RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 028433
(209 letters)
>1ryb_A CRS2; alpha-beta, hydrolase; 1.70A {Zea mays} SCOP: c.56.3.1 PDB:
1rym_A 1ryn_A
Length = 205
Score = 248 bits (636), Expect = 8e-85
Identities = 103/190 (54%), Positives = 137/190 (72%), Gaps = 11/190 (5%)
Query: 18 PWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLA 77
PWL GLGNPG+KY GTRHN VGFEM+D A +GI+MNT+ K+ G G +G+ PVL+
Sbjct: 17 PWLIAGLGNPGNKYYGTRHN-VGFEMVDRIAAEEGITMNTIQSKSLLGIGSIGEVPVLVV 75
Query: 78 KPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMN 137
KPQ+YMN SGE+ GPLAAYY++PL +L+ +DD LP GVLRL+ GGHG HNGL++V+
Sbjct: 76 KPQSYMNYSGEAIGPLAAYYQVPLRHILLIYDDTSLPNGVLRLQKKGGHGRHNGLQNVIE 135
Query: 138 NFR----------GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLT 187
+ GIG PPG+MDP+AFLLQKF++ R +IDTAL++GV+ ++ L+ KG +
Sbjct: 136 HLDGRREFPRLSIGIGSPPGKMDPRAFLLQKFSSEERVQIDTALEQGVDAVRTLVLKGFS 195
Query: 188 ESARHFNTIQ 197
S FN +Q
Sbjct: 196 GSTERFNLVQ 205
>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 = 235 bits (602), Expect = 9e-80
Identities = 73/189 (38%), Positives = 102/189 (53%), Gaps = 11/189 (5%)
Query: 16 ARPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTV-HCKATFGQGFVGDAPV 74
A P L VGLGNPG Y TRHN +GF + D A G A G +
Sbjct: 2 AEPLLVVGLGNPGANYARTRHN-LGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSL 60
Query: 75 LLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKS 134
+LAKP+ YMN SG GPLA +Y + ++V HDD+ L G +RL+ GG GGHNGL+S
Sbjct: 61 VLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRS 120
Query: 135 VM-----NNFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 185
V+ +F+ GIGRPPG+ DP AF+L+ F R + T ++ + +LL+ +G
Sbjct: 121 VVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQG 180
Query: 186 LTESARHFN 194
+ + +
Sbjct: 181 MEPAQNRVH 189
>4fno_A PTH, peptidyl-tRNA hydrolase; 2.25A {Pseudomonas aeruginosa} PDB:
4djj_A* 4erx_A 4dhw_A
Length = 194
Score = 229 bits (586), Expect = 3e-77
Identities = 62/191 (32%), Positives = 99/191 (51%), Gaps = 12/191 (6%)
Query: 16 ARPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPV 74
L VGLGNPG +Y TRHN G ++ A +QG+S+ G+ V
Sbjct: 2 TAVQLIVGLGNPGPEYDQTRHN-AGALFVERLAHAQGVSLVADRKYFGLVGKFSHQGKDV 60
Query: 75 LLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKS 134
L P TYMN SG+S LA ++++ + +LV HD++ +P GV +L+ GGHGGHNGL+
Sbjct: 61 RLLIPTTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMPPGVAKLKTGGGHGGHNGLRD 120
Query: 135 VM------NNFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSK 184
++ N+F GIG P ++L + +E +DT++ + VL +L+
Sbjct: 121 IIAQLGNQNSFHRLRLGIGHPGHSSLVSGYVLGRAPRSEQELLDTSIDFALGVLPEMLAG 180
Query: 185 GLTESARHFNT 195
T + + ++
Sbjct: 181 DWTRAMQKLHS 191
>2pth_A Peptidyl-tRNA hydrolase; 1.20A {Escherichia coli} SCOP: c.56.3.1
PDB: 3ofv_A
Length = 193
Score = 220 bits (564), Expect = 5e-74
Identities = 61/191 (31%), Positives = 95/191 (49%), Gaps = 12/191 (6%)
Query: 19 WLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLA 77
L VGL NPG +Y TRHN G +D AE + + +G V L
Sbjct: 3 KLIVGLANPGAEYAATRHN-AGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLL 61
Query: 78 KPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVM- 136
P T+MNLSG++ +A+++++ + +LV HD++ LP GV + + GGHGGHNGLK ++
Sbjct: 62 VPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIIS 121
Query: 137 -----NNFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLT 187
NF GIG P + F+L K ++ ID A+ E ++ + GLT
Sbjct: 122 KLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGLT 181
Query: 188 ESARHFNTIQK 198
++ + +
Sbjct: 182 KATNRLHAFKA 192
>4fop_A PTH, peptidyl-tRNA hydrolase; 1.86A {Acinetobacter baumannii}
Length = 193
Score = 218 bits (558), Expect = 5e-73
Identities = 62/189 (32%), Positives = 98/189 (51%), Gaps = 10/189 (5%)
Query: 19 WLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLA 77
L VGLGNPG +Y TRHN GF ++ A+ GI++ G+G + V L
Sbjct: 5 SLIVGLGNPGSEYAQTRHN-AGFWFVEQLADKYGITLKNDPKFHGISGRGNIEGHDVRLL 63
Query: 78 KPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVM- 136
P TYMN SG+S P + +Y++ +L+ HD++ + GV+RL+ GGHGGHNGL+ ++
Sbjct: 64 LPMTYMNRSGQSVVPFSKFYQIAPEAILIAHDELDMNPGVIRLKTGGGHGGHNGLRDIVP 123
Query: 137 ---NNFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTES 189
NF GIG P + +L K + + +D A+ + +KLL+ + ++
Sbjct: 124 HIGPNFHRLRIGIGHPGSKERVSGHVLGKAPSNEQSLMDGAIDHALSKVKLLVQGQVPQA 183
Query: 190 ARHFNTIQK 198
N +
Sbjct: 184 MNQINAYKP 192
>3nea_A PTH, peptidyl-tRNA hydrolase; 2.25A {Francisella tularensis subsp}
Length = 207
Score = 215 bits (550), Expect = 1e-71
Identities = 56/183 (30%), Positives = 93/183 (50%), Gaps = 11/183 (6%)
Query: 16 ARPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPV 74
+ + +GLGN G +Y+ TRHN VG I A+ S ++ + + V
Sbjct: 21 PKIKMIIGLGNIGKEYQDTRHN-VGEWFIAKIAQDNNQSFSSNPKLNCNLAKVSIDYNNV 79
Query: 75 LLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKS 134
+L P TYMN SG + +A +YK+ +LV HD++ + G +RL+ GGHGGHNGL+S
Sbjct: 80 VLVFPTTYMNNSGLAVSKVANFYKIAPAEILVVHDELDIDSGEIRLKKGGGHGGHNGLRS 139
Query: 135 VM-----NNFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 185
+ N++ GIG P + ++L + ++ ID+A+ G+ L +++
Sbjct: 140 INQHLGTNDYLRLRIGIGHPGHKSKVANYVLSNPSIAQKKDIDSAIDNGICFLDDIINYK 199
Query: 186 LTE 188
L
Sbjct: 200 LEP 202
>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 = 211 bits (540), Expect = 5e-70
Identities = 61/197 (30%), Positives = 95/197 (48%), Gaps = 21/197 (10%)
Query: 19 WLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLA 77
L VGLGNPG +Y TRHN GF ++D A G ++ + + + V L
Sbjct: 24 KLIVGLGNPGAEYTATRHN-AGFWLVDQLAREAGATLRDERRFHGFYAKARLYGEEVHLL 82
Query: 78 KPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVM- 136
+PQTYMN SG+S LA ++K+ N +LV HD++ LP G ++L+ GG GGHNGLK +
Sbjct: 83 EPQTYMNRSGQSVVALAHFFKILPNEILVAHDELDLPPGAVKLKLGGGSGGHNGLKDISA 142
Query: 137 ----NNFR----GIGRPP----------GQMDPKAFLLQKFNAIARERIDTALQEGVEVL 178
+ GIG P + D F+L+ ++ ID A++ + V+
Sbjct: 143 HLSSQQYWRLRIGIGHPRDMIPESARAGAKPDVANFVLKPPRKEEQDVIDAAIERALAVM 202
Query: 179 KLLLSKGLTESARHFNT 195
++ + +
Sbjct: 203 PAVVKGETERAMMQLHR 219
>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 = 29.9 bits (67), Expect = 0.23
Identities = 17/70 (24%), Positives = 25/70 (35%), Gaps = 10/70 (14%)
Query: 31 YKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGEST 90
+ + F + DAFA+ G H + +A LL+ P +
Sbjct: 42 WFALKFGPSTFGVFDAFADEAGRQ---AHLNGQIAAALMANAATLLSSPPNIEKVE---- 94
Query: 91 GPLAAYYKLP 100
LAA KLP
Sbjct: 95 -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 = 5.0
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 23 GLGNPGDKYKGTRH 36
GLG+ GD+ GT++
Sbjct: 204 GLGDAGDRLFGTKN 217
>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 = 26.6 bits (58), Expect = 9.1
Identities = 8/42 (19%), Positives = 15/42 (35%), Gaps = 9/42 (21%)
Query: 155 LLQKFNA-IARERIDTALQEGVEVLKLLLSKGLTESARHFNT 195
L+ KF ++ + + + +VL L L F
Sbjct: 60 LVGKFLGYVSSLVEPSKVGQFDQVLNLCL--------TEFEN 93
>3csl_A HASR protein; outer membrane protein, beta-barrel, hemophore
receptor, TON heme, iron, metal-binding, secreted; HET:
HEM; 2.70A {Serratia marcescens} PDB: 3csn_A 3ddr_A*
Length = 865
Score = 26.3 bits (57), Expect = 9.7
Identities = 11/59 (18%), Positives = 17/59 (28%), Gaps = 3/59 (5%)
Query: 124 GGHGGHNGLKSVMNNFRGIGRPPGQMD--PKAFLLQKFNAIA-RERIDTALQEGVEVLK 179
L + + GR +D + F ID+ L GV + K
Sbjct: 152 SVSQQDPALSVNIRGIQDYGRVNMNIDGMRQNFQKSGHGQRNGTMYIDSELLSGVTIDK 210
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
0.323 0.141 0.432
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: 3,278,406
Number of extensions: 194696
Number of successful extensions: 531
Number of sequences better than 10.0: 1
Number of HSP's gapped: 509
Number of HSP's successfully gapped: 16
Length of query: 209
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 120
Effective length of database: 4,216,824
Effective search space: 506018880
Effective search space used: 506018880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (24.8 bits)