RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12455
(152 letters)
>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 374
Score = 63.9 bits (155), Expect = 9e-13
Identities = 28/72 (38%), Positives = 39/72 (54%), Gaps = 8/72 (11%)
Query: 36 IPTKHIKGEDKEIS-------GDGECCAICIEFYKPSDIVRILPCKHEYHKNCIDPWLLE 88
IPT KG K +S G CAIC+ + +D +R+LPC H +H C+D WLL
Sbjct: 300 IPTTTTKGSLKPLSIERAVEADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG 359
Query: 89 HR-TCPMCKMDI 99
+ CP+C+ I
Sbjct: 360 YSNKCPVCRTAI 371
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 55.5 bits (134), Expect = 1e-11
Identities = 19/46 (41%), Positives = 30/46 (65%)
Query: 53 ECCAICIEFYKPSDIVRILPCKHEYHKNCIDPWLLEHRTCPMCKMD 98
+ C IC++ ++P + V +LPC H +HK C+D WL TCP+C+
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 = 49.0 bits (117), Expect = 5e-09
Identities = 19/47 (40%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 54 CCAICIEFYKPSDIVRILPCKHEYHKNCIDPWL-LEHRTCPMCKMDI 99
C IC+E ++ + V +LPC H + ++CID WL TCP+C+ I
Sbjct: 1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45
>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 = 43.2 bits (102), Expect = 6e-07
Identities = 20/42 (47%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 55 CAICIEFYKPSDIVRILPCKHEYHKNCIDPWLL-EHRTCPMC 95
C IC+E K D V ILPC H + CI WL + TCP+C
Sbjct: 1 CPICLEEPK--DPVTILPCGHLFCSKCILSWLESGNVTCPLC 40
>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 = 44.0 bits (104), Expect = 8e-07
Identities = 19/54 (35%), Positives = 24/54 (44%), Gaps = 10/54 (18%)
Query: 53 ECCAIC--------IEFYKPSD--IVRILPCKHEYHKNCIDPWLLEHRTCPMCK 96
+ CAIC E P D V C H +H +CI WL TCP+C+
Sbjct: 20 DVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73
>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 = 39.8 bits (93), Expect = 1e-05
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 55 CAICIEFYKPSDIVRILPCKHEYHKNCIDPWLL-EHRTCPMC 95
C IC+E Y ILPC H + ++CI WL + TCP+C
Sbjct: 1 CPICLEEY--LKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 39.8 bits (93), Expect = 2e-05
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 51 DGECCAICIEFYKPSDIVRILPCKHEYHKNCIDPWLLEHRTCPMCKM 97
+ C IC D V + PC H + + CI +L + CP+C+
Sbjct: 1 EELECPIC--LDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 40.3 bits (94), Expect = 1e-04
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 11/63 (17%)
Query: 44 EDKEISGDGECCAICIE--FYKPSDIV--------RILPCKHEYHKNCIDPWLLEHRTCP 93
E++ + D C IC++ F+ + + + LPC H H +C+ WL +TCP
Sbjct: 280 EEQLTNSDR-TCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCP 338
Query: 94 MCK 96
+C+
Sbjct: 339 ICR 341
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 37.7 bits (87), Expect = 0.001
Identities = 25/104 (24%), Positives = 44/104 (42%), Gaps = 18/104 (17%)
Query: 11 GKEKVQLTDVKQRRLCSAAKKALSKIPTKHI-------KGEDKEISGDGECCAICIEFYK 63
G ++V +++ + + + + K + K D++ SG EC AIC
Sbjct: 1422 GIKRVGTSEIGWKSWINLRQNEMIKKNGSFMDLLGLWKKNIDEKFSGHEEC-AICYSVLD 1480
Query: 64 PSDIVRILP------CKHEYHKNCIDPWLLE--HRTCPMCKMDI 99
D R LP CK+++H C+ W CP+C+ +I
Sbjct: 1481 MVD--RSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 37.1 bits (86), Expect = 0.002
Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 30 KKALSKIPTKHIKGEDKEISGDGECCAICIE--FYKP--SDIVRILP-CKHEYHKNCIDP 84
KK L IP+ + E + CAIC+E + K + IL C H + CID
Sbjct: 152 KKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDI 211
Query: 85 WLLEHRTCPMCK 96
W E TCP+C+
Sbjct: 212 WKKEKNTCPVCR 223
>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 = 32.1 bits (73), Expect = 0.022
Identities = 14/46 (30%), Positives = 18/46 (39%), Gaps = 2/46 (4%)
Query: 53 ECCAICIEFYKPSD--IVRILPCKHEYHKNCIDPWLLEHRTCPMCK 96
C C P D V C H +H +CI WL CP+ +
Sbjct: 32 GTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDR 77
>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 = 33.1 bits (75), Expect = 0.047
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 55 CAICIEFYKPSDIVRILPCKHEYHKNCIDPWLLEHRTCPMCK 96
C IC +F+ D+ + C H + CI L CP+C+
Sbjct: 29 CHICKDFF---DVPVLTSCSHTFCSLCIRRCLSNQPKCPLCR 67
>gnl|CDD|128780 smart00504, Ubox, Modified RING finger domain. Modified RING
finger domain, without the full complement of
Zn2+-binding ligands. Probable involvement in
E2-dependent ubiquitination.
Length = 63
Score = 30.3 bits (69), Expect = 0.083
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 54 CCAICIEFYKPSDIVRILPCKHEYHKNCIDPWLLEHRTCPM 94
C I +E D V ILP Y ++ I+ WLL H T P+
Sbjct: 3 LCPISLEV--MKDPV-ILPSGQTYERSAIEKWLLSHGTDPV 40
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase
[Signal transduction mechanisms].
Length = 391
Score = 32.0 bits (72), Expect = 0.10
Identities = 13/44 (29%), Positives = 16/44 (36%), Gaps = 3/44 (6%)
Query: 55 CAICIEFYKPSDIVRILPCKHEYHKNCIDPWLLEHRTCPMCKMD 98
C IC I C H + CI L CP+C+ D
Sbjct: 28 CRICDCRIS---IPCETTCGHTFCSLCIRRHLGTQPFCPVCRED 68
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 28.5 bits (64), Expect = 0.21
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 51 DGECCAICIEFYKPSDIVRILPCKH-EYHKNCIDPWLLEHRTCPMCKMDI 99
+ + C IC+E +P ++V LPC H + C L + CP+C+ I
Sbjct: 1 EDDLCVICLE--RPRNVV-FLPCGHLCLCEECAK-RLRSKKKCPICRQPI 46
>gnl|CDD|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11
RING-H2 finger. Apc11 is one of the subunits of the
anaphase-promoting complex or cyclosome. The APC
subunits are cullin family proteins with ubiquitin
ligase activity. Polyubiquitination marks proteins for
degradation by the 26S proteasome and is carried out by
a cascade of enzymes that includes ubiquitin-activating
enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and
ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and
is responsible for recruiting E2s to the APC and for
mediating the subsequent transfer of ubiquitin to APC
substrates in vivo. In Saccharomyces cerevisiae this
RING-H2 finger protein defines the minimal ubiquitin
ligase activity of the APC, and the integrity of the
RING-H2 finger is essential for budding yeast cell
viability.
Length = 85
Score = 28.2 bits (63), Expect = 0.59
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 73 CKHEYHKNCIDPWLLEHRT---CPMCK 96
CKH +H +CI WL + CPMC+
Sbjct: 52 CKHNFHMHCILKWLATETSKGLCPMCR 78
>gnl|CDD|240441 cd13433, Na_channel_gate, Inactivation gate of the voltage-gated
sodium channel alpha subunits. This region is part of
the intracellular linker between domains III and IV of
the alpha subunits of voltage-gated sodium channels. It
is responsible for fast inactivation of the channel and
essential for proper physiological function.
Length = 54
Score = 26.4 bits (59), Expect = 1.7
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 11 GKEKVQLTDVKQRRLCSAAKKALSKIPTKHIK 42
G + LT+ Q++ +A KK SK P K I
Sbjct: 12 GGLDIFLTE-SQKKYYNAMKKLGSKKPQKPIP 42
>gnl|CDD|219112 pfam06628, Catalase-rel, Catalase-related immune-responsive.
This family represents a small conserved region within
catalase enzymes (EC:1.11.1.6). All members also
contain the Catalase family, pfam00199 domain. Catalase
decomposes hydrogen peroxide into water and oxygen,
serving to protect cells from its toxic effects. This
domain carries the immune-responsive amphipathic
octa-peptide that is recognised by T cells.
Length = 68
Score = 25.8 bits (58), Expect = 2.8
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 17 LTDVKQRRLCSAAKKALSKIPTKHIK 42
++ +Q+RL LSK+ I+
Sbjct: 20 MSPAEQQRLIDNIAFELSKVTDPEIR 45
>gnl|CDD|177491 PHA02825, PHA02825, LAP/PHD finger-like protein; Provisional.
Length = 162
Score = 27.1 bits (60), Expect = 3.3
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 9/48 (18%)
Query: 54 CCAICIEFYKPSDIVR-ILPCKHEY---HKNCIDPWL--LEHRTCPMC 95
CC IC + Y D+V CK+E HK C++ W+ ++++C +C
Sbjct: 10 CCWICKDEY---DVVTNYCNCKNENKIVHKECLEEWINTSKNKSCKIC 54
>gnl|CDD|233277 TIGR01116, ATPase-IIA1_Ca, sarco/endoplasmic reticulum
calcium-translocating P-type ATPase. This model
describes the P-type ATPase responsible for
translocating calcium ions across the endoplasmic
reticulum membrane of eukaryotes , and is of particular
importance in the sarcoplasmic reticulum of skeletal and
cardiac muscle in vertebrates. These pumps transfer Ca2+
from the cytoplasm to the lumen of the endoplasmic
reticulum. In humans and mice, at least, there are
multiple isoforms of the SERCA pump with overlapping but
not redundant functions. Defects in SERCA isoforms are
associated with diseases in humans. The calcium P-type
ATPases have been characterized as Type IIA based on a
phylogenetic analysis which distinguishes this group
from the Type IIB PMCA calcium pump modelled by
TIGR01517. A separate analysis divides Type IIA into
sub-types, SERCA and PMR1 the latter of which is
modelled by TIGR01522 [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 917
Score = 26.3 bits (58), Expect = 9.2
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 10/56 (17%)
Query: 6 GDSKTGKEKVQLTDVKQRRLCSAAKKALSKIPTKH------IKGEDKEI---SGDG 52
S TG+E ++ KQR C +A S++ H + E EI +GDG
Sbjct: 585 FKSFTGREFDEMGPAKQRAACRSA-VLFSRVEPSHKSELVELLQEQGEIVAMTGDG 639
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
0.320 0.137 0.436
Gapped
Lambda K H
0.267 0.0768 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,352,523
Number of extensions: 626336
Number of successful extensions: 474
Number of sequences better than 10.0: 1
Number of HSP's gapped: 468
Number of HSP's successfully gapped: 33
Length of query: 152
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 64
Effective length of database: 7,034,450
Effective search space: 450204800
Effective search space used: 450204800
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 (21.8 bits)
S2: 55 (24.9 bits)