RPS-BLAST 2.2.26 [Sep-21-2011]
Database: scop70_1_75
13,730 sequences; 2,407,596 total letters
Searching..................................................done
Query= psy11157
(111 letters)
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens)
[TaxId: 9606]}
Length = 93
Score = 122 bits (308), Expect = 1e-38
Identities = 80/93 (86%), Positives = 88/93 (94%)
Query: 19 TGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKK 78
TGPLS+LT SVK+NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTE P++GKGKK
Sbjct: 1 TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKK 60
Query: 79 KSKPVNKDRFISKMFLRGDSVILILKNPLALNK 111
KSKPVNKDR+ISKMFLRGDSVI++L+NPL K
Sbjct: 61 KSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK 93
>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein
LSM5 {Cryptosporidium parvum [TaxId: 5807]}
Length = 92
Score = 80.3 bits (198), Expect = 7e-22
Identities = 17/83 (20%), Positives = 40/83 (48%), Gaps = 3/83 (3%)
Query: 21 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPR-AGKGKKK 79
PL+++ + ++ + + +K+ G ++ FD + NMVL++V+E + G K
Sbjct: 6 PLALIDKCI--GNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNK 63
Query: 80 SKPVNKDRFISKMFLRGDSVILI 102
+ + L G++V ++
Sbjct: 64 KLKRVMVNRLETILLSGNNVAML 86
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens)
[TaxId: 9606]}
Length = 81
Score = 66.0 bits (161), Expect = 2e-16
Identities = 15/71 (21%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 32 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISK 91
+ ++ ++ + +G KAFD+H N++L + E P+ K ++ + R +
Sbjct: 8 DYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEK----RVLGL 63
Query: 92 MFLRGDSVILI 102
+ LRG++++ +
Sbjct: 64 VLLRGENLVSM 74
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon
Pyrococcus abyssi [TaxId: 29292]}
Length = 71
Score = 63.2 bits (154), Expect = 2e-15
Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 16/82 (19%)
Query: 21 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 80
PL ++ S+ + VL+ + + GR+ +D H N+VL + + +
Sbjct: 3 PLDVIHRSL--DKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDG----------- 49
Query: 81 KPVNKDRFISKMFLRGDSVILI 102
+ K+ +RGD+V+ I
Sbjct: 50 ---EVVKRYGKIVIRGDNVLAI 68
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon
Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]}
Length = 72
Score = 59.3 bits (144), Expect = 7e-14
Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 16/82 (19%)
Query: 21 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 80
PL +L S+ + V++ + ++ G + +D H N+VL + +E+
Sbjct: 4 PLDVLNRSL--KSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG----------- 50
Query: 81 KPVNKDRFISKMFLRGDSVILI 102
R + + +RGD+V+ +
Sbjct: 51 ---EVVRKVGSVVIRGDTVVFV 69
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein
{Sulfolobus solfataricus [TaxId: 2287]}
Length = 76
Score = 59.0 bits (143), Expect = 9e-14
Identities = 22/85 (25%), Positives = 45/85 (52%), Gaps = 16/85 (18%)
Query: 18 ATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGK 77
A +L +S+ N VL+ + NK++ G ++++D+H N+VL + +E+ ++
Sbjct: 5 AETAHKVLAESL--NNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD-------- 54
Query: 78 KKSKPVNKDRFISKMFLRGDSVILI 102
+ + + +RGD+VILI
Sbjct: 55 ------GSGKKLGTIVIRGDNVILI 73
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon
Methanobacterium thermoautotrophicum [TaxId: 145262]}
Length = 74
Score = 58.9 bits (143), Expect = 1e-13
Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 16/82 (19%)
Query: 21 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 80
PL L +S+ N+ V+I + +++ G +K+FD H N+VL + +E+
Sbjct: 7 PLDALGNSL--NSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDG----------- 53
Query: 81 KPVNKDRFISKMFLRGDSVILI 102
R + + +RGD+++ I
Sbjct: 54 ---EVTRRLGTVLIRGDNIVYI 72
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon
Pyrobaculum aerophilum [TaxId: 13773]}
Length = 71
Score = 58.2 bits (141), Expect = 2e-13
Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 17/84 (20%)
Query: 23 SILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKP 82
+ L DS+ QVL+ R++ ++ G +++FD+H N++LE+ +E+
Sbjct: 5 ATLQDSI--GKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDG------------- 49
Query: 83 VNKDRFISKMFLRGDSVILILKNP 106
M +RG++V+ I P
Sbjct: 50 --NVYKRGTMVVRGENVLFISPVP 71
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon
Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]}
Length = 75
Score = 47.0 bits (112), Expect = 4e-09
Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 17/83 (20%)
Query: 21 PLSILTDSVKHNTQVLINCRNNK-KLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKK 79
P ++ V + + + + +L+G+++ D + N+ L N E E
Sbjct: 6 PNQMVKSMV--GKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGE---------- 53
Query: 80 SKPVNKDRFISKMFLRGDSVILI 102
K R + ++ LRG++V+LI
Sbjct: 54 ----EKVRSLGEIVLRGNNVVLI 72
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens)
[TaxId: 9606]}
Length = 72
Score = 43.6 bits (103), Expect = 7e-08
Identities = 9/82 (10%), Positives = 31/82 (37%), Gaps = 16/82 (19%)
Query: 21 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 80
P+ +L ++ H V + G++ + + N + N+ + + +
Sbjct: 3 PIKVLHEAEGH--IVTCETNTGEVYRGKLIEAEDNMNCQMSNITVT-------YRDGRVA 53
Query: 81 KPVNKDRFISKMFLRGDSVILI 102
+ + ++++RG + +
Sbjct: 54 Q-------LEQVYIRGCKIRFL 68
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf
{Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Length = 68
Score = 38.9 bits (91), Expect = 5e-06
Identities = 13/76 (17%), Positives = 29/76 (38%), Gaps = 15/76 (19%)
Query: 32 NTQVLINCRNNKKLL-GRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFIS 90
N +V + + N G + + D + N+ L +E +
Sbjct: 6 NHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAG--------------VSHGTLG 51
Query: 91 KMFLRGDSVILILKNP 106
++F+R ++V+ I + P
Sbjct: 52 EIFIRCNNVLYIRELP 67
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon
Pyrobaculum aerophilum [TaxId: 13773]}
Length = 127
Score = 39.7 bits (93), Expect = 9e-06
Identities = 13/81 (16%), Positives = 30/81 (37%), Gaps = 20/81 (24%)
Query: 22 LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSK 81
++ L + + +V + N + G + A D N+VL N
Sbjct: 2 VAELNNLL--GREVQVVLSNGEVYKGVLHAVDNQLNIVLANASN---------------- 43
Query: 82 PVNKDRFISKMFLRGDSVILI 102
++F +++F+ ++ I
Sbjct: 44 -KAGEKF-NRVFIMYRYIVHI 62
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens)
[TaxId: 9606]}
Length = 80
Score = 32.0 bits (73), Expect = 0.003
Identities = 12/71 (16%), Positives = 27/71 (38%), Gaps = 14/71 (19%)
Query: 32 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISK 91
+ V I +N ++ G + D N L+ VK K ++ + +
Sbjct: 11 HETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMT-------LKNREPVQ-------LET 56
Query: 92 MFLRGDSVILI 102
+ +RG+++
Sbjct: 57 LSIRGNNIRYF 67
>d1u1sa1 b.38.1.2 (A:6-71) Pleiotropic translational regulator Hfq
{Pseudomonas aeruginosa [TaxId: 287]}
Length = 66
Score = 24.2 bits (53), Expect = 1.6
Identities = 12/41 (29%), Positives = 21/41 (51%)
Query: 30 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEH 70
K V I N KL G++++FD+ ++ V +M +H
Sbjct: 12 KERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKH 52
>d1kq1a_ b.38.1.2 (A:) Pleiotropic translational regulator Hfq
{Staphylococcus aureus [TaxId: 1280]}
Length = 60
Score = 23.4 bits (51), Expect = 3.6
Identities = 6/37 (16%), Positives = 18/37 (48%)
Query: 30 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEM 66
+ T+V + N ++ G ++ +D++ + K+
Sbjct: 12 ANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGKQH 48
>d1vfsa2 c.1.6.1 (A:13-249) Alanine racemase {Streptomyces
lavendulae [TaxId: 1914]}
Length = 237
Score = 23.7 bits (50), Expect = 5.5
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 27 DSVKHNTQVLINCRNNKKLLGRVKA 51
D+V+ N + L L+ VK+
Sbjct: 3 DAVRANVRALRARAPRSALMAVVKS 27
>d1iv8a1 b.71.1.1 (A:654-720) Maltooligosyl trehalose synthase
{Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}
Length = 67
Score = 22.2 bits (47), Expect = 10.0
Identities = 5/19 (26%), Positives = 13/19 (68%)
Query: 93 FLRGDSVILILKNPLALNK 111
F+R + +++I+K ++N
Sbjct: 14 FIRFNKILVIIKTKGSVNY 32
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
0.316 0.132 0.378
Gapped
Lambda K H
0.267 0.0615 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 380,939
Number of extensions: 15390
Number of successful extensions: 50
Number of sequences better than 10.0: 1
Number of HSP's gapped: 39
Number of HSP's successfully gapped: 17
Length of query: 111
Length of database: 2,407,596
Length adjustment: 70
Effective length of query: 41
Effective length of database: 1,446,496
Effective search space: 59306336
Effective search space used: 59306336
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 (21.6 bits)
S2: 47 (22.1 bits)