RPS-BLAST 2.2.22 [Sep-27-2009]

Database: mmdb70 
           33,805 sequences; 4,956,049 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} (A:1-83)
          Length = 83

 Score = 92.5 bits (230), Expect = 2e-20
 Identities = 37/83 (44%), Positives = 58/83 (69%)

Query: 2  VDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEG 61
          +  IP+T +G +K+++EL + +   RP II AI+EAR +GDL ENAEY AA+E Q   EG
Sbjct: 1  MQAIPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEG 60

Query: 62 RMAELENIITRAEVIDISTMSGD 84
          R+ ++E  ++ A+VID++ M  +
Sbjct: 61 RIKDIEAKLSNAQVIDVTKMPNN 83


>1grj_A GREA protein; transcript elongation factor, transcript
           cleavage factor, transcription regulation; 2.20A
           {Escherichia coli} (A:84-158)
          Length = 75

 Score = 89.0 bits (221), Expect = 3e-19
 Identities = 34/74 (45%), Positives = 56/74 (75%)

Query: 85  RIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAP 144
           R+ FGATV+++  +S +++ Y+IVGD EAD +  L+S++SPIAR LIGKE  D++ +  P
Sbjct: 2   RVIFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLISVNSPIARGLIGKEEDDVVVIKTP 61

Query: 145 GGEKTYEILQVLWI 158
           GGE  +E+++V ++
Sbjct: 62  GGEVEFEVIKVEYL 75


>2f23_A Anti-cleavage anti-GREA transcription factor GFH1;
          anti-GREA GFH1 thermus thermophilus; 1.60A {Thermus
          thermophilus HB27} (A:1-80)
          Length = 80

 Score = 88.6 bits (220), Expect = 4e-19
 Identities = 18/80 (22%), Positives = 43/80 (53%), Gaps = 1/80 (1%)

Query: 1  MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNE 60
          M  ++ +T  G++++ Q+L   ++       K + E     D  +++  +AAK+ +   E
Sbjct: 1  MAREVKLTKAGYERLMQQLERERER-LQEATKILQELMESSDDYDDSGLEAAKQEKARIE 59

Query: 61 GRMAELENIITRAEVIDIST 80
           R+  LE+I++RA +++  +
Sbjct: 60 ARIDSLEDILSRAVILEEGS 79


>2p4v_A Transcription elongation factor GREB; transcript cleavage,
          GRE-factors, RNA polymerase; 2.60A {Escherichia coli}
          (A:1-82)
          Length = 82

 Score = 88.3 bits (219), Expect = 4e-19
 Identities = 26/78 (33%), Positives = 45/78 (57%)

Query: 4  KIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRM 63
             VT +G++K++QEL +  +EERP + K ++ A + GD SENA+YQ  K+     + R+
Sbjct: 3  TPLVTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRV 62

Query: 64 AELENIITRAEVIDISTM 81
            L   +   +++D S  
Sbjct: 63 RYLTKCMENLKIVDYSPQ 80


>2f23_A Anti-cleavage anti-GREA transcription factor GFH1; anti-GREA
           GFH1 thermus thermophilus; 1.60A {Thermus thermophilus
           HB27} (A:81-156)
          Length = 76

 Score = 84.4 bits (209), Expect = 6e-18
 Identities = 22/74 (29%), Positives = 46/74 (62%), Gaps = 2/74 (2%)

Query: 84  DRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGL--VSISSPIARALIGKELGDIISV 141
           + I  G+ V L +  SG++ + Q+V   EA+V      +S +SP+ +AL+G  +GD++S+
Sbjct: 1   EVIGLGSVVELEDPLSGERLSVQVVSPAEANVLDTPMKISDASPMGKALLGHRVGDVLSL 60

Query: 142 NAPGGEKTYEILQV 155
           + P G++ + ++ +
Sbjct: 61  DTPKGKREFRVVAI 74


>2p4v_A Transcription elongation factor GREB; transcript cleavage,
           GRE-factors, RNA polymerase; 2.60A {Escherichia coli}
           (A:83-158)
          Length = 76

 Score = 82.8 bits (205), Expect = 2e-17
 Identities = 26/74 (35%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 85  RIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAP 144
           ++ FGA V +   + G    ++IVG  E   +   +SI SP+ARAL+ KE+GD+  VN P
Sbjct: 2   KVFFGAWVEIENDD-GVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDLAVVNTP 60

Query: 145 GGEKTYEILQVLWI 158
            GE ++ +  + ++
Sbjct: 61  AGEASWYVNAIEYV 74


>3bmb_A Regulator of nucleoside diphosphate kinase; RNA polymerase,
           elongation factor, anti-GRE factor, RNA binding protein;
           1.91A {Escherichia coli} (A:52-136)
          Length = 85

 Score = 81.7 bits (202), Expect = 5e-17
 Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 84  DRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNA 143
           D +   + V     + G+ +   +V   +    +  +S+ +P+  AL+G  +GD I    
Sbjct: 1   DVVTMNSRVKFRNLSDGEVRVRTLVYPAKMTDSNTQLSVMAPVGAALLGLRVGDSIHWEL 60

Query: 144 PGG-EKTYEILQVLW 157
           PGG     E+L++ +
Sbjct: 61  PGGVATHLEVLELEY 75


>2pn0_A Prokaryotic transcription elongation factor GREA/GREB;
           structural genomics, APC6349, PSI-2, protein structure
           initiative; HET: MSE; 1.70A {Nitrosomonas europaea}
           (A:55-141)
          Length = 87

 Score = 76.3 bits (188), Expect = 2e-15
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 86  IAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAP- 144
           +   +TV    ++S ++    +V  ++ D     +SI +P+  AL+G   GD I    P 
Sbjct: 3   VTXNSTVRFRVESSAEEFXLTLVYPKDVDTSGEKISILAPVGSALLGLAQGDEIEWPKPG 62

Query: 145 GGEKTYEILQVLW 157
           GG     I++V +
Sbjct: 63  GGVLRVRIVEVTY 75


>2pff_A Fatty acid synthase subunit alpha,
          3-oxoacyl-[acyl-carrier-; fatty acid synthase,
          acyl-carrier-protein, beta-ketoacyl reductase,
          beta-ketoacyl synthase, dehydratase; 4.00A
          {Saccharomyces cerevisiae} (A:1221-1330,A:1541-1688)
          Length = 258

 Score = 29.5 bits (66), Expect = 0.26
 Identities = 12/55 (21%), Positives = 16/55 (29%), Gaps = 1/55 (1%)

Query: 20 RWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAE 74
          R RQ   R   IK          L   AE   +++       R  E+ N      
Sbjct: 29 RKRQLVTREAQIKD-WVENELEALKLEAEEIPSEDQNEFLLERTREIHNEAESQL 82


>3is6_A Putative permease protein, ABC transporter; domain, PSI,
           MCSG, structural genomics, midwest center for structural
           genomics; 1.95A {Porphyromonas gingivalis W83} (A:)
          Length = 244

 Score = 27.4 bits (60), Expect = 0.85
 Identities = 14/97 (14%), Positives = 25/97 (25%), Gaps = 2/97 (2%)

Query: 62  RMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSG--L 119
            +  +E             +  D   +     L E    D    +++             
Sbjct: 50  EIPGVELATRTTLYGTSKXILEDNKTYETKTLLAEPAFLDXFGVELIAGVRDSALRDNXT 109

Query: 120 VSISSPIARALIGKELGDIISVNAPGGEKTYEILQVL 156
             IS  +AR   G  LG  +       ++   I  V 
Sbjct: 110 CLISESLARKXGGDVLGKRLRPAESKSDRAITIGGVF 146


>1g8k_A Arsenite oxidase; molybdopterin, [3Fe-4S] cluster, [2Fe- 2S]
           cluster, rieske, oxidoreductase; HET: MGD; 1.64A
           {Alcaligenes faecalis} (A:1-105)
          Length = 105

 Score = 26.9 bits (60), Expect = 1.2
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 90  ATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSI 122
           A  ++V ++ G + +  +V D+   V SGL S 
Sbjct: 68  AMTNVVTEHDGARYDIMVVPDKACVVNSGLSST 100


  Database: mmdb70
    Posted date:  Jun 20, 2010  3:12 AM
  Number of letters in database: 4,956,049
  Number of sequences in database:  33,805
  
Lambda     K      H
   0.312    0.131    0.354 

Gapped
Lambda     K      H
   0.267   0.0623    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,126,934
Number of extensions: 45599
Number of successful extensions: 98
Number of sequences better than 10.0: 1
Number of HSP's gapped: 96
Number of HSP's successfully gapped: 26
Length of query: 158
Length of database: 4,956,049
Length adjustment: 81
Effective length of query: 77
Effective length of database: 2,217,844
Effective search space: 170773988
Effective search space used: 170773988
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: 51 (23.7 bits)