RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1176
(232 letters)
>gnl|CDD|211338 cd02572, PseudoU_synth_hDyskerin, Pseudouridine synthase, human
dyskerin like. This group consists of eukaryotic and
archeal pseudouridine synthases similar to human
dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila
melanogaster Mfl (minifly protein). Pseudouridine
synthases catalyze the isomerization of specific
uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactor is required. S.
cerevisiae Cbf5 and human dyskerin are nucleolar
proteins that, with the help of guide RNAs, make the
hundreds of psueudouridnes present in rRNA and small
nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic
subunit of eukaryotic box H/ACA small nucleolar
ribonucleoprotein (snoRNP) particles. D. melanogaster
mfl hosts in its fourth intron, a box H/AC snoRNA gene.
In addition dyskerin is likely to have a structural role
in the telomerase complex. Mutations in human dyskerin
cause X-linked dyskeratosis congenitas. Mutations in
Drosophila Mfl results in miniflies that suffer
abnormalities.
Length = 182
Score = 238 bits (610), Expect = 1e-80
Identities = 99/200 (49%), Positives = 117/200 (58%), Gaps = 41/200 (20%)
Query: 31 RAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQ 90
+ G +NLDKPS PSSHEVVAWIKRIL EKTGHSGTLDPK +GCL VCIDRATRLVKSQQ
Sbjct: 1 KYGVINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQ 60
Query: 91 SAGKEYISIFKLHSAV--ENVAKASKKKMMIKQGLLDKHGKPNENTPASYLAELEAAPNK 148
AGKEY+ + +LH V E V + L E A +
Sbjct: 61 EAGKEYVCVMRLHDDVDEEKVRRV--------------------------LEEFTGAIFQ 94
Query: 149 KP-------------TYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGVGAQ 195
+P T +S L+ D + + C+AGTY+RT CVH+GL+LGVGA
Sbjct: 95 RPPLISAVKRQLRVRTIYESKLLEYDGERRLVLFRVSCEAGTYIRTLCVHIGLLLGVGAH 154
Query: 196 MIELRRNRSGIQSEEDGLVT 215
M ELRR RSG SEED +VT
Sbjct: 155 MQELRRTRSGPFSEEDNMVT 174
>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 = 243 bits (621), Expect = 3e-80
Identities = 103/218 (47%), Positives = 134/218 (61%), Gaps = 20/218 (9%)
Query: 1 NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEK 60
NF+ L V+ HYT + +G +PL+R I+EYI G VNLDKPS PSSHEVVAW++RIL EK
Sbjct: 3 NFENLIVKEEHYTNIDYGCNPLKRDIEEYISYGVVNLDKPSGPSSHEVVAWVRRILNVEK 62
Query: 61 TGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIK 120
TGH GTLDPK +G L VCI+RATRLVKSQQ A KEY+ + +LH K+ I
Sbjct: 63 TGHGGTLDPKVTGVLPVCIERATRLVKSQQEAPKEYVCLMRLHRDA--------KEEDIL 114
Query: 121 QGLLDKHGKPNENTPASYLAELEAAPNKK---PTYMKSNLISSDVTLSTGIIWLKCQAGT 177
+ L + G+ + P L++A ++ T +S L+ D + + C+AGT
Sbjct: 115 RVLKEFTGRIFQRPP------LKSAVKRQLRVRTIYESELLEKDG--KDVLFRVSCEAGT 166
Query: 178 YVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVT 215
Y+R CV +G LG GA M ELRR RSG ED +VT
Sbjct: 167 YIRKLCVDIGEALGTGAHMQELRRTRSGC-FGEDDMVT 203
>gnl|CDD|179806 PRK04270, PRK04270, H/ACA RNA-protein complex component Cbf5p;
Reviewed.
Length = 300
Score = 177 bits (451), Expect = 6e-55
Identities = 79/226 (34%), Positives = 113/226 (50%), Gaps = 60/226 (26%)
Query: 13 TPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTS 72
T +G P +R I+E I+ G VNLDKP P+SHEV AW++ IL EK GH GTLDPK +
Sbjct: 3 TNPEYGCPPEKRPIEELIKFGVVNLDKPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVT 62
Query: 73 GCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAV-----ENVAK--------------AS 113
G L V + +AT++V++ +GKEY+ + LH V V K A
Sbjct: 63 GVLPVALGKATKVVQALLESGKEYVCVMHLHGDVPEEDIRKVFKEFTGEIYQKPPLKSAV 122
Query: 114 KKKMMIKQ----GLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGII 169
K+++ ++ +L+ G+ DV +
Sbjct: 123 KRRLRVRTIYELEILEIDGR-------------------------------DV-----LF 146
Query: 170 WLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVT 215
++C++GTY+R C +GL LG GA M ELRR R+G +EED LVT
Sbjct: 147 RVRCESGTYIRKLCHDIGLALGTGAHMQELRRTRTGPFTEED-LVT 191
>gnl|CDD|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal
structure and biogenesis].
Length = 271
Score = 163 bits (415), Expect = 7e-50
Identities = 76/203 (37%), Positives = 101/203 (49%), Gaps = 20/203 (9%)
Query: 21 PLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCID 80
P +R I+ YI G +NLDKP P+SHEVVAW+KRIL EK GH GTLDP +G L +C+
Sbjct: 6 PEKRPIEIYI--GVINLDKPPGPTSHEVVAWVKRILGVEKAGHGGTLDPLATGVLPICLG 63
Query: 81 RATRLVKSQQSAGKEYISIFKLHSAV---ENVAKASKK-KMMIKQGLLDKHGKPNENTPA 136
AT+LV+ A KEY++ +L E V A + I Q P
Sbjct: 64 EATKLVQYLLDADKEYVATVRLGDQTDSEEEVRAALEAFTGEIYQ------------IPP 111
Query: 137 SYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGVGAQM 196
+ A +K T + D + + ++C GTY+RT +G LG GA M
Sbjct: 112 MFSAVKREVERRKITIYDLLELDFD--RNLVTLRVECSKGTYIRTLARDLGEALGCGAHM 169
Query: 197 IELRRNRSGIQSEEDGLVTFRQE 219
ELRR R G SEED + +
Sbjct: 170 SELRRTRVGPFSEEDAVTLELLD 192
>gnl|CDD|211323 cd00506, PseudoU_synth_TruB_like, Pseudouridine synthase, TruB
family. This group consists of eukaryotic, bacterial
and archeal pseudouridine synthases similar to
Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M.
tuberculosis TruB, S. cerevisiae Cbf5 and human
dyskerin. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. E. coli TruB, M. tuberculosis TruB and S.
cerevisiae Pus4, make psi55 in the T loop of tRNAs.
Pus4 catalyses the formation of psi55 in both
cytoplasmic and mitochondrial tRNAs. Psi55 is almost
universally conserved. S. cerevisiae Cbf5 and human
dyskerin are nucleolar proteins that, with the help of
guide RNAs, make the hundreds of psueudouridnes present
in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin
is the catalytic subunit of eukaryotic box H/ACA small
nucleolar ribonucleoprotein (snoRNP) particles.
Mutations in human dyskerin cause X-linked dyskeratosis
congenitas.
Length = 210
Score = 158 bits (402), Expect = 9e-49
Identities = 67/200 (33%), Positives = 94/200 (47%), Gaps = 30/200 (15%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSA 92
G +DKP PSSH+VV I+RI EK GH GTLDP +G L+V I +AT+L+K +A
Sbjct: 1 GLFAVDKPQGPSSHDVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKATKLLKHLLAA 60
Query: 93 GKEYISIFKLHSAVEN------VAKASKKKMMIKQGL---LDKHGKPNENTPASYLA--- 140
K+Y +I +L A + V + + + + L L+ + P Y A
Sbjct: 61 TKDYTAIGRLGQATDTFDATGQVIEETPYDHITHEQLERALETLTGDIQQVPPLYSAVKR 120
Query: 141 ---------------ELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVH 185
EA P PT + I + + + C+ GTY+RT
Sbjct: 121 QGQRAYELARRGLLVPDEARP---PTIYELLCIRFNPPHFLLEVEVVCETGTYIRTLIHD 177
Query: 186 MGLVLGVGAQMIELRRNRSG 205
+GL LGVGA + ELRR R G
Sbjct: 178 LGLELGVGAHVTELRRTRVG 197
>gnl|CDD|211339 cd02573, 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 = 213
Score = 112 bits (283), Expect = 7e-31
Identities = 61/214 (28%), Positives = 90/214 (42%), Gaps = 46/214 (21%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSA 92
G + LDKP+ +SH+VV ++R+L +K GH+GTLDP +G L + + AT+L + A
Sbjct: 1 GILLLDKPAGLTSHDVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEATKLSQYLLDA 60
Query: 93 GKEYISIFKL-----------------------HSAVENVAKASKKKMM--------IKQ 121
K Y + +L +E KA ++ +K
Sbjct: 61 DKTYRATVRLGEATDTDDAEGEIIETSPPPRLTEEEIEAALKAFTGEIEQVPPMYSAVKV 120
Query: 122 GLLDKHGKPNENTPASYLA----ELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGT 177
GK LA E+E P +K T L+S D + C GT
Sbjct: 121 D-----GK-----RLYELARAGEEVERPP-RKVTIYSLELLSFDPENPEADFEVHCSKGT 169
Query: 178 YVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEED 211
Y+R+ +G LG GA + LRR RSG + E
Sbjct: 170 YIRSLARDLGKALGCGAHLSALRRTRSGPFTLEQ 203
>gnl|CDD|203846 pfam08068, DKCLD, DKCLD (NUC011) domain. This is a TruB_N/PUA
domain associated N-terminal domain of Dyskerin-like
proteins.
Length = 59
Score = 91.3 bits (227), Expect = 2e-24
Identities = 34/49 (69%), Positives = 42/49 (85%)
Query: 1 NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVV 49
N+D+LNVR+ HYTP P+G SPL+R I+EYI+ G +NLDKPS PSSHEVV
Sbjct: 11 NYDELNVRSEHYTPPPYGCSPLKRPIEEYIKYGVINLDKPSGPSSHEVV 59
>gnl|CDD|129523 TIGR00431, TruB, tRNA pseudouridine(55) synthase. TruB, the tRNA
pseudouridine 55 synthase, converts uracil to
pseudouridine in the T loop of most tRNAs in all three
domains of life. This model is built on a seed alignment
of bacterial proteins only. Saccharomyces cerevisiae
protein YNL292w (Pus4) has been shown to be the
pseudouridine 55 synthase of both cytosolic and
mitochondrial compartments, active at no other position
on tRNA and the only enzyme active at that position in
the species. A distinct yeast protein YLR175w,
(centromere/microtubule-binding protein CBF5) is an rRNA
pseudouridine synthase, and the archaeal set is much
more similar to CBF5 than to Pus4. It is unclear whether
the archaeal proteins found by this model are tRNA
pseudouridine 55 synthases like TruB, rRNA pseudouridine
synthases like CBF5, or (as suggested by the absence of
paralogs in the Archaea) both. CBF5 likely has
additional, eukaryotic-specific functions. The trusted
cutoff is set above the scores for the archaeal homologs
of unknown function, so yeast Pus4p scores between
trusted and noise [Protein synthesis, tRNA and rRNA base
modification].
Length = 209
Score = 88.6 bits (220), Expect = 1e-21
Identities = 52/197 (26%), Positives = 80/197 (40%), Gaps = 27/197 (13%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSA 92
G + LDKP +S + +A ++R+L +K GH+GTLDP +G L + + +AT+L
Sbjct: 3 GVLLLDKPQGMTSFDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKATKLSPYLTDL 62
Query: 93 GKEYISIFKL-------HSAVENVAKASKKKMM--IKQGLLDKHGKPNENTPASYLAE-- 141
KEY + +L + V ++ L G+ E P Y A
Sbjct: 63 DKEYRAEIRLGVRTDTLDPDGQIVETRPVNPTTEDVEAALPTFRGE-IEQIPPMYSALKV 121
Query: 142 -----LEAAPNKKPTYMKS--------NLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGL 188
E A K+ + + T + + C GTY+RT +G
Sbjct: 122 NGKRLYEYARQGIEVERKARPVTVYDLQFLKYEGPELT--LEVHCSKGTYIRTLARDLGE 179
Query: 189 VLGVGAQMIELRRNRSG 205
LG GA + LRR G
Sbjct: 180 KLGCGAYVSHLRRTAVG 196
>gnl|CDD|178886 PRK00130, truB, tRNA pseudouridine synthase B; Provisional.
Length = 290
Score = 84.2 bits (209), Expect = 2e-19
Identities = 58/205 (28%), Positives = 91/205 (44%), Gaps = 30/205 (14%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSA 92
G +N+ KP +S +VV I++I + +K GH+GTLDP SG L VC+ +AT++V
Sbjct: 3 GILNILKPPGMTSFDVVRKIRKIAKIKKVGHTGTLDPLASGVLPVCLGKATKIVDYLMEG 62
Query: 93 GKEYISIFKLHSAVENVAKASK----------KKMMIKQGLLDKHGKPNENTPASYLA-- 140
K Y + KL + + + + I++ +L G+ + P Y A
Sbjct: 63 KKTYRAEIKLGVETDTYDREGEILKEKEVSHLTEEEIREAILSFQGE-IDQVPPMYSALK 121
Query: 141 --------------ELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHM 186
E+E K Y L ++ L I +KC GTY+R+ C +
Sbjct: 122 INGKKLYELARQGIEVEREARKITIYDIEIL---EIDLPYVIFDVKCSKGTYIRSLCFDI 178
Query: 187 GLVLGVGAQMIELRRNRSGIQSEED 211
G L GA M L R +G + E+
Sbjct: 179 GEKLNCGAYMWNLIRTETGPFNIEN 203
>gnl|CDD|216540 pfam01509, TruB_N, TruB family pseudouridylate synthase (N terminal
domain). 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 TruB, a pseudouridylate synthase that
specifically converts uracil 55 to pseudouridine in most
tRNAs. This family also includes Cbf5p that modifies
rRNA.
Length = 149
Score = 80.2 bits (199), Expect = 4e-19
Identities = 25/53 (47%), Positives = 35/53 (66%)
Query: 53 KRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSA 105
KRIL +K GH+GTLDP +G L VC+ +AT+L++ A KEY + +L A
Sbjct: 1 KRILGAKKVGHTGTLDPLATGVLPVCVGKATKLLQYLLDADKEYRATIRLGVA 53
>gnl|CDD|172614 PRK14124, PRK14124, tRNA pseudouridine synthase B; Provisional.
Length = 308
Score = 82.5 bits (204), Expect = 1e-18
Identities = 58/223 (26%), Positives = 101/223 (45%), Gaps = 29/223 (13%)
Query: 30 IRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQ 89
++ G++ KP P+SH+VV +++ L+ K GH+GTLDP +G LIV +++ATRL++
Sbjct: 1 MKHGFLVAYKPKGPTSHDVVDEVRKKLKTRKVGHAGTLDPFATGVLIVGVNKATRLLEYL 60
Query: 90 QSAGKEY---------ISIFKLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPA---- 136
++ K Y F + V + + + I++ + G+ + PA
Sbjct: 61 KNEKKVYYVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYKQVPPAYSAK 120
Query: 137 SYLAE-----------LEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVH 185
Y E + P + Y ++ +S ++ GTY+R+ C+
Sbjct: 121 KYKGERLYKLAREGKIINLPPKEVKIYEIWDISIEGPDVS---FRVEVSPGTYIRSLCMD 177
Query: 186 MGLVLGVGAQMIELRRNRSGIQSEEDGLVTFR--QEHMFEHIV 226
+G LG GA +EL R G S ED + F E + I+
Sbjct: 178 IGYKLGCGATAVELVRLSVGKFSIEDSINVFEVSPEEIENRII 220
>gnl|CDD|235113 PRK03287, truB, tRNA pseudouridine synthase B; Provisional.
Length = 298
Score = 76.1 bits (188), Expect = 2e-16
Identities = 27/66 (40%), Positives = 42/66 (63%)
Query: 31 RAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQ 90
+G V +DKP+ +SH+VVA +R+ K GH+GTLDP +G L++ ++RAT+L+
Sbjct: 8 GSGLVVVDKPAGMTSHDVVARCRRLFGTRKVGHAGTLDPMATGVLVLGVERATKLLGHLT 67
Query: 91 SAGKEY 96
K Y
Sbjct: 68 LTDKSY 73
Score = 36.4 bits (85), Expect = 0.007
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 173 CQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSG 205
C +GTY+R +G LGVG + LRR R G
Sbjct: 176 CSSGTYIRALARDLGAALGVGGHLTALRRTRVG 208
>gnl|CDD|234986 PRK01851, truB, tRNA pseudouridine synthase B; Provisional.
Length = 303
Score = 71.2 bits (175), Expect = 1e-14
Identities = 60/197 (30%), Positives = 83/197 (42%), Gaps = 35/197 (17%)
Query: 37 LDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEY 96
LDKP SS++ + KR+LR +K GH+GTLDP +G L +C AT+ + A K Y
Sbjct: 21 LDKPLGLSSNDALQRAKRLLRAKKAGHTGTLDPLATGLLPLCFGEATKFSQDLLDADKTY 80
Query: 97 ISIFKL----------------------HSAVENVAKASKKKMMIKQ-----GLLDKHGK 129
+ +L +A+E + I+Q L K GK
Sbjct: 81 EATLRLGVRTSTGDAEGEVLATRPVDCDPAALEAALARFTGE--IRQVPPMYSALKKDGK 138
Query: 130 P-NENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGL 188
P E A E EA + T +L+ L I + C GTY+RT +G
Sbjct: 139 PLYEYARAGITVEREA---RDVTIHALDLL--ACDLPDVTIRVTCSKGTYIRTLAEDIGE 193
Query: 189 VLGVGAQMIELRRNRSG 205
LG GA + LRR G
Sbjct: 194 ALGCGAHLTALRRTGVG 210
>gnl|CDD|234959 PRK01550, truB, tRNA pseudouridine synthase B; Provisional.
Length = 304
Score = 71.2 bits (175), Expect = 1e-14
Identities = 28/64 (43%), Positives = 42/64 (65%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSA 92
G + L KP +SH+ V +++ILR +K GH+GTLDP+ SG L +C+ RAT++ +
Sbjct: 3 GVLLLHKPRGMTSHDCVFKLRKILRTKKVGHTGTLDPEVSGVLPICVGRATKIAEYLTDE 62
Query: 93 GKEY 96
GK Y
Sbjct: 63 GKTY 66
Score = 40.3 bits (95), Expect = 4e-04
Identities = 17/33 (51%), Positives = 18/33 (54%)
Query: 173 CQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSG 205
C GTYVRT V +G LG A M L R SG
Sbjct: 172 CSKGTYVRTLAVMIGEKLGYPAHMSHLVRTASG 204
>gnl|CDD|134035 PRK00020, truB, tRNA pseudouridine synthase B; Provisional.
Length = 244
Score = 68.9 bits (168), Expect = 4e-14
Identities = 55/200 (27%), Positives = 84/200 (42%), Gaps = 30/200 (15%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSA 92
G + LDKP SS+ + KR + K GH+GTLDP +G L+ C+ RAT++ A
Sbjct: 11 GVLLLDKPVGLSSNHALQRAKRTVDAAKAGHTGTLDPFATGLLVCCMGRATKISGRMLEA 70
Query: 93 GKEYISIFKLHSAVEN-------VAKASKKKMMIKQG----LLDKHGKPNENTPASYLA- 140
K Y + + ++ VA+A +++ +L + E P Y A
Sbjct: 71 DKTYQATLQFGEETDSGDLTGHIVARAPDGFAGVEEAALRDVLSRFVGTIEQIPPMYSAL 130
Query: 141 ---------------ELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVH 185
EL+ P ++ T L+S + I + C GTY+RT
Sbjct: 131 KRDGKPLYEYARAGIELDRPP-RQVTIRHIELLS--FSGMQAQIDVACSKGTYIRTLAQD 187
Query: 186 MGLVLGVGAQMIELRRNRSG 205
+G LG A + LRR G
Sbjct: 188 IGRALGCHAHLAALRRTHVG 207
>gnl|CDD|235042 PRK02484, truB, tRNA pseudouridine synthase B; Provisional.
Length = 294
Score = 69.6 bits (171), Expect = 4e-14
Identities = 27/65 (41%), Positives = 41/65 (63%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSA 92
G +NL K + +SH+ V +++IL+ +K GH GTLDP G L + + +ATRL++ A
Sbjct: 4 GIINLKKEAGMTSHDAVFKLRKILQTKKIGHGGTLDPDVVGVLPIAVGKATRLIEYMTEA 63
Query: 93 GKEYI 97
GK Y
Sbjct: 64 GKVYE 68
Score = 39.2 bits (92), Expect = 0.001
Identities = 16/34 (47%), Positives = 17/34 (50%)
Query: 172 KCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSG 205
C GTYVRT V +G LG A M L R S
Sbjct: 172 ACSKGTYVRTLAVDLGEKLGYAAHMSFLTRTASA 205
>gnl|CDD|184522 PRK14123, PRK14123, tRNA pseudouridine synthase B; Provisional.
Length = 305
Score = 67.5 bits (165), Expect = 2e-13
Identities = 56/213 (26%), Positives = 89/213 (41%), Gaps = 35/213 (16%)
Query: 44 SSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEY---ISIF 100
+SH+VV +++IL+ +K GH+GTLDP+ +G L VCI ATR+ GK Y +SI
Sbjct: 15 TSHDVVFKLRKILKTKKIGHTGTLDPEVAGVLPVCIGNATRVSDYVMDMGKAYEATVSIG 74
Query: 101 KLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPASYLAELEAAP--------NKKPTY 152
+ + + + K + D + + + +E P N K Y
Sbjct: 75 RSTTTEDQTGDTLETKGVHSA---DFNKDDIDRLLEQFKGIIEQIPPMYSSVKVNGKKLY 131
Query: 153 -------------MKSNLIS----SDVTLSTGI----IWLKCQAGTYVRTYCVHMGLVLG 191
K N+ S++ I + C GTY+RT +G+ LG
Sbjct: 132 EYARNNETVERPKRKVNIKDIGRISELDFKENECHFKIRVICGKGTYIRTLATDIGVKLG 191
Query: 192 VGAQMIELRRNRSGIQSEEDGLVTFRQEHMFEH 224
A M +L R SG +D L + + + E
Sbjct: 192 FPAHMSKLTRIESGGFVLKDSLTLEQIKELHEQ 224
>gnl|CDD|184521 PRK14122, PRK14122, tRNA pseudouridine synthase B; Provisional.
Length = 312
Score = 66.4 bits (162), Expect = 6e-13
Identities = 38/110 (34%), Positives = 53/110 (48%), Gaps = 17/110 (15%)
Query: 38 DKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYI 97
DKP +SH+VV +R L + GH+GTLDP +G L++C D +T+LV + KEY+
Sbjct: 7 DKPLGLTSHDVVNRARRALGTRRVGHTGTLDPLATGVLVLCTDDSTKLVPFLSAEDKEYL 66
Query: 98 SIFKLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPASYLAE--LEAA 145
+ + LD G +E P S L E LEAA
Sbjct: 67 AWVSFGATTPT---------------LDAEGPISEEAPVSPLDEKDLEAA 101
Score = 32.8 bits (75), Expect = 0.10
Identities = 18/51 (35%), Positives = 26/51 (50%)
Query: 163 TLSTGIIWLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGL 213
T ++ L +GTYVR++ +G LGV A + L R R G ED +
Sbjct: 188 EYPTALLRLVVGSGTYVRSFARDLGAALGVPAHLSGLVRTRVGRYGLEDAV 238
>gnl|CDD|179469 PRK02755, truB, tRNA pseudouridine synthase B; Provisional.
Length = 295
Score = 65.8 bits (161), Expect = 8e-13
Identities = 26/53 (49%), Positives = 40/53 (75%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRL 85
G++NLDKP+ +SH+ VA ++R+LR ++ GH GTLDP +G L + + +ATRL
Sbjct: 4 GFLNLDKPAGLTSHDCVARLRRLLRLKRVGHGGTLDPAATGVLPIALGKATRL 56
Score = 36.5 bits (85), Expect = 0.006
Identities = 16/41 (39%), Positives = 21/41 (51%)
Query: 173 CQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGL 213
C AGTY+R+ +G VLG G + LRR +S L
Sbjct: 168 CGAGTYIRSLARDLGAVLGTGGTLAALRRTQSLGFHLAQSL 208
>gnl|CDD|179300 PRK01528, truB, tRNA pseudouridine synthase B; Provisional.
Length = 292
Score = 63.1 bits (153), Expect = 8e-12
Identities = 58/204 (28%), Positives = 90/204 (44%), Gaps = 25/204 (12%)
Query: 34 YVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAG 93
++N+ KP SS ++V+ +K+IL K GH+GTLD + G L + + AT+LV+ A
Sbjct: 5 WLNIYKPRGISSAKLVSIVKKILGKVKIGHAGTLDVEAEGVLPLAVGEATKLVQLLIDAK 64
Query: 94 KEYISIFKLHSAVENVAKASKKKMMIKQGLLDKH----------GKPNENTPA------- 136
K YI K ++ + K + K + K G + PA
Sbjct: 65 KTYIFTVKFGKQTDS-GDYAGKVIATKDYIPSKEEAYAVCSKFIGNITQIPPAFSALKVN 123
Query: 137 ---SY-LAELEAAPNKKP---TYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLV 189
+Y LA KP T ++ D +T + +C GTY+RT + L
Sbjct: 124 GVRAYKLAREGKEVELKPRNITIYDLKCLNFDEKNATATYYTECSKGTYIRTLAEDLALS 183
Query: 190 LGVGAQMIELRRNRSGIQSEEDGL 213
L +IELRR + GI EE+ +
Sbjct: 184 LQSLGFVIELRRTQVGIFKEENAI 207
>gnl|CDD|179381 PRK02193, truB, tRNA pseudouridine synthase B; Provisional.
Length = 279
Score = 61.3 bits (149), Expect = 3e-11
Identities = 52/201 (25%), Positives = 79/201 (39%), Gaps = 40/201 (19%)
Query: 37 LDKPSNPSSHEVV---AWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAG 93
L KP SS + + A I +K GH+GTLDP SG L+V D T+L+
Sbjct: 5 LYKPKGISSFKFIKNFAKTNNI---KKIGHTGTLDPLASGLLLVATDEDTKLIDYLDQKD 61
Query: 94 KEYISIFKL---------HSAVENVAKASK--KKMMIKQGLLDKHGKPNENTPASYLA-- 140
K YI+ K + NV++ K K+ + + L+ + P + A
Sbjct: 62 KTYIAKIKFGFISTTYDSEGQIINVSQNIKVTKENLEEA--LNNLVGSQKQVPPVFSAKK 119
Query: 141 ----------------ELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCV 184
EL+ K K L++ D L + GTY+R+
Sbjct: 120 VNGKRAYDLARQGKQIELKPIEIK---ISKIELLNFDEKLQNCVFMWVVSRGTYIRSLIH 176
Query: 185 HMGLVLGVGAQMIELRRNRSG 205
+G +L GA M +L R + G
Sbjct: 177 DLGKMLKTGAYMSDLERTKIG 197
>gnl|CDD|237834 PRK14846, truB, tRNA pseudouridine synthase B; Provisional.
Length = 345
Score = 61.2 bits (148), Expect = 4e-11
Identities = 55/204 (26%), Positives = 86/204 (42%), Gaps = 25/204 (12%)
Query: 34 YVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAG 93
++N+ KP SS ++V+ +K+IL K GH+GTLD + G L + AT+L+ A
Sbjct: 5 WLNIYKPRGISSAQLVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEATKLIHLLIDAR 64
Query: 94 KEYISIFKLHSAVENVAKASK----KKMMIKQ----GLLDKHGKPNENTPASYLA----- 140
K YI K + A K K + Q + K P ++ A
Sbjct: 65 KTYIFTVKFGMQTNSGDCAGKVIATKDCIPSQEEAYAVCSKFIGNVTQIPPAFSALKVNG 124
Query: 141 -----------ELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLV 189
++E P Y ++ D +T + +C GTY+RT + L
Sbjct: 125 VRAYKLAREGKKVELKPRNITIY-DLKCLNFDEKNATATYYTECSKGTYIRTLAEDLALS 183
Query: 190 LGVGAQMIELRRNRSGIQSEEDGL 213
L +IELRR + GI EE+ +
Sbjct: 184 LQSLGFVIELRRTQVGIFKEENAI 207
>gnl|CDD|235442 PRK05389, truB, tRNA pseudouridine synthase B; Provisional.
Length = 305
Score = 60.7 bits (148), Expect = 6e-11
Identities = 23/54 (42%), Positives = 35/54 (64%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLV 86
G++ LDKP+ +S E V+ +K + +K GH+GTLDP SG L + + AT+ V
Sbjct: 14 GWLILDKPAGMTSTEAVSKVKWLFDAQKAGHAGTLDPLASGVLPIALGEATKTV 67
Score = 34.9 bits (81), Expect = 0.024
Identities = 17/41 (41%), Positives = 22/41 (53%)
Query: 173 CQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGL 213
C GTYVR+ +G LG + LRR R G +EED +
Sbjct: 176 CGKGTYVRSLARDLGRALGCYGHIAALRRTRVGPFTEEDAI 216
>gnl|CDD|179199 PRK00989, truB, tRNA pseudouridine synthase B; Provisional.
Length = 230
Score = 57.9 bits (140), Expect = 3e-10
Identities = 54/204 (26%), Positives = 91/204 (44%), Gaps = 41/204 (20%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRA-TRLVKSQQS 91
G + +DKP +S ++ + +++ +K GH+GTLDP +G +++ I R TRL
Sbjct: 10 GILLVDKPQGRTSFSLIRSLTKLIGVKKIGHAGTLDPFATGVMVMLIGRKFTRLSDILLF 69
Query: 92 AGKEYISIFKLHSAVEN------VAKASKKKMMIKQGLLDKHGKPNENTPASYL-AELEA 144
KEY ++ L + ++ + SKK +++ L + ASY E++
Sbjct: 70 EDKEYAAVAHLGTTTDSYDCDGKIVGRSKKIPTLEEVL----------SAASYFQGEIQQ 119
Query: 145 AP----------NKKPTYMKSNLI----SSDVTLSTGII---------WLKCQAGTYVRT 181
P K Y + L S V + + ++C GTY+R+
Sbjct: 120 VPPMFSAKKVQGKKLYEYARQGLSIERRPSTVQVHLQLTKYEYPLLHFVVQCSKGTYIRS 179
Query: 182 YCVHMGLVLGVGAQMIELRRNRSG 205
+G +LG GA + ELRR RSG
Sbjct: 180 IAHELGNMLGCGAYLEELRRLRSG 203
>gnl|CDD|235333 PRK05033, truB, tRNA pseudouridine synthase B; Provisional.
Length = 312
Score = 55.6 bits (135), Expect = 3e-09
Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQ-- 90
G + LDKP SS++ + +KR+ K GH+G LDP +G L +C+ AT+ SQ
Sbjct: 11 GVLLLDKPQGMSSNDALQKVKRLFNANKAGHTGALDPLATGMLPICLGEATKF--SQYLL 68
Query: 91 SAGKEYISIFKL 102
+ K Y +L
Sbjct: 69 DSDKRYRVTARL 80
Score = 37.1 bits (87), Expect = 0.004
Identities = 15/34 (44%), Positives = 19/34 (55%)
Query: 172 KCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSG 205
C GTY+RT +G LG GA +I LRR +
Sbjct: 171 HCSKGTYIRTLVDDLGEKLGCGAHVIYLRRTQVA 204
>gnl|CDD|179870 PRK04642, truB, tRNA pseudouridine synthase B; Provisional.
Length = 300
Score = 54.1 bits (130), Expect = 1e-08
Identities = 25/64 (39%), Positives = 38/64 (59%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSA 92
G + LDKP+ SS+ + +R+LR EK GH+G+LDP +G L +C AT++ +
Sbjct: 11 GILLLDKPAGLSSNNALQAARRLLRAEKGGHTGSLDPLATGLLPLCFGEATKIAGLLLGS 70
Query: 93 GKEY 96
K Y
Sbjct: 71 AKAY 74
Score = 34.1 bits (78), Expect = 0.045
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 173 CQAGTYVRTYCVHMGLVLGVGAQMIELRR 201
C +GTY+R+ +G VLG GA + LRR
Sbjct: 173 CGSGTYIRSLARDLGEVLGCGAHIAALRR 201
>gnl|CDD|179739 PRK04099, truB, tRNA pseudouridine synthase B; Provisional.
Length = 273
Score = 46.1 bits (110), Expect = 4e-06
Identities = 22/58 (37%), Positives = 32/58 (55%)
Query: 39 KPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEY 96
KP+ SS+ ++ +KR +K G SGTLDP G LIV + T+L + + K Y
Sbjct: 9 KPAGMSSNAFLSRLKRKYGVKKAGFSGTLDPFAKGVLIVAFGQYTKLFRFLKKTPKTY 66
>gnl|CDD|211344 cd02867, PseudoU_synth_TruB_4, Pseudouridine synthase homolog 4.
This group consists of Eukaryotic TruB proteins similar
to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4,
makes psi55 in the T loop of both cytoplasmic and
mitochondrial tRNAs. Psi55 is almost universally
conserved. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule
to pseudouridines (5-ribosyluracil, psi).
Length = 312
Score = 44.0 bits (104), Expect = 2e-05
Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 29/91 (31%)
Query: 38 DKPSNPSSHEVVAWIKRILRCE-----------------------------KTGHSGTLD 68
+KPS +S +V+ +K + K GH GTLD
Sbjct: 6 NKPSGITSAQVLNDLKPLFLNSALFKDKIQRAVAKRGKKARRRKGRKRSKLKIGHGGTLD 65
Query: 69 PKTSGCLIVCIDRATRLVKSQQSAGKEYISI 99
P +G L+V + T+ ++ S K Y +
Sbjct: 66 PLATGVLVVGVGAGTKQLQDYLSCSKTYEAT 96
>gnl|CDD|211325 cd02550, PseudoU_synth_Rsu_Rlu_like, 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 = 33.5 bits (77), Expect = 0.036
Identities = 24/106 (22%), Positives = 40/106 (37%), Gaps = 9/106 (8%)
Query: 34 YVNLDKPSNPSSH-------EVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDR--ATR 84
+ L+KPS H V L + +G LD TSG L++ D R
Sbjct: 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRR 60
Query: 85 LVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIKQGLLDKHGKP 130
L + ++ KEY+ + E + + + GL+D+
Sbjct: 61 LTEPRREIEKEYLVTVRGELDEEGIEDLATVRRGRLSGLVDEGVPL 106
>gnl|CDD|211324 cd01291, PseudoU_synth, Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule
to pseudouridines (5-ribosyluracil, psi).
Pseudouridine synthases contains the RsuA/RluD, TruA,
TruB and TruD families. This group consists of
eukaryotic, bacterial and archeal pseudouridine
synthases. Some psi sites such as psi55,13,38 and 39
in tRNA are highly conserved, being in the same
position in eubacteria, archeabacteria and eukaryotes.
Other psi sites occur in a more restricted fashion, for
example psi2604in 23S RNA made by E.coli RluF has only
been detected in E.coli. Human dyskerin with the help
of guide RNAs makes the hundreds of psueudouridnes
present in rRNA and small nuclear RNAs (snRNAs).
Mutations in human dyskerin cause X-linked dyskeratosis
congenitas. Missense mutation in human PUS1 causes
mitochondrial myopathy and sideroblastic anemia
(MLASA).
Length = 87
Score = 29.8 bits (68), Expect = 0.26
Identities = 8/43 (18%), Positives = 16/43 (37%), Gaps = 1/43 (2%)
Query: 37 LDKPSNPSSHEVVAWIK-RILRCEKTGHSGTLDPKTSGCLIVC 78
L KP + K + ++ G++G D + +V
Sbjct: 1 LYKPGGDTMEAARQLAKLLGIPPKRVGYAGRKDKRAVTTQLVS 43
>gnl|CDD|173780 cd01030, TOPRIM_TopoIIA_like, TOPRIM_TopoIIA_like:
topoisomerase-primase (TOPRIM) nucleotidyl
transferase/hydrolase domain of the type found in
proteins of the type IIA family of DNA topoisomerases
similar to Saccharomyces cerevisiae Topoisomerase II.
TopoIIA enzymes cut both strands of the duplex DNA to
remove (relax) both positive and negative supercoils in
DNA. These enzymes covalently attach to the 5' ends of
the cut DNA, separate the free ends of the cleaved
strands, pass another region of the duplex through this
gap, then rejoin the ends. These proteins also catenate/
decatenate duplex rings. The TOPRIM domain has two
conserved motifs, one of which centers at a conserved
glutamate and the other one at two conserved aspartates
(DxD). The conserved glutamate may act as a general base
in strand joining and as a general acid in strand
cleavage by topisomerases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 115
Score = 29.8 bits (68), Expect = 0.48
Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 9/62 (14%)
Query: 80 DRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMM-------IKQGLLDKHGKPNE 132
D A K Q + + ++F L + NV KAS KK++ I + L GK +
Sbjct: 9 DSAGGSAK--QGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGKDDF 66
Query: 133 NT 134
+
Sbjct: 67 DL 68
>gnl|CDD|213293 cd05927, LC-FACS_euk, Eukaryotic long-chain fatty acid CoA
synthetase (LC-FACS). The members of this family are
eukaryotic fatty acid CoA synthetases that activate
fatty acids with chain lengths of 12 to 20. LC-FACS
catalyzes the formation of fatty acyl-CoA in a two-step
reaction: the formation of a fatty acyl-AMP molecule as
an intermediate, and the formation of a fatty acyl-CoA.
This is a required step before free fatty acids can
participate in most catabolic and anabolic reactions.
Organisms tend to have multiple isoforms of LC-FACS
genes with multiple splice variants. For example, nine
genes are found in Arabidopsis and six genes are
expressed in mammalian cells.
Length = 539
Score = 29.4 bits (67), Expect = 1.6
Identities = 17/56 (30%), Positives = 23/56 (41%), Gaps = 12/56 (21%)
Query: 60 KTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYIS------IFKLHSAVENV 109
TG G P G L + IDR L K Q EY++ I+K V+ +
Sbjct: 382 HTGDIGEWLPD--GTLKI-IDRKKNLFKLSQG---EYVALEKLENIYKSSPLVDQI 431
>gnl|CDD|171463 PRK12392, PRK12392, bacteriochlorophyll c synthase; Provisional.
Length = 331
Score = 28.1 bits (63), Expect = 3.6
Identities = 13/38 (34%), Positives = 18/38 (47%)
Query: 169 IWLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGI 206
WL G V Y + +GLVL + Q+ R + GI
Sbjct: 241 AWLAWSWGFTVLMYFILVGLVLNIVIQIQLYRDPKGGI 278
>gnl|CDD|221188 pfam11725, AvrE, Pathogenicity factor. This family is secreted by
gram-negative Gammaproteobacteria such as Pseudomonas
syringae of tomato and the fire blight plant pathogen
Erwinia amylovora, amongst others. It is an essential
pathogenicity factor of approximately 198 kDa. Its
injection into the host-plant is dependent upon the
bacterial type III or Hrp secretion system. The family is
long and carries a number of predicted functional
regions, including an ERMS or endoplasmic reticulum
membrane retention signal at both the C- and the
N-termini, a leucine-zipper motif from residues 539-560,
and a nuclear localisation signal at 1358-1361. this
conserved AvrE-family of effectors is among the few that
are required for full virulence of many phytopathogenic
pseudomonads, erwinias and pantoeas.
Length = 1771
Score = 28.6 bits (64), Expect = 3.8
Identities = 8/41 (19%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 112 ASKKKMMI--KQGLLDKHGKPNENTPASYLAELEAAPNKKP 150
++ +++ +QG+L+ HG+ N+ L + N
Sbjct: 981 STTAAILLGQQQGVLNSHGEINKPFKPKKSKALGQSFNVNR 1021
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 28.3 bits (63), Expect = 4.1
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 7/48 (14%)
Query: 93 GKEYISIFKLHSAVENVAKASKKKMM-------IKQGLLDKHGKPNEN 133
G+ Y +F L + NV +AS K++M IKQ L +HGK E+
Sbjct: 474 GRNYYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYES 521
>gnl|CDD|187723 cd08821, FMT_core_like_1, Formyl transferase catalytic core
domain found in a group of proteins with unknown
functions. Formyl transferase catalytic core domain
found in a group of proteins with unknown functions.
Formyl transferase catalyzes the transfer of one-carbon
groups, specifically the formyl- or hydroxymethyl-
group. This domain contains a Rossmann fold and it is
the catalytic domain of the enzyme.
Length = 211
Score = 27.3 bits (61), Expect = 6.7
Identities = 10/18 (55%), Positives = 12/18 (66%), Gaps = 2/18 (11%)
Query: 11 HYTPLPFGK--SPLQRTI 26
H T LP+G+ SPLQ I
Sbjct: 71 HMTDLPYGRGGSPLQNLI 88
>gnl|CDD|130682 TIGR01621, RluA-like, pseudouridine synthase Rlu family protein,
TIGR01621. This model represents a clade of sequences
within the pseudouridine synthase superfamily
(pfam00849). The superfamily includes E. coli proteins:
RluA, RluB, RluC, RluD, and RsuA. The sequences modeled
here are most closely related to RluA. Neisseria, among
those species hitting this model, does not appear to
have an RluA homolog. It is presumed that these
sequences function as pseudouridine synthases, although
perhaps with different specificity [Protein synthesis,
tRNA and rRNA base modification].
Length = 217
Score = 26.8 bits (59), Expect = 8.0
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 67 LDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIKQGL 123
LD TSG L++ ++ + SQ A + I K + A+ + K KK+ +I +
Sbjct: 50 LDKMTSGILLLALNAESASELSQGFAKR---KIEKTYLALSS-KKPKKKQGLICGDM 102
>gnl|CDD|153321 cd07637, BAR_ACAP3, The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP
with Coiled-coil, ANK repeat and PH domain containing
protein 3. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. ACAP3 (ArfGAP with
Coiled-coil, ANK repeat and PH domain containing protein
3), also called centaurin beta-5, is presumed to be an
Arf GTPase activating protein (GAP) based on its
similarity to the Arf6-specific GAPs ACAP1 and ACAP2.
The specific function of ACAP3 is still unknown. ACAP3
contains an N-terminal BAR domain, followed by a
Pleckstrin homology (PH) domain, an Arf GAP domain, and
C-terminal ankyrin (ANK) repeats. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 200
Score = 26.9 bits (59), Expect = 8.4
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 79 IDRATRLVKSQQSAGKEYISIFKLH-SAVENVAKASKKKMMIKQGLLDKHG 128
+D+ +L AGK Y + KL S + ++++ KK MI + LDK G
Sbjct: 18 LDKLVKLCSGMIEAGKAYATTNKLFVSGIRDLSQQCKKDEMISE-CLDKFG 67
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
0.318 0.132 0.395
Gapped
Lambda K H
0.267 0.0653 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,497,013
Number of extensions: 1025564
Number of successful extensions: 738
Number of sequences better than 10.0: 1
Number of HSP's gapped: 735
Number of HSP's successfully gapped: 63
Length of query: 232
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 138
Effective length of database: 6,768,326
Effective search space: 934028988
Effective search space used: 934028988
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 (21.7 bits)
S2: 57 (25.9 bits)