RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4641
(229 letters)
>1i8d_A Riboflavin synthase; riboflavin biosynthesis, antimicrobial target,
structure-based design, transferase; 2.00A {Escherichia
coli} SCOP: b.43.4.3 b.43.4.3 PDB: 1hze_A* 1i18_A*
1pkv_A*
Length = 213
Score = 271 bits (696), Expect = 2e-93
Identities = 100/201 (49%), Positives = 142/201 (70%)
Query: 1 MFTGIVQGIGKVSAVFSYNDFKSMTIWFPSDLLDGISISCSVAINGVCLSVTKIEGNYIS 60
MFTGIVQG K+ ++ +F++ + P +LDG+ SVA NG CL+VT+I GN++S
Sbjct: 1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVS 60
Query: 61 FDVINETLKITNLKAVAVDQFVNLERSAKMNTEVGGHFLSGHIIDVANVRAIQALEKNYR 120
FD++ ETL+ITNL + V +VN+ER+AK + E+GGH +SGHI+ A V I E N +
Sbjct: 61 FDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGHLMSGHIMTTAEVAKILTSENNRQ 120
Query: 121 MEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEKTTMSKKAVGDAL 180
+ ++ + LMKY+ YKG++ IDGISLT+G+V F VHLIPET+E+TT+ KK +G +
Sbjct: 121 IWFKVQDSQLMKYILYKGFIGIDGISLTVGEVTPTRFCVHLIPETLERTTLGKKKLGARV 180
Query: 181 NIEVDSQTQVIVNTVERVLKE 201
NIE+D QTQ +V+TVERVL
Sbjct: 181 NIEIDPQTQAVVDTVERVLAA 201
>3a35_A Lumazine protein, LUMP; luminous bacteria, homologue of riboflavin
synthase, luminescent protein; HET: RBF; 1.42A
{Photobacterium kishitanii} PDB: 3a3b_B* 3a3g_A*
Length = 190
Score = 243 bits (622), Expect = 2e-82
Identities = 49/185 (26%), Positives = 95/185 (51%), Gaps = 2/185 (1%)
Query: 1 MFTGIVQGIGKVSAVFSYNDFKSMTIWFPSDLLDGISISCSVAINGVCLSVTKIEGNYIS 60
MF GIVQG G + + +D + I FP D+L+ + + +NG L+V +I G+ +
Sbjct: 1 MFKGIVQGAGIIKKISKNDDTQRHGITFPKDILESVEKGTVMLVNGCSLTVVRISGDVVY 60
Query: 61 FDVINETLKITNLKAVAVDQFVNLERSAKMNTEVGGHFLSGHIIDVANVRAIQALEKNYR 120
FD+ ++ + T + + V VNLE + + +G L+G+I VA V I E +
Sbjct: 61 FDI-DQAINTTTFRELEVGNKVNLEVRPEFGSLLGKGALTGNIKGVATVDNITEEEDRLK 119
Query: 121 MEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEKTTMSKKAVGDAL 180
+ I++ K L++ + + ++ I+G+S +I ++ +D +++ T + G +
Sbjct: 120 VYIKI-PKDLIENILSEDHIGINGVSHSIEEISDDIIFINYPKNLSITTNLGTLEKGSDV 178
Query: 181 NIEVD 185
N+E
Sbjct: 179 NVETL 183
>3ddy_A Lumazine protein, LUMP; luminescent bacteria, lumazine PR
riboflavin synthase, luminescence, luminescent protein;
HET: RBF; 2.50A {Photobacterium leiognathi}
Length = 186
Score = 237 bits (607), Expect = 3e-80
Identities = 50/187 (26%), Positives = 90/187 (48%), Gaps = 2/187 (1%)
Query: 1 MFTGIVQGIGKVSAVFSYNDFKSMTIWFPSDLLDGISISCSVAINGVCLSVTKIEGNYIS 60
MF GIVQG G + ++ D + I FP + + + + +NG +V +I G+ +
Sbjct: 1 MFRGIVQGRGVIRSISKSEDSQRHGIAFPEGMFQLVDVDTVMLVNGCSNTVVRILGDMVY 60
Query: 61 FDVINETLKITNLKAVAVDQFVNLERSAKMNTEVGGHFLSGHIIDVANVRAIQALEKNYR 120
FD+ ++ L T + VNLE K VG L+G+I A V AI+ + +
Sbjct: 61 FDI-DQALGTTTFDGLKEGDQVNLEIHPKFGEVVGRGGLTGNIKGTALVAAIEENDAGFS 119
Query: 121 MEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEKTTMSKKAVGDAL 180
+ I + K L + + K + IDGISL I + + ++ + + T ++ A +
Sbjct: 120 VLIDI-PKGLAENLTVKDDIGIDGISLPITDMSDSIITLNYSRDLLASTNIASLAKDVKV 178
Query: 181 NIEVDSQ 187
N+E+ ++
Sbjct: 179 NVEILNE 185
>1kzl_A Riboflavin synthase; biosynthesis of riboflavin, ligand binding,
transferase; HET: CRM; 2.10A {Schizosaccharomyces pombe}
SCOP: b.43.4.3 b.43.4.3
Length = 208
Score = 218 bits (559), Expect = 1e-72
Identities = 70/203 (34%), Positives = 111/203 (54%), Gaps = 2/203 (0%)
Query: 1 MFTGIVQGIGKVSAV-FSYNDFKSMTIWFPSDLLDGISISCSVAINGVCLSVTKIEGNYI 59
MFTG+V+ IG V V + ++ +M I +LD S+A+NG CL+VT + +
Sbjct: 1 MFTGLVEAIGVVKDVQGTIDNGFAMKI-EAPQILDDCHTGDSIAVNGTCLTVTDFDRYHF 59
Query: 60 SFDVINETLKITNLKAVAVDQFVNLERSAKMNTEVGGHFLSGHIIDVANVRAIQALEKNY 119
+ + E+L++TNL VNLER+ +T +GGHF+ GH+ VA + + +
Sbjct: 60 TVGIAPESLRLTNLGQCKAGDPVNLERAVLSSTRMGGHFVQGHVDTVAEIVEKKQDGEAI 119
Query: 120 RMEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEKTTMSKKAVGDA 179
+ + ++KY+ YKGY+A+DG SLTI V + F + +I T K M+KK VGD
Sbjct: 120 DFTFRPRDPFVLKYIVYKGYIALDGTSLTITHVDDSTFSIMMISYTQSKVIMAKKNVGDL 179
Query: 180 LNIEVDSQTQVIVNTVERVLKEN 202
+N+EVD + VE + +
Sbjct: 180 VNVEVDQIGKYTEKLVEAHIADW 202
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 39.8 bits (92), Expect = 5e-04
Identities = 22/159 (13%), Positives = 47/159 (29%), Gaps = 37/159 (23%)
Query: 20 DFKSMTIWFPSDLLDGISISCSVAINGVCLSVTKIEGNYISFDVINETLKIT-------- 71
D + + D ++ ++N L + + V + I
Sbjct: 339 DGLATWDNWKHVNCDKLTTIIESSLN--VLEPAEYRKMFDRLSVFPPSAHIPTILLSLIW 396
Query: 72 -NLKAVAVDQFVN-------LERSAKMNTEVGGHFLSGHIIDVANVRAIQALEKNYRMEI 123
++ V VN +E+ K +T + ++ L+ E
Sbjct: 397 FDVIKSDVMVVVNKLHKYSLVEKQPKEST----ISIPSIYLE---------LKVKLENEY 443
Query: 124 QMTNKSLMKYVFYKGYVAIDGISLTIGKVFED-YFYVHL 161
+ + Y K + + D + + D YFY H+
Sbjct: 444 ALHRSIVDHYNIPKTFDSDD-----LIPPYLDQYFYSHI 477
Score = 35.2 bits (80), Expect = 0.017
Identities = 18/96 (18%), Positives = 35/96 (36%), Gaps = 29/96 (30%)
Query: 122 EIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEKTTMSKKAVGDALN 181
E Q K ++ VF +V ++ F + + M K+ +SK+ + +
Sbjct: 13 EHQYQYKDILS-VFEDAFV-------------DN-FDCKDVQD-MPKSILSKEEIDHIIM 56
Query: 182 -------------IEVDSQTQVIVNTVERVLKENYG 204
+ Q +++ VE VL+ NY
Sbjct: 57 SKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYK 92
Score = 30.6 bits (68), Expect = 0.44
Identities = 25/218 (11%), Positives = 75/218 (34%), Gaps = 41/218 (18%)
Query: 26 IWFPSDLLDGISISCSVAI----NGVCLSVTKIEGNYISFDVINETLKITNLKAVAVDQF 81
+ + ++SC + + V ++ +IS D + TL +K++ + ++
Sbjct: 253 VQNAK-AWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL-LLKY 310
Query: 82 VN-----LERSAKMNTEVGGHFLSGHIIDVANVRAIQALEKNYRME--------IQMTNK 128
++ L R + II ++R A N++ I+ +
Sbjct: 311 LDCRPQDLPREVL-----TTNPRRLSII-AESIRDGLATWDNWKHVNCDKLTTIIESSLN 364
Query: 129 SLMKYVFYKGYV--AI--DGISLTIGKVFE------DYFYVHLIPETMEKTTMSKKAVGD 178
L + K + ++ + + V ++ + K ++ +K +
Sbjct: 365 VLEPAEYRKMFDRLSVFPPSAHIPT-ILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKE 423
Query: 179 AL----NIEVDSQTQV-IVNTVERVLKENYGNLRCLCH 211
+ +I ++ + ++ + R + ++Y +
Sbjct: 424 STISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDS 461
Score = 29.1 bits (64), Expect = 1.3
Identities = 35/244 (14%), Positives = 79/244 (32%), Gaps = 70/244 (28%)
Query: 8 GIGK-VSAVFSYNDFKSMTIWFPSDLLDGISISCSVAINGVC-LSVTKIEGNYISFDVIN 65
G GK A+ +K + + L++ N S + +
Sbjct: 160 GSGKTWVALDVCLSYK-VQCKMD---------------FKIFWLNL----KNCNSPETVL 199
Query: 66 ETLKITNLKAVAVDQFVNLERSA---KMNTEVGGHFLSGHII------------DVANVR 110
E L+ L + + + K+ L + +V N +
Sbjct: 200 EMLQ--KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAK 257
Query: 111 AIQALEKNYRMEIQMT--NKSLMKYV--FYKGYVAIDGIS--LTIGKVFEDYF--YVHL- 161
A A N +I +T K + ++ ++++D S LT +V + Y+
Sbjct: 258 AWNAF--NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV-KSLLLKYLDCR 314
Query: 162 ---IPETMEKT-----TMSKKAVGDALN-------IEVDSQTQVIVNTVERV----LKEN 202
+P + T ++ +++ D L + D T +I +++ + ++
Sbjct: 315 PQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKM 374
Query: 203 YGNL 206
+ L
Sbjct: 375 FDRL 378
>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 = 38.5 bits (89), Expect = 0.002
Identities = 34/213 (15%), Positives = 66/213 (30%), Gaps = 72/213 (33%)
Query: 1 MFTGIVQGIGKVSAVFSYNDFKSMTIWF--PSDLLDG----------ISISC-------- 40
+F IV G K +F + S + F LL + +
Sbjct: 1692 IFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKG 1751
Query: 41 -----------S-------VAINGV-----CLSVTKIEGNYISFDVINETLKITNLKAVA 77
S ++ V + V G + V + L +N +A
Sbjct: 1752 LIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIA 1811
Query: 78 VD-----QFVNLERSAKMNTEVGGHFLSGHIIDVAN--------VRA--IQALEKNYRME 122
++ + E + VG +G ++++ N V A ++AL+
Sbjct: 1812 INPGRVAASFSQEALQYVVERVGKR--TGWLVEIVNYNVENQQYVAAGDLRALDT----- 1864
Query: 123 IQMTNKSLMKYVFYKGYVAIDGISLTIGKVFED 155
+TN ++ ++ + ID I L E+
Sbjct: 1865 --VTN--VLNFIKLQK---IDIIELQKSLSLEE 1890
Score = 27.7 bits (61), Expect = 3.7
Identities = 14/94 (14%), Positives = 33/94 (35%), Gaps = 36/94 (38%)
Query: 5 IVQGIGK-----VSAVFSYNDFKSMTIWFPSDLLDGISISCS---VAINGVCLSVTKIEG 56
+V+ +GK V V +YN ++ + A++ V
Sbjct: 1829 VVERVGKRTGWLVEIV-NYN-------------VENQQYVAAGDLRALDTVT-------- 1866
Query: 57 NYISFDVINETLKITNLKAVAVDQFVNLERSAKM 90
+V+N +K+ + + + + ++LE
Sbjct: 1867 -----NVLNF-IKLQKIDIIELQKSLSLEEVEGH 1894
>3t6g_B Breast cancer anti-estrogen resistance protein 1; CDC25-homology
domain, GTPase exchange factor, focal-adhesio targeting
domain, signaling protein; 2.50A {Homo sapiens}
Length = 229
Score = 28.2 bits (62), Expect = 1.9
Identities = 11/37 (29%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 154 EDYFYVHLIPETMEKTTMSKKAVGDALNIEVDSQTQV 190
EDY YVHL + E+ ++K + + +I ++Q+
Sbjct: 19 EDYDYVHL--QGKEEFEKTQKELLEKGSITRQGKSQL 53
>4f4f_A Threonine synthase; structural genomics, niaid, national institute
of allergy AN infectious diseases; HET: PLP; 1.90A
{Brucella melitensis BV}
Length = 468
Score = 27.6 bits (62), Expect = 3.6
Identities = 16/63 (25%), Positives = 25/63 (39%), Gaps = 3/63 (4%)
Query: 98 FLSGHIIDVANVRAI-QALEKNYRMEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDY 156
G D A VR + Q L+++ I S ++ F G +D + TI V
Sbjct: 327 EAHGR--DAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSAGRSTVDETAATIESVLSKD 384
Query: 157 FYV 159
Y+
Sbjct: 385 GYL 387
>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP
ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11
PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A*
1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A*
2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...
Length = 510
Score = 26.9 bits (60), Expect = 6.5
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 84 LERSAKMNTEVGG 96
LER+AKMN GG
Sbjct: 306 LERAAKMNDAFGG 318
>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase,
single analysis, thermoalkaliphilic, hydrolase; 3.06A
{Bacillus SP} PDB: 1sky_B
Length = 502
Score = 26.9 bits (60), Expect = 6.6
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 84 LERSAKMNTEVGG 96
LER+AK++ E GG
Sbjct: 298 LERAAKLSDEKGG 310
>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for
structural genomics, JCSG, protein structure initiative
ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima
MSB8}
Length = 515
Score = 26.9 bits (60), Expect = 6.8
Identities = 6/13 (46%), Positives = 11/13 (84%)
Query: 84 LERSAKMNTEVGG 96
LER+ ++N ++GG
Sbjct: 311 LERAVRLNDKLGG 323
>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability,
potential tentoxin binding hydrolase; 3.20A {Spinacia
oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*
Length = 507
Score = 26.9 bits (60), Expect = 7.0
Identities = 6/13 (46%), Positives = 11/13 (84%)
Query: 84 LERSAKMNTEVGG 96
LER+AK+++ +G
Sbjct: 299 LERAAKLSSLLGE 311
>3v7n_A Threonine synthase; ssgcid, structural genomics, seattle structural
genomics CEN infectious disease, lyase; 1.40A
{Burkholderia thailandensis}
Length = 487
Score = 26.5 bits (59), Expect = 8.3
Identities = 17/80 (21%), Positives = 27/80 (33%), Gaps = 13/80 (16%)
Query: 83 NLERSAKMNTEVGGHFLSGHIIDVANVRAI-QALEKNYRMEIQMTNKSL--MKYVFYKGY 139
N ER L G D A V + + +E+ ++ + ++ F G
Sbjct: 337 NFERFV--------FDLLGR--DPARVVQLFRDVEQKGGFDLAASGDFARVAEFGFVSGR 386
Query: 140 VAIDGISLTIGKVFEDYFYV 159
TI VFE Y +
Sbjct: 387 STHADRIATIRDVFERYRTM 406
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
0.319 0.134 0.382
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,474,237
Number of extensions: 201919
Number of successful extensions: 428
Number of sequences better than 10.0: 1
Number of HSP's gapped: 411
Number of HSP's successfully gapped: 22
Length of query: 229
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 139
Effective length of database: 4,188,903
Effective search space: 582257517
Effective search space used: 582257517
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: 56 (25.3 bits)