RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 030200
(181 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 = 287 bits (737), Expect = e-100
Identities = 108/159 (67%), Positives = 129/159 (81%)
Query: 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLA 76
PWL GLGNPG+KYKGTRHNVGFEM+D AE++GI+MNT+ K+ G G +GD PVLLA
Sbjct: 1 TPWLIAGLGNPGNKYKGTRHNVGFEMVDRIAEAEGITMNTIQFKSLLGIGSIGDVPVLLA 60
Query: 77 KPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMN 136
KPQTYMN SGES GPLAAYYK+PL +LV +DDM LP GVLRL+ GGHG HNGL+SV+
Sbjct: 61 KPQTYMNYSGESVGPLAAYYKVPLRHILVIYDDMSLPNGVLRLQPKGGHGRHNGLQSVIE 120
Query: 137 NFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARER 175
+ G+REF RL IGIG PPG+MDP+AFLLQKF++ RE+
Sbjct: 121 HLDGSREFPRLSIGIGSPPGKMDPRAFLLQKFSSEEREQ 159
>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 = 227 bits (581), Expect = 4e-77
Identities = 83/151 (54%), Positives = 104/151 (68%), Gaps = 1/151 (0%)
Query: 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQ 79
L VGLGNPG KY+ TRHNVGF ++DA AE G+S K G+G +G VLL KPQ
Sbjct: 1 LIVGLGNPGPKYENTRHNVGFMVLDALAERYGVSFKKKKKKGLVGEGRIGGEKVLLLKPQ 60
Query: 80 TYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFR 139
TYMNLSGE+ LA +YK+P +LV HDD+ LP G +RL+ GG GGHNGLKS++ +
Sbjct: 61 TYMNLSGEAVAALANFYKIPPEDILVIHDDLDLPLGKIRLKKGGGSGGHNGLKSIIAHL- 119
Query: 140 GNREFARLRIGIGRPPGQMDPKAFLLQKFNA 170
G +F RLRIGIGRPP +MD ++L KF+
Sbjct: 120 GTEDFPRLRIGIGRPPNKMDVADYVLSKFSK 150
>gnl|CDD|216355 pfam01195, Pept_tRNA_hydro, Peptidyl-tRNA hydrolase.
Length = 183
Score = 213 bits (545), Expect = 2e-71
Identities = 79/152 (51%), Positives = 101/152 (66%), Gaps = 2/152 (1%)
Query: 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTV-HCKATFGQGFVGDAPVLLAKP 78
L VGLGNPG KY+ TRHNVGF +ID AE G+S+ K +G + V+L KP
Sbjct: 1 LIVGLGNPGPKYENTRHNVGFMVIDRLAERLGVSLKKKKKFKGLIAKGRIEGEKVILLKP 60
Query: 79 QTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNF 138
QTYMNLSGE+ +A +YK+P +LV HDD+ LP G LRL+ GG GGHNGLKS++ +
Sbjct: 61 QTYMNLSGEAVRAIARFYKIPPEDILVVHDDLDLPLGKLRLKKGGGAGGHNGLKSIIQHL 120
Query: 139 RGNREFARLRIGIGRPPGQMDPKAFLLQKFNA 170
G +F RLRIGIGRPP + D ++L KF+
Sbjct: 121 -GTNDFKRLRIGIGRPPDKNDVADYVLSKFSP 151
>gnl|CDD|235457 PRK05426, PRK05426, peptidyl-tRNA hydrolase; Provisional.
Length = 189
Score = 208 bits (531), Expect = 3e-69
Identities = 72/154 (46%), Positives = 97/154 (62%), Gaps = 3/154 (1%)
Query: 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLA 76
L VGLGNPG +Y TRHN+GF ++D A G S+ K +G + V+L
Sbjct: 2 MKLIVGLGNPGPEYANTRHNIGFMVVDELARRLGGSLKEKKKFKGLIAEGRINGEKVILL 61
Query: 77 KPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMN 136
KPQTYMNLSG++ LA +YK+P +LV HDD+ LP G +RL+ GG GGHNGLKS++
Sbjct: 62 KPQTYMNLSGKAVAALANFYKIPPEDILVIHDDLDLPPGKIRLKKGGGAGGHNGLKSIIA 121
Query: 137 NFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNA 170
+ G ++F RLRIGIGRP + ++L KF+
Sbjct: 122 HL-GTQDFWRLRIGIGRPDKK-KVVDYVLGKFSK 153
>gnl|CDD|223271 COG0193, Pth, Peptidyl-tRNA hydrolase [Translation, ribosomal
structure and biogenesis].
Length = 190
Score = 198 bits (506), Expect = 2e-65
Identities = 71/153 (46%), Positives = 93/153 (60%), Gaps = 2/153 (1%)
Query: 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGIS-MNTVHCKATFGQGFVGDAPVLLA 76
L VGLGNPG KY TRHNVGF ++D A +S +G + V+L
Sbjct: 2 MKLIVGLGNPGKKYAKTRHNVGFMVVDLLARRLNLSFKEEKKFNGLVAKGTIEGEKVILL 61
Query: 77 KPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMN 136
KP TYMNLSG++ G LA++YK+ +LV HD++ LP G +RL+ GG GGHNGLKS++
Sbjct: 62 KPTTYMNLSGKAVGALASFYKIKPEDILVVHDELDLPLGKVRLKLGGGAGGHNGLKSIIA 121
Query: 137 NFRGNREFARLRIGIGRPPGQMDPKAFLLQKFN 169
+ G F RLRIGIGRP D ++L KF+
Sbjct: 122 HL-GTNNFYRLRIGIGRPGNGEDVADYVLGKFS 153
>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 = 171 bits (436), Expect = 6e-55
Identities = 72/150 (48%), Positives = 94/150 (62%), Gaps = 2/150 (1%)
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 QTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNF 138
TYMNLSGE+ LA++Y++ +LV HD++ LP G +RL+ GG GGHNGLKS++++
Sbjct: 63 LTYMNLSGEAVRALASFYRIKPAELLVVHDELDLPLGKVRLKMGGGAGGHNGLKSIISHL 122
Query: 139 RGNREFARLRIGIGRPPGQMDPKAFLLQKF 168
G F RLRIGIG P G F+L KF
Sbjct: 123 -GTNNFNRLRIGIGSPGGSNKVVEFVLSKF 151
>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 = 31.4 bits (71), Expect = 0.21
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|152211 pfam11775, CobT_C, Cobalamin biosynthesis protein CobT VWA domain.
This family consists of several bacterial cobalamin
biosynthesis (CobT) proteins. CobT is involved in the
transformation of precorrin-3 into cobyrinic acid.
Length = 220
Score = 27.3 bits (60), Expect = 4.9
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 3/72 (4%)
Query: 83 NLSGESTGPLAAYY--KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRG 140
N+ GE+ A + ++ ++L+ D G PC L G G L+ ++
Sbjct: 116 NIDGEALAQAAKLFAGRMEDKKILLMISD-GAPCDDSTLSVAAGDGFEQHLRHIIEEIET 174
Query: 141 NREFARLRIGIG 152
E + IGIG
Sbjct: 175 LSEIDLIAIGIG 186
>gnl|CDD|182322 PRK10234, PRK10234, DNA-binding transcriptional activator GutM;
Provisional.
Length = 118
Score = 25.8 bits (57), Expect = 7.9
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 4/35 (11%)
Query: 139 RGNREFARL----RIGIGRPPGQMDPKAFLLQKFN 169
R NR F L R+G+GR G+ P+ + +
Sbjct: 26 RFNRAFDTLCQQGRVGVGRSSGRFKPRVVVALALD 60
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 0.448
Gapped
Lambda K H
0.267 0.0548 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,622,278
Number of extensions: 890401
Number of successful extensions: 730
Number of sequences better than 10.0: 1
Number of HSP's gapped: 721
Number of HSP's successfully gapped: 14
Length of query: 181
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 90
Effective length of database: 6,901,388
Effective search space: 621124920
Effective search space used: 621124920
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: 56 (25.8 bits)