RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3499
(108 letters)
>3suz_A Amyloid beta A4 precursor protein-binding family 2; APP binding;
2.70A {Rattus norvegicus} PDB: 1u3b_A 1u39_A 1x45_A
1u37_A 1u38_A 2yt8_A
Length = 388
Score = 89.6 bits (221), Expect = 1e-22
Identities = 59/146 (40%), Positives = 77/146 (52%), Gaps = 48/146 (32%)
Query: 5 PSVLIEGVLFRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRI------------------ 46
LI+G++F A YLGSTQL+ E P+K+ RMMQA+EAVSR+
Sbjct: 2 SEDLIDGIIFAANYLGSTQLLSERNPSKNIRMMQAQEAVSRVKRMQKAAKIKKKANSEGD 61
Query: 47 -----------------------KEIMMDHALRTISYIADIGDLVVLMARRRFVSQEADE 83
+E MMDHALRTISYIADIG++VVLMARRR + +
Sbjct: 62 AQTLTEVDLFISTQRIKVLNADTQETMMDHALRTISYIADIGNIVVLMARRRMPRSASQD 121
Query: 84 PPKIS-------RTPKMICHVFESDE 102
+ + + KMICHVFES++
Sbjct: 122 CIETTPGAQEGKKQYKMICHVFESED 147
>1aqc_A X11; PTB domain; 2.30A {Homo sapiens} SCOP: b.55.1.2 PDB: 1x11_A*
Length = 172
Score = 84.5 bits (208), Expect = 3e-22
Identities = 61/143 (42%), Positives = 75/143 (52%), Gaps = 47/143 (32%)
Query: 7 VLIEGVLFRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRIKE------------------ 48
LI+G++F A YLGSTQL+ + P+K+ RMMQA+EAVSRIK
Sbjct: 3 DLIDGIIFAANYLGSTQLLSDKTPSKNVRMMQAQEAVSRIKMAQKLAKSRKKAPEGESQP 62
Query: 49 ----------------------IMMDHALRTISYIADIGDLVVLMARRRFVSQEADEPPK 86
MMDH LRTISYIADIG++VVLMARRR + E +
Sbjct: 63 MTEVDLFILTQRIKVLNADTQETMMDHPLRTISYIADIGNIVVLMARRRIPRSNSQENVE 122
Query: 87 IS-------RTPKMICHVFESDE 102
S R KMICHVFES++
Sbjct: 123 ASHPSQDGKRQYKMICHVFESED 145
>4dbb_A Amyloid beta A4 precursor protein-binding family 1; X11S/mints, PTB
domain, chimera protein, protein transport; HET: IPA
GOL; 1.90A {Rattus norvegicus}
Length = 162
Score = 74.4 bits (182), Expect = 2e-18
Identities = 59/127 (46%), Positives = 73/127 (57%), Gaps = 38/127 (29%)
Query: 4 EPSVLIEGVLFRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRI----------------- 46
+P LI+G++F A YLGSTQL+ + P+K+ RMMQA+EAVSRI
Sbjct: 1 DPEDLIDGIIFAANYLGSTQLLSDKTPSKNVRMMQAQEAVSRIKPEGESQPMTEVDLFIS 60
Query: 47 -----------KEIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEPPKISRTPKMIC 95
+E MMDH LRTISYIADIG++VVLMARRR KMIC
Sbjct: 61 TQRIKVLNADTQEPMMDHPLRTISYIADIGNIVVLMARRR----------MPRSQYKMIC 110
Query: 96 HVFESDE 102
HVFES++
Sbjct: 111 HVFESED 117
>2ela_A Adapter protein containing PH domain, PTB domain and leucine zipper
motif 1; APPL, cell cycle; 2.00A {Homo sapiens}
Length = 175
Score = 67.0 bits (163), Expect = 2e-15
Identities = 22/130 (16%), Positives = 40/130 (30%), Gaps = 30/130 (23%)
Query: 2 PHEPSVLIEGVLFRARYLGSTQLVCEGQPT---KSTRMMQAEEAVSRI------------ 46
H I LF R+LGS ++ + P ++ R + A A+ I
Sbjct: 19 SHMTEDSILHQLFIVRFLGSMEVKSDDHPDVVYETMRQILAARAIHNIFRMTESHLLVTC 78
Query: 47 ----------KEIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEPPKISRTPKMICH 96
+ + L + A + L FV + + +C+
Sbjct: 79 DCLKLIDPQTQVTRLTFPLPCVVLYATHQENKRLFG---FVLR--TSSGRSESNLSSVCY 133
Query: 97 VFESDEIASA 106
+FES+
Sbjct: 134 IFESNNEGEK 143
>2ej8_A DCC-interacting protein 13 alpha; structural genomics, NPPSFA,
national project on protein structural and functional
analyses; 1.84A {Homo sapiens}
Length = 160
Score = 55.4 bits (133), Expect = 5e-11
Identities = 19/135 (14%), Positives = 33/135 (24%), Gaps = 42/135 (31%)
Query: 3 HEPSVLIEGVLFRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRIK--------------- 47
E I LF R+LGS ++ E + +I
Sbjct: 7 GETEDSILHQLFIVRFLGSMEV------KSDDHPDVVYETMRQILAARAIHNIFRMTESH 60
Query: 48 ----------------EIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEPPKISRTP 91
+ L + A + L FV + +
Sbjct: 61 LLVTCDCLKLIDPQTQVTRLTFPLPCVVLYATHQENKRLFG---FVLR--TSSGRSESNL 115
Query: 92 KMICHVFESDEIASA 106
+C++FES+
Sbjct: 116 SSVCYIFESNNEGEK 130
>3f0w_A NUMB-R, NUMB-like protein; PH domain-like, PID domain,
phosphoprotein, signaling protei structural genomics,
structural genomics consortium, SGC; 2.70A {Homo
sapiens} PDB: 1wj1_A 2nmb_A* 1ddm_A
Length = 168
Score = 51.5 bits (123), Expect = 1e-09
Identities = 21/132 (15%), Positives = 47/132 (35%), Gaps = 43/132 (32%)
Query: 3 HEPSVLIEG-VLFRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRIK-------------- 47
+ + +G F RYLG ++ +S M E+AV ++K
Sbjct: 32 ADEDAVRKGTCSFPVRYLGHVEV------EESRGMHVCEDAVKKLKAMGRKSVKSVLWVS 85
Query: 48 ------------EIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEPPKISRTPKMIC 95
++++D + +S+ A +L + ++ ++ T + IC
Sbjct: 86 ADGLRVVDDKTKDLLVDQTIEKVSFCAPDRNLDKAFS---YICRD-------GTTRRWIC 135
Query: 96 HVFESDEIASAP 107
H F + + +
Sbjct: 136 HCFLALKDSGER 147
>3so6_A LDL receptor adaptor protein; PTB, endocytic adaptor, autosomal
reces hypercholesterolemia, ARH, cholesterol; 1.37A
{Rattus norvegicus}
Length = 137
Score = 50.3 bits (120), Expect = 2e-09
Identities = 20/128 (15%), Positives = 40/128 (31%), Gaps = 46/128 (35%)
Query: 9 IEGVLFRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRIK--------------------- 47
+EG++F +YLG T + + + AV RI
Sbjct: 1 MEGMVFSLKYLGMTLV------ERPKGEELSAAAVKRIVATAKASGKKLQKVTLKVSPRG 54
Query: 48 ---------EIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEPPKISRTPKMICHVF 98
+++ + ++ ISY + A +++Q + + CH F
Sbjct: 55 IILTDSLTSQLIENVSIYRISYCTADKMHDKVFA---YIAQS-------QQNESLECHAF 104
Query: 99 ESDEIASA 106
+ A
Sbjct: 105 LCTKRKVA 112
>1p3r_A Disabled homolog 2; PTB, signaling protein; 2.10A {Mus musculus}
SCOP: b.55.1.2 PDB: 1m7e_A
Length = 160
Score = 50.0 bits (119), Expect = 4e-09
Identities = 15/130 (11%), Positives = 37/130 (28%), Gaps = 51/130 (39%)
Query: 10 EGVLFRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRIK---------------------- 47
+GV ++A+ +G V + + K ++ +++ ++K
Sbjct: 15 DGVKYKAKLIGIDD-VPDARGDKMSQ-----DSMMKLKGMAAAGRSQGQHKQRIWVNISL 68
Query: 48 -----------EIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEPPKISRTPKMICH 96
I +H + IS+IA +V +
Sbjct: 69 SGIKIIDEKTGVIEHEHPVNKISFIARDVTDNRAFG---YVCGG---------EGQHQFF 116
Query: 97 VFESDEIASA 106
++ + A
Sbjct: 117 AIKTGQQAEP 126
>1ntv_A Disabled homolog 1; beta-sandwich, signaling protein; 1.50A {Mus
musculus} SCOP: b.55.1.2 PDB: 1nu2_A* 1oqn_A*
Length = 152
Score = 46.8 bits (111), Expect = 6e-08
Identities = 17/136 (12%), Positives = 36/136 (26%), Gaps = 51/136 (37%)
Query: 4 EPSVLIEGVLFRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRIK---------------- 47
EGV ++A+ +G + V + K + +++ ++K
Sbjct: 10 IKRFKGEGVRYKAKLIGIDE-VSAARGDKLCQ-----DSMMKLKGVVAGARSKGEHKQKI 63
Query: 48 -----------------EIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEPPKISRT 90
+ HA+ ISYIA +V +
Sbjct: 64 FLTISFGGIKIFDEKTGALQHHHAVHEISYIAKDITDHRAFG---YVCGKEG-------- 112
Query: 91 PKMICHVFESDEIASA 106
++ + A
Sbjct: 113 -NHRFVAIKTAQAAEP 127
>1n3h_A SHC transforming protein; free protein, beta sandwich, signaling
protein; NMR {Homo sapiens} SCOP: b.55.1.2 PDB: 1oy2_A
2l1c_A* 1shc_A*
Length = 207
Score = 44.8 bits (105), Expect = 6e-07
Identities = 12/48 (25%), Positives = 23/48 (47%), Gaps = 2/48 (4%)
Query: 3 HEPSVLI-EGVLFRARYLGSTQLVCEGQ-PTKSTRMMQAEEAVSRIKE 48
H ++ GV + RY+G +++ + +TR EA+S + E
Sbjct: 40 HPNDKVMGPGVSYLVRYMGCVEVLQSMRALDFNTRTQVTREAISLVCE 87
>3dxe_A Amyloid beta A4 protein-binding family B member 1; alzheimer'S
disease, APP, AICD, Fe65, PTB domain, alternative
splicing, polymorphism, alzheimer disease, apoptosis;
2.00A {Homo sapiens} PDB: 3dxd_A 3dxc_A
Length = 140
Score = 41.8 bits (98), Expect = 3e-06
Identities = 15/121 (12%), Positives = 35/121 (28%), Gaps = 46/121 (38%)
Query: 14 FRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRI--------------------------- 46
F+ YLG+ + K + A+ +
Sbjct: 10 FQVYYLGNVPV------AKPVGVDVINGALESVLSSSSREQWTPSHVSVAPATLTILHQQ 63
Query: 47 -KEIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEPPKISRTPKMICHVFESDEIAS 105
+ ++ + +R +S++A D+ F+ CH+F + A+
Sbjct: 64 TEAVLGECRVRFLSFLAVGRDVHTFA----FIMAAGPA--------SFCCHMFWCEPNAA 111
Query: 106 A 106
+
Sbjct: 112 S 112
>1dci_A Dienoyl-COA isomerase; lyase; 1.50A {Rattus norvegicus} SCOP:
c.14.1.3 PDB: 2vre_A
Length = 275
Score = 31.0 bits (71), Expect = 0.053
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 8/46 (17%)
Query: 35 RMMQAEEA-----VSRI---KEIMMDHALRTISYIADIGDLVVLMA 72
R M A+EA VSR+ K++M++ A + I+ + V +
Sbjct: 177 RKMMADEALDSGLVSRVFPDKDVMLNAAFALAADISSKSPVAVQGS 222
>2dyq_A Amyloid beta A4 precursor protein-binding family 3;
phosphotyrosine-interaction domain (PTB/PID alzheimer'S
disease, structural genomics, NPPSFA; 3.10A {Homo
sapiens}
Length = 144
Score = 29.1 bits (65), Expect = 0.15
Identities = 12/132 (9%), Positives = 31/132 (23%), Gaps = 40/132 (30%)
Query: 3 HEPSVLIEGVL-FRARYLGSTQ--------LVCE-------GQPTKSTRMMQAEEAVSRI 46
+ + + A Y+G+ ++ E + + S +
Sbjct: 6 SGLDAVSQAAQKYEALYMGTLPVTKAMGMDVLNEAIGTLTARGDRNAWVPTMLSVSDSLM 65
Query: 47 ------------KEIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEPPKISRTPKMI 94
+E + +R +++I D ++ +
Sbjct: 66 TAHPIQAEASTEEEPLWQCPVRLVTFIGVGRDPHTFG----LIADLGRQ--------SFQ 113
Query: 95 CHVFESDEIASA 106
C F A
Sbjct: 114 CAAFWCQPHAGG 125
>1wgu_A APBB2, amyloid beta (A4) precursor protein-bindin, family B, member
2; phosphotyrosine-interaction domain, amyloid disease,
structural genomics; NMR {Mus musculus} SCOP: b.55.1.2
PDB: 2roz_B
Length = 136
Score = 28.7 bits (64), Expect = 0.20
Identities = 22/110 (20%), Positives = 41/110 (37%), Gaps = 23/110 (20%)
Query: 14 FRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRIKE---------IMMDHALRTISYIADI 64
FR +YLG + + M A+ + + M+ A T++ I++
Sbjct: 18 FRVQYLGMLPV------DRPVGMDTLNSAIENLMTSSSKEDWPSVNMNVADATVTVISEK 71
Query: 65 GDLVVLMARR-RFVSQEA-DEPPKI------SRTPKMICHVFESDEIASA 106
+ VL+ R RF+S + + + CHVF + A+
Sbjct: 72 NEEEVLVECRVRFLSFMGVGKDVHTFAFIMDTGNQRFECHVFWCEPNAAN 121
>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 = 28.5 bits (63), Expect = 0.38
Identities = 22/117 (18%), Positives = 41/117 (35%), Gaps = 36/117 (30%)
Query: 10 EGVLFRARYLGSTQLVCEGQPTKSTRMMQAEEAVSR-IKE---IMMD-----H------A 54
+G+L ++ TQ P + E+A +K I D H A
Sbjct: 1723 KGLLSATQF---TQ------P----ALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAA 1769
Query: 55 LRTISYIADIGDLVVLMARR-RFVSQ--EADEPPK-----ISRTPKMICHVFESDEI 103
L +++ + I LV ++ R + DE + I+ P + F + +
Sbjct: 1770 LASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEAL 1826
>2yt0_A Amyloid beta A4 protein and amyloid beta A4 precursor
protein-binding family B member...; chimera, Fe65L, PID
domain, amyloid precursor protein; NMR {Mus musculus}
PDB: 2yt1_A
Length = 176
Score = 27.4 bits (60), Expect = 0.80
Identities = 22/110 (20%), Positives = 41/110 (37%), Gaps = 23/110 (20%)
Query: 14 FRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRIKE---------IMMDHALRTISYIADI 64
FR +YLG + + M A+ + + M+ A T++ I++
Sbjct: 64 FRVQYLGMLPV------DRPVGMDTLNSAIENLMTSSSKEDWPSVNMNVADATVTVISEK 117
Query: 65 GDLVVLMARR-RFVS-QEADEPPKI------SRTPKMICHVFESDEIASA 106
+ VL+ R RF+S + + + CHVF + A+
Sbjct: 118 NEEEVLVECRVRFLSFMGVGKDVHTFAFIMDTGNQRFECHVFWCEPNAAN 167
>2ysz_A Amyloid beta A4 precursor protein-binding family B member 2 and
amyloid beta A4 protein...; chimera, Fe65L, PID domain,
amyloid precursor protein; NMR {Mus musculus}
Length = 185
Score = 26.7 bits (58), Expect = 1.3
Identities = 22/110 (20%), Positives = 41/110 (37%), Gaps = 23/110 (20%)
Query: 14 FRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRIKE---------IMMDHALRTISYIADI 64
FR +YLG + + M A+ + + M+ A T++ I++
Sbjct: 18 FRVQYLGMLPV------DRPVGMDTLNSAIENLMTSSSKEDWPSVNMNVADATVTVISEK 71
Query: 65 GDLVVLMARR-RFVS-QEADEPPKI------SRTPKMICHVFESDEIASA 106
+ VL+ R RF+S + + + CHVF + A+
Sbjct: 72 NEEEVLVECRVRFLSFMGVGKDVHTFAFIMDTGNQRFECHVFWCEPNAAN 121
>2ppy_A Enoyl-COA hydratase; beta-oxidation, fatty acid metabol lyase,
structural genomics, NPPSFA; 2.16A {Geobacillus
kaustophilus}
Length = 265
Score = 25.9 bits (58), Expect = 2.5
Identities = 6/45 (13%), Positives = 14/45 (31%), Gaps = 7/45 (15%)
Query: 35 RMMQAEEA-----VSRI--KEIMMDHALRTISYIADIGDLVVLMA 72
+ +EA V+R+ + + +A+ V
Sbjct: 171 ETITPQEALEIGLVNRVFPQAETRERTREYARKLANSATYAVSNI 215
>2xe4_A Oligopeptidase B; hydrolase-inhibitor complex, hydrolase, protease
inhibitor trypanosomes, CLAN SC; HET: FC0 RGL; 1.65A
{Leishmania major}
Length = 751
Score = 26.1 bits (58), Expect = 2.9
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 2 PHEPSVLIEGVLFRARYL 19
H V +E + R+ YL
Sbjct: 364 DHSEDVFMESIAVRSNYL 381
>1wvf_A 4-cresol dehydrogenase [hydroxylating] flavoprote subunit;
flavoprotein, electron-transfer, FAD, oxidoreductase;
HET: FAD; 1.30A {Pseudomonas putida} SCOP: d.58.32.1
d.145.1.1 PDB: 1wve_A* 1dii_A* 1diq_A*
Length = 520
Score = 25.4 bits (56), Expect = 5.3
Identities = 5/65 (7%), Positives = 16/65 (24%), Gaps = 1/65 (1%)
Query: 38 QAEEAVSRIKEIMMDHALRTISYIADIGDLVVLMARRR-FVSQEADEPPKISRTPKMICH 96
Q + + ++ I + GD R + + +
Sbjct: 332 QVDVNWKIVTDVFKKLGKGRIVTQEEAGDTQPFKYRAQLMSGVPNLQEFGLYNWRGGGGS 391
Query: 97 VFESD 101
++ +
Sbjct: 392 MWFAP 396
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 24.7 bits (53), Expect = 7.3
Identities = 12/69 (17%), Positives = 24/69 (34%), Gaps = 9/69 (13%)
Query: 49 IMMDHALRTISYIADIGDLVVLMARRRFVS----QEADEPPK----ISRTP-KMICHVFE 99
I ++++ D D + R VS + + K I+ P + I
Sbjct: 120 IQVNYSSEVKENSVDSDDKAKVPPLIRIVSGLELSDTKQKGKKFLVIAYEPFENIAIELP 179
Query: 100 SDEIASAPD 108
+EI + +
Sbjct: 180 PNEILFSEN 188
>3mca_B Protein DOM34, elongation factor 1 alpha-like protein; protein
protein complex, translation regulation; 2.74A
{Schizosaccharomyces pombe}
Length = 390
Score = 24.7 bits (53), Expect = 9.0
Identities = 9/38 (23%), Positives = 13/38 (34%)
Query: 57 TISYIADIGDLVVLMARRRFVSQEADEPPKISRTPKMI 94
+ I +GD + RR V A SR +
Sbjct: 28 HLYNILQVGDQLKASTVRRVVKVGATGSTSGSRVVMKL 65
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 0.133 0.378
Gapped
Lambda K H
0.267 0.0747 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,643,424
Number of extensions: 89866
Number of successful extensions: 268
Number of sequences better than 10.0: 1
Number of HSP's gapped: 247
Number of HSP's successfully gapped: 44
Length of query: 108
Length of database: 6,701,793
Length adjustment: 72
Effective length of query: 36
Effective length of database: 4,691,481
Effective search space: 168893316
Effective search space used: 168893316
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 (23.4 bits)