RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 027817
(218 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 = 326 bits (837), Expect = e-115
Identities = 124/191 (64%), Positives = 152/191 (79%)
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 NFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLT 196
+ G+REF RL IGIG PPG+MDP+AFLLQKF++ RE+IDTAL++GV+ ++ L+ KG
Sbjct: 121 HLDGSREFPRLSIGIGSPPGKMDPRAFLLQKFSSEEREQIDTALEQGVDAVRTLVLKGFN 180
Query: 197 ESARHFNTIQK 207
SA FN +QK
Sbjct: 181 GSAERFNLVQK 191
>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 = 238 bits (611), Expect = 5e-81
Identities = 88/172 (51%), Positives = 117/172 (68%), Gaps = 1/172 (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 GNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLL 191
G +F RLRIGIGRPP +MD ++L KF+ RE ++ A+++ + L+ +L
Sbjct: 120 GTEDFPRLRIGIGRPPNKMDVADYVLSKFSKEERELLEEAIEKAADALEDIL 171
>gnl|CDD|216355 pfam01195, Pept_tRNA_hydro, Peptidyl-tRNA hydrolase.
Length = 183
Score = 229 bits (586), Expect = 5e-77
Identities = 85/179 (47%), Positives = 115/179 (64%), Gaps = 2/179 (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 RGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTE 197
G +F RLRIGIGRPP + D ++L KF+ E +D A+++ + L+ L+ G +
Sbjct: 121 -GTNDFKRLRIGIGRPPDKNDVADYVLSKFSPEELELLDKAIEKAADALEDLIEGGFDK 178
>gnl|CDD|235457 PRK05426, PRK05426, peptidyl-tRNA hydrolase; Provisional.
Length = 189
Score = 226 bits (578), Expect = 8e-76
Identities = 81/188 (43%), Positives = 116/188 (61%), Gaps = 3/188 (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 NFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLT 196
+ G ++F RLRIGIGRP + ++L KF+ +E +D A+ + + ++LLL G
Sbjct: 122 HL-GTQDFWRLRIGIGRPDKK-KVVDYVLGKFSKEEQELLDKAIDKAADAIELLLEGGFE 179
Query: 197 ESARHFNT 204
++ FN+
Sbjct: 180 KAMNKFNS 187
>gnl|CDD|223271 COG0193, Pth, Peptidyl-tRNA hydrolase [Translation, ribosomal
structure and biogenesis].
Length = 190
Score = 217 bits (555), Expect = 2e-72
Identities = 80/188 (42%), Positives = 109/188 (57%), Gaps = 2/188 (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 NFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLT 196
+ G F RLRIGIGRP D ++L KF+ RE +D A+ + + L+LLL
Sbjct: 122 HL-GTNNFYRLRIGIGRPGNGEDVADYVLGKFSKEERELLDKAIDKAADALELLLEGDFE 180
Query: 197 ESARHFNT 204
++ N
Sbjct: 181 KAMNKLNA 188
>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 = 184 bits (468), Expect = 4e-59
Identities = 79/176 (44%), Positives = 107/176 (60%), Gaps = 2/176 (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 RGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 194
G F RLRIGIG P G F+L KF ++ AL + VE L++ S+G
Sbjct: 123 -GTNNFNRLRIGIGSPGGSNKVVEFVLSKFTKSELPLLEKALDKAVEALEMSFSEG 177
>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 = 31.0 bits (70), Expect = 0.46
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|182322 PRK10234, PRK10234, DNA-binding transcriptional activator GutM;
Provisional.
Length = 118
Score = 29.2 bits (66), Expect = 0.64
Identities = 23/66 (34%), Positives = 30/66 (45%), Gaps = 16/66 (24%)
Query: 139 RGNREFARL----RIGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 194
R NR F L R+G+GR G+ P+ + A+ AL E V+ L KG
Sbjct: 26 RFNRAFDTLCQQGRVGVGRSSGRFKPRVVV-----AL-------ALDEQQRVVDTLFMKG 73
Query: 195 LTESAR 200
LT AR
Sbjct: 74 LTVFAR 79
>gnl|CDD|221853 pfam12919, TcdA_TcdB, TcdA/TcdB catalytic glycosyltransferase
domain. This domain represents the N-terminal
glycosyltransferase from a set of toxins found in some
bacteria. This domain in TcdB glycosylates the host RhoA
protein.
Length = 472
Score = 29.7 bits (67), Expect = 1.3
Identities = 11/30 (36%), Positives = 13/30 (43%), Gaps = 1/30 (3%)
Query: 159 DPKAFLLQKFN-AIARERIDTALQEGVEVL 187
D AFL KF + D AL+ E L
Sbjct: 38 DSNAFLAAKFKSTLKESAFDHALESLRENL 67
>gnl|CDD|232970 TIGR00424, APS_reduc, 5'-adenylylsulfate reductase,
thioredoxin-independent. This enzyme, involved in the
assimilation of inorganic sulfate, is closely related to
the thioredoxin-dependent PAPS reductase of Bacteria
(CysH) and Saccharomyces cerevisiae. However, it has its
own C-terminal thioredoxin-like domain and is not
thioredoxin-dependent. Also, it has a substrate
preference for 5'-adenylylsulfate (APS) over
3'-phosphoadenylylsulfate (PAPS) so the pathway does not
require an APS kinase (CysC) to convert APS to PAPS.
Arabidopsis thaliana appears to have three isozymes, all
able to complement E. coli CysH mutants (even in
backgrounds lacking thioredoxin or APS kinase) but
likely localized to different compartments in
Arabidopsis [Central intermediary metabolism, Sulfur
metabolism].
Length = 463
Score = 27.7 bits (61), Expect = 5.2
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 15/63 (23%)
Query: 143 EFARLRIGIGRP-------PGQMDPKAFLLQKFNAIARE---RIDTALQEGVEVLKLLLS 192
E+A L GRP G+++P+ + F+A+ ++ RI+ + VEV L+ S
Sbjct: 132 EYAHL---TGRPFRVFSLDTGRLNPETYRF--FDAVEKQYGIRIEYMFPDAVEVQALVRS 186
Query: 193 KGL 195
KGL
Sbjct: 187 KGL 189
>gnl|CDD|233237 TIGR01026, fliI_yscN, ATPase FliI/YscN family. This family of
ATPases demonstrates extensive homology with ATP
synthase F1, beta subunit. It is a mixture of members
with two different protein functions. The first group is
exemplified by Salmonella typhimurium FliI protein. It
is needed for flagellar assembly, its ATPase activity is
required for flagellation, and it may be involved in a
specialized protein export pathway that proceeds without
signal peptide cleavage. The second group of proteins
function in the export of virulence proteins;
exemplified by Yersinia sp. YscN protein an ATPase
involved in the type III secretory pathway for the
antihost Yops proteins [Energy metabolism, ATP-proton
motive force interconversion].
Length = 440
Score = 27.3 bits (61), Expect = 6.4
Identities = 11/45 (24%), Positives = 19/45 (42%)
Query: 150 GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 194
G G+ ++ + + N + R I L GV + LL+ G
Sbjct: 117 GKGKFLDNVETEGLITAPINPLKRAPIREILSTGVRSIDGLLTVG 161
>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 = 26.9 bits (59), Expect = 6.8
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|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 = 8.2
Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 2/59 (3%)
Query: 149 IGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHFNTIQK 207
GIG PG KA LL+K + + + +A Q E+ + K ++ TI+
Sbjct: 2 SGIGVSPGIAIGKALLLKKPDLVIDRKKISASQVDQEISR--FLKARAKAKEDLETIKT 58
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 0.141 0.433
Gapped
Lambda K H
0.267 0.0678 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,426,637
Number of extensions: 1090263
Number of successful extensions: 791
Number of sequences better than 10.0: 1
Number of HSP's gapped: 781
Number of HSP's successfully gapped: 15
Length of query: 218
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 125
Effective length of database: 6,812,680
Effective search space: 851585000
Effective search space used: 851585000
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: 41 (22.0 bits)
S2: 57 (25.8 bits)