RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780440|ref|YP_003064853.1| transcription elongation factor GreA [Candidatus Liberibacter asiaticus str. psy62] (158 letters) >gnl|CDD|178936 PRK00226, greA, transcription elongation factor GreA; Reviewed. Length = 157 Score = 212 bits (542), Expect = 4e-56 Identities = 85/155 (54%), Positives = 117/155 (75%) Query: 1 MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNE 60 M+ KIP+T +G++K+++EL + ERP II+AI+EAR +GDLSENAEY AAKE Q E Sbjct: 1 MMKKIPMTQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIE 60 Query: 61 GRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLV 120 GR+ ELE+ ++ AEVID S +SG ++ FG+TV+L + ++ +++ YQIVG EAD + G + Sbjct: 61 GRIRELEDKLSNAEVIDPSKLSGGKVKFGSTVTLKDLDTDEEETYQIVGSDEADPKQGKI 120 Query: 121 SISSPIARALIGKELGDIISVNAPGGEKTYEILQV 155 SI SPIARALIGK++GD + V PGGE YEIL V Sbjct: 121 SIESPIARALIGKKVGDTVEVTTPGGEYEYEILSV 155 >gnl|CDD|130529 TIGR01462, greA, transcription elongation factor GreA. In the Chlamydias and some spirochetes, the region described by this model is found as the C-terminal region of a much larger protein. Length = 151 Score = 180 bits (458), Expect = 2e-46 Identities = 75/150 (50%), Positives = 114/150 (76%) Query: 6 PVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAE 65 P+T +G++K+++EL + + +RP I + I+EAR +GDLSENAEY AAKE Q NEGR+AE Sbjct: 1 PLTQEGYEKLKEELEYLKTVKRPEISEEIAEAREHGDLSENAEYHAAKEEQGFNEGRIAE 60 Query: 66 LENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSP 125 LE+++ A+VID S +S D + FG+TV++ + ++G+++ Y IVG EAD + G +SI SP Sbjct: 61 LEDLLANAQVIDDSKLSTDVVGFGSTVTIKDLDTGEEETYTIVGSWEADPKEGKISIDSP 120 Query: 126 IARALIGKELGDIISVNAPGGEKTYEILQV 155 + +ALIGK++GD++ V P GEK YEIL++ Sbjct: 121 LGKALIGKKVGDVVEVQTPKGEKEYEILKI 150 >gnl|CDD|179345 PRK01885, greB, transcription elongation factor GreB; Reviewed. Length = 157 Score = 124 bits (313), Expect = 1e-29 Identities = 56/151 (37%), Positives = 92/151 (60%), Gaps = 5/151 (3%) Query: 7 VTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNE--GRMA 64 +T +G+ +++QEL + +EERP + + +S A + GD SENA+Y K+ L E R+ Sbjct: 7 ITREGYARLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKR--LREIDRRVR 64 Query: 65 ELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISS 124 L + +V+D S ++ FGA V + E G++K ++IVG E D + G +SI S Sbjct: 65 FLTKRLENLKVVDYSPQQEGKVFFGAWVEI-ENEDGEEKRFRIVGPDEIDGRKGYISIDS 123 Query: 125 PIARALIGKELGDIISVNAPGGEKTYEILQV 155 P+ARAL+ KE+GD ++VN P GE + + ++ Sbjct: 124 PMARALLKKEVGDEVTVNTPAGEAEWYVNEI 154 >gnl|CDD|130528 TIGR01461, greB, transcription elongation factor GreB. The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreB differs functionally in that it releases larger oligonucleotides. This model describes proteobacterial GreB. Length = 156 Score = 109 bits (273), Expect = 4e-25 Identities = 54/152 (35%), Positives = 91/152 (59%), Gaps = 1/152 (0%) Query: 7 VTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAEL 66 +T +G++K++QEL + +EERP + + ++ A + GD SENA+YQ K+ + R+ L Sbjct: 5 ITPEGYEKLKQELNYLWREERPEVTQKVTWAASLGDRSENADYQYGKKRLREIDRRVRFL 64 Query: 67 ENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPI 126 + +V+D S ++ FGA V L E + G ++IVG E D + +SI SP+ Sbjct: 65 TKRLENLKVVDYSPQQEGKVFFGAWVEL-ENDDGVTHRFRIVGYDEIDGRKNYISIDSPL 123 Query: 127 ARALIGKELGDIISVNAPGGEKTYEILQVLWI 158 ARAL+ KE+GD + VN P GE ++ + + ++ Sbjct: 124 ARALLKKEVGDEVVVNTPAGEASWYVNAIEYV 155 >gnl|CDD|184804 PRK14720, PRK14720, transcript cleavage factor/unknown domain fusion protein; Provisional. Length = 906 Score = 102 bits (255), Expect = 6e-23 Identities = 51/149 (34%), Positives = 89/149 (59%) Query: 7 VTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAEL 66 VT + +K ++EL + E P K I EA+ GDL ENAEY+AAKE Q + + L Sbjct: 752 VTRRALNKKKKELEHLKDVEMPENSKDIGEAQELGDLRENAEYKAAKEKQQQLQAALKRL 811 Query: 67 ENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPI 126 E I A+++D++ + ++ FG V L +++G++++Y I+G E+D + G++S SP+ Sbjct: 812 EAEIDSAKILDLTDVKTSKVGFGTKVKLKNEDTGEEESYSILGPWESDPEEGIISYQSPL 871 Query: 127 ARALIGKELGDIISVNAPGGEKTYEILQV 155 ++L+GK+ GD + E Y +L++ Sbjct: 872 GKSLLGKKEGDSLEFVINDTETRYTVLKI 900 >gnl|CDD|180531 PRK06330, PRK06330, transcript cleavage factor/unknown domain fusion protein; Validated. Length = 718 Score = 75.6 bits (186), Expect = 5e-15 Identities = 49/148 (33%), Positives = 83/148 (56%), Gaps = 5/148 (3%) Query: 8 TSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELE 67 TS+ F +++ +L+ +E K I +ARA GDL EN+EY+ A E + + + L Sbjct: 570 TSESFTRMKNKLQSLVGKEMVENAKEIEDARALGDLRENSEYKFALEKRARLQEEIRVLS 629 Query: 68 NIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIA 127 I RA ++ + D++ G V L E + GDK Y I+G +AD + ++S+ S +A Sbjct: 630 EEINRARILTKDDVFTDKVGVGCKVVL-EDDQGDKVCYTILGPWDADPDNKILSLKSKLA 688 Query: 128 RALIGKELGDIISVNAPGGEKTYEILQV 155 + ++GK++GD SV G K Y+I ++ Sbjct: 689 QEMLGKKVGD--SVQFQG--KKYKISRI 712 >gnl|CDD|180535 PRK06342, PRK06342, transcription elongation factor regulatory protein; Validated. Length = 160 Score = 65.1 bits (159), Expect = 8e-12 Identities = 41/118 (34%), Positives = 69/118 (58%), Gaps = 15/118 (12%) Query: 47 AEYQAAKELQNLNEGRMAE---------LENIITRAEVIDISTMSGDRIAFGATVSLVEK 97 A Y+AA+ ++++NE R L A+++ S D +AFG+TV+ + Sbjct: 48 AAYEAAQAIEDVNERRRQMARPLRDLRYLAARRRTAQLMPDPA-STDVVAFGSTVTF-SR 105 Query: 98 NSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQV 155 + G + Y+IVG+ EAD ++G +S SP+ARAL+GK +GD++SV G + EI+ + Sbjct: 106 DDGRVQTYRIVGEDEADPKAGSISYVSPVARALMGKAVGDVVSV----GGQELEIIAI 159 >gnl|CDD|180236 PRK05753, PRK05753, nucleoside diphosphate kinase regulator; Provisional. Length = 137 Score = 49.9 bits (120), Expect = 3e-07 Identities = 39/134 (29%), Positives = 66/134 (49%), Gaps = 15/134 (11%) Query: 27 RPRIIKAISE---ARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSG 83 +P II I+E R L E + + LN AEL RA+V+ + M Sbjct: 4 KPTII--INELDAERLDR-LLEQPAFAGPPIAEALN----AEL----DRAQVVPPAEMPA 52 Query: 84 DRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNA 143 D + + V + +SG+++ +V +AD G +S+ +P+ AL+G +G I Sbjct: 53 DVVTMNSRVRFRDLSSGEERVRTLVYPADADDSEGQLSVLAPVGAALLGLSVGQSIDWPL 112 Query: 144 PGGEKTY-EILQVL 156 PGG++T+ E+L+V Sbjct: 113 PGGKETHLEVLEVE 126 >gnl|CDD|180307 PRK05892, PRK05892, nucleoside diphosphate kinase regulator; Provisional. Length = 158 Score = 44.0 bits (104), Expect = 2e-05 Identities = 36/147 (24%), Positives = 68/147 (46%), Gaps = 10/147 (6%) Query: 13 DKIQQELRWRQQEERPRIIKAISEARAYGDLSENAE-YQAAKELQNLNEGRMAELENIIT 71 D ++ EL R + R R+ +++ GD + AE Q A EL L++ R+ EL+ + Sbjct: 14 DHLEAELA-RLRARRDRLAVEVNDRGMIGDHGDQAEAIQRADELARLDD-RINELDRRLR 71 Query: 72 RAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVG-DQEADV--QSGLVSISSPIAR 128 + + G V+L G+ + ++ +E V ++ ++ SP+ + Sbjct: 72 TGP---TPWSGSETLPGGTEVTL-RFPDGEVETMHVISVVEETPVGREAETLTADSPLGQ 127 Query: 129 ALIGKELGDIISVNAPGGEKTYEILQV 155 AL G + GD ++ + P G E+L V Sbjct: 128 ALAGHQAGDTVTYSTPQGPAQVELLAV 154 >gnl|CDD|179046 PRK00488, pheS, phenylalanyl-tRNA synthetase subunit alpha; Validated. Length = 339 Score = 30.1 bits (69), Expect = 0.27 Identities = 20/70 (28%), Positives = 27/70 (38%), Gaps = 19/70 (27%) Query: 25 EERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELE----NIITRAEVIDIST 80 EER I+E + ++ E R ELE N AE ID+ T Sbjct: 52 EERKEAGALINELKQ--------------AIEAALEERKEELEAAALNARLAAETIDV-T 96 Query: 81 MSGDRIAFGA 90 + G RI G+ Sbjct: 97 LPGRRIELGS 106 >gnl|CDD|179065 PRK00558, uvrC, excinuclease ABC subunit C; Validated. Length = 598 Score = 29.7 bits (68), Expect = 0.31 Identities = 21/72 (29%), Positives = 29/72 (40%), Gaps = 16/72 (22%) Query: 45 ENAEYQAAKEL--QNLNEGRMAE------LENIITRAEVIDISTMSGDRIAFGATV-SLV 95 +NA ++L Q+ + + E L R E DIS + G ATV S+V Sbjct: 350 KNAREALERKLSDQSTQQQALEELAELLGLPEPPYRIECFDISHIQGT-----ATVASMV 404 Query: 96 --EKNSGDKKNY 105 E DK Y Sbjct: 405 VFEDGGPDKSEY 416 >gnl|CDD|165508 PHA03249, PHA03249, DNA packaging tegument protein UL25; Provisional. Length = 653 Score = 27.7 bits (61), Expect = 1.2 Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 16/94 (17%) Query: 6 PVTSKGFD----KIQQELRWRQQEERPRIIKAISEARAYGDL-------SENAEYQAAKE 54 VT + ++ +ELR R E P + + R Y L + A Y + Sbjct: 326 AVTDGQYQACLRRLDEELRKRGTTESPSLTEVYETLRDYNVLFPIAHYTNRGALYLYRQN 385 Query: 55 LQNLNEG-----RMAELENIITRAEVIDISTMSG 83 LQ LN G ++ E + + D++ + G Sbjct: 386 LQKLNNGHRGVLKLLSSEKLNEEHTLNDLAFLVG 419 >gnl|CDD|169417 PRK08384, PRK08384, thiamine biosynthesis protein ThiI; Provisional. Length = 381 Score = 26.5 bits (58), Expect = 3.4 Identities = 14/37 (37%), Positives = 22/37 (59%) Query: 121 SISSPIARALIGKELGDIISVNAPGGEKTYEILQVLW 157 I SP+A L+ K ++I V+ GEKT E ++ +W Sbjct: 190 GIDSPVAAFLMMKRGVEVIPVHIYMGEKTLEKVRKIW 226 >gnl|CDD|182393 PRK10343, PRK10343, RNA-binding protein YhbY; Provisional. Length = 97 Score = 25.8 bits (56), Expect = 5.3 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%) Query: 58 LNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVG 109 L EG +AE+E + E+I + + DR V + + +G N Q++G Sbjct: 29 LTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETG-ACNVQVIG 79 >gnl|CDD|162465 TIGR01652, ATPase-Plipid, phospholipid-translocating P-type ATPase, flippase. This model describes the P-type ATPase responsible for transporting phospholipids from one leaflet of bilayer membranes to the other. These ATPases are found only in eukaryotes. Length = 1057 Score = 25.8 bits (57), Expect = 5.5 Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 5/63 (7%) Query: 95 VEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDI-ISVNAPGGEKTYEIL 153 + ++ YQ EA LV + + + I + + G K YEIL Sbjct: 457 FNDDGPEEITYQAASPDEA----ALVKAARDVGFVFFERTPKSISLLIEMHGETKEYEIL 512 Query: 154 QVL 156 VL Sbjct: 513 NVL 515 >gnl|CDD|149497 pfam08459, UvrC_HhH_N, UvrC Helix-hairpin-helix N-terminal. This domain is found in the C subunits of the bacterial and archaeal UvrABC system which catalyses nucleotide excision repair in a multi-step process. UvrC catalyses the first incision on the fourth or fifth phosphodiester bond 3' and on the eighth phosphodiester bond 5' from the damage that is to be excised. The domain described here is found to the N-terminus of a helix hairpin helix (pfam00633) motif and also co-occurs with the pfam01541 catalytic domain which is found at the N-terminus of the same proteins. Length = 154 Score = 25.5 bits (57), Expect = 6.3 Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 8/44 (18%) Query: 65 ELENIITRAEVIDISTMSGDRIAFGATV-SLV--EKNSGDKKNY 105 L + R E DIS + G TV S+V E DK Y Sbjct: 6 GLPKLPHRIECFDISHIQGT-----DTVGSMVVFEDGKPDKSEY 44 >gnl|CDD|185296 PRK15398, PRK15398, aldehyde dehydrogenase EutE; Provisional. Length = 465 Score = 25.6 bits (57), Expect = 6.5 Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 5/47 (10%) Query: 16 QQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGR 62 QQ + + R RII AI EA L +AE A ++ GR Sbjct: 49 QQRYQQKSLAMRQRIIDAIREA-----LLPHAEELAELAVEETGMGR 90 >gnl|CDD|162462 TIGR01647, ATPase-IIIA_H, plasma-membrane proton-efflux P-type ATPase. This model describes the plasma membrane proton efflux P-type ATPase found in plants, fungi, protozoa, slime molds and archaea. The best studied representative is from yeast. Length = 755 Score = 25.4 bits (56), Expect = 7.1 Identities = 10/48 (20%), Positives = 20/48 (41%) Query: 61 GRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIV 108 G +A + + + E + T +G FG +LV+ + Q + Sbjct: 155 GDIAYSGSTVKQGEAEAVVTATGMNTFFGKAAALVQSTETGSGHLQKI 202 >gnl|CDD|162007 TIGR00713, hemL, glutamate-1-semialdehyde-2,1-aminomutase. This enzyme, glutamate-1-semialdehyde-2,1-aminomutase (glutamate-1-semialdehyde aminotransferase, GSA aminotransferase), contains a pyridoxal phosphate attached at a Lys residue at position 283 of the seed alignment. It is in the family of class III aminotransferases. Length = 423 Score = 25.4 bits (56), Expect = 7.6 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 20/73 (27%) Query: 28 PRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDI--------- 78 PR+++A+ EA G Y A E + L +A+ II+R +++ Sbjct: 67 PRVVEAVKEALERGTS-----YGAPTEAEIL----LAKE--IISRVPSVEMVRFVNSGTE 115 Query: 79 STMSGDRIAFGAT 91 +TMS R+A G T Sbjct: 116 ATMSAVRLARGYT 128 >gnl|CDD|179965 PRK05218, PRK05218, heat shock protein 90; Provisional. Length = 613 Score = 25.1 bits (56), Expect = 8.3 Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 7/41 (17%) Query: 71 TRAEVID-ISTMSGDRIAFGATVSLVEKNSGD-KKNYQIVG 109 TR EVI+ + T IA T +EK GD KK+ Q++G Sbjct: 85 TREEVIENLGT-----IAKSGTKEFLEKLKGDQKKDSQLIG 120 >gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional. Length = 857 Score = 24.8 bits (54), Expect = 9.0 Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 11/62 (17%) Query: 26 ERPRIIKAISEARAYGDLSENAEYQAAK--ELQ------NLNEGR-MAELENIITRAEVI 76 E+ +I AI +AR GDL+ +E Q K EL+ EG+ M L N +T AE+ Sbjct: 480 EQAKI--AIEQARRVGDLARMSELQYGKIPELEKQLAAATQLEGKTMRLLRNKVTDAEIA 537 Query: 77 DI 78 ++ Sbjct: 538 EV 539 >gnl|CDD|179811 PRK04290, PRK04290, 30S ribosomal protein S6e; Validated. Length = 115 Score = 24.8 bits (55), Expect = 9.6 Identities = 10/26 (38%), Positives = 14/26 (53%) Query: 120 VSISSPIARALIGKELGDIISVNAPG 145 + I A LIGK++GD I + G Sbjct: 19 IEIDGAEANRLIGKKIGDEIDGSIVG 44 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.312 0.131 0.354 Gapped Lambda K H 0.267 0.0697 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,541,575 Number of extensions: 152272 Number of successful extensions: 288 Number of sequences better than 10.0: 1 Number of HSP's gapped: 283 Number of HSP's successfully gapped: 43 Length of query: 158 Length of database: 5,994,473 Length adjustment: 86 Effective length of query: 72 Effective length of database: 4,136,185 Effective search space: 297805320 Effective search space used: 297805320 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 (24.3 bits)