RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3767
(246 letters)
>gnl|CDD|234581 PRK00026, trmD, tRNA (guanine-N(1)-)-methyltransferase; Reviewed.
Length = 244
Score = 371 bits (956), Expect = e-132
Identities = 121/247 (48%), Positives = 171/247 (69%), Gaps = 5/247 (2%)
Query: 1 MQFDVITLFPEMFSAITQSGITRRAFEKKQYSLNLWNPRNFSSNNYRKIDDYPYGGGVGM 60
M+ DV+TLFPEMF + I RA EK L + NPR+F+++ +R +DD PYGGG GM
Sbjct: 1 MRIDVLTLFPEMFPGPLEYSILGRALEKGLLELEVHNPRDFTTDKHRTVDDTPYGGGAGM 60
Query: 61 IMLGKPIEDTITAIKKNIKKIPKIIYMSPQGKKLTHNIIIKLLKESNLILLCGRYQAIDQ 120
+M +P+ D I A K + K+I +SPQGK T +L KE +LILLCGRY+ ID+
Sbjct: 61 VMKPEPLFDAIDAAKAAAGEKAKVILLSPQGKPFTQADARELAKEEHLILLCGRYEGIDE 120
Query: 121 RFLDNFIDEEISVGDFILSGGELPAMMLIDAIVRLLPKVLNNKLN-MQDSFINGLLDCSY 179
R +++++DEEIS+GD++L+GGEL AM+LIDA+VRLLP VL N+ + +DSF +GLL+ +
Sbjct: 121 RVIEHYVDEEISIGDYVLTGGELAAMVLIDAVVRLLPGVLGNEESAEEDSFSDGLLEYPH 180
Query: 180 YTKPRIYLNMEVPIVLLSGNHKKIKKWKRKNSLKITNKKRPDLIIKARKNKFLTCTDEEF 239
YT+P + M+VP VLLSGNH KI +W+RK SL+ T +RPDL+ K LT D++
Sbjct: 181 YTRPAEFRGMKVPEVLLSGNHAKIARWRRKQSLERTKLRRPDLLEKLA----LTKEDKKL 236
Query: 240 LKKINKK 246
L ++ K+
Sbjct: 237 LAELKKE 243
>gnl|CDD|223413 COG0336, TrmD, tRNA-(guanine-N1)-methyltransferase [Translation,
ribosomal structure and biogenesis].
Length = 240
Score = 335 bits (862), Expect = e-118
Identities = 113/246 (45%), Positives = 172/246 (69%), Gaps = 8/246 (3%)
Query: 1 MQFDVITLFPEMFSAITQSGITRRAFEKKQYSLNLWNPRNFSSNNYRKIDDYPYGGGVGM 60
M+ D++TLFPEMF I RA EK SL + NPR+F+++ ++ +DD PYGGG GM
Sbjct: 1 MKIDILTLFPEMFDGYLGYSILGRAIEKGLLSLEVVNPRDFATDKHKTVDDTPYGGGAGM 60
Query: 61 IMLGKPIEDTITAIKKNIKKIPKIIYMSPQGKKLTHNIIIKLLKESNLILLCGRYQAIDQ 120
+M +P+ D + ++K K K+I +SPQGK T +L KE +L+L+CGRY+ ID+
Sbjct: 61 VMKPEPLFDALDSVKA--AKKAKVILLSPQGKPFTQARARELAKEEHLVLICGRYEGIDE 118
Query: 121 RFLDNFIDEEISVGDFILSGGELPAMMLIDAIVRLLPKVLNNKLNMQ-DSF-INGLLDCS 178
R ++ ++DEEIS+GD++L+GGEL AM+LIDA+VRL+P VL N+ +++ DSF NGLL+
Sbjct: 119 RVIELYVDEEISIGDYVLTGGELAAMVLIDAVVRLIPGVLGNEESLEEDSFENNGLLEYP 178
Query: 179 YYTKPRIYLNMEVPIVLLSGNHKKIKKWKRKNSLKITNKKRPDLIIKARKNKFLTCTDEE 238
+YT+PR + M+VP VLLSGNH KI +W+ + SL+ T ++RPDL+ + + +++
Sbjct: 179 HYTRPREFEGMKVPEVLLSGNHAKIAQWRLEQSLERTKERRPDLLEAHKLTE----EEKK 234
Query: 239 FLKKIN 244
LK+I+
Sbjct: 235 LLKEIH 240
>gnl|CDD|129196 TIGR00088, trmD, tRNA (guanine-N1)-methyltransferase. This model
is specfic for the tRNA modification enzyme tRNA
(guanine-N1)-methyltransferase (trmD). This enzyme
methylates guanosime-37 in a number of tRNAs.The
enzyme's catalytic activity is as follows:
S-adenosyl-L-methionine + tRNA =
S-adenosyl-L-homocysteine + tRNA containing
N1-methylguanine [Protein synthesis, tRNA and rRNA base
modification].
Length = 233
Score = 275 bits (704), Expect = 6e-94
Identities = 105/231 (45%), Positives = 153/231 (66%), Gaps = 4/231 (1%)
Query: 1 MQFDVITLFPEMFSAITQSGITRRAFEKKQYSLNLWNPRNFSSNNYRKIDDYPYGGGVGM 60
M+ V+TLFPEMF +S I RA +K S + NPR+FS + ++ +DD PYGGG GM
Sbjct: 1 MKIGVLTLFPEMFWPYLESSILGRAQKKNLVSFEVVNPRDFSKDKHKTVDDRPYGGGAGM 60
Query: 61 IMLGKPIEDTITAIKKNIKKIPKIIYMSPQGKKLTHNIIIKLLKESNLILLCGRYQAIDQ 120
++ +PI D + ++K +I +SPQG+K +L + +LIL+CGRY+ D+
Sbjct: 61 VLKPEPIRDALHSVK-APAG--TVILLSPQGRKFDQAGARELAQNEHLILICGRYEGFDE 117
Query: 121 RFLDNFIDEEISVGDFILSGGELPAMMLIDAIVRLLPKVLNNKLNM-QDSFINGLLDCSY 179
R + +DEEIS+GDF+L+GGELPA+ LID++VRL+P VL + ++ ++SF NGLLDC +
Sbjct: 118 RIIQLEVDEEISIGDFVLTGGELPALTLIDSVVRLIPGVLGKEASLIEESFANGLLDCPH 177
Query: 180 YTKPRIYLNMEVPIVLLSGNHKKIKKWKRKNSLKITNKKRPDLIIKARKNK 230
YT+P ++VP VLLSGNH KI++W+ K SL T +RPDL+ K
Sbjct: 178 YTRPYDLKGLKVPEVLLSGNHAKIEQWRLKQSLLRTKLRRPDLLKKYLALT 228
>gnl|CDD|234892 PRK01037, trmD, tRNA (guanine-N(1)-)-methyltransferase/unknown
domain fusion protein; Reviewed.
Length = 357
Score = 196 bits (501), Expect = 1e-61
Identities = 94/246 (38%), Positives = 157/246 (63%), Gaps = 9/246 (3%)
Query: 1 MQFDVITLFPEMFSAITQSGITRRAFEKKQYSLNLWNPRNFSSNNYRKIDDYPYGGGVGM 60
M+ D+++LFP+ F + Q+ I RA ++ S+ + R F ++++DD P+ G GM
Sbjct: 1 MEIDILSLFPDYFDSPLQASILGRAIKQGLLSVQSRDIREFGLGKWKQVDDAPFNGE-GM 59
Query: 61 IMLGKPIEDTITAIKKNIKKIPKIIYMSPQGKKLTHNIIIKLLKESNLILLCGRYQAIDQ 120
+++ +P+ I ++++ + K+IY+SPQG+ LT +L S+LILLCG Y+ ID+
Sbjct: 60 LLMAEPVVQAIRSVRR---EKSKVIYLSPQGQLLTAKKSRELASCSHLILLCGHYEGIDE 116
Query: 121 RFLDNFIDEEISVGDFILSGGELPAMMLIDAIVRLLPKVLNNKLNMQ-DSFINGLLDCSY 179
R L++ +DEEIS+GD++L+ G + A++LIDA+ R +P VL N+ + + DS NGLL+
Sbjct: 117 RALESEVDEEISIGDYVLTNGGIAALVLIDALSRFIPGVLGNQESAEYDSLENGLLEGPQ 176
Query: 180 YTKPRIYLNMEVPIVLLSGNHKKIKKWKRKNSLKITNKKRPDLIIK---ARKNKFLTCTD 236
YT+PR++ EVP VLL G+H+ I W+++ SL+ T ++RPDL ++ R L T
Sbjct: 177 YTRPRVFEGKEVPEVLLQGDHQAIADWRKQVSLERTRERRPDLYLQYLYGRSADCLF-TQ 235
Query: 237 EEFLKK 242
E+ K
Sbjct: 236 EDLPKI 241
>gnl|CDD|173063 PRK14599, trmD, tRNA (guanine-N(1)-)-methyltransferase/unknown
domain fusion protein; Provisional.
Length = 222
Score = 146 bits (369), Expect = 2e-43
Identities = 73/217 (33%), Positives = 120/217 (55%), Gaps = 6/217 (2%)
Query: 1 MQFDVITLFPEMFSAITQSGITRRAFEKKQYSLNLWNPRNFSSNNYRKIDDYPYGGGVGM 60
M+F+ ITLFPE + G+ ++A E +S+N R+FS N + ++DD YGGG GM
Sbjct: 1 MKFNFITLFPEKIQSYFSEGLQQKAIESGVFSINPIQLRDFSGNKHNRVDDTIYGGGPGM 60
Query: 61 IMLGKPIEDTITAIKKNIKKIPKIIYMSPQGKKLTHNIIIKLLKESN-LILLCGRYQAID 119
++ +PI + ++ + +I SP G I +L + L + G Y+ +D
Sbjct: 61 LLRVEPIHKALLSLGEKKG---IVILTSPSGIPFNQTIARELKESGKPLTFISGYYEGVD 117
Query: 120 QRFLDNFIDEEISVGDFILSGGELPAMMLIDAIVRLLPKVLNNKLNMQDSFIN--GLLDC 177
R ++ +D E+S+G++++S G+L ++ + DA+ RLLP L + ++ D N L+
Sbjct: 118 HRVTEHLVDMEMSLGNYVISAGDLASICIADAVSRLLPGFLGAEESLLDESHNEPDELEY 177
Query: 178 SYYTKPRIYLNMEVPIVLLSGNHKKIKKWKRKNSLKI 214
+TKP Y +VP VLLSGNH I W+ +N KI
Sbjct: 178 PQFTKPSEYNGWKVPDVLLSGNHASILAWREQNRKKI 214
>gnl|CDD|216676 pfam01746, tRNA_m1G_MT, tRNA (Guanine-1)-methyltransferase. This
is a family of tRNA (Guanine-1)-methyltransferases
EC:2.1.1.31. In E.coli K12 this enzyme catalyzes the
conversion of a guanosine residue to N1-methylguanine in
position 37, next to the anticodon, in tRNA.
Length = 185
Score = 127 bits (320), Expect = 2e-36
Identities = 67/197 (34%), Positives = 101/197 (51%), Gaps = 14/197 (7%)
Query: 24 RAFEKKQYSLNLWNPRNFSSNNYRKIDDYPYGGGVGMIMLGKPIEDTITAIKKNIKKIPK 83
EK+ SL L R++++N +DD+ YGGG GM++ +P + +
Sbjct: 3 LMIEKELVSLELQILRDYTANRRATVDDHLYGGGFGMVLKPEPDLE-----ALKSVSGWE 57
Query: 84 IIYMSPQGKKLTHNIIIKLLKESNLILLCGRYQAIDQRFLDNFIDEEISVGDFILSGGEL 143
+I ++P G + + +L K+ +L+ L G Y+ + +R D E +G + GGE
Sbjct: 58 VILLTPTGIPFSQELASELFKKEHLVYLTGDYEGVLERLDD--DKAEYIIGGIVDKGGEK 115
Query: 144 PAMMLIDAIVRLLPKVLNNKLNMQDSFINGLLDCSYYTKPRIYLNMEVPIVLLSGNHKKI 203
A+ LIDA+V LLP VLN DSF LL YT+P +VP +LLSGNH KI
Sbjct: 116 GALTLIDAVVALLPGVLNTASLPLDSF---LLGVPNYTRPLTLN--QVPEILLSGNHAKI 170
Query: 204 KKWKRKNSLKITNKKRP 220
+ W + +L T KR
Sbjct: 171 RNW--EEALLRTIPKRK 185
>gnl|CDD|200562 cd10936, CE4_DAC2, Putative catalytic domain of family 2
polysaccharide deacetylases (DACs) from bacteria. This
family contains an uncharacterized protein BH1492 from
Bacillus halodurans, an uncharacterized protein ATU2773
from Agrobacterium tumefaciens C58, and other bacterial
hypothetical proteins. Although their functions are
still unknown, structural superposition and sequence
comparison suggest that BH1492 and ATU2773 might be
divergently related to the 7-stranded barrel catalytic
domain of polysaccharide deacetylases (DACs) from the
carbohydrate esterase 4 (CE4) superfamily, which remove
N-linked acetyl groups from cell wall polysaccharides.
This family is designated as DAC family 2, a divergent
DAC family.
Length = 215
Score = 31.8 bits (73), Expect = 0.24
Identities = 12/67 (17%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 51 DYPYGGGVGMIMLGKPIEDTITAIKKNIKKIPKIIYMS-PQGKKLTHN-----IIIKLLK 104
YP G ++ G E+ ++ + ++P + ++ G + T + +++ LK
Sbjct: 61 GYPKNDPPGALLTGMSAEEIEKRLEAALARVPGAVGVNNHMGSRFTADREAMRQVLEALK 120
Query: 105 ESNLILL 111
E L +
Sbjct: 121 ERGLFFV 127
>gnl|CDD|223582 COG0508, AceF, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide acyltransferase (E2) component, and
related enzymes [Energy production and conversion].
Length = 404
Score = 30.1 bits (68), Expect = 1.1
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 178 SYYTKPRIYLNMEVPIVLLSGNHKKIKKWKRKNSLKITNKKRPDLIIKA 226
S T P + L EV + L KK+K+ K +K+T ++KA
Sbjct: 194 SKQTIPHLTLFNEVDMTKLMALRKKLKEEFEKKGVKLTFL---SFLVKA 239
>gnl|CDD|222983 PHA03098, PHA03098, kelch-like protein; Provisional.
Length = 534
Score = 29.4 bits (66), Expect = 1.9
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 4/41 (9%)
Query: 69 DTITAIKKNIKKIPKIIYMSPQGKKLTHNIIIKLLKESNLI 109
I+ NI+ +IY P L+ N +IK+L + L
Sbjct: 128 AAYNYIRNNIE----LIYNDPDFIYLSKNELIKILSDDKLN 164
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 28.8 bits (65), Expect = 3.1
Identities = 17/80 (21%), Positives = 37/80 (46%), Gaps = 3/80 (3%)
Query: 67 IEDTITAIKKNIKKIP-KIIYMSPQGKKLTHNIIIKLLKESNLIL--LCGRYQAIDQRFL 123
+E+ + IKK +KK+P K P K+ +++ ++ + L L + + +
Sbjct: 346 LEEELEKIKKLLKKLPKKARGQLPPEKREQLEKLLETKEKLSEELEELEEELKELKEELE 405
Query: 124 DNFIDEEISVGDFILSGGEL 143
+ + +ISV I G ++
Sbjct: 406 SLYSEGKISVNKTIYPGVKI 425
>gnl|CDD|217628 pfam03587, EMG1, EMG1/NEP1 methyltransferase. Members of this
family are essential for 40S ribosomal biogenesis. The
structure of EMG1 has revealed that it is a novel member
of the superfamily of alpha/beta knot fold
methyltransferases.
Length = 200
Score = 27.9 bits (63), Expect = 3.7
Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 7/85 (8%)
Query: 58 VGMIMLGKPIEDTITAIKKNIKKIPKIIYMSPQGKKLTHNIIIKLLKESNLILLCG---R 114
G L K +++ +T + + + K I +S +G+K++ ++ L + + G
Sbjct: 107 EGGEPLLKVVKNPLTDL---LPEGAKKILLSEKGEKVSPKELVSELLNKPVAFVIGAFPH 163
Query: 115 YQAIDQRFLDNFIDEEISVGDFILS 139
D+ DE S+ ++ LS
Sbjct: 164 GDFSDEVDYKKA-DESYSISNYPLS 187
>gnl|CDD|216835 pfam01994, Trm56, tRNA ribose 2'-O-methyltransferase, aTrm56.
This family is an aTrm56 that catalyzes the
2'-O-methylation of the cytidine residue in archaeal
tRNA, using S-adenosyl-L-methionine. Biochemical assays
showed that aTrm56 forms a dimer and prefers the
L-shaped tRNA to the lambda form as its substrate.
aTrm56 consists of the SPOUT domain, which contains the
characteristic deep trefoil knot for AdoMet binding,
and a unique C-terminal beta-hairpin.
Length = 121
Score = 27.1 bits (61), Expect = 3.8
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 45 NYRK-IDDYPYGGG--VGMIMLGKPIEDTITAIKKNIKKI 81
N+R I ++ GG V + M G+ I+D I I+++ K I
Sbjct: 12 NWRSYIREWKEKGGIVVHLTMYGENIDDVIPEIRESGKDI 51
>gnl|CDD|216571 pfam01558, POR, Pyruvate ferredoxin/flavodoxin oxidoreductase.
This family includes a region of the large protein
pyruvate-flavodoxin oxidoreductase and the whole
pyruvate ferredoxin oxidoreductase gamma subunit
protein. It is not known whether the gamma subunit has a
catalytic or regulatory role. Pyruvate oxidoreductase
(POR) catalyzes the final step in the fermentation of
carbohydrates in anaerobic microorganisms. This involves
the oxidative decarboxylation of pyruvate with the
participation of thiamine followed by the transfer of an
acetyl moiety to coenzyme A for the synthesis of
acetyl-CoA. The family also includes pyruvate flavodoxin
oxidoreductase as encoded by the nifJ gene in
cyanobacterium which is required for growth on molecular
nitrogen when iron is limited.
Length = 129
Score = 26.8 bits (60), Expect = 6.2
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 7/35 (20%)
Query: 58 VGMIMLGK-------PIEDTITAIKKNIKKIPKII 85
+MLG P+E AI++ K K+I
Sbjct: 85 ANTVMLGALAALLGLPLEALEEAIREQFGKKEKVI 119
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 27.3 bits (61), Expect = 8.9
Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 3/70 (4%)
Query: 179 YYTKPRIYL--NMEVPIVLLSGNHKKIKKWKRKNSLKITNKKRPDLIIKARKNKFLTCTD 236
Y K + YL +E + LS N + K L ITN K+ DL+ + +K ++ D
Sbjct: 992 LYKKRKEYLLGKLERELARLS-NKVRFIKHVINGELVITNAKKKDLVKELKKLGYVRFKD 1050
Query: 237 EEFLKKINKK 246
K
Sbjct: 1051 IIKKKSEKIT 1060
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
0.322 0.140 0.407
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: 13,097,856
Number of extensions: 1305750
Number of successful extensions: 1360
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1345
Number of HSP's successfully gapped: 38
Length of query: 246
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 152
Effective length of database: 6,768,326
Effective search space: 1028785552
Effective search space used: 1028785552
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: 58 (26.1 bits)