RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7115
(132 letters)
>gnl|CDD|191232 pfam05207, zf-CSL, CSL zinc finger. This is a zinc binding motif
which contains four cysteine residues which chelate
zinc. This domain is often found associated with a
pfam00226 domain. This domain is named after the
conserved motif of the final cysteine.
Length = 55
Score = 51.1 bits (123), Expect = 6e-10
Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 39 VSLSDMEHKGESQMFTYPCRCGAEFCIEEQDTEGDGSDDNILIACDTCSLLLEI 92
V L D E E F YPCRCG EF I E+D E + +++ C +CSL +++
Sbjct: 3 VELEDFEFDEEEGSFYYPCRCGDEFEITEEDLE----EGEVVVQCPSCSLWIKV 52
>gnl|CDD|227541 COG5216, COG5216, Uncharacterized conserved protein [Function
unknown].
Length = 67
Score = 39.8 bits (93), Expect = 2e-05
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 4/60 (6%)
Query: 33 MNIYKSVSLSDMEHKGESQMFTYPCRCGAEFCIEEQDTEGDGSDDNILIACDTCSLLLEI 92
M+ Y + + D E + FTYPC CG F I +D + ++ C +CSL++ +
Sbjct: 1 MSFYDEIEIEDFTFSREEKTFTYPCPCGDRFEISLEDLR----NGEVVARCPSCSLIVCV 56
>gnl|CDD|215804 pfam00226, DnaJ, DnaJ domain. DnaJ domains (J-domains) are
associated with hsp70 heat-shock system and it is
thought that this domain mediates the interaction.
DnaJ-domain is therefore part of a chaperone (protein
folding) system. The T-antigens, although not in
Prosite are confirmed as DnaJ containing domains from
literature.
Length = 63
Score = 34.4 bits (80), Expect = 0.002
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 1 MFLKINEAWNILKDEKERKLY 21
F +INEA+ +L D ++R +Y
Sbjct: 42 KFKEINEAYEVLSDPEKRAIY 62
>gnl|CDD|223560 COG0484, DnaJ, DnaJ-class molecular chaperone with C-terminal Zn
finger domain [Posttranslational modification, protein
turnover, chaperones].
Length = 371
Score = 32.2 bits (74), Expect = 0.052
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 2 FLKINEAWNILKDEKERKLY 21
F +INEA+ +L D ++R Y
Sbjct: 47 FKEINEAYEVLSDPEKRAAY 66
>gnl|CDD|237665 PRK14295, PRK14295, chaperone protein DnaJ; Provisional.
Length = 389
Score = 31.4 bits (71), Expect = 0.11
Identities = 11/21 (52%), Positives = 18/21 (85%)
Query: 2 FLKINEAWNILKDEKERKLYE 22
F +I+EA+++L DEK+RK Y+
Sbjct: 52 FKEISEAYDVLSDEKKRKEYD 72
>gnl|CDD|237661 PRK14291, PRK14291, chaperone protein DnaJ; Provisional.
Length = 382
Score = 31.3 bits (71), Expect = 0.13
Identities = 11/21 (52%), Positives = 17/21 (80%)
Query: 2 FLKINEAWNILKDEKERKLYE 22
F +INEA+ +L D ++RKLY+
Sbjct: 45 FKEINEAYQVLSDPEKRKLYD 65
>gnl|CDD|233829 TIGR02349, DnaJ_bact, chaperone protein DnaJ. This model
represents bacterial forms of DnaJ, part of the
DnaK-DnaJ-GrpE chaperone system. The three components
typically are encoded by consecutive genes. DnaJ
homologs occur in many genomes, typically not near DnaK
and GrpE-like genes; most such genes are not included
by this family. Eukaryotic (mitochondrial and
chloroplast) forms are not included in the scope of
this family.
Length = 354
Score = 30.3 bits (69), Expect = 0.25
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 2 FLKINEAWNILKDEKERKLY 21
F +INEA+ +L D ++R Y
Sbjct: 42 FKEINEAYEVLSDPEKRAQY 61
>gnl|CDD|237667 PRK14299, PRK14299, chaperone protein DnaJ; Provisional.
Length = 291
Score = 29.1 bits (65), Expect = 0.61
Identities = 9/22 (40%), Positives = 18/22 (81%)
Query: 2 FLKINEAWNILKDEKERKLYES 23
F +INEA+ +L D ++R++Y++
Sbjct: 46 FKEINEAYTVLSDPEKRRIYDT 67
>gnl|CDD|225124 COG2214, CbpA, DnaJ-class molecular chaperone [Posttranslational
modification, protein turnover, chaperones].
Length = 237
Score = 29.0 bits (64), Expect = 0.72
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 4 KINEAWNILKDEKERKLY 21
+INEA+ IL D + R Y
Sbjct: 52 EINEAYEILSDPERRAEY 69
>gnl|CDD|182347 PRK10266, PRK10266, curved DNA-binding protein CbpA; Provisional.
Length = 306
Score = 28.6 bits (64), Expect = 0.89
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 8/49 (16%)
Query: 2 FLKINEAWNILKDEKERKLYESQLLSQ-------QQTHMNIYKSVSLSD 43
F ++ EAW +L DE+ R Y+ QL +Q +S + D
Sbjct: 46 FKEVAEAWEVLSDEQRRAEYD-QLWQHRNDPQFNRQFQHGDGQSFNAED 93
>gnl|CDD|197617 smart00271, DnaJ, DnaJ molecular chaperone homology domain.
Length = 60
Score = 26.8 bits (60), Expect = 0.99
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 1 MFLKINEAWNILKDEK 16
F +INEA+ +L D +
Sbjct: 44 KFKEINEAYEVLSDPE 59
>gnl|CDD|172776 PRK14288, PRK14288, chaperone protein DnaJ; Provisional.
Length = 369
Score = 28.1 bits (62), Expect = 1.6
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 2 FLKINEAWNILKDEKERKLYE 22
F INEA+ +L DEK+R LY+
Sbjct: 46 FKLINEAYGVLSDEKKRALYD 66
>gnl|CDD|184599 PRK14277, PRK14277, chaperone protein DnaJ; Provisional.
Length = 386
Score = 27.8 bits (62), Expect = 1.7
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 2 FLKINEAWNILKDEKERKLYE 22
F +INEA+ IL D ++R Y+
Sbjct: 48 FKEINEAYEILSDPQKRAQYD 68
>gnl|CDD|99751 cd06257, DnaJ, DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock
protein 40) proteins are highly conserved and play
crucial roles in protein translation, folding,
unfolding, translocation, and degradation. They act
primarily by stimulating the ATPase activity of Hsp70s,
an important chaperonine family. Hsp40 proteins are
characterized by the presence of a J domain, which
mediates the interaction with Hsp70. They may contain
other domains as well, and the architectures provide a
means of classification.
Length = 55
Score = 26.0 bits (58), Expect = 2.0
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 1 MFLKINEAWNILKD 14
F +INEA+ +L D
Sbjct: 42 KFKEINEAYEVLSD 55
>gnl|CDD|185076 PRK15121, PRK15121, right oriC-binding transcriptional activator;
Provisional.
Length = 289
Score = 27.3 bits (61), Expect = 2.2
Identities = 27/111 (24%), Positives = 40/111 (36%), Gaps = 20/111 (18%)
Query: 13 KDEKERKLYESQLLSQQQTHMNIYKSVSLSDMEHKGESQMFTYPCRCGAEFCIEEQDTEG 72
KD+++ Y + L + Y M GE MFTY + G
Sbjct: 190 KDDEQEVFYTTALEPD---QADGYVQTGHPVMLQGGEYVMFTY-------------EGLG 233
Query: 73 DGSDDNILIACDTCSLLLEITARCGAEFCIEEQDTKGDS--SEGNILIACD 121
G + IL TC +L +T R G IE D+ + I + C+
Sbjct: 234 TGLQEFILTVYGTCMPMLNLTRRKG--QDIERYYPAEDAKAGDRPINLRCE 282
>gnl|CDD|172788 PRK14300, PRK14300, chaperone protein DnaJ; Provisional.
Length = 372
Score = 27.3 bits (60), Expect = 3.0
Identities = 10/21 (47%), Positives = 17/21 (80%)
Query: 2 FLKINEAWNILKDEKERKLYE 22
F +IN A+++LKDE++R Y+
Sbjct: 45 FKEINAAYDVLKDEQKRAAYD 65
>gnl|CDD|181927 PRK09522, PRK09522, bifunctional glutamine
amidotransferase/anthranilate phosphoribosyltransferase;
Provisional.
Length = 531
Score = 27.3 bits (60), Expect = 3.0
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 7/32 (21%)
Query: 8 AWNILKDEKE-------RKLYESQLLSQQQTH 32
AW K E KLY++Q LSQQ++H
Sbjct: 188 AWAQQKLEPTNTLQPILEKLYQAQTLSQQESH 219
>gnl|CDD|240236 PTZ00037, PTZ00037, DnaJ_C chaperone protein; Provisional.
Length = 421
Score = 26.7 bits (59), Expect = 4.1
Identities = 8/22 (36%), Positives = 16/22 (72%)
Query: 1 MFLKINEAWNILKDEKERKLYE 22
F +I+ A+ +L D ++RK+Y+
Sbjct: 66 KFKEISRAYEVLSDPEKRKIYD 87
>gnl|CDD|198381 cd10434, GIY-YIG_UvrC_Cho, Catalytic GIY-YIG domain of nucleotide
excision repair endonucleases UvrC, Cho, and similar
proteins. UvrC is essential for nucleotide excision
repair (NER). The N-terminal catalytic GIY-YIG domain
of UvrC (also known as Uri domain) is responsible for
the 3' incision reaction and the C-terminal half of
UvrC, consisting of an UvrB-binding domain (UvrBb),
EndoV-like nuclease domain and a helix-hairpin-helix
(HhH) DNA-binding domain, contains the residues
involved in 5' incision. The N- and C-terminal regions
are joined by a common Cys-rich domain containing four
conserved Cys residues. Besides UvrC, protein Cho (UvrC
homolog) serves as a second endonuclease in E. coli
NER. Cho contains GIY-YIG motif followed by a Cys-rich
region and shares sequence homology with the N-terminal
half of UvrC. It is capable of incising the DNA at the
3' side of a lesion in the presence of the UvrA and
UvrB proteins during NER. The C-terminal half of Cho is
a unique uncharacterized domain, which is distinct from
that of UvrC. Moreover, unlike UvrC, Cho does not
require the UvrC-binding domain of UvrB for the 3'
incision reaction, which might cause the shift in
incision position and the difference in incision
efficiencies between Cho and UvrC on different damaged
substrates. Due to this, the range of NER in E. coli
can be broadened by combining action of Cho and UvrC.
This family also includes many uncharacterized epsilon
proofreading subunits of DNA polymerase III, which have
an additional N-terminal ExoIII domain and a 3'-5'
exonuclease domain homolog, fused to an UvrC-like
region or a Cho-like region. The UvrC-like region
includes a GIY-YIG motif, followed by a Cys-rich
region, and an UvrB-binding domain (UvrBb), but lacks
the EndoV-like nuclease domain and the
helix-hairpin-helix (HhH) DNA-binding domain. The
Cho-like region consists of a GIY-YIG motif, followed
by the Cys-rich region, and the unique uncharacterized
domain presenting in the C-terminal half of Cho. Some
family members may not carry the Cys-rich region. This
family also includes a specific Cho-like protein from
G. violaceus, which possesses only UvrBb domain at the
C-terminus, but lacks the additional N-terminal ExoIII
domain. The oother two remote homologs of UvrC,
Bacillus-I and -II, are included in this family as
well. Both of them contain a GIY-YIG domain, but no
Cys-rich region. Moreover, the whole C-terminal region
of Bacillus-I is replaces by an unknown domain, and
Bacillus-II possesses another unknown N-terminal
extension.
Length = 81
Score = 25.5 bits (57), Expect = 4.5
Identities = 7/27 (25%), Positives = 13/27 (48%)
Query: 9 WNILKDEKERKLYESQLLSQQQTHMNI 35
+ + E E L E+ L+ + + NI
Sbjct: 55 YIVTDSELEALLLEANLIKKYKPRYNI 81
>gnl|CDD|146924 pfam04528, Adeno_E4_34, Adenovirus early E4 34 kDa protein
conserved region. Conserved region found in the
Adenovirus E4 34 kDa protein.
Length = 146
Score = 26.1 bits (58), Expect = 5.3
Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 72 GDGSDDNILI-ACDTCSLLLEITARCGA 98
G +N ++ C +C+ L EI+ARC A
Sbjct: 72 CYGILNNYVVLCCKSCADLSEISARCCA 99
>gnl|CDD|235757 PRK06260, PRK06260, threonine synthase; Validated.
Length = 397
Score = 26.0 bits (58), Expect = 6.3
Identities = 10/34 (29%), Positives = 13/34 (38%), Gaps = 11/34 (32%)
Query: 59 CGAEFCIEEQDTEGDGSDDNILIACDTCSLLLEI 92
CG E+ D I+ C C LLE+
Sbjct: 9 CGKEY-----------DPDEIIYTCPECGGLLEV 31
>gnl|CDD|173239 PRK14778, PRK14778, lipoprotein signal peptidase; Provisional.
Length = 186
Score = 25.9 bits (57), Expect = 6.3
Identities = 10/42 (23%), Positives = 18/42 (42%)
Query: 10 NILKDEKERKLYESQLLSQQQTHMNIYKSVSLSDMEHKGESQ 51
++ +K R L + + T ++I S SD + E Q
Sbjct: 142 SLESRKKRRGLETGSVFEGEDTVLDIEIVDSKSDKRGQSEGQ 183
>gnl|CDD|237658 PRK14284, PRK14284, chaperone protein DnaJ; Provisional.
Length = 391
Score = 26.0 bits (57), Expect = 7.9
Identities = 7/21 (33%), Positives = 16/21 (76%)
Query: 2 FLKINEAWNILKDEKERKLYE 22
F +++EA+ +L D ++R+ Y+
Sbjct: 44 FKEVSEAYEVLSDAQKRESYD 64
>gnl|CDD|222743 pfam14421, LmjF365940-deam, A distinct subfamily of CDD/CDA-like
deaminases. A distinct branch of the CDD/CDA-like
deaminases prototyped by Leishmania LmjF36.5940. Members
of this family are widely distributed across several
microbial eukaryotes such as kinetoplastids, chlorophyte
algae, stramenopiles and the alveolate Perkinsus. Domain
architectures suggest that these proteins might possess
mRNA editing or DNA mutagenizing activity.
Length = 169
Score = 25.5 bits (56), Expect = 8.0
Identities = 9/31 (29%), Positives = 11/31 (35%)
Query: 72 GDGSDDNILIACDTCSLLLEITARCGAEFCI 102
G D N L C C L A +F +
Sbjct: 122 GSARDPNPLFPCGACEEWLRKIAEYNPDFRV 152
>gnl|CDD|215140 PLN02251, PLN02251, pyrophosphate-dependent phosphofructokinase.
Length = 568
Score = 25.9 bits (57), Expect = 8.1
Identities = 12/39 (30%), Positives = 16/39 (41%)
Query: 22 ESQLLSQQQTHMNIYKSVSLSDMEHKGESQMFTYPCRCG 60
E L+ +T + K KG+S F Y RCG
Sbjct: 408 EKMLIQMVETELEKRKQEGSYKGHFKGQSHFFGYEGRCG 446
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
0.318 0.133 0.395
Gapped
Lambda K H
0.267 0.0717 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,043,812
Number of extensions: 487822
Number of successful extensions: 357
Number of sequences better than 10.0: 1
Number of HSP's gapped: 354
Number of HSP's successfully gapped: 40
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.2 bits)