RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1209
(61 letters)
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
Length = 393
Score = 77.0 bits (190), Expect = 8e-19
Identities = 31/64 (48%), Positives = 41/64 (64%), Gaps = 11/64 (17%)
Query: 1 MGILGLAKLVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSV---D 50
MGI GL+K +AD AP++I+E R I IDASM+LYQFLIA+R +Q ++
Sbjct: 1 MGIKGLSKFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIRD-DSQGGNLTNEA 59
Query: 51 GEPT 54
GE T
Sbjct: 60 GEVT 63
>gnl|CDD|189037 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Flap endonuclease-1 (FEN1) is
involved in multiple DNA metabolic pathways, including
DNA replication processes (5' flap DNA endonuclease
activity and double stranded DNA 5'-exonuclease
activity) and DNA repair processes (long-patch base
excision repair) in eukaryotes and archaea. Interaction
between FEN1 and PCNA (Proliferating cell nuclear
antigen) is an essential prerequisite to FEN1's DNA
replication functionality and stimulates FEN1 nuclease
activity by 10-50 fold. FEN1 belongs to the
FEN1-EXO1-like family of structure-specific, 5'
nucleases. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain) of variable length (approximately 45 residues
in FEN1 PIN domains) and a H3TH (helix-3-turn-helix)
domain, an atypical helix-hairpin-helix-2-like region.
Both the H3TH domain (not included here) and the
helical arch/clamp region are involved in DNA binding.
Nucleases within this group also have a
carboxylate-rich active site that is involved in
binding essential divalent metal ion cofactors
(Mg2+/Mn2+). FEN1 has a C-terminal extension
containing residues forming the consensus PIP-box -
Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA.
Length = 261
Score = 63.3 bits (155), Expect = 3e-14
Identities = 28/55 (50%), Positives = 33/55 (60%), Gaps = 5/55 (9%)
Query: 5 GLAKLVADVAPSSIR----ESRKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPT 54
GL+KL+AD A I RKI IDAS +LYQFLIA+R G L + GE T
Sbjct: 2 GLSKLIADGAIKEIELKDLFGRKIAIDASNALYQFLIAIRQPDGTPLTNSAGEVT 56
>gnl|CDD|214690 smart00485, XPGN, Xeroderma pigmentosum G N-region. domain in
nucleases.
Length = 99
Score = 48.8 bits (117), Expect = 1e-09
Identities = 20/51 (39%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 1 MGILGLAKLVADVA-PSSIR--ESRKICIDASMSLYQFLIAVRSE-GNQLM 47
MGI GL L+ V + + + IDAS+ LYQFL A R + G L
Sbjct: 1 MGIKGLWPLLKPVVREVPLEALRGKTLAIDASIWLYQFLTACREKLGTPLP 51
>gnl|CDD|216098 pfam00752, XPG_N, XPG N-terminal domain.
Length = 100
Score = 46.2 bits (110), Expect = 1e-08
Identities = 24/53 (45%), Positives = 31/53 (58%), Gaps = 6/53 (11%)
Query: 2 GILGLAKLVADVA---PSSIR--ESRKICIDASMSLYQFLIAVRSE-GNQLMS 48
GI GL ++ VA P I E + + IDAS+ LYQFL AVR + GN L +
Sbjct: 1 GIKGLLPILKPVALIRPVDIEALEGKTLAIDASIWLYQFLKAVRDQLGNALQN 53
>gnl|CDD|189038 cd09868, PIN_XPG, PIN domain of Xeroderma pigmentosum
complementation group G (XPG) nuclease, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. The Xeroderma pigmentosum
complementation group G (XPG) nuclease plays a central
role in nucleotide excision repair (NER) in cleaving
DNA bubble structures or loops. XPG is a member of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain). In XPG PIN domains, this arch region can be
quite variable and extensive (400 - 800 residues) in
length and is required for NER activity and for
efficient processing of bubble substrates. Inserted
within the PIN domain of these 5' nucleases is a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this
group also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+).
Length = 249
Score = 38.4 bits (90), Expect = 5e-05
Identities = 21/50 (42%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 1 MGILGLAKLVADVA-PSSIR--ESRKICIDASMSLYQFLIAVR-SEGNQL 46
MG+ GL KL+ P + E +++ IDAS+ +YQFL +R EGN L
Sbjct: 1 MGVKGLWKLLEPSGRPVRLETLEGKRLAIDASIWIYQFLKGMRDREGNAL 50
>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2). All
proteins in this family for which functions are known
are flap endonucleases that generate the 3' incision
next to DNA damage as part of nucleotide excision
repair. This family is related to many other flap
endonuclease families including the fen1 family. 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 = 1034
Score = 38.0 bits (88), Expect = 7e-05
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 6/53 (11%)
Query: 1 MGILGLAKLVA----DVAPSSIRESRKICIDASMSLYQFLIAVR-SEGNQLMS 48
MG+ GL KL+ V+P ++ E +++ +D S+ L Q L VR EGN + +
Sbjct: 1 MGVQGLWKLLECSGRPVSPETL-EGKRLAVDISIWLNQALKGVRDREGNAIKN 52
>gnl|CDD|189020 cd00128, PIN_FEN1_EXO1-like, PIN domains of Flap Endonuclease-1
(FEN1)-like and Exonuclease-1 (EXO1)-like nucleases,
structure-specific, divalent-metal-ion dependent, 5'
nucleases. PIN (PilT N terminus) domain of Flap
Endonuclease-1 (FEN1) and Exonuclease-1 (EXO1)-like
nucleases: FEN1, EXO1, Mkt1, Gap endonuclease 1 (GEN1)
and Xeroderma pigmentosum complementation group G (XPG)
nuclease are members of the structure-specific, 5'
nuclease family that catalyzes hydrolysis of DNA
duplex-containing nucleic acid structures during DNA
replication, repair, and recombination. These nucleases
contain a PIN domain with a helical arch/clamp region
(I domain) of variable length (approximately 30 to 800
residues) and a H3TH (helix-3-turn-helix) domain, an
atypical helix-hairpin-helix-2-like region. Both the
H3TH domain (not included here) and the helical
arch/clamp region are involved in DNA binding. Most
nucleases within this family also have a carboxylate
rich active site that is involved in binding essential
divalent metal ion cofactors (Mg2+/Mn2+). Some
nucleases in this family have C-terminal extensions
that act as interaction sites for other proteins.
Length = 209
Score = 32.1 bits (73), Expect = 0.007
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 15 PSSIRE--SRKICIDASMSLYQFLIAVRSEG 43
S+I + +K+ ID + LYQFL + R +
Sbjct: 12 GSAIEDLNGKKVAIDVNHYLYQFLTSKREQY 42
>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease.
Endonuclease that cleaves the 5'-overhanging flap
structure that is generated by displacement synthesis
when DNA polymerase encounters the 5'-end of a
downstream Okazaki fragment. Has 5'-endo-/exonuclease
and 5'-pseudo-Y-endonuclease activities. Cleaves the
junction between single and double-stranded regions of
flap DNA.
Length = 338
Score = 31.5 bits (72), Expect = 0.013
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 22 RKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPT 54
+ + +DA +LYQFL ++R G LM G T
Sbjct: 22 KVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRIT 55
>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of
PolI) [DNA replication, recombination, and repair].
Length = 310
Score = 29.2 bits (66), Expect = 0.079
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 3/40 (7%)
Query: 15 PSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPT 54
+ + + ID S LY+ L A+ L + G+PT
Sbjct: 5 QLMNKSGKLLLIDGSSLLYRALHALPQ---PLGNPLGDPT 41
>gnl|CDD|189023 cd09853, PIN_StructSpec-5'-nucleases, PIN domains of
structure-specific 5' nucleases (or flap
endonuclease-1-like) involved in DNA replication,
repair, and recombination. Structure-specific 5'
nucleases are capable of both 5'-3' exonucleolytic
activity and cleaving bifurcated or branched DNA, in an
endonucleolytic, structure-specific manner. The family
includes the PIN (PilT N terminus) domains of Flap
Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap
Endonuclease 1 (GEN1), and Xeroderma pigmentosum
complementation group G (XPG) nuclease. Also included
are the PIN domains of the 5'-3' exonucleases of DNA
polymerase I and single domain protein homologs, as
well as, the bacteriophage T4- and T5-5' nucleases, and
other homologs. These nucleases contain a PIN domain
with a helical arch/clamp region (I domain) of variable
length (approximately 16 to 800 residues) and a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. With the exception of
Mkt1, the nucleases within this family have a
carboxylate rich active site that is involved in
binding essential divalent metal ion cofactors (Mg2+,
Mn2+, Zn2+, or Co2+).
Length = 163
Score = 28.0 bits (62), Expect = 0.20
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 23 KICIDASMSLYQFLIAVRSEG 43
K+ ID S YQFL R +
Sbjct: 1 KVAIDGSNLGYQFLHNNRKDK 21
>gnl|CDD|223108 COG0029, NadB, Aspartate oxidase [Coenzyme metabolism].
Length = 518
Score = 24.9 bits (55), Expect = 3.0
Identities = 12/20 (60%), Positives = 14/20 (70%), Gaps = 2/20 (10%)
Query: 35 FLI--AVRSEGNQLMSVDGE 52
FLI AVR EG L++ DGE
Sbjct: 244 FLISEAVRGEGAILVNEDGE 263
>gnl|CDD|189026 cd09856, PIN_FEN1-like, PIN domain of Flap Endonuclease-1
(FEN1)-like, structure-specific, divalent-metal-ion
dependent, 5' nucleases. PIN (PilT N terminus) domain
of Flap Endonuclease-1 (FEN1)-like nucleases: FEN1, Gap
endonuclease 1 (GEN1) and Xeroderma pigmentosum
complementation group G (XPG) nuclease are members of
the structure-specific, 5' nuclease family that
catalyzes hydrolysis of DNA duplex-containing nucleic
acid structures during DNA replication, repair, and
recombination. These nucleases contain a PIN domain
with a helical arch/clamp region (I domain) of variable
length (approximately 30 to 800 residues) and a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Most nucleases within this
family also have a carboxylate rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+). Some nucleases in this family
have C-terminal extensions that act as interaction
sites for other proteins.
Length = 207
Score = 24.8 bits (54), Expect = 3.1
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 15 PSSIRESRKICIDASMSLYQFLIAVR 40
P ++I IDAS L++ L R
Sbjct: 14 PKEQLRGKRIAIDASGWLFEALTIQR 39
>gnl|CDD|219361 pfam07277, SapC, SapC. This family contains a number of bacterial
SapC proteins approximately 250 residues long. In
Campylobacter fetus, SapC forms part of a
paracrystalline surface layer (S-layer) that confers
serum resistance.
Length = 220
Score = 24.5 bits (54), Expect = 4.0
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 5/33 (15%)
Query: 24 ICIDASMSLYQFLIAVRSEGNQLMSVDGEPTRY 56
+CID ++ EG L DGEPT Y
Sbjct: 102 VCIDEDSPR----VSED-EGEALFDEDGEPTEY 129
>gnl|CDD|241251 cd01215, PTB_Dab, Disabled (Dab) Phosphotyrosine-binding domain.
Dab is a cystosolic adaptor protein, which binds to the
cytoplasmic tails of lipoprotein receptors, such as
ApoER2 and VLDLR, via its PTB domain. The dab PTB
domain has a preference for unphosphorylated tyrosine
within an NPxY motif. Additionally, the Dab PTB
domain, which is structurally similar to PH domains,
binds to phosphatidlyinositol phosphate 4,5
bisphosphate in a manner characteristic of
phosphoinositide binding PH domains. PTB domains have a
common PH-like fold and are found in various eukaryotic
signaling molecules. This domain was initially shown to
binds peptides with a NPXY motif with differing
requirements for phosphorylation of the tyrosine,
although more recent studies have found that some types
of PTB domains can bind to peptides lack tyrosine
residues altogether. In contrast to SH2 domains, which
recognize phosphotyrosine and adjacent carboxy-terminal
residues, PTB-domain binding specificity is conferred
by residues amino-terminal to the phosphotyrosine. PTB
domains are classified into three groups:
phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 150
Score = 24.1 bits (53), Expect = 4.2
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 9/41 (21%)
Query: 7 AKL--VADVAPSSIRESR--KICIDASMSLYQFLIAVRSEG 43
AKL + +V +R K+C DA M L + A S+G
Sbjct: 20 AKLIGIDEVP-----AARGDKMCQDAMMKLKGIVKAAGSQG 55
>gnl|CDD|235432 PRK05367, PRK05367, glycine dehydrogenase; Provisional.
Length = 954
Score = 24.3 bits (54), Expect = 4.5
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 6 LAKLVADVAPSSIRESRKICIDASMSLYQFL 36
L L+ P+SIR + + + A++S + L
Sbjct: 34 LDALIDQAVPASIRLAEPLDLPAALSEAEAL 64
>gnl|CDD|218359 pfam04981, NMD3, NMD3 family. The NMD3 protein is involved in
nonsense mediated mRNA decay. This amino terminal region
contains four conserved CXXC motifs that could be metal
binding. NMD3 is involved in export of the 60S ribosomal
subunit is mediated by the adapter protein Nmd3p in a
Crm1p-dependent pathway.
Length = 238
Score = 23.8 bits (52), Expect = 6.9
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 6 LAKLVADVAPSSIRESRK-ICIDASMS--LYQFLIAVR 40
L ++ V P ++ES+K + D Y+F +VR
Sbjct: 200 LVDFLSSVLPGKVKESKKLVGEDDDTGKKNYRFTYSVR 237
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 0.135 0.366
Gapped
Lambda K H
0.267 0.0769 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 2,921,977
Number of extensions: 194111
Number of successful extensions: 169
Number of sequences better than 10.0: 1
Number of HSP's gapped: 166
Number of HSP's successfully gapped: 17
Length of query: 61
Length of database: 10,937,602
Length adjustment: 32
Effective length of query: 29
Effective length of database: 9,518,274
Effective search space: 276029946
Effective search space used: 276029946
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: 53 (24.1 bits)