RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12967
(222 letters)
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus
amylolyticus}
Length = 363
Score = 92.6 bits (230), Expect = 2e-22
Identities = 28/101 (27%), Positives = 49/101 (48%), Gaps = 12/101 (11%)
Query: 56 MGVKDLWGILTPICER--KPIWELQDKTIAIDLSAWIC---------DSSTIAEHSSQKN 104
MGV L I+ + + + L K I ID + D + + +++ +
Sbjct: 11 MGVD-LKDIIPGEAKTVIEDLRILHGKIIVIDGYNALYQFLAAIRQPDGTPLMDNNGRIT 69
Query: 105 MYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQ 145
+L LF+RT ++ G+KP++V +GK P LK IE+R+
Sbjct: 70 SHLSGLFYRTINIVEAGIKPVYVFDGKPPELKAREIERRKA 110
>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 = 90.3 bits (224), Expect = 1e-21
Identities = 21/101 (20%), Positives = 45/101 (44%), Gaps = 12/101 (11%)
Query: 56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWIC---------DSSTIAEHSSQKNMY 106
MG + + E + K IA+D + D + + + + +
Sbjct: 1 MGAD-IGDLFER--EEVELEYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSH 57
Query: 107 LRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQ 147
L + +R S ++ +G++P+FV +G+ P K IE+R++ +
Sbjct: 58 LSGILYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKKRR 98
>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 = 90.3 bits (224), Expect = 1e-21
Identities = 23/101 (22%), Positives = 43/101 (42%), Gaps = 12/101 (11%)
Query: 57 GVKDLWGILTPIC----ERKPIWELQDKTIAIDLSAWIC--------DSSTIAEHSSQKN 104
G++ L ++ + I + +AID S I + +
Sbjct: 1 GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETT 60
Query: 105 MYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQ 145
+L +F+RT ++ G+KP++V +GK P LK + KR +
Sbjct: 61 SHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSE 101
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A
{Homo sapiens} PDB: 3qeb_Z* 3qea_Z*
Length = 352
Score = 88.9 bits (220), Expect = 4e-21
Identities = 20/94 (21%), Positives = 39/94 (41%), Gaps = 4/94 (4%)
Query: 56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDS-STIAEHSSQKNM---YLRNLF 111
MG++ L + E + + + + +A+D W+ AE ++ Y+
Sbjct: 1 MGIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAKGEPTDRYVGFCM 60
Query: 112 FRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQ 145
+ LL G+KPI V +G K + R++
Sbjct: 61 KFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRE 94
>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 = 89.2 bits (221), Expect = 4e-21
Identities = 23/101 (22%), Positives = 43/101 (42%), Gaps = 12/101 (11%)
Query: 57 GVKDLWGILTPIC----ERKPIWELQDKTIAIDLSAWIC--------DSSTIAEHSSQKN 104
G++ L ++ + I + +AID S I + +
Sbjct: 1 GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETT 60
Query: 105 MYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQ 145
+L +F+RT ++ G+KP++V +GK P LK + KR +
Sbjct: 61 SHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSE 101
>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 = 88.4 bits (219), Expect = 5e-21
Identities = 33/130 (25%), Positives = 58/130 (44%), Gaps = 17/130 (13%)
Query: 56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWIC---------DSSTIAEHSSQKNMY 106
MGV + I+ + + L K IAID I D + + + + +
Sbjct: 1 MGVP-IGEIIPR--KEIELENLYGKKIAIDALNAIYQFLSTIRQKDGTPLMDSKGRITSH 57
Query: 107 LRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAG-----SRA 161
L LF+RT L+ G+KP++V +G+ P K +EKR++A+ + + +A A
Sbjct: 58 LSGLFYRTINLMEAGIKPVYVFDGEPPEFKKKELEKRREAREEAEEKWREALEKGEIEEA 117
Query: 162 RNLFFRTSYL 171
R R + +
Sbjct: 118 RKYAQRATRV 127
>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 = 85.8 bits (212), Expect = 4e-20
Identities = 24/93 (25%), Positives = 46/93 (49%), Gaps = 9/93 (9%)
Query: 64 ILTPICERKPIWELQDKTIAIDLSAWIC---------DSSTIAEHSSQKNMYLRNLFFRT 114
++ + EL+ K ++ID + D + + + + +L LF+RT
Sbjct: 3 LVKDVKRELSFSELKGKRVSIDGYNALYQFLAAIRQPDGTPLMDSQGRVTSHLSGLFYRT 62
Query: 115 SYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQ 147
+L GV PI+V +GK P K + +E+R++A+
Sbjct: 63 INILEEGVIPIYVFDGKPPEQKSEELERRRKAK 95
>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 = 84.5 bits (209), Expect = 1e-19
Identities = 23/101 (22%), Positives = 43/101 (42%), Gaps = 12/101 (11%)
Query: 56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWI---------CDSSTIAEHSSQKNMY 106
MGV+ + +L+ K +AID + D S + +
Sbjct: 1 MGVQ-FGDFIPK--NIISFEDLKGKKVAIDGMNALYQFLTSIRLRDGSPLRNRKGEITSA 57
Query: 107 LRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQ 147
+F++T +LL + PI+V +G+ P LK T + R++ +
Sbjct: 58 YNGVFYKTIHLLENDITPIWVFDGEPPKLKEKTRKVRREMK 98
>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 = 31.4 bits (70), Expect = 0.24
Identities = 27/138 (19%), Positives = 49/138 (35%), Gaps = 23/138 (16%)
Query: 6 LWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRAIMGVKDLWGIL 65
+W + + +L ++ + +S TI+ S +YL + +++ + +
Sbjct: 395 IWFDVIKSDVMVVVNKLHKYSL---VEKQPKES-TISIPS----IYLELKVKLENEYALH 446
Query: 66 TPICERKPIWELQDKTIAIDLSAWICDS---STIAEHSSQKNMYLRNLFFRTSYLLLLGV 122
I + I + D DL D S I H R FR +L
Sbjct: 447 RSIVDHYNIPKTFDSD---DLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFR-- 501
Query: 123 KPIFVLEGKAPVLKHDTI 140
F LE K ++HD+
Sbjct: 502 ---F-LEQK---IRHDST 512
Score = 29.8 bits (66), Expect = 0.83
Identities = 21/124 (16%), Positives = 39/124 (31%), Gaps = 18/124 (14%)
Query: 12 PICERKPIWELQDKTIAIDLSAWI-------CDSSTIAEHSSQKNMYLRAIMGVKDLWGI 64
+ +P +L+ + + + + + +A + ++ M K W
Sbjct: 130 NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCL-SYKVQCKMDFKIFW-- 186
Query: 65 LTPICERKP---IWELQD--KTIAIDLSAWICDSSTIAEHSSQKNMYLRNLFFRTSY--- 116
L P + LQ I + ++ SS I LR L Y
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246
Query: 117 LLLL 120
LL+L
Sbjct: 247 LLVL 250
>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 = 28.1 bits (62), Expect = 3.2
Identities = 43/274 (15%), Positives = 81/274 (29%), Gaps = 113/274 (41%)
Query: 38 SSTIAEHSSQKNMYLRAIMG-----------VKDLW----GILTPICER--KPIWELQDK 80
+S + + N L AI G ++DL+ ++ + + + + EL
Sbjct: 142 NSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRT 201
Query: 81 TIA--------IDLSAWICDSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVK-P-IFVLE- 129
T+ +++ W+ + S + YLL + + P I V++
Sbjct: 202 TLDAEKVFTQGLNILEWLENPSNTPD---------------KDYLLSIPISCPLIGVIQL 246
Query: 130 ----------GKAPVLKHDTIEKRQQAQGRSA-GRNVQ-----AGSRARNLFFRTS---- 169
G P E R +G + + + A + + FF +
Sbjct: 247 AHYVVTAKLLGFTPG------ELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAI 300
Query: 170 -YLLLLGVK-----PIFVLEGKAPVLKHDTIE---------------KRQQAQGRSAGRN 208
L +GV+ P L P + D++E ++Q Q N
Sbjct: 301 TVLFFIGVRCYEAYPNTSLP---PSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTN 357
Query: 209 --------------------VQAGSRARLKGLQT 222
V +G L GL
Sbjct: 358 SHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNL 391
Score = 28.1 bits (62), Expect = 3.2
Identities = 29/172 (16%), Positives = 51/172 (29%), Gaps = 61/172 (35%)
Query: 11 TPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLR-AIMGV-KDLWGILTPI 68
P ERK + + + HS L A + KDL
Sbjct: 407 IPFSERKLKFSNRFLPV------------ASPFHSH----LLVPASDLINKDLVKNNVSF 450
Query: 69 CE---RKPIW------ELQ--DKTIAIDLSAWIC------DSSTIAEHSSQKNMYLRNLF 111
+ P++ +L+ +I+ + I +++T
Sbjct: 451 NAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTT---------------Q 495
Query: 112 FRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRARN 163
F+ +++L G P G A L T + G R + AG+ N
Sbjct: 496 FKATHILDFG--P-----GGASGLGVLT---HRNKDGTGV-RVIVAGTLDIN 536
>2ree_A CURA; GNAT, S-acetyltransferase, decarboxylase, polyketid synthase,
loading, phosphopantetheine, transferase, lyase; HET:
SO4; 1.95A {Lyngbya majuscula} PDB: 2ref_A*
Length = 224
Score = 26.5 bits (58), Expect = 5.8
Identities = 19/97 (19%), Positives = 32/97 (32%), Gaps = 3/97 (3%)
Query: 74 IWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAP 133
I EL+DK + S I + + + + L LL + + P +G
Sbjct: 58 ILELEDKIVGAIYSQRIDNPQLLDNKTCTQVPLLHTESGVVVQLLAVNILPELQNQGLGD 117
Query: 134 VLKHDTIEKRQQAQGRSAGRNVQAGSRARNLFFRTSY 170
L ++ Q G V A + RN +
Sbjct: 118 RLLEFMLQYCAQISGV---EKVVAVTLCRNYPDYSPM 151
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
0.321 0.136 0.410
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: 3,173,042
Number of extensions: 174243
Number of successful extensions: 247
Number of sequences better than 10.0: 1
Number of HSP's gapped: 231
Number of HSP's successfully gapped: 31
Length of query: 222
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 132
Effective length of database: 4,188,903
Effective search space: 552935196
Effective search space used: 552935196
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: 55 (25.3 bits)