RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|255764511|ref|YP_003065518.2| S-adenosyl-methyltransferase
MraW [Candidatus Liberibacter asiaticus str. psy62]
(341 letters)
>gnl|CDD|178824 PRK00050, PRK00050, 16S rRNA m(4)C1402 methyltranserfase;
Provisional.
Length = 296
Score = 397 bits (1023), Expect = e-111
Identities = 133/304 (43%), Positives = 192/304 (63%), Gaps = 17/304 (5%)
Query: 20 HVPVLLEKVIALLNPAPGKVILDATFGAGGYSRSFCKMGSN---VIALDRDPFAVSCGQE 76
H+PVLL++V+ L P + +D TFG GG+SR+ + +IA+DRDP A++ ++
Sbjct: 3 HIPVLLDEVVDALAIKPDGIYVDGTFGGGGHSRAILERLGPKGRLIAIDRDPDAIAAAKD 62
Query: 77 TMRDYKEQFSLFQATFSQLQDYVPD--KGVDGVVFDLGVSSMQIDCGDRGFSFQKSGPLD 134
++ + +F+L FS L++ + + VDG++ DLGVSS Q+D +RGFSF+K GPLD
Sbjct: 63 RLKPFG-RFTLVHGNFSNLKEVLAEGLGKVDGILLDLGVSSPQLDDAERGFSFRKDGPLD 121
Query: 135 MRMSCS-GISASDVVNQANVKDLTRILGILGEEKQASRIAHAIVKRRQSAPFQTTQDLSS 193
MRM S G++A++VVN + ++L RI GEE+ A RIA AIV+ R P TT +L+
Sbjct: 122 MRMDQSQGLTAAEVVNTYSEEELARIFKEYGEERFARRIARAIVEARPKKPITTTGELAE 181
Query: 194 LIQKTVYFSKNNRIHPATRSFQALRIFVNNEIEELAQGLRSAEKALKAGGLLIVVSFHSL 253
+I K+ + IHPATR+FQALRI VN+E+EEL + L +A LK GG L V+SFHSL
Sbjct: 182 II-KSAVPPRRKGIHPATRTFQALRIEVNDELEELERALEAALDLLKPGGRLAVISFHSL 240
Query: 254 EDRLVKKFFASRSGKVMAVRHMIPSNAHPAVFQSITKKVVVPTQEDVAFNRRSRSAKLRA 313
EDR+VK+FF S P + +TKK + P++E++A N R+RSAKLR
Sbjct: 241 EDRIVKRFFRELSKG--------CCGNKP-KLKLLTKKPIKPSEEEIAANPRARSAKLRV 291
Query: 314 GMRT 317
R
Sbjct: 292 AERL 295
>gnl|CDD|161660 TIGR00006, TIGR00006, S-adenosyl-methyltransferase MraW. Genetics
paper in 1972 links mra cluster to peptidoglycan
biosynthesis in E. coli. Seems to be common in
proteobacteria.wn.
Length = 305
Score = 296 bits (759), Expect = 7e-81
Identities = 131/301 (43%), Positives = 192/301 (63%), Gaps = 12/301 (3%)
Query: 20 HVPVLLEKVIALLNPAPGKVILDATFGAGGYSRS-FCKMGS-NVIALDRDPFAVSCGQET 77
H VLL++V+ LN P + +D T G GG+S++ ++G+ +I +DRDP A++ +E
Sbjct: 4 HQSVLLDEVVEGLNIKPDGIYIDCTLGFGGHSKAILEQLGTGRLIGIDRDPQAIAFAKER 63
Query: 78 MRDYKEQFSLFQATFSQLQDYVPDKGV---DGVVFDLGVSSMQIDCGDRGFSFQKSGPLD 134
+ D++ + L F+ +++ + V DG++ DLGVSS Q+D +RGFSF+ GPLD
Sbjct: 64 LSDFEGRVVLIHDNFANFFEHLDELLVTKIDGILVDLGVSSPQLDDPERGFSFKHDGPLD 123
Query: 135 MRM-SCSGISASDVVNQANVKDLTRILGILGEEKQASRIAHAIVKRRQSAPFQTTQDLSS 193
MRM +SA++++N + +DL RIL GEEK + RIA AIV+RR+ P QTT++L+
Sbjct: 124 MRMDQSQKLSAAEILNTYSEEDLERILKKYGEEKFSKRIARAIVERRKKKPIQTTKELAE 183
Query: 194 LIQKTVY-FSKNNRIHPATRSFQALRIFVNNEIEELAQGLRSAEKALKAGGLLIVVSFHS 252
LI K V FSK+ IHPATR FQA+RI+VN+E+EEL + L+ A L GG L ++SFHS
Sbjct: 184 LISKAVPGFSKHKSIHPATRVFQAIRIYVNDELEELEEALQFAPNLLAPGGRLSIISFHS 243
Query: 253 LEDRLVKKFFASRS-GKVMAVRHMIPSNAHPAVFQSITKKVVVPTQEDVAFNRRSRSAKL 311
LEDR+VK FF S + + + ITKK + P++E++ N RSRSAKL
Sbjct: 244 LEDRIVKNFFRELSKFPQPPGLPVKETPLYAL----ITKKPITPSEEEIKENPRSRSAKL 299
Query: 312 R 312
R
Sbjct: 300 R 300
>gnl|CDD|150199 pfam09445, Methyltransf_15, RNA cap guanine-N2 methyltransferase.
RNA cap guanine-N2 methyltransferases such as
Schizosaccharomyces pombe Tgs1 and Giardia lamblia Tgs2
catalyse methylation of the exocyclic N2 amine of
7-methylguanosine.
Length = 165
Score = 33.0 bits (76), Expect = 0.11
Identities = 15/45 (33%), Positives = 24/45 (53%)
Query: 37 GKVILDATFGAGGYSRSFCKMGSNVIALDRDPFAVSCGQETMRDY 81
++ILD GAGG + F + +VI +D +P ++C Q Y
Sbjct: 1 ARIILDVFCGAGGNTIQFANVFCSVIGIDINPEHLACAQHNAEVY 45
>gnl|CDD|184894 PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional.
Length = 434
Score = 31.8 bits (73), Expect = 0.28
Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 28 VIALLNPAPGKVILDATFGAGGYSRSFCK-MG--SNVIALDRDP 68
V LL+P PG+VILDA GG + + MG + A+DR
Sbjct: 244 VAPLLDPQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSA 287
>gnl|CDD|184897 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
Length = 445
Score = 31.6 bits (72), Expect = 0.30
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 31 LLNPAPGKVILDATFGAGGYSRSFCK--MGS--NVIALDRDP 68
LLNP PG +LD GG S +F M + + A+DR P
Sbjct: 245 LLNPQPGSTVLDLCAAPGGKS-TFMAELMQNRGQITAVDRYP 285
>gnl|CDD|184932 PRK14968, PRK14968, putative methyltransferase; Provisional.
Length = 188
Score = 31.4 bits (72), Expect = 0.34
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 5/76 (6%)
Query: 36 PGKVILDATFGAGGYSRSFCKMGSNVIALDRDPFAVSCGQETMRDYKEQFSLFQATFSQL 95
G +L+ G+G + K G V+ +D +P+AV C + + + + + S L
Sbjct: 23 KGDRVLEVGTGSGIVAIVAAKNGKKVVGVDINPYAVECAKCNAKLNNIRNNGVEVIRSDL 82
Query: 96 QDYVPDKGVDGVVFDL 111
+ G FD+
Sbjct: 83 FE-----PFRGDKFDV 93
>gnl|CDD|115607 pfam06962, rRNA_methylase, Putative rRNA methylase. This family
contains a number of putative rRNA methylases. Note that
many family members are hypothetical proteins.
Length = 140
Score = 31.1 bits (71), Expect = 0.41
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 82 KEQFSLFQATFSQLQDYVPDKGVDGVVFDLG 112
E L + + +Y+P+ V +F+LG
Sbjct: 25 SEIVELILDSHENIDEYIPEGPVKAAIFNLG 55
>gnl|CDD|179944 PRK05134, PRK05134, bifunctional 3-demethylubiquinone-9
3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol
methylase; Provisional.
Length = 233
Score = 30.1 bits (69), Expect = 0.76
Identities = 13/44 (29%), Positives = 21/44 (47%)
Query: 22 PVLLEKVIALLNPAPGKVILDATFGAGGYSRSFCKMGSNVIALD 65
P+ L + GK +LD G G S S ++G++V +D
Sbjct: 34 PLRLNYIREHAGGLFGKRVLDVGCGGGILSESMARLGADVTGID 77
>gnl|CDD|150622 pfam09968, DUF2202, Uncharacterized protein domain (DUF2202). This
domain, found in various hypothetical archaeal proteins,
has no known function.
Length = 162
Score = 30.0 bits (68), Expect = 0.94
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 219 IFVNNEIEEL-----AQGLRSAEKALKAGGLLIVVSFHSLEDRL 257
+F N +++EL +G +S E ALK G + + + LE+ +
Sbjct: 65 VFTNPDLQELYNQLVEKGSKSLEDALKVGATIEDLDIYDLEEAI 108
>gnl|CDD|162239 TIGR01177, TIGR01177, conserved hypothetical protein TIGR01177.
This family is found exclusively in the Archaea.
Length = 329
Score = 29.3 bits (66), Expect = 1.3
Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 6/85 (7%)
Query: 30 ALLNPA---PGKVILDATFGAGGYSRSFCKMGSNVIALDRDPFAVSCGQETMRDYK-EQF 85
A++N A G +LD G GG+ MG+ VI D D V+ + + Y E F
Sbjct: 173 AMVNLARVTEGDRVLDPFCGTGGFLIEAGLMGAKVIGCDIDWKMVAGARINLEHYGIEDF 232
Query: 86 SLFQATFSQLQDYVPDKGVDGVVFD 110
+ + ++L + + VD + D
Sbjct: 233 FVKRGDATKLP--LSSESVDAIATD 255
>gnl|CDD|161931 TIGR00563, rsmB, ribosomal RNA small subunit methyltransferase
RsmB. The seed alignment is built from bacterial
sequences only. Eukaryotic homologs include Nop2, a
protein required for processing pre-rRNA, that is likely
also a rRNA methyltransferase, although the fine
specificity may differ. Cutoff scores are set to avoid
treating archaeal and eukaroytic homologs automatically
as functionally equivalent, although they may have very
similar roles.
Length = 426
Score = 28.7 bits (64), Expect = 2.2
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 2/42 (4%)
Query: 28 VIALLNPAPGKVILDATFGAGGYSRSFCKMG--SNVIALDRD 67
V L P + ILDA GG + ++ + V+ALD
Sbjct: 230 VATWLAPQNEETILDACAAPGGKTTHILELAPQAQVVALDIH 271
>gnl|CDD|177641 PHA03413, PHA03413, putative internal core protein; Provisional.
Length = 1304
Score = 28.5 bits (63), Expect = 2.7
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 5/65 (7%)
Query: 180 RQSAPFQTTQDLSSLIQKTVYFSKNNRIHPATRSFQALRIFVNNEIEELAQGLRSAEKAL 239
Q+A F TTQ+L + FS +R+ + + +E+E + +G A KAL
Sbjct: 1046 NQAAAFNTTQNLGQAARHANGFSMVHRLMANLNAG-----IIADELENMFKGDAEAFKAL 1100
Query: 240 KAGGL 244
+ GL
Sbjct: 1101 EEFGL 1105
>gnl|CDD|162871 TIGR02469, CbiT, precorrin-6Y C5,15-methyltransferase
(decarboxylating), CbiT subunit. This model recognizes
the CbiT methylase which is responsible, in part (along
with CbiE), for methylating precorrin-6y (or
cobalt-precorrin-6y) at both the 5 and 15 positions as
well as the concomitant decarbozylation at C-12. In
many organisms, this protein is fused to the CbiE
subunit. The fused protein, when found in organisms
catalyzing the oxidative version of the cobalamin
biosynthesis pathway, is called CobL.
Length = 124
Score = 28.5 bits (64), Expect = 3.0
Identities = 14/56 (25%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 28 VIALLNPAPGKVILDATFGAGGYSRSFCKMGSN--VIALDRDPFAVSCGQETMRDY 81
++ L PG V+ D G+G + ++ N V A++R+P A+ + R +
Sbjct: 11 TLSKLRLRPGDVLWDIGAGSGSITIEAARLVPNGRVYAIERNPEALRLIERNARRF 66
>gnl|CDD|129628 TIGR00537, hemK_rel_arch, HemK-related putative methylase. The
gene hemK from E. coli was found to contribute to heme
biosynthesis and originally suggested to be
protoporphyrinogen oxidase (Medline 95189105).
Functional analysis of the nearest homolog in
Saccharomyces cerevisiae, YNL063w, finds it is not
protoporphyrinogen oxidase and sequence analysis
suggests that HemK homologs have
S-adenosyl-methionine-dependent methyltransferase
activity (Medline 99237242). Homologs are found,
usually in a single copy, in nearly all completed
genomes, but varying somewhat in apparent domain
architecture. This model represents an archaeal and
eukaryotic protein family that lacks an N-terminal
domain found in HemK and its eubacterial homologs. It
is found in a single copy in the first six completed
archaeal and eukaryotic genomes.
Length = 179
Score = 28.3 bits (63), Expect = 3.0
Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 3/67 (4%)
Query: 23 VLLEKVIALLNPAPGKVILDATFGAGGYSRSFCKMGSNVIALDRDPFAVSCGQETMRDYK 82
+LLE + L P +L+ G G + G ++ D +PFAV +E +
Sbjct: 9 LLLEANLRELKP---DDVLEIGAGTGLVAIRLKGKGKCILTTDINPFAVKELRENAKLNN 65
Query: 83 EQFSLFQ 89
+
Sbjct: 66 VGLDVVM 72
>gnl|CDD|182838 PRK10919, PRK10919, ATP-dependent DNA helicase Rep; Provisional.
Length = 672
Score = 28.3 bits (63), Expect = 3.4
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 224 EIEELAQGLRSAEKALKAGGLLIVVSFHSLEDRL 257
++ +L Q RS+ + LKA +LI + H E RL
Sbjct: 269 QVIKLEQNYRSSGRILKAANILIANNPHVFEKRL 302
>gnl|CDD|182489 PRK10477, PRK10477, outer membrane lipoprotein Blc; Provisional.
Length = 177
Score = 27.7 bits (62), Expect = 4.3
Identities = 14/25 (56%), Positives = 17/25 (68%), Gaps = 3/25 (12%)
Query: 58 GSNVIALDRD-PFAVSCGQETMRDY 81
G NVIALDR+ A+ CG + RDY
Sbjct: 115 GYNVIALDREYRHALVCGPD--RDY 137
>gnl|CDD|162663 TIGR02021, BchM-ChlM, magnesium protoporphyrin
O-methyltransferase. This model represents the
S-adenosylmethionine-dependent O-methyltransferase
responsible for methylation of magnesium protoporphyrin
IX. This step is essentiasl for the biosynthesis of
both chlorophyll and bacteriochlorophyll. This model
encompasses two closely related clades, from
cyanobacteria (and plants) where it is called ChlM and
other photosynthetic bacteria where it is known as
BchM.
Length = 219
Score = 27.5 bits (61), Expect = 5.2
Identities = 14/40 (35%), Positives = 18/40 (45%)
Query: 37 GKVILDATFGAGGYSRSFCKMGSNVIALDRDPFAVSCGQE 76
GK +LDA G G S K G+ V A+D V +
Sbjct: 56 GKRVLDAGCGTGLLSIELAKRGAIVKAVDISEQMVQMARN 95
>gnl|CDD|162613 TIGR01934, MenG_MenH_UbiE, ubiquinone/menaquinone biosynthesis
methyltransferases. Note that a number of
non-orthologous genes which are members of pfam03737
have been erroneously annotated as MenG
methyltransferases.
Length = 223
Score = 27.2 bits (61), Expect = 5.5
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 212 RSFQALRI-FVNNEIEELAQGLRSAEKALKAGGLLIVVSFHSLEDRLVKKFFASRSGKVM 270
SF A+ I F + ++ + LR + LK GG L+++ F + L+KKF+ V+
Sbjct: 105 NSFDAVTIAFGLRNVTDIQKALREMYRVLKPGGRLVILEFSKPANALLKKFYKFYLKNVL 164
>gnl|CDD|182822 PRK10901, PRK10901, 16S rRNA methyltransferase B; Provisional.
Length = 427
Score = 27.5 bits (62), Expect = 5.6
Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 14/46 (30%)
Query: 31 LLNPAPGKVILDATFGAGGYSRSFCKMG--------SNVIALDRDP 68
LL P G+ +LDA GG K + V+ALD D
Sbjct: 239 LLAPQNGERVLDACAAPGG------KTAHILELAPQAQVVALDIDA 278
>gnl|CDD|172732 PRK14244, PRK14244, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 251
Score = 27.5 bits (61), Expect = 5.6
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 6/53 (11%)
Query: 86 SLFQATFSQLQDYVPDKGVDG--VVFDLGVSSMQIDC----GDRGFSFQKSGP 132
S F F+++ D+VP+ V G + + V S+ + G FQK P
Sbjct: 45 STFLRCFNRMNDFVPNCKVKGELDIDGIDVYSVDTNVVLLRAKVGMVFQKPNP 97
>gnl|CDD|181470 PRK08562, rpl32e, 50S ribosomal protein L32e; Validated.
Length = 125
Score = 27.2 bits (61), Expect = 7.2
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 4/29 (13%)
Query: 152 NVKDLTRILGILGEEKQASRIAHAIVKRR 180
NVK+L + L E QA+RIA + KR+
Sbjct: 81 NVKELEK----LDPETQAARIASTVGKRK 105
>gnl|CDD|180083 PRK05441, murQ, N-acetylmuramic acid-6-phosphate etherase;
Reviewed.
Length = 299
Score = 27.1 bits (61), Expect = 8.0
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 221 VNNEIEELAQGLRSAEKALKAGGLLI 246
V + ++A + +A AL+ GG LI
Sbjct: 41 VEKALPQIAAAVDAAAAALRQGGRLI 66
>gnl|CDD|128898 smart00650, rADc, Ribosomal RNA adenine dimethylases.
Length = 169
Score = 26.7 bits (60), Expect = 8.2
Identities = 11/45 (24%), Positives = 23/45 (51%)
Query: 24 LLEKVIALLNPAPGKVILDATFGAGGYSRSFCKMGSNVIALDRDP 68
+++K++ N PG +L+ G G + + + V A++ DP
Sbjct: 1 VIDKIVRAANLRPGDTVLEIGPGKGALTEELLERAARVTAIEIDP 45
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.321 0.134 0.377
Gapped
Lambda K H
0.267 0.0681 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,426,009
Number of extensions: 343897
Number of successful extensions: 733
Number of sequences better than 10.0: 1
Number of HSP's gapped: 722
Number of HSP's successfully gapped: 33
Length of query: 341
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 247
Effective length of database: 3,963,321
Effective search space: 978940287
Effective search space used: 978940287
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 (25.8 bits)