RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3154
(101 letters)
>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 = 113 bits (285), Expect = 8e-35
Identities = 51/89 (57%), Positives = 66/89 (74%)
Query: 7 PTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEE 66
+V EPLDL+RLSLDE V+VK+R +R L G+LHAYD+HLNMVLGD EE VT + +E
Sbjct: 3 SAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEET 62
Query: 67 TYEEIYKTTKRSIPMLFVRGDGVILVSPP 95
++ KT ++ MLFVRGD VIL++PP
Sbjct: 63 DKDKALKTIRKHYEMLFVRGDSVILIAPP 91
>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 = 102 bits (256), Expect = 4e-30
Identities = 20/93 (21%), Positives = 48/93 (51%), Gaps = 2/93 (2%)
Query: 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEET-- 67
++ PL LI + R++V M+ ++ G L +D+++NMVL DV+E + ++ +
Sbjct: 25 NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGG 84
Query: 68 YEEIYKTTKRSIPMLFVRGDGVILVSPPNRTPA 100
+++ + + + + G+ V ++ P +
Sbjct: 85 NKKLKRVMVNRLETILLSGNNVAMLVPGGDPDS 117
>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 = 96.7 bits (241), Expect = 5e-28
Identities = 36/89 (40%), Positives = 55/89 (61%), Gaps = 6/89 (6%)
Query: 11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEE 70
++ PLDL++L+LDERV++K+R R L G L A+D H N+VL D ET+ + +E +
Sbjct: 8 METPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSES- 66
Query: 71 IYKTTKRSIPMLFVRGDGVILVSPPNRTP 99
+R M+F+RGD V L+S P+
Sbjct: 67 -----ERRCEMVFIRGDTVTLISTPSEDD 90
>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 = 95.8 bits (238), Expect = 2e-27
Identities = 29/88 (32%), Positives = 48/88 (54%), Gaps = 3/88 (3%)
Query: 11 VKEPLDLIRLSL--DERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETY 68
PL ++ S+ + +V + RN + L G++ A+D+H NMVL +V+E T V +
Sbjct: 25 NTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGK 84
Query: 69 EEIYKTTK-RSIPMLFVRGDGVILVSPP 95
++ K R I +F+RGD VI+V
Sbjct: 85 KKSKPVNKDRYISKMFLRGDSVIVVLRN 112
>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 = 93.2 bits (232), Expect = 7e-27
Identities = 27/94 (28%), Positives = 47/94 (50%), Gaps = 13/94 (13%)
Query: 1 MEDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTT 60
+ D ++V+ PLD + SL+ V +K++ +R RG L ++D H+N+VL D EE
Sbjct: 3 VIDVSSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELED- 61
Query: 61 VEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP 94
R + + +RGD ++ +SP
Sbjct: 62 ------------GEVTRRLGTVLIRGDNIVYISP 83
>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 = 84.3 bits (209), Expect = 3e-23
Identities = 26/88 (29%), Positives = 44/88 (50%), Gaps = 13/88 (14%)
Query: 11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEE 70
+ ++ SL+ V VK++ + +RG L +YDQH+N+VL D EE +
Sbjct: 7 AETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGS-------- 58
Query: 71 IYKTTKRSIPMLFVRGDGVILVSPPNRT 98
+ + + +RGD VIL+SP +
Sbjct: 59 -----GKKLGTIVIRGDNVILISPLQTS 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 = 82.7 bits (205), Expect = 8e-23
Identities = 28/84 (33%), Positives = 39/84 (46%), Gaps = 13/84 (15%)
Query: 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
PLD++ SL V V+++ R RG L YD H+N+VL D EE
Sbjct: 3 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG----------- 51
Query: 72 YKTTKRSIPMLFVRGDGVILVSPP 95
R + + +RGD V+ VSP
Sbjct: 52 --EVVRKVGSVVIRGDTVVFVSPA 73
>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 = 81.6 bits (202), Expect = 2e-22
Identities = 27/84 (32%), Positives = 39/84 (46%), Gaps = 13/84 (15%)
Query: 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
+ PLD+I SLD+ V V ++ RG+L YD HLN+VL D E
Sbjct: 3 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQD------------ 50
Query: 72 YKTTKRSIPMLFVRGDGVILVSPP 95
+ + +RGD V+ +SP
Sbjct: 51 -GEVVKRYGKIVIRGDNVLAISPT 73
>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 = 79.1 bits (195), Expect = 4e-21
Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 12/97 (12%)
Query: 2 EDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTV 61
Q P PL+LI + + V M++ER G L +D ++N+VL DV E T
Sbjct: 9 HHSQDPMSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVT 68
Query: 62 EIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNRT 98
+ + G+G+ ++ P +
Sbjct: 69 G------------VTEKHSEMLLNGNGMCMLIPGGKP 93
>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 = 76.9 bits (189), Expect = 5e-20
Identities = 26/83 (31%), Positives = 42/83 (50%), Gaps = 7/83 (8%)
Query: 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
+ LDL R D+R+ R + G L +DQ +N+VL DVEE + E + T
Sbjct: 23 ESILDLSRY-QDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGA-- 79
Query: 72 YKTTKRSIPMLFVRGDGVILVSP 94
R + ++ VRG ++L++P
Sbjct: 80 ----IRKLGLVVVRGTTLVLIAP 98
>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 = 74.7 bits (184), Expect = 2e-19
Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 16/94 (17%)
Query: 1 MEDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTT 60
M + + ++ S+ ++V VK+R+ +RG L ++DQH+N++L D EE +
Sbjct: 1 MASDI--SKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIID- 57
Query: 61 VEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP 94
+ VRG+ V+ +SP
Sbjct: 58 -------------GNVYKRGTMVVRGENVLFISP 78
>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 = 70.3 bits (172), Expect = 1e-17
Identities = 20/93 (21%), Positives = 50/93 (53%), Gaps = 8/93 (8%)
Query: 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYE 69
+V + +++ +D R+ +++ R+ G A+D+H+N++L D +E I + +
Sbjct: 2 TVGKSSKMLQH-IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRK---IKPKNSK 57
Query: 70 EIYKTTKRSIPMLFVRGDGVILVS----PPNRT 98
+ + KR + ++ +RG+ ++ ++ PP T
Sbjct: 58 QAEREEKRVLGLVLLRGENLVSMTVEGPPPKDT 90
>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 = 68.9 bits (169), Expect = 2e-17
Identities = 19/86 (22%), Positives = 40/86 (46%), Gaps = 14/86 (16%)
Query: 10 SVKEPLDLIRLSLDERVHVKMRNERV-LRGKLHAYDQHLNMVLGDVEETVTTVEIDEETY 68
++ P +++ + + + V+M+ E L GKL D ++N+ L + E
Sbjct: 2 AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMEC----------- 50
Query: 69 EEIYKTTKRSIPMLFVRGDGVILVSP 94
+ RS+ + +RG+ V+L+ P
Sbjct: 51 --KGEEKVRSLGEIVLRGNNVVLIQP 74
>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 = 68.5 bits (168), Expect = 4e-17
Identities = 18/85 (21%), Positives = 41/85 (48%), Gaps = 14/85 (16%)
Query: 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYE 69
S P +L + +D+++ +K+ R ++G L +D +N+V+ +E E
Sbjct: 2 SKAHPPELKKF-MDKKLSLKLNGGRHVQGILRGFDPFMNLVI-------------DECVE 47
Query: 70 EIYKTTKRSIPMLFVRGDGVILVSP 94
+ +I M+ +RG+ +I++
Sbjct: 48 MATSGQQNNIGMVVIRGNSIIMLEA 72
>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 = 67.7 bits (166), Expect = 6e-17
Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 13/84 (15%)
Query: 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
P + + + ++V +++ + +G L D ++N+ L EE V
Sbjct: 3 SSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVN------------ 50
Query: 72 YKTTKRSIPMLFVRGDGVILVSPP 95
F+RG+ V+ VS
Sbjct: 51 -GKKTNVYGDAFIRGNNVLYVSAL 73
>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 = 14/86 (16%), Positives = 30/86 (34%), Gaps = 13/86 (15%)
Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
P + + V VK++ +G L + D ++NM L + EE +
Sbjct: 7 PKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDG------------- 53
Query: 74 TTKRSIPMLFVRGDGVILVSPPNRTP 99
+ + +R + V+ +
Sbjct: 54 ALSGHLGEVLIRCNNVLYIRGVEEEE 79
>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 = 57.9 bits (140), Expect = 7e-13
Identities = 17/85 (20%), Positives = 39/85 (45%), Gaps = 16/85 (18%)
Query: 14 PLDLIRLSLDER----VHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYE 69
P++LI L R V + + + G + +D+++N+VL D EE + +
Sbjct: 17 PINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTK------- 69
Query: 70 EIYKTTKRSIPMLFVRGDGVILVSP 94
+++ + + ++GD + L+
Sbjct: 70 -----SRKQLGRIMLKGDNITLLQS 89
>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 = 54.5 bits (131), Expect = 2e-11
Identities = 19/95 (20%), Positives = 39/95 (41%), Gaps = 14/95 (14%)
Query: 2 EDEQIPTISVKEPLDLIRLSLDERVHVKMR-NERVLRGKLHAYDQHLNMVLGDVEETVTT 60
E I + P ++ ++ RV VK++ N RG L + D + N+ L + EE
Sbjct: 10 ESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEF--- 66
Query: 61 VEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPP 95
+ + ++ +F+R + V+ +
Sbjct: 67 --VAGV--------SHGTLGEIFIRCNNVLYIREL 91
>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 = 49.7 bits (119), Expect = 2e-09
Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 12/84 (14%)
Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
PL L+ + + V+++N G L D ++N+ L +V T+
Sbjct: 17 PLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPD------------G 64
Query: 74 TTKRSIPMLFVRGDGVILVSPPNR 97
+P ++RG+ + + +
Sbjct: 65 DKFFRLPECYIRGNNIKYLRIQDE 88
>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 = 48.9 bits (116), Expect = 6e-09
Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 13/87 (14%)
Query: 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYE 69
S+ P+ ++ + V + V RGKL + ++N + ++ T
Sbjct: 2 SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR------- 54
Query: 70 EIYKTTKRSIPMLFVRGDGVILVSPPN 96
+ +++RG + + P+
Sbjct: 55 ------VAQLEQVYIRGSKIRFLILPD 75
>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 = 48.9 bits (116), Expect = 2e-08
Identities = 18/81 (22%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEE--TVTTVEIDEETYEEIYKTTKRSI 79
+D R+ +++ R+ G A+D+H+N++L D +E + + EE KR +
Sbjct: 13 IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREE-----KRVL 67
Query: 80 PMLFVRGDGVILVSPPNRTPA 100
++ +RG+ ++ ++ P
Sbjct: 68 GLVLLRGENLVSMTVEGPPPK 88
>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 = 42.8 bits (101), Expect = 4e-07
Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 13/87 (14%)
Query: 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYE 69
S+ P+ ++ + V + V RGKL + ++N + ++ T
Sbjct: 2 SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR------- 54
Query: 70 EIYKTTKRSIPMLFVRGDGVILVSPPN 96
+ +++RG + + P+
Sbjct: 55 ------VAQLEQVYIRGCKIRFLILPD 75
>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 = 41.5 bits (97), Expect = 3e-06
Identities = 14/83 (16%), Positives = 30/83 (36%), Gaps = 13/83 (15%)
Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
+ + E V ++++N + G + D +N L V+ T+ E
Sbjct: 3 LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNRE----------- 51
Query: 74 TTKRSIPMLFVRGDGVILVSPPN 96
+ L +RG+ + P+
Sbjct: 52 --PVQLETLSIRGNNIRYFILPD 72
>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like P;
OB-like fold, B-sheet toroid, 14-MER, cadmium-binding
site, translation; 2.00A {Pyrobaculum aerophilum} SCOP:
b.38.1.1
Length = 130
Score = 30.1 bits (67), Expect = 0.060
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEE 56
L V V + N V +G LHA D LN+VL +
Sbjct: 9 LGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASN 43
>3hkw_A NS5B RNA-dependent RNA polymerase; HCV polymerase,
1,5-benzodiazepine, transferase; HET: IX6; 1.55A
{Hepatitis c virus subtype 1A} PDB: 3qgi_A* 3qgh_A*
2xi3_A* 2xi2_A* 3e51_A* 3bsa_A* 3bsc_A* 3br9_A* 3co9_A*
3cvk_A* 3cwj_A* 3d28_A* 3d5m_A* 3cde_A* 3gyn_A* 3h2l_A*
3igv_A* 2ax0_A* 2awz_A* 2ax1_A* ...
Length = 581
Score = 29.3 bits (65), Expect = 0.18
Identities = 12/49 (24%), Positives = 21/49 (42%)
Query: 27 HVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTT 75
R ++V +L D H VL +V+ + V+ + + EE T
Sbjct: 47 SACQRQKKVTFDRLQVLDSHYQDVLKEVKAAASKVKANLLSVEEACSLT 95
>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 = 0.27
Identities = 12/63 (19%), Positives = 26/63 (41%), Gaps = 18/63 (28%)
Query: 3 DEQIPT--ISVK----EPL-DLIR-----LSLDERVHVKMRNER---VLRG---KLHAYD 44
+E +P+ +S+ E + D + L ++V + + N V+ G L+ +
Sbjct: 331 NEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLN 390
Query: 45 QHL 47
L
Sbjct: 391 LTL 393
Score = 25.4 bits (55), Expect = 3.8
Identities = 12/46 (26%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 45 QHLNMVLGDVEETVTTVEI-DEETYEEIYKTTKRSIPMLF---VRG 86
+L G + VT V I + +++E + + +++I +LF VR
Sbjct: 265 SYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRC 310
Score = 25.0 bits (54), Expect = 5.9
Identities = 3/7 (42%), Positives = 4/7 (57%)
Query: 80 PMLFVRG 86
PML +
Sbjct: 337 PMLSISN 343
>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein;
ATP-binding, nucleotide-binding, membrane,
transmembrane, transport protein; 3.00A {Methanosarcina
acetivorans} SCOP: b.40.6.3 c.37.1.12
Length = 348
Score = 27.1 bits (61), Expect = 1.00
Identities = 14/87 (16%), Positives = 29/87 (33%), Gaps = 5/87 (5%)
Query: 20 LSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETV-----TTVEIDEETYEEIYKT 74
+ + ++V+ +R E + K N + G V E V++D + T
Sbjct: 261 MEVGDQVYAFLRPENIALSKSSTQSSIRNSLQGRVTEAWVLGALVRVKVDCGVPLNVLIT 320
Query: 75 TKRSIPMLFVRGDGVILVSPPNRTPAL 101
+ + M G + + L
Sbjct: 321 RRSAEEMELSPGVQIYARFKASSVHVL 347
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 26.5 bits (57), Expect = 1.3
Identities = 5/26 (19%), Positives = 11/26 (42%), Gaps = 4/26 (15%)
Query: 76 KRSIPMLFVRGDGVILVSPPNRTPAL 101
K+++ L + + + PAL
Sbjct: 19 KQALKKL----QASLKLYADDSAPAL 40
>3brd_A LIN-12 and GLP-1 phenotype protein 1, isoform A; protein-DNA
complex, signaling, transcription, notch; HET: DNA;
2.21A {Caenorhabditis elegans} SCOP: b.1.18.1 b.2.5.8
b.42.7.1 PDB: 2fo1_A 1ttu_A* 3brf_A*
Length = 477
Score = 25.9 bits (56), Expect = 2.5
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 72 YKTTKRSIPMLFVRGDGVILVS 93
T +P+ VR DGV+ S
Sbjct: 445 RTTGDVEVPISLVRDDGVVYSS 466
>1e9y_B Urease subunit beta; hydrolase, dodecamer; HET: KCX; 3.00A
{Helicobacter pylori} SCOP: b.92.1.1 c.1.9.2 PDB:
1e9z_B* 3qga_C* 3qgk_C*
Length = 569
Score = 26.1 bits (57), Expect = 2.7
Identities = 11/48 (22%), Positives = 17/48 (35%), Gaps = 17/48 (35%)
Query: 48 NMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPP 95
+M + T +E++ ETY V DG + S P
Sbjct: 526 DMQFNN---TTAHIEVNPETYH--------------VFVDGKEVTSKP 556
>3iag_C Recombining binding protein suppressor of hairless; protein-DNA
complex, signaling, transcription, notch, activator,
alternative splicing; HET: XYL; 2.00A {Mus musculus}
PDB: 3brg_C* 3nbn_A 2f8x_C 3v79_C*
Length = 422
Score = 25.8 bits (56), Expect = 3.0
Identities = 14/57 (24%), Positives = 19/57 (33%), Gaps = 12/57 (21%)
Query: 45 QHLNMVLGDVEETVTTVEIDEETY-----------EEIYKTTKRSIPMLFVRGDGVI 90
+L + GDVE T E + +P+ VR DGVI
Sbjct: 354 PNLRVWFGDVEAE-TMYRCGESMLCVVPDISAFREGWRWVRQPVQVPVTLVRNDGVI 409
>3la4_A Urease; JACK bean, hydrolase, ME binding, nickel; HET: CME KCX;
2.05A {Canavalia ensiformis}
Length = 840
Score = 25.6 bits (56), Expect = 3.2
Identities = 7/35 (20%), Positives = 12/35 (34%), Gaps = 14/35 (40%)
Query: 61 VEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPP 95
+ +D E+Y V+ DG +L
Sbjct: 807 ITVDPESYT--------------VKADGKLLCVSE 827
>4ubp_C Protein (urease (chain C)); bacillus pasteurii, nickel,
acetohydroxamic acid, metalloenzyme, hydrolase; HET:
KCX; 1.55A {Sporosarcina pasteurii} SCOP: b.92.1.1
c.1.9.2 PDB: 1s3t_C* 2ubp_C* 3ubp_C* 1ubp_C* 1ie7_C*
Length = 570
Score = 25.4 bits (55), Expect = 3.7
Identities = 13/48 (27%), Positives = 19/48 (39%), Gaps = 17/48 (35%)
Query: 48 NMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPP 95
+M D T ++I+ ETYE V+ DG +L P
Sbjct: 527 DMKWND---VTTDIDINPETYE--------------VKVDGEVLTCEP 557
>1cmb_A Met APO-repressor; DNA-binding regulatory protein; 1.80A
{Escherichia coli} SCOP: a.43.1.5 PDB: 1cma_A 1cmc_A*
1mjl_A* 1mj2_A 1mjk_A* 1mjm_A 1mjo_A* 1mjp_A 1mjq_A*
Length = 104
Score = 24.7 bits (53), Expect = 4.5
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 2 EDEQIPTISVKEPLDLIRLSLDERVHVKMRNER 34
+ EQ+ I+V PL ++++ DER ++ N R
Sbjct: 17 KSEQVKKITVSIPLKVLKILTDERTRRQVNNLR 49
>1y14_A B32, RPB4, DNA-directed RNA polymerase II 32 kDa polypeptide;
transferase; 2.30A {Saccharomyces cerevisiae} SCOP:
a.60.8.2
Length = 187
Score = 24.5 bits (52), Expect = 6.5
Identities = 16/100 (16%), Positives = 41/100 (41%), Gaps = 1/100 (1%)
Query: 2 EDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTV 61
E+E++ +++ E +I+ +L ER R+++ + K H ++ N VE+ +
Sbjct: 9 EEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKK-HLKHENANDETTAVEDEDDDL 67
Query: 62 EIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNRTPAL 101
+ D+ ++ + D ++ + L
Sbjct: 68 DEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDL 107
>2ord_A Acoat, acetylornithine aminotransferase; TM1785, acetylornithine
aminotransferase (EC 2.6.1.11) (ACOA structural
genomics; HET: MSE PLP; 1.40A {Thermotoga maritima
MSB8} PDB: 2e54_A*
Length = 397
Score = 24.4 bits (54), Expect = 8.7
Identities = 8/34 (23%), Positives = 13/34 (38%), Gaps = 2/34 (5%)
Query: 59 TTVEIDEETYEE-IYKTTKRSIPMLFVRGDGVIL 91
+ +I + + T R P FV G G +
Sbjct: 2 GSDKIHHHHHHMYLMNTYSRF-PATFVYGKGSWI 34
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
0.317 0.136 0.376
Gapped
Lambda K H
0.267 0.0538 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,556,420
Number of extensions: 87018
Number of successful extensions: 363
Number of sequences better than 10.0: 1
Number of HSP's gapped: 342
Number of HSP's successfully gapped: 58
Length of query: 101
Length of database: 6,701,793
Length adjustment: 67
Effective length of query: 34
Effective length of database: 4,831,086
Effective search space: 164256924
Effective search space used: 164256924
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 (23.9 bits)