RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11827
(336 letters)
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A
{Homo sapiens} PDB: 3qeb_Z* 3qea_Z*
Length = 352
Score = 253 bits (646), Expect = 2e-82
Identities = 124/292 (42%), Positives = 187/292 (64%), Gaps = 6/292 (2%)
Query: 1 MKYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHL 60
MK+++MLL+H IK I+VFDG LP+K+ E RR++R ++ K +LL + SEA+
Sbjct: 60 MKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLREGKVSEARECF 119
Query: 61 RQSVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGA 120
+S+++TH MA VI+A R++GVDC+VAP+EADAQ+AYLN AG +ITEDS LL FG
Sbjct: 120 TRSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAIITEDSALLAFGC 179
Query: 121 KKIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKA 180
KK+I K+D GN +D+ +L ++ FT+ KFRYMCILSGCDY + ++G+GL KA
Sbjct: 180 KKVILKMDQFGNGLEIDQARLGMCRQLGD-VFTEEKFRYMCILSGCDYLSSLRGIGLAKA 238
Query: 181 KDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFHNTNLMFLYQPVYDPVSKEVV 240
+ +PD ++KI Y K+ + + ++++ F N FLYQ V+DP+ ++++
Sbjct: 239 CKVLRLANNPDIVKVIKKIGHYLKMN--ITVPEDYINGFIRANNTFLYQLVFDPIKRKLI 296
Query: 241 PLNPLESEMRDEVFSQLSLKELELPKDQAFQLALGNLDPFSLEEMDQWNPDS 292
PLN E ++ E S + A Q+ALGN D + E++D +NPD+
Sbjct: 297 PLNAYEDDVDPETLSYAGQY---VDDSIALQIALGNKDINTFEQIDDYNPDT 345
>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 = 209 bits (533), Expect = 1e-65
Identities = 58/251 (23%), Positives = 97/251 (38%), Gaps = 10/251 (3%)
Query: 1 MKYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHL 60
++ + IK + VFDG+ K R ++R + + + E +
Sbjct: 67 FYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFT 126
Query: 61 RQSVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGA 120
++ V VT + G+ + AP EA+A A L AG TED D L FG+
Sbjct: 127 KRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGS 186
Query: 121 KKIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKA 180
++ L S + ++ + + +F +CIL G DY I+G+G K+A
Sbjct: 187 PVLMRHLTASEAKK-LPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRA 245
Query: 181 KDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFHNTNLMFLYQPVYDPVSKEVV 240
D + E +R+++ K + +FL V DP S E+
Sbjct: 246 VDLIQKH--KSIEEIVRRLDPN-------KYPVPENWLHKEAHQLFLEPEVLDPESVELK 296
Query: 241 PLNPLESEMRD 251
P E E+
Sbjct: 297 WSEPNEEELIK 307
>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 = 207 bits (528), Expect = 2e-64
Identities = 67/289 (23%), Positives = 111/289 (38%), Gaps = 22/289 (7%)
Query: 1 MKYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHL 60
++ + IK + VFDG+ K R ++R + + + E +
Sbjct: 67 FYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFT 126
Query: 61 RQSVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGA 120
++ V VT + G+ + AP EA+A A L AG TED D L FG+
Sbjct: 127 KRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGS 186
Query: 121 KKIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKA 180
++ L S + ++ + + +F +CIL G DY I+G+G K+A
Sbjct: 187 PVLMRHLTASEAKK-LPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRA 245
Query: 181 KDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFHNTNLMFLYQPVYDPVSKEVV 240
D + E +R+++ K + +FL V DP S E+
Sbjct: 246 VDLIQKH--KSIEEIVRRLDPN-------KYPVPENWLHKEAHQLFLEPEVLDPESVELK 296
Query: 241 PLNPLESEMRDEV-----FSQ----LSLKELELPKDQAFQLALGNLDPF 280
P E E+ + FS+ +K L + + Q G LD F
Sbjct: 297 WSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQ---GRLDDF 342
>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 = 190 bits (485), Expect = 2e-58
Identities = 53/246 (21%), Positives = 101/246 (41%), Gaps = 17/246 (6%)
Query: 1 MKYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHL 60
+ + ++ I+ + VFDG K+A E+R+K+R + L +A+ +
Sbjct: 62 LYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAALQAGD-KDAKKYA 120
Query: 61 RQSVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGA 120
+ + V + + G+ + AP E +AQ AY+ G +Y ++D D L+FG+
Sbjct: 121 QAAGRVDEYIVDSAKTLLSYMGIPFVDAPSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGS 180
Query: 121 KKIIYKLDLSGNCCFMDREKLPSALKMPLA--------KFTDAKFRYMCILSGCDYWTGI 172
++ L ++G + + T + + IL G DY G+
Sbjct: 181 PRLARNLAITGKRKLPGKNVYVDVKPEIIILESNLKRLGLTREQLIDIAILVGTDYNEGV 240
Query: 173 KGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFHNTNLMFLYQPVY 232
KG+G+KKA +Y+ + D AL+ + + +E F N + Y+ +
Sbjct: 241 KGVGVKKALNYIKTY--GDIFRALKALK------VNIDHVEEIRNFFLNPPVTDDYRIEF 292
Query: 233 DPVSKE 238
E
Sbjct: 293 REPDFE 298
>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 = 186 bits (475), Expect = 5e-57
Identities = 60/250 (24%), Positives = 103/250 (41%), Gaps = 23/250 (9%)
Query: 4 IHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQS 63
LL + I I VFDG KE T + RR+ ++ + K E + + EA + ++
Sbjct: 65 TIHLLENDITPIWVFDGEPPKLKEKTRKVRREMKEKAELKMKEAIKKEDFEEAAKYAKRV 124
Query: 64 VDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKI 123
+T KM N G+ + AP E +AQ +Y+ G V+++D D L++GA ++
Sbjct: 125 SYLTPKMVENCKYLLSLMGIPYVEAPSEGEAQASYMAKKGDVWAVVSQDYDALLYGAPRV 184
Query: 124 IYKLDLSGNCC-FMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYW-TGIKGMGLKKAK 181
+ L + ++ ++ L + + + I G DY G+KG+G K+A
Sbjct: 185 VRNLTTTKEMPELIELNEVLEDL-----RISLDDLIDIAIFMGTDYNPGGVKGIGFKRAY 239
Query: 182 DYVFSIMDPDFENALRKINVYGKIGSYVKITK--------------EFLTSFHNTNLMFL 227
+ V S + +++ Y +I K K E + F F
Sbjct: 240 ELVRSG--VAKDVLKKEVEYYDEIKRIFKEPKVTDNYSLSLKLPDKEGIIKFLVDENDFN 297
Query: 228 YQPVYDPVSK 237
Y V V K
Sbjct: 298 YDRVKKHVDK 307
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus
amylolyticus}
Length = 363
Score = 187 bits (476), Expect = 7e-57
Identities = 57/243 (23%), Positives = 90/243 (37%), Gaps = 22/243 (9%)
Query: 1 MKYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHL 60
++ IK + VFDG+ K E R+ ++ K E + A+ +
Sbjct: 76 FYRTINIVEAGIKPVYVFDGKPPELKAREIERRKAVKEEAAKKYEEAVQSGDLELARRYA 135
Query: 61 RQSVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGA 120
S +T +M + A G+ + AP E +AQ AY+ G A ++D D L+FG+
Sbjct: 136 MMSAKLTEEMVRDAKSLLDAMGIPWVQAPAEGEAQAAYIVKKGDAYASASQDYDSLLFGS 195
Query: 121 KKIIYKLDLSGNCCF--------MDREKLPSALKMPLAKFTDAKFRYMCILSGCDYW-TG 171
K++ L +SG + E + + T + IL G DY G
Sbjct: 196 PKLVRNLTISGRRKLPRKNEYVEVKPELIELDKLLVQLGITLENLIDIGILLGTDYNPDG 255
Query: 172 IKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFHNTNLMFLYQPV 231
+G+G KKA V + E + I + I K FL V
Sbjct: 256 FEGIGPKKALQLVKAY--GGIEKIPKPILKSPIEVDVIAIKK-----------YFLQPQV 302
Query: 232 YDP 234
D
Sbjct: 303 TDN 305
>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 = 184 bits (467), Expect = 1e-55
Identities = 53/260 (20%), Positives = 104/260 (40%), Gaps = 21/260 (8%)
Query: 1 MKYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHL 60
+L + I VFDG+ K E RRK ++ + K + E + +
Sbjct: 59 FYRTINILEEGVIPIYVFDGKPPEQKSEELERRRKAKEEAERKLERAKSEGKIEELRKYS 118
Query: 61 RQSVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGA 120
+ + +++ M + RA G+ + AP E +A+ AYLN G + ++D D ++FGA
Sbjct: 119 QAILRLSNIMVEESKKLLRAMGIPIVQAPSEGEAEAAYLNKLGLSWAAASQDYDAILFGA 178
Query: 121 KKIIYKLDLSGNCCFMDREKLPSALKMPLA--------KFTDAKFRYMCILSGCDYW-TG 171
K+++ L ++G +++ + T + + IL G DY G
Sbjct: 179 KRLVRNLTITGKRKLPNKDVYVEIKPELIETEILLKKLGITREQLIDIGILIGTDYNPDG 238
Query: 172 IKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFHNTNLMFLYQPV 231
I+G+G ++A + E A+ + K ++ + +FL V
Sbjct: 239 IRGIGPERALKIIKK--YGKIEKAMEYGEISKKDINF---------NIDEIRGLFLNPQV 287
Query: 232 YDPVSKEVVPLNPLESEMRD 251
P + + P ++ +
Sbjct: 288 VKP-EEALDLNEPNGEDIIN 306
>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 = 183 bits (466), Expect = 1e-55
Identities = 58/260 (22%), Positives = 98/260 (37%), Gaps = 23/260 (8%)
Query: 1 MKYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHL 60
L+ IK + VFDG K+ E RR+ R+ + K E L EA+ +
Sbjct: 62 FYRTINLMEAGIKPVYVFDGEPPEFKKKELEKRREAREEAEEKWREALEKGEIEEARKYA 121
Query: 61 RQSVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGA 120
+++ V + + + G+ + AP E +AQ AY+ G ++D D L+FGA
Sbjct: 122 QRATRVNEMLIEDAKKLLELMGIPIVQAPSEGEAQAAYMAAKGSVYASASQDYDSLLFGA 181
Query: 121 KKIIYKLDLSGNCCFMDREKLPSALK--------MPLAKFTDAKFRYMCILSGCDYW-TG 171
+++ L ++G + + K T K + IL G DY G
Sbjct: 182 PRLVRNLTITGKRKLPGKNVYVEIKPELIILEEVLKELKLTREKLIELAILVGTDYNPGG 241
Query: 172 IKGMGLKKA-------KDYVFSIMDPDFENALRKINVYGKIG-------SYVKITKEFLT 217
IKG+GLKKA KD + + + + +E +
Sbjct: 242 IKGIGLKKALEIVRHSKDPLAKFQKQSDVDLYAIKEFFLNPPVTDNYNLVWRDPDEEGIL 301
Query: 218 SFHNTNLMFLYQPVYDPVSK 237
F F + V + + +
Sbjct: 302 KFLCDEHDFSEERVKNGLER 321
>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 = 56.8 bits (136), Expect = 4e-09
Identities = 47/297 (15%), Positives = 107/297 (36%), Gaps = 87/297 (29%)
Query: 55 EAQSHLRQSVDVT-HKMA------LNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADY 107
+A LR + +V + + + C + V C F ++ +LN+
Sbjct: 142 QALLELRPAKNVLIDGVLGSGKTWV-ALDVCLSYKVQC-KMDF----KIFWLNLK----N 191
Query: 108 VITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCILSGCD 167
+ ++ L + +K++Y++D + + R S +K+ + R +
Sbjct: 192 CNSPETVLEML--QKLLYQIDPN----WTSRSDHSSNIKLRIHSIQAELRRLL------- 238
Query: 168 YWTGIKGMGLKKAKDYVFS--IMDPDFENALRKINVYGKIGSYVKITKEFLTSFHN-TNL 224
K+K Y ++ + +NA + N + + + +T T F T+
Sbjct: 239 -----------KSKPYENCLLVLL-NVQNA-KAWNAFN-LSCKILLT----TRFKQVTDF 280
Query: 225 MFLYQPVYDPVSKEVVPLNPLESEMRDEVFSQ-LSLKELELPKDQAFQLALGNLDPFSL- 282
+ + + + L P E + + + L + +LP+ ++ N P L
Sbjct: 281 LSAATTTHISLDHHSMTLTPDEVK---SLLLKYLDCRPQDLPR----EVLTTN--PRRLS 331
Query: 283 -------EEMDQWNPDSEENLPVTSIWSKQYEKPCDRHSS--EESVS--EPPVFQKL 328
+ + W+ W K CD+ ++ E S++ EP ++K+
Sbjct: 332 IIAESIRDGLATWDN-----------W-KHVN--CDKLTTIIESSLNVLEPAEYRKM 374
Score = 45.6 bits (107), Expect = 2e-05
Identities = 28/216 (12%), Positives = 53/216 (24%), Gaps = 64/216 (29%)
Query: 23 LPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQA----C 78
L E RR + LL+L +V + A C
Sbjct: 225 LRIHSIQAELRRLLKSKPYENC--LLVLL-------------NVQNA---KAWNAFNLSC 266
Query: 79 ------RARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGN 132
R + V D ++ I+ D + + L
Sbjct: 267 KILLTTRFKQV--------TDF------LSAATTTHISLDHHSMTLTPDE---VKSLLLK 309
Query: 133 CCFMDREKLPS-ALK-MPL------AKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYV 184
+ LP L P D + D W + L +
Sbjct: 310 YLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATW-------DNWKHVNCDKLTTIIESS 362
Query: 185 FSIMDP-DFENALRKINVYGKIGSYVKITKEFLTSF 219
++++P ++ +++V+ I L+
Sbjct: 363 LNVLEPAEYRKMFDRLSVFPP---SAHIPTILLSLI 395
Score = 34.8 bits (79), Expect = 0.039
Identities = 21/124 (16%), Positives = 45/124 (36%), Gaps = 20/124 (16%)
Query: 172 IKGMGLKKAKDY---VFS-------IMDPDFENALRKINVYGKIGSYVK-ITKEFLTSFH 220
+ K +D + S IM D + ++ + + S + + ++F+
Sbjct: 30 VDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRL--FWTLLSKQEEMVQKFVEEVL 87
Query: 221 NTNLMFLYQPVY----DPVSKEVVPLNPLESEMRD-EVFSQLSLKELELPKDQAFQLALG 275
N FL P+ P + + + D +VF++ ++ L+ + AL
Sbjct: 88 RINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQ--PYLKLRQALL 145
Query: 276 NLDP 279
L P
Sbjct: 146 ELRP 149
Score = 27.5 bits (60), Expect = 8.2
Identities = 14/115 (12%), Positives = 34/115 (29%), Gaps = 27/115 (23%)
Query: 2 KYIHMLLAHKIKVIMVFDGRHLPAKEATEED-------------RRKKRDSHKAKAAELL 48
+Y + + H HL E E +K R A A
Sbjct: 471 QYFYSHIGH-----------HLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGS 519
Query: 49 ILDRGSEA---QSHLRQSVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLN 100
IL+ + + ++ + ++ ++ + I + + ++A +
Sbjct: 520 ILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMA 574
>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 = 72/392 (18%), Positives = 115/392 (29%), Gaps = 142/392 (36%)
Query: 4 IHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQS 63
IH L A L + T + K+ ++ A+ ++
Sbjct: 101 IHALAAK------------LLQENDTTLVKTKE------------LIKNYITARIMAKRP 136
Query: 64 VDVTHKMALNVIQACRARGVDCIVAPF----EADAQMAYL----NIAGYADY------VI 109
D AL +A +VA F D Y ++ Y Y +I
Sbjct: 137 FDKKSNSAL--FRAVGEGNAQ-LVAIFGGQGNTDD---YFEELRDL--YQTYHVLVGDLI 188
Query: 110 TEDSDLL------VFGAKKIIYK-LDLSGNCCFMDR-EKLPS-------ALKMPLAKFTD 154
++ L A+K+ + L++ +++ P + PL
Sbjct: 189 KFSAETLSELIRTTLDAEKVFTQGLNILE---WLENPSNTPDKDYLLSIPISCPLIGVIQ 245
Query: 155 -AKFRYMCILSGC------DYWTGIKGM--GLKKAKDYVFSIMD--PDF-ENALRKINVY 202
A + L G Y G G GL A + D F + + I V
Sbjct: 246 LAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAV--AIAETDSWESFFVSVRKAITVL 303
Query: 203 GKIGSYVKITKEFLTSFHNTNLMFLYQP--VYDPVSK-EVVPLNPLESEM-------RDE 252
IG ++ NT+L P + D + E VP S M +++
Sbjct: 304 FFIGV------RCYEAYPNTSL----PPSILEDSLENNEGVP-----SPMLSISNLTQEQ 348
Query: 253 VFSQLSLKELELPKDQAFQLALGNLD--------PFSLE-------------EMDQWN-P 290
V ++ LP + +++L N P SL +DQ P
Sbjct: 349 VQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIP 408
Query: 291 DSEEN-------LPVTSIWSKQYEKPCDRHSS 315
SE LPV S P HS
Sbjct: 409 FSERKLKFSNRFLPVAS--------PF--HSH 430
Score = 37.0 bits (85), Expect = 0.010
Identities = 29/154 (18%), Positives = 54/154 (35%), Gaps = 62/154 (40%)
Query: 171 GI--KGMGL------KKAKD------------YVFSIMDPDFENALRKINVY--GKIGSY 208
G +GMG+ K A+D Y FSI+D N + ++ G+ G
Sbjct: 1625 GSQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLT-IHFGGEKGKR 1683
Query: 209 VKITKEFLTSFHNTNLMFLYQPVYD------PVSKEV------VPLNPLESEMRDEVFSQ 256
++ N + M +++ + D + KE+ + + F+Q
Sbjct: 1684 IR---------ENYSAM-IFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQ 1733
Query: 257 -----LS---LKELE----LPKDQAFQLA---LG 275
+ ++L+ +P D F A LG
Sbjct: 1734 PALTLMEKAAFEDLKSKGLIPADATF--AGHSLG 1765
Score = 30.8 bits (69), Expect = 0.84
Identities = 16/116 (13%), Positives = 36/116 (31%), Gaps = 38/116 (32%)
Query: 225 MFLYQPVYDPVSKEVVPLNPLESEMRDEVFSQLSLKELELPKDQAFQLALGNLDPFSLEE 284
M LY+ +++V + D F+ G FS+ +
Sbjct: 1633 MDLYK--TSKAAQDV----------WNRA-------------DNHFKDTYG----FSILD 1663
Query: 285 MDQWNPDSEENLPV--TSIWSKQ----YEKPCDRHSSEESVSEPPVFQKLKPVASS 334
+ NP + L + K+ Y + + +F+++ ++S
Sbjct: 1664 IVINNPVN---LTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTS 1716
>2h3h_A Sugar ABC transporter, periplasmic sugar-binding protein; glucose
binding protein, periplasmic binding protein, GBP; HET:
BGC; 1.70A {Thermotoga maritima} PDB: 2qvc_A* 3c6q_B*
Length = 313
Score = 30.1 bits (68), Expect = 1.0
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 72 LNVIQACRARGVDCI-VAPFEADAQMAYLNIAGYAD-YVITEDSDL 115
L ++++ A GV+ I +AP + A + + A V+T D+D
Sbjct: 47 LQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTDS 92
>3g1w_A Sugar ABC transporter; sugar-binding protein, bacillus halod target
11229F, transport protein, structural genomics; 2.02A
{Bacillus halodurans c-125}
Length = 305
Score = 29.7 bits (67), Expect = 1.3
Identities = 8/46 (17%), Positives = 18/46 (39%), Gaps = 2/46 (4%)
Query: 72 LNVIQACRARGVDCI-VAPFEADAQMAYLNIAGYAD-YVITEDSDL 115
+ V++ A+ I ++ + +N A A ++ DS
Sbjct: 51 ITVLEQAIAKNPAGIAISAIDPVELTDTINKAVDAGIPIVLFDSGA 96
>2gpr_A Glucose-permease IIA component; phosphotransferase, enzyme IIA;
2.50A {Mycoplasma capricolum} SCOP: b.84.3.1
Length = 154
Score = 28.7 bits (65), Expect = 1.7
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 7/35 (20%)
Query: 225 MFLY---QPVYDPVSKEVVPLNPLESEMRDEVFSQ 256
M+ + V P ++ L E+ DEVF +
Sbjct: 1 MWFFNKNLKVLAPCDGTIITL----DEVEDEVFKE 31
>3brs_A Periplasmic binding protein/LACI transcriptional; structural
genomics, protein structure initiative; 2.00A
{Clostridium phytofermentans}
Length = 289
Score = 29.2 bits (66), Expect = 1.9
Identities = 9/46 (19%), Positives = 16/46 (34%), Gaps = 2/46 (4%)
Query: 72 LNVIQACRARGVDCI-VAPFEADAQMAYLNIAGYAD-YVITEDSDL 115
+I+ R D I +A + + A +I DS +
Sbjct: 55 NELIEEAIKRKPDVILLAAADYEKTYDAAKEIKDAGIKLIVIDSGM 100
>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 = 28.4 bits (62), Expect = 1.9
Identities = 7/43 (16%), Positives = 15/43 (34%), Gaps = 19/43 (44%)
Query: 258 SLKELELPKDQAFQLALGNLDPFSLEEMDQWNPDSEENLPVTS 300
+LK+L+ +L ++ DS L + +
Sbjct: 21 ALKKLQ-----------ASLKLYA--------DDSAPALAIKA 44
>3d02_A Putative LACI-type transcriptional regulator; periplasmic
sugar-binding protein, structura genomics; HET: MSE GOL;
1.30A {Klebsiella pneumoniae subsp}
Length = 303
Score = 28.9 bits (65), Expect = 2.5
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 72 LNVIQACRARGVDCI-VAPFEADAQMAYLNIAGYAD-YVITEDSD 114
+ +I+ AR VD I + P +A+ A A V+T +S
Sbjct: 51 VKIIEDLIARKVDAITIVPNDANVLEPVFKKARDAGIVVLTNESP 95
>3rot_A ABC sugar transporter, periplasmic sugar binding; nysgrc,
PSI-biology, structural genomics; 1.91A {Legionella
pneumophila subsp}
Length = 297
Score = 28.5 bits (64), Expect = 2.8
Identities = 9/46 (19%), Positives = 14/46 (30%), Gaps = 2/46 (4%)
Query: 72 LNVIQACRARGVDCI-VAPFEADAQMAYLNIAGYAD-YVITEDSDL 115
+ I++ A I A L A + VI D+
Sbjct: 51 VQFIESALATYPSGIATTIPSDTAFSKSLQRANKLNIPVIAVDTRP 96
>1f3z_A EIIA-GLC, glucose-specific phosphocarrier; phosphotransferase,
signal transduction, sugar transport; 1.98A {Escherichia
coli} SCOP: b.84.3.1 PDB: 1f3g_A 1ggr_A 1gla_F 1glb_F*
1glc_F* 1gld_F* 1gle_F* 1o2f_A 2f3g_A
Length = 161
Score = 27.6 bits (62), Expect = 3.8
Identities = 7/26 (26%), Positives = 15/26 (57%), Gaps = 4/26 (15%)
Query: 231 VYDPVSKEVVPLNPLESEMRDEVFSQ 256
+ P+S E+V + ++ D VF++
Sbjct: 15 IIAPLSGEIVNI----EDVPDVVFAE 36
>3our_B EIIA, phosphotransferase system IIA component; exhibit no hydrolase
activity1, lyase-transferase complex; 2.20A {Vibrio
vulnificus}
Length = 183
Score = 27.7 bits (62), Expect = 4.5
Identities = 7/26 (26%), Positives = 15/26 (57%), Gaps = 4/26 (15%)
Query: 231 VYDPVSKEVVPLNPLESEMRDEVFSQ 256
+ P+S E+V + ++ D VF++
Sbjct: 37 IIAPLSGEIVNI----EDVPDVVFAE 58
>1ax3_A Iiaglc, glucose permease IIA domain; phosphotransferase system,
sugar transport, transferase, phosphorylation,
transmembrane; NMR {Bacillus subtilis} SCOP: b.84.3.1
PDB: 1gpr_A
Length = 162
Score = 27.2 bits (61), Expect = 4.7
Identities = 7/26 (26%), Positives = 15/26 (57%), Gaps = 4/26 (15%)
Query: 231 VYDPVSKEVVPLNPLESEMRDEVFSQ 256
P++ E+ P+ +++ D+VFS
Sbjct: 15 FVSPITGEIHPI----TDVPDQVFSG 36
>1kl7_A Threonine synthase; threonine synthesis, pyridoxal 5-phosphate,
beta-family, MON lyase; HET: PLP; 2.70A {Saccharomyces
cerevisiae} SCOP: c.79.1.1
Length = 514
Score = 27.7 bits (62), Expect = 5.6
Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 14/67 (20%)
Query: 236 SKEVVPLNPLESEMRDEVFSQLSLKELEL---P----KDQAFQLALGNLDPFSLEEMDQW 288
S EV PL + ++ + LEL P KD A Q +GNL + L+ +
Sbjct: 93 SDEVTPLVQNVTGDKENLHI------LELFHGPTYAFKDVALQF-VGNLFEYFLQRTNAN 145
Query: 289 NPDSEEN 295
P+ E+
Sbjct: 146 LPEGEKK 152
>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 354
Score = 27.5 bits (61), Expect = 5.8
Identities = 12/110 (10%), Positives = 31/110 (28%), Gaps = 18/110 (16%)
Query: 71 ALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLDLS 130
+L ++++ + + + I ++ E S + + ++Y L
Sbjct: 233 SLLMLESMALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAH 292
Query: 131 G----------NCCFMDREKLPSALKMPLAK---FTDAKFRYMCILSGCD 167
+D E L + K + + D + G
Sbjct: 293 CIPANIILKELTFSLLDVETLNTTNKSSIIEYSSVFD-----ERLSLGNK 337
>3o1i_D Periplasmic protein TORT; ligand free, two component sensor,
periplasmic binding prote signaling protein; HET: PE4;
2.80A {Vibrio parahaemolyticus} PDB: 3o1h_B* 3o1j_C
Length = 304
Score = 27.4 bits (61), Expect = 6.3
Identities = 12/76 (15%), Positives = 21/76 (27%), Gaps = 11/76 (14%)
Query: 41 KAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQACRARGVDCI-VAPFEADAQMAYL 99
+ + L +L+ G RQ + C G + I + + A L
Sbjct: 32 EKQGVNLRVLEAGGYPNKS-RQ---------EQQLALCTQWGANAIILGTVDPHAYEHNL 81
Query: 100 NIAGYADYVITEDSDL 115
V + L
Sbjct: 82 KSWVGNTPVFATVNQL 97
>3qry_B Putative uncharacterized protein; alpha-alpha six fold, glycoside
hydrolase, mannosidase, 1- deoxymannojirimycin,
hydrolase; HET: DMJ; 1.75A {Streptococcus pneumoniae}
PDB: 3qpf_A* 3qsp_A*
Length = 426
Score = 27.6 bits (61), Expect = 7.0
Identities = 11/39 (28%), Positives = 16/39 (41%)
Query: 118 FGAKKIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAK 156
G K +++D GN MD +PS L P +
Sbjct: 280 KGEKIYAFEVDGLGNASIMDDPNVPSLLAAPYLGYCSVD 318
>3l6u_A ABC-type sugar transport system periplasmic component; structural
genomics, nysgrc, target 11006S, PSI-2, protein
structure initiative; 1.90A {Exiguobacterium sibiricum}
Length = 293
Score = 27.3 bits (61), Expect = 7.7
Identities = 9/85 (10%), Positives = 28/85 (32%), Gaps = 9/85 (10%)
Query: 70 MALNVIQACRARGV-DCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLD 128
+A+ V++A + + IV + + + D + + ++ ++ A +
Sbjct: 206 IAMGVLEALKKAKISGKIVVGIDGNRAILEAVDMKSMDATVVQSAEEMMKVAFSALKLH- 264
Query: 129 LSGNCCFMDREKLPSALKMPLAKFT 153
+K+P +
Sbjct: 265 TKN-------KKIPDRFYTYSYLYD 282
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
0.319 0.135 0.398
Gapped
Lambda K H
0.267 0.0639 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,150,196
Number of extensions: 313345
Number of successful extensions: 949
Number of sequences better than 10.0: 1
Number of HSP's gapped: 925
Number of HSP's successfully gapped: 39
Length of query: 336
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 242
Effective length of database: 4,077,219
Effective search space: 986686998
Effective search space used: 986686998
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 (21.8 bits)
S2: 57 (25.9 bits)