RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11903
(179 letters)
>1lur_A Aldose 1-epimerase; vitamin B12, methyltransferase, structural
genomics, structure-based function assignment,
decarboxylase, PSI; 1.85A {Caenorhabditis elegans}
SCOP: b.30.5.4
Length = 339
Score = 84.9 bits (211), Expect = 3e-20
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 20 ESNGQVLPVRRFTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLGFDDMRE 74
+ + N Q ++ ++ +GAT+ + PDK G D+VLGFD + E
Sbjct: 6 HHHSM--ASGFIEIANKQGLTATLLPFGATLAKLTFPDKNGKNQDLVLGFDTIDE 58
>1snz_A Aldose 1-epimerase; mutarotase, galactosemia, isomerase; 2.20A
{Homo sapiens} SCOP: b.30.5.4 PDB: 1so0_A*
Length = 344
Score = 82.2 bits (204), Expect = 3e-19
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 9 IMEDKFGECINESNGQVLPVRRFTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLG 68
+ FGE + G V +F L + + V +I +G TIT ++V D++G DVVLG
Sbjct: 6 VTRAVFGELPS--GGG--TVEKFQLQSDL-LRVDIISWGCTITALEVKDRQGRASDVVLG 60
Query: 69 FDDMRE 74
F ++
Sbjct: 61 FAELEG 66
>3imh_A Galactose-1-epimerase; structural genomics, PSI-2, protein ST
initiative, NEW YORK SGX research center for structural
GEN nysgxrc; 1.76A {Lactobacillus acidophilus}
Length = 338
Score = 74.1 bits (183), Expect = 2e-16
Identities = 12/66 (18%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 9 IMEDKFGECINESNGQVLPVRRFTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLG 68
++ F + + + + TL N M+V+V++YGAT+ + + + +++L
Sbjct: 2 SLKTNFVK-YERKDNK--DLCEITLENDAGMAVKVLNYGATLEKVLLDGE-----NMILS 53
Query: 69 FDDMRE 74
+ +
Sbjct: 54 LNSPED 59
>1yga_A Hypothetical 37.9 kDa protein in BIO3-HXT17 intergenic region;
aldose_1_epimerase, sugar metabolism, predicted,
structural genomics; 2.00A {Saccharomyces cerevisiae}
Length = 342
Score = 73.8 bits (182), Expect = 3e-16
Identities = 9/48 (18%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 27 PVRRFTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLGFDDMRE 74
T+ + ++ + GAT+ +KV + VV G+ ++++
Sbjct: 9 KYGVITIGDEKKFQATIAPLGATLVDLKVNGQ-----SVVQGYSNVQD 51
>1nsx_A Galactose mutarotase; epimerase, galactose metabolism, isomerase;
HET: GAL; 1.75A {Lactococcus lactis} SCOP: b.30.5.4
PDB: 1nsz_A* 1mmu_A* 1l7k_A* 1l7j_A* 1mmx_A* 1mmy_A*
1mmz_A* 1mn0_A* 1ns0_A* 1ns4_A* 1ns8_A* 1nsr_A* 1nsu_A*
1nsv_A* 1ns7_A* 1ns2_A* 1nsm_A* 1nss_A*
Length = 347
Score = 66.8 bits (164), Expect = 1e-13
Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 27 PVRRFTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLGFDDMRE 74
+LTN +++ + GA I D + + ++LGFD +E
Sbjct: 11 GSDLISLTNKAGVTISFTNLGARIV-----DWQKDGKHLILGFDSAKE 53
>3mwx_A Aldose 1-epimerase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2, isomerase; HET: MSE; 1.45A {Bacillus subtilis}
Length = 326
Score = 34.0 bits (78), Expect = 0.019
Identities = 3/44 (6%), Positives = 13/44 (29%), Gaps = 3/44 (6%)
Query: 31 FTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLGFDDMRE 74
N + V ++G+ + ++ ++ +
Sbjct: 17 IKAGNEHLEMIVVPEWGSNVISLVDKTTNV---QLLREPETAES 57
>3nre_A Aldose 1-epimerase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2, isomerase; HET: MSE; 1.59A {Escherichia coli}
Length = 291
Score = 31.7 bits (72), Expect = 0.089
Identities = 6/41 (14%), Positives = 13/41 (31%), Gaps = 6/41 (14%)
Query: 31 FTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLGFDD 71
+TL++ + + V D G I ++
Sbjct: 5 YTLSHG-SLKLDVSDQGGVIEGFWRDTT-----PLLRPGKK 39
>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 = 30.0 bits (67), Expect = 0.47
Identities = 35/182 (19%), Positives = 53/182 (29%), Gaps = 49/182 (26%)
Query: 10 MEDKFGECINE---SNGQVLPVRRFTLTNSQR-------MSVQVIDYGATITTIKVPDKR 59
+D +G I + +N L + F +R M + I G T + K
Sbjct: 1653 FKDTYGFSILDIVINNPVNLTIH-FGGEKGKRIRENYSAMIFETIVDGKLKT--EKIFKE 1709
Query: 60 GNVDDVVLGFDDMREEIY---F----IMVCSKCE----KKLGKVITPDNWKSG-SRNTIE 107
N F + + F + + K K G +I D +G S
Sbjct: 1710 INEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKG-LIPADATFAGHS----- 1763
Query: 108 SGGRRIGENKALTASKARFNPYTQKFES-CKICRQKVHQVGSHYCQAC---AYKKGICAM 163
+GE AL AS A ES ++ V G A + M
Sbjct: 1764 -----LGEYAAL-ASLADVMS----IESLVEV----VFYRGMTMQVAVPRDELGRSNYGM 1809
Query: 164 CG 165
Sbjct: 1810 IA 1811
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 27.7 bits (61), Expect = 2.4
Identities = 8/71 (11%), Positives = 22/71 (30%)
Query: 102 SRNTIESGGRRIGENKALTASKARFNPYTQKFESCKICRQKVHQVGSHYCQACAYKKGIC 161
+ I+S + + + K R N ++ +C + ++ +
Sbjct: 113 GKLKIDSSNPKFNDTQRYRDPKNRLNAVWNVCKTKMVCDTGLSAGSDNFDLSNPSANMGH 172
Query: 162 AMCGKKLLDVK 172
CG ++
Sbjct: 173 GGCGAAQPTIR 183
>1k3x_A Endonuclease VIII; hydrolase/DNA, hydrolase-DNA complex; HET: BRU
PED; 1.25A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1
g.39.1.8 PDB: 1k3w_A* 1q39_A 2ea0_A* 2oq4_A* 1q3c_A
2opf_A* 1q3b_A*
Length = 262
Score = 27.1 bits (61), Expect = 3.0
Identities = 10/56 (17%), Positives = 19/56 (33%), Gaps = 11/56 (19%)
Query: 106 IESGG--RRIGENKALTASKARFNPYTQKFESCKIC-----RQKVHQVGSHYCQAC 154
+ G + AL RF + + E C+ C + + ++C C
Sbjct: 209 YATRGQVDENKHHGAL----FRFKVFHRDGEPCERCGSIIEKTTLSSRPFYWCPGC 260
>2jne_A Hypothetical protein YFGJ; zinc fingers, two zinc, structural
genomics, PSI-2, protein structure initiative; NMR
{Escherichia coli} SCOP: g.41.18.1
Length = 101
Score = 26.1 bits (57), Expect = 3.6
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 4/37 (10%)
Query: 136 CKICRQKVHQVGSHY-CQACA---YKKGICAMCGKKL 168
C C+ + Q H C++C K +C C + L
Sbjct: 35 CPQCQHVLDQDNGHARCRSCGEFIEMKALCPDCHQPL 71
>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 = 26.6 bits (58), Expect = 4.9
Identities = 8/51 (15%), Positives = 18/51 (35%), Gaps = 16/51 (31%)
Query: 56 PDKRGNVDDVVLGFDDMREEIYFIMVCSKCEKKLGKVITPDN------WKS 100
P+ + +V ++ VC+ C G V++ W++
Sbjct: 25 PECKVYPPKIV--ERFSEGDV----VCALC----GLVLSDKLVDTRSEWRT 65
Score = 25.8 bits (56), Expect = 7.9
Identities = 7/32 (21%), Positives = 14/32 (43%), Gaps = 8/32 (25%)
Query: 136 CKICRQKVHQVGSHYCQACAYKKG--ICAMCG 165
C C+ ++ + +G +CA+CG
Sbjct: 24 CPECKVYPPKI------VERFSEGDVVCALCG 49
>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 = 26.3 bits (59), Expect = 5.3
Identities = 10/35 (28%), Positives = 14/35 (40%), Gaps = 5/35 (14%)
Query: 125 RFNPYTQKFESCKIC-----RQKVHQVGSHYCQAC 154
Y + E C C + KV G+H+C C
Sbjct: 234 ELQVYGKTGEKCSRCGAEIQKIKVAGRGTHFCPVC 268
>3u6p_A Formamidopyrimidine-DNA glycosylase; DNA glycosylase, DNA repair,
sequence context; HET: DNA 08Q; 1.60A {Geobacillus
stearothermophilus} PDB: 3u6d_A* 3u6c_A* 3u6l_A* 3u6m_A*
3u6o_A* 3u6e_A* 3u6q_A* 3u6s_A* 3gp1_A* 3sbj_A* 2f5q_A*
2f5s_A* 3gq4_A* 3gpy_A* 2f5n_A 2f5o_A 2f5p_A 3sau_A*
3sar_A* 3sav_A* ...
Length = 273
Score = 26.3 bits (59), Expect = 5.3
Identities = 10/31 (32%), Positives = 14/31 (45%), Gaps = 5/31 (16%)
Query: 129 YTQKFESCKIC-----RQKVHQVGSHYCQAC 154
Y ++ CK C + V G+HYC C
Sbjct: 241 YGRQGNPCKRCGTPIEKTVVAGRGTHYCPRC 271
>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural
genomics, PSI-2, protein structure initiative; NMR
{Salmonella typhimurium LT2}
Length = 81
Score = 24.9 bits (54), Expect = 5.7
Identities = 7/37 (18%), Positives = 13/37 (35%), Gaps = 4/37 (10%)
Query: 136 CKICRQKVHQVGSHY----CQACAYKKGICAMCGKKL 168
C +C + + G C + +C C + L
Sbjct: 5 CPVCHHALERNGDTAHCETCAKDFSLQALCPDCRQPL 41
>1ee8_A MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns
helix, riken STR genomics/proteomics initiative, RSGI,
structural genomics; 1.90A {Thermus thermophilus} SCOP:
a.156.1.2 b.113.1.1 g.39.1.8
Length = 266
Score = 26.3 bits (59), Expect = 6.4
Identities = 8/26 (30%), Positives = 11/26 (42%), Gaps = 5/26 (19%)
Query: 134 ESCKIC-----RQKVHQVGSHYCQAC 154
C C R+ V G+H+C C
Sbjct: 236 LPCPACGRPVERRVVAGRGTHFCPTC 261
>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 = 8.8
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 125 RFNPYTQKFESCKIC-----RQKVHQVGSHYCQAC 154
Y +K E C++C K Q + YC+ C
Sbjct: 232 ELQVYGRKGEPCRVCGTPIVATKHAQRATFYCRQC 266
>3d00_A Tungsten formylmethanofuran dehydrogenase subunit; FWDE/GAPDH
domain-like fold, structural genomics, joint CENT
structural genomics; HET: MSE; 1.90A {Syntrophus
aciditrophicus}
Length = 191
Score = 25.3 bits (55), Expect = 9.5
Identities = 8/35 (22%), Positives = 11/35 (31%), Gaps = 2/35 (5%)
Query: 123 KARFNPYTQKFES--CKICRQKVHQVGSHYCQACA 155
K F K + C CR+ C +C
Sbjct: 151 KPGFLEKKHKGKIVLCPQCREAYPAQDGELCLSCQ 185
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
0.320 0.135 0.404
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: 2,794,625
Number of extensions: 160071
Number of successful extensions: 417
Number of sequences better than 10.0: 1
Number of HSP's gapped: 412
Number of HSP's successfully gapped: 28
Length of query: 179
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 92
Effective length of database: 4,272,666
Effective search space: 393085272
Effective search space used: 393085272
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 (21.8 bits)
S2: 54 (24.5 bits)