RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 030200
(181 letters)
>1ryb_A CRS2; alpha-beta, hydrolase; 1.70A {Zea mays} SCOP: c.56.3.1 PDB:
1rym_A 1ryn_A
Length = 205
Score = 252 bits (645), Expect = 1e-86
Identities = 96/157 (61%), Positives = 121/157 (77%)
Query: 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAK 77
PWL GLGNPG+KY GTRHNVGFEM+D A +GI+MNT+ K+ G G +G+ PVL+ K
Sbjct: 17 PWLIAGLGNPGNKYYGTRHNVGFEMVDRIAAEEGITMNTIQSKSLLGIGSIGEVPVLVVK 76
Query: 78 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNN 137
PQ+YMN SGE+ GPLAAYY++PL +L+ +DD LP GVLRL+ GGHG HNGL++V+ +
Sbjct: 77 PQSYMNYSGEAIGPLAAYYQVPLRHILLIYDDTSLPNGVLRLQKKGGHGRHNGLQNVIEH 136
Query: 138 FRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARE 174
G REF RL IGIG PPG+MDP+AFLLQKF++ R
Sbjct: 137 LDGRREFPRLSIGIGSPPGKMDPRAFLLQKFSSEERV 173
>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 = 238 bits (609), Expect = 2e-81
Identities = 73/160 (45%), Positives = 93/160 (58%), Gaps = 2/160 (1%)
Query: 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTV-HCKATFGQGFVGDAPVL 74
A P L VGLGNPG Y TRHN+GF + D A G A G ++
Sbjct: 2 AEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLV 61
Query: 75 LAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSV 134
LAKP+ YMN SG GPLA +Y + ++V HDD+ L G +RL+ GG GGHNGL+SV
Sbjct: 62 LAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSV 121
Query: 135 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARE 174
+ G ++F R+RIGIGRPPG+ DP AF+L+ F R
Sbjct: 122 VAAL-GTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERA 160
>4fno_A PTH, peptidyl-tRNA hydrolase; 2.25A {Pseudomonas aeruginosa} PDB:
4djj_A* 4erx_A 4dhw_A
Length = 194
Score = 232 bits (593), Expect = 7e-79
Identities = 58/160 (36%), Positives = 85/160 (53%), Gaps = 1/160 (0%)
Query: 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVL 74
L VGLGNPG +Y TRHN G ++ A +QG+S+ G+ V
Sbjct: 2 TAVQLIVGLGNPGPEYDQTRHNAGALFVERLAHAQGVSLVADRKYFGLVGKFSHQGKDVR 61
Query: 75 LAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSV 134
L P TYMN SG+S LA ++++ + +LV HD++ +P GV +L+ GGHGGHNGL+ +
Sbjct: 62 LLIPTTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMPPGVAKLKTGGGHGGHNGLRDI 121
Query: 135 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARE 174
+ F RLR+GIG P ++L + +E
Sbjct: 122 IAQLGNQNSFHRLRLGIGHPGHSSLVSGYVLGRAPRSEQE 161
>2pth_A Peptidyl-tRNA hydrolase; 1.20A {Escherichia coli} SCOP: c.56.3.1
PDB: 3ofv_A
Length = 193
Score = 225 bits (576), Expect = 3e-76
Identities = 58/157 (36%), Positives = 85/157 (54%), Gaps = 1/157 (0%)
Query: 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAK 77
L VGL NPG +Y TRHN G +D AE + + +G V L
Sbjct: 3 KLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLV 62
Query: 78 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNN 137
P T+MNLSG++ +A+++++ + +LV HD++ LP GV + + GGHGGHNGLK +++
Sbjct: 63 PTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISK 122
Query: 138 FRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARE 174
N F RLRIGIG P + F+L K ++
Sbjct: 123 LGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQK 159
>3nea_A PTH, peptidyl-tRNA hydrolase; 2.25A {Francisella tularensis subsp}
Length = 207
Score = 221 bits (565), Expect = 2e-74
Identities = 54/156 (34%), Positives = 84/156 (53%), Gaps = 2/156 (1%)
Query: 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVL 74
+ + +GLGN G +Y+ TRHNVG I A+ S ++ + + V+
Sbjct: 21 PKIKMIIGLGNIGKEYQDTRHNVGEWFIAKIAQDNNQSFSSNPKLNCNLAKVSIDYNNVV 80
Query: 75 LAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSV 134
L P TYMN SG + +A +YK+ +LV HD++ + G +RL+ GGHGGHNGL+S+
Sbjct: 81 LVFPTTYMNNSGLAVSKVANFYKIAPAEILVVHDELDIDSGEIRLKKGGGHGGHNGLRSI 140
Query: 135 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNA 170
+ G ++ RLRIGIG P + ++L +
Sbjct: 141 NQHL-GTNDYLRLRIGIGHPGHKSKVANYVLSNPSI 175
>4fop_A PTH, peptidyl-tRNA hydrolase; 1.86A {Acinetobacter baumannii}
Length = 193
Score = 214 bits (547), Expect = 9e-72
Identities = 59/153 (38%), Positives = 86/153 (56%), Gaps = 3/153 (1%)
Query: 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAK 77
L VGLGNPG +Y TRHN GF ++ A+ GI++ G+G + V L
Sbjct: 5 SLIVGLGNPGSEYAQTRHNAGFWFVEQLADKYGITLKNDPKFHGISGRGNIEGHDVRLLL 64
Query: 78 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNN 137
P TYMN SG+S P + +Y++ +L+ HD++ + GV+RL+ GGHGGHNGL+ ++ +
Sbjct: 65 PMTYMNRSGQSVVPFSKFYQIAPEAILIAHDELDMNPGVIRLKTGGGHGGHNGLRDIVPH 124
Query: 138 FRGNREFARLRIGIGRPPGQMDPKAFLLQKFNA 170
F RLRIGIG P + +L K +
Sbjct: 125 I--GPNFHRLRIGIGHPGSKERVSGHVLGKAPS 155
>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 = 214 bits (548), Expect = 1e-71
Identities = 61/163 (37%), Positives = 89/163 (54%), Gaps = 12/163 (7%)
Query: 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAK 77
L VGLGNPG +Y TRHN GF ++D A G ++ + + + V L +
Sbjct: 24 KLIVGLGNPGAEYTATRHNAGFWLVDQLAREAGATLRDERRFHGFYAKARLYGEEVHLLE 83
Query: 78 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNN 137
PQTYMN SG+S LA ++K+ N +LV HD++ LP G ++L+ GG GGHNGLK + +
Sbjct: 84 PQTYMNRSGQSVVALAHFFKILPNEILVAHDELDLPPGAVKLKLGGGSGGHNGLKDISAH 143
Query: 138 FRGNREFARLRIGIGRPP----------GQMDPKAFLLQKFNA 170
++++ RLRIGIG P + D F+L+
Sbjct: 144 L-SSQQYWRLRIGIGHPRDMIPESARAGAKPDVANFVLKPPRK 185
>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 = 36.6 bits (84), Expect = 0.003
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
>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 = 28.7 bits (64), Expect = 0.47
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 = 3.9
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 23 GLGNPGDKYKGTRH 36
GLG+ GD+ GT++
Sbjct: 204 GLGDAGDRLFGTKN 217
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 0.143 0.448
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: 2,913,608
Number of extensions: 169491
Number of successful extensions: 339
Number of sequences better than 10.0: 1
Number of HSP's gapped: 329
Number of HSP's successfully gapped: 17
Length of query: 181
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 93
Effective length of database: 4,244,745
Effective search space: 394761285
Effective search space used: 394761285
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: 54 (24.4 bits)