RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1702
(200 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 = 105 bits (262), Expect = 2e-27
Identities = 48/163 (29%), Positives = 67/163 (41%), Gaps = 10/163 (6%)
Query: 22 LAVYTVLFKTAGGKVIEKYISSFSELGSE-YNTIFNCTGLGARTLCNDMHVIPVRGQTIR 80
L T G K ++ + SF E+ E + I NCTG+ A L D + P RGQ ++
Sbjct: 145 LQWLTERLTERGVKFFQRKVESFEEVAREGADVIVNCTGVWAGALQRDPLLQPGRGQIMK 204
Query: 81 IKAPHITNFYK-------NEYDTYIIPNGFDSLVTLGGTQNFGHVNRCVESTDTESILAR 133
+ AP + +F YIIP VTLGG G+ + D +I
Sbjct: 205 VDAPWMKHFILTHDPERGIYNSPYIIPGTQT--VTLGGIFQLGNWSELNNIQDHNTIWEG 262
Query: 134 TEELLPGVGACGGGQCWVGLRPHRYRVRVECEQTPGGKVNAGV 176
L P + G RP R ++R+E EQ G N V
Sbjct: 263 CCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLRTGPSNTEV 305
>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 = 100 bits (249), Expect = 2e-25
Identities = 50/210 (23%), Positives = 77/210 (36%), Gaps = 33/210 (15%)
Query: 5 HYLKPVLPVYKRMSEEEL------AVYTVL--------------FKTAGGKVIEKYISSF 44
H+ K + P Y+ + E Y L + G + ++S
Sbjct: 108 HWYKDITPNYRPLPSSECPPGAIGVTYDTLSVHAPKYCQYLARELQKLGATFERRTVTSL 167
Query: 45 SELGSEYNTIFNCTGLGARTLC--NDMHVIPVRGQTIRIKAPHITNFY---KNEYDTYII 99
+ + + N TGLGA+++ +D P+RGQT+ +K+P YII
Sbjct: 168 EQAFDGADLVVNATGLGAKSIAGIDDQAAEPIRGQTVLVKSPCKRCTMDSSDPASPAYII 227
Query: 100 PNGFDSLVTLGGTQNFGHVNRCVESTDTESILARTEELLPGVGACGGGQ------CWVGL 153
P V GGT G + V + IL L P + + G + VGL
Sbjct: 228 PRP-GGEVICGGTYGVGDWDLSVNPETVQRILKHCLRLDPTISSDGTIEGIEVLRHNVGL 286
Query: 154 RPHRYR-VRVECEQTPGGKVNAGVGVVVGR 182
RP R RVE E+ + +GR
Sbjct: 287 RPARRGGPRVEAERIVLPLDRTKSPLSLGR 316
>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 = 41.6 bits (97), Expect = 1e-04
Identities = 34/249 (13%), Positives = 65/249 (26%), Gaps = 90/249 (36%)
Query: 14 YKRMSEEELAVYTVLFKTAGGK-VIEKYISSFSELGSEYNTIFNCTGLGARTLCNDMHVI 72
++ + E + + F GG+ + Y F EL Y T ++
Sbjct: 146 FRAVGEGNAQLVAI-F---GGQGNTDDY---FEELRDLYQT-YH---------------- 181
Query: 73 PVRGQTIRIKAPHITNFYKNEYDT-YIIPNGFD----------------------SLVTL 109
+ G I+ A ++ + D + G + S +
Sbjct: 182 VLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLI 241
Query: 110 GGTQNFGH-VNRCVESTDTESILARTEELLPGVGACGGG--------------------- 147
G Q H V T L L G G
Sbjct: 242 GVIQ-LAHYVVTAKLLGFTPGELR---SYLKGATGHSQGLVTAVAIAETDSWESFFVSVR 297
Query: 148 QC-----WVGLRPHR-YRVRVECEQTPGGKVNAGVGV------VVG-RKKRLTDLLLTFN 194
+ ++G+R + Y + GV + ++++ D + N
Sbjct: 298 KAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTN 357
Query: 195 A---ENKQI 200
+ KQ+
Sbjct: 358 SHLPAGKQV 366
Score = 37.3 bits (86), Expect = 0.003
Identities = 33/193 (17%), Positives = 55/193 (28%), Gaps = 92/193 (47%)
Query: 21 ELAVYTVLFKTAGGKVIEKYISSFSELGSEYNTIFNCTGLGARTLCNDMHVIPV------ 74
E A + L K+ G + + S LG EY A L + V+ +
Sbjct: 1740 EKAAFEDL-KSKGLIPADATFAGHS-LG-EYA---------A--LASLADVMSIESLVEV 1785
Query: 75 ---RGQTIRIKAPHITNFYKNEYDTYIIPNGFDSLVTLGGTQNFGHV----NRCVESTDT 127
RG T+++ P ++E G N+G + R S
Sbjct: 1786 VFYRGMTMQVAVP------RDE----------------LGRSNYGMIAINPGRVAASFSQ 1823
Query: 128 ESILARTEELLPGVGACGGGQCWVGLRPHRYRVRVECEQTPGGKVNAGVGVVVGRKKRLT 187
E++ + ++ VG G + VN
Sbjct: 1824 EAL----QYVVERVGKRTGWLVEI--------------------VN-------------- 1845
Query: 188 DLLLTFNAENKQI 200
+N EN+Q
Sbjct: 1846 -----YNVENQQY 1853
>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 = 41.0 bits (95), Expect = 1e-04
Identities = 23/116 (19%), Positives = 39/116 (33%), Gaps = 10/116 (8%)
Query: 50 EYNTIFNCTGLGARTL--CNDMHVIPVRGQTIRIKAPHITNFYKN--EYDTYIIP-NGFD 104
+ T+ TG + + + VRGQ I + + + YD Y+ P N +
Sbjct: 457 HHATVILATGHRLPEWEQTHHLPLSAVRGQVSHIPTTPVLSQLQQVLCYDGYLTPVNPAN 516
Query: 105 SLVTLGGTQNFGHVNRCVESTDTESILARTEELLPGVGA-----CGGGQCWVGLRP 155
+G + G + T+ + R LP V Q G+R
Sbjct: 517 QHHCIGASYQRGDIATDFRLTEQQENRERLLRCLPQVSWPQQVDVSDNQARCGVRC 572
>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 = 39.1 bits (92), Expect = 5e-04
Identities = 20/122 (16%), Positives = 40/122 (32%), Gaps = 40/122 (32%)
Query: 56 NCTGLGARTLCN----DMHVIPVRGQTIRIKAP----HITNFYKNEYDTYIIP------- 100
+G+ + + +PV+G+ + + T ++ YI+P
Sbjct: 213 VASGVWSGMFFKQLGLNNAFLPVKGECLSVWNDDIPLTKTLYHD---HCYIVPRKSGRLV 269
Query: 101 -------NGFDSLVTLGGTQNFGHVNRCVESTDTESILARTEELLPGVGACGGGQCWVGL 153
+ LGG ES++ + + +LP + + W GL
Sbjct: 270 VGATMKPGDWSETPDLGGL---------------ESVMKKAKTMLPAIQNMKVDRFWAGL 314
Query: 154 RP 155
RP
Sbjct: 315 RP 316
>2q8o_A GITR ligand; TNF, dimer, unknown function; 1.75A {Mus musculus}
SCOP: b.22.1.1 PDB: 3fc0_A 2qdn_A 3b9i_A
Length = 136
Score = 27.0 bits (59), Expect = 2.6
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 70 HVIPVRGQTIRIKAPHITNFYKNEYDTYIIPNGFDSLVTLGGT 112
VIPV + I+ AP + YK + N F + +GG
Sbjct: 57 QVIPVDKKYIKDNAPFVVQIYKKNDVLQTLMNDFQI-LPIGGV 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
0.320 0.138 0.419
Gapped
Lambda K H
0.267 0.0705 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,123,577
Number of extensions: 181698
Number of successful extensions: 371
Number of sequences better than 10.0: 1
Number of HSP's gapped: 367
Number of HSP's successfully gapped: 10
Length of query: 200
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 111
Effective length of database: 4,216,824
Effective search space: 468067464
Effective search space used: 468067464
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 (21.8 bits)
S2: 55 (25.0 bits)