RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15518
(195 letters)
>2f1v_A Outer membrane protein W; outer membrane protein beta barrel; 2.70A
{Escherichia coli K12} PDB: 2f1t_A
Length = 197
Score = 30.5 bits (68), Expect = 0.27
Identities = 14/77 (18%), Positives = 28/77 (36%), Gaps = 2/77 (2%)
Query: 106 TTYVNANDEVVSNPGLIALHYLRGWFIIDLVAAIPFDLLIFGSETEETLDSRELPLSMSI 165
+ + GL + ++L+AA PF I T + LP ++
Sbjct: 28 LGGFSVTNNTQ--LGLTFTYMATDNIGVELLAATPFRHKIGTRATGDIATVHHLPPTLMA 85
Query: 166 EMHFKLLTSVMTKWIGL 182
+ +F +S ++G
Sbjct: 86 QWYFGDASSKFRPYVGA 102
>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 = 29.6 bits (66), Expect = 0.67
Identities = 23/159 (14%), Positives = 44/159 (27%), Gaps = 56/159 (35%)
Query: 54 TAIFTP---YVAAFLLNEPDFT----NRTRNIRRYSDPIVFVDLIVD-VTFIVD------ 99
+ P + A L E F T +P +L+ + ++
Sbjct: 18 HVLLVPTASFFIASQLQE-QFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSK 76
Query: 100 ---------IAIN-FRTTYVNAND---------EVVSNPGLIALHYLRGWFIIDLVAAIP 140
+ + F Y+ ND + + ++ + ++A P
Sbjct: 77 VGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRP 136
Query: 141 FD------LL------------IFG--SETEETLDSREL 159
FD L IFG T++ + EL
Sbjct: 137 FDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFE--EL 173
Score = 28.9 bits (64), Expect = 1.3
Identities = 17/84 (20%), Positives = 35/84 (41%), Gaps = 27/84 (32%)
Query: 87 FVDLIVDVT-FIVDIAINFRTTYVNANDE--VVSNPG-LIALHYLRGWFIIDLVAAIPFD 142
V+ + T ++V+I N+ N ++ V + G L AL + +++ + D
Sbjct: 1829 VVERVGKRTGWLVEIV-NY-----NVENQQYVAA--GDLRALDTVTN--VLNFIKLQKID 1878
Query: 143 LLIFGSETEETLDSRELPLSMSIE 166
++ EL S+S+E
Sbjct: 1879 II-------------ELQKSLSLE 1889
Score = 27.7 bits (61), Expect = 2.8
Identities = 25/159 (15%), Positives = 48/159 (30%), Gaps = 65/159 (40%)
Query: 37 SP-FKAVWD-----------WLILILVV-----YTAIFTPYVAAFLLNEPDFTNRTRNIR 79
S + VW+ + IL +V+ T F + + IR
Sbjct: 1639 SKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGE-------------KGKRIR 1685
Query: 80 RYSDPIVFVDLIVD---VTFIVDIAINFRTT-YVNANDEVVSN------PGLIALHY--- 126
++F + IVD T + IN +T Y +++ + + P L +
Sbjct: 1686 ENYSAMIF-ETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAF 1744
Query: 127 --LRGWFIID---------------LVA---AIPF-DLL 144
L+ +I L + + L+
Sbjct: 1745 EDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLV 1783
>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 = 29.8 bits (66), Expect = 0.70
Identities = 28/147 (19%), Positives = 57/147 (38%), Gaps = 25/147 (17%)
Query: 16 DVLPEYKLQT---PRIHKWTILHYSPFKAV--WDWLILILVVYTAIFTPYVAAFLLNEPD 70
+ E K++ +H+ + HY+ K D + L Y ++ ++ L
Sbjct: 430 SIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQY--FYS-HIGHHL----- 481
Query: 71 FTNRTRNIRRYSDPIVFVDLIVDVTFIVDIAINFRTTYVNANDEVVSNPGLIALHYLRGW 130
+NI +F + +D F+ + I +T NA+ +++ L L + +
Sbjct: 482 -----KNIEHPERMTLFRMVFLDFRFL-EQKIRHDSTAWNASGSILNT--LQQLKFYKP- 532
Query: 131 FIID---LVAAIPFDLLIFGSETEETL 154
+I D + +L F + EE L
Sbjct: 533 YICDNDPKYERLVNAILDFLPKIEENL 559
Score = 29.1 bits (64), Expect = 1.0
Identities = 29/201 (14%), Positives = 57/201 (28%), Gaps = 70/201 (34%)
Query: 12 SLGADVLPEYKLQTPRIHKWTILHYSPFKAVW---------DWLILILV-VYTAIFTPYV 61
+ DV YK+Q FK W + ++ +L + I +
Sbjct: 165 WVALDVCLSYKVQCKM----------DFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWT 214
Query: 62 A------AFLLNEPDFTNRTRNI---RRYSDPIVFVDLIV--DV--TFIVDIAINFR-TT 107
+ L R + + Y + L+V +V + A N
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRLLKSKPYEN-----CLLVLLNVQNAKAWN-AFNLSCKI 268
Query: 108 YVNANDEVVSNPGLIALHYLRGWFIIDLVAAIPFDLLIFGSETEETLDSRELPLSMSIEM 167
+ + V D L + T +LD + L+
Sbjct: 269 LLTTRFKQV------------------------TDFLSAATTTHISLDHHSMTLT----- 299
Query: 168 HFKLLTSVMTKWIGLKRLTLP 188
++ S++ K++ + LP
Sbjct: 300 PDEVK-SLLLKYLDCRPQDLP 319
Score = 27.5 bits (60), Expect = 3.6
Identities = 26/162 (16%), Positives = 51/162 (31%), Gaps = 38/162 (23%)
Query: 55 AIFTPYVAAFLLNEPDFTNRTRNI----RRYSDPIV--FVD--LIVDVTFIVD-IAINFR 105
+I + ++ D + T + + +V FV+ L ++ F++ I R
Sbjct: 44 SILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQR 103
Query: 106 ------TTYVNANDEVV-SNPGLIALHYLRGWFIIDLVAAI----PFD-LLIFG------ 147
Y+ D + N + R + L A+ P +LI G
Sbjct: 104 QPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK 163
Query: 148 -SETEETLDSRELPLSMSIEMHFKLLTSVMTKWIGLKRLTLP 188
+ S ++ M ++ W+ LK P
Sbjct: 164 TWVALDVCLSYKVQCKMDFKIF----------WLNLKNCNSP 195
>3a4c_A DNA replication factor CDT1; alpha-beta structure, cell cycle, DNA-
binding, nucleus, phosphoprotein, proto-oncogene, UBL
conjugation; HET: DNA; 1.89A {Mus musculus} PDB: 2rqq_A*
Length = 106
Score = 26.1 bits (57), Expect = 4.3
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 127 LRGWFIIDLVAAIPFDLLIFGSETEETLDSRELPLSMS-IEMHFKLLTSVMTKWIGLKRL 185
LR F+ + A+ +++ +DS + LS +E H LL ++ W+ L R+
Sbjct: 22 LRNVFVSERKPALTMEVVC-----ARMVDSCQTALSPGEMEKHLVLLAELLPDWLSLHRI 76
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 0.143 0.442
Gapped
Lambda K H
0.267 0.0725 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,142,553
Number of extensions: 188837
Number of successful extensions: 332
Number of sequences better than 10.0: 1
Number of HSP's gapped: 327
Number of HSP's successfully gapped: 14
Length of query: 195
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 106
Effective length of database: 4,216,824
Effective search space: 446983344
Effective search space used: 446983344
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: 55 (25.0 bits)