RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781032|ref|YP_003065445.1| hypothetical protein
CLIBASIA_04670 [Candidatus Liberibacter asiaticus str. psy62]
(118 letters)
>gnl|CDD|163236 TIGR03367, queuosine_QueD, queuosine biosynthesis protein QueD.
Members of this protein family, closely related to
eukaryotic 6-pyruvoyl tetrahydrobiopterin synthase
enzymes, are the QueD protein of queuosine
biosynthesis. Queuosine is a hypermodified base in the
wobble position of tRNAs for Tyr, His, Asp, and Asn in
many species. This modification, although widespread,
appears not to be important for viability. The
queuosine precursor made by this enzyme may be
converted instead to archeaosine as in some Archaea.
Length = 92
Score = 119 bits (302), Expect = 1e-28
Identities = 44/92 (47%), Positives = 65/92 (70%), Gaps = 2/92 (2%)
Query: 2 KITQAFTFEAAHRLPRVPKTHKCHRMHGHSYRVELVMEGDVDPKTGFVDDFFNIEQYFSP 61
+IT+ FTF+AAHRLP P KC +HGH+Y+VE+ + G+V + G V DF +++
Sbjct: 1 EITKEFTFDAAHRLPGYPG--KCANLHGHTYKVEVTVSGEVLDEAGMVMDFSDLKAIVKE 58
Query: 62 LLEKLDHHCLNEIEELENPTAENIAIWIWKRL 93
++++LDH LN++ LENPTAEN+A WI+ RL
Sbjct: 59 VVDRLDHALLNDVPGLENPTAENLARWIYDRL 90
>gnl|CDD|161674 TIGR00039, 6PTHBS, 6-pyruvoyl tetrahydropterin synthase/QueD family
protein. This model has been downgraded from
hypothetical_equivalog to subfamily. The animal enzymes
are known to be 6-pyruvoyl tetrahydropterin synthase.
The function of the bacterial branch of the sequence
lineage had been thought to be the same, but many are
now taken to be QueD, and enzyme of queuosine
biosynthesis. Queuosine is a hypermodified base in the
wobble position of some tRNAs in most species. A new
model is built to be the QueD equivalog model.
Length = 124
Score = 100 bits (252), Expect = 7e-23
Identities = 48/122 (39%), Positives = 74/122 (60%), Gaps = 7/122 (5%)
Query: 1 MKITQAFTFEAAHRLPRVPKTHKCHRMHGHSYRVELVMEGDVDPKTGFVDDFFNIEQYFS 60
I + F+F AAHRLP KC +HGHSY+V++ + G+ DPKTG V DF ++++
Sbjct: 2 FGIHKEFSFSAAHRLPGHEG--KCGNLHGHSYKVDVEVSGERDPKTGMVMDFSDLKKIVK 59
Query: 61 PLLEK-LDHHCLN-EIEELENPTAENIAIWIW---KRLSTSLSILSSVRVYETPMSWVEY 115
++++ LDH LN ++ LENPT+EN+A++I+ K + L V+ ETP Y
Sbjct: 60 EVIDEPLDHKLLNDDVNYLENPTSENVAVYIFDNLKEYLIPVENLVKVKEEETPAEIRIY 119
Query: 116 QG 117
+G
Sbjct: 120 RG 121
>gnl|CDD|179359 PRK02006, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 498
Score = 28.9 bits (65), Expect = 0.30
Identities = 14/38 (36%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 15 LPRVPKTHKCHRMHGHSYRVELVME-GDVDPKTGFVDD 51
LP P H G +RVELV VD + DD
Sbjct: 337 LPAAPLLHGLREYRGEPHRVELVATIDGVD----YYDD 370
>gnl|CDD|180957 PRK07395, PRK07395, L-aspartate oxidase; Provisional.
Length = 553
Score = 26.5 bits (59), Expect = 1.6
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 6 AFTFEAAHRLPRV 18
A T EAAH PRV
Sbjct: 113 ALTLEAAHSRPRV 125
>gnl|CDD|179505 PRK02936, argD, acetylornithine aminotransferase; Provisional.
Length = 377
Score = 26.1 bits (58), Expect = 2.3
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 55 IEQYFSPLLEKLDHHCLNEIEELENPTAENIA 86
I++ F PLL H N+I+ L+ E +A
Sbjct: 138 IKEGFGPLLPGFTHVPFNDIKALKEVMNEEVA 169
>gnl|CDD|178433 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 25.9 bits (57), Expect = 2.6
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 79 NPTAENIAIWIWKRLSTSLSILSS 102
+P A ++ W RL SL I+ S
Sbjct: 169 DPKARSLPRNDWYRLRRSLEIIKS 192
>gnl|CDD|181430 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau;
Validated.
Length = 535
Score = 25.8 bits (57), Expect = 2.6
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 8/48 (16%)
Query: 38 MEGDVDPKTGFVDDFFNIEQYFSPLLEKLDHHCLNEIEELENPTAENI 85
M G +DP +E +F +L + ++ELE+ AE +
Sbjct: 238 MLGLLDPSK--------LEDFFQAILNQDKEKLFELLKELEDYEAEMV 277
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model
describes peptide chain release factor 1 (PrfA, RF-1),
and excludes the related peptide chain release factor 2
(PrfB, RF-2). RF-1 helps recognize and terminate
translation at UAA and UAG stop codons. The
mitochondrial release factors are prfA-like, although
not included above the trusted cutoff for this model.
RF-1 does not have a translational frameshift.
Length = 360
Score = 25.8 bits (57), Expect = 3.0
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 8/51 (15%)
Query: 9 FEA-AHRLPRVPKTHKCHRMHGHSYRVELVM------EGDVDPKTGFVDDF 52
FE+ HR+ RVP T R+H + V VM E D++P +D F
Sbjct: 179 FESGVHRVQRVPVTESQGRIHTSAATV-AVMPELEEVEVDINPADLRIDTF 228
>gnl|CDD|183863 PRK13107, PRK13107, preprotein translocase subunit SecA; Reviewed.
Length = 908
Score = 25.7 bits (56), Expect = 3.1
Identities = 11/14 (78%), Positives = 11/14 (78%)
Query: 73 EIEELENPTAENIA 86
EIE LENPTAE A
Sbjct: 522 EIEALENPTAEQKA 535
>gnl|CDD|162005 TIGR00707, argD, acetylornithine and succinylornithine
aminotransferases. Members of this family may also act
on ornithine, like ornithine aminotransferase (EC
2.6.1.13) (see MEDLINE:90337349) and on
succinyldiaminopimelate, like
N-succinyldiaminopmelate-aminotransferase (EC 2.6.1.17,
DapC, an enzyme of lysine biosynthesis) (see
MEDLINE:99175097).
Length = 379
Score = 25.4 bits (56), Expect = 3.4
Identities = 8/32 (25%), Positives = 15/32 (46%)
Query: 55 IEQYFSPLLEKLDHHCLNEIEELENPTAENIA 86
++ F PL+ + N+IE L+ + A
Sbjct: 141 YQKGFEPLVPGFSYAPYNDIESLKKAIDDETA 172
>gnl|CDD|180865 PRK07178, PRK07178, pyruvate carboxylase subunit A; Validated.
Length = 472
Score = 25.1 bits (55), Expect = 3.9
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 43 DPKTGFVDDFFNIEQYFSP 61
DPK F+ F I +Y++P
Sbjct: 342 DPKNDFLPSFGKITRYYAP 360
>gnl|CDD|130122 TIGR01050, rpsS_bact, ribosomal protein S19, bacterial/organelle.
the Archaea may be designated S15 or S19.
Length = 92
Score = 25.0 bits (55), Expect = 4.3
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 66 LDHHCLNEIEELENPTAENIAIWIWKRLST 95
+DHH L ++E+L N + + I W R ST
Sbjct: 11 VDHHLLKKVEKL-NESGKKKVIKTWSRRST 39
>gnl|CDD|179074 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 25.0 bits (56), Expect = 4.7
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 25 HRMHGHSYRVELVMEGDVDP 44
HR++ Y+++ VMEGD+D
Sbjct: 321 HRINLTLYKLDEVMEGDLDE 340
>gnl|CDD|148810 pfam07412, Geminin, Geminin. This family contains the eukaryotic
protein geminin (approximately 200 residues long).
Geminin inhibits DNA replication by preventing the
incorporation of MCM complex into prereplication
complex, and is degraded during the mitotic phase of the
cell cycle. It has been proposed that geminin inhibits
DNA replication during S, G2, and M phases and that
geminin destruction at the metaphase-anaphase transition
permits replication in the succeeding cell cycle.
Length = 200
Score = 24.8 bits (54), Expect = 4.9
Identities = 6/23 (26%), Positives = 14/23 (60%)
Query: 57 QYFSPLLEKLDHHCLNEIEELEN 79
QY + ++E+L + +E L++
Sbjct: 159 QYMAEMIERLTGEPPDNLESLKS 181
>gnl|CDD|179453 PRK02627, PRK02627, acetylornithine aminotransferase; Provisional.
Length = 396
Score = 24.7 bits (55), Expect = 5.2
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 57 QYFSPLLEKLDHHCLNEIEELENPTAENIA 86
+ F PL+E + N+IE L+ + A
Sbjct: 155 EGFEPLVEGFIYVPFNDIEALKAAITDKTA 184
>gnl|CDD|151067 pfam10510, PIG-S, Phosphatidylinositol-glycan biosynthesis class S
protein. PIG-S is one of several key, core, components
of the glycosylphosphatidylinositol (GPI) trans-amidase
complex that mediates GPI anchoring in the endoplasmic
reticulum. Anchoring occurs when a protein's C-terminal
GPI attachment signal peptide is replaced with a
pre-assembled GPI. Mammalian GPITransamidase consists of
at least five components: Gaa1, Gpi8, PIG-S, PIG-T, and
PIG-U, all five of which are required for function. It
is possible that Gaa1, Gpi8, PIG-S, and PIG-T form a
tightly associated core that is only weakly associated
with PIG-U. The exact function of PIG-S is unclear.
Length = 500
Score = 24.2 bits (53), Expect = 7.2
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 55 IEQYFSPLLEKLDH 68
+++Y PLLE L
Sbjct: 214 LKEYIQPLLEALSP 227
>gnl|CDD|184161 PRK13580, PRK13580, serine hydroxymethyltransferase; Provisional.
Length = 493
Score = 24.2 bits (53), Expect = 7.8
Identities = 9/24 (37%), Positives = 10/24 (41%), Gaps = 8/24 (33%)
Query: 27 MHGHSYRVELVMEGDVDPKTGFVD 50
H SY VDP TG +D
Sbjct: 193 FHQRSY--------GVDPDTGLLD 208
>gnl|CDD|183035 PRK11199, tyrA, bifunctional chorismate mutase/prephenate
dehydrogenase; Provisional.
Length = 374
Score = 24.1 bits (53), Expect = 8.1
Identities = 10/26 (38%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 34 VELVMEGDVDPKTGFVDDFFNIEQYF 59
+EL+ +GD K F+D F +E +F
Sbjct: 328 LELLEQGD---KQAFIDSFRKVEHWF 350
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.322 0.136 0.430
Gapped
Lambda K H
0.267 0.0787 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,006,288
Number of extensions: 114850
Number of successful extensions: 210
Number of sequences better than 10.0: 1
Number of HSP's gapped: 207
Number of HSP's successfully gapped: 28
Length of query: 118
Length of database: 5,994,473
Length adjustment: 81
Effective length of query: 37
Effective length of database: 4,244,225
Effective search space: 157036325
Effective search space used: 157036325
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: 51 (23.3 bits)