RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780295|ref|YP_003064708.1| tRNA pseudouridine synthase A
[Candidatus Liberibacter asiaticus str. psy62]
(247 letters)
>gnl|CDD|178798 PRK00021, truA, tRNA pseudouridine synthase A; Validated.
Length = 244
Score = 341 bits (878), Expect = 8e-95
Identities = 118/246 (47%), Positives = 151/246 (61%), Gaps = 2/246 (0%)
Query: 1 MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
M+R + IEY+G+ + GWQRQ NG ++QG +EKA+ + GE V V GAGRTD+GVHAL Q
Sbjct: 1 MMRIALTIEYDGTNFHGWQRQPNGRTVQGELEKALSKLAGEPVRVIGAGRTDAGVHALGQ 60
Query: 61 VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
VAHFD P +ALNA L D I++L V FHARFSA R Y YRI R
Sbjct: 61 VAHFDTPAPRPPEKWRRALNALLP--DDIAVLWAEEVPDDFHARFSAKARRYRYRIYNRP 118
Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
A +G W P LD + M AAQ+L+G HDFT+FR+ CQ+ SP+RTI DV
Sbjct: 119 ARPPFLRGYVWHYPYPLDVDAMNEAAQYLLGEHDFTSFRASGCQSKSPVRTIYEADVTRE 178
Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
G+ I + A FLH +R+ VG+L VG GK D+++ L+A+DR GP AP EGLY
Sbjct: 179 GDFIVFDISANGFLHNMVRNIVGTLLEVGKGKRPPEDIKELLEAKDRTLAGPTAPAEGLY 238
Query: 241 FDSVEY 246
V+Y
Sbjct: 239 LVEVDY 244
>gnl|CDD|161691 TIGR00071, hisT_truA, pseudouridylate synthase I. universal so
far, single copy in all prokaryotes, 3 in yeast. Trusted
cutoff for orthology is about 100 based on 1 match only
in complete prokaryote with length > 200.
Length = 227
Score = 204 bits (521), Expect = 2e-53
Identities = 91/235 (38%), Positives = 122/235 (51%), Gaps = 13/235 (5%)
Query: 6 MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
+ I Y+GS Y GWQRQ N ++QG +EKA+ + + + + AGRTD GVHA+ QV FD
Sbjct: 5 LKIAYDGSNYHGWQRQPNKRTVQGELEKALEAIGKKKITIMSAGRTDKGVHAMGQVISFD 64
Query: 66 LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
+E L LNA L I + L+ V+ FHARFSA +R Y Y + +
Sbjct: 65 TPKEIPDNKLNAKLNALLP--PDIRVKALAPVNDNFHARFSASKRHYRYILYNHRH---- 118
Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
LD E MR AA+ L+G+HDF+ F ++ SPIRTI V+ G I
Sbjct: 119 -------YYSPLDLEKMRAAAKQLLGKHDFSNFSKAKSKSRSPIRTISDIKVSESGEYII 171
Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
++ SFL +R VG+L LVG GK + K L A+ R AP GLY
Sbjct: 172 FDIIGNSFLWHMVRKIVGALVLVGRGKLPPEWVAKLLDAKKRNLAPTTAPANGLY 226
>gnl|CDD|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed.
Length = 245
Score = 194 bits (496), Expect = 1e-50
Identities = 92/247 (37%), Positives = 144/247 (58%), Gaps = 3/247 (1%)
Query: 1 MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
M + I+Y+GS Y GWQ+ N ++IQG IE + +TGE + + G GRTD+GVHAL
Sbjct: 1 MRNIKLTIQYDGSRYKGWQKLGNNDNTIQGKIESVLSEMTGEEIEIIGCGRTDAGVHALN 60
Query: 60 QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
QVA+F + + K LN YL + I + N+ VD++FHAR++ ++YLY+I
Sbjct: 61 QVANFQTDEKLSEDKIKKYLNEYL--PNDIVVTNVEEVDERFHARYNVKSKTYLYKIWNE 118
Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
+ + + + + LD + M+ AA++LVG HDFT+F + + S +R I D+
Sbjct: 119 KFHNVFMRKYSMHVNEKLDVKAMKEAAKYLVGSHDFTSFTNAKSKKKSTVREIYSIDIME 178
Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
++IRV FLH +R VG+L VG G+ + D+++ L+A+DR + AP GL
Sbjct: 179 EDGFVQIRVSGNGFLHNMVRIIVGALIEVGLGQLKAEDIKQILEAKDRNQANCTAPASGL 238
Query: 240 YFDSVEY 246
Y ++VEY
Sbjct: 239 YLENVEY 245
>gnl|CDD|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional.
Length = 245
Score = 189 bits (481), Expect = 7e-49
Identities = 91/246 (36%), Positives = 132/246 (53%), Gaps = 5/246 (2%)
Query: 1 MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
M R ++ Y+GS +FG+Q Q + ++QG E A+ + + + AGRTD+GVHA Q
Sbjct: 1 MKRVAAVVSYDGSNFFGYQGQPDVRTVQGVFEDALERIFKQRIYTQAAGRTDTGVHANGQ 60
Query: 61 VAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
V F+ + + K A+NA L D I + + V K FH RF A +R Y Y I+T
Sbjct: 61 VIAFNCPNDRMTEEDIKNAMNANL--PDDIYVKKVFEVPKNFHPRFDAKKRIYHYFILTS 118
Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
+ + W P LD E MR AA++L G HDFT+F++ +P+RTI +
Sbjct: 119 KEKNVFLRKYVWWFPYELDLEAMRKAAKYLEGEHDFTSFKTGS-DERNPVRTIYRIRILR 177
Query: 180 FGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
LI IRV RSFL +R+ VG+L VG G+W +++ L+A+DR + AP G
Sbjct: 178 LKKDLILIRVEGRSFLRRMVRNIVGALVKVGLGQWEPEKIKEVLEARDRSKAAGTAPAHG 237
Query: 239 LYFDSV 244
LY V
Sbjct: 238 LYLYKV 243
>gnl|CDD|173052 PRK14588, PRK14588, tRNA pseudouridine synthase ACD; Provisional.
Length = 272
Score = 156 bits (395), Expect = 6e-39
Identities = 88/245 (35%), Positives = 126/245 (51%), Gaps = 7/245 (2%)
Query: 6 MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
+++EY+G+ + G Q Q +G ++QG++E A +T E + AGRTD+GVHA QVAH
Sbjct: 6 LLLEYDGTDFAGSQWQTDGRTVQGALEAAWQALTQERRRIVLAGRTDAGVHARGQVAHVQ 65
Query: 66 LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
+ + LNA+L I + N FHARFSAI+R Y Y I AP
Sbjct: 66 TDTRHSLATIWRGLNAHLPED--IGVQNAWEAPPDFHARFSAIQREYRYVIDCAPAPSPQ 123
Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS---FGN 182
+ + +LD M A + L+G HDF F + + S+ +RT FG
Sbjct: 124 LRHQVLHYAGTLDVAAMDAALKLLIGTHDFAAFTTAPQEGST-VRTCYWARCTDTEWFGR 182
Query: 183 -LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
L+ I V A +FL +R+ VG+L LVG G+ T L ++DR+ GP AP GLY
Sbjct: 183 PLLAIEVAANAFLQHMVRNIVGTLLLVGRGRMTVDQFGAVLASRDRRLAGPTAPAHGLYL 242
Query: 242 DSVEY 246
+V Y
Sbjct: 243 TAVRY 247
>gnl|CDD|173053 PRK14589, PRK14589, tRNA pseudouridine synthase ACD; Provisional.
Length = 265
Score = 104 bits (262), Expect = 2e-23
Identities = 76/254 (29%), Positives = 107/254 (42%), Gaps = 38/254 (14%)
Query: 2 IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHA 57
+R I Y G+ +FG Q Q + +++G A + AGRTD GVHA
Sbjct: 1 MRLAFRISYIGTRFFGSQYQPDQRTVEGEFIAACRRLGLFSDWREAGFALAGRTDRGVHA 60
Query: 58 LRQVAHF-----DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
QV F + E ALN L I + V + FH R+ AI R+Y
Sbjct: 61 RGQVLAFSTHKPERAVE--------ALNGQL--PPDIWCTGWAEVPESFHPRYDAISRTY 110
Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
Y + P D MR AA +G HDF+ F + + SP+RTI
Sbjct: 111 RYYF--SRPPS--------------DINAMRDAAGEFIGTHDFSCFARV--EGKSPVRTI 152
Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
V S G V A+SFL +R G+L +G+G+ D+E+ L +++ P
Sbjct: 153 LRIRVFSDGGFPVFEVTAQSFLWHMVRCMAGALLQIGEGEMEPDDIERLLSGPCKRKVKP 212
Query: 233 LAPPEGLYFDSVEY 246
AP EGL V+
Sbjct: 213 -APAEGLVLWDVDC 225
>gnl|CDD|173051 PRK14587, PRK14587, tRNA pseudouridine synthase ACD; Provisional.
Length = 256
Score = 69.9 bits (171), Expect = 6e-13
Identities = 71/245 (28%), Positives = 110/245 (44%), Gaps = 37/245 (15%)
Query: 4 YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAG-RTDSGVHALRQVA 62
Y I Y+G+ ++G+ N S+E A+ V GEI+ G G RTD GV A V
Sbjct: 3 YLYRIAYDGTLFYGFTGHPN------SLEPALRRVFGEIL---GRGSRTDPGVSA---VG 50
Query: 63 HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
+ + + +P+ + K+ + ++ V + F+ R A RR YLY AP
Sbjct: 51 NVVMTSQKLPLGYVNS-----KLPRGVWAWAVAEVPEGFNPR-RAKRRRYLY-----VAP 99
Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIRTIDHFDVNSFG 181
E D E MR AA+ L G HD+++F + A+ + T+ V G
Sbjct: 100 HWGE-----------DVEAMREAAELLAGTHDYSSFIQRRGEKATPTVTTVYEIGVELRG 148
Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
+LI + V R F + IR ++ G G + D+ + L+ + R P AP EGL
Sbjct: 149 DLIYLYFVGRGFRNKMIRKMAWAILAAGRGVLSRRDIAELLE-RPRPGAVPSAPAEGLVL 207
Query: 242 DSVEY 246
+EY
Sbjct: 208 LDIEY 212
>gnl|CDD|178627 PLN03078, PLN03078, Putative tRNA pseudouridine synthase;
Provisional.
Length = 513
Score = 39.9 bits (93), Expect = 7e-04
Identities = 35/131 (26%), Positives = 57/131 (43%), Gaps = 21/131 (16%)
Query: 3 RYCMIIEYNGSGYFGWQRQKNGSS---IQGSIEKAIFLVTGEIVVVHG---------AGR 50
+ + + Y G+ Y G Q+Q++ SS I+G +E AIF G +G + R
Sbjct: 72 KVVLRVGYVGTDYRGLQKQRDLSSLSTIEGELETAIFKAGGIRESNYGNLHKIGWARSSR 131
Query: 51 TDSGVHALRQVAHFDL---VREWVP----VILCKALNAYLKISDTISILNLSIVDKQFHA 103
TD GVH+L + + W + L K +N++L D I + ++ + F
Sbjct: 132 TDKGVHSLATMISLKMEIPENAWKDDPDGIALAKFINSHL--PDNIRVFSILPAQRSFDP 189
Query: 104 RFSAIRRSYLY 114
R R Y Y
Sbjct: 190 RRECDLRKYSY 200
>gnl|CDD|178368 PLN02769, PLN02769, Probable galacturonosyltransferase.
Length = 629
Score = 28.1 bits (63), Expect = 2.1
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 16/58 (27%)
Query: 91 ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQH 148
IL+++ + FH + SA +LY+ L ++ +PKS C +MR+ ++
Sbjct: 268 ILDMTEDEAHFHMKQSA----FLYQ-------LGVQT-----MPKSHHCLSMRLTVEY 309
>gnl|CDD|162753 TIGR02188, Ac_CoA_lig_AcsA, acetate--CoA ligase. This model
describes acetate-CoA ligase (EC 6.2.1.1), also called
acetyl-CoA synthetase and acetyl-activating enzyme. It
catalyzes the reaction ATP + acetate + CoA = AMP +
diphosphate + acetyl-CoA and belongs to the family of
AMP-binding enzymes described by Pfam model pfam00501.
Length = 625
Score = 28.0 bits (63), Expect = 2.4
Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
I +FV +LK DG +L K L+ RKE GP+A P+ + F
Sbjct: 540 IYAFV-TLK---DGYEPDDELRKELRKHVRKEIGPIAKPDKIRF 579
>gnl|CDD|184741 PRK14554, PRK14554, putative pseudouridylate synthase; Provisional.
Length = 422
Score = 28.0 bits (63), Expect = 2.6
Identities = 23/111 (20%), Positives = 38/111 (34%), Gaps = 23/111 (20%)
Query: 20 RQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHAL------------RQVAHFDL 66
+++ S++ I K + GE V HGAGR D L + DL
Sbjct: 215 KKQYPESVEELIAKPVIEAFGGEDAVFHGAGREDVDARMLGTGRPFVIEVKEPRKRKVDL 274
Query: 67 VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
+AL + + + NL ++ R + S YR +
Sbjct: 275 ----------EALEEEINADGKVEVENLRFATRKEVERIKEEKASKTYRAL 315
>gnl|CDD|180260 PRK05788, PRK05788, cobalamin biosynthesis protein CbiG; Validated.
Length = 315
Score = 27.5 bits (62), Expect = 3.1
Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 1/59 (1%)
Query: 77 KALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPK 135
K LNA + ++ +N ++V+ + + R+ R L K L PK
Sbjct: 136 KQLNAKIVNRESTKKVNAALVNGE-KVGLWGDELDPVIRVSLRNDVPELPKVTVKLRPK 193
>gnl|CDD|184164 PRK13583, hisG, ATP phosphoribosyltransferase catalytic subunit;
Provisional.
Length = 228
Score = 27.3 bits (61), Expect = 4.0
Identities = 18/49 (36%), Positives = 22/49 (44%), Gaps = 11/49 (22%)
Query: 29 GSIE-----KAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVP 72
G +E + +FL EI GAGR D GV DLVRE +
Sbjct: 39 GRVEGEDDVELLFLSASEIPRELGAGRVDLGVTG------EDLVREKLA 81
>gnl|CDD|178388 PLN02791, PLN02791, Nudix hydrolase homolog.
Length = 770
Score = 26.7 bits (59), Expect = 6.2
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 10/40 (25%)
Query: 97 VDKQFHARFSAIRRSY----------LYRIITRQAPLALE 126
V+ ++ FS I + Y L + + R AP+ LE
Sbjct: 171 VNGEYGQLFSIIEKRYKVNTEARSLTLQKQLNRYAPVNLE 210
>gnl|CDD|179651 PRK03806, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 438
Score = 26.4 bits (59), Expect = 7.4
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 8/37 (21%)
Query: 123 LALEKGRAWLIPKS---LDCENMRIAAQHLVGRHDFT 156
L ++G WL K L+ + M+ L G+H++T
Sbjct: 240 LNRQQGETWLRVKGEKVLNTKEMK-----LSGQHNYT 271
>gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter;
Provisional.
Length = 588
Score = 26.1 bits (58), Expect = 9.4
Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 40 GEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKAL-NAYLKISDTISILNLSIVD 98
G + VV R ++ ALR +A +L+ +PV+ AL + + + TI++L + ++
Sbjct: 203 GNVSVVQSYNRIEAETQALRDIAD-NLLAAQMPVLSWWALASVLNRAASTITMLAILVLG 261
Query: 99 KQFHAR 104
+
Sbjct: 262 AALVQK 267
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.325 0.138 0.421
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,097,190
Number of extensions: 257837
Number of successful extensions: 611
Number of sequences better than 10.0: 1
Number of HSP's gapped: 593
Number of HSP's successfully gapped: 17
Length of query: 247
Length of database: 5,994,473
Length adjustment: 91
Effective length of query: 156
Effective length of database: 4,028,145
Effective search space: 628390620
Effective search space used: 628390620
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.3 bits)