RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10748
(98 letters)
>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2
complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP
biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens}
PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E
Length = 92
Score = 122 bits (308), Expect = 2e-38
Identities = 62/85 (72%), Positives = 76/85 (89%)
Query: 8 APKVQKVMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNI 67
KVQKVMVQPINLIFR+LQNRSR+Q+WLYE VN+RIEG I+GFDEYMN+VL+ AEE +
Sbjct: 7 GQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHS 66
Query: 68 KSKTRKALGTIMLKGDNITLIQNLN 92
K+K+RK LG IMLKGDNITL+Q+++
Sbjct: 67 KTKSRKQLGRIMLKGDNITLLQSVS 91
>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and
PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A
{Schizosaccharomyces pombe} PDB: 3swn_A
Length = 94
Score = 91.1 bits (226), Expect = 6e-26
Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 7/92 (7%)
Query: 1 MSGGFKMAPKVQKVM---VQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNI 57
M Q M + P+ LI + + + +W+ G ++GFD+Y+NI
Sbjct: 1 MGSSHHHHHHSQDPMSMTILPLELIDKCIGSN----LWVIMKSEREFAGTLVGFDDYVNI 56
Query: 58 VLESAEEYNIKSKTRKALGTIMLKGDNITLIQ 89
VL+ EY+ + + ++L G+ + ++
Sbjct: 57 VLKDVTEYDTVTGVTEKHSEMLLNGNGMCMLI 88
>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA
binding protein, unknown F; 1.95A {Archaeoglobus
fulgidus} SCOP: b.38.1.1
Length = 77
Score = 75.0 bits (185), Expect = 9e-20
Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 4/75 (5%)
Query: 15 MVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKA 74
MV P ++ + +++ + N ++ G + G D+YMN+ L +A E + K R
Sbjct: 3 MVLPNQMVKSMVG--KIIRVEMKGEEN-QLVGKLEGVDDYMNLYLTNAMECKGEEKVRS- 58
Query: 75 LGTIMLKGDNITLIQ 89
LG I+L+G+N+ LIQ
Sbjct: 59 LGEIVLRGNNVVLIQ 73
>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics,
structural genomics consortium, SGC, DNA binding
protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1
PDB: 3pgg_A
Length = 121
Score = 66.5 bits (162), Expect = 6e-16
Identities = 24/102 (23%), Positives = 46/102 (45%), Gaps = 18/102 (17%)
Query: 1 MSGGFKMAPKVQKVMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60
+ + + ++ P+ LI + + NR I++ + G + GFDEY+N+VL+
Sbjct: 12 ANKSQGGSNQKGGNIILPLALIDKCIGNR----IYVVMKGDKEFSGVLRGFDEYVNMVLD 67
Query: 61 SAEEY--------------NIKSKTRKALGTIMLKGDNITLI 88
+EY +K L TI+L G+N+ ++
Sbjct: 68 DVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAML 109
>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A
{Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A*
Length = 75
Score = 60.4 bits (147), Expect = 5e-14
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: 4 RPLDVIHRSLD--KDVLVILKKGFEFR--GRLIGYDIHLNVVLADAEMIQDGEVVKR-YG 58
Query: 77 TIMLKGDNITLI 88
I+++GDN+ I
Sbjct: 59 KIVIRGDNVLAI 70
>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2
complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP
biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens}
PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F
Length = 86
Score = 59.8 bits (145), Expect = 1e-13
Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 2/84 (2%)
Query: 15 MVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKA 74
M P+N FL + + + + +G+++ D YMN+ L + EEY I
Sbjct: 1 MSLPLNPK-PFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEY-IDGALSGH 58
Query: 75 LGTIMLKGDNITLIQNLNPDEVKV 98
LG ++++ +N+ I+ + +E
Sbjct: 59 LGEVLIRCNNVLYIRGVEEEEEDG 82
>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein,
SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus
solfataricus} SCOP: b.38.1.1
Length = 81
Score = 55.4 bits (134), Expect = 5e-12
Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 1/80 (1%)
Query: 14 VMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRK 73
M + L + + N + G + +D++MN+VL +EE +K
Sbjct: 2 AMNFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKK 61
Query: 74 ALGTIMLKGDNITLIQNLNP 93
LGTI+++GDN+ LI L
Sbjct: 62 -LGTIVIRGDNVILISPLQT 80
>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding
protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP:
b.38.1.1 PDB: 1i5l_A*
Length = 77
Score = 51.5 bits (124), Expect = 2e-10
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: 3 PRPLDVLNRSLKSPVIVRL----KGGREFRGTLDGYDIHMNLVLLDAEEI-QNGEVVRKV 57
Query: 76 GTIMLKGDNITLI 88
G+++++GD + +
Sbjct: 58 GSVVIRGDTVVFV 70
>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers
form 35-stranded beta-sheet I heptamer, structural
genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1
PDB: 1lnx_A*
Length = 81
Score = 50.1 bits (120), Expect = 5e-10
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 7 MAPKVQKVMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYN 66
MA + K + + + V++ + I G + FD+++N++LE AEE
Sbjct: 1 MASDISKCFATLGATLQDSIGKQVLVKL----RDSHEIRGILRSFDQHVNLLLEDAEEI- 55
Query: 67 IKSKTRKALGTIMLKGDNITLI 88
I K GT++++G+N+ I
Sbjct: 56 IDGNVYK-RGTMVVRGENVLFI 76
>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F;
heptamer, translation; 2.80A {Saccharomyces cerevisiae}
SCOP: b.38.1.1 PDB: 1n9s_A
Length = 93
Score = 50.2 bits (120), Expect = 7e-10
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 5/88 (5%)
Query: 6 KMAPKVQKVMVQPINLIFRFLQN--RSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAE 63
M+ +QP+N FL+ RV + L N + G ++ D Y N+ L AE
Sbjct: 7 HMSESSDISAMQPVNPK-PFLKGLVNHRVGVKLKFN-STEYRGTLVSTDNYFNLQLNEAE 64
Query: 64 EYNIKSKTRKALGTIMLKGDNITLIQNL 91
E+ + + LG I ++ +N+ I+ L
Sbjct: 65 EF-VAGVSHGTLGEIFIRCNNVLYIREL 91
>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein;
1.70A {Methanothermobacterthermautotrophicus} SCOP:
b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A
Length = 83
Score = 49.6 bits (119), Expect = 1e-09
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 5/77 (6%)
Query: 12 QKVMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKT 71
+ + +P++ + L + +++ + G + FD +MN+VL AEE T
Sbjct: 10 RVNVQRPLDALGNSLNSPVIIKL----KGDREFRGVLKSFDLHMNLVLNDAEELEDGEVT 65
Query: 72 RKALGTIMLKGDNITLI 88
R+ LGT++++GDNI I
Sbjct: 66 RR-LGTVLIRGDNIVYI 81
>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing,
spliceosome, core snRNP domain, systemi erythematosus,
SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP:
b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y*
3s6n_B
Length = 118
Score = 48.4 bits (115), Expect = 7e-09
Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 15/84 (17%)
Query: 18 PINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEY------------ 65
P++++ + ++N ++V I N L G + FD + N+VLE+ +E
Sbjct: 28 PLSVLTQSVKNNTQVLINCRNNKKLL--GRVKAFDRHCNMVLENVKEMWTEVPKSGKGKK 85
Query: 66 -NIKSKTRKALGTIMLKGDNITLI 88
+ + + + L+GD++ ++
Sbjct: 86 KSKPVNKDRYISKMFLRGDSVIVV 109
>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and
PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A
{Schizosaccharomyces pombe} PDB: 3swn_B
Length = 75
Score = 46.9 bits (112), Expect = 8e-09
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 30 SRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQ 89
+V I L + + +G + D YMN+ LE EEY + K G ++G+N+ +
Sbjct: 15 KKVLIRL--SSGVDYKGILSCLDGYMNLALERTEEY-VNGKKTNVYGDAFIRGNNVLYVS 71
>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2
complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP
biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens}
PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G
Length = 76
Score = 46.6 bits (111), Expect = 1e-08
Identities = 11/45 (24%), Positives = 28/45 (62%), Gaps = 1/45 (2%)
Query: 44 IEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLI 88
++G + GFD +MN+V++ E + +G ++++G++I ++
Sbjct: 27 VQGILRGFDPFMNLVIDECVEMATSGQQNN-IGMVVIRGNSIIML 70
>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA
decay, LSM proteins, RNA binding protein; 2.70A
{Schizosaccharomyces pombe}
Length = 93
Score = 44.4 bits (105), Expect = 1e-07
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 16/84 (19%)
Query: 17 QPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEY----------- 65
+P++L+ L V + L + L G + +DE++N+VL AEE
Sbjct: 9 EPLDLVRLSL--DEIVYVKLRGDRELN--GRLHAYDEHLNMVLGDAEEIVTIFDDEETDK 64
Query: 66 -NIKSKTRKALGTIMLKGDNITLI 88
RK + ++GD++ LI
Sbjct: 65 DKALKTIRKHYEMLFVRGDSVILI 88
>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3;
RNA-binding protein, SM protein, ring, HOMO octamer,
mRNA processing; 2.50A {Saccharomyces cerevisiae}
Length = 96
Score = 43.6 bits (103), Expect = 3e-07
Identities = 20/88 (22%), Positives = 37/88 (42%), Gaps = 11/88 (12%)
Query: 7 MAPKVQKVMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEY- 65
M + P++L+ L R +++ + G + FD + NIVL A E
Sbjct: 1 MHHHHHHME-TPLDLLKLNLDERVYIKL----RGARTLVGTLQAFDSHCNIVLSDAVETI 55
Query: 66 -----NIKSKTRKALGTIMLKGDNITLI 88
S++ + + ++GD +TLI
Sbjct: 56 YQLNNEELSESERRCEMVFIRGDTVTLI 83
>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP,
splicing, core snRNP domain, systemic lupus eryth SLE,
RNA binding protein; HET: CIT; 2.00A {Homo sapiens}
SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A
Length = 91
Score = 43.3 bits (102), Expect = 4e-07
Identities = 14/83 (16%), Positives = 35/83 (42%), Gaps = 15/83 (18%)
Query: 26 LQNRSRVQIWLYENVNLR------IEGHILGFDEYMNIVLESAEEY---------NIKSK 70
+ S++ + + G FD++MN++L +E+ + +
Sbjct: 3 VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAERE 62
Query: 71 TRKALGTIMLKGDNITLIQNLNP 93
++ LG ++L+G+N+ + P
Sbjct: 63 EKRVLGLVLLRGENLVSMTVEGP 85
>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and
PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A
{Schizosaccharomyces pombe} PDB: 3swn_C
Length = 113
Score = 43.0 bits (101), Expect = 7e-07
Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 10/87 (11%)
Query: 8 APKVQKVMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEY-- 65
+ ++ + I + R+ R + +I G + GFD+ MN+VL+ EE
Sbjct: 14 SQPTERPRKESILDLSRYQDQRIQATF----TGGRQITGILKGFDQLMNLVLDDVEEQLR 69
Query: 66 ----NIKSKTRKALGTIMLKGDNITLI 88
+ + LG ++++G + LI
Sbjct: 70 NPEDGKLTGAIRKLGLVVVRGTTLVLI 96
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_A
Length = 231
Score = 44.3 bits (104), Expect = 7e-07
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 20/88 (22%)
Query: 7 MAPKVQKVMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEY- 65
M M+Q I+ R + R+ I G FD++MN++L +E+
Sbjct: 1 MTVGKSSKMLQHIDYRMRCILQDGRIFI-----------GTFKAFDKHMNLILCDCDEFR 49
Query: 66 NIKSKTRKA--------LGTIMLKGDNI 85
IK K K LG ++L+G+N+
Sbjct: 50 KIKPKNSKQAEREEKRVLGLVLLRGENL 77
>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA
decay, PRE-mRNA splicing, LSM proteins, RNA BI protein;
2.20A {Schizosaccharomyces pombe}
Length = 105
Score = 42.8 bits (101), Expect = 7e-07
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 2/54 (3%)
Query: 44 IEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQNLNPDEVK 97
GH+ D YMN+ L L ++G+NI ++ DEV
Sbjct: 39 FNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGNNIKYLR--IQDEVL 90
>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing,
spliceosome, core snRNP domain, systemi erythematosus,
SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP:
b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B
3pgw_X* 3s6n_A
Length = 119
Score = 38.4 bits (89), Expect = 4e-05
Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 3/77 (3%)
Query: 21 LIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIML 80
+ RFL S + + ++ G I G D MN L++ + K++ L T+ +
Sbjct: 2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTL-KNREPVQLETLSI 60
Query: 81 KGDNITLIQNLNPDEVK 97
+G+NI PD +
Sbjct: 61 RGNNIRYFI--LPDSLP 75
>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex,
PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM
site, SM fold, heteromeric heptameric ring; 3.60A {Homo
sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D
Length = 126
Score = 36.6 bits (84), Expect = 2e-04
Identities = 9/54 (16%), Positives = 22/54 (40%), Gaps = 3/54 (5%)
Query: 44 IEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQNLNPDEVK 97
G ++ ++ MN + + + + L + ++G I + PD +K
Sbjct: 28 YRGKLIEAEDNMNCQMSNITVTYRDGRVAQ-LEQVYIRGSKIRFLI--LPDMLK 78
>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing,
core snRNP domain, systemic lupus eryth SLE, RNA
binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP:
b.38.1.1
Length = 75
Score = 33.9 bits (78), Expect = 0.001
Identities = 6/46 (13%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 44 IEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQ 89
G ++ ++ MN + + + + L + ++G I +
Sbjct: 28 YRGKLIEAEDNMNCQMSNITVTYRDGRVAQ-LEQVYIRGCKIRFLI 72
>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A
{Escherichia coli} PDB: 3qhs_A
Length = 104
Score = 27.2 bits (60), Expect = 0.47
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 9/52 (17%)
Query: 15 MVQPINLIFRFL----QNRSRVQIWLYENVN-LRIEGHILGFDEYMNIVLES 61
M + +L FL + R V I+L VN ++++G I FD+++ I+L++
Sbjct: 3 MAKGQSLQDPFLNALRRERVPVSIYL---VNGIKLQGQIESFDQFV-ILLKN 50
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 27.9 bits (61), Expect = 0.51
Identities = 15/67 (22%), Positives = 24/67 (35%), Gaps = 22/67 (32%)
Query: 23 FRFLQNRSR----------------VQIWLYENVNLRIEGHILGFDEYMNIV---LESAE 63
FRFL+ + R Q+ Y+ I + ++ +N + L E
Sbjct: 500 FRFLEQKIRHDSTAWNASGSILNTLQQLKFYKP---YICDNDPKYERLVNAILDFLPKIE 556
Query: 64 EYNIKSK 70
E I SK
Sbjct: 557 ENLICSK 563
Score = 27.5 bits (60), Expect = 0.76
Identities = 9/58 (15%), Positives = 20/58 (34%), Gaps = 14/58 (24%)
Query: 51 FD-----EYMNIVLESAE------EYNIKSKTRKALGTIMLKGDNIT---LIQNLNPD 94
FD + +L E + S T + T++ K + + + + L +
Sbjct: 33 FDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRIN 90
>2ylb_A Protein HFQ; RNA-binding protein, LSM protein, RNA chaperone;
1.15A {Salmonella enterica subsp} PDB: 2yht_A 1hk9_A
2ylc_A* 3gib_A* 3rer_A* 3qo3_A* 3res_A*
Length = 74
Score = 25.8 bits (57), Expect = 1.3
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 9/52 (17%)
Query: 15 MVQPINLIFRFL----QNRSRVQIWLYENVN-LRIEGHILGFDEYMNIVLES 61
M + +L FL + R V I+L VN ++++G I FD+++ I+L++
Sbjct: 3 MAKGQSLQDPFLNALRRERVPVSIYL---VNGIKLQGQIESFDQFV-ILLKN 50
>1u1s_A HFQ protein; SM-like bacterial protein, riken structural
genomics/proteomics initiative, RSGI, structural
genomics, RNA binding protein; 1.60A {Pseudomonas
aeruginosa} SCOP: b.38.1.2 PDB: 1u1t_A 3qui_A* 3m4g_A
3inz_A
Length = 82
Score = 25.9 bits (57), Expect = 1.4
Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 9/52 (17%)
Query: 15 MVQPINLIFRFL----QNRSRVQIWLYENVN-LRIEGHILGFDEYMNIVLES 61
M + +L +L + R V I+L VN ++++G I FD+++ I+L++
Sbjct: 1 MSKGHSLQDPYLNTLRKERVPVSIYL---VNGIKLQGQIESFDQFV-ILLKN 48
>1kq1_A HFQ, HOST factor for Q beta; hexamer, RNA binding protein,
translational regulator, SM motif; 1.55A
{Staphylococcus aureus} SCOP: b.38.1.2 PDB: 1kq2_A
Length = 77
Score = 25.0 bits (55), Expect = 2.3
Identities = 12/52 (23%), Positives = 27/52 (51%), Gaps = 9/52 (17%)
Query: 15 MVQPINLIFRFL----QNRSRVQIWLYENVN-LRIEGHILGFDEYMNIVLES 61
M+ N+ + L N++ V ++ +N +++G I +D+Y+ + L S
Sbjct: 1 MIANENIQDKALENFKANQTEVTVFF---LNGFQMKGVIEEYDKYV-VSLNS 48
>2iuw_A Alkylated repair protein ALKB homolog 3; oxidoreductase, DNA/RNA
repair, demethylase, beta jellyroll; HET: AKG; 1.50A
{Homo sapiens} SCOP: b.82.2.10
Length = 238
Score = 25.6 bits (55), Expect = 2.8
Identities = 10/40 (25%), Positives = 13/40 (32%), Gaps = 5/40 (12%)
Query: 1 MSGGFKMA-----PKVQKVMVQPINLIFRFLQNRSRVQIW 35
M G + PK +NL FR + R W
Sbjct: 199 MEGATQADWQHRVPKEYHSREPRVNLTFRTVYPDPRGAPW 238
>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA
complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A
Length = 78
Score = 24.7 bits (54), Expect = 3.4
Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 9/50 (18%)
Query: 17 QPINLIFRFL----QNRSRVQIWLYENVN-LRIEGHILGFDEYMNIVLES 61
+PIN+ +FL + + V ++L +N ++ G + GFD + ++LES
Sbjct: 7 KPINIQDQFLNQIRKENTYVTVFL---LNGFQLRGQVKGFDNFT-VLLES 52
>1fiu_A Type II restriction enzyme ngomi; protein-DNA complex, double
helix, restriction endonuclease, restriction-modifiction
systems, hydrolase; HET: DNA; 1.60A {Neisseria
gonorrhoeae} SCOP: c.52.1.10 PDB: 4abt_A
Length = 286
Score = 25.5 bits (55), Expect = 3.5
Identities = 17/66 (25%), Positives = 27/66 (40%), Gaps = 3/66 (4%)
Query: 31 RVQIWLYENVNLRIEGHILGFDEYMNIV-LESAEEYNIKSKTRKALGTIMLKGDNITLIQ 89
R W + V R I + +Y ++ L A E N + ALG+ +I + +
Sbjct: 88 RPGDWNVKQVGSRNRLEIARYQQYAHLTALAKAAEEN--PELAAALGSDYTITPDIIVTR 145
Query: 90 NLNPDE 95
NL D
Sbjct: 146 NLIADA 151
>2x6w_A Tail spike protein; viral protein, beta-helix, hydrolase; HET: RAM
GLC GLA NAG NDG; 1.35A {Enterobacteria phage HK620} PDB:
2vji_A 2vjj_A* 2x85_A* 2x6x_A* 2x6y_A*
Length = 600
Score = 25.2 bits (54), Expect = 4.0
Identities = 10/36 (27%), Positives = 14/36 (38%)
Query: 34 IWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKS 69
I L NVNL IEG I + + ++
Sbjct: 107 IQLRSNVNLNIEGRIHLSPFFDLKPFQVFVGFDNGD 142
>3h28_A Sulfide-quinone reductase; monotopic membrane protein,
flavoprotein, polysulfur, oxidoreductase; HET: FAD DCQ
LMT; 2.00A {Aquifex aeolicus} PDB: 3h27_A* 3h29_A*
3hyv_A* 3hyw_A* 3hyx_A*
Length = 430
Score = 25.1 bits (55), Expect = 4.6
Identities = 9/72 (12%), Positives = 21/72 (29%), Gaps = 1/72 (1%)
Query: 4 GFKMAPKVQKVMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAE 63
G + + ++ + R +V + + + G +V +
Sbjct: 153 GVSCFGPAYEFALM-LHYELKKRGIRYKVPMTFITSEPYLGHFGVGGIGASKRLVEDLFA 211
Query: 64 EYNIKSKTRKAL 75
E NI A+
Sbjct: 212 ERNIDWIANVAV 223
>2aiz_P Outer membrane protein P6; alpha-beta sandwich; HET: UDP AMU DGL
6CL DAL; NMR {Haemophilus influenzae} SCOP: d.79.7.1
Length = 134
Score = 24.7 bits (54), Expect = 5.1
Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 10/40 (25%)
Query: 35 WL--YENVNLRIEGHI--LGFDEYMNIVL-----ESAEEY 65
+L + +EG+ G EY NI L ++ + Y
Sbjct: 55 YLNATPAAKVLVEGNTDERGTPEY-NIALGQRRADAVKGY 93
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.321 0.139 0.391
Gapped
Lambda K H
0.267 0.0581 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,452,630
Number of extensions: 74987
Number of successful extensions: 239
Number of sequences better than 10.0: 1
Number of HSP's gapped: 221
Number of HSP's successfully gapped: 45
Length of query: 98
Length of database: 6,701,793
Length adjustment: 64
Effective length of query: 34
Effective length of database: 4,914,849
Effective search space: 167104866
Effective search space used: 167104866
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: 51 (23.7 bits)