RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780904|ref|YP_003065317.1| tRNA/rRNA methyltransferase
[Candidatus Liberibacter asiaticus str. psy62]
(268 letters)
>gnl|CDD|30911 COG0565, LasT, rRNA methylase [Translation, ribosomal structure and
biogenesis].
Length = 242
Score = 235 bits (602), Expect = 7e-63
Identities = 94/241 (39%), Positives = 150/241 (62%), Gaps = 4/241 (1%)
Query: 12 AKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSV 71
+ I+LV+P NIG VARAM NF L++LRLVNPR G E+AR+ +A A ++++
Sbjct: 2 LENIRIVLVEPSHPGNIGSVARAMKNFGLSELRLVNPRAG-LDEEARALAAGARDILENA 60
Query: 72 RVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWG 131
++ L+EA+AD + ATTAR+R+ + + P+EAA L E+ G V ++FGRER G
Sbjct: 61 KIVDTLEEALADCDLVVATTARSRDLLRPLRTPREAAPELLEK-AKGGKVALVFGRERVG 119
Query: 132 LTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKEQNTPATKGE 191
LTNEE+AL + +++ P NP +PSLN++QAV ++++E + ++ E + ++ ATK E
Sbjct: 120 LTNEELALCDVLVTIPANPDYPSLNLAQAVQVILYELRKAE-LAQEGSSGIEDELATKEE 178
Query: 192 LLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSR 251
L ++LE L+ G+ P KKK ++ L + R L EV +LRGI+ +++ +
Sbjct: 179 LELLYEHLEELLDAIGFPDP-RKKKSLMRKLRRLLGRARLTSREVNILRGILRKIERRIK 237
Query: 252 Q 252
Sbjct: 238 G 238
>gnl|CDD|144253 pfam00588, SpoU_methylase, SpoU rRNA Methylase family. This family
of proteins probably use S-AdoMet.
Length = 142
Score = 107 bits (270), Expect = 3e-24
Identities = 42/158 (26%), Positives = 76/158 (48%), Gaps = 21/158 (13%)
Query: 14 GPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRD-GWPSEKARSSSANADCVIDSVR 72
+++L +PQ N+G +AR F L LV PR + KA +SA A + +
Sbjct: 1 PLIVVLDEPQDPGNLGAIARTAAAFGADGLILVEPRCADLYNPKAIRASAGALFHLP-LV 59
Query: 73 VFSNLKEAIADLH----FIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRE 128
+ NL+EA+ DL +I AT+ + + ++ K V ++FG E
Sbjct: 60 IVDNLEEALKDLKEAGYWIIATSLKGKPLYEIDFPKK---------------VALVFGNE 104
Query: 129 RWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVW 166
GL+NE + L + ++ P++ SLN++ A ++++
Sbjct: 105 GTGLSNEVLELCDRLVRIPMSGEVESLNVAVAAAIILY 142
>gnl|CDD|30912 COG0566, SpoU, rRNA methylases [Translation, ribosomal structure
and biogenesis].
Length = 260
Score = 41.5 bits (97), Expect = 2e-04
Identities = 32/152 (21%), Positives = 62/152 (40%), Gaps = 23/152 (15%)
Query: 21 DPQLGENIGMVARAMWNFNLTQLRLVNPR-DGWPSEKARSSSANADCVIDSVRVFSNLKE 79
DP N+G + R F + + L R D + R+S+ A + +RV + +
Sbjct: 119 DPH---NLGAIIRTADAFGVDGVILPKRRADPLNPKVIRASAGAAF-HVPVIRVTNLART 174
Query: 80 AIADLH----FIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNE 135
+ L ++ AT+ + PK+ A+V G E GL+
Sbjct: 175 LLELLKEAGFWVVATSLDGEVDLYETDLPKKTALV--------------LGNEGEGLSRL 220
Query: 136 EIALSNAIISFPVNPLFPSLNISQAVLLMVWE 167
+ ++ ++ P+ SLN+S A ++++E
Sbjct: 221 LLEHADQLVRIPMAGKVESLNVSVAAGILLYE 252
>gnl|CDD|30568 COG0219, CspR, Predicted rRNA methylase (SpoU class) [Translation,
ribosomal structure and biogenesis].
Length = 155
Score = 36.7 bits (85), Expect = 0.006
Identities = 32/154 (20%), Positives = 58/154 (37%), Gaps = 15/154 (9%)
Query: 17 IILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVID-SVRVFS 75
I+L P++ N G + R +L L+ P G+ + R A D S+
Sbjct: 5 IVLYQPEIPPNTGNIIRTCAATG-AELHLIEPL-GFDLDDKRLKRAGLDYHEKASLTEHD 62
Query: 76 NLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNE 135
+L+ + + + + F + ++FG E GL E
Sbjct: 63 SLEAFLEA----------EPIGGRLFALTTKGTTTYTDVSFQKGDY-LLFGPESRGLPEE 111
Query: 136 EI-ALSNAIISFPVNPLFPSLNISQAVLLMVWEC 168
+ A + I P+ P SLN+S V ++++E
Sbjct: 112 ILDAAPDRCIRIPMRPGVRSLNLSNTVAVVLYEA 145
>gnl|CDD|176209 cd08247, AST1_like, AST1 is a cytoplasmic protein associated with
the periplasmic membrane in yeast. This group contains
members identified in targeting of yeast membrane
proteins ATPase. AST1 is a cytoplasmic protein
associated with the periplasmic membrane in yeast,
identified as a multicopy suppressor of pma1 mutants
which cause temperature sensitive growth arrest due to
the inability of ATPase to target to the cell surface.
This family is homologous to the medium chain family of
dehydrogenases and reductases. Medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of an
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 352
Score = 30.3 bits (69), Expect = 0.50
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 35 MWNFNLTQLRLVNPRDGWPSEKARS--SSANADCVIDSVRVFSNLKEAIADL 84
+W++N Q L++P W EK + IDSV F + KEA L
Sbjct: 290 LWSYNY-QFFLLDPNADWI-EKCAELIADGKVKPPIDSVYPFEDYKEAFERL 339
>gnl|CDD|143948 pfam00185, OTCace, Aspartate/ornithine carbamoyltransferase,
Asp/Orn binding domain.
Length = 155
Score = 29.5 bits (67), Expect = 0.92
Identities = 10/51 (19%), Positives = 19/51 (37%), Gaps = 2/51 (3%)
Query: 43 LRLVNPRDGWPSEK--ARSSSANADCVIDSVRVFSNLKEAIADLHFIYATT 91
+ LV P+ P + + S+ V +L+EA+ +Y
Sbjct: 31 VVLVAPKGLPPDPELVDEAKKNALKSGGISITVTDDLEEALKGADVVYTDR 81
>gnl|CDD|30427 COG0078, ArgF, Ornithine carbamoyltransferase [Amino acid transport
and metabolism].
Length = 310
Score = 28.6 bits (64), Expect = 1.8
Identities = 12/69 (17%), Positives = 27/69 (39%), Gaps = 7/69 (10%)
Query: 25 GENIG---MVARAMWNFNLTQLRLVNPRDGWPSEKARS-SSANADCVIDSVRVFSNLKEA 80
G N+ ++A A ++ R+ P+ P + + NA + + + +EA
Sbjct: 162 GNNVANSLLLAAAKLGMDV---RIATPKGYEPDPEVVEKAKENAKESGGKITLTEDPEEA 218
Query: 81 IADLHFIYA 89
+ +Y
Sbjct: 219 VKGADVVYT 227
>gnl|CDD|35746 KOG0526, KOG0526, KOG0526, Nucleosome-binding factor SPN, POB3
subunit [Transcription, Replication, recombination and
repair, Chromatin structure and dynamics].
Length = 615
Score = 27.2 bits (60), Expect = 4.5
Identities = 16/61 (26%), Positives = 23/61 (37%)
Query: 39 NLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNF 98
L ++R P D E A + V+ V S + +AI I T R R +
Sbjct: 159 GLMEMRFHIPEDQEDGEDRDKVEAFYENVLAKADVSSAVGDAIVSFEEILCLTPRGRYDI 218
Query: 99 K 99
K
Sbjct: 219 K 219
>gnl|CDD|31437 COG1244, COG1244, Predicted Fe-S oxidoreductase [General function
prediction only].
Length = 358
Score = 27.2 bits (60), Expect = 5.3
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 194 SFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFI--RPELMREEV 236
SFLD E+ E R Y ++ D++ + + RPE +REE
Sbjct: 111 SFLDPEEVPREARRYIL---ERISENDNVKEVVVESRPEFIREER 152
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
0.318 0.133 0.380
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,117,920
Number of extensions: 161127
Number of successful extensions: 354
Number of sequences better than 10.0: 1
Number of HSP's gapped: 349
Number of HSP's successfully gapped: 12
Length of query: 268
Length of database: 6,263,737
Length adjustment: 92
Effective length of query: 176
Effective length of database: 4,275,709
Effective search space: 752524784
Effective search space used: 752524784
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.3 bits)