RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6532
(277 letters)
>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse
transcriptases. Ribonuclease H (RNase H) is classified
into two families, type 1 (prokaryotic RNase HI,
eukaryotic RNase H1 and viral RNase H) and type 2
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2). Ribonuclease HI (RNase HI) is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is widely present
in various organisms, including bacteria, archaea and
eukaryotes. RNase HI has also been observed as an
adjunct domain to the reverse transcriptase gene in
retroviruses, long-term repeat (LTR)-bearing
retrotransposons and non-LTR retrotransposons. RNase HI
in LTR retrotransposons perform degradation of the
original RNA template, generation of a polypurine tract
(the primer for plus-strand DNA synthesis), and final
removal of RNA primers from newly synthesized minus and
plus strands. The catalytic residues for RNase H
enzymatic activity, three aspartatic acids and one
glutamatic acid residue (DEDD), are unvaried across all
RNase H domains. The position of the RNase domain of
non-LTR and LTR transposons is at the carboxyl terminal
of the reverse transcriptase (RT) domain and their RNase
domains group together, indicating a common evolutionary
origin. Many non-LTR transposons have lost the RNase
domain because their activity is at the nucleus and
cellular RNase may suffice; however LTR retotransposons
always encode their own RNase domain because it requires
RNase activity in RNA-protein particles in the
cytoplasm. RNase H inhibitors have been explored as an
anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 128
Score = 106 bits (266), Expect = 8e-29
Identities = 45/122 (36%), Positives = 63/122 (51%), Gaps = 6/122 (4%)
Query: 110 DGSKNEQGVGCALTIPEK-DIVKRFGLNKNASIFHAELFALLQSLLTIKQLG--TCKALI 166
DGSK E G I K I + + L S+F AEL A+L++L + G K I
Sbjct: 5 DGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRARKITI 64
Query: 167 ITDSLSCLQAIMNMFHENPLVKRVQ---EELSSTESPVEFLWCPSHVGIAGNETADEEAK 223
+DS + L+A+ + +PLV R++ EL++ V W P H GI GNE AD AK
Sbjct: 65 FSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLAK 124
Query: 224 QA 225
+A
Sbjct: 125 EA 126
>gnl|CDD|215695 pfam00075, RNase_H, RNase H. RNase H digests the RNA strand of an
RNA/DNA hybrid. Important enzyme in retroviral
replication cycle, and often found as a domain
associated with reverse transcriptases. Structure is a
mixed alpha+beta fold with three a/b/a layers.
Length = 126
Score = 71.5 bits (176), Expect = 1e-15
Identities = 40/123 (32%), Positives = 53/123 (43%), Gaps = 10/123 (8%)
Query: 109 IDGSKNEQ-GVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALII 167
DGS N G G A + + + L + AEL AL+++L + L K I
Sbjct: 8 TDGSCNGNPGPGGAGYVTDGGKQRSKPLP-GTTNQRAELLALIEAL---EALSGQKVNIY 63
Query: 168 TDSLSCLQAIMNMF---HE-NPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAK 223
TDS + I N + E P+ + E L V W P H GI GNE AD+ AK
Sbjct: 64 TDSQYVIGGITNGWPTKSESKPIKNEIWELLQKKHK-VYIQWVPGHSGIPGNELADKLAK 122
Query: 224 QAI 226
Q
Sbjct: 123 QGA 125
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 58.1 bits (141), Expect = 1e-10
Identities = 38/149 (25%), Positives = 56/149 (37%), Gaps = 28/149 (18%)
Query: 104 NMKPTI--DG-SKNEQGV-GCA----LTIPEKDIVKRFGLNKNASIFHAELFALLQSLLT 155
K I DG G G EK++ G N AEL AL+++L
Sbjct: 1 MKKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNR---AELRALIEALEA 57
Query: 156 IKQLGTCKALIITDSLSCLQAIMNMFHENP----------------LVKRVQEELSSTES 199
+K+LG C+ + TDS ++ I + L + + E L E
Sbjct: 58 LKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHEL 117
Query: 200 PVEFLWCPSHVGIAGNETADEEAKQAINN 228
V + W H G NE AD+ A++A
Sbjct: 118 -VFWEWVKGHAGHPENERADQLAREAARA 145
>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA
strand of an RNA/DNA hybrid in a sequence non-specific
manner. Ribonuclease H (RNase H) enzymes are divided
into two major families, Type 1 and Type 2, based on
amino acid sequence similarities and biochemical
properties. RNase H is an endonuclease that cleaves the
RNA strand of an RNA/DNA hybrid in a sequence
non-specific manner in the presence of divalent cations.
RNase H is widely present in various organisms,
including bacteria, archaea and eukaryotes. Most
prokaryotic and eukaryotic genomes contain multiple
RNase H genes. Despite the lack of amino acid sequence
homology, Type 1 and type 2 RNase H share a main-chain
fold and steric configurations of the four acidic
active-site residues and have the same catalytic
mechanism and functions in cells. RNase H is involved in
DNA replication, repair and transcription. One of the
important functions of RNase H is to remove Okazaki
fragments during DNA replication. RNase H inhibitors
have been explored as an anti-HIV drug target because
RNase H inactivation inhibits reverse transcription.
Length = 123
Score = 47.0 bits (112), Expect = 7e-07
Identities = 35/126 (27%), Positives = 48/126 (38%), Gaps = 12/126 (9%)
Query: 109 IDGSKNEQG--VGCALTIPEKDIVKRFGL---NKNASIFHAELFALLQSLLTIKQLGTCK 163
DGS G + + + F A+ AEL ALL++L LG K
Sbjct: 2 TDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLKK 61
Query: 164 ALIITDSLSCLQAI---MNMFHENPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADE 220
+I TDS + I + +N L+ L S + F P GNE AD
Sbjct: 62 LIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEVADR 117
Query: 221 EAKQAI 226
AK+A
Sbjct: 118 LAKEAA 123
>gnl|CDD|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in
prokaryotes. Ribonuclease H (RNase H) is classified
into two evolutionarily unrelated families, type 1
(prokaryotic RNase HI, eukaryotic RNase H1 and viral
RNase H) and type 2 (prokaryotic RNase HII and HIII, and
eukaryotic RNase H2). RNase H is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is involved in DNA
replication, repair and transcription. RNase H is widely
present in various organisms, including bacteria,
archaea and eukaryotes and most prokaryotic and
eukaryotic genomes contain multiple RNase H genes.
Despite the lack of amino acid sequence homology, Type 1
and type 2 RNase H share a main-chain fold and steric
configurations of the four acidic active-site (DEDD),
residues and have the same catalytic mechanism and
functions in cells. One of the important functions of
RNase H is to remove Okazaki fragments during DNA
replication. Prokaryotic RNase H varies greatly in
domain structures and substrate specificities.
Prokaryotes and some single-cell eukaryotes do not
require RNase H for viability.
Length = 139
Score = 47.1 bits (113), Expect = 9e-07
Identities = 27/99 (27%), Positives = 42/99 (42%), Gaps = 20/99 (20%)
Query: 145 ELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFH---------------ENP-LVK 188
EL A++++L +K+ C L+ TDS + I H +N L +
Sbjct: 45 ELTAVIEALEALKE--PCPVLLYTDSQYVINGITKWIHGWKKNGWKTADGKPVKNVDLWQ 102
Query: 189 RVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAIN 227
+ L+ + V + W H G GNE ADE A A +
Sbjct: 103 ELDALLAKHQ--VTWHWVKGHAGHPGNERADELANAAAD 139
>gnl|CDD|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term
repeat retroelements. Ribonuclease H (RNase H) enzymes
are divided into two major families, Type 1 and Type 2,
based on amino acid sequence similarities and
biochemical properties. RNase H is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner in the presence of divalent
cations. RNase H is widely present in various organisms,
including bacteria, archaea and eukaryote. RNase HI has
also been observed as adjunct domains to the reverse
transcriptase gene in retroviruses, in long-term repeat
(LTR)-bearing retrotransposons and non-LTR
retrotransposons. RNase HI in LTR retrotransposons
perform degradation of the original RNA template,
generation of a polypurine tract (the primer for
plus-strand DNA synthesis), and final removal of RNA
primers from newly synthesized minus and plus strands.
The catalytic residues for RNase H enzymatic activity,
three aspartatic acids and one glutamatic acid residue
(DEDD), are unvaried across all RNase H domains.
Phylogenetic patterns of RNase HI of LTR retroelements
is classified into five major families, Ty3/Gypsy,
Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate
retroviruses. Bel/Pao family has been described only in
metazoan genomes. RNase H inhibitors have been explored
as an anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 135
Score = 42.3 bits (100), Expect = 4e-05
Identities = 34/141 (24%), Positives = 54/141 (38%), Gaps = 34/141 (24%)
Query: 109 IDGSKNEQGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKAL-II 167
DGS + G A+ D+++ L S AEL AL+++L K K + I
Sbjct: 4 TDGSSFVRKAGYAVVT-GPDVLEIATLPYGTSAQRAELIALIRALELAKG----KPVNIY 58
Query: 168 TDSLSCLQAIMNMFHE------------------NPLVKRVQEELSSTESPVEFLWCPSH 209
TDS + H L+ ++Q+ + + PV + +H
Sbjct: 59 TDS----AYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPK-PVAVIHIRAH 113
Query: 210 VG-----IAGNETADEEAKQA 225
G GN AD+ A+QA
Sbjct: 114 SGLPGPLALGNARADQAARQA 134
>gnl|CDD|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and
more complex than their prokaryotic counterparts and
unlike prokaryote, RNase H are essential in higher
eukaryote. Ribonuclease H (RNase H) is classified into
two families, type 1 (prokaryotic RNase HI, eukaryotic
RNase H1 and viral RNase H) and type 2 (prokaryotic
RNase HII and HIII, and eukaryotic RNase H2). RNase H is
an endonuclease that cleaves the RNA strand of an
RNA/DNA hybrid in a sequence non-specific manner. RNase
H is involved in DNA replication, repair and
transcription. One of the important functions of RNase H
is to remove Okazaki fragments during DNA replication.
RNase H is widely present in various organisms,
including bacteria, archaea and eukaryote and most
prokaryotic and eukaryotic genomes contain multiple
RNase H genes. Despite the lack of amino acid sequence
homology, Type 1 and type 2 RNase H share a main-chain
fold and steric configurations of the four acidic
active-site (DEDD) residues and have the same catalytic
mechanism and functions in cells. Eukaryotic RNase H is
longer and more complex than in prokaryotes. Almost all
eukaryotic RNase HI have highly conserved regions at the
N-terminal called hybrid binding domain (HBD). It is
speculated that the HBD contributes to binding the
RNA/DNA hybrid. Prokaryotes and some single-cell
eukaryotes do not require RNase H for viability, but
RNase H is essential in higher eukaryotes. RNase H
knockout mice lack mitochondrial DNA replication and die
as embryos.
Length = 150
Score = 38.7 bits (91), Expect = 7e-04
Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 21/104 (20%)
Query: 144 AELFALLQSLLTIKQL--GTCKALIITDS---LSCLQAIMNMFHEN--------P----- 185
AEL A++ +L IK++ G K +I TDS ++ + + + +N P
Sbjct: 46 AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105
Query: 186 LVKRVQEELSSTES---PVEFLWCPSHVGIAGNETADEEAKQAI 226
L+K + + L E V+F P H GI GNE AD AK+
Sbjct: 106 LIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGA 149
>gnl|CDD|205634 pfam13456, RVT_3, Reverse transcriptase-like. This domain is found
in plants and appears to be part of a retrotransposon.
Length = 88
Score = 37.2 bits (87), Expect = 0.001
Identities = 26/93 (27%), Positives = 40/93 (43%), Gaps = 9/93 (9%)
Query: 140 SIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMN--MFHEN--PLVKRVQEELS 195
S AE ALL+ L +LG + ++ +DS +Q I L++ +++ L
Sbjct: 1 SPLEAEAEALLEGLQLALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLK 60
Query: 196 STESPVEFLWCPSHVGIAGNETADEEAKQAINN 228
+S V SHV N AD AK A +
Sbjct: 61 KFDS-VSV----SHVPRECNRVADALAKLASAS 88
>gnl|CDD|187699 cd09275, RNase_HI_RT_DIRS1, DIRS1 family of RNase HI in long-term
repeat retroelements. Ribonuclease H (RNase H) enzymes
are divided into two major families, Type 1 and Type 2,
based on amino acid sequence similarities and
biochemical properties. RNase H is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner in the presence of divalent
cations. RNase H is widely present in various organisms,
including bacteria, archaea and eukaryotes. RNase HI
has also been observed as adjunct domains to the reverse
transcriptase gene in retroviruses, in long-term repeat
(LTR)-bearing retrotransposons and non-LTR
retrotransposons. RNase HI in LTR retrotransposons
perform degradation of the original RNA template,
generation of a polypurine tract (the primer for
plus-strand DNA synthesis), and final removal of RNA
primers from newly synthesized minus and plus strands.
The catalytic residues for RNase H enzymatic activity,
three aspartatic acids and one glutamatic acid residue
(DEDD), are unvaried across all RNase H domains.
Phylogenetic patterns of RNase HI of LTR retroelements
is classified into five major families, Ty3/Gypsy,
Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate
retroviruses. The structural features of DIRS1-group
elements are different from typical LTR elements. RNase
H inhibitors have been explored as an anti-HIV drug
target because RNase H inactivation inhibits reverse
transcription.
Length = 120
Score = 32.6 bits (75), Expect = 0.067
Identities = 21/101 (20%), Positives = 34/101 (33%), Gaps = 26/101 (25%)
Query: 138 NASIFHAELFALLQSLLTI-KQLGTCKALIITDSLSCLQAIMNM-----FHENPLVKRVQ 191
N I EL A+L +L +L K L+ +D+ + + I L +++
Sbjct: 30 NKHINFLELLAVLLALQHWGARLSNRKVLVRSDNTTAVAYINRQGGTRSPELLALARQL- 88
Query: 192 EELSSTESPVEFLWCPSH------VGIAG--NETADEEAKQ 224
LWC I G N AD ++
Sbjct: 89 -----------VLWCEERNIWLRARHIPGVLNVAADRLSRL 118
>gnl|CDD|187701 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI containing a
hybrid binding domain (HBD) at the N-terminus.
Ribonuclease H (RNase H) enzymes are divided into two
major families, Type 1 and Type 2, based on amino acid
sequence similarities and biochemical properties. RNase
H is an endonuclease that cleaves the RNA strand of an
RNA/DNA hybrid in a sequence non-specific manner in the
presence of divalent cations. RNase H is involved in
DNA replication, repair and transcription. RNase H is
widely present in various organisms, including bacteria,
archaea and eukaryotes and most prokaryotic and
eukaryotic genomes contain multiple RNase H genes.
Despite the lack of amino acid sequence homology, Type 1
and type 2 RNase H share a main-chain fold and steric
configurations of the four acidic active-site (DEDD)
residues and have the same catalytic mechanism and
functions in cells. One of the important functions of
RNase H is to remove Okazaki fragments during DNA
replication. Prokaryotic RNase H varies greatly in
domain structures and substrate specificities.
Prokaryotes and some single-cell eukaryotes do not
require RNase H for viability. Some bacteria
distinguished from other bacterial RNase HI in the
presence of a hybrid binding domain (HBD) at the
N-terminus which is commonly present at the N-termini of
eukaryotic RNase HI. It has been reported that this
domain is required for dimerization and processivity of
RNase HI upon binding to RNA-DNA hybrids.
Length = 133
Score = 32.1 bits (74), Expect = 0.11
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 201 VEFLWCPSHVGIAGNETADEEAKQAI 226
+ F+ +H G NE AD+ AK+A+
Sbjct: 108 ISFVKVKAHSGDKYNELADKLAKKAL 133
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 32.1 bits (74), Expect = 0.12
Identities = 24/100 (24%), Positives = 39/100 (39%), Gaps = 20/100 (20%)
Query: 145 ELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFH---------------ENP-LVK 188
EL A +++L +K+ C+ + TDS Q I H +N L +
Sbjct: 47 ELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQ 104
Query: 189 RVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINN 228
R+ L + +++ W H G NE DE A+
Sbjct: 105 RLDAALKRHQ--IKWHWVKGHAGHPENERCDELARAGAEE 142
>gnl|CDD|100807 PRK01189, PRK01189, V-type ATP synthase subunit F; Provisional.
Length = 104
Score = 29.0 bits (65), Expect = 0.87
Identities = 34/111 (30%), Positives = 52/111 (46%), Gaps = 13/111 (11%)
Query: 120 CALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMN 179
C I E+D+V F L AE L++ L I CK + +++S N
Sbjct: 4 CITVIGERDVVLGFRLLGIGDTIEAEGKDLVKKFLEIFNNPKCKYIFVSESTK------N 57
Query: 180 MFHENPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINNDV 230
MF +N L R E SS++ V F+ P GI+ E+ +E AK+ + D+
Sbjct: 58 MFDKNTL--RSLE--SSSKPLVVFIPLP---GISEEESIEEMAKRILGIDI 101
>gnl|CDD|187703 cd09279, RNase_HI_archaeal_like, RNAse HI family that includes
Archaeal RNase HI. Ribonuclease H (RNase H) is
classified into two evolutionarily unrelated families,
type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and
viral RNase H) and type 2 (prokaryotic RNase HII and
HIII, and eukaryotic RNase H2). RNase H is an
endonuclease that cleaves the RNA strand of an RNA/DNA
hybrid in a sequence non-specific manner. RNase H is
involved in DNA replication, repair and transcription.
RNase H is widely present in various organisms,
including bacteria, archaea and eukaryotes and most
prokaryotic and eukaryotic genomes contain multiple
RNase H genes. Despite the lack of amino acid sequence
homology, Type 1 and type 2 RNase H share a main-chain
fold and steric configurations of the four acidic
active-site (DEDD) residues and have the same catalytic
mechanism and functions in cells. One of the important
functions of RNase H is to remove Okazaki fragments
during DNA replication. Most archaeal genomes contain
only type 2 RNase H (RNase HII); however, a few contain
RNase HI as well. Although archaeal RNase HI sequences
conserve the DEDD active-site motif, they lack other
common features important for catalytic function, such
as the basic protrusion region. Archaeal RNase HI
homologs are more closely related to retroviral RNase HI
than bacterial and eukaryotic type I RNase H in
enzymatic properties.
Length = 128
Score = 29.0 bits (66), Expect = 1.2
Identities = 34/132 (25%), Positives = 52/132 (39%), Gaps = 23/132 (17%)
Query: 109 IDGSKNEQ----GVGCALTIPEKDIVKR-FGLNKNASIFHAELFALLQSLLTIKQLGTCK 163
DG+ G G + P+ +++++ L A+ AE AL+ L +LG K
Sbjct: 5 FDGASRGNPGPAGAGIVIKSPDGEVLEQSIPLGFPATNNEAEYEALIAGLELALELGIKK 64
Query: 164 ALIITDSLSCLQAIMNMFHEN---------PLVKRVQEELSSTESPVEFLWCPSHVGIAG 214
I DS Q ++N P ++ +E L E VE W P
Sbjct: 65 LEIYGDS----QLVVNQIQGEYEVKNERLAPYLEEARELLKKFEE-VEIKWIPRE----E 115
Query: 215 NETADEEAKQAI 226
N+ AD A QA+
Sbjct: 116 NKEADALANQAL 127
>gnl|CDD|168967 PRK07481, PRK07481, hypothetical protein; Provisional.
Length = 449
Score = 28.9 bits (65), Expect = 2.9
Identities = 15/36 (41%), Positives = 17/36 (47%)
Query: 118 VGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSL 153
V CA + DIV R L NA+ A L LQ L
Sbjct: 325 VACAAALATLDIVVREDLPANAAKRGAYLLEGLQPL 360
>gnl|CDD|216712 pfam01803, LIM_bind, LIM-domain binding protein. The LIM-domain
binding protein, binds to the LIM domain pfam00412 of
LIM homeodomain proteins which are transcriptional
regulators of development. Nuclear LIM interactor (NLI)
/ LIM domain-binding protein 1 (LDB1) is located in the
nuclei of neuronal cells during development, it is
co-expressed with Isl1 in early motor neuron
differentiation and has a suggested role in the Isl1
dependent development of motor neurons. It is suggested
that these proteins act synergistically to enhance
transcriptional efficiency by acting as co-factors for
LIM homeodomain and Otx class transcription factors both
of which have essential roles in development. The
Drosophila protein Chip is required for segmentation and
activity of a remote wing margin enhancer. Chip is a
ubiquitous chromosomal factor required for normal
expression of diverse genes at many stages of
development. It is suggested that Chip cooperates with
different LIM domain proteins and other factors to
structurally support remote enhancer-promoter
interactions.
Length = 230
Score = 28.8 bits (65), Expect = 2.9
Identities = 22/111 (19%), Positives = 36/111 (32%), Gaps = 27/111 (24%)
Query: 80 LSIENH-PNIMRTLNPLYVRKYENSNMKPTIDGSKNEQGVGCALTIPEKDI----VKRFG 134
+H I R++ + + + + SKN Q P + V RFG
Sbjct: 132 FCTRSHEEYIPRSVLEPLASPLHTKSKQQSPELSKNSQLRQQKGPQPITSLPSSNVTRFG 191
Query: 135 LNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFHENP 185
L K + L+ I + LS +Q +M+ NP
Sbjct: 192 LPKA-------VMRFLE---------------IAEILSPMQDLMSFSKANP 220
>gnl|CDD|226375 COG3857, AddB, ATP-dependent nuclease, subunit B [DNA replication,
recombination, and repair].
Length = 1108
Score = 28.2 bits (63), Expect = 6.9
Identities = 10/42 (23%), Positives = 18/42 (42%)
Query: 234 ELFFDEVKIIIKKKYTEEWNTKWVNISPNENKLRKIKNSILP 275
E + I KKK+T+ + + N +L + + IL
Sbjct: 410 ENYVLAAGIKGKKKWTKLFTYEHFRKIENLERLNETRLDILH 451
>gnl|CDD|215162 PLN02288, PLN02288, mannose-6-phosphate isomerase.
Length = 394
Score = 27.7 bits (62), Expect = 7.3
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 69 KILSSNYIAKTLSIENHPN--IMRTLNPLYVRKYENSNMKP 107
K+LS +AK LSI+ HP+ + L+ Y++ N KP
Sbjct: 93 KVLS---VAKALSIQAHPDKKLAEKLHAEQPNVYKDDNHKP 130
>gnl|CDD|132286 TIGR03242, arg_catab_astE, succinylglutamate desuccinylase.
Members of this protein family are succinylglutamate
desuccinylase, the fifth and final enzyme of the
arginine succinyltransferase (AST) pathway for arginine
catabolism. This model excludes the related protein
aspartoacylase [Energy metabolism, Amino acids and
amines].
Length = 319
Score = 27.7 bits (62), Expect = 7.3
Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 14/71 (19%)
Query: 211 GIAGNETADEEAKQAINNDVIHNEL---------FFDEVKIIIKKKYTEE-----WNTKW 256
GI GNETA E + + D+ +L + + K+Y + + ++
Sbjct: 49 GIHGNETAPIEILEQLLGDIAAGKLPLRVRLLVILGNPPAMRTGKRYLHDDLNRMFGGRY 108
Query: 257 VNISPNENKLR 267
++P+ R
Sbjct: 109 QQLAPSFETCR 119
>gnl|CDD|75628 PRK06548, PRK06548, ribonuclease H; Provisional.
Length = 161
Score = 27.1 bits (59), Expect = 7.9
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 201 VEFLWCPSHVGIAGNETADEEAKQAINN 228
+ W +H G NE AD A+QA NN
Sbjct: 115 IRMSWVNAHTGHPLNEAADSLARQAANN 142
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 0.132 0.379
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,681,130
Number of extensions: 1282775
Number of successful extensions: 1110
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1103
Number of HSP's successfully gapped: 26
Length of query: 277
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 181
Effective length of database: 6,679,618
Effective search space: 1209010858
Effective search space used: 1209010858
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: 58 (26.0 bits)