RPS-BLAST 2.2.26 [Sep-21-2011]
Database: scop70_1_75
13,730 sequences; 2,407,596 total letters
Searching..................................................done
Query= psy1178
(144 letters)
>d2apoa1 b.122.1.1 (A:247-331) Pseudouridine synthase II TruB,
C-terminal domain {Archaeon Methanococcus jannaschii
[TaxId: 2190]}
Length = 85
Score = 98.3 bits (245), Expect = 1e-28
Identities = 35/82 (42%), Positives = 54/82 (65%)
Query: 55 KRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMA 114
K++++KDSAV+A+C+GA + + G+ + GI E +++ + KGEAVA+ A M T +
Sbjct: 3 KKVVVKDSAVDAICHGADVYVRGIAKLSKGIGKGETVLVETLKGEAVAVGKALMNTKEIL 62
Query: 115 TCDHGVVAKIKRVIMDRDTYPR 136
D GV ++RV MDR TYPR
Sbjct: 63 NADKGVAVDVERVYMDRGTYPR 84
>d2ey4a1 b.122.1.1 (A:253-336) Pseudouridine synthase II TruB,
C-terminal domain {Archaeon Pyrococcus furiosus [TaxId:
2261]}
Length = 84
Score = 92.1 bits (229), Expect = 4e-26
Identities = 30/81 (37%), Positives = 49/81 (60%)
Query: 56 RIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMAT 115
++ +KDSAV AV +GA + +PG+ + GI+ + + I++ K E VAL A MT+ M
Sbjct: 3 KVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLE 62
Query: 116 CDHGVVAKIKRVIMDRDTYPR 136
G+ +++V M RD YP+
Sbjct: 63 KTKGIAVDVEKVFMPRDWYPK 83
>d1r3ea1 b.122.1.1 (A:238-318) Pseudouridine synthase II TruB,
C-terminal domain {Thermotoga maritima [TaxId: 2336]}
Length = 81
Score = 77.9 bits (192), Expect = 1e-20
Identities = 18/81 (22%), Positives = 38/81 (46%), Gaps = 5/81 (6%)
Query: 55 KRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMA 114
R+++ + + G+QI L + + DG + E + + + +G +ALA A+ +S +
Sbjct: 2 PRVVVHQESTKMILNGSQIHLEMLKEW-DGFKKGEVVRVFNEEGRLLALAEAERNSSFLE 60
Query: 115 TCDHGV----VAKIKRVIMDR 131
T V +++V R
Sbjct: 61 TLRKHERNERVLTLRKVFNTR 81
>d1q7ha1 b.122.1.1 (A:69-153) Hypothetical protein Ta1423,
C-terminal domain {Archaeon Thermoplasma acidophilum
[TaxId: 2303]}
Length = 85
Score = 70.2 bits (172), Expect = 2e-17
Identities = 17/78 (21%), Positives = 35/78 (44%)
Query: 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTM 113
+ + + A + G+ + PG++ +D I + I + S+KG +A+ +A+M +
Sbjct: 2 RNIVTVDEGAEPHILNGSDLFAPGIVSMDDSIRKGDMIFVKSSKGYFIAVGMAEMDAGEV 61
Query: 114 ATCDHGVVAKIKRVIMDR 131
G A+I D
Sbjct: 62 MATKRGKAARIIHFPGDE 79
>d1iq8a3 b.122.1.1 (A:506-582) Archaeosine tRNA-guanine
transglycosylase, C3 domain {Archaeon Pyrococcus
horikoshii [TaxId: 53953]}
Length = 77
Score = 64.9 bits (158), Expect = 1e-15
Identities = 14/74 (18%), Positives = 33/74 (44%)
Query: 55 KRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMA 114
R+++ A G + V+ + GI +E+++V+ E +A A ++ M
Sbjct: 3 MRVVVNKEAEPFARKGKDVFAKFVIFADPGIRPYDEVLVVNENDELLATGQALLSGREMI 62
Query: 115 TCDHGVVAKIKRVI 128
+G K+++ +
Sbjct: 63 VFQYGRAVKVRKGV 76
>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB
{Archaeon Pyrococcus furiosus [TaxId: 2261]}
Length = 245
Score = 61.3 bits (148), Expect = 8e-13
Identities = 21/51 (41%), Positives = 31/51 (60%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLL 51
M ELRR RSG E++ L+TLHD+ D Y + + E R+ I+P+E +
Sbjct: 193 MSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAV 243
>d2q07a1 b.122.1.1 (A:460-527) Uncharacterized protein AF0587
{Archaeoglobus fulgidus [TaxId: 2234]}
Length = 68
Score = 57.0 bits (138), Expect = 1e-12
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 73 IMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVI 128
I GVLR ++ I ++ +V + LA M+ MA + G+ +KR
Sbjct: 14 IFAGGVLRADEKIRPNDVVVFH--NSRIFGVGLAAMSGKEMAGSEKGIAINVKRKF 67
>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB
{Archaeon Methanococcus jannaschii [TaxId: 2190]}
Length = 230
Score = 50.9 bits (121), Expect = 4e-09
Identities = 24/51 (47%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLL 51
M ELRR +SG E+D V L D+ DA + + DE LRRVI+P+E L
Sbjct: 180 MQELRRTKSGCFEEKD-AVYLQDLLDAYVFWKEDGDEEELRRVIKPMEYGL 229
>d2cx1a1 b.122.1.1 (A:91-183) Hypothetical protein APE0525,
C-terminal domain {Archaeon Aeropyrum pernix [TaxId:
56636]}
Length = 93
Score = 42.9 bits (101), Expect = 7e-07
Identities = 14/80 (17%), Positives = 33/80 (41%), Gaps = 5/80 (6%)
Query: 56 RIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTK-GEAVALALAQMTTSTMA 114
+++ A A+ GA +M+PGV+ E + + + + V + +A++ +S +
Sbjct: 3 VVLVDKGAAIALAKGAHLMIPGVVGVEGSFTRGDVVAALYHETRTPVMVGVAEVDSSALE 62
Query: 115 TC----DHGVVAKIKRVIMD 130
G + + D
Sbjct: 63 KLYREKARGRAVRRVHRLGD 82
>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB
{Escherichia coli [TaxId: 562]}
Length = 242
Score = 37.1 bits (85), Expect = 3e-04
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQH--KDESLLRRVIRPLE 48
+I LRR E +VTL +++ + +Q LL ++ P++
Sbjct: 189 VIYLRRLAVSKYPVER-MVTLEHLRELVEQAEQQDIPAAELLDPLLMPMD 237
>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB
{Mycobacterium tuberculosis [TaxId: 1773]}
Length = 233
Score = 31.7 bits (71), Expect = 0.021
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLL 40
+ LRR R G + +L D+ + L DE+ L
Sbjct: 194 VTALRRTRVGRFELDQ-ARSLDDLAERPALSLSL-DEACL 231
>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB
{Thermotoga maritima [TaxId: 2336]}
Length = 228
Score = 30.9 bits (69), Expect = 0.034
Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 12/51 (23%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLL 51
+EL R G H I++++ +++ +E + I PLE L
Sbjct: 188 AVELVRESVGP----------HTIEESLNVFEAAPEE--IENRIIPLEKCL 226
>g1dy9.1 b.47.1.3 (A:,C:) NS3 protease {Human hepatitis C virus
(HCV), different isolates [TaxId: 11103]}
Length = 187
Score = 23.9 bits (52), Expect = 9.0
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 11/32 (34%)
Query: 90 EIVIVSTKGEAVALALAQMTTSTMATCDHGVV 121
E+ ++ST T S +ATC +GV
Sbjct: 32 EVQVLST-----------ATQSFLATCVNGVC 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
0.320 0.137 0.392
Gapped
Lambda K H
0.267 0.0708 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 524,755
Number of extensions: 22079
Number of successful extensions: 79
Number of sequences better than 10.0: 1
Number of HSP's gapped: 75
Number of HSP's successfully gapped: 17
Length of query: 144
Length of database: 2,407,596
Length adjustment: 77
Effective length of query: 67
Effective length of database: 1,350,386
Effective search space: 90475862
Effective search space used: 90475862
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 (21.8 bits)
S2: 49 (22.7 bits)