RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17038
(399 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 = 69.6 bits (171), Expect = 2e-14
Identities = 27/62 (43%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 11 DSLSALQSIQNEFSSNPIAQEIR-NILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEA 69
DS +AL+++++ SS+P+ IR I H + + WVP H GI GNE +DRLAKEA
Sbjct: 67 DSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLAKEA 126
Query: 70 LS 71
Sbjct: 127 AK 128
>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 = 59.2 bits (144), Expect = 7e-11
Identities = 24/65 (36%), Positives = 32/65 (49%), Gaps = 7/65 (10%)
Query: 11 DSLSALQSI----QNEFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLA 66
DS + I + S PI EI +L K + + WVP H GI GNE +D+LA
Sbjct: 65 DSQYVIGGITNGWPTKSESKPIKNEIWELLQKKHKV---YIQWVPGHSGIPGNELADKLA 121
Query: 67 KEALS 71
K+ S
Sbjct: 122 KQGAS 126
>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 = 45.7 bits (109), Expect = 5e-06
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 30 QEIRNILVK-NKHILSLHFTWVPSHVGIVGNEESDRLAKEALS 71
+E+ +L + + + + F VP H GI GNEE+DRLAK+
Sbjct: 108 KELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGAD 150
>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 = 44.8 bits (107), Expect = 7e-06
Identities = 15/45 (33%), Positives = 24/45 (53%)
Query: 26 NPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEAL 70
+E + + K K + + F V +H G NE +D+LAK+AL
Sbjct: 89 KEGTKEYKEFMDKIKKKIKISFVKVKAHSGDKYNELADKLAKKAL 133
>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 = 37.1 bits (87), Expect = 0.004
Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 10/43 (23%)
Query: 37 VKNK-------HILSLH---FTWVPSHVGIVGNEESDRLAKEA 69
VKN +L+ H + WV H G GNE +D LA A
Sbjct: 95 VKNVDLWQELDALLAKHQVTWHWVKGHAGHPGNERADELANAA 137
>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 = 35.0 bits (81), Expect = 0.018
Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 5/61 (8%)
Query: 11 DSLSALQSIQNEFSSNPIAQEIRN-ILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEA 69
DS + I + + IL+ + + F VP GNE +DRLAKEA
Sbjct: 67 DSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEVADRLAKEA 122
Query: 70 L 70
Sbjct: 123 A 123
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 33.9 bits (78), Expect = 0.057
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 47 FTWVPSHVGIVGNEESDRLAKEALSSN 73
+ WV H G NE +D+LA+EA +
Sbjct: 120 WEWVKGHAGHPENERADQLAREAARAA 146
>gnl|CDD|212669 cd10227, ParM_like, Plasmid segregation protein ParM and similar
proteins. ParM is a plasmid-encoded bacterial homolog
of actin, which polymerizes into filaments similar to
F-actin, and plays a vital role in plasmid segregation.
ParM filaments segregate plasmids paired at midcell into
the individual daughter cells. This subfamily also
contains Thermoplasma acidophilum Ta0583, an active
ATPase at physiological temperatures, which has a
propensity to form filaments.
Length = 312
Score = 30.8 bits (70), Expect = 1.1
Identities = 22/101 (21%), Positives = 40/101 (39%), Gaps = 7/101 (6%)
Query: 187 TLDLA----NRIVQSYTGIQADLKYGVSGILSEIMDLVQDVVTSSEAGEDGLELPVARKR 242
T D+ + V+S +G L+ GVS + I + + E+ E+ K
Sbjct: 178 TTDVVVFDNGKPVESSSG---SLELGVSDLYEAIAKELNKEYGIDLSDEEIEEILRNGKI 234
Query: 243 EYQEARQKCQREVRRIREEWWNKKINELQEFANKNDTYNLY 283
+ + + EE+ K +NEL+EF +D +
Sbjct: 235 KNYGKEEDITEIIEEAAEEYAEKILNELKEFLGLSDVDKVI 275
>gnl|CDD|147197 pfam04906, Tweety, Tweety. The tweety (tty) gene has not been
characterized at the protein level. However, it is
thought to form a membrane protein with five potential
membrane-spanning regions. A number of potential
functions have been suggested in.
Length = 406
Score = 30.8 bits (70), Expect = 1.3
Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 11/88 (12%)
Query: 207 YGVSGILSEIMDLVQDVVTSSEAGEDG----LELPVARKREYQEARQKCQREVRRIREE- 261
+ +S I +LV D S + LE A++ +Y + + Q V ++
Sbjct: 99 RNANHTVSGIDNLVSDTTNSLNETLEQHLTRLEEIFAKRTDYLQTLRFLQGNVGNAVQQL 158
Query: 262 -----WWNKKINELQEFANKNDTYNLYR 284
W ++ L E A + D Y YR
Sbjct: 159 TGIPFWKGVGLS-LTELAEQGDFYEYYR 185
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 29.8 bits (68), Expect = 1.4
Identities = 9/29 (31%), Positives = 12/29 (41%)
Query: 46 HFTWVPSHVGIVGNEESDRLAKEALSSNS 74
+ WV H G NE D LA+ +
Sbjct: 116 KWHWVKGHAGHPENERCDELARAGAEEAT 144
>gnl|CDD|172557 PRK14067, PRK14067, exodeoxyribonuclease VII small subunit;
Provisional.
Length = 80
Score = 28.6 bits (64), Expect = 1.5
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 217 MDLVQDVVTSSEAGEDGLELPVARKREYQEARQKCQREVRRIREE 261
+ +Q++V + E G+ LE VA +E + C+ ++ + R E
Sbjct: 13 LARLQEIVDALEGGDLPLEESVALYKEGLGLARACREQLAKARNE 57
>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 = 2.0
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 26 NPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALS 71
P +E R +L K + W+P N+E+D LA +AL
Sbjct: 90 APYLEEARELL---KKFEEVEIKWIPRE----ENKEADALANQALD 128
>gnl|CDD|233149 TIGR00845, caca, sodium/calcium exchanger 1. The Ca2+:Cation
Antiporter (CaCA) Family (TC 2.A.19)Proteins of the CaCA
family are found ubiquitously, having been identified in
animals, plants, yeast, archaea and widely divergent
bacteria.All of the characterized animal proteins
catalyze Ca2+:Na+ exchange although some also transport
K+. The NCX1 plasma membrane protein exchanges 3 Na+ for
1 Ca2+. The E. coli ChaA protein catalyzes Ca2+:H+
antiport but may also catalyze Na+:H+ antiport. All
remaining well-characterized members of the family
catalyze Ca2+:H+ exchange.This model is specific for the
eukaryotic sodium ion/calcium ion exchangers of the Caca
family [Transport and binding proteins, Other].
Length = 928
Score = 30.1 bits (68), Expect = 2.2
Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 221 QDVVTSSEAGEDGLELPVARKREYQEARQKCQREVRRIREEWWNKKINELQEFANKNDTY 280
+V S L V +E+ EAR++ R ++ ++++ +K + +L+E AN
Sbjct: 290 GKMVNSHVDNFLDGAL-VLEVKEFDEARREMIRILKELKQKHPDKDLEQLEEMAN---YQ 345
Query: 281 NLYRGMKS 288
L R KS
Sbjct: 346 VLSRQQKS 353
>gnl|CDD|153203 cd04931, ACT_PAH, ACT domain of the nonheme iron-dependent aromatic
amino acid hydroxylase, phenylalanine hydroxylases
(PAH). ACT domain of the nonheme iron-dependent
aromatic amino acid hydroxylase, phenylalanine
hydroxylases (PAH). PAH catalyzes the hydroxylation of
L-Phe to L-Tyr, the first step in the catabolic
degradation of L-Phe. In PAH, an autoregulatory
sequence, N-terminal of the ACT domain, extends across
the catalytic domain active site and regulates the
enzyme by intrasteric regulation. It appears that the
activation by L-Phe induces a conformational change that
converts the enzyme to a high-affinity and high-activity
state. Modulation of activity is achieved through
inhibition by BH4 and activation by phosphorylation of
serine residues of the autoregulatory region. The
molecular basis for the cooperative activation process
is not fully understood yet. Members of this CD belong
to the superfamily of ACT regulatory domains.
Length = 90
Score = 27.9 bits (62), Expect = 3.0
Identities = 26/90 (28%), Positives = 45/90 (50%), Gaps = 7/90 (7%)
Query: 270 LQEFANKNDTYNLYRGMKSAVGPIRKPLNIIEDKNGN--KISNKEERLERWREHFQHVFN 327
++E +NKN +L +K VG + K L + E+K+ N I ++ RL + F +
Sbjct: 5 IEENSNKNGVISLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSRLNKDEYEFFINLD 64
Query: 328 QQTTVNLEGIEIDPITDNLPNDERPTENEI 357
+++ L DPI +L ND T +E+
Sbjct: 65 KKSAPAL-----DPIIKSLRNDIGATVHEL 89
>gnl|CDD|183506 PRK12406, PRK12406, long-chain-fatty-acid--CoA ligase; Provisional.
Length = 509
Score = 29.7 bits (67), Expect = 3.4
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 8/44 (18%)
Query: 234 LELPVARKREYQ--------EARQKCQREVRRIREEWWNKKINE 269
L+LP + +Y A C +V+R EWW I E
Sbjct: 258 LKLPEEVRAKYDVSSLRHVIHAAAPCPADVKRAMIEWWGPVIYE 301
>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 = 27.5 bits (62), Expect = 3.7
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 3/62 (4%)
Query: 11 DSLSALQSIQNEFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEAL 70
DS +Q IQ E + +L + + +L + SHV N +D LAK A
Sbjct: 30 DSQLVVQQIQGE---YEARSRLAALLREIRKLLKKFDSVSVSHVPRECNRVADALAKLAS 86
Query: 71 SS 72
+S
Sbjct: 87 AS 88
>gnl|CDD|75628 PRK06548, PRK06548, ribonuclease H; Provisional.
Length = 161
Score = 28.2 bits (62), Expect = 5.0
Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 4/54 (7%)
Query: 28 IAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALSSNSPSVNTIP 81
I QEI + L++N++I +WV +H G NE +D LA++A ++ S IP
Sbjct: 102 IIQEIDS-LMENRNI---RMSWVNAHTGHPLNEAADSLARQAANNFSTRSAHIP 151
>gnl|CDD|217715 pfam03759, PRONE, PRONE (Plant-specific Rop nucleotide exchanger).
This is a functional guanine exchange factor (GEF) of
plant Rho GTPase.
Length = 360
Score = 28.9 bits (65), Expect = 5.1
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 180 DLSSHHVTLDLANRI 194
DLSS H L+LANRI
Sbjct: 238 DLSSEHKALELANRI 252
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc gene
is often associated with scpB (TIGR00281) and scpA genes,
where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 28.9 bits (65), Expect = 6.4
Identities = 41/232 (17%), Positives = 86/232 (37%), Gaps = 21/232 (9%)
Query: 107 NKLRQIKEEKRPWNPSLHESRESNSARLPQVSLAELKVIQETLGDLERQGDLDLDLCDS- 165
L + L E E S + ++ AE++ ++E + +LE + + L+ S
Sbjct: 827 ESLERRIAATERRLEDLEEQIEELSEDIESLA-AEIEELEELIEELESELEALLNERASL 885
Query: 166 --WRNLAESQEANDDGDLSSHHVTLDLANRIVQSYTGIQADLKYGVSGILSEIMDLVQDV 223
L S+ +L R ++ A L+ + G+ I +L + +
Sbjct: 886 EEALALLRSELEELSEELRELESKRSELRRELEELREKLAQLELRLEGLEVRIDNLQERL 945
Query: 224 VTSSEAGEDGLELPVARKREYQEARQKCQREVRRIREEWWNKKINEL--------QEFAN 275
SE LE A + + ++ ++ +R ++R+ KI EL +E+
Sbjct: 946 ---SEEYSLTLEEAEALENKIEDDEEEARRRLKRLEN-----KIKELGPVNLAAIEEYEE 997
Query: 276 KNDTYNLYRG-MKSAVGPIRKPLNIIEDKNGNKISNKEERLERWREHFQHVF 326
+ Y+ + IE+ + ++ ++ E+FQ VF
Sbjct: 998 LKERYDFLTAQKEDLTEAKETLEEAIEEIDREARERFKDTFDQVNENFQRVF 1049
>gnl|CDD|221037 pfam11231, DUF3034, Protein of unknown function (DUF3034). This
family of proteins with unknown function appears to be
restricted to Proteobacteria.
Length = 257
Score = 28.4 bits (64), Expect = 7.0
Identities = 13/48 (27%), Positives = 20/48 (41%)
Query: 177 DDGDLSSHHVTLDLANRIVQSYTGIQADLKYGVSGILSEIMDLVQDVV 224
DD L+ + L NR+ SY DL + + +L QD+
Sbjct: 43 DDYTLTVVGAAVGLYNRVELSYARQTFDLGTLGAALGLPGYELKQDIF 90
>gnl|CDD|224846 COG1935, COG1935, Uncharacterized conserved protein [Function
unknown].
Length = 122
Score = 27.4 bits (61), Expect = 7.5
Identities = 12/46 (26%), Positives = 26/46 (56%), Gaps = 3/46 (6%)
Query: 197 SYTGIQADLKYGVSGILSEI--MDLVQDVVTSSEAGEDGLELPVAR 240
+ T ++ DL G SGI++++ +++V + E+ + E+ AR
Sbjct: 48 TSTSLE-DLTKGTSGIIAKVRRVEVVHQRIPWEESYIEEREISAAR 92
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 28.4 bits (64), Expect = 7.7
Identities = 27/104 (25%), Positives = 43/104 (41%), Gaps = 15/104 (14%)
Query: 228 EAGEDGLELPVARKREYQEARQKCQREVRRIREEWWNKKINELQEFANKND--TYNLYRG 285
EA E + K E + R + +RE++ R NELQ + L R
Sbjct: 44 EAETLKKEALLEAKEEVHKLRAELERELKERR--------NELQRLERRLLQREETLDRK 95
Query: 286 MKSAVGPIRKPLNIIEDKNGNKISNKEERLERWREHFQHVFNQQ 329
M+S + K +E K +SNKE+ L+ E + + +Q
Sbjct: 96 MES----LDKKEENLEKKEKE-LSNKEKNLDEKEEELEELIAEQ 134
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
0.313 0.131 0.377
Gapped
Lambda K H
0.267 0.0675 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,001,264
Number of extensions: 1929424
Number of successful extensions: 1589
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1585
Number of HSP's successfully gapped: 47
Length of query: 399
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 300
Effective length of database: 6,546,556
Effective search space: 1963966800
Effective search space used: 1963966800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 60 (27.0 bits)