RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11730
(496 letters)
>gnl|CDD|202224 pfam02373, JmjC, JmjC domain, hydroxylase. The JmjC domain belongs
to the Cupin superfamily. JmjC-domain proteins may be
protein hydroxylases that catalyze a novel histone
modification. This is confirmed to be a hydroxylase: the
human JmjC protein named Tyw5p unexpectedly acts in the
biosynthesis of a hypermodified nucleoside,
hydroxy-wybutosine, in tRNA-Phe by catalyzing
hydroxylation.
Length = 114
Score = 80.0 bits (198), Expect = 3e-18
Identities = 34/124 (27%), Positives = 47/124 (37%), Gaps = 12/124 (9%)
Query: 344 KFYHGDWGSLSAVIHSKFDIILTSETIYSVANYNKL--LTVWCLFPTHTPKDLLKVTSAE 401
Y G GS + + +YS NY VW + P+ + KV S
Sbjct: 1 WLYMGMPGS-------TTPWHIEDQGLYS-INYLHFGGPKVWYIIPSEYAEKFEKVLSKH 52
Query: 402 GGKQRDEAITWFSIIYPRTQLPSWPTEWKPLELVQGPGETVFVPGGWWHVVLNLDTTVAV 461
G ++ + + + I QL VQ PGE VF GW+H V NL +A
Sbjct: 53 NGGEQPDLLLHLNTIISPKQL--LENGIPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAE 110
Query: 462 TQNF 465
NF
Sbjct: 111 AVNF 114
>gnl|CDD|222415 pfam13847, Methyltransf_31, Methyltransferase domain. This family
appears to be have methyltransferase activity.
Length = 151
Score = 51.3 bits (123), Expect = 9e-08
Identities = 25/96 (26%), Positives = 43/96 (44%), Gaps = 7/96 (7%)
Query: 289 DKLSVLDVGCGAGLLG--LYTLMNGAAHVSFQDYNQEVIESLTLPNILMNTDNLEKCKFY 346
+ VLD+GCG G L L + A V D ++E IE E +F
Sbjct: 3 SGIKVLDLGCGTGYLTFILAEKLGPGAEVVGIDISEEAIEKA---KENAKKLGYENVEFI 59
Query: 347 HGDWGSL--SAVIHSKFDIILTSETIYSVANYNKLL 380
GD L + + FD+++++E + + + +K+L
Sbjct: 60 QGDIEELPQLQLEDNSFDVVISNEVLNHLPDPDKVL 95
>gnl|CDD|222269 pfam13621, Cupin_8, Cupin-like domain. This cupin like domain
shares similarity to the JmjC domain.
Length = 247
Score = 48.1 bits (115), Expect = 3e-06
Identities = 38/155 (24%), Positives = 53/155 (34%), Gaps = 37/155 (23%)
Query: 65 PQEFIEKYEKPNKPVVIKGVTENWNATYKWT--LEKLGKKYRNQKFKCGE---------- 112
P+EF +Y KPVV+KG ++W A KWT L+ L +KY + +
Sbjct: 1 PEEFFREYVAKRKPVVLKGAAKDWPAVKKWTDALDYLKEKYGDVEVSVEVTPPGRADRFF 60
Query: 113 DNHGYSKLGKKYRNQKFKCGEDNHGYSHPRRKKLLDDYEVPIYFQ----DDLFQYAGEDK 168
N S + K FK D R + +Y Q D F ED
Sbjct: 61 YNDDLSGVNFKEERMPFK---DFLDLL---RAGSDQETPPYLYLQSSNLDSEFPGLREDN 114
Query: 169 RPPYR-------------WFVMGPARSGTGIHIDP 190
P W +G + T +H D
Sbjct: 115 DLPLAPEAFGKLPQAVNLW--IGNGGTTTSLHYDA 147
Score = 33.5 bits (77), Expect = 0.19
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 430 KPLELVQGPGETVFVPGGWWHVVLNLD-TTVAVTQNF 465
K L PG+ +++P GWWH V +LD +AV F
Sbjct: 205 KALVAELEPGDALYIPAGWWHHVRSLDDFNIAVNYWF 241
>gnl|CDD|203189 pfam05175, MTS, Methyltransferase small domain. This domain is
found in ribosomal RNA small subunit methyltransferase C
as well as other methyltransferases .
Length = 170
Score = 46.8 bits (112), Expect = 4e-06
Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 292 SVLDVGCGAGLLGLYTL-MNGAAHVSFQDYNQEVIESLTLPNILMNTDNLEKCKFYHGDW 350
VLD+GCG G+LG + V+ D N +ES N+ N LE + + D
Sbjct: 34 KVLDLGCGYGVLGAALAKRSPDLEVTMVDINARALESARA-NLAAN--GLENGEVFWSD- 89
Query: 351 GSLSAVIHSKFDIILT 366
SAV KFD+I++
Sbjct: 90 -LYSAVEPGKFDLIIS 104
>gnl|CDD|234248 TIGR03534, RF_mod_PrmC, protein-(glutamine-N5) methyltransferase,
release factor-specific. Members of this protein family
are HemK (PrmC), a protein once thought to be involved
in heme biosynthesis but now recognized to be a
protein-glutamine methyltransferase that modifies the
peptide chain release factors. All members of the seed
alignment are encoded next to the release factor 1 gene
(prfA) and confirmed by phylogenetic analysis. SIMBAL
analysis (manuscript in prep.) shows the motif
[LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers
specificity for the release factors rather than for
ribosomal protein L3 [Protein fate, Protein modification
and repair].
Length = 251
Score = 47.5 bits (114), Expect = 5e-06
Identities = 24/90 (26%), Positives = 38/90 (42%), Gaps = 12/90 (13%)
Query: 279 LNFIKDNVAVDKLSVLDVGCGAGLLGLYTL--MNGAAHVSFQDYNQEVIESLTLPNILMN 336
L +K L VLD+G G+G + L L A V+ D + E + + N
Sbjct: 81 LERLKKG----PLRVLDLGTGSGAIAL-ALAKERPDARVTAVDISPEALA-VARKNAARL 134
Query: 337 TDNLEKCKFYHGDWGSLSAVIHSKFDIILT 366
L+ +F DW + KFD+I++
Sbjct: 135 --GLDNVEFLQSDW--FEPLPGGKFDLIVS 160
>gnl|CDD|237872 PRK14968, PRK14968, putative methyltransferase; Provisional.
Length = 188
Score = 46.4 bits (111), Expect = 7e-06
Identities = 28/106 (26%), Positives = 38/106 (35%), Gaps = 11/106 (10%)
Query: 260 LKPNVYEGGYKIWECTFDLLNFIKDNVAVDKLSVLDVGCGAGLLGLYTLMNGAAHVSFQD 319
L VYE E +F L D VL+VG G+G++ + NG V D
Sbjct: 1 LNDEVYEPA----EDSFLLAENAVD---KKGDRVLEVGTGSGIVAIVAAKNG-KKVVGVD 52
Query: 320 YNQEVIESLTLPNILMNTDNLEKCKFYHGDWGSLSAVIHSKFDIIL 365
N +E N +N + D KFD+IL
Sbjct: 53 INPYAVE-CAKCNAKLNNIRNNGVEVIRSD--LFEPFRGDKFDVIL 95
>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 = 44.3 bits (105), Expect = 8e-06
Identities = 19/73 (26%), Positives = 27/73 (36%), Gaps = 3/73 (4%)
Query: 293 VLDVGCGAGLLGLYTLMNGAAHVSFQDYNQEVIESLTLPNILMNTDNLEKCKFYHGDWGS 352
VLD+GCG G L L A V+ D + +E + + GD
Sbjct: 2 VLDLGCGTGALALALASGPGARVTGVDISPVALELARKAAAA---LLADNVEVLKGDAEE 58
Query: 353 LSAVIHSKFDIIL 365
L FD+I+
Sbjct: 59 LPPEADESFDVII 71
>gnl|CDD|214721 smart00558, JmjC, A domain family that is part of the cupin
metalloenzyme superfamily. Probable enzymes, but of
unknown functions, that regulate chromatin
reorganisation processes (Clissold and Ponting, in
press).
Length = 58
Score = 38.8 bits (91), Expect = 2e-04
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 4/51 (7%)
Query: 145 KLLDDYEVPIYFQDDLFQYAGEDKRPP--YRWFVMGPARSGTGIHIDPLGT 193
+L + ++P F+ +L ED P + MG A S T HID
Sbjct: 1 QLWNLAKLP--FKLNLLSDLPEDIPGPDVGPYLYMGMAGSTTPWHIDDYDL 49
>gnl|CDD|225443 COG2890, HemK, Methylase of polypeptide chain release factors
[Translation, ribosomal structure and biogenesis].
Length = 280
Score = 41.6 bits (98), Expect = 6e-04
Identities = 21/109 (19%), Positives = 37/109 (33%), Gaps = 11/109 (10%)
Query: 259 DLKPNVYEGGYKIWECTFDLLNFIKDNVAVDKLSVLDVGCGAGLLGLYTLMNG-AAHVSF 317
+ V T L+ + +LD+G G+G + + G A V
Sbjct: 84 KVDEGVLIPR----PDTELLVEAALALLLQLDKRILDLGTGSGAIAIALAKEGPDAEVIA 139
Query: 318 QDYNQEVIESLTLPNILMNTDNLEKCKFYHGDWGSLSAVIHSKFDIILT 366
D + + + L N N L + D + KFD+I++
Sbjct: 140 VDISPDALA-LARENAERN--GLVRVLVVQSDLFE---PLRGKFDLIVS 182
>gnl|CDD|235350 PRK05134, PRK05134, bifunctional 3-demethylubiquinone-9
3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol
methylase; Provisional.
Length = 233
Score = 40.5 bits (96), Expect = 0.001
Identities = 12/26 (46%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 279 LNFIKDNVA-VDKLSVLDVGCGAGLL 303
LN+I+++ + VLDVGCG G+L
Sbjct: 37 LNYIREHAGGLFGKRVLDVGCGGGIL 62
>gnl|CDD|219759 pfam08241, Methyltransf_11, Methyltransferase domain. Members of
this family are SAM dependent methyltransferases.
Length = 92
Score = 37.6 bits (88), Expect = 0.001
Identities = 24/87 (27%), Positives = 37/87 (42%), Gaps = 10/87 (11%)
Query: 294 LDVGCGAGLLGLYTLMNGAAHVSFQDYNQEVIESLTLPNILMNTDNLEKCKFYHGDWGSL 353
LDVGCG GLL G A V+ D + E++ KF GD L
Sbjct: 1 LDVGCGTGLLAEALARRGGARVTGVDLSPEMLALAR---------KRAPRKFVVGDAEDL 51
Query: 354 SAVIHSKFDIILTSETIYSVANYNKLL 380
S FD++++S ++ + + + L
Sbjct: 52 PFPDES-FDVVVSSLVLHHLPDPERAL 77
>gnl|CDD|225370 COG2813, RsmC, 16S RNA G1207 methylase RsmC [Translation, ribosomal
structure and biogenesis].
Length = 300
Score = 39.6 bits (93), Expect = 0.003
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 292 SVLDVGCGAGLLGLYTL-MNGAAHVSFQDYNQEVIESLTLPNILMNTDNLEKCKFYHGDW 350
VLD+GCG G+LGL + A ++ D N +ES N+ N +E + + +
Sbjct: 161 KVLDLGCGYGVLGLVLAKKSPQAKLTLVDVNARAVESARK-NLAAN--GVENTEVWASN- 216
Query: 351 GSLSAVIHSKFDIILT 366
L + KFD+I++
Sbjct: 217 --LYEPVEGKFDLIIS 230
>gnl|CDD|233668 TIGR01983, UbiG, ubiquinone biosynthesis O-methyltransferase. This
model represents an O-methyltransferase believed to act
at two points in the ubiquinone biosynthetic pathway in
bacteria (UbiG) and fungi (COQ3). A separate methylase
(MenG/UbiE) catalyzes the single C-methylation step. The
most commonly used names for genes in this family do not
indicate whether this gene is an O-methyl, or C-methyl
transferase [Biosynthesis of cofactors, prosthetic
groups, and carriers, Menaquinone and ubiquinone].
Length = 224
Score = 38.8 bits (91), Expect = 0.004
Identities = 30/102 (29%), Positives = 45/102 (44%), Gaps = 9/102 (8%)
Query: 279 LNFIKDNVA-----VDKLSVLDVGCGAGLLGLYTLMNGAAHVSFQDYNQEVIESLTLPNI 333
L++I+D + + L VLDVGCG GLL GA V+ D ++E IE L
Sbjct: 30 LDYIRDTIRKNKKPLFGLRVLDVGCGGGLLSEPLARLGAN-VTGIDASEENIEVAKLH-- 86
Query: 334 LMNTDNLEKCKFYHGDWGSLSAVIHSKFDIILTSETIYSVAN 375
D L K ++ L+ FD++ E + V +
Sbjct: 87 -AKKDPLLKIEYRCTSVEDLAEKGAKSFDVVTCMEVLEHVPD 127
>gnl|CDD|221804 pfam12847, Methyltransf_18, Methyltransferase domain. Protein in
this family function as methyltransferases.
Length = 104
Score = 36.5 bits (85), Expect = 0.004
Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 7/84 (8%)
Query: 292 SVLDVGCGAGLLGLYT--LMNGAAHVSFQDYNQEVIESLTLPNILMNTDNLEKCKFYHGD 349
VLD+GCG G L + L GA D + E++E N + + F GD
Sbjct: 4 RVLDIGCGTGSLAIELARLFPGARVTGV-DLSPEMLELARE-NAKLA--LGPRITFVQGD 59
Query: 350 WGSLSAVIHSKFDIILTSETIYSV 373
++ FD + +
Sbjct: 60 APDALDLLE-GFDAVFIGGGGGDL 82
>gnl|CDD|222287 pfam13649, Methyltransf_25, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 97
Score = 36.2 bits (84), Expect = 0.005
Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 5/75 (6%)
Query: 293 VLDVGCGAGLLGLYTLMNGAAHVSFQDYNQEVIESLTLPNILMNTDNLEKCKFYHGDWGS 352
+LD+GCG G + G + V+ D ++E +E + K +F D
Sbjct: 1 ILDLGCGTGRVLRALARAGPSSVTGVDISKEALELA---KERLRDKGP-KVRFVVADARD 56
Query: 353 LSAVIHSKFDIILTS 367
L FD+++ +
Sbjct: 57 LP-FEEGSFDLVICA 70
>gnl|CDD|236467 PRK09328, PRK09328, N5-glutamine S-adenosyl-L-methionine-dependent
methyltransferase; Provisional.
Length = 275
Score = 37.4 bits (88), Expect = 0.010
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 8/80 (10%)
Query: 287 AVDKLSVLDVGCGAGLLGLYTLM--NGAAHVSFQDYNQEVIESLTLPNILMNTDNLEKCK 344
+ L VLD+G G+G + L L A V+ D + E + + N + +
Sbjct: 106 LKEPLRVLDLGTGSGAIAL-ALAKERPDAEVTAVDISPEALA-VARRNAKHG--LGARVE 161
Query: 345 FYHGDWGSLSAVIHSKFDII 364
F GDW + +FD+I
Sbjct: 162 FLQGDW--FEPLPGGRFDLI 179
>gnl|CDD|236059 PRK07580, PRK07580, Mg-protoporphyrin IX methyl transferase;
Validated.
Length = 230
Score = 37.1 bits (87), Expect = 0.012
Identities = 42/173 (24%), Positives = 65/173 (37%), Gaps = 43/173 (24%)
Query: 277 DLLNFIKDNVAVDKLSVLDVGCGAGLLGLYTLMNGAAHVSFQDYNQEVIESLT---LPNI 333
+L+++ + + L +LD GCG G L + G A V D + +++E P
Sbjct: 51 TVLSWLPADGDLTGLRILDAGCGVGSLSIPLARRG-AKVVASDISPQMVE-EARERAPEA 108
Query: 334 LMNTDNLEKCKFYHGD----WGSLSAV------IH---SKFDII------LTSET-IYSV 373
+ N+ F GD G V IH + LT + I++
Sbjct: 109 GLA-GNIT---FEVGDLESLLGRFDTVVCLDVLIHYPQEDAARMLAHLASLTRGSLIFTF 164
Query: 374 ANYNKLLTV--WC--LFP---------THTPKDLLKVTSAEGGK-QRDEAITW 412
A Y LL + W LFP H K + + +A G K R E I+
Sbjct: 165 APYTPLLALLHWIGGLFPGPSRTTRIYPHREKGIRRALAAAGFKVVRTERISS 217
>gnl|CDD|225173 COG2264, PrmA, Ribosomal protein L11 methylase [Translation,
ribosomal structure and biogenesis].
Length = 300
Score = 36.5 bits (85), Expect = 0.022
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 14/85 (16%)
Query: 292 SVLDVGCGAGLLGLYTLMNGAAHVSFQDYNQEVIESLTLPNILMN-TDNLEKCKFYHGDW 350
+VLDVGCG+G+L + GA V D + + +E+ N +N + L + K +
Sbjct: 165 TVLDVGCGSGILAIAAAKLGAKKVVGVDIDPQAVEA-ARENARLNGVELLVQAKGFLLL- 222
Query: 351 GSLSAVIHSKFDIILTSETIYSVAN 375
+ FD+I VAN
Sbjct: 223 ---EVPENGPFDVI--------VAN 236
>gnl|CDD|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 117
Score = 33.9 bits (78), Expect = 0.043
Identities = 18/75 (24%), Positives = 26/75 (34%), Gaps = 3/75 (4%)
Query: 293 VLDVGCGAGLLGLYTLMNGA-AHVSFQDYNQEVIESLTLPNILMNTDNLEKCKFYHGDWG 351
VLD G G+G L G A V + + E L + + GD
Sbjct: 4 VLDPGAGSGAFLLAAARAGPDARVVGVELDPEAAALARR--RLALAGLAPRVRVVVGDAR 61
Query: 352 SLSAVIHSKFDIILT 366
L + FD++L
Sbjct: 62 ELLELPDGSFDLVLG 76
>gnl|CDD|233687 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
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Chlorophyll and bacteriochlorphyll].
Length = 219
Score = 34.4 bits (79), Expect = 0.076
Identities = 30/119 (25%), Positives = 47/119 (39%), Gaps = 13/119 (10%)
Query: 264 VYEGGYKIWECTFDLLNFIKDNVAVDKLSVLDVGCGAGLLGLYTLMNGAAHVSFQDYNQE 323
V EG + D L + VLD GCG GLL + L A V D +++
Sbjct: 34 VREGRAAMRRKLLDWLP----KDPLKGKRVLDAGCGTGLLSI-ELAKRGAIVKAVDISEQ 88
Query: 324 VIESLTLPNILMNTDNLEKCKFYHGDWGSLSAVIHSKFDIILTSETI--YSVANYNKLL 380
+++ N D +F D SL +FDI++ + + Y ++ K L
Sbjct: 89 MVQMAR--NRAQGRDVAGNVEFEVNDLLSLCG----EFDIVVCMDVLIHYPASDMAKAL 141
>gnl|CDD|132519 TIGR03479, DMSO_red_II_alp, DMSO reductase family type II enzyme,
molybdopterin subunit. This model represents the
molybdopterin subunit, typically called the alpha
subunit, of various proteins that also contain an
iron-sulfur subunit and a heme b subunit. The group
includes two distinct but very closely related
periplasmic proteins of anaerobic respiration, selenate
reductase and chlorate reductase. Other members of this
family include dimethyl sulphide dehydrogenase,
ethylbenzene dehydrogenase, and an archaeal respiratory
nitrate reductase. This alpha subunit has a
twin-arginine translocation (TAT) signal for
Sec-independent translocation across the plasma
membrane.
Length = 912
Score = 34.8 bits (80), Expect = 0.12
Identities = 17/66 (25%), Positives = 23/66 (34%), Gaps = 9/66 (13%)
Query: 403 GKQRDEAITWFSIIYPRTQLPSW-------PTEWKPLELVQGPGETVFVPGGWWHVVLNL 455
G Q I + + Q +W KPL LV G G F P W ++
Sbjct: 848 GLQPGTCIMYHG--WEAHQYKNWKPYNSLLAGLIKPLHLVGGYGHLRFYPNYWNPAGVDR 905
Query: 456 DTTVAV 461
+ V V
Sbjct: 906 EVRVDV 911
>gnl|CDD|232960 TIGR00406, prmA, ribosomal protein L11 methyltransferase.
Ribosomal protein L11 methyltransferase is an
S-adenosyl-L-methionine-dependent methyltransferase
required for the modification of ribosomal protein L11.
This protein is found in bacteria and (with a probable
transit peptide) in Arabidopsis [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 288
Score = 34.0 bits (78), Expect = 0.14
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 292 SVLDVGCGAGLLGLYTLMNGAAHVSFQDYNQEVIES 327
+V+DVGCG+G+L + L GAA V D + +ES
Sbjct: 162 NVIDVGCGSGILSIAALKLGAAKVVGIDIDPLAVES 197
>gnl|CDD|239177 cd02776, MopB_CT_Nitrate-R-NarG-like, Respiratory nitrate reductase
A (NarGHI), alpha chain (NarG) and related proteins.
Under anaerobic conditions in the presence of nitrate,
E. coli synthesizes the cytoplasmic membrane-bound
quinol-nitrate oxidoreductase (NarGHI), which reduces
nitrate to nitrite and forms part of a redox loop
generating a proton-motive force. Found in prokaryotes
and some archaea, NarGHI usually functions as a
heterotrimer. The alpha chain contains the molybdenum
cofactor-containing Mo-bisMGD catalytic subunit. This CD
(MopB_CT_Nitrate-R-NarG-like) is of the conserved
molybdopterin_binding C-terminal (MopB_CT) region
present in many, but not all, MopB homologs.
Length = 141
Score = 32.7 bits (75), Expect = 0.18
Identities = 14/70 (20%), Positives = 23/70 (32%), Gaps = 13/70 (18%)
Query: 405 QRDEAITWFS----IIYPRTQLPSW---------PTEWKPLELVQGPGETVFVPGGWWHV 451
R + + + P ++L KP LV G G+ + +
Sbjct: 71 PRGTVFMYHAQERHVNVPGSKLTGKRGGIHNSVTRVRIKPTHLVGGYGQLSYGFNYYGPT 130
Query: 452 VLNLDTTVAV 461
+N DT V V
Sbjct: 131 GVNRDTRVVV 140
>gnl|CDD|222171 pfam13489, Methyltransf_23, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 154
Score = 32.5 bits (74), Expect = 0.23
Identities = 20/105 (19%), Positives = 36/105 (34%), Gaps = 20/105 (19%)
Query: 277 DLLNFIKDNVAVDKLSVLDVGCGAGLLGLYTLMNGAAHVSFQDYNQEVIESLTLPNILMN 336
LL + + VLD+GCG G+L + + ++ ++
Sbjct: 11 RLLARLLPRLKPGG-RVLDIGCGTGIL--------LRLLRERGFDVTGVD-------PSP 54
Query: 337 TDNLEKCKFYHGDWGSLSAVIHSKFDIILTSETIYSVANYNKLLT 381
L F D L+ K+D+I E + + + LL
Sbjct: 55 AAVLIFSLFDAPDPAVLAG----KYDLITAFEVLEHLPDPPALLQ 95
>gnl|CDD|218990 pfam06325, PrmA, Ribosomal protein L11 methyltransferase (PrmA).
This family consists of several Ribosomal protein L11
methyltransferase (EC:2.1.1.-) sequences.
Length = 294
Score = 33.4 bits (77), Expect = 0.23
Identities = 25/86 (29%), Positives = 37/86 (43%), Gaps = 19/86 (22%)
Query: 292 SVLDVGCGAGLLGLYTLMNGAAHVSFQDYNQEVIESLTLPNILMN--TDNLEKCKFYHGD 349
+VLDVGCG+G+L + L GA V D + + + N +N LE + GD
Sbjct: 163 TVLDVGCGSGILAIAALKLGAKKVVGVDIDPVAVRA-AKENAELNGVEAQLE--VYLPGD 219
Query: 350 WGSLSAVIHSKFDIILTSETIYSVAN 375
+ K D++ VAN
Sbjct: 220 ------LPEGKADVV--------VAN 231
>gnl|CDD|224017 COG1092, COG1092, Predicted SAM-dependent methyltransferases
[General function prediction only].
Length = 393
Score = 33.1 bits (76), Expect = 0.34
Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 292 SVLDVGCGAGLLGLYTLMNGAAHVSFQDYNQEVIESLTLPNILMNTDNLEKCKFYHGD-W 350
VL++ G ++ + GA+ V+ D ++ +E N +N + ++ +F GD +
Sbjct: 220 RVLNLFSYTGGFSVHAALGGASEVTSVDLSKRALE-WARENAELNGLDGDRHRFIVGDVF 278
Query: 351 GSLSAVI--HSKFDIIL 365
L KFD+I+
Sbjct: 279 KWLRKAERRGEKFDLII 295
>gnl|CDD|184963 PRK15001, PRK15001, SAM-dependent 23S ribosomal RNA mG1835
methyltransferase; Provisional.
Length = 378
Score = 32.7 bits (74), Expect = 0.41
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 293 VLDVGCGAGLLGLYTL-MNGAAHVSFQDYNQEVIESLTLPNILMNT-DNLEKCKFYHGDW 350
++D+GCG G++GL L N A V F D + + S L N+ N + L++C+F +
Sbjct: 232 IVDLGCGNGVIGLTLLDKNPQAKVVFVDESPMAVASSRL-NVETNMPEALDRCEFMINN- 289
Query: 351 GSLSAVIHSKFDIIL 365
+LS V +F+ +L
Sbjct: 290 -ALSGVEPFRFNAVL 303
>gnl|CDD|181902 PRK09489, rsmC, 16S ribosomal RNA m2G1207 methyltransferase;
Provisional.
Length = 342
Score = 32.6 bits (75), Expect = 0.43
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 278 LLNFIKDNVAVDKLSVLDVGCGAGLLGLY 306
LL+ + + K VLDVGCGAG+L
Sbjct: 188 LLSTLTPHT---KGKVLDVGCGAGVLSAV 213
>gnl|CDD|223813 COG0742, COG0742, N6-adenine-specific methylase [DNA replication,
recombination, and repair].
Length = 187
Score = 31.4 bits (72), Expect = 0.63
Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 10/78 (12%)
Query: 293 VLDVGCGAGLLGLYTLMNGAAHVSFQDYNQEVIESLTLPNILMNTDNL---EKCKFYHGD 349
VLD+ G+G LGL L GAA V F + +++ ++ + N L + + D
Sbjct: 47 VLDLFAGSGALGLEALSRGAARVVFVEKDRKAVKI-----LKENLKALGLEGEARVLRND 101
Query: 350 --WGSLSAVIHSKFDIIL 365
FD++
Sbjct: 102 ALRALKQLGTREPFDLVF 119
>gnl|CDD|234786 PRK00517, prmA, ribosomal protein L11 methyltransferase; Reviewed.
Length = 250
Score = 31.7 bits (73), Expect = 0.65
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 292 SVLDVGCGAGLLGLYTLMNGAAHV 315
+VLDVGCG+G+L + GA V
Sbjct: 122 TVLDVGCGSGILAIAAAKLGAKKV 145
>gnl|CDD|233708 TIGR02072, BioC, biotin biosynthesis protein BioC. This enzyme,
which is found in biotin biosynthetic gene clusters in
proteobacteria, firmicutes, green-sulfur bacteria,
fusobacterium and bacteroides, is believed to carry out
an enzymatic step prior to the formation of pimeloyl-CoA
(although attribution of this annotation is not
traceable). The enzyme appears related to
methyltransferases by homology [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 240
Score = 31.1 bits (71), Expect = 0.94
Identities = 13/31 (41%), Positives = 16/31 (51%)
Query: 273 ECTFDLLNFIKDNVAVDKLSVLDVGCGAGLL 303
E LL +K+ SVLD+GCG G L
Sbjct: 18 EMAKRLLALLKEKGIFIPASVLDIGCGTGYL 48
>gnl|CDD|219760 pfam08242, Methyltransf_12, Methyltransferase domain. Members of
this family are SAM dependent methyltransferases.
Length = 98
Score = 28.9 bits (65), Expect = 1.7
Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 4/78 (5%)
Query: 294 LDVGCGAGLLGLYTLM-NGAAHVSFQDYNQEVIESLTLPNILMNTDNLEKCKFYHGDWGS 352
LD+GCG G L L + D + +E+ + L D
Sbjct: 1 LDIGCGTGTLLRALLEALPGLEYTGVDISPAALEAAAE---RLAALGLLDAVRVRLDVLD 57
Query: 353 LSAVIHSKFDIILTSETI 370
+ FD+++ S +
Sbjct: 58 AIDLDPGSFDVVVASNVL 75
>gnl|CDD|215319 PLN02585, PLN02585, magnesium protoporphyrin IX methyltransferase.
Length = 315
Score = 30.6 bits (69), Expect = 1.7
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 279 LNFIKDNVAVDKLSVLDVGCGAGLLGLYTLMNGAAHVSFQD 319
L ++ ++ ++ ++V D GCG G L + + GA VS D
Sbjct: 134 LLWLAEDGSLAGVTVCDAGCGTGSLAIPLALEGAI-VSASD 173
>gnl|CDD|225137 COG2227, UbiG,
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol
methylase [Coenzyme metabolism].
Length = 243
Score = 30.4 bits (69), Expect = 1.8
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 290 KLSVLDVGCGAGLL 303
L VLDVGCG G+L
Sbjct: 60 GLRVLDVGCGGGIL 73
>gnl|CDD|188022 TIGR00095, TIGR00095, RNA methyltransferase, RsmD family. This
model represents a family of uncharacterized bacterial
proteins. Members are present in nearly every complete
bacterial genome, always in a single copy. PSI-BLAST
analysis shows homology to several families of
SAM-dependent methyltransferases, including ribosomal
RNA adenine dimethylases [Protein synthesis, tRNA and
rRNA base modification].
Length = 190
Score = 30.1 bits (68), Expect = 2.0
Identities = 14/41 (34%), Positives = 23/41 (56%)
Query: 288 VDKLSVLDVGCGAGLLGLYTLMNGAAHVSFQDYNQEVIESL 328
+ LD+ G+G LGL L GAA F + +++V ++L
Sbjct: 49 IVGAHFLDLFAGSGALGLEALSRGAASAVFVEQDRKVAQTL 89
>gnl|CDD|131920 TIGR02873, spore_ylxY, probable sporulation protein, polysaccharide
deacetylase family. Members of this protein family are
most closely related to TIGR02764, a subset of
polysaccharide deacetylase family proteins found in a
species if and only if the species forms endospores like
those of Bacillus subtilis or Clostridium tetani. This
family is likewise restricted to spore-formers, but is
not universal among them in having sequences with
full-length matches to the model [Energy metabolism,
Biosynthesis and degradation of polysaccharides,
Cellular processes, Sporulation and germination].
Length = 268
Score = 30.2 bits (68), Expect = 2.1
Identities = 34/130 (26%), Positives = 52/130 (40%), Gaps = 12/130 (9%)
Query: 25 RARPELNGKDAWFELGYAD-----KFD-KFKIVKENVERIHVKDYSPQEFIEKYEKPNKP 78
+A P NG+ E Y +FD K + E +H+ D P + P KP
Sbjct: 28 KATPGYNGRQVDVEASYNKMKQEGRFDEKLLVFDEVSPSVHLDDLPPSPIYRGH--PEKP 85
Query: 79 VVIKGVTENWNATYKWTLEKLGKKY--RNQKFKCGEDNHGYSKLGKKYRNQKFKCGEDNH 136
+V + W Y + ++ KK+ + F G+ S+L K Q + G NH
Sbjct: 86 MVALLINVAWGNEYLPEILQILKKHDVKATFFLEGKWVKENSQLAKMIVEQGHEIG--NH 143
Query: 137 GYSHPRRKKL 146
Y+HP L
Sbjct: 144 AYNHPDMATL 153
>gnl|CDD|129627 TIGR00536, hemK_fam, HemK family putative methylases. 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. Both
E. coli and H. influenzae have two members rather than
one. The members from the Mycoplasmas have an additional
C-terminal domain [Protein fate, Protein modification
and repair].
Length = 284
Score = 30.0 bits (68), Expect = 2.3
Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 9/80 (11%)
Query: 290 KLSVLDVGCGAGLLGL---YTLMNGAAHVSFQDYNQEVIESLTLPNILMNTDNLEKCKFY 346
L +LD+G G+G + L Y N A V D + + + + N N + +F
Sbjct: 115 ILHILDLGTGSGCIALALAYEFPN--AEVIAVDISPDALA-VAEENAEKNQLE-HRVEFI 170
Query: 347 HGDWGSLSAVIHSKFDIILT 366
+ + K DII++
Sbjct: 171 QSNL--FEPLAGQKIDIIVS 188
>gnl|CDD|223574 COG0500, SmtA, SAM-dependent methyltransferases [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 257
Score = 29.9 bits (64), Expect = 2.8
Identities = 22/86 (25%), Positives = 34/86 (39%), Gaps = 6/86 (6%)
Query: 289 DKLSVLDVGCGAGLLGLYT-LMNGAAHVSFQDYNQEVIESLTLPNILMNTDNLEKCKFYH 347
L VLD+GCG G L L L A+V D + E++ L F
Sbjct: 48 GGLGVLDIGCGTGRLALLARLGGRGAYVVGVDLSPEMLALARARAEG---AGLGLVDFVV 104
Query: 348 GDW--GSLSAVIHSKFDIILTSETIY 371
D G L + FD++++ ++
Sbjct: 105 ADALGGVLPFEDSASFDLVISLLVLH 130
>gnl|CDD|220679 pfam10294, Methyltransf_16, Putative methyltransferase.
Length = 170
Score = 29.2 bits (66), Expect = 2.9
Identities = 28/97 (28%), Positives = 46/97 (47%), Gaps = 9/97 (9%)
Query: 291 LSVLDVGCGAGLLGL-YTLMNGAAHVSFQDYNQEVIESLTLPNILMNTDNLEKCKFYHGD 349
L+VL++G G GL+G+ L+ A V+ D +E IE + NI +N + K D
Sbjct: 46 LNVLELGSGTGLVGIAVALLLPGASVTITDL-EEAIELMK-KNIELNGLS-SKVTAKVLD 102
Query: 350 WG----SLSAVIHSKFDIILTSETIYSVANYNKLLTV 382
WG H D+IL ++ +Y+ ++ L
Sbjct: 103 WGEDLPDDVFDPHP-VDLILAADCVYNEDSFPLLEKT 138
>gnl|CDD|225139 COG2230, Cfa, Cyclopropane fatty acid synthase and related
methyltransferases [Cell envelope biogenesis, outer
membrane].
Length = 283
Score = 29.9 bits (68), Expect = 3.2
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 10/39 (25%)
Query: 292 SVLDVGCGAGLLGLYTLMNGAAHVSFQDYNQEVIESLTL 330
++LD+GCG G L +Y AA ++Y V+ +TL
Sbjct: 75 TLLDIGCGWGGLAIY-----AA----EEYGVTVV-GVTL 103
>gnl|CDD|235704 PRK06126, PRK06126, hypothetical protein; Provisional.
Length = 545
Score = 30.0 bits (68), Expect = 3.6
Identities = 9/41 (21%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 149 DYEVPIYFQDDLFQYAGEDKRPPYRWFVMGPARSGTGIHID 189
++ IY + A P + +++ P R G + ID
Sbjct: 205 QRDLSIYIRAPGL-AALVGHDPAWMYWLFNPDRRGVLVAID 244
>gnl|CDD|225051 COG2140, COG2140, Thermophilic glucose-6-phosphate isomerase and
related metalloenzymes [Carbohydrate transport and
metabolism / General function prediction only].
Length = 209
Score = 29.3 bits (66), Expect = 4.0
Identities = 7/27 (25%), Positives = 14/27 (51%)
Query: 428 EWKPLELVQGPGETVFVPGGWWHVVLN 454
E + + G+ ++VP G+ H +N
Sbjct: 122 EGEARVIAVRAGDVIYVPPGYGHYTIN 148
>gnl|CDD|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR;
Provisional.
Length = 638
Score = 29.3 bits (66), Expect = 5.7
Identities = 8/37 (21%), Positives = 13/37 (35%)
Query: 452 VLNLDTTVAVTQNFCSHTNFPVVYHKTIRGRPKLSKK 488
+L LD T + + P V + I+ L
Sbjct: 235 LLRLDATASQGRAITELLTLPAVLQQAIKQAHPLKHV 271
>gnl|CDD|202698 pfam03602, Cons_hypoth95, Conserved hypothetical protein 95.
Length = 183
Score = 28.4 bits (64), Expect = 6.3
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 278 LLNFIKDNVAVDKLSVLDVGCGAGLLGLYTLMNGAAHVSFQDYNQEVIESLTLPNILMNT 337
L N + + VLD+ G+G LGL L GAA V F + +++ + +L
Sbjct: 32 LFNILAPYFEIGGARVLDLFAGSGALGLEALSRGAASVVFVEKDKKAVATL--------K 83
Query: 338 DNLEKCKFY 346
+NLE
Sbjct: 84 ENLEALGLE 92
>gnl|CDD|198008 smart00940, PepX_N, X-Prolyl dipeptidyl aminopeptidase PepX,
N-terminal. This N-terminal domain adopts a secondary
structure consisting of a helical bundle of eight alpha
helices and three beta strands, with the last alpha
helix connecting to the first strand of the catalytic
domain. The first strand of the N-terminus also forms a
small parallel beta sheet with strand five of the
catalytic domain. This domain mediates dimerisation of
the protein, with two proline residues present in the
domain being critical for interaction.
Length = 156
Score = 28.0 bits (63), Expect = 7.0
Identities = 10/32 (31%), Positives = 12/32 (37%), Gaps = 1/32 (3%)
Query: 465 FCSHTNFPVVYHKTIRGRPKLSKKWYRKLKTR 496
F PVV H L + Y+ L TR
Sbjct: 110 FMKKIGLPVVDHIIF-TTENLIEALYQLLNTR 140
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and Arl13.
Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily
of the Arf family of small GTPases. Arl2l1 was
identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been confirmed;
it may be a pseudogene.
Length = 167
Score = 28.1 bits (63), Expect = 7.2
Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 22/96 (22%)
Query: 10 VLDSRARKRIKETKK-----------RARPEL---NGKDAWFELGYADKFDKF---KIVK 52
V+DS R++E K+ +P L N +D L AD + K+V
Sbjct: 73 VVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLGADVIEYLSLEKLVN 132
Query: 53 ENVERIHVKDYSPQEFIEKYEKPNKPVVIKGVTENW 88
EN H++ P IE K P +++G+ W
Sbjct: 133 ENKSLCHIE---PCSAIEGLGKKIDPSIVEGL--RW 163
>gnl|CDD|129570 TIGR00478, tly, hemolysin TlyA family protein. Hemolysins are
exotoxins that attack blood cell membranes and cause
cell rupture, often by forming a pore in the membrane.
At least two members of this protein family have been
characterized indirectly as pore-forming hemolysins, one
from the spirochete Serpula (Treponema) hyodysenteriae
and one from Mycobacterium tuberculosis. However,
homology domains in this protein suggest
methyltransferase activity (pfam01728) and RNA-binding
activity (pfam01479) [Unknown function, General].
Length = 228
Score = 28.2 bits (63), Expect = 7.5
Identities = 21/84 (25%), Positives = 28/84 (33%), Gaps = 6/84 (7%)
Query: 237 SNIKLLRTPLFEYETFVNISHTDLKPNVYEGGYKIWECTFDLLNFIKDNVAVDKLSVLDV 296
N K + P + I V GG K+ E + +K+ + VLDV
Sbjct: 29 VNGKKVDKPSALVDFDAKIELLQNPLFVSRGGEKLKEALEEFNIDVKNKI------VLDV 82
Query: 297 GCGAGLLGLYTLMNGAAHVSFQDY 320
G G L GA V D
Sbjct: 83 GSSTGGFTDCALQKGAKEVYGVDV 106
>gnl|CDD|223618 COG0544, Tig, FKBP-type peptidyl-prolyl cis-trans isomerase
(trigger factor) [Posttranslational modification,
protein turnover, chaperones].
Length = 441
Score = 28.8 bits (65), Expect = 8.0
Identities = 16/41 (39%), Positives = 26/41 (63%), Gaps = 2/41 (4%)
Query: 19 IKETKKRARPELNGKDAWFELGYADKFDKFK-IVKENVERI 58
+KE KKR PEL+ + A +LG D ++ K +++N+ER
Sbjct: 237 VKEVKKRELPELDDEFAK-KLGEEDTLEELKEKLRKNLERE 276
>gnl|CDD|234637 PRK00107, gidB, 16S rRNA methyltransferase GidB; Reviewed.
Length = 187
Score = 28.2 bits (64), Expect = 8.5
Identities = 28/111 (25%), Positives = 41/111 (36%), Gaps = 37/111 (33%)
Query: 289 DKLSVLDVGCGAGLLGL-YTLMNGAAHV----------SFQDYNQEVIESLTLPNILMNT 337
VLDVG GAG G+ + V +F +EV L L N+
Sbjct: 45 GGERVLDVGSGAGFPGIPLAIARPELKVTLVDSLGKKIAFL---REVAAELGLKNV---- 97
Query: 338 DNLEKCKFYHG---DWGSLSAVIHSKFDIILTSETIYSVANYNKLLTVWCL 385
HG ++G KFD++ T +VA+ + L+ CL
Sbjct: 98 ------TVVHGRAEEFG-----QEEKFDVV----TSRAVASLSDLVE-LCL 132
>gnl|CDD|132310 TIGR03266, methan_mark_1, putative methanogenesis marker protein 1.
Members of this protein family represent a distinct
clade among the larger set of proteins that belong to
families TIGR00702 and pfam02624. Proteins from this
clade are found in genome sequence if and only if the
species sequenced is one of the methanogens. All
methanogens belong to the archaea; some but not all of
those sequenced are hyperthermophiles. This protein
family was detected by the method of partial
phylogenetic profiling (see Haft, et al., 2006).
Length = 376
Score = 28.2 bits (63), Expect = 9.9
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 12/61 (19%)
Query: 414 SIIYPRTQLPSWPTEWKPLELVQG----PGETVFVPGGWWHVVLNLDTTVAVTQNFCSHT 469
S+I P+ P+ P EW V+G E V+VP + V + + + F S+T
Sbjct: 102 SLILPQPYYPTSPLEW-----VEGYDLTNNEEVYVPA---NAVFHPYDSPGQGKLFRSNT 153
Query: 470 N 470
N
Sbjct: 154 N 154
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.137 0.425
Gapped
Lambda K H
0.267 0.0746 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,315,398
Number of extensions: 2468838
Number of successful extensions: 2343
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2331
Number of HSP's successfully gapped: 66
Length of query: 496
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 395
Effective length of database: 6,457,848
Effective search space: 2550849960
Effective search space used: 2550849960
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 (21.6 bits)
S2: 61 (27.2 bits)