RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 030459
(177 letters)
>1ryb_A CRS2; alpha-beta, hydrolase; 1.70A {Zea mays} SCOP: c.56.3.1 PDB:
1rym_A 1ryn_A
Length = 205
Score = 221 bits (565), Expect = 1e-74
Identities = 90/165 (54%), Positives = 123/165 (74%)
Query: 1 MIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLN 60
M+D A +GI+MNT+ K+ G G +G+ PVL+ KPQ+YMN SGE+ GPLAAYY++PL
Sbjct: 41 MVDRIAAEEGITMNTIQSKSLLGIGSIGEVPVLVVKPQSYMNYSGEAIGPLAAYYQVPLR 100
Query: 61 RVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPK 120
+L+ +DD LP GVLRL+ GGHG HNGL++V+ + G REF RL IGIG PPG+MDP+
Sbjct: 101 HILLIYDDTSLPNGVLRLQKKGGHGRHNGLQNVIEHLDGRREFPRLSIGIGSPPGKMDPR 160
Query: 121 AFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHFNTIQ 165
AFLLQKF++ R +IDTAL++GV+ ++ L+ KG + S FN +Q
Sbjct: 161 AFLLQKFSSEERVQIDTALEQGVDAVRTLVLKGFSGSTERFNLVQ 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 = 204 bits (521), Expect = 5e-68
Identities = 60/163 (36%), Positives = 89/163 (54%), Gaps = 2/163 (1%)
Query: 1 MIDAFAESQGISMNTV-HCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPL 59
+ D A G A G ++LAKP+ YMN SG GPLA +Y +
Sbjct: 28 VADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFYSVAP 87
Query: 60 NRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDP 119
++V HDD+ L G +RL+ GG GGHNGL+SV+ G ++F R+RIGIGRPPG+ DP
Sbjct: 88 ANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAAL-GTKDFQRVRIGIGRPPGRKDP 146
Query: 120 KAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHFN 162
AF+L+ F R + T ++ + +LL+ +G+ + +
Sbjct: 147 AAFVLENFTPAERAEVPTICEQAADATELLIEQGMEPAQNRVH 189
>4fno_A PTH, peptidyl-tRNA hydrolase; 2.25A {Pseudomonas aeruginosa} PDB:
4djj_A* 4erx_A 4dhw_A
Length = 194
Score = 200 bits (512), Expect = 1e-66
Identities = 50/164 (30%), Positives = 86/164 (52%), Gaps = 1/164 (0%)
Query: 1 MIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPL 59
++ A +QG+S+ G+ V L P TYMN SG+S LA ++++
Sbjct: 28 FVERLAHAQGVSLVADRKYFGLVGKFSHQGKDVRLLIPTTYMNRSGQSVAALAGFFRIAP 87
Query: 60 NRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDP 119
+ +LV HD++ +P GV +L+ GGHGGHNGL+ ++ F RLR+GIG P
Sbjct: 88 DAILVAHDELDMPPGVAKLKTGGGHGGHNGLRDIIAQLGNQNSFHRLRLGIGHPGHSSLV 147
Query: 120 KAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHFNT 163
++L + +E +DT++ + VL +L+ T + + ++
Sbjct: 148 SGYVLGRAPRSEQELLDTSIDFALGVLPEMLAGDWTRAMQKLHS 191
>2pth_A Peptidyl-tRNA hydrolase; 1.20A {Escherichia coli} SCOP: c.56.3.1
PDB: 3ofv_A
Length = 193
Score = 195 bits (499), Expect = 1e-64
Identities = 52/166 (31%), Positives = 86/166 (51%), Gaps = 1/166 (0%)
Query: 2 IDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLN 60
+D AE + + +G V L P T+MNLSG++ +A+++++ +
Sbjct: 27 VDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLVPTTFMNLSGKAVAAMASFFRINPD 86
Query: 61 RVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPK 120
+LV HD++ LP GV + + GGHGGHNGLK +++ N F RLRIGIG P +
Sbjct: 87 EILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISKLGNNPNFHRLRIGIGHPGDKNKVV 146
Query: 121 AFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHFNTIQK 166
F+L K ++ ID A+ E ++ + GLT++ + +
Sbjct: 147 GFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGLTKATNRLHAFKA 192
>3nea_A PTH, peptidyl-tRNA hydrolase; 2.25A {Francisella tularensis subsp}
Length = 207
Score = 185 bits (473), Expect = 2e-60
Identities = 48/156 (30%), Positives = 81/156 (51%), Gaps = 2/156 (1%)
Query: 2 IDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLN 60
I A+ S ++ + + V+L P TYMN SG + +A +YK+
Sbjct: 48 IAKIAQDNNQSFSSNPKLNCNLAKVSIDYNNVVLVFPTTYMNNSGLAVSKVANFYKIAPA 107
Query: 61 RVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPK 120
+LV HD++ + G +RL+ GGHGGHNGL+S+ + G ++ RLRIGIG P +
Sbjct: 108 EILVVHDELDIDSGEIRLKKGGGHGGHNGLRSINQHL-GTNDYLRLRIGIGHPGHKSKVA 166
Query: 121 AFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTE 156
++L + ++ ID+A+ G+ L +++ L
Sbjct: 167 NYVLSNPSIAQKKDIDSAIDNGICFLDDIINYKLEP 202
>4fop_A PTH, peptidyl-tRNA hydrolase; 1.86A {Acinetobacter baumannii}
Length = 193
Score = 183 bits (467), Expect = 8e-60
Identities = 50/166 (30%), Positives = 86/166 (51%), Gaps = 3/166 (1%)
Query: 2 IDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLN 60
++ A+ GI++ G+G + V L P TYMN SG+S P + +Y++
Sbjct: 29 VEQLADKYGITLKNDPKFHGISGRGNIEGHDVRLLLPMTYMNRSGQSVVPFSKFYQIAPE 88
Query: 61 RVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPK 120
+L+ HD++ + GV+RL+ GGHGGHNGL+ ++ + F RLRIGIG P +
Sbjct: 89 AILIAHDELDMNPGVIRLKTGGGHGGHNGLRDIVPHI--GPNFHRLRIGIGHPGSKERVS 146
Query: 121 AFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHFNTIQK 166
+L K + + +D A+ + +KLL+ + ++ N +
Sbjct: 147 GHVLGKAPSNEQSLMDGAIDHALSKVKLLVQGQVPQAMNQINAYKP 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 = 183 bits (466), Expect = 2e-59
Identities = 50/173 (28%), Positives = 86/173 (49%), Gaps = 12/173 (6%)
Query: 2 IDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLN 60
+D A G ++ + + + V L +PQTYMN SG+S LA ++K+ N
Sbjct: 48 VDQLAREAGATLRDERRFHGFYAKARLYGEEVHLLEPQTYMNRSGQSVVALAHFFKILPN 107
Query: 61 RVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPP------ 114
+LV HD++ LP G ++L+ GG GGHNGLK + + ++++ RLRIGIG P
Sbjct: 108 EILVAHDELDLPPGAVKLKLGGGSGGHNGLKDISAHL-SSQQYWRLRIGIGHPRDMIPES 166
Query: 115 ----GQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHFNT 163
+ D F+L+ ++ ID A++ + V+ ++ + +
Sbjct: 167 ARAGAKPDVANFVLKPPRKEEQDVIDAAIERALAVMPAVVKGETERAMMQLHR 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 = 26.0 bits (57), Expect = 3.9
Identities = 16/58 (27%), Positives = 22/58 (37%), Gaps = 10/58 (17%)
Query: 1 MIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 58
+ DAFA+ G H + +A LL+ P + LAA KLP
Sbjct: 54 VFDAFADEAGRQ---AHLNGQIAAALMANAATLLSSPPNIEKVE-----LLAA--KLP 101
>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 = 6.5
Identities = 8/42 (19%), Positives = 15/42 (35%), Gaps = 9/42 (21%)
Query: 123 LLQKFNA-IARERIDTALQEGVEVLKLLLSKGLTESARHFNT 163
L+ KF ++ + + + +VL L L F
Sbjct: 60 LVGKFLGYVSSLVEPSKVGQFDQVLNLCL--------TEFEN 93
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
0.322 0.139 0.416
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: 2,741,096
Number of extensions: 163121
Number of successful extensions: 460
Number of sequences better than 10.0: 1
Number of HSP's gapped: 454
Number of HSP's successfully gapped: 12
Length of query: 177
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 90
Effective length of database: 4,272,666
Effective search space: 384539940
Effective search space used: 384539940
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 (21.9 bits)
S2: 54 (24.4 bits)