RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10835
(80 letters)
>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 = 92.9 bits (231), Expect = 6e-27
Identities = 35/76 (46%), Positives = 48/76 (63%)
Query: 1 MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
MS + F+ + G+PV+VKL G++Y+G L +DGYMN+ L TEEYI+G L G
Sbjct: 1 MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLG 60
Query: 61 DTFIRGNNVLYISTQK 76
+ IR NNVLYI +
Sbjct: 61 EVLIRCNNVLYIRGVE 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 = 91.6 bits (228), Expect = 2e-26
Identities = 23/66 (34%), Positives = 37/66 (56%)
Query: 8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGN 67
+ PV++KL ++RGVL D +MN+ L EE +G++ + G IRG+
Sbjct: 17 LDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGD 76
Query: 68 NVLYIS 73
N++YIS
Sbjct: 77 NIVYIS 82
>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 = 91.2 bits (227), Expect = 2e-26
Identities = 23/67 (34%), Positives = 37/67 (55%)
Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
+ + PV+V+L G ++RG L D +MN+ L EE NG++ K G IRG+ V
Sbjct: 8 VLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTV 67
Query: 70 LYISTQK 76
+++S
Sbjct: 68 VFVSPAP 74
>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 = 90.5 bits (225), Expect = 3e-26
Identities = 42/67 (62%), Positives = 58/67 (86%)
Query: 8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGN 67
++F+ ++ G+ V+++L SGVDY+G+LSCLDGYMN+ALE+TEEY+NG+ N YGD FIRGN
Sbjct: 6 NEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGN 65
Query: 68 NVLYIST 74
NVLY+S
Sbjct: 66 NVLYVSA 72
>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 = 90.0 bits (224), Expect = 5e-26
Identities = 23/67 (34%), Positives = 37/67 (55%)
Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
I + + V+V L G ++RG L D ++N+ L E +G++ +YG IRG+NV
Sbjct: 8 VIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNV 67
Query: 70 LYISTQK 76
L IS +
Sbjct: 68 LAISPTE 74
>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 = 89.1 bits (221), Expect = 2e-25
Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 9/82 (10%)
Query: 1 MSRKESLSQ--------FIQQIHGRPVVVKL-VSGVDYRGVLSCLDGYMNIALEQTEEYI 51
MS +S F++ + V VKL + +YRG L D Y N+ L + EE++
Sbjct: 8 MSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFV 67
Query: 52 NGQLKNKYGDTFIRGNNVLYIS 73
G G+ FIR NNVLYI
Sbjct: 68 AGVSHGTLGEIFIRCNNVLYIR 89
>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 = 86.7 bits (215), Expect = 1e-24
Identities = 27/72 (37%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 2 SRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGD 61
+L +Q G+ V+VKL + RG+L D ++N+ LE EE I+G K G
Sbjct: 7 KCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGN-VYKRGT 65
Query: 62 TFIRGNNVLYIS 73
+RG NVL+IS
Sbjct: 66 MVVRGENVLFIS 77
>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 = 85.8 bits (213), Expect = 3e-24
Identities = 22/64 (34%), Positives = 33/64 (51%)
Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
+ + V+VKL + RG+L D +MN+ L +EE + K G IRG+NV
Sbjct: 13 VLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNV 72
Query: 70 LYIS 73
+ IS
Sbjct: 73 ILIS 76
>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 = 80.2 bits (198), Expect = 8e-22
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQ-TEEYINGQLKNKYGDTFIRGNN 68
+ GRP++V+L +G + G L D YMN+ L + +G + + +IRGNN
Sbjct: 20 LLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGNN 79
Query: 69 VLYIS 73
+ Y+
Sbjct: 80 IKYLR 84
>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 = 78.1 bits (193), Expect = 2e-21
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 8 SQFIQQIHGRPVVVKLVSG-VDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRG 66
+Q ++ + G+ + V++ G L +D YMN+ L E + G+ +RG
Sbjct: 7 NQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRG 66
Query: 67 NNVLYIS 73
NNV+ I
Sbjct: 67 NNVVLIQ 73
>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 = 74.3 bits (183), Expect = 7e-20
Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 2/77 (2%)
Query: 1 MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
MS+ +++ + + +KL G +G+L D +MN+ +++ E +N G
Sbjct: 1 MSKAHPP--ELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIG 58
Query: 61 DTFIRGNNVLYISTQKR 77
IRGN+++ + +R
Sbjct: 59 MVVIRGNSIIMLEALER 75
>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 = 67.4 bits (165), Expect = 5e-17
Identities = 12/64 (18%), Positives = 23/64 (35%)
Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
+ + G V + +G YRG L + MN + + +IRG +
Sbjct: 9 VLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKI 68
Query: 70 LYIS 73
++
Sbjct: 69 RFLI 72
>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 = 68.5 bits (167), Expect = 5e-17
Identities = 16/66 (24%), Positives = 32/66 (48%)
Query: 7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRG 66
L +F+ ++ V ++L +G G ++ +D MN L+ + + + + IRG
Sbjct: 3 LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRG 62
Query: 67 NNVLYI 72
NN+ Y
Sbjct: 63 NNIRYF 68
>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 = 64.1 bits (156), Expect = 2e-15
Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 13/80 (16%)
Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN-------------GQLK 56
++ V VKL + G L D ++N+ L EE + ++
Sbjct: 13 LVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIR 72
Query: 57 NKYGDTFIRGNNVLYISTQK 76
Y F+RG++V+ I+ +
Sbjct: 73 KHYEMLFVRGDSVILIAPPR 92
>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 = 64.7 bits (157), Expect = 2e-15
Identities = 12/64 (18%), Positives = 24/64 (37%)
Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
+ + G V + +G YRG L + MN + + +IRG+ +
Sbjct: 9 VLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKI 68
Query: 70 LYIS 73
++
Sbjct: 69 RFLI 72
>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 = 57.5 bits (139), Expect = 6e-13
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 1/66 (1%)
Query: 9 QFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN-GQLKNKYGDTFIRGN 67
+ I + G + V + S ++ G L D Y+NI L+ EY + K+ + + GN
Sbjct: 23 ELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEMLLNGN 82
Query: 68 NVLYIS 73
+ +
Sbjct: 83 GMCMLI 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 = 51.6 bits (124), Expect = 1e-10
Identities = 19/74 (25%), Positives = 27/74 (36%), Gaps = 7/74 (9%)
Query: 11 IQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI-------NGQLKNKYGDTF 63
++ V +KL G L D + NI L E I + + + F
Sbjct: 15 LKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVF 74
Query: 64 IRGNNVLYISTQKR 77
IRG+ V IST
Sbjct: 75 IRGDTVTLISTPSE 88
>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 = 51.9 bits (124), Expect = 2e-10
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 11/75 (14%)
Query: 6 SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN-------GQLKNK 58
LS++ + + G G+L D MN+ L+ EE + K
Sbjct: 27 DLSRYQ----DQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRK 82
Query: 59 YGDTFIRGNNVLYIS 73
G +RG ++ I+
Sbjct: 83 LGLVVVRGTTLVLIA 97
>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 = 51.5 bits (123), Expect = 2e-10
Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 15/80 (18%)
Query: 9 QFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYING--------------- 53
I + G + V + ++ GVL D Y+N+ L+ +EY
Sbjct: 31 ALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKR 90
Query: 54 QLKNKYGDTFIRGNNVLYIS 73
+ N+ + GNNV +
Sbjct: 91 VMVNRLETILLSGNNVAMLV 110
>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 = 50.2 bits (120), Expect = 4e-10
Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 14/83 (16%)
Query: 1 MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI--------- 51
+ + + Q I + L G + G D +MN+ L +E+
Sbjct: 3 VGKSSKMLQHI----DYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQ 58
Query: 52 -NGQLKNKYGDTFIRGNNVLYIS 73
+ K G +RG N++ ++
Sbjct: 59 AEREEKRVLGLVLLRGENLVSMT 81
>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 = 44.8 bits (106), Expect = 5e-08
Identities = 13/70 (18%), Positives = 31/70 (44%), Gaps = 1/70 (1%)
Query: 5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN-GQLKNKYGDTF 63
+ +++Q V + + G + D YMN+ L+ EE + + + + G
Sbjct: 19 NLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIM 78
Query: 64 IRGNNVLYIS 73
++G+N+ +
Sbjct: 79 LKGDNITLLQ 88
>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 = 35.7 bits (82), Expect = 2e-04
Identities = 13/73 (17%), Positives = 27/73 (36%), Gaps = 14/73 (19%)
Query: 15 HGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDT------------ 62
+ V++ + G + D + N+ LE +E K+ G
Sbjct: 38 NNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYIS 97
Query: 63 --FIRGNNVLYIS 73
F+RG++V+ +
Sbjct: 98 KMFLRGDSVIVVL 110
>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 = 31.2 bits (70), Expect = 0.017
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 11/79 (13%)
Query: 8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEY----------INGQLKN 57
S+ +Q I R + L G + G D +MN+ L +E+ + K
Sbjct: 7 SKMLQHIDYR-MRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKR 65
Query: 58 KYGDTFIRGNNVLYISTQK 76
G +RG N++ ++ +
Sbjct: 66 VLGLVLLRGENLVSMTVEG 84
>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 = 30.8 bits (69), Expect = 0.017
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 4/68 (5%)
Query: 11 IQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVL 70
+ + GR V V L +G Y+GVL +D +NI L K+ FI ++
Sbjct: 5 LNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAG----EKFNRVFIMYRYIV 60
Query: 71 YISTQKRR 78
+I + +RR
Sbjct: 61 HIDSTERR 68
>3ln6_A Glutathione biosynthesis bifunctional protein GSH; gamma-glutamyl
cysteine ligase domain, ATP-grAsp domain, HYB enzyme;
2.95A {Streptococcus agalactiae serogroup V}
Length = 750
Score = 27.9 bits (62), Expect = 0.26
Identities = 15/66 (22%), Positives = 25/66 (37%), Gaps = 13/66 (19%)
Query: 2 SRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGY--------MNIALEQT-----E 48
+ ++ + QI +P+VVK S G+ ++IA + E
Sbjct: 506 TDRKEALNYFSQIQDKPIVVKPKSTNFGLGISIFKTSANLASYEKAIDIAFTEDSAILVE 565
Query: 49 EYINGQ 54
EYI G
Sbjct: 566 EYIEGT 571
>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum
spherical virus}
Length = 165
Score = 25.1 bits (54), Expect = 2.6
Identities = 6/28 (21%), Positives = 18/28 (64%)
Query: 50 YINGQLKNKYGDTFIRGNNVLYISTQKR 77
++N LK YG+ +++ + +Y++ ++
Sbjct: 130 FLNHLLKMIYGEPYVKTDETVYLTANRK 157
>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 = 24.3 bits (53), Expect = 2.7
Identities = 9/43 (20%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 1 MSRKESL-SQFIQQI--HGRPVVVKLVSGVDYRGVLSCLDGYM 40
M E++ + ++ + V V ++G +GV+ D Y+
Sbjct: 1 MIANENIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYV 43
>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A
{Escherichia coli} PDB: 3qhs_A
Length = 104
Score = 24.8 bits (54), Expect = 2.8
Identities = 11/43 (25%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 1 MSRKESL-SQFIQQI--HGRPVVVKLVSGVDYRGVLSCLDGYM 40
M++ +SL F+ + PV + LV+G+ +G + D ++
Sbjct: 3 MAKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFV 45
>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 = 24.3 bits (53), Expect = 3.2
Identities = 11/43 (25%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 1 MSRKESL-SQFIQQI--HGRPVVVKLVSGVDYRGVLSCLDGYM 40
MS+ SL ++ + PV + LV+G+ +G + D ++
Sbjct: 1 MSKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFV 43
>1uc8_A LYSX, lysine biosynthesis enzyme; alpha-aminoadipate pathway, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; 2.00A {Thermus thermophilus} SCOP:
c.30.1.6 d.142.1.7 PDB: 1uc9_A*
Length = 280
Score = 24.7 bits (54), Expect = 3.3
Identities = 9/29 (31%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 4 KESLSQFIQQIHGRPVVVKLVSGVDYRGV 32
+E + ++ G PVV+K V G R +
Sbjct: 112 REEALRLMEAF-GYPVVLKPVIGSWGRLL 139
>1m6b_A C-ER, receptor protein-tyrosine kinase ERBB-3; cell surface
receptor, immunity, signaling transferase; HET: NAG NDG;
2.60A {Homo sapiens} SCOP: c.10.2.5 c.10.2.5 g.3.9.1
g.3.9.1 PDB: 3p11_A*
Length = 621
Score = 25.0 bits (53), Expect = 3.5
Identities = 6/35 (17%), Positives = 14/35 (40%)
Query: 38 GYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYI 72
GY+ +A+ + L+ G G +++
Sbjct: 66 GYVLVAMNEFSTLPLPNLRVVRGTQVYDGKFAIFV 100
>3ncv_A DNA mismatch repair protein MUTL; endonuclease, dimer, hydrolase;
HET: DNA; 2.40A {Neisseria gonorrhoeae}
Length = 220
Score = 24.5 bits (54), Expect = 3.7
Identities = 7/9 (77%), Positives = 7/9 (77%)
Query: 15 HGRPVVVKL 23
HGRP VKL
Sbjct: 199 HGRPTWVKL 207
>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 = 23.9 bits (52), Expect = 4.0
Identities = 11/43 (25%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 1 MSRKESL-SQFIQQI--HGRPVVVKLVSGVDYRGVLSCLDGYM 40
M++ +SL F+ + PV + LV+G+ +G + D ++
Sbjct: 3 MAKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFV 45
>3kdg_A DNA mismatch repair protein MUTL; endonuclease, DNA damage, DNA
repair, hydrolase; HET: DNA; 2.00A {Bacillus subtilis}
PDB: 3gab_A* 3kdk_A*
Length = 197
Score = 24.4 bits (54), Expect = 4.1
Identities = 4/9 (44%), Positives = 7/9 (77%)
Query: 15 HGRPVVVKL 23
HGRP+++
Sbjct: 176 HGRPIIIHH 184
>2btv_A T2A, T2B, protein (VP3 core protein); virus/viral protein,
icosahedral virus; 3.50A {Bluetongue virus} SCOP:
e.28.1.1
Length = 901
Score = 24.3 bits (52), Expect = 5.5
Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 3/53 (5%)
Query: 14 IHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI---NGQLKNKYGDTF 63
G V V GV+++ VL L ++ + NG + + D F
Sbjct: 153 HRGMEVAEPEVLGVEFKNVLPVLTAEHRAMIQNALDGSIIENGNVATRDVDVF 205
>3ln7_A Glutathione biosynthesis bifunctional protein GSH;
gamma-glutamylcysteine ligase domain, ATP-grAsp domain,
HYBR enzyme, ATP-binding; 3.20A {Pasteurella multocida}
Length = 757
Score = 24.1 bits (52), Expect = 6.9
Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 15/67 (22%)
Query: 2 SRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMN---------IALEQT----- 47
S +++++ + R VV+K S G+ G N IA +
Sbjct: 512 SLEKAVASYALFE-NRAVVIKPKSTNYGLGITIFQQGVQNREDFAKALEIAFREDKEVMV 570
Query: 48 EEYINGQ 54
E+Y+ G
Sbjct: 571 EDYLVGT 577
>2dwc_A PH0318, 433AA long hypothetical phosphoribosylglycinamide
transferase; purine ribonucleotide biosynthesis; HET:
ADP; 1.70A {Pyrococcus horikoshii} PDB: 2czg_A*
Length = 433
Score = 23.8 bits (52), Expect = 7.5
Identities = 6/29 (20%), Positives = 12/29 (41%), Gaps = 1/29 (3%)
Query: 4 KESLSQFIQQIHGRPVVVKLVSGVDYRGV 32
+ L + ++I G P K + +G
Sbjct: 145 LDELYEACEKI-GYPCHTKAIMSSSGKGS 172
>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A
{Herbaspirillum seropedicae}
Length = 79
Score = 22.8 bits (49), Expect = 9.8
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 1 MSRKESLSQ--FIQQI--HGRPVVVKLVSGVDYRGVLSCLDGYM 40
MS K L Q F+ + PV + LV+G+ +G + D Y+
Sbjct: 1 MSNKGQLLQDPFLNALRKEHVPVSIYLVNGIKLQGHVESFDQYV 44
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
0.320 0.138 0.389
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: 1,195,250
Number of extensions: 60454
Number of successful extensions: 160
Number of sequences better than 10.0: 1
Number of HSP's gapped: 149
Number of HSP's successfully gapped: 42
Length of query: 80
Length of database: 6,701,793
Length adjustment: 49
Effective length of query: 31
Effective length of database: 5,333,664
Effective search space: 165343584
Effective search space used: 165343584
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)