RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780225|ref|YP_003064638.1| peptidyl-tRNA hydrolase
[Candidatus Liberibacter asiaticus str. psy62]
(189 letters)
>2z2i_A PTH, peptidyl-tRNA hydrolase; protein synthesis; 1.98A
{Mycobacterium tuberculosis H37RV} PDB: 2z2j_A 2z2k_A
2jrc_A
Length = 191
Score = 150 bits (380), Expect = 2e-37
Identities = 73/184 (39%), Positives = 106/184 (57%), Gaps = 3/184 (1%)
Query: 3 IVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAW-KKKFHAEISEGQLDGLRTILIKP 61
+V GLGNPG Y RHN+GF+ D + + K+ AE++ G+ G +L KP
Sbjct: 6 LVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKP 65
Query: 62 QTFMNLSGQSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSISEK 121
+ +MN SG+ + + FY + N +VIHDDLDL+FG +RLK GGG+ GHNGL+S+
Sbjct: 66 RCYMNESGRQIGPLAKFYSVA-PANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAA 124
Query: 122 CG-KNYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLPIIDNIARSLPLLAKREDVSF 180
G K+++R+RIGIGRPP VL NF+ ER + I + A + LL ++
Sbjct: 125 LGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQGMEPA 184
Query: 181 LNHI 184
N +
Sbjct: 185 QNRV 188
>2pth_A Peptidyl-tRNA hydrolase; 1.20A {Escherichia coli K12} SCOP:
c.56.3.1
Length = 193
Score = 142 bits (360), Expect = 4e-35
Identities = 67/192 (34%), Positives = 94/192 (48%), Gaps = 4/192 (2%)
Query: 1 MFIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFP-AWKKKFHAEISEGQLDGLRTILI 59
+ ++ GL NPG EY RHN G +D + P + KF S L G L+
Sbjct: 2 IKLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLL 61
Query: 60 KPQTFMNLSGQSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSIS 119
P TFMNLSG+++ + +F+++ + LV HD+LDL G + K GGG GHNGLK I
Sbjct: 62 VPTTFMNLSGKAVAAMASFFRIN-PDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDII 120
Query: 120 EKC--GKNYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLPIIDNIARSLPLLAKRED 177
K N+ RLRIGIG P D ++ VLG E+ + ID AR +
Sbjct: 121 SKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGL 180
Query: 178 VSFLNHIVSVRK 189
N + + +
Sbjct: 181 TKATNRLHAFKA 192
>1ryb_A CRS2; alpha-beta, hydrolase; 1.70A {Zea mays} SCOP: c.56.3.1 PDB:
1rym_A 1ryn_A
Length = 205
Score = 139 bits (352), Expect = 3e-34
Identities = 57/186 (30%), Positives = 98/186 (52%), Gaps = 3/186 (1%)
Query: 1 MFIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIK 60
+++AGLGNPG++Y RHN+GF +DRI + + + + G + + +++K
Sbjct: 17 PWLIAGLGNPGNKYYGTRHNVGFEMVDRIAAEEGITMNTIQSKSLLGIGSIGEVPVLVVK 76
Query: 61 PQTFMNLSGQSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSISE 120
PQ++MN SG+++ + +Y++ L + L+I+DD L G LRL+ GG HNGL+++ E
Sbjct: 77 PQSYMNYSGEAIGPLAAYYQV-PLRHILLIYDDTSLPNGVLRLQKKGGHGRHNGLQNVIE 135
Query: 121 KCG--KNYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLPIIDNIARSLPLLAKREDV 178
+ + RL IGIG PP +L FSS ER + ++ ++ L +
Sbjct: 136 HLDGRREFPRLSIGIGSPPGKMDPRAFLLQKFSSEERVQIDTALEQGVDAVRTLVLKGFS 195
Query: 179 SFLNHI 184
Sbjct: 196 GSTERF 201
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 36.5 bits (84), Expect = 0.004
Identities = 41/209 (19%), Positives = 61/209 (29%), Gaps = 84/209 (40%)
Query: 30 HSF-----HFFPA--WKKKFHAEISEGQLDGLRTILIKPQT-------FMNL-------- 67
H FF A +++F+ + E +G +P T F+
Sbjct: 18 HVLLVPTASFFIASQLQEQFNKILPE-PTEGF-AADDEPTTPAELVGKFLGYVSSLVEPS 75
Query: 68 -SGQS---LLEVMNFYKLPNLENYLV---IHD---DLDLDFGTLRLKTGGGDAGHNGLKS 117
GQ L + ++ YL IH L + T +KT K
Sbjct: 76 KVGQFDQVLNLCLTEFE----NCYLEGNDIHALAAKLLQENDTTLVKT----------KE 121
Query: 118 ISEKCGKNYKRLRIGIGRPPDTAH---IIRHVL-------------GNFSSPERYF---- 157
+ KNY RI RP D + R V GN + YF
Sbjct: 122 LI----KNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNT---DDYFEELR 174
Query: 158 --------LL-PIIDNIARSLPLLAKRED 177
L+ +I A +L L +
Sbjct: 175 DLYQTYHVLVGDLIKFSAETLSELIRTTL 203
>3bl9_A Scavenger mRNA-decapping enzyme DCPS; ligand complex, cytoplasm,
hydrolase, nonsense-mediated mRNA decay, nucleus,
polymorphism, structural genomics; HET: DD2; 1.80A {Homo
sapiens} SCOP: d.13.1.3 d.246.1.1 PDB: 3bl7_A* 3bla_A*
Length = 301
Score = 29.4 bits (66), Expect = 0.59
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 114 GLKSISEKCGKNYKRLRIGIGRPPDTAHIIRHVLG-NFSSP----ERYFLLP-IIDNI 165
G ++I ++ LR+ + P H+ H F +P ER LL +I+N+
Sbjct: 212 GQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENL 269
>2wk0_A Beta-lactamase; hydrolase, iodopenicillanate, antibiotic
resistance; HET: BIY CIT; 1.65A {Bacillus licheniformis}
PDB: 3b3x_A* 1i2s_A* 1i2w_A* 2blm_A 4blm_A 1mbl_A
Length = 265
Score = 28.3 bits (62), Expect = 1.2
Identities = 17/162 (10%), Positives = 42/162 (25%), Gaps = 21/162 (12%)
Query: 8 GNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQTFMNL 67
G + + +R + + L+ ++ + +
Sbjct: 116 GPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDK-LPSE 174
Query: 68 SGQSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSISEKCGKNYK 127
+ L++ M + + + + KTG G G
Sbjct: 175 KRELLIDWMKRNTTGDALIRAGVPEG-----WEVADKTGAGSYGTRND------------ 217
Query: 128 RLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLPIIDNIARSL 169
I I PP ++ VL + + + +I + +
Sbjct: 218 ---IAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVV 256
>1w7f_A Beta-lactamase; hydrolase, isocitrate, bacillus licheniformis
hydrolase; HET: ICT; 1.80A {Bacillus licheniformis}
Length = 307
Score = 27.9 bits (61), Expect = 1.5
Identities = 19/164 (11%), Positives = 44/164 (26%), Gaps = 22/164 (13%)
Query: 7 LGNPGHEYCE-NRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQTFM 65
+G P E + +R + + L+ ++ +
Sbjct: 156 IGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDK-LP 214
Query: 66 NLSGQSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSISEKCGKN 125
+ + L++ M + + + + KTG G G
Sbjct: 215 SEKRELLIDWMKRNTTGDALIRAGVPEG-----WEVADKTGAGSYGTRND---------- 259
Query: 126 YKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLPIIDNIARSL 169
I I PP ++ VL + + + +I + +
Sbjct: 260 -----IAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVV 298
>1bue_A Protein (imipenem-hydrolysing beta-lactamase); hydrolase,
antibiotic resistance, class A carbapenemase; 1.64A
{Enterobacter cloacae} SCOP: e.3.1.1 PDB: 1bul_A* 1dy6_A
Length = 265
Score = 27.5 bits (60), Expect = 1.9
Identities = 14/111 (12%), Positives = 25/111 (22%), Gaps = 21/111 (18%)
Query: 58 LIKPQTFMNLSGQSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKTG-GGDAGHNGLK 116
L ++ + + D + KTG G G
Sbjct: 168 LALGNILSEHEKETYQTWLKGNTTGAARIRASVPSD-----WVVGDKTGSCGAYGTAND- 221
Query: 117 SISEKCGKNYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLPIIDNIAR 167
+ P + A +I V + E +I +R
Sbjct: 222 --------------YAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASR 258
>1vlr_A MRNA decapping enzyme; 16740816, structural genomics, JCSG, protein
structure initiative, PSI, joint center for structural
genomics; 1.83A {Mus musculus} SCOP: d.13.1.3 d.246.1.1
PDB: 1xmm_B* 1xml_B 1st0_B* 1st4_B*
Length = 350
Score = 27.5 bits (61), Expect = 2.2
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 114 GLKSISEKCGKNYKRLRIGIGRPPDTAHIIRHVLG-NFSSP----ERYFLLP-IIDNI 165
G ++I ++ RLR+ + P H+ H F +P ER LL +I+N+
Sbjct: 259 GQEAILKRYQVTGDRLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAQVIENL 316
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.325 0.144 0.445
Gapped
Lambda K H
0.267 0.0460 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,741,554
Number of extensions: 80621
Number of successful extensions: 262
Number of sequences better than 10.0: 1
Number of HSP's gapped: 255
Number of HSP's successfully gapped: 21
Length of query: 189
Length of database: 5,693,230
Length adjustment: 87
Effective length of query: 102
Effective length of database: 3,584,002
Effective search space: 365568204
Effective search space used: 365568204
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 (25.2 bits)