RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15048
(207 letters)
>3ssc_A ECOKMCRBC, 5-methylcytosine-specific restriction enzyme B;
protein-DNA complex; HET: DNA 5CM; 2.10A {Escherichia
coli} PDB: 3ssd_A* 3sse_A*
Length = 170
Score = 30.1 bits (67), Expect = 0.29
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 163 FGWATFASV---SFLGDSQPVGRKGLAVYPIFLFYFVIAWLILS 203
FG+ F S+ +FLG+ Q +YP+ L+Y L+L+
Sbjct: 39 FGYGNFTSIPWFAFLGEGQEASN---GIYPVILYYKDFDELVLA 79
>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 = 31.2 bits (70), Expect = 0.30
Identities = 24/142 (16%), Positives = 37/142 (26%), Gaps = 46/142 (32%)
Query: 2 ASPGTDQHRVTFYASETPQAEGSMNIPGINQNKATGH--------PEYNTLDEPIRTTIM 53
A G DQ R+ F ++ K P ++ L P I
Sbjct: 398 APSGLDQSRIPF-----------------SERKLKFSNRFLPVASPFHSHLLVPASDLIN 440
Query: 54 RDLSAVGDLWGPLLL-----CTFMAIVLQGSSDESINDGGPQFAEVFV------------ 96
+DL + + TF L+ S + V
Sbjct: 441 KDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATH 500
Query: 97 IVWIG----SGVVTLNSKLLGG 114
I+ G SG+ L + G
Sbjct: 501 ILDFGPGGASGLGVLTHRNKDG 522
>2hur_A NDK, nucleoside diphosphate kinase, NDP kinase; type II tetramer,
signaling protein,transferase; 1.62A {Escherichia coli}
Length = 142
Score = 27.5 bits (62), Expect = 2.2
Identities = 13/46 (28%), Positives = 16/46 (34%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L FM +S GP + V V G V + LLG
Sbjct: 62 LVEFM------TS-------GP----IVVSVLEGENAVQRHRDLLG 90
>1w7w_A Nucleoside diphosphate kinase; NDPK3, transferase; 2.80A {Pisum
sativum} SCOP: d.58.6.1
Length = 182
Score = 27.6 bits (62), Expect = 2.3
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
LC F+ SS GP V +VW G GV+T KL+G
Sbjct: 92 LCDFL------SS-------GP----VIAMVWEGEGVITYGRKLIG 120
>1nhk_R Nucleoside diphosphate kinase; phosphotransferase; HET: CMP; 1.90A
{Myxococcus xanthus} SCOP: d.58.6.1 PDB: 1nlk_R* 2nck_R
3pj9_A
Length = 144
Score = 27.1 bits (61), Expect = 2.6
Identities = 12/46 (26%), Positives = 16/46 (34%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L FM S GP V ++V G V N ++G
Sbjct: 62 LVQFM------IS-------GP----VVLMVLEGENAVLANRDIMG 90
>4ek2_A Nucleoside diphosphate kinase; seattle structural genomics center
for infectious disease, S DAMP, niaid; HET: DA; 2.00A
{Burkholderia thailandensis} PDB: 4dut_A*
Length = 145
Score = 27.1 bits (61), Expect = 3.0
Identities = 12/46 (26%), Positives = 15/46 (32%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L FM S GP V + V G + N L+G
Sbjct: 67 LVEFM------IS-------GP----VMIQVLEGEDAILKNRDLMG 95
>4fkx_A NDK B, nucleoside diphosphate kinase; structural genomics, niaid,
national institute of allergy AN infectious diseases;
HET: CDP; 1.70A {Trypanosoma brucei brucei} PDB: 4fky_A*
4f4a_A* 4f36_A* 3prv_A 3ngs_A 3ngr_A 3ngt_A* 3ngu_A*
Length = 161
Score = 27.2 bits (61), Expect = 3.1
Identities = 14/46 (30%), Positives = 18/46 (39%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L ++ SS GP + +VW G GVV LLG
Sbjct: 71 LVSYF------SS-------GP----IVGMVWEGLGVVKGGRVLLG 99
>3mpd_A Nucleoside diphosphate kinase; ssgcid, NIH, niaid, SBRI, UW,
emerald biostructures, encepha cuniculi, structural
genomics; 2.08A {Encephalitozoon cuniculi}
Length = 151
Score = 26.7 bits (60), Expect = 3.3
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
+ M S G V +VW+G V++ KL+G
Sbjct: 65 MVEDM------MS-------GM----VLAMVWVGKDAVSIGRKLIG 93
>3ztp_A Nucleoside diphosphate kinase; transferase; HET: GOL; 1.37A
{Aquifex aeolicus} PDB: 3zto_A* 3ztq_A 3ztr_A 3zts_A
Length = 142
Score = 26.7 bits (60), Expect = 3.6
Identities = 11/46 (23%), Positives = 15/46 (32%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L FM SS GP V V G + +++G
Sbjct: 63 LVEFM------SS-------GP----VVAAVLEGEDAIKRVREIIG 91
>2dxe_A Nucleoside diphosphate kinase; nucleoside binding, structural
genomics, NPPSFA, NAT project on protein structural and
functional analyses; HET: GDP; 1.70A {Pyrococcus
horikoshii} SCOP: d.58.6.1 PDB: 2dxd_A* 2cwk_A* 2dxf_A*
2dy9_A* 2dya_A*
Length = 160
Score = 26.8 bits (60), Expect = 3.7
Identities = 9/46 (19%), Positives = 15/46 (32%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L ++ + P V V+V G V + K+ G
Sbjct: 67 LIDYI------TK-------TP----VVVMVLEGRYAVEVVRKMAG 95
>3evo_A NDP kinase, NDK, nucleoside diphosphate kinase; phosphotransferase
nucleotide binding, ATP-binding, magnesium,
metal-binding; HET: TYD; 1.50A {Acanthamoeba polyphaga
mimivirus} PDB: 3ejm_A* 3emt_A* 3em1_A* 3fc9_A* 3g2x_A*
3ena_A* 3dkd_A* 3ddi_A* 3etm_A* 3evm_A* 3fcv_A* 3b6b_A*
2b8p_A* 3gp9_A* 2b8q_A* 3ee3_A* 3elh_A* 3eic_A* 3evw_A*
3gpa_A* ...
Length = 146
Score = 26.7 bits (60), Expect = 3.8
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
C FM S GP + IV+ G+ ++ +L G
Sbjct: 67 NCDFM------VS-------GP----IISIVYEGTDAISKIRRLQG 95
>1ehw_A NDPK H4, nucleoside diphosphate kinase; NM23, mitochondrial,
killer-O transferase; 2.40A {Homo sapiens} SCOP:
d.58.6.1
Length = 162
Score = 26.8 bits (60), Expect = 3.9
Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L +M SS GP V +VW G VV + ++G
Sbjct: 84 LIRYM------SS-------GP----VVAMVWEGYNVVRASRAMIG 112
>3q8u_A Nucleoside diphosphate kinase; ferridoxin fold, alpha-beta protein
family; HET: ADP; 2.22A {Staphylococcus aureus subsp}
PDB: 3q83_A* 3q89_A* 3q86_A* 3q8v_A* 3q8y_A*
Length = 157
Score = 26.8 bits (60), Expect = 4.1
Identities = 10/46 (21%), Positives = 18/46 (39%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L +F+ +S P VF +V G V ++ ++G
Sbjct: 61 LISFI------TS-------AP----VFAMVVEGEDAVNVSRHIIG 89
>1u8w_A Nucleoside diphosphate kinase I; nucleotide diphosphate,
transferase; 2.40A {Arabidopsis thaliana} SCOP: d.58.6.1
Length = 149
Score = 26.4 bits (59), Expect = 4.5
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L ++ S GP V ++W G VV K++G
Sbjct: 61 LVDYI------VS-------GP----VVAMIWEGKNVVLTGRKIIG 89
>1s57_A Nucleoside diphosphate kinase II; transferase; HET: EPE; 1.80A
{Arabidopsis thaliana} SCOP: d.58.6.1 PDB: 1s59_A*
Length = 153
Score = 26.4 bits (59), Expect = 4.7
Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L ++ +S GP V + W G GVV KL+G
Sbjct: 65 LIEYI------TS-------GP----VVCMAWEGVGVVASARKLIG 93
>3r9l_A Nucleoside diphosphate kinase; structural genomics, seattle
structural genomics center for infectious disease,
ssgcid, giardiasis; 2.65A {Giardia lamblia}
Length = 155
Score = 26.4 bits (59), Expect = 5.1
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
LC F+ SS GP V +VW G+ VV+++ ++G
Sbjct: 67 LCKFL------SS-------GP----VCAMVWEGANVVSISRTMMG 95
>4dz6_A Nucleoside diphosphate kinase; ssgcid, niaid, vanada transition
state mimic, transition state analog, transferas; HET:
ADP; 2.20A {Borrelia burgdorferi} PDB: 4di6_A*
Length = 190
Score = 26.6 bits (59), Expect = 5.1
Identities = 11/46 (23%), Positives = 15/46 (32%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L F+ S+ P VF V G + + KL G
Sbjct: 91 LIKFI------SN-------SP----VFTFVVEGVESIEVVRKLCG 119
>1pku_A Nucleoside diphosphate kinase I; RICE, transferase; 2.50A {Oryza
sativa} SCOP: d.58.6.1
Length = 150
Score = 26.4 bits (59), Expect = 5.4
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L ++ S GP V +VW G VV +++G
Sbjct: 62 LVEYI------IS-------GP----VVAMVWEGKDVVATGRRIIG 90
>1nb2_A Nucleoside diphosphate kinase; bacillus halodenitrifians,
transferase; 2.20A {Virgibacillus halodenitrificans}
SCOP: d.58.6.1
Length = 150
Score = 26.0 bits (58), Expect = 5.8
Identities = 11/46 (23%), Positives = 15/46 (32%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L +S GP VF +VW G ++LG
Sbjct: 62 LVGGA------TS-------GP----VFAMVWEGLNAAATARQILG 90
>3l7u_A Nucleoside diphosphate kinase A; ATP-binding, nucleotide-binding,
transferase, tumor suppressor; 2.10A {Homo sapiens}
Length = 172
Score = 26.1 bits (58), Expect = 6.2
Identities = 13/46 (28%), Positives = 16/46 (34%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L +M S GP V +VW G VV +LG
Sbjct: 84 LVKYM------HS-------GP----VVAMVWEGLNVVKTGRVMLG 112
>3b54_A NDK, NDP kinase, nucleoside diphosphate kinase; alpha/beta
sandwich, ATP-binding, magnesium, metal-B mitochondrion;
3.10A {Saccharomyces cerevisiae}
Length = 161
Score = 26.0 bits (58), Expect = 7.3
Identities = 12/46 (26%), Positives = 16/46 (34%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
+ +FM S GP + VW G VV +LG
Sbjct: 73 MVSFM------KS-------GP----ILATVWEGKDVVRQGRTILG 101
>1wkj_A Nucleoside diphosphate kinase; thermus thermophilus HB8, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; 2.00A {Thermus thermophilus} SCOP:
d.58.6.1 PDB: 1wkk_A* 1wkl_A*
Length = 137
Score = 25.9 bits (58), Expect = 7.4
Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L F+ +S GP V +V G GVV K++G
Sbjct: 61 LVRFI------TS-------GP----VVAMVLEGPGVVAEVRKMMG 89
>2az3_A Nucleoside diphosphate kinase; halophilic, transferase; HET: CDP;
2.20A {Halobacterium salinarum} SCOP: d.58.6.1 PDB:
2az1_A 2zua_A
Length = 164
Score = 26.0 bits (58), Expect = 7.4
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L +F+ +S GP VF +VW G+ +L+G
Sbjct: 68 LVSFI------TS-------GP----VFAMVWEGADATRQVRQLMG 96
>2vu5_A Nucleoside diphosphate kinase; nucleotide-binding, ATP-binding,
metal-binding, phosphoprotein, nucleotide metabolism,
cytoplasm, magnesium; 2.0A {Bacillus anthracis}
Length = 148
Score = 26.0 bits (58), Expect = 7.5
Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L F+ +S GP VF +VW G GVV ++G
Sbjct: 61 LVDFI------TS-------GP----VFAMVWQGEGVVDTARNMMG 89
>3fkb_A NDP kinase, NDK, nucleoside diphosphate kinase, cytosolic; AN
hexamer structure, ATP-binding, magnesium, metal-
nucleotide metabolism; HET: TNM TNV; 1.65A
{Dictyostelium discoideum} PDB: 1b4s_A* 1mn9_A* 1f3f_A*
1hlw_A 1ndk_A 1pae_X 1f6t_A* 1bux_A* 1b99_A* 1hiy_A*
1kdn_A* 1ndc_A* 1ndp_A* 1nsp_A* 1s5z_A* 2bef_A* 1mn7_A*
1hhq_A 1lwx_A* 1npk_A ...
Length = 155
Score = 26.0 bits (58), Expect = 7.6
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L +F+ +S GP V +V+ G GVV ++G
Sbjct: 68 LVSFI------TS-------GP----VVAMVFEGKGVVASARLMIG 96
>1xiq_A Nucleoside diphosphate kinase B; protein structure initiative,
structural genomics, SGPP; 3.05A {Plasmodium falciparum}
SCOP: d.58.6.1
Length = 157
Score = 26.0 bits (58), Expect = 7.6
Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L ++ S GP V +VW G +V KL+G
Sbjct: 69 LVAYI------SK-------GP----VVAMVWEGVDMVKQGRKLIG 97
>3bbb_A Nucleoside diphosphate kinase B; transcription factor, cancer, NM23
GEN, hexamer, activator, oncogene, ATP-binding, cell
cycle, DNA-binding; HET: DG DA; 1.30A {Homo sapiens}
SCOP: d.58.6.1 PDB: 1nue_A* 3bbf_A* 1nsk_R 3bbc_A
1be4_A* 1bhn_A* 2hvd_A* 1jxv_A* 2hve_A* 1ucn_A* 1nsq_A*
1ndl_A*
Length = 151
Score = 25.6 bits (57), Expect = 8.2
Identities = 13/46 (28%), Positives = 17/46 (36%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L +M +S GP V +VW G VV +LG
Sbjct: 63 LVKYM------NS-------GP----VVAMVWEGLNVVKTGRVMLG 91
>1k44_A Nucleoside diphosphate kinase; nucleoside triphosphate,
transferase; 2.60A {Mycobacterium tuberculosis} SCOP:
d.58.6.1
Length = 136
Score = 25.5 bits (57), Expect = 8.6
Identities = 9/46 (19%), Positives = 15/46 (32%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
L F+ +S GP V + G+ + +L G
Sbjct: 62 LLEFI------TS-------GP----VVAAIVEGTRAIAAVRQLAG 90
>3js9_A Nucleoside diphosphate kinase family protein; niaid, ssgcid,
seattle structural genomics center for infect disease,
babesiosis; 2.50A {Babesia bovis}
Length = 156
Score = 25.6 bits (57), Expect = 8.7
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 17/46 (36%)
Query: 68 LCTFMAIVLQGSSDESINDGGPQFAEVFVIVWIGSGVVTLNSKLLG 113
LC F+ S GP VF ++W G + + L+G
Sbjct: 69 LCDFI------SH-------GP----VFCMIWEGPEAIKIGRNLVG 97
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
0.327 0.142 0.444
Gapped
Lambda K H
0.267 0.0786 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,055,666
Number of extensions: 169583
Number of successful extensions: 377
Number of sequences better than 10.0: 1
Number of HSP's gapped: 377
Number of HSP's successfully gapped: 34
Length of query: 207
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 118
Effective length of database: 4,216,824
Effective search space: 497585232
Effective search space used: 497585232
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 55 (24.9 bits)