RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17815
(599 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 = 104 bits (262), Expect = 1e-26
Identities = 40/125 (32%), Positives = 59/125 (47%), Gaps = 5/125 (4%)
Query: 339 ICFTDGSKTIQNTSCAVYA--GGSA-KSYILNNINSIFTAELLALVFCLDSVKNRPD-VN 394
+ +TDGSK T G+ +SY L S+F AELLA++ L
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60
Query: 395 TLIVC-DSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVD 453
+ + DS +AL ++ + +S PL+ I L + G KV W P H+GI GNE D
Sbjct: 61 KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120
Query: 454 RATRQ 458
R ++
Sbjct: 121 RLAKE 125
>gnl|CDD|238827 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat)
retrotransposon and non-LTR retrovirus reverse
transcriptase (RT). This subfamily contains both non-LTR
retrotransposons and non-LTR retrovirus RTs. RTs
catalyze the conversion of single-stranded RNA into
double-stranded DNA for integration into host
chromosomes. RT is a multifunctional enzyme with
RNA-directed DNA polymerase, DNA directed DNA polymerase
and ribonuclease hybrid (RNase H) activities.
Length = 220
Score = 79.6 bits (197), Expect = 7e-17
Identities = 34/123 (27%), Positives = 58/123 (47%), Gaps = 18/123 (14%)
Query: 10 GIPQGSSLSPLLFIIFLNDLLKII---------KLPLRSMLFIDDLLIISRGKDLSAILG 60
G+ QG LSPLLF + L+DLL+++ + + + DD+++ S GK
Sbjct: 106 GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEGKSRKL--- 162
Query: 61 RFQTTLNAIKTWSDTNGLIFSADPQKSVCVDFTRLRSRSVPLTLYYSDKELKFVDKTKFL 120
Q L ++ WS +GL + P KS + + R +TL ++ V+ K+L
Sbjct: 163 --QELLQRLQEWSKESGLKIN--PSKSKVMLIGNKKKRLKDITLN--GTPIEAVETFKYL 216
Query: 121 GLI 123
G+
Sbjct: 217 GVT 219
>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 = 66.5 bits (163), Expect = 2e-13
Identities = 37/126 (29%), Positives = 52/126 (41%), Gaps = 13/126 (10%)
Query: 339 ICFTDGSKTIQN-TSCAVY-AGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTL 396
+TDGS A Y G + + AELLAL+ L+++ + VN
Sbjct: 5 TVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALEALSGQK-VN-- 61
Query: 397 IVCDSMSALTSI----ANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIV 452
I DS + I K+ S P+ I L KV W P H+GI GNE+
Sbjct: 62 IYTDSQYVIGGITNGWPTKSESKPIKNEIWE----LLQKKHKVYIQWVPGHSGIPGNELA 117
Query: 453 DRATRQ 458
D+ +Q
Sbjct: 118 DKLAKQ 123
>gnl|CDD|215698 pfam00078, RVT_1, Reverse transcriptase (RNA-dependent DNA
polymerase). A reverse transcriptase gene is usually
indicative of a mobile element such as a retrotransposon
or retrovirus. Reverse transcriptases occur in a variety
of mobile elements, including retrotransposons,
retroviruses, group II introns, bacterial msDNAs,
hepadnaviruses, and caulimoviruses.
Length = 194
Score = 57.0 bits (138), Expect = 2e-09
Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 9/85 (10%)
Query: 2 SRSFPLENGIPQGSSLSPLLFIIFLNDLLKIIKLPLRSM---LFIDDLLIISRGKDLSAI 58
G+PQGS LSPLLF +F+N+LL+ ++ + + DD+LI S+ +
Sbjct: 99 PGGRYEWRGLPQGSVLSPLLFNLFMNELLRPLRKRFPGLTYLRYADDILIFSKSPE---- 154
Query: 59 LGRFQTTLNAIKTWSDTNGLIFSAD 83
Q L + + GL + +
Sbjct: 155 --ELQEILEEVLEFLKELGLKLNPE 177
>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 = 47.3 bits (113), Expect = 2e-06
Identities = 41/137 (29%), Positives = 54/137 (39%), Gaps = 23/137 (16%)
Query: 340 CFTDGSKTIQNTSCAVYAGGSAKSYI-LNNINSIFTAELLALVFCLDSVKNRPDVNTLIV 398
FTDGS ++ AV G L S AEL+AL+ L+ K +P VN I
Sbjct: 2 VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKGKP-VN--IY 58
Query: 399 CDS---MSALTSIA------NKNTSIPLIAH---ILNTWHTLKSCGKKVAFLWCPSHTG- 445
DS L ++ T P IA IL + K VA + +H+G
Sbjct: 59 TDSAYAFGILHALETIWKERGFLTGKP-IALASLILQLQKAI-QRPKPVAVIHIRAHSGL 116
Query: 446 ----ISGNEIVDRATRQ 458
GN D+A RQ
Sbjct: 117 PGPLALGNARADQAARQ 133
>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 = 46.2 bits (110), Expect = 3e-06
Identities = 27/125 (21%), Positives = 42/125 (33%), Gaps = 11/125 (8%)
Query: 341 FTDGSKTIQNTSCAVYA------GGSAKSYILNNIN-SIFTAELLALVFCLDSVKNRPDV 393
TDGS G + L+ + AELLAL+ L+ +
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60
Query: 394 NTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVD 453
+I DS + I + + +L L S + F P GNE+ D
Sbjct: 61 KLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPR----EGNEVAD 116
Query: 454 RATRQ 458
R ++
Sbjct: 117 RLAKE 121
>gnl|CDD|238826 cd01648, TERT, TERT: Telomerase reverse transcriptase (TERT).
Telomerase is a ribonucleoprotein (RNP) that
synthesizes telomeric DNA repeats. The telomerase RNA
subunit provides the template for synthesis of these
repeats. The catalytic subunit of RNP is known as
telomerase reverse transcriptase (TERT). The reverse
transcriptase (RT) domain is located in the C-terminal
region of the TERT polypeptide. Single amino acid
substitutions in this region lead to telomere
shortening and senescence. Telomerase is an enzyme
that, in certain cells, maintains the physical ends of
chromosomes (telomeres) during replication. In somatic
cells, replication of the lagging strand requires the
continual presence of an RNA primer approximately 200
nucleotides upstream, which is complementary to the
template strand. Since there is a region of DNA less
than 200 base pairs from the end of the chromosome
where this is not possible, the chromosome is
continually shortened. However, a surplus of repetitive
DNA at the chromosome ends protects against the erosion
of gene-encoding DNA. Telomerase is not normally
expressed in somatic cells. It has been suggested that
exogenous TERT may extend the lifespan of, or even
immortalize, the cell. However, recent studies have
shown that telomerase activity can be induced by a
number of oncogenes. Conversely, the oncogene c-myc can
be activated in human TERT immortalized cells. Sequence
comparisons place the telomerase proteins in the RT
family but reveal hallmarks that distinguish them from
retroviral and retrotransposon relatives.
Length = 119
Score = 41.9 bits (99), Expect = 8e-05
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 7/48 (14%)
Query: 10 GIPQGSSLSPLLFIIFLNDLLK-----IIKLPLRSML--FIDDLLIIS 50
GIPQGS LS LL ++ DL + + S+L +DD L+I+
Sbjct: 19 GIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLIT 66
>gnl|CDD|238828 cd01651, RT_G2_intron, RT_G2_intron: Reverse transcriptases (RTs)
with group II intron origin. RT transcribes DNA using
RNA as template. Proteins in this subfamily are found in
bacterial and mitochondrial group II introns. Their most
probable ancestor was a retrotransposable element with
both gag-like and pol-like genes. This subfamily of
proteins appears to have captured the RT sequences from
transposable elements, which lack long terminal repeats
(LTRs).
Length = 226
Score = 42.2 bits (100), Expect = 3e-04
Identities = 24/89 (26%), Positives = 34/89 (38%), Gaps = 22/89 (24%)
Query: 5 FPLENGIPQGSSLSPLLFIIFLNDLLKII-----------KLPLRSMLFI---DDLLIIS 50
E G PQG +SPLL I+L++L K + R + ++ DD +I
Sbjct: 121 VETEKGTPQGGVISPLLANIYLHELDKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGV 180
Query: 51 RGKD--------LSAILGRFQTTLNAIKT 71
RG + L LN KT
Sbjct: 181 RGPKEAEEIKELIREFLEELGLELNPEKT 209
>gnl|CDD|238185 cd00304, RT_like, RT_like: Reverse transcriptase (RT,
RNA-dependent DNA polymerase)_like family. An RT gene
is usually indicative of a mobile element such as a
retrotransposon or retrovirus. RTs occur in a variety
of mobile elements, including retrotransposons,
retroviruses, group II introns, bacterial msDNAs,
hepadnaviruses, and caulimoviruses. These elements can
be divided into two major groups. One group contains
retroviruses and DNA viruses whose propagation involves
an RNA intermediate. They are grouped together with
transposable elements containing long terminal repeats
(LTRs). The other group, also called poly(A)-type
retrotransposons, contain fungal mitochondrial introns
and transposable elements that lack LTRs.
Length = 98
Score = 37.3 bits (87), Expect = 0.002
Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 11 IPQGSSLSPLLFIIFLNDLLK---IIKLPLRSMLFIDDLLIISRGKDLSAILGRFQTTL 66
+PQGS LSP L +++ L L + + ++DDL++I++ + + + L
Sbjct: 12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSEQQAVKKRELEEFL 70
>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 = 34.1 bits (79), Expect = 0.067
Identities = 28/102 (27%), Positives = 38/102 (37%), Gaps = 26/102 (25%)
Query: 375 AELLALVFCLDSVKNR--PDVNTLIVCDSM--------------------SALTSIANKN 412
AEL A++ L +K +I DS S +ANK+
Sbjct: 46 AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105
Query: 413 TSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDR 454
LI + L+ G +V F P H+GI GNE DR
Sbjct: 106 ----LIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADR 143
>gnl|CDD|238824 cd01646, RT_Bac_retron_I, RT_Bac_retron_I: Reverse transcriptases
(RTs) in bacterial retrotransposons or retrons. The
polymerase reaction of this enzyme leads to the
production of a unique RNA-DNA complex called msDNA
(multicopy single-stranded (ss)DNA) in which a small
ssDNA branches out from a small ssRNA molecule via a
2'-5'phosphodiester linkage. Bacterial retron RTs
produce cDNA corresponding to only a small portion of
the retron genome.
Length = 158
Score = 33.1 bits (76), Expect = 0.21
Identities = 23/77 (29%), Positives = 33/77 (42%), Gaps = 17/77 (22%)
Query: 9 NGIPQGSSLSPLLFIIFLNDLLKIIKLPL------RSMLFIDDLLIISRGKD-------- 54
NG+P G S L I+LND+ +K L R ++DD+ I + K+
Sbjct: 52 NGLPIGPLTSRFLANIYLNDVDHELKSKLKGVDYVR---YVDDIRIFADSKEEAEEILEE 108
Query: 55 LSAILGRFQTTLNAIKT 71
L L +LN KT
Sbjct: 109 LKEFLAELGLSLNLSKT 125
>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 = 32.5 bits (75), Expect = 0.22
Identities = 10/30 (33%), Positives = 12/30 (40%), Gaps = 1/30 (3%)
Query: 432 GKKVAFLWCPSHTGISGNEIVDR-ATRQLD 460
+V + W H G GNE D A D
Sbjct: 110 KHQVTWHWVKGHAGHPGNERADELANAAAD 139
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 31.9 bits (73), Expect = 0.43
Identities = 25/105 (23%), Positives = 37/105 (35%), Gaps = 17/105 (16%)
Query: 367 NNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDS---MSALTSIANKN------TSIPL 417
NN AEL AL+ L+++K + DS + +T K T+
Sbjct: 43 NN-----RAELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKK 97
Query: 418 IAHILNTWHTLKSCGK---KVAFLWCPSHTGISGNEIVDRATRQL 459
+ W L K V + W H G NE D+ R+
Sbjct: 98 PVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREA 142
>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 = 30.5 bits (70), Expect = 1.1
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 434 KVAFLWCPSHTGISGNEIVDR 454
K++F+ +H+G NE+ D+
Sbjct: 107 KISFVKVKAHSGDKYNELADK 127
>gnl|CDD|238823 cd01645, RT_Rtv, RT_Rtv: Reverse transcriptases (RTs) from
retroviruses (Rtvs). RTs catalyze the conversion of
single-stranded RNA into double-stranded viral DNA for
integration into host chromosomes. Proteins in this
subfamily contain long terminal repeats (LTRs) and are
multifunctional enzymes with RNA-directed DNA
polymerase, DNA directed DNA polymerase, and
ribonuclease hybrid (RNase H) activities. The viral RNA
genome enters the cytoplasm as part of a nucleoprotein
complex, and the process of reverse transcription
generates in the cytoplasm forming a linear DNA duplex
via an intricate series of steps. This duplex DNA is
colinear with its RNA template, but contains terminal
duplications known as LTRs that are not present in viral
RNA. It has been proposed that two specialized template
switches, known as strand-transfer reactions or "jumps",
are required to generate the LTRs.
Length = 213
Score = 31.1 bits (71), Expect = 1.1
Identities = 16/63 (25%), Positives = 25/63 (39%), Gaps = 4/63 (6%)
Query: 9 NGIPQGSSLSPLLFIIFLNDLLKIIKLPLRSMLFI---DDLLIIS-RGKDLSAILGRFQT 64
+PQG SP + F+ L+ + ++ DD+LI S L I +
Sbjct: 127 KVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQ 186
Query: 65 TLN 67
TL
Sbjct: 187 TLL 189
>gnl|CDD|168661 PRK06753, PRK06753, hypothetical protein; Provisional.
Length = 373
Score = 31.2 bits (71), Expect = 1.8
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 143 NAMNVLKIVSN-KNYGLHRQTLLKLYQSYVSP 173
+N +K+ SN N LHRQTL+ + +SYV
Sbjct: 79 TLLNKVKLKSNTLNVTLHRQTLIDIIKSYVKE 110
>gnl|CDD|223970 COG1040, ComFC, Predicted amidophosphoribosyltransferases [General
function prediction only].
Length = 225
Score = 29.7 bits (67), Expect = 4.1
Identities = 15/54 (27%), Positives = 20/54 (37%), Gaps = 2/54 (3%)
Query: 546 QCGLPLTIRHLLECRSYIDPSRPAFHRIPSLDDDRDSVENLFEFLKYINVYNLI 599
CGLPL+ P P F R+ SL + L LK+ +L
Sbjct: 43 LCGLPLSSHACRCGECLAKP--PPFERLRSLGSYNGPLRELISQLKFQGDLDLA 94
>gnl|CDD|219683 pfam07986, TBCC, Tubulin binding cofactor C. Members of this
family are involved in the folding pathway of tubulins
and form a beta helix structure.
Length = 119
Score = 27.6 bits (62), Expect = 9.7
Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 1/53 (1%)
Query: 490 SDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDP 542
+ + + P G + DC N V ++RI YL T S P
Sbjct: 26 DNCKDCTIILG-PVSGSVFIRDCENCTIVVACRQLRIHDCTNCDFYLHTTSRP 77
>gnl|CDD|217402 pfam03170, BcsB, Bacterial cellulose synthase subunit. This family
includes bacterial proteins involved in cellulose
synthesis. Cellulose synthesis has been identified in
several bacteria. In Agrobacterium tumefaciens, for
instance, cellulose has a pathogenic role: it allows the
bacteria to bind tightly to their host plant cells.
While several enzymatic steps are involved in cellulose
synthesis, potentially the only step unique to this
pathway is that catalyzed by cellulose synthase. This
enzyme is a multi subunit complex. This family encodes a
subunit that is thought to bind the positive effector
cyclic di-GMP. This subunit is found in several
different bacterial cellulose synthase enzymes. The
first recognised sequence for this subunit is BcsB. In
the AcsII cellulose synthase, this subunit and the
subunit corresponding to BcsA are found in the same
protein. Indeed, this alignment only includes the
C-terminal half of the AcsAII synthase, which
corresponds to BcsB.
Length = 614
Score = 28.8 bits (65), Expect = 9.7
Identities = 30/165 (18%), Positives = 50/165 (30%), Gaps = 25/165 (15%)
Query: 439 WCPSHTGISGNEIVDRATRQLDGAEF----VNLSSPADLISVGKKYIH----------EK 484
W P+ + E+ D + Q+ G VN P DL + I
Sbjct: 298 WVPTDRPVRFGELGDPSQLQVSGRTPGPIRVNFRLPPDLFLWRGRGIPLDLDYRYTAGLD 357
Query: 485 WQKSWSDLTNN-------KLKCVKPTIGPWNVSD-CNNRYEEVVLTRVRI-GHTRLTHSY 535
S D++ N L + + D V + + + G +L +
Sbjct: 358 RDGSRLDVSVNGQFVQSFPLSPEGELLRLPLLGDGSLQERATVTIPALLLGGRNQLQFEF 417
Query: 536 LFTRSDPPSCQCGLPLTIRHLLECRSYIDPSRPAFHRIPSLDDDR 580
+C P +R ++ S ID S F +L D
Sbjct: 418 NLDPPKDGACATVAPDNLRAAIDPDSTIDLSG--FAHYAALPDLA 460
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 0.137 0.415
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,981,343
Number of extensions: 2865187
Number of successful extensions: 2165
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2154
Number of HSP's successfully gapped: 26
Length of query: 599
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 497
Effective length of database: 6,413,494
Effective search space: 3187506518
Effective search space used: 3187506518
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: 62 (27.6 bits)