RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14489
(284 letters)
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 352 bits (906), Expect = e-115
Identities = 133/284 (46%), Positives = 181/284 (63%), Gaps = 11/284 (3%)
Query: 2 QNTLLLVDGSSCIYRAFYAL-PDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDA 60
TLLL+DGSS ++RAFYAL P +RN D P GA+YG + ML KL K + T++A FDA
Sbjct: 1 MKTLLLIDGSSLLFRAFYALLPTLRNSDGLPTGAVYGFLNMLLKLLKEEKPTHVAVAFDA 60
Query: 61 KGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQ 120
KGK FR+ LYP YKA R MP +L QI LI ++++A+G P+L ++G EADDVIGTLAKQ
Sbjct: 61 KGKTFRHELYPEYKANRPPMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQ 120
Query: 121 AVTKHNLKVIISTNDKDMAQLVSNKIALIN-----NNKIHDRTTIISRFGVSPEKIVDYF 175
A +V+I T DKD+ QLV + + L++ N+ D ++ ++GV+PE+I+DY
Sbjct: 121 A-EAAGYEVLIVTGDKDLLQLVDDNVTLLDTMGVSKNEELDPEEVVEKYGVTPEQIIDYL 179
Query: 176 SLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLK 235
+L+GD SDN+PGV IG KTA KLL +Y SLE + N + IKG + LR +
Sbjct: 180 ALMGDSSDNIPGVPGIGEKTAAKLLQEYGSLEGLYENLDEIKGKKKEKLRENKEQAFLSR 239
Query: 236 KILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKL 279
K+ TIKTD L + E L LQP D + L+ LF + + L
Sbjct: 240 KLATIKTDVPLEVD----LEDLELQPPDREKLIALFKELEFKSL 279
>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease.
Length = 259
Score = 272 bits (699), Expect = 4e-92
Identities = 113/254 (44%), Positives = 165/254 (64%), Gaps = 7/254 (2%)
Query: 3 NTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKG 62
LLLVDGSS +RA++ALP ++N P A+YG ++ML KL K + TY+A +FDAKG
Sbjct: 1 KKLLLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYVAVVFDAKG 60
Query: 63 KNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAV 122
K FR+ LYP YKA R K P L+ QI LI +++ A+G P+L ++G EADDVI TLAK+A
Sbjct: 61 KTFRHELYPEYKANRPKTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKA- 119
Query: 123 TKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTT------IISRFGVSPEKIVDYFS 176
+V I + DKD+ QLVS+K+++++ K +I ++G++PE+I+DY +
Sbjct: 120 EAEGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFELYTPENVIEKYGLTPEQIIDYKA 179
Query: 177 LIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKK 236
L+GD SDN+PGV IG KTA KLL ++ SLENI+ N + +K + + L +K
Sbjct: 180 LMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLDKLKKKLREKLLAHKEDAKLSRK 239
Query: 237 ILTIKTDCDLTKNI 250
+ TI+TD L ++
Sbjct: 240 LATIETDVPLEVDL 253
>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 = 259 bits (665), Expect = 2e-80
Identities = 114/278 (41%), Positives = 158/278 (56%), Gaps = 13/278 (4%)
Query: 5 LLLVDGSSCIYRAFYALP--DIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKG 62
LLL+DG S +RA++AL + N P A+YG KML KL K + TY+A FD+
Sbjct: 1 LLLIDGHSLAFRAYFALKNKPLTNSKGEPTNAVYGFTKMLLKLLKEEKPTYVAVAFDSGT 60
Query: 63 KNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAV 122
FR+ Y YKA R P LI QI LI +++ A+G PIL ++G EADDVI TLAKQA
Sbjct: 61 PTFRHEAYAEYKANRAPTPEELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQA- 119
Query: 123 TKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTI-----ISRFGVSPEKIVDYFSL 177
K +V I + DKD+ QLVS+ + ++ T I + ++GV+P+++VD +L
Sbjct: 120 EKEGYEVRIISGDKDLLQLVSDNVKVLIPKGKTSFTEITPEYVVEKYGVTPDQLVDLKAL 179
Query: 178 IGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKG-VIGKNLRFALNWLPKLKK 236
+GD SDN+PGVK IG KTA KLL ++ SLENI N + IK + + L K+
Sbjct: 180 VGDSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQIKSAKMREKLIAHKEDAFLSKE 239
Query: 237 ILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKY 274
+ TI TD L ++ E L L D + L L +
Sbjct: 240 LATIVTDVPLEVDL----EDLRLSEPDRERLYALLQEL 273
>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of
PolI) [DNA replication, recombination, and repair].
Length = 310
Score = 234 bits (599), Expect = 3e-76
Identities = 110/285 (38%), Positives = 160/285 (56%), Gaps = 10/285 (3%)
Query: 3 NTLLLVDGSSCIYRAFYALP-DIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61
LLL+DGSS +YRA +ALP + N P GA+ G + ML +L + T+ +FD K
Sbjct: 11 GKLLLIDGSSLLYRALHALPQPLGNPLGDPTGAVSGFLGMLYRLIRLLEPTHPVVVFDGK 70
Query: 62 GKNFRNILYPSYKATRKK-MPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQ 120
FR+ L YKA R+K MP L QI ++ +++ A+G P+L + G+EADD I TLA Q
Sbjct: 71 PPTFRHELLEEYKANREKEMPDELAPQIPILTELLVALGIPLLELMGIEADDPIETLA-Q 129
Query: 121 AVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIH-----DRTTIISRF-GVSPEKIVDY 174
K V+I + DKD+ QLVS + +IN K D + +F G++PE+++D
Sbjct: 130 KAYKKGDVVLIISGDKDLLQLVSPNVLVINGKKGEPEKFLDLEEVEEKFKGLTPEQLIDL 189
Query: 175 FSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKL 234
+L+GD SDN+PGVK IGPKTA+KLL +Y SLE + N + IK + L
Sbjct: 190 KALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIKKKTREKLLEDKEKAFLS 249
Query: 235 KKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKL 279
K + TIKTD L ++ I L++ D L++ + +L
Sbjct: 250 KPLATIKTDVPLEFDLEDI-LELLVPEHDFSKLLEERVELGFKRL 293
>gnl|CDD|189029 cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuclease of Taq DNA
polymerase I and homologs. The 5'-3' exonuclease
(53EXO) PIN (PilT N terminus) domain of multi-domain DNA
polymerase I and single domain protein homologs are
included in this family. Taq contains a polymerase
domain for synthesizing a new DNA strand and a 53EXO PIN
domain for cleaving RNA primers or damaged DNA strands.
Taq's 53EXO PIN domain recognizes and
endonucleolytically cleaves a structure-specific DNA
substrate that has a bifurcated downstream duplex and an
upstream template-primer duplex that overlaps the
downstream duplex by 1 bp. The 53EXO PIN domain cleaves
the unpaired 5'-arm of the overlap flap DNA substrate.
5'-3' exonucleases are members of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN domain with
a helical arch/clamp region (I domain) of variable
length (approximately 16 residues in 53EXO PIN domains)
and a H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA/RNA binding. The active site
includes a set of conserved acidic residues that are
essential for binding divalent metal ions required for
nuclease activity.
Length = 174
Score = 206 bits (528), Expect = 2e-67
Identities = 73/157 (46%), Positives = 104/157 (66%), Gaps = 2/157 (1%)
Query: 5 LLLVDGSSCIYRAFYALPDIRNIDN-FPVGALYGTIKMLRKLYKNYRATYIACIFDAKGK 63
LLL+DGSS ++RA+YALP + N D+ P A+YG + ML KL K + T++A FDAKG
Sbjct: 1 LLLIDGSSLLFRAYYALPPLTNSDDGEPTNAVYGFLNMLLKLLKEEKPTHVAVAFDAKGP 60
Query: 64 NFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVT 123
FR+ LYP YKA R MP L Q+ LI ++++A+G P+L ++G EADDVIGTLAK+A
Sbjct: 61 TFRHELYPEYKANRPPMPEELRPQLPLIKELLEALGIPVLEVEGYEADDVIGTLAKKAE- 119
Query: 124 KHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTI 160
+ +V+I + DKD+ QLVS + +++ K
Sbjct: 120 EEGYEVVIVSGDKDLLQLVSENVRVLDPKKGSKFELY 156
>gnl|CDD|237877 PRK14976, PRK14976, 5'-3' exonuclease; Provisional.
Length = 281
Score = 206 bits (527), Expect = 7e-66
Identities = 111/286 (38%), Positives = 162/286 (56%), Gaps = 14/286 (4%)
Query: 1 MQNTLLLVDGSSCIYRAFYAL----PDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIAC 56
M LL+DG+S I+R++YA P ++N P A++ + M+ K+ K +YI
Sbjct: 1 MMKKALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTNAIHTFLTMIFKILKKLNPSYILI 60
Query: 57 IFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGT 116
FDA K FR+ LY YK RKK P +LI QI L+ +++K G G EADD+IG+
Sbjct: 61 AFDAGRKTFRHQLYDEYKQGRKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGS 120
Query: 117 LAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNK-----IHDRTTIISRFGVSPEKI 171
LAK+ +K N+ V+I ++DKD+ QLV+ ++ K I + +G+ P++I
Sbjct: 121 LAKKL-SKQNITVLIYSSDKDLLQLVNENTDVLLKKKGTSHFILNTNNFFELYGIEPKQI 179
Query: 172 VDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWL 231
+DY L+GD SDN+ GVK IGPKTA+KLLN+Y ++ENI N + IK I L A
Sbjct: 180 IDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENIDKIKKKIKNKLSEAKEKA 239
Query: 232 PKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLN 277
KK+ TIKTD L I I L+ D+ L ++F + +L
Sbjct: 240 LLSKKLATIKTDVPLDFQIEDI----KLKKLDQPELKKIFEELELK 281
>gnl|CDD|145734 pfam02739, 5_3_exonuc_N, 5'-3' exonuclease, N-terminal
resolvase-like domain.
Length = 169
Score = 186 bits (475), Expect = 2e-59
Identities = 73/155 (47%), Positives = 97/155 (62%), Gaps = 5/155 (3%)
Query: 3 NTLLLVDGSSCIYRAFYALPD--IRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDA 60
LLL+DGSS +RAF+ALP + N P A+YG ++ML KL K + TY+A +FDA
Sbjct: 1 KKLLLIDGSSLAFRAFFALPKVPLTNSKGEPTNAVYGFLRMLLKLLKEEKPTYVAVVFDA 60
Query: 61 KGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQ 120
FR+ LY YKA R K P L QI LI +++ A+G P+L + G EADDVIGTLAK+
Sbjct: 61 GAPTFRHELYEEYKANRAKTPDELPPQIPLIKELLDALGIPVLEVPGYEADDVIGTLAKK 120
Query: 121 AVTKHNLKVIISTNDKDMAQLVS--NKIALINNNK 153
A K V I + DKD+ QLVS +A++N +
Sbjct: 121 A-EKEGYDVRIVSGDKDLLQLVSDKVNVAVLNPGR 154
>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional.
Length = 256
Score = 141 bits (359), Expect = 5e-41
Identities = 81/257 (31%), Positives = 123/257 (47%), Gaps = 17/257 (6%)
Query: 1 MQNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKM----LRKLYKNYRATYIAC 56
M N LL++D + I R P +I+ ++ L KL ++ + T+
Sbjct: 1 MMNHLLIIDALNLIRRIHAVQPSPNDINA--------CVETCQHALDKLIRHSQPTHAVA 52
Query: 57 IFD--AKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVI 114
+FD A+ +R+ L P YKA RK MP L + I + +G G EADD+I
Sbjct: 53 VFDGDARSSGWRHQLLPDYKAGRKPMPEALQQGLPAIRAAFEELGIDSWHADGNEADDLI 112
Query: 115 GTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN--NNKIHDRTTIISRFGVSPEKIV 172
TLA + V + + I + DK QL+S I + + + D I FGV P+++
Sbjct: 113 ATLAVK-VAQAGHQATIVSTDKGYCQLLSPTIQIRDYFQKRWLDAPFIEQEFGVEPQQLP 171
Query: 173 DYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLP 232
DY+ L G S +PGV IGPK+A +LLNQ+ SLENI + + + K L
Sbjct: 172 DYWGLAGISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLDALPEKWRKKLEEHKEMAR 231
Query: 233 KLKKILTIKTDCDLTKN 249
+K+ ++TD L N
Sbjct: 232 LCRKLAQLQTDLPLGGN 248
>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 = 93.6 bits (234), Expect = 1e-24
Identities = 35/73 (47%), Positives = 49/73 (67%)
Query: 168 PEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFA 227
PE+I+DY +L+GD SDN+PGV IGPKTA KLL +Y SLENI+ N + +KG + + L
Sbjct: 1 PEQIIDYLALVGDSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDELKGKLREKLEEN 60
Query: 228 LNWLPKLKKILTI 240
+K+ T+
Sbjct: 61 KEQALLSRKLATL 73
>gnl|CDD|216458 pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-terminal SAM fold.
Length = 100
Score = 93.8 bits (234), Expect = 3e-24
Identities = 42/102 (41%), Positives = 63/102 (61%), Gaps = 3/102 (2%)
Query: 166 VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLR 225
++PE+I+DY +L+GD SDN+PGV IG KTA KLL +Y SLENI N + +KG + + L
Sbjct: 1 LTPEQIIDYKALVGDSSDNIPGVPGIGEKTAAKLLKEYGSLENIYENLDKLKGKLREKLL 60
Query: 226 FALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLL 267
+K+ TIKTD L +++ + + P E+L+
Sbjct: 61 NGKEDAFLSRKLATIKTDVPLE---LTLEDLRLKPPDKEELI 99
>gnl|CDD|189019 cd00008, PIN_53EXO-like, PIN domains of the 5'-3' exonucleases of
DNA polymerase I, bacteriophage T4 RNase H and T5-5'
nucleases, and homologs. PIN (PilT N terminus) domains
of the 5'-3' exonucleases (53EXO) of mutli-domain DNA
polymerase I and single domain protein homologs, as well
as, the PIN domains of bacteriophage T5-5'nuclease
(T5FEN or 5'-3'exonuclease), bacteriophage T4 RNase H
(T4FEN), bacteriophage T3 (T3 phage
exodeoxyribonuclease) and other similar nucleases are
included in this family. The 53EXO of DNA polymerase I
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
T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also
exhibits endonucleolytic activity on flap structures
(branched duplex DNA containing a free single-stranded
5'end). T4 RNase H, which removes the RNA primers that
initiate lagging strand fragments, has 5'- 3'exonuclease
activity on DNA/DNA and RNA/DNA duplexes and has
endonuclease activity on flap or forked DNA structures.
These nucleases 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. They contain a
PIN domain with a helical arch/clamp region (I domain)
of variable length (approximately 16 to 30 residues in
53EXO-like 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. The
active site of the 53EXO of Taq DNA polymerase I
includes a set of conserved acidic residues that are
essential for binding three divalent metal ions (two
Mn2+ ions and one Zn2+ ion) required for nuclease
activity. T5-5'nuclease requires at least two bound
divalent metal ions for nuclease activity and is
reported to be able to use Mg2+, Mn2+ or Co2+ as
co-factors.
Length = 160
Score = 81.9 bits (202), Expect = 4e-19
Identities = 37/150 (24%), Positives = 61/150 (40%), Gaps = 11/150 (7%)
Query: 5 LLLVDGSSCIYRAFYAL-PDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGK 63
L+LVDG++ +R + I+ + ++ L K+Y A + D
Sbjct: 1 LMLVDGTNLAFRTKHNNSKKKEKIN--LSPFASSYVSSIQSLAKSYSARTTIVLGDKGKS 58
Query: 64 NFRNILYPSYKATR-------KKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGT 116
FR P YK R K + + ++ KA +P I+G EADD+
Sbjct: 59 VFRLEHLPEYKGNRDEKYAEEKALDEQFFEYLKDAFELCKATTFPTFTIRGYEADDMAAY 118
Query: 117 LAKQAVTKHNLKVIISTNDKDMAQLVSNKI 146
L K+ V I + D D QL+++K+
Sbjct: 119 LVKKI-GHEGDHVWIISTDGDWDQLLTDKV 147
>gnl|CDD|189030 cd09860, PIN_T4-like, PIN domain of bacteriophage T3, T4 RNase H,
T5-5'nuclease, and homologs. PIN (PilT N terminus)
domain of bacteriophage T5-5'nuclease (5'-3' exonuclease
or T5FEN), bacteriophage T4 RNase H (T4FEN),
bacteriophage T3 (T3 phage exodeoxyribonuclease) and
other similar 5' nucleases are included in this family.
T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also
exhibits endonucleolytic activity on flap structures
(branched duplex DNA containing a free single-stranded
5'end). T4 RNase H, which removes the RNA primers that
initiate lagging strand fragments, has 5'- 3'exonuclease
activity on DNA/DNA and RNA/DNA duplexes and has
endonuclease activity on flap or forked DNA structures.
Bacteriophage T3 is believed to function in the removal
of DNA-linked RNA primers and is essential for phage DNA
replication and also necessary for host DNA degradation
and phage genetic recombination. These nucleases 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. They have a PIN domain with a helical
arch/clamp region (I domain) of variable length
(approximately 20 to 30 residues in PIN T5-like domains)
and a H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA/RNA binding. The active site
includes a set of conserved acidic residues that are
essential for binding divalent metal ions required for
nuclease activity. In the T5-5'nuclease,
structure-specific endonuclease activity requires
binding of a single metal ion in the high-affinity,
metal binding site 1, whereas exonuclease activity
requires both, the high-affinity, metal binding site 1
and the low-affinity, metal binding site 2 to be
occupied by a divalent cofactor. The T5-5'nuclease is
reported to be able to bind several metal ions
including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors.
Length = 170
Score = 65.1 bits (159), Expect = 7e-13
Identities = 41/150 (27%), Positives = 67/150 (44%), Gaps = 13/150 (8%)
Query: 5 LLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKN 64
+LL+DG+ + A Y+ V A +G + +++ K Y+ ++D K
Sbjct: 2 ILLIDGNQLGFAAMYS-NFKDESGIMEVMARHGLLDSIKRNAKRYKYAIPIVLWD-GRKY 59
Query: 65 FRNILYPSYKATRKKMP-------YNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTL 117
+R L P YKA R K P Y + I +M + + + I G EADDV L
Sbjct: 60 WRRDLLPYYKANRDKTPDKRAWEGYFEAQKP-YIEEMKENMPVIQIRIPGAEADDVAAVL 118
Query: 118 AKQ-AVTKHNLKVIISTNDKDMAQLVSNKI 146
K+ + H KV++ ++D D QL +
Sbjct: 119 VKKLSAFGH--KVLLISSDGDWTQLHKPNV 146
>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 = 57.4 bits (139), Expect = 4e-11
Identities = 30/72 (41%), Positives = 42/72 (58%), Gaps = 2/72 (2%)
Query: 169 EKIVDYFSLIG-DMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFA 227
E+ +D +L+G D SDN PGV IGPKTA KL +Y SLE I+ N + +KG + L
Sbjct: 1 EQFIDLCALVGCDYSDN-PGVPGIGPKTAAKLALKYGSLEGILENLDELKGKKREKLEEP 59
Query: 228 LNWLPKLKKILT 239
+ +K+ T
Sbjct: 60 KEYAFLSRKLAT 71
>gnl|CDD|197623 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol1 family) motifs.
Length = 36
Score = 55.1 bits (134), Expect = 1e-10
Identities = 23/36 (63%), Positives = 30/36 (83%)
Query: 168 PEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQY 203
PE+ +DY L+GD SDN+PGVK IGPKTA+KLL ++
Sbjct: 1 PEQFIDYAILVGDYSDNIPGVKGIGPKTALKLLREF 36
>gnl|CDD|222794 PHA00439, PHA00439, exonuclease.
Length = 286
Score = 57.9 bits (140), Expect = 8e-10
Identities = 44/175 (25%), Positives = 68/175 (38%), Gaps = 25/175 (14%)
Query: 35 LYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRK--KMP--YNLILQINL 90
L +IK + K ++ I F N+R + P+YKA RK + P Y L+ +
Sbjct: 48 LEDSIKSYKTRKKAWKDAPIVLAFTDS-VNWRKEVVPTYKANRKAKRKPVGYRKFLEELM 106
Query: 91 IHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN 150
+ K+I P G+E DDV+G + K ++ + DKD + +
Sbjct: 107 AREEWKSILEP-----GLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKTIPNCDFLWCT 161
Query: 151 NNKIHDRTTIISRFGVSPEKIVDYFSLI----GDMSDNLPGVKKIGPKTAVKLLN 201
I +T PE D + L GD +D G+ G TA L
Sbjct: 162 TGNILTQT---------PET-ADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLE 205
>gnl|CDD|222882 PHA02567, rnh, RnaseH; Provisional.
Length = 304
Score = 50.8 bits (122), Expect = 2e-07
Identities = 28/111 (25%), Positives = 50/111 (45%), Gaps = 12/111 (10%)
Query: 42 LRKLYKNYRATY---IACIFDAKGKNFRNILYPSYKATRKK----MPYNLILQINLIHQM 94
+R K ++ Y + ++K +R + YK RKK P++ I+++
Sbjct: 52 IRYNVKKFKEEYPEIVLAFDNSKSGYWRRDIAWYYKKNRKKDREESPWDWEGLFEAINKI 111
Query: 95 VKAI----GWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQL 141
V I + ++ I EADD+I L K+ + V+I ++D D QL
Sbjct: 112 VDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAE-GRPVLIVSSDGDFTQL 161
>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 = 42.5 bits (101), Expect = 9e-06
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 183 DNLPGVKKIGPKTAVKLLNQYNSLENIINN 212
D LP + IGPKTA KL+ ++ S+E ++
Sbjct: 13 DYLPSIPGIGPKTAYKLIKKHKSIEKVLKA 42
>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 = 42.1 bits (100), Expect = 1e-05
Identities = 19/58 (32%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 169 EKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRF 226
E+ +D L+G D +K IGPKTA+KL+ ++ S+E I+ N + K + ++ +
Sbjct: 1 EQFIDLCILLG--CDYCESIKGIGPKTALKLIKKHKSIEKILENIDKSKYPVPEDWPY 56
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 44.8 bits (107), Expect = 2e-05
Identities = 19/46 (41%), Positives = 33/46 (71%), Gaps = 2/46 (4%)
Query: 165 GVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENII 210
G++ E+++D L+G +D PG+K IGPKTA+KL+ ++ LE ++
Sbjct: 173 GITREQLIDIAILVG--TDYNPGIKGIGPKTALKLIKKHGDLEKVL 216
>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 = 41.4 bits (98), Expect = 2e-05
Identities = 21/49 (42%), Positives = 30/49 (61%), Gaps = 2/49 (4%)
Query: 169 EKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIK 217
E+ +D L G D LPG+ IGPKTA+KL+ +Y SLE ++ + K
Sbjct: 1 EQFIDLCILSG--CDYLPGLPGIGPKTALKLIKEYGSLEKVLKALRDDK 47
>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 = 43.8 bits (104), Expect = 4e-05
Identities = 20/49 (40%), Positives = 33/49 (67%), Gaps = 2/49 (4%)
Query: 162 SRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENII 210
S G++ E+++D L+G +D GVK IGPKTA+KL+ ++ LE ++
Sbjct: 217 SELGITREQLIDIAILVG--TDYNEGVKGIGPKTALKLIKEHGDLEKVL 263
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
Length = 393
Score = 43.1 bits (102), Expect = 9e-05
Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 159 TIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKG 218
T++ G+S ++ +D L G D +K IGPKTA KL+ +Y S+E I+ + + K
Sbjct: 213 TVLEELGLSMDQFIDLCILCG--CDYCDTIKGIGPKTAYKLIKKYKSIEEILEHLDKTKY 270
Query: 219 VIGKNLRF 226
+ +N +
Sbjct: 271 PVPENFDY 278
>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 = 41.4 bits (97), Expect = 1e-04
Identities = 34/161 (21%), Positives = 61/161 (37%), Gaps = 19/161 (11%)
Query: 5 LLLVDGSSCIYRAFYAL---PDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61
+ +DGS+ Y+ + + + +F G Y I + KNY A +FD
Sbjct: 1 KVAIDGSNLGYQFLHNNRKDKEKGELTSFASGYFYTIISLA----KNYSAITPIVVFDGG 56
Query: 62 GKNFRNILYPSYKATR-----------KKMPYNLILQINLIHQMVKAIGWPILIIKGVEA 110
R P YK R K++ + +++K +G P I+ EA
Sbjct: 57 KPVLRLEHLPEYKENRDEAEAEATEEEKRLDEQTFEYLKDCKELLKLMGIPYFDIRPSEA 116
Query: 111 DDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINN 151
+D+ L K V + + D D L ++K++ +
Sbjct: 117 EDMAAYLVK-KGGHLYDVVALISTDGDWLTLGTDKVSRFSF 156
>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 = 36.0 bits (84), Expect = 0.002
Identities = 20/43 (46%), Positives = 30/43 (69%), Gaps = 3/43 (6%)
Query: 169 EKIVDYFSLIGDMSD-NLPGVKKIGPKTAVKLLNQYNSLENII 210
E+++D L+G +D N GVK IGPKTA+KL+ +Y LE ++
Sbjct: 1 EQLIDIAILVG--TDYNPGGVKGIGPKTALKLVKEYGDLEKVL 41
>gnl|CDD|188620 cd09900, H3TH_XPG-like, H3TH domains of Flap endonuclease-1
(FEN1)-like structure specific 5' nucleases: FEN1
(archaeal), GEN1, YEN1, and XPG. The 5' nucleases
within this family are capable of both 5'-3'
exonucleolytic activity and cleaving bifurcated or
branched DNA, in an endonucleolytic, structure-specific
manner, and are involved in DNA replication, repair, and
recombination. This family includes the H3TH
(helix-3-turn-helix) domains of archaeal Flap
Endonuclease-1 (FEN1), Gap Endonuclease 1 (GEN1), Yeast
Endonuclease 1 (YEN1), Xeroderma pigmentosum
complementation group G (XPG) nuclease, and other
eukaryotic and archaeal homologs. These nucleases
contain a PIN (PilT N terminus) domain with a helical
arch/clamp region/I domain (not included here) and
inserted within the PIN domain is an atypical
helix-hairpin-helix-2 (HhH2)-like region. This atypical
HhH2 region, the H3TH domain, has an extended loop with
at least three turns between the first two helices, and
only three of the four helices appear to be conserved.
Both the H3TH domain and the helical arch/clamp region
are involved in DNA binding. Studies suggest that a
glycine-rich loop in the H3TH domain contacts the
phosphate backbone of the template strand in the
downstream DNA duplex. With the except of the Mkt1-like
proteins, the nucleases within this family have a
carboxylate rich active site that is involved in binding
essential divalent metal ion cofactors (i. e., Mg2+,
Mn2+, Zn2+, or Co2+) required for nuclease activity. The
first metal binding site is composed entirely of Asp/Glu
residues from the PIN domain, whereas, the second metal
binding site is composed generally of two Asp residues
from the PIN domain and one Asp residue from the H3TH
domain. Together with the helical arch and network of
amino acids interacting with metal binding ions, the
H3TH region defines a positively charged active-site
DNA-binding groove in structure-specific 5' nucleases.
Length = 52
Score = 34.4 bits (80), Expect = 0.003
Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 3/45 (6%)
Query: 169 EKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNS-LENIINN 212
E+++ L+G +D PGV IGPKTA++LL ++ LE + +
Sbjct: 1 EQLILLALLLG--TDYNPGVPGIGPKTALELLKEFGEDLEKFLES 43
>gnl|CDD|188619 cd09899, H3TH_T4-like, H3TH domain of bacteriophage T3, T4 RNase H,
T5-5' nucleases, and homologs. H3TH
(helix-3-turn-helix) domains of bacteriophage
T5-5'nuclease (5'-3' exonuclease or T5FEN),
bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3
phage exodeoxyribonuclease) and other similar 5'
nucleases are included in this family. The T5-5'nuclease
is a 5'-3' exodeoxyribonuclease that also exhibits
endonucleolytic activity on flap structures (branched
duplex DNA containing a free single-stranded 5'end). T4
RNase H, which removes the RNA primers that initiate
lagging strand fragments, has 5'- 3' exonuclease
activity on DNA/DNA and RNA/DNA duplexes and has
endonuclease activity on flap or forked DNA structures.
Bacteriophage T3 is believed to function in the removal
of DNA-linked RNA primers and is essential for phage DNA
replication and also necessary for host DNA degradation
and phage genetic recombination. These nucleases 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. They 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 required for nuclease activity. The first
metal binding site (MBS-1) is composed entirely of
Asp/Glu residues from the PIN domain, whereas, the
second metal binding site (MBS-2) is composed generally
of two Asp residues from the PIN domain and two Asp
residues from the H3TH domain. In the T5-5'nuclease,
structure-specific endonuclease activity requires
binding of a single metal ion in the high-affinity,
MBS-1, whereas exonuclease activity requires both, the
high-affinity, MBS-1 and the low-affinity, MBS-2 to be
occupied by a divalent cofactor. The T5-5'nuclease is
reported to be able to bind several metal ions
including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors.
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 = 74
Score = 34.8 bits (80), Expect = 0.006
Identities = 15/38 (39%), Positives = 20/38 (52%)
Query: 177 LIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNAN 214
L GD DN+ GV IG A KLL + + +II+
Sbjct: 11 LAGDTKDNIAGVPGIGTGRATKLLEEIGDVADIIDALL 48
>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 = 34.1 bits (79), Expect = 0.008
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 183 DNLPGVKKIGPKTAVKLLNQYNSLENIIN 211
D LP + IG K A KL+ ++ ++E +I
Sbjct: 13 DYLPSLPGIGLKKAYKLVRRHRTIEKVIK 41
>gnl|CDD|184199 PRK13639, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 275
Score = 31.6 bits (72), Expect = 0.44
Identities = 10/31 (32%), Positives = 22/31 (70%)
Query: 124 KHNLKVIISTNDKDMAQLVSNKIALINNNKI 154
K + +IIST+D D+ + ++K+ ++++ KI
Sbjct: 185 KEGITIIISTHDVDLVPVYADKVYVMSDGKI 215
>gnl|CDD|213193 cd03226, ABC_cobalt_CbiO_domain2, Second domain of the ATP-binding
cassette component of cobalt transport system. Domain
II of the ABC component of a cobalt transport family
found in bacteria, archaea, and eukaryota. The
transition metal cobalt is an essential component of
many enzymes and must be transported into cells in
appropriate amounts when needed. The CbiMNQO family ABC
transport system is involved in cobalt transport in
association with the cobalamin (vitamin B12)
biosynthetic pathways. Most cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are encoded
by the conserved gene cluster cbiMNQO. Both the CbiM and
CbiQ proteins are integral cytoplasmic membrane
proteins, and the CbiO protein has the linker peptide
and the Walker A and B motifs commonly found in the
ATPase components of the ABC-type transport systems.
Length = 205
Score = 30.3 bits (69), Expect = 0.78
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 112 DVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIH 155
++I LA Q VI+ T+D + V +++ L+ N I
Sbjct: 167 ELIRELAAQGKA-----VIVITHDYEFLAKVCDRVLLLANGAIV 205
>gnl|CDD|205093 pfam12826, HHH_2, Helix-hairpin-helix motif. The HhH domain of
DisA, a bacterial checkpoint control protein, is a
DNA-binding domain.
Length = 64
Score = 27.4 bits (62), Expect = 1.7
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 187 GVKKIGPKTAVKLLNQYNSLENIIN 211
G++ +G KTA L + SL+ + N
Sbjct: 7 GIRHVGEKTAKLLAKHFGSLDALAN 31
>gnl|CDD|213197 cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the
drug resistance transporter and related proteins,
subfamily A. This family of ATP-binding proteins
belongs to a multi-subunit transporter involved in drug
resistance (BcrA and DrrA), nodulation, lipid transport,
and lantibiotic immunity. In bacteria and archaea, these
transporters usually include an ATP-binding protein and
one or two integral membrane proteins. Eukaryotic
systems of the ABCA subfamily display ABC domains that
are quite similar to this family. The ATP-binding domain
shows the highest similarity between all members of the
ABC transporter family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 173
Score = 28.9 bits (66), Expect = 2.1
Identities = 9/43 (20%), Positives = 27/43 (62%), Gaps = 5/43 (11%)
Query: 112 DVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKI 154
+++ L K+ T +++S++ + A+ + +++A++NN +I
Sbjct: 136 ELLRELKKEGKT-----ILLSSHILEEAERLCDRVAILNNGRI 173
>gnl|CDD|234600 PRK00053, alr, alanine racemase; Reviewed.
Length = 363
Score = 29.0 bits (66), Expect = 2.6
Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 17/95 (17%)
Query: 101 PILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIH---DR 157
PILI+ G + + + +NL + + + + + K L K+H D
Sbjct: 77 PILILGGFFPAEDLPLIIA-----YNLTTAV--HSLEQLEALE-KAELGKPLKVHLKID- 127
Query: 158 TTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIG 192
T + R GV PE+ + P V+ G
Sbjct: 128 -TGMHRLGVRPEEAEAALERL----LACPNVRLEG 157
>gnl|CDD|234755 PRK00419, PRK00419, DNA primase small subunit; Reviewed.
Length = 376
Score = 29.2 bits (66), Expect = 2.8
Identities = 18/93 (19%), Positives = 31/93 (33%), Gaps = 5/93 (5%)
Query: 169 EKIVDYFS-LIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFA 227
++ + L + L IG TA K+L + N+ G R A
Sbjct: 206 RRLGYFIDHLRELALERLEEFDGIGEGTAKKILKAARDNTEFL-RKGNLDAFHGIGPRLA 264
Query: 228 LNWLPKLKKILTIKTDCDLT---KNIVSIPESL 257
+ + D +T K ++ +P SL
Sbjct: 265 ARLFAESVRFSKAPIDEPVTIDIKRLIRLPGSL 297
>gnl|CDD|224051 COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase
component [Amino acid transport and metabolism].
Length = 240
Score = 28.6 bits (65), Expect = 3.1
Identities = 12/45 (26%), Positives = 27/45 (60%), Gaps = 5/45 (11%)
Query: 112 DVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHD 156
DV+ LA++ +T +II T++ A+ V++++ ++ KI +
Sbjct: 177 DVMKDLAEEGMT-----MIIVTHEMGFAREVADRVIFMDQGKIIE 216
>gnl|CDD|223350 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type
II) [DNA replication, recombination, and repair].
Length = 667
Score = 29.1 bits (66), Expect = 3.3
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 187 GVKKIGPKTAVKLLNQYNSLENII 210
G++ +G TA L + +LE ++
Sbjct: 515 GIRHVGETTAKSLARHFGTLEALL 538
>gnl|CDD|237785 PRK14671, uvrC, excinuclease ABC subunit C; Provisional.
Length = 621
Score = 28.9 bits (65), Expect = 3.8
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 185 LPGVKKIGPKTAVKLLNQYNSLENI 209
L + IG KTA KLL + S+E +
Sbjct: 571 LTDIAGIGEKTAEKLLEHFGSVEKV 595
>gnl|CDD|237635 PRK14184, PRK14184, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 286
Score = 28.6 bits (64), Expect = 3.9
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 166 VSPEKIVDYFSL--IGDMSDNLPGVKKIGPKTAVKLLNQYN 204
+ P K VD F +G ++ LPG + P + LL +Y
Sbjct: 112 IDPAKDVDGFHPENMGRLALGLPGFRPCTPAGVMTLLERYG 152
>gnl|CDD|173066 PRK14602, ruvA, Holliday junction DNA helicase RuvA; Provisional.
Length = 203
Score = 28.1 bits (63), Expect = 4.8
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 185 LPGVKKIGPKTAVKLLNQY 203
L + K+G KTA+ +L+Q+
Sbjct: 76 LISISKVGAKTALAILSQF 94
>gnl|CDD|221393 pfam12044, Metallopep, Putative peptidase family. This family of
proteins is functionally uncharacterized. However, it
does contain an HEXXH motif characteristic of
metallopeptidases. This protein is found in bacteria and
eukaryotes. Proteins in this family are typically
between 625 to 773 amino acids in length.
Length = 419
Score = 28.5 bits (64), Expect = 5.1
Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 7/79 (8%)
Query: 109 EADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN-----NNKIHDRTT--II 161
E + TL++ ++ KV + +DK +A+L +A N + D +
Sbjct: 159 EEEWTTDTLSQNTTMRNEAKVHVLRSDKTVAELRDPNLAQQNPDAKDGGGLFDIAADALK 218
Query: 162 SRFGVSPEKIVDYFSLIGD 180
P + + L D
Sbjct: 219 KYGLPQPGQKLKVAVLFLD 237
>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 = 28.3 bits (63), Expect = 5.1
Identities = 18/67 (26%), Positives = 37/67 (55%), Gaps = 7/67 (10%)
Query: 150 NNNK---IHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQY--N 204
N NK + I ++ G+ K+++ L+G SD G+ +GP +A+++LN++ +
Sbjct: 832 NQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLG--SDYTEGIPTVGPVSAMEILNEFPGD 889
Query: 205 SLENIIN 211
LE ++
Sbjct: 890 GLEPLLK 896
>gnl|CDD|187550 cd05239, GDP_FS_SDR_e, GDP-fucose synthetase, extended (e) SDRs.
GDP-fucose synthetase (aka 3, 5-epimerase-4-reductase)
acts in the NADP-dependent synthesis of GDP-fucose from
GDP-mannose. Two activities have been proposed for the
same active site: epimerization and reduction. Proteins
in this subgroup are extended SDRs, which have a
characteristic active site tetrad and an NADP-binding
motif, [AT]GXXGXXG, that is a close match to the
archetypical form. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 27.9 bits (63), Expect = 5.2
Identities = 17/66 (25%), Positives = 22/66 (33%), Gaps = 17/66 (25%)
Query: 6 LLVDGSSCIYRAFYALPDIRNID------------NFPVG-ALYGTIKMLRKLYKNYRAT 52
L+ GSSCIY P ID N A +K+ K Y
Sbjct: 98 LVFLGSSCIYPDLAPQP----IDESDLLTGPPEPTNEGYAIAKRAGLKLCEAYRKQYGCD 153
Query: 53 YIACIF 58
YI+ +
Sbjct: 154 YISVMP 159
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 28.3 bits (64), Expect = 5.9
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 191 IGPKTAVKLLNQYNSLENIIN 211
+GP A LL + S+E ++
Sbjct: 723 VGPVLARNLLEHFGSVEAVMT 743
>gnl|CDD|221659 pfam12597, DUF3767, Protein of unknown function (DUF3767). This
family of proteins is found in eukaryotes. Proteins in
this family are typically between 112 and 199 amino
acids in length.
Length = 119
Score = 26.9 bits (60), Expect = 6.5
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 216 IKGVIGKNLRFALNW 230
++ +IGKN+ A NW
Sbjct: 58 VRFLIGKNIWKAANW 72
>gnl|CDD|234792 PRK00558, uvrC, excinuclease ABC subunit C; Validated.
Length = 598
Score = 27.8 bits (63), Expect = 7.2
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 183 DNLPGVKKIGPKTAVKLLNQYNSLENI 209
D++PG IGPK LL + SL+ I
Sbjct: 546 DDIPG---IGPKRRKALLKHFGSLKAI 569
>gnl|CDD|184317 PRK13774, PRK13774, formimidoylglutamase; Provisional.
Length = 311
Score = 27.5 bits (61), Expect = 7.4
Identities = 25/88 (28%), Positives = 35/88 (39%), Gaps = 7/88 (7%)
Query: 9 DGSSCIYRAFYALPDIRNIDN-FPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNF-- 65
+G I +AF LPD+ + G +Y + L K + A A + F
Sbjct: 68 EGPDAIKQAFAGLPDLNQCETLVDYGNVYHDHEELIDTQKEF-AMLAAKSIANHRQTFLL 126
Query: 66 ---RNILYPSYKATRKKMPYNLILQINL 90
+I Y Y ATRK P I IN+
Sbjct: 127 GGGHDIAYAQYLATRKVYPTQSIGVINI 154
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component of
iron-siderophores, vitamin B12 and hemin transporters
and related proteins. ABC transporters, involved in the
uptake of siderophores, heme, and vitamin B12, are
widely conserved in bacteria and archaea. Only very few
species lack representatives of the siderophore family
transporters. The E. coli BtuCD protein is an ABC
transporter mediating vitamin B12 uptake. The two
ATP-binding cassettes (BtuD) are in close contact with
each other, as are the two membrane-spanning subunits
(BtuC); this arrangement is distinct from that observed
for the E. coli lipid flippase MsbA. The BtuC subunits
provide 20 transmembrane helices grouped around a
translocation pathway that is closed to the cytoplasm by
a gate region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 27.0 bits (61), Expect = 7.7
Identities = 6/39 (15%), Positives = 21/39 (53%)
Query: 117 LAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIH 155
L ++ + V++ +D ++A ++++ L+ + +I
Sbjct: 139 LLRRLARERGKTVVMVLHDLNLAARYADRVILLKDGRIV 177
>gnl|CDD|237678 PRK14335, PRK14335, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 455
Score = 27.6 bits (61), Expect = 9.7
Identities = 22/111 (19%), Positives = 46/111 (41%), Gaps = 10/111 (9%)
Query: 87 QINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVI--ISTNDKDMAQLVSN 144
+I L+ Q V + V ++ + ++A ++ I +S++ KD++ +
Sbjct: 200 EITLLGQNVNSYRGRDREGNIVTFPQLLRHIVRRAEVTDQIRWIRFMSSHPKDLSDDLIA 259
Query: 145 KIA-------LINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGV 188
IA L++ H ++ R S Y SL+G + ++P V
Sbjct: 260 TIAQESRLCRLVHLPVQHGSNGVLKRMNRS-YTREHYLSLVGKLKASIPNV 309
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 0.139 0.401
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,413,388
Number of extensions: 1403496
Number of successful extensions: 1533
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1491
Number of HSP's successfully gapped: 83
Length of query: 284
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 188
Effective length of database: 6,679,618
Effective search space: 1255768184
Effective search space used: 1255768184
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: 58 (26.0 bits)