RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780610|ref|YP_003065023.1| RNA-pseudouridylate synthase
protein, ribosomal large subunit D [Candidatus Liberibacter asiaticus
str. psy62]
(340 letters)
>gnl|CDD|30910 COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific
[Translation, ribosomal structure and biogenesis].
Length = 289
Score = 296 bits (760), Expect = 5e-81
Identities = 143/313 (45%), Positives = 199/313 (63%), Gaps = 31/313 (9%)
Query: 17 SDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVP 76
+ A R+D++LA L SRS ++ LI G + +NG K P+ K+ PGD I +P
Sbjct: 7 PEEEAGQRLDKFLAKLLP--ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLP 63
Query: 77 -AAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSS 135
++ + E+IPLDILYED+D++V+NKPAGLVVHP G+ GTLVNALL HC +
Sbjct: 64 EEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDG--- 120
Query: 136 INGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLP 195
V+RPGIVHRLDKDT+G+++VAKN A ++LSEQF ++K+ Y A+V G
Sbjct: 121 ---VERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQR----KVKKTYLALVRGHLPE 173
Query: 196 DSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETG 255
D G I+AP+GR NR + AV + + + AITHY+ +E + N +L++ ETG
Sbjct: 174 DEGTIDAPIGRDPKNRKKMAV--VKEGSGKPAITHYEVLERFGDN----YTLVELKPETG 227
Query: 256 RTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPR 315
RTHQIRVH+AH G+P++GDPLYG KSA L RQALHA+ LSF+HP
Sbjct: 228 RTHQIRVHLAHLGHPIVGDPLYG-----------GKDKSAGAGLKRQALHAYKLSFTHPL 276
Query: 316 NNQDMDFQVPIPE 328
++++F+ P+PE
Sbjct: 277 TGEELEFEAPLPE 289
>gnl|CDD|30029 cd02869, PseudoU_synth_RluCD_like, PseudoU_synth_RsuA/RluD:
Pseudouridine synthase, RsuA/RluD family. This group is
comprised of eukaryotic, bacterial and archeal proteins
similar to eight site specific Escherichia coli
pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD,
RluE, RluF and TruA. Pseudouridine synthases catalyze
the isomerization of specific uridines in a n RNA
molecule to pseudouridines (5-ribosyluracil, psi)
requiring no cofactors. E. coli RluC for example makes
psi955, 2504 and 2580 in 23S RNA. Some psi sites such
as psi1917 in 23S RNA made by RluD are universally
conserved. Other psi sites occur in a more restricted
fashion, for example psi2819 in 21S mitochondrial
ribosomal RNA made by S. cerevisiae Pus5p is only found
in mitochondrial large subunit rRNAs from some other
species and in gram negative bacteria. The E. coli
counterpart of this psi residue is psi2580 in 23S rRNA.
psi2604in 23S RNA made by RluF has only been detected in
E.coli. .
Length = 185
Score = 207 bits (528), Expect = 4e-54
Identities = 99/213 (46%), Positives = 129/213 (60%), Gaps = 28/213 (13%)
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158
++V+NKPAGL VHP PG+ TGTLVNALL L + RPG+VHRLDKDT+G+++V
Sbjct: 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKL----LLLLGEEFRPGLVHRLDKDTSGLLLV 56
Query: 159 AKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKG 218
AKN A KLS+QF + ++K+ Y A+V G P D G I+APLGR K + R V
Sbjct: 57 AKNKKAAAKLSKQFKER----KVKKTYLALVDGKPPEDEGTIDAPLGRKKRKKRARVVVS 112
Query: 219 IDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYG 278
D K A ITHY+ +E + V+L++ LETGRTHQIRVH+A G+P++GDP YG
Sbjct: 113 EDGKPA---ITHYKVLERFGN-----VTLVELQLETGRTHQIRVHLASIGHPIVGDPKYG 164
Query: 279 KGFKTKANIVNNNAKSAILSLARQALHAHSLSF 311
+ R ALHA+ LSF
Sbjct: 165 GKASDSPGL------------KRLALHAYRLSF 185
>gnl|CDD|37130 KOG1919, KOG1919, KOG1919, RNA pseudouridylate synthases [RNA
processing and modification].
Length = 371
Score = 135 bits (342), Expect = 1e-32
Identities = 73/258 (28%), Positives = 115/258 (44%), Gaps = 26/258 (10%)
Query: 25 IDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIA 84
+ + + + R+Y + I G +++NG + V GD TV +
Sbjct: 46 LVDVFVSEFRLR-ERAYYESAIKLGRVTVNG-EQVRVSLIVKNGDVLCHTVHRHEPPVAY 103
Query: 85 QENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGI 144
P+ I++ED D +V+NKP G+ VHP G + + +L H V+
Sbjct: 104 L---PIRIVFEDKDYVVVNKPHGIPVHPT-GRYRENTITKILAALH-------KVEGLRP 152
Query: 145 VHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPL 204
HRLD+ T+G++V+AK A K E + +K+ Y P P G +
Sbjct: 153 CHRLDRLTSGLLVLAKTKEAADKFHEVL----RKRTVKKEYVVARVEGPFPVVGEVEIKE 208
Query: 205 GRCKSNRLRR----AVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQI 260
+ R R AV D+ A A T ++ + + SL++C TGRTHQI
Sbjct: 209 PIGEEERPLRMGLNAVGVRDEVAAKDAKTLFKVLS-----YDGGSSLVECRPLTGRTHQI 263
Query: 261 RVHMAHKGNPLIGDPLYG 278
RVH+ + G+P+ GDP YG
Sbjct: 264 RVHLQYLGHPIAGDPKYG 281
>gnl|CDD|30016 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomerase C:
Pseudouridine synthases catalyze the isomerization of
specific uridines in an tRNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required. TruC
makes psi65 in tRNAs. This psi residue is not
universally conserved..
Length = 223
Score = 135 bits (342), Expect = 1e-32
Identities = 77/245 (31%), Positives = 117/245 (47%), Gaps = 29/245 (11%)
Query: 90 LDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLD 149
L+ILY+D+ ++ INKP+GL+VH + + T L + L + VHRLD
Sbjct: 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRF--ALQTLRDQLG-----QHVYPVHRLD 53
Query: 150 KDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKS 209
+ T+GV++ A + +KL EQF +H R+ + Y A+V G P+SG I+ PL
Sbjct: 54 RPTSGVLLFALSSEVARKLGEQFTEH----RVHKTYLAVVRGYV-PESGTIDYPL---SE 105
Query: 210 NRLRRAVKGIDDKTA-DSAITHY---QTIEIYNKNSNFAV---SLLKCHLETGRTHQIRV 262
+ A K D A +A THY E+ + SL++ TGR HQ+R
Sbjct: 106 ELDKLADKFASDDKAPQAATTHYRLLAVEELPVVVGKYPTSRYSLVELTPHTGRKHQLRR 165
Query: 263 HMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDF 322
H+AH +P+IGD +G G +N R L A L F+HP + +
Sbjct: 166 HLAHIRHPIIGDTTHGDG-------RHNRFFREHFGCHRLLLAATRLEFTHPVTGERLLI 218
Query: 323 QVPIP 327
+ P+
Sbjct: 219 EAPLD 223
>gnl|CDD|144443 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase. Members
of this family are involved in modifying bases in RNA
molecules. They carry out the conversion of uracil bases
to pseudouridine. This family includes RluD, a
pseudouridylate synthase that converts specific uracils
to pseudouridine in 23S rRNA. RluA from E. coli converts
bases in both rRNA and tRNA.
Length = 151
Score = 132 bits (334), Expect = 1e-31
Identities = 58/169 (34%), Positives = 90/169 (53%), Gaps = 19/169 (11%)
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLS-SINGVKRPGIVHRLDKDTTGVMV 157
IV+NKPAG+ VHP + L L + G R VHRLD+DT+G+++
Sbjct: 1 YIVVNKPAGVPVHPTDLS--------DLLSLTELLLVAELGKFRLYPVHRLDRDTSGLLL 52
Query: 158 VAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVK 217
+AK+ A KL++ F + +++ Y A+V P + G I AP+ + K+ RR +
Sbjct: 53 LAKDGEAANKLNKLFPERK----VEKEYLALV-DGPEEEEGTIKAPIKKDKNKVPRRKKE 107
Query: 218 GIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAH 266
+D K A+TH + + +K + VSL++ L TGR HQIR H+A
Sbjct: 108 ELDGK---KAVTHLRVLRSGSKIED--VSLVELELVTGRKHQIRAHLAA 151
>gnl|CDD|73313 cd02557, PseudoU_synth_ScRIB2, PseudoU_synth_ScRIB2_like:
Pseudouridine synthase, Saccharomyces cerevisiae
RIB2_like. This group is comprised of eukaryotic and
bacterial proteins similar to Saccharomyces cerevisiae
RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S.
cerevisiae RIB2 displays two distinct catalytic
activities. The N-terminal domain of RIB2 is
RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs.
Psi32 is highly phylogenetically conserved. The
C-terminal domain of RIB2 has a DRAP deaminase activity
which catalyses the formation of
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione
5'-phosphate from
2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone
5'-phosphate during riboflavin biosynthesis. S.
cerevisiae Pus6p makes the psi31 of cytoplasmic and
mitochondrial tRNAs..
Length = 213
Score = 119 bits (301), Expect = 8e-28
Identities = 60/192 (31%), Positives = 102/192 (53%), Gaps = 18/192 (9%)
Query: 87 NIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVH 146
N P+ I++EDDD++V++KP+G+ VHP G + V +L L+ + RP H
Sbjct: 13 NDPIKIVHEDDDLLVVDKPSGIPVHPT-GRYRYNTVTEILKS-EYGLTEL----RP--CH 64
Query: 147 RLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGR 206
RLD+ T+G+++ AK +L +Q +K+ Y A V G +++ P+G
Sbjct: 65 RLDRLTSGLLLFAKTSQTASRLQQQIRSR----EVKKEYLARVKGEFPDGEVVVDQPIG- 119
Query: 207 CKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAH 266
+ ++ D+ A T ++ + YN + N S++ C TGRTHQIRVH+ +
Sbjct: 120 --LVSPKGGLRNDVDEKGKDARTIFKRL-SYNGDLNT--SVVLCKPITGRTHQIRVHLQY 174
Query: 267 KGNPLIGDPLYG 278
G+P++ DP+Y
Sbjct: 175 LGHPIVNDPIYN 186
>gnl|CDD|30008 cd02550, PseudoU_synth_Rsu_Rlu_like, PseudoU_synth_Rsu_Rlu:
Pseudouridine synthase, Rsu/Rlu family. This group is
comprised of eukaryotic, bacterial and archeal proteins
similar to eight site specific Escherichia coli
pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD,
RluE, RluF and TruA. Pseudouridine synthases catalyze
the isomerization of specific uridines in a n RNA
molecule to pseudouridines (5-ribosyluracil, psi)
requiring no cofactors. E. coli RluC for example makes
psi955, 2504 and 2580 in 23S RNA. Some psi sites such
as psi1917 in 23S RNA made by RluD are universally
conserved. Other psi sites occur in a more restricted
fashion, for example psi2819 in 21S mitochondrial
ribosomal RNA made by S. cerevisiae Pus5p is only found
in mitochondrial large subunit rRNAs from some other
species and in gram negative bacteria. The E. coli
counterpart of this psi residue is psi2580 in 23S rRNA.
psi2604in 23S RNA made by RluF has only been detected in
E.coli..
Length = 154
Score = 95.3 bits (237), Expect = 2e-20
Identities = 50/174 (28%), Positives = 79/174 (45%), Gaps = 27/174 (15%)
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158
I+V+NKP+GLV HP + T+V L R RLDKDT+G++++
Sbjct: 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDK---------LHGPRVHAAGRLDKDTSGLLLL 51
Query: 159 AKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKG 218
+ ++L+E + ++ Y V G L + GI + R R + G
Sbjct: 52 TNDGRLQRRLTEPRREI------EKEYLVTVRG-ELDEEGIEDLATVR------RGRLSG 98
Query: 219 IDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLI 272
+ D+ A+T + I + L+ L+TGRTHQIR H A G P++
Sbjct: 99 LVDEGVPLAVTKVRVIGEHGGTG-----RLRLTLKTGRTHQIRRHCAAVGFPVL 147
>gnl|CDD|30015 cd02558, PSRA_1, PSRA_1: Pseudouridine synthase, a subgroup of the
RluA family. This group is comprised of bacterial
proteins assigned to the RluA family of pseudouridine
synthases. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. The RluA family is comprised of proteins
related to Escherichia coli RluA. .
Length = 246
Score = 79.1 bits (195), Expect = 2e-15
Identities = 47/201 (23%), Positives = 80/201 (39%), Gaps = 33/201 (16%)
Query: 84 AQENIPLD--ILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKR 141
+ IP + IL++D+ ++V +KP L V P T TL+ L ++
Sbjct: 31 DEPPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRL-------------RRQ 77
Query: 142 PGI-----VHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPD 196
G HRLD+ T G+++ +K F + + Y A+ +P
Sbjct: 78 TGNPDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARR----EVSKTYEAVAPYVPA-- 131
Query: 197 SGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGR 256
+R+ + + + IE+ + + + L H TG+
Sbjct: 132 -----LTFPLTVRSRIVKGRGFFQAREVEGEPNAETRIELLARRGGWGLYRLSPH--TGK 184
Query: 257 THQIRVHMAHKGNPLIGDPLY 277
THQ+RVHMA G P++ DP Y
Sbjct: 185 THQLRVHMAALGVPILNDPFY 205
>gnl|CDD|31380 COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and
related pseudouridylate synthases [Translation,
ribosomal structure and biogenesis].
Length = 248
Score = 68.0 bits (166), Expect = 3e-12
Identities = 53/248 (21%), Positives = 98/248 (39%), Gaps = 46/248 (18%)
Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNI 83
R++++LA + SR + LI G +++NG V+ V P D ++ V +++ +
Sbjct: 4 RLNKFLAEAG--VGSRREAEKLIEEGRVTVNGKVATLGGVVVDP-DDDVVEVD-GKRIEL 59
Query: 84 AQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPG 143
+E + +++NKP G V T+ + L KR
Sbjct: 60 KEERV----------YLLLNKPRGYVSSTEDDEGRPTVFDLLPERLPRK-------KRLF 102
Query: 144 IVHRLDKDTTGVMVVAKN-DLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINA 202
V RLDKDT G++++ + +LAH+ + S+ +++ Y V G +
Sbjct: 103 PVGRLDKDTEGLLLLTNDGELAHRLMHP-------SSEVEKEYLVRVEGPVTEE------ 149
Query: 203 PLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRV 262
L + KG+ ++ ++E +N S L+ L GR Q+R
Sbjct: 150 --------DLEKLRKGVTLDDGETKPAKPASLEKEPGKNN---SWLRITLTEGRNRQVRR 198
Query: 263 HMAHKGNP 270
G
Sbjct: 199 MFEAVGLE 206
>gnl|CDD|29105 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The domain
surface is populated by conserved, charged residues that
define a likely RNA-binding site; Found in stress
proteins, ribosomal proteins and tRNA synthetases; This
may imply a hitherto unrecognized functional similarity
between these three protein classes..
Length = 70
Score = 46.0 bits (109), Expect = 2e-05
Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 11/80 (13%)
Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNI 83
R+D+ LA SRS + LI +G + +NG V P+ KV PGD + +
Sbjct: 2 RLDKILARLGLA-PSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGD----------VIEV 50
Query: 84 AQENIPLDILYEDDDIIVIN 103
++I DI+YED ++V+N
Sbjct: 51 DGKSIEEDIVYEDKKLLVVN 70
>gnl|CDD|30030 cd02870, PseudoU_synth_RsuA_like, Pseudouridine synthases are
responsible for the synthesis of pseudouridine from
uracil in ribosomal RNA. The RsuA subfamily includes
Pseudouridine Synthase similar to Ribosomal small
subunit pseudouridine 516 synthase. Most of the proteins
in this family are bacterial proteins..
Length = 146
Score = 37.4 bits (87), Expect = 0.005
Identities = 31/129 (24%), Positives = 57/129 (44%), Gaps = 27/129 (20%)
Query: 145 VHRLDKDTTGVMVVAKN-DLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAP 203
V RLD DT G++++ + +LA++ ++ +++ Y V G+P +
Sbjct: 37 VGRLDYDTEGLLLLTNDGELANRLTHPRY-------GVEKTYLVKVRGVPSEEEL----- 84
Query: 204 LGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVH 263
RLR V+ D KTA + + + KN+ V+L + GR Q+R
Sbjct: 85 ------RRLRAGVELDDGKTAPAKVKV---LSRDPKNTLLEVTLHE-----GRNRQVRRM 130
Query: 264 MAHKGNPLI 272
G+P++
Sbjct: 131 FEAVGHPVL 139
>gnl|CDD|31382 COG1189, COG1189, Predicted rRNA methylase [Translation,
ribosomal structure and biogenesis].
Length = 245
Score = 35.6 bits (82), Expect = 0.022
Identities = 18/62 (29%), Positives = 24/62 (38%), Gaps = 7/62 (11%)
Query: 38 SRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVP-------AAQKLNIAQENIPL 90
SR K LIL G + +NG P++ V D + KL A E L
Sbjct: 17 SREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKGEEQPYVSRGGLKLEKALEEFEL 76
Query: 91 DI 92
D+
Sbjct: 77 DV 78
>gnl|CDD|144902 pfam01479, S4, S4 domain. The S4 domain is a small domain
consisting of 60-65 amino acid residues that was
detected in the bacterial ribosomal protein S4,
eukaryotic ribosomal S9, two families of pseudouridine
synthases, a novel family of predicted RNA methylases,
a yeast protein containing a pseudouridine synthetase
and a deaminase domain, bacterial tyrosyl-tRNA
synthetases, and a number of uncharacterized, small
proteins that may be involved in translation
regulation. The S4 domain probably mediates binding to
RNA.
Length = 48
Score = 34.4 bits (80), Expect = 0.050
Identities = 19/46 (41%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGD 69
R+D+ LA SRS + LI +G + +NG V K+P+ +V PGD
Sbjct: 2 RLDKVLARLGLAS-SRSEARQLIRHGHVRVNGKVVKDPSYRVKPGD 46
>gnl|CDD|30022 cd02573, PseudoU_synth_EcTruB, PseudoU_synth_EcTruB: Pseudouridine
synthase, Escherichia coli TruB like. This group
consists of bacterial pseudouridine synthases similar to
E. coli TruB and Mycobacterium tuberculosis TruB.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). E. coli TruB and M.
tuberculosis TruB make psi55 in the T loop of tRNAs.
Psi55 is nearly universally conserved. E. coli TruB is
not inhibited by RNA containing 5-fluorouridine. .
Length = 277
Score = 33.6 bits (77), Expect = 0.076
Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 18/82 (21%)
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158
I++++KPAGL H + + G K+ G LD TGV+ +
Sbjct: 2 ILLLDKPAGLTSH----------------DVVQKVRRLLGTKKVGHTGTLDPLATGVLPI 45
Query: 159 AKNDLAHQKLSEQFVDHGKSTR 180
A + KLS+ +D K+ R
Sbjct: 46 ALGEAT--KLSQYLLDADKTYR 65
>gnl|CDD|30017 cd02566, PseudoU_synth_RluE, PseudoU_synth_RluE: Pseudouridine
synthase, Escherichia coli RluE. This group is comprised
of bacterial proteins similar to E. coli RluE.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required.
Escherichia coli RluE makes psi2457 in 23S RNA. psi2457
is not universally conserved..
Length = 168
Score = 33.7 bits (77), Expect = 0.078
Identities = 33/179 (18%), Positives = 63/179 (35%), Gaps = 35/179 (19%)
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158
+I+ NKP G++ + H L RLD+D+ G++++
Sbjct: 1 LILFNKPYGVLSQFTDES-----------EKHKTLKDYIDDPGVYAAGRLDRDSEGLLLL 49
Query: 159 AKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKG 218
+ ++++ H K+ YY V G+P D+ +LR V+
Sbjct: 50 TDDGRLQHRITDPSFKHPKT------YYVQVEGVPTEDA-----------LEQLRNGVEL 92
Query: 219 IDDKT-ADSAITHYQTIEIYNKN------SNFAVSLLKCHLETGRTHQIRVHMAHKGNP 270
D T + ++ + N S ++ + G+ Q+R A G P
Sbjct: 93 GDGLTLPAKVEKVDEPPWLWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAAVGFP 151
>gnl|CDD|30010 cd02553, PseudoU_synth_RsuA, PseudoU_synth_RsuA: Pseudouridine
synthase, Escherichia coli RsuA like. This group is
comprised of eukaryotic and bacterial proteins similar
to Escherichia coli RsuA. Pseudouridine synthases
catalyze the isomerization of specific uridines in an
RNA molecule to pseudouridines (5-ribosyluracil, psi).
No cofactors are required. E.coli RsuA makes psi516 in
16S RNA. Psi at this position is not generally conserved
in other organisms..
Length = 167
Score = 31.3 bits (71), Expect = 0.41
Identities = 27/130 (20%), Positives = 48/130 (36%), Gaps = 30/130 (23%)
Query: 144 IVHRLDKDTTGVMVVAKN-DLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINA 202
V RLDKDTTG++++ + LAH+ S + + + Y +
Sbjct: 38 PVGRLDKDTTGLLLLTNDGQLAHRLTSPK-------KHVPKTYEV-----------TLAG 79
Query: 203 PLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRV 262
PL V D A +EI + + ++ + G+ HQ++
Sbjct: 80 PLTEDDIEAFAEGVLLHDGYPTKPA-----KLEILSPTT------VRLTITEGKYHQVKR 128
Query: 263 HMAHKGNPLI 272
A GN ++
Sbjct: 129 MFAAVGNKVV 138
>gnl|CDD|30428 COG0079, HisC, Histidinol-phosphate/aromatic aminotransferase and
cobyric acid decarboxylase [Amino acid transport and
metabolism].
Length = 356
Score = 31.1 bits (70), Expect = 0.52
Identities = 24/69 (34%), Positives = 28/69 (40%), Gaps = 9/69 (13%)
Query: 65 VVPGDSFLITVP-------AAQKLNIAQENIPLDILYEDDDIIV--INKPAGLVVHPAPG 115
V PGD+ LI P AAQ +PL D D I+ I LV P
Sbjct: 96 VEPGDTVLIPEPTFSMYEIAAQLAGAEVVKVPLKEFRLDLDAILAAIRDKTKLVFLCNPN 155
Query: 116 NWTGTLVNA 124
N TGTL+
Sbjct: 156 NPTGTLLPR 164
>gnl|CDD|36342 KOG1127, KOG1127, KOG1127, TPR repeat-containing protein [RNA
processing and modification].
Length = 1238
Score = 28.9 bits (64), Expect = 1.9
Identities = 24/104 (23%), Positives = 45/104 (43%), Gaps = 4/104 (3%)
Query: 201 NAPLGRCKSNRLRRAVKGIDDKTADSAITHYQT-IEIYNKNSNFAVSLLKCHLETGR-TH 258
AP CK N ++R ++ A+ +Q+ + K+ N + L + + E+GR +H
Sbjct: 555 KAPAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTDPKDYNLWLGLGEAYPESGRYSH 614
Query: 259 QIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQ 302
++V K + L YG+ + N K A+ +L
Sbjct: 615 ALKV--FTKASLLRPLSKYGRFKEAVMECDNGKYKEALDALGLI 656
>gnl|CDD|35482 KOG0261, KOG0261, KOG0261, RNA polymerase III, large subunit
[Transcription].
Length = 1386
Score = 28.4 bits (63), Expect = 3.3
Identities = 16/45 (35%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 199 IINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNF 243
II A L R R VKG +KT + Y E+Y +S F
Sbjct: 1081 IITAELENPHDERSARVVKGRIEKTTLGDVCSYIE-EVYGPDSCF 1124
>gnl|CDD|144119 pfam00405, Transferrin, Transferrin.
Length = 328
Score = 27.4 bits (61), Expect = 5.1
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 229 THYQTIEIYNKNSNFAVSLLK----CHLETGRT 257
THY + + K SNF ++ L+ CH GR+
Sbjct: 85 THYYAVAVVKKGSNFQLNQLQGKKSCHTGLGRS 117
>gnl|CDD|32457 COG2302, COG2302, Uncharacterized conserved protein, contains
S4-like domain [Function unknown].
Length = 257
Score = 27.5 bits (61), Expect = 5.4
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 4/64 (6%)
Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNI 83
R+D ++ SR+ + LI G + +N V + +V GD LI++ +L I
Sbjct: 182 RLDVVISEGFG--LSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGD--LISIRGFGRLKI 237
Query: 84 AQEN 87
+ N
Sbjct: 238 LEIN 241
>gnl|CDD|30600 COG0251, TdcF, Putative translation initiation inhibitor, yjgF
family [Translation, ribosomal structure and
biogenesis].
Length = 130
Score = 27.2 bits (60), Expect = 6.4
Identities = 6/31 (19%), Positives = 17/31 (54%)
Query: 41 YVKILILNGFISINGMVSKNPNRKVVPGDSF 71
Y + ++ G + ++G + +P ++V G+
Sbjct: 19 YSQAVVAGGLVFVSGQIPLDPTGELVGGEDI 49
>gnl|CDD|133126 cd06595, GH31_xylosidase_XylS-like, This family represents an
uncharacterized glycosyl hydrolase family 31 (GH31)
enzyme found in bacteria and eukaryotes that is related
to the XylS xylosidase of Sulfolobus solfataricus.
Alpha-xylosidases catalyze the release of an
alpha-xylose residue from the non-reducing end of
alpha-xyloside substrates. Enzymes of the GH31 family
possess a wide range of different hydrolytic activities
including alpha-glucosidase (glucoamylase and
sucrase-isomaltase), alpha-xylosidase,
6-alpha-glucosyltransferase,
3-alpha-isomaltosyltransferase and alpha-1,4-glucan
lyase. All GH31 enzymes cleave a terminal carbohydrate
moiety from a substrate that varies considerably in
size, depending on the enzyme, and may be either a
starch or a glycoprotein.
Length = 292
Score = 27.3 bits (61), Expect = 6.7
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 82 NIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTG 119
+ NIPLD+L D D V + P WTG
Sbjct: 33 RFKKHNIPLDVLVIDMDWHVTDIP-----SKYGSGWTG 65
>gnl|CDD|36139 KOG0921, KOG0921, KOG0921, Dosage compensation complex, subunit MLE
[Transcription].
Length = 1282
Score = 27.2 bits (59), Expect = 7.3
Identities = 11/41 (26%), Positives = 19/41 (46%)
Query: 286 NIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPI 326
N+ K +L+ + + H S + P + Q+MDF P
Sbjct: 999 NVAYYVEKRKVLTTEQSSALIHKYSVNCPNSRQEMDFPSPF 1039
>gnl|CDD|37352 KOG2141, KOG2141, KOG2141, Protein involved in high osmolarity
signaling pathway [Signal transduction mechanisms].
Length = 822
Score = 26.9 bits (59), Expect = 7.9
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 211 RLRRAVKGIDDKTADSAITHYQT--IEIYNKNSNFAV--SLLKCHLET 254
RLRR V G +K +D+ I E+Y NS + V SL K L+
Sbjct: 318 RLRRKVNGSLNKLSDANIIKIIAGIAELYMNNSRYDVTSSLTKLLLKA 365
>gnl|CDD|30803 COG0455, COG0455, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 262
Score = 26.8 bits (59), Expect = 9.9
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 46 ILNGFISINGMVSKNP--NRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVIN 103
+L G SI ++ + P V+PG S + KL+ + L E D I+I+
Sbjct: 63 VLAGEASIEDIIYETPQDGLYVLPGGS---GLEDLAKLDPEDLEDVIKELEELYDYILID 119
Query: 104 KPAGL 108
AGL
Sbjct: 120 TGAGL 124
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.318 0.134 0.395
Gapped
Lambda K H
0.267 0.0871 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,011,727
Number of extensions: 207267
Number of successful extensions: 509
Number of sequences better than 10.0: 1
Number of HSP's gapped: 481
Number of HSP's successfully gapped: 31
Length of query: 340
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 246
Effective length of database: 4,232,491
Effective search space: 1041192786
Effective search space used: 1041192786
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 (21.7 bits)
S2: 58 (25.9 bits)