RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10264
(426 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 = 119 bits (300), Expect = 1e-32
Identities = 48/148 (32%), Positives = 69/148 (46%), Gaps = 28/148 (18%)
Query: 189 CFTDGSKTSDHTGAAYII---GDEVCSMKLNPVCSIFTAELVAIEKCLEKIKDLIRTELI 245
+TDGSK TGA + I G S KL P CS+F AEL+AI + L+
Sbjct: 2 IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLA--------- 52
Query: 246 SELVAIEKCLEKIKDLIRTELILQNFIICSDSKSSLQALQNVYHASPLVCNIISTIQDIR 305
+R + I SDS+++L+AL++ +SPLV I I+++
Sbjct: 53 ----------------LREGRRARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELA 96
Query: 306 ELGTRVSFFWIPSHLGIRENENVDHAAR 333
G +V W+P H GI NE D A+
Sbjct: 97 NHGVKVRLHWVPGHSGIEGNERADRLAK 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 = 58.8 bits (143), Expect = 8e-11
Identities = 34/148 (22%), Positives = 54/148 (36%), Gaps = 34/148 (22%)
Query: 189 CFTDGS--KTSDHTGAAYII-GDEVCSMKLNPVCSIFTAELVAIEKCLEKIKDLIRTELI 245
+TDGS GA Y+ G + S L P + AEL+A+ + LE +
Sbjct: 6 VYTDGSCNGNPGPGGAGYVTDGGKQRSKPL-PGTTNQRAELLALIEALEALSG------- 57
Query: 246 SELVAIEKCLEKIKDLIRTELILQNFIICSDSKSSLQALQNVYHASPLVCNIISTIQDIR 305
Q I +DS+ + + N + I + I ++
Sbjct: 58 -----------------------QKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWELL 94
Query: 306 ELGTRVSFFWIPSHLGIRENENVDHAAR 333
+ +V W+P H GI NE D A+
Sbjct: 95 QKKHKVYIQWVPGHSGIPGNELADKLAK 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 = 45.4 bits (108), Expect = 4e-06
Identities = 32/153 (20%), Positives = 51/153 (33%), Gaps = 40/153 (26%)
Query: 190 FTDGSKTSD--HTGAAYIIGDEVCSMKL-----NPVCSIFTAELVAIEKCLEKIKDLIRT 242
TDGS + GA ++ D + P + AEL+A+ + LE DL
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60
Query: 243 ELISELVAIEKCLEKIKDLIRTELILQNFIICSDSKSSLQALQNVYHASPLVCNIISTIQ 302
+LI IE +DSK + + + ++ I
Sbjct: 61 KLI-----IE----------------------TDSKYVVDLINSWSKGWKKNNLLLWDIL 93
Query: 303 DIRELGTRVSFFWIPSHLGIRE-NENVDHAARH 334
+ + F +P RE NE D A+
Sbjct: 94 LLLSKFIDIRFEHVP-----REGNEVADRLAKE 121
>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 = 6e-05
Identities = 35/163 (21%), Positives = 53/163 (32%), Gaps = 46/163 (28%)
Query: 188 LCFTDGSKTSDHTGAAYIIGDEVCSMK-LNPVCSIFTAELVAIEKCLEKIKDLIRTELIS 246
FTDGS G A + G +V + L S AEL+A+ + LE K
Sbjct: 1 TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKG-------- 52
Query: 247 ELVAIEKCLEKIKDLIRTELILQNFIICSDSK---SSLQALQNVYHASPLVC-------N 296
+ I +DS L AL+ ++ + +
Sbjct: 53 ----------------------KPVNIYTDSAYAFGILHALETIWKERGFLTGKPIALAS 90
Query: 297 IISTIQDIRELGTRVSFFWIPSHLG-----IRENENVDHAARH 334
+I +Q + V+ I +H G N D AAR
Sbjct: 91 LILQLQKAIQRPKPVAVIHIRAHSGLPGPLALGNARADQAARQ 133
>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 = 40.7 bits (96), Expect = 3e-04
Identities = 24/104 (23%), Positives = 43/104 (41%), Gaps = 21/104 (20%)
Query: 247 ELVAIEKCLEKIKDLIRTELILQNFIICSDSKSSLQAL-----------------QNVYH 289
EL A+ L IK++ L +I +DS+ + + + V +
Sbjct: 47 ELRAVIHALRLIKEVGEG---LTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVAN 103
Query: 290 ASPLVCNIISTIQDIRELGTRVSFFWIPSHLGIRENENVDHAAR 333
+ + ++++ E G RV F+ +P H GI NE D A+
Sbjct: 104 KDLIKE-LDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146
>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 = 33.3 bits (77), Expect = 0.033
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 265 ELILQNFIICSDSKSSLQALQNVYHASPLVCNIISTIQDIRELGTRVSFFWIPSHLGIRE 324
EL ++ I+ SDS+ +Q +Q Y A + ++ I+ + + VS +P RE
Sbjct: 19 ELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLKKFDSVSVSHVP-----RE 73
Query: 325 -NENVDHAARH 334
N D A+
Sbjct: 74 CNRVADALAKL 84
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 33.5 bits (77), Expect = 0.096
Identities = 27/100 (27%), Positives = 41/100 (41%), Gaps = 19/100 (19%)
Query: 247 ELVAIEKCLEKIKDLIRTELILQNFIICSDSKSSLQALQNVYH----------ASPLVCN 296
EL A+ + LE +K+L E+ L +DSK ++ + V N
Sbjct: 47 ELRALIEALEALKELGACEVTL-----YTDSKYVVEGITRWIVKWKKNGWKTADKKPVKN 101
Query: 297 IISTIQDIRELGTR---VSFFWIPSHLGIRENENVDHAAR 333
+++ EL R V + W+ H G ENE D AR
Sbjct: 102 K-DLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140
>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 = 33.3 bits (77), Expect = 0.098
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 310 RVSFFWIPSHLGIRENENVDHAAR 333
+V++ W+ H G NE D A
Sbjct: 112 QVTWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|99879 cd06070, H2MP_like-2, Putative [NiFe] hydrogenase-specific
C-terminal protease. Sequence comparison shows
similarity to hydrogenase specific C-terminal
endopeptidases, also called Hydrogen Maturation
Proteases (H2MP). Maturation of [FeNi] hydrogenases
includes formation of the nickel metallocenter,
proteolytic processing and assembly with other subunits.
Hydrogenase maturation endopeptidases are responsible
for the proteolytic processing, liberating a short
C-terminal peptide by cleaving after a His or an Arg
residue, e.g., HycI (E. coli) is involved in processing
of HypE (the large subunit of hydrogenases 3). This
cleavage is nickel dependent.
Length = 140
Score = 32.0 bits (73), Expect = 0.25
Identities = 17/72 (23%), Positives = 27/72 (37%), Gaps = 2/72 (2%)
Query: 169 KEEVVQHFLKFKDQHKFDTLCFTDGSKTSDHTGAAYIIGDEVCSMKLNPVCSIFTAELVA 228
V + D H+ K+S AYI+G V + + A +
Sbjct: 71 PASVAEQISFETDAHRLGPAHLLLLLKSSGRRPKAYIVG--VKPESIEFARGLSEAVIAR 128
Query: 229 IEKCLEKIKDLI 240
EK LE++K L+
Sbjct: 129 AEKALEELKKLL 140
>gnl|CDD|241322 cd13168, PTB_LOC417372, uncharacterized protein LOC417372
Phosphotyrosine-binding (PTB) PH-like fold. The
function of LOC417372 and its related proteins are
unknown to date. Members here contain a N-terminal RUN
domain, followed by a PDZ domain, and a C-terminal PTB
domain. The RUN domain is involved in Ras-like GTPase
signaling. The PDZ domain (also called DHR/Dlg
homologous region or GLGF after its conserved sequence
motif) binds C-terminal polypeptides, internal
(non-C-terminal) polypeptides, and lipids. PTB domains
have a common PH-like fold and are found in various
eukaryotic signaling molecules. This domain was
initially shown to binds peptides with a NPXY motif with
differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 120
Score = 30.4 bits (69), Expect = 0.59
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 4/41 (9%)
Query: 189 CFTD----GSKTSDHTGAAYIIGDEVCSMKLNPVCSIFTAE 225
F + G + D AYI GD C++ + VC +F A
Sbjct: 65 SFPEISSCGRRVDDPKYFAYIAGDTPCTLAKHFVCYVFEAA 105
>gnl|CDD|164775 PHA00009, F, capsid protein.
Length = 427
Score = 31.4 bits (71), Expect = 0.89
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 346 SDDYKIQFKKIQLNEWNHSWRDNSTTGQKLTMLRDTAMT 384
+D+Y F+ +QL WN + N T + + RD+ MT
Sbjct: 388 TDNYDECFQSMQLAHWNMQTKFNVTVYRHMPTTRDSIMT 426
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 31.6 bits (72), Expect = 0.91
Identities = 19/47 (40%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 222 FTAELVAIEKCLEKIKDLIRTELISELVAIEKCLEKIKDLIRTELIL 268
+TAEL IEK L++I++ R +L EL +EK L+K +LI+ + +
Sbjct: 457 YTAELKRIEKELKEIEEKER-KLRKELRELEKVLKKESELIKLKELA 502
>gnl|CDD|215514 PLN02954, PLN02954, phosphoserine phosphatase.
Length = 224
Score = 30.8 bits (70), Expect = 0.96
Identities = 17/37 (45%), Positives = 21/37 (56%), Gaps = 9/37 (24%)
Query: 52 TGVRLISGAFR--TSPIVSILAESGIPPLSVRRNILA 86
T V L+SG FR +P+ +IL GIPP NI A
Sbjct: 101 TDVYLVSGGFRQMIAPVAAIL---GIPP----ENIFA 130
>gnl|CDD|218679 pfam05661, DUF808, Protein of unknown function (DUF808). This
family consists of several bacterial proteins of unknown
function.
Length = 293
Score = 31.0 bits (71), Expect = 0.98
Identities = 15/27 (55%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 247 ELVAIEKCLEKIKDLIRTELILQNFII 273
+LVA EK +KIK IRT+ IL II
Sbjct: 132 DLVAFEK--DKIKGAIRTDFILSAEII 156
Score = 29.8 bits (68), Expect = 2.2
Identities = 14/29 (48%), Positives = 20/29 (68%), Gaps = 4/29 (13%)
Query: 225 ELVAIEKCLEKIKDLIRTELI--SELVAI 251
+LVA EK +KIK IRT+ I +E++ I
Sbjct: 132 DLVAFEK--DKIKGAIRTDFILSAEIIVI 158
>gnl|CDD|217143 pfam02614, UxaC, Glucuronate isomerase. This is a family of
Glucuronate isomerases also known as D-glucuronate
isomerase, uronic isomerase, uronate isomerase, or
uronic acid isomerase, EC:5.3.1.12. This enzyme
catalyzes the reactions: D-glucuronate <=>
D-fructuronate and D-galacturonate <=> D-tagaturonate.
It is not however clear where the experimental evidence
for this functional assignment came from and thus this
family has no literature reference.
Length = 469
Score = 31.0 bits (71), Expect = 1.2
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 1 MKILSNRNWGLRRETLRRLYYSFV--LPILDY 30
MK + ++ L ET RRLY+ LPI+DY
Sbjct: 1 MKPFLDEDFLLSNETARRLYHDHAKDLPIIDY 32
>gnl|CDD|237167 PRK12667, PRK12667, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 520
Score = 29.6 bits (67), Expect = 4.1
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 9/42 (21%)
Query: 48 VVHHTGVRLI---SGAFRTSPIVSI------LAESGIPPLSV 80
+H G R I +G R PI S L+ GIPPL+
Sbjct: 370 FIHAAGTRDIDELAGLGRKMPIASFAFLIGALSLVGIPPLNG 411
>gnl|CDD|226561 COG4075, COG4075, Uncharacterized conserved protein, homolog of
nitrogen regulatory protein PII [Function unknown].
Length = 110
Score = 27.8 bits (62), Expect = 4.6
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 229 IEKCLEKIKDLIRTELISELVAIEKCLEKIKDLIRTEL 266
E ++ I+DL ++ V E+ +EKI++L++ +L
Sbjct: 53 PESAIKAIRDLSDKAVLIGTVVKEEKVEKIEELLKEKL 90
>gnl|CDD|239614 cd03541, Rieske_RO_Alpha_CMO, Rieske non-heme iron oxygenase (RO)
family, Choline monooxygenase (CMO) subfamily,
N-terminal Rieske domain of the oxygenase alpha subunit;
ROs comprise a large class of aromatic
ring-hydroxylating dioxygenases that enable
microorganisms to tolerate and utilize aromatic
compounds for growth. The oxygenase alpha subunit
contains an N-terminal Rieske domain with an [2Fe-2S]
cluster and a C-terminal catalytic domain with a
mononuclear Fe(II) binding site. The Rieske [2Fe-2S]
cluster accepts electrons from a reductase or ferredoxin
component and transfers them to the mononuclear iron for
catalysis. CMO is a novel RO found in certain plants
which catalyzes the first step in betaine synthesis. CMO
is not found in animals or bacteria. In these organisms,
the first step in betaine synthesis is catalyzed by
either the membrane-bound choline dehydrogenase (CDH) or
the soluble choline oxidase (COX).
Length = 118
Score = 27.9 bits (62), Expect = 4.8
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 271 FIICSDSKSSLQALQNV--YHASPLVC 295
+++C D L A NV + AS L C
Sbjct: 27 YVVCRDGNGKLHAFHNVCTHRASILAC 53
>gnl|CDD|118654 pfam10126, Nit_Regul_Hom, Uncharacterized protein, homolog of
nitrogen regulatory protein PII. This domain, found in
various hypothetical archaeal proteins, has no known
function. It is distantly similar to the nitrogen
regulatory protein PII.
Length = 110
Score = 27.4 bits (61), Expect = 5.2
Identities = 11/38 (28%), Positives = 22/38 (57%)
Query: 229 IEKCLEKIKDLIRTELISELVAIEKCLEKIKDLIRTEL 266
E ++ I+DL ++ V E+ +EKI +L++ +L
Sbjct: 53 PEMAIKAIRDLSEDAVMINTVVSEEKVEKIVELLKEKL 90
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 28.7 bits (65), Expect = 6.6
Identities = 22/106 (20%), Positives = 37/106 (34%), Gaps = 17/106 (16%)
Query: 222 FTAELVAIEKCLEKIKDLIRTEL-----ISELVAIEKCLEKIKDLIRTELILQNFIICSD 276
E+ K++DL EL I E L+ IK+ I EL + +
Sbjct: 231 ELEPPSLDEELEAKVRDLAEDELKEAVGIREKQERSAALDAIKEKIEEELSGEEESSLKE 290
Query: 277 SKSSLQALQNVYHASPLVCNIIS--------TIQDIRELGTRVSFF 314
K+ L+ L+ P+ I+ ++R +G V
Sbjct: 291 IKAILEKLEK----KPVRRLILEGKVRIDGRFGDEVRPIGIEVGVL 332
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 27.9 bits (63), Expect = 6.7
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 310 RVSFFWIPSHLGIRENENVDHAAR 333
++ + W+ H G ENE D AR
Sbjct: 114 QIKWHWVKGHAGHPENERCDELAR 137
>gnl|CDD|150197 pfam09442, DUF2018, Domain of unknown function (DUF2018).
Acid-adaptive protein possibly of physiological
significance when H.pylori colonises the human stomach,
which adopts a unique four alpha-helical triangular
conformations. The biologically active form is thought
to be a tetramer. The protein is expressed along with
six other proteins, some of which are related to iron
storage and haem biosynthesis.
Length = 80
Score = 26.5 bits (59), Expect = 7.5
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 11/53 (20%)
Query: 221 IFTAELVAIEKCLEKIKDLIRTELISELVAIEKCLEKIKDLIRTELILQNFII 273
IF A +E LEK+ + L A+E+ LEK K L E ++NFI+
Sbjct: 13 IFHANRNLVENELEKL--------LERLAALEELLEK-KGL--DENDIKNFIL 54
>gnl|CDD|197850 smart00738, NGN, In Spt5p, this domain may confer affinity for
Spt4p. It possesses a RNP-like fold. In Spt5p, this
domain may confer affinity for Spt4p.Spt4p.
Length = 106
Score = 26.6 bits (59), Expect = 9.9
Identities = 8/74 (10%), Positives = 24/74 (32%), Gaps = 8/74 (10%)
Query: 224 AELVAIEKCLEKIKDLIRTELISELVAIEKCLEKIKDLIRTE--------LILQNFIICS 275
E E K + L + I ++ + +++I+ + I +
Sbjct: 11 QEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLED 70
Query: 276 DSKSSLQALQNVYH 289
+ ++++ V
Sbjct: 71 EVWTAIRGTPGVRG 84
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.136 0.405
Gapped
Lambda K H
0.267 0.0698 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,296,907
Number of extensions: 2038445
Number of successful extensions: 1752
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1746
Number of HSP's successfully gapped: 29
Length of query: 426
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 326
Effective length of database: 6,502,202
Effective search space: 2119717852
Effective search space used: 2119717852
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: 60 (27.0 bits)