RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= 537021.9.peg.888_1
(217 letters)
>gnl|CDD|30672 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 194 bits (495), Expect = 1e-50
Identities = 87/217 (40%), Positives = 125/217 (57%), Gaps = 2/217 (0%)
Query: 1 MLSKKLQRYKKRF-LPIIVGGTGLYFRALTGQLSIMPEIPTAIREKIREKLKQYGSHILH 59
+ R LPI+VGGTGLY +AL LS++PE +R ++ +L + G+ LH
Sbjct: 80 DALAAIDDILARGKLPILVGGTGLYLKALLEGLSLLPEADPEVRRRLEAELAELGNDALH 139
Query: 60 DELSSLDSIVARQIHPSDGQRIARALEIKLVSGQSIIEFWKQAPNPFIPLESAHKIIILP 119
EL +D A +IHP+D QRI RALE+ ++G+ I E K++ P + I +
Sbjct: 140 AELKKIDPEAAAKIHPNDPQRIIRALEVYYLTGKPISELQKRSRPILEPYD-ILIIALAA 198
Query: 120 ERSALKERIRRRFTQMLESGAIDEIRSLMKMNLSLDLPIMKAIGVRDIIALLKGEINYDE 179
+R L ERI RR MLE G I+E+++L L LDLP M+AIG ++I+A L G I+ +E
Sbjct: 199 DREVLYERINRRVDAMLEQGLIEEVKALYARGLHLDLPAMQAIGYKEILAYLDGGISLEE 258
Query: 180 TLQRGIIATNKYAKRQKTWLCHQFQADWIRISSIDDL 216
++R AT +YAKRQ TW +Q W+ S D L
Sbjct: 259 AIERIKTATRQYAKRQLTWFRNQLGVHWLDSESPDTL 295
>gnl|CDD|145065 pfam01715, IPPT, IPP transferase. This is a family of IPP
transferases EC:2.5.1.8 also known as tRNA
delta(2)-isopentenylpyrophosphate transferase. These
enzymes modify both cytoplasmic and mitochondrial tRNAs
at A(37) to give isopentenyl A(37).
Length = 253
Score = 190 bits (485), Expect = 3e-49
Identities = 83/197 (42%), Positives = 121/197 (61%), Gaps = 2/197 (1%)
Query: 14 LPIIVGGTGLYFRALTGQLSIMPEIPTAIREKIREKLKQYGSHILHDELSSLDSIVARQI 73
+P++VGGTGLYF+AL LS P +R K+ E+L++ G+ LH EL+S+D A +I
Sbjct: 58 IPLLVGGTGLYFKALLDGLSDTPSADPKVRAKLEEQLEELGNDYLHAELASVDPEAAAKI 117
Query: 74 HPSDGQRIARALEIKLVSGQSIIEFWKQAPNPFIPLESAHKIIILPERSALKERIRRRFT 133
HP+DG+RI RALE+ +G+ I EF K+ N +I + +R L ERI RR
Sbjct: 118 HPNDGRRIVRALEVFYATGKPISEFQKEQKNALPY--DIVQIGLARDREVLHERIARRVD 175
Query: 134 QMLESGAIDEIRSLMKMNLSLDLPIMKAIGVRDIIALLKGEINYDETLQRGIIATNKYAK 193
MLESG ++E+++L L+ DLP ++AIG ++ + L GE +E ++R I AT +YAK
Sbjct: 176 DMLESGLVEEVKALYAQGLNEDLPSIRAIGYKEFLLYLDGECTLEEAIERIIKATRQYAK 235
Query: 194 RQKTWLCHQFQADWIRI 210
RQ TW Q W+ I
Sbjct: 236 RQMTWFRKDSQVHWLDI 252
>gnl|CDD|36598 KOG1384, KOG1384, KOG1384, tRNA delta(2)-isopentenylpyrophosphate
transferase [Translation, ribosomal structure and
biogenesis].
Length = 348
Score = 42.6 bits (100), Expect = 9e-05
Identities = 24/93 (25%), Positives = 40/93 (43%), Gaps = 13/93 (13%)
Query: 120 ERSALKERIRRRFTQMLESGAIDEIRSLMKMNLS-LDLPIMKAIGVRDIIALLKGEI--- 175
+++ L ER+ +R MLESG ++E+R S I KAIGV + +
Sbjct: 147 DQAVLFERLDKRVDDMLESGLLEELRDFYDPYNSSYRSGIRKAIGVPEFDGFKEFYPWLT 206
Query: 176 ---------NYDETLQRGIIATNKYAKRQKTWL 199
++ ++ T + AKRQK +
Sbjct: 207 DKWDLARKELLEKAIEAIKENTRRLAKRQKRKI 239
Score = 27.2 bits (60), Expect = 3.7
Identities = 10/26 (38%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 3 SKKLQRYKKRFLPIIVGGTGLYFRAL 28
+++ K LPI+VGG+ Y +AL
Sbjct: 89 IEEIHSRGK--LPIVVGGSNSYLQAL 112
>gnl|CDD|37150 KOG1939, KOG1939, KOG1939, Oxoprolinase [Amino acid transport and
metabolism].
Length = 1247
Score = 28.8 bits (64), Expect = 1.1
Identities = 19/69 (27%), Positives = 27/69 (39%), Gaps = 7/69 (10%)
Query: 35 MPEIPTAIREKIREKLKQYGSHILHDELSSLDSIVARQIHPSDGQRIARALEIKLVSGQS 94
M I +RE LK+ G +L LS+ D DG I + I G++
Sbjct: 945 MKHIQNNAELAVREMLKKVGRRVLEKTLSAED-------FMDDGSPIKLKVTIDPEKGEA 997
Query: 95 IIEFWKQAP 103
I +F P
Sbjct: 998 IFDFTGTGP 1006
>gnl|CDD|132854 cd07215, Pat17_PNPLA8_PNPLA9_like2, Patatin-like phospholipase of
bacteria. Patatin is a storage protein of the potato
tuber that shows Phospholipase A2 activity (PLA2; EC
3.1.1.4). Patatin catalyzes the nonspecific hydrolysis
of phospholipids, glycolipids, sulfolipids, and mono-
and diacylglycerols, thereby showing lipid acyl
hydrolase activity. The active site includes an oxyanion
hole with a conserved GGxR motif; it is found in almost
all the members of this family. The catalytic dyad is
formed by a serine and an aspartate. Patatin belongs to
the alpha-beta hydrolase family which is identified by a
characteristic nucleophile elbow with a consensus
sequence of Sm-X-Nu-Sm (Sm = small residue, X = any
residue and Nu = nucleophile). Members of this family
have been found also in vertebrates. This family
includes subfamily of PNPLA8 (iPLA2-gamma) and PNPLA9
(iPLA2-beta) like phospholipases from human as well as
the Pat17 isozyme from Solanum cardiophyllum.
Length = 329
Score = 28.5 bits (64), Expect = 1.6
Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 24 YFRALTGQLSIMPEIPTAIREKIREKLKQYGSHILHDELSSLDSIVAR 71
Y R PE+ A E + EKL++ G + D LD IV R
Sbjct: 282 YLRIQPELEDADPEMDDASPENL-EKLREVGQALAEDHKDQLDEIVDR 328
>gnl|CDD|112154 pfam03326, Herpes_TAF50, Herpesvirus transcription activation
factor (transactivator). This family includes EBV BRLF1
and similar ORF 50 proteins from other herpesviruses.
Length = 500
Score = 28.2 bits (63), Expect = 1.6
Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 3/85 (3%)
Query: 21 TGLYFRALTGQLSIMPEIPTAIREKIREKLKQYGSHILHDELSSLDSIVARQIHPSDGQR 80
TG++ ++ Q ++PE + E L L + L + + I+ + P Q
Sbjct: 157 TGIFSGLVSQQSFVLPEP--LLLEISEPGLLAASDADLSELLQNPEEILETRASPLS-QF 213
Query: 81 IARALEIKLVSGQSIIEFWKQAPNP 105
L QS ++ + P
Sbjct: 214 HGFTPHPSLPQPQSPLKPSPSSARP 238
>gnl|CDD|146078 pfam03264, Cytochrom_NNT, NapC/NirT cytochrome c family, N-terminal
region. Within the NapC/NirT family of cytochrome c
proteins, some members, such as NapC and NirT, bind four
haem groups, while others, such as TorC, bind five
haems. This family aligns the common N-terminal region
that contains four haem-binding C-X(2)-CH motifs.
Length = 174
Score = 28.0 bits (63), Expect = 1.9
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 7/53 (13%)
Query: 160 KAIGVRDIIALLKGEINYDETLQ--RGIIATNKYAKRQKTWL-----CHQFQA 205
KA +++ A L G I+ E + R +A +A+ + CH F +
Sbjct: 84 KAQASKEVYAELTGTIDTPEKFEAHRLEMAERVWARMKANDSRECRNCHSFDS 136
>gnl|CDD|147180 pfam04882, Peroxin-3, Peroxin-3. Peroxin-3 is a peroxisomal
protein. It is thought to be involve in membrane vesicle
assembly prior to the translocation of matrix proteins.
Length = 393
Score = 27.3 bits (61), Expect = 3.1
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 4/49 (8%)
Query: 125 KERIRRRFTQMLESGAIDEIRSLMKMNLSLDLPIMKAIGVRDIIALLKG 173
KE+I+RRF Q + + +L+ L PI++A+ V +I L+
Sbjct: 50 KEQIKRRFEQ-TQRDCNYTVLALLPT---LSEPILEALDVEEITEKLQQ 94
>gnl|CDD|33325 COG3522, COG3522, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 446
Score = 27.1 bits (60), Expect = 3.7
Identities = 23/104 (22%), Positives = 39/104 (37%), Gaps = 6/104 (5%)
Query: 50 LKQYGSHILHDELSSLDSIVARQIHPSDGQRIARALEIKLVSGQSIIEFWKQAPNPFIPL 109
L Y L L + R + RA+ I L W +
Sbjct: 288 LPVYDHDDLTASFKPLFDALRRLLSTV---LEPRAVAIPLEERA--YGVWVARLHDPKLR 342
Query: 110 ESAHKIIILPERSALKERIRRRFTQMLESGAIDEIRSLMKMNLS 153
+SA ++ + E++RR+F Q + GA ++IR L+ + L
Sbjct: 343 DSASFVLAVRADMPA-EQLRRQFPQQTKVGAPEKIRELVNVQLP 385
>gnl|CDD|30460 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 26.4 bits (58), Expect = 5.8
Identities = 11/73 (15%), Positives = 27/73 (36%), Gaps = 4/73 (5%)
Query: 77 DGQRIARALEIKLVSGQSIIEFWKQAPNPFIPLESAHKIIILPERSALKERIRRRFTQML 136
D + AL+ ++G ++ F ++ PL +I+ P + + R ++
Sbjct: 239 DEDALLAALDSGKIAGAALDVFEEEPLPADSPLWDLPNVILTPHIGGSTDEAQERVAEI- 297
Query: 137 ESGAIDEIRSLMK 149
+ I +
Sbjct: 298 ---VAENIVRYLA 307
>gnl|CDD|35466 KOG0245, KOG0245, KOG0245, Kinesin-like protein [Cytoskeleton].
Length = 1221
Score = 26.5 bits (58), Expect = 5.9
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 167 IIALLKGEINYDETLQRGIIATNKYAKRQKTWLC 200
I AL +INY+ETL +T +YA R K +
Sbjct: 322 IAALSPADINYEETL-----STLRYADRAKQIVN 350
>gnl|CDD|73161 cd03714, RT_DIRS1, RT_DIRS1: Reverse transcriptases (RTs)
occurring in the DIRS1 group of retransposons. Members
of the subfamily include the Dictyostelium DIRS-1,
Volvox carteri kangaroo, and Panagrellus redivivus PAT
elements. These elements differ from LTR and
conventional non-LTR retrotransposons. They contain
split direct repeat (SDR) termini, and have been
proposed to integrate via double-stranded closed-circle
DNA intermediates assisted by an encoded recombinase
which is similar to gamma-site-specific integrase..
Length = 119
Score = 26.4 bits (58), Expect = 6.2
Identities = 13/49 (26%), Positives = 20/49 (40%)
Query: 11 KRFLPIIVGGTGLYFRALTGQLSIMPEIPTAIREKIREKLKQYGSHILH 59
+ L G F+AL LS+ P + T + E + L+ G I
Sbjct: 17 RDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFS 65
>gnl|CDD|132752 cd06954, NR_LBD_LXR, The ligand binding domain of Liver X
receptors, a family of nuclear receptors of
ligand-activated transcription factors. The ligand
binding domain of Liver X receptors: Liver X receptors
(LXRs) belong to a family of nuclear receptors of
ligand-activated transcription factors. LXRs operate as
cholesterol sensors which protect from cholesterol
overload by stimulating reverse cholesterol transport
from peripheral tissues to the liver and its excretion
in the bile. Oxidized cholesterol derivatives or
oxysterols were identified as specific ligands for LXRs.
Upon ligand binding a conformational change leads to
recruitment of co-factors, which stimulates expression
of target genes. Among the LXR target genes are several
genes involved in cholesterol efflux from peripheral
tissues such as the ATP-binding-cassette transporters
ABCA1, ABCG1 and ApoE. There are two LXR isoforms in
mammals, LXRalpha and LXRbeta. LXRalpha is expressed
mainly in the liver, intestine, kidney, spleen, and
adipose tissue, whereas LXRbeta is ubiquitously
expressed at lower level. Both LXRalpha and LXRbeta
function as heterodimers with the retinoid X receptor
(RX R) which may be activated by either LXR ligands or
9-cis retinoic acid, a specific RXR ligand. The LXR/RXR
complex binds to a liver X receptor response element
(LXRE) in the promoter region of target genes. LXR has
typical NR modular structure with a central well
conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and the ligand
binding domain (LBD) at the C-terminal.
Length = 236
Score = 26.3 bits (58), Expect = 7.8
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 79 QRIARALEIKLVSGQSIIEFWKQAPNPFIPLESAHKIIIL 118
QR A E+ ++S Q I++F KQ P F+ L +I +L
Sbjct: 43 QRFAHFTELAILSVQEIVDFAKQLPG-FLTLTREDQIALL 81
>gnl|CDD|163621 cd07378, MPP_ACP5, Homo sapiens acid phosphatase 5 and related
proteins, metallophosphatase domain. Acid phosphatase 5
(ACP5) removes the mannose 6-phosphate recognition
marker from lysosomal proteins. The exact site of
dephosphorylation is not clear. Evidence suggests
dephosphorylation may take place in a prelysosomal
compartment as well as in the lysosome. ACP5 belongs to
the metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 277
Score = 25.7 bits (57), Expect = 9.0
Identities = 10/36 (27%), Positives = 12/36 (33%), Gaps = 3/36 (8%)
Query: 176 NYDETLQRGIIATNKYAKRQKTWLCHQFQ---ADWI 208
N D+ K A+ Q WL ADW
Sbjct: 134 NSDDIASPYGPPNGKLAEEQLAWLEKTLAASTADWK 169
>gnl|CDD|33261 COG3458, COG3458, Acetyl esterase (deacetylase) [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 321
Score = 25.7 bits (56), Expect = 9.6
Identities = 10/50 (20%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 129 RRRFTQMLESGAIDEIRSLMKMNLSLDLPIMKAIGVRDII---ALLKGEI 175
R ++ G DEI++ K + + + + + DI+ A +K +
Sbjct: 213 FPRAIELATEGPYDEIQTYFKRHDPKEAEVFETLSYFDIVNLAARIKVPV 262
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
0.323 0.139 0.399
Gapped
Lambda K H
0.267 0.0733 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,720,701
Number of extensions: 143042
Number of successful extensions: 479
Number of sequences better than 10.0: 1
Number of HSP's gapped: 476
Number of HSP's successfully gapped: 31
Length of query: 217
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 127
Effective length of database: 4,318,927
Effective search space: 548503729
Effective search space used: 548503729
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.0 bits)