RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12553
(401 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 = 370 bits (953), Expect = e-129
Identities = 140/237 (59%), Positives = 168/237 (70%), Gaps = 16/237 (6%)
Query: 43 LGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAW 102
LGIDEAGRGPVLGPMVYG AYCP EEL K LG ADSK LTE+KR+++ + +++
Sbjct: 1 LGIDEAGRGPVLGPMVYGAAYCPISYKEEL-KKLGFADSKTLTEEKREELFKKLKEKDDA 59
Query: 103 LGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPES 162
LGW I+SP I ML R KY+LNE+SHDAAIGLIR+V+ GVNV EVYVDTVGPPE
Sbjct: 60 LGWATRILSPQYISTKMLARTKYNLNEISHDAAIGLIREVLDKGVNVTEVYVDTVGPPEK 119
Query: 163 YKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALKSW 222
Y+ KL + FP + TV KADS YP+V AASI AKV+RD ALK+W
Sbjct: 120 YQAKLQKKFPGIKFTV---------------EKKADSLYPIVSAASIVAKVTRDRALKNW 164
Query: 223 TFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKEKAV 279
F E + ++ GSGYP DP TKK+L +N+DPVFG+PQLVRFSWSTA IL++KAV
Sbjct: 165 QFDETLIKDSGDLGSGYPSDPKTKKWLKKNVDPVFGYPQLVRFSWSTAKTILEKKAV 221
>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 = 330 bits (849), Expect = e-114
Identities = 132/229 (57%), Positives = 159/229 (69%), Gaps = 19/229 (8%)
Query: 43 LGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAW 102
LGIDEAGRGPVLGPMVY AYCP E+L ++LG ADSK LTE+KR+++ D I KE+
Sbjct: 1 LGIDEAGRGPVLGPMVYAAAYCPISYLEKL-ESLGFADSKQLTEEKREELFDEI-KEDKA 58
Query: 103 LGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPES 162
+GW V I+SP I ML R KY+LNE+SHDAAIGLIR ++ GV V EVYVDTVGPPE
Sbjct: 59 VGWAVRILSPEYISRKMLARSKYNLNEISHDAAIGLIRNLLDKGVKVTEVYVDTVGPPEK 118
Query: 163 YKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALKSW 222
Y+ KL + FP + TV KADS YP+V AASI AKV+RD AL+ W
Sbjct: 119 YQAKLLKRFPGIKFTV---------------EKKADSKYPIVSAASIVAKVTRDRALEQW 163
Query: 223 TFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTAS 271
F EG+ + +GSGYP DP TK++L +N+DPVFGFP LVRFSWST
Sbjct: 164 KFDEGLD--SGDFGSGYPSDPKTKEWLKKNVDPVFGFPSLVRFSWSTVK 210
>gnl|CDD|216451 pfam01351, RNase_HII, Ribonuclease HII.
Length = 199
Score = 162 bits (413), Expect = 2e-48
Identities = 74/239 (30%), Positives = 100/239 (41%), Gaps = 51/239 (21%)
Query: 43 LGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAW 102
GIDE GRGP+ GP+V Y P + + L+ LG DSK L++KKR+++ + I K
Sbjct: 1 AGIDEVGRGPLAGPLVVAAVYLPPE-RLDELRKLGVKDSKKLSDKKREELAELIKK---- 55
Query: 103 LGWMVEIISPNVICNSMLRRQ---KYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGP 159
I + ++ + +LN + H + +IR V GV E+ VD P
Sbjct: 56 ------RIETRKLVAGNIKYAEANEINLNNILHALHLAMIRAVQKLGVKPDEILVDGFRP 109
Query: 160 PESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSAL 219
P+S K IF A KADS Y V AASI AKV+RD
Sbjct: 110 PKSLPMKQEAIFKI--KVTAEH--------------KADSKYLSVAAASIIAKVTRD--- 150
Query: 220 KSWTFQEGIQIENN--------AWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTA 270
+E GSGYP DP T+ L P P R S++T
Sbjct: 151 --------EMLELLKRFPGYGLDKGSGYPSDPHTEALLKLGATP--WLPDFHRRSFATV 199
>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 = 152 bits (386), Expect = 2e-44
Identities = 80/236 (33%), Positives = 112/236 (47%), Gaps = 34/236 (14%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
V GIDEAGRGPV+GP+V G + ++ EE L+ LG DSK LT +R+++ I N
Sbjct: 1 VAGIDEAGRGPVIGPLVVG-VFAIEEKREEELRKLGVKDSKKLTPGRREELFSKI--RNK 57
Query: 102 WLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPE 161
+ V I+P I R + +LNE + + I EVYVD+V
Sbjct: 58 LGRYEVLKITPEEID----RERNINLNENEIEK---FSKAAIILIEKPSEVYVDSVDVNP 110
Query: 162 S---YKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSA 218
+ K+ E + + KAD+ YPVV AA SI AKV RD
Sbjct: 111 KRFKREIKIKERIEGIKVIAEHKADAKYPVVSAA---------------SIIAKVERDRE 155
Query: 219 LKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKIL 274
++S + G +GSGYP DP T+++L E P +VR +W T K+L
Sbjct: 156 IESLKRKYGD------FGSGYPSDPRTREWLEEYFKSHGELPDIVRRTWKTVRKLL 205
>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 = 147 bits (374), Expect = 2e-42
Identities = 82/237 (34%), Positives = 112/237 (47%), Gaps = 38/237 (16%)
Query: 43 LGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKR----DDILDSICK 98
GIDEAGRGPV+GPMV + + + L+ LG DSK LT KKR ++IL
Sbjct: 1 CGIDEAGRGPVIGPMVVA-GVAIDEEDLKKLEELGVKDSKKLTPKKREELFNEILKVADD 59
Query: 99 ENAWLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVG 158
+ ++SP I R +LNE+ +A LI ++ VYVD
Sbjct: 60 VV------IVVVSPEEIDERRERG---NLNELEVEAFAELINRLKLKPE---IVYVDACD 107
Query: 159 P-PESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDS 217
E + ++L E + V ++ KAD+ YPVV AASI AKV+RD
Sbjct: 108 VNEERFAERLRE-RLNTGVEVIAE-------------HKADAKYPVVSAASIIAKVTRDR 153
Query: 218 ALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKIL 274
+ E ++ E +GSGYP DP T KFL E P +VR SW T ++L
Sbjct: 154 EI------EELKKEYGDFGSGYPSDPRTIKFLREYYREHGELPPIVRKSWKTVKRLL 204
>gnl|CDD|223242 COG0164, RnhB, Ribonuclease HII [DNA replication, recombination,
and repair].
Length = 199
Score = 140 bits (355), Expect = 6e-40
Identities = 66/248 (26%), Positives = 95/248 (38%), Gaps = 54/248 (21%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
V G+DEAGRGP+ GP+V P D L K LG DSK L+ KKR+++ + I ++
Sbjct: 2 VAGVDEAGRGPLAGPVVAAAVILPPDR---LPKKLGLKDSKKLSPKKREELFEEIKEKA- 57
Query: 102 WLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPE 161
L W V II I + ++ E + A + + V VD P
Sbjct: 58 -LAWGVGIIPAEEI-------DELNILEATKLAMRRAVAGLS---SQPDLVLVDGNDLPL 106
Query: 162 SYK-KKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRD---S 217
++ I K D+ P + AASI AKV+RD
Sbjct: 107 GLPQPAVAII-------------------------KGDAKSPSIAAASILAKVTRDRLME 141
Query: 218 ALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKEK 277
L + G GSGYP DP T+ L + P + R S++ ++L
Sbjct: 142 ELAKEYPEYGF-----DKGSGYPTDPHTEALLKKGGTPG-----IHRRSFAPVRRLLGLA 191
Query: 278 AVLVEGDE 285
Sbjct: 192 KKRQLKLF 199
>gnl|CDD|237752 PRK14551, rnhB, ribonuclease HII; Provisional.
Length = 212
Score = 100 bits (252), Expect = 6e-25
Identities = 64/237 (27%), Positives = 97/237 (40%), Gaps = 35/237 (14%)
Query: 41 CVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKEN 100
G+DEAG+GPVLG M L + G DSK L+ ++R+++ + +E+
Sbjct: 1 MRFGVDEAGKGPVLGSMFAAAVRAD----PAALPD-GIDDSKRLSPERREELAAEL-RED 54
Query: 101 AWLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPP 160
+ V I P I + +N ++ A + V G+ D
Sbjct: 55 DAIAVGVAEIPPARI-----DDPETDMNTLTVAAHAEALSGVATDGI---TGLCDAGDVD 106
Query: 161 ES-YKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSAL 219
+ +++ AD V + AD P+VGAASI AKV+RD+ +
Sbjct: 107 AGRFARRV--------------ADRVALDVSVSAEHGADEEDPLVGAASIVAKVARDAHV 152
Query: 220 KSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKE 276
+ E GSGYP DP T++FL E + P R SWST +L
Sbjct: 153 ------AALAAEYGDVGSGYPSDPTTREFLREYVREHGELPACARRSWSTCDDVLAA 203
>gnl|CDD|234574 PRK00015, rnhB, ribonuclease HII; Validated.
Length = 197
Score = 98.7 bits (247), Expect = 2e-24
Identities = 59/230 (25%), Positives = 92/230 (40%), Gaps = 53/230 (23%)
Query: 41 CVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKEN 100
+ G+DEAGRGP+ GP+V D G DSK L+EKKR+++ + I KE
Sbjct: 19 LIAGVDEAGRGPLAGPVVAAAVILDPDRP-----IEGLNDSKKLSEKKREELYEEI-KEK 72
Query: 101 AWLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPP 160
A L + V I SP I + ++ E + A R+ + V V VD P
Sbjct: 73 A-LAYSVGIASPEEID-------ELNILEATLLAM----RRAVEGLVKPDYVLVDGNRVP 120
Query: 161 ESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALK 220
+ + + +A +V K D+ P + AASI AKV+RD ++
Sbjct: 121 K--------------LPIPQEA-----IV------KGDAKSPSIAAASILAKVTRDRLME 155
Query: 221 SWTFQ-EGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWST 269
+ G + GY + +G + R S++
Sbjct: 156 ELDKEYPGYGFAKH---KGYGTKEHLEALAK------YGPTPIHRRSFAP 196
>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 = 73.6 bits (182), Expect = 2e-15
Identities = 52/179 (29%), Positives = 72/179 (40%), Gaps = 54/179 (30%)
Query: 44 GIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWL 103
G+DEAGRGP+ GP+V P D E L DSK L+EKKR+++ + I ++ L
Sbjct: 2 GVDEAGRGPLAGPVVAAAVILPPDFEIEGLN-----DSKKLSEKKREELYEEIKEKA--L 54
Query: 104 GWMVEIISPNVI--CN----SMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTV 157
W + I S I N ++L + R V V V VD
Sbjct: 55 AWGIGIASVEEIDRINILQATLL----------------AMKRAVEGLKVKPDLVLVDGN 98
Query: 158 GPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRD 216
P + + I+ K D+ +IA AASI AKV+RD
Sbjct: 99 RLPPLPIPQEA------IV----KGDAKSA----SIA-----------AASILAKVTRD 132
>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 = 64.9 bits (159), Expect = 3e-12
Identities = 43/157 (27%), Positives = 68/157 (43%), Gaps = 19/157 (12%)
Query: 43 LGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAW 102
+G DE G+G GP+V Y K+ N E LK LG DSK LT++K + I K+
Sbjct: 1 IGSDEVGKGDYFGPLVVAAVYVDKE-NIEKLKELGVKDSKKLTDEKIIQLAPKIKKKIP- 58
Query: 103 LGWMVEIISP---NVICNSMLRRQKYSLNEV---SHDAAIGLIRKVIAAGVNVREVYVDT 156
V + P N L ++ +LN++ H+ A I ++ + +D
Sbjct: 59 --HSVLSLGPEKYNE-----LIKKGNNLNKIKALLHNKA---INNLLQKPKKPEAILIDQ 108
Query: 157 VGPPESYKKKL-SEIFPELIITVASKADSTYPVVGAA 192
+ Y L E + + +KA+S + V AA
Sbjct: 109 FASEKVYFNYLKKEKIVKEPLYFRTKAESKHLAVAAA 145
>gnl|CDD|184399 PRK13925, rnhB, ribonuclease HII; Provisional.
Length = 198
Score = 53.1 bits (128), Expect = 3e-08
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICK 98
+ G+DE GRG + GP+ + E L G DSK L+ K+R ++ I
Sbjct: 10 IAGVDEVGRGALFGPVFAAAVILSEKA-EPQLLQAGLTDSKKLSPKRRAQLVPLILT 65
Score = 32.3 bits (74), Expect = 0.28
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 196 KADSTYPVVGAASICAKVSRDSALK 220
K DS + AASI AKV RD +K
Sbjct: 127 KGDSKSAAIAAASILAKVWRDDLIK 151
>gnl|CDD|234886 PRK00996, PRK00996, ribonuclease HIII; Provisional.
Length = 304
Score = 54.1 bits (131), Expect = 4e-08
Identities = 47/181 (25%), Positives = 76/181 (41%), Gaps = 37/181 (20%)
Query: 29 SSTIPESCKSQPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKK 88
P S ++ +G DE G+G GP+ Y K+ LK LG DSK LT+ K
Sbjct: 77 GYEEPLSFQNLSL-IGSDEVGKGDYFGPLTVAAVYVDKEQ-IPFLKKLGVKDSKKLTDTK 134
Query: 89 RDDILDSICKENAWLGWMVEIISPNVICNSM-LRRQKYSLNEV-------------SHDA 134
I + + + + + + L +KY NE+ H+
Sbjct: 135 -------IRQ-------IAPQLREKIPHSVLLLSPEKY--NELQAKGYNQNKLKAWLHNQ 178
Query: 135 AIGLIRKVIAAGVNVREVYVDTVGPPESYKKKLSE---IFPELIITVASKADSTYPVVGA 191
AI + + I AG+ ++ +D PE Y+K L + F + +T +KA+S + V A
Sbjct: 179 AIDNLLQKI-AGIQPEKIVIDQFASPEVYQKYLKKEKNKFRD-NVTFETKAESKHLAVAA 236
Query: 192 A 192
A
Sbjct: 237 A 237
>gnl|CDD|223969 COG1039, RnhC, Ribonuclease HIII [DNA replication, recombination,
and repair].
Length = 297
Score = 49.2 bits (118), Expect = 2e-06
Identities = 58/239 (24%), Positives = 93/239 (38%), Gaps = 54/239 (22%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
++G DE G+G GP+V Y K+N LK LG DSK L++KK I +
Sbjct: 85 LIGSDEVGKGDYFGPLVVCAVYVSKENL-PKLKELGVKDSKKLSDKK-------IQQ--- 133
Query: 102 WLGWMVEIISPNVIC----------NSMLRRQKYSLNEVS---HDAAIGLIRKVIAAGVN 148
+ II P + N + ++ + N + H+ AI + A
Sbjct: 134 ----LAPIIKPLIPHSVLTLDPKKYNELYKK-FNNANSMKTFLHNQAIQNLLPQKGAQPE 188
Query: 149 VREVYVDTVGPPESYKKKL-SEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAA 207
+ +D E+YK L E + +KA+S V A
Sbjct: 189 --FIVIDQFASSENYKNYLQKETNKFSEPVL--------------FLTKAESKSLAVAVA 232
Query: 208 SICAKVSRDSALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFS 266
SI A+ + +LK + Q G+Q+ G+G P + +E I GF +L + +
Sbjct: 233 SIIARYAFLQSLKQLSRQYGVQLPK---GAG----PAVDQAAAEIIQK-RGFSKLEQVA 283
>gnl|CDD|184400 PRK13926, PRK13926, ribonuclease HII; Provisional.
Length = 207
Score = 44.9 bits (106), Expect = 2e-05
Identities = 42/175 (24%), Positives = 66/175 (37%), Gaps = 45/175 (25%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
V G+DEAGRG GP+V P DSK L+ R+ + + + + A
Sbjct: 24 VAGVDEAGRGAWAGPVVVAAVILPPGEYP-------FRDSKTLSPAAREALAEEV-RRVA 75
Query: 102 WLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPE 161
L W V I + ++ + +H AA + +A +
Sbjct: 76 -LAWAVGHAEAAEI-------DRLNVLKATHLAA----ARALAR-----------LAVA- 111
Query: 162 SYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRD 216
PE ++T + + P++ KAD+ P V AAS+ AK RD
Sbjct: 112 ----------PEALVTDYLRLPTPLPLLA---PPKADALSPTVAAASLLAKTERD 153
>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 = 42.2 bits (99), Expect = 3e-04
Identities = 52/213 (24%), Positives = 90/213 (42%), Gaps = 30/213 (14%)
Query: 25 NLIISSTIPESCKSQPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKAL 84
NL+ +P +S V+G DE+G+G + GP+V Y P++ N + +L DSK L
Sbjct: 69 NLLEKKKLPADPRS---VIGCDESGKGDIFGPLVLCCVYIPEE-NYLKVSSLNPRDSKRL 124
Query: 85 TEKKRDDI---LDSICKENAWLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRK 141
++K+ + + L + K + P N + R+ + +LN++ LI +
Sbjct: 125 SDKRIERLALNLKPLVK------AYCYELKPEKY-NKLYRKFR-NLNKMMAHFHKLLIER 176
Query: 142 VIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTY 201
++ V EV VD P + F L D + ++A+
Sbjct: 177 LLKEECGVSEVVVDQFAPSNPF-------FNHLKGRDIVGEDVIF-------ETEAERNL 222
Query: 202 PVVGAASICAKVSRDSALKSWTFQEGIQIENNA 234
V AASI A+ +LK + GI++ A
Sbjct: 223 -AVAAASIFARYKFLQSLKELERELGIKLPKGA 254
>gnl|CDD|173015 PRK14550, rnhB, ribonuclease HII; Provisional.
Length = 204
Score = 41.5 bits (97), Expect = 3e-04
Identities = 30/74 (40%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
LGIDEAGRG + G + C + E LK +G DSK L+ KKR + D I K +
Sbjct: 2 TLGIDEAGRGCLAGSLFVAGVACNEKTALEFLK-MGLKDSKKLSPKKRFFLEDKI-KTHG 59
Query: 102 WLGWMVEIISPNVI 115
+G+ V S N I
Sbjct: 60 EVGFFVVKKSANEI 73
>gnl|CDD|223977 COG1048, AcnA, Aconitase A [Energy production and conversion].
Length = 861
Score = 31.9 bits (73), Expect = 0.75
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 160 PESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYP-VVGAASICAK--VSRD 216
E+++K L EI + + ++ K VV AAI S +++ P V+ AA + AK V +
Sbjct: 379 AENFEKILREIEIKRVYSLLGKELGDGKVVIAAITSCTNTSNPDVLIAAGLLAKKAVEKG 438
Query: 217 SALKSWT 223
+K W
Sbjct: 439 LKVKPWV 445
>gnl|CDD|181370 PRK08305, spoVFB, dipicolinate synthase subunit B; Reviewed.
Length = 196
Score = 31.0 bits (71), Expect = 0.76
Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 10/62 (16%)
Query: 131 SH---DAAIGLIRKVIAAGVNVREVYVDTV-------GPPESYKKKLSEIFPELIITVAS 180
SH D + I K++ G V + TV G E + KK+ EI +I
Sbjct: 15 SHCTYDEVMPEIEKLVDEGAEVTPIVSYTVQTTDTRFGKAEEWIKKIEEITGNKVINTIV 74
Query: 181 KA 182
+A
Sbjct: 75 EA 76
>gnl|CDD|233336 TIGR01272, gluP, glucose/galactose transporter. This model
describes the glucose/galactose transporter in bacteria.
This belongs to the larger facilitator superfamily.
Disruption of the loci leads to the total loss of
glucose or galactose uptake in E.coli. Putative
transporters in other bacterial species were isolated by
functional complementation, which restored it functional
activity [Transport and binding proteins, Carbohydrates,
organic alcohols, and acids].
Length = 310
Score = 30.6 bits (69), Expect = 1.3
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 15/80 (18%)
Query: 142 VIAAGVNVREV----YVDTVGPPESYKKKLS--EIFPELIITVASKADSTYPVVGAA--I 193
V+A+G+ + +V YV +GP E+ +L+ + F +L TVA P+ G + +
Sbjct: 19 VLASGLTILQVAANPYVSILGPIETAASRLALTQAFNKLGTTVA-------PLFGGSLIL 71
Query: 194 ASKADSTYPVVGAASICAKV 213
+ D + V A + AKV
Sbjct: 72 SGAGDLSMQVATANAEAAKV 91
>gnl|CDD|147609 pfam05517, p25-alpha, p25-alpha. This family encodes a 25 kDa
protein that is phosphorylated by a Ser/Thr-Pro kinase.
It has been described as a brain specific protein, but
it is found in Tetrahymena thermophila.
Length = 151
Score = 29.6 bits (67), Expect = 1.4
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 323 AFFKESPYGGSKVFEVLNSTYLNILEMAHFIGKKLNLTSIDLLF 366
AF K + +G + E+ T+ +L+ I KK+ T +D++F
Sbjct: 4 AFKKFASFGTASGKEMDGKTFAKMLKDCKVIDKKVTATDVDIIF 47
>gnl|CDD|218652 pfam05602, CLPTM1, Cleft lip and palate transmembrane protein 1
(CLPTM1). This family consists of several eukaryotic
cleft lip and palate transmembrane protein 1 sequences.
Cleft lip with or without cleft palate is a common birth
defect that is genetically complex. The nonsyndromic
forms have been studied genetically using linkage and
candidate-gene association studies with only partial
success in defining the loci responsible for orofacial
clefting. CLPTM1 encodes a transmembrane protein and has
strong homology to two Caenorhabditis elegans genes,
suggesting that CLPTM1 may belong to a new gene family.
This family also contains the human cisplatin resistance
related protein CRR9p which is associated with
CDDP-induced apoptosis.
Length = 437
Score = 30.0 bits (68), Expect = 2.7
Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 6/77 (7%)
Query: 237 SGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKEKAVLVEGDEIDDEEEEGENK 296
SGY DP K + S F FP L + K +K+K +L E ++ EEE
Sbjct: 121 SGYSLDPTDKGYDSGKAVH-FVFP-LTTY---LPKKKVKKKNLLGGKSEKEEPEEEKTPA 175
Query: 297 KTRSIRNFFKPKADENV 313
I + + P +V
Sbjct: 176 PD-KIVSHWHPNLTLSV 191
>gnl|CDD|222837 PHA01794, PHA01794, hypothetical protein.
Length = 134
Score = 28.4 bits (63), Expect = 3.9
Identities = 19/74 (25%), Positives = 28/74 (37%), Gaps = 6/74 (8%)
Query: 247 KFLSENIDPVFGFPQLVRFSWSTASKILKEKAVLVEGDEIDDEEEEG---ENKKTRSIRN 303
L + + +L T +IL A VE E ++ EG E +K
Sbjct: 29 NILERDESAIVDLVRLSAKKALTEDEILDAIADFVETFEDEEGTTEGLFAELEKEMVDSG 88
Query: 304 FFKPKAD---ENVE 314
FF+ K EN+E
Sbjct: 89 FFRAKIKKYIENME 102
>gnl|CDD|227409 COG5077, COG5077, Ubiquitin carboxyl-terminal hydrolase
[Posttranslational modification, protein turnover,
chaperones].
Length = 1089
Score = 29.5 bits (66), Expect = 3.9
Identities = 27/136 (19%), Positives = 41/136 (30%), Gaps = 18/136 (13%)
Query: 254 DPVFGFPQLVRFSWSTASKI-LKEKAVLVEGDEIDDEEE-EGENKKTRSIRNFFKPKADE 311
+ + S S+ + L E+ D I D G T I F P A E
Sbjct: 708 LKISSISPWIEDSISSNLPLTLYEEIKPGMVDTIGDNITFIGSEIGTGDIICFEVPGAVE 767
Query: 312 NVESPVVEE--------RH----AFFKESPYGGSKVFEVLNSTYLNILEMAHFIGKKLNL 359
S + + AF + S VFE L ++ + KL++
Sbjct: 768 FDTSSAYDSALKLYDFLQGRVLVAFRRFSDEYRENVFEFLLFIGDFYDDLCRNVSCKLHV 827
Query: 360 TSIDLLFYIPLLTRNL 375
T FY+
Sbjct: 828 TP----FYLRGTKSTE 839
>gnl|CDD|182964 PRK11102, PRK11102, bicyclomycin/multidrug efflux system;
Provisional.
Length = 377
Score = 29.1 bits (66), Expect = 4.8
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 171 FPELIITVASKADS----TYPVVGAAIAS-KADSTYPVVGAASICAKVS 214
FP + T +S A + +VGA ++ S +P+V + + C+ +S
Sbjct: 316 FPHMAGTASSLAGTLRFGIGAIVGALLSLAPFTSAWPMVWSMAFCSILS 364
>gnl|CDD|236676 PRK10376, PRK10376, putative oxidoreductase; Provisional.
Length = 290
Score = 28.4 bits (64), Expect = 5.9
Identities = 11/25 (44%), Positives = 17/25 (68%), Gaps = 4/25 (16%)
Query: 132 HDAAIGLIRKVIAAGVNVREVYVDT 156
DAAI ++R+ +A GVN ++DT
Sbjct: 39 RDAAIAVLREAVALGVN----HIDT 59
>gnl|CDD|222928 PHA02778, PHA02778, major capsid L1 protein; Provisional.
Length = 503
Score = 28.2 bits (64), Expect = 7.6
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 76 LGCADSKALTEKKRD---DILDSICK 98
G + KAL K D DI++SICK
Sbjct: 205 FGAMNFKALQANKSDVPLDIVNSICK 230
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
0.316 0.134 0.388
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,513,735
Number of extensions: 2002379
Number of successful extensions: 1853
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1810
Number of HSP's successfully gapped: 40
Length of query: 401
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 302
Effective length of database: 6,546,556
Effective search space: 1977059912
Effective search space used: 1977059912
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 (21.6 bits)
S2: 60 (26.8 bits)