RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5379
(341 letters)
>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 = 45.6 bits (107), Expect = 2e-05
Identities = 43/337 (12%), Positives = 101/337 (29%), Gaps = 75/337 (22%)
Query: 39 QPLRWFKPRLYWTIEGKFF-HWLLAMAGDDIR--ACIES-----RTLVLVNHQSTGDVPM 90
+ + L ++ K + + LL + +++ + + L+ + D
Sbjct: 225 LRIHSIQAELRRLLKSKPYENCLLVL--LNVQNAKAWNAFNLSCKILLTTRFKQVTDF-- 280
Query: 91 LMAAFNPRRGVLPNIMWIMDR-----IF-KYTNFGVGIAQLRQHIRSSYIPRKRKWMMLF 144
++A L + + + KY + L + + ++ PR+ + +
Sbjct: 281 -LSAATTTHISLDHHSMTLTPDEVKSLLLKYLD--CRPQDLPREVLTT-NPRR---LSII 333
Query: 145 PEGGFLRKRREASQRYAAKNNLPQCQYVSLPRLG-ALGAIFEELHPEEEEICTDKHGNTA 203
E +R + ++V+ +L + + L P E D+ +
Sbjct: 334 AE--SIRDGLATWDNW---------KHVNCDKLTTIIESSLNVLEPAEYRKMFDR---LS 379
Query: 204 IFPPDND---DTLS--WVLDITIGYPQGNPIDLPTII-------MGQRDPCTTTLFYRLY 251
+FPP LS W D+ ++ + ++ P +T +
Sbjct: 380 VFPPSAHIPTILLSLIW--------FDVIKSDVMVVVNKLHKYSLVEKQPKEST--ISIP 429
Query: 252 PINSVPSGKEALTRWLYDRWEEKEHMLDVFYRNGQFPSR-------HTGYTSSPIPPTQV 304
I K L+ + ++ F + P H G+ I +
Sbjct: 430 SIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPE- 488
Query: 305 AQSPLRFLLLHLFFMTSSFFHYKLIEVGYEYFYPVPL 341
R L + F+ F K+ + +
Sbjct: 489 -----RMTLFRMVFLDFRFLEQKIRHDSTAWNASGSI 520
Score = 28.7 bits (63), Expect = 4.1
Identities = 29/198 (14%), Positives = 57/198 (28%), Gaps = 56/198 (28%)
Query: 103 PNIMWIMDRIFKYTNFGVGIAQLRQHIRSSYIP-RKRKW--MMLFPEGGFLRKRREASQR 159
N ++M I + YI R R + +F + R + R
Sbjct: 89 INYKFLMSPIKTEQR-------QPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLR 141
Query: 160 YAAKNNLPQCQYVSLPRLGALGA-----IFEELHPEEEEICTDKHGNTAIFPPDNDDTLS 214
A L + V + G LG+ + + + D IF
Sbjct: 142 QALL-ELRPAKNVLI--DGVLGSGKTWVALDVCLSYKVQCKMDFK----IF--------- 185
Query: 215 WVLDITIGYPQGNPIDLPTIIMGQRDPCTTTLFYRLYP--------INSVPSGKEALTRW 266
W + + +P + + M Q L Y++ P +++ ++
Sbjct: 186 W---LNLKN-CNSPETV--LEMLQ------KLLYQIDPNWTSRSDHSSNIKLRIHSIQAE 233
Query: 267 LYDRWEEKEH-----MLD 279
L + K + +L
Sbjct: 234 LRRLLKSKPYENCLLVLL 251
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 32.2 bits (72), Expect = 0.13
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 11/35 (31%)
Query: 152 KRREAS-QRYAAKNNLPQCQYVSLPRLGALGAIFE 185
K+ +AS + YA S P L A+ A E
Sbjct: 23 KKLQASLKLYA-----DD----SAPAL-AIKATME 47
>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 = 30.8 bits (69), Expect = 0.87
Identities = 15/82 (18%), Positives = 26/82 (31%), Gaps = 25/82 (30%)
Query: 60 LLAMAG-----DDIRACIESRTLV---------LVNHQSTGDVPMLMAAFNPRRGVLP-- 103
L ++A + +V V G M A NP R
Sbjct: 1770 LASLADVMSIESLVE-------VVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFS 1822
Query: 104 --NIMWIMDRIFKYTNFGVGIA 123
+ ++++R+ K T + V I
Sbjct: 1823 QEALQYVVERVGKRTGWLVEIV 1844
Score = 29.6 bits (66), Expect = 1.9
Identities = 38/214 (17%), Positives = 60/214 (28%), Gaps = 65/214 (30%)
Query: 148 GFLRKRREASQRYAAKNNLPQCQYVSLPRLGALGAIFEELHPEEEEICTDKHGNTAIFPP 207
G++ E S+ Q+ + L L FE + E +I H A
Sbjct: 66 GYVSSLVEPSK---------VGQFDQVLNL-CLTE-FENCYLEGNDI----HALAAKLLQ 110
Query: 208 DNDDTLSWVLDITIGYPQ-----GNPIDLPTIIMGQRDPCTTTLF-------YRLYPI-- 253
+ND TL ++ Y P D + + LF +L I
Sbjct: 111 ENDTTLVKTKELIKNYITARIMAKRPFDKKS---------NSALFRAVGEGNAQLVAIFG 161
Query: 254 ---NSVPSGKEALTRWLYDRW--------EEKEHMLDVFYRNGQFPSRH--TGY------ 294
N+ +E L R LY + + L R + G
Sbjct: 162 GQGNTDDYFEE-L-RDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWL 219
Query: 295 -TSSPIPPTQ-VAQSPLRFLLLHLFFMTSSFFHY 326
S P + P+ L+ + HY
Sbjct: 220 ENPSNTPDKDYLLSIPISCPLIGVI----QLAHY 249
>3k49_A MRNA-binding protein PUF3; PUF3, pumilio, RNA binding,
mitochondrial mRNA,, membrane, mitochondrion; HET: CIT;
2.50A {Saccharomyces cerevisiae} PDB: 3k4e_A
Length = 369
Score = 30.1 bits (68), Expect = 0.99
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 182 AIFEELHPEEEEICTDKHGNTAI 204
IF E+ + E+ D GN I
Sbjct: 60 VIFNEIRDDAIELSNDVFGNYVI 82
>3gvo_A Pumilio 2, pumilio homolog 2; RNA-binding, PUF domain, RNA binding
protein; HET: DTD; 1.60A {Mus musculus} PDB: 3gvt_A
3q0q_A 3q0r_A 3q0s_A 1ib2_A 1m8w_A 1m8x_A 1m8y_A 1m8z_A
3q0l_A 3q0m_A 3q0n_A 3q0o_A 3q0p_A 2yjy_A 3bsx_A 3bsb_A
3h3d_X
Length = 351
Score = 30.0 bits (68), Expect = 1.1
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 182 AIFEELHPEEEEICTDKHGNTAI 204
+F E+ ++ TD GN I
Sbjct: 55 IVFNEILQAAYQLMTDVFGNYVI 77
>3bwt_A Protein PUF4; pumilio, RNA binding, HO endonuclease, transcription,
RNA binding protein; 2.69A {Saccharomyces cerevisiae}
PDB: 4dzs_A 3bx2_A 3bx3_A
Length = 333
Score = 29.4 bits (66), Expect = 1.8
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 182 AIFEELHPEEEEICTDKHGNTAI 204
AIFEE E+ TD GN I
Sbjct: 42 AIFEETKDYTVELMTDSFGNYLI 64
>3v71_A PUF (pumilio/FBF) domain-containing protein 7, CO transcript
evidence; PUF repeats, RNA binding protein-RNA complex;
HET: EPE; 2.90A {Caenorhabditis elegans}
Length = 382
Score = 27.7 bits (61), Expect = 6.4
Identities = 5/23 (21%), Positives = 9/23 (39%)
Query: 182 AIFEELHPEEEEICTDKHGNTAI 204
F E +C ++GN +
Sbjct: 53 EKFTESTTLFVGLCHSRNGNFIV 75
>3gix_A Thioredoxin-like protein 4B; PRE-mRNA splicing, TXNL4B, DLP, cell
cycle, mRNA processing, mRNA splicing, nucleus,
phosphoprotein, splicing; HET: SUC; 1.33A {Homo sapiens}
PDB: 1xbs_A
Length = 149
Score = 26.8 bits (59), Expect = 6.9
Identities = 10/75 (13%), Positives = 21/75 (28%), Gaps = 6/75 (8%)
Query: 239 RDPCTTTLFYRLYPINSV--PSGKEALTRWLYDRWEEKEHMLDVFYRNGQFPSRHTGYTS 296
+T F+ + + K+ +D+ + R
Sbjct: 76 SYIPSTVFFFNGQHMKVDYGSPDHTKFVGSF----KTKQDFIDLIEVIYRGAMRGKLIVQ 131
Query: 297 SPIPPTQVAQSPLRF 311
SPI P + + L +
Sbjct: 132 SPIDPKNIPKYDLLY 146
>2gai_A DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A {Thermotoga
maritima} PDB: 2gaj_A*
Length = 633
Score = 27.5 bits (62), Expect = 8.0
Identities = 5/13 (38%), Positives = 6/13 (46%)
Query: 44 FKPRLYWTIEGKF 56
F P+ Y I F
Sbjct: 186 FVPKKYHRITVNF 198
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
0.327 0.143 0.467
Gapped
Lambda K H
0.267 0.0543 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,672,574
Number of extensions: 344717
Number of successful extensions: 717
Number of sequences better than 10.0: 1
Number of HSP's gapped: 712
Number of HSP's successfully gapped: 16
Length of query: 341
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 247
Effective length of database: 4,077,219
Effective search space: 1007073093
Effective search space used: 1007073093
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 (21.7 bits)
S2: 58 (26.5 bits)