RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14489
(284 letters)
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition,
helix-coil dynamics, inhibitor design, complex
(polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP:
a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A*
1taq_A*
Length = 832
Score = 354 bits (912), Expect = e-117
Identities = 94/279 (33%), Positives = 146/279 (52%), Gaps = 9/279 (3%)
Query: 2 QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61
+ +LLVDG YR F+AL + PV A+YG K L K K + +FDAK
Sbjct: 11 KGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALK-EDGDAVIVVFDAK 69
Query: 62 GKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQA 121
+FR+ Y YKA R P + Q+ LI ++V +G L + G EADDV+ +LAK+A
Sbjct: 70 APSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKA 129
Query: 122 VTKHNLKVIISTNDKDMAQLVSNKIALIN-NNKIHDRTTIISRFGVSPEKIVDYFSLIGD 180
K +V I T DKD+ QL+S++I +++ + + ++G+ P++ DY +L GD
Sbjct: 130 -EKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWADYRALTGD 188
Query: 181 MSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTI 240
SDNLPGVK IG KTA KLL ++ SLE ++ N + +K I + + ++ L + +
Sbjct: 189 ESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIREKILAHMDDLKLSWDLAKV 248
Query: 241 KTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKL 279
+TD L + + D + L + + L
Sbjct: 249 RTDLPLE------VDFAKRREPDRERLRAFLERLEFGSL 281
>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage
T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A
Length = 290
Score = 284 bits (729), Expect = 2e-96
Identities = 49/280 (17%), Positives = 105/280 (37%), Gaps = 23/280 (8%)
Query: 2 QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61
+ L++VDG++ +R + + ++ L K+Y A + D
Sbjct: 18 RRNLMIVDGTNLGFRFKHNNS--------KKPFASSYVSTIQSLAKSYSARTTIVLGDKG 69
Query: 62 GKNFRNILYPSYKATRKKMPYNLILQINLIHQM----------VKAIGWPILIIKGVEAD 111
FR P YK R + + + + + +P I+GVEAD
Sbjct: 70 KSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEAD 129
Query: 112 DVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN--NNKIHDRTTIISRFGVSP- 168
D+ + K V + + D D L+++K++ + + + + V
Sbjct: 130 DMAAYIVKLI-GHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDV 188
Query: 169 EKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGV-IGKNLRFA 227
E+ + +++GD+ DN+ GV+ IG K ++ ++ ++ +II+ +NL +
Sbjct: 189 EQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNAS 248
Query: 228 LNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLL 267
L + ++ + T C V ++
Sbjct: 249 EELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIA 288
>3h7i_A Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonuclease,
hydrolase, endonuclease; 1.50A {Enterobacteria phage T4}
PDB: 2ihn_A 3h8w_A 3h8j_A 1tfr_A 3h8s_A
Length = 305
Score = 122 bits (308), Expect = 2e-33
Identities = 48/294 (16%), Positives = 88/294 (29%), Gaps = 21/294 (7%)
Query: 1 MQNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALY----GTIKMLRKLYKNYRATYIAC 56
+ + L+D S + + + + + +IK K K T I
Sbjct: 11 YKEGICLIDFSQIALSTALV--NFPDKEKINLSMVRHLILNSIKFNVKKAKTLGYTKIVL 68
Query: 57 IFDAKGKN-FRNILYPSYKATRKKMPYNL--------ILQINLIHQMVKAIGWPILIIKG 107
D +R YK R K +I ++ + + ++ I
Sbjct: 69 CIDNAKSGYWRRDFAYYYKKNRGKAREESTWDWEGYFESSHKVIDELKAYMPYIVMDIDK 128
Query: 108 VEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVS 167
EA+D I L K+ + K++I ++D D QL + + S
Sbjct: 129 YEANDHIAVLVKKF-SLEGHKILIISSDGDFTQLHKYPNVKQWSPM---HKKWVKIKSGS 184
Query: 168 PEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFA 227
E L GD DN+ VK ++ + +
Sbjct: 185 AEIDCMTKILKGDKKDNVASVKVRSDFWFTRVEGERTPSMKTSIVEAIANDREQAKVLLT 244
Query: 228 LNWLPKLKKILTIKTDCDLTKNIVS--IPESLILQPKDEKLLMQLFNKYKLNKL 279
+ + K+ L + + NI S + + + F K L+KL
Sbjct: 245 ESEYNRYKENLVLIDFDYIPDNIASNIVNYYNSYKLPPRGKIYSYFVKAGLSKL 298
>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 = 55.2 bits (132), Expect = 9e-09
Identities = 44/300 (14%), Positives = 96/300 (32%), Gaps = 78/300 (26%)
Query: 10 GSSCIYRAFYALPDIRNIDNFPVGALY----------GTIKMLRKLYKNYRATYIACIFD 59
G + + A + + ++ML+KL I +
Sbjct: 162 GKTWV--ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQ-----IDPNWT 214
Query: 60 AKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAK 119
++ + NI + + L+ L++ +V
Sbjct: 215 SRSDHSSNIKLRIHSIQAELR--RLLKS----KPYENC-----LLV----LLNV---QNA 256
Query: 120 QAVTKHNL--KVIISTNDKDMAQLVSN----KIALINNNKIHDRTTIISRFGVSPEKIVD 173
+A NL K++++T K + +S I+L +++ ++P+++
Sbjct: 257 KAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSM-----------TLTPDEVKS 305
Query: 174 YFSLIGDMS-DNLPG-VKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFA---- 227
D +LP V P + ++ + S+ + + +N K V L
Sbjct: 306 LLLKYLDCRPQDLPREVLTTNP-RRLSIIAE--SIRDGLATWDNWKHVNCDKLTTIIESS 362
Query: 228 LNWLP-----KLKKILTIKTDCDLTKNIVSIPESLI------LQPKDEKLLMQLFNKYKL 276
LN L K+ L++ + IP L+ + D +++ +KY L
Sbjct: 363 LNVLEPAEYRKMFDRLSV-----FPPS-AHIPTILLSLIWFDVIKSDVMVVVNKLHKYSL 416
Score = 50.2 bits (119), Expect = 4e-07
Identities = 47/276 (17%), Positives = 92/276 (33%), Gaps = 68/276 (24%)
Query: 39 IKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKK-----MPYNL--------I 85
+ ++ + ++ AT+ N++++ + P +
Sbjct: 330 LSIIAESIRDGLATW---------DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV 380
Query: 86 LQINL-IHQMVKAIGWPILIIKGVEADDVIGTLAKQA-VTKHNLKVIISTND--KDMAQL 141
+ I ++ ++ W +I V V+ L K + V K + IS ++
Sbjct: 381 FPPSAHIPTILLSLIWFDVIKSDVM--VVVNKLHKYSLVEKQPKESTISIPSIYLELKVK 438
Query: 142 VSNKIALINNNKIHDRTTIISRF---GVSPEKIVDYF-SLIG---------DMSDNLPGV 188
+ N+ AL + I D I F + P + YF S IG + V
Sbjct: 439 LENEYAL--HRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMV 496
Query: 189 --------KKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKN-------LRFALNWLPK 233
+KI + N S+ N + K I N + L++LPK
Sbjct: 497 FLDFRFLEQKI--RHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPK 554
Query: 234 LKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQ 269
+++ L DL + + L +DE + +
Sbjct: 555 IEENLICSKYTDLLR--------IALMAEDEAIFEE 582
Score = 34.1 bits (77), Expect = 0.051
Identities = 37/229 (16%), Positives = 66/229 (28%), Gaps = 44/229 (19%)
Query: 73 YKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIS 132
++ + Y IL + A + + DV K ++K + II
Sbjct: 9 FETGEHQYQYKDILSVFE-----DAF------VDNFDCKDVQDMP-KSILSKEEIDHIIM 56
Query: 133 TNDKDMAQLVSNKIALINNNKIHDRTT----------IISRFGV---SPEKIVDYFSLIG 179
+ D L L ++ + ++S P + +
Sbjct: 57 SKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYI--- 113
Query: 180 DMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVI-------GKNLRFALNWLP 232
+ D L ++ K V L Y L + K V+ GK W+
Sbjct: 114 EQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK------TWV- 166
Query: 233 KLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKLNF 281
L L+ K C + I + +L E +L L N+
Sbjct: 167 ALDVCLSYKVQCKMDFKIFWL--NLKNCNSPETVLEMLQKLLYQIDPNW 213
Score = 27.5 bits (60), Expect = 6.6
Identities = 20/163 (12%), Positives = 46/163 (28%), Gaps = 41/163 (25%)
Query: 4 TLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIF-DAKG 62
+D + + L +I + + + R ++ ++R F + K
Sbjct: 465 IPPYLDQYFYSHIG-HHLKNIEHPERM---------TLFRMVFLDFR-------FLEQK- 506
Query: 63 KNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAV 122
I + S N + Q+ I + + +
Sbjct: 507 -----IRHDSTAWNASGSILNTLQQLKFYKPY---------ICDNDPKYERLVNAILDFL 552
Query: 123 TKHNLKVIISTNDKDMAQLVSNKIALINNNK--IHDRTTIISR 163
K +I S D+ + IAL+ ++ + + R
Sbjct: 553 PKIEENLICS-KYTDLLR-----IALMAEDEAIFEEAHKQVQR 589
>3q8k_A Flap endonuclease 1; helix-3 turn-helix, hydrophobic wedge, 3' flap
binding site, hydrolase-DNA complex, DNA repair,
replication; HET: DNA; 2.20A {Homo sapiens} PDB: 3q8l_A*
3q8m_A*
Length = 341
Score = 51.4 bits (123), Expect = 1e-07
Identities = 25/104 (24%), Positives = 47/104 (45%), Gaps = 10/104 (9%)
Query: 131 ISTNDKDM----AQLVSNKIALINNNKIH----DRTTIISRFGVSPEKIVDYFSLIGDMS 182
+T D D + ++ + K+ + I+ G++ E+ VD L+G S
Sbjct: 174 AATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLG--S 231
Query: 183 DNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRF 226
D ++ IGPK AV L+ ++ S+E I+ + K + +N
Sbjct: 232 DYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLH 275
>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap
DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A
{Homo sapiens} SCOP: a.60.7.1 c.120.1.2
Length = 379
Score = 51.4 bits (123), Expect = 1e-07
Identities = 44/256 (17%), Positives = 89/256 (34%), Gaps = 49/256 (19%)
Query: 8 VDGSSCIYRAFYALPD----IRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIF----- 58
+D S IY+ A+ ++N + L G ++ +N I ++
Sbjct: 32 IDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENG----IKPVYVFDGK 87
Query: 59 ---------------DAKGKNFRNILYPSYKATRKKMPYNLILQINLIH-----QMVKAI 98
A+ + + + ++++ H ++ +
Sbjct: 88 PPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLM 147
Query: 99 GWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDM----AQLVSNKIALINNNKI 154
G P L EA+ L K +T D D + ++ + K+
Sbjct: 148 GIPYLDAPS-EAEASCAALVKAGKVY-----AAATEDMDCLTFGSPVLMRHLTASEAKKL 201
Query: 155 H----DRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENII 210
+ I+ G++ E+ VD L+G SD ++ IGPK AV L+ ++ S+E I+
Sbjct: 202 PIQEFHLSRILQELGLNQEQFVDLCILLG--SDYCESIRGIGPKRAVDLIQKHKSIEEIV 259
Query: 211 NNANNIKGVIGKNLRF 226
+ K + +N
Sbjct: 260 RRLDPNKYPVPENWLH 275
>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3
turn-helix, hydrophobic wedge, 3' FLA site,
hydrolase-DNA complex; 2.00A {Archaeoglobus fulgidus}
SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A
Length = 336
Score = 50.2 bits (120), Expect = 2e-07
Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 160 IISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINN 212
+ R G++ E+++D L+G +D GVK +G K A+ + Y + +
Sbjct: 214 NLKRLGLTREQLIDIAILVG--TDYNEGVKGVGVKKALNYIKTYGDIFRALKA 264
>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 = 48.9 bits (116), Expect = 1e-06
Identities = 45/297 (15%), Positives = 86/297 (28%), Gaps = 101/297 (34%)
Query: 41 MLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIH---QMVKA 97
M LYK +A +++ +F++ S P NL IH + K
Sbjct: 1631 MGMDLYKTSKA--AQDVWNRADNHFKDTYGFSILDIVINNPVNLT-----IHFGGEKGKR 1683
Query: 98 I--GWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDM-----AQ----LVSNKI 146
I + +I + + + + + +H+ + + Q L+
Sbjct: 1684 IRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLME--K 1741
Query: 147 ALINNNKIHDRTTIISRFGVSPEKIVDYF---SLIG------------DMSDNLPGVKK- 190
A + G+ P F SL G + + V
Sbjct: 1742 AAFE---------DLKSKGLIPAD--ATFAGHSL-GEYAALASLADVMSIESLVEVVFYR 1789
Query: 191 ----------------------IGPKTAVKLLNQYNSLENIINN-----------AN-NI 216
I P +Q +L+ ++ N N+
Sbjct: 1790 GMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQ-EALQYVVERVGKRTGWLVEIVNYNV 1848
Query: 217 KG---VIGKNLRFALNWLPKLKKIL-TIKTDCDLTKNI--VSIPESLILQPKDEKLL 267
+ V +LR AL+ + +L IK + I + + +SL L+ + L
Sbjct: 1849 ENQQYVAAGDLR-ALD---TVTNVLNFIKL-----QKIDIIELQKSLSLEEVEGHLF 1896
Score = 41.2 bits (96), Expect = 4e-04
Identities = 60/361 (16%), Positives = 101/361 (27%), Gaps = 143/361 (39%)
Query: 15 YRAFYALPDIRNIDNFPVGALY-----GTIKM----------------LRKLYKNYRATY 53
A R D AL+ G ++ LR LY+ Y
Sbjct: 127 ITARIMAK--RPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYH-VL 183
Query: 54 IACIFDAKGKNFRNI---------LYP---------SYKATRKKMPY--------NLILQ 87
+ + + + ++ + Y LI
Sbjct: 184 VGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGV 243
Query: 88 INLIHQMV--KAIGW-PILIIKGVEADDVIGTLAK--QAVTKHNLKVI----ISTND--K 136
I L H +V K +G+ P G L + T H+ ++ I+ D +
Sbjct: 244 IQLAHYVVTAKLLGFTP-------------GELRSYLKGATGHSQGLVTAVAIAETDSWE 290
Query: 137 DMAQLVSNKIALINNNKIHDRTTII--------SRFGVSPEKIVDYFSL---IGDMSDNL 185
V I ++ I + P + D SL G S
Sbjct: 291 SFFVSVRKAITVL---------FFIGVRCYEAYPNTSLPPSILED--SLENNEGVPS--- 336
Query: 186 P--GVKKIGPKTAVKLLNQYN-----------SLENIINNANNIKGVI-G--KNLRFALN 229
P + + + +N+ N SL +N A N+ V+ G ++L LN
Sbjct: 337 PMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISL---VNGAKNL--VVSGPPQSLY-GLN 390
Query: 230 -WLPKLKKILTIKTDCDLTKNI---------------VSIPE-SLILQPKDEKLLMQLFN 272
L K K + D ++ I V+ P S +L P + + L
Sbjct: 391 LTLRKAK----APSGLDQSR-IPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVK 445
Query: 273 K 273
Sbjct: 446 N 446
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair,
DNA-binding, endonuclease, metal-BIND excision repair,
DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus
solfataricus}
Length = 346
Score = 46.1 bits (109), Expect = 6e-06
Identities = 19/69 (27%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 160 IISRFGVSPEKIVDYFSLIGDMSD-NLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKG 218
++ + G++ E+++D LIG +D N G++ IGP+ A+K++ +Y +E + K
Sbjct: 212 LLKKLGITREQLIDIGILIG--TDYNPDGIRGIGPERALKIIKKYGKIEKAMEYGEISKK 269
Query: 219 VIGKNLRFA 227
I N+
Sbjct: 270 DINFNIDEI 278
>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA
replication, RTH, RAD27, DNA repair; 2.00A
{Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2
PDB: 1a77_A
Length = 326
Score = 44.4 bits (105), Expect = 2e-05
Identities = 17/95 (17%), Positives = 38/95 (40%), Gaps = 8/95 (8%)
Query: 131 ISTNDKDM-----AQLVSNKIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSD-N 184
+ + D D ++V N ++ + ++ +S + ++D +G +D N
Sbjct: 169 VVSQDYDALLYGAPRVVRNLTTTKEMPELIELNEVLEDLRISLDDLIDIAIFMG--TDYN 226
Query: 185 LPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGV 219
GVK IG K A +L+ + + + +
Sbjct: 227 PGGVKGIGFKRAYELVRSGVAKDVLKKEVEYYDEI 261
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus
amylolyticus}
Length = 363
Score = 44.5 bits (105), Expect = 2e-05
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 160 IISRFGVSPEKIVDYFSLIGDMSDNLP-GVKKIGPKTAVKLLNQYNSLENIINN 212
++ + G++ E ++D L+G +D P G + IGPK A++L+ Y +E I
Sbjct: 229 LLVQLGITLENLIDIGILLG--TDYNPDGFEGIGPKKALQLVKAYGGIEKIPKP 280
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication,
transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1
c.120.1.2 PDB: 1mc8_A
Length = 340
Score = 41.1 bits (96), Expect = 2e-04
Identities = 12/59 (20%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 160 IISRFGVSPEKIVDYFSLIGDMSDNLP-GVKKIGPKTAVKLLNQYNSLENIINNANNIK 217
++ ++ EK+++ L+G +D P G+K IG K A++++ +++
Sbjct: 215 VLKELKLTREKLIELAILVG--TDYNPGGIKGIGLKKALEIVRHSKDPLAKFQKQSDVD 271
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A
{Homo sapiens} PDB: 3qeb_Z* 3qea_Z*
Length = 352
Score = 37.7 bits (87), Expect = 0.003
Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 3/73 (4%)
Query: 164 FGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKN 223
+ EK L G D L ++ IG A K+L N+ + I+ I + N
Sbjct: 208 DVFTEEKFRYMCILSG--CDYLSSLRGIGLAKACKVLRLANNPD-IVKVIKKIGHYLKMN 264
Query: 224 LRFALNWLPKLKK 236
+ +++ +
Sbjct: 265 ITVPEDYINGFIR 277
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase;
HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5
Length = 89
Score = 32.5 bits (74), Expect = 0.029
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 181 MSDNLPGVKKIGPKTAVKLLNQYNSLENIIN 211
+++ L VK + + LL + SLE +I
Sbjct: 17 VTECLTTVKSVNKTDSQTLLTTFGSLEQLIA 47
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA
repair, endonuclease, helix-hairpin-helix, DNA binding
protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5
Length = 91
Score = 31.7 bits (72), Expect = 0.047
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 181 MSDNLPGVKKIGPKTAVKLLNQYNSLENIIN 211
+++ L VK + + LL + SLE +I
Sbjct: 30 VTECLTTVKSVNKTDSQTLLTTFGSLEQLIA 60
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding
domain, homodimer, hydrolase; 1.45A {Pyrococcus
furiosus} SCOP: a.60.2.5
Length = 75
Score = 31.1 bits (71), Expect = 0.063
Identities = 8/29 (27%), Positives = 13/29 (44%), Gaps = 3/29 (10%)
Query: 183 DNLPGVKKIGPKTAVKLLNQYNSLENIIN 211
+ LP V A +LL + S+E +
Sbjct: 17 EGLPHV---SATLARRLLKHFGSVERVFT 42
>1l4a_C S-SNAP25 fusion protein; snare, snare complex, membrane fusion,
neurotransmission, endocytosis/exocytosis complex; 2.95A
{Loligo pealei} SCOP: h.1.15.1
Length = 83
Score = 30.3 bits (68), Expect = 0.17
Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 4/48 (8%)
Query: 189 KKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKK 236
K+ G +T V L Q L+ I + I ++++ A L ++K
Sbjct: 40 KEAGIRTLVMLDEQGEQLDRIEEGLDQIN----QDMKDAEKNLEGMEK 83
>1n7s_C SNAP-25A; neuronal snare protein complex, four helix bundle,
transport protein; 1.45A {Rattus norvegicus} SCOP:
h.1.15.1 PDB: 1sfc_C 1urq_C 3hd7_C* 3hd9_C 3ipd_C 3rk2_C
3rk3_C 3rl0_C 1kil_C 1jth_A
Length = 79
Score = 29.1 bits (65), Expect = 0.38
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 4/48 (8%)
Query: 189 KKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKK 236
K G +T V L Q L+ + N+I ++++ A L L K
Sbjct: 36 KDAGIRTLVMLDEQGEQLDRVEEGMNHIN----QDMKEAEKNLKDLGK 79
>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin
helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB:
2nrv_A 2nrw_A 2nrx_A 2nrz_A
Length = 220
Score = 30.2 bits (69), Expect = 0.64
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 183 DNLPGVKKIGPKTAVKLLNQYNSLENI 209
DN+PG IGP KL+ + SLENI
Sbjct: 171 DNVPG---IGPIRKKKLIEHFGSLENI 194
>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision
repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA
excision; 1.90A {Bacillus stearothermophilus}
Length = 226
Score = 29.8 bits (68), Expect = 0.84
Identities = 9/27 (33%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 183 DNLPGVKKIGPKTAVKLLNQYNSLENI 209
D++PG +G K LLN + S++ +
Sbjct: 176 DDIPG---VGEKRKKALLNYFGSVKKM 199
>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural
genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}
Length = 263
Score = 28.5 bits (64), Expect = 2.5
Identities = 16/93 (17%), Positives = 35/93 (37%), Gaps = 8/93 (8%)
Query: 129 VIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGV 188
I+ T++ DM L A + S ++++ + G+ +D L +
Sbjct: 178 GILVTHELDMLNLYKEYKAYFLVGN------RLQGPI-SVSELLESSIVEGERNDALLVL 230
Query: 189 KKIGPKTAVKLLNQYNSLENIINNANNIKGVIG 221
+ K ++ + + + N I G+IG
Sbjct: 231 DIMDKKVSI-VKGDLGMKFGALGSLNRIYGIIG 262
>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 = 3.5
Identities = 9/40 (22%), Positives = 15/40 (37%), Gaps = 17/40 (42%)
Query: 1 MQNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIK 40
+Q +L L YA D + P A+ T++
Sbjct: 25 LQASLKL-----------YA-DD-----SAPALAIKATME 47
>3maj_A DNA processing chain A; MCSG, PSI-2, structural genomics, protein
structure initiati midwest center for structural
genomics; HET: DNA; 2.05A {Rhodopseudomonas palustris}
Length = 382
Score = 28.0 bits (63), Expect = 4.0
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 185 LPGVKKIGPKTAVKLLNQYNSLENI 209
L + +GP+T L+N + S
Sbjct: 28 LIRAENVGPRTFRSLINHFGSARAA 52
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
0.322 0.139 0.401
Gapped
Lambda K H
0.267 0.0558 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,194,367
Number of extensions: 252637
Number of successful extensions: 626
Number of sequences better than 10.0: 1
Number of HSP's gapped: 605
Number of HSP's successfully gapped: 37
Length of query: 284
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 191
Effective length of database: 4,105,140
Effective search space: 784081740
Effective search space used: 784081740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (26.1 bits)