RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11598
(457 letters)
>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse
transcriptases. Ribonuclease H (RNase H) is classified
into two families, type 1 (prokaryotic RNase HI,
eukaryotic RNase H1 and viral RNase H) and type 2
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2). Ribonuclease HI (RNase HI) is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is widely present
in various organisms, including bacteria, archaea and
eukaryotes. RNase HI has also been observed as an
adjunct domain to the reverse transcriptase gene in
retroviruses, long-term repeat (LTR)-bearing
retrotransposons and non-LTR retrotransposons. RNase HI
in LTR retrotransposons perform degradation of the
original RNA template, generation of a polypurine tract
(the primer for plus-strand DNA synthesis), and final
removal of RNA primers from newly synthesized minus and
plus strands. The catalytic residues for RNase H
enzymatic activity, three aspartatic acids and one
glutamatic acid residue (DEDD), are unvaried across all
RNase H domains. The position of the RNase domain of
non-LTR and LTR transposons is at the carboxyl terminal
of the reverse transcriptase (RT) domain and their RNase
domains group together, indicating a common evolutionary
origin. Many non-LTR transposons have lost the RNase
domain because their activity is at the nucleus and
cellular RNase may suffice; however LTR retotransposons
always encode their own RNase domain because it requires
RNase activity in RNA-protein particles in the
cytoplasm. RNase H inhibitors have been explored as an
anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 128
Score = 72.7 bits (179), Expect = 1e-15
Identities = 28/105 (26%), Positives = 47/105 (44%), Gaps = 8/105 (7%)
Query: 264 CYTDGSKNDNFTGGA---YILNETIEQFQLNQIASIYTAELMAIDLCLNAILTYVQNNFC 320
YTDGSK + TG ++L S++ AEL+AI L L +
Sbjct: 2 IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRA-- 59
Query: 321 FKDFVICSDSKSSLQALK--FNLNDSFKRWEEIWTQNAVLGRQLR 363
+ I SDS+++L+AL+ + + R + + A G ++R
Sbjct: 60 -RKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVR 103
>gnl|CDD|215695 pfam00075, RNase_H, RNase H. RNase H digests the RNA strand of an
RNA/DNA hybrid. Important enzyme in retroviral
replication cycle, and often found as a domain
associated with reverse transcriptases. Structure is a
mixed alpha+beta fold with three a/b/a layers.
Length = 126
Score = 39.5 bits (93), Expect = 5e-04
Identities = 21/96 (21%), Positives = 36/96 (37%), Gaps = 13/96 (13%)
Query: 262 ILCYTDGS--KNDNFTGGAYILNETIEQFQLNQIASIYTAELMAIDLCLNAILTYVQNNF 319
+ YTDGS N G Y+ + ++ + + AEL+A+ L A+
Sbjct: 4 VTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALEALSG------ 57
Query: 320 CFKDFVICSDSKSSLQA--LKFNLNDSFKRW-EEIW 352
+ I +DS+ + + K EIW
Sbjct: 58 --QKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIW 91
>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 = 38.9 bits (91), Expect = 0.001
Identities = 20/95 (21%), Positives = 32/95 (33%), Gaps = 12/95 (12%)
Query: 265 YTDGSKNDNF---TGGAYILNETIE----QFQLNQIASIYTAELMAIDLCLNAILTYVQN 317
TDGS N G + + A+ AEL+A+ L A+ +
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLAL---LEALELALDL 57
Query: 318 NFCFKDFVICSDSKSSLQALKFNLNDSFKRWEEIW 352
K +I +DSK + + K +W
Sbjct: 58 GL--KKLIIETDSKYVVDLINSWSKGWKKNNLLLW 90
>gnl|CDD|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao 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 eukaryote. 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. Bel/Pao family has been described only in
metazoan genomes. RNase H inhibitors have been explored
as an anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 135
Score = 38.4 bits (90), Expect = 0.001
Identities = 33/151 (21%), Positives = 47/151 (31%), Gaps = 34/151 (22%)
Query: 263 LCYTDGSKNDNFTGGA-YILNETIEQFQLNQIASIYTAELMAIDLCLNAILTYVQNNFCF 321
+TDGS G A + +E L S AEL+A+ + A+
Sbjct: 1 TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIAL---IRALEL-----AKG 52
Query: 322 KDFVICSDSKSSLQALKFNLNDSFKRWEEIWTQNAVLGRQLRQIKTDVRKWKSSNRNIRQ 381
K I +DS + L E IW + L T I Q
Sbjct: 53 KPVNIYTDSAYAFGIL--------HALETIWKERGFL--------TGKPIA--LASLILQ 94
Query: 382 EEVVLCR---LRIGHCLATHKHLLERKDPPA 409
+ + R + + H A H L P A
Sbjct: 95 LQKAIQRPKPVAVIHIRA-HSGL---PGPLA 121
>gnl|CDD|151410 pfam10963, DUF2765, Protein of unknown function (DUF2765). This
family of proteins has no known function.
Length = 82
Score = 29.9 bits (68), Expect = 0.55
Identities = 12/38 (31%), Positives = 20/38 (52%)
Query: 211 VRCVIKQQKEEPQWLLHQPKVTMLISGKKDEELPSEIN 248
+R V +QKE + LL P M ++G +EE ++
Sbjct: 40 MRTVDPEQKEALKELLEVPGAAMQLAGAVNEEYAPDLE 77
>gnl|CDD|237339 PRK13299, PRK13299, tRNA CCA-pyrophosphorylase; Provisional.
Length = 394
Score = 30.6 bits (70), Expect = 2.0
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 328 SDSKSSLQALKFNLNDSFKRWEEIWTQNAVLGRQLRQIKTDVRKWKSSNRNIRQ 381
+ +L L L SF+ E+ W ++ ++ IK+ ++ WK SN+ I+
Sbjct: 229 KGKEENLLKLTQLLWFSFETSEQAWA-ALLISLKIENIKSFLKAWKLSNKFIKD 281
>gnl|CDD|131035 TIGR01980, sufB, FeS assembly protein SufB. This protein, SufB,
forms a cytosolic complex SufBCD. This complex enhances
the cysteine desulfurase of SufSE. The system, together
with SufA, is believed to act in iron-sulfur cluster
formation during oxidative stress. Note that SufC
belongs to the family of ABC transporter ATP binding
proteins, so this protein, encoded by an adjacent gene,
has often been annotated as a transporter component
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 448
Score = 30.4 bits (69), Expect = 2.1
Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 28/90 (31%)
Query: 172 EVRCVIKQQKEEPQWLLHQPRYPLNIRLRAEAMDDYKLEVRCVIKQQKEEPQWLLHQPKV 231
EV I ++K EP W+ L+ RLRA LE + ++ P W +
Sbjct: 24 EVVEEISEKKGEPDWM-------LDFRLRA-------LE----LFEKMPMPTWGPDLSGI 65
Query: 232 TM--LI-----SGKKD---EELPSEINNKY 251
++ KK +E+P EI + +
Sbjct: 66 DYEDIVYYSKPDKKKATSWDEVPDEIKDTF 95
>gnl|CDD|185210 PRK15310, PRK15310, fimbrial outer membrane usher protein TcfC;
Provisional.
Length = 895
Score = 30.4 bits (68), Expect = 2.4
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 179 QQKEEPQWLLHQP---RYPLNIRLRAEAMDDYKLEVRCVIKQQKEEPQWLLHQPKVTMLI 235
+ KE WLL + R P+++ R + M +VRC + PQ L P+V L+
Sbjct: 824 EHKESSLWLLSKNRILRCPMSVHKRRDVMQVVG-DVRCELSDVDALPQALQISPRVIRLL 882
Query: 236 S 236
+
Sbjct: 883 N 883
>gnl|CDD|225323 COG2603, COG2603, Predicted ATPase [General function prediction
only].
Length = 334
Score = 30.2 bits (68), Expect = 2.4
Identities = 25/130 (19%), Positives = 38/130 (29%), Gaps = 21/130 (16%)
Query: 204 MDDYKLEVRCVIKQQKEEPQWLLHQPKVTMLISGKKDEELPSEINNKYLEFKNENKNKIL 263
DD + E+ K+Q Q L E+ + F+ EN IL
Sbjct: 42 NDDERQEIGTCYKKQ--------GQDAAKALGHALVCGEIRQQRLEASKAFQEENPVGIL 93
Query: 264 CYTDGSKNDNFTGGAYILNETIEQFQLNQIASIYTAELMAIDLCLNAILT-YVQNNFCFK 322
C G + I Q L A I ++ + L K
Sbjct: 94 CARGGLR------------SKIVQKWLGYAAGIDYPRVIGGEKALRTFAIQATIKEIAQK 141
Query: 323 DFVICSDSKS 332
DF++C +
Sbjct: 142 DFILCGCTGC 151
>gnl|CDD|205913 pfam13739, DUF4163, Domain of unknown function (DUF4163). The
structure of this domain is and alpha-beta-two layer
sandwich, identified from a Fervidobacterium nodosum
Rt17-B1 like protein. The function is not known except
that it is found in association with Heat-shock cognate
70kd protein 44kd ATPase, pfam11738.
Length = 101
Score = 28.4 bits (64), Expect = 2.7
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 1/65 (1%)
Query: 235 ISGKKDEELPSEINNKYLEFKNENKNKILCYTDGSKNDNFTGGAYILNETIE-QFQLNQI 293
SG K++EL +IN+ + N++ +K +F Y LN + + N I
Sbjct: 23 FSGLKNKELQKKINDFIKNKILKFINELEKEAKEAKKKDFPFRPYELNIDYKVTYNDNNI 82
Query: 294 ASIYT 298
S Y
Sbjct: 83 LSFYF 87
>gnl|CDD|225712 COG3171, COG3171, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 119
Score = 28.6 bits (64), Expect = 2.7
Identities = 13/69 (18%), Positives = 25/69 (36%), Gaps = 1/69 (1%)
Query: 335 QALKFNLNDSFKRWEEIWTQNAVLGRQLRQIKTDVRKWKSSNRNIRQEEVVLCRLRIGHC 394
Q L F++ SF + + R + ++ + E ++C RIG C
Sbjct: 27 QELGFSVQWSFHEGTSAEDVDEAVDRFIDEV-IAPNGLAFAGSGYLDWEGLVCLQRIGKC 85
Query: 395 LATHKHLLE 403
H+ +
Sbjct: 86 DEEHRASVR 94
>gnl|CDD|234605 PRK00059, prsA, peptidylprolyl isomerase; Provisional.
Length = 336
Score = 29.3 bits (66), Expect = 4.1
Identities = 30/97 (30%), Positives = 46/97 (47%), Gaps = 15/97 (15%)
Query: 205 DDYK--LEVRCVIKQQKEEPQWLLHQPKVTMLISGKK------DEELPSEINNKYLEFKN 256
D+Y+ +V+ IKQQKE+ L KV +L K+ +EEL E++ K E K
Sbjct: 70 DNYEKNEQVKEQIKQQKEQILDSLITEKV-LLQKAKELKLIPSEEELNKEVDKKINEIKK 128
Query: 257 ENKNKILCYTDGSKNDNFTGGAYILNETIEQFQLNQI 293
+ N + + K FT ET +++ NQI
Sbjct: 129 QFNNDEEQFEEALKATGFT------EETFKEYLKNQI 159
>gnl|CDD|145542 pfam02456, Adeno_IVa2, Adenovirus IVa2 protein. IVa2 protein can
interact with the adenoviral packaging signal and that
this interaction involves DNA sequences that have
previously been demonstrated to be required for
packaging. During the course of lytic infection, the
adenovirus major late promoter (MLP) is induced to high
levels after replication of viral DNA has started. IVa2
is a transcriptional activator of the major late
promoter.
Length = 370
Score = 29.3 bits (66), Expect = 4.3
Identities = 13/49 (26%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 279 YILNETIEQFQLNQIASIYTAEL-MAIDLCLNAILTYVQNNFCFKDFVI 326
+IL+ ++ FQL++ + YT + A+ + L I +Y Q N + +++
Sbjct: 265 HILSPKMQPFQLSRFINTYTKGMPKALTVLLKDIFSYHQQNQKY-SWIV 312
>gnl|CDD|168698 PRK06839, PRK06839, acyl-CoA synthetase; Validated.
Length = 496
Score = 29.4 bits (66), Expect = 4.6
Identities = 31/125 (24%), Positives = 52/125 (41%), Gaps = 22/125 (17%)
Query: 194 PLNIRLRAEAMDDYKLE---VRCVIKQQKEEPQWLLHQPKVTM----LISGKKDEELPSE 246
PLNIRL E ++L+ + ++ + L Q + I+ K+ E
Sbjct: 82 PLNIRL-TENELIFQLKDSGTTVLFVEKTFQNMALSMQKVSYVQRVISITSLKEIEDRKI 140
Query: 247 INNKYLEFKNENKNKILCYTDGSKNDNFTG---GAYILNETIEQFQLNQIASIYTAELMA 303
N KNE+ + I+CYT G+ TG GA +L + E N + + + +L
Sbjct: 141 DN---FVEKNESASFIICYTSGT-----TGKPKGA-VLTQ--ENMFWNALNNTFAIDLTM 189
Query: 304 IDLCL 308
D +
Sbjct: 190 HDRSI 194
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 28.9 bits (65), Expect = 7.4
Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 2/53 (3%)
Query: 302 MAIDLCLNAILTYVQNNFCFKDFVICSDSKSSLQALKFNLNDSFKRWEEIWTQ 354
+ +N +F F + S L LKF D+F ++E +TQ
Sbjct: 300 TPVSPEMNPTFNLENLSFIFNYTTEDGIALSWL--LKFKDADAFTHFQEGFTQ 350
>gnl|CDD|180982 PRK07452, PRK07452, DNA polymerase III subunit delta; Validated.
Length = 326
Score = 28.3 bits (64), Expect = 7.6
Identities = 20/44 (45%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 76 LQELDKLNVVHHTALRIV---TGAFRTSPIVSLLAECGQPTLQV 116
L LD L + ALRIV TG FRT V LL E G+ ++V
Sbjct: 219 LALLDDLLDANEPALRIVATLTGQFRTWLWVKLLVESGERDVKV 262
>gnl|CDD|236990 PRK11814, PRK11814, cysteine desulfurase activator complex subunit
SufB; Provisional.
Length = 486
Score = 28.3 bits (64), Expect = 9.2
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 19/56 (33%)
Query: 177 IKQQKEEPQWLLHQPRYPLNIRLRAEAMDDYKLEVRCVIKQQKEEPQWL-LHQPKV 231
I +K EP+W+ L RL+A Y+ EEP W +H P +
Sbjct: 44 ISAKKNEPEWM-------LEWRLKA-----YRH------WLTMEEPHWAKVHYPPI 81
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 0.136 0.427
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,879,596
Number of extensions: 2195620
Number of successful extensions: 2125
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2118
Number of HSP's successfully gapped: 29
Length of query: 457
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 357
Effective length of database: 6,502,202
Effective search space: 2321286114
Effective search space used: 2321286114
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)