254780937

254780937

DNA-directed RNA polymerase subunit omega

GeneID in NCBI database:8209959Locus tag:CLIBASIA_04180
Protein GI in NCBI database:254780937Protein Accession:YP_003065350.1
Gene range:+(928042, 928410)Protein Length:122aa
Gene description:DNA-directed RNA polymerase subunit omega
COG prediction:[K] DNA-directed RNA polymerase, subunit K/omega
KEGG prediction:ropZ; DNA-directed RNA polymerase subunit omega (EC:2.7.7.6); K03060 DNA-directed RNA polymerase subunit omega [EC:2.7.7.6]
SEED prediction:DNA-directed RNA polymerase omega subunit (EC 2.7.7.6)
Pathway involved in KEGG:Purine metabolism [PATH:las00230]
Pyrimidine metabolism [PATH:las00240]
RNA polymerase [PATH:las03020]
Subsystem involved in SEED:RNA polymerase bacterial
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120--
MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVEIDEPDSPTENSDFSWHKPEALSFGQMSEGDLLEGINNIVTPDKRDD
cccccHHHHHHHcccHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccccHHHHHHHHHcccccccccc
cccEEHHHHHHHcccHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHcccccHHHHHHHHHHHHccEEEccccccccHHHccccccccccccccccHHHHHHHHccccccccccc
MARTTVEDCIDKVDNRFLLVLLASHrtrhlsqgakptvdvgkdkNTVVALREIasgtlspddleEDFIHSLQKhveidepdsptensdfswhkpealsfgqmsegdlleginnivtpdkrdd
marttvedcidkvdNRFLLVLLAShrtrhlsqgakptvdvgkdkNTVVALREiasgtlspddlEEDFIHSLQKHVEIDEPDSPTENSDFSWHKPEALSfgqmsegdlleginnivtpdkrdd
MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVEIDEPDSPTENSDFSWHKPEALSFGQMSEGDLLEGINNIVTPDKRDD
*ARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAK******KDKNTVVALREIASGTLSPDDLEE*********************************************************
MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVEID**********FSWHKPEALSFGQMSEGDLLEGINNIVTPDKRDD
*ARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVEID*********************GQ*S*GDLLEGINNIVTP*****
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVEIDEPDSPTENSDFSWHKPEALSFGQMSEGDLLEGINNIVTPDKRDD
MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVEIDEPDSPTENSDFSWHKPEALSFGQMSEGDLLEGINNIVTPDKRDD
MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVEIDEPDSPTENSDFSWHKPEALSFGQMSEGDLLEGINNIVTPDKRDD

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

Original result of BLAST against C. L. asiaticus genome

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

Original result of PSI-BLAST first 2 iterations

IdentityAlignment graphLength Definition Round E-value
Target122 DNA-directed RNA polymerase subunit omega [Candidatus L
315122350126 DNA-directed RNA polymerase subunit omega [Candidatus L 1 8e-50
222148077132 DNA-directed RNA polymerase subunit omega [Agrobacteriu 1 1e-35
222085385134 DNA-directed RNA polymerase, omega subunit [Agrobacteri 1 1e-34
159184585129 DNA-directed RNA polymerase subunit omega [Agrobacteriu 1 2e-34
240850191132 DNA-directed RNA polymerase subunit omega [Bartonella g 1 5e-34
325292408130 DNA-directed RNA polymerase subunit omega [Agrobacteriu 1 5e-34
49474060132 DNA-directed RNA polymerase subunit omega [Bartonella q 1 6e-34
241203883134 DNA-directed RNA polymerase subunit omega [Rhizobium le 1 8e-34
190891067134 DNA-directed RNA polymerase omega chain protein [Rhizob 1 9e-34
163867986132 DNA-directed RNA polymerase subunit omega [Bartonella t 1 1e-33
>gi|315122350|ref|YP_004062839.1| DNA-directed RNA polymerase subunit omega [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 126 Back     alignment and organism information
 Score =  199 bits (507), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 96/124 (77%), Positives = 109/124 (87%), Gaps = 4/124 (3%)

Query: 3   RTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDD 62
           R TVEDCIDKV+NRF LVLLAS+R RH+SQG+ PTV+VG DKNTV++LREIASG LSPDD
Sbjct: 2   RITVEDCIDKVENRFELVLLASYRARHISQGSPPTVEVGNDKNTVISLREIASGALSPDD 61

Query: 63  LEEDFIHSLQKHVEIDEPDSPTE----NSDFSWHKPEALSFGQMSEGDLLEGINNIVTPD 118
           LEEDFIHSLQ+HVE+DEPD+P E    N DF W+KPE+LSF QMSEGDLLEGI+NIV PD
Sbjct: 62  LEEDFIHSLQRHVEVDEPDTPVEDSDLNRDFPWNKPESLSFRQMSEGDLLEGIDNIVVPD 121

Query: 119 KRDD 122
           KRDD
Sbjct: 122 KRDD 125



Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222148077|ref|YP_002549034.1| DNA-directed RNA polymerase subunit omega [Agrobacterium vitis S4] Length = 132 Back     alignment and organism information
>gi|222085385|ref|YP_002543915.1| DNA-directed RNA polymerase, omega subunit [Agrobacterium radiobacter K84] Length = 134 Back     alignment and organism information
>gi|159184585|ref|NP_354052.2| DNA-directed RNA polymerase subunit omega [Agrobacterium tumefaciens str. C58] Length = 129 Back     alignment and organism information
>gi|240850191|ref|YP_002971584.1| DNA-directed RNA polymerase subunit omega [Bartonella grahamii as4aup] Length = 132 Back     alignment and organism information
>gi|325292408|ref|YP_004278272.1| DNA-directed RNA polymerase subunit omega [Agrobacterium sp. H13-3] Length = 130 Back     alignment and organism information
>gi|49474060|ref|YP_032102.1| DNA-directed RNA polymerase subunit omega [Bartonella quintana str. Toulouse] Length = 132 Back     alignment and organism information
>gi|241203883|ref|YP_002974979.1| DNA-directed RNA polymerase subunit omega [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 134 Back     alignment and organism information
>gi|190891067|ref|YP_001977609.1| DNA-directed RNA polymerase omega chain protein [Rhizobium etli CIAT 652] Length = 134 Back     alignment and organism information
>gi|163867986|ref|YP_001609190.1| DNA-directed RNA polymerase subunit omega [Bartonella tribocorum CIP 105476] Length = 132 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Original result of RPS-BLASTagainst CDD database part II

IdentityAlignment graphLength Definition E-value
Target122 DNA-directed RNA polymerase subunit omega [Candidatus L
PRK0039269 PRK00392, rpoZ, DNA-directed RNA polymerase subunit ome 1e-21
pfam0119257 pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6 2e-09
TIGR0069059 TIGR00690, rpoZ, DNA-directed RNA polymerase, omega sub 5e-09
COG175874 COG1758, RpoZ, DNA-directed RNA polymerase, subunit K/o 2e-15
>gnl|CDD|178998 PRK00392, rpoZ, DNA-directed RNA polymerase subunit omega; Reviewed Back     alignment and domain information
>gnl|CDD|144692 pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6 Back     alignment and domain information
>gnl|CDD|161999 TIGR00690, rpoZ, DNA-directed RNA polymerase, omega subunit Back     alignment and domain information
>gnl|CDD|31944 COG1758, RpoZ, DNA-directed RNA polymerase, subunit K/omega [Transcription] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

Original result of HHsearch against CDD database

IdentityAlignment graphLength Definition Probability
Target 122 DNA-directed RNA polymerase subunit omega [Candidatus L
PRK02756128 DNA-directed RNA polymerase subunit omega; Provisional 100.0
PRK01481127 rpoZ DNA-directed RNA polymerase subunit omega; Provisi 100.0
PRK0039287 rpoZ DNA-directed RNA polymerase subunit omega; Reviewe 100.0
PRK0447499 DNA-directed RNA polymerase subunit omega; Provisional 99.97
PRK0495191 rpoZ DNA-directed RNA polymerase subunit omega; Validat 99.97
PRK0212867 DNA-directed RNA polymerase subunit omega; Provisional 99.97
PRK0042569 rpoZ DNA-directed RNA polymerase subunit omega; Reviewe 99.88
PRK0254498 DNA-directed RNA polymerase subunit omega; Provisional 99.87
COG175874 RpoZ DNA-directed RNA polymerase, subunit K/omega [Tran 99.8
PRK0295089 DNA-directed RNA polymerase subunit omega; Provisional 99.7
pfam0119257 RNA_pol_Rpb6 RNA polymerase Rpb6. Rpb6 is an essential 99.59
PRK0385373 DNA-directed RNA polymerase subunit omega; Provisional 99.46
PRK0181467 rpoZ DNA-directed RNA polymerase subunit omega; Validat 99.44
TIGR0069073 rpoZ DNA-directed RNA polymerase, omega subunit; InterP 98.92
PRK01099106 rpoK DNA-directed RNA polymerase subunit K; Provisional 96.7
PRK0372157 rpoK DNA-directed RNA polymerase subunit K; Provisional 95.9
PRK0116861 rpoK DNA-directed RNA polymerase subunit K; Provisional 95.9
KOG3405136 consensus 94.55
>PRK02756 DNA-directed RNA polymerase subunit omega; Provisional Back     alignment and domain information
>PRK01481 rpoZ DNA-directed RNA polymerase subunit omega; Provisional Back     alignment and domain information
>PRK00392 rpoZ DNA-directed RNA polymerase subunit omega; Reviewed Back     alignment and domain information
>PRK04474 DNA-directed RNA polymerase subunit omega; Provisional Back     alignment and domain information
>PRK04951 rpoZ DNA-directed RNA polymerase subunit omega; Validated Back     alignment and domain information
>PRK02128 DNA-directed RNA polymerase subunit omega; Provisional Back     alignment and domain information
>PRK00425 rpoZ DNA-directed RNA polymerase subunit omega; Reviewed Back     alignment and domain information
>PRK02544 DNA-directed RNA polymerase subunit omega; Provisional Back     alignment and domain information
>COG1758 RpoZ DNA-directed RNA polymerase, subunit K/omega [Transcription] Back     alignment and domain information
>PRK02950 DNA-directed RNA polymerase subunit omega; Provisional Back     alignment and domain information
>pfam01192 RNA_pol_Rpb6 RNA polymerase Rpb6 Back     alignment and domain information
>PRK03853 DNA-directed RNA polymerase subunit omega; Provisional Back     alignment and domain information
>PRK01814 rpoZ DNA-directed RNA polymerase subunit omega; Validated Back     alignment and domain information
>TIGR00690 rpoZ DNA-directed RNA polymerase, omega subunit; InterPro: IPR003716 Bacterial DNA-dependent RNA polymerase (RNAP) has the core composition of alpha(2)-beta-beta'-omega, where omega is the smallest of the subunits Back     alignment and domain information
>PRK01099 rpoK DNA-directed RNA polymerase subunit K; Provisional Back     alignment and domain information
>PRK03721 rpoK DNA-directed RNA polymerase subunit K; Provisional Back     alignment and domain information
>PRK01168 rpoK DNA-directed RNA polymerase subunit K; Provisional Back     alignment and domain information
>KOG3405 consensus Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

Original result of PSI-BLAST

IdentityAlignment graphLength Definition E-value
Target122 DNA-directed RNA polymerase subunit omega [Candidatus L
3lu0_E91 Molecular Model Of Escherichia Coli Core Rna Polyme 5e-15
3iyd_E90 Three-Dimensional Em Structure Of An Intact Activat 6e-14
gi|307776499|pdb|3LU0|E Chain E, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 91 Back     alignment and structure 
 Score = 84.1 bits (207), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 30/65 (46%), Positives = 41/65 (63%), Gaps = 1/65 (1%)

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

Query: 60 PDDLE 64
             L+
Sbjct: 61 NQILD 65
>gi|266618719|pdb|3IYD|E Chain E, Three-Dimensional Em Structure Of An Intact Activator- Dependent Transcription Initiation Complex Length = 90 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

IdentityAlignment graphLength Definition E-value
Target122 DNA-directed RNA polymerase subunit omega [Candidatus L
3lu0_E91 DNA-directed RNA polymerase subunit omega; E. coli RNA 3e-22
3iyd_E90 DNA-directed RNA polymerase subunit omega; transcriptio 1e-20
>3lu0_E DNA-directed RNA polymerase subunit omega; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_E* Length = 91 Back     alignment and structure
 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 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

Original result of HHsearch against PDB70 database

IdentityAlignment graphLength Definition Probability
Target122 DNA-directed RNA polymerase subunit omega [Candidatus L
3lu0_E91 DNA-directed RNA polymerase subunit omega; E. coli RNA 99.96
3h0g_F142 DNA-directed RNA polymerases I, II, and III subunit rpa 97.57
1twf_F155 ABC23, DNA-directed RNA polymerases I, II, and III 23 k 97.54
1qkl_A127 RPB6, DNA-directed RNA polymerase II 14.4 KD polypeptid 97.47
2waq_K95 DNA-directed RNA polymerase RPO6 subunit; multi-subunit 97.14
2a6h_E99 RNA polymerase omega chain; RNA polymerase holoenzyme, 96.72
>3lu0_E DNA-directed RNA polymerase subunit omega; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_E* Back     alignment and structure
Probab=99.96  E-value=1.4e-30  Score=191.28  Aligned_cols=64  Identities=47%  Similarity=0.733  Sum_probs=60.8

Q ss_pred             CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCC-CCCCCCCCCCCHHHHHHHHHCCCCCHHHHH
Q ss_conf             9600089985128789999999999999985788-776774468541156756540587999999
Q gi|254780937|r    1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGA-KPTVDVGKDKNTVVALREIASGTLSPDDLE   64 (122)
Q Consensus         1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~-~~~v~~~ndK~~ViALREIa~gki~~~~l~   64 (122)
                      ||||||||||+||+|||.||++||||||||+.|+ +|+++.+||||+|+||||||+|||+++.+.
T Consensus         1 MARvtVEDcl~kv~nRy~LV~lAakRARql~~g~~~~~~~~~~~K~~viALrEIa~gki~~~~l~   65 (91)
T 3lu0_E            1 MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILD   65 (91)
T ss_dssp             -CCTTHHHHHHHSSSHHHHHHHHHHHHHHHHHTCCCSCCSSSCCCSSCCSHHHHHSSSCEEESSS
T ss_pred             CCEEEHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHCC
T ss_conf             97132999988547796999999999999984898886787689607899999990897677623
>3h0g_F DNA-directed RNA polymerases I, II, and III subunit rpabc2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>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* ... Back     alignment and structure
>1qkl_A RPB6, DNA-directed RNA polymerase II 14.4 KD polypeptide; transcription; NMR {Homo sapiens} SCOP: a.143.1.2 Back     alignment and structure
>2waq_K DNA-directed RNA polymerase RPO6 subunit; multi-subunit, transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_I 2pmz_K 3hkz_K Back     alignment and structure
>2a6h_E RNA polymerase omega chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.143.1.1 PDB: 1smy_E* 1zyr_E* 1iw7_E* 2a69_E* 2a6e_E 2a68_E* 2be5_E* 2cw0_E 3dxj_E* 2o5i_E 2o5j_E* 2ppb_E* 3eql_E* 1ynj_K* 1i6v_E* 1l9u_E 1l9z_E 1hqm_E* 1ynn_K* Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

IdentityAlignment graphLength Definition Probability
Target122 DNA-directed RNA polymerase subunit omega [Candidatus L
d1twff_84 RPB6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 97.54
d1qkla_127 RPB6 {Human (Homo sapiens) [TaxId: 9606]} 97.49
d1smye_95 RNA polymerase omega subunit {Thermus thermophilus [Tax 96.15
>d1twff_ a.143.1.2 (F:) RPB6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.54  E-value=6.4e-05  Score=45.46  Aligned_cols=47  Identities=17%  Similarity=0.294  Sum_probs=41.3

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHH-HHHHHHHCCCCCH
Q ss_conf             7899999999999999857887767744685411-5675654058799
Q gi|254780937|r   14 DNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTV-VALREIASGTLSP   60 (122)
Q Consensus        14 ~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~V-iALREIa~gki~~   60 (122)
                      =++|+..-+-+.||.||+.|++|+|+.++..+++ ||..|.-.|++-+
T Consensus        14 LTkYE~ariiG~Ra~Ql~~Ga~p~I~~~~~~d~~~IA~~El~~~kiP~   61 (84)
T d1twff_          14 MTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPL   61 (84)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCCCSSCCSSCCSHHHHHHHHHHTTCCCE
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCE
T ss_conf             229999999999999997699824547888799999999998399877
>d1qkla_ a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1smye_ a.143.1.1 (E:) RNA polymerase omega subunit {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against MMDB70 database

IdentityAlignment graphLength Definition E-value
Target 122 DNA-directed RNA polymerase subunit omega [Candida
3iyd_E_90 (E:) DNA-directed RNA polymerase subunit omega; tr 9e-21
2a6h_E_1-7777 (E:1-77) RNA polymerase omega chain; RNA polymeras 3e-18
>3iyd_E (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 Back     alignment and structure
 Score = 93.6 bits (233), Expect = 9e-21
 Identities = 31/81 (38%), Positives = 45/81 (55%), Gaps = 4/81 (4%)

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

Query: 61 DDLEEDFIHSLQKHVEIDEPD 81
            L+       Q+  E +  +
Sbjct: 61 QILDVR---ERQEQQEQEAAE 78
>2a6h_E (E:1-77) RNA polymerase omega chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus}Length = 77 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

Original result of HHsearch against MMDB70 database

IdentityAlignment graphLength Definition Probability
Target122 DNA-directed RNA polymerase subunit omega [Candidatus L
2a6h_E_1-7777 RNA polymerase omega chain; RNA polymerase holoenz 99.84
3iyd_E_90 DNA-directed RNA polymerase subunit omega; transcr 99.83
3h0g_F_142 DNA-directed RNA polymerases I, II, and III subuni 97.27
1twf_F_155 ABC23, DNA-directed RNA polymerases I, II, and III 97.23
1qkl_A_127 RPB6, DNA-directed RNA polymerase II 14.4 KD polyp 97.1
2waq_K_27-9569 DNA-directed RNA polymerase RPO6 subunit; multi-su 96.74
>2a6h_E (E:1-77) RNA polymerase omega chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} Back     alignment and structure
Probab=99.84  E-value=1.6e-21  Score=141.25  Aligned_cols=61  Identities=18%  Similarity=0.322  Sum_probs=57.0

Q ss_pred             CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCC---------------CCCCCHHHHHHHHHCCCCCHH
Q ss_conf             9600089985128789999999999999985788776774---------------468541156756540587999
Q gi|254780937|r    1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDV---------------GKDKNTVVALREIASGTLSPD   61 (122)
Q Consensus         1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~---------------~ndK~~ViALREIa~gki~~~   61 (122)
                      |+|.++++|++||+|||.||++||+|||||++|++|+++.               +++|++++||+|||+|+|+++
T Consensus         1 M~~psid~ll~kv~srY~Lvi~aAKRArql~~g~~~~~~~~~~~~~~~~~~~~~~~~~Kpv~~Al~EIa~gkv~~~   76 (77)
T 2a6h_E            1 MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGRLVFG   76 (77)
T ss_dssp             -CCTTHHHHHHHSSSHHHHHHHHHHHHHHHHHTCTTCCSCCSSSCCCCSSSSGGGTSSCSHHHHHHHHTTTCCEEE
T ss_pred             CCCCCHHHHHHCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCEEEC
T ss_conf             9863577886224442244135389899998716985636965625564025567997588999999873735533
>3iyd_E (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} Back     alignment and structure
>3h0g_F (F:) DNA-directed RNA polymerases I, II, and III subunit rpabc2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1twf_F (F:) ABC23, DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} Back     alignment and structure
>1qkl_A (A:) RPB6, DNA-directed RNA polymerase II 14.4 KD polypeptide; transcription; NMR {Homo sapiens} Back     alignment and structure
>2waq_K (K:27-95) DNA-directed RNA polymerase RPO6 subunit; multi-subunit, transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_I 2pmz_K 3hkz_K Back     alignment and structure