RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5607
(769 letters)
>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 = 156 bits (397), Expect = 1e-43
Identities = 73/267 (27%), Positives = 119/267 (44%), Gaps = 58/267 (21%)
Query: 164 ESLILPLLKPGKDRLVPSNYRPISLLNCSGKILEKMVNKRLFWVLENRGLINPFQSGGRF 223
++ I+ + K GK P NYRPISLL+ K+LEK++ RL VLE L P Q G R
Sbjct: 1 KARIILIPKKGKPSD-PKNYRPISLLSVLYKLLEKILANRLRPVLEENIL--PNQFGFRP 57
Query: 224 RRSTIDNLVFLEKEAAQGLAKKECTVALLLDGQKAFDMTWRFKIIETLKGFNINGYMLRY 283
RST D ++ L + + KK+ V + LD +KAFD +++ L
Sbjct: 58 GRSTTDAILLLREVIEKAKEKKKSLVLVFLDFEKAFDSVDHEFLLKAL------------ 105
Query: 284 LCNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSLSPVLFIIFMNDILDII---------K 334
G+ QG LSP+LF + ++D+L ++
Sbjct: 106 --------------------------GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGG 139
Query: 335 VPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSACILFSR 394
+ L + DD ++ + GK K+Q+ L + +WS ++GL + P KS +L
Sbjct: 140 PGITHLAYADDIVLFSEGK-----SRKLQELLQRLQEWSKESGLKIN--PSKSKVMLIGN 192
Query: 395 ARNPTFPPLFYNGSELKFESNIKFLGL 421
+ + NG+ ++ K+LG+
Sbjct: 193 -KKKRLKDITLNGTPIEAVETFKYLGV 218
Score = 36.9 bits (86), Expect = 0.021
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 29 HKSGSRNLPSNFRPVCNYSIIPKTFEKLVYDKLSP 63
K G + P N+RP+ S++ K EK++ ++L P
Sbjct: 8 PKKGKPSDPKNYRPISLLSVLYKLLEKILANRLRP 42
>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 = 87.4 bits (217), Expect = 9e-20
Identities = 64/221 (28%), Positives = 94/221 (42%), Gaps = 49/221 (22%)
Query: 172 KPGKDRLVPSNYRPISLLNCSGKILEKMVNKRLFWVLENRGLINPFQSGGRFR--RSTID 229
K GK YRPIS + KIL K KRL + +P Q G FR RST +
Sbjct: 3 KKGK-----GKYRPIS--SVDYKILNKATKKRL------EPIFSPPQPG--FRPGRSTHN 47
Query: 230 NLVFLEKEAAQGLAKKECTVALLLDGQKAFDMTWRFKIIETLKGFNINGYMLRYLCNFLY 289
L K L LD +KAFD + L F + F+
Sbjct: 48 LL-------------KGSKWFLKLDLKKAFDSIPHDPLDRPLTAFGLPQ-------RFIR 87
Query: 290 NRSFKVKCNGSFSNSFPLQNGIVQGSSLSPVLFIIFMNDILDIIKVPLRR---LLFIDDF 346
R+F V NG G+ QGS LSP+LF +FMN++L ++ L + DD
Sbjct: 88 WRTFSVLVNG-NPGGRYEWRGLPQGSVLSPLLFNLFMNELLRPLRKRFPGLTYLRYADDI 146
Query: 347 LVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKS 387
L+ ++ +Q+ L ++L++ + GL + P+K+
Sbjct: 147 LIFSKSPEE------LQEILEEVLEFLKELGLKLN--PEKT 179
>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 = 71.9 bits (177), Expect = 4e-15
Identities = 25/70 (35%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 641 PHSKFLLVSDSMSAIQAIANI-CSSYKNSLTSKIYSAWMDLKSGGKEVTLMWCPSHCGIS 699
K + SDS +A++A+ + SS +I A +L + G +V L W P H GI
Sbjct: 58 RARKITIFSDSQAALKALRSPRSSSPLVL---RIRKAIRELANHGVKVRLHWVPGHSGIE 114
Query: 700 GNEAVDMAAK 709
GNE D AK
Sbjct: 115 GNERADRLAK 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 = 59.2 bits (144), Expect = 1e-10
Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 6/72 (8%)
Query: 640 LPHSKFLLVSDSMSAIQAI--ANICSSYKNSLTSKIYSAWMDLKSGGKEVTLMWCPSHCG 697
L K + +DS I I S + ++I+ +L +V + W P H G
Sbjct: 55 LSGQKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIW----ELLQKKHKVYIQWVPGHSG 110
Query: 698 ISGNEAVDMAAK 709
I GNE D AK
Sbjct: 111 IPGNELADKLAK 122
>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 = 41.5 bits (98), Expect = 2e-04
Identities = 26/97 (26%), Positives = 39/97 (40%), Gaps = 13/97 (13%)
Query: 296 KCNGSFSNSFPLQNGIVQGSSLSPVLFIIFMNDILD-----IIKVPLRRLL--FIDDFLV 348
KC S + + GI QGS LS +L ++ D+ + + + LL +DDFL+
Sbjct: 5 KCYDSIPQYYRQKVGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLL 64
Query: 349 IARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPK 385
I K K LN +L+ F K
Sbjct: 65 IT------TSLDKAIKFLNLLLRGFINQYKTFVNFDK 95
>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 = 36.2 bits (84), Expect = 0.012
Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 6/75 (8%)
Query: 637 CIYLPHSKFLLVSDSMSAIQAIANICSSYKNSLTSKIYSAWMDLKSGGKEVTLMWCPSHC 696
+ L K ++ +DS + I + S + + + L S ++ P
Sbjct: 54 ALDLGLKKLIIETDSKYVVDLINS--WSKGWKKNNLLLWDILLLLSKFIDIRFEHVPR-- 109
Query: 697 GISGNEAVDMAAKNP 711
GNE D AK
Sbjct: 110 --EGNEVADRLAKEA 122
>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 = 37.6 bits (88), Expect = 0.012
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 15/79 (18%)
Query: 305 FPLQNGIVQGSSLSPVLFIIFMNDILDII-----------KVPLRRLLFI---DDFLVIA 350
+ G QG +SP+L I+++++ + RRL ++ DDF++
Sbjct: 121 VETEKGTPQGGVISPLLANIYLHELDKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGV 180
Query: 351 RG-KVIELLRIKIQKALND 368
RG K E ++ I++ L +
Sbjct: 181 RGPKEAEEIKELIREFLEE 199
>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 = 31.9 bits (73), Expect = 0.22
Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 13/82 (15%)
Query: 313 QGSSLSPVLFIIFMN----DILDIIKVPLRRLLFIDDFLVIARGKVIELLRIKIQKALND 368
QGS LSP L ++M IL + + + ++DD +VIA+ + +K + L +
Sbjct: 14 QGSPLSPALANLYMEKLEAPILKQLL-DITLIRYVDDLVVIAKSEQ---QAVKK-RELEE 68
Query: 369 ILKWSNQNGLIFSADPKKSACI 390
L + +D K
Sbjct: 69 FL----ARLGLNLSDEKTQFTE 86
>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 = 32.9 bits (76), Expect = 0.23
Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 1/47 (2%)
Query: 666 KNSLTSKIYSAWMDLKSGGKEVTLMWCPSHCGISGNEAVDMAAKNPC 712
T K Y +MD +++ + +H G NE D AK
Sbjct: 88 NKEGT-KEYKEFMDKIKKKIKISFVKVKAHSGDKYNELADKLAKKAL 133
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 31.6 bits (72), Expect = 0.83
Identities = 9/32 (28%), Positives = 12/32 (37%)
Query: 678 MDLKSGGKEVTLMWCPSHCGISGNEAVDMAAK 709
+L + V W H G NE D A+
Sbjct: 109 DELLKRHELVFWEWVKGHAGHPENERADQLAR 140
>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 = 30.6 bits (70), Expect = 1.3
Identities = 13/31 (41%), Positives = 15/31 (48%)
Query: 679 DLKSGGKEVTLMWCPSHCGISGNEAVDMAAK 709
+L+ G V P H GI GNE D AK
Sbjct: 116 ELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146
>gnl|CDD|222211 pfam13542, HTH_Tnp_ISL3, Helix-turn-helix domain of transposase
family ISL3.
Length = 65
Score = 28.4 bits (64), Expect = 2.3
Identities = 10/40 (25%), Positives = 12/40 (30%), Gaps = 7/40 (17%)
Query: 677 WMDLKSGGKEVTLMW------CPSHCGISGNEAVDMAAKN 710
L GGK V L C CG + E +
Sbjct: 25 IRHLPIGGKPVYLRLRKRRYRCK-ECGKTFTEELPWVDPG 63
>gnl|CDD|226091 COG3561, COG3561, Phage anti-repressor protein [Transcription].
Length = 110
Score = 28.9 bits (65), Expect = 4.0
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 7/45 (15%)
Query: 408 SELKFESNIKFLGLY-------WDAKMNWALHINHTKSRAMVALN 445
SE F NI ++G M++AL I+ K AMV N
Sbjct: 37 SEYGFIENIDYIGCSDYGEEFSGVIGMDYALTIDMAKEIAMVERN 81
>gnl|CDD|219952 pfam08645, PNK3P, Polynucleotide kinase 3 phosphatase.
Polynucleotide kinase 3 phosphatases play a role in the
repair of single breaks in DNA induced by DNA-damaging
agents such as gamma radiation and camptothecin.
Length = 158
Score = 29.1 bits (66), Expect = 5.3
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 7/51 (13%)
Query: 288 LYNRSFKVKCNGSFSNSFPLQNGIVQGSSLSPVLFIIFMNDILDIIKVPLR 338
L+ +K+ F+N Q GI S F + IL + VPL+
Sbjct: 41 LHEDGYKI---VIFTN----QGGISTKGKKSAESFKNKIESILKKLDVPLQ 84
>gnl|CDD|188163 TIGR01735, FGAM_synt, phosphoribosylformylglycinamidine synthase,
single chain form. This model represents a
single-molecule form of
phosphoribosylformylglycinamidine synthase, also called
FGAM synthase, an enzyme of purine de novo biosynthesis.
This form is found mostly in eukaryotes and
Proteobacteria. In Bacillus subtilis PurL (FGAM synthase
II) and PurQ (FGAM synthase I), homologous to different
parts of this model, perform the equivalent function;
the unrelated small protein PurS is also required and
may be a third subunit [Purines, pyrimidines,
nucleosides, and nucleotides, Purine ribonucleotide
biosynthesis].
Length = 1310
Score = 30.1 bits (68), Expect = 5.9
Identities = 8/52 (15%), Positives = 20/52 (38%), Gaps = 2/52 (3%)
Query: 96 IKVTSGCGQGGHMKNLAPPTDSNESIDMDMDIVPEKGKK--RALTQSPPPQD 145
+ + + + AP N +D+ ++++ K K R + + P
Sbjct: 587 LTLVDDTPVRRNGQGDAPSHFPNNPVDLPLEVLLGKMPKMTRFVQRKAPMLQ 638
>gnl|CDD|215091 PLN00179, PLN00179, acyl- [acyl-carrier protein] desaturase.
Length = 390
Score = 29.7 bits (67), Expect = 6.1
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 7/58 (12%)
Query: 128 VPEKGKKRALTQSPPPQDNEKKFDFSSVGKFPKSWGESLILPLLKPGKDRLVPSNYRP 185
P + +T S PP+ E + K + W E +LPLLKP + P ++ P
Sbjct: 44 APPREVHVQVTHSMPPEKLE-------IFKSLEGWAEENLLPLLKPVEKSWQPQDFLP 94
>gnl|CDD|225110 COG2200, Rtn, c-di-GMP phosphodiesterase class I (EAL domain)
[Signal transduction mechanisms].
Length = 256
Score = 29.2 bits (66), Expect = 6.7
Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 336 PLRRLLFIDDFLVIA--RGKVIELLRIKIQKALNDILKWSNQNGLIFS 381
P L+ +F+ +A G ++EL R +++A + W L +
Sbjct: 44 PDGGLISPGEFIPLAEETGLIVELGRWVLEEACRQLRTWPRAGPLRLA 91
>gnl|CDD|188709 cd08755, RGS_p115RhoGEF, Regulator of G protein signaling (RGS)
domain found in the Rho guanine nucleotide exchange
factor (GEF), p115 RhoGEF. The RGS (Regulator of
G-protein Signaling) domain is an essential part of the
p115RhoGEF protein, a member of the RhoGEF (Rho guanine
nucleotide exchange factor) subfamily of the RGS protein
family. The RhoGEFs are peripheral membrane proteins
that regulate essential cellular processes, including
cell shape, cell migration, cell cycle progression of
cells, and gene transcription by linking signals from
heterotrimeric G-alpha12/13 protein-coupled receptors to
Rho GTPase activation, leading to various cellular
responses, such as actin reorganization and gene
expression. The RhoGEF subfamily includes p115RhoGEF,
LARG, PDZ-RhoGEF and its rat specific splice variant
GTRAP48. The RGS domain of RhoGEFs has very little
sequence similarity with the canonical RGS domain of the
RGS proteins and is often refered to as RH (RGS
Homology) domain. In addition to being a G-alpha13/12
effector, the p115RhoGEF protein also functions as a
GTPase-activating protein (GAP) for G-alpha13. RGS
proteins play critical regulatory role as GTPase
activating proteins (GAPs) of the heterotrimeric
G-protein G-alpha-subunits. RGS proteins play critical
regulatory role as GTPase activating proteins (GAPs) of
the heterotrimeric G-protein G-alpha-subunits. RGS
proteins regulate many aspects of embryonic development
such as glial differentiation, embryonic axis formation,
skeletal and muscle development, cell migration during
early embryogenesis, as well as apoptosis, cell
proliferation, and modulation of cardiac development.
Length = 193
Score = 28.7 bits (64), Expect = 8.0
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 600 FQAPPVDTSLHVDRKKNISPSVFQKHFLD 628
F P+ LH D KN++ +KHF D
Sbjct: 19 FDPAPLLCYLHADMLKNLNTKETKKHFGD 47
>gnl|CDD|217376 pfam03122, Herpes_MCP, Herpes virus major capsid protein. This
family represents the major capsid protein (MCP) of
herpes viruses. The capsid shell consists of 150 MCP
hexamers and 12 MCP pentamers. One pentamer is found at
each of the 12 apices of the icosahedral shell, and the
hexamers form the edges and 20 faces.
Length = 1352
Score = 29.5 bits (67), Expect = 8.4
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 14/60 (23%)
Query: 395 ARNPTFPPLFY------NGSELKFESNIKFLGL----YWDAKMNWALHINHTKSRAMVAL 444
+P +P LFY +G+E F + + + YW+ A +N S MV
Sbjct: 596 LFDPNYPELFYVIEALIHGNEEAFCALARLIAQCINSYWNNSGRLAF-VN---SFDMVKY 651
>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 = 28.2 bits (64), Expect = 9.3
Identities = 10/26 (38%), Positives = 11/26 (42%)
Query: 684 GKEVTLMWCPSHCGISGNEAVDMAAK 709
+VT W H G GNE D A
Sbjct: 110 KHQVTWHWVKGHAGHPGNERADELAN 135
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 0.136 0.420
Gapped
Lambda K H
0.267 0.0747 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 39,076,322
Number of extensions: 3820928
Number of successful extensions: 2773
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2760
Number of HSP's successfully gapped: 33
Length of query: 769
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 665
Effective length of database: 6,324,786
Effective search space: 4205982690
Effective search space used: 4205982690
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: 63 (28.0 bits)