RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13811
(297 letters)
>2nwl_A GLTPH, glutamate symport protein; alpha helical, membrane protein,
helical hairpin, unwound RE transport protein; HET: PLM;
2.96A {Pyrococcus horikoshii} PDB: 2nww_A* 1xfh_A*
2nwx_A* 3v8g_A 3v8f_A 3kbc_A
Length = 422
Score = 141 bits (358), Expect = 2e-39
Identities = 68/273 (24%), Positives = 119/273 (43%), Gaps = 38/273 (13%)
Query: 35 PDAWSERERMYVQFPGELFLKMLKCLIVPLLVSSIVSAIGSLDLSLSKRVGFRSIAYYCA 94
++ YV+ G+LF+++LK L++P++ +S+V S+ + RVG + + YY
Sbjct: 32 HYGYAHAVHTYVKPFGDLFVRLLKMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLL 91
Query: 95 TTSIAVVEGIILVCTIRPGVG-HASMKGAQAGNYSKTSLTTDTLMDL--SRVLFYILCVT 151
T++ AV GII+ PG G H ++ G Q + L L+D+ +
Sbjct: 92 TSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPHQAPPLV-HILLDIVPTNPF------- 143
Query: 152 ELYFILCVTELWQMRGEWVVGSNVLGLVFFSIAMGIAIA--------RIGKAGKPLLSVF 203
+ VL +FF+I +GIAI ++ K+ + LL
Sbjct: 144 ----------------GALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAI 187
Query: 204 ESLSEVVMTITTWVIWISPFGIFFLVAEKIIDMKSLSHTVGQLGLYFITVLLGLLIHGFI 263
L+E + I V+ +P G+F L+A + + H VG+L V +GL + +
Sbjct: 188 NGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQG--VHVVGELAKVTAAVYVGLTLQILL 245
Query: 264 LLPAMYTFFVREWPFRFTANMGQAIATAFGTAS 296
+ + + P F + A+ TAF T S
Sbjct: 246 VYFVLLKIY-GIDPISFIKHAKDAMLTAFVTRS 277
>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 = 38.7 bits (89), Expect = 0.002
Identities = 13/72 (18%), Positives = 18/72 (25%), Gaps = 18/72 (25%)
Query: 12 DRTVMDGMDEMRVVERRTVLDSMPDAWSERERMYVQFPGELFLKMLK----------CLI 61
+ V D + LD + E L LK L
Sbjct: 274 FKQVTDFLSAATTTHIS--LDHHSMTLTPDEVK------SLLLKYLDCRPQDLPREVLTT 325
Query: 62 VPLLVSSIVSAI 73
P +S I +I
Sbjct: 326 NPRRLSIIAESI 337
Score = 28.7 bits (63), Expect = 3.2
Identities = 24/153 (15%), Positives = 50/153 (32%), Gaps = 50/153 (32%)
Query: 119 MKGAQAGNYS--KTSLTTDTLMDLSRVLFYILCVTELY-----FI-LCVT---ELWQMR- 166
++ NY + + T+ YI LY F V+ ++R
Sbjct: 83 VEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQ 142
Query: 167 -------GEWVVGSNVLGLVFFSIAMGIAIARIGKAGKPLLSVFESLSEVVMTITTWVIW 219
+ V+ + G + G +GK +++ +V ++ V
Sbjct: 143 ALLELRPAKNVL---IDG-------VL------G-SGKTWVAL-----DVCLSYK--VQC 178
Query: 220 ISPFGIFFL------VAEKIIDM-KSLSHTVGQ 245
F IF+L E +++M + L + +
Sbjct: 179 KMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDP 211
Score = 28.3 bits (62), Expect = 4.4
Identities = 8/47 (17%), Positives = 15/47 (31%), Gaps = 15/47 (31%)
Query: 110 IRPGVG---HASMKGAQAGNYSKTSLTTDTLMDLSRVL------FYI 147
+RP + G+ G KT + D + F++
Sbjct: 147 LRPAKNVLIDG-VLGS--G---KTWVALDVCLSYKVQCKMDFKIFWL 187
>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 = 37.7 bits (87), Expect = 0.004
Identities = 40/259 (15%), Positives = 75/259 (28%), Gaps = 77/259 (29%)
Query: 66 VSSIVSAI-GSLDLSLSKRVGFRSI--AYYCATTSIAVVEGIILVCTIRPGV-GHAS--M 119
+ ++ + + D +L K + + Y A + RP S
Sbjct: 101 IHALAAKLLQENDTTLVKT---KELIKNYITA-----------RIMAKRPFDKKSNSALF 146
Query: 120 KGAQAGNYSKTSLTTDTLMDLSRVLFYILC----VTELYFILCVTELWQMRGEWVVGSNV 175
+ GN + T+ YF EL R + +
Sbjct: 147 RAVGEGNAQ----------------LVAIFGGQGNTDDYF----EEL---RDLYQTYHVL 183
Query: 176 LGLVFFSIAMGIA-IARIGKAGKPLLS-VFESLSEVVMTITTWVIWIS-----PFGIFFL 228
+G + A ++ + R + + + L W+ P + L
Sbjct: 184 VGDLIKFSAETLSELIRTTLDAEKVFTQGLNILE-----------WLENPSNTPDKDYLL 232
Query: 229 ---VAEKIIDMKSLSH---TVGQLGLY---FITVLLGLLIHGFILLPAMYTFFVREWPFR 279
++ +I + L+H T LG + L G H L+ A+ W
Sbjct: 233 SIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWE-S 291
Query: 280 FTANMGQAIATAF--GTAS 296
F ++ +AI F G
Sbjct: 292 FFVSVRKAITVLFFIGVRC 310
Score = 33.9 bits (77), Expect = 0.072
Identities = 27/223 (12%), Positives = 61/223 (27%), Gaps = 71/223 (31%)
Query: 23 RVVERRTVLDSMPDAW-----SERERMYVQFPG----ELFLKMLKCL--IVPLLVSSIVS 71
R++ +R A ++ F G + + + L+ L +LV ++
Sbjct: 130 RIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIK 189
Query: 72 AIGSLDLSLSKRVGFRSIAYYCATTSIAVVEGIILVC-----TIRPGVGHASMKGAQAGN 126
L + + +G+ ++ + P +
Sbjct: 190 FSAETLSELIRTTLDAEKVFT---------QGLNILEWLENPSNTPDK-----------D 229
Query: 127 YSKTSLTTDTLMDLSRVLFYILCVTEL--YFILCVT------ELWQ-MRGEWVVGSNVLG 177
Y + + ++ V +L Y + EL ++G ++
Sbjct: 230 Y----------LLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLV- 278
Query: 178 LVFFSIAMGIAIARIGKAGKPLLSVFESLSEVVMTITTWVIWI 220
A+ IA +ES V T + +I
Sbjct: 279 -----TAVAIAET----------DSWESFFVSVRKAITVLFFI 306
>1eys_M Photosynthetic reaction center; membrane protein complex, electron
transport; HET: BGL BCL BPH MQ8 HEM CRT LDA PEF; 2.20A
{Thermochromatium tepidum} SCOP: f.26.1.1
Length = 324
Score = 28.9 bits (64), Expect = 1.7
Identities = 26/132 (19%), Positives = 43/132 (32%), Gaps = 8/132 (6%)
Query: 166 RGEWVVGSNVLGLVFFSIAMGIAIARIGKAGKPLLSVFESLSEVVMTI-TTWVIWISPFG 224
R + S LG + + I + G V S+ M W ++
Sbjct: 29 RIGRPIFSYWLGKIGDAQIGPIYLGLTGTLSIFFGLVAISIIGFNMLASVHWDVFQFLKH 88
Query: 225 IFFLVAEKIIDMKSLSHTVGQLGLYFITVLLGLLIHGFILLPAMYTFFVREWPFRFTANM 284
F+L E L G ++ LI G L ++ ++VR + M
Sbjct: 89 FFWLGLEPPPPQYGLRIPPLSEGGWW-------LIAGLFLTLSILLWWVRTYKRAEALGM 141
Query: 285 GQAIATAFGTAS 296
Q ++ AF A
Sbjct: 142 SQHLSWAFAAAI 153
>3ksy_A SOS-1, SON of sevenless homolog 1; RAS, RAS activator, disease
mutation, guanine-nucleotide releasing factor, signaling
protein; 3.18A {Homo sapiens} PDB: 1xd4_A 1xdv_A 1q9c_A
Length = 1049
Score = 29.0 bits (64), Expect = 2.4
Identities = 15/102 (14%), Positives = 28/102 (27%), Gaps = 1/102 (0%)
Query: 53 FLKMLKCLIVPLLVSSIVSAIGSLDLSLSKRVGFRSIAYYCATTSIAVVEGIILVCTIRP 112
L ++ + S +GS L++ + F Y L +P
Sbjct: 259 LLGHIEDTVEMTDEGSPHPLVGSCFEDLAEELAFDPYESYARDILRPGFHDRFLSQLSKP 318
Query: 113 GVGHASMKGAQAGNY-SKTSLTTDTLMDLSRVLFYILCVTEL 153
G + + L L + L Y + +L
Sbjct: 319 GAALYLQSIGEGFKEAVQYVLPRLLLAPVYHCLHYFELLKQL 360
>2wjn_L Reaction center protein L chain; bacteriochlorophyll,
lipidic-sponge phase, photosynthesis, R center, electron
transport, cell membrane; HET: HEM FME BCB BPB MPG MQ7
NS5; 1.86A {Rhodopseudomonas viridis} PDB: 2wjm_L*
2x5u_L* 2x5v_L* 4ac5_L* 3t6e_L* 1r2c_L* 1prc_L* 1vrn_L*
2jbl_L* 2prc_L* 3d38_L* 3g7f_L* 3prc_L* 2i5n_L* 3t6d_L*
5prc_L* 6prc_L* 7prc_L* 1dxr_L*
Length = 274
Score = 26.9 bits (59), Expect = 8.4
Identities = 7/38 (18%), Positives = 12/38 (31%)
Query: 258 LIHGFILLPAMYTFFVREWPFRFTANMGQAIATAFGTA 295
L A ++ +RE +G + AF
Sbjct: 88 QAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVP 125
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
0.329 0.141 0.430
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,568,031
Number of extensions: 270318
Number of successful extensions: 554
Number of sequences better than 10.0: 1
Number of HSP's gapped: 550
Number of HSP's successfully gapped: 17
Length of query: 297
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 204
Effective length of database: 4,105,140
Effective search space: 837448560
Effective search space used: 837448560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 57 (25.7 bits)