BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 044842
(602 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex
Length = 346
Score = 97.1 bits (240), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 80/259 (30%), Positives = 127/259 (49%), Gaps = 31/259 (11%)
Query: 9 DLLKPYARFEGLDFLRDKRVAVDLSYWIVQHETAIKK-NSVP--------KPHLRLTFFR 59
DL+K R L+ KRV++D + Q AI++ + P HL F+R
Sbjct: 2 DLVKDVKRELSFSELKGKRVSIDGYNALYQFLAAIRQPDGTPLMDSQGRVTSHLSGLFYR 61
Query: 60 TINLFAKFGAFPVFVVDGTPSPLKSQARLARFYRSTIDAS-TLPVAE-EGILVE---RNQ 114
TIN+ + G P++V DG P KS+ L R ++ +A L A+ EG + E +Q
Sbjct: 62 TINILEE-GVIPIYVFDGKPPEQKSE-ELERRRKAKEEAERKLERAKSEGKIEELRKYSQ 119
Query: 115 TFLKC----VQECVELLELFGMPVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGAK 170
L+ V+E +LL G+P+++A E EA A LN G A + D DA LFGAK
Sbjct: 120 AILRLSNIMVEESKKLLRAMGIPIVQAPSEGEAEAAYLNKLGLSWAAASQDYDAILFGAK 179
Query: 171 CVVKCIRPNTKEPF-----------ECYCISDIEAGLGLKRKHLIAMSLLIGNDHDLNGV 219
+V+ + K E + LG+ R+ LI + +LIG D++ +G+
Sbjct: 180 RLVRNLTITGKRKLPNKDVYVEIKPELIETEILLKKLGITREQLIDIGILIGTDYNPDGI 239
Query: 220 QGIGLDTALQFVQNFSEDE 238
+GIG + AL+ ++ + + E
Sbjct: 240 RGIGPERALKIIKKYGKIE 258
>pdb|1B43|A Chain A, Fen-1 From P. Furiosus
pdb|1B43|B Chain B, Fen-1 From P. Furiosus
Length = 340
Score = 92.4 bits (228), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 69/242 (28%), Positives = 115/242 (47%), Gaps = 29/242 (11%)
Query: 20 LDFLRDKRVAVDLSYWIVQHETAIK-KNSVP--------KPHLRLTFFRTINLFAKFGAF 70
L+ L K++A+D I Q + I+ K+ P HL F+RTINL + G
Sbjct: 16 LENLYGKKIAIDALNAIYQFLSTIRQKDGTPLMDSKGRITSHLSGLFYRTINLM-EAGIK 74
Query: 71 PVFVVDGTPSPLKSQARLARFYRSTIDASTLPVAEEGILVERNQTFLK--------CVQE 122
PV+V DG P K + R A E +E + + + +++
Sbjct: 75 PVYVFDGEPPEFKKKELEKRREAREEAEEKWREALEKGEIEEARKYAQRATRVNEMLIED 134
Query: 123 CVELLELFGMPVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGAKCVVKCIRPNTKE 182
+LLEL G+P+++A E EA A + ++G V A + D D+ LFGA +V+ + K
Sbjct: 135 AKKLLELMGIPIVQAPSEGEAQAAYMAAKGSVYASASQDYDSLLFGAPRLVRNLTITGKR 194
Query: 183 PF-----------ECYCISDIEAGLGLKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFV 231
E + ++ L L R+ LI +++L+G D++ G++GIGL AL+ V
Sbjct: 195 KLPGKNVYVEIKPELIILEEVLKELKLTREKLIELAILVGTDYNPGGIKGIGLKKALEIV 254
Query: 232 QN 233
++
Sbjct: 255 RH 256
>pdb|1MC8|A Chain A, Crystal Structure Of Flap Endonuclease-1 R42e Mutant From
Pyrococcus Horikoshii
pdb|1MC8|B Chain B, Crystal Structure Of Flap Endonuclease-1 R42e Mutant From
Pyrococcus Horikoshii
Length = 343
Score = 86.3 bits (212), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 34/250 (13%)
Query: 20 LDFLRDKRVAVDLSYWIVQHETAIKK-NSVP--------KPHLRLTFFRTINLFAKFGAF 70
L+ L K++A+D I Q + I++ + P HL F+RTINL + G
Sbjct: 16 LENLYGKKIAIDALNAIYQFLSTIRQEDGTPLMDSKGRITSHLSGLFYRTINLM-EAGIK 74
Query: 71 PVFVVDGTPSPLKSQARLARFYRSTIDASTLPVAE---EGILVERNQTFLKC-------V 120
P +V DG P K + R R + + L E +G L E + + +
Sbjct: 75 PAYVFDGKPPEFKRKELEKR--REAREEAELKWKEALAKGNLEEARKYAQRATKVNEMLI 132
Query: 121 QECVELLELFGMPVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGAKCVVKCIRPNT 180
++ +LL+L G+P+++A E EA A + S+G V A + D D+ LFGA +++ +
Sbjct: 133 EDAKKLLQLMGIPIIQAPSEGEAQAAYMASKGDVYASASQDYDSLLFGAPRLIRNLTITG 192
Query: 181 KEPF-----------ECYCISDIEAGLGLKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQ 229
K E + ++ L + R+ LI +++L+G D++ GV+GIG AL+
Sbjct: 193 KRKMPGKDVYVEIKPELVVLDEVLKELKITREKLIELAILVGTDYNPGGVKGIGPKKALE 252
Query: 230 FVQNFSEDEI 239
V+ +S D +
Sbjct: 253 IVR-YSRDPL 261
>pdb|1UL1|X Chain X, Crystal Structure Of The Human Fen1-Pcna Complex
pdb|1UL1|Y Chain Y, Crystal Structure Of The Human Fen1-Pcna Complex
pdb|1UL1|Z Chain Z, Crystal Structure Of The Human Fen1-Pcna Complex
Length = 379
Score = 85.9 bits (211), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 74/249 (29%), Positives = 113/249 (45%), Gaps = 22/249 (8%)
Query: 26 KRVAVDLSYWIVQHETAIKKNS--------VPKPHLRLTFFRTINLFAKFGAFPVFVVDG 77
++VA+D S I Q A+++ HL F+RTI + G PV+V DG
Sbjct: 28 RKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMEN-GIKPVYVFDG 86
Query: 78 TPSPLKSQARLARFYRSTIDASTLPVAEEGILVERNQTFLKCV--------QECVELLEL 129
P LKS R R L A+ + + F K + EC LL L
Sbjct: 87 KPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSL 146
Query: 130 FGMPVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGAKCVVKCIRPN--TKEPFECY 187
G+P L A EAEA CA L G V A T D D FG+ +++ + + K P + +
Sbjct: 147 MGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEF 206
Query: 188 CISDIEAGLGLKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNF-SEDEILNILHKI 246
+S I LGL ++ + + +L+G+D+ ++GIG A+ +Q S +EI+ L
Sbjct: 207 HLSRILQELGLNQEQFVDLCILLGSDY-CESIRGIGPKRAVDLIQKHKSIEEIVRRLDP- 264
Query: 247 GNGDIPQYW 255
+P+ W
Sbjct: 265 NKYPVPENW 273
>pdb|3Q8K|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (Wt) In
Complex With Product 5'-Flap Dna, Sm3+, And K+
pdb|3Q8L|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (Wt) In
Complex With Substrate 5'-Flap Dna, Sm3+, And K+
Length = 341
Score = 85.5 bits (210), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 74/249 (29%), Positives = 113/249 (45%), Gaps = 22/249 (8%)
Query: 26 KRVAVDLSYWIVQHETAIKKNS--------VPKPHLRLTFFRTINLFAKFGAFPVFVVDG 77
++VA+D S I Q A+++ HL F+RTI + G PV+V DG
Sbjct: 28 RKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMEN-GIKPVYVFDG 86
Query: 78 TPSPLKSQARLARFYRSTIDASTLPVAEEGILVERNQTFLKCV--------QECVELLEL 129
P LKS R R L A+ + + F K + EC LL L
Sbjct: 87 KPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSL 146
Query: 130 FGMPVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGAKCVVKCIRPN--TKEPFECY 187
G+P L A EAEA CA L G V A T D D FG+ +++ + + K P + +
Sbjct: 147 MGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEF 206
Query: 188 CISDIEAGLGLKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNF-SEDEILNILHKI 246
+S I LGL ++ + + +L+G+D+ ++GIG A+ +Q S +EI+ L
Sbjct: 207 HLSRILQELGLNQEQFVDLCILLGSDY-CESIRGIGPKRAVDLIQKHKSIEEIVRRLDP- 264
Query: 247 GNGDIPQYW 255
+P+ W
Sbjct: 265 NKYPVPENW 273
>pdb|1A76|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii
pdb|1A77|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii
Length = 326
Score = 84.7 bits (208), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 73/258 (28%), Positives = 127/258 (49%), Gaps = 27/258 (10%)
Query: 3 VGGKFWDLL-KPYARFEGLDFLRDKRVAVDLSYWIVQHETAIK-KNSVPKPHLRL----- 55
+G +F D + K FE L + K+VA+D + Q T+I+ ++ P + +
Sbjct: 1 MGVQFGDFIPKNIISFEDL---KGKKVAIDGMNALYQFLTSIRLRDGSPLRNRKGEITSA 57
Query: 56 ---TFFRTINLFAKFGAFPVFVVDGTPSPLKSQARLARFYRSTIDASTLPVAE------- 105
F++TI+L P++V DG P LK + R R R + + L + E
Sbjct: 58 YNGVFYKTIHLLEN-DITPIWVFDGEPPKLKEKTRKVR--REMKEKAELKMKEAIKKEDF 114
Query: 106 -EGILVERNQTFL--KCVQECVELLELFGMPVLKAKGEAEALCAQLNSEGYVDACITADS 162
E + ++L K V+ C LL L G+P ++A E EA + + +G V A ++ D
Sbjct: 115 EEAAKYAKRVSYLTPKMVENCKYLLSLMGIPYVEAPSEGEAQASYMAKKGDVWAVVSQDY 174
Query: 163 DAFLFGAKCVVKCIRPNTKEPFECYCISDIEAGLGLKRKHLIAMSLLIGNDHDLNGVQGI 222
DA L+GA VV+ + TKE E ++++ L + LI +++ +G D++ GV+GI
Sbjct: 175 DALLYGAPRVVRNL-TTTKEMPELIELNEVLEDLRISLDDLIDIAIFMGTDYNPGGVKGI 233
Query: 223 GLDTALQFVQNFSEDEIL 240
G A + V++ ++L
Sbjct: 234 GFKRAYELVRSGVAKDVL 251
>pdb|3Q8M|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (D181a)
In Complex With Substrate 5'-Flap Dna And K+
pdb|3Q8M|B Chain B, Crystal Structure Of Human Flap Endonuclease Fen1 (D181a)
In Complex With Substrate 5'-Flap Dna And K+
Length = 341
Score = 82.0 bits (201), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 73/249 (29%), Positives = 112/249 (44%), Gaps = 22/249 (8%)
Query: 26 KRVAVDLSYWIVQHETAIKKNS--------VPKPHLRLTFFRTINLFAKFGAFPVFVVDG 77
++VA+D S I Q A+++ HL F+RTI + G PV+V DG
Sbjct: 28 RKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMEN-GIKPVYVFDG 86
Query: 78 TPSPLKSQARLARFYRSTIDASTLPVAEEGILVERNQTFLKCV--------QECVELLEL 129
P LKS R R L A+ + + F K + EC LL L
Sbjct: 87 KPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSL 146
Query: 130 FGMPVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGAKCVVKCIRPN--TKEPFECY 187
G+P L A EAEA CA L G V A T D FG+ +++ + + K P + +
Sbjct: 147 MGIPYLDAPSEAEASCAALVKAGKVYAAATEDMACLTFGSPVLMRHLTASEAKKLPIQEF 206
Query: 188 CISDIEAGLGLKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNF-SEDEILNILHKI 246
+S I LGL ++ + + +L+G+D+ ++GIG A+ +Q S +EI+ L
Sbjct: 207 HLSRILQELGLNQEQFVDLCILLGSDY-CESIRGIGPKRAVDLIQKHKSIEEIVRRLDP- 264
Query: 247 GNGDIPQYW 255
+P+ W
Sbjct: 265 NKYPVPENW 273
>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From
Hyperthermophilic Archaeon Desulfurococcus Amylolyticus
Length = 363
Score = 80.5 bits (197), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 64/248 (25%), Positives = 112/248 (45%), Gaps = 31/248 (12%)
Query: 17 FEGLDFLRDKRVAVDLSYWIVQHETAIKK---------NSVPKPHLRLTFFRTINLFAKF 67
E L L K + +D + Q AI++ N HL F+RTIN+ +
Sbjct: 27 IEDLRILHGKIIVIDGYNALYQFLAAIRQPDGTPLMDNNGRITSHLSGLFYRTINI-VEA 85
Query: 68 GAFPVFVVDGTPSPLKS---------QARLARFYRSTIDASTLPVAEEGILVERNQTFLK 118
G PV+V DG P LK+ + A+ Y + + L +A ++ T +
Sbjct: 86 GIKPVYVFDGKPPELKAREIERRKAVKEEAAKKYEEAVQSGDLELARRYAMMSAKLTE-E 144
Query: 119 CVQECVELLELFGMPVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGAKCVVKCIRP 178
V++ LL+ G+P ++A E EA A + +G A + D D+ LFG+ +V+ +
Sbjct: 145 MVRDAKSLLDAMGIPWVQAPAEGEAQAAYIVKKGDAYASASQDYDSLLFGSPKLVRNLTI 204
Query: 179 NTKEPF-----------ECYCISDIEAGLGLKRKHLIAMSLLIGNDHDLNGVQGIGLDTA 227
+ + E + + LG+ ++LI + +L+G D++ +G +GIG A
Sbjct: 205 SGRRKLPRKNEYVEVKPELIELDKLLVQLGITLENLIDIGILLGTDYNPDGFEGIGPKKA 264
Query: 228 LQFVQNFS 235
LQ V+ +
Sbjct: 265 LQLVKAYG 272
>pdb|1RXV|A Chain A, Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna
pdb|1RXV|B Chain B, Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna
pdb|1RXW|A Chain A, Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna
Length = 336
Score = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 58/246 (23%), Positives = 105/246 (42%), Gaps = 33/246 (13%)
Query: 20 LDFLRDKRVAVDLSYWIVQHETAIKK-NSVP--------KPHLRLTFFRTINLFAKFGAF 70
L++ K++AVD + Q + I++ + P HL +R N+ + G
Sbjct: 16 LEYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNM-VEVGIR 74
Query: 71 PVFVVDGTPSPLKS---------QARLARFYRSTIDASTLPVAEEGILVERNQTFLKCVQ 121
PVFV DG P K +A + + + A + R ++ V
Sbjct: 75 PVFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAALQAGDKDAKKYAQAAGRVDEYI--VD 132
Query: 122 ECVELLELFGMPVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGAKCVVKCIRPNTK 181
LL G+P + A E EA A + ++G V+ + D D+ LFG+ + + + K
Sbjct: 133 SAKTLLSYMGIPFVDAPSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAITGK 192
Query: 182 EPF-----------ECYCISDIEAGLGLKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQF 230
E + LGL R+ LI +++L+G D++ GV+G+G+ AL +
Sbjct: 193 RKLPGKNVYVDVKPEIIILESNLKRLGLTREQLIDIAILVGTDYN-EGVKGVGVKKALNY 251
Query: 231 VQNFSE 236
++ + +
Sbjct: 252 IKTYGD 257
>pdb|3QEA|Z Chain Z, Crystal Structure Of Human Exonuclease 1 Exo1 (Wt) In
Complex With Dna (Complex Ii)
pdb|3QEB|Z Chain Z, Crystal Structure Of Human Exonuclease 1 Exo1 (Wt) In
Complex With Dna And Mn2+ (Complex Iii)
Length = 352
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 65/243 (26%), Positives = 107/243 (44%), Gaps = 32/243 (13%)
Query: 28 VAVDLSYWIVQHETAI---KKNSVPKPHLRLTFF--RTINLFAKFGAFPVFVVDGTPSPL 82
VAVD W+ H+ AI +K + +P R F + +N+ G P+ V DG P
Sbjct: 27 VAVDTYCWL--HKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLP- 83
Query: 83 KSQARLARFYRSTIDASTLP---VAEEGILVERNQTFLKCV-------QECVELLELFGM 132
S+ + R R A+ L + EG + E + F + + + ++ G+
Sbjct: 84 -SKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGV 142
Query: 133 PVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGAKCVV-------KCIRPNTKEPFE 185
L A EA+A A LN G V A IT DSD FG K V+ + +
Sbjct: 143 DCLVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQARLGM 202
Query: 186 CYCISDIEAGLGLKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSEDEILNILHK 245
C + D+ + M +L G D+ L+ ++GIGL A + ++ + +I+ ++ K
Sbjct: 203 CRQLGDV-----FTEEKFRYMCILSGCDY-LSSLRGIGLAKACKVLRLANNPDIVKVIKK 256
Query: 246 IGN 248
IG+
Sbjct: 257 IGH 259
>pdb|3QE9|Y Chain Y, Crystal Structure Of Human Exonuclease 1 Exo1 (D173a) In
Complex With Dna (Complex I)
pdb|3QE9|Z Chain Z, Crystal Structure Of Human Exonuclease 1 Exo1 (D173a) In
Complex With Dna (Complex I)
Length = 352
Score = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 64/243 (26%), Positives = 106/243 (43%), Gaps = 32/243 (13%)
Query: 28 VAVDLSYWIVQHETAI---KKNSVPKPHLRLTFF--RTINLFAKFGAFPVFVVDGTPSPL 82
VAVD W+ H+ AI +K + +P R F + +N+ G P+ V DG P
Sbjct: 27 VAVDTYCWL--HKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLP- 83
Query: 83 KSQARLARFYRSTIDASTLP---VAEEGILVERNQTFLKCV-------QECVELLELFGM 132
S+ + R R A+ L + EG + E + F + + + ++ G+
Sbjct: 84 -SKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGV 142
Query: 133 PVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGAKCVV-------KCIRPNTKEPFE 185
L A EA+A A LN G V A IT DS FG K V+ + +
Sbjct: 143 DCLVAPYEADAQLAYLNKAGIVQAIITEDSALLAFGCKKVILKMDQFGNGLEIDQARLGM 202
Query: 186 CYCISDIEAGLGLKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSEDEILNILHK 245
C + D+ + M +L G D+ L+ ++GIGL A + ++ + +I+ ++ K
Sbjct: 203 CRQLGDV-----FTEEKFRYMCILSGCDY-LSSLRGIGLAKACKVLRLANNPDIVKVIKK 256
Query: 246 IGN 248
IG+
Sbjct: 257 IGH 259
>pdb|1BGX|T Chain T, Taq Polymerase In Complex With Tp7, An Inhibitory Fab
pdb|1TAU|A Chain A, Taq Polymerase (E.C.2.7.7.7)DNAB-Octylglucoside Complex
Length = 832
Score = 35.8 bits (81), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 37/135 (27%), Positives = 61/135 (45%), Gaps = 15/135 (11%)
Query: 114 QTFLKCVQECVELLELFGMPVLKAKG-EAEALCAQL----NSEGYVDACITADSDAFLFG 168
+ F + + EL++L G+ L+ G EA+ + A L EGY +TAD D +
Sbjct: 90 EDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKAEKEGYEVRILTADKDLYQLL 149
Query: 169 AKCVVKCIRPNTKEPFECYCISD--IEAGLGLKRKHLIAMSLLIGNDHD-LNGVQGIGLD 225
+ + + P E Y I+ + GL+ L G++ D L GV+GIG
Sbjct: 150 SDR-IHVLHP------EGYLITPAWLWEKYGLRPDQWADYRALTGDESDNLPGVKGIGEK 202
Query: 226 TALQFVQNFSEDEIL 240
TA + ++ + E L
Sbjct: 203 TARKLLEEWGSLEAL 217
>pdb|1TAQ|A Chain A, Structure Of Taq Dna Polymerase
Length = 832
Score = 35.4 bits (80), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 37/135 (27%), Positives = 61/135 (45%), Gaps = 15/135 (11%)
Query: 114 QTFLKCVQECVELLELFGMPVLKAKG-EAEALCAQL----NSEGYVDACITADSDAFLFG 168
+ F + + EL++L G+ L+ G EA+ + A L EGY +TAD D +
Sbjct: 90 EDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKAEKEGYEVRILTADKDLYQLL 149
Query: 169 AKCVVKCIRPNTKEPFECYCISD--IEAGLGLKRKHLIAMSLLIGNDHD-LNGVQGIGLD 225
+ + + P E Y I+ + GL+ L G++ D L GV+GIG
Sbjct: 150 SDR-IHVLHP------EGYLITPAWLWEKYGLRPDQWADYRALTGDESDNLPGVKGIGEK 202
Query: 226 TALQFVQNFSEDEIL 240
TA + ++ + E L
Sbjct: 203 TARKLLEEWGSLEAL 217
>pdb|2ZE3|A Chain A, Crystal Structure Of Dfa0005 Complexed With
Alpha-Ketoglutarate: A Novel Member Of The IclPEPM
SUPERFAMILY FROM ALKALI-Tolerant Deinococcus Ficus
Length = 275
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 31/66 (46%), Gaps = 10/66 (15%)
Query: 59 RTINLFAKFGAFPVFVVDGT---PSPL---KSQARLARFYRSTIDASTLPVAEEGILVER 112
RT+ FA G V + D T P+ L SQ R R+ IDAS +PV L R
Sbjct: 96 RTVEHFAALGVAGVNLEDATGLTPTELYDLDSQLRRIEAARAAIDASGVPV----FLNAR 151
Query: 113 NQTFLK 118
TFLK
Sbjct: 152 TDTFLK 157
>pdb|1V0D|A Chain A, Crystal Structure Of Caspase-Activated Dnase (Cad)
Length = 329
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 490 FLLTDENMKLVHSAFPKKVDHFLQENERRELKRKRTSS 527
L T EN+KLVH A KK H L E +R + R +T S
Sbjct: 293 LLFTAENLKLVHIACHKKTTHKL-ECDRSRIYRPQTGS 329
>pdb|3HG0|D Chain D, Crystal Structure Of A Darpin In Complex With Orf49 From
Lactococcal Phage Tp901-1
Length = 136
Score = 30.0 bits (66), Expect = 4.0, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 193 EAGLGLKRKHLIAMS-------LLIGNDHDLNGVQGIGLDTALQFVQNFSEDEILNILHK 245
E +GL HL AM+ +L+ N D+N + IG +T L V + EI+ +L K
Sbjct: 43 EDKVGLTPLHLAAMNDHLEIVEVLLKNGADVNAIDAIG-ETPLHLVAMYGHLEIVEVLLK 101
Query: 246 IG 247
G
Sbjct: 102 HG 103
>pdb|3NBN|A Chain A, Crystal Structure Of A Dimer Of Notch Transcription
Complex Trimers On Hes1 Dna
pdb|3NBN|D Chain D, Crystal Structure Of A Dimer Of Notch Transcription
Complex Trimers On Hes1 Dna
Length = 433
Score = 29.6 bits (65), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 30/132 (22%), Positives = 53/132 (40%), Gaps = 15/132 (11%)
Query: 264 AVSHSDESMPMIKSSHCSFCG------HPGTKRAHFKFSCE-YCINDNNEGCLKKPDGFK 316
+ +SD+ M + ++C KR HF S + + N ++ G
Sbjct: 83 GIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIGVF-----LS 137
Query: 317 CNCSLCNKNRKEKEQKKHENWWIKVCSKIALETNFPNDEIVTMYLCENNGTFTATDGPSI 376
+ +K K+K+ K+ + I +K+AL + + T YL G F A+ S
Sbjct: 138 KRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHAS---SQ 194
Query: 377 SWGSPMTEMLVD 388
WG+ +L D
Sbjct: 195 QWGAFFIHLLDD 206
>pdb|2F8X|C Chain C, Crystal Structure Of Activated Notch, Csl And Maml On
Hes-1 Promoter Dna Sequence
pdb|3V79|C Chain C, Structure Of Human Notch1 Transcription Complex Including
Csl, Ram, Ank, And Maml-1 On Hes-1 Promoter Dna Sequence
Length = 434
Score = 29.6 bits (65), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 30/132 (22%), Positives = 53/132 (40%), Gaps = 15/132 (11%)
Query: 264 AVSHSDESMPMIKSSHCSFCG------HPGTKRAHFKFSCE-YCINDNNEGCLKKPDGFK 316
+ +SD+ M + ++C KR HF S + + N ++ G
Sbjct: 83 GIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIGVF-----LS 137
Query: 317 CNCSLCNKNRKEKEQKKHENWWIKVCSKIALETNFPNDEIVTMYLCENNGTFTATDGPSI 376
+ +K K+K+ K+ + I +K+AL + + T YL G F A+ S
Sbjct: 138 KRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHAS---SQ 194
Query: 377 SWGSPMTEMLVD 388
WG+ +L D
Sbjct: 195 QWGAFFIHLLDD 206
>pdb|3BRG|C Chain C, Csl (Rbp-Jk) Bound To Dna
Length = 427
Score = 29.3 bits (64), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 30/132 (22%), Positives = 53/132 (40%), Gaps = 15/132 (11%)
Query: 264 AVSHSDESMPMIKSSHCSFCG------HPGTKRAHFKFSCE-YCINDNNEGCLKKPDGFK 316
+ +SD+ M + ++C KR HF S + + N ++ G
Sbjct: 83 GIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIGVF-----LS 137
Query: 317 CNCSLCNKNRKEKEQKKHENWWIKVCSKIALETNFPNDEIVTMYLCENNGTFTATDGPSI 376
+ +K K+K+ K+ + I +K+AL + + T YL G F A+ S
Sbjct: 138 KRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHAS---SQ 194
Query: 377 SWGSPMTEMLVD 388
WG+ +L D
Sbjct: 195 QWGAFYIHLLDD 206
>pdb|3IAG|C Chain C, Csl (Rbp-Jk) Bound To Hes-1 Nonconsensus Site
Length = 422
Score = 29.3 bits (64), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 30/132 (22%), Positives = 53/132 (40%), Gaps = 15/132 (11%)
Query: 264 AVSHSDESMPMIKSSHCSFCG------HPGTKRAHFKFSCE-YCINDNNEGCLKKPDGFK 316
+ +SD+ M + ++C KR HF S + + N ++ G
Sbjct: 78 GIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIGVF-----LS 132
Query: 317 CNCSLCNKNRKEKEQKKHENWWIKVCSKIALETNFPNDEIVTMYLCENNGTFTATDGPSI 376
+ +K K+K+ K+ + I +K+AL + + T YL G F A+ S
Sbjct: 133 KRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHAS---SQ 189
Query: 377 SWGSPMTEMLVD 388
WG+ +L D
Sbjct: 190 QWGAFYIHLLDD 201
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.135 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,147,091
Number of Sequences: 62578
Number of extensions: 778721
Number of successful extensions: 1601
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1562
Number of HSP's gapped (non-prelim): 21
length of query: 602
length of database: 14,973,337
effective HSP length: 104
effective length of query: 498
effective length of database: 8,465,225
effective search space: 4215682050
effective search space used: 4215682050
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)