RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11729
(281 letters)
>3uby_A DNA-3-methyladenine glycosylase; alkyladenine DNA glycosylase fold,
AAG, DNA repair, DNA BIND nucleus, hydrolase-DNA
complex; HET: DNA EDC; 2.00A {Homo sapiens} PDB: 3qi5_A*
1f4r_A* 1f6o_A* 1ewn_A* 1bnk_A*
Length = 219
Score = 204 bits (520), Expect = 6e-66
Identities = 99/264 (37%), Positives = 136/264 (51%), Gaps = 52/264 (19%)
Query: 18 LDQAFFDQPCIDLANALLGKYLVRRLSCGTLLIGKIVETESYLGVEDRASHSYNNRRTPR 77
L FFDQP + LA A LG+ LVRRL GT L G+IVETE+YLG ED A+HS R+TPR
Sbjct: 7 LGLEFFDQPAVPLARAFLGQVLVRRLPNGTELRGRIVETEAYLGPEDEAAHSRGGRQTPR 66
Query: 78 NEPMYMKPGTIYVYFTYGMYHCFNLSSQESGGAVLIRSLEPVHGLDIMNRLRNQFNENQN 137
N M+MKPGT+YVY YGMY C N+SSQ G VL+R+LEP+ GL+ M +LR+ +
Sbjct: 67 NRGMFMKPGTLYVYIIYGMYFCMNISSQGDGACVLLRALEPLEGLETMRQLRSTLRKGTA 126
Query: 138 KSKRNNHLPNSQNNEETHSQSNRNSPAKKQKLIKSKQTLSSNDWDQPNKKSKLQDRDLCN 197
+DR+LC+
Sbjct: 127 SRVL-------------------------------------------------KDRELCS 137
Query: 198 GPSKLCISMDITIEYLNKRHICESEEMWVQDLD-CESNITIVESSRIGIGDFAKEWKAKL 256
GPSKLC ++ I ++R + + E +W++ S +V ++R+G+ A EW K
Sbjct: 138 GPSKLCQALAINKS-FDQRDLAQDEAVWLERGPLEPSEPAVVAAARVGV-GHAGEWARKP 195
Query: 257 LRFYILGNKCVSKTDKKMESQMLS 280
LRFY+ G+ VS D+ E +
Sbjct: 196 LRFYVRGSPWVSVVDRVAEQDTQA 219
>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 = 42.1 bits (98), Expect = 2e-04
Identities = 38/218 (17%), Positives = 72/218 (33%), Gaps = 44/218 (20%)
Query: 93 TYGMYHCFNLSSQESGGAVLIRS-LEPVHGLDIMNRLRNQFNENQNKSKR-NNHLPNSQN 150
T ++ LS QE + L + +M+ ++ + + ++ N
Sbjct: 64 TLRLFWTL-LSKQEEMVQKFVEEVLRINYKF-LMSPIKTEQRQPSMMTRMYIEQRDRLYN 121
Query: 151 NEETHSQSNRNSPAKKQKLIKSKQTLSSNDWDQPNK-----------KSKL-----QDRD 194
+ + ++ N + KL +Q L +P K K+ +
Sbjct: 122 DNQVFAKYNVSRLQPYLKL---RQALLE---LRPAKNVLIDGVLGSGKTWVALDVCLSYK 175
Query: 195 L-CNGPSKL-------CISMDITIEYLNKRHICESEEMWVQDLDCESNITI-VESSRIGI 245
+ C K+ C S + +E L K + + W D SNI + + S + +
Sbjct: 176 VQCKMDFKIFWLNLKNCNSPETVLEMLQKLLY-QIDPNWTSRSDHSSNIKLRIHSIQAEL 234
Query: 246 GDFAKEWKAK--LLRFYILGNKCVSKTDKKMESQMLSC 281
K + LL +L N +K LSC
Sbjct: 235 RRLLKSKPYENCLL---VLLNVQNAKAWNAFN---LSC 266
Score = 35.2 bits (80), Expect = 0.021
Identities = 38/290 (13%), Positives = 78/290 (26%), Gaps = 106/290 (36%)
Query: 33 ALLGKYL------VRRLSCGT--LLIGKIVETESYLGVEDRASHSYNNRRTPRNEPM--- 81
+LL KYL + R T + I E+ + D + ++N + + +
Sbjct: 305 SLLLKYLDCRPQDLPREVLTTNPRRLSIIAES-----IRDGLAT-WDNWKHVNCDKLTTI 358
Query: 82 ------YMKPGTIYVYFTYGMYHCF----NLSSQESGGAVLIR---SLEPVHGLDIMNRL 128
++P F F ++ + +L + + ++N+L
Sbjct: 359 IESSLNVLEPAEYRKMFD--RLSVFPPSAHIPTI-----LLSLIWFDVIKSDVMVVVNKL 411
Query: 129 RNQFNENQNKSKRNNHLPNSQNNEETHS---------QSNRNSPAKKQKLIKSKQTLSSN 179
S L Q E T S N A + ++ +
Sbjct: 412 -------HKYS-----LVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTF 459
Query: 180 DWDQPNK-------------------------------------KSKL-QDRDLCNGPSK 201
D D + K+ D N
Sbjct: 460 DSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGS 519
Query: 202 LCISMDITIEYLNKRHICESE---EMWVQDL-----DCESNITIVESSRI 243
+ ++ Y K +IC+++ E V + E N+ + + +
Sbjct: 520 ILNTLQQLKFY--KPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDL 567
>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 = 32.3 bits (73), Expect = 0.19
Identities = 49/269 (18%), Positives = 78/269 (28%), Gaps = 83/269 (30%)
Query: 18 LDQAFFDQPCIDLANALLGKYLV------------RRLSCGTLLIGKIVETESYLGVEDR 65
L P I + L Y+V R G + + T + D
Sbjct: 231 LLSIPISCPLIGVIQ--LAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDS 288
Query: 66 ASHSYNNRRTPRNEPMYMKPGTIYVYFTYGMYHC---FNLSSQESGGAVLIRSLEPVHG- 121
+ + R I V F G C + +S ++L SLE G
Sbjct: 289 WESFFVSVRK-----------AITVLFFIG-VRCYEAYPNTSLPP--SILEDSLENNEGV 334
Query: 122 ----LDIMNRLRNQFNENQNKSKRNNHLPNSQNNEETH-SQSNRNSP------------- 163
L I N + Q + NK N+HLP S N
Sbjct: 335 PSPMLSISNLTQEQVQDYVNK--TNSHLP-----AGKQVEISLVNGAKNLVVSGPPQSLY 387
Query: 164 AKKQKLIKSKQTLSSNDWDQPNKKSKLQDRDLCNGPSKLCISMD---ITI----EYLNKR 216
L K+K + + DQ + +R KL S + L
Sbjct: 388 GLNLTLRKAK---APSGLDQ--SRIPFSER-------KLKFSNRFLPVASPFHSHLLV-- 433
Query: 217 HICESEEMWVQDLDCESNITIVESSRIGI 245
+ ++ +DL ++N++ + I I
Sbjct: 434 ---PASDLINKDLV-KNNVSF-NAKDIQI 457
Score = 32.3 bits (73), Expect = 0.20
Identities = 12/58 (20%), Positives = 16/58 (27%), Gaps = 13/58 (22%)
Query: 86 GTIYVYF-----TYGMYHCFNLSSQESGGAVLIRSLEPV--------HGLDIMNRLRN 130
G YF Y YH + L + GL+I+ L N
Sbjct: 164 GNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLEN 221
Score = 28.9 bits (64), Expect = 2.7
Identities = 28/150 (18%), Positives = 55/150 (36%), Gaps = 35/150 (23%)
Query: 110 AVLIRSLEPVHGLDIMNRLRNQFNENQNKSKRNNHLPNSQNNEETHS------QSNRNSP 163
+ L+ + ++N +F N +L + N+ H+ Q N +
Sbjct: 69 SSLVEPSKVGQFDQVLNLCLTEFE--------NCYL---EGND-IHALAAKLLQENDTTL 116
Query: 164 AKKQKLIKS--KQTLSSNDWDQPNKKSKLQDRDLCNGPSKLCISMDITI--------EYL 213
K ++LIK+ + + S L R + G ++L + I +Y
Sbjct: 117 VKTKELIKNYITARIMAKRPFDKKSNSAL-FRAVGEGNAQL-----VAIFGGQGNTDDYF 170
Query: 214 NK-RHICESEEMWVQDLDCESNITIVESSR 242
+ R + ++ + V DL S T+ E R
Sbjct: 171 EELRDLYQTYHVLVGDLIKFSAETLSELIR 200
>2k53_A A3DK08 protein; NESG, CMR9, structural genomics, PSI-2, protein
structure initiative; NMR {Clostridium thermocellum atcc
27405}
Length = 76
Score = 26.7 bits (59), Expect = 2.2
Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 11/70 (15%)
Query: 79 EPMYMKPGTIYVYFTYGMYHCFN--LSSQESGGAVLIRSLEPVHGLDIMNRLRNQFNE-- 134
+ + M GT ++ GM HC S ES I VHG+D ++L + NE
Sbjct: 11 DVLQMDRGTAPIFINNGM-HCLGCPSSMGES-----IEDACAVHGIDA-DKLVKELNEYF 63
Query: 135 NQNKSKRNNH 144
+ + ++H
Sbjct: 64 EKKEVLEHHH 73
>3t7k_A RTT107, regulator of TY1 transposition protein 107; BRCT, DNA
repair, phospho-peptide, protein binding; HET: SEP;
2.03A {Saccharomyces cerevisiae} PDB: 3t7j_A* 3t7i_A
Length = 256
Score = 26.6 bits (58), Expect = 8.1
Identities = 16/89 (17%), Positives = 35/89 (39%), Gaps = 4/89 (4%)
Query: 98 HCFNLSSQESGGAVLIRSLEPVHGLDIMNRLRNQFNENQNKSKRNNHLPNSQNNEETHSQ 157
C NL + GG I S+ HG++ +N LR++ ++ + + +
Sbjct: 142 RCINLVNDIPGGVDTIGSVLKAHGIEKINVLRSKKCTFEDIIPNDVSKQENGGIFKYVLI 201
Query: 158 SNRNSPAKKQKLIKSKQTLSSN----DWD 182
+ S KK + + + + +W+
Sbjct: 202 VTKASQVKKFTKLINDRDKNETILIVEWN 230
>2k5e_A Uncharacterized protein; helix protein, structural genomic,
structural genomics, PSI-2, protein structure
initiative; NMR {Methanococcus jannaschii}
Length = 73
Score = 25.1 bits (55), Expect = 8.4
Identities = 12/68 (17%), Positives = 24/68 (35%), Gaps = 9/68 (13%)
Query: 79 EPMYMKPGTIYVYFTYGMYHCFN--LSSQESGGAVLIRSLEPVHGLDIMNRLRNQFNENQ 136
+ + PG V +Y + C + ES + HGL++ + N
Sbjct: 13 QALQTHPGVAGVLRSYNL-GCIGCMGAQNES-----LEQGANAHGLNV-EDILRDLNALA 65
Query: 137 NKSKRNNH 144
+ ++H
Sbjct: 66 LEHHHHHH 73
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
0.316 0.131 0.389
Gapped
Lambda K H
0.267 0.0521 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,919,680
Number of extensions: 210084
Number of successful extensions: 389
Number of sequences better than 10.0: 1
Number of HSP's gapped: 386
Number of HSP's successfully gapped: 13
Length of query: 281
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 189
Effective length of database: 4,133,061
Effective search space: 781148529
Effective search space used: 781148529
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: 57 (26.2 bits)