RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase
subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
         (340 letters)



>gnl|CDD|30551 COG0202, RpoA, DNA-directed RNA polymerase, alpha subunit/40 kD
           subunit [Transcription].
          Length = 317

 Score =  303 bits (777), Expect = 5e-83
 Identities = 148/319 (46%), Positives = 206/319 (64%), Gaps = 5/319 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++     +  +     + EPL RGF  TLGNALRRVL+SS+ GAA+TAV+IDGV
Sbjct: 1   FLKPKKVKIE---ELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE  SI+GV ED+    LN+K + +K+ GD    + + K GPG VTA DI    D+EV+
Sbjct: 58  LHEFDSIEGVQEDVLAHRLNLKPLAVKLDGDEEVTLELDKEGPGEVTASDITVPLDLEVV 117

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPDHVI  L  DA + MEL V  G GYVPA+ +R ++ P+G I +DA +SP++KV Y VE
Sbjct: 118 NPDHVIATLTEDAKLEMELRVYSGDGYVPAEGNREDDPPVGPIAVDAPFSPVRKVQYIVE 177

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
            AR GQ  D D L    +T+GSI  E+++A+A++IL + L +F+       E++E+    
Sbjct: 178 EARVGQGTDKDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCPKAVEIEEE--KP 235

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
             P    L   ++EL+LSVRS NCL+ E I  +G+L+QRTE ++L++ N G+KSL EIK 
Sbjct: 236 EFPILLVLEAPIDELDLSVRSYNCLKREGIETIGELVQRTEEELLKVENLGKKSLEEIKE 295

Query: 309 VLGTMGLFLGMNLPDWPPE 327
            L  +GL LGM L +WPP 
Sbjct: 296 KLAELGLELGMELENWPPS 314


>gnl|CDD|132904 cd06928, RNAP_alpha_NTD, N-terminal domain of the Alpha subunit of
           Bacterial RNA polymerase.  The bacterial alpha subunit
           of RNA polymerase (RNAP) consists of two independently
           folded domains: an amino-terminal domain (alphaNTD) and
           a carboxy-terminal domain (alphaCTD). AlphaCTD is not
           required for RNAP assembly but interacts with
           transcription activators. AlphaNTD is essential in vivo
           and in vitro for RNAP assembly and basal transcription.
           It is similar to the eukaryotic RPB3/AC40/archaeal D
           subunit, and contains two subdomains: one subdomain is
           similar the eukaryotic Rpb11/AC19/archaeal L subunit
           which is involved in dimerization; and the other is an
           inserted beta sheet subdomain. The alphaNTDs of plant
           plastid RNAP (PEP) are also included in this subfamily.
           PEP is largely responsible for the transcription of
           photosynthetic genes and is closely related to the
           multi-subunit bacterial RNAP, which is a large
           multi-subunit complex responsible for the synthesis of
           all bacterial RNAs. The bacterial RNAP core enzyme
           consists of four subunits (beta', beta, alpha and
           omega). All residues in the alpha subunit that is
           involved in dimerization or in the interaction with
           other subunits are located within alphaNTD.
          Length = 215

 Score =  288 bits (740), Expect = 1e-78
 Identities = 108/211 (51%), Positives = 149/211 (70%), Gaps = 1/211 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            + EN    + EPL RG   TLGNALRRVL+SSL GAAITAV+I+GVLHE S+I GV ED
Sbjct: 5   NKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGVLHEFSTIPGVRED 64

Query: 82  LTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           + +I+LN+K I  K  S D  + + +  +GPGVVTA DI+  + +E++NPD  I  L  D
Sbjct: 65  VLEILLNLKEIVFKSDSEDEPQVLRLKVKGPGVVTAADIELPSGVEIVNPDQYIATLTED 124

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           A + MEL + KG GYVPA+ +++E  PIG I IDA++SP++KV+Y+VES R GQ  DY+K
Sbjct: 125 ASLEMELRIEKGRGYVPAEENKSEEKPIGFIPIDAIFSPVRKVNYSVESTRVGQRTDYEK 184

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           L + I T+GSI+ E+++A A++IL +    F
Sbjct: 185 LILEIWTNGSISPEEALAQAAKILINHFSPF 215


>gnl|CDD|176956 CHL00013, rpoA, RNA polymerase alpha subunit.
          Length = 327

 Score =  195 bits (499), Expect = 1e-50
 Identities = 105/307 (34%), Positives = 165/307 (53%), Gaps = 22/307 (7%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           I  PL +G A T+G ALRR L+  + G  IT  +I+GV HE S+I G+ E + +I+LN+K
Sbjct: 25  ILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEGVPHEYSTIPGIRESVLEILLNLK 84

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            I LK +    ++ +I  +GP  VTA DI     +E+++P   I  +     + +EL + 
Sbjct: 85  EIVLKSNLYGPQKASICVQGPKYVTAQDIILPPSVEIVDPTQHIATITEPIDLEIELKIE 144

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GY   +    +N   G   IDA++ P++ V+Y++ S   G     + L + I T+GS
Sbjct: 145 KGRGY---RLKTPKNFQDGSFPIDAVFMPVRNVNYSIHSYGNGNEKQ-EILFLEIWTNGS 200

Query: 211 ITGEDSVALASRILQDQLGMFINFEEP--KKEVKEDINVKSLPFNPALLKK--------- 259
           IT ++++  ASR L D    F++ EE   K E  E+       F+  L            
Sbjct: 201 ITPKEALHEASRNLIDLFIPFLHAEEENLKLENNENRVTLLFTFHDRLTDLKKNKKEIAL 260

Query: 260 ----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
               +E+LELSVR+ NCL+  NI  + DL+  ++ D+L++ NFG+KS    K VL  +  
Sbjct: 261 KQIFIEQLELSVRAYNCLKRANIHTLLDLLNYSQEDLLKIKNFGQKS---AKEVLEALQK 317

Query: 316 FLGMNLP 322
             G++LP
Sbjct: 318 RFGIDLP 324


>gnl|CDD|110031 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA insert domain.
           Members of this family include: alpha subunit from
           eubacteria alpha subunits from chloroplasts Rpb3
           subunits from eukaryotes RpoD subunits from archaeal.
          Length = 117

 Score =  126 bits (319), Expect = 7e-30
 Identities = 47/118 (39%), Positives = 72/118 (61%), Gaps = 3/118 (2%)

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQ 120
           V I+GV HE   I GV ED+ +IILN+K +  K+ G     VT+    +GPG VTAGD++
Sbjct: 1   VYINGVAHEFGLIPGVSEDVLEIILNLKELVCKIEGCEECSVTLTLDVKGPGEVTAGDLE 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           +  D+E++NPD +I  L     + +E    KG GYV AK ++ + +  G I +D+++S
Sbjct: 61  SDPDVEIVNPDILIATLRKGQELELEAYAKKGRGYVHAKENKEDEEE-GRIPVDSIFS 117


>gnl|CDD|145976 pfam03118, RNA_pol_A_CTD, Bacterial RNA polymerase, alpha chain C
           terminal domain.  The alpha subunit of RNA polymerase
           consists of two independently folded domains, referred
           to as amino-terminal and carboxyl terminal domains. The
           amino terminal domain is involved in the interaction
           with the other subunits of the RNA polymerase. The
           carboxyl-terminal domain interacts with the DNA and
           activators. The amino acid sequence of the alpha subunit
           is conserved in prokaryotic and chloroplast RNA
           polymerases. There are three regions of particularly
           strong conservation, two in the amino-terminal and one
           in the carboxyl- terminal.
          Length = 62

 Score = 84.1 bits (209), Expect = 5e-17
 Identities = 30/60 (50%), Positives = 40/60 (66%)

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELELSVRS NCL+   I  +GDL+ ++E D+L++ NFG+KSL EIK  L
Sbjct: 1   EELALLSIPIEELELSVRSYNCLKRAGINTVGDLLSKSEEDLLKIKNFGKKSLEEIKEKL 60


>gnl|CDD|144693 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerization
           domain.  The two eukaryotic subunits Rpb3 and Rpb11
           dimerize to from a platform onto which the other
           subunits of the RNA polymerase assemble (D/L in
           archaea). The prokaryotic equivalent of the Rpb3/Rpb11
           platform is the alpha-alpha dimer. The dimerization
           domain of the alpha subunit/Rpb3 is interrupted by an
           insert domain (pfam01000). Some of the alpha subunits
           also contain iron-sulphur binding domains (pfam00037).
           Rpb11 is found as a continuous domain. Members of this
           family include: alpha subunit from eubacteria, alpha
           subunits from chloroplasts, Rpb3 subunits from
           eukaryotes, Rpb11 subunits from eukaryotes, RpoD
           subunits from archaeal spp, and RpoL subunits from
           archaeal spp.
          Length = 91

 Score = 62.3 bits (152), Expect = 2e-10
 Identities = 32/63 (50%), Positives = 44/63 (69%)

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I  DA +SP+KKV+Y VE  R GQ  DYDKL + I+TDGSIT E+++  A++IL D+L  
Sbjct: 29  IAGDAKFSPVKKVNYRVEPTRVGQNTDYDKLILEIETDGSITPEEALLEAAKILIDKLDE 88

Query: 231 FIN 233
            + 
Sbjct: 89  LLE 91



 Score = 50.3 bits (121), Expect = 7e-07
 Identities = 17/31 (54%), Positives = 20/31 (64%)

Query: 32 AEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           E L  G  HTLGNALRR+L+S + G AI  
Sbjct: 1  IEFLLEGEDHTLGNALRRILLSEVPGVAIAG 31


>gnl|CDD|132901 cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits of RNA
           polymerase.  The eukaryotic RPB11 and RPB3 subunits of
           RNA polymerase (RNAP), as well as their archaeal (L and
           D subunits) and bacterial (alpha subunit) counterparts,
           are involved in the assembly of RNAP, a large
           multi-subunit complex responsible for the synthesis of
           RNA. It is the principal enzyme of the transcription
           process, and is a final target in many regulatory
           pathways that control gene expression in all living
           cells. At least three distinct RNAP complexes are found
           in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for
           the synthesis of ribosomal RNA precursor, mRNA
           precursor, and 5S and tRNA, respectively. A single
           distinct RNAP complex is found in prokaryotes and
           archaea, which may be responsible for the synthesis of
           all RNAs. The assembly of the two largest eukaryotic
           RNAP subunits that provide most of the enzyme's
           catalytic functions depends on the presence of
           RPB3/RPB11 heterodimer subunits. This is also true for
           the archaeal (D/L subunits) and bacterial (alpha
           subunit) counterparts.
          Length = 86

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 20/56 (35%), Positives = 31/56 (55%)

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           L SP++  +Y VE   + Q  D DK  + I+T GSI  E+++  A  IL+ +L   
Sbjct: 31  LKSPVEFAAYYVEHPVKLQRTDEDKFILRIETVGSIPPEEALRRAVEILRKKLEHL 86



 Score = 30.1 bits (68), Expect = 0.97
 Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 12/68 (17%)

Query: 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
          ++E+N    + E       HTLGN+LRR+L+ S       A  ++        +K    D
Sbjct: 5  EKEKNYVDFVLENED----HTLGNSLRRILLKS--PVEFAAYYVE------HPVKLQRTD 52

Query: 82 LTDIILNI 89
              IL I
Sbjct: 53 EDKFILRI 60


>gnl|CDD|35413 KOG0192, KOG0192, KOG0192, Tyrosine kinase specific for activated
           (GTP-bound) p21cdc42Hs [Signal transduction mechanisms].
          Length = 362

 Score = 30.5 bits (68), Expect = 0.73
 Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 8/92 (8%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGV-- 68
           PN +++            ++ E +P G    L +  R+  +  L+     A+ I  G+  
Sbjct: 99  PNIVQFYGACTSPPGSLCIVTEYMPGGSLSVLLHKKRKRKL-PLKVRLRIALDIARGMEY 157

Query: 69  LHEISSIKGVHEDL--TDIILNIKGINLKMSG 98
           LH    I  +H DL   +I++++KG  LK++ 
Sbjct: 158 LHSEGPI--IHRDLKSDNILVDLKGKTLKIAD 187


>gnl|CDD|31955 COG1769, COG1769, Uncharacterized protein predicted to be involved
           in DNA repair (RAMP superfamily) [DNA replication,
           recombination, and repair].
          Length = 335

 Score = 30.4 bits (68), Expect = 0.82
 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 4/90 (4%)

Query: 155 YVPAKHHRTENDPI-GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           YVP+  +  + D +  ++ ID LY P     Y ++S        + + S       +   
Sbjct: 79  YVPSPRNVYKTDSVTPIVEIDGLYLPWL-PEYKMDSKESTN--GFIEFSDLELLRSNGIC 135

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  +  A +I + +  + I  E+ +K+VKE
Sbjct: 136 KFDLVSAEKIFKKETRVGIALEKNRKKVKE 165


>gnl|CDD|132908 cd07030, RNAP_D, D subunit of Archaeal RNA polymerase.  The D
           subunit of archaeal RNA polymerase (RNAP) is involved in
           the assembly of RNAP subunits. RNAP is a large
           multi-subunit complex responsible for the synthesis of
           RNA. It is the principal enzyme of the transcription
           process, and is a final target in many regulatory
           pathways that control gene expression in all living
           cells. A single distinct RNAP complex is found in
           archaea, which may be responsible for the synthesis of
           all RNAs. The archaeal RNAP harbors homologues of all
           eukaryotic RNAP II subunits with two exceptions (RPB8
           and RPB9). The 12 archaeal subunits are designated by
           letters and can be divided into three functional groups
           that are engaged in: (I) catalysis (A'/A", B'/B" or B);
           (II) assembly (L, N, D and P); and (III) auxiliary
           functions (F, E, H and K). The D subunit is equivalent
           to the RPB3 subunit of eukaryotic RNAP II. It contains
           two subdomains: one subdomain is similar the eukaryotic
           Rpb11/AC19/archaeal L subunit which is involved in
           dimerization, and the other is an inserted beta sheet
           subdomain. The assembly of the two largest archaeal RNAP
           subunits that provide most of the enzyme's catalytic
           functions depends on the presence of the archaeal D/L
           heterodimer.
          Length = 259

 Score = 29.9 bits (68), Expect = 0.90
 Identities = 59/268 (22%), Positives = 105/268 (39%), Gaps = 58/268 (21%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI--------TAVQI 65
            IE + L   +++R   + E +P  FA    NA+RR ++S +   AI        T+V  
Sbjct: 2   EIEVLEL---DDDRARFVLEGVPPAFA----NAIRRAIISEVPTLAIDDVNIYENTSVLF 54

Query: 66  DGVL-HEISSIKGVHEDLTDIILN--IKGINLKMSGDSHKRVT--IFKRGPGVVTAGDIQ 120
           D +L H +  I       TD+ L       +   +G     VT  +   GPG V +GD++
Sbjct: 55  DEMLAHRLGLIPLR----TDLDLYKYRSECSCGGAGCPLCTVTLTLSVEGPGTVYSGDLK 110

Query: 121 TVN-DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT-----ENDPIGLI--T 172
           + + D++ +  +  I  L     + +E     G G   AK   T     +  P+  I   
Sbjct: 111 SSDPDVKPVYDNIPIVKLGKGQKLVLEAYARLGRGKEHAKWQPTTACGYKYYPVIEIDED 170

Query: 173 IDALYSPIKKVSYTVESAREGQVL--------------------------DYDKLSMTID 206
            D     +++    V    EG+V+                          D D+    ++
Sbjct: 171 CDGCGKCVEECPRGVLELEEGKVVVEDLEDCSLCKLCERACDAGAIRVGWDEDRFIFEVE 230

Query: 207 TDGSITGEDSVALASRILQDQLGMFINF 234
           +DGS+  ++ +  A RIL+++    I  
Sbjct: 231 SDGSLPPKEILLEALRILKEKADELIEA 258


>gnl|CDD|132907 cd07029, RNAP_I_III_AC19, AC19 subunit of Eukaryotic RNA
          polymerase (RNAP) I and RNAP III.  The eukaryotic AC19
          subunit of RNA polymerase (RNAP) I and RNAP III is
          involved in the assembly of RNAP subunits. RNAP is a
          large multi-subunit complex responsible for the
          synthesis of RNA. It is the principal enzyme of the
          transcription process, and is a final target in many
          regulatory pathways that control gene expression in all
          living cells. At least three distinct RNAP complexes
          are found in eukaryotic nuclei:  RNAP I, RNAP II, and
          RNAP III. RNAP I is responsible for the synthesis of
          ribosomal RNA precursor, while RNAP III functions in
          the synthesis of 5S and tRNA. The AC19 subunit is the
          equivalent of the RPB11 subunit of RNAP II. The RPB11
          subunit heterodimerizes with the RPB3 subunit, and
          together with RPB10 and RPB12, anchors the two largest
          subunits, RPB1 and RPB2, and stabilizes their
          association. The homology of AC19 to RPB11 suggests a
          similar function. The AC19 subunit is likely to
          associate with the RPB3 counterpart, AC40, to form a
          heterodimer, which stabilizes the association of the
          two largest subunits of RNAP I and RNAP III.
          Length = 85

 Score = 29.5 bits (67), Expect = 1.5
 Identities = 9/12 (75%), Positives = 11/12 (91%)

Query: 41 HTLGNALRRVLM 52
          HTLGN+LR V+M
Sbjct: 20 HTLGNSLRYVIM 31


>gnl|CDD|146686 pfam04177, TAP42, TAP42-like family.  The TOR signalling pathway
           activates a cell-growth program in response to
           nutrients. TIP41 (pfam04176) interacts with TAP42 and
           negatively regulates the TOR signaling pathway.
          Length = 335

 Score = 28.0 bits (63), Expect = 4.1
 Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 17/82 (20%)

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           ++  L+    K+   +E +        DK+  TI+          +  A+R++  QL +F
Sbjct: 1   SLSELFDEALKLFDELEESASDSEEYQDKVKKTIE---------LLEKATRLV-SQLSLF 50

Query: 232 -INFEEPKKEVKEDINVKSLPF 252
             N      E  EDI+  SL +
Sbjct: 51  SSN------ETLEDISTSSLKY 66


>gnl|CDD|36735 KOG1522, KOG1522, KOG1522, RNA polymerase II, subunit POLR2C/RPB3
           [Transcription].
          Length = 285

 Score = 27.6 bits (61), Expect = 5.1
 Identities = 47/230 (20%), Positives = 86/230 (37%), Gaps = 44/230 (19%)

Query: 43  LGNALRRVLMSSLRGAAITAVQID---GVLHE--ISSIKGVHEDLTDIILNIK------- 90
           + N+LRRV+++ +   AI  V+I+    VL +  I+   G+   ++D I+ ++       
Sbjct: 29  VANSLRRVMIAEVPTIAIDLVEIEVNSSVLPDEFIAHRLGLIPLISDRIVELQYTRDCEC 88

Query: 91  -----------GINLKMSGDSHKRVT---IFKRGPGVVTAGDIQTVNDIEVLNPDH-VIC 135
                       +++K + D  + VT   +    P V      +     +       +I 
Sbjct: 89  DEFCPECSVEFTLDVKCTDDQTRDVTSRDLVSLDPTVTPVDSNRGSEIDDDSESKGILIV 148

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRT-----ENDPIGLI--------TIDALYSPIKK 182
            L     +++     KG G   AK   T     E DP   +          D +  P  K
Sbjct: 149 KLRKGQELKLRAIAKKGIGKEHAKWSPTAAVAFEYDPDNKLRHTLYWFEEDDLIEWPKSK 208

Query: 183 VSYTVESAREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQL 228
            S   E   EG   D     DK    +++ G++     V +   IL+++L
Sbjct: 209 NSELEEDPEEGAPYDPEGKPDKFYFNVESVGALPPSQIVLMGIDILKEKL 258


>gnl|CDD|132909 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic RNA polymerase
          II.  The eukaryotic RPB3 subunit of RNA polymerase
          (RNAP) II is involved in the assembly of RNAP subunits.
          RNAP is a large multi-subunit complex responsible for
          the synthesis of RNA. It is the principal enzyme of the
          transcription process, and is a final target in many
          regulatory pathways that control gene expression in all
          living cells. At least three distinct RNAP complexes
          are found in eukaryotic nuclei: RNAP I, RNAP II, and
          RNAP III. RNAP II is responsible for the synthesis of
          mRNA precursor. The RPB3 subunit is similar to the
          bacterial RNAP alpha subunit in that it contains two
          subdomains: one subdomain is similar the eukaryotic
          Rpb11/AC19/archaeal L subunit which is involved in
          dimerization, and the other is an inserted beta sheet
          subdomain. The RPB3 subunit heterodimerizes with the
          RPB11 subunit, and together with RPB10 and RPB12,
          anchors the two largest subunits, RPB1 and RPB2, and
          stabilizes their association.
          Length = 265

 Score = 27.2 bits (61), Expect = 6.4
 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 20/64 (31%)

Query: 10 IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG-- 67
          +  + +++I+     EN  L +A            N+LRRV+++ +   AI  V+I+   
Sbjct: 8  LTDDKVKFIL-----ENTDLSVA------------NSLRRVMIAEVPTLAIDLVEIEENT 50

Query: 68 -VLH 70
           VLH
Sbjct: 51 SVLH 54


>gnl|CDD|36604 KOG1390, KOG1390, KOG1390, Acetyl-CoA acetyltransferase [Lipid
           transport and metabolism].
          Length = 396

 Score = 26.8 bits (59), Expect = 8.3
 Identities = 10/23 (43%), Positives = 13/23 (56%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVND 124
           K   +FK   G VTA +  T+ND
Sbjct: 233 KLRPVFKEDGGTVTAANASTLND 255


>gnl|CDD|112628 pfam03824, NicO, High-affinity nickel-transport protein.  High
          affinity nickel transporters involved in the
          incorporation of nickel into H2-uptake hydrogenase and
          urease enzymes. Essential for the expression of
          catalytically active hydrogenase and urease. Ion uptake
          is dependent on proton motive force. HoxN in
          Alcaligenes eutrophus is thought to be an integral
          membrane protein with seven transmembrane helices. The
          family also includes a cobalt transporter.
          Length = 278

 Score = 27.0 bits (60), Expect = 8.3
 Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 2/53 (3%)

Query: 27 RTLMIA--EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
          R+ M A   PL  G   +LG++    L++ L    +  V     L EI S  G
Sbjct: 28 RSYMQAGKTPLKVGILFSLGHSSVVGLVALLLALGVKLVLRLPSLQEIGSTIG 80


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.317    0.136    0.386 

Gapped
Lambda     K      H
   0.267   0.0737    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,963,820
Number of extensions: 205796
Number of successful extensions: 508
Number of sequences better than 10.0: 1
Number of HSP's gapped: 500
Number of HSP's successfully gapped: 21
Length of query: 340
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 246
Effective length of database: 4,232,491
Effective search space: 1041192786
Effective search space used: 1041192786
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 (21.6 bits)
S2: 58 (26.1 bits)