RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780225|ref|YP_003064638.1| peptidyl-tRNA hydrolase
[Candidatus Liberibacter asiaticus str. psy62]
(189 letters)
>gnl|CDD|144695 pfam01195, Pept_tRNA_hydro, Peptidyl-tRNA hydrolase.
Length = 184
Score = 227 bits (581), Expect = 1e-60
Identities = 86/184 (46%), Positives = 115/184 (62%), Gaps = 3/184 (1%)
Query: 3 IVAGLGNPGHEYCENRHNIGFMCIDRIHS-FHFFPAWKKKFHAEISEGQLDGLRTILIKP 61
++ GLGNPG +Y RHN+GFM IDR+ KKKF I++G+++G + +L+KP
Sbjct: 1 LIVGLGNPGPKYENTRHNVGFMVIDRLAERLGVSLKKKKKFKGLIAKGRINGEKVLLLKP 60
Query: 62 QTFMNLSGQSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSISEK 121
QT+MNLSG+++ + FYK+P E+ LV+HDDLDL G LRLK GGG GHNGLKSI
Sbjct: 61 QTYMNLSGEAVRAIARFYKIP-PEDILVVHDDLDLPLGKLRLKKGGGAGGHNGLKSIISH 119
Query: 122 CG-KNYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLPIIDNIARSLPLLAKREDVSF 180
G ++KRLRIGIGRPPD + +VL FS E L I+ A +L L +
Sbjct: 120 LGTNDFKRLRIGIGRPPDKNDVADYVLSKFSPEELELLDKAIEKAADALEDLIEGGFDKA 179
Query: 181 LNHI 184
+N
Sbjct: 180 MNRF 183
>gnl|CDD|30542 COG0193, Pth, Peptidyl-tRNA hydrolase [Translation, ribosomal
structure and biogenesis].
Length = 190
Score = 218 bits (558), Expect = 6e-58
Identities = 82/186 (44%), Positives = 119/186 (63%), Gaps = 3/186 (1%)
Query: 1 MFIVAGLGNPGHEYCENRHNIGFMCIDRI-HSFHFFPAWKKKFHAEISEGQLDGLRTILI 59
M ++ GLGNPG +Y + RHN+GFM +D + + +KKF+ +++G ++G + IL+
Sbjct: 2 MKLIVGLGNPGKKYAKTRHNVGFMVVDLLARRLNLSFKEEKKFNGLVAKGTIEGEKVILL 61
Query: 60 KPQTFMNLSGQSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSIS 119
KP T+MNLSG+++ + +FYK+ E+ LV+HD+LDL G +RLK GGG GHNGLKSI
Sbjct: 62 KPTTYMNLSGKAVGALASFYKI-KPEDILVVHDELDLPLGKVRLKLGGGAGGHNGLKSII 120
Query: 120 EKCG-KNYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLPIIDNIARSLPLLAKREDV 178
G N+ RLRIGIGRP + + +VLG FS ER L ID A +L LL + +
Sbjct: 121 AHLGTNNFYRLRIGIGRPGNGEDVADYVLGKFSKEERELLDKAIDKAADALELLLEGDFE 180
Query: 179 SFLNHI 184
+N +
Sbjct: 181 KAMNKL 186
>gnl|CDD|73208 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 = 208 bits (531), Expect = 8e-55
Identities = 81/171 (47%), Positives = 111/171 (64%), Gaps = 2/171 (1%)
Query: 3 IVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQ 62
++ GLGNPG +Y RHN+GFM +D + + KKK + EG++ G + +L+KPQ
Sbjct: 1 LIVGLGNPGPKYENTRHNVGFMVLDALAERYGVSFKKKKKKGLVGEGRIGGEKVLLLKPQ 60
Query: 63 TFMNLSGQSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSISEKC 122
T+MNLSG+++ + NFYK+P E+ LVIHDDLDL G +RLK GGG GHNGLKSI
Sbjct: 61 TYMNLSGEAVAALANFYKIP-PEDILVIHDDLDLPLGKIRLKKGGGSGGHNGLKSIIAHL 119
Query: 123 G-KNYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLPIIDNIARSLPLL 172
G +++ RLRIGIGRPP+ + +VL FS ER L I+ A +L +
Sbjct: 120 GTEDFPRLRIGIGRPPNKMDVADYVLSKFSKEERELLEEAIEKAADALEDI 170
>gnl|CDD|48347 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 = 135 bits (342), Expect = 5e-33
Identities = 64/156 (41%), Positives = 92/156 (58%), Gaps = 3/156 (1%)
Query: 2 FIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKP 61
+++AGLGNPG++Y RHN+GF +DRI +F + + G + + +L KP
Sbjct: 3 WLIAGLGNPGNKYKGTRHNVGFEMVDRIAEAEGITMNTIQFKSLLGIGSIGDVPVLLAKP 62
Query: 62 QTFMNLSGQSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSISE- 120
QT+MN SG+S+ + +YK+P L + LVI+DD+ L G LRL+ GG HNGL+S+ E
Sbjct: 63 QTYMNYSGESVGPLAAYYKVP-LRHILVIYDDMSLPNGVLRLQPKGGHGRHNGLQSVIEH 121
Query: 121 -KCGKNYKRLRIGIGRPPDTAHIIRHVLGNFSSPER 155
+ + RL IGIG PP +L FSS ER
Sbjct: 122 LDGSREFPRLSIGIGSPPGKMDPRAFLLQKFSSEER 157
>gnl|CDD|37466 KOG2255, KOG2255, KOG2255, Peptidyl-tRNA hydrolase [Translation,
ribosomal structure and biogenesis].
Length = 224
Score = 120 bits (302), Expect = 2e-28
Identities = 66/183 (36%), Positives = 102/183 (55%), Gaps = 3/183 (1%)
Query: 2 FIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKP 61
+++ GLGNPG +Y RHN+GF +D + P A G + + +L++P
Sbjct: 40 WLIVGLGNPGSKYVGTRHNVGFEMLDMLARRLGVPMNTISSKALEGLGLVGDVPILLLRP 99
Query: 62 QTFMNLSGQSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSISEK 121
Q +MN SG+S+ +V YK+P L + +VIHD+L+L G LRL+ GG GHNG++S+
Sbjct: 100 QQYMNFSGESVGKVAALYKIP-LRHIVVIHDELELPLGKLRLRPGGSHRGHNGVRSVFNC 158
Query: 122 CG--KNYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLPIIDNIARSLPLLAKREDVS 179
+++ RL IGIGRPP + VL FS E+ LL + ++L L ++ +S
Sbjct: 159 LNGRRSFPRLSIGIGRPPGNEDVKAFVLSKFSPAEQKELLETLLEHVKTLILQGLQQSIS 218
Query: 180 FLN 182
N
Sbjct: 219 RFN 221
>gnl|CDD|31282 COG1085, GalT, Galactose-1-phosphate uridylyltransferase [Energy
production and conversion].
Length = 338
Score = 29.2 bits (65), Expect = 0.75
Identities = 25/93 (26%), Positives = 37/93 (39%), Gaps = 3/93 (3%)
Query: 16 ENRHNIGFMCIDRIHSFHF--FPAWKKKFHAEISEGQLDGLRTILIK-PQTFMNLSGQSL 72
EN H + F+ F +P F ++S+ +L L IL K + NL G S
Sbjct: 206 ENDHFLAFVPFWARWPFEVLIYPKEHVSFLTDLSDEELKDLAEILKKLLARYDNLFGNSF 265
Query: 73 LEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKT 105
M F++ P E H ++ LR T
Sbjct: 266 PYSMGFHQAPFNEVNEHYHLHAEIYPPLLRSAT 298
>gnl|CDD|37585 KOG2374, KOG2374, KOG2374, Uncharacterized conserved protein
[Function unknown].
Length = 661
Score = 29.0 bits (64), Expect = 0.82
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 115 LKSISEKCGKNYKRLRIGI 133
L+ +EK G +YK LR+G
Sbjct: 120 LEKWNEKFGFHYKELRLGF 138
>gnl|CDD|176561 cd08624, PI-PLCc_beta2, Catalytic domain of metazoan
phosphoinositide-specific phospholipase C-beta2. This
subfamily corresponds to the catalytic domain present in
metazoan phosphoinositide-specific phospholipase C
(PI-PLC, EC 3.1.4.11)-beta isozyme 2. PI-PLC is a
signaling enzyme that hydrolyzes the membrane
phospholipids phosphatidylinositol-4,5-bisphosphate
(PIP2) to generate two important second messengers in
eukaryotic signal transduction cascades, Inositol
1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG).
InsP3 triggers inflow of calcium from intracellular
stores, while DAG, together with calcium, activates
protein kinase C, which goes on to phosphorylate other
molecules, leading to altered cellular activity. Calcium
is required for the catalysis. PLC-beta represents a
class of mammalian PI-PLC that has an N-terminal
pleckstrin homology (PH) domain, an array of EF hands, a
PLC catalytic core domain, a C2 domain, and a unique
C-terminal coiled-coil (CT) domain necessary for
homodimerization. The PLC catalytic core domain is a TIM
barrel with two highly conserved regions (X and Y) split
by a highly degenerate linker sequence. PI-PLC-beta2 is
expressed at highest levels in cells of hematopoietic
origin. It is activated by the heterotrimeric G protein
alpha q subunits through their C2 domain and long
C-terminal extension. It is also activated by the
beta-gamma subunits of heterotrimeric G proteins.
Length = 261
Score = 28.5 bits (63), Expect = 1.3
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 4/57 (7%)
Query: 134 GRPPDTAHIIRHVLGNFSSPERYFLLPIIDNIARSLPLLAKREDV-SFLNHIVSVRK 189
G+PPD II H F+ I+ IA S + + SF NH+ S ++
Sbjct: 53 GKPPDEEPIITH---GFTMTTEILFKDAIEAIAESAFKTSPYPVILSFENHVDSPKQ 106
>gnl|CDD|36387 KOG1172, KOG1172, KOG1172, Na+-independent Cl/HCO3 exchanger AE1
and related transporters (SLC4 family) [Inorganic ion
transport and metabolism].
Length = 876
Score = 27.2 bits (60), Expect = 2.9
Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 5/60 (8%)
Query: 38 WKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMNFYKLPNLENYLVIHDDLDLD 97
W K A +S L LR+ L ++L SL E+ + + +V L +
Sbjct: 37 WSKPHVATLSLHSLFELRSCLANGTVLLDLDATSLPEIADQ-----VVEKMVESGQLKPE 91
>gnl|CDD|145275 pfam02006, DUF137, Protein of unknown function DUF137. This family
of archaeal proteins has no known function.
Length = 178
Score = 27.2 bits (61), Expect = 3.3
Identities = 7/16 (43%), Positives = 12/16 (75%)
Query: 159 LPIIDNIARSLPLLAK 174
+ I+DNI R++P L +
Sbjct: 130 ITIVDNITRAIPNLTE 145
>gnl|CDD|37242 KOG2031, KOG2031, KOG2031, Tyrosyl-DNA phosphodiesterase
[Replication, recombination and repair].
Length = 519
Score = 25.7 bits (56), Expect = 7.4
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 9/62 (14%)
Query: 70 QSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRL---------KTGGGDAGHNGLKSISE 120
Q L+E +N Y+LP L+ ++ +D +R +G GHN LK I +
Sbjct: 231 QDLIEYLNSYRLPQLKEWIASLKKVDFSAINVRFIGSTPGKFQGSGLLSWGHNKLKKILK 290
Query: 121 KC 122
+
Sbjct: 291 EH 292
>gnl|CDD|176552 cd08610, GDPD_GDE6, Glycerophosphodiester phosphodiesterase domain
of mammalian glycerophosphodiester phosphodiesterase
GDE6 and similar proteins. This subfamily corresponds
to the glycerophosphodiester phosphodiesterase domain
(GDPD) present in mammalian GDE6 (also known as
glycerophosphodiester phosphodiesterase
domain-containing protein 4 (GDPD4)) and their metazoan
homologs. Mammalian GDE6 is a transmembrane protein
predominantly expressed in the spermatocytes of testis.
Although the specific physiological function of
mammalian GDE6 has not been elucidated, its different
pattern of tissue distribution suggests it might play a
critical role in the completion of meiosis during male
germ cell differentiation.
Length = 316
Score = 25.6 bits (56), Expect = 9.6
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 11/45 (24%)
Query: 59 IKPQTFMNLS-----------GQSLLEVMNFYKLPNLENYLVIHD 92
+KP+ F N+ QS+ ++ NF +L EN LVI D
Sbjct: 110 VKPRPFYNMKPLSEADKERARNQSIPKLSNFLRLAEKENKLVIFD 154
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.325 0.144 0.445
Gapped
Lambda K H
0.267 0.0785 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,486,666
Number of extensions: 131024
Number of successful extensions: 364
Number of sequences better than 10.0: 1
Number of HSP's gapped: 349
Number of HSP's successfully gapped: 15
Length of query: 189
Length of database: 6,263,737
Length adjustment: 88
Effective length of query: 101
Effective length of database: 4,362,145
Effective search space: 440576645
Effective search space used: 440576645
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: 40 (21.5 bits)
S2: 54 (24.5 bits)