RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1206
(531 letters)
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
Length = 393
Score = 262 bits (672), Expect = 8e-83
Identities = 93/143 (65%), Positives = 117/143 (81%)
Query: 60 KAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVL 119
+APCEAEAQCA +VK GKVYA ATEDMDALTFG+ +LLR++ FSEA+K P+QE +L VL
Sbjct: 156 EAPCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVL 215
Query: 120 EGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEG 179
E + LS ++FIDLCIL GCDYCD+I+GIGPK A +LIK+++SIE+ILE++D KY VPE
Sbjct: 216 EELGLSMDQFIDLCILCGCDYCDTIKGIGPKTAYKLIKKYKSIEEILEHLDKTKYPVPEN 275
Query: 180 WLYKEARELFRHPEVADPETIEF 202
+ YKEARELF +PEV E I+
Sbjct: 276 FDYKEARELFLNPEVTPAEEIDL 298
Score = 159 bits (403), Expect = 1e-43
Identities = 63/115 (54%), Positives = 82/115 (71%), Gaps = 11/115 (9%)
Query: 303 IELVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSV---DGEPTSH 352
+ +AD AP++I+E R I IDASM+LYQFLIA+R +Q ++ GE TSH
Sbjct: 7 SKFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIRD-DSQGGNLTNEAGEVTSH 65
Query: 353 LMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQG 407
+ G F RTIRL+E G+KP+YVFDGKPP LKSGEL KR E+RE+A++ L KA E+G
Sbjct: 66 ISGLFNRTIRLLEAGIKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEG 120
Score = 137 bits (348), Expect = 5e-36
Identities = 48/74 (64%), Positives = 61/74 (82%)
Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAREL 291
FIDLCIL GCDYCD+I+GIGPK A +LIK+++SIE+ILE++D KY VPE + YKEAREL
Sbjct: 225 FIDLCILCGCDYCDTIKGIGPKTAYKLIKKYKSIEEILEHLDKTKYPVPENFDYKEAREL 284
Query: 292 FRHPEIADPETIEL 305
F +PE+ E I+L
Sbjct: 285 FLNPEVTPAEEIDL 298
Score = 87.8 bits (218), Expect = 1e-18
Identities = 30/63 (47%), Positives = 45/63 (71%)
Query: 405 EQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRREEK 464
E+ LKW++PDE+GL K+L +KNF E+R+ ++L KA++ TQ RLDSFFT ++
Sbjct: 294 EEIDLKWNEPDEEGLKKFLVKEKNFNEERVEKYIERLKKAKTKKTQTRLDSFFTATKKPI 353
Query: 465 RKS 467
+KS
Sbjct: 354 KKS 356
Score = 85.1 bits (211), Expect = 9e-18
Identities = 29/64 (45%), Positives = 46/64 (71%)
Query: 3 LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFFTIRREEKRKAP 62
LKW++PDE+GL K+L +KNF E+R+ ++L KA++ TQ RLDSFFT ++ +K+
Sbjct: 298 LKWNEPDEEGLKKFLVKEKNFNEERVEKYIERLKKAKTKKTQTRLDSFFTATKKPIKKSN 357
Query: 63 CEAE 66
+A+
Sbjct: 358 SKAK 361
>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 = 167 bits (425), Expect = 4e-48
Identities = 73/147 (49%), Positives = 91/147 (61%), Gaps = 17/147 (11%)
Query: 304 ELVADVAPSSIR----ESRKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTSHLMGTFY 358
+L+AD A I RKI IDAS +LYQFLIA+R G L + GE TSHL G FY
Sbjct: 5 KLIADGAIKEIELKDLFGRKIAIDASNALYQFLIAIRQPDGTPLTNSAGEVTSHLSGLFY 64
Query: 359 RTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDG 418
RTIRL+E+G+KP+YVFDGKPP LKSGEL KR E+RE+A++ L +A+E+G D +
Sbjct: 65 RTIRLLENGIKPVYVFDGKPPELKSGELEKRRERREEAEEKLEEAKEEG-------DAEE 117
Query: 419 LVKYLCGDK--NFAEDRIRNGAKKLLK 443
KY K I KKLL+
Sbjct: 118 ARKY---AKRTVRVTKEIVEECKKLLR 141
Score = 125 bits (316), Expect = 1e-32
Identities = 36/65 (55%), Positives = 48/65 (73%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
AP EAEAQCA +VK G VYA A++D D+L FG+ L+R++T S +K+P +E LEKVLE
Sbjct: 150 APSEAEAQCAYLVKKGDVYAVASQDYDSLLFGAPRLVRNLTISGKKKVPPEEIELEKVLE 209
Query: 121 GMELS 125
+EL
Sbjct: 210 ELELK 214
Score = 87.9 bits (219), Expect = 2e-19
Identities = 30/58 (51%), Positives = 44/58 (75%)
Query: 400 LAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFF 457
L K E+ +LKW +PDE+GL+K+L + +F+EDR+R ++L KA+ +TQGRLDSFF
Sbjct: 204 LEKVLEELELKWKEPDEEGLIKFLVEEHDFSEDRVRKAIERLKKAKKKSTQGRLDSFF 261
Score = 87.2 bits (217), Expect = 3e-19
Identities = 27/51 (52%), Positives = 40/51 (78%)
Query: 1 MTLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFF 51
+ LKW +PDE+GL+K+L + +F+EDR+R ++L KA+ +TQGRLDSFF
Sbjct: 211 LELKWKEPDEEGLIKFLVEEHDFSEDRVRKAIERLKKAKKKSTQGRLDSFF 261
>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 = 144 bits (366), Expect = 4e-42
Identities = 54/70 (77%), Positives = 62/70 (88%)
Query: 127 EEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAR 186
E+FIDLCILLGCDYC+SI+GIGPK A++LIK+H+SIEKILENID KY VPE W YKEAR
Sbjct: 1 EQFIDLCILLGCDYCESIKGIGPKTALKLIKKHKSIEKILENIDKSKYPVPEDWPYKEAR 60
Query: 187 ELFRHPEVAD 196
ELF +PEV D
Sbjct: 61 ELFLNPEVTD 70
Score = 139 bits (354), Expect = 2e-40
Identities = 52/68 (76%), Positives = 60/68 (88%)
Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAREL 291
FIDLCILLGCDYC+SI+GIGPK A++LIK+H+SIEKILENID KY VPE W YKEAREL
Sbjct: 3 FIDLCILLGCDYCESIKGIGPKTALKLIKKHKSIEKILENIDKSKYPVPEDWPYKEAREL 62
Query: 292 FRHPEIAD 299
F +PE+ D
Sbjct: 63 FLNPEVTD 70
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 146 bits (370), Expect = 7e-40
Identities = 60/151 (39%), Positives = 88/151 (58%), Gaps = 15/151 (9%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFH------ 114
AP E EAQ A M K G +A ++D D+L FG+ L+R++T S RKLP + +
Sbjct: 102 APSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVEVKPE 161
Query: 115 ---LEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 171
LE+VL+ + ++ E+ ID+ IL+G DY I+GIGPK A++LIK+H +EK+LE
Sbjct: 162 LIELEEVLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEERG- 220
Query: 172 KKYTVPEGWLYKEARELFRHPEVADPETIEF 202
E Y E RE F +P V D +++
Sbjct: 221 -----FEIENYDEIREFFLNPPVTDDYELKW 246
Score = 99.5 bits (249), Expect = 3e-23
Identities = 45/104 (43%), Positives = 62/104 (59%), Gaps = 12/104 (11%)
Query: 343 MSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAK 402
M G TSHL G FYRTI L+E+G+KP+YVFDGKPP LK+ E+ +R E RE+A++ +
Sbjct: 1 MDSKGRITSHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEE 60
Query: 403 AQEQGKLKWSDPDEDGLVKYLCGDK--NFAEDRIRNGAKKLLKA 444
A+E+G D + KY + + D I +KKLL
Sbjct: 61 AKEEG-------DLEEARKY---AQRSSRLTDEIVEDSKKLLDL 94
Score = 73.7 bits (182), Expect = 1e-14
Identities = 30/73 (41%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 233 IDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELF 292
ID+ IL+G DY I+GIGPK A++LIK+H +EK+LE E Y E RE F
Sbjct: 180 IDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEERG------FEIENYDEIREFF 233
Query: 293 RHPEIADPETIEL 305
+P + D ++
Sbjct: 234 LNPPVTDDYELKW 246
Score = 65.2 bits (160), Expect = 1e-11
Identities = 18/50 (36%), Positives = 35/50 (70%)
Query: 408 KLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFF 457
+LKW +PD++G++++L + +F+E+R++ ++L KA Q LDS+F
Sbjct: 243 ELKWKEPDKEGIIEFLVEEHDFSEERVKKALERLEKAVKEKKQTTLDSWF 292
Score = 65.2 bits (160), Expect = 1e-11
Identities = 18/50 (36%), Positives = 34/50 (68%)
Query: 2 TLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFF 51
LKW +PD++G++++L + +F+E+R++ ++L KA Q LDS+F
Sbjct: 243 ELKWKEPDKEGIIEFLVEEHDFSEERVKKALERLEKAVKEKKQTTLDSWF 292
>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 = 139 bits (352), Expect = 5e-37
Identities = 58/152 (38%), Positives = 88/152 (57%), Gaps = 15/152 (9%)
Query: 60 KAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFH----- 114
+AP E EAQ A M K G V ++D D+L FG+ L+R++T S RKLP + +
Sbjct: 148 QAPSEGEAQAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVKP 207
Query: 115 ----LEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENID 170
LE+VL + ++ E+ ID+ IL+G DY + ++GIGPK A++LIKEH +EK+L
Sbjct: 208 ELIELEEVLSELGITREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEHGDLEKVL---K 264
Query: 171 TKKYTVPEGWLYKEARELFRHPEVADPETIEF 202
+ + Y E RE F +P V D +++
Sbjct: 265 ARGEDIEN---YDEIREFFLNPPVTDDYELKW 293
Score = 122 bits (308), Expect = 7e-31
Identities = 59/152 (38%), Positives = 83/152 (54%), Gaps = 20/152 (13%)
Query: 296 EIADPETIELVADVAPSSIRESRKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTSHLM 354
++ E IEL D+ + + +DA +LYQFL ++R G LM G TSHL
Sbjct: 7 DLLAKEEIEL-EDL------SGKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLS 59
Query: 355 GTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDP 414
G FYRTI L+E+G+KP+YVFDGKPP LK+ L +R E RE+A++ +A E+G
Sbjct: 60 GLFYRTINLLENGIKPVYVFDGKPPELKAETLEERREIREEAEEKWEEALEKG------- 112
Query: 415 DEDGLVKYLCGDK--NFAEDRIRNGAKKLLKA 444
D + KY + + I +KKLL
Sbjct: 113 DLEEARKY---AQRSSRLTSEIVESSKKLLDL 141
Score = 69.6 bits (171), Expect = 7e-13
Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 233 IDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELF 292
ID+ IL+G DY + ++GIGPK A++LIKEH +EK+L + + Y E RE F
Sbjct: 227 IDIAILVGTDYNEGVKGIGPKTALKLIKEHGDLEKVL---KARGEDIEN---YDEIREFF 280
Query: 293 RHPEIADPETIEL 305
+P + D ++
Sbjct: 281 LNPPVTDDYELKW 293
Score = 62.7 bits (153), Expect = 1e-10
Identities = 19/50 (38%), Positives = 32/50 (64%), Gaps = 1/50 (2%)
Query: 2 TLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFF 51
LKW PD++G++++LC + +F+EDR+ ++L A S Q LD +F
Sbjct: 290 ELKWRKPDKEGIIEFLCDEHDFSEDRVERALERLEAAYKS-KQKTLDRWF 338
Score = 61.5 bits (150), Expect = 3e-10
Identities = 18/50 (36%), Positives = 33/50 (66%), Gaps = 1/50 (2%)
Query: 408 KLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFF 457
+LKW PD++G++++LC + +F+EDR+ ++L A + Q LD +F
Sbjct: 290 ELKWRKPDKEGIIEFLCDEHDFSEDRVERALERLEAAYK-SKQKTLDRWF 338
>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 = 119 bits (301), Expect = 7e-33
Identities = 40/73 (54%), Positives = 49/73 (67%), Gaps = 3/73 (4%)
Query: 127 EEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKY---TVPEGWLYK 183
E+FIDLCIL GCDY SI GIGPK A +LIK+H+SIEK+L+ + + K VP +K
Sbjct: 1 EQFIDLCILSGCDYLPSIPGIGPKTAYKLIKKHKSIEKVLKALRSNKKKKVPVPYEEPFK 60
Query: 184 EARELFRHPEVAD 196
EAR F H V D
Sbjct: 61 EARLTFLHQRVYD 73
Score = 114 bits (289), Expect = 4e-31
Identities = 38/71 (53%), Positives = 47/71 (66%), Gaps = 3/71 (4%)
Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKY---TVPEGWLYKEA 288
FIDLCIL GCDY SI GIGPK A +LIK+H+SIEK+L+ + + K VP +KEA
Sbjct: 3 FIDLCILSGCDYLPSIPGIGPKTAYKLIKKHKSIEKVLKALRSNKKKKVPVPYEEPFKEA 62
Query: 289 RELFRHPEIAD 299
R F H + D
Sbjct: 63 RLTFLHQRVYD 73
>gnl|CDD|216098 pfam00752, XPG_N, XPG N-terminal domain.
Length = 100
Score = 102 bits (256), Expect = 3e-26
Identities = 47/97 (48%), Positives = 62/97 (63%), Gaps = 8/97 (8%)
Query: 303 IELVADVAPSSIR--ESRKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTSHLMGTFYR 359
++ VA + P I E + + IDAS+ LYQFL AVR + GN L + TSHLMG F R
Sbjct: 9 LKPVALIRPVDIEALEGKTLAIDASIWLYQFLKAVRDQLGNALQN-----TSHLMGFFSR 63
Query: 360 TIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDA 396
RL + G+KPI+VFDG PP LK+ L KR +R++A
Sbjct: 64 LCRLKDFGIKPIFVFDGGPPPLKAETLQKRSARRQEA 100
>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of
PolI) [DNA replication, recombination, and repair].
Length = 310
Score = 108 bits (271), Expect = 4e-26
Identities = 44/142 (30%), Positives = 68/142 (47%), Gaps = 9/142 (6%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
P E AQ A K G V + D D L S + + + P + LE+V E
Sbjct: 122 DPIETLAQKAY--KKGDVVLIISGDKDLLQLVSP---NVLVINGKKGEPEKFLDLEEVEE 176
Query: 121 -GMELSHEEFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVP 177
L+ E+ IDL L+G D ++GIGPK A++L++E+ S+E + EN+D K
Sbjct: 177 KFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIKKKTR 236
Query: 178 EGWLYKEARELFRHPEVADPET 199
E L ++ + F +A +T
Sbjct: 237 E-KLLEDKEKAFLSKPLATIKT 257
Score = 73.9 bits (182), Expect = 2e-14
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 232 FIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAR 289
IDL L+G D ++GIGPK A++L++E+ S+E + EN+D K E L ++
Sbjct: 186 LIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIKKKTRE-KLLEDKE 244
Query: 290 ELFRHPEIADPET 302
+ F +A +T
Sbjct: 245 KAFLSKPLATIKT 257
Score = 72.0 bits (177), Expect = 8e-14
Identities = 31/91 (34%), Positives = 43/91 (47%), Gaps = 7/91 (7%)
Query: 311 PSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPT---SHLMGTFYRTIRLVEHG 367
+ + + ID S LY+ L A+ L + G+PT S +G YR IRL+E
Sbjct: 5 QLMNKSGKLLLIDGSSLLYRALHALPQ---PLGNPLGDPTGAVSGFLGMLYRLIRLLEP- 60
Query: 368 LKPIYVFDGKPPTLKSGELNKRMEKREDAQK 398
P+ VFDGKPPT + L + RE
Sbjct: 61 THPVVVFDGKPPTFRHELLEEYKANREKEMP 91
Score = 36.1 bits (84), Expect = 0.038
Identities = 29/100 (29%), Positives = 43/100 (43%), Gaps = 8/100 (8%)
Query: 363 LVEHG-LKPIYV-FDGKPPTLKSGELNKRMEKREDA--QKALAKAQEQGKLKWSDPDEDG 418
L E+G L+ +Y D + K +E +E A K LA + L++ D
Sbjct: 215 LQEYGSLEGLYENLDIIKKKTR----EKLLEDKEKAFLSKPLATIKTDVPLEFDLEDILE 270
Query: 419 LVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFT 458
L+ E+R+ G K+LLKA + Q LD FF
Sbjct: 271 LLVPEHDFSKLLEERVELGFKRLLKAIGSVEQATLDEFFR 310
Score = 35.4 bits (82), Expect = 0.056
Identities = 17/50 (34%), Positives = 23/50 (46%)
Query: 3 LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFFT 52
L++ D L+ E+R+ G K+LLKA S Q LD FF
Sbjct: 261 LEFDLEDILELLVPEHDFSKLLEERVELGFKRLLKAIGSVEQATLDEFFR 310
>gnl|CDD|214690 smart00485, XPGN, Xeroderma pigmentosum G N-region. domain in
nucleases.
Length = 99
Score = 101 bits (255), Expect = 4e-26
Identities = 45/82 (54%), Positives = 55/82 (67%), Gaps = 6/82 (7%)
Query: 316 ESRKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVF 374
+ + IDAS+ LYQFL A R + G L + HLMG FYRT RL+E G+KPI+VF
Sbjct: 23 RGKTLAIDASIWLYQFLTACREKLGTPLPNS-----KHLMGLFYRTCRLLEFGIKPIFVF 77
Query: 375 DGKPPTLKSGELNKRMEKREDA 396
DGKPP LKS L KR E+RE+A
Sbjct: 78 DGKPPPLKSETLAKRRERREEA 99
>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 = 99.2 bits (248), Expect = 2e-25
Identities = 37/68 (54%), Positives = 48/68 (70%), Gaps = 3/68 (4%)
Query: 127 EEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKY---TVPEGWLYK 183
E+FIDLCIL GCDY + GIGPK A++LIKE+ S+EK+L+ + K VP + YK
Sbjct: 1 EQFIDLCILSGCDYLPGLPGIGPKTALKLIKEYGSLEKVLKALRDDKKDKVPVPYDFPYK 60
Query: 184 EARELFRH 191
+ARELF H
Sbjct: 61 KARELFLH 68
Score = 96.5 bits (241), Expect = 1e-24
Identities = 36/66 (54%), Positives = 46/66 (69%), Gaps = 3/66 (4%)
Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKY---TVPEGWLYKEA 288
FIDLCIL GCDY + GIGPK A++LIKE+ S+EK+L+ + K VP + YK+A
Sbjct: 3 FIDLCILSGCDYLPGLPGIGPKTALKLIKEYGSLEKVLKALRDDKKDKVPVPYDFPYKKA 62
Query: 289 RELFRH 294
RELF H
Sbjct: 63 RELFLH 68
>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 = 95.3 bits (237), Expect = 2e-22
Identities = 44/99 (44%), Positives = 59/99 (59%), Gaps = 5/99 (5%)
Query: 311 PSSIRE--SRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGL 368
S+I + +K+ ID + LYQFL + R Q + GE TS L G FYRTI+L E+G+
Sbjct: 12 GSAIEDLNGKKVAIDVNHYLYQFLTSKRE---QYLDAIGEFTSSLKGYFYRTIKLFENGI 68
Query: 369 KPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQG 407
PI+VFDG PP LKS KR E R +A+ + +A G
Sbjct: 69 TPIFVFDGGPPYLKSEASGKRTEARAEAEISSTEASYIG 107
Score = 85.7 bits (212), Expect = 4e-19
Identities = 29/65 (44%), Positives = 36/65 (55%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
AP EAEAQ A + K+G V A TED D L +G +R MTF K + F L K+L
Sbjct: 144 APYEAEAQLAYLAKSGHVIAAITEDTDCLMYGVPRFIRGMTFPNKEKRFIDRFRLSKILG 203
Query: 121 GMELS 125
+EL
Sbjct: 204 KLELF 208
>gnl|CDD|214689 smart00484, XPGI, Xeroderma pigmentosum G I-region. domain in
nucleases.
Length = 73
Score = 90.7 bits (226), Expect = 2e-22
Identities = 31/64 (48%), Positives = 40/64 (62%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
AP EAEAQCA + K+G V A TED D L FG+ L R++ FS +KL + LE VL+
Sbjct: 10 APYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVLK 69
Query: 121 GMEL 124
+ L
Sbjct: 70 ELGL 73
>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 = 76.9 bits (189), Expect = 1e-16
Identities = 34/95 (35%), Positives = 46/95 (48%), Gaps = 10/95 (10%)
Query: 319 KICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHG--LKPIYVFDG 376
K+ ID S YQFL R + + GE TS G FY I L ++ + PI VFDG
Sbjct: 1 KVAIDGSNLGYQFLHNNRKDKEK-----GELTSFASGYFYTIISLAKNYSAITPIVVFDG 55
Query: 377 KPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKW 411
P L+ L + E R+ +A A+A E+ K
Sbjct: 56 GKPVLRLEHLPEYKENRD---EAEAEATEEEKRLD 87
Score = 44.5 bits (105), Expect = 2e-05
Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 10/57 (17%)
Query: 62 PCEAEAQCAAMVKAGK----VYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFH 114
P EAE A +VK G V A + D D LT G++ S L +E+H
Sbjct: 113 PSEAEDMAAYLVKKGGHLYDVVALISTDGDWLTLGTD------KVSRFSFLTRREYH 163
>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 = 77.7 bits (192), Expect = 4e-16
Identities = 40/109 (36%), Positives = 59/109 (54%), Gaps = 13/109 (11%)
Query: 309 VAPSSIR------ESRKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPTSHLMGTFYRTI 361
+ PS E +++ IDAS+ +YQFL +R EGN L +HL+G F R
Sbjct: 10 LEPSGRPVRLETLEGKRLAIDASIWIYQFLKGMRDREGNAL------KNAHLLGFFRRIC 63
Query: 362 RLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLK 410
+L+ +G+KP++VFDG P LK L KR ++RE A+ K E+
Sbjct: 64 KLLFYGIKPVFVFDGGAPELKRRTLAKRRQQREKAEINAKKTAEKLLAS 112
Score = 51.5 bits (124), Expect = 3e-07
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEAR 106
AP EAEAQCA + + G V T+D D FG+ + ++ F+ +
Sbjct: 155 APMEAEAQCAILNQLGLVDGVITDDSDVFLFGAKRVYKNF-FNGNK 199
>gnl|CDD|188623 cd09903, H3TH_FEN1-Arc, H3TH domain of Flap Endonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease: Archaeal homologs. Members of this subgroup
include the H3TH (helix-3-turn-helix) domains of
archaeal 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 = 65
Score = 71.5 bits (176), Expect = 1e-15
Identities = 27/71 (38%), Positives = 45/71 (63%), Gaps = 7/71 (9%)
Query: 127 EEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEA 185
E+ ID+ IL+G DY ++GIGPK A++L+KE+ +EK+L + + + + +E
Sbjct: 1 EQLIDIAILVGTDYNPGGVKGIGPKTALKLVKEYGDLEKVLR---SVEDEIVD---PEEI 54
Query: 186 RELFRHPEVAD 196
RE+F +P V D
Sbjct: 55 REIFLNPPVTD 65
Score = 67.2 bits (165), Expect = 3e-14
Identities = 25/68 (36%), Positives = 43/68 (63%), Gaps = 7/68 (10%)
Query: 233 IDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAREL 291
ID+ IL+G DY ++GIGPK A++L+KE+ +EK+L + + + + +E RE+
Sbjct: 4 IDIAILVGTDYNPGGVKGIGPKTALKLVKEYGDLEKVLR---SVEDEIVD---PEEIREI 57
Query: 292 FRHPEIAD 299
F +P + D
Sbjct: 58 FLNPPVTD 65
>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 = 70.9 bits (174), Expect = 2e-15
Identities = 27/71 (38%), Positives = 39/71 (54%), Gaps = 10/71 (14%)
Query: 127 EEFIDLCILLGCDYCD--SIRGIGPKRAIELIKEHRSIEKILENID--------TKKYTV 176
E+FIDLC L+GCDY D + GIGPK A +L ++ S+E ILEN+D +
Sbjct: 1 EQFIDLCALVGCDYSDNPGVPGIGPKTAAKLALKYGSLEGILENLDELKGKKREKLEEPK 60
Query: 177 PEGWLYKEARE 187
+L ++
Sbjct: 61 EYAFLSRKLAT 71
Score = 69.3 bits (170), Expect = 6e-15
Identities = 26/69 (37%), Positives = 37/69 (53%), Gaps = 10/69 (14%)
Query: 232 FIDLCILLGCDYCD--SIRGIGPKRAIELIKEHRSIEKILENID--------TKKYTVPE 281
FIDLC L+GCDY D + GIGPK A +L ++ S+E ILEN+D +
Sbjct: 3 FIDLCALVGCDYSDNPGVPGIGPKTAAKLALKYGSLEGILENLDELKGKKREKLEEPKEY 62
Query: 282 GWLYKEARE 290
+L ++
Sbjct: 63 AFLSRKLAT 71
>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 = 65.7 bits (161), Expect = 1e-13
Identities = 29/73 (39%), Positives = 45/73 (61%), Gaps = 3/73 (4%)
Query: 127 EEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT-KKYTVPEGWL--YK 183
E+F +CIL GCDY S+ GIG K+A +L++ HR+IEK+++ + K VP + ++
Sbjct: 1 EKFRHMCILSGCDYLPSLPGIGLKKAYKLVRRHRTIEKVIKALRFDGKKEVPPDYEEGFQ 60
Query: 184 EARELFRHPEVAD 196
+A F H V D
Sbjct: 61 KALLTFLHQRVFD 73
Score = 63.4 bits (155), Expect = 8e-13
Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 3/67 (4%)
Query: 231 SFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT-KKYTVPEGWL--YKE 287
F +CIL GCDY S+ GIG K+A +L++ HR+IEK+++ + K VP + +++
Sbjct: 2 KFRHMCILSGCDYLPSLPGIGLKKAYKLVRRHRTIEKVIKALRFDGKKEVPPDYEEGFQK 61
Query: 288 ARELFRH 294
A F H
Sbjct: 62 ALLTFLH 68
>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 = 72.2 bits (177), Expect = 3e-13
Identities = 35/99 (35%), Positives = 57/99 (57%), Gaps = 8/99 (8%)
Query: 309 VAPSSIRESRKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPTSHLMGTFYRTIRLVEHG 367
V+P ++ E +++ +D S+ L Q L VR EGN + + SHL+ F+R +L+
Sbjct: 17 VSPETL-EGKRLAVDISIWLNQALKGVRDREGNAIKN------SHLLTLFHRLCKLLFFR 69
Query: 368 LKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQ 406
++PI+VFDG P LK L KR ++R+ A + K E+
Sbjct: 70 IRPIFVFDGGAPLLKRQTLAKRRQRRDGASEDARKTAEK 108
Score = 58.8 bits (142), Expect = 5e-09
Identities = 31/98 (31%), Positives = 52/98 (53%), Gaps = 3/98 (3%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
AP EAEAQCA + + T T+D D FG+ + ++ F++ + V+ + +
Sbjct: 791 APMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNF-FNQNKF--VEYYQYVDIHN 847
Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKE 158
+ L + I+L LLG DY + I +GP A+E++ E
Sbjct: 848 QLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNE 885
Score = 32.6 bits (74), Expect = 0.56
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 203 IDLCILLGCDYCDSIRGIGPKRAIELLYSF 232
I+L LLG DY + I +GP A+E+L F
Sbjct: 857 INLAYLLGSDYTEGIPTVGPVSAMEILNEF 886
Score = 32.2 bits (73), Expect = 0.87
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 233 IDLCILLGCDYCDSIRGIGPKRAIELIKE 261
I+L LLG DY + I +GP A+E++ E
Sbjct: 857 INLAYLLGSDYTEGIPTVGPVSAMEILNE 885
>gnl|CDD|216163 pfam00867, XPG_I, XPG I-region.
Length = 46
Score = 62.8 bits (154), Expect = 6e-13
Identities = 20/33 (60%), Positives = 23/33 (69%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGS 93
AP EAEAQCA +VK G V A +ED D L FG+
Sbjct: 10 APYEAEAQCAYLVKTGLVDAVISEDSDLLLFGA 42
>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 = 59.0 bits (144), Expect = 1e-11
Identities = 22/49 (44%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 127 EEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSI-EKILENIDTKKY 174
E+ I L +LLG DY + GIGPK A+EL+KE EK LE+ + +
Sbjct: 1 EQLILLALLLGTDYNPGVPGIGPKTALELLKEFGEDLEKFLESEEILEA 49
Score = 57.1 bits (139), Expect = 7e-11
Identities = 21/47 (44%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSI-EKILENIDTKKY 277
I L +LLG DY + GIGPK A+EL+KE EK LE+ + +
Sbjct: 3 LILLALLLGTDYNPGVPGIGPKTALELLKEFGEDLEKFLESEEILEA 49
Score = 49.8 bits (120), Expect = 2e-08
Identities = 17/39 (43%), Positives = 22/39 (56%)
Query: 201 EFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILL 239
+ I L +LLG DY + GIGPK A+ELL F +
Sbjct: 2 QLILLALLLGTDYNPGVPGIGPKTALELLKEFGEDLEKF 40
>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 = 62.9 bits (153), Expect = 2e-11
Identities = 26/83 (31%), Positives = 38/83 (45%), Gaps = 1/83 (1%)
Query: 301 ETIELVADVAPSSIRESRKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPTSHLMGTFYR 359
E +E P ++I IDAS L++ L R G + L+ F R
Sbjct: 4 EFLEPQKSRIPKEQLRGKRIAIDASGWLFEALTIQRIRIGPRSSRSYSTTGPALINLFSR 63
Query: 360 TIRLVEHGLKPIYVFDGKPPTLK 382
L+ ++PI+VFDG+PP LK
Sbjct: 64 LKELLSLDVEPIFVFDGEPPKLK 86
Score = 44.4 bits (105), Expect = 4e-05
Identities = 17/49 (34%), Positives = 23/49 (46%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLP 109
AP E EAQCA + +G V + D D L FG+ + R+ T
Sbjct: 114 APGEGEAQCAYLQVSGAVDGILSNDSDTLLFGAEKVYRNFTKFYKESFV 162
>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease.
Length = 259
Score = 56.1 bits (136), Expect = 8e-09
Identities = 27/62 (43%), Positives = 37/62 (59%), Gaps = 4/62 (6%)
Query: 112 EFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRG---IGPKRAIELIKEHRSIEKILEN 168
+ E V+E L+ E+ ID L+G D D+I G IG K A +L+KE S+E ILEN
Sbjct: 157 LYTPENVIEKYGLTPEQIIDYKALMG-DSSDNIPGVPGIGEKTAAKLLKEFGSLENILEN 215
Query: 169 ID 170
+D
Sbjct: 216 LD 217
Score = 51.1 bits (123), Expect = 4e-07
Identities = 22/45 (48%), Positives = 28/45 (62%), Gaps = 4/45 (8%)
Query: 232 FIDLCILLGCDYCDSIRG---IGPKRAIELIKEHRSIEKILENID 273
ID L+G D D+I G IG K A +L+KE S+E ILEN+D
Sbjct: 174 IIDYKALMG-DSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLD 217
>gnl|CDD|197623 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol1 family) motifs.
Length = 36
Score = 49.8 bits (120), Expect = 2e-08
Identities = 18/36 (50%), Positives = 26/36 (72%), Gaps = 4/36 (11%)
Query: 127 EEFIDLCILLGCDYCD---SIRGIGPKRAIELIKEH 159
E+FID IL+G DY D ++GIGPK A++L++E
Sbjct: 2 EQFIDYAILVG-DYSDNIPGVKGIGPKTALKLLREF 36
Score = 47.8 bits (115), Expect = 8e-08
Identities = 17/34 (50%), Positives = 24/34 (70%), Gaps = 4/34 (11%)
Query: 232 FIDLCILLGCDYCD---SIRGIGPKRAIELIKEH 262
FID IL+G DY D ++GIGPK A++L++E
Sbjct: 4 FIDYAILVG-DYSDNIPGVKGIGPKTALKLLREF 36
Score = 43.6 bits (104), Expect = 3e-06
Identities = 17/31 (54%), Positives = 22/31 (70%), Gaps = 4/31 (12%)
Query: 202 FIDLCILLGCDYCD---SIRGIGPKRAIELL 229
FID IL+G DY D ++GIGPK A++LL
Sbjct: 4 FIDYAILVG-DYSDNIPGVKGIGPKTALKLL 33
>gnl|CDD|188618 cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exonuclease of Taq
DNA polymerase I and homologs. H3TH
(helix-3-turn-helix) domains of the 5'-3' exonuclease
(53EXO) of mutli-domain DNA polymerase I and single
domain protein homologs are included in this family. Taq
DNA polymerase I contains a polymerase domain for
synthesizing a new DNA strand and a 53EXO domain for
cleaving RNA primers or damaged DNA strands. Taq's 53EXO
recognizes and endonucleolytically cleaves a
structure-specific DNA substrate that has a bifurcated
downstream duplex and an upstream template-primer duplex
that overlaps the downstream duplex by 1 bp. The 53EXO
cleaves the unpaired 5'-arm of the overlap flap DNA
substrate. 5'-3' exonucleases are members of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN (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+ or Mn2+ or Zn2+) 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 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 = 73
Score = 50.9 bits (123), Expect = 2e-08
Identities = 22/53 (41%), Positives = 31/53 (58%), Gaps = 10/53 (18%)
Query: 127 EEFIDLCILLGCDYCDS------IRGIGPKRAIELIKEHRSIEKILENIDTKK 173
E+ ID L+G DS + GIGPK A +L++E+ S+E IL N+D K
Sbjct: 2 EQIIDYLALVG----DSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDELK 50
Score = 50.1 bits (121), Expect = 4e-08
Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 10/51 (19%)
Query: 232 FIDLCILLGCDYCDS------IRGIGPKRAIELIKEHRSIEKILENIDTKK 276
ID L+G DS + GIGPK A +L++E+ S+E IL N+D K
Sbjct: 4 IIDYLALVG----DSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDELK 50
>gnl|CDD|216458 pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-terminal SAM fold.
Length = 100
Score = 51.4 bits (124), Expect = 2e-08
Identities = 23/50 (46%), Positives = 31/50 (62%), Gaps = 4/50 (8%)
Query: 127 EEFIDLCILLGCDYCDSI---RGIGPKRAIELIKEHRSIEKILENIDTKK 173
E+ ID L+G D D+I GIG K A +L+KE+ S+E I EN+D K
Sbjct: 4 EQIIDYKALVG-DSSDNIPGVPGIGEKTAAKLLKEYGSLENIYENLDKLK 52
Score = 51.0 bits (123), Expect = 4e-08
Identities = 22/48 (45%), Positives = 29/48 (60%), Gaps = 4/48 (8%)
Query: 232 FIDLCILLGCDYCDSI---RGIGPKRAIELIKEHRSIEKILENIDTKK 276
ID L+G D D+I GIG K A +L+KE+ S+E I EN+D K
Sbjct: 6 IIDYKALVG-DSSDNIPGVPGIGEKTAAKLLKEYGSLENIYENLDKLK 52
>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 = 49.9 bits (120), Expect = 8e-08
Identities = 23/97 (23%), Positives = 44/97 (45%), Gaps = 3/97 (3%)
Query: 201 EFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIK 260
+ I L +LLG DY + + GIGP A+E+L F L + D P+++ +
Sbjct: 2 KLIRLALLLGSDYTEGVSGIGPVNAMEILSEFPGEEDL--EKFKDWWENAQPEKSEDSDN 59
Query: 261 EHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEI 297
+ + ++ +N K +P G+ + +P +
Sbjct: 60 DKQEFKRKHKNY-LKNLILPPGFPSPAVINAYLNPNV 95
Score = 49.6 bits (119), Expect = 1e-07
Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 27/95 (28%)
Query: 127 EEFIDLCILLGCDYCDSIRGIGPKRAIELIKE--------------HRSIEKILENIDT- 171
++ I L +LLG DY + + GIGP A+E++ E + + E+ D
Sbjct: 1 DKLIRLALLLGSDYTEGVSGIGPVNAMEILSEFPGEEDLEKFKDWWENAQPEKSEDSDND 60
Query: 172 ------------KKYTVPEGWLYKEARELFRHPEV 194
K +P G+ + +P V
Sbjct: 61 KQEFKRKHKNYLKNLILPPGFPSPAVINAYLNPNV 95
>gnl|CDD|233038 TIGR00593, pola, DNA polymerase I. All proteins in this family for
which functions are known are DNA polymerases Many also
have an exonuclease motif. 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 = 887
Score = 53.1 bits (128), Expect = 3e-07
Identities = 25/65 (38%), Positives = 39/65 (60%), Gaps = 4/65 (6%)
Query: 112 EFHLEKVLEGMELSHEEFIDLCILLGCDYCDSI---RGIGPKRAIELIKEHRSIEKILEN 168
E E V+E ++ ++ +DL L+G D D+I +GIG K A +L++E S+E I EN
Sbjct: 156 EITPEYVVEKYGVTPDQLVDLKALVG-DSSDNIPGVKGIGEKTAAKLLQEFGSLENIYEN 214
Query: 169 IDTKK 173
+D K
Sbjct: 215 LDQIK 219
Score = 47.7 bits (114), Expect = 1e-05
Identities = 21/48 (43%), Positives = 30/48 (62%), Gaps = 4/48 (8%)
Query: 232 FIDLCILLGCDYCDSI---RGIGPKRAIELIKEHRSIEKILENIDTKK 276
+DL L+G D D+I +GIG K A +L++E S+E I EN+D K
Sbjct: 173 LVDLKALVG-DSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQIK 219
>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 = 49.2 bits (118), Expect = 1e-06
Identities = 18/38 (47%), Positives = 25/38 (65%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLR 98
AP EAEA+CA + + G V A + D DAL FG+ ++R
Sbjct: 129 APGEAEAECARLQRLGIVDAVLSNDSDALMFGATRVIR 166
Score = 37.7 bits (88), Expect = 0.008
Identities = 29/89 (32%), Positives = 43/89 (48%), Gaps = 10/89 (11%)
Query: 319 KICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDG-- 376
+I IDAS+ L+Q A +G Q GE L FYR RL+ + P++VFDG
Sbjct: 37 RIAIDASIWLFQ---AQFIQGGQARRQAGE-NPELRTLFYRLKRLLALPITPVFVFDGPN 92
Query: 377 KPPTLKSGELNKRMEKREDAQKALAKAQE 405
+P K G KR+ ++ + +E
Sbjct: 93 RPS-FKRG---KRVGLKKKEHWLIKLVKE 117
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 49.7 bits (120), Expect = 3e-06
Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 10/61 (16%)
Query: 116 EKVLEGMELSHEEFIDLCILLGCDYCDS------IRGIGPKRAIELIKEHRSIEKILENI 169
E+V+E ++ E+ ID L+G DS + GIG K A +L++E+ S+E + EN+
Sbjct: 162 EEVVEKYGVTPEQIIDYLALMG----DSSDNIPGVPGIGEKTAAKLLQEYGSLEGLYENL 217
Query: 170 D 170
D
Sbjct: 218 D 218
Score = 46.6 bits (112), Expect = 3e-05
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 17/61 (27%)
Query: 219 GIGPKRAIELLYSFIDLCILLGCDYCDS------IRGIGPKRAIELIKEHRSIEKILENI 272
G+ P++ ID L+G DS + GIG K A +L++E+ S+E + EN+
Sbjct: 169 GVTPEQ-------IIDYLALMG----DSSDNIPGVPGIGEKTAAKLLQEYGSLEGLYENL 217
Query: 273 D 273
D
Sbjct: 218 D 218
>gnl|CDD|237877 PRK14976, PRK14976, 5'-3' exonuclease; Provisional.
Length = 281
Score = 45.7 bits (109), Expect = 3e-05
Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 106 RKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRG---IGPKRAIELIKEHRSI 162
+ + E + ++ ID L+G D D+I+G IGPK AI+L+ ++ +I
Sbjct: 156 KGTSHFILNTNNFFELYGIEPKQIIDYKGLVG-DSSDNIKGVKGIGPKTAIKLLNKYGNI 214
Query: 163 EKILENID 170
E I ENID
Sbjct: 215 ENIYENID 222
Score = 43.8 bits (104), Expect = 1e-04
Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 13/72 (18%)
Query: 214 CDSIRGIGPK----RAIELLYS-----FIDLCILLGCDYCDSIRG---IGPKRAIELIKE 261
+G LY ID L+G D D+I+G IGPK AI+L+ +
Sbjct: 152 LLKKKGTSHFILNTNNFFELYGIEPKQIIDYKGLVG-DSSDNIKGVKGIGPKTAIKLLNK 210
Query: 262 HRSIEKILENID 273
+ +IE I ENID
Sbjct: 211 YGNIENIYENID 222
>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 = 44.7 bits (106), Expect = 5e-05
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 8/76 (10%)
Query: 318 RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGK 377
+++ +D S + + V+ P HL F+RT L+ G+ P++V DG
Sbjct: 25 KRVAVDLSCWVVESQTVVKYFV--------VPKPHLRNLFFRTRYLIALGVLPVFVVDGA 76
Query: 378 PPTLKSGELNKRMEKR 393
P LK + KR + +
Sbjct: 77 APPLKLPVIIKRNQLQ 92
Score = 43.5 bits (103), Expect = 1e-04
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 6/78 (7%)
Query: 60 KAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVL 119
+A EAEA CA + G V T+D DA +G+ + R+ SE V + + +
Sbjct: 136 QAAGEAEALCAELNSEGLVDGCITQDSDAFLYGARTVYRNFQMSEKGG-YVDCYDMSDIK 194
Query: 120 EGMELS-----HEEFIDL 132
++LS E FID
Sbjct: 195 SKLDLSWRQPDLELFIDF 212
>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 = 43.6 bits (104), Expect = 7e-05
Identities = 27/101 (26%), Positives = 47/101 (46%), Gaps = 8/101 (7%)
Query: 311 PSSIRESR--KICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEH-G 367
P I E + ++ +DA L++ + E G+PT + + + ++ H G
Sbjct: 16 PVHISEYKGKRVAVDAYSWLHRGAYSCAEELAL-----GKPTDKYVQYCMKRVNMLLHYG 70
Query: 368 LKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGK 408
+KPI VFDG P K G +R E+RE+ + + +G
Sbjct: 71 IKPILVFDGGPLPSKKGTEEERRERREENLEKALELLREGN 111
Score = 34.0 bits (79), Expect = 0.100
Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
AP EA+AQ A + K G V A TED D L +G + F + QE L +L+
Sbjct: 147 APYEADAQLAYLAKTGYVDAVITEDSDLLAYGC----PKVLFKLDKNGSCQEIDLADLLK 202
Query: 121 GMELSH 126
+L
Sbjct: 203 CRKLVP 208
>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 = 39.4 bits (92), Expect = 6e-04
Identities = 19/72 (26%), Positives = 22/72 (30%)
Query: 21 KNFAEDRIRNGAKKLLKARSSTTQGRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYA 80
E + KK A L I EA+AQ AA+ K G V A
Sbjct: 41 LLKLEAQKGLRRKKGRVAELLLRDLELLDLMGIPVVHAPGDLYEADAQIAALAKKGHVVA 100
Query: 81 TATEDMDALTFG 92
T D D
Sbjct: 101 LITNDSDLRQKA 112
>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional.
Length = 256
Score = 39.9 bits (94), Expect = 0.002
Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 16/75 (21%)
Query: 124 LSHEEFIDLCILLGCDYCDS------IRGIGPKRAIELIKEHRSIEKILENIDTKKYTVP 177
+ ++ D L G S + GIGPK A EL+ + RS+E I E++D +P
Sbjct: 165 VEPQQLPDYWGLAG----ISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLD----ALP 216
Query: 178 EGWLYK--EARELFR 190
E W K E +E+ R
Sbjct: 217 EKWRKKLEEHKEMAR 231
Score = 38.7 bits (91), Expect = 0.004
Identities = 21/49 (42%), Positives = 30/49 (61%), Gaps = 6/49 (12%)
Query: 247 IRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYK--EARELFR 293
+ GIGPK A EL+ + RS+E I E++D +PE W K E +E+ R
Sbjct: 187 VAGIGPKSAAELLNQFRSLENIYESLD----ALPEKWRKKLEEHKEMAR 231
>gnl|CDD|188622 cd09902, H3TH_MKT1, H3TH 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 (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
(helix-3-turn-helix) 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.
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 = 81
Score = 35.3 bits (82), Expect = 0.007
Identities = 17/80 (21%), Positives = 36/80 (45%), Gaps = 13/80 (16%)
Query: 127 EEFIDLCILLGCDYCDSI---------RGIGPKRAIELIKEHRSIEKILENI-DTKKYTV 176
E+F+D C+L G + C + + + A++++K+ RS + + DT
Sbjct: 1 EQFLDACLLAGTELCPTFPPLQDSPFPKPQNFRDALDMVKQARSGISVCQQFPDTPSVND 60
Query: 177 PEGWL--YKEARELFRHPEV 194
+L Y +A+ ++ V
Sbjct: 61 KN-YLDQYCKAKSAVKYHLV 79
Score = 32.3 bits (74), Expect = 0.077
Identities = 15/76 (19%), Positives = 33/76 (43%), Gaps = 13/76 (17%)
Query: 232 FIDLCILLGCDYCDSI---------RGIGPKRAIELIKEHRSIEKILENI-DTKKYTVPE 281
F+D C+L G + C + + + A++++K+ RS + + DT
Sbjct: 3 FLDACLLAGTELCPTFPPLQDSPFPKPQNFRDALDMVKQARSGISVCQQFPDTPSVNDKN 62
Query: 282 GWL--YKEARELFRHP 295
+L Y +A+ ++
Sbjct: 63 -YLDQYCKAKSAVKYH 77
Score = 30.0 bits (68), Expect = 0.51
Identities = 6/14 (42%), Positives = 10/14 (71%)
Query: 201 EFIDLCILLGCDYC 214
+F+D C+L G + C
Sbjct: 2 QFLDACLLAGTELC 15
>gnl|CDD|188625 cd09905, H3TH_GEN1, H3TH domain of Gap Endonuclease 1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease. Gap Endonuclease 1 (GEN1): 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. Members of this
subgroup include the H3TH (helix-3-turn-helix) domains
of GEN1 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 = 108
Score = 34.3 bits (79), Expect = 0.036
Identities = 15/44 (34%), Positives = 27/44 (61%), Gaps = 2/44 (4%)
Query: 127 EEFIDLCILLGCDYCDS-IRGIGPKRAIELIKEHRSIEKILENI 169
E+ I L +L GCDY + G+G +RA+ L+ S +++L+ +
Sbjct: 2 EKLIALALLCGCDYNPKGVPGVGKERALRLVNIVSS-DEVLDRL 44
Score = 33.5 bits (77), Expect = 0.063
Identities = 14/41 (34%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 233 IDLCILLGCDYCDS-IRGIGPKRAIELIKEHRSIEKILENI 272
I L +L GCDY + G+G +RA+ L+ S +++L+ +
Sbjct: 5 IALALLCGCDYNPKGVPGVGKERALRLVNIVSS-DEVLDRL 44
Score = 30.4 bits (69), Expect = 0.76
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 203 IDLCILLGCDYCDS-IRGIGPKRAIELLYSFIDLCIL 238
I L +L GCDY + G+G +RA+ L+ +L
Sbjct: 5 IALALLCGCDYNPKGVPGVGKERALRLVNIVSSDEVL 41
>gnl|CDD|223972 COG1042, COG1042, Acyl-CoA synthetase (NDP forming) [Energy
production and conversion].
Length = 598
Score = 36.2 bits (84), Expect = 0.042
Identities = 22/95 (23%), Positives = 33/95 (34%), Gaps = 15/95 (15%)
Query: 245 DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIAD-PETI 303
SI IG + + + +LE K Y V Y E + + +AD P+
Sbjct: 11 KSIAVIGASERPGKL-GYEILRNLLEYGQGKIYPVNPK--YDEVLGVKAYTSVADLPDAP 67
Query: 304 ELV-----ADVAPSSIRESRK------ICIDASMS 327
+L A V P + E + I I A
Sbjct: 68 DLAVIVVPAKVVPEIVHELGEKGVKGAIVISAGFR 102
>gnl|CDD|219354 pfam07264, EI24, Etoposide-induced protein 2.4 (EI24). This family
contains a number of eukaryotic etoposide-induced 2.4
(EI24) proteins approximately 350 residues long as well
as bacterial CysZ proteins (formerly known as DUF540).
In cells treated with the cytotoxic drug etoposide, EI24
is induced by p53. It has been suggested to play an
important role in negative cell growth control.
Length = 205
Score = 34.9 bits (81), Expect = 0.053
Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 5/36 (13%)
Query: 228 LLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHR 263
LL ++ LLG +Y D + L++ +R
Sbjct: 152 LLNAW-----LLGFEYLDYAADRSFEERRALLRRNR 182
Score = 33.3 bits (77), Expect = 0.18
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 135 LLGCDYCDSIRGIGPKRAIELIKEHR 160
LLG +Y D + L++ +R
Sbjct: 157 LLGFEYLDYAADRSFEERRALLRRNR 182
>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 = 34.9 bits (81), Expect = 0.063
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 365 EHGLKPIYVFDGKPPTLK---SGELNKRMEKREDAQKALAKAQEQGKLK 410
EH +KPI+VFDG P + S + + + E A + Q ++
Sbjct: 72 EHNIKPIFVFDGLSPKSQLEPSSQREQSARQLEQAWELYVNGQASQAVE 120
>gnl|CDD|113452 pfam04684, BAF1_ABF1, BAF1 / ABF1 chromatin reorganising factor.
ABF1 is a sequence-specific DNA binding protein involved
in transcription activation, gene silencing and
initiation of DNA replication. ABF1 is known to remodel
chromatin, and it is proposed that it mediates its
effects on transcription and gene expression by
modifying local chromatin architecture. These functions
require a conserved stretch of 20 amino acids in the
C-terminal region of ABF1 (amino acids 639 to 662 S.
cerevisiae). The N-terminal two thirds of the protein
are necessary for DNA binding, and the N-terminus (amino
acids 9 to 91 in S. cerevisiae) is thought to contain a
novel zinc-finger motif which may stabilise the protein
structure.
Length = 508
Score = 34.3 bits (78), Expect = 0.18
Identities = 29/132 (21%), Positives = 47/132 (35%), Gaps = 19/132 (14%)
Query: 417 DGLVKYLCGDKNFAEDRIR-------NGAKKLLKARSTTTQGRLD-----------SFFT 458
D +++ LC D + + R +G ++K R T +D +
Sbjct: 206 DAILESLCNDDDNTVAKFRVAQYVEESGIIDIIKQRYGLTDAEMDKKMLSNIARRVTTDK 265
Query: 459 IRREEKRKSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQ 518
R KRK Y Q Q Q Q+Q +Q+ +Q+ +Q+Q
Sbjct: 266 ARFVLKRKKDGVYALPNAHQISGADHHQHQHHHHPSIPAHHQHQLPEGHQHDHQHHHQHQ 325
Query: 519 CQCQCQCQCQYQ 530
Q Q Q Q+Q
Sbjct: 326 QQ-DLQHQEQHQ 336
>gnl|CDD|217555 pfam03433, EspA, EspA-like secreted protein. EspA is the
prototypical member of this family. EspA, together with
EspB, EspD and Tir are exported by a type III secretion
system. These proteins are essential for attaching and
effacing lesion formation. EspA is a structural protein
and a major component of a large, transiently expressed,
filamentous surface organelle which forms a direct link
between the bacterium and the host cell.
Length = 188
Score = 32.9 bits (75), Expect = 0.26
Identities = 17/90 (18%), Positives = 36/90 (40%), Gaps = 16/90 (17%)
Query: 382 KSGELNKRMEKREDAQK-------ALAKAQEQG-KLKWSDPDEDGLVKYLCGD------K 427
K ++ K+ E+ +AQ+ +AK + K K P + ++KY+ + K
Sbjct: 60 KFAQMQKKAERSRNAQEMANRVDAVIAKVAKSDDKKKVKLPQD--VIKYMKDNGILVDGK 117
Query: 428 NFAEDRIRNGAKKLLKARSTTTQGRLDSFF 457
+ + + K L K + L++
Sbjct: 118 SILDYLDKYPDKGLDKGDLQAVKAALENDS 147
>gnl|CDD|240343 PTZ00280, PTZ00280, Actin-related protein 3; Provisional.
Length = 414
Score = 32.4 bits (74), Expect = 0.61
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 7/75 (9%)
Query: 259 IKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELVADVAPSSIRESR 318
K++ ++ + K YTV G+ E+F HPEI E + +V +I+
Sbjct: 250 FKKYTAVNSV----TKKPYTVDVGYERFLGPEMFFHPEIFSSEWTTPLPEVVDDAIQSCP 305
Query: 319 KICIDASMSLYQFLI 333
ID LY+ ++
Sbjct: 306 ---IDCRRPLYKNIV 317
>gnl|CDD|151935 pfam11498, Activator_LAG-3, Transcriptional activator LAG-3. The
C.elegans Notch pathway, involved in the control of
growth, differentiation and patterning in animal
development, relies on either of the receptors GLP-1 or
LIN-12. Both these receptors promote signalling by the
recruitment of LAG-3 to target promoters, where it then
acts as a transcriptional activator. LAG-3 works as a
ternary complex together with the DNA binding protein,
LAG-1.
Length = 476
Score = 31.9 bits (71), Expect = 0.99
Identities = 17/72 (23%), Positives = 26/72 (36%)
Query: 460 RREEKRKSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQC 519
++E +++ Q Q Q Q +Q Q Q Y Q Q+ + Q
Sbjct: 362 QQEHQQQQMLLQQQQQMHQLQQHHQMNGGGQFATQAHQHAAYLQQMQHMRLQEQIQHQQQ 421
Query: 520 QCQCQCQCQYQY 531
Q Q Q Q Q+
Sbjct: 422 QAQHHQQAQQQH 433
Score = 30.3 bits (67), Expect = 2.8
Identities = 18/66 (27%), Positives = 28/66 (42%)
Query: 459 IRREEKRKSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQ 518
++++E R + Q Q Q +Q Q Q Q + Q Q Q Q +Q Q +Q Q+
Sbjct: 335 LQQQEMEMQRIEQQRQQQIMHQHQQQQQQEHQQQQMLLQQQQQMHQLQQHHQMNGGGQFA 394
Query: 519 CQCQCQ 524
Q
Sbjct: 395 TQAHQH 400
Score = 29.2 bits (64), Expect = 6.1
Identities = 16/61 (26%), Positives = 20/61 (32%)
Query: 470 QYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQCQCQCQCQCQY 529
Q Q +Q Q Q Q Q Q Q+ + Q Q Q Q Q Q+
Sbjct: 374 QQQQMHQLQQHHQMNGGGQFATQAHQHAAYLQQMQHMRLQEQIQHQQQQAQHHQQAQQQH 433
Query: 530 Q 530
Q
Sbjct: 434 Q 434
>gnl|CDD|234792 PRK00558, uvrC, excinuclease ABC subunit C; Validated.
Length = 598
Score = 31.6 bits (73), Expect = 1.0
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 142 DSIRGIGPKRAIELIKEHRSIEKILE 167
D I GIGPKR L+K S++ I E
Sbjct: 546 DDIPGIGPKRRKALLKHFGSLKAIKE 571
Score = 31.6 bits (73), Expect = 1.0
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 245 DSIRGIGPKRAIELIKEHRSIEKILE 270
D I GIGPKR L+K S++ I E
Sbjct: 546 DDIPGIGPKRRKALLKHFGSLKAIKE 571
>gnl|CDD|171782 PRK12865, PRK12865, YciI-like protein; Reviewed.
Length = 97
Score = 29.4 bits (66), Expect = 1.1
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 382 KSGELNKRMEKREDAQKALAKAQEQGKLKWSDP--DEDG 418
K G LN RM+ R + L K +G LK + P D+DG
Sbjct: 10 KPGHLNVRMDTRPTHLEYLNKLNAEGTLKIAGPFLDDDG 48
>gnl|CDD|181146 PRK07851, PRK07851, acetyl-CoA acetyltransferase; Provisional.
Length = 406
Score = 31.1 bits (71), Expect = 1.7
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 395 DAQKALAKAQEQGKLKWSDPDEDGLV 420
+AQ A E G W DP EDGL+
Sbjct: 141 EAQARTAARAEGGAEAWHDPREDGLL 166
>gnl|CDD|226993 COG4646, COG4646, DNA methylase [Transcription / DNA replication,
recombination, and repair].
Length = 637
Score = 31.0 bits (70), Expect = 1.8
Identities = 24/97 (24%), Positives = 36/97 (37%), Gaps = 10/97 (10%)
Query: 373 VFDGKPPTLKSGELNKRMEKRE----DAQKALAKAQE----QGKLKWSDPDEDGLVKYLC 424
+ + P + + EKR D + A K Q+ LK DP+ L
Sbjct: 402 ALNSRVPQIFDTVKDDHAEKRVLNVVDTEAAKEKLQKIKTAMSTLKGVDPNGSQRAWDLY 461
Query: 425 GDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRR 461
FAE RN + L+ A T L F+++R
Sbjct: 462 VKSRFAET--RNPGRALVLASGTPITNTLGEMFSVQR 496
>gnl|CDD|184325 PRK13786, PRK13786, adenylosuccinate synthetase; Provisional.
Length = 424
Score = 30.5 bits (69), Expect = 2.3
Identities = 41/164 (25%), Positives = 70/164 (42%), Gaps = 29/164 (17%)
Query: 172 KKYTVPEGWLYKEARELFRHPEVADPETI-EFIDLCILLGCDYCDSIRGIGPKRAIELLY 230
K + +P G+L +AR L V +PE + E ID+ G GI K +I + Y
Sbjct: 50 KLHLIPSGFLL-DARVLIGPGVVLNPEVLAEEIDMLEKHGVKVDAEKLGIDAKTSIIMPY 108
Query: 231 SFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARE 290
I+L D +R + R+ E I T K + ++ K AR+
Sbjct: 109 H-IEL---------DGLR-----------ESART-----EKIGTTKRGIGFAYIDKIARD 142
Query: 291 LFRHPEIADPET-IELVADVAPSSIRESRKICIDASMSLYQFLI 333
R ++ D E + + ++AP +E +++ D S+ + LI
Sbjct: 143 EVRMSDLVDKERLMRRLEELAPQKEKEIKELGGDPSIVRDEALI 186
>gnl|CDD|184529 PRK14133, PRK14133, DNA polymerase IV; Provisional.
Length = 347
Score = 30.5 bits (69), Expect = 2.3
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 115 LEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSI--EKILENIDTK 172
+ + + ++LS E I+ G + + IRGI R +E+ +E +SI E L+ DTK
Sbjct: 194 IYTIEDLLKLSREFLIEYFGKFGVEIYERIRGID-YREVEVSRERKSIGKETTLKK-DTK 251
>gnl|CDD|223350 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type
II) [DNA replication, recombination, and repair].
Length = 667
Score = 30.6 bits (70), Expect = 2.6
Identities = 32/123 (26%), Positives = 40/123 (32%), Gaps = 35/123 (28%)
Query: 153 IELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCD 212
+E E S E +L I+ K +LY LG
Sbjct: 484 LEGFGEK-SAENLLNAIEKSKKQPLARFLYA-------------------------LG-- 515
Query: 213 YCDSIRGIGPKRAIELLYSFIDLCILLGCDYCD--SIRGIGPKRAIELIKEHRSIEKILE 270
IR +G A L F L LL + SI GIG A I E + E+ E
Sbjct: 516 ----IRHVGETTAKSLARHFGTLEALLAASEEELASIPGIGEVVA-RSIIEFFANEENRE 570
Query: 271 NID 273
ID
Sbjct: 571 LID 573
>gnl|CDD|203813 pfam07943, PBP5_C, Penicillin-binding protein 5, C-terminal domain.
Penicillin-binding protein 5 expressed by E. coli
functions as a D-alanyl-D-alanine carboxypeptidase. It
is composed of two domains that are oriented at
approximately right angles to each other. The N-terminal
domain (pfam00768) is the catalytic domain. The
C-terminal domain featured in this family is organised
into a sandwich of two anti-parallel beta-sheets, and
has a relatively hydrophobic surface as compared to the
N-terminal domain. Its precise function is unknown; it
may mediate interactions with other cell
wall-synthesising enzymes, thus allowing the protein to
be recruited to areas of active cell wall synthesis. It
may also function as a linker domain that positions the
active site in the catalytic domain closer to the
peptidoglycan layer, to allow it to interact with cell
wall peptides.
Length = 91
Score = 28.0 bits (63), Expect = 3.8
Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 17/77 (22%)
Query: 358 YRTIRLVEHG--LKPIYVFDGKP------------PTLKSGE---LNKRMEKREDAQKAL 400
+ T +L + G +K + V+ GK TL GE L ++ ++ + +
Sbjct: 1 FETKKLYKKGDVVKKVKVWKGKKKTVPLGAKEDVYVTLPKGEKKKLKAKVTLKKPLEAPI 60
Query: 401 AKAQEQGKLKWSDPDED 417
K Q GKL+ +
Sbjct: 61 KKGQVVGKLEVYLDGKL 77
>gnl|CDD|221794 pfam12825, DUF3818, Domain of unknown function in PX-proteins
(DUF3818). This domain is found on proteins carrying a
PX domain. Its function is unknown.
Length = 340
Score = 29.6 bits (67), Expect = 3.9
Identities = 27/138 (19%), Positives = 49/138 (35%), Gaps = 22/138 (15%)
Query: 183 KEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCD 242
KE +EL P + + + D D+IR K +LL L IL
Sbjct: 114 KEIKEL-EAKIDDYPVICQKLKNFVEADEDIKDAIREEAVKEDEDLL-----LAILRSSR 167
Query: 243 YCDSIRGIGPKRAI-ELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRH------- 294
+ K + E+I+ + + + +E+ + E LY ++L +
Sbjct: 168 ----LAPKLSKEQLQEVIESYTAWKNAVESEPVDEEESEEAELYSNLKQLLQLYLRERDK 223
Query: 295 ----PEIADPETIELVAD 308
+PE +L+ D
Sbjct: 224 DLMKKLWQEPELTQLLKD 241
>gnl|CDD|226760 COG4310, COG4310, Uncharacterized protein conserved in bacteria
with an aminopeptidase-like domain [General function
prediction only].
Length = 435
Score = 29.8 bits (67), Expect = 4.0
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 141 CDSIRGIGPKRAIELIKEHRSIEKILENIDTKKY--TVPEGWLYKEA 185
C SI G G + ++++ ++ +E TK + TVP+ W KEA
Sbjct: 29 CRSITGQGVRDTLDILNKYLPLEIHEVKSGTKVFDWTVPQEWNVKEA 75
Score = 29.8 bits (67), Expect = 4.0
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 244 CDSIRGIGPKRAIELIKEHRSIEKILENIDTKKY--TVPEGWLYKEA 288
C SI G G + ++++ ++ +E TK + TVP+ W KEA
Sbjct: 29 CRSITGQGVRDTLDILNKYLPLEIHEVKSGTKVFDWTVPQEWNVKEA 75
>gnl|CDD|240947 cd12503, RRM1_hnRNPH_GRSF1_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, G-rich sequence factor 1 (GRSF-1) and
similar proteins. This subfamily corresponds to the
RRM1 of hnRNP H proteins and GRSF-1. The hnRNP H protein
family includes hnRNP H (also termed mcs94-1), hnRNP H2
(also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3
(also termed hnRNP 2H9), which represent a group of
nuclear RNA binding proteins that are involved in
pre-mRNA processing. These proteins have similar RNA
binding affinities and specifically recognize the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA only
in the presence of cap-binding proteins. hnRNP H and
hnRNP H2 are almost identical; both have been found to
bind nuclear-matrix proteins. hnRNP H activates exon
inclusion by binding G-rich intronic elements downstream
of the 5' splice site in the transcripts of c-src, human
immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and
myelin. It silences exons when bound to exonic elements
in the transcripts of beta-tropomyosin, HIV-1, and
alpha-tropomyosin. hnRNP H2 has been implicated in
pre-mRNA 3' end formation. hnRNP H3 may be involved in
splicing arrest induced by heat shock. Most family
members contain three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), except for hnRNP H3, in
which the RRM1 is absent. RRM1 and RRM2 are responsible
for the binding to the RNA at DGGGD motifs, and play an
important role in efficiently silencing the exon.
Members in this family can regulate the alternative
splicing of fibroblast growth factor receptor 2 (FGFR2)
transcripts, and function as silencers of FGFR2 exon
IIIc through an interaction with the exonic GGG motifs.
The lack of RRM1 could account for the reduced silencing
activity within hnRNP H3. Members in this family have an
extensive glycine-rich region near the C-terminus, which
may allow them to homo- or heterodimerize. They also
include a cytoplasmic poly(A)+ mRNA binding protein,
GRSF-1, which interacts with RNA in a G-rich
element-dependent manner. They may function in RNA
packaging, stabilization of RNA secondary structure, or
other macromolecular interactions. GRSF-1 contains three
potential RRMs responsible for the RNA binding, and two
auxiliary domains (an acidic alpha-helical domain and an
N-terminal alanine-rich region) that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 77
Score = 27.3 bits (61), Expect = 4.5
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 360 TIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQE 405
I+ E+G+ Y +G+P SGE +E ED +KAL K E
Sbjct: 24 RIKGGENGIHFTYSREGRP----SGEAFIELESEEDVEKALEKHNE 65
>gnl|CDD|237393 PRK13477, PRK13477, bifunctional pantoate ligase/cytidylate kinase;
Provisional.
Length = 512
Score = 29.5 bits (67), Expect = 4.5
Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 4/35 (11%)
Query: 139 DYCDSIRGIGPKR----AIELIKEHRSIEKILENI 169
D DS R I P R AIELI + SIE++++ I
Sbjct: 463 DRLDSTREIAPLRKADDAIELITDGLSIEEVVDKI 497
Score = 29.5 bits (67), Expect = 4.5
Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 4/35 (11%)
Query: 242 DYCDSIRGIGPKR----AIELIKEHRSIEKILENI 272
D DS R I P R AIELI + SIE++++ I
Sbjct: 463 DRLDSTREIAPLRKADDAIELITDGLSIEEVVDKI 497
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 29.3 bits (67), Expect = 5.6
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 252 PKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELVAD 308
KR +L KE+ +E I+E K + +EA+E+ E +DPE E+ +
Sbjct: 31 QKRFRKLSKEYAELEPIVEAYREYKQAQED---LEEAKEMLE--EESDPEMREMAKE 82
>gnl|CDD|241174 cd12730, RRM1_GRSF1, RNA recognition motif 1 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subgroup
corresponds to the RRM1 of GRSF-1, a cytoplasmic
poly(A)+ mRNA binding protein which interacts with RNA
in a G-rich element-dependent manner. It may function in
RNA packaging, stabilization of RNA secondary structure,
or other macromolecular interactions. GRSF-1 contains
three potential RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which are responsible for
the RNA binding. In addition, GRSF-1 has two auxiliary
domains, an acidic alpha-helical domain and an
N-terminal alanine-rich region, that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 79
Score = 27.1 bits (60), Expect = 6.0
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 361 IRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAK 402
IR E+G+ + DGKP G+ +E ED QKAL +
Sbjct: 27 IRNGENGVHFLLNRDGKP----RGDALIELESEEDVQKALEQ 64
>gnl|CDD|224859 COG1948, MUS81, ERCC4-type nuclease [DNA replication,
recombination, and repair].
Length = 254
Score = 28.8 bits (65), Expect = 7.1
Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 143 SIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRH 191
SI GIGPK A L+K+ S+E +L + + V +G K+ARE++R
Sbjct: 186 SIPGIGPKLAERLLKKFGSVEDVLTASEEELMKV-KGIGEKKAREIYRF 233
Score = 28.8 bits (65), Expect = 7.1
Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 246 SIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRH 294
SI GIGPK A L+K+ S+E +L + + V +G K+ARE++R
Sbjct: 186 SIPGIGPKLAERLLKKFGSVEDVLTASEEELMKV-KGIGEKKAREIYRF 233
>gnl|CDD|224240 COG1321, TroR, Mn-dependent transcriptional regulator
[Transcription].
Length = 154
Score = 27.7 bits (62), Expect = 9.9
Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 8/76 (10%)
Query: 148 GPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCI 207
G ++A EL+++HR +E+ L + ++EA L ET E +D +
Sbjct: 68 GREKAKELLRKHRLLERFL----VDVLGLDWEEAHEEAEGLEHA---LSDETAERLDE-L 119
Query: 208 LLGCDYCDSIRGIGPK 223
L C + I +
Sbjct: 120 LGFPTRCPHGKPIEVE 135
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
0.322 0.137 0.424
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: 26,958,361
Number of extensions: 2679016
Number of successful extensions: 3937
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3795
Number of HSP's successfully gapped: 167
Length of query: 531
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 430
Effective length of database: 6,457,848
Effective search space: 2776874640
Effective search space used: 2776874640
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 (21.9 bits)
S2: 61 (27.2 bits)