RPS-BLAST 2.2.26 [Sep-21-2011]
Database: scop70_1_75
13,730 sequences; 2,407,596 total letters
Searching..................................................done
Query= psy10748
(98 letters)
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens)
[TaxId: 9606]}
Length = 93
Score = 61.8 bits (150), Expect = 8e-15
Identities = 17/85 (20%), Positives = 40/85 (47%), Gaps = 15/85 (17%)
Query: 17 QPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEY----------- 65
P++++ + ++N ++V I N L G + FD + N+VLE+ +E
Sbjct: 2 GPLSVLTQSVKNNTQVLINCRNNKKLL--GRVKAFDRHCNMVLENVKEMWTEVPKSGKGK 59
Query: 66 --NIKSKTRKALGTIMLKGDNITLI 88
+ + + + L+GD++ ++
Sbjct: 60 KKSKPVNKDRYISKMFLRGDSVIVV 84
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein
{Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]}
Length = 75
Score = 59.8 bits (145), Expect = 3e-14
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 4/75 (5%)
Query: 15 MVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKA 74
MV P ++ + RV++ + ++ G + G D+YMN+ L +A E + K R
Sbjct: 3 MVLPNQMVKSMVGKIIRVEM---KGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRS- 58
Query: 75 LGTIMLKGDNITLIQ 89
LG I+L+G+N+ LIQ
Sbjct: 59 LGEIVLRGNNVVLIQ 73
>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein
LSM5 {Cryptosporidium parvum [TaxId: 5807]}
Length = 92
Score = 54.1 bits (130), Expect = 7e-12
Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 18/88 (20%)
Query: 15 MVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEY--------- 65
++ P+ LI + + NR I++ + G + GFDEY+N+VL+ +EY
Sbjct: 3 IILPLALIDKCIGNR----IYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDI 58
Query: 66 -----NIKSKTRKALGTIMLKGDNITLI 88
+K L TI+L G+N+ ++
Sbjct: 59 SGGNKKLKRVMVNRLETILLSGNNVAML 86
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein
{Archaeon Pyrococcus abyssi [TaxId: 29292]}
Length = 71
Score = 52.8 bits (127), Expect = 2e-11
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 17 QPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALG 76
+P+++I R L V + L + R G ++G+D ++N+VL AE ++ G
Sbjct: 2 RPLDVIHRSLD--KDVLVILKKGFEFR--GRLIGYDIHLNVVLADAEMIQDGEVVKR-YG 56
Query: 77 TIMLKGDNITLI 88
I+++GDN+ I
Sbjct: 57 KIVIRGDNVLAI 68
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein
{Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]}
Length = 72
Score = 50.9 bits (122), Expect = 8e-11
Identities = 17/73 (23%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 16 VQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKAL 75
+P++++ R L++ V++ G + G+D +MN+VL AEE + + +
Sbjct: 2 PRPLDVLNRSLKSPVIVRL----KGGREFRGTLDGYDIHMNLVLLDAEEI-QNGEVVRKV 56
Query: 76 GTIMLKGDNITLI 88
G+++++GD + +
Sbjct: 57 GSVVIRGDTVVFV 69
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein
{Archaeon Methanobacterium thermoautotrophicum [TaxId:
145262]}
Length = 74
Score = 50.1 bits (120), Expect = 2e-10
Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 13 KVMVQ-PINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKT 71
+V VQ P++ + L + +++ + G + FD +MN+VL AEE +
Sbjct: 1 RVNVQRPLDALGNSLNSPVIIKL----KGDREFRGVLKSFDLHMNLVLNDAEEL-EDGEV 55
Query: 72 RKALGTIMLKGDNITLI 88
+ LGT++++GDNI I
Sbjct: 56 TRRLGTVLIRGDNIVYI 72
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens)
[TaxId: 9606]}
Length = 81
Score = 47.9 bits (114), Expect = 2e-09
Identities = 15/82 (18%), Positives = 35/82 (42%), Gaps = 13/82 (15%)
Query: 22 IFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEY---------NIKSKTR 72
+ + + R R + G FD++MN++L +E+ + + +
Sbjct: 3 MLQHIDYRMRCIL----QDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEK 58
Query: 73 KALGTIMLKGDNITLIQNLNPD 94
+ LG ++L+G+N+ + P
Sbjct: 59 RVLGLVLLRGENLVSMTVEGPP 80
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf
{Baker's yeast (Saccharomyces cerevisiae) [TaxId:
4932]}
Length = 68
Score = 47.0 bits (112), Expect = 3e-09
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 31 RVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQN 90
RV + L N + G ++ D Y N+ L AEE+ + + LG I ++ +N+ I+
Sbjct: 8 RVGVKLKFN-STEYRGTLVSTDNYFNLQLNEAEEF-VAGVSHGTLGEIFIRCNNVLYIRE 65
Query: 91 LNPD 94
L P+
Sbjct: 66 L-PN 68
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein
{Archaeon Pyrobaculum aerophilum [TaxId: 13773]}
Length = 71
Score = 46.6 bits (111), Expect = 5e-09
Identities = 19/59 (32%), Positives = 36/59 (61%), Gaps = 4/59 (6%)
Query: 30 SRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLI 88
+V + L ++ +R G + FD+++N++LE AEE I K GT++++G+N+ I
Sbjct: 13 KQVLVKLRDSHEIR--GILRSFDQHVNLLLEDAEEI-IDGNVYK-RGTMVVRGENVLFI 67
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein
{Sulfolobus solfataricus [TaxId: 2287]}
Length = 76
Score = 45.5 bits (108), Expect = 1e-08
Identities = 19/48 (39%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 41 NLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLI 88
N + G + +D++MN+VL +EE + K LGTI+++GDN+ LI
Sbjct: 27 NKEVRGMLRSYDQHMNLVLSDSEEI-QSDGSGKKLGTIVIRGDNVILI 73
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens)
[TaxId: 9606]}
Length = 72
Score = 40.9 bits (96), Expect = 6e-07
Identities = 9/72 (12%), Positives = 25/72 (34%), Gaps = 5/72 (6%)
Query: 18 PINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGT 77
PI ++ + + N G ++ ++ MN + + + + L
Sbjct: 3 PIKVLHEAEGHIVTCET----NTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQ-LEQ 57
Query: 78 IMLKGDNITLIQ 89
+ ++G I +
Sbjct: 58 VYIRGCKIRFLI 69
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens)
[TaxId: 9606]}
Length = 80
Score = 37.4 bits (87), Expect = 2e-05
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 24 RFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGD 83
RFL S + + ++ G I G D MN L++ + +K++ L T+ ++G+
Sbjct: 4 RFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMT-LKNREPVQLETLSIRGN 62
Query: 84 NITLI 88
NI
Sbjct: 63 NIRYF 67
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon
Pyrobaculum aerophilum [TaxId: 13773]}
Length = 127
Score = 35.1 bits (81), Expect = 3e-04
Identities = 10/45 (22%), Positives = 17/45 (37%), Gaps = 5/45 (11%)
Query: 44 IEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLI 88
+G + D +NIVL +A K + + + I I
Sbjct: 23 YKGVLHAVDNQLNIVLANASN-----KAGEKFNRVFIMYRYIVHI 62
>d2akka1 b.34.11.2 (A:1-72) Hypothetical protein RPA4501
{Rhodopseudomonas palustris [TaxId: 1076]}
Length = 72
Score = 23.1 bits (50), Expect = 4.6
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 72 RKALGTIMLKGDNITLIQNLN 92
R G ++ GDN++LI++L
Sbjct: 6 RDCNGALLADGDNVSLIKDLK 26
>d2akla1 b.34.11.2 (A:41-114) Hypothetical protein PA0128,
C-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}
Length = 74
Score = 22.7 bits (49), Expect = 6.8
Identities = 7/21 (33%), Positives = 15/21 (71%)
Query: 72 RKALGTIMLKGDNITLIQNLN 92
+ ++G ++ GD IT+I++L
Sbjct: 8 KDSVGNVLQDGDTITVIKDLK 28
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
0.321 0.139 0.391
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: 355,031
Number of extensions: 14731
Number of successful extensions: 63
Number of sequences better than 10.0: 1
Number of HSP's gapped: 50
Number of HSP's successfully gapped: 19
Length of query: 98
Length of database: 2,407,596
Length adjustment: 60
Effective length of query: 38
Effective length of database: 1,583,796
Effective search space: 60184248
Effective search space used: 60184248
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: 47 (22.1 bits)