RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8593
(204 letters)
>1rw3_A POL polyprotein; RNA and DNA dependent DNA polymerase, reverse
transcriptase, transferase, replication; 3.00A {Moloney
murine leukemia virus} SCOP: e.8.1.2
Length = 455
Score = 44.2 bits (105), Expect = 1e-05
Identities = 8/65 (12%), Positives = 21/65 (32%), Gaps = 2/65 (3%)
Query: 80 ELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFE 139
+A + G +V++ H + + + N R+ + L
Sbjct: 393 MVAAIAVLTKDAGKLTMGQP-LVIKAPHAVEALVKQPPDRWLSNARMTHYQALLLDTD-R 450
Query: 140 LKYLP 144
+++ P
Sbjct: 451 VQFGP 455
>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 = 0.002
Identities = 36/188 (19%), Positives = 56/188 (29%), Gaps = 74/188 (39%)
Query: 22 RNTQSAETAGEKCSALDQHFEFRLITMQLIGSAQRDLFFIIFYKLGH---------AFST 72
+ TQ A T EK A F + + G D F GH + +
Sbjct: 1730 QFTQPALTLMEK--AA-----FEDLKSK--GLIPADATFA-----GHSLGEYAALASLAD 1775
Query: 73 SL------------------AIPRDEL----------------AGFRSEA-TEFCYYVYG 97
+ A+PRDEL A F EA V
Sbjct: 1776 VMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGK 1835
Query: 98 HRNIVVQT------DHQPLLAINKKDLYKIQN--NRLKRLKIKLFPYQFELKYLPGKYMH 149
+V+ + Q + A + + L + N N +K KI + L +
Sbjct: 1836 RTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIE-------LQKS-LS 1887
Query: 150 IAELADYL 157
+ E+ +L
Sbjct: 1888 LEEVEGHL 1895
Score = 32.7 bits (74), Expect = 0.094
Identities = 23/128 (17%), Positives = 39/128 (30%), Gaps = 41/128 (32%)
Query: 66 LGH-AFSTSLAIP----------RDELAGFRSEATEFCYYVYGHRNIVVQTDHQP----- 109
L H + L +P +++ E TE D +P
Sbjct: 11 LSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTE-----------GFAADDEPTTPAE 59
Query: 110 LLA-----INKKDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMH--IAEL-----ADYL 157
L+ ++ + L + L +FE YL G +H A+L +
Sbjct: 60 LVGKFLGYVSSLVEPSKVGQFDQVLNLCL--TEFENCYLEGNDIHALAAKLLQENDTTLV 117
Query: 158 SRNLLVKN 165
L+KN
Sbjct: 118 KTKELIKN 125
Score = 32.3 bits (73), Expect = 0.12
Identities = 23/105 (21%), Positives = 43/105 (40%), Gaps = 34/105 (32%)
Query: 97 GHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKL------FPY-----QFELKYLP- 144
G +N+VV + P + LY + N L++ K P+ +F ++LP
Sbjct: 373 GAKNLVV-SGP-P------QSLYGL-NLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPV 423
Query: 145 -----GKYMHIAELADYLSRNLLVKNVQEDILMKDM---V-HTVN 180
+ A +D ++++L+ NV KD+ V T +
Sbjct: 424 ASPFHSHLLVPA--SDLINKDLVKNNVS--FNAKDIQIPVYDTFD 464
>1i1r_B Viral IL-6; cytokine/receptor complex, GP130; 2.40A {Human
herpesvirus 8} SCOP: a.26.1.1
Length = 181
Score = 29.1 bits (64), Expect = 0.78
Identities = 13/69 (18%), Positives = 24/69 (34%), Gaps = 2/69 (2%)
Query: 126 LKRLKIKLFPYQFELKYLPGKYMHIAELAD--YLSRNLLVKNVQEDILMKDMVHTVNKFE 183
LK+L F ++ K+L ++ D L L ++QE++ H
Sbjct: 71 LKKLADGFFEFEVLFKFLTTEFGKSVINVDVMELLTKTLGWDIQEELNKLTKTHYSPPKF 130
Query: 184 INFSPEKFQ 192
+ Q
Sbjct: 131 DRGLLGRLQ 139
>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 = 29.1 bits (64), Expect = 1.2
Identities = 25/199 (12%), Positives = 66/199 (33%), Gaps = 39/199 (19%)
Query: 7 ILRYD-QFLIAKISTIRNTQSAETAG-----EKCSALDQHFEFRLIT-MQLIGSAQRDLF 59
+LR + +FL++ I T + S T ++ +Q F ++ +Q ++ L
Sbjct: 86 VLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALL 145
Query: 60 ------FIIFYKLGHAFSTSLAIPRDELAGFRSEATEFCYYVY----GHRNIVVQTDHQP 109
++ + + T +A+ ++ + + ++ + N
Sbjct: 146 ELRPAKNVLIDGVLGSGKTWVAL---DVCLSYKVQCKMDFKIFWLNLKNCNS-------- 194
Query: 110 LLAINKKDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMHIAELADYLSRNLLVKNVQED 169
+ + ++ L ++ + + I + L R L K +
Sbjct: 195 -----PETVLEMLQKLLYQIDPNWTSRSDHSSNIK---LRIHSIQAELRRLLKSKPYENC 246
Query: 170 ILMKDMV---HTVNKFEIN 185
+L+ V N F ++
Sbjct: 247 LLVLLNVQNAKAWNAFNLS 265
Score = 29.1 bits (64), Expect = 1.3
Identities = 24/171 (14%), Positives = 46/171 (26%), Gaps = 55/171 (32%)
Query: 55 QRDLF--FIIFYKLGHAFSTSLAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLA 112
R +F +F S IP L+ + + +V + L+
Sbjct: 371 YRKMFDRLSVFPP-------SAHIPTILLSLIWFDVIKSDV-----MVVVNKLHKYSLVE 418
Query: 113 INKK-------DLY---KIQNNRLKRLKIKLF-PYQFELKYLPGK----------YMHIA 151
K +Y K++ L + Y + Y HI
Sbjct: 419 KQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIG 478
Query: 152 ELADY-LSRNLLVKNVQEDILMKDMVHTVNKFEINFSPEKFQWFQQEILND 201
+ L + + F + F F++ +Q+I +D
Sbjct: 479 ----HHLKN-------------IEHPERMTLFRMVFL--DFRFLEQKIRHD 510
>1alu_A Interleukin-6; cytokine, receptor, signaling, glycoprotein; HET:
TLA; 1.90A {Homo sapiens} SCOP: a.26.1.1 PDB: 1il6_A
2il6_A 1p9m_B
Length = 186
Score = 28.3 bits (62), Expect = 1.3
Identities = 14/69 (20%), Positives = 29/69 (42%), Gaps = 2/69 (2%)
Query: 126 LKRLKIKLFPYQFELKYLPGKYMHIAELAD--YLSRNLLVKNVQEDILMKDMVHTVNKFE 183
L ++ L ++ L+YL ++ E A +S +L++ +Q+ D + T +
Sbjct: 86 LVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAKNLDAITTPDPTT 145
Query: 184 INFSPEKFQ 192
K Q
Sbjct: 146 NASLLTKLQ 154
>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 = 27.2 bits (59), Expect = 2.5
Identities = 7/31 (22%), Positives = 10/31 (32%), Gaps = 14/31 (45%)
Query: 115 KKDLYKIQNNRLKRLKIKLFPYQFELKYLPG 145
K+ L K+Q LK+ Y
Sbjct: 19 KQALKKLQA----SLKL----------YADD 35
Score = 26.8 bits (58), Expect = 3.2
Identities = 5/9 (55%), Positives = 5/9 (55%)
Query: 106 DHQPLLAIN 114
D P LAI
Sbjct: 35 DSAPALAIK 43
Score = 25.7 bits (55), Expect = 7.8
Identities = 5/15 (33%), Positives = 8/15 (53%)
Query: 122 QNNRLKRLKIKLFPY 136
+ LK+L+ L Y
Sbjct: 18 EKQALKKLQASLKLY 32
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_D*
Length = 1407
Score = 27.2 bits (61), Expect = 4.4
Identities = 10/16 (62%), Positives = 12/16 (75%), Gaps = 3/16 (18%)
Query: 117 DLYK---IQNNRLKRL 129
DLY+ +NNRLKRL
Sbjct: 267 DLYRRVINRNNRLKRL 282
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D-
structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB:
1i6v_D* 2gho_D
Length = 1265
Score = 26.9 bits (60), Expect = 5.7
Identities = 9/16 (56%), Positives = 12/16 (75%), Gaps = 3/16 (18%)
Query: 117 DLYK---IQNNRLKRL 129
DLY+ +NNRLK+L
Sbjct: 282 DLYRRLINRNNRLKKL 297
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
0.325 0.139 0.405
Gapped
Lambda K H
0.267 0.0719 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,032,511
Number of extensions: 169583
Number of successful extensions: 414
Number of sequences better than 10.0: 1
Number of HSP's gapped: 411
Number of HSP's successfully gapped: 29
Length of query: 204
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 115
Effective length of database: 4,216,824
Effective search space: 484934760
Effective search space used: 484934760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.0 bits)