RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 032899
(131 letters)
>1ryb_A CRS2; alpha-beta, hydrolase; 1.70A {Zea mays} SCOP: c.56.3.1 PDB:
1rym_A 1ryn_A
Length = 205
Score = 195 bits (499), Expect = 3e-65
Identities = 70/113 (61%), Positives = 87/113 (76%)
Query: 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAK 77
PWL GLGNPG+KY GTRHNVGFEM+D A +GI+MNT+ K+ G G +G+ PVL+ K
Sbjct: 17 PWLIAGLGNPGNKYYGTRHNVGFEMVDRIAAEEGITMNTIQSKSLLGIGSIGEVPVLVVK 76
Query: 78 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNG 130
PQ+YMN SGE+ GPLAAYY++PL +L+ +DD LP GVLRL+ GGHG HNG
Sbjct: 77 PQSYMNYSGEAIGPLAAYYQVPLRHILLIYDDTSLPNGVLRLQKKGGHGRHNG 129
>2z2i_A PTH, peptidyl-tRNA hydrolase; protein synthesis; 1.98A
{Mycobacterium tuberculosis} PDB: 2z2j_A 2z2k_A 3tck_A
3tcn_A 3td2_A 3td6_A 2jrc_A 3p2j_A 3kk0_A 3kjz_A
Length = 191
Score = 185 bits (473), Expect = 2e-61
Identities = 51/116 (43%), Positives = 63/116 (54%), Gaps = 1/116 (0%)
Query: 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTV-HCKATFGQGFVGDAPVL 74
A P L VGLGNPG Y TRHN+GF + D A G A G ++
Sbjct: 2 AEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLV 61
Query: 75 LAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNG 130
LAKP+ YMN SG GPLA +Y + ++V HDD+ L G +RL+ GG GGHNG
Sbjct: 62 LAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNG 117
>4fno_A PTH, peptidyl-tRNA hydrolase; 2.25A {Pseudomonas aeruginosa} PDB:
4djj_A* 4erx_A 4dhw_A
Length = 194
Score = 181 bits (463), Expect = 7e-60
Identities = 47/116 (40%), Positives = 66/116 (56%), Gaps = 1/116 (0%)
Query: 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVL 74
L VGLGNPG +Y TRHN G ++ A +QG+S+ G+ V
Sbjct: 2 TAVQLIVGLGNPGPEYDQTRHNAGALFVERLAHAQGVSLVADRKYFGLVGKFSHQGKDVR 61
Query: 75 LAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNG 130
L P TYMN SG+S LA ++++ + +LV HD++ +P GV +L+ GGHGGHNG
Sbjct: 62 LLIPTTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMPPGVAKLKTGGGHGGHNG 117
>2pth_A Peptidyl-tRNA hydrolase; 1.20A {Escherichia coli} SCOP: c.56.3.1
PDB: 3ofv_A
Length = 193
Score = 176 bits (449), Expect = 8e-58
Identities = 43/113 (38%), Positives = 63/113 (55%), Gaps = 1/113 (0%)
Query: 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAK 77
L VGL NPG +Y TRHN G +D AE + + +G V L
Sbjct: 3 KLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLV 62
Query: 78 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNG 130
P T+MNLSG++ +A+++++ + +LV HD++ LP GV + + GGHGGHNG
Sbjct: 63 PTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNG 115
>3v2i_A PTH, peptidyl-tRNA hydrolase; ssgcid, seattle structural genomics
center for infectious DI RNA; HET: CIT; 1.65A
{Burkholderia thailandensis E264}
Length = 222
Score = 176 bits (449), Expect = 2e-57
Identities = 48/113 (42%), Positives = 67/113 (59%), Gaps = 1/113 (0%)
Query: 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAK 77
L VGLGNPG +Y TRHN GF ++D A G ++ + + + V L +
Sbjct: 24 KLIVGLGNPGAEYTATRHNAGFWLVDQLAREAGATLRDERRFHGFYAKARLYGEEVHLLE 83
Query: 78 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNG 130
PQTYMN SG+S LA ++K+ N +LV HD++ LP G ++L+ GG GGHNG
Sbjct: 84 PQTYMNRSGQSVVALAHFFKILPNEILVAHDELDLPPGAVKLKLGGGSGGHNG 136
>4fop_A PTH, peptidyl-tRNA hydrolase; 1.86A {Acinetobacter baumannii}
Length = 193
Score = 175 bits (445), Expect = 3e-57
Identities = 47/113 (41%), Positives = 67/113 (59%), Gaps = 1/113 (0%)
Query: 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAK 77
L VGLGNPG +Y TRHN GF ++ A+ GI++ G+G + V L
Sbjct: 5 SLIVGLGNPGSEYAQTRHNAGFWFVEQLADKYGITLKNDPKFHGISGRGNIEGHDVRLLL 64
Query: 78 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNG 130
P TYMN SG+S P + +Y++ +L+ HD++ + GV+RL+ GGHGGHNG
Sbjct: 65 PMTYMNRSGQSVVPFSKFYQIAPEAILIAHDELDMNPGVIRLKTGGGHGGHNG 117
>3nea_A PTH, peptidyl-tRNA hydrolase; 2.25A {Francisella tularensis subsp}
Length = 207
Score = 174 bits (444), Expect = 6e-57
Identities = 42/116 (36%), Positives = 63/116 (54%), Gaps = 1/116 (0%)
Query: 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVL 74
+ + +GLGN G +Y+ TRHNVG I A+ S ++ + + V+
Sbjct: 21 PKIKMIIGLGNIGKEYQDTRHNVGEWFIAKIAQDNNQSFSSNPKLNCNLAKVSIDYNNVV 80
Query: 75 LAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNG 130
L P TYMN SG + +A +YK+ +LV HD++ + G +RL+ GGHGGHNG
Sbjct: 81 LVFPTTYMNNSGLAVSKVANFYKIAPAEILVVHDELDIDSGEIRLKKGGGHGGHNG 136
>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 = 36.2 bits (83), Expect = 0.002
Identities = 32/127 (25%), Positives = 46/127 (36%), Gaps = 31/127 (24%)
Query: 20 LFVGLGNPGD-------KYKGTRHNVGFEMIDAFAES-QGISMNTVHCKATFGQGFVGDA 71
+F G GN D Y+ VG ++I AE+ + T+ + F QG +
Sbjct: 159 IFGGQGNTDDYFEELRDLYQTYHVLVG-DLIKFSAETLSELIRTTLDAEKVFTQGL--NI 215
Query: 72 PVLLAKPQT-----YMNLSGESTGPL-----AAYYKLPLNRVLVFHDDMGLPCGVLRLRH 121
L P Y+ LS + PL A+Y +V +G G LR
Sbjct: 216 LEWLENPSNTPDKDYL-LSIPISCPLIGVIQLAHY-------VVTAKLLGFTPGELRSYL 267
Query: 122 NG--GHG 126
G GH
Sbjct: 268 KGATGHS 274
Score = 25.8 bits (56), Expect = 6.9
Identities = 21/107 (19%), Positives = 39/107 (36%), Gaps = 30/107 (28%)
Query: 11 FCTA-VARPWLFVG-LGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFV 68
+ ++ P + V L + Y T +GF + + +G T H QG V
Sbjct: 231 LLSIPISCPLIGVIQLAH----YVVTAKLLGFTPGELRSYLKGA---TGH-----SQGLV 278
Query: 69 GDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLNRV-LVFHDDMGLPC 114
V +A+ S ES ++ + ++F +G+ C
Sbjct: 279 --TAVAIAETD-----SWES------FFVSVRKAITVLFF--IGVRC 310
>2pd1_A Hypothetical protein; unknown function, NE2512 protein, structural
genomics, APC72 2, protein structure initiative; 1.86A
{Nitrosomonas europaea} SCOP: d.58.4.11
Length = 104
Score = 29.1 bits (65), Expect = 0.19
Identities = 17/60 (28%), Positives = 23/60 (38%), Gaps = 10/60 (16%)
Query: 40 FEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99
F + DAFA+ G H + +A LL+ P + LAA KLP
Sbjct: 52 FGVFDAFADEAGRQ---AHLNGQIAAALMANAATLLSSPPNIEKVE-----LLAA--KLP 101
>3dmp_A Uracil phosphoribosyltransferase; structural genomics, seattle
structural genomics center for infectious disease,
ssgcid; 2.60A {Burkholderia pseudomallei}
Length = 217
Score = 26.8 bits (59), Expect = 2.2
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 23 GLGNPGDKYKGTRH 36
GLG+ GD+ GT++
Sbjct: 204 GLGDAGDRLFGTKN 217
>1nox_A NADH oxidase; flavoenzyme, flavoprotein FMN, oxidoreductase,
thermophIle; HET: FMN; 1.59A {Thermus thermophilus}
SCOP: d.90.1.1
Length = 205
Score = 25.7 bits (57), Expect = 4.8
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 60 KATFGQGFVGDAPVLLA 76
+A FGQ V +APV+L
Sbjct: 68 EAAFGQAHVEEAPVVLV 84
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein,
ATP-binding, nucleotide-binding, HYD; 2.20A
{Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*
Length = 574
Score = 25.8 bits (57), Expect = 4.8
Identities = 4/18 (22%), Positives = 11/18 (61%)
Query: 38 VGFEMIDAFAESQGISMN 55
+GF D +++G +++
Sbjct: 52 IGFLTADKLWQARGGALD 69
>3eof_A Putative oxidoreductase; YP_213212.1, structural genomics, J
center for structural genomics, JCSG, protein structure
INI PSI-2; HET: FMN; 1.99A {Bacteroides fragilis nctc
9343}
Length = 248
Score = 25.8 bits (57), Expect = 5.2
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 60 KATFGQGFVGDAPVLLA 76
A F Q V +APV+L
Sbjct: 60 PAHFNQPMVKEAPVVLT 76
>1v9s_A Uracil phosphoribosyltransferase; pyrimidine salvage,
oligomerization, structural genomics, RI structural
genomics/proteomics initiative; 2.10A {Thermus
thermophilus} SCOP: c.61.1.1
Length = 208
Score = 25.2 bits (55), Expect = 7.1
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 23 GLGNPGDKYKGTR 35
GLG+ GD+ GT+
Sbjct: 196 GLGDAGDRIYGTK 208
>1i5e_A Uracil phosphoribosyltransferase; salvage pathway; HET: U5P; 3.00A
{Bacillus caldolyticus} SCOP: c.61.1.1
Length = 209
Score = 25.2 bits (55), Expect = 7.2
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 23 GLGNPGDKYKGTR 35
GLG+ GD+ GT+
Sbjct: 197 GLGDAGDRLFGTK 209
>2ehj_A Uracil phosphoribosyltransferase; structural genomics; 2.80A
{Escherichia coli}
Length = 208
Score = 24.9 bits (54), Expect = 9.2
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 23 GLGNPGDKYKGTR 35
GLG+ GDK GT+
Sbjct: 196 GLGDAGDKIFGTK 208
>1o5o_A Uracil phosphoribosyltransferase; TM0721, structural genomic PSI,
protein structure initiative, joint center for structu
genomics; HET: U5P; 2.30A {Thermotoga maritima} SCOP:
c.61.1.1
Length = 221
Score = 24.9 bits (54), Expect = 9.5
Identities = 6/13 (46%), Positives = 9/13 (69%)
Query: 23 GLGNPGDKYKGTR 35
GLG+ GD+ T+
Sbjct: 209 GLGDAGDRLFRTK 221
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
0.325 0.144 0.468
Gapped
Lambda K H
0.267 0.0826 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,100,903
Number of extensions: 113949
Number of successful extensions: 281
Number of sequences better than 10.0: 1
Number of HSP's gapped: 275
Number of HSP's successfully gapped: 20
Length of query: 131
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 48
Effective length of database: 4,384,350
Effective search space: 210448800
Effective search space used: 210448800
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: 40 (21.5 bits)
S2: 52 (23.6 bits)