RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15484
(1233 letters)
>gnl|CDD|239209 cd02843, PAZ_dicer_like, PAZ domain, dicer_like subfamily. Dicer is
an RNAse involved in cleaving dsRNA in the RNA
interference pathway. It generates dsRNAs which are
approximately 20 bp long (siRNAs), which in turn target
hydrolysis of homologous RNAs. PAZ domains are named
after the proteins Piwi Argonaut and Zwille. PAZ is
found in two families of proteins that are essential
components of RNA-mediated gene-silencing pathways,
including RNA interference, the piwi and Dicer families.
PAZ functions as a nucleic-acid binding domain, with a
strong preference for single-stranded nucleic acids (RNA
or DNA) or RNA duplexes with single-stranded 3'
overhangs. It has been suggested that the PAZ domain
provides a unique mode for the recognition of the two
3'-terminal nucleotides in single-stranded nucleic acids
and buries the 3' OH group, and that it might recognize
characteristic 3' overhangs in siRNAs within RISC
(RNA-induced silencing) and other complexes.
Length = 122
Score = 168 bits (427), Expect = 1e-48
Identities = 71/124 (57%), Positives = 85/124 (68%), Gaps = 2/124 (1%)
Query: 261 DSEQIVIDWKFMTLISEHHNDVIQDIPEKERENFVFDESKFRDAVVMPWYRNQFEPTYFY 320
DS + IDW+FM I + + P++ R+ F FD ++DAVVMPWYRN +P YFY
Sbjct: 1 DSSTLDIDWEFMEKIEANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFY 60
Query: 321 VAEIMTNVHPRSMFPSRTNTYQTFEEYYSLKYGLQIQNLEQPLLDVDHTSCRLNFLTPRY 380
VAEI T++ P S FP Y+TFEEYY KY L IQNL QPLLDVDHTS RLN LTPRY
Sbjct: 61 VAEICTDLRPLSKFPG--PEYETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRY 118
Query: 381 VNRK 384
VN+K
Sbjct: 119 VNQK 122
>gnl|CDD|223644 COG0571, Rnc, dsRNA-specific ribonuclease [Transcription].
Length = 235
Score = 136 bits (345), Expect = 4e-36
Identities = 80/261 (30%), Positives = 116/261 (44%), Gaps = 42/261 (16%)
Query: 979 FDKFEESINYRFKDKSYLLQAMTHASYFL-NTLTDCYQRLEFLGDAILDYLITRHLYEDE 1037
+ E+ + Y FKDK L QA+TH SY + + +RLEFLGDA+L ++ +L++
Sbjct: 8 LEALEKKLGYTFKDKELLEQALTHRSYANEHKAVENNERLEFLGDAVLGLVVAEYLFKKY 67
Query: 1038 RAHSPGTLTDLRSALVNNIIFASLAVRLGFHHFFKHLSPGLHEVIQRFVKMQAENDFTLN 1097
G L+ LR+ALV+ A +A LG + + L G E
Sbjct: 68 PNLPEGELSKLRAALVSEESLAEIARELGLGDYLR-LGKG------------EEKSGGRR 114
Query: 1098 QEYYLMEGECDEAEDIEVPKALGDLFESVAGAIYLDSGMSLDTVWKVYYEIMKSEIERLS 1157
+ L D FE++ GAIYLDSG L+ K ++ +E +
Sbjct: 115 R-----------------ESILADAFEALIGAIYLDSG--LEAARKFILKLFLPRLEEID 155
Query: 1158 VSV----PKSPIRELL----ELEPENARFSKPEKLADGRRVRVTVEVFGKGSYKGIGRNY 1209
PK+ ++ELL + PE R K E A + V V V GK G GR+
Sbjct: 156 AGDQFKDPKTRLQELLQAQGLVLPE-YRLVKEEGPAHDKEFTVEVAVGGKELGTGKGRSK 214
Query: 1210 CIAKCTAAKCALKHLKSAKPA 1230
A+ AA+ ALK L +PA
Sbjct: 215 KEAEQAAAEQALKKLGVKEPA 235
Score = 56.1 bits (136), Expect = 2e-08
Identities = 23/74 (31%), Positives = 42/74 (56%)
Query: 774 ENHTGPSPKRLETIGDSFLKYAITIFLYCTYPNVHEGKLSHLRSKQVSNYNLFKLGKQKV 833
E+ + +RLE +GD+ L + +L+ YPN+ EG+LS LR+ VS +L ++ ++
Sbjct: 37 EHKAVENNERLEFLGDAVLGLVVAEYLFKKYPNLPEGELSKLRAALVSEESLAEIARELG 96
Query: 834 FGESMIATKFEPRD 847
G+ + K E +
Sbjct: 97 LGDYLRLGKGEEKS 110
>gnl|CDD|238333 cd00593, RIBOc, RIBOc. Ribonuclease III C terminal domain. This group
consists of eukaryotic, bacterial and archeal
ribonuclease III (RNAse III) proteins. RNAse III is a
double stranded RNA-specific endonuclease. Prokaryotic
RNAse III is important in post-transcriptional control of
mRNA stability and translational efficiency. It is
involved in the processing of ribosomal RNA precursors.
Prokaryotic RNAse III also plays a role in the maturation
of tRNA precursors and in the processing of phage and
plasmid transcripts. Eukaryotic RNase III's participate
(through direct cleavage) in rRNA processing, in
processing of small nucleolar RNAs (snoRNAs) and snRNA's
(components of the spliceosome). In eukaryotes RNase III
or RNaseIII like enzymes such as Dicer are involved in
RNAi (RNA interference) and miRNA (micro-RNA) gene
silencing.
Length = 133
Score = 130 bits (330), Expect = 3e-35
Identities = 55/164 (33%), Positives = 79/164 (48%), Gaps = 32/164 (19%)
Query: 994 SYLLQAMTHASYFLNTLTDCYQRLEFLGDAILDYLITRHLYEDERAHSPGTLTDLRSALV 1053
S LL+A+TH SY +RLEFLGDA+L+ ++T +L++ S G LT LRSALV
Sbjct: 1 SLLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALV 60
Query: 1054 NNIIFASLAVRLGFHHFFKHLSPGLHEVIQRFVKMQAENDFTLNQEYYLMEGECDEAEDI 1113
+N A LA LG + + L +GE +++
Sbjct: 61 SNETLARLARELGLGKYLR-----------------------------LGKGE-EKSGGR 90
Query: 1114 EVPKALGDLFESVAGAIYLDSGMSLDTVWKVYYEIMKSEIERLS 1157
PK L D+FE++ GAIYLD G + K ++ IE +S
Sbjct: 91 LRPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPLIEEIS 132
Score = 79.6 bits (197), Expect = 2e-17
Identities = 24/75 (32%), Positives = 42/75 (56%)
Query: 774 ENHTGPSPKRLETIGDSFLKYAITIFLYCTYPNVHEGKLSHLRSKQVSNYNLFKLGKQKV 833
H + +RLE +GD+ L+ +T +L+ +P++ EG L+ LRS VSN L +L ++
Sbjct: 14 NEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELG 73
Query: 834 FGESMIATKFEPRDN 848
G+ + K E +
Sbjct: 74 LGKYLRLGKGEEKSG 88
Score = 43.8 bits (104), Expect = 7e-05
Identities = 14/44 (31%), Positives = 22/44 (50%)
Query: 921 HSIPDKSIADCVEALIGAYLIECGPRGALLFMSWLGLKVIPPVT 964
+ K +AD EALIGA ++ G A F+ L +I ++
Sbjct: 89 GRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEIS 132
>gnl|CDD|233772 TIGR02191, RNaseIII, ribonuclease III, bacterial. This family
consists of bacterial examples of ribonuclease III. This
enzyme cleaves double-stranded rRNA. It is involved in
processing ribosomal RNA precursors. It is found even in
minimal genones such as Mycoplasma genitalium and
Buchnera aphidicola, and in some cases has been shown to
be an essential gene. These bacterial proteins contain a
double-stranded RNA binding motif (pfam00035) and a
ribonuclease III domain (pfam00636). Eukaryotic homologs
tend to be much longer proteins with additional domains,
localized to the nucleus, and not included in this family
[Transcription, RNA processing].
Length = 220
Score = 128 bits (323), Expect = 3e-33
Identities = 69/257 (26%), Positives = 108/257 (42%), Gaps = 51/257 (19%)
Query: 982 FEESINYRFKDKSYLLQAMTHASYFLNT--LTDCYQRLEFLGDAILDYLITRHLYEDERA 1039
E+ + Y+FK+K L QA+TH+SY +RLEFLGDA+L ++ +L+++
Sbjct: 1 LEKRLGYKFKNKELLEQALTHSSYANEHHKGVKNNERLEFLGDAVLGLVVAEYLFKNFPD 60
Query: 1040 HSPGTLTDLRSALVNNIIFASLAVRLGFHHFFKHLSPGLHEVIQRFVKMQAENDFTLNQE 1099
S G L+ LR+ALV+ A +A LG F L G E +
Sbjct: 61 LSEGELSKLRAALVSEESLAEVARELGLGKFLL-LGKG--EEKSGGRRR----------- 106
Query: 1100 YYLMEGECDEAEDIEVPKALGDLFESVAGAIYLDSGMSLDTVW--KVYYEIMKSEIERLS 1157
L D FE++ GAIYLDSG+ + K+ + + + +
Sbjct: 107 ----------------ESILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIEKEET 150
Query: 1158 VSVPKSPIRELL----------ELEPENARFSKPEKLADGRRVRVTVEVFGKGSYKGIGR 1207
+ K+ ++E L E E + V V V G+ +G G+
Sbjct: 151 LKDYKTALQEWAQARGKPLPEYRLIKE-------EGPDHDKEFTVEVSVNGEPYGEGKGK 203
Query: 1208 NYCIAKCTAAKCALKHL 1224
+ A+ AAK AL+ L
Sbjct: 204 SKKEAEQNAAKAALEKL 220
Score = 46.4 bits (111), Expect = 3e-05
Identities = 20/66 (30%), Positives = 39/66 (59%)
Query: 783 RLETIGDSFLKYAITIFLYCTYPNVHEGKLSHLRSKQVSNYNLFKLGKQKVFGESMIATK 842
RLE +GD+ L + +L+ +P++ EG+LS LR+ VS +L ++ ++ G+ ++ K
Sbjct: 37 RLEFLGDAVLGLVVAEYLFKNFPDLSEGELSKLRAALVSEESLAEVARELGLGKFLLLGK 96
Query: 843 FEPRDN 848
E +
Sbjct: 97 GEEKSG 102
>gnl|CDD|197778 smart00535, RIBOc, Ribonuclease III family.
Length = 129
Score = 121 bits (305), Expect = 5e-32
Identities = 57/163 (34%), Positives = 83/163 (50%), Gaps = 34/163 (20%)
Query: 994 SYLLQAMTHASYFLNTLTDCYQRLEFLGDAILDYLITRHLYEDERAHSPGTLTDLRSALV 1053
S LL+A+THASY + +RLEFLGDA+L+ ++T +LY+ S G L+ LRSALV
Sbjct: 1 SLLLRALTHASYSNEH--EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALV 58
Query: 1054 NNIIFASLAVRLGFHHFFKHLSPGLHEVIQRFVKMQAENDFTLNQEYYLMEGECDEAEDI 1113
+N A LA +LG F + L G + G D+
Sbjct: 59 SNETLARLAKKLGLGEFIR-LGRGE-----------------------AISGGRDK---- 90
Query: 1114 EVPKALGDLFESVAGAIYLDSGMSLDTVWKVYYEIMKSEIERL 1156
PK L D+FE++ GAIYLDSG L+ + +++ ++ L
Sbjct: 91 --PKILADVFEALIGAIYLDSG--LEAAREFIRDLLGPRLDEL 129
Score = 83.8 bits (208), Expect = 6e-19
Identities = 32/89 (35%), Positives = 45/89 (50%), Gaps = 1/89 (1%)
Query: 779 PSPKRLETIGDSFLKYAITIFLYCTYPNVHEGKLSHLRSKQVSNYNLFKLGKQKVFGESM 838
+RLE +GD+ L+ +T +LY YP++ EG LS LRS VSN L +L K+ GE +
Sbjct: 17 EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFI 76
Query: 839 IATKFEPRDNWLPPGYFVPKYLETALIEA 867
+ E + E ALI A
Sbjct: 77 RLGRGEAISGGRDKPKILADVFE-ALIGA 104
Score = 33.7 bits (78), Expect = 0.19
Identities = 13/39 (33%), Positives = 18/39 (46%)
Query: 924 PDKSIADCVEALIGAYLIECGPRGALLFMSWLGLKVIPP 962
K +AD EALIGA ++ G A F+ L +
Sbjct: 90 KPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDE 128
>gnl|CDD|234633 PRK00102, rnc, ribonuclease III; Reviewed.
Length = 229
Score = 119 bits (301), Expect = 3e-30
Identities = 76/264 (28%), Positives = 115/264 (43%), Gaps = 56/264 (21%)
Query: 979 FDKFEESINYRFKDKSYLLQAMTHASYFLNTLTDC--YQRLEFLGDAILDYLITRHLYED 1036
++ ++ + Y FKD L+QA+TH SY N +RLEFLGDA+L+ +++ +L++
Sbjct: 5 LEELQKKLGYTFKDPELLIQALTHRSY-ANENKGLKHNERLEFLGDAVLELVVSEYLFKR 63
Query: 1037 ERAHSPGTLTDLRSALVNNIIFASLAVRLGFHHFFKHLSPGLHEVIQRFVKMQAENDFTL 1096
G L+ LR+ALV A +A LG
Sbjct: 64 FPDLDEGDLSKLRAALVREESLAEIARELGL----------------------------- 94
Query: 1097 NQEYYLM-EGECDEAEDIEVPKALGDLFESVAGAIYLDSGMSLDTVWKVYYEIMKSEIER 1155
EY L+ +GE +++ P L D FE++ GAIYLD G L+ K + + IE
Sbjct: 95 -GEYLLLGKGE-EKSGGRRRPSILADAFEALIGAIYLDQG--LEAARKFILRLFEPRIEE 150
Query: 1156 LSVSV----PKSPIRELLELEPENARFSKP--------EKLADGRRV-RVTVEVFGKGSY 1202
+ + K+ ++ELL P E+ + V V V GK
Sbjct: 151 IDLGDLVKDYKTRLQELL------QGRGLPLPEYELVKEEGPAHDKEFTVEVTVNGKELG 204
Query: 1203 KGIGRNYCIAKCTAAKCALKHLKS 1226
+G G + A+ AAK ALK LK
Sbjct: 205 EGTGSSKKEAEQAAAKQALKKLKE 228
Score = 47.0 bits (113), Expect = 2e-05
Identities = 20/63 (31%), Positives = 37/63 (58%)
Query: 774 ENHTGPSPKRLETIGDSFLKYAITIFLYCTYPNVHEGKLSHLRSKQVSNYNLFKLGKQKV 833
EN +RLE +GD+ L+ ++ +L+ +P++ EG LS LR+ V +L ++ ++
Sbjct: 34 ENKGLKHNERLEFLGDAVLELVVSEYLFKRFPDLDEGDLSKLRAALVREESLAEIARELG 93
Query: 834 FGE 836
GE
Sbjct: 94 LGE 96
>gnl|CDD|190615 pfam03368, dsRNA_bind, Double stranded RNA binding domain. This
domain is a divergent double stranded RNA-binding
domain. It is found in members of the Dicer protein
family which function in RNA interference, an
evolutionarily conserved mechanism for gene silencing
using double-stranded RNA (dsRNA) molecules.
Length = 91
Score = 99.2 bits (248), Expect = 9e-25
Identities = 41/92 (44%), Positives = 60/92 (65%), Gaps = 5/92 (5%)
Query: 4 AIFIVNRYCARLPSDIFTRLAPIITISEIKEDDSIMFTCSIRLPINSPLKRSVTGHKMPT 63
AI ++NRYCA LPSD FT L P ++ D + C++ LP+NSP+ R + G M +
Sbjct: 1 AIQLLNRYCATLPSDPFTSLRPEFSV--EPVDGG--YVCTVILPLNSPV-REIVGKPMRS 55
Query: 64 KLLAWRIAAMEACRVLYELKELDNDLMPVTKE 95
K LA + AA +AC+ L+EL EL++ L+P+ KE
Sbjct: 56 KRLAKQSAAFKACKKLHELGELNDHLLPIGKE 87
>gnl|CDD|198017 smart00949, PAZ, This domain is named PAZ after the proteins Piwi
Argonaut and Zwille. This domain is found in two
families of proteins that are involved in
post-transcriptional gene silencing. These are the Piwi
family and the Dicer family, that includes the Carpel
factory protein. The function of the domains is unknown
but has been suggested to mediate complex formation
between proteins of the Piwi and Dicer families by
hetero-dimerisation. The three-dimensional structure of
this domain has been solved. The PAZ domain is composed
of two subdomains. One subdomain is similar to the OB
fold, albeit with a different topology. The OB-fold is
well known as a single-stranded nucleic acid binding
fold. The second subdomain is composed of a beta-hairpin
followed by an alpha-helix. The PAZ domains shows
low-affinity nucleic acid binding and appears to
interact with the 3' ends of single-stranded regions of
RNA in the cleft between the two subdomains. PAZ can
bind the characteristic two-base 3' overhangs of siRNAs,
indicating that although PAZ may not be a primary
nucleic acid binding site in Dicer or RISC, it may
contribute to the specific and productive incorporation
of siRNAs and miRNAs into the RNAi pathway.
Length = 138
Score = 95.4 bits (238), Expect = 7e-23
Identities = 38/175 (21%), Positives = 62/175 (35%), Gaps = 39/175 (22%)
Query: 268 DWKFMTLISEHHNDVIQDIPEKERENFVFDESKFRDAVVMPWYRNQFEPTYFYVAEIMTN 327
FM + N + ++ ++ +V+ Y N+ + + +I N
Sbjct: 3 VLDFMRQLPSQGNR--SNFQDRCAKDLK-------GLIVLTRYNNKT----YRIDDIDWN 49
Query: 328 VHPRSMFPSRTNTYQTFEEYYSLKYGLQIQNLEQPLLDVDHTSCRLNFLTPRYVNRKGIN 387
+ P+S F + TF EYY KY + I++ QPLL
Sbjct: 50 LAPKSTFEKSDGSEITFVEYYKQKYNITIRDPNQPLL----------------------- 86
Query: 388 LATTSEETRREIRESLGKKQLLVPELCLIHPFPASLWRKSVSLPSILYRLNALLL 442
S RR + G+ LL PELC I + + + + SI R L
Sbjct: 87 ---VSRPKRRRNQNGKGEPVLLPPELCFITGLTDRMRKDFMLMKSIADRTRLSPL 138
>gnl|CDD|216036 pfam00636, Ribonuclease_3, Ribonuclease III domain.
Length = 91
Score = 89.6 bits (223), Expect = 2e-21
Identities = 45/122 (36%), Positives = 57/122 (46%), Gaps = 32/122 (26%)
Query: 1015 QRLEFLGDAILDYLITRHLYEDERAHSPGTLTDLRSALVNNIIFASLAVRLGFHHFFKHL 1074
+RLEFLGDA+L+ ++ +LYE S G L LRSALV+N A LA +LG
Sbjct: 1 ERLEFLGDAVLELYVSEYLYEKFPDLSEGELHRLRSALVSNEALAKLARKLGLDK----- 55
Query: 1075 SPGLHEVIQRFVKMQAENDFTLNQEYYLMEGECDEAEDIEV-PKALGDLFESVAGAIYLD 1133
YL EGE D + V K L D FE++ GA+YLD
Sbjct: 56 --------------------------YLREGEGDIVKRASVKDKVLADAFEALIGALYLD 89
Query: 1134 SG 1135
G
Sbjct: 90 GG 91
Score = 70.0 bits (172), Expect = 1e-14
Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 5/85 (5%)
Query: 783 RLETIGDSFLKYAITIFLYCTYPNVHEGKLSHLRSKQVSNYNLFKLGKQKVFGESMIATK 842
RLE +GD+ L+ ++ +LY +P++ EG+L LRS VSN L KL ++ + + +
Sbjct: 2 RLEFLGDAVLELYVSEYLYEKFPDLSEGELHRLRSALVSNEALAKLARKLGLDKYLREGE 61
Query: 843 FEPRDNWLPPGYFVPKYLETALIEA 867
+ K L A EA
Sbjct: 62 GDIVKRASVK----DKVLADAF-EA 81
Score = 34.9 bits (81), Expect = 0.029
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 917 LVTQHSIPDKSIADCVEALIGAYLIECG 944
+V + S+ DK +AD EALIGA ++ G
Sbjct: 64 IVKRASVKDKVLADAFEALIGALYLDGG 91
>gnl|CDD|216914 pfam02170, PAZ, PAZ domain. This domain is named PAZ after the
proteins Piwi Argonaut and Zwille. This domain is found
in two families of proteins that are involved in
post-transcriptional gene silencing. These are the Piwi
family and the Dicer family, that includes the Carpel
factory protein. The function of the domains is unknown
but has been suggested to mediate complex formation
between proteins of the Piwi and Dicer families by
hetero-dimerisation. The three-dimensional structure of
this domain has been solved. The PAZ domain is composed
of two subdomains. One subdomain is similar to the OB
fold, albeit with a different topology. The OB-fold is
well known as a single-stranded nucleic acid binding
fold. The second subdomain is composed of a beta-hairpin
followed by an alpha-helix. The PAZ domains shows
low-affinity nucleic acid binding and appears to
interact with the 3' ends of single-stranded regions of
RNA in the cleft between the two subdomains. PAZ can
bind the characteristic two-base 3' overhangs of siRNAs,
indicating that although PAZ may not be a primary
nucleic acid binding site in Dicer or RISC, it may
contribute to the specific and productive incorporation
of siRNAs and miRNAs into the RNAi pathway.
Length = 114
Score = 73.5 bits (181), Expect = 2e-15
Identities = 26/148 (17%), Positives = 41/148 (27%), Gaps = 42/148 (28%)
Query: 281 DVIQDIPEKERENFVF----DESKFRDAVVMPWYRNQFEPTYFYVAEIMTNVHPRSMFPS 336
D + DI + + +V Y N+ + + I + P S FP
Sbjct: 5 DFLTDILTQRTPLGDDFREKFTKALKGLIVETTYNNRT----YRIDGITWDPTPNSTFPL 60
Query: 337 RTNTYQTFEEYYSLKYGLQIQNLEQPLLDVDHTSCRLNFLTPRYVNRKGINLATTSEETR 396
+ + EY+ KY + ++ PLL V
Sbjct: 61 KDGGEISVAEYFKEKYNITLKYPNLPLLVVGRKK-------------------------- 94
Query: 397 REIRESLGKKQLLVPELCLIHPFPASLW 424
K L PELC I +
Sbjct: 95 --------KPNYLPPELCFITGGQRYMK 114
>gnl|CDD|171444 PRK12371, PRK12371, ribonuclease III; Reviewed.
Length = 235
Score = 65.1 bits (159), Expect = 2e-11
Identities = 42/157 (26%), Positives = 67/157 (42%), Gaps = 31/157 (19%)
Query: 980 DKFEESINYRFKDKSYLLQAMTHASYFLNTLTDCYQRLEFLGDAILDYLITRHLYEDERA 1039
EE +RF +K L +A+TH+S + + Y+RLEFLGD +L + L+E
Sbjct: 13 SILEERTGHRFANKERLERALTHSSARASKQGN-YERLEFLGDRVLGLCVAEMLFEAFPD 71
Query: 1040 HSPGTLTDLRSALVNNIIFASLAVRLGFHHFFKHLSPGLHEVIQRFVKMQAENDFTLNQE 1099
S G L+ + LVN A++A +G H + S +R + ++A
Sbjct: 72 ASEGELSVRLNQLVNAETCAAIADEIGLHDLIRTGSDVKKLTGKRLLNVRA--------- 122
Query: 1100 YYLMEGECDEAEDIEVPKALGDLFESVAGAIYLDSGM 1136
D+ E++ AIYLD G+
Sbjct: 123 ---------------------DVVEALIAAIYLDGGL 138
Score = 31.6 bits (72), Expect = 2.4
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 783 RLETIGDSFLKYAITIFLYCTYPNVHEGKLS 813
RLE +GD L + L+ +P+ EG+LS
Sbjct: 48 RLEFLGDRVLGLCVAEMLFEAFPDASEGELS 78
>gnl|CDD|239210 cd02844, PAZ_CAF_like, PAZ domain, CAF_like subfamily. CAF (for
carpel factory) is a plant homolog of Dicer. CAF has
been implicated in flower morphogenesis and in early
Arabidopsis development and might function through
posttranscriptional regulation of specific mRNA
molecules. PAZ domains are named after the proteins
Piwi, Argonaut, and Zwille. PAZ is found in two families
of proteins that are essential components of
RNA-mediated gene-silencing pathways, including RNA
interference, the Piwi and Dicer families. PAZ functions
as a nucleic-acid binding domain, with a strong
preference for single-stranded nucleic acids (RNA or
DNA) or RNA duplexes with single-stranded 3' overhangs.
It has been suggested that the PAZ domain provides a
unique mode for the recognition of the two 3'-terminal
nucleotides in single-stranded nucleic acids and buries
the 3' OH group, and that it might recognize
characteristic 3' overhangs in siRNAs within RISC
(RNA-induced silencing) and other complexes.
Length = 135
Score = 57.0 bits (138), Expect = 1e-09
Identities = 29/104 (27%), Positives = 43/104 (41%), Gaps = 12/104 (11%)
Query: 318 YFYVAEIMTNVHPRSMFPSRTN-TYQTFEEYYSLKYGLQIQNLEQPLLDVDHTSCRLNFL 376
FYV + +++ S FP + Y T+ EY+ KYG+ + + QPLL N L
Sbjct: 43 RFYVISGILDLNANSSFPGKEGLGYATYAEYFKEKYGIVLNHPNQPLLKGKQIFNLHNLL 102
Query: 377 TPRYVNRKGINLATTSEETRREIRESLGKKQLLVPELCLIHPFP 420
R+ E+ E +E L PELC + P
Sbjct: 103 HNRF-----------EEKGESEEKEKDRYFVELPPELCSVIDLP 135
>gnl|CDD|239211 cd02845, PAZ_piwi_like, PAZ domain, Piwi_like subfamily. In
multi-cellular organisms, the Piwi protein appears to be
essential for the maintenance of germline stem cells. In
the Drosophila male germline, Piwi was shown to be
involved in the silencing of retrotransposons in the
male gametes. The Piwi proteins share their domain
architecture with other members of the argonaute family.
The PAZ domain has been named after the proteins Piwi,
Argonaut, and Zwille. PAZ is found in two families of
proteins that are essential components of RNA-mediated
gene-silencing pathways, including RNA interference, the
Piwi and Dicer families. PAZ functions as a nucleic acid
binding domain, with a strong preference for
single-stranded nucleic acids (RNA or DNA) or RNA
duplexes with single-stranded 3' overhangs. It has been
suggested that the PAZ domain provides a unique mode for
the recognition of the two 3'-terminal nucleotides in
single-stranded nucleic acids and buries the 3' OH
group, and that it might recognize characteristic 3'
overhangs in siRNAs within RISC (RNA-induced silencing)
and other complexes.
Length = 117
Score = 51.5 bits (124), Expect = 1e-07
Identities = 36/136 (26%), Positives = 54/136 (39%), Gaps = 32/136 (23%)
Query: 281 DVIQDIPEKER-ENFV-FDESKFRDAVVMPWYRNQFEPTYFYVAEIMTNVHPRSMFPSRT 338
D + + +E E F E + ++V+ Y N+ TY + +I + P S F
Sbjct: 6 DRMHKLYRQETDERFREECEKELIGSIVLTRYNNK---TY-RIDDIDFDKTPLSTFKKSD 61
Query: 339 NTYQTFEEYYSLKYGLQIQNLEQPLLDVDHTSCRLNFLTPRYVNRKGINLATTSEETRRE 398
T TF EYY +Y ++I +L QPLL S RR+
Sbjct: 62 GTEITFVEYYKKQYNIEITDLNQPLL--------------------------VSRPKRRD 95
Query: 399 IRESLGKKQLLVPELC 414
R + L+PELC
Sbjct: 96 PRGGEKEPIYLIPELC 111
>gnl|CDD|239207 cd02825, PAZ, PAZ domain, named PAZ after the proteins Piwi
Argonaut and Zwille. PAZ is found in two families of
proteins that are essential components of RNA-mediated
gene-silencing pathways, including RNA interference, the
piwi and Dicer families. PAZ functions as a nucleic-acid
binding domain, with a strong preference for
single-stranded nucleic acids (RNA or DNA) or RNA
duplexes with single-stranded 3' overhangs. It has been
suggested that the PAZ domain provides a unique mode for
the recognition of the two 3'-terminal nucleotides in
single-stranded nucleic acids and buries the 3' OH
group, and that it might recognize characteristic 3'
overhangs in siRNAs within RISC (RNA-induced silencing)
and other complexes. This parent model also contains
structures of an archaeal PAZ domain.
Length = 115
Score = 50.9 bits (122), Expect = 1e-07
Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 2/66 (3%)
Query: 319 FYVAEIMTNVHPRSMFPSRTNTYQTFEEYYSLKYGLQIQNLEQPLLDVDHTSC--RLNFL 376
Y + T + S TF +Y+ +Y L + +L QPLL V +S L
Sbjct: 48 VYRPDGETRLKAPSQLKHSDGKEITFADYFKERYNLTLTDLNQPLLIVKFSSKKSYSILL 107
Query: 377 TPRYVN 382
P
Sbjct: 108 PPELCV 113
>gnl|CDD|173181 PRK14718, PRK14718, ribonuclease III; Provisional.
Length = 467
Score = 50.6 bits (120), Expect = 3e-06
Identities = 47/180 (26%), Positives = 75/180 (41%), Gaps = 44/180 (24%)
Query: 981 KFEESINYRFKDKSYLLQAMTHASYFLNTLTDCYQRLEFLGDAILDYLITRHLYEDERAH 1040
+ E + Y F++ L QA+TH S+ +RLEFLGD++L+ + L++
Sbjct: 5 QLESRLRYEFRNAELLRQALTHRSHSATH----NERLEFLGDSVLNCAVAALLFQRFGKL 60
Query: 1041 SPGTLTDLRSALVNNIIFASLAVRLGFHHFFKHLSPGLHEVIQRFVKMQAENDFTLNQEY 1100
G L+ +R+ LV +A L ++S GL
Sbjct: 61 DEGDLSRVRANLVKQQSLYEIAQAL-------NISDGLR--------------------- 92
Query: 1101 YLMEGECDEAEDIEVPKALGDLFESVAGAIYLDSGMSLDTVWKVYYEIMKSEIERLSVSV 1160
L EGE + P L D FE++ GA++LD G +E + I+RL V +
Sbjct: 93 -LGEGEL-RSGGFRRPSILADAFEAIIGAVFLDGG----------FEAAQGVIKRLYVPI 140
Score = 37.5 bits (86), Expect = 0.041
Identities = 17/56 (30%), Positives = 32/56 (57%)
Query: 775 NHTGPSPKRLETIGDSFLKYAITIFLYCTYPNVHEGKLSHLRSKQVSNYNLFKLGK 830
+H+ +RLE +GDS L A+ L+ + + EG LS +R+ V +L+++ +
Sbjct: 28 SHSATHNERLEFLGDSVLNCAVAALLFQRFGKLDEGDLSRVRANLVKQQSLYEIAQ 83
>gnl|CDD|237081 PRK12372, PRK12372, ribonuclease III; Reviewed.
Length = 413
Score = 48.4 bits (115), Expect = 2e-05
Identities = 50/178 (28%), Positives = 80/178 (44%), Gaps = 44/178 (24%)
Query: 983 EESINYRFKDKSYLLQAMTHASYFLNTLTDCYQRLEFLGDAILDYLITRHLYEDERAHSP 1042
E + Y F++ L QA+TH S+ + T +RLEFLGD++L+ + L++
Sbjct: 7 ESRLRYEFRNAELLRQALTHRSH---SATH-NERLEFLGDSVLNCAVAALLFQRFGKLDE 62
Query: 1043 GTLTDLRSALVNNIIFASLAVRLGFHHFFKHLSPGLHEVIQRFVKMQAENDFTLNQEYYL 1102
G L+ +R+ LV K S L+E+ QA N +++ L
Sbjct: 63 GDLSRVRANLV------------------KQQS--LYEI------AQALN---ISEGLRL 93
Query: 1103 MEGECDEAEDIEVPKALGDLFESVAGAIYLDSGMSLDTVWKVYYEIMKSEIERLSVSV 1160
EGE + P L D FE++ GA++LD G +E + I+RL V +
Sbjct: 94 GEGEL-RSGGFRRPSILADAFEAIIGAVFLDGG----------FEAAQGVIKRLYVPI 140
Score = 34.9 bits (80), Expect = 0.27
Identities = 17/55 (30%), Positives = 31/55 (56%)
Query: 776 HTGPSPKRLETIGDSFLKYAITIFLYCTYPNVHEGKLSHLRSKQVSNYNLFKLGK 830
H+ +RLE +GDS L A+ L+ + + EG LS +R+ V +L+++ +
Sbjct: 29 HSATHNERLEFLGDSVLNCAVAALLFQRFGKLDEGDLSRVRANLVKQQSLYEIAQ 83
>gnl|CDD|238007 cd00048, DSRM, Double-stranded RNA binding motif. Binding is not
sequence specific but is highly specific for double
stranded RNA. Found in a variety of proteins including
dsRNA dependent protein kinase PKR, RNA helicases,
Drosophila staufen protein, E. coli RNase III, RNases H1,
and dsRNA dependent adenosine deaminases.
Length = 68
Score = 35.7 bits (83), Expect = 0.009
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 1188 RRVRVTVEVFGKGSYKGIGRNYCIAKCTAAKCALKHL 1224
R V V V GK + +G G + AK AA+ AL+ L
Sbjct: 32 PRFTVEVTVGGKITGEGEGSSKKEAKQNAAEAALRKL 68
>gnl|CDD|117044 pfam08467, Luteo_P1-P2, Luteovirus RNA polymerase P1-P2/replicase.
This domain is found in RNA-dependent RNA polymerase
P1-P2 fusion/replicase proteins in plant Luteoviruses.
Length = 361
Score = 32.6 bits (74), Expect = 1.1
Identities = 37/145 (25%), Positives = 55/145 (37%), Gaps = 17/145 (11%)
Query: 415 LIHPFPASLWRKSVSLPSILYRLNALL-LADEIRTAVASEIGLGKVILDEKVEWPPFNFG 473
LI P S S R+ + L A+E+ + K +E E PF
Sbjct: 126 LIPSVPPSKDGCEDKSKSNPVRVEKFINLVKAKEVLQATEVRIKKTYEEEIGE-SPFG-C 183
Query: 474 WK---------MKKLKEKYGWDTKDANDVIVDDTEVNDTKEDDSAVNEICTEIAKVEIVD 524
W +K+ K+K + K A V TEVN + S C E+ +VE +
Sbjct: 184 WFNTLPSRMHYIKRAKDKAADNAKRAKKVGSMMTEVNVIPDFYS-----CCEVVQVETGE 238
Query: 525 KKETVCDSGNEQENEDEEKLDKIKS 549
K T + E+ E E KL ++
Sbjct: 239 TKPTKKNVNGEEVGEPEPKLKMVRR 263
>gnl|CDD|213552 TIGR00691, spoT_relA, (p)ppGpp synthetase, RelA/SpoT family. The
functions of E. coli RelA and SpoT differ somewhat. RelA
(EC 2.7.6.5) produces pppGpp (or ppGpp) from ATP and GTP
(or GDP). SpoT (EC 3.1.7.2) degrades ppGpp, but may also
act as a secondary ppGpp synthetase. The two proteins are
strongly similar. In many species, a single homolog to
SpoT and RelA appears reponsible for both ppGpp synthesis
and ppGpp degradation. (p)ppGpp is a regulatory
metabolite of the stringent response, but appears also to
be involved in antibiotic biosynthesis in some species
[Cellular processes, Adaptations to atypical conditions].
Length = 683
Score = 33.1 bits (76), Expect = 1.1
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 8/44 (18%)
Query: 1057 IFASLAVRLGFHHF--------FKHLSPGLHEVIQRFVKMQAEN 1092
I+A LA RLG FK+L P +E I+ V Q N
Sbjct: 140 IYAPLAHRLGMSSIKTELEDLSFKYLYPKEYENIKSLVNEQKVN 183
>gnl|CDD|148152 pfam06374, NDUF_C2, NADH-ubiquinone oxidoreductase subunit b14.5b
(NDUFC2). This family consists of several
NADH-ubiquinone oxidoreductase subunit b14.5b proteins
(EC:1.6.5.3).
Length = 117
Score = 31.0 bits (70), Expect = 1.3
Identities = 14/45 (31%), Positives = 21/45 (46%)
Query: 1163 SPIRELLELEPENARFSKPEKLADGRRVRVTVEVFGKGSYKGIGR 1207
P+ + LE P+ AR P KL D R + + + G + GR
Sbjct: 2 RPVNDPLEFLPDEARSLPPPKLWDPRLIACGLLGYCSGLFDNWGR 46
>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 32.9 bits (75), Expect = 1.4
Identities = 22/141 (15%), Positives = 51/141 (36%), Gaps = 20/141 (14%)
Query: 661 NSKAEFVKVIQDKLTFYEGQLELIKNRIDVE--------------NTIKENQPVHIVRQS 706
++ +F K+ ++ + + + + I+N D+E K I ++
Sbjct: 363 ENEIKFKKIEENSIDNLDIKEKKIENENDIEGKSDTKNLEEGFETKDNKNKNSSFI-NKT 421
Query: 707 FDNASNPSKNTAILTEILENINKLNT----YGSVEKDVKTEPKSPGKSCEHGI-IRNTST 761
+ +N +L + E IN N +G + D+ + + ++ I
Sbjct: 422 ENILTNSPLKDELLEKTTEIINIENPQEFEFGQIGNDIISTEIAQLDENQNLIDTGEFDL 481
Query: 762 PSDFSFDFQPDLENHTGPSPK 782
++FS F P+ N +
Sbjct: 482 ENNFSNSFNPENGNKIDENIN 502
>gnl|CDD|215670 pfam00035, dsrm, Double-stranded RNA binding motif. Sequences
gathered for seed by HMM_iterative_training Putative
motif shared by proteins that bind to dsRNA. At least
some DSRM proteins seem to bind to specific RNA targets.
Exemplified by Staufen, which is involved in localisation
of at least five different mRNAs in the early Drosophila
embryo. Also by interferon-induced protein kinase in
humans, which is part of the cellular response to dsRNA.
Length = 66
Score = 29.6 bits (67), Expect = 1.5
Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 1161 PKSPIRELLELEPENARFSKPEKL--ADGRRVRVTVEVFGKGSYKGIGRNYCIAKCTAAK 1218
PKS ++EL + + + E+ VTV V GK G G + AK AA+
Sbjct: 1 PKSLLQELCQKKGPKPPYEYVEEEGPPHSPTFTVTVTVNGKKYGTGTGSSKKEAKQLAAE 60
Query: 1219 CALKHL 1224
AL+ L
Sbjct: 61 KALQKL 66
>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional.
Length = 211
Score = 31.6 bits (72), Expect = 1.8
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 492 DVIVDDTEVNDTKEDDSAVNEICTEIAKVEIVDKKETVCDSGNEQENEDEEKLDKIKS-- 549
++ D + N+ KE+D E ++ E ++K+E + DS E + EE D+
Sbjct: 12 NMEEDCCKENENKEEDKGKEE---DLE-FEEIEKEEIIEDSEESNEVKIEELKDENNKLK 67
Query: 550 DENKTESQGVE 560
+ENK +E
Sbjct: 68 EENKKLENELE 78
>gnl|CDD|237293 PRK13185, chlL, protochlorophyllide reductase iron-sulfur
ATP-binding protein; Provisional.
Length = 270
Score = 31.1 bits (71), Expect = 2.9
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 12/61 (19%)
Query: 60 KMPTKLLAWRIAAMEACRV-------LYELKELDNDLMPVTKEFIN----LYENTEPVVP 108
+ K+LA + ++A R L+E++E D L V E++ L EP+VP
Sbjct: 196 AVGLKVLA-HVPDLDAIRRSRLKGKTLFEMEETDPGLEEVQNEYLRLAEQLLAGPEPLVP 254
Query: 109 K 109
K
Sbjct: 255 K 255
>gnl|CDD|227726 COG5439, COG5439, Uncharacterized conserved protein [Function
unknown].
Length = 112
Score = 29.9 bits (67), Expect = 3.1
Identities = 15/38 (39%), Positives = 20/38 (52%)
Query: 856 VPKYLETALIEAGFPASLWNCLSLPNLKELSPEKVLEI 893
V K +T+ + G W SLPNLK+L P+ LE
Sbjct: 74 VRKKPDTSFVVRGSKNIPWQMKSLPNLKKLHPDLTLEF 111
>gnl|CDD|185297 PRK15399, PRK15399, lysine decarboxylase LdcC; Provisional.
Length = 713
Score = 31.6 bits (72), Expect = 3.6
Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 9/71 (12%)
Query: 663 KAEFVKVIQDKLTFYEGQLELIKNRIDVENTIKENQPVHIVRQSFDNASNPSKNTAILTE 722
K E +K ++ L Q +N +D+ I+ N + V +D S +
Sbjct: 15 KDEPIKELESALQAQGFQTIWPQNSVDLLKFIEHNPRICGVIFDWDEYSL---------D 65
Query: 723 ILENINKLNTY 733
+ +IN+LN Y
Sbjct: 66 LCSDINQLNEY 76
>gnl|CDD|236843 PRK11092, PRK11092, bifunctional (p)ppGpp synthetase II/
guanosine-3',5'-bis pyrophosphate
3'-pyrophosphohydrolase; Provisional.
Length = 702
Score = 30.9 bits (70), Expect = 4.8
Identities = 22/65 (33%), Positives = 29/65 (44%), Gaps = 14/65 (21%)
Query: 1037 ERAHSPGTLTDLRSALVNNI------IFASLAVRLGFHHF--------FKHLSPGLHEVI 1082
+R H+ TL LR I I++ LA RLG HH F+ L P + VI
Sbjct: 139 DRTHNMRTLGSLRPDKRRRIARETLEIYSPLAHRLGIHHIKTELEELGFEALYPNRYRVI 198
Query: 1083 QRFVK 1087
+ VK
Sbjct: 199 KEVVK 203
>gnl|CDD|217943 pfam04180, LTV, Low temperature viability protein. The
low-temperature viability protein LTV1 is involved in
ribosome biogenesis 40S subunit production.
Length = 426
Score = 30.7 bits (69), Expect = 5.1
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 5/73 (6%)
Query: 588 FSDDE--DSNDDLSSVDFD--VEDDFRENEKEDTLQIQFKGKYSAEAICEGEEESA-LKI 642
E ++ +D + V D E+D E +E + + SA + E E+ SA
Sbjct: 157 PRLREVLEALEDEAYVRNDEESEEDDGEEWEEMDDEEGSDDRSSAGFLDEFEDLSAPGSP 216
Query: 643 QDWIESNFFWEEI 655
Q+ ++ + F EE
Sbjct: 217 QEAMKKHLFVEEE 229
>gnl|CDD|218939 pfam06207, DUF1002, Protein of unknown function (DUF1002). This
protein family has no known function. Its members are
about 300 amino acids in length. It has so far been
detected in Firmicute bacteria and some archaebacteria.
Length = 222
Score = 29.8 bits (68), Expect = 6.2
Identities = 14/72 (19%), Positives = 30/72 (41%), Gaps = 8/72 (11%)
Query: 486 DTKDANDVIVDDTEVNDTKEDDSAVNEICTEIAKVEIVDKKETVCDSGNEQENEDEEKLD 545
+ AN+ +V +E+N D + EI K EI +K + + E + ++
Sbjct: 128 QKEAANEELVTTSELNGDGIGDDKAANLVAEI-KKEIAKQK-------PKTKEEIRKIVN 179
Query: 546 KIKSDENKTESQ 557
+ ++ N +
Sbjct: 180 NVLNNLNINLTD 191
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 30.7 bits (69), Expect = 7.0
Identities = 34/146 (23%), Positives = 55/146 (37%), Gaps = 25/146 (17%)
Query: 497 DTEVNDTKEDDS-AVNEICTEIAKVEIVDKKETVCDSGNEQENEDEEKLDKIKSDENKTE 555
D EVND ED S ++NE + E D ET S + +E L + D E
Sbjct: 3889 DEEVNDIPEDLSNSLNEKLWDEPNEE--DLLETEQKSNEQSAANNESDLVSKEDDNKALE 3946
Query: 556 SQGVEPWVEIGTWSNEMAAGVECKP-----YPMTPPMFSD--------------DEDSND 596
+ + + S+++ E +P PP D D +
Sbjct: 3947 DKDRQEKEDEEEMSDDVGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLDEKEGDVSKDS 4006
Query: 597 DLSSVDFDVEDDFRE---NEKEDTLQ 619
DL +D + D+ +E EK++ +Q
Sbjct: 4007 DLEDMDMEAADENKEEADAEKDEPMQ 4032
>gnl|CDD|204655 pfam11468, PTase_Orf2, Aromatic prenyltransferase Orf2. In vivo Orf2
attaches a geranyl group to a
1,3,6,8-tetrahydroxynaphthalene-derived polyketide during
naphterpin biosynthesis. In vitro, Orf2 catalyzes
carbon-carbon based and carbon-oxygen based prenylation
of hydroxyl-containing aromatic acceptors of synthetic,
microbial and plant origin.
Length = 294
Score = 30.1 bits (68), Expect = 7.0
Identities = 19/66 (28%), Positives = 26/66 (39%), Gaps = 5/66 (7%)
Query: 1151 SEIERLSVSVPKSPIRELLE----LEPENARFSKPEKLADGRRVRVTVEVFG-KGSYKGI 1205
+IER+ +V K P R E LEP +F + A V FG +G Y +
Sbjct: 213 GDIERVCFAVLKRPGRAPGELPARLEPRIEKFLRAAPSAYEGEKNVYAASFGPEGEYLKL 272
Query: 1206 GRNYCI 1211
Y
Sbjct: 273 EAYYQG 278
>gnl|CDD|218538 pfam05285, SDA1, SDA1. This family consists of several SDA1
protein homologues. SDA1 is a Saccharomyces cerevisiae
protein which is involved in the control of the actin
cytoskeleton. The protein is essential for cell
viability and is localised in the nucleus.
Length = 317
Score = 30.0 bits (68), Expect = 8.7
Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 2/76 (2%)
Query: 481 EKYGWDTKDANDVIVDDTEVNDTKEDDSAVNEICTEIAKVEIVDKKETVCDSGNEQENED 540
E+ W+ ++ D + ++ E D + +E + + K+ DS E ED
Sbjct: 100 EEEEWEVEEDEDSDDEGEWIDV--ESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEED 157
Query: 541 EEKLDKIKSDENKTES 556
EE+ + + E + E
Sbjct: 158 EEEAAEEEEAEAEKEK 173
>gnl|CDD|219915 pfam08578, DUF1765, Protein of unknown function (DUF1765). This
region represents a conserved region found in
hypothetical proteins from fungi, mycetozoa and
entamoebidae.
Length = 123
Score = 28.3 bits (64), Expect = 9.4
Identities = 14/68 (20%), Positives = 21/68 (30%), Gaps = 19/68 (27%)
Query: 253 YFIVPTVSDSEQIVIDWKF------MTLISEHHN-------------DVIQDIPEKEREN 293
F S DW+F M L S+H +I K+ +
Sbjct: 32 IFQFNRSLPSIPTFFDWEFWLKGIRMMLNSDHAQSLLRALAFLFNIWPLIPADLRKKILD 91
Query: 294 FVFDESKF 301
F+ +E F
Sbjct: 92 FLLEEEVF 99
>gnl|CDD|239212 cd02846, PAZ_argonaute_like, PAZ domain, argonaute_like subfamily.
Argonaute is part of the RNA-induced silencing complex
(RISC), and is an endonuclease that plays a key role in
the RNA interference pathway. The PAZ domain has been
named after the proteins Piwi,Argonaut, and Zwille. PAZ
is found in two families of proteins that are essential
components of RNA-mediated gene-silencing pathways,
including RNA interference, the Piwi and Dicer families.
PAZ functions as a nucleic acid binding domain, with a
strong preference for single-stranded nucleic acids (RNA
or DNA) or RNA duplexes with single-stranded 3'
overhangs. It has been suggested that the PAZ domain
provides a unique mode for the recognition of the two
3'-terminal nucleotides in single-stranded nucleic acids
and buries the 3' OH group, and that it might recognize
characteristic 3' overhangs in siRNAs within RISC
(RNA-induced silencing) and other complexes.
Length = 114
Score = 28.4 bits (64), Expect = 9.6
Identities = 9/61 (14%), Positives = 20/61 (32%), Gaps = 8/61 (13%)
Query: 314 FEPTYFYVAEIMTNVH-------PRSMFPSRT-NTYQTFEEYYSLKYGLQIQNLEQPLLD 365
E T+ + + F + + +Y+ KY ++++ P L
Sbjct: 37 VEVTHRGNTNRKYKIKGLSAEPASQQTFELKDGEKEISVADYFKEKYNIRLKYPNLPCLQ 96
Query: 366 V 366
V
Sbjct: 97 V 97
>gnl|CDD|221373 pfam12006, DUF3500, Protein of unknown function (DUF3500). This
family of proteins is functionally uncharacterized. This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 335 to 438 amino acids
in length. This protein has a conserved GHH sequence
motif. This protein has two completely conserved G
residues that may be functionally important.
Length = 314
Score = 29.6 bits (67), Expect = 10.0
Identities = 11/37 (29%), Positives = 15/37 (40%)
Query: 363 LLDVDHTSCRLNFLTPRYVNRKGINLATTSEETRREI 399
L D D R P + RKG+ L ++E R
Sbjct: 32 LYDFDDPERRTWSNPPFPLPRKGLRLDDLTDEQRDAA 68
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
0.318 0.135 0.402
Gapped
Lambda K H
0.267 0.0741 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 63,278,707
Number of extensions: 6345282
Number of successful extensions: 5655
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5600
Number of HSP's successfully gapped: 82
Length of query: 1233
Length of database: 10,937,602
Length adjustment: 108
Effective length of query: 1125
Effective length of database: 6,147,370
Effective search space: 6915791250
Effective search space used: 6915791250
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: 65 (28.8 bits)