RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14488
(368 letters)
>2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily,
SH3-like domain, produc structure, DNA damage, DNA
repair, exonuclease; HET: TMP; 1.50A {Escherichia coli}
SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A 3hl8_A*
3hp9_A*
Length = 482
Score = 171 bits (433), Expect = 4e-49
Identities = 110/371 (29%), Positives = 193/371 (52%), Gaps = 12/371 (3%)
Query: 1 MFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNN 60
+F+RN +PY W+++ SRWDL++V++A Y L P GI WP ++G PSF+LEHL+ N
Sbjct: 115 IFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANG 174
Query: 61 LSHKKAHDALSDVRATLGLARLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITH 120
+ H AHDA++DV AT+ +A+L++ PRLF+++ + R K ++A I P +P +++
Sbjct: 175 IEHSNAHDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSG 234
Query: 121 MFSSKHSYISLMWPICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFK--E 178
MF + S + P+ HP N+N +I +L D L D + +R+ L K
Sbjct: 235 MFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNA 294
Query: 179 DIPISMIHLNRSPIVISNLKVLSSNLMFRYKFDLNCAFKNIKCASSILNNTYIWKKIFLD 238
+P+ ++H+N+ P++ + + + +N N K + +
Sbjct: 295 AVPVKLVHINKCPVLAQANTLRPED---ADRLGINRQHCLDNLKILRENPQVREKVVAIF 351
Query: 239 YKINNSDLELNIDEELYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKKLEELIFLYR 298
+ N+D +LYN F S D + I+ P+ L ++ F +K++E+L+F YR
Sbjct: 352 AEAEPFTPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYR 411
Query: 299 ARNFIETLSYKELKRWKKYRISRFYNKKNNLYNINMFYLEIESLLKKA--NEHDTKILNA 356
ARNF TL Y E +RW ++R F + + + E++ L+++ ++ +L A
Sbjct: 412 ARNFPGTLDYAEQQRWLEHRRQVFTPE-----FLQGYADELQMLVQQYADDKEKVALLKA 466
Query: 357 LLMYGKSITQK 367
L Y I +
Sbjct: 467 LWQYADEIVEH 477
>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 = 56.0 bits (134), Expect = 1e-08
Identities = 55/360 (15%), Positives = 110/360 (30%), Gaps = 107/360 (29%)
Query: 21 WDLINVIKAF------YVLSPY-GITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDV 73
+ AF + + + +T L+H S L+ + L
Sbjct: 254 QNA-KAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHS--MTLTPDEVKSLLLKY 310
Query: 74 RATLG-----LARLIRNNNPRLFNFI-LSLRKKKYVLAEIGWPIARPFFY-------ITH 120
L L R + NPR + I S+R +A + +T
Sbjct: 311 ---LDCRPQDLPREVLTTNPRRLSIIAESIRD----------GLATWDNWKHVNCDKLTT 357
Query: 121 MFSS----------KHSYISLMWPICIHPMNKNI----L-ITWNLLHDPKKFLLNDI-NK 164
+ S + + L + P + +I L + W D K + + NK
Sbjct: 358 IIESSLNVLEPAEYRKMFDRLS----VFPPSAHIPTILLSLIWF---DVIKSDVMVVVNK 410
Query: 165 IRDYLCFKKNSFKEDIPISMIHLNRSPIVISNLKVLSSNLMFRYKFDLNCAFKNIKCASS 224
+ Y +K + I I I+L + + N L +++ Y + F +
Sbjct: 411 LHKYSLVEKQPKESTISIPSIYL-ELKVKLENEYALHRSIVDHYN--IPKTFDSDDLIPP 467
Query: 225 ILNNTYIW-------------------KKIFLDY-----KINNSDLELN---------ID 251
L+ Y + + +FLD+ KI + N
Sbjct: 468 YLDQ-YFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQ 526
Query: 252 EELYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKKLEELIFLYRARNFIE-TLSYKE 310
+ Y +I D ++ ++ ++F K+EE + + + + L ++
Sbjct: 527 LKFYKPYICDNDPKYERLVNAI-------LDFLP---KIEENLICSKYTDLLRIALMAED 576
Score = 38.3 bits (88), Expect = 0.004
Identities = 59/424 (13%), Positives = 125/424 (29%), Gaps = 140/424 (33%)
Query: 25 NVIKAFY--VLSP-YGITW-PYKNNGK-PSFKLE-HLSFVNNLSHKKAHDALSDVRATLG 78
+++ F VL Y P K + PS ++ + L +D +
Sbjct: 77 EMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLY--------NDNQ---- 124
Query: 79 LARLIRNNNPR------LFNFILSLRKKKYV------------LA-----EIGWPIARPF 115
+ N R L +L LR K V +A F
Sbjct: 125 --VFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF 182
Query: 116 --FYITHMFSSKHSYISLM---WPICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLC 170
F++ + +S +++ + + ++ N W D + I+ I+ L
Sbjct: 183 KIFWLN--LKNCNSPETVLEMLQKLL-YQIDPN----WTSRSDHSSNIKLRIHSIQAEL- 234
Query: 171 FKKNSFKE-DIPISMIHLNRSPIVISNLKVLSSNLMFRYKFDLNCAF----KNIKCASSI 225
+ K ++ L + N K ++ F+L+C + + +
Sbjct: 235 --RRLLKSKPYENCLLVLLN----VQNAKAWNA-------FNLSCKILLTTRFKQVTDFL 281
Query: 226 LNNTYIWKKIFLDYKINNSDLELNIDE--ELYNNFIS-KKDNLK--------LAILRSMS 274
T I LD + + L DE L ++ + +L + S+
Sbjct: 282 SAATT--THISLD----HHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRL--SII 333
Query: 275 PKKLSNVNFCFEN------KKLEELIFLYRARNFIETLSYKELKR--------------- 313
+ + + ++N KL +I + + L E ++
Sbjct: 334 AESIRDGLATWDNWKHVNCDKLTTII-----ESSLNVLEPAEYRKMFDRLSVFPPSAHIP 388
Query: 314 -------W--KKYR-----ISRFYNK-------KNNLYNINMFYLEIESLLKKANEHDTK 352
W +++ + K + +I YLE++ L+
Sbjct: 389 TILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRS 448
Query: 353 ILNA 356
I++
Sbjct: 449 IVDH 452
Score = 34.4 bits (78), Expect = 0.067
Identities = 32/242 (13%), Positives = 69/242 (28%), Gaps = 69/242 (28%)
Query: 1 MFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNN 60
+ W ++I N ++ L+ +S I K + + L H S V++
Sbjct: 394 LIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL-HRSIVDH 452
Query: 61 LSHKKAHDALSDVRATLGLARLIRNNN---PRLFNFILSLRKKKYVLAEIGWPIARPFFY 117
+ K D +++ P L + + +
Sbjct: 453 YNIPKTFD----------------SDDLIPPYLDQYF--------------------YSH 476
Query: 118 IT-HMFSSKHS---------YISLMWPICIHPMNKNILITWNLLHDPKKFL--LNDINKI 165
I H+ + +H ++ + + + I + L L +
Sbjct: 477 IGHHLKNIEHPERMTLFRMVFLDFRF------LEQKIRHDSTAWNASGSILNTLQQLKFY 530
Query: 166 RDYLCFKKNSFKE---DI----PISMIHLNRSPIVISNLKVLSSNLMFRYKFDLNCAFKN 218
+ Y+C ++ I P +L S +L LM + A K
Sbjct: 531 KPYICDNDPKYERLVNAILDFLPKIEENLICSK----YTDLLRIALMAEDEAIFEEAHKQ 586
Query: 219 IK 220
++
Sbjct: 587 VQ 588
Score = 34.1 bits (77), Expect = 0.090
Identities = 30/158 (18%), Positives = 67/158 (42%), Gaps = 31/158 (19%)
Query: 230 YIWKKIFLDYKIN-NSDLELNIDEELYNNFISKKDNLKLAILRSMSPKKLSNVNF-CFEN 287
Y +K I ++ + + +++ + +SK++ + I+ S + F +
Sbjct: 16 YQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEE-ID-HIIMSKDAVSGTLRLFWTLLS 73
Query: 288 KKLEELIFLYRARNFIETL---SYKELK-RWK-----KYRISRFYN-KKNNLYNIN-MF- 335
K+ EE++ + F+E + +YK L K ++R Y +++ LYN N +F
Sbjct: 74 KQ-EEMV-----QKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFA 127
Query: 336 ---------YLEIESLLKKANEHDTKILNALLMYGKSI 364
YL++ L + +++ +L GK+
Sbjct: 128 KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTW 165
>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 = 51.6 bits (123), Expect = 3e-07
Identities = 44/240 (18%), Positives = 77/240 (32%), Gaps = 109/240 (45%)
Query: 21 WD--LINVIKA----FYV------------LSPYGITWPYKNN-GKPSFKLEHLSFVNNL 61
W+ ++V KA F++ L P + +NN G PS L ++NL
Sbjct: 289 WESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLS----ISNL 344
Query: 62 SHKKAHDALSDVRATLGLARLIR---NNNPR----------LFNFILSLRKKKYVLAEIG 108
+ ++ D ++ + L + + N + L+ L+LRK K A G
Sbjct: 345 TQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAK---APSG 401
Query: 109 W-------------------PIARPFFYITHMFSSKHSYISLMWPICIHPMNKNILITWN 149
P+A PF HS +
Sbjct: 402 LDQSRIPFSERKLKFSNRFLPVASPF----------HS---------------------H 430
Query: 150 LLHDPKKFLLNDINKIRDYLCFKKNSFKEDIPISMIHLNRSPIVI-----SNLKVLSSNL 204
LL + D+ +++ + F + IP V S+L+VLS ++
Sbjct: 431 LLVPASDLINKDL--VKNNVSFNAKDIQ--IP-----------VYDTFDGSDLRVLSGSI 475
Score = 28.1 bits (62), Expect = 5.5
Identities = 23/138 (16%), Positives = 39/138 (28%), Gaps = 46/138 (33%)
Query: 253 ELYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKKLEELIFLYRARNFIETLSYKELK 312
+LY + +D A S ++ N L +
Sbjct: 1634 DLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPV--NLTIHFGGE------------ 1679
Query: 313 RWKKYRISRFYNKKNNLYNINMFY-------LEIESLLKKANEHDTKI--------LN-- 355
K RI Y+ M + L+ E + K+ NEH T L+
Sbjct: 1680 --KGKRIRENYSA--------MIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSAT 1729
Query: 356 -----ALLMYGKSITQKI 368
AL + K+ + +
Sbjct: 1730 QFTQPALTLMEKAAFEDL 1747
>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics,
exonuclease, PSI-2, protein structure initiative; HET:
DNA; 2.50A {Thermotoga maritima MSB8}
Length = 186
Score = 30.2 bits (69), Expect = 0.79
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 48 PSFKLEHLSFVNNLSHKKAHDALSDVRAT 76
S+ L+ + L + H AL D R T
Sbjct: 137 RSYSLDSVVEKLGLGPFRHHRALDDARVT 165
>3u3y_B Three prime repair exonuclease 1; RNAse H fold, 3' exonuclease,
homodimer, hydrolase-DNA compl; HET: BU1; 2.28A {Mus
musculus} PDB: 3u6f_B*
Length = 314
Score = 30.5 bits (68), Expect = 0.80
Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 3/55 (5%)
Query: 24 INVIKAFYVLSPYGITWPYKNNGKPSFKLEHL-SFVNNLSHKKAHDALSDVRATL 77
++ I A L + P N + S+ L + + + + +H A V L
Sbjct: 153 VDSIAALKALEQ--ASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGHVLTLL 205
>3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline
type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus
musculus} PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A*
3b6p_A* 2o4i_A 2oa8_A
Length = 242
Score = 29.6 bits (66), Expect = 1.5
Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 3/55 (5%)
Query: 24 INVIKAFYVLSPYGITWPYKNNGKPSFKLEHL-SFVNNLSHKKAHDALSDVRATL 77
++ I A L + P N + S+ L + + + + +H A D L
Sbjct: 153 VDSIAALKALEQ--ASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDDLTLL 205
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo
sapiens} SCOP: c.55.3.5
Length = 238
Score = 28.7 bits (64), Expect = 2.5
Identities = 9/38 (23%), Positives = 12/38 (31%), Gaps = 1/38 (2%)
Query: 41 PYKNNGKPSFKLEHL-SFVNNLSHKKAHDALSDVRATL 77
+ G+ + L L AH A DV L
Sbjct: 163 GTRARGRQGYSLGSLFHRYFRAEPSAAHSAEGDVHTLL 200
>3tr8_A Oligoribonuclease; transcription, hydrolase; 2.50A {Coxiella
burnetii}
Length = 186
Score = 28.3 bits (62), Expect = 3.4
Identities = 13/89 (14%), Positives = 33/89 (37%), Gaps = 7/89 (7%)
Query: 2 FWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNL 61
F ++ + N D + + L+ + + Y++ + K+ + +
Sbjct: 95 FLEKYVSAGKSPLCGNSVCQDRRFLSRYMPRLNQF---FHYRHLDVTTLKILAQRWAPQI 151
Query: 62 SH----KKAHDALSDVRATLGLARLIRNN 86
+ + H AL D+R ++ R R +
Sbjct: 152 AAAHIKESQHLALQDIRDSIEELRYYRAH 180
>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, hydrolase;
2.30A {Xanthomonas campestris PV}
Length = 194
Score = 27.1 bits (59), Expect = 7.7
Identities = 19/90 (21%), Positives = 29/90 (32%), Gaps = 7/90 (7%)
Query: 1 MFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHL----S 56
F I N D + + L Y + Y+N + K +
Sbjct: 94 AFLGEWIRAGASPMCGNSICQDRRFLHRQMSRLERY---FHYRNLDVSTIKELARRWAPA 150
Query: 57 FVNNLSHKKAHDALSDVRATLGLARLIRNN 86
+ + AH ALSDVR ++ R R
Sbjct: 151 VASGFAKSSAHTALSDVRDSIDELRHYRQF 180
>3a79_B TLR6, VLRB.59, TOLL-like receptor 6, variable lymphocyte recepto;
diacyl lipopeptide, innate immunity, Leu repeat, cell
membrane, cytoplasmic vesicle; HET: PXS NAG BMA NDG;
2.90A {Mus musculus}
Length = 562
Score = 27.5 bits (61), Expect = 8.3
Identities = 24/212 (11%), Positives = 58/212 (27%), Gaps = 14/212 (6%)
Query: 128 YISLMWPICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFKEDIPISMIHL 187
+I + N +L + +N +L ++ ++
Sbjct: 182 HIKGGETESLQIPNTTVLHLVFHPNSLFSVQVNMSVNALGHLQLSNIKLNDENCQRLMTF 241
Query: 188 NRSPIVISNLKVLSSNLMFRYKFDLNCAFKNIKCAS----SILNNTYIWKKIFLDYKINN 243
L ++ + F+ +I N T + ++ +
Sbjct: 242 LSELTRGPTLLNVTLQHIETTWKCSVKLFQFFWPRPVEYLNIYNLTITERIDREEFTYSE 301
Query: 244 SDLELNIDEELYNNFISKKDNLKLAILRSMSPKKLSNVN------FCFENKKLEELIFLY 297
+ L+ + E + N ++ M+ K LS + C FL
Sbjct: 302 TALKSLMIEHVKNQVFLFSKEALYSVFAEMNIKMLSISDTPFIHMVCP--PSPSSFTFLN 359
Query: 298 RARNFIETLSYKELKRWKKYRISRFYNKKNNL 329
+N ++ K+ + ++N L
Sbjct: 360 FTQNVFTDSVFQGCSTLKR--LQTLILQRNGL 389
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A
{Homo sapiens}
Length = 349
Score = 27.3 bits (60), Expect = 8.8
Identities = 9/75 (12%), Positives = 20/75 (26%), Gaps = 18/75 (24%)
Query: 18 CSRWDLINVIKAFYVLSPYGITWP---------------YKNNGKPSFKLEHLSFVNNLS 62
WD+ + L + +P + + KL + +
Sbjct: 230 DGSWDMSKFLNIQCQL--SRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMD 287
Query: 63 HK-KAHDALSDVRAT 76
+ + H L D +
Sbjct: 288 YDGRPHCGLDDSKNI 302
>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A
{Homo sapiens} SCOP: c.55.3.5
Length = 204
Score = 27.1 bits (60), Expect = 9.0
Identities = 9/75 (12%), Positives = 20/75 (26%), Gaps = 18/75 (24%)
Query: 18 CSRWDLINVIKAFYVLSPYGITWP---------------YKNNGKPSFKLEHLSFVNNLS 62
WD+ + L + +P + + KL + +
Sbjct: 112 DGSWDMSKFLNIQCQL--SRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMD 169
Query: 63 HK-KAHDALSDVRAT 76
+ + H L D +
Sbjct: 170 YDGRPHCGLDDSKNI 184
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
0.324 0.139 0.429
Gapped
Lambda K H
0.267 0.0570 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,637,726
Number of extensions: 333453
Number of successful extensions: 891
Number of sequences better than 10.0: 1
Number of HSP's gapped: 879
Number of HSP's successfully gapped: 61
Length of query: 368
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 273
Effective length of database: 4,049,298
Effective search space: 1105458354
Effective search space used: 1105458354
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 (21.5 bits)
S2: 58 (26.5 bits)