RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4044
(460 letters)
>gnl|CDD|187699 cd09275, RNase_HI_RT_DIRS1, DIRS1 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 eukaryotes. 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. The structural features of DIRS1-group
elements are different from typical LTR elements. RNase
H inhibitors have been explored as an anti-HIV drug
target because RNase H inactivation inhibits reverse
transcription.
Length = 120
Score = 133 bits (338), Expect = 6e-38
Identities = 51/117 (43%), Positives = 69/117 (58%)
Query: 280 VSTDASNSGWGAIVDNHSLGGVWSDHQEMWHINLKEMFAVRSALERKLPVLQDKVVLIQS 339
+ TDAS SGWGA++ G+WS + HIN E+ AV AL+ L ++ VL++S
Sbjct: 2 LFTDASLSGWGAVLSGSWAQGLWSAEERNKHINFLELLAVLLALQHWGARLSNRKVLVRS 61
Query: 340 DNQTVVSYIHKEGGTKSFKLLREVEALFDLAVRHNITLMARYIPGKFNTWADSLSRQ 396
DN T V+YI+++GGT+S +LL L NI L AR+IPG N AD LSR
Sbjct: 62 DNTTAVAYINRQGGTRSPELLALARQLVLWCEERNIWLRARHIPGVLNVAADRLSRL 118
>gnl|CDD|239684 cd03714, RT_DIRS1, RT_DIRS1: Reverse transcriptases (RTs) occurring
in the DIRS1 group of retransposons. Members of the
subfamily include the Dictyostelium DIRS-1, Volvox
carteri kangaroo, and Panagrellus redivivus PAT
elements. These elements differ from LTR and
conventional non-LTR retrotransposons. They contain
split direct repeat (SDR) termini, and have been
proposed to integrate via double-stranded closed-circle
DNA intermediates assisted by an encoded recombinase
which is similar to gamma-site-specific integrase.
Length = 119
Score = 93.2 bits (232), Expect = 6e-23
Identities = 44/117 (37%), Positives = 64/117 (54%), Gaps = 1/117 (0%)
Query: 114 IDLSQAYFHVPIRPSHQRFLSVVYRDTLYCMTCLPFGLASAPQVFAKLTNWIANYLRNLG 173
+DL AYFH+PI P + L ++ Y LPFGL+ AP+VF K+ + LR LG
Sbjct: 1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLG 60
Query: 174 MRVIVYLDDLLLGNQDSVLLRSQARA-AVATLQSLRWSVNLERSVLWPVQTCQYLGI 229
+R+ YLDDLL+ + R L +L +++NLE+S L P Q +LG+
Sbjct: 61 VRIFSYLDDLLIIASSIKTSEAVLRHLRATLLANLGFTLNLEKSKLGPTQRITFLGL 117
>gnl|CDD|238825 cd01647, RT_LTR, RT_LTR: Reverse transcriptases (RTs) from
retrotransposons and retroviruses which have long
terminal repeats (LTRs) in their DNA copies but not in
their RNA template. RT catalyzes DNA replication from an
RNA template, and is responsible for the replication of
retroelements. An RT gene is usually indicative of a
mobile element such as a retrotransposon or retrovirus.
RTs are present in a variety of mobile elements,
including retrotransposons, retroviruses, group II
introns, bacterial msDNAs, hepadnaviruses, and
Caulimoviruses.
Length = 177
Score = 65.3 bits (160), Expect = 1e-12
Identities = 29/81 (35%), Positives = 38/81 (46%), Gaps = 4/81 (4%)
Query: 105 LQRGDFLVKIDLSQAYFHVPIRPSHQRFLSVVYRDTLYCMTCLPFGLASAPQVFAKLTNW 164
L K+DL Y +P+ + + LY T +PFGL +AP F +L N
Sbjct: 54 LAGAKVFSKLDLRSGYHQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNK 113
Query: 165 IANYLR-NLGMRVIVYLDDLL 184
I L LG V VYLDD+L
Sbjct: 114 I---LGDLLGDFVEVYLDDIL 131
>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 = 62.4 bits (152), Expect = 2e-11
Identities = 31/144 (21%), Positives = 57/144 (39%), Gaps = 19/144 (13%)
Query: 105 LQRGDFLVKIDLSQAYFHVPIRP---------SHQRFLSVVYR--------DTLYCMTCL 147
L+ + +K+DL +A+ +P P QRF+ Y L
Sbjct: 49 LKGSKWFLKLDLKKAFDSIPHDPLDRPLTAFGLPQRFIRWRTFSVLVNGNPGGRYEWRGL 108
Query: 148 PFGLASAPQVFAKLTNWIANYLRNL--GMRVIVYLDDLLLGNQDSVLLRSQARAAVATLQ 205
P G +P +F N + LR G+ + Y DD+L+ ++ L+ + L+
Sbjct: 109 PQGSVLSPLLFNLFMNELLRPLRKRFPGLTYLRYADDILIFSKSPEELQEILEEVLEFLK 168
Query: 206 SLRWSVNLERSVLWPVQTCQYLGI 229
L +N E++ + ++LG
Sbjct: 169 ELGLKLNPEKTKITHSDEVKFLGY 192
>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 = 52.0 bits (125), Expect = 3e-08
Identities = 29/126 (23%), Positives = 53/126 (42%), Gaps = 17/126 (13%)
Query: 282 TDAS------NSGWGAIVDNHSLGGVWSDHQEMW----HINLKEMFAVRSALERKLPVLQ 331
TD S +G G ++ +H G W + N E+ A+ ALE L
Sbjct: 2 TDGSCKGNPGPAGAGGVLRDHE--GAWLFAGSLSIPAATNNEAELLALLEALE-LALDLG 58
Query: 332 DKVVLIQSDNQTVVSYIHKEGGTKSFKLLREVEALFDLAVR-HNITLMARYIPGKFNTWA 390
K ++I++D++ VV I+ K + + L + +I ++P + N A
Sbjct: 59 LKKLIIETDSKYVVDLINSWSKGWK-KNNLLLWDILLLLSKFIDIRFE--HVPREGNEVA 115
Query: 391 DSLSRQ 396
D L+++
Sbjct: 116 DRLAKE 121
>gnl|CDD|239685 cd03715, RT_ZFREV_like, RT_ZFREV_like: A subfamily of reverse
transcriptases (RTs) found in sequences similar to the
intact endogenous retrovirus ZFERV from zebrafish and to
Moloney murine leukemia virus RT. 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. Phylogenetic analysis suggests
that ZFERV belongs to a distinct group of retroviruses.
Length = 210
Score = 53.1 bits (128), Expect = 4e-08
Identities = 30/127 (23%), Positives = 57/127 (44%), Gaps = 9/127 (7%)
Query: 110 FLVKIDLSQAYFHVPIRPSHQRFLSVVYRDTLYCMTCLPFGLASAPQVF-----AKLTNW 164
+ +DL+ A+F +P+ P Q + + Y T LP G ++P +F L +
Sbjct: 88 WYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEALARDLAPF 147
Query: 165 IANYLRNLGMRVIVYLDDLLLGNQDSVLLRSQARAAVATLQSLRWSVNLERSVLWPVQTC 224
L + G ++ Y+DDLLL A + L L + V+ +++ +
Sbjct: 148 ---PLEHEGTILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQI-CRAEV 203
Query: 225 QYLGIMW 231
++LG++W
Sbjct: 204 KFLGVVW 210
>gnl|CDD|187698 cd09274, RNase_HI_RT_Ty3, Ty3/Gypsy 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 eukaryotes. 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. Ty3/Gypsy family widely distributed among
the genomes of plants, fungi and animals. RNase H
inhibitors have been explored as an anti-HIV drug target
because RNase H inactivation inhibits reverse
transcription.
Length = 121
Score = 49.4 bits (119), Expect = 1e-07
Identities = 31/129 (24%), Positives = 56/129 (43%), Gaps = 23/129 (17%)
Query: 279 FVSTDASNSGWGAIVDNHSLGGVW----------SDHQEMWHINLKEMFAVRSALERKLP 328
+ TDAS+ G GA++ + G + + + KE+ A+ AL++
Sbjct: 1 VLETDASDFGIGAVL-SQLDDGKERPIAFASRKLTPAERNYSTYEKELLAIVFALKKFRH 59
Query: 329 VLQDKVVLIQSDNQTVVSYIHKEGGTKSFKLLREVEAL--FDLAVRHNITLMARYIPGKF 386
L + + +D++++ Y+ + +L R + L FD + Y PGK
Sbjct: 60 YLLGRKFTVYTDHKSLK-YLLTKKDLNP-RLARWLLLLQEFDFEIE--------YRPGKE 109
Query: 387 NTWADSLSR 395
N AD+LSR
Sbjct: 110 NVVADALSR 118
>gnl|CDD|238822 cd01644, RT_pepA17, RT_pepA17: Reverse transcriptase (RTs) in
retrotransposons. This subfamily represents the RT
domain of a multifunctional enzyme. C-terminal to the RT
domain is a domain homologous to aspartic proteinases
(corresponding to Merops family A17) encoded by
retrotransposons and retroviruses. RT catalyzes DNA
replication from an RNA template and is responsible for
the replication of retroelements.
Length = 213
Score = 39.2 bits (92), Expect = 0.002
Identities = 35/155 (22%), Positives = 60/155 (38%), Gaps = 39/155 (25%)
Query: 115 DLSQAYFHVPIRPSHQRFLSVVYRDT-------LYCMTCLPFGLASAP-------QVFAK 160
D+ + + V +RP + L ++R Y MT +PFG ASAP + A+
Sbjct: 65 DIEKMFHQVKVRPEDRDVLRFLWRKDGDEPKPIEYRMTVVPFGAASAPFLANRALKQHAE 124
Query: 161 L--TNWIANYLRNLGMRVIVYLDDLLLGNQDSVLLRSQARAAVATLQSL-----RWSVNL 213
A ++ Y+DD+L+ + A+ +A L+ +W+ N
Sbjct: 125 DHPHEAAAKIIKR-----NFYVDDILVSTDTLNEAVNVAKRLIALLKKGGFNLRKWASN- 178
Query: 214 ERSVLWPVQTCQY------------LGIMWNPTLD 236
+ VL + + LG+ WNP D
Sbjct: 179 SQEVLDDLPEERVLLDRDSDVTEKTLGLRWNPKTD 213
>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 = 34.9 bits (81), Expect = 0.011
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 335 VLIQSDNQTVVSYIHKEGGTKS--FKLLREVEALFDLAVRHNITLMARYIPGKFNTWADS 392
++++SD+Q VV I E +S LLRE+ L ++ ++P + N AD+
Sbjct: 25 LIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLK----KFDSVSVSHVPRECNRVADA 80
Query: 393 LSR 395
L++
Sbjct: 81 LAK 83
>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 = 35.6 bits (83), Expect = 0.012
Identities = 25/84 (29%), Positives = 36/84 (42%), Gaps = 12/84 (14%)
Query: 316 MFAVRSALERKLPVLQDKVVLIQSDNQTVVSYIHKEGGTKSFKL---LREVEALFDLAVR 372
+ + ALE L K + I D+Q VV+ I E K+ +L L E L
Sbjct: 51 IAGLELALE-----LGIKKLEIYGDSQLVVNQIQGEYEVKNERLAPYLEEARELLKKFEE 105
Query: 373 HNITLMARYIPGKFNTWADSLSRQ 396
I +IP + N AD+L+ Q
Sbjct: 106 VEIK----WIPREENKEADALANQ 125
>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 = 0.94
Identities = 26/115 (22%), Positives = 45/115 (39%), Gaps = 9/115 (7%)
Query: 101 VPDFLQRGDFLVKIDLSQAYFHVPIRPSH-QRF----LSVVYR--DTLYCMTCLPFGLAS 153
P L +G L+ +DL +F +P+ P +RF S+ + Y LP G+ +
Sbjct: 76 HPAALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKN 135
Query: 154 APQVFAKLTNWIANYLR--NLGMRVIVYLDDLLLGNQDSVLLRSQARAAVATLQS 206
+P + R + + Y+DD+L+ + LR TL
Sbjct: 136 SPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLR 190
>gnl|CDD|176513 cd08571, GDPD_SHV3_plant, Glycerophosphodiester phosphodiesterase
domain of glycerophosphodiester phosphodiesterase-like
protein SHV3 and SHV3-like proteins. This subfamily
corresponds to the glycerophosphodiester
phosphodiesterase (GDPD) domain present in
glycerophosphodiester phosphodiesterase (GP-GDE)-like
protein SHV3 and SHV3-like proteins (SVLs), which may
play an important role in cell wall organization. The
prototype of this family is a
glycosylphosphatidylinositol (GPI) anchored protein SHV3
encoded by shaven3 (shv3) gene from Arabidopsis
thaliana. Members in this family show sequence homology
to bacterial GP-GDEs (EC 3.1.4.46) that catalyze the
hydrolysis of various glycerophosphodiesters, and
produce sn-glycerol-3-phosphate (G3P) and the
corresponding alcohols. Both, SHV3 and SVLs, have two
tandemly repeated GDPD domains whose biochemical
functions remain unclear. The residues essential for
interactions with the substrates and calcium ions in
bacterial GP-GDEs are not conserved in SHV3 and SVLs,
which suggests that the function of GDPD domains in
these proteins might be distinct from those in typical
bacterial GP-GDEs. In addition, the two tandem repeats
show low sequence similarity to each other, suggesting
they have different biochemical function. Most members
of this family are Arabidopsis-specific gene products.
To date, SHV3 orthologues are only found in
Physcomitrella patens.
Length = 302
Score = 30.7 bits (70), Expect = 1.6
Identities = 32/152 (21%), Positives = 58/152 (38%), Gaps = 26/152 (17%)
Query: 253 LTLTQIQWWSVALHRSSPIFPQAPQVFVSTDASNSGWGAIV---------DNHSLGGVWS 303
LT +IQ ++ S+P + + N G I+ SL GVW
Sbjct: 84 LTWAEIQ--TLKPIISNPFSV------LFRNPRNDNAGKILTLEDFLTLAKPKSLSGVWI 135
Query: 304 DHQE----MWHINLKEMFAVRSALERKLPVLQDKVVLIQSDNQTVVSYIHKEGGTKSFKL 359
+ + H L + AV ++L + K V I S + +V+ K GTK
Sbjct: 136 NVENAAFLAEHKGLLSVDAVLTSLSKAGYDQTAKKVYISSPDSSVLKSFKKRVGTKLVFR 195
Query: 360 LREVEALFDLAVRHNITLMARY-----IPGKF 386
+ +V+ + N+T + ++ +P +
Sbjct: 196 VLDVDDTEPDTLLSNLTEIKKFASGVLVPKSY 227
>gnl|CDD|143390 cd05400, NT_2-5OAS_ClassI-CCAase, Nucleotidyltransferase (NT)
domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS)
and class I CCA-adding enzyme. In vertebrates, 2-5OASs
are induced by interferon during the innate immune
response to protect against RNA virus infections. In the
presence of an RNA activator, 2-5OASs catalyze the
oligomerization of ATP into 2-5A. 2-5A activates
endoribonuclease L, which leads to degradation of the
viral RNA. 2-5OASs are also implicated in cell growth
control, differentiation, and apoptosis. This family
includes human OAS1, -2, -3, and OASL. CCA-adding
enzymes add the sequence [cytidine(C)-cytidine-adenosine
(A)], one nucleotide at a time, onto the 3' end of tRNA,
in a template-independent reaction. This class I group
includes the archaeal Sulfolobus shibatae and
Archeoglobus fulgidus CCA-adding enzymes. It belongs to
the Pol beta-like NT superfamily. In the majority of
enzymes in this superfamily, two carboxylates, Dx[D/E],
together with a third more distal carboxylate,
coordinate two divalent metal cations involved in a
two-metal ion mechanism of nucleotide addition. These
carboxylate residues are conserved in this family.
Length = 143
Score = 29.7 bits (67), Expect = 1.7
Identities = 17/81 (20%), Positives = 29/81 (35%), Gaps = 9/81 (11%)
Query: 50 VARHTAILLLLCSGRRVHDLTLL--LSSRDGFQDLGDRAFLSLKKFHLINHFRVPDFLQR 107
AR TA+ R D+ L+ L F + G L L ++ + ++
Sbjct: 36 YARGTAL-------RGDSDIDLVVVLPDDTSFAEYGPAELLDELGEALKEYYGANEEVKA 88
Query: 108 GDFLVKIDLSQAYFHVPIRPS 128
V + FHV + P+
Sbjct: 89 QHRSVTVKFKGQGFHVDVVPA 109
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 29.3 bits (67), Expect = 3.0
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 165 IANYLRNLGMRVIVYLDDL 183
IA Y R+ G V++ LD L
Sbjct: 97 IAEYFRDQGKDVLLLLDSL 115
>gnl|CDD|215474 PLN02877, PLN02877, alpha-amylase/limit dextrinase.
Length = 970
Score = 29.7 bits (67), Expect = 3.9
Identities = 18/58 (31%), Positives = 24/58 (41%), Gaps = 2/58 (3%)
Query: 21 LLEKREIWDVSTLISWISDHPPNQDSFFEVARHTAILLLLCSGRRVHDLTLLLSSRDG 78
LL R W ++I+W D S F A TA L + G +DL + L G
Sbjct: 92 LLYSRAYWVTESIIAWNVD--VGDGSCFLYASKTAGLSVSDDGVEGYDLVVKLEEDSG 147
>gnl|CDD|219791 pfam08317, Spc7, Spc7 kinetochore protein. This domain is found in
cell division proteins which are required for
kinetochore-spindle association.
Length = 321
Score = 29.2 bits (66), Expect = 4.2
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 327 LPVLQDKVVLIQSDNQTVVSYIHKEGGTKSFKLLREVEALFDLA 370
+ L+ KV L+Q T ++ G T S R +E +FD A
Sbjct: 276 ISKLKAKVSLLQK--LTGWKFLSLSGSTLSMSYNRTIELVFDPA 317
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of unknown
function.
Length = 248
Score = 29.0 bits (66), Expect = 4.4
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 36 WISDHPPNQDSFFEVARHTA 55
W+ HP +QD + + R A
Sbjct: 187 WLGFHPFDQDEYLAIVRGYA 206
>gnl|CDD|213530 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a
histidyl-tRNA synthetase in every completed genome.
Apparent second copies from Bacillus subtilis,
Synechocystis sp., and Aquifex aeolicus are slightly
shorter, more closely related to each other than to
other hisS proteins, and actually serve as regulatory
subunits for an enzyme of histidine biosynthesis. They
were excluded from the seed alignment and score much
lower than do single copy histidyl-tRNA synthetases of
other genomes not included in the seed alignment. These
putative second copies of HisS score below the trusted
cutoff. The regulatory protein kinase GCN2 of
Saccharomyces cerevisiae (YDR283c), and related proteins
from other species designated eIF-2 alpha kinase, have a
domain closely related to histidyl-tRNA synthetase that
may serve to detect and respond to uncharged tRNA(his),
an indicator of amino acid starvation; these regulatory
proteins are not orthologous and so score below the
noise cutoff [Protein synthesis, tRNA aminoacylation].
Length = 397
Score = 28.6 bits (65), Expect = 7.2
Identities = 14/37 (37%), Positives = 17/37 (45%)
Query: 165 IANYLRNLGMRVIVYLDDLLLGNQDSVLLRSQARAAV 201
+A LR G+RV V L L Q + AR AV
Sbjct: 341 LAQKLRKAGIRVEVDLGGRKLKKQLKYADKLGARFAV 377
>gnl|CDD|223202 COG0124, HisS, Histidyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 28.3 bits (64), Expect = 8.1
Identities = 12/38 (31%), Positives = 15/38 (39%)
Query: 164 WIANYLRNLGMRVIVYLDDLLLGNQDSVLLRSQARAAV 201
+A LR G+ V V L Q + AR AV
Sbjct: 353 KLAQKLRAAGISVEVDYSGRKLKKQFKYADKLGARFAV 390
>gnl|CDD|234066 TIGR02940, anfO_nitrog, Fe-only nitrogenase accessory protein AnfO.
Members of this protein family, called Anf1 in
Rhodobacter capsulatus and AnfO in Azotobacter
vinelandii, are found only in species with the Fe-only
nitrogenase and are encoded immediately downstream of
the structural genes in the above named species.
Length = 214
Score = 28.2 bits (63), Expect = 8.4
Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 4/77 (5%)
Query: 299 GGVWSDHQEMWHINLKE---MFAVRSALERKLPVLQDKVVLIQSDNQTVVSYIHKEGGTK 355
GG W + + + AVR+A+ + L D V + S+ + + + +E G +
Sbjct: 28 GGEWK-LLKDIENAVCPAKGLAAVRAAVADMVKQLDDCRVFLASEVRGIAYSLLQEMGFQ 86
Query: 356 SFKLLREVEALFDLAVR 372
+ V D +
Sbjct: 87 VWLSEGPVLDQLDSVAK 103
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
0.324 0.137 0.430
Gapped
Lambda K H
0.267 0.0721 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,767,068
Number of extensions: 2321671
Number of successful extensions: 2585
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2570
Number of HSP's successfully gapped: 28
Length of query: 460
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 360
Effective length of database: 6,502,202
Effective search space: 2340792720
Effective search space used: 2340792720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 61 (27.3 bits)