RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 028433
(209 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 = 295 bits (756), Expect = e-103
Identities = 117/192 (60%), Positives = 144/192 (75%), Gaps = 11/192 (5%)
Query: 17 RPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLL 76
PWL GLGNPG+KYKGTRHN VGFEM+D AE++GI+MNT+ K+ G G +GD PVLL
Sbjct: 1 TPWLIAGLGNPGNKYKGTRHN-VGFEMVDRIAEAEGITMNTIQFKSLLGIGSIGDVPVLL 59
Query: 77 AKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVM 136
AKPQTYMN SGES GPLAAYYK+PL +LV +DDM LP GVLRL+ GGHG HNGL+SV+
Sbjct: 60 AKPQTYMNYSGESVGPLAAYYKVPLRHILVIYDDMSLPNGVLRLQPKGGHGRHNGLQSVI 119
Query: 137 NNFR----------GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGL 186
+ GIG PPG+MDP+AFLLQKF++ RE+IDTAL++GV+ ++ L+ KG
Sbjct: 120 EHLDGSREFPRLSIGIGSPPGKMDPRAFLLQKFSSEEREQIDTALEQGVDAVRTLVLKGF 179
Query: 187 TESARHFNTIQK 198
SA FN +QK
Sbjct: 180 NGSAERFNLVQK 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 = 213 bits (546), Expect = 3e-71
Identities = 82/172 (47%), Positives = 110/172 (63%), Gaps = 10/172 (5%)
Query: 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKP 79
L VGLGNPG KY+ TRHN VGF ++DA AE G+S K G+G +G VLL KP
Sbjct: 1 LIVGLGNPGPKYENTRHN-VGFMVLDALAERYGVSFKKKKKKGLVGEGRIGGEKVLLLKP 59
Query: 80 QTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNF 139
QTYMNLSGE+ LA +YK+P +LV HDD+ LP G +RL+ GG GGHNGLKS++ +
Sbjct: 60 QTYMNLSGEAVAALANFYKIPPEDILVIHDDLDLPLGKIRLKKGGGSGGHNGLKSIIAHL 119
Query: 140 R---------GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLL 182
GIGRPP +MD ++L KF+ RE ++ A+++ + L+ +L
Sbjct: 120 GTEDFPRLRIGIGRPPNKMDVADYVLSKFSKEERELLEEAIEKAADALEDIL 171
>gnl|CDD|216355 pfam01195, Pept_tRNA_hydro, Peptidyl-tRNA hydrolase.
Length = 183
Score = 205 bits (525), Expect = 5e-68
Identities = 81/179 (45%), Positives = 111/179 (62%), Gaps = 11/179 (6%)
Query: 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTV-HCKATFGQGFVGDAPVLLAK 78
L VGLGNPG KY+ TRHN VGF +ID AE G+S+ K +G + V+L K
Sbjct: 1 LIVGLGNPGPKYENTRHN-VGFMVIDRLAERLGVSLKKKKKFKGLIAKGRIEGEKVILLK 59
Query: 79 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVM-- 136
PQTYMNLSGE+ +A +YK+P +LV HDD+ LP G LRL+ GG GGHNGLKS++
Sbjct: 60 PQTYMNLSGEAVRAIARFYKIPPEDILVVHDDLDLPLGKLRLKKGGGAGGHNGLKSIIQH 119
Query: 137 ---NNFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTE 188
N+F+ GIGRPP + D ++L KF+ E +D A+++ + L+ L+ G +
Sbjct: 120 LGTNDFKRLRIGIGRPPDKNDVADYVLSKFSPEELELLDKAIEKAADALEDLIEGGFDK 178
>gnl|CDD|235457 PRK05426, PRK05426, peptidyl-tRNA hydrolase; Provisional.
Length = 189
Score = 202 bits (517), Expect = 1e-66
Identities = 76/188 (40%), Positives = 109/188 (57%), Gaps = 12/188 (6%)
Query: 18 PWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLL 76
L VGLGNPG +Y TRHN +GF ++D A G S+ K +G + V+L
Sbjct: 2 MKLIVGLGNPGPEYANTRHN-IGFMVVDELARRLGGSLKEKKKFKGLIAEGRINGEKVIL 60
Query: 77 AKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVM 136
KPQTYMNLSG++ LA +YK+P +LV HDD+ LP G +RL+ GG GGHNGLKS++
Sbjct: 61 LKPQTYMNLSGKAVAALANFYKIPPEDILVIHDDLDLPPGKIRLKKGGGAGGHNGLKSII 120
Query: 137 -----NNFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLT 187
+F GIGRP + ++L KF+ +E +D A+ + + ++LLL G
Sbjct: 121 AHLGTQDFWRLRIGIGRPDKK-KVVDYVLGKFSKEEQELLDKAIDKAADAIELLLEGGFE 179
Query: 188 ESARHFNT 195
++ FN+
Sbjct: 180 KAMNKFNS 187
>gnl|CDD|223271 COG0193, Pth, Peptidyl-tRNA hydrolase [Translation, ribosomal
structure and biogenesis].
Length = 190
Score = 197 bits (503), Expect = 1e-64
Identities = 77/188 (40%), Positives = 105/188 (55%), Gaps = 11/188 (5%)
Query: 18 PWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGIS-MNTVHCKATFGQGFVGDAPVLL 76
L VGLGNPG KY TRHN VGF ++D A +S +G + V+L
Sbjct: 2 MKLIVGLGNPGKKYAKTRHN-VGFMVVDLLARRLNLSFKEEKKFNGLVAKGTIEGEKVIL 60
Query: 77 AKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVM 136
KP TYMNLSG++ G LA++YK+ +LV HD++ LP G +RL+ GG GGHNGLKS++
Sbjct: 61 LKPTTYMNLSGKAVGALASFYKIKPEDILVVHDELDLPLGKVRLKLGGGAGGHNGLKSII 120
Query: 137 -----NNFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLT 187
NNF GIGRP D ++L KF+ RE +D A+ + + L+LLL
Sbjct: 121 AHLGTNNFYRLRIGIGRPGNGEDVADYVLGKFSKEERELLDKAIDKAADALELLLEGDFE 180
Query: 188 ESARHFNT 195
++ 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 = 164 bits (417), Expect = 1e-51
Identities = 76/176 (43%), Positives = 102/176 (57%), Gaps = 11/176 (6%)
Query: 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCK-ATFGQGFVGDAPVLLAK 78
L VGLGNPG KY GTRHN GF ++D A G+S+ T +G + V+L K
Sbjct: 3 LIVGLGNPGKKYAGTRHN-AGFWVLDLLASRLGLSLRTEKKFFGYTERGLLSGKKVILLK 61
Query: 79 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVM-- 136
P TYMNLSGE+ LA++Y++ +LV HD++ LP G +RL+ GG GGHNGLKS++
Sbjct: 62 PLTYMNLSGEAVRALASFYRIKPAELLVVHDELDLPLGKVRLKMGGGAGGHNGLKSIISH 121
Query: 137 ---NNFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 185
NNF GIG P G F+L KF ++ AL + VE L++ S+G
Sbjct: 122 LGTNNFNRLRIGIGSPGGSNKVVEFVLSKFTKSELPLLEKALDKAVEALEMSFSEG 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 = 30.2 bits (68), Expect = 0.59
Identities = 23/103 (22%), Positives = 38/103 (36%), Gaps = 12/103 (11%)
Query: 1 MLINRFLRRGFCTAVARPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHC 60
+L+ ++G R F+G+ +P DK G + A+ ES +
Sbjct: 162 LLMANLYQQG-----HRHISFLGV-DPSDKTTGLMRHNAYL----AYCESANLEPIYQTG 211
Query: 61 KATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLNR 103
+ + G+V VL KP+T + T L A L
Sbjct: 212 QLSHESGYVLTDKVL--KPETTALVCATDTLALGAAKYLQELD 252
>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 = 1.1
Identities = 11/30 (36%), Positives = 13/30 (43%), Gaps = 1/30 (3%)
Query: 150 DPKAFLLQKFN-AIARERIDTALQEGVEVL 178
D AFL KF + D AL+ E L
Sbjct: 38 DSNAFLAAKFKSTLKESAFDHALESLRENL 67
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 29.3 bits (65), Expect = 1.7
Identities = 19/99 (19%), Positives = 39/99 (39%), Gaps = 32/99 (32%)
Query: 127 GGHNGLKSVMNNFRGIGRPP--GQMDPKAFL----LQKFNAIARERIDTALQEGVEVLKL 180
G + L+ ++NF I PP +D + + LQK + + + R ALQ+ ++
Sbjct: 18 GSFSSLQIALDNFSTIYEPPDLSGLDAEMIVIVKNLQKRDIVTKCR---ALQDLIQ---- 70
Query: 181 LLSKGLTESARHFN--------------TIQKYKHIRLQ 205
+ ++ N +I+ + RL+
Sbjct: 71 -----WNDPSQFDNEQFLNALAVLFPRLSIEVEMNPRLE 104
>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 = 27.7 bits (62), Expect = 5.1
Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 4/62 (6%)
Query: 128 GHNGLKSVMNNF----RGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLS 183
G L V++ G G+ ++ + + N + R I L GV + LL+
Sbjct: 100 GDGLLGRVLDGLGKPIDGKGKFLDNVETEGLITAPINPLKRAPIREILSTGVRSIDGLLT 159
Query: 184 KG 185
G
Sbjct: 160 VG 161
>gnl|CDD|225319 COG2521, COG2521, Predicted archaeal methyltransferase [General
function prediction only].
Length = 287
Score = 27.4 bits (61), Expect = 6.1
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 15/57 (26%)
Query: 5 RFLRRGFCTAVARPWLFVGLGNPGDKYKGT--------RHNQVGFEMIDAFAESQGI 53
R L+RG R LF +GNPG +Y+G R +VGFE++ E+ G+
Sbjct: 233 RILKRG-----GR--LFHYVGNPGKRYRGLDLPKGVAERLRRVGFEVVKKVREALGV 282
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
0.323 0.141 0.432
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: 10,876,001
Number of extensions: 1024101
Number of successful extensions: 771
Number of sequences better than 10.0: 1
Number of HSP's gapped: 754
Number of HSP's successfully gapped: 19
Length of query: 209
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 116
Effective length of database: 6,812,680
Effective search space: 790270880
Effective search space used: 790270880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (25.8 bits)