RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1207
(113 letters)
>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 = 139 bits (352), Expect = 2e-42
Identities = 45/91 (49%), Positives = 57/91 (62%), Gaps = 15/91 (16%)
Query: 10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
GDA+E K+ +R VRV+ V+ECK+LL LMGIPY+E AP EAEAQ
Sbjct: 113 GDAEEARKYAKRTVRVTKEIVEECKKLLRLMGIPYVE---------------APSEAEAQ 157
Query: 70 CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
CA +VK G VYA A++D D+L FG L+R
Sbjct: 158 CAYLVKKGDVYAVASQDYDSLLFGAPRLVRN 188
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
Length = 393
Score = 128 bits (324), Expect = 5e-37
Identities = 51/91 (56%), Positives = 60/91 (65%), Gaps = 15/91 (16%)
Query: 10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
GD +EI K ++R VRV+ ++ K+LL LMGIP IE APCEAEAQ
Sbjct: 120 GDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIE---------------APCEAEAQ 164
Query: 70 CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
CA +VK GKVYA ATEDMDALTFGT +LLR
Sbjct: 165 CAELVKKGKVYAVATEDMDALTFGTPVLLRN 195
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 90.7 bits (226), Expect = 2e-23
Identities = 34/91 (37%), Positives = 49/91 (53%), Gaps = 15/91 (16%)
Query: 10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
GD +E K+ +R R++ V++ K+LL LMGIPY++ AP E EAQ
Sbjct: 65 GDLEEARKYAQRSSRLTDEIVEDSKKLLDLMGIPYVQ---------------APSEGEAQ 109
Query: 70 CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
A M K G +A ++D D+L FG L+R
Sbjct: 110 AAYMAKKGDAWAVGSQDYDSLLFGAPRLVRN 140
>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 = 84.1 bits (208), Expect = 2e-21
Identities = 34/90 (37%), Positives = 43/90 (47%), Gaps = 15/90 (16%)
Query: 10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
G E K +R V ++ + CK LLSL GIPY+ AP EAEAQ
Sbjct: 107 GQFIEAQKPFKRNVTITPKAYQNCKILLSLEGIPYVV---------------APYEAEAQ 151
Query: 70 CAAMVKAGKVYATATEDMDALTFGTNILLR 99
A + K+G V A TED D L +G +R
Sbjct: 152 LAYLAKSGHVIAAITEDTDCLMYGVPRFIR 181
>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 = 85.8 bits (213), Expect = 3e-21
Identities = 35/91 (38%), Positives = 48/91 (52%), Gaps = 15/91 (16%)
Query: 10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
GD +E K+ +R R++S V+ K+LL LMGIPY++ AP E EAQ
Sbjct: 112 GDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQ---------------APSEGEAQ 156
Query: 70 CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
A M K G V ++D D+L FG L+R
Sbjct: 157 AAYMAKKGDVDYVGSQDYDSLLFGAPRLVRN 187
>gnl|CDD|214689 smart00484, XPGI, Xeroderma pigmentosum G I-region. domain in
nucleases.
Length = 73
Score = 72.6 bits (179), Expect = 2e-18
Identities = 29/62 (46%), Positives = 31/62 (50%), Gaps = 15/62 (24%)
Query: 38 SLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNIL 97
LMGIPYI AP EAEAQCA + K+G V A TED D L FG L
Sbjct: 1 RLMGIPYIV---------------APYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRL 45
Query: 98 LR 99
R
Sbjct: 46 YR 47
>gnl|CDD|216163 pfam00867, XPG_I, XPG I-region.
Length = 46
Score = 69.0 bits (170), Expect = 2e-17
Identities = 26/55 (47%), Positives = 29/55 (52%), Gaps = 15/55 (27%)
Query: 39 LMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFG 93
LMGIPY+ AP EAEAQCA +VK G V A +ED D L FG
Sbjct: 2 LMGIPYVV---------------APYEAEAQCAYLVKTGLVDAVISEDSDLLLFG 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 = 72.3 bits (177), Expect = 3e-17
Identities = 31/86 (36%), Positives = 41/86 (47%), Gaps = 18/86 (20%)
Query: 13 QEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAA 72
E + +RL + ++K+CKELL LMGIPY ++ P EAE A
Sbjct: 77 AEATEEEKRLDEQTFEYLKDCKELLKLMGIPYFDIR--------------PSEAEDMAAY 122
Query: 73 MVKAGK----VYATATEDMDALTFGT 94
+VK G V A + D D LT GT
Sbjct: 123 LVKKGGHLYDVVALISTDGDWLTLGT 148
>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 = 69.2 bits (170), Expect = 1e-15
Identities = 29/93 (31%), Positives = 37/93 (39%), Gaps = 19/93 (20%)
Query: 5 LFLLTGDAQEIDKFNRRLVRVSSVH----VKECKELLSLMGIPYIEVSRSPRLLPNFLGV 60
L + ++ R + EC+ELL L GIPYI
Sbjct: 109 LLASQLKKSAVKSQQQQQERDADEITQEMYDECQELLRLFGIPYIV-------------- 154
Query: 61 LAPCEAEAQCAAMVKAGKVYATATEDMDALTFG 93
AP EAEAQCA + + G V T+D D FG
Sbjct: 155 -APMEAEAQCAILNQLGLVDGVITDDSDVFLFG 186
>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 = 64.8 bits (158), Expect = 4e-14
Identities = 30/95 (31%), Positives = 44/95 (46%), Gaps = 18/95 (18%)
Query: 5 LFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPC 64
+F+ G+ K R+ + + EC++LL LMGIPY++ AP
Sbjct: 75 IFVFDGEPP---KLKRKTNPSTPEMISECRKLLDLMGIPYVQ---------------APG 116
Query: 65 EAEAQCAAMVKAGKVYATATEDMDALTFGTNILLR 99
E EAQCA + +G V + D D L FG + R
Sbjct: 117 EGEAQCAYLQVSGAVDGILSNDSDTLLFGAEKVYR 151
>gnl|CDD|189040 cd09870, PIN_YEN1, PIN domain of Yeast Endonuclease 1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and fungal homologs. Yeast Endonuclease 1
(YEN1) is a Holliday junction resolvase which promotes
reciprocal exchange during mitotic recombination to
maintain genome integrity in budding yeast. YEN1 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) of variable length (approximately 15 - 50
residues in YEN1 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+).
Length = 239
Score = 59.6 bits (145), Expect = 5e-12
Identities = 31/85 (36%), Positives = 40/85 (47%), Gaps = 17/85 (20%)
Query: 17 KFNRRLVRVSSVH--VKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMV 74
K +R+ H +K KELL L GIPY AP EAEA+CA +
Sbjct: 97 KRGKRVGLKKKEHWLIKLVKELLDLFGIPYHT---------------APGEAEAECARLQ 141
Query: 75 KAGKVYATATEDMDALTFGTNILLR 99
+ G V A + D DAL FG ++R
Sbjct: 142 RLGIVDAVLSNDSDALMFGATRVIR 166
>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 = 56.1 bits (135), Expect = 2e-10
Identities = 26/69 (37%), Positives = 32/69 (46%), Gaps = 15/69 (21%)
Query: 25 VSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATAT 84
V+ + E +ELL L GIPYI AP EAEAQCA + + T T
Sbjct: 769 VTGQMILESQELLRLFGIPYIV---------------APMEAEAQCAILDLLDQTSGTIT 813
Query: 85 EDMDALTFG 93
+D D FG
Sbjct: 814 DDSDIWLFG 822
>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of
PolI) [DNA replication, recombination, and repair].
Length = 310
Score = 52.7 bits (127), Expect = 2e-09
Identities = 19/81 (23%), Positives = 27/81 (33%), Gaps = 18/81 (22%)
Query: 14 EIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAM 73
D+ ++ ++ + V LL LMGI P E AQ A
Sbjct: 90 MPDELAPQIPILTELLVALGIPLLELMGIE----------------ADDPIETLAQKAY- 132
Query: 74 VKAGKVYATATEDMDALTFGT 94
K G V + D D L +
Sbjct: 133 -KKGDVVLIISGDKDLLQLVS 152
>gnl|CDD|189039 cd09869, PIN_GEN1, PIN domain of Gap Endonuclease 1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Gap Endonuclease 1 (GEN1) is a
Holliday junction resolvase reported to symmetrically
cleave Holliday junctions and allow religation without
additional processing. GEN1 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) of variable length (approximately 30 - 50
residues in GEN1 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+).
Length = 233
Score = 51.2 bits (123), Expect = 5e-09
Identities = 24/64 (37%), Positives = 31/64 (48%), Gaps = 15/64 (23%)
Query: 30 VKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDA 89
+KEC ELL L+GIP ++ A EAEA CA + G V T+D DA
Sbjct: 120 LKECVELLELLGIPCLQ---------------AAGEAEALCAELNSEGLVDGCITQDSDA 164
Query: 90 LTFG 93
+G
Sbjct: 165 FLYG 168
>gnl|CDD|189022 cd09852, PIN_SF, PIN (PilT N terminus) domain: Superfamily. PIN_SF
The PIN (PilT N terminus) domain belongs to a large
nuclease superfamily with representatives from
eukaryota, eubacteria, and archaea. PIN domains were
originally named for their sequence similarity to the
N-terminal domain of an annotated pili biogenesis
protein, PilT, a domain fusion between a PIN-domain and
a PilT ATPase domain. The structural properties of the
PIN domain indicate its putative active center,
consisting of invariant acidic amino acid residues
(putative metal-binding residues) is geometrically
similar in the active center of structure-specific 5'
nucleases (also known as Flap endonuclease-1-like),
PIN-domain ribonucleases of eukaryotic rRNA editing
proteins, and bacterial toxins of toxin-antitoxin (TA)
operons. Seen here, are two major divisions in the PIN
domain superfamily. The first major division, the
structure-specific 5' nuclease family, is represented by
FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4
RNase H nuclease PIN domains. These 5' nucleases are
involved in DNA replication, repair, and recombination.
They are capable of both 5'-3' exonucleolytic activity
and cleaving bifurcated DNA, in an endonucleolytic,
structure-specific manner. Unique to FEN1-like
nucleases, the PIN domain has a helical arch/clamp
region (I domain) of variable length (approximately 16
to 800 residues) and, inserted within the C-terminal
region of the PIN domain, 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, these nucleases have a carboxylate
rich active site that is involved in binding essential
divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or
Co2+). The second major division of the PIN domain
superfamily, the VapC-Smg6 family, includes such
eukaryotic ribonucleases as, Smg6, an essential factor
in nonsense-mediated mRNA decay; Rrp44, the catalytic
subunit of the exosome; and Nob1, a ribosome assembly
factor critical in pre-rRNA processing. A large
percentage of members in this family are bacterial
ribonuclease toxins of TA operons such as Mycobacterium
tuberculosis VapC and Neisseria gonorrhoeae FitB, as
well as, archaeal homologs, Pyrobaculum aerophilum
Pea0151 and P. aerophilum Pae2754. Also included are the
eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U
three-associated protein 24) and Utp23-like proteins.
Components of the small subunit processome, Fcf1/Utp24
and Utp23 are essential proteins involved in pre-rRNA
processing and 40S ribosomal subunit assembly.
Length = 120
Score = 43.7 bits (103), Expect = 9e-07
Identities = 25/82 (30%), Positives = 30/82 (36%), Gaps = 12/82 (14%)
Query: 13 QEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAA 72
E K RR + + ELL LMGIP + EA+AQ AA
Sbjct: 44 LEAQKGLRRKKGRVAELLLRDLELLDLMGIPVVHA------------PGDLYEADAQIAA 91
Query: 73 MVKAGKVYATATEDMDALTFGT 94
+ K G V A T D D
Sbjct: 92 LAKKGHVVALITNDSDLRQKAK 113
>gnl|CDD|189027 cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Exonuclease-1 (EXO1) is involved
in multiple, eukaryotic DNA metabolic pathways,
including DNA replication processes (5' flap DNA
endonuclease activity and double stranded DNA
5'-exonuclease activity), DNA repair processes (DNA
mismatch repair (MMR) and post-replication repair
(PRR)), recombination, and telomere integrity. EXO1
functions in the MMS2 error-free branch of the PRR
pathway in the maintenance and repair of stalled
replication forks. Studies also suggest that EXO1 plays
both structural and catalytic roles during MMR-mediated
mutation avoidance. EXO1 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 43 residues in EXO1 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+). EXO1 nucleases also have
C-terminal Mlh1- and Msh2-binding domains which allow
interaction with MMR and PRR proteins, respectively.
Length = 210
Score = 38.6 bits (91), Expect = 2e-04
Identities = 26/84 (30%), Positives = 37/84 (44%), Gaps = 15/84 (17%)
Query: 10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
G+ E + +R V ++ E + L G+ YI +AP EA+AQ
Sbjct: 110 GNRSEARECFQRAVDITPEMAHELIKALRKEGVEYI---------------VAPYEADAQ 154
Query: 70 CAAMVKAGKVYATATEDMDALTFG 93
A + K G V A TED D L +G
Sbjct: 155 LAYLAKTGYVDAVITEDSDLLAYG 178
>gnl|CDD|217111 pfam02570, CbiC, Precorrin-8X methylmutase. This is a family
Precorrin-8X methylmutases also known as Precorrin
isomerase, CbiC/CobH, EC:5.4.1.2. This enzyme catalyzes
the reaction: Precorrin-8X <=> hydrogenobyrinate. This
enzyme is part of the Cobalamin (vitamin B12)
biosynthetic pathway and catalyzes a methyl
rearrangement.
Length = 198
Score = 27.8 bits (63), Expect = 0.95
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 28 VHVKECKELLSLMGIPYI 45
V E KE L+ G+PYI
Sbjct: 157 VGAAESKEALAESGVPYI 174
>gnl|CDD|239549 cd03466, Nitrogenase_NifN_2, Nitrogenase_nifN_2: A subgroup of the
NifN subunit of the NifEN complex: NifN forms an
alpha2beta2 tetramer with NifE. NifN and nifE are
structurally homologous to nitrogenase MoFe protein beta
and alpha subunits respectively. NifEN participates in
the synthesis of the iron-molybdenum cofactor (FeMoco)
of the MoFe protein. NifB-co (an iron and sulfur
containing precursor of the FeMoco) from NifB is
transferred to the NifEN complex where it is further
processed to FeMoco. The nifEN bound precursor of FeMoco
has been identified as a molybdenum-free, iron- and
sulfur- containing analog of FeMoco. It has been
suggested that this nifEN bound precursor also acts as a
cofactor precursor in nitrogenase systems which require
a cofactor other than FeMoco: i.e. iron-vanadium
cofactor (FeVco) or iron only cofactor (FeFeco). This
group also contains the Clostidium fused NifN-NifB
protein.
Length = 429
Score = 27.7 bits (62), Expect = 1.1
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 8 LTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYI 45
+ D +I+K N +S ++E KE+L GI YI
Sbjct: 148 IAVDPDKIEKINVIAGMMSPADIREIKEILREFGIEYI 185
>gnl|CDD|206661 cd01869, Rab1_Ypt1, Rab GTPase family 1 includes the yeast homolog
Ypt1. Rab1/Ypt1 subfamily. Rab1 is found in every
eukaryote and is a key regulatory component for the
transport of vesicles from the ER to the Golgi
apparatus. Studies on mutations of Ypt1, the yeast
homolog of Rab1, showed that this protein is necessary
for the budding of vesicles of the ER as well as for
their transport to, and fusion with, the Golgi
apparatus. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 166
Score = 26.9 bits (60), Expect = 1.9
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 16/50 (32%)
Query: 13 QEIDKF-----NRRLV---------RVSSVHVKECKELLSLMGIPYIEVS 48
QEID++ N+ LV +V V E KE +GIP++E S
Sbjct: 98 QEIDRYASENVNKLLVGNKCDLTDKKV--VDYTEAKEFADELGIPFLETS 145
>gnl|CDD|189029 cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuclease of Taq DNA
polymerase I and homologs. The 5'-3' exonuclease
(53EXO) PIN (PilT N terminus) domain of multi-domain DNA
polymerase I and single domain protein homologs are
included in this family. Taq contains a polymerase
domain for synthesizing a new DNA strand and a 53EXO PIN
domain for cleaving RNA primers or damaged DNA strands.
Taq's 53EXO PIN domain recognizes and
endonucleolytically cleaves a structure-specific DNA
substrate that has a bifurcated downstream duplex and an
upstream template-primer duplex that overlaps the
downstream duplex by 1 bp. The 53EXO PIN domain cleaves
the unpaired 5'-arm of the overlap flap DNA substrate.
5'-3' exonucleases 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 16 residues in 53EXO 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/RNA binding. The active site
includes a set of conserved acidic residues that are
essential for binding divalent metal ions required for
nuclease activity.
Length = 174
Score = 27.0 bits (61), Expect = 1.9
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 33 CKELLSLMGIPYIEV 47
KELL +GIP +EV
Sbjct: 88 IKELLEALGIPVLEV 102
>gnl|CDD|239502 cd03408, Band_7_5, A subgroup of the band 7 domain of flotillin
(reggie) like proteins. This subgroup contains proteins
similar to stomatin, prohibitin, flotillin, HlfK/C and
podicin. Many of these band 7 domain-containing
proteins are lipid raft-associated. Individual proteins
of this band 7 domain family may cluster to form
membrane microdomains which may in turn recruit
multiprotein complexes. Microdomains formed from
flotillin proteins may in addition be dynamic units with
their own regulatory functions. Flotillins have been
implicated in signal transduction, vesicle trafficking,
cytoskeleton rearrangement and are known to interact
with a variety of proteins. Stomatin interacts with and
regulates members of the degenerin/epithelia Na+ channel
family in mechanosensory cells of Caenorhabditis elegans
and vertebrate neurons and participates in trafficking
of Glut1 glucose transporters. Prohibitin may act as a
chaperone for the stabilization of mitochondrial
proteins. Prokaryotic HflK/C plays a role in the
decision between lysogenic and lytic cycle growth during
lambda phage infection. Flotillins have been implicated
in the progression of prion disease, in the pathogenesis
of neurodegenerative diseases such as Parkinson's and
Alzheimer's disease and, in cancer invasion and
metastasis. Mutations in the podicin gene give rise to
autosomal recessive steroid resistant nephritic
syndrome.
Length = 207
Score = 26.9 bits (60), Expect = 2.0
Identities = 12/38 (31%), Positives = 13/38 (34%)
Query: 67 EAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLSW 104
E Q A V GKV LT +L LS
Sbjct: 21 EGQAAVFVNEGKVADVFAPGGYYLTTNNLPVLAFLLSG 58
>gnl|CDD|238934 cd01974, Nitrogenase_MoFe_beta, Nitrogenase_MoFe_beta: Nitrogenase
MoFe protein, beta subunit. The nitrogenase enzyme
catalyzes the ATP-dependent reduction of dinitrogen to
ammonia. The Molybdenum (Mo-) nitrogenase is the most
widespread and best characterized of these systems.
Mo-nitrogenase consists of the MoFe protein (component
1) and the Fe protein (component 2). MoFe is an
alpha2beta2 tetramer. This group contains the beta
subunit of the MoFe protein. Each alphabeta pair of MoFe
contains one P-cluster (at the alphabeta interface) and,
one molecule of iron molybdenum cofactor (FeMoco)
contained within the alpha subunit. The Fe protein
contains a single [4Fe-4S] cluster. Electrons are
transferred from the [4Fe-4S] cluster of the Fe protein
to the P-cluster of the MoFe and in turn to FeMoCo, the
site of substrate reduction.
Length = 435
Score = 27.2 bits (61), Expect = 2.1
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 7/35 (20%)
Query: 27 SVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVL 61
+ +++E K LL LMG+ Y +LP+ VL
Sbjct: 173 AGNMREIKRLLELMGVDYT-------ILPDTSDVL 200
>gnl|CDD|216746 pfam01862, PvlArgDC, Pyruvoyl-dependent arginine decarboxylase
(PvlArgDC). Methanococcus jannaschii contains
homologues of most genes required for spermidine
polyamine biosynthesis. Yet genomes from neither this
organism nor any other euryarchaeon have orthologues of
the pyridoxal 5'-phosphate- dependent ornithine or
arginine decarboxylase genes, required to produce
putrescine. Instead,these organisms have a new class of
arginine decarboxylase (PvlArgDC) formed by the
self-cleavage of a proenzyme into a 5-kDa subunit and a
12-kDa subunit that contains a reactive pyruvoyl group.
Although this extremely thermostable enzyme has no
significant sequence similarity to previously
characterized proteins, conserved active site residues
are similar to those of the pyruvoyl-dependent
histidine decarboxylase enzyme, and its subunits form a
similar (alpha-beta)(3) complex. Homologues of PvlArgDC
are found in several bacterial genomes, including those
of Chlamydia spp., which have no agmatine ureohydrolase
enzyme to convert agmatine (decarboxylated arginine)
into putrescine. In these intracellular pathogens,
PvlArgDC may function analogously to pyruvoyl-dependent
histidine decarboxylase; the cells are proposed to
import arginine and export agmatine, increasing the pH
and affecting the host cell's metabolism. Phylogenetic
analysis of Pvl- ArgDC proteins suggests that this gene
has been recruited from the euryarchaeal polyamine
biosynthetic pathway to function as a degradative
enzyme in bacteria.
Length = 159
Score = 26.8 bits (60), Expect = 2.3
Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 13/50 (26%)
Query: 15 IDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPC 64
I+ FN LVRVSS+ + + + + LP G + C
Sbjct: 30 IENFN--LVRVSSILPPNAEI---------VSLEEGLKELPP--GSIVFC 66
>gnl|CDD|226576 COG4091, COG4091, Predicted homoserine dehydrogenase [Amino acid
transport and metabolism].
Length = 438
Score = 26.6 bits (59), Expect = 3.0
Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 14/62 (22%)
Query: 21 RLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVY 80
+V +S ++ K G P IE + + ++ A ++AGK+
Sbjct: 43 EVVAISDRNLDAAKRAYDRAGGPKIEAVEA--------------DDASKMADAIEAGKIA 88
Query: 81 AT 82
T
Sbjct: 89 VT 90
>gnl|CDD|214454 MTH00198, ND2, NADH dehydrogenase subunit 2; Provisional.
Length = 607
Score = 26.7 bits (59), Expect = 3.5
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 22 LVRVSSVHVKECKELLSLMGIPYIEVSRSPR 52
+V+ +S EC LLSLMG+ ++ R PR
Sbjct: 158 MVKENSHWASECVILLSLMGLLFLTNERGPR 188
>gnl|CDD|133338 cd04138, H_N_K_Ras_like, Ras GTPase family containing H-Ras,N-Ras
and K-Ras4A/4B. H-Ras/N-Ras/K-Ras subfamily. H-Ras,
N-Ras, and K-Ras4A/4B are the prototypical members of
the Ras family. These isoforms generate distinct signal
outputs despite interacting with a common set of
activators and effectors, and are strongly associated
with oncogenic progression in tumor initiation. Mutated
versions of Ras that are insensitive to GAP stimulation
(and are therefore constitutively active) are found in a
significant fraction of human cancers. Many Ras guanine
nucleotide exchange factors (GEFs) have been identified.
They are sequestered in the cytosol until activation by
growth factors triggers recruitment to the plasma
membrane or Golgi, where the GEF colocalizes with Ras.
Active (GTP-bound) Ras interacts with several effector
proteins that stimulate a variety of diverse cytoplasmic
signaling activities. Some are known to positively
mediate the oncogenic properties of Ras, including Raf,
phosphatidylinositol 3-kinase (PI3K), RalGEFs, and
Tiam1. Others are proposed to play negative regulatory
roles in oncogenesis, including RASSF and NORE/MST1.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 162
Score = 25.8 bits (57), Expect = 4.5
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 27 SVHVKECKELLSLMGIPYIEVSRSPRL 53
+V ++ ++L GIPYIE S R
Sbjct: 122 TVSTRQGQDLAKSYGIPYIETSAKTRQ 148
>gnl|CDD|178791 PRK00010, rplE, 50S ribosomal protein L5; Validated.
Length = 179
Score = 25.8 bits (58), Expect = 5.0
Identities = 5/14 (35%), Positives = 8/14 (57%)
Query: 31 KECKELLSLMGIPY 44
+E + LL G P+
Sbjct: 164 EEARALLKAFGFPF 177
>gnl|CDD|145734 pfam02739, 5_3_exonuc_N, 5'-3' exonuclease, N-terminal
resolvase-like domain.
Length = 169
Score = 25.3 bits (56), Expect = 6.6
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 34 KELLSLMGIPYIEV 47
KELL +GIP +EV
Sbjct: 92 KELLDALGIPVLEV 105
>gnl|CDD|173776 cd01026, TOPRIM_OLD, TOPRIM_OLD: topoisomerase-primase (TOPRIM)
nucleotidyl transferase/hydrolase domain of the type
found in bacterial and archaeal nucleases of the OLD
(overcome lysogenization defect) family. The
bacteriophage P2 OLD protein, which has DNase as well
as RNase activity, consists of an N-terminal ABC-type
ATPase domain and a C-terminal Toprim domain; the
nuclease activity of OLD is stimulated by ATP, though
the ATPase activity is not DNA-dependent. Functional
details on OLD are scant and further experimentation is
required to define the relationship between the ATPase
and Toprim nuclease domains. The TOPRIM domain has two
conserved motifs, one of which centers at a conserved
glutamate and the other one at two conserved aspartates
(DxD). The conserved glutamate may act as a general
acid in strand cleavage by nucleases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full
catalytic function.
Length = 97
Score = 24.9 bits (55), Expect = 6.8
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 22 LVRVSSVHVKECKELLSLMGIPY 44
++ V + K +LL+ +GIP
Sbjct: 36 IIPVGGKNFKPFIKLLNALGIPV 58
>gnl|CDD|233021 TIGR00555, panK_eukar, pantothenate kinase,
eukaryotic/staphyloccocal type. This model describes a
eukaryotic form of pantothenate kinase, characterized
from the fungus Aspergillus nidulans and with similar
forms known in several other eukaryotes. It also
includes forms from several Gram-positive bacteria
suggested to have originated from the eukaryotic form by
lateral transfer. It differs in a number of biochemical
properties (such as inhibition by acetyl-CoA) from most
bacterial CoaA and lacks sequence similarity. This
enzyme is the key regulatory step in the biosynthesis of
coenzyme A (CoA) [Biosynthesis of cofactors, prosthetic
groups, and carriers, Pantothenate and coenzyme A].
Length = 296
Score = 25.4 bits (56), Expect = 8.1
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 84 TEDMDALTFGTNILLRQQ 101
++ DAL G N LL+++
Sbjct: 78 FDEFDALIQGLNYLLKEE 95
>gnl|CDD|193566 cd08019, M20_Acy1_subfamily5, M20 Peptidase Aminoacylase 1
subfamily. Peptidase M20 family, Uncharacterized
subfamily of bacterial proteins predicted as putative
amidohydrolases. These are a class of zinc binding
homodimeric enzymes involved in hydrolysis of
N-acetylated proteins. N-terminal acetylation of
proteins is a widespread and highly conserved process
that is involved in protection and stability of
proteins. Several types of aminoacylases can be
distinguished on the basis of substrate specificity.
Aminoacylase 1 (ACY1) breaks down cytosolic aliphatic
N-acyl-alpha-amino acids (except L-aspartate),
especially N-acetyl-methionine and acetyl-glutamate
into L-amino acids and an acyl group. However, ACY1 can
also catalyze the reverse reaction, the synthesis of
acetylated amino acids. ACY1 may also play a role in
xenobiotic bioactivation as well as the inter-organ
processing of amino acid-conjugated xenobiotic
derivatives (S-substituted-N-acetyl-L-cysteine).
Length = 372
Score = 25.2 bits (56), Expect = 8.5
Identities = 20/60 (33%), Positives = 26/60 (43%), Gaps = 16/60 (26%)
Query: 31 KECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDAL 90
K KE L +GIPY V+ + GV+A + K GK A D+DAL
Sbjct: 23 KRIKEELDKLGIPYERVAET--------GVIATIKGG-------KPGKTVALRA-DIDAL 66
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 25.4 bits (57), Expect = 8.7
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 33 CKELLSLMGIPYIEV 47
+ELL +GIP +E+
Sbjct: 91 IRELLRALGIPLLEL 105
>gnl|CDD|202421 pfam02833, DHHA2, DHHA2 domain. This domain is often found
adjacent to the DHH domain pfam01368 and is called
DHHA2 for DHH associated domain. This domain is
diagnostic of DHH subfamily 2 members. The domain is
about 120 residues long and contains a conserved DXK
motif at its amino terminus.
Length = 127
Score = 24.8 bits (55), Expect = 9.7
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 7 LLTGDAQEIDKFNRRLVRVSSVHVKECKELLSL 39
LL D +E F + V + V + +ELL
Sbjct: 19 LLRKDYKEFT-FGGKKVGIGQVETVDLEELLER 50
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
0.324 0.134 0.406
Gapped
Lambda K H
0.267 0.0817 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,628,881
Number of extensions: 472719
Number of successful extensions: 709
Number of sequences better than 10.0: 1
Number of HSP's gapped: 691
Number of HSP's successfully gapped: 46
Length of query: 113
Length of database: 10,937,602
Length adjustment: 77
Effective length of query: 36
Effective length of database: 7,522,344
Effective search space: 270804384
Effective search space used: 270804384
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: 53 (24.0 bits)