RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 026552
(237 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 = 269 bits (689), Expect = 7e-92
Identities = 94/162 (58%), Positives = 116/162 (71%)
Query: 12 SNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGD 71
+ GWA I+ P+ +S KML + K NLNEISHD+AIGLI VL+ G+ +TEVY+DTVG
Sbjct: 57 DDALGWATRILSPQYISTKMLARTKYNLNEISHDAAIGLIREVLDKGVNVTEVYVDTVGP 116
Query: 72 AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN 131
EKYQAKL ++FP IKF V KKADSLYP+VS ASIVAKVTRDR L+ W F+ET +
Sbjct: 117 PEKYQAKLQKKFPGIKFTVEKKADSLYPIVSAASIVAKVTRDRALKNWQFDETLIKDSGD 176
Query: 132 FGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKD 173
GSGYP DP+TK WL + +FG+P LVRFSW T + +
Sbjct: 177 LGSGYPSDPKTKKWLKKNVDPVFGYPQLVRFSWSTAKTILEK 218
>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 = 246 bits (630), Expect = 4e-83
Identities = 96/153 (62%), Positives = 114/153 (74%), Gaps = 2/153 (1%)
Query: 15 FGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEK 74
GWAV I+ P +S KML ++K NLNEISHD+AIGLI +L+ G+ +TEVY+DTVG EK
Sbjct: 59 VGWAVRILSPEYISRKMLARSKYNLNEISHDAAIGLIRNLLDKGVKVTEVYVDTVGPPEK 118
Query: 75 YQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGS 134
YQAKL +RFP IKF V KKADS YP+VS ASIVAKVTRDR L W F+E ++ FGS
Sbjct: 119 YQAKLLKRFPGIKFTVEKKADSKYPIVSAASIVAKVTRDRALEQWKFDEGLDSGD--FGS 176
Query: 135 GYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
GYP DP+TK WL + +FGFPSLVRFSW T
Sbjct: 177 GYPSDPKTKEWLKKNVDPVFGFPSLVRFSWSTV 209
>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 = 118 bits (298), Expect = 3e-33
Identities = 53/155 (34%), Positives = 77/155 (49%), Gaps = 16/155 (10%)
Query: 16 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEK- 74
+ V I P E+ + INLNE + + +EVY+D+V K
Sbjct: 60 RYEVLKITPEEIDRER----NINLNENEIEKFSKAAI---ILIEKPSEVYVDSVDVNPKR 112
Query: 75 --YQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 132
+ K+ +R IK + KAD+ YPVVS ASI+AKV RDR + E+ + + +F
Sbjct: 113 FKREIKIKERIEGIKVIAEHKADAKYPVVSAASIIAKVERDREI------ESLKRKYGDF 166
Query: 133 GSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
GSGYP DP T+ WL ++ P +VR +W T
Sbjct: 167 GSGYPSDPRTREWLEEYFKSHGELPDIVRRTWKTV 201
>gnl|CDD|216451 pfam01351, RNase_HII, Ribonuclease HII.
Length = 199
Score = 109 bits (273), Expect = 2e-29
Identities = 48/150 (32%), Positives = 65/150 (43%), Gaps = 9/150 (6%)
Query: 21 IIDPRELSAKMLNK---NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQA 77
I+ R+L A + N+INLN I H + +I V +G+ E+ +D +
Sbjct: 56 RIETRKLVAGNIKYAEANEINLNNILHALHLAMIRAVQKLGVKPDEILVDGFRPPKSLPM 115
Query: 78 KLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYP 137
K F KADS Y V+ ASI+AKVTRD L + + GSGYP
Sbjct: 116 KQEAIFKIKV-TAEHKADSKYLSVAAASIIAKVTRDEMLE---LLKRFPGYGLDKGSGYP 171
Query: 138 GDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
DP T+A L P R S+ T
Sbjct: 172 SDPHTEALL--KLGATPWLPDFHRRSFATV 199
>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 = 106 bits (267), Expect = 2e-28
Identities = 54/150 (36%), Positives = 82/150 (54%), Gaps = 16/150 (10%)
Query: 21 IIDPRELSAKMLNKNKINLNEISHDSAIGLITRV-LNIGILLTEVYLDTVG-DAEKYQAK 78
++ P E+ + + NLNE+ ++ LI R+ L I VY+D + E++ +
Sbjct: 64 VVSPEEIDERR---ERGNLNELEVEAFAELINRLKLKPEI----VYVDACDVNEERFAER 116
Query: 79 LSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYP 137
L +R + V+++ KAD+ YPVVS ASI+AKVTRDR EE + + +FGSGYP
Sbjct: 117 LRERLNTGVEVIAEHKADAKYPVVSAASIIAKVTRDR-----EIEELKK-EYGDFGSGYP 170
Query: 138 GDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
DP T +L ++ P +VR SW T
Sbjct: 171 SDPRTIKFLREYYREHGELPPIVRKSWKTV 200
>gnl|CDD|223242 COG0164, RnhB, Ribonuclease HII [DNA replication, recombination,
and repair].
Length = 199
Score = 81.5 bits (202), Expect = 5e-19
Identities = 43/156 (27%), Positives = 64/156 (41%), Gaps = 34/156 (21%)
Query: 16 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 75
W V II E+ +++N+ E + + V + V +D
Sbjct: 59 AWGVGIIPAEEI-------DELNILEATKL---AMRRAVAGLSSQPDLVLVDGND----L 104
Query: 76 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHR----N 131
L Q +I K D+ P ++ ASI+AKVTRDR + EE A+ + +
Sbjct: 105 PLGLPQPAVAII-----KGDAKSPSIAAASILAKVTRDR-----LMEELAK-EYPEYGFD 153
Query: 132 FGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
GSGYP DP T+A L G P + R S+
Sbjct: 154 KGSGYPTDPHTEALLKKG-----GTPGIHRRSFAPV 184
>gnl|CDD|234574 PRK00015, rnhB, ribonuclease HII; Validated.
Length = 197
Score = 64.0 bits (157), Expect = 1e-12
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 16/79 (20%)
Query: 93 KADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG----SGYPGDPETKAWLTD 148
K D+ P ++ ASI+AKVTRDR + EE + + +G GY +A
Sbjct: 131 KGDAKSPSIAAASILAKVTRDR-----LMEELDK-EYPGYGFAKHKGYGTKEHLEALAK- 183
Query: 149 HKHIIFGFPSLVRFSWGTC 167
+G + R S+
Sbjct: 184 -----YGPTPIHRRSFAPV 197
>gnl|CDD|237752 PRK14551, rnhB, ribonuclease HII; Provisional.
Length = 212
Score = 60.9 bits (148), Expect = 2e-11
Identities = 32/98 (32%), Positives = 47/98 (47%), Gaps = 7/98 (7%)
Query: 71 DAEKYQAKLSQRF-PSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMH 129
DA ++ +++ R + AD P+V ASIVAKV RD + A +
Sbjct: 106 DAGRFARRVADRVALDVSVSAEHGADEEDPLVGAASIVAKVARDAHV-----AALAAE-Y 159
Query: 130 RNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
+ GSGYP DP T+ +L ++ P+ R SW TC
Sbjct: 160 GDVGSGYPSDPTTREFLREYVREHGELPACARRSWSTC 197
>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 = 44.7 bits (107), Expect = 7e-06
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 93 KADSLYPVVSGASIVAKVTRDR 114
K D+ ++ ASI+AKVTRDR
Sbjct: 112 KGDAKSASIAAASILAKVTRDR 133
>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 = 36.0 bits (84), Expect = 0.009
Identities = 23/97 (23%), Positives = 40/97 (41%), Gaps = 9/97 (9%)
Query: 17 WAVDIIDPRELSAKMLNKNKINLNEI---SHDSAIGLITRVLNIGILLTEVYLDTVGDAE 73
+V + P + + L K NLN+I H+ AI +L + +D +
Sbjct: 59 HSVLSLGPEKYNE--LIKKGNNLNKIKALLHNKAI---NNLLQKPKKPEAILIDQFASEK 113
Query: 74 KYQAKL-SQRFPSIKFVVSKKADSLYPVVSGASIVAK 109
Y L ++ KA+S + V+ ASI+A+
Sbjct: 114 VYFNYLKKEKIVKEPLYFRTKAESKHLAVAAASIIAR 150
>gnl|CDD|184400 PRK13926, PRK13926, ribonuclease HII; Provisional.
Length = 207
Score = 35.2 bits (81), Expect = 0.017
Identities = 14/25 (56%), Positives = 19/25 (76%)
Query: 93 KADSLYPVVSGASIVAKVTRDRTLR 117
KAD+L P V+ AS++AK RDR +R
Sbjct: 133 KADALSPTVAAASLLAKTERDRLMR 157
>gnl|CDD|113793 pfam05036, SPOR, Sporulation related domain. This 70 residue
domain is composed of two 35 residue repeats found in
proteins involved in sporulation and cell division such
as FtsN, DedD, and CwlM. This domain is involved in
binding peptidoglycan. Two tandem repeats fold into a
pseudo-2-fold symmetric single-domain structure
containing numerous contacts between the repeats. FtsN
is an essential cell division protein with a simple
bitopic topology, a short N-terminal cytoplasmic segment
fused to a large carboxy periplasmic domain through a
single transmembrane domain. These repeats lay at the
periplasmic C-terminus. FtsN localises to the septum
ring complex.
Length = 75
Score = 31.5 bits (72), Expect = 0.068
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 71 DAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSG 103
+AE AKL + + K V+ LY V G
Sbjct: 17 NAEALAAKLRAKGFAAKEAVTSGGGGLYRVRVG 49
>gnl|CDD|184399 PRK13925, rnhB, ribonuclease HII; Provisional.
Length = 198
Score = 32.3 bits (74), Expect = 0.13
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 93 KADSLYPVVSGASIVAKVTRDRTLR 117
K DS ++ ASI+AKV RD ++
Sbjct: 127 KGDSKSAAIAAASILAKVWRDDLIK 151
>gnl|CDD|173015 PRK14550, rnhB, ribonuclease HII; Provisional.
Length = 204
Score = 28.8 bits (64), Expect = 1.9
Identities = 12/39 (30%), Positives = 25/39 (64%), Gaps = 2/39 (5%)
Query: 79 LSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLR 117
L++R+P+I+ ++ K D ++ AS++AK +DR +
Sbjct: 110 LNKRYPNIQTII--KGDETIAQIAMASVLAKAFKDREML 146
>gnl|CDD|179241 PRK01185, ppnK, inorganic polyphosphate/ATP-NAD kinase;
Provisional.
Length = 271
Score = 28.6 bits (64), Expect = 2.6
Identities = 32/126 (25%), Positives = 54/126 (42%), Gaps = 28/126 (22%)
Query: 20 DIIDPRELSAKMLNKNKINLNEISHDSAI-----GLITRVL----------NIGIL--LT 62
+II E AK L + +++ EI+ D I G I R L N+G L LT
Sbjct: 30 EIIYEMEA-AKALGMDGLDIEEINADVIITIGGDGTILRTLQRAKGPILGINMGGLGFLT 88
Query: 63 EVYLDTVGDA----EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASI-VAKVTRDRTLR 117
E+ +D VG A + + + +R +K V + L + A I ++ + R +
Sbjct: 89 EIEIDEVGSAIKKLIRGEYFIDER---MKLKVYINGERLEDCTNEAVIHTDRIAKIRQFK 145
Query: 118 GWIFEE 123
I+ +
Sbjct: 146 --IYYD 149
>gnl|CDD|222826 PHA01627, PHA01627, DNA binding protein.
Length = 107
Score = 27.3 bits (61), Expect = 3.0
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 5/63 (7%)
Query: 24 PRELSAKMLNKNKINLNEISHDSAIGLITRVL--NIGILLTEVYLDTVGDAEKYQAKLSQ 81
E + ++L + ++ I HD+ L++ + N+ E+ LD GD + L Q
Sbjct: 27 DIEEAKELLENEEF-VSAIGHDATANLLSNLCGVNLPKNRIEIKLD-KGD-KALAIMLKQ 83
Query: 82 RFP 84
R
Sbjct: 84 RLE 86
>gnl|CDD|216126 pfam00798, Arena_glycoprot, Arenavirus glycoprotein.
Length = 473
Score = 28.8 bits (65), Expect = 3.1
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 6/43 (13%)
Query: 169 SHFKDIVEVLWESDEMDEDVSSR----RSGKRQLKLSDIGFSS 207
SHF++ E + ESD + ++ S+ R GK L L D+ F S
Sbjct: 385 SHFRN--EWILESDHLISEMLSKEYEERQGKTPLTLVDLCFWS 425
>gnl|CDD|212963 cd12030, SH3_DLG4, Src Homology 3 domain of Disks Large homolog 4.
DLG4, also called postsynaptic density-95 (PSD95) or
synapse-associated protein 90 (SAP90), is a scaffolding
protein that clusters at synapses and plays an important
role in synaptic development and plasticity. It is
responsible for the membrane clustering and retention of
many transporters and receptors such as potassium
channels and PMCA4b, a P-type ion transport ATPase,
among others. DLG4 is a member of the MAGUK
(membrane-associated guanylate kinase) protein family,
which is characterized by the presence of a core of
three domains: PDZ, SH3, and guanylate kinase (GuK). The
GuK domain in MAGUK proteins is enzymatically inactive;
instead, the domain mediates protein-protein
interactions and associates intramolecularly with the
SH3 domain. DLG4 contains three PDZ domains. The SH3
domain of DLG4 binds and clusters the kainate subgroup
of glutamate receptors via two proline-rich sequences in
their C-terminal tail. It also binds AKAP79/150
(A-kinase anchoring protein). SH3 domains are protein
interaction domains that bind to proline-rich ligands
with moderate affinity and selectivity, preferentially
to PxxP motifs. They play versatile and diverse roles in
the cell including the regulation of enzymes, changing
the subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 66
Score = 26.4 bits (58), Expect = 3.8
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 171 FKDIVEVLWESDEMDEDVSSRRSGKRQLKLSDIGFSSSKRRSE 213
F D++ V+ D DE+ R + +IGF SKRR E
Sbjct: 27 FGDVLHVI---DAGDEEWWQARRVHSDSETEEIGFIPSKRRVE 66
>gnl|CDD|119073 pfam10553, MSV199, MSV199 domain. This domain was identified by
Iyer and colleagues.
Length = 135
Score = 27.3 bits (61), Expect = 3.9
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 29 AKMLNKNKINLNEISHD 45
K+L +N I EI ++
Sbjct: 57 KKILKRNNIPYKEIKYN 73
>gnl|CDD|221182 pfam11715, Nup160, Nucleoporin Nup120/160. Nup120 is conserved
from fungi to plants to humans, and is homologous with
the Nup160 of vertebrates. The nuclear core complex, or
NPC, mediates macromolecular transport across the
nuclear envelope. Deletion of the NUP120 gene causes
clustering of NPCs at one side of the nuclear envelope,
moderate nucleolar fragmentation and slower cell growth.
The vertebrate NPC is estimated to contain between 30
and 60 different proteins. most of which are not known.
Two important ones in creating the nucleoporin basket
are Nup98 and Nup153, and Nup120, in conjunction with
Nup 133, interacts with these two and itself plays a
role in mRNA export. Nup160, Nup133, Nup96, and Nup107
are all targets of phosphorylation. The phosphorylation
sites are clustered mainly at the N-terminal regions of
these proteins, which are predicted to be natively
disordered. The entire Nup107-160 subcomplex is stable
throughout the cell cycle, thus it seems unlikely that
phosphorylation affects interactions within the
Nup107-160 subcomplex, but rather that it regulates the
association of the subcomplex with the NPC and other
proteins.
Length = 511
Score = 28.2 bits (63), Expect = 3.9
Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 8/79 (10%)
Query: 49 GLITRV-LNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPV------- 100
G + ++ + G V+ +T+ + L P ++ + A S
Sbjct: 169 GGLLKLTRSSGDTDGAVWKETLYGPSSWLRSLRGLLPFQRYGKDRLASSAAASTIVSSSE 228
Query: 101 VSGASIVAKVTRDRTLRGW 119
V+G + + ++ D TLR W
Sbjct: 229 VNGQTFLFTLSLDGTLRVW 247
>gnl|CDD|237678 PRK14335, PRK14335, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 455
Score = 28.3 bits (63), Expect = 4.0
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 72 AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN 131
AE+ ++ + FP I +VV A + + I AK+ +D + FE +E +
Sbjct: 81 AERLHDEIQKEFPRIDYVVGTFAHARLESIFQ-EIEAKLKQD----DYRFEFISERYREH 135
Query: 132 FGSGY 136
SGY
Sbjct: 136 PVSGY 140
>gnl|CDD|112730 pfam03930, Flp_N, Recombinase Flp protein N-terminus.
Length = 82
Score = 26.2 bits (58), Expect = 5.2
Identities = 9/39 (23%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 70 GDAEKYQAKLSQRFPSIKFVVS--KKADSLYPVVSGASI 106
+ + LS+ F FV+ KK S+ + S +
Sbjct: 41 KRPTELKEGLSKAFKPYNFVIKSHKKPTSMTTLFSSLHL 79
>gnl|CDD|220082 pfam08960, DUF1874, Domain of unknown function (DUF1874). This
domain is found in a set of hypothetical viral and
bacterial proteins.
Length = 105
Score = 26.5 bits (59), Expect = 6.4
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 5/63 (7%)
Query: 24 PRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILL--TEVYLDTVGDAEKYQAKLSQ 81
E + ++L + ++ I HD+ L++ +L + I + +V L VGD + L Q
Sbjct: 26 DIEEAKELLENERF-ISAIGHDATAQLLSNLLGVNIPMNRIQVKLQ-VGD-KALAFVLKQ 82
Query: 82 RFP 84
R
Sbjct: 83 RLE 85
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
0.317 0.133 0.396
Gapped
Lambda K H
0.267 0.0637 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,134,915
Number of extensions: 1123221
Number of successful extensions: 964
Number of sequences better than 10.0: 1
Number of HSP's gapped: 951
Number of HSP's successfully gapped: 30
Length of query: 237
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 143
Effective length of database: 6,768,326
Effective search space: 967870618
Effective search space used: 967870618
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 (21.7 bits)
S2: 57 (25.9 bits)