RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1209
(61 letters)
>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 = 69.9 bits (171), Expect = 2e-16
Identities = 37/62 (59%), Positives = 46/62 (74%), Gaps = 7/62 (11%)
Query: 2 GILGLAKLVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPT 54
GI GLAKL+ADVAPS+IRE+ RK+ IDASMS+YQFLIAVR G+ L + +GE T
Sbjct: 1 GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETT 60
Query: 55 RY 56
+
Sbjct: 61 SH 62
>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 = 69.5 bits (170), Expect = 3e-16
Identities = 37/62 (59%), Positives = 46/62 (74%), Gaps = 7/62 (11%)
Query: 2 GILGLAKLVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPT 54
GI GLAKL+ADVAPS+IRE+ RK+ IDASMS+YQFLIAVR G+ L + +GE T
Sbjct: 1 GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETT 60
Query: 55 RY 56
+
Sbjct: 61 SH 62
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus
amylolyticus}
Length = 363
Score = 60.3 bits (146), Expect = 5e-13
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 1 MGILGLAKLVADVAPSSIRE-----SRKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPT 54
MG+ L ++ A + I + + I ID +LYQFL A+R G LM +G T
Sbjct: 11 MGV-DLKDIIPGEAKTVIEDLRILHGKIIVIDGYNALYQFLAAIRQPDGTPLMDNNGRIT 69
Query: 55 RYSVY 59
+
Sbjct: 70 SHLSG 74
>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 = 54.8 bits (132), Expect = 3e-11
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 1 MGILGLAKLVADVAPSSIRE--SRKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPTRY 56
MG+ + S + +K+ ID +LYQFL ++R +G+ L + GE T
Sbjct: 1 MGVQFGDFIPK--NIISFEDLKGKKVAIDGMNALYQFLTSIRLRDGSPLRNRKGEITSA 57
>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 = 52.2 bits (125), Expect = 3e-10
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 1 MGILGLAKLVADVAPSSIRE--SRKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTRYS 57
MG+ + +++ + +KI IDA ++YQFL +R + G LM G T +
Sbjct: 1 MGV-PIGEIIPR-KEIELENLYGKKIAIDALNAIYQFLSTIRQKDGTPLMDSKGRITSHL 58
Query: 58 VY 59
Sbjct: 59 SG 60
>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 = 51.5 bits (123), Expect = 6e-10
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 8/53 (15%)
Query: 12 DVAPSSIRES-------RKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPTRY 56
D+ RE +++ ID +LYQFL A+R +G LM G T +
Sbjct: 2 DLVKDVKRELSFSELKGKRVSIDGYNALYQFLAAIRQPDGTPLMDSQGRVTSH 54
>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 = 51.0 bits (122), Expect = 1e-09
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 5/59 (8%)
Query: 1 MGILGLAKLVADVAPSSIRE--SRKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTRY 56
MG + L + +KI +DA +LYQF+ +R G L G T +
Sbjct: 1 MGA-DIGDLFERE-EVELEYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSH 57
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA;
2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z*
Length = 352
Score = 47.3 bits (112), Expect = 2e-08
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 1 MGILGLAKLVADVA-PSSIRE--SRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTR 55
MGI GL + + + + P +R+ + + +D L++ IA + + GEPT
Sbjct: 1 MGIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAK-----GEPTD 53
>2ch5_A NAGK protein; transferase, N-acetylglucosamine, glcnac, sugar
kinase, RIBO H fold, sugar kinase/HSP70/actin
superfamily, domain rotati conformation; HET: NAG NDG;
1.9A {Homo sapiens} SCOP: c.55.1.5 c.55.1.5 PDB: 2ch6_A*
Length = 347
Score = 23.8 bits (51), Expect = 3.6
Identities = 11/53 (20%), Positives = 20/53 (37%)
Query: 3 ILGLAKLVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTR 55
G + +A+ A SR I A L + ++AV E + ++
Sbjct: 216 FAGFCRKIAEGAQQGDPLSRYIFRKAGEMLGRHIVAVLPEIDPVLFQGKIGLP 268
>1chu_A Protein (L-aspartate oxidase); flavoenzyme, NAD biosynthesis, FAD,
oxidoreductase; 2.20A {Escherichia coli} SCOP: a.7.3.1
c.3.1.4 d.168.1.1 PDB: 1knr_A* 1knp_A*
Length = 540
Score = 23.4 bits (51), Expect = 5.3
Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 2/22 (9%)
Query: 34 QFLI--AVRSEGNQLMSVDGEP 53
FL+ A+R EG L DG
Sbjct: 255 NFLLTEALRGEGAYLKRPDGTR 276
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
0.320 0.135 0.366
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: 842,692
Number of extensions: 34456
Number of successful extensions: 57
Number of sequences better than 10.0: 1
Number of HSP's gapped: 52
Number of HSP's successfully gapped: 10
Length of query: 61
Length of database: 6,701,793
Length adjustment: 32
Effective length of query: 29
Effective length of database: 5,808,321
Effective search space: 168441309
Effective search space used: 168441309
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: 51 (23.8 bits)