RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12378
(260 letters)
>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 = 34.6 bits (79), Expect = 0.034
Identities = 40/289 (13%), Positives = 75/289 (25%), Gaps = 108/289 (37%)
Query: 5 YVIFDIKIGEGQYNWKG---KYFVVPQQGL-GIF-TSETFLDTKTENQNKAHENLWFVWF 59
IF G GQ G YF + L ++ T + + + E L
Sbjct: 157 VAIF----G-GQ----GNTDDYF----EELRDLYQTYHVLVGDLIKF---SAETLS---- 196
Query: 60 FDRGGDDNEGDYQKDIHNSSPQIHKNFNFQLPFFGFRFNYTRVSRHGYLEFSD--PPDHF 117
+ + ++ + N +LE P +
Sbjct: 197 ----------ELIRTTLDAEKVFTQGLNI----------------LEWLENPSNTPDKDY 230
Query: 118 --TYPLSFPNKDWPKKNDPSFIGI-----FYSKCRIGSIRTTDIDQRTPGVYFRFDIVDV 170
+ P+S P IG+ + ++ ++ G
Sbjct: 231 LLSIPISCP-----------LIGVIQLAHYVVTAKLLGFTPGELRSYLKGA-----TGHS 274
Query: 171 VGTVVDRNRAICV------QPFL-MAEGYVIFDIKIG-EGQYNWKGKYFVETPATA-TER 221
G V A+ + + F + IG + + P T+
Sbjct: 275 QGLVT----AVAIAETDSWESFFVSVRKAITVLFFIGVRCY-----EAY---PNTSLPPS 322
Query: 222 IYFETDAVHERYP-----------EEIKITWDKYNLTSNLNTPVSISLK 259
I ++ +E P E+++ +K N V ISL
Sbjct: 323 ILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLV 371
Score = 32.7 bits (74), Expect = 0.15
Identities = 39/243 (16%), Positives = 61/243 (25%), Gaps = 104/243 (42%)
Query: 105 HGYLEFSDP-P-----------DHFTYPLSFPNKDWPKKNDPS--------FIGIFYSKC 144
HG LE P + F L P + + ++P+ F+G + S
Sbjct: 13 HGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLG-YVSSL 71
Query: 145 ----RIGS----------------IRTTDI---------DQRTPGV--------YFRFDI 167
++G + DI + T V Y
Sbjct: 72 VEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYIT--- 128
Query: 168 VDVVGTVVDRNRAICVQPFLM---AEG----YVIFDIKIGEGQ----------------Y 204
+ R L EG IF G GQ Y
Sbjct: 129 ---ARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF----G-GQGNTDDYFEELRDLYQTY 180
Query: 205 NWKGKYFVETPATATERIYFETDAVHERYPEEIKI-TW--------DKYNLTSNLNTPVS 255
+ ++ A + T + + + + I W DK L S P+S
Sbjct: 181 HVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLS---IPIS 237
Query: 256 ISL 258
L
Sbjct: 238 CPL 240
Score = 31.9 bits (72), Expect = 0.25
Identities = 28/186 (15%), Positives = 55/186 (29%), Gaps = 55/186 (29%)
Query: 73 KDIHNSSPQIHKNFN----FQLPFFGFRFNYTRVSRHGYLEFSDPPD---HFTYPLSFPN 125
D++ +S +N +GF + + +P + HF
Sbjct: 1633 MDLYKTSKAAQDVWNRADNHFKDTYGFSI--LDIVIN------NPVNLTIHFGGEKG--- 1681
Query: 126 KDWPKKNDPSFIGIFYSKCRIGSIRTT----DIDQRTPGVYFRFDIVDVVGTVVDRNRAI 181
K+ ++ + + G ++T +I++ + FR + + T +
Sbjct: 1682 ----KRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSAT---QF--- 1731
Query: 182 CVQPFLMAEGYVIF-DIKIGEGQYNWKGKYFVETPA-------TA----TERIYFETDA- 228
QP L F D+K +G F A A + + E
Sbjct: 1732 -TQPALTLMEKAAFEDLK-SKGLIP-ADATF----AGHSLGEYAALASLADVMSIE-SLV 1783
Query: 229 --VHER 232
V R
Sbjct: 1784 EVVFYR 1789
>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 = 32.5 bits (73), Expect = 0.16
Identities = 32/278 (11%), Positives = 65/278 (23%), Gaps = 82/278 (29%)
Query: 20 KGKYFVVPQQGLG-----IFTSETFLDTKTENQ--NKAHENLWFVWFFDRGGDDNEGDYQ 72
K ++ G+ + L K + + K W N +
Sbjct: 149 PAKNVLI--DGVLGSGKTWVALDVCLSYKVQCKMDFKIF------WL-------NLKNCN 193
Query: 73 KDIHNSSPQIHKNFNFQL-PFFGFRFNYTRVSRHGYLEFSDPPDHFTYPLSFPNK----D 127
+ ++ + +Q+ P + R +++ + + N
Sbjct: 194 SP--ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL 251
Query: 128 --WPKKNDPSFIGIFYSKCRIGSIRTT----DIDQRTPGVYFRFDIVDVVGTVVDRN--- 178
+ F C+I + TT D + + T+
Sbjct: 252 NVQ----NAKAWNAFNLSCKI--LLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS 305
Query: 179 --------------RAIC-VQPFLMAEGYVIF--DIKIGEGQY-NWKGKYFVETPATATE 220
R + P ++ I I+ G + NWK + T E
Sbjct: 306 LLLKYLDCRPQDLPREVLTTNPRRLS----IIAESIRDGLATWDNWK-HVNCDKLTTIIE 360
Query: 221 RIY--FETDAVHERY------PEEIKIT-------WDK 243
E + + P I W
Sbjct: 361 SSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFD 398
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_C*
Length = 1342
Score = 28.9 bits (65), Expect = 1.9
Identities = 10/30 (33%), Positives = 13/30 (43%)
Query: 163 FRFDIVDVVGTVVDRNRAICVQPFLMAEGY 192
F FD D + +DR R + L A Y
Sbjct: 186 FEFDPKDNLFVRIDRRRKLPATIILRALNY 215
>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA
degradation, exoribonuclease, S1domain, KH domain,
archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5
b.84.4.2 d.51.1.1
Length = 229
Score = 27.4 bits (60), Expect = 5.0
Identities = 14/91 (15%), Positives = 28/91 (30%), Gaps = 4/91 (4%)
Query: 151 TTDIDQRTPGVYFRFD--IVDVVGTVVDRNRAICVQPFLMAEGYVIFDIKIGEGQYNWKG 208
+T+ G Y ++G + V P + D+ IG +
Sbjct: 12 STNPRAAGYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGRYTPSVGDVVIGIIREVAAN 71
Query: 209 KYFVET--PATATERIYFETDAVHERYPEEI 237
+ V+ P A + + + P E+
Sbjct: 72 GWAVDIYSPYQAFLPVSENPEMKPNKKPNEV 102
>2rcj_C Light chain; immunoglobulin M, polymeric antibodies, immunology,
X-RAY solution scattering, constrained modelling, immune
system; NMR {Homo sapiens}
Length = 523
Score = 26.7 bits (59), Expect = 8.9
Identities = 6/20 (30%), Positives = 14/20 (70%)
Query: 233 YPEEIKITWDKYNLTSNLNT 252
+P+ + ++W+ LTS ++T
Sbjct: 247 FPQPVTVSWNSGALTSGVHT 266
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
0.322 0.141 0.452
Gapped
Lambda K H
0.267 0.0501 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,279,148
Number of extensions: 256082
Number of successful extensions: 657
Number of sequences better than 10.0: 1
Number of HSP's gapped: 656
Number of HSP's successfully gapped: 16
Length of query: 260
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 168
Effective length of database: 4,133,061
Effective search space: 694354248
Effective search space used: 694354248
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: 56 (25.9 bits)