Psyllid ID: psy3868

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------7
Protein Sequence
MSYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKREL
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHccEEEEEEccHHHccccHHHHHHHHHHHHHHHHccccEEEEEcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHcccEEEEEccHHHHHHHHcccHHHHHHHHHHHHHcccEEEEEEcHHHHccccccccc
Coil and Loop (DISEMBL)
MSYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEeadknspsiifideldaiapkrekrel
Flexible Loop (DISEMBL)
msyrlttlcrdSLGAFFFLINGPEIMSKLAGESESNLRKAFEeadknspsiifideldaiapkrekrel
Low Complexity Region (SEG)
MSYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKREL
Disordered region (IsUnstruct)
***RLTTLCRDSLGAFFFLINGPEIM************************IIFIDEL************
Disordered Region (DISOPRED)
*SYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIA*KR*****
Disordered Region (DISEMBL)
MSYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKREL
Disordered Region (DISPRO)
*SYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK******
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKREL
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	69	2.2.26 [Sep-21-2011]
P23787	805	Transitional endoplasmic	N/A	N/A	0.768	0.065	0.943	2e-22
Q01853	806	Transitional endoplasmic	yes	N/A	0.768	0.065	0.943	2e-22
P55072	806	Transitional endoplasmic	yes	N/A	0.768	0.065	0.943	2e-22
P46462	806	Transitional endoplasmic	yes	N/A	0.768	0.065	0.943	2e-22
Q3ZBT1	806	Transitional endoplasmic	yes	N/A	0.768	0.065	0.943	2e-22
Q6GL04	805	Transitional endoplasmic	yes	N/A	0.768	0.065	0.943	2e-22
P03974	806	Transitional endoplasmic	yes	N/A	0.768	0.065	0.943	2e-22
Q7ZU99	806	Transitional endoplasmic	no	N/A	0.768	0.065	0.943	2e-22
Q9P3A7	815	Cell division cycle prote	yes	N/A	0.768	0.065	0.905	4e-22
Q7KN62	801	Transitional endoplasmic	yes	N/A	0.768	0.066	0.924	4e-22

>sp|P23787|TERA_XENLA Transitional endoplasmic reticulum ATPase OS=Xenopus laevis GN=vcp PE=1 SV=3

 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct: 263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process.
Xenopus laevis (taxid: 8355)

>sp|Q01853|TERA_MOUSE Transitional endoplasmic reticulum ATPase OS=Mus musculus GN=Vcp PE=1 SV=4

 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct: 263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process. The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope. Regulates E3 ubiquitin-protein ligase activity of RNF19A (By similarity). Component of the VCP/p97-AMFR/gp78 complex that participates in the final step of the sterol-mediated ubiquitination and endoplasmic reticulum-associated degradation (ERAD) of HMGCR.

Mus musculus (taxid: 10090)

>sp|P55072|TERA_HUMAN Transitional endoplasmic reticulum ATPase OS=Homo sapiens GN=VCP PE=1 SV=4

 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct: 263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process. The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope. Regulates E3 ubiquitin-protein ligase activity of RNF19A (By similarity). Component of the VCP/p97-AMFR/gp78 complex that participates in the final step of the sterol-mediated ubiquitination and endoplasmic reticulum-associated degradation (ERAD) of HMGCR.

Homo sapiens (taxid: 9606)

>sp|P46462|TERA_RAT Transitional endoplasmic reticulum ATPase OS=Rattus norvegicus GN=Vcp PE=1 SV=3

 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct: 263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process. The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope. Regulates E3 ubiquitin-protein ligase activity of RNF19A (By similarity). Component of the VCP/p97-AMFR/gp78 complex that participates in the final step of the sterol-mediated ubiquitination and endoplasmic reticulum-associated degradation (ERAD) of HMGCR.

Rattus norvegicus (taxid: 10116)

>sp|Q3ZBT1|TERA_BOVIN Transitional endoplasmic reticulum ATPase OS=Bos taurus GN=VCP PE=2 SV=1

 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct: 263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process. The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope. Regulates E3 ubiquitin-protein ligase activity of RNF19A (By similarity). Component of the VCP/p97-AMFR/gp78 complex that participates in the final step of the sterol-mediated ubiquitination and endoplasmic reticulum-associated degradation (ERAD) of HMGCR.

Bos taurus (taxid: 9913)

>sp|Q6GL04|TERA_XENTR Transitional endoplasmic reticulum ATPase OS=Xenopus tropicalis GN=vcp PE=2 SV=1

 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct: 263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the nuclear envelope and of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process.

Xenopus tropicalis (taxid: 8364)

>sp|P03974|TERA_PIG Transitional endoplasmic reticulum ATPase OS=Sus scrofa GN=VCP PE=1 SV=5

 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct: 263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process. The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope. Regulates E3 ubiquitin-protein ligase activity of RNF19A (By similarity). Component of the VCP/p97-AMFR/gp78 complex that participates in the final step of the sterol-mediated ubiquitination and endoplasmic reticulum-associated degradation (ERAD) of HMGCR.

Sus scrofa (taxid: 9823)

>sp|Q7ZU99|TERA_DANRE Transitional endoplasmic reticulum ATPase OS=Danio rerio GN=vcp PE=1 SV=1

 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct: 263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process (By similarity). Enhances cell cycle progression and inhibits apoptosis at low temperatures.

Danio rerio (taxid: 7955)

>sp|Q9P3A7|CDC48_SCHPO Cell division cycle protein 48 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=cdc48 PE=1 SV=2

 Score =  103 bits (256), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 48/53 (90%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSK+AGESESNLRKAFEEA+KNSP+IIFIDE+D+IAPKREK
Sbjct: 283 GAFFFLINGPEIMSKMAGESESNLRKAFEEAEKNSPAIIFIDEIDSIAPKREK 335

Involved in spindle disassembly, degradation of ubiquitinated proteins and protein export from the endoplasmic reticulum to the cytoplasm.

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

>sp|Q7KN62|TERA_DROME Transitional endoplasmic reticulum ATPase TER94 OS=Drosophila melanogaster GN=TER94 PE=1 SV=1

 Score =  103 bits (256), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 49/53 (92%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KNSP+IIFIDE+DAIAPKR+K
Sbjct: 260 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNSPAIIFIDEIDAIAPKRDK 312

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process (By similarity). Involved in the ubiquitin-proteasome system. Important for oskar mRNA localization and/or anchoring during oogenesis.

Drosophila melanogaster (taxid: 7227)

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	69
357623246	1316	transitional endoplasmic reticulum ATPas	0.768	0.040	0.981	7e-22
112983322	805	transitional endoplasmic reticulum ATPas	0.768	0.065	0.981	1e-21
242008814	804	conserved hypothetical protein [Pediculu	0.768	0.065	0.981	1e-21
91086235	803	PREDICTED: similar to transitional endop	0.768	0.066	0.981	1e-21
344251788	2171	Transitional endoplasmic reticulum ATPas	0.768	0.024	0.943	1e-21
193617621	804	PREDICTED: transitional endoplasmic reti	0.768	0.065	0.962	2e-21
443694341	812	hypothetical protein CAPTEDRAFT_161400,	0.768	0.065	0.962	3e-21
380016377	893	PREDICTED: LOW QUALITY PROTEIN: transiti	0.768	0.059	0.962	3e-21
383861759	811	PREDICTED: transitional endoplasmic reti	0.768	0.065	0.962	3e-21
307211146	796	Transitional endoplasmic reticulum ATPas	0.768	0.066	0.962	4e-21

>gi|357623246|gb|EHJ74479.1| transitional endoplasmic reticulum ATPase TER94 [Danaus plexippus]

 Score =  107 bits (268), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 52/53 (98%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSP+IIFIDELDAIAPKREK
Sbjct: 772 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPAIIFIDELDAIAPKREK 824

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|112983322|ref|NP_001037003.1| transitional endoplasmic reticulum ATPase TER94 [Bombyx mori] gi|83423461|dbj|BAE54254.1| transitional endoplasmic reticulum ATPase TER94 [Bombyx mori] gi|95102992|gb|ABF51437.1| transitional endoplasmic reticulum ATPase TER94 [Bombyx mori]

 Score =  107 bits (267), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 52/53 (98%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSP+IIFIDELDAIAPKREK
Sbjct: 261 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPAIIFIDELDAIAPKREK 313

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242008814|ref|XP_002425193.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212508909|gb|EEB12455.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  107 bits (267), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 52/53 (98%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSP+IIFIDELDAIAPKREK
Sbjct: 261 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPAIIFIDELDAIAPKREK 313

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91086235|ref|XP_966692.1| PREDICTED: similar to transitional endoplasmic reticulum ATPase TER94 isoform 1 [Tribolium castaneum] gi|270011017|gb|EFA07465.1| transitional endoplasmic reticulum ATPase TER94 [Tribolium castaneum]

 Score =  107 bits (266), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 52/53 (98%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSP+IIFIDELDAIAPKREK
Sbjct: 261 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPAIIFIDELDAIAPKREK 313

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|344251788|gb|EGW07892.1| Transitional endoplasmic reticulum ATPase [Cricetulus griseus]

 Score =  106 bits (265), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query: 14   GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
            GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct: 1606 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 1658

Source: Cricetulus griseus

Species: Cricetulus griseus

Genus: Cricetulus

Family: Cricetidae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|193617621|ref|XP_001949588.1| PREDICTED: transitional endoplasmic reticulum ATPase TER94-like [Acyrthosiphon pisum]

 Score =  106 bits (264), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 51/53 (96%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEAD+NSP+IIFIDELDAIAPKREK
Sbjct: 261 GAFFFLINGPEIMSKLAGESESNLRKAFEEADRNSPAIIFIDELDAIAPKREK 313

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443694341|gb|ELT95504.1| hypothetical protein CAPTEDRAFT_161400, partial [Capitella teleta]

 Score =  105 bits (263), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 51/53 (96%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KNSP+IIFIDELDAIAPKREK
Sbjct: 261 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNSPAIIFIDELDAIAPKREK 313

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|380016377|ref|XP_003692162.1| PREDICTED: LOW QUALITY PROTEIN: transitional endoplasmic reticulum ATPase TER94-like [Apis florea]

 Score =  105 bits (263), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 51/53 (96%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KNSP+IIFIDELDAIAPKREK
Sbjct: 260 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNSPAIIFIDELDAIAPKREK 312

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383861759|ref|XP_003706352.1| PREDICTED: transitional endoplasmic reticulum ATPase TER94-like isoform 2 [Megachile rotundata]

 Score =  105 bits (262), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 51/53 (96%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KNSP+IIFIDELDAIAPKREK
Sbjct: 260 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNSPAIIFIDELDAIAPKREK 312

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307211146|gb|EFN87364.1| Transitional endoplasmic reticulum ATPase TER94 [Harpegnathos saltator]

 Score =  105 bits (262), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 51/53 (96%), Positives = 53/53 (100%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KNSP+IIFIDELDAIAPKREK
Sbjct: 261 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNSPAIIFIDELDAIAPKREK 313

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

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	69
UNIPROTKB|P23787	805	vcp "Transitional endoplasmic	0.768	0.065	0.943	1.2e-20
UNIPROTKB|Q6GL04	805	vcp "Transitional endoplasmic	0.768	0.065	0.943	1.2e-20
ZFIN|ZDB-GENE-060312-22	805	zgc:136908 "zgc:136908" [Danio	0.768	0.065	0.943	1.2e-20
UNIPROTKB|G3X757	806	VCP "Transitional endoplasmic	0.768	0.065	0.943	1.2e-20
UNIPROTKB|Q3ZBT1	806	VCP "Transitional endoplasmic	0.768	0.065	0.943	1.2e-20
UNIPROTKB|P55072	806	VCP "Transitional endoplasmic	0.768	0.065	0.943	1.2e-20
UNIPROTKB|P03974	806	VCP "Transitional endoplasmic	0.768	0.065	0.943	1.2e-20
MGI|MGI:99919	806	Vcp "valosin containing protei	0.768	0.065	0.943	1.2e-20
RGD|621595	806	Vcp "valosin-containing protei	0.768	0.065	0.943	1.2e-20
ZFIN|ZDB-GENE-030131-5408	806	vcp "valosin containing protei	0.768	0.065	0.943	1.2e-20

UNIPROTKB|P23787 vcp "Transitional endoplasmic reticulum ATPase" [Xenopus laevis (taxid:8355)]

 Score = 254 (94.5 bits), Expect = 1.2e-20, P = 1.2e-20
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query:    14 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
             GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct:   263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

GO:0000785 "chromatin" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006200 "ATP catabolic process" evidence=IDA

GO:0006302 "double-strand break repair" evidence=ISS

GO:0006974 "response to DNA damage stimulus" evidence=ISS

GO:0016567 "protein ubiquitination" evidence=ISS

GO:0016887 "ATPase activity" evidence=IDA

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISS

GO:0019985 "translesion synthesis" evidence=ISS

GO:0030433 "ER-associated protein catabolic process" evidence=ISS

GO:0032403 "protein complex binding" evidence=IPI

GO:0034214 "protein hexamerization" evidence=IDA

GO:0035861 "site of double-strand break" evidence=ISS

GO:0035101 "FACT complex" evidence=IPI

UNIPROTKB|Q6GL04 vcp "Transitional endoplasmic reticulum ATPase" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 254 (94.5 bits), Expect = 1.2e-20, P = 1.2e-20
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query:    14 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
             GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct:   263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

GO:0000785 "chromatin" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0006200 "ATP catabolic process" evidence=ISS

GO:0006302 "double-strand break repair" evidence=ISS

GO:0006974 "response to DNA damage stimulus" evidence=ISS

GO:0016567 "protein ubiquitination" evidence=ISS

GO:0016887 "ATPase activity" evidence=ISS

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISS

GO:0019985 "translesion synthesis" evidence=ISS

GO:0030433 "ER-associated protein catabolic process" evidence=ISS

GO:0032403 "protein complex binding" evidence=ISS

GO:0034214 "protein hexamerization" evidence=ISS

GO:0035861 "site of double-strand break" evidence=ISS

GO:0035101 "FACT complex" evidence=ISS

ZFIN|ZDB-GENE-060312-22 zgc:136908 "zgc:136908" [Danio rerio (taxid:7955)]

 Score = 254 (94.5 bits), Expect = 1.2e-20, P = 1.2e-20
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query:    14 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
             GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct:   265 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 317

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

GO:0005524 "ATP binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|G3X757 VCP "Transitional endoplasmic reticulum ATPase" [Bos taurus (taxid:9913)]

 Score = 254 (94.5 bits), Expect = 1.2e-20, P = 1.2e-20
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query:    14 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
             GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct:   263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

GO:0070842 "aggresome assembly" evidence=IEA

GO:0045732 "positive regulation of protein catabolic process" evidence=IEA

GO:0035861 "site of double-strand break" evidence=IEA

GO:0031593 "polyubiquitin binding" evidence=IEA

GO:0031334 "positive regulation of protein complex assembly" evidence=IEA

GO:0030970 "retrograde protein transport, ER to cytosol" evidence=IEA

GO:0019904 "protein domain specific binding" evidence=IEA

GO:0019903 "protein phosphatase binding" evidence=IEA

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=IEA

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0006302 "double-strand break repair" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|Q3ZBT1 VCP "Transitional endoplasmic reticulum ATPase" [Bos taurus (taxid:9913)]

 Score = 254 (94.5 bits), Expect = 1.2e-20, P = 1.2e-20
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query:    14 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
             GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct:   263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

GO:0019985 "translesion synthesis" evidence=ISS

GO:0016567 "protein ubiquitination" evidence=ISS

GO:0006974 "response to DNA damage stimulus" evidence=ISS

GO:0006302 "double-strand break repair" evidence=ISS

GO:0035861 "site of double-strand break" evidence=ISS

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISS

GO:0030433 "ER-associated protein catabolic process" evidence=ISS

GO:0005829 "cytosol" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008289 "lipid binding" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|P55072 VCP "Transitional endoplasmic reticulum ATPase" [Homo sapiens (taxid:9606)]

 Score = 254 (94.5 bits), Expect = 1.2e-20, P = 1.2e-20
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query:    14 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
             GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct:   263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

GO:0008289 "lipid binding" evidence=IEA

GO:0005102 "receptor binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006888 "ER to Golgi vesicle-mediated transport" evidence=IEA

GO:0032403 "protein complex binding" evidence=IEA

GO:0042802 "identical protein binding" evidence=IEA

GO:0051260 "protein homooligomerization" evidence=IEA

GO:0070842 "aggresome assembly" evidence=IEA

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

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=ISS

GO:0006281 "DNA repair" evidence=NAS

GO:0006974 "response to DNA damage stimulus" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA;TAS

GO:0005829 "cytosol" evidence=IDA

GO:0006302 "double-strand break repair" evidence=IDA

GO:0019904 "protein domain specific binding" evidence=IPI

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=NAS

GO:0030970 "retrograde protein transport, ER to cytosol" evidence=IDA

GO:0030433 "ER-associated protein catabolic process" evidence=IMP;TAS

GO:0030968 "endoplasmic reticulum unfolded protein response" evidence=TAS

GO:0016887 "ATPase activity" evidence=TAS

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0016567 "protein ubiquitination" evidence=IDA;NAS

GO:0042981 "regulation of apoptotic process" evidence=TAS

GO:0045184 "establishment of protein localization" evidence=TAS

GO:0019985 "translesion synthesis" evidence=IMP

GO:0035861 "site of double-strand break" evidence=IDA

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=IMP

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IDA

GO:0000502 "proteasome complex" evidence=IDA

GO:0019903 "protein phosphatase binding" evidence=IPI

GO:0045732 "positive regulation of protein catabolic process" evidence=IDA

GO:0031334 "positive regulation of protein complex assembly" evidence=IDA

GO:0031593 "polyubiquitin binding" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|P03974 VCP "Transitional endoplasmic reticulum ATPase" [Sus scrofa (taxid:9823)]

 Score = 254 (94.5 bits), Expect = 1.2e-20, P = 1.2e-20
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query:    14 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
             GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct:   263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

GO:0019985 "translesion synthesis" evidence=ISS

GO:0016567 "protein ubiquitination" evidence=ISS

GO:0006974 "response to DNA damage stimulus" evidence=ISS

GO:0035861 "site of double-strand break" evidence=ISS

GO:0006302 "double-strand break repair" evidence=ISS

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISS

GO:0030433 "ER-associated protein catabolic process" evidence=ISS

GO:0005829 "cytosol" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008289 "lipid binding" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

MGI|MGI:99919 Vcp "valosin containing protein" [Mus musculus (taxid:10090)]

 Score = 254 (94.5 bits), Expect = 1.2e-20, P = 1.2e-20
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query:    14 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
             GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct:   263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000502 "proteasome complex" evidence=ISO

GO:0005102 "receptor binding" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005524 "ATP binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=ISO

GO:0005829 "cytosol" evidence=ISO

GO:0006200 "ATP catabolic process" evidence=ISO

GO:0006281 "DNA repair" evidence=IEA

GO:0006302 "double-strand break repair" evidence=ISO

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IGI

GO:0006810 "transport" evidence=IEA

GO:0006888 "ER to Golgi vesicle-mediated transport" evidence=ISO

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IDA

GO:0006974 "response to DNA damage stimulus" evidence=ISO

GO:0008289 "lipid binding" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=ISO

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=ISO

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

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISO

GO:0019903 "protein phosphatase binding" evidence=ISO

GO:0019904 "protein domain specific binding" evidence=ISO

GO:0019985 "translesion synthesis" evidence=ISO

GO:0030433 "ER-associated protein catabolic process" evidence=ISO

GO:0030970 "retrograde protein transport, ER to cytosol" evidence=ISO

GO:0031334 "positive regulation of protein complex assembly" evidence=ISO

GO:0031593 "polyubiquitin binding" evidence=ISO;IDA

GO:0032403 "protein complex binding" evidence=ISO

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=ISO

GO:0035861 "site of double-strand break" evidence=ISO

GO:0042802 "identical protein binding" evidence=ISO

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

GO:0043234 "protein complex" evidence=IPI

GO:0043531 "ADP binding" evidence=ISO

GO:0045732 "positive regulation of protein catabolic process" evidence=ISO

GO:0051260 "protein homooligomerization" evidence=ISO

GO:0070842 "aggresome assembly" evidence=IGI

RGD|621595 Vcp "valosin-containing protein" [Rattus norvegicus (taxid:10116)]

 Score = 254 (94.5 bits), Expect = 1.2e-20, P = 1.2e-20
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query:    14 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
             GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct:   263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

GO:0000502 "proteasome complex" evidence=IEA;ISO

GO:0005102 "receptor binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005524 "ATP binding" evidence=IDA;IMP

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005783 "endoplasmic reticulum" evidence=ISO;IDA

GO:0005829 "cytosol" evidence=ISO;IDA

GO:0006200 "ATP catabolic process" evidence=IDA

GO:0006302 "double-strand break repair" evidence=ISO;ISS

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=ISO

GO:0006888 "ER to Golgi vesicle-mediated transport" evidence=IMP

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA;ISO

GO:0006974 "response to DNA damage stimulus" evidence=ISO;ISS

GO:0008289 "lipid binding" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=ISO;ISS

GO:0016887 "ATPase activity" evidence=IDA

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISO;ISS

GO:0019903 "protein phosphatase binding" evidence=IEA;ISO

GO:0019904 "protein domain specific binding" evidence=IEA;ISO

GO:0019985 "translesion synthesis" evidence=ISO;ISS

GO:0030433 "ER-associated protein catabolic process" evidence=ISO;ISS

GO:0030970 "retrograde protein transport, ER to cytosol" evidence=IEA;ISO

GO:0031334 "positive regulation of protein complex assembly" evidence=IEA;ISO

GO:0031593 "polyubiquitin binding" evidence=IEA;ISO

GO:0032403 "protein complex binding" evidence=IPI

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=ISO;IMP

GO:0035861 "site of double-strand break" evidence=ISO;ISS

GO:0042802 "identical protein binding" evidence=IDA

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

GO:0043234 "protein complex" evidence=ISO

GO:0043531 "ADP binding" evidence=IMP

GO:0045732 "positive regulation of protein catabolic process" evidence=ISO

GO:0051260 "protein homooligomerization" evidence=IDA

GO:0070842 "aggresome assembly" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

ZFIN|ZDB-GENE-030131-5408 vcp "valosin containing protein" [Danio rerio (taxid:7955)]

 Score = 254 (94.5 bits), Expect = 1.2e-20, P = 1.2e-20
 Identities = 50/53 (94%), Positives = 53/53 (100%)

Query:    14 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
             GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct:   263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

GO:0016787 "hydrolase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA;ISS

GO:0016567 "protein ubiquitination" evidence=ISS

GO:0035861 "site of double-strand break" evidence=ISS

GO:0006302 "double-strand break repair" evidence=ISS

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISS

GO:0019985 "translesion synthesis" evidence=ISS

GO:0030433 "ER-associated protein catabolic process" evidence=ISS

GO:0009790 "embryo development" evidence=IMP

GO:2000058 "regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process" evidence=IMP

GO:0005634 "nucleus" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0008289 "lipid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

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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)
Q07590	SAV_SULAC	No assigned EC number	0.6190	0.8695	0.0769	yes	N/A
Q58556	Y1156_METJA	No assigned EC number	0.6557	0.8840	0.0675	yes	N/A
P54609	CD48A_ARATH	No assigned EC number	0.9056	0.7681	0.0655	yes	N/A
Q9SCN8	CD48D_ARATH	No assigned EC number	0.9056	0.7681	0.0650	no	N/A
P46462	TERA_RAT	No assigned EC number	0.9433	0.7681	0.0657	yes	N/A
Q3ZBT1	TERA_BOVIN	No assigned EC number	0.9433	0.7681	0.0657	yes	N/A
Q9P3A7	CDC48_SCHPO	No assigned EC number	0.9056	0.7681	0.0650	yes	N/A
P55072	TERA_HUMAN	No assigned EC number	0.9433	0.7681	0.0657	yes	N/A
Q01853	TERA_MOUSE	No assigned EC number	0.9433	0.7681	0.0657	yes	N/A
Q5AWS6	CDC48_EMENI	No assigned EC number	0.9056	0.7681	0.0643	yes	N/A
Q8SSJ5	CDC48_ENCCU	No assigned EC number	0.8545	0.7391	0.0653	yes	N/A
Q7KN62	TERA_DROME	No assigned EC number	0.9245	0.7681	0.0661	yes	N/A
Q96372	CDC48_CAPAN	No assigned EC number	0.9056	0.7681	0.0658	N/A	N/A
P54812	TERA2_CAEEL	No assigned EC number	0.8490	0.7681	0.0654	yes	N/A
Q7ZU99	TERA_DANRE	No assigned EC number	0.9433	0.7681	0.0657	no	N/A
Q6GL04	TERA_XENTR	No assigned EC number	0.9433	0.7681	0.0658	yes	N/A
O05209	VAT_THEAC	No assigned EC number	0.6415	0.7681	0.0711	yes	N/A
P54774	CDC48_SOYBN	No assigned EC number	0.9056	0.7681	0.0656	no	N/A
P25694	CDC48_YEAST	No assigned EC number	0.8490	0.7681	0.0634	yes	N/A
P23787	TERA_XENLA	No assigned EC number	0.9433	0.7681	0.0658	N/A	N/A
Q9LZF6	CD48E_ARATH	No assigned EC number	0.9056	0.7681	0.0654	yes	N/A
P03974	TERA_PIG	No assigned EC number	0.9433	0.7681	0.0657	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	69
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	4e-23
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	2e-19
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	3e-15
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	4e-14
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	1e-12
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	7e-11
COG1223	368	COG1223, COG1223, Predicted ATPase (AAA+ superfami	1e-09
TIGR01241	495	TIGR01241, FtsH_fam, ATP-dependent metalloprotease	1e-09
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	1e-09
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	2e-09
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	3e-09
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	5e-09
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	5e-08
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	5e-08
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	3e-07
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	5e-06
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	1e-05
smart00382	148	smart00382, AAA, ATPases associated with a variety	2e-04

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

 Score = 90.0 bits (223), Expect = 4e-23
 Identities = 38/53 (71%), Positives = 46/53 (86%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GA+F  INGPEIMSK  GESE  LR+ F+EA++N+PSIIFIDE+DAIAPKRE+
Sbjct: 237 GAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREE 289

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 = 74.9 bits (185), Expect = 2e-19
 Identities = 32/66 (48%), Positives = 41/66 (62%), Gaps = 3/66 (4%)

Query: 6  TTLCR---DSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 62
          TTL +     LGA F  I+G E++SK  GESE  LR+ FE A K +P +IFIDE+DA+A 
Sbjct: 12 TTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAG 71

Query: 63 KREKRE 68
           R    
Sbjct: 72 SRGSGG 77

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

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

 Score = 67.6 bits (165), Expect = 3e-15
 Identities = 29/55 (52%), Positives = 38/55 (69%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68
           GA F  + GPEI+SK  GESE  +R+ F +A + +P+IIF DE+DAIAP R  R 
Sbjct: 512 GANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARF 566

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

 Score = 64.5 bits (157), Expect = 4e-14
 Identities = 26/53 (49%), Positives = 37/53 (69%)

Query: 12  SLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
              + F  + G E++SK  GESE N+R+ FE+A K +PSIIFIDE+D++A  R
Sbjct: 299 ESRSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGR 351

Length = 494

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

 Score = 60.2 bits (146), Expect = 1e-12
 Identities = 36/57 (63%), Positives = 44/57 (77%)

Query: 12 SLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68
          + GA F  INGPEI+SK  GESE  LR+ FEEA+K +PSIIFIDE+DA+APKR   +
Sbjct: 40 NEGAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPSIIFIDEIDALAPKRSSDQ 96

Length = 494

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

 Score = 55.3 bits (134), Expect = 7e-11
 Identities = 24/51 (47%), Positives = 32/51 (62%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
            A F  + G E++ K  GE    +R+ FE A + +PSIIFIDE+DAI  KR
Sbjct: 210 DATFIRVVGSELVQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKR 260

Length = 406

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

 Score = 51.7 bits (124), Expect = 1e-09
 Identities = 20/53 (37%), Positives = 31/53 (58%)

Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKREL 69
             L+   E++ +  G+    + + +E A K +P I+FIDELDAIA  R  +EL
Sbjct: 179 LLLVKATELIGEHVGDGARRIHELYERARKAAPCIVFIDELDAIALDRRYQEL 231

Length = 368

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

 Score = 51.5 bits (124), Expect = 1e-09
 Identities = 22/48 (45%), Positives = 31/48 (64%)

Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           FF I+G + +    G   S +R  FE+A KN+P IIFIDE+DA+  +R
Sbjct: 116 FFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQR 163

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

 Score = 51.7 bits (124), Expect = 1e-09
 Identities = 24/50 (48%), Positives = 31/50 (62%)

Query: 15  AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           A F  + G E + K  GE    +R  F  A +N+PSIIFIDE+D+IA KR
Sbjct: 205 ATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKR 254

Length = 398

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

 Score = 51.0 bits (122), Expect = 2e-09
 Identities = 25/50 (50%), Positives = 33/50 (66%)

Query: 15  AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           A F  + G E++ K  GE    +R+ FE A + +PSIIFIDE+DAIA KR
Sbjct: 182 ATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKR 231

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

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

 Score = 50.5 bits (121), Expect = 3e-09
 Identities = 22/50 (44%), Positives = 33/50 (66%)

Query: 15  AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           A F  + G E++ K  G+    +R+ F  A++N+PSI+FIDE+DAI  KR
Sbjct: 243 ATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKR 292

Length = 438

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

 Score = 49.8 bits (120), Expect = 5e-09
 Identities = 25/51 (49%), Positives = 33/51 (64%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
            A F  + G E++ K  GE    +R+ FE A + +PSIIFIDE+DAIA KR
Sbjct: 190 NATFIRVVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKR 240

Length = 389

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

 Score = 47.3 bits (112), Expect = 5e-08
 Identities = 21/48 (43%), Positives = 30/48 (62%)

Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           FF I+G + +    G   S +R  FE+A K +P IIFIDE+DA+  +R
Sbjct: 213 FFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQR 260

Length = 644

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

 Score = 47.0 bits (112), Expect = 5e-08
 Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 4/50 (8%)

Query: 15  AFFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFIDELDAI 60
           ++F  I GPE+++K  GE+E  +R  F+ A +      P I+F DE+D++
Sbjct: 252 SYFLNIKGPELLNKYVGETERQIRLIFQRAREKASEGRPVIVFFDEMDSL 301

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|214386 CHL00176, ftsH, cell division protein; Validated

 Score = 45.0 bits (107), Expect = 3e-07
 Identities = 20/48 (41%), Positives = 31/48 (64%)

Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           FF I+G E +    G   + +R  F++A +NSP I+FIDE+DA+  +R
Sbjct: 244 FFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQR 291

Length = 638

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

 Score = 41.5 bits (98), Expect = 5e-06
 Identities = 22/48 (45%), Positives = 31/48 (64%)

Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           FF I+G + +    G   S +R  FE+A KN+P IIFIDE+DA+  +R
Sbjct: 211 FFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQR 258

Length = 596

>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 = 39.4 bits (92), Expect = 1e-05
 Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 14  GAFFFLINGPEIMSKLAGESE---SNLRKAFEEADKNSPSIIFIDELDAIAPKREKREL 69
           GA F  +N  +++  L          +R  FE A+K  P ++FIDE+D+++   +   L
Sbjct: 47  GAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALL 105

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

>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular activities

 Score = 36.6 bits (84), Expect = 2e-04
 Identities = 13/56 (23%), Positives = 23/56 (41%)

Query: 14 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKREL 69
               L+       K +G  E  LR A   A K  P ++ +DE+ ++    ++  L
Sbjct: 44 EVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALL 99

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. Length = 148

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	69
KOG0733|consensus	802		99.89
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	99.87
KOG0739|consensus	439		99.87
KOG0738|consensus	491		99.86
KOG0736|consensus	953		99.86
KOG0733|consensus	802		99.85
KOG0730|consensus	693		99.84
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.81
KOG0734|consensus	752		99.79
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.78
KOG0740|consensus	428		99.74
KOG0735|consensus	952		99.73
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.73
KOG0727|consensus	408		99.72
KOG0728|consensus	404		99.72
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.71
KOG0726|consensus	440		99.7
KOG0737|consensus	386		99.69
KOG0731|consensus	774		99.68
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.67
CHL00195	489	ycf46 Ycf46; Provisional	99.66
KOG0729|consensus	435		99.63
KOG0652|consensus	424		99.62
KOG0651|consensus	388		99.62
KOG0730|consensus	693		99.61
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	99.55
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.55
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.55
CHL00206	2281	ycf2 Ycf2; Provisional	99.52
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.49
PF00004	132	AAA: ATPase family associated with various cellula	99.49
CHL00176	638	ftsH cell division protein; Validated	99.47
KOG0741|consensus	744		99.43
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.42
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.4
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.39
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.37
KOG0732|consensus	1080		99.34
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.09
KOG0744|consensus	423		99.05
CHL00095	821	clpC Clp protease ATP binding subunit	98.93
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	98.9
CHL00181	287	cbbX CbbX; Provisional	98.88
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	98.84
PRK10865	857	protein disaggregation chaperone; Provisional	98.75
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	98.72
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.72
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	98.69
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	98.66
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.64
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	98.62
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	98.61
KOG0736|consensus	953		98.59
KOG0742|consensus	630		98.55
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	98.55
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.55
KOG0745|consensus	564		98.52
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.46
KOG2028|consensus	554		98.4
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	98.2
smart00382	148	AAA ATPases associated with a variety of cellular	98.04
KOG0735|consensus	952		98.02
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	98.02
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	97.82
PRK13342	413	recombination factor protein RarA; Reviewed	97.8
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	97.78
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.66
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	97.56
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.54
PRK04195	482	replication factor C large subunit; Provisional	97.51
PRK04132	846	replication factor C small subunit; Provisional	97.5
KOG0741|consensus	744		97.46
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	97.44
KOG1969|consensus	877		97.4
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.4
KOG2004|consensus	906		97.34
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	97.33
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.32
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.31
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	97.3
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.21
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.21
PRK13341	725	recombination factor protein RarA/unknown domain f	97.2
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.17
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	97.14
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.12
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.96
PHA02544	316	44 clamp loader, small subunit; Provisional	96.92
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.81
PF13173	128	AAA_14: AAA domain	96.73
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	96.71
PRK07952	244	DNA replication protein DnaC; Validated	96.51
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	96.48
PRK12422	445	chromosomal replication initiation protein; Provis	96.48
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.41
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	96.41
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	96.39
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	96.37
PLN03025	319	replication factor C subunit; Provisional	96.29
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	96.08
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	96.07
CHL00095	821	clpC Clp protease ATP binding subunit	96.02
PRK06893	229	DNA replication initiation factor; Validated	95.99
PRK12402	337	replication factor C small subunit 2; Reviewed	95.89
PRK14087	450	dnaA chromosomal replication initiation protein; P	95.83
COG0714	329	MoxR-like ATPases [General function prediction onl	95.65
PRK07940	394	DNA polymerase III subunit delta'; Validated	95.65
PTZ00112	1164	origin recognition complex 1 protein; Provisional	95.65
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	95.64
PHA02244	383	ATPase-like protein	95.58
PRK08181	269	transposase; Validated	95.55
PRK08116	268	hypothetical protein; Validated	95.47
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	95.33
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	95.31
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	95.22
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	95.22
PRK09183	259	transposase/IS protein; Provisional	95.22
PRK05642	234	DNA replication initiation factor; Validated	95.16
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	95.12
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	95.09
PRK08903	227	DnaA regulatory inactivator Hda; Validated	95.09
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	94.99
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	94.96
PRK09376	416	rho transcription termination factor Rho; Provisio	94.86
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	94.81
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	94.79
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	94.75
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	94.71
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	94.71
PRK08727	233	hypothetical protein; Validated	94.63
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	94.6
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	94.55
KOG0743|consensus	457		94.52
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	94.49
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	94.45
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	94.41
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	94.41
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	94.37
PRK12377	248	putative replication protein; Provisional	94.34
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	94.28
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	94.26
PRK10865	857	protein disaggregation chaperone; Provisional	94.19
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	94.15
PRK08939	306	primosomal protein DnaI; Reviewed	94.09
COG1484	254	DnaC DNA replication protein [DNA replication, rec	93.96
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	93.95
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	93.95
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	93.66
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	93.6
PRK08084	235	DNA replication initiation factor; Provisional	93.6
PRK06526	254	transposase; Provisional	93.5
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	93.26
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	93.19
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	93.19
PRK06921	266	hypothetical protein; Provisional	93.17
PF14516	331	AAA_35: AAA-like domain	92.97
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	92.94
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	92.9
KOG1051|consensus	898		92.72
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	92.7
PRK06835	329	DNA replication protein DnaC; Validated	92.66
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	92.63
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	92.51
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	92.3
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	92.28
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	92.21
KOG0732|consensus	1080		92.19
COG0593	408	DnaA ATPase involved in DNA replication initiation	92.16
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	92.09
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	91.82
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	91.61
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	91.61
PRK15424	538	propionate catabolism operon regulatory protein Pr	91.55
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	91.35
PRK05022	509	anaerobic nitric oxide reductase transcription reg	91.33
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	91.22
PRK00440	319	rfc replication factor C small subunit; Reviewed	91.14
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	91.03
PRK08118	167	topology modulation protein; Reviewed	90.73
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	90.66
KOG1051|consensus	898		90.45
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	90.06
PRK10365	441	transcriptional regulatory protein ZraR; Provision	89.93
KOG0989|consensus	346		89.75
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	89.56
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	89.1
COG2204	464	AtoC Response regulator containing CheY-like recei	88.76
cd01128	249	rho_factor Transcription termination factor rho is	88.54
cd00338	137	Ser_Recombinase Serine Recombinase family, catalyt	88.32
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	88.31
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	88.31
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	88.21
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	87.98
PRK11823	446	DNA repair protein RadA; Provisional	87.71
PRK11608	326	pspF phage shock protein operon transcriptional ac	87.63
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	87.19
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	86.91
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	86.69
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	86.07
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	85.96
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	85.76
PF13304	303	AAA_21: AAA domain; PDB: 3QKS_B 1US8_B 1F2U_B 1F2T	85.64
KOG1942|consensus	456		85.54
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	85.48
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	85.25
PRK15115	444	response regulator GlrR; Provisional	84.96
PRK07261	171	topology modulation protein; Provisional	84.65
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	84.41
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	84.07
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	83.62
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	83.42
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	83.41
PRK13531	498	regulatory ATPase RavA; Provisional	83.38
PF07931	174	CPT: Chloramphenicol phosphotransferase-like prote	83.36
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	82.06
PRK06620	214	hypothetical protein; Validated	81.98
COG4130	272	Predicted sugar epimerase [Carbohydrate transport	81.88
PF01202	158	SKI: Shikimate kinase; InterPro: IPR000623 Shikima	81.6
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	81.38
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	80.87
PRK13947	171	shikimate kinase; Provisional	80.84
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	80.73
PRK07631	475	amidophosphoribosyltransferase; Provisional	80.69
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	80.27
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	80.25
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	80.21
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	80.18

>KOG0733|consensus

Probab=99.89  E-value=1.7e-23  Score=147.48  Aligned_cols=66  Identities=36%  Similarity=0.702  Sum_probs=64.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE   68 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~   68 (69)
                      |+||||+|+|.|.+|+.|.+++|+++|+||+|+.||++|++|+.++||||||||+|+|+++|++..
T Consensus       559 TLlAKAVANEag~NFisVKGPELlNkYVGESErAVR~vFqRAR~saPCVIFFDEiDaL~p~R~~~~  624 (802)
T KOG0733|consen  559 TLLAKAVANEAGANFISVKGPELLNKYVGESERAVRQVFQRARASAPCVIFFDEIDALVPRRSDEG  624 (802)
T ss_pred             HHHHHHHhhhccCceEeecCHHHHHHHhhhHHHHHHHHHHHhhcCCCeEEEecchhhcCcccCCCC
Confidence            899999999999999999999999999999999999999999999999999999999999999764

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

Probab=99.87  E-value=1.7e-22  Score=135.60  Aligned_cols=66  Identities=38%  Similarity=0.540  Sum_probs=64.0

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE   68 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~   68 (69)
                      |+||||+|++++++|+.+.+|+|+.+|+||+.+.||++|+.|++++||||||||||+|+.+|.+.+
T Consensus       199 TLLAkAVA~~T~AtFIrvvgSElVqKYiGEGaRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~  264 (406)
T COG1222         199 TLLAKAVANQTDATFIRVVGSELVQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSG  264 (406)
T ss_pred             HHHHHHHHhccCceEEEeccHHHHHHHhccchHHHHHHHHHHhhcCCeEEEEechhhhhcccccCC
Confidence            899999999999999999999999999999999999999999999999999999999999998753

>KOG0739|consensus

Probab=99.87  E-value=2.9e-22  Score=133.14  Aligned_cols=66  Identities=36%  Similarity=0.585  Sum_probs=63.6

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE   68 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~   68 (69)
                      ++||+|+|.+.+.+||.|+.++|+++|.||+|+.|+++|+.|++++|+||||||||++|++|+.++
T Consensus       180 SYLAKAVATEAnSTFFSvSSSDLvSKWmGESEkLVknLFemARe~kPSIIFiDEiDslcg~r~enE  245 (439)
T KOG0739|consen  180 SYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKNLFEMARENKPSIIFIDEIDSLCGSRSENE  245 (439)
T ss_pred             HHHHHHHHhhcCCceEEeehHHHHHHHhccHHHHHHHHHHHHHhcCCcEEEeehhhhhccCCCCCc
Confidence            579999999999999999999999999999999999999999999999999999999999998764

>KOG0738|consensus

Probab=99.86  E-value=3.6e-22  Score=135.42  Aligned_cols=65  Identities=35%  Similarity=0.497  Sum_probs=63.6

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |+||||+|.|++.+||+|+.+.+.|+|-||+|+.||-+|+.|+-++|++|||||||+||.+|++.
T Consensus       259 TlLAKAvATEc~tTFFNVSsstltSKwRGeSEKlvRlLFemARfyAPStIFiDEIDslcs~RG~s  323 (491)
T KOG0738|consen  259 TLLAKAVATECGTTFFNVSSSTLTSKWRGESEKLVRLLFEMARFYAPSTIFIDEIDSLCSQRGGS  323 (491)
T ss_pred             HHHHHHHHHhhcCeEEEechhhhhhhhccchHHHHHHHHHHHHHhCCceeehhhHHHHHhcCCCc
Confidence            89999999999999999999999999999999999999999999999999999999999999875

>KOG0736|consensus

Probab=99.86  E-value=4.5e-22  Score=142.56  Aligned_cols=65  Identities=35%  Similarity=0.658  Sum_probs=63.4

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|||+|.|++..|+.|.+++++.+|+|++|+|||++|++||+.+|||||+||+|+++|+|+..
T Consensus       719 TLlAKAVATEcsL~FlSVKGPELLNMYVGqSE~NVR~VFerAR~A~PCVIFFDELDSlAP~RG~s  783 (953)
T KOG0736|consen  719 TLLAKAVATECSLNFLSVKGPELLNMYVGQSEENVREVFERARSAAPCVIFFDELDSLAPNRGRS  783 (953)
T ss_pred             HHHHHHHHhhceeeEEeecCHHHHHHHhcchHHHHHHHHHHhhccCCeEEEeccccccCccCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999864

>KOG0733|consensus

Probab=99.85  E-value=1.3e-21  Score=138.04  Aligned_cols=65  Identities=46%  Similarity=0.781  Sum_probs=63.5

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |+||+++|+++++||+.++++++++.+.||+|++||++|++|+.++|||+||||||+|.++|+..
T Consensus       237 T~lA~AiAgel~vPf~~isApeivSGvSGESEkkiRelF~~A~~~aPcivFiDeIDAI~pkRe~a  301 (802)
T KOG0733|consen  237 TSLANAIAGELGVPFLSISAPEIVSGVSGESEKKIRELFDQAKSNAPCIVFIDEIDAITPKREEA  301 (802)
T ss_pred             HHHHHHHhhhcCCceEeecchhhhcccCcccHHHHHHHHHHHhccCCeEEEeecccccccchhhH
Confidence            89999999999999999999999999999999999999999999999999999999999999864

>KOG0730|consensus

Probab=99.84  E-value=1.6e-21  Score=137.67  Aligned_cols=65  Identities=38%  Similarity=0.633  Sum_probs=63.2

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++||++|++.+.+|+.+++++++++|+||+|+.|+++|++|++.+|||||+||||+++..|+++
T Consensus       482 T~lAkalAne~~~nFlsvkgpEL~sk~vGeSEr~ir~iF~kAR~~aP~IiFfDEiDsi~~~R~g~  546 (693)
T KOG0730|consen  482 TLLAKALANEAGMNFLSVKGPELFSKYVGESERAIREVFRKARQVAPCIIFFDEIDALAGSRGGS  546 (693)
T ss_pred             HHHHHHHhhhhcCCeeeccCHHHHHHhcCchHHHHHHHHHHHhhcCCeEEehhhHHhHhhccCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999754

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

Probab=99.81  E-value=8.5e-20  Score=123.54  Aligned_cols=65  Identities=26%  Similarity=0.300  Sum_probs=61.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh-----cCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK-----NSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-----~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|+++|++++.+++++|.++|+||+|++||++|+.|++     .+||||||||||+++++|++.
T Consensus       162 TllAraiA~elg~~~i~vsa~eL~sk~vGEsEk~IR~~F~~A~~~a~~~~aPcVLFIDEIDA~~g~r~~~  231 (413)
T PLN00020        162 SFQCELVFKKMGIEPIVMSAGELESENAGEPGKLIRQRYREAADIIKKKGKMSCLFINDLDAGAGRFGTT  231 (413)
T ss_pred             HHHHHHHHHHcCCCeEEEEHHHhhcCcCCcHHHHHHHHHHHHHHHhhccCCCeEEEEehhhhcCCCCCCC
Confidence            88999999999999999999999999999999999999999975     479999999999999998754

>KOG0734|consensus

Probab=99.79  E-value=1.1e-19  Score=127.32  Aligned_cols=66  Identities=32%  Similarity=0.524  Sum_probs=63.7

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE   68 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~   68 (69)
                      |+||||+|.|.++|||+.+++++-..|+|.+.++||.+|+.|++++||||||||||+++++|...+
T Consensus       351 TlLARAvAGEA~VPFF~~sGSEFdEm~VGvGArRVRdLF~aAk~~APcIIFIDEiDavG~kR~~~~  416 (752)
T KOG0734|consen  351 TLLARAVAGEAGVPFFYASGSEFDEMFVGVGARRVRDLFAAAKARAPCIIFIDEIDAVGGKRNPSD  416 (752)
T ss_pred             hHHHHHhhcccCCCeEeccccchhhhhhcccHHHHHHHHHHHHhcCCeEEEEechhhhcccCCccH
Confidence            899999999999999999999999999999999999999999999999999999999999997653

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

Probab=99.78  E-value=5.2e-19  Score=121.73  Aligned_cols=65  Identities=42%  Similarity=0.598  Sum_probs=63.1

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|++++.+|+.+++++++++|+||++++|+++|..|++.+||||||||+|++++.|+..
T Consensus       290 T~lAkava~~~~~~fi~v~~~~l~sk~vGesek~ir~~F~~A~~~~p~iiFiDEiDs~~~~r~~~  354 (494)
T COG0464         290 TLLAKAVALESRSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPS  354 (494)
T ss_pred             HHHHHHHHhhCCCeEEEeeCHHHhccccchHHHHHHHHHHHHHcCCCcEEEEEchhhhhccCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999864

>KOG0740|consensus

Probab=99.74  E-value=3.2e-18  Score=116.96  Aligned_cols=65  Identities=38%  Similarity=0.550  Sum_probs=62.7

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |+|++++|.|++..||.+++++|.++|+|++|+.||.+|+.|+..+|+|+||||+|+++.+|.+.
T Consensus       200 tmL~~aiAsE~~atff~iSassLtsK~~Ge~eK~vralf~vAr~~qPsvifidEidslls~Rs~~  264 (428)
T KOG0740|consen  200 TMLAKAIATESGATFFNISASSLTSKYVGESEKLVRALFKVARSLQPSVIFIDEIDSLLSKRSDN  264 (428)
T ss_pred             HHHHHHHHhhhcceEeeccHHHhhhhccChHHHHHHHHHHHHHhcCCeEEEechhHHHHhhcCCc
Confidence            79999999999999999999999999999999999999999999999999999999999998653

>KOG0735|consensus

Probab=99.73  E-value=6.1e-18  Score=121.13  Aligned_cols=66  Identities=39%  Similarity=0.651  Sum_probs=63.8

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE   68 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~   68 (69)
                      |+||.++|..++..|+.|.+++++++|+|.+|+++|.+|.+|+..+|||+|+||+|+++|+|+..+
T Consensus       715 T~la~a~a~~~~~~fisvKGPElL~KyIGaSEq~vR~lF~rA~~a~PCiLFFDEfdSiAPkRGhDs  780 (952)
T KOG0735|consen  715 TLLASAIASNSNLRFISVKGPELLSKYIGASEQNVRDLFERAQSAKPCILFFDEFDSIAPKRGHDS  780 (952)
T ss_pred             HHHHHHHHhhCCeeEEEecCHHHHHHHhcccHHHHHHHHHHhhccCCeEEEeccccccCcccCCCC
Confidence            889999999999999999999999999999999999999999999999999999999999998653

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

Probab=99.73  E-value=4.8e-18  Score=111.49  Aligned_cols=63  Identities=29%  Similarity=0.517  Sum_probs=61.4

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |++|+++|+++++|++.+++.++++.++|++.++++++|+.|++.+|||+||||+|+|+-+|.
T Consensus       165 Tm~Akalane~kvp~l~vkat~liGehVGdgar~Ihely~rA~~~aPcivFiDE~DAiaLdRr  227 (368)
T COG1223         165 TMMAKALANEAKVPLLLVKATELIGEHVGDGARRIHELYERARKAAPCIVFIDELDAIALDRR  227 (368)
T ss_pred             HHHHHHHhcccCCceEEechHHHHHHHhhhHHHHHHHHHHHHHhcCCeEEEehhhhhhhhhhh
Confidence            899999999999999999999999999999999999999999999999999999999998775

>KOG0727|consensus

Probab=99.72  E-value=4.6e-18  Score=111.67  Aligned_cols=66  Identities=39%  Similarity=0.549  Sum_probs=63.4

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE   68 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~   68 (69)
                      |+|++++|+++...|+.+.+++++.+|.||+.+.+|.+|..|++++|+||||||||+|+.+|-+.+
T Consensus       203 tml~kava~~t~a~firvvgsefvqkylgegprmvrdvfrlakenapsiifideidaiatkrfdaq  268 (408)
T KOG0727|consen  203 TMLAKAVANHTTAAFIRVVGSEFVQKYLGEGPRMVRDVFRLAKENAPSIIFIDEIDAIATKRFDAQ  268 (408)
T ss_pred             HHHHHHHhhccchheeeeccHHHHHHHhccCcHHHHHHHHHHhccCCcEEEeehhhhHhhhhcccc
Confidence            899999999999999999999999999999999999999999999999999999999999886654

>KOG0728|consensus

Probab=99.72  E-value=1.1e-17  Score=109.83  Aligned_cols=65  Identities=31%  Similarity=0.513  Sum_probs=62.9

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|.++.+.|+.+++++++.+|.||+.+.+|++|-.|++++|+|||.||||+|++.|..+
T Consensus       195 tLlaraVahht~c~firvsgselvqk~igegsrmvrelfvmarehapsiifmdeidsigs~r~e~  259 (404)
T KOG0728|consen  195 TLLARAVAHHTDCTFIRVSGSELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSSRVES  259 (404)
T ss_pred             hHHHHHHHhhcceEEEEechHHHHHHHhhhhHHHHHHHHHHHHhcCCceEeeecccccccccccC
Confidence            78999999999999999999999999999999999999999999999999999999999988764

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

Probab=99.71  E-value=7.7e-18  Score=118.72  Aligned_cols=65  Identities=37%  Similarity=0.617  Sum_probs=62.8

Q ss_pred             hhHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           2 SYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         2 ~T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      .|+|||++|.+.++|||.+++|+++..|+|-+.+.+|.+|++|++++||||||||||++++.|+.
T Consensus       196 KTLLAkAvAgEA~VPFf~iSGS~FVemfVGvGAsRVRdLF~qAkk~aP~IIFIDEiDAvGr~Rg~  260 (596)
T COG0465         196 KTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGA  260 (596)
T ss_pred             cHHHHHHHhcccCCCceeccchhhhhhhcCCCcHHHHHHHHHhhccCCCeEEEehhhhcccccCC
Confidence            38999999999999999999999999999999999999999999999999999999999999963

>KOG0726|consensus

Probab=99.70  E-value=1.3e-17  Score=111.01  Aligned_cols=66  Identities=33%  Similarity=0.558  Sum_probs=63.4

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE   68 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~   68 (69)
                      |+||+|+|++++.+|+.+-+++++.+|.|++.+.+|++|+.|..++|+|+||||||+++.+|=+++
T Consensus       233 TLLAKAVANqTSATFlRvvGseLiQkylGdGpklvRqlF~vA~e~apSIvFiDEIdAiGtKRyds~  298 (440)
T KOG0726|consen  233 TLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSN  298 (440)
T ss_pred             hHHHHHHhcccchhhhhhhhHHHHHHHhccchHHHHHHHHHHHhcCCceEEeehhhhhccccccCC
Confidence            799999999999999999999999999999999999999999999999999999999999986654

>KOG0737|consensus

Probab=99.69  E-value=1.3e-17  Score=112.13  Aligned_cols=64  Identities=33%  Similarity=0.453  Sum_probs=61.8

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++.|.+|+.|+.+.+.++|+||+++.++.+|..|.+.+||||||||+|++.+.|..
T Consensus       141 TmlAKA~Akeaga~fInv~~s~lt~KWfgE~eKlv~AvFslAsKl~P~iIFIDEvds~L~~R~s  204 (386)
T KOG0737|consen  141 TMLAKAIAKEAGANFINVSVSNLTSKWFGEAQKLVKAVFSLASKLQPSIIFIDEVDSFLGQRRS  204 (386)
T ss_pred             HHHHHHHHHHcCCCcceeeccccchhhHHHHHHHHHHHHhhhhhcCcceeehhhHHHHHhhccc
Confidence            8999999999999999999999999999999999999999999999999999999999988744

>KOG0731|consensus

Probab=99.68  E-value=6e-17  Score=116.43  Aligned_cols=63  Identities=40%  Similarity=0.603  Sum_probs=61.8

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |+||||+|.|.|+||+.+++++++..++|....++|.+|..|+.++||||||||||+++.+|.
T Consensus       358 TLLAKAiAGEAgVPF~svSGSEFvE~~~g~~asrvr~lf~~ar~~aP~iifideida~~~~r~  420 (774)
T KOG0731|consen  358 TLLAKAIAGEAGVPFFSVSGSEFVEMFVGVGASRVRDLFPLARKNAPSIIFIDEIDAVGRKRG  420 (774)
T ss_pred             HHHHHHHhcccCCceeeechHHHHHHhcccchHHHHHHHHHhhccCCeEEEeccccccccccc
Confidence            899999999999999999999999999999999999999999999999999999999999995

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.67  E-value=1.6e-16  Score=113.91  Aligned_cols=64  Identities=45%  Similarity=0.725  Sum_probs=62.0

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++++.+|+.+++++++++|+|+++++++++|+.|+..+||||||||+|+++++|+.
T Consensus       501 T~lakalA~e~~~~fi~v~~~~l~~~~vGese~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~  564 (733)
T TIGR01243       501 TLLAKAVATESGANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGA  564 (733)
T ss_pred             HHHHHHHHHhcCCCEEEEehHHHhhcccCcHHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCC
Confidence            7899999999999999999999999999999999999999999999999999999999998864

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.

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.66  E-value=2.6e-16  Score=109.31  Aligned_cols=63  Identities=24%  Similarity=0.353  Sum_probs=60.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |++|+++|++++.|++.++++++.++|+|+++++++++|+.|+..+||||||||||.++++++
T Consensus       273 TllAkaiA~e~~~~~~~l~~~~l~~~~vGese~~l~~~f~~A~~~~P~IL~IDEID~~~~~~~  335 (489)
T CHL00195        273 SLTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSE  335 (489)
T ss_pred             HHHHHHHHHHhCCCEEEEEhHHhcccccChHHHHHHHHHHHHHhcCCcEEEehhhhhhhcccc
Confidence            789999999999999999999999999999999999999999999999999999999987644

>KOG0729|consensus

Probab=99.63  E-value=3.9e-16  Score=103.23  Aligned_cols=64  Identities=31%  Similarity=0.443  Sum_probs=61.8

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+|+|+.++.-|+.|=+|+++.+|+||+.+.+|++|+.|+..+.||||+||||++++.|-+
T Consensus       225 tl~aravanrtdacfirvigselvqkyvgegarmvrelf~martkkaciiffdeidaiggarfd  288 (435)
T KOG0729|consen  225 TLCARAVANRTDACFIRVIGSELVQKYVGEGARMVRELFEMARTKKACIIFFDEIDAIGGARFD  288 (435)
T ss_pred             hHHHHHHhcccCceEEeehhHHHHHHHhhhhHHHHHHHHHHhcccceEEEEeeccccccCcccc
Confidence            7899999999999999999999999999999999999999999999999999999999998854

>KOG0652|consensus

Probab=99.62  E-value=3.3e-16  Score=103.35  Aligned_cols=66  Identities=36%  Similarity=0.627  Sum_probs=63.6

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE   68 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~   68 (69)
                      |++||+.|++++.+|+.+.++.++.+|+|++.+.+|..|..|++.+|+||||||+|+|+.+|-+++
T Consensus       219 TlmARAcAaqT~aTFLKLAgPQLVQMfIGdGAkLVRDAFaLAKEkaP~IIFIDElDAIGtKRfDSe  284 (424)
T KOG0652|consen  219 TLMARACAAQTNATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSE  284 (424)
T ss_pred             HHHHHHHHHhccchHHHhcchHHHhhhhcchHHHHHHHHHHhhccCCeEEEEechhhhcccccccc
Confidence            789999999999999999999999999999999999999999999999999999999999997753

>KOG0651|consensus

Probab=99.62  E-value=8.3e-16  Score=102.46  Aligned_cols=64  Identities=31%  Similarity=0.482  Sum_probs=62.1

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|+..+++|+.+.++.+.++|.||+.+.||+.|..|+...|||||+||||+++++|..
T Consensus       180 Tlla~~Vaa~mg~nfl~v~ss~lv~kyiGEsaRlIRemf~yA~~~~pciifmdeiDAigGRr~s  243 (388)
T KOG0651|consen  180 TLLARAVAATMGVNFLKVVSSALVDKYIGESARLIRDMFRYAREVIPCIIFMDEIDAIGGRRFS  243 (388)
T ss_pred             hHHHHHHHHhcCCceEEeeHhhhhhhhcccHHHHHHHHHHHHhhhCceEEeehhhhhhccEEec
Confidence            7899999999999999999999999999999999999999999999999999999999999854

>KOG0730|consensus

Probab=99.61  E-value=9.6e-16  Score=108.71  Aligned_cols=67  Identities=61%  Similarity=0.912  Sum_probs=63.9

Q ss_pred             hhHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcC-CeEEEEccccccccccccCC
Q psy3868           2 SYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNS-PSIIFIDELDAIAPKREKRE   68 (69)
Q Consensus         2 ~T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~-p~iifiDEid~i~~~r~~~~   68 (69)
                      .|++++++|++.++.++.++++++++++.||+++++|++|+.+.+++ |++|||||+|++|++|.+.+
T Consensus       231 kt~l~~aVa~e~~a~~~~i~~peli~k~~gEte~~LR~~f~~a~k~~~psii~IdEld~l~p~r~~~~  298 (693)
T KOG0730|consen  231 KTFLVRAVANEYGAFLFLINGPELISKFPGETESNLRKAFAEALKFQVPSIIFIDELDALCPKREGAD  298 (693)
T ss_pred             hHHHHHHHHHHhCceeEecccHHHHHhcccchHHHHHHHHHHHhccCCCeeEeHHhHhhhCCcccccc
Confidence            48899999999999999999999999999999999999999999999 99999999999999998753

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

Probab=99.55  E-value=1.4e-14  Score=98.57  Aligned_cols=64  Identities=39%  Similarity=0.536  Sum_probs=61.2

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++++.+|+.+.++++.++|+|++++.++++|+.|+..+|+||||||+|+++++|.+
T Consensus       193 T~LAkalA~~l~~~fi~i~~s~l~~k~~ge~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r~~  256 (398)
T PTZ00454        193 TMLAKAVAHHTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFD  256 (398)
T ss_pred             HHHHHHHHHhcCCCEEEEehHHHHHHhcchhHHHHHHHHHHHHhcCCeEEEEECHhhhcccccc
Confidence            7899999999999999999999999999999999999999999999999999999999988743

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.55  E-value=1.9e-14  Score=97.47  Aligned_cols=64  Identities=41%  Similarity=0.594  Sum_probs=61.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++++.+|+.++++++.++|.|++++.++.+|+.++..+|+||||||+|+++++|.+
T Consensus       179 T~lAkaia~~~~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~  242 (389)
T PRK03992        179 TLLAKAVAHETNATFIRVVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTD  242 (389)
T ss_pred             HHHHHHHHHHhCCCEEEeehHHHhHhhccchHHHHHHHHHHHHhcCCeEEEEechhhhhccccc
Confidence            7899999999999999999999999999999999999999999999999999999999988764

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.55  E-value=9.8e-15  Score=101.01  Aligned_cols=64  Identities=38%  Similarity=0.626  Sum_probs=61.6

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++++++|++++.+|+.++++++.+.++|+++++++++|+.|+..+||||||||+|+++++|+.
T Consensus       102 T~la~alA~~~~~~~~~i~~~~~~~~~~g~~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~  165 (495)
T TIGR01241       102 TLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGA  165 (495)
T ss_pred             HHHHHHHHHHcCCCeeeccHHHHHHHHhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhcccc
Confidence            7899999999999999999999999999999999999999999999999999999999988764

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.

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.52  E-value=2.9e-14  Score=109.54  Aligned_cols=63  Identities=16%  Similarity=0.139  Sum_probs=54.7

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcc-----------------------------------------cChHHH--HHHH
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKL-----------------------------------------AGESES--NLRK   39 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~-----------------------------------------~ges~~--~l~~   39 (69)
                      |+||||+|+++++||+.++++++++++                                         +|+++.  .|+.
T Consensus      1644 TlLAKALA~es~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~~~~e~~e~~n~~~~~m~~~e~~~rIr~ 1723 (2281)
T CHL00206       1644 SYLVKYLATNSYVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRDLDTELLTMMNALTMDMMPKIDRFYITL 1723 (2281)
T ss_pred             HHHHHHHHHhcCCceEEEEHHHHhhcccccccccccccccccccccccccccccchhhhhhcchhhhhhhhhhhHHHHHH
Confidence            789999999999999999999999765                                         223333  4999


Q ss_pred             HHHHHHhcCCeEEEEccccccccccc
Q psy3868          40 AFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus        40 if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      +|+.|++.+||||||||||+++++.+
T Consensus      1724 lFelARk~SPCIIFIDEIDaL~~~ds 1749 (2281)
T CHL00206       1724 QFELAKAMSPCIIWIPNIHDLNVNES 1749 (2281)
T ss_pred             HHHHHHHCCCeEEEEEchhhcCCCcc
Confidence            99999999999999999999998643

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

Probab=99.49  E-value=4.2e-14  Score=97.33  Aligned_cols=64  Identities=36%  Similarity=0.585  Sum_probs=61.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++++.+|+.++++++.++|+|++++.++++|+.|+.++|+||||||+|+++.+|..
T Consensus       231 T~LAraIA~el~~~fi~V~~seL~~k~~Ge~~~~vr~lF~~A~~~~P~ILfIDEID~l~~kR~~  294 (438)
T PTZ00361        231 TLLAKAVANETSATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYD  294 (438)
T ss_pred             HHHHHHHHHhhCCCEEEEecchhhhhhcchHHHHHHHHHHHHHhCCCcEEeHHHHHHHhccCCC
Confidence            8899999999999999999999999999999999999999999999999999999999988753

>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=99.49  E-value=1.7e-13  Score=78.73  Aligned_cols=62  Identities=39%  Similarity=0.672  Sum_probs=59.7

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcC-CeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNS-PSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~-p~iifiDEid~i~~~r   64 (69)
                      |++++.+|+.++.+++.++++++.+.+.+++++.++++|+.++... |+||||||+|.++++.
T Consensus        12 T~l~~~la~~l~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~vl~iDe~d~l~~~~   74 (132)
T PF00004_consen   12 TTLARALAQYLGFPFIEIDGSELISSYAGDSEQKIRDFFKKAKKSAKPCVLFIDEIDKLFPKS   74 (132)
T ss_dssp             HHHHHHHHHHTTSEEEEEETTHHHTSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGTSHHC
T ss_pred             eHHHHHHHhhcccccccccccccccccccccccccccccccccccccceeeeeccchhccccc
Confidence            7899999999999999999999999999999999999999999887 9999999999999877

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 ....

>CHL00176 ftsH cell division protein; Validated

Probab=99.47  E-value=1.1e-13  Score=98.63  Aligned_cols=64  Identities=33%  Similarity=0.556  Sum_probs=60.9

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++.+.||+.++++++.+.++|.+.+.++.+|+.|+..+||||||||+|+++++|+.
T Consensus       230 T~LAralA~e~~~p~i~is~s~f~~~~~g~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~  293 (638)
T CHL00176        230 TLLAKAIAGEAEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGA  293 (638)
T ss_pred             HHHHHHHHHHhCCCeeeccHHHHHHHhhhhhHHHHHHHHHHHhcCCCcEEEEecchhhhhcccC
Confidence            7899999999999999999999999999999999999999999999999999999999987753

>KOG0741|consensus

Probab=99.43  E-value=1.5e-13  Score=96.72  Aligned_cols=65  Identities=38%  Similarity=0.555  Sum_probs=57.9

Q ss_pred             hHHHHHHHHHhCC-cEEEEchhhhhhcccChHHHHHHHHHHHHHh--------cCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGA-FFFLINGPEIMSKLAGESESNLRKAFEEADK--------NSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~-~~~~v~~~~l~~~~~ges~~~l~~if~~a~~--------~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++||.|.+-++. +--.||+++++++|+||+|++||++|..|.+        ..-.||.+||||+||..|++.
T Consensus       270 TLiARqIGkMLNArePKIVNGPeIL~KYVGeSE~NvR~LFaDAEeE~r~~g~~SgLHIIIFDEiDAICKqRGS~  343 (744)
T KOG0741|consen  270 TLIARQIGKMLNAREPKIVNGPEILNKYVGESEENVRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSM  343 (744)
T ss_pred             hHHHHHHHHHhcCCCCcccCcHHHHHHhhcccHHHHHHHHHhHHHHHHhhCccCCceEEEehhhHHHHHhcCCC
Confidence            7899999999984 5667999999999999999999999999964        345899999999999999874

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.42  E-value=4.3e-13  Score=95.58  Aligned_cols=64  Identities=34%  Similarity=0.566  Sum_probs=61.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |+++++++++++.||+.++++++.+.++|.+++.++++|+.++..+||||||||+|+++++|+.
T Consensus       199 t~~~~~~a~~~~~~f~~is~~~~~~~~~g~~~~~~~~~f~~a~~~~P~IifIDEiD~l~~~r~~  262 (644)
T PRK10733        199 TLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGA  262 (644)
T ss_pred             HHHHHHHHHHcCCCEEEEehHHhHHhhhcccHHHHHHHHHHHHhcCCcEEEehhHhhhhhccCC
Confidence            7899999999999999999999999999999999999999999999999999999999988864

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.40  E-value=6e-13  Score=93.08  Aligned_cols=64  Identities=34%  Similarity=0.617  Sum_probs=57.6

Q ss_pred             hHHHHHHHHHhCCc----------EEEEchhhhhhcccChHHHHHHHHHHHHHhc----CCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAF----------FFLINGPEIMSKLAGESESNLRKAFEEADKN----SPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~----------~~~v~~~~l~~~~~ges~~~l~~if~~a~~~----~p~iifiDEid~i~~~r~~   66 (69)
                      |++++++|++++.+          |+.+++++++++|+|+++++++.+|+.++..    .|+||||||+|+++++|+.
T Consensus       230 T~LAKAlA~eL~~~i~~~~~~~~~fl~v~~~eLl~kyvGete~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~  307 (512)
T TIGR03689       230 TLIAKAVANSLAQRIGAETGDKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGS  307 (512)
T ss_pred             HHHHHHHHHhhccccccccCCceeEEeccchhhcccccchHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCC
Confidence            78999999998654          7788899999999999999999999999764    7999999999999998864

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.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.39  E-value=1.1e-12  Score=94.33  Aligned_cols=64  Identities=61%  Similarity=0.934  Sum_probs=61.5

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++++++|++++.+++.++++++.+++.|+++++++++|+.+..+.|+||||||+|+++++|+.
T Consensus       226 T~laraia~~~~~~~i~i~~~~i~~~~~g~~~~~l~~lf~~a~~~~p~il~iDEid~l~~~r~~  289 (733)
T TIGR01243       226 TLLAKAVANEAGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREE  289 (733)
T ss_pred             HHHHHHHHHHhCCeEEEEecHHHhcccccHHHHHHHHHHHHHHhcCCcEEEeehhhhhcccccC
Confidence            7899999999999999999999999999999999999999999999999999999999998764

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.

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.37  E-value=1.6e-12  Score=87.09  Aligned_cols=64  Identities=41%  Similarity=0.588  Sum_probs=60.7

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++++.+|+.+.++++..+|.|++++.++.+|+.++...|+||||||+|.++.+|.+
T Consensus       170 T~lakaia~~l~~~~~~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~  233 (364)
T TIGR01242       170 TLLAKAVAHETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTD  233 (364)
T ss_pred             HHHHHHHHHhCCCCEEecchHHHHHHhhhHHHHHHHHHHHHHHhcCCcEEEhhhhhhhcccccc
Confidence            7899999999999999999999999999999999999999999999999999999999887754

Many proteins may score above the trusted cutoff because an internal

>KOG0732|consensus

Probab=99.34  E-value=9.9e-13  Score=97.25  Aligned_cols=64  Identities=41%  Similarity=0.644  Sum_probs=60.3

Q ss_pred             hHHHHHHHHHhC-----CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLG-----AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~-----~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|..+.     ..|+.-++++..++|+||.|++++.+|+.|++.+|+|||+||||.+++.|+.
T Consensus       313 Tl~araLa~~~s~~~~kisffmrkgaD~lskwvgEaERqlrllFeeA~k~qPSIIffdeIdGlapvrSs  381 (1080)
T KOG0732|consen  313 TLMARALAAACSRGNRKISFFMRKGADCLSKWVGEAERQLRLLFEEAQKTQPSIIFFDEIDGLAPVRSS  381 (1080)
T ss_pred             hHHHHhhhhhhcccccccchhhhcCchhhccccCcHHHHHHHHHHHHhccCceEEeccccccccccccc
Confidence            789999999984     6889999999999999999999999999999999999999999999999964

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

Probab=99.09  E-value=3.6e-10  Score=81.58  Aligned_cols=62  Identities=21%  Similarity=0.349  Sum_probs=56.6

Q ss_pred             hHHHHHHHHHh----------CCcEEEEchhhhh--hcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSL----------GAFFFLINGPEIM--SKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~----------~~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |++++++|.++          +.+++.++.+.+.  .+|.|+.+++++++|+.++...|+||||||+|.|++.+
T Consensus       217 T~l~~~la~~~~~~~~p~~l~~~~~~~~~~~~l~a~~~~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g  290 (731)
T TIGR02639       217 TAIAEGLALRIAEGKVPENLKNAKIYSLDMGSLLAGTKYRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAG  290 (731)
T ss_pred             HHHHHHHHHHHHhCCCchhhcCCeEEEecHHHHhhhccccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccC
Confidence            78999999987          7889999999998  57999999999999999988889999999999998764

>KOG0744|consensus

Probab=99.05  E-value=1.8e-10  Score=77.73  Aligned_cols=64  Identities=23%  Similarity=0.316  Sum_probs=55.1

Q ss_pred             hHHHHHHHHHhCC---------cEEEEchhhhhhcccChHHHHHHHHHHHHHhc-----CCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGA---------FFFLINGPEIMSKLAGESESNLRKAFEEADKN-----SPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~---------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~-----~p~iifiDEid~i~~~r~~   66 (69)
                      |+|+|++|.++..         .++++|+..+++||++|+.+.|.++|++..+.     .-..++|||+++++..|..
T Consensus       191 TSLCKaLaQkLSIR~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvLIDEVESLa~aR~s  268 (423)
T KOG0744|consen  191 TSLCKALAQKLSIRTNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVLIDEVESLAAARTS  268 (423)
T ss_pred             hHHHHHHHHhheeeecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEEeHHHHHHHHHHHh
Confidence            7899999999963         67999999999999999999999999998762     2345668999999988843

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.93  E-value=3.9e-09  Score=77.11  Aligned_cols=63  Identities=19%  Similarity=0.334  Sum_probs=56.1

Q ss_pred             hHHHHHHHHHh----------CCcEEEEchhhhh--hcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSL----------GAFFFLINGPEIM--SKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~----------~~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |.+|+.+|.+.          +.+++.++.+.++  .+|.|+.+++++++|+.++...|+||||||+|.|.+.+.
T Consensus       214 Tal~~~la~~i~~~~vp~~l~~~~i~~l~~~~l~ag~~~~ge~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~  288 (821)
T CHL00095        214 TAIAEGLAQRIVNRDVPDILEDKLVITLDIGLLLAGTKYRGEFEERLKRIFDEIQENNNIILVIDEVHTLIGAGA  288 (821)
T ss_pred             HHHHHHHHHHHHhCCCChhhcCCeEEEeeHHHHhccCCCccHHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCC
Confidence            78889998886          4789999999988  469999999999999999888899999999999987654

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=98.90  E-value=4e-09  Score=67.94  Aligned_cols=57  Identities=14%  Similarity=0.322  Sum_probs=50.3

Q ss_pred             hHHHHHHHHHh-------CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL-------GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~-------~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++|+++|+.+       ..++++++++++.++|+|+++..++++|+.+   .++||||||+|.|.+
T Consensus        56 TtlA~~ia~~l~~~~~~~~~~~v~~~~~~l~~~~~g~~~~~~~~~~~~a---~~~VL~IDE~~~L~~  119 (261)
T TIGR02881        56 TTVARILGKLFKEMNVLSKGHLIEVERADLVGEYIGHTAQKTREVIKKA---LGGVLFIDEAYSLAR  119 (261)
T ss_pred             HHHHHHHHHHHHhcCcccCCceEEecHHHhhhhhccchHHHHHHHHHhc---cCCEEEEechhhhcc
Confidence            78999999874       2488999999999999999999999999887   368999999999974

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.

>CHL00181 cbbX CbbX; Provisional

Probab=98.88  E-value=4.4e-09  Score=69.14  Aligned_cols=59  Identities=14%  Similarity=0.263  Sum_probs=50.8

Q ss_pred             hHHHHHHHHHhC-------CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLG-------AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~-------~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |++|+++|..+.       .+++.++.+++.++|+|+++.+++++|+.+   .+.||||||+|.+++.+
T Consensus        73 T~lAr~la~~~~~~g~~~~~~~~~v~~~~l~~~~~g~~~~~~~~~l~~a---~ggVLfIDE~~~l~~~~  138 (287)
T CHL00181         73 TTVALKMADILYKLGYIKKGHLLTVTRDDLVGQYIGHTAPKTKEVLKKA---MGGVLFIDEAYYLYKPD  138 (287)
T ss_pred             HHHHHHHHHHHHHcCCCCCCceEEecHHHHHHHHhccchHHHHHHHHHc---cCCEEEEEccchhccCC
Confidence            789999988762       369999999999999999999899998886   45899999999997654

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=98.84  E-value=7.4e-09  Score=67.86  Aligned_cols=59  Identities=12%  Similarity=0.229  Sum_probs=50.7

Q ss_pred             hHHHHHHHHHhC-------CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLG-------AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~-------~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |++|+++|..+.       -+++.++++++.++|+|+++.+++++|+.+   .+++|||||+|.+.+++
T Consensus        72 T~lA~~ia~~l~~~g~~~~~~~v~v~~~~l~~~~~g~~~~~~~~~~~~a---~~gvL~iDEi~~L~~~~  137 (284)
T TIGR02880        72 TTVALRMAQILHRLGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEILKRA---MGGVLFIDEAYYLYRPD  137 (284)
T ss_pred             HHHHHHHHHHHHHcCCcccceEEEecHHHHhHhhcccchHHHHHHHHHc---cCcEEEEechhhhccCC
Confidence            788988888763       279999999999999999999999999887   45899999999997544

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=98.75  E-value=3.3e-08  Score=72.77  Aligned_cols=63  Identities=21%  Similarity=0.344  Sum_probs=54.9

Q ss_pred             hHHHHHHHHHh----------CCcEEEEchhhhh--hcccChHHHHHHHHHHHHHh-cCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSL----------GAFFFLINGPEIM--SKLAGESESNLRKAFEEADK-NSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~----------~~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~~-~~p~iifiDEid~i~~~r~   65 (69)
                      |++++++|...          +.+++.++.+.++  .+|.|+.++.++++|+.+.+ ..|+||||||+|.|.+.++
T Consensus       213 T~l~~~la~~i~~~~vp~~l~~~~~~~l~l~~l~ag~~~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~  288 (857)
T PRK10865        213 TAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGK  288 (857)
T ss_pred             HHHHHHHHHHhhcCCCchhhCCCEEEEEehhhhhhccchhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCC
Confidence            78999999988          7899999998887  55899999999999998654 5799999999999987653

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.72  E-value=3.7e-08  Score=66.58  Aligned_cols=66  Identities=30%  Similarity=0.413  Sum_probs=55.1

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhh-cccChHHHH-HHHHHHHHH----hcCCeEEEEccccccccccccCC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMS-KLAGESESN-LRKAFEEAD----KNSPSIIFIDELDAIAPKREKRE   68 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~-~~~ges~~~-l~~if~~a~----~~~p~iifiDEid~i~~~r~~~~   68 (69)
                      |+||+.+|+.+++||-.-++..|.. .|+||...+ +.++.+.|.    +.+..||||||||.|+++.++.+
T Consensus       111 TlLAqTLAk~LnVPFaiADATtLTEAGYVGEDVENillkLlqaadydV~rAerGIIyIDEIDKIarkSeN~S  182 (408)
T COG1219         111 TLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVERAERGIIYIDEIDKIARKSENPS  182 (408)
T ss_pred             HHHHHHHHHHhCCCeeeccccchhhccccchhHHHHHHHHHHHcccCHHHHhCCeEEEechhhhhccCCCCC
Confidence            8999999999999999999999984 599998554 677776652    34689999999999998876654

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=98.72  E-value=2.3e-08  Score=68.74  Aligned_cols=57  Identities=26%  Similarity=0.389  Sum_probs=50.0

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhc----CCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKN----SPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~----~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+.||..++.+|..+|+..-       +.+.+|++|+.|++.    +..|||+||||.+...+.+
T Consensus        62 TTlA~liA~~~~~~f~~~sAv~~-------gvkdlr~i~e~a~~~~~~gr~tiLflDEIHRfnK~QQD  122 (436)
T COG2256          62 TTLARLIAGTTNAAFEALSAVTS-------GVKDLREIIEEARKNRLLGRRTILFLDEIHRFNKAQQD  122 (436)
T ss_pred             HHHHHHHHHhhCCceEEeccccc-------cHHHHHHHHHHHHHHHhcCCceEEEEehhhhcChhhhh
Confidence            89999999999999999999654       789999999999663    3699999999999877654

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

Probab=98.69  E-value=5.5e-08  Score=70.96  Aligned_cols=63  Identities=16%  Similarity=0.316  Sum_probs=54.6

Q ss_pred             hHHHHHHHHHh----------CCcEEEEchhhhh--hcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSL----------GAFFFLINGPEIM--SKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~----------~~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |++|+++|...          +..++.++.+.++  .+|.|+.+++++++|+.+++..++||||||+|.|++.+.
T Consensus       221 T~lae~la~~i~~~~vP~~l~~~~~~~l~~~~llaG~~~~Ge~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~  295 (758)
T PRK11034        221 TAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGA  295 (758)
T ss_pred             HHHHHHHHHHHHhcCCCchhcCCeEEeccHHHHhcccchhhhHHHHHHHHHHHHHhcCCCEEEeccHHHHhccCC
Confidence            67888888764          6778888888887  468999999999999999888899999999999987764

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=98.66  E-value=8.3e-08  Score=65.99  Aligned_cols=63  Identities=29%  Similarity=0.378  Sum_probs=50.7

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhh-cccChHHH-HHHHHHHHH----HhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMS-KLAGESES-NLRKAFEEA----DKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~-~~~ges~~-~l~~if~~a----~~~~p~iifiDEid~i~~~r~   65 (69)
                      |++|+++|+.+++||+.++++.+.. .|+|+... .+..+++.+    ....++||||||||.+.+++.
T Consensus       122 T~lAr~lA~~l~~pf~~id~~~l~~~gyvG~d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~~~~~  190 (412)
T PRK05342        122 TLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIARKSE  190 (412)
T ss_pred             HHHHHHHHHHhCCCceecchhhcccCCcccchHHHHHHHHHHhccccHHHcCCcEEEEechhhhccccC
Confidence            7899999999999999999998864 69998644 456666542    345789999999999987643

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.64  E-value=1.1e-07  Score=69.99  Aligned_cols=62  Identities=21%  Similarity=0.344  Sum_probs=53.5

Q ss_pred             hHHHHHHHHHh----------CCcEEEEchhhhh--hcccChHHHHHHHHHHHHHh-cCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSL----------GAFFFLINGPEIM--SKLAGESESNLRKAFEEADK-NSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~----------~~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~~-~~p~iifiDEid~i~~~r   64 (69)
                      |++++++|...          +.+++.++.+.++  .+|.|+.+++++++|+.+.+ ..|+||||||+|.|++.+
T Consensus       208 T~l~~~la~~i~~~~~p~~l~~~~~~~l~~~~l~a~~~~~g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g  282 (852)
T TIGR03346       208 TAIVEGLAQRIVNGDVPESLKNKRLLALDMGALIAGAKYRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAG  282 (852)
T ss_pred             HHHHHHHHHHHhccCCchhhcCCeEEEeeHHHHhhcchhhhhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCC
Confidence            77888888885          6789999988886  56999999999999999865 469999999999998644

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.

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=98.62  E-value=9.9e-08  Score=65.70  Aligned_cols=64  Identities=30%  Similarity=0.410  Sum_probs=50.9

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhh-cccChH-HHHHHHHHHHH----HhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMS-KLAGES-ESNLRKAFEEA----DKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~-~~~ges-~~~l~~if~~a----~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|..++.||..++++.+.. +|+|+. +..+..+++.+    ....|+||||||+|.+.+++++
T Consensus       130 T~lAraLA~~l~~pf~~~da~~L~~~gyvG~d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~~~~~~  199 (413)
T TIGR00382       130 TLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSEN  199 (413)
T ss_pred             HHHHHHHHHhcCCCeEEechhhccccccccccHHHHHHHHHHhCcccHHhcccceEEecccchhchhhcc
Confidence            7899999999999999999998763 589986 45566665533    2457899999999999986543

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

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

Probab=98.61  E-value=7.6e-08  Score=66.66  Aligned_cols=64  Identities=58%  Similarity=0.838  Sum_probs=60.0

Q ss_pred             hhHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           2 SYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         2 ~T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      -|+++++++++ +..++.++++.+.++|.|+++.+++.+|+.++..+|+++++||+|.+.++|..
T Consensus        31 ~t~~~~~~a~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~ii~~d~~~~~~~~~~~   94 (494)
T COG0464          31 KTLLARALANE-GAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPSIIFIDEIDALAPKRSS   94 (494)
T ss_pred             hhHHHHHHHhc-cCcccccCcchhhhhhhhHHHHHHHHHHHHHHHhCCCeEeechhhhcccCccc
Confidence            37899999999 87779999999999999999999999999999999999999999999999876

>KOG0736|consensus

Probab=98.59  E-value=1.6e-07  Score=68.80  Aligned_cols=65  Identities=20%  Similarity=0.422  Sum_probs=61.2

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++++++|.++|.+++.++|.++.+.-.+-+|.++...|..|+.+.|+|||+-..|.+..+++++
T Consensus       445 ~t~V~~vas~lg~h~~evdc~el~~~s~~~~etkl~~~f~~a~~~~pavifl~~~dvl~id~dgg  509 (953)
T KOG0736|consen  445 TTVVRAVASELGLHLLEVDCYELVAESASHTETKLQAIFSRARRCSPAVLFLRNLDVLGIDQDGG  509 (953)
T ss_pred             HHHHHHHHHHhCCceEeccHHHHhhcccchhHHHHHHHHHHHhhcCceEEEEeccceeeecCCCc
Confidence            67899999999999999999999999999999999999999999999999999999999777654

>KOG0742|consensus

Probab=98.55  E-value=8.4e-08  Score=66.88  Aligned_cols=66  Identities=23%  Similarity=0.360  Sum_probs=57.5

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh-cCCeEEEEccccccccccccCCC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK-NSPSIIFIDELDAIAPKREKREL   69 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-~~p~iifiDEid~i~~~r~~~~~   69 (69)
                      |++|+.+|.+.|..+-...+.++ .+.-.+....|+++|+++++ ++.-+|||||.|++...|....|
T Consensus       398 Tm~ArelAr~SGlDYA~mTGGDV-APlG~qaVTkiH~lFDWakkS~rGLllFIDEADAFLceRnktym  464 (630)
T KOG0742|consen  398 TMFARELARHSGLDYAIMTGGDV-APLGAQAVTKIHKLFDWAKKSRRGLLLFIDEADAFLCERNKTYM  464 (630)
T ss_pred             hHHHHHHHhhcCCceehhcCCCc-cccchHHHHHHHHHHHHHhhcccceEEEehhhHHHHHHhchhhh
Confidence            89999999999999999999887 55566788899999999987 56789999999999998887644

>TIGR00763 lon ATP-dependent protease La

Probab=98.55  E-value=1.2e-07  Score=69.02  Aligned_cols=61  Identities=16%  Similarity=0.280  Sum_probs=50.5

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhh---------hcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIM---------SKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~---------~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |++|+++|+.++.+++.++.+.+.         ..|+|.....+.+.|..+....| ||||||||.+.++.
T Consensus       361 T~lAk~iA~~l~~~~~~i~~~~~~~~~~i~g~~~~~~g~~~g~i~~~l~~~~~~~~-villDEidk~~~~~  430 (775)
T TIGR00763       361 TSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQGLKKAKTKNP-LFLLDEIDKIGSSF  430 (775)
T ss_pred             HHHHHHHHHHhcCCeEEEeCCCcccHHHHcCCCCceeCCCCchHHHHHHHhCcCCC-EEEEechhhcCCcc
Confidence            889999999999999998764431         36888888889999998866666 78999999998753

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.55  E-value=2.8e-07  Score=67.99  Aligned_cols=63  Identities=17%  Similarity=0.250  Sum_probs=53.3

Q ss_pred             hHHHHHHHHHh----------CCcEEEEchhhhhh--cccChHHHHHHHHHHHHHh-cCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSL----------GAFFFLINGPEIMS--KLAGESESNLRKAFEEADK-NSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~----------~~~~~~v~~~~l~~--~~~ges~~~l~~if~~a~~-~~p~iifiDEid~i~~~r~   65 (69)
                      |.+++.+|...          +.+++.++.+.+.+  ++.|+.+++++++|+.++. ..++||||||+|.+.+.++
T Consensus       222 Tal~~~La~~i~~~~v~~~l~~~~i~~l~l~~l~ag~~~~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~  297 (852)
T TIGR03345       222 TAVVEGLALRIAAGDVPPALRNVRLLSLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGG  297 (852)
T ss_pred             HHHHHHHHHHHhhCCCCccccCCeEEEeehhhhhcccccchHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCC
Confidence            78889999876          35688888888774  6999999999999999965 4789999999999997654

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.

>KOG0745|consensus

Probab=98.52  E-value=2.6e-07  Score=64.51  Aligned_cols=63  Identities=30%  Similarity=0.440  Sum_probs=54.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhh-hcccChH-HHHHHHHHHHHH----hcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIM-SKLAGES-ESNLRKAFEEAD----KNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~-~~~~ges-~~~l~~if~~a~----~~~p~iifiDEid~i~~~r~   65 (69)
                      |+||+.+|.-+++||...+|..+. ..|+||. |.-|.++...|.    +.+..|+|+||+|.|..+-.
T Consensus       240 TllaqTLAr~ldVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVekAQqGIVflDEvDKi~~~~~  308 (564)
T KOG0745|consen  240 TLLAQTLARVLDVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGIVFLDEVDKITKKAE  308 (564)
T ss_pred             hHHHHHHHHHhCCCeEEecccchhhcccccccHHHHHHHHHHHccCCHHHHhcCeEEEehhhhhcccCc
Confidence            889999999999999999999997 4599997 777899998873    45789999999999985433

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=98.46  E-value=1.1e-07  Score=61.33  Aligned_cols=54  Identities=26%  Similarity=0.495  Sum_probs=35.8

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |+||+.+|++++.+|..++++.+      +....+..++...  ....||||||||.+.+..
T Consensus        64 TTLA~IIA~e~~~~~~~~sg~~i------~k~~dl~~il~~l--~~~~ILFIDEIHRlnk~~  117 (233)
T PF05496_consen   64 TTLARIIANELGVNFKITSGPAI------EKAGDLAAILTNL--KEGDILFIDEIHRLNKAQ  117 (233)
T ss_dssp             HHHHHHHHHHCT--EEEEECCC--------SCHHHHHHHHT----TT-EEEECTCCC--HHH
T ss_pred             hHHHHHHHhccCCCeEeccchhh------hhHHHHHHHHHhc--CCCcEEEEechhhccHHH
Confidence            89999999999999999998765      2234555565554  346899999999987653

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>KOG2028|consensus

Probab=98.40  E-value=5.6e-07  Score=62.16  Aligned_cols=57  Identities=21%  Similarity=0.419  Sum_probs=48.6

Q ss_pred             hHHHHHHHHHhCCc---EEEEchhhhhhcccChHHHHHHHHHHHHHh-----cCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAF---FFLINGPEIMSKLAGESESNLRKAFEEADK-----NSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~---~~~v~~~~l~~~~~ges~~~l~~if~~a~~-----~~p~iifiDEid~i~~~r~~   66 (69)
                      |+||+.+++....+   |+++++.+-       +.+.+|.+|+++++     .+..||||||||.+...+.+
T Consensus       176 TtlArlia~tsk~~SyrfvelSAt~a-------~t~dvR~ife~aq~~~~l~krkTilFiDEiHRFNksQQD  240 (554)
T KOG2028|consen  176 TTLARLIASTSKKHSYRFVELSATNA-------KTNDVRDIFEQAQNEKSLTKRKTILFIDEIHRFNKSQQD  240 (554)
T ss_pred             HHHHHHHHhhcCCCceEEEEEecccc-------chHHHHHHHHHHHHHHhhhcceeEEEeHHhhhhhhhhhh
Confidence            78999999998876   888888654       67889999999976     46899999999999887665

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=98.20  E-value=1.7e-06  Score=57.70  Aligned_cols=53  Identities=23%  Similarity=0.519  Sum_probs=44.0

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      |+||..+|+|+|+++-..+++.+      +....+-.++...+  ...|+||||||++.+.
T Consensus        66 TTLA~IIA~Emgvn~k~tsGp~l------eK~gDlaaiLt~Le--~~DVLFIDEIHrl~~~  118 (332)
T COG2255          66 TTLAHIIANELGVNLKITSGPAL------EKPGDLAAILTNLE--EGDVLFIDEIHRLSPA  118 (332)
T ss_pred             HHHHHHHHHHhcCCeEecccccc------cChhhHHHHHhcCC--cCCeEEEehhhhcChh
Confidence            88999999999999999999888      45666777776653  3599999999999764

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.04  E-value=1.4e-05  Score=44.69  Aligned_cols=62  Identities=26%  Similarity=0.435  Sum_probs=50.2

Q ss_pred             hHHHHHHHHHhCCc---EEEEchhhhhhc--------------ccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLGAF---FFLINGPEIMSK--------------LAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~~~---~~~v~~~~l~~~--------------~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |++++.++..+...   ++.++++.....              ........++.+++.++...|.+|++||++.+....
T Consensus        16 Ttl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDei~~~~~~~   94 (148)
T smart00382       16 TTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDVLILDEITSLLDAE   94 (148)
T ss_pred             HHHHHHHHhccCCCCCCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHHhcCCCEEEEECCcccCCHH
Confidence            78899999999875   888888765432              334567788899999988889999999999997654

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.

>KOG0735|consensus

Probab=98.02  E-value=1.5e-05  Score=58.65  Aligned_cols=61  Identities=25%  Similarity=0.279  Sum_probs=53.6

Q ss_pred             hHHHHHHHHHhC----CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLG----AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~----~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      |.|+++++++..    +++..++|+.+-.+-+....+.++.+|..+..++|+||++|++|.|++.
T Consensus       445 T~L~kal~~~~~k~~~~hv~~v~Cs~l~~~~~e~iQk~l~~vfse~~~~~PSiIvLDdld~l~~~  509 (952)
T KOG0735|consen  445 TNLVKALFDYYSKDLIAHVEIVSCSTLDGSSLEKIQKFLNNVFSEALWYAPSIIVLDDLDCLASA  509 (952)
T ss_pred             hHHHHHHHHHhccccceEEEEEechhccchhHHHHHHHHHHHHHHHHhhCCcEEEEcchhhhhcc
Confidence            679999999886    5778899999977767777888999999999999999999999999983

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=98.02  E-value=2.8e-05  Score=57.24  Aligned_cols=52  Identities=23%  Similarity=0.413  Sum_probs=46.5

Q ss_pred             CCcEEEEchhhhhhc--ccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868          14 GAFFFLINGPEIMSK--LAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus        14 ~~~~~~v~~~~l~~~--~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      +..++.++.+.++..  |-|+-|.+++.+.+..++..+.||||||+|.|.+.-.
T Consensus       226 ~~~i~sLD~g~LvAGakyRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~  279 (786)
T COG0542         226 DKRIYSLDLGSLVAGAKYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGA  279 (786)
T ss_pred             CCEEEEecHHHHhccccccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCc
Confidence            568899999999854  9999999999999999988899999999999977554

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=97.82  E-value=1.2e-05  Score=55.87  Aligned_cols=57  Identities=19%  Similarity=0.239  Sum_probs=48.9

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhh-cccC-hHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMS-KLAG-ESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~-~~~g-es~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|..++.||+.++++.+.. .|+| +.+..++.+|+.|...      +| +|.+++.|..
T Consensus        61 T~lAraLA~~l~~~fi~vdat~~~e~g~vG~dvE~i~r~l~e~A~~~------i~-~d~i~~~r~~  119 (441)
T TIGR00390        61 TEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESMVRDLTDAAVKL------VK-EEAIEKVRDR  119 (441)
T ss_pred             HHHHHHHHHHhCCeEEEeecceeecCCcccCCHHHHHHHHHHHHHHH------HH-HHHHhHHHHH
Confidence            7899999999999999999998874 7999 6899999999999663      34 6888887743

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=97.80  E-value=6.6e-05  Score=51.37  Aligned_cols=53  Identities=25%  Similarity=0.357  Sum_probs=43.0

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifiDEid~i~~   62 (69)
                      |++|+++++.++.+|+.+++...       +.+.++++++.++.    .++.+|||||+|.+..
T Consensus        50 TtLA~~ia~~~~~~~~~l~a~~~-------~~~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l~~  106 (413)
T PRK13342         50 TTLARIIAGATDAPFEALSAVTS-------GVKDLREVIEEARQRRSAGRRTILFIDEIHRFNK  106 (413)
T ss_pred             HHHHHHHHHHhCCCEEEEecccc-------cHHHHHHHHHHHHHhhhcCCceEEEEechhhhCH
Confidence            78999999999999999988642       45667788877753    3678999999998864

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

Probab=97.78  E-value=3.8e-05  Score=56.55  Aligned_cols=61  Identities=13%  Similarity=0.248  Sum_probs=47.0

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhh---------hcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIM---------SKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~---------~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |++++.+|+.++.+++.++.+...         ..|.|.....+.+.+..+....| ++|+||+|.+.++.
T Consensus       363 Ttl~~~ia~~l~~~~~~i~~~~~~d~~~i~g~~~~~~g~~~G~~~~~l~~~~~~~~-villDEidk~~~~~  432 (784)
T PRK10787        363 TSLGQSIAKATGRKYVRMALGGVRDEAEIRGHRRTYIGSMPGKLIQKMAKVGVKNP-LFLLDEIDKMSSDM  432 (784)
T ss_pred             HHHHHHHHHHhCCCEEEEEcCCCCCHHHhccchhccCCCCCcHHHHHHHhcCCCCC-EEEEEChhhccccc
Confidence            789999999999999988765532         24777777777777776654444 78999999998764

>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=97.66  E-value=0.00018  Score=40.59  Aligned_cols=58  Identities=31%  Similarity=0.543  Sum_probs=40.6

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHH---HHHHHHHHHhcCCeEEEEcccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESN---LRKAFEEADKNSPSIIFIDELDAI   60 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~---l~~if~~a~~~~p~iifiDEid~i   60 (69)
                      |++++.+++.+   +.+++.+++......+.......   ....+.......+.+|++||++.+
T Consensus        33 T~l~~~i~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lilDe~~~~   96 (151)
T cd00009          33 TTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSL   96 (151)
T ss_pred             HHHHHHHHHHhhcCCCCeEEEehhhhhhhhHHHHHhhhhhHhHHHHhhccCCCeEEEEeChhhh
Confidence            67899999998   89999999988765433332222   122233344567899999999976

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.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=97.56  E-value=0.00019  Score=47.65  Aligned_cols=52  Identities=19%  Similarity=0.476  Sum_probs=38.8

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++|+++|++++..+...+++.+.      ....+..++...  ..+++|||||+|.+..
T Consensus        65 T~la~~ia~~l~~~~~~~~~~~~~------~~~~l~~~l~~l--~~~~vl~IDEi~~l~~  116 (328)
T PRK00080         65 TTLANIIANEMGVNIRITSGPALE------KPGDLAAILTNL--EEGDVLFIDEIHRLSP  116 (328)
T ss_pred             HHHHHHHHHHhCCCeEEEeccccc------ChHHHHHHHHhc--ccCCEEEEecHhhcch
Confidence            789999999999998887766442      233455555543  3579999999999864

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

Probab=97.54  E-value=7.5e-05  Score=54.91  Aligned_cols=60  Identities=18%  Similarity=0.295  Sum_probs=40.8

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhh-----cccChHH-----HHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMS-----KLAGESE-----SNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~-----~~~ges~-----~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |.+|+++|..++.+++.++++++..     +++|...     ..-..+.+..+.+..+||||||+|.+.+
T Consensus       502 T~lAk~LA~~l~~~~i~id~se~~~~~~~~~LiG~~~gyvg~~~~g~L~~~v~~~p~sVlllDEieka~~  571 (758)
T PRK11034        502 TEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHP  571 (758)
T ss_pred             HHHHHHHHHHhCCCcEEeechhhcccccHHHHcCCCCCcccccccchHHHHHHhCCCcEEEeccHhhhhH
Confidence            7899999999999999999887632     2333210     1111233334455669999999998854

>PRK04195 replication factor C large subunit; Provisional

Probab=97.51  E-value=0.00034  Score=48.80  Aligned_cols=54  Identities=19%  Similarity=0.257  Sum_probs=41.1

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh------cCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK------NSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~------~~p~iifiDEid~i~~   62 (69)
                      |++|+++|++++.+++.+++++..      +...++.+...+..      ..+.+|+|||+|.+..
T Consensus        53 Ttla~ala~el~~~~ielnasd~r------~~~~i~~~i~~~~~~~sl~~~~~kvIiIDEaD~L~~  112 (482)
T PRK04195         53 TSLAHALANDYGWEVIELNASDQR------TADVIERVAGEAATSGSLFGARRKLILLDEVDGIHG  112 (482)
T ss_pred             HHHHHHHHHHcCCCEEEEcccccc------cHHHHHHHHHHhhccCcccCCCCeEEEEecCccccc
Confidence            789999999999999999998752      23345555544432      2578999999999976

>PRK04132 replication factor C small subunit; Provisional

Probab=97.50  E-value=0.00032  Score=52.25  Aligned_cols=54  Identities=22%  Similarity=0.282  Sum_probs=42.0

Q ss_pred             hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcC------CeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNS------PSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~------p~iifiDEid~i~~   62 (69)
                      |++|+++|+++     +.+++++|+++-.      +...||++.+.+....      ..|++|||+|.+-.
T Consensus       580 TT~A~ala~~l~g~~~~~~~lElNASd~r------gid~IR~iIk~~a~~~~~~~~~~KVvIIDEaD~Lt~  644 (846)
T PRK04132        580 TTAALALARELFGENWRHNFLELNASDER------GINVIREKVKEFARTKPIGGASFKIIFLDEADALTQ  644 (846)
T ss_pred             HHHHHHHHHhhhcccccCeEEEEeCCCcc------cHHHHHHHHHHHHhcCCcCCCCCEEEEEECcccCCH
Confidence            88999999998     5689999999841      3457888777654433      36999999999964

>KOG0741|consensus

Probab=97.46  E-value=0.00034  Score=50.47  Aligned_cols=57  Identities=26%  Similarity=0.367  Sum_probs=45.5

Q ss_pred             hHHHHHHHHHhCCcEEEE-chhhhhhcccChHH--HHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLI-NGPEIMSKLAGESE--SNLRKAFEEADKNSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v-~~~~l~~~~~ges~--~~l~~if~~a~~~~p~iifiDEid~i~   61 (69)
                      |.||-.+|...+.||+.+ ++.++.+  ..|++  ..++++|+.|++..-+||++|+|+.|.
T Consensus       552 TaLAA~iA~~S~FPFvKiiSpe~miG--~sEsaKc~~i~k~F~DAYkS~lsiivvDdiErLi  611 (744)
T KOG0741|consen  552 TALAAKIALSSDFPFVKIISPEDMIG--LSESAKCAHIKKIFEDAYKSPLSIIVVDDIERLL  611 (744)
T ss_pred             HHHHHHHHhhcCCCeEEEeChHHccC--ccHHHHHHHHHHHHHHhhcCcceEEEEcchhhhh
Confidence            788999999999999985 5555533  23333  349999999999999999999999874

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=97.44  E-value=0.00017  Score=50.31  Aligned_cols=47  Identities=19%  Similarity=0.162  Sum_probs=41.4

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhh-cccC-hHHHHHHHHHHHHHhcCC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMS-KLAG-ESESNLRKAFEEADKNSP   49 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~-~~~g-es~~~l~~if~~a~~~~p   49 (69)
                      |++|+++|+.++.||+.++++.+.. .|+| +.+..++++|+.|....|
T Consensus        64 T~LAr~LAk~l~~~fi~vD~t~f~e~GyvG~d~e~~ir~L~~~A~~~~~  112 (443)
T PRK05201         64 TEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESIIRDLVEIAVKMVR  112 (443)
T ss_pred             HHHHHHHHHHhCChheeecchhhccCCcccCCHHHHHHHHHHHHHHHhH
Confidence            7899999999999999999999986 6999 668999999999954444

>KOG1969|consensus

Probab=97.40  E-value=0.00042  Score=51.24  Aligned_cols=52  Identities=21%  Similarity=0.322  Sum_probs=42.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh--------cCCeEEEEcccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK--------NSPSIIFIDELDAI   60 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~--------~~p~iifiDEid~i   60 (69)
                      |+||+.+|++.|..++++|+|+=      .+...+++....|..        .+|..|++||||.-
T Consensus       340 TTLAHViAkqaGYsVvEINASDe------Rt~~~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa  399 (877)
T KOG1969|consen  340 TTLAHVIAKQAGYSVVEINASDE------RTAPMVKEKIENAVQNHSVLDADSRPVCLVIDEIDGA  399 (877)
T ss_pred             hHHHHHHHHhcCceEEEeccccc------ccHHHHHHHHHHHHhhccccccCCCcceEEEecccCC
Confidence            78999999999999999999984      456666666666543        47999999999963

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.40  E-value=0.00031  Score=48.56  Aligned_cols=60  Identities=15%  Similarity=0.241  Sum_probs=41.6

Q ss_pred             hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHHHH-HHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESESN-LRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~~~-l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |+|++++++++     +..++++++.++...+.+.-... ..+..+..  ..+.+|+|||+|.+.+++
T Consensus       162 ThL~~ai~~~~~~~~~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~--~~~dlLiiDDi~~l~~~~  227 (450)
T PRK00149        162 THLLHAIGNYILEKNPNAKVVYVTSEKFTNDFVNALRNNTMEEFKEKY--RSVDVLLIDDIQFLAGKE  227 (450)
T ss_pred             HHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHHcCcHHHHHHHH--hcCCEEEEehhhhhcCCH
Confidence            78999999987     56789999998876654443221 22222222  257899999999997754

>KOG2004|consensus

Probab=97.34  E-value=0.00035  Score=51.65  Aligned_cols=59  Identities=20%  Similarity=0.383  Sum_probs=48.4

Q ss_pred             hHHHHHHHHHhCCcEEEEchh------hhh---hcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGP------EIM---SKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~------~l~---~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++++.||..+|..||.++..      ++-   ..|+|....++=+..+....+.| +++|||||.+++
T Consensus       452 TSI~kSIA~ALnRkFfRfSvGG~tDvAeIkGHRRTYVGAMPGkiIq~LK~v~t~NP-liLiDEvDKlG~  519 (906)
T KOG2004|consen  452 TSIAKSIARALNRKFFRFSVGGMTDVAEIKGHRRTYVGAMPGKIIQCLKKVKTENP-LILIDEVDKLGS  519 (906)
T ss_pred             ccHHHHHHHHhCCceEEEeccccccHHhhcccceeeeccCChHHHHHHHhhCCCCc-eEEeehhhhhCC
Confidence            789999999999999998764      333   34999998888888888877666 555999999985

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=97.33  E-value=0.00056  Score=42.03  Aligned_cols=59  Identities=19%  Similarity=0.266  Sum_probs=39.9

Q ss_pred             hHHHHHHHHHhCC----cEEEEchhhhhhcccChHHHHHHHHHHHHH----hcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLGA----FFFLINGPEIMSKLAGESESNLRKAFEEAD----KNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~~----~~~~v~~~~l~~~~~ges~~~l~~if~~a~----~~~p~iifiDEid~i~~~   63 (69)
                      |.+|+++|..+..    +++.++++++..  -++.+..+.++...+.    .....|||+||||.+.++
T Consensus        17 T~la~~la~~l~~~~~~~~~~~d~s~~~~--~~~~~~~~~~l~~~~~~~v~~~~~gVVllDEidKa~~~   83 (171)
T PF07724_consen   17 TELAKALAELLFVGSERPLIRIDMSEYSE--GDDVESSVSKLLGSPPGYVGAEEGGVVLLDEIDKAHPS   83 (171)
T ss_dssp             HHHHHHHHHHHT-SSCCEEEEEEGGGHCS--HHHCSCHCHHHHHHTTCHHHHHHHTEEEEETGGGCSHT
T ss_pred             HHHHHHHHHHhccCCccchHHHhhhcccc--cchHHhhhhhhhhcccceeeccchhhhhhHHHhhcccc
Confidence            6799999999996    999999999865  1122333334443321    112349999999999873

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 ATPase AAA-2 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 []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

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

Probab=97.32  E-value=0.00059  Score=49.87  Aligned_cols=58  Identities=21%  Similarity=0.298  Sum_probs=41.7

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhc------------ccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSK------------LAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~------------~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |.+|+++|..++.+++.++++++..+            |+|..+  -..+.+..+.+..+||||||+|.+-+
T Consensus       498 T~lA~~la~~l~~~~~~~d~se~~~~~~~~~lig~~~gyvg~~~--~~~l~~~~~~~p~~VvllDEieka~~  567 (731)
T TIGR02639       498 TELAKQLAEALGVHLERFDMSEYMEKHTVSRLIGAPPGYVGFEQ--GGLLTEAVRKHPHCVLLLDEIEKAHP  567 (731)
T ss_pred             HHHHHHHHHHhcCCeEEEeCchhhhcccHHHHhcCCCCCcccch--hhHHHHHHHhCCCeEEEEechhhcCH
Confidence            78999999999999999998876431            333221  22344444556678999999998754

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.31  E-value=0.00043  Score=47.13  Aligned_cols=60  Identities=13%  Similarity=0.237  Sum_probs=40.4

Q ss_pred             hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHHH-HHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESES-NLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~~-~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |+|++++++++     +..++++++.++...+.+.-.. .+....+..  ..+.+|+|||+|.+.+++
T Consensus       150 ThL~~ai~~~l~~~~~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~--~~~dlLiiDDi~~l~~~~  215 (405)
T TIGR00362       150 THLLHAIGNEILENNPNAKVVYVSSEKFTNDFVNALRNNKMEEFKEKY--RSVDLLLIDDIQFLAGKE  215 (405)
T ss_pred             HHHHHHHHHHHHHhCCCCcEEEEEHHHHHHHHHHHHHcCCHHHHHHHH--HhCCEEEEehhhhhcCCH
Confidence            78999999887     6789999998886654433211 122222222  236899999999997753

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).

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=97.30  E-value=0.00052  Score=44.70  Aligned_cols=53  Identities=19%  Similarity=0.465  Sum_probs=36.8

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      |++++++|++++.++..++++.+..      ...+...+...  ..+.+|||||+|.+.+.
T Consensus        44 T~la~~ia~~~~~~~~~~~~~~~~~------~~~l~~~l~~~--~~~~vl~iDEi~~l~~~   96 (305)
T TIGR00635        44 TTLAHIIANEMGVNLKITSGPALEK------PGDLAAILTNL--EEGDVLFIDEIHRLSPA   96 (305)
T ss_pred             HHHHHHHHHHhCCCEEEeccchhcC------chhHHHHHHhc--ccCCEEEEehHhhhCHH
Confidence            7899999999999887776654321      22333333332  35789999999998654

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.

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=97.21  E-value=0.00076  Score=49.67  Aligned_cols=60  Identities=22%  Similarity=0.359  Sum_probs=49.4

Q ss_pred             hHHHHHHHHHhCCcEEEEchh------hhh---hcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGP------EIM---SKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~------~l~---~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      |+|++.||..+|..|+.++-.      ++-   ..|+|.-..++-+-.+.|....| ++++||||.+..+
T Consensus       364 TSLgkSIA~al~RkfvR~sLGGvrDEAEIRGHRRTYIGamPGrIiQ~mkka~~~NP-v~LLDEIDKm~ss  432 (782)
T COG0466         364 TSLGKSIAKALGRKFVRISLGGVRDEAEIRGHRRTYIGAMPGKIIQGMKKAGVKNP-VFLLDEIDKMGSS  432 (782)
T ss_pred             hhHHHHHHHHhCCCEEEEecCccccHHHhccccccccccCChHHHHHHHHhCCcCC-eEEeechhhccCC
Confidence            899999999999999998763      333   34899988888888888877666 4559999999875

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.21  E-value=0.0014  Score=42.41  Aligned_cols=58  Identities=19%  Similarity=0.240  Sum_probs=38.2

Q ss_pred             hHHHHHHHHHhCCcEEEEch------hhhhhcccChHHHHHHHHH--------------------HHHHhcCCeEEEEcc
Q psy3868           3 YRLTTLCRDSLGAFFFLING------PEIMSKLAGESESNLRKAF--------------------EEADKNSPSIIFIDE   56 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~------~~l~~~~~ges~~~l~~if--------------------~~a~~~~p~iifiDE   56 (69)
                      |++|+++|+.+|.+++.+++      +++++.|.|...+.+..-|                    -.|. ..+.+|++||
T Consensus        35 T~lA~~la~~lg~~~~~i~~~~~~~~~dllg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~l~~A~-~~g~~lllDE  113 (262)
T TIGR02640        35 TTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQFIHNVVKLEDIVRQNWVDNRLTLAV-REGFTLVYDE  113 (262)
T ss_pred             HHHHHHHHHHhCCCEEEEeCCccCCHHHHhhhhcccchhhHHHHHHHHhhhhhcccceeecCchHHHHH-HcCCEEEEcc
Confidence            78999999999999998865      4566655543322221111                    1121 2457999999


Q ss_pred             ccccc
Q psy3868          57 LDAIA   61 (69)
Q Consensus        57 id~i~   61 (69)
                      ++.+-
T Consensus       114 i~r~~  118 (262)
T TIGR02640       114 FTRSK  118 (262)
T ss_pred             hhhCC
Confidence            99864

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).

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=97.20  E-value=0.00097  Score=49.03  Aligned_cols=54  Identities=22%  Similarity=0.335  Sum_probs=40.2

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh-----cCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK-----NSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-----~~p~iifiDEid~i~~~   63 (69)
                      |++|+++++..+.+|+.+++...       +.+.++++++.+..     ..+.+|||||+|.+...
T Consensus        66 TTLA~aIA~~~~~~f~~lna~~~-------~i~dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~~  124 (725)
T PRK13341         66 TTLARIIANHTRAHFSSLNAVLA-------GVKDLRAEVDRAKERLERHGKRTILFIDEVHRFNKA  124 (725)
T ss_pred             HHHHHHHHHHhcCcceeehhhhh-------hhHHHHHHHHHHHHHhhhcCCceEEEEeChhhCCHH
Confidence            78999999999999999988642       23445666665532     34679999999998653

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.17  E-value=0.00086  Score=46.55  Aligned_cols=61  Identities=16%  Similarity=0.297  Sum_probs=40.3

Q ss_pred             hHHHHHHHHHh-----CCcEEEEchhhhhhcccChH-HHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGES-ESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges-~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |+|++++++++     +..++++++.+++..+...- ...+.+ |.......+.+|+|||++.+.++.
T Consensus       144 THLl~ai~~~l~~~~~~~~v~yi~~~~f~~~~~~~~~~~~~~~-f~~~~~~~~dvLlIDDi~~l~~~~  210 (440)
T PRK14088        144 THLLQSIGNYVVQNEPDLRVMYITSEKFLNDLVDSMKEGKLNE-FREKYRKKVDVLLIDDVQFLIGKT  210 (440)
T ss_pred             HHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHhcccHHH-HHHHHHhcCCEEEEechhhhcCcH
Confidence            78999999986     46788999988766543221 112222 222222468999999999987643

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=97.14  E-value=0.00031  Score=47.40  Aligned_cols=59  Identities=20%  Similarity=0.112  Sum_probs=42.1

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhc--ccChHHHHHH----------HHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSK--LAGESESNLR----------KAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~--~~ges~~~l~----------~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++++.+|++++++++.++++..++.  ++|...-.++          ..+-.|. ..++++++||+|..-+
T Consensus        78 Ttla~~lA~~l~~~~~rV~~~~~l~~~DliG~~~~~l~~g~~~~~f~~GpL~~A~-~~g~illlDEin~a~p  148 (327)
T TIGR01650        78 STHIEQIAARLNWPCVRVNLDSHVSRIDLVGKDAIVLKDGKQITEFRDGILPWAL-QHNVALCFDEYDAGRP  148 (327)
T ss_pred             HHHHHHHHHHHCCCeEEEEecCCCChhhcCCCceeeccCCcceeEEecCcchhHH-hCCeEEEechhhccCH
Confidence            78999999999999999988777666  6665422211          1223332 3578999999998743

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.12  E-value=0.0018  Score=43.52  Aligned_cols=59  Identities=17%  Similarity=0.164  Sum_probs=38.4

Q ss_pred             hHHHHHHHHHh-----CCcEEEEchhhh----------hhcccC-------h-HHHHHHHHHHHHHh-cCCeEEEEcccc
Q psy3868           3 YRLTTLCRDSL-----GAFFFLINGPEI----------MSKLAG-------E-SESNLRKAFEEADK-NSPSIIFIDELD   58 (69)
Q Consensus         3 T~la~aia~~~-----~~~~~~v~~~~l----------~~~~~g-------e-s~~~l~~if~~a~~-~~p~iifiDEid   58 (69)
                      |++++.+++++     +..++++++...          .....+       . ....+..+++..++ ..+.||+|||+|
T Consensus        69 T~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d  148 (394)
T PRK00411         69 TTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDIN  148 (394)
T ss_pred             HHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHh
Confidence            67888888776     577888988532          222222       1 23344555555443 457899999999


Q ss_pred             ccc
Q psy3868          59 AIA   61 (69)
Q Consensus        59 ~i~   61 (69)
                      .+.
T Consensus       149 ~l~  151 (394)
T PRK00411        149 YLF  151 (394)
T ss_pred             Hhh
Confidence            998

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.96  E-value=0.0018  Score=46.96  Aligned_cols=61  Identities=11%  Similarity=0.194  Sum_probs=43.5

Q ss_pred             hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |+|++++++++     +..++++++.+++..+...-......-|+.-. ..+.+|+||||+.+..+.
T Consensus       328 THLL~AIa~~a~~~~~g~~V~Yitaeef~~el~~al~~~~~~~f~~~y-~~~DLLlIDDIq~l~gke  393 (617)
T PRK14086        328 THLLHAIGHYARRLYPGTRVRYVSSEEFTNEFINSIRDGKGDSFRRRY-REMDILLVDDIQFLEDKE  393 (617)
T ss_pred             HHHHHHHHHHHHHhCCCCeEEEeeHHHHHHHHHHHHHhccHHHHHHHh-hcCCEEEEehhccccCCH
Confidence            78999999987     56889999999887765543332223344322 247999999999997754

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.92  E-value=0.0028  Score=41.46  Aligned_cols=56  Identities=18%  Similarity=0.335  Sum_probs=36.1

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHH-hcCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEAD-KNSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~-~~~p~iifiDEid~i~   61 (69)
                      |+++++++++.+.+++.+++++  .+ +..-...+........ ...+.+|+|||+|.+.
T Consensus        57 T~la~~l~~~~~~~~~~i~~~~--~~-~~~i~~~l~~~~~~~~~~~~~~vliiDe~d~l~  113 (316)
T PHA02544         57 TTVAKALCNEVGAEVLFVNGSD--CR-IDFVRNRLTRFASTVSLTGGGKVIIIDEFDRLG  113 (316)
T ss_pred             HHHHHHHHHHhCccceEeccCc--cc-HHHHHHHHHHHHHhhcccCCCeEEEEECccccc
Confidence            7899999999999999999876  21 1111122222111111 1357899999999884

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.81  E-value=0.0028  Score=47.31  Aligned_cols=58  Identities=19%  Similarity=0.249  Sum_probs=40.6

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhc------------ccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSK------------LAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~------------~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |.+|+++|..+   +..++.++++++..+            |+|..+.-  .+.+..+++..+||+|||||..-+
T Consensus       610 T~lA~~La~~l~~~~~~~~~~dmse~~~~~~~~~l~g~~~gyvg~~~~g--~L~~~v~~~p~svvllDEieka~~  682 (852)
T TIGR03345       610 TETALALAELLYGGEQNLITINMSEFQEAHTVSRLKGSPPGYVGYGEGG--VLTEAVRRKPYSVVLLDEVEKAHP  682 (852)
T ss_pred             HHHHHHHHHHHhCCCcceEEEeHHHhhhhhhhccccCCCCCcccccccc--hHHHHHHhCCCcEEEEechhhcCH
Confidence            78999999998   468889998876432            44443221  233445567789999999997654

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.

>PF13173 AAA_14: AAA domain

Probab=96.73  E-value=0.0042  Score=35.96  Aligned_cols=57  Identities=23%  Similarity=0.218  Sum_probs=34.9

Q ss_pred             hHHHHHHHHHhC--CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSLG--AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~~--~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~   61 (69)
                      |++++.++.++.  -.++.++..+.......+..  +.+.|......++.+|||||++.+-
T Consensus        16 Ttll~~~~~~~~~~~~~~yi~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~i~iDEiq~~~   74 (128)
T PF13173_consen   16 TTLLKQLAKDLLPPENILYINFDDPRDRRLADPD--LLEYFLELIKPGKKYIFIDEIQYLP   74 (128)
T ss_pred             HHHHHHHHHHhcccccceeeccCCHHHHHHhhhh--hHHHHHHhhccCCcEEEEehhhhhc
Confidence            678888888876  67778877765332111111  2233333222378999999998773

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=96.71  E-value=0.0059  Score=40.57  Aligned_cols=60  Identities=20%  Similarity=0.344  Sum_probs=38.2

Q ss_pred             hHHHHHHHHHhC---------CcEEEEchhhhh----------hccc--C--------hHHHHHHHHHHHHHh-cCCeEE
Q psy3868           3 YRLTTLCRDSLG---------AFFFLINGPEIM----------SKLA--G--------ESESNLRKAFEEADK-NSPSII   52 (69)
Q Consensus         3 T~la~aia~~~~---------~~~~~v~~~~l~----------~~~~--g--------es~~~l~~if~~a~~-~~p~ii   52 (69)
                      |++++.+++++.         ++++++++....          ..+.  |        ...+.++.+++.... ..+.||
T Consensus        54 T~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vl  133 (365)
T TIGR02928        54 TAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLII  133 (365)
T ss_pred             HHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEE
Confidence            677888877653         578888875432          1111  1        123445667766643 457899


Q ss_pred             EEcccccccc
Q psy3868          53 FIDELDAIAP   62 (69)
Q Consensus        53 fiDEid~i~~   62 (69)
                      +|||+|.+..
T Consensus       134 vIDE~d~L~~  143 (365)
T TIGR02928       134 VLDEIDYLVG  143 (365)
T ss_pred             EECchhhhcc
Confidence            9999999973

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.51  E-value=0.0063  Score=39.49  Aligned_cols=57  Identities=21%  Similarity=0.364  Sum_probs=39.5

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccCh---HHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGE---SESNLRKAFEEADKNSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ge---s~~~l~~if~~a~~~~p~iifiDEid~i~   61 (69)
                      |+|+.++|+++   +..++.++.+++++...+.   +.....++++..  ....+|+|||++...
T Consensus       113 ThLa~aia~~l~~~g~~v~~it~~~l~~~l~~~~~~~~~~~~~~l~~l--~~~dlLvIDDig~~~  175 (244)
T PRK07952        113 NHLAAAICNELLLRGKSVLIITVADIMSAMKDTFSNSETSEEQLLNDL--SNVDLLVIDEIGVQT  175 (244)
T ss_pred             HHHHHHHHHHHHhcCCeEEEEEHHHHHHHHHHHHhhccccHHHHHHHh--ccCCEEEEeCCCCCC
Confidence            77899999888   6788999999987643321   112233444443  257899999998865

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.48  E-value=0.0091  Score=42.33  Aligned_cols=54  Identities=13%  Similarity=0.216  Sum_probs=36.4

Q ss_pred             hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++|+.+|+.+++.                        +++++++.      ..+...+|++.+.+..    .+..|++|
T Consensus        54 TTlAriLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~dviEIdaas------~~gVd~IReL~e~l~~~p~~g~~KV~II  127 (484)
T PRK14956         54 TTIARILAKRLNCENPIGNEPCNECTSCLEITKGISSDVLEIDAAS------NRGIENIRELRDNVKFAPMGGKYKVYII  127 (484)
T ss_pred             HHHHHHHHHhcCcccccCccccCCCcHHHHHHccCCccceeechhh------cccHHHHHHHHHHHHhhhhcCCCEEEEE
Confidence            78999999998863                        44555432      1234566776666542    34679999


Q ss_pred             cccccccc
Q psy3868          55 DELDAIAP   62 (69)
Q Consensus        55 DEid~i~~   62 (69)
                      ||+|.+..
T Consensus       128 DEah~Ls~  135 (484)
T PRK14956        128 DEVHMLTD  135 (484)
T ss_pred             echhhcCH
Confidence            99999854

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.48  E-value=0.0068  Score=42.32  Aligned_cols=60  Identities=15%  Similarity=0.263  Sum_probs=38.9

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      |+|++++++++   +..++++++.++...+...-...-...|.... ..+.+|+|||++.+.++
T Consensus       155 THLl~Ai~~~l~~~~~~v~yi~~~~f~~~~~~~l~~~~~~~f~~~~-~~~dvLiIDDiq~l~~k  217 (445)
T PRK12422        155 THLMQAAVHALRESGGKILYVRSELFTEHLVSAIRSGEMQRFRQFY-RNVDALFIEDIEVFSGK  217 (445)
T ss_pred             HHHHHHHHHHHHHcCCCEEEeeHHHHHHHHHHHHhcchHHHHHHHc-ccCCEEEEcchhhhcCC
Confidence            78999999876   68889999887754432211110112243332 35789999999998764

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.41  E-value=0.01  Score=36.84  Aligned_cols=51  Identities=16%  Similarity=0.235  Sum_probs=36.1

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      |+++++++++.   +.++++++++++....        ..+++..+  .+.+|+|||+|.+...
T Consensus        52 T~la~~~~~~~~~~~~~~~~i~~~~~~~~~--------~~~~~~~~--~~~lLvIDdi~~l~~~  105 (226)
T TIGR03420        52 SHLLQAACAAAEERGKSAIYLPLAELAQAD--------PEVLEGLE--QADLVCLDDVEAIAGQ  105 (226)
T ss_pred             HHHHHHHHHHHHhcCCcEEEEeHHHHHHhH--------HHHHhhcc--cCCEEEEeChhhhcCC
Confidence            67899998876   4788999998885321        23443332  3469999999998654

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.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.41  E-value=0.0099  Score=41.84  Aligned_cols=54  Identities=13%  Similarity=0.206  Sum_probs=37.9

Q ss_pred             hHHHHHHHHHhCC------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGA------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++|+++|+.+++                        .++.++++.      ..+...+|++.+.++.    ....++||
T Consensus        50 TTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~dv~el~aa~------~~gid~iR~i~~~~~~~p~~~~~kVvII  123 (472)
T PRK14962         50 TTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVIELDAAS------NRGIDEIRKIRDAVGYRPMEGKYKVYII  123 (472)
T ss_pred             HHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCccEEEeCcc------cCCHHHHHHHHHHHhhChhcCCeEEEEE
Confidence            7899999999875                        456665532      1234567777776643    23579999


Q ss_pred             cccccccc
Q psy3868          55 DELDAIAP   62 (69)
Q Consensus        55 DEid~i~~   62 (69)
                      ||+|.+..
T Consensus       124 DE~h~Lt~  131 (472)
T PRK14962        124 DEVHMLTK  131 (472)
T ss_pred             EChHHhHH
Confidence            99999853

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.39  E-value=0.011  Score=41.93  Aligned_cols=54  Identities=11%  Similarity=0.241  Sum_probs=37.6

Q ss_pred             hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++|+++|+.+++.                        ++++++++      ..+...+|++.+.+.-    .+..|++|
T Consensus        52 Tt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~eidaas------~~~v~~iR~l~~~~~~~p~~~~~kV~iI  125 (509)
T PRK14958         52 TTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLFEVDAAS------RTKVEDTRELLDNIPYAPTKGRFKVYLI  125 (509)
T ss_pred             HHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceEEEEcccc------cCCHHHHHHHHHHHhhccccCCcEEEEE
Confidence            78999999999763                        56666542      1244557777766532    23469999


Q ss_pred             cccccccc
Q psy3868          55 DELDAIAP   62 (69)
Q Consensus        55 DEid~i~~   62 (69)
                      ||+|.+.+
T Consensus       126 DE~~~ls~  133 (509)
T PRK14958        126 DEVHMLSG  133 (509)
T ss_pred             EChHhcCH
Confidence            99999864

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.37  E-value=0.0076  Score=44.33  Aligned_cols=54  Identities=13%  Similarity=0.255  Sum_probs=36.4

Q ss_pred             hHHHHHHHHHhCC-----------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHH----hcCC
Q psy3868           3 YRLTTLCRDSLGA-----------------------------FFFLINGPEIMSKLAGESESNLRKAFEEAD----KNSP   49 (69)
Q Consensus         3 T~la~aia~~~~~-----------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~----~~~p   49 (69)
                      |++|+.+|+.+++                             .++++++++      ..+...+|++.+.+.    ..+.
T Consensus        52 TTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC~~I~aG~hpDviEIdAas------~~gVDdIReLie~~~~~P~~gr~  125 (700)
T PRK12323         52 TTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEIDAGRFVDYIEMDAAS------NRGVDEMAQLLDKAVYAPTAGRF  125 (700)
T ss_pred             HHHHHHHHHHhcCCCccccccCCCCCCcccHHHHHHHcCCCCcceEecccc------cCCHHHHHHHHHHHHhchhcCCc
Confidence            7899999999876                             344444431      123456777766653    2346


Q ss_pred             eEEEEcccccccc
Q psy3868          50 SIIFIDELDAIAP   62 (69)
Q Consensus        50 ~iifiDEid~i~~   62 (69)
                      .|++|||+|.|..
T Consensus       126 KViIIDEah~Ls~  138 (700)
T PRK12323        126 KVYMIDEVHMLTN  138 (700)
T ss_pred             eEEEEEChHhcCH
Confidence            7999999999854

>PLN03025 replication factor C subunit; Provisional

Probab=96.29  E-value=0.015  Score=38.58  Aligned_cols=55  Identities=13%  Similarity=0.123  Sum_probs=35.1

Q ss_pred             hHHHHHHHHHhC-----CcEEEEchhhhhhcccChHHHHHHHHHHHHHh-------cCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLG-----AFFFLINGPEIMSKLAGESESNLRKAFEEADK-------NSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~-----~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-------~~p~iifiDEid~i~~~   63 (69)
                      |++|+++|+++.     ..++++++++..      +...++...+....       ..+.+++|||+|.+...
T Consensus        48 Ttla~~la~~l~~~~~~~~~~eln~sd~~------~~~~vr~~i~~~~~~~~~~~~~~~kviiiDE~d~lt~~  114 (319)
T PLN03025         48 TTSILALAHELLGPNYKEAVLELNASDDR------GIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTSG  114 (319)
T ss_pred             HHHHHHHHHHHhcccCccceeeecccccc------cHHHHHHHHHHHHhccccCCCCCeEEEEEechhhcCHH
Confidence            789999999973     347778876542      12234444332211       24679999999998653

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=96.08  E-value=0.013  Score=43.85  Aligned_cols=54  Identities=13%  Similarity=0.221  Sum_probs=36.3

Q ss_pred             hHHHHHHHHHhCC------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGA------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++++++|+.+++                        .++++++++      ..+...++++.+.+..    .+..|++|
T Consensus        52 TTlAriLAKaLnCe~~~~~~PCG~C~sCr~I~~G~h~DviEIDAas------~rgVDdIReLIe~a~~~P~~gr~KVIII  125 (830)
T PRK07003         52 TTLSRIFAKALNCETGVTSQPCGVCRACREIDEGRFVDYVEMDAAS------NRGVDEMAALLERAVYAPVDARFKVYMI  125 (830)
T ss_pred             HHHHHHHHHHhcCccCCCCCCCcccHHHHHHhcCCCceEEEecccc------cccHHHHHHHHHHHHhccccCCceEEEE
Confidence            7889999998875                        244444432      1234567777776542    34579999


Q ss_pred             cccccccc
Q psy3868          55 DELDAIAP   62 (69)
Q Consensus        55 DEid~i~~   62 (69)
                      ||+|.|-.
T Consensus       126 DEah~LT~  133 (830)
T PRK07003        126 DEVHMLTN  133 (830)
T ss_pred             eChhhCCH
Confidence            99999854

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.07  E-value=0.021  Score=42.12  Aligned_cols=54  Identities=11%  Similarity=0.207  Sum_probs=37.3

Q ss_pred             hHHHHHHHHHhCC------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGA------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++|+++|+.+++                        .++++++++-      .+...+|++.+.+..    .+..|++|
T Consensus        51 TTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hpDviEIDAAs~------~~VddIReli~~~~y~P~~gk~KV~II  124 (702)
T PRK14960         51 TTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFIDLIEIDAASR------TKVEDTRELLDNVPYAPTQGRFKVYLI  124 (702)
T ss_pred             HHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCCceEEeccccc------CCHHHHHHHHHHHhhhhhcCCcEEEEE
Confidence            7899999999876                        4555555421      234567777766532    34679999


Q ss_pred             cccccccc
Q psy3868          55 DELDAIAP   62 (69)
Q Consensus        55 DEid~i~~   62 (69)
                      ||+|.+-.
T Consensus       125 DEVh~LS~  132 (702)
T PRK14960        125 DEVHMLST  132 (702)
T ss_pred             echHhcCH
Confidence            99998853

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.02  E-value=0.0096  Score=44.23  Aligned_cols=58  Identities=21%  Similarity=0.277  Sum_probs=39.1

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhh-----c-------ccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMS-----K-------LAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~-----~-------~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |.+|+++|..+   +.+++.++.+++..     +       |+|-.+  ...+.+..+....+||+|||+|.+-+
T Consensus       553 t~lA~~LA~~l~~~~~~~~~~d~s~~~~~~~~~~l~g~~~gyvg~~~--~~~l~~~~~~~p~~VvllDeieka~~  625 (821)
T CHL00095        553 TELTKALASYFFGSEDAMIRLDMSEYMEKHTVSKLIGSPPGYVGYNE--GGQLTEAVRKKPYTVVLFDEIEKAHP  625 (821)
T ss_pred             HHHHHHHHHHhcCCccceEEEEchhccccccHHHhcCCCCcccCcCc--cchHHHHHHhCCCeEEEECChhhCCH
Confidence            67999999987   36888888877632     2       333222  22355555555558999999998754

>PRK06893 DNA replication initiation factor; Validated

Probab=95.99  E-value=0.013  Score=37.18  Aligned_cols=52  Identities=12%  Similarity=0.131  Sum_probs=31.1

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |+|++++|++.   +....+++....        .....++++..  .+..+|+|||++.+.+++
T Consensus        53 ThL~~ai~~~~~~~~~~~~y~~~~~~--------~~~~~~~~~~~--~~~dlLilDDi~~~~~~~  107 (229)
T PRK06893         53 SHLLKAVSNHYLLNQRTAIYIPLSKS--------QYFSPAVLENL--EQQDLVCLDDLQAVIGNE  107 (229)
T ss_pred             HHHHHHHHHHHHHcCCCeEEeeHHHh--------hhhhHHHHhhc--ccCCEEEEeChhhhcCCh
Confidence            78999999886   234444444321        11112333333  246899999999987654

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=95.89  E-value=0.044  Score=35.90  Aligned_cols=60  Identities=15%  Similarity=0.159  Sum_probs=37.1

Q ss_pred             hHHHHHHHHHhC-----CcEEEEchhhhhhcc-------------cCh-------HHHHHHHHHHHHHhc-----CCeEE
Q psy3868           3 YRLTTLCRDSLG-----AFFFLINGPEIMSKL-------------AGE-------SESNLRKAFEEADKN-----SPSII   52 (69)
Q Consensus         3 T~la~aia~~~~-----~~~~~v~~~~l~~~~-------------~ge-------s~~~l~~if~~a~~~-----~p~ii   52 (69)
                      |++|+++++++.     .+++.++++++...+             .+.       ....++.+.+.....     .+.+|
T Consensus        50 T~la~~~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl  129 (337)
T PRK12402         50 TAAVRALARELYGDPWENNFTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTI  129 (337)
T ss_pred             HHHHHHHHHHhcCcccccceEEechhhhhhcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEE
Confidence            788999999874     357888887764321             111       123344444343332     34699


Q ss_pred             EEcccccccc
Q psy3868          53 FIDELDAIAP   62 (69)
Q Consensus        53 fiDEid~i~~   62 (69)
                      +|||+|.+..
T Consensus       130 ilDe~~~l~~  139 (337)
T PRK12402        130 LLDNAEALRE  139 (337)
T ss_pred             EEeCcccCCH
Confidence            9999998853

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=95.83  E-value=0.028  Score=39.31  Aligned_cols=60  Identities=13%  Similarity=0.205  Sum_probs=40.2

Q ss_pred             hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHHH---HHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESES---NLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~~---~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |+|++++++++     +..++++++.++...+...-..   .+.+..+..  ..+.+|+|||++.+.+++
T Consensus       155 THLl~Ai~~~l~~~~~~~~v~yv~~~~f~~~~~~~l~~~~~~~~~~~~~~--~~~dvLiIDDiq~l~~k~  222 (450)
T PRK14087        155 THLLKAAKNYIESNFSDLKVSYMSGDEFARKAVDILQKTHKEIEQFKNEI--CQNDVLIIDDVQFLSYKE  222 (450)
T ss_pred             HHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHHHhhhHHHHHHHHh--ccCCEEEEeccccccCCH
Confidence            77889998854     4788899999987665543221   222222222  356799999999987654

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

Probab=95.65  E-value=0.014  Score=38.78  Aligned_cols=60  Identities=20%  Similarity=0.213  Sum_probs=36.4

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhc--ccChHHHHHH----HHHHHHHh--cCC--eEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSK--LAGESESNLR----KAFEEADK--NSP--SIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~--~~ges~~~l~----~if~~a~~--~~p--~iifiDEid~i~~   62 (69)
                      |++|+.+|..++.+|+.+.+..-+..  .+|...-.-+    ..|.....  ...  +++|+|||+...+
T Consensus        57 T~la~~lA~~l~~~~~~i~~t~~l~p~d~~G~~~~~~~~~~~~~~~~~~gpl~~~~~~ill~DEInra~p  126 (329)
T COG0714          57 TLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVPGPLFAAVRVILLLDEINRAPP  126 (329)
T ss_pred             HHHHHHHHHHhCCCeEEEecCCCCCHHHhcCchhHhhhhccCCeEEEecCCcccccceEEEEeccccCCH
Confidence            78999999999999999988644322  3343221111    11111110  111  4999999998654

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=95.65  E-value=0.035  Score=38.30  Aligned_cols=30  Identities=17%  Similarity=0.315  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEccccccccc
Q psy3868          34 ESNLRKAFEEADK----NSPSIIFIDELDAIAPK   63 (69)
Q Consensus        34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~~   63 (69)
                      ...+|++++.+..    ....|+||||+|.+...
T Consensus        99 i~~iR~l~~~~~~~p~~~~~kViiIDead~m~~~  132 (394)
T PRK07940         99 VDEVRELVTIAARRPSTGRWRIVVIEDADRLTER  132 (394)
T ss_pred             HHHHHHHHHHHHhCcccCCcEEEEEechhhcCHH
Confidence            4568899988754    23469999999999653

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=95.65  E-value=0.028  Score=43.13  Aligned_cols=32  Identities=34%  Similarity=0.479  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHHHh--cCCeEEEEcccccccccc
Q psy3868          33 SESNLRKAFEEADK--NSPSIIFIDELDAIAPKR   64 (69)
Q Consensus        33 s~~~l~~if~~a~~--~~p~iifiDEid~i~~~r   64 (69)
                      +...+.++|.....  ....||+|||||.|..+.
T Consensus       852 S~evLerLF~~L~k~~r~v~IIILDEID~L~kK~  885 (1164)
T PTZ00112        852 SFKILDRLFNQNKKDNRNVSILIIDEIDYLITKT  885 (1164)
T ss_pred             HHHHHHHHHhhhhcccccceEEEeehHhhhCccH
Confidence            34567788877632  346799999999998653

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=95.64  E-value=0.027  Score=41.27  Aligned_cols=54  Identities=13%  Similarity=0.233  Sum_probs=35.2

Q ss_pred             hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++|+++|+.+++.                        ++++++++      ..+...+|++.+.+..    ....|++|
T Consensus        52 TTlAr~lAk~L~c~~~~~~~pCg~C~~C~~i~~g~~~D~ieidaas------~~~VddiR~li~~~~~~p~~g~~KV~II  125 (647)
T PRK07994         52 TTIARLLAKGLNCETGITATPCGECDNCREIEQGRFVDLIEIDAAS------RTKVEDTRELLDNVQYAPARGRFKVYLI  125 (647)
T ss_pred             HHHHHHHHHhhhhccCCCCCCCCCCHHHHHHHcCCCCCceeecccc------cCCHHHHHHHHHHHHhhhhcCCCEEEEE
Confidence            78999999998773                        34444432      0123456666665532    34579999


Q ss_pred             cccccccc
Q psy3868          55 DELDAIAP   62 (69)
Q Consensus        55 DEid~i~~   62 (69)
                      ||+|.+..
T Consensus       126 DEah~Ls~  133 (647)
T PRK07994        126 DEVHMLSR  133 (647)
T ss_pred             echHhCCH
Confidence            99998864

>PHA02244 ATPase-like protein

Probab=95.58  E-value=0.023  Score=39.26  Aligned_cols=59  Identities=25%  Similarity=0.340  Sum_probs=34.6

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccC---hHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAG---ESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~g---es~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++|+++|..++.||+.++...-.....|   ....-...-|-.|. ..+.++++||++.+.+
T Consensus       133 TtLA~aLA~~lg~pfv~In~l~d~~~L~G~i~~~g~~~dgpLl~A~-~~GgvLiLDEId~a~p  194 (383)
T PHA02244        133 NHIAEQIAEALDLDFYFMNAIMDEFELKGFIDANGKFHETPFYEAF-KKGGLFFIDEIDASIP  194 (383)
T ss_pred             HHHHHHHHHHhCCCEEEEecChHHHhhcccccccccccchHHHHHh-hcCCEEEEeCcCcCCH
Confidence            78999999999999999885311111111   11100001122222 3578999999997643

>PRK08181 transposase; Validated

Probab=95.55  E-value=0.026  Score=37.12  Aligned_cols=60  Identities=17%  Similarity=0.268  Sum_probs=40.0

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccC-hHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAG-ESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~g-es~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |+|+.++++++   |..++.++.++++..... .......+.++..  .++.+|+|||++.+..++
T Consensus       120 THLa~Aia~~a~~~g~~v~f~~~~~L~~~l~~a~~~~~~~~~l~~l--~~~dLLIIDDlg~~~~~~  183 (269)
T PRK08181        120 SHLAAAIGLALIENGWRVLFTRTTDLVQKLQVARRELQLESAIAKL--DKFDLLILDDLAYVTKDQ  183 (269)
T ss_pred             HHHHHHHHHHHHHcCCceeeeeHHHHHHHHHHHHhCCcHHHHHHHH--hcCCEEEEeccccccCCH
Confidence            67888888654   678888999888765421 1112334445443  357899999999876543

>PRK08116 hypothetical protein; Validated

Probab=95.47  E-value=0.042  Score=35.93  Aligned_cols=55  Identities=15%  Similarity=0.359  Sum_probs=35.6

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhccc----ChHHHHHHHHHHHHHhcCCeEEEEccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLA----GESESNLRKAFEEADKNSPSIIFIDELDA   59 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~----ges~~~l~~if~~a~~~~p~iifiDEid~   59 (69)
                      |+|+.++++++   +.+++.++.++++..+.    +.+.....++++..  ....+|+|||+..
T Consensus       128 ThLa~aia~~l~~~~~~v~~~~~~~ll~~i~~~~~~~~~~~~~~~~~~l--~~~dlLviDDlg~  189 (268)
T PRK08116        128 TYLAACIANELIEKGVPVIFVNFPQLLNRIKSTYKSSGKEDENEIIRSL--VNADLLILDDLGA  189 (268)
T ss_pred             HHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHHHHhccccccHHHHHHHh--cCCCEEEEecccC
Confidence            78999999986   78999999988766432    11111222333333  2346999999954

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=95.33  E-value=0.067  Score=38.14  Aligned_cols=30  Identities=27%  Similarity=0.477  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868          33 SESNLRKAFEEADK----NSPSIIFIDELDAIAP   62 (69)
Q Consensus        33 s~~~l~~if~~a~~----~~p~iifiDEid~i~~   62 (69)
                      +...++.+.+.+..    ....|++|||+|.+..
T Consensus       109 ~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~  142 (507)
T PRK06645        109 SVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSK  142 (507)
T ss_pred             CHHHHHHHHHHHHhccccCCcEEEEEEChhhcCH
Confidence            46678888888754    2457999999998853

>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=95.31  E-value=0.0025  Score=36.97  Aligned_cols=56  Identities=18%  Similarity=0.195  Sum_probs=32.1

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhh------hhcccChHHHHHHHHHHHH---H-hcCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEI------MSKLAGESESNLRKAFEEA---D-KNSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l------~~~~~ges~~~l~~if~~a---~-~~~p~iifiDEid~i~   61 (69)
                      |.+++.+|+.++.+++.++++..      .+.|.-.   .-..-|...   + -..++++||||++..-
T Consensus        13 t~l~~~la~~~~~~~~~i~~~~~~~~~dl~g~~~~~---~~~~~~~~~~l~~a~~~~~il~lDEin~a~   78 (139)
T PF07728_consen   13 TTLARELAALLGRPVIRINCSSDTTEEDLIGSYDPS---NGQFEFKDGPLVRAMRKGGILVLDEINRAP   78 (139)
T ss_dssp             HHHHHHHHHHHTCEEEEEE-TTTSTHHHHHCEEET----TTTTCEEE-CCCTTHHEEEEEEESSCGG--
T ss_pred             HHHHHHHHHHhhcceEEEEeccccccccceeeeeec---ccccccccccccccccceeEEEECCcccCC
Confidence            78999999999999988877653      2222211   000000000   0 0158999999999653

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.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.22  E-value=0.07  Score=36.11  Aligned_cols=54  Identities=15%  Similarity=0.246  Sum_probs=34.7

Q ss_pred             hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++|+++|+++++.                        ++.+++++      ..+...++++.+.+..    ....|++|
T Consensus        52 Ttla~~la~~l~c~~~~~~~pc~~c~~c~~~~~~~~~d~~~~~~~~------~~~v~~ir~i~~~~~~~p~~~~~kviII  125 (363)
T PRK14961         52 TTIARLLAKSLNCQNGITSNPCRKCIICKEIEKGLCLDLIEIDAAS------RTKVEEMREILDNIYYSPSKSRFKVYLI  125 (363)
T ss_pred             HHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceEEecccc------cCCHHHHHHHHHHHhcCcccCCceEEEE
Confidence            78999999998742                        23333321      1234557777776542    23469999


Q ss_pred             cccccccc
Q psy3868          55 DELDAIAP   62 (69)
Q Consensus        55 DEid~i~~   62 (69)
                      ||+|.+-.
T Consensus       126 DEa~~l~~  133 (363)
T PRK14961        126 DEVHMLSR  133 (363)
T ss_pred             EChhhcCH
Confidence            99998853

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.22  E-value=0.051  Score=39.60  Aligned_cols=54  Identities=13%  Similarity=0.239  Sum_probs=35.5

Q ss_pred             hHHHHHHHHHhCC-----------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCC
Q psy3868           3 YRLTTLCRDSLGA-----------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSP   49 (69)
Q Consensus         3 T~la~aia~~~~~-----------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p   49 (69)
                      |++|+++|+.+++                             .++++++++      ..+...+|++.+.+..    .+-
T Consensus        52 TtlAr~lAk~LnC~~~~~~~~~~~~pCg~C~~C~~i~~g~h~D~~eldaas------~~~Vd~iReli~~~~~~p~~g~~  125 (618)
T PRK14951         52 TTVSRILAKSLNCQGPDGQGGITATPCGVCQACRDIDSGRFVDYTELDAAS------NRGVDEVQQLLEQAVYKPVQGRF  125 (618)
T ss_pred             HHHHHHHHHHhcCCCcccccCCCCCCCCccHHHHHHHcCCCCceeecCccc------ccCHHHHHHHHHHHHhCcccCCc
Confidence            7899999999875                             244444432      1234567777776532    224


Q ss_pred             eEEEEcccccccc
Q psy3868          50 SIIFIDELDAIAP   62 (69)
Q Consensus        50 ~iifiDEid~i~~   62 (69)
                      .|++|||+|.+..
T Consensus       126 KV~IIDEvh~Ls~  138 (618)
T PRK14951        126 KVFMIDEVHMLTN  138 (618)
T ss_pred             eEEEEEChhhCCH
Confidence            6999999999864

>PRK09183 transposase/IS protein; Provisional

Probab=95.22  E-value=0.041  Score=35.76  Aligned_cols=62  Identities=13%  Similarity=0.268  Sum_probs=40.4

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccC-hHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAG-ESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~g-es~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |+++.+++.+.   |..+..++..++...+.. .....+..+|+.. ...+.+++|||++.....+.
T Consensus       116 ThLa~al~~~a~~~G~~v~~~~~~~l~~~l~~a~~~~~~~~~~~~~-~~~~dlLiiDdlg~~~~~~~  181 (259)
T PRK09183        116 THLAIALGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRG-VMAPRLLIIDEIGYLPFSQE  181 (259)
T ss_pred             HHHHHHHHHHHHHcCCeEEEEeHHHHHHHHHHHHHCCcHHHHHHHH-hcCCCEEEEcccccCCCChH
Confidence            67888886653   677888888887644321 1122355566554 34678999999988755543

>PRK05642 DNA replication initiation factor; Validated

Probab=95.16  E-value=0.087  Score=33.62  Aligned_cols=52  Identities=17%  Similarity=0.252  Sum_probs=35.0

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |+|+++++++.   +..+++++..++...        ...+.+..+.  ..+|+|||++.+.+++
T Consensus        59 THLl~a~~~~~~~~~~~v~y~~~~~~~~~--------~~~~~~~~~~--~d~LiiDDi~~~~~~~  113 (234)
T PRK05642         59 SHLLQAACLRFEQRGEPAVYLPLAELLDR--------GPELLDNLEQ--YELVCLDDLDVIAGKA  113 (234)
T ss_pred             HHHHHHHHHHHHhCCCcEEEeeHHHHHhh--------hHHHHHhhhh--CCEEEEechhhhcCCh
Confidence            77889988754   578888988887642        1223333322  2588999999887654

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.12  E-value=0.076  Score=37.89  Aligned_cols=54  Identities=15%  Similarity=0.269  Sum_probs=35.8

Q ss_pred             hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++|+.+|+.+++.                        +++++++.      ..+...+|++.+.+..    ....|++|
T Consensus        52 Tt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d~~ei~~~~------~~~vd~ir~l~~~~~~~p~~~~~kVvII  125 (527)
T PRK14969         52 TTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDLIEVDAAS------NTQVDAMRELLDNAQYAPTRGRFKVYII  125 (527)
T ss_pred             HHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceeEeeccc------cCCHHHHHHHHHHHhhCcccCCceEEEE
Confidence            78999999998763                        23333221      1235568888877643    23569999


Q ss_pred             cccccccc
Q psy3868          55 DELDAIAP   62 (69)
Q Consensus        55 DEid~i~~   62 (69)
                      ||+|.+..
T Consensus       126 DEad~ls~  133 (527)
T PRK14969        126 DEVHMLSK  133 (527)
T ss_pred             cCcccCCH
Confidence            99998854

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.09  E-value=0.088  Score=37.90  Aligned_cols=54  Identities=13%  Similarity=0.204  Sum_probs=34.4

Q ss_pred             hHHHHHHHHHhCC------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGA------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++|+.+|+.+++                        .++++++..-    .  +...++++.+.+..    ....|++|
T Consensus        52 TTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dlieidaas~----~--gvd~ir~ii~~~~~~p~~g~~kViII  125 (546)
T PRK14957         52 TTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIEIDAASR----T--GVEETKEILDNIQYMPSQGRYKVYLI  125 (546)
T ss_pred             HHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEEeecccc----c--CHHHHHHHHHHHHhhhhcCCcEEEEE
Confidence            7899999998865                        3333433211    1  23456666666542    34679999


Q ss_pred             cccccccc
Q psy3868          55 DELDAIAP   62 (69)
Q Consensus        55 DEid~i~~   62 (69)
                      ||+|.+..
T Consensus       126 DEa~~ls~  133 (546)
T PRK14957        126 DEVHMLSK  133 (546)
T ss_pred             echhhccH
Confidence            99998854

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=95.09  E-value=0.052  Score=34.00  Aligned_cols=46  Identities=9%  Similarity=0.139  Sum_probs=31.9

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |+++++++++.   +.++..+++.++...            +..  ...+.+|+|||+|.+.+
T Consensus        56 T~La~ai~~~~~~~~~~~~~i~~~~~~~~------------~~~--~~~~~~liiDdi~~l~~  104 (227)
T PRK08903         56 SHLLQALVADASYGGRNARYLDAASPLLA------------FDF--DPEAELYAVDDVERLDD  104 (227)
T ss_pred             HHHHHHHHHHHHhCCCcEEEEehHHhHHH------------Hhh--cccCCEEEEeChhhcCc
Confidence            78899998875   568888888776321            111  23467899999998754

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=94.99  E-value=0.038  Score=41.36  Aligned_cols=58  Identities=24%  Similarity=0.301  Sum_probs=37.6

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhc-----c-------cChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSK-----L-------AGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~-----~-------~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |.+|+++|..+   +.+++.++++.+...     +       +|-.+  -..+.+..+....+|||+||||.+-+
T Consensus       609 t~lA~~La~~l~~~~~~~i~~d~s~~~~~~~~~~l~g~~~g~~g~~~--~g~l~~~v~~~p~~vlllDeieka~~  681 (852)
T TIGR03346       609 TELAKALAEFLFDDEDAMVRIDMSEYMEKHSVARLIGAPPGYVGYEE--GGQLTEAVRRKPYSVVLFDEVEKAHP  681 (852)
T ss_pred             HHHHHHHHHHhcCCCCcEEEEechhhcccchHHHhcCCCCCccCccc--ccHHHHHHHcCCCcEEEEeccccCCH
Confidence            67999999887   468898988776332     1       22111  12344444455567999999997643

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.

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=94.96  E-value=0.06  Score=30.47  Aligned_cols=28  Identities=18%  Similarity=0.271  Sum_probs=18.4

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868          34 ESNLRKAFEEADKNSPSIIFIDELDAIA   61 (69)
Q Consensus        34 ~~~l~~if~~a~~~~p~iifiDEid~i~   61 (69)
                      ....+.+.+...+....+|+|||+|.+.
T Consensus        73 ~~l~~~~~~~l~~~~~~~lviDe~~~l~  100 (131)
T PF13401_consen   73 DELRSLLIDALDRRRVVLLVIDEADHLF  100 (131)
T ss_dssp             HHHHHHHHHHHHHCTEEEEEEETTHHHH
T ss_pred             HHHHHHHHHHHHhcCCeEEEEeChHhcC
Confidence            3334444455555555699999999974

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=94.86  E-value=0.065  Score=37.48  Aligned_cols=63  Identities=16%  Similarity=0.270  Sum_probs=38.5

Q ss_pred             hHHHHHHHHHhCC-----c-EEEEchhh---------------hhhcccChHHHHHH---HHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGA-----F-FFLINGPE---------------IMSKLAGESESNLR---KAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~-----~-~~~v~~~~---------------l~~~~~ges~~~l~---~if~~a~~----~~p~iifi   54 (69)
                      |+|++.+++....     . ++.+....               +.+.+-...+..++   .+.+.|+.    .+..+||+
T Consensus       183 TTLaK~Ian~I~~nhFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~ie~Ae~~~e~G~dVlL~i  262 (416)
T PRK09376        183 TVLLQNIANSITTNHPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVIEKAKRLVEHGKDVVILL  262 (416)
T ss_pred             hHHHHHHHHHHHhhcCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEE
Confidence            6788888887743     2 22222221               33444455566655   55555543    36889999


Q ss_pred             ccccccccccc
Q psy3868          55 DELDAIAPKRE   65 (69)
Q Consensus        55 DEid~i~~~r~   65 (69)
                      ||+++++....
T Consensus       263 DsItR~arAqr  273 (416)
T PRK09376        263 DSITRLARAYN  273 (416)
T ss_pred             EChHHHHHHHH
Confidence            99999986543

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=94.81  E-value=0.18  Score=30.85  Aligned_cols=54  Identities=17%  Similarity=0.295  Sum_probs=33.5

Q ss_pred             hHHHHHHHHHhC---CcEEEEchhhhhhcccChHHHHHHHHHHHH---------------HhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLG---AFFFLINGPEIMSKLAGESESNLRKAFEEA---------------DKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~---~~~~~v~~~~l~~~~~ges~~~l~~if~~a---------------~~~~p~iifiDEid~i~~   62 (69)
                      +++|++|-+...   .||+.++|+.+-.      +..-.++|-..               .......|||||||.+-+
T Consensus        36 ~~lA~~IH~~s~r~~~pfi~vnc~~~~~------~~~e~~LFG~~~~~~~~~~~~~~G~l~~A~~GtL~Ld~I~~L~~  107 (168)
T PF00158_consen   36 ELLARAIHNNSPRKNGPFISVNCAALPE------ELLESELFGHEKGAFTGARSDKKGLLEQANGGTLFLDEIEDLPP  107 (168)
T ss_dssp             HHHHHHHHHCSTTTTS-EEEEETTTS-H------HHHHHHHHEBCSSSSTTTSSEBEHHHHHTTTSEEEEETGGGS-H
T ss_pred             HHHHHHHHHhhhcccCCeEEEehhhhhc------chhhhhhhccccccccccccccCCceeeccceEEeecchhhhHH
Confidence            467888877653   6999999988721      22223444321               122567999999999864

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.79  E-value=0.085  Score=38.59  Aligned_cols=53  Identities=13%  Similarity=0.216  Sum_probs=32.2

Q ss_pred             hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHH----hcCCeEEEE
Q psy3868           3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEAD----KNSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~----~~~p~iifi   54 (69)
                      |++|+.+|+.+.+.                        ++++++..-      .+-..+|++-+.+.    .....||+|
T Consensus        52 TtiArilAk~L~C~~~~~~~pCg~C~sC~~i~~g~hpDv~eId~a~~------~~Id~iR~L~~~~~~~p~~g~~kVIII  125 (624)
T PRK14959         52 TTIARIFAKALNCETAPTGEPCNTCEQCRKVTQGMHVDVVEIDGASN------RGIDDAKRLKEAIGYAPMEGRYKVFII  125 (624)
T ss_pred             HHHHHHHHHhccccCCCCCCCCcccHHHHHHhcCCCCceEEEecccc------cCHHHHHHHHHHHHhhhhcCCceEEEE
Confidence            67899999998763                        445544211      12233444333322    235679999


Q ss_pred             ccccccc
Q psy3868          55 DELDAIA   61 (69)
Q Consensus        55 DEid~i~   61 (69)
                      ||+|.+-
T Consensus       126 DEad~Lt  132 (624)
T PRK14959        126 DEAHMLT  132 (624)
T ss_pred             EChHhCC
Confidence            9999985

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=94.75  E-value=0.12  Score=38.30  Aligned_cols=54  Identities=19%  Similarity=0.320  Sum_probs=35.6

Q ss_pred             hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++|+++|+.++++                        +++++++      .+.+...+|++.+.++.    ....|++|
T Consensus        52 TTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~~DvlEidaA------s~~gVd~IRelle~a~~~P~~gk~KVIII  125 (709)
T PRK08691         52 TTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLLEIDAA------SNTGIDNIREVLENAQYAPTAGKYKVYII  125 (709)
T ss_pred             HHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCccceEEEecc------ccCCHHHHHHHHHHHHhhhhhCCcEEEEE
Confidence            78999999987653                        2233321      12345678888876632    24579999


Q ss_pred             cccccccc
Q psy3868          55 DELDAIAP   62 (69)
Q Consensus        55 DEid~i~~   62 (69)
                      ||+|.+..
T Consensus       126 DEad~Ls~  133 (709)
T PRK08691        126 DEVHMLSK  133 (709)
T ss_pred             ECccccCH
Confidence            99998753

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.71  E-value=0.086  Score=40.18  Aligned_cols=54  Identities=13%  Similarity=0.212  Sum_probs=34.4

Q ss_pred             hHHHHHHHHHhCCcE------------------------EEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGAFF------------------------FLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~~~------------------------~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++|+++|+.+++.-                        +++++++      -.+...+|++.+.+..    .+..|++|
T Consensus        52 TTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~DviEidAas------~~kVDdIReLie~v~~~P~~gk~KViII  125 (944)
T PRK14949         52 TSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFVDLIEVDAAS------RTKVDDTRELLDNVQYRPSRGRFKVYLI  125 (944)
T ss_pred             HHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCceEEEecccc------ccCHHHHHHHHHHHHhhhhcCCcEEEEE
Confidence            789999999998741                        2222211      0124456776665532    34579999


Q ss_pred             cccccccc
Q psy3868          55 DELDAIAP   62 (69)
Q Consensus        55 DEid~i~~   62 (69)
                      ||+|.|-.
T Consensus       126 DEAh~LT~  133 (944)
T PRK14949        126 DEVHMLSR  133 (944)
T ss_pred             echHhcCH
Confidence            99999853

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.71  E-value=0.12  Score=36.76  Aligned_cols=54  Identities=13%  Similarity=0.145  Sum_probs=37.2

Q ss_pred             hHHHHHHHHHhCC------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGA------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++|+.+|+.+++                        .++++++++-      .+...+|++.+.+..    ....|++|
T Consensus        49 TT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~eidaas~------~~vddIR~Iie~~~~~P~~~~~KVvII  122 (491)
T PRK14964         49 TTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEIDAASN------TSVDDIKVILENSCYLPISSKFKVYII  122 (491)
T ss_pred             HHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEEEEecccC------CCHHHHHHHHHHHHhccccCCceEEEE
Confidence            6788888886543                        4566666431      245678888877743    34579999


Q ss_pred             cccccccc
Q psy3868          55 DELDAIAP   62 (69)
Q Consensus        55 DEid~i~~   62 (69)
                      ||+|.+..
T Consensus       123 DEah~Ls~  130 (491)
T PRK14964        123 DEVHMLSN  130 (491)
T ss_pred             eChHhCCH
Confidence            99998853

>PRK08727 hypothetical protein; Validated

Probab=94.63  E-value=0.16  Score=32.34  Aligned_cols=53  Identities=25%  Similarity=0.270  Sum_probs=33.9

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |++++++++++   +....+++..++.        ..+.++++..  .+..+|+|||+|.+..++.
T Consensus        55 ThL~~a~~~~~~~~~~~~~y~~~~~~~--------~~~~~~~~~l--~~~dlLiIDDi~~l~~~~~  110 (233)
T PRK08727         55 THLALALCAAAEQAGRSSAYLPLQAAA--------GRLRDALEAL--EGRSLVALDGLESIAGQRE  110 (233)
T ss_pred             HHHHHHHHHHHHHcCCcEEEEeHHHhh--------hhHHHHHHHH--hcCCEEEEeCcccccCChH
Confidence            67888886654   4566666655542        2344455544  3457999999999876543

>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A

Probab=94.60  E-value=0.081  Score=34.07  Aligned_cols=52  Identities=19%  Similarity=0.292  Sum_probs=40.5

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~   61 (69)
                      |..++.+|+-+|.+++.++|++-+      ..+.+.++|.-+-. ..+-+.+||++.+-
T Consensus        46 tetik~La~~lG~~~~vfnc~~~~------~~~~l~ril~G~~~-~GaW~cfdefnrl~   97 (231)
T PF12774_consen   46 TETIKDLARALGRFVVVFNCSEQM------DYQSLSRILKGLAQ-SGAWLCFDEFNRLS   97 (231)
T ss_dssp             HHHHHHHHHCTT--EEEEETTSSS-------HHHHHHHHHHHHH-HT-EEEEETCCCSS
T ss_pred             hhHHHHHHHHhCCeEEEecccccc------cHHHHHHHHHHHhh-cCchhhhhhhhhhh
Confidence            567999999999999999998864      57889999988755 47888899999874

>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=94.55  E-value=0.046  Score=37.95  Aligned_cols=18  Identities=44%  Similarity=0.739  Sum_probs=15.3

Q ss_pred             CCeEEEEccccccccccc
Q psy3868          48 SPSIIFIDELDAIAPKRE   65 (69)
Q Consensus        48 ~p~iifiDEid~i~~~r~   65 (69)
                      +-.|+||||||.++.+.+
T Consensus       250 ~~GIvFIDEIDKIa~~~~  267 (444)
T COG1220         250 QNGIVFIDEIDKIAKRGG  267 (444)
T ss_pred             hcCeEEEehhhHHHhcCC
Confidence            458999999999998764

>KOG0743|consensus

Probab=94.52  E-value=0.093  Score=37.09  Aligned_cols=54  Identities=19%  Similarity=0.241  Sum_probs=42.5

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |+++-|+|+.++..++.++-++..    ..++  ++++.-.+  ...+||+|.+||+=+..|
T Consensus       249 SS~IaAmAn~L~ydIydLeLt~v~----~n~d--Lr~LL~~t--~~kSIivIEDIDcs~~l~  302 (457)
T KOG0743|consen  249 SSFIAAMANYLNYDIYDLELTEVK----LDSD--LRHLLLAT--PNKSILLIEDIDCSFDLR  302 (457)
T ss_pred             HHHHHHHHhhcCCceEEeeecccc----CcHH--HHHHHHhC--CCCcEEEEeecccccccc
Confidence            578889999999999999887762    2233  88988665  456999999999886533

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=94.49  E-value=0.054  Score=40.53  Aligned_cols=55  Identities=25%  Similarity=0.344  Sum_probs=38.9

Q ss_pred             hHHHHHHHHHhC---CcEEEEchhhhhhc------------ccChHHHHHHHHHHHH-HhcCCeEEEEcccccc
Q psy3868           3 YRLTTLCRDSLG---AFFFLINGPEIMSK------------LAGESESNLRKAFEEA-DKNSPSIIFIDELDAI   60 (69)
Q Consensus         3 T~la~aia~~~~---~~~~~v~~~~l~~~------------~~ges~~~l~~if~~a-~~~~p~iifiDEid~i   60 (69)
                      |-+|+++|..+.   ..++.++.|+.+.+            |+|-.+.   -.+..+ +++..|||++|||+.-
T Consensus       535 TELAkaLA~~Lfg~e~aliR~DMSEy~EkHsVSrLIGaPPGYVGyeeG---G~LTEaVRr~PySViLlDEIEKA  605 (786)
T COG0542         535 TELAKALAEALFGDEQALIRIDMSEYMEKHSVSRLIGAPPGYVGYEEG---GQLTEAVRRKPYSVILLDEIEKA  605 (786)
T ss_pred             HHHHHHHHHHhcCCCccceeechHHHHHHHHHHHHhCCCCCCceeccc---cchhHhhhcCCCeEEEechhhhc
Confidence            779999999997   89999999888542            4443331   133334 3444589999999864

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=94.45  E-value=0.14  Score=33.21  Aligned_cols=59  Identities=15%  Similarity=0.120  Sum_probs=40.4

Q ss_pred             hHHHHHHHHHhC------------------------CcEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLG------------------------AFFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~------------------------~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |.+|.++|+++.                        ..++++++++....-  -....++++-+....    ...-|++|
T Consensus        38 tt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~--i~~~~vr~~~~~~~~~~~~~~~kviii  115 (325)
T COG0470          38 TTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKID--IIVEQVRELAEFLSESPLEGGYKVVII  115 (325)
T ss_pred             HHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecccccCCCc--chHHHHHHHHHHhccCCCCCCceEEEe
Confidence            677888888887                        588999998863321  234455555554432    34689999


Q ss_pred             ccccccccc
Q psy3868          55 DELDAIAPK   63 (69)
Q Consensus        55 DEid~i~~~   63 (69)
                      ||+|.+-..
T Consensus       116 dead~mt~~  124 (325)
T COG0470         116 DEADKLTED  124 (325)
T ss_pred             CcHHHHhHH
Confidence            999998653

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=94.41  E-value=0.082  Score=33.50  Aligned_cols=60  Identities=15%  Similarity=0.282  Sum_probs=37.1

Q ss_pred             hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHH-HHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESE-SNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~-~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |+|.++++++.     +..++++++.++...+...-. ..+.++.+..  ....+|+||++|.+..+.
T Consensus        48 THLL~Ai~~~~~~~~~~~~v~y~~~~~f~~~~~~~~~~~~~~~~~~~~--~~~DlL~iDDi~~l~~~~  113 (219)
T PF00308_consen   48 THLLQAIANEAQKQHPGKRVVYLSAEEFIREFADALRDGEIEEFKDRL--RSADLLIIDDIQFLAGKQ  113 (219)
T ss_dssp             HHHHHHHHHHHHHHCTTS-EEEEEHHHHHHHHHHHHHTTSHHHHHHHH--CTSSEEEEETGGGGTTHH
T ss_pred             HHHHHHHHHHHHhccccccceeecHHHHHHHHHHHHHcccchhhhhhh--hcCCEEEEecchhhcCch
Confidence            67888888764     567888988887554332211 1122222222  256889999999997653

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=94.41  E-value=0.1  Score=39.27  Aligned_cols=29  Identities=28%  Similarity=0.394  Sum_probs=18.6

Q ss_pred             HHHHHHHHHHH----HhcCCeEEEEcccccccc
Q psy3868          34 ESNLRKAFEEA----DKNSPSIIFIDELDAIAP   62 (69)
Q Consensus        34 ~~~l~~if~~a----~~~~p~iifiDEid~i~~   62 (69)
                      ...+|++-+.+    ......|++|||+|.|..
T Consensus       102 Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~  134 (824)
T PRK07764        102 VDDARELRERAFFAPAESRYKIFIIDEAHMVTP  134 (824)
T ss_pred             HHHHHHHHHHHHhchhcCCceEEEEechhhcCH
Confidence            34455544333    234567999999999854

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.37  E-value=0.17  Score=36.84  Aligned_cols=53  Identities=19%  Similarity=0.244  Sum_probs=36.6

Q ss_pred             hHHHHHHHHHhCCc--------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEE
Q psy3868           3 YRLTTLCRDSLGAF--------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSII   52 (69)
Q Consensus         3 T~la~aia~~~~~~--------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~ii   52 (69)
                      |++|+++|+.+++.                          ++++++      ..+.+...+|++.+.+..    ....|+
T Consensus        52 ttlA~~lAk~L~c~~~~~~~~~~Cg~C~~C~~i~~g~h~D~~ei~~------~~~~~vd~IReii~~a~~~p~~~~~KVi  125 (620)
T PRK14948         52 TSSARILAKSLNCLNSDKPTPEPCGKCELCRAIAAGNALDVIEIDA------ASNTGVDNIRELIERAQFAPVQARWKVY  125 (620)
T ss_pred             HHHHHHHHHHhcCCCcCCCCCCCCcccHHHHHHhcCCCccEEEEec------cccCCHHHHHHHHHHHhhChhcCCceEE
Confidence            67899999998763                          223322      123456788999888753    234799


Q ss_pred             EEccccccc
Q psy3868          53 FIDELDAIA   61 (69)
Q Consensus        53 fiDEid~i~   61 (69)
                      +|||+|.+-
T Consensus       126 IIDEad~Lt  134 (620)
T PRK14948        126 VIDECHMLS  134 (620)
T ss_pred             EEECccccC
Confidence            999999884

>PRK12377 putative replication protein; Provisional

Probab=94.34  E-value=0.11  Score=33.83  Aligned_cols=57  Identities=19%  Similarity=0.314  Sum_probs=36.0

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChH--HHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGES--ESNLRKAFEEADKNSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges--~~~l~~if~~a~~~~p~iifiDEid~i~   61 (69)
                      |+|+.++++++   |..++.++.++++......-  .....++++..  ....+|+|||+....
T Consensus       115 ThLa~AIa~~l~~~g~~v~~i~~~~l~~~l~~~~~~~~~~~~~l~~l--~~~dLLiIDDlg~~~  176 (248)
T PRK12377        115 NHLAAAIGNRLLAKGRSVIVVTVPDVMSRLHESYDNGQSGEKFLQEL--CKVDLLVLDEIGIQR  176 (248)
T ss_pred             HHHHHHHHHHHHHcCCCeEEEEHHHHHHHHHHHHhccchHHHHHHHh--cCCCEEEEcCCCCCC
Confidence            67888888887   57788888888866432100  00111233332  467999999997654

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=94.28  E-value=0.15  Score=31.12  Aligned_cols=29  Identities=10%  Similarity=0.312  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868          34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP   62 (69)
Q Consensus        34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~   62 (69)
                      ...++++.+.+..    ....|++|||+|.+..
T Consensus        78 ~~~i~~i~~~~~~~~~~~~~kviiide~~~l~~  110 (188)
T TIGR00678        78 VDQVRELVEFLSRTPQESGRRVVIIEDAERMNE  110 (188)
T ss_pred             HHHHHHHHHHHccCcccCCeEEEEEechhhhCH
Confidence            4567777777654    4567999999999864

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.

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.26  E-value=0.098  Score=35.14  Aligned_cols=54  Identities=13%  Similarity=0.229  Sum_probs=35.2

Q ss_pred             hHHHHHHHHHhCCcE------------EEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGAFF------------FLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~~~------------~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifiDEid~i~~   62 (69)
                      |++++++++.++.+.            +.+++.      ...+...++++++.+..    ..+.+++|||+|.+..
T Consensus        53 t~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~------~~~~~~~i~~l~~~~~~~p~~~~~kiviIDE~~~l~~  122 (367)
T PRK14970         53 TTCARILARKINQPGYDDPNEDFSFNIFELDAA------SNNSVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLSS  122 (367)
T ss_pred             HHHHHHHHHHhcCCCCCCCCCCCCcceEEeccc------cCCCHHHHHHHHHHHhhccccCCcEEEEEeChhhcCH
Confidence            678888988876521            222211      12345678888887753    2457999999998754

>PRK10865 protein disaggregation chaperone; Provisional

Probab=94.19  E-value=0.12  Score=38.79  Aligned_cols=57  Identities=23%  Similarity=0.281  Sum_probs=35.3

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhc-----cc-------ChHHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSK-----LA-------GESESNLRKAFEEADKNSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~-----~~-------ges~~~l~~if~~a~~~~p~iifiDEid~i~   61 (69)
                      |.+|++++..+   +.+++.++++++...     .+       |..+.  ..+-+..+....++|||||+|.+-
T Consensus       612 T~lA~aLa~~l~~~~~~~i~id~se~~~~~~~~~LiG~~pgy~g~~~~--g~l~~~v~~~p~~vLllDEieka~  683 (857)
T PRK10865        612 TELCKALANFMFDSDDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEG--GYLTEAVRRRPYSVILLDEVEKAH  683 (857)
T ss_pred             HHHHHHHHHHhhcCCCcEEEEEhHHhhhhhhHHHHhCCCCcccccchh--HHHHHHHHhCCCCeEEEeehhhCC
Confidence            67999999887   457888988876432     11       22111  112222333344899999999764

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.15  E-value=0.18  Score=35.87  Aligned_cols=53  Identities=13%  Similarity=0.154  Sum_probs=35.1

Q ss_pred             hHHHHHHHHHhCC-----------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEEc
Q psy3868           3 YRLTTLCRDSLGA-----------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFID   55 (69)
Q Consensus         3 T~la~aia~~~~~-----------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifiD   55 (69)
                      |++|+++|+.+.+                       .++.++++.      ..+...+|++-+.+..    ..+.+++||
T Consensus        50 TTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~dv~el~~~~------~~~vd~iR~l~~~~~~~p~~~~~kVVIID  123 (504)
T PRK14963         50 TTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPDVLEIDAAS------NNSVEDVRDLREKVLLAPLRGGRKVYILD  123 (504)
T ss_pred             HHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCCCCceEEecccc------cCCHHHHHHHHHHHhhccccCCCeEEEEE
Confidence            7889999998864                       155566532      1234556776555532    357799999


Q ss_pred             cccccc
Q psy3868          56 ELDAIA   61 (69)
Q Consensus        56 Eid~i~   61 (69)
                      |+|.+.
T Consensus       124 Ead~ls  129 (504)
T PRK14963        124 EAHMMS  129 (504)
T ss_pred             CccccC
Confidence            999774

>PRK08939 primosomal protein DnaI; Reviewed

Probab=94.09  E-value=0.1  Score=34.82  Aligned_cols=56  Identities=18%  Similarity=0.370  Sum_probs=36.1

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccCh-HHHHHHHHHHHHHhcCCeEEEEcccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGE-SESNLRKAFEEADKNSPSIIFIDELDAI   60 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ge-s~~~l~~if~~a~~~~p~iifiDEid~i   60 (69)
                      |+|+.++|+++   |.++..+..++++...... ....+.+.++..  ....+|+|||+.+-
T Consensus       170 ThLa~Aia~~l~~~g~~v~~~~~~~l~~~lk~~~~~~~~~~~l~~l--~~~dlLiIDDiG~e  229 (306)
T PRK08939        170 SYLLAAIANELAKKGVSSTLLHFPEFIRELKNSISDGSVKEKIDAV--KEAPVLMLDDIGAE  229 (306)
T ss_pred             HHHHHHHHHHHHHcCCCEEEEEHHHHHHHHHHHHhcCcHHHHHHHh--cCCCEEEEecCCCc
Confidence            78889999888   6788888888875543211 011123333333  35789999999754

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=93.96  E-value=0.14  Score=33.27  Aligned_cols=51  Identities=25%  Similarity=0.481  Sum_probs=33.7

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHH-------HH-hcCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEE-------AD-KNSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~-------a~-~~~p~iifiDEid~i~   61 (69)
                      |+|+-|+++++   |.+++.++.+++++.        |+..|..       .+ -....+|+|||+-+.-
T Consensus       119 ThLa~Ai~~~l~~~g~sv~f~~~~el~~~--------Lk~~~~~~~~~~~l~~~l~~~dlLIiDDlG~~~  180 (254)
T COG1484         119 THLAIAIGNELLKAGISVLFITAPDLLSK--------LKAAFDEGRLEEKLLRELKKVDLLIIDDIGYEP  180 (254)
T ss_pred             HHHHHHHHHHHHHcCCeEEEEEHHHHHHH--------HHHHHhcCchHHHHHHHhhcCCEEEEecccCcc
Confidence            56666666666   788999999998654        3333321       11 1356899999987653

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.95  E-value=0.18  Score=36.37  Aligned_cols=54  Identities=19%  Similarity=0.299  Sum_probs=35.2

Q ss_pred             hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++|+++|+.++++                        ++++++..      ..+...++++.+.++.    ....|++|
T Consensus        52 tt~A~~lak~l~c~~~~~~~~c~~c~~c~~i~~g~~~d~~eid~~s------~~~v~~ir~l~~~~~~~p~~~~~KVvII  125 (576)
T PRK14965         52 TSTARILAKALNCEQGLTAEPCNVCPPCVEITEGRSVDVFEIDGAS------NTGVDDIRELRENVKYLPSRSRYKIFII  125 (576)
T ss_pred             HHHHHHHHHhhcCCCCCCCCCCCccHHHHHHhcCCCCCeeeeeccC------ccCHHHHHHHHHHHHhccccCCceEEEE
Confidence            67889999888653                        34444322      1235567888777642    23369999


Q ss_pred             cccccccc
Q psy3868          55 DELDAIAP   62 (69)
Q Consensus        55 DEid~i~~   62 (69)
                      ||+|.+..
T Consensus       126 dev~~Lt~  133 (576)
T PRK14965        126 DEVHMLST  133 (576)
T ss_pred             EChhhCCH
Confidence            99998854

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=93.95  E-value=0.21  Score=35.87  Aligned_cols=53  Identities=9%  Similarity=0.194  Sum_probs=36.6

Q ss_pred             hHHHHHHHHHhCC------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGA------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++|+.+|+.+++                        .+++++++      .+.+...+|++.+.+..    ....|++|
T Consensus        52 Tt~Ak~lAkal~c~~~~~~~pC~~C~~C~~i~~g~~~dv~eidaa------s~~~vd~ir~i~~~v~~~p~~~~~kViII  125 (559)
T PRK05563         52 TSAAKIFAKAVNCLNPPDGEPCNECEICKAITNGSLMDVIEIDAA------SNNGVDEIRDIRDKVKYAPSEAKYKVYII  125 (559)
T ss_pred             HHHHHHHHHHhcCCCCCCCCCCCccHHHHHHhcCCCCCeEEeecc------ccCCHHHHHHHHHHHhhCcccCCeEEEEE
Confidence            6788888888764                        34445442      23456778888887753    34579999


Q ss_pred             ccccccc
Q psy3868          55 DELDAIA   61 (69)
Q Consensus        55 DEid~i~   61 (69)
                      ||+|.+.
T Consensus       126 DE~~~Lt  132 (559)
T PRK05563        126 DEVHMLS  132 (559)
T ss_pred             ECcccCC
Confidence            9999884

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=93.66  E-value=0.1  Score=36.81  Aligned_cols=17  Identities=59%  Similarity=0.851  Sum_probs=15.1

Q ss_pred             CCeEEEEcccccccccc
Q psy3868          48 SPSIIFIDELDAIAPKR   64 (69)
Q Consensus        48 ~p~iifiDEid~i~~~r   64 (69)
                      +..||||||||.|+.+.
T Consensus       247 ~~GIVfiDEiDKIa~~~  263 (441)
T TIGR00390       247 QSGIIFIDEIDKIAKKG  263 (441)
T ss_pred             cCCEEEEEchhhhcccC
Confidence            57899999999999765

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=93.60  E-value=0.095  Score=36.97  Aligned_cols=18  Identities=44%  Similarity=0.756  Sum_probs=15.5

Q ss_pred             CCeEEEEccccccccccc
Q psy3868          48 SPSIIFIDELDAIAPKRE   65 (69)
Q Consensus        48 ~p~iifiDEid~i~~~r~   65 (69)
                      +-.||||||||.|+.+.+
T Consensus       249 ~~GIVfiDEiDKIa~~~~  266 (443)
T PRK05201        249 QNGIVFIDEIDKIAARGG  266 (443)
T ss_pred             cCCEEEEEcchhhcccCC
Confidence            568999999999998753

>PRK08084 DNA replication initiation factor; Provisional

Probab=93.60  E-value=0.13  Score=32.83  Aligned_cols=52  Identities=15%  Similarity=0.131  Sum_probs=30.0

Q ss_pred             hHHHHHHHHHhC---CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLG---AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~---~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |+++++++++..   ..+.+++......        ...++.+...+  ..+|+|||++.+.++.
T Consensus        59 ThLl~a~~~~~~~~~~~v~y~~~~~~~~--------~~~~~~~~~~~--~dlliiDdi~~~~~~~  113 (235)
T PRK08084         59 SHLLHAACAELSQRGRAVGYVPLDKRAW--------FVPEVLEGMEQ--LSLVCIDNIECIAGDE  113 (235)
T ss_pred             HHHHHHHHHHHHhCCCeEEEEEHHHHhh--------hhHHHHHHhhh--CCEEEEeChhhhcCCH
Confidence            678888887754   3455555544321        11122222222  3689999999987643

>PRK06526 transposase; Provisional

Probab=93.50  E-value=0.1  Score=33.99  Aligned_cols=60  Identities=13%  Similarity=0.178  Sum_probs=36.4

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccCh-HHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGE-SESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ge-s~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |+++.+++.++   |..+...+.++++...... ....+.+.++..  ..+.+|+|||++.+...+
T Consensus       112 ThLa~al~~~a~~~g~~v~f~t~~~l~~~l~~~~~~~~~~~~l~~l--~~~dlLIIDD~g~~~~~~  175 (254)
T PRK06526        112 THLAIGLGIRACQAGHRVLFATAAQWVARLAAAHHAGRLQAELVKL--GRYPLLIVDEVGYIPFEP  175 (254)
T ss_pred             HHHHHHHHHHHHHCCCchhhhhHHHHHHHHHHHHhcCcHHHHHHHh--ccCCEEEEcccccCCCCH
Confidence            67888887765   6677778887776543211 111222233222  357899999999876543

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

Probab=93.26  E-value=0.35  Score=31.81  Aligned_cols=47  Identities=15%  Similarity=0.248  Sum_probs=35.9

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHh-cCCeEEEEcccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADK-NSPSIIFIDELD   58 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-~~p~iifiDEid   58 (69)
                      |+++|++.++.   |+.+++|...++         ..+.++++..+. ..+-|||+|++.
T Consensus        66 SSlVkall~~y~~~GLRlIev~k~~L---------~~l~~l~~~l~~~~~kFIlf~DDLs  116 (249)
T PF05673_consen   66 SSLVKALLNEYADQGLRLIEVSKEDL---------GDLPELLDLLRDRPYKFILFCDDLS  116 (249)
T ss_pred             HHHHHHHHHHHhhcCceEEEECHHHh---------ccHHHHHHHHhcCCCCEEEEecCCC
Confidence            67899998866   689999988777         346667777653 468999999853

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=93.19  E-value=0.19  Score=33.77  Aligned_cols=53  Identities=13%  Similarity=0.169  Sum_probs=32.2

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHH-HHHHHHH---------------HhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNL-RKAFEEA---------------DKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l-~~if~~a---------------~~~~p~iifiDEid~i~~   62 (69)
                      +++|+++-...   +.||+.++|+.+-.       ..+ ..+|...               .......|||||||.+-.
T Consensus        36 ~~lAr~iH~~s~r~~~pfv~vnc~~~~~-------~~l~~~lfG~~~g~~~ga~~~~~G~~~~a~gGtL~Ldei~~L~~  107 (329)
T TIGR02974        36 ELIAARLHYLSKRWQGPLVKLNCAALSE-------NLLDSELFGHEAGAFTGAQKRHQGRFERADGGTLFLDELATASL  107 (329)
T ss_pred             HHHHHHHHHhcCccCCCeEEEeCCCCCh-------HHHHHHHhccccccccCcccccCCchhhCCCCEEEeCChHhCCH
Confidence            45777775544   46999999987622       111 1222211               112468899999998754

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=93.19  E-value=0.23  Score=34.58  Aligned_cols=41  Identities=34%  Similarity=0.431  Sum_probs=31.6

Q ss_pred             hHHHHHHHHHhC--CcEEEEchhhhhhcccChHHHHHHHHHHHH
Q psy3868           3 YRLTTLCRDSLG--AFFFLINGPEIMSKLAGESESNLRKAFEEA   44 (69)
Q Consensus         3 T~la~aia~~~~--~~~~~v~~~~l~~~~~ges~~~l~~if~~a   44 (69)
                      |.+|-++|.++|  +||..++++++.|.-+..+| .|.+.|.++
T Consensus        64 TAlA~~ia~eLG~~~PF~~isgSEiyS~e~kKTE-~L~qa~Rra  106 (398)
T PF06068_consen   64 TALAMAIAKELGEDVPFVSISGSEIYSSEVKKTE-ALTQAFRRA  106 (398)
T ss_dssp             HHHHHHHHHHCTTTS-EEEEEGGGG-BTTC-HHH-HHHHHHHCS
T ss_pred             hHHHHHHHHHhCCCCCeeEcccceeeecccCchH-HHHHHHHHh
Confidence            789999999998  89999999999998887776 455566554

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>PRK06921 hypothetical protein; Provisional

Probab=93.17  E-value=0.31  Score=31.90  Aligned_cols=54  Identities=20%  Similarity=0.220  Sum_probs=32.5

Q ss_pred             hHHHHHHHHHh----CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccc
Q psy3868           3 YRLTTLCRDSL----GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDA   59 (69)
Q Consensus         3 T~la~aia~~~----~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~   59 (69)
                      |+|+.++|+++    |..++.++..+++..... .-....+..+..  ....+|+|||++.
T Consensus       131 ThLa~aia~~l~~~~g~~v~y~~~~~l~~~l~~-~~~~~~~~~~~~--~~~dlLiIDDl~~  188 (266)
T PRK06921        131 THLLTAAANELMRKKGVPVLYFPFVEGFGDLKD-DFDLLEAKLNRM--KKVEVLFIDDLFK  188 (266)
T ss_pred             HHHHHHHHHHHhhhcCceEEEEEHHHHHHHHHH-HHHHHHHHHHHh--cCCCEEEEecccc
Confidence            67888888876    567788888776543211 111112222222  3578999999944

>PF14516 AAA_35: AAA-like domain

Probab=92.97  E-value=0.28  Score=32.88  Aligned_cols=17  Identities=35%  Similarity=0.741  Sum_probs=14.9

Q ss_pred             cCCeEEEEccccccccc
Q psy3868          47 NSPSIIFIDELDAIAPK   63 (69)
Q Consensus        47 ~~p~iifiDEid~i~~~   63 (69)
                      .+|-||+|||+|++...
T Consensus       126 ~~~lVL~iDEiD~l~~~  142 (331)
T PF14516_consen  126 DKPLVLFIDEIDRLFEY  142 (331)
T ss_pred             CCCEEEEEechhhhccC
Confidence            57999999999999863

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=92.94  E-value=0.49  Score=31.27  Aligned_cols=30  Identities=13%  Similarity=0.340  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHHHHhc----CCeEEEEcccccccc
Q psy3868          33 SESNLRKAFEEADKN----SPSIIFIDELDAIAP   62 (69)
Q Consensus        33 s~~~l~~if~~a~~~----~p~iifiDEid~i~~   62 (69)
                      +...++++++.+...    ...+++|||+|.+..
T Consensus        98 ~~~~~~~l~~~~~~~p~~~~~~vviidea~~l~~  131 (355)
T TIGR02397        98 GVDDIREILDNVKYAPSSGKYKVYIIDEVHMLSK  131 (355)
T ss_pred             CHHHHHHHHHHHhcCcccCCceEEEEeChhhcCH
Confidence            455688888877542    346999999998843

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.

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=92.90  E-value=0.69  Score=26.47  Aligned_cols=25  Identities=24%  Similarity=0.383  Sum_probs=18.7

Q ss_pred             HHHHHHHhcCCeEEEEccccccccc
Q psy3868          39 KAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus        39 ~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      .....+....|.+++|||+..+...
T Consensus        76 ~~~~~~~~~~~~~lviDe~~~~~~~  100 (165)
T cd01120          76 KAERLRERGGDDLIILDELTRLVRA  100 (165)
T ss_pred             HHHHHHhCCCCEEEEEEcHHHHHHH
Confidence            3445556678999999999988643

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>KOG1051|consensus

Probab=92.72  E-value=0.39  Score=36.61  Aligned_cols=56  Identities=14%  Similarity=0.307  Sum_probs=40.2

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhh------hhhc---ccChHHHHHHHHHHHHHhcCCeEEEEcccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPE------IMSK---LAGESESNLRKAFEEADKNSPSIIFIDELDAI   60 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~------l~~~---~~ges~~~l~~if~~a~~~~p~iifiDEid~i   60 (69)
                      |-||+++|..+   .-.++.++.++      +.+.   |+|..+-  -++.+..++..-+||||||||.-
T Consensus       605 t~lAkaLA~~~Fgse~~~IriDmse~~evskligsp~gyvG~e~g--g~LteavrrrP~sVVLfdeIEkA  672 (898)
T KOG1051|consen  605 TELAKALAEYVFGSEENFIRLDMSEFQEVSKLIGSPPGYVGKEEG--GQLTEAVKRRPYSVVLFEEIEKA  672 (898)
T ss_pred             HHHHHHHHHHHcCCccceEEechhhhhhhhhccCCCcccccchhH--HHHHHHHhcCCceEEEEechhhc
Confidence            56888998887   35788888885      2222   5666543  36777777777799999999964

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=92.70  E-value=0.15  Score=31.38  Aligned_cols=56  Identities=13%  Similarity=0.298  Sum_probs=33.4

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccCh-HHHHHHHHHHHHHhcCCeEEEEcccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGE-SESNLRKAFEEADKNSPSIIFIDELDAI   60 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ge-s~~~l~~if~~a~~~~p~iifiDEid~i   60 (69)
                      |++|.++++++   |.++..++.++++...-.. ......+.++..  ..+.+|+|||+-..
T Consensus        61 ThLa~ai~~~~~~~g~~v~f~~~~~L~~~l~~~~~~~~~~~~~~~l--~~~dlLilDDlG~~  120 (178)
T PF01695_consen   61 THLAVAIANEAIRKGYSVLFITASDLLDELKQSRSDGSYEELLKRL--KRVDLLILDDLGYE  120 (178)
T ss_dssp             HHHHHHHHHHHHHTT--EEEEEHHHHHHHHHCCHCCTTHCHHHHHH--HTSSCEEEETCTSS
T ss_pred             HHHHHHHHHHhccCCcceeEeecCceeccccccccccchhhhcCcc--ccccEeccccccee
Confidence            56777776654   7888999999987653221 111233344443  24688889998654

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>PRK06835 DNA replication protein DnaC; Validated

Probab=92.66  E-value=0.36  Score=32.63  Aligned_cols=57  Identities=16%  Similarity=0.241  Sum_probs=36.7

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccCh---HHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGE---SESNLRKAFEEADKNSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ge---s~~~l~~if~~a~~~~p~iifiDEid~i~   61 (69)
                      |+|+.++|+++   |..++.++.++++......   ........++..  ....+|+|||+....
T Consensus       197 ThLa~aIa~~l~~~g~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~~~l--~~~DLLIIDDlG~e~  259 (329)
T PRK06835        197 TFLSNCIAKELLDRGKSVIYRTADELIEILREIRFNNDKELEEVYDLL--INCDLLIIDDLGTEK  259 (329)
T ss_pred             HHHHHHHHHHHHHCCCeEEEEEHHHHHHHHHHHHhccchhHHHHHHHh--ccCCEEEEeccCCCC
Confidence            78999999887   6788999999886653211   111112223332  245899999997654

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

Probab=92.63  E-value=0.3  Score=34.66  Aligned_cols=62  Identities=8%  Similarity=0.083  Sum_probs=35.9

Q ss_pred             hHHHHHHHHHhCCc-------EEEEc----hhhhhhcccCh--H----HHHHHHHHHHHHh--cCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLGAF-------FFLIN----GPEIMSKLAGE--S----ESNLRKAFEEADK--NSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~~~-------~~~v~----~~~l~~~~~ge--s----~~~l~~if~~a~~--~~p~iifiDEid~i~~~   63 (69)
                      |++|+.+|..++..       .+.+.    ..+++.++.-.  +    ...+.++.+.|+.  ..|++|+||||+.--.+
T Consensus       208 T~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~rP~~vgy~~~~G~f~~~~~~A~~~p~~~~vliIDEINRani~  287 (459)
T PRK11331        208 TFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINRANLS  287 (459)
T ss_pred             HHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccCCCCCCeEecCchHHHHHHHHHhcccCCcEEEEehhhccCHH
Confidence            78899999887531       22222    23444333111  1    1134455566655  36899999999976544


Q ss_pred             c
Q psy3868          64 R   64 (69)
Q Consensus        64 r   64 (69)
                      +
T Consensus       288 k  288 (459)
T PRK11331        288 K  288 (459)
T ss_pred             H
Confidence            3

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=92.51  E-value=0.6  Score=32.03  Aligned_cols=63  Identities=24%  Similarity=0.403  Sum_probs=37.6

Q ss_pred             hHHHHHHHHHhCCc-----EEEEchhhh----------hh-----cccChHHH-HHHHHHHHHHh-cCCeEEEEcccccc
Q psy3868           3 YRLTTLCRDSLGAF-----FFLINGPEI----------MS-----KLAGESES-NLRKAFEEADK-NSPSIIFIDELDAI   60 (69)
Q Consensus         3 T~la~aia~~~~~~-----~~~v~~~~l----------~~-----~~~ges~~-~l~~if~~a~~-~~p~iifiDEid~i   60 (69)
                      |..++-+..++.-+     ++++||-..          ..     +..|.+.. ..+.+++.... ....||.+||+|.|
T Consensus        56 T~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L  135 (366)
T COG1474          56 TATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDAL  135 (366)
T ss_pred             hHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhh
Confidence            45566666666433     788888433          23     22333322 24444444433 46789999999999


Q ss_pred             ccccc
Q psy3868          61 APKRE   65 (69)
Q Consensus        61 ~~~r~   65 (69)
                      ..+.+
T Consensus       136 ~~~~~  140 (366)
T COG1474         136 VDKDG  140 (366)
T ss_pred             ccccc
Confidence            88753

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=92.30  E-value=0.19  Score=35.15  Aligned_cols=41  Identities=29%  Similarity=0.302  Sum_probs=34.0

Q ss_pred             hHHHHHHHHHhC--CcEEEEchhhhhhcccChHHHHHHHHHHHH
Q psy3868           3 YRLTTLCRDSLG--AFFFLINGPEIMSKLAGESESNLRKAFEEA   44 (69)
Q Consensus         3 T~la~aia~~~~--~~~~~v~~~~l~~~~~ges~~~l~~if~~a   44 (69)
                      |.||-++|.++|  .||..++++++.|.-+..+|.. .+.|..+
T Consensus        79 TAlA~gIa~eLG~dvPF~~isgsEiYS~E~kKTE~L-~qa~Rra  121 (450)
T COG1224          79 TALAMGIARELGEDVPFVAISGSEIYSLEVKKTEAL-TQALRRA  121 (450)
T ss_pred             HHHHHHHHHHhCCCCCceeeccceeeeecccHHHHH-HHHHHHh
Confidence            779999999998  8999999999999888877765 4455555

>TIGR01817 nifA Nif-specific regulatory protein

Probab=92.28  E-value=0.24  Score=35.07  Aligned_cols=53  Identities=17%  Similarity=0.257  Sum_probs=33.9

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHH-HHHHHHH---------------HhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNL-RKAFEEA---------------DKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l-~~if~~a---------------~~~~p~iifiDEid~i~~   62 (69)
                      +++|++|....   +.||+.++|+.+-.       ..+ ..+|...               .......|||||||.+-.
T Consensus       233 ~~lA~~ih~~s~r~~~pfv~i~c~~~~~-------~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~GtL~ldei~~L~~  304 (534)
T TIGR01817       233 ELIAKAIHYLSPRAKRPFVKVNCAALSE-------TLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEISP  304 (534)
T ss_pred             HHHHHHHHHhCCCCCCCeEEeecCCCCH-------HHHHHHHcCCCCCccCCCCcCCCCcccccCCCeEEEechhhCCH
Confidence            57888888775   46999999987622       111 1222211               112467899999998754

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>TIGR00602 rad24 checkpoint protein rad24

Probab=92.21  E-value=0.18  Score=37.01  Aligned_cols=60  Identities=13%  Similarity=-0.004  Sum_probs=37.1

Q ss_pred             hHHHHHHHHHhCCcEEE-Echhhhh-------------hc--ccChHHHHHHHHHHHHHh----------cCCeEEEEcc
Q psy3868           3 YRLTTLCRDSLGAFFFL-INGPEIM-------------SK--LAGESESNLRKAFEEADK----------NSPSIIFIDE   56 (69)
Q Consensus         3 T~la~aia~~~~~~~~~-v~~~~l~-------------~~--~~ges~~~l~~if~~a~~----------~~p~iifiDE   56 (69)
                      |++++.+|++++..+.+ .++....             ..  .+....+.++++...+..          ....||||||
T Consensus       124 TTl~~~la~~l~~~~~Ew~npv~~~~~~~~~~~~~s~~~~~~~~~s~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDE  203 (637)
T TIGR00602       124 STTIKILSKELGIQVQEWSNPTLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVED  203 (637)
T ss_pred             HHHHHHHHHHhhhHHHHHhhhhhhcccccccccchhhhhccccccchHHHHHHHHHHHHhhhcccccccCCceeEEEeec
Confidence            67899999998876644 3332111             00  011234556666766642          3567999999


Q ss_pred             cccccc
Q psy3868          57 LDAIAP   62 (69)
Q Consensus        57 id~i~~   62 (69)
                      +|.+..
T Consensus       204 iPn~~~  209 (637)
T TIGR00602       204 LPNQFY  209 (637)
T ss_pred             chhhch
Confidence            988764

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG0732|consensus

Probab=92.19  E-value=0.14  Score=39.58  Aligned_cols=61  Identities=26%  Similarity=0.309  Sum_probs=46.2

Q ss_pred             HHHHHHHHHh-CCcEEEEchhhhhhcc-cChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           4 RLTTLCRDSL-GAFFFLINGPEIMSKL-AGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         4 ~la~aia~~~-~~~~~~v~~~~l~~~~-~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      .+..+|-+.+ +.++....-+.+++.. .++.+..|..+|-.|++.+|||+||-.+|--....
T Consensus       607 ~lg~aIlh~~~~~~v~s~~issll~d~~~~~~~~~iv~i~~eaR~~~psi~~ip~~d~w~~~~  669 (1080)
T KOG0732|consen  607 YLGPAILHRLEGLPVQSLDISSLLSDEGTEDLEEEIVHIFMEARKTTPSIVFIPNVDEWARVI  669 (1080)
T ss_pred             cccHHHHHHHhccchHHHHHHHHHhccccccHHHHHHHHHHHHhccCCceeeccchhhhhhcC
Confidence            3445555555 4677777777777765 77788999999999999999999999888665443

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=92.16  E-value=0.38  Score=33.65  Aligned_cols=60  Identities=17%  Similarity=0.216  Sum_probs=41.4

Q ss_pred             hHHHHHHHHHhC-----CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLG-----AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~-----~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |+|.+|++++..     ..+++++..+++..++-.--.+=-+-|+.-.  .-.+++||+++.+.++.
T Consensus       127 THLl~Aign~~~~~~~~a~v~y~~se~f~~~~v~a~~~~~~~~Fk~~y--~~dlllIDDiq~l~gk~  191 (408)
T COG0593         127 THLLQAIGNEALANGPNARVVYLTSEDFTNDFVKALRDNEMEKFKEKY--SLDLLLIDDIQFLAGKE  191 (408)
T ss_pred             HHHHHHHHHHHHhhCCCceEEeccHHHHHHHHHHHHHhhhHHHHHHhh--ccCeeeechHhHhcCCh
Confidence            788898888873     4688888888866655443332223344433  45789999999998874

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.09  E-value=0.6  Score=33.15  Aligned_cols=28  Identities=14%  Similarity=0.228  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEccccccc
Q psy3868          34 ESNLRKAFEEADK----NSPSIIFIDELDAIA   61 (69)
Q Consensus        34 ~~~l~~if~~a~~----~~p~iifiDEid~i~   61 (69)
                      ...+|.+-+.+..    ..+.|++|||+|.+.
T Consensus       101 vd~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt  132 (486)
T PRK14953        101 IDDIRALRDAVSYTPIKGKYKVYIIDEAHMLT  132 (486)
T ss_pred             HHHHHHHHHHHHhCcccCCeeEEEEEChhhcC
Confidence            4456666665543    345799999999884

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=91.82  E-value=0.67  Score=33.98  Aligned_cols=53  Identities=8%  Similarity=0.208  Sum_probs=34.1

Q ss_pred             hHHHHHHHHHhCC------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHhc----CCeEEEE
Q psy3868           3 YRLTTLCRDSLGA------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADKN----SPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~----~p~iifi   54 (69)
                      |++|+++|+.+.+                        .+++++++.      ..+...+|++.+.+...    ...|++|
T Consensus        52 TTlA~~lAk~L~C~~~~~~~~Cg~C~sCr~i~~~~h~DiieIdaas------~igVd~IReIi~~~~~~P~~~~~KVIII  125 (605)
T PRK05896         52 TSIAKIFAKAINCLNPKDGDCCNSCSVCESINTNQSVDIVELDAAS------NNGVDEIRNIIDNINYLPTTFKYKVYII  125 (605)
T ss_pred             HHHHHHHHHHhcCCCCCCCCCCcccHHHHHHHcCCCCceEEecccc------ccCHHHHHHHHHHHHhchhhCCcEEEEE
Confidence            6788888888753                        334444322      12345678877766432    3469999


Q ss_pred             ccccccc
Q psy3868          55 DELDAIA   61 (69)
Q Consensus        55 DEid~i~   61 (69)
                      ||+|.+-
T Consensus       126 DEad~Lt  132 (605)
T PRK05896        126 DEAHMLS  132 (605)
T ss_pred             echHhCC
Confidence            9999874

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.61  E-value=0.75  Score=31.57  Aligned_cols=29  Identities=17%  Similarity=0.225  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868          34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP   62 (69)
Q Consensus        34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~   62 (69)
                      ...++++-+.+..    ....+++|||+|.+..
T Consensus       109 id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~  141 (397)
T PRK14955        109 VDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSI  141 (397)
T ss_pred             HHHHHHHHHHHhhchhcCCeEEEEEeChhhCCH
Confidence            4567776655532    2346999999998853

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.61  E-value=0.62  Score=33.91  Aligned_cols=29  Identities=17%  Similarity=0.197  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868          34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP   62 (69)
Q Consensus        34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~   62 (69)
                      ...+|++-+.+..    ....|++|||+|.+-.
T Consensus       100 vd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~  132 (584)
T PRK14952        100 VDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTT  132 (584)
T ss_pred             HHHHHHHHHHHHhhhhcCCceEEEEECCCcCCH
Confidence            4556666555432    3456999999998853

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=91.55  E-value=0.32  Score=35.01  Aligned_cols=57  Identities=21%  Similarity=0.218  Sum_probs=32.9

Q ss_pred             hHHHHHHHHH-----------hCCcEEEEchhhhhhc-----ccChHHH--------HHHHHHHHHHhcCCeEEEEcccc
Q psy3868           3 YRLTTLCRDS-----------LGAFFFLINGPEIMSK-----LAGESES--------NLRKAFEEADKNSPSIIFIDELD   58 (69)
Q Consensus         3 T~la~aia~~-----------~~~~~~~v~~~~l~~~-----~~ges~~--------~l~~if~~a~~~~p~iifiDEid   58 (69)
                      +++|+++-+.           .+.||+.+||+.+-..     .+|..+.        .-.-+|+.|   ....||+|||+
T Consensus       256 e~~A~~IH~~~~~~~~~~S~r~~~pfv~inCaal~e~lleseLFG~~~gaftga~~~~~~Gl~e~A---~gGTLfLdeI~  332 (538)
T PRK15424        256 ELAAQAIHREYFARHDARQGKKSHPFVAVNCGAIAESLLEAELFGYEEGAFTGSRRGGRAGLFEIA---HGGTLFLDEIG  332 (538)
T ss_pred             HHHHHHHHHhhcccccccCccCCCCeEEeecccCChhhHHHHhcCCccccccCccccccCCchhcc---CCCEEEEcChH
Confidence            4678887665           4579999999876321     1111000        000123332   35689999999


Q ss_pred             cccc
Q psy3868          59 AIAP   62 (69)
Q Consensus        59 ~i~~   62 (69)
                      .+-.
T Consensus       333 ~Lp~  336 (538)
T PRK15424        333 EMPL  336 (538)
T ss_pred             hCCH
Confidence            8754

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=91.35  E-value=0.77  Score=33.21  Aligned_cols=29  Identities=21%  Similarity=0.256  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868          34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP   62 (69)
Q Consensus        34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~   62 (69)
                      ...++++.+.+..    ....|++|||+|.+-.
T Consensus       101 vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~  133 (563)
T PRK06647        101 VQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSN  133 (563)
T ss_pred             HHHHHHHHHHHHhchhcCCCEEEEEEChhhcCH
Confidence            4566776655432    3567999999998853

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=91.33  E-value=0.4  Score=33.89  Aligned_cols=57  Identities=19%  Similarity=0.250  Sum_probs=33.6

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhc-----ccChHH-------HHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSK-----LAGESE-------SNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~-----~~ges~-------~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      +++|+++-...   +.||+.++|+.+-..     .+|...       ..-.-.|+.|   ....|||||||.+..
T Consensus       224 ~~~A~~ih~~s~r~~~p~v~v~c~~~~~~~~e~~lfG~~~g~~~ga~~~~~g~~~~a---~gGtL~ldeI~~L~~  295 (509)
T PRK05022        224 ELVARAIHAASPRADKPLVYLNCAALPESLAESELFGHVKGAFTGAISNRSGKFELA---DGGTLFLDEIGELPL  295 (509)
T ss_pred             HHHHHHHHHhCCcCCCCeEEEEcccCChHHHHHHhcCccccccCCCcccCCcchhhc---CCCEEEecChhhCCH
Confidence            56888887764   479999999877321     111100       0000123222   356799999999864

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=91.22  E-value=0.81  Score=33.37  Aligned_cols=29  Identities=17%  Similarity=0.334  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868          34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP   62 (69)
Q Consensus        34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~   62 (69)
                      ...||++.+.++.    ....|++|||+|.+..
T Consensus       114 vd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~  146 (598)
T PRK09111        114 VDDIREIIESVRYRPVSARYKVYIIDEVHMLST  146 (598)
T ss_pred             HHHHHHHHHHHHhchhcCCcEEEEEEChHhCCH
Confidence            4568888887753    2457999999999853

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=91.14  E-value=1  Score=29.22  Aligned_cols=54  Identities=20%  Similarity=0.266  Sum_probs=30.8

Q ss_pred             hHHHHHHHHHhC-----CcEEEEchhhhhhcccChHHHHHHHHHHHHHh------cCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLG-----AFFFLINGPEIMSKLAGESESNLRKAFEEADK------NSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~-----~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~------~~p~iifiDEid~i~~   62 (69)
                      |++++++++++.     .+++.+++++-      .....+++.+.....      ..+.+|+|||+|.+..
T Consensus        52 t~~~~~l~~~l~~~~~~~~~i~~~~~~~------~~~~~~~~~i~~~~~~~~~~~~~~~vviiDe~~~l~~  116 (319)
T PRK00440         52 TTAALALARELYGEDWRENFLELNASDE------RGIDVIRNKIKEFARTAPVGGAPFKIIFLDEADNLTS  116 (319)
T ss_pred             HHHHHHHHHHHcCCccccceEEeccccc------cchHHHHHHHHHHHhcCCCCCCCceEEEEeCcccCCH
Confidence            678889988873     34566655432      111223333222211      2356999999998854

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=91.03  E-value=0.87  Score=33.19  Aligned_cols=23  Identities=17%  Similarity=0.274  Sum_probs=17.3

Q ss_pred             hHHHHHHHHHh----------CCcEEEEchhhh
Q psy3868           3 YRLTTLCRDSL----------GAFFFLINGPEI   25 (69)
Q Consensus         3 T~la~aia~~~----------~~~~~~v~~~~l   25 (69)
                      |++|+++.+..          +.+|+.+++..+
T Consensus       189 TTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l  221 (615)
T TIGR02903       189 TTAARLALEEAKKLKHTPFAEDAPFVEVDGTTL  221 (615)
T ss_pred             HHHHHHHHHhhhhccCCcccCCCCeEEEechhc
Confidence            67888887655          357899988765

Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.

>PRK08118 topology modulation protein; Reviewed

Probab=90.73  E-value=1  Score=27.34  Aligned_cols=42  Identities=10%  Similarity=0.001  Sum_probs=28.6

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHH
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEA   44 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a   44 (69)
                      |++|+.+++.++.+++.++.--....|...+...+.++.+..
T Consensus        15 STlak~L~~~l~~~~~~lD~l~~~~~w~~~~~~~~~~~~~~~   56 (167)
T PRK08118         15 STLARQLGEKLNIPVHHLDALFWKPNWEGVPKEEQITVQNEL   56 (167)
T ss_pred             HHHHHHHHHHhCCCceecchhhcccCCcCCCHHHHHHHHHHH
Confidence            789999999999999888764433345555554555554443

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=90.66  E-value=0.35  Score=34.94  Aligned_cols=53  Identities=8%  Similarity=0.183  Sum_probs=33.7

Q ss_pred             hHHHHHHHHHhC---CcEEEEchhhhhhcccChHHHH-HHHHHHHH------------HhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLG---AFFFLINGPEIMSKLAGESESN-LRKAFEEA------------DKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~---~~~~~v~~~~l~~~~~ges~~~-l~~if~~a------------~~~~p~iifiDEid~i~~   62 (69)
                      +++|+++-+...   .||+.+||..+-       +.. -.++|...            .......|||||||.+-.
T Consensus       362 ~~~A~~ih~~s~r~~~pfv~vnc~~~~-------~~~~~~elfg~~~~~~~~~~~g~~~~a~~GtL~ldei~~l~~  430 (638)
T PRK11388        362 ALLAQAIHNESERAAGPYIAVNCQLYP-------DEALAEEFLGSDRTDSENGRLSKFELAHGGTLFLEKVEYLSP  430 (638)
T ss_pred             HHHHHHHHHhCCccCCCeEEEECCCCC-------hHHHHHHhcCCCCcCccCCCCCceeECCCCEEEEcChhhCCH
Confidence            468898877654   699999997762       111 12333211            112467899999998754

>KOG1051|consensus

Probab=90.45  E-value=1.3  Score=33.95  Aligned_cols=51  Identities=20%  Similarity=0.322  Sum_probs=39.8

Q ss_pred             CcEEEEchhhhh--hcccChHHHHHHHHHHHHH-hcCCeEEEEccccccccccc
Q psy3868          15 AFFFLINGPEIM--SKLAGESESNLRKAFEEAD-KNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus        15 ~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~-~~~p~iifiDEid~i~~~r~   65 (69)
                      ..++.++-..+.  .++-|+-+.+++.+-+.+. .....|||+||++-+.+...
T Consensus       244 ~~l~~l~~g~l~aGa~~rge~E~rlk~l~k~v~~~~~gvILfigelh~lvg~g~  297 (898)
T KOG1051|consen  244 KKLIALDFGSLVAGAKRRGEFEERLKELLKEVESGGGGVILFLGELHWLVGSGS  297 (898)
T ss_pred             cceEEEEhhhcccCcccchHHHHHHHHHHHHHhcCCCcEEEEecceeeeecCCC
Confidence            455666665444  4588999999999999988 45788999999999977654

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

Probab=90.06  E-value=1.7  Score=29.03  Aligned_cols=46  Identities=17%  Similarity=0.229  Sum_probs=35.6

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHh-cCCeEEEEccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADK-NSPSIIFIDEL   57 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-~~p~iifiDEi   57 (69)
                      ++++||+-++.   +..+++|+..++.         .+-.+++..+. ..+-|||+|+.
T Consensus        99 SSLVKA~~~e~~~~glrLVEV~k~dl~---------~Lp~l~~~Lr~~~~kFIlFcDDL  148 (287)
T COG2607          99 SSLVKALLNEYADEGLRLVEVDKEDLA---------TLPDLVELLRARPEKFILFCDDL  148 (287)
T ss_pred             HHHHHHHHHHHHhcCCeEEEEcHHHHh---------hHHHHHHHHhcCCceEEEEecCC
Confidence            57889888877   4789999998873         45667777765 46789999985

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=89.93  E-value=0.27  Score=33.47  Aligned_cols=53  Identities=19%  Similarity=0.253  Sum_probs=32.4

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHH-HHHHHH---------------HhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLR-KAFEEA---------------DKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~-~if~~a---------------~~~~p~iifiDEid~i~~   62 (69)
                      +.+|+++-...   +.||+.++|+.+..       ..+. .+|...               ....+..|||||||.+.+
T Consensus       176 ~~~a~~ih~~s~~~~~~~i~~~c~~~~~-------~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ldei~~l~~  247 (441)
T PRK10365        176 ELVARAIHASSARSEKPLVTLNCAALNE-------SLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISP  247 (441)
T ss_pred             HHHHHHHHHcCCCCCCCeeeeeCCCCCH-------HHHHHHhcCCCCCCcCCCCcCCCCceeECCCCEEEEeccccCCH
Confidence            35677775443   47999999987632       2222 223211               122467899999999865

>KOG0989|consensus

Probab=89.75  E-value=0.36  Score=33.04  Aligned_cols=60  Identities=17%  Similarity=0.141  Sum_probs=33.8

Q ss_pred             hHHHHHHHHHhCC------cEEEEchhhhhhcccCh-HHHHHHHHHHHHH-----hcCC-eEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGA------FFFLINGPEIMSKLAGE-SESNLRKAFEEAD-----KNSP-SIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~------~~~~v~~~~l~~~~~ge-s~~~l~~if~~a~-----~~~p-~iifiDEid~i~~   62 (69)
                      |+.++++|.++..      .+...++++-.+.-++. .-++-.++-..-.     .+.| -|+.+||+|++..
T Consensus        71 TStalafar~L~~~~~~~~rvl~lnaSderGisvvr~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmts  143 (346)
T KOG0989|consen   71 TSTALAFARALNCEQLFPCRVLELNASDERGISVVREKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTS  143 (346)
T ss_pred             hHHHHHHHHHhcCccccccchhhhcccccccccchhhhhcCHHHHhhccccccCCCCCcceEEEEechhhhhH
Confidence            7789999999876      34455666654433222 2222222211111     1223 7999999999865

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=89.56  E-value=0.71  Score=33.14  Aligned_cols=57  Identities=21%  Similarity=0.211  Sum_probs=32.8

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhc-----ccChHH--------HHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSK-----LAGESE--------SNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~-----~~ges~--------~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      +++|+++-+..   +.||+.+||..+-..     ..|..+        ..-.-+|+.|   ....||+||||.+-.
T Consensus       249 e~lA~~IH~~S~r~~~pfv~inC~~l~e~lleseLFG~~~gaftga~~~~~~Gl~e~A---~gGTLfLdeI~~Lp~  321 (526)
T TIGR02329       249 ELVAQAIHQLSGRRDFPFVAINCGAIAESLLEAELFGYEEGAFTGARRGGRTGLIEAA---HRGTLFLDEIGEMPL  321 (526)
T ss_pred             HHHHHHHHHhcCcCCCCEEEeccccCChhHHHHHhcCCcccccccccccccccchhhc---CCceEEecChHhCCH
Confidence            46788876554   469999999876221     111000        0001122222   356799999998854

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=89.10  E-value=1.6  Score=32.76  Aligned_cols=59  Identities=14%  Similarity=0.213  Sum_probs=35.0

Q ss_pred             hHHHHHHHHHhCCcEEE---Echhhhh------------hcccChHHHHHHHHHHHHHh----cCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFL---INGPEIM------------SKLAGESESNLRKAFEEADK----NSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~~~~~~~---v~~~~l~------------~~~~ges~~~l~~if~~a~~----~~p~iifiDEid~i~   61 (69)
                      |++|+++|+.+.++-..   -.|..+.            ......+...+|++.+.+..    ....|++|||+|.+-
T Consensus        54 Tt~AriLAk~LnC~~~~~~~~pC~~C~~~~~~~~Dvieidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT  131 (725)
T PRK07133         54 TSVAKIFANALNCSHKTDLLEPCQECIENVNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLS  131 (725)
T ss_pred             HHHHHHHHHHhcccccCCCCCchhHHHHhhcCCCcEEEEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCC
Confidence            67899999988763210   0111110            00001235668888887754    345799999999875

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=88.76  E-value=0.47  Score=33.72  Aligned_cols=51  Identities=18%  Similarity=0.318  Sum_probs=33.4

Q ss_pred             HHHHHHHHHhC---CcEEEEchhhhhhcccChHHHHHHH-HHHHHH---------------hcCCeEEEEccccccc
Q psy3868           4 RLTTLCRDSLG---AFFFLINGPEIMSKLAGESESNLRK-AFEEAD---------------KNSPSIIFIDELDAIA   61 (69)
Q Consensus         4 ~la~aia~~~~---~~~~~v~~~~l~~~~~ges~~~l~~-if~~a~---------------~~~p~iifiDEid~i~   61 (69)
                      ++|++|=....   .||+.+||..+       .+..+.. +|-..+               ......||+|||..+.
T Consensus       179 lvAr~IH~~S~R~~~PFVavNcaAi-------p~~l~ESELFGhekGAFTGA~~~r~G~fE~A~GGTLfLDEI~~mp  248 (464)
T COG2204         179 LVARAIHQASPRAKGPFIAVNCAAI-------PENLLESELFGHEKGAFTGAITRRIGRFEQANGGTLFLDEIGEMP  248 (464)
T ss_pred             HHHHHHHhhCcccCCCceeeecccC-------CHHHHHHHhhcccccCcCCcccccCcceeEcCCceEEeeccccCC
Confidence            45666655543   59999999877       4444444 554322               1246789999998764

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=88.54  E-value=2.1  Score=27.87  Aligned_cols=18  Identities=17%  Similarity=0.370  Sum_probs=14.7

Q ss_pred             cCCeEEEEcccccccccc
Q psy3868          47 NSPSIIFIDELDAIAPKR   64 (69)
Q Consensus        47 ~~p~iifiDEid~i~~~r   64 (69)
                      .++.++|+||+.++...-
T Consensus       102 G~~vll~iDei~r~a~a~  119 (249)
T cd01128         102 GKDVVILLDSITRLARAY  119 (249)
T ss_pred             CCCEEEEEECHHHhhhhh
Confidence            468999999999987543

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>cd00338 Ser_Recombinase Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain

Probab=88.32  E-value=1.7  Score=24.71  Aligned_cols=58  Identities=9%  Similarity=0.062  Sum_probs=35.8

Q ss_pred             HHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           7 TLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         7 ~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      +..|...|+.+..+-...-.+.+....-..+.++.+.++.....+|++.++|.|++.-
T Consensus        24 ~~~a~~~g~~i~~~~~d~~~s~~~~~~R~~~~~ll~~~~~~~~d~ivv~~~~Rl~R~~   81 (137)
T cd00338          24 REYAARNGLEVVGEYEDAGSSATSLVDRPGLQRLLADVKAGKIDVVLVEKLDRLSRNL   81 (137)
T ss_pred             HHHHHHCCCEEEEEEEeCCCCcccccCCHHHHHHHHHHHcCCCCEEEEEecchhhCCH
Confidence            3445555665433222111122212335568888888887788999999999998754

These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are protei

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=88.31  E-value=1.2  Score=31.75  Aligned_cols=57  Identities=23%  Similarity=0.367  Sum_probs=32.6

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhc-----ccChHH-------HHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSK-----LAGESE-------SNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~-----~~ges~-------~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      +++|+++-...   +.||+.++|+.+-..     .+|...       ..-..+|+.|   ....|||||||.+.+
T Consensus       241 ~~lA~aiH~~s~r~~~pfv~inca~~~~~~~e~elFG~~~~~~~~~~~~~~g~~e~a---~~GtL~LdeI~~L~~  312 (520)
T PRK10820        241 DLLAYACHLRSPRGKKPFLALNCASIPDDVVESELFGHAPGAYPNALEGKKGFFEQA---NGGSVLLDEIGEMSP  312 (520)
T ss_pred             HHHHHHHHHhCCCCCCCeEEeccccCCHHHHHHHhcCCCCCCcCCcccCCCChhhhc---CCCEEEEeChhhCCH
Confidence            46788875443   369999999876321     111100       0001123332   357789999998864

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=88.31  E-value=0.85  Score=33.38  Aligned_cols=56  Identities=20%  Similarity=0.249  Sum_probs=34.6

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhc-----ccCh--------HHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSK-----LAGE--------SESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~-----~~ge--------s~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++|+++-...   +.||+.++|..+-..     ++|.        ..+.. ..|+.+   ....|||||||.+-.
T Consensus       413 ~~lA~~ih~~s~r~~~~~v~i~c~~~~~~~~~~~lfg~~~~~~~g~~~~~~-g~le~a---~~GtL~Ldei~~L~~  484 (686)
T PRK15429        413 ELIARAIHNLSGRNNRRMVKMNCAAMPAGLLESDLFGHERGAFTGASAQRI-GRFELA---DKSSLFLDEVGDMPL  484 (686)
T ss_pred             HHHHHHHHHhcCCCCCCeEEEecccCChhHhhhhhcCcccccccccccchh-hHHHhc---CCCeEEEechhhCCH
Confidence            57889887754   469999999875321     2221        11111 123333   467899999998754

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=88.21  E-value=0.64  Score=28.29  Aligned_cols=29  Identities=38%  Similarity=0.472  Sum_probs=21.4

Q ss_pred             HHHHHHHHHHHHHhc-CCeEEEEccccccc
Q psy3868          33 SESNLRKAFEEADKN-SPSIIFIDELDAIA   61 (69)
Q Consensus        33 s~~~l~~if~~a~~~-~p~iifiDEid~i~   61 (69)
                      ....+.++++...+. .+.+|+|||++.+.
T Consensus       102 ~~~~l~~~~~~l~~~~~~~iiviDe~~~~~  131 (234)
T PF01637_consen  102 SFSALERLLEKLKKKGKKVIIVIDEFQYLA  131 (234)
T ss_dssp             -G--HHHHHHHHHHCHCCEEEEEETGGGGG
T ss_pred             HHHHHHHHHHHHHhcCCcEEEEEecHHHHh
Confidence            456678888887664 35999999999998

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=87.98  E-value=1.9  Score=31.19  Aligned_cols=29  Identities=17%  Similarity=0.290  Sum_probs=19.1

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868          34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP   62 (69)
Q Consensus        34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~   62 (69)
                      ...+|++-+.+..    ....|++|||+|.+..
T Consensus       102 vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~  134 (585)
T PRK14950        102 VDDAREIIERVQFRPALARYKVYIIDEVHMLST  134 (585)
T ss_pred             HHHHHHHHHHHhhCcccCCeEEEEEeChHhCCH
Confidence            4456666555432    2457999999998853

>PRK11823 DNA repair protein RadA; Provisional

Probab=87.71  E-value=1.8  Score=30.41  Aligned_cols=28  Identities=18%  Similarity=0.482  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868          36 NLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus        36 ~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      .+.++++..++.+|.+|+||++..+...
T Consensus       144 ~l~~i~~~i~~~~~~lVVIDSIq~l~~~  171 (446)
T PRK11823        144 NLEAILATIEEEKPDLVVIDSIQTMYSP  171 (446)
T ss_pred             CHHHHHHHHHhhCCCEEEEechhhhccc
Confidence            4667777777789999999999988753

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=87.63  E-value=1.2  Score=29.83  Aligned_cols=57  Identities=18%  Similarity=0.206  Sum_probs=32.2

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhh-----cccChHH-------HHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMS-----KLAGESE-------SNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~-----~~~ges~-------~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      +++|+++-...   +.||+.++|..+-.     .++|...       ..-...|+.   .....|||||||.+..
T Consensus        43 ~~lA~~iH~~s~r~~~pfv~v~c~~~~~~~~~~~lfg~~~~~~~g~~~~~~g~l~~---a~gGtL~l~~i~~L~~  114 (326)
T PRK11608         43 ELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGAFTGAQKRHPGRFER---ADGGTLFLDELATAPM  114 (326)
T ss_pred             HHHHHHHHHhCCccCCCeEEEeCCCCCHHHHHHHHccccccccCCcccccCCchhc---cCCCeEEeCChhhCCH
Confidence            46777775544   36999999987621     1112110       000112222   2457899999999864

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=87.19  E-value=0.68  Score=33.12  Aligned_cols=15  Identities=33%  Similarity=0.806  Sum_probs=12.5

Q ss_pred             CCeEEEEcccccccc
Q psy3868          48 SPSIIFIDELDAIAP   62 (69)
Q Consensus        48 ~p~iifiDEid~i~~   62 (69)
                      ...+|||||||.+-+
T Consensus       175 ~gG~L~IdEI~~L~~  189 (531)
T TIGR02902       175 HGGVLFIDEIGELHP  189 (531)
T ss_pred             CCcEEEEechhhCCH
Confidence            457999999998864

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.

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=86.91  E-value=0.53  Score=29.05  Aligned_cols=19  Identities=37%  Similarity=0.477  Sum_probs=13.9

Q ss_pred             CCeEEEEcccccccccccc
Q psy3868          48 SPSIIFIDELDAIAPKREK   66 (69)
Q Consensus        48 ~p~iifiDEid~i~~~r~~   66 (69)
                      ..++|+|||+..+++.|..
T Consensus        79 ~~~liviDEa~~~~~~r~~   97 (193)
T PF05707_consen   79 KGSLIVIDEAQNFFPSRSW   97 (193)
T ss_dssp             TT-EEEETTGGGTSB---T
T ss_pred             CCcEEEEECChhhcCCCcc
Confidence            6899999999999998876

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.69  E-value=2.7  Score=30.89  Aligned_cols=29  Identities=17%  Similarity=0.297  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868          34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP   62 (69)
Q Consensus        34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~   62 (69)
                      ...|+.+-+.+..    ....|++|||+|.+..
T Consensus       109 vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~  141 (620)
T PRK14954        109 VDDIRQLRENVRYGPQKGRYRVYIIDEVHMLST  141 (620)
T ss_pred             HHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCH
Confidence            4566666555522    3456999999998853

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=86.07  E-value=2  Score=30.53  Aligned_cols=63  Identities=19%  Similarity=0.380  Sum_probs=42.7

Q ss_pred             hhHHHHHHHHHh-CCcEEEEchhhhhhcc------cC--------hHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           2 SYRLTTLCRDSL-GAFFFLINGPEIMSKL------AG--------ESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         2 ~T~la~aia~~~-~~~~~~v~~~~l~~~~------~g--------es~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      ||+|-+..++-. ..++++|++.+-...+      .|        -.|.++..+.+...+.+|.+++||-|-.+....
T Consensus       107 STLLLQva~~lA~~~~vLYVsGEES~~QiklRA~RL~~~~~~l~l~aEt~~e~I~~~l~~~~p~lvVIDSIQT~~s~~  184 (456)
T COG1066         107 STLLLQVAARLAKRGKVLYVSGEESLQQIKLRADRLGLPTNNLYLLAETNLEDIIAELEQEKPDLVVIDSIQTLYSEE  184 (456)
T ss_pred             HHHHHHHHHHHHhcCcEEEEeCCcCHHHHHHHHHHhCCCccceEEehhcCHHHHHHHHHhcCCCEEEEeccceeeccc
Confidence            566655444433 1278888775433222      12        156778999999999999999999998887654

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=85.96  E-value=2.6  Score=29.64  Aligned_cols=16  Identities=25%  Similarity=0.389  Sum_probs=13.1

Q ss_pred             cCCeEEEEcccccccc
Q psy3868          47 NSPSIIFIDELDAIAP   62 (69)
Q Consensus        47 ~~p~iifiDEid~i~~   62 (69)
                      ....|++|||+|.+..
T Consensus       120 ~~~kvvIIdead~lt~  135 (451)
T PRK06305        120 SRYKIYIIDEVHMLTK  135 (451)
T ss_pred             CCCEEEEEecHHhhCH
Confidence            4578999999998853

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=85.76  E-value=1.1  Score=30.79  Aligned_cols=54  Identities=15%  Similarity=0.207  Sum_probs=32.4

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHH---------------HHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEE---------------ADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~---------------a~~~~p~iifiDEid~i~~   62 (69)
                      +++|+++....   +.||+.++|..+-..+.      -..+|..               .....+..|||||||.+-.
T Consensus       171 ~~~A~~ih~~~~~~~~~~~~~~c~~~~~~~~------~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~ei~~l~~  242 (463)
T TIGR01818       171 ELVARALHRHSPRANGPFIALNMAAIPKDLI------ESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDMPL  242 (463)
T ss_pred             HHHHHHHHHhCCCCCCCeEEEeCCCCCHHHH------HHHhcCCCCCCCCCcccCCCCcEEECCCCeEEEEchhhCCH
Confidence            46777776654   46999999977622111      1112221               1122467899999998764

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>PF13304 AAA_21: AAA domain; PDB: 3QKS_B 1US8_B 1F2U_B 1F2T_B 3QKT_A 1II8_B 3QKR_B 3QKU_A

Probab=85.64  E-value=1.5  Score=26.14  Aligned_cols=31  Identities=23%  Similarity=0.208  Sum_probs=20.7

Q ss_pred             cChHHHHHHHHHHHHHhcCC--eEEEEcccccc
Q psy3868          30 AGESESNLRKAFEEADKNSP--SIIFIDELDAI   60 (69)
Q Consensus        30 ~ges~~~l~~if~~a~~~~p--~iifiDEid~i   60 (69)
                      .|.+++++-.++.......+  .+++|||.|.-
T Consensus       237 ~S~G~~~~l~l~~~l~~~~~~~~illiDEpE~~  269 (303)
T PF13304_consen  237 LSSGEKRLLSLLSLLLSAKKNGSILLIDEPENH  269 (303)
T ss_dssp             --HHHHHHHHHHHHHHTTTTT-SEEEEESSSTT
T ss_pred             CCHHHHHHHHHHHHHhCcCCCCeEEEecCCcCC
Confidence            37778887566666554433  99999999864

>KOG1942|consensus

Probab=85.54  E-value=0.58  Score=32.31  Aligned_cols=38  Identities=32%  Similarity=0.546  Sum_probs=22.3

Q ss_pred             hhhhhcccChHHHHHHHHHHHHH-hcCCeEEEEcccccc
Q psy3868          23 PEIMSKLAGESESNLRKAFEEAD-KNSPSIIFIDELDAI   60 (69)
Q Consensus        23 ~~l~~~~~ges~~~l~~if~~a~-~~~p~iifiDEid~i   60 (69)
                      .++..+..||-.+.+.+-.++-. +.-|.++||||++-+
T Consensus       270 TEITdkLR~eiNkvVn~Yid~GvAElvPGVLFIDEVhML  308 (456)
T KOG1942|consen  270 TEITDKLRGEINKVVNKYIDQGVAELVPGVLFIDEVHML  308 (456)
T ss_pred             chhHHHHHHHHHHHHHHHHhcchhhhcCcceEeeehhhh
Confidence            33444444444444444444322 356999999999865

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=85.48  E-value=2.8  Score=29.00  Aligned_cols=56  Identities=23%  Similarity=0.248  Sum_probs=28.9

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAI   60 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i   60 (69)
                      |++.+.+..+..-+++.++-.++.....  .-......+..+.......||+|||+..
T Consensus        51 Ttll~~l~~~~~~~~iy~~~~d~~~~~~--~l~d~~~~~~~~~~~~~~yifLDEIq~v  106 (398)
T COG1373          51 TTLLKLLIKGLLEEIIYINFDDLRLDRI--ELLDLLRAYIELKEREKSYIFLDEIQNV  106 (398)
T ss_pred             HHHHHHHHhhCCcceEEEEecchhcchh--hHHHHHHHHHHhhccCCceEEEecccCc
Confidence            4444777766654455555555432211  1122222222222224589999999875

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=85.25  E-value=0.81  Score=32.96  Aligned_cols=59  Identities=14%  Similarity=0.249  Sum_probs=36.1

Q ss_pred             hHHHHHHHHHhCCcE--E-----------EEchh---hh--hhcccChHHHHHHHHHHHHHh----cCCeEEEEcccccc
Q psy3868           3 YRLTTLCRDSLGAFF--F-----------LINGP---EI--MSKLAGESESNLRKAFEEADK----NSPSIIFIDELDAI   60 (69)
Q Consensus         3 T~la~aia~~~~~~~--~-----------~v~~~---~l--~~~~~ges~~~l~~if~~a~~----~~p~iifiDEid~i   60 (69)
                      |++||.+|+.+++.=  .           .++..   ++  ++.-...+...+|++-+.++-    .+.-|++|||+|-+
T Consensus        52 Tt~Ari~AkalNC~~~~~~ePC~~C~~Ck~I~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHML  131 (515)
T COG2812          52 TTIARILAKALNCENGPTAEPCGKCISCKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHML  131 (515)
T ss_pred             hhHHHHHHHHhcCCCCCCCCcchhhhhhHhhhcCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhh
Confidence            778999999887641  0           01111   11  011222356678888888742    45679999999987


Q ss_pred             c
Q psy3868          61 A   61 (69)
Q Consensus        61 ~   61 (69)
                      -
T Consensus       132 S  132 (515)
T COG2812         132 S  132 (515)
T ss_pred             h
Confidence            4

>PRK15115 response regulator GlrR; Provisional

Probab=84.96  E-value=1.3  Score=30.27  Aligned_cols=55  Identities=18%  Similarity=0.244  Sum_probs=33.8

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHH---------------HhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEA---------------DKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a---------------~~~~p~iifiDEid~i~~~   63 (69)
                      +++|+++....   +.+|+.++|..+-..+      .-..+|..+               .......|||||||.+.+.
T Consensus       171 ~~lA~~ih~~s~r~~~~f~~i~c~~~~~~~------~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~~  243 (444)
T PRK15115        171 EILAQAIHNASPRASKPFIAINCGALPEQL------LESELFGHARGAFTGAVSNREGLFQAAEGGTLFLDEIGDMPAP  243 (444)
T ss_pred             HHHHHHHHHhcCCCCCCeEEEeCCCCCHHH------HHHHhcCCCcCCCCCCccCCCCcEEECCCCEEEEEccccCCHH
Confidence            56788776664   4799999998762211      111233221               1123578999999988653

>PRK07261 topology modulation protein; Provisional

Probab=84.65  E-value=3.4  Score=25.03  Aligned_cols=31  Identities=3%  Similarity=-0.009  Sum_probs=22.6

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChH
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGES   33 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges   33 (69)
                      |++|+.++..++.+++.++.-.....|....
T Consensus        14 STla~~l~~~~~~~~i~~D~~~~~~~~~~~~   44 (171)
T PRK07261         14 STLARKLSQHYNCPVLHLDTLHFQPNWQERD   44 (171)
T ss_pred             HHHHHHHHHHhCCCeEecCCEEeccccccCC
Confidence            6799999999999988877654444454444

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=84.41  E-value=2.6  Score=28.52  Aligned_cols=25  Identities=12%  Similarity=0.294  Sum_probs=18.8

Q ss_pred             HHHHHHHHhcCCeEEEEcccccccc
Q psy3868          38 RKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus        38 ~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      .++....+..++-+|+|||+|.+..
T Consensus       135 ~~~~~llr~~~vrmLIIDE~H~lLa  159 (302)
T PF05621_consen  135 QQVLRLLRRLGVRMLIIDEFHNLLA  159 (302)
T ss_pred             HHHHHHHHHcCCcEEEeechHHHhc
Confidence            3344555667999999999999743

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=84.07  E-value=0.97  Score=32.99  Aligned_cols=14  Identities=29%  Similarity=0.674  Sum_probs=11.7

Q ss_pred             CeEEEEcccccccc
Q psy3868          49 PSIIFIDELDAIAP   62 (69)
Q Consensus        49 p~iifiDEid~i~~   62 (69)
                      ..+|||||++.+-+
T Consensus       127 ~GiL~lDEi~~l~~  140 (633)
T TIGR02442       127 RGILYIDEVNLLDD  140 (633)
T ss_pred             CCeEEeChhhhCCH
Confidence            46999999998865

A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=83.62  E-value=1.3  Score=27.61  Aligned_cols=36  Identities=19%  Similarity=0.264  Sum_probs=23.9

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHH
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEE   43 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~   43 (69)
                      |++.+++|+.++.+|+-.+  .++.+-.|.   .+.++|+.
T Consensus        16 STIGr~LAk~L~~~F~D~D--~~Ie~~~g~---sI~eIF~~   51 (172)
T COG0703          16 STIGRALAKALNLPFIDTD--QEIEKRTGM---SIAEIFEE   51 (172)
T ss_pred             hHHHHHHHHHcCCCcccch--HHHHHHHCc---CHHHHHHH
Confidence            7899999999999997654  344444443   24444444

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=83.42  E-value=0.92  Score=29.57  Aligned_cols=17  Identities=35%  Similarity=0.679  Sum_probs=14.3

Q ss_pred             cCCeEEEEccccccccc
Q psy3868          47 NSPSIIFIDELDAIAPK   63 (69)
Q Consensus        47 ~~p~iifiDEid~i~~~   63 (69)
                      ..+-||+|||+|++-+.
T Consensus       171 ~~~iViiIDdLDR~~~~  187 (325)
T PF07693_consen  171 KKRIVIIIDDLDRCSPE  187 (325)
T ss_pred             CceEEEEEcchhcCCcH
Confidence            57899999999998654

Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=83.41  E-value=1.8  Score=31.56  Aligned_cols=48  Identities=23%  Similarity=0.127  Sum_probs=35.9

Q ss_pred             hHHHHHHHHHhCCcE-----EEEch-----hhhhhcccChHHHHHHHHHHHHHhcCCe
Q psy3868           3 YRLTTLCRDSLGAFF-----FLING-----PEIMSKLAGESESNLRKAFEEADKNSPS   50 (69)
Q Consensus         3 T~la~aia~~~~~~~-----~~v~~-----~~l~~~~~ges~~~l~~if~~a~~~~p~   50 (69)
                      |++++++++.++.+.     +..|+     +-+..-+.|.+++.++..|+.|++..|+
T Consensus        51 T~la~~la~~l~~~~~~~~~~~~n~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~  108 (608)
T TIGR00764        51 SMLAKAMAELLPDEELEDILVYPNPEDPNMPRIVEVPAGEGREIVEDYKKKAFKQPSS  108 (608)
T ss_pred             HHHHHHHHHHcCchhheeEEEEeCCCCCchHHHHHHHHhhchHHHHHHHHHhhcccch
Confidence            789999999997652     23333     3344558899999999999999886654

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=83.38  E-value=0.91  Score=32.60  Aligned_cols=56  Identities=16%  Similarity=0.239  Sum_probs=29.0

Q ss_pred             hHHHHHHHHHhCC--cEEEEc-----hhhhhhcccChH-HHHH--HHHHHHHHhc---CCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGA--FFFLIN-----GPEIMSKLAGES-ESNL--RKAFEEADKN---SPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~--~~~~v~-----~~~l~~~~~ges-~~~l--~~if~~a~~~---~p~iifiDEid~i~~   62 (69)
                      |++|++++...+.  +|..++     ++++    +|.. -...  ..-|......   ...++|+|||..+.+
T Consensus        53 T~LAraLa~~~~~~~~F~~~~~~fttp~DL----fG~l~i~~~~~~g~f~r~~~G~L~~A~lLfLDEI~rasp  121 (498)
T PRK13531         53 SLIARRLKFAFQNARAFEYLMTRFSTPEEV----FGPLSIQALKDEGRYQRLTSGYLPEAEIVFLDEIWKAGP  121 (498)
T ss_pred             HHHHHHHHHHhcccCcceeeeeeecCcHHh----cCcHHHhhhhhcCchhhhcCCccccccEEeecccccCCH
Confidence            7899999987653  333332     3344    3321 1111  1123221111   234999999986654

>PF07931 CPT: Chloramphenicol phosphotransferase-like protein; InterPro: IPR012853 The members of this family are all similar to chloramphenicol 3-O phosphotransferase (CPT, Q56148 from SWISSPROT) expressed by Streptomyces venezuelae

Probab=83.36  E-value=8  Score=23.93  Aligned_cols=26  Identities=4%  Similarity=0.079  Sum_probs=22.7

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSK   28 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~   28 (69)
                      |++|+++.+.+.-|++.++...+...
T Consensus        15 Ssia~~Lq~~~~~p~~~l~~D~f~~~   40 (174)
T PF07931_consen   15 SSIARALQERLPEPWLHLSVDTFVDM   40 (174)
T ss_dssp             HHHHHHHHHHSSS-EEEEEHHHHHHH
T ss_pred             HHHHHHHHHhCcCCeEEEecChHHhh
Confidence            78999999999999999999888773

Chloramphenicol (Cm) is a metabolite produced by this bacterium that can inhibit ribosomal peptidyl transferase activity and therefore protein production. By transferring a phosphate group to the C-3 hydroxyl group of Cm, CPT inactivates this potentially lethal metabolite [, ]. ; GO: 0005524 ATP binding, 0016740 transferase activity; PDB: 1QHX_A 1QHN_A 1GRR_A 1QHY_A 1QHS_A 1GRQ_A.

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=82.06  E-value=2  Score=29.38  Aligned_cols=54  Identities=11%  Similarity=0.182  Sum_probs=32.3

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHH---------------HhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEA---------------DKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a---------------~~~~p~iifiDEid~i~~   62 (69)
                      +++|+++....   +.+|+.++|..+-..+      .-..+|-..               .......|||||||.+.+
T Consensus       180 ~~lA~~ih~~s~~~~~~~~~i~c~~~~~~~------~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ld~i~~l~~  251 (457)
T PRK11361        180 ELIARAIHYNSRRAKGPFIKVNCAALPESL------LESELFGHEKGAFTGAQTLRQGLFERANEGTLLLDEIGEMPL  251 (457)
T ss_pred             HHHHHHHHHhCCCCCCCeEEEECCCCCHHH------HHHHhcCCCCCCCCCCCCCCCCceEECCCCEEEEechhhCCH
Confidence            45777776554   4699999998762211      111222211               112356899999999865

>PRK06620 hypothetical protein; Validated

Probab=81.98  E-value=2.2  Score=26.98  Aligned_cols=12  Identities=8%  Similarity=0.329  Sum_probs=9.7

Q ss_pred             CeEEEEcccccc
Q psy3868          49 PSIIFIDELDAI   60 (69)
Q Consensus        49 p~iifiDEid~i   60 (69)
                      ..+++|||||.+
T Consensus        86 ~d~lliDdi~~~   97 (214)
T PRK06620         86 YNAFIIEDIENW   97 (214)
T ss_pred             CCEEEEeccccc
Confidence            478999999954

>COG4130 Predicted sugar epimerase [Carbohydrate transport and metabolism]

Probab=81.88  E-value=6.3  Score=25.99  Aligned_cols=46  Identities=13%  Similarity=0.034  Sum_probs=41.0

Q ss_pred             HHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCe
Q psy3868           5 LTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPS   50 (69)
Q Consensus         5 la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~   50 (69)
                      -+|++|.+.|+.++.+|+-.=+..|.++-.+.-+.+-++|+.+...
T Consensus        53 ~vka~Aek~Gl~IvSINAlypFn~wt~~~~a~a~~la~yA~acGA~   98 (272)
T COG4130          53 EVKALAEKAGLTIVSINALYPFNEWTEERVAEARGLADYAAACGAK   98 (272)
T ss_pred             HHHHHHHHcCcEEEEeeccccccccChHHHHHHHHHHHHHHhcCCc
Confidence            3689999999999999998888999999999999999999886543

>PF01202 SKI: Shikimate kinase; InterPro: IPR000623 Shikimate kinase (2

Probab=81.60  E-value=2.6  Score=25.04  Aligned_cols=29  Identities=21%  Similarity=0.261  Sum_probs=22.2

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChH
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGES   33 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges   33 (69)
                      |++++.+|..++++|+.++-  ++....|.+
T Consensus         6 Stvg~~lA~~L~~~fiD~D~--~i~~~~g~s   34 (158)
T PF01202_consen    6 STVGKLLAKRLGRPFIDLDD--EIEERTGMS   34 (158)
T ss_dssp             HHHHHHHHHHHTSEEEEHHH--HHHHHHTSH
T ss_pred             HHHHHHHHHHhCCCccccCH--HHHHHhCCc
Confidence            78999999999999977644  455556643

7.1.71 from EC) catalyses the fifth step in the biosynthesis of aromatic amino acids from chorismate (the so-called shikimate pathway) []. The enzyme catalyses the following reaction: ATP + shikimate = ADP + shikimate-3-phosphate The protein is found in bacteria (gene aroK or aroL), plants and fungi (where it is part of a multifunctional enzyme that catalyses five consecutive steps in this pathway). In 1994, the 3D structure of shikimate kinase was predicted to be very close to that of adenylate kinase, suggesting a functional similarity as well as an evolutionary relationship []. This prediction has since been confirmed experimentally. The protein is reported to possess an alpha/beta fold, consisting of a central sheet of five parallel beta-strands flanked by alpha-helices. Such a topology is very similar to that of adenylate kinase [].; GO: 0004765 shikimate kinase activity, 0005524 ATP binding; PDB: 3VAA_C 1KO8_B 1KO4_B 1KO1_A 1KOF_A 1KNQ_A 1KO5_A 1KAG_A 2PT5_D 1SHK_A ....

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=81.38  E-value=2  Score=29.67  Aligned_cols=54  Identities=15%  Similarity=0.183  Sum_probs=32.9

Q ss_pred             hHHHHHHHHHhC---CcEEEEchhhhhhcccChHHHHHHHHHHHH---------------HhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLG---AFFFLINGPEIMSKLAGESESNLRKAFEEA---------------DKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~---~~~~~v~~~~l~~~~~ges~~~l~~if~~a---------------~~~~p~iifiDEid~i~~   62 (69)
                      +++|+++.....   .||+.++|+.+-.      +..-..+|...               ....+..|||||||.+..
T Consensus       175 ~~lA~~ih~~s~~~~~~~i~i~c~~~~~------~~~~~~lfg~~~g~~~~~~~~~~g~~~~a~~Gtl~l~~i~~l~~  246 (469)
T PRK10923        175 ELVAHALHRHSPRAKAPFIALNMAAIPK------DLIESELFGHEKGAFTGANTIRQGRFEQADGGTLFLDEIGDMPL  246 (469)
T ss_pred             HHHHHHHHhcCCCCCCCeEeeeCCCCCH------HHHHHHhcCCCCCCCCCCCcCCCCCeeECCCCEEEEeccccCCH
Confidence            567888777653   6999999987722      11122233211               012356789999997754

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=80.87  E-value=2.1  Score=29.26  Aligned_cols=53  Identities=19%  Similarity=0.209  Sum_probs=32.5

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHH-HHHHHH---------------HhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLR-KAFEEA---------------DKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~-~if~~a---------------~~~~p~iifiDEid~i~~   62 (69)
                      +.+|+++-...   +.||+.++|..+-.       ..+. .+|...               ....+..|||||||.+.+
T Consensus       176 ~~lA~~ih~~s~~~~~~~v~v~c~~~~~-------~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~  247 (445)
T TIGR02915       176 EVLARALHQLSDRKDKRFVAINCAAIPE-------NLLESELFGYEKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDLPL  247 (445)
T ss_pred             HHHHHHHHHhCCcCCCCeEEEECCCCCh-------HHHHHHhcCCCCCCcCCCccCCCCceeECCCCEEEEechhhCCH
Confidence            45777776554   36899999987622       2221 223211               112467899999998864

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>PRK13947 shikimate kinase; Provisional

Probab=80.84  E-value=8.6  Score=22.66  Aligned_cols=28  Identities=14%  Similarity=0.148  Sum_probs=20.1

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccCh
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGE   32 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ge   32 (69)
                      |++++.+|+.+|++|+..+  .+.....|.
T Consensus        15 st~a~~La~~lg~~~id~d--~~~~~~~g~   42 (171)
T PRK13947         15 TTVGKRVATTLSFGFIDTD--KEIEKMTGM   42 (171)
T ss_pred             HHHHHHHHHHhCCCEEECc--hhhhhhcCC
Confidence            7899999999999997654  344443443

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=80.73  E-value=7  Score=28.69  Aligned_cols=29  Identities=21%  Similarity=0.345  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEcccccccc
Q psy3868          34 ESNLRKAFEEADKN----SPSIIFIDELDAIAP   62 (69)
Q Consensus        34 ~~~l~~if~~a~~~----~p~iifiDEid~i~~   62 (69)
                      ...++.+.+.+...    ..-|++|||+|.+..
T Consensus       103 vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls~  135 (614)
T PRK14971        103 VDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLSQ  135 (614)
T ss_pred             HHHHHHHHHHHhhCcccCCcEEEEEECcccCCH
Confidence            45677777776432    345999999998853

>PRK07631 amidophosphoribosyltransferase; Provisional

Probab=80.69  E-value=2.8  Score=29.89  Aligned_cols=53  Identities=13%  Similarity=0.214  Sum_probs=33.0

Q ss_pred             hhHHHHHHHHHhCCcEEEEchhhhhhcccC---------hHHHHHHHHHHHHHh--cCCeEEEEccc
Q psy3868           2 SYRLTTLCRDSLGAFFFLINGPEIMSKLAG---------ESESNLRKAFEEADK--NSPSIIFIDEL   57 (69)
Q Consensus         2 ~T~la~aia~~~~~~~~~v~~~~l~~~~~g---------es~~~l~~if~~a~~--~~p~iifiDEi   57 (69)
                      |..+|+.+|+++|.|+..   .-+..++.|         +-.++++..|...+.  ....|+++||+
T Consensus       294 ~~~~A~gla~~~gip~~~---~lik~~~~~Rt~i~~~~~~R~~nv~~~f~~~~~~v~gk~VlLVDDs  357 (475)
T PRK07631        294 SISAAIGYAEATGIPYEL---GLIKNRYVGRTFIQPSQALREQGVKMKLSPVRGVVEGKRVVMVDDS  357 (475)
T ss_pred             HHHHHHHHHHHHCCCccc---ceEEEecCCCCCcCCCHHHHHHHHhhhhhhcccccCCceEEEEeee
Confidence            456899999999998843   001111222         244567778864322  34679999986

>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=80.27  E-value=4.1  Score=28.63  Aligned_cols=42  Identities=21%  Similarity=0.254  Sum_probs=34.8

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhh-cccChH-HHHHHHHHHHH
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMS-KLAGES-ESNLRKAFEEA   44 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~-~~~ges-~~~l~~if~~a   44 (69)
                      |-+||-+|+-.+.||+.|.++.+.. +|+|.. +..+|.+-+.+
T Consensus        64 TEIARRLAkl~~aPFiKVEATKfTEVGYVGrDVesivRDLve~a  107 (444)
T COG1220          64 TEIARRLAKLAGAPFIKVEATKFTEVGYVGRDVESIIRDLVEIA  107 (444)
T ss_pred             HHHHHHHHHHhCCCeEEEEeeeeeecccccccHHHHHHHHHHHH
Confidence            6799999999999999999998864 488875 66677777665

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=80.25  E-value=11  Score=22.98  Aligned_cols=13  Identities=31%  Similarity=0.629  Sum_probs=10.6

Q ss_pred             cCCeEEEEccccc
Q psy3868          47 NSPSIIFIDELDA   59 (69)
Q Consensus        47 ~~p~iifiDEid~   59 (69)
                      ..|.++++||.-+
T Consensus        77 ~~~~llllDEp~~   89 (185)
T smart00534       77 TENSLVLLDELGR   89 (185)
T ss_pred             CCCeEEEEecCCC
Confidence            4799999999743

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=80.21  E-value=1.1  Score=25.94  Aligned_cols=45  Identities=18%  Similarity=0.386  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhC---CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           4 RLTTLCRDSLG---AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         4 ~la~aia~~~~---~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      ++|+.+....+   .+|+.+++..+-           .++++.+   .+..|||+|+|.+-+
T Consensus        36 ~~A~~lh~~~~~~~~~~~~~~~~~~~-----------~~~l~~a---~~gtL~l~~i~~L~~   83 (138)
T PF14532_consen   36 LLARALHRYSGRANGPFIVIDCASLP-----------AELLEQA---KGGTLYLKNIDRLSP   83 (138)
T ss_dssp             HHHHCCHHTTTTCCS-CCCCCHHCTC-----------HHHHHHC---TTSEEEEECGCCS-H
T ss_pred             HHHHHHHhhcCccCCCeEEechhhCc-----------HHHHHHc---CCCEEEECChHHCCH
Confidence            46666666554   366666666542           3345444   778999999999865

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=80.18  E-value=4.5  Score=27.86  Aligned_cols=29  Identities=17%  Similarity=0.477  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868          35 SNLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus        35 ~~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      ..+.++++.....+|.+|+||++..+...
T Consensus       145 ~~le~I~~~i~~~~~~lVVIDSIq~l~~~  173 (372)
T cd01121         145 TNLEDILASIEELKPDLVIIDSIQTVYSS  173 (372)
T ss_pred             CcHHHHHHHHHhcCCcEEEEcchHHhhcc
Confidence            34667777777789999999999988643

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	69
1e32_A	458	Structure Of The N-Terminal Domain And The D1 Aaa D		1e-23
3hu3_A	489	Structure Of P97 N-D1 R155h Mutant In Complex With		1e-23
3hu2_A	489	Structure Of P97 N-D1 R86a Mutant In Complex With A		1e-23
3hu1_A	489	Structure Of P97 N-D1 R95g Mutant In Complex With A		1e-23
3cf1_A	806	Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Len		2e-23
1r7r_A	816	The Crystal Structure Of Murine P97VCP AT 3.6A Leng		2e-23
2x8a_A	274	Human Nuclear Valosin Containing Protein Like (Nvl)		4e-09
4b4t_K	428	Near-Atomic Resolution Structural Model Of The Yeas		7e-08
3cf0_A	301	Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH		1e-07
2zam_A	444	Crystal Structure Of Mouse Skd1VPS4B APO-Form Lengt		7e-07
1xwi_A	322	Crystal Structure Of Vps4b Length = 322		8e-07
3h4m_A	285	Aaa Atpase Domain Of The Proteasome- Activating Nuc		1e-06
4b4t_I	437	Near-Atomic Resolution Structural Model Of The Yeas		2e-06
4b4t_M	434	Near-Atomic Resolution Structural Model Of The Yeas		3e-06
2rko_A	331	Crystal Structure Of The Vps4p-Dimer Length = 331		3e-06
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		3e-06
3eie_A	322	Crystal Structure Of S.Cerevisiae Vps4 In The So4-B		5e-06
3eih_A	340	Crystal Structure Of S.Cerevisiae Vps4 In The Prese		6e-06
2qp9_X	355	Crystal Structure Of S.Cerevisiae Vps4 Length = 355		7e-06
2r62_A	268	Crystal Structure Of Helicobacter Pylori Atp Depend		1e-05
3d8b_A	357	Crystal Structure Of Human Fidgetin-Like Protein 1		3e-05
4b4t_J	405	Near-Atomic Resolution Structural Model Of The Yeas		1e-04
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		2e-04
1ixz_A	254	Crystal Structure Of The Ftsh Atpase Domain From Th		3e-04
4eiw_A	508	Whole Cytosolic Region Of Atp-Dependent Metalloprot		3e-04
2ce7_A	476	Edta Treated Length = 476		3e-04
1iy2_A	278	Crystal Structure Of The Ftsh Atpase Domain From Th		3e-04
3kds_E	465	Apo-ftsh Crystal Structure Length = 465		3e-04
2qz4_A	262	Human Paraplegin, Aaa Domain In Complex With Adp Le		3e-04
2dhr_A	499	Whole Cytosolic Region Of Atp-Dependent Metalloprot		4e-04
3vfd_A	389	Human Spastin Aaa Domain Length = 389		4e-04

>pdb|1E32|A Chain A, Structure Of The N-Terminal Domain And The D1 Aaa Domain Of Membrane Fusion Atpase P97 Length = 458

Iteration: 1
 Score =  104 bits (260), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 53/53 (100%)
Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct: 263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  104 bits (260), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 53/53 (100%)
Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct: 263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  104 bits (260), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 53/53 (100%)
Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct: 263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

>pdb|3HU1|A Chain A, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  104 bits (260), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 53/53 (100%)
Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct: 263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

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

Iteration: 1
 Score =  104 bits (259), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 53/53 (100%)
Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct: 263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

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

Iteration: 1
 Score =  104 bits (259), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 53/53 (100%)
Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKREK
Sbjct: 263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK 315

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 36/55 (65%)
Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68
           G  F  + GPE+++   GESE  +R+ F+ A  ++P +IF DE+DA+ P+R  RE
Sbjct: 69  GLNFISVKGPELLNMYVGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRE 123

>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 428

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 27/60 (45%), Positives = 35/60 (58%)
Query: 5   LTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           L     +S  A F  +NG E + K  GE    +R  F  A +N+PSIIFIDE+D+IA KR
Sbjct: 222 LVKAVANSTKAAFIRVNGSEFVHKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKR 281

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 36/50 (72%)
Query: 15  AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           A F  I GPE+++   GESE+N+R+ F++A + +P ++F DELD+IA  R
Sbjct: 75  ANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKAR 124

>pdb|2ZAM|A Chain A, Crystal Structure Of Mouse Skd1VPS4B APO-Form Length = 444

Iteration: 1
 Score = 48.9 bits (115), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 41/67 (61%)
Query: 2   SYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIA 61
           SY    +  ++  + FF I+  +++SK  GESE  ++  F+ A +N PSIIFIDE+D++ 
Sbjct: 181 SYLAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLC 240
Query: 62  PKREKRE 68
             R + E
Sbjct: 241 GSRSENE 247

>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b Length = 322

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 41/67 (61%)
Query: 2   SYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIA 61
           SY    +  ++  + FF I+  +++SK  GESE  ++  F+ A +N PSIIFIDE+D++ 
Sbjct: 59  SYLAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLC 118
Query: 62  PKREKRE 68
             R + E
Sbjct: 119 GSRSENE 125

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 33/50 (66%)
Query: 15  AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           A F  + G E++ K  GE  S ++  F+ A + +PSIIFIDE+DAIA KR
Sbjct: 77  ATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKR 126

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 32/50 (64%)
Query: 15  AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           A F  I G E++ K  G+     R+ F+ A +N+PSI+FIDE+DAI  KR
Sbjct: 242 ATFLRIVGSELIQKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKR 291

>pdb|4B4T|M Chain M, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 434

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 32/60 (53%)
Query: 5   LTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           L   C     A F  +  P+++    GE    +R AF  A + +P+IIFIDELDAI  KR
Sbjct: 231 LARACAAQTNATFLKLAAPQLVQMYIGEGAKLVRDAFALAKEKAPTIIFIDELDAIGTKR 290

>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer Length = 331

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 35/52 (67%)
Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68
           FF ++  +++SK  GESE  +++ F  A +N PSIIFIDE+DA+   R + E
Sbjct: 88  FFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDEVDALTGTRGEGE 139

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 21/48 (43%), Positives = 30/48 (62%)
Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           FF I+G + +    G   S +R  FE+A K +P IIFIDE+DA+  +R
Sbjct: 73  FFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQR 120

>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound State Length = 322

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 35/52 (67%)
Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68
           FF ++  +++SK  GESE  +++ F  A +N PSIIFID++DA+   R + E
Sbjct: 79  FFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGE 130

>pdb|3EIH|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of Atpgammas Length = 340

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 35/52 (67%)
Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68
           FF ++  +++SK  GESE  +++ F  A +N PSIIFID++DA+   R + E
Sbjct: 97  FFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGE 148

>pdb|2QP9|X Chain X, Crystal Structure Of S.Cerevisiae Vps4 Length = 355

Iteration: 1
 Score = 45.4 bits (106), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 35/52 (67%)
Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68
           FF ++  +++SK  GESE  +++ F  A +N PSIIFID++DA+   R + E
Sbjct: 112 FFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGE 163

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/48 (45%), Positives = 27/48 (56%)
Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           FF + G   +    G   S +R  FE A K +PSIIFIDE+DAI   R
Sbjct: 72  FFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSR 119

>pdb|3D8B|A Chain A, Crystal Structure Of Human Fidgetin-Like Protein 1 In Complex With Adp Length = 357

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 30/51 (58%)
Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           GA FF I+   + SK  GE E  +R  F  A    P++IFIDE+D++  +R
Sbjct: 142 GATFFSISASSLTSKWVGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQR 192

>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 405

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/48 (39%), Positives = 31/48 (64%)
Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           F  ++G E++ K  GE    +R+ F  A +++PSIIF+DE+D+I   R
Sbjct: 210 FIRVSGAELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTR 257

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 31/53 (58%)
Query: 12  SLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           ++GA F       I+ K  GES   +R+ F  A ++ P IIF+DE+DAI  +R
Sbjct: 238 TIGANFIFSPASGIVDKYIGESARIIREMFAYAKEHEPCIIFMDEVDAIGGRR 290

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           F   +G + +    G   + +R  FE A +++P I+FIDE+DA+  KR
Sbjct: 77  FITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKR 124

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           F   +G + +    G   + +R  FE A +++P I+FIDE+DA+  KR
Sbjct: 101 FITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKR 148

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           FF I+G + +    G   + +R  F +A  ++P I+FIDE+DA+   R
Sbjct: 77  FFHISGSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHR 124

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           F   +G + +    G   + +R  FE A +++P I+FIDE+DA+  KR
Sbjct: 101 FITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKR 148

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           FF I+G + +    G   + +R  F +A  ++P I+FIDE+DA+   R
Sbjct: 77  FFHISGSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHR 124

>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp Length = 262

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           F  + G E +  + G   + +R  F+EA   +P I++IDE+DA+  KR
Sbjct: 67  FLAMAGAEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKR 114

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           F   +G + +    G   + +R  FE A +++P I+FIDE+DA+  KR
Sbjct: 92  FITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKR 139

>pdb|3VFD|A Chain A, Human Spastin Aaa Domain Length = 389

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 32/54 (59%)
Query: 15  AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68
           A FF I+   + SK  GE E  +R  F  A +  PSIIFID++D++  +R + E
Sbjct: 174 ATFFNISAASLTSKYVGEGEKLVRALFAVARELQPSIIFIDQVDSLLCERREGE 227

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	69
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	6e-27
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	3e-24
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	8e-20
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	4e-21
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	1e-19
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	6e-19
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	9e-19
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	5e-16
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	5e-16
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	2e-15
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	2e-15
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	4e-15
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	1e-14
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	1e-14
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	5e-14
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	1e-09
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	2e-09
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	3e-09
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	3e-09
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	4e-09
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	5e-08
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	5e-08

>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 = 99.9 bits (249), Expect = 6e-27
 Identities = 52/64 (81%), Positives = 57/64 (89%), Gaps = 3/64 (4%)

Query: 6   TTLCR---DSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 62
           T + R   +  GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAP
Sbjct: 252 TLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAP 311

Query: 63  KREK 66
           KREK
Sbjct: 312 KREK 315

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

 Score = 81.9 bits (203), Expect = 4e-21
 Identities = 24/54 (44%), Positives = 33/54 (61%)

Query: 12  SLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE 65
              A F  + G E++ K  GE  S ++  F+ A + +PSIIFIDE+DAIA KR 
Sbjct: 74  ETNATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRT 127

>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 = 78.2 bits (193), Expect = 1e-19
 Identities = 10/53 (18%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 14  GAFFFLINGPEIMSKLAGESESN-LRKAFEEADKNSPSIIFIDELDAIAPKRE 65
              F  I  P+ M   +  ++   ++K F++A K+  S + +D+++ +     
Sbjct: 89  NFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVP 141

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

 Score = 76.1 bits (188), Expect = 6e-19
 Identities = 21/51 (41%), Positives = 34/51 (66%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           G  F  + GPE+++   GESE  +R+ F+ A  ++P +IF DE+DA+ P+R
Sbjct: 69  GLNFISVKGPELLNMYVGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRR 119

>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 = 76.1 bits (188), Expect = 9e-19
 Identities = 23/51 (45%), Positives = 36/51 (70%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
            A F  I GPE+++   GESE+N+R+ F++A + +P ++F DELD+IA  R
Sbjct: 74  QANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKAR 124

>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 = 68.9 bits (169), Expect = 5e-16
 Identities = 22/55 (40%), Positives = 36/55 (65%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68
            + FF ++  +++SK  GESE  +++ F  A +N PSIIFID++DA+   R + E
Sbjct: 76  NSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGE 130

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

 Score = 68.9 bits (169), Expect = 5e-16
 Identities = 23/57 (40%), Positives = 37/57 (64%)

Query: 12  SLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68
           +  + FF I+  +++SK  GESE  ++  F+ A +N PSIIFIDE+D++   R + E
Sbjct: 69  ANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENE 125

>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 = 67.3 bits (164), Expect = 2e-15
 Identities = 23/61 (37%), Positives = 39/61 (63%)

Query: 8   LCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR 67
           +  ++  + FF I+  +++SK  GESE  ++  F+ A +N PSIIFIDE+D++   R + 
Sbjct: 187 VATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSEN 246

Query: 68  E 68
           E
Sbjct: 247 E 247

>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 = 67.2 bits (164), Expect = 2e-15
 Identities = 22/55 (40%), Positives = 36/55 (65%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68
            + FF ++  +++SK  GESE  +++ F  A +N PSIIFID++DA+   R + E
Sbjct: 109 NSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGE 163

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

 Score = 66.0 bits (161), Expect = 4e-15
 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 7/66 (10%)

Query: 6   TTLCR---DSLGAFFFLINGPEIMSKLAGESESNLRKAFEEAD----KNSPSIIFIDELD 58
           +  C      +G    +++  E+ S  AGE    +R+ + EA     K +   +FI++LD
Sbjct: 50  SFQCELVFRKMGINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLD 109

Query: 59  AIAPKR 64
           A A + 
Sbjct: 110 AGAGRM 115

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

 Score = 65.0 bits (159), Expect = 1e-14
 Identities = 21/55 (38%), Positives = 29/55 (52%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68
            A F  I+   + SK  G+ E  +R  F  A    PSIIFIDE+D++  +R   E
Sbjct: 79  SATFLNISAASLTSKYVGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSE 133

>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 = 64.8 bits (158), Expect = 1e-14
 Identities = 22/55 (40%), Positives = 31/55 (56%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68
           GA FF I+   + SK  GE E  +R  F  A    P++IFIDE+D++  +R   E
Sbjct: 142 GATFFSISASSLTSKWVGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGE 196

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

 Score = 63.3 bits (154), Expect = 5e-14
 Identities = 22/55 (40%), Positives = 32/55 (58%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68
            A FF I+   + SK  GE E  +R  F  A +  PSIIFID++D++  +R + E
Sbjct: 173 NATFFNISAASLTSKYVGEGEKLVRALFAVARELQPSIIFIDQVDSLLCERREGE 227

>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 = 51.1 bits (123), Expect = 1e-09
 Identities = 17/50 (34%), Positives = 28/50 (56%)

Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66
           F  + G E +  + G   + +R  F+EA   +P I++IDE+DA+  KR  
Sbjct: 67  FLAMAGAEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRST 116

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

 Score = 50.4 bits (121), Expect = 2e-09
 Identities = 17/48 (35%), Positives = 28/48 (58%)

Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           F   +G + +    G   + +R  FE A +++P I+FIDE+DA+  KR
Sbjct: 101 FITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKR 148

>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 = 49.6 bits (119), Expect = 3e-09
 Identities = 17/48 (35%), Positives = 28/48 (58%)

Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           F   +G + +    G   + +R  FE A +++P I+FIDE+DA+  KR
Sbjct: 77  FITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKR 124

>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 = 49.6 bits (119), Expect = 3e-09
 Identities = 22/48 (45%), Positives = 27/48 (56%)

Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           FF + G   +    G   S +R  FE A K +PSIIFIDE+DAI   R
Sbjct: 72  FFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSR 119

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

 Score = 49.2 bits (118), Expect = 4e-09
 Identities = 21/48 (43%), Positives = 30/48 (62%)

Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           FF I+G + +    G   S +R  FE+A K +P IIFIDE+DA+  +R
Sbjct: 73  FFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQR 120

>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 = 46.4 bits (111), Expect = 5e-08
 Identities = 17/48 (35%), Positives = 28/48 (58%)

Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           FF I+G + +    G   + +R  F +A  ++P I+FIDE+DA+   R
Sbjct: 77  FFHISGSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHR 124

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

 Score = 46.4 bits (111), Expect = 5e-08
 Identities = 17/48 (35%), Positives = 28/48 (58%)

Query: 17  FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
           F   +G + +    G   + +R  FE A +++P I+FIDE+DA+  KR
Sbjct: 92  FITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKR 139

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	69
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	99.84
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	99.82
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	99.81
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	99.8
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	99.8
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	99.78
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.78
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.74
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.59
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.56
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.56
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.53
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.5
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.49
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.46
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.46
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.46
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.43
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.43
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.43
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.41
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.4
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.37
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.36
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.34
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.27
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.26
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.21
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.11
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.09
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.03
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.01
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.93
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.74
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.71
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.67
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	98.63
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	98.6
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.6
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	98.55
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	98.53
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.25
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.25
3pvs_A	447	Replication-associated recombination protein A; ma	98.23
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.18
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.15
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	98.14
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.06
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.04
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.97
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.94
3co5_A	143	Putative two-component system transcriptional RES	97.92
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	97.91
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	97.91
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.89
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.88
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	97.74
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.7
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	97.69
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	97.64
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.45
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.43
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	97.11
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	97.1
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.09
2chg_A	226	Replication factor C small subunit; DNA-binding pr	97.06
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	96.88
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	96.84
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	96.83
3bos_A	242	Putative DNA replication factor; P-loop containing	96.81
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.76
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.7
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	96.63
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	96.49
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	96.47
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	96.47
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.25
2chq_A	319	Replication factor C small subunit; DNA-binding pr	96.14
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	96.09
2r44_A	331	Uncharacterized protein; putative ATPase, structur	95.84
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	95.72
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	95.6
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	95.58
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	95.54
2fna_A	357	Conserved hypothetical protein; structural genomic	95.52
2qgz_A	308	Helicase loader, putative primosome component; str	95.38
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	95.14
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	94.84
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	94.7
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	94.33
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	93.94
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	93.79
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	92.34
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	92.21
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	91.64
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	90.17
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	89.72
1xp8_A	366	RECA protein, recombinase A; recombination, radior	86.44
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	86.05
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	85.22
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	84.57
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	84.5
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	83.52
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	82.82
3imk_A	158	Putative molybdenum carrier protein; YP_461806.1,	82.35
2cvh_A	220	DNA repair and recombination protein RADB; filamen	81.06

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

Probab=99.84  E-value=4e-21  Score=129.74  Aligned_cols=65  Identities=31%  Similarity=0.502  Sum_probs=62.8

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|++++.+|+.++++++.++|+|+++++|+++|+.|+.++||||||||+|+++++|...
T Consensus       196 TllAkAiA~e~~~~f~~v~~s~l~sk~vGese~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~  260 (405)
T 4b4t_J          196 TLLARAVAHHTDCKFIRVSGAELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEG  260 (405)
T ss_dssp             HHHHHHHHHHHTCEEEEEEGGGGSCSSTTHHHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCS
T ss_pred             HHHHHHHHHhhCCCceEEEhHHhhccccchHHHHHHHHHHHHHHhCCceEeeecchhhccCCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999988653

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

Probab=99.82  E-value=3.2e-20  Score=126.25  Aligned_cols=65  Identities=37%  Similarity=0.555  Sum_probs=62.9

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|++++.+|+.++++++.++|+|+++++++.+|+.|+.++||||||||+|+++++|...
T Consensus       230 TlLAkAiA~e~~~~fi~v~~s~l~sk~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~  294 (437)
T 4b4t_I          230 TLLAKAVANQTSATFLRIVGSELIQKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDS  294 (437)
T ss_dssp             HHHHHHHHHHHTCEEEEEESGGGCCSSSSHHHHHHHHHHHHHHHTCSEEEEEEEESSSSCCCSCS
T ss_pred             HHHHHHHHHHhCCCEEEEEHHHhhhccCchHHHHHHHHHHHHHhcCCcEEEEehhhhhcccCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999654

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

Probab=99.81  E-value=4.9e-20  Score=125.22  Aligned_cols=65  Identities=37%  Similarity=0.588  Sum_probs=62.8

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|++++.+|+.++++++.++|+|+++++++.+|..|+.++||||||||+|+++++|.+.
T Consensus       229 TllAkAiA~e~~~~f~~v~~s~l~~~~vGese~~ir~lF~~A~~~aP~IifiDEiDal~~~R~~~  293 (434)
T 4b4t_M          229 TLLARACAAQTNATFLKLAAPQLVQMYIGEGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDS  293 (434)
T ss_dssp             HHHHHHHHHHHTCEEEEEEGGGGCSSCSSHHHHHHHHHHHHHHHHCSEEEEEECTHHHHCCCSSG
T ss_pred             HHHHHHHHHHhCCCEEEEehhhhhhcccchHHHHHHHHHHHHHhcCCeEEeecchhhhhhccCCC
Confidence            89999999999999999999999999999999999999999999999999999999999998653

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

Probab=99.80  E-value=1e-19  Score=123.71  Aligned_cols=65  Identities=34%  Similarity=0.519  Sum_probs=62.8

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|++++++|+.+++++++++|+|+++++++.+|..|+.++||||||||+|+++++|.+.
T Consensus       229 TllAkAiA~e~~~~~~~v~~s~l~sk~~Gese~~ir~~F~~A~~~~P~IifiDEiDai~~~R~~~  293 (437)
T 4b4t_L          229 TLLAKAVAATIGANFIFSPASGIVDKYIGESARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSE  293 (437)
T ss_dssp             HHHHHHHHHHHTCEEEEEEGGGTCCSSSSHHHHHHHHHHHHHHHSCSEEEEEECCCSSSCCCSSS
T ss_pred             HHHHHHHHHHhCCCEEEEehhhhccccchHHHHHHHHHHHHHHhcCCceeeeecccccccccccC
Confidence            89999999999999999999999999999999999999999999999999999999999998653

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

Probab=99.80  E-value=1.5e-19  Score=123.73  Aligned_cols=65  Identities=29%  Similarity=0.423  Sum_probs=62.9

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|++++.+|+.++++++.++|+|+++++++.+|..|+.++||||||||+|+++++|++.
T Consensus       257 TlLAkAiA~e~~~~fi~vs~s~L~sk~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~  321 (467)
T 4b4t_H          257 TLCARAVANRTDATFIRVIGSELVQKYVGEGARMVRELFEMARTKKACIIFFDEIDAVGGARFDD  321 (467)
T ss_dssp             HHHHHHHHHHHTCEEEEEEGGGGCCCSSSHHHHHHHHHHHHHHHTCSEEEEEECCTTTSBCCSSS
T ss_pred             HHHHHHHHhccCCCeEEEEhHHhhcccCCHHHHHHHHHHHHHHhcCCceEeecccccccccccCc
Confidence            89999999999999999999999999999999999999999999999999999999999998653

>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=2.8e-19  Score=121.34  Aligned_cols=65  Identities=42%  Similarity=0.571  Sum_probs=62.6

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|++++.+|+.++++++.++|+|+++++|+++|+.|+.++||||||||+|+++++|.+.
T Consensus       220 T~lakAiA~~~~~~~~~v~~~~l~~~~~Ge~e~~ir~lF~~A~~~aP~IifiDEiD~i~~~R~~~  284 (428)
T 4b4t_K          220 TMLVKAVANSTKAAFIRVNGSEFVHKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDA  284 (428)
T ss_dssp             HHHHHHHHHHHTCEEEEEEGGGTCCSSCSHHHHHHHHHHHHHHHTCSEEEEEECTHHHHCSCSSS
T ss_pred             HHHHHHHHHHhCCCeEEEecchhhccccchhHHHHHHHHHHHHHcCCCeeechhhhhhhccccCC
Confidence            89999999999999999999999999999999999999999999999999999999999998543

>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=1.7e-19  Score=129.48  Aligned_cols=64  Identities=38%  Similarity=0.621  Sum_probs=58.4

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++++.+|+.+++++++++|+|++|++++++|+.|++.+||||||||+|+++++|+.
T Consensus       525 T~lAkaiA~e~~~~f~~v~~~~l~s~~vGese~~vr~lF~~Ar~~~P~IifiDEiDsl~~~R~~  588 (806)
T 3cf2_A          525 TLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGG  588 (806)
T ss_dssp             HHHHHHHHHTTTCEEEECCHHHHHTTTCSSCHHHHHHHHHHHHTTCSEEEECSCGGGCC-----
T ss_pred             hHHHHHHHHHhCCceEEeccchhhccccchHHHHHHHHHHHHHHcCCceeechhhhHHhhccCC
Confidence            7999999999999999999999999999999999999999999999999999999999999863

>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=99.74  E-value=3.3e-18  Score=122.83  Aligned_cols=65  Identities=77%  Similarity=1.114  Sum_probs=63.0

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|++++.+|+.++++++.++|+|+++++++++|+.|+.++||||||||+|+|+++|++.
T Consensus       252 T~LAraiA~elg~~~~~v~~~~l~sk~~gese~~lr~lF~~A~~~~PsIIfIDEiDal~~~r~~~  316 (806)
T 3cf2_A          252 TLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKT  316 (806)
T ss_dssp             HHHHHHHHTTTTCEEEEEEHHHHHSSCTTHHHHHHHHHHHHHTTSCSEEEEEESGGGTCCTTTTC
T ss_pred             HHHHHHHHHHhCCeEEEEEhHHhhcccchHHHHHHHHHHHHHHHcCCeEEEEehhcccccccCCC
Confidence            89999999999999999999999999999999999999999999999999999999999998764

>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=99.59  E-value=4.9e-15  Score=96.05  Aligned_cols=64  Identities=34%  Similarity=0.555  Sum_probs=59.7

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++++.+|+.++++++.++|+|++++.++.+|+.++..+|+||||||+|.++++|+.
T Consensus        65 T~la~aia~~~~~~~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~  128 (322)
T 3eie_A           65 SYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGE  128 (322)
T ss_dssp             HHHHHHHHHHHTCEEEEEEHHHHHTTTGGGHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC---
T ss_pred             HHHHHHHHHHHCCCEEEEchHHHhhcccchHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCC
Confidence            7899999999999999999999999999999999999999999999999999999999987754

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

Probab=99.56  E-value=3.9e-15  Score=95.89  Aligned_cols=64  Identities=27%  Similarity=0.312  Sum_probs=51.0

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHH----HhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEA----DKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a----~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++++.+|+.++++++.++|+|++++.++++|+.+    +..+|+||||||||++++++++
T Consensus        50 T~la~aiA~~l~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~~~~~~~vl~iDEiD~~~~~~~~  117 (293)
T 3t15_A           50 SFQCELVFRKMGINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLDAGAGRMGG  117 (293)
T ss_dssp             HHHHHHHHHHHTCCCEEEEHHHHHCC---HHHHHHHHHHHHHHHHHTTSSCCCEEEECCC--------
T ss_pred             HHHHHHHHHHhCCCEEEEeHHHhhhccCchhHHHHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCCC
Confidence            789999999999999999999999999999999999999999    5678999999999999986653

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

Probab=99.56  E-value=6.6e-15  Score=95.91  Aligned_cols=65  Identities=35%  Similarity=0.564  Sum_probs=61.7

Q ss_pred             hHHHHHHHHHh-CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSL-GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~-~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|+++ +.+|+.++++++.++|+|++++.++.+|+.++..+|+||||||+|.++++|...
T Consensus        59 T~la~ala~~~~~~~~~~i~~~~l~~~~~g~~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~  124 (322)
T 1xwi_A           59 SYLAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSEN  124 (322)
T ss_dssp             HHHHHHHHHHTTSCEEEEEECCSSCCSSCCSCHHHHHHHHHHHHHTSSEEEEEETTTGGGCCSSSC
T ss_pred             HHHHHHHHHHcCCCcEEEEEhHHHHhhhhhHHHHHHHHHHHHHHhcCCcEEEeecHHHhccccccc
Confidence            78999999999 899999999999999999999999999999999999999999999999887653

>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=99.53  E-value=2.1e-14  Score=94.56  Aligned_cols=64  Identities=34%  Similarity=0.555  Sum_probs=55.7

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++++.+|+.++++++.++|+|++++.++.+|..++..+|+||||||+|.+.++|+.
T Consensus        98 T~la~ala~~~~~~~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~  161 (355)
T 2qp9_X           98 SYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGE  161 (355)
T ss_dssp             HHHHHHHHHHHTCEEEEEEHHHHHSCC---CHHHHHHHHHHHHHTSSEEEEEECGGGGTC----
T ss_pred             HHHHHHHHHHhCCCEEEeeHHHHhhhhcchHHHHHHHHHHHHHHcCCeEEEEechHhhcccCCC
Confidence            7899999999999999999999999999999999999999999999999999999999987754

>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=99.50  E-value=6.2e-14  Score=96.08  Aligned_cols=64  Identities=28%  Similarity=0.524  Sum_probs=59.5

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++++++|++++.+|+.++++++...|+|.++++++.+|+.|+..+||||||||+|.++++|+.
T Consensus        63 T~Laraia~~~~~~f~~is~~~~~~~~~g~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~~  126 (476)
T 2ce7_A           63 TLLARAVAGEANVPFFHISGSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGA  126 (476)
T ss_dssp             HHHHHHHHHHHTCCEEEEEGGGTTTCCTTHHHHHHHHHHHHHHHTCSEEEEEETGGGTCCC---
T ss_pred             HHHHHHHHHHcCCCeeeCCHHHHHHHHhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhhccc
Confidence            7899999999999999999999999999999999999999999999999999999999998753

>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=99.49  E-value=2.4e-14  Score=92.17  Aligned_cols=63  Identities=38%  Similarity=0.636  Sum_probs=60.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |++|+++|++++.+++.++++++.++|+|++++.++.+|+.++...|++|||||+|.+++.|+
T Consensus        63 T~la~ala~~~~~~~i~v~~~~l~~~~~g~~~~~~~~~f~~a~~~~p~il~iDEid~l~~~~~  125 (301)
T 3cf0_A           63 TLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARG  125 (301)
T ss_dssp             HHHHHHHHHHTTCEEEEECHHHHHHHHHTTCTTHHHHHHHHHHHTCSEEEEECSTTHHHHHHT
T ss_pred             HHHHHHHHHHhCCCEEEEEhHHHHhhhcCchHHHHHHHHHHHHhcCCeEEEEEChHHHhhccC
Confidence            789999999999999999999999999999999999999999999999999999999988764

>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=99.46  E-value=1.5e-13  Score=94.24  Aligned_cols=64  Identities=78%  Similarity=1.132  Sum_probs=61.5

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|++++++++.+|+.++++++.+.|.|+++..++.+|+.+...+|++|||||||.++++|+.
T Consensus       252 T~lAraia~~~~~~fv~vn~~~l~~~~~g~~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~~~~  315 (489)
T 3hu3_A          252 TLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK  315 (489)
T ss_dssp             HHHHHHHHHHCSSEEEEEEHHHHHTSCTTHHHHHHHHHHHHHHHTCSEEEEEESHHHHCBCTTS
T ss_pred             HHHHHHHHHHhCCCEEEEEchHhhhhhcchhHHHHHHHHHHHHhcCCcEEEecchhhhcccccc
Confidence            7899999999999999999999999999999999999999999999999999999999998764

>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=99.46  E-value=4e-14  Score=95.66  Aligned_cols=64  Identities=20%  Similarity=0.298  Sum_probs=57.8

Q ss_pred             hHHHHHHHHHhC--CcEEEEchhhhhhcccChHHHHHHHHHHHH---HhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLG--AFFFLINGPEIMSKLAGESESNLRKAFEEA---DKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~--~~~~~v~~~~l~~~~~ges~~~l~~if~~a---~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|++++  .+|+.++++++.++|+|++++ ++++|+.|   +..+|+||||||+|+++++|+..
T Consensus        77 T~la~ala~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~f~~a~~~~~~~~~il~iDEid~l~~~r~~~  145 (456)
T 2c9o_A           77 TALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEV-LMENFRRAIGLRIKETKEVYEGEVTELTPCETEN  145 (456)
T ss_dssp             HHHHHHHHHHHCTTSCEEEEEGGGGCCSSSCHHHH-HHHHHHHTEEEEEEEEEEEEEEEEEEEEEC----
T ss_pred             HHHHHHHHHHhCCCceEEEEeHHHHHHHhhhhhHH-HHHHHHHHHhhhhcCCcEEEEechhhcccccCCC
Confidence            789999999999  999999999999999999998 99999999   77899999999999999988654

>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=99.46  E-value=5e-14  Score=95.13  Aligned_cols=65  Identities=35%  Similarity=0.564  Sum_probs=52.5

Q ss_pred             hHHHHHHHHHh-CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSL-GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~-~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|+++ +.+|+.++++++.++|+|++++.++.+|+.++..+|+||||||+|.++++|...
T Consensus       181 T~lA~aia~~~~~~~~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~  246 (444)
T 2zan_A          181 SYLAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSEN  246 (444)
T ss_dssp             HHHHHHHHHHCCSSEEEEECCC---------CCCTHHHHHHHHHHSCSEEEEESCTTTTCCCSSCC
T ss_pred             HHHHHHHHHHcCCCCEEEEeHHHHHhhhcchHHHHHHHHHHHHHHcCCeEEEEechHhhccCCCCc
Confidence            78999999999 899999999999999999999999999999999999999999999999877653

>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=99.43  E-value=3.3e-13  Score=88.70  Aligned_cols=64  Identities=33%  Similarity=0.515  Sum_probs=59.2

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++++.+|+.++++++.++|.|++++.++.+|..++..+|++|||||+|.++++|+.
T Consensus       131 T~la~aia~~~~~~~~~i~~~~l~~~~~g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~  194 (357)
T 3d8b_A          131 TLIGKCIASQSGATFFSISASSLTSKWVGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGD  194 (357)
T ss_dssp             HHHHHHHHHHTTCEEEEEEGGGGCCSSTTHHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC---
T ss_pred             HHHHHHHHHHcCCeEEEEehHHhhccccchHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCC
Confidence            7899999999999999999999999999999999999999999999999999999999887653

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

Probab=99.43  E-value=2.1e-13  Score=90.19  Aligned_cols=64  Identities=34%  Similarity=0.485  Sum_probs=50.8

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++++.+|+.++++++.+.|.|+++..++.+|+.++..+|+||||||||.++.+|..
T Consensus       162 T~la~aia~~~~~~~~~v~~~~l~~~~~g~~~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~  225 (389)
T 3vfd_A          162 TMLAKAVAAESNATFFNISAASLTSKYVGEGEKLVRALFAVARELQPSIIFIDQVDSLLCERRE  225 (389)
T ss_dssp             HHHHHHHHHHTTCEEEEECSCCC-------CHHHHHHHHHHHHHSSSEEEEEETGGGGC-----
T ss_pred             HHHHHHHHHhhcCcEEEeeHHHhhccccchHHHHHHHHHHHHHhcCCeEEEEECchhhcccCCC
Confidence            7899999999999999999999999999999999999999999999999999999999877654

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

Probab=99.43  E-value=5.1e-13  Score=84.34  Aligned_cols=64  Identities=39%  Similarity=0.583  Sum_probs=61.0

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++++.+++.++++++.+.+.|+++..++.+|..++...|+||||||+|.++++|.+
T Consensus        65 T~la~~la~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~  128 (285)
T 3h4m_A           65 TLLAKAVATETNATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTD  128 (285)
T ss_dssp             HHHHHHHHHHTTCEEEEEEGGGGCCCSTTHHHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSS
T ss_pred             HHHHHHHHHHhCCCEEEEehHHHHHhccchHHHHHHHHHHHHHHcCCeEEEEECHHHhcccCcc
Confidence            7899999999999999999999999999999999999999999999999999999999887754

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

Probab=99.41  E-value=8.3e-13  Score=83.90  Aligned_cols=64  Identities=33%  Similarity=0.477  Sum_probs=59.8

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++++.+|+.++++++.+++.|++++.++.+|..+...+|++|||||+|.+..++..
T Consensus        68 T~la~~la~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~  131 (297)
T 3b9p_A           68 TLLARAVATECSATFLNISAASLTSKYVGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSS  131 (297)
T ss_dssp             HHHHHHHHHHTTCEEEEEESTTTSSSSCSCHHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC--
T ss_pred             HHHHHHHHHHhCCCeEEeeHHHHhhcccchHHHHHHHHHHHHHHcCCcEEEeccHHHhcccccc
Confidence            7899999999999999999999999999999999999999999999999999999999887653

>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=99.40  E-value=6.9e-13  Score=82.54  Aligned_cols=63  Identities=29%  Similarity=0.515  Sum_probs=53.5

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |++|+++|++++.+++.++++++.+.+.|++++.++.+|+.++...|++|||||+|.++.+|.
T Consensus        53 T~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~  115 (262)
T 2qz4_A           53 TLLAKAVATEAQVPFLAMAGAEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRS  115 (262)
T ss_dssp             HHHHHHHHHHHTCCEEEEETTTTSSSSTTHHHHHHHHHHHHHHHTCSEEEEEECC--------
T ss_pred             HHHHHHHHHHhCCCEEEechHHHHhhccChhHHHHHHHHHHHHhcCCeEEEEeCcchhhcccc
Confidence            789999999999999999999999999999999999999999999999999999999987764

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

Probab=99.36  E-value=1.4e-12  Score=81.66  Aligned_cols=64  Identities=34%  Similarity=0.566  Sum_probs=60.2

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |+++++++++++.+++.++++++.+.+.|++++.++.+|+.++...|+++|+||+|.+.+.+..
T Consensus        59 T~la~~la~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~il~iDeid~l~~~~~~  122 (257)
T 1lv7_A           59 TLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGA  122 (257)
T ss_dssp             HHHHHHHHHHHTCCEEEECSCSSTTSCCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCST
T ss_pred             HHHHHHHHHHcCCCEEEEeHHHHHHHhhhhhHHHHHHHHHHHHHcCCeeehhhhhhhhccCCCC
Confidence            7899999999999999999999999999999999999999999889999999999999987653

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

Probab=99.34  E-value=2.1e-12  Score=82.70  Aligned_cols=63  Identities=35%  Similarity=0.694  Sum_probs=58.0

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |++++++|++++.+++.+++.++.++|.|+++++++.+|+.++...|+++|+||+|.+++.|+
T Consensus        58 TtLakala~~~~~~~i~i~g~~l~~~~~~~~~~~i~~vf~~a~~~~p~i~~~Deid~~~~~r~  120 (274)
T 2x8a_A           58 TLLAKAVANESGLNFISVKGPELLNMYVGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRS  120 (274)
T ss_dssp             HHHHHHHHHHTTCEEEEEETTTTCSSTTHHHHHHHHHHHHHHHHTCSEEEEEETCTTTCC---
T ss_pred             HHHHHHHHHHcCCCEEEEEcHHHHhhhhhHHHHHHHHHHHHHHhcCCCeEeeehhhhhhcccC
Confidence            789999999999999999999999999999999999999999889999999999999987764

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

Probab=99.27  E-value=4.8e-12  Score=87.19  Aligned_cols=63  Identities=29%  Similarity=0.531  Sum_probs=59.9

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |++++++|++++.+++.++++++.+.++|+..++++.+|+.++...|+++||||||.++++|.
T Consensus        78 TtLaraIa~~~~~~~i~i~g~~~~~~~~g~~~~~v~~lfq~a~~~~p~il~IDEId~l~~~r~  140 (499)
T 2dhr_A           78 THLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRG  140 (499)
T ss_dssp             HHHHHHHHHHTTCCEEEEEGGGGTSSCTTHHHHHHHHHTTTSSSSSSCEEEEECGGGTCCCSS
T ss_pred             HHHHHHHHHHhCCCEEEEehhHHHHhhhhhHHHHHHHHHHHHHhcCCCEEEEehHHHHHHhhc
Confidence            789999999999999999999999999999999999999999888999999999999998775

>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=99.26  E-value=7.4e-13  Score=83.12  Aligned_cols=62  Identities=37%  Similarity=0.569  Sum_probs=57.7

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |++|+++|++++.+++.++++++.+.+.|++++.++.+|+.+...+|++|||||+|.+.++|
T Consensus        58 T~la~~la~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~  119 (268)
T 2r62_A           58 TLLAKAVAGEAHVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSR  119 (268)
T ss_dssp             HHHHHHHHHHHTCCCCCCCSCTTTTSCSSSCSSSSSTTHHHHHHSCSCEEEESCGGGTTC--
T ss_pred             HHHHHHHHHHhCCCEEEechHHHHHhhcchHHHHHHHHHHHHHhcCCeEEEEeChhhhcccc
Confidence            78999999999999999999999999999999999999999999999999999999998876

>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=99.11  E-value=1.9e-10  Score=71.73  Aligned_cols=63  Identities=29%  Similarity=0.531  Sum_probs=57.1

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |++++++++.++.+++.+++.++.+.+.|+..+.++.+|+.+....|+++|+||+|.++++|.
T Consensus        63 Ttl~~~i~~~~~~~~i~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~i~~~Deid~l~~~~~  125 (254)
T 1ixz_A           63 THLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRG  125 (254)
T ss_dssp             HHHHHHHHHHTTCCEEEEEHHHHHHSCTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---
T ss_pred             HHHHHHHHHHhCCCEEEeeHHHHHHHHhhHHHHHHHHHHHHHHhcCCeEEEehhhhhhhcccC
Confidence            789999999999999999999999999999999999999999888899999999999987664

>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=99.09  E-value=6.1e-11  Score=77.63  Aligned_cols=65  Identities=22%  Similarity=0.379  Sum_probs=56.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhc-ccChH-HHHHHHHHHHH----HhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSK-LAGES-ESNLRKAFEEA----DKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~-~~ges-~~~l~~if~~a----~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|+.++.+|+.++++++... |+|++ ++.++.+|+.+    ....|+||||||+|.+.+.|++.
T Consensus        65 T~la~~ia~~~~~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l~~~~~~~  135 (363)
T 3hws_A           65 TLLAETLARLLDVPFTMADATTLTEAGYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRKSDNP  135 (363)
T ss_dssp             HHHHHHHHHHTTCCEEEEEHHHHTTCHHHHHHHTHHHHHHHHHTTTCHHHHHHCEEEEECHHHHCCCSSCC
T ss_pred             HHHHHHHHHHcCCCEEEechHHhcccccccccHHHHHHHHHHHhhhhHHhcCCcEEEEeChhhhccccccc
Confidence            78999999999999999999999855 88987 67788999886    44578999999999999886553

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

Probab=99.03  E-value=7.5e-10  Score=70.12  Aligned_cols=63  Identities=29%  Similarity=0.531  Sum_probs=57.6

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |++++++++.++.+++.+++.++...+.|+..+.++.+|+.+....|+++|+||+|.++..+.
T Consensus        87 Ttl~~~i~~~~~~~~i~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~i~~iDeid~l~~~~~  149 (278)
T 1iy2_A           87 THLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRG  149 (278)
T ss_dssp             HHHHHHHHHHTTCCEEEEEHHHHHHSTTTHHHHHHHHHHHHHHTSCSEEEEEETHHHHHCC--
T ss_pred             HHHHHHHHHHcCCCEEEecHHHHHHHHhhHHHHHHHHHHHHHHhcCCcEEehhhhHhhhcccc
Confidence            789999999999999999999999999999999999999999888899999999999987654

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

Probab=99.01  E-value=1.4e-09  Score=69.10  Aligned_cols=60  Identities=12%  Similarity=0.230  Sum_probs=53.3

Q ss_pred             hHHHHHHHHHhC-------CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLG-------AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~-------~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |++|+++|+.++       .+++.++++++.+.++|.+++.++.+|+.+   .+++|||||+|.+++.++
T Consensus        81 T~la~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~~~~~~~~~---~~~vl~iDEid~l~~~~~  147 (309)
T 3syl_A           81 TTVALKMAGLLHRLGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEVLKRA---MGGVLFIDEAYYLYRPDN  147 (309)
T ss_dssp             HHHHHHHHHHHHHTTSSSSCCEEEECGGGTCCSSTTCHHHHHHHHHHHH---TTSEEEEETGGGSCCCC-
T ss_pred             HHHHHHHHHHHHhcCCcCCCcEEEEcHHHhhhhcccccHHHHHHHHHhc---CCCEEEEEChhhhccCCC
Confidence            789999999984       489999999999999999999999999887   578999999999987664

>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=98.93  E-value=2.7e-09  Score=67.18  Aligned_cols=60  Identities=18%  Similarity=0.281  Sum_probs=49.9

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccCh----HHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGE----SESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ge----s~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |++|+++|++++.+|+.+++++.   +.|.    ....++.+|+.+....+++|||||+|.+++.+.
T Consensus        78 T~la~~ia~~~~~~~~~i~~~~~---~~g~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~  141 (272)
T 1d2n_A           78 TALAAKIAEESNFPFIKICSPDK---MIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVP  141 (272)
T ss_dssp             HHHHHHHHHHHTCSEEEEECGGG---CTTCCHHHHHHHHHHHHHHHHTSSEEEEEECCHHHHTTCBT
T ss_pred             HHHHHHHHHHhCCCEEEEeCHHH---hcCCchHHHHHHHHHHHHHHHhcCCcEEEEEChhhhhccCC
Confidence            78999999999999999988753   3443    346789999999888899999999999976554

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

Probab=98.74  E-value=6.1e-08  Score=56.62  Aligned_cols=63  Identities=16%  Similarity=0.310  Sum_probs=52.7

Q ss_pred             hHHHHHHHHHh----------CCcEEEEchhhhhh--cccChHHHHHHHHHHHHHhc-CCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSL----------GAFFFLINGPEIMS--KLAGESESNLRKAFEEADKN-SPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~----------~~~~~~v~~~~l~~--~~~ges~~~l~~if~~a~~~-~p~iifiDEid~i~~~r~   65 (69)
                      |++++++++++          +.+++.+++..+..  .+.|..+..+++++..+... .|.+|||||+|.+.+.+.
T Consensus        57 T~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~  132 (187)
T 2p65_A           57 TAIVEGLAIKIVQGDVPDSLKGRKLVSLDLSSLIAGAKYRGDFEERLKSILKEVQDAEGQVVMFIDEIHTVVGAGA  132 (187)
T ss_dssp             HHHHHHHHHHHHTTCSCTTTTTCEEEEECHHHHHHHCCSHHHHHHHHHHHHHHHHHTTTSEEEEETTGGGGSSSSS
T ss_pred             HHHHHHHHHHHHhcCCcchhcCCeEEEEeHHHhhcCCCchhHHHHHHHHHHHHHHhcCCceEEEEeCHHHhccccc
Confidence            68899999987          78999999988873  36677888899999888765 789999999999986543

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

Probab=98.71  E-value=5.8e-08  Score=56.62  Aligned_cols=62  Identities=21%  Similarity=0.343  Sum_probs=51.4

Q ss_pred             hHHHHHHHHHh----------CCcEEEEchhhhh--hcccChHHHHHHHHHHHHHh-cCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSL----------GAFFFLINGPEIM--SKLAGESESNLRKAFEEADK-NSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~----------~~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~~-~~p~iifiDEid~i~~~r   64 (69)
                      |++++++++++          +.+++.+++..+.  ..+.|+.++.++++++.+.. ..|++|+|||+|.+.+.+
T Consensus        57 T~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~  131 (195)
T 1jbk_A           57 TAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAG  131 (195)
T ss_dssp             HHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT--
T ss_pred             HHHHHHHHHHHHhCCCchhhcCCcEEEeeHHHHhccCCccccHHHHHHHHHHHHhhcCCCeEEEEeCHHHHhccC
Confidence            78899999986          7899999999987  45778888899999987754 568999999999998654

>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=98.67  E-value=4.2e-08  Score=70.46  Aligned_cols=63  Identities=21%  Similarity=0.331  Sum_probs=42.8

Q ss_pred             hHHHHHHHHHh----------CCcEEEEchhhhh--hcccChHHHHHHHHHHHHHhc-CCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSL----------GAFFFLINGPEIM--SKLAGESESNLRKAFEEADKN-SPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~----------~~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~~~-~p~iifiDEid~i~~~r~   65 (69)
                      |++++++|..+          +.+++.++++.+.  .++.|+.+..++.+|+.+... .|+||||||+|.+.+.++
T Consensus       205 T~la~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~g~~~~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~  280 (854)
T 1qvr_A          205 TAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGK  280 (854)
T ss_dssp             HHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC--------
T ss_pred             HHHHHHHHHHHhcCCCchhhcCCeEEEeehHHhhccCccchHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCC
Confidence            78999999998          8999999999997  568999999999999999875 799999999999986553

>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=98.63  E-value=5e-08  Score=63.95  Aligned_cols=63  Identities=24%  Similarity=0.371  Sum_probs=43.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhh-hcccChH-HHHHHHHHHHHH----hcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIM-SKLAGES-ESNLRKAFEEAD----KNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~-~~~~ges-~~~l~~if~~a~----~~~p~iifiDEid~i~~~r~   65 (69)
                      |++|+++|+.++.+|+.++++.+. ..|.|+. +..+..+|..+.    ...+++|||||+|.+.++|+
T Consensus        86 T~la~~la~~l~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~  154 (376)
T 1um8_A           86 TLMAQTLAKHLDIPIAISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSE  154 (376)
T ss_dssp             HHHHHHHHHHTTCCEEEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC-----
T ss_pred             HHHHHHHHHHhCCCEEEecchhhhhcCcCCccHHHHHHHHHhhccchhhhcCCeEEEEcCHHHHhhhcC
Confidence            789999999999999999999876 4577775 556777776543    34789999999999988754

>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=98.60  E-value=4.6e-08  Score=61.67  Aligned_cols=62  Identities=23%  Similarity=0.341  Sum_probs=50.2

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhh-cccChH-HHHHHHHHHHH-----HhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMS-KLAGES-ESNLRKAFEEA-----DKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~-~~~ges-~~~l~~if~~a-----~~~~p~iifiDEid~i~~~r   64 (69)
                      |++|+++++.++.+++.++++++.. .|+|.. +..++++|..+     ....+++|||||+|.+.+.+
T Consensus        64 T~la~~la~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~  132 (310)
T 1ofh_A           64 TEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKG  132 (310)
T ss_dssp             HHHHHHHHHHHTCCEEEEEGGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCS
T ss_pred             HHHHHHHHHHhCCCEEEEcchhcccCCccCccHHHHHHHHHHHhhHHHhhccCCCEEEEEChhhcCccc
Confidence            7899999999999999999999876 577753 46678887743     12347999999999998765

>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=98.60  E-value=1.1e-07  Score=67.20  Aligned_cols=64  Identities=16%  Similarity=0.309  Sum_probs=53.6

Q ss_pred             hHHHHHHHHHh----------CCcEEEEchhhhh--hcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSL----------GAFFFLINGPEIM--SKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~----------~~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|++++..+          +.+++.++.+.+.  .++.|+.++.++.+|+.+....+++|||||+|.+.++++.
T Consensus       221 T~la~~la~~l~~~~v~~~~~~~~~~~~~~~~l~~~~~~~g~~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~~~~~  296 (758)
T 1r6b_X          221 TAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAA  296 (758)
T ss_dssp             HHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCS
T ss_pred             HHHHHHHHHHHHhCCCChhhcCCEEEEEcHHHHhccccccchHHHHHHHHHHHHHhcCCeEEEEechHHHhhcCCC
Confidence            78999999987          7788999888887  4689999999999999998888999999999999876543

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=98.55  E-value=4.8e-08  Score=74.79  Aligned_cols=63  Identities=22%  Similarity=0.239  Sum_probs=51.8

Q ss_pred             hHHHHHHHHHhC---CcEEEEchhh----hh--------hcccCh----HHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLG---AFFFLINGPE----IM--------SKLAGE----SESNLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~---~~~~~v~~~~----l~--------~~~~ge----s~~~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      |++|++++.+..   -|...++...    +.        ++|+++    +|+.|+.+|..|++..||+||+||+|+|+++
T Consensus      1096 T~la~~~~~~~~~~g~~~~fi~~~~~~~~~~~~~~G~d~~~~~~~~~~~~e~~l~~~~~~ar~~~~~~i~~d~~~al~~~ 1175 (1706)
T 3cmw_A         1096 TTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTPK 1175 (1706)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCGGGCCCH
T ss_pred             HHHHHHHHHHhhhcCCceeEEEcccchHHHHHHHhCCCHHHHhhccccchHHHHHHHHHHHHhcCCeEEEeCchHhcCcc
Confidence            789999998774   3444444444    33        788999    9999999999999999999999999999998


Q ss_pred             cc
Q psy3868          64 RE   65 (69)
Q Consensus        64 r~   65 (69)
                      |+
T Consensus      1176 ~~ 1177 (1706)
T 3cmw_A         1176 AE 1177 (1706)
T ss_dssp             HH
T ss_pred             cc
Confidence            53

>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=98.53  E-value=3.9e-08  Score=67.92  Aligned_cols=62  Identities=21%  Similarity=0.336  Sum_probs=42.7

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhh---------cccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMS---------KLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~---------~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |++++++|+.++.++..++++.+..         +|+|.....+.+.|..+....| ++|+||+|.+.+++.
T Consensus       122 Ttlar~ia~~l~~~~~~i~~~~~~~~~~~~g~~~~~ig~~~~~~~~~~~~a~~~~~-vl~lDEid~l~~~~~  192 (543)
T 3m6a_A          122 TSLAKSIAKSLGRKFVRISLGGVRDESEIRGHRRTYVGAMPGRIIQGMKKAGKLNP-VFLLDEIDKMSSDFR  192 (543)
T ss_dssp             HHHHHHHHHHHTCEEEEECCCC--------------------CHHHHHHTTCSSSE-EEEEEESSSCC----
T ss_pred             HHHHHHHHHhcCCCeEEEEecccchhhhhhhHHHHHhccCchHHHHHHHHhhccCC-EEEEhhhhhhhhhhc
Confidence            7899999999999999998876544         6888888999999998876666 999999999988753

>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=98.25  E-value=1.5e-06  Score=55.80  Aligned_cols=60  Identities=10%  Similarity=0.192  Sum_probs=45.2

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      |++++++++++   +.+++.+++.++...+.+.........|.... ..+.+|||||+|.+..+
T Consensus        51 T~la~~i~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~vL~iDEi~~l~~~  113 (324)
T 1l8q_A           51 THLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMY-KSVDLLLLDDVQFLSGK  113 (324)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEEEHHHHHHHHHHHHHHTCHHHHHHHH-HTCSEEEEECGGGGTTC
T ss_pred             HHHHHHHHHHHHHCCCEEEEEEHHHHHHHHHHHHHcCcHHHHHHHh-cCCCEEEEcCcccccCC
Confidence            78999999999   89999999999876666554433333343332 24899999999999764

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

Probab=98.25  E-value=1.3e-06  Score=56.53  Aligned_cols=30  Identities=27%  Similarity=0.282  Sum_probs=23.5

Q ss_pred             hHHHHHHHHHhCC--cEEEEchhhhhhcccCh
Q psy3868           3 YRLTTLCRDSLGA--FFFLINGPEIMSKLAGE   32 (69)
Q Consensus         3 T~la~aia~~~~~--~~~~v~~~~l~~~~~ge   32 (69)
                      |++|++++++++.  +++.+++..+.+.+.++
T Consensus        84 T~la~~la~~l~~~~~~~~~~~~~~~~~~~~~  115 (368)
T 3uk6_A           84 TAIAMGMAQALGPDTPFTAIAGSEIFSLEMSK  115 (368)
T ss_dssp             HHHHHHHHHHHCSSCCEEEEEGGGGSCSSSCH
T ss_pred             HHHHHHHHHHhcccCCcccccchhhhhcccch
Confidence            7899999999985  88899887765554444

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=98.23  E-value=2.4e-06  Score=57.97  Aligned_cols=55  Identities=20%  Similarity=0.254  Sum_probs=43.2

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifiDEid~i~~~r   64 (69)
                      |++|+++++.++.+|+.+++...       +.+.++++|+.+..    ..+.+|||||||.+....
T Consensus        64 TtlAr~ia~~~~~~f~~l~a~~~-------~~~~ir~~~~~a~~~~~~~~~~iLfIDEI~~l~~~~  122 (447)
T 3pvs_A           64 TTLAEVIARYANADVERISAVTS-------GVKEIREAIERARQNRNAGRRTILFVDEVHRFNKSQ  122 (447)
T ss_dssp             HHHHHHHHHHTTCEEEEEETTTC-------CHHHHHHHHHHHHHHHHTTCCEEEEEETTTCC----
T ss_pred             HHHHHHHHHHhCCCeEEEEeccC-------CHHHHHHHHHHHHHhhhcCCCcEEEEeChhhhCHHH
Confidence            78999999999999999987543       46678888888764    468999999999997543

>1sxj_A Activator 1 95 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=98.18  E-value=2.2e-07  Score=63.61  Aligned_cols=62  Identities=18%  Similarity=0.200  Sum_probs=43.2

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHH-------HHHHHHHHH-----HhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESES-------NLRKAFEEA-----DKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~-------~l~~if~~a-----~~~~p~iifiDEid~i~~~r   64 (69)
                      |++|+++|++++.+++.++++++.+.+..+..-       .++.+|+.+     ...++++|||||+|.+....
T Consensus        91 Ttla~~la~~l~~~~i~in~s~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~~  164 (516)
T 1sxj_A           91 TTAAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGD  164 (516)
T ss_dssp             HHHHHHHHHHTTCEEEEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTS
T ss_pred             HHHHHHHHHHcCCCEEEEeCCCcchHHHHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCCccchhh
Confidence            789999999999999999998875543222111       123344433     23578999999999997643

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.15  E-value=2.5e-06  Score=55.95  Aligned_cols=59  Identities=17%  Similarity=0.220  Sum_probs=45.7

Q ss_pred             hHHHHHHHHHh----------CCcEEEEchhhhhh----------cc------cChHHHHHHHHHHHH--HhcCCeEEEE
Q psy3868           3 YRLTTLCRDSL----------GAFFFLINGPEIMS----------KL------AGESESNLRKAFEEA--DKNSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~----------~~~~~~v~~~~l~~----------~~------~ges~~~l~~if~~a--~~~~p~iifi   54 (69)
                      |++++.+++++          +..++++||..+.+          .+      .|++...+++.|+..  ....++|+|+
T Consensus        59 T~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~l  138 (318)
T 3te6_A           59 FQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILI  138 (318)
T ss_dssp             HHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHHHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEE
T ss_pred             HHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEE
Confidence            78999999998          45788899865432          22      345678899999985  3567899999


Q ss_pred             ccccccc
Q psy3868          55 DELDAIA   61 (69)
Q Consensus        55 DEid~i~   61 (69)
                      ||+|.+.
T Consensus       139 DE~d~l~  145 (318)
T 3te6_A          139 QNPENLL  145 (318)
T ss_dssp             ECCSSSC
T ss_pred             ecHHHhh
Confidence            9999997

>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=98.14  E-value=1.4e-06  Score=59.55  Aligned_cols=57  Identities=14%  Similarity=0.125  Sum_probs=46.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhh-cccCh-HHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMS-KLAGE-SESNLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~-~~~ge-s~~~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      |++|+++|+.++.+|+.++++.+.+ +|+|+ .++.++++|+.++...    ++||+|.+...
T Consensus        64 T~lar~lA~~l~~~~~~v~~~~~~~~g~vG~d~e~~lr~lf~~a~~~~----~~De~d~~~~~  122 (444)
T 1g41_A           64 TEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAMKLV----RQQEIAKNRAR  122 (444)
T ss_dssp             HHHHHHHHHHTTCCEEEEEGGGGC----CCCCTHHHHHHHHHHHHHHH----HHHHHHSCC--
T ss_pred             HHHHHHHHHHcCCCceeecchhhcccceeeccHHHHHHHHHHHHHhcc----hhhhhhhhhcc
Confidence            7899999999999999999999998 59995 8999999999987653    48888877543

>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=98.06  E-value=4.5e-06  Score=56.32  Aligned_cols=61  Identities=15%  Similarity=0.237  Sum_probs=43.9

Q ss_pred             hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      |++++++++++     +.+++.+++.++...+.+.-.......|.......|.+|||||+|.+..+
T Consensus       144 TtLa~aia~~l~~~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vL~IDEi~~l~~~  209 (440)
T 2z4s_A          144 THLLQSIGNYVVQNEPDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLIGK  209 (440)
T ss_dssp             HHHHHHHHHHHHHHCCSSCEEEEEHHHHHHHHHHHHHTTCHHHHHHHHTTTCSEEEEECGGGGSSC
T ss_pred             HHHHHHHHHHHHHhCCCCeEEEeeHHHHHHHHHHHHHcccHHHHHHHhcCCCCEEEEeCcccccCC
Confidence            78999999998     88999999998865554433322222343333337999999999999864

>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=98.04  E-value=6.4e-06  Score=52.62  Aligned_cols=52  Identities=17%  Similarity=0.269  Sum_probs=41.6

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhc-----CCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKN-----SPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~-----~p~iifiDEid~i~   61 (69)
                      |+++++++++++.+++++++++.       ....+++.+......     .+.+|||||+|.+.
T Consensus        62 T~la~~la~~l~~~~~~i~~~~~-------~~~~i~~~~~~~~~~~~~~~~~~vliiDEi~~l~  118 (324)
T 3u61_B           62 TTVAKALCHDVNADMMFVNGSDC-------KIDFVRGPLTNFASAASFDGRQKVIVIDEFDRSG  118 (324)
T ss_dssp             HHHHHHHHHHTTEEEEEEETTTC-------CHHHHHTHHHHHHHBCCCSSCEEEEEEESCCCGG
T ss_pred             HHHHHHHHHHhCCCEEEEccccc-------CHHHHHHHHHHHHhhcccCCCCeEEEEECCcccC
Confidence            78999999999999999998774       255666666554332     67999999999986

>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=97.97  E-value=8.2e-06  Score=57.71  Aligned_cols=58  Identities=17%  Similarity=0.299  Sum_probs=43.4

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhc------------ccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSK------------LAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~------------~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++|+++|+.++.+++.++++++..+            |+|..+.  ..+....+...++||||||+|.+-+
T Consensus       502 T~la~~la~~l~~~~~~i~~s~~~~~~~~~~l~g~~~g~~g~~~~--~~l~~~~~~~~~~vl~lDEi~~~~~  571 (758)
T 1r6b_X          502 TEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQG--GLLTDAVIKHPHAVLLLDEIEKAHP  571 (758)
T ss_dssp             HHHHHHHHHHHTCEEEEEEGGGCSSSSCCSSSCCCCSCSHHHHHT--THHHHHHHHCSSEEEEEETGGGSCH
T ss_pred             HHHHHHHHHHhcCCEEEEechhhcchhhHhhhcCCCCCCcCcccc--chHHHHHHhCCCcEEEEeCccccCH
Confidence            78999999999999999999988653            4443332  2234444556689999999998753

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

Probab=97.94  E-value=1.8e-05  Score=50.69  Aligned_cols=52  Identities=21%  Similarity=0.348  Sum_probs=40.9

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++|++++++++.+|+.++++.+.      ....+...+..  ...+++|||||+|.+.+
T Consensus        69 T~la~~ia~~~~~~~~~~~~~~~~------~~~~~~~~~~~--~~~~~vl~lDEi~~l~~  120 (338)
T 3pfi_A           69 TTLANIISYEMSANIKTTAAPMIE------KSGDLAAILTN--LSEGDILFIDEIHRLSP  120 (338)
T ss_dssp             HHHHHHHHHHTTCCEEEEEGGGCC------SHHHHHHHHHT--CCTTCEEEEETGGGCCH
T ss_pred             HHHHHHHHHHhCCCeEEecchhcc------chhHHHHHHHh--ccCCCEEEEechhhcCH
Confidence            789999999999999999998762      34455555543  35689999999998864

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.92  E-value=2.4e-06  Score=49.43  Aligned_cols=50  Identities=4%  Similarity=0.110  Sum_probs=39.9

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      |++|+++++..+ +|+.++++++...+       .+.+|+.+   .+.+|||||+|.+.+.
T Consensus        41 t~lA~~i~~~~~-~~~~~~~~~~~~~~-------~~~~~~~a---~~~~l~lDei~~l~~~   90 (143)
T 3co5_A           41 ETVARYFHKNGT-PWVSPARVEYLIDM-------PMELLQKA---EGGVLYVGDIAQYSRN   90 (143)
T ss_dssp             HHHHGGGCCTTS-CEECCSSTTHHHHC-------HHHHHHHT---TTSEEEEEECTTCCHH
T ss_pred             HHHHHHHHHhCC-CeEEechhhCChHh-------hhhHHHhC---CCCeEEEeChHHCCHH
Confidence            689999999888 99999999885443       56677665   3689999999998653

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

Probab=97.91  E-value=8.1e-06  Score=55.38  Aligned_cols=50  Identities=22%  Similarity=0.329  Sum_probs=37.4

Q ss_pred             hHHHHHHHHHh----------CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEc
Q psy3868           3 YRLTTLCRDSL----------GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFID   55 (69)
Q Consensus         3 T~la~aia~~~----------~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiD   55 (69)
                      |++|+++|..+          +.+++.++++   .+|.|+.+..++.+|+.++...|.|||||
T Consensus       215 T~la~~la~~l~~~~~p~~l~~~~~~~l~~~---~~~~g~~e~~~~~~~~~~~~~~~~iLfiD  274 (468)
T 3pxg_A          215 TAIAEGLAQQIINNEVPEILRDKRVMTLDMG---TKYRGEFEDRLKKVMDEIRQAGNIILFID  274 (468)
T ss_dssp             HHHHHHHHHHHHSSCSCTTTSSCCEECC-------------CTTHHHHHHHHHTCCCCEEEEC
T ss_pred             HHHHHHHHHHHHhCCCChhhcCCeEEEeeCC---ccccchHHHHHHHHHHHHHhcCCeEEEEe
Confidence            78999999997          8899999988   78899999999999999998899999999

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=97.91  E-value=5.2e-06  Score=47.99  Aligned_cols=51  Identities=6%  Similarity=-0.031  Sum_probs=39.2

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      |++|+++++..   +.+|+ ++++.+.+.      ......|+.+   .+.+|||||+|.+.+.
T Consensus        38 t~lA~~i~~~~~~~~~~~v-~~~~~~~~~------~~~~~~~~~a---~~g~l~ldei~~l~~~   91 (145)
T 3n70_A           38 MTGARYLHQFGRNAQGEFV-YRELTPDNA------PQLNDFIALA---QGGTLVLSHPEHLTRE   91 (145)
T ss_dssp             HHHHHHHHHSSTTTTSCCE-EEECCTTTS------SCHHHHHHHH---TTSCEEEECGGGSCHH
T ss_pred             HHHHHHHHHhCCccCCCEE-EECCCCCcc------hhhhcHHHHc---CCcEEEEcChHHCCHH
Confidence            78999999987   67999 999887543      3345566665   4689999999998653

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

Probab=97.89  E-value=1.9e-05  Score=55.98  Aligned_cols=56  Identities=18%  Similarity=0.259  Sum_probs=43.3

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++|+++|..+   +.+|+.++++++...+.+.    -..+++..+...+++|||||||.+.+
T Consensus       535 T~lA~ala~~l~~~~~~~i~i~~s~~~~~~~~~----~~~l~~~~~~~~~~vl~lDEi~~~~~  593 (758)
T 3pxi_A          535 TELARALAESIFGDEESMIRIDMSEYMEKHSTS----GGQLTEKVRRKPYSVVLLDAIEKAHP  593 (758)
T ss_dssp             HHHHHHHHHHHHSCTTCEEEEEGGGGCSSCCCC-------CHHHHHHCSSSEEEEECGGGSCH
T ss_pred             HHHHHHHHHHhcCCCcceEEEechhcccccccc----cchhhHHHHhCCCeEEEEeCccccCH
Confidence            78999999998   6899999999998887765    22334444556779999999998753

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

Probab=97.88  E-value=9.1e-06  Score=57.67  Aligned_cols=50  Identities=22%  Similarity=0.316  Sum_probs=37.8

Q ss_pred             hHHHHHHHHHh----------CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEc
Q psy3868           3 YRLTTLCRDSL----------GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFID   55 (69)
Q Consensus         3 T~la~aia~~~----------~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiD   55 (69)
                      |++|+++|..+          +.+++.+++   ..+|.|+.+.+++.+|+.+....|+|||||
T Consensus       215 T~la~~la~~l~~~~~p~~l~~~~~~~~~~---g~~~~G~~e~~l~~~~~~~~~~~~~iLfiD  274 (758)
T 3pxi_A          215 TAIAEGLAQQIINNEVPEILRDKRVMTLDM---GTKYRGEFEDRLKKVMDEIRQAGNIILFID  274 (758)
T ss_dssp             HHHHHHHHHHHHSSCSCTTTSSCCEECC-------------CTTHHHHHHHHHTCCCCEEEEC
T ss_pred             HHHHHHHHHHHhcCCCChhhcCCeEEEecc---cccccchHHHHHHHHHHHHHhcCCEEEEEc
Confidence            78999999997          889999988   677899999999999999999999999999

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

Probab=97.74  E-value=3.2e-05  Score=49.61  Aligned_cols=61  Identities=16%  Similarity=0.171  Sum_probs=42.6

Q ss_pred             hHHHHHHHHHh---------CCcEEEEchhhhhh------c----------ccChHH-HHHHHHHHHHHhc-CCeEEEEc
Q psy3868           3 YRLTTLCRDSL---------GAFFFLINGPEIMS------K----------LAGESE-SNLRKAFEEADKN-SPSIIFID   55 (69)
Q Consensus         3 T~la~aia~~~---------~~~~~~v~~~~l~~------~----------~~ges~-~~l~~if~~a~~~-~p~iifiD   55 (69)
                      |++++++++++         +.+++.+++....+      .          ..|.+. ..++.+++..... +|++||||
T Consensus        58 T~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilD  137 (387)
T 2v1u_A           58 TAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLD  137 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEE
T ss_pred             HHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEc
Confidence            78899999988         88999999865321      1          123323 3356666665443 48999999


Q ss_pred             cccccccc
Q psy3868          56 ELDAIAPK   63 (69)
Q Consensus        56 Eid~i~~~   63 (69)
                      |+|.+...
T Consensus       138 Ei~~l~~~  145 (387)
T 2v1u_A          138 EIDFLPKR  145 (387)
T ss_dssp             TTTHHHHS
T ss_pred             cHhhhccc
Confidence            99998765

>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=97.70  E-value=7.4e-05  Score=47.36  Aligned_cols=53  Identities=23%  Similarity=0.414  Sum_probs=39.5

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++|++++++++.+++.++++.+.      ....+...|..+ ...+.+|||||+|.+..
T Consensus        52 T~la~~i~~~~~~~~~~~~~~~~~------~~~~l~~~l~~~-~~~~~~l~lDEi~~l~~  104 (324)
T 1hqc_A           52 TTLAHVIAHELGVNLRVTSGPAIE------KPGDLAAILANS-LEEGDILFIDEIHRLSR  104 (324)
T ss_dssp             HHHHHHHHHHHTCCEEEECTTTCC------SHHHHHHHHTTT-CCTTCEEEETTTTSCCH
T ss_pred             HHHHHHHHHHhCCCEEEEeccccC------ChHHHHHHHHHh-ccCCCEEEEECCccccc
Confidence            789999999999999999987762      233444444331 14689999999999864

>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=97.69  E-value=4.7e-05  Score=49.13  Aligned_cols=61  Identities=18%  Similarity=0.243  Sum_probs=41.8

Q ss_pred             hHHHHHHHHHh-----------CCcEEEEchhhhh-h----------c-------ccChH-HHHHHHHHHHHHhcCCeEE
Q psy3868           3 YRLTTLCRDSL-----------GAFFFLINGPEIM-S----------K-------LAGES-ESNLRKAFEEADKNSPSII   52 (69)
Q Consensus         3 T~la~aia~~~-----------~~~~~~v~~~~l~-~----------~-------~~ges-~~~l~~if~~a~~~~p~ii   52 (69)
                      |++++++++++           +.+++.+++.... +          .       ..|.+ ...+..+++.+....+ +|
T Consensus        59 T~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~-vl  137 (384)
T 2qby_B           59 TFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRA-II  137 (384)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCE-EE
T ss_pred             HHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCC-EE
Confidence            78899999987           9999999987643 1          1       11222 3345566665544444 99


Q ss_pred             EEcccccccccc
Q psy3868          53 FIDELDAIAPKR   64 (69)
Q Consensus        53 fiDEid~i~~~r   64 (69)
                      ||||+|.+...+
T Consensus       138 ilDEi~~l~~~~  149 (384)
T 2qby_B          138 YLDEVDTLVKRR  149 (384)
T ss_dssp             EEETTHHHHHST
T ss_pred             EEECHHHhccCC
Confidence            999999997643

>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=97.64  E-value=0.00014  Score=46.55  Aligned_cols=62  Identities=21%  Similarity=0.266  Sum_probs=43.0

Q ss_pred             hHHHHHHHHHh------CCcEEEEchhhhhh------c----------ccChH-HHHHHHHHHHHHhcC-CeEEEEcccc
Q psy3868           3 YRLTTLCRDSL------GAFFFLINGPEIMS------K----------LAGES-ESNLRKAFEEADKNS-PSIIFIDELD   58 (69)
Q Consensus         3 T~la~aia~~~------~~~~~~v~~~~l~~------~----------~~ges-~~~l~~if~~a~~~~-p~iifiDEid   58 (69)
                      |++++++++++      +.+++.+++.....      .          ..|.+ ....+.+++...... |++|+|||+|
T Consensus        59 Ttl~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~  138 (386)
T 2qby_A           59 TAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEID  138 (386)
T ss_dssp             HHHHHHHHHHHHHHTCSSCEEEEEEHHHHCSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHH
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChh
Confidence            78999999988      88999999765321      1          12222 333566666665543 9999999999


Q ss_pred             cccccc
Q psy3868          59 AIAPKR   64 (69)
Q Consensus        59 ~i~~~r   64 (69)
                      .+...+
T Consensus       139 ~l~~~~  144 (386)
T 2qby_A          139 AFVKKY  144 (386)
T ss_dssp             HHHHSS
T ss_pred             hhhccC
Confidence            987543

>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=97.45  E-value=0.00013  Score=52.47  Aligned_cols=58  Identities=24%  Similarity=0.298  Sum_probs=38.8

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhc------------ccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSK------------LAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~------------~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++|+++++.+   +.+|+.++++.+...            |+|..+  ...+....+...+++|||||+|.+-+
T Consensus       602 T~lA~~la~~~~~~~~~~i~i~~~~~~~~~~~s~l~g~~~~~~G~~~--~g~l~~~~~~~~~~vl~lDEi~~l~~  674 (854)
T 1qvr_A          602 TELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEE--GGQLTEAVRRRPYSVILFDEIEKAHP  674 (854)
T ss_dssp             HHHHHHHHHHHHSSGGGEEEECTTTCCSSGGGGGC----------------CHHHHHHHCSSEEEEESSGGGSCH
T ss_pred             HHHHHHHHHHhcCCCCcEEEEechhccchhHHHHHcCCCCCCcCccc--cchHHHHHHhCCCeEEEEecccccCH
Confidence            78999999999   789999999876543            223322  12344444455679999999998743

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

Probab=97.43  E-value=9.3e-05  Score=46.65  Aligned_cols=58  Identities=24%  Similarity=0.323  Sum_probs=37.9

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhc-----cc-------ChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSK-----LA-------GESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~-----~~-------ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++|+++++.+   +.+++.++++.+...     ++       |....  ..+....+...+++|||||+|.+.+
T Consensus        61 t~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~--~~~~~~~~~~~~~vl~lDEi~~l~~  133 (311)
T 4fcw_A           61 TELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEG--GQLTEAVRRRPYSVILFDAIEKAHP  133 (311)
T ss_dssp             HHHHHHHHHHHHSCGGGEEEEEGGGCCSTTHHHHHHCCCTTSTTTTTC--CHHHHHHHHCSSEEEEEETGGGSCH
T ss_pred             HHHHHHHHHHHcCCCcceEEeecccccccccHHHhcCCCCcccccccc--chHHHHHHhCCCeEEEEeChhhcCH
Confidence            78999999998   567999998876322     11       11110  1233333445569999999998854

>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=97.11  E-value=0.0023  Score=41.10  Aligned_cols=58  Identities=17%  Similarity=0.088  Sum_probs=37.3

Q ss_pred             hHHHHHHHHHh----CCcEEEEchhhhhh------c----------ccChH-HHHHHHHHHHHHh-cCCeEEEEcccccc
Q psy3868           3 YRLTTLCRDSL----GAFFFLINGPEIMS------K----------LAGES-ESNLRKAFEEADK-NSPSIIFIDELDAI   60 (69)
Q Consensus         3 T~la~aia~~~----~~~~~~v~~~~l~~------~----------~~ges-~~~l~~if~~a~~-~~p~iifiDEid~i   60 (69)
                      |++++++++++    +.+++.+++....+      .          ..|.+ ....+.+.+.... ..|.+|+|||+|.+
T Consensus        58 Ttl~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l  137 (389)
T 1fnn_A           58 TVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNL  137 (389)
T ss_dssp             HHHHHHHHHHHTTSCCCEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGS
T ss_pred             HHHHHHHHHHHhhhcCeeEEEEeCccCCCHHHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECcccc
Confidence            78899999998    67889998754321      1          01222 2233333333333 45899999999988

>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=97.10  E-value=0.0012  Score=42.76  Aligned_cols=52  Identities=15%  Similarity=0.379  Sum_probs=38.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++++++|++++.++...+++.+.      ....+..++..  ...+.|+||||+|.+.+
T Consensus        65 TTLa~~ia~~l~~~~~~~sg~~~~------~~~~l~~~~~~--~~~~~v~~iDE~~~l~~  116 (334)
T 1in4_A           65 TTLAHIIASELQTNIHVTSGPVLV------KQGDMAAILTS--LERGDVLFIDEIHRLNK  116 (334)
T ss_dssp             HHHHHHHHHHHTCCEEEEETTTCC------SHHHHHHHHHH--CCTTCEEEEETGGGCCH
T ss_pred             HHHHHHHHHHhCCCEEEEechHhc------CHHHHHHHHHH--ccCCCEEEEcchhhcCH
Confidence            789999999999998887776542      23345555433  23578999999999865

>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=97.09  E-value=0.0014  Score=40.62  Aligned_cols=57  Identities=18%  Similarity=0.214  Sum_probs=35.6

Q ss_pred             hHHHHHHHHHhC---CcEEEEchhhhhhc-----ccChHHH-------HHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLG---AFFFLINGPEIMSK-----LAGESES-------NLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~---~~~~~v~~~~l~~~-----~~ges~~-------~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++|+++++.++   .+|+.++++.+...     ..|....       .....|+.   ..+.+|||||+|.+.+
T Consensus        43 t~la~~i~~~~~~~~~~~~~v~~~~~~~~~~~~~l~g~~~~~~~g~~~~~~~~l~~---a~~~~l~lDEi~~l~~  114 (265)
T 2bjv_A           43 ELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGAFTGAQKRHPGRFER---ADGGTLFLDELATAPM  114 (265)
T ss_dssp             HHHHHHHHHTSTTTTSCEEEEEGGGSCHHHHHHHHHCCC---------CCCCHHHH---TTTSEEEEESGGGSCH
T ss_pred             HHHHHHHHHhcCccCCCeEEEecCCCChhHHHHHhcCCcccccccccccccchhhh---cCCcEEEEechHhcCH
Confidence            789999999875   68999999876321     1111000       00112222   2468999999999864

>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=97.06  E-value=0.0018  Score=38.01  Aligned_cols=54  Identities=22%  Similarity=0.250  Sum_probs=35.3

Q ss_pred             hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHHHHHHHHHHHHH------hcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESESNLRKAFEEAD------KNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~------~~~p~iifiDEid~i~~   62 (69)
                      |++++++++++     +.+++.++++...+      ...++..+....      ...+.+|+|||+|.+.+
T Consensus        52 T~l~~~l~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~  116 (226)
T 2chg_A           52 TATAIALARDLFGENWRDNFIEMNASDERG------IDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTA  116 (226)
T ss_dssp             HHHHHHHHHHHHGGGGGGGEEEEETTCTTC------HHHHHHHHHHHHTSCCSTTCSCEEEEEETGGGSCH
T ss_pred             HHHHHHHHHHHhccccccceEEeccccccC------hHHHHHHHHHHhcccCCCccCceEEEEeChhhcCH
Confidence            77889998876     45688887765421      223333333322      25689999999999864

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=96.88  E-value=0.00022  Score=45.82  Aligned_cols=56  Identities=20%  Similarity=0.287  Sum_probs=36.2

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhc-----ccC--------hHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSK-----LAG--------ESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~-----~~g--------es~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++|+++++..   +.||+.++|+.+...     .+|        ... .....|+.+   .+.+|||||||.+..
T Consensus        39 t~lAr~i~~~~~~~~~~~v~v~~~~~~~~l~~~~lfg~~~g~~tg~~~-~~~g~~~~a---~~g~L~LDEi~~l~~  110 (304)
T 1ojl_A           39 ELVARALHACSARSDRPLVTLNCAALNESLLESELFGHEKGAFTGADK-RREGRFVEA---DGGTLFLDEIGDISP  110 (304)
T ss_dssp             HHHHHHHHHHSSCSSSCCCEEECSSCCHHHHHHHHTCCCSSCCC---C-CCCCHHHHH---TTSEEEEESCTTCCH
T ss_pred             HHHHHHHHHhCcccCCCeEEEeCCCCChHHHHHHhcCccccccCchhh-hhcCHHHhc---CCCEEEEeccccCCH
Confidence            68999999965   578999998765321     111        111 122344444   357999999998864

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=96.84  E-value=0.0014  Score=43.36  Aligned_cols=61  Identities=15%  Similarity=0.130  Sum_probs=39.5

Q ss_pred             hHHHHHHHHHhCCc--EEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSLGAF--FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~~~~--~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |+|+.++|.+.|.+  |+.+...+.++.+..+.+..++.+++...+..  +|+|||++++...+.
T Consensus       137 TtLAlqlA~~~G~~VlyIs~~~eE~v~~~~~~le~~l~~i~~~l~~~~--LLVIDsI~aL~~~~~  199 (331)
T 2vhj_A          137 TPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHR--VIVIDSLKNVIGAAG  199 (331)
T ss_dssp             HHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHCS--EEEEECCTTTC----
T ss_pred             HHHHHHHHHhCCCCEEEEEecchhhhhhhhcCHHHHHHHHHHHHhhCC--EEEEecccccccccc
Confidence            67888888765544  44442233344444666777888888776654  999999999976543

>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=96.83  E-value=0.0015  Score=40.93  Aligned_cols=54  Identities=13%  Similarity=0.155  Sum_probs=38.4

Q ss_pred             hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHHHHHHHHHHHHH-------hcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESESNLRKAFEEAD-------KNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~-------~~~p~iifiDEid~i~~   62 (69)
                      |++++++++++     +.+++.+++++..      +...++++++...       ...+.+|+|||+|.+..
T Consensus        56 t~la~~l~~~l~~~~~~~~~~~~~~~~~~------~~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~  121 (323)
T 1sxj_B           56 TTSVHCLAHELLGRSYADGVLELNASDDR------GIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTA  121 (323)
T ss_dssp             HHHHHHHHHHHHGGGHHHHEEEECTTSCC------SHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCH
T ss_pred             HHHHHHHHHHhcCCcccCCEEEecCcccc------ChHHHHHHHHHHHhccccCCCCCceEEEEECcccCCH
Confidence            67899999886     4567888876531      2456666666654       23489999999999854

>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=96.81  E-value=0.0013  Score=39.45  Aligned_cols=52  Identities=21%  Similarity=0.110  Sum_probs=36.6

Q ss_pred             hHHHHHHHHHhC---CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLG---AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~---~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |+++++++++++   .+++.++++++...+.        +.++.  -..|.+|+|||+|.+....
T Consensus        66 T~la~~l~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~--~~~~~vliiDe~~~~~~~~  120 (242)
T 3bos_A           66 THLIHAACARANELERRSFYIPLGIHASIST--------ALLEG--LEQFDLICIDDVDAVAGHP  120 (242)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEEEGGGGGGSCG--------GGGTT--GGGSSEEEEETGGGGTTCH
T ss_pred             HHHHHHHHHHHHHcCCeEEEEEHHHHHHHHH--------HHHHh--ccCCCEEEEeccccccCCH
Confidence            678888888775   7888899888755431        11111  1458999999999987643

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.76  E-value=0.0011  Score=39.39  Aligned_cols=57  Identities=16%  Similarity=0.306  Sum_probs=35.7

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccCh-HHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGE-SESNLRKAFEEADKNSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ge-s~~~l~~if~~a~~~~p~iifiDEid~i~   61 (69)
                      |++++++++++   +.+++.++++++...+.+. ....+.++++...  .+.+|+|||++...
T Consensus        68 T~la~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~lilDei~~~~  128 (202)
T 2w58_A           68 TYLLAAIANELAKRNVSSLIVYVPELFRELKHSLQDQTMNEKLDYIK--KVPVLMLDDLGAEA  128 (202)
T ss_dssp             HHHHHHHHHHHHTTTCCEEEEEHHHHHHHHHHC---CCCHHHHHHHH--HSSEEEEEEECCC-
T ss_pred             HHHHHHHHHHHHHcCCeEEEEEhHHHHHHHHHHhccchHHHHHHHhc--CCCEEEEcCCCCCc
Confidence            78899999888   6788889988876543211 0111233344333  34699999997754

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.70  E-value=0.0015  Score=38.02  Aligned_cols=45  Identities=9%  Similarity=0.092  Sum_probs=33.7

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |++++++++..   |...+.+++.++...               +...+|.+|++||++.+..
T Consensus        50 TtL~~~i~~~~~~~g~~~~~~~~~~~~~~---------------~~~~~~~lLilDE~~~~~~   97 (149)
T 2kjq_A           50 SHLLQAWVAQALEAGKNAAYIDAASMPLT---------------DAAFEAEYLAVDQVEKLGN   97 (149)
T ss_dssp             CHHHHHHHHHHHTTTCCEEEEETTTSCCC---------------GGGGGCSEEEEESTTCCCS
T ss_pred             HHHHHHHHHHHHhcCCcEEEEcHHHhhHH---------------HHHhCCCEEEEeCccccCh
Confidence            67888898887   777888888777543               1123689999999998754

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=96.63  E-value=0.0033  Score=49.55  Aligned_cols=62  Identities=21%  Similarity=0.263  Sum_probs=44.2

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhh----hhcccC------------hHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEI----MSKLAG------------ESESNLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l----~~~~~g------------es~~~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      |+||.+++.+.   |..+..++....    ..+..|            .+|+.++.++..+++.+|++|+|||++++.+.
T Consensus      1441 T~LA~ala~ea~~~G~~v~Fi~~e~~~~~l~a~~~G~dl~~l~v~~~~~~E~~l~~~~~lvr~~~~~lVVIDsi~al~p~ 1520 (2050)
T 3cmu_A         1441 TTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTPK 1520 (2050)
T ss_dssp             HHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCGGGCCCH
T ss_pred             HHHHHHHHHHHHHcCCcEEEEEcccccCHHHHHHcCCCchhceeecCChHHHHHHHHHHHHhcCCCCEEEEcChhHhccc
Confidence            67787777765   334444554422    222233            56788999999999999999999999999985


Q ss_pred             c
Q psy3868          64 R   64 (69)
Q Consensus        64 r   64 (69)
                      +
T Consensus      1521 ~ 1521 (2050)
T 3cmu_A         1521 A 1521 (2050)
T ss_dssp             H
T ss_pred             c
Confidence            4

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

Probab=96.49  E-value=0.00047  Score=47.55  Aligned_cols=59  Identities=15%  Similarity=0.246  Sum_probs=32.2

Q ss_pred             hHHHHHHHHHhCC--cEEEEc-----hhhhhhcccChHHHHHHHHHHHHHhc---CCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGA--FFFLIN-----GPEIMSKLAGESESNLRKAFEEADKN---SPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~--~~~~v~-----~~~l~~~~~ges~~~l~~if~~a~~~---~p~iifiDEid~i~~   62 (69)
                      |++|+++|+.++.  +|..++     ++++++.+.+..... ...|..+...   .++|||||||+.+.+
T Consensus        55 T~LAraLa~~l~~~~~f~~~~~~~~t~~dL~G~~~~~~~~~-~g~~~~~~~g~l~~~~IL~IDEI~r~~~  123 (500)
T 3nbx_X           55 SLIARRLKFAFQNARAFEYLMTRFSTPEEVFGPLSIQALKD-EGRYERLTSGYLPEAEIVFLDEIWKAGP  123 (500)
T ss_dssp             HHHHHHGGGGBSSCCEEEEECCTTCCHHHHHCCBC-----------CBCCTTSGGGCSEEEEESGGGCCH
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHhcCCHHHhcCcccHHHHhh-chhHHhhhccCCCcceeeeHHhHhhhcH
Confidence            7899999998853  444433     356655554443222 1223322221   578999999987654

>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=96.47  E-value=0.0047  Score=36.45  Aligned_cols=29  Identities=14%  Similarity=0.360  Sum_probs=20.8

Q ss_pred             HHHHHHHHHHHHH----hcCCeEEEEccccccc
Q psy3868          33 SESNLRKAFEEAD----KNSPSIIFIDELDAIA   61 (69)
Q Consensus        33 s~~~l~~if~~a~----~~~p~iifiDEid~i~   61 (69)
                      ....++++++.+.    ..+|.+|+|||+|.+.
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~  139 (250)
T 1njg_A          107 KVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLS  139 (250)
T ss_dssp             GHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSC
T ss_pred             cHHHHHHHHHHhhhchhcCCceEEEEECccccc
Confidence            3455677776653    2358999999999874

>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=96.47  E-value=0.0023  Score=40.73  Aligned_cols=55  Identities=16%  Similarity=0.173  Sum_probs=34.7

Q ss_pred             hHHHHHHHHHhC------CcEEEEchhhhhhcccChHHHHHHHHHHHHHh----------------cCCeEEEEcccccc
Q psy3868           3 YRLTTLCRDSLG------AFFFLINGPEIMSKLAGESESNLRKAFEEADK----------------NSPSIIFIDELDAI   60 (69)
Q Consensus         3 T~la~aia~~~~------~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----------------~~p~iifiDEid~i   60 (69)
                      |+++++++++++      ..+..+++++..      +...+++.+.....                ..+.+|||||+|.+
T Consensus        72 T~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~~~l  145 (353)
T 1sxj_D           72 TSTILALTKELYGPDLMKSRILELNASDER------GISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSM  145 (353)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSEEEECSSSCC------CHHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGS
T ss_pred             HHHHHHHHHHhCCCcccccceEEEcccccc------chHHHHHHHHHHhhhcccccchhhcccCCCCCceEEEEECCCcc
Confidence            788999998864      458888877641      12233333322211                24569999999998


Q ss_pred             ccc
Q psy3868          61 APK   63 (69)
Q Consensus        61 ~~~   63 (69)
                      .+.
T Consensus       146 ~~~  148 (353)
T 1sxj_D          146 TAD  148 (353)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            653

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=96.25  E-value=0.0021  Score=37.63  Aligned_cols=57  Identities=11%  Similarity=0.200  Sum_probs=34.6

Q ss_pred             hHHHHHHHHHh----CCcEEEEchhhhhhcccChHHHH-HHHHHHHHHhcCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSL----GAFFFLINGPEIMSKLAGESESN-LRKAFEEADKNSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~----~~~~~~v~~~~l~~~~~ges~~~-l~~if~~a~~~~p~iifiDEid~i~   61 (69)
                      |++++++++.+    |..++.++..++...+...-... ..++.+.  -..|.+|++||++...
T Consensus        52 TtL~~~i~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~llilDE~~~~~  113 (180)
T 3ec2_A           52 THLAVATLKAIYEKKGIRGYFFDTKDLIFRLKHLMDEGKDTKFLKT--VLNSPVLVLDDLGSER  113 (180)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCEEEHHHHHHHHHHHHHHTCCSHHHHH--HHTCSEEEEETCSSSC
T ss_pred             HHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHHHhcCchHHHHHHH--hcCCCEEEEeCCCCCc
Confidence            67888888876    66778888887754432111000 0112222  1368999999998643

>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=96.14  E-value=0.002  Score=40.32  Aligned_cols=58  Identities=19%  Similarity=0.193  Sum_probs=35.0

Q ss_pred             hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHHHHHHHHHHHH-H-hcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESESNLRKAFEEA-D-KNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~~~l~~if~~a-~-~~~p~iifiDEid~i~~   62 (69)
                      |++++++++++     +.+++.+++++..+  .......+....... . ...+.+|+|||+|.+..
T Consensus        52 t~la~~l~~~l~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~  116 (319)
T 2chq_A           52 TATAIALARDLFGENWRDNFIEMNASDERG--IDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTA  116 (319)
T ss_dssp             HHHHHHHHHHHHTTCHHHHCEEEETTSTTC--TTTSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCH
T ss_pred             HHHHHHHHHHhcCCcccCCeEEEeCccccC--hHHHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCH
Confidence            78899999986     45688888876422  111112222222110 0 14589999999999854

>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=96.09  E-value=0.012  Score=36.76  Aligned_cols=54  Identities=24%  Similarity=0.265  Sum_probs=34.1

Q ss_pred             hHHHHHHHHHhC-----CcEEEEchhhhhhcccChHHHHHHHHHHHHHh------cCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLG-----AFFFLINGPEIMSKLAGESESNLRKAFEEADK------NSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~-----~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~------~~p~iifiDEid~i~~   62 (69)
                      |++++++++++.     .+++.+++++..+      ...++..+.....      ..+.+|+|||+|.+.+
T Consensus        60 T~la~~l~~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~  124 (327)
T 1iqp_A           60 TTAALALARELFGENWRHNFLELNASDERG------INVIREKVKEFARTKPIGGASFKIIFLDEADALTQ  124 (327)
T ss_dssp             HHHHHHHHHHHHGGGHHHHEEEEETTCHHH------HHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCH
T ss_pred             HHHHHHHHHHhcCCcccCceEEeeccccCc------hHHHHHHHHHHHhhCCcCCCCCeEEEEeCCCcCCH
Confidence            788999998863     3577888765421      1223332222211      4588999999999854

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

Probab=95.84  E-value=0.0058  Score=38.96  Aligned_cols=56  Identities=16%  Similarity=0.207  Sum_probs=34.1

Q ss_pred             hHHHHHHHHHhCCcEEEEchh------hhhhcccChHHHHHHHHHHHHHhcC---CeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGP------EIMSKLAGESESNLRKAFEEADKNS---PSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~------~l~~~~~ges~~~l~~if~~a~~~~---p~iifiDEid~i~~~   63 (69)
                      |++|+++|+.++.+++.+++.      ++.+...-....   .-|.  ...+   .+++||||+|.+.++
T Consensus        60 T~la~~la~~~~~~~~~i~~~~~~~~~~l~g~~~~~~~~---~~~~--~~~g~l~~~vl~iDEi~~~~~~  124 (331)
T 2r44_A           60 TLSVNTLAKTMDLDFHRIQFTPDLLPSDLIGTMIYNQHK---GNFE--VKKGPVFSNFILADEVNRSPAK  124 (331)
T ss_dssp             HHHHHHHHHHTTCCEEEEECCTTCCHHHHHEEEEEETTT---TEEE--EEECTTCSSEEEEETGGGSCHH
T ss_pred             HHHHHHHHHHhCCCeEEEecCCCCChhhcCCceeecCCC---CceE--eccCcccccEEEEEccccCCHH
Confidence            789999999999999988863      233221110000   0000  0112   379999999997653

>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=95.72  E-value=0.03  Score=36.09  Aligned_cols=55  Identities=4%  Similarity=0.080  Sum_probs=39.0

Q ss_pred             hHHHHHHHHHh------CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhc----CCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL------GAFFFLINGPEIMSKLAGESESNLRKAFEEADKN----SPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~------~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~----~p~iifiDEid~i~~   62 (69)
                      |++++++|+.+      ...++.++++.   +  ..+...+|++.+.+...    ...|++|||+|.+-.
T Consensus        32 tt~a~~la~~~~~~~~~~~d~~~l~~~~---~--~~~id~ir~li~~~~~~p~~~~~kvviIdead~lt~   96 (305)
T 2gno_A           32 REVSLELPEYVEKFPPKASDVLEIDPEG---E--NIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMTQ   96 (305)
T ss_dssp             HHHHHHHHHHHHTSCCCTTTEEEECCSS---S--CBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBCH
T ss_pred             HHHHHHHHHhCchhhccCCCEEEEcCCc---C--CCCHHHHHHHHHHHhhccccCCceEEEeccHHHhCH
Confidence            67889998874      35777887652   0  12456788898888542    247999999999854

>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=95.60  E-value=0.011  Score=37.52  Aligned_cols=16  Identities=19%  Similarity=0.461  Sum_probs=13.3

Q ss_pred             CCeEEEEccccccccc
Q psy3868          48 SPSIIFIDELDAIAPK   63 (69)
Q Consensus        48 ~p~iifiDEid~i~~~   63 (69)
                      .+.+|||||+|.+.+.
T Consensus       144 ~~~vl~iDEi~~l~~~  159 (350)
T 1g8p_A          144 NRGYLYIDECNLLEDH  159 (350)
T ss_dssp             TTEEEEETTGGGSCHH
T ss_pred             CCCEEEEeChhhCCHH
Confidence            4789999999998654

>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=95.58  E-value=0.0098  Score=38.03  Aligned_cols=28  Identities=14%  Similarity=0.326  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868          35 SNLRKAFEEADK----NSPSIIFIDELDAIAP   62 (69)
Q Consensus        35 ~~l~~if~~a~~----~~p~iifiDEid~i~~   62 (69)
                      ..++++++.+..    ..+.+|+|||+|.+..
T Consensus       102 ~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~  133 (373)
T 1jr3_A          102 EDTRDLLDNVQYAPARGRFKVYLIDEVHMLSR  133 (373)
T ss_dssp             SCHHHHHHHTTSCCSSSSSEEEEEECGGGSCH
T ss_pred             HHHHHHHHHHhhccccCCeEEEEEECcchhcH
Confidence            346677777643    3578999999998853

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=95.54  E-value=0.026  Score=36.42  Aligned_cols=60  Identities=15%  Similarity=0.216  Sum_probs=35.7

Q ss_pred             hHHHHHHHHHh---------CCcEEEEchhh------hhhcc----------cChH-HHHHHHHHHHHH-hcCCeEEEEc
Q psy3868           3 YRLTTLCRDSL---------GAFFFLINGPE------IMSKL----------AGES-ESNLRKAFEEAD-KNSPSIIFID   55 (69)
Q Consensus         3 T~la~aia~~~---------~~~~~~v~~~~------l~~~~----------~ges-~~~l~~if~~a~-~~~p~iifiD   55 (69)
                      |++++.++++.         +.+++.+++..      +....          .|.+ ...++.+.+... ..+|.+|+||
T Consensus        66 T~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlD  145 (412)
T 1w5s_A           66 TTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILD  145 (412)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEE
T ss_pred             HHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEe
Confidence            67888888776         56778888632      11110          1222 222334443333 3569999999


Q ss_pred             ccccccc
Q psy3868          56 ELDAIAP   62 (69)
Q Consensus        56 Eid~i~~   62 (69)
                      |+|.+..
T Consensus       146 e~~~l~~  152 (412)
T 1w5s_A          146 EFQSMLS  152 (412)
T ss_dssp             STHHHHS
T ss_pred             CHHHHhh
Confidence            9999865

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=95.52  E-value=0.032  Score=35.08  Aligned_cols=26  Identities=19%  Similarity=0.363  Sum_probs=19.0

Q ss_pred             HHHHHHHHHhc--CCeEEEEcccccccc
Q psy3868          37 LRKAFEEADKN--SPSIIFIDELDAIAP   62 (69)
Q Consensus        37 l~~if~~a~~~--~p~iifiDEid~i~~   62 (69)
                      +.++++...+.  +|.+|+|||++.+..
T Consensus       124 ~~~l~~~l~~~~~~~~vlvlDe~~~~~~  151 (357)
T 2fna_A          124 FANLLESFEQASKDNVIIVLDEAQELVK  151 (357)
T ss_dssp             HHHHHHHHHHTCSSCEEEEEETGGGGGG
T ss_pred             HHHHHHHHHhcCCCCeEEEEECHHHhhc
Confidence            55566555443  499999999999865

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=95.38  E-value=0.0085  Score=38.53  Aligned_cols=57  Identities=12%  Similarity=0.235  Sum_probs=33.9

Q ss_pred             hHHHHHHHHHhC----CcEEEEchhhhhhcccCh-HHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSLG----AFFFLINGPEIMSKLAGE-SESNLRKAFEEADKNSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~~----~~~~~v~~~~l~~~~~ge-s~~~l~~if~~a~~~~p~iifiDEid~i~   61 (69)
                      |++++++++++.    .++..+++++++..+.+. ....+.+.++..  ..+.+|+|||++...
T Consensus       166 T~La~aia~~~~~~~g~~v~~~~~~~l~~~l~~~~~~~~~~~~~~~~--~~~~lLiiDdig~~~  227 (308)
T 2qgz_A          166 SYLLAAMAHELSEKKGVSTTLLHFPSFAIDVKNAISNGSVKEEIDAV--KNVPVLILDDIGAEQ  227 (308)
T ss_dssp             HHHHHHHHHHHHHHSCCCEEEEEHHHHHHHHHCCCC----CCTTHHH--HTSSEEEEETCCC--
T ss_pred             HHHHHHHHHHHHHhcCCcEEEEEHHHHHHHHHHHhccchHHHHHHHh--cCCCEEEEcCCCCCC
Confidence            778888888654    788889988876543321 111222333332  245799999997654

>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=95.14  E-value=0.056  Score=34.79  Aligned_cols=57  Identities=7%  Similarity=0.109  Sum_probs=37.3

Q ss_pred             hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++|+++|+.+.++                        ++.+++.+-   ..+.+...++++.+.+..    ..+.|++|
T Consensus        38 t~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~---~~~~~i~~ir~l~~~~~~~~~~~~~kvviI  114 (334)
T 1a5t_A           38 DALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKG---KNTLGVDAVREVTEKLNEHARLGGAKVVWV  114 (334)
T ss_dssp             HHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTT---CSSBCHHHHHHHHHHTTSCCTTSSCEEEEE
T ss_pred             HHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEecccc---CCCCCHHHHHHHHHHHhhccccCCcEEEEE
Confidence            67899999888643                        334433210   011245678888888753    34789999


Q ss_pred             cccccccc
Q psy3868          55 DELDAIAP   62 (69)
Q Consensus        55 DEid~i~~   62 (69)
                      ||+|.+..
T Consensus       115 dead~l~~  122 (334)
T 1a5t_A          115 TDAALLTD  122 (334)
T ss_dssp             SCGGGBCH
T ss_pred             CchhhcCH
Confidence            99999854

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=94.84  E-value=0.013  Score=35.80  Aligned_cols=19  Identities=37%  Similarity=0.599  Sum_probs=16.0

Q ss_pred             hcCCeEEEEcccccccccc
Q psy3868          46 KNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus        46 ~~~p~iifiDEid~i~~~r   64 (69)
                      ...+++|+|||++.+.+.|
T Consensus        85 ~~~~~vliIDEAq~l~~~~  103 (199)
T 2r2a_A           85 ENIGSIVIVDEAQDVWPAR  103 (199)
T ss_dssp             GGTTCEEEETTGGGTSBCC
T ss_pred             ccCceEEEEEChhhhccCc
Confidence            3568999999999998766

>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=94.70  E-value=0.04  Score=44.57  Aligned_cols=52  Identities=12%  Similarity=0.123  Sum_probs=43.6

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~   61 (69)
                      |.+++++|+.+|.+++.++|++-+      ..+.+.++|..+... ++.+++||++.+-
T Consensus       659 Te~vk~LA~~lg~~~v~~nc~e~l------d~~~lg~~~~g~~~~-Gaw~~~DE~nr~~  710 (2695)
T 4akg_A          659 TETVKAFGQNLGRVVVVFNCDDSF------DYQVLSRLLVGITQI-GAWGCFDEFNRLD  710 (2695)
T ss_dssp             HHHHHHHHHTTTCCCEEEETTSSC------CHHHHHHHHHHHHHH-TCEEEEETTTSSC
T ss_pred             HHHHHHHHHHhCCcEEEEECCCCC------ChhHhhHHHHHHHhc-CCEeeehhhhhcC
Confidence            789999999999999999998764      356778899888554 6899999998864

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=94.33  E-value=0.23  Score=31.08  Aligned_cols=16  Identities=19%  Similarity=0.088  Sum_probs=13.5

Q ss_pred             cCCeEEEEcccccccc
Q psy3868          47 NSPSIIFIDELDAIAP   62 (69)
Q Consensus        47 ~~p~iifiDEid~i~~   62 (69)
                      .+|.+|+|||++.+..
T Consensus       127 ~~~~vlvlDe~~~~~~  142 (350)
T 2qen_A          127 LGEFIVAFDEAQYLRF  142 (350)
T ss_dssp             HSCEEEEEETGGGGGG
T ss_pred             cCCEEEEEeCHHHHhc
Confidence            3599999999999864

>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=93.94  E-value=0.13  Score=32.87  Aligned_cols=54  Identities=15%  Similarity=0.212  Sum_probs=35.0

Q ss_pred             hHHHHHHHHHhC-----CcEEEEchhhhhhcccChHHHHHHHHHHHHHh------cCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLG-----AFFFLINGPEIMSKLAGESESNLRKAFEEADK------NSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~-----~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~------~~p~iifiDEid~i~~   62 (69)
                      |++++++|+.+.     ..+..+++++.    .|  ...+++.......      ..+.+++|||+|.+..
T Consensus        60 Ttla~~la~~l~~~~~~~~~~~~~~~~~----~~--~~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l~~  124 (340)
T 1sxj_C           60 TSTIVALAREIYGKNYSNMVLELNASDD----RG--IDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTN  124 (340)
T ss_dssp             HHHHHHHHHHHHTTSHHHHEEEECTTSC----CS--HHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCH
T ss_pred             HHHHHHHHHHHcCCCccceEEEEcCccc----cc--HHHHHHHHHHHHhhcccCCCCceEEEEeCCCCCCH
Confidence            789999999864     24677777652    12  3445554443321      2378999999998753

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=93.79  E-value=0.16  Score=33.54  Aligned_cols=56  Identities=20%  Similarity=0.262  Sum_probs=33.7

Q ss_pred             hHHHHHHHHHhC---CcEEEEchhhhhhc-------------ccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLG---AFFFLINGPEIMSK-------------LAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~---~~~~~v~~~~l~~~-------------~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      +++|+++....+   .||+.++|+.+-..             |.|... .-...|+.|   ....||+|||+.+-.
T Consensus       174 ~~lAr~ih~~s~r~~~~fv~v~~~~~~~~~~~~elfg~~~g~~tga~~-~~~g~~~~a---~~gtlfldei~~l~~  245 (387)
T 1ny5_A          174 EVVARLIHKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVS-SKEGFFELA---DGGTLFLDEIGELSL  245 (387)
T ss_dssp             HHHHHHHHHHSTTTTSCEEEEETTTSCHHHHHHHHHCBCTTSSTTCCS-CBCCHHHHT---TTSEEEEESGGGCCH
T ss_pred             HHHHHHHHHhcCCCCCCeEEEecCCCCHHHHHHHhcCCCCCCCCCccc-ccCCceeeC---CCcEEEEcChhhCCH
Confidence            567888877654   69999999876221             111100 011233333   357999999998853

>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=92.34  E-value=0.23  Score=40.45  Aligned_cols=56  Identities=14%  Similarity=0.076  Sum_probs=35.8

Q ss_pred             hHHH-HHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHH---------------hcCCeEEEEcccccccccc
Q psy3868           3 YRLT-TLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEAD---------------KNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la-~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~---------------~~~p~iifiDEid~i~~~r   64 (69)
                      |++| +.+++..+.+++.++.+...      +...+.+.++..-               ..+++||||||+|.-...+
T Consensus      1281 T~la~~~l~~~~~~~~~~infsa~t------s~~~~~~~i~~~~~~~~~~~g~~~~P~~~gk~~VlFiDEinmp~~d~ 1352 (2695)
T 4akg_A         1281 TMIMNNALRNSSLYDVVGINFSKDT------TTEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVLFCDEINLPKLDK 1352 (2695)
T ss_dssp             HHHHHHHHHSCSSCEEEEEECCTTC------CHHHHHHHHHHHBCCEEETTTEEEEEBSSSSCEEEEEETTTCSCCCS
T ss_pred             HHHHHHHHhcCCCCceEEEEeecCC------CHHHHHHHHHHHhhhccccCCccccCCCCCceEEEEecccccccccc
Confidence            6778 55666557788888876653      2344555555431               1235799999999765554

>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=92.21  E-value=0.33  Score=30.79  Aligned_cols=14  Identities=14%  Similarity=0.361  Sum_probs=12.0

Q ss_pred             CCeEEEEccccccc
Q psy3868          48 SPSIIFIDELDAIA   61 (69)
Q Consensus        48 ~p~iifiDEid~i~   61 (69)
                      .|.++++||+|.+-
T Consensus       134 ~~~vlilDE~~~L~  147 (354)
T 1sxj_E          134 RYKCVIINEANSLT  147 (354)
T ss_dssp             CCEEEEEECTTSSC
T ss_pred             CCeEEEEeCccccC
Confidence            67899999999864

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=91.64  E-value=0.21  Score=32.78  Aligned_cols=54  Identities=26%  Similarity=0.363  Sum_probs=32.6

Q ss_pred             hHHHHHHHHHhCC--cEEEEchhhhhhcccChHHHHH---------------HHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGA--FFFLINGPEIMSKLAGESESNL---------------RKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~--~~~~v~~~~l~~~~~ges~~~l---------------~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      +.+|+++....+.  +|+.+||+.+-...   .+..+               .-.|+.|   ....||+|||+.+-.
T Consensus       166 e~lAr~ih~~s~r~~~fv~vnc~~~~~~~---~~~~lfg~~~g~~tga~~~~~g~~~~a---~~gtlfldei~~l~~  236 (368)
T 3dzd_A          166 EIVARLIHRYSGRKGAFVDLNCASIPQEL---AESELFGHEKGAFTGALTRKKGKLELA---DQGTLFLDEVGELDQ  236 (368)
T ss_dssp             HHHHHHHHHHHCCCSCEEEEESSSSCTTT---HHHHHHEECSCSSSSCCCCEECHHHHT---TTSEEEEETGGGSCH
T ss_pred             HHHHHHHHHhccccCCcEEEEcccCChHH---HHHHhcCccccccCCcccccCChHhhc---CCCeEEecChhhCCH
Confidence            4678888777654  39999998762110   01110               1134443   346899999998854

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

Probab=90.17  E-value=0.011  Score=41.29  Aligned_cols=58  Identities=14%  Similarity=0.170  Sum_probs=32.3

Q ss_pred             hHHHHHHHHHhCCcEEEE----chhhhhhcccChHHHH----HHHHHHHHHhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLI----NGPEIMSKLAGESESN----LRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v----~~~~l~~~~~ges~~~----l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      |++|+++|+.++..++..    ++..+...........    -...+..|   .+.++||||+|.+.+.
T Consensus       341 T~LAr~la~~~~r~~~~~~~~~~~~~l~~~~~~~~~~g~~~~~~G~l~~A---~~gil~IDEid~l~~~  406 (595)
T 3f9v_A          341 SQMLQFISRVAPRAVYTTGKGSTAAGLTAAVVREKGTGEYYLEAGALVLA---DGGIAVIDEIDKMRDE  406 (595)
T ss_dssp             HHHHHSSSTTCSCEECCCTTCSTTTTSEEECSSGGGTSSCSEEECHHHHH---SSSEECCTTTTCCCSH
T ss_pred             HHHHHHHHHhCCCceecCCCccccccccceeeeccccccccccCCeeEec---CCCcEEeehhhhCCHh
Confidence            789999999988766553    3333332222111000    00012222   4589999999998653

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=89.72  E-value=0.25  Score=39.39  Aligned_cols=60  Identities=20%  Similarity=0.319  Sum_probs=40.6

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcc----cC--------hHHHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKL----AG--------ESESNLRKAFEEADK----NSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~----~g--------es~~~l~~if~~a~~----~~p~iifiDEid~i~~   62 (69)
                      |.|+..+|...   +.++++++..+...++    .|        .++.++..+++.+++    ..|++|+||.+..+.+
T Consensus       746 TtLalqlA~~~a~~g~~VlyiS~Ees~~ql~A~rlG~~~~~l~i~~~~~i~~i~~~~r~l~~~~~~~LVIIDsLq~i~~  824 (2050)
T 3cmu_A          746 TTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTP  824 (2050)
T ss_dssp             HHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCGGGCCC
T ss_pred             HHHHHHHHHHHHhcCCcEEEEECCCcHHHHHHHHcCCCccceEEecCCCHHHHHHHHHHHhhccCCCEEEEcchhhhcc
Confidence            56677666655   3468888887655543    33        223345666666654    6899999999999986

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=86.44  E-value=2.2  Score=28.13  Aligned_cols=20  Identities=15%  Similarity=0.429  Sum_probs=16.2

Q ss_pred             HHHhcCCeEEEEcccccccc
Q psy3868          43 EADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus        43 ~a~~~~p~iifiDEid~i~~   62 (69)
                      ..+...+.+|+||.+..+.+
T Consensus       147 l~~~~~~~lVVIDsl~~l~~  166 (366)
T 1xp8_A          147 LVRSGAIDVVVVDSVAALTP  166 (366)
T ss_dssp             HHTTTCCSEEEEECTTTCCC
T ss_pred             HHhcCCCCEEEEeChHHhcc
Confidence            33456799999999999985

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=86.05  E-value=2.7  Score=27.38  Aligned_cols=28  Identities=29%  Similarity=0.315  Sum_probs=19.6

Q ss_pred             HHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868          35 SNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus        35 ~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      ..+..+...+++..|.+|+||++.++.+
T Consensus       126 ~~l~~~~~l~~~~~~~lIVIDsl~~l~~  153 (349)
T 2zr9_A          126 QALEIADMLVRSGALDIIVIDSVAALVP  153 (349)
T ss_dssp             HHHHHHHHHHTTTCCSEEEEECGGGCCC
T ss_pred             HHHHHHHHHHhcCCCCEEEEcChHhhcc
Confidence            3333333344456799999999999985

>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=85.22  E-value=1.3  Score=30.21  Aligned_cols=15  Identities=53%  Similarity=0.888  Sum_probs=13.1

Q ss_pred             eEEEEcccccccccc
Q psy3868          50 SIIFIDELDAIAPKR   64 (69)
Q Consensus        50 ~iifiDEid~i~~~r   64 (69)
                      .++|+||+|.++.+.
T Consensus       252 ~il~~DEidki~~~~  266 (444)
T 1g41_A          252 GIVFIDEIDKICKKG  266 (444)
T ss_dssp             CEEEEETGGGGSCCS
T ss_pred             CeeeHHHHHHHhhcc
Confidence            689999999999764

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=84.57  E-value=3.8  Score=23.10  Aligned_cols=23  Identities=4%  Similarity=0.018  Sum_probs=19.2

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhh
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEI   25 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l   25 (69)
                      |++++.++..++.+++.++...+
T Consensus        17 ST~a~~La~~l~~~~~~~~~D~~   39 (178)
T 1qhx_A           17 SGIVRCLQSVLPEPWLAFGVDSL   39 (178)
T ss_dssp             HHHHHHHHHHSSSCEEEEEHHHH
T ss_pred             HHHHHHHHHhcCCCeEEeccchH
Confidence            78999999999999888766544

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=84.50  E-value=4.4  Score=24.60  Aligned_cols=15  Identities=13%  Similarity=0.341  Sum_probs=12.6

Q ss_pred             CCeEEEEcccccccc
Q psy3868          48 SPSIIFIDELDAIAP   62 (69)
Q Consensus        48 ~p~iifiDEid~i~~   62 (69)
                      ...+|+|||+|.+..
T Consensus       192 ~~~llIiDEaH~l~~  206 (237)
T 2fz4_A          192 RFMLLIFDEVHHLPA  206 (237)
T ss_dssp             TCSEEEEECSSCCCT
T ss_pred             cCCEEEEECCccCCC
Confidence            478999999999854

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=83.52  E-value=1.4  Score=36.70  Aligned_cols=52  Identities=13%  Similarity=0.156  Sum_probs=42.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIA   61 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~   61 (69)
                      |.+++.+|+.+|.+++.++|++-+      ..+.+.++|.-+-. ..+-..+||++.+-
T Consensus       618 Tet~k~La~~lgr~~~vfnC~~~~------d~~~~g~i~~G~~~-~GaW~cfDEfNrl~  669 (3245)
T 3vkg_A          618 TETVKALGSQLGRFVLVFCCDEGF------DLQAMSRIFVGLCQ-CGAWGCFDEFNRLE  669 (3245)
T ss_dssp             HHHHHHHHHHTTCCEEEEECSSCC------CHHHHHHHHHHHHH-HTCEEEEETTTSSC
T ss_pred             HHHHHHHHHHhCCeEEEEeCCCCC------CHHHHHHHHhhHhh-cCcEEEehhhhcCC
Confidence            678999999999999999997643      45677888888755 47778899998863

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=82.82  E-value=1.5  Score=34.62  Aligned_cols=42  Identities=21%  Similarity=0.347  Sum_probs=36.0

Q ss_pred             hhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868          24 EIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus        24 ~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      +++-.++...|+.+..+...+++.+|.+|+||.+.++.++.+
T Consensus      1485 ~l~~~~p~~~e~~l~~~~~~~~s~~~~~vvvDsv~al~~~~e 1526 (1706)
T 3cmw_A         1485 NLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTPKAE 1526 (1706)
T ss_dssp             GCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCSTTCCCTTT
T ss_pred             HeEEeCCCcHHHHHHHHHHHHHcCCCCEEEEccHHhCCcccc
Confidence            344447777899999999999999999999999999998764

>3imk_A Putative molybdenum carrier protein; YP_461806.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE MES PG4 PG6; 1.45A {Syntrophus aciditrophicus SB}

Probab=82.35  E-value=5.9  Score=23.61  Aligned_cols=45  Identities=11%  Similarity=0.005  Sum_probs=36.9

Q ss_pred             hhHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEE
Q psy3868           2 SYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSII   52 (69)
Q Consensus         2 ~T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~ii   52 (69)
                      +|.+...+|.+.+.|++.++...+      ........+.++...+...+|
T Consensus        88 GT~lT~~~a~~~~KP~l~i~l~~~------~~~~~~~~v~~wl~~~~i~vL  132 (158)
T 3imk_A           88 GSALTEFFAEQYKKPCLHIDLDRI------SIEDAATLINSWTVSHHIQVL  132 (158)
T ss_dssp             HHHHHHHHHHHTTCCEEEEETTTS------CHHHHHHHHHHHHHHTTCCEE
T ss_pred             chHHHHHHHHHhCCCEEEEecccc------cccchHHHHHHHHHHCCceEE
Confidence            588899999999999999988764      135678888899988887777

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=81.06  E-value=4.2  Score=23.61  Aligned_cols=15  Identities=13%  Similarity=0.271  Sum_probs=12.9

Q ss_pred             CCeEEEEcccccccc
Q psy3868          48 SPSIIFIDELDAIAP   62 (69)
Q Consensus        48 ~p~iifiDEid~i~~   62 (69)
                      .|.+|+|||+..+..
T Consensus       105 ~~~lliiD~~~~~l~  119 (220)
T 2cvh_A          105 NFALVVVDSITAHYR  119 (220)
T ss_dssp             TEEEEEEECCCCCTT
T ss_pred             CCCEEEEcCcHHHhh
Confidence            599999999998854

---

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	69
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	7e-18
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	2e-17
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	3e-10
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	2e-07
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	1e-04

>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 = 71.8 bits (176), Expect = 7e-18
 Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 3/68 (4%)

Query: 1   MSYRLTTLCR---DSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDEL 57
                T L +         FF I+G + +    G   S +R  FE+A K +P IIFIDE+
Sbjct: 54  PGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEI 113

Query: 58  DAIAPKRE 65
           DA+  +R 
Sbjct: 114 DAVGRQRG 121

>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 = 71.0 bits (174), Expect = 2e-17
 Identities = 17/54 (31%), Positives = 28/54 (51%)

Query: 12  SLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE 65
                F   +G + +    G   + +R  FE A +++P I+FIDE+DA+  KR 
Sbjct: 65  EARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRG 118

>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 = 51.6 bits (123), Expect = 3e-10
 Identities = 6/51 (11%), Positives = 14/51 (27%), Gaps = 2/51 (3%)

Query: 14  GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64
              +  +   E +S    +    +        +    +I ID L  +    
Sbjct: 150 KDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQ--HRVIVIDSLKNVIGAA 198

>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 = 43.9 bits (102), Expect = 2e-07
 Identities = 49/57 (85%), Positives = 53/57 (92%)

Query: 9   CRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE 65
             +  GAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIFIDELDAIAPKRE
Sbjct: 58  VANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKRE 114

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]} Length = 362

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]

 Score = 35.8 bits (82), Expect = 1e-04
 Identities = 14/70 (20%), Positives = 23/70 (32%), Gaps = 10/70 (14%)

Query: 6   TTLCR---DSLGAFFFLINGPEIMSK-LAGESESNLRKAFEEAD------KNSPSIIFID 55
           TTL     +  G     +N P        G +       FE+        ++ PS   I+
Sbjct: 168 TTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGIN 227

Query: 56  ELDAIAPKRE 65
            LD +    +
Sbjct: 228 NLDNLRDYLD 237

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	69
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	99.78
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.78
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.73
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.68
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.66
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.61
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.47
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.48
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.46
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	98.26
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.12
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.02
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.82
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	97.75
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.7
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.62
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.14
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.03
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	96.88
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.66
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	96.16
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	95.72
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	95.53
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	95.35
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	93.69
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	93.51
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	91.62
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	89.83
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	88.87
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	87.85
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	87.67
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	87.65
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	86.2
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	85.7
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	85.55
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	84.85
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	82.66
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	81.14

>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=99.78  E-value=1.5e-19  Score=113.58  Aligned_cols=65  Identities=28%  Similarity=0.510  Sum_probs=59.1

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|++++++++.++++++.++|+|+++++++++|+.|+.++||||||||+|+|+++|+..
T Consensus        56 T~la~aia~~~~~~~~~i~~~~l~~~~~g~~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~  120 (247)
T d1ixza_          56 THLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSG  120 (247)
T ss_dssp             HHHHHHHHHHTTCCEEEEEHHHHHHSCTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC-----
T ss_pred             hHHHHHHHHHcCCCEEEEEhHHhhhccccHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999988653

>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=99.78  E-value=1.7e-19  Score=113.84  Aligned_cols=65  Identities=34%  Similarity=0.552  Sum_probs=62.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|++++.+++.++++++.++|+|+++++++++|+.|++++||||||||+|++++.|+..
T Consensus        59 T~la~~iA~~~~~~~~~i~~~~l~~~~~g~~~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~  123 (256)
T d1lv7a_          59 TLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAG  123 (256)
T ss_dssp             HHHHHHHHHHHTCCEEEECSCSSTTSCCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTT
T ss_pred             cHHHHHHHHHcCCCEEEEEhHHhhhcchhHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999988653

>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=99.73  E-value=1.5e-18  Score=112.87  Aligned_cols=63  Identities=14%  Similarity=0.105  Sum_probs=54.6

Q ss_pred             hHHHHHHHHHhC--CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLG--AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~--~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|.+++  .+|+.+++++++++|+|+++++++++|+.|+.  ||||||||||+++++|+++
T Consensus       137 T~la~ala~~~~~~~~~~~~~~~~~~~~~~G~~e~~~~~~f~~a~~--~~ilf~DEid~~~~~r~~~  201 (321)
T d1w44a_         137 TPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQ--HRVIVIDSLKNVIGAAGGN  201 (321)
T ss_dssp             HHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHH--CSEEEEECCTTTC------
T ss_pred             HHHHHHHHHHhcCCCCeEEEEhhHhhhcccchHHHHHHHHHHHHhh--ccEEEeehhhhhccccccC
Confidence            899999999987  78999999999999999999999999999975  8999999999999999653

>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=99.68  E-value=3.9e-17  Score=102.44  Aligned_cols=65  Identities=77%  Similarity=1.114  Sum_probs=62.5

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++++++|++++.+++.++++++.++|+|+++++++++|+.|+.++||||||||+|.++++|++.
T Consensus        52 T~l~~ala~~~~~~~~~i~~~~l~~~~~g~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~  116 (258)
T d1e32a2          52 TLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKT  116 (258)
T ss_dssp             HHHHHHHHHHTTCEEEEECHHHHTTSCTTHHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHC
T ss_pred             hHHHHHHHHHhCCeEEEEEchhhcccccccHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999988754

>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=99.66  E-value=1.1e-16  Score=100.90  Aligned_cols=64  Identities=38%  Similarity=0.621  Sum_probs=61.7

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++++++|++++.+|+.++++++.+.|.|+++.+++++|+.|+.++||||||||+|.++.+|+.
T Consensus        55 T~l~~ala~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~f~~A~~~~p~il~ideid~l~~~~~~  118 (265)
T d1r7ra3          55 TLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGG  118 (265)
T ss_dssp             HHHHHHHHHHTTCEEEEECHHHHHTSCTTTHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHH
T ss_pred             hhHHHHHHHHhCCcEEEEEHHHhhhccccchHHHHHHHHHHHHhcCCcceeHHhhhhccccCCC
Confidence            7899999999999999999999999999999999999999999999999999999999998754

>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=99.61  E-value=5.3e-16  Score=96.93  Aligned_cols=64  Identities=17%  Similarity=0.274  Sum_probs=58.1

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHH-HHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESE-SNLRKAFEEADKNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~-~~l~~if~~a~~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|++++.+|+.+++++++.++.+.++ +.++++|+.|++++||||||||||.+++.+..
T Consensus        54 T~la~alA~~~~~~~~~i~~~~~~~g~~~~~~~~~i~~if~~A~~~~p~il~iDEid~l~~~~~~  118 (246)
T d1d2na_          54 TALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPI  118 (246)
T ss_dssp             HHHHHHHHHHHTCSEEEEECGGGCTTCCHHHHHHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTT
T ss_pred             HHHHHHHhhcccccccccccccccccccccchhhhhhhhhhhhhhcccceeehhhhhhHhhhccc
Confidence            78999999999999999999998888887774 67999999999999999999999999887653

>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=99.47  E-value=1.9e-14  Score=91.99  Aligned_cols=65  Identities=23%  Similarity=0.311  Sum_probs=58.8

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhh--hcccChHHHHHHHHHHHHHh-----cCCeEEEEccccccccccccC
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIM--SKLAGESESNLRKAFEEADK-----NSPSIIFIDELDAIAPKREKR   67 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~~-----~~p~iifiDEid~i~~~r~~~   67 (69)
                      |++|+++|++++.+++.++++++.  +.|.|++++.++.+|..|..     .+||||||||||++++++.+.
T Consensus        63 T~lAkalA~~~~~~~~~i~~s~~~~~~~~~~~~~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki~~~~~~~  134 (309)
T d1ofha_          63 TEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYS  134 (309)
T ss_dssp             HHHHHHHHHHHTCCEEEEEGGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCC
T ss_pred             HHHHHHHhhccccchhcccccccccceeEeeeccccccccchhhhcccccccCCceEEehhhhhhhhhccCc
Confidence            899999999999999999999998  45899999999999999865     368999999999999987653

>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=98.48  E-value=2e-07  Score=58.51  Aligned_cols=61  Identities=16%  Similarity=0.308  Sum_probs=49.9

Q ss_pred             hHHHHHHHHH----------hCCcEEEEchhhhhh--cccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDS----------LGAFFFLINGPEIMS--KLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~----------~~~~~~~v~~~~l~~--~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~   63 (69)
                      |.+++.+|..          .+.+++.++.+.+++  +|.|+-+..++.+++.+.+....|+||||+|.|.+.
T Consensus        53 Talv~~la~ri~~~~vp~~l~~~~i~~l~~~~liag~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~  125 (268)
T d1r6bx2          53 TAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGA  125 (268)
T ss_dssp             HHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTS
T ss_pred             HHHHHHHHHHHHhCCcccccccceeEEeeechHhccCccchhHHHHHHHHHHHhhccCCceEEecchHHHhcC
Confidence            5677777764          357899999999997  599999999999999998888999999999999764

>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=98.46  E-value=3.6e-07  Score=55.16  Aligned_cols=61  Identities=20%  Similarity=0.328  Sum_probs=49.1

Q ss_pred             hHHHHHHHHHh----------CCcEEEEchhhhhhc--ccChHHHHHHHHHHHHHhcC-CeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSL----------GAFFFLINGPEIMSK--LAGESESNLRKAFEEADKNS-PSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~----------~~~~~~v~~~~l~~~--~~ges~~~l~~if~~a~~~~-p~iifiDEid~i~~~   63 (69)
                      |.+++.+|...          +.+++.++.+.+++.  |.|+-|.+++.+++.+.+.. +.||||||++.+.+.
T Consensus        57 Talv~~LA~ri~~~~vp~~L~~~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~  130 (195)
T d1jbka_          57 TAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGA  130 (195)
T ss_dssp             HHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT-
T ss_pred             HHHHHHHHHHHHhCCCCHHHcCceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcC
Confidence            55666666533          578999999999954  77899999999999986654 789999999999764

>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=98.26  E-value=2.1e-09  Score=69.96  Aligned_cols=64  Identities=19%  Similarity=0.137  Sum_probs=52.6

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhc-ccChHHHHHHHHHHHHH------hcCCeEEEEcccccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSK-LAGESESNLRKAFEEAD------KNSPSIIFIDELDAIAPKREK   66 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~-~~ges~~~l~~if~~a~------~~~p~iifiDEid~i~~~r~~   66 (69)
                      |++|+++|+.++.+|+.+|+++..+. |+|........+|+.+.      ...|+++++||+|.+...+++
T Consensus       168 ~~~~~~~~~~~~~~~i~in~s~~rs~~~l~~~~~~~~~l~d~~~~~~~~~~~~~~~~~~DeiD~l~~~~dg  238 (362)
T d1svma_         168 TTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDG  238 (362)
T ss_dssp             HHHHHHHHHHHCCEEECCSSCTTTHHHHHGGGTTCSCEEETTCCCSTTTTTTCCCCSHHHHHHTTHHHHHC
T ss_pred             HHHHHHHHHHcCCCEEEEECcchhhHHHHHhHHHHHHHHHHHHHHhhhhccCCCCeEEEehHhhcccccCC
Confidence            78999999999999999999998777 57777777767777763      356899999999998765544

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {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: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=98.12  E-value=3.4e-06  Score=55.06  Aligned_cols=50  Identities=24%  Similarity=0.404  Sum_probs=31.2

Q ss_pred             CCcEEEEchhhhhhc--ccChHHHHHHHHHHHHHhcC-CeEEEEccccccccc
Q psy3868          14 GAFFFLINGPEIMSK--LAGESESNLRKAFEEADKNS-PSIIFIDELDAIAPK   63 (69)
Q Consensus        14 ~~~~~~v~~~~l~~~--~~ges~~~l~~if~~a~~~~-p~iifiDEid~i~~~   63 (69)
                      +..++.++.+.++++  |.|+-+..++.+.+.+.... +.||||||+|.+.+.
T Consensus        78 ~~~i~~ld~~~l~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~  130 (387)
T d1qvra2          78 GKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGA  130 (387)
T ss_dssp             TCEEEEECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC------
T ss_pred             CceEEEeeHhhhhcccCcchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcC
Confidence            367999999999964  88999999999999987764 789999999999764

>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=98.02  E-value=3.7e-06  Score=50.18  Aligned_cols=54  Identities=15%  Similarity=0.350  Sum_probs=42.5

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |++|+++|++++.+++.+++++..      ....+..++..  ....+++|+||+|.+.+.+
T Consensus        49 T~lA~~la~~~~~~~~~~~~~~~~------~~~~~~~~~~~--~~~~~~~~ide~~~~~~~~  102 (238)
T d1in4a2          49 TTLAHIIASELQTNIHVTSGPVLV------KQGDMAAILTS--LERGDVLFIDEIHRLNKAV  102 (238)
T ss_dssp             HHHHHHHHHHHTCCEEEEETTTCC------SHHHHHHHHHH--CCTTCEEEEETGGGCCHHH
T ss_pred             HHHHHHHHhccCCCcccccCcccc------cHHHHHHHHHh--hccCCchHHHHHHHhhhHH
Confidence            899999999999999999987763      34456666554  3457999999999997543

>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=97.82  E-value=7.8e-06  Score=48.79  Aligned_cols=55  Identities=24%  Similarity=0.450  Sum_probs=38.5

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r   64 (69)
                      |++|+++|++++.++..++++....  .+.    ........ ...++++|+||+|.+.+..
T Consensus        49 Ttla~~la~~~~~~~~~~~~~~~~~--~~~----~~~~~~~~-~~~~~i~~iDe~~~~~~~~  103 (239)
T d1ixsb2          49 TTLAHVIAHELGVNLRVTSGPAIEK--PGD----LAAILANS-LEEGDILFIDEIHRLSRQA  103 (239)
T ss_dssp             HHHHHHHHHHHTCCEEEEETTTCCS--HHH----HHHHHHTT-CCTTCEEEEETGGGCCHHH
T ss_pred             HHHHHHHHHHhCCCeEeccCCcccc--chh----hHHHHHhh-ccCCCeeeeecccccchhH
Confidence            8899999999999999999887632  111    22222111 1346899999999997643

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

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: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=97.75  E-value=3e-05  Score=49.95  Aligned_cols=61  Identities=21%  Similarity=0.342  Sum_probs=43.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhc-ccChH-HHHHHHHHHHH----HhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSK-LAGES-ESNLRKAFEEA----DKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~-~~ges-~~~l~~if~~a----~~~~p~iifiDEid~i~~~   63 (69)
                      |.+||++|..++.||+.++++.+... |+|.- +..++++...+    +....+|+++||+|.+.+.
T Consensus        82 TElAk~LA~~~~~~~ir~D~s~~~e~gyvg~dv~~~i~~l~~~~~~~v~~~~~~iv~lDEieK~~~~  148 (364)
T d1um8a_          82 TLMAQTLAKHLDIPIAISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRL  148 (364)
T ss_dssp             HHHHHHHHHHTTCCEEEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC---
T ss_pred             HHHHHHHHhhcccceeehhhhhcccchhhHhhhccchhhhhhhchhHHHHhhcccchhhhhhhhccc
Confidence            78999999999999999999999764 77763 45577777654    3456799999999998764

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {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: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.70  E-value=1.7e-05  Score=50.12  Aligned_cols=58  Identities=22%  Similarity=0.301  Sum_probs=38.2

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhh------------cccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMS------------KLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~------------~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |.+|+.+|..+   +.+++.++.+++..            +|+|..+.  ..+.+..+++.-+|+|+||||...+
T Consensus        67 t~lak~la~~l~~~~~~~~~~~~~~~~~~~~~~~L~g~~~gyvG~~~~--~~l~~~~~~~p~~Vvl~DEieK~~~  139 (315)
T d1qvra3          67 TELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEG--GQLTEAVRRRPYSVILFDEIEKAHP  139 (315)
T ss_dssp             HHHHHHHHHHHHSSGGGEEEECTTTCCSSGGGGGC----------------CHHHHHHHCSSEEEEESSGGGSCH
T ss_pred             HHHHHHHHHHhcCCCcceEEEeccccccchhhhhhcCCCCCCcCcccC--ChHHHHHHhCCCcEEEEehHhhcCH
Confidence            78999999988   68999999877653            24443322  2234445566679999999998753

>d1r6bx3 c.37.1.20 (X:437-751) 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=97.62  E-value=2.3e-05  Score=49.43  Aligned_cols=60  Identities=18%  Similarity=0.292  Sum_probs=42.4

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhc-----ccCh----HHHHH-HHHHHHHHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSK-----LAGE----SESNL-RKAFEEADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~-----~~ge----s~~~l-~~if~~a~~~~p~iifiDEid~i~~   62 (69)
                      |.+|+++|..++.+|+.++++++...     ..|.    ..... ..+....+.+..+|+++||+|...+
T Consensus        66 T~lak~la~~l~~~~i~~d~s~~~~~~~~~~l~g~~~gy~g~~~~~~l~~~~~~~~~~vvl~DeieKa~~  135 (315)
T d1r6bx3          66 TEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHP  135 (315)
T ss_dssp             HHHHHHHHHHHTCEEEEEEGGGCSSSSCCSSSCCCCSCSHHHHHTTHHHHHHHHCSSEEEEEETGGGSCH
T ss_pred             HHHHHHHHhhccCCeeEeccccccchhhhhhhcccCCCccccccCChhhHHHHhCccchhhhcccccccc
Confidence            78999999999999999999987432     2222    11111 2234445566779999999998754

>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=97.14  E-value=0.00016  Score=42.62  Aligned_cols=55  Identities=24%  Similarity=0.246  Sum_probs=37.3

Q ss_pred             hHHHHHHHHHhC-----CcEEEEchhhhhhcccChHHHHHHHHHHHH------HhcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLG-----AFFFLINGPEIMSKLAGESESNLRKAFEEA------DKNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~-----~~~~~v~~~~l~~~~~ges~~~l~~if~~a------~~~~p~iifiDEid~i~~~   63 (69)
                      |++|+++|++++     .+++++++++..+.      ..++..+...      ....+.++++||+|.+...
T Consensus        59 Ttla~~iak~l~~~~~~~~~~e~n~s~~~~~------~~~~~~~~~~~~~~~~~~~~~~iilide~d~~~~~  124 (231)
T d1iqpa2          59 TTAALALARELFGENWRHNFLELNASDERGI------NVIREKVKEFARTKPIGGASFKIIFLDEADALTQD  124 (231)
T ss_dssp             HHHHHHHHHHHHGGGHHHHEEEEETTCHHHH------HTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCHH
T ss_pred             HHHHHHHHHHHHhcccCCCeeEEecCcccch------hHHHHHHHHHHhhhhccCCCceEEeehhhhhcchh
Confidence            789999999875     47888888765322      2233333332      2346899999999987653

>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=97.03  E-value=0.00048  Score=40.73  Aligned_cols=56  Identities=20%  Similarity=0.216  Sum_probs=39.7

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHH------------------HhcCCeEEEEcccccccccc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEA------------------DKNSPSIIFIDELDAIAPKR   64 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a------------------~~~~p~iifiDEid~i~~~r   64 (69)
                      |++|+++|++++.+++.+++++..+.+..      +...+.+                  ....+.++++||+|.+....
T Consensus        66 Tt~a~~la~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~~~  139 (253)
T d1sxja2          66 TTAAHLVAQELGYDILEQNASDVRSKTLL------NAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGD  139 (253)
T ss_dssp             HHHHHHHHHHTTCEEEEECTTSCCCHHHH------HHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTS
T ss_pred             HHHHHHHHHHHHhhhhccccccchhhHHH------HHHHHHHhhcchhhhhhhhhhhcccccccceEEEeeeccccccch
Confidence            78999999999999999999877544322      2221111                  11357899999999987643

>d1g41a_ 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=96.88  E-value=0.00079  Score=44.20  Aligned_cols=42  Identities=14%  Similarity=0.195  Sum_probs=34.3

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhc-ccChH-HHHHHHHHHHH
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSK-LAGES-ESNLRKAFEEA   44 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~-~~ges-~~~l~~if~~a   44 (69)
                      |+|||.+|+.+++||+.++++.+..- |+|+. +..++++.+.+
T Consensus        63 TlLAr~LAk~l~VPFv~~daT~fTeaGYvG~DVesii~~L~~~a  106 (443)
T d1g41a_          63 TEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSA  106 (443)
T ss_dssp             HHHHHHHHHHTTCCEEEEEGGGGC----CCCCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCEEEeecceeeecceeecchhHHHHHHHHHH
Confidence            89999999999999999999999855 88885 66677777665

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

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]

Probab=96.66  E-value=4.1e-05  Score=45.67  Aligned_cols=51  Identities=6%  Similarity=-0.012  Sum_probs=34.1

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccC---hHHHHHHHHHHHHHhcCCeEEE
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAG---ESESNLRKAFEEADKNSPSIIF   53 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~g---es~~~l~~if~~a~~~~p~iif   53 (69)
                      |++|+++|++++.+|+.++++++...+.+   ......+..++.++...+++.+
T Consensus        46 T~la~~la~~~~~~~~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (273)
T d1gvnb_          46 TSLRSAIFEETQGNVIVIDNDTFKQQHPNFDELVKLYEKDVVKHVTPYSNRMTE   99 (273)
T ss_dssp             HHHHHHHHHHTTTCCEEECTHHHHTTSTTHHHHHHHHGGGCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcceEEEecHHHHHHhccCcccchhhhHHHHHHHHhhccchHH
Confidence            78999999999999999999998654333   3333344445554443333333

>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=96.16  E-value=0.00084  Score=39.22  Aligned_cols=55  Identities=13%  Similarity=0.170  Sum_probs=33.0

Q ss_pred             hHHHHHHHHHhCC-----cEEEEchhhhhhcccChHHHHHHHHHHHHH------hcCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLGA-----FFFLINGPEIMSKLAGESESNLRKAFEEAD------KNSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~~-----~~~~v~~~~l~~~~~ges~~~l~~if~~a~------~~~p~iifiDEid~i~~~   63 (69)
                      |++++++|++++.     .+++.+.++..+.      ......+....      .....+|+|||+|.+...
T Consensus        49 ttl~~~la~~l~~~~~~~~~~e~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~kiiiiDe~d~~~~~  114 (227)
T d1sxjc2          49 TSTIVALAREIYGKNYSNMVLELNASDDRGI------DVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNA  114 (227)
T ss_dssp             HHHHHHHHHHHHTTSHHHHEEEECTTSCCSH------HHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCHH
T ss_pred             hHHHHHHHHHhhcCCCcceeEEecccccCCe------eeeecchhhccccccccCCCeEEEEEeccccchhh
Confidence            7899999999753     4566776654321      11222222221      134569999999988643

>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=95.72  E-value=0.01  Score=34.39  Aligned_cols=55  Identities=13%  Similarity=0.133  Sum_probs=37.0

Q ss_pred             hHHHHHHHHHhCC-----cEEEEchhhhhhcccChHHHHHHHHHHHHHh-------cCCeEEEEccccccccc
Q psy3868           3 YRLTTLCRDSLGA-----FFFLINGPEIMSKLAGESESNLRKAFEEADK-------NSPSIIFIDELDAIAPK   63 (69)
Q Consensus         3 T~la~aia~~~~~-----~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-------~~p~iifiDEid~i~~~   63 (69)
                      |++|+.+|++++.     .++++++++..      +...++..+.....       ....++++||+|.+...
T Consensus        50 Tt~a~~la~~l~~~~~~~~~~~~n~~~~~------~~~~i~~~~~~~~~~~~~~~~~~~kviiiDe~d~~~~~  116 (224)
T d1sxjb2          50 TTSVHCLAHELLGRSYADGVLELNASDDR------GIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAG  116 (224)
T ss_dssp             HHHHHHHHHHHHGGGHHHHEEEECTTSCC------SHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCHH
T ss_pred             hhhHHHHHHHHhccccccccccccccccC------CceehhhHHHHHHHhhccCCCcceEEEEEecccccchh
Confidence            7899999998874     47788877642      23444444443322       34679999999998654

>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=95.53  E-value=0.0071  Score=35.76  Aligned_cols=54  Identities=13%  Similarity=0.220  Sum_probs=34.3

Q ss_pred             hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868           3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI   54 (69)
Q Consensus         3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi   54 (69)
                      |++|++++++++.+                        ++++++++.      .+...++++.+.++.    ....|++|
T Consensus        48 tt~a~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~------~~i~~ir~~~~~~~~~~~~~~~kviiI  121 (239)
T d1njfa_          48 TSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASR------TKVEDTRDLLDNVQYAPARGRFKVYLI  121 (239)
T ss_dssp             HHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHHTCCTTEEEEETTCS------SSHHHHHHHHHSCCCSCSSSSSEEEEE
T ss_pred             HHHHHHHHHHhcCccccccCccccchHHHHHHcCCCCeEEEecchhc------CCHHHHHHHHHHHHhccccCCCEEEEE
Confidence            67888988887542                        445544322      123456777766532    24569999


Q ss_pred             cccccccc
Q psy3868          55 DELDAIAP   62 (69)
Q Consensus        55 DEid~i~~   62 (69)
                      ||+|.+..
T Consensus       122 de~d~l~~  129 (239)
T d1njfa_         122 DEVHMLSR  129 (239)
T ss_dssp             ETGGGSCH
T ss_pred             ECcccCCH
Confidence            99999853

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

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: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=95.35  E-value=0.016  Score=34.00  Aligned_cols=61  Identities=8%  Similarity=0.161  Sum_probs=37.8

Q ss_pred             hHHHHHHHHHh---CCcEEEEchhhhhhcccChHH-HHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868           3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESE-SNLRKAFEEADKNSPSIIFIDELDAIAPKRE   65 (69)
Q Consensus         3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~-~~l~~if~~a~~~~p~iifiDEid~i~~~r~   65 (69)
                      |+|++|++++.   +..+++++..++.......-. +.....++..  ....+|+|||+|.+.+++.
T Consensus        50 THLl~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~dll~iDDi~~i~~~~~  114 (213)
T d1l8qa2          50 THLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMY--KSVDLLLLDDVQFLSGKER  114 (213)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEEEHHHHHHHHHHHHHHTCHHHHHHHH--HTCSEEEEECGGGGTTCHH
T ss_pred             HHHHHHHHHHhccCccceEEechHHHHHHHHHHHHccchhhHHHHH--hhccchhhhhhhhhcCchH
Confidence            67888888887   357777887777544322211 1122333322  2468899999999987643

>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=93.69  E-value=0.045  Score=31.42  Aligned_cols=57  Identities=14%  Similarity=0.121  Sum_probs=31.9

Q ss_pred             hHHHHHHHHHh------CCcEEEEchhhhhhc-ccChHHHHHHHHHHH------------HHhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSL------GAFFFLINGPEIMSK-LAGESESNLRKAFEE------------ADKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~------~~~~~~v~~~~l~~~-~~ges~~~l~~if~~------------a~~~~p~iifiDEid~i~~   62 (69)
                      |++++++|+++      +...+.++++...+. ...+.   ++.....            .......+++|||+|.+..
T Consensus        47 Ttl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe~d~l~~  122 (237)
T d1sxjd2          47 TSTILALTKELYGPDLMKSRILELNASDERGISIVREK---VKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTA  122 (237)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTH---HHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCH
T ss_pred             HHHHHHHHHHHcCCcccccchhheeccccccchHHHHH---HHHHhhhhhhhhhHHHHhhccccCceEEEEecccccCH
Confidence            78999999986      456666666544221 11111   1111111            1112345899999998864

>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=93.51  E-value=0.11  Score=29.97  Aligned_cols=63  Identities=13%  Similarity=0.199  Sum_probs=37.1

Q ss_pred             hHHHHHHHHHhC---------CcEEEEchhhhhh----------------cccChHHHHHHHHHHHH-H-hcCCeEEEEc
Q psy3868           3 YRLTTLCRDSLG---------AFFFLINGPEIMS----------------KLAGESESNLRKAFEEA-D-KNSPSIIFID   55 (69)
Q Consensus         3 T~la~aia~~~~---------~~~~~v~~~~l~~----------------~~~ges~~~l~~if~~a-~-~~~p~iifiD   55 (69)
                      |+++++++++++         ..+..+++.....                ...|.+...+.+.+... + ...+.++++|
T Consensus        60 T~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iid  139 (287)
T d1w5sa2          60 TTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILD  139 (287)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEE
T ss_pred             HHHHHHHHHHHHhhcccccCCceeeeeccccccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCcccccee
Confidence            788899998863         3344444433211                23344544544444433 2 2467888999


Q ss_pred             cccccccccc
Q psy3868          56 ELDAIAPKRE   65 (69)
Q Consensus        56 Eid~i~~~r~   65 (69)
                      |+|.+...+.
T Consensus       140 e~d~l~~~~~  149 (287)
T d1w5sa2         140 EFQSMLSSPR  149 (287)
T ss_dssp             STHHHHSCTT
T ss_pred             EEEEeccccc
Confidence            9999976554

>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=91.62  E-value=0.22  Score=28.67  Aligned_cols=55  Identities=4%  Similarity=0.029  Sum_probs=36.7

Q ss_pred             hHHHHHHHHHhCC------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLGA------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~~------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifiDEid~i~~   62 (69)
                      |.+|+.+++....      .++.+.+..   +-  -+-..+|++.+.+..    .+.-|++|||+|.+..
T Consensus        29 ~~~a~~l~~~i~~~~~~h~D~~~i~~~~---~~--I~Id~IR~i~~~~~~~~~~~~~KviIId~ad~l~~   93 (198)
T d2gnoa2          29 REVSLELPEYVEKFPPKASDVLEIDPEG---EN--IGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMTQ   93 (198)
T ss_dssp             HHHHHHHHHHHHTSCCCTTTEEEECCSS---SC--BCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBCH
T ss_pred             HHHHHHHHHHHhccccCCCCEEEEeCCc---CC--CCHHHHHHHHHHHhhCcccCCCEEEEEeCccccch
Confidence            5678888876642      477776631   11  135678888877743    2456999999999864

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {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: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=89.83  E-value=0.31  Score=25.45  Aligned_cols=28  Identities=14%  Similarity=0.172  Sum_probs=19.7

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcccCh
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGE   32 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~~ge   32 (69)
                      |++|+.+|.+++.+++.  ...+.....|.
T Consensus        16 STvak~La~~L~~~~id--~~~~~~~~~~~   43 (169)
T d1kaga_          16 STIGRQLAQQLNMEFYD--SDQEIEKRTGA   43 (169)
T ss_dssp             HHHHHHHHHHTTCEEEE--HHHHHHHHHTS
T ss_pred             HHHHHHHHHHhCCCeEe--echhHHhhhcc
Confidence            78999999999999864  34443333333

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {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: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=88.87  E-value=0.17  Score=27.16  Aligned_cols=27  Identities=11%  Similarity=-0.069  Sum_probs=22.9

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhhhcc
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIMSKL   29 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~~~~   29 (69)
                      |++|+++|+.+|.+++......+...+
T Consensus        21 TTla~~La~~~~~~~i~~~~~~~~~~~   47 (192)
T d1lw7a2          21 SVLVNKLAAVFNTTSAWEYGREFVFEK   47 (192)
T ss_dssp             HHHHHHHHHHTTCEEECCTTHHHHHHS
T ss_pred             HHHHHHHHHHhCCCeEeeehHHHhhhh
Confidence            789999999999999988877765553

>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=87.85  E-value=0.21  Score=28.66  Aligned_cols=29  Identities=7%  Similarity=0.320  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868          34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP   62 (69)
Q Consensus        34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~   62 (69)
                      ...+|++.+....    .+..|++|||+|.+-.
T Consensus        90 ~~~ir~l~~~~~~~~~~~~~kviIide~d~l~~  122 (207)
T d1a5ta2          90 VDAVREVTEKLNEHARLGGAKVVWVTDAALLTD  122 (207)
T ss_dssp             HHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCH
T ss_pred             cchhhHHhhhhhhccccCccceEEechhhhhhh
Confidence            4457777766532    4567999999999864

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

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: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=87.67  E-value=1.4  Score=24.76  Aligned_cols=23  Identities=4%  Similarity=0.124  Sum_probs=18.0

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhh
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEI   25 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l   25 (69)
                      |++++.++.+.+..+..+++...
T Consensus        43 TsLl~~~~~~~~~~~~~i~~~~~   65 (283)
T d2fnaa2          43 SSIIKIGINELNLPYIYLDLRKF   65 (283)
T ss_dssp             HHHHHHHHHHHTCCEEEEEGGGG
T ss_pred             HHHHHHHHHHCCCCeEEEEeccc
Confidence            67888899999988887776544

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=87.65  E-value=0.87  Score=24.64  Aligned_cols=19  Identities=16%  Similarity=0.149  Sum_probs=16.9

Q ss_pred             hHHHHHHHHHhCCcEEEEc
Q psy3868           3 YRLTTLCRDSLGAFFFLIN   21 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~   21 (69)
                      |++++.+|+.+|++|+.++
T Consensus        14 sTi~k~La~~l~~~~~d~d   32 (161)
T d1viaa_          14 STLARALAKDLDLVFLDSD   32 (161)
T ss_dssp             HHHHHHHHHHHTCEEEEHH
T ss_pred             HHHHHHHHHHhCCCEEecC
Confidence            7899999999999998753

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=86.20  E-value=0.47  Score=25.74  Aligned_cols=19  Identities=11%  Similarity=0.069  Sum_probs=16.7

Q ss_pred             hHHHHHHHHHhCCcEEEEc
Q psy3868           3 YRLTTLCRDSLGAFFFLIN   21 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~   21 (69)
                      |++++.+|..+|++|+..+
T Consensus        15 STig~~La~~l~~~fiD~D   33 (165)
T d2iyva1          15 STIGRRLAKALGVGLLDTD   33 (165)
T ss_dssp             HHHHHHHHHHHTCCEEEHH
T ss_pred             HHHHHHHHHHhCCCeEeec
Confidence            7899999999999998654

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=85.70  E-value=0.3  Score=26.16  Aligned_cols=24  Identities=4%  Similarity=0.001  Sum_probs=21.0

Q ss_pred             hHHHHHHHHHhCCcEEEEchhhhh
Q psy3868           3 YRLTTLCRDSLGAFFFLINGPEIM   26 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v~~~~l~   26 (69)
                      |++|+++++++|.+++.++...+.
T Consensus        18 STia~~La~~lg~~~~~~~~d~~~   41 (176)
T d1zp6a1          18 STIAEALANLPGVPKVHFHSDDLW   41 (176)
T ss_dssp             HHHHHHHHTCSSSCEEEECTTHHH
T ss_pred             HHHHHHHHHHhCCCEEEecHHHHH
Confidence            679999999999999999886654

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

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: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=85.55  E-value=1.3  Score=25.95  Aligned_cols=54  Identities=15%  Similarity=0.169  Sum_probs=32.0

Q ss_pred             hHHHHHHHHHhC---CcEEEEchhhhhhcccChHHHHHHHHHHHH---------------HhcCCeEEEEcccccccc
Q psy3868           3 YRLTTLCRDSLG---AFFFLINGPEIMSKLAGESESNLRKAFEEA---------------DKNSPSIIFIDELDAIAP   62 (69)
Q Consensus         3 T~la~aia~~~~---~~~~~v~~~~l~~~~~ges~~~l~~if~~a---------------~~~~p~iifiDEid~i~~   62 (69)
                      +.+|+++.....   .+++.+++..+..      ......+|...               .......|||||||.+-.
T Consensus        37 ~~~A~~ih~~s~~~~~~~~~~~~~~~~~------~~~~~~lfg~~~~~~~~~~~~~~g~l~~a~gGtL~l~~i~~L~~  108 (247)
T d1ny5a2          37 EVVARLIHKLSDRSKEPFVALNVASIPR------DIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGELSL  108 (247)
T ss_dssp             HHHHHHHHHHSTTTTSCEEEEETTTSCH------HHHHHHHHCBCTTSSTTCCSCBCCHHHHTTTSEEEEESGGGCCH
T ss_pred             HHHHHHHHHhcCCcccccccchhhhhhh------cccHHHhcCcccCCcCCcccccCCHHHccCCCEEEEeChHhCCH
Confidence            568888876543   5788888876521      12223333211               112346899999998754

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

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: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=84.85  E-value=0.6  Score=25.06  Aligned_cols=25  Identities=36%  Similarity=0.647  Sum_probs=19.1

Q ss_pred             HHHHHHHHHHhcCCeEEEEcccccc
Q psy3868          36 NLRKAFEEADKNSPSIIFIDELDAI   60 (69)
Q Consensus        36 ~l~~if~~a~~~~p~iifiDEid~i   60 (69)
                      ..+..+..+....|.++++||+...
T Consensus        87 ~~~~~l~~~~~~~~~vlllDE~~~~  111 (178)
T d1ye8a1          87 ILERAYREAKKDRRKVIIIDEIGKM  111 (178)
T ss_dssp             HHHHHHHHHHHCTTCEEEECCCSTT
T ss_pred             hHHHHHHHHHhcCCCceeecCCCcc
Confidence            4556666677789999999998654

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=81.14  E-value=0.43  Score=26.01  Aligned_cols=18  Identities=17%  Similarity=0.026  Sum_probs=16.0

Q ss_pred             hHHHHHHHHHhCCcEEEE
Q psy3868           3 YRLTTLCRDSLGAFFFLI   20 (69)
Q Consensus         3 T~la~aia~~~~~~~~~v   20 (69)
                      |++++.+|.++|++|+..
T Consensus        16 STia~~LA~~Lg~~~id~   33 (170)
T d1e6ca_          16 TTVGRELARALGYEFVDT   33 (170)
T ss_dssp             HHHHHHHHHHHTCEEEEH
T ss_pred             HHHHHHHHHHhCCCEEeh
Confidence            689999999999998754