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= psy12967
(222 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From
Hyperthermophilic Archaeon Desulfurococcus Amylolyticus
Length = 363
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 40/66 (60%)
Query: 92 DSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSA 151
D + + +++ + +L LF+RT ++ G+KP++V +GK P LK IE+R+ + +A
Sbjct: 57 DGTPLMDNNGRITSHLSGLFYRTINIVEAGIKPVYVFDGKPPELKAREIERRKAVKEEAA 116
Query: 152 GRNVQA 157
+ +A
Sbjct: 117 KKYEEA 122
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 34/58 (58%)
Query: 154 NVQAGSRARNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQA 211
N + S LF+RT ++ G+KP++V +GK P LK IE+R+ + +A + +A
Sbjct: 65 NGRITSHLSGLFYRTINIVEAGIKPVYVFDGKPPELKAREIERRKAVKEEAAKKYEEA 122
>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 = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 30/80 (37%), Positives = 42/80 (52%), Gaps = 9/80 (11%)
Query: 77 LQDKTIAID-LSAWICDSSTIAEHSSQKNM--------YLRNLFFRTSYLLLLGVKPIFV 127
L K IAID L+A STI + M +L LF+RT L+ G+KP +V
Sbjct: 19 LYGKKIAIDALNAIYQFLSTIRQEDGTPLMDSKGRITSHLSGLFYRTINLMEAGIKPAYV 78
Query: 128 LEGKAPVLKHDTIEKRQQAQ 147
+GK P K +EKR++A+
Sbjct: 79 FDGKPPEFKRKELEKRREAR 98
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex
Length = 346
Score = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 33/119 (27%), Positives = 59/119 (49%), Gaps = 9/119 (7%)
Query: 76 ELQDKTIAID----LSAWIC-----DSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIF 126
EL+ K ++ID L ++ D + + + + +L LF+RT +L GV PI+
Sbjct: 15 ELKGKRVSIDGYNALYQFLAAIRQPDGTPLMDSQGRVTSHLSGLFYRTINILEEGVIPIY 74
Query: 127 VLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRARNLFFRTSYLLLLGVKPIFVLEGK 185
V +GK P K + +E+R++A+ + + +A S + R +L + I V E K
Sbjct: 75 VFDGKPPEQKSEELERRRKAKEEAERKLERAKSEGKIEELRKYSQAILRLSNIMVEESK 133
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 37/58 (63%)
Query: 164 LFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRARLKGLQ 221
LF+RT +L GV PI+V +GK P K + +E+R++A+ + + +A S +++ L+
Sbjct: 58 LFYRTINILEEGVIPIYVFDGKPPEQKSEELERRRKAKEEAERKLERAKSEGKIEELR 115
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 14/96 (14%)
Query: 92 DSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQ------- 144
D + + + + +L + +R S ++ +G++P+FV +G+ P K IE+R+
Sbjct: 43 DGTPLKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKKRRAEAE 102
Query: 145 -------QAQGRSAGRNVQAGSRARNLFFRTSYLLL 173
QA + A + QA R ++ LL
Sbjct: 103 EMWIAALQAGDKDAKKYAQAAGRVDEYIVDSAKTLL 138
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 14/70 (20%)
Query: 159 SRARNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQ--------------QAQGRS 204
S + +R S ++ +G++P+FV +G+ P K IE+R+ QA +
Sbjct: 56 SHLSGILYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAALQAGDKD 115
Query: 205 AGRNVQAGSR 214
A + QA R
Sbjct: 116 AKKYAQAAGR 125
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 80 KTIAIDLSAWICD--------SSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGK 131
+ +AID S I + + +L +F+RT ++ G+KP++V +GK
Sbjct: 28 RKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGK 87
Query: 132 APVLKHDTIEKRQQ 145
P LK + KR +
Sbjct: 88 PPQLKSGELAKRSE 101
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 24/36 (66%)
Query: 164 LFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQ 199
+F+RT ++ G+KP++V +GK P LK + KR +
Sbjct: 66 MFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSE 101
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 80 KTIAIDLSAWICD--------SSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGK 131
+ +AID S I + + +L +F+RT ++ G+KP++V +GK
Sbjct: 28 RKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGK 87
Query: 132 APVLKHDTIEKRQQ 145
P LK + KR +
Sbjct: 88 PPQLKSGELAKRSE 101
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 26/44 (59%)
Query: 156 QAGSRARNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQ 199
+ S +F+RT ++ G+KP++V +GK P LK + KR +
Sbjct: 58 ETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSE 101
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 80 KTIAIDLSAWICD--------SSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGK 131
+ +AID S I + + +L +F+RT ++ G+KP++V +GK
Sbjct: 28 RKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGK 87
Query: 132 APVLKHDTIEKRQQ 145
P LK + KR +
Sbjct: 88 PPQLKSGELAKRSE 101
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 26/44 (59%)
Query: 156 QAGSRARNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQ 199
+ S +F+RT ++ G+KP++V +GK P LK + KR +
Sbjct: 58 ETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSE 101
>pdb|1B43|A Chain A, Fen-1 From P. Furiosus
pdb|1B43|B Chain B, Fen-1 From P. Furiosus
Length = 340
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 41/85 (48%), Gaps = 14/85 (16%)
Query: 66 TPICERKPIWELQ-----DKTIAID-LSAWICDSSTIAEHSSQKNM--------YLRNLF 111
PI E P E++ K IAID L+A STI + M +L LF
Sbjct: 3 VPIGEIIPRKEIELENLYGKKIAIDALNAIYQFLSTIRQKDGTPLMDSKGRITSHLSGLF 62
Query: 112 FRTSYLLLLGVKPIFVLEGKAPVLK 136
+RT L+ G+KP++V +G+ P K
Sbjct: 63 YRTINLMEAGIKPVYVFDGEPPEFK 87
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 159 SRARNLFFRTSYLLLLGVKPIFVLEGKAPVLK 190
S LF+RT L+ G+KP++V +G+ P K
Sbjct: 56 SHLSGLFYRTINLMEAGIKPVYVFDGEPPEFK 87
>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 = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 9/84 (10%)
Query: 76 ELQDKTIAID---------LSAWICDSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIF 126
+L+ K +AID S + D S + + +F++T +LL + PI+
Sbjct: 18 DLKGKKVAIDGMNALYQFLTSIRLRDGSPLRNRKGEITSAYNGVFYKTIHLLENDITPIW 77
Query: 127 VLEGKAPVLKHDTIEKRQQAQGRS 150
V +G+ P LK T + R++ + ++
Sbjct: 78 VFDGEPPKLKEKTRKVRREMKEKA 101
Score = 30.8 bits (68), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 30/53 (56%)
Query: 152 GRNVQAGSRARNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRS 204
R + S +F++T +LL + PI+V +G+ P LK T + R++ + ++
Sbjct: 49 NRKGEITSAYNGVFYKTIHLLENDITPIWVFDGEPPKLKEKTRKVRREMKEKA 101
>pdb|3IDF|A Chain A, The Crystal Structure Of A Usp-Like Protein From Wolinella
Succinogenes To 2.0a
pdb|3IDF|B Chain B, The Crystal Structure Of A Usp-Like Protein From Wolinella
Succinogenes To 2.0a
Length = 138
Score = 30.8 bits (68), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 24/102 (23%), Positives = 49/102 (48%), Gaps = 17/102 (16%)
Query: 89 WICDSSTIAEHSSQKNMYLRNLFFRTS--YLLLLGVKPIFVLEGKAPVLKHDTIEKRQQA 146
+ D + E ++Q Y+ ++F + + L L+ VKP F+L G+A + +D IE +++
Sbjct: 6 FAIDDTEACERAAQ---YILDMFGKDADCTLTLIHVKPEFMLYGEAVLAAYDEIEMKEEE 62
Query: 147 QGRSAGRNVQAGSRARNLFFRTSYLLLLGVKPIFVLEGKAPV 188
+ + ++ + FF G+ P V++ PV
Sbjct: 63 KAKLL-------TQKFSTFFTEK-----GINPFVVIKEGEPV 92
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 171 LLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGR 203
L L+ VKP F+L G+A + +D IE +++ + +
Sbjct: 33 LTLIHVKPEFMLYGEAVLAAYDEIEMKEEEKAK 65
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
0.321 0.136 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,087,286
Number of Sequences: 62578
Number of extensions: 220275
Number of successful extensions: 372
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 351
Number of HSP's gapped (non-prelim): 21
length of query: 222
length of database: 14,973,337
effective HSP length: 95
effective length of query: 127
effective length of database: 9,028,427
effective search space: 1146610229
effective search space used: 1146610229
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)