RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12750
(93 letters)
>3g2s_A C-terminal fragment of sortilin-related receptor; ADP-ribosylation
factor binding protein GGA1, VHS, acidic- cluster
dileucine signal, sorla; 1.70A {Homo sapiens} PDB:
3g2t_A* 3g2u_A 3g2v_A* 3g2w_A 1ujk_A* 1jwf_A 1ujj_A
1jwg_A* 1py1_A*
Length = 149
Score = 97.7 bits (243), Expect = 6e-28
Identities = 51/85 (60%), Positives = 66/85 (77%)
Query: 7 VILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELLYLW 66
I + VLE CM+ CG +FH EVGKFRFLNELIK++SPKYLG+ T + V+ +I+ELLY W
Sbjct: 65 AIQALTVLETCMKSCGKRFHDEVGKFRFLNELIKVVSPKYLGSRTSEKVKNKILELLYSW 124
Query: 67 TLEYPRESKIREAYEMLKKQQVVQA 91
T+ P E KI EAY+MLKKQ +V++
Sbjct: 125 TVGLPEEVKIAEAYQMLKKQGIVKS 149
>1mhq_A ADP-ribosylation factor binding protein GGA2; super helix, protein
transport; 2.20A {Homo sapiens} SCOP: a.118.9.2
Length = 148
Score = 94.6 bits (235), Expect = 1e-26
Identities = 45/83 (54%), Positives = 63/83 (75%)
Query: 7 VILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELLYLW 66
+ + VLE CM HCG +FH+EV KFRFLNELIK++SPKYLG+ V+ +IE+L+ W
Sbjct: 55 ALYALTVLEMCMNHCGEKFHSEVAKFRFLNELIKVLSPKYLGSWATGKVKGRVIEILFSW 114
Query: 67 TLEYPRESKIREAYEMLKKQQVV 89
T+ +P + KIR+AY+MLKKQ ++
Sbjct: 115 TVWFPEDIKIRDAYQMLKKQGII 137
>1juq_A ADP-ribosylation factor binding protein GGA3; protein-peptide
compelx, VHS domain, DXXLL sorting signal, signaling
protein; 2.20A {Homo sapiens} SCOP: a.118.9.2 PDB:
1jpl_A 1lf8_A*
Length = 171
Score = 92.7 bits (230), Expect = 1e-25
Identities = 49/85 (57%), Positives = 67/85 (78%)
Query: 5 RLVILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELLY 64
+ + VLEACM++CG +FH EVGKFRFLNELIK++SPKYLG+ + V+T++IELLY
Sbjct: 65 WEALQALTVLEACMKNCGRRFHNEVGKFRFLNELIKVVSPKYLGDRVSEKVKTKVIELLY 124
Query: 65 LWTLEYPRESKIREAYEMLKKQQVV 89
WT+ P E+KI++AY MLK+Q +V
Sbjct: 125 SWTMALPEEAKIKDAYHMLKRQGIV 149
>1x5b_A Signal transducing adaptor molecule 2; VHS domain, ubiquitin
binding, STAM2, structural genomics, NPPSFA; NMR {Homo
sapiens} PDB: 2l0t_B
Length = 163
Score = 72.3 bits (177), Expect = 8e-18
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 8/83 (9%)
Query: 7 VILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELLYLW 66
+ + +L AC+ +CG FH EV F E+ +I K V ++ L+ W
Sbjct: 69 ALQALTLLGACVANCGKIFHLEVCSRDFATEVRAVIKNK-----AHPKVCEKLKSLMVEW 123
Query: 67 TLEY---PRESKIREAYEMLKKQ 86
+ E+ P+ S I + +K++
Sbjct: 124 SEEFQKDPQFSLISATIKSMKEE 146
>3rru_A TOM1L1 protein; structural genomics, PSI-biology, northeast
structural genom consortium, NESG, super-helical
protein; 3.00A {Homo sapiens}
Length = 152
Score = 71.6 bits (175), Expect = 1e-17
Identities = 24/86 (27%), Positives = 49/86 (56%), Gaps = 7/86 (8%)
Query: 5 RLVILTIWVLEACMQHCGPQFHAEVGKFRFLNE-LIKLISPKYLGNLTPDAVRTEIIELL 63
+ + LT+ +++ C+Q+CGP F + + K F+ E L+KL++P+Y P ++ I+ +
Sbjct: 69 KEIQLTLSLIDMCVQNCGPSFQSLIVKKEFVKENLVKLLNPRY---NLPLDIQNRILNFI 125
Query: 64 YLWTLEY---PRESKIREAYEMLKKQ 86
W+ + S+++E Y L K+
Sbjct: 126 KTWSQGFPGGVDVSEVKEVYLDLVKK 151
>1elk_A Target of MYB1; superhelix of helices, endocytosis/exocytosis
complex; 1.50A {Homo sapiens} SCOP: a.118.9.2
Length = 157
Score = 70.0 bits (171), Expect = 5e-17
Identities = 24/84 (28%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 7 VILTIWVLEACMQHCGPQFHAEVGKFRFLNE-LIKLISPKYLGNLTPDAVRTEIIELLYL 65
V+L + VLE C+++CG +FH V F+ L++ I PK P V +++ L+
Sbjct: 71 VMLALTVLETCVKNCGHRFHVLVASQDFVESVLVRTILPKN---NPPTIVHDKVLNLIQS 127
Query: 66 WTLEY---PRESKIREAYEMLKKQ 86
W + P + + YE L+++
Sbjct: 128 WADAFRSSPDLTGVVTIYEDLRRK 151
>3ldz_A STAM-1, signal transducing adapter molecule 1; ubiquitin-binding,
cytoplasm, UBL conjugation, endosome, membrane, protein
transport, SH3 domain; 2.60A {Homo sapiens}
Length = 140
Score = 66.9 bits (163), Expect = 5e-16
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 9/83 (10%)
Query: 7 VILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELLYLW 66
+ + +L AC+ +CG FH EV F +E+ +++ V ++ L+ W
Sbjct: 59 AMQALTLLGACVSNCGKIFHLEVCSRDFASEVSNVLNK------GHPKVCEKLKALMVEW 112
Query: 67 TLEY---PRESKIREAYEMLKKQ 86
T E+ P+ S I + LK+Q
Sbjct: 113 TDEFKNDPQLSLISAMIKNLKEQ 135
>3zyq_A Hepatocyte growth factor-regulated tyrosine kinas substrate;
signaling; 1.48A {Homo sapiens} PDB: 4avx_A*
Length = 226
Score = 58.2 bits (140), Expect = 5e-12
Identities = 19/91 (20%), Positives = 43/91 (47%), Gaps = 8/91 (8%)
Query: 5 RLVILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELLY 64
+ + + V+E+ +++CG H EV + + EL L+ + VR +I+ L+
Sbjct: 60 HVALYALEVMESVVKNCGQTVHDEVANKQTMEELKDLLKRQ-----VEVNVRNKILYLIQ 114
Query: 65 LWTLEY---PRESKIREAYEMLKKQQVVQAW 92
W + P+ +++ Y+++K + V
Sbjct: 115 AWAHAFRNEPKYKVVQDTYQIMKVEGHVFPE 145
>1dvp_A HRS, hepatocyte growth factor-regulated tyrosine kinase substrate;
VHS, FYVE, zinc finger, superhelix, transferase; HET:
CIT; 2.00A {Drosophila melanogaster} SCOP: a.118.9.2
g.50.1.1
Length = 220
Score = 54.0 bits (129), Expect = 2e-10
Identities = 16/91 (17%), Positives = 34/91 (37%), Gaps = 8/91 (8%)
Query: 5 RLVILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELLY 64
++ VLE+ +++CG H EV + + VR +++EL+
Sbjct: 57 HSSCYSLLVLESIVKNCGAPVHEEVFTKENCEMFSSFLEST-----PHENVRQKMLELVQ 111
Query: 65 LWTLEY---PRESKIREAYEMLKKQQVVQAW 92
W + + I++ +LK +
Sbjct: 112 TWAYAFRSSDKYQAIKDTMTILKAKGHTFPE 142
>1nmr_A Poly(A)-binding protein; all helical domain, peptide binding
protein; NMR {Trypanosoma cruzi} SCOP: a.144.1.1
Length = 85
Score = 28.7 bits (64), Expect = 0.11
Identities = 12/50 (24%), Positives = 23/50 (46%)
Query: 38 LIKLISPKYLGNLTPDAVRTEIIELLYLWTLEYPRESKIREAYEMLKKQQ 87
I I+P +T + + E+L L ++K++EA E+L +
Sbjct: 34 HIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDAKVQEALEVLNRHM 83
>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 = 27.1 bits (59), Expect = 0.61
Identities = 13/49 (26%), Positives = 23/49 (46%)
Query: 39 IKLISPKYLGNLTPDAVRTEIIELLYLWTLEYPRESKIREAYEMLKKQQ 87
I+ + P G +T + + ELL++ SK+ EA +L+ Q
Sbjct: 78 IQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQ 126
>2bkl_A Prolyl endopeptidase; mechanistic study, celiac sprue, hydrolase,
protease; HET: ZAH MES; 1.5A {Myxococcus xanthus}
Length = 695
Score = 27.1 bits (61), Expect = 0.80
Identities = 8/33 (24%), Positives = 13/33 (39%), Gaps = 1/33 (3%)
Query: 53 DAVRTEIIELLYLWTLEYPRESKIREAYEMLKK 85
D VR + W EY ++ E ++ L
Sbjct: 561 DMVRYHLFGSGRTWIPEYG-TAEKPEDFKTLHA 592
>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 = 25.4 bits (55), Expect = 2.0
Identities = 15/55 (27%), Positives = 25/55 (45%)
Query: 33 RFLNELIKLISPKYLGNLTPDAVRTEIIELLYLWTLEYPRESKIREAYEMLKKQQ 87
L LI+ + P G +T + + ELL++ SK+ EA +L+ Q
Sbjct: 26 ERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQ 80
>3u0r_A Apoptosis inhibitor 5; heat repeat, armadillo repeat, lysine
acetylation; 2.50A {Homo sapiens} PDB: 3v6a_A
Length = 507
Score = 26.1 bits (56), Expect = 2.2
Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 9/80 (11%)
Query: 14 LEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELL--------YL 65
L C + P F V RF+ + + P TP +E+L +
Sbjct: 241 LLQCTRQAVPLFSKNVHSTRFVTYFCEQVLPNLGTLTTPVEGLDIQLEVLKLLAEMSSFC 300
Query: 66 WTLEYPRESKIREAYEMLKK 85
+E E+ +R+ ++ L +
Sbjct: 301 GDMEKL-ETNLRKLFDKLLE 319
>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA,
transcription, arrest, BACKTRACKING cleavage,
transferase-DNA-RNA complex; HET: DNA BRU EPE PGE;
3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S
3gtm_S* 1enw_A
Length = 178
Score = 24.8 bits (53), Expect = 4.2
Identities = 3/16 (18%), Positives = 9/16 (56%)
Query: 49 NLTPDAVRTEIIELLY 64
+ +R ++++ LY
Sbjct: 11 AIYHHKLRDQVLKALY 26
>2o5v_A DNA replication and repair protein RECF; ABC ATPase, walker A
motif, P-loop, signature motif,
replication/recombination complex; HET: DNA; 1.61A
{Deinococcus radiodurans}
Length = 359
Score = 24.9 bits (55), Expect = 4.7
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 33 RFLNELIKLISPKYLGNL 50
+L+ L+ +S +Y L
Sbjct: 133 AYLDSLLSRLSARYGEQL 150
>1ou5_A TRNA CCA-adding enzyme, tRNA-nucleotidyltransferase; polymerase,
translation; 3.40A {Homo sapiens} SCOP: a.173.1.1
d.218.1.4
Length = 448
Score = 24.8 bits (54), Expect = 4.7
Identities = 6/33 (18%), Positives = 14/33 (42%)
Query: 33 RFLNELIKLISPKYLGNLTPDAVRTEIIELLYL 65
R EL K++ ++ +L ++ + L
Sbjct: 251 RIWVELKKILVGNHVNHLIHLIYDLDVAPYIGL 283
>2guz_A Mitochondrial import inner membrane translocase subunit TIM14;
DNAJ-fold, chaperone, protein transport; HET: FLC;
2.00A {Saccharomyces cerevisiae}
Length = 71
Score = 23.9 bits (52), Expect = 5.0
Identities = 6/14 (42%), Positives = 10/14 (71%)
Query: 74 SKIREAYEMLKKQQ 87
+KI EA + L+K+
Sbjct: 55 TKINEAKDFLEKRG 68
>3hko_A Calcium/calmodulin-dependent protein kinase with domain and 2
calmodulin-like EF...; structural genomics, protist
parasite; HET: ANP; 1.80A {Cryptosporidium parvum iowa
II}
Length = 345
Score = 24.4 bits (53), Expect = 6.3
Identities = 10/43 (23%), Positives = 21/43 (48%)
Query: 39 IKLISPKYLGNLTPDAVRTEIIELLYLWTLEYPRESKIREAYE 81
IK+++ + + P V E+ + L +P +++ E YE
Sbjct: 56 IKIMNKNKIRQINPKDVERIKTEVRLMKKLHHPNIARLYEVYE 98
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
0.327 0.141 0.446
Gapped
Lambda K H
0.267 0.0580 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,436,340
Number of extensions: 69170
Number of successful extensions: 250
Number of sequences better than 10.0: 1
Number of HSP's gapped: 244
Number of HSP's successfully gapped: 28
Length of query: 93
Length of database: 6,701,793
Length adjustment: 60
Effective length of query: 33
Effective length of database: 5,026,533
Effective search space: 165875589
Effective search space used: 165875589
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (23.8 bits)