RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780714|ref|YP_003065127.1| tRNA
(guanine-N(1)-)-methyltransferase [Candidatus Liberibacter asiaticus
str. psy62]
(236 letters)
>gnl|CDD|30684 COG0336, TrmD, tRNA-(guanine-N1)-methyltransferase [Translation,
ribosomal structure and biogenesis].
Length = 240
Score = 323 bits (830), Expect = 2e-89
Identities = 117/229 (51%), Positives = 166/229 (72%), Gaps = 4/229 (1%)
Query: 3 FHASILTLYPEMFPGHLEKSVAGKALACNLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGM 62
ILTL+PEMF G+L S+ G+A+ L S++ + R+F+TD+H +VDDTP GGGAGM
Sbjct: 1 MKIDILTLFPEMFDGYLGYSILGRAIEKGLLSLEVVNPRDFATDKHKTVDDTPYGGGAGM 60
Query: 63 VLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGID 122
V++ + L A+D + IL+SP+GK TQ R R+L+++ ++++CGR+EGID
Sbjct: 61 VMKPEPLFDALDSVKAAKKA---KVILLSPQGKPFTQARARELAKEEHLVLICGRYEGID 117
Query: 123 ERIIEARDLEEISVGDYILSGGEPAALILLDAVVRLLPGVLGNQQSTIHESFE-NGLLEF 181
ER+IE EEIS+GDY+L+GGE AA++L+DAVVRL+PGVLGN++S +SFE NGLLE+
Sbjct: 118 ERVIELYVDEEISIGDYVLTGGELAAMVLIDAVVRLIPGVLGNEESLEEDSFENNGLLEY 177
Query: 182 PQYTRPQIWEGLAIPPILNSGDHERIKKWRKEQSFALTKKHRPDLLSKK 230
P YTRP+ +EG+ +P +L SG+H +I +WR EQS TK+ RPDLL
Sbjct: 178 PHYTRPREFEGMKVPEVLLSGNHAKIAQWRLEQSLERTKERRPDLLEAH 226
>gnl|CDD|110724 pfam01746, tRNA_m1G_MT, tRNA (Guanine-1)-methyltransferase. This
is a family of tRNA (Guanine-1)-methyltransferases
EC:2.1.1.31. In E.coli K12 this enzyme catalyses the
conversion of a guanosine residue to N1-methylguanine in
position 37, next to the anticodon, in tRNA.
Length = 185
Score = 137 bits (346), Expect = 3e-33
Identities = 68/184 (36%), Positives = 102/184 (55%), Gaps = 16/184 (8%)
Query: 41 RNFSTDRHHSVDDTPAGGGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQK 100
R+++ +R +VDD GGG GMVL+ + +A+ +VS + IL++P G +Q+
Sbjct: 18 RDYTANRRATVDDHLYGGGFGMVLKPEPDLEAL-KSVSGWEV-----ILLTPTGIPFSQE 71
Query: 101 RVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSGGEPAALILLDAVVRLLP 160
+L +K ++ + G +EG+ ER+ + D E +G + GGE AL L+DAVV LLP
Sbjct: 72 LASELFKKEHLVYLTGDYEGVLERLDD--DKAEYIIGGIVDKGGEKGALTLIDAVVALLP 129
Query: 161 GVLGNQQSTIHESFENGLLEFPQYTRPQIWEGLAIPPILNSGDHERIKKWRKEQSFALTK 220
GVL N S +SF LL P YTRP +P IL SG+H +I+ W E++ T
Sbjct: 130 GVL-NTASLPLDSF---LLGVPNYTRPLTLN--QVPEILLSGNHAKIRNW--EEALLRTI 181
Query: 221 KHRP 224
R
Sbjct: 182 PKRK 185
>gnl|CDD|32804 COG2985, COG2985, Predicted permease [General function prediction
only].
Length = 544
Score = 31.4 bits (71), Expect = 0.19
Identities = 21/95 (22%), Positives = 33/95 (34%), Gaps = 2/95 (2%)
Query: 63 VLRVDILGKAIDHAVS-QYTHEDIPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGI 121
+ +V++ +A A +P I L +R L + C R +
Sbjct: 179 LFKVNLDTEAQQIARERGLDTVYLPVIRAYVVNPNLDGLNLRDLPILRQEGVYCSRIKRD 238
Query: 122 DERIIEARDLEEISVGDYILSGGEPAALILLDAVV 156
+ D I VGD + G P AL LD +
Sbjct: 239 GILAVPDPD-TIIQVGDELHLVGYPDALARLDLRI 272
>gnl|CDD|144620 pfam01094, ANF_receptor, Receptor family ligand binding region.
This family includes extracellular ligand binding
domains of a wide range of receptors. This family also
includes the bacterial amino acid binding proteins of
known structure.
Length = 344
Score = 30.5 bits (69), Expect = 0.40
Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 7/87 (8%)
Query: 100 KRVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSGGEPAALILLDAVVRLL 159
K ++ + K VI+VCG + + + + +AR+L +S G Y+ + LL +
Sbjct: 169 KELKDIKSKARVIVVCGSSDDLRQILQQARELGMMS-GGYVWILTDLWGDSLLPDNDKAR 227
Query: 160 P---GVLGNQQSTIHESFENGLLEFPQ 183
GVLG T+ G EF +
Sbjct: 228 EAAKGVLG---FTLKPPDSPGFQEFLE 251
>gnl|CDD|145056 pfam01702, TGT, Queuine tRNA-ribosyltransferase. This is a family
of queuine tRNA-ribosyltransferases EC:2.4.2.29, also
known as tRNA-guanine transglycosylase and guanine
insertion enzyme. Queuine tRNA-ribosyltransferase
modifies tRNAs for asparagine, aspartic acid, histidine
and tyrosine with queuine. It catalyses the exchange of
guanine-34 at the wobble position with
7-aminomethyl-7-deazaguanine, and the addition of a
cyclopentenediol moiety to
7-aminomethyl-7-deazaguanine-34 tRNA; giving a
hypermodified base queuine in the wobble position. The
aligned region contains a zinc binding motif
C-x-C-x2-C-x29-H, and important tRNA and
7-aminomethyl-7deazaguanine binding residues.
Length = 238
Score = 28.8 bits (65), Expect = 1.4
Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 107 QKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSG---GEPAALI--LLDAVVRLLP 160
Q L I+ G +E D R A +L E+ Y + G GE + L+DAV LLP
Sbjct: 55 QALFGIVQGGLYE--DLREESAEELAELDFDGYAIGGLSVGEEKEEMLELVDAVTPLLP 111
>gnl|CDD|38283 KOG3073, KOG3073, KOG3073, Protein required for 18S rRNA maturation
and 40S ribosome biogenesis [Translation, ribosomal
structure and biogenesis].
Length = 236
Score = 28.0 bits (62), Expect = 2.0
Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 8/78 (10%)
Query: 69 LGKAIDHAVSQYTHEDIPRILMSPRGKTLT--QKRVRQLSQKLGVIIVCGRF--EGIDER 124
L K + + V+ + + +I +S G L+ + V L V+ V G I
Sbjct: 144 LLKVVKNPVTDHLPVNSRKIGLSFSGPKLSNVRDLVASLDDDDSVVFVIGAMAHGKISVE 203
Query: 125 IIEARDLEEISVGDYILS 142
++ E++S+ +Y LS
Sbjct: 204 YVD----EKVSISNYPLS 217
>gnl|CDD|146300 pfam03587, EMG1, EMG1/NEP1 methyltransferase. Members of this
family are essential for 40S ribosomal biogenesis. The
structure of EMG1 has revealed that it is a novel member
of the superfamily of alpha/beta knot fold
methyltransferases.
Length = 202
Score = 28.3 bits (64), Expect = 2.1
Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 2/76 (2%)
Query: 69 LGKAIDHAVSQYTHEDIPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRF--EGIDERII 126
L K + + ++ E +IL+S +G+ ++ K + + V V G F + +
Sbjct: 114 LLKVVKNPLTDLLPEGSKKILLSEKGEKVSPKELASELKNEPVAFVIGAFPHGDFSDEVD 173
Query: 127 EARDLEEISVGDYILS 142
+ E S+ +Y LS
Sbjct: 174 YKKADESYSISNYPLS 189
>gnl|CDD|31942 COG1756, Mra1, Uncharacterized conserved protein [Function
unknown].
Length = 223
Score = 27.9 bits (62), Expect = 2.2
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 88 ILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILS 142
IL+ +G+ + K + L K +I+ G G D R E+ S+ D LS
Sbjct: 151 ILLHEKGELIPPKELISLLLKGIAVIIGGFPHG-DFREETEFVAEKYSIYDEPLS 204
>gnl|CDD|176347 cd01271, Fe65_C, Fe65 C-terminal Phosphotyrosine-binding (PTB)
domain. Fe65 C-terminal Phosphotyrosine-binding (PTB)
domain. Fe65 is an amyloid beta A4 precursor (APP)
protein-binding. It contains an N-terminal WW domain
followed by two PTB domains. The C-terminal PTB domain
is responsible for APP binding. PTB domains have a
PH-like fold and are found in various eukaryotic
signaling molecules. They were initially identified
based upon their ability to recognize phosphorylated
tyrosine residues In contrast to SH2 domains, which
recognize phosphotyrosine and adjacent carboxy-terminal
residues, PTB-domain binding specificity is conferred by
residues amino-terminal to the phosphotyrosine. More
recent studies have found that some types of PTB domains
can bind to peptides which are not tyrosine
phosphorylated or lack tyrosine residues altogether.
Length = 124
Score = 26.8 bits (59), Expect = 6.2
Identities = 20/72 (27%), Positives = 26/72 (36%), Gaps = 16/72 (22%)
Query: 47 RHHSVDDTPAGGGAGMVLRVDILGKAIDHAVSQYTHED------------IPRILMSPRG 94
R + P GM +IL AID+ +S ED I I
Sbjct: 5 RVQYLGMLPVDKPTGM----EILNSAIDNLMSSSNKEDWLSVNVNVAPSTITVISEKNEE 60
Query: 95 KTLTQKRVRQLS 106
+ L + RVR LS
Sbjct: 61 EVLVECRVRYLS 72
>gnl|CDD|30836 COG0490, COG0490, Putative regulatory, ligand-binding protein
related to C-terminal domains of K+ channels [Inorganic
ion transport and metabolism].
Length = 162
Score = 26.4 bits (58), Expect = 6.4
Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 1/51 (1%)
Query: 96 TLTQKRVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSGGEP 146
+LT + RQ++ LG+ RFE E + +E + G+
Sbjct: 53 SLTDEEARQVAAILGMSYKTERFEQT-EPALPGLIIEWFKIEAGSPFIGKT 102
>gnl|CDD|144312 pfam00665, rve, Integrase core domain. Integrase mediates
integration of a DNA copy of the viral genome into the
host chromosome. Integrase is composed of three domains.
The amino-terminal domain is a zinc binding domain
pfam02022. This domain is the central catalytic domain.
The carboxyl terminal domain that is a non-specific DNA
binding domain pfam00552. The catalytic domain acts as
an endonuclease when two nucleotides are removed from
the 3' ends of the blunt-ended viral DNA made by reverse
transcription. This domain also catalyses the DNA strand
transfer reaction of the 3' ends of the viral DNA to the
5' ends of the integration site.
Length = 120
Score = 26.1 bits (58), Expect = 8.8
Identities = 21/98 (21%), Positives = 35/98 (35%), Gaps = 18/98 (18%)
Query: 32 LWSMDAIQIRNFSTDR----HHSVDDTPAGGGAGMVL--------RVDILGKAIDHAVSQ 79
LW MD I S VDD + V+ +++ + AV +
Sbjct: 8 LWQMDITGIPIPSKGGKKYLLVIVDDF-----SRFVVAYALKSKTDAELVFDLLKAAVER 62
Query: 80 YTHEDIPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGR 117
P+ + S G T K ++L ++LG+ R
Sbjct: 63 R-GGKKPKTIHSDNGSEFTSKAFQELLKELGIKHSFSR 99
>gnl|CDD|144614 pfam01086, Clathrin_lg_ch, Clathrin light chain.
Length = 225
Score = 25.8 bits (57), Expect = 9.6
Identities = 7/35 (20%), Positives = 17/35 (48%), Gaps = 3/35 (8%)
Query: 196 PPILNSGDHERIKKWRKEQSFALTKKHRPDLLSKK 230
+ + E I++WR+ + + ++ D S+K
Sbjct: 103 ADRVEGEEPESIREWRERRDLRIEER---DEASEK 134
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
0.320 0.138 0.408
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,941,232
Number of extensions: 156094
Number of successful extensions: 393
Number of sequences better than 10.0: 1
Number of HSP's gapped: 386
Number of HSP's successfully gapped: 16
Length of query: 236
Length of database: 6,263,737
Length adjustment: 91
Effective length of query: 145
Effective length of database: 4,297,318
Effective search space: 623111110
Effective search space used: 623111110
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 (21.8 bits)
S2: 56 (25.2 bits)