RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1207
(113 letters)
>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 = 104 bits (260), Expect = 2e-28
Identities = 30/87 (34%), Positives = 41/87 (47%), Gaps = 15/87 (17%)
Query: 13 QEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAA 72
++ K+ + RV V K LLS MGIP+++ AP E EAQ A
Sbjct: 114 KDAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVD---------------APSEGEAQAAY 158
Query: 73 MVKAGKVYATATEDMDALTFGTNILLR 99
M G V T ++D D+L FG+ L R
Sbjct: 159 MAAKGDVEYTGSQDYDSLLFGSPRLAR 185
>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 = 103 bits (259), Expect = 3e-28
Identities = 51/90 (56%), Positives = 62/90 (68%), Gaps = 15/90 (16%)
Query: 10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
G QE++KF +RLV+V+ H ECK LLSLMGIPY++ AP EAEA
Sbjct: 117 GAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEAS 161
Query: 70 CAAMVKAGKVYATATEDMDALTFGTNILLR 99
CAA+VKAGKVYA ATEDMD LTFG+ +L+R
Sbjct: 162 CAALVKAGKVYAAATEDMDCLTFGSPVLMR 191
>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 = 102 bits (257), Expect = 5e-28
Identities = 34/94 (36%), Positives = 50/94 (53%), Gaps = 15/94 (15%)
Query: 6 FLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCE 65
+ D +E K+ +R+ ++ V+ CK LLSLMGIPY+E AP E
Sbjct: 108 AIKKEDFEEAAKYAKRVSYLTPKMVENCKYLLSLMGIPYVE---------------APSE 152
Query: 66 AEAQCAAMVKAGKVYATATEDMDALTFGTNILLR 99
EAQ + M K G V+A ++D DAL +G ++R
Sbjct: 153 GEAQASYMAKKGDVWAVVSQDYDALLYGAPRVVR 186
>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 = 101 bits (254), Expect = 2e-27
Identities = 51/90 (56%), Positives = 62/90 (68%), Gaps = 15/90 (16%)
Query: 10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
G QE++KF +RLV+V+ H ECK LLSLMGIPY++ AP EAEA
Sbjct: 117 GAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEAS 161
Query: 70 CAAMVKAGKVYATATEDMDALTFGTNILLR 99
CAA+VKAGKVYA ATEDMD LTFG+ +L+R
Sbjct: 162 CAALVKAGKVYAAATEDMDCLTFGSPVLMR 191
>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 = 101 bits (253), Expect = 3e-27
Identities = 31/91 (34%), Positives = 52/91 (57%), Gaps = 15/91 (16%)
Query: 9 TGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEA 68
G +E+ K+++ ++R+S++ V+E K+LL MGIP ++ AP E EA
Sbjct: 108 EGKIEELRKYSQAILRLSNIMVEESKKLLRAMGIPIVQ---------------APSEGEA 152
Query: 69 QCAAMVKAGKVYATATEDMDALTFGTNILLR 99
+ A + K G +A A++D DA+ FG L+R
Sbjct: 153 EAAYLNKLGLSWAAASQDYDAILFGAKRLVR 183
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus
amylolyticus}
Length = 363
Score = 100 bits (250), Expect = 9e-27
Identities = 30/91 (32%), Positives = 49/91 (53%), Gaps = 15/91 (16%)
Query: 9 TGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEA 68
+GD + ++ +++ V++ K LL MGIP+++ AP E EA
Sbjct: 125 SGDLELARRYAMMSAKLTEEMVRDAKSLLDAMGIPWVQ---------------APAEGEA 169
Query: 69 QCAAMVKAGKVYATATEDMDALTFGTNILLR 99
Q A +VK G YA+A++D D+L FG+ L+R
Sbjct: 170 QAAYIVKKGDAYASASQDYDSLLFGSPKLVR 200
>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 = 98.8 bits (246), Expect = 2e-26
Identities = 34/91 (37%), Positives = 51/91 (56%), Gaps = 15/91 (16%)
Query: 9 TGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEA 68
G+ +E K+ +R RV+ + +++ K+LL LMGIP ++ AP E EA
Sbjct: 111 KGEIEEARKYAQRATRVNEMLIEDAKKLLELMGIPIVQ---------------APSEGEA 155
Query: 69 QCAAMVKAGKVYATATEDMDALTFGTNILLR 99
Q A M G VYA+A++D D+L FG L+R
Sbjct: 156 QAAYMAAKGSVYASASQDYDSLLFGAPRLVR 186
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A
{Homo sapiens} PDB: 3qeb_Z* 3qea_Z*
Length = 352
Score = 86.6 bits (214), Expect = 1e-21
Identities = 22/95 (23%), Positives = 35/95 (36%), Gaps = 15/95 (15%)
Query: 9 TGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEA 68
G E + R + ++ + + G+ + AP EA+A
Sbjct: 109 EGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLV---------------APYEADA 153
Query: 69 QCAAMVKAGKVYATATEDMDALTFGTNILLRQQLS 103
Q A + KAG V A TED L FG ++ +
Sbjct: 154 QLAYLNKAGIVQAIITEDSALLAFGCKKVILKMDQ 188
>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 = 45.4 bits (107), Expect = 6e-07
Identities = 22/130 (16%), Positives = 39/130 (30%), Gaps = 37/130 (28%)
Query: 6 FLLTGDAQEIDKFNRRLVRVS-SVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPC 64
+++G Q + N L + + + + IP+ E R + FL V +P
Sbjct: 377 LVVSGPPQSLYGLNLTLRKAKAPSGLDQSR-------IPFSE--RKLKFSNRFLPVASPF 427
Query: 65 ------EAEAQCAAMVKAGK-----------VYATAT-EDMDALTFGTNILLR--QQLSW 104
A + VY T D+ L+ +I R +
Sbjct: 428 HSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLS--GSISERIVDCI-- 483
Query: 105 ATFSMHC-WE 113
+ WE
Sbjct: 484 --IRLPVKWE 491
Score = 28.5 bits (63), Expect = 0.46
Identities = 19/113 (16%), Positives = 34/113 (30%), Gaps = 20/113 (17%)
Query: 12 AQEI----DKFNRRLVRVSSVH-VKEC-KELLSLMGIPYIEVSRSPRLLPNFLGVLAPCE 65
AQ++ D + S + V L G + R+ N+ ++
Sbjct: 1642 AQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGE-----KGKRIRENYSAMIF--- 1693
Query: 66 AEAQCAAMVKAGKVYATATEDMDALTF-GTNILLRQ----QLSWATFSMHCWE 113
E +K K++ E + TF LL Q + +E
Sbjct: 1694 -ETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFE 1745
Score = 24.6 bits (53), Expect = 9.3
Identities = 12/87 (13%), Positives = 29/87 (33%), Gaps = 21/87 (24%)
Query: 15 IDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLA----PCEAEAQC 70
+ +F + + +H L+ + ++ L+ N++ P + ++
Sbjct: 88 LTEFENCYLEGNDIHAL----AAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNS 143
Query: 71 A--AMVKAG--KVYATATEDMDALTFG 93
A V G ++ A FG
Sbjct: 144 ALFRAVGEGNAQLVA---------IFG 161
>3c5h_A Glucocorticoid receptor DNA-binding factor 1; RAS, GTPase,
glucorticoid receptor, structural genomics consortium,
SGC, alternative splicing; HET: GNP; 1.80A {Homo
sapiens}
Length = 255
Score = 26.9 bits (59), Expect = 1.3
Identities = 7/34 (20%), Positives = 11/34 (32%), Gaps = 6/34 (17%)
Query: 15 IDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVS 48
D+ R +R LS + +E S
Sbjct: 208 CDEGVERYIR------DAHTFALSKKNLQVVETS 235
>1ou0_A Precorrin-8X methylmutase related protein; structural genomics,
PSI, protein structure initiative; 2.10A {Thermoplasma
acidophilum dsm 1728} SCOP: c.23.17.1
Length = 207
Score = 26.5 bits (58), Expect = 1.8
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 25 VSSVHVKECKELLSLMGIPYI 45
V ++ + KE L I YI
Sbjct: 163 VGFINASKAKEGLVSSHIEYI 183
>1v9c_A Precorrin-8X methyl mutase; alpha-beta WIND, doubly wound sheet,
riken structural genomics/proteomics initiative, RSGI,
structural genomics; 2.20A {Thermus thermophilus} SCOP:
c.23.17.1
Length = 218
Score = 26.6 bits (58), Expect = 2.0
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 25 VSSVHVKECKELLSLMGIPYI 45
V V+V E K L +P+I
Sbjct: 161 VGFVNVLEAKRALMEAPVPWI 181
>2gjf_A Designed protein; procarboxypeptidase, de novo protein; NMR {}
Length = 78
Score = 25.1 bits (55), Expect = 2.6
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 23 VRVSSVHVKECKELLSLMGIPY 44
+ + S V+ E+L GIP+
Sbjct: 51 ILIPSDMVEWFLEMLKAKGIPF 72
>1vjq_A Designed protein; structural genomics, engineered protein, PSI,
protein struct initiative, structural genomics of
pathogenic protozoa CONS SGPP; 2.10A {} SCOP: k.43.1.1
Length = 79
Score = 25.1 bits (55), Expect = 2.7
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 23 VRVSSVHVKECKELLSLMGIPY 44
+ + S V+ E+L GIP+
Sbjct: 43 ILIPSDMVEWFLEMLKAKGIPF 64
>3fkr_A L-2-keto-3-deoxyarabonate dehydratase; DHDPS/NAL family, complex,
pyruvate, lyase; HET: KPI; 1.80A {Azospirillum
brasilense} PDB: 3fkk_A
Length = 309
Score = 25.9 bits (57), Expect = 3.3
Identities = 10/81 (12%), Positives = 22/81 (27%), Gaps = 11/81 (13%)
Query: 2 ELTLFLLTGDAQEIDKFNRRLVRVSSVHVKEC-----KELLSLMGIPYIEVSRSPRLLPN 56
+ G + + + + + ++ K L+ G+ E R P +
Sbjct: 227 PILEAWREGRHDDAYARYQAWLPLINHENRQSGILTAKALMREGGVIASERPRHP-MPE- 284
Query: 57 FLGVLAPCEAEAQCAAMVKAG 77
L P A +
Sbjct: 285 ----LHPDTRAELLAIARRLD 301
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition,
helix-coil dynamics, inhibitor design, complex
(polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP:
a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A*
1taq_A*
Length = 832
Score = 25.2 bits (56), Expect = 6.0
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 34 KELLSLMGIPYIEV 47
KEL+ L+G+ +EV
Sbjct: 100 KELVDLLGLARLEV 113
>4e51_A Histidine--tRNA ligase; seattle structural genomics center for
infectious disease, S aminoacylation, tRNA activation,
charged tRNA; HET: HIS; 2.65A {Burkholderia
thailandensis}
Length = 467
Score = 24.9 bits (55), Expect = 7.7
Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 26 SSVHVKECKELLSLMGIPYIEVSRSPRL 53
S H + + LL +P+ +PRL
Sbjct: 260 SRAHFEGLQRLLKANNVPFTI---NPRL 284
>1htt_A Histidyl-tRNA synthetase; complex (tRNA synthetase/His-adenylate),
aminoacyl-tRNA synthase, ligase; HET: HIS AMP; 2.60A
{Escherichia coli} SCOP: c.51.1.1 d.104.1.1 PDB: 1kmm_A*
1kmn_A* 2el9_A*
Length = 423
Score = 24.8 bits (55), Expect = 8.3
Identities = 9/28 (32%), Positives = 11/28 (39%), Gaps = 3/28 (10%)
Query: 26 SSVHVKECKELLSLMGIPYIEVSRSPRL 53
S H +LL GI Y + RL
Sbjct: 232 SREHFAGLCKLLESAGIAYTV---NQRL 256
>1h4v_B Histidyl-tRNA synthetase; class IIA aminoacyl-tRNA synthetase, ATP
+ L-histidine tRNA(His)-> AMP + PPI +
L-histidyl-tRNA(His); 2.4A {Thermus thermophilus} SCOP:
c.51.1.1 d.104.1.1 PDB: 1ady_A* 1adj_A
Length = 421
Score = 24.8 bits (55), Expect = 8.5
Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 26 SSVHVKECKELLSLMGIPYIEVSRSPRL 53
+ H+KE + L + +PY P L
Sbjct: 233 ARAHLKEVERHLERLSVPYEL---EPAL 257
>1qe0_A Histidyl-tRNA synthetase; class II tRNA synthetase, beta sheet,
ligase; 2.70A {Staphylococcus aureus} SCOP: c.51.1.1
d.104.1.1
Length = 420
Score = 24.8 bits (55), Expect = 8.7
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 26 SSVHVKECKELLSLMGIPYIEVSRSPRL 53
S + ++ K L +GIPY E P L
Sbjct: 231 SKAYYEQVKAYLDDLGIPYTE---DPNL 255
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
0.324 0.134 0.406
Gapped
Lambda K H
0.267 0.0747 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,679,220
Number of extensions: 86995
Number of successful extensions: 393
Number of sequences better than 10.0: 1
Number of HSP's gapped: 384
Number of HSP's successfully gapped: 26
Length of query: 113
Length of database: 6,701,793
Length adjustment: 77
Effective length of query: 36
Effective length of database: 4,551,876
Effective search space: 163867536
Effective search space used: 163867536
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.4 bits)