RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032666
(136 letters)
>gnl|CDD|239090 cd02406, CRS2, Chloroplast RNA splicing 2 (CRS2) is a
nuclear-encoded protein required for the splicing of
group II introns in the chloroplast. CRS2 forms stable
complexes with two CRS2-associated factors, CAF1 and
CAF2, which are required for the splicing of distinct
subsets of CRS2-dependent introns. CRS2 is closely
related to bacterial peptidyl-tRNA hydrolases (PTH).
Length = 191
Score = 216 bits (551), Expect = 4e-73
Identities = 80/114 (70%), Positives = 92/114 (80%)
Query: 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLA 76
PWL GLGNPG+KYKGTRHNVGFEM+D AE++GI+MNT+ K+ G G +GD PVLLA
Sbjct: 1 TPWLIAGLGNPGNKYKGTRHNVGFEMVDRIAEAEGITMNTIQFKSLLGIGSIGDVPVLLA 60
Query: 77 KPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNG 130
KPQTYMN SGES GPLAAYYK+PL +LV +DDM LP GVLRL+ GGHG HNG
Sbjct: 61 KPQTYMNYSGESVGPLAAYYKVPLRHILVIYDDMSLPNGVLRLQPKGGHGRHNG 114
>gnl|CDD|238259 cd00462, PTH, Peptidyl-tRNA hydrolase (PTH) is a monomeric protein
that cleaves the ester bond linking the nascent peptide
and tRNA when peptidyl-tRNA is released prematurely from
the ribosome. This ensures the recycling of
peptidyl-tRNAs into tRNAs produced through abortion of
translation and is essential for cell viability.This
group also contains chloroplast RNA splicing 2 (CRS2),
which is closely related nuclear-encoded protein
required for the splicing of nine group II introns in
chloroplasts.
Length = 171
Score = 179 bits (458), Expect = 4e-59
Identities = 63/111 (56%), Positives = 76/111 (68%)
Query: 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQ 79
L VGLGNPG KY+ TRHNVGF ++DA AE G+S K G+G +G VLL KPQ
Sbjct: 1 LIVGLGNPGPKYENTRHNVGFMVLDALAERYGVSFKKKKKKGLVGEGRIGGEKVLLLKPQ 60
Query: 80 TYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNG 130
TYMNLSGE+ LA +YK+P +LV HDD+ LP G +RL+ GG GGHNG
Sbjct: 61 TYMNLSGEAVAALANFYKIPPEDILVIHDDLDLPLGKIRLKKGGGSGGHNG 111
>gnl|CDD|235457 PRK05426, PRK05426, peptidyl-tRNA hydrolase; Provisional.
Length = 189
Score = 171 bits (437), Expect = 1e-55
Identities = 55/114 (48%), Positives = 71/114 (62%), Gaps = 1/114 (0%)
Query: 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLA 76
L VGLGNPG +Y TRHN+GF ++D A G S+ K +G + V+L
Sbjct: 2 MKLIVGLGNPGPEYANTRHNIGFMVVDELARRLGGSLKEKKKFKGLIAEGRINGEKVILL 61
Query: 77 KPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNG 130
KPQTYMNLSG++ LA +YK+P +LV HDD+ LP G +RL+ GG GGHNG
Sbjct: 62 KPQTYMNLSGKAVAALANFYKIPPEDILVIHDDLDLPPGKIRLKKGGGAGGHNG 115
>gnl|CDD|216355 pfam01195, Pept_tRNA_hydro, Peptidyl-tRNA hydrolase.
Length = 183
Score = 169 bits (431), Expect = 6e-55
Identities = 60/112 (53%), Positives = 74/112 (66%), Gaps = 1/112 (0%)
Query: 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTV-HCKATFGQGFVGDAPVLLAKP 78
L VGLGNPG KY+ TRHNVGF +ID AE G+S+ K +G + V+L KP
Sbjct: 1 LIVGLGNPGPKYENTRHNVGFMVIDRLAERLGVSLKKKKKFKGLIAKGRIEGEKVILLKP 60
Query: 79 QTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNG 130
QTYMNLSGE+ +A +YK+P +LV HDD+ LP G LRL+ GG GGHNG
Sbjct: 61 QTYMNLSGEAVRAIARFYKIPPEDILVVHDDLDLPLGKLRLKKGGGAGGHNG 112
>gnl|CDD|223271 COG0193, Pth, Peptidyl-tRNA hydrolase [Translation, ribosomal
structure and biogenesis].
Length = 190
Score = 158 bits (402), Expect = 2e-50
Identities = 54/115 (46%), Positives = 70/115 (60%), Gaps = 3/115 (2%)
Query: 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCK--ATFGQGFVGDAPVLL 75
L VGLGNPG KY TRHNVGF ++D A +S K +G + V+L
Sbjct: 2 MKLIVGLGNPGKKYAKTRHNVGFMVVDLLARRLNLS-FKEEKKFNGLVAKGTIEGEKVIL 60
Query: 76 AKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNG 130
KP TYMNLSG++ G LA++YK+ +LV HD++ LP G +RL+ GG GGHNG
Sbjct: 61 LKPTTYMNLSGKAVGALASFYKIKPEDILVVHDELDLPLGKVRLKLGGGAGGHNG 115
>gnl|CDD|213531 TIGR00447, pth, peptidyl-tRNA hydrolase. The natural substrate for
this enzyme may be peptidyl-tRNAs that drop off the
ribosome during protein synthesis. Peptidyl-tRNA
hydrolase is a bacterial protein; YHR189W from
Saccharomyces cerevisiae appears to be orthologous and
likely has the same function [Protein synthesis, Other].
Length = 188
Score = 137 bits (347), Expect = 3e-42
Identities = 54/112 (48%), Positives = 71/112 (63%), Gaps = 1/112 (0%)
Query: 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCK-ATFGQGFVGDAPVLLAKP 78
L VGLGNPG KY GTRHN GF ++D A G+S+ T +G + V+L KP
Sbjct: 3 LIVGLGNPGKKYAGTRHNAGFWVLDLLASRLGLSLRTEKKFFGYTERGLLSGKKVILLKP 62
Query: 79 QTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNG 130
TYMNLSGE+ LA++Y++ +LV HD++ LP G +RL+ GG GGHNG
Sbjct: 63 LTYMNLSGEAVRALASFYRIKPAELLVVHDELDLPLGKVRLKMGGGAGGHNG 114
>gnl|CDD|131458 TIGR02405, trehalos_R_Ecol, trehalose operon repressor,
proteobacterial. This family consists of repressors of
the LacI family typically associated with trehalose
utilization operons. Trehalose is imported as
trehalose-6-phosphate and then hydrolyzed by
alpha,alpha-phosphotrehalase to glucose and glucose-6-P.
This family includes repressors mostly from
Gammaproteobacteria and does not include the GntR family
TreR of Bacillus subtilis [Regulatory functions, DNA
interactions].
Length = 311
Score = 31.8 bits (72), Expect = 0.075
Identities = 26/103 (25%), Positives = 40/103 (38%), Gaps = 13/103 (12%)
Query: 1 MLINRFLRRGFCTAVARPWLFVGLGNPGDKYKG-TRHNVGFEMIDAFAESQGISMNTVHC 59
+L+ ++G R F+G+ +P DK G RHN A+ ES +
Sbjct: 162 LLMANLYQQG-----HRHISFLGV-DPSDKTTGLMRHNAYL----AYCESANLEPIYQTG 211
Query: 60 KATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLNR 102
+ + G+V VL KP+T + T L A L
Sbjct: 212 QLSHESGYVLTDKVL--KPETTALVCATDTLALGAAKYLQELD 252
>gnl|CDD|232961 TIGR00408, proS_fam_I, prolyl-tRNA synthetase, family I.
Prolyl-tRNA synthetase is a class II tRNA synthetase and
is recognized by pfam model tRNA-synt_2b, which
recognizes tRNA synthetases for Gly, His, Ser, and Pro.
The prolyl-tRNA synthetases are divided into two widely
divergent families. This family includes the archaeal
enzyme, the Pro-specific domain of a human
multifunctional tRNA ligase, and the enzyme from the
spirochete Borrelia burgdorferi. The other family
includes enzymes from Escherichia coli, Bacillus
subtilis, Synechocystis PCC6803, and one of the two
prolyL-tRNA synthetases of Saccharomyces cerevisiae
[Protein synthesis, tRNA aminoacylation].
Length = 472
Score = 26.6 bits (59), Expect = 4.2
Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 5/47 (10%)
Query: 21 FVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGF 67
FVG +K+ G + FE I + + + + T H GQ F
Sbjct: 190 FVGRKPEWEKFAGAEYTWAFETI--MPDGRTLQIATSH---NLGQNF 231
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 0.143 0.473
Gapped
Lambda K H
0.267 0.0749 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,089,235
Number of extensions: 617208
Number of successful extensions: 520
Number of sequences better than 10.0: 1
Number of HSP's gapped: 516
Number of HSP's successfully gapped: 11
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
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: 54 (24.5 bits)