RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781160|ref|YP_003065573.1| 16S rRNA m3U1498
methyltransferase [Candidatus Liberibacter asiaticus str. psy62]
(245 letters)
>gnl|CDD|146878 pfam04452, Methyltrans_RNA, RNA methyltransferase. RNA
methyltransferases modify nucleotides during ribosomal
RNA maturation in a site-specific manner. The
Escherichia coli member is specific for U1498
methylation.
Length = 225
Score = 188 bits (480), Expect = 1e-48
Identities = 77/222 (34%), Positives = 124/222 (55%), Gaps = 9/222 (4%)
Query: 26 GDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG-KSIRFKVEYQSRSQTKQSD-VQ 83
++ H+L VLR+KEGD I LF+G GE+L++I + KS+ K+ + + +
Sbjct: 5 DEEAHHLVRVLRLKEGDEIKLFDGDGGEYLAEIEEISKKSVLVKILEKLEVNKELPLKIT 64
Query: 84 YIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHY------NMDRVRTYTISAAEQ 137
+ K +RL+ ++QK+ E+G+ I P+I+ + ++R + I AAEQ
Sbjct: 65 LAQALPKGDRLELILQKATELGVDRIVPLISERSVVKLDGKRADKKLERWQKIAIEAAEQ 124
Query: 138 CDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPE 197
LP + PP +L+ LL+ D +++ +E S L +L A V ++IGPE
Sbjct: 125 SGRTRLPEVLPPISLKELLEELDDADKLILHEEAAKSLGELSELLASLKGGKVLLIIGPE 184
Query: 198 GGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQA 239
GG+ EE E L TP+SLGPRILR++TAA+AA++ +QA
Sbjct: 185 GGFSPEEIELLKEA-GFTPVSLGPRILRTETAALAALSALQA 225
>gnl|CDD|31575 COG1385, COG1385, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 246
Score = 184 bits (468), Expect = 2e-47
Identities = 90/245 (36%), Positives = 132/245 (53%), Gaps = 9/245 (3%)
Query: 7 LKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGK-SI 65
+ RLFVD L +GD+ H+L VLR+KEGD + LF+G GE+L++I+ +GK
Sbjct: 3 MPRLFVDEELAEGATVILTGDEAHHLKRVLRLKEGDELRLFDGSGGEFLAEITKIGKKEA 62
Query: 66 RFKVEYQSRSQTKQSDVQYIFSPI-KTNRLDYMIQKSVEMGMGAIRPVITRYTQ-----N 119
K+ Q + + I K ++L+ +IQK+ E+G+ I P+IT +
Sbjct: 63 LLKIVEQLEPNPELPLKITLAQAIPKGDKLELIIQKATELGVSKIIPLITERSVVKLDGK 122
Query: 120 THYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLE 179
++R + I AAEQ +P I PP +L+ LLK D + E E L
Sbjct: 123 KAAKLERWQKIAIEAAEQSGRNVVPEIKPPESLKELLKEIDDEDALKLIYEEKAKEGLLA 182
Query: 180 KLHAIAHIP-NVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQ 238
A V ++IGPEGG+ +E E L F TP+SLGPRILR++TAA+AA+A +Q
Sbjct: 183 LPLLEALPEGKVLLIIGPEGGFSEDEIELLREAGF-TPVSLGPRILRTETAALAALAALQ 241
Query: 239 AICGD 243
A+ GD
Sbjct: 242 ALLGD 246
>gnl|CDD|35259 KOG0036, KOG0036, KOG0036, Predicted mitochondrial carrier protein
[Nucleotide transport and metabolism].
Length = 463
Score = 29.9 bits (67), Expect = 0.69
Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 3/44 (6%)
Query: 124 MDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVF 167
MD+ TI E D L L YP + LE + W H I
Sbjct: 127 MDKDGKATIDLEEWRDHLLL---YPESDLEDIYDFWRHVLLIDI 167
>gnl|CDD|39880 KOG4682, KOG4682, KOG4682, Uncharacterized conserved protein,
contains BTB/POZ domain [General function prediction
only].
Length = 488
Score = 28.8 bits (64), Expect = 1.3
Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 2/74 (2%)
Query: 58 ISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRP--VITR 115
I V + F Y+ + K SDV + + +LD +IQ+ E+ + + P
Sbjct: 119 IDVVALQVAFGSLYRDEVEIKLSDVVGVLAAACLLQLDGLIQRCGEVMIETLSPKTACGY 178
Query: 116 YTQNTHYNMDRVRT 129
Y Y ++ V+
Sbjct: 179 YEAACKYGLESVKK 192
>gnl|CDD|39719 KOG4519, KOG4519, KOG4519, Phosphomevalonate kinase [Lipid
transport and metabolism].
Length = 459
Score = 27.4 bits (60), Expect = 3.4
Identities = 13/46 (28%), Positives = 20/46 (43%)
Query: 50 KDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLD 95
D EWL KIS +I+ SR+ + +QY+ + L
Sbjct: 61 SDREWLYKISLNHLTIQVVSASDSRNPFVEHAIQYVIAYFHLATLH 106
>gnl|CDD|38182 KOG2971, KOG2971, KOG2971, RNA-binding protein required for
biogenesis of the ribosomal 60S subunit [Translation,
ribosomal structure and biogenesis].
Length = 299
Score = 27.7 bits (61), Expect = 3.6
Identities = 14/72 (19%), Positives = 25/72 (34%), Gaps = 6/72 (8%)
Query: 4 HSHLKRLFVDF-PLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGE----WLSKI 58
HL + P K + L + +K ++ L F + + W+S
Sbjct: 64 TRHLMKDISSLLPHSKKDSKLDRKKKLGVLNELAELKNCNSCLFFESRKRKDLYLWMSNS 123
Query: 59 SYVGKSIRFKVE 70
G S++F V
Sbjct: 124 PN-GPSVKFLVH 134
>gnl|CDD|119356 cd02877, GH18_hevamine_XipI_class_III, This conserved domain family
includes xylanase inhibitor Xip-I, and the class III
plant chitinases such as hevamine, concanavalin B, and
PPL2, all of which have a glycosyl hydrolase family 18
(GH18) domain. Hevamine is a class III endochitinase
that hydrolyzes the linear polysaccharide chains of
chitin and peptidoglycan and is important for defense
against pathogenic bacteria and fungi. PPL2 (Parkia
platycephala lectin 2) is a class III chitinase from
Parkia platycephala seeds that hydrolyzes beta(1-4)
glycosidic bonds linking
2-acetoamido-2-deoxy-beta-D-glucopyranose units in
chitin..
Length = 280
Score = 26.8 bits (60), Expect = 5.7
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 121 HYNMDRVRTYTISAAEQC 138
+ D + Y ++AA QC
Sbjct: 147 LFASDPSKKYYLTAAPQC 164
>gnl|CDD|143602 cd07578, nitrilase_1_R1, First nitrilase domain of an
uncharacterized subgroup of the nitrilase superfamily
(putative class 13 nitrilases). Members of this
subgroup have two nitrilase domains. This is the first
of those two domains. The nitrilase superfamily is
comprised of nitrile- or amide-hydrolyzing enzymes and
amide-condensing enzymes, which depend on a Glu-Lys-Cys
catalytic triad. This superfamily has been classified in
the literature based on global and structure based
sequence analysis into thirteen different enzyme classes
(referred to as 1-13). Class 13 represents proteins that
at the time were difficult to place in a distinct
similarity group; this subgroup represents either a new
class or one that was included previously in class 13.
Members of this superfamily generally form homomeric
complexes, the basic building block of which is a
homodimer.
Length = 258
Score = 26.7 bits (59), Expect = 6.8
Identities = 33/119 (27%), Positives = 44/119 (36%), Gaps = 29/119 (24%)
Query: 144 PFIYP---PTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEG-- 198
PF+ P PTT F +H+C IV S + + N A+LIGP G
Sbjct: 57 PFVEPIPGPTTARFAELAREHDCYIVVGLPEVDSRSGI--------YYNSAVLIGPSGVI 108
Query: 199 GYH-------SEEKET----LHSLPFVTPLSLGPRILRSD-----TAAVAAMALVQAIC 241
G H SE K L F T + ++ D TA + A+ IC
Sbjct: 109 GRHRKTHPYISEPKWAADGDLGHQVFDTEIGRIALLICMDIHFFETARLLALGGADVIC 167
>gnl|CDD|33901 COG4149, ModC, ABC-type molybdate transport system, permease
component [Inorganic ion transport and metabolism].
Length = 225
Score = 25.9 bits (57), Expect = 9.5
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 122 YNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLL 156
Y + R R S E ++ LP + PP L FLL
Sbjct: 32 YLLARRRFRGKSLLES--LVLLPLVLPPVVLGFLL 64
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
0.321 0.136 0.414
Gapped
Lambda K H
0.267 0.0776 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,972,896
Number of extensions: 149223
Number of successful extensions: 315
Number of sequences better than 10.0: 1
Number of HSP's gapped: 308
Number of HSP's successfully gapped: 12
Length of query: 245
Length of database: 6,263,737
Length adjustment: 91
Effective length of query: 154
Effective length of database: 4,297,318
Effective search space: 661786972
Effective search space used: 661786972
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: 56 (25.3 bits)