RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15213
(139 letters)
>gnl|CDD|236790 PRK10901, PRK10901, 16S rRNA methyltransferase B; Provisional.
Length = 427
Score = 160 bits (408), Expect = 1e-48
Identities = 57/117 (48%), Positives = 72/117 (61%), Gaps = 9/117 (7%)
Query: 27 FDRILADLPCTGSGVVRRNPDIPWLRRKNDIKKLSKYSCKILNNLWKMLKPGGKLLFVTC 86
FDRIL D PC+ +GV+RR+PDI WLRR DI L+ +IL+ LW +LKPGG LL+ TC
Sbjct: 314 FDRILLDAPCSATGVIRRHPDIKWLRRPEDIAALAALQSEILDALWPLLKPGGTLLYATC 373
Query: 87 SLWFEESEEQAIIFSKNHKDSIRL------NSPGQLLPTVNKKQDYDGFFYSLFQKR 137
S+ EE+E+Q F H D+ L QLLP +D DGFFY+L KR
Sbjct: 374 SILPEENEQQIKAFLARHPDAELLDTGTPQQPGRQLLPGE---EDGDGFFYALLIKR 427
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 115 bits (290), Expect = 5e-32
Identities = 51/130 (39%), Positives = 71/130 (54%), Gaps = 20/130 (15%)
Query: 26 YFDRILADLPCTGSGVVRRNPDIPWLRRKNDIKKLSKYSCKILNNLWKMLKPGGKLLFVT 85
FDRIL D PC+G+GV+RR+PD+ W R DI +L+K +IL K+LKPGG L++ T
Sbjct: 229 KFDRILLDAPCSGTGVIRRDPDVKWRRTPEDIAELAKLQKEILAAALKLLKPGGVLVYST 288
Query: 86 CSLWFEESEEQAIIFSKNHKD----SIRLNSPG-------------QLLPTVNKKQDYDG 128
CSL EE+EE F + H D +RL +L P V+ DG
Sbjct: 289 CSLTPEENEEVVERFLERHPDFELEPVRLPWGPLFEGLGSELGKTRRLYPHVHGT---DG 345
Query: 129 FFYSLFQKRK 138
FF + +K++
Sbjct: 346 FFIAKLRKKR 355
>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 = 101 bits (254), Expect = 2e-26
Identities = 49/123 (39%), Positives = 72/123 (58%), Gaps = 12/123 (9%)
Query: 24 NKYFDRILADLPCTGSGVVRRNPDIPWLRRKNDIKKLSKYSCKILNNLWKMLKPGGKLLF 83
N+ FDRIL D PC+ +GV+RR+PDI WLR+ DI +L++ +IL+ +W +LK GG L++
Sbjct: 307 NEQFDRILLDAPCSATGVIRRHPDIKWLRKPRDIAELAELQSEILDAIWPLLKTGGTLVY 366
Query: 84 VTCSLWFEESEEQAIIFSKNHKD-----SIRLNSPG----QLLPTVNKKQDYDGFFYSLF 134
TCS+ EE+ EQ F + H D + Q+LP + DGFFY+
Sbjct: 367 ATCSVLPEENSEQIKAFLQEHPDFPFEKTGTPEQVRDGGLQILPHAEEG---DGFFYAKL 423
Query: 135 QKR 137
K+
Sbjct: 424 IKK 426
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 99.1 bits (248), Expect = 2e-25
Identities = 45/129 (34%), Positives = 68/129 (52%), Gaps = 22/129 (17%)
Query: 27 FDRILADLPCTGSGVVRRNPDIPWLRRKNDIKKLSKYSCKILNNLWKMLKPGGKLLFVTC 86
FD+IL D PC+G GV+RR PDI + + K DI+ L + +IL ++ + LK GG L++ TC
Sbjct: 321 FDKILVDAPCSGLGVIRRKPDIKYNKTKEDIESLQEIQLEILESVAQYLKKGGILVYSTC 380
Query: 87 SLWFEESEEQAIIFSKNHKD-------------SIRLNSPG--QLLPTVNKKQDY--DGF 129
++ EE+EE F + H + + G Q+LP DY DGF
Sbjct: 381 TIEKEENEEVIEAFLEEHPEFELVPLQHEKPDELVYEVKDGYLQILP-----NDYGTDGF 435
Query: 130 FYSLFQKRK 138
F + +K+
Sbjct: 436 FIAKLRKKG 444
>gnl|CDD|201649 pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family.
Length = 277
Score = 89.8 bits (223), Expect = 1e-22
Identities = 46/123 (37%), Positives = 68/123 (55%), Gaps = 15/123 (12%)
Query: 27 FDRILADLPCTGSGVVRRNPDIPWLRRKNDIKKLSKYSCKILNNLWKMLKPGGKLLFVTC 86
FDRIL D PC+G+GV+RR+PDI WLRR+ DI +L++ ++L W ++KPGG L++ TC
Sbjct: 156 FDRILLDAPCSGTGVIRRDPDIKWLRREADIAQLAELQKELLKAAWDLVKPGGVLVYSTC 215
Query: 87 SLWFEESEEQAIIFSKNHKDSIRL------NSPGQLLPTVNK--KQDY------DGFFYS 132
S+ EE+E F + D + L L + K Q DGFF++
Sbjct: 216 SVLPEENEAVIKYFLQKRPD-VELVPTGLSEGKIALAKRIVKGGLQSLPHELNRDGFFFA 274
Query: 133 LFQ 135
+
Sbjct: 275 KLR 277
>gnl|CDD|237856 PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional.
Length = 434
Score = 85.0 bits (211), Expect = 3e-20
Identities = 45/114 (39%), Positives = 67/114 (58%), Gaps = 5/114 (4%)
Query: 26 YFDRILADLPCTGSGVVRRNPDIPWLRRKNDIKKLSKYSCKILNNLWKMLKPGGKLLFVT 85
YFDRIL D PC+G G + R+PD W + I++L+ ++L +L +LKPGG L++ T
Sbjct: 325 YFDRILLDAPCSGLGTLHRHPDARWRQTPEKIQELAPLQAELLESLAPLLKPGGTLVYAT 384
Query: 86 CSLWFEESEEQAIIFSKNHKDSIRLNSPGQ-LLPTVNKKQDYDGFFYSLFQKRK 138
C+L E+E Q F H D +L P Q + P +QD DGFF ++ +K+
Sbjct: 385 CTLHPAENEAQIEQFLARHPD-WKLEPPKQKIWP---HRQDGDGFFMAVLRKKS 434
>gnl|CDD|188051 TIGR00446, nop2p, NOL1/NOP2/sun family putative RNA methylase.
[Protein synthesis, tRNA and rRNA base modification].
Length = 264
Score = 76.0 bits (187), Expect = 1e-17
Identities = 40/133 (30%), Positives = 60/133 (45%), Gaps = 15/133 (11%)
Query: 18 RFRFYKNKYFDRILADLPCTGSGVVRRNPDIPWLRRKNDIKKLSKYSCKILNNLWKMLKP 77
+F Y K FD IL D PC+G GV+R++P + DIK S ++++ LKP
Sbjct: 133 KFGAYLLK-FDAILLDAPCSGEGVIRKDPSRKRNWSEEDIKYCSLLQKELIDAAIDALKP 191
Query: 78 GGKLLFVTCSLWFEESEEQAIIFSKNHKDSIRLNSPGQLLPTVNKKQDY----------- 126
GG L++ TCSL EE+EE + D + G +N +
Sbjct: 192 GGVLVYSTCSLEVEENEEVIDYILRKRPDVVEEIIKGDEFFGINIGKGEVKGALRVFPQN 251
Query: 127 ---DGFFYSLFQK 136
+GFF + +K
Sbjct: 252 YDCEGFFVAKLRK 264
>gnl|CDD|237858 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
Length = 445
Score = 76.3 bits (188), Expect = 3e-17
Identities = 36/114 (31%), Positives = 57/114 (50%)
Query: 20 RFYKNKYFDRILADLPCTGSGVVRRNPDIPWLRRKNDIKKLSKYSCKILNNLWKMLKPGG 79
F + D IL D PCTG+GV+ R ++ W + +L ++L++ +LKPGG
Sbjct: 312 SFSPEEQPDAILLDAPCTGTGVLGRRAELRWKLTPEKLAELVGLQAELLDHAASLLKPGG 371
Query: 80 KLLFVTCSLWFEESEEQAIIFSKNHKDSIRLNSPGQLLPTVNKKQDYDGFFYSL 133
L++ TCS+ EE+E Q F + H + SPG L ++ G +L
Sbjct: 372 VLVYATCSIEPEENELQIEAFLQRHPEFSAEPSPGSLPEPFHEVAHPKGAILTL 425
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 75.3 bits (185), Expect = 6e-17
Identities = 39/91 (42%), Positives = 52/91 (57%), Gaps = 4/91 (4%)
Query: 18 RFRFYKNKYFDRILADLPCTGSGVVRRNPDIPWLRR--KNDIKKLSKYSCKILNNLWKML 75
R Y FDRIL D PCT G R +P++ LRR K D KKLS+ +I++ WK+L
Sbjct: 299 RLTEYVQDTFDRILVDAPCTSLGTARNHPEV--LRRVNKEDFKKLSEIQLRIVSQAWKLL 356
Query: 76 KPGGKLLFVTCSLWFEESEEQAIIFSKNHKD 106
+ GG LL+ TC++ EE+ E F KD
Sbjct: 357 EKGGILLYSTCTVTKEENTEVVKRFVYEQKD 387
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 46.1 bits (110), Expect = 1e-06
Identities = 39/129 (30%), Positives = 59/129 (45%), Gaps = 23/129 (17%)
Query: 26 YFDRILADLPCTGSGVVRRNPDI--PW-LRRKNDIKKLSKYSCKILNNLWKMLKPGGKLL 82
FD IL D PC+G G VR++PD W +I + +++ + + LKPGG L+
Sbjct: 183 TFDAILLDAPCSGEGTVRKDPDALKNWSPESNLEIAATQR---ELIESAFHALKPGGTLV 239
Query: 83 FVTCSLWFEESEEQAIIFS--KNHKDSIRLNSPGQLLPTVNKK-----------QDYD-- 127
+ TC+L E QA+ + + D++ G L P K Q YD
Sbjct: 240 YSTCTL--NREENQAVCLWLKETYPDAVEFEPLGDLFPGAEKALTEEGFLHVFPQIYDSE 297
Query: 128 GFFYSLFQK 136
GFF + +K
Sbjct: 298 GFFVARLRK 306
>gnl|CDD|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 117
Score = 32.4 bits (74), Expect = 0.030
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 14/61 (22%)
Query: 27 FDRILADLPCTGSGVVRRNPDIPWLRRKNDIKKLSKYSCKILNNLWKMLKPGGKLLFVTC 86
FD +L NP P+ R D K + L ++LKPGG L+ +T
Sbjct: 71 FDLVLG------------NP--PYGPRAGDPKDNRDLYDRFLAAALRLLKPGGVLVVITP 116
Query: 87 S 87
+
Sbjct: 117 A 117
>gnl|CDD|221804 pfam12847, Methyltransf_18, Methyltransferase domain. Protein in
this family function as methyltransferases.
Length = 104
Score = 29.6 bits (67), Expect = 0.25
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 66 KILNNLWKMLKPGGKLLFVTC 86
++L+ L +LKPGG+L+
Sbjct: 84 ELLDALASLLKPGGRLVLNAV 104
>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 = 29.3 bits (66), Expect = 0.30
Identities = 13/66 (19%), Positives = 22/66 (33%), Gaps = 21/66 (31%)
Query: 19 FRFYKNKYFDRILADLPCTGSGVVRRNPDIPWLRRKNDIKKLSKYSCKILNNLWKMLKPG 78
++ FD I++D P D+ + L ++LKPG
Sbjct: 59 LPPEADESFDVIISDPPLHHLV-----EDLA----------------RFLEEARRLLKPG 97
Query: 79 GKLLFV 84
G L+
Sbjct: 98 GVLVLT 103
>gnl|CDD|129739 TIGR00654, PhzF_family, phenazine biosynthesis protein PhzF family.
Members of this family show a distant global similarity
to diaminopimelate epimerases, which can be taken as the
outgroup. One member of this family has been shown to
act as an enzyme in the biosynthesis of the antibiotic
phenazine in Pseudomonas aureofaciens. The function in
other species is unclear [Cellular processes, Toxin
production and resistance].
Length = 297
Score = 29.4 bits (66), Expect = 0.48
Identities = 10/65 (15%), Positives = 22/65 (33%), Gaps = 8/65 (12%)
Query: 75 LKPGGKLLFVTCSLWFEESEEQAIIFSKNHKDSIRLNSPGQLLPTVNKKQDYDGFFYSLF 134
G + ++ + +I K+ + + +L K+ D+ G F
Sbjct: 150 FIKGLPIQLLSTGPEW------IVIPLKDEEACFNASPNFAMLAHQLKQNDHVGVI--PF 201
Query: 135 QKRKE 139
+KE
Sbjct: 202 GPKKE 206
>gnl|CDD|222415 pfam13847, Methyltransf_31, Methyltransferase domain. This family
appears to be have methyltransferase activity.
Length = 151
Score = 28.9 bits (65), Expect = 0.49
Identities = 12/54 (22%), Positives = 19/54 (35%)
Query: 65 CKILNNLWKMLKPGGKLLFVTCSLWFEESEEQAIIFSKNHKDSIRLNSPGQLLP 118
K+L + ++LKPGG L+ L E + +LL
Sbjct: 92 DKVLEEIIRVLKPGGVLIVSDPVLLSELPALLEDLERLYAGVLEGAIGKKKLLT 145
>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 = 29.2 bits (66), Expect = 0.66
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 67 ILNNLWKMLKPGGKLLFVT 85
+ ++LKPGG L F T
Sbjct: 131 FIRACAQLLKPGGILFFST 149
>gnl|CDD|232819 TIGR00087, surE, 5'/3'-nucleotidase SurE. This protein family
originally was named SurE because of its role in
stationary phase survivalin Escherichia coli. In E.
coli, surE is next to pcm, an L-isoaspartyl protein
repair methyltransferase that is also required for
stationary phase survival. Recent work (PMID:15489502)
shows that viewing SurE as an acid phosphatase (3.1.3.2)
is not accurate. Rather, SurE in E. coli, Thermotoga
maritima, and Pyrobaculum aerophilum acts strictly on
nucleoside 5'- and 3'-monophosphates. E. coli SurE is
Recommended cutoffs are 15 for homology, 40 for probable
orthology, and 200 for orthology with full-length
homology [Cellular processes, Adaptations to atypical
conditions].
Length = 244
Score = 28.9 bits (65), Expect = 0.75
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 61 SKYSCKILNNLWKMLKPGGKLLFVTCSLW 89
+K + I+ NL K PGG LL V L
Sbjct: 146 AKVTNAIVKNLLKNGLPGGDLLNVNVPLV 174
>gnl|CDD|222171 pfam13489, Methyltransf_23, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 154
Score = 28.2 bits (63), Expect = 0.98
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 66 KILNNLWKMLKPGGKLLFVT 85
+L L ++LKPGG LL T
Sbjct: 92 ALLQQLRELLKPGGVLLIST 111
>gnl|CDD|216177 pfam00891, Methyltransf_2, O-methyltransferase. This family
includes a range of O-methyltransferases. These enzymes
utilise S-adenosyl methionine.
Length = 239
Score = 28.4 bits (64), Expect = 1.1
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 66 KILNNLWKMLKPGGKLLFVTCSL 88
KIL ++ L PGGK++ V L
Sbjct: 179 KILKRCYEALPPGGKVIVVEMVL 201
>gnl|CDD|224017 COG1092, COG1092, Predicted SAM-dependent methyltransferases
[General function prediction only].
Length = 393
Score = 28.4 bits (64), Expect = 1.3
Identities = 12/48 (25%), Positives = 19/48 (39%)
Query: 52 RRKNDIKKLSKYSCKILNNLWKMLKPGGKLLFVTCSLWFEESEEQAII 99
R K + + + ++L PGG L+ +CS F II
Sbjct: 303 RSKKQEFSAQRDYKDLNDLALRLLAPGGTLVTSSCSRHFSSDLFLEII 350
>gnl|CDD|223048 PHA03333, PHA03333, putative ATPase subunit of terminase;
Provisional.
Length = 752
Score = 28.2 bits (63), Expect = 1.7
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 4/45 (8%)
Query: 22 YKNKYFDRILADLPCTGSGVVRRNPDIPWLRRKNDIKKLSKYSCK 66
YK+K D + P VV NP+ P R +I ++ K
Sbjct: 147 YKHKLLDLLGLASP----DVVAFNPEAPSPRTLREIDRIFDEYGK 187
>gnl|CDD|219759 pfam08241, Methyltransf_11, Methyltransferase domain. Members of
this family are SAM dependent methyltransferases.
Length = 92
Score = 26.9 bits (60), Expect = 1.7
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 66 KILNNLWKMLKPGGKLLF 83
+ L + ++LKPGGKL+
Sbjct: 75 RALREIARVLKPGGKLVI 92
>gnl|CDD|219760 pfam08242, Methyltransf_12, Methyltransferase domain. Members of
this family are SAM dependent methyltransferases.
Length = 98
Score = 27.0 bits (60), Expect = 1.8
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 66 KILNNLWKMLKPGGKL 81
+L NL ++LKPGG L
Sbjct: 83 AVLRNLRRLLKPGGVL 98
>gnl|CDD|225137 COG2227, UbiG,
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol
methylase [Coenzyme metabolism].
Length = 243
Score = 27.7 bits (62), Expect = 2.2
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 67 ILNNLWKMLKPGGKLLFVT 85
L K++KPGG L T
Sbjct: 143 FLRACAKLVKPGGILFLST 161
>gnl|CDD|225151 COG2242, CobL, Precorrin-6B methylase 2 [Coenzyme metabolism].
Length = 187
Score = 26.8 bits (60), Expect = 3.0
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 66 KILNNLWKMLKPGGKLLFVTCSLWFEESEEQAI 98
+IL W+ LKPGG+L+ E+ +A+
Sbjct: 116 EILEAAWERLKPGGRLV-ANAIT--LETLAKAL 145
>gnl|CDD|225443 COG2890, HemK, Methylase of polypeptide chain release factors
[Translation, ribosomal structure and biogenesis].
Length = 280
Score = 27.3 bits (61), Expect = 3.1
Identities = 16/73 (21%), Positives = 25/73 (34%), Gaps = 14/73 (19%)
Query: 66 KILNNLWKMLKPGGKLLFVTCSLWFEESEEQAIIFSKNHKDSIRLNSPGQLLPTVNKKQD 125
+IL +LKPGG L+ L E+ + +F I V +D
Sbjct: 219 RILGEAPDILKPGGVLILE-IGLTQGEAVKA--LFEDTGFFEI-----------VETLKD 264
Query: 126 YDGFFYSLFQKRK 138
G + K +
Sbjct: 265 LFGRDRVVLAKLR 277
>gnl|CDD|115814 pfam07184, CTV_P33, Citrus tristeza virus P33 protein. This
family consists of several Citrus tristeza virus (CTV)
P33 proteins. The function of P33 is unclear although
it is known that the protein is not needed for virion
formation.
Length = 303
Score = 26.9 bits (59), Expect = 3.7
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 1 MIAGEIESSDINKKTNNRFRFYKNKYFDRILADLPC-TGSGVVRRNPDI 48
M A E+ DI ++ R R KYFD ++ D G +V R+P +
Sbjct: 1 MFAFASENQDILEEKIFRRRTCHRKYFDDVVRDFTIDIGYDIVDRDPTV 49
>gnl|CDD|180961 PRK07402, PRK07402, precorrin-6B methylase; Provisional.
Length = 196
Score = 26.9 bits (60), Expect = 3.8
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 67 ILNNLWKMLKPGGKLLFVTCSL 88
IL +W+ LKPGG+L+ SL
Sbjct: 124 ILQAVWQYLKPGGRLVATASSL 145
>gnl|CDD|234609 PRK00068, PRK00068, hypothetical protein; Validated.
Length = 970
Score = 26.9 bits (60), Expect = 4.3
Identities = 7/19 (36%), Positives = 9/19 (47%)
Query: 106 DSIRLNSPGQLLPTVNKKQ 124
+IRL P L P + Q
Sbjct: 367 SNIRLLDPTILSPFFTQVQ 385
>gnl|CDD|182918 PRK11036, PRK11036, putative S-adenosyl-L-methionine-dependent
methyltransferase; Provisional.
Length = 255
Score = 26.5 bits (59), Expect = 5.4
Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 5/24 (20%)
Query: 67 ILNNLWKMLKPGGKLLFVTCSLWF 90
+L LW +L+PGG L SL F
Sbjct: 131 VLQTLWSVLRPGGAL-----SLMF 149
>gnl|CDD|114142 pfam05401, NodS, Nodulation protein S (NodS). This family consists
of nodulation S (NodS) proteins. The products of the
rhizobial nodulation genes are involved in the
biosynthesis of lipochitin oligosaccharides (LCOs),
which are host-specific signal molecules required for
nodule formation. NodS is an S-adenosyl-L-methionine
(SAM)-dependent methyltransferase involved in N
methylation of LCOs. NodS uses N-deacetylated
chitooligosaccharides, the products of the NodBC
proteins, as its methyl acceptors.
Length = 201
Score = 26.3 bits (58), Expect = 5.6
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 5/27 (18%)
Query: 68 LNNLWKMLKPGGKLLF-----VTCSLW 89
+ NL ML P G+L+F C W
Sbjct: 129 VRNLVSMLAPDGQLVFGSARDANCRRW 155
>gnl|CDD|132737 cd06939, NR_LBD_ROR_like, The ligand binding domain of
Retinoid-related orphan receptors, of the nuclear
receptor superfamily. The ligand binding domain (LBD)
of Retinoid-related orphan receptors (RORs):
Retinoid-related orphan receptors (RORs) are
transcription factors belonging to the nuclear receptor
superfamily. RORs are key regulators of many
physiological processes during embryonic development.
RORs bind as monomers to specific ROR response elements
(ROREs) consisting of the consensus core motif AGGTCA
preceded by a 5-bp A/T-rich sequence. Transcription
regulation by RORs is mediated through certain
corepressors, as well as coactivators. There are three
subtypes of retinoid-related orphan receptors (RORs),
alpha, beta, and gamma that differ only in N-terminal
sequence and are distributed in distinct tissues.
RORalpha plays a key role in the development of the
cerebellum, particularly in the regulation of the
maturation and survival of Purkinje cells. RORbeta
expression is largely restricted to several regions of
the brain, the retina, and pineal gland. RORgamma is
essential for lymph node organogenesis. Recently, it has
been su ggested that cholesterol or a cholesterol
derivative is the natural ligand of RORalpha. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, retinoid-related
orphan receptors have a central well conserved DNA
binding domain (DBD), a variable N-terminal domain, a
non-conserved hinge and a C-terminal ligand binding
domain (LBD).
Length = 241
Score = 26.2 bits (58), Expect = 5.8
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 39 SGVVRRNPDIPWLRRKNDIKKLSKYSCKILNNLWKML 75
S +V + D P L+ K ++KL KI L +L
Sbjct: 154 SALVLISADRPGLQEKRKVEKL---QQKIELALRHVL 187
>gnl|CDD|165253 PHA02943, PHA02943, hypothetical protein; Provisional.
Length = 165
Score = 26.0 bits (57), Expect = 6.2
Identities = 8/37 (21%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 29 RILADLPCTGSGVVRRNPDIPWLRRKNDIKKLSKYSC 65
R+LAD C + + + +N + +L+K
Sbjct: 18 RLLAD-GCKTTSRIANKLGVSHSMARNALYQLAKEGM 53
>gnl|CDD|235350 PRK05134, PRK05134, bifunctional 3-demethylubiquinone-9
3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol
methylase; Provisional.
Length = 233
Score = 26.3 bits (59), Expect = 6.3
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 67 ILNNLWKMLKPGGKLLFVT 85
+ K++KPGG + F T
Sbjct: 133 FVRACAKLVKPGGLVFFST 151
>gnl|CDD|215386 PLN02727, PLN02727, NAD kinase.
Length = 986
Score = 26.4 bits (58), Expect = 6.8
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 106 DSIRLNSPGQLLPTVNKKQDYDGFFYSL 133
DS+R++ LPTVNK +F SL
Sbjct: 944 DSVRISMSQHPLPTVNKSDQTGDWFRSL 971
>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 = 25.9 bits (58), Expect = 8.1
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 66 KILNNLWKMLKPGGKLLF 83
+I+ ++LKPGG LL
Sbjct: 198 RIIAQAPRLLKPGGWLLL 215
>gnl|CDD|225661 COG3119, AslA, Arylsulfatase A and related enzymes [Inorganic ion
transport and metabolism].
Length = 475
Score = 25.9 bits (57), Expect = 9.1
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 33 DLPCTGSGVVRRNPDIPWL 51
DL G VV P+I L
Sbjct: 19 DLGAYGGPVVGPTPNIDRL 37
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
0.320 0.138 0.424
Gapped
Lambda K H
0.267 0.0668 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,288,501
Number of extensions: 644217
Number of successful extensions: 643
Number of sequences better than 10.0: 1
Number of HSP's gapped: 637
Number of HSP's successfully gapped: 49
Length of query: 139
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 52
Effective length of database: 7,078,804
Effective search space: 368097808
Effective search space used: 368097808
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 (21.8 bits)
S2: 54 (24.7 bits)