RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17706
(154 letters)
>3rfo_A Methionyl-tRNA formyltransferase; structural genomics, center for
structural genomics of infec diseases, csgid, alpha-beta
structure, cytosol; HET: PGE; 2.40A {Bacillus anthracis}
Length = 317
Score = 35.9 bits (84), Expect = 0.003
Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 1/52 (1%)
Query: 42 PITPELTPGFVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTAVDFKNGY 93
P+T G + V + + +++ +GKK+M+ F G
Sbjct: 255 PVTKSAEAGTI-VAIEEDGFVVATGNETGVKITELQPSGKKRMSCSQFLRGT 305
>3tqq_A Methionyl-tRNA formyltransferase; protein synthesis; 2.00A
{Coxiella burnetii}
Length = 314
Score = 35.5 bits (83), Expect = 0.004
Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 2/57 (3%)
Query: 42 PITPELTPGFVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTAVDFKNGYLGKVK 98
+ PG + D K + + G + Q+ + GK+ +A DF N + K+
Sbjct: 253 DEKTDFEPGVL-VDADKKGISIAAGSG-ILRLHQLQLPGKRVCSAGDFINAHGDKLI 307
>1fmt_A Methionyl-tRNA FMet formyltransferase; initiator tRNA, translation
initiation; 2.00A {Escherichia coli} SCOP: b.46.1.1
c.65.1.1 PDB: 2fmt_A* 3r8x_A
Length = 314
Score = 35.2 bits (82), Expect = 0.004
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 2/52 (3%)
Query: 42 PITPELTPGFVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTAVDFKNGY 93
PG + + + ++V DG + + AGKK M+A D N
Sbjct: 254 DTATNAAPGTI-LEANKQGIQVATGDG-ILNLLSLQPAGKKAMSAQDLLNSR 303
>3q0i_A Methionyl-tRNA formyltransferase; structural genomics, center for
structural genomics of infec diseases, csgid; 1.89A
{Vibrio cholerae}
Length = 318
Score = 34.8 bits (81), Expect = 0.006
Identities = 9/57 (15%), Positives = 16/57 (28%), Gaps = 2/57 (3%)
Query: 42 PITPELTPGFVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTAVDFKNGYLGKVK 98
TPG + + V ++ + + GKK + D N
Sbjct: 258 TRAVTQTPGTI-IQADKSGIYVATGQD-VLVLESLQIPGKKALPVQDILNARADWFS 312
>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 = 34.3 bits (78), Expect = 0.012
Identities = 25/131 (19%), Positives = 38/131 (29%), Gaps = 54/131 (41%)
Query: 3 EHKGSLQHFRDTSSKPPSE-----------TKEPPERSKEPTDRLTEETNPITP-ELTPG 50
H GSL+H P + K PE PT+ + P TP EL
Sbjct: 12 SH-GSLEH---VLLVPTASFFIASQLQEQFNKILPE----PTEGFAADDEPTTPAELVGK 63
Query: 51 FVSF-----DRGSKLLRVRCVDGKSILCSQITVAGKKKMTAVDFKNGYLGKVKNESDKRY 105
F+ + + + + L +F+N YL N+
Sbjct: 64 FLGYVSSLVEPSKVGQFDQVL--NLCLT--------------EFENCYLE--GND----- 100
Query: 106 KGMSTCPHSLT 116
H+L
Sbjct: 101 ------IHALA 105
Score = 28.5 bits (63), Expect = 1.2
Identities = 9/45 (20%), Positives = 16/45 (35%), Gaps = 8/45 (17%)
Query: 74 SQITVAGKKKMTAVDFKNGYLGKVKNESD-KRYKGMSTCPHSLTT 117
Q AG + A+D + V N ++ + SL+
Sbjct: 1851 QQYVAAGDLR--ALD----TVTNVLNFIKLQKID-IIELQKSLSL 1888
Score = 27.7 bits (61), Expect = 2.3
Identities = 7/45 (15%), Positives = 18/45 (40%), Gaps = 12/45 (26%)
Query: 50 GFVSFDRGSKLLRVRCVDGKSILCSQITVAGKKK------MTAVD 88
+S + +++ R G ++ Q+ V + M A++
Sbjct: 1775 DVMSIESLVEVVFYR---GMTM---QVAVPRDELGRSNYGMIAIN 1813
>2bln_A Protein YFBG; transferase, formyltransferase, L-ARA4N biosynthesis,
methyltransferase; HET: FON U5P; 1.2A {Escherichia coli}
SCOP: b.46.1.1 c.65.1.1 PDB: 1yrw_A
Length = 305
Score = 32.8 bits (76), Expect = 0.028
Identities = 10/53 (18%), Positives = 14/53 (26%), Gaps = 6/53 (11%)
Query: 42 PITPELTPGFV-SFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTAVDFKNGY 93
P + PG V S L + C DG ++ M
Sbjct: 249 PHASKAQPGSVISVAP----LLIACGDG-ALEIVTGQAGDGITMQGSQLAQTL 296
>2bw0_A 10-FTHFDH, 10-formyltetrahydrofolate dehydrogenase; nucleotide
biosynthesis, oxidoreductase; 1.7A {Homo sapiens} SCOP:
b.46.1.1 c.65.1.1 PDB: 2cfi_A* 1s3i_A
Length = 329
Score = 30.3 bits (69), Expect = 0.23
Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 4/51 (7%)
Query: 39 ETNPITPELTPGFVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTAVDF 89
+ PI PG V+ L+ D +L I + K + A +F
Sbjct: 281 DALPIPGAHRPGVVTKA---GLILFGNDDK-MLLVKNIQLEDGKMILASNF 327
>1z7e_A Protein aRNA; rossmann fold, OB-like fold, hydrolase; HET: ATP UGA;
3.00A {Escherichia coli} SCOP: b.46.1.1 c.2.1.2 c.65.1.1
Length = 660
Score = 30.0 bits (68), Expect = 0.30
Identities = 9/52 (17%), Positives = 13/52 (25%), Gaps = 4/52 (7%)
Query: 42 PITPELTPGFVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTAVDFKNGY 93
P + PG V L + C DG ++ M
Sbjct: 249 PHASKAQPGSVISVAP---LLIACGDG-ALEIVTGQAGDGITMQGSQLAQTL 296
>1tc5_A Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA;
SGPP, structural genomics, PSI; 1.93A {Leishmania major}
SCOP: c.110.1.1
Length = 194
Score = 26.4 bits (58), Expect = 3.2
Identities = 8/25 (32%), Positives = 11/25 (44%), Gaps = 1/25 (4%)
Query: 66 VDGKSILC-SQITVAGKKKMTAVDF 89
IL Q ++ GK K +V F
Sbjct: 89 CPEMDILIVPQASLGGKVKGRSVQF 113
>3l0q_A Xylulose kinase; xlylulose kinase, SGX, PSI, structural genomics,
protein structure initiative; HET: MSE XUL EPE; 1.61A
{Yersinia pseudotuberculosis} PDB: 3gg4_A*
Length = 554
Score = 26.5 bits (59), Expect = 4.1
Identities = 4/41 (9%), Positives = 13/41 (31%)
Query: 6 GSLQHFRDTSSKPPSETKEPPERSKEPTDRLTEETNPITPE 46
+ H + P+ ++ + + + L + E
Sbjct: 329 ALIDHIIQSHPCYPALLEQAKNKGETIYEALNYILRQMAGE 369
>2dgy_A MGC11102 protein; EIF-1A, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 111
Score = 25.3 bits (55), Expect = 5.4
Identities = 6/19 (31%), Positives = 8/19 (42%)
Query: 56 RGSKLLRVRCVDGKSILCS 74
G+ L V G+ L S
Sbjct: 25 PGNNLHEVETAQGQRFLVS 43
>2oqk_A Putative translation initiation factor EIF-1A; malaria,
eukaryotic initiation facto SGC, structural genomics;
1.80A {Cryptosporidium parvum iowa II}
Length = 117
Score = 25.4 bits (55), Expect = 5.8
Identities = 14/58 (24%), Positives = 20/58 (34%), Gaps = 3/58 (5%)
Query: 28 RSKEPTDRLTEETNPITPELTPGFVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMT 85
R K ++ E G V G+ L C DG+ LC + GK +
Sbjct: 14 RGKNDSEGDKRELVFKEEGQEYGQVQRMLGNGRLDAYCFDGQKRLCH---IRGKMRKK 68
>3gdb_A Endo-D, putative uncharacterized protein SPR0440;
alpha-beta-barrels, cell WALL, peptidoglycan-anchor,
secreted, hydrolase; HET: PGE; 1.87A {Streptococcus
pneumoniae} PDB: 2xqx_A
Length = 937
Score = 26.1 bits (56), Expect = 7.1
Identities = 4/36 (11%), Positives = 11/36 (30%)
Query: 14 TSSKPPSETKEPPERSKEPTDRLTEETNPITPELTP 49
+ +E + E E + + + +P
Sbjct: 46 NEADKQNEGEHARENKLEKAEGVATASETASPASNE 81
>1jt8_A EIF-1A, probable translation initiation factor 1A; beta barrel,
translation factor; NMR {Methanocaldococcus jannaschii}
SCOP: b.40.4.5
Length = 102
Score = 24.5 bits (53), Expect = 9.5
Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 56 RGSKLLRVRCVDGKSILCSQITVAGKKK 83
G+ +RVRC+DGK+ L + G+ K
Sbjct: 30 LGASRVRVRCLDGKTRLGR---IPGRLK 54
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
0.313 0.131 0.391
Gapped
Lambda K H
0.267 0.0840 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,262,775
Number of extensions: 121034
Number of successful extensions: 171
Number of sequences better than 10.0: 1
Number of HSP's gapped: 171
Number of HSP's successfully gapped: 18
Length of query: 154
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 69
Effective length of database: 4,328,508
Effective search space: 298667052
Effective search space used: 298667052
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.0 bits)