RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11827
(336 letters)
>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 = 226 bits (578), Expect = 1e-73
Identities = 73/147 (49%), Positives = 103/147 (70%)
Query: 1 MKYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHL 60
MK ++MLL + IK I+VFDG LP+K+ TEE+RR++R+ + KA ELL SEA+
Sbjct: 60 MKRVNMLLHYGIKPILVFDGGPLPSKKGTEEERRERREENLEKALELLREGNRSEARECF 119
Query: 61 RQSVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGA 120
+++VD+T +MA +I+A R GV+ IVAP+EADAQ+AYL GY D VITEDSDLL +G
Sbjct: 120 QRAVDITPEMAHELIKALRKEGVEYIVAPYEADAQLAYLAKTGYVDAVITEDSDLLAYGC 179
Query: 121 KKIIYKLDLSGNCCFMDREKLPSALKM 147
K+++KLD +G+C +D L K+
Sbjct: 180 PKVLFKLDKNGSCQEIDLADLLKCRKL 206
>gnl|CDD|214689 smart00484, XPGI, Xeroderma pigmentosum G I-region. domain in
nucleases.
Length = 73
Score = 88.0 bits (219), Expect = 4e-22
Identities = 31/70 (44%), Positives = 42/70 (60%), Gaps = 4/70 (5%)
Query: 82 GVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGN----CCFMD 137
G+ IVAP+EA+AQ AYL +G D +ITEDSDLL+FGA ++ L SG +D
Sbjct: 4 GIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIID 63
Query: 138 REKLPSALKM 147
E + L +
Sbjct: 64 LESVLKELGL 73
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
Length = 393
Score = 93.9 bits (234), Expect = 2e-21
Identities = 57/188 (30%), Positives = 85/188 (45%), Gaps = 27/188 (14%)
Query: 6 MLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVD 65
LL IK + VFDG+ K E RR++R+ + + + + E + +++V
Sbjct: 75 RLLEAGIKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVR 134
Query: 66 VTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGA----- 120
VT + + + R G+ I AP EA+AQ A L G V TED D L FG
Sbjct: 135 VTKEQNEDAKKLLRLMGIPVIEAPCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLR 194
Query: 121 --------KKIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGI 172
K+ I +++LS + L + + +F D +CIL GCDY I
Sbjct: 195 NLNFSEAKKRPIQEINLS---------TVLEELGLSMDQFID-----LCILCGCDYCDTI 240
Query: 173 KGMGLKKA 180
KG+G K A
Sbjct: 241 KGIGPKTA 248
>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 = 90.3 bits (224), Expect = 2e-21
Identities = 38/125 (30%), Positives = 60/125 (48%)
Query: 6 MLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVD 65
L + I I VFDG K R + R + + E + + EAQ +++V
Sbjct: 62 KLFENGITPIFVFDGGPPYLKSEASGKRTEARAEAEISSTEASYIGQFIEAQKPFKRNVT 121
Query: 66 VTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIY 125
+T K N G+ +VAP+EA+AQ+AYL +G+ ITED+D L++G + I
Sbjct: 122 ITPKAYQNCKILLSLEGIPYVVAPYEAEAQLAYLAKSGHVIAAITEDTDCLMYGVPRFIR 181
Query: 126 KLDLS 130
+
Sbjct: 182 GMTFP 186
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 89.9 bits (224), Expect = 1e-20
Identities = 63/225 (28%), Positives = 105/225 (46%), Gaps = 26/225 (11%)
Query: 7 LLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGS--EAQSHLRQSV 64
LL + IK + VFDG+ K E+RR+ R+ + K E + G EA+ + ++S
Sbjct: 21 LLENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAK--EEGDLEEARKYAQRSS 78
Query: 65 DVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKII 124
+T ++ + + G+ + AP E +AQ AY+ G A V ++D D L+FGA +++
Sbjct: 79 RLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLV 138
Query: 125 YKLDLSGNCCF-------------MDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTG 171
L +SG ++ E++ L + + D + IL G DY G
Sbjct: 139 RNLTISGKRKLPGKNVYVEVKPELIELEEVLKELGITREQLID-----IAILVGTDYNPG 193
Query: 172 IKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFL 216
IKG+G K A + D E L + +I +Y +I + FL
Sbjct: 194 IKGIGPKTALKLIKK--HGDLEKVLEERGF--EIENYDEIREFFL 234
>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 = 89.6 bits (223), Expect = 3e-20
Identities = 66/224 (29%), Positives = 105/224 (46%), Gaps = 24/224 (10%)
Query: 7 LLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDV 66
LL + IK + VFDG+ K T E+RR+ R+ + K E L EA+ + ++S +
Sbjct: 68 LLENGIKPVYVFDGKPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRL 127
Query: 67 THKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYK 126
T ++ + + G+ + AP E +AQ AY+ G DYV ++D D L+FGA +++
Sbjct: 128 TSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRN 187
Query: 127 LDLSGNCCFMDREKLPSALK--------MPLAKF------TDAKFRYMCILSGCDYWTGI 172
L +SG + KLP + L + T + + IL G DY G+
Sbjct: 188 LTISG------KRKLPGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVGTDYNEGV 241
Query: 173 KGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFL 216
KG+G K A + D E L+ I +Y +I + FL
Sbjct: 242 KGIGPKTALKLIKE--HGDLEKVLKARGED--IENYDEIREFFL 281
>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 = 86.5 bits (215), Expect = 1e-19
Identities = 50/130 (38%), Positives = 69/130 (53%), Gaps = 12/130 (9%)
Query: 7 LLAHKIKVIMVFDGRHLPAKEATEEDRRKKR----DSHKAKAAELLILD------RGSEA 56
LL + IK + VFDG K T RR++R + K K AE L+ S+
Sbjct: 65 LLFYGIKPVFVFDGGAPELKRRTLAKRRQQREKAEINAK-KTAEKLLASQLKKSAVKSQQ 123
Query: 57 QSHLRQSVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLL 116
Q R + ++T +M + R G+ IVAP EA+AQ A LN G D VIT+DSD+
Sbjct: 124 QQQERDADEITQEMYDECQELLRLFGIPYIVAPMEAEAQCAILNQLGLVDGVITDDSDVF 183
Query: 117 VFGAKKIIYK 126
+FGAK+ +YK
Sbjct: 184 LFGAKR-VYK 192
>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of
PolI) [DNA replication, recombination, and repair].
Length = 310
Score = 85.1 bits (211), Expect = 7e-19
Identities = 42/204 (20%), Positives = 70/204 (34%), Gaps = 26/204 (12%)
Query: 6 MLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVD 65
+ L ++VFDG+ + E+ + R K EL Q
Sbjct: 55 IRLLEPTHPVVVFDGKPPTFRHELLEEYKANR--EKEMPDELA------------PQIPI 100
Query: 66 VTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKI-I 124
+T + I G+ P E AQ AY G +I+ D DLL + + +
Sbjct: 101 LTELLVALGIPLLELMGI-EADDPIETLAQKAYK--KGDVVLIISGDKDLLQLVSPNVLV 157
Query: 125 YKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKD 182
F+D E++ K T + + L G D G+KG+G K A
Sbjct: 158 INGKKGEPEKFLDLEEVEEKFK----GLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALK 213
Query: 183 YV--FSIMDPDFENALRKINVYGK 204
+ + ++ +EN +
Sbjct: 214 LLQEYGSLEGLYENLDIIKKKTRE 237
>gnl|CDD|216163 pfam00867, XPG_I, XPG I-region.
Length = 46
Score = 78.3 bits (194), Expect = 8e-19
Identities = 25/43 (58%), Positives = 31/43 (72%)
Query: 79 RARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAK 121
R G+ +VAP+EA+AQ AYL G D VI+EDSDLL+FGA
Sbjct: 1 RLMGIPYVVAPYEAEAQCAYLVKTGLVDAVISEDSDLLLFGAP 43
>gnl|CDD|188628 cd09908, H3TH_EXO1, H3TH domain of Exonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease. 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. Members of
this subgroup include the H3TH (helix-3-turn-helix)
domains of EXO1 and other similar eukaryotic 5'
nucleases. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region/I
domain (not included here) and inserted within the PIN
domain is an atypical helix-hairpin-helix-2 (HhH2)-like
region. This atypical HhH2 region, the H3TH domain, has
an extended loop with at least three turns between the
first two helices, and only three of the four helices
appear to be conserved. Both the H3TH domain and the
helical arch/clamp region are involved in DNA binding.
Studies suggest that a glycine-rich loop in the H3TH
domain contacts the phosphate backbone of the template
strand in the downstream DNA duplex. These nucleases
have a carboxylate rich active site that is involved in
binding essential divalent metal ion cofactors (Mg2+ or
Mn2+) required for nuclease activity. The first metal
binding site is composed entirely of Asp/Glu residues
from the PIN domain, whereas, the second metal binding
site is composed generally of two Asp residues from the
PIN domain and one Asp residue from the H3TH domain.
Together with the helical arch and network of amino
acids interacting with metal binding ions, the H3TH
region defines a positively charged active-site
DNA-binding groove in structure-specific 5' nucleases.
EXO1 nucleases also have C-terminal Mlh1- and
Msh2-binding domains which allow interaction with MMR
and PRR proteins, respectively.
Length = 73
Score = 75.7 bits (187), Expect = 1e-17
Identities = 29/78 (37%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 156 KFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEF 215
KFR+MCILSGCDY + G+GLKKA Y E ++ + GK ++ ++
Sbjct: 2 KFRHMCILSGCDYLPSLPGIGLKKA--YKLVRRHRTIEKVIKALRFDGK----KEVPPDY 55
Query: 216 LTSFHNTNLMFLYQPVYD 233
F L FL+Q V+D
Sbjct: 56 EEGFQKALLTFLHQRVFD 73
>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 = 79.5 bits (197), Expect = 4e-17
Identities = 42/125 (33%), Positives = 67/125 (53%)
Query: 7 LLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDV 66
LL + IK + VFDG+ K E RR++R+ + K E EA+ + +++V V
Sbjct: 69 LLENGIKPVYVFDGKPPELKSGELEKRRERREEAEEKLEEAKEEGDAEEARKYAKRTVRV 128
Query: 67 THKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYK 126
T ++ + R G+ + AP EA+AQ AYL G V ++D D L+FGA +++
Sbjct: 129 TKEIVEECKKLLRLMGIPYVEAPSEAEAQCAYLVKKGDVYAVASQDYDSLLFGAPRLVRN 188
Query: 127 LDLSG 131
L +SG
Sbjct: 189 LTISG 193
>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 = 78.1 bits (193), Expect = 9e-17
Identities = 32/118 (27%), Positives = 46/118 (38%), Gaps = 29/118 (24%)
Query: 7 LLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDV 66
LLA I + VFDG + P+ KR + L +
Sbjct: 77 LLALPITPVFVFDGPNRPSF---------KRGKRVGLKKKEHWLIK-------------- 113
Query: 67 THKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKII 124
V + G+ AP EA+A+ A L G D V++ DSD L+FGA ++I
Sbjct: 114 ------LVKELLDLFGIPYHTAPGEAEAECARLQRLGIVDAVLSNDSDALMFGATRVI 165
>gnl|CDD|188621 cd09901, H3TH_FEN1-like, H3TH domains of Flap endonuclease-1
(FEN1)-like structure specific 5' nucleases: FEN1
(eukaryotic) and EXO1. The 5' nucleases within this
family are capable of both 5'-3' exonucleolytic activity
and cleaving bifurcated or branched DNA, in an
endonucleolytic, structure-specific manner, and are
involved in DNA replication, repair, and recombination.
This family includes the H3TH (helix-3-turn-helix)
domains of eukaryotic Flap Endonuclease-1 (FEN1),
Exonuclease-1 (EXO1), and other eukaryotic homologs.
These nucleases contain a PIN (PilT N terminus) domain
with a helical arch/clamp region/I domain (not included
here) and inserted within the PIN domain is an atypical
helix-hairpin-helix-2 (HhH2)-like region. This atypical
HhH2 region, the H3TH domain, has an extended loop with
at least three turns between the first two helices, and
only three of the four helices appear to be conserved.
Both the H3TH domain and the helical arch/clamp region
are involved in DNA binding. Studies suggest that a
glycine-rich loop in the H3TH domain contacts the
phosphate backbone of the template strand in the
downstream DNA duplex. The nucleases within this family
have a carboxylate rich active site that is involved in
binding essential divalent metal ion cofactors (i. e.,
Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease
activity. The first metal binding site is composed
entirely of Asp/Glu residues from the PIN domain,
whereas, the second metal binding site is composed
generally of two Asp residues from the PIN domain and
one Asp residue from the H3TH domain. Together with the
helical arch and network of amino acids interacting with
metal binding ions, the H3TH region defines a positively
charged active-site DNA-binding groove in
structure-specific 5' nucleases.
Length = 73
Score = 70.6 bits (174), Expect = 8e-16
Identities = 26/78 (33%), Positives = 35/78 (44%), Gaps = 6/78 (7%)
Query: 156 KFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEF 215
+F +CILSGCDY I G+G K A + E L+ + K K+ +
Sbjct: 2 QFIDLCILSGCDYLPSIPGIGPKTAYKLIKKHKSI--EKVLKALRSNKK----KKVPVPY 55
Query: 216 LTSFHNTNLMFLYQPVYD 233
F L FL+Q VYD
Sbjct: 56 EEPFKEARLTFLHQRVYD 73
>gnl|CDD|189028 cd09858, PIN_MKT1, PIN domain of Mkt1: A global regulator of mRNAs
encoding mitochondrial proteins and eukaryotic homologs.
The Mkt1 gene product interacts with the
Poly(A)-binding protein associated factor, Pbp1, and is
present at the 3' end of RNA transcripts during
translation. The Mkt1-Pbp1 complex is involved in the
post-transcriptional regulation of HO endonuclease
expression. Mkt1 and eukaryotic homologs are atypical
members of the structure-specific, 5' nuclease family.
Conical members of this family possess a PIN (PilT N
terminus) domain with a helical arch/clamp region/I
domain (approximately 40 to 55 residues in MKT1 PIN
domains) and inserted within the PIN domain is a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Although Mkt1 appears
to possess both a PIN and H3TH domain, the Mkt1 PIN
domain lacks several of the active site residues
necessary to bind essential divalent metal ion cofactors
(Mg2+/Mn2+) required for nuclease activity in this
family. Also, Mkt1 lacks the glycine-rich loop in the
H3TH domain which is proposed to facilitate duplex DNA
binding.
Length = 215
Score = 64.5 bits (158), Expect = 3e-12
Identities = 37/140 (26%), Positives = 68/140 (48%), Gaps = 14/140 (10%)
Query: 9 AHKIKVIMVFDG-----RHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQS 63
H IK I VFDG + P+ +R++ +A EL + + S+A ++
Sbjct: 72 EHNIKPIFVFDGLSPKSQLEPSS------QREQSARQLEQAWELYVNGQASQAVEAFSEA 125
Query: 64 VDVTHKMALNVIQA-CRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKK 122
+ + + + +G++ +VAP+ A AQ+AYL GY D + ++LL+F K
Sbjct: 126 GSIQPEDLYRFLIRILKEKGIEYLVAPYLASAQLAYLERHGYVD-AVYGPTELLLFDVDK 184
Query: 123 IIYKLDL-SGNCCFMDREKL 141
+I +D ++D++KL
Sbjct: 185 VILSIDFQKKTFRWVDKKKL 204
>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 = 54.0 bits (130), Expect = 1e-08
Identities = 22/64 (34%), Positives = 37/64 (57%)
Query: 61 RQSVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGA 120
R++ T +M + G+ + AP E +AQ AYL ++G D +++ DSD L+FGA
Sbjct: 87 RKTNPSTPEMISECRKLLDLMGIPYVQAPGEGEAQCAYLQVSGAVDGILSNDSDTLLFGA 146
Query: 121 KKII 124
+K+
Sbjct: 147 EKVY 150
>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 = 53.4 bits (128), Expect = 9e-08
Identities = 38/125 (30%), Positives = 61/125 (48%), Gaps = 8/125 (6%)
Query: 54 SEAQSHLRQSVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDS 113
++ Q R + +VT +M L + R G+ IVAP EA+AQ A L++ IT+DS
Sbjct: 757 AQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDS 816
Query: 114 DLLVFGAKKIIYKLDLSGN--CCFMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTG 171
D+ +FGA+ +YK + N + + + L + K + + L G DY G
Sbjct: 817 DIWLFGARH-VYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLIN-----LAYLLGSDYTEG 870
Query: 172 IKGMG 176
I +G
Sbjct: 871 IPTVG 875
>gnl|CDD|188617 cd09897, H3TH_FEN1-XPG-like, H3TH domains of Flap endonuclease-1
(FEN1)-like structure specific 5' nucleases. The 5'
nucleases within this family are capable of both 5'-3'
exonucleolytic activity and cleaving bifurcated or
branched DNA, in an endonucleolytic, structure-specific
manner, and are involved in DNA replication, repair, and
recombination. This family includes the H3TH
(helix-3-turn-helix) domains of Flap Endonuclease-1
(FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1
(GEN1), Xeroderma pigmentosum complementation group G
(XPG) nuclease, and other eukaryotic and archaeal
homologs. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region/I
domain (not included here) and inserted within the PIN
domain is an atypical helix-hairpin-helix-2 (HhH2)-like
region. This atypical HhH2 region, the H3TH domain, has
an extended loop with at least three turns between the
first two helices, and only three of the four helices
appear to be conserved. Both the H3TH domain and the
helical arch/clamp region are involved in DNA binding.
Studies suggest that a glycine-rich loop in the H3TH
domain contacts the phosphate backbone of the template
strand in the downstream DNA duplex. With the except of
the Mkt1-like proteins, the nucleases within this family
have a carboxylate rich active site that is involved in
binding essential divalent metal ion cofactors (i. e.,
Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease
activity. The first metal binding site is composed
entirely of Asp/Glu residues from the PIN domain,
whereas, the second metal binding site is composed
generally of two Asp residues from the PIN domain and
one Asp residue from the H3TH domain. Together with the
helical arch and network of amino acids interacting with
metal binding ions, the H3TH region defines a positively
charged active-site DNA-binding groove in
structure-specific 5' nucleases.
Length = 68
Score = 47.6 bits (114), Expect = 1e-07
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 156 KFRYMCILSGCDYWTGIKGMGLKKA 180
+F +CILSGCDY G+ G+G K A
Sbjct: 2 QFIDLCILSGCDYLPGLPGIGPKTA 26
>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 = 48.7 bits (116), Expect = 2e-07
Identities = 27/116 (23%), Positives = 42/116 (36%), Gaps = 30/116 (25%)
Query: 11 KIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKM 70
I VI+VFD K ++ R+K+ ++
Sbjct: 28 DITVIIVFDVVAELLKLEAQKGLRRKKG---------------------------RVAEL 60
Query: 71 ALNVIQACRARGVDCIVAPF---EADAQMAYLNIAGYADYVITEDSDLLVFGAKKI 123
L ++ G+ + AP EADAQ+A L G+ +IT DSDL +
Sbjct: 61 LLRDLELLDLMGIPVVHAPGDLYEADAQIAALAKKGHVVALITNDSDLRQKAKPGV 116
>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 = 50.4 bits (121), Expect = 2e-07
Identities = 33/124 (26%), Positives = 53/124 (42%), Gaps = 18/124 (14%)
Query: 7 LLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAEL------LILDRGSEAQSHL 60
L+A + + V DG P K +R + S AK + +R S L
Sbjct: 62 LIALGVLPVFVVDGAAPPLKLPVII-KRNQLQSGIAKPGDNPTPKNGSKRNRRSRFSHVL 120
Query: 61 RQSVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGA 120
++ V++ + G+ C+ A EA+A A LN G D IT+DSD ++GA
Sbjct: 121 KECVELLELL-----------GIPCLQAAGEAEALCAELNSEGLVDGCITQDSDAFLYGA 169
Query: 121 KKII 124
+ +
Sbjct: 170 RTVY 173
>gnl|CDD|214690 smart00485, XPGN, Xeroderma pigmentosum G N-region. domain in
nucleases.
Length = 99
Score = 46.1 bits (110), Expect = 9e-07
Identities = 15/37 (40%), Positives = 18/37 (48%)
Query: 1 MKYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKR 37
LL IK I VFDG+ P K T RR++R
Sbjct: 60 FYRTCRLLEFGIKPIFVFDGKPPPLKSETLAKRRERR 96
>gnl|CDD|197623 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol1 family) motifs.
Length = 36
Score = 38.6 bits (91), Expect = 1e-04
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 156 KFRYMCILSG--CDYWTGIKGMGLKKAKDYV 184
+F IL G D G+KG+G K A +
Sbjct: 3 QFIDYAILVGDYSDNIPGVKGIGPKTALKLL 33
>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 = 40.3 bits (94), Expect = 4e-04
Identities = 27/128 (21%), Positives = 47/128 (36%), Gaps = 18/128 (14%)
Query: 2 KYIHMLLAHK-IKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHL 60
I + + I I+VFDG K + + ++ +A EA
Sbjct: 36 TIISLAKNYSAITPIVVFDG----GKPVLRLEHLPEYKENRDEAEA--------EATEEE 83
Query: 61 RQSVDVTHKMALNVIQACRARGVDCIVA-PFEADAQMAYLNIAGYADY----VITEDSDL 115
++ + T + + + + G+ P EA+ AYL G Y +I+ D D
Sbjct: 84 KRLDEQTFEYLKDCKELLKLMGIPYFDIRPSEAEDMAAYLVKKGGHLYDVVALISTDGDW 143
Query: 116 LVFGAKKI 123
L G K+
Sbjct: 144 LTLGTDKV 151
>gnl|CDD|188627 cd09907, H3TH_FEN1-Euk, H3TH domain of Flap Endonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease: Eukaryotic homologs. Members of this subgroup
include the H3TH (helix-3-turn-helix) domains of
eukaryotic Flap endonuclease-1 (FEN1), 5' nucleases.
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. These
nucleases contain a PIN (PilT N terminus) domain with a
helical arch/clamp region/I domain (not included here)
and inserted within the PIN domain is an atypical
helix-hairpin-helix-2 (HhH2)-like region. This atypical
HhH2 region, the H3TH domain, has an extended loop with
at least three turns between the first two helices, and
only three of the four helices appear to be conserved.
Both the H3TH domain and the helical arch/clamp region
are involved in DNA binding. Studies suggest that a
glycine-rich loop in the H3TH domain contacts the
phosphate backbone of the template strand in the
downstream DNA duplex. The nucleases within this
subfamily have a carboxylate rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+ or Mn2+) required for nuclease activity.
The first metal binding site is composed entirely of
Asp/Glu residues from the PIN domain, whereas, the
second metal binding site is composed generally of two
Asp residues from the PIN domain and one Asp residue
from the H3TH domain. Together with the helical arch and
network of amino acids interacting with metal binding
ions, the H3TH region defines a positively charged
active-site DNA-binding groove in structure-specific 5'
nucleases. Also, 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 = 70
Score = 36.8 bits (86), Expect = 0.001
Identities = 13/20 (65%), Positives = 14/20 (70%)
Query: 161 CILSGCDYWTGIKGMGLKKA 180
CIL GCDY IKG+G K A
Sbjct: 7 CILLGCDYCESIKGIGPKTA 26
>gnl|CDD|221785 pfam12813, XPG_I_2, XPG domain containing. This family is largely
of fungal proteins and is related to the XP-G protein
family.
Length = 223
Score = 39.3 bits (92), Expect = 0.001
Identities = 22/54 (40%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 70 MALNVIQACRAR--GVDCIVAPFEADAQMAYLNIAGYAD-YVITEDSDLLVFGA 120
M V++A + R GV +V P EAD A L A V+T DSDLLV
Sbjct: 5 MVPAVVEALKYRNWGVITVVVPGEADVYCASL--ARKLGCAVLTGDSDLLVHDL 56
>gnl|CDD|188620 cd09900, H3TH_XPG-like, H3TH domains of Flap endonuclease-1
(FEN1)-like structure specific 5' nucleases: FEN1
(archaeal), GEN1, YEN1, and XPG. The 5' nucleases
within this family are capable of both 5'-3'
exonucleolytic activity and cleaving bifurcated or
branched DNA, in an endonucleolytic, structure-specific
manner, and are involved in DNA replication, repair, and
recombination. This family includes the H3TH
(helix-3-turn-helix) domains of archaeal Flap
Endonuclease-1 (FEN1), Gap Endonuclease 1 (GEN1), Yeast
Endonuclease 1 (YEN1), Xeroderma pigmentosum
complementation group G (XPG) nuclease, and other
eukaryotic and archaeal homologs. These nucleases
contain a PIN (PilT N terminus) domain with a helical
arch/clamp region/I domain (not included here) and
inserted within the PIN domain is an atypical
helix-hairpin-helix-2 (HhH2)-like region. This atypical
HhH2 region, the H3TH domain, has an extended loop with
at least three turns between the first two helices, and
only three of the four helices appear to be conserved.
Both the H3TH domain and the helical arch/clamp region
are involved in DNA binding. Studies suggest that a
glycine-rich loop in the H3TH domain contacts the
phosphate backbone of the template strand in the
downstream DNA duplex. With the except of the Mkt1-like
proteins, the nucleases within this family have a
carboxylate rich active site that is involved in binding
essential divalent metal ion cofactors (i. e., Mg2+,
Mn2+, Zn2+, or Co2+) required for nuclease activity. The
first metal binding site is composed entirely of Asp/Glu
residues from the PIN domain, whereas, the second metal
binding site is composed generally of two Asp residues
from the PIN domain and one Asp residue from the H3TH
domain. Together with the helical arch and network of
amino acids interacting with metal binding ions, the
H3TH region defines a positively charged active-site
DNA-binding groove in structure-specific 5' nucleases.
Length = 52
Score = 35.9 bits (84), Expect = 0.002
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 160 MCILSGCDYWTGIKGMGLKKA 180
+ +L G DY G+ G+G K A
Sbjct: 6 LALLLGTDYNPGVPGIGPKTA 26
>gnl|CDD|188616 cd00080, H3TH_StructSpec-5'-nucleases, H3TH domains of
structure-specific 5' nucleases (or flap
endonuclease-1-like) involved in DNA replication,
repair, and recombination. The 5' nucleases of this
superfamily are capable of both 5'-3' exonucleolytic
activity and cleaving bifurcated or branched DNA, in an
endonucleolytic, structure-specific manner, and are
involved in DNA replication, repair, and recombination.
The superfamily includes the H3TH (helix-3-turn-helix)
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 H3TH domains of the 5'-3' exonucleases
of DNA polymerase I and single domain protein homologs,
as well as, the bacteriophage T4 RNase H, T5-5'nuclease,
and other homologs. These nucleases contain a PIN (PilT
N terminus) domain with a helical arch/clamp region/I
domain (not included here) and inserted within the
C-terminal region of the PIN domain is an atypical
helix-hairpin-helix-2 (HhH2)-like region. This atypical
HhH2 region, the H3TH domain, has an extended loop with
at least three turns between the first two helices, and
only three of the four helices appear to be conserved.
Both the H3TH domain and the helical arch/clamp region
are involved in DNA binding. Studies suggest that a
glycine-rich loop in the H3TH domain contacts the
phosphate backbone of the template strand in the
downstream DNA duplex. Typically, the nucleases within
this superfamily have a carboxylate rich active site
that is involved in binding essential divalent metal ion
cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required
for nuclease activity. The first metal binding site is
composed entirely of Asp/Glu residues from the PIN
domain, whereas, the second metal binding site is
composed generally of two Asp residues from the PIN
domain and one or two Asp residues from the H3TH domain.
Together with the helical arch and network of amino
acids interacting with metal binding ions, the H3TH
region defines a positively charged active-site
DNA-binding groove in structure-specific 5' nucleases.
Length = 71
Score = 36.2 bits (84), Expect = 0.002
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 155 AKFRYMCILSGCDY--WTGIKGMGLKKA 180
+F +C L GCDY G+ G+G K A
Sbjct: 1 EQFIDLCALVGCDYSDNPGVPGIGPKTA 28
>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease.
Length = 259
Score = 34.5 bits (80), Expect = 0.051
Identities = 28/121 (23%), Positives = 44/121 (36%), Gaps = 26/121 (21%)
Query: 76 QACRARGVDCIVAP-FEADAQMAYL----NIAGYADYVITEDSDLL--------VFGAKK 122
+ A G+ + +EAD +A L GY +++ D DLL V K
Sbjct: 91 ELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPTK 150
Query: 123 IIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKA 180
I + +L +++ L + D K L G D G+ G+G K A
Sbjct: 151 GIKEFELYTPENVIEKYGLTPE------QIIDYK-----ALMGDSSDNIPGVPGIGEKTA 199
Query: 181 K 181
Sbjct: 200 A 200
>gnl|CDD|227661 COG5366, COG5366, Protein involved in propagation of M2 dsRNA
satellite of L-A virus [General function prediction
only].
Length = 531
Score = 34.2 bits (78), Expect = 0.089
Identities = 39/190 (20%), Positives = 61/190 (32%), Gaps = 48/190 (25%)
Query: 82 GVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKL 141
GV I+AP+ A Q AYL A Y LL+ G +II + + +D +
Sbjct: 142 GVAVIIAPYSATFQCAYLMSAETCSYAFGPSDILLLDGVDRIILDMSFGSDKPPLDVFHV 201
Query: 142 PSALKMPLAK----------------------FTDAKFRYMCILSGCDYWTGIKGMGLKK 179
P L+M L TDA F ++ +K
Sbjct: 202 PRFLEMFLLSSRLFYALGLLLGCDFCSTIPRCATDADFSLNQVIG-----------DMKG 250
Query: 180 AKDYVFSI---------MDPDFENALRKIN-----VYGKI-GSYVKITKEFLTSFHNTNL 224
+ + +I LR + + + GSY ++E + N L
Sbjct: 251 QELFSKAIRGTCEYEGSRKKYTLEFLRSLGLVTYLLVMGVSGSYHAYSEESVPGNLNKIL 310
Query: 225 MFLYQPVYDP 234
P +DP
Sbjct: 311 GLKLAPGFDP 320
>gnl|CDD|216098 pfam00752, XPG_N, XPG N-terminal domain.
Length = 100
Score = 31.2 bits (71), Expect = 0.19
Identities = 13/34 (38%), Positives = 15/34 (44%)
Query: 6 MLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDS 39
L IK I VFDG P K T + R +R
Sbjct: 66 RLKDFGIKPIFVFDGGPPPLKAETLQKRSARRQE 99
>gnl|CDD|185767 cd09244, BRO1_Rhophilin, Protein-interacting Bro1-like domain of
RhoA-binding protein Rhophilin and related domains.
This family contains the Bro1-like domain of
RhoA-binding proteins, Rhophilin-1 and -2, and related
domains. It belongs to the BRO1_Alix_like superfamily
which also includes the Bro1-like domains of mammalian
Alix (apoptosis-linked gene-2 interacting protein X),
His-Domain type N23 protein tyrosine phosphatase
(HD-PTP, also known as PTPN23), Brox, Bro1 and Rim20
(also known as PalA) from Saccharomyces cerevisiae,
Ustilago maydis Rim23 (also known as PalC), and related
domains. Rhophilin-1 and -2 bind both GDP- and GTP-bound
RhoA. Bro1-like domains are boomerang-shaped, and part
of the domain is a tetratricopeptide repeat (TPR)-like
structure. In addition to this Bro1-like domain,
Rhophilin-1 and -2, contain an N-terminal Rho-binding
domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1)
domain. Their PDZ domains have limited homology.
Rhophilin-1 and -2 have different activities. The
Drosophila knockout of Rhophilin-1 is embryonic lethal,
suggesting an essential role in embryonic development.
Roles of Rhophilin-2 may include limiting stress fiber
formation or increasing the turnover of F-actin in the
absence of high levels of RhoA signaling activity. The
isolated Bro1-like domain of Rhophilin-1 binds human
immunodeficiency virus type 1 (HIV-1) nucleocapsid. This
family lacks the V-shaped (V) domain found in many
members of the BRO1_Alix _like superfamily.
Length = 350
Score = 32.7 bits (75), Expect = 0.22
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 39 SHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQACRA-RGVD 84
+H A LL+ +R ++HL++++ + H+ AL + + CR R VD
Sbjct: 246 AHYYAAMGLLLEERRLLGKAHLKEAL-LLHEEALRLHRMCRFLRNVD 291
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms this
enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 31.9 bits (73), Expect = 0.47
Identities = 20/102 (19%), Positives = 35/102 (34%), Gaps = 16/102 (15%)
Query: 4 IHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQ- 62
+L H I V D R L +A + R A + + + L++
Sbjct: 14 APLLARHGDLEITVAD-RSLEKAQALAAPKLGLR----FIAIAVDADNY-EALVALLKEG 67
Query: 63 ------SVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAY 98
+ L V++AC GV + + +AQ+A
Sbjct: 68 DLVINLAPPFLS---LTVLKACIETGVHYVDTSYLREAQLAL 106
>gnl|CDD|119389 cd01427, HAD_like, Haloacid dehalogenase-like hydrolases. The
haloacid dehalogenase-like (HAD) superfamily includes
L-2-haloacid dehalogenase, epoxide hydrolase,
phosphoserine phosphatase, phosphomannomutase,
phosphoglycolate phosphatase, P-type ATPase, and many
others, all of which use a nucleophilic aspartate in
their phosphoryl transfer reaction. All members possess
a highly conserved alpha/beta core domain, and many also
possess a small cap domain, the fold and function of
which is variable. Members of this superfamily are
sometimes referred to as belonging to the DDDD
superfamily of phosphohydrolases.
Length = 139
Score = 30.4 bits (69), Expect = 0.57
Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 5/81 (6%)
Query: 71 ALNVIQACRARGVDCIVA----PFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYK 126
++ + +G+ +A E + L + Y D VIT + ++ K+ ++
Sbjct: 29 VKEALKELKEKGIKLALATNKSRREVLELLEELGLDDYFDPVITSN-GAAIYYPKEGLFL 87
Query: 127 LDLSGNCCFMDREKLPSALKM 147
+ + +KL +ALK+
Sbjct: 88 GGGPFDIGKPNPDKLLAALKL 108
>gnl|CDD|221234 pfam11805, DUF3326, Protein of unknown function (DUF3326). This
protein is functionally uncharacterized. It is about
300-500 amino acids in length. This family is found in
plants and bacteria.
Length = 339
Score = 31.5 bits (72), Expect = 0.58
Identities = 13/40 (32%), Positives = 16/40 (40%), Gaps = 10/40 (25%)
Query: 47 LLILDRGSEAQSHLRQSVDVTHKMALNVIQACRAR-GVDC 85
L+LD G E + R L V A RA G+D
Sbjct: 82 GLLLDAGIEPELRQR---------HLQVADAARATLGLDI 112
>gnl|CDD|237737 PRK14507, PRK14507, putative bifunctional
4-alpha-glucanotransferase/malto-oligosyltrehalose
synthase; Provisional.
Length = 1693
Score = 31.6 bits (72), Expect = 0.70
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 10/49 (20%)
Query: 21 RHLPAKEATEEDRRKKR----DSHKAKAAELLILDRGSEAQSHLRQSVD 65
RHLP ++ T+ +RR +R + K + AEL A L ++
Sbjct: 948 RHLPPRDETDPERRAERPRDKELLKRRLAEL------VAASPQLAAAIA 990
>gnl|CDD|187673 cd09813, 3b-HSD-NSDHL-like_SDR_e, human NSDHL (NAD(P)H steroid
dehydrogenase-like protein)-like, extended (e) SDRs.
This subgroup includes human NSDHL and related proteins.
These proteins have the characteristic active site
tetrad of extended SDRs, and also have a close match to
their NAD(P)-binding motif. Human NSDHL is a
3beta-hydroxysteroid dehydrogenase (3 beta-HSD) which
functions in the cholesterol biosynthetic pathway. 3
beta-HSD catalyzes the oxidative conversion of delta 5-3
beta-hydroxysteroids to the delta 4-3-keto
configuration; this activity is essential for the
biosynthesis of all classes of hormonal steroids.
Mutations in the gene encoding NSDHL cause CHILD
syndrome (congenital hemidysplasia with ichthyosiform
nevus and limb defects), an X-linked dominant,
male-lethal trait. This subgroup also includes an
unusual bifunctional [3beta-hydroxysteroid dehydrogenase
(3b-HSD)/C-4 decarboxylase from Arabidopsis thaliana,
and Saccharomyces cerevisiae ERG26, a 3b-HSD/C-4
decarboxylase, involved in the synthesis of ergosterol,
the major sterol of yeast. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase have
a GGXGXXG NAD(P)-binding motif and an altered active
site motif (YXXXN). Fungal type ketoacyl reductases have
a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 335
Score = 30.4 bits (69), Expect = 1.1
Identities = 24/97 (24%), Positives = 36/97 (37%), Gaps = 15/97 (15%)
Query: 4 IHMLLAHKIKVIMVFDGRHLPAKEATEEDR--------RKKRDSHKA---KAAELLILDR 52
+ LL + VFD R + + R +D KA K ++
Sbjct: 16 VEQLLRRGNPTVHVFDIRPTFELDPSSSGRVQFHTGDLTDPQDLEKAFNEKGPNVVFHTA 75
Query: 53 GSEAQSH--LRQSVDVTHKMALNVIQACRARGVDCIV 87
+ S+ L V+V NVI+ACR GV +V
Sbjct: 76 SPDHGSNDDLYYKVNVQGTR--NVIEACRKCGVKKLV 110
>gnl|CDD|238571 cd01166, KdgK, 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates
2-keto-3-deoxygluconate (KDG) to form
2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the
common intermediate product, that allows organisms to
channel D-glucuronate and/or D-galacturinate into the
glycolysis and therefore use polymers, like pectin and
xylan as carbon sources.
Length = 294
Score = 30.2 bits (69), Expect = 1.2
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 8/59 (13%)
Query: 71 ALNVIQACRARGV----DCIVAPF---EADAQMAYLNIAGYADYVI-TEDSDLLVFGAK 121
L ++A +ARGV D P +A+ A + Y D V+ +E+ + G +
Sbjct: 145 LLEALEAAKARGVTVSFDLNYRPKLWSAEEAREALEELLPYVDIVLPSEEEAEALLGDE 203
>gnl|CDD|224837 COG1926, COG1926, Predicted phosphoribosyltransferases [General
function prediction only].
Length = 220
Score = 30.0 bits (68), Expect = 1.5
Identities = 18/76 (23%), Positives = 29/76 (38%), Gaps = 11/76 (14%)
Query: 34 RKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQACRARGVDCIVAPFEAD 93
R R K ++++D G + T K A ++A RA+G IV
Sbjct: 114 RGGRPVPSLKGRTVILVDDGIATGA--------TMKAA---VRALRAKGPKEIVIAVPVA 162
Query: 94 AQMAYLNIAGYADYVI 109
+ A + AD V+
Sbjct: 163 PEDAAAELESEADEVV 178
>gnl|CDD|188624 cd09904, H3TH_XPG, H3TH domain of Xeroderma pigmentosum
complementation group G (XPG) nuclease, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease. 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. Members of this subgroup include the
H3TH (helix-3-turn-helix) domains of XPG and other
similar eukaryotic 5' nucleases. These nucleases contain
a PIN (PilT N terminus) domain with a helical arch/clamp
region/I domain (not included here) and inserted within
the PIN domain is an atypical helix-hairpin-helix-2
(HhH2)-like region. This atypical HhH2 region, the H3TH
domain, has an extended loop with at least three turns
between the first two helices, and only three of the
four helices appear to be conserved. Both the H3TH
domain and the helical arch/clamp region are involved in
DNA binding. Studies suggest that a glycine-rich loop
in the H3TH domain contacts the phosphate backbone of
the template strand in the downstream DNA duplex. These
nucleases have a carboxylate rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+ or Mn2+) required for nuclease activity.
The first metal binding site is composed entirely of
Asp/Glu residues from the PIN domain, whereas, the
second metal binding site is composed generally of two
Asp residues from the PIN domain and one Asp residue
from the H3TH domain. Together with the helical arch and
network of amino acids interacting with metal binding
ions, the H3TH region defines a positively charged
active-site DNA-binding groove in structure-specific 5'
nucleases.
Length = 97
Score = 28.0 bits (63), Expect = 2.4
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 162 ILSGCDYWTGIKGMG 176
+L G DY G+ G+G
Sbjct: 8 LLLGSDYTEGVSGIG 22
>gnl|CDD|177899 PLN02257, PLN02257, phosphoribosylamine--glycine ligase.
Length = 434
Score = 29.7 bits (67), Expect = 2.4
Identities = 29/96 (30%), Positives = 42/96 (43%), Gaps = 19/96 (19%)
Query: 64 VDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKI 123
+D++ A VI CR GV +V EA +AG AD ++ + + FG
Sbjct: 46 LDISDSAA--VISFCRKWGVGLVVVGPEAPL------VAGLADDLV--KAGIPTFGPSAE 95
Query: 124 IYKLDLSGNCCFM----DREKLPSALKMPLAKFTDA 155
L+ S N FM D+ K+P+A FTD
Sbjct: 96 AAALEGSKN--FMKDLCDKYKIPTA---KYETFTDP 126
>gnl|CDD|225101 COG2190, NagE, Phosphotransferase system IIA components
[Carbohydrate transport and metabolism].
Length = 156
Score = 28.7 bits (65), Expect = 2.8
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 4/26 (15%)
Query: 231 VYDPVSKEVVPLNPLESEMRDEVFSQ 256
+Y P+S EVVPL S++ D VFS+
Sbjct: 8 IYSPLSGEVVPL----SDVPDPVFSE 29
>gnl|CDD|107313 cd06318, PBP1_ABC_sugar_binding_like_9, Periplasmic sugar-binding
domain of uncharacterized ABC-type transport systems.
Periplasmic sugar-binding domain of uncharacterized
ABC-type transport systems that share homology with a
family of pentose/hexose sugar-binding proteins of the
type I periplasmic binding protein superfamily, which
consists of two domains connected by a three-stranded
hinge. The substrate specificity of this group is not
known, but it is predicted to be involved in the
transport of sugar-containing molecules and chemotaxis.
Length = 282
Score = 29.0 bits (65), Expect = 3.1
Identities = 14/49 (28%), Positives = 18/49 (36%), Gaps = 2/49 (4%)
Query: 70 MALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVIT--EDSDLL 116
MAL ++ G V AD Q L + Y T D DL+
Sbjct: 201 MALGAMRVLAEAGKTDDVKVAAADGQKEALALIKGGKYGATALNDPDLV 249
>gnl|CDD|233677 TIGR01995, PTS-II-ABC-beta, PTS system, beta-glucoside-specific
IIABC component. This model represents a family of PTS
enzyme II proteins in which all three domains are found
in the same polypeptide chain and which appear to have a
broad specificity for beta-glucosides including salicin
(beta-D-glucose-1-salicylate) and arbutin
(Hydroquinone-O-beta-D-glucopyranoside). These are
distinct from the closely related sucrose-specific and
trehalose-specific PTS transporters.
Length = 610
Score = 29.2 bits (66), Expect = 3.8
Identities = 13/28 (46%), Positives = 19/28 (67%), Gaps = 4/28 (14%)
Query: 229 QPVYDPVSKEVVPLNPLESEMRDEVFSQ 256
+ +Y PV+ E++PLN E+ DEVFS
Sbjct: 463 ESLYAPVAGEMLPLN----EVPDEVFSS 486
>gnl|CDD|129405 TIGR00305, TIGR00305, putative toxin-antitoxin system toxin
component, PIN family. This uncharacterized protein
family, part of the PIN domain superfamily, is
restricted to bacteria and archaea. A comprehensive in
silico study of toxin-antitoxin systems by Makarova, et
al. (2009) finds evidence this family represents the
toxin-like component of one class of type 2
toxin-antitoxin systems [Cellular processes, Other,
Transcription, Degradation of RNA].
Length = 114
Score = 27.8 bits (62), Expect = 3.8
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 91 EADAQMAYLNIAGYADYVITEDSDLLV 117
+ D + A A+ +IT D+DLLV
Sbjct: 87 KKDNKFLNTAYASKANALITGDTDLLV 113
>gnl|CDD|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional.
Length = 567
Score = 29.1 bits (65), Expect = 4.4
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 15/88 (17%)
Query: 16 MVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVI 75
M F+ R A+E E ++R+++ K K L+R +A+ + + A+
Sbjct: 1 MDFELRR--AREKLEREQRERKQRAKLK------LERERKAKEEAAKQRE-----AIEAA 47
Query: 76 QACRARGVDCIVAPFEADAQMAYLNIAG 103
Q R+R +D I A +AD QM AG
Sbjct: 48 Q--RSRRLDAIEAQIKADQQMQESLQAG 73
>gnl|CDD|200521 cd11260, Sema_4E, The Sema domain, a protein interacting module, of
semaphorin 4E (Sema4E). Sema4E is expressed in the
epithelial cells that line the pharyngeal arches in
zebrafish. It may act as a guidance molecule to restrict
the branchiomotor axons to the mesenchymal cells.
Gain-of-function and loss-of-function studies
demonstrate that Sema4E is essential for the guidance of
facial axons from the hindbrain into their pharyngeal
arch targets and is sufficient for guidance of gill
motor axons. Sema4E guides facial motor axons by a
repulsive action. Sema4E belongs to the class 4
transmembrane semaphorin family of proteins. Semaphorins
are regulatory molecules involved in the development of
the nervous system and in axonal guidance. They also
play important roles in other biological processes, such
as angiogenesis, immune regulation, respiration systems
and cancer. The Sema domain is located at the N-terminus
and contains four disulfide bonds formed by eight
conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 456
Score = 28.7 bits (64), Expect = 4.7
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 101 IAGYADYVITEDSDLLVFGAKKIIYKLDL 129
I Y+ ++ ED LLV GA++ ++ LDL
Sbjct: 6 IWNYSTMLLREDLGLLVLGAREAVFALDL 34
>gnl|CDD|217112 pfam02571, CbiJ, Precorrin-6x reductase CbiJ/CobK. This family
consists of Precorrin-6x reductase EC:1.3.1.54. This
enzyme catalyzes the reaction: precorrin-6Y + NADP(+)
<=> precorrin-6X + NADPH. CbiJ and CobK both catalyze
the reduction of macocycle in the colbalmin
biosynthesis pathway.
Length = 246
Score = 28.3 bits (64), Expect = 4.8
Identities = 8/27 (29%), Positives = 14/27 (51%), Gaps = 4/27 (14%)
Query: 64 VDVTH----KMALNVIQACRARGVDCI 86
+D TH +++ N AC+ GV +
Sbjct: 69 IDATHPFAAQISRNAAAACKELGVPLL 95
>gnl|CDD|236711 PRK10537, PRK10537, voltage-gated potassium channel; Provisional.
Length = 393
Score = 28.4 bits (64), Expect = 5.0
Identities = 18/68 (26%), Positives = 24/68 (35%), Gaps = 11/68 (16%)
Query: 70 MALNVIQACRARG--VDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVF---GAKKII 124
+A+N R RG V IV + AD + + SD V GA +
Sbjct: 251 LAINTYLGLRQRGQAVTVIVPLGLEH------RLPDDADLIPGDSSDSAVLKKAGAARAR 304
Query: 125 YKLDLSGN 132
L L N
Sbjct: 305 AILALRDN 312
>gnl|CDD|221386 pfam12029, DUF3516, Domain of unknown function (DUF3516). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria. This domain is typically
between 460 to 473 amino acids in length. This domain
is found associated with pfam00270, pfam00271.
Length = 462
Score = 28.8 bits (65), Expect = 5.1
Identities = 22/71 (30%), Positives = 29/71 (40%), Gaps = 13/71 (18%)
Query: 25 AKEATEEDRRKKRDSHKAKAAELLI------LDRGSEAQSH-LRQSVDVTHKMALNVIQA 77
AK +D +K R + K E + +R EA+ L V+H M LNVI
Sbjct: 13 AKAG--DDPKKLRKVVRKKPPEGFVSWSESTFERLVEAEPEPLTSRFRVSHSMLLNVI-- 68
Query: 78 CRARGVDCIVA 88
AR D A
Sbjct: 69 --ARPGDAFAA 77
>gnl|CDD|235265 PRK04250, PRK04250, dihydroorotase; Provisional.
Length = 398
Score = 28.6 bits (64), Expect = 5.4
Identities = 10/36 (27%), Positives = 18/36 (50%)
Query: 171 GIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIG 206
GIK G+++ F++ D E ++ +Y K G
Sbjct: 325 GIKNYGIEEGNYANFAVFDMKKEWTIKAEELYTKAG 360
>gnl|CDD|202623 pfam03414, Glyco_transf_6, Glycosyltransferase family 6.
Length = 289
Score = 28.2 bits (63), Expect = 6.3
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 6/48 (12%)
Query: 205 IGSYVKITKEFLTSFHNTNLMFLYQPVY-----DPVSKEVVPLNPLES 247
+G Y++ + FL S M ++ +Y DP VPL P S
Sbjct: 60 VGKYIEFLELFLES-AEKYFMVGHRVIYYIFTDDPARVPRVPLGPGRS 106
>gnl|CDD|204975 pfam12598, TBX, T-box transcription factor. This domain family is
found in eukaryotes, and is typically between 77 and 89
amino acids in length. The family is found in
association with pfam00907. There are two completely
conserved residues (S and P) that may be functionally
important. T-box genes encode transcription factors
involved in morphogenesis and organogenesis of
vertebrates and invertebrates.
Length = 91
Score = 26.7 bits (59), Expect = 7.1
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 306 YEKPC----DRHSSEESVSEPPVFQKLKPVASSPL 336
YE+ C D +S+ S SE + SSP
Sbjct: 3 YEEQCKPDKDGGTSDASSSEQAAGRCFDQ-PSSPA 36
>gnl|CDD|239200 cd02801, DUS_like_FMN, Dihydrouridine synthase-like (DUS-like)
FMN-binding domain. Members of this family catalyze the
reduction of the 5,6-double bond of a uridine residue on
tRNA. Dihydrouridine modification of tRNA is widely
observed in prokaryotes and eukaryotes, and also in some
archaea. Most dihydrouridines are found in the D loop of
t-RNAs. The role of dihydrouridine in tRNA is currently
unknown, but may increase conformational flexibility of
the tRNA. It is likely that different family members
have different substrate specificities, which may
overlap. 1VHN, a putative flavin oxidoreductase, has
high sequence similarity to DUS. The enzymatic
mechanism of 1VHN is not known at the present.
Length = 231
Score = 27.8 bits (63), Expect = 7.8
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 148 PLAKFTDAKFRYMCILSGCD-YWT 170
P+ TD FR +C G D +T
Sbjct: 6 PMVGVTDLPFRLLCRRYGADLVYT 29
>gnl|CDD|107309 cd06314, PBP1_tmGBP, Periplasmic sugar-binding domain of Thermotoga
maritima glucose-binding protein (tmGBP) and its close
homologs. Periplasmic sugar-binding domain of
Thermotoga maritima glucose-binding protein (tmGBP) and
its close homologs from other bacteria. They are a
member of the type I periplasmic binding protein
superfamily which consists of two domains connected by a
three-stranded hinge. TmGBP is specific for glucose and
its binding pocket is buried at the interface of the two
domains. TmGBP also exhibits high thermostability and
the highest structural similarity to E. coli glucose
binding protein (ecGBP).
Length = 271
Score = 27.4 bits (61), Expect = 9.4
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 80 ARGVDCI-VAPFEADAQMAYLNIAGYADYVITEDSD 114
A GVD I ++P + A + LN A +IT DSD
Sbjct: 53 AEGVDGIAISPIDPKAVIPALNKAAAGIKLITTDSD 88
>gnl|CDD|173241 PRK14780, PRK14780, lipoprotein signal peptidase; Provisional.
Length = 263
Score = 27.6 bits (61), Expect = 9.5
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 177 LKKAKDYVFSIMDPDFENALRKINVYGKI 205
+KK K+ F I+ F N+LRKIN + KI
Sbjct: 2 IKKIKNSNFYIIIKKFNNSLRKINFFSKI 30
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
0.319 0.135 0.398
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: 17,152,437
Number of extensions: 1651714
Number of successful extensions: 1572
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1550
Number of HSP's successfully gapped: 69
Length of query: 336
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 239
Effective length of database: 6,635,264
Effective search space: 1585828096
Effective search space used: 1585828096
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: 59 (26.4 bits)