RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6026
(98 letters)
>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 = 113 bits (285), Expect = 9e-35
Identities = 24/90 (26%), Positives = 48/90 (53%), Gaps = 1/90 (1%)
Query: 4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
+L + + G+ ++VELKN + G L + D Y+N+ L ++ T PD + C
Sbjct: 15 MLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDG-DKFFRLPEC 73
Query: 64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEA 93
+IRG+ ++Y+++ + + Q A ++E
Sbjct: 74 YIRGNNIKYLRIQDEVLSQVAKQQAQQREN 103
>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 = 104 bits (260), Expect = 8e-31
Identities = 27/88 (30%), Positives = 39/88 (44%), Gaps = 2/88 (2%)
Query: 5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCF 64
F L + V +ELKN + GT+ VD +N L + +T ++ P L +
Sbjct: 2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQL--ETLS 59
Query: 65 IRGSVVRYVQLPGDEVDTQLLQDATRKE 92
IRG+ +RY LP LL D K
Sbjct: 60 IRGNNIRYFILPDSLPLDTLLVDVEPKV 87
>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 = 97.4 bits (242), Expect = 6e-28
Identities = 21/96 (21%), Positives = 38/96 (39%), Gaps = 2/96 (2%)
Query: 1 MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSV 60
M + G V E G L + +N ++++I+VT D L
Sbjct: 1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQL-- 58
Query: 61 KNCFIRGSVVRYVQLPGDEVDTQLLQDATRKEAVNA 96
+ +IRGS +R++ LP + +L+ K +
Sbjct: 59 EQVYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSG 94
>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 = 85.5 bits (212), Expect = 5e-24
Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 2/76 (2%)
Query: 1 MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSV 60
M + G V E G L + +N ++++I+VT D L
Sbjct: 1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQL-- 58
Query: 61 KNCFIRGSVVRYVQLP 76
+ +IRG +R++ LP
Sbjct: 59 EQVYIRGCKIRFLILP 74
>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 = 74.4 bits (183), Expect = 2e-19
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 2/79 (2%)
Query: 9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
F L GK V+V+LK + G L SVD Y+N++L + L IR +
Sbjct: 10 FLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHL--GEVLIRCN 67
Query: 69 VVRYVQLPGDEVDTQLLQD 87
V Y++ +E + +++
Sbjct: 68 NVLYIRGVEEEEEDGEMRE 86
>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 = 65.2 bits (159), Expect = 8e-16
Identities = 23/71 (32%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 9 FFKSLVGKDVVVELK-NDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG 67
F K LV V V+LK N GTL S D Y N++L + L FIR
Sbjct: 25 FLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTL--GEIFIRC 82
Query: 68 SVVRYVQLPGD 78
+ V Y++ +
Sbjct: 83 NNVLYIRELPN 93
>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 = 62.7 bits (153), Expect = 6e-15
Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
F ++GK V++ L + V G L +D Y+N+ L K ++ + FIRG+
Sbjct: 8 FLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYG--DAFIRGN 65
Query: 69 VVRYVQLPGD 78
V YV D
Sbjct: 66 NVLYVSALDD 75
>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 = 51.9 bits (125), Expect = 9e-11
Identities = 19/71 (26%), Positives = 27/71 (38%), Gaps = 3/71 (4%)
Query: 9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
+ KDV+V LK G L D +LN+ L D + + IRG
Sbjct: 8 VIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRY--GKIVIRGD 65
Query: 69 VVRYVQLPGDE 79
V + P +E
Sbjct: 66 NVLAIS-PTEE 75
>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 = 49.2 bits (118), Expect = 1e-09
Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 3/72 (4%)
Query: 9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
+ V+V LK GTL D ++N+ L D + + + IRG
Sbjct: 8 VLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKV--GSVVIRGD 65
Query: 69 VVRYVQ-LPGDE 79
V +V PG E
Sbjct: 66 TVVFVSPAPGGE 77
>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 = 48.1 bits (115), Expect = 3e-09
Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 2/65 (3%)
Query: 9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
+ + V+++LK D G L S D ++N+ L D + + L IRG
Sbjct: 19 ALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRL--GTVLIRGD 76
Query: 69 VVRYV 73
+ Y+
Sbjct: 77 NIVYI 81
>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 = 47.7 bits (114), Expect = 5e-09
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 4/72 (5%)
Query: 9 FFKSLVGKDVVVELKND-VSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG 67
KS+VGK + VE+K + + G L VD Y+N+ LT+ ++ L +RG
Sbjct: 9 MVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSL--GEIVLRG 66
Query: 68 SVVRYVQLPGDE 79
+ V +Q P +E
Sbjct: 67 NNVVLIQ-PQEE 77
>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 = 45.8 bits (109), Expect = 3e-08
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDIS-VTDPDKYPHMLSVKNCFIR 66
+ + +GK V+V+L++ I G L S DQ++N+ L D + D + Y +R
Sbjct: 14 ATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGT----MVVR 69
Query: 67 GSVVRYV 73
G V ++
Sbjct: 70 GENVLFI 76
>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 = 44.6 bits (106), Expect = 9e-08
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 2/65 (3%)
Query: 9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
+ V+V+LK + + G L S DQ++N+ L+D D L IRG
Sbjct: 13 VLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGT--IVIRGD 70
Query: 69 VVRYV 73
V +
Sbjct: 71 NVILI 75
>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 = 38.9 bits (91), Expect = 2e-05
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 11 KSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDI--SVTDPDKYPHMLSVKNC---FI 65
K + + V ++L+ ++ GTL + D + NI L+D ++ + S + C FI
Sbjct: 16 KLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFI 75
Query: 66 RGSVVRYVQLPGDEVD 81
RG V + P ++ D
Sbjct: 76 RGDTVTLISTPSEDDD 91
>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 = 37.6 bits (87), Expect = 8e-05
Identities = 12/66 (18%), Positives = 26/66 (39%), Gaps = 6/66 (9%)
Query: 11 KSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDI--SVTDPDKYPHMLSVKN---CFI 65
+ + I G L DQ +N+ L D+ + +P+ +++ +
Sbjct: 29 SRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVV 88
Query: 66 RG-SVV 70
RG ++V
Sbjct: 89 RGTTLV 94
>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 = 37.1 bits (86), Expect = 1e-04
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 11/82 (13%)
Query: 8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD-------ISVTDPDKYPHMLSV 60
+ + + V V+L+ D + G LH+ D++LN+ L D + DK + ++
Sbjct: 12 DLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTI 71
Query: 61 KN----CFIRGSVVRYVQLPGD 78
+ F+RG V + P +
Sbjct: 72 RKHYEMLFVRGDSVILIAPPRN 93
>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 = 36.7 bits (85), Expect = 1e-04
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 3/72 (4%)
Query: 10 FKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSV 69
K + G ++ V +K++ GTL D Y+NI L D++ D + G+
Sbjct: 26 DKCI-GSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVT-GVTEKHSEMLLNGNG 83
Query: 70 VRYVQLPGDEVD 81
+ + PG + +
Sbjct: 84 MCMLI-PGGKPE 94
>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 = 36.9 bits (85), Expect = 1e-04
Identities = 14/60 (23%), Positives = 26/60 (43%)
Query: 14 VGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYV 73
+G + V +K D G L D+Y+N+ L D+ +S N ++ +V +
Sbjct: 37 IGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRL 96
>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 = 35.4 bits (82), Expect = 3e-04
Identities = 11/65 (16%), Positives = 26/65 (40%), Gaps = 6/65 (9%)
Query: 11 KSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDIS--VTDPDKYPHMLSVKNCFIRGS 68
K + K + ++L + G L D ++N+ + + T + + IRG+
Sbjct: 10 KKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGM----VVIRGN 65
Query: 69 VVRYV 73
+ +
Sbjct: 66 SIIML 70
>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 = 34.3 bits (78), Expect = 0.002
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 6/76 (7%)
Query: 6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFI 65
F + +L+G++V V L N G LH+VD LNI L + S +K+ + FI
Sbjct: 1 FVAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRV------FI 54
Query: 66 RGSVVRYVQLPGDEVD 81
+ ++ +D
Sbjct: 55 MYRYIVHIDSTERRID 70
>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 = 32.5 bits (74), Expect = 0.005
Identities = 7/35 (20%), Positives = 16/35 (45%)
Query: 11 KSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45
+ + L++ GT + D+++N+ L D
Sbjct: 10 LQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCD 44
>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 = 30.9 bits (70), Expect = 0.020
Identities = 9/41 (21%), Positives = 21/41 (51%)
Query: 5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45
L + + ++ V + + ++ I G + D+Y+N+ L D
Sbjct: 20 LIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDD 60
>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 = 31.2 bits (70), Expect = 0.041
Identities = 17/104 (16%), Positives = 31/104 (29%), Gaps = 32/104 (30%)
Query: 6 FYSFFKSL--VGKDVVV------------ELKNDVSI------CGTLHSVDQY----LNI 41
S+ K + +V + G + + Y L
Sbjct: 263 LRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIG-VRCYEAYPNTSLPP 321
Query: 42 KLTDISVTDPDKYP-HMLSVKNCFIRGSVVRYVQ-----LPGDE 79
+ + S+ + + P MLS+ N + V YV LP +
Sbjct: 322 SILEDSLENNEGVPSPMLSISNL-TQEQVQDYVNKTNSHLPAGK 364
>2a8x_A Dihydrolipoyl dehydrogenase, E3 component of alpha; lipoamide
dehydrogenase, pyruvate dehydrogenase, alpha keto acid
dehydrogenase; HET: FAD; 2.40A {Mycobacterium
tuberculosis} PDB: 3ii4_A*
Length = 464
Score = 28.2 bits (64), Expect = 0.38
Identities = 9/37 (24%), Positives = 14/37 (37%), Gaps = 3/37 (8%)
Query: 46 ISVTDPDKYPHMLSVKNCFI-RGSVVRYVQLPGDEVD 81
+ V D ++ N I GS R +PG +
Sbjct: 121 LLVDLNDGGTESVTFDNAIIATGSSTR--LVPGTSLS 155
>1i16_A Interleukin 16, LCF; cytokine, lymphocyte chemoattractant factor,
PDZ domain; NMR {Homo sapiens} SCOP: b.36.1.2
Length = 130
Score = 26.3 bits (58), Expect = 1.2
Identities = 10/26 (38%), Positives = 13/26 (50%), Gaps = 3/26 (11%)
Query: 76 PGDE---VDTQLLQDATRKEAVNATR 98
PGDE + +Q TR EA N +
Sbjct: 78 PGDEILQLGGTAMQGLTRFEAWNIIK 103
>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 = 1.2
Identities = 7/39 (17%), Positives = 14/39 (35%), Gaps = 14/39 (35%)
Query: 59 SVKNCFIRGSVVRYVQLPGDEVDTQLLQDATRKEAVNAT 97
++K ++ S+ Y D+ A+ AT
Sbjct: 21 ALKK--LQASLKLYA--D----------DSAPALAIKAT 45
>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex,
RNA binding protein; 2.00A {Homo sapiens}
Length = 86
Score = 24.7 bits (53), Expect = 3.4
Identities = 5/27 (18%), Positives = 11/27 (40%)
Query: 10 FKSLVGKDVVVELKNDVSICGTLHSVD 36
++ + K+V V G + + D
Sbjct: 12 WQDYIYKEVRVTASEKNEYKGWVLTTD 38
>3k1r_A Harmonin; protein-protein complex, alternative splicing, coiled
coil, deafness, hearing, non-syndromic deafness,
polymorphism; 2.30A {Homo sapiens} PDB: 2kbq_A 2kbr_A
Length = 192
Score = 25.3 bits (55), Expect = 3.9
Identities = 5/20 (25%), Positives = 9/20 (45%)
Query: 79 EVDTQLLQDATRKEAVNATR 98
+VD + DA + + R
Sbjct: 12 KVDFLIENDAEKDYLYDVLR 31
>3n6o_A Guanine nucleotide exchange factor;
phosphatidylinositol-4-phosphate, membrane, RAB, LCV, P
rabgef, signaling protein; 2.50A {Legionella
pneumophila} PDB: 3l0m_A
Length = 311
Score = 24.8 bits (53), Expect = 6.5
Identities = 12/55 (21%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 33 HSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQLLQD 87
++ +YL+ K T + H + + +Y Q+ GD + T++L D
Sbjct: 188 ENLSEYLSYKYA----TKDEGREHRYTASTENFKNVKEKYQQMRGDALKTEILAD 238
>1wfg_A Regulating synaptic membrane exocytosis protein 2; PDZ domain,
RAB3-interacting molecule, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: b.36.1.1 PDB: 2css_A 1zub_A
Length = 131
Score = 24.4 bits (53), Expect = 6.6
Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 3/24 (12%)
Query: 76 PGDE---VDTQLLQDATRKEAVNA 96
PGDE + +LLQ AT +E N
Sbjct: 86 PGDEVLEWNGRLLQGATFEEVYNI 109
>2d92_A INAD-like protein; PDZ domain, inadl protein, hinadl, PALS1-
associated tight junction protein, protein associated
to tight junctions, PATJ; NMR {Homo sapiens}
Length = 108
Score = 23.9 bits (52), Expect = 7.8
Identities = 8/24 (33%), Positives = 11/24 (45%), Gaps = 3/24 (12%)
Query: 76 PGD---EVDTQLLQDATRKEAVNA 96
PGD V+ L + + EAV
Sbjct: 65 PGDRLVSVNEYCLDNTSLAEAVEI 88
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 0.137 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: 1,440,670
Number of extensions: 71931
Number of successful extensions: 201
Number of sequences better than 10.0: 1
Number of HSP's gapped: 191
Number of HSP's successfully gapped: 37
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 (21.9 bits)
S2: 51 (23.7 bits)