RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5480
(446 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 = 112 bits (283), Expect = 5e-30
Identities = 43/123 (34%), Positives = 68/123 (55%), Gaps = 4/123 (3%)
Query: 154 CFTDGSKTANNTSCAY-IIDKTLIS-SFVLNNVNSVYTSELIAVLLCLKHLKFLPKE--K 209
+TDGSK T + I+ K IS S+ L SV+ +EL+A+L L+ + K
Sbjct: 2 IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRARK 61
Query: 210 FVVISDSKSTLLALSNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDR 269
+ SDS++ L AL +P +++P+V I +L +G ++ W P H+GI+GNE DR
Sbjct: 62 ITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADR 121
Query: 270 AAR 272
A+
Sbjct: 122 LAK 124
>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 = 79.6 bits (197), Expect = 5e-18
Identities = 32/125 (25%), Positives = 52/125 (41%), Gaps = 14/125 (11%)
Query: 154 CFTDGS--KTANNTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFV 211
+TDGS Y+ D S L + +EL+A++ L+ L +K
Sbjct: 6 VYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPG-TTNQRAELLALIEALEAL---SGQKVN 61
Query: 212 VISDSKST----LLALSNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAV 267
+ +DS+ S + PI + I +LL ++ W P H+GI GNE
Sbjct: 62 IYTDSQYVIGGITNGWPTKSESKPIKNEIW----ELLQKKHKVYIQWVPGHSGIPGNELA 117
Query: 268 DRAAR 272
D+ A+
Sbjct: 118 DKLAK 122
>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 = 58.1 bits (141), Expect = 2e-10
Identities = 29/128 (22%), Positives = 51/128 (39%), Gaps = 14/128 (10%)
Query: 155 FTDGSKTAN--NTSCAYII---DKTLISSFVLNNVNSVYTS---ELIAVLLCLKHLKFLP 206
TDGS N ++ + + + L+ T+ EL+A+L L+ L
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSI--PAATNNEAELLALLEALELALDLG 58
Query: 207 KEKFVVISDSKSTLLALSNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEA 266
+K ++ +DSK + +++ S +L+ LL + F P GNE
Sbjct: 59 LKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEV 114
Query: 267 VDRAARNP 274
DR A+
Sbjct: 115 ADRLAKEA 122
>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 = 55.7 bits (135), Expect = 1e-09
Identities = 30/139 (21%), Positives = 49/139 (35%), Gaps = 26/139 (18%)
Query: 153 LCFTDGSKTANNTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVV 212
FTDGS A + ++ L S +ELIA++ L+ K + +
Sbjct: 1 TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKG---KPVNI 57
Query: 213 ISDSK---STLLAL-----------SNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSH 258
+DS L AL P ++ + + K +A + +H
Sbjct: 58 YTDSAYAFGILHALETIWKERGFLTGKPIALASLILQL----QKAIQRPKPVAVIHIRAH 113
Query: 259 TG-----IQGNEAVDRAAR 272
+G GN D+AAR
Sbjct: 114 SGLPGPLALGNARADQAAR 132
>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 = 45.6 bits (109), Expect = 5e-06
Identities = 34/142 (23%), Positives = 52/142 (36%), Gaps = 35/142 (24%)
Query: 155 FTDGSKTANNTS--CAYIID-----KTLISSFVL--NNVNSVYTSELIAVLLCLKHLKFL 205
+TDG+ N A I+ K L NN EL AV+ L+ LK
Sbjct: 5 YTDGACLGNPGPGGWAAILRYGDHEKELSGGEAGTTNNR-----MELTAVIEALEALK-- 57
Query: 206 PKEKFVVISDSKSTLLALSN-----------PSNTNPI--VSLIHSCWTDL--LCYGKQL 250
++ +DS+ + ++ ++ P+ V L W +L L Q+
Sbjct: 58 EPCPVLLYTDSQYVINGITKWIHGWKKNGWKTADGKPVKNVDL----WQELDALLAKHQV 113
Query: 251 AFLWCPSHTGIQGNEAVDRAAR 272
+ W H G GNE D A
Sbjct: 114 TWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 36.6 bits (85), Expect = 0.008
Identities = 23/94 (24%), Positives = 33/94 (35%), Gaps = 12/94 (12%)
Query: 191 ELIAVLLCLKHLKFLPKEKFVVISDSKS-----TLLALSNPSNTNPIVSLIHSCWTDLLC 245
EL A++ L+ LK L + + +DSK T + N DL
Sbjct: 47 ELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWE 106
Query: 246 YGKQLA-------FLWCPSHTGIQGNEAVDRAAR 272
+L + W H G NE D+ AR
Sbjct: 107 ELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140
>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 = 0.20
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 252 FLWCPSHTGIQGNEAVDRAARN 273
F+ +H+G + NE D+ A+
Sbjct: 110 FVKVKAHSGDKYNELADKLAKK 131
>gnl|CDD|187698 cd09274, RNase_HI_RT_Ty3, Ty3/Gypsy 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. Ty3/Gypsy family widely distributed among
the genomes of plants, fungi and animals. RNase H
inhibitors have been explored as an anti-HIV drug target
because RNase H inactivation inhibits reverse
transcription.
Length = 121
Score = 31.7 bits (73), Expect = 0.25
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 186 SVYTSELIAVLLCLKHLK-FLPKEKFVVISDSKSTLLALSNPSNTNP 231
S Y EL+A++ LK + +L KF V +D KS L L + NP
Sbjct: 41 STYEKELLAIVFALKKFRHYLLGRKFTVYTDHKS-LKYLLTKKDLNP 86
>gnl|CDD|223929 COG0860, AmiC, N-acetylmuramoyl-L-alanine amidase [Cell envelope
biogenesis, outer membrane].
Length = 231
Score = 32.0 bits (73), Expect = 0.45
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 3 LNKLNPVHNSGIRIATGA-LRSSPIPSLLVESG 34
L K + + G++ A A LR++ +PS+LVE G
Sbjct: 164 LVKKLNLRDRGVKGANLAVLRNTQMPSVLVELG 196
>gnl|CDD|182376 PRK10319, PRK10319, N-acetylmuramoyl-l-alanine amidase I;
Provisional.
Length = 287
Score = 31.3 bits (71), Expect = 0.83
Identities = 16/37 (43%), Positives = 22/37 (59%), Gaps = 4/37 (10%)
Query: 1 HILNKLNPVH----NSGIRIATGALRSSPIPSLLVES 33
HIL K+ PVH + + A L+S IPS+LVE+
Sbjct: 207 HILKKIKPVHKLHSRNTEQAAFVVLKSPSIPSVLVET 243
>gnl|CDD|236692 PRK10431, PRK10431, N-acetylmuramoyl-l-alanine amidase II;
Provisional.
Length = 445
Score = 31.4 bits (71), Expect = 1.0
Identities = 16/32 (50%), Positives = 19/32 (59%), Gaps = 5/32 (15%)
Query: 3 LNKLNPVHNSGIRIATGALRSSPIPSLLVESG 34
L+K P H S G LRS IPS+LVE+G
Sbjct: 358 LHKRRPEHAS-----LGVLRSPDIPSVLVETG 384
>gnl|CDD|236471 PRK09344, PRK09344, phosphoenolpyruvate carboxykinase; Provisional.
Length = 526
Score = 31.0 bits (71), Expect = 1.3
Identities = 21/59 (35%), Positives = 26/59 (44%), Gaps = 16/59 (27%)
Query: 115 ATPVIDNALSFDKK-ENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIID 172
A P I +A+ F ENV VV + T+ F DGS T NT AY I+
Sbjct: 280 AEPEIYDAIRFGAVLENV--VVDEDG------------TVDFDDGSLTE-NTRAAYPIE 323
>gnl|CDD|216549 pfam01520, Amidase_3, N-acetylmuramoyl-L-alanine amidase. This
enzyme domain cleaves the amide bond between
N-acetylmuramoyl and L-amino acids in bacterial cell
walls.
Length = 172
Score = 29.9 bits (68), Expect = 1.4
Identities = 12/33 (36%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 3 LNKLNPVHNSGIRIATGA-LRSSPIPSLLVESG 34
L K+ + N G++ A LR++ +P++LVE G
Sbjct: 111 LVKVLGLKNRGVKPANLYVLRNTNMPAVLVELG 143
>gnl|CDD|163004 TIGR02761, TraE_TIGR, type IV conjugative transfer system protein
TraE. TraE is a component of type IV secretion systems
involved in conjugative transfer of plasmid DNA. The
function of the TraE protein is unknown.
Length = 181
Score = 29.7 bits (67), Expect = 1.9
Identities = 10/72 (13%), Positives = 21/72 (29%), Gaps = 8/72 (11%)
Query: 106 CKFFPP--WSIATPVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDF----TLCFTDGS 159
+ P + + KK N SSV + + + L G
Sbjct: 97 LGYVEPQNYGQIKSRLAKEAEEIKKANASSVFYPKSVE--WNPQEGTVKVRGHLKRFVGG 154
Query: 160 KTANNTSCAYII 171
+ ++ Y++
Sbjct: 155 RLLSDERKTYLL 166
>gnl|CDD|168927 PRK07374, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1170
Score = 30.5 bits (69), Expect = 2.0
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 328 LKLCSPEDFKPFI---MIGRTGSIKPVIGPWPSSDRQSRYEEVVICRMRIGH 376
LKLC + KP I M GSI P ++ RY VV+ + G+
Sbjct: 51 LKLCKGKGIKPIIGNEMYVINGSIDD-----PQPKKEKRYHLVVLAKNATGY 97
>gnl|CDD|119407 cd02696, MurNAc-LAA, N-acetylmuramoyl-L-alanine amidase or
MurNAc-LAA (also known as peptidoglycan aminohydrolase,
NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan
amidase; EC 3.5.1.28) is an autolysin that hydrolyzes
the amide bond between N-acetylmuramoyl and L-amino
acids in certain cell wall glycopeptides. These proteins
are Zn-dependent peptidases with highly conserved
residues involved in cation co-ordination. MurNAc-LAA in
this family is one of several peptidoglycan hydrolases
(PGHs) found in bacterial and bacteriophage or prophage
genomes that are involved in the degradation of the
peptidoglycan. In Escherichia coli, there are five
MurNAc-LAAs present: AmiA, AmiB, AmiC and AmiD that are
periplasmic, and AmpD that is cytoplasmic. Three of
these (AmiA, AmiB and AmiC) belong to this family, the
other two (AmiD and AmpD) do not. E. coli AmiA, AmiB and
AmiC play an important role in cleaving the septum to
release daughter cells after cell division. In general,
bacterial MurNAc-LAAs are members of the bacterial
autolytic system and carry a signal peptide in their
N-termini that allows their transport across the
cytoplasmic membrane. However, the bacteriophage
MurNAc-LAAs are endolysins since these phage-encoded
enzymes break down bacterial peptidoglycan at the
terminal stage of the phage reproduction cycle. As
opposed to autolysins, almost all endolysins have no
signal peptides and their translocation through the
cytoplasmic membrane is thought to proceed with the help
of phage-encoded holin proteins. The amidase catalytic
module is fused to another functional module (cell wall
binding module or CWBM) either at the N- or C-terminus,
which is responsible for high affinity binding of the
protein to the cell wall.
Length = 172
Score = 29.4 bits (67), Expect = 2.6
Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 3 LNKLNPVHNSGIRIAT-GALRSSPIPSLLVESG 34
L K + N G++ A LR++ +P++LVE G
Sbjct: 111 LVKALGLRNRGVKQANLYVLRNTKMPAVLVELG 143
>gnl|CDD|188606 TIGR04091, LTA_dltB, D-alanyl-lipoteichoic acid biosynthesis
protein DltB. Members of this protein family are DltB,
part of a four-gene operon for D-alanyl-lipoteichoic
acid biosynthesis that is present in the vast majority
of low-GC Gram-positive organisms. This protein may be
involved in transport of D-alanine across the plasma
membrane [Cell envelope, Biosynthesis and degradation of
murein sacculus and peptidoglycan].
Length = 380
Score = 29.8 bits (68), Expect = 3.0
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 285 SPEDF-KPFICKLIKDLWQNSW 305
+P +F KPF+ K IKD W N W
Sbjct: 250 TPMNFNKPFLSKDIKDFW-NRW 270
>gnl|CDD|152066 pfam11630, DUF3254, Protein of unknown function (DUF3254). This
family of proteins is most likely a family of
anti-lipopolysaccharide factor proteins however this
cannot be confirmed.
Length = 97
Score = 27.7 bits (62), Expect = 3.6
Identities = 14/69 (20%), Positives = 23/69 (33%), Gaps = 12/69 (17%)
Query: 237 HSCWTDLLCYGKQL-----AFLWCPSHTGIQGN-------EAVDRAARNPSASLPPLKLC 284
H C + K+ +WCP T I G V+ A R+ L
Sbjct: 28 HECNYRVKPTIKRFQLYYKGKMWCPGWTPITGESRTRSRSGVVEHAVRDFVQKALQAGLI 87
Query: 285 SPEDFKPFI 293
+ E+ ++
Sbjct: 88 TEEEANAWL 96
>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 = 28.3 bits (64), Expect = 4.6
Identities = 25/100 (25%), Positives = 42/100 (42%), Gaps = 18/100 (18%)
Query: 191 ELIAVLLCLKHLKFL--PKEKFVVISDSKSTLLALSN-----------PSNTNPIV---- 233
EL AV+ L+ +K + K V+ +DS+ + ++ S P+
Sbjct: 47 ELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKDL 106
Query: 234 -SLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAAR 272
+ +L G ++ F P H+GI GNE DR A+
Sbjct: 107 IKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146
>gnl|CDD|238366 cd00714, GFAT, Glutamine amidotransferases class-II
(Gn-AT)_GFAT-type. This domain is found at the
N-terminus of glucosamine-6P synthase (GlmS, or GFAT in
humans). The glutaminase domain catalyzes amide
nitrogen transfer from glutamine to the appropriate
substrate. In this process, glutamine is hydrolyzed to
glutamic acid and ammonia. In humans, GFAT catalyzes the
first and rate-limiting step of hexosamine metabolism,
the conversion of D-fructose-6P (Fru6P) into
D-glucosamine-6P using L-glutamine as a nitrogen source.
The end product of this pathway, UDP-N-acetyl
glucosamine, is a major building block of the bacterial
peptidoglycan and fungal chitin.
Length = 215
Score = 28.6 bits (65), Expect = 4.9
Identities = 9/10 (90%), Positives = 9/10 (90%), Gaps = 1/10 (10%)
Query: 374 IGHTR-ATHG 382
IGHTR ATHG
Sbjct: 68 IGHTRWATHG 77
>gnl|CDD|224779 COG1866, PckA, Phosphoenolpyruvate carboxykinase (ATP) [Energy
production and conversion].
Length = 529
Score = 29.2 bits (66), Expect = 5.5
Identities = 10/18 (55%), Positives = 11/18 (61%), Gaps = 1/18 (5%)
Query: 155 FTDGSKTANNTSCAYIID 172
F DGS T NT AY I+
Sbjct: 309 FDDGSLT-ENTRAAYPIE 325
>gnl|CDD|240558 cd13115, POLO_box_Plk4_2, Second (cryptic) polo-box domain (PBD) of
polo-like kinase 4 (Plk4/Sak). The polo-like Ser/Thr
kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the
inactive kinase Plk5) play various roles in cytokinesis
and mitosis. At their C-terminus, they contain a
tandemly repeated polo-box domain (in the case of Plk4,
a tandem repeat of cryptic PBDs is found in the middle
of the protein followed by a C-terminal single repeat),
which appears to be involved in autoinhibition and in
mediating the subcellular localization. The latter may
be controlled via interactions between the polo-box
domain and phospho-peptide motifs. The phosphopeptide
binding site is formed at the interface between the two
tandemly repeated PBDs. The PBDs of Plk4/Sak appear
unique in participating in homodimer interactions,
though it is not clear whether and how they interact
with phosphopeptides.
Length = 108
Score = 27.3 bits (61), Expect = 7.0
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 4/57 (7%)
Query: 149 QDFTLCFTDGSKTANNTSCAYIIDKTLISSFVLNNVNSVYTSELIA----VLLCLKH 201
DF CF DG+K + IIDK+ S + + S + EL C +H
Sbjct: 23 ADFEACFYDGAKVHKTSGGIKIIDKSGKSYTLKESDLSSLSPELRKLLDHFNECRQH 79
>gnl|CDD|211835 TIGR03548, mutarot_permut, cyclically-permuted mutarotase family
protein. Members of this protein family show
essentially full-length homology, cyclically permuted,
to YjhT from Escherichia coli. YjhT was shown to act as
a mutarotase for sialic acid, and by this ability to be
able to act as a virulence factor. Members of the YjhT
family (TIGR03547) and this cyclically-permuted family
have multiple repeats of the beta-propeller-forming
Kelch repeat.
Length = 323
Score = 28.2 bits (63), Expect = 8.6
Identities = 19/58 (32%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 264 NEAVDRAARNPSASLPPLK---LCSPEDFKPFICK-LIKDLWQNSWSNIPNSEAVDRA 317
N+AV R A SL P D+ + K LI D+ W +I NS V R
Sbjct: 238 NDAVIRLATMKDESLKSYAAEYFLHPPDWYRWNDKVLIYDVRSGKWKSIGNSPFVARC 295
>gnl|CDD|234252 TIGR03545, TIGR03545, TIGR03545 family protein. This model
represents a relatively rare but broadly distributed
uncharacterized protein family, distributed in 1-2
percent of bacterial genomes, all of which have outer
membranes. In many of these genomes, it is part of a
two-gene pair.
Length = 555
Score = 28.5 bits (64), Expect = 9.0
Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 2/80 (2%)
Query: 310 NSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRTGSIKPVIGPWPSSDRQSRYEEVVI 369
VD S+ L++ P+ KP + I + + EE+ I
Sbjct: 46 EIAQVDTGLFPLQLSIQGLQVTDPD--KPMRNLFEIDRINASLDWDALLRGKVVIEELAI 103
Query: 370 CRMRIGHTRATHGHLFKRAP 389
+ G R+T G + +
Sbjct: 104 EGLAFGTERSTSGAVPETKD 123
>gnl|CDD|227093 COG4750, LicC, CTP:phosphocholine cytidylyltransferase involved in
choline phosphorylation for cell surface LPS epitopes
[Cell envelope biogenesis, outer membrane].
Length = 231
Score = 27.8 bits (62), Expect = 9.7
Identities = 14/75 (18%), Positives = 34/75 (45%), Gaps = 7/75 (9%)
Query: 116 TPVIDNALSFDKKENVSSVV-----FQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYI 170
P+I+ + ++ + + +++F L KY D TL + + NN Y+
Sbjct: 31 EPLIERQIEQLREAGIDDITIVVGYLKEQFEYLKD-KY-DVTLVYNPKYREYNNIYSLYL 88
Query: 171 IDKTLISSFVLNNVN 185
L +++++++ N
Sbjct: 89 ARDFLNNTYIIDSDN 103
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
0.321 0.135 0.418
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,422,084
Number of extensions: 2107051
Number of successful extensions: 1534
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1526
Number of HSP's successfully gapped: 28
Length of query: 446
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 346
Effective length of database: 6,502,202
Effective search space: 2249761892
Effective search space used: 2249761892
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: 61 (27.3 bits)