RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780313|ref|YP_003064726.1| ribosomal RNA
methyltransferase RrmJ/FtsJ [Candidatus Liberibacter asiaticus str.
psy62]
(227 letters)
>gnl|CDD|30641 COG0293, FtsJ, 23S rRNA methylase [Translation, ribosomal structure
and biogenesis].
Length = 205
Score = 242 bits (618), Expect = 8e-65
Identities = 102/205 (49%), Positives = 143/205 (69%), Gaps = 4/205 (1%)
Query: 24 GSSRDWLNRHINDPYVQRAQLEGWRARSAYKLLQINEKHQILQSNRRIVDLGSSPGSWSQ 83
GSS+ WL H+ DPY ++A+ EG+R+R+AYKLL++NEK ++ + +VDLG++PG WSQ
Sbjct: 2 GSSQRWLAEHLRDPYYKKAKKEGYRSRAAYKLLELNEKFKLFKPGMVVVDLGAAPGGWSQ 61
Query: 84 VAARITGSNANNTRVVAIDILDMEPILGVKFFKFDFLDLDSWEFIRQAIGGNP-DLVLSD 142
VAA+ G+ ++VA+DIL M+PI GV F + D D D+ E + +A+GG P D+VLSD
Sbjct: 62 VAAKKLGAG---GKIVAVDILPMKPIPGVIFLQGDITDEDTLEKLLEALGGAPVDVVLSD 118
Query: 143 MAYPTIGHRKIDHLRTMSLCEAATFFALEMLNIGGDFLVKTFQGGTTNDILCLLKKHFQK 202
MA T G+R +DH R+M LCE A FALE+L GG F+ K FQG D+L L++ F+K
Sbjct: 119 MAPNTSGNRSVDHARSMYLCELALEFALEVLKPGGSFVAKVFQGEDFEDLLKALRRLFRK 178
Query: 203 VIHVKPVASRAESVEMFLLAKGFRK 227
V KP ASR S E++L+AKGF+
Sbjct: 179 VKIFKPKASRKRSREIYLVAKGFKG 203
>gnl|CDD|145073 pfam01728, FtsJ, FtsJ-like methyltransferase. This family consists
of FtsJ from various bacterial and archaeal sources FtsJ
is a methyltransferase, but actually has no effect on
cell division. FtsJ's substrate is the 23S rRNA. The 1.5
A crystal structure of FtsJ in complex with its cofactor
S-adenosylmethionine revealed that FtsJ has a
methyltransferase fold. This family also includes the N
terminus of flaviviral NS5 protein. It has been
hypothesized that the N-terminal domain of NS5 is a
methyltransferase involved in viral RNA capping.
Length = 176
Score = 191 bits (488), Expect = 1e-49
Identities = 69/180 (38%), Positives = 104/180 (57%), Gaps = 5/180 (2%)
Query: 47 WRARSAYKLLQINEKHQILQSNRRIVDLGSSPGSWSQVAARITGSNANNTRVVAIDILDM 106
+ +R+A+KLL+I+E+ + + ++DLG++PG +SQV RVVA+D+ M
Sbjct: 1 YVSRAAFKLLEIDERFGLKPGGKTVLDLGAAPGGFSQVLLERGA----KGRVVAVDLGPM 56
Query: 107 EPILGVKFFKFDFLDLDSWEFIRQAIGGNPDLVLSDMAYPTIGHRKIDHLRTMSLCEAAT 166
+PI GV F + D D ++ E + + + G DLVL D A G D ++ L AA
Sbjct: 57 KPIQGVTFLRGDITDPETLEKLLELLPGKVDLVLCDGAPNVSGLENTDSFISLRLVLAAL 116
Query: 167 FFALEMLNIGGDFLVKTFQGGTTN-DILCLLKKHFQKVIHVKPVASRAESVEMFLLAKGF 225
ALE+L GG+F+VK F+G + ++L LKK F+KV KP ASR S E +L+ GF
Sbjct: 117 LLALEVLRPGGNFVVKLFKGFEFSVELLYKLKKGFEKVGIFKPPASRPSSSEEYLVCLGF 176
>gnl|CDD|39789 KOG4589, KOG4589, KOG4589, Cell division protein FtsJ [Cell cycle
control, cell division, chromosome partitioning].
Length = 232
Score = 185 bits (471), Expect = 8e-48
Identities = 80/220 (36%), Positives = 126/220 (57%), Gaps = 5/220 (2%)
Query: 10 RRGLTQKVKNRSCQGSSRDWLNRHINDPYVQRAQLEGWRARSAYKLLQINEKHQILQSNR 69
R + + +R S WL R + DPYV++A+++ +R+RSA+KL++IN+K++ L+
Sbjct: 12 IRSMFGTIGSRYRSKSLHRWLTRQLKDPYVKKAKVQNYRSRSAFKLIEINDKYRFLRPED 71
Query: 70 RIVDLGSSPGSWSQVAARITGSNANNTRVVAIDILDMEPILGVKFFK-FDFLDLDSWEFI 128
++D G++PGSWSQVA + N V+ +D+L +EP G + D D +++ I
Sbjct: 72 TVLDCGAAPGSWSQVAVQRVN---PNGMVLGVDLLHIEPPEGATIIQGNDVTDPETYRKI 128
Query: 129 RQAIGGNP-DLVLSDMAYPTIGHRKIDHLRTMSLCEAATFFALEMLNIGGDFLVKTFQGG 187
+A+ P D+VLSDMA G R DH R++ LC++A FAL +L G F+ K + G
Sbjct: 129 FEALPNRPVDVVLSDMAPNATGVRIRDHYRSIELCDSALLFALTLLIPNGSFVCKLWDGS 188
Query: 188 TTNDILCLLKKHFQKVIHVKPVASRAESVEMFLLAKGFRK 227
+ L+ F V VKP ASR ES E +L+ F+
Sbjct: 189 EEALLQRRLQAVFTNVKKVKPDASRDESAETYLVCLNFKG 228
>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 = 148 bits (375), Expect = 1e-36
Identities = 76/196 (38%), Positives = 110/196 (56%), Gaps = 6/196 (3%)
Query: 36 DPYVQRAQLEGWRARSAYKLLQINEKHQILQSNRRIVDLGSSPGSWSQVAAR-----ITG 90
D Y + A+ GWRARSA+KLLQI+E+ QI + +R+VDL ++PGSWSQV +R +
Sbjct: 10 DIYYRLAKENGWRARSAFKLLQIDEEFQIFEGVKRVVDLCAAPGSWSQVLSRKLYKPLPS 69
Query: 91 SNANNTRVVAIDILDMEPILGVKFFKFDFLDLDSWEFIRQAIGGNP-DLVLSDMAYPTIG 149
S + ++VA+D+ M PI GV + D + E I + GG DLV+ D A G
Sbjct: 70 SGERDKKIVAVDLQPMAPIEGVIQLQGDITSASTAEAIIEHFGGEKADLVVCDGAPDVTG 129
Query: 150 HRKIDHLRTMSLCEAATFFALEMLNIGGDFLVKTFQGGTTNDILCLLKKHFQKVIHVKPV 209
+D L AA A +L GG F+ K F+G T+ + L+K F+KV KP
Sbjct: 130 LHDLDEYVQAQLLLAALNIATCVLKPGGSFVAKIFRGRDTSLLYSQLRKFFKKVTCAKPR 189
Query: 210 ASRAESVEMFLLAKGF 225
+SR S+E F++ G+
Sbjct: 190 SSRNSSIEAFVVCLGY 205
>gnl|CDD|36314 KOG1098, KOG1098, KOG1098, Putative SAM-dependent rRNA
methyltransferase SPB1 [RNA processing and modification,
General function prediction only].
Length = 780
Score = 113 bits (283), Expect = 5e-26
Identities = 61/197 (30%), Positives = 103/197 (52%), Gaps = 4/197 (2%)
Query: 32 RHINDPYVQRAQLEGWRARSAYKLLQINEKHQILQSNRRIVDLGSSPGSWSQVAARITGS 91
+ D Y + A+ G+R+RSA+KLLQ+N+K++ L+ ++DL ++PG W QVA++
Sbjct: 9 KGRLDKYYRLAKELGYRSRSAFKLLQLNKKYKFLEKAHVVLDLCAAPGGWLQVASQSMPV 68
Query: 92 NANNTRVVAIDILDMEPILGVKFFKFDFLDLDSWEFIRQAIGGNP-DLVLSDMAYPTIGH 150
+ +V +D++ ++PI D + +R+ + D+VL D A G+
Sbjct: 69 GS---LIVGVDLVPIKPIPNCDTLVEDITTDECRSKLRKILKTWKADVVLHDGAPNVGGN 125
Query: 151 RKIDHLRTMSLCEAATFFALEMLNIGGDFLVKTFQGGTTNDILCLLKKHFQKVIHVKPVA 210
D + L A A E L GG F+ K F+ N +L + + F+KV KP A
Sbjct: 126 WVQDAFQQACLTLRALKLATEFLAKGGTFVTKVFRSEDYNGLLRVFGQLFKKVEATKPAA 185
Query: 211 SRAESVEMFLLAKGFRK 227
SR+ES E+F++ G+
Sbjct: 186 SRSESAEIFVVCLGYLA 202
>gnl|CDD|38878 KOG3674, KOG3674, KOG3674, FtsJ-like RNA methyltransferase [RNA
processing and modification].
Length = 696
Score = 44.7 bits (105), Expect = 2e-05
Identities = 29/113 (25%), Positives = 50/113 (44%), Gaps = 4/113 (3%)
Query: 118 DFLDLDSWEFIRQAI--GGNPDLVLSDMAYPTIGHRKIDHLRTMSLCEAATFFALEMLNI 175
D ++Q + G DLV +D + G SL A AL++L
Sbjct: 207 DIEKFTEEYLLKQEVKLAGTVDLVTADGSTDCQGKPGEQESIVSSLISAEVEVALKLLRR 266
Query: 176 GGDFLVKTFQ--GGTTNDILCLLKKHFQKVIHVKPVASRAESVEMFLLAKGFR 226
GG F++K F + D++ LL +F V KP S+ + E++++ G++
Sbjct: 267 GGRFILKMFTFFEKCSRDLMYLLNCNFSSVHAFKPATSKPGNSEVYVVCLGYK 319
>gnl|CDD|31382 COG1189, COG1189, Predicted rRNA methylase [Translation, ribosomal
structure and biogenesis].
Length = 245
Score = 41.7 bits (98), Expect = 2e-04
Identities = 20/106 (18%), Positives = 44/106 (41%), Gaps = 17/106 (16%)
Query: 47 WRARSAYKLLQINEKHQILQSNRRIVDLGSSPGSWSQVAARITGSNANNTRVVAIDI--- 103
+ +R KL + E+ ++ + ++D+GSS G ++ V + V A+D+
Sbjct: 59 YVSRGGLKLEKALEEFELDVKGKVVLDIGSSTGGFTDVLLQRGAK-----HVYAVDVGYG 113
Query: 104 ---LDMEPILGVKFF-KFDFLDLDSWEFIRQAIGGNPDLVLSDMAY 145
+ V + + L +F PDL++ D+++
Sbjct: 114 QLHWKLRNDPRVIVLERTNVRYLTPEDF-----TEKPDLIVIDVSF 154
>gnl|CDD|38877 KOG3673, KOG3673, KOG3673, FtsJ-like RNA methyltransferase [RNA
processing and modification].
Length = 845
Score = 39.6 bits (92), Expect = 6e-04
Identities = 31/115 (26%), Positives = 52/115 (45%), Gaps = 4/115 (3%)
Query: 117 FDFLDLDSWE-FIRQAIGG-NPDLVLSDMAYPTIGHRKIDHLRTMSLCEAATFFALEMLN 174
D +++DS E I + G +++D + G I + + L AL ++
Sbjct: 332 MDPVNIDSLEAHISRGTSGLGVHFMMADGGFSVEGQENIQEILSKQLYLCQFLVALCIVR 391
Query: 175 IGGDFLVKTFQGGT--TNDILCLLKKHFQKVIHVKPVASRAESVEMFLLAKGFRK 227
GG+F K F T + ++ L+ FQ V KP SR + E +++ KG RK
Sbjct: 392 EGGNFFCKLFDLFTPFSVGLVYLMYVCFQSVSLHKPHTSRPANSERYIVCKGLRK 446
>gnl|CDD|100107 cd02440, AdoMet_MTases, S-adenosylmethionine-dependent
methyltransferases (SAM or AdoMet-MTase), class I;
AdoMet-MTases are enzymes that use
S-adenosyl-L-methionine (SAM or AdoMet) as a substrate
for methyltransfer, creating the product
S-adenosyl-L-homocysteine (AdoHcy). There are at least
five structurally distinct families of AdoMet-MTases,
class I being the largest and most diverse. Within this
class enzymes can be classified by different substrate
specificities (small molecules, lipids, nucleic acids,
etc.) and different target atoms for methylation
(nitrogen, oxygen, carbon, sulfur, etc.)..
Length = 107
Score = 39.7 bits (93), Expect = 7e-04
Identities = 22/126 (17%), Positives = 38/126 (30%), Gaps = 32/126 (25%)
Query: 70 RIVDLGSSPGSWSQVAARITGSNANNTRVVAIDILDM-----------EPILGVKFFKFD 118
R++DLG G+ + A RV +DI + V+ K D
Sbjct: 1 RVLDLGCGTGALALALAS-----GPGARVTGVDISPVALELARKAAAALLADNVEVLKGD 55
Query: 119 FLDLDSWEFIRQAIGGNPDLVLSDMAYPTIGHRKIDHLRTMSLCEAATFFALEMLNIGGD 178
+L + D+++SD + L A +L GG
Sbjct: 56 AEELPPEAD------ESFDVIISDPPLHHLVEDLARFLEE----------ARRLLKPGGV 99
Query: 179 FLVKTF 184
++
Sbjct: 100 LVLTLV 105
>gnl|CDD|32757 COG2933, COG2933, Predicted SAM-dependent methyltransferase
[General function prediction only].
Length = 358
Score = 31.5 bits (71), Expect = 0.20
Identities = 20/69 (28%), Positives = 28/69 (40%), Gaps = 13/69 (18%)
Query: 49 ARSAYKL-------LQINEKHQILQSNRRIVDLGSSPGSWSQVAARITGSNANNTRVVAI 101
+RS KL + +E + L VDLG+ PG W+ + N RV A+
Sbjct: 186 SRSTLKLEEAFHTFIPRDEWDKRLAPGMWAVDLGACPGGWTYQLVK------RNMRVYAV 239
Query: 102 DILDMEPIL 110
D M L
Sbjct: 240 DNGPMAQSL 248
>gnl|CDD|31053 COG0709, SelD, Selenophosphate synthase [Amino acid transport and
metabolism].
Length = 346
Score = 30.2 bits (68), Expect = 0.47
Identities = 21/101 (20%), Positives = 37/101 (36%), Gaps = 14/101 (13%)
Query: 56 LQINEKHQILQSNRRIVDLGSSPGSWSQVAARITGSNANNTRVVAIDILDM--EPILGVK 113
+ H I+ + + + P + ++AA +NA D+ M +PI+ +
Sbjct: 55 YDLGNGHSIISTTDFFMPIVDDPFDFGRIAA----TNA------ISDVFAMGGKPIMAIA 104
Query: 114 FFKFDFLDLDSWEFIRQAIGGNPDLVLSDMAYPTIGHRKID 154
F LD E ++ I G D + G ID
Sbjct: 105 ILGFPNDLLDK-EIAQEVIEGGRD-ACREAGIALAGGHSID 143
>gnl|CDD|34129 COG4449, COG4449, Predicted protease of the Abi (CAAX) family
[General function prediction only].
Length = 827
Score = 30.0 bits (67), Expect = 0.53
Identities = 22/84 (26%), Positives = 33/84 (39%), Gaps = 18/84 (21%)
Query: 12 GLTQKVKNRSCQGSSRDWLNRHINDPYVQRAQLEGWRARSAYKLLQINEKHQILQSNRRI 71
GL QKV+N WL +H N P QR Q +L Q+ ++ +
Sbjct: 514 GLQQKVQNSP---EIITWLAQHGNSPENQRFQ----------RLQQLGDRLL-----TML 555
Query: 72 VDLGSSPGSWSQVAARITGSNANN 95
G + W AA + G + +N
Sbjct: 556 KPRGITREDWQNNAATLAGLDPDN 579
>gnl|CDD|33863 COG4106, Tam, Trans-aconitate methyltransferase [General function
prediction only].
Length = 257
Score = 29.1 bits (65), Expect = 1.0
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 40 QRAQLEGWRARSAYKLLQINEKHQILQSNRRIVDLGSSPGSWSQVAAR 87
Q Q E R R A LL L+ RR+VDLG PG+ +++ AR
Sbjct: 7 QYLQFEDERTRPARDLLA----RVPLERPRRVVDLGCGPGNSTELLAR 50
>gnl|CDD|79364 cd03682, ClC_sycA_like, ClC sycA-like chloride channel proteins.
This ClC family presents in bacteria, where it
facilitates acid resistance in acidic soil. Mutation of
this gene (sycA) in Rhizobium tropici CIAT899 causes
serious deficiencies in nodule development, nodulation
competitiveness, and N2 fixation on Phaseolus vulgaris
plants, due to its reduced ability for acid resistance.
This family is part of the ClC chloride channel
superfamiy. These proteins catalyse the selective flow
of Cl- ions across cell membranes and Cl-/H+ exchange
transport. These proteins share two characteristics that
are apparently inherent to the entire ClC chloride
channel superfamily: a unique double-barreled
architecture and voltage-dependent gating mechanism. The
gating is conferred by the permeating anion itself,
acting as the gating charge..
Length = 378
Score = 27.0 bits (60), Expect = 4.6
Identities = 15/67 (22%), Positives = 22/67 (32%), Gaps = 5/67 (7%)
Query: 164 AATFFALEMLNIGG---DFLVKTFQGGTTNDILCLL--KKHFQKVIHVKPVASRAESVEM 218
A FALE+L +G L+ D + +H I P V++
Sbjct: 144 AGAIFALEVLVLGRLRYSALIPCLVAAIVADWVSHALGLEHTHYHIVFIPTLDPLLFVKV 203
Query: 219 FLLAKGF 225
L F
Sbjct: 204 ILAGIIF 210
>gnl|CDD|30932 COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication,
recombination, and repair].
Length = 1139
Score = 26.0 bits (57), Expect = 9.0
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 105 DMEPILGVKFFKFDFLDLDSWEFIRQAI 132
DM+ + V KFDFL L + I++A+
Sbjct: 540 DMDDLEAVGLLKFDFLGLKTLTIIQRAL 567
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 0.137 0.410
Gapped
Lambda K H
0.267 0.0779 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,785,838
Number of extensions: 142186
Number of successful extensions: 321
Number of sequences better than 10.0: 1
Number of HSP's gapped: 310
Number of HSP's successfully gapped: 19
Length of query: 227
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 137
Effective length of database: 4,318,927
Effective search space: 591692999
Effective search space used: 591692999
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)