RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13857
(259 letters)
>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation,
exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB:
4a4k_A
Length = 997
Score = 147 bits (372), Expect = 2e-40
Identities = 53/161 (32%), Positives = 86/161 (53%), Gaps = 4/161 (2%)
Query: 97 KFYHIYKRKED-HNRLSELKHLLSHKGMSLYADYDSKVKVLQELNYINSQGIVQLKGNIA 155
+ + ++ EL HL+S + +SL DY+ ++ VL++ +I+ V LKG +A
Sbjct: 769 QHIVPKFKAHVIKKKIEELYHLMSDQNLSLLPDYEKRLAVLKDTEFIDQNHNVLLKGRVA 828
Query: 156 CEMGSKNELLITELLFQNKLVNFTPEEIAALLSCLVFQSKTT--TPTELPESLKQGMSII 213
CE+ S EL++TEL+ N L +F PEEI ALLS V++ KT P + L +G I
Sbjct: 829 CEINSGYELVLTELILDNFLGSFEPEEIVALLSVFVYEGKTREEEPPIVTPRLAKGKQRI 888
Query: 214 ADMNIEVESIEKKHGVERDKSSEE-ADNLNFGLVQVVYEWA 253
++ ++ + H + + E D F ++ VVYEWA
Sbjct: 889 EEIYKKMLCVFNTHQIPLTQDEAEFLDRKRFAMMNVVYEWA 929
>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase,
tramp, exosome, DEAD, nucleotide-binding; HET: ADP;
2.90A {Saccharomyces cerevisiae}
Length = 1010
Score = 145 bits (366), Expect = 1e-39
Identities = 49/159 (30%), Positives = 81/159 (50%), Gaps = 3/159 (1%)
Query: 97 KFYHIYKRKED-HNRLSELKHLLSH-KGMSLYADYDSKVKVLQELNYINSQGIVQLKGNI 154
+ Y Y RK D H + +LK +S + + D + +VL+ L + I++LKG +
Sbjct: 785 ELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRV 844
Query: 155 ACEMGSKNELLITELLFQNKLVNFTPEEIAALLSCLVFQSKTTTPTELPESLKQGMSIIA 214
ACE+ S +ELL+TEL+F PE+ AALLSC FQ + L L + + +
Sbjct: 845 ACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEAPRLKPELAEPLKAMR 904
Query: 215 DMNIEVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWA 253
++ ++ I K +E + ++ L++VVYEW
Sbjct: 905 EIAAKIAKIMKDSKIEVV-EKDYVESFRHELMEVVYEWC 942
>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix,
antiparallel-coiled-COI domain, ATP-binding, helicase,
hydrolase; 3.39A {Saccharomyces cerevisiae}
Length = 1108
Score = 143 bits (362), Expect = 4e-39
Identities = 49/159 (30%), Positives = 81/159 (50%), Gaps = 3/159 (1%)
Query: 97 KFYHIYKRKED-HNRLSELKHLLSH-KGMSLYADYDSKVKVLQELNYINSQGIVQLKGNI 154
+ Y Y RK D H + +LK +S + + D + +VL+ L + I++LKG +
Sbjct: 883 ELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRV 942
Query: 155 ACEMGSKNELLITELLFQNKLVNFTPEEIAALLSCLVFQSKTTTPTELPESLKQGMSIIA 214
ACE+ S +ELL+TEL+F PE+ AALLSC FQ + L L + + +
Sbjct: 943 ACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEAPRLKPELAEPLKAMR 1002
Query: 215 DMNIEVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWA 253
++ ++ I K +E + ++ L++VVYEW
Sbjct: 1003 EIAAKIAKIMKDSKIEVV-EKDYVESFRHELMEVVYEWC 1040
>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 = 45.2 bits (106), Expect = 1e-05
Identities = 43/246 (17%), Positives = 84/246 (34%), Gaps = 62/246 (25%)
Query: 37 GPSVNASDPNSSDPPKPALYYQM--LTL---LTSDPVMLGSLSMNHTIVNIQVQNIWGVV 91
G + A D S + + +++ L L + + V+ + + I
Sbjct: 162 GKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSS 221
Query: 92 NTPILKFYHIYKRKEDHNRLSELKHLLSHKGMSLYADYDSKVKVLQELNYINSQGIVQLK 151
N + R +EL+ LL K Y L L + +
Sbjct: 222 NIKL--------RIHSIQ--AELRRLLKSK------PY---ENCLLVLLNVQNAKAWN-A 261
Query: 152 GNIACEMGSKNELLIT---------------ELLFQNKLVNFTPEEIAALLS-CLVFQSK 195
N++C++ LL T + + + TP+E+ +LL L
Sbjct: 262 FNLSCKI-----LLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYL----- 311
Query: 196 TTTPTELPESLKQG----MSIIADMNIE-VESIEK-KHGVERDKSSE--EA--DNLNFGL 245
P +LP + +SIIA+ + + + + KH V DK + E+ + L
Sbjct: 312 DCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKH-VNCDKLTTIIESSLNVLEPAE 370
Query: 246 VQVVYE 251
+ +++
Sbjct: 371 YRKMFD 376
Score = 40.2 bits (93), Expect = 5e-04
Identities = 29/214 (13%), Positives = 62/214 (28%), Gaps = 65/214 (30%)
Query: 74 SMNHTIVNIQVQNIWGVVNTPILKFYHIYKRKEDHNRLSE-LKHLLSHK-----GM---- 123
SM + Q ++ + Y++ R + + +L + L L K G+
Sbjct: 106 SMMTRMYIEQRDRLYNDN--QVFAKYNVS-RLQPYLKLRQALLELRPAKNVLIDGVLGSG 162
Query: 124 ------SLYADY---------------------DSKVKVLQELNYINSQGIVQLKGNIAC 156
+ Y ++ +++LQ+L Y + +
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSN 222
Query: 157 EMGSKNEL------LITELLFQNKL-----VNFTPEEIAAL-LSC--LVFQSKTTTPTEL 202
+ + L+ ++N L V + A LSC L+ TT ++
Sbjct: 223 IKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ-NAKAWNAFNLSCKILL----TTRFKQV 277
Query: 203 PESLKQGMSIIADMNIEVESIEKKHGVERDKSSE 236
+ L A + + D+
Sbjct: 278 TDFLS------AATTTHISLDHHSMTLTPDEVKS 305
Score = 29.8 bits (66), Expect = 1.0
Identities = 13/67 (19%), Positives = 22/67 (32%), Gaps = 2/67 (2%)
Query: 170 LFQNKLVNFTPEEIAALL-SCLVFQSKTTTPTELPESLKQGMSIIADMNIEVESIEKKHG 228
+ ++ L P E + VF PT L + + M + V + K
Sbjct: 358 IIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVV-VNKLHKYSL 416
Query: 229 VERDKSS 235
VE+
Sbjct: 417 VEKQPKE 423
>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 = 31.6 bits (71), Expect = 0.28
Identities = 30/180 (16%), Positives = 52/180 (28%), Gaps = 64/180 (35%)
Query: 119 SHK---GMSLYADYDS--KV-----KVLQELNYINSQGIVQLKGN---IACEMGSKNELL 165
S + GM LY + V ++ + IV N + G +
Sbjct: 1626 SQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIV--INNPVNLTIHFGGEKGKR 1683
Query: 166 ITE----LLFQNKLVNFTP-----EEIAALLSCLVFQSKTTTPTELPESLKQ-------- 208
I E ++F+ + +EI + F+S L L
Sbjct: 1684 IRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRS----EKGL---LSATQFTQPAL 1736
Query: 209 ---GMSIIADMNIEVESIEKKHGVERDKS-----S--E------EADNLNFG-LVQVVYE 251
+ D+ K G+ + S E AD ++ LV+VV+
Sbjct: 1737 TLMEKAAFEDL--------KSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFY 1788
>3cnc_A Fiber protein; adenovirus fiber KNOB, viral protein; 2.40A {Human
adenovirus 16}
Length = 220
Score = 29.7 bits (66), Expect = 0.67
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 13/61 (21%)
Query: 15 ITKESRTIWCRRVLIFTDTTTPGPSVNASDPNSSDPPKPALYYQMLTLLTSDPVMLGSLS 74
IT E+ T+W T PS N D P L L L+ + ++ G ++
Sbjct: 23 ITIENNTLW----------TGAKPSANCVIKEGEDSPDCKLT---LVLVKNGGLINGYIT 69
Query: 75 M 75
+
Sbjct: 70 L 70
>2oka_A Hypothetical protein; PAR82, NESG, structural genomics, PSI-2,
protein structure initiative, northeast structural
genomics consortium; 2.50A {Pseudomonas aeruginosa}
PDB: 2obk_A
Length = 104
Score = 27.4 bits (61), Expect = 2.1
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 11 GVFKITKESRTIWCRRV 27
GVF+IT + +W R+
Sbjct: 48 GVFRITCDGVQVWERKA 64
>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 = 27.6 bits (60), Expect = 2.8
Identities = 5/32 (15%), Positives = 14/32 (43%), Gaps = 9/32 (28%)
Query: 14 KITK-ESRTIWCRRVL-IFTDTTTPGPSVNAS 43
+ K ++ L ++ D + P ++ A+
Sbjct: 21 ALKKLQAS-------LKLYADDSAPALAIKAT 45
>3dex_A SAV_2001; alpha-beta protein, structural genomics, PSI-2, protein
structure initiative, northeast structural genomics
consortium, NESG; 2.70A {Streptomyces avermitilis}
Length = 107
Score = 26.3 bits (58), Expect = 4.4
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 11 GVFKITKESRTIWCRRVLIFTDTT 34
GVF + + +W RR F + T
Sbjct: 55 GVFVVRVDDEVVWDRREQGFPEPT 78
>1xq1_A Putative tropinone reducatse; structural genomics, protein
structure initiative, CESG, AT1 reductively methylated
protein; 2.10A {Arabidopsis thaliana} SCOP: c.2.1.2 PDB:
2q45_A
Length = 266
Score = 26.7 bits (60), Expect = 6.7
Identities = 13/66 (19%), Positives = 22/66 (33%), Gaps = 28/66 (42%)
Query: 146 GIVQLKGNIACEMGSKNELLI--------------TELLFQNKLVNF-----------TP 180
+ QL N+ACE S I E ++ ++ P
Sbjct: 170 ALNQLARNLACEWASDG---IRANAVAPAVIATPLAEAVYDDEFKKVVISRKPLGRFGEP 226
Query: 181 EEIAAL 186
EE+++L
Sbjct: 227 EEVSSL 232
>2wst_A Putative fiber protein; viral protein; 3.20A {Porcine adenovirus
4}
Length = 208
Score = 26.6 bits (58), Expect = 6.8
Identities = 14/67 (20%), Positives = 24/67 (35%), Gaps = 14/67 (20%)
Query: 16 TKESRTIWCRRVLIFTDTTTPGPSVNASDPNSSDPPKPALYYQMLTLLTSDPVMLGSLSM 75
T+W T P P N + + P L L L + ++G+LS+
Sbjct: 32 ILVYPTLW----------TGPAPEANVTFSGENS-PSGILR---LCLSRTGGTVIGTLSV 77
Query: 76 NHTIVNI 82
++ N
Sbjct: 78 QGSLTNP 84
>2ztg_A Alanyl-tRNA synthetase; class-II aminoacyl-tRNA synthetase,
aminoacyl-tRNA synthetase, ATP-binding, cytoplasm,
ligase; HET: A5A; 2.20A {Archaeoglobus fulgidus}
Length = 739
Score = 27.2 bits (61), Expect = 7.0
Identities = 6/13 (46%), Positives = 7/13 (53%)
Query: 8 GPIGVFKITKESR 20
G IG+ KI K
Sbjct: 712 GEIGMLKILKVES 724
>2e1b_A PH0108, 216AA long hypothetical alanyl-tRNA synthetase;
zinc-binding motif, trans-editing enzyme, structural
genomics, NPPSFA; 2.70A {Pyrococcus horikoshii} SCOP:
b.43.3.6 d.67.1.2
Length = 216
Score = 26.4 bits (59), Expect = 9.4
Identities = 5/13 (38%), Positives = 5/13 (38%)
Query: 8 GPIGVFKITKESR 20
IG K K S
Sbjct: 191 KEIGHIKKLKRSS 203
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
0.317 0.133 0.389
Gapped
Lambda K H
0.267 0.0489 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,710,331
Number of extensions: 207288
Number of successful extensions: 486
Number of sequences better than 10.0: 1
Number of HSP's gapped: 483
Number of HSP's successfully gapped: 23
Length of query: 259
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 167
Effective length of database: 4,133,061
Effective search space: 690221187
Effective search space used: 690221187
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.9 bits)