RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 027817
(218 letters)
>1ryb_A CRS2; alpha-beta, hydrolase; 1.70A {Zea mays} SCOP: c.56.3.1 PDB:
1rym_A 1ryn_A
Length = 205
Score = 278 bits (714), Expect = 2e-96
Identities = 110/189 (58%), Positives = 144/189 (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 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNN 137
PQ+YMN SGE+ GPLAAYY++PL +L+ +DD LP GVLRL+ GGHG HNGL++V+ +
Sbjct: 77 PQSYMNYSGEAIGPLAAYYQVPLRHILLIYDDTSLPNGVLRLQKKGGHGRHNGLQNVIEH 136
Query: 138 FRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTE 197
G REF RL IGIG PPG+MDP+AFLLQKF++ R +IDTAL++GV+ ++ L+ KG +
Sbjct: 137 LDGRREFPRLSIGIGSPPGKMDPRAFLLQKFSSEERVQIDTALEQGVDAVRTLVLKGFSG 196
Query: 198 SARHFNTIQ 206
S FN +Q
Sbjct: 197 STERFNLVQ 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 = 260 bits (668), Expect = 1e-89
Identities = 77/189 (40%), Positives = 107/189 (56%), Gaps = 2/189 (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 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 194
+ G ++F R+RIGIGRPPG+ DP AF+L+ F R + T ++ + +LL+ +G
Sbjct: 122 VAAL-GTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQG 180
Query: 195 LTESARHFN 203
+ + +
Sbjct: 181 MEPAQNRVH 189
>4fno_A PTH, peptidyl-tRNA hydrolase; 2.25A {Pseudomonas aeruginosa} PDB:
4djj_A* 4erx_A 4dhw_A
Length = 194
Score = 255 bits (653), Expect = 3e-87
Identities = 64/190 (33%), Positives = 101/190 (53%), Gaps = 1/190 (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 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 194
+ F RLR+GIG P ++L + +E +DT++ + VL +L+
Sbjct: 122 IAQLGNQNSFHRLRLGIGHPGHSSLVSGYVLGRAPRSEQELLDTSIDFALGVLPEMLAGD 181
Query: 195 LTESARHFNT 204
T + + ++
Sbjct: 182 WTRAMQKLHS 191
>2pth_A Peptidyl-tRNA hydrolase; 1.20A {Escherichia coli} SCOP: c.56.3.1
PDB: 3ofv_A
Length = 193
Score = 247 bits (632), Expect = 3e-84
Identities = 65/190 (34%), Positives = 100/190 (52%), Gaps = 1/190 (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 FRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTE 197
N F RLRIGIG P + F+L K ++ ID A+ E ++ + GLT+
Sbjct: 123 LGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGLTK 182
Query: 198 SARHFNTIQK 207
+ + +
Sbjct: 183 ATNRLHAFKA 192
>3nea_A PTH, peptidyl-tRNA hydrolase; 2.25A {Francisella tularensis subsp}
Length = 207
Score = 239 bits (611), Expect = 9e-81
Identities = 60/183 (32%), Positives = 98/183 (53%), Gaps = 2/183 (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 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 194
+ G ++ RLRIGIG P + ++L + ++ ID+A+ G+ L +++
Sbjct: 141 NQHL-GTNDYLRLRIGIGHPGHKSKVANYVLSNPSIAQKKDIDSAIDNGICFLDDIINYK 199
Query: 195 LTE 197
L
Sbjct: 200 LEP 202
>4fop_A PTH, peptidyl-tRNA hydrolase; 1.86A {Acinetobacter baumannii}
Length = 193
Score = 236 bits (604), Expect = 6e-80
Identities = 65/190 (34%), Positives = 102/190 (53%), Gaps = 3/190 (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 FRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTE 197
F RLRIGIG P + +L K + + +D A+ + +KLL+ + +
Sbjct: 125 I--GPNFHRLRIGIGHPGSKERVSGHVLGKAPSNEQSLMDGAIDHALSKVKLLVQGQVPQ 182
Query: 198 SARHFNTIQK 207
+ N +
Sbjct: 183 AMNQINAYKP 192
>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 = 236 bits (604), Expect = 2e-79
Identities = 65/197 (32%), Positives = 103/197 (52%), Gaps = 12/197 (6%)
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----------GQMDPKAFLLQKFNAIARERIDTALQEGVEVL 187
++++ RLRIGIG P + D F+L+ ++ ID A++ + V+
Sbjct: 144 L-SSQQYWRLRIGIGHPRDMIPESARAGAKPDVANFVLKPPRKEEQDVIDAAIERALAVM 202
Query: 188 KLLLSKGLTESARHFNT 204
++ + +
Sbjct: 203 PAVVKGETERAMMQLHR 219
>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 = 40.8 bits (95), Expect = 2e-04
Identities = 51/255 (20%), Positives = 85/255 (33%), Gaps = 81/255 (31%)
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--GHGG------------------HNGLKSVMNNF----RGNREFARLRI-------- 149
G GH + K++ F R + +
Sbjct: 268 KGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDS 327
Query: 150 ---GIGRP-PGQM-----DPKAFL---LQKFNAI--ARERIDTALQEGVEVLKLLLSKGL 195
G P P M + + + K N+ A ++++ +L G + L++S G
Sbjct: 328 LENNEGVPSP--MLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAK--NLVVS-GP 382
Query: 196 TESARHFNT-IQKYK 209
+S N ++K K
Sbjct: 383 PQSLYGLNLTLRKAK 397
Score = 26.6 bits (58), Expect = 9.5
Identities = 8/42 (19%), Positives = 15/42 (35%), Gaps = 9/42 (21%)
Query: 164 LLQKFNA-IARERIDTALQEGVEVLKLLLSKGLTESARHFNT 204
L+ KF ++ + + + +VL L L F
Sbjct: 60 LVGKFLGYVSSLVEPSKVGQFDQVLNLCL--------TEFEN 93
>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 = 28.3 bits (63), Expect = 0.86
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 = 5.4
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
0.324 0.141 0.433
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: 3,441,613
Number of extensions: 207042
Number of successful extensions: 528
Number of sequences better than 10.0: 1
Number of HSP's gapped: 517
Number of HSP's successfully gapped: 16
Length of query: 218
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 128
Effective length of database: 4,188,903
Effective search space: 536179584
Effective search space used: 536179584
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: 41 (22.0 bits)
S2: 55 (24.8 bits)