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)