RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 011036
(495 letters)
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 105 bits (265), Expect = 3e-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 = 95.5 bits (238), Expect = 1e-21
Identities = 33/103 (32%), Positives = 52/103 (50%), Gaps = 2/103 (1%)
Query: 395 RKNMRRMRNGPGRNQCLGGRAENSKGFSPNSFDRVLLDAPCSALGLRPRLFAA--EETIQ 452
R+N++R+ R FDR+LLDAPCS G+ R T +
Sbjct: 199 RENLKRLGVRNVIVVNKDARRLAELLPGGEKFDRILLDAPCSGTGVIRRDPDVKWRRTPE 258
Query: 453 SLRNHGKYQRRMFDQAVQLVRPGGIIVYSTCTINPGENEALCA 495
+ K Q+ + A++L++PGG++VYSTC++ P ENE +
Sbjct: 259 DIAELAKLQKEILAAALKLLKPGGVLVYSTCSLTPEENEEVVE 301
Score = 38.1 bits (89), Expect = 0.007
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 = 105 bits (265), 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 = 84.8 bits (211), Expect = 1e-17
Identities = 30/73 (41%), Positives = 45/73 (61%), Gaps = 8/73 (10%)
Query: 424 NSFDRVLLDAPCSALGL---RP--RLFAAEETIQSLRNHGKYQRRMFDQAVQLVRPGGII 478
FD++L+DAPCS LG+ +P + +E I+SL+ + Q + + Q ++ GGI+
Sbjct: 319 EKFDKILVDAPCSGLGVIRRKPDIKYNKTKEDIESLQ---EIQLEILESVAQYLKKGGIL 375
Query: 479 VYSTCTINPGENE 491
VYSTCTI ENE
Sbjct: 376 VYSTCTIEKEENE 388
Score = 42.9 bits (102), 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 = 3e-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
Score = 85.4 bits (212), Expect = 8e-18
Identities = 36/95 (37%), Positives = 47/95 (49%), Gaps = 15/95 (15%)
Query: 409 QCLGGRAENSKGFSP---NSFDRVLLDAPCSALG-------LRPRLFAAEETIQSLRNHG 458
+ L + N P FDR+LLDAPCS LG R R E IQ L
Sbjct: 306 KILAADSRNLLELKPQWRGYFDRILLDAPCSGLGTLHRHPDARWRQ--TPEKIQEL---A 360
Query: 459 KYQRRMFDQAVQLVRPGGIIVYSTCTINPGENEAL 493
Q + + L++PGG +VY+TCT++P ENEA
Sbjct: 361 PLQAELLESLAPLLKPGGTLVYATCTLHPAENEAQ 395
>gnl|CDD|237858 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
Length = 445
Score = 88.6 bits (220), Expect = 6e-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
Score = 69.3 bits (170), Expect = 1e-12
Identities = 32/86 (37%), Positives = 46/86 (53%), Gaps = 13/86 (15%)
Query: 414 RAENSKGFSPN-SFDRVLLDAPCSALG-------LRPRLFAAEETIQSLRNHGKYQRRMF 465
+++ FSP D +LLDAPC+ G LR +L E + L Q +
Sbjct: 306 IEGDARSFSPEEQPDAILLDAPCTGTGVLGRRAELRWKL--TPEKLAELVG---LQAELL 360
Query: 466 DQAVQLVRPGGIIVYSTCTINPGENE 491
D A L++PGG++VY+TC+I P ENE
Sbjct: 361 DHAASLLKPGGVLVYATCSIEPEENE 386
>gnl|CDD|188051 TIGR00446, nop2p, NOL1/NOP2/sun family putative RNA methylase.
[Protein synthesis, tRNA and rRNA base modification].
Length = 264
Score = 71.7 bits (176), Expect = 5e-14
Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 10/77 (12%)
Query: 424 NSFDRVLLDAPCSALGL------RPRLFAAEETIQSLRNHGKYQRRMFDQAVQLVRPGGI 477
FD +LLDAPCS G+ R R ++ E+ Q+ + D A+ ++PGG+
Sbjct: 139 LKFDAILLDAPCSGEGVIRKDPSRKRNWSEEDIKYC----SLLQKELIDAAIDALKPGGV 194
Query: 478 IVYSTCTINPGENEALC 494
+VYSTC++ ENE +
Sbjct: 195 LVYSTCSLEVEENEEVI 211
Score = 70.2 bits (172), Expect = 2e-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
>gnl|CDD|201649 pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family.
Length = 277
Score = 68.6 bits (168), Expect = 6e-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
Score = 60.5 bits (147), Expect = 4e-10
Identities = 32/76 (42%), Positives = 43/76 (56%), Gaps = 8/76 (10%)
Query: 422 SPNSFDRVLLDAPCSALGL---RP--RLFAAEETIQSLRNHGKYQRRMFDQAVQLVRPGG 476
FDR+LLDAPCS G+ P + E I L + Q+ + A LV+PGG
Sbjct: 152 LGGEFDRILLDAPCSGTGVIRRDPDIKWLRREADIAQL---AELQKELLKAAWDLVKPGG 208
Query: 477 IIVYSTCTINPGENEA 492
++VYSTC++ P ENEA
Sbjct: 209 VLVYSTCSVLPEENEA 224
Score = 32.7 bits (75), Expect = 0.30
Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 5/70 (7%)
Query: 429 VLLDAPCSALG-LRPRLFAA--EETIQSLRNHGKYQRRMFDQAVQLVRPGGIIVYSTCTI 485
+L CS G LR + +Q+L G Q + + P G + YS ++
Sbjct: 1 ILEANNCSPPGTLRKNVLKTKRWSLLQALELAG-VQLEPLGRYPHAL-PVGDLPYSIGSL 58
Query: 486 NPGENEALCA 495
P EN A+
Sbjct: 59 PPFENGAVTV 68
>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 = 2e-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
Score = 62.6 bits (152), Expect = 2e-10
Identities = 27/72 (37%), Positives = 38/72 (52%), Gaps = 8/72 (11%)
Query: 426 FDRVLLDAPCSALGL---RP--RLFAAEETIQSLRNHGKYQRRMFDQAVQLVRPGGIIVY 480
FDR+LLDAPCSA G+ P + I L + Q + D L++ GG +VY
Sbjct: 310 FDRILLDAPCSATGVIRRHPDIKWLRKPRDIAEL---AELQSEILDAIWPLLKTGGTLVY 366
Query: 481 STCTINPGENEA 492
+TC++ P EN
Sbjct: 367 ATCSVLPEENSE 378
>gnl|CDD|236790 PRK10901, PRK10901, 16S rRNA methyltransferase B; Provisional.
Length = 427
Score = 67.1 bits (165), Expect = 5e-12
Identities = 32/77 (41%), Positives = 41/77 (53%), Gaps = 18/77 (23%)
Query: 426 FDRVLLDAPCSALG----------LRPRLFAAEETIQSLRNHGKYQRRMFDQAVQLVRPG 475
FDR+LLDAPCSA G LR R E I +L Q + D L++PG
Sbjct: 314 FDRILLDAPCSATGVIRRHPDIKWLR-R----PEDIAAL---AALQSEILDALWPLLKPG 365
Query: 476 GIIVYSTCTINPGENEA 492
G ++Y+TC+I P ENE
Sbjct: 366 GTLLYATCSILPEENEQ 382
Score = 61.4 bits (150), Expect = 4e-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 = 64.9 bits (159), Expect = 4e-11
Identities = 31/84 (36%), Positives = 45/84 (53%), Gaps = 22/84 (26%)
Query: 423 PNSFDRVLLDAPCSALGLRPRLFAAEETIQ----SLRNH--------GKYQRRMFDQAVQ 470
P +FD +LLDAPCS E T++ +L+N QR + + A
Sbjct: 181 PETFDAILLDAPCSG----------EGTVRKDPDALKNWSPESNLEIAATQRELIESAFH 230
Query: 471 LVRPGGIIVYSTCTINPGENEALC 494
++PGG +VYSTCT+N EN+A+C
Sbjct: 231 ALKPGGTLVYSTCTLNREENQAVC 254
Score = 48.8 bits (117), Expect = 4e-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 = 5.2
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|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 64.1 bits (156), Expect = 6e-11
Identities = 32/100 (32%), Positives = 54/100 (54%), Gaps = 10/100 (10%)
Query: 396 KNMRRMRNGPGRNQCLGGRAENSKGFSPNSFDRVLLDAPCSALGL---RPRLF--AAEET 450
K+ +R++ + AE + ++FDR+L+DAPC++LG P + +E
Sbjct: 280 KHAKRLKLSSIEIKIAD--AERLTEYVQDTFDRILVDAPCTSLGTARNHPEVLRRVNKED 337
Query: 451 IQSLRNHGKYQRRMFDQAVQLVRPGGIIVYSTCTINPGEN 490
+ L + Q R+ QA +L+ GGI++YSTCT+ EN
Sbjct: 338 FKKL---SEIQLRIVSQAWKLLEKGGILLYSTCTVTKEEN 374
Score = 63.7 bits (155), Expect = 7e-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|179806 PRK04270, PRK04270, H/ACA RNA-protein complex component Cbf5p;
Reviewed.
Length = 300
Score = 48.7 bits (117), 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 = 42.8 bits (101), Expect = 7e-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 = 40.2 bits (95), 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|214635 smart00359, PUA, Putative RNA-binding Domain in PseudoUridine
synthase and Archaeosine transglycosylase.
Length = 76
Score = 38.0 bits (89), Expect = 6e-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|181382 PRK08317, PRK08317, hypothetical protein; Provisional.
Length = 241
Score = 41.1 bits (97), Expect = 7e-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|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 117
Score = 38.2 bits (89), Expect = 0.002
Identities = 24/102 (23%), Positives = 39/102 (38%), Gaps = 13/102 (12%)
Query: 383 GVERTYVSKADTRKNMRRMRNGPGRNQCLGGRAENSKGFSPNSFDRVLLDAPCSALGLRP 442
GVE + A R+ + P R + + G A SFD VL + P P
Sbjct: 29 GVELDPEAAALARRRLALAGLAP-RVRVVVGDARELLELPDGSFDLVLGNPPYGPRAGDP 87
Query: 443 RLFAAEETIQSLRNHGKYQRRMFDQAVQLVRPGGIIVYSTCT 484
+ ++ R A++L++PGG++V T
Sbjct: 88 K------------DNRDLYDRFLAAALRLLKPGGVLVVITPA 117
>gnl|CDD|223370 COG0293, FtsJ, 23S rRNA methylase [Translation, ribosomal structure
and biogenesis].
Length = 205
Score = 38.4 bits (90), Expect = 0.004
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 = 0.015
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 260 QKGERILDMCAAPGGKTTAIASLLRDEGEVVAVD 293
+ G+ +LD+ AAPGG + + +G V+AVD
Sbjct: 31 KPGDTVLDLGAAPGGWSQVAVEQVGGKGRVIAVD 64
>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 = 34.7 bits (80), Expect = 0.018
Identities = 18/88 (20%), Positives = 32/88 (36%), Gaps = 21/88 (23%)
Query: 396 KNMRRMRNGPGRNQC--LGGRAENSKGFSPNSFDRVLLDAPCSALGLRPRLFAAEETIQS 453
+ R+ + L G AE + SFD ++ D P L
Sbjct: 35 ELARKAAAALLADNVEVLKGDAEELPPEADESFDVIISDPPLHHLVED------------ 82
Query: 454 LRNHGKYQRRMFDQAVQLVRPGGIIVYS 481
R ++A +L++PGG++V +
Sbjct: 83 -------LARFLEEARRLLKPGGVLVLT 103
Score = 32.4 bits (74), Expect = 0.14
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|224927 COG2016, COG2016, Predicted RNA-binding protein (contains PUA
domain) [Translation, ribosomal structure and
biogenesis].
Length = 161
Score = 35.7 bits (83), Expect = 0.022
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|224017 COG1092, COG1092, Predicted SAM-dependent methyltransferases
[General function prediction only].
Length = 393
Score = 36.1 bits (84), Expect = 0.032
Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 11/59 (18%)
Query: 426 FDRVLLDAPCSALGLRPRLFAAEETIQSLRNHGKYQRRMFDQAVQLVRPGGIIVYSTCT 484
FD ++LD P + + + + R++ + D A++L+ PGG +V S+C+
Sbjct: 291 FDLIILDPP--SFARSKK-----QEFSAQRDYKD----LNDLALRLLAPGGTLVTSSCS 338
>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 = 35.1 bits (81), Expect = 0.072
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|237510 PRK13795, PRK13795, hypothetical protein; Provisional.
Length = 636
Score = 35.4 bits (82), Expect = 0.084
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|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 = 33.7 bits (78), 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 = 0.18
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|234689 PRK00216, ubiE, ubiquinone/menaquinone biosynthesis
methyltransferase; Reviewed.
Length = 239
Score = 32.8 bits (76), Expect = 0.34
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|183245 PRK11630, PRK11630, hypothetical protein; Provisional.
Length = 206
Score = 32.2 bits (73), Expect = 0.39
Identities = 13/22 (59%), Positives = 19/22 (86%)
Query: 461 QRRMFDQAVQLVRPGGIIVYST 482
Q+R+ +QAV++VR GG+IVY T
Sbjct: 13 QQRLINQAVEIVRKGGVIVYPT 34
>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 = 31.1 bits (71), Expect = 0.48
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 = 31.4 bits (72), Expect = 0.54
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 = 31.9 bits (73), Expect = 0.68
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|220999 pfam11144, DUF2920, Protein of unknown function (DUF2920). This
bacterial family of proteins has no known function.
Length = 403
Score = 31.9 bits (73), Expect = 0.75
Identities = 15/87 (17%), Positives = 38/87 (43%), Gaps = 12/87 (13%)
Query: 410 CLGGRAENSKGFSPNSFDRVLLDAPCSALGLRPRLFAAEETIQSLRNHGKYQRRMFDQAV 469
C+G R + F + D+ +L+ A+ + + I + N + + ++ +
Sbjct: 75 CIGNRPQYGAKFYLDDEDKEILEKSLKAINI------DIKPINTYDNAEEIFEYL-NKKI 127
Query: 470 QLVRPGGIIVYS-----TCTINPGENE 491
+ ++ GI+ + + T+ P +NE
Sbjct: 128 KELKQAGILDENYKLNLSVTLIPPKNE 154
>gnl|CDD|221804 pfam12847, Methyltransf_18, Methyltransferase domain. Protein in
this family function as methyltransferases.
Length = 104
Score = 29.6 bits (67), Expect = 1.0
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|226608 COG4123, COG4123, Predicted O-methyltransferase [General function
prediction only].
Length = 248
Score = 31.1 bits (71), Expect = 1.1
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 = 1.3
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|223574 COG0500, SmtA, SAM-dependent methyltransferases [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 257
Score = 31.0 bits (67), Expect = 1.4
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|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 = 30.9 bits (71), 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|225316 COG2518, Pcm, Protein-L-isoaspartate carboxylmethyltransferase
[Posttranslational modification, protein turnover,
chaperones].
Length = 209
Score = 30.7 bits (70), Expect = 1.4
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|187782 cd09651, Cas5_I-C, CRISPR/Cas system-associated RAMP superfamily
protein Cas5. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas5 is a RAMP superfamily protein; Subunit of the
Cascade complex; in subtype I-C this protein might be
the endoribonuclease that generates crRNAs; also known
as DevS family.
Length = 198
Score = 30.3 bits (69), Expect = 1.5
Identities = 11/31 (35%), Positives = 12/31 (38%), Gaps = 2/31 (6%)
Query: 398 MRRMRNGPGRNQ-CLGGRAENSKGFSPNSFD 427
RR R G + LG R E F P F
Sbjct: 124 ARRARKGQCFHDPYLGTR-EFPAYFEPCDFG 153
>gnl|CDD|187534 cd09752, Cas5_I-C, CRISPR/Cas system-associated RAMP superfamily
protein Cas5. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas5 is a RAMP superfamily protein; Subunit of the
Cascade complex; in subtype I-C this protein might be
the endoribonuclease that generates crRNAs; also known
as DevS family.
Length = 198
Score = 30.3 bits (69), Expect = 1.5
Identities = 11/31 (35%), Positives = 12/31 (38%), Gaps = 2/31 (6%)
Query: 398 MRRMRNGPGRNQ-CLGGRAENSKGFSPNSFD 427
RR R G + LG R E F P F
Sbjct: 124 ARRARKGQCFHDPYLGTR-EFPAYFEPCDFG 153
>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 = 30.7 bits (70), Expect = 1.5
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|227595 COG5270, COG5270, PUA domain (predicted RNA-binding domain)
[Translation, ribosomal structure and biogenesis].
Length = 202
Score = 30.5 bits (69), Expect = 1.5
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|225136 COG2226, UbiE, Methylase involved in ubiquinone/menaquinone
biosynthesis [Coenzyme metabolism].
Length = 238
Score = 30.7 bits (70), Expect = 1.6
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|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 = 29.9 bits (68), Expect = 1.7
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|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 = 1.8
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 = 28.8 bits (65), Expect = 1.8
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|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 30.6 bits (70), Expect = 2.0
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|225319 COG2521, COG2521, Predicted archaeal methyltransferase [General
function prediction only].
Length = 287
Score = 30.5 bits (69), Expect = 2.0
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|222019 pfam13276, HTH_21, HTH-like domain. This domain contains a
predicted helix-turn-helix suggesting a DNA-binding
function.
Length = 60
Score = 27.9 bits (63), Expect = 2.1
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|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 = 28.9 bits (65), Expect = 2.1
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|183025 PRK11188, rrmJ, 23S rRNA methyltransferase J; Provisional.
Length = 209
Score = 29.7 bits (67), Expect = 2.6
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|178645 PLN03097, FHY3, Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional.
Length = 846
Score = 30.3 bits (68), Expect = 3.0
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|177877 PLN02233, PLN02233, ubiquinone biosynthesis methyltransferase.
Length = 261
Score = 29.9 bits (67), Expect = 3.0
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|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 = 3.1
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|223434 COG0357, GidB, Predicted S-adenosylmethionine-dependent
methyltransferase involved in bacterial cell division
[Cell envelope biogenesis, outer membrane].
Length = 215
Score = 29.6 bits (67), Expect = 3.2
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|176181 cd05278, FDH_like, Formaldehyde dehydrogenases. Formaldehyde
dehydrogenase (FDH) is a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. Formaldehyde dehydrogenase (aka ADH3) may be
the ancestral form of alcohol dehydrogenase, which
evolved to detoxify formaldehyde. This CD contains
glutathione dependant FDH, glutathione independent FDH,
and related alcohol dehydrogenases. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. Unlike typical FDH, Pseudomonas
putida aldehyde-dismutating FDH (PFDH) is
glutathione-independent. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 347
Score = 29.9 bits (68), Expect = 3.3
Identities = 10/14 (71%), Positives = 13/14 (92%)
Query: 465 FDQAVQLVRPGGII 478
F+QAV++VRPGG I
Sbjct: 250 FEQAVKVVRPGGTI 263
>gnl|CDD|232802 TIGR00057, TIGR00057, tRNA threonylcarbamoyl adenosine modification
protein, Sua5/YciO/YrdC/YwlC family. Has paralogs, but
YrdC called a tRNA modification protein. Ref 2 authors
say probably heteromultimeric complex. Paralogs may mean
its does the final binding to the tRNA [Protein
synthesis, tRNA and rRNA base modification].
Length = 201
Score = 29.2 bits (66), Expect = 3.4
Identities = 12/25 (48%), Positives = 19/25 (76%)
Query: 461 QRRMFDQAVQLVRPGGIIVYSTCTI 485
+R +QAV+++R GGI+VY T T+
Sbjct: 7 SQRGIEQAVKILRKGGIVVYPTDTV 31
>gnl|CDD|219763 pfam08245, Mur_ligase_M, Mur ligase middle domain.
Length = 178
Score = 28.8 bits (65), Expect = 4.1
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|237757 PRK14560, PRK14560, putative RNA-binding protein; Provisional.
Length = 160
Score = 28.7 bits (65), Expect = 4.2
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|232955 TIGR00395, leuS_arch, leucyl-tRNA synthetase, archaeal and
cytosolic family. The leucyl-tRNA synthetases belong to
two families so broadly different that they are
represented by separate models. This model includes both
archaeal and cytosolic eukaryotic leucyl-tRNA
synthetases; the eubacterial and mitochondrial forms
differ so substantially that some other tRNA ligases
score higher by this model than does any eubacterial
LeuS [Protein synthesis, tRNA aminoacylation].
Length = 938
Score = 29.4 bits (66), Expect = 5.0
Identities = 23/104 (22%), Positives = 38/104 (36%), Gaps = 14/104 (13%)
Query: 285 DEGEVVAVDRSHNKVMDIQKLAAEMGLKCITTY-------KLDALKAVRRKNESNDEPNM 337
D+ A + N V DIQ++A K Y K LK V + D
Sbjct: 796 DKEVEAAEEYLRNLVRDIQEIAKIDASKPKRVYLYTSEDWKSQCLKIVA-ELFGED---- 850
Query: 338 CNSKDNNYITSQTSDSMKLHKEVPSIAAEGLNGDKSCKEKVSNE 381
+ ++ + + K KEV S+ + + +K E +E
Sbjct: 851 --TGEDMKKVMEEPEERKRGKEVISLVKQIIKDEKKEDELQISE 892
>gnl|CDD|225151 COG2242, CobL, Precorrin-6B methylase 2 [Coenzyme metabolism].
Length = 187
Score = 28.7 bits (65), Expect = 5.1
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|211415 cd11574, GH99, Glycoside hydrolase family 99, an
endo-alpha-1,2-mannosidase. This family of glycoside
hydrolases 99 (following the CAZY nomenclature) includes
endo-alpha-1,2-mannosidase (EC 3.2.1.130), which is an
important membrane-associated eukaryotic enzyme involved
in the maturation of N-linked glycans. Specifically, it
cleaves mannoside linkages internal to N-linked glycan
chains by hydrolyzing an alpha-1,2-mannosidic bond
between a glucose-substituted mannose and the remainder
of the chain. The biological function and significance
of the soluble bacterial orthologs, which may have
obtained the genes via horizontal transfer, is not
clear.
Length = 338
Score = 29.2 bits (66), Expect = 5.5
Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 455 RNHGKYQRRMFDQAVQLVRPGGIIVYS 481
R +GKY +M+ A++ V P I + S
Sbjct: 270 RENGKYYEKMWKAALK-VDPDIISITS 295
>gnl|CDD|216379 pfam01234, NNMT_PNMT_TEMT, NNMT/PNMT/TEMT family.
Length = 255
Score = 28.5 bits (64), Expect = 8.2
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|226196 COG3670, COG3670, Lignostilbene-alpha,beta-dioxygenase and related
enzymes [Secondary metabolites biosynthesis, transport,
and catabolism].
Length = 490
Score = 28.5 bits (64), Expect = 9.1
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|176125 cd08434, PBP2_GltC_like, The substrate binding domain of LysR-type
transcriptional regulator GltC, which activates gltA
expression of glutamate synthase operon, contains type 2
periplasmic binding fold. GltC, a member of the LysR
family of bacterial transcriptional factors, activates
the expression of gltA gene of glutamate synthase operon
and is essential for cell growth in the absence of
glutamate. Glutamate synthase is a heterodimeric protein
that encoded by gltA and gltB, whose expression is
subject to nutritional regulation. GltC also negatively
auto-regulates its own expression. This
substrate-binding domain has strong homology to the type
2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis.
Length = 195
Score = 27.9 bits (63), Expect = 9.7
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 420 GFSPNSFDRVLLDAPCSALGLRPRL-FAAEE--TIQSL 454
SP R ++D C+A G P++ F EE TI L
Sbjct: 102 LLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGL 139
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
0.316 0.133 0.387
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: 24,689,416
Number of extensions: 2377055
Number of successful extensions: 2506
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2490
Number of HSP's successfully gapped: 97
Length of query: 495
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 394
Effective length of database: 6,457,848
Effective search space: 2544392112
Effective search space used: 2544392112
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)