RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16216
(129 letters)
>3osn_A DNA polymerase IOTA; hoogsteen base PAIR, protein-DNA complex,
Y-family DNA polym translesion synthesis, nucleoside
triphosphate; HET: DNA DOC 6OG TTP; 1.90A {Homo sapiens}
PDB: 2dpj_A* 2fll_A* 2fln_A* 2flp_A* 3epg_A* 3epi_A*
2dpi_A* 3g6v_A* 3g6y_A* 3g6x_A* 3gv7_B* 3gv8_B* 3ngd_A*
3gv5_B* 3q8p_B* 3q8q_B* 3q8r_B* 3q8s_B* 3h4d_A* 3h4b_A*
...
Length = 420
Score = 99.8 bits (249), Expect = 4e-26
Identities = 31/127 (24%), Positives = 51/127 (40%), Gaps = 25/127 (19%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGP 60
YR +V +L EFS +VER DE ++DLT++V +R++ + S ++ + V
Sbjct: 102 YREMSYKVTELLEEFSPVVERLGFDENFVDLTEMVEKRLQQLQSDELSAVTVSGHVYNNQ 161
Query: 61 DNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCS 120
N D L + I E+R A+ ++
Sbjct: 162 SINLLDVLH-------------------------IRLLVGSQIAAEMREAMYNQLGLTGC 196
Query: 121 AGIAHNK 127
AG+A NK
Sbjct: 197 AGVASNK 203
>4ecq_A DNA polymerase ETA; transferase-DNA complex; HET: DNA DTP; 1.50A
{Homo sapiens} PDB: 3mr2_A* 3mr4_A* 3mr5_A* 3si8_A*
4dl2_A* 4dl3_A* 4dl4_A* 4dl5_A* 4dl6_A* 4dl7_A* 3mr3_A*
4ecr_A* 4ecs_A* 4ect_A* 4ecu_A* 4ecv_A* 4ecw_A* 4ecx_A*
4ecy_A* 4ecz_A* ...
Length = 435
Score = 90.1 bits (223), Expect = 2e-22
Identities = 55/137 (40%), Positives = 78/137 (56%), Gaps = 16/137 (11%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSI--GHIAASQLSNTFVVGF 58
YR A EV+ ++S F+ ++ERASIDEAY+DLT V ER++ + I+A L +T++ G
Sbjct: 95 YREASVEVMEIMSRFA-VIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGL 153
Query: 59 GPD-------NNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAV 111
E RK G+ +WL + D T +L + VIVEE+RAA+
Sbjct: 154 PQGPTTAEETVQKEGMRKQGLFQWLDSLQID------NLTSPDLQLTVGAVIVEEMRAAI 207
Query: 112 LSKTQFHCSAGIAHNKV 128
+T F CSAGI+HNKV
Sbjct: 208 ERETGFQCSAGISHNKV 224
>3mfi_A DNA polymerase ETA; DNA damage, DNA repair, DNA replication, DNA
synthesis, NUCL binding, magnesium; HET: DNA DOC TTD
DTP; 1.76A {Saccharomyces cerevisiae} PDB: 3mfh_A*
3oha_A* 3ohb_A* 2r8j_A* 2r8k_A* 2wtf_A* 2xgp_A* 2xgq_A*
1jih_A*
Length = 520
Score = 74.1 bits (181), Expect = 8e-17
Identities = 30/140 (21%), Positives = 58/140 (41%), Gaps = 13/140 (9%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGH----------IAASQL 50
YR R+ +A+ ++VERASIDE ++DL + + A S +
Sbjct: 138 YRRESRKALAIFKWACDLVERASIDEVFLDLGRICFNMLMFDNEYELTGDLKLKDALSNI 197
Query: 51 SNTFVVGFGP--DNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIR 108
F+ G + K +++ G V++ L+ + +D LA+ + + IR
Sbjct: 198 REAFIGGNYDINSHLPLIPEKIKSLKFEGDVFNPEGRDLITDWDDVI-LALGSQVCKGIR 256
Query: 109 AAVLSKTQFHCSAGIAHNKV 128
++ + S G++ K
Sbjct: 257 DSIKDILGYTTSCGLSSTKN 276
>1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family
DNA polymerase, translesion DNA synthesis, lesion
bypass; 2.40A {Homo sapiens} SCOP: d.240.1.1 e.8.1.7
PDB: 2oh2_A* 2w7o_A* 2w7p_A* 3hed_A* 3in5_A*
Length = 459
Score = 61.9 bits (150), Expect = 2e-12
Identities = 31/145 (21%), Positives = 49/145 (33%), Gaps = 17/145 (11%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVG--- 57
YR +EV +L+++ S+DEAY+++T + ER + V
Sbjct: 107 YRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDN 166
Query: 58 --------------FGPDNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVI 103
P +E QV + + A +
Sbjct: 167 PGKEVNKLSEHERSISPLLFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEV 226
Query: 104 VEEIRAAVLSKTQFHCSAGIAHNKV 128
V+EIR + KT SAGIA N +
Sbjct: 227 VKEIRFRIEQKTTLTASAGIAPNTM 251
>3pzp_A DNA polymerase kappa; DNA nucleotidyltransferase, DNA binding
nucleotide binding M binding, nucleus; HET: DNA TTD DTP;
3.34A {Homo sapiens}
Length = 517
Score = 62.0 bits (150), Expect = 2e-12
Identities = 31/145 (21%), Positives = 49/145 (33%), Gaps = 17/145 (11%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVG--- 57
YR +EV +L+++ S+DEAY+++T + ER + V
Sbjct: 163 YRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDN 222
Query: 58 --------------FGPDNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVI 103
P +E QV + + A +
Sbjct: 223 PGKEVNKLSEHERSISPLLFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEV 282
Query: 104 VEEIRAAVLSKTQFHCSAGIAHNKV 128
V+EIR + KT SAGIA N +
Sbjct: 283 VKEIRFRIEQKTTLTASAGIAPNTM 307
>3bq0_A POL IV, DBH, DNA polymerase IV; Y-family, lesion bypass; HET: DNA;
2.60A {Sulfolobus acidocaldarius} SCOP: d.240.1.1
e.8.1.7 PDB: 3bq1_A* 3bq2_A* 1k1q_A 1k1s_A
Length = 354
Score = 52.2 bits (126), Expect = 4e-09
Identities = 14/47 (29%), Positives = 28/47 (59%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAA 47
Y ++ +L++ ++ +E ASIDEAY+D+T+ V ++ +A
Sbjct: 81 YEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELAR 127
Score = 36.4 bits (85), Expect = 0.001
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 89 ENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNK 127
E E I + +I+ +L K + + G+A NK
Sbjct: 113 NKVEGNFENGIE--LARKIKQEILEKEKITVTVGVAPNK 149
>1im4_A DBH; DNA polymerase PALM, thumb, fingers, helix-hairpin-helix,
fidelity, processivity, transferase; 2.30A {Sulfolobus
solfataricus} SCOP: e.8.1.7
Length = 221
Score = 51.4 bits (124), Expect = 5e-09
Identities = 14/47 (29%), Positives = 28/47 (59%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAA 47
Y ++ +L++ ++ +E ASIDEAY+D+T+ V ++ +A
Sbjct: 86 YEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELAR 132
Score = 37.5 bits (88), Expect = 4e-04
Identities = 7/28 (25%), Positives = 14/28 (50%)
Query: 100 AGVIVEEIRAAVLSKTQFHCSAGIAHNK 127
+ +I+ +L K + + G+A NK
Sbjct: 127 GIELARKIKQEILEKEKITVTVGVAPNK 154
>3gqc_A DNA repair protein REV1; protein-DNA complex, DNA damage, DNA
repair, DNA synthesis, binding, magnesium,
metal-binding; HET: DNA DOC DCP; 2.50A {Homo sapiens}
Length = 504
Score = 46.4 bits (110), Expect = 4e-07
Identities = 11/46 (23%), Positives = 25/46 (54%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIA 46
Y+ + + L+ +++ +E S DEA +D+T+++ E + A
Sbjct: 217 YKEVAQTLYETLASYTHNIEAVSCDEALVDITEILAETKLTPDEFA 262
Score = 39.4 bits (92), Expect = 1e-04
Identities = 6/28 (21%), Positives = 10/28 (35%)
Query: 100 AGVIVEEIRAAVLSKTQFHCSAGIAHNK 127
+R + +T+ S GI N
Sbjct: 258 PDEFANAVRMEIKDQTKCAASVGIGSNI 285
>1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family,
transferase-D complex; HET: DNA MSE ADI; 1.70A
{Sulfolobus solfataricus} SCOP: d.240.1.1 e.8.1.7 PDB:
1jxl_A* 1n48_A* 1n56_A* 1ryr_A* 1rys_A* 1s0m_A* 1s0n_A*
1s0o_A* 1s10_A* 1s97_A* 1s9f_A* 2ia6_A* 2ibk_A* 2r8g_A*
2r8h_A* 2r8i_A* 2rdj_A* 3fds_A* 3m9m_B* 3m9n_B* ...
Length = 352
Score = 46.0 bits (110), Expect = 4e-07
Identities = 14/33 (42%), Positives = 23/33 (69%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTD 33
Y+ ++ +L E+S +E ASIDEAY+D++D
Sbjct: 81 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISD 113
Score = 37.2 bits (87), Expect = 5e-04
Identities = 9/37 (24%), Positives = 19/37 (51%)
Query: 91 TEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNK 127
++ ++ A + EI+ +L K + + GI+ NK
Sbjct: 112 SDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNK 148
>2aq4_A DNA repair protein REV1; polymerase, PAD, N-digit, G-loop,
transferase; HET: DNA DOC DCP; 2.32A {Saccharomyces
cerevisiae} PDB: 3bjy_A* 3osp_A*
Length = 434
Score = 38.9 bits (91), Expect = 2e-04
Identities = 7/35 (20%), Positives = 13/35 (37%), Gaps = 2/35 (5%)
Query: 1 YRNAGREVIAVLSEFS--NIVERASIDEAYIDLTD 33
++ + L + N++ SIDEA
Sbjct: 137 FQLKSEAFYSTLKRLNIFNLILPISIDEAVCVRII 171
Score = 35.4 bits (82), Expect = 0.003
Identities = 7/40 (17%), Positives = 12/40 (30%), Gaps = 1/40 (2%)
Query: 89 ENTEDFQELAIAGVIVEEIRAAVLSKTQF-HCSAGIAHNK 127
+ + EEIR + T S G + +
Sbjct: 171 IPDNIHNTNTLNARLCEEIRQEIFQGTNGCTVSIGCSDSL 210
>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 = 38.1 bits (88), Expect = 4e-04
Identities = 23/86 (26%), Positives = 32/86 (37%), Gaps = 15/86 (17%)
Query: 44 HIAASQLSNTFVV-------GFGPDNNDEDARKAG-VMEWLGQVYSDTDTSLMENTEDFQ 95
ASQL F GF D DE A V ++LG V +SL+E ++ Q
Sbjct: 27 FFIASQLQEQFNKILPEPTEGFAAD--DEPTTPAELVGKFLGYV-----SSLVEPSKVGQ 79
Query: 96 ELAIAGVIVEEIRAAVLSKTQFHCSA 121
+ + + E L H A
Sbjct: 80 FDQVLNLCLTEFENCYLEGNDIHALA 105
Score = 36.6 bits (84), Expect = 0.001
Identities = 26/139 (18%), Positives = 48/139 (34%), Gaps = 36/139 (25%)
Query: 4 AGREVIAVLS--EFSNIVERA---SIDEAYIDLTDVVHERMKSIGHIAASQ---LSNTFV 55
AG S E++ + A SI+ L +VV R ++ SN +
Sbjct: 1760 AG------HSLGEYAALASLADVMSIE----SLVEVVFYRGMTMQVAVPRDELGRSNYGM 1809
Query: 56 VGFGPDNNDEDARKAGVMEWLGQVYSDTDTSLME----NTEDFQELAIAGVIVEEIRA-A 110
+ P + + + +V T L+E N E+ Q AG ++RA
Sbjct: 1810 IAINPGRVAASFSQEALQYVVERVGKRTG-WLVEIVNYNVENQQ-YVAAG----DLRALD 1863
Query: 111 VLSKTQFHCSAGIAHNKVK 129
++ + K++
Sbjct: 1864 TVTNV-------LNFIKLQ 1875
Score = 29.2 bits (65), Expect = 0.39
Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 14/58 (24%)
Query: 9 IAVLSEF--SNI-VERASIDEAYID--LTDVVH-ERMKSIGHIAASQLSNTFVVGFGP 60
I V F S++ V SI E +D + V E +Q T ++ FGP
Sbjct: 457 IPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWE--------TTTQFKATHILDFGP 506
>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 = 28.7 bits (63), Expect = 0.68
Identities = 12/103 (11%), Positives = 31/103 (30%), Gaps = 29/103 (28%)
Query: 20 ERASIDEAYIDLTDVVH-----------ERMKSIGHI--AASQL-SNTFVV-----GFG- 59
+ + + YI+ D ++ R++ + A +L V+ G G
Sbjct: 104 QPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK 163
Query: 60 --------PDNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDF 94
+ + WL ++ +++E +
Sbjct: 164 TWVALDVCLSYKVQCKMDFKIF-WLNLKNCNSPETVLEMLQKL 205
>1pt6_A Integrin alpha-1; cell adhesion; 1.87A {Homo sapiens} SCOP:
c.62.1.1 PDB: 4a0q_A 1qcy_A 1qc5_A 1qc5_B 1ck4_A 1mhp_A
Length = 213
Score = 25.1 bits (55), Expect = 7.5
Identities = 10/55 (18%), Positives = 17/55 (30%), Gaps = 1/55 (1%)
Query: 54 FVVGFGPDNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQEL-AIAGVIVEEI 107
F + N + +E + + S+ N D L I + E I
Sbjct: 142 FSIAILGSYNRGNLSTEKFVEEIKSIASEPTEKHFFNVSDELALVTIVKTLGERI 196
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
0.316 0.131 0.362
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,037,212
Number of extensions: 119604
Number of successful extensions: 313
Number of sequences better than 10.0: 1
Number of HSP's gapped: 304
Number of HSP's successfully gapped: 46
Length of query: 129
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 46
Effective length of database: 4,384,350
Effective search space: 201680100
Effective search space used: 201680100
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 (21.6 bits)
S2: 52 (23.9 bits)