RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11828
(443 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 = 84.1 bits (209), Expect = 1e-18
Identities = 33/57 (57%), Positives = 42/57 (73%), Gaps = 1/57 (1%)
Query: 21 YVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSG 77
YV YCMK +NMLL + IK I+VFDG LP+K+ TEE+RR+R E + +KA ELL G
Sbjct: 55 YVQYCMKRVNMLLHYGIKPILVFDGGPLPSKKGTEEERRERRE-ENLEKALELLREG 110
Score = 70.6 bits (174), Expect = 4e-14
Identities = 22/48 (45%), Positives = 30/48 (62%)
Query: 198 NIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALKM 245
GY D VITEDSDLL +G K+++KLD +G+C +D L K+
Sbjct: 159 AKTGYVDAVITEDSDLLAYGCPKVLFKLDKNGSCQEIDLADLLKCRKL 206
Score = 29.0 bits (66), Expect = 3.6
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 78 SSIIYKLDLSGNCCFMDREKLPSALKM 104
+++KLD +G+C +D L K+
Sbjct: 180 PKVLFKLDKNGSCQEIDLADLLKCRKL 206
>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 = 57.2 bits (139), Expect = 1e-10
Identities = 22/49 (44%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 113 KFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGK 161
KFR+MCILSGCDY + G+GLKKA Y E ++ + GK
Sbjct: 2 KFRHMCILSGCDYLPSLPGIGLKKA--YKLVRRHRTIEKVIKALRFDGK 48
Score = 54.5 bits (132), Expect = 9e-10
Identities = 18/25 (72%), Positives = 21/25 (84%)
Query: 254 KFRYMCILSGCDYWTGIKGMGLKKA 278
KFR+MCILSGCDY + G+GLKKA
Sbjct: 2 KFRHMCILSGCDYLPSLPGIGLKKA 26
>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 = 53.3 bits (129), Expect = 2e-09
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 113 KFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKI 162
+F +CILSGCDY I G+G K A + E L+ + K
Sbjct: 2 QFIDLCILSGCDYLPSIPGIGPKTAYKLIKKHKSI--EKVLKALRSNKKK 49
Score = 51.8 bits (125), Expect = 9e-09
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 254 KFRYMCILSGCDYWTGIKGMGLKKA 278
+F +CILSGCDY I G+G K A
Sbjct: 2 QFIDLCILSGCDYLPSIPGIGPKTA 26
>gnl|CDD|214689 smart00484, XPGI, Xeroderma pigmentosum G I-region. domain in
nucleases.
Length = 73
Score = 52.6 bits (127), Expect = 4e-09
Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 200 AGYADYVITEDSDLLVFGAKKIIYKLDLSGN----CCFMDREKLPSALKM 245
+G D +ITEDSDLL+FGA ++ L SG +D E + L +
Sbjct: 24 SGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVLKELGL 73
>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of
PolI) [DNA replication, recombination, and repair].
Length = 310
Score = 54.6 bits (132), Expect = 3e-08
Identities = 22/98 (22%), Positives = 39/98 (39%), Gaps = 9/98 (9%)
Query: 200 AGYADYVITEDSDLLVFGAKKI-IYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYM 258
G +I+ D DLL + + + F+D E++ K T + +
Sbjct: 134 KGDVVLIISGDKDLLQLVSPNVLVINGKKGEPEKFLDLEEVEEKFK----GLTPEQLIDL 189
Query: 259 CILSG--CDYWTGIKGMGLKKAKDYV--FSIMDPDFEN 292
L G D G+KG+G K A + + ++ +EN
Sbjct: 190 KALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYEN 227
Score = 36.5 bits (85), Expect = 0.021
Identities = 11/54 (20%), Positives = 21/54 (38%), Gaps = 4/54 (7%)
Query: 112 AKFRYMCILSG--CDYWTGIKGMGLKKAKDYV--FSIMDPDFENALRKINVYGK 161
+ + L G D G+KG+G K A + + ++ +EN +
Sbjct: 184 EQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIKKKTRE 237
>gnl|CDD|214690 smart00485, XPGN, Xeroderma pigmentosum G N-region. domain in
nucleases.
Length = 99
Score = 49.2 bits (118), Expect = 1e-07
Identities = 16/46 (34%), Positives = 20/46 (43%)
Query: 16 LLQHLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKR 61
L ++ LL IK I VFDG+ P K T RR+R
Sbjct: 50 LPNSKHLMGLFYRTCRLLEFGIKPIFVFDGKPPPLKSETLAKRRER 95
>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 = 45.7 bits (109), Expect = 9e-07
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 113 KFRYMCILSGCDYWTGIKGMGLKKA 137
+F +CILSGCDY G+ G+G K A
Sbjct: 2 QFIDLCILSGCDYLPGLPGIGPKTA 26
Score = 45.7 bits (109), Expect = 9e-07
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 254 KFRYMCILSGCDYWTGIKGMGLKKA 278
+F +CILSGCDY G+ G+G K A
Sbjct: 2 QFIDLCILSGCDYLPGLPGIGPKTA 26
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
Length = 393
Score = 49.6 bits (119), Expect = 2e-06
Identities = 29/92 (31%), Positives = 39/92 (42%), Gaps = 27/92 (29%)
Query: 200 AGYADYVITEDSDLLVFGA-------------KKIIYKLDLSGNCCFMDREKLPSALKMP 246
G V TED D L FG K+ I +++LS + L +
Sbjct: 171 KGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLS---------TVLEELGLS 221
Query: 247 LAKFTDAKFRYMCILSGCDYWTGIKGMGLKKA 278
+ +F D +CIL GCDY IKG+G K A
Sbjct: 222 MDQFID-----LCILCGCDYCDTIKGIGPKTA 248
Score = 37.7 bits (88), Expect = 0.011
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 93 MDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKA 137
++ + L + + +F D +CIL GCDY IKG+G K A
Sbjct: 209 INLSTVLEELGLSMDQFID-----LCILCGCDYCDTIKGIGPKTA 248
Score = 28.4 bits (64), Expect = 7.4
Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 31 MLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELL 74
LL IK + VFDG+ K E RR+R E +A E L
Sbjct: 75 RLLEAGIKPVYVFDGKPPELKSGELEKRRERRE-----EAEEEL 113
>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 = 46.2 bits (110), Expect = 1e-05
Identities = 24/85 (28%), Positives = 36/85 (42%), Gaps = 18/85 (21%)
Query: 145 MDPDFENALRKINVYGKIGSY--VKITKEFLTSGAPQPFG-----ARNEGRSLLSAVTER 197
P F+ R V K + +K+ KE L FG A E + + +
Sbjct: 92 NRPSFK---RGKRVGLKKKEHWLIKLVKELLDL-----FGIPYHTAPGEAEAECARL--- 140
Query: 198 NIAGYADYVITEDSDLLVFGAKKII 222
G D V++ DSD L+FGA ++I
Sbjct: 141 QRLGIVDAVLSNDSDALMFGATRVI 165
>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 = 44.9 bits (107), Expect = 5e-05
Identities = 32/117 (27%), Positives = 51/117 (43%), Gaps = 22/117 (18%)
Query: 201 GYADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALK--------MPLAKF-- 250
G DYV ++D D L+FGA +++ L +SG + KLP + L +
Sbjct: 164 GDVDYVGSQDYDSLLFGAPRLVRNLTISG------KRKLPGKNIYVEVKPELIELEEVLS 217
Query: 251 ----TDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPD--FENRKEYVKYAK 301
T + + IL G DY G+KG+G K A + D + + R E ++
Sbjct: 218 ELGITREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEHGDLEKVLKARGEDIENYD 274
Score = 36.1 bits (84), Expect = 0.027
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 27 KYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSG 77
+ IN LL + IK + VFDG+ K T E+RR+ E ++K E L G
Sbjct: 64 RTIN-LLENGIKPVYVFDGKPPELKAETLEERREIRE-EAEEKWEEALEKG 112
Score = 31.5 bits (72), Expect = 0.76
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 116 YMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFL 173
+ IL G DY G+KG+G K A + D E L+ I +Y +I + FL
Sbjct: 228 DIAILVGTDYNEGVKGIGPKTALKLIKE--HGDLEKVLKARGED--IENYDEIREFFL 281
>gnl|CDD|216163 pfam00867, XPG_I, XPG I-region.
Length = 46
Score = 39.7 bits (94), Expect = 6e-05
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 198 NIAGYADYVITEDSDLLVFGAK 219
G D VI+EDSDLL+FGA
Sbjct: 22 VKTGLVDAVISEDSDLLLFGAP 43
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 44.0 bits (105), Expect = 8e-05
Identities = 33/118 (27%), Positives = 48/118 (40%), Gaps = 29/118 (24%)
Query: 201 GYADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALK--------MPLAKFTD 252
G A V ++D D L+FGA +++ L +SG + KLP + L +
Sbjct: 117 GDAWAVGSQDYDSLLFGAPRLVRNLTISG------KRKLPGKNVYVEVKPELIELEEVLK 170
Query: 253 A------KFRYMCILSGCDYWTGIKGMGLKKA----KDY-----VFSIMDPDFENRKE 295
+ + IL G DY GIKG+G K A K + V + EN E
Sbjct: 171 ELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEERGFEIENYDE 228
Score = 36.3 bits (85), Expect = 0.022
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 6/46 (13%)
Query: 27 KYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAE 72
+ IN LL + IK + VFDG+ K E+RR+ +++A E
Sbjct: 17 RTIN-LLENGIKPVYVFDGKPPELKAEEIEERRE-----VREEAEE 56
Score = 30.6 bits (70), Expect = 1.5
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 119 ILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFL 173
IL G DY GIKG+G K A + D E L + +I +Y +I + FL
Sbjct: 184 ILVGTDYNPGIKGIGPKTALKLIKK--HGDLEKVLEERGF--EIENYDEIREFFL 234
>gnl|CDD|197623 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol1 family) motifs.
Length = 36
Score = 36.7 bits (86), Expect = 8e-04
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 113 KFRYMCILSG--CDYWTGIKGMGLKKAKDYV 141
+F IL G D G+KG+G K A +
Sbjct: 3 QFIDYAILVGDYSDNIPGVKGIGPKTALKLL 33
Score = 36.7 bits (86), Expect = 8e-04
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 254 KFRYMCILSG--CDYWTGIKGMGLKKAKDYV 282
+F IL G D G+KG+G K A +
Sbjct: 3 QFIDYAILVGDYSDNIPGVKGIGPKTALKLL 33
>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 = 36.0 bits (84), Expect = 0.003
Identities = 13/20 (65%), Positives = 14/20 (70%)
Query: 118 CILSGCDYWTGIKGMGLKKA 137
CIL GCDY IKG+G K A
Sbjct: 7 CILLGCDYCESIKGIGPKTA 26
Score = 36.0 bits (84), Expect = 0.003
Identities = 13/20 (65%), Positives = 14/20 (70%)
Query: 259 CILSGCDYWTGIKGMGLKKA 278
CIL GCDY IKG+G K A
Sbjct: 7 CILLGCDYCESIKGIGPKTA 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 = 35.0 bits (81), Expect = 0.005
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 112 AKFRYMCILSGCDY--WTGIKGMGLKKA 137
+F +C L GCDY G+ G+G K A
Sbjct: 1 EQFIDLCALVGCDYSDNPGVPGIGPKTA 28
Score = 35.0 bits (81), Expect = 0.005
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 253 AKFRYMCILSGCDY--WTGIKGMGLKKA 278
+F +C L GCDY G+ G+G K A
Sbjct: 1 EQFIDLCALVGCDYSDNPGVPGIGPKTA 28
>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 = 34.4 bits (80), Expect = 0.006
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 117 MCILSGCDYWTGIKGMGLKKA 137
+ +L G DY G+ G+G K A
Sbjct: 6 LALLLGTDYNPGVPGIGPKTA 26
Score = 34.4 bits (80), Expect = 0.006
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 258 MCILSGCDYWTGIKGMGLKKA 278
+ +L G DY G+ G+G K A
Sbjct: 6 LALLLGTDYNPGVPGIGPKTA 26
>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 = 37.5 bits (87), Expect = 0.008
Identities = 13/51 (25%), Positives = 16/51 (31%), Gaps = 3/51 (5%)
Query: 21 YVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDR---RKRAEIRHKQ 68
+ L + I I VFDG K R R AEI +
Sbjct: 52 SLKGYFYRTIKLFENGITPIFVFDGGPPYLKSEASGKRTEARAEAEISSTE 102
Score = 31.4 bits (71), Expect = 0.74
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 200 AGYADYVITEDSDLLVFGAKKIIYKLDLS 228
+G+ ITED+D L++G + I +
Sbjct: 158 SGHVIAAITEDTDCLMYGVPRFIRGMTFP 186
>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 = 36.8 bits (86), Expect = 0.012
Identities = 20/49 (40%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 29 INMLLAHKIKVIMVFDGRHLPAKEATEEDRRKR---AEIRHKQKAAELL 74
I LL + IK + VFDG K T RR++ AEI K+ A +LL
Sbjct: 62 ICKLLFYGIKPVFVFDGGAPELKRRTLAKRRQQREKAEINAKKTAEKLL 110
Score = 33.7 bits (78), Expect = 0.12
Identities = 15/27 (55%), Positives = 20/27 (74%), Gaps = 1/27 (3%)
Query: 198 NIAGYADYVITEDSDLLVFGAKKIIYK 224
N G D VIT+DSD+ +FGAK+ +YK
Sbjct: 167 NQLGLVDGVITDDSDVFLFGAKR-VYK 192
>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 = 33.6 bits (78), Expect = 0.15
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 27 KYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRK-RAEIRHKQKAAE 72
+ I +L + IK + VFDG+ K E RR+ R E K + A+
Sbjct: 65 RTIRLL-ENGIKPVYVFDGKPPELKSGELEKRRERREEAEEKLEEAK 110
Score = 32.1 bits (74), Expect = 0.48
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 200 AGYADYVITEDSDLLVFGAKKIIYKLDLSG 229
G V ++D D L+FGA +++ L +SG
Sbjct: 164 KGDVYAVASQDYDSLLFGAPRLVRNLTISG 193
>gnl|CDD|187554 cd05243, SDR_a5, atypical (a) SDRs, subgroup 5. This subgroup
contains atypical SDRs, some of which are identified as
putative NAD(P)-dependent epimerases, one as a putative
NAD-dependent epimerase/dehydratase. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
have a glycine-rich NAD(P)-binding motif that is very
similar to the extended SDRs, GXXGXXG, and binds NADP.
Generally, this subgroup has poor conservation of the
active site tetrad; however, individual sequences do
contain matches to the YXXXK active site motif, the
upstream Ser, and there is a highly conserved Asp in
place of the usual active site Asn throughout the
subgroup. 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. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. 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. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase 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 = 203
Score = 31.4 bits (72), Expect = 0.58
Identities = 10/38 (26%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 45 GRHLPAKEATEEDRRKRAEIRHKQKAAELLHSGSSIIY 82
GRH+ +E + + RA +R +A +L +G+ ++
Sbjct: 12 GRHV-VRELLDRGYQVRALVRDPSQAEKLEAAGAEVVV 48
>gnl|CDD|216098 pfam00752, XPG_N, XPG N-terminal domain.
Length = 100
Score = 29.6 bits (67), Expect = 0.83
Identities = 15/47 (31%), Positives = 17/47 (36%), Gaps = 5/47 (10%)
Query: 15 KLLQHLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKR 61
L + C L IK I VFDG P K T + R R
Sbjct: 55 SHLMGFFSRLCR-----LKDFGIKPIFVFDGGPPPLKAETLQKRSAR 96
>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 = 31.0 bits (70), Expect = 1.2
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 196 ERNIAGYADYVITEDSDLLVFGAKKIIYKLDL 227
E+ I Y+ ++ ED LLV GA++ ++ LDL
Sbjct: 3 EQGIWNYSTMLLREDLGLLVLGAREAVFALDL 34
>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 = 30.2 bits (68), Expect = 1.6
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 198 NIAGYADYVITEDSDLLVFGAKKII 222
++G D +++ DSD L+FGA+K+
Sbjct: 126 QVSGAVDGILSNDSDTLLFGAEKVY 150
>gnl|CDD|130253 TIGR01185, devC, DevC protein. This model describes a predicted
membrane subunit, DevC, of an ABC transporter known so
far from two species of cyanobacteria. Some experimental
data from mutational analysis suggest that this protein
along with DevA and DevB encoded in the same operon may
be involved in the transport/export of glycolipids
[Transport and binding proteins, Other].
Length = 380
Score = 29.9 bits (67), Expect = 2.9
Identities = 29/112 (25%), Positives = 45/112 (40%), Gaps = 9/112 (8%)
Query: 141 VFSIMDPDFENALRKINVY---GKIGSYVKITKEFLTSGAPQPFGARNEGRSLLSAVTER 197
+ M F +AL NV G V + K+ A +PF R +SL +
Sbjct: 27 ILMFMQIGFRDALYYSNVRLHTSLQGDIVLLNKQSNAVLAMKPFSQRRLYKSLELPSVQS 86
Query: 198 NIAGYADYVITEDSD------LLVFGAKKIIYKLDLSGNCCFMDREKLPSAL 243
Y DY I ++ +LVFG ++L+G +D+ KLP +
Sbjct: 87 VHPIYLDYSIWKNPYTGLTRSILVFGINPETNIINLAGVQENLDKLKLPDVV 138
>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 = 2.9
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 119 ILSGCDYWTGIKGMG 133
+L G DY G+ G+G
Sbjct: 8 LLLGSDYTEGVSGIG 22
Score = 28.0 bits (63), Expect = 2.9
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 260 ILSGCDYWTGIKGMG 274
+L G DY G+ G+G
Sbjct: 8 LLLGSDYTEGVSGIG 22
>gnl|CDD|182978 PRK11122, artM, arginine transporter permease subunit ArtM;
Provisional.
Length = 222
Score = 29.2 bits (66), Expect = 3.7
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 187 GRSLLSAVTERNIAGYADYVITEDSDLLVFGAKKIIY 223
SL +T ++ GY+ + D++VFGA IIY
Sbjct: 161 STSLAYTITLMDVMGYSQLLYGRTYDVMVFGAAGIIY 197
>gnl|CDD|237737 PRK14507, PRK14507, putative bifunctional
4-alpha-glucanotransferase/malto-oligosyltrehalose
synthase; Provisional.
Length = 1693
Score = 29.3 bits (66), Expect = 5.1
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 46 RHLPAKEATEEDRRK---RAEIRHKQKAAEL 73
RHLP ++ T+ +RR R + K++ AEL
Sbjct: 948 RHLPPRDETDPERRAERPRDKELLKRRLAEL 978
>gnl|CDD|239125 cd02660, Peptidase_C19D, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 328
Score = 28.9 bits (65), Expect = 5.1
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 6/38 (15%)
Query: 167 KITKEFLTSGAPQPFGARNEGRSLLSAV--TERNIAGY 202
+I +EF SG P+G N LL RN+AGY
Sbjct: 53 EIFQEFYYSGDRSPYGPIN----LLYLSWKHSRNLAGY 86
>gnl|CDD|235265 PRK04250, PRK04250, dihydroorotase; Provisional.
Length = 398
Score = 28.6 bits (64), Expect = 8.3
Identities = 10/36 (27%), Positives = 18/36 (50%)
Query: 128 GIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIG 163
GIK G+++ F++ D E ++ +Y K G
Sbjct: 325 GIKNYGIEEGNYANFAVFDMKKEWTIKAEELYTKAG 360
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
0.326 0.140 0.435
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: 23,332,750
Number of extensions: 2332048
Number of successful extensions: 2478
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2469
Number of HSP's successfully gapped: 63
Length of query: 443
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 343
Effective length of database: 6,502,202
Effective search space: 2230255286
Effective search space used: 2230255286
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 61 (27.2 bits)