RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 022427
(297 letters)
>gnl|CDD|187694 cd07181, RNase_HII_eukaryota_like, Mammalian RNase HII is
functional when it forms a complex with two other
accessory protein. Ribonuclease H (RNase H) is
classified into two families, type I (prokaryotic RNase
HI, eukaryotic RNase H1 and viral RNase H) and type II
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2/HII). RNase H endonucleolytically hydrolyzes an RNA
strand when it is annealed to a complementary DNA strand
in the presence of divalent cations, in DNA replication
and repair. The enzyme can be found in bacteria,
archaea, and eukaryotes. Most prokaryotic and eukaryotic
genomes contain multiple RNase H genes. Despite a lack
of evidence for homology from sequence comparisons, type
I and type II RNase H share a common fold and similar
steric configurations of the four acidic active-site
residues, suggesting identical or very similar catalytic
mechanisms. Eukaryotic RNase HII is active during
replication and is believed to play a role in removal of
Okazaki fragment primers and single ribonucleotides in
DNA-DNA duplexes. Eukaryotic RNase HII is functional
when it forms a complex with two other accessory
proteins. It is speculated that the two accessory
subunits are required for correct folding of the
catalytic subunit of RNase HII. Mutations in the three
subunits of human RNase HII cause neurological disorder.
Length = 221
Score = 372 bits (957), Expect = e-131
Identities = 136/218 (62%), Positives = 164/218 (75%), Gaps = 1/218 (0%)
Query: 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKV-NDSV 75
+GIDEAGRGPVLGPMVYG YCP SY++ L L FADSKTL EEKREELF+ LK +D++
Sbjct: 1 LGIDEAGRGPVLGPMVYGAAYCPISYKEELKKLGFADSKTLTEEKREELFKKLKEKDDAL 60
Query: 76 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
GWA I+ P+ +S KML + K NLNEISHD+AIGLI VL+ G+ +TEVY+DTVG EKY
Sbjct: 61 GWATRILSPQYISTKMLARTKYNLNEISHDAAIGLIREVLDKGVNVTEVYVDTVGPPEKY 120
Query: 136 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSG 195
QAKL ++FP IKF V KKADSLYP+VS ASIVAKVTRDR L+ W F+ET + GSG
Sbjct: 121 QAKLQKKFPGIKFTVEKKADSLYPIVSAASIVAKVTRDRALKNWQFDETLIKDSGDLGSG 180
Query: 196 YPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKD 233
YP DP+TK WL + +FG+P LVRFSW T + +
Sbjct: 181 YPSDPKTKKWLKKNVDPVFGYPQLVRFSWSTAKTILEK 218
>gnl|CDD|187691 cd06266, RNase_HII, Ribonuclease H (RNase H) type II family
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2/HII). Ribonuclease H (RNase H) is classified into
two families, type I (prokaryotic RNase HI, eukaryotic
RNase H1 and viral RNase H) and type II (prokaryotic
RNase HII and HIII, and eukaryotic RNase H2/HII). RNase
H endonucleolytically hydrolyzes an RNA strand when it
is annealed to a complementary DNA strand in the
presence of divalent cations. The enzyme can be found in
bacteria, archaea, and eukaryotes. Most prokaryotic and
eukaryotic genomes contain multiple RNase H genes, but
no prokaryotic genome contains the combination of only
RNase HI and HIII. Despite a lack of evidence for
homology from sequence comparisons, type I and type II
RNase H share a common fold and similar steric
configurations of the four acidic active-site residues,
suggesting identical or very similar catalytic
mechanisms. It appears that type I and type II RNases H
also have overlapping functions in cells, as
over-expression of Escherichia coli RNase HII can
complement an RNase HI deletion phenotype in E. coli.
Length = 210
Score = 349 bits (899), Expect = e-123
Identities = 135/211 (63%), Positives = 161/211 (76%), Gaps = 2/211 (0%)
Query: 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVG 76
+GIDEAGRGPVLGPMVY YCP SY + L +L FADSK L EEKREELF+++K + +VG
Sbjct: 1 LGIDEAGRGPVLGPMVYAAAYCPISYLEKLESLGFADSKQLTEEKREELFDEIKEDKAVG 60
Query: 77 WAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQ 136
WAV I+ P +S KML ++K NLNEISHD+AIGLI +L+ G+ +TEVY+DTVG EKYQ
Sbjct: 61 WAVRILSPEYISRKMLARSKYNLNEISHDAAIGLIRNLLDKGVKVTEVYVDTVGPPEKYQ 120
Query: 137 AKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGY 196
AKL +RFP IKF V KKADS YP+VS ASIVAKVTRDR L W F+E ++ FGSGY
Sbjct: 121 AKLLKRFPGIKFTVEKKADSKYPIVSAASIVAKVTRDRALEQWKFDEGLDSGD--FGSGY 178
Query: 197 PGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 227
P DP+TK WL + +FGFPSLVRFSW T
Sbjct: 179 PSDPKTKEWLKKNVDPVFGFPSLVRFSWSTV 209
>gnl|CDD|129812 TIGR00729, TIGR00729, ribonuclease H, mammalian HI/archaeal HII
subfamily. This enzyme cleaves RNA from DNA-RNA
hybrids. Archaeal members of this subfamily of RNase H
are designated RNase HII and one has been shown to be
active as a monomer. A member from Homo sapiens was
characterized as RNase HI, large subunit [DNA
metabolism, DNA replication, recombination, and repair].
Length = 206
Score = 174 bits (443), Expect = 5e-54
Identities = 78/216 (36%), Positives = 112/216 (51%), Gaps = 19/216 (8%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQT-LATLNFADSKTLKEEKREELFEDLKVNDS 74
+ GIDEAGRGPV+GP+V ++ ++ L L DSK L +REELF ++ N
Sbjct: 1 VAGIDEAGRGPVIGPLVV-GVFAIEEKREEELRKLGVKDSKKLTPGRREELFSKIR-NKL 58
Query: 75 VGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEK 134
+ V I P E+ + INLNE + + +EVY+D+V K
Sbjct: 59 GRYEVLKITPEEIDRER----NINLNENEIEKFSKAAI---ILIEKPSEVYVDSVDVNPK 111
Query: 135 ---YQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN 191
+ K+ +R IK + KAD+ YPVVS ASI+AKV RDR + E+ + + +
Sbjct: 112 RFKREIKIKERIEGIKVIAEHKADAKYPVVSAASIIAKVERDREI------ESLKRKYGD 165
Query: 192 FGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 227
FGSGYP DP T+ WL ++ P +VR +W T
Sbjct: 166 FGSGYPSDPRTREWLEEYFKSHGELPDIVRRTWKTV 201
>gnl|CDD|216451 pfam01351, RNase_HII, Ribonuclease HII.
Length = 199
Score = 173 bits (441), Expect = 7e-54
Identities = 74/214 (34%), Positives = 97/214 (45%), Gaps = 18/214 (8%)
Query: 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVG 76
GIDE GRGP+ GP+V +Y P L L DSK L ++KREEL E +K
Sbjct: 1 AGIDEVGRGPLAGPLVVAAVYLPPERLDELRKLGVKDSKKLSDKKREELAELIK------ 54
Query: 77 WAVDIIDPRELSAKMLNK---NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAE 133
I+ R+L A + N+INLN I H + +I V +G+ E+ +D +
Sbjct: 55 ---KRIETRKLVAGNIKYAEANEINLNNILHALHLAMIRAVQKLGVKPDEILVDGFRPPK 111
Query: 134 KYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG 193
K F KADS Y V+ ASI+AKVTRD L + + G
Sbjct: 112 SLPMKQEAIFKIKV-TAEHKADSKYLSVAAASIIAKVTRDEMLE---LLKRFPGYGLDKG 167
Query: 194 SGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 227
SGYP DP T+A L P R S+ T
Sbjct: 168 SGYPSDPHTEALL--KLGATPWLPDFHRRSFATV 199
>gnl|CDD|187693 cd07180, RNase_HII_Archaea_like, Archaeal ribonuclease HII.
Ribonuclease (RNase) H is classified into two families,
type I (prokaryotic RNase HI, eukaryotic RNase H1 and
viral RNase H) and type II (prokaryotic RNase HII and
HIII, archaeal RNase HII and eukaryotic RNase H2/HII).
RNase H endonucleolytically hydrolyzes an RNA strand
when it is annealed to a complementary DNA strand in the
presence of divalent cations, in DNA replication or
repair. Some archaeal RNase HII show broad divalent
cation specificity. It is proposed that three of the
four acidic residues at the active site are involved in
metal binding and the fourth one involved in the
catalytic process in archaea. Most archaeal genomes
contain multiple RNase H genes. Despite a lack of
evidence for homology from sequence comparisons, type I
and type II RNase H share a common fold and similar
steric configurations of the four acidic active-site
residues, suggesting identical or very similar catalytic
mechanisms. It appears that type I and type II RNases H
also have overlapping functions in cells, as
over-expression of Escherichia coli RNase HII can
complement an RNase HI deletion phenotype in E. coli.
Length = 204
Score = 162 bits (413), Expect = 1e-49
Identities = 82/216 (37%), Positives = 118/216 (54%), Gaps = 21/216 (9%)
Query: 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVG 76
GIDEAGRGPV+GPMV + + L L DSK L +KREELF ++ V
Sbjct: 1 CGIDEAGRGPVIGPMVVAGVAIDEEDLKKLEELGVKDSKKLTPKKREELFNEIL---KVA 57
Query: 77 WAVDIIDPRELSAKMLNK--NKINLNEISHDSAIGLITRV-LNIGILLTEVYLDTVG-DA 132
V I+ +S + +++ + NLNE+ ++ LI R+ L I VY+D +
Sbjct: 58 DDVVIV---VVSPEEIDERRERGNLNELEVEAFAELINRLKLKPEI----VYVDACDVNE 110
Query: 133 EKYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN 191
E++ +L +R + V+++ KAD+ YPVVS ASI+AKVTRDR EE + + +
Sbjct: 111 ERFAERLRERLNTGVEVIAEHKADAKYPVVSAASIIAKVTRDR-----EIEELKK-EYGD 164
Query: 192 FGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 227
FGSGYP DP T +L ++ P +VR SW T
Sbjct: 165 FGSGYPSDPRTIKFLREYYREHGELPPIVRKSWKTV 200
>gnl|CDD|223242 COG0164, RnhB, Ribonuclease HII [DNA replication, recombination,
and repair].
Length = 199
Score = 148 bits (375), Expect = 7e-44
Identities = 68/216 (31%), Positives = 98/216 (45%), Gaps = 37/216 (17%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
+ G+DEAGRGP+ GP+V + P L DSK L +KREELFE++K +
Sbjct: 2 VAGVDEAGRGPLAGPVVAAAVILPPDRLPKKLGLK--DSKKLSPKKREELFEEIKEKA-L 58
Query: 76 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
W V II E+ +++N+ E + + V + V +D
Sbjct: 59 AWGVGIIPAEEI-------DELNILEATKL---AMRRAVAGLSSQPDLVLVDGND----L 104
Query: 136 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHR----N 191
L Q +I K D+ P ++ ASI+AKVTRDR + EE A+ + +
Sbjct: 105 PLGLPQPAVAI-----IKGDAKSPSIAAASILAKVTRDR-----LMEELAK-EYPEYGFD 153
Query: 192 FGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 227
GSGYP DP T+A L G P + R S+
Sbjct: 154 KGSGYPTDPHTEALLKKG-----GTPGIHRRSFAPV 184
>gnl|CDD|234574 PRK00015, rnhB, ribonuclease HII; Validated.
Length = 197
Score = 117 bits (297), Expect = 3e-32
Identities = 57/217 (26%), Positives = 99/217 (45%), Gaps = 42/217 (19%)
Query: 15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDS 74
I G+DEAGRGP+ GP+V + + + LN DSK L E+KREEL+E++K +
Sbjct: 19 LIAGVDEAGRGPLAGPVVAAAVILDPD--RPIEGLN--DSKKLSEKKREELYEEIK-EKA 73
Query: 75 VGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEK 134
+ ++V I P E+ +++N+ E + + + ++ +L D
Sbjct: 74 LAYSVGIASPEEI-------DELNILEATLLAMRRAVEGLVKPDYVLV--------DG-- 116
Query: 135 YQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG- 193
++ + + +V K D+ P ++ ASI+AKVTRDR + EE + + +G
Sbjct: 117 --NRVPKLPIPQEAIV--KGDAKSPSIAAASILAKVTRDR-----LMEELDK-EYPGYGF 166
Query: 194 ---SGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 227
GY +A +G + R S+
Sbjct: 167 AKHKGYGTKEHLEALAK------YGPTPIHRRSFAPV 197
>gnl|CDD|237752 PRK14551, rnhB, ribonuclease HII; Provisional.
Length = 212
Score = 104 bits (261), Expect = 6e-27
Identities = 65/216 (30%), Positives = 95/216 (43%), Gaps = 22/216 (10%)
Query: 15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDS 74
G+DEAG+GPVLG M + DSK L E+REEL +L+ +D+
Sbjct: 1 MRFGVDEAGKGPVLGSMFAAAVRAD----PAALPDGIDDSKRLSPERREELAAELREDDA 56
Query: 75 VGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGD--A 132
+ V I P + + N + + +H A+ V GI D GD A
Sbjct: 57 IAVGVAEIPPARIDDPETDMNTLTVA--AHAEALS---GVATDGI---TGLCDA-GDVDA 107
Query: 133 EKYQAKLSQRF-PSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN 191
++ +++ R + AD P+V ASIVAKV RD + A + +
Sbjct: 108 GRFARRVADRVALDVSVSAEHGADEEDPLVGAASIVAKVARDAHV-----AALAAE-YGD 161
Query: 192 FGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 227
GSGYP DP T+ +L ++ P+ R SW TC
Sbjct: 162 VGSGYPSDPTTREFLREYVREHGELPACARRSWSTC 197
>gnl|CDD|187695 cd07182, RNase_HII_bacteria_HII_like, bacterial Ribonuclease
HII-like. Ribonuclease H (RNase H) is classified into
two families, type I (prokaryotic RNase HI, eukaryotic
RNase H1 and viral RNase H) and type II (prokaryotic
RNase HII and HIII, and eukaryotic RNase H2). RNase H
endonucleolytically hydrolyzes an RNA strand when it is
annealed to a complementary DNA strand in the presence
of divalent cations, in DNA replication and repair.
Bacterial RNase HII has a role in primer removal based
on its involvement in ribonucleotide-specific catalytic
activity in the presence of RNA/DNA hybrid substrates.
Several bacteria, such as Bacillus subtilis, have two
different type II RNases H, RNases HII and HIII; double
deletion of these leads to cellular lethality. It
appears that type I and type II RNases H also have
overlapping functions in cells, as over-expression of
Escherichia coli RNase HII can complement an RNase HI
deletion phenotype.
Length = 179
Score = 88.6 bits (221), Expect = 2e-21
Identities = 49/160 (30%), Positives = 76/160 (47%), Gaps = 31/160 (19%)
Query: 18 GIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGW 77
G+DEAGRGP+ GP+V + P + LN DSK L E+KREEL+E++K ++ W
Sbjct: 2 GVDEAGRGPLAGPVVAAAVILP--PDFEIEGLN--DSKKLSEKKREELYEEIK-EKALAW 56
Query: 78 AVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLD---TVGDAEK 134
+ I E+ ++IN I + + + V + + V +D
Sbjct: 57 GIGIASVEEI-------DRIN---ILQATLLAMKRAVEGLKVKPDLVLVDGNRLPPLPIP 106
Query: 135 YQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174
+A +V K D+ ++ ASI+AKVTRDR
Sbjct: 107 QEA-----------IV--KGDAKSASIAAASILAKVTRDR 133
>gnl|CDD|187692 cd06590, RNase_HII_bacteria_HIII_like, bacterial Ribonuclease
HIII-like. Ribonuclease H (RNase H) is classified into
two families, type I (prokaryotic RNase HI, eukaryotic
RNase H1 and viral RNase H) and type II (prokaryotic
RNase HII and HIII, and eukaryotic RNase H2). RNase H
endonucleolytically hydrolyzes an RNA strand when it is
annealed to a complementary DNA strand in the presence
of divalent cations, in DNA replication and repair.
Several bacteria, such as Bacillus subtilis, have two
different type II RNases H, RNases HII and HIII. RNases
HIII are distinguished by having a large (70-90
residues) N-terminal extension of unknown function. In
addition, the active site of RNase HIII differs from
that of other RNases H; replacing the fourth residue
(aspartate) of the acidic "DEDD" motif with a glutamate.
Most prokaryotic and eukaryotic genomes contain multiple
RNase H genes, however, no prokaryotic genomes contain
the combination of both RNase HI and HIII. This mutual
exclusive gene inheritance might be the result of
functional redundancy of RNase HI and HIII in
prokaryotes.
Length = 207
Score = 71.1 bits (175), Expect = 1e-14
Identities = 42/156 (26%), Positives = 67/156 (42%), Gaps = 11/156 (7%)
Query: 18 GIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGW 77
G DE G+G GP+V +Y + L L DSK L +EK +L +K +
Sbjct: 2 GSDEVGKGDYFGPLVVAAVYVDKENIEKLKELGVKDSKKLTDEKIIQLAPKIK--KKIPH 59
Query: 78 AVDIIDPRELSAKMLNKNKINLNEI---SHDSAIGLITRVLNIGILLTEVYLDTVGDAEK 134
+V + P + + L K NLN+I H+ A I +L + +D +
Sbjct: 60 SVLSLGPEKYNE--LIKKGNNLNKIKALLHNKA---INNLLQKPKKPEAILIDQFASEKV 114
Query: 135 YQAKL-SQRFPSIKFVVSKKADSLYPVVSGASIVAK 169
Y L ++ KA+S + V+ ASI+A+
Sbjct: 115 YFNYLKKEKIVKEPLYFRTKAESKHLAVAAASIIAR 150
>gnl|CDD|184400 PRK13926, PRK13926, ribonuclease HII; Provisional.
Length = 207
Score = 61.8 bits (150), Expect = 2e-11
Identities = 50/164 (30%), Positives = 80/164 (48%), Gaps = 32/164 (19%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCP-CSYQQTLATLNFADSKTLKEEKREELFEDLKVNDS 74
+ G+DEAGRG GP+V + P Y F DSKTL RE L E+++ +
Sbjct: 24 VAGVDEAGRGAWAGPVVVAAVILPPGEYP-------FRDSKTLSPAAREALAEEVR-RVA 75
Query: 75 VGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRV-LNIGILLTEVYLDTVGDAE 133
+ WAV + E+ +++N+ + +H +A + R+ + L+T+ YL
Sbjct: 76 LAWAVGHAEAAEI-------DRLNVLKATHLAAARALARLAVAPEALVTD-YL------- 120
Query: 134 KYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLR 177
+L P + KAD+L P V+ AS++AK RDR +R
Sbjct: 121 ----RLPTPLP---LLAPPKADALSPTVAAASLLAKTERDRLMR 157
>gnl|CDD|223969 COG1039, RnhC, Ribonuclease HIII [DNA replication, recombination,
and repair].
Length = 297
Score = 54.2 bits (131), Expect = 1e-08
Identities = 41/161 (25%), Positives = 69/161 (42%), Gaps = 13/161 (8%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
++G DE G+G GP+V +Y L L DSK L ++K ++L +K +
Sbjct: 85 LIGSDEVGKGDYFGPLVVCAVYVSKENLPKLKELGVKDSKKLSDKKIQQLAPIIK--PLI 142
Query: 76 GWAVDIIDPR---ELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLD---TV 129
+V +DP+ EL K N N + H+ AI + + +D +
Sbjct: 143 PHSVLTLDPKKYNELYKKFNNANSMKT--FLHNQAIQNLLPQKGAQ--PEFIVIDQFASS 198
Query: 130 GDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKV 170
+ + Y K + +F KA+S V+ ASI+A+
Sbjct: 199 ENYKNYLQKETNKFSEPVL-FLTKAESKSLAVAVASIIARY 238
>gnl|CDD|129799 TIGR00716, rnhC, ribonuclease HIII. This enzyme cleaves RNA from
DNA-RNA hybrids. Two types of ribonuclease H in Bacillus
subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are
both known experimentally and are quite similar to each
other. The only RNase H homolog in the Mycoplasmas
resembles rnhC. Archaeal forms resemble HII more closely
than HIII. This model describes bacterial RNase III [DNA
metabolism, DNA replication, recombination, and repair].
Length = 284
Score = 52.2 bits (125), Expect = 8e-08
Identities = 42/155 (27%), Positives = 73/155 (47%), Gaps = 6/155 (3%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
++G DE+G+G + GP+V C+Y P +++LN DSK L +++ E L +LK V
Sbjct: 83 VIGCDESGKGDIFGPLVLCCVYIPEENYLKVSSLNPRDSKRLSDKRIERLALNLK--PLV 140
Query: 76 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
+ P + + L + NLN++ LI R+L ++EV +D + +
Sbjct: 141 KAYCYELKPEKYNK--LYRKFRNLNKMMAHFHKLLIERLLKEECGVSEVVVDQFAPSNPF 198
Query: 136 QAKLSQRFPS-IKFVVSKKADSLYPVVSGASIVAK 169
L R + +A+ V+ ASI A+
Sbjct: 199 FNHLKGRDIVGEDVIFETEAER-NLAVAAASIFAR 232
>gnl|CDD|184399 PRK13925, rnhB, ribonuclease HII; Provisional.
Length = 198
Score = 51.2 bits (123), Expect = 9e-08
Identities = 37/162 (22%), Positives = 64/162 (39%), Gaps = 20/162 (12%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
I G+DE GRG + GP+ + + L DSK L ++R +L + +
Sbjct: 10 IAGVDEVGRGALFGPVFAAAVILSEKAEPQLLQAGLTDSKKLSPKRRAQLVPLILTL-AS 68
Query: 76 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
W + RE I+ I + + ++ + + + +D G+
Sbjct: 69 DWGIGQASARE----------IDRLGIRQATELAMLRALKKLKSPPSLCLVD--GNLPLR 116
Query: 136 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLR 177
QR +V K DS ++ ASI+AKV RD ++
Sbjct: 117 LWPGPQR-----TIV--KGDSKSAAIAAASILAKVWRDDLIK 151
>gnl|CDD|173015 PRK14550, rnhB, ribonuclease HII; Provisional.
Length = 204
Score = 47.6 bits (113), Expect = 2e-06
Identities = 45/167 (26%), Positives = 76/167 (45%), Gaps = 27/167 (16%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
+GIDEAGRG + G + + C + DSK L +KR L + +K + V
Sbjct: 2 TLGIDEAGRGCLAGSLFVAGVACNEKTALEFLKMGLKDSKKLSPKKRFFLEDKIKTHGEV 61
Query: 76 GWAV-----DIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG 130
G+ V + ID L A + K+ + EI + N L E+ +D G
Sbjct: 62 GFFVVKKSANEIDSLGLGACL----KLAIQEI-----------LENGCSLANEIKID--G 104
Query: 131 DAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLR 177
+ L++R+P+I+ ++ K D ++ AS++AK +DR +
Sbjct: 105 NT---AFGLNKRYPNIQTII--KGDETIAQIAMASVLAKAFKDREML 146
>gnl|CDD|234886 PRK00996, PRK00996, ribonuclease HIII; Provisional.
Length = 304
Score = 45.3 bits (108), Expect = 1e-05
Identities = 46/167 (27%), Positives = 70/167 (41%), Gaps = 25/167 (14%)
Query: 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVND 73
I G DE G+G GP+ +Y L L DSK L + K ++ L+ +
Sbjct: 88 SLI-GSDEVGKGDYFGPLTVAAVYVDKEQIPFLKKLGVKDSKKLTDTKIRQIAPQLR--E 144
Query: 74 SVGWAVDIIDPR---ELSAKMLNKNKINLNEISHDSAIGLITRVLN----IGILL----- 121
+ +V ++ P EL AK N+NK L H+ AI + + + I++
Sbjct: 145 KIPHSVLLLSPEKYNELQAKGYNQNK--LKAWLHNQAIDNLLQKIAGIQPEKIVIDQFAS 202
Query: 122 TEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVA 168
EVY KY K +F KA+S + V+ ASI+A
Sbjct: 203 PEVYQ-------KYLKKEKNKFRD-NVTFETKAESKHLAVAAASIIA 241
>gnl|CDD|113793 pfam05036, SPOR, Sporulation related domain. This 70 residue
domain is composed of two 35 residue repeats found in
proteins involved in sporulation and cell division such
as FtsN, DedD, and CwlM. This domain is involved in
binding peptidoglycan. Two tandem repeats fold into a
pseudo-2-fold symmetric single-domain structure
containing numerous contacts between the repeats. FtsN
is an essential cell division protein with a simple
bitopic topology, a short N-terminal cytoplasmic segment
fused to a large carboxy periplasmic domain through a
single transmembrane domain. These repeats lay at the
periplasmic C-terminus. FtsN localises to the septum
ring complex.
Length = 75
Score = 31.9 bits (73), Expect = 0.061
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 131 DAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSG 163
+AE AKL + + K V+ LY V G
Sbjct: 17 NAEALAAKLRAKGFAAKEAVTSGGGGLYRVRVG 49
>gnl|CDD|179241 PRK01185, ppnK, inorganic polyphosphate/ATP-NAD kinase;
Provisional.
Length = 271
Score = 29.0 bits (65), Expect = 2.6
Identities = 32/126 (25%), Positives = 54/126 (42%), Gaps = 28/126 (22%)
Query: 80 DIIDPRELSAKMLNKNKINLNEISHDSAI-----GLITRVL----------NIGIL--LT 122
+II E AK L + +++ EI+ D I G I R L N+G L LT
Sbjct: 30 EIIYEMEA-AKALGMDGLDIEEINADVIITIGGDGTILRTLQRAKGPILGINMGGLGFLT 88
Query: 123 EVYLDTVGDA----EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASI-VAKVTRDRTLR 177
E+ +D VG A + + + +R +K V + L + A I ++ + R +
Sbjct: 89 EIEIDEVGSAIKKLIRGEYFIDER---MKLKVYINGERLEDCTNEAVIHTDRIAKIRQFK 145
Query: 178 GWIFEE 183
I+ +
Sbjct: 146 --IYYD 149
>gnl|CDD|227403 COG5071, RPN5, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 439
Score = 29.1 bits (65), Expect = 2.7
Identities = 16/61 (26%), Positives = 23/61 (37%), Gaps = 1/61 (1%)
Query: 20 DEAGRGPVLGPMVYGCLYCPC-SYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWA 78
D A VL +V L P + Q L AD K ++L + VN+ + W
Sbjct: 247 DPAKWKEVLSNVVCFALLTPYDNEQADLLHKINADHKLNSLPLLQQLVKCFIVNELMRWP 306
Query: 79 V 79
Sbjct: 307 K 307
>gnl|CDD|221182 pfam11715, Nup160, Nucleoporin Nup120/160. Nup120 is conserved
from fungi to plants to humans, and is homologous with
the Nup160 of vertebrates. The nuclear core complex, or
NPC, mediates macromolecular transport across the
nuclear envelope. Deletion of the NUP120 gene causes
clustering of NPCs at one side of the nuclear envelope,
moderate nucleolar fragmentation and slower cell growth.
The vertebrate NPC is estimated to contain between 30
and 60 different proteins. most of which are not known.
Two important ones in creating the nucleoporin basket
are Nup98 and Nup153, and Nup120, in conjunction with
Nup 133, interacts with these two and itself plays a
role in mRNA export. Nup160, Nup133, Nup96, and Nup107
are all targets of phosphorylation. The phosphorylation
sites are clustered mainly at the N-terminal regions of
these proteins, which are predicted to be natively
disordered. The entire Nup107-160 subcomplex is stable
throughout the cell cycle, thus it seems unlikely that
phosphorylation affects interactions within the
Nup107-160 subcomplex, but rather that it regulates the
association of the subcomplex with the NPC and other
proteins.
Length = 511
Score = 29.0 bits (65), Expect = 3.2
Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 8/79 (10%)
Query: 109 GLITRV-LNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPV------- 160
G + ++ + G V+ +T+ + L P ++ + A S
Sbjct: 169 GGLLKLTRSSGDTDGAVWKETLYGPSSWLRSLRGLLPFQRYGKDRLASSAAASTIVSSSE 228
Query: 161 VSGASIVAKVTRDRTLRGW 179
V+G + + ++ D TLR W
Sbjct: 229 VNGQTFLFTLSLDGTLRVW 247
>gnl|CDD|212963 cd12030, SH3_DLG4, Src Homology 3 domain of Disks Large homolog 4.
DLG4, also called postsynaptic density-95 (PSD95) or
synapse-associated protein 90 (SAP90), is a scaffolding
protein that clusters at synapses and plays an important
role in synaptic development and plasticity. It is
responsible for the membrane clustering and retention of
many transporters and receptors such as potassium
channels and PMCA4b, a P-type ion transport ATPase,
among others. DLG4 is a member of the MAGUK
(membrane-associated guanylate kinase) protein family,
which is characterized by the presence of a core of
three domains: PDZ, SH3, and guanylate kinase (GuK). The
GuK domain in MAGUK proteins is enzymatically inactive;
instead, the domain mediates protein-protein
interactions and associates intramolecularly with the
SH3 domain. DLG4 contains three PDZ domains. The SH3
domain of DLG4 binds and clusters the kainate subgroup
of glutamate receptors via two proline-rich sequences in
their C-terminal tail. It also binds AKAP79/150
(A-kinase anchoring protein). SH3 domains are protein
interaction domains that bind to proline-rich ligands
with moderate affinity and selectivity, preferentially
to PxxP motifs. They play versatile and diverse roles in
the cell including the regulation of enzymes, changing
the subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 66
Score = 26.8 bits (59), Expect = 3.4
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 231 FKDIVEVLWESDEMDEDVSSRRSGKRQLKLSDIGFSSSKRRSE 273
F D++ V+ D DE+ R + +IGF SKRR E
Sbjct: 27 FGDVLHVI---DAGDEEWWQARRVHSDSETEEIGFIPSKRRVE 66
>gnl|CDD|222826 PHA01627, PHA01627, DNA binding protein.
Length = 107
Score = 27.7 bits (62), Expect = 3.5
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 5/63 (7%)
Query: 84 PRELSAKMLNKNKINLNEISHDSAIGLITRVL--NIGILLTEVYLDTVGDAEKYQAKLSQ 141
E + ++L + ++ I HD+ L++ + N+ E+ LD GD + L Q
Sbjct: 27 DIEEAKELLENEEF-VSAIGHDATANLLSNLCGVNLPKNRIEIKLD-KGD-KALAIMLKQ 83
Query: 142 RFP 144
R
Sbjct: 84 RLE 86
>gnl|CDD|112730 pfam03930, Flp_N, Recombinase Flp protein N-terminus.
Length = 82
Score = 27.0 bits (60), Expect = 3.8
Identities = 9/39 (23%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 130 GDAEKYQAKLSQRFPSIKFVVS--KKADSLYPVVSGASI 166
+ + LS+ F FV+ KK S+ + S +
Sbjct: 41 KRPTELKEGLSKAFKPYNFVIKSHKKPTSMTTLFSSLHL 79
>gnl|CDD|216126 pfam00798, Arena_glycoprot, Arenavirus glycoprotein.
Length = 473
Score = 28.8 bits (65), Expect = 4.2
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 6/43 (13%)
Query: 229 SHFKDIVEVLWESDEMDEDVSSR----RSGKRQLKLSDIGFSS 267
SHF++ E + ESD + ++ S+ R GK L L D+ F S
Sbjct: 385 SHFRN--EWILESDHLISEMLSKEYEERQGKTPLTLVDLCFWS 425
>gnl|CDD|119073 pfam10553, MSV199, MSV199 domain. This domain was identified by
Iyer and colleagues.
Length = 135
Score = 27.6 bits (62), Expect = 4.3
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 89 AKMLNKNKINLNEISHD 105
K+L +N I EI ++
Sbjct: 57 KKILKRNNIPYKEIKYN 73
>gnl|CDD|237678 PRK14335, PRK14335, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 455
Score = 28.3 bits (63), Expect = 5.3
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 132 AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN 191
AE+ ++ + FP I +VV A + + I AK+ +D + FE +E +
Sbjct: 81 AERLHDEIQKEFPRIDYVVGTFAHARLESIFQ-EIEAKLKQD----DYRFEFISERYREH 135
Query: 192 FGSGY 196
SGY
Sbjct: 136 PVSGY 140
>gnl|CDD|143399 cd07080, ALDH_Acyl-CoA-Red_LuxC, Acyl-CoA reductase LuxC. Acyl-CoA
reductase, LuxC, (EC=1.2.1.50) is the fatty acid
reductase enzyme responsible for synthesis of the
aldehyde substrate for the luminescent reaction
catalyzed by luciferase. The fatty acid reductase, a
luminescence-specific, multienzyme complex (LuxCDE),
reduces myristic acid to generate the long chain fatty
aldehyde required for the luciferase-catalyzed reaction
resulting in the emission of blue-green light.
Mutational studies of conserved cysteines of LuxC
revealed that the cysteine which aligns with the
catalytic cysteine conserved throughout the ALDH
superfamily is the LuxC acylation site. This CD is
composed of mainly bacterial sequences but also includes
a few archaeal sequences similar to the Methanospirillum
hungateiacyl acyl-CoA reductase RfbN.
Length = 422
Score = 28.0 bits (63), Expect = 6.0
Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 13/86 (15%)
Query: 47 ATLNFADSKTLKEEKREELFEDLK--VNDSVGWAVDIIDPRELSAKMLNKNKINLNEISH 104
+L+ A+S + + E F +LK V+ +GW V I D L A LN+ +N+ ++
Sbjct: 297 LSLSAAESAKIARARLEAEFYELKGGVSRDLGWTVIISDEIGLEASPLNRT-VNVKPVAS 355
Query: 105 DSAIGLITRVLNIGILLTEVYLDTVG 130
+ VL YL TVG
Sbjct: 356 ------LDDVLR----PVTPYLQTVG 371
>gnl|CDD|233702 TIGR02061, aprA, adenosine phosphosulphate reductase, alpha
subunit. During dissimilatory sulfate reduction or
sulfur oxidation, adenylylsulfate (APS) reductase
catalyzes reversibly the two-electron reduction of APS
to sulfite and AMP. Found in several bacterial lineages
and in Archaeoglobales, APS reductase is a heterodimer
composed of an alpha subunit containing a noncovalently
bound FAD, and a beta subunit containing two [4Fe-4S]
clusters. Described by this model is the alpha subunit
of APS reductase, sharing common evolutionary origin
with fumarate reductase/succinate dehydrogenase
flavoproteins [Central intermediary metabolism, Sulfur
metabolism].
Length = 614
Score = 28.3 bits (63), Expect = 6.1
Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 22 AGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDI 81
GRGP+ + + Q AT K L+EE E+ F D+ V + WA
Sbjct: 302 EGRGPIY-------MDTKEALQDPFATDK-KQQKHLEEEAWED-FLDMTVGQANLWAATN 352
Query: 82 IDPRE 86
+DP E
Sbjct: 353 VDPEE 357
>gnl|CDD|223675 COG0602, NrdG, Organic radical activating enzymes
[Posttranslational modification, protein turnover,
chaperones].
Length = 212
Score = 27.7 bits (62), Expect = 7.1
Identities = 15/53 (28%), Positives = 21/53 (39%), Gaps = 6/53 (11%)
Query: 23 GRGPVLG-PMVY----GCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLK 70
G G +G P V+ GC C T T +F K +E+ D+K
Sbjct: 15 GEGKNIGRPSVFVRFAGCNLR-CPGCDTKYTWDFNYGKPGTPMSADEILADIK 66
>gnl|CDD|220082 pfam08960, DUF1874, Domain of unknown function (DUF1874). This
domain is found in a set of hypothetical viral and
bacterial proteins.
Length = 105
Score = 26.5 bits (59), Expect = 7.5
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 5/63 (7%)
Query: 84 PRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILL--TEVYLDTVGDAEKYQAKLSQ 141
E + ++L + ++ I HD+ L++ +L + I + +V L VGD + L Q
Sbjct: 26 DIEEAKELLENERF-ISAIGHDATAQLLSNLLGVNIPMNRIQVKLQ-VGD-KALAFVLKQ 82
Query: 142 RFP 144
R
Sbjct: 83 RLE 85
>gnl|CDD|233602 TIGR01856, hisJ_fam, histidinol phosphate phosphatase, HisJ family.
This model represents the histidinol phosphate
phosphatase HisJ of Bacillus subtilis, and related
proteins from a number of species within a larger family
of phosphatases in the PHP hydrolase family. HisJ
catalyzes the penultimate step of histidine biosynthesis
but shows no homology to the functionally equivalent
sequence in E. coli, a domain of the bifunctional HisB
protein. Note, however, that many species have two
members and that Clostridium perfringens, predicted not
to make histidine, has five members of this family; this
family is designated subfamily rather than equivalog to
indicate that members may not all act as HisJ.
Length = 253
Score = 27.4 bits (61), Expect = 8.0
Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 5/52 (9%)
Query: 30 PMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDI 81
P+V G + + D + +E E L LK+ S G A++
Sbjct: 157 PLVIGHIDLVQKFGP-----LDTDVSSFSDEVYELLQRILKLVASQGKALEF 203
>gnl|CDD|224833 COG1922, WecG, Teichoic acid biosynthesis proteins [Cell envelope
biogenesis, outer membrane].
Length = 253
Score = 27.2 bits (61), Expect = 8.6
Identities = 32/116 (27%), Positives = 43/116 (37%), Gaps = 20/116 (17%)
Query: 43 QQTLATLNFADSKTLKEEKREELFE-----DLKVNDSVGWAVDIIDPRELSAKMLNKNKI 97
T+ TLN K L K E E DL + D +G V R L +
Sbjct: 38 PTTVVTLNA--EKVLLARKDPEFREILNQADLILPDGIG--VVRAARRLLGQPL----PE 89
Query: 98 NLNEISHDSAIGLITRVLNIGILLTEVYL--DTVGDAEKYQAKLSQRFPSIKFVVS 151
+ D L+ R G V+L G AE+ AKL ++P +K V S
Sbjct: 90 RVAGT--DLVEALLKRAAEEG---KRVFLLGGKPGVAEQAAAKLRAKYPGLKIVGS 140
>gnl|CDD|237108 PRK12467, PRK12467, peptide synthase; Provisional.
Length = 3956
Score = 27.8 bits (62), Expect = 9.0
Identities = 7/16 (43%), Positives = 13/16 (81%)
Query: 62 REELFEDLKVNDSVGW 77
RE+LF+++ + +VGW
Sbjct: 2450 REDLFDEIDLTRTVGW 2465
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
0.317 0.134 0.401
Gapped
Lambda K H
0.267 0.0637 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,057,183
Number of extensions: 1415960
Number of successful extensions: 1280
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1245
Number of HSP's successfully gapped: 43
Length of query: 297
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 201
Effective length of database: 6,679,618
Effective search space: 1342603218
Effective search space used: 1342603218
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 (26.7 bits)