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)