RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 030459
(177 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 = 268 bits (688), Expect = 2e-93
Identities = 103/166 (62%), Positives = 130/166 (78%)
Query: 1 MIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLN 60
M+D AE++GI+MNT+ K+ G G +GD PVLLAKPQTYMN SGES GPLAAYYK+PL
Sbjct: 26 MVDRIAEAEGITMNTIQFKSLLGIGSIGDVPVLLAKPQTYMNYSGESVGPLAAYYKVPLR 85
Query: 61 RVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPK 120
+LV +DDM LP GVLRL+ GGHG HNGL+SV+ + G+REF RL IGIG PPG+MDP+
Sbjct: 86 HILVIYDDMSLPNGVLRLQPKGGHGRHNGLQSVIEHLDGSREFPRLSIGIGSPPGKMDPR 145
Query: 121 AFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHFNTIQK 166
AFLLQKF++ RE+IDTAL++GV+ ++ L+ KG SA FN +QK
Sbjct: 146 AFLLQKFSSEEREQIDTALEQGVDAVRTLVLKGFNGSAERFNLVQK 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 = 189 bits (484), Expect = 2e-62
Identities = 71/150 (47%), Positives = 99/150 (66%), Gaps = 1/150 (0%)
Query: 1 MIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLN 60
++DA AE G+S K G+G +G VLL KPQTYMNLSGE+ LA +YK+P
Sbjct: 23 VLDALAERYGVSFKKKKKKGLVGEGRIGGEKVLLLKPQTYMNLSGEAVAALANFYKIPPE 82
Query: 61 RVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPK 120
+LV HDD+ LP G +RL+ GG GGHNGLKS++ + G +F RLRIGIGRPP +MD
Sbjct: 83 DILVIHDDLDLPLGKIRLKKGGGSGGHNGLKSIIAHL-GTEDFPRLRIGIGRPPNKMDVA 141
Query: 121 AFLLQKFNAIARERIDTALQEGVEVLKLLL 150
++L KF+ RE ++ A+++ + L+ +L
Sbjct: 142 DYVLSKFSKEERELLEEAIEKAADALEDIL 171
>gnl|CDD|216355 pfam01195, Pept_tRNA_hydro, Peptidyl-tRNA hydrolase.
Length = 183
Score = 181 bits (461), Expect = 8e-59
Identities = 68/157 (43%), Positives = 97/157 (61%), Gaps = 2/157 (1%)
Query: 1 MIDAFAESQGISMNTV-HCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPL 59
+ID AE G+S+ K +G + V+L KPQTYMNLSGE+ +A +YK+P
Sbjct: 23 VIDRLAERLGVSLKKKKKFKGLIAKGRIEGEKVILLKPQTYMNLSGEAVRAIARFYKIPP 82
Query: 60 NRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDP 119
+LV HDD+ LP G LRL+ GG GGHNGLKS++ + G +F RLRIGIGRPP + D
Sbjct: 83 EDILVVHDDLDLPLGKLRLKKGGGAGGHNGLKSIIQHL-GTNDFKRLRIGIGRPPDKNDV 141
Query: 120 KAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTE 156
++L KF+ E +D A+++ + L+ L+ G +
Sbjct: 142 ADYVLSKFSPEELELLDKAIEKAADALEDLIEGGFDK 178
>gnl|CDD|235457 PRK05426, PRK05426, peptidyl-tRNA hydrolase; Provisional.
Length = 189
Score = 174 bits (445), Expect = 3e-56
Identities = 66/163 (40%), Positives = 98/163 (60%), Gaps = 3/163 (1%)
Query: 2 IDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLN 60
+D A G S+ K +G + V+L KPQTYMNLSG++ LA +YK+P
Sbjct: 27 VDELARRLGGSLKEKKKFKGLIAEGRINGEKVILLKPQTYMNLSGKAVAALANFYKIPPE 86
Query: 61 RVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPK 120
+LV HDD+ LP G +RL+ GG GGHNGLKS++ + G ++F RLRIGIGRP +
Sbjct: 87 DILVIHDDLDLPPGKIRLKKGGGAGGHNGLKSIIAHL-GTQDFWRLRIGIGRPDKK-KVV 144
Query: 121 AFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHFNT 163
++L KF+ +E +D A+ + + ++LLL G ++ FN+
Sbjct: 145 DYVLGKFSKEEQELLDKAIDKAADAIELLLEGGFEKAMNKFNS 187
>gnl|CDD|223271 COG0193, Pth, Peptidyl-tRNA hydrolase [Translation, ribosomal
structure and biogenesis].
Length = 190
Score = 170 bits (434), Expect = 2e-54
Identities = 63/164 (38%), Positives = 92/164 (56%), Gaps = 2/164 (1%)
Query: 1 MIDAFAESQGIS-MNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPL 59
++D A +S +G + V+L KP TYMNLSG++ G LA++YK+
Sbjct: 26 VVDLLARRLNLSFKEEKKFNGLVAKGTIEGEKVILLKPTTYMNLSGKAVGALASFYKIKP 85
Query: 60 NRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDP 119
+LV HD++ LP G +RL+ GG GGHNGLKS++ + G F RLRIGIGRP D
Sbjct: 86 EDILVVHDELDLPLGKVRLKLGGGAGGHNGLKSIIAHL-GTNNFYRLRIGIGRPGNGEDV 144
Query: 120 KAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHFNT 163
++L KF+ RE +D A+ + + L+LLL ++ N
Sbjct: 145 ADYVLGKFSKEERELLDKAIDKAADALELLLEGDFEKAMNKLNA 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 = 143 bits (362), Expect = 8e-44
Identities = 62/154 (40%), Positives = 90/154 (58%), Gaps = 2/154 (1%)
Query: 1 MIDAFAESQGISMNTVHCK-ATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPL 59
++D A G+S+ T +G + V+L KP TYMNLSGE+ LA++Y++
Sbjct: 25 VLDLLASRLGLSLRTEKKFFGYTERGLLSGKKVILLKPLTYMNLSGEAVRALASFYRIKP 84
Query: 60 NRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDP 119
+LV HD++ LP G +RL+ GG GGHNGLKS++++ G F RLRIGIG P G
Sbjct: 85 AELLVVHDELDLPLGKVRLKMGGGAGGHNGLKSIISHL-GTNNFNRLRIGIGSPGGSNKV 143
Query: 120 KAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 153
F+L KF ++ AL + VE L++ S+G
Sbjct: 144 VEFVLSKFTKSELPLLEKALDKAVEALEMSFSEG 177
>gnl|CDD|182322 PRK10234, PRK10234, DNA-binding transcriptional activator GutM;
Provisional.
Length = 118
Score = 29.2 bits (66), Expect = 0.45
Identities = 23/66 (34%), Positives = 30/66 (45%), Gaps = 16/66 (24%)
Query: 98 RGNREFARL----RIGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 153
R NR F L R+G+GR G+ P+ + A+ AL E V+ L KG
Sbjct: 26 RFNRAFDTLCQQGRVGVGRSSGRFKPRVVV-----AL-------ALDEQQRVVDTLFMKG 73
Query: 154 LTESAR 159
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 = 29.3 bits (66), Expect = 0.97
Identities = 11/30 (36%), Positives = 13/30 (43%), Gaps = 1/30 (3%)
Query: 118 DPKAFLLQKFN-AIARERIDTALQEGVEVL 146
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 = 3.6
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 15/63 (23%)
Query: 102 EFARLRIGIGRP-------PGQMDPKAFLLQKFNAIARE---RIDTALQEGVEVLKLLLS 151
E+A L GRP G+++P+ + F+A+ ++ RI+ + VEV L+ S
Sbjct: 132 EYAHL---TGRPFRVFSLDTGRLNPETYRF--FDAVEKQYGIRIEYMFPDAVEVQALVRS 186
Query: 152 KGL 154
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 = 4.7
Identities = 11/45 (24%), Positives = 19/45 (42%)
Query: 109 GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 153
G G+ ++ + + N + R I L GV + LL+ G
Sbjct: 117 GKGKFLDNVETEGLITAPINPLKRAPIREILSTGVRSIDGLLTVG 161
>gnl|CDD|165155 PHA02792, PHA02792, ankyrin-like protein; Provisional.
Length = 631
Score = 27.6 bits (61), Expect = 4.8
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 8/43 (18%)
Query: 127 FNAIARERIDTALQEGVEVLKLLLSKGL-TESARH-FNTIQKY 167
F + + ID +E+LKLL+SKGL S ++ N ++KY
Sbjct: 75 FEYLCSDNID------IELLKLLISKGLEINSIKNGINIVEKY 111
>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 = 5.0
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 3/72 (4%)
Query: 42 NLSGESTGPLAAYY--KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRG 99
N+ GE+ A + ++ ++L+ D G PC L G G L+ ++
Sbjct: 116 NIDGEALAQAAKLFAGRMEDKKILLMISD-GAPCDDSTLSVAAGDGFEQHLRHIIEEIET 174
Query: 100 NREFARLRIGIG 111
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 = 26.7 bits (59), Expect = 7.6
Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 2/59 (3%)
Query: 108 IGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHFNTIQK 166
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
0.322 0.139 0.416
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: 9,146,188
Number of extensions: 860241
Number of successful extensions: 655
Number of sequences better than 10.0: 1
Number of HSP's gapped: 649
Number of HSP's successfully gapped: 21
Length of query: 177
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 86
Effective length of database: 6,901,388
Effective search space: 593519368
Effective search space used: 593519368
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (25.5 bits)