RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12139
(65 letters)
>1ifw_A Polyadenylate-binding protein, cytoplasmic and nuclear;
all-helical domain, RNA binding protein; NMR
{Saccharomyces cerevisiae} SCOP: a.144.1.1
Length = 92
Score = 43.7 bits (103), Expect = 1e-07
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 1 MLLELSPAQLLMLLASDEALRQKVEEAMDI 30
M+L+L P ++ LL SDE Q +EA
Sbjct: 48 MILDLPPQEVFPLLESDELFEQHYKEASAA 77
>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding
protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A
1jh4_A
Length = 144
Score = 44.1 bits (103), Expect = 1e-07
Identities = 15/30 (50%), Positives = 23/30 (76%)
Query: 1 MLLELSPAQLLMLLASDEALRQKVEEAMDI 30
MLLE+ ++LL +L S E+LR KV+EA+ +
Sbjct: 92 MLLEIDNSELLHMLESPESLRSKVDEAVAV 121
>1i2t_A HYD protein; four alpha-helical domain, ligase; 1.04A {Homo
sapiens} SCOP: a.144.1.1 PDB: 3ntw_A
Length = 61
Score = 40.5 bits (95), Expect = 8e-07
Identities = 21/30 (70%), Positives = 29/30 (96%)
Query: 1 MLLELSPAQLLMLLASDEALRQKVEEAMDI 30
MLLELSPAQLL+LLAS+++LR +V+EAM++
Sbjct: 27 MLLELSPAQLLLLLASEDSLRARVDEAMEL 56
>2dyd_A Poly(A)-binding protein; alpha helical protein, RNA binding
protein; NMR {Triticum aestivum}
Length = 85
Score = 40.6 bits (95), Expect = 1e-06
Identities = 15/30 (50%), Positives = 22/30 (73%)
Query: 1 MLLELSPAQLLMLLASDEALRQKVEEAMDI 30
MLLE+ ++L LL S +AL+ KV EAM++
Sbjct: 48 MLLEMDQTEVLHLLESPDALKAKVAEAMEV 77
>1nmr_A Poly(A)-binding protein; all helical domain, peptide binding
protein; NMR {Trypanosoma cruzi} SCOP: a.144.1.1
Length = 85
Score = 38.7 bits (90), Expect = 7e-06
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 1 MLLELSPAQLLMLLASDEALRQKVEEAMDI 30
MLLE+ ++L LL + L KV+EA+++
Sbjct: 49 MLLEMDNGEILNLLDTPGLLDAKVQEALEV 78
>3kuj_A Polyadenylate-binding protein 1; protein-protein complex,
methylation, mRNA processing, mRNA nucleus,
phosphoprotein, RNA-binding, spliceosome; 1.40A {Homo
sapiens} PDB: 3ktr_A 3kui_A 3ktp_A 3kus_A* 3kut_A
3pkn_A 2rqg_B 2rqh_B 3kur_A 3pth_A 2x04_A
Length = 88
Score = 37.7 bits (87), Expect = 2e-05
Identities = 15/30 (50%), Positives = 23/30 (76%)
Query: 1 MLLELSPAQLLMLLASDEALRQKVEEAMDI 30
MLLE+ ++LL +L S E+LR KV+EA+ +
Sbjct: 46 MLLEIDNSELLHMLESPESLRSKVDEAVAV 75
>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 = 31.0 bits (69), Expect = 0.016
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 14/57 (24%)
Query: 2 LLELSPAQLLML----------LASDEALRQKVEEAMD--IV-MNLSGHDLSSENLL 45
LLEL PA+ +++ +A D L KV+ MD I +NL + S E +L
Sbjct: 144 LLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNL-KNCNSPETVL 199
>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 = 27.7 bits (61), Expect = 0.21
Identities = 19/65 (29%), Positives = 25/65 (38%), Gaps = 15/65 (23%)
Query: 7 PAQLLMLLASDEALRQKVEEAMDIVMNLSGHDLSS--EN--LLGSSDGIDIHSSTVK--- 59
PA LM A+ E L+ K D +GH S E L +D + I S V+
Sbjct: 1734 PALTLMEKAAFEDLKSKGLIPADATF--AGH---SLGEYAALASLADVMSI-ESLVEVVF 1787
Query: 60 --GEL 62
G
Sbjct: 1788 YRGMT 1792
Score = 26.9 bits (59), Expect = 0.41
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 3 LELSPAQLLMLLASDEALRQKVEEAMDIVMNLSGHDLSSENLLGSSDGIDIHS 55
EL + L ++S + D V+NL + + L G+ DIH+
Sbjct: 58 AELV-GKFLGYVSSL--VEPSKVGQFDQVLNLCLTEFENCYLEGN----DIHA 103
>2inf_A URO-D, UPD, uroporphyrinogen decarboxylase; (alpha-beta)8 barrel,
eight parallel beta strands surrounded by eight alpha
helices, lyase; 2.30A {Bacillus subtilis}
Length = 359
Score = 26.7 bits (60), Expect = 0.47
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 12 MLLASDEALRQKVEEAMDIVMNLSGH 37
+LLA E + QK +E +D M G
Sbjct: 297 ILLAPWEVIEQKTKEILDQGMESDGF 322
>2eja_A URO-D, UPD, uroporphyrinogen decarboxylase; dimer, X-RAY
diffraction, structural genomics, NPPSFA; 1.90A {Aquifex
aeolicus}
Length = 338
Score = 26.3 bits (59), Expect = 0.65
Identities = 5/26 (19%), Positives = 13/26 (50%)
Query: 12 MLLASDEALRQKVEEAMDIVMNLSGH 37
+L AS+E + +K + + + +
Sbjct: 283 VLYASEEVIEEKTLGLLRRIPVKTRY 308
>3cyv_A URO-D, UPD, uroporphyrinogen decarboxylase; alpha/beta barrel,
cytoplasm, lyase, porphyrin biosynthesis; 2.80A
{Shigella flexneri}
Length = 354
Score = 25.5 bits (57), Expect = 1.1
Identities = 6/26 (23%), Positives = 11/26 (42%)
Query: 12 MLLASDEALRQKVEEAMDIVMNLSGH 37
ML A + ++V + + GH
Sbjct: 296 MLYAPPARIEEEVATILAGFGHGEGH 321
>2eqx_A Kelch repeat and BTB domain-containing protein 4; BACK domain,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 105
Score = 25.3 bits (56), Expect = 1.1
Identities = 6/39 (15%), Positives = 11/39 (28%), Gaps = 3/39 (7%)
Query: 3 LELSPAQLLMLLASDEALRQKVEEAMDIVMNLSGHDLSS 41
L L L +++ Q EA + +
Sbjct: 50 LHLPHRLLTDIISDGVPCSQNPTEA---IEAWINFNKEE 85
>4exq_A UPD, URO-D, uroporphyrinogen decarboxylase; ssgcid, NIH, SBRI, heme
biosynthesis, structural GENO niaid; 1.65A {Burkholderia
thailandensis}
Length = 368
Score = 25.6 bits (57), Expect = 1.2
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 12 MLLASDEALRQKVEEAMDIVMNLSGH 37
+L A EA+R + +D N GH
Sbjct: 306 ILFAPPEAIRAEARAVLDSYGNHPGH 331
>3hve_A Gigaxonin; ubiquitin, cytoplasm, cytoskeleton, disease mutation,
kelch repeat, neurodegeneration, phosphoprotein,
polymorphism, UBL conjugation; 2.80A {Homo sapiens} PDB:
3hve_B
Length = 256
Score = 25.2 bits (56), Expect = 1.5
Identities = 6/28 (21%), Positives = 15/28 (53%)
Query: 5 LSPAQLLMLLASDEALRQKVEEAMDIVM 32
L + L + ++ +R+ V+E +I +
Sbjct: 228 LDSSYLREQMLNEPLVREIVKECSNIPL 255
Score = 23.3 bits (51), Expect = 6.1
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 3 LELSPAQLLMLLASDEALRQKVEEAM-DIVMNLSGHDLSS 41
LELSP +L +++ ++ L E + + V+ HD
Sbjct: 173 LELSPQKLKEVISLEK-LNVGNERYVFEAVIRWIAHDTEI 211
>1a8r_A GTP cyclohydrolase I; purine hydrolysis, pterine synthesis; HET:
GTP; 2.10A {Escherichia coli} SCOP: d.96.1.1 PDB:
1n3r_A* 1fbx_A 1gtp_A 1n3s_A* 1n3t_F* 1a9c_A* 4du6_A*
Length = 221
Score = 24.5 bits (54), Expect = 2.5
Identities = 7/31 (22%), Positives = 15/31 (48%)
Query: 16 SDEALRQKVEEAMDIVMNLSGHDLSSENLLG 46
+E + + M +M L DL+ ++L+
Sbjct: 31 DNETRKSLIAGHMTEIMQLLNLDLADDSLME 61
>3i3n_A Kelch-like protein 11; structural genomics, BTB, KLHL11A, SGC,
structural genomics consortium, kelch repeat, secreted,
protein binding; 2.60A {Homo sapiens}
Length = 279
Score = 23.8 bits (52), Expect = 5.1
Identities = 6/40 (15%), Positives = 13/40 (32%), Gaps = 2/40 (5%)
Query: 3 LELSPAQLLMLLASDEALRQKVEEAM-DIVMNLSGHDLSS 41
L + L+ E + EE + + V+ +
Sbjct: 181 YTLPFHLIRDWLSDLE-ITVDSEEVLFETVLKWVQRNAEE 219
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
0.312 0.130 0.330
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 900,063
Number of extensions: 42609
Number of successful extensions: 221
Number of sequences better than 10.0: 1
Number of HSP's gapped: 221
Number of HSP's successfully gapped: 21
Length of query: 65
Length of database: 6,701,793
Length adjustment: 36
Effective length of query: 29
Effective length of database: 5,696,637
Effective search space: 165202473
Effective search space used: 165202473
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (23.3 bits)