RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14294
(314 letters)
>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 = 240 bits (614), Expect = 6e-79
Identities = 88/184 (47%), Positives = 115/184 (62%), Gaps = 21/184 (11%)
Query: 152 DVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTI- 210
D SIW++Q KG D G ++ NAHL+G + RICKLLF+ IKPVFVFDGG P+LK++T+
Sbjct: 30 DASIWIYQFLKGMRDREGNALKNAHLLGFFRRICKLLFYGIKPVFVFDGGAPELKRRTLA 89
Query: 211 ----------STLEKDRDQLLL----------ERGKQTRLASTITEQMSREAQELLQLFG 250
+K ++LL ++ +Q R A IT++M E QELL+LFG
Sbjct: 90 KRRQQREKAEINAKKTAEKLLASQLKKSAVKSQQQQQERDADEITQEMYDECQELLRLFG 149
Query: 251 VPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDI 310
+P+IVAP EAEAQCA L GVITDDSD++LFGA+ VYKNFF+ +V Y A DI
Sbjct: 150 IPYIVAPMEAEAQCAILNQLGLVDGVITDDSDVFLFGAKRVYKNFFNGNKYVEYYLAEDI 209
Query: 311 RYYF 314
Sbjct: 210 EKEL 213
>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 = 150 bits (380), Expect = 2e-44
Identities = 58/167 (34%), Positives = 82/167 (49%), Gaps = 30/167 (17%)
Query: 152 DVSIWLHQLTKGTHDLAGG------SVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQL 205
D S WL + G S LI L+ R+ +LL ++P+FVFDG P+L
Sbjct: 26 DASGWLFEALTIQRIRIGPRSSRSYSTTGPALINLFSRLKELLSLDVEPIFVFDGEPPKL 85
Query: 206 KKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCA 265
K++T T +M E ++LL L G+P++ APGE EAQCA
Sbjct: 86 KRKTN----------------------PSTPEMISECRKLLDLMGIPYVQAPGEGEAQCA 123
Query: 266 SLELGNHTQGVITDDSDIWLFGARTVYKNF--FDKKSHVLRYTAPDI 310
L++ G++++DSD LFGA VY+NF F K+S V P I
Sbjct: 124 YLQVSGAVDGILSNDSDTLLFGAEKVYRNFTKFYKESFVEVIDLPKI 170
>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 = 129 bits (327), Expect = 4e-36
Identities = 61/169 (36%), Positives = 82/169 (48%), Gaps = 13/169 (7%)
Query: 152 DVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTI- 210
D+S W+ + VP HL L+ R L+ + PVFV DG P LK I
Sbjct: 30 DLSCWVVESQTVVKYFV---VPKPHLRNLFFRTRYLIALGVLPVFVVDGAAPPLKLPVII 86
Query: 211 ------STLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQC 264
S + K D + G + S + + +E ELL+L G+P + A GEAEA C
Sbjct: 87 KRNQLQSGIAKPGDNPTPKNGSKRNRRSRFSH-VLKECVELLELLGIPCLQAAGEAEALC 145
Query: 265 ASLELGNHTQGVITDDSDIWLFGARTVYKNFF--DKKSHVLRYTAPDIR 311
A L G IT DSD +L+GARTVY+NF +K +V Y DI+
Sbjct: 146 AELNSEGLVDGCITQDSDAFLYGARTVYRNFQMSEKGGYVDCYDMSDIK 194
>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 = 126 bits (317), Expect = 3e-32
Identities = 55/100 (55%), Positives = 73/100 (73%)
Query: 211 STLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELG 270
+ L +++ L ++ +Q R+A+ +T QM E+QELL+LFG+P+IVAP EAEAQCA L+L
Sbjct: 746 ANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLL 805
Query: 271 NHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDI 310
+ T G ITDDSDIWLFGAR VYKNFF++ V Y DI
Sbjct: 806 DQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDI 845
Score = 98.4 bits (245), Expect = 1e-22
Identities = 37/67 (55%), Positives = 52/67 (77%)
Query: 152 DVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTIS 211
D+SIWL+Q KG D G ++ N+HL+ L+HR+CKLLFF+I+P+FVFDGG P LK+QT++
Sbjct: 30 DISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGAPLLKRQTLA 89
Query: 212 TLEKDRD 218
+ RD
Sbjct: 90 KRRQRRD 96
Score = 65.3 bits (159), Expect = 1e-11
Identities = 41/140 (29%), Positives = 68/140 (48%), Gaps = 13/140 (9%)
Query: 1 AQRKTLKSKAASNADKVRSDLLKNLLEQQ-LLNDVLGKNEMALPPPSVS---REVDMFEL 56
A+R+ + A+ +A K LL L++Q + K PSV R D++ L
Sbjct: 89 AKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKKSTPEALPSVQQVPRPQDLYVL 148
Query: 57 PPAPAQTVQDEEEDSDSDDTE--------AKFRYADLHSVDINSEQFSALPPDMRHEILT 108
PP P + EE+S+ + E + + + ++DI SE+FS+LPP+++HEILT
Sbjct: 149 PPLPEEEKHSSEEESEKEWEERMNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEILT 208
Query: 109 ELLEQRKLSSWHKMHEMPQN 128
++ K MP+N
Sbjct: 209 DMKLFTKRRR-TLFEAMPEN 227
>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 = 111 bits (279), Expect = 4e-29
Identities = 58/178 (32%), Positives = 77/178 (43%), Gaps = 36/178 (20%)
Query: 152 DVSIWLHQLTKGTHDLAGGSVP-NAHLIGLYHRICKLLFFKIKPVFVFDG-GVPQLKKQT 209
D SIWL Q A N L L++R+ +LL I PVFVFDG P K
Sbjct: 41 DASIWLFQAQFIQGGQARRQAGENPELRTLFYRLKRLLALPITPVFVFDGPNRPSFK--- 97
Query: 210 ISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLEL 269
RGK+ L + + +ELL LFG+P+ APGEAEA+CA L+
Sbjct: 98 --------------RGKRVGLKKKEHW-LIKLVKELLDLFGIPYHTAPGEAEAECARLQR 142
Query: 270 GNHTQGVITDDSDIWLFGARTVYKNF----------------FDKKSHVLRYTAPDIR 311
V+++DSD +FGA V +N + HV Y +IR
Sbjct: 143 LGIVDAVLSNDSDALMFGATRVIRNPSKEGEDSLASSSNVKSKKDEDHVTVYDLDEIR 200
>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 = 107 bits (270), Expect = 1e-27
Identities = 50/135 (37%), Positives = 71/135 (52%), Gaps = 18/135 (13%)
Query: 176 HLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRD---------QLLLERG- 225
HL GL++R +LL IKPV+VFDG P+LK LEK R+ + E G
Sbjct: 58 HLSGLFYRTIRLLENGIKPVYVFDGKPPELKSGE---LEKRRERREEAEEKLEEAKEEGD 114
Query: 226 -----KQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDD 280
K + +T+++ E ++LL+L G+P++ AP EAEAQCA L V + D
Sbjct: 115 AEEARKYAKRTVRVTKEIVEECKKLLRLMGIPYVEAPSEAEAQCAYLVKKGDVYAVASQD 174
Query: 281 SDIWLFGARTVYKNF 295
D LFGA + +N
Sbjct: 175 YDSLLFGAPRLVRNL 189
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
Length = 393
Score = 106 bits (267), Expect = 3e-26
Identities = 58/167 (34%), Positives = 86/167 (51%), Gaps = 25/167 (14%)
Query: 152 DVSIWLHQLTKGTHDLA-GGSVPNA------HLIGLYHRICKLLFFKIKPVFVFDGGVPQ 204
D S+ L+Q D + GG++ N H+ GL++R +LL IKPV+VFDG P+
Sbjct: 34 DASMALYQFLIAIRDDSQGGNLTNEAGEVTSHISGLFNRTIRLLEAGIKPVYVFDGKPPE 93
Query: 205 LKKQTISTLEKDRD-----QLLLERG----------KQTRLASTITEQMSREAQELLQLF 249
LK LEK R+ + LE+ KQ++ +T++ + +A++LL+L
Sbjct: 94 LKS---GELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLM 150
Query: 250 GVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFF 296
G+P I AP EAEAQCA L V T+D D FG + +N
Sbjct: 151 GIPVIEAPCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLN 197
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 99.5 bits (249), Expect = 2e-24
Identities = 44/133 (33%), Positives = 71/133 (53%), Gaps = 12/133 (9%)
Query: 175 AHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTIS----TLEKDRDQLL--LERG--- 225
+HL G+++R LL IKPV+VFDG P+LK + I E+ ++ E G
Sbjct: 9 SHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLE 68
Query: 226 ---KQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSD 282
K + +S +T+++ ++++LL L G+P++ AP E EAQ A + V + D D
Sbjct: 69 EARKYAQRSSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYD 128
Query: 283 IWLFGARTVYKNF 295
LFGA + +N
Sbjct: 129 SLLFGAPRLVRNL 141
>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 = 97.7 bits (244), Expect = 2e-23
Identities = 46/133 (34%), Positives = 72/133 (54%), Gaps = 12/133 (9%)
Query: 175 AHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRDQLL------LERG--- 225
+HL GL++R LL IKPV+VFDG P+LK +T+ + R++ LE+G
Sbjct: 56 SHLSGLFYRTINLLENGIKPVYVFDGKPPELKAETLEERREIREEAEEKWEEALEKGDLE 115
Query: 226 ---KQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSD 282
K + +S +T ++ +++LL L G+P++ AP E EAQ A + V + D D
Sbjct: 116 EARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDVDYVGSQDYD 175
Query: 283 IWLFGARTVYKNF 295
LFGA + +N
Sbjct: 176 SLLFGAPRLVRNL 188
>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 = 91.4 bits (228), Expect = 4e-22
Identities = 54/166 (32%), Positives = 79/166 (47%), Gaps = 16/166 (9%)
Query: 152 DVSIWLHQ-LTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTI 210
D WLH+ +LA G + ++ R+ LL + IKP+ VFDGG KK T
Sbjct: 30 DAYSWLHRGAYSCAEELALGKPTDKYVQYCMKRVNMLLHYGIKPILVFDGGPLPSKKGTE 89
Query: 211 STLEKDRDQ------LLLERGKQT------RLASTITEQMSREAQELLQLFGVPFIVAPG 258
+ R++ LL G ++ + A IT +M+ E + L+ GV +IVAP
Sbjct: 90 EERRERREENLEKALELLREGNRSEARECFQRAVDITPEMAHELIKALRKEGVEYIVAPY 149
Query: 259 EAEAQCASLELGNHTQGVITDDSDIWLFGARTV-YKNFFDKKSHVL 303
EA+AQ A L + VIT+DSD+ +G V +K DK
Sbjct: 150 EADAQLAYLAKTGYVDAVITEDSDLLAYGCPKVLFK--LDKNGSCQ 193
>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 = 91.5 bits (227), Expect = 5e-22
Identities = 51/158 (32%), Positives = 75/158 (47%), Gaps = 16/158 (10%)
Query: 152 DVSIWLHQL---TKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQ 208
DV+ +L+Q + + A G + L G ++R KL I P+FVFDGG P LK +
Sbjct: 26 DVNHYLYQFLTSKREQYLDAIGEFT-SSLKGYFYRTIKLFENGITPIFVFDGGPPYLKSE 84
Query: 209 T------------ISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVA 256
IS+ E +E K + TIT + + + LL L G+P++VA
Sbjct: 85 ASGKRTEARAEAEISSTEASYIGQFIEAQKPFKRNVTITPKAYQNCKILLSLEGIPYVVA 144
Query: 257 PGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKN 294
P EAEAQ A L H IT+D+D ++G +
Sbjct: 145 PYEAEAQLAYLAKSGHVIAAITEDTDCLMYGVPRFIRG 182
>gnl|CDD|214689 smart00484, XPGI, Xeroderma pigmentosum G I-region. domain in
nucleases.
Length = 73
Score = 85.7 bits (213), Expect = 2e-21
Identities = 28/56 (50%), Positives = 35/56 (62%)
Query: 248 LFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVL 303
L G+P+IVAP EAEAQCA L +IT+DSD+ LFGA +Y+N F L
Sbjct: 2 LMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKL 57
>gnl|CDD|214690 smart00485, XPGN, Xeroderma pigmentosum G N-region. domain in
nucleases.
Length = 99
Score = 79.2 bits (196), Expect = 1e-18
Identities = 32/69 (46%), Positives = 44/69 (63%), Gaps = 4/69 (5%)
Query: 152 DVSIWLHQLTKGTHDLAGGSVPN-AHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTI 210
D SIWL+Q + G +PN HL+GL++R C+LL F IKP+FVFDG P LK +T+
Sbjct: 30 DASIWLYQFLTACREKLGTPLPNSKHLMGLFYRTCRLLEFGIKPIFVFDGKPPPLKSETL 89
Query: 211 STLEKDRDQ 219
K R++
Sbjct: 90 ---AKRRER 95
>gnl|CDD|216098 pfam00752, XPG_N, XPG N-terminal domain.
Length = 100
Score = 78.9 bits (195), Expect = 2e-18
Identities = 30/61 (49%), Positives = 41/61 (67%), Gaps = 1/61 (1%)
Query: 152 DVSIWLHQLTKGTHDLAGGSVPN-AHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTI 210
D SIWL+Q K D G ++ N +HL+G + R+C+L F IKP+FVFDGG P LK +T+
Sbjct: 31 DASIWLYQFLKAVRDQLGNALQNTSHLMGFFSRLCRLKDFGIKPIFVFDGGPPPLKAETL 90
Query: 211 S 211
Sbjct: 91 Q 91
>gnl|CDD|216163 pfam00867, XPG_I, XPG I-region.
Length = 46
Score = 73.2 bits (181), Expect = 5e-17
Identities = 23/42 (54%), Positives = 29/42 (69%)
Query: 248 LFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGAR 289
L G+P++VAP EAEAQCA L VI++DSD+ LFGA
Sbjct: 2 LMGIPYVVAPYEAEAQCAYLVKTGLVDAVISEDSDLLLFGAP 43
>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of
PolI) [DNA replication, recombination, and repair].
Length = 310
Score = 74.3 bits (183), Expect = 4e-15
Identities = 38/181 (20%), Positives = 71/181 (39%), Gaps = 10/181 (5%)
Query: 131 HSMLEFRCNIVINKLLVDLISDVSIWLHQLTKGTHDLAGGSVP-NAHLIGLYHRICKLLF 189
L + LL+D S + LH L + + G + +G+ +R+ +LL
Sbjct: 3 EIQLMNKSG---KLLLIDGSSLLYRALHALPQPLGNPLGDPTGAVSGFLGMLYRLIRLLE 59
Query: 190 FKIKPVFVFDGGVPQLKKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLF 249
PV VFDG P + + + + +R++ + + + +TE + LL+L
Sbjct: 60 P-THPVVVFDGKPPTFRHELLEEYKANREKEMPD--ELAPQIPILTELLVALGIPLLELM 116
Query: 250 GVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPD 309
G+ P E AQ A + G+ +I+ D D+ + V K +
Sbjct: 117 GIE-ADDPIETLAQKAY-KKGDVV-LIISGDKDLLQLVSPNVLVINGKKGEPEKFLDLEE 173
Query: 310 I 310
+
Sbjct: 174 V 174
>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 = 61.9 bits (150), Expect = 1e-11
Identities = 33/123 (26%), Positives = 56/123 (45%), Gaps = 7/123 (5%)
Query: 176 HLIGLYHRICKLL--FFKIKPVFVFDGGVPQLKKQTISTLEKDRDQLLLERGKQTRLAST 233
G ++ I L + I P+ VFDGG P L+ + + +++RD+ E ++ +
Sbjct: 29 FASGYFYTIISLAKNYSAITPIVVFDGGKPVLRLEHLPEYKENRDEAEAEATEEEKRLDE 88
Query: 234 ITEQMSREAQELLQLFGVPFIVA-PGEAEAQCASL----ELGNHTQGVITDDSDIWLFGA 288
T + ++ +ELL+L G+P+ P EAE A L +I+ D D G
Sbjct: 89 QTFEYLKDCKELLKLMGIPYFDIRPSEAEDMAAYLVKKGGHLYDVVALISTDGDWLTLGT 148
Query: 289 RTV 291
V
Sbjct: 149 DKV 151
>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 = 59.5 bits (144), Expect = 3e-11
Identities = 40/143 (27%), Positives = 53/143 (37%), Gaps = 32/143 (22%)
Query: 152 DVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTIS 211
D S L +L I L + +LL I + VFD LK
Sbjct: 3 DTSALLFRL--------------LTEIRLRKSLKRLLEGDITVIIVFDVVAELLK----- 43
Query: 212 TLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPG---EAEAQCASLE 268
LE K R ++ ELL L G+P + APG EA+AQ A+L
Sbjct: 44 ----------LEAQKGLRRKKGRVAELLLRDLELLDLMGIPVVHAPGDLYEADAQIAALA 93
Query: 269 LGNHTQGVITDDSDIWLFGARTV 291
H +IT+DSD+ V
Sbjct: 94 KKGHVVALITNDSDLRQKAKPGV 116
>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 = 51.4 bits (124), Expect = 8e-08
Identities = 41/155 (26%), Positives = 64/155 (41%), Gaps = 24/155 (15%)
Query: 152 DVSIWLHQL--TKGTH-DLAGGSVPNAHLIGLYHRI---CKLL-FFKIKPVFVFDGGVPQ 204
D + +L +L K LA G +P L I +L IKP+FVFDG P+
Sbjct: 32 DATHYLSRLLTLKDEQEPLALGGLP----PSLKSYIESDLRLFKEHNIKPIFVFDGLSPK 87
Query: 205 LKKQ---TISTLEKDRDQ--LLLERG------KQTRLASTIT-EQMSREAQELLQLFGVP 252
+ + + +Q L G + A +I E + R +L+ G+
Sbjct: 88 SQLEPSSQREQSARQLEQAWELYVNGQASQAVEAFSEAGSIQPEDLYRFLIRILKEKGIE 147
Query: 253 FIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFG 287
++VAP A AQ A LE + V +++ LF
Sbjct: 148 YLVAPYLASAQLAYLERHGYVDAVY-GPTELLLFD 181
>gnl|CDD|221785 pfam12813, XPG_I_2, XPG domain containing. This family is largely
of fungal proteins and is related to the XP-G protein
family.
Length = 223
Score = 42.4 bits (100), Expect = 1e-04
Identities = 21/73 (28%), Positives = 29/73 (39%), Gaps = 4/73 (5%)
Query: 242 AQELLQ--LFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYK-NFFDK 298
E L+ +GV +V PGEA+ CASL V+T DSD+ + F
Sbjct: 9 VVEALKYRNWGVITVVVPGEADVYCASL-ARKLGCAVLTGDSDLLVHDLGPDGSVIFLQS 67
Query: 299 KSHVLRYTAPDIR 311
+ IR
Sbjct: 68 IEVTSTASYRGIR 80
>gnl|CDD|222719 pfam14377, DUF4414, Domain of unknown function (DUF4414). This
family is frequently found on DNA binding proteins of
the URE-B1 type and on ligases.
Length = 105
Score = 33.1 bits (76), Expect = 0.044
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 86 HSVDINSEQFSALPPDMRHEILTELLEQR 114
+IN E +ALPP++R E+L + ++R
Sbjct: 36 EPTEINPEFLAALPPEIREEVLQQERQER 64
>gnl|CDD|233288 TIGR01139, cysK, cysteine synthase A. This model distinguishes
cysteine synthase A (CysK) from cysteine synthase B
(CysM). CysM differs in having a broader specificity
that also allows the use of thiosulfate to produce
cysteine thiosulfonate [Amino acid biosynthesis, Serine
family].
Length = 298
Score = 30.0 bits (68), Expect = 1.4
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 229 RLASTITEQMSREAQELLQLFGVPFIVAPGE 259
+L T+ E MS E ++LL+ +G ++ PG
Sbjct: 82 KLILTMPETMSIERRKLLKAYGAELVLTPGA 112
>gnl|CDD|182237 PRK10094, PRK10094, DNA-binding transcriptional activator AllS;
Provisional.
Length = 308
Score = 29.8 bits (67), Expect = 1.6
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 7/55 (12%)
Query: 110 LLEQ-RKLSSWHKMHEMPQNDQ--HSMLEFRCNIVINKLLVD--LISDVSIWLHQ 159
LL Q R SW + MP Q + +E + NIVIN LL + ++ + WL++
Sbjct: 65 LLSQARDWLSW--LESMPSELQQVNDGVERQVNIVINNLLYNPQAVAQLLAWLNE 117
>gnl|CDD|182716 PRK10771, thiQ, thiamine transporter ATP-binding subunit;
Provisional.
Length = 232
Score = 29.2 bits (66), Expect = 2.3
Identities = 12/21 (57%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 93 EQFSALPPDMRHEILTELLEQ 113
E FSAL P +R E+LT L+ Q
Sbjct: 155 EPFSALDPALRQEMLT-LVSQ 174
>gnl|CDD|193227 pfam12751, Vac7, Vacuolar segregation subunit 7. Vac7 is
localised at the vacuole membrane, a location which is
consistent with its involvement in vacuole morphology
and inheritance. Vac7 has been shown to function as an
upstream regulator of the Fab1 lipid kinase pathway.
The Fab1 lipid kinase pathway is important for correct
regulation of membrane trafficking events.
Length = 386
Score = 29.4 bits (66), Expect = 2.6
Identities = 16/36 (44%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 41 ALPPPSVSREVDMFELPPAPAQTVQDEEEDSDSDDT 76
ALP + S + D+FE A A DE + SDSD+T
Sbjct: 57 ALPSGTASSKADIFEAKVASA---VDEADVSDSDET 89
>gnl|CDD|147601 pfam05505, Ebola_NP, Ebola nucleoprotein. This family consists of
Ebola and Marburg virus nucleoproteins. These proteins
are responsible for encapsidation of genomic RNA. It has
been found that nucleoprotein DNA vaccines can offer
protection from the virus.
Length = 717
Score = 28.8 bits (64), Expect = 4.1
Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 10/85 (11%)
Query: 43 PPPSVSREVDMFELPPAPAQTVQDEEEDSDSDDTEAKFRYADLHSVDINSEQFSALPPDM 102
PP V R+ + P PAQ QD + D++ + NS+ + L +
Sbjct: 585 PPAPVYRDEKEQDEIPHPAQNPQDPTGSIGNVDSDI---------LRSNSKPSAPL-EET 634
Query: 103 RHEILTELLEQRKLSSWHKMHEMPQ 127
+L ++ +H M + P
Sbjct: 635 YMHLLRTQGPFDAINYYHMMKDEPV 659
>gnl|CDD|226135 COG3608, COG3608, Predicted deacylase [General function prediction
only].
Length = 331
Score = 28.5 bits (64), Expect = 5.1
Identities = 14/41 (34%), Positives = 14/41 (34%)
Query: 161 TKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGG 201
T D GG V L Y R PVFVF G
Sbjct: 6 IVLTGDFDGGGVQLGVLRFPYSRDDSAYGHVGTPVFVFGNG 46
>gnl|CDD|226360 COG3840, ThiQ, ABC-type thiamine transport system, ATPase component
[Coenzyme metabolism].
Length = 231
Score = 28.1 bits (63), Expect = 5.3
Identities = 12/28 (42%), Positives = 19/28 (67%), Gaps = 3/28 (10%)
Query: 93 EQFSALPPDMRHEILT---ELLEQRKLS 117
E FSAL P +R E+L +L ++RK++
Sbjct: 155 EPFSALDPALRAEMLALVSQLCDERKMT 182
>gnl|CDD|233286 TIGR01136, cysKM, cysteine synthase. This model discriminates
cysteine synthases (EC 2.5.1.47) (both CysK and CysM)
from cystathionine beta-synthase, a protein found
primarily in eukaryotes and carrying a C-terminal CBS
domain lacking from this protein. Bacterial proteins
lacking the CBS domain but otherwise showing
resemblamnce to cystathionine beta-synthases and
considerable phylogenetic distance from known cysteine
synthases were excluded from the seed and score below
the trusted cutoff [Amino acid biosynthesis, Serine
family].
Length = 299
Score = 28.4 bits (64), Expect = 5.4
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 229 RLASTITEQMSREAQELLQLFGVPFIVAPGE 259
+L T+ E MS E ++LL+ +G I+ P E
Sbjct: 83 KLILTMPETMSLERRKLLRAYGAELILTPAE 113
>gnl|CDD|222975 PHA03083, PHA03083, poxvirus myristoylprotein; Provisional.
Length = 334
Score = 28.1 bits (63), Expect = 6.4
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 137 RCNIVINKLLVDLISDVSIWLHQLTKGT 164
RCNI IN L +D S + + + +
Sbjct: 267 RCNISINNLNMDSKSSLRMSCNNNDLLS 294
>gnl|CDD|149788 pfam08841, DDR, Diol dehydratase reactivase ATPase-like domain.
Diol dehydratase (DDH, EC:4.2.1.28) and its
isofunctional homologue glycerol dehydratase (GDH,
EC.4.2.1.30) are enzymes which catalyze the conversion
of glycerol 1,2-propanediol, and 1,2-ethanediol to
aldehydes. These reactions require coenzyme B12.
Cleavage of the Co-C bond of coenzyme B12 by substrates
or coenzyme analogues results in inactivation during
which coenzyme B12 remains tightly bound to the
apoenzyme. This family comprises of the large subunit of
the diol dehydratase and glycerol dehydratase
reactivating factors whose function is to reactivate the
holoenzyme by exchange of a damaged cofactor for intact
coenzyme.
Length = 332
Score = 28.1 bits (63), Expect = 6.5
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 237 QMSREAQELLQLFGVPFIVAPGEAEA 262
QM+ A EL + GVP + EAEA
Sbjct: 96 QMAIIAAELEEELGVPVEIGGVEAEA 121
>gnl|CDD|131231 TIGR02176, pyruv_ox_red, pyruvate:ferredoxin (flavodoxin)
oxidoreductase, homodimeric. This model represents a
single chain form of pyruvate:ferredoxin (or flavodoxin)
oxidoreductase. This enzyme may transfer electrons to
nitrogenase in nitrogen-fixing species. Portions of this
protein are homologous to gamma subunit of the four
subunit pyruvate:ferredoxin (flavodoxin) oxidoreductase.
Length = 1165
Score = 28.2 bits (63), Expect = 6.7
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 175 AHLIGLYHRICKLL---FFKIKPVFVFDGGVPQLKK 207
A +GL RI ++ FFK+ V F+ V LKK
Sbjct: 545 AQEVGLGGRINTIMQTAFFKLAGVLPFEKAVDLLKK 580
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 28.1 bits (62), Expect = 7.4
Identities = 10/42 (23%), Positives = 20/42 (47%)
Query: 36 GKNEMALPPPSVSREVDMFELPPAPAQTVQDEEEDSDSDDTE 77
G +M + +R + ++ P + D++ED D DD +
Sbjct: 125 GDLDMIIIKRRRARHLAEEDMSPRDNFVIDDDDEDEDEDDDD 166
>gnl|CDD|237722 PRK14476, PRK14476, nitrogenase molybdenum-cofactor biosynthesis
protein NifN; Provisional.
Length = 455
Score = 27.5 bits (62), Expect = 9.5
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 234 ITEQMSREAQELLQLFGVPFIVAP 257
I E M + A+ L GVP++V P
Sbjct: 241 IGESMRKAAEALEARTGVPYLVFP 264
>gnl|CDD|226643 COG4175, ProV, ABC-type proline/glycine betaine transport system,
ATPase component [Amino acid transport and metabolism].
Length = 386
Score = 27.3 bits (61), Expect = 10.0
Identities = 15/25 (60%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 93 EQFSALPPDMRHEILTELLE-QRKL 116
E FSAL P +R E+ ELLE Q KL
Sbjct: 190 EAFSALDPLIRTEMQDELLELQAKL 214
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
0.318 0.134 0.389
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: 16,032,488
Number of extensions: 1548375
Number of successful extensions: 1788
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1767
Number of HSP's successfully gapped: 61
Length of query: 314
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 217
Effective length of database: 6,635,264
Effective search space: 1439852288
Effective search space used: 1439852288
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.4 bits)