RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8858
(121 letters)
>3r8n_M 30S ribosomal protein S13; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_M 3oaq_M 3ofa_M 3ofx_M
3ofo_M 3r8o_M 4a2i_M 3i1m_M 1vs7_M* 3e1a_F 3e1c_F 1vs5_M
3i1o_M 3i1q_M 3i1s_M 3i1z_M 3i21_M 3iyx_M 3iyy_M 3izv_Q*
...
Length = 114
Score = 191 bits (488), Expect = 6e-65
Identities = 66/112 (58%), Positives = 93/112 (83%)
Query: 3 RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK 62
RI GINIP+++H +I LT+IYG+G++R+K I I+ KI +L++ +++ LR+E++K
Sbjct: 2 RIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAK 61
Query: 63 FIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
F++EGDLRRE SM+IKRL+DL CYRG+RHR+ LP RGQRT+TNARTRKGPR+
Sbjct: 62 FVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK 113
>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP:
a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M
1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P*
1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M*
1xmq_M* ...
Length = 126
Score = 188 bits (480), Expect = 1e-63
Identities = 64/122 (52%), Positives = 88/122 (72%), Gaps = 1/122 (0%)
Query: 1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
M RI G+ IP N+ + + LT IYGIG++RAK+ E T I+ ++KDL + E+ +LRE +
Sbjct: 1 MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYV 60
Query: 61 SK-FIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSL 119
+ +EG+LR E + NIKRL+D+ CYRG+RHR+ LP RGQRTRTNARTRKGPR+
Sbjct: 61 ENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGK 120
Query: 120 RK 121
+K
Sbjct: 121 KK 122
>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 145
Score = 162 bits (412), Expect = 5e-53
Identities = 45/111 (40%), Positives = 63/111 (56%), Gaps = 11/111 (9%)
Query: 1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
RI G+ IPN++ + L I+GIGRSR+++I K KDL++ E+ LR
Sbjct: 46 CIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFDN-KVTKDLSEEEVIILR--- 101
Query: 61 SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKG 111
+R + I+RL ++ CYRGIRH+ LP RGQRT+ N RT KG
Sbjct: 102 -------KEKRFNRVAIERLKEIRCYRGIRHKLGLPVRGQRTKNNCRTLKG 145
>3u5c_S 40S ribosomal protein S18-A, 40S ribosomal protein S17-A;
translation, ribosome, ribosomal, ribosomal R ribosomal
protein, eukaryotic ribosome, RNA-protein C; 3.00A
{Saccharomyces cerevisiae} PDB: 3izb_M 3o30_L 3o2z_L
3u5g_S 1s1h_M 3jyv_M* 2zkq_m
Length = 146
Score = 147 bits (373), Expect = 4e-47
Identities = 31/132 (23%), Positives = 57/132 (43%), Gaps = 23/132 (17%)
Query: 1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
+ R++ N+ N I+ LT I G+GR + +C+ + K+ +L ELE++ + +
Sbjct: 14 ILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIM 73
Query: 61 S-----------------------KFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPC 97
+ ++ + +++RL + +RGIRH L
Sbjct: 74 QNPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIRAHRGIRHFWGLRV 133
Query: 98 RGQRTRTNARTR 109
RGQ T+T R R
Sbjct: 134 RGQHTKTTGRRR 145
>3iz6_M 40S ribosomal protein S18 (S13P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 152
Score = 142 bits (359), Expect = 6e-45
Identities = 29/133 (21%), Positives = 58/133 (43%), Gaps = 23/133 (17%)
Query: 1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
+ R++ N+ Q I+ LT+I G+GR + +C+ I K+ +L+ E+++L +
Sbjct: 12 ILRVLNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELSAEEMDRLMAVV 71
Query: 61 SKF-----------------------IIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPC 97
++ + + +++RL + +RG+RH +
Sbjct: 72 HNPRQFKVPDWFLNRKKDYKDGRFSQVVSNAVDMKLRDDLERLKKIRNHRGLRHYWGVRV 131
Query: 98 RGQRTRTNARTRK 110
RGQ T+T R K
Sbjct: 132 RGQHTKTTGRRGK 144
>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_M
Length = 155
Score = 139 bits (352), Expect = 1e-43
Identities = 35/133 (26%), Positives = 56/133 (42%), Gaps = 23/133 (17%)
Query: 1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
+ RI+ NI + I LT I GIGR A IC+V KI + L +++ K+ + I
Sbjct: 14 IHRILNTNIDGKRITPIALTGIRGIGRRFAYIICKVLKIDPNARAGLLTEDQCNKITDLI 73
Query: 61 SKF-----------------------IIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPC 97
+ + L + +++RL + +RG+RH L
Sbjct: 74 ADPEAHGIPTWLLNRINDFKDGKNYQMASNTLDTKMREDLERLKKIKSHRGLRHFWGLKV 133
Query: 98 RGQRTRTNARTRK 110
RGQ T+T+ R
Sbjct: 134 RGQHTKTSGRHGV 146
>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 = 46.6 bits (110), Expect = 3e-07
Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 15/67 (22%)
Query: 4 IVGINIPNNQHIIIGLTAIYGIGRSRA-KKICEVTKISTTKKIKDLNDNELEKLREEISK 62
IV N+ N Q + G RA + V +KI + +L++ +S
Sbjct: 1843 IVNYNVENQQ-YVAA-------GDLRALDTVTNVLNFIKLQKID------IIELQKSLSL 1888
Query: 63 FIIEGDL 69
+EG L
Sbjct: 1889 EEVEGHL 1895
Score = 35.0 bits (80), Expect = 0.004
Identities = 24/131 (18%), Positives = 47/131 (35%), Gaps = 45/131 (34%)
Query: 26 GRSRAKKICEVTKISTTKKI-----KDLNDNE-------------LEKLREEISKFIIE- 66
G+ + +KI + +T L+ + E L+ + +I
Sbjct: 1699 GKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSK---GLIPA 1755
Query: 67 ---------GDLRREFS--------MNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNAR-T 108
G E++ M+I+ L+++ YRG+ + ++P R + R+N
Sbjct: 1756 DATFAGHSLG----EYAALASLADVMSIESLVEVVFYRGMTMQVAVP-RDELGRSNYGMI 1810
Query: 109 RKGPRRAAQSL 119
P R A S
Sbjct: 1811 AINPGRVAASF 1821
Score = 31.2 bits (70), Expect = 0.081
Identities = 18/132 (13%), Positives = 46/132 (34%), Gaps = 50/132 (37%)
Query: 2 TRIVGIN--IPNNQHIIIGLT-------------AIYGIG----RSRAKKICEVTKI-ST 41
+ N +P + + I L ++YG+ +++A + ++I +
Sbjct: 351 DYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFS 410
Query: 42 TKKIK--------------DLNDNELEKLREEISKFIIE---GDLR------------RE 72
+K+K L + + +++ K + D++ R
Sbjct: 411 ERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRV 470
Query: 73 FSMNI-KRLIDL 83
S +I +R++D
Sbjct: 471 LSGSISERIVDC 482
Score = 27.3 bits (60), Expect = 1.6
Identities = 14/88 (15%), Positives = 27/88 (30%), Gaps = 26/88 (29%)
Query: 45 IKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDLSCYRGIRHR------KSLPCR 98
I +L +++ ++K + +++S G ++ +SL
Sbjct: 341 ISNLTQEQVQDY---VNKT------NSHLPAG--KQVEISLVNGAKNLVVSGPPQSL--- 386
Query: 99 GQRTRTNARTRKGPRRAAQ-----SLRK 121
R K P Q S RK
Sbjct: 387 -YGLNLTLRKAKAPSGLDQSRIPFSERK 413
>2o1s_A 1-deoxy-D-xylulose-5-phosphate synthase; DXS, thiamine,
isoprenoid, transferase; HET: TDP; 2.40A {Escherichia
coli}
Length = 621
Score = 30.2 bits (69), Expect = 0.15
Identities = 6/29 (20%), Positives = 19/29 (65%)
Query: 38 KISTTKKIKDLNDNELEKLREEISKFIIE 66
+ +T++++ L L KL +E+ +++++
Sbjct: 13 LVDSTQELRLLPKESLPKLCDELRRYLLD 41
>2o1x_A 1-deoxy-D-xylulose-5-phosphate synthase; thiamin, isoprenoid,
DXS, transferase; HET: TDP; 2.90A {Deinococcus
radiodurans}
Length = 629
Score = 30.2 bits (69), Expect = 0.15
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 38 KISTTKKIKDLNDNELEKLREEISKFIIE 66
+I K +K L+ +L L EE+ I+
Sbjct: 15 QIHGPKDLKRLSREQLPALTEELRGEIVR 43
>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal
helicase, DNA repair,, DNA binding protein/DNA complex;
3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2
c.37.1.19 c.37.1.19 PDB: 2p6u_A
Length = 702
Score = 28.6 bits (64), Expect = 0.54
Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 16 IIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIE 66
++ L I IGR RA+K+ I + I + + I++ ++E
Sbjct: 631 LLELVRIRHIGRVRARKLYN-AGIRNAEDIVRHREKVASLIGRGIAERVVE 680
>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 = 27.9 bits (61), Expect = 0.97
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 43 KKIKDLNDNELEKLREEISKFI--IEGDLRREFSMNIKRL 80
I D ND + E+L I F+ IE +L ++ R+
Sbjct: 532 PYICD-NDPKYERLVNAILDFLPKIEENLICSKYTDLLRI 570
>2w3p_A Benzoyl-COA-dihydrodiol lyase; BOXC, crotonase, ring cleaving,
burkholderia xenovorans LB400 crotonase; 1.50A
{Burkholderia xenovorans}
Length = 556
Score = 27.3 bits (60), Expect = 1.3
Identities = 13/107 (12%), Positives = 32/107 (29%), Gaps = 9/107 (8%)
Query: 19 LTAIYGIGRSRAKKICEVTKISTTKKIKDL--------NDNELEKLREEISKFIIEGDL- 69
+T + RA C V + ++ K + + ++ + + D
Sbjct: 184 VTDKRKVRHDRADIFCTVVEGVRGERAKAWRLVDEVVKPNQFDQAIQARALELAAQSDRP 243
Query: 70 RREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAA 116
+ + R+ G+ ++ + R T K P+
Sbjct: 244 AHAQGVPLTRIERTDREDGLTYKTLDVTIDRAKRIATFTAKAPQTEP 290
>3f2b_A DNA-directed DNA polymerase III alpha chain; DNA polymerase C, DNA
polymerase III; HET: DGT; 2.39A {Geobacillus
kaustophilus} PDB: 3f2c_A* 3f2d_A*
Length = 1041
Score = 26.5 bits (59), Expect = 2.5
Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 9 IPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIE 66
+ + +I AI G+G + A+ I + + D L++ R ++SK ++E
Sbjct: 959 VIDGNSLIPPFNAIPGLGTNVAQAIVRARE---EGEFLSKED--LQQ-RGKLSKTLLE 1010
>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain,
helix turn helix motif, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: a.60.2.7
Length = 98
Score = 25.5 bits (56), Expect = 2.8
Identities = 6/49 (12%), Positives = 21/49 (42%), Gaps = 7/49 (14%)
Query: 19 LTAIYGIGRSRAKKICE-------VTKISTTKKIKDLNDNELEKLREEI 60
L ++ IG +A+ I +++ ++++ + ++E +
Sbjct: 42 LRSLQRIGPKKAQLIVGWRELHGPFSQVEDLERVEGITGKQMESFLKAN 90
>1sqw_A Saccharomyces cerevisiae NIP7P homolog; PUA, unknown function;
1.90A {Homo sapiens} SCOP: b.122.1.1 d.17.6.3 PDB:
1t5y_A
Length = 188
Score = 26.0 bits (57), Expect = 2.9
Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 13/51 (25%)
Query: 46 KDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDLS----CYRGIRHR 92
+ L + E + E+I+K+I G+ N++ L+D C+R R
Sbjct: 2 RPLTEEETRVMFEKIAKYI--GE-------NLQLLVDRPDGTYCFRLHNDR 43
>2duy_A Competence protein comea-related protein; helix-hairpin-helix,
structural genomics, NPPSFA; 1.75A {Thermus
thermophilus} SCOP: a.60.2.7
Length = 75
Score = 25.0 bits (55), Expect = 3.3
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 19 LTAIYGIGRSRAKKICE---VTKISTTKKIKDLNDNELEKLREEI 60
L A+ GIG A++I E ++ K+K + LE+LR +
Sbjct: 29 LMALPGIGPVLARRIVEGRPYARVEDLLKVKGIGPATLERLRPYL 73
>1k82_A Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA
repair, beta sandwich, zinc finger, helix two-turns
helix, hydrolase/DNA complex; HET: PED; 2.10A
{Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8
Length = 268
Score = 25.9 bits (58), Expect = 3.9
Identities = 10/52 (19%), Positives = 17/52 (32%), Gaps = 12/52 (23%)
Query: 12 NQHIIIGLTAIYGIGRSRAKKICEV---TKISTTKKIKDLNDNELEKLREEI 60
+ +++G+ IY E I + L+ E E L I
Sbjct: 159 DNKLVVGVGNIY---------ASESLFAAGIHPDRLASSLSLAECELLARVI 201
>1j03_A Putative steroid binding protein; alpha and beta, structural
genomics, riken structural genomics/proteomics
initiative, RSGI; NMR {Arabidopsis thaliana} SCOP:
d.120.1.2 PDB: 1t0g_A
Length = 102
Score = 25.3 bits (55), Expect = 3.9
Identities = 9/40 (22%), Positives = 17/40 (42%)
Query: 24 GIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKF 63
G SRA + + ++ L + E+ L + +KF
Sbjct: 51 GKDASRALGKMSKNEEDVSPSLEGLTEKEINTLNDWETKF 90
>2z1q_A Acyl-COA dehydrogenase; FAD, structural genomics, NPPSFA, Na
project on protein structural and functional analyses;
HET: FAD; 2.30A {Thermus thermophilus}
Length = 577
Score = 25.8 bits (57), Expect = 4.8
Identities = 13/96 (13%), Positives = 29/96 (30%), Gaps = 7/96 (7%)
Query: 6 GINIPNNQHIIIGL----TAIYGI--GRSRAKKICEVTKISTTKKIKDLNDNELEKLREE 59
G + Q ++ + Y RA+++ + + + D
Sbjct: 469 GQGVEEEQEVLGAVADILIDAYAAESALLRARRLGGLAPVLARIYLAQALDRAQAGALSV 528
Query: 60 ISKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSL 95
+ + + EGD R +RL + R+
Sbjct: 529 LPRLV-EGDEARVVYSAARRLTKREPGDLVALRRQA 563
>1n8i_A Probable malate synthase G; glyoxylate pathway, acetyl coenzyme A,
isocitrate lyase, persistence, GLCB, structural
genomics, PSI; 2.10A {Mycobacterium tuberculosis} SCOP:
c.1.13.1 PDB: 1n8w_A* 2gq3_A*
Length = 741
Score = 25.5 bits (56), Expect = 5.2
Identities = 17/99 (17%), Positives = 33/99 (33%), Gaps = 11/99 (11%)
Query: 11 NNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK------FI 64
+ HI I + +G + + +V S I D D+ + +
Sbjct: 235 HGLHIEILIDPESQVGTTDRAGVKDVILESAITTIMDFEDSVAAVDAADKVLGYRNWLGL 294
Query: 65 IEGDLRREFSMN---IKRLI--DLSCYRGIRHRKSLPCR 98
+GDL + R++ D + + +LP R
Sbjct: 295 NKGDLAAAVDKDGTAFLRVLNRDRNYTAPGGGQFTLPGR 333
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding,
hydrolase, nucleotide- binding; 2.00A {Pyrococcus
furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*
Length = 720
Score = 25.6 bits (56), Expect = 5.2
Identities = 10/41 (24%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 16 IIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL 56
+I L + +GR RA+ + + + + I EL K+
Sbjct: 645 LIPLMQLPLVGRRRARALYN-SGFRSIEDISQARPEELLKI 684
>1ryp_D 20S proteasome; multicatalytic proteinase, protein degradation,
antigen processing, hydrolase, protease; 1.90A
{Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_C*
1g65_C 2f16_C* 2fak_C* 2fny_C* 2gpl_C* 3d29_C* 3dy3_C*
3dy4_C* 3e47_C* 3gpj_C* 3gpt_C* 3gpw_C* 3hye_C* 3mg0_C*
3mg4_C* 3oeu_C* 3oev_C* 3okj_C* 3shj_C* ...
Length = 241
Score = 25.3 bits (56), Expect = 5.4
Identities = 9/48 (18%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK 62
+ + + ++ + ++ AK I E+T + I L+ E+ + +I +
Sbjct: 190 VKLTVRSLLEVVQTGAKNI-EITVVKPDSDIVALSSEEINQYVTQIEQ 236
>1iru_D 20S proteasome; cell cycle, immune response, proteolysis,
ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
PDB: 3unf_C* 3une_C* 3unh_C 3unb_C*
Length = 248
Score = 25.3 bits (56), Expect = 5.5
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK 62
I + + A+ + +S K I E+ + + +K LN E+EK EI K
Sbjct: 188 IKLVIKALLEVVQSGGKNI-ELAVMRRDQSLKILNPEEIEKYVAEIEK 234
>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis,
mutation, deletion, streisinger, slippage, transferase,
lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP:
a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A*
2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A*
1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A*
1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ...
Length = 335
Score = 25.6 bits (55), Expect = 5.7
Identities = 9/34 (26%), Positives = 20/34 (58%)
Query: 19 LTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNE 52
+I GIG+ A+KI E+ + +K+ ++++
Sbjct: 59 ACSIPGIGKRMAEKIIEILESGHLRKLDHISESV 92
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA
complex; HET: DNA D3T; 2.40A {Mus musculus}
Length = 360
Score = 25.3 bits (54), Expect = 6.6
Identities = 11/67 (16%), Positives = 28/67 (41%), Gaps = 2/67 (2%)
Query: 19 LTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIEGD--LRREFSMN 76
L + G + I E+ + T +++K + +E + + ++ G R +
Sbjct: 63 LHGLPYFGEHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVGVKTANRWYQEG 122
Query: 77 IKRLIDL 83
++ L +L
Sbjct: 123 LRTLDEL 129
>2w8d_A Processed glycerol phosphate lipoteichoic acid SY; transferase,
phosphatase, cell membrane, transmembrane, LTA,
membrane, secreted, cell WALL; HET: TPO PG4; 2.35A
{Bacillus subtilis}
Length = 436
Score = 25.2 bits (55), Expect = 6.7
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 5/52 (9%)
Query: 35 EVTKISTTKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDLSCY 86
E+ + K L ELE +S II GDL R + + ++ S Y
Sbjct: 371 ELDESEVDKSEDSLVKKELE-----MSDKIINGDLLRFYEPKGFKKVNPSDY 417
>3twl_A Formamidopyrimidine-DNA glycosylase 1; helix two turns helix,
zinc-LESS finger, hydrolase, DNA DAMA repair,
DNA-binding, glycosidase, lyase; 1.70A {Arabidopsis
thaliana} PDB: 3twm_A* 3twk_A
Length = 310
Score = 24.9 bits (55), Expect = 7.5
Identities = 10/52 (19%), Positives = 16/52 (30%), Gaps = 12/52 (23%)
Query: 12 NQHIIIGLTAIYGIGRSRAKKICEV---TKISTTKKIKDLNDNELEKLREEI 60
+Q I G+ EV +I + L+ + E L I
Sbjct: 177 DQGYISGIGNWIA---------DEVLYQARIHPLQTASSLSKEQCEALHTSI 219
>1y6z_A Heat shock protein, putative; chaperone, structural genomics,
structural genom consortium, SGC, unknown function;
1.88A {Plasmodium falciparum}
Length = 263
Score = 24.8 bits (55), Expect = 7.9
Identities = 7/47 (14%), Positives = 15/47 (31%), Gaps = 6/47 (12%)
Query: 32 KICEVTKISTTKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIK 78
K+ + K + E ++ +KF+ F +K
Sbjct: 119 KMLSIINKRIVLKSISMMKGLKETGGDKWTKFL------NTFGKYLK 159
>2xzf_A Formamidopyrimidine-DNA glycosylase; hydrolase-DNA complex; HET:
VET; 1.80A {Lactococcus lactis subsp} PDB: 1pm5_A*
1xc8_A* 1pji_A* 2xzu_A* 3c58_A* 1tdz_A* 1nnj_A 1kfv_A
1pjj_A*
Length = 271
Score = 24.7 bits (55), Expect = 8.3
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 12/52 (23%)
Query: 12 NQHIIIGLTAIYGIGRSRAKKICEV---TKISTTKKIKDLNDNELEKLREEI 60
Q ++ GL IY + EV KI K+ L ++ + L + I
Sbjct: 162 EQTLVAGLGNIY---------VDEVLWLAKIHPEKETNQLIESSIHLLHDSI 204
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication;
2.46A {Deinococcus radiodurans}
Length = 578
Score = 24.7 bits (53), Expect = 9.9
Identities = 6/41 (14%), Positives = 15/41 (36%)
Query: 18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLRE 58
T I +G+ A ++ + + T ++ L +
Sbjct: 58 EFTGIPKVGKGIAAELSDFARSGTFAPLEAAAGQLPPGLLD 98
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
0.322 0.138 0.390
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,827,509
Number of extensions: 103782
Number of successful extensions: 423
Number of sequences better than 10.0: 1
Number of HSP's gapped: 415
Number of HSP's successfully gapped: 59
Length of query: 121
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 39
Effective length of database: 4,412,271
Effective search space: 172078569
Effective search space used: 172078569
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 (21.9 bits)
S2: 51 (23.4 bits)