RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014571
(422 letters)
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 105 bits (265), Expect = 2e-25
Identities = 40/100 (40%), Positives = 61/100 (61%), Gaps = 4/100 (4%)
Query: 229 IFQLPSFYDVLEGEIFLQNLPSIVTAHALDPQKGERILDMCAAPGGKTTAIASLLRDEGE 288
I +LP F EG I++Q+ S + A LDP+ GER+LD+CAAPGGKTT +A L+ +EG
Sbjct: 127 IGRLPEF---AEGLIYVQDEASQLPALVLDPKPGERVLDLCAAPGGKTTHLAELMENEGA 183
Query: 289 -VVAVDRSHNKVMDIQKLAAEMGLKCITTYKLDALKAVRR 327
VVAVD S ++ +++ +G++ + DA +
Sbjct: 184 IVVAVDVSPKRLKRLRENLKRLGVRNVIVVNKDARRLAEL 223
Score = 38.1 bits (89), Expect = 0.006
Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 7/59 (11%)
Query: 6 RYSYSPLLRWNPQVEEYFIRAYGADHFSRISKALTRPSCYSCIRVNTLKTTTDDVIQKL 64
RYS+ W + E A G D I+ AL RP S +RVNTLK +++++ L
Sbjct: 51 RYSHP---EW---LVEKLPDALGEDEAEAIAAALLRPPPRS-LRVNTLKADVEELLEAL 102
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 104 bits (263), Expect = 1e-24
Identities = 47/117 (40%), Positives = 69/117 (58%), Gaps = 4/117 (3%)
Query: 217 ASEGIAVDMHNRIFQLPSFYDVLEGEIFLQNLPSIVTAHALDPQKGERILDMCAAPGGKT 276
+ E + ++ N I F +G I +Q+ S++ A ALDP+ G+ +LD CAAPGGKT
Sbjct: 210 SPEALVIEKGN-IAGTDLF---KDGLITIQDESSMLVAPALDPKGGDTVLDACAAPGGKT 265
Query: 277 TAIASLLRDEGEVVAVDRSHNKVMDIQKLAAEMGLKCITTYKLDALKAVRRKNESND 333
T IA LL++ G+VVA+D +K+ I++ A +GL I T LDA K + E D
Sbjct: 266 THIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDARKVHEKFAEKFD 322
Score = 42.5 bits (101), Expect = 3e-04
Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 7/62 (11%)
Query: 3 LSGRYSYSPLLRWNPQVEEYFIRAYGADHFSRISKALTRPSCYSCIRVNTLKTTTDDVIQ 62
LS +YS+ L V+ +I YG + +I ++L P + IRVNTLK + +++I+
Sbjct: 143 LSIKYSHPVWL-----VK-RWIDQYGEEKAEKILESLNEPP-KASIRVNTLKISVEELIE 195
Query: 63 KL 64
KL
Sbjct: 196 KL 197
>gnl|CDD|237856 PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional.
Length = 434
Score = 95.8 bits (239), Expect = 2e-21
Identities = 44/93 (47%), Positives = 59/93 (63%), Gaps = 3/93 (3%)
Query: 229 IFQLPSFYDVLEGEIFLQNLPSIVTAHALDPQKGERILDMCAAPGGKTTAIASLLRDEGE 288
I QLP + EG +Q+ + + A LDPQ GE ILD CAAPGGKTT IA L+ D+GE
Sbjct: 223 IRQLPGYE---EGWWTVQDRSAQLVAPLLDPQPGEVILDACAAPGGKTTHIAELMGDQGE 279
Query: 289 VVAVDRSHNKVMDIQKLAAEMGLKCITTYKLDA 321
+ AVDRS +++ +Q+ A +GLK I D+
Sbjct: 280 IWAVDRSASRLKKLQENAQRLGLKSIKILAADS 312
>gnl|CDD|237858 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
Length = 445
Score = 88.6 bits (220), Expect = 4e-19
Identities = 32/83 (38%), Positives = 51/83 (61%)
Query: 240 EGEIFLQNLPSIVTAHALDPQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRSHNKV 299
G + +QN + L+PQ G +LD+CAAPGGK+T +A L+++ G++ AVDR K+
Sbjct: 229 LGLVSVQNPTQALACLLLNPQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKL 288
Query: 300 MDIQKLAAEMGLKCITTYKLDAL 322
I+ A+ +G+ I T + DA
Sbjct: 289 EKIRSHASALGITIIETIEGDAR 311
>gnl|CDD|188051 TIGR00446, nop2p, NOL1/NOP2/sun family putative RNA methylase.
[Protein synthesis, tRNA and rRNA base modification].
Length = 264
Score = 70.2 bits (172), Expect = 1e-13
Identities = 26/61 (42%), Positives = 42/61 (68%)
Query: 239 LEGEIFLQNLPSIVTAHALDPQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRSHNK 298
L G + Q S++ AL+P++ ER+LDM AAPGGKTT I+ L++++G +VA + S ++
Sbjct: 49 LFGYYYPQEASSMIPPIALEPREDERVLDMAAAPGGKTTQISQLMKNKGCIVANEISKSR 108
Query: 299 V 299
Sbjct: 109 T 109
Score = 27.8 bits (62), Expect = 9.0
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 48 IRVNTLKTTTDDVIQKL 64
IRVNTLK +D++++L
Sbjct: 1 IRVNTLKINVEDLLERL 17
>gnl|CDD|201649 pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family.
Length = 277
Score = 68.6 bits (168), Expect = 5e-13
Identities = 41/94 (43%), Positives = 55/94 (58%), Gaps = 4/94 (4%)
Query: 203 GQGTAMMSRAGIFRASEGIAV-DMHNRIFQLPSFYDVLEGEIFLQNLPSIVTAHALDPQK 261
A + + R + V D+ I LP F G + +Q+ S + A AL+PQ+
Sbjct: 28 ALELAGVQLEPLGRYPHALPVGDLPYSIGSLPPF---ENGAVTVQDASSQLDAIALNPQE 84
Query: 262 GERILDMCAAPGGKTTAIASLLRDEGEVVAVDRS 295
E ILDMCAAPGGKTT IA L+++EG VVAVDR+
Sbjct: 85 DEFILDMCAAPGGKTTHIAELMKNEGTVVAVDRN 118
>gnl|CDD|233025 TIGR00563, rsmB, ribosomal RNA small subunit methyltransferase
RsmB. This protein is also known as sun protein. The
reading frame was originally interpreted as two reading
frames, fmu and fmv. The recombinant protein from E.
coli was shown to methylate only C967 of small subunit
(16S) ribosomal RNA and to produce only m5C at that
position. 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 [Protein synthesis, tRNA and rRNA base
modification].
Length = 426
Score = 68.7 bits (168), Expect = 1e-12
Identities = 32/90 (35%), Positives = 46/90 (51%), Gaps = 4/90 (4%)
Query: 229 IFQLPSFYDVLEGEIFLQNLPSIVTAHALDPQKGERILDMCAAPGGKTTAIASLLRDEGE 288
+ LP F EG + +Q+ + A L PQ E ILD CAAPGGKTT I L + +
Sbjct: 209 VHALPGFE---EGWVTVQDASAQWVATWLAPQNEETILDACAAPGGKTTHILELAP-QAQ 264
Query: 289 VVAVDRSHNKVMDIQKLAAEMGLKCITTYK 318
VVA+D +++ + + +GL K
Sbjct: 265 VVALDIHEHRLKRVYENLKRLGLTIKAETK 294
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 63.7 bits (155), Expect = 6e-11
Identities = 33/82 (40%), Positives = 50/82 (60%)
Query: 240 EGEIFLQNLPSIVTAHALDPQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRSHNKV 299
+G +Q S + ++ + G R+LD CAAPGGKTTAIA L++D+G+++AVD S K+
Sbjct: 216 DGLATVQGESSQIVPLLMELEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKI 275
Query: 300 MDIQKLAAEMGLKCITTYKLDA 321
++K A + L I DA
Sbjct: 276 QLVEKHAKRLKLSSIEIKIADA 297
>gnl|CDD|236790 PRK10901, PRK10901, 16S rRNA methyltransferase B; Provisional.
Length = 427
Score = 61.4 bits (150), Expect = 3e-10
Identities = 23/40 (57%), Positives = 27/40 (67%), Gaps = 1/40 (2%)
Query: 254 AHALDPQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVD 293
A L PQ GER+LD CAAPGGKT I L + +VVA+D
Sbjct: 237 ATLLAPQNGERVLDACAAPGGKTAHILE-LAPQAQVVALD 275
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 48.8 bits (117), Expect = 3e-06
Identities = 22/44 (50%), Positives = 29/44 (65%), Gaps = 2/44 (4%)
Query: 248 LPSIVTAHALDPQKGERILDMCAAPGGKTTAIASLLRDEGEVVA 291
LP V A D +R+LDM AAPG KTT IA+L+ ++G +VA
Sbjct: 102 LP--VAALFADDNAPQRVLDMAAAPGSKTTQIAALMNNQGAIVA 143
Score = 29.5 bits (67), Expect = 4.2
Identities = 11/22 (50%), Positives = 13/22 (59%), Gaps = 4/22 (18%)
Query: 41 RPSCYSCIRVNTLKTTTDDVIQ 62
R S IRVNTLK + D +Q
Sbjct: 34 RRS----IRVNTLKISVADFLQ 51
>gnl|CDD|179806 PRK04270, PRK04270, H/ACA RNA-protein complex component Cbf5p;
Reviewed.
Length = 300
Score = 47.9 bits (115), Expect = 3e-06
Identities = 31/108 (28%), Positives = 45/108 (41%), Gaps = 34/108 (31%)
Query: 123 PKEVIVSRKCAEAVLRGAQVYVPGVMACSSHVEKGDVVAVSVAVEQPTLDGGWGLGITRG 182
PK +I+ +A+ GA +Y PG+ ++KGD+VAV TL G
Sbjct: 226 PK-IIIKDSAVDAIAHGAPLYAPGIAKLEKGIKKGDLVAVF------TLKG--------- 269
Query: 183 TVLQGSQTDPYYFERSGLYIGQGTAMMSRAGIFRASEGIAVDMHNRIF 230
E L G A+M I +A +GI VD+ R+F
Sbjct: 270 -------------ELVAL----GKALMDSDEILKAEKGIVVDL-ERVF 299
>gnl|CDD|222415 pfam13847, Methyltransf_31, Methyltransferase domain. This family
appears to be have methyltransferase activity.
Length = 151
Score = 42.0 bits (99), Expect = 9e-05
Identities = 15/65 (23%), Positives = 30/65 (46%)
Query: 259 PQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRSHNKVMDIQKLAAEMGLKCITTYK 318
+ G ++LD+ G T +A L EVV +D S + ++ A ++G + + +
Sbjct: 1 LKSGIKVLDLGCGTGYLTFILAEKLGPGAEVVGIDISEEAIEKAKENAKKLGYENVEFIQ 60
Query: 319 LDALK 323
D +
Sbjct: 61 GDIEE 65
>gnl|CDD|201816 pfam01472, PUA, PUA domain. The PUA domain named after
Pseudouridine synthase and Archaeosine transglycosylase,
was detected in archaeal and eukaryotic pseudouridine
synthases, archaeal archaeosine synthases, a family of
predicted ATPases that may be involved in RNA
modification, a family of predicted archaeal and
bacterial rRNA methylases. Additionally, the PUA domain
was detected in a family of eukaryotic proteins that
also contain a domain homologous to the translation
initiation factor eIF1/SUI1; these proteins may comprise
a novel type of translation factors. Unexpectedly, the
PUA domain was detected also in bacterial and yeast
glutamate kinases; this is compatible with the
demonstrated role of these enzymes in the regulation of
the expression of other genes. It is predicted that the
PUA domain is an RNA binding domain.
Length = 74
Score = 39.8 bits (94), Expect = 1e-04
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 124 KEVIVSRKCAEAVLRGAQVYVPGVMACSSHVEKGDVVAV 162
V+V EA+L GA + PGV+ +GD V V
Sbjct: 1 GRVVVDDGAVEAILNGASLLAPGVVEVDGDFRRGDEVVV 39
>gnl|CDD|181382 PRK08317, PRK08317, hypothetical protein; Provisional.
Length = 241
Score = 41.1 bits (97), Expect = 5e-04
Identities = 16/40 (40%), Positives = 22/40 (55%)
Query: 256 ALDPQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRS 295
L Q G+R+LD+ PG +A + EG VV +DRS
Sbjct: 14 LLAVQPGDRVLDVGCGPGNDARELARRVGPEGRVVGIDRS 53
>gnl|CDD|214635 smart00359, PUA, Putative RNA-binding Domain in PseudoUridine
synthase and Archaeosine transglycosylase.
Length = 76
Score = 37.6 bits (88), Expect = 8e-04
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 124 KEVIVSRKCAEAVLRGAQVYVPGVMACSSHVEKGDVVAV 162
+V+V +A+L GA + PGV+ +++GDVV +
Sbjct: 1 GKVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVI 39
>gnl|CDD|223370 COG0293, FtsJ, 23S rRNA methylase [Translation, ribosomal structure
and biogenesis].
Length = 205
Score = 38.4 bits (90), Expect = 0.003
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 261 KGERILDMCAAPGGKTTAIASLLRDEGEVVAVD----RSHNKVMDIQK 304
G ++D+ AAPGG + A L G++VAVD + V+ +Q
Sbjct: 45 PGMVVVDLGAAPGGWSQVAAKKLGAGGKIVAVDILPMKPIPGVIFLQG 92
>gnl|CDD|232976 TIGR00438, rrmJ, cell division protein FtsJ. Methylates the 23S
rRNA. Previously known as cell division protein ftsJ.//
Trusted cutoff too high? [SS 10/1/04] [Protein
synthesis, tRNA and rRNA base modification].
Length = 188
Score = 36.3 bits (84), Expect = 0.012
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 260 QKGERILDMCAAPGGKTTAIASLLRDEGEVVAVD 293
+ G+ +LD+ AAPGG + + +G V+AVD
Sbjct: 31 KPGDTVLDLGAAPGGWSQVAVEQVGGKGRVIAVD 64
>gnl|CDD|224927 COG2016, COG2016, Predicted RNA-binding protein (contains PUA
domain) [Translation, ribosomal structure and
biogenesis].
Length = 161
Score = 35.0 bits (81), Expect = 0.027
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 115 YGYEPDKPPKEVIVSRKCAEAVLRGAQVYVPGVMACSSHVEKGDVVAV 162
P K V+V + VL GA V PG+++ +++GD+V V
Sbjct: 70 LKLPPGKY--VVVVDEGAVKFVLNGADVMAPGIVSADGEIKEGDIVVV 115
>gnl|CDD|237510 PRK13795, PRK13795, hypothetical protein; Provisional.
Length = 636
Score = 35.4 bits (82), Expect = 0.063
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 124 KEVIVSRKCAEAVLRGAQVYVPGVMACSSHVEKGDVVAVSVAVEQPTLDGGWGLGITR 181
K VIV + E + G V PGV+ ++KGD V V + G+G +
Sbjct: 127 KWVIVDKGALEPIKNGKNVLAPGVVEADLDIKKGDEVVVVTEDGEVV-----GVGRAK 179
>gnl|CDD|232971 TIGR00425, CBF5, rRNA pseudouridine synthase, putative. This
family, found in archaea and eukaryotes, includes the
only archaeal proteins markedly similar to bacterial
TruB, the tRNA pseudouridine 55 synthase. However, among
two related yeast proteins, the archaeal set matches
yeast YLR175w far better than YNL292w. The first, termed
centromere/microtubule binding protein 5 (CBF5), is an
apparent rRNA pseudouridine synthase, while the second
is the exclusive tRNA pseudouridine 55 synthase for both
cytosolic and mitochondrial compartments. It is unclear
whether archaeal proteins found by this model modify
tRNA, rRNA, or both [Protein synthesis, tRNA and rRNA
base modification].
Length = 322
Score = 34.7 bits (80), Expect = 0.070
Identities = 25/113 (22%), Positives = 37/113 (32%), Gaps = 33/113 (29%)
Query: 124 KEVIVSRKCAEAVLRGAQVYVPGVMACSSHVEKGDVVAVSVAVEQPTLDGGWGLGITRGT 183
K V+V +A+ GA + V G+ +EKGD V V
Sbjct: 238 KRVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVVV--------------------- 276
Query: 184 VLQGSQTDPYYFERSGLYIGQGTAMMSRAGIFRASEGIAVDMHNRIFQLPSFY 236
G + G A+MS I A +G+ D+ R+ Y
Sbjct: 277 -----------ITLKGEAVAVGIALMSTKDIANADKGVVADV-KRVIMERGTY 317
>gnl|CDD|216666 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
hypothesised that the N-terminal domain of NS5 is a
methyltransferase involved in viral RNA capping.
Length = 177
Score = 33.4 bits (77), Expect = 0.12
Identities = 17/40 (42%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 254 AHALDPQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVD 293
L P KG+ +LD+ AAPGG + + G+VVAVD
Sbjct: 15 RFGLKPGKGKTVLDLGAAPGGFSQVLLERGGA-GKVVAVD 53
>gnl|CDD|131799 TIGR02752, MenG_heptapren, demethylmenaquinone methyltransferase.
MenG is a generic term for a methyltransferase that
catalyzes the last step in menaquinone biosynthesis; the
exact enzymatic activity differs for different MenG
because the menaquinone differ in their prenoid side
chains in different species. Members of this MenG
protein family are 2-heptaprenyl-1,4-naphthoquinone
methyltransferase, and are found together in operons
with the two subunits of the heptaprenyl diphosphate
synthase in Bacillus subtilis and related species
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 231
Score = 33.6 bits (77), Expect = 0.14
Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 2/64 (3%)
Query: 236 YDVLEGEIFLQNLPSIV--TAHALDPQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVD 293
YD + I Q T ++ Q G LD+C + A+A + EG V+ +D
Sbjct: 18 YDRMNSVISFQRHKKWRKDTMKRMNVQAGTSALDVCCGTADWSIALAEAVGPEGHVIGLD 77
Query: 294 RSHN 297
S N
Sbjct: 78 FSEN 81
>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 = 31.6 bits (72), Expect = 0.18
Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 2/68 (2%)
Query: 264 RILDMCAAPGGKTTAIASLLRDEGEVVAVDRSHNKVMDIQKLAAEMGLKCITTYKLDALK 323
R+LD+ G A+AS V VD S + +K AA + + K DA +
Sbjct: 1 RVLDLGCGTGALALALAS--GPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEE 58
Query: 324 AVRRKNES 331
+ES
Sbjct: 59 LPPEADES 66
>gnl|CDD|234689 PRK00216, ubiE, ubiquinone/menaquinone biosynthesis
methyltransferase; Reviewed.
Length = 239
Score = 32.4 bits (75), Expect = 0.29
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 256 ALDPQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRS 295
L + G+++LD+ G A+A + GEVV +D S
Sbjct: 46 WLGVRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLDFS 85
>gnl|CDD|233880 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 [Biosynthesis of cofactors,
prosthetic groups, and carriers, Heme, porphyrin, and
cobalamin].
Length = 124
Score = 30.8 bits (70), Expect = 0.43
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 1/75 (1%)
Query: 251 IVTAHALDPQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRSHNKVMDIQKLAAEMG 310
+T L + G+ + D+ A G T A+ L G V A++R+ + I++ G
Sbjct: 9 ALTLSKLRLRPGDVLWDIGAGTGSVTIE-AARLVPNGRVYAIERNPEALDLIERNLRRFG 67
Query: 311 LKCITTYKLDALKAV 325
+ I + DA +A
Sbjct: 68 VSNIVIVEGDAPEAP 82
>gnl|CDD|216746 pfam01862, PvlArgDC, Pyruvoyl-dependent arginine decarboxylase
(PvlArgDC). Methanococcus jannaschii contains
homologues of most genes required for spermidine
polyamine biosynthesis. Yet genomes from neither this
organism nor any other euryarchaeon have orthologues of
the pyridoxal 5'-phosphate- dependent ornithine or
arginine decarboxylase genes, required to produce
putrescine. Instead,these organisms have a new class of
arginine decarboxylase (PvlArgDC) formed by the
self-cleavage of a proenzyme into a 5-kDa subunit and a
12-kDa subunit that contains a reactive pyruvoyl group.
Although this extremely thermostable enzyme has no
significant sequence similarity to previously
characterized proteins, conserved active site residues
are similar to those of the pyruvoyl-dependent histidine
decarboxylase enzyme, and its subunits form a similar
(alpha-beta)(3) complex. Homologues of PvlArgDC are
found in several bacterial genomes, including those of
Chlamydia spp., which have no agmatine ureohydrolase
enzyme to convert agmatine (decarboxylated arginine)
into putrescine. In these intracellular pathogens,
PvlArgDC may function analogously to pyruvoyl-dependent
histidine decarboxylase; the cells are proposed to
import arginine and export agmatine, increasing the pH
and affecting the host cell's metabolism. Phylogenetic
analysis of Pvl- ArgDC proteins suggests that this gene
has been recruited from the euryarchaeal polyamine
biosynthetic pathway to function as a degradative enzyme
in bacteria.
Length = 159
Score = 31.0 bits (71), Expect = 0.59
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 122 PPKEVIVSRKCAEAVLR-GAQVYVPGVMACSSHVEKGDVVAVSVAVEQPTLDGGWGL 177
PP IVS + L G+ V+ VMA ++ E G ++ +V V P +G
Sbjct: 43 PPNAEIVSLEEGLKELPPGSIVFC--VMARNTSNEPGRTISAAVGVAIPKDKSIYGY 97
>gnl|CDD|225443 COG2890, HemK, Methylase of polypeptide chain release factors
[Translation, ribosomal structure and biogenesis].
Length = 280
Score = 31.2 bits (71), Expect = 0.84
Identities = 27/93 (29%), Positives = 42/93 (45%), Gaps = 15/93 (16%)
Query: 240 EGEIFLQNLPSIVTAHALDPQKGERILDMCAAPGGKTTAIASLLRDEG---EVVAVDRSH 296
+ E+ ++ AL Q +RILD+ G AIA L EG EV+AVD S
Sbjct: 95 DTELLVEAAL------ALLLQLDKRILDLGTGSG----AIAIALAKEGPDAEVIAVDIS- 143
Query: 297 NKVMDI-QKLAAEMGLKCITTYKLDALKAVRRK 328
+ + ++ A GL + + D + +R K
Sbjct: 144 PDALALARENAERNGLVRVLVVQSDLFEPLRGK 176
>gnl|CDD|222019 pfam13276, HTH_21, HTH-like domain. This domain contains a
predicted helix-turn-helix suggesting a DNA-binding
function.
Length = 60
Score = 28.6 bits (65), Expect = 0.86
Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 6/40 (15%)
Query: 279 IASLLRDEGEVVAVDRSHNKVMDIQKLAAEMGLKCITTYK 318
I + LR EG + + +V ++L E+GL+ K
Sbjct: 26 ITAELRREGGIKV---NRKRV---RRLMRELGLRSRIRRK 59
>gnl|CDD|226608 COG4123, COG4123, Predicted O-methyltransferase [General function
prediction only].
Length = 248
Score = 31.1 bits (71), Expect = 1.0
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 13/65 (20%)
Query: 250 SIVTAHALDPQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRSHNKV--MDIQKLAA 307
+I+ A K RILD+ A G LL +A K+ ++IQ+ AA
Sbjct: 33 AILLAAFAPVPKKGRILDLGAGNG-----ALGLL------LAQRTEKAKIVGVEIQEEAA 81
Query: 308 EMGLK 312
EM +
Sbjct: 82 EMAQR 86
>gnl|CDD|110227 pfam01209, Ubie_methyltran, ubiE/COQ5 methyltransferase family.
Length = 233
Score = 30.9 bits (70), Expect = 1.1
Identities = 15/56 (26%), Positives = 27/56 (48%)
Query: 259 PQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRSHNKVMDIQKLAAEMGLKCI 314
++G + LD+ G T ++ G+VV +D + N + + +K A E G I
Sbjct: 45 VKRGNKFLDVAGGTGDWTFGLSDSAGSSGKVVGLDINENMLKEGEKKAKEEGKYNI 100
>gnl|CDD|221804 pfam12847, Methyltransf_18, Methyltransferase domain. Protein in
this family function as methyltransferases.
Length = 104
Score = 29.2 bits (66), Expect = 1.2
Identities = 12/48 (25%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 261 KGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRSHNKVMDIQKLAAE 308
G R+LD+ G +A L V VD S + ++ A
Sbjct: 1 PGARVLDIGCGTGSLAIELARLFPG-ARVTGVDLSPEMLELARENAKL 47
>gnl|CDD|227595 COG5270, COG5270, PUA domain (predicted RNA-binding domain)
[Translation, ribosomal structure and biogenesis].
Length = 202
Score = 30.5 bits (69), Expect = 1.2
Identities = 15/42 (35%), Positives = 19/42 (45%)
Query: 121 KPPKEVIVSRKCAEAVLRGAQVYVPGVMACSSHVEKGDVVAV 162
K K + R E V G V PGV+ +E+GD V V
Sbjct: 126 KGKKGRKIDRGAVEPVKNGKNVLPPGVIEAEDSIERGDEVIV 167
>gnl|CDD|233645 TIGR01934, MenG_MenH_UbiE, ubiquinone/menaquinone biosynthesis
methyltransferases. This model represents a family of
methyltransferases involved in the biosynthesis of
menaquinone and ubiqinone. Some members such as the UbiE
enzyme from E. coli are believed to act in both
pathways, while others may act in only the menaquinone
pathway. These methyltransferases are members of the
UbiE/CoQ family of methyltransferases (pfam01209) which
also contains ubiquinone methyltransferases and other
methyltransferases. Members of this clade include a wide
distribution of bacteria and eukaryotes, but no archaea.
An outgroup for this clade is provided by the
phosphatidylethanolamine methyltransferase (EC 2.1.1.17)
from Rhodobacter sphaeroides. Note that a number of
non-orthologous genes which are members of pfam03737
have been erroneously annotated as MenG
methyltransferases [Biosynthesis of cofactors,
prosthetic groups, and carriers, Menaquinone and
ubiquinone].
Length = 223
Score = 30.3 bits (69), Expect = 1.3
Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 259 PQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRSHNKVMDIQK 304
KG+++LD+ G +A D G+V VD S ++++++ K
Sbjct: 37 VFKGQKVLDVACGTGDLAIELAKSAPDRGKVTGVDFS-SEMLEVAK 81
>gnl|CDD|234247 TIGR03533, L3_gln_methyl, protein-(glutamine-N5) methyltransferase,
ribosomal protein L3-specific. Members of this protein
family methylate ribosomal protein L3 on a glutamine
side chain. This family is related to HemK, a
protein-glutamine methyltranferase for peptide chain
release factors [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 284
Score = 30.6 bits (70), Expect = 1.4
Identities = 18/40 (45%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 257 LDPQKGERILDMCAAPGGKTTAIASLLR-DEGEVVAVDRS 295
L+P+ +RILD+C G AIA E EV AVD S
Sbjct: 117 LEPEPVKRILDLCT--GSGCIAIACAYAFPEAEVDAVDIS 154
>gnl|CDD|225136 COG2226, UbiE, Methylase involved in ubiquinone/menaquinone
biosynthesis [Coenzyme metabolism].
Length = 238
Score = 30.3 bits (69), Expect = 1.4
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 256 ALDPQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRS 295
L + G+++LD+ G +A GEVV +D S
Sbjct: 46 LLGIKPGDKVLDVACGTGDMALLLAK-SVGTGEVVGLDIS 84
>gnl|CDD|225316 COG2518, Pcm, Protein-L-isoaspartate carboxylmethyltransferase
[Posttranslational modification, protein turnover,
chaperones].
Length = 209
Score = 30.3 bits (69), Expect = 1.5
Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 5/77 (6%)
Query: 249 PSIVT--AHALDPQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRSHNKVMDIQKLA 306
P +V L+ + G+R+L++ G A+ + L G VV+++R ++
Sbjct: 58 PHMVARMLQLLELKPGDRVLEI-GTGSGYQAAVLARL--VGRVVSIERIEELAEQARRNL 114
Query: 307 AEMGLKCITTYKLDALK 323
+G + +T D K
Sbjct: 115 ETLGYENVTVRHGDGSK 131
>gnl|CDD|225319 COG2521, COG2521, Predicted archaeal methyltransferase [General
function prediction only].
Length = 287
Score = 30.5 bits (69), Expect = 1.5
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 259 PQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRSHNKVMDIQKL 305
++GER+LD C G TAI +L R V+ V++ N V+++ KL
Sbjct: 132 VKRGERVLDTCTGLG--YTAIEALERGAIHVITVEKDPN-VLELAKL 175
>gnl|CDD|185710 cd07900, Adenylation_DNA_ligase_I_Euk, Adenylation domain of
eukaryotic DNA Ligase I. ATP-dependent polynucleotide
ligases catalyze phosphodiester bond formation using
nicked nucleic acid substrates with the high energy
nucleotide of ATP as a cofactor in a three step reaction
mechanism. DNA ligases play a vital role in the diverse
processes of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms such
as viruses, bacteriophages, eukarya, archaea and
bacteria. Some organisms express a variety of different
ligases which appear to be targeted to specific
functions. There are three classes of ATP-dependent DNA
ligases in eukaryotic cells (I, III and IV). DNA ligase
I is required for the ligation of Okazaki fragments
during lagging-strand DNA synthesis and for base
excision repair (BER). DNA ligases have a highly modular
architecture consisting of a unique arrangement of two
or more discrete domains. The adenylation and C-terminal
oligonucleotide/oligosaccharide binding (OB)-fold
domains comprise a catalytic core unit that is common to
most members of the ATP-dependent DNA ligase family. The
adenylation domain binds ATP and contains many of the
active-site residues. DNA ligase I is the main
replicative ligase in eukaryotes. The common catalytic
core unit comprises six conserved sequence motifs (I,
III, IIIa, IV, V and VI) that define this family of
related nucleotidyltransferases.
Length = 219
Score = 30.2 bits (69), Expect = 1.5
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 286 EGEVVAVDRSHNKVMDIQKL 305
+ E+VA DR K++ Q L
Sbjct: 89 DSEIVAYDRETGKILPFQVL 108
>gnl|CDD|176363 cd01768, RA, RA (Ras-associating) ubiquitin domain. The RA
(Ras-associating) domain is structurally similar to
ubiquitin and is present in one or two copies in a
number of signalling molecules that bind and regulate a
small GTPase called Ras or the Ras-related GTPases, Ral
and Rap. RA-containing proteins include RalGDS, AF6,
RIN1, RASSF1, SNX27, CYR1, STE50, and phospholipase C
epsilon.
Length = 87
Score = 28.4 bits (64), Expect = 1.7
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 34 RISKALTRPSCYSCIRVNTLKTTTDDVIQKLL 65
R+ Y +RV + TT DVIQ+LL
Sbjct: 3 RVYPEDPSGGTYKTLRV-SKDTTAQDVIQQLL 33
>gnl|CDD|178645 PLN03097, FHY3, Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional.
Length = 846
Score = 30.7 bits (69), Expect = 1.9
Identities = 15/45 (33%), Positives = 22/45 (48%)
Query: 123 PKEVIVSRKCAEAVLRGAQVYVPGVMACSSHVEKGDVVAVSVAVE 167
P E VS AV + QV V G +AC +E D +++ V+
Sbjct: 516 PLEKSVSGVYTHAVFKKFQVEVLGAVACHPKMESQDETSITFRVQ 560
>gnl|CDD|223574 COG0500, SmtA, SAM-dependent methyltransferases [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 257
Score = 30.3 bits (65), Expect = 1.9
Identities = 25/120 (20%), Positives = 40/120 (33%), Gaps = 12/120 (10%)
Query: 206 TAMMSRAGIFRASEGIAVDMHNRIFQLPSFYDVLEGEIFLQNLPSIVTAHALDPQKGERI 265
+ + I + +A + + D+L L+ LP G +
Sbjct: 4 LSAELLSRILELYDRLAELLDAFLLLAEELLDLLLVLRLLRLLP-----------GGLGV 52
Query: 266 LDMCAAPGGKTTAIASLLRDEGEVVAVDRSHNKVMDIQKLAAEMGLKCITTYKLDALKAV 325
LD+ G + +A L VV VD S + + A GL + DAL V
Sbjct: 53 LDIGCGTG-RLALLARLGGRGAYVVGVDLSPEMLALARARAEGAGLGLVDFVVADALGGV 111
>gnl|CDD|234310 TIGR03684, arCOG00985, arCOG04150 universal archaeal PUA-domain
protein. This universal archaeal protein contains a
domain possibly associated with RNA binding (pfam01472,
TIGR00451).
Length = 150
Score = 29.5 bits (67), Expect = 2.0
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 117 YEPDKPPKEVIVSRKCAEAVLRGAQVYVPGVMACSSHVEKGDVVAV 162
PDK V+V + ++ GA + PG++ +++GD+V V
Sbjct: 65 LNPDKN--VVVVDEGAVKFIINGADIMAPGIVEADPSIKEGDIVFV 108
>gnl|CDD|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 30.2 bits (69), Expect = 2.1
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 288 EVVAVDRSHNKVMDIQKLAAEMGLKCITTYKLDALKAVRRK 328
EV+A+ RS K+ +KL A+ I + DAL+AV+
Sbjct: 192 EVIAITRSEEKLELAKKLGADHV---INSSDSDALEAVKEI 229
>gnl|CDD|183025 PRK11188, rrmJ, 23S rRNA methyltransferase J; Provisional.
Length = 209
Score = 29.7 bits (67), Expect = 2.2
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 260 QKGERILDMCAAPGGKTTAIASLLRDEGEVVAVD 293
+ G ++D+ AAPGG + + + D+G V+A D
Sbjct: 50 KPGMTVVDLGAAPGGWSQYAVTQIGDKGRVIACD 83
>gnl|CDD|177877 PLN02233, PLN02233, ubiquinone biosynthesis methyltransferase.
Length = 261
Score = 29.9 bits (67), Expect = 2.3
Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 260 QKGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRSHNKVM---DIQKLAAEMGLKCITT 316
+ G+R+LD+C G ++ + +G+V+ +D S ++ Q+L A+ K I
Sbjct: 72 KMGDRVLDLCCGSGDLAFLLSEKVGSDGKVMGLDFSSEQLAVAASRQELKAKSCYKNIEW 131
Query: 317 YKLDALK 323
+ DA
Sbjct: 132 IEGDATD 138
>gnl|CDD|212501 cd11642, SUMT, Uroporphyrin-III C-methyltransferase
(S-Adenosyl-L-methionine:uroporphyrinogen III
methyltransferase, SUMT). SUMT, an enzyme of the
cobalamin and siroheme biosynthetic pathway, catalyzes
the transformation of uroporphyrinogen III into
precorrin-2. It transfers two methyl groups from
S-adenosyl-L-methionine to the C-2 and C-7 atoms of
uroporphyrinogen III to yield precorrin-2 via the
intermediate formation of precorrin-1. SUMT is the first
enzyme committed to the biosynthesis of siroheme or
cobalamin (vitamin B12), and precorrin-2 is a common
intermediate in the biosynthesis of corrinoids such as
vitamin B12, siroheme and coenzyme F430. In some
organisms, the SUMT domain is fused to the precorrin-2
oxidase/ferrochelatase domain to form siroheme synthase
or to uroporphyrinogen-III synthase to form bifunctional
uroporphyrinogen-III methylase/uroporphyrinogen-III
synthase.
Length = 233
Score = 29.7 bits (68), Expect = 2.7
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 378 GRTCGECGMAQEEINALVV 396
G+ G+ + QEEIN L+V
Sbjct: 53 GKRPGKHSLPQEEINELLV 71
>gnl|CDD|129543 TIGR00451, unchar_dom_2, uncharacterized domain 2. This
uncharacterized domain is found a number of enzymes and
uncharacterized proteins, often at the C-terminus. It is
found in some but not all members of a family of related
tRNA-guanine transglycosylases (tgt), which exchange a
guanine base for some modified base without breaking the
phosphodiester backbone of the tRNA. It is also found in
rRNA pseudouridine synthase, another enzyme of RNA base
modification not otherwise homologous to tgt. It is
found, again at the C-terminus, in two putative
glutamate 5-kinases. It is also found in a family of
small, uncharacterized archaeal proteins consisting
mostly of this domain.
Length = 107
Score = 28.2 bits (63), Expect = 2.7
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 118 EPDKPPKEVIVSRKCAEAVLRGAQVYVPGVMACSSHVEKGDVVAVSV 164
DK V+V + + GA V PG++ +++GD V V
Sbjct: 27 MEDKK--IVVVDNGAVKFLKNGADVMRPGIVDADEDIKEGDDVVVVD 71
>gnl|CDD|201444 pfam00788, RA, Ras association (RalGDS/AF-6) domain. RasGTP
effectors (in cases of AF6, canoe and RalGDS); putative
RasGTP effectors in other cases. Recent evidence (not
yet in MEDLINE) shows that some RA domains do NOT bind
RasGTP. Predicted structure similar to that determined,
and that of the RasGTP-binding domain of Raf kinase.
Length = 87
Score = 28.1 bits (63), Expect = 2.8
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 10/43 (23%)
Query: 23 FIRAYGADHFSRISKALTRPSCYSCIRVNTLKTTTDDVIQKLL 65
+R Y D P Y I V + TT +VI+ L
Sbjct: 1 VLRVYTEDG---------TPGTYKTILV-SSTTTAQEVIRAAL 33
>gnl|CDD|145511 pfam02405, Permease, Permease. This domain functions as a
permease. In a hypothetical protein from Neisseria it is
involved in L-glutamate import into the cell. In
Arabidopsis ABC transporter I family member 14 it is
involved in lipid transfer within the cell.
Length = 215
Score = 28.9 bits (66), Expect = 4.0
Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 389 EEINAL-VVGLRIQKVLVLTALIESFLMLPVL 419
EEI+AL V+G+ + LVL ++ + LP+L
Sbjct: 86 EEIDALEVMGIDPIRYLVLPRVLAGVIALPLL 117
>gnl|CDD|223434 COG0357, GidB, Predicted S-adenosylmethionine-dependent
methyltransferase involved in bacterial cell division
[Cell envelope biogenesis, outer membrane].
Length = 215
Score = 28.8 bits (65), Expect = 4.0
Identities = 17/82 (20%), Positives = 35/82 (42%), Gaps = 13/82 (15%)
Query: 247 NLPSIVTAHALD--------PQKGERILDMCAAPG--GKTTAIASLLRDEGEVVAVDRSH 296
+ + H LD K +R+LD+ + G G AIA + +V ++
Sbjct: 45 DPEELWQRHILDSLVLLPYLDGKAKRVLDIGSGAGFPGIPLAIA---FPDLKVTLLESLG 101
Query: 297 NKVMDIQKLAAEMGLKCITTYK 318
K+ ++++ E+GL+ +
Sbjct: 102 KKIAFLREVKKELGLENVEIVH 123
>gnl|CDD|219763 pfam08245, Mur_ligase_M, Mur ligase middle domain.
Length = 178
Score = 28.8 bits (65), Expect = 4.2
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 274 GKTT---AIASLLRDEGEVVAVDRSHNKVMDIQKLAAEM 309
GKTT IA++L G VV + N + + L A M
Sbjct: 5 GKTTTTELIAAILSAAGGVVGTGGNTNNAIGLPLLLALM 43
>gnl|CDD|225151 COG2242, CobL, Precorrin-6B methylase 2 [Coenzyme metabolism].
Length = 187
Score = 28.4 bits (64), Expect = 4.7
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 251 IVTAHALDPQKGERILDMCAAPGGKTTAIASLLRDEGEVVAVDRSHNKVMDIQKLAAEMG 310
+T L P+ G+R+ D+ A G T A L G V+A++R + I++ AA G
Sbjct: 24 ALTLSKLRPRPGDRLWDIGAGTGSITIEWA-LAGPSGRVIAIERDEEALELIERNAARFG 82
Query: 311 LKCITTYKLDALKA 324
+ + + DA +A
Sbjct: 83 VDNLEVVEGDAPEA 96
>gnl|CDD|237757 PRK14560, PRK14560, putative RNA-binding protein; Provisional.
Length = 160
Score = 28.3 bits (64), Expect = 5.0
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 117 YEPDKPPKEVIVSRKCAEAVLRGAQVYVPGVMACSSHVEKGDVVAV 162
+P+K V+V + V GA V PG++ +++GD+V V
Sbjct: 72 LKPEKR--RVVVDAGAVKFVSNGADVMAPGIVEADEDIKEGDIVFV 115
>gnl|CDD|226196 COG3670, COG3670, Lignostilbene-alpha,beta-dioxygenase and related
enzymes [Secondary metabolites biosynthesis, transport,
and catabolism].
Length = 490
Score = 28.9 bits (65), Expect = 6.4
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 3/38 (7%)
Query: 229 IFQLPSFYDVLEGEIFLQNLPSIVTAHALDPQKGERIL 266
F LP +D + L P+ A P+ RIL
Sbjct: 243 FFDLPVTFDPVP---RLLGRPADGHAMRWRPELPTRIL 277
>gnl|CDD|240314 PTZ00208, PTZ00208, 65 kDa invariant surface glycoprotein;
Provisional.
Length = 436
Score = 28.4 bits (63), Expect = 7.6
Identities = 16/76 (21%), Positives = 29/76 (38%), Gaps = 10/76 (13%)
Query: 108 SGPHTIDYGYEPDKPPKEVIVSRKCAEAVLRGAQVYVPGVMACSSHVEKGDVVAVSVAVE 167
+ + ++ E +KP EVIV+ K EA +GA++ +P ++ E
Sbjct: 290 NTAYAVNTKVEQEKPLSEVIVAAK--EAGKKGAKIIIPAAAPATATESTKG--------E 339
Query: 168 QPTLDGGWGLGITRGT 183
+ GI
Sbjct: 340 DSAISEHVDRGIATNE 355
>gnl|CDD|216379 pfam01234, NNMT_PNMT_TEMT, NNMT/PNMT/TEMT family.
Length = 255
Score = 28.1 bits (63), Expect = 7.7
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 232 LPSFY-----DVLEGEIFLQNLPSIVTAHALDPQKGERILDMCAAP 272
L ++Y D E +I L LP+++ KG+ +LD+ A P
Sbjct: 22 LNTYYKFASGDAAEMQIVLFFLPNLLQTFGPGGVKGDTLLDIGAGP 67
>gnl|CDD|234997 PRK02090, PRK02090, phosphoadenosine phosphosulfate reductase;
Provisional.
Length = 241
Score = 27.9 bits (63), Expect = 8.6
Identities = 7/25 (28%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 5 GRYSYSPLLRWNP-QVEEYFIRAYG 28
GR+ +PL W V Y ++ +
Sbjct: 168 GRFKINPLADWTNEDVWAY-LKEHD 191
>gnl|CDD|172614 PRK14124, PRK14124, tRNA pseudouridine synthase B; Provisional.
Length = 308
Score = 28.2 bits (63), Expect = 9.3
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 123 PKEVIVSRKCAEAVLRGAQVYVPGVMACSSHVEKGDVVAV 162
PK V++ ++ E +L G+Q+Y+ V + +K DVV V
Sbjct: 229 PK-VVIHQESTEKILNGSQIYLEMVKEWDN-FKKDDVVRV 266
>gnl|CDD|223363 COG0286, HsdM, Type I restriction-modification system
methyltransferase subunit [Defense mechanisms].
Length = 489
Score = 28.2 bits (63), Expect = 9.9
Identities = 13/52 (25%), Positives = 18/52 (34%), Gaps = 6/52 (11%)
Query: 240 EGEIFLQNLPSIVT---AHALDPQKGERILDMCAAPGGKTTAIASLLRDEGE 288
GE + P V+ LDP+ I D GG A L+ +
Sbjct: 165 AGEFYT---PREVSELIVELLDPEPRNSIYDPACGSGGMLLQAAKYLKRHQD 213
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 0.134 0.386
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,013,351
Number of extensions: 2013749
Number of successful extensions: 2065
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2060
Number of HSP's successfully gapped: 76
Length of query: 422
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 323
Effective length of database: 6,546,556
Effective search space: 2114537588
Effective search space used: 2114537588
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: 60 (26.8 bits)