RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2610
(133 letters)
>1n0u_A EF-2, elongation factor 2; G-protein, CIS-proline, translation;
HET: SO1; 2.12A {Saccharomyces cerevisiae} SCOP:
b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 d.58.11.1 PDB:
1n0v_C 1s1h_T 2e1r_A* 2npf_A* 2p8w_T* 3dny_T 3b82_A*
1zm2_A* 1zm3_A* 1zm4_A* 1zm9_A* 2p8x_T* 2p8y_T* 2p8z_T*
2zit_A* 1u2r_A* 3b78_A* 3b8h_A*
Length = 842
Score = 92.4 bits (229), Expect = 4e-23
Identities = 33/102 (32%), Positives = 45/102 (44%), Gaps = 3/102 (2%)
Query: 35 LEDADDSDLYFSPDRGNVVFASAFDGWGFTIDDFARLYSAKLGIREDILRKTLWGDYYLN 94
D D+ P RG V F S GW FTI FA Y+ K G+ + + LWGD + N
Sbjct: 192 YADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKMMDRLWGDSFFN 251
Query: 95 AKAKRILKG---AQEKAKAPLFVEFVLKNVVTLYETVAVRKK 133
K K+ A+ K F F+L + L+ + KK
Sbjct: 252 PKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKK 293
>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 = 30.4 bits (68), Expect = 0.16
Identities = 17/107 (15%), Positives = 33/107 (30%), Gaps = 27/107 (25%)
Query: 19 STSSPSDTVYT------DWGTGLEDADDSDLYFS------PDRGNVV-----FASAFDGW 61
T+ ++ V+T +W + D D Y P V +
Sbjct: 200 RTTLDAEKVFTQGLNILEWLENPSNTPDKD-YLLSIPISCP--LIGVIQLAHYVVTAKLL 256
Query: 62 GFTIDDFARLYSAKLGIREDILRKTL------WGDYYLNA-KAKRIL 101
GFT + G + ++ W ++++ KA +L
Sbjct: 257 GFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVL 303
Score = 25.8 bits (56), Expect = 6.0
Identities = 21/114 (18%), Positives = 38/114 (33%), Gaps = 26/114 (22%)
Query: 40 DSDLYFSPDRGNVVFASAFDGWGFT---IDDFARLYSAKLGIREDILR---KTLWGDYYL 93
+S L+ + GN + F G G T ++ LY + D+++ +TL
Sbjct: 142 NSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRT 201
Query: 94 NAKAKRI----------LKGAQEK------AKAPLFVEFVLKNVVTL--YETVA 129
A+++ L+ P + L V+ L Y A
Sbjct: 202 TLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIP--ISCPLIGVIQLAHYVVTA 253
>3irs_A Uncharacterized protein BB4693; structural genomics, PSI-2, protein
structure initiative, TI protein; HET: GOL; 1.76A
{Bordetella bronchiseptica} PDB: 3k4w_A
Length = 291
Score = 29.4 bits (66), Expect = 0.32
Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 15/66 (22%)
Query: 47 PDRGNVVFASAFDGWGF--TIDDFARLYSAKLGIREDILRKTLWGDYYLNAKAKRILKGA 104
DR ++F +A+ + F L I+ D + K L G N A+R+L A
Sbjct: 235 ADR--MLFGTAYPMCPLKEYTEWFLTL-----PIKPDAMEKILHG----N--AERLLAQA 281
Query: 105 QEKAKA 110
+
Sbjct: 282 GREGHH 287
>3af5_A Putative uncharacterized protein PH1404; archaeal CPSF, beta-CAsp
family, KH domain, ribonuclease, ME beta-lactamase
superfamily, archaea; 2.60A {Pyrococcus horikoshii} PDB:
3af6_A*
Length = 651
Score = 28.5 bits (64), Expect = 0.71
Identities = 16/79 (20%), Positives = 30/79 (37%), Gaps = 11/79 (13%)
Query: 11 LVLRPGPQSTSSPSDTVYTDWGTGLEDADDSDLYFSPDRGNVVFASAFDGWGFTIDDFAR 70
+ +RP P+ P + + ++A+ +++ F P G V+ + G
Sbjct: 70 ISVRPDPEVLLPPEEAEKLIFEIVPKEAEITNIAFDPSVGEVLIEAKKPG---------- 119
Query: 71 LYSAKLG-IREDILRKTLW 88
L K G I +K W
Sbjct: 120 LVIGKNGETLRLITQKVKW 138
>2ycb_A Beta-CAsp RNAse, cleavage and polyadenylation specificity factor;
hydrolase, KH, metallo-beta-lactamase; 3.10A
{Methanothermobacter thermautotrophicusorganism_taxid}
Length = 636
Score = 28.4 bits (64), Expect = 0.73
Identities = 13/79 (16%), Positives = 26/79 (32%), Gaps = 11/79 (13%)
Query: 11 LVLRPGPQSTSSPSDTVYTDWGTGLEDADDSDLYFSPDRGNVVFASAFDGWGFTIDDFAR 70
+++R P + E+A +++ F V+ + G
Sbjct: 61 IIIRSDRSVLMDPEKAIRKIHEIVPEEAKITNISFDDVTCEVIIEARKPG---------- 110
Query: 71 LYSAKLG-IREDILRKTLW 88
L K G +I++ T W
Sbjct: 111 LVIGKYGSTSREIVKNTGW 129
>2xr1_A Cleavage and polyadenylation specificity factor 1 subunit;
hydrolase, metallo-beta-lactamase, beta-CAsp, RNA
processing; 2.59A {Methanosarcina mazei}
Length = 640
Score = 28.4 bits (64), Expect = 0.77
Identities = 18/79 (22%), Positives = 33/79 (41%), Gaps = 11/79 (13%)
Query: 11 LVLRPGPQSTSSPSDTVYTDWGTGLEDADDSDLYFSPDRGNVVFASAFDGWGFTIDDFAR 70
+ +RP P+ ++P D++ +++ S YF PD G V+ + G
Sbjct: 65 IAMRPDPRVLATPEDSISIIEEVVPKESVISSYYFDPDSGEVIIEAEKPG---------- 114
Query: 71 LYSAKLG-IREDILRKTLW 88
L K G +I ++ W
Sbjct: 115 LVIGKHGATLREITKQIGW 133
>3k6o_A Uncharacterized protein DUF1344; protein of unknown function
DUF1344, structural genomics, JO center for structural
genomics; HET: PG4; 2.00A {Bacteroides vulgatus atcc
8482}
Length = 224
Score = 28.1 bits (62), Expect = 0.81
Identities = 6/47 (12%), Positives = 12/47 (25%)
Query: 27 VYTDWGTGLEDADDSDLYFSPDRGNVVFASAFDGWGFTIDDFARLYS 73
V T + Y D G ++ + R++
Sbjct: 15 VTIAMATVEKQPQYDAPYLVLDNGEKLWVVQHIVPYRDLKAGERIFG 61
>2uzz_A N-methyl-L-tryptophan oxidase; N-methyltryptophan oxidase (MTOX),
oxidative demethylation of N-methyl-L-tryptophan, FAD,
flavoenzyme; HET: FAD; 3.2A {Escherichia coli}
Length = 372
Score = 26.6 bits (59), Expect = 2.5
Identities = 5/19 (26%), Positives = 7/19 (36%)
Query: 45 FSPDRGNVVFASAFDGWGF 63
P N + + G GF
Sbjct: 322 TLPGHDNTLLITGLSGHGF 340
>1l5a_A Amide synthase, VIBH; nonribosomal peptide synthetase, NRPS
condensation domain, vibriobactin, biosynthetic protein;
2.55A {Vibrio cholerae} SCOP: c.43.1.2 c.43.1.2
Length = 436
Score = 26.8 bits (60), Expect = 2.7
Identities = 4/20 (20%), Positives = 9/20 (45%), Gaps = 2/20 (10%)
Query: 57 AFDGWGFTI--DDFARLYSA 74
DG+G + ++ Y +
Sbjct: 128 VLDGYGMMLFEQRLSQHYQS 147
>3op0_A Signal transduction protein CBL-C; structural genomics, structural
genomics consortium, SGC, SI transduction protein,
SH3-binding protein; HET: PTR; 2.52A {Homo sapiens}
Length = 323
Score = 26.7 bits (58), Expect = 3.0
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 1 NGRNHNPNLTLVLRPGP 17
+G+ HNP+LT +
Sbjct: 304 DGKTHNPDLTELGAENL 320
>3fes_A ATP-dependent CLP endopeptidase; alpha-helical bundles, structural
genomics, PSI-2, protein S initiative; HET: PG4 EPE;
1.82A {Clostridium difficile}
Length = 145
Score = 25.6 bits (57), Expect = 4.1
Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 10/46 (21%)
Query: 74 AKLGIREDILRKTLW----------GDYYLNAKAKRILKGAQEKAK 109
+K+G E L + D L+ ++K+IL+ + A
Sbjct: 53 SKVGFTEAYLEGKIVDMEGKGEEISEDIVLSPRSKQILELSGMFAN 98
>2gf3_A MSOX, monomeric sarcosine oxidase; flavoprotein oxidase, inhibitor
2-furoic acid, oxidoreductas; HET: FAD; 1.30A {Bacillus
SP} SCOP: c.3.1.2 d.16.1.3 PDB: 1el7_A* 1el8_A* 1el9_A*
1eli_A* 1l9e_A* 2a89_A* 2gb0_A* 1el5_A* 3qse_A* 3qsm_A*
3qss_A* 3bhk_A* 3bhf_A* 3m12_A* 3m13_A* 3m0o_A* 1l9c_A*
1l9d_A* 1zov_A*
Length = 389
Score = 26.1 bits (58), Expect = 4.5
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 45 FSPDRGNVVFASAFDGWGF 63
P+ NVV A+ F G GF
Sbjct: 329 LHPEHSNVVIAAGFSGHGF 347
>1zy9_A Alpha-galactosidase; TM1192, struc genomics, joint center for
structural genomics, JCSG, prote structure initiative,
PSI, hydrolase; 2.34A {Thermotoga maritima} SCOP:
b.30.5.11 c.1.8.13
Length = 564
Score = 26.2 bits (57), Expect = 4.8
Identities = 12/70 (17%), Positives = 22/70 (31%), Gaps = 4/70 (5%)
Query: 52 VVFASAFDGWGFTIDDFARLYSAKLGIREDILRKTL---WGDYYLNAKAKRILKGAQEKA 108
+ ++ +A L + R T W Y+L+ + LK +
Sbjct: 163 PLVVLEDPNTPLLLEKYAELVGMENNARVPKHTPTGWCSWYHYFLDLTWEETLKNLKLAK 222
Query: 109 KAPLFVEFVL 118
P V F +
Sbjct: 223 NFPFEV-FQI 231
>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 = 25.6 bits (55), Expect = 8.1
Identities = 11/91 (12%), Positives = 22/91 (24%), Gaps = 31/91 (34%)
Query: 61 WGFTIDDFARLYSAKLGIREDILRK---------------------TLWGDYYLNA---K 96
T D+ L L R L + W D + + K
Sbjct: 296 MTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATW-DNWKHVNCDK 354
Query: 97 AKRILKGAQEKAKAP----LFVEFVL--KNV 121
I++ + + +F + +
Sbjct: 355 LTTIIESSLNVLEPAEYRKMFDRLSVFPPSA 385
>3mpk_A Virulence sensor protein BVGS; venus flytrap, sensor domain,
signaling protein; 2.04A {Bordetella pertussis} PDB:
3mpl_A
Length = 267
Score = 25.0 bits (55), Expect = 9.6
Identities = 4/39 (10%), Positives = 13/39 (33%), Gaps = 1/39 (2%)
Query: 62 GFTIDDFARLYSAKLGIREDILRKTLWGDYYLNAKAKRI 100
G + +L + G+ +I+ + ++
Sbjct: 56 GISAA-VLQLLQLRTGLDFEIIGVDTVEELIAKLRSGEA 93
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
0.318 0.136 0.412
Gapped
Lambda K H
0.267 0.0463 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,136,921
Number of extensions: 123916
Number of successful extensions: 285
Number of sequences better than 10.0: 1
Number of HSP's gapped: 284
Number of HSP's successfully gapped: 28
Length of query: 133
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 50
Effective length of database: 4,384,350
Effective search space: 219217500
Effective search space used: 219217500
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: 41 (21.7 bits)
S2: 52 (24.5 bits)