RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3362
(550 letters)
>gnl|CDD|234633 PRK00102, rnc, ribonuclease III; Reviewed.
Length = 229
Score = 170 bits (433), Expect = 1e-49
Identities = 79/238 (33%), Positives = 124/238 (52%), Gaps = 28/238 (11%)
Query: 227 KQLQYLEYSSGVIFNHIRLLARVFTTRSMGYTNLTLGSNQRLEFLGDTVLQLITSDYLYN 286
K L+ L+ G F LL + T RS N L N+RLEFLGD VL+L+ S+YL+
Sbjct: 3 KDLEELQKKLGYTFKDPELLIQALTHRSYANENKGLKHNERLEFLGDAVLELVVSEYLFK 62
Query: 287 HFPEHHEGHLSLLRSSLVNNRTQSVVCNDIGMPFFANIINPKVDLKM---------KDR- 336
FP+ EG LS LR++LV + + + ++G+ + L + + R
Sbjct: 63 RFPDLDEGDLSKLRAALVREESLAEIARELGLGEY---------LLLGKGEEKSGGRRRP 113
Query: 337 ---ADLLEAFLGAMYIDKGMEACEQFCKVCFFPRLQYFILNQEWNDPKSKLQQCCLTLRT 393
AD EA +GA+Y+D+G+EA +F F PR++ L D K++LQ+ L
Sbjct: 114 SILADAFEALIGAIYLDQGLEAARKFILRLFEPRIEEIDLGDLVKDYKTRLQE--LLQGR 171
Query: 394 LDGGEPDIPIYKVIEHVGPTNSRSYTVAVYFKNERLAKATGNSIQQAEMNAAKVALQK 451
+P Y++++ GP + + +TV V + L + TG+S ++AE AAK AL+K
Sbjct: 172 GLP----LPEYELVKEEGPAHDKEFTVEVTVNGKELGEGTGSSKKEAEQAAAKQALKK 225
Score = 81.7 bits (203), Expect = 2e-17
Identities = 33/101 (32%), Positives = 57/101 (56%), Gaps = 14/101 (13%)
Query: 98 QFITSIHLFHVFPDIEEGGLATYRAAIVQNQHLAHLAKRIGLEDFMLYAHGSDLCHEVEL 157
+ + S +LF FPD++EG L+ RAA+V+ + LA +A+ +GL +++L G E
Sbjct: 53 ELVVSEYLFKRFPDLDEGDLSKLRAALVREESLAEIARELGLGEYLLLGKG-------EE 105
Query: 158 KH-------AMANCFEALMGALFLDGGIDVADQVFSSVLYK 191
K +A+ FEAL+GA++LD G++ A + +
Sbjct: 106 KSGGRRRPSILADAFEALIGAIYLDQGLEAARKFILRLFEP 146
>gnl|CDD|223644 COG0571, Rnc, dsRNA-specific ribonuclease [Transcription].
Length = 235
Score = 164 bits (417), Expect = 3e-47
Identities = 76/231 (32%), Positives = 123/231 (53%), Gaps = 14/231 (6%)
Query: 227 KQLQYLEYSSGVIFNHIRLLARVFTTRSMGYTNLTLGSNQRLEFLGDTVLQLITSDYLYN 286
K+L+ LE G F LL + T RS + + +N+RLEFLGD VL L+ ++YL+
Sbjct: 6 KKLEALEKKLGYTFKDKELLEQALTHRSYANEHKAVENNERLEFLGDAVLGLVVAEYLFK 65
Query: 287 HFPEHHEGHLSLLRSSLVNNRTQSVVCNDIGMPFFANIINPKVDLKMKDR------ADLL 340
+P EG LS LR++LV+ + + + ++G+ + + K + K R AD
Sbjct: 66 KYPNLPEGELSKLRAALVSEESLAEIARELGLGDY--LRLGKGEEKSGGRRRESILADAF 123
Query: 341 EAFLGAMYIDKGMEACEQFCKVCFFPRLQYFILNQEWNDPKSKLQQCCLTLRTLDGGEPD 400
EA +GA+Y+D G+EA +F F PRL+ ++ DPK++LQ+ G
Sbjct: 124 EALIGAIYLDSGLEAARKFILKLFLPRLEEIDAGDQFKDPKTRLQELL-----QAQGLVL 178
Query: 401 IPIYKVIEHVGPTNSRSYTVAVYFKNERLAKATGNSIQQAEMNAAKVALQK 451
P Y++++ GP + + +TV V + L G S ++AE AA+ AL+K
Sbjct: 179 -PEYRLVKEEGPAHDKEFTVEVAVGGKELGTGKGRSKKEAEQAAAEQALKK 228
Score = 80.4 bits (199), Expect = 4e-17
Identities = 31/114 (27%), Positives = 59/114 (51%), Gaps = 4/114 (3%)
Query: 93 GNNFSQFITSIHLFHVFPDIEEGGLATYRAAIVQNQHLAHLAKRIGLEDFMLYAHGSDLC 152
G+ + + +LF +P++ EG L+ RAA+V + LA +A+ +GL D++ G +
Sbjct: 51 GDAVLGLVVAEYLFKKYPNLPEGELSKLRAALVSEESLAEIARELGLGDYLRLGKGEEKS 110
Query: 153 HEVELKHAMANCFEALMGALFLDGGIDVADQVFSSVLYKDNEVRFKQWMYYPQH 206
+ +A+ FEAL+GA++LD G++ A + + R ++ Q
Sbjct: 111 GGRRRESILADAFEALIGAIYLDSGLEAARKFILKLFLP----RLEEIDAGDQF 160
>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 = 162 bits (413), Expect = 7e-47
Identities = 76/234 (32%), Positives = 120/234 (51%), Gaps = 22/234 (9%)
Query: 225 LLKQLQYLEYSSGVIFNHIRLLARVFTTRSMGY-TNLTLGSNQRLEFLGDTVLQLITSDY 283
L K+L G F + LL + T S + + +N+RLEFLGD VL L+ ++Y
Sbjct: 1 LEKRL-------GYKFKNKELLEQALTHSSYANEHHKGVKNNERLEFLGDAVLGLVVAEY 53
Query: 284 LYNHFPEHHEGHLSLLRSSLVNNRTQSVVCNDIGMPFFANIINPKVDLKMKDR------A 337
L+ +FP+ EG LS LR++LV+ + + V ++G+ F ++ K + K R A
Sbjct: 54 LFKNFPDLSEGELSKLRAALVSEESLAEVARELGLGKF--LLLGKGEEKSGGRRRESILA 111
Query: 338 DLLEAFLGAMYIDKGMEACEQFCKVCFFPRLQYFILNQEWNDPKSKLQQCCLTLRTLDGG 397
D EA +GA+Y+D G+EA +F PR+ + D K+ LQ+
Sbjct: 112 DAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIEKEETLKDYKTALQE--WAQARGKP- 168
Query: 398 EPDIPIYKVIEHVGPTNSRSYTVAVYFKNERLAKATGNSIQQAEMNAAKVALQK 451
+P Y++I+ GP + + +TV V E + G S ++AE NAAK AL+K
Sbjct: 169 ---LPEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALEK 219
Score = 77.6 bits (192), Expect = 2e-16
Identities = 32/94 (34%), Positives = 54/94 (57%)
Query: 98 QFITSIHLFHVFPDIEEGGLATYRAAIVQNQHLAHLAKRIGLEDFMLYAHGSDLCHEVEL 157
+ + +LF FPD+ EG L+ RAA+V + LA +A+ +GL F+L G +
Sbjct: 47 GLVVAEYLFKNFPDLSEGELSKLRAALVSEESLAEVARELGLGKFLLLGKGEEKSGGRRR 106
Query: 158 KHAMANCFEALMGALFLDGGIDVADQVFSSVLYK 191
+ +A+ FEAL+GA++LD G++ A + +L
Sbjct: 107 ESILADAFEALIGAIYLDSGLEAARKFILKLLIP 140
>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 = 136 bits (344), Expect = 4e-38
Identities = 47/136 (34%), Positives = 74/136 (54%), Gaps = 9/136 (6%)
Query: 244 RLLARVFTTRSMGYTNLTLGSNQRLEFLGDTVLQLITSDYLYNHFPEHHEGHLSLLRSSL 303
LL T S + +N+RLEFLGD VL+L+ ++YL+ FP+ EG L+ LRS+L
Sbjct: 1 SLLLEALTHPSYANEHGRF-NNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSAL 59
Query: 304 VNNRTQSVVCNDIGMPFFANIINPKVDLKMKDR------ADLLEAFLGAMYIDKGMEACE 357
V+N T + + ++G+ + + K + K R AD+ EA +GA+Y+D G EA
Sbjct: 60 VSNETLARLARELGLGKY--LRLGKGEEKSGGRLRPKILADVFEALIGAIYLDGGFEAAR 117
Query: 358 QFCKVCFFPRLQYFIL 373
+F P ++ L
Sbjct: 118 KFLLRLLGPLIEEISL 133
Score = 105 bits (265), Expect = 4e-27
Identities = 33/97 (34%), Positives = 54/97 (55%)
Query: 98 QFITSIHLFHVFPDIEEGGLATYRAAIVQNQHLAHLAKRIGLEDFMLYAHGSDLCHEVEL 157
+ + + +LF FPD+ EG L R+A+V N+ LA LA+ +GL ++ G +
Sbjct: 33 ELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKGEEKSGGRLR 92
Query: 158 KHAMANCFEALMGALFLDGGIDVADQVFSSVLYKDNE 194
+A+ FEAL+GA++LDGG + A + +L E
Sbjct: 93 PKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIE 129
>gnl|CDD|197778 smart00535, RIBOc, Ribonuclease III family.
Length = 129
Score = 126 bits (320), Expect = 9e-35
Identities = 49/131 (37%), Positives = 72/131 (54%), Gaps = 9/131 (6%)
Query: 244 RLLARVFTTRSMGYTNLTLGSNQRLEFLGDTVLQLITSDYLYNHFPEHHEGHLSLLRSSL 303
LL R T S + N+RLEFLGD VL+L+ ++YLY +P+ EG LS LRS+L
Sbjct: 1 SLLLRALTHASYSNEH---EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSAL 57
Query: 304 VNNRTQSVVCNDIGMPFFANIINPKVDLKM-----KDRADLLEAFLGAMYIDKGMEACEQ 358
V+N T + + +G+ F + + K AD+ EA +GA+Y+D G+EA +
Sbjct: 58 VSNETLARLAKKLGLGEFI-RLGRGEAISGGRDKPKILADVFEALIGAIYLDSGLEAARE 116
Query: 359 FCKVCFFPRLQ 369
F + PRL
Sbjct: 117 FIRDLLGPRLD 127
Score = 108 bits (272), Expect = 4e-28
Identities = 32/97 (32%), Positives = 59/97 (60%)
Query: 93 GNNFSQFITSIHLFHVFPDIEEGGLATYRAAIVQNQHLAHLAKRIGLEDFMLYAHGSDLC 152
G+ + + + +L+ +PD+ EG L+ R+A+V N+ LA LAK++GL +F+ G +
Sbjct: 26 GDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRGEAIS 85
Query: 153 HEVELKHAMANCFEALMGALFLDGGIDVADQVFSSVL 189
+ +A+ FEAL+GA++LD G++ A + +L
Sbjct: 86 GGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLL 122
>gnl|CDD|216036 pfam00636, Ribonuclease_3, Ribonuclease III domain.
Length = 91
Score = 95.4 bits (238), Expect = 8e-24
Identities = 38/91 (41%), Positives = 54/91 (59%), Gaps = 4/91 (4%)
Query: 266 QRLEFLGDTVLQLITSDYLYNHFPEHHEGHLSLLRSSLVNNRTQSVVCNDIGMPFF---- 321
+RLEFLGD VL+L S+YLY FP+ EG L LRS+LV+N + + +G+ +
Sbjct: 1 ERLEFLGDAVLELYVSEYLYEKFPDLSEGELHRLRSALVSNEALAKLARKLGLDKYLREG 60
Query: 322 ANIINPKVDLKMKDRADLLEAFLGAMYIDKG 352
I + +K K AD EA +GA+Y+D G
Sbjct: 61 EGDIVKRASVKDKVLADAFEALIGALYLDGG 91
Score = 81.1 bits (201), Expect = 8e-19
Identities = 32/85 (37%), Positives = 51/85 (60%)
Query: 93 GNNFSQFITSIHLFHVFPDIEEGGLATYRAAIVQNQHLAHLAKRIGLEDFMLYAHGSDLC 152
G+ + S +L+ FPD+ EG L R+A+V N+ LA LA+++GL+ ++ G +
Sbjct: 7 GDAVLELYVSEYLYEKFPDLSEGELHRLRSALVSNEALAKLARKLGLDKYLREGEGDIVK 66
Query: 153 HEVELKHAMANCFEALMGALFLDGG 177
+A+ FEAL+GAL+LDGG
Sbjct: 67 RASVKDKVLADAFEALIGALYLDGG 91
>gnl|CDD|171444 PRK12371, PRK12371, ribonuclease III; Reviewed.
Length = 235
Score = 93.2 bits (232), Expect = 2e-21
Identities = 59/204 (28%), Positives = 91/204 (44%), Gaps = 46/204 (22%)
Query: 263 GSNQRLEFLGDTVLQLITSDYLYNHFPEHHEGHLSLLRSSLVNNRTQSVVCNDIGMPFFA 322
G+ +RLEFLGD VL L ++ L+ FP+ EG LS+ + LVN T + + ++IG+
Sbjct: 44 GNYERLEFLGDRVLGLCVAEMLFEAFPDASEGELSVRLNQLVNAETCAAIADEIGLH--- 100
Query: 323 NIINPKVDLK-------MKDRADLLEAFLGAMYIDKGMEACEQFCKVCFFPR-------- 367
++I D+K + RAD++EA + A+Y+D G+EA F + + R
Sbjct: 101 DLIRTGSDVKKLTGKRLLNVRADVVEALIAAIYLDGGLEAARPFIQRYWQKRALETDAAR 160
Query: 368 ------LQYFILNQEWNDPKSKLQQCCLTLRTLDGGEPDIPIYKVIEHVGPTNSRSYTVA 421
L QEW + + P+Y+V GP + +TV
Sbjct: 161 RDAKTEL------QEWAHAQFGVT----------------PVYRVDSRSGPDHDPRFTVE 198
Query: 422 VYFKNERLAKATGNSIQQAEMNAA 445
V K G S + AE AA
Sbjct: 199 VEVKGFAPETGEGRSKRAAEQVAA 222
Score = 49.3 bits (118), Expect = 1e-06
Identities = 29/81 (35%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 104 HLFHVFPDIEEGGLATYRAAIVQNQHLAHLAKRIGLEDFMLYAHGSDLCHEVELKHAM-- 161
LF FPD EG L+ +V + A +A IGL D + GSD+ ++ K +
Sbjct: 64 MLFEAFPDASEGELSVRLNQLVNAETCAAIADEIGLHDLI--RTGSDV-KKLTGKRLLNV 120
Query: 162 -ANCFEALMGALFLDGGIDVA 181
A+ EAL+ A++LDGG++ A
Sbjct: 121 RADVVEALIAAIYLDGGLEAA 141
>gnl|CDD|173181 PRK14718, PRK14718, ribonuclease III; Provisional.
Length = 467
Score = 81.4 bits (200), Expect = 2e-16
Identities = 75/259 (28%), Positives = 119/259 (45%), Gaps = 25/259 (9%)
Query: 224 PLLKQLQYLEYSSGVIFNHIRLLARVFTTRSMGYTNLTLGSNQRLEFLGDTVLQLITSDY 283
PL + L Y F + LL + T RS T+ N+RLEFLGD+VL +
Sbjct: 2 PLSQLESRLRYE----FRNAELLRQALTHRSHSATH-----NERLEFLGDSVLNCAVAAL 52
Query: 284 LYNHFPEHHEGHLSLLRSSLVNNRT-----QSVVCNDIGMPFFANIINPKVDLKMKDRAD 338
L+ F + EG LS +R++LV ++ Q++ +D G+ + + AD
Sbjct: 53 LFQRFGKLDEGDLSRVRANLVKQQSLYEIAQALNISD-GLRLGEGELRSGGFRRPSILAD 111
Query: 339 LLEAFLGAMYIDKGMEACEQFCKVCFFPRLQYFILNQEWNDPKSKLQQCCLTLRTLDGGE 398
EA +GA+++D G EA + K + P L + D K+ LQ+ L G +
Sbjct: 112 AFEAIIGAVFLDGGFEAAQGVIKRLYVPILDHIDPRTLGKDAKTLLQE------YLQGHK 165
Query: 399 PDIPIYKVIEHVGPTNSRSYTVAVYF-KNERLAKATGNSIQQAEMNAAKVALQKCPSICP 457
+P Y V+ G +++ + V K + +G S + AE AAK AL + ++ P
Sbjct: 166 IALPTYTVVATHGAAHNQQFEVECTVPKLDIKVSGSGASRRAAEQAAAKKALDEVTAVAP 225
Query: 458 QLDHQ-KRVIAKSIELQKH 475
L + KR +KS KH
Sbjct: 226 MLAAKPKR--SKSARGAKH 242
Score = 53.6 bits (128), Expect = 1e-07
Identities = 27/80 (33%), Positives = 43/80 (53%)
Query: 105 LFHVFPDIEEGGLATYRAAIVQNQHLAHLAKRIGLEDFMLYAHGSDLCHEVELKHAMANC 164
LF F ++EG L+ RA +V+ Q L +A+ + + D + G +A+
Sbjct: 53 LFQRFGKLDEGDLSRVRANLVKQQSLYEIAQALNISDGLRLGEGELRSGGFRRPSILADA 112
Query: 165 FEALMGALFLDGGIDVADQV 184
FEA++GA+FLDGG + A V
Sbjct: 113 FEAIIGAVFLDGGFEAAQGV 132
>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 = 69.6 bits (171), Expect = 4e-15
Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 379 DPKSKLQQCCLTLRTLDGGEPDIPIYKVIEHVGPTNSRSYTVAVYFKNERLAKATGNSIQ 438
+PKS LQ+ +P Y+++E GP ++ +TV V + + G+S +
Sbjct: 1 NPKSLLQELAQKRG------KPLPEYELVEEEGPDHAPRFTVEVTVGGKITGEGEGSSKK 54
Query: 439 QAEMNAAKVALQK 451
+A+ NAA+ AL+K
Sbjct: 55 EAKQNAAEAALRK 67
>gnl|CDD|237081 PRK12372, PRK12372, ribonuclease III; Reviewed.
Length = 413
Score = 75.3 bits (185), Expect = 2e-14
Identities = 77/269 (28%), Positives = 121/269 (44%), Gaps = 44/269 (16%)
Query: 222 QSPLLKQLQYLEYSSGVIFNHIRLLARVFTTRSMGYTNLTLGSNQRLEFLGDTVLQLITS 281
S L +L+Y F + LL + T RS T+ N+RLEFLGD+VL +
Sbjct: 3 LSQLESRLRYE-------FRNAELLRQALTHRSHSATH-----NERLEFLGDSVLNCAVA 50
Query: 282 DYLYNHFPEHHEGHLSLLRSSLVNNRTQSVVCNDIGMPFFANIINPKVDLKMKD------ 335
L+ F + EG LS +R++LV + QS+ +I A +N L++ +
Sbjct: 51 ALLFQRFGKLDEGDLSRVRANLV--KQQSLY--EI-----AQALNISEGLRLGEGELRSG 101
Query: 336 -------RADLLEAFLGAMYIDKGMEACEQFCKVCFFPRLQYFILNQEWNDPKSKLQQCC 388
AD EA +GA+++D G EA + K + P L + D K+ LQ+
Sbjct: 102 GFRRPSILADAFEAIIGAVFLDGGFEAAQGVIKRLYVPILDHIDPRTLGKDAKTLLQE-- 159
Query: 389 LTLRTLDGGEPDIPIYKVIEHVGPTNSRSYTVAVYF-KNERLAKATGNSIQQAEMNAAKV 447
L G + +P Y V+ G +++ + V K + +G S + AE AAK
Sbjct: 160 ----YLQGHKIALPTYTVVATHGAAHNQQFEVECTVPKLDVKVSGSGASRRAAEQAAAKK 215
Query: 448 ALQKCPSICPQLDHQ-KRVIAKSIELQKH 475
AL + + P L + KR +K+ KH
Sbjct: 216 ALDEVMAAAPMLAAKPKR--SKNARASKH 242
Score = 51.4 bits (123), Expect = 7e-07
Identities = 28/87 (32%), Positives = 46/87 (52%), Gaps = 14/87 (16%)
Query: 105 LFHVFPDIEEGGLATYRAAIVQNQHLAHLAKRIGLEDFMLYAHGSDLCHEVELKHA---- 160
LF F ++EG L+ RA +V+ Q L +A+ + + + + G EL+
Sbjct: 53 LFQRFGKLDEGDLSRVRANLVKQQSLYEIAQALNISEGLRLGEG-------ELRSGGFRR 105
Query: 161 ---MANCFEALMGALFLDGGIDVADQV 184
+A+ FEA++GA+FLDGG + A V
Sbjct: 106 PSILADAFEAIIGAVFLDGGFEAAQGV 132
>gnl|CDD|214634 smart00358, DSRM, Double-stranded RNA binding motif.
Length = 67
Score = 67.3 bits (165), Expect = 3e-14
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 7/72 (9%)
Query: 380 PKSKLQQCCLTLRTLDGGEPDIPIYKVIEHVGPTNSRSYTVAVYFKNERLAKATGNSIQQ 439
PKS LQ+ + P Y++++ GP ++ +TV V +R + G+S ++
Sbjct: 1 PKSLLQELAQKRKL-------PPEYELVKEEGPDHAPRFTVTVKVGGKRTGEGEGSSKKE 53
Query: 440 AEMNAAKVALQK 451
A+ AA+ AL+
Sbjct: 54 AKQRAAEAALRS 65
>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 = 62.7 bits (153), Expect = 1e-12
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 380 PKSKLQQCCLTLRTLDGGEPDIPIYKVIEHVGPTNSRSYTVAVYFKNERLAKATGNSIQQ 439
PKS LQ+ C P Y+ +E GP +S ++TV V ++ TG+S ++
Sbjct: 1 PKSLLQELCQKKGPK-------PPYEYVEEEGPPHSPTFTVTVTVNGKKYGTGTGSSKKE 53
Query: 440 AEMNAAKVALQK 451
A+ AA+ ALQK
Sbjct: 54 AKQLAAEKALQK 65
>gnl|CDD|222987 PHA03103, PHA03103, double-strand RNA-binding protein; Provisional.
Length = 183
Score = 31.3 bits (71), Expect = 0.84
Identities = 15/45 (33%), Positives = 28/45 (62%)
Query: 407 IEHVGPTNSRSYTVAVYFKNERLAKATGNSIQQAEMNAAKVALQK 451
I GP++S ++T +V + A G++ ++A+ NAAK+A+ K
Sbjct: 130 ITSSGPSHSPTFTASVIISGIKFKPAIGSTKKEAKNNAAKLAMDK 174
>gnl|CDD|220970 pfam11077, DUF2616, Protein of unknown function (DUF2616). This
cysteine-rich family is expressed by the double-stranded
Nucleopolyhedrovirus, a member of the Baculoviridae
family of dsDNA viruses. The function is not known.
Length = 172
Score = 30.0 bits (68), Expect = 1.9
Identities = 9/20 (45%), Positives = 11/20 (55%), Gaps = 1/20 (5%)
Query: 358 QFCKVCFFPRLQYFILNQEW 377
FCK CFFP I ++E
Sbjct: 68 LFCKQCFFPLCDLGI-DEEL 86
>gnl|CDD|220496 pfam09972, DUF2207, Predicted membrane protein (DUF2207). This
domain, found in various hypothetical bacterial
proteins, has no known function.
Length = 503
Score = 30.8 bits (70), Expect = 2.1
Identities = 5/60 (8%), Positives = 17/60 (28%), Gaps = 8/60 (13%)
Query: 55 FLVTWASQAY-CNYTIFVGVVLFVISVIQIYRMYMY-------IHKGNNFSQFITSIHLF 106
F++ A I + + + +++ + + F ++ I
Sbjct: 412 FILISLVLAALVLLAIVLVIGSVIAAILPRKLFGRWTPEGAEEYLEWKGFKNYLKDISRL 471
>gnl|CDD|173976 cd08211, RuBisCO_large_II, Ribulose bisphosphate carboxylase large
chain, Form II. Ribulose bisphosphate carboxylase
(Rubisco) plays an important role in the Calvin
reductive pentose phosphate pathway. It catalyzes the
primary CO2 fixation step. Rubisco is activated by
carbamylation of an active site lysine, stabilized by a
divalent cation, which then catalyzes the proton
abstraction from the substrate ribulose 1,5 bisphosphate
(RuBP) and leads to the formation of two molecules of
3-phosphoglycerate. Members of the Rubisco family can be
divided into 4 subgroups, Form I-IV , which differ in
their taxonomic distribution and subunit composition.
Form II is mainly found in bacteria, and forms large
subunit oligomers (dimers, tetramers, etc.) that do not
include small subunits.
Length = 439
Score = 30.5 bits (69), Expect = 2.5
Identities = 21/84 (25%), Positives = 30/84 (35%), Gaps = 16/84 (19%)
Query: 412 PTNSRSYTVAVYFKNERLAKATGNSIQQAEMNAAKVALQKCPSICPQLDHQKRVIAKSIE 471
P + R YT V K RL A+G I M K+ + + +VIA IE
Sbjct: 296 PQSKRGYTAFVLSKMARLQGASG--IHTGTMGFGKM----------EGESSDKVIAYMIE 343
Query: 472 LQKHEGIFGAWASFSCWVGLGVCA 495
+ +G W G+
Sbjct: 344 RDEAQGPL----FNQKWYGMKPTT 363
>gnl|CDD|233663 TIGR01974, NDH_I_L, proton-translocating NADH-quinone
oxidoreductase, chain L. This model describes the 12th
(based on E. coli) structural gene, L, of bacterial NADH
dehydrogenase I, as well as chain 5 of the corresponding
mitochondrial complex I and subunit 5 (or F) of the
chloroplast NAD(P)H-plastoquinone dehydrogenase complex
[Energy metabolism, Electron transport].
Length = 609
Score = 30.3 bits (69), Expect = 2.9
Identities = 21/95 (22%), Positives = 38/95 (40%), Gaps = 5/95 (5%)
Query: 12 IAGYVIAWMLSLCIIIPMTLHQDEFKGHCLLFSTGAWQEADGQFLVTWASQAYCNYTIFV 71
I ++ LS + + L+ + LF W G F V + + +
Sbjct: 34 IGSVGLSAALSAFVFVDFFLNGEGEAFTQSLFP---WISVGG-FQVDFGLRLDGLSLTML 89
Query: 72 GVVLFVISVIQIYRMYMYIHKGNNFSQFITSIHLF 106
VV V S++ IY + Y+ +S+F ++LF
Sbjct: 90 VVVTGVGSLVHIYSIG-YMAHDEGYSRFFAYLNLF 123
>gnl|CDD|183911 PRK13239, PRK13239, alkylmercury lyase; Provisional.
Length = 206
Score = 29.6 bits (67), Expect = 3.1
Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 7/46 (15%)
Query: 427 ERLAKATGNSIQQAEMNAAKVALQKCPSICPQLDHQKRVIAKSIEL 472
LA A G +++ E L+ P + D R+I + L
Sbjct: 40 TTLAAALGWPVEEVEA-----VLEAMPDT--EYDEDGRIIGYGLTL 78
>gnl|CDD|234517 TIGR04238, seadorna_dsRNA, seadornavirus double-stranded
RNA-binding protein. This protein family occurs in the
seadornavirus virus group, with an N-terminal domain for
binding double-stranded RNA, is designated VP12 in Banna
virus, VP8 in Kadipiro virus, and VP11 in Liao ning
virus.
Length = 201
Score = 29.5 bits (66), Expect = 3.5
Identities = 15/67 (22%), Positives = 31/67 (46%), Gaps = 7/67 (10%)
Query: 379 DPKSKLQQCCLTLRTLDGGEPDIPIYKVIEHVGPTNSRSYTVAVYFKNERLAKATGNSIQ 438
+ LQ+ + G +P+Y+ + GP ++ ++T+ + N+ +S +
Sbjct: 1 NVVGMLQELAVKR-----GLE-LPVYEKVGKEGPDHAPTFTIKLTA-NDIEVIEAASSKK 53
Query: 439 QAEMNAA 445
QAE AA
Sbjct: 54 QAEKLAA 60
>gnl|CDD|185724 cd08983, GH43_4, Glycosyl hydrolase family 43. This glycosyl
hydrolase family 43 (GH43) includes enzymes with
beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC
3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-),
alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase
(EC 3.2.1.99), xylanase (EC 3.2.1.8),
endo-alpha-L-arabinanase and galactan
1,3-beta-galactosidase (EC 3.2.1.145) activities. These
are inverting enzymes (i.e. they invert the
stereochemistry of the anomeric carbon atom of the
substrate) that have an aspartate as the catalytic
general base, a glutamate as the catalytic general acid
and another aspartate that is responsible for pKa
modulation and orienting the catalytic acid. Many of the
enzymes in this family display both
alpha-L-arabinofuranosidase and beta-D-xylosidase
activity using aryl-glycosides as substrates. A common
structural feature of GH43 enzymes is a 5-bladed
beta-propeller domain that contains the catalytic acid
and catalytic base. A long V-shaped groove, partially
enclosed at one end, forms a single extended
substrate-binding surface across the face of the
propeller.
Length = 276
Score = 29.6 bits (67), Expect = 4.0
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 48 WQEADGQFLVTWASQAYCNYTIFVGVVLFVI 78
W GQ++V W+S+ Y N F L+
Sbjct: 85 WDAERGQYVVYWSSRLYDNTGGFYNYRLYAT 115
>gnl|CDD|217471 pfam03278, IpaB_EvcA, IpaB/EvcA family. This family includes IpaB,
which is an invasion plasmid antigen from Shigella, as
well as EvcA from E. coli. Members of this family seem
to be involved in pathogenicity of some enterobacteria.
However the exact function of this component is not
clear.
Length = 147
Score = 28.5 bits (64), Expect = 5.3
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 304 VNNRTQSVVCNDIGMPFFANIINPKVDLK 332
V N TQ+ + N + FF NP +D+K
Sbjct: 114 VKNNTQTKMANLVSDQFFEKNFNPDIDIK 142
>gnl|CDD|214444 MTH00165, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 573
Score = 29.0 bits (66), Expect = 8.7
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 55 FLVTWASQAYCNYTIFVGVVLFVISVIQIYRMYMYIHKGNNFSQFITSIHLF 106
FL W S +F+ VLF+ S++ Y Y+ N ++FI + LF
Sbjct: 50 FLFDWMS------LLFMSFVLFISSMVIYYSKS-YMSGDKNINRFIYLVLLF 94
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 0.138 0.426
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,994,648
Number of extensions: 2718270
Number of successful extensions: 2818
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2793
Number of HSP's successfully gapped: 42
Length of query: 550
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 448
Effective length of database: 6,413,494
Effective search space: 2873245312
Effective search space used: 2873245312
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 (21.6 bits)
S2: 61 (27.2 bits)