RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 026076
(244 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 = 346 bits (889), Expect = e-122
Identities = 149/191 (78%), Positives = 169/191 (88%)
Query: 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLA 107
TPWLI GLGNPG KY GTRHNVGFEM+D IA+A+ I MNTIQ K+L+GIGSIG+VP+LLA
Sbjct: 1 TPWLIAGLGNPGNKYKGTRHNVGFEMVDRIAEAEGITMNTIQFKSLLGIGSIGDVPVLLA 60
Query: 108 KPQAYMNFSGESVGPLAAHYQVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMN 167
KPQ YMN+SGESVGPLAA+Y+VPLRHILVIYD+MSL NGVLRLQPKGGHG HNGL+SV+
Sbjct: 61 KPQTYMNYSGESVGPLAAYYKVPLRHILVIYDDMSLPNGVLRLQPKGGHGRHNGLQSVIE 120
Query: 168 HLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFD 227
HLDG REFPRL IGIG+PPGKMD +A+LLQKFS EREQID ALEQGV+AVRTLVL GF+
Sbjct: 121 HLDGSREFPRLSIGIGSPPGKMDPRAFLLQKFSSEEREQIDTALEQGVDAVRTLVLKGFN 180
Query: 228 QNISRFNMGQK 238
+ RFN+ 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 = 240 bits (615), Expect = 4e-81
Identities = 87/172 (50%), Positives = 117/172 (68%), Gaps = 1/172 (0%)
Query: 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQ 110
LIVGLGNPG KY TRHNVGF ++D +A+ ++ + K L+G G IG +LL KPQ
Sbjct: 1 LIVGLGNPGPKYENTRHNVGFMVLDALAERYGVSFKKKKKKGLVGEGRIGGEKVLLLKPQ 60
Query: 111 AYMNFSGESVGPLAAHYQVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLD 170
YMN SGE+V LA Y++P ILVI+D++ L G +RL+ GG G HNGLKS++ HL
Sbjct: 61 TYMNLSGEAVAALANFYKIPPEDILVIHDDLDLPLGKIRLKKGGGSGGHNGLKSIIAHL- 119
Query: 171 GCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLV 222
G +FPRL IGIG PP KMD+ Y+L KFS ERE ++ A+E+ +A+ ++
Sbjct: 120 GTEDFPRLRIGIGRPPNKMDVADYVLSKFSKEERELLEEAIEKAADALEDIL 171
>gnl|CDD|216355 pfam01195, Pept_tRNA_hydro, Peptidyl-tRNA hydrolase.
Length = 183
Score = 232 bits (593), Expect = 9e-78
Identities = 90/184 (48%), Positives = 122/184 (66%), Gaps = 2/184 (1%)
Query: 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQS-KALIGIGSIGEVPILLAKP 109
LIVGLGNPG KY TRHNVGF +ID +A+ +++ + K LI G I ++L KP
Sbjct: 1 LIVGLGNPGPKYENTRHNVGFMVIDRLAERLGVSLKKKKKFKGLIAKGRIEGEKVILLKP 60
Query: 110 QAYMNFSGESVGPLAAHYQVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHL 169
Q YMN SGE+V +A Y++P ILV++D++ L G LRL+ GG G HNGLKS++ HL
Sbjct: 61 QTYMNLSGEAVRAIARFYKIPPEDILVVHDDLDLPLGKLRLKKGGGAGGHNGLKSIIQHL 120
Query: 170 DGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQN 229
G +F RL IGIG PP K D+ Y+L KFSP E E +D A+E+ +A+ L+ GFD+
Sbjct: 121 -GTNDFKRLRIGIGRPPDKNDVADYVLSKFSPEELELLDKAIEKAADALEDLIEGGFDKA 179
Query: 230 ISRF 233
++RF
Sbjct: 180 MNRF 183
>gnl|CDD|235457 PRK05426, PRK05426, peptidyl-tRNA hydrolase; Provisional.
Length = 189
Score = 222 bits (568), Expect = 8e-74
Identities = 82/187 (43%), Positives = 119/187 (63%), Gaps = 3/187 (1%)
Query: 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQA-QRIAMNTIQSKALIGIGSIGEVPILLA 107
LIVGLGNPG +Y TRHN+GF ++D +A+ + K LI G I ++L
Sbjct: 2 MKLIVGLGNPGPEYANTRHNIGFMVVDELARRLGGSLKEKKKFKGLIAEGRINGEKVILL 61
Query: 108 KPQAYMNFSGESVGPLAAHYQVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMN 167
KPQ YMN SG++V LA Y++P ILVI+D++ L G +RL+ GG G HNGLKS++
Sbjct: 62 KPQTYMNLSGKAVAALANFYKIPPEDILVIHDDLDLPPGKIRLKKGGGAGGHNGLKSIIA 121
Query: 168 HLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFD 227
HL G ++F RL IGIG P K + Y+L KFS E+E +D A+++ +A+ L+ GF+
Sbjct: 122 HL-GTQDFWRLRIGIGR-PDKKKVVDYVLGKFSKEEQELLDKAIDKAADAIELLLEGGFE 179
Query: 228 QNISRFN 234
+ +++FN
Sbjct: 180 KAMNKFN 186
>gnl|CDD|223271 COG0193, Pth, Peptidyl-tRNA hydrolase [Translation, ribosomal
structure and biogenesis].
Length = 190
Score = 205 bits (525), Expect = 3e-67
Identities = 81/189 (42%), Positives = 118/189 (62%), Gaps = 4/189 (2%)
Query: 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSK--ALIGIGSIGEVPIL 105
LIVGLGNPG KY TRHNVGF ++D +A+ ++ + K L+ G+I ++
Sbjct: 1 MMKLIVGLGNPGKKYAKTRHNVGFMVVDLLARRLNLS-FKEEKKFNGLVAKGTIEGEKVI 59
Query: 106 LAKPQAYMNFSGESVGPLAAHYQVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSV 165
L KP YMN SG++VG LA+ Y++ ILV++DE+ L G +RL+ GG G HNGLKS+
Sbjct: 60 LLKPTTYMNLSGKAVGALASFYKIKPEDILVVHDELDLPLGKVRLKLGGGAGGHNGLKSI 119
Query: 166 MNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNG 225
+ HL G F RL IGIG P D+ Y+L KFS ERE +D A+++ +A+ L+
Sbjct: 120 IAHL-GTNNFYRLRIGIGRPGNGEDVADYVLGKFSKEERELLDKAIDKAADALELLLEGD 178
Query: 226 FDQNISRFN 234
F++ +++ N
Sbjct: 179 FEKAMNKLN 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 = 172 bits (437), Expect = 4e-54
Identities = 77/186 (41%), Positives = 114/186 (61%), Gaps = 3/186 (1%)
Query: 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSK-ALIGIGSIGEVPILLAKP 109
LIVGLGNPG KY GTRHN GF ++D +A +++ T + G + ++L KP
Sbjct: 3 LIVGLGNPGKKYAGTRHNAGFWVLDLLASRLGLSLRTEKKFFGYTERGLLSGKKVILLKP 62
Query: 110 QAYMNFSGESVGPLAAHYQVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHL 169
YMN SGE+V LA+ Y++ +LV++DE+ L G +RL+ GG G HNGLKS+++HL
Sbjct: 63 LTYMNLSGEAVRALASFYRIKPAELLVVHDELDLPLGKVRLKMGGGAGGHNGLKSIISHL 122
Query: 170 DGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAALEQGVEAV-RTLVLNGFDQ 228
G F RL IGIG+P G + ++L KF+ E ++ AL++ VEA+ + F +
Sbjct: 123 -GTNNFNRLRIGIGSPGGSNKVVEFVLSKFTKSELPLLEKALDKAVEALEMSFSEGAFLK 181
Query: 229 NISRFN 234
++RFN
Sbjct: 182 AMNRFN 187
>gnl|CDD|182708 PRK10763, PRK10763, phospholipase A; Provisional.
Length = 289
Score = 33.6 bits (77), Expect = 0.074
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 32 VHASLPADNGGFKVEYTPWLIVGL--GNPGI-KYHGT-RHNVGFEMIDHIAQAQ 81
++ L A NG + VE PW +G NP I KY G + +G+ + D + A+
Sbjct: 178 LYTRLMAQNGNWLVEVKPWYRIGSTDDNPDITKYMGYYQLKIGYHLGDAVFSAK 231
>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 = 28.4 bits (64), Expect = 1.7
Identities = 10/44 (22%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 191 MKAYLLQKFSPIERE-QIDAALEQGVEAVRTLVLNGFDQNISRF 233
++ LL++ + E + +E G + TL+ + D+N +F
Sbjct: 32 VEKVLLKRLPIMGAEIAPEEEIENGTAKLETLLESRVDKNFDKF 75
>gnl|CDD|232796 TIGR00043, TIGR00043, probable rRNA maturation factor YbeY. This
metalloprotein family is represented by a single member
sequence only in nearly every bacterium. Crystallography
demonstrated metal-binding activity, possibly to nickel.
It is a predicted to be a metallohydrolase, and more
recently it was shown that mutants have a ribosomal RNA
processing defect [Protein synthesis, Other].
Length = 110
Score = 28.0 bits (63), Expect = 2.1
Identities = 9/35 (25%), Positives = 17/35 (48%), Gaps = 3/35 (8%)
Query: 63 HGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIG 97
HG H +G+ DH + + M ++ + L +G
Sbjct: 79 HGLLHLLGY---DHETEDEEKEMFALEEEILALLG 110
>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 = 27.2 bits (61), Expect = 2.3
Identities = 9/41 (21%), Positives = 14/41 (34%), Gaps = 4/41 (9%)
Query: 139 DEMSLMNGVLRLQPKGGHGHHNGLKSVMNHL---DGCREFP 176
E+ L + +P G H H + + L R F
Sbjct: 2 QEIRLFKAIEGFKPVGIHKHFR-MICISERLRSSGLDRHFS 41
>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 = 28.3 bits (64), Expect = 2.6
Identities = 14/28 (50%), Positives = 15/28 (53%)
Query: 205 EQIDAALEQGVEAVRTLVLNGFDQNISR 232
E +D LE VE R LV G D ISR
Sbjct: 12 EVVDGGLEDAVEVARALVAEGVDVIISR 39
>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 = 28.6 bits (64), Expect = 2.7
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 5/35 (14%)
Query: 186 PGKMDMKAYLLQ-----KFSPIEREQIDAALEQGV 215
Y +Q FSPIE+ ++DA+ EQG
Sbjct: 137 YATKLKAEYCMQYQVGVTFSPIEKVELDASWEQGK 171
>gnl|CDD|224948 COG2037, Ftr, Formylmethanofuran:tetrahydromethanopterin
formyltransferase [Energy production and conversion].
Length = 297
Score = 28.2 bits (63), Expect = 3.5
Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 175 FPRLCIGIGNPPGKM---DMKAYLLQKFSPIEREQI-DAALEQGVEAVRTLVLNGFDQNI 230
FP + G+ G + A K+ P ++ + D+ + +GV+A+ +V+NG D+
Sbjct: 197 FPGGIVASGSKVGTNKYPFLGATTNHKYCPTLKDVVEDSEVPEGVKAIYEIVINGLDEEA 256
Query: 231 SRFNMGQ 237
+ 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 = 4.0
Identities = 10/37 (27%), Positives = 22/37 (59%)
Query: 191 MKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFD 227
+ A + P ++Q+++ L +GV AV +V++G +
Sbjct: 208 LPASTNDAYCPTLKDQVESELPEGVNAVYEIVIDGLN 244
>gnl|CDD|171490 PRK12425, PRK12425, fumarate hydratase; Provisional.
Length = 464
Score = 27.6 bits (61), Expect = 7.1
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 159 HNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYL 195
HN L+S+ DGCR F + C+ G P M A+L
Sbjct: 365 HNLLQSIRLLADGCRNFQQHCVA-GLEPDAEQMAAHL 400
>gnl|CDD|201301 pfam00554, RHD, Rel homology domain (RHD). Proteins containing the
Rel homology domain (RHD) are eukaryotic transcription
factors. The RHD is composed of two structural domains.
This is the N-terminal domain that is similar to that
found in P53. The C-terminal domain has an
immunoglobulin-like fold (See pfam01833) that binds to
DNA.
Length = 169
Score = 26.5 bits (59), Expect = 9.0
Identities = 9/21 (42%), Positives = 9/21 (42%)
Query: 29 RLCVHASLPADNGGFKVEYTP 49
RLC A LP G F P
Sbjct: 140 RLCFQAFLPDTRGNFTTPLPP 160
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 0.140 0.431
Gapped
Lambda K H
0.267 0.0627 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,616,481
Number of extensions: 1203022
Number of successful extensions: 1096
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1085
Number of HSP's successfully gapped: 27
Length of query: 244
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 150
Effective length of database: 6,768,326
Effective search space: 1015248900
Effective search space used: 1015248900
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: 58 (26.3 bits)