RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4226
(183 letters)
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 59.7 bits (145), Expect = 7e-13
Identities = 19/46 (41%), Positives = 30/46 (65%)
Query: 124 ECCAICIEFYKPSDIVRILPCKHEYHKNCIDPWLLEHRTCPMCKMD 169
+ C IC++ ++P + V +LPC H +HK C+D WL TCP+C+
Sbjct: 1 DECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRAP 46
>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 374
Score = 62.7 bits (152), Expect = 6e-12
Identities = 28/72 (38%), Positives = 39/72 (54%), Gaps = 8/72 (11%)
Query: 107 IPTKHIKGEDKEIS-------GDGECCAICIEFYKPSDIVRILPCKHEYHKNCIDPWLLE 159
IPT KG K +S G CAIC+ + +D +R+LPC H +H C+D WLL
Sbjct: 300 IPTTTTKGSLKPLSIERAVEADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG 359
Query: 160 HR-TCPMCKMDI 170
+ CP+C+ I
Sbjct: 360 YSNKCPVCRTAI 371
>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 = 53.2 bits (128), Expect = 3e-10
Identities = 19/47 (40%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 125 CCAICIEFYKPSDIVRILPCKHEYHKNCIDPWL-LEHRTCPMCKMDI 170
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 = 46.7 bits (111), Expect = 5e-08
Identities = 20/42 (47%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 126 CAICIEFYKPSDIVRILPCKHEYHKNCIDPWLL-EHRTCPMC 166
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 = 46.7 bits (111), Expect = 1e-07
Identities = 19/54 (35%), Positives = 24/54 (44%), Gaps = 10/54 (18%)
Query: 124 ECCAIC--------IEFYKPSD--IVRILPCKHEYHKNCIDPWLLEHRTCPMCK 167
+ 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 = 43.3 bits (102), Expect = 1e-06
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 126 CAICIEFYKPSDIVRILPCKHEYHKNCIDPWLL-EHRTCPMC 166
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 = 42.9 bits (101), Expect = 1e-06
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 122 DGECCAICIEFYKPSDIVRILPCKHEYHKNCIDPWLLEHRTCPMCKM 168
+ 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 = 42.3 bits (99), Expect = 7e-05
Identities = 26/116 (22%), Positives = 43/116 (37%), Gaps = 20/116 (17%)
Query: 63 LPRAVSLTLFQTEL-IFYQQYSSDNIFEIMELRRLCSAAKKALSKIPTKHIKGEDKEISG 121
V + L + FY + I E RR E++ +
Sbjct: 235 PYVRVPIYLIRQMYTCFYALFRR--IREHARFRRATKDLNAMYPTAT------EEQLTNS 286
Query: 122 DGECCAICIE--FYKPSDIV--------RILPCKHEYHKNCIDPWLLEHRTCPMCK 167
D C IC++ F+ + + + LPC H H +C+ WL +TCP+C+
Sbjct: 287 DR-TCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICR 341
>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: 101 KKALSKIPTKHIKGEDKEISGDGECCAICIE--FYKP--SDIVRILP-CKHEYHKNCIDP 155
KK L IP+ + E + CAIC+E + K + IL C H + CID
Sbjct: 152 KKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDI 211
Query: 156 WLLEHRTCPMCK 167
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 = 33.7 bits (77), Expect = 0.009
Identities = 14/46 (30%), Positives = 18/46 (39%), Gaps = 2/46 (4%)
Query: 124 ECCAICIEFYKPSD--IVRILPCKHEYHKNCIDPWLLEHRTCPMCK 167
C C P D V C H +H +CI WL CP+ +
Sbjct: 32 GTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDR 77
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 35.8 bits (82), Expect = 0.010
Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 11/63 (17%)
Query: 116 DKEISGDGECCAICIEFYKPSDIVRILP------CKHEYHKNCIDPWLLE--HRTCPMCK 167
D++ SG EC AIC D R LP CK+++H C+ W CP+C+
Sbjct: 1463 DEKFSGHEEC-AICYSVLDMVD--RSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCR 1519
Query: 168 MDI 170
+I
Sbjct: 1520 SEI 1522
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 32.0 bits (73), Expect = 0.016
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 122 DGECCAICIEFYKPSDIVRILPCKH-EYHKNCIDPWLLEHRTCPMCKMDI 170
+ + C IC+E +P ++V LPC H + C L + CP+C+ I
Sbjct: 1 EDDLCVICLE--RPRNVV-FLPCGHLCLCEECAK-RLRSKKKCPICRQPI 46
>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 = 34.2 bits (78), Expect = 0.029
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 126 CAICIEFYKPSDIVRILPCKHEYHKNCIDPWLLEHRTCPMCK 167
C IC +F+ D+ + C H + CI L CP+C+
Sbjct: 29 CHICKDFF---DVPVLTSCSHTFCSLCIRRCLSNQPKCPLCR 67
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal
transduction mechanisms].
Length = 391
Score = 33.1 bits (75), Expect = 0.068
Identities = 13/44 (29%), Positives = 16/44 (36%), Gaps = 3/44 (6%)
Query: 126 CAICIEFYKPSDIVRILPCKHEYHKNCIDPWLLEHRTCPMCKMD 169
C IC I C H + CI L CP+C+ D
Sbjct: 28 CRICDCRIS---IPCETTCGHTFCSLCIRRHLGTQPFCPVCRED 68
>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 = 0.098
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 125 CCAICIEFYKPSDIVRILPCKHEYHKNCIDPWLLEHRTCPM 165
C I +E D V ILP Y ++ I+ WLL H T P+
Sbjct: 3 LCPISLEV--MKDPV-ILPSGQTYERSAIEKWLLSHGTDPV 40
>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 = 30.1 bits (68), Expect = 0.18
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 144 CKHEYHKNCIDPWLLEHRT---CPMCK 167
CKH +H +CI WL + CPMC+
Sbjct: 52 CKHNFHMHCILKWLATETSKGLCPMCR 78
>gnl|CDD|185056 PRK15101, PRK15101, protease3; Provisional.
Length = 961
Score = 29.9 bits (68), Expect = 0.87
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 6/47 (12%)
Query: 73 QTELI-FYQQYSSDN-----IFEIMELRRLCSAAKKALSKIPTKHIK 113
Q L+ FYQ+Y S N I+ L L A ++P K+
Sbjct: 215 QDALVDFYQRYYSANLMKAVIYSNQPLPELAKLAADTFGRVPNKNAS 261
>gnl|CDD|177491 PHA02825, PHA02825, LAP/PHD finger-like protein; Provisional.
Length = 162
Score = 27.5 bits (61), Expect = 3.6
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 9/48 (18%)
Query: 125 CCAICIEFYKPSDIVR-ILPCKHEY---HKNCIDPWL--LEHRTCPMC 166
CC IC + Y D+V CK+E HK C++ W+ ++++C +C
Sbjct: 10 CCWICKDEY---DVVTNYCNCKNENKIVHKECLEEWINTSKNKSCKIC 54
>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 = 25.2 bits (56), Expect = 5.8
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 78 FYQQ----YSSDNIFEIMELRRLCSAAKKALSKIPTKHIK 113
F Q +IF ++ +A KK SK P K I
Sbjct: 3 FNQLKKKYGGGLDIFLTESQKKYYNAMKKLGSKKPQKPIP 42
>gnl|CDD|212667 cd10170, HSP70_NBD, Nucleotide-binding domain of the HSP70 family.
HSP70 (70-kDa heat shock protein) family chaperones
assist in protein folding and assembly and can direct
incompetent "client" proteins towards degradation.
Typically, HSP70s have a nucleotide-binding domain (NBD)
and a substrate-binding domain (SBD). The nucleotide
sits in a deep cleft formed between the two lobes of the
NBD. The two subdomains of each lobe change conformation
between ATP-bound, ADP-bound, and nucleotide-free
states. ATP binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
HSP70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs). Some HSP70 family members are not
chaperones but instead, function as NEFs to remove ADP
from their HSP70 chaperone partners during the ATP
hydrolysis cycle, some may function as both chaperones
and NEFs.
Length = 369
Score = 26.8 bits (60), Expect = 6.7
Identities = 12/38 (31%), Positives = 15/38 (39%), Gaps = 3/38 (7%)
Query: 78 FYQQYSSDNIFEIMELRRL---CSAAKKALSKIPTKHI 112
F ++ D + LRRL AK ALS I
Sbjct: 237 FKEKGGIDLRLDPRALRRLKEAAEKAKIALSSSEEATI 274
>gnl|CDD|162866 TIGR02460, osmo_MPGsynth, mannosyl-3-phosphoglycerate synthase.
This family consists of examples of
mannosyl-3-phosphoglycerate synthase (MPGS), which
together mannosyl-3-phosphoglycerate phosphatase (MPGP)
comprises a two-step pathway for mannosylglycerate
biosynthesis. Mannosylglycerate is a compatible solute
that tends to be restricted to extreme thermophiles of
archaea and bacteria. Note that in Rhodothermus marinus,
this pathway is one of two; the other is condensation of
GDP-mannose with D-glycerate by mannosylglycerate
synthase.
Length = 381
Score = 26.3 bits (58), Expect = 9.6
Identities = 14/54 (25%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 72 FQTELIFYQQYSSDNIFEIMELRRLCSAAKKALSKIPTKHIKGEDKEI-SGDGE 124
F+ E+ + +S+ +I+ + + A +AL ++ I GE+ + SG GE
Sbjct: 93 FKMEVDLIRHFSNLTHRKIIIIHQKDPALAEALKEVGYTSILGENGLVRSGKGE 146
>gnl|CDD|107145 PHA02135, PHA02135, hypothetical protein.
Length = 122
Score = 25.8 bits (56), Expect = 9.8
Identities = 9/59 (15%), Positives = 26/59 (44%), Gaps = 5/59 (8%)
Query: 60 IGDLPRAVSLTLFQTELIF-YQQYSSDNIFEIMELRRLCSAAKKALSKIPTKHIKGEDK 117
+G++ R + + E ++++ +N +I+ + + A S+ P + +K
Sbjct: 61 LGEMTRLFFIQRYNKENNKDWRKWCRENPGKILVIEVVGDAK----SEKPCQLEMQYEK 115
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
0.323 0.138 0.429
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: 9,162,659
Number of extensions: 812854
Number of successful extensions: 719
Number of sequences better than 10.0: 1
Number of HSP's gapped: 713
Number of HSP's successfully gapped: 30
Length of query: 183
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 92
Effective length of database: 6,901,388
Effective search space: 634927696
Effective search space used: 634927696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (25.3 bits)