RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= 537021.9.peg.816_1 (97 letters) >2qlc_A DNA repair protein RADC homolog; MCSG, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; HET: DNA; 2.30A {Chlorobium tepidum tls} Length = 126 Score = 101 bits (252), Expect = 6e-23 Identities = 36/97 (37%), Positives = 57/97 (58%) Query: 1 LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADI 60 LFL N ++ E + GT+ ++ REI + + SA SIILVHNHPSG+ PS+AD Sbjct: 30 LFLSTKNQILRHETITIGTLTASLIHPREIFKAAIRESAHSIILVHNHPSGDVQPSNADK 89 Query: 61 NMTQNIITTLNPLNIIVHDHIIIGKDAFVSFKGLRII 97 +T + + L I + DH+I+G + + SF+ ++ Sbjct: 90 QVTSILKKAGDLLQIELLDHVIVGNNDWFSFRDHALL 126 >2kcq_A MOV34/MPN/PAD-1 family; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Salinibacter ruber dsm 13855} Length = 153 Score = 30.1 bits (67), Expect = 0.13 Identities = 8/39 (20%), Positives = 12/39 (30%) Query: 24 PVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADINM 62 R E + + H+HP PS D+ Sbjct: 61 ADDYRAADAAAQEQGLDVVGVYHSHPDHPARPSATDLEE 99 >1oi0_A AF2198, hypothetical protein AF2198; proteasome, deubiquitination, archaea, hydrolase; 1.5A {Archaeoglobus fulgidus} SCOP: c.97.3.1 PDB: 1r5x_A Length = 124 Score = 28.5 bits (63), Expect = 0.38 Identities = 8/18 (44%), Positives = 14/18 (77%) Query: 45 VHNHPSGNPNPSDADINM 62 VH+HPS + PS+ D+++ Sbjct: 69 VHSHPSPSCRPSEEDLSL 86 >1giq_A IOTA toxin component IA; enzymatic component; HET: NAD; 1.80A {Clostridium perfringens} SCOP: d.166.1.1 d.166.1.1 PDB: 1gir_A* 3buz_A* Length = 413 Score = 27.0 bits (59), Expect = 1.0 Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 2/43 (4%) Query: 38 SATSIILVHNHPSGNPNPS-DADINMTQNIIT-TLNPLNIIVH 78 +A + L+ N P NPNP D+ +N +N + T P N+IV+ Sbjct: 252 TAINNYLISNGPLNNPNPELDSKVNNIENALKLTPIPSNLIVY 294 >2kks_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiative; NMR {Desulfitobacterium hafniense Y51} Length = 146 Score = 27.0 bits (59), Expect = 1.1 Identities = 8/39 (20%), Positives = 14/39 (35%) Query: 24 PVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADINM 62 P V+ + + H+HP+ PS D + Sbjct: 59 PREQLTAVKDMRKNGWVMLGNFHSHPATPARPSAEDKRL 97 >2cxh_A Probable BRIX-domain ribosomal biogenesis protein; 18S rRNA, IMP4, U3 snoRNP, RNA-binding, structural genomics, NPPSFA; 1.80A {Aeropyrum pernix K1} SCOP: c.51.1.2 Length = 217 Score = 26.0 bits (57), Expect = 2.3 Identities = 7/28 (25%), Positives = 13/28 (46%), Gaps = 1/28 (3%) Query: 27 IREIVQRCLELSATSIILVHNHPSGNPN 54 + E+ + + A I++V GNP Sbjct: 72 MEELAREAIIRGADRIVVVGERR-GNPG 98 >1dmg_A Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon; HET: CIT; 1.70A {Thermotoga maritima} SCOP: c.22.1.1 Length = 225 Score = 25.5 bits (55), Expect = 2.6 Identities = 12/54 (22%), Positives = 27/54 (50%), Gaps = 2/54 (3%) Query: 35 LELSATSIILVHNHPSGNPNPSDADINMTQNIITTLNPLNIIVHDHIIIGKDAF 88 ++LS ++ V + NPN S + I LN +++ +D++++ +D Sbjct: 166 VKLSGRNLPDVKVIIADNPNNSKNGEKAVR--IDGLNVFDMLKYDYLVLTRDMV 217 >2h6f_B Protein farnesyltransferase beta subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.102.4.3 PDB: 1jcq_B* 1ld7_B* 1mzc_B* 1s63_B* 1sa4_B* 1tn6_B* 2f0y_B* 1ld8_B* 2iej_B* 3e37_B* 2h6h_B* 2h6g_B* 2h6i_B* 1o1t_B* 1o1s_B* 1o1r_B* 3eu5_B* 3e33_B* 1d8e_B* 1fpp_B* ... Length = 437 Score = 25.7 bits (56), Expect = 2.7 Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 3/46 (6%) Query: 34 CLELSATSIILVHNHPSGNPNPSDADINMTQNIITTLNPLNIIVHD 79 C LS SI H D + + +N + +P+ I D Sbjct: 364 CYCLSGLSIA---QHFGSGAMLHDVVLGVPENALQPTHPVYNIGPD 406 >3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197 Score = 25.3 bits (55), Expect = 3.4 Identities = 8/57 (14%), Positives = 16/57 (28%), Gaps = 21/57 (36%) Query: 29 EIVQRCLELSATSIILVHNHPSGNPNPSDADINMTQNIITT---LNPLNIIVHDHII 82 IV C E +V G +++ L ++ D ++ Sbjct: 19 NIVLTCPECKVYPPKIVERFSEG-------------DVVCALCGL-----VLSDKLV 57 >2znr_A AMSH-like protease; metal binding protein, alternative splicing, hydrolase, metal-binding, metalloprotease, UBL conjugation pathway, zinc; 1.20A {Homo sapiens} PDB: 2znv_A Length = 178 Score = 24.9 bits (54), Expect = 4.4 Identities = 12/65 (18%), Positives = 22/65 (33%) Query: 15 QSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADINMTQNIITTLNPLN 74 QS G + E+ + ++ +H HP+ S D++ + L Sbjct: 58 QSAGPDYCDMENVEELFNVQDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAI 117 Query: 75 IIVHD 79 IV Sbjct: 118 AIVCS 122 >2ftc_D Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_D Length = 175 Score = 24.8 bits (53), Expect = 4.9 Identities = 8/57 (14%), Positives = 19/57 (33%), Gaps = 1/57 (1%) Query: 33 RCLELSATSIILVHNHPSGNPNPSDADINMTQNI-ITTLNPLNIIVHDHIIIGKDAF 88 R S + L H + + + + I LN +++ H +++ Sbjct: 114 RRWGDSVLLVDLTHEEMPQSIVEATSRLKTFNLIPAVGLNVHSMLKHQTLVLTLPTV 170 >1g01_A Endoglucanase; alpha/beta barrel, TIM barrel, hydrolase; 1.90A {Bacillus SP} SCOP: c.1.8.3 PDB: 1g0c_A* Length = 364 Score = 24.7 bits (53), Expect = 4.9 Identities = 7/33 (21%), Positives = 12/33 (36%) Query: 27 IREIVQRCLELSATSIILVHNHPSGNPNPSDAD 59 + E ++ E I+ H H G+P Sbjct: 92 VYEGIELAFEHDMYVIVDWHVHAPGDPRADVYS 124 >3ofq_E 50S ribosomal protein L4; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_C 1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E 2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E* 2qbk_E* 2qov_E 2qox_E 2qoz_E* ... Length = 201 Score = 24.5 bits (53), Expect = 6.0 Identities = 5/19 (26%), Positives = 13/19 (68%) Query: 70 LNPLNIIVHDHIIIGKDAF 88 ++P+++I D +++ DA Sbjct: 175 IDPVSLIAFDKVVMTADAV 193 >1z7d_A Ornithine aminotransferase; structural genomics consortium, SGC, malaria; 2.10A {Plasmodium yoelii yoelii} SCOP: c.67.1.4 Length = 433 Score = 23.9 bits (51), Expect = 8.8 Identities = 7/14 (50%), Positives = 11/14 (78%), Gaps = 1/14 (7%) Query: 4 DKHNI-LIADEVQS 16 K+N+ +ADEVQ+ Sbjct: 243 KKYNVLFVADEVQT 256 >1c3p_A Protein (HDLP (histone deacetylase-like protein) ); alpha/beta fold, lyase; 1.80A {Aquifex aeolicus} SCOP: c.42.1.2 PDB: 1c3r_A* 1c3s_A* Length = 375 Score = 23.7 bits (50), Expect = 9.9 Identities = 8/77 (10%), Positives = 19/77 (24%) Query: 5 KHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADINMTQ 64 L + ID + + + + ++ +H P + Sbjct: 150 GIEYLRKKGFKRILYIDLDAHHCDGVQEAFYDTDQVFVLSLHQSPEYAFPFEKGFLEEIG 209 Query: 65 NIITTLNPLNIIVHDHI 81 LNI + + Sbjct: 210 EGKGKGYNLNIPLPKGL 226 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.324 0.142 0.413 Gapped Lambda K H 0.267 0.0571 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 856,591 Number of extensions: 34752 Number of successful extensions: 108 Number of sequences better than 10.0: 1 Number of HSP's gapped: 108 Number of HSP's successfully gapped: 25 Length of query: 97 Length of database: 5,693,230 Length adjustment: 63 Effective length of query: 34 Effective length of database: 4,165,858 Effective search space: 141639172 Effective search space used: 141639172 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: 41 (22.0 bits) S2: 50 (23.4 bits)