RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12450
(168 letters)
>3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA
replication, DNA-BI DNA-directed DNA polymerase,
exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A
{Saccharomyces cerevisiae}
Length = 919
Score = 161 bits (408), Expect = 1e-46
Identities = 65/124 (52%), Positives = 86/124 (69%), Gaps = 1/124 (0%)
Query: 45 QKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLT 104
+ + +IP +DQ+EGATVIEP +GYY PIATLDF+SLYPSIMMAHNLCYTTL
Sbjct: 504 EIDTVIPNMQSQASDDQYEGATVIEPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCN 563
Query: 105 PQTITKLELTPD-QYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELT 163
T+ +L L D Y TP G++F+ + R+G+LP IL+ L+SARK+AK DL+ E D
Sbjct: 564 KATVERLNLKIDEDYVITPNGDYFVTTKRRRGILPIILDELISARKRAKKDLRDEKDPFK 623
Query: 164 QVLY 167
+ +
Sbjct: 624 RDVL 627
Score = 53.8 bits (129), Expect = 4e-09
Identities = 17/35 (48%), Positives = 26/35 (74%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRDPDGAVT 44
GL +VRRD+ LV+ ++N L+K+LI R+ DGA+
Sbjct: 768 GLASVRRDSCSLVSIVMNKVLKKILIERNVDGALA 802
>1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B
polymer alpha family polymerase, transferase; 2.10A
{Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A
2xhb_A* 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 4ahc_A*
4ail_C* 3a2f_A* 2jgu_A* 1d5a_A
Length = 775
Score = 142 bits (360), Expect = 3e-40
Identities = 36/127 (28%), Positives = 56/127 (44%), Gaps = 14/127 (11%)
Query: 45 QKNFIIPTYH----GGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYT 100
++N + P + + G V EP++G + D I LDF SLYPSI++ HN+
Sbjct: 363 KRNELAPNKPDERELARRRGGYAGGYVKEPERGLW-DNIVYLDFRSLYPSIIITHNVSPD 421
Query: 101 TLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETD 160
TL + G+ F K G +P +L +LL R++ K +K D
Sbjct: 422 TLNREG-------CKEYDVAPEVGHKFCKD--FPGFIPSLLGDLLEERQKIKRKMKATVD 472
Query: 161 ELTQVLY 167
L + L
Sbjct: 473 PLEKKLL 479
Score = 52.4 bits (126), Expect = 9e-09
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRDPDGAV 43
GLE VRRD S + L+ +L + D + AV
Sbjct: 607 GLEIVRRDWSEIAKETQARVLEAILKHGDVEEAV 640
>3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA
repair, DNA-binding; HET: DNA DOC DCP; 1.92A
{Escherichia coli} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A*
3k5n_A* 3k5o_A* 3maq_A* 1q8i_A*
Length = 786
Score = 136 bits (344), Expect = 6e-38
Identities = 29/122 (23%), Positives = 48/122 (39%), Gaps = 12/122 (9%)
Query: 45 QKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLT 104
+ ++ P G V++ + G Y D + LD+ SLYPSI+ + L+
Sbjct: 386 RAGYVAPNLGEVPPH-ASPGGYVMDSRPGLY-DSVLVLDYKSLYPSIIRTFLIDPVGLV- 442
Query: 105 PQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQ 164
+ + G S K LPEI+ N+ R +AK ++ L+Q
Sbjct: 443 ------EGMAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAK---RQGNKPLSQ 493
Query: 165 VL 166
L
Sbjct: 494 AL 495
Score = 45.9 bits (109), Expect = 2e-06
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRDPDGAVTQ 45
GLETVR D +PL ++ N V +
Sbjct: 636 GLETVRTDWTPLAQQFQQELYLRIFRNEPYQEYVRE 671
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A
{Human herpesvirus 1} PDB: 1dml_B*
Length = 1193
Score = 129 bits (324), Expect = 2e-35
Identities = 40/166 (24%), Positives = 70/166 (42%), Gaps = 3/166 (1%)
Query: 4 HVTWRDGLETVRRDNSPLVANMINTCLQKLLINRDPDGAVTQKNFIIPTYHGGQGEDQFE 63
R P A ++ + D + ++
Sbjct: 596 DTQGRFRGAGGEAPKRPAAAREDEERPEEEGEDEDEREEGGGEREPEGARETAGRHVGYQ 655
Query: 64 GATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPC 123
GA V++P G++ +P+ DF+SLYPSI+ AHNLC++TL Y +
Sbjct: 656 GAKVLDPTSGFHVNPVVVFDFASLYPSIIQAHNLCFSTLSLRADAVAHLEAGKDYLEIEV 715
Query: 124 G---NFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
G FF+K+ +R+ LL +L + L+ RKQ ++ + + + E +L
Sbjct: 716 GGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRIPQSSPEEAVLL 761
Score = 51.8 bits (123), Expect = 2e-08
Identities = 7/34 (20%), Positives = 14/34 (41%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRDPDGAV 43
G++ VR++N + + L + GA
Sbjct: 912 GVDLVRKNNCAFINRTSRALVDLLFYDDTVSGAA 945
>1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET:
DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5
e.8.1.1
Length = 847
Score = 127 bits (321), Expect = 7e-35
Identities = 31/129 (24%), Positives = 48/129 (37%), Gaps = 18/129 (13%)
Query: 45 QKNFIIP------------TYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIM 92
++N++IP ++GA VI+P G + I LDF+SLYPSI+
Sbjct: 430 KRNWLIPLKEEILAKSSNIRTSALIKGKGYKGAVVIDPPAGIF-FNITVLDFASLYPSII 488
Query: 93 MAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAK 152
NL Y T+ Q E+ + + R G+ I L R +
Sbjct: 489 RTWNLSYETVDIQQCKKPYEVKDE-----TGEVLHIVCMDRPGITAVITGLLRDFRVKIY 543
Query: 153 NDLKKETDE 161
K +
Sbjct: 544 KKKAKNPNN 552
Score = 48.3 bits (115), Expect = 3e-07
Identities = 7/41 (17%), Positives = 16/41 (39%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRDPDGAVTQKNFII 50
G+ +R+ V + N + ++ P+ K I+
Sbjct: 680 GMLVKKRNTPEFVKKVFNEVKELMISINSPNDVKEIKRKIV 720
>3qex_A DNA polymerase, GP43; difluorotoluene nucleoside; HET: DNA DOC DGT;
1.73A {Enterobacteria phage RB69} PDB: 3qei_A* 3qer_A*
3qes_A* 3qet_A* 3qep_A* 3qew_A* 3qev_A* 3s9h_A* 3sq0_A*
3spz_A* 3ne6_A* 3nhg_A* 3si6_A* 3scx_A* 3sjj_A* 3snn_A*
3ngi_A* 3lzi_A* 3lzj_A* 3ndk_A* ...
Length = 903
Score = 49.1 bits (116), Expect = 1e-07
Identities = 22/115 (19%), Positives = 40/115 (34%), Gaps = 7/115 (6%)
Query: 46 KNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTP 105
+ + + GA V EP Y ++ D +SLYPSI+ N+ T+
Sbjct: 375 EQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMS-FDLTSLYPSIIRQVNISPETIAGT 433
Query: 106 QTIT------KLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKND 154
+ + N + R G++P + + + RK+ K
Sbjct: 434 FKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGY 488
>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 = 36.8 bits (84), Expect = 0.002
Identities = 26/167 (15%), Positives = 51/167 (30%), Gaps = 49/167 (29%)
Query: 7 WRDGLETVRRDNSPLVANMINTCLQKLLINRDPDGAVTQKNFIIPTYHG------GQGED 60
W D +++ V ++N + L+ + P K I + + E+
Sbjct: 396 WFDVIKSD-------VMVVVNKLHKYSLVEKQP------KESTI-SIPSIYLELKVKLEN 441
Query: 61 QFEG-ATVIE----PKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTP 115
++ ++++ PK D I Y I H L + ++ L
Sbjct: 442 EYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH-H------LKNIEHPERMTLFR 494
Query: 116 DQYSKTPCGNF-FLKSSLRKGLLPEI----LENLLSARKQAKNDLKK 157
+ +F FL+ +R + N L LK
Sbjct: 495 MVFL-----DFRFLEQKIRHDSTAWNASGSILNTL-------QQLKF 529
Score = 26.0 bits (56), Expect = 7.8
Identities = 33/212 (15%), Positives = 58/212 (27%), Gaps = 70/212 (33%)
Query: 19 SPLVANMI----------------------NTCLQKLLINRDPDG--------AVTQKNF 48
+P ++I T ++ L +P +V +
Sbjct: 326 NPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSA 385
Query: 49 IIPT------YHGGQGED------QFEGATVIE--PKKGYYADPIATLDFSSLYPSIMMA 94
IPT + D + +++E PK+ + P L+ +
Sbjct: 386 HIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL 445
Query: 95 HNL---CYTTLLTPQTITKLELTPDQYSKTPCGNFF------LKS---SLRKGLLPEI-- 140
H Y T + + DQY F+ LK+ R L +
Sbjct: 446 HRSIVDHYNIPKTFDSDDLIPPYLDQY-------FYSHIGHHLKNIEHPERMTLFRMVFL 498
Query: 141 ----LENLLSARKQAKNDLKKETDELTQV-LY 167
LE + A N + L Q+ Y
Sbjct: 499 DFRFLEQKIRHDSTAWNASGSILNTLQQLKFY 530
>2py5_A DNA polymerase; protein-DNA complex, replication, transferase/DNA
complex; HET: DNA; 1.60A {Bacillus phage PHI29} SCOP:
c.55.3.5 e.8.1.1 PDB: 1xhz_A* 1xhx_A* 2ex3_A* 1xi1_A*
2pyj_A* 2pyl_A* 2pzs_A*
Length = 575
Score = 34.1 bits (77), Expect = 0.014
Identities = 16/94 (17%), Positives = 31/94 (32%), Gaps = 11/94 (11%)
Query: 47 NFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQ 106
+ Y GG + + K D +SLYP+ M + L Y + +
Sbjct: 220 KEVRYAYRGGFTW-------LNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFE 272
Query: 107 TITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEI 140
+ + + + L++G +P I
Sbjct: 273 GKYVWDEDYPLH----IQHIRCEFELKEGYIPTI 302
>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 = 32.3 bits (73), Expect = 0.072
Identities = 33/192 (17%), Positives = 50/192 (26%), Gaps = 83/192 (43%)
Query: 21 LVANMINTCLQKLLINRDPDGAVTQKNFIIPTYH-------------------------- 54
L N I+ KLL ++ D + + +I Y
Sbjct: 96 LEGNDIHALAAKLL--QENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGN 153
Query: 55 -------GGQG--EDQFEGATVIEPKKGY--YADPIATLDFSSLYPSIMMAHNLCYTTLL 103
GGQG +D FE E + Y Y + L I + +
Sbjct: 154 AQLVAIFGGQGNTDDYFE-----ELRDLYQTYHVLVGDL--------IKFSAETLSELIR 200
Query: 104 TPQTITKL--------------ELTPDQ-YSKT-----P------CGNF--FLKSSLRKG 135
T K+ TPD+ Y + P ++ K G
Sbjct: 201 TTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLL---G 257
Query: 136 LLPEILENLLSA 147
P L + L
Sbjct: 258 FTPGELRSYLKG 269
Score = 27.7 bits (61), Expect = 2.4
Identities = 18/101 (17%), Positives = 30/101 (29%), Gaps = 29/101 (28%)
Query: 18 NSPLVANMINTCLQKLLINRDPDGAVTQKNFIIPTYHGGQGEDQFEGATVIEPKKGYYAD 77
+S L+ + + L+ + + K+ IP Y G D + I + D
Sbjct: 428 HSHLLVPASDLINKDLV---KNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISER---IVD 481
Query: 78 PIAT----------------LDF-----SSLYPSIMMAHNL 97
I LDF S L ++ N
Sbjct: 482 CIIRLPVKWETTTQFKATHILDFGPGGASGL--GVLTHRNK 520
>3mkh_A Nitroalkane oxidase; oxidoreductase flavoenzyme, acyl-COA
dehydrogen flavoprotein, oxidoreductase; HET: FAD; 2.00A
{Podospora anserina}
Length = 438
Score = 28.0 bits (63), Expect = 1.6
Identities = 13/50 (26%), Positives = 18/50 (36%), Gaps = 12/50 (24%)
Query: 50 IPTYHGGQGEDQFEGATVIEPKKGYYADP-IATLDFSSLYPSIMMAHNLC 98
I HGG G E A ++E + Y +P A + A L
Sbjct: 64 ISPAHGGTGGTLIESAILVE--ECYSVEPSAAL---------TIFATGLG 102
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 27.6 bits (60), Expect = 1.7
Identities = 7/32 (21%), Positives = 13/32 (40%), Gaps = 10/32 (31%)
Query: 106 QTITKLE--L---TPDQYSKTPCGNFFLKSSL 132
Q + KL+ L D P +K+++
Sbjct: 20 QALKKLQASLKLYADDS---APA--LAIKATM 46
>1rx0_A Acyl-COA dehydrogenase family member 8, mitochondrial;
flavoprotein, coenzyme A, oxidoreductase; HET: FAD 2MC;
1.77A {Homo sapiens} SCOP: a.29.3.1 e.6.1.1
Length = 393
Score = 27.5 bits (62), Expect = 2.1
Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 10/49 (20%)
Query: 50 IPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLC 98
I T GG G + + + + E +AT S+ + + HN+C
Sbjct: 69 IQTDVGGSGLSRLDTSVIFE--------ALATGCTST--TAYISIHNMC 107
>1r2j_A Protein FKBI; polyketide synthase, polyketide, acyl-COA
dehydrogenase, , aldehyde dehydrogenase, oxidoreductase;
HET: FAD; 2.10A {Streptomyces hygroscopicus} SCOP:
a.29.3.1 e.6.1.1
Length = 366
Score = 26.7 bits (60), Expect = 3.8
Identities = 10/55 (18%), Positives = 17/55 (30%), Gaps = 10/55 (18%)
Query: 50 IPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLT 104
+ HGG G E + +L S S+M + + T+
Sbjct: 43 VAAEHGGLGLGSRENGEFTA--------HVGSLCSSL--RSVMTSQGMAAWTVQR 87
>1egd_A Medium chain acyl-COA dehydrogenase; flavoprotein, electron
transfer; HET: FAD; 2.40A {Homo sapiens} SCOP: a.29.3.1
e.6.1.1 PDB: 1egc_A* 1ege_A* 1t9g_A* 2a1t_A* 1udy_A*
3mdd_A* 3mde_A*
Length = 396
Score = 26.7 bits (60), Expect = 4.2
Identities = 10/52 (19%), Positives = 17/52 (32%), Gaps = 10/52 (19%)
Query: 47 NFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLC 98
N IP GG G F+ + E +A + + ++L
Sbjct: 63 NTHIPENCGGLGLGTFDACLISE--------ELAYGCTGV--QTAIEGNSLG 104
>1q8f_A Pyrimidine nucleoside hydrolase; open alpha-beta structure,
NH-fold; 1.70A {Escherichia coli} SCOP: c.70.1.1 PDB:
3b9x_A* 3mkn_A* 3mkm_A*
Length = 313
Score = 25.6 bits (57), Expect = 8.5
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 74 YYADPIAT-LDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFF 127
+ADP A + F+S P +MM +L T+ TP I ++E + P G F
Sbjct: 167 IFADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIARME-----RAGGPAGELF 216
>3t8j_A Purine nucleosidase, (IUNH-1); nucleoside hydrolase, thermostable
protein, open (alpha,beta structure, rossmann fold,
NH-fold; 1.60A {Sulfolobus solfataricus}
Length = 311
Score = 25.6 bits (57), Expect = 8.7
Identities = 8/56 (14%), Positives = 20/56 (35%), Gaps = 8/56 (14%)
Query: 74 YYADPIATLD--FSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFF 127
+ DP A F++ + M+ ++ +T + ++ KT +
Sbjct: 165 IWVDPDAA-KIVFNAGFDITMIPWDVIINYPVTDEEWNVIK-----NMKTRMSELY 214
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
0.318 0.135 0.402
Gapped
Lambda K H
0.267 0.0771 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,457,189
Number of extensions: 132805
Number of successful extensions: 258
Number of sequences better than 10.0: 1
Number of HSP's gapped: 249
Number of HSP's successfully gapped: 24
Length of query: 168
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 81
Effective length of database: 4,272,666
Effective search space: 346085946
Effective search space used: 346085946
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (24.5 bits)