254780391

254780391

DNA polymerase III subunit chi

GeneID in NCBI database:8209376Locus tag:CLIBASIA_01380
Protein GI in NCBI database:254780391Protein Accession:YP_003064804.1
Gene range:-(290437, 290862)Protein Length:141aa
Gene description:DNA polymerase III subunit chi
COG prediction:[L] DNA polymerase III, chi subunit
KEGG prediction:DNA polymerase III subunit chi; K02339 DNA polymerase III subunit chi [EC:2.7.7.7]
SEED prediction:DNA polymerase III chi subunit (EC 2.7.7.7)
Pathway involved in KEGG:Purine metabolism [PATH:las00230]
Pyrimidine metabolism [PATH:las00240]
DNA replication [PATH:las03030]
Mismatch repair [PATH:las03430]
Homologous recombination [PATH:las03440]
Subsystem involved in SEED:DNA-replication
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
TOPPRED1 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-------130-------140-
MRTLLFYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDVI
ccEEEEEEEcccHHHHHHHHHHHHHHcccEEEEEEccHHHHHHHHHHcccccccccccccccccccccccccccEEEEcccccccccEEEEEEEcccccHHHHHcccEEEEEEccccHHHHHHHHHHHHHHHHcccccccc
cccEEEEcccccHHHHHHHHHHHHHHcccEEEEEEccHHHHHHHHHHHcccccHccccccccccccccccccccEEEEccccccccccEEEEEccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHcccccccc
MRTLLFYRFKNDWEYNLLVLLQDEyekgkrvsvqcgsERVRDSLNEYLWTWkkdgflphgvdvgdegdfssfqpVLLTISSLNANTSTIRFLVDEAsmhigdvdyYEKVVFIINtddqgslewGRAHWRSLknsgyapdvi
mrtllfyrfkndweyNLLVLLQDeyekgkrvsvqcgservRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWrslknsgyapdvi
MRTLLFYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDVI
MRTLLFYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDVI
MRTLLFYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDVI
*RTLLFYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDVI
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MRTLLFYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDVI
MRTLLFYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDVI
MRTLLFYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDVI

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

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

IdentityAlignment graphLength Definition Round E-value
Target141 DNA polymerase III subunit chi [Candidatus Liberibacter
315122197141 DNA polymerase III subunit chi [Candidatus Liberibacter 1 4e-51
209548674149 DNA polymerase III subunit chi [Rhizobium leguminosarum 1 5e-24
327188013149 DNA polymerase III subunit chi [Rhizobium etli CNPAF512 1 5e-24
218509824149 DNA polymerase III subunit chi [Rhizobium etli Brasil 5 1 1e-23
190891139149 DNA polymerase III protein, chi subunit [Rhizobium etli 1 1e-23
241203952149 DNA polymerase III subunit chi [Rhizobium leguminosarum 1 4e-23
116251338149 DNA polymerase III subunit chi [Rhizobium leguminosarum 1 1e-22
86357095149 DNA polymerase III subunit chi [Rhizobium etli CFN 42] 1 1e-22
218459999149 DNA polymerase III subunit chi [Rhizobium etli Kim 5] L 1 2e-22
222085456149 DNA polymerase III [Agrobacterium radiobacter K84] Leng 1 6e-21
>gi|315122197|ref|YP_004062686.1| DNA polymerase III subunit chi [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 141 Back     alignment and organism information
 Score =  204 bits (519), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 86/136 (63%), Positives = 117/136 (86%)

Query: 1   MRTLLFYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHG 60
           M   LF RFK++W+ + L+LL+ EY+ G R+S+QCGSER+RD+LNE LWTWKKD F+PHG
Sbjct: 1   MTDFLFCRFKHNWQNDFLILLESEYQNGLRISIQCGSERIRDALNERLWTWKKDSFMPHG 60

Query: 61  VDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGS 120
           +DVG+E   +SFQP+LLT+SS NAN S +RF VD+ASMHIGD+D+Y+K++FII+TDDQ S
Sbjct: 61  IDVGEEEALASFQPILLTVSSNNANASMVRFFVDQASMHIGDMDHYKKIIFIIDTDDQAS 120

Query: 121 LEWGRAHWRSLKNSGY 136
           L+WGRA+W++LK++GY
Sbjct: 121 LKWGRANWKNLKSNGY 136


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|209548674|ref|YP_002280591.1| DNA polymerase III subunit chi [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 149 Back     alignment and organism information
>gi|327188013|gb|EGE55243.1| DNA polymerase III subunit chi [Rhizobium etli CNPAF512] Length = 149 Back     alignment and organism information
>gi|218509824|ref|ZP_03507702.1| DNA polymerase III subunit chi [Rhizobium etli Brasil 5] Length = 149 Back     alignment and organism information
>gi|190891139|ref|YP_001977681.1| DNA polymerase III protein, chi subunit [Rhizobium etli CIAT 652] Length = 149 Back     alignment and organism information
>gi|241203952|ref|YP_002975048.1| DNA polymerase III subunit chi [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 149 Back     alignment and organism information
>gi|116251338|ref|YP_767176.1| DNA polymerase III subunit chi [Rhizobium leguminosarum bv. viciae 3841] Length = 149 Back     alignment and organism information
>gi|86357095|ref|YP_468987.1| DNA polymerase III subunit chi [Rhizobium etli CFN 42] Length = 149 Back     alignment and organism information
>gi|218459999|ref|ZP_03500090.1| DNA polymerase III subunit chi [Rhizobium etli Kim 5] Length = 149 Back     alignment and organism information
>gi|222085456|ref|YP_002543986.1| DNA polymerase III [Agrobacterium radiobacter K84] Length = 149 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

IdentityAlignment graphLength Definition E-value
Target141 DNA polymerase III subunit chi [Candidatus Liberibacter
PRK05728142 PRK05728, PRK05728, DNA polymerase III subunit chi; Val 3e-20
COG2927144 COG2927, HolC, DNA polymerase III, chi subunit [DNA rep 5e-16
pfam04364136 pfam04364, DNA_pol3_chi, DNA polymerase III chi subunit 9e-22
>gnl|CDD|180224 PRK05728, PRK05728, DNA polymerase III subunit chi; Validated Back     alignment and domain information
>gnl|CDD|32751 COG2927, HolC, DNA polymerase III, chi subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|146811 pfam04364, DNA_pol3_chi, DNA polymerase III chi subunit, HolC Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 141 DNA polymerase III subunit chi [Candidatus Liberibacter
PRK05728143 DNA polymerase III subunit chi; Validated 100.0
pfam04364136 DNA_pol3_chi DNA polymerase III chi subunit, HolC. The 100.0
COG2927144 HolC DNA polymerase III, chi subunit [DNA replication, 100.0
PRK06646154 DNA polymerase III subunit chi; Provisional 100.0
TIGR00963 904 secA preprotein translocase, SecA subunit; InterPro: IP 91.68
cd00079131 HELICc Helicase superfamily c-terminal domain; associat 91.42
>PRK05728 DNA polymerase III subunit chi; Validated Back     alignment and domain information
>pfam04364 DNA_pol3_chi DNA polymerase III chi subunit, HolC Back     alignment and domain information
>COG2927 HolC DNA polymerase III, chi subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK06646 DNA polymerase III subunit chi; Provisional Back     alignment and domain information
>TIGR00963 secA preprotein translocase, SecA subunit; InterPro: IPR000185 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway Back     alignment and domain information
>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process 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

IdentityAlignment graphLength Definition E-value
Target141 DNA polymerase III subunit chi [Candidatus Liberibacter
1em8_A147 Crystal Structure Of Chi And Psi Subunit Heterodime 2e-21
gi|34810156|pdb|1EM8|A Chain A, Crystal Structure Of Chi And Psi Subunit Heterodimer From Dna Pol Iii Length = 147 Back     alignment and structure
 Score =  106 bits (264), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 27/148 (18%), Positives = 55/148 (37%), Gaps = 13/148 (8%)

Query: 1   MRTLLFYRFKND--------WEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWK 52
           M+   FY   ND         E  +  +  + +  GKRV + C  E+    L+E LW   
Sbjct: 1   MKNATFYLLDNDTTVDGLSAVEQLVCEIAAERWRSGKRVLIACEDEKQAYRLDEALWARP 60

Query: 53  KDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFI 112
            + F+PH +        +   PV +       ++S    L+   +        + +VV  
Sbjct: 61  AESFVPHNLAGEGPRGGA---PVEIAW-PQKRSSSRRDILISLRTSFADFATAFTEVVD- 115

Query: 113 INTDDQGSLEWGRAHWRSLKNSGYAPDV 140
               +    +  R  +++ + +G+  + 
Sbjct: 116 FVPYEDSLKQLARERYKAYRVAGFNLNT 143


Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target141 DNA polymerase III subunit chi [Candidatus Liberibacter
1em8_A147 DNA polymerase III CHI subunit; DNA POL III, heterodime 2e-19
>1em8_A DNA polymerase III CHI subunit; DNA POL III, heterodimer, clamp-loader, alpha-beta fold, gene regulation; HET: DNA; 2.10A {Escherichia coli} SCOP: c.128.1.1 Length = 147 Back     alignment and structure
 Score = 90.3 bits (224), Expect = 2e-19
 Identities = 27/146 (18%), Positives = 55/146 (37%), Gaps = 13/146 (8%)

Query: 1   MRTLLFYRFKNDWEYNLLV--------LLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWK 52
           M+   FY   ND   + L         +  + +  GKRV + C  E+    L+E LW   
Sbjct: 1   MKNATFYLLDNDTTVDGLSAVEQLVCEIAAERWRSGKRVLIACEDEKQAYRLDEALWARP 60

Query: 53  KDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFI 112
            + F+PH +            PV +      +++     L+   +        + +VV  
Sbjct: 61  AESFVPHNLAGEGP---RGGAPVEIAWPQKRSSSRRDI-LISLRTSFADFATAFTEVVDF 116

Query: 113 INTDDQGSLEWGRAHWRSLKNSGYAP 138
           +  +D    +  R  +++ + +G+  
Sbjct: 117 VPYEDS-LKQLARERYKAYRVAGFNL 141


Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target141 DNA polymerase III subunit chi [Candidatus Liberibacter
1em8_A147 DNA polymerase III CHI subunit; DNA POL III, heterodime 100.0
>1em8_A DNA polymerase III CHI subunit; DNA POL III, heterodimer, clamp-loader, alpha-beta fold, gene regulation; HET: DNA; 2.10A {Escherichia coli} SCOP: c.128.1.1 Back     alignment and structure
Probab=100.00  E-value=8.7e-41  Score=264.98  Aligned_cols=135  Identities=19%  Similarity=0.368  Sum_probs=120.0

Q ss_pred             CCEEEEEECCCC--------HHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             982799631674--------899999999999977984999829989999999985218823331332247776544422
Q gi|254780391|r    1 MRTLLFYRFKND--------WEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSF   72 (141)
Q Consensus         1 Mt~v~FY~l~~~--------~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~   72 (141)
                      ||+|+||++.++        .+.++|||++|+|++|+|++|+|+|+++++.||++||+|+++|||||++.+++.   ...
T Consensus         1 M~~~~FY~l~~~~~~~~l~~~~~~~crL~~K~~~~g~ri~I~~~d~~~a~~LD~~LWt~~~~sFlPH~i~~~~~---~~~   77 (147)
T 1em8_A            1 MKNATFYLLDNDTTVDGLSAVEQLVCEIAAERWRSGKRVLIACEDEKQAYRLDEALWARPAESFVPHNLAGEGP---RGG   77 (147)
T ss_dssp             CEEEEEEECSCCCCBTTBCHHHHHHHHHHHHHHHTTCCEEEECSSHHHHHHHHHHHHHCSTTCCCCEEETTCSS---TTC
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCEEEECCCCCCCC---CCC
T ss_conf             98269998579855667768999999999999977997999949999999999998679988585244378886---467


Q ss_pred             CEEEEECCCCCCCCCCEEEEEECCCCCCCHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             06998328667899819999816877821131175799997598989999999999999988998603
Q gi|254780391|r   73 QPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDV  140 (141)
Q Consensus        73 ~PV~i~~~~~~~~~~~~~~linl~~~~p~~~~~f~rvieiv~~~d~~~~~~aR~rwk~yk~~G~~~~~  140 (141)
                      +||+|+++...++. ..++|||+++..|+++++|+||+|||+ +|++.|+.||+|||+||++||+++.
T Consensus        78 ~pI~l~~~~~~~~~-~~~vliNl~~~~p~~~~~f~Rvieiv~-~de~~~~~aR~r~k~yk~~G~~i~~  143 (147)
T 1em8_A           78 APVEIAWPQKRSSS-RRDILISLRTSFADFATAFTEVVDFVP-YEDSLKQLARERYKAYRVAGFNLNT  143 (147)
T ss_dssp             CSEEEECTTSCCCS-CCSEEEECCSSCCGGGGGCSEEEEEEC-SSHHHHHHHHHHHHHHHHTTEEEEE
T ss_pred             CCEEEECCCCCCCC-CCEEEEECCCCCCCCCCCCCEEEEEEC-CCHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             99674068767876-674999899878312146788999969-8999999999999999987998605




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

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

IdentityAlignment graphLength Definition E-value
Target 141 DNA polymerase III subunit chi [Candidatus Liberibacter
d1em8a_147 c.128.1.1 (A:) DNA polymerase III chi subunit {Escheric 3e-18
>d1em8a_ c.128.1.1 (A:) DNA polymerase III chi subunit {Escherichia coli [TaxId: 562]} Length = 147 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: DNA polymerase III chi subunit
superfamily: DNA polymerase III chi subunit
family: DNA polymerase III chi subunit
domain: DNA polymerase III chi subunit
species: Escherichia coli [TaxId: 562]
 Score = 84.6 bits (209), Expect = 3e-18
 Identities = 27/145 (18%), Positives = 55/145 (37%), Gaps = 13/145 (8%)

Query: 1   MRTLLFYRFKNDWEYNLLV--------LLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWK 52
           M+   FY   ND   + L         +  + +  GKRV + C  E+    L+E LW   
Sbjct: 1   MKNATFYLLDNDTTVDGLSAVEQLVCEIAAERWRSGKRVLIACEDEKQAYRLDEALWARP 60

Query: 53  KDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFI 112
            + F+PH +            PV +      +++     L+   +        + +VV  
Sbjct: 61  AESFVPHNL---AGEGPRGGAPVEIAWPQKRSSSRRD-ILISLRTSFADFATAFTEVVDF 116

Query: 113 INTDDQGSLEWGRAHWRSLKNSGYA 137
           +  +D    +  R  +++ + +G+ 
Sbjct: 117 VPYEDS-LKQLARERYKAYRVAGFN 140


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

IdentityAlignment graphLength Definition Probability
Target141 DNA polymerase III subunit chi [Candidatus Liberibacter
d1em8a_147 DNA polymerase III chi subunit {Escherichia coli [TaxId 100.0
d1s2ma2171 Putative ATP-dependent RNA helicase DHH1 {Baker's yeast 93.89
>d1em8a_ c.128.1.1 (A:) DNA polymerase III chi subunit {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: DNA polymerase III chi subunit
superfamily: DNA polymerase III chi subunit
family: DNA polymerase III chi subunit
domain: DNA polymerase III chi subunit
species: Escherichia coli [TaxId: 562]
Probab=100.00  E-value=3.8e-41  Score=265.72  Aligned_cols=135  Identities=19%  Similarity=0.368  Sum_probs=120.5

Q ss_pred             CCEEEEEECCCC--------HHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             982799631674--------899999999999977984999829989999999985218823331332247776544422
Q gi|254780391|r    1 MRTLLFYRFKND--------WEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSF   72 (141)
Q Consensus         1 Mt~v~FY~l~~~--------~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~   72 (141)
                      ||+|+||+|.++        .+.++|||++|+|++|+|++|+|+|+++++.||++||+|+++|||||++.+++.   ...
T Consensus         1 Mt~v~FY~L~~~~~~~~l~~~~~~~crL~~K~~~~g~ri~I~~~d~~~~~~lD~~LWt~~~~sFiPH~~~~~~~---~~~   77 (147)
T d1em8a_           1 MKNATFYLLDNDTTVDGLSAVEQLVCEIAAERWRSGKRVLIACEDEKQAYRLDEALWARPAESFVPHNLAGEGP---RGG   77 (147)
T ss_dssp             CEEEEEEECSCCCCBTTBCHHHHHHHHHHHHHHHTTCCEEEECSSHHHHHHHHHHHHHCSTTCCCCEEETTCSS---TTC
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCC---CCC
T ss_conf             98269998579865667778999999999999977997999939999999999998579974364433367886---678


Q ss_pred             CEEEEECCCCCCCCCCEEEEEECCCCCCCHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             06998328667899819999816877821131175799997598989999999999999988998603
Q gi|254780391|r   73 QPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDV  140 (141)
Q Consensus        73 ~PV~i~~~~~~~~~~~~~~linl~~~~p~~~~~f~rvieiv~~~d~~~~~~aR~rwk~yk~~G~~~~~  140 (141)
                      +||+|++....++.. .++|||+++..|+++++|+|++|||+ +|++.++.||+|||+||++||+++.
T Consensus        78 ~PI~l~~~~~~~~~~-~dvlinl~~~~p~~~~~f~Rvieiv~-~de~~~~~aR~rwk~yk~~G~~l~~  143 (147)
T d1em8a_          78 APVEIAWPQKRSSSR-RDILISLRTSFADFATAFTEVVDFVP-YEDSLKQLARERYKAYRVAGFNLNT  143 (147)
T ss_dssp             CSEEEECTTSCCCSC-CSEEEECCSSCCGGGGGCSEEEEEEC-SSHHHHHHHHHHHHHHHHTTEEEEE
T ss_pred             CCEEECCCCCCCCCC-CEEEEECCCCCCHHHHCCCEEEEEEC-CCHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             988723787778866-62999999989403213388999979-6999999999999999987998611



>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 141 DNA polymerase III subunit chi [Candidatus Liberib
1em8_A_147 (A:) DNA polymerase III CHI subunit; DNA POL III, 5e-22
>1em8_A (A:) DNA polymerase III CHI subunit; DNA POL III, heterodimer, clamp-loader, alpha-beta fold, gene regulation; HET: DNA; 2.10A {Escherichia coli}Length = 147 Back     alignment and structure
 Score = 97.6 bits (243), Expect = 5e-22
 Identities = 26/146 (17%), Positives = 54/146 (36%), Gaps = 13/146 (8%)

Query: 1   MRTLLFYRFKNDWEYNLLV--------LLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWK 52
           M+   FY   ND   + L         +  + +  GKRV + C  E+    L+E LW   
Sbjct: 1   MKNATFYLLDNDTTVDGLSAVEQLVCEIAAERWRSGKRVLIACEDEKQAYRLDEALWARP 60

Query: 53  KDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFI 112
            + F+PH +            PV +      +++     +    +        + +VV  
Sbjct: 61  AESFVPHNL---AGEGPRGGAPVEIAWPQKRSSSRRDILISL-RTSFADFATAFTEVVDF 116

Query: 113 INTDDQGSLEWGRAHWRSLKNSGYAP 138
           +  +D    +  R  +++ + +G+  
Sbjct: 117 VPYEDS-LKQLARERYKAYRVAGFNL 141


Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target141 DNA polymerase III subunit chi [Candidatus Liberibacter
1em8_A_147 DNA polymerase III CHI subunit; DNA POL III, heter 100.0
1nkt_A_427-523_579-641160 Preprotein translocase SECA 1 subunit; preprotein 94.38
1c4o_A_410-664 255 DNA nucleotide excision repair enzyme UVRB; uvrabc 94.19
>1em8_A (A:) DNA polymerase III CHI subunit; DNA POL III, heterodimer, clamp-loader, alpha-beta fold, gene regulation; HET: DNA; 2.10A {Escherichia coli} Back     alignment and structure
Probab=100.00  E-value=4.5e-41  Score=267.65  Aligned_cols=135  Identities=19%  Similarity=0.355  Sum_probs=122.4

Q ss_pred             CCEEEEEECCC--------CHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             98279963167--------4899999999999977984999829989999999985218823331332247776544422
Q gi|254780391|r    1 MRTLLFYRFKN--------DWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSF   72 (141)
Q Consensus         1 Mt~v~FY~l~~--------~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~   72 (141)
                      ||+|+||+|.+        ....++|+|++|++++|+|++|+|+|.++++.||++||+|+++|||||++.+++   ..+.
T Consensus         1 Mt~v~FY~L~~~~~~~~l~~~~~~~c~L~~k~~~~g~rv~I~~~d~~~a~~lD~~LW~~~~~sFiPH~~~~~~---~~~~   77 (147)
T 1em8_A            1 MKNATFYLLDNDTTVDGLSAVEQLVCEIAAERWRSGKRVLIACEDEKQAYRLDEALWARPAESFVPHNLAGEG---PRGG   77 (147)
T ss_dssp             CEEEEEEECSCCCCBTTBCHHHHHHHHHHHHHHHTTCCEEEECSSHHHHHHHHHHHHHCSTTCCCCEEETTCS---STTC
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCC---CCCC
T ss_conf             9846999857986566566799999999999997699799985999999999999629999866189868888---7778


Q ss_pred             CEEEEECCCCCCCCCCEEEEEECCCCCCCHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             06998328667899819999816877821131175799997598989999999999999988998603
Q gi|254780391|r   73 QPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDV  140 (141)
Q Consensus        73 ~PV~i~~~~~~~~~~~~~~linl~~~~p~~~~~f~rvieiv~~~d~~~~~~aR~rwk~yk~~G~~~~~  140 (141)
                      +||+|+++.+.++.+. ++|||+++..|+++++|+||+||| ++|++.|+.||+|||+||++||++++
T Consensus        78 ~PV~i~~~~~~~~~~~-~vliNl~~~~~~~~~~f~rvie~v-~~d~~~~~~aR~r~k~Yr~~G~~l~~  143 (147)
T 1em8_A           78 APVEIAWPQKRSSSRR-DILISLRTSFADFATAFTEVVDFV-PYEDSLKQLARERYKAYRVAGFNLNT  143 (147)
T ss_dssp             CSEEEECTTSCCCSCC-SEEEECCSSCCGGGGGCSEEEEEE-CSSHHHHHHHHHHHHHHHHTTEEEEE
T ss_pred             CCEEEECCCCCCCCCC-EEEEECCCCCCCHHCCCCEEEEEE-CCCHHHHHHHHHHHHHHHHCCCCCEE
T ss_conf             8878747877788777-199989988953110478899997-98989999999999999987997411



>1nkt_A (A:427-523,A:579-641) Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} Back     alignment and structure
>1c4o_A (A:410-664) DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hyperthermostable protein; HET: DNA BOG; 1.50A {Thermus thermophilus} Back     alignment and structure