RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 029652
(190 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 = 290 bits (744), Expect = e-101
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 = 228 bits (583), Expect = 3e-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 (546), 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 = 209 bits (534), Expect = 2e-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 = 200 bits (510), Expect = 7e-66
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 = 173 bits (440), Expect = 2e-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 = 0.25
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|219884 pfam08529, NusA_N, NusA N-terminal domain. This domain represents
the RNA polymerase binding domain of NusA.
Length = 122
Score = 29.0 bits (66), Expect = 0.77
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 164 LLQKFNAIARERDISFDCII 183
LL+ +AIARE+ I + +I
Sbjct: 2 LLEAIDAIAREKGIDKEVLI 21
>gnl|CDD|203934 pfam08414, NADPH_Ox, Respiratory burst NADPH oxidase. This domain
is found in plant proteins such as respiratory burst
NADPH oxidase proteins which produce reactive oxygen
species as a defence mechanism. It tends to occur to the
N-terminus of an EF-hand (pfam00036), which suggests a
direct regulatory effect of Ca2+ on the activity of the
NADPH oxidase in plants.
Length = 96
Score = 28.4 bits (64), Expect = 0.83
Identities = 21/61 (34%), Positives = 26/61 (42%), Gaps = 7/61 (11%)
Query: 126 GGHNGLKSVMNNFRGNREFAR----LRIGIGRPPGQMDPKAFLLQKFNAIARERDISFDC 181
GG +G V F + A R G G D K F L+ F+A+AR R I D
Sbjct: 20 GGVDGWNEVEKRFD---KLAVDGYLPRSKFGECIGMNDSKEFALELFDALARRRRIKVDS 76
Query: 182 I 182
I
Sbjct: 77 I 77
>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 = 4.2
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|237061 PRK12327, nusA, transcription elongation factor NusA; Provisional.
Length = 362
Score = 27.1 bits (61), Expect = 5.3
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 164 LLQKFNAIARERDISFDCII 183
L+ A+ E+ IS + +I
Sbjct: 5 DLEALRALEEEKGISKEDLI 24
>gnl|CDD|213617 TIGR01417, PTS_I_fam, phosphoenolpyruvate-protein
phosphotransferase. This model recognizes a distinct
clade of phophoenolpyruvate (PEP)-dependent enzymes.
Most members are known or deduced to function as the
phosphoenolpyruvate-protein phosphotransferase (or
enzyme I) of PTS sugar transport systems. However, some
species with both a member of this family and a homolog
of the phosphocarrier protein HPr lack a IIC component
able to serve as a permease. An HPr homolog designated
NPr has been implicated in the regulation of nitrogen
assimilation, which demonstrates that not all
phosphotransferase system components are associated
directly with PTS transport.
Length = 565
Score = 27.1 bits (60), Expect = 8.0
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 149 IGIGRPPGQMDPKAFLLQKFNAIARERDISFD 180
GIG PG KA LL+K + + + IS
Sbjct: 2 SGIGVSPGIAIGKALLLKKPDLVIDRKKISAS 33
>gnl|CDD|182322 PRK10234, PRK10234, DNA-binding transcriptional activator GutM;
Provisional.
Length = 118
Score = 25.8 bits (57), Expect = 8.6
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
0.326 0.145 0.457
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: 10,140,654
Number of extensions: 951755
Number of successful extensions: 799
Number of sequences better than 10.0: 1
Number of HSP's gapped: 790
Number of HSP's successfully gapped: 16
Length of query: 190
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 99
Effective length of database: 6,901,388
Effective search space: 683237412
Effective search space used: 683237412
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.8 bits)