RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1084
(110 letters)
>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 = 135 bits (341), Expect = 6e-43
Identities = 87/108 (80%), Positives = 99/108 (91%), Gaps = 1/108 (0%)
Query: 3 TREEPKQQEEEESFATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENV 62
T EE +++EEEE F TGPLS+LT SVK+NTQVLINCRNNKKLLGRVKAFDRHCNMVLENV
Sbjct: 12 TPEELQKREEEE-FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENV 70
Query: 63 KEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILILKNPLALKQ 110
KEMWTE P++GKGKKKSKPVNKDR+ISKMFLRGDSVI++L+NPL +
Sbjct: 71 KEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK 118
>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 = 101 bits (252), Expect = 1e-29
Identities = 29/90 (32%), Positives = 47/90 (52%), Gaps = 3/90 (3%)
Query: 12 EEESFATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPR 71
E PL ++ S+ + V + R +++L GR+ A+D H NMVL + +E+ T
Sbjct: 2 ESAQAVAEPLDLVRLSL--DEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDD 59
Query: 72 AGKGKKKSKPVNKDRFISKMFLRGDSVILI 101
K K+ + + +F+RGDSVILI
Sbjct: 60 EETDKDKALKTIR-KHYEMLFVRGDSVILI 88
>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 = 88.5 bits (219), Expect = 2e-24
Identities = 17/101 (16%), Positives = 43/101 (42%), Gaps = 3/101 (2%)
Query: 2 ATREEPKQQEEEESFATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 61
+ ++ PL+++ + ++ + + +K+ G ++ FD + NMVL++
Sbjct: 11 PANKSQGGSNQKGGNIILPLALIDKCI--GNRIYVVMKGDKEFSGVLRGFDEYVNMVLDD 68
Query: 62 VKEMWTE-HPRAGKGKKKSKPVNKDRFISKMFLRGDSVILI 101
V+E + G K + + L G++V ++
Sbjct: 69 VQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAML 109
>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 = 84.0 bits (208), Expect = 7e-23
Identities = 25/90 (27%), Positives = 42/90 (46%), Gaps = 9/90 (10%)
Query: 12 EEESFATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPR 71
PL +L ++ + +V I R + L+G ++AFD HCN+VL + E +
Sbjct: 3 HHHHHMETPLDLLKLNL--DERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQ--- 57
Query: 72 AGKGKKKSKPVNKDRFISKMFLRGDSVILI 101
+ +R +F+RGD+V LI
Sbjct: 58 ----LNNEELSESERRCEMVFIRGDTVTLI 83
>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 = 55.0 bits (133), Expect = 1e-11
Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 16/82 (19%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 79
PL ++ S+ + VL+ + + GR+ +D H N+VL + + +
Sbjct: 5 PLDVIHRSL--DKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVV-------- 54
Query: 80 KPVNKDRFISKMFLRGDSVILI 101
+ K+ +RGD+V+ I
Sbjct: 55 ------KRYGKIVIRGDNVLAI 70
>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 = 52.9 bits (127), Expect = 8e-11
Identities = 17/99 (17%), Positives = 40/99 (40%), Gaps = 15/99 (15%)
Query: 3 TREEPKQQEEEESFATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENV 62
+ ++ S PL ++ + + + + ++ ++ G + FD + N+VL++V
Sbjct: 4 SHHHHHHSQDPMSMTILPLELIDKCI--GSNLWVIMKSEREFAGTLVGFDDYVNIVLKDV 61
Query: 63 KEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILI 101
E T K S+M L G+ + ++
Sbjct: 62 TEYDT------VTGVTEK-------HSEMLLNGNGMCML 87
>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 = 52.4 bits (126), Expect = 1e-10
Identities = 20/90 (22%), Positives = 41/90 (45%), Gaps = 17/90 (18%)
Query: 12 EEESFATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPR 71
+ + L DS+ QVL+ R++ ++ G +++FD+H N++LE+ +E+
Sbjct: 4 DISKCFATLGATLQDSI--GKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDG--- 58
Query: 72 AGKGKKKSKPVNKDRFISKMFLRGDSVILI 101
M +RG++V+ I
Sbjct: 59 ------------NVYKRGTMVVRGENVLFI 76
>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 = 51.6 bits (124), Expect = 2e-10
Identities = 22/92 (23%), Positives = 44/92 (47%), Gaps = 16/92 (17%)
Query: 10 QEEEESFATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEH 69
+ PL L +S+ N+ V+I + +++ G +K+FD H N+VL + +E+
Sbjct: 6 VSSQRVNVQRPLDALGNSL--NSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELED-- 61
Query: 70 PRAGKGKKKSKPVNKDRFISKMFLRGDSVILI 101
G+ R + + +RGD+++ I
Sbjct: 62 -----GEVT-------RRLGTVLIRGDNIVYI 81
>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 = 51.1 bits (123), Expect = 3e-10
Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 16/82 (19%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 79
PL +L S+ + V++ + ++ G + +D H N+VL + +E+
Sbjct: 5 PLDVLNRSL--KSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVV-------- 54
Query: 80 KPVNKDRFISKMFLRGDSVILI 101
R + + +RGD+V+ +
Sbjct: 55 ------RKVGSVVIRGDTVVFV 70
>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 = 51.1 bits (123), Expect = 4e-10
Identities = 21/82 (25%), Positives = 44/82 (53%), Gaps = 16/82 (19%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 79
+L +S+ N VL+ + NK++ G ++++D+H N+VL + +E+ ++
Sbjct: 10 AHKVLAESL--NNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD----------- 56
Query: 80 KPVNKDRFISKMFLRGDSVILI 101
+ + + +RGD+VILI
Sbjct: 57 ---GSGKKLGTIVIRGDNVILI 75
>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 = 49.5 bits (118), Expect = 2e-09
Identities = 15/71 (21%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 31 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISK 90
+ ++ ++ + +G KAFD+H N++L + E P+ K ++ + R +
Sbjct: 14 DYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEK----RVLGL 69
Query: 91 MFLRGDSVILI 101
+ LRG++++ +
Sbjct: 70 VLLRGENLVSM 80
>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 = 48.8 bits (116), Expect = 6e-09
Identities = 15/71 (21%), Positives = 34/71 (47%), Gaps = 7/71 (9%)
Query: 31 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISK 90
+ ++ +++ G +K FD+ N+VL++V+E + K R +
Sbjct: 33 DQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNP-------EDGKLTGAIRKLGL 85
Query: 91 MFLRGDSVILI 101
+ +RG +++LI
Sbjct: 86 VVVRGTTLVLI 96
>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 = 44.2 bits (105), Expect = 1e-07
Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 16/82 (19%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 79
P L + +VLI + G + D + N+ LE +E GKK +
Sbjct: 5 PNEFLNKVI--GKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEY-------VNGKKTN 55
Query: 80 KPVNKDRFISKMFLRGDSVILI 101
F+RG++V+ +
Sbjct: 56 V-------YGDAFIRGNNVLYV 70
>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 = 44.2 bits (105), Expect = 1e-07
Identities = 12/71 (16%), Positives = 30/71 (42%), Gaps = 14/71 (19%)
Query: 31 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISK 90
+ ++ + + + G ++ FD N+V++ EM + I
Sbjct: 14 DKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEM--------------ATSGQQNNIGM 59
Query: 91 MFLRGDSVILI 101
+ +RG+S+I++
Sbjct: 60 VVIRGNSIIML 70
>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 = 44.2 bits (105), Expect = 2e-07
Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 17/83 (20%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKKLL-GRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKK 78
P ++ V + + + + L G+++ D + N+ L N E E
Sbjct: 6 PNQMVKSMV--GKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGE---------- 53
Query: 79 SKPVNKDRFISKMFLRGDSVILI 101
K R + ++ LRG++V+LI
Sbjct: 54 ----EKVRSLGEIVLRGNNVVLI 72
>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 = 44.4 bits (105), Expect = 2e-07
Identities = 17/84 (20%), Positives = 47/84 (55%), Gaps = 15/84 (17%)
Query: 20 PLSILTDSVKHNT--QVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKK 77
P++++ +++ + QV + + N ++ G + FD + N+VL++ +E+ ++ K +K
Sbjct: 17 PINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSK----TKSRK 72
Query: 78 KSKPVNKDRFISKMFLRGDSVILI 101
+ + ++ L+GD++ L+
Sbjct: 73 Q---------LGRIMLKGDNITLL 87
>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 = 42.1 bits (99), Expect = 1e-06
Identities = 14/82 (17%), Positives = 29/82 (35%), Gaps = 16/82 (19%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 79
P L V++ + + G + + D + NM L N +E G
Sbjct: 7 PKPFLNGLT--GKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEY-------IDGALSG 57
Query: 80 KPVNKDRFISKMFLRGDSVILI 101
+ ++ +R ++V+ I
Sbjct: 58 H-------LGEVLIRCNNVLYI 72
>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 = 40.8 bits (95), Expect = 2e-05
Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 14/82 (17%)
Query: 27 SVKHNTQV--LINCR------NNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKK 78
+V ++++ I+ R + + +G KAFD+H N++L + + R K K
Sbjct: 2 TVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCD-----CDEFRKIKPKNS 56
Query: 79 SKPVNKD-RFISKMFLRGDSVI 99
+ ++ R + + LRG++++
Sbjct: 57 KQAEREEKRVLGLVLLRGENLV 78
>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 = 38.3 bits (89), Expect = 4e-05
Identities = 17/86 (19%), Positives = 33/86 (38%), Gaps = 15/86 (17%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 79
P L V H V + N+ + G + + D + N+ L +E G
Sbjct: 22 PKPFLKGLVNHRVGVKLKF-NSTEYRGTLVSTDNYFNLQLNEAEEF-------VAGVSHG 73
Query: 80 KPVNKDRFISKMFLRGDSVILILKNP 105
+ ++F+R ++V+ I + P
Sbjct: 74 T-------LGEIFIRCNNVLYIRELP 92
>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 = 35.1 bits (81), Expect = 9e-04
Identities = 12/82 (14%), Positives = 34/82 (41%), Gaps = 15/82 (18%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 79
PL++L + +L+ +N + G ++ D + N+ L V + + +
Sbjct: 17 PLTLLNATQ--GRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFR----- 69
Query: 80 KPVNKDRFISKMFLRGDSVILI 101
+ + ++RG+++ +
Sbjct: 70 --------LPECYIRGNNIKYL 83
>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 = 32.4 bits (74), Expect = 0.005
Identities = 9/79 (11%), Positives = 30/79 (37%), Gaps = 16/79 (20%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 79
P+ +L ++ H V + G++ + + N + N+ + + +
Sbjct: 6 PIKVLHEAEGH--IVTCETNTGEVYRGKLIEAEDNMNCQMSNITVT-------YRDGRVA 56
Query: 80 KPVNKDRFISKMFLRGDSV 98
+ + ++++RG +
Sbjct: 57 Q-------LEQVYIRGCKI 68
>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 = 34.1 bits (77), Expect = 0.005
Identities = 20/135 (14%), Positives = 40/135 (29%), Gaps = 34/135 (25%)
Query: 1 MATREEPKQQEEEESFATGPLSILTDSVKHNTQVLINCRNNKK-LL--------GRVKAF 51
+ + +P + + L I S++ + L+ + + LL AF
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLRI--HSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAF 262
Query: 52 DRHCNMVL-------------ENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSV 98
+ C ++L + +H + K + K +L
Sbjct: 263 NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVK-----SLLLK-YLDCRPQ 316
Query: 99 IL---ILK-NPLALK 109
L +L NP L
Sbjct: 317 DLPREVLTTNPRRLS 331
>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 = 31.6 bits (71), Expect = 0.021
Identities = 9/82 (10%), Positives = 32/82 (39%), Gaps = 16/82 (19%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 79
P+ +L ++ H V + G++ + + N + N+ + + + +
Sbjct: 6 PIKVLHEAEGH--IVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTY-------RDGRVA 56
Query: 80 KPVNKDRFISKMFLRGDSVILI 101
+ + ++++RG + +
Sbjct: 57 Q-------LEQVYIRGSKIRFL 71
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 28.9 bits (64), Expect = 0.34
Identities = 20/112 (17%), Positives = 38/112 (33%), Gaps = 49/112 (43%)
Query: 20 PLSILTDSVKHNTQV---LINCRN--NKKLLGRVKAFDRHC---------------NMVL 59
P SIL DS+++N V +++ N +++ V + H N+V+
Sbjct: 320 PPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVV 379
Query: 60 ENVKEMWTEHPR-------------AGKGKKKS-------KPVNKDRF--IS 89
+ P+ A G +S K +RF ++
Sbjct: 380 -------SGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVA 424
Score = 28.9 bits (64), Expect = 0.38
Identities = 22/93 (23%), Positives = 34/93 (36%), Gaps = 20/93 (21%)
Query: 21 LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSK 80
SIL D V +N L +K G+ + EN M E GK K++
Sbjct: 1659 FSIL-DIVINNPVNLTIHFGGEK--GK---------RIRENYSAMIFETIV--DGKLKTE 1704
Query: 81 PVNK--DRFISKMFLRGDSVILIL-KN--PLAL 108
+ K + + R + +L + P AL
Sbjct: 1705 KIFKEINEHSTSYTFRSEKGLLSATQFTQP-AL 1736
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 26.6 bits (58), Expect = 1.8
Identities = 14/67 (20%), Positives = 21/67 (31%), Gaps = 21/67 (31%)
Query: 1 MATREEPKQQEEEESFATGP-LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDR------ 53
M TRE ++ GP L+I C+ + V+ F
Sbjct: 1 MMTRESIDKRAGRR----GPNLNI--------VLTCPECKVYPPKI--VERFSEGDVVCA 46
Query: 54 HCNMVLE 60
C +VL
Sbjct: 47 LCGLVLS 53
>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 = 25.1 bits (55), Expect = 2.7
Identities = 11/37 (29%), Positives = 19/37 (51%)
Query: 29 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEM 65
K V I N KL G++++FD+ ++ V +M
Sbjct: 17 KERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQM 53
>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 = 24.6 bits (54), Expect = 3.2
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 29 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEM 65
+ V I N KL G++++FD+ ++ V +M
Sbjct: 19 RERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQM 55
>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 = 24.9 bits (54), Expect = 4.2
Identities = 10/45 (22%), Positives = 17/45 (37%), Gaps = 2/45 (4%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKE 64
+ L + V I +N ++ G + D N L+ VK
Sbjct: 3 LVRFLMKLS--HETVTIELKNGTQVHGTITGVDVSMNTHLKAVKM 45
>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A
{Herbaspirillum seropedicae}
Length = 79
Score = 24.3 bits (53), Expect = 4.9
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 29 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEM 65
K + V I N KL G V++FD++ ++ V +M
Sbjct: 18 KEHVPVSIYLVNGIKLQGHVESFDQYVVLLRNTVTQM 54
>3na5_A Phosphoglucomutase; isomerase, metal binding; HET: BTB; 1.70A
{Salmonella enterica subsp} PDB: 3olp_A 2fuv_A*
Length = 570
Score = 25.0 bits (55), Expect = 5.9
Identities = 6/30 (20%), Positives = 14/30 (46%)
Query: 63 KEMWTEHPRAGKGKKKSKPVNKDRFISKMF 92
H RAG+ ++S +N + ++ +
Sbjct: 22 SNAMAIHNRAGQPAQQSDLINVAQLTAQYY 51
>2gnx_A Hypothetical protein; structural genomics, protein structure
initiative, PSI, center for eukaryotic structural
genomics, CESG, unknown function; 2.45A {Mus musculus}
SCOP: a.246.3.1 d.109.3.1
Length = 344
Score = 25.2 bits (54), Expect = 6.2
Identities = 7/34 (20%), Positives = 15/34 (44%), Gaps = 2/34 (5%)
Query: 74 KGKKKSKPVNKDRFISKM--FLRGDSVILILKNP 105
+ KK + + F++++ L+ V LK
Sbjct: 308 ESKKSERDSHFISFLNELSLALKNPKVFASLKPG 341
>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A
{Escherichia coli} PDB: 3qhs_A
Length = 104
Score = 24.5 bits (53), Expect = 6.4
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 29 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEM 65
+ V I N KL G++++FD+ ++ V +M
Sbjct: 19 RERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQM 55
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
0.316 0.132 0.377
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: 1,533,133
Number of extensions: 75788
Number of successful extensions: 154
Number of sequences better than 10.0: 1
Number of HSP's gapped: 135
Number of HSP's successfully gapped: 37
Length of query: 110
Length of database: 6,701,793
Length adjustment: 74
Effective length of query: 36
Effective length of database: 4,635,639
Effective search space: 166883004
Effective search space used: 166883004
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: 51 (23.7 bits)