RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11828
(443 letters)
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A
{Homo sapiens} PDB: 3qeb_Z* 3qea_Z*
Length = 352
Score = 95.8 bits (238), Expect = 5e-22
Identities = 46/113 (40%), Positives = 63/113 (55%), Gaps = 5/113 (4%)
Query: 196 ERNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKF 255
N AG +ITEDS LL FG KK+I K+D GN +D+ +L ++ FT+ KF
Sbjct: 157 YLNKAGIVQAIITEDSALLAFGCKKVILKMDQFGNGLEIDQARLGMCRQLGD-VFTEEKF 215
Query: 256 RYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPD----FENRKEYVKYAKVFP 304
RYMCILSGCDY + ++G+GL KA + +PD + Y+K P
Sbjct: 216 RYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVP 268
Score = 75.0 bits (184), Expect = 6e-15
Identities = 46/173 (26%), Positives = 79/173 (45%), Gaps = 11/173 (6%)
Query: 9 WKTNLKKLLQHLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHK- 67
K L++ + IN+ A KVI + + A E + A +
Sbjct: 103 GKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAG 162
Query: 68 -------QKAAELLHSGSSIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCIL 120
+ +A L +I K+D GN +D+ +L ++ FT+ KFRYMCIL
Sbjct: 163 IVQAIITEDSALLAFGCKKVILKMDQFGNGLEIDQARLGMCRQLGD-VFTEEKFRYMCIL 221
Query: 121 SGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFL 173
SGCDY + ++G+GL KA + +PD ++KI Y K+ + + ++++
Sbjct: 222 SGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMN--ITVPEDYI 272
Score = 52.3 bits (125), Expect = 1e-07
Identities = 24/43 (55%), Positives = 33/43 (76%)
Query: 21 YVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAE 63
YV +CMK++NMLL+H IK I+VFDG LP+K+ E RR+R +
Sbjct: 55 YVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQ 97
>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 = 92.6 bits (230), Expect = 4e-21
Identities = 24/118 (20%), Positives = 50/118 (42%), Gaps = 9/118 (7%)
Query: 198 NIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCC-FMDREKLPSALKMPLAKFTDAKFR 256
G V+++D D L++GA +++ L + ++ ++ L + +
Sbjct: 161 AKKGDVWAVVSQDYDALLYGAPRVVRNLTTTKEMPELIELNEVLEDL-----RISLDDLI 215
Query: 257 YMCILSGCDYW-TGIKGMGLKKAKDYV--FSIMDPDFENRKEYVKYAKVFPLTAILDM 311
+ I G DY G+KG+G K+A + V D + + Y + ++F + D
Sbjct: 216 DIAIFMGTDYNPGGVKGIGFKRAYELVRSGVAKDVLKKEVEYYDEIKRIFKEPKVTDN 273
Score = 58.3 bits (141), Expect = 1e-09
Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 7/71 (9%)
Query: 73 LLHSGSSIIYKLDLSGNCC-FMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYW-TGIK 130
LL+ ++ L + ++ ++ L+ + + I G DY G+K
Sbjct: 177 LLYGAPRVVRNLTTTKEMPELIELNEVLEDLR-----ISLDDLIDIAIFMGTDYNPGGVK 231
Query: 131 GMGLKKAKDYV 141
G+G K+A + V
Sbjct: 232 GIGFKRAYELV 242
Score = 40.2 bits (94), Expect = 0.001
Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 1/55 (1%)
Query: 21 YVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLH 75
Y K I+ LL + I I VFDG KE T + RR+ E + +
Sbjct: 58 YNGVFYKTIH-LLENDITPIWVFDGEPPKLKEKTRKVRREMKEKAELKMKEAIKK 111
>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 = 91.8 bits (228), Expect = 1e-20
Identities = 24/114 (21%), Positives = 48/114 (42%), Gaps = 10/114 (8%)
Query: 198 NIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALKMPLA--------K 249
G +Y ++D D L+FG+ ++ L ++G + +
Sbjct: 160 AAKGDVEYTGSQDYDSLLFGSPRLARNLAITGKRKLPGKNVYVDVKPEIIILESNLKRLG 219
Query: 250 FTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYV--FSIMDPDFENRKEYVKYAK 301
T + + IL G DY G+KG+G+KKA +Y+ + + + K + + +
Sbjct: 220 LTREQLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKVNIDHVE 273
Score = 65.6 bits (160), Expect = 6e-12
Identities = 25/109 (22%), Positives = 41/109 (37%), Gaps = 12/109 (11%)
Query: 73 LLHSGSSIIYKLDLSGNCCFMDREKLPSALKMPLA--------KFTDAKFRYMCILSGCD 124
LL + L ++G + + T + + IL G D
Sbjct: 176 LLFGSPRLARNLAITGKRKLPGKNVYVDVKPEIIILESNLKRLGLTREQLIDIAILVGTD 235
Query: 125 YWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFL 173
Y G+KG+G+KKA +Y+ + D AL+ + V +I FL
Sbjct: 236 YNEGVKGVGVKKALNYIKTY--GDIFRALKALKVNIDH--VEEIRNFFL 280
Score = 46.4 bits (110), Expect = 1e-05
Identities = 14/64 (21%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 21 YVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSGSSI 80
+++ + ++ ++ I+ + VFDG K+A E+R+KR ++ L +G
Sbjct: 57 HLSGILYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKKRRA-EAEEMWIAALQAGDKD 115
Query: 81 IYKL 84
K
Sbjct: 116 AKKY 119
>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 = 90.7 bits (225), Expect = 2e-20
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 1/85 (1%)
Query: 198 NIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRY 257
AG TED D L FG+ ++ L S + ++ + + +F
Sbjct: 166 VKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKK-LPIQEFHLSRILQELGLNQEQFVD 224
Query: 258 MCILSGCDYWTGIKGMGLKKAKDYV 282
+CIL G DY I+G+G K+A D +
Sbjct: 225 LCILLGSDYCESIRGIGPKRAVDLI 249
Score = 66.4 bits (162), Expect = 3e-12
Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 2/81 (2%)
Query: 77 GSSIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKK 136
GS ++ + + + ++ + + +F +CIL G DY I+G+G K+
Sbjct: 185 GSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKR 244
Query: 137 AKDYVFSIMDPDFENALRKIN 157
A D + E +R+++
Sbjct: 245 AVDLIQKH--KSIEEIVRRLD 263
Score = 45.2 bits (107), Expect = 2e-05
Identities = 10/57 (17%), Positives = 23/57 (40%), Gaps = 1/57 (1%)
Query: 21 YVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSG 77
++ ++ + IK + VFDG+ K R +R +++ + +G
Sbjct: 62 HLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRA-EAEKQLQQAQAAG 117
>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 = 89.6 bits (222), Expect = 9e-20
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 1/85 (1%)
Query: 198 NIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRY 257
AG TED D L FG+ ++ L S + ++ + + +F
Sbjct: 166 VKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKK-LPIQEFHLSRILQELGLNQEQFVD 224
Query: 258 MCILSGCDYWTGIKGMGLKKAKDYV 282
+CIL G DY I+G+G K+A D +
Sbjct: 225 LCILLGSDYCESIRGIGPKRAVDLI 249
Score = 66.5 bits (162), Expect = 4e-12
Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 2/81 (2%)
Query: 77 GSSIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKK 136
GS ++ + + + ++ + + +F +CIL G DY I+G+G K+
Sbjct: 185 GSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKR 244
Query: 137 AKDYVFSIMDPDFENALRKIN 157
A D + E +R+++
Sbjct: 245 AVDLIQKH--KSIEEIVRRLD 263
Score = 46.0 bits (109), Expect = 1e-05
Identities = 10/57 (17%), Positives = 23/57 (40%), Gaps = 1/57 (1%)
Query: 21 YVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSG 77
++ ++ + IK + VFDG+ K R +R +++ + +G
Sbjct: 62 HLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRA-EAEKQLQQAQAAG 117
>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 = 88.1 bits (218), Expect = 2e-19
Identities = 27/94 (28%), Positives = 40/94 (42%), Gaps = 9/94 (9%)
Query: 198 NIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALK--------MPLAK 249
G ++D D L+FGA +++ L ++G + + K
Sbjct: 161 AAKGSVYASASQDYDSLLFGAPRLVRNLTITGKRKLPGKNVYVEIKPELIILEEVLKELK 220
Query: 250 FTDAKFRYMCILSGCDYW-TGIKGMGLKKAKDYV 282
T K + IL G DY GIKG+GLKKA + V
Sbjct: 221 LTREKLIELAILVGTDYNPGGIKGIGLKKALEIV 254
Score = 58.0 bits (140), Expect = 2e-09
Identities = 22/78 (28%), Positives = 31/78 (39%), Gaps = 9/78 (11%)
Query: 73 LLHSGSSIIYKLDLSGNCCFMDREKLPSALK--------MPLAKFTDAKFRYMCILSGCD 124
LL ++ L ++G + + K T K + IL G D
Sbjct: 177 LLFGAPRLVRNLTITGKRKLPGKNVYVEIKPELIILEEVLKELKLTREKLIELAILVGTD 236
Query: 125 YW-TGIKGMGLKKAKDYV 141
Y GIKG+GLKKA + V
Sbjct: 237 YNPGGIKGIGLKKALEIV 254
Score = 42.6 bits (100), Expect = 1e-04
Identities = 14/64 (21%), Positives = 23/64 (35%)
Query: 21 YVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSGSSI 80
+++ L+ IK + VFDG K+ E RR+ E ++ L
Sbjct: 57 HLSGLFYRTINLMEAGIKPVYVFDGEPPEFKKKELEKRREAREEAEEKWREALEKGEIEE 116
Query: 81 IYKL 84
K
Sbjct: 117 ARKY 120
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus
amylolyticus}
Length = 363
Score = 85.7 bits (212), Expect = 2e-18
Identities = 25/94 (26%), Positives = 38/94 (40%), Gaps = 9/94 (9%)
Query: 198 NIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCCF--------MDREKLPSALKMPLAK 249
G A ++D D L+FG+ K++ L +SG + E + +
Sbjct: 175 VKKGDAYASASQDYDSLLFGSPKLVRNLTISGRRKLPRKNEYVEVKPELIELDKLLVQLG 234
Query: 250 FTDAKFRYMCILSGCDYW-TGIKGMGLKKAKDYV 282
T + IL G DY G +G+G KKA V
Sbjct: 235 ITLENLIDIGILLGTDYNPDGFEGIGPKKALQLV 268
Score = 61.4 bits (149), Expect = 2e-10
Identities = 25/110 (22%), Positives = 37/110 (33%), Gaps = 11/110 (10%)
Query: 73 LLHSGSSIIYKLDLSGNCCF--------MDREKLPSALKMPLAKFTDAKFRYMCILSGCD 124
LL ++ L +SG + E + + T + IL G D
Sbjct: 191 LLFGSPKLVRNLTISGRRKLPRKNEYVEVKPELIELDKLLVQLGITLENLIDIGILLGTD 250
Query: 125 YW-TGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFL 173
Y G +G+G KKA V + E + I + I K FL
Sbjct: 251 YNPDGFEGIGPKKALQLVKAY--GGIEKIPKPILKSPIEVDVIAIKKYFL 298
Score = 47.9 bits (114), Expect = 3e-06
Identities = 11/48 (22%), Positives = 20/48 (41%)
Query: 21 YVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQ 68
+++ ++ IK + VFDG+ K E R+ E K+
Sbjct: 71 HLSGLFYRTINIVEAGIKPVYVFDGKPPELKAREIERRKAVKEEAAKK 118
>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 = 83.1 bits (205), Expect = 9e-18
Identities = 25/142 (17%), Positives = 53/142 (37%), Gaps = 25/142 (17%)
Query: 198 NIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALKMPLA--------K 249
N G + ++D D ++FGAK+++ L ++G +++ +
Sbjct: 158 NKLGLSWAAASQDYDAILFGAKRLVRNLTITGKRKLPNKDVYVEIKPELIETEILLKKLG 217
Query: 250 FTDAKFRYMCILSGCDYW-TGIKGMGLKKAKDYVFS----------------IMDPDFEN 292
T + + IL G DY GI+G+G ++A + ++ + +
Sbjct: 218 ITREQLIDIGILIGTDYNPDGIRGIGPERALKIIKKYGKIEKAMEYGEISKKDINFNIDE 277
Query: 293 RKEYVKYAKVFPLTAILDMKVP 314
+ +V LD+ P
Sbjct: 278 IRGLFLNPQVVKPEEALDLNEP 299
Score = 58.8 bits (142), Expect = 1e-09
Identities = 34/232 (14%), Positives = 65/232 (28%), Gaps = 81/232 (34%)
Query: 21 YVNYCMKYINMLLAHKIKVIMVFDG------------RHLPAKEATEEDRRKRAEIRHKQ 68
+++ +L + I VFDG R +EA + R ++E + ++
Sbjct: 54 HLSGLFYRTINILEEGVIPIYVFDGKPPEQKSEELERRRKAKEEAERKLERAKSEGKIEE 113
Query: 69 K---------------------------------------AAELLHSG------------ 77
AA L G
Sbjct: 114 LRKYSQAILRLSNIMVEESKKLLRAMGIPIVQAPSEGEAEAAYLNKLGLSWAAASQDYDA 173
Query: 78 -----SSIIYKLDLSGNCCFMDREKLPSALKMPLA--------KFTDAKFRYMCILSGCD 124
++ L ++G +++ + T + + IL G D
Sbjct: 174 ILFGAKRLVRNLTITGKRKLPNKDVYVEIKPELIETEILLKKLGITREQLIDIGILIGTD 233
Query: 125 YW-TGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGS--YVKITKEFL 173
Y GI+G+G ++A + E A+ + K + +I FL
Sbjct: 234 YNPDGIRGIGPERALKIIKK--YGKIEKAMEYGEISKKDINFNIDEIRGLFL 283
>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 = 50.8 bits (121), Expect = 7e-07
Identities = 65/434 (14%), Positives = 135/434 (31%), Gaps = 138/434 (31%)
Query: 92 FMDREKLPSA-------LKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSI 144
++ PS L + L +F + L G D + ++
Sbjct: 67 YVSSLVEPSKVGQFDQVLNLCLTEFENC------YLEGND----------------IHAL 104
Query: 145 ---MDPDFENALRKINVYGKIGSYVK---ITKEFLTSGAPQP-FGARNEGRSLLSAV--- 194
+ + + L K I +Y+ + K + F A EG + L A+
Sbjct: 105 AAKLLQENDTTLVKTKEL--IKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGG 162
Query: 195 --------TE-RNIAGYADY------VITEDSDLL------VFGAKKIIYK-LDLSGNCC 232
E R++ Y Y +I ++ L A+K+ + L++
Sbjct: 163 QGNTDDYFEELRDL--YQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILE--- 217
Query: 233 FMDR-EKLPS-------ALKMPLAKFTD-AKFRYMCILSGC------DYWTGIKGM--GL 275
+++ P + PL A + L G Y G G GL
Sbjct: 218 WLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGL 277
Query: 276 KKAKDYVFSIMD--PDF-ENRKEYVKYA--------KVFPLTAILDMKVPAKWYRRIIGS 324
A + D F + ++ + + +P T++ P + +
Sbjct: 278 VTAV--AIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSL-----PPSILEDSLEN 330
Query: 325 IE-------VICGFSMATI-----PFNMKVPAKWYRRIIGSIEVICGFSMATIPFILAG- 371
E I + + N +PA +++ I ++ G +++G
Sbjct: 331 NEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAG--KQV--EISLVNGAKN----LVVSGP 382
Query: 372 --------KAILDMKVPAKWYR-RIIGS---IEVICGFSMATIPFSTYYLL--VCKLDEM 417
+ K P+ + RI S ++ F PF ++ L+ +++
Sbjct: 383 PQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKD 442
Query: 418 ILRKNVQYTPAVIK 431
+++ NV + I+
Sbjct: 443 LVKNNVSFNAKDIQ 456
Score = 38.9 bits (90), Expect = 0.004
Identities = 39/221 (17%), Positives = 65/221 (29%), Gaps = 97/221 (43%)
Query: 128 GI--KGMGL------KKAKD------------YVFSIMDPDFENALRKINVYGKIGSYVK 167
G +GMG+ K A+D Y FSI+D N + ++
Sbjct: 1625 GSQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLT-IH-------- 1675
Query: 168 ITKEFLTSGAPQPFGARNEGRSLLSAVTERNIAGYADYVITEDSDLLVFGAKKIIYKLDL 227
FG G+ + E Y+ + D + +KI +++
Sbjct: 1676 -------------FGGEK-GKRI----REN----YSAMIFETIVDGKL-KTEKIFKEINE 1712
Query: 228 SGN-CCFM-DREKL-------PSALKMPLAKFTD--AKFRYMCILSGCDYWTGIKGMGLK 276
F ++ L P AL A F + K GL
Sbjct: 1713 HSTSYTFRSEKGLLSATQFTQP-AL------TLMEKAAFEDL------------KSKGLI 1753
Query: 277 KAKDYVF---SIMDPDFENRKEY---VKYAKVFPLTAILDM 311
A D F S+ EY A V + +++++
Sbjct: 1754 PA-DATFAGHSL--------GEYAALASLADVMSIESLVEV 1785
Score = 38.1 bits (88), Expect = 0.006
Identities = 76/445 (17%), Positives = 121/445 (27%), Gaps = 150/445 (33%)
Query: 17 LQHLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHS 76
L+ LY Y + ++ F L IR A ++
Sbjct: 173 LRDLYQTY---------HVLVGDLIKFSAETL------------SELIRTTLDAEKVFTQ 211
Query: 77 GSSIIYKLDLSGNCCFMDREKLPS-------ALKMPLAKFTD-AKFRYMCILSGC----- 123
G +I+ L+ + P + PL A + L G
Sbjct: 212 GLNILEWLE--------NPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGEL 263
Query: 124 -DYWTGIKGM--GLKKAKDYVFSIMD--PDF-ENALRKINVYGKIGSYV----------- 166
Y G G GL A + D F + + I V IG
Sbjct: 264 RSYLKGATGHSQGLVTAV--AIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPP 321
Query: 167 KITKEFLTS--GAPQP-FGARNEGRS-LLSAVTERN----------IA---GYADYVITE 209
I ++ L + G P P N + + V + N I+ G + V++
Sbjct: 322 SILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVS- 380
Query: 210 DSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFR-YMCIL------- 261
G L G + + K PS L F++ K + L
Sbjct: 381 -------G-----PPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFH 428
Query: 262 SGCDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKYAKVFPLTAILDMKVP------A 315
S L A D + D D+++P
Sbjct: 429 S--HL--------LVPASDLINK----DLVKNNVSFNAK---------DIQIPVYDTFDG 465
Query: 316 KWYRRIIGSI-EVICGFSMATIPFNMKVPAKWYRRIIGSIEVICGFSMATI----PFILA 370
R + GSI E I ++P KW E F I P +
Sbjct: 466 SDLRVLSGSISERIV--DCII-----RLPVKW--------ETTTQFKATHILDFGPGGAS 510
Query: 371 GKAILDMK-VPAKWYRRII-GSIEV 393
G +L + R I+ G++++
Sbjct: 511 GLGVLTHRNKDGTGVRVIVAGTLDI 535
>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 = 41.8 bits (97), Expect = 4e-04
Identities = 67/483 (13%), Positives = 144/483 (29%), Gaps = 141/483 (29%)
Query: 27 KYINMLLAHKIKVIMVFDGRHLPAKEATEEDRR--KRAEIRH--KQKAAE---------L 73
+Y ++L + + FD + + + + + EI H K A L
Sbjct: 17 QYKDILSVFEDAFVDNFDCKDVQ-----DMPKSILSKEEIDHIIMSKDAVSGTLRLFWTL 71
Query: 74 LHSGSSIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMG 133
L ++ K F++ L+ KF + +
Sbjct: 72 LSKQEEMVQK--------FVE-----EVLR-INYKFLMSPIKTEQRQPSMMT-------- 109
Query: 134 LKKAKDYVFSIMDPDFEN--ALRKINVYGKIGSYVKITKEFLTSGAPQPF----GARNEG 187
+ Y+ D + + K NV ++ Y+K+ ++ L P G G
Sbjct: 110 ----RMYI-EQRDRLYNDNQVFAKYNVS-RLQPYLKL-RQALLELRPAKNVLIDGVLGSG 162
Query: 188 RSLLSAVTERNIA-----GYADYVIT----EDSDLLVFGAKKIIYKLDLSGNCCFMDREK 238
++ ++ + + + + + ++ +K++Y++D + + R
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPN----WTSRSD 218
Query: 239 LPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFS--IMDPDFENRKEY 296
S +K+ + R + K+K Y ++ + +N +
Sbjct: 219 HSSNIKLRIHSIQAELRRLL------------------KSKPYENCLLVLL-NVQN-AKA 258
Query: 297 VKY----AKVFPLT---AILDMKVPAKWYRRIIGSIEVICGFSMATIPFNMKVPAKWYRR 349
K+ T + D A I T + K+
Sbjct: 259 WNAFNLSCKILLTTRFKQVTDFLSAAT--TTHISLDHHSMTL---TPDEVKSLLLKYLDC 313
Query: 350 IIGSI-EVICGFSMATIPFILA--GKAILDMKVPAKW--YR--------RIIG-SIEVIC 395
+ + T P L+ ++I D A W ++ II S+ V+
Sbjct: 314 RPQDLPREVLT----TNPRRLSIIAESIRDG--LATWDNWKHVNCDKLTTIIESSLNVLE 367
Query: 396 ---------GFSM----ATIPFSTYYLLVCKLD----EMILRKNVQYTPAVIKQ---SYY 435
S+ A IP L+ + +++ K +Y+ V KQ S
Sbjct: 368 PAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYS-LVEKQPKESTI 426
Query: 436 YLH 438
+
Sbjct: 427 SIP 429
Score = 38.7 bits (89), Expect = 0.005
Identities = 53/449 (11%), Positives = 100/449 (22%), Gaps = 184/449 (40%)
Query: 4 IPIIWWKTNLKKLLQHLYVNYCMKYINMLLAHKI-------KVIMVFDG--------RHL 48
+ I + L++LL+ Y N LL + K F+ R
Sbjct: 225 LRIHSIQAELRRLLKS------KPYENCLL---VLLNVQNAKAWNAFNLSCKILLTTRFK 275
Query: 49 PAKEATEEDRRKRAEIRHKQKAAELLHSGSSIIYKLDLSGNCCFMDREKLPS-ALK-MPL 106
+ + H L L + LP L P
Sbjct: 276 QVTDFLSAATTTHISLDHHSMT--LTPDEV-----KSLLLKYLDCRPQDLPREVLTTNPR 328
Query: 107 ------AKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYG 160
D + D W + +N
Sbjct: 329 RLSIIAESIRDGLATW-------DNW---------------------------KHVN-CD 353
Query: 161 KIGSYVKITKEFLTSGAPQPFGARNEGRSLLSAVTERNIAGYADYVITEDSDLLVFGAKK 220
K+ + ++ + L E R + + +
Sbjct: 354 KLTTIIESSLNVLEP---------AEYRKM-----------FDRLSV------------- 380
Query: 221 IIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGI---------- 270
F +P+ L + ++ W +
Sbjct: 381 ------------FPPSAHIPTIL--------------LSLI-----WFDVIKSDVMVVVN 409
Query: 271 ----KGMGLKKAKDYVFSIMDPDFENRK-------------EYVKYAKVFPLTAILDMKV 313
+ K+ K+ SI E + ++ K F ++ +
Sbjct: 410 KLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYL 469
Query: 314 PAKWYRRI------IGSIEVICGFSMATIPFNMKVPAKWYRRII---GSIEVICGFSMAT 364
+Y I I E + F M + F + + I + G + T
Sbjct: 470 DQYFYSHIGHHLKNIEHPERMTLFRMVFLDFR------FLEQKIRHDSTAWNASGSILNT 523
Query: 365 IP-FILAGKAILDMKVPAKWYRRIIGSIE 392
+ I D P Y R++ +I
Sbjct: 524 LQQLKFYKPYICD-NDPK--YERLVNAIL 549
>1vqt_A Orotidine 5'-phosphate decarboxylase; TM0332, structural GEN joint
center for structural genomics, JCSG, protein structu
initiative, PSI; 2.00A {Thermotoga maritima} SCOP:
c.1.2.3
Length = 213
Score = 30.2 bits (69), Expect = 0.92
Identities = 8/29 (27%), Positives = 12/29 (41%), Gaps = 1/29 (3%)
Query: 148 DFENALRKINVYGKIGSYVKITKEFLTSG 176
D E+ +R I+ G VK+ G
Sbjct: 20 DMEDPIRFIDENGSF-EVVKVGHNLAIHG 47
>3qvo_A NMRA family protein; structural genomics, PSI-biology, midwest
center for structu genomics, MCSG, unknown function;
HET: MNB; 2.30A {Shigella flexneri 2A}
Length = 236
Score = 29.0 bits (65), Expect = 2.5
Identities = 11/59 (18%), Positives = 24/59 (40%), Gaps = 7/59 (11%)
Query: 45 GRHLPAKEATEEDRRKRAEIRHKQKAAELLHSGSSIIYKLDLSGNCCFMDREKLPSALK 103
RH+ + A ++ ++ R K + + S II D+ ++ L A++
Sbjct: 36 ARHVINQLADKQTIKQTLFARQPAKIHKPYPTNSQII-MGDV------LNHAALKQAMQ 87
>1hdo_A Biliverdin IX beta reductase; foetal metabolism, HAEM degradation,
flavin reductase, diaphorase, green HAEM binding
protein; HET: NAP; 1.15A {Homo sapiens} SCOP: c.2.1.2
PDB: 1he2_A* 1he3_A* 1he4_A* 1he5_A*
Length = 206
Score = 28.0 bits (63), Expect = 5.2
Identities = 4/59 (6%), Positives = 15/59 (25%), Gaps = 8/59 (13%)
Query: 45 GRHLPAKEATEEDRRKRAEIRHKQKAAELLHSGSSIIYKLDLSGNCCFMDREKLPSALK 103
G +A + +R + + ++ D+ + + +
Sbjct: 16 GLTT-LAQAVQAGYEVTVLVRDSSRLPSEGPRPAHVV-VGDV------LQAADVDKTVA 66
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
0.326 0.140 0.435
Gapped
Lambda K H
0.267 0.0644 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,201,425
Number of extensions: 455540
Number of successful extensions: 1279
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1253
Number of HSP's successfully gapped: 37
Length of query: 443
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 346
Effective length of database: 3,993,456
Effective search space: 1381735776
Effective search space used: 1381735776
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 59 (26.7 bits)