RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3979
(286 letters)
>gnl|CDD|223644 COG0571, Rnc, dsRNA-specific ribonuclease [Transcription].
Length = 235
Score = 111 bits (280), Expect = 1e-29
Identities = 38/95 (40%), Positives = 61/95 (64%), Gaps = 1/95 (1%)
Query: 114 TQLEKRINYTFQDKSFLLQALSHPTY-NANRITTSYQRLEFLGDAIIDFLVTAYLYENFS 172
LEK++ YTF+DK L QAL+H +Y N ++ + +RLEFLGDA++ +V YL++ +
Sbjct: 9 EALEKKLGYTFKDKELLEQALTHRSYANEHKAVENNERLEFLGDAVLGLVVAEYLFKKYP 68
Query: 173 HLSPGEISDIRSAMVNNVTFASYAVRLDLHKHLLH 207
+L GE+S +R+A+V+ + A A L L +L
Sbjct: 69 NLPEGELSKLRAALVSEESLAEIARELGLGDYLRL 103
Score = 27.6 bits (62), Expect = 6.8
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 13/53 (24%)
Query: 33 YNFLDRIKLG-----------DKVVADVVESLTG-VYLRSCGIEGAMLFLQAL 73
D ++LG + ++AD E+L G +YL S G+E A F+ L
Sbjct: 95 LGLGDYLRLGKGEEKSGGRRRESILADAFEALIGAIYLDS-GLEAARKFILKL 146
>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 = 108 bits (272), Expect = 2e-28
Identities = 41/93 (44%), Positives = 61/93 (65%), Gaps = 2/93 (2%)
Query: 116 LEKRINYTFQDKSFLLQALSHPTYN--ANRITTSYQRLEFLGDAIIDFLVTAYLYENFSH 173
LEKR+ Y F++K L QAL+H +Y ++ + +RLEFLGDA++ +V YL++NF
Sbjct: 1 LEKRLGYKFKNKELLEQALTHSSYANEHHKGVKNNERLEFLGDAVLGLVVAEYLFKNFPD 60
Query: 174 LSPGEISDIRSAMVNNVTFASYAVRLDLHKHLL 206
LS GE+S +R+A+V+ + A A L L K LL
Sbjct: 61 LSEGELSKLRAALVSEESLAEVARELGLGKFLL 93
>gnl|CDD|234633 PRK00102, rnc, ribonuclease III; Reviewed.
Length = 229
Score = 108 bits (272), Expect = 2e-28
Identities = 38/94 (40%), Positives = 63/94 (67%), Gaps = 1/94 (1%)
Query: 114 TQLEKRINYTFQDKSFLLQALSHPTY-NANRITTSYQRLEFLGDAIIDFLVTAYLYENFS 172
+L+K++ YTF+D L+QAL+H +Y N N+ +RLEFLGDA+++ +V+ YL++ F
Sbjct: 6 EELQKKLGYTFKDPELLIQALTHRSYANENKGLKHNERLEFLGDAVLELVVSEYLFKRFP 65
Query: 173 HLSPGEISDIRSAMVNNVTFASYAVRLDLHKHLL 206
L G++S +R+A+V + A A L L ++LL
Sbjct: 66 DLDEGDLSKLRAALVREESLAEIARELGLGEYLL 99
>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 = 105 bits (263), Expect = 3e-28
Identities = 36/85 (42%), Positives = 54/85 (63%)
Query: 128 SFLLQALSHPTYNANRITTSYQRLEFLGDAIIDFLVTAYLYENFSHLSPGEISDIRSAMV 187
S LL+AL+HP+Y + +RLEFLGDA+++ +VT YL++ F LS G+++ +RSA+V
Sbjct: 1 SLLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALV 60
Query: 188 NNVTFASYAVRLDLHKHLLHDSPRL 212
+N T A A L L K+L
Sbjct: 61 SNETLARLARELGLGKYLRLGKGEE 85
Score = 29.9 bits (68), Expect = 0.61
Identities = 14/38 (36%), Positives = 18/38 (47%)
Query: 36 LDRIKLGDKVVADVVESLTGVYLRSCGIEGAMLFLQAL 73
+L K++ADV E+L G G E A FL L
Sbjct: 86 KSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRL 123
>gnl|CDD|197778 smart00535, RIBOc, Ribonuclease III family.
Length = 129
Score = 89.6 bits (223), Expect = 2e-22
Identities = 34/91 (37%), Positives = 53/91 (58%), Gaps = 2/91 (2%)
Query: 128 SFLLQALSHPTYNANRITTSYQRLEFLGDAIIDFLVTAYLYENFSHLSPGEISDIRSAMV 187
S LL+AL+H +Y+ +RLEFLGDA+++ +VT YLY+ + LS G++S +RSA+V
Sbjct: 1 SLLLRALTHASYSNEHE--HNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALV 58
Query: 188 NNVTFASYAVRLDLHKHLLHDSPRLYENVTR 218
+N T A A +L L + +
Sbjct: 59 SNETLARLAKKLGLGEFIRLGRGEAISGGRD 89
>gnl|CDD|216036 pfam00636, Ribonuclease_3, Ribonuclease III domain.
Length = 91
Score = 76.9 bits (190), Expect = 4e-18
Identities = 29/70 (41%), Positives = 43/70 (61%)
Query: 149 QRLEFLGDAIIDFLVTAYLYENFSHLSPGEISDIRSAMVNNVTFASYAVRLDLHKHLLHD 208
+RLEFLGDA+++ V+ YLYE F LS GE+ +RSA+V+N A A +L L K+L
Sbjct: 1 ERLEFLGDAVLELYVSEYLYEKFPDLSEGELHRLRSALVSNEALAKLARKLGLDKYLREG 60
Query: 209 SPRLYENVTR 218
+ + +
Sbjct: 61 EGDIVKRASV 70
>gnl|CDD|171444 PRK12371, PRK12371, ribonuclease III; Reviewed.
Length = 235
Score = 65.9 bits (161), Expect = 1e-12
Identities = 33/88 (37%), Positives = 51/88 (57%), Gaps = 1/88 (1%)
Query: 115 QLEKRINYTFQDKSFLLQALSHPTYNANRITTSYQRLEFLGDAIIDFLVTAYLYENFSHL 174
LE+R + F +K L +AL+H + A++ +Y+RLEFLGD ++ V L+E F
Sbjct: 14 ILEERTGHRFANKERLERALTHSSARASK-QGNYERLEFLGDRVLGLCVAEMLFEAFPDA 72
Query: 175 SPGEISDIRSAMVNNVTFASYAVRLDLH 202
S GE+S + +VN T A+ A + LH
Sbjct: 73 SEGELSVRLNQLVNAETCAAIADEIGLH 100
>gnl|CDD|173181 PRK14718, PRK14718, ribonuclease III; Provisional.
Length = 467
Score = 63.3 bits (153), Expect = 2e-11
Identities = 32/92 (34%), Positives = 55/92 (59%), Gaps = 4/92 (4%)
Query: 114 TQLEKRINYTFQDKSFLLQALSHPTYNANRITTSYQRLEFLGDAIIDFLVTAYLYENFSH 173
+QLE R+ Y F++ L QAL+H +++A T +RLEFLGD++++ V A L++ F
Sbjct: 4 SQLESRLRYEFRNAELLRQALTHRSHSA----THNERLEFLGDSVLNCAVAALLFQRFGK 59
Query: 174 LSPGEISDIRSAMVNNVTFASYAVRLDLHKHL 205
L G++S +R+ +V + A L++ L
Sbjct: 60 LDEGDLSRVRANLVKQQSLYEIAQALNISDGL 91
>gnl|CDD|237081 PRK12372, PRK12372, ribonuclease III; Reviewed.
Length = 413
Score = 62.6 bits (152), Expect = 4e-11
Identities = 29/74 (39%), Positives = 49/74 (66%), Gaps = 4/74 (5%)
Query: 114 TQLEKRINYTFQDKSFLLQALSHPTYNANRITTSYQRLEFLGDAIIDFLVTAYLYENFSH 173
+QLE R+ Y F++ L QAL+H +++A T +RLEFLGD++++ V A L++ F
Sbjct: 4 SQLESRLRYEFRNAELLRQALTHRSHSA----THNERLEFLGDSVLNCAVAALLFQRFGK 59
Query: 174 LSPGEISDIRSAMV 187
L G++S +R+ +V
Sbjct: 60 LDEGDLSRVRANLV 73
>gnl|CDD|219424 pfam07485, DUF1529, Domain of Unknown Function (DUF1259). This
family is the lppY/lpqO homologue family.
Length = 123
Score = 29.5 bits (67), Expect = 0.98
Identities = 7/13 (53%), Positives = 8/13 (61%)
Query: 201 LHKHLLHDSPRLY 213
LH H L + PRL
Sbjct: 87 LHNHWLFEQPRLM 99
>gnl|CDD|232918 TIGR00321, dhys, deoxyhypusine synthase. Deoxyhypusine synthase is
responsible for the first step in creating hypusine.
Hypusine is a modified amino acid found in eukaryotes
and in archaea in their respective forms of initiation
factor 5A. Its presence is confirmed in archaeal genera
Pyrococcus (PMID:12761201), Sulfolobus, Halobacterium,
and Haloferax (PMID:10648545), but in an older report
was not detected in Methanococcus voltae (J Biol Chem
1987 Dec 5;262(34):16585-9). This family of apparent
orthologs has an unusual UPGMA difference tree, in which
the members from the archaea M. jannaschii and P.
horikoshii cluster with the known eukaryotic
deoxyhypusine synthases. Separated by a fairly deep
branch, although still strongly related, is a small
cluster of proteins from Methanobacterium
thermoautotrophicum and Archeoglobus fulgidus, the
latter of which has two [Protein fate, Protein
modification and repair].
Length = 301
Score = 30.1 bits (68), Expect = 1.4
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 42 GDKVVADVVESLTGVYLRSCGIEGAMLFLQALN 74
G + D++E+L +L ++ L + +N
Sbjct: 81 GANLEHDLIEALGPTHLGDFAVDDKKLREEGIN 113
>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein.
Length = 306
Score = 29.4 bits (66), Expect = 1.9
Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 15/76 (19%)
Query: 213 YENVTRFAQNQEARNH-EISDEEEEEEEEEGIVRCLIFFLIEEKDVQTDVYGRVVEYV-- 269
Y N F ++ E R IS++ EEEE EEG E+D + + E+
Sbjct: 57 YGNPDPFGEDDEGRIEVRISEDGEEEEVEEG-----------EEDEEEEGEEESEEFEPL 105
Query: 270 -DVPKALGDVFEALVE 284
D P+ L + E L E
Sbjct: 106 GDTPEELTEASEQLEE 121
>gnl|CDD|145208 pfam01916, DS, Deoxyhypusine synthase. Eukaryotic initiation
factor 5A (eIF-5A) contains an unusual amino acid,
hypusine [N epsilon-(4-aminobutyl-2-hydroxy)lysine]. The
first step in the post-translational formation of
hypusine is catalyzed by the enzyme deoxyhypusine
synthase (DS) EC:1.1.1.249. The modified version of
eIF-5A, and DS, are required for eukaryotic cell
proliferation.
Length = 297
Score = 29.3 bits (66), Expect = 2.2
Identities = 7/30 (23%), Positives = 14/30 (46%)
Query: 45 VVADVVESLTGVYLRSCGIEGAMLFLQALN 74
V D+++ L YL ++ L + +N
Sbjct: 76 VEEDLIKCLGPTYLGDFEVDDKELREEGIN 105
>gnl|CDD|235536 PRK05627, PRK05627, bifunctional riboflavin kinase/FMN
adenylyltransferase; Reviewed.
Length = 305
Score = 29.0 bits (66), Expect = 2.5
Identities = 10/36 (27%), Positives = 18/36 (50%)
Query: 143 RITTSYQRLEFLGDAIIDFLVTAYLYENFSHLSPGE 178
R+T + E L + +D+++ E F+ LS E
Sbjct: 68 RLTPLRDKAELLAELGVDYVLVLPFDEEFAKLSAEE 103
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 29.2 bits (65), Expect = 2.9
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 220 AQNQEARNHEISDEEEEEEEEE 241
++ +E E +EEEEEEEEE
Sbjct: 863 SEEEEEEEEEEEEEEEEEEEEE 884
>gnl|CDD|216868 pfam02084, Bindin, Bindin.
Length = 239
Score = 28.7 bits (64), Expect = 3.3
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 201 LHKHLLHDSPRLYENVTRFAQNQEARNHEISDEEEEEEEEE 241
L +HL H S L N+ + E R +S +EEEEEEE
Sbjct: 131 LLRHLRHHS-NLLANIG----DPEVREQVLSAMQEEEEEEE 166
>gnl|CDD|132208 TIGR03164, UHCUDC, OHCU decarboxylase. Previously thought to only
proceed spontaneously, the decarboxylation of
2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU)
has been recently been shown to be catalyzed by this
enzyme in Mus musculus. Homologs of this enzyme are
found adjacent to and fused with uricase in a number of
prokaryotes and are represented by this model.
Length = 157
Score = 27.7 bits (62), Expect = 4.8
Identities = 18/69 (26%), Positives = 27/69 (39%), Gaps = 14/69 (20%)
Query: 179 ISDIRSAMVNNVTFASYAVRLDL-HKHLLHDSPRLYENVTRFAQNQEARNHEISDEEEEE 237
I D+ +AMV V AS +L L H P L + A E++ E E
Sbjct: 33 IEDLHAAMVGAVRAASPEQQLALIRAH-----PDL--------AGKLAVAGELTAESTSE 79
Query: 238 EEEEGIVRC 246
+ G+ +
Sbjct: 80 QASAGLDQL 88
>gnl|CDD|226258 COG3735, COG3735, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 299
Score = 28.1 bits (63), Expect = 6.0
Identities = 15/67 (22%), Positives = 28/67 (41%), Gaps = 13/67 (19%)
Query: 5 SNLDFDLYQDPTEDGKKV---SSPEK-------LPSSSY--NFLDRIKLGDKVVADVVES 52
+D+ L Q K + + E+ LP +D + LGD AD++E+
Sbjct: 156 YGIDYQLLQAAKAQNKPILGLETAEEQLAALASLPLDFGIELLIDTLALGDT-NADLLET 214
Query: 53 LTGVYLR 59
+ ++L
Sbjct: 215 MIDLWLN 221
>gnl|CDD|238355 cd00659, Topo_IB_C, DNA topoisomerase IB, C-terminal catalytic
domain. Topoisomerase I promotes the relaxation of both
positive and negative DNA superhelical tension by
introducing a transient single-stranded break in duplex
DNA. This function is vital for the processes of
replication, transcription, and recombination. Unlike
Topo IA enzymes, Topo IB enzymes do not require a
single-stranded region of DNA or metal ions for their
function. The type IB family of DNA topoisomerases
includes eukaryotic nuclear topoisomerase I,
topoisomerases of poxviruses and bacterial versions of
Topo IB. They belong to the superfamily of DNA
breaking-rejoining enzymes, which share the same fold in
their C-terminal catalytic domain and the overall
reaction mechanism with tyrosine recombinases. The
C-terminal catalytic domain in topoisomerases is linked
to a divergent N-terminal domain that shows no sequence
or structure similarity to the N-terminal domains of
tyrosine recombinases.
Length = 218
Score = 27.2 bits (61), Expect = 9.8
Identities = 10/45 (22%), Positives = 19/45 (42%), Gaps = 7/45 (15%)
Query: 187 VNNVTFASYAVRLDL-------HKHLLHDSPRLYENVTRFAQNQE 224
+VT VR D +++ + PRL++N+ +F
Sbjct: 76 KEHVTLKPNVVRFDFLGKDSIRYENEVEVEPRLFKNLRKFLDKLP 120
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 0.137 0.391
Gapped
Lambda K H
0.267 0.0887 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,170,193
Number of extensions: 1487716
Number of successful extensions: 2069
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2039
Number of HSP's successfully gapped: 38
Length of query: 286
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 190
Effective length of database: 6,679,618
Effective search space: 1269127420
Effective search space used: 1269127420
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: 58 (25.8 bits)