RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 029850
(186 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 = 296 bits (760), Expect = e-104
Identities = 131/170 (77%), Positives = 151/170 (88%)
Query: 11 VGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQ 70
VGFEM+D IA+A+ I MNTIQ K+L+GIGSIG+VP+LLAKPQ YMN+SGESVGPLAA+Y+
Sbjct: 22 VGFEMVDRIAEAEGITMNTIQFKSLLGIGSIGDVPVLLAKPQTYMNYSGESVGPLAAYYK 81
Query: 71 VPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGK 130
VPLRHILVIYD+MSL NGVLRLQPKGGHG HNGL+SV+ HLDG REFPRL IGIG+PPGK
Sbjct: 82 VPLRHILVIYDDMSLPNGVLRLQPKGGHGRHNGLQSVIEHLDGSREFPRLSIGIGSPPGK 141
Query: 131 MDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISRFNMGQK 180
MD +A+LLQKFS EREQID ALEQGV+AVRTLVL GF+ + RFN+ QK
Sbjct: 142 MDPRAFLLQKFSSEEREQIDTALEQGVDAVRTLVLKGFNGSAERFNLVQK 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 = 194 bits (496), Expect = 4e-64
Identities = 72/154 (46%), Positives = 102/154 (66%), Gaps = 1/154 (0%)
Query: 11 VGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQ 70
VGF ++D +A+ ++ + K L+G G IG +LL KPQ YMN SGE+V LA Y+
Sbjct: 19 VGFMVLDALAERYGVSFKKKKKKGLVGEGRIGGEKVLLLKPQTYMNLSGEAVAALANFYK 78
Query: 71 VPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGK 130
+P ILVI+D++ L G +RL+ GG G HNGLKS++ HL G +FPRL IGIG PP K
Sbjct: 79 IPPEDILVIHDDLDLPLGKIRLKKGGGSGGHNGLKSIIAHL-GTEDFPRLRIGIGRPPNK 137
Query: 131 MDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLV 164
MD+ Y+L KFS ERE ++ A+E+ +A+ ++
Sbjct: 138 MDVADYVLSKFSKEERELLEEAIEKAADALEDIL 171
>gnl|CDD|216355 pfam01195, Pept_tRNA_hydro, Peptidyl-tRNA hydrolase.
Length = 183
Score = 187 bits (478), Expect = 4e-61
Identities = 75/166 (45%), Positives = 107/166 (64%), Gaps = 2/166 (1%)
Query: 11 VGFEMIDHIAQAQRIAMNTIQS-KALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHY 69
VGF +ID +A+ +++ + K LI G I ++L KPQ YMN SGE+V +A Y
Sbjct: 19 VGFMVIDRLAERLGVSLKKKKKFKGLIAKGRIEGEKVILLKPQTYMNLSGEAVRAIARFY 78
Query: 70 QVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPG 129
++P ILV++D++ L G LRL+ GG G HNGLKS++ HL G +F RL IGIG PP
Sbjct: 79 KIPPEDILVVHDDLDLPLGKLRLKKGGGAGGHNGLKSIIQHL-GTNDFKRLRIGIGRPPD 137
Query: 130 KMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISRF 175
K D+ Y+L KFSP E E +D A+E+ +A+ L+ GFD+ ++RF
Sbjct: 138 KNDVADYVLSKFSPEELELLDKAIEKAADALEDLIEGGFDKAMNRF 183
>gnl|CDD|235457 PRK05426, PRK05426, peptidyl-tRNA hydrolase; Provisional.
Length = 189
Score = 173 bits (441), Expect = 2e-55
Identities = 68/167 (40%), Positives = 104/167 (62%), Gaps = 3/167 (1%)
Query: 11 VGFEMIDHIAQA-QRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHY 69
+GF ++D +A+ + K LI G I ++L KPQ YMN SG++V LA Y
Sbjct: 22 IGFMVVDELARRLGGSLKEKKKFKGLIAEGRINGEKVILLKPQTYMNLSGKAVAALANFY 81
Query: 70 QVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPG 129
++P ILVI+D++ L G +RL+ GG G HNGLKS++ HL G ++F RL IGIG P
Sbjct: 82 KIPPEDILVIHDDLDLPPGKIRLKKGGGAGGHNGLKSIIAHL-GTQDFWRLRIGIGR-PD 139
Query: 130 KMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISRFN 176
K + Y+L KFS E+E +D A+++ +A+ L+ GF++ +++FN
Sbjct: 140 KKKVVDYVLGKFSKEEQELLDKAIDKAADAIELLLEGGFEKAMNKFN 186
>gnl|CDD|223271 COG0193, Pth, Peptidyl-tRNA hydrolase [Translation, ribosomal
structure and biogenesis].
Length = 190
Score = 160 bits (407), Expect = 2e-50
Identities = 66/168 (39%), Positives = 103/168 (61%), Gaps = 4/168 (2%)
Query: 11 VGFEMIDHIAQAQRIAMNTIQSK--ALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAH 68
VGF ++D +A+ ++ + K L+ G+I ++L KP YMN SG++VG LA+
Sbjct: 22 VGFMVVDLLARRLNLS-FKEEKKFNGLVAKGTIEGEKVILLKPTTYMNLSGKAVGALASF 80
Query: 69 YQVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPP 128
Y++ ILV++DE+ L G +RL+ GG G HNGLKS++ HL G F RL IGIG P
Sbjct: 81 YKIKPEDILVVHDELDLPLGKVRLKLGGGAGGHNGLKSIIAHL-GTNNFYRLRIGIGRPG 139
Query: 129 GKMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISRFN 176
D+ Y+L KFS ERE +D A+++ +A+ L+ F++ +++ N
Sbjct: 140 NGEDVADYVLGKFSKEERELLDKAIDKAADALELLLEGDFEKAMNKLN 187
>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 = 134 bits (339), Expect = 3e-40
Identities = 61/168 (36%), Positives = 98/168 (58%), Gaps = 3/168 (1%)
Query: 11 VGFEMIDHIAQAQRIAMNTIQSK-ALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHY 69
GF ++D +A +++ T + G + ++L KP YMN SGE+V LA+ Y
Sbjct: 21 AGFWVLDLLASRLGLSLRTEKKFFGYTERGLLSGKKVILLKPLTYMNLSGEAVRALASFY 80
Query: 70 QVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPG 129
++ +LV++DE+ L G +RL+ GG G HNGLKS+++HL G F RL IGIG+P G
Sbjct: 81 RIKPAELLVVHDELDLPLGKVRLKMGGGAGGHNGLKSIISHL-GTNNFNRLRIGIGSPGG 139
Query: 130 KMDMKAYLLQKFSPIEREQIDAALEQGVEAV-RTLVLNGFDQNISRFN 176
+ ++L KF+ E ++ AL++ VEA+ + F + ++RFN
Sbjct: 140 SNKVVEFVLSKFTKSELPLLEKALDKAVEALEMSFSEGAFLKAMNRFN 187
>gnl|CDD|153116 cd01058, AAMH_B, Aromatic and Alkene Monooxygenase Hydroxylase,
subunit B, ferritin-like diiron-binding domain.
Aromatic and Alkene Monooxygenase Hydroxylases, subunit
B (AAMH_B). Subunit B (beta) of the soluble hydroxylase
of multicomponent, aromatic and alkene monooxygenases
are members of a superfamily of ferritin-like
iron-storage proteins. AAMH exists as a hexamer (an
alpha2-beta2-gamma2 homodimer) with each alpha-subunit
housing one nonheme diiron center embedded in a
four-helix bundle. The N-terminal domain of the alpha-
and noncatalytic beta-subunits possess nearly identical
folds; the beta-subunit lacks the C-terminal domain
found in the alpha-subunit. Methane monooxygenase is a
multicomponent enzyme found in methanotrophic bacteria
that catalyzes the hydroxylation of methane and higher
alkenes (as large as octane). Phenol monooxygenase,
found in a diverse group of bacteria, catalyses the
hydroxylation of phenol, chloro- and methyl-phenol and
naphthol. Both enzyme systems consist of three
components: the hydroxylase, a coupling protein and a
reductase. In the MMO hydroxylase, dioxygen and
substrate interact with the diiron center in a
hydrophobic cavity at the active site. The reductase
component and protein coupling factor provide electrons
from NADH for reducing the oxidized binuclear iron-oxo
cluster to its reduced form. Reaction with dioxygen
produces a peroxy-bridged complex and dehydration leads
to the formation of complex Q, which is thought to be
the oxygenating species that carries out the insertion
of an oxygen atom into a C-H bond of the substrate. The
toluene monooxygenase systems, toluene 2-, 3-, and
4-monooxygenase, are similar to MMO but with an
additional component, a Rieske-type ferredoxin. The
alkene monooxygenase from Xanthobacter strain Py2 is
closely related to aromatic monooxygenases and catalyzes
aromatic monohydroxylation of benzene, toluene, and
phenol. Alkane omega-hydroxylase (AlkB) and xylene
monooxygenase are members of a distinct class of
integral membrane diiron proteins and are not included
in this CD.
Length = 304
Score = 31.5 bits (72), Expect = 0.20
Identities = 22/85 (25%), Positives = 32/85 (37%), Gaps = 20/85 (23%)
Query: 1 MALGTIISCQVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGE 60
A T I+ F+ +D + AQ IA + L G+ AK +A+
Sbjct: 125 YAPSTTITNAAAFQAMDKLRIAQDIAY---RGLEL--DGNTPGFDGDAAK-EAWEE---- 174
Query: 61 SVGPLAAHYQVPLR----HILVIYD 81
P +Q LR +LV YD
Sbjct: 175 --DPA---WQ-GLRELVEKLLVTYD 193
>gnl|CDD|217201 pfam02722, MOSP_C, Major Outer Sheath Protein C-terminal region.
This is a family of spirochete major outer sheath
protein C-terminal regions. These proteins are present
on the bacterial cell surface. In T. denticola the major
outer sheath protein (Msp) binds immobilised laminin and
fibronectin supporting the hypothesis that Msp mediates
the extracellular matrix binding activity of T.
denticola.
Length = 201
Score = 29.0 bits (65), Expect = 1.1
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 5/35 (14%)
Query: 128 PGKMDMKAYLLQ-----KFSPIEREQIDAALEQGV 157
Y +Q FSPIE+ ++DA+ EQG
Sbjct: 137 YATKLKAEYCMQYQVGVTFSPIEKVELDASWEQGK 171
>gnl|CDD|219632 pfam07904, Eaf7, Chromatin modification-related protein EAF7. The
S. cerevisiae member of this family is part of NuA4, the
only essential histone acetyltransferase complex in
Saccharomyces cerevisiae involved in global histone
acetylation.
Length = 83
Score = 26.9 bits (60), Expect = 2.2
Identities = 9/41 (21%), Positives = 14/41 (34%), Gaps = 4/41 (9%)
Query: 81 DEMSLMNGVLRLQPKGGHGHHNGLKSVMNHL---DGCREFP 118
E+ L + +P G H H + + L R F
Sbjct: 2 QEIRLFKAIEGFKPVGIHKHFR-MICISERLRSSGLDRHFS 41
>gnl|CDD|218782 pfam05859, Mis12, Mis12 protein. Kinetochores are the chromosomal
sites for spindle interaction and play a vital role in
chromosome segregation. Fission yeast kinetochore
protein Mis12, is required for correct spindle
morphogenesis, determining metaphase spindle length.
Thirty-five to sixty percent extension of metaphase
spindle length takes place in Mis12 mutants. It has been
shown that Mis12 genetically interacts with Mal2,
another inner centromere core complex protein in S.
pombe.
Length = 141
Score = 27.7 bits (62), Expect = 2.2
Identities = 10/44 (22%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 133 MKAYLLQKFSPIERE-QIDAALEQGVEAVRTLVLNGFDQNISRF 175
++ LL++ + E + +E G + TL+ + D+N +F
Sbjct: 32 VEKVLLKRLPIMGAEIAPEEEIENGTAKLETLLESRVDKNFDKF 75
>gnl|CDD|224948 COG2037, Ftr, Formylmethanofuran:tetrahydromethanopterin
formyltransferase [Energy production and conversion].
Length = 297
Score = 28.2 bits (63), Expect = 2.5
Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 117 FPRLCIGIGNPPGKM---DMKAYLLQKFSPIEREQI-DAALEQGVEAVRTLVLNGFDQNI 172
FP + G+ G + A K+ P ++ + D+ + +GV+A+ +V+NG D+
Sbjct: 197 FPGGIVASGSKVGTNKYPFLGATTNHKYCPTLKDVVEDSEVPEGVKAIYEIVINGLDEEA 256
Query: 173 SRFNMGQ 179
+ M
Sbjct: 257 VKEAMRV 263
>gnl|CDD|132163 TIGR03119, one_C_fhcD, formylmethanofuran--tetrahydromethanopterin
N-formyltransferase. Members of this protein family are
the FhcD protein of tetrahydromethanopterin
(H4MPT)-dependent C-1 carrier metabolism. In the
archaea, FhcD is designated
formylmethanofuran--tetrahydromethanopterin
N-formyltransferase, while in bacteria it is commonly
designated as formyltransferase/hydrolase complex
subunit D. FhcD is essential for one-carbon metabolism
in at least three groups of prokaryotes: methanogenic
archaea, sulfate-reducing archaea, and methylotrophic
bacteria [Central intermediary metabolism, One-carbon
metabolism].
Length = 287
Score = 28.1 bits (63), Expect = 2.7
Identities = 10/37 (27%), Positives = 22/37 (59%)
Query: 133 MKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFD 169
+ A + P ++Q+++ L +GV AV +V++G +
Sbjct: 208 LPASTNDAYCPTLKDQVESELPEGVNAVYEIVIDGLN 244
>gnl|CDD|219065 pfam06506, PrpR_N, Propionate catabolism activator. This domain is
found at the N terminus of several sigma54- dependent
transcriptional activators including PrpR, which
activates catabolism of propionate.
Length = 169
Score = 27.5 bits (62), Expect = 3.4
Identities = 14/28 (50%), Positives = 15/28 (53%)
Query: 147 EQIDAALEQGVEAVRTLVLNGFDQNISR 174
E +D LE VE R LV G D ISR
Sbjct: 12 EVVDGGLEDAVEVARALVAEGVDVIISR 39
>gnl|CDD|237558 PRK13920, PRK13920, putative anti-sigmaE protein; Provisional.
Length = 206
Score = 27.5 bits (61), Expect = 4.1
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 133 MKAYLLQKFSPIEREQIDAALE 154
+ Y L SP ER +++AALE
Sbjct: 1 LPLYALGALSPEERARVEAALE 22
>gnl|CDD|171490 PRK12425, PRK12425, fumarate hydratase; Provisional.
Length = 464
Score = 27.6 bits (61), Expect = 5.1
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 101 HNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYL 137
HN L+S+ DGCR F + C+ G P M A+L
Sbjct: 365 HNLLQSIRLLADGCRNFQQHCVA-GLEPDAEQMAAHL 400
>gnl|CDD|181826 PRK09406, gabD1, succinic semialdehyde dehydrogenase; Reviewed.
Length = 457
Score = 27.0 bits (60), Expect = 6.3
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 138 LQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQ 170
++ F+ + +++DAA+ + R F Q
Sbjct: 14 VKTFTALTDDEVDAAIARAHARFRDYRTTTFAQ 46
>gnl|CDD|233412 TIGR01438, TGR, thioredoxin and glutathione reductase
selenoprotein. This homodimeric, FAD-containing member
of the pyridine nucleotide disulfide oxidoreductase
family contains a C-terminal motif Cys-SeCys-Gly, where
SeCys is selenocysteine encoded by TGA (in some sequence
reports interpreted as a stop codon). In some members of
this subfamily, Cys-SeCys-Gly is replaced by
Cys-Cys-Gly. The reach of the selenium atom at the
C-term arm of the protein is proposed to allow broad
substrate specificity.
Length = 484
Score = 26.7 bits (59), Expect = 8.4
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 7/43 (16%)
Query: 151 AALEQGVE-AVRTLVLNGFDQNISRFNM------GQKYKYHAV 186
A + V VR+++L GFDQ+ + G K+K V
Sbjct: 200 AGIGLDVTVMVRSILLRGFDQDCANKVGEHMEEHGVKFKRQFV 242
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 0.140 0.413
Gapped
Lambda K H
0.267 0.0754 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,663,896
Number of extensions: 913122
Number of successful extensions: 911
Number of sequences better than 10.0: 1
Number of HSP's gapped: 901
Number of HSP's successfully gapped: 33
Length of query: 186
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 95
Effective length of database: 6,901,388
Effective search space: 655631860
Effective search space used: 655631860
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 (25.3 bits)