RPS-BLAST 2.2.22 [Sep-27-2009]
Database: scop70_1_75
13,730 sequences; 2,407,596 total letters
Searching..................................................done
Query= gi|254780406|ref|YP_003064819.1| putative ribosomal large
subunit pseudouridine synthase B [Candidatus Liberibacter asiaticus
str. psy62]
(354 letters)
>d1kska4 d.265.1.3 (A:60-231) Ribosomal small subunit pseudouridine
516 synthase RsuA {Escherichia coli [TaxId: 562]}
Length = 172
Score = 118 bits (296), Expect = 7e-28
Identities = 41/167 (24%), Positives = 74/167 (44%), Gaps = 3/167 (1%)
Query: 74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
R ++ +KP G V + DPD + ++ + ++ + GRLDI+T GL+L+T+DG +
Sbjct: 2 RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 61
Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
+ P + Y V V D KG+ + L+ + +T +
Sbjct: 62 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVITPTQVRLT--I 119
Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
EG+ ++K++F V L R G L L G R ++++
Sbjct: 120 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 166
>d1vioa1 d.265.1.3 (A:58-231) Ribosomal small subunit pseudouridine
516 synthase RsuA {Haemophilus influenzae [TaxId: 727]}
Length = 174
Score = 108 bits (271), Expect = 7e-25
Identities = 43/175 (24%), Positives = 81/175 (46%), Gaps = 5/175 (2%)
Query: 71 ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGG 129
E + ++ +KP G V ++ D T++ + ++ S GRLD++T GL+LLT+DG
Sbjct: 1 EEGQYFMLNKPQGCVCSNDDG-DYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQ 59
Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
+ + P + Y V V+++ +GI+++G L+ N +
Sbjct: 60 WSHRITSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEILDDYNVNL 119
Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILRE 243
T + EG+ ++K++F KV L R G L L G R +++ + +
Sbjct: 120 T--ISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEK 172
>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal
domain {Escherichia coli [TaxId: 562]}
Length = 59
Score = 57.1 bits (138), Expect = 2e-09
Identities = 18/55 (32%), Positives = 27/55 (49%)
Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
R+ K IA+ SR R I RV V+G ++ AA ++ + DG PL +
Sbjct: 2 RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQ 56
>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal
domain {Haemophilus influenzae [TaxId: 727]}
Length = 58
Score = 56.6 bits (137), Expect = 3e-09
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
R+ K IA +R + + I Q VK+NG +++ +V + D I + L
Sbjct: 3 RLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELL 55
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli
[TaxId: 562]}
Length = 79
Score = 46.0 bits (109), Expect = 4e-06
Identities = 10/55 (18%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
+ ++ G + S + + IA+ +VKV+G + R +++ + G ++
Sbjct: 22 ELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQ 76
>d1ejea_ b.45.1.2 (A:) FMN-binding protein MTH152 {Archaeon
Methanobacterium thermoautotrophicum [TaxId: 145262]}
Length = 192
Score = 29.8 bits (66), Expect = 0.32
Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 59 HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGR 94
++ + P+ A R L +P +VTT D +G
Sbjct: 9 SMDFEDFPVESAHR---ILTPRPTVMVTTV-DEEGN 40
>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal
domain {Bacillus stearothermophilus [TaxId: 1422]}
Length = 99
Score = 29.0 bits (65), Expect = 0.60
Identities = 12/55 (21%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 16 VSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
+ +++ AGI+ S+R+ I + VNG L+ + + +E +R+
Sbjct: 34 LVELLVSAGISPSKRQAREDIQNGAIYVNGERLQDVGAILTAEHRLEGRFTVIRR 88
>d1rkda_ c.72.1.1 (A:) Ribokinase {Escherichia coli [TaxId: 562]}
Length = 306
Score = 29.0 bits (63), Expect = 0.64
Identities = 6/24 (25%), Positives = 14/24 (58%)
Query: 16 VSKVIARAGIASRREVERMIAQQR 39
V++ A+ + R E++ + +QR
Sbjct: 283 VTRKGAQPSVPWREEIDAFLDRQR 306
>d2vk9a1 c.68.1.22 (A:2-541) Alpha-toxin {Clostridium novyi [TaxId:
1542]}
Length = 540
Score = 27.6 bits (61), Expect = 1.6
Identities = 6/52 (11%), Positives = 20/52 (38%), Gaps = 3/52 (5%)
Query: 273 NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV---HRRNLASNVWMAKGIH 321
+ ++E+ D++ +S + L + +N ++ +K +
Sbjct: 49 SKLNELVDNYQTKYPSSGRNLALENFRDSLYSELRELIKNSRTSTIASKNLS 100
>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS),
C-terminal domain {Thermus thermophilus [TaxId: 274]}
Length = 81
Score = 25.9 bits (57), Expect = 5.2
Identities = 10/46 (21%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 16 VSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
V+++ AG+ S E R+I + ++++G +L + V +
Sbjct: 20 VARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPR 65
>d1k3ea_ d.198.1.1 (A:) Secretion chaperone CesT {Escherichia coli
[TaxId: 562]}
Length = 146
Score = 25.7 bits (56), Expect = 5.7
Identities = 9/48 (18%), Positives = 18/48 (37%)
Query: 98 FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
+ L F+ I +G + N L D L + +++ +Y
Sbjct: 5 SELLLEKFAEKIGIGSISFNENRLCSFAIDEIYYISLSDANDEYMMIY 52
Database: scop70_1_75
Posted date: Mar 27, 2010 6:21 PM
Number of letters in database: 2,407,596
Number of sequences in database: 13,730
Lambda K H
0.318 0.134 0.385
Gapped
Lambda K H
0.267 0.0603 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,278,816
Number of extensions: 60620
Number of successful extensions: 157
Number of sequences better than 10.0: 1
Number of HSP's gapped: 155
Number of HSP's successfully gapped: 13
Length of query: 354
Length of database: 2,407,596
Length adjustment: 86
Effective length of query: 268
Effective length of database: 1,226,816
Effective search space: 328786688
Effective search space used: 328786688
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: 53 (24.5 bits)