RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780322|ref|YP_003064735.1| SAM-dependent
methyltransferase protein [Candidatus Liberibacter asiaticus str.
psy62]
(273 letters)
>gnl|CDD|38151 KOG2940, KOG2940, KOG2940, Predicted methyltransferase [General
function prediction only].
Length = 325
Score = 153 bits (388), Expect = 5e-38
Identities = 82/270 (30%), Positives = 130/270 (48%), Gaps = 13/270 (4%)
Query: 4 LFDMQLINRNRLRSFRQKDFSVYFLLDRVAKEIAFRLNMINQTFENALELHGITGIVG-- 61
+FD L R R+ D +L + + +A R+ ++F A ++ G V
Sbjct: 30 IFDRDLKRIQRDRAAWLSDQKNDYLKEEIGDRLADRVFDCKKSFPTAFDIGCSLGAVKRH 89
Query: 62 --------YTCMETKKIHRMIRAEISTEFSTLKREVISCPLEEIPSISQSVDLILSPLNL 113
M+T + MI++ + +++ E + SVDLI+S L+L
Sbjct: 90 LRGEGVEKLIMMDTS--YDMIKSCRDAQDPSIETSYFVGDEEFLDFKENSVDLIISSLSL 147
Query: 114 HIINDTLEMFSKINHMLKPGGMFLAAIPGIGTLHELRKALLKAETELTGGASPRVIPFMD 173
H ND + LKP G+F+A++ G TL+ELR +L AE E GG SP + PF
Sbjct: 148 HWTNDLPGSMIQCKLALKPDGLFIASMLGGDTLYELRCSLQLAELEREGGISPHISPFTQ 207
Query: 174 IKSAGTLMEKSGFISPIIDQDTYTVYYKSMLHLMHDLRGMGMSNPLIRRSKTPPYKSLFK 233
++ G L+ ++GF +D D V Y M LM DL+GMG SN + R+ +++
Sbjct: 208 VRDIGNLLTRAGFSMLTVDTDEIVVGYPRMFELMEDLQGMGESNAALNRNAILNRETMVA 267
Query: 234 RASTIYTEENSDLTGNVTASFSIIYVMGWK 263
A+ IY + G + A+F IIY++GWK
Sbjct: 268 -AAAIYQSMYATEDGTIPATFQIIYMIGWK 296
>gnl|CDD|38255 KOG3045, KOG3045, KOG3045, Predicted RNA methylase involved in rRNA
processing [RNA processing and modification].
Length = 325
Score = 32.3 bits (73), Expect = 0.15
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 64 CMETKKIHRMIRAEISTEFSTLKREVISCPLEEIPSISQSVDLILSPLNLHIINDTLEMF 123
C E K S + + VI+C + +P +SVD+ + L+L + + +
Sbjct: 189 CGEAKIASSERHKVHSFDLVAVNERVIACDMRNVPLEDESVDVAVFCLSL-MGTNLADFI 247
Query: 124 SKINHMLKPGGMFLAA 139
+ N +LKPGG+ A
Sbjct: 248 KEANRILKPGGLLYIA 263
>gnl|CDD|147365 pfam05148, Methyltransf_8, Hypothetical methyltransferase. This
family consists of several uncharacterized eukaryotic
proteins which are related to methyltransferases
pfam01209.
Length = 214
Score = 32.1 bits (73), Expect = 0.17
Identities = 25/93 (26%), Positives = 39/93 (41%), Gaps = 10/93 (10%)
Query: 64 CMETKKIHRMIRAE--ISTEFSTLKREVISCPLEEIPSISQSVDLILSPLNLHIINDTLE 121
C E + R E S + + + VI C + +P +SVD+ + L+L N +
Sbjct: 76 CGEARIAFRKREFENVHSFDLVAVNKRVIPCDMARVPLEDESVDVAVFCLSLMGTN--IA 133
Query: 122 MFSK-INHMLKPGGMFLAA-----IPGIGTLHE 148
F K N +LK GG+ A P +G
Sbjct: 134 DFLKEANRILKNGGLLKIAEVRSRFPSVGLFER 166
>gnl|CDD|163681 cd07943, DRE_TIM_HOA, 4-hydroxy-2-oxovalerate aldolase, N-terminal
catalytic TIM barrel domain. 4-hydroxy 2-ketovalerate
aldolase (Also known as 4-hydroxy-2-ketovalerate
aldolase and 4-hydroxy-2-oxopentanoate aldolase (HOA))
converts 4-hydroxy-2-oxopentanoate to acetaldehyde and
pyruvate, the penultimate step in the meta-cleavage
pathway for the degradation of phenols, cresols and
catechol. This family includes the Escherichia coli
MhpE aldolase, the Pseudomonas DmpG aldolase, and the
Burkholderia xenovorans BphI pyruvate aldolase. In
Pseudomonas, the DmpG aldolase tightly associates with a
dehydrogenase (DmpF ) and is inactive without it. HOA
has a canonical TIM-barrel fold with a C-terminal
extension that forms a funnel leading to the active
site. This family belongs to the DRE-TIM metallolyase
superfamily. DRE-TIM metallolyases include
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 263
Score = 31.7 bits (73), Expect = 0.20
Identities = 9/20 (45%), Positives = 14/20 (70%), Gaps = 2/20 (10%)
Query: 134 GMFLAAIPGIGTLHELRKAL 153
G+ L +PGIGT+ +L+ A
Sbjct: 78 GVLL--LPGIGTVDDLKMAA 95
>gnl|CDD|37932 KOG2721, KOG2721, KOG2721, Uncharacterized conserved protein
[Function unknown].
Length = 260
Score = 29.6 bits (66), Expect = 0.85
Identities = 10/36 (27%), Positives = 20/36 (55%)
Query: 228 YKSLFKRASTIYTEENSDLTGNVTASFSIIYVMGWK 263
Y +FK+++ ++ S + V + F+ +YV WK
Sbjct: 72 YSFVFKKSTELFKRRASKILSLVASFFASVYVTKWK 107
>gnl|CDD|32408 COG2226, UbiE, Methylase involved in ubiquinone/menaquinone
biosynthesis [Coenzyme metabolism].
Length = 238
Score = 29.1 bits (65), Expect = 1.4
Identities = 22/122 (18%), Positives = 44/122 (36%), Gaps = 12/122 (9%)
Query: 27 FLLDRVAKEIAFRLNMINQTFENALELHGITGIVGYTCMETKKIHRMIRAEIST------ 80
F L R+ + A + + + L++ TG + ++ ++ +IS
Sbjct: 33 FGLHRLWRR-ALISLLGIKPGDKVLDVACGTGDMALLLAKSVGTGEVVGLDISESMLEVA 91
Query: 81 -----EFSTLKREVISCPLEEIPSISQSVDLILSPLNLHIINDTLEMFSKINHMLKPGGM 135
+ E + E +P S D + L + D + ++ +LKPGG
Sbjct: 92 REKLKKKGVQNVEFVVGDAENLPFPDNSFDAVTISFGLRNVTDIDKALKEMYRVLKPGGR 151
Query: 136 FL 137
L
Sbjct: 152 LL 153
>gnl|CDD|146872 pfam04446, Thg1, tRNAHis guanylyltransferase. The Thg1 protein
from Saccharomyces cerevisiae is responsible for adding
a GMP residue to the 5' end of tRNA His.
Length = 181
Score = 29.2 bits (66), Expect = 1.5
Identities = 11/37 (29%), Positives = 19/37 (51%)
Query: 228 YKSLFKRASTIYTEENSDLTGNVTASFSIIYVMGWKS 264
Y LF++++ ++ S L V + F+ YV WK
Sbjct: 78 YSFLFRKSTKLFNRRLSKLLSLVVSLFTSSYVFLWKE 114
>gnl|CDD|33863 COG4106, Tam, Trans-aconitate methyltransferase [General function
prediction only].
Length = 257
Score = 28.3 bits (63), Expect = 2.1
Identities = 11/42 (26%), Positives = 19/42 (45%)
Query: 101 SQSVDLILSPLNLHIINDTLEMFSKINHMLKPGGMFLAAIPG 142
Q DL+ + L + D E+ ++ L PGG+ +P
Sbjct: 90 EQPTDLLFANAVLQWLPDHPELLPRLVSQLAPGGVLAVQMPD 131
>gnl|CDD|38220 KOG3010, KOG3010, KOG3010, Methyltransferase [General function
prediction only].
Length = 261
Score = 28.3 bits (63), Expect = 2.3
Identities = 10/51 (19%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 89 VISCPLEEIPSISQSVDLILSPLNLHIINDTLEMFSKINHMLKPGGMFLAA 139
+ S + ++ +SVDLI + +H + + + +L+ G +A
Sbjct: 86 MSSDEMVDLLGGEESVDLITAAQAVHWFDLE-RFYKEAYRVLRKDGGLIAV 135
>gnl|CDD|36315 KOG1099, KOG1099, KOG1099, SAM-dependent methyltransferase/cell
division protein FtsJ [Cell cycle control, cell
division, chromosome partitioning, General function
prediction only].
Length = 294
Score = 28.0 bits (62), Expect = 3.0
Identities = 22/98 (22%), Positives = 38/98 (38%), Gaps = 20/98 (20%)
Query: 50 ALELHGITGIVGYTCMETKKIHRMIRAEISTEFSTLKREVISCP-------LEEIPSISQ 102
A++L + I G ++ I F K +++ C L ++ Q
Sbjct: 79 AVDLQPMAPIEGVIQLQGDITSASTAEAIIEHFGGEKADLVVCDGAPDVTGLHDLDEYVQ 138
Query: 103 SVDLILSPLNLHIINDTLEMFSKINHMLKPGGMFLAAI 140
+ L+L+ LN+ +LKPGG F+A I
Sbjct: 139 A-QLLLAALNI------------ATCVLKPGGSFVAKI 163
>gnl|CDD|119430 cd05170, PIKKc_SMG1, Suppressor of morphogenetic effect on
genitalia-1 (SMG-1), catalytic domain; The SMG-1
catalytic domain subfamily is part of a larger
superfamily that includes the catalytic domains of other
kinases such as the typical serine/threonine/tyrosine
protein kinases (PKs), aminoglycoside
phosphotransferase, choline kinase, and RIO kinases.
SMG-1 is a member of the phosphoinositide
3-kinase-related protein kinase (PIKK) subfamily. PIKKs
have intrinsic serine/threonine kinase activity and are
distinguished from other PKs by their unique catalytic
domain, similar to that of lipid PI3K, and their large
molecular weight (240-470 kDa). In addition to its
catalytic domain, SMG-1 contains a FATC (FRAP, ATM and
TRRAP, C-terminal) domain at the C-terminus. SMG-1 plays
a critical role in the mRNA surveillance mechanism known
as non-sense mediated mRNA decay (NMD). NMD protects the
cells from the accumulation of aberrant mRNAs with
premature termination codons (PTCs) generated by genome
mutations and by errors during transcription and
splicing. SMG-1 phosphorylates Upf1, another central
component of NMD, at the C-terminus upon recognition of
PTCs. The phosphorylation/dephosphorylation cycle of
Upf1 is essential for promoting NMD..
Length = 307
Score = 27.8 bits (62), Expect = 3.1
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 31 RVAKEIAFRLNMINQTFENALELHGITGIVGYTCMETKKIHR 72
R+ +++ FR+ Q E AL L G+ G+ +C + I R
Sbjct: 246 RIPEKVPFRMT---QNIETALGLTGVEGVFRLSCEQVLHIMR 284
>gnl|CDD|39501 KOG4300, KOG4300, KOG4300, Predicted methyltransferase [General
function prediction only].
Length = 252
Score = 27.6 bits (61), Expect = 3.6
Identities = 11/46 (23%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 93 PLEEIPSISQ-SVDLILSPLNLHIINDTLEMFSKINHMLKPGGMFL 137
E +P ++ S D ++ L L + D ++ +++ +L+PGG +
Sbjct: 134 DGENLPQLADGSYDTVVCTLVLCSVEDPVKQLNEVRRLLRPGGRII 179
>gnl|CDD|36312 KOG1096, KOG1096, KOG1096, Adenosine monophosphate deaminase
[Nucleotide transport and metabolism].
Length = 768
Score = 27.6 bits (61), Expect = 3.7
Identities = 36/159 (22%), Positives = 64/159 (40%), Gaps = 27/159 (16%)
Query: 12 RNRLRSFRQKDFSVYFLLDRVAKEIAFRLNMINQTFENALELHGITGIVGYTCMETKKIH 71
RL+ K F ++ LL+ KE+ + + ++ F N ++ T I CM K +
Sbjct: 281 HRRLQYLESK-FQLHQLLNEK-KELLAQKKVPHRDFYNVRKVD--THIHASACMNQKHLL 336
Query: 72 RMIRAEISTEFSTLKREVISCPLEEIPSISQ--------SVDLILSPLNLHIINDTLEMF 123
R I+ ++ E R VI ++ ++ + + DL + L++H +T F
Sbjct: 337 RFIKKKLRKE---PDRVVIQRDGRKL-TLREVFKSLGLTAYDLSVDTLDVHADRNTFHRF 392
Query: 124 SKINHMLKPGGMFLAAIPGIGTLHELRKALLKAETELTG 162
K N P G LR+ LK + + G
Sbjct: 393 DKFNAKYNPVGE-----------SRLREIFLKTDNYING 420
>gnl|CDD|36109 KOG0891, KOG0891, KOG0891, DNA-dependent protein kinase [Replication,
recombination and repair].
Length = 2341
Score = 27.2 bits (60), Expect = 5.0
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 23 FSVYFLLDRVAKEIAFRLNMINQTFENALELHGITGIVGYTCMETKKIHR 72
F V L ++ +++ FRL + NA+E+ GI G TC ++ R
Sbjct: 2168 FEVAMLREKFPEKVPFRLT---RMLINAMEVTGIEGTYRITCEHVMRVLR 2214
>gnl|CDD|37572 KOG2361, KOG2361, KOG2361, Predicted methyltransferase [General
function prediction only].
Length = 264
Score = 26.9 bits (59), Expect = 5.8
Identities = 23/89 (25%), Positives = 32/89 (35%), Gaps = 4/89 (4%)
Query: 123 FSKINHMLKPGGMFLAAIPGIGTLHELR--KALLKAETELTGGASPRVIPFMDIKSAGTL 180
+ +LKPGG L G L +LR K +E G R F + L
Sbjct: 166 IKNLRTLLKPGGSLLFRDYGRYDLAQLRFKKGQCISENFYVRGDGTRAYFF-TEEELDEL 224
Query: 181 MEKSGFISPIIDQD-TYTVYYKSMLHLMH 208
K+GF ++ D V K L +
Sbjct: 225 FTKAGFEEVQLEVDCRLLVNRKKQLKMYR 253
>gnl|CDD|30790 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 589
Score = 26.8 bits (59), Expect = 7.6
Identities = 9/35 (25%), Positives = 18/35 (51%)
Query: 14 RLRSFRQKDFSVYFLLDRVAKEIAFRLNMINQTFE 48
R+R F Q D ++ D++ E L +I + ++
Sbjct: 324 RVRGFTQDDAHIFCTPDQIKDEFKGILELILEVYK 358
>gnl|CDD|112099 pfam03269, DUF268, Caenorhabditis protein of unknown function,
DUF268.
Length = 177
Score = 26.3 bits (58), Expect = 8.2
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 120 LEMFSKINHMLKPGGMFLAAIPGIGT 145
L KI +LK GG+ +P +GT
Sbjct: 91 LREMLKIKCVLKKGGLLFLGLP-LGT 115
>gnl|CDD|37186 KOG1975, KOG1975, KOG1975, mRNA cap methyltransferase [RNA
processing and modification].
Length = 389
Score = 26.5 bits (58), Expect = 9.4
Identities = 16/69 (23%), Positives = 25/69 (36%), Gaps = 7/69 (10%)
Query: 95 EEIPSISQSVDLILSPLNLHIINDTLE----MFSKINHMLKPGGMFLAAIPGIGTLHELR 150
+ + D++ H +T E + LKPGG+F+ IP +
Sbjct: 188 DLLEFKDPRFDIVSCQFAFHYAFETEESARIALRNVAKCLKPGGVFIGTIP---DSDVII 244
Query: 151 KALLKAETE 159
K L E E
Sbjct: 245 KRLRAGEVE 253
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
0.322 0.136 0.389
Gapped
Lambda K H
0.267 0.0636 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,238,728
Number of extensions: 168736
Number of successful extensions: 396
Number of sequences better than 10.0: 1
Number of HSP's gapped: 395
Number of HSP's successfully gapped: 23
Length of query: 273
Length of database: 6,263,737
Length adjustment: 92
Effective length of query: 181
Effective length of database: 4,275,709
Effective search space: 773903329
Effective search space used: 773903329
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: 57 (25.9 bits)