 DFDCILCRST--IWKPVTTPCGHSYCWMCLDRCLDYSSSCPLCK 110
D C C+S V CGH++ C+ R L ++CPLC+
Sbjct: 30 DGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73
>gnl|CDD|181563 PRK08841, PRK08841, aspartate kinase; Validated.
Length = 392
Score = 26.6 bits (59), Expect = 5.9
Identities = 7/28 (25%), Positives = 12/28 (42%)
Query: 12 EYVHNSANILSDKFSLSSEARKIPVLLT 39
V +ANIL + S + + P+
Sbjct: 363 ANVDRAANILHKTYVTSEQPQDNPLKQA 390
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
0.321 0.134 0.412
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,168,678
Number of extensions: 582864
Number of successful extensions: 494
Number of sequences better than 10.0: 1
Number of HSP's gapped: 490
Number of HSP's successfully gapped: 38
Length of query: 156
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 67
Effective length of database: 6,990,096
Effective search space: 468336432
Effective search space used: 468336432
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 (21.9 bits)
S2: 55 (25.0 bits)