RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

Searching..................................................done

Query= gi|254781067|ref|YP_003065480.1| elongation factor P
[Candidatus Liberibacter asiaticus str. psy62]
         (189 letters)



>3a5z_B EF-P, elongation factor P; aminoacyl-tRNA synthetase paralog,
           translation, tRNA, lysyl- synthetase, structural
           genomics, NPPSFA; HET: KAA; 2.50A {Escherichia coli}
          Length = 191

 Score =  196 bits (501), Expect = 2e-51
 Identities = 63/188 (33%), Positives = 97/188 (51%)

Query: 1   MVKVIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTE 60
           M    ++  R G  + +DG+ Y V  ++   PGKG    +V++RR+  G +V   +++T+
Sbjct: 4   MATYYSNDFRAGLKIMLDGEPYAVEASEFVKPGKGQAFARVKLRRLLTGTRVEKTFKSTD 63

Query: 61  QVERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEG 120
             E A V D    +LY D E +HFMN ET++Q++   + IGD   +  +  E  + +  G
Sbjct: 64  SAEGADVVDMNLTYLYNDGEFWHFMNNETFEQLSADAKAIGDNAKWLLDQAECIVTLWNG 123

Query: 121 VALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTED 180
             +SV  P  V   ++DT+P  KG T     KPA LS      VP  + IG+ I + T  
Sbjct: 124 QPISVTPPNFVELEIVDTDPGLKGDTAGTGGKPATLSTGAVVKVPLFVQIGEVIKVDTRS 183

Query: 181 NSYVERVK 188
             YV RVK
Sbjct: 184 GEYVSRVK 191


>1yby_A Translation elongation factor P; conserved hypothetical protein,
           structural genomics, PSI, protein structure initiative;
           1.95A {Clostridium thermocellum}
          Length = 215

 Score =  163 bits (415), Expect = 1e-41
 Identities = 60/187 (32%), Positives = 103/187 (55%)

Query: 1   MVKVIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTE 60
            + + A   + G   ++DG+++ V+  ++  PGKG    + +++ I  G  +   +  T+
Sbjct: 29  GLMISAGDFKNGVTFELDGQIFQVIEFQHVKPGKGAAFVRTKLKNIVTGATIEKTFNPTD 88

Query: 61  QVERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEG 120
           ++ +A +E +  Q+LY D + ++FM+ ET++Q+ + ++ IGD   + +E   VK+L H+G
Sbjct: 89  KMPKAHIERKDMQYLYNDGDLYYFMDTETFEQLPLGKDKIGDALKFVKENEIVKVLSHKG 148

Query: 121 VALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTED 180
               +E P  V   V DTEP  KG T T + KPAI+       VP  +N GD I I T  
Sbjct: 149 NVFGIEPPNFVELEVTDTEPGFKGDTATGATKPAIVETGASIKVPLFVNKGDIIRIDTRT 208

Query: 181 NSYVERV 187
             Y+ERV
Sbjct: 209 GEYMERV 215


>1ueb_A EF-P, TT0860, elongation factor P; beta barrel, riken structural
           genomics/proteomics initiative, RSGI, structural
           genomics; 1.65A {Thermus thermophilus} SCOP: b.34.5.2
           b.40.4.5 b.40.4.5 PDB: 3huw_V 3huy_V
          Length = 184

 Score =  150 bits (379), Expect = 2e-37
 Identities = 52/181 (28%), Positives = 87/181 (48%), Gaps = 1/181 (0%)

Query: 6   ASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVERA 65
            + +R G  + +DG L+  +  ++   G+G      + + +  G  V   + + E++E  
Sbjct: 4   VTDLRPGTKVKMDGGLWECVEYQHQKLGRGGAKVVAKFKNLETGATVERTFNSGEKLEDI 63

Query: 66  FVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSV 125
           +VE +  Q+LY + E   FM+ ETY+Q  V    +   + +F+EGM     ++EG  + V
Sbjct: 64  YVETRELQYLYPEGEEMVFMDLETYEQFAVPRSRVVGAE-FFKEGMTALGDMYEGQPIKV 122

Query: 126 EVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVE 185
             P  V   V+DT P  +G TV+   KPA L       VP  +  G+ I + T    YV 
Sbjct: 123 TPPTVVELKVVDTPPGVRGDTVSGGSKPATLETGAVVQVPLFVEPGEVIKVDTRTGEYVG 182

Query: 186 R 186
           R
Sbjct: 183 R 183


>1iz6_A Initiation factor 5A; SH3-like barrel, OB fold, biosynthetic
           protein; 2.00A {Pyrococcus horikoshii OT3} SCOP:
           b.34.5.2 b.40.4.5
          Length = 138

 Score = 98.1 bits (244), Expect = 1e-21
 Identities = 27/123 (21%), Positives = 52/123 (42%), Gaps = 3/123 (2%)

Query: 1   MVKVIASAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTT 59
             KV  S ++ G  + +D +   ++      PGK G+   ++E   I DG   S    T+
Sbjct: 4   KTKVQVSKLKPGRYIIIDDEPCRIVNITVSSPGKHGSAKARIEAVGIFDGKVRSIVKPTS 63

Query: 60  EQVERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVS--EEVIGDQKVYFQEGMEVKLLI 117
            +V+   ++ +  Q +    +    M+ ETY+   V     V  + +   +EG+ V+   
Sbjct: 64  AEVDVPIIDKKTAQVIAITPDTVQIMDMETYETFEVPIDTGVADEIRDQLKEGINVEYWE 123

Query: 118 HEG 120
             G
Sbjct: 124 TLG 126


>1bkb_A Translation initiation factor 5A; 1.75A {Pyrobaculum aerophilum}
           SCOP: b.34.5.2 b.40.4.5
          Length = 136

 Score = 89.6 bits (222), Expect = 4e-19
 Identities = 24/117 (20%), Positives = 48/117 (41%), Gaps = 2/117 (1%)

Query: 6   ASAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTTEQVER 64
           A  +++G+ + +DG+   V+  +    GK G+   ++    + DG K +       QVE 
Sbjct: 11  AGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGKRTLSLPVDAQVEV 70

Query: 65  AFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQ-KVYFQEGMEVKLLIHEG 120
             +E    Q L    +    M+   Y  + V  + + ++ K     G EV++     
Sbjct: 71  PIIEKFTAQILSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPGAEVEVWQILD 127


>3er0_A Eukaryotic translation initiation factor 5A-2; yeast, low
           resolution, acetylation, hypusine, phosphoprotein,
           protein biosynthesis; 3.35A {Saccharomyces cerevisiae}
          Length = 167

 Score = 87.2 bits (216), Expect = 2e-18
 Identities = 27/116 (23%), Positives = 47/116 (40%), Gaps = 4/116 (3%)

Query: 6   ASAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTTEQVER 64
            SA+RK   + +  +   ++       GK G     +    I  G K+ +   +T  +E 
Sbjct: 33  CSALRKNGFVVIKSRPCKIVDMSTSKTGKHGHAKVHLVAIDIFTGKKLEDLSPSTHNMEV 92

Query: 65  AFVEDQRFQFLYQDQE--GFHFMNPETYDQVTVSEEVIGDQ-KVYFQEGMEVKLLI 117
             V+   +Q L  D        M+ +T D V   E  +GD  +  F EG ++ + I
Sbjct: 93  PVVKRNEYQLLDIDDGFLSLMNMDGDTKDDVKAPEGELGDSLQTAFDEGKDLMVTI 148


>2eif_A IF-5A, protein (eukaryotic translation initiation factor 5A);
           EIF-5A, OB-fold, structural genomics; 1.80A
           {Methanocaldococcus jannaschii DSM2661} SCOP: b.34.5.2
           b.40.4.5 PDB: 1eif_A
          Length = 136

 Score = 85.7 bits (212), Expect = 6e-18
 Identities = 25/120 (20%), Positives = 51/120 (42%), Gaps = 4/120 (3%)

Query: 2   VKVIASAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTTE 60
            +V   +++ G  + +DG    ++      PGK G    +V    I + VK      T+ 
Sbjct: 9   KQVNVGSLKVGQYVMIDGVPCEIVDISVSKPGKHGGAKARVVGIGIFEKVKKEFVAPTSS 68

Query: 61  QVERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEG 120
           +VE   ++ ++ Q L    +    M+ +TY+ + +    I +     + G EV+ +   G
Sbjct: 69  KVEVPIIDRRKGQVLAIMGDMVQIMDLQTYETLELP---IPEGIEGLEPGGEVEYIEAVG 125


>3hks_A EIF-5A-2, eukaryotic translation initiation factor 5A-2; beta
           barrel, alternative splicing, hypusine, protein
           biosynthesis; 2.30A {Arabidopsis thaliana}
          Length = 167

 Score = 80.8 bits (199), Expect = 2e-16
 Identities = 19/118 (16%), Positives = 44/118 (37%), Gaps = 6/118 (5%)

Query: 6   ASAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTTEQVER 64
           A  +RKG  + +  +   V+       GK G          I    K+ +   ++   + 
Sbjct: 31  AGNIRKGGHIVIKNRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTAKKLEDIVPSSHNCDV 90

Query: 65  AFVEDQRFQFLYQDQEGFH---FMNPETYDQVTVS--EEVIGDQKVYFQEGMEVKLLI 117
             V    +Q +   ++GF      +  T D + +   + +    ++ F EG ++ + +
Sbjct: 91  PHVNRVDYQLIDITEDGFVSLLTDSGGTKDDLKLPTDDGLTAQMRLGFDEGKDIVVSV 148


>3cpf_A Eukaryotic translation initiation factor 5A-1; structural genomics
           consortium, leukemia, apoptosis, SGC, acetylation,
           alternative splicing; 2.50A {Homo sapiens}
          Length = 138

 Score = 78.1 bits (192), Expect = 1e-15
 Identities = 17/116 (14%), Positives = 42/116 (36%), Gaps = 4/116 (3%)

Query: 6   ASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTP-ITQVEMRRISDGVKVSNRWRTTEQVER 64
            SA+RK   + + G+   ++       GK       +    I  G K  +   +T  ++ 
Sbjct: 9   CSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDICPSTHNMDV 68

Query: 65  AFVEDQRFQFLYQDQEGFHFMNPETY--DQVTVSEEVIGDQ-KVYFQEGMEVKLLI 117
             ++   FQ +         +       + + + E  +G + +  +  G E+ + +
Sbjct: 69  PNIKRNDFQLIGIQDGYLSLLQDSGEVREDLRLPEGDLGKEIEQKYDCGEEILITV 124


>1x6o_A Eukaryotic initiation factor 5A; SGPP, structural genomics, PSI,
           protein structure initiative; 1.60A {Leishmania
           braziliensis} SCOP: b.34.5.2 b.40.4.5 PDB: 1xtd_A
          Length = 174

 Score = 71.6 bits (175), Expect = 1e-13
 Identities = 23/126 (18%), Positives = 46/126 (36%), Gaps = 12/126 (9%)

Query: 6   ASAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTTEQVER 64
           A A++KG  + ++G+   V+       GK G     +    I  G ++ ++  +T  VE 
Sbjct: 33  AGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVSIVATDIFTGNRLEDQAPSTHNVEV 92

Query: 65  AFVEDQRFQFLYQDQEG-------FHFMNPETYDQVTVS----EEVIGDQKVYFQEGMEV 113
            FV+   +  L                M+ E   +  +       +    K  F  G +V
Sbjct: 93  PFVKTYTYSVLDIQANEDPSLPAHLSLMDDEGESREDLDMPPDPALATQIKEQFDSGKDV 152

Query: 114 KLLIHE 119
            +++  
Sbjct: 153 LVVVVS 158


>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 = 27.6 bits (61), Expect = 1.9
 Identities = 16/102 (15%), Positives = 29/102 (28%), Gaps = 28/102 (27%)

Query: 73  QFLYQDQEGF--HFMNPETYDQVT-VSEEVIGDQKVYFQEGMEVKLL----IHEGVALSV 125
           +FL     G+    + P    Q   V    + +    F    E   L    IH   AL+ 
Sbjct: 63  KFL-----GYVSSLVEPSKVGQFDQVLNLCLTE----F----ENCYLEGNDIH---ALAA 106

Query: 126 EVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPH 167
           ++ +       DT      + +       I++          
Sbjct: 107 KLLQE-----NDTTLVKTKELIKNYITARIMAKRPFDKKSNS 143


>2zci_A Phosphoenolpyruvate carboxykinase [GTP], phosphoenolpyruvate;
           GTP-dependent, signaling protein, lyase; 2.30A
           {Corynebacterium glutamicum}
          Length = 610

 Score = 26.8 bits (59), Expect = 3.5
 Identities = 14/61 (22%), Positives = 21/61 (34%), Gaps = 7/61 (11%)

Query: 122 ALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDN 181
            L +  P    + +    PS+ G+T  A   P I     +        +GDDI  L    
Sbjct: 253 ILKLINPEGKAYHIAAAFPSACGKTNLAMITPTIPGWTAQV-------VGDDIAWLKLRE 305

Query: 182 S 182
            
Sbjct: 306 D 306


>2izw_A Coat protein, ryegrass mottle virus coat protein; RNA, assembly,
           capsid protein; 2.90A {Ryegrass mottle virus}
          Length = 234

 Score = 26.1 bits (57), Expect = 5.2
 Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 3/41 (7%)

Query: 138 TEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILT 178
            +P+ +   V+A   PA +   I    P  +    DI    
Sbjct: 28  QQPTRQVTPVSA---PAAMGTQITYRGPQVVTQYGDITPAK 65


>3gfz_A Klebsiella pneumoniae BLRP1; TIM-barrel, EAL domain, BLUF domain,
           hydrolase, signaling protein; HET: C2E FMN; 2.05A
           {Klebsiella pneumoniae subsp} PDB: 3gfy_A* 3gfx_A*
           3gg0_A* 3gg1_A* 2kb2_A*
          Length = 413

 Score = 25.7 bits (56), Expect = 7.1
 Identities = 7/27 (25%), Positives = 9/27 (33%), Gaps = 3/27 (11%)

Query: 54  NRWRTTEQVERAF---VEDQRFQFLYQ 77
           +RW        A    +  Q  QF  Q
Sbjct: 156 SRWMMMPASGTAAPQHLPGQPCQFALQ 182


  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
   0.318    0.135    0.381 

Gapped
Lambda     K      H
   0.267   0.0563    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,617,102
Number of extensions: 72322
Number of successful extensions: 233
Number of sequences better than 10.0: 1
Number of HSP's gapped: 218
Number of HSP's successfully gapped: 17
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: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.0 bits)