RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780440|ref|YP_003064853.1| transcription elongation factor GreA [Candidatus Liberibacter asiaticus str. psy62] (158 letters) >1grj_A GREA protein; transcript elongation factor, transcript cleavage factor, transcription regulation; 2.20A {Escherichia coli} SCOP: a.2.1.1 d.26.1.2 Length = 158 Score = 145 bits (366), Expect = 6e-36 Identities = 71/157 (45%), Positives = 113/157 (71%), Gaps = 1/157 (0%) Query: 3 DKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGR 62 IP+T +G +K+++EL + + RP II AI+EAR +GDL ENAEY AA+E Q EGR Sbjct: 2 QAIPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGR 61 Query: 63 MAELENIITRAEVIDISTMSGD-RIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVS 121 + ++E ++ A+VID++ M + R+ FGATV+++ +S +++ Y+IVGD EAD + L+S Sbjct: 62 IKDIEAKLSNAQVIDVTKMPNNGRVIFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLIS 121 Query: 122 ISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI 158 ++SPIAR LIGKE D++ + PGGE +E+++V ++ Sbjct: 122 VNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKVEYL 158 >2f23_A Anti-cleavage anti-GREA transcription factor GFH1; anti-GREA GFH1 thermus thermophilus; 1.60A {Thermus thermophilus HB27} SCOP: a.2.1.1 d.26.1.2 PDB: 2eul_A 2etn_A Length = 156 Score = 127 bits (321), Expect = 9e-31 Identities = 43/157 (27%), Positives = 90/157 (57%), Gaps = 5/157 (3%) Query: 1 MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNE 60 M ++ +T G++++ Q+L R++E K + E D +++ +AAK+ + E Sbjct: 1 MAREVKLTKAGYERLMQQLE-RERERLQEATKILQELMESSDDYDDSGLEAAKQEKARIE 59 Query: 61 GRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADV--QSG 118 R+ LE+I++R + + SG+ I G+ V L + SG++ + Q+V EA+V Sbjct: 60 ARIDSLEDILSR--AVILEEGSGEVIGLGSVVELEDPLSGERLSVQVVSPAEANVLDTPM 117 Query: 119 LVSISSPIARALIGKELGDIISVNAPGGEKTYEILQV 155 +S +SP+ +AL+G +GD++S++ P G++ + ++ + Sbjct: 118 KISDASPMGKALLGHRVGDVLSLDTPKGKREFRVVAI 154 >2p4v_A Transcription elongation factor GREB; transcript cleavage, GRE-factors, RNA polymerase; 2.60A {Escherichia coli} Length = 158 Score = 124 bits (312), Expect = 8e-30 Identities = 53/155 (34%), Positives = 90/155 (58%), Gaps = 1/155 (0%) Query: 4 KIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRM 63 VT +G++K++QEL + +EERP + K ++ A + GD SENA+YQ K+ + R+ Sbjct: 3 TPLVTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRV 62 Query: 64 AELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSIS 123 L + +++D S ++ FGA V +E + G ++IVG E + +SI Sbjct: 63 RYLTKCMENLKIVDYSPQQEGKVFFGAWV-EIENDDGVTHRFRIVGYDEIFGRKDYISID 121 Query: 124 SPIARALIGKELGDIISVNAPGGEKTYEILQVLWI 158 SP+ARAL+ KE+GD+ VN P GE ++ + + ++ Sbjct: 122 SPMARALLKKEVGDLAVVNTPAGEASWYVNAIEYV 156 >2pn0_A Prokaryotic transcription elongation factor GREA/GREB; structural genomics, APC6349, PSI-2, protein structure initiative; HET: MSE; 1.70A {Nitrosomonas europaea} Length = 141 Score = 113 bits (284), Expect = 2e-26 Identities = 32/134 (23%), Positives = 57/134 (42%), Gaps = 9/134 (6%) Query: 25 EERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGD 84 +P+I+ + +A L E A +LE + RAEV+D + Sbjct: 4 SIKPKIMISSLDAERLEILLETLSQNAFPGRD--------DLEAELARAEVVDPEEIPPT 55 Query: 85 RIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAP 144 + +TV ++S ++ +V ++ D +SI +P+ AL+G GD I P Sbjct: 56 VVTMNSTVRFRVESSAEEFCLTLVYPKDVDTSGEKISILAPVGSALLGLAQGDEIEWPKP 115 Query: 145 -GGEKTYEILQVLW 157 GG I++V + Sbjct: 116 GGGVLRVRIVEVTY 129 >3bmb_A Regulator of nucleoside diphosphate kinase; RNA polymerase, elongation factor, anti-GRE factor, RNA binding protein; 1.91A {Escherichia coli} Length = 136 Score = 111 bits (280), Expect = 5e-26 Identities = 29/133 (21%), Positives = 51/133 (38%), Gaps = 9/133 (6%) Query: 26 ERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDR 85 RP II +A L E Y L + RA++ M D Sbjct: 2 SRPTIIINDLDAERIDILLEQPAYAGLPIAD--------ALNAELDRAQMCSPEEMPHDV 53 Query: 86 IAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPG 145 + + V + G+ + +V + + +S+ +P+ AL+G +GD I PG Sbjct: 54 VTMNSRVKFRNLSDGEVRVRTLVYPAKMTDSNTQLSVMAPVGAALLGLRVGDSIHWELPG 113 Query: 146 G-EKTYEILQVLW 157 G E+L++ + Sbjct: 114 GVATHLEVLELEY 126 >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 = 37.2 bits (86), Expect = 0.002 Identities = 27/137 (19%), Positives = 44/137 (32%), Gaps = 38/137 (27%) Query: 24 QEERPRIIKAISEARAYGD-----LSENAEYQAAKE----L------QNLNEGRMAELEN 68 + +IK AR S +A ++A E L Q + EL Sbjct: 116 LVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEEL-- 173 Query: 69 IITRAEVIDI-STMSGDRIAFGATV--SLVEKNSGDKKNYQIVGDQEADVQSGLVS---- 121 ++ + GD I F A L+ +K + Q ++ L + Sbjct: 174 ----RDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFT----QGLNILEWLENPSNT 225 Query: 122 ------ISSPIARALIG 132 +S PI+ LIG Sbjct: 226 PDKDYLLSIPISCPLIG 242 Score = 26.4 bits (58), Expect = 3.3 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 10/52 (19%) Query: 45 ENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVE 96 EN +Y AA +L+ L+ + + N I + + IDI I ++SL E Sbjct: 1849 ENQQYVAAGDLRALDT--VTNVLNFI-KLQKIDI-------IELQKSLSLEE 1890 >3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190 Score = 33.0 bits (74), Expect = 0.034 Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 14/66 (21%) Query: 13 DKIQQE----LRWRQQEERPRI--IKAISEA-------RAYGDLSENAEYQAAKELQNLN 59 D++ QE +WR+ E+R R+ + A S+ +A DL E + Q+ + +N Sbjct: 78 DRLTQEPESIRKWRE-EQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKI 136 Query: 60 EGRMAE 65 R+A+ Sbjct: 137 NNRIAD 142 Score = 27.6 bits (60), Expect = 1.4 Identities = 25/114 (21%), Positives = 44/114 (38%), Gaps = 39/114 (34%) Query: 3 DKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGR 62 D++ + K ++E R R QE + A S+ + + +A K+L+ N+ + Sbjct: 78 DRLTQEPESIRKWREEQRKRLQE-----LDAASKV-----MEQEWREKAKKDLEEWNQRQ 127 Query: 63 MAELE-NIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADV 115 ++E N I +RIA DK YQ +AD+ Sbjct: 128 SEQVEKNKIN------------NRIA-------------DKAFYQ---QPDADI 153 >1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154 Score = 31.9 bits (71), Expect = 0.066 Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 1/28 (3%) Query: 10 KGFDKIQQELRWRQQEERPRI-IKAISE 36 + K+Q L+ + P + IKA E Sbjct: 20 QALKKLQASLKLYADDSAPALAIKATME 47 Score = 31.9 bits (71), Expect = 0.072 Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 16/45 (35%) Query: 48 EYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATV 92 E QA K+LQ A L+ A+ D S +A AT+ Sbjct: 18 EKQALKKLQ-------ASLK---LYAD--D----SAPALAIKATM 46 >3n6r_A Propionyl-COA carboxylase, alpha subunit; protein complex, biotin-dependent carboxylase, ligase; HET: BTI; 3.20A {Ruegeria pomeroyi} Length = 681 Score = 31.1 bits (70), Expect = 0.11 Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 17/67 (25%) Query: 28 PRIIKAISEARA------YGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTM 81 +++ AI A YG LSEN+++ A+ L+ + + I+ Sbjct: 64 DKVMAAIRATGAQAVHPGYGFLSENSKF--AEALEA------EGVIFVGPPKGAIE---A 112 Query: 82 SGDRIAF 88 GD+I Sbjct: 113 MGDKITS 119 >3hbl_A Pyruvate carboxylase; TIM barrel, ligase; HET: BTI ADP; 2.71A {Staphylococcus aureus subsp} PDB: 3bg5_A* 3ho8_A* 3hb9_A* Length = 1150 Score = 28.8 bits (64), Expect = 0.57 Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 17/67 (25%) Query: 28 PRIIKAISEARA------YGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTM 81 RII +A YG LSEN ++ A+ ++ I E +D M Sbjct: 67 ERIIDVAKQANVDAIHPGYGFLSENEQF--ARRCAE------EGIKFIGPHLEHLD---M 115 Query: 82 SGDRIAF 88 GD++ Sbjct: 116 FGDKVKA 122 >3jrx_A Acetyl-COA carboxylase 2; BC domain, soraphen A, alternative splicing, ATP-binding, biotin, fatty acid biosynthesis, ligase, lipid synthesis; HET: S1A; 2.50A {Homo sapiens} PDB: 3jrw_A* Length = 587 Score = 28.1 bits (62), Expect = 0.91 Identities = 11/67 (16%), Positives = 20/67 (29%), Gaps = 17/67 (25%) Query: 28 PRIIKAISEARA------YGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTM 81 I+ +G SEN + + L + + +E + Sbjct: 129 ELIVDIAKRIPVQAVWAGWGHASENPKL--PELLCK------NGVAFLGPPSEAMW---A 177 Query: 82 SGDRIAF 88 GD+IA Sbjct: 178 LGDKIAS 184 >2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A Length = 220 Score = 28.1 bits (62), Expect = 0.98 Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 5/39 (12%) Query: 46 NAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGD 84 +A +EL L +++ R E IDIS + G Sbjct: 3 GLRKEALEELMKL-----LNMKDFPYRIEGIDISHLQGK 36 >1wle_A Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bos taurus} Length = 501 Score = 28.2 bits (62), Expect = 0.99 Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 5/73 (6%) Query: 2 VDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEG 61 + I T + ++++++R +EE+ + +A+ D N++ Q + Q+L Sbjct: 69 LPGIISTWQELRQLREQIR-SLEEEKEAVTEAVRALVVNQD---NSQVQQDPQYQSLRA- 123 Query: 62 RMAELENIITRAE 74 R E+ +T Sbjct: 124 RGREIRKQLTLLY 136 >2qf7_A Pyruvate carboxylase protein; multi-domain, multi-functional, biotin-dependent, ligase; HET: KCX COA SAP; 2.00A {Rhizobium etli cfn 42} Length = 1165 Score = 27.8 bits (61), Expect = 1.2 Identities = 13/67 (19%), Positives = 25/67 (37%), Gaps = 17/67 (25%) Query: 28 PRIIKAISEARA------YGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTM 81 +I+ + A YG LSE+ E+ A + I +A+ + Sbjct: 83 DEVIRVAKLSGADAIHPGYGLLSESPEFVDACNKAGIIF--------IGPKADTMR---Q 131 Query: 82 SGDRIAF 88 G+++A Sbjct: 132 LGNKVAA 138 >1w96_A ACC, acetyl-coenzyme A carboxylase; ligase, obesity, diabetes, fatty acid metabolism, structure-based drug design; HET: S1A; 1.8A {Saccharomyces cerevisiae} SCOP: b.84.2.1 c.30.1.1 d.142.1.2 PDB: 1w93_A Length = 554 Score = 26.7 bits (58), Expect = 2.6 Identities = 6/38 (15%), Positives = 8/38 (21%), Gaps = 6/38 (15%) Query: 28 PRIIKAISEARA------YGDLSENAEYQAAKELQNLN 59 I+ A +G SEN Sbjct: 120 DLIVDIAERADVDAVWAGWGHASENPLLPEKLSQSKRK 157 >3krb_A Aldose reductase; ssgcid, SBRI, emerald biostructures, university of washington, NIH, niaid, oxidoreductase, structural genomics; HET: NAP; 1.75A {Giardia lamblia atcc 50803} Length = 334 Score = 25.7 bits (55), Expect = 4.6 Identities = 12/60 (20%), Positives = 23/60 (38%), Gaps = 4/60 (6%) Query: 10 KGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENI 69 KG L W ++ + I +++ + N E+Q L++ M + NI Sbjct: 258 KGTSPHCVALAWHVKKWNTSMYSVIPKSQTPARIEANF---KCTEVQ-LSDDDMDAINNI 313 >3ir3_A HTD2, 3-hydroxyacyl-thioester dehydratase 2; structural genomics, structural genomics consortium, SGC, lyase; 1.99A {Homo sapiens} Length = 148 Score = 25.9 bits (56), Expect = 4.9 Identities = 9/30 (30%), Positives = 15/30 (50%) Query: 56 QNLNEGRMAELENIITRAEVIDISTMSGDR 85 ++ G AEL T+ +V S ++GD Sbjct: 14 MHIKVGDRAELRRAFTQTDVATFSELTGDV 43 >1omo_A Alanine dehydrogenase; two-domain, beta-sandwich-dimer, rossmann-fold NAD domain, human MU crystallin homolog; HET: NAD; 2.32A {Archaeoglobus fulgidus} SCOP: c.2.1.13 PDB: 1vll_A Length = 322 Score = 25.2 bits (54), Expect = 7.9 Identities = 21/129 (16%), Positives = 45/129 (34%), Gaps = 18/129 (13%) Query: 42 DLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMS------GDRIAFGATVSLV 95 D+ E A + ++ + +R +V+ +T S + + G ++ + Sbjct: 157 DVREKAAKKFVSYCEDRGISASVQPAEEASRCDVLVTTTPSRKPVVKAEWVEEGTHINAI 216 Query: 96 EKNSGD---------KKNYQIVGDQEADVQSGLVSI---SSPIARALIGKELGDIISVNA 143 + KK +V D E G +++ I + +G++I+ Sbjct: 217 GADGPGKQELDVEILKKAKIVVDDLEQAKHGGEINVAVSKGVIGVEDVHATIGEVIAGLK 276 Query: 144 PGGEKTYEI 152 G E EI Sbjct: 277 DGRESDEEI 285 >3glk_A Acetyl-COA carboxylase 2; ATP binding, alternative splicing, ATP-binding, biotin, fatty acid biosynthesis, ligase, lipid synthesis, manganese; 2.10A {Homo sapiens} PDB: 3gid_A 2hjw_A Length = 540 Score = 24.8 bits (53), Expect = 8.5 Identities = 5/27 (18%), Positives = 8/27 (29%), Gaps = 6/27 (22%) Query: 28 PRIIKAISEARA------YGDLSENAE 48 I+ +G SEN + Sbjct: 113 ELIVDIAKRIPVQAVWAGWGHASENPK 139 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 0.312 0.131 0.354 Gapped Lambda K H 0.267 0.0584 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,292,198 Number of extensions: 55012 Number of successful extensions: 173 Number of sequences better than 10.0: 1 Number of HSP's gapped: 165 Number of HSP's successfully gapped: 32 Length of query: 158 Length of database: 5,693,230 Length adjustment: 85 Effective length of query: 73 Effective length of database: 3,632,490 Effective search space: 265171770 Effective search space used: 265171770 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 53 (24.5 bits)