RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5260
(142 letters)
>3g3e_A D-amino-acid oxidase; FAD, flavoprotein, oxidoreductase, PER; HET:
FAD G3E; 2.20A {Homo sapiens} PDB: 3cuk_A* 2e48_A*
2e49_A* 2e4a_A* 2e82_A* 2du8_A* 1ve9_A* 1dao_A* 1ddo_A*
1kif_A* 1an9_A* 1evi_A*
Length = 351
Score = 111 bits (279), Expect = 1e-30
Identities = 52/146 (35%), Positives = 73/146 (50%), Gaps = 15/146 (10%)
Query: 11 LQVWAPWLSHFYYL-------DYDVYIIPHSNGAVTLGGCRHYDSYSRDISRHDTASILE 63
++V APW+ HF YIIP + VTLGG ++S + D +I E
Sbjct: 203 MKVDAPWMKHFILTHDPERGIYNSPYIIPGTQT-VTLGGIFQLGNWSELNNIQDHNTIWE 261
Query: 64 RCYSLLPRLEEAPVLYEWCGLRPHRSLVRVEIEQI----GRLKVIHNYGHGGYGVTTAPG 119
C L P L+ A ++ E G RP R +R+E EQ+ +VIHNYGHGGYG+T G
Sbjct: 262 GCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLRTGPSNTEVIHNYGHGGYGLTIHWG 321
Query: 120 TSRYAVQLVKQALD--PTSSL-KSKL 142
+ A +L + L+ S + S L
Sbjct: 322 CALEAAKLFGRILEEKKLSRMPPSHL 347
>1c0p_A D-amino acid oxidase; alpha-beta-alpha motif, flavin containing
protein, oxidoreductase; HET: FAD; 1.20A {Rhodosporidium
toruloides} SCOP: c.4.1.2 d.16.1.3 PDB: 1c0i_A* 1c0l_A*
1c0k_A*
Length = 363
Score = 99.8 bits (248), Expect = 5e-26
Identities = 37/156 (23%), Positives = 51/156 (32%), Gaps = 33/156 (21%)
Query: 11 LQVWAPWLSHFYYLD---YDVYIIPHSNGAVTLGGCRHYDSYSRDISRHDTASILERCYS 67
+ V +P YIIP G V GG + ++ IL+ C
Sbjct: 204 VLVKSPCKRCTMDSSDPASPAYIIPRPGGEVICGGTYGVGDWDLSVNPETVQRILKHCLR 263
Query: 68 LLPR------LEEAPVLYEWCGLRPHR-SLVRVEIEQI---------------------- 98
L P +E VL GLRP R RVE E+I
Sbjct: 264 LDPTISSDGTIEGIEVLRHNVGLRPARRGGPRVEAERIVLPLDRTKSPLSLGRGSARAAK 323
Query: 99 -GRLKVIHNYGHGGYGVTTAPGTSRYAVQLVKQALD 133
+ ++H YG G + G + QLV +A
Sbjct: 324 EKEVTLVHAYGFSSAGYQQSWGAAEDVAQLVDEAFQ 359
>1ryi_A Glycine oxidase; flavoprotein, protein-inhibitor complex,
oxidoreductase; HET: FAD; 1.80A {Bacillus subtilis}
SCOP: c.3.1.2 d.16.1.3 PDB: 3if9_A* 1ng4_A* 1ng3_A*
Length = 382
Score = 60.7 bits (148), Expect = 5e-12
Identities = 28/126 (22%), Positives = 46/126 (36%), Gaps = 16/126 (12%)
Query: 11 LQVWAPWLSHFYYLDYDVYIIPHSNGAVTLGGCRHYDSYSRDISRHDTASILERCYSLLP 70
+ L+ Y D YI+P +G + +G +S S++++ ++LP
Sbjct: 242 VWNDDIPLTKTLYHD-HCYIVPRKSGRLVVGATMKPGDWSETPDLGGLESVMKKAKTMLP 300
Query: 71 RLEEAPVLYEWCGLRP----HRSLVRVEIEQIGRLKVIHNY----GHGGYGVTTAPGTSR 122
++ V W GLRP + IGR GH G+ AP T
Sbjct: 301 AIQNMKVDRFWAGLRPGTKDGKPY-------IGRHPEDSRILFAAGHFRNGILLAPATGA 353
Query: 123 YAVQLV 128
L+
Sbjct: 354 LISDLI 359
>3nyc_A D-arginine dehydrogenase; FAD, imino-arginine, oxidoreductas; HET:
FAD IAR; 1.06A {Pseudomonas aeruginosa} PDB: 3nye_A*
3nyf_A* 3sm8_A*
Length = 381
Score = 37.6 bits (88), Expect = 6e-04
Identities = 14/67 (20%), Positives = 20/67 (29%), Gaps = 13/67 (19%)
Query: 69 LPRLEEAPVLYEWCGLR---PHRSLVRVEIEQIGRLKVIHNY----GHGGYGVTTAPGTS 121
L + W GLR LV G + GGYG+ T+
Sbjct: 295 ATTLTIRRPEHTWAGLRSFVADGDLV------AGYAANAEGFFWVAAQGGYGIQTSAAMG 348
Query: 122 RYAVQLV 128
+ L+
Sbjct: 349 EASAALI 355
>2gag_B Heterotetrameric sarcosine oxidase beta-subunit; flavoenzyme,
electron transfer, folate-ME enzyme, oxidoreductase;
HET: NAD FAD FMN; 1.85A {Stenotrophomonas maltophilia}
PDB: 2gah_B* 1x31_B* 1vrq_B* 3ad7_B* 3ad8_B* 3ad9_B*
3ada_B*
Length = 405
Score = 35.7 bits (83), Expect = 0.003
Identities = 22/115 (19%), Positives = 33/115 (28%), Gaps = 21/115 (18%)
Query: 25 DYDVYIIPHSNGAVTLGG-CRHYDSYSRDISRHDTASILERCYSLLPRLEEAPVLYEWCG 83
VY+ G + +G Y+ Y + + H + L P A VL W G
Sbjct: 268 HIHVYVSQAHKGELVMGAGIDSYNGYGQRGAFHVIQEQMAAAVELFPIFARAHVLRTWGG 327
Query: 84 L-------RPHRSLVRVEIEQIGRLKV---IHNYGHGGYGVTTAPGTSRYAVQLV 128
+ P I + + N G G G PG +
Sbjct: 328 IVDTTMDASPI----------ISKTPIQNLYVNCGWGTGGFKGTPGAGFTLAHTI 372
>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 = 32.7 bits (74), Expect = 0.035
Identities = 29/159 (18%), Positives = 47/159 (29%), Gaps = 36/159 (22%)
Query: 2 VCLLVCSTPLQVWAPWLSHFYYLDYDVYIIPHSNG---A-VTLGGCRHYDSYSRDISRHD 57
L + + S + D HS G A +L +S
Sbjct: 1734 PALTLME--KAAFEDLKSKGL-IPADATFAGHSLGEYAALASLADV---------MSIES 1781
Query: 58 TASIL-ER---CYSLLPRLEEAPVLYEWCGLRPHR-------SLVRVEIEQI----GRLK 102
++ R +PR E Y + P R ++ +E++ G L
Sbjct: 1782 LVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLV 1841
Query: 103 VIHNYGHGGYGVTTAPGTSRYAVQLVKQALDPTSSLKSK 141
I NY A G R A+ V L+ +K +
Sbjct: 1842 EIVNYNVENQQYVAA-GDLR-ALDTVTNVLN---FIKLQ 1875
Score = 25.8 bits (56), Expect = 8.3
Identities = 23/142 (16%), Positives = 43/142 (30%), Gaps = 41/142 (28%)
Query: 17 WLSH------FYYLDYDVYIIPHSNGAVTLGGCRHY--------------DSYSRDISRH 56
WL + YL IP S + + HY SY + + H
Sbjct: 218 WLENPSNTPDKDYLLS----IPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGH 273
Query: 57 D----TASILERCYS---LLPRLEEAPVLYEWCGLRPHRSLVRVEIEQIGRLKVIHNYGH 109
TA + S + +A + + G+R + + + ++ +
Sbjct: 274 SQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPP----SILEDSLE 329
Query: 110 GGYGVTTAP-----GTSRYAVQ 126
GV + P ++ VQ
Sbjct: 330 NNEGVPS-PMLSISNLTQEQVQ 350
>3nix_A Flavoprotein/dehydrogenase; structural genomics, PSI-2, NES protein
structure initiative, northeast structural genomics
consortium; HET: FAD; 2.60A {Cytophaga hutchinsonii}
Length = 421
Score = 31.3 bits (71), Expect = 0.096
Identities = 18/137 (13%), Positives = 37/137 (27%), Gaps = 29/137 (21%)
Query: 14 WAPWLSHFYYLDYDVYIIPHSNGAVTLGGCRHYDSYSRDISRHDTA--SILERCYSLLPR 71
+ + +++IP SNG ++G + + +++ + R
Sbjct: 203 GNRITAVVHKPKVWIWVIPFSNGNTSVGFVGEPSYFDEYTGTPEERMRAMIANEGHIAER 262
Query: 72 LEEAPVLYEWCGLRPHRSLVRVEIEQIGRLKVIHNYGHG---------------GYGVTT 116
+ L+E + + YG G G T
Sbjct: 263 FKSEEFLFEPRTIEGYAISAS------------KLYGDGFVLTGNATEFLDPIFSSGATF 310
Query: 117 APGTSRYAVQLVKQALD 133
A + +L Q L
Sbjct: 311 AMESGSKGGKLAVQFLK 327
>3pvc_A TRNA 5-methylaminomethyl-2-thiouridine biosynthes bifunctional
protein MNMC; structural genomics, PSI-biology; HET:
FAD; 2.31A {Yersinia pestis} PDB: 3sgl_A*
Length = 689
Score = 31.0 bits (69), Expect = 0.12
Identities = 21/146 (14%), Positives = 35/146 (23%), Gaps = 37/146 (25%)
Query: 10 PLQVWAPWLSHFYYLDYDVYIIPHSNGAVTLGGCRHYDSYSRDISRHDTASILERCYSLL 69
P L D + + +N +G + D + ER L
Sbjct: 491 PTTPVLSQLQQVLCYDGYLTPVNPANQHHCIGASYQRGDIATDFRLTEQQENRERLLRCL 550
Query: 70 PRLE-----EAPVLYEWCGLRP----------------------------HRSLVRVEIE 96
P++ + CG+R + E+
Sbjct: 551 PQVSWPQQVDVSDNQARCGVRCAIRDHLPMVGAVPDYAATLAQYQDLSRRIQHGGESEVN 610
Query: 97 QIGRLKVIHN----YGHGGYGVTTAP 118
I V G G G+ +AP
Sbjct: 611 DIAVAPVWPELFMVGGLGSRGLCSAP 636
>3axb_A Putative oxidoreductase; dinucleotide-binding fold; HET: FAD; 1.92A
{Aeropyrum pernix} PDB: 3vqr_A*
Length = 448
Score = 30.5 bits (69), Expect = 0.16
Identities = 18/119 (15%), Positives = 34/119 (28%), Gaps = 21/119 (17%)
Query: 24 LDYDVYIIP-HSNGAVTLGGCRH-------YDSYSRDISRHDTASILERCYSLLPRLEEA 75
L V + P G+ + + + + + A IL LP+ ++A
Sbjct: 304 LPKRVLVRPAPREGSFWVQLSDNLGRPFALEEDPQPEEHYYSLA-ILPILSLYLPQFQDA 362
Query: 76 PVLYEWCGLR---PHRSLVRVEIEQIGRLKV---IHNYGHGGYGVTTAPGTSRYAVQLV 128
W G + V + + G G G+ + R A +
Sbjct: 363 YPSGGWAGHYDISFDANPV------VFEPWESGIVVAAGTSGSGIMKSDSIGRVAAAVA 415
>1y56_B Sarcosine oxidase; dehydrogenase, protein-protein complex,
oxidoreductase; HET: FAD FMN ATP CXS; 2.86A {Pyrococcus
horikoshii}
Length = 382
Score = 30.2 bits (69), Expect = 0.19
Identities = 20/116 (17%), Positives = 38/116 (32%), Gaps = 22/116 (18%)
Query: 25 DYDVYIIPHSNGAVTLGGCR-HYDSYSRDISRHDTASILERCYSLLPRLEEAPVLYEWCG 83
Y+ +G + G +Y + + ++P L+ +L W G
Sbjct: 247 YGHAYLTQTFHGGIIGGIGYEIGPTYDLTPTYEFLREVSYYFTKIIPALKNLLILRTWAG 306
Query: 84 L-------RPHRSLVRVEIEQIGRLKVIHNY----GHGGYGVTTAPGTSRYAVQLV 128
P IGR++ +++Y G G+G AP +L+
Sbjct: 307 YYAKTPDSNPA----------IGRIEELNDYYIAAGFSGHGFMMAPAVGEMVAELI 352
>3dje_A Fructosyl amine: oxygen oxidoreductase; fructosyl-amino acid,
amadoriase, deglycation, fructosamine oxidase; HET: MSE
FAD FSA EPE; 1.60A {Aspergillus fumigatus} PDB: 3djd_A*
Length = 438
Score = 29.8 bits (67), Expect = 0.27
Identities = 18/138 (13%), Positives = 35/138 (25%), Gaps = 22/138 (15%)
Query: 13 VWAPWLSHFYYL----DYDVYIIPHSNGAVTL-----GGCRHYDSYSRDISRHDTASILE 63
V F++ ++ I G + G I + +
Sbjct: 256 VIFNIERGFFFEPDEERGEIKICDEHPGYTNMVQSADGTMMSIPFEKTQIPKEAETRVRA 315
Query: 64 RCYSLLPRLEEAPVLYEWCGLR---PHRSLVRVEIEQIGRLKVIHNY----GHGGYGVTT 116
+P+L + P + +R + I R H+ G G G
Sbjct: 316 LLKETMPQLADRPFSFARICWCADTANREFL------IDRHPQYHSLVLGCGASGRGFKY 369
Query: 117 APGTSRYAVQLVKQALDP 134
P V ++ +
Sbjct: 370 LPSIGNLIVDAMEGKVPQ 387
>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 = 28.5 bits (64), Expect = 0.73
Identities = 21/142 (14%), Positives = 31/142 (21%), Gaps = 20/142 (14%)
Query: 1 MVCLLVCSTPLQVWAPWLSHFYYLDYD--VYIIPHSNGAVTLGGCRHYDSYSRDISRHDT 58
+ V + + L Y P N A+ +G R
Sbjct: 219 VFAWYQADGRYSVKNKFPAFTGELPNGDQYYGFPAENDALKIGKHNGGQVIHSADERVPF 278
Query: 59 ASILERCYSLLPRLEE-----APVLYEWCGLR---PHRSLVRVEIEQIGRL----KVIHN 106
A ++ P L LY P + I L +
Sbjct: 279 AEVVSDGSEAFPFLRNVLPGIGCCLYGAACTYDNSPDEDFI------IDTLPGHDNTLLI 332
Query: 107 YGHGGYGVTTAPGTSRYAVQLV 128
G G+G A A
Sbjct: 333 TGLSGHGFKFASVLGEIAADFA 354
>3dz1_A Dihydrodipicolinate synthase; lysine biosynthesis, pyruvate, TIM
barrel, NYSGXRC, PSI2, structural genomics; 1.87A
{Rhodopseudomonas palustris}
Length = 313
Score = 28.0 bits (63), Expect = 1.1
Identities = 9/47 (19%), Positives = 20/47 (42%), Gaps = 9/47 (19%)
Query: 87 HRSLVRVEIEQIGRLKVIHNYGHGGYGVTTAPGTSRYAVQLVKQALD 133
++ I++ ++VI G +APG +L + ++D
Sbjct: 63 AEAVATRFIKRAKSMQVI-----VG---VSAPGF-AAMRRLARLSMD 100
>1tzj_A ACC deaminase, 1-aminocyclopropane-1-carboxylate deaminase;
substrate, PLP, crystal, complex, hydrolase; HET: PLP;
1.99A {Pseudomonas SP} SCOP: c.79.1.1 PDB: 1rqx_A*
1tz2_A* 1tyz_A* 1tzk_A* 1tzm_A*
Length = 338
Score = 27.9 bits (62), Expect = 1.2
Identities = 8/42 (19%), Positives = 14/42 (33%), Gaps = 6/42 (14%)
Query: 103 VIHNYGHGGYGVTTAPGTSRYAVQLVKQA----LDPTSSLKS 140
+ + YG+ A++L + DP KS
Sbjct: 259 LDERFAGPEYGLPNEGTLE--AIRLCARTEGMLTDPVYEGKS 298
>2fxu_A Alpha-actin-1, actin, alpha skeletal muscle; actin complexed to
bistramide A, structural protein; HET: HIC ATP BID;
1.35A {Oryctolagus cuniculus} SCOP: c.55.1.1 c.55.1.1
PDB: 1h1v_A* 1kxp_A* 1lot_B* 1m8q_7* 1ma9_B* 1mvw_1*
1nwk_A* 1o18_1* 1o19_1* 1o1a_1* 1o1b_0* 1o1c_0* 1o1d_0*
1o1e_1* 1o1f_0* 1o1g_1* 1j6z_A* 1qz6_A* 1rdw_X* 1rfq_A*
...
Length = 375
Score = 27.7 bits (62), Expect = 1.5
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 26 YDVYIIPHSNGAVTLGGCRHYDSYSRDISRHDTASILERCYSLLPRLE 73
Y+ Y +PH+ + L G RD++ + + ER YS + E
Sbjct: 166 YEGYALPHAIMRLDLAG--------RDLTDYLMKILTERGYSFVTTAE 205
>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 = 27.5 bits (60), Expect = 1.7
Identities = 12/98 (12%), Positives = 33/98 (33%), Gaps = 17/98 (17%)
Query: 20 HFYYLDYDVYIIPHSNGAVTLGGCRHY-DSYSRDISRHDTASILERCYS--------LLP 70
H +++D++ + + + D++ + D + + S +
Sbjct: 3 HHHHMDFETGEHQYQYKDILS----VFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSK 58
Query: 71 RLEEAPVLYEWCGLRPHRSLVRVEIEQIGRLKVIHNYG 108
+ W L +V+ +E++ R+ NY
Sbjct: 59 DAVSGTLRLFWTLLSKQEEMVQKFVEEVLRI----NYK 92
>2p10_A MLL9387 protein; putative phosphonopyruvate hydrolase, structural
genomics, J center for structural genomics, JCSG; HET:
MSE; 2.15A {Mesorhizobium loti} SCOP: c.1.12.9
Length = 286
Score = 27.2 bits (60), Expect = 2.2
Identities = 14/75 (18%), Positives = 26/75 (34%), Gaps = 10/75 (13%)
Query: 61 ILERCYSLLPRLEEAPVLYEWCGLRPHRSLVRVEIEQIGRLKVIHNYGHGGYGVTTAPGT 120
+++ +LP + PVL G P + + ++ + G GV P
Sbjct: 81 VVDMAREVLPVVRHTPVLAGVNGTDPFMVMSTF-LRELKEI--------GFAGVQNFPTV 131
Query: 121 SRYAVQLVKQALDPT 135
+Q L+ T
Sbjct: 132 GLIDGLF-RQNLEET 145
>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI,
protein structure initiative, midwest center for
structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga
maritima} SCOP: c.37.1.12
Length = 240
Score = 26.3 bits (59), Expect = 3.4
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 48 SYSRDISRHDTASILERCYSLLPRLEE 74
+Y+R + LE +SL PRL+E
Sbjct: 106 AYNRK-DKEGIKRDLEWIFSLFPRLKE 131
>3sm3_A SAM-dependent methyltransferases; NESG, structural genomics,
PSI-biology, protein structure in northeast structural
genomics; 2.20A {Methanosarcina mazei}
Length = 235
Score = 25.9 bits (57), Expect = 5.7
Identities = 8/28 (28%), Positives = 9/28 (32%), Gaps = 1/28 (3%)
Query: 5 LVCSTPLQVWAPWLSHFYYLDYDVYIIP 32
L Q W L YL +D I
Sbjct: 137 LYLVEFGQNWHLKLYRKRYL-HDFPITK 163
>1j0a_A 1-aminocyclopropane-1-carboxylate deaminase; PLP dependent, lyase;
HET: PLP; 2.50A {Pyrococcus horikoshii} SCOP: c.79.1.1
PDB: 1j0b_A*
Length = 325
Score = 25.8 bits (56), Expect = 5.7
Identities = 10/48 (20%), Positives = 19/48 (39%), Gaps = 6/48 (12%)
Query: 97 QIGRLKVIHNYGHGGYGVTTAPGTSRYAVQLVKQA----LDPTSSLKS 140
++ +++Y G YG T ++ V LDP + K+
Sbjct: 241 KVEVRPELYDYSFGEYGKITGEVAQ--IIRKVGTREGIILDPVYTGKA 286
>1k8k_A ARP3, actin-like protein 3, actin-2; beta-propeller, structural
protein; 2.00A {Bos taurus} SCOP: c.55.1.1 c.55.1.1 PDB:
1tyq_A* 1u2v_A* 2p9i_A* 2p9k_A* 2p9l_A 2p9n_A* 2p9p_A*
2p9s_A* 2p9u_A* 3dxk_A* 3dxm_A* 3rse_A
Length = 418
Score = 25.8 bits (57), Expect = 6.1
Identities = 8/48 (16%), Positives = 16/48 (33%), Gaps = 8/48 (16%)
Query: 26 YDVYIIPHSNGAVTLGGCRHYDSYSRDISRHDTASILERCYSLLPRLE 73
+ Y+I + + G RDI+ + +R + P
Sbjct: 181 AEGYVIGSCIKHIPIAG--------RDITYFIQQLLRDREVGIPPEQS 220
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
0.323 0.139 0.450
Gapped
Lambda K H
0.267 0.0569 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,258,505
Number of extensions: 126310
Number of successful extensions: 319
Number of sequences better than 10.0: 1
Number of HSP's gapped: 311
Number of HSP's successfully gapped: 31
Length of query: 142
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 58
Effective length of database: 4,356,429
Effective search space: 252672882
Effective search space used: 252672882
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.2 bits)