RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8987
(173 letters)
>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 = 34.0 bits (78), Expect = 0.002
Identities = 11/59 (18%), Positives = 21/59 (35%), Gaps = 20/59 (33%)
Query: 33 CVLCRGYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKSCIVKYIK-TSRYCPIC 90
C +C + +I+ C H C CI+ +++ + CP+C
Sbjct: 1 CPICLEEPKDPVTILPCGHLF-------------------CSKCILSWLESGNVTCPLC 40
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 30.9 bits (70), Expect = 0.032
Identities = 14/60 (23%), Positives = 21/60 (35%), Gaps = 19/60 (31%)
Query: 31 LLCVLCRGYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKSCIVKYIKTSRYCPIC 90
L C +C + + C H C+ CI++Y+K CPIC
Sbjct: 3 LECPICLDLLRDPVVLTPCGHVF-------------------CRECILRYLKKKSKCPIC 43
>gnl|CDD|237514 PRK13804, ileS, isoleucyl-tRNA synthetase; Provisional.
Length = 961
Score = 31.5 bits (72), Expect = 0.19
Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 3/33 (9%)
Query: 111 ASDDYDNDTRIYEQVLQIVLRIYLRKNVLRGTI 143
AS DY +D RI +++L+ V Y RK LR T+
Sbjct: 658 ASVDYSDDQRIGKEILKQVSETY-RK--LRNTL 687
>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 = 28.2 bits (63), Expect = 0.37
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 20/59 (33%)
Query: 33 CVLCRGYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKSCIVKYIKTSRY-CPIC 90
C +C F E ++ C H C+SCI K++K+ + CP+C
Sbjct: 2 CPICLEEFREPVVLLPCGH-------------------VFCRSCIDKWLKSGKNTCPLC 41
>gnl|CDD|146106 pfam03302, VSP, Giardia variant-specific surface protein.
Length = 397
Score = 30.7 bits (69), Expect = 0.39
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 11/54 (20%)
Query: 38 GYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKSCIVKYIKTSRYCPICD 91
GY + +V C C + +VC +C+ Y+KTS C CD
Sbjct: 248 GYKLNNGDLVTCSPGCKTCTS-----------NTVCTTCMDGYVKTSDSCTKCD 290
>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 = 27.5 bits (61), Expect = 0.61
Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 20/59 (33%)
Query: 33 CVLCRGYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKSCIVKYIKTS-RYCPIC 90
C +C +++ I+ C H + C+SCI K++++ CPIC
Sbjct: 1 CPICLEEYLKDPVILPCGH-------------------TFCRSCIRKWLESGNNTCPIC 40
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase
[Signal transduction mechanisms].
Length = 391
Score = 28.9 bits (64), Expect = 1.3
Identities = 15/61 (24%), Positives = 23/61 (37%), Gaps = 22/61 (36%)
Query: 31 LLCVLCRGYFVEATSIVECLHSCDFVSYFSH-FCKLLFGFVSVCKSCIVKYIKTSRYCPI 89
L C +C + C +C H FC L CI +++ T +CP+
Sbjct: 26 LRCRICDCRIS-----IPCETTC------GHTFCSL----------CIRRHLGTQPFCPV 64
Query: 90 C 90
C
Sbjct: 65 C 65
>gnl|CDD|227521 COG5194, APC11, Component of SCF ubiquitin ligase and
anaphase-promoting complex [Posttranslational
modification, protein turnover, chaperones / Cell
division and chromosome partitioning].
Length = 88
Score = 27.5 bits (61), Expect = 1.6
Identities = 16/72 (22%), Positives = 25/72 (34%), Gaps = 14/72 (19%)
Query: 33 CVLCRGYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKS-----CIVKYIKTSRYC 87
C +CR I+ C F C +++G VC CI +++ T C
Sbjct: 23 CAICR------NHIMGTCPECQFGMTPGDECPVVWG---VCNHAFHDHCIYRWLDTKGVC 73
Query: 88 PICDVQLNRQDP 99
P+ D
Sbjct: 74 PLDRQTWVLADG 85
>gnl|CDD|236891 PRK11278, PRK11278, NADH dehydrogenase I subunit F; Provisional.
Length = 448
Score = 28.6 bits (64), Expect = 1.9
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 17/51 (33%)
Query: 9 NAIEMRPTSRSDKLLVRDVNPHLLC----------------VLCRGYFVEA 43
NA EM P + D+LL+ + PHLL + RG ++EA
Sbjct: 91 NADEMEPGTYKDRLLMEQL-PHLLVEGMLISAFALKAYRGYIFLRGEYIEA 140
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 25.8 bits (57), Expect = 2.4
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 17/58 (29%)
Query: 33 CVLCRGYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKSCIVKYIKTSRYCPIC 90
C +C F +V C H K C+ K++++S CP+C
Sbjct: 3 CPICLDEFEPGEEVVVL--PC------GHVF---------HKECLDKWLRSSNTCPLC 43
>gnl|CDD|226585 COG4100, COG4100, Cystathionine beta-lyase family protein involved
in aluminum resistance [Inorganic ion transport and
metabolism].
Length = 416
Score = 28.2 bits (63), Expect = 2.6
Identities = 10/43 (23%), Positives = 20/43 (46%), Gaps = 7/43 (16%)
Query: 14 RPTSRSDKL-----LVRDVNPHLLCVL--CRGYFVEATSIVEC 49
RP+ ++ V+++NP+++ + C G FVE
Sbjct: 180 RPSLSIAEIEEMITFVKEINPNVIVFVDNCYGEFVEEKEPTHV 222
>gnl|CDD|216556 pfam01532, Glyco_hydro_47, Glycosyl hydrolase family 47. Members
of this family are alpha-mannosidases that catalyze the
hydrolysis of the terminal 1,2-linked alpha-D-mannose
residues in the oligo-mannose oligosaccharide
Man(9)(GlcNAc)(2).
Length = 445
Score = 27.6 bits (62), Expect = 4.0
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 10/49 (20%)
Query: 77 IVKYIKTSR-YCPICDV------QLNRQDPFL---SLKYSYIAFASDDY 115
I KY +T Y I DV +R + F +LKY Y+ F+ DD
Sbjct: 380 IEKYTRTPCGYAGIKDVTTPPPEPRDRMESFWLAETLKYLYLLFSDDDL 428
>gnl|CDD|215452 PLN02843, PLN02843, isoleucyl-tRNA synthetase.
Length = 974
Score = 27.4 bits (61), Expect = 4.3
Identities = 17/36 (47%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 111 ASDDYDNDTRIYEQVLQIVLRIYLRKNVLRGTIHQL 146
AS DY D I Q+L+ + IY RK LRGT+ L
Sbjct: 648 ASVDYTGDVLIGPQILKQMSDIY-RK--LRGTLRYL 680
>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 = 27.3 bits (60), Expect = 5.0
Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 20/60 (33%)
Query: 31 LLCVLCRGYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKSCIVKYIKTSRYCPIC 90
L C +C+ +F + + C H+ FC L CI + + CP+C
Sbjct: 27 LRCHICKDFF-DVPVLTSCSHT---------FCSL----------CIRRCLSNQPKCPLC 66
>gnl|CDD|223138 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 933
Score = 26.8 bits (60), Expect = 6.9
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 110 FASDDYDNDTRIYEQVLQIVLRIYLR-KNVLR 140
AS DY D R +++L+ V +Y + +N R
Sbjct: 629 VASSDYWEDLRFSDEILKQVREVYRKIRNTYR 660
>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 = 25.1 bits (55), Expect = 7.2
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 76 CIVKYIKTSRYCPIC 90
CI +++KT CP+C
Sbjct: 58 CISRWLKTRNTCPLC 72
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 26.8 bits (59), Expect = 8.3
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 65 LLFGFVSVCKSCIVKYIKTSRYCPICDVQLNRQDPFLSLKYSYIAFASDDYDND 118
L+ G + +S +VKY+ T+ Y P V LN+ FL K F DD D D
Sbjct: 1634 LVIGSIGTGRSYLVKYLATNSYVPFITVFLNK---FLDNKPK--GFLIDDIDID 1682
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
0.332 0.143 0.467
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,563,601
Number of extensions: 750759
Number of successful extensions: 810
Number of sequences better than 10.0: 1
Number of HSP's gapped: 802
Number of HSP's successfully gapped: 34
Length of query: 173
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 83
Effective length of database: 6,945,742
Effective search space: 576496586
Effective search space used: 576496586
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 55 (25.2 bits)