RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780937|ref|YP_003065350.1| DNA-directed RNA polymerase
subunit omega [Candidatus Liberibacter asiaticus str. psy62]
         (122 letters)



>3lu0_E DNA-directed RNA polymerase subunit omega; E. coli RNA
          polymerase, nucleotidyltransferase, transcription,
          transferase; 11.20A {Escherichia coli} PDB: 3iyd_E*
          Length = 91

 Score = 98.8 bits (246), Expect = 3e-22
 Identities = 35/89 (39%), Positives = 50/89 (56%), Gaps = 2/89 (2%)

Query: 1  MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAK-PTVDVGKDKNTVVALREIASGTLS 59
          MAR TV+D ++K+ NRF LVL+A+ R R +  G K P V    DK TV+ALREI  G ++
Sbjct: 1  MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN 60

Query: 60 PDDLEEDFIHSLQKHVEIDEPDSPTENSD 88
             L+       Q+  E  E  + T  ++
Sbjct: 61 NQILDVR-ERQEQQEQEAAELQAVTAIAE 88


>3iyd_E DNA-directed RNA polymerase subunit omega; transcription,
          initiation, class I, activator, RNA polymerase,
          holoenzyme, sigma70, open complex, CAP, CRP,
          CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli
          k-12}
          Length = 90

 Score = 93.3 bits (232), Expect = 1e-20
 Identities = 34/88 (38%), Positives = 49/88 (55%), Gaps = 2/88 (2%)

Query: 2  ARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAK-PTVDVGKDKNTVVALREIASGTLSP 60
          AR TV+D ++K+ NRF LVL+A+ R R +  G K P V    DK TV+ALREI  G ++ 
Sbjct: 1  ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINN 60

Query: 61 DDLEEDFIHSLQKHVEIDEPDSPTENSD 88
            L+       Q+  E  E  + T  ++
Sbjct: 61 QILDVR-ERQEQQEQEAAELQAVTAIAE 87


>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 = 34.5 bits (79), Expect = 0.006
 Identities = 23/98 (23%), Positives = 32/98 (32%), Gaps = 33/98 (33%)

Query: 49  ALRE--IASGTLS-----PDD-------LEEDFIHSLQKHVEI----DEPDSPTENS--- 87
           + R   ++ G+L      P         L+E F   L +  E     DEP +P E     
Sbjct: 5   STRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKF 64

Query: 88  -DFSWHKPEALSFGQMS----------EGDLLEGINNI 114
             +     E    GQ            E   LEG N+I
Sbjct: 65  LGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEG-NDI 101



 Score = 30.7 bits (69), Expect = 0.090
 Identities = 15/108 (13%), Positives = 29/108 (26%), Gaps = 36/108 (33%)

Query: 20  VLLASHRTRHLSQGAKPTV-------DVGKDKNTVVA--------------LREIASGTL 58
           ++      R +++              VG+    +VA              LR++   T 
Sbjct: 122 LIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQ-TY 180

Query: 59  SPDDLEEDFIHSLQKHVEIDEPDSPTENSDF---------SW-HKPEA 96
               L  D I    + +   E    T +++           W   P  
Sbjct: 181 HV--LVGDLIKFSAETL--SELIRTTLDAEKVFTQGLNILEWLENPSN 224



 Score = 29.9 bits (67), Expect = 0.15
 Identities = 14/109 (12%), Positives = 25/109 (22%), Gaps = 48/109 (44%)

Query: 12  KVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDL-------- 63
           K  NRFL V    H +  L      +  + KD    +    +   + +  D+        
Sbjct: 415 KFSNRFLPVASPFH-SHLL---VPASDLINKD----LVKNNV---SFNAKDIQIPVYDTF 463

Query: 64  --------EEDFIHSL-----QKHVEIDEPDSPTENSDFSWHKPEALSF 99
                          +     +  V+              W       F
Sbjct: 464 DGSDLRVLSGSISERIVDCIIRLPVK--------------W--ETTTQF 496


>2kxo_A Cell division topological specificity factor; MINE, MIND-binding,
           to specificity, cell cycle; NMR {Neisseria gonorrhoeae}
          Length = 95

 Score = 28.5 bits (64), Expect = 0.45
 Identities = 15/89 (16%), Positives = 33/89 (37%), Gaps = 18/89 (20%)

Query: 35  KPTVDVGKDKNTVVALREIASGTLSPDDLE---EDFIHSLQKHVEIDEPDSPTENSDFSW 91
           + T  V +D+  ++  +E A    +PD L    +  +  L K+V +              
Sbjct: 12  QKTATVARDRLQIIIAQERAQEGQTPDYLPTLRKALMEVLSKYVNVS------------- 58

Query: 92  HKPEALSFGQMSEGDLLEGINNIVTPDKR 120
              + +   Q  +  +     NI  P+++
Sbjct: 59  --LDNIRISQEKQDGMDVLELNITLPEQK 85


>3ke8_A 4-hydroxy-3-methylbut-2-ENYL diphosphate reductase; induced FIT
           mechanism, FS4-iron-sulfure-cluster, 3Fe-4S, iron,
           iron-sulfur; HET: EIP; 1.70A {Escherichia coli} PDB:
           3ke9_A* 3kef_A* 3kel_A 3kem_A* 3f7t_A
          Length = 326

 Score = 26.8 bits (59), Expect = 1.3
 Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 2/40 (5%)

Query: 53  IASGTLSPDDLEEDFIHSLQKH--VEIDEPDSPTENSDFS 90
           + +G  +PD L ++ +  LQ+    E    +   EN  F 
Sbjct: 274 VTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFE 313


>2waq_K DNA-directed RNA polymerase RPO6 subunit; multi-subunit,
          transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_I
          2pmz_K 3hkz_K
          Length = 95

 Score = 26.3 bits (58), Expect = 1.8
 Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 3/47 (6%)

Query: 15 NRFLLVLLASHRTRHLSQGAKPTVDVGKDKNT---VVALREIASGTL 58
           R+ +  + S R   L+ GA   +D+    +T    +A  E   G L
Sbjct: 28 TRYEIARVISARALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVL 74


>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}
          Length = 1688

 Score = 25.5 bits (55), Expect = 2.9
 Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 22/80 (27%)

Query: 51  REIASGTLSPDDLE---------EDFIHSLQKHVEIDE-PDSPTENSDFS--------WH 92
           +E+    +  +DLE         E F H     V+I E P    E  ++S         +
Sbjct: 920 KEMIQEVIVEEDLEPFEASKETAEQFKHQHGDKVDIFEIP----ETGEYSVKLLKGATLY 975

Query: 93  KPEALSFGQMSEGDLLEGIN 112
            P+AL F ++  G +  G N
Sbjct: 976 IPKALRFDRLVAGQIPTGWN 995


>1mw9_X DNA topoisomerase I; decatenase enzyme, toprim domain; HET: DNA;
           1.67A {Escherichia coli} SCOP: e.10.1.1 PDB: 1mw8_X*
           1cy1_A* 1cy0_A* 1cy2_A* 1cy4_A* 1cy6_A* 1cy7_A* 1cy8_A*
           1ecl_A 1cy9_A* 1cyy_A*
          Length = 592

 Score = 25.5 bits (55), Expect = 3.5
 Identities = 3/27 (11%), Positives = 11/27 (40%)

Query: 50  LREIASGTLSPDDLEEDFIHSLQKHVE 76
           L ++A+       + + F     + ++
Sbjct: 550 LDQVANHEAEWKAVLDHFFSDFTQQLD 576


>3kpk_A Sulfide-quinone reductase, putative; oxidoreductases,
          sulfide:quinone oxidoreductase, C160A mutan
          oxidoreductase; HET: FAD LMT; 2.05A {Acidithiobacillus
          ferrooxidans atcc 23} PDB: 3kpg_A* 3kpi_A*
          Length = 434

 Score = 25.2 bits (54), Expect = 3.8
 Identities = 7/49 (14%), Positives = 17/49 (34%), Gaps = 3/49 (6%)

Query: 28 RHLSQGAKPTVDVGKDKNTVV--ALREIASGTLSPDDLEEDFIHSLQKH 74
            L  G + T+ +  +       +   +  G    DD+     H +++ 
Sbjct: 22 EALGSGHEVTL-ISANDYFQFVPSNPWVGVGWKERDDIAFPIRHYVERK 69


>1m22_A Peptide amidase, PAM; eleven-stranded beta sheet, covered double
          layers of alpha helices on TOP and bottom, hydrolase;
          HET: EPE; 1.40A {Stenotrophomonas maltophilia} SCOP:
          c.117.1.1 PDB: 1m21_A*
          Length = 503

 Score = 25.3 bits (54), Expect = 4.2
 Identities = 9/53 (16%), Positives = 20/53 (37%), Gaps = 6/53 (11%)

Query: 46 TVVALRE-IASGTLSPDDLEEDFIHSLQKHVEIDEPDSPTENSDFSWHKPEAL 97
           V  L+  + +G L    L + ++    + +   +   P   +      P+AL
Sbjct: 12 DVADLQARMTAGELDSTTLTQAYL----QRIAALDRTGPRLRA-VIELNPDAL 59


>1k9a_A Carboxyl-terminal SRC kinase; COOH-terminal SRC kinase, CSK, SFK,
           signal transduction, SH2, SH3, SRC homology, tyrosine
           kinase; 2.50A {Rattus norvegicus} SCOP: b.34.2.1
           d.93.1.1 d.144.1.7 PDB: 1jeg_A
          Length = 450

 Score = 24.5 bits (53), Expect = 6.2
 Identities = 9/47 (19%), Positives = 21/47 (44%)

Query: 28  RHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKH 74
           + + +G    V +G  +   VA++ I +   +   L E  + +  +H
Sbjct: 199 QTIGKGEFGDVMLGDYRGNKVAVKCIKNDATAQAFLAEASVMTQLRH 245


>1r42_A Angiotensin I converting enzyme 2; zinc metallopeptidase domain,
           native or open conformation, chloride ION binding site;
           HET: NAG; 2.20A {Homo sapiens} SCOP: d.92.1.5 PDB:
           1r4l_A* 2ajf_A* 3d0g_A* 3d0h_A* 3d0i_A*
          Length = 615

 Score = 24.0 bits (51), Expect = 8.5
 Identities = 6/41 (14%), Positives = 13/41 (31%), Gaps = 1/41 (2%)

Query: 52  EIASGTLSPDDLEEDFIHSLQKHVEIDEPDSPTENSDFSWH 92
            +  G +  D   + +    ++ V + EP    E       
Sbjct: 462 MVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDET-YCDPA 501


>1twf_F ABC23, DNA-directed RNA polymerases I, II, and III 23 kDa
           polypeptide; transcription, mRNA, multiprotein complex;
           HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP:
           a.143.1.2 PDB: 1i3q_F 1i6h_F 1k83_F* 1nik_F 1nt9_F
           1pqv_F 1r5u_F 1r9s_F* 1r9t_F* 1sfo_F* 1twa_F* 1twc_F*
           1i50_F* 1twg_F* 1twh_F* 1wcm_F 1y1v_F 1y1w_F 1y1y_F
           1y77_F* ...
          Length = 155

 Score = 24.1 bits (52), Expect = 9.7
 Identities = 8/45 (17%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 15  NRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTV-VALREIASGTL 58
            ++    +   R   +S  A   VD+  + + + +A++E+A   +
Sbjct: 86  TKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKI 130


  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
   0.313    0.132    0.380 

Gapped
Lambda     K      H
   0.267   0.0628    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,047,823
Number of extensions: 44286
Number of successful extensions: 90
Number of sequences better than 10.0: 1
Number of HSP's gapped: 87
Number of HSP's successfully gapped: 20
Length of query: 122
Length of database: 5,693,230
Length adjustment: 81
Effective length of query: 41
Effective length of database: 3,729,466
Effective search space: 152908106
Effective search space used: 152908106
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: 50 (23.3 bits)