Psyllid ID: psy3374

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--
Protein Sequence
IITGYRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFAS
Secondary Structure (PSIPRED)
cccccccccccccHHHHHHHHHHHHHHcccccccEEEEEEcccccccccccccccccccEEEEccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccHHHHHHHHHHHHHccccccccEEEEEEccccccccHHHccccccccEEEcccccccccc
Coil and Loop (DISEMBL)
iitgyrrgndstgvKDRVVNQLLTeldgvegleGVYVvgatsrpdiidpallrpgrlgssvhctmpdlafas
Flexible Loop (DISEMBL)
iitgyrrgndstgvkdRVVNQLLteldgveglEGVYVVGatsrpdiidpallrpgrlgssvhctmpdlafas
Low Complexity Region (SEG)
IITGYRRGNDSTGVKDRVVNQllteldgveglegvyvvgATSRPDIIDPALLRPGRLGSSVHCTMPDLAFAS
Disordered region (IsUnstruct)
**************KDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHC*********
Disordered Region (DISOPRED)
******************VNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD*****
Disordered Region (DISEMBL)
***********TGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFAS
Disordered Region (DISPRO)
***********TGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD*****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
IITGYRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFAS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	72	2.2.26 [Sep-21-2011]
O43933	1283	Peroxisome biogenesis fac	yes	N/A	0.861	0.048	0.774	1e-23
Q5BL07	1284	Peroxisome biogenesis fac	yes	N/A	0.861	0.048	0.774	4e-23
Q54GX5	1227	Peroxisome biogenesis fac	yes	N/A	0.875	0.051	0.714	9e-23
P46463	1157	Peroxisome biosynthesis p	yes	N/A	0.875	0.054	0.730	8e-22
P24004	1043	Peroxisomal ATPase PEX1 O	yes	N/A	0.847	0.058	0.721	2e-21
O74941	937	Peroxisomal ATPase pex1 O	yes	N/A	0.861	0.066	0.677	3e-21
Q9FNP1	1130	Peroxisome biogenesis pro	yes	N/A	0.847	0.053	0.688	2e-18
Q9SCN8	815	Cell division control pro	no	N/A	0.861	0.076	0.569	2e-15
P54774	807	Cell division cycle prote	no	N/A	0.805	0.071	0.586	8e-15
Q96372	805	Cell division cycle prote	N/A	N/A	0.805	0.072	0.586	8e-15

>sp|O43933|PEX1_HUMAN Peroxisome biogenesis factor 1 OS=Homo sapiens GN=PEX1 PE=1 SV=1

 Score =  107 bits (268), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 48/62 (77%), Positives = 55/62 (88%)

Query: 6    RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
            RRG+D+TGV DRVVNQLLT+LDGVEGL+GVYV+ ATSRPD+IDPALLRPGRL   V+C  
Sbjct: 948  RRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 1007

Query: 66   PD 67
            PD
Sbjct: 1008 PD 1009

Required for stability of PEX5 and protein import into the peroxisome matrix. Anchored by PEX26 to peroxisome membranes, possibly to form heteromeric AAA ATPase complexes required for the import of proteins into peroxisomes.
Homo sapiens (taxid: 9606)

>sp|Q5BL07|PEX1_MOUSE Peroxisome biogenesis factor 1 OS=Mus musculus GN=Pex1 PE=1 SV=2

 Score =  106 bits (265), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 48/62 (77%), Positives = 55/62 (88%)

Query: 6    RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
            RRG+D+TGV DRVVNQLLT+LDGVEGL+GVYV+ ATSRPD+IDPALLRPGRL   V+C  
Sbjct: 949  RRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 1008

Query: 66   PD 67
            PD
Sbjct: 1009 PD 1010

Required for stability of PEX5 and protein import into the peroxisome matrix. Anchored by PEX26 to peroxisome membranes, possibly to form heteromeric AAA ATPase complexes required for the import of proteins into peroxisomes.

Mus musculus (taxid: 10090)

>sp|Q54GX5|PEX1_DICDI Peroxisome biogenesis factor 1 OS=Dictyostelium discoideum GN=pex1 PE=3 SV=1

 Score =  105 bits (262), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 45/63 (71%), Positives = 55/63 (87%)

Query: 6    RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
            RRG+D++GV DRVVNQ LT+LDGVEGL GVYV+ ATSRPD+IDPALLRPGRL  S++C +
Sbjct: 974  RRGHDNSGVTDRVVNQFLTQLDGVEGLTGVYVLAATSRPDLIDPALLRPGRLDKSLYCNI 1033

Query: 66   PDL 68
            P+ 
Sbjct: 1034 PEF 1036

Involved in peroxisome biosynthesis.

Dictyostelium discoideum (taxid: 44689)

>sp|P46463|PEX1_PICPA Peroxisome biosynthesis protein PAS1 OS=Komagataella pastoris GN=PEX1 PE=3 SV=1

 Score =  102 bits (254), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 46/63 (73%), Positives = 54/63 (85%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
           +RG+DSTGV DRVVNQ+LT++DG EGL+GVYV+ ATSRPD+ID ALLRPGRL  SV C M
Sbjct: 907 KRGHDSTGVTDRVVNQMLTQMDGAEGLDGVYVLAATSRPDLIDSALLRPGRLDKSVICDM 966

Query: 66  PDL 68
           PD 
Sbjct: 967 PDF 969

Involved in peroxisome biosynthesis. May play a direct or indirect role in delivering membrane material to developing peroxisomes. It may also be involved in intracellular membrane movement.

Pichia pastoris (taxid: 4922)

>sp|P24004|PEX1_YEAST Peroxisomal ATPase PEX1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PEX1 PE=1 SV=2

 Score =  101 bits (251), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 44/61 (72%), Positives = 53/61 (86%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
           +RG+DSTGV DRVVNQLLT++DG EGL+GVY++ ATSRPD+ID ALLRPGRL  SV C +
Sbjct: 805 KRGHDSTGVTDRVVNQLLTQMDGAEGLDGVYILAATSRPDLIDSALLRPGRLDKSVICNI 864

Query: 66  P 66
           P
Sbjct: 865 P 865

Component of the peroxisomal protein import machinery. Together with PEX6, mediates the ATP-dependent relocation and recycling of the peroxisomal targeting signal-1 (PTS1) import receptor PEX5 from the peroxisomal membrane to the cytosol, where it is then available for another round of protein import into the organelle.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|O74941|PEX1_SCHPO Peroxisomal ATPase pex1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=pex1 PE=3 SV=1

 Score =  100 bits (249), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 42/62 (67%), Positives = 52/62 (83%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
           RRG DSTGV DRVVNQ+LT++DG E L+GVY+V AT+RPD+IDPALLRPGRL   + C +
Sbjct: 714 RRGQDSTGVTDRVVNQILTQMDGAESLDGVYIVAATTRPDMIDPALLRPGRLDKLIFCDL 773

Query: 66  PD 67
           P+
Sbjct: 774 PN 775

Component of the peroxisomal protein import machinery. Together with pex6, mediates the ATP-dependent relocation and recycling of the peroxisomal targeting signal-1 (PTS1) import receptor pex5 from the peroxisomal membrane to the cytosol, where it is then available for another round of protein import into the organelle.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q9FNP1|PEX1_ARATH Peroxisome biogenesis protein 1 OS=Arabidopsis thaliana GN=PEX1 PE=2 SV=2

 Score = 90.9 bits (224), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 42/61 (68%), Positives = 49/61 (80%)

Query: 6    RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
            +RG+D+TGV DRVVNQ LTELDGVE L GV+V  ATSRPD++DPALLRPGRL   + C  
Sbjct: 952  KRGHDNTGVTDRVVNQFLTELDGVEVLTGVFVFAATSRPDLLDPALLRPGRLDRLLLCDF 1011

Query: 66   P 66
            P
Sbjct: 1012 P 1012

Involved in PTS1- and PTS2-dependent protein import into peroxisomes. May form heteromeric AAA ATPase complexes required for the import of proteins.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SCN8|CD48D_ARATH Cell division control protein 48 homolog D OS=Arabidopsis thaliana GN=CDC48D PE=1 SV=1

 Score = 80.5 bits (197), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 37/65 (56%), Positives = 50/65 (76%), Gaps = 3/65 (4%)

Query: 6   RRGN---DSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVH 62
           +RGN   D+ G  DRV+NQLLTE+DG+   + V+++GAT+RPDIIDPALLRPGRL   ++
Sbjct: 589 QRGNSVGDAGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIIDPALLRPGRLDQLIY 648

Query: 63  CTMPD 67
             +PD
Sbjct: 649 IPLPD 653

Probably functions in cell division and growth processes. Interacts with certain SNAREs as part of specialized membrane fusion events where vesicles from the same organelle fuse (homotypic fusion).

Arabidopsis thaliana (taxid: 3702)

>sp|P54774|CDC48_SOYBN Cell division cycle protein 48 homolog OS=Glycine max GN=CDC48 PE=2 SV=1

 Score = 79.0 bits (193), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 34/58 (58%), Positives = 46/58 (79%)

Query: 10  DSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD 67
           D+ G  DRV+NQLLTE+DG+   + V+++GAT+RPDIIDPALLRPGRL   ++  +PD
Sbjct: 596 DAGGAADRVLNQLLTEMDGMSAKKTVFIIGATNRPDIIDPALLRPGRLDQLIYIPLPD 653

Probably functions in cell division and growth processes.

Glycine max (taxid: 3847)

>sp|Q96372|CDC48_CAPAN Cell division cycle protein 48 homolog OS=Capsicum annuum GN=CAFP PE=2 SV=1

 Score = 79.0 bits (193), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 34/58 (58%), Positives = 46/58 (79%)

Query: 10  DSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD 67
           D+ G  DRV+NQLLTE+DG+   + V+++GAT+RPDIIDPALLRPGRL   ++  +PD
Sbjct: 596 DAGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIIDPALLRPGRLDQLIYIPLPD 653

Probably functions in cell division and growth processes.

Capsicum annuum (taxid: 4072)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	72
443732886	1072	hypothetical protein CAPTEDRAFT_183010 [	0.847	0.056	0.803	2e-23
410910898	1120	PREDICTED: peroxisome biogenesis factor	0.875	0.056	0.793	4e-23
348513282	1221	PREDICTED: peroxisome biogenesis factor	0.875	0.051	0.793	1e-22
326921757	1263	PREDICTED: LOW QUALITY PROTEIN: peroxiso	0.888	0.050	0.75	3e-22
126341344	1250	PREDICTED: peroxisome biogenesis factor	0.861	0.049	0.790	3e-22
126341342	1290	PREDICTED: peroxisome biogenesis factor	0.861	0.048	0.790	3e-22
431908908	1323	Peroxisome biogenesis factor 1 [Pteropus	0.861	0.046	0.774	4e-22
395540081	1276	PREDICTED: peroxisome biogenesis factor	0.861	0.048	0.790	4e-22
281208808	1212	peroxisomal biogenesis factor 1 [Polysph	0.861	0.051	0.774	4e-22
440893433	1239	Peroxisome biogenesis factor 1, partial	0.888	0.051	0.765	4e-22

>gi|443732886|gb|ELU17449.1| hypothetical protein CAPTEDRAFT_183010 [Capitella teleta]

 Score =  113 bits (282), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 49/61 (80%), Positives = 57/61 (93%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
           RRG+DSTGV DRVVNQLLT+LDGVEGL+GVYV+GATSRPD+IDPALLRPGRL  ++HC +
Sbjct: 846 RRGHDSTGVTDRVVNQLLTQLDGVEGLQGVYVLGATSRPDLIDPALLRPGRLDKALHCNL 905

Query: 66  P 66
           P
Sbjct: 906 P 906

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|410910898|ref|XP_003968927.1| PREDICTED: peroxisome biogenesis factor 1-like [Takifugu rubripes]

 Score =  111 bits (278), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 50/63 (79%), Positives = 57/63 (90%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
           RRG+DSTGV DRVVNQLLT++DGVEGL+GVYV+ ATSRPD+IDPALLRPGRL  S+HC  
Sbjct: 797 RRGHDSTGVTDRVVNQLLTQMDGVEGLQGVYVIAATSRPDLIDPALLRPGRLDKSLHCPP 856

Query: 66  PDL 68
           PDL
Sbjct: 857 PDL 859

Source: Takifugu rubripes

Species: Takifugu rubripes

Genus: Takifugu

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|348513282|ref|XP_003444171.1| PREDICTED: peroxisome biogenesis factor 1 [Oreochromis niloticus]

 Score =  110 bits (274), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 50/63 (79%), Positives = 57/63 (90%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
           RRG+DSTGV DRVVNQLLT+LDGVEGL+GVYV+ ATSRPD+IDPALLRPGRL  S++C  
Sbjct: 912 RRGHDSTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKSLYCPP 971

Query: 66  PDL 68
           PDL
Sbjct: 972 PDL 974

Source: Oreochromis niloticus

Species: Oreochromis niloticus

Genus: Oreochromis

Family: Cichlidae

Order: Perciformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|326921757|ref|XP_003207122.1| PREDICTED: LOW QUALITY PROTEIN: peroxisome biogenesis factor 1-like [Meleagris gallopavo]

 Score =  108 bits (271), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 48/64 (75%), Positives = 57/64 (89%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
           RRG+D+TGV DRVVNQLLT+LDGVEGL+GVYV+ ATSRPD+IDPALLRPGRL   ++C  
Sbjct: 929 RRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCLYCPP 988

Query: 66  PDLA 69
           PDL+
Sbjct: 989 PDLS 992

Source: Meleagris gallopavo

Species: Meleagris gallopavo

Genus: Meleagris

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|126341344|ref|XP_001368801.1| PREDICTED: peroxisome biogenesis factor 1 isoform 2 [Monodelphis domestica]

 Score =  108 bits (271), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 49/62 (79%), Positives = 55/62 (88%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
           RRG+D+TGV DRVVNQLLT+LDGVEGLEGVYV+ ATSRPD+IDPALLRPGRL   V+C  
Sbjct: 915 RRGHDNTGVTDRVVNQLLTQLDGVEGLEGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 974

Query: 66  PD 67
           PD
Sbjct: 975 PD 976

Source: Monodelphis domestica

Species: Monodelphis domestica

Genus: Monodelphis

Family: Didelphidae

Order: Didelphimorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|126341342|ref|XP_001368768.1| PREDICTED: peroxisome biogenesis factor 1 isoform 1 [Monodelphis domestica]

 Score =  108 bits (271), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 49/62 (79%), Positives = 55/62 (88%)

Query: 6    RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
            RRG+D+TGV DRVVNQLLT+LDGVEGLEGVYV+ ATSRPD+IDPALLRPGRL   V+C  
Sbjct: 955  RRGHDNTGVTDRVVNQLLTQLDGVEGLEGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 1014

Query: 66   PD 67
            PD
Sbjct: 1015 PD 1016

Source: Monodelphis domestica

Species: Monodelphis domestica

Genus: Monodelphis

Family: Didelphidae

Order: Didelphimorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|431908908|gb|ELK12499.1| Peroxisome biogenesis factor 1 [Pteropus alecto]

 Score =  108 bits (270), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 48/62 (77%), Positives = 56/62 (90%)

Query: 6    RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
            RRG+D+TGV DRVVNQLLT+LDGVEGL+GVYV+ ATSRPD+IDPALLRPGRL   V+C+ 
Sbjct: 988  RRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCSP 1047

Query: 66   PD 67
            PD
Sbjct: 1048 PD 1049

Source: Pteropus alecto

Species: Pteropus alecto

Genus: Pteropus

Family: Pteropodidae

Order: Chiroptera

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|395540081|ref|XP_003771988.1| PREDICTED: peroxisome biogenesis factor 1 [Sarcophilus harrisii]

 Score =  108 bits (270), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 49/62 (79%), Positives = 55/62 (88%)

Query: 6    RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
            RRG+D+TGV DRVVNQLLT+LDGVEGLEGVYV+ ATSRPD+IDPALLRPGRL   V+C  
Sbjct: 940  RRGHDNTGVTDRVVNQLLTQLDGVEGLEGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 999

Query: 66   PD 67
            PD
Sbjct: 1000 PD 1001

Source: Sarcophilus harrisii

Species: Sarcophilus harrisii

Genus: Sarcophilus

Family: Dasyuridae

Order: Dasyuromorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|281208808|gb|EFA82983.1| peroxisomal biogenesis factor 1 [Polysphondylium pallidum PN500]

 Score =  108 bits (270), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 48/62 (77%), Positives = 55/62 (88%)

Query: 6    RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
            RRG+DSTGV DRVVNQ LTELDGVEGL GVYV+ ATSRPD+IDPALLRPGRL  S++C +
Sbjct: 963  RRGHDSTGVTDRVVNQFLTELDGVEGLRGVYVLAATSRPDLIDPALLRPGRLDKSLYCNI 1022

Query: 66   PD 67
            P+
Sbjct: 1023 PE 1024

Source: Polysphondylium pallidum PN500

Species: Polysphondylium pallidum

Genus: Polysphondylium

Order: Dictyosteliida

Superkingdom: Eukaryota

>gi|440893433|gb|ELR46198.1| Peroxisome biogenesis factor 1, partial [Bos grunniens mutus]

 Score =  108 bits (270), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 49/64 (76%), Positives = 56/64 (87%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
           RRG+D+TGV DRVVNQLLT+LDGVEGL+GVYV+ ATSRPD+IDPALLRPGRL   V+C  
Sbjct: 905 RRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 964

Query: 66  PDLA 69
           PD A
Sbjct: 965 PDQA 968

Source: Bos grunniens mutus

Species: Bos grunniens

Genus: Bos

Family: Bovidae

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	72
ASPGD|ASPL0000002697	1225	pexA [Emericella nidulans (tax	0.888	0.052	0.546	5.7e-11
UNIPROTKB|E1BPU3	1281	PEX1 "Uncharacterized protein"	0.888	0.049	0.546	6e-11
UNIPROTKB|E9PE75	961	PEX1 "Peroxisome biogenesis fa	0.861	0.064	0.548	6.8e-11
ZFIN|ZDB-GENE-070530-1	1237	pex1 "peroxisome biogenesis fa	0.888	0.051	0.531	7.3e-11
UNIPROTKB|E2RLT2	1267	PEX1 "Uncharacterized protein"	0.861	0.048	0.548	9.7e-11
UNIPROTKB|O43933	1283	PEX1 "Peroxisome biogenesis fa	0.861	0.048	0.548	9.8e-11
RGD|1559939	1283	Pex1 "peroxisomal biogenesis f	0.861	0.048	0.548	9.8e-11
MGI|MGI:1918632	1284	Pex1 "peroxisomal biogenesis f	0.861	0.048	0.548	9.8e-11
UNIPROTKB|I3LPI5	1286	PEX1 "Uncharacterized protein"	0.861	0.048	0.548	9.8e-11
UNIPROTKB|E2RCK9	1416	PEX1 "Uncharacterized protein"	0.861	0.043	0.548	1.1e-10

ASPGD|ASPL0000002697 pexA [Emericella nidulans (taxid:162425)]

 Score = 166 (63.5 bits), Expect = 5.7e-11, P = 5.7e-11
 Identities = 35/64 (54%), Positives = 40/64 (62%)

Query:     6 RRGNDSTGVKDRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVHCTM 65
             +RG+DSTGV DRVVNQ                  ATSRPD+IDPALLRPGRL  S+ C M
Sbjct:   958 KRGHDSTGVTDRVVNQLLTQMDGAEGLSGVYVLAATSRPDLIDPALLRPGRLDKSLLCDM 1017

Query:    66 PDLA 69
             P+ A
Sbjct:  1018 PNHA 1021

GO:0006631 "fatty acid metabolic process" evidence=IMP

GO:0005829 "cytosol" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005778 "peroxisomal membrane" evidence=IEA

GO:0006625 "protein targeting to peroxisome" evidence=IEA

GO:0042623 "ATPase activity, coupled" evidence=IEA

UNIPROTKB|E1BPU3 PEX1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 166 (63.5 bits), Expect = 6.0e-11, P = 6.0e-11
 Identities = 35/64 (54%), Positives = 39/64 (60%)

Query:     6 RRGNDSTGVKDRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVHCTM 65
             RRG+D+TGV DRVVNQ                  ATSRPD+IDPALLRPGRL   V+C  
Sbjct:   947 RRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 1006

Query:    66 PDLA 69
             PD A
Sbjct:  1007 PDQA 1010

GO:0060152 "microtubule-based peroxisome localization" evidence=IEA

GO:0042623 "ATPase activity, coupled" evidence=IEA

GO:0032403 "protein complex binding" evidence=IEA

GO:0016558 "protein import into peroxisome matrix" evidence=IEA

GO:0008022 "protein C-terminus binding" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0005778 "peroxisomal membrane" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|E9PE75 PEX1 "Peroxisome biogenesis factor 1" [Homo sapiens (taxid:9606)]

 Score = 164 (62.8 bits), Expect = 6.8e-11, P = 6.8e-11
 Identities = 34/62 (54%), Positives = 38/62 (61%)

Query:     6 RRGNDSTGVKDRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVHCTM 65
             RRG+D+TGV DRVVNQ                  ATSRPD+IDPALLRPGRL   V+C  
Sbjct:   626 RRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 685

Query:    66 PD 67
             PD
Sbjct:   686 PD 687

GO:0005778 "peroxisomal membrane" evidence=IEA

GO:0006625 "protein targeting to peroxisome" evidence=IEA

GO:0042623 "ATPase activity, coupled" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IDA

ZFIN|ZDB-GENE-070530-1 pex1 "peroxisome biogenesis factor 1" [Danio rerio (taxid:7955)]

 Score = 165 (63.1 bits), Expect = 7.3e-11, P = 7.3e-11
 Identities = 34/64 (53%), Positives = 40/64 (62%)

Query:     6 RRGNDSTGVKDRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVHCTM 65
             RRG+D+TGV DRVVNQ                  A+SRPD+IDPALLRPGRL  S++C  
Sbjct:   904 RRGHDNTGVTDRVVNQLLTQLDGVEGLTGVYVLAASSRPDLIDPALLRPGRLDKSLYCPP 963

Query:    66 PDLA 69
             PD A
Sbjct:   964 PDRA 967

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005777 "peroxisome" evidence=IEA

GO:0007031 "peroxisome organization" evidence=IEA

GO:0042623 "ATPase activity, coupled" evidence=IEA

GO:0005778 "peroxisomal membrane" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0006625 "protein targeting to peroxisome" evidence=IEA

UNIPROTKB|E2RLT2 PEX1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 164 (62.8 bits), Expect = 9.7e-11, P = 9.7e-11
 Identities = 34/62 (54%), Positives = 38/62 (61%)

Query:     6 RRGNDSTGVKDRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVHCTM 65
             RRG+D+TGV DRVVNQ                  ATSRPD+IDPALLRPGRL   V+C  
Sbjct:   932 RRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 991

Query:    66 PD 67
             PD
Sbjct:   992 PD 993

GO:0060152 "microtubule-based peroxisome localization" evidence=IEA

GO:0042623 "ATPase activity, coupled" evidence=IEA

GO:0032403 "protein complex binding" evidence=IEA

GO:0016558 "protein import into peroxisome matrix" evidence=IEA

GO:0008022 "protein C-terminus binding" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0005778 "peroxisomal membrane" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|O43933 PEX1 "Peroxisome biogenesis factor 1" [Homo sapiens (taxid:9606)]

 Score = 164 (62.8 bits), Expect = 9.8e-11, P = 9.8e-11
 Identities = 34/62 (54%), Positives = 38/62 (61%)

Query:     6 RRGNDSTGVKDRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVHCTM 65
             RRG+D+TGV DRVVNQ                  ATSRPD+IDPALLRPGRL   V+C  
Sbjct:   948 RRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 1007

Query:    66 PD 67
             PD
Sbjct:  1008 PD 1009

GO:0016558 "protein import into peroxisome matrix" evidence=IMP

GO:0008022 "protein C-terminus binding" evidence=IPI

GO:0006625 "protein targeting to peroxisome" evidence=IMP

GO:0032403 "protein complex binding" evidence=IDA

GO:0005777 "peroxisome" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0042623 "ATPase activity, coupled" evidence=IMP

GO:0060152 "microtubule-based peroxisome localization" evidence=IMP

GO:0005737 "cytoplasm" evidence=IDA

GO:0005778 "peroxisomal membrane" evidence=IDA

GO:0005524 "ATP binding" evidence=IMP

GO:0007031 "peroxisome organization" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IDA

RGD|1559939 Pex1 "peroxisomal biogenesis factor 1" [Rattus norvegicus (taxid:10116)]

 Score = 164 (62.8 bits), Expect = 9.8e-11, P = 9.8e-11
 Identities = 34/62 (54%), Positives = 38/62 (61%)

Query:     6 RRGNDSTGVKDRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVHCTM 65
             RRG+D+TGV DRVVNQ                  ATSRPD+IDPALLRPGRL   V+C  
Sbjct:   948 RRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 1007

Query:    66 PD 67
             PD
Sbjct:  1008 PD 1009

GO:0003674 "molecular_function" evidence=ND

GO:0005524 "ATP binding" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005777 "peroxisome" evidence=ISO

GO:0005778 "peroxisomal membrane" evidence=ISO;IDA

GO:0005829 "cytosol" evidence=IEA;ISO

GO:0006625 "protein targeting to peroxisome" evidence=ISO

GO:0007031 "peroxisome organization" evidence=ISO

GO:0008022 "protein C-terminus binding" evidence=IEA;ISO

GO:0008150 "biological_process" evidence=ND

GO:0016558 "protein import into peroxisome matrix" evidence=IEA;ISO

GO:0032403 "protein complex binding" evidence=IEA;ISO

GO:0042623 "ATPase activity, coupled" evidence=IEA;ISO

GO:0043231 "intracellular membrane-bounded organelle" evidence=ISO

GO:0060152 "microtubule-based peroxisome localization" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

MGI|MGI:1918632 Pex1 "peroxisomal biogenesis factor 1" [Mus musculus (taxid:10090)]

 Score = 164 (62.8 bits), Expect = 9.8e-11, P = 9.8e-11
 Identities = 34/62 (54%), Positives = 38/62 (61%)

Query:     6 RRGNDSTGVKDRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVHCTM 65
             RRG+D+TGV DRVVNQ                  ATSRPD+IDPALLRPGRL   V+C  
Sbjct:   949 RRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 1008

Query:    66 PD 67
             PD
Sbjct:  1009 PD 1010

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005777 "peroxisome" evidence=ISO;IDA

GO:0005778 "peroxisomal membrane" evidence=ISO

GO:0005829 "cytosol" evidence=ISO

GO:0006625 "protein targeting to peroxisome" evidence=ISO

GO:0006810 "transport" evidence=IEA

GO:0007031 "peroxisome organization" evidence=ISO

GO:0008022 "protein C-terminus binding" evidence=ISO

GO:0008289 "lipid binding" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016558 "protein import into peroxisome matrix" evidence=ISO

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0032403 "protein complex binding" evidence=ISO

GO:0042623 "ATPase activity, coupled" evidence=ISO

GO:0060152 "microtubule-based peroxisome localization" evidence=ISO

UNIPROTKB|I3LPI5 PEX1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 164 (62.8 bits), Expect = 9.8e-11, P = 9.8e-11
 Identities = 34/62 (54%), Positives = 38/62 (61%)

Query:     6 RRGNDSTGVKDRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVHCTM 65
             RRG+D+TGV DRVVNQ                  ATSRPD+IDPALLRPGRL   V+C  
Sbjct:   952 RRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 1011

Query:    66 PD 67
             PD
Sbjct:  1012 PD 1013

GO:0060152 "microtubule-based peroxisome localization" evidence=IEA

GO:0042623 "ATPase activity, coupled" evidence=IEA

GO:0032403 "protein complex binding" evidence=IEA

GO:0016558 "protein import into peroxisome matrix" evidence=IEA

GO:0008022 "protein C-terminus binding" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0005778 "peroxisomal membrane" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|E2RCK9 PEX1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 164 (62.8 bits), Expect = 1.1e-10, P = 1.1e-10
 Identities = 34/62 (54%), Positives = 38/62 (61%)

Query:     6 RRGNDSTGVKDRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVHCTM 65
             RRG+D+TGV DRVVNQ                  ATSRPD+IDPALLRPGRL   V+C  
Sbjct:  1081 RRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 1140

Query:    66 PD 67
             PD
Sbjct:  1141 PD 1142

GO:0005524 "ATP binding" evidence=IEA

GO:0042623 "ATPase activity, coupled" evidence=IEA

GO:0006625 "protein targeting to peroxisome" evidence=IEA

GO:0005778 "peroxisomal membrane" evidence=IEA

GO:0005509 "calcium ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q58556	Y1156_METJA	No assigned EC number	0.6190	0.8611	0.0686	yes	N/A
P46463	PEX1_PICPA	No assigned EC number	0.7301	0.875	0.0544	yes	N/A
O74941	PEX1_SCHPO	No assigned EC number	0.6774	0.8611	0.0661	yes	N/A
Q9FNP1	PEX1_ARATH	No assigned EC number	0.6885	0.8472	0.0539	yes	N/A
P24004	PEX1_YEAST	No assigned EC number	0.7213	0.8472	0.0584	yes	N/A
Q5BL07	PEX1_MOUSE	No assigned EC number	0.7741	0.8611	0.0482	yes	N/A
O05209	VAT_THEAC	No assigned EC number	0.5873	0.8611	0.0832	yes	N/A
Q54GX5	PEX1_DICDI	No assigned EC number	0.7142	0.875	0.0513	yes	N/A
O43933	PEX1_HUMAN	No assigned EC number	0.7741	0.8611	0.0483	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	72
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	1e-20
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	3e-20
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	9e-17
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	1e-16
TIGR01241	495	TIGR01241, FtsH_fam, ATP-dependent metalloprotease	1e-16
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	2e-15
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	2e-15
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	5e-15
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	1e-14
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	3e-14
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	5e-13
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	3e-12
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	1e-10
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	2e-09
COG1223	368	COG1223, COG1223, Predicted ATPase (AAA+ superfami	3e-08
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	1e-07
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	2e-04

>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

 Score = 83.3 bits (206), Expect = 1e-20
 Identities = 36/64 (56%), Positives = 43/64 (67%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
            RG    G   RVV QLLTELDG+E  EGV V+ AT+RPD +DPALLRPGR    ++  +
Sbjct: 350 GRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPL 409

Query: 66  PDLA 69
           PDL 
Sbjct: 410 PDLE 413

Length = 494

>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily

 Score = 81.9 bits (202), Expect = 3e-20
 Identities = 35/62 (56%), Positives = 43/62 (69%), Gaps = 1/62 (1%)

Query: 7   RGND-STGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
           RG    T V DR+VNQLLTE+DG++ L  V V+ AT+RPDI+DPALLRPGR    +    
Sbjct: 562 RGARFDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPP 621

Query: 66  PD 67
           PD
Sbjct: 622 PD 623

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. Length = 733

>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

 Score = 71.9 bits (177), Expect = 9e-17
 Identities = 30/70 (42%), Positives = 40/70 (57%), Gaps = 5/70 (7%)

Query: 4   GYRRGNDSTGVKDRVVN----QLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGS 59
           G +R +  T   DR V     +LL +LDG +    V V+ AT+RPDI+DPALLRPGR   
Sbjct: 257 GAKRFDSGTS-GDREVQRTMLELLNQLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDR 315

Query: 60  SVHCTMPDLA 69
            +   +PD  
Sbjct: 316 KIEFPLPDEE 325

Length = 406

>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase

 Score = 71.7 bits (176), Expect = 1e-16
 Identities = 31/57 (54%), Positives = 41/57 (71%)

Query: 11  STGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD 67
           S+ V+  VV QLL E+DGVE L+ V V+GA++R D+IDPA+LRPGRL   +    PD
Sbjct: 310 SSDVETTVVPQLLAEIDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPD 366

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity [Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 512

>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH

 Score = 71.5 bits (176), Expect = 1e-16
 Identities = 30/62 (48%), Positives = 41/62 (66%), Gaps = 3/62 (4%)

Query: 8   GNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD 67
           GND    +++ +NQLL E+DG     GV V+ AT+RPD++DPALLRPGR    V   +PD
Sbjct: 170 GND---EREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPD 226

Query: 68  LA 69
           + 
Sbjct: 227 IK 228

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH [Cellular processes, Cell division, Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 495

>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated

 Score = 68.5 bits (168), Expect = 2e-15
 Identities = 31/65 (47%), Positives = 44/65 (67%), Gaps = 3/65 (4%)

Query: 3   TGYRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVH 62
            G   GND    +++ +NQLLTE+DG +G +GV V+ AT+R DI+D ALLRPGR    + 
Sbjct: 293 AGIGGGNDE---REQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQIT 349

Query: 63  CTMPD 67
            ++PD
Sbjct: 350 VSLPD 354

Length = 638

>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed

 Score = 68.1 bits (166), Expect = 2e-15
 Identities = 28/54 (51%), Positives = 41/54 (75%)

Query: 15  KDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDL 68
           +++ +NQ+L E+DG EG EG+ V+ AT+RPD++DPALLRPGR    V   +PD+
Sbjct: 271 REQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDV 324

Length = 644

>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase; Provisional

 Score = 66.8 bits (164), Expect = 5e-15
 Identities = 27/68 (39%), Positives = 38/68 (55%), Gaps = 5/68 (7%)

Query: 4   GYRRGNDSTGVKDRVVN----QLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGS 59
             +R +  T   DR V     QLL E+DG +    V ++ AT+R DI+DPA+LRPGR   
Sbjct: 237 AAKRTDSGTS-GDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDR 295

Query: 60  SVHCTMPD 67
            +   +PD
Sbjct: 296 IIEVPLPD 303

Length = 389

>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

 Score = 65.8 bits (161), Expect = 1e-14
 Identities = 28/50 (56%), Positives = 36/50 (72%)

Query: 20  NQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLA 69
           NQLL E+DG  G EGV V+ AT+RPD++DPALLRPGR    +   +PD+ 
Sbjct: 274 NQLLVEMDGFGGNEGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIK 323

Length = 596

>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family

 Score = 64.8 bits (158), Expect = 3e-14
 Identities = 31/69 (44%), Positives = 39/69 (56%), Gaps = 5/69 (7%)

Query: 4   GYRRGNDSTGVKDRVVN----QLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGS 59
             +R +  T   DR V     QLL ELDG +    V V+ AT+RPDI+DPALLRPGR   
Sbjct: 228 AAKRTDSGTS-GDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDR 286

Query: 60  SVHCTMPDL 68
            +   +PD 
Sbjct: 287 IIEVPLPDF 295

Many proteins may score above the trusted cutoff because an internal. Length = 364

>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily

 Score = 61.5 bits (149), Expect = 5e-13
 Identities = 29/54 (53%), Positives = 38/54 (70%)

Query: 14  VKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD 67
           V+ RVV QLLT +DG++G   V V+GAT+RPD +DPAL RPGR    +   +PD
Sbjct: 294 VEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPD 347

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. Length = 733

>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular activities (AAA)

 Score = 56.8 bits (138), Expect = 3e-12
 Identities = 30/53 (56%), Positives = 34/53 (64%), Gaps = 2/53 (3%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEG-LEGVYVVGATSRPDIIDPALLRPGRL 57
            RG+       RVVNQLLTELDG    L  V V+ AT+RPD +DPALLR GR 
Sbjct: 72  SRGSGGDSESRRVVNQLLTELDGFTSSLSKVIVIAATNRPDKLDPALLR-GRF 123

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. Length = 131

>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like protein; Provisional

 Score = 54.8 bits (132), Expect = 1e-10
 Identities = 23/51 (45%), Positives = 34/51 (66%)

Query: 17  RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD 67
           R++ +LL ++DG +    V V+ AT+R D +DPALLRPGRL   +   +PD
Sbjct: 267 RILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD 317

Length = 398

>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like protein; Provisional

 Score = 50.9 bits (122), Expect = 2e-09
 Identities = 25/64 (39%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 6   RRGNDSTGVKD--RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHC 63
           R    S G K+  R + +LL +LDG +    V V+ AT+R + +DPAL+RPGR+   +  
Sbjct: 292 RYDATSGGEKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEF 351

Query: 64  TMPD 67
             PD
Sbjct: 352 PNPD 355

Length = 438

>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General function prediction only]

 Score = 47.9 bits (114), Expect = 3e-08
 Identities = 19/34 (55%), Positives = 28/34 (82%)

Query: 18  VVNQLLTELDGVEGLEGVYVVGATSRPDIIDPAL 51
           +VN LLTELDG++  EGV  + AT+RP+++DPA+
Sbjct: 238 IVNALLTELDGIKENEGVVTIAATNRPELLDPAI 271

Length = 368

>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

 Score = 46.4 bits (110), Expect = 1e-07
 Identities = 29/64 (45%), Positives = 41/64 (64%), Gaps = 1/64 (1%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
           +R +D   V+ RVV QLL  +DG++  + V V+GAT+RPD +DPA  RPGR    +   +
Sbjct: 91  KRSSDQGEVERRVVAQLLALMDGLKRGQ-VIVIGATNRPDGLDPAKRRPGRFDREIEVNL 149

Query: 66  PDLA 69
           PD A
Sbjct: 150 PDEA 153

Length = 494

>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

 Score = 36.7 bits (85), Expect = 2e-04
 Identities = 16/52 (30%), Positives = 24/52 (46%)

Query: 11  STGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVH 62
           S G ++ ++  L T  D     E V V+GAT+RP + D       RL   + 
Sbjct: 97  SRGAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIV 148

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases. Length = 151

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	72
KOG0730|consensus	693		99.87
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	99.86
KOG0733|consensus	802		99.85
KOG0734|consensus	752		99.81
KOG0736|consensus	953		99.81
KOG0733|consensus	802		99.77
KOG0735|consensus	952		99.76
KOG0738|consensus	491		99.75
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.72
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.71
KOG0731|consensus	774		99.7
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.7
KOG0741|consensus	744		99.69
KOG0728|consensus	404		99.67
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.66
KOG0727|consensus	408		99.66
KOG0729|consensus	435		99.64
KOG0726|consensus	440		99.63
KOG0739|consensus	439		99.63
KOG0732|consensus	1080		99.62
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.6
KOG0652|consensus	424		99.6
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.59
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.58
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	99.56
CHL00195	489	ycf46 Ycf46; Provisional	99.55
KOG0651|consensus	388		99.55
CHL00206	2281	ycf2 Ycf2; Provisional	99.54
KOG0737|consensus	386		99.5
KOG0730|consensus	693		99.49
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.47
CHL00176	638	ftsH cell division protein; Validated	99.46
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.44
KOG0743|consensus	457		99.42
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.39
KOG0740|consensus	428		99.36
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.35
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.3
PF00004	132	AAA: ATPase family associated with various cellula	98.99
KOG0744|consensus	423		98.74
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	98.47
KOG0742|consensus	630		98.46
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	97.18
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.96
CHL00181	287	cbbX CbbX; Provisional	96.78
COG0714	329	MoxR-like ATPases [General function prediction onl	96.47
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.37
PRK06964	342	DNA polymerase III subunit delta'; Validated	96.19
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	96.13
PRK10865	857	protein disaggregation chaperone; Provisional	96.12
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.11
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	95.87
PRK07940	394	DNA polymerase III subunit delta'; Validated	95.81
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	95.66
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	95.38
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	95.32
KOG0735|consensus	952		95.28
KOG0736|consensus	953		94.87
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	94.82
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	94.77
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	94.69
PRK05707	328	DNA polymerase III subunit delta'; Validated	94.68
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	94.63
PHA02544	316	44 clamp loader, small subunit; Provisional	93.92
PRK06090	319	DNA polymerase III subunit delta'; Validated	93.58
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	93.4
PRK08769	319	DNA polymerase III subunit delta'; Validated	93.22
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	92.59
PRK07993	334	DNA polymerase III subunit delta'; Validated	92.57
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	92.39
PRK06871	325	DNA polymerase III subunit delta'; Validated	92.31
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	92.17
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	91.89
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	91.72
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	91.56
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	91.45
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	91.29
PRK09112	351	DNA polymerase III subunit delta'; Validated	90.81
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	90.68
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	90.42
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	90.36
PRK07471	365	DNA polymerase III subunit delta'; Validated	90.15
PRK00149	450	dnaA chromosomal replication initiation protein; R	90.07
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	90.06
PRK08058	329	DNA polymerase III subunit delta'; Validated	90.02
PRK06893	229	DNA replication initiation factor; Validated	89.93
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	89.85
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	89.64
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	89.5
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	88.87
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	87.95
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	87.94
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	87.71
PHA02244	383	ATPase-like protein	87.54
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	87.16
PRK09862	506	putative ATP-dependent protease; Provisional	86.9
PRK08699	325	DNA polymerase III subunit delta'; Validated	86.62
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	85.71
PRK05564	313	DNA polymerase III subunit delta'; Validated	85.69
CHL00095	821	clpC Clp protease ATP binding subunit	85.67
PRK13342	413	recombination factor protein RarA; Reviewed	85.28
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	85.04
KOG2004|consensus	906		84.88
PRK06581	263	DNA polymerase III subunit delta'; Validated	84.81
PRK07276	290	DNA polymerase III subunit delta'; Validated	84.61
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	84.27
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	84.26
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	84.14
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	83.92
smart00350	509	MCM minichromosome maintenance proteins.	83.17
PRK04132	846	replication factor C small subunit; Provisional	82.92
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	82.28
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	82.02
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	81.63
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	81.38
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	81.32
PRK00411	394	cdc6 cell division control protein 6; Reviewed	81.28
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	81.05
PRK12422	445	chromosomal replication initiation protein; Provis	80.99
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	80.94
PRK13531	498	regulatory ATPase RavA; Provisional	80.72
PRK07399	314	DNA polymerase III subunit delta'; Validated	80.63
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	80.62
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	80.38
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	80.18
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	80.09
smart00382	148	AAA ATPases associated with a variety of cellular	80.08
PRK12402	337	replication factor C small subunit 2; Reviewed	80.03

>KOG0730|consensus

Probab=99.87  E-value=1.3e-22  Score=150.67  Aligned_cols=68  Identities=56%  Similarity=0.909  Sum_probs=62.9

Q ss_pred             ecccCCCCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           4 GYRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         4 ~~~r~~~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ++.|++++++...|+++|||++|||+...++|+||||||||+.||+||+||||||+.||||+||.+++
T Consensus       540 ~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~V~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR  607 (693)
T KOG0730|consen  540 AGSRGGSSSGVTDRVLSQLLTEMDGLEALKNVLVIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEAR  607 (693)
T ss_pred             hhccCCCccchHHHHHHHHHHHcccccccCcEEEEeccCChhhcCHHHcCCcccceeEeecCccHHHH
Confidence            45666666688999999999999999888899999999999999999999999999999999999876

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.86  E-value=4e-22  Score=140.98  Aligned_cols=62  Identities=40%  Similarity=0.634  Sum_probs=57.7

Q ss_pred             CCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          10 DSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        10 ~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ++..+.+|.+-|||+||||++..++|-||+||||++.|||||+||||||++|+||+||.+++
T Consensus       266 ~gDrEVQRTmleLL~qlDGFD~~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR  327 (406)
T COG1222         266 SGDREVQRTMLELLNQLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGR  327 (406)
T ss_pred             CchHHHHHHHHHHHHhccCCCCCCCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHH
Confidence            34556779999999999999999999999999999999999999999999999999999886

>KOG0733|consensus

Probab=99.85  E-value=1.8e-21  Score=144.70  Aligned_cols=69  Identities=54%  Similarity=0.829  Sum_probs=64.8

Q ss_pred             eecccCCCCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           3 TGYRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         3 ~~~~r~~~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ++++|+.+.++...|++||||++|||+....+|+||||||||+.||||++||||||+.+||++|+.+++
T Consensus       616 L~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR  684 (802)
T KOG0733|consen  616 LVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEER  684 (802)
T ss_pred             cCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHHHH
Confidence            578888887888899999999999999888899999999999999999999999999999999999875

>KOG0734|consensus

Probab=99.81  E-value=1.7e-20  Score=138.30  Aligned_cols=68  Identities=38%  Similarity=0.636  Sum_probs=60.8

Q ss_pred             ecccCCCCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           4 GYRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         4 ~~~r~~~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +++|........+..+||||.+|||++.+++|+||||||+|++||+||.||||||++|.||.||..++
T Consensus       409 G~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe~LD~AL~RPGRFD~~v~Vp~PDv~GR  476 (752)
T KOG0734|consen  409 GGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNFPEALDKALTRPGRFDRHVTVPLPDVRGR  476 (752)
T ss_pred             cccCCccHHHHHHHHHHHHHHHhcCcCcCCceEEEeccCChhhhhHHhcCCCccceeEecCCCCcccH
Confidence            44555554447889999999999999999999999999999999999999999999999999998775

>KOG0736|consensus

Probab=99.81  E-value=3.6e-20  Score=139.99  Aligned_cols=68  Identities=53%  Similarity=0.795  Sum_probs=59.3

Q ss_pred             eecccC--CCCcchhHHHHHHHHHHhhCCC--CCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374           3 TGYRRG--NDSTGVKDRVVNQLLTELDGVE--GLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus         3 ~~~~r~--~~~~~~~~~~~~~ll~~ld~~~--~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      +++.|+  +++++.++|+++|||.+|||++  ..+.|+||||||||+.|||||+||||||+.+|++.++.++
T Consensus       776 lAP~RG~sGDSGGVMDRVVSQLLAELDgls~~~s~~VFViGATNRPDLLDpALLRPGRFDKLvyvG~~~d~e  847 (953)
T KOG0736|consen  776 LAPNRGRSGDSGGVMDRVVSQLLAELDGLSDSSSQDVFVIGATNRPDLLDPALLRPGRFDKLVYVGPNEDAE  847 (953)
T ss_pred             cCccCCCCCCccccHHHHHHHHHHHhhcccCCCCCceEEEecCCCccccChhhcCCCccceeEEecCCccHH
Confidence            345555  4457789999999999999996  5678999999999999999999999999999999987654

>KOG0733|consensus

Probab=99.77  E-value=2.1e-19  Score=133.75  Aligned_cols=70  Identities=34%  Similarity=0.548  Sum_probs=62.4

Q ss_pred             eecccCCCCcchhHHHHHHHHHHhhCCCCC----CCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhhC
Q psy3374           3 TGYRRGNDSTGVKDRVVNQLLTELDGVEGL----EGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFAS   72 (72)
Q Consensus         3 ~~~~r~~~~~~~~~~~~~~ll~~ld~~~~~----~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~~   72 (72)
                      ++++|...+.+..+|+++|||+.||++...    +.|+||||||||+.|||||+|+||||++|.++.|+..+++
T Consensus       294 I~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g~~VlVIgATnRPDslDpaLRRaGRFdrEI~l~vP~e~aR~  367 (802)
T KOG0733|consen  294 ITPKREEAQREMERRIVAQLLTSMDELSNEKTKGDPVLVIGATNRPDSLDPALRRAGRFDREICLGVPSETARE  367 (802)
T ss_pred             cccchhhHHHHHHHHHHHHHHHhhhcccccccCCCCeEEEecCCCCcccCHHHhccccccceeeecCCchHHHH
Confidence            456777777778889999999999999543    5699999999999999999999999999999999998874

>KOG0735|consensus

Probab=99.76  E-value=8.8e-19  Score=132.05  Aligned_cols=69  Identities=68%  Similarity=1.081  Sum_probs=65.6

Q ss_pred             eecccCCCCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           3 TGYRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         3 ~~~~r~~~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ++++||.++.+..+|++||||++|||...-.+|+|+|||.||+.|||||+||||||+.++-++|++.+|
T Consensus       772 iAPkRGhDsTGVTDRVVNQlLTelDG~Egl~GV~i~aaTsRpdliDpALLRpGRlD~~v~C~~P~~~eR  840 (952)
T KOG0735|consen  772 IAPKRGHDSTGVTDRVVNQLLTELDGAEGLDGVYILAATSRPDLIDPALLRPGRLDKLVYCPLPDEPER  840 (952)
T ss_pred             cCcccCCCCCCchHHHHHHHHHhhccccccceEEEEEecCCccccCHhhcCCCccceeeeCCCCCcHHH
Confidence            578899888899999999999999999988999999999999999999999999999999999998875

>KOG0738|consensus

Probab=99.75  E-value=3.7e-19  Score=127.38  Aligned_cols=68  Identities=37%  Similarity=0.474  Sum_probs=59.2

Q ss_pred             eecccC-CCCcchhHHHHHHHHHHhhCCCC----CCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhhC
Q psy3374           3 TGYRRG-NDSTGVKDRVVNQLLTELDGVEG----LEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFAS   72 (72)
Q Consensus         3 ~~~~r~-~~~~~~~~~~~~~ll~~ld~~~~----~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~~   72 (72)
                      +|++|+ +++++..+|+.++||.||||+..    .+.|+|+||||.||+||+||+|  ||.++|+||+||.++++
T Consensus       316 lcs~RG~s~EHEaSRRvKsELLvQmDG~~~t~e~~k~VmVLAATN~PWdiDEAlrR--RlEKRIyIPLP~~~~R~  388 (491)
T KOG0738|consen  316 LCSQRGGSSEHEASRRVKSELLVQMDGVQGTLENSKVVMVLAATNFPWDIDEALRR--RLEKRIYIPLPDAEARS  388 (491)
T ss_pred             HHhcCCCccchhHHHHHHHHHHHHhhccccccccceeEEEEeccCCCcchHHHHHH--HHhhheeeeCCCHHHHH
Confidence            466666 45688899999999999999932    2349999999999999999999  99999999999999874

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=99.72  E-value=9.9e-18  Score=120.80  Aligned_cols=68  Identities=53%  Similarity=0.811  Sum_probs=60.6

Q ss_pred             ecccCCCCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           4 GYRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         4 ~~~r~~~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ++.|+.+.++...+++++||.+||++...++|+||+|||+|+.+|+|++||||||++|+|++||.+++
T Consensus       348 ~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~r  415 (494)
T COG0464         348 ASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEER  415 (494)
T ss_pred             hccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcccCccceEeecCCCCHHHH
Confidence            34555555555579999999999999988899999999999999999999999999999999999876

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=99.71  E-value=1e-17  Score=124.17  Aligned_cols=62  Identities=45%  Similarity=0.821  Sum_probs=56.7

Q ss_pred             CCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          10 DSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        10 ~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +++.+.+..+||+|.+|||+..+++|+|+++||||+-+|+||+||||||++|.|++||..++
T Consensus       264 ggnderEQTLNQlLvEmDGF~~~~gviviaaTNRpdVlD~ALlRpgRFDRqI~V~~PDi~gR  325 (596)
T COG0465         264 GGNDEREQTLNQLLVEMDGFGGNEGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGR  325 (596)
T ss_pred             CCchHHHHHHHHHHhhhccCCCCCceEEEecCCCcccchHhhcCCCCcceeeecCCcchhhH
Confidence            34556668999999999999988899999999999999999999999999999999998765

>KOG0731|consensus

Probab=99.70  E-value=2.6e-17  Score=124.44  Aligned_cols=62  Identities=45%  Similarity=0.797  Sum_probs=57.0

Q ss_pred             CCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          10 DSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        10 ~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +.+.+.+..+||||.+|||+...++|+|+|+||+|+.||+||+||||||++|++++||..++
T Consensus       426 ~~~~e~e~tlnQll~emDgf~~~~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r  487 (774)
T KOG0731|consen  426 GGQDEREQTLNQLLVEMDGFETSKGVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGR  487 (774)
T ss_pred             CCChHHHHHHHHHHHHhcCCcCCCcEEEEeccCCccccCHHhcCCCccccceeccCCchhhh
Confidence            34556778999999999999888889999999999999999999999999999999998875

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.70  E-value=2.8e-17  Score=120.40  Aligned_cols=67  Identities=52%  Similarity=0.827  Sum_probs=57.9

Q ss_pred             cccCCC-CcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           5 YRRGND-STGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         5 ~~r~~~-~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+|+++ ++....+++++||++||++...++++||+|||+++.||||++||||||.+|+|++|+.+++
T Consensus       303 ~~R~~~~s~d~e~~il~~LL~~LDgl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r  370 (512)
T TIGR03689       303 RTRGSGVSSDVETTVVPQLLSELDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAA  370 (512)
T ss_pred             cccCCCccchHHHHHHHHHHHHhcccccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHH
Confidence            344433 3344568899999999999877789999999999999999999999999999999999876

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>KOG0741|consensus

Probab=99.69  E-value=9.9e-18  Score=123.74  Aligned_cols=69  Identities=49%  Similarity=0.762  Sum_probs=62.6

Q ss_pred             eecccCCCC--cchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           3 TGYRRGNDS--TGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         3 ~~~~r~~~~--~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +|.+|++..  .+..+.++||||+.|||+..-++++|||.|||++.||+||+|||||..++++.+||+++|
T Consensus       336 ICKqRGS~~g~TGVhD~VVNQLLsKmDGVeqLNNILVIGMTNR~DlIDEALLRPGRlEVqmEIsLPDE~gR  406 (744)
T KOG0741|consen  336 ICKQRGSMAGSTGVHDTVVNQLLSKMDGVEQLNNILVIGMTNRKDLIDEALLRPGRLEVQMEISLPDEKGR  406 (744)
T ss_pred             HHHhcCCCCCCCCccHHHHHHHHHhcccHHhhhcEEEEeccCchhhHHHHhcCCCceEEEEEEeCCCccCc
Confidence            577787543  567889999999999999888899999999999999999999999999999999999875

>KOG0728|consensus

Probab=99.67  E-value=8.4e-17  Score=111.41  Aligned_cols=61  Identities=38%  Similarity=0.602  Sum_probs=56.8

Q ss_pred             CcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          11 STGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        11 ~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ++++.+|..-+||+||||+...+++-||.|||+.+-|||||+||||.|++|+||.|+++++
T Consensus       263 gdsevqrtmlellnqldgfeatknikvimatnridild~allrpgridrkiefp~p~e~ar  323 (404)
T KOG0728|consen  263 GDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDILDPALLRPGRIDRKIEFPPPNEEAR  323 (404)
T ss_pred             ccHHHHHHHHHHHHhccccccccceEEEEeccccccccHhhcCCCcccccccCCCCCHHHH
Confidence            3556678889999999999999999999999999999999999999999999999999886

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.66  E-value=1.9e-16  Score=119.05  Aligned_cols=67  Identities=52%  Similarity=0.814  Sum_probs=58.6

Q ss_pred             cccCCC-CcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           5 YRRGND-STGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         5 ~~r~~~-~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ++|+.. .+...++++++||.+||++...++++||+|||+|+.||+|++||||||+.|+|++||.+++
T Consensus       560 ~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R  627 (733)
T TIGR01243       560 PARGARFDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEAR  627 (733)
T ss_pred             ccCCCCCCccHHHHHHHHHHHHhhcccCCCCEEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHH
Confidence            344433 3445679999999999999888899999999999999999999999999999999999876

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>KOG0727|consensus

Probab=99.66  E-value=1.4e-16  Score=110.42  Aligned_cols=61  Identities=38%  Similarity=0.631  Sum_probs=56.5

Q ss_pred             CcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          11 STGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        11 ~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.+..+++-+||++|||+....+|-||.|||+.+.|||||+||||+|++|+||+||.-+.
T Consensus       271 adrevqril~ellnqmdgfdq~~nvkvimatnradtldpallrpgrldrkiefplpdrrqk  331 (408)
T KOG0727|consen  271 ADREVQRILIELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQK  331 (408)
T ss_pred             ccHHHHHHHHHHHHhccCcCcccceEEEEecCcccccCHhhcCCccccccccCCCCchhhh
Confidence            4456779999999999999999999999999999999999999999999999999998764

>KOG0729|consensus

Probab=99.64  E-value=3.9e-16  Score=108.86  Aligned_cols=62  Identities=40%  Similarity=0.642  Sum_probs=56.7

Q ss_pred             CCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          10 DSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        10 ~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +++.+.++..-+++.||||+...+++-|+.|||+|+.|||||+||||+|++++|++||.+++
T Consensus       292 ggdnevqrtmleli~qldgfdprgnikvlmatnrpdtldpallrpgrldrkvef~lpdlegr  353 (435)
T KOG0729|consen  292 GGDNEVQRTMLELINQLDGFDPRGNIKVLMATNRPDTLDPALLRPGRLDRKVEFGLPDLEGR  353 (435)
T ss_pred             CCcHHHHHHHHHHHHhccCCCCCCCeEEEeecCCCCCcCHhhcCCcccccceeccCCccccc
Confidence            34455678888999999999999999999999999999999999999999999999999875

>KOG0726|consensus

Probab=99.63  E-value=3.4e-16  Score=109.88  Aligned_cols=58  Identities=36%  Similarity=0.603  Sum_probs=53.7

Q ss_pred             hhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          14 VKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +.+|..-+||+||||+...+.|-||.|||+.+.|||||+||||.|++|+|++||...+
T Consensus       304 EiQrtmLELLNQldGFdsrgDvKvimATnrie~LDPaLiRPGrIDrKIef~~pDe~Tk  361 (440)
T KOG0726|consen  304 EIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTK  361 (440)
T ss_pred             HHHHHHHHHHHhccCccccCCeEEEEecccccccCHhhcCCCccccccccCCCchhhh
Confidence            4567778999999999998899999999999999999999999999999999998764

>KOG0739|consensus

Probab=99.63  E-value=1.6e-16  Score=111.64  Aligned_cols=67  Identities=25%  Similarity=0.459  Sum_probs=62.4

Q ss_pred             eecccCCCCcchhHHHHHHHHHHhhCC-CCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           3 TGYRRGNDSTGVKDRVVNQLLTELDGV-EGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         3 ~~~~r~~~~~~~~~~~~~~ll~~ld~~-~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +|++|+.++++..+|+.++||.||.|+ ..+.+|+|+||||-||.||.|++|  ||+++||||+|+..++
T Consensus       237 lcg~r~enEseasRRIKTEfLVQMqGVG~d~~gvLVLgATNiPw~LDsAIRR--RFekRIYIPLPe~~AR  304 (439)
T KOG0739|consen  237 LCGSRSENESEASRRIKTEFLVQMQGVGNDNDGVLVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHAR  304 (439)
T ss_pred             hccCCCCCchHHHHHHHHHHHHhhhccccCCCceEEEecCCCchhHHHHHHH--HhhcceeccCCcHHHh
Confidence            578888999999999999999999999 456689999999999999999999  9999999999998876

>KOG0732|consensus

Probab=99.62  E-value=3.6e-16  Score=121.12  Aligned_cols=67  Identities=37%  Similarity=0.629  Sum_probs=59.8

Q ss_pred             cccCCCCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           5 YRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         5 ~~r~~~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +.|++-....+..+++.||..|||+...+.|+||||||||+++||||+||||||+.++|++|+.+++
T Consensus       377 pvrSskqEqih~SIvSTLLaLmdGldsRgqVvvigATnRpda~dpaLRRPgrfdref~f~lp~~~ar  443 (1080)
T KOG0732|consen  377 PVRSSKQEQIHASIVSTLLALMDGLDSRGQVVVIGATNRPDAIDPALRRPGRFDREFYFPLPDVDAR  443 (1080)
T ss_pred             ccccchHHHhhhhHHHHHHHhccCCCCCCceEEEcccCCccccchhhcCCcccceeEeeeCCchHHH
Confidence            3444444456678999999999999999999999999999999999999999999999999999886

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.60  E-value=1.1e-15  Score=114.09  Aligned_cols=60  Identities=47%  Similarity=0.846  Sum_probs=55.1

Q ss_pred             cchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          12 TGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        12 ~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +....+++++||.+||++...++++||+|||+|+.||+|++||||||++|+|++||.+++
T Consensus       268 ~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd~~~R  327 (644)
T PRK10733        268 HDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGR  327 (644)
T ss_pred             chHHHHHHHHHHHhhhcccCCCCeeEEEecCChhhcCHHHhCCcccceEEEcCCCCHHHH
Confidence            345568999999999999888899999999999999999999999999999999998765

>KOG0652|consensus

Probab=99.60  E-value=1.1e-15  Score=106.47  Aligned_cols=60  Identities=38%  Similarity=0.570  Sum_probs=56.0

Q ss_pred             cchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          12 TGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        12 ~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ..+.+|..-+||+||||++++.+|-||+|||+.+-|||||+|.||+|++|+||.|+.+++
T Consensus       288 DREVQRTMLELLNQLDGFss~~~vKviAATNRvDiLDPALlRSGRLDRKIEfP~Pne~aR  347 (424)
T KOG0652|consen  288 DREVQRTMLELLNQLDGFSSDDRVKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEAR  347 (424)
T ss_pred             cHHHHHHHHHHHHhhcCCCCccceEEEeecccccccCHHHhhcccccccccCCCCChHHH
Confidence            445678888999999999999999999999999999999999999999999999999886

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=99.59  E-value=2.1e-15  Score=107.78  Aligned_cols=67  Identities=19%  Similarity=0.209  Sum_probs=52.9

Q ss_pred             eecccCCCCcchhHHHH-HHHHHHhhCC------------CCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChh
Q psy3374           3 TGYRRGNDSTGVKDRVV-NQLLTELDGV------------EGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLA   69 (72)
Q Consensus         3 ~~~~r~~~~~~~~~~~~-~~ll~~ld~~------------~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~   69 (72)
                      +++++++.+.....+++ ++||++||+.            ...++|+||+|||+|+.|||||+||||||+.|  .+|+.+
T Consensus       224 ~~g~r~~~~~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~VIaTTNrpd~LDpALlRpGRfDk~i--~lPd~e  301 (413)
T PLN00020        224 GAGRFGTTQYTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGNDFSTLYAPLIRDGRMEKFY--WAPTRE  301 (413)
T ss_pred             cCCCCCCCCcchHHHHHHHHHHHHhcCCccccccccccccccCCCceEEEeCCCcccCCHhHcCCCCCCcee--CCCCHH
Confidence            35566555545545665 8999999873            23567999999999999999999999999975  589998


Q ss_pred             hh
Q psy3374          70 FA   71 (72)
Q Consensus        70 ~~   71 (72)
                      ++
T Consensus       302 ~R  303 (413)
T PLN00020        302 DR  303 (413)
T ss_pred             HH
Confidence            76

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.58  E-value=2.6e-15  Score=108.78  Aligned_cols=60  Identities=45%  Similarity=0.784  Sum_probs=55.1

Q ss_pred             cchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          12 TGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        12 ~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +....+++++||.+||++.+.++++||+|||+|+.||+|++||||||++|+|++||.+++
T Consensus       171 ~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R  230 (495)
T TIGR01241       171 NDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGR  230 (495)
T ss_pred             cHHHHHHHHHHHhhhccccCCCCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHH
Confidence            344568999999999999888889999999999999999999999999999999999876

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=99.56  E-value=7.1e-15  Score=104.95  Aligned_cols=59  Identities=39%  Similarity=0.645  Sum_probs=54.5

Q ss_pred             chhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          13 GVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        13 ~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ....+.+.+||.+||++....+++||+|||+|+.||||++||||||++|+|++|+.+++
T Consensus       263 ~~~~r~l~~LL~~ld~~~~~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R  321 (398)
T PTZ00454        263 REVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQK  321 (398)
T ss_pred             HHHHHHHHHHHHHhhccCCCCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHH
Confidence            34568899999999999877789999999999999999999999999999999999876

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.55  E-value=9e-15  Score=106.74  Aligned_cols=61  Identities=25%  Similarity=0.424  Sum_probs=53.9

Q ss_pred             CCCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           9 NDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         9 ~~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.++...+++++||++|+..  ..+|+||||||+++.||+|++|+||||+.|+|++|+.+++
T Consensus       337 ~~d~~~~~rvl~~lL~~l~~~--~~~V~vIaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR  397 (489)
T CHL00195        337 KGDSGTTNRVLATFITWLSEK--KSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEER  397 (489)
T ss_pred             CCCchHHHHHHHHHHHHHhcC--CCceEEEEecCChhhCCHHHhCCCcCCeEEEeCCcCHHHH
Confidence            344556789999999999953  4579999999999999999999999999999999999876

>KOG0651|consensus

Probab=99.55  E-value=5.5e-15  Score=103.83  Aligned_cols=61  Identities=41%  Similarity=0.652  Sum_probs=55.7

Q ss_pred             CcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          11 STGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        11 ~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.+.++.+-+||.+||+++..++|-+|.|||+|+.|||||+||||+|+++++|+|+..++
T Consensus       248 ~dreiqrTLMeLlnqmdgfd~l~rVk~ImatNrpdtLdpaLlRpGRldrk~~iPlpne~~r  308 (388)
T KOG0651|consen  248 SDREIQRTLMELLNQMDGFDTLHRVKTIMATNRPDTLDPALLRPGRLDRKVEIPLPNEQAR  308 (388)
T ss_pred             hhHHHHHHHHHHHHhhccchhcccccEEEecCCccccchhhcCCccccceeccCCcchhhc
Confidence            3456678888999999999999999999999999999999999999999999999998764

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.54  E-value=6.9e-15  Score=118.81  Aligned_cols=54  Identities=20%  Similarity=0.350  Sum_probs=48.6

Q ss_pred             HHHHHHHHhhCCC---CCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          18 VVNQLLTELDGVE---GLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        18 ~~~~ll~~ld~~~---~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+++||.+||+..   ...+|+||||||+|+.|||||+||||||++|+|++|+..++
T Consensus      1753 tL~qLLneLDg~~~~~s~~~VIVIAATNRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R 1809 (2281)
T CHL00206       1753 SLGLLVNSLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQ 1809 (2281)
T ss_pred             hHHHHHHHhccccccCCCCCEEEEEeCCCcccCCHhHcCCCCCCeEEEeCCCCchhH
Confidence            4899999999873   35679999999999999999999999999999999998654

>KOG0737|consensus

Probab=99.50  E-value=1e-14  Score=103.49  Aligned_cols=64  Identities=30%  Similarity=0.468  Sum_probs=57.9

Q ss_pred             cCCCCcchhHHHHHHHHHHhhCCCCCC--CeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhhC
Q psy3374           7 RGNDSTGVKDRVVNQLLTELDGVEGLE--GVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFAS   72 (72)
Q Consensus         7 r~~~~~~~~~~~~~~ll~~ld~~~~~~--~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~~   72 (72)
                      |.+++++....+.+||+..|||+..++  +|+|+||||||.+||.|++|  ||.+.++|++|+.++++
T Consensus       202 R~s~dHEa~a~mK~eFM~~WDGl~s~~~~rVlVlgATNRP~DlDeAiiR--R~p~rf~V~lP~~~qR~  267 (386)
T KOG0737|consen  202 RRSTDHEATAMMKNEFMALWDGLSSKDSERVLVLGATNRPFDLDEAIIR--RLPRRFHVGLPDAEQRR  267 (386)
T ss_pred             cccchHHHHHHHHHHHHHHhccccCCCCceEEEEeCCCCCccHHHHHHH--hCcceeeeCCCchhhHH
Confidence            367778889999999999999996554  49999999999999999999  99999999999988763

>KOG0730|consensus

Probab=99.49  E-value=5.4e-14  Score=105.22  Aligned_cols=67  Identities=42%  Similarity=0.551  Sum_probs=59.9

Q ss_pred             eecccCCCCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           3 TGYRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         3 ~~~~r~~~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +|++|..... ...++++|++.+||++....+++|++|||+|+.||++++| ||||+.++++.|+..++
T Consensus       290 l~p~r~~~~~-~e~Rv~sqlltL~dg~~~~~~vivl~atnrp~sld~alRR-gRfd~ev~IgiP~~~~R  356 (693)
T KOG0730|consen  290 LCPKREGADD-VESRVVSQLLTLLDGLKPDAKVIVLAATNRPDSLDPALRR-GRFDREVEIGIPGSDGR  356 (693)
T ss_pred             hCCcccccch-HHHHHHHHHHHHHhhCcCcCcEEEEEecCCccccChhhhc-CCCcceeeecCCCchhH
Confidence            4666665554 6789999999999999888899999999999999999999 99999999999998765

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.47  E-value=1.1e-13  Score=98.26  Aligned_cols=58  Identities=40%  Similarity=0.643  Sum_probs=53.4

Q ss_pred             hhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          14 VKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ...+.+.+|++++|++....++.||+|||+++.+|+|++||||||+.|+|++|+.+++
T Consensus       250 ~~~~~l~~lL~~ld~~~~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R  307 (389)
T PRK03992        250 EVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGR  307 (389)
T ss_pred             HHHHHHHHHHHhccccCCCCCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHH
Confidence            4567888999999999777789999999999999999999999999999999999876

>CHL00176 ftsH cell division protein; Validated

Probab=99.46  E-value=8.4e-14  Score=104.24  Aligned_cols=60  Identities=45%  Similarity=0.762  Sum_probs=55.3

Q ss_pred             cchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          12 TGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        12 ~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +.....++++||.+||++....+|+||+|||+++.+|+|++||||||++|+|++||.+++
T Consensus       299 ~~e~~~~L~~LL~~~dg~~~~~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R  358 (638)
T CHL00176        299 NDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGR  358 (638)
T ss_pred             cHHHHHHHHHHHhhhccccCCCCeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHH
Confidence            445568899999999999888899999999999999999999999999999999999876

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=99.44  E-value=1.3e-13  Score=99.68  Aligned_cols=58  Identities=36%  Similarity=0.567  Sum_probs=53.3

Q ss_pred             hhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          14 VKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ...+.+.+||.+||++....++.||+|||+++.||+|++||||||++|+|++||.+++
T Consensus       302 e~qr~ll~LL~~Ldg~~~~~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R  359 (438)
T PTZ00361        302 EIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTK  359 (438)
T ss_pred             HHHHHHHHHHHHHhhhcccCCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHH
Confidence            4567888999999999777789999999999999999999999999999999999876

>KOG0743|consensus

Probab=99.42  E-value=2.1e-13  Score=98.68  Aligned_cols=54  Identities=30%  Similarity=0.410  Sum_probs=47.5

Q ss_pred             HHHHHHHHHhhCCCCC--CCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGL--EGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~--~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      -.++.||+.+||+-+.  +--++|.|||+++.|||||+||||+|.+|+++.|+.++
T Consensus       319 VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDmhI~mgyCtf~~  374 (457)
T KOG0743|consen  319 VTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDMHIYMGYCTFEA  374 (457)
T ss_pred             eehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCcceeEEEcCCCCHHH
Confidence            5689999999999322  34678899999999999999999999999999999876

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=99.39  E-value=1.7e-13  Score=95.12  Aligned_cols=56  Identities=38%  Similarity=0.638  Sum_probs=52.8

Q ss_pred             hhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          14 VKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ....++|.||++|||+.++.+|+.||+||+|+.||+|++.  ||..+|+|.+|+.+++
T Consensus       234 DVsEiVNALLTelDgi~eneGVvtIaaTN~p~~LD~aiRs--RFEeEIEF~LP~~eEr  289 (368)
T COG1223         234 DVSEIVNALLTELDGIKENEGVVTIAATNRPELLDPAIRS--RFEEEIEFKLPNDEER  289 (368)
T ss_pred             cHHHHHHHHHHhccCcccCCceEEEeecCChhhcCHHHHh--hhhheeeeeCCChHHH
Confidence            4557999999999999999999999999999999999999  9999999999999875

>KOG0740|consensus

Probab=99.36  E-value=3.5e-13  Score=97.23  Aligned_cols=65  Identities=28%  Similarity=0.416  Sum_probs=57.7

Q ss_pred             cccCCCCcchhHHHHHHHHHHhhCC--CCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           5 YRRGNDSTGVKDRVVNQLLTELDGV--EGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         5 ~~r~~~~~~~~~~~~~~ll~~ld~~--~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+|..+.++...++.++||.++++.  ...++|+||||||+||.+|.|++|  ||-+.++|++||.+++
T Consensus       259 s~Rs~~e~e~srr~ktefLiq~~~~~s~~~drvlvigaTN~P~e~Dea~~R--rf~kr~yiplPd~etr  325 (428)
T KOG0740|consen  259 SKRSDNEHESSRRLKTEFLLQFDGKNSAPDDRVLVIGATNRPWELDEAARR--RFVKRLYIPLPDYETR  325 (428)
T ss_pred             hhcCCcccccchhhhhHHHhhhccccCCCCCeEEEEecCCCchHHHHHHHH--HhhceeeecCCCHHHH
Confidence            3456666777889999999999998  445689999999999999999999  9999999999999986

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.35  E-value=2.4e-12  Score=90.17  Aligned_cols=58  Identities=47%  Similarity=0.745  Sum_probs=52.9

Q ss_pred             hhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          14 VKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ...+.+.+++.+++++...+++.||+|||+++.+|++++||||||+.|+|++|+.+++
T Consensus       241 ~~~~~l~~ll~~ld~~~~~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r  298 (364)
T TIGR01242       241 EVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGR  298 (364)
T ss_pred             HHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHH
Confidence            4557888999999998777789999999999999999999999999999999998875

Many proteins may score above the trusted cutoff because an internal

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.30  E-value=4.4e-12  Score=95.64  Aligned_cols=67  Identities=45%  Similarity=0.689  Sum_probs=58.0

Q ss_pred             cccCCCCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           5 YRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         5 ~~r~~~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ++++...++...+++++|++.||++.....++||++||+++.||++++|+||||+.|++++|+.+++
T Consensus       285 ~~r~~~~~~~~~~~~~~Ll~~ld~l~~~~~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R  351 (733)
T TIGR01243       285 PKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRAR  351 (733)
T ss_pred             ccccCCcchHHHHHHHHHHHHhhccccCCCEEEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHH
Confidence            3444444455678999999999999877889999999999999999999999999999999998865

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=98.99  E-value=1e-09  Score=65.37  Aligned_cols=54  Identities=39%  Similarity=0.620  Sum_probs=46.7

Q ss_pred             CcchhHHHHHHHHHHhhCCCCC-CCeEEEEecCCCCCCcccccCCCccccEEEeCC
Q psy3374          11 STGVKDRVVNQLLTELDGVEGL-EGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM   65 (72)
Q Consensus        11 ~~~~~~~~~~~ll~~ld~~~~~-~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~   65 (72)
                      .+.....++++|+..|+..... .+++||+|||+++.+|++++| |||+.+|++++
T Consensus        78 ~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~~i~~~l~~-~rf~~~i~~~~  132 (132)
T PF00004_consen   78 SSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPDKIDPALLR-SRFDRRIEFPL  132 (132)
T ss_dssp             SSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGGGSCHHHHS-TTSEEEEEE-S
T ss_pred             cccccccccceeeecccccccccccceeEEeeCChhhCCHhHHh-CCCcEEEEcCC
Confidence            4455678899999999998654 569999999999999999999 99999999985

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>KOG0744|consensus

Probab=98.74  E-value=8e-09  Score=73.54  Aligned_cols=58  Identities=28%  Similarity=0.313  Sum_probs=53.4

Q ss_pred             cchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          12 TGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        12 ~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+..-|++|.+|+|||.++..++|++++|+|-.+.||-|+..  |-|-+.|||.|+.++.
T Consensus       275 psDaIRvVNalLTQlDrlK~~~NvliL~TSNl~~siD~AfVD--RADi~~yVG~Pt~~ai  332 (423)
T KOG0744|consen  275 PSDAIRVVNALLTQLDRLKRYPNVLILATSNLTDSIDVAFVD--RADIVFYVGPPTAEAI  332 (423)
T ss_pred             CchHHHHHHHHHHHHHHhccCCCEEEEeccchHHHHHHHhhh--HhhheeecCCccHHHH
Confidence            334559999999999999999999999999999999999999  9999999999998764

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=98.47  E-value=3.9e-07  Score=66.02  Aligned_cols=65  Identities=45%  Similarity=0.693  Sum_probs=55.9

Q ss_pred             ccCCCCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           6 RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         6 ~r~~~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ++.........+++++++..||++.... ++++++||++..+|++++++|||++.+++..|+.+.+
T Consensus        91 ~~~~~~~~~~~~v~~~l~~~~d~~~~~~-v~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  155 (494)
T COG0464          91 KRSSDQGEVERRVVAQLLALMDGLKRGQ-VIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGR  155 (494)
T ss_pred             CccccccchhhHHHHHHHHhcccccCCc-eEEEeecCCccccChhHhCccccceeeecCCCCHHHH
Confidence            3334445567799999999999998444 9999999999999999999999999999999998753

>KOG0742|consensus

Probab=98.46  E-value=1.5e-07  Score=69.12  Aligned_cols=66  Identities=21%  Similarity=0.238  Sum_probs=53.2

Q ss_pred             eeecccCCCCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           2 ITGYRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         2 ~~~~~r~~~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      |+|.+....-++..+..+|.||-.-.  ..+..++++.+||+|.++|.|+-.  |||..|+|++|..|++
T Consensus       455 FLceRnktymSEaqRsaLNAlLfRTG--dqSrdivLvlAtNrpgdlDsAV~D--Ride~veFpLPGeEER  520 (630)
T KOG0742|consen  455 FLCERNKTYMSEAQRSALNALLFRTG--DQSRDIVLVLATNRPGDLDSAVND--RIDEVVEFPLPGEEER  520 (630)
T ss_pred             HHHHhchhhhcHHHHHHHHHHHHHhc--ccccceEEEeccCCccchhHHHHh--hhhheeecCCCChHHH
Confidence            34555444556777888999886554  345579999999999999999999  9999999999999886

>TIGR00763 lon ATP-dependent protease La

Probab=97.18  E-value=0.00048  Score=53.00  Aligned_cols=35  Identities=17%  Similarity=0.147  Sum_probs=30.9

Q ss_pred             CCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          33 EGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        33 ~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      .++++|+|||.++.||++|++  ||+ .|+++.|+.++
T Consensus       462 s~v~~I~TtN~~~~i~~~L~~--R~~-vi~~~~~~~~e  496 (775)
T TIGR00763       462 SKVIFIATANSIDTIPRPLLD--RME-VIELSGYTEEE  496 (775)
T ss_pred             CCEEEEEecCCchhCCHHHhC--Cee-EEecCCCCHHH
Confidence            468999999999999999999  995 78999888654

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=96.96  E-value=0.0011  Score=51.29  Aligned_cols=37  Identities=27%  Similarity=0.374  Sum_probs=32.2

Q ss_pred             CCCeEEEEecCCCC-----CCcccccCCCccccEEEeCCCChhhh
Q psy3374          32 LEGVYVVGATSRPD-----IIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        32 ~~~v~vi~aTn~~~-----~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.+.||||||.++     ..|+||.|  ||+ .|+|+.|+.+++
T Consensus       313 ~g~i~vIgATt~~E~~~~~~~D~AL~r--RFq-~I~v~ePs~~~~  354 (758)
T PRK11034        313 SGKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEET  354 (758)
T ss_pred             CCCeEEEecCChHHHHHHhhccHHHHh--hCc-EEEeCCCCHHHH
Confidence            45799999999875     58999999  995 899999999875

>CHL00181 cbbX CbbX; Provisional

Probab=96.78  E-value=0.003  Score=43.61  Aligned_cols=54  Identities=15%  Similarity=0.131  Sum_probs=40.6

Q ss_pred             hhHHHHHHHHHHhhCCCCCCCeEEEEecCCCC-----CCcccccCCCccccEEEeCCCChhhh
Q psy3374          14 VKDRVVNQLLTELDGVEGLEGVYVVGATSRPD-----IIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~-----~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ....++..|+..|+..  .++++||+|++...     .++|++.+  ||+..|+|+.++.++.
T Consensus       143 ~~~e~~~~L~~~me~~--~~~~~vI~ag~~~~~~~~~~~np~L~s--R~~~~i~F~~~t~~el  201 (287)
T CHL00181        143 YGSEAIEILLQVMENQ--RDDLVVIFAGYKDRMDKFYESNPGLSS--RIANHVDFPDYTPEEL  201 (287)
T ss_pred             hHHHHHHHHHHHHhcC--CCCEEEEEeCCcHHHHHHHhcCHHHHH--hCCceEEcCCcCHHHH
Confidence            3457788899999854  34677888775321     34699999  9999999999988653

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=96.47  E-value=0.0063  Score=42.27  Aligned_cols=52  Identities=23%  Similarity=0.212  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHhhCC----------CCCCCeEEEEecC-----CCCCCcccccCCCccccEEEeCCCChh
Q psy3374          16 DRVVNQLLTELDGV----------EGLEGVYVVGATS-----RPDIIDPALLRPGRLGSSVHCTMPDLA   69 (72)
Q Consensus        16 ~~~~~~ll~~ld~~----------~~~~~v~vi~aTn-----~~~~lD~al~r~GRfd~~i~v~~Pd~~   69 (72)
                      ..+.+.||..|+.-          .-....+|++|+|     .-..+++|+++  ||-..+++++|+.+
T Consensus       126 p~~q~aLl~~l~e~~vtv~~~~~~~~~~~f~viaT~Np~e~~g~~~l~eA~ld--Rf~~~~~v~yp~~~  192 (329)
T COG0714         126 PEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNPGEYEGTYPLPEALLD--RFLLRIYVDYPDSE  192 (329)
T ss_pred             HHHHHHHHHHHhCcEEEECCcCCcCCCCCCEEEEccCccccCCCcCCCHHHHh--hEEEEEecCCCCch
Confidence            46777888888772          2235689999999     77889999999  99999999999544

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.37  E-value=0.0031  Score=49.28  Aligned_cols=37  Identities=32%  Similarity=0.383  Sum_probs=31.1

Q ss_pred             CCCeEEEEecCCCC-----CCcccccCCCccccEEEeCCCChhhh
Q psy3374          32 LEGVYVVGATSRPD-----IIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        32 ~~~v~vi~aTn~~~-----~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.+.+||||+..+     .+|+||.|  || ..|+|+.|+.++.
T Consensus       314 ~G~l~~IgaTT~~e~~~~~~~d~AL~r--Rf-~~i~v~eps~~~~  355 (852)
T TIGR03345       314 RGELRTIAATTWAEYKKYFEKDPALTR--RF-QVVKVEEPDEETA  355 (852)
T ss_pred             CCCeEEEEecCHHHHhhhhhccHHHHH--hC-eEEEeCCCCHHHH
Confidence            45689999999754     49999999  99 5899999998864

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=96.19  E-value=0.0099  Score=42.25  Aligned_cols=50  Identities=26%  Similarity=0.314  Sum_probs=42.1

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ...|.||..|+.  ..+++++|.+|++|+.|.|.++.  |+ ..|.|+.|+.++.
T Consensus       147 ~AaNaLLKtLEE--Pp~~t~fiL~t~~~~~LLpTI~S--Rc-q~i~~~~~~~~~~  196 (342)
T PRK06964        147 AAANALLKTLEE--PPPGTVFLLVSARIDRLLPTILS--RC-RQFPMTVPAPEAA  196 (342)
T ss_pred             HHHHHHHHHhcC--CCcCcEEEEEECChhhCcHHHHh--cC-EEEEecCCCHHHH
Confidence            456889999984  45578899999999999999999  99 7899999987653

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=96.13  E-value=0.02  Score=38.48  Aligned_cols=51  Identities=12%  Similarity=0.131  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCC-----CCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRP-----DIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~-----~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+..|+..|+..  ..++++|++++..     ..++|++.+  ||+..|+++.++.++
T Consensus       127 ~~~i~~Ll~~~e~~--~~~~~vila~~~~~~~~~~~~~p~L~s--Rf~~~i~f~~~~~~e  182 (261)
T TIGR02881       127 KEAIDTLVKGMEDN--RNEFVLILAGYSDEMDYFLSLNPGLRS--RFPISIDFPDYTVEE  182 (261)
T ss_pred             HHHHHHHHHHHhcc--CCCEEEEecCCcchhHHHHhcChHHHh--ccceEEEECCCCHHH
Confidence            45778889988865  3345555554322     236889999  999999999888764

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.12  E-value=0.0052  Score=48.07  Aligned_cols=37  Identities=30%  Similarity=0.310  Sum_probs=31.8

Q ss_pred             CCCeEEEEecCCCC-----CCcccccCCCccccEEEeCCCChhhh
Q psy3374          32 LEGVYVVGATSRPD-----IIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        32 ~~~v~vi~aTn~~~-----~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.+.+||||+..+     .+|+|+.|  ||+ .|.++.|+.+++
T Consensus       305 ~g~l~~IgaTt~~e~r~~~~~d~al~r--Rf~-~i~v~eP~~~~~  346 (857)
T PRK10865        305 RGELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDT  346 (857)
T ss_pred             cCCCeEEEcCCCHHHHHHhhhcHHHHh--hCC-EEEeCCCCHHHH
Confidence            45799999999987     48999999  997 689999998754

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=96.11  E-value=0.007  Score=46.40  Aligned_cols=37  Identities=22%  Similarity=0.234  Sum_probs=31.1

Q ss_pred             CCCeEEEEecCCC-----CCCcccccCCCccccEEEeCCCChhhh
Q psy3374          32 LEGVYVVGATSRP-----DIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        32 ~~~v~vi~aTn~~-----~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.+.+|||||..     ..+|+|+.|  ||. .|+|+.|+.++.
T Consensus       309 ~g~i~~IgaTt~~e~~~~~~~d~al~r--Rf~-~i~v~~p~~~~~  350 (731)
T TIGR02639       309 SGKLRCIGSTTYEEYKNHFEKDRALSR--RFQ-KIDVGEPSIEET  350 (731)
T ss_pred             CCCeEEEEecCHHHHHHHhhhhHHHHH--hCc-eEEeCCCCHHHH
Confidence            3569999999974     368999999  996 799999998864

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=95.87  E-value=0.022  Score=38.68  Aligned_cols=36  Identities=22%  Similarity=0.308  Sum_probs=32.0

Q ss_pred             CeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          34 GVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        34 ~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.++++||++..++++++.  ||...+.++.|+.++.
T Consensus       129 ~~~li~~t~~~~~l~~~l~s--R~~~~~~l~~l~~~e~  164 (305)
T TIGR00635       129 PFTLVGATTRAGMLTSPLRD--RFGIILRLEFYTVEEL  164 (305)
T ss_pred             CeEEEEecCCccccCHHHHh--hcceEEEeCCCCHHHH
Confidence            47899999999999999999  9999999999987653

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=95.81  E-value=0.014  Score=42.12  Aligned_cols=50  Identities=24%  Similarity=0.365  Sum_probs=37.6

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ...|.||..|+.-.. +.++|++|+| ++.|.|++++  |+ ..++|+.|+.++.
T Consensus       132 ~aanaLLk~LEep~~-~~~fIL~a~~-~~~llpTIrS--Rc-~~i~f~~~~~~~i  181 (394)
T PRK07940        132 RAANALLKAVEEPPP-RTVWLLCAPS-PEDVLPTIRS--RC-RHVALRTPSVEAV  181 (394)
T ss_pred             HHHHHHHHHhhcCCC-CCeEEEEECC-hHHChHHHHh--hC-eEEECCCCCHHHH
Confidence            456789998886422 3455555555 9999999999  88 7999999987753

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=95.66  E-value=0.0091  Score=41.02  Aligned_cols=53  Identities=17%  Similarity=0.164  Sum_probs=40.0

Q ss_pred             hhHHHHHHHHHHhhCCCCCCCeEEEEecCC--CCC---CcccccCCCccccEEEeCCCChhh
Q psy3374          14 VKDRVVNQLLTELDGVEGLEGVYVVGATSR--PDI---IDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~--~~~---lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....+.+.|++.|+.-  ..+++||++++.  ++.   ++|++.+  ||+..|+|+.++.++
T Consensus       142 ~~~~~~~~Ll~~le~~--~~~~~vI~a~~~~~~~~~~~~np~L~s--R~~~~i~fp~l~~ed  199 (284)
T TIGR02880       142 YGQEAIEILLQVMENQ--RDDLVVILAGYKDRMDSFFESNPGFSS--RVAHHVDFPDYSEAE  199 (284)
T ss_pred             hHHHHHHHHHHHHhcC--CCCEEEEEeCCcHHHHHHHhhCHHHHh--hCCcEEEeCCcCHHH
Confidence            3456778899999853  346778887664  232   4899999  999999999988664

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=95.38  E-value=0.013  Score=40.55  Aligned_cols=36  Identities=19%  Similarity=0.285  Sum_probs=32.2

Q ss_pred             CeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          34 GVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        34 ~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.+|++||++..++++|+.  ||...++++.|+.++.
T Consensus       150 ~~~li~at~~~~~l~~~L~s--Rf~~~~~l~~~~~~e~  185 (328)
T PRK00080        150 PFTLIGATTRAGLLTSPLRD--RFGIVQRLEFYTVEEL  185 (328)
T ss_pred             CceEEeecCCcccCCHHHHH--hcCeeeecCCCCHHHH
Confidence            47889999999999999998  9999999999998754

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=95.32  E-value=0.024  Score=41.92  Aligned_cols=48  Identities=25%  Similarity=0.407  Sum_probs=35.5

Q ss_pred             hHHHHHHHHHHhhC--------------------CCCCCCeEEEEecCCCC----CCcccccCCCccccEEEeCC
Q psy3374          15 KDRVVNQLLTELDG--------------------VEGLEGVYVVGATSRPD----IIDPALLRPGRLGSSVHCTM   65 (72)
Q Consensus        15 ~~~~~~~ll~~ld~--------------------~~~~~~v~vi~aTn~~~----~lD~al~r~GRfd~~i~v~~   65 (72)
                      ..++.+++++.|+.                    +.-..++.+|||+|..+    .+|.|++|  || ..|++..
T Consensus       286 i~kiFGel~~lLE~~~rg~~~~v~l~y~e~d~e~f~iP~Nl~IIgTMNt~Drs~~~lD~AlrR--RF-~fi~i~p  357 (459)
T PRK11331        286 LSKVFGEVMMLMEHDKRGENWSVPLTYSENDEERFYVPENVYIIGLMNTADRSLAVVDYALRR--RF-SFIDIEP  357 (459)
T ss_pred             HHHhhhhhhhhccccccccccceeeeccccccccccCCCCeEEEEecCccccchhhccHHHHh--hh-heEEecC
Confidence            34666777776662                    22335799999999998    89999999  99 5566654

>KOG0735|consensus

Probab=95.28  E-value=0.032  Score=43.85  Aligned_cols=61  Identities=13%  Similarity=0.207  Sum_probs=47.7

Q ss_pred             CcchhHHHHHHHHHHhhC-C-CCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          11 STGVKDRVVNQLLTELDG-V-EGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        11 ~~~~~~~~~~~ll~~ld~-~-~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ..+.....++.||.++-. + +.+..+.|||+.+....|.|-|..|++|+.++.++.|+..+|
T Consensus       516 q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~ap~~~~R  578 (952)
T KOG0735|consen  516 QDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPAPAVTRR  578 (952)
T ss_pred             cchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecCCcchhHH
Confidence            334445566677755443 3 444458999999999999999999999999999999998876

>KOG0736|consensus

Probab=94.87  E-value=0.051  Score=42.94  Aligned_cols=52  Identities=15%  Similarity=0.118  Sum_probs=41.3

Q ss_pred             HHHHHHHHHhhCC-CCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          17 RVVNQLLTELDGV-EGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        17 ~~~~~ll~~ld~~-~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .++.++++ .|-+ ....+++|+++|+..+.|++.+.+  -|-.+|.++.|++++|
T Consensus       516 ~~i~~~ls-~e~~~~~~~~~ivv~t~~s~~~lp~~i~~--~f~~ei~~~~lse~qR  568 (953)
T KOG0736|consen  516 KVIRHLLS-NEDFKFSCPPVIVVATTSSIEDLPADIQS--LFLHEIEVPALSEEQR  568 (953)
T ss_pred             HHHHHHHh-cccccCCCCceEEEEeccccccCCHHHHH--hhhhhccCCCCCHHHH
Confidence            34444554 3333 355679999999999999999999  8888999999999986

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=94.82  E-value=0.034  Score=43.49  Aligned_cols=37  Identities=27%  Similarity=0.300  Sum_probs=31.0

Q ss_pred             CCCeEEEEecCCCC-----CCcccccCCCccccEEEeCCCChhhh
Q psy3374          32 LEGVYVVGATSRPD-----IIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        32 ~~~v~vi~aTn~~~-----~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.+.+||+|+..+     .+|+|+.|  ||. .|+++.|+.++.
T Consensus       300 ~g~i~~IgaTt~~e~r~~~~~d~al~r--Rf~-~i~v~~p~~~~~  341 (852)
T TIGR03346       300 RGELHCIGATTLDEYRKYIEKDAALER--RFQ-PVFVDEPTVEDT  341 (852)
T ss_pred             cCceEEEEeCcHHHHHHHhhcCHHHHh--cCC-EEEeCCCCHHHH
Confidence            45699999999874     58999999  995 689999997763

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=94.77  E-value=0.094  Score=30.32  Aligned_cols=45  Identities=38%  Similarity=0.467  Sum_probs=33.8

Q ss_pred             HHHHHHHHhhCCCC----CCCeEEEEecCCCC--CCcccccCCCccccEEEeC
Q psy3374          18 VVNQLLTELDGVEG----LEGVYVVGATSRPD--IIDPALLRPGRLGSSVHCT   64 (72)
Q Consensus        18 ~~~~ll~~ld~~~~----~~~v~vi~aTn~~~--~lD~al~r~GRfd~~i~v~   64 (72)
                      ....++..+.....    ..++.+|++||...  .+++.+..  ||+..|+++
T Consensus       100 ~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~--r~~~~i~~~  150 (151)
T cd00009         100 AQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYD--RLDIRIVIP  150 (151)
T ss_pred             HHHHHHHHHHhcCceeccCCCeEEEEecCccccCCcChhHHh--hhccEeecC
Confidence            44566666666643    35788899999887  78888888  999888876

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=94.69  E-value=0.062  Score=36.35  Aligned_cols=34  Identities=24%  Similarity=0.290  Sum_probs=28.4

Q ss_pred             CeEEEEecCCC-----CCCcccccCCCccccEEEeCCCChhh
Q psy3374          34 GVYVVGATSRP-----DIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        34 ~v~vi~aTn~~-----~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ++.||+|+|..     ..+++|+++  || ..+++++|+.+.
T Consensus       151 ~frvIaTsN~~~~~g~~~l~~aL~~--R~-~~i~i~~P~~~~  189 (262)
T TIGR02640       151 EFRVIFTSNPVEYAGVHETQDALLD--RL-ITIFMDYPDIDT  189 (262)
T ss_pred             CCEEEEeeCCccccceecccHHHHh--hc-EEEECCCCCHHH
Confidence            56799999976     367999999  99 789999999764

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=94.68  E-value=0.066  Score=37.73  Aligned_cols=52  Identities=17%  Similarity=0.293  Sum_probs=42.0

Q ss_pred             hHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          15 KDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .....|.||..|+.-  .+++++|.+|+.++.|.|.++.  |+ ..+.|+.|+.++.
T Consensus       119 ~~~aaNaLLK~LEEP--p~~~~fiL~t~~~~~ll~TI~S--Rc-~~~~~~~~~~~~~  170 (328)
T PRK05707        119 NRNAANALLKSLEEP--SGDTVLLLISHQPSRLLPTIKS--RC-QQQACPLPSNEES  170 (328)
T ss_pred             CHHHHHHHHHHHhCC--CCCeEEEEEECChhhCcHHHHh--hc-eeeeCCCcCHHHH
Confidence            446788899999864  3568888999999999999999  98 4588988887653

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=94.63  E-value=0.074  Score=33.84  Aligned_cols=49  Identities=16%  Similarity=0.154  Sum_probs=36.9

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.||..|+..  .+..++|.+||.+..|.+++.+  |+ ..+++..|+.++
T Consensus       111 ~~~~~Ll~~le~~--~~~~~~il~~~~~~~l~~~i~s--r~-~~~~~~~~~~~~  159 (188)
T TIGR00678       111 AAANALLKTLEEP--PPNTLFILITPSPEKLLPTIRS--RC-QVLPFPPLSEEA  159 (188)
T ss_pred             HHHHHHHHHhcCC--CCCeEEEEEECChHhChHHHHh--hc-EEeeCCCCCHHH
Confidence            4567788888764  2345566667788999999998  77 489999888765

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=93.92  E-value=0.11  Score=35.46  Aligned_cols=46  Identities=11%  Similarity=0.086  Sum_probs=34.6

Q ss_pred             HHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          20 NQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        20 ~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ..|...|+...  .++.+|.+||.++.+++++++  ||. .+.++.|+.+.
T Consensus       119 ~~L~~~le~~~--~~~~~Ilt~n~~~~l~~~l~s--R~~-~i~~~~p~~~~  164 (316)
T PHA02544        119 RHLRSFMEAYS--KNCSFIITANNKNGIIEPLRS--RCR-VIDFGVPTKEE  164 (316)
T ss_pred             HHHHHHHHhcC--CCceEEEEcCChhhchHHHHh--hce-EEEeCCCCHHH
Confidence            34445566542  356778899999999999999  994 78898888765

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=93.58  E-value=0.17  Score=35.78  Aligned_cols=51  Identities=22%  Similarity=0.223  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ....|.||..|+.  ..+++++|..|+.++.|-|.++.  |+ ..+.|+.|+.+..
T Consensus       122 ~~AaNaLLKtLEE--Pp~~t~fiL~t~~~~~lLpTI~S--RC-q~~~~~~~~~~~~  172 (319)
T PRK06090        122 ESASNALLKTLEE--PAPNCLFLLVTHNQKRLLPTIVS--RC-QQWVVTPPSTAQA  172 (319)
T ss_pred             HHHHHHHHHHhcC--CCCCeEEEEEECChhhChHHHHh--cc-eeEeCCCCCHHHH
Confidence            4677889999985  45568888889999999999999  88 5888998887754

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=93.40  E-value=0.2  Score=35.53  Aligned_cols=52  Identities=29%  Similarity=0.400  Sum_probs=39.6

Q ss_pred             hHHHHHHHHHHhhCCC-----------CCCCeEEEEecCCCC-CCcccccCCCccccEEEeCCCCh
Q psy3374          15 KDRVVNQLLTELDGVE-----------GLEGVYVVGATSRPD-IIDPALLRPGRLGSSVHCTMPDL   68 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~-----------~~~~v~vi~aTn~~~-~lD~al~r~GRfd~~i~v~~Pd~   68 (72)
                      ...+.+.|+..|+.-.           ...++++++|+|-.+ .++++++.  ||...|.++.|..
T Consensus       141 ~~~~q~~Lle~mee~~v~v~r~G~~~~~p~rfiviAt~NP~e~~l~~aLld--RF~~~v~v~~~~~  204 (334)
T PRK13407        141 EDHIVDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEEGELRPQLLD--RFGLSVEVRSPRD  204 (334)
T ss_pred             CHHHHHHHHHHHHcCCeEEEECCeEEecCCCEEEEecCCcccCCCCHHHHh--hcceEEEcCCCCc
Confidence            4466777888776421           234689999999644 58999999  9999999998876

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=93.22  E-value=0.18  Score=35.61  Aligned_cols=52  Identities=19%  Similarity=0.276  Sum_probs=40.8

Q ss_pred             hHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          15 KDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .....|.||..|+.-  ..++++|-+|+.++.|-|.++.  |+ ..+.|+.|+.++.
T Consensus       126 ~~~AaNaLLKtLEEP--p~~~~fiL~~~~~~~lLpTIrS--RC-q~i~~~~~~~~~~  177 (319)
T PRK08769        126 NRAACNALLKTLEEP--SPGRYLWLISAQPARLPATIRS--RC-QRLEFKLPPAHEA  177 (319)
T ss_pred             CHHHHHHHHHHhhCC--CCCCeEEEEECChhhCchHHHh--hh-eEeeCCCcCHHHH
Confidence            346778899988854  4467778888999999999999  88 6788888877653

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=92.59  E-value=0.072  Score=32.07  Aligned_cols=40  Identities=25%  Similarity=0.409  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHhhCCC-----------CCC------CeEEEEecCCCC----CCcccccCCCcc
Q psy3374          16 DRVVNQLLTELDGVE-----------GLE------GVYVVGATSRPD----IIDPALLRPGRL   57 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~-----------~~~------~v~vi~aTn~~~----~lD~al~r~GRf   57 (72)
                      ..+++.|+..++.-.           ...      ++.+|+|+|...    .+++|+++  ||
T Consensus        79 ~~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~~~~~~l~~al~~--Rf  139 (139)
T PF07728_consen   79 PEVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRDKGRKELSPALLD--RF  139 (139)
T ss_dssp             HHHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST--TTTTCHHHHT--T-
T ss_pred             HHHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCCCCcCcCCHHHHh--hC
Confidence            466667777776531           111      389999999999    99999999  98

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=92.57  E-value=0.2  Score=35.43  Aligned_cols=51  Identities=22%  Similarity=0.210  Sum_probs=41.9

Q ss_pred             hHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          15 KDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      .....|.||..|+.  ...++++|..|+.++.|-|.++.  |.- .+.++.|+.+.
T Consensus       121 ~~~AaNaLLKtLEE--Pp~~t~fiL~t~~~~~lLpTIrS--RCq-~~~~~~~~~~~  171 (334)
T PRK07993        121 TDAAANALLKTLEE--PPENTWFFLACREPARLLATLRS--RCR-LHYLAPPPEQY  171 (334)
T ss_pred             CHHHHHHHHHHhcC--CCCCeEEEEEECChhhChHHHHh--ccc-cccCCCCCHHH
Confidence            34678899999995  45578888889999999999999  885 67888887765

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=92.39  E-value=0.27  Score=38.50  Aligned_cols=48  Identities=23%  Similarity=0.182  Sum_probs=34.3

Q ss_pred             HHHHHHHhhCC-------------CCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          19 VNQLLTELDGV-------------EGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        19 ~~~ll~~ld~~-------------~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      .+.|+..||.-             -.-.+|++|+|+|.. .|++||+.  ||+ .|.+..++.++
T Consensus       437 ~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~TaN~~-~i~~aLl~--R~~-ii~~~~~t~ee  497 (784)
T PRK10787        437 ASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSM-NIPAPLLD--RME-VIRLSGYTEDE  497 (784)
T ss_pred             HHHHHHHhccccEEEEecccccccccCCceEEEEcCCCC-CCCHHHhc--cee-eeecCCCCHHH
Confidence            46777777741             012479999999998 59999999  996 56666555543

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=92.31  E-value=0.31  Score=34.51  Aligned_cols=51  Identities=16%  Similarity=0.199  Sum_probs=41.0

Q ss_pred             hHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          15 KDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      .....|.||..|+.  ..+++++|.+|+.++.|-|.++.  |. ..+.+..|+.+.
T Consensus       120 ~~~AaNaLLKtLEE--Pp~~~~fiL~t~~~~~llpTI~S--RC-~~~~~~~~~~~~  170 (325)
T PRK06871        120 TEAAANALLKTLEE--PRPNTYFLLQADLSAALLPTIYS--RC-QTWLIHPPEEQQ  170 (325)
T ss_pred             CHHHHHHHHHHhcC--CCCCeEEEEEECChHhCchHHHh--hc-eEEeCCCCCHHH
Confidence            34677889999985  45568888899999999999999  88 677888887654

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=92.17  E-value=0.16  Score=35.01  Aligned_cols=49  Identities=27%  Similarity=0.258  Sum_probs=37.1

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.|+..|+..  ..++++|.+||.++.+.+++.+  |+ ..++++.|+.++
T Consensus       132 ~~~~~Ll~~le~~--~~~~~lIl~~~~~~~l~~~l~s--r~-~~~~~~~~~~~~  180 (355)
T TIGR02397       132 SAFNALLKTLEEP--PEHVVFILATTEPHKIPATILS--RC-QRFDFKRIPLED  180 (355)
T ss_pred             HHHHHHHHHHhCC--ccceeEEEEeCCHHHHHHHHHh--he-eEEEcCCCCHHH
Confidence            4567788888753  3456777778889999999998  88 578888887654

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.89  E-value=0.35  Score=35.75  Aligned_cols=48  Identities=21%  Similarity=0.234  Sum_probs=35.4

Q ss_pred             HHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          18 VVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        18 ~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ..+.||..|+..  .+.+++|++|+.+..++++++.  |+ ..+++..|+.++
T Consensus       133 a~~~LLk~LE~p--~~~vv~Ilattn~~kl~~~L~S--R~-~vv~f~~l~~~e  180 (472)
T PRK14962        133 AFNALLKTLEEP--PSHVVFVLATTNLEKVPPTIIS--RC-QVIEFRNISDEL  180 (472)
T ss_pred             HHHHHHHHHHhC--CCcEEEEEEeCChHhhhHHHhc--Cc-EEEEECCccHHH
Confidence            445677777753  3457777777778999999999  88 578888887654

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=91.72  E-value=0.16  Score=36.18  Aligned_cols=49  Identities=16%  Similarity=0.240  Sum_probs=33.9

Q ss_pred             HHHHHhhCCCCCCCeEEEEecCCCCC---CcccccCCCcccc--EEEeCCCChhhh
Q psy3374          21 QLLTELDGVEGLEGVYVVGATSRPDI---IDPALLRPGRLGS--SVHCTMPDLAFA   71 (72)
Q Consensus        21 ~ll~~ld~~~~~~~v~vi~aTn~~~~---lD~al~r~GRfd~--~i~v~~Pd~~~~   71 (72)
                      +|+..++.+...+..+|+++++.|+.   +++.+..  ||..  .++++.||.+.+
T Consensus       220 ~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~S--Rl~~g~~v~i~~pd~~~r  273 (405)
T TIGR00362       220 EFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRS--RFEWGLVVDIEPPDLETR  273 (405)
T ss_pred             HHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhh--hccCCeEEEeCCCCHHHH
Confidence            45555555533445577777777765   4577887  9974  799999998865

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=91.56  E-value=0.3  Score=33.65  Aligned_cols=53  Identities=17%  Similarity=0.248  Sum_probs=40.9

Q ss_pred             HHHHHHHHhhCC--CCCCCeEEEEecCCCCCCcccccC---------------------CCccccEEEeCCCChhh
Q psy3374          18 VVNQLLTELDGV--EGLEGVYVVGATSRPDIIDPALLR---------------------PGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        18 ~~~~ll~~ld~~--~~~~~v~vi~aTn~~~~lD~al~r---------------------~GRfd~~i~v~~Pd~~~   70 (72)
                      --.+|.+.|||-  ...++|++.+|+|+-..+.+-...                     ..||..+|.|..||.+.
T Consensus       123 ~yk~LKs~LeGgle~~P~NvliyATSNRRHLv~E~~~d~~~~~~~eih~~d~~eEklSLsDRFGL~l~F~~~~q~~  198 (249)
T PF05673_consen  123 EYKALKSVLEGGLEARPDNVLIYATSNRRHLVPESFSDREDIQDDEIHPSDTIEEKLSLSDRFGLWLSFYPPDQEE  198 (249)
T ss_pred             HHHHHHHHhcCccccCCCcEEEEEecchhhccchhhhhccCCCccccCcchHHHHHHhHHHhCCcEEEecCCCHHH
Confidence            346788888886  456689999999998877764432                     35899999999998764

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.45  E-value=0.32  Score=36.35  Aligned_cols=48  Identities=23%  Similarity=0.216  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCCh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDL   68 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~   68 (72)
                      ....+.||..|+.  ...++++|.+|+.++.|.++++.  |+ ..++|..++.
T Consensus       135 ~~A~NALLKtLEE--Pp~~viFILaTte~~kI~~TI~S--RC-q~~~f~~ls~  182 (484)
T PRK14956        135 DQSFNALLKTLEE--PPAHIVFILATTEFHKIPETILS--RC-QDFIFKKVPL  182 (484)
T ss_pred             HHHHHHHHHHhhc--CCCceEEEeecCChhhccHHHHh--hh-heeeecCCCH
Confidence            4567888888874  34578888889999999999999  98 4566665554

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.29  E-value=0.13  Score=39.85  Aligned_cols=50  Identities=22%  Similarity=0.221  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....|.||..|+.-  .+++++|.+||.++.|.+.++.  |+ ..+.|..++.++
T Consensus       138 ~~AaNALLKTLEEP--P~~v~FILaTtep~kLlpTIrS--RC-q~f~f~~ls~ee  187 (700)
T PRK12323        138 NHAFNAMLKTLEEP--PEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPGH  187 (700)
T ss_pred             HHHHHHHHHhhccC--CCCceEEEEeCChHhhhhHHHH--HH-HhcccCCCChHH
Confidence            45678888888753  4568888889999999999999  88 778887776653

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=90.81  E-value=0.6  Score=33.23  Aligned_cols=50  Identities=12%  Similarity=0.090  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....|.||..|+..  ..+.++|..|+.|+.+.|.++.  |+ ..+.++.|+.++
T Consensus       155 ~~aanaLLk~LEEp--p~~~~fiLit~~~~~llptIrS--Rc-~~i~l~pl~~~~  204 (351)
T PRK09112        155 RNAANAILKTLEEP--PARALFILISHSSGRLLPTIRS--RC-QPISLKPLDDDE  204 (351)
T ss_pred             HHHHHHHHHHHhcC--CCCceEEEEECChhhccHHHHh--hc-cEEEecCCCHHH
Confidence            34567788888764  2345555667889999999988  98 799999988765

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=90.68  E-value=0.27  Score=36.71  Aligned_cols=32  Identities=22%  Similarity=0.142  Sum_probs=24.6

Q ss_pred             eEEEEecCCCCCCcccccCCCccccEEEeCCCChh
Q psy3374          35 VYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLA   69 (72)
Q Consensus        35 v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~   69 (72)
                      .++.+|||.|+.|+|++++  |+. .|+++.++.+
T Consensus       235 rlI~ATt~~p~~L~paLrs--R~~-~I~f~pL~~e  266 (531)
T TIGR02902       235 RLIGATTRNPEEIPPALRS--RCV-EIFFRPLLDE  266 (531)
T ss_pred             EEEEEecCCcccCChHHhh--hhh-eeeCCCCCHH
Confidence            5666778889999999999  984 5666665544

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=90.42  E-value=0.67  Score=32.90  Aligned_cols=51  Identities=22%  Similarity=0.263  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHhhCC-----------CCCCCeEEEEecCCCC-CCcccccCCCccccEEEeCCCCh
Q psy3374          16 DRVVNQLLTELDGV-----------EGLEGVYVVGATSRPD-IIDPALLRPGRLGSSVHCTMPDL   68 (72)
Q Consensus        16 ~~~~~~ll~~ld~~-----------~~~~~v~vi~aTn~~~-~lD~al~r~GRfd~~i~v~~Pd~   68 (72)
                      ..+.+.|+..|+.-           ....++++++++|-.+ .+.++++.  ||..++.++.|+.
T Consensus       145 ~~~Q~~Ll~~l~~g~~~v~r~G~~~~~~~r~iviat~np~eg~l~~~Lld--Rf~l~i~l~~p~~  207 (337)
T TIGR02030       145 DHLVDVLLDVAASGWNVVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--RFGLHAEIRTVRD  207 (337)
T ss_pred             HHHHHHHHHHHHhCCeEEEECCEEEEcCCCEEEEeccccccCCCCHHHHh--hcceEEECCCCCC
Confidence            35566677777531           1123689999998655 69999999  9999999999975

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=90.36  E-value=0.53  Score=37.32  Aligned_cols=48  Identities=21%  Similarity=0.195  Sum_probs=37.2

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLA   69 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~   69 (72)
                      ...|.||..|+.-  .+++.+|.+||.++.|.+.++.  |+ .++.|..++.+
T Consensus       134 ~A~NALLKtLEEP--P~~v~FILaTtd~~KIp~TIrS--RC-q~f~Fk~Ls~e  181 (830)
T PRK07003        134 HAFNAMLKTLEEP--PPHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPAG  181 (830)
T ss_pred             HHHHHHHHHHHhc--CCCeEEEEEECChhhccchhhh--he-EEEecCCcCHH
Confidence            4567788888754  3468888888999999999999  88 67777766554

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=90.15  E-value=0.87  Score=32.60  Aligned_cols=50  Identities=14%  Similarity=0.085  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....|.||..+...  ..+.++|.+|+.++.+.+.++.  |+ ..|.++.|+.++
T Consensus       155 ~~aanaLLK~LEep--p~~~~~IL~t~~~~~llpti~S--Rc-~~i~l~~l~~~~  204 (365)
T PRK07471        155 ANAANALLKVLEEP--PARSLFLLVSHAPARLLPTIRS--RC-RKLRLRPLAPED  204 (365)
T ss_pred             HHHHHHHHHHHhcC--CCCeEEEEEECCchhchHHhhc--cc-eEEECCCCCHHH
Confidence            46677888888854  3356777789999999999888  87 678888887665

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=90.07  E-value=0.21  Score=36.24  Aligned_cols=50  Identities=16%  Similarity=0.278  Sum_probs=35.1

Q ss_pred             HHHHHHhhCCCCCCCeEEEEecCCCCC---CcccccCCCccc--cEEEeCCCChhhh
Q psy3374          20 NQLLTELDGVEGLEGVYVVGATSRPDI---IDPALLRPGRLG--SSVHCTMPDLAFA   71 (72)
Q Consensus        20 ~~ll~~ld~~~~~~~v~vi~aTn~~~~---lD~al~r~GRfd--~~i~v~~Pd~~~~   71 (72)
                      .+|+..++.+...+..+|++++..|..   +++.+..  ||.  ..++++.||.+.+
T Consensus       231 ~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~S--Rl~~gl~v~i~~pd~~~r  285 (450)
T PRK00149        231 EEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRS--RFEWGLTVDIEPPDLETR  285 (450)
T ss_pred             HHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHh--HhcCCeeEEecCCCHHHH
Confidence            345555555533444577777777766   6788888  997  4899999998864

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=90.06  E-value=0.58  Score=32.37  Aligned_cols=36  Identities=19%  Similarity=0.174  Sum_probs=29.1

Q ss_pred             CCeEEEEecCCCC---CCcccccCCCccc-cEEEeCCCChhh
Q psy3374          33 EGVYVVGATSRPD---IIDPALLRPGRLG-SSVHCTMPDLAF   70 (72)
Q Consensus        33 ~~v~vi~aTn~~~---~lD~al~r~GRfd-~~i~v~~Pd~~~   70 (72)
                      .++.+|++||.++   .+++.+.+  ||. ..|+++.++.++
T Consensus       164 ~~v~lI~i~n~~~~~~~l~~~~~s--~~~~~~i~f~p~~~~e  203 (365)
T TIGR02928       164 AKVGVIGISNDLKFRENLDPRVKS--SLCEEEIIFPPYDAEE  203 (365)
T ss_pred             CeEEEEEEECCcchHhhcCHHHhc--cCCcceeeeCCCCHHH
Confidence            4688999999986   58888887  885 679999888765

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=90.02  E-value=0.58  Score=32.76  Aligned_cols=50  Identities=22%  Similarity=0.147  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....|.||..|+.-  .+++++|.+|+.++.|-|+++.  |. ..+++..|+.+.
T Consensus       124 ~~a~NaLLK~LEEP--p~~~~~Il~t~~~~~ll~TIrS--Rc-~~i~~~~~~~~~  173 (329)
T PRK08058        124 ASAANSLLKFLEEP--SGGTTAILLTENKHQILPTILS--RC-QVVEFRPLPPES  173 (329)
T ss_pred             HHHHHHHHHHhcCC--CCCceEEEEeCChHhCcHHHHh--hc-eeeeCCCCCHHH
Confidence            45677889888864  3456677788889999999999  87 678888877654

>PRK06893 DNA replication initiation factor; Validated

Probab=89.93  E-value=0.24  Score=32.81  Aligned_cols=50  Identities=10%  Similarity=0.139  Sum_probs=33.8

Q ss_pred             HHHHhhCCCCCC-CeEEEEecCCCCCCc---ccccCCCccccEEEeCCCChhhh
Q psy3374          22 LLTELDGVEGLE-GVYVVGATSRPDIID---PALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        22 ll~~ld~~~~~~-~v~vi~aTn~~~~lD---~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      |...++.....+ .++|++++..|..++   +.|....++...+.++.||.+.+
T Consensus       113 l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~  166 (229)
T PRK06893        113 IFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQK  166 (229)
T ss_pred             HHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHH
Confidence            444455443333 456777777788776   78888444567899999998864

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=89.85  E-value=0.59  Score=35.19  Aligned_cols=50  Identities=22%  Similarity=0.220  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....+.||..|+..  ...+++|.+|+.++.|.+.++.  |+ ..++|..|+.++
T Consensus       133 ~~a~naLLKtLEep--p~~~ifIlatt~~~ki~~tI~S--Rc-~~~~f~~~~~~e  182 (559)
T PRK05563        133 TGAFNALLKTLEEP--PAHVIFILATTEPHKIPATILS--RC-QRFDFKRISVED  182 (559)
T ss_pred             HHHHHHHHHHhcCC--CCCeEEEEEeCChhhCcHHHHh--Hh-eEEecCCCCHHH
Confidence            45677888888754  3456666667789999999988  87 467787776643

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=89.64  E-value=0.66  Score=32.82  Aligned_cols=49  Identities=18%  Similarity=0.158  Sum_probs=36.6

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.||..|+..  .+++.+|.+|+.++.+.+++..  |+ ..++++.|+.++
T Consensus       134 ~a~naLLk~lEe~--~~~~~fIl~t~~~~~l~~tI~S--Rc-~~~~~~~l~~~e  182 (363)
T PRK14961        134 HSFNALLKTLEEP--PQHIKFILATTDVEKIPKTILS--RC-LQFKLKIISEEK  182 (363)
T ss_pred             HHHHHHHHHHhcC--CCCeEEEEEcCChHhhhHHHHh--hc-eEEeCCCCCHHH
Confidence            4566788887754  3456666677888999999988  88 678898887765

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=89.50  E-value=0.71  Score=35.64  Aligned_cols=50  Identities=26%  Similarity=0.273  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....|.||..|+.-  .+++.+|.+|+.+..|.+.++.  |+ ..++|..++.++
T Consensus       133 ~~a~NALLKtLEEP--p~~v~FIL~Tt~~~kLl~TI~S--RC-~~~~f~~Ls~~e  182 (647)
T PRK07994        133 RHSFNALLKTLEEP--PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQ  182 (647)
T ss_pred             HHHHHHHHHHHHcC--CCCeEEEEecCCccccchHHHh--hh-eEeeCCCCCHHH
Confidence            35677888888853  4467777778889999999999  87 788888877654

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=88.87  E-value=0.74  Score=36.01  Aligned_cols=49  Identities=20%  Similarity=0.153  Sum_probs=38.1

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.||..|+..  .+.+++|.+|+.++.|.+.++.  |+ ..++|..|+.++
T Consensus       133 ~A~NALLKtLEEP--P~~tifILaTte~~KLl~TI~S--Rc-q~ieF~~L~~ee  181 (725)
T PRK07133        133 SAFNALLKTLEEP--PKHVIFILATTEVHKIPLTILS--RV-QRFNFRRISEDE  181 (725)
T ss_pred             HHHHHHHHHhhcC--CCceEEEEEcCChhhhhHHHHh--hc-eeEEccCCCHHH
Confidence            4577788888854  3467777788889999999999  88 478888877654

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=87.95  E-value=1.5  Score=32.77  Aligned_cols=50  Identities=24%  Similarity=0.271  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....+.|+..|+.-  ..++++|.+||.++.+.+++..  |+. .++|..|+.++
T Consensus       130 ~~a~naLLk~LEep--~~~t~~Il~t~~~~kl~~~I~S--Rc~-~~~f~~ls~~e  179 (504)
T PRK14963        130 KSAFNALLKTLEEP--PEHVIFILATTEPEKMPPTILS--RTQ-HFRFRRLTEEE  179 (504)
T ss_pred             HHHHHHHHHHHHhC--CCCEEEEEEcCChhhCChHHhc--ceE-EEEecCCCHHH
Confidence            35577788887753  3456777788999999999998  874 78888887664

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=87.94  E-value=0.78  Score=32.87  Aligned_cols=51  Identities=22%  Similarity=0.284  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHhhCC-----------CCCCCeEEEEecCCCC-CCcccccCCCccccEEEeCCCCh
Q psy3374          16 DRVVNQLLTELDGV-----------EGLEGVYVVGATSRPD-IIDPALLRPGRLGSSVHCTMPDL   68 (72)
Q Consensus        16 ~~~~~~ll~~ld~~-----------~~~~~v~vi~aTn~~~-~lD~al~r~GRfd~~i~v~~Pd~   68 (72)
                      ..+.+.||..|+.-           ....++++++|.|-.+ .+.++++.  ||..++.++.|+.
T Consensus       158 ~~~Q~~LLeam~e~~~~ier~G~s~~~p~rfiviaT~np~eg~l~~~Lld--Rf~l~i~l~~~~~  220 (350)
T CHL00081        158 DHLVDILLDSAASGWNTVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--RFGMHAEIRTVKD  220 (350)
T ss_pred             HHHHHHHHHHHHhCCeEEeeCCeeeecCCCEEEEeccCcccCCCCHHHHH--HhCceeecCCCCC
Confidence            35566677777541           1233688999888655 69999999  9999999999874

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=87.71  E-value=1.2  Score=28.06  Aligned_cols=46  Identities=24%  Similarity=0.365  Sum_probs=33.5

Q ss_pred             hhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeC
Q psy3374          14 VKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCT   64 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~   64 (72)
                      ......|.||..|+.-  .+++.+|.+|+.++.|-|.++.  |+ ..|.++
T Consensus       114 l~~~a~NaLLK~LEep--p~~~~fiL~t~~~~~il~TI~S--Rc-~~i~~~  159 (162)
T PF13177_consen  114 LTEEAQNALLKTLEEP--PENTYFILITNNPSKILPTIRS--RC-QVIRFR  159 (162)
T ss_dssp             S-HHHHHHHHHHHHST--TTTEEEEEEES-GGGS-HHHHT--TS-EEEEE-
T ss_pred             hhHHHHHHHHHHhcCC--CCCEEEEEEECChHHChHHHHh--hc-eEEecC
Confidence            4557889999999965  4578888899999999999999  77 444443

...

>PHA02244 ATPase-like protein

Probab=87.54  E-value=1.2  Score=32.47  Aligned_cols=34  Identities=24%  Similarity=0.300  Sum_probs=28.6

Q ss_pred             CCeEEEEecCCC-----------CCCcccccCCCccccEEEeCCCChh
Q psy3374          33 EGVYVVGATSRP-----------DIIDPALLRPGRLGSSVHCTMPDLA   69 (72)
Q Consensus        33 ~~v~vi~aTn~~-----------~~lD~al~r~GRfd~~i~v~~Pd~~   69 (72)
                      .++-+|+|+|.+           ..+++|++.  || ..|+++.|...
T Consensus       220 ~~FRlIATsN~~~~G~~~~y~G~k~L~~AllD--RF-v~I~~dyp~~~  264 (383)
T PHA02244        220 EDFRVISAGNTLGKGADHIYVARNKIDGATLD--RF-APIEFDYDEKI  264 (383)
T ss_pred             CCEEEEEeeCCCccCcccccCCCcccCHHHHh--hc-EEeeCCCCcHH
Confidence            568999999973           788999999  99 57999999743

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=87.16  E-value=1.1  Score=33.57  Aligned_cols=49  Identities=16%  Similarity=0.137  Sum_probs=36.8

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.||..|+.-  ...+++|.+|+.++.++++++.  |+ ..+++..++.++
T Consensus       143 ~a~naLLk~LEep--p~~~vfI~aTte~~kI~~tI~S--Rc-~~~ef~~ls~~e  191 (507)
T PRK06645        143 GAFNALLKTLEEP--PPHIIFIFATTEVQKIPATIIS--RC-QRYDLRRLSFEE  191 (507)
T ss_pred             HHHHHHHHHHhhc--CCCEEEEEEeCChHHhhHHHHh--cc-eEEEccCCCHHH
Confidence            4567778777743  4467777778889999999998  88 678888777654

>PRK09862 putative ATP-dependent protease; Provisional

Probab=86.90  E-value=1.6  Score=32.73  Aligned_cols=53  Identities=15%  Similarity=0.219  Sum_probs=38.1

Q ss_pred             hHHHHHHHHHHhhCCC-----------CCCCeEEEEecCCCC---------------------CCcccccCCCccccEEE
Q psy3374          15 KDRVVNQLLTELDGVE-----------GLEGVYVVGATSRPD---------------------IIDPALLRPGRLGSSVH   62 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~-----------~~~~v~vi~aTn~~~---------------------~lD~al~r~GRfd~~i~   62 (72)
                      ...+...|++.|+.=.           ...++.+|+|+|...                     .|..+++.  |||.++.
T Consensus       307 ~~~~~~~L~~~LE~g~v~I~r~g~~~~~pa~f~lIAa~NP~pcG~~~~~~c~c~~~~~~~Y~~~ls~plLD--RfdL~v~  384 (506)
T PRK09862        307 ERRTLDALREPIESGQIHLSRTRAKITYPARFQLVAAMNPSPTGHYQGNHNRCTPEQTLRYLNRLSGPFLD--RFDLSLE  384 (506)
T ss_pred             CHHHHHHHHHHHHcCcEEEecCCcceeccCCEEEEEeecCccceecCCCCCCcCHHHHHHHHhhCCHhHHh--hccEEEE
Confidence            3456677777774321           123689999999753                     47778888  9999999


Q ss_pred             eCCCChh
Q psy3374          63 CTMPDLA   69 (72)
Q Consensus        63 v~~Pd~~   69 (72)
                      ++.|+.+
T Consensus       385 v~~~~~~  391 (506)
T PRK09862        385 IPLPPPG  391 (506)
T ss_pred             eCCCCHH
Confidence            9998754

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=86.62  E-value=0.7  Score=32.55  Aligned_cols=50  Identities=18%  Similarity=0.163  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....+.||..|+...  +++.+|.+|..++.+.+.+.+  |+ ..+.|+.|+.+.
T Consensus       127 ~~a~naLLk~LEep~--~~~~~Ilvth~~~~ll~ti~S--Rc-~~~~~~~~~~~~  176 (325)
T PRK08699        127 LQAANSLLKVLEEPP--PQVVFLLVSHAADKVLPTIKS--RC-RKMVLPAPSHEE  176 (325)
T ss_pred             HHHHHHHHHHHHhCc--CCCEEEEEeCChHhChHHHHH--Hh-hhhcCCCCCHHH
Confidence            356677888888763  345666688889999999988  87 778888887765

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=85.71  E-value=1.5  Score=32.25  Aligned_cols=49  Identities=22%  Similarity=0.158  Sum_probs=36.7

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.|+..|+..  .+.+++|.+||.++.|.++++.  |+ ..+++..++.++
T Consensus       136 ~~~n~LLk~lEep--~~~~~~Il~t~~~~kl~~tI~s--Rc-~~v~f~~l~~~e  184 (451)
T PRK06305        136 EAFNSLLKTLEEP--PQHVKFFLATTEIHKIPGTILS--RC-QKMHLKRIPEET  184 (451)
T ss_pred             HHHHHHHHHhhcC--CCCceEEEEeCChHhcchHHHH--hc-eEEeCCCCCHHH
Confidence            3556778888754  3466777778889999999998  88 468888877654

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=85.69  E-value=1.8  Score=29.85  Aligned_cols=50  Identities=12%  Similarity=0.131  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....|.||..|+.-  ..++++|.+|+.++.|-+.++.  |+ ..+++..|+.++
T Consensus       107 ~~a~naLLK~LEep--p~~t~~il~~~~~~~ll~TI~S--Rc-~~~~~~~~~~~~  156 (313)
T PRK05564        107 EQAQNAFLKTIEEP--PKGVFIILLCENLEQILDTIKS--RC-QIYKLNRLSKEE  156 (313)
T ss_pred             HHHHHHHHHHhcCC--CCCeEEEEEeCChHhCcHHHHh--hc-eeeeCCCcCHHH
Confidence            35677888888854  3455555566779999999998  87 588888887664

>CHL00095 clpC Clp protease ATP binding subunit

Probab=85.67  E-value=0.81  Score=35.81  Aligned_cols=37  Identities=30%  Similarity=0.351  Sum_probs=29.9

Q ss_pred             CCCeEEEEecCCCC-----CCcccccCCCccccEEEeCCCChhhh
Q psy3374          32 LEGVYVVGATSRPD-----IIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        32 ~~~v~vi~aTn~~~-----~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.+.+||+|+..+     ..|+++.+  ||. .|.++.|+.++.
T Consensus       305 rg~l~~IgaTt~~ey~~~ie~D~aL~r--Rf~-~I~v~ep~~~e~  346 (821)
T CHL00095        305 RGELQCIGATTLDEYRKHIEKDPALER--RFQ-PVYVGEPSVEET  346 (821)
T ss_pred             CCCcEEEEeCCHHHHHHHHhcCHHHHh--cce-EEecCCCCHHHH
Confidence            34688999999764     58999999  996 589999987653

>PRK13342 recombination factor protein RarA; Reviewed

Probab=85.28  E-value=2  Score=30.90  Aligned_cols=44  Identities=23%  Similarity=0.254  Sum_probs=30.5

Q ss_pred             HHHHHHhhCCCCCCCeEEEEec--CCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          20 NQLLTELDGVEGLEGVYVVGAT--SRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        20 ~~ll~~ld~~~~~~~v~vi~aT--n~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      +.|+..|+    .+.+++|++|  |....+++++++  || ..+.++.|+.++
T Consensus       110 ~~LL~~le----~~~iilI~att~n~~~~l~~aL~S--R~-~~~~~~~ls~e~  155 (413)
T PRK13342        110 DALLPHVE----DGTITLIGATTENPSFEVNPALLS--RA-QVFELKPLSEED  155 (413)
T ss_pred             HHHHHHhh----cCcEEEEEeCCCChhhhccHHHhc--cc-eeeEeCCCCHHH
Confidence            44555554    2456777665  335689999999  98 778888888765

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=85.04  E-value=1.2  Score=31.71  Aligned_cols=35  Identities=9%  Similarity=0.033  Sum_probs=29.2

Q ss_pred             CeEEEEecCCCC------------CCcccccCCCccccEEEeCCCChhh
Q psy3374          34 GVYVVGATSRPD------------IIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        34 ~v~vi~aTn~~~------------~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      .+.||||.|-.+            .+++|++.  ||-..+.+++|+.+.
T Consensus       178 ~FrviAT~Np~g~Gd~~G~y~Gt~~l~~A~lD--RF~i~~~~~Yp~~e~  224 (327)
T TIGR01650       178 AFRLFATANTIGLGDTTGLYHGTQQINQAQMD--RWSIVTTLNYLEHDN  224 (327)
T ss_pred             CeEEEEeeCCCCcCCCCcceeeeecCCHHHHh--heeeEeeCCCCCHHH
Confidence            588999999765            45788998  998889999998764

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>KOG2004|consensus

Probab=84.88  E-value=1  Score=35.79  Aligned_cols=23  Identities=30%  Similarity=0.446  Sum_probs=21.5

Q ss_pred             CeEEEEecCCCCCCcccccCCCccc
Q psy3374          34 GVYVVGATSRPDIIDPALLRPGRLG   58 (72)
Q Consensus        34 ~v~vi~aTn~~~~lD~al~r~GRfd   58 (72)
                      +|++|||.|..+.|+++|+.  |+.
T Consensus       554 kVLFicTAN~idtIP~pLlD--RME  576 (906)
T KOG2004|consen  554 KVLFICTANVIDTIPPPLLD--RME  576 (906)
T ss_pred             heEEEEeccccccCChhhhh--hhh
Confidence            59999999999999999999  885

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=84.81  E-value=2.6  Score=29.35  Aligned_cols=50  Identities=20%  Similarity=0.167  Sum_probs=38.8

Q ss_pred             hHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChh
Q psy3374          15 KDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLA   69 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~   69 (72)
                      .....|.||..|+.  ...+++++..|..++.|.|.++.  |+ ..+.+..|+..
T Consensus       102 t~~AANALLKtLEE--PP~~t~fILit~~~~~LLpTIrS--RC-q~i~~~~p~~~  151 (263)
T PRK06581        102 NLNAANSCLKILED--APKNSYIFLITSRAASIISTIRS--RC-FKINVRSSILH  151 (263)
T ss_pred             CHHHHHHHHHhhcC--CCCCeEEEEEeCChhhCchhHhh--ce-EEEeCCCCCHH
Confidence            34677889998885  34567777778889999999999  88 67778877763

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=84.61  E-value=1.8  Score=30.24  Aligned_cols=47  Identities=17%  Similarity=0.236  Sum_probs=37.0

Q ss_pred             hHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCC
Q psy3374          15 KDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMP   66 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~P   66 (72)
                      .....|.||..|+.-  ..++++|..|+.++.|-|.++.  |+ ..|.|+.+
T Consensus       117 ~~~AaNaLLKtLEEP--p~~t~~iL~t~~~~~lLpTI~S--Rc-q~i~f~~~  163 (290)
T PRK07276        117 HVNAANSLLKVIEEP--QSEIYIFLLTNDENKVLPTIKS--RT-QIFHFPKN  163 (290)
T ss_pred             CHHHHHHHHHHhcCC--CCCeEEEEEECChhhCchHHHH--cc-eeeeCCCc
Confidence            346788899999863  4467888888889999999999  88 67777653

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=84.27  E-value=0.91  Score=34.29  Aligned_cols=49  Identities=22%  Similarity=0.223  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLA   69 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~   69 (72)
                      ....|.||..|+.-  ..++++|.+||.++.|.+.++.  |+ ..++|..++.+
T Consensus       133 ~~a~naLLk~LEep--p~~~~fIl~t~~~~kl~~tI~S--Rc-~~~~f~~l~~~  181 (576)
T PRK14965        133 TNAFNALLKTLEEP--PPHVKFIFATTEPHKVPITILS--RC-QRFDFRRIPLQ  181 (576)
T ss_pred             HHHHHHHHHHHHcC--CCCeEEEEEeCChhhhhHHHHH--hh-hhhhcCCCCHH
Confidence            35567888888854  3467777888889999999988  77 46777666554

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=84.26  E-value=1.3  Score=34.14  Aligned_cols=49  Identities=24%  Similarity=0.175  Sum_probs=36.7

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.||..|+.-  .+++++|.+||.++.+.+.++.  |+ ..|+|+.++.++
T Consensus       134 ~a~naLLk~LEEP--~~~~ifILaTt~~~kll~TI~S--Rc-q~i~F~pLs~~e  182 (624)
T PRK14959        134 EAFNALLKTLEEP--PARVTFVLATTEPHKFPVTIVS--RC-QHFTFTRLSEAG  182 (624)
T ss_pred             HHHHHHHHHhhcc--CCCEEEEEecCChhhhhHHHHh--hh-hccccCCCCHHH
Confidence            4567788888753  3467788888889999999888  87 467887776554

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=84.14  E-value=2.7  Score=29.41  Aligned_cols=48  Identities=19%  Similarity=0.161  Sum_probs=33.1

Q ss_pred             HHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          18 VVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        18 ~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ..+.|+..|+..  ....++|.+|+.+..+.+++.+  |+ ..++++.|+.++
T Consensus       124 ~~~~ll~~le~~--~~~~~~Il~~~~~~kl~~~l~s--r~-~~v~~~~~~~~~  171 (367)
T PRK14970        124 AFNAFLKTLEEP--PAHAIFILATTEKHKIIPTILS--RC-QIFDFKRITIKD  171 (367)
T ss_pred             HHHHHHHHHhCC--CCceEEEEEeCCcccCCHHHHh--cc-eeEecCCccHHH
Confidence            456677767653  2345566667778899999988  76 458888887654

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=83.92  E-value=2.3  Score=29.88  Aligned_cols=52  Identities=15%  Similarity=0.159  Sum_probs=38.0

Q ss_pred             HHHHHHHhhCC--CCCCCeEEEEecCCCCCCcccccC--------------------CCccccEEEeCCCChhh
Q psy3374          19 VNQLLTELDGV--EGLEGVYVVGATSRPDIIDPALLR--------------------PGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        19 ~~~ll~~ld~~--~~~~~v~vi~aTn~~~~lD~al~r--------------------~GRfd~~i~v~~Pd~~~   70 (72)
                      --.|-+.|||-  ....+|++-||+||-..|++-...                    ..||..++.|..||.+.
T Consensus       157 yK~LKs~LeG~ve~rP~NVl~YATSNRRHLl~e~~~dn~~~~~eih~~eaveEKlSlSDRFGLwL~F~~~~Q~~  230 (287)
T COG2607         157 YKALKSALEGGVEGRPANVLFYATSNRRHLLPEDMKDNEGSTGEIHPSEAVEEKLSLSDRFGLWLSFYPCDQDE  230 (287)
T ss_pred             HHHHHHHhcCCcccCCCeEEEEEecCCcccccHhhhhCCCcccccChhHHHHHhhchhhhcceeecccCCCHHH
Confidence            34566777775  345689999999999888744321                    45888899988888753

>smart00350 MCM minichromosome maintenance proteins

Probab=83.17  E-value=1.6  Score=32.43  Aligned_cols=36  Identities=14%  Similarity=0.043  Sum_probs=28.3

Q ss_pred             CCeEEEEecCCCC-------------CCcccccCCCccccEEEe-CCCChhh
Q psy3374          33 EGVYVVGATSRPD-------------IIDPALLRPGRLGSSVHC-TMPDLAF   70 (72)
Q Consensus        33 ~~v~vi~aTn~~~-------------~lD~al~r~GRfd~~i~v-~~Pd~~~   70 (72)
                      .+..||||+|-.+             .|+++++.  |||..+.+ +.||.+.
T Consensus       342 ~~~~viAa~NP~~g~y~~~~~~~~n~~l~~~lLs--RFdLi~~~~d~~~~~~  391 (509)
T smart00350      342 ARCSVLAAANPIGGRYDPKLTPEENIDLPAPILS--RFDLLFVVLDEVDEER  391 (509)
T ss_pred             CCcEEEEEeCCCCcccCCCcChhhccCCChHHhC--ceeeEEEecCCCChHH
Confidence            4688999999643             69999999  99986554 6787764

>PRK04132 replication factor C small subunit; Provisional

Probab=82.92  E-value=2.7  Score=33.51  Aligned_cols=49  Identities=8%  Similarity=-0.032  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLA   69 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~   69 (72)
                      ....+.|+..|+..  .+++.+|.+||.++.+-++++.  |+ ..+.|+.|+.+
T Consensus       644 ~~AQnALLk~lEep--~~~~~FILi~N~~~kIi~tIrS--RC-~~i~F~~ls~~  692 (846)
T PRK04132        644 QDAQQALRRTMEMF--SSNVRFILSCNYSSKIIEPIQS--RC-AIFRFRPLRDE  692 (846)
T ss_pred             HHHHHHHHHHhhCC--CCCeEEEEEeCChhhCchHHhh--hc-eEEeCCCCCHH
Confidence            34567788888754  3467888999999999999998  88 77888888754

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=82.28  E-value=1.4  Score=32.92  Aligned_cols=50  Identities=22%  Similarity=0.217  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....|.||..|+..  .+.+.+|.+|+.++.+.+.++.  |+ ..++|..|+.++
T Consensus       133 ~~a~naLLK~LEep--p~~~~fIL~t~d~~kil~tI~S--Rc-~~~~f~~l~~~~  182 (527)
T PRK14969        133 KSAFNAMLKTLEEP--PEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPPL  182 (527)
T ss_pred             HHHHHHHHHHHhCC--CCCEEEEEEeCChhhCchhHHH--HH-HHHhcCCCCHHH
Confidence            45678888888864  3457777777888899888887  77 777887776653

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=82.02  E-value=0.91  Score=29.19  Aligned_cols=48  Identities=19%  Similarity=0.225  Sum_probs=27.7

Q ss_pred             HHHHHhhCCCCCCCeEEEEecCCCCCCc---ccccCCCcc--ccEEEeCCCChhh
Q psy3374          21 QLLTELDGVEGLEGVYVVGATSRPDIID---PALLRPGRL--GSSVHCTMPDLAF   70 (72)
Q Consensus        21 ~ll~~ld~~~~~~~v~vi~aTn~~~~lD---~al~r~GRf--d~~i~v~~Pd~~~   70 (72)
                      .+...++.....+..+|++++..+..++   +.+.+  ||  ...|.++.|+.++
T Consensus       111 ~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~--r~~~~~~i~l~~l~~~e  163 (226)
T TIGR03420       111 ALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRT--RLAWGLVFQLPPLSDEE  163 (226)
T ss_pred             HHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHH--HHhcCeeEecCCCCHHH
Confidence            3444444332223355565555555543   66777  66  4788899888754

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=81.63  E-value=3.1  Score=31.63  Aligned_cols=50  Identities=22%  Similarity=0.191  Sum_probs=37.1

Q ss_pred             hHHHHHHHHHHhhCCC-----------CCCCeEEEEecCCCC---CCcccccCCCccccEEEeCCC
Q psy3374          15 KDRVVNQLLTELDGVE-----------GLEGVYVVGATSRPD---IIDPALLRPGRLGSSVHCTMP   66 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~-----------~~~~v~vi~aTn~~~---~lD~al~r~GRfd~~i~v~~P   66 (72)
                      ...+.+.|+..|+.-.           ...++.||+|+|..+   .+.++|+.  ||+.+|.+..|
T Consensus        97 ~~~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g~L~~~Lld--Rf~l~v~~~~~  160 (589)
T TIGR02031        97 DDGLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGGGLPDHLLD--RLALHVSLEDV  160 (589)
T ss_pred             CHHHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccCCCCHHHHH--hccCeeecCCC
Confidence            3466777888886321           123588999999875   79999999  99999888764

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=81.38  E-value=1.8  Score=33.29  Aligned_cols=49  Identities=18%  Similarity=0.095  Sum_probs=37.2

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.||..|+..  .+.+++|.+|+.+..|.+++++  |+. .+++..|+.++
T Consensus       134 ~A~NaLLKtLEEP--p~~tvfIL~Tt~~~KLl~TI~S--Rcq-~ieF~~Ls~~e  182 (605)
T PRK05896        134 SAWNALLKTLEEP--PKHVVFIFATTEFQKIPLTIIS--RCQ-RYNFKKLNNSE  182 (605)
T ss_pred             HHHHHHHHHHHhC--CCcEEEEEECCChHhhhHHHHh--hhh-hcccCCCCHHH
Confidence            4567788888854  3457777788889999999999  884 68888877654

>smart00763 AAA_PrkA PrkA AAA domain

Probab=81.32  E-value=2.6  Score=30.47  Aligned_cols=51  Identities=18%  Similarity=0.169  Sum_probs=38.1

Q ss_pred             hHHHHHHHHHHhhCC--CCC-------CCeEEEEecCCC-------CCCcccccCCCccccEEEeCCCCh
Q psy3374          15 KDRVVNQLLTELDGV--EGL-------EGVYVVGATSRP-------DIIDPALLRPGRLGSSVHCTMPDL   68 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~--~~~-------~~v~vi~aTn~~-------~~lD~al~r~GRfd~~i~v~~Pd~   68 (72)
                      ....++.||..++.-  +..       -..++|++||-.       ....+||++  |+. .|+|+.|..
T Consensus       249 ~~~~l~~LL~~~qE~~v~~~~~~~~~~~d~liia~sNe~e~~~~~~~k~~eaf~d--R~~-~i~vpY~l~  315 (361)
T smart00763      249 DIKFLHPLLTATQEGNIKGTGGFAMIPIDGLIIAHSNESEWQRFKSNKKNEALLD--RII-KVKVPYCLR  315 (361)
T ss_pred             CHHHHHHHhhhhhcceEecCCcccccccceEEEEeCCHHHHhhhhccccchhhhh--ceE-EEeCCCcCC
Confidence            457888888888753  111       136899999988       377899999  997 888888753

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=81.28  E-value=3.5  Score=28.82  Aligned_cols=51  Identities=20%  Similarity=0.228  Sum_probs=34.5

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCC---CCcccccCCCccc-cEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPD---IIDPALLRPGRLG-SSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~---~lD~al~r~GRfd-~~i~v~~Pd~~~   70 (72)
                      ..+..|+..++.... .++.+|+++|.++   .+++.+..  ||. ..|+++.++.++
T Consensus       157 ~~l~~l~~~~~~~~~-~~v~vI~i~~~~~~~~~l~~~~~s--~~~~~~i~f~py~~~e  211 (394)
T PRK00411        157 DVLYSLLRAHEEYPG-ARIGVIGISSDLTFLYILDPRVKS--VFRPEEIYFPPYTADE  211 (394)
T ss_pred             hHHHHHHHhhhccCC-CeEEEEEEECCcchhhhcCHHHHh--cCCcceeecCCCCHHH
Confidence            356666666665533 2688888888764   46777766  664 578888888765

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=81.05  E-value=3.2  Score=31.40  Aligned_cols=51  Identities=20%  Similarity=0.149  Sum_probs=38.2

Q ss_pred             hHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          15 KDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      .....+.||..|+..  ...+.+|.+|+.+..|.++++.  |. ..++|..++.++
T Consensus       130 t~~A~NALLK~LEEp--p~~t~FIL~ttd~~kL~~tI~S--Rc-~~~~F~~Ls~~e  180 (535)
T PRK08451        130 TKEAFNALLKTLEEP--PSYVKFILATTDPLKLPATILS--RT-QHFRFKQIPQNS  180 (535)
T ss_pred             CHHHHHHHHHHHhhc--CCceEEEEEECChhhCchHHHh--hc-eeEEcCCCCHHH
Confidence            346678888888865  3345666667778999999999  86 688888877654

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=80.99  E-value=1.2  Score=32.65  Aligned_cols=37  Identities=14%  Similarity=0.180  Sum_probs=26.6

Q ss_pred             CCeEEEEecCCCC---CCcccccCCCccc--cEEEeCCCChhhh
Q psy3374          33 EGVYVVGATSRPD---IIDPALLRPGRLG--SSVHCTMPDLAFA   71 (72)
Q Consensus        33 ~~v~vi~aTn~~~---~lD~al~r~GRfd--~~i~v~~Pd~~~~   71 (72)
                      +..+|+++++.|.   .+++.|+.  ||.  ..+.+..|+.+.+
T Consensus       235 ~k~IIlts~~~p~~l~~l~~rL~S--R~~~Gl~~~l~~pd~e~r  276 (445)
T PRK12422        235 GKLIVISSTCAPQDLKAMEERLIS--RFEWGIAIPLHPLTKEGL  276 (445)
T ss_pred             CCcEEEecCCCHHHHhhhHHHHHh--hhcCCeEEecCCCCHHHH
Confidence            3456666655554   56789999  996  6888888998754

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=80.94  E-value=2.3  Score=32.25  Aligned_cols=50  Identities=14%  Similarity=0.140  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....+.||..|+..  ...+++|.+|+.++.|.++++.  |+. .+++..++.++
T Consensus       133 ~~a~naLLK~LEep--p~~~vfI~~tte~~kL~~tI~S--Rc~-~~~f~~l~~~e  182 (563)
T PRK06647        133 NSAFNALLKTIEEP--PPYIVFIFATTEVHKLPATIKS--RCQ-HFNFRLLSLEK  182 (563)
T ss_pred             HHHHHHHHHhhccC--CCCEEEEEecCChHHhHHHHHH--hce-EEEecCCCHHH
Confidence            34567788887743  3467777777889999999998  874 57887776554

>PRK13531 regulatory ATPase RavA; Provisional

Probab=80.72  E-value=2.9  Score=31.49  Aligned_cols=52  Identities=17%  Similarity=0.084  Sum_probs=33.2

Q ss_pred             hHHHHHHHHHHhhCCC--------CCCCeEEEEecCCCCC---CcccccCCCccccEEEeCCCCh
Q psy3374          15 KDRVVNQLLTELDGVE--------GLEGVYVVGATSRPDI---IDPALLRPGRLGSSVHCTMPDL   68 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~--------~~~~v~vi~aTn~~~~---lD~al~r~GRfd~~i~v~~Pd~   68 (72)
                      .....+.||..|..-.        .-...++++|||....   ..+|+.-  ||-.+|.+++|+.
T Consensus       120 sp~~QsaLLeam~Er~~t~g~~~~~lp~rfiv~ATN~LPE~g~~leAL~D--RFliri~vp~l~~  182 (498)
T PRK13531        120 GPAILNTLLTAINERRFRNGAHEEKIPMRLLVTASNELPEADSSLEALYD--RMLIRLWLDKVQD  182 (498)
T ss_pred             CHHHHHHHHHHHHhCeEecCCeEEeCCCcEEEEECCCCcccCCchHHhHh--hEEEEEECCCCCc
Confidence            4567788888884321        1112456666674321   2248888  9988999999974

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=80.63  E-value=3.2  Score=29.06  Aligned_cols=49  Identities=14%  Similarity=0.163  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....|.||..|+.-.   +.++|..|+.++.|-|.++.  |+ ..++|+.|+.+.
T Consensus       138 ~~aaNaLLK~LEEPp---~~~fILi~~~~~~Ll~TI~S--Rc-q~i~f~~l~~~~  186 (314)
T PRK07399        138 EAAANALLKTLEEPG---NGTLILIAPSPESLLPTIVS--RC-QIIPFYRLSDEQ  186 (314)
T ss_pred             HHHHHHHHHHHhCCC---CCeEEEEECChHhCcHHHHh--hc-eEEecCCCCHHH
Confidence            356778888888653   33456667789999999999  87 778888877654

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=80.62  E-value=2.4  Score=31.53  Aligned_cols=49  Identities=22%  Similarity=0.241  Sum_probs=34.2

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.||..|+..  ...+++|.+|+.++.+.+++.+  |+. .+.+..|+.++
T Consensus       134 ~a~naLLk~LEep--p~~~v~Il~tt~~~kl~~tI~S--Rc~-~i~f~~ls~~e  182 (486)
T PRK14953        134 EAFNALLKTLEEP--PPRTIFILCTTEYDKIPPTILS--RCQ-RFIFSKPTKEQ  182 (486)
T ss_pred             HHHHHHHHHHhcC--CCCeEEEEEECCHHHHHHHHHH--hce-EEEcCCCCHHH
Confidence            4567778887754  2345555566778889999988  774 68888877654

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=80.38  E-value=2.8  Score=31.99  Aligned_cols=49  Identities=18%  Similarity=0.175  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLA   69 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~   69 (72)
                      ....|.||..|+..  .+++++|.+|+.++.|.++++.  |. ..++|..++.+
T Consensus       132 ~~A~NALLK~LEEp--p~~~~fIL~tte~~kll~TI~S--Rc-~~~~F~~l~~~  180 (584)
T PRK14952        132 TAGFNALLKIVEEP--PEHLIFIFATTEPEKVLPTIRS--RT-HHYPFRLLPPR  180 (584)
T ss_pred             HHHHHHHHHHHhcC--CCCeEEEEEeCChHhhHHHHHH--hc-eEEEeeCCCHH
Confidence            35677888888854  3467778888889999999988  75 67888777654

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=80.18  E-value=3  Score=33.09  Aligned_cols=49  Identities=18%  Similarity=0.148  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLA   69 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~   69 (72)
                      ....|.||..|+...  .++++|.+|+.++.|-+.|+.  |+ ..++|..++.+
T Consensus       134 ~~a~NaLLK~LEEpP--~~~~fIl~tt~~~kLl~TIrS--Rc-~~v~F~~l~~~  182 (824)
T PRK07764        134 PQGFNALLKIVEEPP--EHLKFIFATTEPDKVIGTIRS--RT-HHYPFRLVPPE  182 (824)
T ss_pred             HHHHHHHHHHHhCCC--CCeEEEEEeCChhhhhHHHHh--he-eEEEeeCCCHH
Confidence            356678888888653  356777777888889999988  77 66777776554

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=80.09  E-value=3.2  Score=31.85  Aligned_cols=49  Identities=24%  Similarity=0.270  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLA   69 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~   69 (72)
                      ....+.||..|+.-  ...+++|.+|+.++.|-+.++.  |+ ..++|..++.+
T Consensus       135 ~~a~naLLK~LEeP--p~~tvfIL~t~~~~~llpTIrS--Rc-~~~~f~~l~~~  183 (620)
T PRK14948        135 TAAFNALLKTLEEP--PPRVVFVLATTDPQRVLPTIIS--RC-QRFDFRRIPLE  183 (620)
T ss_pred             HHHHHHHHHHHhcC--CcCeEEEEEeCChhhhhHHHHh--he-eEEEecCCCHH
Confidence            35677888888853  3457777778889999999988  77 55777666554

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=80.08  E-value=2.5  Score=23.75  Aligned_cols=33  Identities=18%  Similarity=0.159  Sum_probs=23.6

Q ss_pred             CCeEEEEecCC-CCCCcccccCCCccccEEEeCCCC
Q psy3374          33 EGVYVVGATSR-PDIIDPALLRPGRLGSSVHCTMPD   67 (72)
Q Consensus        33 ~~v~vi~aTn~-~~~lD~al~r~GRfd~~i~v~~Pd   67 (72)
                      .+..+|+++|. ....+..+.+  |++.++.++.|+
T Consensus       115 ~~~~~i~~~~~~~~~~~~~~~~--~~~~~~~~~~~~  148 (148)
T smart00382      115 KNLTVILTTNDEKDLGPALLRR--RFDRRIVLLLIL  148 (148)
T ss_pred             CCCEEEEEeCCCccCchhhhhh--ccceEEEecCCC
Confidence            45788888887 4445555555  999999987663

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=80.03  E-value=5.6  Score=27.01  Aligned_cols=47  Identities=15%  Similarity=0.121  Sum_probs=29.9

Q ss_pred             HHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          19 VNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        19 ~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      .+.|+..|+....  ...+|.+|+.+..+.+.+..  |+ ..+++..|+.++
T Consensus       142 ~~~L~~~le~~~~--~~~~Il~~~~~~~~~~~L~s--r~-~~v~~~~~~~~~  188 (337)
T PRK12402        142 QQALRRIMEQYSR--TCRFIIATRQPSKLIPPIRS--RC-LPLFFRAPTDDE  188 (337)
T ss_pred             HHHHHHHHHhccC--CCeEEEEeCChhhCchhhcC--Cc-eEEEecCCCHHH
Confidence            4455666665433  23344456667778888887  76 568888887764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	72
2x8a_A	274	Human Nuclear Valosin Containing Protein Like (Nvl)		4e-07
3cf0_A	301	Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH		5e-07
1r7r_A	816	The Crystal Structure Of Murine P97VCP AT 3.6A Leng		8e-07
3cf1_A	806	Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Len		8e-07
1iy2_A	278	Crystal Structure Of The Ftsh Atpase Domain From Th		8e-05
2ce7_A	476	Edta Treated Length = 476		9e-05
3kds_E	465	Apo-ftsh Crystal Structure Length = 465		9e-05
4b4t_H	467	Near-Atomic Resolution Structural Model Of The Yeas		1e-04
4eiw_A	508	Whole Cytosolic Region Of Atp-Dependent Metalloprot		1e-04
2dhr_A	499	Whole Cytosolic Region Of Atp-Dependent Metalloprot		1e-04
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		1e-04
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		1e-04
1ixz_A	254	Crystal Structure Of The Ftsh Atpase Domain From Th		2e-04
3h4m_A	285	Aaa Atpase Domain Of The Proteasome- Activating Nuc		2e-04
2r62_A	268	Crystal Structure Of Helicobacter Pylori Atp Depend		4e-04

>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C- Terminal Aaa-Atpase Domain Length = 274

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 26/61 (42%), Positives = 32/61 (52%)
Query: 6   RRGNDSTGVKDRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVHCTM 65
           RR +  TG   RVVNQ                  AT+RPDIIDPA+LRPGRL  ++   +
Sbjct: 118 RRSDRETGASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGL 177
Query: 66  P 66
           P
Sbjct: 178 P 178

>pdb|3CF0|A Chain A, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP Length = 301

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 23/52 (44%), Positives = 29/52 (55%)
Query: 16  DRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVHCTMPD 67
           DRV+NQ                  AT+RPDIIDPA+LRPGRL   ++  +PD
Sbjct: 136 DRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPD 187

>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A Length = 816

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 23/52 (44%), Positives = 29/52 (55%)
Query: 16  DRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVHCTMPD 67
           DRV+NQ                  AT+RPDIIDPA+LRPGRL   ++  +PD
Sbjct: 598 DRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPD 649

>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Length = 806

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 23/52 (44%), Positives = 29/52 (55%)
Query: 16  DRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVHCTMPD 67
           DRV+NQ                  AT+RPDIIDPA+LRPGRL   ++  +PD
Sbjct: 598 DRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPD 649

>pdb|1IY2|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 278

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 3   TGYRRGNDSTGVKDRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVH 62
           +G   GND    +++ +NQ                  AT+RPDI+DPALLRPGR    + 
Sbjct: 150 SGVGGGNDE---REQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA 206
Query: 63  CTMPDL 68
              PD+
Sbjct: 207 IDAPDV 212

>pdb|2CE7|A Chain A, Edta Treated Length = 476

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 17/29 (58%), Positives = 21/29 (72%)
Query: 40  ATSRPDIIDPALLRPGRLGSSVHCTMPDL 68
           AT+RPDI+DPALLRPGR    +    PD+
Sbjct: 160 ATNRPDILDPALLRPGRFDKKIVVDPPDM 188

>pdb|3KDS|E Chain E, Apo-ftsh Crystal Structure Length = 465

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 17/29 (58%), Positives = 21/29 (72%)
Query: 40  ATSRPDIIDPALLRPGRLGSSVHCTMPDL 68
           AT+RPDI+DPALLRPGR    +    PD+
Sbjct: 160 ATNRPDILDPALLRPGRFDKKIVVDPPDM 188

>pdb|4B4T|H Chain H, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 467

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 17/29 (58%), Positives = 23/29 (79%)
Query: 40  ATSRPDIIDPALLRPGRLGSSVHCTMPDL 68
           AT+RP+ +DPALLRPGR+   V  ++PDL
Sbjct: 354 ATNRPNTLDPALLRPGRIDRKVEFSLPDL 382

>pdb|4EIW|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 508

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 3   TGYRRGNDSTGVKDRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVH 62
           +G   GND    +++ +NQ                  AT+RPDI+DPALLRPGR    + 
Sbjct: 150 SGVGGGNDE---REQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA 206
Query: 63  CTMPDL 68
              PD+
Sbjct: 207 IDAPDV 212

>pdb|2DHR|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 499

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 3   TGYRRGNDSTGVKDRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVH 62
           +G   GND    +++ +NQ                  AT+RPDI+DPALLRPGR    + 
Sbjct: 141 SGVGGGNDE---REQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA 197
Query: 63  CTMPDL 68
              PD+
Sbjct: 198 IDAPDV 203

>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/30 (60%), Positives = 22/30 (73%)
Query: 40  ATSRPDIIDPALLRPGRLGSSVHCTMPDLA 69
           AT+RPD +DPALLRPGRL   V   +P+ A
Sbjct: 326 ATNRPDTLDPALLRPGRLDRKVEIPLPNEA 355

>pdb|1LV7|A Chain A, Crystal Structure Of The Aaa Domain Of Ftsh Length = 257

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 17/29 (58%), Positives = 22/29 (75%)
Query: 40  ATSRPDIIDPALLRPGRLGSSVHCTMPDL 68
           AT+RPD++DPALLRPGR    V   +PD+
Sbjct: 156 ATNRPDVLDPALLRPGRFDRQVVVGLPDV 184

>pdb|1IXZ|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 254

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 3   TGYRRGNDSTGVKDRVVNQXXXXXXXXXXXXXXXXXXATSRPDIIDPALLRPGRLGSSVH 62
           +G   GND    +++ +NQ                  AT+RPDI+DPALLRPGR    + 
Sbjct: 126 SGVGGGNDE---REQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA 182
Query: 63  CTMPDL 68
              PD+
Sbjct: 183 IDAPDV 188

>pdb|3H4M|A Chain A, Aaa Atpase Domain Of The Proteasome- Activating Nucleotidase Length = 285

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/28 (57%), Positives = 20/28 (71%)
Query: 40  ATSRPDIIDPALLRPGRLGSSVHCTMPD 67
           AT+RPDI+DPA+LRPGR    +    PD
Sbjct: 162 ATNRPDILDPAILRPGRFDRIIEVPAPD 189

>pdb|2R62|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent Protease, Ftsh Length = 268

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 16/29 (55%), Positives = 20/29 (68%)
Query: 40  ATSRPDIIDPALLRPGRLGSSVHCTMPDL 68
           AT+RP+I+DPAL+RPGR    V    PD 
Sbjct: 157 ATNRPEILDPALMRPGRFDRQVLVDKPDF 185

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	72
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	2e-36
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	1e-31
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	2e-28
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	1e-16
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	3e-19
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	6e-19
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	1e-17
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	2e-17
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	4e-17
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	4e-17
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	4e-17
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	4e-17
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	5e-17
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	3e-15
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	1e-14
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	1e-14
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	1e-14
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	3e-14
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	7e-13
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	3e-12
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	5e-12
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	6e-09

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens} Length = 274

 Score =  121 bits (307), Expect = 2e-36
 Identities = 35/64 (54%), Positives = 47/64 (73%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
           RR +  TG   RVVNQLLTE+DG+E  + V+++ AT+RPDIIDPA+LRPGRL  ++   +
Sbjct: 118 RRSDRETGASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGL 177

Query: 66  PDLA 69
           P  A
Sbjct: 178 PPPA 181

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus} Length = 301

 Score =  110 bits (276), Expect = 1e-31
 Identities = 34/67 (50%), Positives = 47/67 (70%), Gaps = 3/67 (4%)

Query: 6   RRGN---DSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVH 62
            RG    D  G  DRV+NQ+LTE+DG+   + V+++GAT+RPDIIDPA+LRPGRL   ++
Sbjct: 123 ARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIY 182

Query: 63  CTMPDLA 69
             +PD  
Sbjct: 183 IPLPDEK 189

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A* 2pjh_B Length = 489

 Score = 78.3 bits (193), Expect = 3e-19
 Identities = 27/62 (43%), Positives = 38/62 (61%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
           +R      V+ R+V+QLLT +DG++    V V+ AT+RP+ IDPAL R GR    V   +
Sbjct: 312 KREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGI 371

Query: 66  PD 67
           PD
Sbjct: 372 PD 373

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii} Length = 285

 Score = 76.5 bits (189), Expect = 6e-19
 Identities = 28/67 (41%), Positives = 39/67 (58%), Gaps = 3/67 (4%)

Query: 4   GYRRGNDSTGVK---DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSS 60
             +R +  TG      R + QLL E+DG +    V ++GAT+RPDI+DPA+LRPGR    
Sbjct: 123 AAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRI 182

Query: 61  VHCTMPD 67
           +    PD
Sbjct: 183 IEVPAPD 189

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A Length = 293

 Score = 73.3 bits (180), Expect = 1e-17
 Identities = 11/78 (14%), Positives = 23/78 (29%), Gaps = 12/78 (15%)

Query: 2   ITGYRRGNDSTGVKDRVVNQLLTEL------------DGVEGLEGVYVVGATSRPDIIDP 49
             G   G     V +++VN  L  +               +    V ++   +    +  
Sbjct: 111 GAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYA 170

Query: 50  ALLRPGRLGSSVHCTMPD 67
            L+R GR+         +
Sbjct: 171 PLIRDGRMEKFYWAPTRE 188

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens} Length = 262

 Score = 71.9 bits (177), Expect = 2e-17
 Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 3/61 (4%)

Query: 8   GNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD 67
            N     +++ +NQLL E+DG+   + V V+ +T+R DI+D AL+RPGRL   V   +P 
Sbjct: 122 SNTE---EEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPT 178

Query: 68  L 68
           L
Sbjct: 179 L 179

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20 Length = 278

 Score = 71.6 bits (176), Expect = 4e-17
 Identities = 29/61 (47%), Positives = 40/61 (65%), Gaps = 3/61 (4%)

Query: 8   GNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD 67
           GND    +++ +NQLL E+DG E    + V+ AT+RPDI+DPALLRPGR    +    PD
Sbjct: 155 GNDE---REQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPD 211

Query: 68  L 68
           +
Sbjct: 212 V 212

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20 Length = 257

 Score = 71.2 bits (175), Expect = 4e-17
 Identities = 30/61 (49%), Positives = 44/61 (72%), Gaps = 3/61 (4%)

Query: 8   GNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD 67
           G+D    +++ +NQ+L E+DG EG EG+ V+ AT+RPD++DPALLRPGR    V   +PD
Sbjct: 127 GHDE---REQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPD 183

Query: 68  L 68
           +
Sbjct: 184 V 184

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A* Length = 254

 Score = 71.2 bits (175), Expect = 4e-17
 Identities = 29/61 (47%), Positives = 40/61 (65%), Gaps = 3/61 (4%)

Query: 8   GNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD 67
           GND    +++ +NQLL E+DG E    + V+ AT+RPDI+DPALLRPGR    +    PD
Sbjct: 131 GNDE---REQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPD 187

Query: 68  L 68
           +
Sbjct: 188 V 188

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E* Length = 476

 Score = 72.2 bits (178), Expect = 4e-17
 Identities = 27/49 (55%), Positives = 35/49 (71%)

Query: 20  NQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDL 68
           NQLL E+DG +  EG+ V+ AT+RPDI+DPALLRPGR    +    PD+
Sbjct: 140 NQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDM 188

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus} Length = 499

 Score = 71.9 bits (177), Expect = 5e-17
 Identities = 26/49 (53%), Positives = 33/49 (67%)

Query: 20  NQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDL 68
           NQLL E+DG E    + V+ AT+RPDI+DPALLRPGR    +    PD+
Sbjct: 155 NQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDV 203

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A* Length = 268

 Score = 66.5 bits (163), Expect = 3e-15
 Identities = 25/50 (50%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 20  NQLLTELDG-VEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDL 68
           NQLL E+DG       V V+ AT+RP+I+DPAL+RPGR    V    PD 
Sbjct: 136 NQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDF 185

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A Length = 444

 Score = 65.4 bits (159), Expect = 1e-14
 Identities = 16/65 (24%), Positives = 33/65 (50%), Gaps = 3/65 (4%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEG-LEGVYVVGATSRPDIIDPALLRPGRLGSSVHCT 64
            R  + +    R+  + L ++ GV    +G+ V+GAT+ P ++D A+ R  R    ++  
Sbjct: 242 SRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRIYIP 299

Query: 65  MPDLA 69
           +P+  
Sbjct: 300 LPEAH 304

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A* Length = 355

 Score = 65.2 bits (159), Expect = 1e-14
 Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 3/65 (4%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGV-EGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCT 64
            RG   +    R+  +LL +++GV    +GV V+GAT+ P  +D A+ R  R    ++  
Sbjct: 158 TRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIP 215

Query: 65  MPDLA 69
           +PDLA
Sbjct: 216 LPDLA 220

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C Length = 322

 Score = 65.1 bits (159), Expect = 1e-14
 Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 3/65 (4%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGV-EGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCT 64
            RG   +    R+  +LL +++GV    +GV V+GAT+ P  +D A+ R  R    ++  
Sbjct: 125 TRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIP 182

Query: 65  MPDLA 69
           +PDLA
Sbjct: 183 LPDLA 187

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Length = 322

 Score = 63.9 bits (156), Expect = 3e-14
 Identities = 16/65 (24%), Positives = 33/65 (50%), Gaps = 3/65 (4%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVE-GLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCT 64
            R  + +    R+  + L ++ GV    +G+ V+GAT+ P ++D A+ R  R    ++  
Sbjct: 120 SRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRIYIP 177

Query: 65  MPDLA 69
           +P+  
Sbjct: 178 LPEPH 182

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens} Length = 357

 Score = 60.5 bits (147), Expect = 7e-13
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 4/64 (6%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGV--EGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHC 63
           +RG+       R+  + L +LDG      + + VVGAT+RP  ID A  R  RL   ++ 
Sbjct: 191 QRGDGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARR--RLVKRLYI 248

Query: 64  TMPD 67
            +P+
Sbjct: 249 PLPE 252

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Length = 297

 Score = 58.5 bits (142), Expect = 3e-12
 Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 6/71 (8%)

Query: 2   ITGYRRGNDSTGVKDRVVNQLLTELDGV---EGLEGVYVVGATSRPDIIDPALLRPGRLG 58
           +   R  ++      R+  + L E DG+      + + V+ AT+RP  +D A LR  R  
Sbjct: 125 LLSERSSSEH-EASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR--RFT 181

Query: 59  SSVHCTMPDLA 69
             V+ ++PD  
Sbjct: 182 KRVYVSLPDEQ 192

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens} Length = 389

 Score = 57.9 bits (140), Expect = 5e-12
 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 4/64 (6%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVE--GLEGVYVVGATSRPDIIDPALLRPGRLGSSVHC 63
            R         R+  + L E DGV+  G + V V+GAT+RP  +D A+LR  R    V+ 
Sbjct: 222 ERREGEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLR--RFIKRVYV 279

Query: 64  TMPD 67
           ++P+
Sbjct: 280 SLPN 283

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A* Length = 272

 Score = 49.0 bits (117), Expect = 6e-09
 Identities = 11/53 (20%), Positives = 24/53 (45%), Gaps = 4/53 (7%)

Query: 17  RVVNQLLTELDGVEGL-EGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDL 68
            V+  LL  L         + ++G TSR D++   +       +++H  +P++
Sbjct: 149 LVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQ-EMEMLNAFSTTIH--VPNI 198

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	72
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	99.81
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	99.8
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	99.8
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	99.79
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	99.78
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.78
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	99.76
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.69
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.55
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.44
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.38
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.38
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.36
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.34
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.31
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.3
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.28
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.26
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.24
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.22
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.21
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.2
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.17
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.13
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.1
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.01
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	98.97
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	98.94
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	98.88
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	98.85
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	98.59
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	97.78
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	97.5
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.48
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.44
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.38
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.17
2r44_A	331	Uncharacterized protein; putative ATPase, structur	97.1
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	97.01
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	96.85
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.72
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	96.69
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	96.58
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	96.51
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	96.49
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.47
2chg_A	226	Replication factor C small subunit; DNA-binding pr	96.45
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	96.42
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.29
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	96.26
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	96.19
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.04
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	96.0
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	95.92
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	95.65
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	95.58
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	95.46
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	95.25
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	94.98
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	94.91
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	94.84
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	94.81
2chq_A	319	Replication factor C small subunit; DNA-binding pr	94.6
3bos_A	242	Putative DNA replication factor; P-loop containing	94.49
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	94.37
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	94.36
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	94.31
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	94.23
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	94.22
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	94.08
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	93.93
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	93.76
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	92.08
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	91.47
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	91.34
3pvs_A	447	Replication-associated recombination protein A; ma	90.57
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	90.54
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	89.7
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	88.49
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	88.02
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	87.57
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	84.86
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	84.32
3f8t_A	506	Predicted ATPase involved in replication control,	83.64

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.81  E-value=2.9e-20  Score=131.92  Aligned_cols=59  Identities=39%  Similarity=0.636  Sum_probs=55.4

Q ss_pred             chhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          13 GVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        13 ~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ....+++++||++||++...++|+||||||+|+.||||++||||||++|+|++||.+++
T Consensus       266 ~~~~~~l~~lL~~lDg~~~~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R  324 (405)
T 4b4t_J          266 SEVQRTMLELLNQLDGFETSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAAR  324 (405)
T ss_dssp             GHHHHHHHHHHHHHHTTTCCCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHH
T ss_pred             HHHHHHHHHHHHhhhccCCCCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHH
Confidence            34568999999999999888899999999999999999999999999999999999876

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.80  E-value=8.2e-20  Score=130.40  Aligned_cols=60  Identities=42%  Similarity=0.660  Sum_probs=55.7

Q ss_pred             cchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          12 TGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        12 ~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +....+++++||++||++...++|+||+|||+|+.|||||+||||||++|+|++||.+++
T Consensus       298 ~~~~~~~l~~lL~~lDg~~~~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R  357 (437)
T 4b4t_L          298 DREIQRTLMELLTQMDGFDNLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGR  357 (437)
T ss_dssp             TTHHHHHHHHHHHHHHSSSCTTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHH
T ss_pred             chHHHHHHHHHHHHhhcccCCCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHH
Confidence            344668899999999999888899999999999999999999999999999999999876

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.80  E-value=8.6e-20  Score=130.18  Aligned_cols=58  Identities=38%  Similarity=0.591  Sum_probs=54.6

Q ss_pred             hhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          14 VKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ...+++++||++||++...++|+||||||+|+.||||++||||||++|+|++||.+++
T Consensus       300 ~~~~~~~~lL~~ldg~~~~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R  357 (434)
T 4b4t_M          300 EVQRTMLELLNQLDGFSSDDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSR  357 (434)
T ss_dssp             HHHHHHHHHHHHHTTSCSSCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHH
T ss_pred             HHHHHHHHHHHHhhccCCCCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHH
Confidence            4567899999999999888899999999999999999999999999999999999886

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.79  E-value=9e-20  Score=130.41  Aligned_cols=59  Identities=36%  Similarity=0.579  Sum_probs=55.5

Q ss_pred             chhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          13 GVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        13 ~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ....+++++||++||++...++|+||+|||+|+.|||||+||||||++|+|++||.+++
T Consensus       300 ~~~~~~l~~LL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R  358 (437)
T 4b4t_I          300 REIQRTMLELLNQLDGFDDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTK  358 (437)
T ss_dssp             CHHHHHHHHHHHHHHHCCCSSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHH
T ss_pred             HHHHHHHHHHHHHhhCcCCCCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHH
Confidence            45678999999999999888899999999999999999999999999999999999886

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.78  E-value=1.6e-19  Score=128.61  Aligned_cols=60  Identities=38%  Similarity=0.587  Sum_probs=55.5

Q ss_pred             cchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeC-CCChhhh
Q psy3374          12 TGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCT-MPDLAFA   71 (72)
Q Consensus        12 ~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~-~Pd~~~~   71 (72)
                      +....+++++||++|||+....+|+||||||+|+.||||++||||||++|+|+ +||.+++
T Consensus       289 ~~~~~r~l~~lL~~ldg~~~~~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R  349 (428)
T 4b4t_K          289 DREVQRILIELLTQMDGFDQSTNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRER  349 (428)
T ss_dssp             CCHHHHHHHHHHHHHHHSCSSCSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHH
T ss_pred             ChHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHH
Confidence            44567999999999999988889999999999999999999999999999995 8999876

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=99.78  E-value=8.1e-20  Score=137.79  Aligned_cols=61  Identities=51%  Similarity=0.890  Sum_probs=48.3

Q ss_pred             CcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          11 STGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        11 ~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +++..++++++||++||++...++|+||||||+|+.||+|++||||||++|+|++||.+++
T Consensus       593 ~~~~~~rv~~~lL~~mdg~~~~~~V~vi~aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R  653 (806)
T 3cf2_A          593 GGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSR  653 (806)
T ss_dssp             -----CHHHHHHHHHHHSSCSSSSEEEECC-CCSSSSCHHHHSTTTSCCEEEC-----CHH
T ss_pred             CchHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCchhCCHhHcCCCcceEEEEECCcCHHHH
Confidence            3456779999999999999888899999999999999999999999999999999999876

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.76  E-value=7.6e-19  Score=126.44  Aligned_cols=59  Identities=41%  Similarity=0.666  Sum_probs=55.0

Q ss_pred             chhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          13 GVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        13 ~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ....+++++||++||++...++|+||+|||+|+.||+|++||||||++|+|++||.++|
T Consensus       327 ~~~~~~l~~lL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R  385 (467)
T 4b4t_H          327 NEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGR  385 (467)
T ss_dssp             GHHHHHHHHHHHHHHSSCCTTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHH
T ss_pred             HHHHHHHHHHHHHhhccCCCCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHH
Confidence            34567899999999999888899999999999999999999999999999999999886

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=99.69  E-value=1.9e-17  Score=125.00  Aligned_cols=69  Identities=39%  Similarity=0.546  Sum_probs=62.8

Q ss_pred             eecccCCCCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           3 TGYRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         3 ~~~~r~~~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ++++|+++.++..++++++||.+||++...++|+||+|||+|+.||+||+||||||++|+|++||.++|
T Consensus       309 l~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R  377 (806)
T 3cf2_A          309 IAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGR  377 (806)
T ss_dssp             TCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEEEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHH
T ss_pred             cccccCCCCChHHHHHHHHHHHHHhcccccCCEEEEEecCChhhcCHHHhCCcccceEEecCCCCHHHH
Confidence            356677666777889999999999999888899999999999999999999999999999999999876

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.55  E-value=2.6e-15  Score=100.56  Aligned_cols=58  Identities=53%  Similarity=0.853  Sum_probs=53.1

Q ss_pred             hhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          14 VKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ...+++++++.+|++......++++++||+|+.||+|++||||||+.|++++||.+++
T Consensus       126 ~~~~~~~~~l~~Lsgg~~~~~~i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r  183 (274)
T 2x8a_A          126 ASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADR  183 (274)
T ss_dssp             -CTTHHHHHHHHHHTCCSTTCEEEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHH
T ss_pred             HHHHHHHHHHHhhhcccccCCEEEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHH
Confidence            3457889999999999877789999999999999999999999999999999999875

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=99.44  E-value=1.6e-13  Score=92.27  Aligned_cols=59  Identities=53%  Similarity=0.924  Sum_probs=54.0

Q ss_pred             chhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          13 GVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        13 ~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +...+++++||.+|+++....+++||+|||+++.||++++|+|||+..|++++|+.+++
T Consensus       133 ~~~~~~~~~lL~~l~~~~~~~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r  191 (301)
T 3cf0_A          133 GAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSR  191 (301)
T ss_dssp             CSCCHHHHHHHHHHHSSCTTSSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHH
T ss_pred             hHHHHHHHHHHHHhhcccCCCCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHH
Confidence            34568899999999999777789999999999999999999999999999999999875

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=99.38  E-value=3.3e-13  Score=97.03  Aligned_cols=60  Identities=45%  Similarity=0.794  Sum_probs=53.9

Q ss_pred             cchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          12 TGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        12 ~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +....+++++||.+||++....+++||+|||+|+.||++++||||||+.|+|++||.+++
T Consensus       132 ~~~~~~~l~~LL~~ld~~~~~~~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R  191 (476)
T 2ce7_A          132 HDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGR  191 (476)
T ss_dssp             -CHHHHHHHHHHHHHHHSCGGGTEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHH
T ss_pred             cHHHHHHHHHHHHHHhccCCCCCEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHH
Confidence            344568899999999998777789999999999999999999999999999999998765

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.38  E-value=1.7e-12  Score=84.73  Aligned_cols=58  Identities=48%  Similarity=0.877  Sum_probs=53.2

Q ss_pred             hhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          14 VKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ...+.++++|.+|+++....+++||+|||+++.+|++++|+|||++.+++++|+.+++
T Consensus       130 ~~~~~~~~ll~~l~~~~~~~~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r  187 (257)
T 1lv7_A          130 EREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGR  187 (257)
T ss_dssp             HHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHH
T ss_pred             HHHHHHHHHHHHhhCcccCCCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHH
Confidence            4457899999999999777789999999999999999999999999999999998865

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.34  E-value=1.7e-12  Score=88.29  Aligned_cols=65  Identities=25%  Similarity=0.472  Sum_probs=56.1

Q ss_pred             cccCCCCcchhHHHHHHHHHHhhCCC-CCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           5 YRRGNDSTGVKDRVVNQLLTELDGVE-GLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         5 ~~r~~~~~~~~~~~~~~ll~~ld~~~-~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +++.....+...+++++||.+||++. ...+++||+|||+|+.||++++|  ||+..|++++|+.+++
T Consensus       119 ~~~~~~~~~~~~~~~~~ll~~ld~~~~~~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r  184 (322)
T 1xwi_A          119 GSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEPHAR  184 (322)
T ss_dssp             CCSSSCCTTHHHHHHHHHHHHHHCSSSCCTTEEEEEEESCTTTSCHHHHH--TCCEEEECCCCCHHHH
T ss_pred             cccccccchHHHHHHHHHHHHHhcccccCCCEEEEEecCCcccCCHHHHh--hcCeEEEeCCcCHHHH
Confidence            34444455667799999999999985 45789999999999999999999  9999999999998875

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.31  E-value=3.5e-12  Score=92.11  Aligned_cols=60  Identities=43%  Similarity=0.736  Sum_probs=54.3

Q ss_pred             cchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          12 TGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        12 ~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +....+.++++|.+|++......++++++||+|+.||++++|+||||+.|+|++||.+++
T Consensus       147 ~~e~~~~l~~LL~~Ldg~~~~~~viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R  206 (499)
T 2dhr_A          147 NDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGR  206 (499)
T ss_dssp             SHHHHHHHHHHHHHGGGCCSSCCCEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHH
T ss_pred             cHHHHHHHHHHHHHhcccccCccEEEEEecCChhhcCcccccccccceEEecCCCCHHHH
Confidence            344568899999999999777789999999999999999999999999999999999865

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=99.30  E-value=5.4e-12  Score=82.17  Aligned_cols=59  Identities=44%  Similarity=0.746  Sum_probs=53.4

Q ss_pred             chhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          13 GVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        13 ~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ....+.+++++.+|++......++++++||+|+.||++++|+||||+.|++++||.+++
T Consensus       133 ~~~~~~~~~ll~~l~g~~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r  191 (254)
T 1ixz_A          133 DEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGR  191 (254)
T ss_dssp             HHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHH
T ss_pred             hHHHHHHHHHHHHHhCCCCCCCEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHHH
Confidence            34567889999999998777779999999999999999999999999999999999865

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=99.28  E-value=5.4e-12  Score=90.67  Aligned_cols=67  Identities=40%  Similarity=0.563  Sum_probs=58.8

Q ss_pred             cccCCCCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           5 YRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         5 ~~r~~~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +++....++...++.++||..|+++....+++||+|||+++.||++++|+|||+..|++++|+.+++
T Consensus       311 ~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR  377 (489)
T 3hu3_A          311 PKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGR  377 (489)
T ss_dssp             BCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHH
T ss_pred             cccccccchHHHHHHHHHHHHhhccccCCceEEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHH
Confidence            3444444566778999999999998777889999999999999999999999999999999998875

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=99.26  E-value=4.6e-13  Score=95.81  Aligned_cols=57  Identities=11%  Similarity=0.050  Sum_probs=0.0

Q ss_pred             CcchhHHHHHHHHHHhhCCCCCCCeEEEEe-cCCCCCCcccccCCCccccEEEeCCCChh
Q psy3374          11 STGVKDRVVNQLLTELDGVEGLEGVYVVGA-TSRPDIIDPALLRPGRLGSSVHCTMPDLA   69 (72)
Q Consensus        11 ~~~~~~~~~~~ll~~ld~~~~~~~v~vi~a-Tn~~~~lD~al~r~GRfd~~i~v~~Pd~~   69 (72)
                      .+...++++++||.+||++.....+  +++ ||+|+.||+||+|+||||++|+|++|+..
T Consensus       124 ~~~~e~rvl~~LL~~~dg~~~~~~v--~a~~TN~~~~ld~aL~rggr~D~~i~i~lP~~~  181 (444)
T 1g41_A          124 EDVAEERILDALLPPAKNQWGEVEN--HDSHSSTRQAFRKKLREGQLDDKEIEIDVSAGV  181 (444)
T ss_dssp             ------------------------------------------------------------
T ss_pred             hhhHHHHHHHHHHHHhhcccccccc--ccccccCHHHHHHHHHcCCCcceEEEEcCCCCc
Confidence            3445679999999999999665554  444 99999999999999999999999999986

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=99.24  E-value=1.1e-11  Score=80.28  Aligned_cols=58  Identities=41%  Similarity=0.679  Sum_probs=51.9

Q ss_pred             hhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          14 VKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .....+++|+.++++.....++++|+|||.++.+|++++|+|||+..+++++|+.+++
T Consensus       125 ~~~~~l~~ll~~~~~~~~~~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r  182 (262)
T 2qz4_A          125 EEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQER  182 (262)
T ss_dssp             --CHHHHHHHHHHHTCCTTCCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHH
T ss_pred             hHHHHHHHHHHHhhCcCCCCCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHH
Confidence            3457889999999998777789999999999999999999999999999999998875

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=99.22  E-value=5.9e-12  Score=85.13  Aligned_cols=65  Identities=34%  Similarity=0.545  Sum_probs=52.7

Q ss_pred             cccCCCCcchhHHHHHHHHHHhhCCC-CCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           5 YRRGNDSTGVKDRVVNQLLTELDGVE-GLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         5 ~~r~~~~~~~~~~~~~~ll~~ld~~~-~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ++++++.++...++.++|+.+|+++. ...+++||+|||+|+.||++++|  ||+..|++++|+.+++
T Consensus       124 ~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~atn~~~~ld~al~~--Rf~~~i~~~~p~~~~r  189 (322)
T 3eie_A          124 GTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAAR  189 (322)
T ss_dssp             CC------CCTHHHHHHHHHHHGGGGTSCCCEEEEEEESCGGGSCHHHHH--HCCEEEECCCCCHHHH
T ss_pred             ccCCCCcchHHHHHHHHHHHHhccccccCCceEEEEecCChhhCCHHHHc--ccCeEEEeCCCCHHHH
Confidence            33444445567789999999999984 55679999999999999999999  9999999999999875

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.21  E-value=2.6e-11  Score=80.15  Aligned_cols=59  Identities=44%  Similarity=0.746  Sum_probs=53.1

Q ss_pred             chhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          13 GVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        13 ~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ......+++++.+|++......++++++||+|+.||++++|+|||++.|++++|+.+++
T Consensus       157 ~~~~~~~~~ll~~lsgg~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r  215 (278)
T 1iy2_A          157 DEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGR  215 (278)
T ss_dssp             HHHHHHHHHHHHHHTTCCTTCCEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHH
T ss_pred             hHHHHHHHHHHHHHhCCCCCCCEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHH
Confidence            34567889999999998766679999999999999999999999999999999998865

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=99.20  E-value=1.6e-11  Score=86.73  Aligned_cols=65  Identities=25%  Similarity=0.477  Sum_probs=55.8

Q ss_pred             cccCCCCcchhHHHHHHHHHHhhCCC-CCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           5 YRRGNDSTGVKDRVVNQLLTELDGVE-GLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         5 ~~r~~~~~~~~~~~~~~ll~~ld~~~-~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +++.....+...+++++||.+|+++. ...+++||+|||+|+.||++++|  ||+..+++++|+.+++
T Consensus       241 ~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r  306 (444)
T 2zan_A          241 GSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHAR  306 (444)
T ss_dssp             CCSSCCCCGGGHHHHHHHHTTTTCSSCCCSSCEEEEEESCGGGSCHHHHT--TCCEEEECCCCCHHHH
T ss_pred             cCCCCccccHHHHHHHHHHHHHhCcccCCCCEEEEecCCCccccCHHHHh--hcceEEEeCCcCHHHH
Confidence            34444455667899999999999985 35689999999999999999999  9999999999998865

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=99.17  E-value=1.3e-11  Score=84.90  Aligned_cols=64  Identities=34%  Similarity=0.576  Sum_probs=51.3

Q ss_pred             ccCCCCcchhHHHHHHHHHHhhCCCC-CCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           6 RRGNDSTGVKDRVVNQLLTELDGVEG-LEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         6 ~r~~~~~~~~~~~~~~ll~~ld~~~~-~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +++.+.+....++.++||.+|+++.. ..+++||+|||+|+.||++++|  ||+..+++++|+.+++
T Consensus       158 ~r~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r  222 (355)
T 2qp9_X          158 TRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAAR  222 (355)
T ss_dssp             ------CTHHHHHHHHHHHHHHHCC---CCEEEEEEESCGGGSCHHHHH--TCCEEEECCCCCHHHH
T ss_pred             cCCCCcchHHHHHHHHHHHHhhcccccCCCeEEEeecCCcccCCHHHHc--ccCEEEEeCCcCHHHH
Confidence            33344455677899999999999853 5679999999999999999999  9999999999998875

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.13  E-value=7.1e-11  Score=77.56  Aligned_cols=59  Identities=42%  Similarity=0.707  Sum_probs=53.1

Q ss_pred             chhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          13 GVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        13 ~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ......+.+++.+++++....+++||+|||.++.+|++++|+|||+..++++.|+.+++
T Consensus       135 ~~~~~~l~~ll~~~~~~~~~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r  193 (285)
T 3h4m_A          135 REVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGR  193 (285)
T ss_dssp             GHHHHHHHHHHHHHHTTCSSSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHH
T ss_pred             HHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHH
Confidence            34557888999999998777789999999999999999999999999999999998875

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.10  E-value=3.8e-11  Score=80.66  Aligned_cols=56  Identities=16%  Similarity=0.119  Sum_probs=44.8

Q ss_pred             hhHHHHHHHHHHhhCCC-----------CCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          14 VKDRVVNQLLTELDGVE-----------GLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~-----------~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ....+.+.|++.||+..           ...+++||+|||+++.||++++|+||||..|+  +|+.+++
T Consensus       124 ~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~~ld~al~R~~R~d~~i~--~P~~~~r  190 (293)
T 3t15_A          124 NNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYW--APTREDR  190 (293)
T ss_dssp             CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCCC--CHHHHHHHEEEEEE--CCCHHHH
T ss_pred             hHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcccCCHHHhCCCCCceeEe--CcCHHHH
Confidence            34467799999998553           44579999999999999999999999999998  5787764

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=99.01  E-value=3.6e-11  Score=78.50  Aligned_cols=55  Identities=45%  Similarity=0.744  Sum_probs=48.4

Q ss_pred             HHHHHHHHHhhCCCC-CCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          17 RVVNQLLTELDGVEG-LEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~-~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +.+++|+..|++... ..+++||+|||.++.+|++++|+|||+..|++++|+.+++
T Consensus       133 ~~~~~ll~~l~~~~~~~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r  188 (268)
T 2r62_A          133 QTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGR  188 (268)
T ss_dssp             SSTTTTTTTTTCSSCSCSCCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTTTH
T ss_pred             HHHHHHHHHhhCcccCCCCEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHHHH
Confidence            567888999998743 3459999999999999999999999999999999998865

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=98.94  E-value=8.6e-10  Score=75.65  Aligned_cols=61  Identities=31%  Similarity=0.490  Sum_probs=49.5

Q ss_pred             CCCcchhHHHHHHHHHHhhCCC--CCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           9 NDSTGVKDRVVNQLLTELDGVE--GLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         9 ~~~~~~~~~~~~~ll~~ld~~~--~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.+....+++++||..|++..  ...+++||+|||+++.||++++|  ||+..+++++|+.+++
T Consensus       194 ~~~~~~~~~~~~~lL~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~--Rf~~~i~i~~p~~~~r  256 (357)
T 3d8b_A          194 DGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARR--RLVKRLYIPLPEASAR  256 (357)
T ss_dssp             ----CHHHHHHHHHHHHHHC----CCCCEEEEEEESCGGGBCHHHHT--TCCEEEECCCCCHHHH
T ss_pred             CCcchHHHHHHHHHHHHHhcccccCCCCEEEEEecCChhhCCHHHHh--hCceEEEeCCcCHHHH
Confidence            3344556788999999999984  34579999999999999999999  9999999999998865

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=98.88  E-value=7.9e-10  Score=73.03  Aligned_cols=58  Identities=33%  Similarity=0.539  Sum_probs=48.6

Q ss_pred             cchhHHHHHHHHHHhhCCCCC---CCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          12 TGVKDRVVNQLLTELDGVEGL---EGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        12 ~~~~~~~~~~ll~~ld~~~~~---~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+...+..++||..+++....   .+++||++||+|+.+|++++|  ||+..+++++|+.+++
T Consensus       134 ~~~~~~~~~~ll~~l~~~~~~~~~~~v~vi~~tn~~~~l~~~l~~--R~~~~i~~~~p~~~~r  194 (297)
T 3b9p_A          134 HEASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR--RFTKRVYVSLPDEQTR  194 (297)
T ss_dssp             -CCSHHHHHHHHHHHHHCC------CEEEEEEESCGGGBCHHHHH--HCCEEEECCCCCHHHH
T ss_pred             chHHHHHHHHHHHHHhcccccCCCCcEEEEeecCChhhCCHHHHh--hCCeEEEeCCcCHHHH
Confidence            344567889999999988542   579999999999999999999  9999999999998764

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=98.85  E-value=1.5e-09  Score=74.93  Aligned_cols=60  Identities=33%  Similarity=0.531  Sum_probs=49.3

Q ss_pred             CCcchhHHHHHHHHHHhhCCCC--CCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          10 DSTGVKDRVVNQLLTELDGVEG--LEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        10 ~~~~~~~~~~~~ll~~ld~~~~--~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +......++.++|+..|+++..  ..+++||+|||+++.||++++|  ||+..|++++|+.+++
T Consensus       226 ~~~~~~~~~~~~ll~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~--R~~~~i~i~~p~~~~r  287 (389)
T 3vfd_A          226 GEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLR--RFIKRVYVSLPNEETR  287 (389)
T ss_dssp             ---CTHHHHHHHHHHHHHHHC-----CEEEEEEESCGGGCCHHHHT--TCCEEEECCCCCHHHH
T ss_pred             ccchHHHHHHHHHHHHhhcccccCCCCEEEEEecCCchhcCHHHHc--CcceEEEcCCcCHHHH
Confidence            3344567889999999998854  4579999999999999999999  9999999999998875

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=98.59  E-value=1e-08  Score=72.31  Aligned_cols=51  Identities=10%  Similarity=0.083  Sum_probs=41.0

Q ss_pred             HHHHHHHHhh--CCCCCCCeEEEEecCCCCCCcccccCCCcccc--EEEeCCCCh
Q psy3374          18 VVNQLLTELD--GVEGLEGVYVVGATSRPDIIDPALLRPGRLGS--SVHCTMPDL   68 (72)
Q Consensus        18 ~~~~ll~~ld--~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~--~i~v~~Pd~   68 (72)
                      +.++++.+|+  ++...+.++|++|||+++.+|+|+.|+||||+  .+++++|+.
T Consensus       172 ~~~~ll~~l~~~~~~~~~~v~i~attn~~~~ld~a~~r~~rfd~~~~~~v~~p~~  226 (456)
T 2c9o_A          172 LDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKG  226 (456)
T ss_dssp             ECHHHHHHHHHTTCCTTEEEEEETTTCCEEEEEEETTSCCTTSCSSSSEECCCCS
T ss_pred             hhHHHHHHHhhccCCCCCEEEEEcCCCCcccCChhhcCCcccCcceeEecCCCch
Confidence            3456777776  34445557778999999999999999999999  778888864

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=97.78  E-value=7.5e-06  Score=59.15  Aligned_cols=51  Identities=16%  Similarity=0.114  Sum_probs=39.4

Q ss_pred             HHHHHHHHhhCCCC-------------CCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          18 VVNQLLTELDGVEG-------------LEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        18 ~~~~ll~~ld~~~~-------------~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ..+.||..||....             ..++++|+|||.++.+|++|++  ||+ .|+++.|+.++.
T Consensus       195 ~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI~ttN~~~~l~~aL~~--R~~-vi~~~~~~~~e~  258 (543)
T 3m6a_A          195 PSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFIATANNLATIPGPLRD--RME-IINIAGYTEIEK  258 (543)
T ss_dssp             ---CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEEEECSSTTTSCHHHHH--HEE-EEECCCCCHHHH
T ss_pred             HHHHHHHHHhhhhcceeecccCCeeecccceEEEeccCccccCCHHHHh--hcc-eeeeCCCCHHHH
Confidence            45678888875421             1468999999999999999999  996 799999998764

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=97.50  E-value=0.0001  Score=48.00  Aligned_cols=52  Identities=25%  Similarity=0.299  Sum_probs=42.0

Q ss_pred             HHHHHHHHHhhCCC--------CCCCeEEEEe----cCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVE--------GLEGVYVVGA----TSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~--------~~~~v~vi~a----Tn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      .+.+.|+..|++..        ...++++|++    ++.+..+++++++  ||+..|+|+.|+.++
T Consensus       143 ~~~~~Ll~~le~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~--R~~~~i~~~~~~~~~  206 (310)
T 1ofh_A          143 GVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAAD  206 (310)
T ss_dssp             HHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHH--TCCEEEECCCCCHHH
T ss_pred             HHHHHHHHHhcCCeEecccccccCCcEEEEEcCCcccCCcccCCHHHHh--hCCceEEcCCcCHHH
Confidence            45788999998741        2246788888    6789999999998  999999999999875

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=97.48  E-value=0.00016  Score=48.19  Aligned_cols=54  Identities=17%  Similarity=0.226  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHhhCCCC----------------CCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          16 DRVVNQLLTELDGVEG----------------LEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~----------------~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ....+.|+..|+....                ..++.+|++||+...++++|++  ||+..++++.|+.++.
T Consensus       120 ~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~atn~~~~l~~~L~~--R~~~~i~l~~~~~~e~  189 (338)
T 3pfi_A          120 PAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTLIGATTRAGMLSNPLRD--RFGMQFRLEFYKDSEL  189 (338)
T ss_dssp             HHHHHHHHHHHHTSCC---------CCCCCCCCCCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHH
T ss_pred             HHHHHHHHHHHHhccchhhcccCccccceecCCCCeEEEEeCCCccccCHHHHh--hcCEEeeCCCcCHHHH
Confidence            3556677777765320                1148999999999999999999  9999999999988763

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=97.44  E-value=6.3e-05  Score=49.01  Aligned_cols=53  Identities=21%  Similarity=0.364  Sum_probs=40.6

Q ss_pred             hhHHHHHHHHHHhhCCC-CCCCeEEEEecCCCCCCcc-cccCCCccccEEEeCCCCh
Q psy3374          14 VKDRVVNQLLTELDGVE-GLEGVYVVGATSRPDIIDP-ALLRPGRLGSSVHCTMPDL   68 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~-~~~~v~vi~aTn~~~~lD~-al~r~GRfd~~i~v~~Pd~   68 (72)
                      ....+++.|+..+++.. ...++++|+|||.++.+|+ .+.+  ||+..|+++.++.
T Consensus       146 ~~~~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~~l~~~~l~~--rf~~~i~~p~l~~  200 (272)
T 1d2n_A          146 FSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLN--AFSTTIHVPNIAT  200 (272)
T ss_dssp             CCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTT--TSSEEEECCCEEE
T ss_pred             HHHHHHHHHHHHhcCccCCCCCEEEEEecCChhhcchhhhhc--ccceEEcCCCccH
Confidence            34567777888888764 3446899999999999998 5565  9999998876543

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.38  E-value=4.8e-05  Score=49.96  Aligned_cols=53  Identities=11%  Similarity=0.098  Sum_probs=43.3

Q ss_pred             hHHHHHHHHHHhhCCCCCCCeEEEEecCCCC-----CCcccccCCCccccEEEeCCCChhhh
Q psy3374          15 KDRVVNQLLTELDGVEGLEGVYVVGATSRPD-----IIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~-----~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ...+.+.|+..|+..  ..++++|++||.++     .++|+|++  ||+..|+|+.|+.++.
T Consensus       152 ~~~~~~~Ll~~l~~~--~~~~~~i~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~~~~~~~  209 (309)
T 3syl_A          152 GQEAIEILLQVMENN--RDDLVVILAGYADRMENFFQSNPGFRS--RIAHHIEFPDYSDEEL  209 (309)
T ss_dssp             THHHHHHHHHHHHHC--TTTCEEEEEECHHHHHHHHHHSTTHHH--HEEEEEEECCCCHHHH
T ss_pred             cHHHHHHHHHHHhcC--CCCEEEEEeCChHHHHHHHhhCHHHHH--hCCeEEEcCCcCHHHH
Confidence            457888999999864  44688999998764     36799999  9999999999998763

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=97.17  E-value=0.00066  Score=44.65  Aligned_cols=36  Identities=31%  Similarity=0.418  Sum_probs=32.7

Q ss_pred             CeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          34 GVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        34 ~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ++.+|++||++..+++++.+  ||+..+.++.|+.++.
T Consensus       138 ~~~~i~~t~~~~~~~~~l~~--R~~~~i~l~~~~~~e~  173 (324)
T 1hqc_A          138 RFTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEEL  173 (324)
T ss_dssp             CCEEEEEESCCSSCSCSTTT--TCSCEEECCCCCHHHH
T ss_pred             CEEEEEeCCCcccCCHHHHh--cccEEEecCCCCHHHH
Confidence            57899999999999999999  9999999999988653

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=97.10  E-value=0.0006  Score=45.39  Aligned_cols=54  Identities=17%  Similarity=0.122  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHhhCC---------CCCCCeEEEEecCCCC-----CCcccccCCCccccEEEeCCCChhhh
Q psy3374          16 DRVVNQLLTELDGV---------EGLEGVYVVGATSRPD-----IIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        16 ~~~~~~ll~~ld~~---------~~~~~v~vi~aTn~~~-----~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ....+.|+..|+.-         ....++++++|+|..+     .+++++++  ||+..++++.|+.++.
T Consensus       123 ~~~~~~Ll~~l~~~~~~~~g~~~~~~~~~~viat~np~~~~~~~~l~~~l~~--Rf~~~i~i~~p~~~~~  190 (331)
T 2r44_A          123 AKVQSALLECMQEKQVTIGDTTYPLDNPFLVLATQNPVEQEGTYPLPEAQVD--RFMMKIHLTYLDKESE  190 (331)
T ss_dssp             HHHHHHHHHHHHHSEEEETTEEEECCSSCEEEEEECTTCCSCCCCCCHHHHT--TSSEEEECCCCCHHHH
T ss_pred             HHHHHHHHHHHhcCceeeCCEEEECCCCEEEEEecCCCcccCcccCCHHHHh--heeEEEEcCCCCHHHH
Confidence            35666777777642         1234688889998443     39999999  9999999999998764

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=97.01  E-value=0.00091  Score=44.33  Aligned_cols=49  Identities=31%  Similarity=0.445  Sum_probs=37.0

Q ss_pred             HHHHHHHHHhhC----CCC-------CCCeEEEEecCCCC-CCcccccCCCccccEEEeCCCC
Q psy3374          17 RVVNQLLTELDG----VEG-------LEGVYVVGATSRPD-IIDPALLRPGRLGSSVHCTMPD   67 (72)
Q Consensus        17 ~~~~~ll~~ld~----~~~-------~~~v~vi~aTn~~~-~lD~al~r~GRfd~~i~v~~Pd   67 (72)
                      ...+.|+..|+.    +..       ..++++|+|||..+ .++++|++  ||+.+++++.|+
T Consensus       159 ~~~~~Ll~~le~~~~~~~~~g~~~~~~~~~~li~~~n~~~~~l~~~L~~--R~~~~~~l~~~~  219 (350)
T 1g8p_A          159 HIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPR  219 (350)
T ss_dssp             HHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCC
T ss_pred             HHHHHHHHHHhcCceEEEecceEEeeCCceEEEEEeCCCCCCCCHHHHh--hcceEEEcCCCC
Confidence            455667776663    111       12689999999745 89999999  999999999994

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=96.85  E-value=7.3e-05  Score=44.78  Aligned_cols=36  Identities=31%  Similarity=0.338  Sum_probs=31.1

Q ss_pred             CCeEEEEecCCCC-----CCcccccCCCccccEEEeCCCChhhh
Q psy3374          33 EGVYVVGATSRPD-----IIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        33 ~~v~vi~aTn~~~-----~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .++.+|++||.++     .+|+++.+  ||+ .|+++.|+.+++
T Consensus       150 ~~~~~i~~~~~~~~~~~~~~~~~l~~--r~~-~i~~~~p~~~~~  190 (195)
T 1jbk_A          150 GELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDT  190 (195)
T ss_dssp             TSCCEEEEECHHHHHHHTTTCHHHHT--TEE-EEECCCCCHHHH
T ss_pred             CCeEEEEeCCHHHHHHHHhcCHHHHH--Hhc-eeecCCCCHHHH
Confidence            4578889999887     89999999  998 699999998865

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.72  E-value=0.0012  Score=48.94  Aligned_cols=37  Identities=24%  Similarity=0.345  Sum_probs=32.5

Q ss_pred             CCCeEEEEecCCCC-----CCcccccCCCccccEEEeCCCChhhh
Q psy3374          32 LEGVYVVGATSRPD-----IIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        32 ~~~v~vi~aTn~~~-----~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.+.+|+|||..+     .+|+++.|  || ..|+|+.|+.+++
T Consensus       289 ~~~v~~I~at~~~~~~~~~~~d~al~r--Rf-~~i~v~~p~~~~~  330 (758)
T 3pxi_A          289 RGELQCIGATTLDEYRKYIEKDAALER--RF-QPIQVDQPSVDES  330 (758)
T ss_dssp             SSSCEEEEECCTTTTHHHHTTCSHHHH--SE-EEEECCCCCHHHH
T ss_pred             cCCEEEEeCCChHHHHHHhhccHHHHh--hC-cEEEeCCCCHHHH
Confidence            45689999999999     79999999  99 5699999998764

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=96.69  E-value=0.0012  Score=46.71  Aligned_cols=37  Identities=24%  Similarity=0.334  Sum_probs=32.2

Q ss_pred             CCCeEEEEecCCCC-----CCcccccCCCccccEEEeCCCChhhh
Q psy3374          32 LEGVYVVGATSRPD-----IIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        32 ~~~v~vi~aTn~~~-----~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.+.+|++||.++     .+|+++.|  ||. .|.|+.|+.++.
T Consensus       289 ~g~v~vI~at~~~e~~~~~~~~~al~~--Rf~-~i~v~~p~~e~~  330 (468)
T 3pxg_A          289 RGELQCIGATTLDEYRKYIEKDAALER--RFQ-PIQVDQPSVDES  330 (468)
T ss_dssp             SSSCEEEEECCTTTTHHHHTTCSHHHH--SEE-EEECCCCCHHHH
T ss_pred             CCCEEEEecCCHHHHHHHhhcCHHHHH--hCc-cceeCCCCHHHH
Confidence            44689999999998     79999999  998 599999998763

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=96.58  E-value=7.2e-05  Score=44.96  Aligned_cols=32  Identities=28%  Similarity=0.390  Sum_probs=27.6

Q ss_pred             CCeEEEEecCCCC-----CCcccccCCCccccEEEeCCCC
Q psy3374          33 EGVYVVGATSRPD-----IIDPALLRPGRLGSSVHCTMPD   67 (72)
Q Consensus        33 ~~v~vi~aTn~~~-----~lD~al~r~GRfd~~i~v~~Pd   67 (72)
                      .++.+|++||.++     .+|+++++  ||+. |+++.|+
T Consensus       151 ~~~~ii~~~~~~~~~~~~~~~~~l~~--R~~~-i~i~~p~  187 (187)
T 2p65_A          151 GELRCIGATTVSEYRQFIEKDKALER--RFQQ-ILVEQPS  187 (187)
T ss_dssp             TCSCEEEEECHHHHHHHTTTCHHHHH--HEEE-EECCSCC
T ss_pred             CCeeEEEecCHHHHHHHHhccHHHHH--hcCc-ccCCCCC
Confidence            4678999999876     69999999  9995 9999996

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=96.51  E-value=0.0036  Score=41.56  Aligned_cols=54  Identities=13%  Similarity=0.113  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCC---CCCcccccCCCcccc-EEEeCCCChhhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRP---DIIDPALLRPGRLGS-SVHCTMPDLAFA   71 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~---~~lD~al~r~GRfd~-~i~v~~Pd~~~~   71 (72)
                      ...+..++.+++......++.+|++||.+   +.+++++.+  ||.. .|+++.|+.++.
T Consensus       149 ~~~l~~l~~~~~~~~~~~~~~~I~~t~~~~~~~~l~~~l~~--r~~~~~i~l~~l~~~~~  206 (387)
T 2v1u_A          149 QDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKS--SLGEVELVFPPYTAPQL  206 (387)
T ss_dssp             HHHHHHHHHGGGCC-----CEEEEECSCSTTSSSSCHHHHT--TTTSEECCBCCCCHHHH
T ss_pred             ChHHHhHhhchhhcCCCceEEEEEEECCCchHhhhCHHHHh--cCCCeEEeeCCCCHHHH
Confidence            35566666666654324578999999998   789999999  9986 899999987653

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=96.49  E-value=0.0025  Score=46.61  Aligned_cols=51  Identities=12%  Similarity=0.052  Sum_probs=38.1

Q ss_pred             HHHHHHHHHhhCCC-----------CCCCeEEEEecCCCC-------------CCcccccCCCcccc-EEEeCCCChh
Q psy3374          17 RVVNQLLTELDGVE-----------GLEGVYVVGATSRPD-------------IIDPALLRPGRLGS-SVHCTMPDLA   69 (72)
Q Consensus        17 ~~~~~ll~~ld~~~-----------~~~~v~vi~aTn~~~-------------~lD~al~r~GRfd~-~i~v~~Pd~~   69 (72)
                      ...+.|+..|+.-.           ...++.||||||.+.             .|++|+++  |||. .+..+.|+.+
T Consensus       406 ~~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vIaatNp~~G~~~~~~~~~~ni~l~~aLl~--RFDl~~~~~~~~~~e  481 (595)
T 3f9v_A          406 EDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIAAGNPKFGRYISERPVSDNINLPPTILS--RFDLIFILKDQPGEQ  481 (595)
T ss_dssp             HHHHHHHHHHHSSSEEEESSSSEEEECCCCEEEEEECCTTCCSCTTSCSCTTTCSCSSSGG--GCSCCEEECCTTHHH
T ss_pred             hHhhhhHHHHhCCEEEEecCCcEEEecCceEEEEEcCCcCCccCcccCchhccCCCHHHHh--hCeEEEEeCCCCCHH
Confidence            45677788877421           123688999999987             99999999  9995 6666777654

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.47  E-value=0.0028  Score=46.99  Aligned_cols=54  Identities=13%  Similarity=0.198  Sum_probs=40.6

Q ss_pred             hHHHHHHHHHHhhCCC---------CCCCeEEEEecCCCCC------------CcccccCCCccccEEEeCCCChhh
Q psy3374          15 KDRVVNQLLTELDGVE---------GLEGVYVVGATSRPDI------------IDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~---------~~~~v~vi~aTn~~~~------------lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.+.|++.|+.-.         ...++++|+|||.+..            +.|+++.  |||..|.|+.|+.+.
T Consensus       592 ~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~~~~~~~~~~~~~f~p~l~~--Rl~~~i~~~~l~~~~  666 (758)
T 3pxi_A          592 HPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGASEKDKVMGELKRAFRPEFIN--RIDEIIVFHSLEKKH  666 (758)
T ss_dssp             CHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTTCCHHHHHHHHHHSCHHHHT--TSSEEEECC--CHHH
T ss_pred             CHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChhhHHHHHHHHHhhCCHHHHh--hCCeEEecCCCCHHH
Confidence            4577888888888631         2236899999998665            7888888  999999999998865

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=96.45  E-value=0.0037  Score=37.96  Aligned_cols=50  Identities=6%  Similarity=-0.088  Sum_probs=38.9

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ...+.|+..++..  ..++.+|++||.++.+++++.+  ||. .++++.|+.++.
T Consensus       117 ~~~~~l~~~l~~~--~~~~~~i~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~  166 (226)
T 2chg_A          117 DAQAALRRTMEMY--SKSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEAM  166 (226)
T ss_dssp             HHHHHHHHHHHHT--TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHH
T ss_pred             HHHHHHHHHHHhc--CCCCeEEEEeCChhhcCHHHHH--hCc-eeecCCCCHHHH
Confidence            3455666666653  3467888999999999999999  997 899998887653

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=96.42  E-value=0.0012  Score=43.21  Aligned_cols=53  Identities=21%  Similarity=0.209  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHhhCCC--C-------CCCeEEEEecCC--------------------------CCCCcccccCCCccccE
Q psy3374          16 DRVVNQLLTELDGVE--G-------LEGVYVVGATSR--------------------------PDIIDPALLRPGRLGSS   60 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~--~-------~~~v~vi~aTn~--------------------------~~~lD~al~r~GRfd~~   60 (72)
                      ..+.+.|+..|+.-.  .       -.++++|+|||.                          ...++++|+.  ||+..
T Consensus       133 ~~~~~~Ll~~le~~~~~~~~~~~~~~~~~iiI~ttn~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~--R~~~~  210 (311)
T 4fcw_A          133 PDVFNILLQMLDDGRLTDSHGRTVDFRNTVIIMTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEI  210 (311)
T ss_dssp             HHHHHHHHHHHHHSEEECTTSCEEECTTEEEEEEESTTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHHHT--TCSEE
T ss_pred             HHHHHHHHHHHhcCEEEcCCCCEEECCCcEEEEecccCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHHHh--cCCeE
Confidence            356778888887541  1       126789999999                          5578899998  99999


Q ss_pred             EEeCCCChhh
Q psy3374          61 VHCTMPDLAF   70 (72)
Q Consensus        61 i~v~~Pd~~~   70 (72)
                      +.+..|+.+.
T Consensus       211 ~~~~p~~~~~  220 (311)
T 4fcw_A          211 VVFRPLTKEQ  220 (311)
T ss_dssp             EECCCCCHHH
T ss_pred             EEeCCCCHHH
Confidence            9999998765

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=96.29  E-value=0.0017  Score=43.01  Aligned_cols=50  Identities=12%  Similarity=0.029  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....+.|+..++..  ..++.+|++||.+..+++++++  ||. .++|+.|+.++
T Consensus       120 ~~~~~~L~~~le~~--~~~~~iI~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~e  169 (324)
T 3u61_B          120 AESQRHLRSFMEAY--SSNCSIIITANNIDGIIKPLQS--RCR-VITFGQPTDED  169 (324)
T ss_dssp             HHHHHHHHHHHHHH--GGGCEEEEEESSGGGSCTTHHH--HSE-EEECCCCCHHH
T ss_pred             HHHHHHHHHHHHhC--CCCcEEEEEeCCccccCHHHHh--hCc-EEEeCCCCHHH
Confidence            34556677777754  2357888899999999999999  995 79999999664

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=96.26  E-value=0.0028  Score=46.75  Aligned_cols=54  Identities=22%  Similarity=0.242  Sum_probs=42.5

Q ss_pred             hHHHHHHHHHHhhCCC---------CCCCeEEEEecCCCC-------------------------CCcccccCCCccccE
Q psy3374          15 KDRVVNQLLTELDGVE---------GLEGVYVVGATSRPD-------------------------IIDPALLRPGRLGSS   60 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~---------~~~~v~vi~aTn~~~-------------------------~lD~al~r~GRfd~~   60 (72)
                      ...+.+.|++.||.-.         ...++++|+|||.+.                         .++|+++.  |||..
T Consensus       570 ~~~~~~~Ll~~le~~~~~~~~g~~~~~~~~~iI~tsN~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~--R~~~~  647 (758)
T 1r6b_X          570 HPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNI  647 (758)
T ss_dssp             CHHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHHHT--TCSEE
T ss_pred             CHHHHHHHHHHhcCcEEEcCCCCEEecCCeEEEEecCcchhhhhhcccCccccchHHHHHHHHHHhcCHHHHh--hCCcc
Confidence            3568888999998531         014688999999865                         67889998  99999


Q ss_pred             EEeCCCChhh
Q psy3374          61 VHCTMPDLAF   70 (72)
Q Consensus        61 i~v~~Pd~~~   70 (72)
                      |.|+.|+.+.
T Consensus       648 i~~~~l~~~~  657 (758)
T 1r6b_X          648 IWFDHLSTDV  657 (758)
T ss_dssp             EECCCCCHHH
T ss_pred             eeeCCCCHHH
Confidence            9999999865

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=96.19  E-value=0.0072  Score=50.94  Aligned_cols=35  Identities=17%  Similarity=0.175  Sum_probs=31.7

Q ss_pred             CeEEEEecCCC-----CCCcccccCCCccccEEEeCCCChhhh
Q psy3374          34 GVYVVGATSRP-----DIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        34 ~v~vi~aTn~~-----~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ++.+|||||.|     ..||++++|  || ..|+++.|+.++.
T Consensus      1384 ~i~lIaA~Npp~~gGR~~l~~rllR--rf-~vi~i~~P~~~~l 1423 (2695)
T 4akg_A         1384 RIHIVGACNPPTDPGRIPMSERFTR--HA-AILYLGYPSGKSL 1423 (2695)
T ss_dssp             SEEEEEEECCTTSTTCCCCCHHHHT--TE-EEEECCCCTTTHH
T ss_pred             CEEEEEecCCCccCCCccCChhhhh--ee-eEEEeCCCCHHHH
Confidence            58999999999     489999999  99 8899999998763

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=96.04  E-value=0.01  Score=39.88  Aligned_cols=50  Identities=22%  Similarity=0.225  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....+.||..|+.-  ..++++|.+||.++.+.+++++  |+ ..++++.|+.++
T Consensus       122 ~~a~naLLk~lEep--~~~~~~Il~t~~~~~l~~ti~S--Rc-~~~~~~~~~~~~  171 (334)
T 1a5t_A          122 DAAANALLKTLEEP--PAETWFFLATREPERLLATLRS--RC-RLHYLAPPPEQY  171 (334)
T ss_dssp             HHHHHHHHHHHTSC--CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHH
T ss_pred             HHHHHHHHHHhcCC--CCCeEEEEEeCChHhCcHHHhh--cc-eeeeCCCCCHHH
Confidence            35678899988853  4468888889999999999999  88 479999998765

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=96.00  E-value=0.013  Score=35.78  Aligned_cols=51  Identities=25%  Similarity=0.262  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ....+.|+..++..  ..++.+|.+||.+..+++++.+  |+ ..++++.|+.++.
T Consensus       140 ~~~~~~l~~~l~~~--~~~~~~i~~t~~~~~~~~~l~~--r~-~~i~l~~l~~~e~  190 (250)
T 1njg_A          140 RHSFNALLKTLEEP--PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQI  190 (250)
T ss_dssp             HHHHHHHHHHHHSC--CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHH
T ss_pred             HHHHHHHHHHHhcC--CCceEEEEEeCChHhCCHHHHH--Hh-hhccCCCCCHHHH
Confidence            35667788888754  3468899999999999999998  76 6899998887653

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=95.92  E-value=0.0051  Score=45.39  Aligned_cols=38  Identities=26%  Similarity=0.368  Sum_probs=31.3

Q ss_pred             CCCCeEEEEecCCCC-----CCcccccCCCccccEEEeCCCChhhh
Q psy3374          31 GLEGVYVVGATSRPD-----IIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        31 ~~~~v~vi~aTn~~~-----~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ...++.+|++||.++     .+|++|.|  ||+ .|+|+.|+.+++
T Consensus       312 ~~~~~~~I~at~~~~~~~~~~~d~aL~~--Rf~-~i~v~~p~~~e~  354 (758)
T 1r6b_X          312 SSGKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEET  354 (758)
T ss_dssp             SSCCCEEEEEECHHHHHCCCCCTTSSGG--GEE-EEECCCCCHHHH
T ss_pred             hCCCeEEEEEeCchHHhhhhhcCHHHHh--Cce-EEEcCCCCHHHH
Confidence            345688999999753     68999999  998 799999998764

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=95.65  E-value=0.015  Score=38.77  Aligned_cols=37  Identities=24%  Similarity=0.297  Sum_probs=32.3

Q ss_pred             CCeEEEEecCCC---CCCcccccCCCccccEEEeCCCChhhh
Q psy3374          33 EGVYVVGATSRP---DIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        33 ~~v~vi~aTn~~---~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .++.+|++||.+   +.+++++.+  ||...|+++.|+.++.
T Consensus       163 ~~~~iI~~t~~~~~~~~l~~~l~s--r~~~~i~l~~l~~~~~  202 (384)
T 2qby_B          163 ANISVIMISNDINVRDYMEPRVLS--SLGPSVIFKPYDAEQL  202 (384)
T ss_dssp             SCEEEEEECSSTTTTTTSCHHHHH--TCCCEEEECCCCHHHH
T ss_pred             cceEEEEEECCCchHhhhCHHHHh--cCCCeEEECCCCHHHH
Confidence            578999999988   789999999  9988999999987753

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=95.58  E-value=0.014  Score=38.91  Aligned_cols=50  Identities=22%  Similarity=0.109  Sum_probs=35.1

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEec-----------CCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGAT-----------SRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aT-----------n~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ...+.|+..++...  ..++++++.           |.+..+++++++  ||.. |+++.|+.++.
T Consensus       204 ~~~~~L~~~le~~~--~~~~ii~t~~~~~~i~~t~~~~~~~l~~~l~s--R~~~-i~~~~~~~~e~  264 (368)
T 3uk6_A          204 ESFSFLNRALESDM--APVLIMATNRGITRIRGTSYQSPHGIPIDLLD--RLLI-VSTTPYSEKDT  264 (368)
T ss_dssp             HHHHHHHHHTTCTT--CCEEEEEESCSEEECBTSSCEEETTCCHHHHT--TEEE-EEECCCCHHHH
T ss_pred             HHHHHHHHHhhCcC--CCeeeeecccceeeeeccCCCCcccCCHHHHh--hccE-EEecCCCHHHH
Confidence            44556666665432  246555554           458899999999  9977 89999988753

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=95.46  E-value=0.0049  Score=46.41  Aligned_cols=46  Identities=30%  Similarity=0.337  Sum_probs=33.1

Q ss_pred             HHHHHHHhhCCCCCCCeEEEEecCCCC----CCcccccCCCccccEEEeCCCChhhh
Q psy3374          19 VNQLLTELDGVEGLEGVYVVGATSRPD----IIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        19 ~~~ll~~ld~~~~~~~v~vi~aTn~~~----~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.|...++    ...+.+|++||.++    .+|+++.|  ||+. |+|+.|+.+++
T Consensus       288 ~~~L~~~l~----~~~i~~I~at~~~~~~~~~~d~aL~r--Rf~~-i~l~~p~~~e~  337 (854)
T 1qvr_A          288 GNMLKPALA----RGELRLIGATTLDEYREIEKDPALER--RFQP-VYVDEPTVEET  337 (854)
T ss_dssp             ----HHHHH----TTCCCEEEEECHHHHHHHTTCTTTCS--CCCC-EEECCCCHHHH
T ss_pred             HHHHHHHHh----CCCeEEEEecCchHHhhhccCHHHHh--CCce-EEeCCCCHHHH
Confidence            344444444    24578999999875    58999999  9986 99999998754

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=95.25  E-value=0.017  Score=41.66  Aligned_cols=53  Identities=19%  Similarity=0.110  Sum_probs=36.1

Q ss_pred             hHHHHHHHHHHhhCC--------CCCCCeEEEEecCCCCC---CcccccCCCccccEEEeCCCChh
Q psy3374          15 KDRVVNQLLTELDGV--------EGLEGVYVVGATSRPDI---IDPALLRPGRLGSSVHCTMPDLA   69 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~--------~~~~~v~vi~aTn~~~~---lD~al~r~GRfd~~i~v~~Pd~~   69 (72)
                      ...+.+.|+..|+.-        ...+..++|+|||.+..   ..+++++  ||..+|+++.|+.+
T Consensus       122 ~~~~q~~LL~~lee~~v~i~G~~~~~~~~~iI~ATN~lpe~~~~~~aLld--RF~~~i~v~~p~~~  185 (500)
T 3nbx_X          122 GPAILNTLLTAINERQFRNGAHVEKIPMRLLVAASNELPEADSSLEALYD--RMLIRLWLDKVQDK  185 (500)
T ss_dssp             CHHHHHHHHHHHHSSEEECSSSEEECCCCEEEEEESSCCCTTCTTHHHHT--TCCEEEECCSCCCH
T ss_pred             cHHHHHHHHHHHHHHhccCCCCcCCcchhhhhhccccCCCccccHHHHHH--HHHHHHHHHHhhhh
Confidence            346778888888642        11112356778885332   3359999  99999999999873

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=94.98  E-value=0.066  Score=36.07  Aligned_cols=22  Identities=14%  Similarity=0.084  Sum_probs=19.1

Q ss_pred             CcccccCCCccccEEEeCCCChhh
Q psy3374          47 IDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        47 lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      +.|+|+.  |||..+.+..|+.+.
T Consensus       239 ~~~~l~~--R~~~~~~~~pl~~~~  260 (363)
T 3hws_A          239 LIPEFIG--RLPVVATLNELSEEA  260 (363)
T ss_dssp             CCHHHHT--TCCEEEECCCCCHHH
T ss_pred             CCHHHhc--ccCeeeecCCCCHHH
Confidence            6788887  999999999998775

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=94.91  E-value=0.033  Score=36.72  Aligned_cols=52  Identities=15%  Similarity=0.190  Sum_probs=38.2

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCC---CCCcccccCCCccc-cEEEeCCCChhhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRP---DIIDPALLRPGRLG-SSVHCTMPDLAFA   71 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~---~~lD~al~r~GRfd-~~i~v~~Pd~~~~   71 (72)
                      ..+..|+..++.. ...++.+|++||.+   +.+++.+.+  ||. +.|+++.++.++.
T Consensus       147 ~~l~~l~~~~~~~-~~~~~~~I~~~~~~~~~~~~~~~~~~--r~~~~~i~l~~l~~~~~  202 (386)
T 2qby_A          147 DILYKLSRINSEV-NKSKISFIGITNDVKFVDLLDPRVKS--SLSEEEIIFPPYNAEEL  202 (386)
T ss_dssp             THHHHHHHHHHSC-CC--EEEEEEESCGGGGGGCTTHHHH--TTTTEEEEECCCCHHHH
T ss_pred             HHHHHHhhchhhc-CCCeEEEEEEECCCChHhhhCHHHhc--cCCCeeEEeCCCCHHHH
Confidence            4566777777765 34478899999987   578888888  886 4899999987753

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=94.84  E-value=0.049  Score=36.06  Aligned_cols=49  Identities=8%  Similarity=0.108  Sum_probs=38.9

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.|+..|+...  .+..+|.+||.++.+.+++.+  |+ ..+.++.|+.++
T Consensus       149 ~~~~~L~~~le~~~--~~~~~Il~t~~~~~l~~~l~s--R~-~~~~~~~~~~~~  197 (354)
T 1sxj_E          149 DAQAALRRTMEKYS--KNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPSDSE  197 (354)
T ss_dssp             HHHHHHHHHHHHST--TTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCCHHH
T ss_pred             HHHHHHHHHHHhhc--CCCEEEEEeCCHHHHHHHHHh--hc-eEEecCCcCHHH
Confidence            44566777777653  357788889999999999999  98 889999998765

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=94.81  E-value=0.016  Score=39.28  Aligned_cols=47  Identities=15%  Similarity=0.138  Sum_probs=35.2

Q ss_pred             HHHHHHHHHhhCCC-------------------CCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCC
Q psy3374          17 RVVNQLLTELDGVE-------------------GLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD   67 (72)
Q Consensus        17 ~~~~~ll~~ld~~~-------------------~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd   67 (72)
                      .+.+.|+..|++..                   ...++++|+||| .+.+|+++.|  ||+ ...+++|.
T Consensus       166 ~~~~~Ll~~le~~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~-~~~l~~~l~~--R~~-~~~~g~~~  231 (376)
T 1um8_A          166 GVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGA-FDGLAEIIKK--RTT-QNVLGFTQ  231 (376)
T ss_dssp             HHHHHHHHHHHCCEEC---------------CEECTTCEEEEEEC-CTTHHHHTTT--SCS-SCCCSCCC
T ss_pred             HHHHHHHHHhhccceecccccccccCCcceEEEecCCeEEEecCC-HHHHHHHHHH--Hhc-ccccCCCc
Confidence            37888999998631                   114578888888 7899999999  998 55666654

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=94.60  E-value=0.021  Score=36.99  Aligned_cols=49  Identities=6%  Similarity=-0.085  Sum_probs=37.2

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.|+..++..  ..++.+|.+||.+..+++++.+  ||. .++++.|+.++
T Consensus       117 ~~~~~L~~~le~~--~~~~~~i~~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~  165 (319)
T 2chq_A          117 DAQAALRRTMEMY--SKSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEA  165 (319)
T ss_dssp             HHHHTTGGGTSSS--SSSEEEEEEESCGGGSCHHHHT--TCE-EEECCCCCHHH
T ss_pred             HHHHHHHHHHHhc--CCCCeEEEEeCChhhcchHHHh--hCe-EEEecCCCHHH
Confidence            3345556555543  3468889999999999999999  886 89999888765

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=94.49  E-value=0.011  Score=36.57  Aligned_cols=51  Identities=14%  Similarity=0.113  Sum_probs=33.2

Q ss_pred             HHHHHHHhhCCCCCCCe-EEEEecCCCC---CCcccccCCCccc--cEEEeCCCChhhh
Q psy3374          19 VNQLLTELDGVEGLEGV-YVVGATSRPD---IIDPALLRPGRLG--SSVHCTMPDLAFA   71 (72)
Q Consensus        19 ~~~ll~~ld~~~~~~~v-~vi~aTn~~~---~lD~al~r~GRfd--~~i~v~~Pd~~~~   71 (72)
                      ...|+..++.......+ +|+++++.+.   .+++++.+  ||.  ..++++.|+.+++
T Consensus       123 ~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~~~l~~--r~~~~~~i~l~~~~~~~~  179 (242)
T 3bos_A          123 EEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLVS--RMHWGLTYQLQPMMDDEK  179 (242)
T ss_dssp             HHHHHHHHHHHHHHCSCEEEEEESSCTTTTTCCCHHHHH--HHHHSEEEECCCCCGGGH
T ss_pred             HHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHHhhhhhhh--HhhcCceEEeCCCCHHHH
Confidence            34455555544333344 6666665554   56688888  886  8999999998764

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=94.37  E-value=0.074  Score=35.22  Aligned_cols=50  Identities=26%  Similarity=0.273  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....+.|+..++..  ..++++|.+||.+..+++++.+  |+ ..++++.|+.++
T Consensus       133 ~~~~~~Ll~~le~~--~~~~~~Il~~~~~~~l~~~l~s--r~-~~i~~~~l~~~~  182 (373)
T 1jr3_A          133 RHSFNALLKTLEEP--PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQ  182 (373)
T ss_dssp             HHHHHHHHHHHHSC--CSSEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHH
T ss_pred             HHHHHHHHHHHhcC--CCceEEEEEeCChHhCcHHHHh--he-eEeeCCCCCHHH
Confidence            35567788888754  3468888889999999999998  87 789999988765

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=94.36  E-value=0.011  Score=41.52  Aligned_cols=51  Identities=14%  Similarity=0.199  Sum_probs=36.0

Q ss_pred             HHHHHHHhhCCCCCCCeEEEEecCCCCC---CcccccCCCccc--cEEEeCCCChhhh
Q psy3374          19 VNQLLTELDGVEGLEGVYVVGATSRPDI---IDPALLRPGRLG--SSVHCTMPDLAFA   71 (72)
Q Consensus        19 ~~~ll~~ld~~~~~~~v~vi~aTn~~~~---lD~al~r~GRfd--~~i~v~~Pd~~~~   71 (72)
                      ...|+..++.+...+..+|+++.+.+..   +++++++  ||+  ..++++.|+.+++
T Consensus       213 q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~s--R~~~g~~i~l~~p~~e~r  268 (440)
T 2z4s_A          213 QTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVS--RFQMGLVAKLEPPDEETR  268 (440)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHH--HHHSSBCCBCCCCCHHHH
T ss_pred             HHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHh--hccCCeEEEeCCCCHHHH
Confidence            3345555554434445677777666665   8899999  997  7899999998764

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=94.31  E-value=0.015  Score=38.56  Aligned_cols=49  Identities=14%  Similarity=0.184  Sum_probs=33.4

Q ss_pred             HHHHHHhhCCCCCCCeEEEEecCCCC---CCcccccCCCccc--cEEEeCCCChhhh
Q psy3374          20 NQLLTELDGVEGLEGVYVVGATSRPD---IIDPALLRPGRLG--SSVHCTMPDLAFA   71 (72)
Q Consensus        20 ~~ll~~ld~~~~~~~v~vi~aTn~~~---~lD~al~r~GRfd--~~i~v~~Pd~~~~   71 (72)
                      ..|+..++.+...+..+|+++++.+.   .+++++++  ||+  ..++++. +.+++
T Consensus       118 ~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L~s--R~~~~~~i~l~~-~~~e~  171 (324)
T 1l8q_A          118 IEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVS--RFEGGILVEIEL-DNKTR  171 (324)
T ss_dssp             HHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHH--HHHTSEEEECCC-CHHHH
T ss_pred             HHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHhhh--cccCceEEEeCC-CHHHH
Confidence            34444444433344578888888877   68999999  997  5778877 76653

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=94.23  E-value=0.038  Score=37.16  Aligned_cols=48  Identities=19%  Similarity=0.136  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....+.||..|+.-  .+++++|.+||.++.|.++++.  |   .++++.|+.++
T Consensus        96 ~~a~naLLk~LEep--~~~t~fIl~t~~~~kl~~tI~S--R---~~~f~~l~~~~  143 (305)
T 2gno_A           96 QQAANAFLKALEEP--PEYAVIVLNTRRWHYLLPTIKS--R---VFRVVVNVPKE  143 (305)
T ss_dssp             HHHHHHTHHHHHSC--CTTEEEEEEESCGGGSCHHHHT--T---SEEEECCCCHH
T ss_pred             HHHHHHHHHHHhCC--CCCeEEEEEECChHhChHHHHc--e---eEeCCCCCHHH
Confidence            45678899999854  4467777778889999999999  8   88888887664

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=94.22  E-value=0.045  Score=35.51  Aligned_cols=49  Identities=8%  Similarity=-0.073  Sum_probs=38.3

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.|+..|+..  ..++.+|.+||.++.+++++.+  ||. .++++.|+.++
T Consensus       125 ~~~~~L~~~le~~--~~~~~~i~~~~~~~~l~~~l~s--r~~-~~~~~~l~~~~  173 (327)
T 1iqp_A          125 DAQQALRRTMEMF--SSNVRFILSCNYSSKIIEPIQS--RCA-IFRFRPLRDED  173 (327)
T ss_dssp             HHHHHHHHHHHHT--TTTEEEEEEESCGGGSCHHHHH--TEE-EEECCCCCHHH
T ss_pred             HHHHHHHHHHHhc--CCCCeEEEEeCCccccCHHHHh--hCc-EEEecCCCHHH
Confidence            4566777777753  3457788899999999999998  886 78888888654

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=94.08  E-value=0.0075  Score=42.07  Aligned_cols=40  Identities=20%  Similarity=0.169  Sum_probs=31.9

Q ss_pred             HHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCC
Q psy3374          20 NQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM   65 (72)
Q Consensus        20 ~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~   65 (72)
                      ..+.+.+||.     +.|+.+||+++.+ +++++|||+|..++...
T Consensus       245 ~~l~~~ldG~-----v~v~~~tn~~~~l-~alf~pg~ld~~~~~l~  284 (377)
T 1svm_A          245 DNLRDYLDGS-----VKVNLEKKHLNKR-TQIFPPGIVTMNEYSVP  284 (377)
T ss_dssp             HTTHHHHHCS-----SCEEECCSSSCCE-EECCCCEEEEECSCCCC
T ss_pred             HHHHHHhcCC-----CeEeeccCchhhH-HHhhcCcccChhHHhhc
Confidence            4566667763     5578889999999 79999999998877754

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=93.93  E-value=0.044  Score=36.09  Aligned_cols=49  Identities=10%  Similarity=-0.023  Sum_probs=37.6

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.|+..|+....  +..+|.+||.+..+++++.+  ||. .+.++.|+.++
T Consensus       148 ~~~~~Ll~~le~~~~--~~~~il~~~~~~~l~~~l~s--R~~-~i~~~~~~~~~  196 (353)
T 1sxj_D          148 DAQSALRRTMETYSG--VTRFCLICNYVTRIIDPLAS--QCS-KFRFKALDASN  196 (353)
T ss_dssp             HHHHHHHHHHHHTTT--TEEEEEEESCGGGSCHHHHH--HSE-EEECCCCCHHH
T ss_pred             HHHHHHHHHHHhcCC--CceEEEEeCchhhCcchhhc--cCc-eEEeCCCCHHH
Confidence            455678888876533  45666788999999999999  996 78888887654

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=93.76  E-value=0.051  Score=35.16  Aligned_cols=50  Identities=8%  Similarity=-0.067  Sum_probs=38.0

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ...+.|+..++..  ..++.+|.+||.+..+++++.+  |+. .++++.|+.++.
T Consensus       122 ~~~~~L~~~le~~--~~~~~~il~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~~  171 (323)
T 1sxj_B          122 GAQQALRRTMELY--SNSTRFAFACNQSNKIIEPLQS--QCA-ILRYSKLSDEDV  171 (323)
T ss_dssp             HHHHTTHHHHHHT--TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHH
T ss_pred             HHHHHHHHHHhcc--CCCceEEEEeCChhhchhHHHh--hce-EEeecCCCHHHH
Confidence            3455667777643  3457788889999999999999  875 899999987653

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=92.08  E-value=0.065  Score=35.57  Aligned_cols=53  Identities=8%  Similarity=0.059  Sum_probs=39.5

Q ss_pred             HHHHHHHHHHhhCCCC--CCCeEEEEecCCC---CCCcccccCCCcccc-EEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEG--LEGVYVVGATSRP---DIIDPALLRPGRLGS-SVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~--~~~v~vi~aTn~~---~~lD~al~r~GRfd~-~i~v~~Pd~~~   70 (72)
                      ...+..|+..++....  ..++.+|++||.+   +.+++.+.+  ||.. .|+++.++.++
T Consensus       139 ~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~--r~~~~~i~~~pl~~~~  197 (389)
T 1fnn_A          139 PDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTKDQ  197 (389)
T ss_dssp             HHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCCBHHH
T ss_pred             hHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHhCHHhhh--cCCCceEEeCCCCHHH
Confidence            3556667777765422  1478899999988   778888888  8886 89999888764

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=91.47  E-value=0.12  Score=38.96  Aligned_cols=54  Identities=20%  Similarity=0.190  Sum_probs=39.8

Q ss_pred             hHHHHHHHHHHhhCCC---------CCCCeEEEEecCCC--------------------------CCCcccccCCCcccc
Q psy3374          15 KDRVVNQLLTELDGVE---------GLEGVYVVGATSRP--------------------------DIIDPALLRPGRLGS   59 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~---------~~~~v~vi~aTn~~--------------------------~~lD~al~r~GRfd~   59 (72)
                      ...+.+.|++.|+.-.         ...++++|+|||..                          ..+.|+|+.  |||.
T Consensus       673 ~~~~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~tsn~~~~~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~l~~--Rl~~  750 (854)
T 1qvr_A          673 HPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDE  750 (854)
T ss_dssp             CHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSB
T ss_pred             CHHHHHHHHHHhccCceECCCCCEeccCCeEEEEecCcChHHHhhhcccccchHHHHHHHHHHHHhhCCHHHHH--hcCe
Confidence            4578889999998531         11368899999972                          345677777  9999


Q ss_pred             EEEeCCCChhh
Q psy3374          60 SVHCTMPDLAF   70 (72)
Q Consensus        60 ~i~v~~Pd~~~   70 (72)
                      .+.+..|+.+.
T Consensus       751 ~i~~~pl~~ed  761 (854)
T 1qvr_A          751 IVVFRPLTKEQ  761 (854)
T ss_dssp             CCBCCCCCHHH
T ss_pred             EEeCCCCCHHH
Confidence            99998888654

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=91.34  E-value=0.24  Score=33.76  Aligned_cols=51  Identities=4%  Similarity=-0.006  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCC----CcccccCCCccc-cEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDI----IDPALLRPGRLG-SSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~----lD~al~r~GRfd-~~i~v~~Pd~~~   70 (72)
                      +.++..|+.+...  ...+++||+.+|..+.    |++++..  ||. ..|.|+..+.++
T Consensus       147 q~~L~~l~~~~~~--~~s~~~vI~i~n~~d~~~~~L~~~v~S--R~~~~~i~F~pYt~~e  202 (318)
T 3te6_A          147 EKILQYFEKWISS--KNSKLSIICVGGHNVTIREQINIMPSL--KAHFTEIKLNKVDKNE  202 (318)
T ss_dssp             THHHHHHHHHHHC--SSCCEEEEEECCSSCCCHHHHHTCHHH--HTTEEEEECCCCCHHH
T ss_pred             chHHHHHHhcccc--cCCcEEEEEEecCcccchhhcchhhhc--cCCceEEEeCCCCHHH
Confidence            3556666665432  3446999999999875    4556667  887 689999888765

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=90.57  E-value=0.11  Score=36.70  Aligned_cols=45  Identities=18%  Similarity=0.176  Sum_probs=30.9

Q ss_pred             HHHHHHHhhCCCCCCCeEEEEec--CCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          19 VNQLLTELDGVEGLEGVYVVGAT--SRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        19 ~~~ll~~ld~~~~~~~v~vi~aT--n~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      .+.||..|+.    ..+++|++|  |....++++|++  ||. .+.++.|+.++
T Consensus       123 q~~LL~~le~----~~v~lI~att~n~~~~l~~aL~s--R~~-v~~l~~l~~ed  169 (447)
T 3pvs_A          123 QDAFLPHIED----GTITFIGATTENPSFELNSALLS--RAR-VYLLKSLSTED  169 (447)
T ss_dssp             --CCHHHHHT----TSCEEEEEESSCGGGSSCHHHHT--TEE-EEECCCCCHHH
T ss_pred             HHHHHHHHhc----CceEEEecCCCCcccccCHHHhC--cee-EEeeCCcCHHH
Confidence            3445555553    346677766  555689999999  986 67788888765

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=90.54  E-value=0.15  Score=34.19  Aligned_cols=35  Identities=23%  Similarity=0.333  Sum_probs=31.2

Q ss_pred             CeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          34 GVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        34 ~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      .+.++++||++..|++++++  ||...+.++.|+.++
T Consensus       150 ~~~li~at~~~~~Ls~~l~s--R~~l~~~Ld~~~~~~  184 (334)
T 1in4_A          150 PFTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKE  184 (334)
T ss_dssp             CCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHH
T ss_pred             CeEEEEecCCcccCCHHHHH--hcCceeeCCCCCHHH
Confidence            46778899999999999999  999889999998865

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=89.70  E-value=0.46  Score=33.18  Aligned_cols=50  Identities=16%  Similarity=0.122  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEe---------cC---CCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGA---------TS---RPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~a---------Tn---~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....+.|+..|+.-..  .+++++|         |+   .|..|+|.++.  ||-. +.++.++.++
T Consensus       309 ~~a~~aLlk~lEe~~~--~~~il~tn~~~~~i~~~~~~~~~~~l~~~i~s--R~~~-~~~~~~~~~e  370 (456)
T 2c9o_A          309 IECFTYLHRALESSIA--PIVIFASNRGNCVIRGTEDITSPHGIPLDLLD--RVMI-IRTMLYTPQE  370 (456)
T ss_dssp             HHHHHHHHHHTTSTTC--CEEEEEECCSEEECBTTSSCEEETTCCHHHHT--TEEE-EECCCCCHHH
T ss_pred             HHHHHHHHHHhhccCC--CEEEEecCCccccccccccccccccCChhHHh--hcce-eeCCCCCHHH
Confidence            4678888888885433  3666666         43   28889999999  9966 6898888765

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=88.49  E-value=0.64  Score=33.11  Aligned_cols=52  Identities=25%  Similarity=0.292  Sum_probs=38.9

Q ss_pred             HHHHHHHHHhhCCC--------CCCCeEEEEec----CCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVE--------GLEGVYVVGAT----SRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~--------~~~~v~vi~aT----n~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      .+-..||..|++..        ...+|++|+|.    +.|.++-|.|+.  ||+..|+++..+.++
T Consensus       277 gvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~~~~~dlipel~~--R~~i~i~l~~lt~~e  340 (444)
T 1g41_A          277 GVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAAD  340 (444)
T ss_dssp             HHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHT--TCCEEEECCCCCHHH
T ss_pred             HHHHHHHHHhcccccccccceecCCcEEEEeccccccCChhhcchHHhc--ccceeeeCCCCCHHH
Confidence            46678999999851        23468888886    345556678888  999999998887764

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=88.02  E-value=0.43  Score=31.65  Aligned_cols=51  Identities=27%  Similarity=0.260  Sum_probs=30.3

Q ss_pred             HHHHHHHHHhhCCC---------CCCCeEEEEecCCC-------CCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVE---------GLEGVYVVGATSRP-------DIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~---------~~~~v~vi~aTn~~-------~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      .....|+..|+.-.         ...++.+|+|||.+       ..+++.|..  ||. .+.+.+|...+
T Consensus       111 ~~q~~Ll~~l~~~~~~~~g~~~~~~~~~riI~atn~~l~~~v~~g~fr~~L~~--Rl~-~~~i~lPpL~e  177 (304)
T 1ojl_A          111 LMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYY--RLN-VVAIEMPSLRQ  177 (304)
T ss_dssp             HHHHHHHHHHHSSBCCBTTBCCCCBCCCEEEEEESSCHHHHHHHTSSCHHHHH--HHS-SEEEECCCSGG
T ss_pred             HHHHHHHHHHhcCEeeecCCcccccCCeEEEEecCccHHHHHHhCCcHHHHHh--hcC-eeEEeccCHHH
Confidence            45566777777532         12358899999986       123444444  554 56666666543

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=87.57  E-value=0.73  Score=30.54  Aligned_cols=49  Identities=12%  Similarity=0.058  Sum_probs=34.9

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.|+..|+...  ..+.++.+||.+..+.+++++  |+. .+.+..++.++
T Consensus       125 ~~~~~L~~~le~~~--~~~~~il~~n~~~~i~~~i~s--R~~-~~~~~~l~~~~  173 (340)
T 1sxj_C          125 AAQNALRRVIERYT--KNTRFCVLANYAHKLTPALLS--QCT-RFRFQPLPQEA  173 (340)
T ss_dssp             HHHHHHHHHHHHTT--TTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHH
T ss_pred             HHHHHHHHHHhcCC--CCeEEEEEecCccccchhHHh--hce-eEeccCCCHHH
Confidence            34556666666542  346677788999999999999  885 67777666543

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=84.86  E-value=0.52  Score=29.99  Aligned_cols=50  Identities=26%  Similarity=0.197  Sum_probs=31.9

Q ss_pred             HHHHHHHHHhhCCC---------CCCCeEEEEecCCC-------CCCcccccCCCccccEEEeCCCChh
Q psy3374          17 RVVNQLLTELDGVE---------GLEGVYVVGATSRP-------DIIDPALLRPGRLGSSVHCTMPDLA   69 (72)
Q Consensus        17 ~~~~~ll~~ld~~~---------~~~~v~vi~aTn~~-------~~lD~al~r~GRfd~~i~v~~Pd~~   69 (72)
                      .....|+..|+.-.         ...++.+|+|||.+       ..++++|..  ||+. +.+.+|+..
T Consensus       115 ~~q~~Ll~~l~~~~~~~~g~~~~~~~~~~iI~atn~~~~~~~~~~~~~~~L~~--Rl~~-~~i~lp~L~  180 (265)
T 2bjv_A          115 MVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLD--ALAF-DVVQLPPLR  180 (265)
T ss_dssp             HHHHHHHHHHHHCEECCCCC--CEECCCEEEEEESSCHHHHHHHTSSCHHHHH--HHCS-EEEECCCGG
T ss_pred             HHHHHHHHHHHhCCeecCCCcccccCCeEEEEecCcCHHHHHHcCCccHHHHH--hhcC-cEEeCCChh
Confidence            45566777776420         12357899999985       246788888  8864 456666554

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=84.32  E-value=0.43  Score=30.18  Aligned_cols=44  Identities=16%  Similarity=0.207  Sum_probs=33.2

Q ss_pred             HHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCCh
Q psy3374          22 LLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDL   68 (72)
Q Consensus        22 ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~   68 (72)
                      +++.+..- ...++-+|.+|+.++.||.++++  |++.++++..|..
T Consensus       112 ll~~l~~~-r~~~~~iil~tq~~~~l~~~lr~--ri~~~~~l~~~~~  155 (199)
T 2r2a_A          112 NVQWLNTH-RHQGIDIFVLTQGPKLLDQNLRT--LVRKHYHIASNKM  155 (199)
T ss_dssp             HHHGGGGT-TTTTCEEEEEESCGGGBCHHHHT--TEEEEEEEEECSS
T ss_pred             HHHHHHhc-CcCCeEEEEECCCHHHHhHHHHH--HhheEEEEcCccc
Confidence            55666543 23356677778889999999998  9999999987654

>3f8t_A Predicted ATPase involved in replication control, CDC46/MCM family; helicase, MCM homolog, DNA replication, ATP-binding, DNA-binding; 1.90A {Methanopyrus kandleri AV19}

Probab=83.64  E-value=0.45  Score=34.75  Aligned_cols=53  Identities=13%  Similarity=0.051  Sum_probs=34.2

Q ss_pred             hHHHHHHHHHHhhCC-------CCCCCeEEEEecCCCC-----------CCcccccCCCccccE-EEeCCCChh
Q psy3374          15 KDRVVNQLLTELDGV-------EGLEGVYVVGATSRPD-----------IIDPALLRPGRLGSS-VHCTMPDLA   69 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~-------~~~~~v~vi~aTn~~~-----------~lD~al~r~GRfd~~-i~v~~Pd~~   69 (72)
                      .....+.|+..|+.=       .-..++.||||+|...           .|+++++.  |||.. +.++.||.+
T Consensus       313 ~~~~qsaLlEaMEe~~VtI~G~~lparf~VIAA~NP~~~yd~~~s~~~~~Lp~alLD--RFDLi~i~~d~pd~e  384 (506)
T 3f8t_A          313 PEPHRWALMEAMDKGTVTVDGIALNARCAVLAAINPGEQWPSDPPIARIDLDQDFLS--HFDLIAFLGVDPRPG  384 (506)
T ss_dssp             CHHHHHHHHHHHHHSEEEETTEEEECCCEEEEEECCCC--CCSCGGGGCCSCHHHHT--TCSEEEETTC-----
T ss_pred             CHHHHHHHHHHHhCCcEEECCEEcCCCeEEEEEeCcccccCCCCCccccCCChHHhh--heeeEEEecCCCChh
Confidence            345667777777632       1123689999999875           88999999  99974 446777765

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	72
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	1e-21
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	2e-21
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	4e-18
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	2e-16
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	4e-08
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	3e-05
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	0.002

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]} Length = 256

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

 Score = 82.2 bits (203), Expect = 1e-21
 Identities = 32/69 (46%), Positives = 46/69 (66%), Gaps = 3/69 (4%)

Query: 4   GYRRGNDSTG---VKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSS 60
           G +RG    G    +++ +NQ+L E+DG EG EG+ V+ AT+RPD++DPALLRPGR    
Sbjct: 117 GRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQ 176

Query: 61  VHCTMPDLA 69
           V   +PD+ 
Sbjct: 177 VVVGLPDVR 185

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]} Length = 247

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

 Score = 81.0 bits (200), Expect = 2e-21
 Identities = 30/69 (43%), Positives = 43/69 (62%), Gaps = 3/69 (4%)

Query: 4   GYRRGNDSTG---VKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSS 60
           G +RG+   G    +++ +NQLL E+DG E    + V+ AT+RPDI+DPALLRPGR    
Sbjct: 114 GRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQ 173

Query: 61  VHCTMPDLA 69
           +    PD+ 
Sbjct: 174 IAIDAPDVK 182

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 265

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 72.9 bits (178), Expect = 4e-18
 Identities = 31/59 (52%), Positives = 44/59 (74%)

Query: 8   GNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMP 66
             D  G  DRV+NQ+LTE+DG+   + V+++GAT+RPDIIDPA+LRPGRL   ++  +P
Sbjct: 120 IGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLP 178

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]} Length = 321

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

 Score = 68.9 bits (168), Expect = 2e-16
 Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 3/71 (4%)

Query: 2   ITGYRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSR---PDIIDPALLRPGRLG 58
           + G   GN ++G   R    LL+++  +    G  V+ + +     D I   +    R  
Sbjct: 194 VIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSN 253

Query: 59  SSVHCTMPDLA 69
           S+      D+ 
Sbjct: 254 STSLVISTDVD 264

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 258

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.4 bits (106), Expect = 4e-08
 Identities = 27/64 (42%), Positives = 38/64 (59%)

Query: 4   GYRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHC 63
             +R      V+ R+V+QLLT +DG++    V V+ AT+RP+ IDPAL R GR    V  
Sbjct: 110 APKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDI 169

Query: 64  TMPD 67
            +PD
Sbjct: 170 GIPD 173

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]} Length = 273

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

 Score = 37.6 bits (86), Expect = 3e-05
 Identities = 4/38 (10%), Positives = 11/38 (28%)

Query: 20  NQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRL 57
               T++  +   +    +G   R + +        R 
Sbjct: 134 KGYETKMYVMAVPKINSYLGTIERYETMYADDPMTARA 171

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]} Length = 246

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

 Score = 32.2 bits (72), Expect = 0.002
 Identities = 12/65 (18%), Positives = 25/65 (38%), Gaps = 4/65 (6%)

Query: 6   RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYV-VGATSRPDIIDPALLRPGRLGSSVHCT 64
                     + V+  LL  L          + +G TSR D++    +      +++H  
Sbjct: 114 DYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEML-NAFSTTIH-- 170

Query: 65  MPDLA 69
           +P++A
Sbjct: 171 VPNIA 175

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	72
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.74
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.71
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	99.7
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.62
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.46
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	98.85
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	97.98
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	96.61
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	96.6
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	96.57
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	96.53
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	95.94
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	94.59
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	94.24
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	93.2
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	92.64
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	92.49
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	89.82
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	89.29
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	87.63
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	84.92
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	84.58
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	82.25

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=99.74  E-value=3.1e-18  Score=113.16  Aligned_cols=59  Identities=47%  Similarity=0.862  Sum_probs=55.2

Q ss_pred             chhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          13 GVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        13 ~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ....+++++||++||++...++|+||||||+|+.||+|++||||||.+|+|++|+.+++
T Consensus       129 ~~~~~~~~~ll~~~d~~~~~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R  187 (256)
T d1lv7a_         129 DEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGR  187 (256)
T ss_dssp             CHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHH
T ss_pred             HHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHH
Confidence            45668999999999999888899999999999999999999999999999999999886

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=3.1e-18  Score=112.44  Aligned_cols=67  Identities=40%  Similarity=0.563  Sum_probs=60.0

Q ss_pred             cccCCCCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           5 YRRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         5 ~~r~~~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ++++++.++...++++.++..+++.....+|+||+|||+|+.||+|++||||||++|+|++|+.++|
T Consensus       111 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R  177 (258)
T d1e32a2         111 PKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGR  177 (258)
T ss_dssp             CHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHH
T ss_pred             cCCCCCCCchHHHHHHHhccccccccccCCccEEEeCCCccccchhhhhcccccceeECCCCCHHHH
Confidence            3444455666778999999999999888899999999999999999999999999999999999987

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=99.70  E-value=1.2e-17  Score=109.59  Aligned_cols=60  Identities=43%  Similarity=0.736  Sum_probs=55.7

Q ss_pred             cchhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          12 TGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        12 ~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +....+++++||++||++....+|+||||||+|+.||++++|+||||.+|+|++|+.+++
T Consensus       125 ~~~~~~~~~~ll~~~d~~~~~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR  184 (247)
T d1ixza_         125 NDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGR  184 (247)
T ss_dssp             CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHH
T ss_pred             cHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHH
Confidence            345668999999999999888899999999999999999999999999999999999986

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.62  E-value=1.6e-16  Score=104.63  Aligned_cols=59  Identities=53%  Similarity=0.924  Sum_probs=49.5

Q ss_pred             chhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          13 GVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        13 ~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ....++++.||++||++...++|+||||||+|+.||+|++|+||||.+|+|++|+.+++
T Consensus       125 ~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R  183 (265)
T d1r7ra3         125 GAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSR  183 (265)
T ss_dssp             HHHHHHHHHHHHTCC------CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHH
T ss_pred             HHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCchhCCHHHhCCCCccEEEEecchHHHHH
Confidence            34567899999999999777789999999999999999999999999999999999886

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=99.46  E-value=1.9e-16  Score=107.91  Aligned_cols=67  Identities=19%  Similarity=0.213  Sum_probs=49.4

Q ss_pred             cccC-CCCcchhHHHHHHHHHHhhCCCCCCCeEEEEecCC---CCCCcccccCCCccccEEEeCCCChhhh
Q psy3374           5 YRRG-NDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSR---PDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus         5 ~~r~-~~~~~~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~---~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ++|+ +..+...++++||||++||++...++|+||||||+   ++.||+++.||||||++|+|+.||.+++
T Consensus       196 ~~r~~~~~~~~~~r~v~~lL~e~dg~~~~~~v~viaatN~~~~~~~i~~~~~r~~Rf~~~v~v~~pd~~~r  266 (321)
T d1w44a_         196 GAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGE  266 (321)
T ss_dssp             -----------CCHHHHHHHHHHHHHHHHHTCEEEEECCCCCCCHHHHHHHHHHHHHSCSEEEEECSSTTE
T ss_pred             cccccCCCCCcchhhhhhhhhhccccccCCCeEEEEeCCCcccccchhhhhhccCcccceeecCCCChHHH
Confidence            4443 33344556899999999999987778999999995   2446666789999999999999998764

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=98.85  E-value=5.4e-10  Score=72.40  Aligned_cols=52  Identities=19%  Similarity=0.316  Sum_probs=42.3

Q ss_pred             hhHHHHHHHHHHhhCCCC-CCCeEEEEecCCCCCCcccccCCCccccEEEeCCC
Q psy3374          14 VKDRVVNQLLTELDGVEG-LEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMP   66 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~~-~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~P   66 (72)
                      ..++++++|+.+|++... ..+|+||||||+|+.+|++.++ +||+.+|++|.+
T Consensus       122 ~~~~~~~~ll~~l~~~~~~~~~v~vi~tTn~~~~ld~~~~~-~rF~~~i~~P~~  174 (246)
T d1d2na_         122 FSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEML-NAFSTTIHVPNI  174 (246)
T ss_dssp             CCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCT-TTSSEEEECCCE
T ss_pred             hhHHHHHHHHHHhcCCCccccceeeeeccCChhhccchhhc-CccceEEecCCc
Confidence            346889999999999843 4469999999999999987554 599999998543

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=97.98  E-value=3.6e-06  Score=55.27  Aligned_cols=55  Identities=24%  Similarity=0.302  Sum_probs=43.3

Q ss_pred             hHHHHHHHHHHhhCCC--------CCCCeEEEEe----cCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          15 KDRVVNQLLTELDGVE--------GLEGVYVVGA----TSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~--------~~~~v~vi~a----Tn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ...++++||..||+..        ...+++++++    +|+++.++|+++.  |||..++++.|+.+..
T Consensus       140 ~~gv~~~LL~~~dg~~~~~~~~~i~~s~ilfi~~ga~~~~~~~~~~p~l~~--R~~~~i~~~~~~~~~~  206 (309)
T d1ofha_         140 REGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAADF  206 (309)
T ss_dssp             HHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHH--TCCEEEECCCCCHHHH
T ss_pred             hhHHHHHhhHHhcCCEEecCCeEEEccceeEEeccchhhcCcccchhhhhh--hhheeeeccCCCHHHH
Confidence            3458899999999852        1224667766    6888899999885  9999999999998764

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=96.61  E-value=0.00025  Score=47.59  Aligned_cols=31  Identities=6%  Similarity=-0.060  Sum_probs=26.7

Q ss_pred             EEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          37 VVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        37 vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      +|+|||.   ++.++.||||||+.|++..|+...
T Consensus       259 ~i~ttN~---~~~~~~r~~Rf~~~i~~~~~~~~~  289 (362)
T d1svma_         259 GIVTMNE---YSVPKTLQARFVKQIDFRPKDYLK  289 (362)
T ss_dssp             EEEEECS---CCCCHHHHTTEEEEEECCCCHHHH
T ss_pred             ceeeccc---ccccccccccCceEEeecCCCcHH
Confidence            7889994   688889999999999999998654

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=96.60  E-value=0.00052  Score=42.11  Aligned_cols=37  Identities=22%  Similarity=0.319  Sum_probs=33.5

Q ss_pred             CCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          33 EGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        33 ~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .++++|++||++..+++++++  ||+..+.++.|+.+..
T Consensus       133 ~~~~~I~at~~~~~~~~~~~~--r~~~~~~~~~~~~~~~  169 (238)
T d1in4a2         133 QPFTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKEL  169 (238)
T ss_dssp             CCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHH
T ss_pred             CCeEEEEecCCCcccccccee--eeeEEEEecCCCHHHH
Confidence            368999999999999999999  9999999999997653

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=96.57  E-value=0.0017  Score=39.79  Aligned_cols=51  Identities=22%  Similarity=0.221  Sum_probs=43.0

Q ss_pred             hHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          15 KDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        15 ~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      .....+.||..|+.-  .+++++|.+||.++.|.++++.  |+ ..|.|+.|+.+.
T Consensus       121 ~~~a~n~Llk~lEep--~~~~~fIl~t~~~~~ll~tI~S--Rc-~~i~~~~~~~~~  171 (207)
T d1a5ta2         121 TDAAANALLKTLEEP--PAETWFFLATREPERLLATLRS--RC-RLHYLAPPPEQY  171 (207)
T ss_dssp             CHHHHHHHHHHHTSC--CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHH
T ss_pred             hhhhhHHHHHHHHhh--cccceeeeeecChhhhhhhhcc--ee-EEEecCCCCHHH
Confidence            345678899999964  4578999999999999999999  98 899999888764

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.53  E-value=0.0021  Score=39.26  Aligned_cols=49  Identities=8%  Similarity=0.092  Sum_probs=39.1

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.|+..++..  ..++.+|++||.++.++++++.  || ..|+|+.|+.++
T Consensus       146 ~~~~~l~~~~e~~--~~~~~~Il~tn~~~~i~~~l~s--R~-~~i~~~~~~~~~  194 (252)
T d1sxje2         146 DAQAALRRTMEKY--SKNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPSDSE  194 (252)
T ss_dssp             HHHHHHHHHHHHS--TTTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCCHHH
T ss_pred             ccchhhhcccccc--cccccceeeeccccchhhhhhc--ch-heeeecccchhh
Confidence            4455667777643  4467889999999999999998  99 689999998775

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=95.94  E-value=0.0059  Score=37.65  Aligned_cols=50  Identities=26%  Similarity=0.273  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....+.|+..|+..  .+++.+|.+||.++.+.++++.  |+ ..+.++.|+.++
T Consensus       129 ~~~q~~Llk~lE~~--~~~~~~il~tn~~~~i~~~i~S--Rc-~~i~~~~~~~~~  178 (239)
T d1njfa_         129 RHSFNALLKTLEEP--PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQ  178 (239)
T ss_dssp             HHHHHHHHHHHHSC--CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHH
T ss_pred             HHHHHHHHHHHhcC--CCCeEEEEEcCCccccChhHhh--hh-cccccccCcHHH
Confidence            45567899999854  4567889999999999999999  98 678888888654

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.59  E-value=0.017  Score=35.10  Aligned_cols=50  Identities=22%  Similarity=0.253  Sum_probs=40.6

Q ss_pred             hhHHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCCh
Q psy3374          14 VKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDL   68 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~   68 (72)
                      ......|.||..|+.-  .+++++|.+||.++.|.|+++.  |+ ..+.++.|..
T Consensus        91 l~~~aqNaLLK~LEEP--p~~t~fiLit~~~~~ll~TI~S--RC-~~i~~~~p~~  140 (198)
T d2gnoa2          91 MTQQAANAFLKALEEP--PEYAVIVLNTRRWHYLLPTIKS--RV-FRVVVNVPKE  140 (198)
T ss_dssp             BCHHHHHHTHHHHHSC--CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCHH
T ss_pred             cchhhhhHHHHHHhCC--CCCceeeeccCChhhCHHHHhc--ce-EEEeCCCchH
Confidence            3456778899999954  4568888889999999999999  98 7888887754

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=94.24  E-value=0.029  Score=33.90  Aligned_cols=37  Identities=32%  Similarity=0.449  Sum_probs=32.1

Q ss_pred             CCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          32 LEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        32 ~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ..+++++++||++...+++.++  |+...+.+..|+.+.
T Consensus       133 ~~~~~~i~~~~~~~~~~~~~l~--~~~~~~~~~~~~~~~  169 (239)
T d1ixsb2         133 LPRFTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEE  169 (239)
T ss_dssp             CCCCEEEEEESCCSSCSCGGGG--GCSEEEECCCCCHHH
T ss_pred             CCCEEEEeeccCcccccchhhc--ccceeeEeeccChhh
Confidence            3467889999999999999999  888999999998765

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=93.20  E-value=0.053  Score=34.58  Aligned_cols=52  Identities=29%  Similarity=0.406  Sum_probs=40.1

Q ss_pred             hhHHHHHHHHHHhhCCC-----------CCCCeEEEEecCC-CCCCcccccCCCccccEEEeCCCC
Q psy3374          14 VKDRVVNQLLTELDGVE-----------GLEGVYVVGATSR-PDIIDPALLRPGRLGSSVHCTMPD   67 (72)
Q Consensus        14 ~~~~~~~~ll~~ld~~~-----------~~~~v~vi~aTn~-~~~lD~al~r~GRfd~~i~v~~Pd   67 (72)
                      ...++.+.|++-|+.-.           -..+.++++|+|- +..+.++++.  |||..|.++.|.
T Consensus       139 ~~~~~~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~Np~~~~l~~~llD--Rf~~~i~v~~~~  202 (333)
T d1g8pa_         139 LEDHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPR  202 (333)
T ss_dssp             SCHHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCC
T ss_pred             HHHHHHHHHhhhhcCCeEEecccCceecCCCCEEEEEecCccccccccchhh--hhcceeeccCcc
Confidence            34578899999997421           0125788999887 4568999999  999999999875

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=92.64  E-value=0.054  Score=32.48  Aligned_cols=49  Identities=8%  Similarity=-0.069  Sum_probs=37.9

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.|+..++..  ..++.+|++||.+..+++++..  || ..+.+..|+.++
T Consensus       124 ~~~~~ll~~l~~~--~~~~~~i~~~n~~~~i~~~l~s--R~-~~i~~~~~~~~~  172 (231)
T d1iqpa2         124 DAQQALRRTMEMF--SSNVRFILSCNYSSKIIEPIQS--RC-AIFRFRPLRDED  172 (231)
T ss_dssp             HHHHHHHHHHHHT--TTTEEEEEEESCGGGSCHHHHH--TE-EEEECCCCCHHH
T ss_pred             hHHHHHhhhcccC--CcceEEEeccCChhhchHhHhC--cc-ccccccccchhh
Confidence            4445677777643  3468899999999999999998  98 468888888764

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.49  E-value=0.08  Score=31.53  Aligned_cols=50  Identities=12%  Similarity=0.081  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          16 DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        16 ~~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ....+.|+..|+..  .+.+.++.+||.+..+++++++  |+ ..+.|..|+.++
T Consensus       113 ~~~~~~Ll~~le~~--~~~~~~~~~~~~~~~i~~~i~s--r~-~~i~~~~~~~~~  162 (227)
T d1sxjc2         113 NAAQNALRRVIERY--TKNTRFCVLANYAHKLTPALLS--QC-TRFRFQPLPQEA  162 (227)
T ss_dssp             HHHHHHHHHHHHHT--TTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHH
T ss_pred             hhHHHHHHHHhhhc--ccceeeccccCcHHHhHHHHHH--HH-hhhccccccccc
Confidence            34566788888754  3468889999999999999999  87 677888887654

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.82  E-value=0.32  Score=28.99  Aligned_cols=48  Identities=15%  Similarity=0.122  Sum_probs=32.2

Q ss_pred             HHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          18 VVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        18 ~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      ....++......  ...++++++++....+++  ++  |+...|+|+.|+.++.
T Consensus       142 ~~~~~~~~~~~~--~~~ii~i~~~~~~~~~~~--l~--~~~~~i~f~~~~~~~i  189 (253)
T d1sxja2         142 GVGQLAQFCRKT--STPLILICNERNLPKMRP--FD--RVCLDIQFRRPDANSI  189 (253)
T ss_dssp             HHHHHHHHHHHC--SSCEEEEESCTTSSTTGG--GT--TTSEEEECCCCCHHHH
T ss_pred             hhHHHhhhhccc--cccccccccccccccccc--cc--ceeeeeeccccchhHH
Confidence            344455544433  235777777777777775  44  6779999999998753

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=89.29  E-value=0.1  Score=31.21  Aligned_cols=51  Identities=12%  Similarity=0.170  Sum_probs=35.9

Q ss_pred             HHHHHHHHhhCCCCCCCeEEEEecCCCCCCc------ccccCCCccccEEEeCCCChhh
Q psy3374          18 VVNQLLTELDGVEGLEGVYVVGATSRPDIID------PALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        18 ~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD------~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      .+..++..+..........+|+.+|.++..+      +++.+  ||...++++.++.++
T Consensus       157 ~l~~l~~~l~~~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~--r~~~~i~f~~y~~~e  213 (287)
T d1w5sa2         157 TLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVES--QIGFKLHLPAYKSRE  213 (287)
T ss_dssp             HHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHT--TCSEEEECCCCCHHH
T ss_pred             HHHHHHHhcchhhcccceeEEeecccHHHHHHHHhhccchhc--ccceeeeccCCcHHH
Confidence            3444555565655556677777777766443      66777  999999999998875

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.63  E-value=0.22  Score=29.58  Aligned_cols=49  Identities=8%  Similarity=-0.065  Sum_probs=37.3

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.|+..++..  .....++.+||..+.+.++++.  |+ ..|.|+.|+.++
T Consensus       116 ~~~~~ll~~~e~~--~~~~~~i~~~~~~~~i~~~l~s--r~-~~i~~~~~~~~~  164 (224)
T d1sxjb2         116 GAQQALRRTMELY--SNSTRFAFACNQSNKIIEPLQS--QC-AILRYSKLSDED  164 (224)
T ss_dssp             HHHHTTHHHHHHT--TTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHH
T ss_pred             hHHHHHhhhcccc--ccceeeeeccCchhhhhhHHHH--HH-HHhhhcccchhh
Confidence            3445566666643  3457788889999999999999  98 579999998765

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=84.92  E-value=0.41  Score=28.13  Aligned_cols=49  Identities=10%  Similarity=-0.077  Sum_probs=36.8

Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEecCCCCCCcccccCCCccccEEEeCCCChhh
Q psy3374          17 RVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDLAF   70 (72)
Q Consensus        17 ~~~~~ll~~ld~~~~~~~v~vi~aTn~~~~lD~al~r~GRfd~~i~v~~Pd~~~   70 (72)
                      ...+.++..++..  .....++.+||..+.+.+++..  || ..|.|..|+.++
T Consensus       123 ~~~~~l~~~~~~~--~~~~~~i~~~~~~~~~~~~l~s--r~-~~i~f~~~~~~~  171 (237)
T d1sxjd2         123 DAQSALRRTMETY--SGVTRFCLICNYVTRIIDPLAS--QC-SKFRFKALDASN  171 (237)
T ss_dssp             HHHHHHHHHHHHT--TTTEEEEEEESCGGGSCHHHHH--HS-EEEECCCCCHHH
T ss_pred             HHHHHHhhccccc--cccccccccccccccccccccc--hh-hhhccccccccc
Confidence            3445555555533  3456778889999999999998  98 789999998765

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=84.58  E-value=1  Score=28.34  Aligned_cols=37  Identities=27%  Similarity=0.318  Sum_probs=29.2

Q ss_pred             CCCeEEEEecC-----CCCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          32 LEGVYVVGATS-----RPDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        32 ~~~v~vi~aTn-----~~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      .+.+-+||+|.     ....-|+||.|  || .+|.|.-|+.++.
T Consensus       145 rg~i~vIgatT~eey~~~~e~d~al~r--rF-~~I~V~Eps~e~t  186 (268)
T d1r6bx2         145 SGKIRVIGSTTYQEFSNIFEKDRALAR--RF-QKIDITEPSIEET  186 (268)
T ss_dssp             SCCCEEEEEECHHHHHCCCCCTTSSGG--GE-EEEECCCCCHHHH
T ss_pred             CCCCeEEEeCCHHHHHHHHhhcHHHHh--hh-cccccCCCCHHHH
Confidence            44688888886     34466999999  99 7899999998763

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=82.25  E-value=0.14  Score=31.34  Aligned_cols=36  Identities=31%  Similarity=0.267  Sum_probs=26.9

Q ss_pred             CCeEEEEecCC-----CCCCcccccCCCccccEEEeCCCChhhh
Q psy3374          33 EGVYVVGATSR-----PDIIDPALLRPGRLGSSVHCTMPDLAFA   71 (72)
Q Consensus        33 ~~v~vi~aTn~-----~~~lD~al~r~GRfd~~i~v~~Pd~~~~   71 (72)
                      +.+-+|+||.-     .-.-|+||.|  || .+|.|.-|+.++.
T Consensus       150 g~l~~IgatT~eey~~~~e~d~aL~r--rF-~~I~V~Ep~~e~t  190 (195)
T d1jbka_         150 GELHCVGATTLDEYRQYIEKDAALER--RF-QKVFVAEPSVEDT  190 (195)
T ss_dssp             TSCCEEEEECHHHHHHHTTTCHHHHT--TE-EEEECCCCCHHHH
T ss_pred             CCceEEecCCHHHHHHHHHcCHHHHh--cC-CEeecCCCCHHHH
Confidence            34667777762     2355999999  99 7799999998763