RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8593
(204 letters)
>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 = 67.1 bits (165), Expect = 1e-14
Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 90 EFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMH 149
+F +Y+ G + V TDH+ L + K K N RL R + L + FE++Y PGK
Sbjct: 56 KFRHYLLGRK-FTVYTDHKSLKYLLTK---KDLNPRLARWLLLLQEFDFEIEYRPGKENV 111
Query: 150 IAELADYLSRN 160
+ AD LSR
Sbjct: 112 V---ADALSRL 119
>gnl|CDD|180875 PRK07196, fliI, flagellum-specific ATP synthase; Validated.
Length = 434
Score = 29.9 bits (67), Expect = 0.89
Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 39 QHFEFRLITMQLIGSAQRDLFFIIFYKLGH---AFSTSLAIPRDELAGFRSEATEFCYYV 95
++ + ++ + LIG R++ I + L A S +A P DE R +ATE C+ +
Sbjct: 177 RYTQADVVVVGLIGERGREVKEFIEHSLQAAGMAKSVVVAAPADESPLMRIKATELCHAI 236
Query: 96 YGH-----RNIVVQTD 106
+ ++++ D
Sbjct: 237 ATYYRDKGHDVLLLVD 252
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 29.1 bits (65), Expect = 1.9
Identities = 14/87 (16%), Positives = 37/87 (42%)
Query: 116 KDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMHIAELADYLSRNLLVKNVQEDILMKDM 175
+ N + RL+ K+ + E+K + K + + + +YL + K++ E ++
Sbjct: 468 NHIINHYNEKKSRLEEKIREIEIEVKDIDEKIVDLKKRKEYLESEEINKSINEYNKIESA 527
Query: 176 VHTVNKFEINFSPEKFQWFQQEILNDE 202
+ +I + K + + E + +
Sbjct: 528 RADLEDIKIKINELKDKHDKYEEIKNR 554
>gnl|CDD|182898 PRK11010, ampG, muropeptide transporter; Validated.
Length = 491
Score = 28.5 bits (64), Expect = 2.9
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 58 LFFIIFYKLGHAFSTSL 74
L I+ YKLG AF+ SL
Sbjct: 228 LLLIVLYKLGDAFAMSL 244
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 27.7 bits (63), Expect = 4.8
Identities = 10/16 (62%), Positives = 12/16 (75%), Gaps = 3/16 (18%)
Query: 117 DLYK---IQNNRLKRL 129
DLY+ +NNRLKRL
Sbjct: 257 DLYRRVINRNNRLKRL 272
>gnl|CDD|220813 pfam10567, Nab6_mRNP_bdg, RNA-recognition motif. This conserved
domain is found in fungal proteins and appears to be
involved in RNA-processing. It binds to poly-adenylated
RNA, interacts genetically with mRNA 3'-end processing
factors, copurifies with the nuclear cap-binding protein
Cbp20p, and is found in complexes containing other
translation factors, such as EIF4G.
Length = 309
Score = 27.1 bits (60), Expect = 6.9
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 156 YLSRNLLVKNVQEDILMKDMVHTVNKFEINFSP-EKFQWFQQEILNDED 203
Y +R+LL +NV ++ D+ + KF + F P E + ++D
Sbjct: 13 YRTRSLLFENVDSEL---DLHEFLKKF-VKFGPIESIYLIKDNDKPNDD 57
>gnl|CDD|233392 TIGR01391, dnaG, DNA primase, catalytic core. Members of this
family are DNA primase, a ubiquitous bacteria protein.
Most members of this family contain nearly two hundred
additional residues C-terminal to the region represented
here, but conservation between species is poor and the
C-terminal region was not included in the seed
alignment. This protein contains a CHC2 zinc finger
(pfam01807) and a Toprim domain (pfam01751) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 415
Score = 27.2 bits (61), Expect = 7.6
Identities = 14/75 (18%), Positives = 29/75 (38%), Gaps = 6/75 (8%)
Query: 132 KLFPYQFELKYLPGKYMHIAELADYLSRNLLVKNVQEDILMKDMVH------TVNKFEIN 185
K + E K K + ELA +N L + + + T+++FE+
Sbjct: 98 KDQQEKKEQKSKRKKLYELLELAAKFFKNQLKHTPENRAALDYLQSRGLSDETIDRFELG 157
Query: 186 FSPEKFQWFQQEILN 200
++P + + + N
Sbjct: 158 YAPNNWDFLFDFLQN 172
>gnl|CDD|198321 cd03212, GST_C_Metaxin1_3, C-terminal, alpha helical domain of
Metaxin 1, Metaxin 3, and similar proteins. Glutathione
S-transferase (GST) C-terminal domain family, Metaxin
subfamily, Metaxin 1-like proteins; composed of metaxins
1 and 3, and similar proteins. Mammalian metaxin (or
metaxin 1) is a component of the preprotein import
complex of the mitochondrial outer membrane. Metaxin
extends to the cytosol and is anchored to the
mitochondrial membrane through its C-terminal domain. In
mice, metaxin is required for embryonic development.
Like the murine gene, the human metaxin gene is located
downstream to the glucocerebrosidase (GBA) pseudogene
and is convergently transcribed. Inherited deficiency of
GBA results in Gaucher disease, which presents many
diverse clinical phenotypes. Alterations in the metaxin
gene, in addition to GBA mutations, may be associated
with Gaucher disease. Genome sequencing shows that a
third metaxin gene also exists in zebrafish, Xenopus,
chicken, and mammals.
Length = 137
Score = 26.1 bits (58), Expect = 8.2
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 6/50 (12%)
Query: 134 FPYQFELKYLPGKYMHIAELADYLSRNLLVKNVQEDI---LMKDMVHTVN 180
FP F Y PG+Y A+ L R L + +E++ L KD +N
Sbjct: 28 FPLNF---YYPGRYQRRAKDRLQLLRGLSELDSEEEVEKELYKDAKECLN 74
>gnl|CDD|227382 COG5049, XRN1, 5'-3' exonuclease [DNA replication, recombination,
and repair / Cell division and chromosome partitioning /
Translation].
Length = 953
Score = 26.8 bits (59), Expect = 9.3
Identities = 16/67 (23%), Positives = 27/67 (40%), Gaps = 6/67 (8%)
Query: 107 HQPLLAINKKDLYKIQNNRLKRLKIKL------FPYQFELKYLPGKYMHIAELADYLSRN 160
H+P I ++D++ +R KR K L + P +HI+ L +YL R
Sbjct: 230 HEPHFLILREDVFFGSKSRRKRKCTKCGRTGHSDEECKVLTHQPFYLLHISLLREYLERE 289
Query: 161 LLVKNVQ 167
+
Sbjct: 290 FREPTLP 296
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
0.325 0.139 0.405
Gapped
Lambda K H
0.267 0.0688 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,376,878
Number of extensions: 966652
Number of successful extensions: 980
Number of sequences better than 10.0: 1
Number of HSP's gapped: 976
Number of HSP's successfully gapped: 26
Length of query: 204
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 112
Effective length of database: 6,857,034
Effective search space: 767987808
Effective search space used: 767987808
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: 57 (25.8 bits)