RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy313
(93 letters)
>3a98_B Engulfment and cell motility protein 1; protein-protein complex,
DOCK2, ELMO1, SH3 domain, PH domain bundle, proline-rich
sequence, cytoskeleton; 2.10A {Homo sapiens} PDB: 2vsz_A
Length = 203
Score = 103 bits (258), Expect = 1e-29
Identities = 48/91 (52%), Positives = 65/91 (71%), Gaps = 2/91 (2%)
Query: 3 KIPDIAFSLTLDSVEITSLDFVAPDEEVFDYWTDGINALLGNKMTSKEADNDLETLLSME 62
++ ++AFS+ DS L+F+APD+ + WTDG+NALLG M S NDL+TLLSME
Sbjct: 112 EVLELAFSILYDSNC--QLNFIAPDKHEYCIWTDGLNALLGKDMMSDLTRNDLDTLLSME 169
Query: 63 IKIRLLDAEGVEIPHHPPEVPEEPRNYDFNF 93
IK+RLLD E ++IP PP +P+EP NYDF +
Sbjct: 170 IKLRLLDLENIQIPDAPPPIPKEPSNYDFVY 200
>1mai_A Phospholipase C delta-1; pleckstrin, inositol trisphosphate, signal
transduction protein, hydrolase; HET: I3P; 1.90A {Rattus
norvegicus} SCOP: b.55.1.1
Length = 131
Score = 46.4 bits (110), Expect = 4e-08
Identities = 10/48 (20%), Positives = 21/48 (43%), Gaps = 3/48 (6%)
Query: 5 PDIAFSLTLDSVEITSLDFVAPDEEVFDYWTDGINALLGN--KMTSKE 50
D FS+ + +LD +AP +W G+ ++ + M ++
Sbjct: 84 EDRCFSIVFKD-QRNTLDLIAPSPADAQHWVQGLRKIIHHSGSMDQRQ 130
>3ohm_B 1-phosphatidylinositol-4,5-bisphosphate phosphodi beta-3; PH
domain, EF hand, TIM barrel, C2 domain, GTPase, lipase,
C binding, GTP binding; HET: GDP; 2.70A {Homo sapiens}
Length = 885
Score = 35.8 bits (81), Expect = 9e-04
Identities = 8/35 (22%), Positives = 16/35 (45%)
Query: 14 DSVEITSLDFVAPDEEVFDYWTDGINALLGNKMTS 48
D V L+F+A ++ W++ + L N +
Sbjct: 110 DPVNTVFLNFMAVQDDTAKVWSEELFKLAMNILAQ 144
>3qr0_A Phospholipase C-beta (PLC-beta); PH domain, EF hand, C2 domain, TIM
barrel domain, hydrolase, calcium binding, phospholipid
binding; 2.00A {Sepia officinalis} PDB: 3qr1_A
Length = 816
Score = 31.8 bits (71), Expect = 0.017
Identities = 5/34 (14%), Positives = 16/34 (47%)
Query: 14 DSVEITSLDFVAPDEEVFDYWTDGINALLGNKMT 47
+ +++ VA + V W++ + + N ++
Sbjct: 113 NYIDLEWTHLVAENSSVAKKWSEEVFSYAYNLLS 146
>2zkm_X 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-2;
phospholipase C, phosphoinositide phospholipase,
PLC-beta-2, calcium, coiled coil; 1.62A {Homo sapiens}
SCOP: a.39.1.7 b.7.1.1 b.55.1.1 c.1.18.1 PDB: 2fju_B
Length = 799
Score = 31.5 bits (70), Expect = 0.027
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 14 DSVEITSLDFVAPDEEVFDYWTDGINALLGNKMT 47
D V++T +FV+ E V W + + AL+ + +T
Sbjct: 106 DMVDLTFHNFVSYKENVGKAWAEDVLALVKHPLT 139
>3a06_A 1-deoxy-D-xylulose 5-phosphate reductoisomerase; MEP pathway,
isoprene biosynthesis, metal- NADP, oxidoreductase; HET:
NDP; 2.00A {Thermotoga maritima} PDB: 3a14_A*
Length = 376
Score = 28.2 bits (64), Expect = 0.26
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 9/37 (24%)
Query: 3 KIPDIAFSLT--------LDSVEITSLDFVAPDEEVF 31
+IP I+++L + SL F PD E +
Sbjct: 255 RIP-ISYALFYPRRVALEPFFLRTISLSFEDPDPEKY 290
>3au8_A 1-deoxy-D-xylulose 5-phosphate reductoisomerase; NADPH binding;
HET: NDP; 1.86A {Plasmodium falciparum} PDB: 3au9_A*
3aua_A*
Length = 488
Score = 28.4 bits (64), Expect = 0.32
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 12/40 (30%)
Query: 3 KIPDIAFSLT-----------LDSVEITSLDFVAPDEEVF 31
+IP I +SLT LD ++++L F P E F
Sbjct: 361 QIP-ILYSLTWPDRIKTNLKPLDLAQVSTLTFHKPSLEHF 399
>1r0k_A 1-deoxy-D-xylulose 5-phosphate reductoisomerase; NADPH dependent,
fosmidomycin, non- mevalonate pathway, oxidoreductase;
1.91A {Zymomonas mobilis} SCOP: a.69.3.1 c.2.1.3
d.81.1.3 PDB: 1r0l_A*
Length = 388
Score = 27.5 bits (62), Expect = 0.52
Identities = 13/42 (30%), Positives = 17/42 (40%), Gaps = 15/42 (35%)
Query: 5 PD----IAFSLT-----------LDSVEITSLDFVAPDEEVF 31
PD I +L LD ++ +DF APD E F
Sbjct: 264 PDMRTPIGHTLAWPKRMETPAESLDFTKLRQMDFEAPDYERF 305
>2y1e_A 1-deoxy-D-xylulose 5-phosphate reductoisomerase; oxidoreductase,
DOXP/MEP pathway; 1.65A {Mycobacterium tuberculosis}
PDB: 2jcv_A* 2jcz_A* 2jd2_A 2jd1_A 2y1d_A* 2y1c_A
2y1f_A* 2y1g_A* 3ras_A* 4a03_A* 4aic_A* 2jcx_A* 2jcy_A
2jd0_A* 2c82_A
Length = 398
Score = 27.5 bits (62), Expect = 0.53
Identities = 10/42 (23%), Positives = 15/42 (35%), Gaps = 15/42 (35%)
Query: 5 PD----IAFSLT-----------LDSVEITSLDFVAPDEEVF 31
PD I+ +L D +S +F D +VF
Sbjct: 274 PDMKLPISLALGWPRRVSGAAAACDFHTASSWEFEPLDTDVF 315
>1q0q_A 1-deoxy-D-xylulose 5-phosphate reductoisomerase; oxidoreductase;
HET: DXP NDP; 1.90A {Escherichia coli} SCOP: a.69.3.1
c.2.1.3 d.81.1.3 PDB: 1q0l_A* 1q0h_A* 3r0i_A* 1k5h_A
1onn_A 1ono_A 1onp_A* 1jvs_A* 1t1r_A* 1t1s_A* 2egh_A*
3anm_A* 3anl_A* 3ann_A* 3iie_A
Length = 406
Score = 27.1 bits (61), Expect = 0.82
Identities = 10/40 (25%), Positives = 19/40 (47%), Gaps = 12/40 (30%)
Query: 3 KIPDIAFSLT-----------LDSVEITSLDFVAPDEEVF 31
+ P IA ++ LD ++++L F APD + +
Sbjct: 285 RTP-IAHTMAWPNRVNSGVKPLDFCKLSALTFAAPDYDRY 323
>2lf2_A Uncharacterized protein; NESG, structural genomics, PSI-biology,
protein structure in northeast structural genomics
consortium; NMR {Cytophaga hutchinsonii}
Length = 175
Score = 26.4 bits (58), Expect = 1.3
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 1 MAKIPDIAFSLTLDSVEIT-SLDFVAPDEEVFDYWTD 36
M + FS+ ++ IT +F A V++ +T
Sbjct: 1 MRTDLALDFSVNKENKTITIKREFAAVRAIVWEAFTR 37
>1umd_A E1-alpha, 2-OXO acid dehydrogenase alpha subunit; alpha(2)beta(2)
tetramer, structural genomics; HET: TDP; 1.90A {Thermus
thermophilus} SCOP: c.36.1.11 PDB: 1um9_A* 1umc_A*
1umb_A*
Length = 367
Score = 26.4 bits (59), Expect = 1.3
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 65 IRLLDAEGVEIPHHPPEVPEE 85
IRL+ EG + P ++ E
Sbjct: 16 IRLIGEEGEWLGDFPLDLEGE 36
>3ggn_A Uncharacterized protein DR_A0006; structural genomics, PSI- 2,
protein structure initiative, northeast structural
genomics consortium; 2.00A {Deinococcus radiodurans R1}
PDB: 2kcz_A
Length = 155
Score = 25.4 bits (55), Expect = 3.0
Identities = 5/23 (21%), Positives = 12/23 (52%)
Query: 14 DSVEITSLDFVAPDEEVFDYWTD 36
++V ++ P E+++ W D
Sbjct: 3 ETVVRDAVTIGKPAEQLYAVWRD 25
>1v5u_A SBF1, SET binding factor 1; MTMR5, the pleckstrin homology domain,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus musculus}
SCOP: b.55.1.1
Length = 117
Score = 24.7 bits (54), Expect = 3.9
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 23 FVAPDEEVFDYWTDGINALLGNKMTS 48
F A D W D I + L + +S
Sbjct: 91 FCAQDVPSAQQWVDRIQSCLSSGPSS 116
>3uid_A Putative uncharacterized protein; SRPBCC superfamily, beta
sandwich, function, structural genomics, TB structural
genomics conso TBSGC; 1.57A {Mycobacterium smegmatis}
Length = 168
Score = 24.9 bits (54), Expect = 3.9
Identities = 8/33 (24%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 5 PDIAFSLTLDSVEIT-SLDFVAPDEEVFDYWTD 36
P LD++ +T + +F AP ++ + D
Sbjct: 2 PVTDVKHDLDTLTLTITAEFAAPVTRIWQIYAD 34
>1qs0_A 2-oxoisovalerate dehydrogenase alpha-subunit; heterotetramer,
THDP cofactor, oxidoreductase; HET: TDP; 2.40A
{Pseudomonas putida} SCOP: c.36.1.11 PDB: 2bp7_A
Length = 407
Score = 25.0 bits (55), Expect = 4.4
Identities = 4/21 (19%), Positives = 10/21 (47%)
Query: 65 IRLLDAEGVEIPHHPPEVPEE 85
+R+LD +G ++ +
Sbjct: 54 VRVLDEQGDAQGPWAEDIDPQ 74
>1xuv_A Hypothetical protein MM0500; alpha-beta protein, northeast
structural genomics consortium, NESG, structural
genomics; 2.10A {Methanosarcina mazei GO1} SCOP:
d.129.3.5
Length = 178
Score = 24.6 bits (53), Expect = 4.9
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 1 MAKIPDIAFSLTLDSVEIT-SLDFVAPDEEVFDYWTD 36
MAK + EI + +F AP E VF +TD
Sbjct: 7 MAKNNPTRITAEPGKQEIIITREFDAPRELVFKAFTD 43
>2kif_A O6-methylguanine-DNA methyltransferase; methods development,
solution structure, DNA base repair methylguanine
methyltransferase; NMR {Vibrio parahaemolyticus AQ3810}
PDB: 2kim_A
Length = 108
Score = 24.1 bits (53), Expect = 5.5
Identities = 5/14 (35%), Positives = 11/14 (78%)
Query: 62 EIKIRLLDAEGVEI 75
+ + + L+AEG+E+
Sbjct: 72 DRQKQKLEAEGIEV 85
>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 = 24.8 bits (53), Expect = 5.7
Identities = 12/84 (14%), Positives = 28/84 (33%), Gaps = 19/84 (22%)
Query: 11 LTLDSVE----ITSLDF------VAPDEEVFDYWTDGINALLGNKMTSKEADNDLETLLS 60
L L +V+ + + ++V TD ++A ++ L
Sbjct: 248 LVLLNVQNAKAWNAFNLSCKILLTTRFKQV----TDFLSAATTTHISLDHHSMTLTPDEV 303
Query: 61 MEIKIRLLDAEGVEIPH-----HP 79
+ ++ LD ++P +P
Sbjct: 304 KSLLLKYLDCRPQDLPREVLTTNP 327
>3q64_A MLL3774 protein; structural genomics, PSI-biology, protein
structure initiati northeast structural genomics
consortium, NESG; 1.50A {Mesorhizobium loti}
Length = 162
Score = 24.4 bits (53), Expect = 6.7
Identities = 4/15 (26%), Positives = 7/15 (46%)
Query: 22 DFVAPDEEVFDYWTD 36
+ AP +VF +
Sbjct: 16 LYPAPPSKVFFALGN 30
>2l8o_A Uncharacterized protein; mixed alpha-beta protein, PSI-biology,
structural genomics, structure initiative; NMR
{Cytophaga hutchinsonii}
Length = 144
Score = 24.1 bits (52), Expect = 7.6
Identities = 5/15 (33%), Positives = 8/15 (53%)
Query: 22 DFVAPDEEVFDYWTD 36
A E+V+ YW +
Sbjct: 9 TVYAAIEKVWKYWNE 23
>2ldk_A Uncharacterized protein; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative; NMR {Arthrobacter aurescens}
Length = 172
Score = 24.1 bits (52), Expect = 8.4
Identities = 5/15 (33%), Positives = 8/15 (53%)
Query: 22 DFVAPDEEVFDYWTD 36
+F A + V+ W D
Sbjct: 19 EFDADVKRVWAIWED 33
>3put_A Hypothetical conserved protein; structural genomics, PSI-biology,
protein structure initiati northeast structural
genomics consortium; 1.83A {Rhizobium etli cfn 42} PDB:
3otl_A*
Length = 166
Score = 24.0 bits (52), Expect = 8.6
Identities = 5/15 (33%), Positives = 6/15 (40%)
Query: 22 DFVAPDEEVFDYWTD 36
AP VF W+
Sbjct: 16 RLTAPVARVFRAWST 30
>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 = 24.1 bits (51), Expect = 8.7
Identities = 5/16 (31%), Positives = 7/16 (43%), Gaps = 1/16 (6%)
Query: 12 TLDSVEITSLDFVAPD 27
L ++ SL A D
Sbjct: 21 ALKKLQ-ASLKLYADD 35
>3rd6_A MLL3558 protein; structural genomics, PSI-biology, northeast
structural genom consortium, NESG, unknown function;
2.80A {Mesorhizobium loti}
Length = 161
Score = 24.0 bits (52), Expect = 8.8
Identities = 3/15 (20%), Positives = 6/15 (40%)
Query: 22 DFVAPDEEVFDYWTD 36
+ + VF + D
Sbjct: 15 TYPQSPDRVFHAFAD 29
>2lcg_A Uncharacterized protein; start domain, structural genomics,
northeast structural GENO consortium, NESG, unknown
function, AHSA1; NMR {Ralstonia metallidurans}
Length = 142
Score = 23.7 bits (51), Expect = 9.0
Identities = 4/15 (26%), Positives = 7/15 (46%)
Query: 22 DFVAPDEEVFDYWTD 36
AP +V+ +T
Sbjct: 8 TVAAPVGKVWRAYTT 22
>1xfs_A NC_840354, conserved hypothetical protein; structural genomics,
protein structure initiative, NESG, ALP protein, PSI;
1.70A {Nitrosomonas europaea} SCOP: d.129.3.5
Length = 178
Score = 23.8 bits (51), Expect = 9.3
Identities = 3/15 (20%), Positives = 6/15 (40%)
Query: 22 DFVAPDEEVFDYWTD 36
+ P V+ T+
Sbjct: 17 ELAVPVNLVWRGLTE 31
>2lgh_A Uncharacterized protein; AHSA1, start domain, COG3832, PF08327,
HSP90, heat shock, ST genomics, PSI-biology; NMR
{Aeromonas hydrophila subsp}
Length = 144
Score = 23.6 bits (51), Expect = 9.6
Identities = 4/15 (26%), Positives = 5/15 (33%)
Query: 22 DFVAPDEEVFDYWTD 36
E V+ W D
Sbjct: 8 HIEQEIEAVWWAWND 22
>1wrj_A Methylated-DNA--protein-cysteine methyltransferase; 2.00A
{Sulfolobus tokodaii}
Length = 156
Score = 23.7 bits (52), Expect = 9.6
Identities = 6/20 (30%), Positives = 13/20 (65%)
Query: 61 MEIKIRLLDAEGVEIPHHPP 80
+E+K +LL+ EG+++
Sbjct: 136 VELKRKLLELEGIDVAKFIE 155
>2l9p_A Uncharacterized protein; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative; NMR {Staphylococcus epidermidis}
Length = 164
Score = 23.7 bits (51), Expect = 9.7
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 22 DFVAPDEEVFDYWTD 36
F AP +VFD +T
Sbjct: 15 TFSAPINKVFDAYTK 29
>1xn5_A BH1534 unknown conserved protein; structural genomics, protein
structure initiative, PSI, BACI halodurans protein
BH1534, alpha + beta; NMR {Bacillus halodurans} SCOP:
d.129.3.5
Length = 146
Score = 23.6 bits (51), Expect = 9.9
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 10/36 (27%)
Query: 1 MAKIPDIAFSLTLDSVEITSLDFVAPDEEVFDYWTD 36
M ++PDI + + AP E+V++ +
Sbjct: 1 MTRLPDIKKEVRFN----------APIEKVWEAVST 26
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
0.315 0.137 0.397
Gapped
Lambda K H
0.267 0.0579 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,544,576
Number of extensions: 82319
Number of successful extensions: 217
Number of sequences better than 10.0: 1
Number of HSP's gapped: 217
Number of HSP's successfully gapped: 51
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: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (23.8 bits)