RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3978
(243 letters)
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 58.8 bits (142), Expect = 2e-10
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 2/63 (3%)
Query: 74 IQQIRGFGNEDIKCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEAVH 133
+ D KC +CL+ P P T CGH FC C+L ++ + K + CP+C V+
Sbjct: 205 KNGLPFIPLADYKCFLCLEEPEVPSCTPCGHLFCLSCLL--ISWTKKKYEFCPLCRAKVY 262
Query: 134 LGD 136
Sbjct: 263 PKK 265
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 51.0 bits (122), Expect = 3e-09
Identities = 26/47 (55%), Positives = 30/47 (63%), Gaps = 5/47 (10%)
Query: 83 EDIKCPICLDLPRAPQM-TRCGHCFCWPCILHYLALSDKSWRKCPIC 128
E+++CPICLDL R P + T CGH FC CIL YL KCPIC
Sbjct: 1 EELECPICLDLLRDPVVLTPCGHVFCRECILRYLKKK----SKCPIC 43
>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 = 49.4 bits (118), Expect = 1e-08
Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 86 KCPICLDLPRAP-QMTRCGHCFCWPCILHYLALSDKSWRKCPIC 128
+CPICL+ R P + CGH FC CI +L CP+C
Sbjct: 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWL---KSGKNTCPLC 41
>gnl|CDD|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2; Provisional.
Length = 193
Score = 51.2 bits (122), Expect = 5e-08
Identities = 25/61 (40%), Positives = 30/61 (49%), Gaps = 12/61 (19%)
Query: 84 DIKCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWR------------KCPICYEA 131
D C ICLD R P +T CGH FCWPCI + S+ S + KCP+C
Sbjct: 18 DFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSD 77
Query: 132 V 132
V
Sbjct: 78 V 78
>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 = 46.0 bits (109), Expect = 2e-07
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 87 CPICLD-LPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPIC 128
CPICL+ + P + CGH FC CI +L + CPIC
Sbjct: 1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGN---NTCPIC 40
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 42.8 bits (101), Expect = 3e-06
Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 87 CPICLD---LPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPIC 128
CPICLD + CGH F C+ +L +S CP+C
Sbjct: 3 CPICLDEFEPGEEVVVLPCGHVFHKECLDKWL----RSSNTCPLC 43
>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 = 40.5 bits (95), Expect = 2e-05
Identities = 19/43 (44%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 87 CPICLDLPRAP-QMTRCGHCFCWPCILHYLALSDKSWRKCPIC 128
CPICL+ P+ P + CGH FC CIL +L + CP+C
Sbjct: 1 CPICLEEPKDPVTILPCGHLFCSKCILSWL---ESGNVTCPLC 40
>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 = 43.5 bits (102), Expect = 5e-05
Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 85 IKCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPIC 128
++C IC D P +T C H FC CI L+ KCP+C
Sbjct: 27 LRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQP----KCPLC 66
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 43.2 bits (101), Expect = 7e-05
Identities = 27/66 (40%), Positives = 31/66 (46%), Gaps = 11/66 (16%)
Query: 64 DPDQLVKWEYIQQIRGFGNEDIKCPICLDLPRAPQMTR-CGHCFCWPCILHYLALSDKSW 122
PDQ+ K + N +KCP+C L R P T CGH FC CI L SD
Sbjct: 261 IPDQVYKMQ-------PPNISLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDF-- 311
Query: 123 RKCPIC 128
KCP C
Sbjct: 312 -KCPNC 316
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 38.9 bits (91), Expect = 7e-05
Identities = 19/47 (40%), Positives = 22/47 (46%), Gaps = 6/47 (12%)
Query: 83 EDIKCPICLDLPRAPQMTRCGH-CFCWPCILHYLALSDKSWRKCPIC 128
ED C ICL+ PR CGH C C C + +KCPIC
Sbjct: 1 EDDLCVICLERPRNVVFLPCGHLCLCEECAKRLRSK-----KKCPIC 42
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal
transduction mechanisms].
Length = 391
Score = 42.4 bits (99), Expect = 1e-04
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 4/46 (8%)
Query: 85 IKCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPICYE 130
++C IC P T CGH FC CI +L CP+C E
Sbjct: 26 LRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQP----FCPVCRE 67
>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 = 35.8 bits (83), Expect = 0.001
Identities = 12/45 (26%), Positives = 16/45 (35%), Gaps = 6/45 (13%)
Query: 87 CPICLDL----PRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPI 127
CPI ++ P M CGH + + K KCP
Sbjct: 13 CPISKEVMTDEENPPVMLPCGHVYSRKALEKLAKNGGK--FKCPY 55
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 34.9 bits (80), Expect = 0.027
Identities = 23/72 (31%), Positives = 29/72 (40%), Gaps = 18/72 (25%)
Query: 81 GNEDIKCPICLD---------LPRAPQMTR----CGHCFCWPCILHYLALSDKSWRKCPI 127
N D C IC+D LPR MT CGH C+ ++L + CPI
Sbjct: 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ----QTCPI 339
Query: 128 CYEAVHLGDLKS 139
C V + D S
Sbjct: 340 CRRPV-IFDQSS 350
>gnl|CDD|227481 COG5152, COG5152, Uncharacterized conserved protein, contains RING
and CCCH-type Zn-fingers [General function prediction
only].
Length = 259
Score = 33.9 bits (77), Expect = 0.058
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 6/53 (11%)
Query: 83 EDI--KCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEAVH 133
E I C IC +P +T CGH FC C + D +C +C +A +
Sbjct: 193 EKIPFLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGD----ECGVCGKATY 241
>gnl|CDD|193137 pfam12660, zf-TFIIIC, Putative zinc-finger of transcription factor
IIIC complex. This zinc-finger domain is at the very
C-terminus of a number of different TFIIIC subunit
proteins. This domain might be involved in protein-DNA
and/or protein-protein interactions.
Length = 92
Score = 29.7 bits (67), Expect = 0.35
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 9/49 (18%)
Query: 86 KCPIC---LDLPRAPQMTRC--GHCFCWP-CILHYLALSDKSWRKCPIC 128
CPIC + A +C GH W C L +LA+ + + C +C
Sbjct: 12 FCPICKSGIPFTDART-AQCANGHV--WLRCALTFLAIQEPGVKYCSVC 57
>gnl|CDD|225783 COG3243, PhaC, Poly(3-hydroxyalkanoate) synthetase [Lipid
metabolism].
Length = 445
Score = 29.6 bits (67), Expect = 1.4
Identities = 12/67 (17%), Positives = 25/67 (37%), Gaps = 5/67 (7%)
Query: 158 LMKRERGSTVVSPVAQWDF-HPTDMLMNVSAKCNAYIAINLDYPAIAPIFSVQLEL---- 212
LM +R ++ + DF H D+ + + + ++ I P + + +
Sbjct: 201 LMAAKRIKSLTLLTSPVDFSHAGDLGIFANEATIEALDADIVQKGILPGWYMAIVFFLLR 260
Query: 213 PGKLIKT 219
P LI
Sbjct: 261 PNDLIWN 267
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 28.2 bits (63), Expect = 3.1
Identities = 20/75 (26%), Positives = 29/75 (38%), Gaps = 28/75 (37%)
Query: 83 EDIKCPICLDLPRAPQM--------TRCGHCFCWPCILHYLALSDKSWRK----CPICYE 130
+D +C IC++ ++ + C H FC CI W+K CP+C
Sbjct: 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECI--------DIWKKEKNTCPVCR- 223
Query: 131 AVHLGDLKSFRSVIK 145
F SVIK
Sbjct: 224 -------TPFISVIK 231
>gnl|CDD|223352 COG0275, COG0275, Predicted S-adenosylmethionine-dependent
methyltransferase involved in cell envelope biogenesis
[Cell envelope biogenesis, outer membrane].
Length = 314
Score = 28.3 bits (64), Expect = 3.6
Identities = 15/57 (26%), Positives = 20/57 (35%), Gaps = 17/57 (29%)
Query: 156 FQLMKRERGSTVVSPVAQWDF-----HPTDMLMNVSAKCNAYIAIN-LDYPAIAPIF 206
QL ERG F P DM M+ + +A +N +A IF
Sbjct: 109 PQLDDAERG-----------FSFRKDGPLDMRMDQTQGLSAAEVVNTYSEEDLARIF 154
>gnl|CDD|216706 pfam01795, Methyltransf_5, MraW methylase family. Members of this
family are probably SAM dependent methyltransferases
based on Escherichia coli rsmH. This family appears to
be related to pfam01596.
Length = 310
Score = 28.0 bits (63), Expect = 4.5
Identities = 17/55 (30%), Positives = 21/55 (38%), Gaps = 13/55 (23%)
Query: 156 FQLMKRERGSTVVSPVAQWDF---HPTDMLMNVSAKCNAYIAIN-LDYPAIAPIF 206
QL ERG + F P DM M+ SA A +N +A IF
Sbjct: 106 PQLDGAERG---------FSFKHDAPLDMRMDQSAGLTAAEVLNTYSEEDLARIF 151
>gnl|CDD|188996 cd06457, M3A_MIP, Peptidase M3 mitochondrial intermediate peptidase
(MIP). Peptidase M3 mitochondrial intermediate
peptidase (MIP; EC 3.4.24.59) belongs to the widespread
subfamily M3A, that show similarity to the Thimet
oligopeptidase (TOP). It is one of three peptidases
responsible for the proteolytic processing of both,
nuclear and mitochondrial encoded precursor polypeptides
targeted to the various subcompartments of the
mitochondria. It cleaves intermediate-size proteins
initially processed by mitochondrial processing
peptidase (MPP) to yield a processing intermediate with
a typical N-terminal octapeptide that is sequentially
cleaved by MIP to mature-size protein. MIP cleaves
precursor proteins of respiratory components, including
subunits of the electron transport chain and
tri-carboxylic acid cycle enzymes, and components of the
mitochondrial genetic machinery, including ribosomal
proteins, translation factors, and proteins required for
mitochondrial DNA metabolism. It has been suggested that
the human MIP (HMIP polypeptide; gene symbol MIPEP) may
be one of the loci predicted to influence the clinical
manifestations of Friedreich's ataxia (FRDA), an
autosomal recessive neurodegenerative disease caused by
lack of human frataxin. These proteins are enriched in
cysteine residues, two of which are highly conserved,
suggesting their importance to stability as well as in
formation of metal binding sites, thus playing a role in
MIP activity.
Length = 606
Score = 28.3 bits (64), Expect = 4.6
Identities = 24/99 (24%), Positives = 37/99 (37%), Gaps = 20/99 (20%)
Query: 113 HYLALSDKSWRKCPICYEAVHLGDLKSF-RSVIK--RARAVNEEVTFQLMKRERGSTVVS 169
H ALSDK + E V F ++ K R +A E +KR+ +
Sbjct: 209 HR-ALSDKMAKN----PENVR-----EFLEALSKKLRPKAEKELSVLARLKRKHSGKSLP 258
Query: 170 PVAQWDFHPTDMLMNVSAKCNAYIAINLDYPAIAPIFSV 208
+ WD D + A+ A D ++P FS+
Sbjct: 259 TLQPWD---RDYYTSK-ARQAAC---PSDSQELSPYFSL 290
>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 = 26.3 bits (58), Expect = 6.1
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 9/42 (21%)
Query: 87 CPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPIC 128
CP+ C H F CIL +LA ++ S CP+C
Sbjct: 45 CPLVWGK--------CKHNFHMHCILKWLA-TETSKGLCPMC 77
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 27.7 bits (61), Expect = 6.2
Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 2/46 (4%)
Query: 83 EDIKCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPIC 128
E++ C IC CGH C C + AL + CP+C
Sbjct: 60 ENMNCQICAGSTTYSARYPCGHQICHACAVRLRALYMQK--GCPLC 103
>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein
complex aNOP56 subunit; Provisional.
Length = 414
Score = 27.6 bits (62), Expect = 7.3
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 50 FVVRLGEDYGIHLGDPDQLVK--WEYIQQIRGFGNED 84
F RL E Y +H + D+LVK EY++ + G+ +
Sbjct: 158 FSERLREWYSLHFPELDELVKKHEEYVKLVSELGDRE 194
>gnl|CDD|151913 pfam11474, N-Term_TEN, Telomerase reverse transcriptase TEN domain.
This is the N terminal domain of the protein telomerase
reverse transcriptase called TEN. The TEN domain is able
to bind both RNA and telomeric DNA and contributes
towards telomerase catalysis. The TEN domain has a
structure that consists of a core beta sheet surrounded
by seven alpha helices and a short beta hairpin.
Length = 188
Score = 27.0 bits (59), Expect = 7.3
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 28 QSLASVHKHKYNKEQFLQANCQFVVRLGEDYGIHLGDPDQLVKWEYIQQI 77
Q+L +K KYN+ F Q + V+ +D I LG+ K Y+QQI
Sbjct: 66 QNLVENYKQKYNQPNFSQLTIKQVI---DDSIILLGN-----KQNYVQQI 107
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
0.325 0.139 0.451
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: 12,037,077
Number of extensions: 1081443
Number of successful extensions: 1087
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1073
Number of HSP's successfully gapped: 32
Length of query: 243
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 149
Effective length of database: 6,768,326
Effective search space: 1008480574
Effective search space used: 1008480574
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.3 bits)