Psyllid ID: psy2779

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-
Protein Sequence
MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNTSMIIDSWVEGSRG
Secondary Structure (PSIPRED)
ccEEEEEccccccccccccccccccccccccccccccccccHHHHHHHcccEEEHHHHccccccccEEEEcccccccccccccccccEEEEEEEEEccccc
Secondary Structure Prediction (SSPRO)
ccEEEEcccccHHHEEccHcccccccccccccccHccccccHHHHHHHHcEEEEccccHHHHHHHcccccEEEEEEccccccccccccHHEEccccccccc
Coil and Loop (DISEMBL)
MKIEEVKSTVktqrisshshvkglglkengeanEMAAGLVGQQAAREVSRAVTWEKSFQFerckshslfrggravaggrtkcpkppntsmiidswvegsrg
Flexible Loop (DISEMBL)
mkieevkstvktqrisshshvkglglkENGEANEMAAGLVGQQAAREVSRAVTWEKSfqferckshslfrggravaggrtkcpkppntsmiidswvegsrg
Low Complexity Region (SEG)
MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNTSMIIDSWVEGSRG
Disordered region (IsUnstruct)
***********************************************VSRAVTWEKSFQFERCKSHSLFRGGRAV**************************
Disordered Region (DISOPRED)
*KIEE***********SHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNTSMIIDSWVEG***
Disordered Region (DISEMBL)
********************VKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNTSMIIDSWVEGSRG
Disordered Region (DISPRO)
*KIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNTSMIIDSWV*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNTSMIIDSWVEGSRG
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	101	2.2.26 [Sep-21-2011]
Q0IFL2	456	RuvB-like helicase 1 OS=A	N/A	N/A	0.514	0.114	0.75	3e-14
Q9DE26	456	RuvB-like 1 OS=Xenopus la	N/A	N/A	0.465	0.103	0.787	2e-13
Q29AK9	456	RuvB-like helicase 1 OS=D	yes	N/A	0.514	0.114	0.730	2e-13
Q8AWW7	456	RuvB-like 1 OS=Danio reri	yes	N/A	0.524	0.116	0.698	2e-13
Q9VH07	456	RuvB-like helicase 1 OS=D	yes	N/A	0.514	0.114	0.730	4e-13
P60123	456	RuvB-like 1 OS=Rattus nor	yes	N/A	0.465	0.103	0.765	6e-13
P60122	456	RuvB-like 1 OS=Mus muscul	yes	N/A	0.465	0.103	0.765	6e-13
Q9Y265	456	RuvB-like 1 OS=Homo sapie	yes	N/A	0.465	0.103	0.765	6e-13
Q9C0X6	456	RuvB-like helicase 1 OS=S	yes	N/A	0.524	0.116	0.452	1e-07
Q4ICA8	458	RuvB-like helicase 1 OS=G	yes	N/A	0.465	0.102	0.531	2e-07

>sp|Q0IFL2|RUVB1_AEDAE RuvB-like helicase 1 OS=Aedes aegypti GN=pont PE=3 SV=1

 Score = 77.0 bits (188), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 39/52 (75%), Positives = 44/52 (84%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAV 52
          MKIEEVKSTVKTQRI++HSHVKGLGL ENG   +MAAGLVGQ+ ARE +  V
Sbjct: 1  MKIEEVKSTVKTQRIAAHSHVKGLGLDENGVPLQMAAGLVGQKDAREAAGIV 52

Proposed core component of the chromatin remodeling Ino80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair.
Aedes aegypti (taxid: 7159)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 2

>sp|Q9DE26|RUVB1_XENLA RuvB-like 1 OS=Xenopus laevis GN=ruvbl1 PE=2 SV=1

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 37/47 (78%), Positives = 41/47 (87%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
          MKIEEVKST KTQRI++HSHVKGLGL ENG A + AAGLVGQ+ ARE
Sbjct: 1  MKIEEVKSTTKTQRIATHSHVKGLGLDENGIAKQAAAGLVGQENARE 47

Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair.

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q29AK9|RUVB1_DROPS RuvB-like helicase 1 OS=Drosophila pseudoobscura pseudoobscura GN=pont PE=3 SV=1

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 38/52 (73%), Positives = 44/52 (84%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAV 52
          MKIEEVKSTV+TQRI++HSHVKGLGL E G A + AAGLVGQ+AARE +  V
Sbjct: 1  MKIEEVKSTVRTQRIAAHSHVKGLGLDEAGSALQSAAGLVGQKAAREAAGIV 52

Proposed core component of the chromatin remodeling Ino80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair.

Drosophila pseudoobscura pseudoobscura (taxid: 46245)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q8AWW7|RUVB1_DANRE RuvB-like 1 OS=Danio rerio GN=ruvbl1 PE=2 SV=1

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 37/53 (69%), Positives = 43/53 (81%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVT 53
          MKIEEVKST KTQRI+SHSHVKGLGL E G A + A+GLVGQ++ARE    +T
Sbjct: 1  MKIEEVKSTTKTQRIASHSHVKGLGLDEAGNAKQSASGLVGQESAREACGIIT 53

Proposed core component of the chromatin remodeling Ino80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair.

Danio rerio (taxid: 7955)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9VH07|RUVB1_DROME RuvB-like helicase 1 OS=Drosophila melanogaster GN=pont PE=1 SV=1

 Score = 73.2 bits (178), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/52 (73%), Positives = 43/52 (82%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAV 52
          MKIEEVKSTV+TQRI++HSHVKGLGL E G A   AAGLVGQ+AARE +  V
Sbjct: 1  MKIEEVKSTVRTQRIAAHSHVKGLGLDEVGAAVHSAAGLVGQKAAREAAGIV 52

Proposed core component of the chromatin remodeling Ino80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair.

Drosophila melanogaster (taxid: 7227)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P60123|RUVB1_RAT RuvB-like 1 OS=Rattus norvegicus GN=Ruvbl1 PE=1 SV=1

 Score = 72.8 bits (177), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/47 (76%), Positives = 41/47 (87%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
          MKIEEVKST KTQRI+SHSHVKGLGL E+G A + A+GLVGQ+ ARE
Sbjct: 1  MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENARE 47

May be able to bind plasminogen at cell surface and enhance plasminogen activation.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P60122|RUVB1_MOUSE RuvB-like 1 OS=Mus musculus GN=Ruvbl1 PE=1 SV=1

 Score = 72.8 bits (177), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/47 (76%), Positives = 41/47 (87%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
          MKIEEVKST KTQRI+SHSHVKGLGL E+G A + A+GLVGQ+ ARE
Sbjct: 1  MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENARE 47

May be able to bind plasminogen at cell surface and enhance plasminogen activation.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9Y265|RUVB1_HUMAN RuvB-like 1 OS=Homo sapiens GN=RUVBL1 PE=1 SV=1

 Score = 72.8 bits (177), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/47 (76%), Positives = 41/47 (87%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
          MKIEEVKST KTQRI+SHSHVKGLGL E+G A + A+GLVGQ+ ARE
Sbjct: 1  MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENARE 47

May be able to bind plasminogen at cell surface and enhance plasminogen activation.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9C0X6|RUVB1_SCHPO RuvB-like helicase 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rvb1 PE=3 SV=1

 Score = 55.1 bits (131), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 24/53 (45%), Positives = 35/53 (66%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVT 53
          ++I EVK   +  RI++HSH+KGLGLKE+G    +  G +GQ+ ARE    +T
Sbjct: 2  VQISEVKGNGRDNRITTHSHIKGLGLKEDGTCESVGGGFIGQEKAREACGIIT 54

DNA helicase which participates in several chromatin remodeling complexes, including the SWR1 and the INO80 complexes. The SWR1 complex mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. The INO80 complex remodels chromatin by shifting nucleosomes and is involved in DNA repair. Also involved in pre-rRNA processing.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q4ICA8|RUVB1_GIBZE RuvB-like helicase 1 OS=Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) GN=RVB1 PE=3 SV=1

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 25/47 (53%), Positives = 34/47 (72%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
          ++I EVK   +  R ++H+H+KGLGLK +G A + AAG VGQ AARE
Sbjct: 2  VQISEVKGNKRDNRTAAHTHIKGLGLKSDGYAEKQAAGFVGQAAARE 48

DNA helicase which participates in several chromatin remodeling complexes, including the SWR1 and the INO80 complexes. The SWR1 complex mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. The INO80 complex remodels chromatin by shifting nucleosomes and is involved in DNA repair. Also involved in pre-rRNA processing.

Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (taxid: 229533)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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	101
312373428	847	hypothetical protein AND_17438 [Anophele	0.524	0.062	0.735	5e-13
170034306	456	pontin [Culex quinquefasciatus] gi|16787	0.514	0.114	0.75	8e-13
193713703	456	PREDICTED: ruvB-like helicase 1-like [Ac	0.514	0.114	0.769	1e-12
194740952	456	GF17460 [Drosophila ananassae] gi|190626	0.514	0.114	0.75	1e-12
157107057	456	TATA-binding protein, putative [Aedes ae	0.514	0.114	0.75	1e-12
156382397	455	predicted protein [Nematostella vectensi	0.514	0.114	0.711	3e-12
260816078	456	hypothetical protein BRAFLDRAFT_127120 [	0.514	0.114	0.75	3e-12
195388750	456	GJ23553 [Drosophila virilis] gi|19415112	0.524	0.116	0.716	4e-12
301607045	456	PREDICTED: ruvB-like 1 [Xenopus (Siluran	0.465	0.103	0.787	4e-12
357623020	443	putative pontin [Danaus plexippus]	0.514	0.117	0.711	4e-12

>gi|312373428|gb|EFR21173.1| hypothetical protein AND_17438 [Anopheles darlingi]

 Score = 78.6 bits (192), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 39/53 (73%), Positives = 44/53 (83%)

Query: 1   MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVT 53
           MKIEEVKSTVKTQRI++HSHVKGLGL ENG   +MAAGLVGQ+ ARE +  V 
Sbjct: 392 MKIEEVKSTVKTQRIAAHSHVKGLGLDENGAPLQMAAGLVGQKNAREAAGVVV 444

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170034306|ref|XP_001845015.1| pontin [Culex quinquefasciatus] gi|167875648|gb|EDS39031.1| pontin [Culex quinquefasciatus]

 Score = 77.8 bits (190), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 39/52 (75%), Positives = 44/52 (84%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAV 52
          MKIEEVKSTVKTQRI++HSHVKGLGL ENG   +MAAGLVGQ+ ARE +  V
Sbjct: 1  MKIEEVKSTVKTQRIAAHSHVKGLGLDENGVPLQMAAGLVGQKDAREAAGVV 52

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193713703|ref|XP_001952030.1| PREDICTED: ruvB-like helicase 1-like [Acyrthosiphon pisum]

 Score = 77.4 bits (189), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 40/52 (76%), Positives = 45/52 (86%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAV 52
          MKIEEVKSTVKTQRISSHSHVKGLGL E GEA +MA+GLVGQ+ AR+ +  V
Sbjct: 1  MKIEEVKSTVKTQRISSHSHVKGLGLDEFGEAIQMASGLVGQEDARQAAGIV 52

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194740952|ref|XP_001952953.1| GF17460 [Drosophila ananassae] gi|190626012|gb|EDV41536.1| GF17460 [Drosophila ananassae]

 Score = 77.4 bits (189), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/52 (75%), Positives = 45/52 (86%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAV 52
          MKIEEVKSTV+TQRI++HSHVKGLGL ENG A + AAGLVGQ+AARE +  V
Sbjct: 1  MKIEEVKSTVRTQRIAAHSHVKGLGLDENGAALQSAAGLVGQKAAREAAGIV 52

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157107057|ref|XP_001649604.1| TATA-binding protein, putative [Aedes aegypti] gi|122115038|sp|Q0IFL2.1|RUVB1_AEDAE RecName: Full=RuvB-like helicase 1; AltName: Full=Pontin gi|108879667|gb|EAT43892.1| AAEL004686-PA [Aedes aegypti]

 Score = 77.0 bits (188), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/52 (75%), Positives = 44/52 (84%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAV 52
          MKIEEVKSTVKTQRI++HSHVKGLGL ENG   +MAAGLVGQ+ ARE +  V
Sbjct: 1  MKIEEVKSTVKTQRIAAHSHVKGLGLDENGVPLQMAAGLVGQKDAREAAGIV 52

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156382397|ref|XP_001632540.1| predicted protein [Nematostella vectensis] gi|156219597|gb|EDO40477.1| predicted protein [Nematostella vectensis]

 Score = 75.9 bits (185), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 37/52 (71%), Positives = 44/52 (84%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAV 52
          MKIEEVKST KTQRI++HSH+KGLGL ENG A+ MA+GLVGQ+ ARE S  +
Sbjct: 1  MKIEEVKSTTKTQRIAAHSHIKGLGLDENGFAHPMASGLVGQETAREGSGVI 52

Source: Nematostella vectensis

Species: Nematostella vectensis

Genus: Nematostella

Family: Edwardsiidae

Order: Actiniaria

Class: Anthozoa

Phylum: Cnidaria

Superkingdom: Eukaryota

>gi|260816078|ref|XP_002602799.1| hypothetical protein BRAFLDRAFT_127120 [Branchiostoma floridae] gi|229288111|gb|EEN58811.1| hypothetical protein BRAFLDRAFT_127120 [Branchiostoma floridae]

 Score = 75.9 bits (185), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 39/52 (75%), Positives = 43/52 (82%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAV 52
          MKIEEVKST KTQRI+SHSHVKGLGL ENG A + AAG+VGQ+ ARE S  V
Sbjct: 1  MKIEEVKSTTKTQRIASHSHVKGLGLDENGFALQAAAGMVGQELAREASGVV 52

Source: Branchiostoma floridae

Species: Branchiostoma floridae

Genus: Branchiostoma

Family: Branchiostomidae

Phylum: Chordata

Superkingdom: Eukaryota

>gi|195388750|ref|XP_002053042.1| GJ23553 [Drosophila virilis] gi|194151128|gb|EDW66562.1| GJ23553 [Drosophila virilis]

 Score = 75.5 bits (184), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 38/53 (71%), Positives = 44/53 (83%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVT 53
          MKIEEVKSTV+TQRI++HSHVKGLGL E G A + AAGLVGQ+AARE +  V 
Sbjct: 1  MKIEEVKSTVRTQRIAAHSHVKGLGLDETGAAIQSAAGLVGQKAAREAAGIVV 53

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|301607045|ref|XP_002933113.1| PREDICTED: ruvB-like 1 [Xenopus (Silurana) tropicalis]

 Score = 75.5 bits (184), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 37/47 (78%), Positives = 41/47 (87%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
          MKIEEVKST KTQRI++HSHVKGLGL ENG A + AAGLVGQ+ ARE
Sbjct: 1  MKIEEVKSTTKTQRIATHSHVKGLGLDENGMAKQAAAGLVGQENARE 47

Source: Xenopus (Silurana) tropicalis

Species: Xenopus (Silurana) tropicalis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|357623020|gb|EHJ74338.1| putative pontin [Danaus plexippus]

 Score = 75.1 bits (183), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 37/52 (71%), Positives = 44/52 (84%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAV 52
          MKIEEVKST KTQRIS+H+H+KGLGL ENG   +MAAGLVGQ++ARE +  V
Sbjct: 1  MKIEEVKSTAKTQRISAHTHIKGLGLDENGVPIQMAAGLVGQESAREAAGIV 52

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

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	101
UNIPROTKB|F1SPF6	269	LOC100518399 "Uncharacterized	0.465	0.174	0.787	3.8e-14
UNIPROTKB|Q0IFL2	456	pont "RuvB-like helicase 1" [A	0.514	0.114	0.75	8.8e-14
ZFIN|ZDB-GENE-030109-2	456	ruvbl1 "RuvB-like 1 (E. coli)"	0.524	0.116	0.698	1.4e-13
UNIPROTKB|Q29AK9	456	pont "RuvB-like helicase 1" [D	0.514	0.114	0.730	2.4e-13
UNIPROTKB|Q9DE26	456	ruvbl1 "RuvB-like 1" [Xenopus	0.465	0.103	0.787	2.4e-13
FB|FBgn0040078	456	pont "pontin" [Drosophila mela	0.514	0.114	0.730	6.5e-13
UNIPROTKB|A7MBG8	456	RUVBL1 "Uncharacterized protei	0.465	0.103	0.765	8.4e-13
UNIPROTKB|E2RQC9	456	RUVBL1 "Uncharacterized protei	0.465	0.103	0.765	8.4e-13
UNIPROTKB|Q9Y265	456	RUVBL1 "RuvB-like 1" [Homo sap	0.465	0.103	0.765	8.4e-13
MGI|MGI:1928760	456	Ruvbl1 "RuvB-like protein 1" [	0.465	0.103	0.765	8.4e-13

UNIPROTKB|F1SPF6 LOC100518399 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 182 (69.1 bits), Expect = 3.8e-14, P = 3.8e-14
 Identities = 37/47 (78%), Positives = 41/47 (87%)

Query:     1 MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
             MKIEEVKST KTQRI+SHSHVKGLGL ENG A + A+GLVGQ+ ARE
Sbjct:     1 MKIEEVKSTTKTQRIASHSHVKGLGLDENGLAKQAASGLVGQENARE 47

GO:0043141 "ATP-dependent 5'-3' DNA helicase activity" evidence=IEA

GO:0031011 "Ino80 complex" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q0IFL2 pont "RuvB-like helicase 1" [Aedes aegypti (taxid:7159)]

 Score = 186 (70.5 bits), Expect = 8.8e-14, P = 8.8e-14
 Identities = 39/52 (75%), Positives = 44/52 (84%)

Query:     1 MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAV 52
             MKIEEVKSTVKTQRI++HSHVKGLGL ENG   +MAAGLVGQ+ ARE +  V
Sbjct:     1 MKIEEVKSTVKTQRIAAHSHVKGLGLDENGVPLQMAAGLVGQKDAREAAGIV 52

GO:0003713 "transcription coactivator activity" evidence=ISS

GO:0030111 "regulation of Wnt receptor signaling pathway" evidence=ISS

GO:0031011 "Ino80 complex" evidence=ISS

GO:0042127 "regulation of cell proliferation" evidence=ISS

ZFIN|ZDB-GENE-030109-2 ruvbl1 "RuvB-like 1 (E. coli)" [Danio rerio (taxid:7955)]

 Score = 184 (69.8 bits), Expect = 1.4e-13, P = 1.4e-13
 Identities = 37/53 (69%), Positives = 43/53 (81%)

Query:     1 MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVT 53
             MKIEEVKST KTQRI+SHSHVKGLGL E G A + A+GLVGQ++ARE    +T
Sbjct:     1 MKIEEVKSTTKTQRIASHSHVKGLGLDEAGNAKQSASGLVGQESAREACGIIT 53

GO:0031011 "Ino80 complex" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0043141 "ATP-dependent 5'-3' DNA helicase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003678 "DNA helicase activity" evidence=IEA

GO:0060420 "regulation of heart growth" evidence=IMP

GO:0007507 "heart development" evidence=IMP

GO:0071339 "MLL1 complex" evidence=ISS

GO:0004386 "helicase activity" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

UNIPROTKB|Q29AK9 pont "RuvB-like helicase 1" [Drosophila pseudoobscura pseudoobscura (taxid:46245)]

 Score = 182 (69.1 bits), Expect = 2.4e-13, P = 2.4e-13
 Identities = 38/52 (73%), Positives = 44/52 (84%)

Query:     1 MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAV 52
             MKIEEVKSTV+TQRI++HSHVKGLGL E G A + AAGLVGQ+AARE +  V
Sbjct:     1 MKIEEVKSTVRTQRIAAHSHVKGLGLDEAGSALQSAAGLVGQKAAREAAGIV 52

GO:0003713 "transcription coactivator activity" evidence=ISS

GO:0030111 "regulation of Wnt receptor signaling pathway" evidence=ISS

GO:0031011 "Ino80 complex" evidence=ISS

GO:0042127 "regulation of cell proliferation" evidence=ISS

UNIPROTKB|Q9DE26 ruvbl1 "RuvB-like 1" [Xenopus laevis (taxid:8355)]

 Score = 182 (69.1 bits), Expect = 2.4e-13, P = 2.4e-13
 Identities = 37/47 (78%), Positives = 41/47 (87%)

Query:     1 MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
             MKIEEVKST KTQRI++HSHVKGLGL ENG A + AAGLVGQ+ ARE
Sbjct:     1 MKIEEVKSTTKTQRIATHSHVKGLGLDENGIAKQAAAGLVGQENARE 47

GO:0071339 "MLL1 complex" evidence=ISS

FB|FBgn0040078 pont "pontin" [Drosophila melanogaster (taxid:7227)]

 Score = 178 (67.7 bits), Expect = 6.5e-13, P = 6.5e-13
 Identities = 38/52 (73%), Positives = 43/52 (82%)

Query:     1 MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAV 52
             MKIEEVKSTV+TQRI++HSHVKGLGL E G A   AAGLVGQ+AARE +  V
Sbjct:     1 MKIEEVKSTVRTQRIAAHSHVKGLGLDEVGAAVHSAAGLVGQKAAREAAGIV 52

GO:0008013 "beta-catenin binding" evidence=ISS

GO:0017025 "TBP-class protein binding" evidence=ISS

GO:0003678 "DNA helicase activity" evidence=ISS

GO:0005524 "ATP binding" evidence=IEA

GO:0043141 "ATP-dependent 5'-3' DNA helicase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0035267 "NuA4 histone acetyltransferase complex" evidence=IDA

GO:0031011 "Ino80 complex" evidence=IDA

GO:0035060 "brahma complex" evidence=IDA

GO:0010628 "positive regulation of gene expression" evidence=IMP

GO:0005875 "microtubule associated complex" evidence=IDA

GO:0090307 "spindle assembly involved in mitosis" evidence=IMP

GO:0007095 "mitotic G2 DNA damage checkpoint" evidence=IGI

UNIPROTKB|A7MBG8 RUVBL1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 177 (67.4 bits), Expect = 8.4e-13, P = 8.4e-13
 Identities = 36/47 (76%), Positives = 41/47 (87%)

Query:     1 MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
             MKIEEVKST KTQRI+SHSHVKGLGL E+G A + A+GLVGQ+ ARE
Sbjct:     1 MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENARE 47

GO:0071339 "MLL1 complex" evidence=IEA

GO:0043968 "histone H2A acetylation" evidence=IEA

GO:0043967 "histone H4 acetylation" evidence=IEA

GO:0035267 "NuA4 histone acetyltransferase complex" evidence=IEA

GO:0031011 "Ino80 complex" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0043141 "ATP-dependent 5'-3' DNA helicase activity" evidence=IEA

UNIPROTKB|E2RQC9 RUVBL1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 177 (67.4 bits), Expect = 8.4e-13, P = 8.4e-13
 Identities = 36/47 (76%), Positives = 41/47 (87%)

Query:     1 MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
             MKIEEVKST KTQRI+SHSHVKGLGL E+G A + A+GLVGQ+ ARE
Sbjct:     1 MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENARE 47

GO:0071339 "MLL1 complex" evidence=IEA

GO:0043968 "histone H2A acetylation" evidence=IEA

GO:0043967 "histone H4 acetylation" evidence=IEA

GO:0035267 "NuA4 histone acetyltransferase complex" evidence=IEA

GO:0031011 "Ino80 complex" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0043141 "ATP-dependent 5'-3' DNA helicase activity" evidence=IEA

UNIPROTKB|Q9Y265 RUVBL1 "RuvB-like 1" [Homo sapiens (taxid:9606)]

 Score = 177 (67.4 bits), Expect = 8.4e-13, P = 8.4e-13
 Identities = 36/47 (76%), Positives = 41/47 (87%)

Query:     1 MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
             MKIEEVKST KTQRI+SHSHVKGLGL E+G A + A+GLVGQ+ ARE
Sbjct:     1 MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENARE 47

GO:0005524 "ATP binding" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0007067 "mitosis" evidence=IEA

GO:0040008 "regulation of growth" evidence=IEA

GO:0051301 "cell division" evidence=IEA

GO:0005815 "microtubule organizing center" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

GO:0016887 "ATPase activity" evidence=IDA

GO:0035267 "NuA4 histone acetyltransferase complex" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0003678 "DNA helicase activity" evidence=IDA

GO:0043968 "histone H2A acetylation" evidence=IDA

GO:0043967 "histone H4 acetylation" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0071339 "MLL1 complex" evidence=IDA

GO:0031011 "Ino80 complex" evidence=IDA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=TAS

GO:0007283 "spermatogenesis" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006334 "nucleosome assembly" evidence=TAS

GO:0034080 "CENP-A containing nucleosome assembly at centromere" evidence=TAS

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=IDA

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

GO:0032508 "DNA duplex unwinding" evidence=IDA

MGI|MGI:1928760 Ruvbl1 "RuvB-like protein 1" [Mus musculus (taxid:10090)]

 Score = 177 (67.4 bits), Expect = 8.4e-13, P = 8.4e-13
 Identities = 36/47 (76%), Positives = 41/47 (87%)

Query:     1 MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
             MKIEEVKST KTQRI+SHSHVKGLGL E+G A + A+GLVGQ+ ARE
Sbjct:     1 MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENARE 47

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003678 "DNA helicase activity" evidence=ISO

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

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

GO:0007049 "cell cycle" evidence=IEA

GO:0007067 "mitosis" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

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

GO:0030529 "ribonucleoprotein complex" evidence=IDA

GO:0031011 "Ino80 complex" evidence=ISO

GO:0032508 "DNA duplex unwinding" evidence=ISO

GO:0035267 "NuA4 histone acetyltransferase complex" evidence=ISO

GO:0040008 "regulation of growth" evidence=IEA

GO:0043234 "protein complex" evidence=ISO

GO:0043967 "histone H4 acetylation" evidence=ISO

GO:0043968 "histone H2A acetylation" evidence=ISO

GO:0051301 "cell division" evidence=IEA

GO:0071339 "MLL1 complex" evidence=ISO

---

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)
Q8AWW7	RUVB1_DANRE	3, ., 6, ., 4, ., 1, 2	0.6981	0.5247	0.1162	yes	N/A
Q29AK9	RUVB1_DROPS	3, ., 6, ., 4, ., 1, 2	0.7307	0.5148	0.1140	yes	N/A
Q9VH07	RUVB1_DROME	3, ., 6, ., 4, ., 1, 2	0.7307	0.5148	0.1140	yes	N/A
P60123	RUVB1_RAT	3, ., 6, ., 4, ., 1, 2	0.7659	0.4653	0.1030	yes	N/A
P60122	RUVB1_MOUSE	3, ., 6, ., 4, ., 1, 2	0.7659	0.4653	0.1030	yes	N/A
Q4ICA8	RUVB1_GIBZE	3, ., 6, ., 4, ., 1, 2	0.5319	0.4653	0.1026	yes	N/A
Q9Y265	RUVB1_HUMAN	3, ., 6, ., 4, ., 1, 2	0.7659	0.4653	0.1030	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	101
COG1224	450	COG1224, TIP49, DNA helicase TIP49, TBP-interactin	5e-11
pfam06068	395	pfam06068, TIP49, TIP49 C-terminus	1e-10

>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein [Transcription]

 Score = 57.0 bits (138), Expect = 5e-11
 Identities = 25/46 (54%), Positives = 32/46 (69%), Gaps = 1/46 (2%)

Query: 2  KIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
          KI E     +  RI++HSH+KGLGL ENG+A  +  GLVGQ+ ARE
Sbjct: 5  KIREEDVGERE-RIAAHSHIKGLGLDENGKAKFIGDGLVGQEEARE 49

Length = 450

>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus

 Score = 56.2 bits (136), Expect = 1e-10
 Identities = 21/34 (61%), Positives = 29/34 (85%)

Query: 14 RISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
          RI++HSH++GLGL E+GEA  ++ GLVGQ+ ARE
Sbjct: 1  RIAAHSHIRGLGLDEDGEARYVSEGLVGQEKARE 34

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. The N-terminal domain contains the pfam00004 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. Length = 395

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	101
KOG1942|consensus	456		99.95
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	99.94
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	99.94
KOG2680|consensus	454		99.92
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	97.13
COG0606	490	Predicted ATPase with chaperone activity [Posttran	96.58
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	96.43
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	96.39
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	96.02
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	95.94
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	95.93
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	95.91
PRK13342	413	recombination factor protein RarA; Reviewed	95.61
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	95.59
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	95.47
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	95.31
PRK06893	229	DNA replication initiation factor; Validated	95.27
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	95.23
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	95.22
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	95.17
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	94.9
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	94.89
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	94.7
PF13245	76	AAA_19: Part of AAA domain	94.65
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	94.57
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	94.55
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	94.43
PRK12402	337	replication factor C small subunit 2; Reviewed	94.31
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	94.28
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	94.18
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	94.01
PRK04195	482	replication factor C large subunit; Provisional	93.84
TIGR02237	209	recomb_radB DNA repair and recombination protein R	93.81
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	93.79
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	93.76
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	93.69
PF13654	509	AAA_32: AAA domain; PDB: 3K1J_B.	93.65
PLN03025	319	replication factor C subunit; Provisional	93.59
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	93.45
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	93.39
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	93.36
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	93.35
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	93.33
cd01394	218	radB RadB. The archaeal protein radB shares simila	93.23
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	93.23
KOG0734|consensus	752		93.21
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	93.13
PHA02544	316	44 clamp loader, small subunit; Provisional	93.06
KOG0744|consensus	423		93.03
KOG1970|consensus	634		92.95
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	92.88
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	92.84
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	92.75
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	92.69
COG2256	436	MGS1 ATPase related to the helicase subunit of the	92.67
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	92.66
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	92.59
PRK13531	498	regulatory ATPase RavA; Provisional	92.57
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	92.51
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	92.5
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	92.48
PRK05973	237	replicative DNA helicase; Provisional	92.35
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	92.32
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	92.08
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	92.06
CHL00181	287	cbbX CbbX; Provisional	91.97
PRK13341	725	recombination factor protein RarA/unknown domain f	91.9
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	91.87
PRK07940	394	DNA polymerase III subunit delta'; Validated	91.78
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	91.78
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	91.77
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	91.67
PRK08903	227	DnaA regulatory inactivator Hda; Validated	91.5
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	91.48
PRK08084	235	DNA replication initiation factor; Provisional	91.42
PRK06067	234	flagellar accessory protein FlaH; Validated	91.41
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	91.38
KOG0731|consensus	774		91.35
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	91.34
PRK14737	186	gmk guanylate kinase; Provisional	91.26
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	91.23
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	91.23
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	91.23
PF07088	484	GvpD: GvpD gas vesicle protein; InterPro: IPR00978	91.22
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	91.21
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	91.18
PRK04328	249	hypothetical protein; Provisional	91.16
PRK06526	254	transposase; Provisional	91.08
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	91.07
CHL00195	489	ycf46 Ycf46; Provisional	91.04
PRK00300	205	gmk guanylate kinase; Provisional	91.02
PRK03992	389	proteasome-activating nucleotidase; Provisional	90.96
PRK05642	234	DNA replication initiation factor; Validated	90.91
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	90.9
KOG0733|consensus	802		90.85
PRK00131	175	aroK shikimate kinase; Reviewed	90.82
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	90.78
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	90.77
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	90.75
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	90.69
PRK07471	365	DNA polymerase III subunit delta'; Validated	90.62
CHL00095	821	clpC Clp protease ATP binding subunit	90.61
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	90.5
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	90.49
COG0714	329	MoxR-like ATPases [General function prediction onl	90.39
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	90.39
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	90.34
PRK00440	319	rfc replication factor C small subunit; Reviewed	90.33
PRK13765	637	ATP-dependent protease Lon; Provisional	90.33
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	90.28
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	90.26
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	90.13
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	90.08
TIGR02236	310	recomb_radA DNA repair and recombination protein R	90.01
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	90.01
PRK14738	206	gmk guanylate kinase; Provisional	89.95
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	89.91
PRK09112	351	DNA polymerase III subunit delta'; Validated	89.89
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	89.88
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	89.68
PRK04301	317	radA DNA repair and recombination protein RadA; Va	89.55
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	89.46
PRK12377	248	putative replication protein; Provisional	89.4
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	89.36
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	89.12
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	89.03
PRK14527	191	adenylate kinase; Provisional	89.01
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	88.98
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	88.98
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	88.96
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	88.93
KOG0727|consensus	408		88.92
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	88.76
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	88.62
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	88.56
PRK06620	214	hypothetical protein; Validated	88.5
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	88.44
KOG2028|consensus	554		88.4
CHL00176	638	ftsH cell division protein; Validated	88.19
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	88.09
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	88.03
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	88.01
PRK00411	394	cdc6 cell division control protein 6; Reviewed	87.89
KOG0730|consensus	693		87.87
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	87.85
PRK08533	230	flagellar accessory protein FlaH; Reviewed	87.83
PRK10865	857	protein disaggregation chaperone; Provisional	87.66
KOG0733|consensus	802		87.6
PRK09183	259	transposase/IS protein; Provisional	87.59
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	87.44
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	87.44
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	87.39
PRK05541	176	adenylylsulfate kinase; Provisional	87.35
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	87.26
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	87.2
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	87.16
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	87.08
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	87.07
KOG0991|consensus	333		87.03
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	86.99
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	86.76
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	86.64
PF00005	137	ABC_tran: ABC transporter This structure is on hol	86.55
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	86.43
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	86.41
PRK00889	175	adenylylsulfate kinase; Provisional	86.35
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	86.3
PRK00149	450	dnaA chromosomal replication initiation protein; R	86.27
PRK09302	509	circadian clock protein KaiC; Reviewed	86.25
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	86.08
PRK08181	269	transposase; Validated	85.96
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	85.91
PRK09862	506	putative ATP-dependent protease; Provisional	85.83
PRK05480	209	uridine/cytidine kinase; Provisional	85.81
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	85.76
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	85.74
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	85.74
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	85.7
PRK08356	195	hypothetical protein; Provisional	85.65
TIGR00235	207	udk uridine kinase. Model contains a number of lon	85.64
KOG0738|consensus	491		85.58
PLN02200	234	adenylate kinase family protein	85.42
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	85.3
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	85.03
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	84.96
cd03272	243	ABC_SMC3_euk Eukaryotic SMC3 proteins; SMC protein	84.91
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	84.81
cd00983	325	recA RecA is a bacterial enzyme which has roles in	84.57
PHA00729	226	NTP-binding motif containing protein	84.47
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	84.34
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	84.3
PRK10436	462	hypothetical protein; Provisional	84.28
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	84.24
PRK13851	344	type IV secretion system protein VirB11; Provision	84.17
PRK09302	509	circadian clock protein KaiC; Reviewed	84.0
PRK05564	313	DNA polymerase III subunit delta'; Validated	83.98
smart00487	201	DEXDc DEAD-like helicases superfamily.	83.97
PRK13833	323	conjugal transfer protein TrbB; Provisional	83.94
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	83.93
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	83.85
PRK08727	233	hypothetical protein; Validated	83.67
PLN02165	334	adenylate isopentenyltransferase	83.66
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	83.59
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	83.58
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	83.49
PRK11823	446	DNA repair protein RadA; Provisional	83.39
COG3839	338	MalK ABC-type sugar transport systems, ATPase comp	83.33
TIGR02533	486	type_II_gspE general secretory pathway protein E.	83.25
PRK07667	193	uridine kinase; Provisional	83.19
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	83.19
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	83.15
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	83.1
PF13476	202	AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V	83.09
KOG0989|consensus	346		83.05
TIGR00665	434	DnaB replicative DNA helicase. This model describe	83.04
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	82.86
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	82.83
PRK15455	644	PrkA family serine protein kinase; Provisional	82.72
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	82.69
KOG0741|consensus	744		82.44
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	82.35
PRK09354	349	recA recombinase A; Provisional	82.22
PTZ00035	337	Rad51 protein; Provisional	82.21
KOG0739|consensus	439		81.86
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	81.77
TIGR00376	637	DNA helicase, putative. The gene product may repre	81.67
KOG0735|consensus	952		81.59
PRK09087	226	hypothetical protein; Validated	81.46
PRK10875	615	recD exonuclease V subunit alpha; Provisional	81.44
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	81.39
PRK14088	440	dnaA chromosomal replication initiation protein; P	81.29
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	81.28
PHA02244	383	ATPase-like protein	81.26
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	81.19
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	81.17
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	80.99
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	80.96
PRK05748	448	replicative DNA helicase; Provisional	80.83
KOG3078|consensus	235		80.72
PRK06547	172	hypothetical protein; Provisional	80.64
KOG1807|consensus	1025		80.57
cd03278	197	ABC_SMC_barmotin Barmotin is a tight junction-asso	80.51
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	80.38
KOG0736|consensus	953		80.26
KOG0737|consensus	386		80.23
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	80.2
PTZ00202	550	tuzin; Provisional	80.18

>KOG1942|consensus

Probab=99.95  E-value=6.8e-30  Score=212.64  Aligned_cols=83  Identities=49%  Similarity=0.646  Sum_probs=77.4

Q ss_pred             CccceeecceeeeeeccccccccccCCCCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCC
Q psy2779           1 MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRT   80 (101)
Q Consensus         1 ~~i~ev~~~~r~~RIaaHSHIkGLGLde~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p   80 (101)
                      ++|+||+++.+.+||++||||||||||+.|.|.+.++|||||++|||||||||||       +|++ +++||++|++|||
T Consensus         2 ~~ieeVkst~~~~ria~HsHvkgLGlde~g~~~~~~~g~vGQ~~AReAagiivdl-------ik~K-kmaGravLlaGpp   73 (456)
T KOG1942|consen    2 VKIEEVKSTGRTQRIAAHSHVKGLGLDETGNAVEVAAGFVGQENAREAAGIIVDL-------IKSK-KMAGRAVLLAGPP   73 (456)
T ss_pred             cchhhhcccccchhhhhhhhccccCcCCCCCeeecccccccchhhhhhhhHHHHH-------HHhh-hccCcEEEEecCC
Confidence            5899999999999999999999999999999999999999999999999999999       5554 5689999999999


Q ss_pred             CCC--------------CCCCceee
Q psy2779          81 KCP--------------KPPNTSMI   91 (101)
Q Consensus        81 ~~g--------------~~~~~~~~   91 (101)
                      |||              |.||++|.
T Consensus        74 gtGKTAlAlaisqELG~kvPFcpmv   98 (456)
T KOG1942|consen   74 GTGKTALALAISQELGPKVPFCPMV   98 (456)
T ss_pred             CCchhHHHHHHHHHhCCCCCccccc
Confidence            999              56999986

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

Probab=99.94  E-value=2.4e-28  Score=204.87  Aligned_cols=74  Identities=35%  Similarity=0.516  Sum_probs=67.5

Q ss_pred             eeeeeeccccccccccCCCCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCC------
Q psy2779          10 VKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCP------   83 (101)
Q Consensus        10 ~r~~RIaaHSHIkGLGLde~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g------   83 (101)
                      ...+|+++||||||||||+||+|++.++|||||++|||||||||+|       +|+++ ++||.+|++||||||      
T Consensus        12 ~~~~~i~aHSHI~GLGLdeng~~k~~~dG~VGQ~~AReAaGvIv~m-------ik~gk-~aGrgiLi~GppgTGKTAlA~   83 (450)
T COG1224          12 GERERIAAHSHIKGLGLDENGKAKFIGDGLVGQEEAREAAGVIVKM-------IKQGK-MAGRGILIVGPPGTGKTALAM   83 (450)
T ss_pred             chhcccchhccccccccCCCCCEeEcCCcccchHHHHHhhhHHHHH-------HHhCc-ccccEEEEECCCCCcHHHHHH
Confidence            4557999999999999999999999999999999999999999999       66665 589999999999999      


Q ss_pred             --------CCCCceee
Q psy2779          84 --------KPPNTSMI   91 (101)
Q Consensus        84 --------~~~~~~~~   91 (101)
                              ++||++|.
T Consensus        84 gIa~eLG~dvPF~~is   99 (450)
T COG1224          84 GIARELGEDVPFVAIS   99 (450)
T ss_pred             HHHHHhCCCCCceeec
Confidence                    57999885

>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=99.94  E-value=1.6e-28  Score=204.25  Aligned_cols=70  Identities=41%  Similarity=0.577  Sum_probs=53.0

Q ss_pred             eeccccccccccCCCCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCC----------
Q psy2779          14 RISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCP----------   83 (101)
Q Consensus        14 RIaaHSHIkGLGLde~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g----------   83 (101)
                      ||++||||||||||++++|.+.++|||||++||||||+||||       +|++| ++||++|++||||||          
T Consensus         1 Ri~~HSHI~GLGld~~~~~~~~~~GlVGQ~~AReAagiiv~m-------Ik~~K-~aGr~iLiaGppGtGKTAlA~~ia~   72 (398)
T PF06068_consen    1 RIGAHSHIKGLGLDENGEARYIADGLVGQEKAREAAGIIVDM-------IKEGK-IAGRAILIAGPPGTGKTALAMAIAK   72 (398)
T ss_dssp             HHGCCTT--S--B-TTS-B-SEETTEES-HHHHHHHHHHHHH-------HHTT---TT-EEEEEE-TTSSHHHHHHHHHH
T ss_pred             CcccccccccCCcCCCCCEeeccccccChHHHHHHHHHHHHH-------Hhccc-ccCcEEEEeCCCCCCchHHHHHHHH
Confidence            799999999999999999999999999999999999999999       55554 689999999999999          


Q ss_pred             ----CCCCceee
Q psy2779          84 ----KPPNTSMI   91 (101)
Q Consensus        84 ----~~~~~~~~   91 (101)
                          |+||++|.
T Consensus        73 eLG~~~PF~~is   84 (398)
T PF06068_consen   73 ELGEDVPFVSIS   84 (398)
T ss_dssp             HCTTTS-EEEEE
T ss_pred             HhCCCCCeeEcc
Confidence                58999885

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.

>KOG2680|consensus

Probab=99.92  E-value=3.5e-26  Score=190.70  Aligned_cols=81  Identities=30%  Similarity=0.467  Sum_probs=74.6

Q ss_pred             cceeecceeeeeeccccccccccCCCCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCC
Q psy2779           3 IEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKC   82 (101)
Q Consensus         3 i~ev~~~~r~~RIaaHSHIkGLGLde~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~   82 (101)
                      ..|+++..+.+||++||||+|||||+..+|++.++|||||.+||+|||+|++|     +|.   .+++||++|++|+|||
T Consensus         6 ~~e~rDv~~veri~aHSHI~GlGldd~le~~~~s~GmVGQ~~AR~Aagvi~km-----i~e---gkiaGraiLiaG~pgt   77 (454)
T KOG2680|consen    6 LIEIRDVTRVERIGAHSHIRGLGLDDVLEPRYVSEGMVGQVKARKAAGVILKM-----IRE---GKIAGRAILIAGQPGT   77 (454)
T ss_pred             cccccchhhhhhccchhhccccCCCcccCcccccccchhhHHHHHHhHHHHHH-----HHc---CcccceEEEEecCCCC
Confidence            45788999999999999999999999999999999999999999999999999     555   5679999999999999


Q ss_pred             CC--------------CCCceee
Q psy2779          83 PK--------------PPNTSMI   91 (101)
Q Consensus        83 g~--------------~~~~~~~   91 (101)
                      ||              +||||++
T Consensus        78 GKtAiAmg~sksLG~~tpF~~i~  100 (454)
T KOG2680|consen   78 GKTAIAMGMSKSLGDDTPFTSIS  100 (454)
T ss_pred             CceeeeeehhhhhCCCCceeeee
Confidence            96              6888875

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

Probab=97.13  E-value=0.00012  Score=61.29  Aligned_cols=44  Identities=16%  Similarity=0.149  Sum_probs=36.4

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccc---cceEEecCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFR---GGRAVAGGRTKCPKP   85 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~---g~~ll~~G~p~~g~~   85 (101)
                      .-+-.||||+|.++|.||++-       .++-.+|+   -+-+|.-||||||||
T Consensus       119 t~ddViGqEeAK~kcrli~~y-------LenPe~Fg~WAPknVLFyGppGTGKT  165 (368)
T COG1223         119 TLDDVIGQEEAKRKCRLIMEY-------LENPERFGDWAPKNVLFYGPPGTGKT  165 (368)
T ss_pred             cHhhhhchHHHHHHHHHHHHH-------hhChHHhcccCcceeEEECCCCccHH
Confidence            446689999999999999988       66655554   578999999999965

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=96.58  E-value=0.00091  Score=58.11  Aligned_cols=36  Identities=17%  Similarity=0.123  Sum_probs=30.0

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ..-.+||+.||+|+-|               --++|.=||+-||||||||=
T Consensus       178 ~~DV~GQ~~AKrAlei---------------AAAGgHnLl~~GpPGtGKTm  213 (490)
T COG0606         178 FKDVKGQEQAKRALEI---------------AAAGGHNLLLVGPPGTGKTM  213 (490)
T ss_pred             hhhhcCcHHHHHHHHH---------------HHhcCCcEEEecCCCCchHH
Confidence            4568999999999754               34579999999999999973

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=96.43  E-value=0.00095  Score=51.82  Aligned_cols=34  Identities=21%  Similarity=0.234  Sum_probs=25.1

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      +-.+||+.|++|+-|-               -+++.=||+.||||||||
T Consensus         3 ~dI~GQe~aKrAL~iA---------------AaG~h~lLl~GppGtGKT   36 (206)
T PF01078_consen    3 SDIVGQEEAKRALEIA---------------AAGGHHLLLIGPPGTGKT   36 (206)
T ss_dssp             CCSSSTHHHHHHHHHH---------------HHCC--EEEES-CCCTHH
T ss_pred             hhhcCcHHHHHHHHHH---------------HcCCCCeEEECCCCCCHH
Confidence            4579999999998653               335778999999999985

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=96.39  E-value=0.00072  Score=51.27  Aligned_cols=45  Identities=16%  Similarity=0.056  Sum_probs=29.9

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCCc
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      -+.||||++..+.....++.       .+... -.-.-+|+.||||||||-..
T Consensus         3 ~~~~iG~~~~~~~l~~~l~~-------~~~~~-~~~~~~ll~Gp~G~GKT~la   47 (305)
T TIGR00635         3 LAEFIGQEKVKEQLQLFIEA-------AKMRQ-EALDHLLLYGPPGLGKTTLA   47 (305)
T ss_pred             HHHHcCHHHHHHHHHHHHHH-------HHhcC-CCCCeEEEECCCCCCHHHHH
Confidence            45799999999986665554       11111 01234789999999998543

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.

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

Probab=96.02  E-value=0.0015  Score=54.34  Aligned_cols=45  Identities=18%  Similarity=0.292  Sum_probs=29.3

Q ss_pred             cccchHHHHhhcceeeecccceeeeeccc------cccccceEEecCCCCCCCC
Q psy2779          38 GLVGQQAAREVSRAVTWEKSFQFERCKSH------SLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        38 GlVGQ~~AREAaGIVVdm~~~~~~~~~~~------~~~~g~~ll~~G~p~~g~~   85 (101)
                      =+|||+.|.++.-+-|--   .+.|++..      --...+-+|+.||||||||
T Consensus        72 ~ViGq~~ak~~l~~av~~---~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT  122 (412)
T PRK05342         72 YVIGQERAKKVLSVAVYN---HYKRLRHGDKKDDDVELQKSNILLIGPTGSGKT  122 (412)
T ss_pred             HeeChHHHHHHHHHHHHH---HHHhhhcccccccccccCCceEEEEcCCCCCHH
Confidence            479999999998765521   11223211      1123466889999999986

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=95.94  E-value=0.002  Score=50.33  Aligned_cols=44  Identities=14%  Similarity=0.083  Sum_probs=32.0

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ..+-||||++..++....++.       .+..+. .-..+|+.||||||||-
T Consensus        23 ~~~~~vG~~~~~~~l~~~l~~-------~~~~~~-~~~~~ll~GppG~GKT~   66 (328)
T PRK00080         23 SLDEFIGQEKVKENLKIFIEA-------AKKRGE-ALDHVLLYGPPGLGKTT   66 (328)
T ss_pred             CHHHhcCcHHHHHHHHHHHHH-------HHhcCC-CCCcEEEECCCCccHHH
Confidence            457799999999998777765       211111 23568899999999984

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=95.93  E-value=0.001  Score=50.45  Aligned_cols=53  Identities=9%  Similarity=0.007  Sum_probs=30.4

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccccccc--cceEEecCCCCCCCCCCce
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFR--GGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~--g~~ll~~G~p~~g~~~~~~   89 (101)
                      +.|||++++.++.-=++.....+..|.+.+....  ..-+|+.||||||||-...
T Consensus         6 ~~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~   60 (261)
T TIGR02881         6 SRMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVAR   60 (261)
T ss_pred             HHhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHH
Confidence            5689999998877544333111111221111112  2356899999999986543

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.

>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=95.91  E-value=0.0019  Score=51.40  Aligned_cols=48  Identities=10%  Similarity=0.031  Sum_probs=31.0

Q ss_pred             CCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          30 GEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        30 g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ..|. +-+-||||++..+-..+..+.       ++..+. .=--+|+.||||||||-
T Consensus        18 lRP~-~L~efiGQ~~l~~~l~i~i~a-------a~~r~~-~l~h~lf~GPPG~GKTT   65 (233)
T PF05496_consen   18 LRPK-SLDEFIGQEHLKGNLKILIRA-------AKKRGE-ALDHMLFYGPPGLGKTT   65 (233)
T ss_dssp             TS-S-SCCCS-S-HHHHHHHHHHHHH-------HHCTTS----EEEEESSTTSSHHH
T ss_pred             cCCC-CHHHccCcHHHHhhhHHHHHH-------HHhcCC-CcceEEEECCCccchhH
Confidence            4444 367899999999999988887       321110 01247899999999964

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.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=95.61  E-value=0.0032  Score=51.14  Aligned_cols=41  Identities=12%  Similarity=0.060  Sum_probs=31.4

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+++-+..+++..+       +++..   -..+|+.||||||||-
T Consensus        11 l~d~vGq~~~v~~~~~L~~~-------i~~~~---~~~ilL~GppGtGKTt   51 (413)
T PRK13342         11 LDEVVGQEHLLGPGKPLRRM-------IEAGR---LSSMILWGPPGTGKTT   51 (413)
T ss_pred             HHHhcCcHHHhCcchHHHHH-------HHcCC---CceEEEECCCCCCHHH
Confidence            45699999988777778777       54444   2367889999999974

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=95.59  E-value=0.004  Score=53.43  Aligned_cols=48  Identities=15%  Similarity=0.163  Sum_probs=30.6

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeecc----ccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKS----HSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~----~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ..-+|||.+|.+|.-+.+-.   .|.|..-    ..-...+-+|+.||||||||-
T Consensus        11 d~~IiGQ~eAkk~lsvAl~n---~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~   62 (441)
T TIGR00390        11 DKYIIGQDNAKKSVAIALRN---RYRRSQLNEELKDEVTPKNILMIGPTGVGKTE   62 (441)
T ss_pred             hhhccCHHHHHHHHHHHHHh---hhhhhccccccccccCCceEEEECCCCCCHHH
Confidence            35589999999999776654   1111110    001123567899999999863

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.

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=95.47  E-value=0.0039  Score=42.72  Aligned_cols=41  Identities=20%  Similarity=0.149  Sum_probs=21.1

Q ss_pred             ccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCCce
Q psy2779          39 LVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        39 lVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      |||-++..+..-=.+++       .+++.   ++.+++.|++|||||=...
T Consensus         2 fvgR~~e~~~l~~~l~~-------~~~~~---~~~~ll~G~~G~GKT~ll~   42 (185)
T PF13191_consen    2 FVGREEEIERLRDLLDA-------AQSGS---PRNLLLTGESGSGKTSLLR   42 (185)
T ss_dssp             -TT-HHHHHHHHHTTGG-------TSS--------EEE-B-TTSSHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHH-------HHcCC---CcEEEEECCCCCCHHHHHH
Confidence            56666666655444444       43333   6899999999999985543

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

Probab=95.31  E-value=0.0072  Score=50.81  Aligned_cols=49  Identities=16%  Similarity=0.216  Sum_probs=30.2

Q ss_pred             cCcccchHHHHhhcceeeecccceeeee-cccc-----ccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERC-KSHS-----LFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~-~~~~-----~~~g~~ll~~G~p~~g~~   85 (101)
                      ..=.|||++|.++.-+.|-- ++.-++. +...     -.....+|+.||||||||
T Consensus        76 ~~~ViGQe~A~~~l~~av~~-h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT  130 (413)
T TIGR00382        76 DEYVIGQEQAKKVLSVAVYN-HYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKT  130 (413)
T ss_pred             cceecCHHHHHHHHHHHHHH-HHhhhccccccccccccccCCceEEEECCCCcCHH
Confidence            34479999999998776621 0000111 0011     123567899999999986

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=95.27  E-value=0.009  Score=44.84  Aligned_cols=51  Identities=8%  Similarity=-0.121  Sum_probs=32.3

Q ss_pred             CCCCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          26 LKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        26 Lde~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      |+=...+....+-||+|.++.-+..+.-.+     .   +   .....+++.||||||||-.
T Consensus         5 l~~~~~~~~~fd~f~~~~~~~~~~~~~~~~-----~---~---~~~~~l~l~G~~G~GKThL   55 (229)
T PRK06893          5 LPIHQIDDETLDNFYADNNLLLLDSLRKNF-----I---D---LQQPFFYIWGGKSSGKSHL   55 (229)
T ss_pred             cCCCCCCcccccccccCChHHHHHHHHHHh-----h---c---cCCCeEEEECCCCCCHHHH
Confidence            343344566778899888876554443222     1   1   1245689999999999843

>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=95.23  E-value=0.009  Score=37.67  Aligned_cols=26  Identities=12%  Similarity=-0.001  Sum_probs=19.9

Q ss_pred             ccceEEecCCCCCCCCCCceeeeeee
Q psy2779          70 RGGRAVAGGRTKCPKPPNTSMIIDSW   95 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~~~~~~~   95 (101)
                      .++.+++.||||||||-....+.+.|
T Consensus        18 ~~~~v~i~G~~G~GKT~l~~~i~~~~   43 (151)
T cd00009          18 PPKNLLLYGPPGTGKTTLARAIANEL   43 (151)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHh
Confidence            46789999999999997655555444

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.

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=95.22  E-value=0.0053  Score=42.75  Aligned_cols=13  Identities=15%  Similarity=0.107  Sum_probs=10.6

Q ss_pred             eEEecCCCCCCCC
Q psy2779          73 RAVAGGRTKCPKP   85 (101)
Q Consensus        73 ~ll~~G~p~~g~~   85 (101)
                      +.|+.||||||||
T Consensus        19 ~~~i~GpPGTGKT   31 (236)
T PF13086_consen   19 ITLIQGPPGTGKT   31 (236)
T ss_dssp             -EEEE-STTSSHH
T ss_pred             CEEEECCCCCChH
Confidence            6899999999998

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=95.17  E-value=0.0065  Score=45.81  Aligned_cols=25  Identities=20%  Similarity=0.109  Sum_probs=21.9

Q ss_pred             cccccccceEEecCCCCCCCCCCce
Q psy2779          65 SHSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        65 ~~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      .+....|+.+|+.|+||||||.|+.
T Consensus        17 ~GG~p~g~~~lI~G~pGsGKT~f~~   41 (260)
T COG0467          17 GGGLPRGSVVLITGPPGTGKTIFAL   41 (260)
T ss_pred             cCCCcCCcEEEEEcCCCCcHHHHHH
Confidence            4677889999999999999998864

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=94.90  E-value=0.01  Score=48.97  Aligned_cols=51  Identities=14%  Similarity=0.149  Sum_probs=35.1

Q ss_pred             CCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCCceee
Q psy2779          28 ENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNTSMI   91 (101)
Q Consensus        28 e~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~~~~   91 (101)
                      +.-.+.+...-+|||++++.|.-+-.--          .+.  |+ +|+.|++||||+-+-.++
T Consensus         8 ~~~~~~~pf~~ivGq~~~k~al~~~~~~----------p~~--~~-vli~G~~GtGKs~~ar~~   58 (350)
T CHL00081          8 KKERPVFPFTAIVGQEEMKLALILNVID----------PKI--GG-VMIMGDRGTGKSTTIRAL   58 (350)
T ss_pred             hccCCCCCHHHHhChHHHHHHHHHhccC----------CCC--Ce-EEEEcCCCCCHHHHHHHH
Confidence            3344566778899999999997654322          232  44 559999999997655443

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=94.89  E-value=0.011  Score=48.19  Aligned_cols=37  Identities=16%  Similarity=0.153  Sum_probs=27.5

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .+-+|||+.+++|+-+-.-.             .+++-+|+.|+||||||
T Consensus         7 f~~i~Gq~~~~~~l~~~~~~-------------~~~~~vLl~G~pG~gKT   43 (334)
T PRK13407          7 FSAIVGQEEMKQAMVLTAID-------------PGIGGVLVFGDRGTGKS   43 (334)
T ss_pred             HHHhCCHHHHHHHHHHHHhc-------------cCCCcEEEEcCCCCCHH
Confidence            45689999999998763221             12345889999999996

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.70  E-value=0.011  Score=47.34  Aligned_cols=39  Identities=10%  Similarity=0.038  Sum_probs=27.4

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+.+|||+.+.+..   ..+       ++.++.  -.++|+.||||||||-
T Consensus        15 ~~~iiGq~~~~~~l---~~~-------~~~~~~--~h~~L~~Gp~G~GKTt   53 (363)
T PRK14961         15 FRDIIGQKHIVTAI---SNG-------LSLGRI--HHAWLLSGTRGVGKTT   53 (363)
T ss_pred             hhhccChHHHHHHH---HHH-------HHcCCC--CeEEEEecCCCCCHHH
Confidence            56799999998874   233       222222  3468999999999984

>PF13245 AAA_19: Part of AAA domain

Probab=94.65  E-value=0.015  Score=37.83  Aligned_cols=16  Identities=19%  Similarity=0.038  Sum_probs=13.9

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      ..+.+++.||||||||
T Consensus         9 ~~~~~vv~g~pGtGKT   24 (76)
T PF13245_consen    9 GSPLFVVQGPPGTGKT   24 (76)
T ss_pred             hCCeEEEECCCCCCHH
Confidence            3677888999999998

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.57  E-value=0.0097  Score=50.37  Aligned_cols=40  Identities=18%  Similarity=0.180  Sum_probs=27.4

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      -+-+|||+.+.+..   ..+       +++++.  ...+|+.||||||||-.
T Consensus        13 ~~divGq~~i~~~L---~~~-------i~~~~l--~~~~Lf~GPpGtGKTTl   52 (472)
T PRK14962         13 FSEVVGQDHVKKLI---INA-------LKKNSI--SHAYIFAGPRGTGKTTV   52 (472)
T ss_pred             HHHccCcHHHHHHH---HHH-------HHcCCC--CeEEEEECCCCCCHHHH
Confidence            45699999986643   334       333332  34588999999999754

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.55  E-value=0.011  Score=47.99  Aligned_cols=39  Identities=13%  Similarity=0.124  Sum_probs=27.8

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+.+.+.   +..+       ++++++  .-++|+.|||||||+.
T Consensus        15 ~~eiiGq~~~~~~---L~~~-------~~~~~~--~ha~lf~Gp~G~GKtt   53 (397)
T PRK14955         15 FADITAQEHITRT---IQNS-------LRMGRV--GHGYIFSGLRGVGKTT   53 (397)
T ss_pred             HhhccChHHHHHH---HHHH-------HHhCCc--ceeEEEECCCCCCHHH
Confidence            4678999999874   3444       333332  4568899999999974

>smart00763 AAA_PrkA PrkA AAA domain

Probab=94.43  E-value=0.014  Score=48.78  Aligned_cols=42  Identities=17%  Similarity=0.023  Sum_probs=27.1

Q ss_pred             cccchHHHHhhcceeeecccceeeeeccc-cccccceEEecCCCCCCCCCC
Q psy2779          38 GLVGQQAAREVSRAVTWEKSFQFERCKSH-SLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        38 GlVGQ~~AREAaGIVVdm~~~~~~~~~~~-~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      -++||++|.+..  |-.+      +.... ..-.+++|++.|||||||+-+
T Consensus        52 ~~~G~~~~i~~l--v~~l------~~~a~g~~~~r~il~L~GPPGsGKStl   94 (361)
T smart00763       52 DFFGMEEAIERF--VNYF------KSAAQGLEERKQILYLLGPVGGGKSSL   94 (361)
T ss_pred             hccCcHHHHHHH--HHHH------HHHHhcCCCCCcEEEEECCCCCCHHHH
Confidence            699999986542  2222      22111 122468999999999999754

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

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=94.31  E-value=0.018  Score=43.66  Aligned_cols=38  Identities=13%  Similarity=0.039  Sum_probs=25.1

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      -+.++||..+++...-.+.-           +.  -..+|+.||||||||-
T Consensus        14 ~~~~~g~~~~~~~L~~~~~~-----------~~--~~~lll~Gp~GtGKT~   51 (337)
T PRK12402         14 LEDILGQDEVVERLSRAVDS-----------PN--LPHLLVQGPPGSGKTA   51 (337)
T ss_pred             HHHhcCCHHHHHHHHHHHhC-----------CC--CceEEEECCCCCCHHH
Confidence            46689999987764322221           11  1258899999999973

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

Probab=94.28  E-value=0.012  Score=48.82  Aligned_cols=67  Identities=12%  Similarity=-0.022  Sum_probs=37.6

Q ss_pred             cccccccCCCCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          19 SHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        19 SHIkGLGLde~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +.|.-+.+.+  .|...-+-+.|.+...+..--.+++--......+....-..+-+|+.||||||||-.
T Consensus       129 ~~~~~~~~~~--~p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~L  195 (398)
T PTZ00454        129 SSIQLLQMSE--KPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTML  195 (398)
T ss_pred             chhhhhcccC--CCCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHH
Confidence            3344445544  234445568888888877665555400000011111333467788999999999754

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.18  E-value=0.018  Score=49.70  Aligned_cols=39  Identities=18%  Similarity=0.089  Sum_probs=27.7

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+.+.+.   +..+       ++++++  +.++|+.||||||||-
T Consensus        17 f~dvVGQe~iv~~---L~~~-------i~~~ri--~ha~Lf~GP~GtGKTT   55 (484)
T PRK14956         17 FRDVIHQDLAIGA---LQNA-------LKSGKI--GHAYIFFGPRGVGKTT   55 (484)
T ss_pred             HHHHhChHHHHHH---HHHH-------HHcCCC--CeEEEEECCCCCCHHH
Confidence            4679999999876   2233       333332  4578999999999984

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=94.01  E-value=0.0095  Score=46.57  Aligned_cols=52  Identities=12%  Similarity=-0.026  Sum_probs=28.1

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccccc--cccceEEecCCCCCCCCCCc
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSL--FRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~--~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +-|||++.+.+..-=++.+-..+-.|.+-+-.  ..+.-+|+.||||||||-..
T Consensus        22 ~~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        22 RELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             HhccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHH
Confidence            46899888888753333320000011110100  02345889999999998643

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.

>PRK04195 replication factor C large subunit; Provisional

Probab=93.84  E-value=0.019  Score=47.63  Aligned_cols=46  Identities=15%  Similarity=0.125  Sum_probs=29.1

Q ss_pred             CcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          31 EANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        31 ~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .|.. .+-+|||+++.+..--.++-  ++     .+.  ..+.+|+.||||||||-
T Consensus         9 rP~~-l~dlvg~~~~~~~l~~~l~~--~~-----~g~--~~~~lLL~GppG~GKTt   54 (482)
T PRK04195          9 RPKT-LSDVVGNEKAKEQLREWIES--WL-----KGK--PKKALLLYGPPGVGKTS   54 (482)
T ss_pred             CCCC-HHHhcCCHHHHHHHHHHHHH--Hh-----cCC--CCCeEEEECCCCCCHHH
Confidence            3444 34599999998764322221  11     111  16789999999999983

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=93.81  E-value=0.03  Score=40.26  Aligned_cols=23  Identities=17%  Similarity=0.021  Sum_probs=19.2

Q ss_pred             ccccccceEEecCCCCCCCCCCc
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +.+..|.+.++.||||||||=+.
T Consensus         7 GGi~~g~i~~i~G~~GsGKT~l~   29 (209)
T TIGR02237         7 GGVERGTITQIYGPPGSGKTNIC   29 (209)
T ss_pred             CCCCCCeEEEEECCCCCCHHHHH
Confidence            45667899999999999998653

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

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

Probab=93.79  E-value=0.019  Score=49.47  Aligned_cols=50  Identities=12%  Similarity=0.064  Sum_probs=30.0

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeec--cccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCK--SHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~--~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ..-+|||++|.+|+-+-+-- .+...+..  ...-...+-+|+.||||||||.
T Consensus        14 d~~IiGQe~AkkalavAl~~-~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~   65 (443)
T PRK05201         14 DKYIIGQDDAKRAVAIALRN-RWRRMQLPEELRDEVTPKNILMIGPTGVGKTE   65 (443)
T ss_pred             ccccCCHHHHHHHHHHHHHH-HHHHhcCCcccccccCCceEEEECCCCCCHHH
Confidence            45699999999998765521 00000000  0011124568899999999874

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=93.76  E-value=0.025  Score=48.75  Aligned_cols=17  Identities=18%  Similarity=0.243  Sum_probs=14.7

Q ss_pred             ccceEEecCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~   86 (101)
                      ..++|||+||||||||-
T Consensus        44 ~~~iLlLtGP~G~GKtt   60 (519)
T PF03215_consen   44 PKRILLLTGPSGCGKTT   60 (519)
T ss_pred             CcceEEEECCCCCCHHH
Confidence            46799999999999874

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=93.69  E-value=0.022  Score=42.79  Aligned_cols=25  Identities=8%  Similarity=-0.013  Sum_probs=21.0

Q ss_pred             cccccccceEEecCCCCCCCCCCce
Q psy2779          65 SHSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        65 ~~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      .+....|..+|+.|+||||||.+..
T Consensus        15 ~GG~~~gs~~lI~G~pGsGKT~la~   39 (237)
T TIGR03877        15 HGGIPERNVVLLSGGPGTGKSIFSQ   39 (237)
T ss_pred             cCCCcCCeEEEEEcCCCCCHHHHHH
Confidence            3466679999999999999998764

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>PF13654 AAA_32: AAA domain; PDB: 3K1J_B

Probab=93.65  E-value=0.019  Score=49.33  Aligned_cols=47  Identities=15%  Similarity=0.079  Sum_probs=0.0

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCCceeeeee
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNTSMIIDS   94 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~~~~~~~   94 (101)
                      ..++|||+.|.+|...=++|       -     ..|==+.+.|+|||||.-++.-.+..
T Consensus         7 ~~~~iGQ~RA~~Al~~gl~i-------~-----~~GYNIfv~G~~GtGr~t~v~~~l~~   53 (509)
T PF13654_consen    7 LEGIIGQERAVEALEFGLGI-------R-----KPGYNIFVMGPPGTGRRTYVRRFLEE   53 (509)
T ss_dssp             -----------------------------------------------------------
T ss_pred             cccccccccccccccccccc-------c-----cccccccccccccccccccccccccc
Confidence            47999999999999999999       1     13667889999999998877655543

>PLN03025 replication factor C subunit; Provisional

Probab=93.59  E-value=0.027  Score=44.02  Aligned_cols=37  Identities=14%  Similarity=0.107  Sum_probs=25.2

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      -+-+|||+++.+..-   .+       +++.+   -.-+|+.||||||||
T Consensus        12 l~~~~g~~~~~~~L~---~~-------~~~~~---~~~lll~Gp~G~GKT   48 (319)
T PLN03025         12 LDDIVGNEDAVSRLQ---VI-------ARDGN---MPNLILSGPPGTGKT   48 (319)
T ss_pred             HHHhcCcHHHHHHHH---HH-------HhcCC---CceEEEECCCCCCHH
Confidence            466899999887643   22       22222   124789999999998

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=93.45  E-value=0.02  Score=47.59  Aligned_cols=51  Identities=14%  Similarity=0.042  Sum_probs=29.8

Q ss_pred             cccccCcccchHHHHhhcceeeec-ccce-eeeeccccccccceEEecCCCCCCCC
Q psy2779          32 ANEMAAGLVGQQAAREVSRAVTWE-KSFQ-FERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        32 a~~~a~GlVGQ~~AREAaGIVVdm-~~~~-~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      +...-+-++|++++++...=+++. +..+ |.+. ..+  .-+-+|+.||||||||
T Consensus        50 ~~~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~-g~~--~~~giLL~GppGtGKT  102 (495)
T TIGR01241        50 PKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKL-GAK--IPKGVLLVGPPGTGKT  102 (495)
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhc-CCC--CCCcEEEECCCCCCHH
Confidence            444556789999998776544443 1110 1111 011  1234789999999997

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.

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=93.39  E-value=0.039  Score=42.68  Aligned_cols=49  Identities=18%  Similarity=0.091  Sum_probs=30.5

Q ss_pred             CcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCCc
Q psy2779          31 EANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        31 ~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      .+.+...-|+|+++.-+..--.+.-       +.++.  ....+++.||||||||-..
T Consensus         9 ~~~~~p~~l~gRe~e~~~l~~~l~~-------~~~~~--~~~~i~I~G~~GtGKT~l~   57 (365)
T TIGR02928         9 EPDYVPDRIVHRDEQIEELAKALRP-------ILRGS--RPSNVFIYGKTGTGKTAVT   57 (365)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHH-------HHcCC--CCCcEEEECCCCCCHHHHH
Confidence            3445556789998877664332221       11112  2457899999999998544

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.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=93.36  E-value=0.041  Score=42.31  Aligned_cols=28  Identities=7%  Similarity=-0.142  Sum_probs=22.1

Q ss_pred             cccccccceEEecCCCCCCCCCCceeee
Q psy2779          65 SHSLFRGGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        65 ~~~~~~g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      .+....|.+.|+.|+||||||=|....+
T Consensus        30 ~GGip~gs~~lI~G~pGtGKT~l~~qf~   57 (259)
T TIGR03878        30 LGGIPAYSVINITGVSDTGKSLMVEQFA   57 (259)
T ss_pred             CCCeECCcEEEEEcCCCCCHHHHHHHHH
Confidence            3455668899999999999998776543

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

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

Probab=93.35  E-value=0.02  Score=37.48  Aligned_cols=18  Identities=17%  Similarity=0.017  Sum_probs=11.4

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .++.+++.|+||||||=.
T Consensus         3 ~~~~~~i~G~~G~GKT~~   20 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTL   20 (131)
T ss_dssp             ----EEEEE-TTSSHHHH
T ss_pred             CCcccEEEcCCCCCHHHH
Confidence            367899999999999843

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

Probab=93.33  E-value=0.03  Score=47.96  Aligned_cols=46  Identities=17%  Similarity=0.294  Sum_probs=30.5

Q ss_pred             CcccchHHHHhhcceeeecccceeeeecccc-----ccccceEEecCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHS-----LFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~-----~~~g~~ll~~G~p~~g~~   85 (101)
                      +=.|||+.|.++..+-|==   .|-|+.+..     -.+.--+|+-||||||||
T Consensus        61 ~YVIGQe~AKKvLsVAVYN---HYKRl~~~~~~~dvEL~KSNILLiGPTGsGKT  111 (408)
T COG1219          61 EYVIGQEQAKKVLSVAVYN---HYKRLNNKEDNDDVELSKSNILLIGPTGSGKT  111 (408)
T ss_pred             hheecchhhhceeeeeehh---HHHHHhccCCCCceeeeeccEEEECCCCCcHH
Confidence            3468999999998887743   223332211     134455778999999987

>cd01394 radB RadB

Probab=93.23  E-value=0.044  Score=39.76  Aligned_cols=25  Identities=16%  Similarity=0.007  Sum_probs=20.2

Q ss_pred             ccccccceEEecCCCCCCCCCCcee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      +.+..|.++++.|+||||||=+...
T Consensus        14 GGi~~g~i~~i~G~~GsGKT~l~~~   38 (218)
T cd01394          14 GGVERGTVTQVYGPPGTGKTNIAIQ   38 (218)
T ss_pred             CCccCCeEEEEECCCCCCHHHHHHH
Confidence            4566789999999999999866443

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=93.23  E-value=0.032  Score=48.55  Aligned_cols=41  Identities=15%  Similarity=0.178  Sum_probs=30.8

Q ss_pred             cccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          32 ANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        32 a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      |..-.+-++||++|.+++-..+..               ++-+|+.||||||||=.
T Consensus        13 ~~~~~~~viG~~~a~~~l~~a~~~---------------~~~~ll~G~pG~GKT~l   53 (608)
T TIGR00764        13 PERLIDQVIGQEEAVEIIKKAAKQ---------------KRNVLLIGEPGVGKSML   53 (608)
T ss_pred             chhhHhhccCHHHHHHHHHHHHHc---------------CCCEEEECCCCCCHHHH
Confidence            345566789999999987665554               34677999999999843

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

>KOG0734|consensus

Probab=93.21  E-value=0.036  Score=50.26  Aligned_cols=57  Identities=18%  Similarity=0.194  Sum_probs=41.0

Q ss_pred             ccccCCCCCCcccc----cCcccchHHHHhhcceeeecccceeeeecccccc---ccc---eEEecCCCCCCCC
Q psy2779          22 KGLGLKENGEANEM----AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLF---RGG---RAVAGGRTKCPKP   85 (101)
Q Consensus        22 kGLGLde~g~a~~~----a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~---~g~---~ll~~G~p~~g~~   85 (101)
                      .++||+..-.+...    ..-.-|-.+|+.-..=|||.       .|+-.+|   +|+   =+|+.||||||||
T Consensus       285 ~~~gl~~ev~p~~~~nv~F~dVkG~DEAK~ELeEiVef-------LkdP~kftrLGGKLPKGVLLvGPPGTGKT  351 (752)
T KOG0734|consen  285 STTGLDSEVDPEQMKNVTFEDVKGVDEAKQELEEIVEF-------LKDPTKFTRLGGKLPKGVLLVGPPGTGKT  351 (752)
T ss_pred             cccccccccChhhhcccccccccChHHHHHHHHHHHHH-------hcCcHHhhhccCcCCCceEEeCCCCCchh
Confidence            46777766665543    45567889999999999998       5555444   332   3679999999987

>TIGR00763 lon ATP-dependent protease La

Probab=93.13  E-value=0.029  Score=49.61  Aligned_cols=43  Identities=14%  Similarity=0.043  Sum_probs=27.3

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .-.+||+++.+..--.+..      + +......|..+|+.||||||||-
T Consensus       320 ~~~~G~~~~k~~i~~~~~~------~-~~~~~~~~~~lll~GppG~GKT~  362 (775)
T TIGR00763       320 EDHYGLKKVKERILEYLAV------Q-KLRGKMKGPILCLVGPPGVGKTS  362 (775)
T ss_pred             hhcCChHHHHHHHHHHHHH------H-HhhcCCCCceEEEECCCCCCHHH
Confidence            3478999998874322111      0 01122346789999999999974

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.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=93.06  E-value=0.031  Score=42.66  Aligned_cols=41  Identities=10%  Similarity=-0.040  Sum_probs=28.0

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +.+-+|||+..++..-   ..       +++++.  -.++|+.||||+|||-.
T Consensus        19 ~~~~~~~~~~~~~~l~---~~-------~~~~~~--~~~lll~G~~G~GKT~l   59 (316)
T PHA02544         19 TIDECILPAADKETFK---SI-------VKKGRI--PNMLLHSPSPGTGKTTV   59 (316)
T ss_pred             cHHHhcCcHHHHHHHH---HH-------HhcCCC--CeEEEeeCcCCCCHHHH
Confidence            4577999999988532   22       222221  35788899999999854

>KOG0744|consensus

Probab=93.03  E-value=0.049  Score=46.83  Aligned_cols=19  Identities=11%  Similarity=0.018  Sum_probs=15.9

Q ss_pred             ccccceEEecCCCCCCCCC
Q psy2779          68 LFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~   86 (101)
                      +.-.|.+|+.||||||||-
T Consensus       174 It~NRliLlhGPPGTGKTS  192 (423)
T KOG0744|consen  174 ITWNRLILLHGPPGTGKTS  192 (423)
T ss_pred             eeeeeEEEEeCCCCCChhH
Confidence            3347899999999999984

>KOG1970|consensus

Probab=92.95  E-value=0.055  Score=48.59  Aligned_cols=21  Identities=14%  Similarity=0.224  Sum_probs=18.2

Q ss_pred             ccccccceEEecCCCCCCCCC
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+.+++++||++||+||||+-
T Consensus       105 ~~~l~~~iLLltGPsGcGKST  125 (634)
T KOG1970|consen  105 TPKLGSRILLLTGPSGCGKST  125 (634)
T ss_pred             ccCCCceEEEEeCCCCCCchh
Confidence            366789999999999999973

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=92.88  E-value=0.035  Score=42.66  Aligned_cols=40  Identities=13%  Similarity=0.106  Sum_probs=26.9

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      -+-+|||+++.+..-   ..       +++++.  ..++|+.||||+|||..
T Consensus        13 ~~~iig~~~~~~~l~---~~-------~~~~~~--~~~~Ll~G~~G~GKt~~   52 (355)
T TIGR02397        13 FEDVIGQEHIVQTLK---NA-------IKNGRI--AHAYLFSGPRGTGKTSI   52 (355)
T ss_pred             HhhccCcHHHHHHHH---HH-------HHcCCC--CeEEEEECCCCCCHHHH
Confidence            345799999987432   22       233332  45789999999999743

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.

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.84  E-value=0.038  Score=51.40  Aligned_cols=39  Identities=18%  Similarity=0.126  Sum_probs=28.7

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+.+.+.   +.++       ++.+++  ..++|+.||||||||-
T Consensus        15 FddIIGQe~Iv~~---Lkna-------I~~~rl--~HAyLFtGPpGtGKTT   53 (944)
T PRK14949         15 FEQMVGQSHVLHA---LTNA-------LTQQRL--HHAYLFTGTRGVGKTS   53 (944)
T ss_pred             HHHhcCcHHHHHH---HHHH-------HHhCCC--CeEEEEECCCCCCHHH
Confidence            4679999999887   3344       444443  5677899999999983

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=92.75  E-value=0.038  Score=40.42  Aligned_cols=23  Identities=13%  Similarity=0.167  Sum_probs=19.4

Q ss_pred             ccccccceEEecCCCCCCCCCCc
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +....|..+|+.|+||||||-|.
T Consensus        14 GGip~gs~~li~G~~GsGKT~l~   36 (226)
T PF06745_consen   14 GGIPKGSVVLISGPPGSGKTTLA   36 (226)
T ss_dssp             TSEETTSEEEEEESTTSSHHHHH
T ss_pred             CCCCCCcEEEEEeCCCCCcHHHH
Confidence            45677999999999999998654

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=92.69  E-value=0.046  Score=47.45  Aligned_cols=37  Identities=19%  Similarity=0.293  Sum_probs=26.6

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .-+|||+.+++|+-+..--          .+ . |. +|+.|+|||||+=
T Consensus         4 ~~ivGq~~~~~al~~~av~----------~~-~-g~-vli~G~~GtgKs~   40 (633)
T TIGR02442         4 TAIVGQEDLKLALLLNAVD----------PR-I-GG-VLIRGEKGTAKST   40 (633)
T ss_pred             chhcChHHHHHHHHHHhhC----------CC-C-Ce-EEEEcCCCCcHHH
Confidence            4689999999998544322          12 2 33 8899999999963

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.

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

Probab=92.67  E-value=0.036  Score=47.87  Aligned_cols=52  Identities=13%  Similarity=0.106  Sum_probs=38.9

Q ss_pred             CCCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCCce
Q psy2779          27 KENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        27 de~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      .+...|+. -+-+|||+.-----+++-.|       ++++.+.   -+++-||||||||-..+
T Consensus        15 A~rmRP~~-lde~vGQ~HLlg~~~~lrr~-------v~~~~l~---SmIl~GPPG~GKTTlA~   66 (436)
T COG2256          15 AERLRPKS-LDEVVGQEHLLGEGKPLRRA-------VEAGHLH---SMILWGPPGTGKTTLAR   66 (436)
T ss_pred             HHHhCCCC-HHHhcChHhhhCCCchHHHH-------HhcCCCc---eeEEECCCCCCHHHHHH
Confidence            33444444 57799999988778899999       8777753   35689999999986544

>TIGR00368 Mg chelatase-related protein

Probab=92.66  E-value=0.061  Score=46.04  Aligned_cols=38  Identities=18%  Similarity=0.114  Sum_probs=29.3

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCCc
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      .+-++||..|++|..+.+               .+|..+|+.|||||||+=+.
T Consensus       191 ~~dv~Gq~~~~~al~~aa---------------~~g~~vlliG~pGsGKTtla  228 (499)
T TIGR00368       191 LKDIKGQQHAKRALEIAA---------------AGGHNLLLFGPPGSGKTMLA  228 (499)
T ss_pred             HHHhcCcHHHHhhhhhhc---------------cCCCEEEEEecCCCCHHHHH
Confidence            456899999998865543               24778999999999986543

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=92.59  E-value=0.041  Score=40.21  Aligned_cols=25  Identities=16%  Similarity=-0.028  Sum_probs=20.6

Q ss_pred             ccccccceEEecCCCCCCCCCCcee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      +..-.|..+++.|+||||||-+...
T Consensus        15 GGi~~G~~~~i~G~~G~GKT~l~~~   39 (229)
T TIGR03881        15 GGIPRGFFVAVTGEPGTGKTIFCLH   39 (229)
T ss_pred             CCCcCCeEEEEECCCCCChHHHHHH
Confidence            3556788999999999999987653

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=92.57  E-value=0.041  Score=47.92  Aligned_cols=40  Identities=15%  Similarity=0.118  Sum_probs=31.2

Q ss_pred             cccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCCc
Q psy2779          34 EMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        34 ~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +...+++||+++-+.+.++.-               +|+-+|+-||||||||=..
T Consensus        17 ~l~~~i~gre~vI~lll~aal---------------ag~hVLL~GpPGTGKT~LA   56 (498)
T PRK13531         17 ALEKGLYERSHAIRLCLLAAL---------------SGESVFLLGPPGIAKSLIA   56 (498)
T ss_pred             HHhhhccCcHHHHHHHHHHHc---------------cCCCEEEECCCChhHHHHH
Confidence            456899999998887766543               4778889999999997443

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

Probab=92.51  E-value=0.045  Score=48.53  Aligned_cols=53  Identities=23%  Similarity=0.206  Sum_probs=40.1

Q ss_pred             CcccchHHHHhhcceeeecccceeeeecccccc-------ccceEEecCCCCCCCC------------CCceeeeeeecc
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSLF-------RGGRAVAGGRTKCPKP------------PNTSMIIDSWVE   97 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~-------~g~~ll~~G~p~~g~~------------~~~~~~~~~~~~   97 (101)
                      .=.-|..+|+|...=|||-       .|+.+++       -.+ +|+.||||||||            ||-|+...++||
T Consensus       150 ~DVAG~dEakeel~EiVdf-------Lk~p~ky~~lGakiPkG-vlLvGpPGTGKTLLAkAvAgEA~VPFf~iSGS~FVe  221 (596)
T COG0465         150 ADVAGVDEAKEELSELVDF-------LKNPKKYQALGAKIPKG-VLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVE  221 (596)
T ss_pred             hhhcCcHHHHHHHHHHHHH-------HhCchhhHhcccccccc-eeEecCCCCCcHHHHHHHhcccCCCceeccchhhhh
Confidence            3456889999999988888       6655533       334 458899999976            888888777766

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=92.50  E-value=0.053  Score=41.58  Aligned_cols=16  Identities=19%  Similarity=0.082  Sum_probs=14.2

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      .|+-+|+.||||||||
T Consensus        20 ~g~~vLL~G~~GtGKT   35 (262)
T TIGR02640        20 SGYPVHLRGPAGTGKT   35 (262)
T ss_pred             cCCeEEEEcCCCCCHH
Confidence            4778899999999997

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).

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.48  E-value=0.044  Score=46.81  Aligned_cols=38  Identities=18%  Similarity=0.114  Sum_probs=27.2

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .+-+|||+.+.++..   .+       ++++++  ..++|+.||||||||
T Consensus        15 f~divGq~~v~~~L~---~~-------i~~~~~--~ha~Lf~Gp~G~GKT   52 (527)
T PRK14969         15 FSELVGQEHVVRALT---NA-------LEQQRL--HHAYLFTGTRGVGKT   52 (527)
T ss_pred             HHHhcCcHHHHHHHH---HH-------HHcCCC--CEEEEEECCCCCCHH
Confidence            467999999988533   33       223332  457889999999998

>PRK05973 replicative DNA helicase; Provisional

Probab=92.35  E-value=0.059  Score=42.22  Aligned_cols=25  Identities=20%  Similarity=0.078  Sum_probs=20.7

Q ss_pred             ccccccceEEecCCCCCCCCCCcee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      +.+..|..+|++|+||+|||=|.-.
T Consensus        59 GGl~~Gsl~LIaG~PG~GKT~lalq   83 (237)
T PRK05973         59 SQLKPGDLVLLGARPGHGKTLLGLE   83 (237)
T ss_pred             CCCCCCCEEEEEeCCCCCHHHHHHH
Confidence            4667899999999999999976543

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

Probab=92.32  E-value=0.05  Score=48.87  Aligned_cols=45  Identities=20%  Similarity=0.070  Sum_probs=29.2

Q ss_pred             cCcccchHHHHhhcceeeecccceeeee--ccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERC--KSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~--~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ..-+|||.+|-++.--.+..     .+.  .+..+. -+.+|+.||||||||-
T Consensus       457 ~~~ViGQ~~ai~~l~~~i~~-----~~~gl~~~~kp-~~~~Lf~GP~GvGKT~  503 (758)
T PRK11034        457 KMLVFGQDKAIEALTEAIKM-----SRAGLGHEHKP-VGSFLFAGPTGVGKTE  503 (758)
T ss_pred             cceEeCcHHHHHHHHHHHHH-----HhccccCCCCC-cceEEEECCCCCCHHH
Confidence            34589999999876665554     111  111111 2368899999999983

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.08  E-value=0.061  Score=47.09  Aligned_cols=38  Identities=21%  Similarity=0.277  Sum_probs=27.3

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .+-+|||+.+.+.   +..+       ++++++  ..++|+.||+|||||
T Consensus        12 f~eivGq~~i~~~---L~~~-------i~~~r~--~ha~Lf~Gp~G~GKT   49 (584)
T PRK14952         12 FAEVVGQEHVTEP---LSSA-------LDAGRI--NHAYLFSGPRGCGKT   49 (584)
T ss_pred             HHHhcCcHHHHHH---HHHH-------HHcCCC--CeEEEEECCCCCCHH
Confidence            5679999998886   3333       333332  447899999999997

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=92.06  E-value=0.072  Score=38.91  Aligned_cols=26  Identities=19%  Similarity=0.134  Sum_probs=21.0

Q ss_pred             cccccceEEecCCCCCCCCCCceeee
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      .+..|..++++|+||+|||=|..-++
T Consensus         9 Gl~~G~l~lI~G~~G~GKT~~~~~~~   34 (242)
T cd00984           9 GLQPGDLIIIAARPSMGKTAFALNIA   34 (242)
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHH
Confidence            45678899999999999997765443

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>CHL00181 cbbX CbbX; Provisional

Probab=91.97  E-value=0.034  Score=43.81  Aligned_cols=19  Identities=16%  Similarity=0.015  Sum_probs=14.6

Q ss_pred             cceEEecCCCCCCCCCCce
Q psy2779          71 GGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~~   89 (101)
                      |--+|+.||||||||-...
T Consensus        59 ~~~ill~G~pGtGKT~lAr   77 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVAL   77 (287)
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4458899999999975433

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

Probab=91.90  E-value=0.052  Score=48.52  Aligned_cols=52  Identities=17%  Similarity=0.137  Sum_probs=34.9

Q ss_pred             ccCCCCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          24 LGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        24 LGLde~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +-|.+...|.. -+.+|||+..-.--.++..+       +++.+   -.-+|+.||||||||-
T Consensus        16 ~PLaek~RP~t-ldd~vGQe~ii~~~~~L~~~-------i~~~~---~~slLL~GPpGtGKTT   67 (725)
T PRK13341         16 APLADRLRPRT-LEEFVGQDHILGEGRLLRRA-------IKADR---VGSLILYGPPGVGKTT   67 (725)
T ss_pred             CChHHhcCCCc-HHHhcCcHHHhhhhHHHHHH-------HhcCC---CceEEEECCCCCCHHH
Confidence            34555555544 46799999876555556666       43333   2357899999999984

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.87  E-value=0.06  Score=46.00  Aligned_cols=39  Identities=26%  Similarity=0.277  Sum_probs=26.3

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+.+-+..--   .       +.++++  ..++|+.||||||||-
T Consensus        13 ~~dvvGq~~v~~~L~~---~-------i~~~~l--~ha~Lf~GppGtGKTT   51 (504)
T PRK14963         13 FDEVVGQEHVKEVLLA---A-------LRQGRL--GHAYLFSGPRGVGKTT   51 (504)
T ss_pred             HHHhcChHHHHHHHHH---H-------HHcCCC--CeEEEEECCCCCCHHH
Confidence            4568999998554322   2       223332  4567999999999984

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=91.78  E-value=0.063  Score=44.56  Aligned_cols=49  Identities=16%  Similarity=0.071  Sum_probs=28.0

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      -+-+|||+++.+...=.+.-..-.+-.. ..+  -..++|+.||||+||+.+
T Consensus         4 f~~IiGq~~~~~~L~~~i~~~~~~~~~~-~~~--l~ha~Lf~Gp~G~GKt~l   52 (394)
T PRK07940          4 WDDLVGQEAVVAELRAAARAARADVAAA-GSG--MTHAWLFTGPPGSGRSVA   52 (394)
T ss_pred             hhhccChHHHHHHHHHHHHhcccccccc-CCC--CCeEEEEECCCCCcHHHH
Confidence            3458999999887443333200000000 001  146799999999999743

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.78  E-value=0.061  Score=45.96  Aligned_cols=39  Identities=13%  Similarity=0.053  Sum_probs=28.0

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+.+|||+...++.-   .+       ++++++  ..++|+.||||||||-
T Consensus        15 f~divGq~~v~~~L~---~~-------~~~~~l--~ha~Lf~Gp~G~GKTt   53 (509)
T PRK14958         15 FQEVIGQAPVVRALS---NA-------LDQQYL--HHAYLFTGTRGVGKTT   53 (509)
T ss_pred             HHHhcCCHHHHHHHH---HH-------HHhCCC--CeeEEEECCCCCCHHH
Confidence            467999999988643   33       233332  4578999999999973

>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []

Probab=91.77  E-value=0.075  Score=38.70  Aligned_cols=22  Identities=9%  Similarity=0.129  Sum_probs=14.9

Q ss_pred             cceEEecCCCCCCCCCCceeee
Q psy2779          71 GGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      -.+++++|+|||||+-...+++
T Consensus        15 P~~~i~aG~~GsGKSt~~~~~~   36 (199)
T PF06414_consen   15 PTLIIIAGQPGSGKSTLARQLL   36 (199)
T ss_dssp             -EEEEEES-TTSTTHHHHHHHH
T ss_pred             CEEEEEeCCCCCCHHHHHHHhh
Confidence            5689999999999964444333

It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].; GO: 0005524 ATP binding, 0016301 kinase activity; PDB: 2P5T_H 1GVN_B 3Q8X_D.

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=91.67  E-value=0.059  Score=47.93  Aligned_cols=40  Identities=18%  Similarity=0.054  Sum_probs=28.1

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +.+-+|||+.+.++.-   ..       ++++++  -.++|+.||||||||-
T Consensus        14 ~f~divGQe~vv~~L~---~~-------l~~~rl--~hAyLf~Gp~GvGKTT   53 (647)
T PRK07994         14 TFAEVVGQEHVLTALA---NA-------LDLGRL--HHAYLFSGTRGVGKTT   53 (647)
T ss_pred             CHHHhcCcHHHHHHHH---HH-------HHcCCC--CeEEEEECCCCCCHHH
Confidence            3578999999998543   33       323332  3458899999999973

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=91.50  E-value=0.079  Score=38.79  Aligned_cols=20  Identities=5%  Similarity=-0.170  Sum_probs=16.0

Q ss_pred             ccceEEecCCCCCCCCCCce
Q psy2779          70 RGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~   89 (101)
                      ..+.+++.||||||||=...
T Consensus        41 ~~~~~~l~G~~G~GKT~La~   60 (227)
T PRK08903         41 ADRFFYLWGEAGSGRSHLLQ   60 (227)
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            46789999999999985443

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.48  E-value=0.068  Score=45.92  Aligned_cols=40  Identities=20%  Similarity=0.106  Sum_probs=27.6

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .+-+|||+.+.+..-   ..       +.+++  -+.++|+.||||||||..
T Consensus        15 ~~eiiGq~~~~~~L~---~~-------i~~~~--i~~a~Lf~Gp~G~GKTtl   54 (585)
T PRK14950         15 FAELVGQEHVVQTLR---NA-------IAEGR--VAHAYLFTGPRGVGKTST   54 (585)
T ss_pred             HHHhcCCHHHHHHHH---HH-------HHhCC--CceEEEEECCCCCCHHHH
Confidence            467999999988642   22       22223  256789999999999843

>PRK08084 DNA replication initiation factor; Provisional

Probab=91.42  E-value=0.12  Score=38.99  Aligned_cols=16  Identities=13%  Similarity=0.063  Sum_probs=13.8

Q ss_pred             cceEEecCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPP   86 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~   86 (101)
                      +..+++.||||||||=
T Consensus        45 ~~~l~l~Gp~G~GKTh   60 (235)
T PRK08084         45 SGYIYLWSREGAGRSH   60 (235)
T ss_pred             CCeEEEECCCCCCHHH
Confidence            4678999999999984

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=91.41  E-value=0.071  Score=39.42  Aligned_cols=27  Identities=7%  Similarity=-0.032  Sum_probs=21.7

Q ss_pred             ccccccceEEecCCCCCCCCCCceeee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      +..-.|.++++.|+||||||.+...++
T Consensus        20 gG~~~g~~~~i~G~~GsGKt~l~~~~~   46 (234)
T PRK06067         20 GGIPFPSLILIEGDHGTGKSVLSQQFV   46 (234)
T ss_pred             CCCcCCcEEEEECCCCCChHHHHHHHH
Confidence            456678999999999999998765443

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=91.38  E-value=0.13  Score=37.17  Aligned_cols=27  Identities=11%  Similarity=-0.066  Sum_probs=21.4

Q ss_pred             ccccccceEEecCCCCCCCCCCceeee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      +....|.+..+.|+||||||-+...++
T Consensus        14 GG~~~g~v~~I~G~~GsGKT~l~~~ia   40 (226)
T cd01393          14 GGIPTGRITEIFGEFGSGKTQLCLQLA   40 (226)
T ss_pred             CCCcCCcEEEEeCCCCCChhHHHHHHH
Confidence            455678999999999999997765443

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>KOG0731|consensus

Probab=91.35  E-value=0.064  Score=49.05  Aligned_cols=59  Identities=20%  Similarity=0.128  Sum_probs=38.2

Q ss_pred             cCcccchHHHHhhcceeeec-ccc-eeeeeccccccccceEEecCCCCCCCC------------CCceeeeeeecc
Q psy2779          36 AAGLVGQQAAREVSRAVTWE-KSF-QFERCKSHSLFRGGRAVAGGRTKCPKP------------PNTSMIIDSWVE   97 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm-~~~-~~~~~~~~~~~~g~~ll~~G~p~~g~~------------~~~~~~~~~~~~   97 (101)
                      ..-..|+++|++-.-=||+. |+- ||.+.  +-++-+++| |.||||||||            ||-||.-..+||
T Consensus       310 FkDVAG~deAK~El~E~V~fLKNP~~Y~~l--GAKiPkGvL-L~GPPGTGKTLLAKAiAGEAgVPF~svSGSEFvE  382 (774)
T KOG0731|consen  310 FKDVAGVDEAKEELMEFVKFLKNPEQYQEL--GAKIPKGVL-LVGPPGTGKTLLAKAIAGEAGVPFFSVSGSEFVE  382 (774)
T ss_pred             cccccCcHHHHHHHHHHHHHhcCHHHHHHc--CCcCcCceE-EECCCCCcHHHHHHHHhcccCCceeeechHHHHH
Confidence            45578999999888777775 110 12221  223344554 8999999997            888877655555

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.34  E-value=0.076  Score=46.21  Aligned_cols=41  Identities=17%  Similarity=0.077  Sum_probs=27.9

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +.+-+|||+.+.+..   ...       +++++.  ..++|+.||||||||-.
T Consensus        14 ~f~diiGq~~~v~~L---~~~-------i~~~rl--~ha~Lf~Gp~GvGKTTl   54 (546)
T PRK14957         14 SFAEVAGQQHALNSL---VHA-------LETQKV--HHAYLFTGTRGVGKTTL   54 (546)
T ss_pred             cHHHhcCcHHHHHHH---HHH-------HHcCCC--CeEEEEECCCCCCHHHH
Confidence            356799999998762   233       322221  34688999999999853

>PRK14737 gmk guanylate kinase; Provisional

Probab=91.26  E-value=0.092  Score=38.81  Aligned_cols=18  Identities=6%  Similarity=-0.164  Sum_probs=15.6

Q ss_pred             cccceEEecCCCCCCCCC
Q psy2779          69 FRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~~   86 (101)
                      ++++.+++.||+|+||+.
T Consensus         2 ~~~~~ivl~GpsG~GK~t   19 (186)
T PRK14737          2 ASPKLFIISSVAGGGKST   19 (186)
T ss_pred             CCCeEEEEECCCCCCHHH
Confidence            568999999999999863

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.23  E-value=0.08  Score=46.67  Aligned_cols=39  Identities=13%  Similarity=0.140  Sum_probs=27.6

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ...+|||+.+.+.   +..+       ++++++  .-++|+.||||||||-
T Consensus        15 f~eivGQe~i~~~---L~~~-------i~~~ri--~ha~Lf~Gp~GvGKtt   53 (620)
T PRK14954         15 FADITAQEHITHT---IQNS-------LRMDRV--GHGYIFSGLRGVGKTT   53 (620)
T ss_pred             HHHhcCcHHHHHH---HHHH-------HHcCCC--CeeEEEECCCCCCHHH
Confidence            5679999999885   3333       333332  3468899999999974

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=91.23  E-value=0.11  Score=38.15  Aligned_cols=23  Identities=17%  Similarity=0.042  Sum_probs=18.5

Q ss_pred             ccccccceEEecCCCCCCCCCCc
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +....|.++++.|+||+|||=|.
T Consensus        11 gGi~~g~~~li~G~~G~GKt~~~   33 (224)
T TIGR03880        11 GGFPEGHVIVVIGEYGTGKTTFS   33 (224)
T ss_pred             CCCCCCeEEEEECCCCCCHHHHH
Confidence            34556889999999999998653

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.23  E-value=0.085  Score=47.82  Aligned_cols=40  Identities=18%  Similarity=0.078  Sum_probs=29.0

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +.+-+|||+.+.++.   ..+       ++++++  -.++|+.||||||||-
T Consensus        13 tFddVIGQe~vv~~L---~~a-------I~~grl--~HAyLF~GPpGvGKTT   52 (702)
T PRK14960         13 NFNELVGQNHVSRAL---SSA-------LERGRL--HHAYLFTGTRGVGKTT   52 (702)
T ss_pred             CHHHhcCcHHHHHHH---HHH-------HHcCCC--CeEEEEECCCCCCHHH
Confidence            357799999997764   344       333443  3688999999999984

>PF07088 GvpD: GvpD gas vesicle protein; InterPro: IPR009788 This family consists of several archaeal GvpD gas vesicle proteins

Probab=91.22  E-value=0.11  Score=45.55  Aligned_cols=26  Identities=15%  Similarity=0.171  Sum_probs=21.9

Q ss_pred             ccceEEecCCCCCCCCCCceeeeeee
Q psy2779          70 RGGRAVAGGRTKCPKPPNTSMIIDSW   95 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~~~~~~~   95 (101)
                      .|..||+-|.||||||-||--+.|+.
T Consensus         9 ~G~TLLIKG~PGTGKTtfaLelL~~l   34 (484)
T PF07088_consen    9 PGQTLLIKGEPGTGKTTFALELLNSL   34 (484)
T ss_pred             CCcEEEEecCCCCCceeeehhhHHHH
Confidence            48899999999999999986666553

GvpD is thought to be involved in the regulation of gas vesicle formation [,].; GO: 0005524 ATP binding

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

Probab=91.21  E-value=0.068  Score=44.89  Aligned_cols=43  Identities=16%  Similarity=0.131  Sum_probs=31.7

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccc---eEEecCCCCCCCCCCc
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGG---RAVAGGRTKCPKPPNT   88 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~---~ll~~G~p~~g~~~~~   88 (101)
                      .-+-||||++.++-..|..+-       .    +.++.   -+|+.||||.|||-..
T Consensus        24 ~l~efiGQ~~vk~~L~ifI~A-------A----k~r~e~lDHvLl~GPPGlGKTTLA   69 (332)
T COG2255          24 TLDEFIGQEKVKEQLQIFIKA-------A----KKRGEALDHVLLFGPPGLGKTTLA   69 (332)
T ss_pred             cHHHhcChHHHHHHHHHHHHH-------H----HhcCCCcCeEEeeCCCCCcHHHHH
Confidence            357899999999988877655       2    11232   3689999999998543

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=91.18  E-value=0.11  Score=37.76  Aligned_cols=26  Identities=12%  Similarity=-0.018  Sum_probs=21.1

Q ss_pred             ccccccceEEecCCCCCCCCCCceee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSMI   91 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~~   91 (101)
                      +....|.+.++.|+||||||-+...+
T Consensus        14 GGi~~g~i~~i~G~~GsGKT~l~~~l   39 (235)
T cd01123          14 GGIETGSITEIFGEFGSGKTQLCHQL   39 (235)
T ss_pred             CCCCCCeEEEEECCCCCCHHHHHHHH
Confidence            45667999999999999999776544

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>PRK04328 hypothetical protein; Provisional

Probab=91.16  E-value=0.11  Score=39.69  Aligned_cols=23  Identities=9%  Similarity=0.008  Sum_probs=19.1

Q ss_pred             cccccceEEecCCCCCCCCCCce
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      ....|..+|+.|+||||||-+..
T Consensus        19 Gip~gs~ili~G~pGsGKT~l~~   41 (249)
T PRK04328         19 GIPERNVVLLSGGPGTGKSIFSQ   41 (249)
T ss_pred             CCcCCcEEEEEcCCCCCHHHHHH
Confidence            45578999999999999987643

>PRK06526 transposase; Provisional

Probab=91.08  E-value=0.094  Score=40.85  Aligned_cols=17  Identities=18%  Similarity=-0.056  Sum_probs=14.0

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      +.-+++.||||||||-.
T Consensus        98 ~~nlll~Gp~GtGKThL  114 (254)
T PRK06526         98 KENVVFLGPPGTGKTHL  114 (254)
T ss_pred             CceEEEEeCCCCchHHH
Confidence            45689999999999843

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=91.07  E-value=0.085  Score=45.39  Aligned_cols=39  Identities=23%  Similarity=0.170  Sum_probs=26.4

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+.+.+..--   .       ++++++  ...+|+.||||||||-
T Consensus        20 f~dliGq~~vv~~L~~---a-------i~~~ri--~~a~Lf~Gp~G~GKTT   58 (507)
T PRK06645         20 FAELQGQEVLVKVLSY---T-------ILNDRL--AGGYLLTGIRGVGKTT   58 (507)
T ss_pred             HHHhcCcHHHHHHHHH---H-------HHcCCC--CceEEEECCCCCCHHH
Confidence            4678999998874322   1       222222  3578999999999984

>CHL00195 ycf46 Ycf46; Provisional

Probab=91.04  E-value=0.064  Score=45.87  Aligned_cols=56  Identities=14%  Similarity=0.066  Sum_probs=28.0

Q ss_pred             CCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          28 ENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        28 e~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +...+....+-+.|.+.+.+...-..+.  |. .+.+...+-..+-+|+.||||||||-
T Consensus       219 e~~~~~~~~~dvgGl~~lK~~l~~~~~~--~~-~~~~~~gl~~pkGILL~GPpGTGKTl  274 (489)
T CHL00195        219 EFYSVNEKISDIGGLDNLKDWLKKRSTS--FS-KQASNYGLPTPRGLLLVGIQGTGKSL  274 (489)
T ss_pred             cccCCCCCHHHhcCHHHHHHHHHHHHHH--hh-HHHHhcCCCCCceEEEECCCCCcHHH
Confidence            3333334445566766666544322211  10 01111122234568899999999963

>PRK00300 gmk guanylate kinase; Provisional

Probab=91.02  E-value=0.11  Score=37.09  Aligned_cols=23  Identities=22%  Similarity=0.251  Sum_probs=18.5

Q ss_pred             ccceEEecCCCCCCCCCCceeee
Q psy2779          70 RGGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      .|.++++.||+||||+....++.
T Consensus         4 ~g~~i~i~G~sGsGKstl~~~l~   26 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLVKALL   26 (205)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHH
Confidence            58899999999999986554443

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=90.96  E-value=0.1  Score=42.48  Aligned_cols=17  Identities=12%  Similarity=-0.122  Sum_probs=13.7

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      -+-+|+.||||||||-.
T Consensus       165 p~gvLL~GppGtGKT~l  181 (389)
T PRK03992        165 PKGVLLYGPPGTGKTLL  181 (389)
T ss_pred             CCceEEECCCCCChHHH
Confidence            34588999999999854

>PRK05642 DNA replication initiation factor; Validated

Probab=90.91  E-value=0.11  Score=39.26  Aligned_cols=56  Identities=11%  Similarity=0.006  Sum_probs=32.0

Q ss_pred             ccCCCCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          24 LGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        24 LGLde~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      |-||=...+.++.+.||...+ +.|...+.+.       .++..-+.-.-+++.|++|||||=.
T Consensus         6 l~l~~~~~~~~tfdnF~~~~~-~~a~~~~~~~-------~~~~~~~~~~~l~l~G~~G~GKTHL   61 (234)
T PRK05642          6 LPLGVRLRDDATFANYYPGAN-AAALGYVERL-------CEADAGWTESLIYLWGKDGVGRSHL   61 (234)
T ss_pred             cccCCCCCCcccccccCcCCh-HHHHHHHHHH-------hhccccCCCCeEEEECCCCCCHHHH
Confidence            455655666677788873333 2343334333       1111111236788999999999844

>TIGR03689 pup_AAA proteasome ATPase

Probab=90.90  E-value=0.053  Score=46.93  Aligned_cols=50  Identities=18%  Similarity=0.073  Sum_probs=26.9

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +.+.|+..+-+..--.+.+-..+-...+.+.+-..+-+|+.||||||||-
T Consensus       182 ~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~  231 (512)
T TIGR03689       182 ADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTL  231 (512)
T ss_pred             HHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHH
Confidence            44667776665554443331011011122233334558899999999984

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.

>KOG0733|consensus

Probab=90.85  E-value=0.089  Score=48.21  Aligned_cols=15  Identities=20%  Similarity=0.322  Sum_probs=12.2

Q ss_pred             cceEEecCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKP   85 (101)
Q Consensus        71 g~~ll~~G~p~~g~~   85 (101)
                      -.=+|+.||||||||
T Consensus       545 PsGvLL~GPPGCGKT  559 (802)
T KOG0733|consen  545 PSGVLLCGPPGCGKT  559 (802)
T ss_pred             CCceEEeCCCCccHH
Confidence            334679999999997

>PRK00131 aroK shikimate kinase; Reviewed

Probab=90.82  E-value=0.12  Score=35.13  Aligned_cols=17  Identities=24%  Similarity=0.075  Sum_probs=14.4

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      +..+++.|+|||||+-.
T Consensus         4 ~~~i~l~G~~GsGKstl   20 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTI   20 (175)
T ss_pred             CCeEEEEcCCCCCHHHH
Confidence            56889999999999754

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=90.78  E-value=0.074  Score=46.47  Aligned_cols=49  Identities=8%  Similarity=0.013  Sum_probs=26.7

Q ss_pred             CcccchHHHHhhcceeeecccceeee-eccccccccceEEecCCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFER-CKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~-~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +-++|++.+++..-=.+.+ .+++-. .+.-..-..+-+|+.||||||||-
T Consensus       453 ~di~g~~~~k~~l~~~v~~-~~~~~~~~~~~g~~~~~giLL~GppGtGKT~  502 (733)
T TIGR01243       453 SDIGGLEEVKQELREAVEW-PLKHPEIFEKMGIRPPKGVLLFGPPGTGKTL  502 (733)
T ss_pred             hhcccHHHHHHHHHHHHHh-hhhCHHHHHhcCCCCCceEEEECCCCCCHHH
Confidence            4467888888776554443 001100 000011123447789999999973

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.

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=90.77  E-value=0.12  Score=37.19  Aligned_cols=18  Identities=11%  Similarity=-0.136  Sum_probs=14.9

Q ss_pred             cceEEecCCCCCCCCCCc
Q psy2779          71 GGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~   88 (101)
                      .+-+++.||||||||-..
T Consensus        38 ~~~lll~G~~G~GKT~la   55 (226)
T TIGR03420        38 DRFLYLWGESGSGKSHLL   55 (226)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            678899999999997543

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=90.75  E-value=0.12  Score=43.37  Aligned_cols=25  Identities=16%  Similarity=0.088  Sum_probs=20.7

Q ss_pred             ccccccceEEecCCCCCCCCCCcee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      +....|+..|+.|+||||||=|...
T Consensus        16 GGlp~g~~~Li~G~pGsGKT~la~q   40 (484)
T TIGR02655        16 GGLPIGRSTLVSGTSGTGKTLFSIQ   40 (484)
T ss_pred             CCCCCCeEEEEEcCCCCCHHHHHHH
Confidence            4667799999999999999876543

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=90.69  E-value=0.075  Score=39.98  Aligned_cols=19  Identities=21%  Similarity=0.181  Sum_probs=16.0

Q ss_pred             ccceEEecCCCCCCCCCCc
Q psy2779          70 RGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~   88 (101)
                      +++.+|++|+||||||-+-
T Consensus       126 ~~~~ili~G~tGSGKTT~l  144 (270)
T PF00437_consen  126 GRGNILISGPTGSGKTTLL  144 (270)
T ss_dssp             TTEEEEEEESTTSSHHHHH
T ss_pred             cceEEEEECCCccccchHH
Confidence            4788999999999998544

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=90.62  E-value=0.15  Score=41.76  Aligned_cols=40  Identities=23%  Similarity=0.170  Sum_probs=28.6

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ...-+|||+.|.+..-   ++       +.++++  .-++|+.||+|+||+.
T Consensus        17 ~~~~iiGq~~~~~~L~---~~-------~~~~rl--~HA~Lf~Gp~G~GK~~   56 (365)
T PRK07471         17 ETTALFGHAAAEAALL---DA-------YRSGRL--HHAWLIGGPQGIGKAT   56 (365)
T ss_pred             chhhccChHHHHHHHH---HH-------HHcCCC--CceEEEECCCCCCHHH
Confidence            3478999999987653   43       333332  4589999999999863

>CHL00095 clpC Clp protease ATP binding subunit

Probab=90.61  E-value=0.092  Score=46.79  Aligned_cols=44  Identities=18%  Similarity=0.108  Sum_probs=27.9

Q ss_pred             cCcccchHHHHhhcceeeecccceeeee--ccccccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERC--KSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~--~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      ..-++||..|.++.--.+..     .|.  ...++- -..+|+.||||||||
T Consensus       508 ~~~v~GQ~~ai~~l~~~i~~-----~~~gl~~~~~p-~~~~lf~Gp~GvGKt  553 (821)
T CHL00095        508 HKRIIGQDEAVVAVSKAIRR-----ARVGLKNPNRP-IASFLFSGPTGVGKT  553 (821)
T ss_pred             cCcCcChHHHHHHHHHHHHH-----HhhcccCCCCC-ceEEEEECCCCCcHH
Confidence            46789999999887544443     111  011111 135789999999998

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=90.50  E-value=0.1  Score=45.25  Aligned_cols=39  Identities=18%  Similarity=0.165  Sum_probs=27.8

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+.+.+..   ...       +++++.  ..++|+.||||+|||-
T Consensus        15 f~diiGqe~iv~~L---~~~-------i~~~~i--~hayLf~Gp~G~GKTt   53 (563)
T PRK06647         15 FNSLEGQDFVVETL---KHS-------IESNKI--ANAYIFSGPRGVGKTS   53 (563)
T ss_pred             HHHccCcHHHHHHH---HHH-------HHcCCC--CeEEEEECCCCCCHHH
Confidence            46799999998852   222       333342  4678999999999863

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=90.49  E-value=0.092  Score=46.57  Aligned_cols=40  Identities=13%  Similarity=0.119  Sum_probs=28.4

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .+.+|||+.+.+..   ...       ++.++.  ..++|+.||||+|||-+
T Consensus        15 F~dIIGQe~iv~~L---~~a-------I~~~rl--~hA~Lf~GP~GvGKTTl   54 (605)
T PRK05896         15 FKQIIGQELIKKIL---VNA-------ILNNKL--THAYIFSGPRGIGKTSI   54 (605)
T ss_pred             HHHhcCcHHHHHHH---HHH-------HHcCCC--CceEEEECCCCCCHHHH
Confidence            57899999998653   233       333332  37899999999999854

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

Probab=90.39  E-value=0.11  Score=40.83  Aligned_cols=35  Identities=23%  Similarity=0.355  Sum_probs=24.4

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      ...++|++.+-+++-+-               +..|+-+|+-|+||||||
T Consensus        23 ~~~~~g~~~~~~~~l~a---------------~~~~~~vll~G~PG~gKT   57 (329)
T COG0714          23 EKVVVGDEEVIELALLA---------------LLAGGHVLLEGPPGVGKT   57 (329)
T ss_pred             CCeeeccHHHHHHHHHH---------------HHcCCCEEEECCCCccHH
Confidence            34477776665554322               235888999999999997

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.39  E-value=0.089  Score=47.68  Aligned_cols=39  Identities=21%  Similarity=0.152  Sum_probs=28.5

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+.+.+..   .++       ++++++  ..++|+.|++|+|||-
T Consensus        15 FddVIGQe~vv~~L---~~a-------l~~gRL--pHA~LFtGP~GvGKTT   53 (700)
T PRK12323         15 FTTLVGQEHVVRAL---THA-------LEQQRL--HHAYLFTGTRGVGKTT   53 (700)
T ss_pred             HHHHcCcHHHHHHH---HHH-------HHhCCC--ceEEEEECCCCCCHHH
Confidence            56799999998843   344       334443  4578999999999984

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=90.34  E-value=0.15  Score=37.31  Aligned_cols=23  Identities=17%  Similarity=0.024  Sum_probs=18.9

Q ss_pred             ccccccceEEecCCCCCCCCCCc
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +....|.+.++.|+||+|||-+.
T Consensus        18 GGi~~g~i~~i~G~~GsGKT~l~   40 (225)
T PRK09361         18 GGFERGTITQIYGPPGSGKTNIC   40 (225)
T ss_pred             CCCCCCeEEEEECCCCCCHHHHH
Confidence            34556889999999999998764

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=90.33  E-value=0.1  Score=39.13  Aligned_cols=44  Identities=16%  Similarity=0.079  Sum_probs=27.0

Q ss_pred             CCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          30 GEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        30 g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      -.|.. -+-++||.++-+...   +.       ++.++   -..+|+.||||||||-.
T Consensus        11 yrP~~-~~~~~g~~~~~~~l~---~~-------i~~~~---~~~~ll~G~~G~GKt~~   54 (319)
T PRK00440         11 YRPRT-LDEIVGQEEIVERLK---SY-------VKEKN---MPHLLFAGPPGTGKTTA   54 (319)
T ss_pred             hCCCc-HHHhcCcHHHHHHHH---HH-------HhCCC---CCeEEEECCCCCCHHHH
Confidence            34433 345899988776633   33       22222   12479999999999743

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=90.33  E-value=0.1  Score=46.16  Aligned_cols=40  Identities=18%  Similarity=0.173  Sum_probs=29.8

Q ss_pred             ccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          33 NEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        33 ~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      ...-+-++||++|-++.-..++.               ++-+|+.||||||||-.
T Consensus        27 ~~~~~~vigq~~a~~~L~~~~~~---------------~~~~l~~G~~G~GKttl   66 (637)
T PRK13765         27 ERLIDQVIGQEHAVEVIKKAAKQ---------------RRHVMMIGSPGTGKSML   66 (637)
T ss_pred             cccHHHcCChHHHHHHHHHHHHh---------------CCeEEEECCCCCcHHHH
Confidence            34567799999998876554443               34688999999999743

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.28  E-value=0.11  Score=44.72  Aligned_cols=40  Identities=18%  Similarity=0.137  Sum_probs=28.3

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +.+-+|||+.+.+...   +.       ++++++  -.++|+.||||+|||-
T Consensus        11 ~f~dliGQe~vv~~L~---~a-------~~~~ri--~ha~Lf~Gp~G~GKTT   50 (491)
T PRK14964         11 SFKDLVGQDVLVRILR---NA-------FTLNKI--PQSILLVGASGVGKTT   50 (491)
T ss_pred             CHHHhcCcHHHHHHHH---HH-------HHcCCC--CceEEEECCCCccHHH
Confidence            3578999999887543   33       223332  3578999999999974

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=90.26  E-value=0.12  Score=41.04  Aligned_cols=62  Identities=19%  Similarity=0.124  Sum_probs=31.3

Q ss_pred             cccccCCCCCCcccccCcccchHHHHhhcceeeec--ccce-eeeeccccccccceEEecCCCCCCCCCC
Q psy2779          21 VKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWE--KSFQ-FERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        21 IkGLGLde~g~a~~~a~GlVGQ~~AREAaGIVVdm--~~~~-~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +.++-+.+.  +...-+-+.|.+++.+..--.++.  +.-. |..+   ..-..+-+|+.||||||||-.
T Consensus       108 ~~~~~~~~~--p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~---g~~~p~gvLL~GppGtGKT~l  172 (364)
T TIGR01242       108 VKGMEVEER--PNVSYEDIGGLEEQIREIREAVELPLKHPELFEEV---GIEPPKGVLLYGPPGTGKTLL  172 (364)
T ss_pred             cccceeccC--CCCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhc---CCCCCceEEEECCCCCCHHHH
Confidence            344444433  334445678877776555433322  0000 0001   111234588999999999743

Many proteins may score above the trusted cutoff because an internal

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=90.13  E-value=0.14  Score=37.06  Aligned_cols=18  Identities=17%  Similarity=0.078  Sum_probs=15.5

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .|..+++.||||||||-+
T Consensus        24 ~g~~i~I~G~tGSGKTTl   41 (186)
T cd01130          24 ARKNILISGGTGSGKTTL   41 (186)
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            588999999999999744

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=90.08  E-value=0.14  Score=37.82  Aligned_cols=43  Identities=9%  Similarity=0.013  Sum_probs=26.1

Q ss_pred             ccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          33 NEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        33 ~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ......|.-...-++|...+..-       +    ..+.+.+++.||||+|||-
T Consensus        16 ~~~~~~~~~~~~~~~~~~~l~~~-------~----~~~~~~~~l~G~~G~GKTt   58 (269)
T TIGR03015        16 LPDPDFFYPSKGHKRAMAYLEYG-------L----SQREGFILITGEVGAGKTT   58 (269)
T ss_pred             CCCHHHhCCCHHHHHHHHHHHHH-------H----hcCCCEEEEEcCCCCCHHH
Confidence            33344555555555655544332       1    1135688999999999974

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=90.01  E-value=0.16  Score=39.44  Aligned_cols=24  Identities=8%  Similarity=-0.133  Sum_probs=19.3

Q ss_pred             ccccccceEEecCCCCCCCCCCce
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      +.+..|.+.++.|+||||||-|.-
T Consensus        90 GGi~~g~i~ei~G~~g~GKT~l~~  113 (310)
T TIGR02236        90 GGIETQAITEVFGEFGSGKTQICH  113 (310)
T ss_pred             CCCCCCeEEEEECCCCCCHHHHHH
Confidence            345568899999999999998744

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=90.01  E-value=0.12  Score=44.51  Aligned_cols=40  Identities=15%  Similarity=0.136  Sum_probs=27.3

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .+-+|||+...+..-   +.       +++++.  ..++|+.||||||||-.
T Consensus        15 f~~viGq~~v~~~L~---~~-------i~~~~~--~hayLf~Gp~GtGKTt~   54 (559)
T PRK05563         15 FEDVVGQEHITKTLK---NA-------IKQGKI--SHAYLFSGPRGTGKTSA   54 (559)
T ss_pred             HHhccCcHHHHHHHH---HH-------HHcCCC--CeEEEEECCCCCCHHHH
Confidence            567999999766432   22       222332  57889999999999743

>PRK14738 gmk guanylate kinase; Provisional

Probab=89.95  E-value=0.15  Score=37.73  Aligned_cols=19  Identities=16%  Similarity=0.010  Sum_probs=16.0

Q ss_pred             cccceEEecCCCCCCCCCC
Q psy2779          69 FRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~~~   87 (101)
                      ..++.+++.||+||||+-.
T Consensus        11 ~~~~~ivi~GpsG~GK~tl   29 (206)
T PRK14738         11 AKPLLVVISGPSGVGKDAV   29 (206)
T ss_pred             CCCeEEEEECcCCCCHHHH
Confidence            4688999999999998753

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=89.91  E-value=0.18  Score=41.15  Aligned_cols=46  Identities=13%  Similarity=0.052  Sum_probs=30.4

Q ss_pred             cCcccchHHHHhhccee-eecccceeeeeccccccccceEEecCCCCCCCCCCceeeeeee
Q psy2779          36 AAGLVGQQAAREVSRAV-TWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNTSMIIDSW   95 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIV-Vdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~~~~~~~~   95 (101)
                      .+-+|||+++.+|.-+. |+=              +.+-+|+.|+||+||+-.-..+-..|
T Consensus         3 f~~ivgq~~~~~al~~~~~~~--------------~~g~vli~G~~G~gKttl~r~~~~~~   49 (337)
T TIGR02030         3 FTAIVGQDEMKLALLLNVIDP--------------KIGGVMVMGDRGTGKSTAVRALAALL   49 (337)
T ss_pred             ccccccHHHHHHHHHHHhcCC--------------CCCeEEEEcCCCCCHHHHHHHHHHhh
Confidence            35689999999996432 221              13446699999999975544443333

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

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=89.89  E-value=0.12  Score=42.14  Aligned_cols=40  Identities=15%  Similarity=0.053  Sum_probs=27.4

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      ..-++||++|.+..--.+.-          ++  .-.++|+.||+|+||+-+
T Consensus        22 ~~~l~Gh~~a~~~L~~a~~~----------gr--l~ha~L~~G~~G~GKttl   61 (351)
T PRK09112         22 NTRLFGHEEAEAFLAQAYRE----------GK--LHHALLFEGPEGIGKATL   61 (351)
T ss_pred             hhhccCcHHHHHHHHHHHHc----------CC--CCeeEeeECCCCCCHHHH
Confidence            46799999998765332222          22  123799999999998744

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

Probab=89.88  E-value=0.1  Score=45.88  Aligned_cols=45  Identities=20%  Similarity=0.156  Sum_probs=27.7

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeee--ccccccccceEEecCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERC--KSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~--~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      -...++||.+|-++.--.+..     .|.  .+..+ -...+|+.||||||||
T Consensus       452 l~~~v~GQ~~ai~~l~~~i~~-----~~~g~~~~~~-p~~~~lf~Gp~GvGKT  498 (731)
T TIGR02639       452 LKAKIFGQDEAIDSLVSSIKR-----SRAGLGNPNK-PVGSFLFTGPTGVGKT  498 (731)
T ss_pred             HhcceeCcHHHHHHHHHHHHH-----HhcCCCCCCC-CceeEEEECCCCccHH
Confidence            356789999998874333222     111  11111 1235789999999998

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

Probab=89.68  E-value=0.12  Score=42.52  Aligned_cols=16  Identities=13%  Similarity=-0.039  Sum_probs=13.2

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      ..+-+|+.||||||||
T Consensus       275 ~~~giLl~GpPGtGKT  290 (494)
T COG0464         275 PPKGVLLYGPPGTGKT  290 (494)
T ss_pred             CCCeeEEECCCCCCHH
Confidence            3457889999999986

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=89.55  E-value=0.21  Score=39.19  Aligned_cols=24  Identities=8%  Similarity=-0.151  Sum_probs=19.4

Q ss_pred             ccccccceEEecCCCCCCCCCCce
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      +....|.+.++.|+||||||-+.-
T Consensus        97 GGi~~g~vtei~G~~GsGKT~l~~  120 (317)
T PRK04301         97 GGIETQSITEFYGEFGSGKTQICH  120 (317)
T ss_pred             CCccCCcEEEEECCCCCCHhHHHH
Confidence            345568899999999999997654

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=89.46  E-value=0.14  Score=46.64  Aligned_cols=38  Identities=21%  Similarity=0.282  Sum_probs=27.5

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .+.+|||+.+.+.   +..+       ++++++  ..++|+.||+|||||
T Consensus        14 f~eiiGqe~v~~~---L~~~-------i~~~ri--~Ha~Lf~Gp~G~GKT   51 (824)
T PRK07764         14 FAEVIGQEHVTEP---LSTA-------LDSGRI--NHAYLFSGPRGCGKT   51 (824)
T ss_pred             HHHhcCcHHHHHH---HHHH-------HHhCCC--CceEEEECCCCCCHH
Confidence            5679999998876   3333       333332  467899999999997

>PRK12377 putative replication protein; Provisional

Probab=89.40  E-value=0.12  Score=40.42  Aligned_cols=35  Identities=20%  Similarity=0.181  Sum_probs=23.0

Q ss_pred             chHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          41 GQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        41 GQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ||..|..+|.-+++-    |.   .    ...-+++.|+||||||=
T Consensus        82 ~~~~a~~~a~~~a~~----~~---~----~~~~l~l~G~~GtGKTh  116 (248)
T PRK12377         82 GQRYALSQAKSIADE----LM---T----GCTNFVFSGKPGTGKNH  116 (248)
T ss_pred             hHHHHHHHHHHHHHH----HH---h----cCCeEEEECCCCCCHHH
Confidence            566666666655554    11   1    13568899999999974

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=89.36  E-value=0.15  Score=40.17  Aligned_cols=38  Identities=16%  Similarity=0.104  Sum_probs=26.0

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      -+-+|||+.+.+..   .+.       +++++.  -..+|+.||||+|||
T Consensus        16 ~~~iig~~~~~~~l---~~~-------i~~~~~--~~~~L~~G~~G~GKt   53 (367)
T PRK14970         16 FDDVVGQSHITNTL---LNA-------IENNHL--AQALLFCGPRGVGKT   53 (367)
T ss_pred             HHhcCCcHHHHHHH---HHH-------HHcCCC--CeEEEEECCCCCCHH
Confidence            46789999987653   222       233332  357889999999986

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=89.12  E-value=0.15  Score=42.68  Aligned_cols=40  Identities=15%  Similarity=0.111  Sum_probs=26.7

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +.+-+|||+.+-+.   +.+.       ++.++.  ..++|+.||||+||+-
T Consensus        15 ~~~diiGq~~~v~~---L~~~-------i~~~~i--~ha~Lf~Gp~G~GKtt   54 (451)
T PRK06305         15 TFSEILGQDAVVAV---LKNA-------LRFNRA--AHAYLFSGIRGTGKTT   54 (451)
T ss_pred             CHHHhcCcHHHHHH---HHHH-------HHcCCC--ceEEEEEcCCCCCHHH
Confidence            35678999988652   2333       222332  4678899999999974

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

Probab=89.03  E-value=0.1  Score=44.23  Aligned_cols=20  Identities=10%  Similarity=-0.105  Sum_probs=15.5

Q ss_pred             ccccceEEecCCCCCCCCCC
Q psy2779          68 LFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~~   87 (101)
                      ....+.+|+.||||||||-.
T Consensus       214 i~~p~gVLL~GPPGTGKT~L  233 (438)
T PTZ00361        214 IKPPKGVILYGPPGTGKTLL  233 (438)
T ss_pred             CCCCcEEEEECCCCCCHHHH
Confidence            33466788999999999754

>PRK14527 adenylate kinase; Provisional

Probab=89.01  E-value=0.19  Score=36.10  Aligned_cols=20  Identities=10%  Similarity=0.057  Sum_probs=16.4

Q ss_pred             ccceEEecCCCCCCCCCCce
Q psy2779          70 RGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~   89 (101)
                      .+.++++.|+|||||+-+..
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~   24 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAE   24 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            36789999999999986544

>TIGR00602 rad24 checkpoint protein rad24

Probab=88.98  E-value=0.15  Score=45.27  Aligned_cols=47  Identities=11%  Similarity=0.015  Sum_probs=29.4

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCCcee
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      .+.++||++.-+..--+++-        .......++++++.||||||||-...+
T Consensus        83 ldel~~~~~ki~~l~~~l~~--------~~~~~~~~~illL~GP~GsGKTTl~~~  129 (637)
T TIGR00602        83 QHELAVHKKKIEEVETWLKA--------QVLENAPKRILLITGPSGCGKSTTIKI  129 (637)
T ss_pred             HHHhcCcHHHHHHHHHHHHh--------cccccCCCcEEEEECCCCCCHHHHHHH
Confidence            56799999765542221111        011123578899999999999865443

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

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=88.98  E-value=0.18  Score=40.38  Aligned_cols=21  Identities=19%  Similarity=0.172  Sum_probs=16.9

Q ss_pred             ccceEEecCCCCCCCCCCcee
Q psy2779          70 RGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      .++.+|++||||||||-+-..
T Consensus       121 ~~g~ili~G~tGSGKTT~l~a  141 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTLAS  141 (343)
T ss_pred             cCcEEEEECCCCCCHHHHHHH
Confidence            478899999999999855443

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=88.96  E-value=0.16  Score=45.94  Aligned_cols=39  Identities=21%  Similarity=0.163  Sum_probs=27.8

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+.+.+...-.          ++++++  ...+|+.||||||||-
T Consensus        15 FddIIGQe~vv~~L~~a----------i~~~rl--~Ha~Lf~GP~GvGKTT   53 (709)
T PRK08691         15 FADLVGQEHVVKALQNA----------LDEGRL--HHAYLLTGTRGVGKTT   53 (709)
T ss_pred             HHHHcCcHHHHHHHHHH----------HHcCCC--CeEEEEECCCCCcHHH
Confidence            56799999998854332          222332  4578999999999984

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=88.93  E-value=0.046  Score=39.97  Aligned_cols=51  Identities=25%  Similarity=0.173  Sum_probs=33.4

Q ss_pred             ccCcccchHHHHhhcceeeec-ccceeeeeccccccccceEE--ecCCCCCCCCCCceeeeee
Q psy2779          35 MAAGLVGQQAAREVSRAVTWE-KSFQFERCKSHSLFRGGRAV--AGGRTKCPKPPNTSMIIDS   94 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm-~~~~~~~~~~~~~~~g~~ll--~~G~p~~g~~~~~~~~~~~   94 (101)
                      -..-+.||..|.+.   |++. +.|.    .+.  -..+.|+  +-|+|||||+=.++||.++
T Consensus        23 L~~~l~GQhla~~~---v~~ai~~~l----~~~--~p~KpLVlSfHG~tGtGKn~v~~liA~~   76 (127)
T PF06309_consen   23 LQRNLFGQHLAVEV---VVNAIKGHL----ANP--NPRKPLVLSFHGWTGTGKNFVSRLIAEH   76 (127)
T ss_pred             HHHHccCcHHHHHH---HHHHHHHHH----cCC--CCCCCEEEEeecCCCCcHHHHHHHHHHH
Confidence            34568999999886   4444 1111    111  1334444  7899999999888888766

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>KOG0727|consensus

Probab=88.92  E-value=0.28  Score=41.73  Aligned_cols=63  Identities=19%  Similarity=0.116  Sum_probs=35.8

Q ss_pred             cccccccCCCCCCcccccC-cccch-HHHHhhcceeeecccce-eeeeccccccccceEEecCCCCCCCCC
Q psy2779          19 SHVKGLGLKENGEANEMAA-GLVGQ-QAAREVSRAVTWEKSFQ-FERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        19 SHIkGLGLde~g~a~~~a~-GlVGQ-~~AREAaGIVVdm~~~~-~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      |.|-=|+-|+.-...+..- |+==| .+-|||..+-+--  ++ |.++   .+---|-+|+-||||||||-
T Consensus       139 ssi~ml~~~ekpdvsy~diggld~qkqeireavelplt~--~~ly~qi---gidpprgvllygppg~gktm  204 (408)
T KOG0727|consen  139 SSISMLGPDEKPDVSYADIGGLDVQKQEIREAVELPLTH--ADLYKQI---GIDPPRGVLLYGPPGTGKTM  204 (408)
T ss_pred             ccccccCCCCCCCccccccccchhhHHHHHHHHhccchH--HHHHHHh---CCCCCcceEEeCCCCCcHHH
Confidence            3344555555544444332 34333 4679997765421  11 2233   44445668899999999973

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

Probab=88.76  E-value=0.16  Score=43.65  Aligned_cols=17  Identities=12%  Similarity=-0.322  Sum_probs=14.3

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      -+.|++-||||||||=+
T Consensus       148 PlgllL~GPPGcGKTll  164 (413)
T PLN00020        148 PLILGIWGGKGQGKSFQ  164 (413)
T ss_pred             CeEEEeeCCCCCCHHHH
Confidence            56789999999999743

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.62  E-value=0.16  Score=43.24  Aligned_cols=38  Identities=13%  Similarity=0.130  Sum_probs=26.6

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .+-+|||+.+.+..   .+.       +++++.  ..++|+.||||+|||
T Consensus        15 f~diiGq~~i~~~L---~~~-------i~~~~i--~hayLf~Gp~G~GKT   52 (486)
T PRK14953         15 FKEVIGQEIVVRIL---KNA-------VKLQRV--SHAYIFAGPRGTGKT   52 (486)
T ss_pred             HHHccChHHHHHHH---HHH-------HHcCCC--CeEEEEECCCCCCHH
Confidence            46789999988743   344       333332  457789999999994

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.56  E-value=0.14  Score=45.35  Aligned_cols=40  Identities=18%  Similarity=0.112  Sum_probs=27.8

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +.+-+|||+.+.++.   .++       ++++++  -.++|+.|++|||||-
T Consensus        14 ~f~dviGQe~vv~~L---~~~-------l~~~rl--~ha~Lf~Gp~GvGKTt   53 (618)
T PRK14951         14 SFSEMVGQEHVVQAL---TNA-------LTQQRL--HHAYLFTGTRGVGKTT   53 (618)
T ss_pred             CHHHhcCcHHHHHHH---HHH-------HHcCCC--CeEEEEECCCCCCHHH
Confidence            357799999988743   333       333332  4568999999999973

>PRK06620 hypothetical protein; Validated

Probab=88.50  E-value=0.19  Score=37.89  Aligned_cols=16  Identities=13%  Similarity=-0.074  Sum_probs=13.4

Q ss_pred             ceEEecCCCCCCCCCC
Q psy2779          72 GRAVAGGRTKCPKPPN   87 (101)
Q Consensus        72 ~~ll~~G~p~~g~~~~   87 (101)
                      +.+++.||||||||=.
T Consensus        45 ~~l~l~Gp~G~GKThL   60 (214)
T PRK06620         45 FTLLIKGPSSSGKTYL   60 (214)
T ss_pred             ceEEEECCCCCCHHHH
Confidence            5689999999999843

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=88.44  E-value=0.17  Score=45.88  Aligned_cols=47  Identities=17%  Similarity=0.087  Sum_probs=29.2

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeecccccc---ccceEEecCCCCCCCCCCc
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLF---RGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~---~g~~ll~~G~p~~g~~~~~   88 (101)
                      -..-++||..|-++.--.+..       ++++-.-   .-+.+|+.||||+|||-..
T Consensus       564 L~~~v~GQ~~Av~~v~~~i~~-------~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA  613 (852)
T TIGR03345       564 LAERVIGQDHALEAIAERIRT-------ARAGLEDPRKPLGVFLLVGPSGVGKTETA  613 (852)
T ss_pred             hcCeEcChHHHHHHHHHHHHH-------HhcCCCCCCCCceEEEEECCCCCCHHHHH
Confidence            345789999998865433332       2211100   1236899999999998544

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.

>KOG2028|consensus

Probab=88.40  E-value=0.12  Score=45.38  Aligned_cols=56  Identities=13%  Similarity=0.033  Sum_probs=44.6

Q ss_pred             cccccCCCCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          21 VKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        21 IkGLGLde~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      |.++=|.|...|+. -+-.|||.++----|++-.+       ++++.+   --+++-||||||||-.
T Consensus       123 ~qh~PLaermRPkt-L~dyvGQ~hlv~q~gllrs~-------ieq~~i---pSmIlWGppG~GKTtl  178 (554)
T KOG2028|consen  123 LQHKPLAERMRPKT-LDDYVGQSHLVGQDGLLRSL-------IEQNRI---PSMILWGPPGTGKTTL  178 (554)
T ss_pred             hccCChhhhcCcch-HHHhcchhhhcCcchHHHHH-------HHcCCC---CceEEecCCCCchHHH
Confidence            36778888888876 57799999988878888888       766664   3467999999999854

>CHL00176 ftsH cell division protein; Validated

Probab=88.19  E-value=0.16  Score=44.87  Aligned_cols=45  Identities=18%  Similarity=0.055  Sum_probs=29.2

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeecccccc------ccceEEecCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLF------RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~------~g~~ll~~G~p~~g~~~   86 (101)
                      ..+-++|++++.+...-+++.       .+....+      --+-+|+.||||||||-
T Consensus       181 ~f~dv~G~~~~k~~l~eiv~~-------lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~  231 (638)
T CHL00176        181 TFRDIAGIEEAKEEFEEVVSF-------LKKPERFTAVGAKIPKGVLLVGPPGTGKTL  231 (638)
T ss_pred             CHHhccChHHHHHHHHHHHHH-------HhCHHHHhhccCCCCceEEEECCCCCCHHH
Confidence            445688998888877666655       2211110      12348899999999974

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=88.09  E-value=0.18  Score=43.91  Aligned_cols=41  Identities=17%  Similarity=0.074  Sum_probs=27.5

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCCc
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +.+-+|||..+.+++   ++.       +.+.   ....+++.||||||||-..
T Consensus       152 ~~~~iiGqs~~~~~l---~~~-------ia~~---~~~~vlL~Gp~GtGKTTLA  192 (615)
T TIGR02903       152 AFSEIVGQERAIKAL---LAK-------VASP---FPQHIILYGPPGVGKTTAA  192 (615)
T ss_pred             cHHhceeCcHHHHHH---HHH-------HhcC---CCCeEEEECCCCCCHHHHH
Confidence            345689999998863   233       2221   2345889999999997543

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.

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=88.03  E-value=0.18  Score=39.51  Aligned_cols=17  Identities=18%  Similarity=0.138  Sum_probs=14.7

Q ss_pred             cccceEEecCCCCCCCC
Q psy2779          69 FRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~   85 (101)
                      ..++-+|+.||||||||
T Consensus        31 ~~~~pvLl~G~~GtGKT   47 (272)
T PF12775_consen   31 SNGRPVLLVGPSGTGKT   47 (272)
T ss_dssp             HCTEEEEEESSTTSSHH
T ss_pred             HcCCcEEEECCCCCchh
Confidence            35788999999999986

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

Probab=88.01  E-value=0.2  Score=43.08  Aligned_cols=61  Identities=21%  Similarity=0.131  Sum_probs=36.6

Q ss_pred             cccccCCCCCCccccc-Ccccch-HHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          21 VKGLGLKENGEANEMA-AGLVGQ-QAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        21 IkGLGLde~g~a~~~a-~GlVGQ-~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      +..+.+++.-+..|.. .|+==| ++-|||.-+-+.- .--|.++   .+---+=+|+.||||||||
T Consensus       137 V~~M~v~e~PdvtY~dIGGL~~Qi~EirE~VELPL~~-PElF~~~---GI~PPKGVLLYGPPGTGKT  199 (406)
T COG1222         137 VSVMEVEEKPDVTYEDIGGLDEQIQEIREVVELPLKN-PELFEEL---GIDPPKGVLLYGPPGTGKT  199 (406)
T ss_pred             hheeeeccCCCCChhhccCHHHHHHHHHHHhcccccC-HHHHHHc---CCCCCCceEeeCCCCCcHH
Confidence            5566666665554432 345445 4578887665532 1224444   4434455779999999998

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=87.89  E-value=0.24  Score=38.80  Aligned_cols=47  Identities=13%  Similarity=0.005  Sum_probs=28.7

Q ss_pred             cccccCcccchHHHHhhcceee-ecccceeeeeccccccccceEEecCCCCCCCCCCc
Q psy2779          32 ANEMAAGLVGQQAAREVSRAVT-WEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        32 a~~~a~GlVGQ~~AREAaGIVV-dm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +.+...-|+|.++-.+...-.+ +.       ++. .  ....+++.||||||||-..
T Consensus        25 ~~~~P~~l~~Re~e~~~l~~~l~~~-------~~~-~--~~~~~lI~G~~GtGKT~l~   72 (394)
T PRK00411         25 PDYVPENLPHREEQIEELAFALRPA-------LRG-S--RPLNVLIYGPPGTGKTTTV   72 (394)
T ss_pred             CCCcCCCCCCHHHHHHHHHHHHHHH-------hCC-C--CCCeEEEECCCCCCHHHHH
Confidence            3345566888887766533222 32       211 1  2456889999999998543

>KOG0730|consensus

Probab=87.87  E-value=0.22  Score=45.33  Aligned_cols=42  Identities=14%  Similarity=0.130  Sum_probs=26.4

Q ss_pred             chHHHHhhcceeeecc---cceeeeeccccccccceEEecCCCCCCCC
Q psy2779          41 GQQAAREVSRAVTWEK---SFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        41 GQ~~AREAaGIVVdm~---~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      ||++-++...--|.+-   +-.|.|.   .+-.-+-+|+.||||||||
T Consensus       438 GlE~lK~elq~~V~~p~~~pe~F~r~---Gi~ppkGVLlyGPPGC~KT  482 (693)
T KOG0730|consen  438 GLEELKRELQQAVEWPLKHPEKFARF---GISPPKGVLLYGPPGCGKT  482 (693)
T ss_pred             CHHHHHHHHHHHHhhhhhchHHHHHh---cCCCCceEEEECCCCcchH
Confidence            4666666655322221   2235666   4445677889999999987

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=87.85  E-value=0.19  Score=41.56  Aligned_cols=17  Identities=18%  Similarity=0.108  Sum_probs=14.5

Q ss_pred             cccceEEecCCCCCCCC
Q psy2779          69 FRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~   85 (101)
                      ..++-+|+.|+||||||
T Consensus        62 ~~~~~ilL~G~pGtGKT   78 (327)
T TIGR01650        62 AYDRRVMVQGYHGTGKS   78 (327)
T ss_pred             hcCCcEEEEeCCCChHH
Confidence            34778999999999987

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.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=87.83  E-value=0.29  Score=37.10  Aligned_cols=21  Identities=14%  Similarity=0.085  Sum_probs=17.7

Q ss_pred             cccccceEEecCCCCCCCCCC
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      ..-.|..+++.|+||||||-+
T Consensus        20 gi~~g~~~~i~G~~G~GKTtl   40 (230)
T PRK08533         20 GIPAGSLILIEGDESTGKSIL   40 (230)
T ss_pred             CCCCCcEEEEECCCCCCHHHH
Confidence            344588999999999999876

>PRK10865 protein disaggregation chaperone; Provisional

Probab=87.66  E-value=0.18  Score=45.59  Aligned_cols=46  Identities=17%  Similarity=0.078  Sum_probs=28.0

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeecccccccc---ceEEecCCCCCCCCCCc
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRG---GRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g---~~ll~~G~p~~g~~~~~   88 (101)
                      ..-++||..|-++.---+..       ++.+-.-..   ..+|+.||||||||-..
T Consensus       567 ~~~viGQ~~ai~~l~~~i~~-------~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA  615 (857)
T PRK10865        567 HHRVIGQNEAVEAVSNAIRR-------SRAGLSDPNRPIGSFLFLGPTGVGKTELC  615 (857)
T ss_pred             CCeEeCCHHHHHHHHHHHHH-------HHhcccCCCCCCceEEEECCCCCCHHHHH
Confidence            45689999997764333322       321111011   37889999999998544

>KOG0733|consensus

Probab=87.60  E-value=0.22  Score=45.77  Aligned_cols=15  Identities=20%  Similarity=0.304  Sum_probs=12.4

Q ss_pred             cceEEecCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKP   85 (101)
Q Consensus        71 g~~ll~~G~p~~g~~   85 (101)
                      -|=+|+-||||||||
T Consensus       223 prGvLlHGPPGCGKT  237 (802)
T KOG0733|consen  223 PRGVLLHGPPGCGKT  237 (802)
T ss_pred             CCceeeeCCCCccHH
Confidence            345779999999987

>PRK09183 transposase/IS protein; Provisional

Probab=87.59  E-value=0.26  Score=38.14  Aligned_cols=19  Identities=21%  Similarity=0.106  Sum_probs=15.3

Q ss_pred             ccceEEecCCCCCCCCCCc
Q psy2779          70 RGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~   88 (101)
                      .|..+++.||||||||=..
T Consensus       101 ~~~~v~l~Gp~GtGKThLa  119 (259)
T PRK09183        101 RNENIVLLGPSGVGKTHLA  119 (259)
T ss_pred             cCCeEEEEeCCCCCHHHHH
Confidence            3677889999999998543

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=87.44  E-value=0.24  Score=44.92  Aligned_cols=39  Identities=18%  Similarity=0.124  Sum_probs=27.0

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+.+|||+.+.+..   ...       +++++.  ..+.|+.||||+|||.
T Consensus        17 f~dIiGQe~~v~~L---~~a-------I~~~rl--~HAYLF~GP~GtGKTt   55 (725)
T PRK07133         17 FDDIVGQDHIVQTL---KNI-------IKSNKI--SHAYLFSGPRGTGKTS   55 (725)
T ss_pred             HHHhcCcHHHHHHH---HHH-------HHcCCC--CeEEEEECCCCCcHHH
Confidence            46799999987642   233       333332  4677899999999973

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=87.44  E-value=0.23  Score=33.44  Aligned_cols=16  Identities=19%  Similarity=0.208  Sum_probs=13.8

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      .|+-+|+.+|||+|||
T Consensus        13 ~~~~~li~aptGsGKT   28 (169)
T PF00270_consen   13 SGKNVLISAPTGSGKT   28 (169)
T ss_dssp             TTSEEEEECSTTSSHH
T ss_pred             cCCCEEEECCCCCccH
Confidence            4667889999999997

Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=87.39  E-value=0.25  Score=40.46  Aligned_cols=18  Identities=22%  Similarity=0.183  Sum_probs=15.4

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .++.+|++||||||||-.
T Consensus       133 ~~glilI~GpTGSGKTTt  150 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTL  150 (358)
T ss_pred             cCCEEEEECCCCCCHHHH
Confidence            478999999999999743

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>PRK05541 adenylylsulfate kinase; Provisional

Probab=87.35  E-value=0.28  Score=34.55  Aligned_cols=19  Identities=16%  Similarity=-0.011  Sum_probs=15.7

Q ss_pred             ccceEEecCCCCCCCCCCc
Q psy2779          70 RGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~   88 (101)
                      .|..+++.|+|||||+-..
T Consensus         6 ~~~~I~i~G~~GsGKst~a   24 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIA   24 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHH
Confidence            4779999999999996443

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=87.26  E-value=0.3  Score=38.03  Aligned_cols=23  Identities=17%  Similarity=0.130  Sum_probs=18.1

Q ss_pred             ccceEEecCCCCCCCCCCceeee
Q psy2779          70 RGGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      .++.+|++|+||||||-+...++
T Consensus        79 ~~GlilisG~tGSGKTT~l~all  101 (264)
T cd01129          79 PHGIILVTGPTGSGKTTTLYSAL  101 (264)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHH
Confidence            36789999999999987665443

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=87.20  E-value=0.3  Score=39.15  Aligned_cols=25  Identities=12%  Similarity=-0.008  Sum_probs=20.2

Q ss_pred             ccccccceEEecCCCCCCCCCCcee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      +..-.|.++++.||||||||.+.-.
T Consensus        91 gGi~~g~i~~i~G~~g~GKT~l~~~  115 (316)
T TIGR02239        91 GGIETGSITEIFGEFRTGKTQLCHT  115 (316)
T ss_pred             CCCCCCeEEEEECCCCCCcCHHHHH
Confidence            3455688999999999999987644

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=87.16  E-value=0.047  Score=38.33  Aligned_cols=28  Identities=14%  Similarity=0.164  Sum_probs=22.5

Q ss_pred             ccceEEecCCCCCCCCCCceeeeeeecc
Q psy2779          70 RGGRAVAGGRTKCPKPPNTSMIIDSWVE   97 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~~~~~~~~~   97 (101)
                      .|...+++|+||+|||=+..-++-+|..
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~~   58 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALAT   58 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            5889999999999999887666555544

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=87.08  E-value=0.25  Score=43.36  Aligned_cols=46  Identities=15%  Similarity=0.108  Sum_probs=30.4

Q ss_pred             CCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          28 ENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        28 e~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +...|. +.+.+|||+.+.+..   ..+       ++++++  -.++|+.||+|+|||-
T Consensus        16 ~KyRP~-~f~dliGq~~~v~~L---~~~-------~~~gri--~ha~L~~Gp~GvGKTt   61 (598)
T PRK09111         16 RKYRPQ-TFDDLIGQEAMVRTL---TNA-------FETGRI--AQAFMLTGVRGVGKTT   61 (598)
T ss_pred             hhhCCC-CHHHhcCcHHHHHHH---HHH-------HHcCCC--CceEEEECCCCCCHHH
Confidence            334443 457899999988763   233       223332  3478899999999974

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=87.07  E-value=0.27  Score=36.68  Aligned_cols=27  Identities=15%  Similarity=0.036  Sum_probs=21.7

Q ss_pred             ccccccceEEecCCCCCCCCCCceeee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      +....|...+++|+||+|||=+...+.
T Consensus        25 gG~~~g~~~~i~g~~G~GKT~l~~~~~   51 (271)
T cd01122          25 KGLRKGELIILTAGTGVGKTTFLREYA   51 (271)
T ss_pred             EEEcCCcEEEEEcCCCCCHHHHHHHHH
Confidence            467778999999999999997665443

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>KOG0991|consensus

Probab=87.03  E-value=0.3  Score=40.92  Aligned_cols=37  Identities=16%  Similarity=0.228  Sum_probs=25.4

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +-+||-|+.-+-..++..-          +.+   --++++||||||||-
T Consensus        27 ~dIVGNe~tv~rl~via~~----------gnm---P~liisGpPG~GKTT   63 (333)
T KOG0991|consen   27 QDIVGNEDTVERLSVIAKE----------GNM---PNLIISGPPGTGKTT   63 (333)
T ss_pred             HHhhCCHHHHHHHHHHHHc----------CCC---CceEeeCCCCCchhh
Confidence            5678888876665554332          332   347899999999983

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

Probab=86.99  E-value=0.24  Score=37.11  Aligned_cols=15  Identities=13%  Similarity=0.000  Sum_probs=13.2

Q ss_pred             eEEecCCCCCCCCCC
Q psy2779          73 RAVAGGRTKCPKPPN   87 (101)
Q Consensus        73 ~ll~~G~p~~g~~~~   87 (101)
                      ++|+.||||+||+..
T Consensus        26 alL~~Gp~G~Gktt~   40 (325)
T COG0470          26 ALLFYGPPGVGKTTA   40 (325)
T ss_pred             eeeeeCCCCCCHHHH
Confidence            799999999999753

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=86.76  E-value=0.26  Score=30.71  Aligned_cols=15  Identities=13%  Similarity=0.091  Sum_probs=12.0

Q ss_pred             EEecCCCCCCCCCCc
Q psy2779          74 AVAGGRTKCPKPPNT   88 (101)
Q Consensus        74 ll~~G~p~~g~~~~~   88 (101)
                      +.+.|+|||||+-+.
T Consensus         2 i~i~G~~gsGKst~~   16 (69)
T cd02019           2 IAITGGSGSGKSTVA   16 (69)
T ss_pred             EEEECCCCCCHHHHH
Confidence            568999999997543

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=86.64  E-value=0.26  Score=45.60  Aligned_cols=39  Identities=21%  Similarity=0.131  Sum_probs=27.6

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||++..+..-   +.       ++++++  ..++|+.|++|||||-
T Consensus        15 FdEVIGQe~Vv~~L~---~a-------L~~gRL--~HAyLFtGPpGvGKTT   53 (830)
T PRK07003         15 FASLVGQEHVVRALT---HA-------LDGGRL--HHAYLFTGTRGVGKTT   53 (830)
T ss_pred             HHHHcCcHHHHHHHH---HH-------HhcCCC--CeEEEEECCCCCCHHH
Confidence            577999999988543   22       222232  4578899999999984

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=86.55  E-value=0.26  Score=32.76  Aligned_cols=20  Identities=15%  Similarity=0.042  Sum_probs=16.4

Q ss_pred             ccccceEEecCCCCCCCCCC
Q psy2779          68 LFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .-.|..+.+.|++||||+-+
T Consensus         8 i~~g~~~~i~G~nGsGKStL   27 (137)
T PF00005_consen    8 IKPGEIVAIVGPNGSGKSTL   27 (137)
T ss_dssp             EETTSEEEEEESTTSSHHHH
T ss_pred             EcCCCEEEEEccCCCccccc
Confidence            34688999999999998643

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.43  E-value=0.27  Score=42.49  Aligned_cols=39  Identities=13%  Similarity=0.131  Sum_probs=26.9

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+.+.+..-=.          +++++.  ..++|+.||||+|||-
T Consensus        15 f~~iiGq~~v~~~L~~~----------i~~~~~--~hayLf~Gp~G~GKtt   53 (576)
T PRK14965         15 FSDLTGQEHVSRTLQNA----------IDTGRV--AHAFLFTGARGVGKTS   53 (576)
T ss_pred             HHHccCcHHHHHHHHHH----------HHcCCC--CeEEEEECCCCCCHHH
Confidence            56799999987665322          222332  4567899999999863

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=86.41  E-value=0.35  Score=40.52  Aligned_cols=26  Identities=23%  Similarity=0.202  Sum_probs=20.6

Q ss_pred             cccccccceEEecCCCCCCCCCCcee
Q psy2779          65 SHSLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        65 ~~~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      .+.+..|.++|+.||||+|||-+...
T Consensus       257 gGG~~~gs~~li~G~~G~GKt~l~~~  282 (484)
T TIGR02655       257 GGGFFKDSIILATGATGTGKTLLVSK  282 (484)
T ss_pred             cCCccCCcEEEEECCCCCCHHHHHHH
Confidence            34667788999999999999865443

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=86.35  E-value=0.32  Score=34.20  Aligned_cols=19  Identities=21%  Similarity=0.121  Sum_probs=16.1

Q ss_pred             ccceEEecCCCCCCCCCCc
Q psy2779          70 RGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~   88 (101)
                      .|.++++.|.|||||+-..
T Consensus         3 ~g~~i~~~G~~GsGKST~a   21 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIA   21 (175)
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3779999999999998754

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=86.30  E-value=0.23  Score=44.60  Aligned_cols=43  Identities=21%  Similarity=0.087  Sum_probs=27.8

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeecccccc---ccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLF---RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~---~g~~ll~~G~p~~g~~   85 (101)
                      ..-++||..|-++.--.+..       +..+-.-   -...+|+.||||||||
T Consensus       564 ~~~v~GQ~~av~~v~~~i~~-------~~~gl~~~~~p~~~~Lf~Gp~GvGKt  609 (852)
T TIGR03346       564 HERVVGQDEAVEAVSDAIRR-------SRAGLSDPNRPIGSFLFLGPTGVGKT  609 (852)
T ss_pred             hcccCCChHHHHHHHHHHHH-------HhccCCCCCCCCeEEEEEcCCCCCHH
Confidence            45689999998876544443       2111000   1346889999999987

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.

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=86.27  E-value=0.26  Score=40.46  Aligned_cols=51  Identities=10%  Similarity=-0.130  Sum_probs=27.4

Q ss_pred             CCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          29 NGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        29 ~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      ...+.++.+-||--..-+.|...+..+       .+.-. -...-+++.||||||||=.
T Consensus       114 ~l~~~~tfd~fv~g~~n~~a~~~~~~~-------~~~~~-~~~~~l~l~G~~G~GKThL  164 (450)
T PRK00149        114 PLNPKYTFDNFVVGKSNRLAHAAALAV-------AENPG-KAYNPLFIYGGVGLGKTHL  164 (450)
T ss_pred             CCCCCCcccccccCCCcHHHHHHHHHH-------HhCcC-ccCCeEEEECCCCCCHHHH
Confidence            344555666655333333344444443       21111 0135689999999999843

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=86.25  E-value=0.35  Score=40.31  Aligned_cols=23  Identities=17%  Similarity=0.163  Sum_probs=19.4

Q ss_pred             cccccceEEecCCCCCCCCCCce
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      ..-.|..+|+.|+||||||-|..
T Consensus        27 G~p~Gs~~li~G~pGsGKT~l~~   49 (509)
T PRK09302         27 GLPKGRPTLVSGTAGTGKTLFAL   49 (509)
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHH
Confidence            45579999999999999997754

>TIGR02012 tigrfam_recA protein RecA

Probab=86.08  E-value=0.35  Score=39.56  Aligned_cols=24  Identities=21%  Similarity=0.040  Sum_probs=20.1

Q ss_pred             ccccccceEEecCCCCCCCCCCce
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      +..-.|++.++.||||||||-+.-
T Consensus        50 GGlp~G~iteI~G~~GsGKTtLaL   73 (321)
T TIGR02012        50 GGLPRGRIIEIYGPESSGKTTLAL   73 (321)
T ss_pred             CCCcCCeEEEEECCCCCCHHHHHH
Confidence            466778999999999999987643

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>PRK08181 transposase; Validated

Probab=85.96  E-value=0.37  Score=38.13  Aligned_cols=16  Identities=19%  Similarity=0.111  Sum_probs=13.5

Q ss_pred             cceEEecCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPP   86 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~   86 (101)
                      +.-+++.||||||||=
T Consensus       106 ~~nlll~Gp~GtGKTH  121 (269)
T PRK08181        106 GANLLLFGPPGGGKSH  121 (269)
T ss_pred             CceEEEEecCCCcHHH
Confidence            4558999999999983

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=85.91  E-value=0.54  Score=37.83  Aligned_cols=23  Identities=13%  Similarity=0.072  Sum_probs=19.3

Q ss_pred             ccccccceEEecCCCCCCCCCCc
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +..-.|.+.++.||||||||-+.
T Consensus        91 GGi~~G~iteI~G~~GsGKTql~  113 (313)
T TIGR02238        91 GGIESMSITEVFGEFRCGKTQLS  113 (313)
T ss_pred             CCCcCCeEEEEECCCCCCcCHHH
Confidence            45566789999999999999765

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>PRK09862 putative ATP-dependent protease; Provisional

Probab=85.83  E-value=0.52  Score=40.85  Aligned_cols=36  Identities=14%  Similarity=0.122  Sum_probs=26.5

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ..=..||..+.++.-+-               ..+|..+++.|+|||||+=
T Consensus       190 ~~~v~Gq~~~~~al~la---------------a~~G~~llliG~~GsGKTt  225 (506)
T PRK09862        190 LSDVIGQEQGKRGLEIT---------------AAGGHNLLLIGPPGTGKTM  225 (506)
T ss_pred             eEEEECcHHHHhhhhee---------------ccCCcEEEEECCCCCcHHH
Confidence            34467999888884322               2258899999999999863

>PRK05480 uridine/cytidine kinase; Provisional

Probab=85.81  E-value=0.35  Score=35.05  Aligned_cols=22  Identities=18%  Similarity=0.028  Sum_probs=17.0

Q ss_pred             ccceEEecCCCCCCCCCCceee
Q psy2779          70 RGGRAVAGGRTKCPKPPNTSMI   91 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~~~   91 (101)
                      .+.++.++|++|||||-++..+
T Consensus         5 ~~~iI~I~G~sGsGKTTl~~~l   26 (209)
T PRK05480          5 KPIIIGIAGGSGSGKTTVASTI   26 (209)
T ss_pred             CCEEEEEECCCCCCHHHHHHHH
Confidence            3668899999999998655443

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=85.76  E-value=0.27  Score=36.23  Aligned_cols=17  Identities=18%  Similarity=0.059  Sum_probs=14.5

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      .+..++.|+||||||-.
T Consensus        18 ~~~~~l~G~aGtGKT~~   34 (196)
T PF13604_consen   18 DRVSVLQGPAGTGKTTL   34 (196)
T ss_dssp             CSEEEEEESTTSTHHHH
T ss_pred             CeEEEEEECCCCCHHHH
Confidence            57889999999999843

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=85.74  E-value=0.28  Score=33.06  Aligned_cols=18  Identities=17%  Similarity=0.040  Sum_probs=14.7

Q ss_pred             cceEEecCCCCCCCCCCc
Q psy2779          71 GGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~   88 (101)
                      .+.+|+.+|||||||---
T Consensus        25 ~~~~ll~~~tGsGKT~~~   42 (184)
T PF04851_consen   25 ERRVLLNAPTGSGKTIIA   42 (184)
T ss_dssp             CSEEEEEESTTSSHHHHH
T ss_pred             CCCEEEEECCCCCcChhh
Confidence            577889999999998543

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=85.74  E-value=0.38  Score=38.22  Aligned_cols=23  Identities=13%  Similarity=0.114  Sum_probs=17.5

Q ss_pred             ccceEEecCCCCCCCCCCceeee
Q psy2779          70 RGGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      .++.+|++|+||||||-+...++
T Consensus       131 ~~~~ilI~G~tGSGKTTll~al~  153 (299)
T TIGR02782       131 ARKNILVVGGTGSGKTTLANALL  153 (299)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHH
Confidence            46678899999999986654443

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=85.70  E-value=0.41  Score=39.21  Aligned_cols=24  Identities=13%  Similarity=0.016  Sum_probs=19.5

Q ss_pred             ccccccceEEecCCCCCCCCCCce
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      +..-.|.+.++.|+||||||.+.-
T Consensus       118 GG~~~g~i~~i~G~~g~GKT~l~~  141 (342)
T PLN03186        118 GGIETGSITEIYGEFRTGKTQLCH  141 (342)
T ss_pred             CCCcCceEEEEECCCCCCccHHHH
Confidence            345567899999999999998763

>PRK08356 hypothetical protein; Provisional

Probab=85.65  E-value=0.35  Score=35.11  Aligned_cols=15  Identities=13%  Similarity=-0.035  Sum_probs=12.5

Q ss_pred             ceEEecCCCCCCCCC
Q psy2779          72 GRAVAGGRTKCPKPP   86 (101)
Q Consensus        72 ~~ll~~G~p~~g~~~   86 (101)
                      .+++++|||||||+-
T Consensus         6 ~~i~~~G~~gsGK~t   20 (195)
T PRK08356          6 MIVGVVGKIAAGKTT   20 (195)
T ss_pred             EEEEEECCCCCCHHH
Confidence            367899999999864

>TIGR00235 udk uridine kinase

Probab=85.64  E-value=0.33  Score=35.46  Aligned_cols=19  Identities=21%  Similarity=0.184  Sum_probs=15.7

Q ss_pred             ccceEEecCCCCCCCCCCc
Q psy2779          70 RGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~   88 (101)
                      .|.++.+.|++|||||-+.
T Consensus         5 ~g~vi~I~G~sGsGKSTl~   23 (207)
T TIGR00235         5 KGIIIGIGGGSGSGKTTVA   23 (207)
T ss_pred             CeEEEEEECCCCCCHHHHH
Confidence            3788999999999998544

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>KOG0738|consensus

Probab=85.58  E-value=0.34  Score=42.50  Aligned_cols=40  Identities=20%  Similarity=0.145  Sum_probs=23.8

Q ss_pred             cchHHH----Hhhcceeeecc-cceeeeeccccccccceEEecCCCCCCCC
Q psy2779          40 VGQQAA----REVSRAVTWEK-SFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        40 VGQ~~A----REAaGIVVdm~-~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .|-.+|    +||.=+-+.|- .||=+|-      -=+-+|+.||||||||
T Consensus       215 agl~~AK~lL~EAVvlPi~mPe~F~Girr------PWkgvLm~GPPGTGKT  259 (491)
T KOG0738|consen  215 AGLHEAKKLLKEAVVLPIWMPEFFKGIRR------PWKGVLMVGPPGTGKT  259 (491)
T ss_pred             cchHHHHHHHHHHHhhhhhhHHHHhhccc------ccceeeeeCCCCCcHH
Confidence            444555    45655555551 2333332      2356889999999997

>PLN02200 adenylate kinase family protein

Probab=85.42  E-value=0.38  Score=36.81  Aligned_cols=18  Identities=11%  Similarity=-0.141  Sum_probs=14.5

Q ss_pred             cceEEecCCCCCCCCCCc
Q psy2779          71 GGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~   88 (101)
                      ..++++.|+|||||+-..
T Consensus        43 ~~ii~I~G~PGSGKsT~a   60 (234)
T PLN02200         43 PFITFVLGGPGSGKGTQC   60 (234)
T ss_pred             CEEEEEECCCCCCHHHHH
Confidence            357899999999997543

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=85.30  E-value=0.53  Score=38.74  Aligned_cols=23  Identities=13%  Similarity=-0.071  Sum_probs=19.0

Q ss_pred             ccccccceEEecCCCCCCCCCCc
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +.+..|.+..+.|+||||||-+.
T Consensus       121 GGi~~G~ItEI~G~~GsGKTql~  143 (344)
T PLN03187        121 GGIETRCITEAFGEFRSGKTQLA  143 (344)
T ss_pred             CCCCCCeEEEEecCCCCChhHHH
Confidence            35567889999999999999754

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=85.03  E-value=0.25  Score=38.91  Aligned_cols=23  Identities=13%  Similarity=0.055  Sum_probs=18.1

Q ss_pred             ccccceEEecCCCCCCCCCCcee
Q psy2779          68 LFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      .-.|..++++|++|||||-+-..
T Consensus       141 v~~~~~ili~G~tGsGKTTll~a  163 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTFLKS  163 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHHHHH
Confidence            33688999999999999865443

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=84.96  E-value=0.43  Score=39.58  Aligned_cols=23  Identities=22%  Similarity=0.219  Sum_probs=17.1

Q ss_pred             ccceEEecCCCCCCCCCCceeee
Q psy2779          70 RGGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      ..+.+|++||||||||-+-..++
T Consensus       148 ~~GlilI~G~TGSGKTT~l~al~  170 (372)
T TIGR02525       148 AAGLGLICGETGSGKSTLAASIY  170 (372)
T ss_pred             cCCEEEEECCCCCCHHHHHHHHH
Confidence            35678899999999986554443

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>cd03272 ABC_SMC3_euk Eukaryotic SMC3 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains

Probab=84.91  E-value=0.6  Score=34.31  Aligned_cols=22  Identities=23%  Similarity=0.178  Sum_probs=17.5

Q ss_pred             cccceEEecCCCCCCCCCCcee
Q psy2779          69 FRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      +.+...++.||+||||+-.-.+
T Consensus        21 ~~~~~~~i~GpNGsGKStll~a   42 (243)
T cd03272          21 FSPKHNVVVGRNGSGKSNFFAA   42 (243)
T ss_pred             CCCCcEEEECCCCCCHHHHHHH
Confidence            4578999999999999865433

Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (fo

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=84.81  E-value=0.48  Score=35.17  Aligned_cols=19  Identities=11%  Similarity=0.062  Sum_probs=16.2

Q ss_pred             ccceEEecCCCCCCCCCCc
Q psy2779          70 RGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~   88 (101)
                      .|+++++.||+||||+-+-
T Consensus        24 ~g~~~~ltGpNg~GKSTll   42 (199)
T cd03283          24 KKNGILITGSNMSGKSTFL   42 (199)
T ss_pred             CCcEEEEECCCCCChHHHH
Confidence            4789999999999998553

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form slid

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=84.57  E-value=0.48  Score=38.88  Aligned_cols=25  Identities=12%  Similarity=-0.059  Sum_probs=20.0

Q ss_pred             ccccccceEEecCCCCCCCCCCcee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      +.+-.|++.++.||||||||-+.-.
T Consensus        50 GGlp~G~iteI~Gp~GsGKTtLal~   74 (325)
T cd00983          50 GGYPKGRIIEIYGPESSGKTTLALH   74 (325)
T ss_pred             CCccCCeEEEEECCCCCCHHHHHHH
Confidence            4556689999999999999866543

RecA couples ATP hydrolysis to DNA strand exchange.

>PHA00729 NTP-binding motif containing protein

Probab=84.47  E-value=0.38  Score=37.80  Aligned_cols=15  Identities=27%  Similarity=0.186  Sum_probs=12.7

Q ss_pred             eEEecCCCCCCCCCC
Q psy2779          73 RAVAGGRTKCPKPPN   87 (101)
Q Consensus        73 ~ll~~G~p~~g~~~~   87 (101)
                      .+++.|+||||||=.
T Consensus        19 nIlItG~pGvGKT~L   33 (226)
T PHA00729         19 SAVIFGKQGSGKTTY   33 (226)
T ss_pred             EEEEECCCCCCHHHH
Confidence            578999999999843

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=84.34  E-value=0.44  Score=41.84  Aligned_cols=16  Identities=25%  Similarity=0.239  Sum_probs=14.2

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      .-+++|++||||||||
T Consensus       257 p~GliLvTGPTGSGKT  272 (500)
T COG2804         257 PQGLILVTGPTGSGKT  272 (500)
T ss_pred             CCeEEEEeCCCCCCHH
Confidence            3678999999999987

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=84.30  E-value=0.5  Score=40.40  Aligned_cols=36  Identities=17%  Similarity=0.274  Sum_probs=24.5

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      +-+|||..+-+++-..  +       + +.   ...-+|+.|||||||+
T Consensus        65 ~~iiGqs~~i~~l~~a--l-------~-~~---~~~~vLi~Ge~GtGKt  100 (531)
T TIGR02902        65 DEIIGQEEGIKALKAA--L-------C-GP---NPQHVIIYGPPGVGKT  100 (531)
T ss_pred             HHeeCcHHHHHHHHHH--H-------h-CC---CCceEEEECCCCCCHH
Confidence            4599999887766421  1       1 11   1356789999999994

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.

>PRK10436 hypothetical protein; Provisional

Probab=84.28  E-value=0.53  Score=40.11  Aligned_cols=17  Identities=24%  Similarity=0.190  Sum_probs=15.2

Q ss_pred             ccceEEecCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~   86 (101)
                      ..+++|++||||||||-
T Consensus       217 ~~GliLvtGpTGSGKTT  233 (462)
T PRK10436        217 PQGLILVTGPTGSGKTV  233 (462)
T ss_pred             cCCeEEEECCCCCChHH
Confidence            57899999999999984

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

Probab=84.24  E-value=0.39  Score=43.31  Aligned_cols=44  Identities=9%  Similarity=-0.055  Sum_probs=28.5

Q ss_pred             cccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCCc
Q psy2779          38 GLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        38 GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      -..|++++.|+.--.+..       .+..+...|..+++.||||||||-..
T Consensus       323 ~~~g~~~vK~~i~~~l~~-------~~~~~~~~g~~i~l~GppG~GKTtl~  366 (784)
T PRK10787        323 DHYGLERVKDRILEYLAV-------QSRVNKIKGPILCLVGPPGVGKTSLG  366 (784)
T ss_pred             hccCHHHHHHHHHHHHHH-------HHhcccCCCceEEEECCCCCCHHHHH
Confidence            378999999876322221       01112235789999999999987443

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=84.17  E-value=0.24  Score=40.59  Aligned_cols=25  Identities=16%  Similarity=0.102  Sum_probs=19.3

Q ss_pred             ccceEEecCCCCCCCCCCceeeeee
Q psy2779          70 RGGRAVAGGRTKCPKPPNTSMIIDS   94 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~~~~~~   94 (101)
                      +++-+|++|+||||||-+-..+++.
T Consensus       161 ~~~nilI~G~tGSGKTTll~aLl~~  185 (344)
T PRK13851        161 GRLTMLLCGPTGSGKTTMSKTLISA  185 (344)
T ss_pred             cCCeEEEECCCCccHHHHHHHHHcc
Confidence            5778999999999998665544443

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=84.00  E-value=0.37  Score=40.16  Aligned_cols=25  Identities=28%  Similarity=0.315  Sum_probs=20.8

Q ss_pred             ccccccceEEecCCCCCCCCCCcee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      +....|..+|+.|+||||||.+..-
T Consensus       268 GG~~~g~~~li~G~~G~GKT~l~~~  292 (509)
T PRK09302        268 GGFFRGSIILVSGATGTGKTLLASK  292 (509)
T ss_pred             CCCCCCcEEEEEcCCCCCHHHHHHH
Confidence            4566789999999999999987644

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=83.98  E-value=0.44  Score=37.11  Aligned_cols=40  Identities=8%  Similarity=0.065  Sum_probs=26.6

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCCc
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +-+|||+.+.+..   .+.       ++.+++  ..++|+.||+|+||+.+-
T Consensus         4 ~~i~g~~~~~~~l---~~~-------~~~~~~--~ha~Lf~G~~G~Gk~~la   43 (313)
T PRK05564          4 HTIIGHENIKNRI---KNS-------IIKNRF--SHAHIIVGEDGIGKSLLA   43 (313)
T ss_pred             hhccCcHHHHHHH---HHH-------HHcCCC--CceEEeECCCCCCHHHHH
Confidence            4578999987652   233       233332  457899999999987543

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=83.97  E-value=0.6  Score=30.82  Aligned_cols=15  Identities=13%  Similarity=0.040  Sum_probs=13.4

Q ss_pred             ceEEecCCCCCCCCC
Q psy2779          72 GRAVAGGRTKCPKPP   86 (101)
Q Consensus        72 ~~ll~~G~p~~g~~~   86 (101)
                      +.+++.|++|||||=
T Consensus        25 ~~~~i~~~~GsGKT~   39 (201)
T smart00487       25 RDVILAAPTGSGKTL   39 (201)
T ss_pred             CcEEEECCCCCchhH
Confidence            678899999999985

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=83.94  E-value=0.47  Score=38.72  Aligned_cols=19  Identities=21%  Similarity=0.081  Sum_probs=15.3

Q ss_pred             cceEEecCCCCCCCCCCce
Q psy2779          71 GGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~~   89 (101)
                      ++-+|++|+||||||-+..
T Consensus       144 ~~nilI~G~tGSGKTTll~  162 (323)
T PRK13833        144 RLNIVISGGTGSGKTTLAN  162 (323)
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            5568899999999986543

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=83.93  E-value=0.55  Score=41.12  Aligned_cols=52  Identities=12%  Similarity=-0.012  Sum_probs=28.4

Q ss_pred             ccCcccchHHHHhhcceeeecccceee-eeccccccccceEEecCCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFE-RCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~-~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .-+.++|..++.+.+-=.+.+- +..- ..+.-..-.++-+|+.||||||||-.
T Consensus       176 ~~~di~G~~~~~~~l~~~i~~~-~~~~~~~~~~gi~~~~giLL~GppGtGKT~l  228 (733)
T TIGR01243       176 TYEDIGGLKEAKEKIREMVELP-MKHPELFEHLGIEPPKGVLLYGPPGTGKTLL  228 (733)
T ss_pred             CHHHhcCHHHHHHHHHHHHHHH-hhCHHHHHhcCCCCCceEEEECCCCCChHHH
Confidence            3445778877766554333320 0000 00111223456788999999999854

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.

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=83.85  E-value=0.49  Score=41.58  Aligned_cols=39  Identities=21%  Similarity=0.115  Sum_probs=26.1

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+.+.+-.   ..+       +.++++  ..++|+.||||+||+.
T Consensus        15 f~~liGq~~i~~~L---~~~-------l~~~rl--~~a~Lf~Gp~G~GKtt   53 (620)
T PRK14948         15 FDELVGQEAIATTL---KNA-------LISNRI--APAYLFTGPRGTGKTS   53 (620)
T ss_pred             HhhccChHHHHHHH---HHH-------HHcCCC--CceEEEECCCCCChHH
Confidence            46689999886642   222       222232  3578999999999984

>PRK08727 hypothetical protein; Validated

Probab=83.67  E-value=0.44  Score=35.95  Aligned_cols=16  Identities=13%  Similarity=-0.045  Sum_probs=13.4

Q ss_pred             ceEEecCCCCCCCCCC
Q psy2779          72 GRAVAGGRTKCPKPPN   87 (101)
Q Consensus        72 ~~ll~~G~p~~g~~~~   87 (101)
                      ..+++.|++|||||=.
T Consensus        42 ~~l~l~G~~G~GKThL   57 (233)
T PRK08727         42 DWLYLSGPAGTGKTHL   57 (233)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4589999999999843

>PLN02165 adenylate isopentenyltransferase

Probab=83.66  E-value=0.54  Score=39.00  Aligned_cols=16  Identities=25%  Similarity=0.102  Sum_probs=14.4

Q ss_pred             cceEEecCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPP   86 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~   86 (101)
                      |.+++|.||||||||-
T Consensus        43 g~iivIiGPTGSGKSt   58 (334)
T PLN02165         43 DKVVVIMGATGSGKSR   58 (334)
T ss_pred             CCEEEEECCCCCcHHH
Confidence            7799999999999973

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=83.59  E-value=0.5  Score=32.37  Aligned_cols=15  Identities=13%  Similarity=0.167  Sum_probs=12.0

Q ss_pred             cceEEecCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKP   85 (101)
Q Consensus        71 g~~ll~~G~p~~g~~   85 (101)
                      ..-+|+.|+|||||.
T Consensus        21 ~~pvli~GE~GtGK~   35 (138)
T PF14532_consen   21 SSPVLITGEPGTGKS   35 (138)
T ss_dssp             SS-EEEECCTTSSHH
T ss_pred             CCcEEEEcCCCCCHH
Confidence            456889999999974

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=83.58  E-value=0.82  Score=33.23  Aligned_cols=24  Identities=21%  Similarity=0.076  Sum_probs=18.7

Q ss_pred             ccccceEEecCCCCCCCCCCceee
Q psy2779          68 LFRGGRAVAGGRTKCPKPPNTSMI   91 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~~~~~~   91 (101)
                      +-.|..+++.||+||||+-+-.++
T Consensus        26 l~~~~~~~l~G~Ng~GKStll~~i   49 (202)
T cd03243          26 LGSGRLLLITGPNMGGKSTYLRSI   49 (202)
T ss_pred             EcCCeEEEEECCCCCccHHHHHHH
Confidence            335689999999999998665544

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=83.49  E-value=0.68  Score=34.15  Aligned_cols=25  Identities=16%  Similarity=-0.064  Sum_probs=19.4

Q ss_pred             cccccceEEecCCCCCCCCCCceee
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTSMI   91 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~~~   91 (101)
                      ..-.|.++.+.||+|||||-.-.++
T Consensus        17 ~i~~G~~~~l~G~nG~GKSTLl~~i   41 (176)
T cd03238          17 SIPLNVLVVVTGVSGSGKSTLVNEG   41 (176)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHH
Confidence            4456899999999999998654433

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>PRK11823 DNA repair protein RadA; Provisional

Probab=83.39  E-value=0.54  Score=39.40  Aligned_cols=27  Identities=19%  Similarity=0.201  Sum_probs=20.6

Q ss_pred             ccccccceEEecCCCCCCCCCCceeee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      +....|.++|+.|+||+|||-+...+.
T Consensus        75 GGi~~Gs~~lI~G~pG~GKTtL~lq~a  101 (446)
T PRK11823         75 GGLVPGSVVLIGGDPGIGKSTLLLQVA  101 (446)
T ss_pred             CCccCCEEEEEECCCCCCHHHHHHHHH
Confidence            355567899999999999987654443

>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]

Probab=83.33  E-value=0.6  Score=38.76  Aligned_cols=24  Identities=25%  Similarity=0.267  Sum_probs=18.7

Q ss_pred             cccccceEEecCCCCCCCCCCcee
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      +.-.|..+++-||.||||+-+--|
T Consensus        25 ~i~~Gef~vllGPSGcGKSTlLr~   48 (338)
T COG3839          25 DIEDGEFVVLLGPSGCGKSTLLRM   48 (338)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHH
Confidence            455688999999999999754433

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=83.25  E-value=0.58  Score=39.88  Aligned_cols=19  Identities=21%  Similarity=0.179  Sum_probs=15.7

Q ss_pred             ccceEEecCCCCCCCCCCc
Q psy2779          70 RGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~   88 (101)
                      ..+++|++||||||||-..
T Consensus       241 ~~GlilitGptGSGKTTtL  259 (486)
T TIGR02533       241 PHGIILVTGPTGSGKTTTL  259 (486)
T ss_pred             CCCEEEEEcCCCCCHHHHH
Confidence            4678999999999998544

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>PRK07667 uridine kinase; Provisional

Probab=83.19  E-value=0.35  Score=35.33  Aligned_cols=19  Identities=11%  Similarity=-0.090  Sum_probs=15.6

Q ss_pred             cceEEecCCCCCCCCCCce
Q psy2779          71 GGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~~   89 (101)
                      ..++.++|+||||||.++.
T Consensus        17 ~~iIgI~G~~gsGKStla~   35 (193)
T PRK07667         17 RFILGIDGLSRSGKTTFVA   35 (193)
T ss_pred             CEEEEEECCCCCCHHHHHH
Confidence            3677899999999998654

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=83.19  E-value=0.59  Score=36.57  Aligned_cols=20  Identities=25%  Similarity=0.280  Sum_probs=16.2

Q ss_pred             ccceEEecCCCCCCCCCCce
Q psy2779          70 RGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~   89 (101)
                      .++++++.||+|+|||-...
T Consensus       193 ~~~vi~~vGptGvGKTTt~~  212 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLA  212 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            47799999999999985443

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=83.15  E-value=0.36  Score=43.04  Aligned_cols=39  Identities=13%  Similarity=0.210  Sum_probs=25.9

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+.+.+   ++..+       +++++.  --++|+.||||||||-
T Consensus        15 f~dIiGQe~v~~---~L~~a-------i~~~ri--~ha~Lf~GPpG~GKTt   53 (624)
T PRK14959         15 FAEVAGQETVKA---ILSRA-------AQENRV--APAYLFSGTRGVGKTT   53 (624)
T ss_pred             HHHhcCCHHHHH---HHHHH-------HHcCCC--CceEEEECCCCCCHHH
Confidence            467899998733   33344       333332  2478899999999974

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

Probab=83.10  E-value=0.38  Score=35.30  Aligned_cols=17  Identities=18%  Similarity=0.092  Sum_probs=12.8

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      +.-|++.|+||||||=.
T Consensus        47 ~~~l~l~G~~G~GKThL   63 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHL   63 (178)
T ss_dssp             --EEEEEESTTSSHHHH
T ss_pred             CeEEEEEhhHhHHHHHH
Confidence            44588999999999844

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.

>PF13476 AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V_A 3QG5_B 3QF7_A 3THO_A

Probab=83.09  E-value=0.66  Score=31.80  Aligned_cols=18  Identities=28%  Similarity=0.283  Sum_probs=14.0

Q ss_pred             cccceEEecCCCCCCCCC
Q psy2779          69 FRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~~   86 (101)
                      |..++-++.||+|||||-
T Consensus        17 f~~g~~vi~G~Ng~GKSt   34 (202)
T PF13476_consen   17 FSPGLNVIYGPNGSGKST   34 (202)
T ss_dssp             --SEEEEEEESTTSSHHH
T ss_pred             cCCCcEEEECCCCCCHHH
Confidence            356789999999999964

>KOG0989|consensus

Probab=83.05  E-value=0.56  Score=39.75  Aligned_cols=38  Identities=16%  Similarity=-0.033  Sum_probs=24.1

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-++||+.+-.+.-   .-       ++  + .-.-.+|+-||||||||-
T Consensus        35 ~de~~gQe~vV~~L~---~a-------~~--~-~~lp~~LFyGPpGTGKTS   72 (346)
T KOG0989|consen   35 FDELAGQEHVVQVLK---NA-------LL--R-RILPHYLFYGPPGTGKTS   72 (346)
T ss_pred             HHhhcchHHHHHHHH---HH-------Hh--h-cCCceEEeeCCCCCcHhH
Confidence            577899987543321   00       11  1 124568899999999984

>TIGR00665 DnaB replicative DNA helicase

Probab=83.04  E-value=0.64  Score=37.72  Aligned_cols=26  Identities=15%  Similarity=0.050  Sum_probs=21.2

Q ss_pred             cccccceEEecCCCCCCCCCCceeee
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      .+-.|..++++|+||+|||-|...++
T Consensus       191 G~~~G~l~vi~g~pg~GKT~~~l~~a  216 (434)
T TIGR00665       191 GLQPSDLIILAARPSMGKTAFALNIA  216 (434)
T ss_pred             CCCCCeEEEEEeCCCCChHHHHHHHH
Confidence            45668899999999999998876544

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=82.86  E-value=0.25  Score=40.05  Aligned_cols=24  Identities=17%  Similarity=0.149  Sum_probs=18.3

Q ss_pred             ccceEEecCCCCCCCCCCceeeee
Q psy2779          70 RGGRAVAGGRTKCPKPPNTSMIID   93 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~~~~~   93 (101)
                      +++-+|++|+||||||-+.-.+++
T Consensus       159 ~~~nili~G~tgSGKTTll~aL~~  182 (332)
T PRK13900        159 SKKNIIISGGTSTGKTTFTNAALR  182 (332)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHh
Confidence            477889999999999866544333

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=82.83  E-value=0.6  Score=40.18  Aligned_cols=18  Identities=22%  Similarity=0.222  Sum_probs=15.5

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      ..+.+|++||||||||-.
T Consensus       315 ~~Glilv~G~tGSGKTTt  332 (564)
T TIGR02538       315 PQGMVLVTGPTGSGKTVS  332 (564)
T ss_pred             cCCeEEEECCCCCCHHHH
Confidence            468899999999999854

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=82.72  E-value=0.75  Score=41.64  Aligned_cols=44  Identities=14%  Similarity=-0.079  Sum_probs=27.7

Q ss_pred             CcccchHHHHhhcceeeecccceeee--eccccccccceEEecCCCCCCCCCCce
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFER--CKSHSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~--~~~~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      .-+.|++++-+..   |+-     .+  .+. -.-.+++|++.||||+|||.+..
T Consensus        76 ~d~yGlee~ieri---v~~-----l~~Aa~g-l~~~~~IL~LvGPpG~GKSsLa~  121 (644)
T PRK15455         76 EEFYGMEEAIEQI---VSY-----FRHAAQG-LEEKKQILYLLGPVGGGKSSLAE  121 (644)
T ss_pred             hcccCcHHHHHHH---HHH-----HHHHHHh-cCCCCceEEEecCCCCCchHHHH
Confidence            3578999887752   121     10  000 01147899999999999987644

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=82.69  E-value=0.63  Score=38.88  Aligned_cols=22  Identities=32%  Similarity=0.318  Sum_probs=17.6

Q ss_pred             ccccceEEecCCCCCCCCCCce
Q psy2779          68 LFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      ...|+++++.||||+|||-...
T Consensus       134 ~~~g~ii~lvGptGvGKTTtia  155 (374)
T PRK14722        134 MERGGVFALMGPTGVGKTTTTA  155 (374)
T ss_pred             ccCCcEEEEECCCCCCHHHHHH
Confidence            3458899999999999985443

>KOG0741|consensus

Probab=82.44  E-value=0.67  Score=42.32  Aligned_cols=48  Identities=21%  Similarity=0.306  Sum_probs=29.6

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccc-------cccc--------------------cceEEecCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSH-------SLFR--------------------GGRAVAGGRTKCPKP   85 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~-------~~~~--------------------g~~ll~~G~p~~g~~   85 (101)
                      =-++|+-+-|.+.-+|.+- .|.|+..-=+       ++|+                    =+=+|+-||||||||
T Consensus       196 lnL~~~~~~k~~~n~ii~P-df~Fe~mGIGGLd~EFs~IFRRAFAsRvFpp~vie~lGi~HVKGiLLyGPPGTGKT  270 (744)
T KOG0741|consen  196 LNLIGKSKTKPASNSIINP-DFNFESMGIGGLDKEFSDIFRRAFASRVFPPEVIEQLGIKHVKGILLYGPPGTGKT  270 (744)
T ss_pred             eEeeccccccchhccccCC-CCChhhcccccchHHHHHHHHHHHHhhcCCHHHHHHcCccceeeEEEECCCCCChh
Confidence            3467777777777777765 5666543111       1111                    123679999999997

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=82.35  E-value=0.5  Score=41.24  Aligned_cols=40  Identities=15%  Similarity=0.159  Sum_probs=27.1

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +.+-+|||+.+.+..--.+          +++++  ..++|+.||||+|||-
T Consensus        12 ~fdeiiGqe~v~~~L~~~I----------~~grl--~hayLf~Gp~G~GKTt   51 (535)
T PRK08451         12 HFDELIGQESVSKTLSLAL----------DNNRL--AHAYLFSGLRGSGKTS   51 (535)
T ss_pred             CHHHccCcHHHHHHHHHHH----------HcCCC--CeeEEEECCCCCcHHH
Confidence            3567999999875543222          22332  4567899999999874

>PRK09354 recA recombinase A; Provisional

Probab=82.22  E-value=0.68  Score=38.48  Aligned_cols=27  Identities=22%  Similarity=0.070  Sum_probs=21.1

Q ss_pred             ccccccceEEecCCCCCCCCCCceeee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      +..-.|++.++.||||||||-+.-.++
T Consensus        55 GGip~G~IteI~G~~GsGKTtLal~~~   81 (349)
T PRK09354         55 GGLPRGRIVEIYGPESSGKTTLALHAI   81 (349)
T ss_pred             CCCcCCeEEEEECCCCCCHHHHHHHHH
Confidence            456668899999999999997655433

>PTZ00035 Rad51 protein; Provisional

Probab=82.21  E-value=0.86  Score=36.96  Aligned_cols=22  Identities=14%  Similarity=0.018  Sum_probs=18.3

Q ss_pred             cccccceEEecCCCCCCCCCCc
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      ..-.|.+..+.|+||||||-+.
T Consensus       114 Gi~~G~iteI~G~~GsGKT~l~  135 (337)
T PTZ00035        114 GIETGSITELFGEFRTGKTQLC  135 (337)
T ss_pred             CCCCCeEEEEECCCCCchhHHH
Confidence            4556788999999999999765

>KOG0739|consensus

Probab=81.86  E-value=0.98  Score=39.05  Aligned_cols=43  Identities=16%  Similarity=-0.008  Sum_probs=28.2

Q ss_pred             cchHHHHhhcc--eeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          40 VGQQAAREVSR--AVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        40 VGQ~~AREAaG--IVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      -|-+.|.||..  +|+-+|.-||   =++++.-=+.+|+-|||||||.
T Consensus       136 AGLE~AKeALKEAVILPIKFPql---FtGkR~PwrgiLLyGPPGTGKS  180 (439)
T KOG0739|consen  136 AGLEGAKEALKEAVILPIKFPQL---FTGKRKPWRGILLYGPPGTGKS  180 (439)
T ss_pred             ccchhHHHHHHhheeecccchhh---hcCCCCcceeEEEeCCCCCcHH
Confidence            35566666653  5666644444   3446555677899999999984

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=81.77  E-value=0.65  Score=37.52  Aligned_cols=24  Identities=21%  Similarity=0.144  Sum_probs=18.0

Q ss_pred             ccceEEecCCCCCCCCCCceeeee
Q psy2779          70 RGGRAVAGGRTKCPKPPNTSMIID   93 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~~~~~   93 (101)
                      +++-+|++|+||||||-+...+++
T Consensus       147 ~~~~ilI~G~tGSGKTTll~aL~~  170 (319)
T PRK13894        147 AHRNILVIGGTGSGKTTLVNAIIN  170 (319)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHH
Confidence            467788999999999965544443

>TIGR00376 DNA helicase, putative

Probab=81.67  E-value=0.64  Score=40.81  Aligned_cols=22  Identities=14%  Similarity=0.034  Sum_probs=16.1

Q ss_pred             cceEEecCCCCCCCCCCceeee
Q psy2779          71 GGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      ...+|+-||||||||-.-.-++
T Consensus       173 ~~~~lI~GpPGTGKT~t~~~ii  194 (637)
T TIGR00376       173 KDLFLIHGPPGTGKTRTLVELI  194 (637)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHH
Confidence            3678899999999985433333

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

>KOG0735|consensus

Probab=81.59  E-value=0.34  Score=45.29  Aligned_cols=25  Identities=20%  Similarity=0.118  Sum_probs=19.5

Q ss_pred             cceEEecCCCCCCCCCCceeeeeee
Q psy2779          71 GGRAVAGGRTKCPKPPNTSMIIDSW   95 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~~~~~~~~   95 (101)
                      ..=+|+-||||||||-..|-++.+|
T Consensus       701 ~~giLLyGppGcGKT~la~a~a~~~  725 (952)
T KOG0735|consen  701 RTGILLYGPPGCGKTLLASAIASNS  725 (952)
T ss_pred             ccceEEECCCCCcHHHHHHHHHhhC
Confidence            3346799999999998877776665

>PRK09087 hypothetical protein; Validated

Probab=81.46  E-value=0.76  Score=34.92  Aligned_cols=50  Identities=14%  Similarity=-0.012  Sum_probs=29.0

Q ss_pred             cCCCCCCcccccCcccc-hHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          25 GLKENGEANEMAAGLVG-QQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        25 GLde~g~a~~~a~GlVG-Q~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      -|+=...+.+..+-||. ..+ ++|..++.+.       . + .  ....+++.||+|||||=
T Consensus         9 ~l~~~~~~~~~~~~Fi~~~~N-~~a~~~l~~~-------~-~-~--~~~~l~l~G~~GsGKTh   59 (226)
T PRK09087          9 PLNFSHDPAYGRDDLLVTESN-RAAVSLVDHW-------P-N-W--PSPVVVLAGPVGSGKTH   59 (226)
T ss_pred             eeCCCCCCCCChhceeecCch-HHHHHHHHhc-------c-c-C--CCCeEEEECCCCCCHHH
Confidence            34433444556677764 434 3354444443       1 1 1  25678999999999974

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=81.44  E-value=0.6  Score=41.19  Aligned_cols=26  Identities=12%  Similarity=0.147  Sum_probs=18.9

Q ss_pred             ccceEEecCCCCCCCCCCceeeeeee
Q psy2779          70 RGGRAVAGGRTKCPKPPNTSMIIDSW   95 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~~~~~~~   95 (101)
                      ..+..++.|+||||||-....++..+
T Consensus       166 ~~~~~vItGgpGTGKTt~v~~ll~~l  191 (615)
T PRK10875        166 TRRISVISGGPGTGKTTTVAKLLAAL  191 (615)
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHHHH
Confidence            36789999999999985544444443

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=81.39  E-value=0.81  Score=33.30  Aligned_cols=19  Identities=16%  Similarity=-0.003  Sum_probs=15.5

Q ss_pred             ceEEecCCCCCCCCCCcee
Q psy2779          72 GRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        72 ~~ll~~G~p~~g~~~~~~~   90 (101)
                      +++++.||+|+||+-+--+
T Consensus        29 ~~~~ltG~Ng~GKStll~~   47 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKT   47 (200)
T ss_pred             eEEEEECCCCCChHHHHHH
Confidence            6899999999999865443

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, a

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=81.29  E-value=0.54  Score=39.20  Aligned_cols=47  Identities=13%  Similarity=-0.076  Sum_probs=26.2

Q ss_pred             CCcccccCccc-chHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          30 GEANEMAAGLV-GQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        30 g~a~~~a~GlV-GQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .++.+..+-|| |..+ +.|...+..+       .++...  -.-+++.||||||||-
T Consensus        98 l~~~~tFdnFv~g~~n-~~a~~~~~~~-------~~~~~~--~n~l~lyG~~G~GKTH  145 (440)
T PRK14088         98 LNPDYTFENFVVGPGN-SFAYHAALEV-------AKNPGR--YNPLFIYGGVGLGKTH  145 (440)
T ss_pred             CCCCCcccccccCCch-HHHHHHHHHH-------HhCcCC--CCeEEEEcCCCCcHHH
Confidence            45556666666 5433 2333333333       221111  2358999999999974

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

Probab=81.28  E-value=0.68  Score=40.12  Aligned_cols=16  Identities=13%  Similarity=0.048  Sum_probs=14.3

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      .++-+++.|+||||||
T Consensus       193 ~~~~iil~GppGtGKT  208 (459)
T PRK11331        193 IKKNIILQGPPGVGKT  208 (459)
T ss_pred             cCCCEEEECCCCCCHH
Confidence            5778889999999998

>PHA02244 ATPase-like protein

Probab=81.26  E-value=0.67  Score=39.39  Aligned_cols=16  Identities=13%  Similarity=-0.045  Sum_probs=13.5

Q ss_pred             cceEEecCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPP   86 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~   86 (101)
                      +.-+||.||||||||-
T Consensus       119 ~~PVLL~GppGtGKTt  134 (383)
T PHA02244        119 NIPVFLKGGAGSGKNH  134 (383)
T ss_pred             CCCEEEECCCCCCHHH
Confidence            5568899999999973

>TIGR00416 sms DNA repair protein RadA

Probab=81.19  E-value=0.72  Score=38.91  Aligned_cols=26  Identities=15%  Similarity=0.189  Sum_probs=20.7

Q ss_pred             ccccccceEEecCCCCCCCCCCceee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSMI   91 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~~   91 (101)
                      +....|.++|++|+||+|||=+.-.+
T Consensus        89 GGi~~GsvilI~G~pGsGKTTL~lq~  114 (454)
T TIGR00416        89 GGIVPGSLILIGGDPGIGKSTLLLQV  114 (454)
T ss_pred             CCccCCeEEEEEcCCCCCHHHHHHHH
Confidence            35667889999999999998765443

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=81.17  E-value=0.49  Score=34.22  Aligned_cols=23  Identities=13%  Similarity=-0.025  Sum_probs=18.7

Q ss_pred             cccceEEecCCCCCCCCCCceee
Q psy2779          69 FRGGRAVAGGRTKCPKPPNTSMI   91 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~~~~~~~   91 (101)
                      ..|.++++.|+.|||||-|+..+
T Consensus        20 ~~~~~i~l~G~lGaGKTtl~~~l   42 (133)
T TIGR00150        20 DFGTVVLLKGDLGAGKTTLVQGL   42 (133)
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHH
Confidence            35789999999999998776544

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=80.99  E-value=0.61  Score=37.59  Aligned_cols=18  Identities=11%  Similarity=-0.202  Sum_probs=14.6

Q ss_pred             cceEEecCCCCCCCCCCc
Q psy2779          71 GGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~   88 (101)
                      ...+++.|+||||||-..
T Consensus       136 ~n~l~l~G~~G~GKThL~  153 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLL  153 (405)
T ss_pred             CCeEEEECCCCCcHHHHH
Confidence            356899999999998554

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).

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

Probab=80.96  E-value=0.6  Score=41.11  Aligned_cols=38  Identities=16%  Similarity=0.203  Sum_probs=23.3

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +-+|||++--+-  + +++     . + . +  ...-+|+.||||||||-.
T Consensus       182 ~~~igr~~ei~~--~-~~~-----L-~-~-~--~~~n~lL~G~pG~GKT~l  219 (731)
T TIGR02639       182 DPLIGREDELER--T-IQV-----L-C-R-R--KKNNPLLVGEPGVGKTAI  219 (731)
T ss_pred             CcccCcHHHHHH--H-HHH-----H-h-c-C--CCCceEEECCCCCCHHHH
Confidence            468888876663  2 232     1 1 1 1  234467899999999754

>PRK05748 replicative DNA helicase; Provisional

Probab=80.83  E-value=0.98  Score=37.22  Aligned_cols=26  Identities=15%  Similarity=0.078  Sum_probs=21.3

Q ss_pred             cccccceEEecCCCCCCCCCCceeee
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      .+-.|..++++|+||+|||-|..-++
T Consensus       199 G~~~G~livIaarpg~GKT~~al~ia  224 (448)
T PRK05748        199 GLQPNDLIIVAARPSVGKTAFALNIA  224 (448)
T ss_pred             CCCCCceEEEEeCCCCCchHHHHHHH
Confidence            56678899999999999998765444

>KOG3078|consensus

Probab=80.72  E-value=0.65  Score=37.09  Aligned_cols=26  Identities=23%  Similarity=0.224  Sum_probs=22.3

Q ss_pred             cceEEecCCCCCCCCCCceeeeeeec
Q psy2779          71 GGRAVAGGRTKCPKPPNTSMIIDSWV   96 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~~~~~~~~~   96 (101)
                      +..+++-|+||+||.|++.++.+.|-
T Consensus        15 ~~~~v~~G~pg~gkgt~a~~l~~~~~   40 (235)
T KOG3078|consen   15 GVRAVLLGAPGSGKGTQAPRLTKNFG   40 (235)
T ss_pred             ceEEEEEeCCCCCCCccCHHHHHhcC
Confidence            56677899999999999999888773

>PRK06547 hypothetical protein; Provisional

Probab=80.64  E-value=0.72  Score=33.82  Aligned_cols=21  Identities=14%  Similarity=0.109  Sum_probs=16.1

Q ss_pred             cceEEecCCCCCCCCCCceee
Q psy2779          71 GGRAVAGGRTKCPKPPNTSMI   91 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~~~~   91 (101)
                      -.++++.|++|||||-++..+
T Consensus        15 ~~~i~i~G~~GsGKTt~a~~l   35 (172)
T PRK06547         15 MITVLIDGRSGSGKTTLAGAL   35 (172)
T ss_pred             CEEEEEECCCCCCHHHHHHHH
Confidence            346778899999998766543

>KOG1807|consensus

Probab=80.57  E-value=0.2  Score=46.93  Aligned_cols=40  Identities=23%  Similarity=0.130  Sum_probs=32.6

Q ss_pred             cceeeeeccccccccceEEecCCCCCCCCCCceeeeeeecccC
Q psy2779          57 SFQFERCKSHSLFRGGRAVAGGRTKCPKPPNTSMIIDSWVEGS   99 (101)
Q Consensus        57 ~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~~~~~~~~~~~~   99 (101)
                      |-||..+   +++..+.-|+-|||||||+=-|+-|+|.-.+.+
T Consensus       382 Sq~~A~q---s~ltyelsliqgppGTgkt~vtlkav~tLL~n~  421 (1025)
T KOG1807|consen  382 SQQFAKQ---SKLTYELSLIQGPPGTGKTLVTLKAVDTLLLNS  421 (1025)
T ss_pred             HHHHHHH---HHhhhhhheeecCCCCCceeehHHHHHHHHhcc
Confidence            4566667   777899999999999999999999888655443

>cd03278 ABC_SMC_barmotin Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function

Probab=80.51  E-value=1.1  Score=33.02  Aligned_cols=17  Identities=18%  Similarity=0.073  Sum_probs=14.2

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .| ++++.||+||||+-.
T Consensus        22 ~g-~~~i~G~nGsGKStl   38 (197)
T cd03278          22 PG-LTAIVGPNGSGKSNI   38 (197)
T ss_pred             CC-cEEEECCCCCCHHHH
Confidence            35 889999999999754

Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, w

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=80.38  E-value=0.7  Score=40.54  Aligned_cols=39  Identities=18%  Similarity=0.163  Sum_probs=27.5

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+.+.+.   +.++       ++++++  ..++|+.||+|+||+-
T Consensus        16 f~~viGq~~~~~~---L~~~-------i~~~~l--~hayLf~Gp~G~GKtt   54 (614)
T PRK14971         16 FESVVGQEALTTT---LKNA-------IATNKL--AHAYLFCGPRGVGKTT   54 (614)
T ss_pred             HHHhcCcHHHHHH---HHHH-------HHcCCC--CeeEEEECCCCCCHHH
Confidence            4568999999775   3333       333332  4678999999999864

>KOG0736|consensus

Probab=80.26  E-value=0.79  Score=43.05  Aligned_cols=13  Identities=15%  Similarity=0.020  Sum_probs=11.4

Q ss_pred             eEEecCCCCCCCC
Q psy2779          73 RAVAGGRTKCPKP   85 (101)
Q Consensus        73 ~ll~~G~p~~g~~   85 (101)
                      =+|+-||||||||
T Consensus       707 GILLYGPPGTGKT  719 (953)
T KOG0736|consen  707 GILLYGPPGTGKT  719 (953)
T ss_pred             eeEEECCCCCchH
Confidence            3679999999998

>KOG0737|consensus

Probab=80.23  E-value=0.62  Score=39.91  Aligned_cols=14  Identities=14%  Similarity=-0.007  Sum_probs=11.9

Q ss_pred             ceEEecCCCCCCCC
Q psy2779          72 GRAVAGGRTKCPKP   85 (101)
Q Consensus        72 ~~ll~~G~p~~g~~   85 (101)
                      +-+|+-||||||||
T Consensus       128 kGiLL~GPpG~GKT  141 (386)
T KOG0737|consen  128 KGILLYGPPGTGKT  141 (386)
T ss_pred             ccceecCCCCchHH
Confidence            45679999999987

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=80.20  E-value=0.79  Score=37.85  Aligned_cols=23  Identities=22%  Similarity=0.234  Sum_probs=18.5

Q ss_pred             ccccccceEEecCCCCCCCCCCc
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +.+..|.++|++|+||+||+=+.
T Consensus        77 GGi~~GslvLI~G~pG~GKStLl   99 (372)
T cd01121          77 GGLVPGSVILIGGDPGIGKSTLL   99 (372)
T ss_pred             CCccCCeEEEEEeCCCCCHHHHH
Confidence            34566889999999999998643

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.

>PTZ00202 tuzin; Provisional

Probab=80.18  E-value=0.93  Score=40.43  Aligned_cols=42  Identities=19%  Similarity=0.124  Sum_probs=30.9

Q ss_pred             ccCcccchHHHHhhcceeee-cccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTW-EKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVd-m~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      ...+|||.+..-.+..-+++ +           ..-..++++++|++|||||-.
T Consensus       260 ~~~~FVGReaEla~Lr~VL~~~-----------d~~~privvLtG~~G~GKTTL  302 (550)
T PTZ00202        260 VIRQFVSREAEESWVRQVLRRL-----------DTAHPRIVVFTGFRGCGKSSL  302 (550)
T ss_pred             CccCCCCcHHHHHHHHHHHhcc-----------CCCCceEEEEECCCCCCHHHH
Confidence            36799999988888776664 3           111235899999999999743

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	101
2c9o_A	456	3d Structure Of The Human Ruvb-Like Helicase Ruvbl1		5e-14
2xsz_A	367	The Dodecameric Human Ruvbl1:ruvbl2 Complex With Tr		3e-13
3uk6_A	368	Crystal Structure Of The Tip48 (Tip49b) Hexamer Len		3e-06
2xsz_D	378	The Dodecameric Human Ruvbl1:ruvbl2 Complex With Tr		6e-06

>pdb|2C9O|A Chain A, 3d Structure Of The Human Ruvb-Like Helicase Ruvbl1 Length = 456

Iteration: 1
 Score = 72.8 bits (177), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 36/47 (76%), Positives = 41/47 (87%)
Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
          MKIEEVKST KTQRI+SHSHVKGLGL E+G A + A+GLVGQ+ ARE
Sbjct: 1  MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENARE 47

>pdb|2XSZ|A Chain A, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated Domains Ii Length = 367

Iteration: 1
 Score = 70.1 bits (170), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 35/46 (76%), Positives = 40/46 (86%)
Query: 2  KIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
          KIEEVKST KTQRI+SHSHVKGLGL E+G A + A+GLVGQ+ ARE
Sbjct: 16 KIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENARE 61

>pdb|3UK6|A Chain A, Crystal Structure Of The Tip48 (Tip49b) Hexamer Length = 368

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 20/51 (39%), Positives = 33/51 (64%)
Query: 2  KIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAV 52
          K+ E++   + +RI +HSH++GLGL +  E  + + G+VGQ AAR  +  V
Sbjct: 9  KVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVV 59

>pdb|2XSZ|D Chain D, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated Domains Ii Length = 378

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 20/51 (39%), Positives = 32/51 (62%)
Query: 2  KIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAV 52
          K+ E++   + +RI +HSH++GLGL +  E  + + G VGQ AAR  +  V
Sbjct: 24 KVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGXVGQLAARRAAGVV 74
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	101
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	2e-18
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	3e-14

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D* Length = 368

 Score = 77.3 bits (190), Expect = 2e-18
 Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 5/85 (5%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQF 60
           K+ E++   + +RI +HSH++GLGL +  E  + + G+VGQ AAR  +      +  + 
Sbjct: 8  TKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAG--VVLEMIRE 65

Query: 61 ERCKSHS-LFRGGRAVAGGRTKCPK 84
           +    + L  G      G+T    
Sbjct: 66 GKIAGRAVLIAGQPGT--GKTAIAM 88

>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* Length = 456

 Score = 65.8 bits (160), Expect = 3e-14
 Identities = 36/47 (76%), Positives = 41/47 (87%)

Query: 1  MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAARE 47
          MKIEEVKST KTQRI+SHSHVKGLGL E+G A + A+GLVGQ+ ARE
Sbjct: 1  MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENARE 47

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	101
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.56
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.52
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.69
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	96.61
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	96.27
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	96.18
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	96.17
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	96.06
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	96.04
3bos_A	242	Putative DNA replication factor; P-loop containing	95.92
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	95.92
3pvs_A	447	Replication-associated recombination protein A; ma	95.9
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	95.89
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	95.89
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	95.78
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	95.71
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	95.7
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	95.64
2r44_A	331	Uncharacterized protein; putative ATPase, structur	95.63
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	95.61
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	95.59
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	95.47
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	95.46
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	95.41
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	95.34
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	95.23
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	95.22
2chg_A	226	Replication factor C small subunit; DNA-binding pr	95.21
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	95.1
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	95.08
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	95.03
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	94.86
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	94.86
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	94.6
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	94.6
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	94.49
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	94.47
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	94.43
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	94.42
2chq_A	319	Replication factor C small subunit; DNA-binding pr	94.42
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	94.36
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	94.35
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	94.27
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	94.2
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	94.12
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	94.1
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	94.09
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	94.06
3co5_A	143	Putative two-component system transcriptional RES	94.01
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	93.98
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	93.92
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	93.9
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	93.85
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	93.84
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	93.79
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	93.77
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	93.71
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	93.67
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	93.61
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	93.36
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	93.34
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	93.07
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	93.05
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	93.04
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	93.02
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	92.98
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	92.97
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	92.9
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	92.85
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	92.72
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	92.69
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	92.41
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	92.37
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	92.29
2cvh_A	220	DNA repair and recombination protein RADB; filamen	92.25
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	92.22
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	92.1
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	92.07
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	92.05
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	92.04
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	91.93
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	91.92
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	91.86
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	91.85
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	91.84
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	91.77
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	91.7
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	91.6
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	91.58
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	91.53
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	91.46
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	91.45
2vli_A	183	Antibiotic resistance protein; transferase, tunica	91.25
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	91.03
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	91.01
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	90.98
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	90.92
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	90.85
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	90.83
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	90.75
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	90.7
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	90.47
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	90.43
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	90.4
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	90.4
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	90.36
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	90.35
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	90.24
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	90.17
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	90.06
4a74_A	231	DNA repair and recombination protein RADA; hydrola	89.85
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	89.57
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	89.39
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	89.17
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	89.13
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	89.07
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	88.99
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	88.91
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	88.89
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	88.85
1tue_A	212	Replication protein E1; helicase, replication, E1E	88.82
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	88.47
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	88.43
2qgz_A	308	Helicase loader, putative primosome component; str	88.43
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	88.31
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	88.18
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	88.18
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	88.05
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	88.02
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	87.86
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	87.66
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	87.65
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	87.62
2z43_A	324	DNA repair and recombination protein RADA; archaea	87.43
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	87.25
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	87.05
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	87.03
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	86.9
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	86.75
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	86.64
1via_A	175	Shikimate kinase; structural genomics, transferase	86.53
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	86.46
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	86.26
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	86.22
2eyu_A	261	Twitching motility protein PILT; pilus retraction	86.19
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	86.03
2r6a_A	454	DNAB helicase, replicative helicase; replication,	85.99
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	85.65
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	85.57
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	85.3
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	85.29
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	85.22
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	85.14
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	85.12
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	85.12
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	85.03
1u94_A	356	RECA protein, recombinase A; homologous recombinat	84.85
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	84.76
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	84.68
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	84.63
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	84.62
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	84.61
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	84.59
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	84.58
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	84.56
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	84.44
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	84.05
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	83.95
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	83.81
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	83.7
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	83.62
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	83.52
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	83.44
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	83.37
2ewv_A	372	Twitching motility protein PILT; pilus retraction	83.35
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	83.21
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	83.18
1p9r_A	418	General secretion pathway protein E; bacterial typ	83.02
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	82.9
3kta_A	182	Chromosome segregation protein SMC; structural mai	82.83
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	82.48
2fna_A	357	Conserved hypothetical protein; structural genomic	82.33
1xp8_A	366	RECA protein, recombinase A; recombination, radior	82.03
1yks_A	440	Genome polyprotein [contains: flavivirin protease	81.97
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	81.95
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	81.83
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	81.7
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	81.41
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	81.33
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	81.25
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	81.12
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	80.98
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	80.93
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	80.9
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	80.62
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	80.59
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	80.3

>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=99.56  E-value=2.1e-16  Score=125.13  Aligned_cols=77  Identities=53%  Similarity=0.683  Sum_probs=61.2

Q ss_pred             CccceeecceeeeeeccccccccccCCCCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCC
Q psy2779           1 MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRT   80 (101)
Q Consensus         1 ~~i~ev~~~~r~~RIaaHSHIkGLGLde~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p   80 (101)
                      |+++||+++.+.+|+++||||+|+||++...+.+..+.+|||+++++++..++++       ++.+. ..++-+|+.|||
T Consensus         1 ~~~~~~~~~~~~~~~~~~s~i~~~~l~~~~~~~~~~~~iiG~~~~~~~l~~~~~~-------~~~~~-~~~~~iLl~Gpp   72 (456)
T 2c9o_A            1 MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVEL-------IKSKK-MAGRAVLLAGPP   72 (456)
T ss_dssp             --------CHHHHHHHTTTTCCSCCBCTTSCBCSEETTEESCHHHHHHHHHHHHH-------HHTTC-CTTCEEEEECCT
T ss_pred             CCcccccccccccchhhhhcccCCCCCcccChhhchhhccCHHHHHHHHHHHHHH-------HHhCC-CCCCeEEEECCC
Confidence            5688999988999999999999999999999999999999999999999988888       44433 355678899999


Q ss_pred             CCCCC
Q psy2779          81 KCPKP   85 (101)
Q Consensus        81 ~~g~~   85 (101)
                      |||||
T Consensus        73 GtGKT   77 (456)
T 2c9o_A           73 GTGKT   77 (456)
T ss_dssp             TSSHH
T ss_pred             cCCHH
Confidence            99996

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

Probab=99.52  E-value=1.4e-15  Score=113.16  Aligned_cols=78  Identities=29%  Similarity=0.503  Sum_probs=54.8

Q ss_pred             CccceeecceeeeeeccccccccccCCCCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCC
Q psy2779           1 MKIEEVKSTVKTQRISSHSHVKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRT   80 (101)
Q Consensus         1 ~~i~ev~~~~r~~RIaaHSHIkGLGLde~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p   80 (101)
                      ++++++++..+.+|++.||||+||+|++...|....+.||||++++++...++++       ++..+ ..++.+|+.|||
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~l~l~~~~~p~~~~~~ivG~~~~~~~l~~l~~~-------~~~~~-~~~~~vLl~Gpp   79 (368)
T 3uk6_A            8 TKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEM-------IREGK-IAGRAVLIAGQP   79 (368)
T ss_dssp             ----------------CCTTCCSCCBCTTSCBCSEETTEESCHHHHHHHHHHHHH-------HHTTC-CTTCEEEEEEST
T ss_pred             eeehhccccchhhccchhhhhhccCcccccCcCcchhhccChHHHHHHHHHHHHH-------HHcCC-CCCCEEEEECCC
Confidence            4567888888899999999999999999999999889999999999999999988       54443 346889999999


Q ss_pred             CCCCCC
Q psy2779          81 KCPKPP   86 (101)
Q Consensus        81 ~~g~~~   86 (101)
                      |||||-
T Consensus        80 GtGKT~   85 (368)
T 3uk6_A           80 GTGKTA   85 (368)
T ss_dssp             TSSHHH
T ss_pred             CCCHHH
Confidence            999873

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

Probab=97.69  E-value=4.8e-06  Score=60.20  Aligned_cols=67  Identities=10%  Similarity=0.058  Sum_probs=33.4

Q ss_pred             eeeccccccccccCCCCCCcccccCcccchHHH----HhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          13 QRISSHSHVKGLGLKENGEANEMAAGLVGQQAA----REVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        13 ~RIaaHSHIkGLGLde~g~a~~~a~GlVGQ~~A----REAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      -|-++|++-...|++++--......++|||..+    .+++..++++       ++....-..+.+|+.||||||||-
T Consensus         9 ~~~~~~~~~~~fg~~~~~l~~~~~~~~i~~~~~~~~i~~~~~~l~~~-------l~~~~~~~~~~vLl~G~~GtGKT~   79 (272)
T 1d2n_A            9 HHGSTMDIKPAFGTNQEDYASYIMNGIIKWGDPVTRVLDDGELLVQQ-------TKNSDRTPLVSVLLEGPPHSGKTA   79 (272)
T ss_dssp             ----------------CCSTTTCTTCCCCCSHHHHHHHHHHHHHHHH-------HHHCSSCSEEEEEEECSTTSSHHH
T ss_pred             cCCCccccCCCCCCCHHHHHHHHhcCCCCccHHHHHHHHHHHHHHHH-------HhccCCCCCeEEEEECCCCCcHHH
Confidence            355778888889999876666667899999766    3333334544       322222345678999999999974

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

Probab=96.61  E-value=0.00013  Score=52.37  Aligned_cols=55  Identities=13%  Similarity=-0.061  Sum_probs=32.5

Q ss_pred             CcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          31 EANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        31 ~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .+...-+.++|++++.+..--.+..-...-...+.-.....+-+|+.||||||||
T Consensus        11 ~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT   65 (285)
T 3h4m_A           11 RPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKT   65 (285)
T ss_dssp             SCCCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHH
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHH
Confidence            4455667899999998887544433000000000001224567899999999997

>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=96.27  E-value=0.00088  Score=46.98  Aligned_cols=48  Identities=21%  Similarity=0.099  Sum_probs=28.0

Q ss_pred             cCcccchHHHHhhcceeeec-cc-ceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWE-KS-FQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm-~~-~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-++|++++.+..--+++. +. -.|.+.   ..-..+-+|+.||||||||-
T Consensus         5 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~---g~~~~~~vll~G~~GtGKT~   54 (262)
T 2qz4_A            5 FKDVAGMHEAKLEVREFVDYLKSPERFLQL---GAKVPKGALLLGPPGCGKTL   54 (262)
T ss_dssp             TTSSCSCHHHHHHHHHHHHHHHCCC---------CCCCCEEEEESCTTSSHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHHc---CCCCCceEEEECCCCCCHHH
Confidence            45689999988776544443 00 001110   11234568899999999973

>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=96.18  E-value=0.0015  Score=47.63  Aligned_cols=41  Identities=15%  Similarity=0.021  Sum_probs=26.7

Q ss_pred             ccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          33 NEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        33 ~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+..+.++||.++.++.-  ...       + . .  ..+-+|+.||||||||-
T Consensus        20 ~~~f~~i~G~~~~~~~l~--~~~-------~-~-~--~~~~vLl~G~~GtGKT~   60 (350)
T 1g8p_A           20 VFPFSAIVGQEDMKLALL--LTA-------V-D-P--GIGGVLVFGDRGTGKST   60 (350)
T ss_dssp             CCCGGGSCSCHHHHHHHH--HHH-------H-C-G--GGCCEEEECCGGGCTTH
T ss_pred             CCCchhccChHHHHHHHH--HHh-------h-C-C--CCceEEEECCCCccHHH
Confidence            345567999999888732  112       1 0 1  12338899999999973

>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=96.17  E-value=0.00092  Score=49.99  Aligned_cols=50  Identities=14%  Similarity=0.088  Sum_probs=30.6

Q ss_pred             cccCcccchHHHHhhcceeeecccceeee-eccccccccceEEecCCCCCCCC
Q psy2779          34 EMAAGLVGQQAAREVSRAVTWEKSFQFER-CKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        34 ~~a~GlVGQ~~AREAaGIVVdm~~~~~~~-~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      ..-+.++||+.+.++.--.+.+- ..+-. .+. .....+-+|+.||||||||
T Consensus        15 ~~~~di~G~~~~~~~l~~~i~~~-~~~~~~~~~-~~~~~~~vLl~GppGtGKT   65 (322)
T 3eie_A           15 VKWEDVAGLEGAKEALKEAVILP-VKFPHLFKG-NRKPTSGILLYGPPGTGKS   65 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHH-HHCGGGCCT-TCCCCCEEEEECSSSSCHH
T ss_pred             CCHHHhcChHHHHHHHHHHHHHH-HhCHHHHhc-CCCCCCeEEEECCCCCcHH
Confidence            34567999999998876555220 00000 111 1223456899999999997

>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=96.06  E-value=0.0012  Score=49.82  Aligned_cols=46  Identities=17%  Similarity=0.259  Sum_probs=28.2

Q ss_pred             cccchHHHHhhcceeeecccceeeeeccc-----cccccceEEecCCCCCCCCC
Q psy2779          38 GLVGQQAAREVSRAVTWEKSFQFERCKSH-----SLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        38 GlVGQ~~AREAaGIVVdm~~~~~~~~~~~-----~~~~g~~ll~~G~p~~g~~~   86 (101)
                      -+|||..|.++.-..+..   .+.+.+..     .....+-+|+.||||||||-
T Consensus        16 ~i~G~~~~~~~l~~~i~~---~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~   66 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYN---HYKRLRNGDTSNGVELGKSNILLIGPTGSGKTL   66 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHH---HHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHH
T ss_pred             hccCHHHHHHHHHHHHHH---HHhhhccccccccccCCCCeEEEECCCCCCHHH
Confidence            479999999986654421   00111100     11135678899999999974

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

Probab=96.04  E-value=0.00051  Score=49.64  Aligned_cols=47  Identities=15%  Similarity=0.116  Sum_probs=28.5

Q ss_pred             cccchHHHHhhcceeeecccceeeeec-c---ccccccceEEecCCCCCCCCC
Q psy2779          38 GLVGQQAAREVSRAVTWEKSFQFERCK-S---HSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        38 GlVGQ~~AREAaGIVVdm~~~~~~~~~-~---~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      -+|||..+.++.--+++.  +.+-+.. .   ...-.+.-+|+.||||||||-
T Consensus        32 ~i~G~~~~~~~l~~~~~~--~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~   82 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAAL--LLVERARQKLGLAHETPTLHMSFTGNPGTGKTT   82 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHH--HHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHH
T ss_pred             HccChHHHHHHHHHHHHH--HHhHHHHHHcCCCCCCCCceEEEECCCCCCHHH
Confidence            589999999987654443  0000000 0   001135578999999999973

>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=95.92  E-value=0.001  Score=45.18  Aligned_cols=55  Identities=13%  Similarity=0.001  Sum_probs=32.0

Q ss_pred             cccCCCCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          23 GLGLKENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        23 GLGLde~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .+-++....+....+.+|+...-+++...+.++       +.. .  .++.+|+.||||||||=.
T Consensus        14 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-------~~~-~--~~~~~ll~G~~G~GKT~l   68 (242)
T 3bos_A           14 QLSLPVHLPDDETFTSYYPAAGNDELIGALKSA-------ASG-D--GVQAIYLWGPVKSGRTHL   68 (242)
T ss_dssp             CCEEECCCCTTCSTTTSCC--CCHHHHHHHHHH-------HHT-C--SCSEEEEECSTTSSHHHH
T ss_pred             hcCCCCCCCCCCChhhccCCCCCHHHHHHHHHH-------HhC-C--CCCeEEEECCCCCCHHHH
Confidence            345556666656677888722122333333333       211 1  468899999999999743

>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=95.92  E-value=0.00053  Score=48.90  Aligned_cols=52  Identities=13%  Similarity=0.077  Sum_probs=29.7

Q ss_pred             cccccCcccchHHHHhhcceeeecccceee-eeccccccccceEEecCCCCCCCC
Q psy2779          32 ANEMAAGLVGQQAAREVSRAVTWEKSFQFE-RCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        32 a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~-~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      +....+-+|||..+.++.--+++.  +.+- ....-..-..+-+|+.||||||||
T Consensus         6 ~~~~~~~i~G~~~~~~~l~~~~~~--~~~~~~~~~~~~~~~~~vll~G~~GtGKT   58 (268)
T 2r62_A            6 PNVRFKDMAGNEEAKEEVVEIVDF--LKYPERYANLGAKIPKGVLLVGPPGTGKT   58 (268)
T ss_dssp             CCCCSTTSSSCTTTHHHHHHHHHH--HHCHHHHHHHSCCCCSCCCCBCSSCSSHH
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHHH--HHChHHHHHCCCCCCceEEEECCCCCcHH
Confidence            344556799999998887655543  0000 000000001234789999999986

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=95.90  E-value=0.0013  Score=52.86  Aligned_cols=42  Identities=17%  Similarity=0.144  Sum_probs=31.9

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +.+.+|||..+......+..+       +++.+.   ..+|+.||||||||=
T Consensus        24 ~l~~ivGq~~~~~~~~~L~~~-------i~~~~~---~~vLL~GppGtGKTt   65 (447)
T 3pvs_A           24 NLAQYIGQQHLLAAGKPLPRA-------IEAGHL---HSMILWGPPGTGKTT   65 (447)
T ss_dssp             STTTCCSCHHHHSTTSHHHHH-------HHHTCC---CEEEEECSTTSSHHH
T ss_pred             CHHHhCCcHHHHhchHHHHHH-------HHcCCC---cEEEEECCCCCcHHH
Confidence            357799999998776667676       544442   568999999999974

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

Probab=95.89  E-value=0.0015  Score=47.16  Aligned_cols=49  Identities=14%  Similarity=0.001  Sum_probs=30.6

Q ss_pred             cccCcccchHHHHhhcceeeeccc---ceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          34 EMAAGLVGQQAAREVSRAVTWEKS---FQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        34 ~~a~GlVGQ~~AREAaGIVVdm~~---~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ...+.++||..+.++.--.+....   -.|.+.    ....+.+|+.||||||||-
T Consensus        18 ~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~----~~~~~~vll~Gp~GtGKT~   69 (297)
T 3b9p_A           18 VEWTDIAGQDVAKQALQEMVILPSVRPELFTGL----RAPAKGLLLFGPPGNGKTL   69 (297)
T ss_dssp             CCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGG----GCCCSEEEEESSSSSCHHH
T ss_pred             CCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcC----CCCCCeEEEECcCCCCHHH
Confidence            345679999999887754443200   001111    1135788999999999973

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

Probab=95.89  E-value=0.0018  Score=46.13  Aligned_cols=51  Identities=14%  Similarity=0.042  Sum_probs=29.5

Q ss_pred             cccccCcccchHHHHhhcceeeec-ccce-eeeeccccccccceEEecCCCCCCCC
Q psy2779          32 ANEMAAGLVGQQAAREVSRAVTWE-KSFQ-FERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        32 a~~~a~GlVGQ~~AREAaGIVVdm-~~~~-~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      +....+-++|+..+.++.--+++. +... |.+.   ..--.+-+|+.||||||||
T Consensus         7 ~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~---~~~~~~~vll~G~~GtGKT   59 (257)
T 1lv7_A            7 IKTTFADVAGCDEAKEEVAELVEYLREPSRFQKL---GGKIPKGVLMVGPPGTGKT   59 (257)
T ss_dssp             SCCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHH
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHc---CCCCCCeEEEECcCCCCHH
Confidence            344567799999998877654443 0000 0000   0011234889999999987

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

Probab=95.78  E-value=0.0015  Score=48.03  Aligned_cols=50  Identities=12%  Similarity=0.078  Sum_probs=31.7

Q ss_pred             CCCCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          28 ENGEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        28 e~g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +...|. ..+.+|||..+.++..-.++.       .+.... .-..+|+.||||||||=
T Consensus        21 ~~~~p~-~~~~iiG~~~~~~~l~~~l~~-------~~~~~~-~~~~vll~G~~GtGKT~   70 (338)
T 3pfi_A           21 TSLRPS-NFDGYIGQESIKKNLNVFIAA-------AKKRNE-CLDHILFSGPAGLGKTT   70 (338)
T ss_dssp             --CCCC-SGGGCCSCHHHHHHHHHHHHH-------HHHTTS-CCCCEEEECSTTSSHHH
T ss_pred             hccCCC-CHHHhCChHHHHHHHHHHHHH-------HHhcCC-CCCeEEEECcCCCCHHH
Confidence            334444 457899999999886655544       211111 12468899999999973

>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=95.71  E-value=0.0024  Score=43.17  Aligned_cols=37  Identities=16%  Similarity=-0.002  Sum_probs=24.3

Q ss_pred             chHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          41 GQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        41 GQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +|++|.+.+--.++-          -..-.|..+++.||||||||-.
T Consensus        18 ~~~~~~~~~~~~~~~----------~~~~~g~~~~l~G~~G~GKTtL   54 (180)
T 3ec2_A           18 SQNRALLTIRVFVHN----------FNPEEGKGLTFVGSPGVGKTHL   54 (180)
T ss_dssp             HHHHHHHHHHHHHHS----------CCGGGCCEEEECCSSSSSHHHH
T ss_pred             HHHHHHHHHHHHHHh----------ccccCCCEEEEECCCCCCHHHH
Confidence            466666655433322          2333588999999999999743

>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=95.70  E-value=0.0011  Score=50.19  Aligned_cols=46  Identities=17%  Similarity=0.246  Sum_probs=28.8

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccc--------------------cccccceEEecCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSH--------------------SLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~--------------------~~~~g~~ll~~G~p~~g~~   85 (101)
                      .-+|||++|.++.-..+..   .+.|.+.+                    .......+|+.||||||||
T Consensus        21 ~~viGq~~ak~~l~~~~~~---~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT   86 (376)
T 1um8_A           21 NYVIGQEQAKKVFSVAVYN---HYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKT   86 (376)
T ss_dssp             TTCCSCHHHHHHHHHHHHH---HHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHH
T ss_pred             hHccCcHHHHHHHHHHHHH---HHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHH
Confidence            4579999999988765521   01111110                    0012456889999999997

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

Probab=95.64  E-value=0.0021  Score=48.70  Aligned_cols=49  Identities=12%  Similarity=-0.058  Sum_probs=29.5

Q ss_pred             ccCcccchHHHHhhcceeeec--ccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWE--KSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm--~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .-+-++|+++++++.--.+.+  +.-+..+   +.....+-+|+.||||||||-
T Consensus        10 ~~~di~G~~~~k~~l~~~v~~p~~~~~~~~---~~~~~~~~iLL~GppGtGKT~   60 (322)
T 1xwi_A           10 KWSDVAGLEGAKEALKEAVILPIKFPHLFT---GKRTPWRGILLFGPPGTGKSY   60 (322)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHHHHHCGGGSC---TTCCCCSEEEEESSSSSCHHH
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHHhCHHHHh---CCCCCCceEEEECCCCccHHH
Confidence            345689999998887644432  0000000   111234678899999999973

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

Probab=95.63  E-value=0.0012  Score=48.79  Aligned_cols=36  Identities=19%  Similarity=0.135  Sum_probs=26.8

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      ....+|||+.+.+++-.-  +             ..++-+|+.||||||||
T Consensus        25 ~~~~i~g~~~~~~~l~~~--l-------------~~~~~vll~G~pGtGKT   60 (331)
T 2r44_A           25 VGKVVVGQKYMINRLLIG--I-------------CTGGHILLEGVPGLAKT   60 (331)
T ss_dssp             HTTTCCSCHHHHHHHHHH--H-------------HHTCCEEEESCCCHHHH
T ss_pred             hccceeCcHHHHHHHHHH--H-------------HcCCeEEEECCCCCcHH
Confidence            346799999988765432  2             23567889999999997

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

Probab=95.61  E-value=0.0036  Score=45.53  Aligned_cols=45  Identities=16%  Similarity=-0.006  Sum_probs=29.6

Q ss_pred             cccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          34 EMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        34 ~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +..+-++|+++..+..--.++-    +  ++. .  .++.+++.||||||||=.
T Consensus        16 ~~p~~~~gr~~~~~~l~~~l~~----~--~~~-~--~~~~vll~G~~G~GKT~l   60 (387)
T 2v1u_A           16 YVPDVLPHREAELRRLAEVLAP----A--LRG-E--KPSNALLYGLTGTGKTAV   60 (387)
T ss_dssp             CCCSCCTTCHHHHHHHHHTTGG----G--TSS-C--CCCCEEECBCTTSSHHHH
T ss_pred             cCCCCCCCHHHHHHHHHHHHHH----H--HcC-C--CCCcEEEECCCCCCHHHH
Confidence            3447799999887765433322    0  111 1  367899999999999743

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

Probab=95.59  E-value=0.0019  Score=53.19  Aligned_cols=36  Identities=17%  Similarity=0.197  Sum_probs=28.4

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      ....+|||+++.+++-+.+               .+++-+|+.||||||||
T Consensus        20 l~~~ivGq~~~i~~l~~al---------------~~~~~VLL~GpPGtGKT   55 (500)
T 3nbx_X           20 LEKGLYERSHAIRLCLLAA---------------LSGESVFLLGPPGIAKS   55 (500)
T ss_dssp             HHTTCSSCHHHHHHHHHHH---------------HHTCEEEEECCSSSSHH
T ss_pred             HHhhhHHHHHHHHHHHHHH---------------hcCCeeEeecCchHHHH
Confidence            4578999999998764433               34678899999999997

>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=95.47  E-value=0.0041  Score=45.83  Aligned_cols=47  Identities=13%  Similarity=-0.026  Sum_probs=28.3

Q ss_pred             CCCcccccCccc-ch--HHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          29 NGEANEMAAGLV-GQ--QAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        29 ~g~a~~~a~GlV-GQ--~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ..++.+..+-|| ||  ..|..++   ..+       ++... -.+.-+|+.||||||||=
T Consensus         3 ~l~~~~~f~~fv~g~~~~~a~~~~---~~~-------~~~~~-~~~~~lll~G~~GtGKT~   52 (324)
T 1l8q_A            3 FLNPKYTLENFIVGEGNRLAYEVV---KEA-------LENLG-SLYNPIFIYGSVGTGKTH   52 (324)
T ss_dssp             CCCTTCCSSSCCCCTTTHHHHHHH---HHH-------HHTTT-TSCSSEEEECSSSSSHHH
T ss_pred             CCCCCCCcccCCCCCcHHHHHHHH---HHH-------HhCcC-CCCCeEEEECCCCCcHHH
Confidence            345666777887 54  4444443   333       22211 135678999999999974

>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=95.46  E-value=0.002  Score=45.90  Aligned_cols=49  Identities=14%  Similarity=0.171  Sum_probs=28.0

Q ss_pred             cCcccchHHHHhhcceeeec--ccceeee-eccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWE--KSFQFER-CKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm--~~~~~~~-~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ..-+|||.+|.++....+.-  +..++.. .+  ..-....+|+.||||||||-
T Consensus        14 ~~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~--~~~~~~~vll~G~~GtGKT~   65 (310)
T 1ofh_A           14 DQHIIGQADAKRAVAIALRNRWRRMQLQEPLR--HEVTPKNILMIGPTGVGKTE   65 (310)
T ss_dssp             HTTCCSCHHHHHHHHHHHHHHHHTTSSCHHHH--HHCCCCCEEEECCTTSSHHH
T ss_pred             hhhcCChHHHHHHHHHHHHHHHhhhhhccccc--ccCCCceEEEECCCCCCHHH
Confidence            35689999999887543321  0000000 00  00124678899999999973

>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=95.41  E-value=0.0025  Score=47.33  Aligned_cols=49  Identities=10%  Similarity=0.093  Sum_probs=30.0

Q ss_pred             ccCcccchHHHHhhcceeeec--ccc-eeeeeccccccccceEEecCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWE--KSF-QFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm--~~~-~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .-+.++|+..+.+..--.+..  +.- .|.+.   ..-.++.+|+.||||||||-
T Consensus        13 ~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~---~~~~~~~vLL~Gp~GtGKT~   64 (301)
T 3cf0_A           13 TWEDIGGLEDVKRELQELVQYPVEHPDKFLKF---GMTPSKGVLFYGPPGCGKTL   64 (301)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHH---CCCCCSEEEEECSSSSSHHH
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHc---CCCCCceEEEECCCCcCHHH
Confidence            445689999988776544432  000 01111   22346778999999999973

>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=95.34  E-value=0.0028  Score=48.57  Aligned_cols=53  Identities=13%  Similarity=0.032  Sum_probs=29.9

Q ss_pred             ccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          33 NEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        33 ~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ...-+-++||+.+.++.--.+.+- ..+-+.-.......+-+|+.||||||||=
T Consensus        47 ~~~~~di~G~~~~~~~l~~~v~~~-~~~~~~~~~~~~~~~~iLL~GppGtGKT~   99 (355)
T 2qp9_X           47 NVKWEDVAGLEGAKEALKEAVILP-VKFPHLFKGNRKPTSGILLYGPPGTGKSY   99 (355)
T ss_dssp             CCCGGGSCCGGGHHHHHHHHTHHH-HHCGGGGCSSCCCCCCEEEECSTTSCHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHH-HhCHHHHhcCCCCCceEEEECCCCCcHHH
Confidence            334567999999988775444220 00000000111124557899999999973

>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=95.23  E-value=0.0039  Score=45.14  Aligned_cols=45  Identities=13%  Similarity=0.006  Sum_probs=29.2

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      ..+.+|||..+.+...-.++.       ..... -....+|+.||||||||-.
T Consensus        10 ~~~~~ig~~~~~~~l~~~l~~-------~~~~~-~~~~~vll~G~~GtGKT~l   54 (324)
T 1hqc_A           10 TLDEYIGQERLKQKLRVYLEA-------AKARK-EPLEHLLLFGPPGLGKTTL   54 (324)
T ss_dssp             STTTCCSCHHHHHHHHHHHHH-------HHHHC-SCCCCCEEECCTTCCCHHH
T ss_pred             cHHHhhCHHHHHHHHHHHHHH-------HHccC-CCCCcEEEECCCCCCHHHH
Confidence            457799999887765444333       21111 1246788999999999743

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

Probab=95.22  E-value=0.0029  Score=45.59  Aligned_cols=44  Identities=18%  Similarity=0.073  Sum_probs=27.3

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccc---cccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSH---SLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~---~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ...++||..|-+..-..+.-       .+.+   ..-....+|+.||||||||-
T Consensus        16 ~~~i~G~~~~~~~l~~~i~~-------~~~~~~~~~~~~~~~ll~G~~GtGKt~   62 (311)
T 4fcw_A           16 HKRVVGQDEAIRAVADAIRR-------ARAGLKDPNRPIGSFLFLGPTGVGKTE   62 (311)
T ss_dssp             HTTCCSCHHHHHHHHHHHHH-------HHHTCSCTTSCSEEEEEESCSSSSHHH
T ss_pred             hhhcCCHHHHHHHHHHHHHH-------HhcCCCCCCCCceEEEEECCCCcCHHH
Confidence            34688999998775444433       1100   00012478999999999974

>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=95.21  E-value=0.004  Score=41.06  Aligned_cols=39  Identities=13%  Similarity=0.061  Sum_probs=25.7

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .+.+||+.++.+..-   +.       ++..+   ...+|+.||||||||-.
T Consensus        16 ~~~~~g~~~~~~~l~---~~-------l~~~~---~~~~ll~G~~G~GKT~l   54 (226)
T 2chg_A           16 LDEVVGQDEVIQRLK---GY-------VERKN---IPHLLFSGPPGTGKTAT   54 (226)
T ss_dssp             GGGCCSCHHHHHHHH---HH-------HHTTC---CCCEEEECSTTSSHHHH
T ss_pred             HHHHcCcHHHHHHHH---HH-------HhCCC---CCeEEEECCCCCCHHHH
Confidence            456999988876543   22       22221   23489999999999743

>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=95.10  E-value=0.0067  Score=43.94  Aligned_cols=46  Identities=9%  Similarity=-0.029  Sum_probs=29.6

Q ss_pred             ccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          33 NEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        33 ~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .+..+-|||+++..+..--.+.-       +....  .++.+++.||||||||-.
T Consensus        16 ~~~p~~~~gr~~e~~~l~~~l~~-------~~~~~--~~~~vli~G~~G~GKTtl   61 (386)
T 2qby_A           16 DYIPDELPHREDQIRKIASILAP-------LYREE--KPNNIFIYGLTGTGKTAV   61 (386)
T ss_dssp             SCCCSCCTTCHHHHHHHHHSSGG-------GGGTC--CCCCEEEEECTTSSHHHH
T ss_pred             ccCCCCCCChHHHHHHHHHHHHH-------HHcCC--CCCeEEEECCCCCCHHHH
Confidence            34447799999887764322221       11112  367899999999999743

>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=95.08  E-value=0.0043  Score=41.07  Aligned_cols=40  Identities=15%  Similarity=-0.037  Sum_probs=26.0

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      ...+||++++.+..--.++          ..+  ....+|+.||||||||=.
T Consensus        22 ~~~~~g~~~~~~~l~~~l~----------~~~--~~~~~ll~G~~G~GKT~l   61 (250)
T 1njg_A           22 FADVVGQEHVLTALANGLS----------LGR--IHHAYLFSGTRGVGKTSI   61 (250)
T ss_dssp             GGGCCSCHHHHHHHHHHHH----------HTC--CCSEEEEECSTTSCHHHH
T ss_pred             HHHHhCcHHHHHHHHHHHH----------cCC--CCeEEEEECCCCCCHHHH
Confidence            3569999988775432221          111  134789999999999743

>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=95.03  E-value=0.0042  Score=49.24  Aligned_cols=49  Identities=12%  Similarity=-0.039  Sum_probs=29.8

Q ss_pred             cccCcccchHHHHhhcceeeec--ccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          34 EMAAGLVGQQAAREVSRAVTWE--KSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        34 ~~a~GlVGQ~~AREAaGIVVdm--~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      ..-+-++||+.++++.--.+.+  +..++.   ....-..+-+|+.||||||||
T Consensus       131 ~~~~di~G~~~~k~~l~~~v~~p~~~~~~~---~~~~~~~~~vLL~GppGtGKT  181 (444)
T 2zan_A          131 VKWSDVAGLEGAKEALKEAVILPIKFPHLF---TGKRTPWRGILLFGPPGTGKS  181 (444)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHTHHHHCTTTT---SGGGCCCSEEEEECSTTSSHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHh---hccCCCCceEEEECCCCCCHH
Confidence            3446689999999887644422  000000   011123467889999999996

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=94.86  E-value=0.0061  Score=42.31  Aligned_cols=23  Identities=22%  Similarity=0.108  Sum_probs=17.9

Q ss_pred             cccccccceEEecCCCCCCCCCC
Q psy2779          65 SHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        65 ~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      -|-|+.|..+++.|||||||+-.
T Consensus         6 ~~~~~~~~~i~l~G~sGsGKsTl   28 (204)
T 2qor_A            6 HHHMARIPPLVVCGPSGVGKGTL   28 (204)
T ss_dssp             ---CCCCCCEEEECCTTSCHHHH
T ss_pred             ccccccCCEEEEECCCCCCHHHH
Confidence            36788999999999999998643

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

Probab=94.86  E-value=0.0042  Score=47.57  Aligned_cols=47  Identities=15%  Similarity=0.081  Sum_probs=30.3

Q ss_pred             ccCcccchHHHHhhcceeeecccc---eeeeeccccccccceEEecCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSF---QFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~---~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      ..+.+|||..+.++.--.+..-..   .|.+.    ....+-+||.||||||||
T Consensus       113 ~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~----~~~~~~vLL~GppGtGKT  162 (389)
T 3vfd_A          113 KFDDIAGQDLAKQALQEIVILPSLRPELFTGL----RAPARGLLLFGPPGNGKT  162 (389)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGG----GCCCSEEEEESSTTSCHH
T ss_pred             ChHHhCCHHHHHHHHHHHHHHhccCHHHhccc----CCCCceEEEECCCCCCHH
Confidence            356799999999887655533000   01111    113578999999999997

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=94.60  E-value=0.005  Score=50.52  Aligned_cols=38  Identities=18%  Similarity=0.217  Sum_probs=29.9

Q ss_pred             cccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          34 EMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        34 ~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ...+.++||..+.+.....+.-               |..+++.||||||||-
T Consensus        38 ~~l~~i~G~~~~l~~l~~~i~~---------------g~~vll~Gp~GtGKTt   75 (604)
T 3k1j_A           38 KLIDQVIGQEHAVEVIKTAANQ---------------KRHVLLIGEPGTGKSM   75 (604)
T ss_dssp             SHHHHCCSCHHHHHHHHHHHHT---------------TCCEEEECCTTSSHHH
T ss_pred             cccceEECchhhHhhccccccC---------------CCEEEEEeCCCCCHHH
Confidence            4567899999999876554433               6789999999999863

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=94.60  E-value=0.0084  Score=41.48  Aligned_cols=19  Identities=16%  Similarity=0.045  Sum_probs=15.9

Q ss_pred             ccceEEecCCCCCCCCCCc
Q psy2779          70 RGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~   88 (101)
                      .|.++++.|+|||||+-..
T Consensus        28 ~g~~i~l~G~~GsGKSTl~   46 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIA   46 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4789999999999997543

>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=94.49  E-value=0.0073  Score=49.56  Aligned_cols=49  Identities=12%  Similarity=0.094  Sum_probs=29.0

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccc--cccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSH--SLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~--~~~~g~~ll~~G~p~~g~~   85 (101)
                      .+-+|||++|.++.-+.+.. .|...+....  .....+-+|+.||||||||
T Consensus        14 d~~IvGqe~ak~~l~~av~~-~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT   64 (444)
T 1g41_A           14 DQHIIGQADAKRAVAIALRN-RWRRMQLQEPLRHEVTPKNILMIGPTGVGKT   64 (444)
T ss_dssp             HTTCCSCHHHHHHHHHHHHH-HHHHHHSCTTTTTTCCCCCEEEECCTTSSHH
T ss_pred             HHHhCCHHHHHHHHHHHHHH-HHhhhccccccccccCCceEEEEcCCCCCHH
Confidence            34589999999998776632 0000000000  0112345789999999985

>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=94.47  E-value=0.0088  Score=43.78  Aligned_cols=40  Identities=5%  Similarity=-0.150  Sum_probs=27.2

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +.+-+|||+++.+..-   +.       +++++  -...+|++||||||||-
T Consensus        24 ~~~~ivg~~~~~~~l~---~~-------l~~~~--~~~~~L~~G~~G~GKT~   63 (324)
T 3u61_B           24 TIDECILPAFDKETFK---SI-------TSKGK--IPHIILHSPSPGTGKTT   63 (324)
T ss_dssp             STTTSCCCHHHHHHHH---HH-------HHTTC--CCSEEEECSSTTSSHHH
T ss_pred             CHHHHhCcHHHHHHHH---HH-------HHcCC--CCeEEEeeCcCCCCHHH
Confidence            3577999998876543   33       22222  13678999999999973

>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=94.43  E-value=0.0063  Score=44.77  Aligned_cols=46  Identities=7%  Similarity=-0.216  Sum_probs=29.7

Q ss_pred             ccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          33 NEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        33 ~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .+..+-+||+++..+...-.++-       .....  ..+.+++.||||||||-.
T Consensus        16 ~~~p~~l~gr~~~~~~l~~~l~~-------~~~~~--~~~~vll~G~~G~GKT~l   61 (384)
T 2qby_B           16 LSVFKEIPFREDILRDAAIAIRY-------FVKNE--VKFSNLFLGLTGTGKTFV   61 (384)
T ss_dssp             HHHCSSCTTCHHHHHHHHHHHHH-------HHTTC--CCCEEEEEECTTSSHHHH
T ss_pred             ccCCCCCCChHHHHHHHHHHHHH-------HHcCC--CCCcEEEECCCCCCHHHH
Confidence            34447799999887765432222       11112  256899999999999743

>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=94.42  E-value=0.005  Score=43.99  Aligned_cols=39  Identities=13%  Similarity=0.022  Sum_probs=20.7

Q ss_pred             ccCcccchHHHHhhc-ceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVS-RAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        35 ~a~GlVGQ~~AREAa-GIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      ..+.+|||..+-+.+ ..+...       .     ..+.-+|+.||||||||
T Consensus         4 ~f~~~ig~~~~~~~~~~~~~~~-------~-----~~~~~vll~G~~GtGKt   43 (265)
T 2bjv_A            4 YKDNLLGEANSFLEVLEQVSHL-------A-----PLDKPVLIIGERGTGKE   43 (265)
T ss_dssp             ------CCCHHHHHHHHHHHHH-------T-----TSCSCEEEECCTTSCHH
T ss_pred             ccccceeCCHHHHHHHHHHHHH-------h-----CCCCCEEEECCCCCcHH
Confidence            346689987765443 222222       1     12467889999999986

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=94.42  E-value=0.013  Score=41.69  Aligned_cols=39  Identities=13%  Similarity=0.038  Sum_probs=25.7

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .+.+|||+.+.+..   .+.       +++++   ...+|+.||||||||-.
T Consensus        16 ~~~~~g~~~~~~~l---~~~-------l~~~~---~~~~ll~G~~G~GKt~l   54 (319)
T 2chq_A           16 LDEVVGQDEVIQRL---KGY-------VERKN---IPHLLFSGPPGTGKTAT   54 (319)
T ss_dssp             GGGSCSCHHHHHHH---HTT-------TTTTC---CCCEEEESSSSSSHHHH
T ss_pred             HHHHhCCHHHHHHH---HHH-------HhCCC---CCeEEEECcCCcCHHHH
Confidence            45699999887753   233       22222   12388999999999743

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

Probab=94.36  E-value=0.01  Score=38.19  Aligned_cols=39  Identities=10%  Similarity=0.055  Sum_probs=24.9

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .+.+||++++-+..   .+.       ++..   ..+.+|+.||||||||=.
T Consensus        21 ~~~~~g~~~~~~~l---~~~-------l~~~---~~~~~ll~G~~G~GKT~l   59 (195)
T 1jbk_A           21 LDPVIGRDEEIRRT---IQV-------LQRR---TKNNPVLIGEPGVGKTAI   59 (195)
T ss_dssp             SCCCCSCHHHHHHH---HHH-------HTSS---SSCEEEEECCTTSCHHHH
T ss_pred             ccccccchHHHHHH---HHH-------HhcC---CCCceEEECCCCCCHHHH
Confidence            46689998765442   222       1111   256788999999999743

>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=94.35  E-value=0.0091  Score=43.73  Aligned_cols=44  Identities=14%  Similarity=0.021  Sum_probs=28.0

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccc--eEEecCCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGG--RAVAGGRTKCPKPPN   87 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~--~ll~~G~p~~g~~~~   87 (101)
                      ...-++|+++..+..--.++-       ...+.  .+.  .+++.||||||||-.
T Consensus        15 ~p~~l~gr~~~~~~l~~~l~~-------~~~~~--~~~~~~~li~G~~G~GKTtl   60 (389)
T 1fnn_A           15 VPKRLPHREQQLQQLDILLGN-------WLRNP--GHHYPRATLLGRPGTGKTVT   60 (389)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHH-------HHHST--TSSCCEEEEECCTTSSHHHH
T ss_pred             CCCCCCChHHHHHHHHHHHHH-------HHcCC--CCCCCeEEEECCCCCCHHHH
Confidence            346799999887764332222       11111  234  899999999999743

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=94.27  E-value=0.0083  Score=42.90  Aligned_cols=39  Identities=18%  Similarity=0.126  Sum_probs=26.2

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .+.+|||+++.+..-   ++       +++++   ..-+|+.||||||||-.
T Consensus        24 ~~~~~g~~~~~~~l~---~~-------l~~~~---~~~~ll~G~~G~GKT~l   62 (327)
T 1iqp_A           24 LDDIVGQEHIVKRLK---HY-------VKTGS---MPHLLFAGPPGVGKTTA   62 (327)
T ss_dssp             TTTCCSCHHHHHHHH---HH-------HHHTC---CCEEEEESCTTSSHHHH
T ss_pred             HHHhhCCHHHHHHHH---HH-------HHcCC---CCeEEEECcCCCCHHHH
Confidence            456999998877543   33       22222   12489999999999743

>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=94.20  E-value=0.0076  Score=43.83  Aligned_cols=39  Identities=18%  Similarity=0.115  Sum_probs=25.1

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .+-+|||+++.+..--   .       +++++ .  .-+|+.||||||||-.
T Consensus        36 ~~~i~g~~~~~~~l~~---~-------l~~~~-~--~~~ll~G~~G~GKT~l   74 (353)
T 1sxj_D           36 LDEVTAQDHAVTVLKK---T-------LKSAN-L--PHMLFYGPPGTGKTST   74 (353)
T ss_dssp             TTTCCSCCTTHHHHHH---H-------TTCTT-C--CCEEEECSTTSSHHHH
T ss_pred             HHHhhCCHHHHHHHHH---H-------HhcCC-C--CEEEEECCCCCCHHHH
Confidence            4668999887765322   2       22222 1  2388999999999843

>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=94.12  E-value=0.0068  Score=45.70  Aligned_cols=43  Identities=12%  Similarity=0.063  Sum_probs=27.3

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      -+-++||..+.+...+.++-       .+.... .-..+++.||||||||=
T Consensus        24 l~~~~g~~~~~~~l~~~i~~-------~~~~~~-~~~~~ll~Gp~G~GKTT   66 (334)
T 1in4_A           24 LDEFIGQENVKKKLSLALEA-------AKMRGE-VLDHVLLAGPPGLGKTT   66 (334)
T ss_dssp             GGGCCSCHHHHHHHHHHHHH-------HHHHTC-CCCCEEEESSTTSSHHH
T ss_pred             HHHccCcHHHHHHHHHHHHH-------HHhcCC-CCCeEEEECCCCCcHHH
Confidence            45588999888876554433       100000 11568899999999973

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=94.10  E-value=0.013  Score=42.97  Aligned_cols=39  Identities=8%  Similarity=0.049  Sum_probs=25.5

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+.+.++.--.+.         ++++ . .. +|+.||||||||-
T Consensus        13 ~~~~vg~~~~~~~l~~~~~---------~~~~-~-~~-~ll~Gp~G~GKTt   51 (354)
T 1sxj_E           13 LNALSHNEELTNFLKSLSD---------QPRD-L-PH-LLLYGPNGTGKKT   51 (354)
T ss_dssp             GGGCCSCHHHHHHHHTTTT---------CTTC-C-CC-EEEECSTTSSHHH
T ss_pred             HHHhcCCHHHHHHHHHHHh---------hCCC-C-Ce-EEEECCCCCCHHH
Confidence            4569999998776533220         2222 1 23 8899999999864

>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=94.09  E-value=0.011  Score=48.61  Aligned_cols=52  Identities=17%  Similarity=0.081  Sum_probs=30.1

Q ss_pred             CcccccCcccchHHHHhhcceeeec-ccce-eeeeccccccccceEEecCCCCCCCC
Q psy2779          31 EANEMAAGLVGQQAAREVSRAVTWE-KSFQ-FERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        31 ~a~~~a~GlVGQ~~AREAaGIVVdm-~~~~-~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .+....+-++|+.++.+..-=+++. +..+ |.++ ..+.  .+-+|+.||||||||
T Consensus        10 ~~~~~f~di~G~~~~~~~l~e~v~~l~~~~~~~~~-g~~~--p~gvLL~GppGtGKT   63 (476)
T 2ce7_A           10 NKRVTFKDVGGAEEAIEELKEVVEFLKDPSKFNRI-GARM--PKGILLVGPPGTGKT   63 (476)
T ss_dssp             SCCCCGGGCCSCHHHHHHHHHHHHHHHCTHHHHTT-TCCC--CSEEEEECCTTSSHH
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHHHhhChHHHhhc-CCCC--CCeEEEECCCCCCHH
Confidence            4445566799999998776555543 1000 0001 0011  223789999999986

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=94.06  E-value=0.009  Score=47.38  Aligned_cols=47  Identities=13%  Similarity=-0.067  Sum_probs=29.1

Q ss_pred             CCCCcccccCccc-ch--HHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          28 ENGEANEMAAGLV-GQ--QAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        28 e~g~a~~~a~GlV-GQ--~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ....+.+..+-|| ||  ..|+.++-   .+       +++...  ..-+++.||||||||-
T Consensus        96 ~~l~~~~tfd~fv~g~~n~~a~~~~~---~~-------a~~~~~--~~~lll~Gp~G~GKTt  145 (440)
T 2z4s_A           96 TPLNPDYTFENFVVGPGNSFAYHAAL---EV-------AKHPGR--YNPLFIYGGVGLGKTH  145 (440)
T ss_dssp             CCCCTTCSGGGCCCCTTTHHHHHHHH---HH-------HHSTTS--SCCEEEECSSSSSHHH
T ss_pred             cCCCCCCChhhcCCCCchHHHHHHHH---HH-------HhCCCC--CCeEEEECCCCCCHHH
Confidence            3455666777888 64  34444443   33       222221  5678999999999974

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=94.01  E-value=0.0044  Score=41.28  Aligned_cols=15  Identities=13%  Similarity=0.151  Sum_probs=12.9

Q ss_pred             cceEEecCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKP   85 (101)
Q Consensus        71 g~~ll~~G~p~~g~~   85 (101)
                      ..-+|+.|||||||+
T Consensus        27 ~~~vll~G~~GtGKt   41 (143)
T 3co5_A           27 TSPVFLTGEAGSPFE   41 (143)
T ss_dssp             SSCEEEEEETTCCHH
T ss_pred             CCcEEEECCCCccHH
Confidence            456889999999996

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

Probab=93.98  E-value=0.0064  Score=49.68  Aligned_cols=60  Identities=18%  Similarity=0.123  Sum_probs=34.0

Q ss_pred             cccccCCCCCCcccccCcccchHHHHhhcceeeec--ccce-eeeeccccccccceEEecCCCCCCCC
Q psy2779          21 VKGLGLKENGEANEMAAGLVGQQAAREVSRAVTWE--KSFQ-FERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        21 IkGLGLde~g~a~~~a~GlVGQ~~AREAaGIVVdm--~~~~-~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      ++.+.+++  .|...-+-+.|.+++.+..-=.|.+  +.-+ |.+.   ..--.+-+|+.||||||||
T Consensus       167 ~~~~~~~~--~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~---g~~~prGvLLyGPPGTGKT  229 (434)
T 4b4t_M          167 VKAMEVDE--KPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDM---GIRAPKGALMYGPPGTGKT  229 (434)
T ss_dssp             CSCCEEES--SCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHH---CCCCCCEEEEESCTTSSHH
T ss_pred             hhhcccCC--CCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhC---CCCCCCeeEEECcCCCCHH
Confidence            34444443  3444557788888888876533322  1111 1111   2223466789999999997

>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=93.92  E-value=0.0093  Score=42.33  Aligned_cols=52  Identities=13%  Similarity=0.155  Sum_probs=29.7

Q ss_pred             CcccccCcccchHHHHhhcceeeeccccee-eeec--cccccccceEEecCCCCCCCCC
Q psy2779          31 EANEMAAGLVGQQAAREVSRAVTWEKSFQF-ERCK--SHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        31 ~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~-~~~~--~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+...-+-++|++++.+...-++..  |.. ...+  +-..-.|  +++.||||||||=
T Consensus        10 ~~~~~~~~i~g~~~~~~~l~~l~~~--~~~~~~~~~~~~~~~~g--~ll~G~~G~GKTt   64 (254)
T 1ixz_A           10 APKVTFKDVAGAEEAKEELKEIVEF--LKNPSRFHEMGARIPKG--VLLVGPPGVGKTH   64 (254)
T ss_dssp             CCSCCGGGCCSCHHHHHHHHHHHHH--HHCHHHHHHTTCCCCSE--EEEECCTTSSHHH
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHHH--HHCHHHHHHcCCCCCCe--EEEECCCCCCHHH
Confidence            3455566789999887776544433  100 0000  0011123  8899999999973

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=93.90  E-value=0.0097  Score=40.58  Aligned_cols=16  Identities=13%  Similarity=-0.170  Sum_probs=13.9

Q ss_pred             ceEEecCCCCCCCCCC
Q psy2779          72 GRAVAGGRTKCPKPPN   87 (101)
Q Consensus        72 ~~ll~~G~p~~g~~~~   87 (101)
                      +.+++.||||||||-.
T Consensus        55 ~~~~l~G~~GtGKT~l   70 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYL   70 (202)
T ss_dssp             CEEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            6789999999999754

>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=93.85  E-value=0.012  Score=44.90  Aligned_cols=49  Identities=10%  Similarity=-0.093  Sum_probs=29.7

Q ss_pred             cccCcccchHHHHhhcceeeec--cc-ceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          34 EMAAGLVGQQAAREVSRAVTWE--KS-FQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        34 ~~a~GlVGQ~~AREAaGIVVdm--~~-~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ..-+-++||+.+.+..--.+..  +. ..|.+.   . -..+.+|+.||||||||=
T Consensus        81 ~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~---~-~~~~~vLl~GppGtGKT~  132 (357)
T 3d8b_A           81 VNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGL---R-GPPKGILLFGPPGTGKTL  132 (357)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGG---G-SCCSEEEEESSTTSSHHH
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHhhChHhHhhc---c-CCCceEEEECCCCCCHHH
Confidence            3446799999998876544432  00 001111   1 135678899999999973

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

Probab=93.84  E-value=0.0067  Score=49.60  Aligned_cols=48  Identities=19%  Similarity=0.109  Sum_probs=29.5

Q ss_pred             ccCcccchHHHHhhcceeeec--ccce-eeeeccccccccceEEecCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWE--KSFQ-FERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm--~~~~-~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .-+-+.|.+++.+..-=.|.+  +.-+ |.+.   ..---+-+|+.||||||||
T Consensus       179 ~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~---g~~~prGvLL~GPPGtGKT  229 (437)
T 4b4t_L          179 TFDGIGGLTEQIRELREVIELPLKNPEIFQRV---GIKPPKGVLLYGPPGTGKT  229 (437)
T ss_dssp             CSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHH---CCCCCCEEEEESCTTSSHH
T ss_pred             ChhHhCChHHHHHHHHHHHHHHHhCHHHHHhC---CCCCCCeEEEECCCCCcHH
Confidence            346678888888877655554  1111 1111   2223456779999999997

>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=93.79  E-value=0.01  Score=48.54  Aligned_cols=41  Identities=17%  Similarity=0.102  Sum_probs=27.8

Q ss_pred             cccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          38 GLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        38 GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      -.+||+++.+..+-.+.++.     + +.+. .|..+|+.||||||||
T Consensus        82 di~G~~~vk~~i~~~~~l~~-----~-~~~~-~g~~vll~Gp~GtGKT  122 (543)
T 3m6a_A           82 EHHGLEKVKERILEYLAVQK-----L-TKSL-KGPILCLAGPPGVGKT  122 (543)
T ss_dssp             HCSSCHHHHHHHHHHHHHHH-----H-SSSC-CSCEEEEESSSSSSHH
T ss_pred             HhccHHHHHHHHHHHHHHHH-----h-cccC-CCCEEEEECCCCCCHH
Confidence            37999999887753332210     1 1122 5889999999999986

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

Probab=93.77  E-value=0.012  Score=43.76  Aligned_cols=16  Identities=13%  Similarity=-0.357  Sum_probs=13.4

Q ss_pred             cceEEecCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPP   86 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~   86 (101)
                      -+.+|+.||||||||-
T Consensus        36 p~~lLl~GppGtGKT~   51 (293)
T 3t15_A           36 PLILGIWGGKGQGKSF   51 (293)
T ss_dssp             CSEEEEEECTTSCHHH
T ss_pred             CeEEEEECCCCCCHHH
Confidence            4678899999999973

>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=93.71  E-value=0.011  Score=43.97  Aligned_cols=35  Identities=17%  Similarity=0.080  Sum_probs=23.1

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccccccccce--EEecCCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGR--AVAGGRTKCPKPP   86 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~--ll~~G~p~~g~~~   86 (101)
                      +-++||+.+-+...   ..       +++     |+.  +|+.||||||||-
T Consensus        25 ~~~~g~~~~~~~L~---~~-------i~~-----g~~~~~ll~Gp~G~GKTt   61 (340)
T 1sxj_C           25 DEVYGQNEVITTVR---KF-------VDE-----GKLPHLLFYGPPGTGKTS   61 (340)
T ss_dssp             GGCCSCHHHHHHHH---HH-------HHT-----TCCCCEEEECSSSSSHHH
T ss_pred             HHhcCcHHHHHHHH---HH-------Hhc-----CCCceEEEECCCCCCHHH
Confidence            44789987765322   22       222     344  8899999999974

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=93.67  E-value=0.018  Score=39.65  Aligned_cols=22  Identities=18%  Similarity=0.149  Sum_probs=18.3

Q ss_pred             cccccceEEecCCCCCCCCCCc
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      .+-.|.+++++|+||+|||-|.
T Consensus        26 Gl~~G~l~~i~G~pG~GKT~l~   47 (251)
T 2zts_A           26 GFPEGTTVLLTGGTGTGKTTFA   47 (251)
T ss_dssp             SEETTCEEEEECCTTSSHHHHH
T ss_pred             CCCCCeEEEEEeCCCCCHHHHH
Confidence            4556889999999999998664

>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=93.61  E-value=0.015  Score=42.63  Aligned_cols=40  Identities=15%  Similarity=-0.017  Sum_probs=25.9

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .+.+|||+++.+..-   +.       +++++  ...++|+.||||||||-.
T Consensus        15 ~~~~vg~~~~~~~L~---~~-------l~~~~--~~~~~ll~G~~G~GKT~l   54 (373)
T 1jr3_A           15 FADVVGQEHVLTALA---NG-------LSLGR--IHHAYLFSGTRGVGKTSI   54 (373)
T ss_dssp             TTTSCSCHHHHHHHH---HH-------HHHTC--CCSEEEEESCTTSSHHHH
T ss_pred             hhhccCcHHHHHHHH---HH-------HHhCC--CCeEEEEECCCCCCHHHH
Confidence            345999998876432   22       22222  134789999999999743

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

Probab=93.36  E-value=0.014  Score=37.91  Aligned_cols=38  Identities=8%  Similarity=0.022  Sum_probs=24.4

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+||+.++-+.+   .+.       +++   -..+-+|+.||||||||-
T Consensus        21 ~~~~~g~~~~~~~l---~~~-------l~~---~~~~~vll~G~~G~GKT~   58 (187)
T 2p65_A           21 LDPVIGRDTEIRRA---IQI-------LSR---RTKNNPILLGDPGVGKTA   58 (187)
T ss_dssp             SCCCCSCHHHHHHH---HHH-------HTS---SSSCEEEEESCGGGCHHH
T ss_pred             cchhhcchHHHHHH---HHH-------HhC---CCCCceEEECCCCCCHHH
Confidence            45689998755442   222       111   135678999999999974

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

Probab=93.34  E-value=0.024  Score=47.08  Aligned_cols=50  Identities=10%  Similarity=0.023  Sum_probs=27.3

Q ss_pred             cccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          34 EMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        34 ~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      ..+..++||+.+.+|.-+.+--  -.--..++.+.-+.--+|+.||||||||
T Consensus       292 ~l~~~I~G~e~vk~al~~~l~~--g~~~~~~~~~~r~~~~vLL~GppGtGKT  341 (595)
T 3f9v_A          292 SIAPSIYGHWELKEALALALFG--GVPKVLEDTRIRGDIHILIIGDPGTAKS  341 (595)
T ss_dssp             HTSSTTSCCHHHHHHHTTTTTC--CCCEETTTTEECCSCCEEEEESSCCTHH
T ss_pred             hhcchhcChHHHHHHHHHHHhC--CCcccccCCCcCCCcceEEECCCchHHH
Confidence            3456799999999886332111  0000000001111125889999999986

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

Probab=93.07  E-value=0.01  Score=48.34  Aligned_cols=48  Identities=13%  Similarity=0.035  Sum_probs=28.8

Q ss_pred             ccCcccchHHHHhhcceeeec--ccce-eeeeccccccccceEEecCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWE--KSFQ-FERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm--~~~~-~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .-+-..|.+++.+..-=.|++  +.-+ |.+.   ..--.+-+|+.||||||||
T Consensus       170 ~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~---g~~~prGiLL~GPPGtGKT  220 (428)
T 4b4t_K          170 TYADVGGLDMQKQEIREAVELPLVQADLYEQI---GIDPPRGVLLYGPPGTGKT  220 (428)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHH---CCCCCCEEEEESCTTTTHH
T ss_pred             CHHHhccHHHHHHHHHHHHHHHHhCHHHHHhC---CCCCCceEEEECCCCCCHH
Confidence            345677888888776555543  1111 1111   2223455889999999997

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

Probab=93.05  E-value=0.011  Score=42.94  Aligned_cols=51  Identities=14%  Similarity=0.153  Sum_probs=29.5

Q ss_pred             cccccCcccchHHHHhhcceeeecccceee-eec--cccccccceEEecCCCCCCCCC
Q psy2779          32 ANEMAAGLVGQQAAREVSRAVTWEKSFQFE-RCK--SHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        32 a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~-~~~--~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +...-+-++|++++.+.+.=++..  |.-. ..+  +-..-.|  +++.||||||||=
T Consensus        35 ~~~~~~~i~g~~~~~~~l~~l~~~--~~~~~~l~~~~~~~~~g--vll~Gp~GtGKTt   88 (278)
T 1iy2_A           35 PKVTFKDVAGAEEAKEELKEIVEF--LKNPSRFHEMGARIPKG--VLLVGPPGVGKTH   88 (278)
T ss_dssp             CCCCGGGSSSCHHHHHHHHHHHHH--HHCHHHHHHTTCCCCCE--EEEECCTTSSHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHH--HHCHHHHHHcCCCCCCe--EEEECCCcChHHH
Confidence            445567799999987776544433  1000 000  0011123  8899999999973

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

Probab=93.04  E-value=0.027  Score=44.84  Aligned_cols=38  Identities=13%  Similarity=0.039  Sum_probs=24.8

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+.+|||.+.-+.   +.++       +..   ....-+|+.||||||||-
T Consensus       179 ld~iiGr~~~i~~---l~~~-------l~r---~~~~~~LL~G~pG~GKT~  216 (468)
T 3pxg_A          179 LDPVIGRSKEIQR---VIEV-------LSR---RTKNNPVLIGEPGVGKTA  216 (468)
T ss_dssp             SCCCCCCHHHHHH---HHHH-------HHC---SSSCEEEEESCTTTTTHH
T ss_pred             CCCccCcHHHHHH---HHHH-------Hhc---cCCCCeEEECCCCCCHHH
Confidence            3568999887765   2222       111   124457899999999974

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

Probab=93.02  E-value=0.0089  Score=44.45  Aligned_cols=48  Identities=15%  Similarity=0.065  Sum_probs=23.8

Q ss_pred             cCcccchHHHHhhcce-ee-ecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRA-VT-WEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGI-VV-dm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      -+-+.|.+++++..-- |+ -++..+..+--+-..-.|  +|+.||||||||
T Consensus         9 ~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~G--vlL~Gp~GtGKT   58 (274)
T 2x8a_A            9 WADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAG--VLLAGPPGCGKT   58 (274)
T ss_dssp             ---CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSE--EEEESSTTSCHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCe--EEEECCCCCcHH
Confidence            3456788888877642 22 221111000001111123  889999999997

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

Probab=92.98  E-value=0.0094  Score=48.68  Aligned_cols=47  Identities=15%  Similarity=0.022  Sum_probs=28.1

Q ss_pred             cCcccchHHHHhhcceeeec--ccce-eeeeccccccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWE--KSFQ-FERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm--~~~~-~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      -+-+.|.+++.+..-=.|.+  +.-+ |.+.   ..--.+-+|+.||||||||
T Consensus       147 ~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~---gi~~prGvLL~GPPGTGKT  196 (405)
T 4b4t_J          147 YDMVGGLTKQIKEIKEVIELPVKHPELFESL---GIAQPKGVILYGPPGTGKT  196 (405)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCHHHHHHH---TCCCCCCEEEESCSSSSHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhCHHHHHhC---CCCCCCceEEeCCCCCCHH
Confidence            35567888888777544443  1111 1111   2223455779999999987

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=92.97  E-value=0.025  Score=38.17  Aligned_cols=23  Identities=4%  Similarity=0.005  Sum_probs=17.3

Q ss_pred             ccccceEEecCCCCCCCCCCcee
Q psy2779          68 LFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      |..|.++.+.||+||||+-...+
T Consensus         4 m~~g~ii~l~Gp~GsGKSTl~~~   26 (205)
T 3tr0_A            4 MNKANLFIISAPSGAGKTSLVRA   26 (205)
T ss_dssp             -CCCCEEEEECCTTSCHHHHHHH
T ss_pred             CCCCcEEEEECcCCCCHHHHHHH
Confidence            34688999999999999754333

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=92.90  E-value=0.021  Score=37.91  Aligned_cols=15  Identities=7%  Similarity=-0.208  Sum_probs=12.9

Q ss_pred             cceEEecCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKP   85 (101)
Q Consensus        71 g~~ll~~G~p~~g~~   85 (101)
                      +.-+|+.|||||||+
T Consensus        24 ~~~vll~G~~GtGKt   38 (145)
T 3n70_A           24 DIAVWLYGAPGTGRM   38 (145)
T ss_dssp             CSCEEEESSTTSSHH
T ss_pred             CCCEEEECCCCCCHH
Confidence            456889999999985

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=92.85  E-value=0.024  Score=38.09  Aligned_cols=18  Identities=17%  Similarity=0.119  Sum_probs=14.8

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .+..+++.|+|||||+-.
T Consensus         3 ~~~~I~i~G~~GsGKsT~   20 (213)
T 2plr_A            3 KGVLIAFEGIDGSGKSSQ   20 (213)
T ss_dssp             CCEEEEEECCTTSSHHHH
T ss_pred             CCeEEEEEcCCCCCHHHH
Confidence            467899999999998643

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=92.72  E-value=0.024  Score=37.87  Aligned_cols=20  Identities=20%  Similarity=0.140  Sum_probs=15.9

Q ss_pred             ccceEEecCCCCCCCCCCce
Q psy2779          70 RGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~   89 (101)
                      .|..+++.|+|||||+-...
T Consensus         3 ~g~~I~l~G~~GsGKST~~~   22 (186)
T 3cm0_A            3 VGQAVIFLGPPGAGKGTQAS   22 (186)
T ss_dssp             CEEEEEEECCTTSCHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            46788999999999975443

>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=92.69  E-value=0.022  Score=40.64  Aligned_cols=39  Identities=13%  Similarity=0.168  Sum_probs=25.5

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .+.+|||+.+.+..   .+.       +++++.   ..+|+.||||+|||-.
T Consensus        20 ~~~~~g~~~~~~~l---~~~-------l~~~~~---~~~ll~G~~G~GKt~l   58 (323)
T 1sxj_B           20 LSDIVGNKETIDRL---QQI-------AKDGNM---PHMIISGMPGIGKTTS   58 (323)
T ss_dssp             GGGCCSCTHHHHHH---HHH-------HHSCCC---CCEEEECSTTSSHHHH
T ss_pred             HHHHHCCHHHHHHH---HHH-------HHcCCC---CeEEEECcCCCCHHHH
Confidence            35699999887643   222       222221   2288999999999743

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=92.41  E-value=0.03  Score=38.49  Aligned_cols=22  Identities=9%  Similarity=-0.043  Sum_probs=18.4

Q ss_pred             ccccccceEEecCCCCCCCCCC
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +..-.|.++++.||||||||-+
T Consensus        18 gGl~~G~~~~i~G~~GsGKTtl   39 (247)
T 2dr3_A           18 GGIPERNVVLLSGGPGTGKTIF   39 (247)
T ss_dssp             TSEETTCEEEEEECTTSSHHHH
T ss_pred             CCCCCCcEEEEECCCCCCHHHH
Confidence            3455788999999999999866

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=92.37  E-value=0.033  Score=38.04  Aligned_cols=21  Identities=10%  Similarity=-0.086  Sum_probs=16.7

Q ss_pred             cccceEEecCCCCCCCCCCce
Q psy2779          69 FRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      +.|+.+++.||+||||+-...
T Consensus         3 ~~g~~i~i~GpsGsGKSTL~~   23 (180)
T 1kgd_A            3 HMRKTLVLLGAHGVGRRHIKN   23 (180)
T ss_dssp             CCCCEEEEECCTTSSHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHH
Confidence            468899999999999864433

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

Probab=92.29  E-value=0.025  Score=47.25  Aligned_cols=44  Identities=16%  Similarity=0.059  Sum_probs=26.8

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeecccccc---ccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLF---RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~---~g~~ll~~G~p~~g~~~   86 (101)
                      ..-+|||..|.++.--.+..       .+....-   .-+.+|+.||||||||-
T Consensus       490 ~~~viGq~~a~~~l~~~i~~-------~~~~~~~~~~p~~~~Ll~Gp~GtGKT~  536 (758)
T 3pxi_A          490 HSRVIGQDEAVVAVAKAVRR-------ARAGLKDPKRPIGSFIFLGPTGVGKTE  536 (758)
T ss_dssp             HTTSCSCHHHHHHHHHHHHH-------HTTTCSCTTSCSEEEEEESCTTSSHHH
T ss_pred             hCcCcChHHHHHHHHHHHHH-------HHcccCCCCCCceEEEEECCCCCCHHH
Confidence            35689999998775443333       2111000   01258899999999973

>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=92.25  E-value=0.039  Score=37.40  Aligned_cols=22  Identities=14%  Similarity=-0.022  Sum_probs=18.3

Q ss_pred             cccccceEEecCCCCCCCCCCc
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      .+-.|.++++.||||||||-+.
T Consensus        16 gi~~G~~~~i~G~~GsGKTtl~   37 (220)
T 2cvh_A           16 GFAPGVLTQVYGPYASGKTTLA   37 (220)
T ss_dssp             SBCTTSEEEEECSTTSSHHHHH
T ss_pred             CCcCCEEEEEECCCCCCHHHHH
Confidence            4556889999999999998654

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=92.22  E-value=0.037  Score=37.37  Aligned_cols=23  Identities=13%  Similarity=-0.041  Sum_probs=18.2

Q ss_pred             cccccceEEecCCCCCCCCCCce
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      ..-.|.++++.||||||||-+..
T Consensus        19 gi~~G~~~~i~G~~GsGKTtl~~   41 (235)
T 2w0m_A           19 GIPQGFFIALTGEPGTGKTIFSL   41 (235)
T ss_dssp             SEETTCEEEEECSTTSSHHHHHH
T ss_pred             CCcCCCEEEEEcCCCCCHHHHHH
Confidence            34468899999999999986543

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

Probab=92.10  E-value=0.018  Score=47.79  Aligned_cols=50  Identities=10%  Similarity=0.033  Sum_probs=30.9

Q ss_pred             ccccCcccchHHHHhhcceeeec--ccce-eeeeccccccccceEEecCCCCCCCC
Q psy2779          33 NEMAAGLVGQQAAREVSRAVTWE--KSFQ-FERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        33 ~~~a~GlVGQ~~AREAaGIVVdm--~~~~-~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .-.-+-+.|.+++.+..-=.|++  +.-+ |.+.   ..--.+-+|+.||||||||
T Consensus       178 ~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~---Gi~~prGvLLyGPPGTGKT  230 (437)
T 4b4t_I          178 TESYSDIGGLESQIQEIKESVELPLTHPELYEEM---GIKPPKGVILYGAPGTGKT  230 (437)
T ss_dssp             CCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHH---TCCCCSEEEEESSTTTTHH
T ss_pred             CCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhC---CCCCCCCCceECCCCchHH
Confidence            34446677888888887665554  1111 1111   2223456789999999997

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=92.07  E-value=0.038  Score=38.06  Aligned_cols=18  Identities=17%  Similarity=-0.058  Sum_probs=15.2

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .+..+++.|+||||||-.
T Consensus        24 ~~~~i~l~G~~GsGKsTl   41 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTL   41 (199)
T ss_dssp             CCCEEEEECCTTSCHHHH
T ss_pred             CCCEEEEEcCCCCCHHHH
Confidence            477899999999999743

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=92.05  E-value=0.036  Score=36.58  Aligned_cols=17  Identities=12%  Similarity=-0.060  Sum_probs=14.1

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      +..+++.|+|||||+-.
T Consensus         4 ~~~i~l~G~~GsGKSTl   20 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTI   20 (173)
T ss_dssp             CCCEEEECCTTSCHHHH
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            56789999999998643

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

Probab=92.04  E-value=0.019  Score=47.96  Aligned_cols=48  Identities=17%  Similarity=-0.002  Sum_probs=29.4

Q ss_pred             ccCcccchHHHHhhcceeeec--ccc-eeeeeccccccccceEEecCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWE--KSF-QFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm--~~~-~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .-+-+.|.+++.+..-=+|.+  +.- .|.+.   .+---+-+|+.||||||||
T Consensus       207 t~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~---Gi~pprGILLyGPPGTGKT  257 (467)
T 4b4t_H          207 TYSDVGGCKDQIEKLREVVELPLLSPERFATL---GIDPPKGILLYGPPGTGKT  257 (467)
T ss_dssp             CCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHH---TCCCCSEEEECSCTTSSHH
T ss_pred             CHHHhccHHHHHHHHHHHHHHHhcCHHHHHHC---CCCCCCceEeeCCCCCcHH
Confidence            345678888888887644443  111 11111   2223566789999999997

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=91.93  E-value=0.032  Score=37.37  Aligned_cols=17  Identities=18%  Similarity=0.233  Sum_probs=14.7

Q ss_pred             ccceEEecCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~   86 (101)
                      .|.++++.|+||||||-
T Consensus         8 ~g~~i~l~G~~GsGKST   24 (191)
T 1zp6_A            8 GGNILLLSGHPGSGKST   24 (191)
T ss_dssp             TTEEEEEEECTTSCHHH
T ss_pred             CCeEEEEECCCCCCHHH
Confidence            47889999999999864

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=91.92  E-value=0.078  Score=36.05  Aligned_cols=18  Identities=17%  Similarity=0.028  Sum_probs=15.4

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .|..+++.||||||||=.
T Consensus        35 ~g~~~~l~G~~G~GKTtL   52 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHL   52 (149)
T ss_dssp             CCSEEEEESSSTTTTCHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            478899999999999743

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=91.86  E-value=0.033  Score=37.14  Aligned_cols=18  Identities=11%  Similarity=0.058  Sum_probs=14.9

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .+..+++.|+|||||+-.
T Consensus         4 ~~~~I~l~G~~GsGKST~   21 (193)
T 2rhm_A            4 TPALIIVTGHPATGKTTL   21 (193)
T ss_dssp             CCEEEEEEESTTSSHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            467899999999999744

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=91.85  E-value=0.042  Score=37.04  Aligned_cols=18  Identities=33%  Similarity=0.359  Sum_probs=15.0

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .|..+++.|+|||||+-.
T Consensus         3 ~~~~I~l~G~~GsGKsT~   20 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTTQ   20 (204)
T ss_dssp             CCCEEEEECCTTSSHHHH
T ss_pred             CCcEEEEEcCCCCCHHHH
Confidence            477899999999998743

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

Probab=91.84  E-value=0.04  Score=45.40  Aligned_cols=51  Identities=16%  Similarity=0.180  Sum_probs=29.5

Q ss_pred             cccccCcccchHHHHhhcceeeec-ccce-eeeeccccccccceEEecCCCCCCCC
Q psy2779          32 ANEMAAGLVGQQAAREVSRAVTWE-KSFQ-FERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        32 a~~~a~GlVGQ~~AREAaGIVVdm-~~~~-~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      +....+-++||.++.+..-=+++. +..+ |-.+ +-+.-.|  +|+.||||||||
T Consensus        26 ~~~~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~l-g~~ip~G--vLL~GppGtGKT   78 (499)
T 2dhr_A           26 PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEM-GARIPKG--VLLVGPPGVGKT   78 (499)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHHHHHCGGGTTTT-SCCCCSE--EEEECSSSSSHH
T ss_pred             CCCCHHHcCCcHHHHHHHHHHHHHhhchhhhhhc-cCCCCce--EEEECCCCCCHH
Confidence            344556799999998877655443 1000 0000 0111123  889999999986

>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=91.77  E-value=0.031  Score=46.34  Aligned_cols=45  Identities=20%  Similarity=0.090  Sum_probs=26.3

Q ss_pred             cCcccchHHHHhhcceeeecccceeeee--ccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERC--KSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~--~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ...+|||.+|.++.--.+..     .+.  ++.++ .-..+|+.||||||||-
T Consensus       457 ~~~v~g~~~~~~~l~~~i~~-----~~~g~~~~~~-p~~~~ll~G~~GtGKT~  503 (758)
T 1r6b_X          457 KMLVFGQDKAIEALTEAIKM-----ARAGLGHEHK-PVGSFLFAGPTGVGKTE  503 (758)
T ss_dssp             TTTSCSCHHHHHHHHHHHHH-----HHTTCSCTTS-CSEEEEEECSTTSSHHH
T ss_pred             HhhccCHHHHHHHHHHHHHH-----HhcccCCCCC-CceEEEEECCCCCcHHH
Confidence            45689999988764332222     110  00000 11368899999999973

>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=91.70  E-value=0.052  Score=47.65  Aligned_cols=47  Identities=11%  Similarity=0.094  Sum_probs=29.7

Q ss_pred             cCcccchHHHHhhcceeeeccc---ceeeeeccccccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKS---FQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~---~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      -+-+.|.+++.+...-.+.+-.   ..|.+.   .+--.+-+|+.||||||||
T Consensus       476 w~diggl~~~k~~l~e~v~~p~~~p~~f~~~---g~~~~~gvLl~GPPGtGKT  525 (806)
T 3cf2_A          476 WEDIGGLEDVKRELQELVQYPVEHPDKFLKF---GMTPSKGVLFYGPPGCGKT  525 (806)
T ss_dssp             STTCCSCHHHHHHHTTTTTTTTTCSGGGSSS---CCCCCSCCEEESSTTSSHH
T ss_pred             HHHhCCHHHHHHHHHHHHHhhhhCHHHHHhc---CCCCCceEEEecCCCCCch
Confidence            4557788898888776665411   112222   2223455789999999986

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=91.60  E-value=0.047  Score=36.30  Aligned_cols=18  Identities=17%  Similarity=-0.068  Sum_probs=15.5

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .|..+++.|+|||||+-.
T Consensus         7 ~g~~i~l~G~~GsGKSTl   24 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAV   24 (175)
T ss_dssp             TSEEEEEECSTTSCHHHH
T ss_pred             CCcEEEEEcCCCCCHHHH
Confidence            578899999999999754

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=91.58  E-value=0.051  Score=37.38  Aligned_cols=24  Identities=13%  Similarity=0.015  Sum_probs=19.0

Q ss_pred             cccccceEEecCCCCCCCCCCcee
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      .+-.|.++++.||||||||-+..+
T Consensus        20 gi~~G~~~~i~G~~GsGKTtl~~~   43 (243)
T 1n0w_A           20 GIETGSITEMFGEFRTGKTQICHT   43 (243)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHH
T ss_pred             CCcCCeEEEEECCCCCcHHHHHHH
Confidence            455688999999999999865443

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=91.53  E-value=0.044  Score=45.11  Aligned_cols=16  Identities=19%  Similarity=0.140  Sum_probs=13.8

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      .....|+.||||||||
T Consensus       204 ~~~~~lI~GPPGTGKT  219 (646)
T 4b3f_X          204 QKELAIIHGPPGTGKT  219 (646)
T ss_dssp             CSSEEEEECCTTSCHH
T ss_pred             CCCceEEECCCCCCHH
Confidence            3458899999999997

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=91.46  E-value=0.047  Score=37.02  Aligned_cols=20  Identities=20%  Similarity=0.154  Sum_probs=16.1

Q ss_pred             ccccceEEecCCCCCCCCCC
Q psy2779          68 LFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +..+..+++.|+|||||+-.
T Consensus         7 ~~~~~~I~l~G~~GsGKST~   26 (212)
T 2wwf_A            7 KKKGKFIVFEGLDRSGKSTQ   26 (212)
T ss_dssp             CBCSCEEEEEESTTSSHHHH
T ss_pred             hhcCCEEEEEcCCCCCHHHH
Confidence            33578899999999998743

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=91.45  E-value=0.048  Score=36.55  Aligned_cols=20  Identities=10%  Similarity=-0.021  Sum_probs=15.9

Q ss_pred             ccccceEEecCCCCCCCCCC
Q psy2779          68 LFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +..+..+++.|+|||||+-.
T Consensus         8 ~~~~~~i~i~G~~GsGKst~   27 (180)
T 3iij_A            8 FMLLPNILLTGTPGVGKTTL   27 (180)
T ss_dssp             TCCCCCEEEECSTTSSHHHH
T ss_pred             cccCCeEEEEeCCCCCHHHH
Confidence            33567899999999999743

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=91.25  E-value=0.082  Score=35.01  Aligned_cols=19  Identities=16%  Similarity=0.027  Sum_probs=11.0

Q ss_pred             ccceEEecCCCCCCCCCCc
Q psy2779          70 RGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~   88 (101)
                      .+..+++.|+|||||+-..
T Consensus         4 ~~~~I~l~G~~GsGKST~a   22 (183)
T 2vli_A            4 RSPIIWINGPFGVGKTHTA   22 (183)
T ss_dssp             -CCEEEEECCC----CHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3568999999999998543

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=91.03  E-value=0.047  Score=36.46  Aligned_cols=18  Identities=11%  Similarity=0.025  Sum_probs=15.1

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .+..+++.|+|||||+-.
T Consensus         8 ~~~~I~l~G~~GsGKsT~   25 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQ   25 (196)
T ss_dssp             TSCEEEEEECTTSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            467899999999999743

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=91.01  E-value=0.093  Score=36.81  Aligned_cols=24  Identities=17%  Similarity=0.199  Sum_probs=15.3

Q ss_pred             cccceEEecCCCCCCCCCCceeee
Q psy2779          69 FRGGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      -.|.++.+.||+||||+-.-.++.
T Consensus        25 ~~G~ii~l~Gp~GsGKSTl~~~L~   48 (231)
T 3lnc_A           25 SVGVILVLSSPSGCGKTTVANKLL   48 (231)
T ss_dssp             ECCCEEEEECSCC----CHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHH
Confidence            358899999999999987655544

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=90.92  E-value=0.049  Score=36.90  Aligned_cols=19  Identities=26%  Similarity=0.310  Sum_probs=15.6

Q ss_pred             cccceEEecCCCCCCCCCC
Q psy2779          69 FRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~~~   87 (101)
                      ..+..+++.|+|||||+-.
T Consensus         7 ~~~~~I~l~G~~GsGKsT~   25 (215)
T 1nn5_A            7 RRGALIVLEGVDRAGKSTQ   25 (215)
T ss_dssp             CCCCEEEEEESTTSSHHHH
T ss_pred             cCCcEEEEECCCCCCHHHH
Confidence            3578899999999998743

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=90.85  E-value=0.034  Score=43.49  Aligned_cols=17  Identities=6%  Similarity=-0.134  Sum_probs=14.6

Q ss_pred             ccceEEecCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~   86 (101)
                      .+..+|+.||||||||-
T Consensus        44 ~~~~lli~GpPGTGKT~   60 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQ   60 (318)
T ss_dssp             CCCEEEEECCCSHHHHH
T ss_pred             CCCeEEEECCCCCCHHH
Confidence            37788999999999973

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=90.83  E-value=0.061  Score=36.20  Aligned_cols=18  Identities=22%  Similarity=0.159  Sum_probs=15.1

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .|..+++.|++||||+-.
T Consensus         5 ~g~~i~l~G~~GsGKSTl   22 (207)
T 2j41_A            5 KGLLIVLSGPSGVGKGTV   22 (207)
T ss_dssp             CCCEEEEECSTTSCHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            478899999999998643

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=90.75  E-value=0.059  Score=36.00  Aligned_cols=18  Identities=11%  Similarity=-0.197  Sum_probs=14.4

Q ss_pred             cceEEecCCCCCCCCCCc
Q psy2779          71 GGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~   88 (101)
                      ++.+++.|+||||||-..
T Consensus         5 ~~~i~l~G~~GsGKst~a   22 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVG   22 (185)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            467889999999997543

>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=90.70  E-value=0.047  Score=44.47  Aligned_cols=47  Identities=9%  Similarity=-0.033  Sum_probs=26.7

Q ss_pred             cCcccchHHHHhhcceeeec--ccce-eeeeccccccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWE--KSFQ-FERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm--~~~~-~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .+.++|+..+.+..-=.+..  +.-+ |.+.   ..-..+-+|+.||||||||
T Consensus       203 ~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~---g~~~~~~vLL~GppGtGKT  252 (489)
T 3hu3_A          203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAI---GVKPPRGILLYGPPGTGKT  252 (489)
T ss_dssp             GGGCCSCHHHHHHHHHHTHHHHHCHHHHHHH---TCCCCCEEEEECSTTSSHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhhCHHHHHhc---CCCCCCcEEEECcCCCCHH
Confidence            35689998887765433332  0000 0000   1122456889999999997

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=90.47  E-value=0.071  Score=36.31  Aligned_cols=20  Identities=15%  Similarity=-0.021  Sum_probs=16.9

Q ss_pred             ccceEEecCCCCCCCCCCce
Q psy2779          70 RGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~   89 (101)
                      .|.++.+.||+||||+-+-.
T Consensus         8 ~gei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHH
Confidence            58899999999999986544

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=90.40  E-value=0.039  Score=41.43  Aligned_cols=15  Identities=13%  Similarity=0.167  Sum_probs=13.0

Q ss_pred             cceEEecCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKP   85 (101)
Q Consensus        71 g~~ll~~G~p~~g~~   85 (101)
                      ..-+|+.|||||||+
T Consensus        25 ~~~vLi~Ge~GtGKt   39 (304)
T 1ojl_A           25 DATVLIHGDSGTGKE   39 (304)
T ss_dssp             TSCEEEESCTTSCHH
T ss_pred             CCcEEEECCCCchHH
Confidence            567889999999986

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=90.40  E-value=0.084  Score=39.49  Aligned_cols=17  Identities=18%  Similarity=0.212  Sum_probs=14.5

Q ss_pred             ccceEEecCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~   86 (101)
                      .+.++++.|+|||||+-
T Consensus        32 ~~~livl~G~sGsGKST   48 (287)
T 1gvn_B           32 SPTAFLLGGQPGSGKTS   48 (287)
T ss_dssp             SCEEEEEECCTTSCTHH
T ss_pred             CCeEEEEECCCCCCHHH
Confidence            36789999999999963

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

Probab=90.36  E-value=0.089  Score=43.89  Aligned_cols=38  Identities=13%  Similarity=0.041  Sum_probs=25.0

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+++-+..--++.          .   -...-+|+.||||||||-
T Consensus       179 ld~iiG~~~~i~~l~~~l~----------~---~~~~~vLL~G~pGtGKT~  216 (758)
T 3pxi_A          179 LDPVIGRSKEIQRVIEVLS----------R---RTKNNPVLIGEPGVGKTA  216 (758)
T ss_dssp             SCCCCCCHHHHHHHHHHHH----------C---SSSCEEEEESCTTTTTHH
T ss_pred             CCCccCchHHHHHHHHHHh----------C---CCCCCeEEECCCCCCHHH
Confidence            4569999988775322211          1   123457899999999973

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=90.35  E-value=0.073  Score=36.31  Aligned_cols=18  Identities=17%  Similarity=0.169  Sum_probs=15.1

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .+..+++.|+|||||+-.
T Consensus         9 ~~~~I~l~G~~GsGKSTv   26 (184)
T 1y63_A            9 KGINILITGTPGTGKTSM   26 (184)
T ss_dssp             SSCEEEEECSTTSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            467899999999999744

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=90.24  E-value=0.08  Score=39.91  Aligned_cols=24  Identities=13%  Similarity=-0.007  Sum_probs=19.9

Q ss_pred             ccccccceEEecCCCCCCCCCCce
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      +.+-.|..++++|+||+|||-|..
T Consensus        63 gGl~~G~l~li~G~pG~GKTtl~l   86 (315)
T 3bh0_A           63 YGYKRRNFVLIAARPSMGKTAFAL   86 (315)
T ss_dssp             SSBCTTCEEEEECCTTSSHHHHHH
T ss_pred             CCCCCCcEEEEEeCCCCCHHHHHH
Confidence            456678999999999999987653

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=90.17  E-value=0.076  Score=37.13  Aligned_cols=20  Identities=25%  Similarity=0.177  Sum_probs=16.1

Q ss_pred             ccceEEecCCCCCCCCCCce
Q psy2779          70 RGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~   89 (101)
                      .|.++++.||+||||+-...
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~   26 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVRE   26 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHHH
Confidence            58899999999999864433

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=89.85  E-value=0.068  Score=36.32  Aligned_cols=24  Identities=8%  Similarity=-0.110  Sum_probs=18.6

Q ss_pred             cccccceEEecCCCCCCCCCCcee
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      ..-.|.++.+.||||||||-+-.+
T Consensus        21 gi~~G~~~~l~G~nGsGKSTll~~   44 (231)
T 4a74_A           21 GIETQAITEVFGEFGSGKTQLAHT   44 (231)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHH
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHH
Confidence            444688999999999999755443

>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=89.57  E-value=0.076  Score=42.59  Aligned_cols=23  Identities=17%  Similarity=0.343  Sum_probs=18.6

Q ss_pred             ccccccceEEecCCCCCCCCCCc
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +....|+.+|+.||||||||-+.
T Consensus       118 GGi~~gsviLI~GpPGsGKTtLA  140 (331)
T 2vhj_A          118 GHRYASGMVIVTGKGNSGKTPLV  140 (331)
T ss_dssp             TEEEESEEEEEECSCSSSHHHHH
T ss_pred             CCCCCCcEEEEEcCCCCCHHHHH
Confidence            45567788899999999998654

>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=89.39  E-value=0.072  Score=45.38  Aligned_cols=43  Identities=19%  Similarity=0.058  Sum_probs=26.5

Q ss_pred             CcccchHHHHhhcceeeecccceeeeecccccc---ccceEEecCCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSLF---RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~---~g~~ll~~G~p~~g~~~   86 (101)
                      ..+|||..|-++..-.+..       ...+-.-   .-..+|+.||||||||=
T Consensus       558 ~~viG~~~a~~~l~~~i~~-------~~~g~~~~~~p~~~vLl~Gp~GtGKT~  603 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRR-------ARAGLKDPNRPIGSFLFLGPTGVGKTE  603 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHH-------HGGGCSCSSSCSEEEEEBSCSSSSHHH
T ss_pred             cccCCcHHHHHHHHHHHHH-------HhcccCCCCCCceEEEEECCCCCCHHH
Confidence            4689999987775444333       2111000   01478899999999963

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=89.17  E-value=0.089  Score=37.23  Aligned_cols=17  Identities=24%  Similarity=0.384  Sum_probs=15.3

Q ss_pred             cccceEEecCCCCCCCC
Q psy2779          69 FRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~   85 (101)
                      ..|+.+++.||||||||
T Consensus        74 ~~g~~~~i~g~TGsGKT   90 (235)
T 3llm_A           74 SQNSVVIIRGATGCGKT   90 (235)
T ss_dssp             HHCSEEEEECCTTSSHH
T ss_pred             hcCCEEEEEeCCCCCcH
Confidence            35889999999999998

>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=89.13  E-value=0.089  Score=42.21  Aligned_cols=51  Identities=10%  Similarity=-0.035  Sum_probs=27.4

Q ss_pred             cCcccchHHHHhhcceeeec-cc---ceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWE-KS---FQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm-~~---~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+-+|||+++.+..--.++- ..   ..|.+......-..+.+|+.||||||||-
T Consensus        38 ~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTt   92 (516)
T 1sxj_A           38 LQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTT   92 (516)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHH
T ss_pred             HHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHH
Confidence            35699999887764433322 00   00000000000023689999999999973

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=89.07  E-value=0.088  Score=38.29  Aligned_cols=24  Identities=8%  Similarity=-0.062  Sum_probs=19.3

Q ss_pred             cccccceEEecCCCCCCCCCCcee
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      .+-.|.++++.||||||||-+..+
T Consensus        31 ~l~~G~~~~i~G~~G~GKTTl~~~   54 (296)
T 1cr0_A           31 GARGGEVIMVTSGSGMGKSTFVRQ   54 (296)
T ss_dssp             SBCTTCEEEEEESTTSSHHHHHHH
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHH
Confidence            455789999999999999866443

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=88.99  E-value=0.087  Score=36.76  Aligned_cols=22  Identities=14%  Similarity=0.065  Sum_probs=15.9

Q ss_pred             ccceEEecCCCCCCCCCCceee
Q psy2779          70 RGGRAVAGGRTKCPKPPNTSMI   91 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~~~   91 (101)
                      .|+.+.+.||+||||+-...++
T Consensus         3 ~g~~i~lvGpsGaGKSTLl~~L   24 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLLKKL   24 (198)
T ss_dssp             --CCEEEECCTTSSHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHH
Confidence            5788999999999987544443

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=88.91  E-value=0.21  Score=39.33  Aligned_cols=20  Identities=15%  Similarity=-0.041  Sum_probs=16.7

Q ss_pred             cccccceEEecCCCCCCCCC
Q psy2779          67 SLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~   86 (101)
                      -+..++.+|+.+|||||||=
T Consensus        17 ~l~~~~~vlv~a~TGsGKT~   36 (459)
T 2z83_A           17 MLRKRQMTVLDLHPGSGKTR   36 (459)
T ss_dssp             GGSTTCEEEECCCTTSCTTT
T ss_pred             HHhcCCcEEEECCCCCCHHH
Confidence            34457889999999999985

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=88.89  E-value=0.14  Score=37.64  Aligned_cols=19  Identities=11%  Similarity=-0.027  Sum_probs=15.1

Q ss_pred             cccceEEecCCCCCCCCCC
Q psy2779          69 FRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~~~   87 (101)
                      ...+++++-|||||||.-.
T Consensus        27 ~k~kiI~llGpPGsGKgTq   45 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQ   45 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHH
T ss_pred             cCCcEEEEECCCCCCHHHH
Confidence            3467889999999999643

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=88.85  E-value=0.07  Score=35.68  Aligned_cols=18  Identities=11%  Similarity=-0.058  Sum_probs=15.0

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .+..+++.|+|||||+-.
T Consensus        11 ~~~~I~l~G~~GsGKsT~   28 (199)
T 2bwj_A           11 KCKIIFIIGGPGSGKGTQ   28 (199)
T ss_dssp             HSCEEEEEECTTSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            467899999999999744

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=88.82  E-value=0.073  Score=40.48  Aligned_cols=17  Identities=18%  Similarity=-0.048  Sum_probs=14.2

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      .+.+|+.||||||||-+
T Consensus        58 kn~ili~GPPGtGKTt~   74 (212)
T 1tue_A           58 KNCLVFCGPANTGKSYF   74 (212)
T ss_dssp             CSEEEEESCGGGCHHHH
T ss_pred             ccEEEEECCCCCCHHHH
Confidence            45699999999999844

>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=88.47  E-value=0.1  Score=43.21  Aligned_cols=37  Identities=16%  Similarity=0.097  Sum_probs=23.6

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +-+|||.+.-+.   +.++       ..   ...+.-+|+.||||||||-
T Consensus       186 d~~iGr~~~i~~---l~~~-------l~---~~~~~~vlL~G~~GtGKT~  222 (758)
T 1r6b_X          186 DPLIGREKELER---AIQV-------LC---RRRKNNPLLVGESGVGKTA  222 (758)
T ss_dssp             CCCCSCHHHHHH---HHHH-------HT---SSSSCEEEEECCTTSSHHH
T ss_pred             CCccCCHHHHHH---HHHH-------Hh---ccCCCCeEEEcCCCCCHHH
Confidence            457888776554   2222       11   1135668899999999973

>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=88.43  E-value=0.088  Score=38.90  Aligned_cols=46  Identities=13%  Similarity=-0.005  Sum_probs=26.5

Q ss_pred             cccCcccchHHHHhhcceee-ecccceeeeeccccccccceEEe--cCCCCCCCCC
Q psy2779          34 EMAAGLVGQQAAREVSRAVT-WEKSFQFERCKSHSLFRGGRAVA--GGRTKCPKPP   86 (101)
Q Consensus        34 ~~a~GlVGQ~~AREAaGIVV-dm~~~~~~~~~~~~~~~g~~ll~--~G~p~~g~~~   86 (101)
                      +...-|||+++..+..--.+ +-       +..+-.-.++.+++  .||||+|||-
T Consensus        19 ~~p~~l~gR~~el~~l~~~l~~~-------~~~~~~~~~~~~li~i~G~~G~GKT~   67 (412)
T 1w5s_A           19 YIPPELRVRRGEAEALARIYLNR-------LLSGAGLSDVNMIYGSIGRVGIGKTT   67 (412)
T ss_dssp             CCCSSCSSSCHHHHHHHHHHHHH-------HHTSSCBCCEEEEEECTTCCSSSHHH
T ss_pred             cCCCCCCChHHHHHHHHHHHhHH-------HhcCCCCCCCEEEEeCcCcCCCCHHH
Confidence            34467999887555432222 11       11110013568889  9999999974

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=88.43  E-value=0.11  Score=39.21  Aligned_cols=16  Identities=13%  Similarity=-0.168  Sum_probs=13.9

Q ss_pred             cceEEecCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPP   86 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~   86 (101)
                      +.-+++.||||||||=
T Consensus       152 ~~~lll~G~~GtGKT~  167 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSY  167 (308)
T ss_dssp             CCEEEEECSTTSSHHH
T ss_pred             CceEEEECCCCCCHHH
Confidence            5778999999999973

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=88.31  E-value=0.12  Score=37.41  Aligned_cols=21  Identities=14%  Similarity=0.237  Sum_probs=15.0

Q ss_pred             cccccccceEEecCCCCCCCC
Q psy2779          65 SHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        65 ~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      -|-|-.|.++++.||+||||+
T Consensus        10 ~~~~~~G~ii~l~GpsGsGKS   30 (219)
T 1s96_A           10 HHHMAQGTLYIVSAPSGAGKS   30 (219)
T ss_dssp             -----CCCEEEEECCTTSCHH
T ss_pred             cccCCCCcEEEEECCCCCCHH
Confidence            456778999999999999975

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=88.18  E-value=0.094  Score=34.55  Aligned_cols=18  Identities=11%  Similarity=-0.040  Sum_probs=14.5

Q ss_pred             cceEEecCCCCCCCCCCc
Q psy2779          71 GGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~   88 (101)
                      ...+++.|+|||||+-..
T Consensus         6 ~~~I~l~G~~GsGKsT~~   23 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQC   23 (194)
T ss_dssp             CEEEEEEESTTSSHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            357899999999997543

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=88.18  E-value=0.11  Score=35.68  Aligned_cols=17  Identities=18%  Similarity=0.157  Sum_probs=14.9

Q ss_pred             ccceEEecCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~   86 (101)
                      .|.++.+.|++||||+-
T Consensus        24 ~g~~i~l~G~sGsGKST   40 (200)
T 3uie_A           24 KGCVIWVTGLSGSGKST   40 (200)
T ss_dssp             CCEEEEEECSTTSSHHH
T ss_pred             CCeEEEEECCCCCCHHH
Confidence            47899999999999974

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=88.05  E-value=0.13  Score=37.13  Aligned_cols=20  Identities=10%  Similarity=-0.054  Sum_probs=16.2

Q ss_pred             ccceEEecCCCCCCCCCCce
Q psy2779          70 RGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~   89 (101)
                      .|..+++.|+|||||+-...
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~   44 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVIN   44 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHH
Confidence            57889999999999975443

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=88.02  E-value=0.11  Score=37.73  Aligned_cols=25  Identities=8%  Similarity=-0.031  Sum_probs=20.3

Q ss_pred             cccccceEEecCCCCCCCCCCceee
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTSMI   91 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~~~   91 (101)
                      .+..|.++++.||||||||-+...+
T Consensus        26 gl~~G~i~~i~G~~GsGKTtl~~~l   50 (279)
T 1nlf_A           26 NMVAGTVGALVSPGGAGKSMLALQL   50 (279)
T ss_dssp             TEETTSEEEEEESTTSSHHHHHHHH
T ss_pred             CccCCCEEEEEcCCCCCHHHHHHHH
Confidence            5667999999999999998765443

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=87.86  E-value=0.11  Score=38.53  Aligned_cols=24  Identities=13%  Similarity=-0.101  Sum_probs=19.4

Q ss_pred             ccccccceEEecCCCCCCCCCCce
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      +.+-.|.++++.||||||||-+.-
T Consensus        93 GGl~~g~i~~i~G~~gsGKT~la~  116 (322)
T 2i1q_A           93 GGLESQSVTEFAGVFGSGKTQIMH  116 (322)
T ss_dssp             SSEETTEEEEEEESTTSSHHHHHH
T ss_pred             CCccCCeEEEEECCCCCCHHHHHH
Confidence            345668899999999999987653

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=87.66  E-value=0.14  Score=37.40  Aligned_cols=21  Identities=10%  Similarity=-0.081  Sum_probs=16.9

Q ss_pred             cccccceEEecCCCCCCCCCC
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      ..+.|+.+++.||+||||+-.
T Consensus        15 ~~~~g~~ivl~GPSGaGKsTL   35 (197)
T 3ney_A           15 YFQGRKTLVLIGASGVGRSHI   35 (197)
T ss_dssp             -CCSCCEEEEECCTTSSHHHH
T ss_pred             CCCCCCEEEEECcCCCCHHHH
Confidence            346799999999999998643

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=87.65  E-value=0.12  Score=37.29  Aligned_cols=18  Identities=17%  Similarity=0.172  Sum_probs=14.9

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .+..+++.|+|||||+-.
T Consensus        31 ~~~~i~l~G~~GsGKSTl   48 (253)
T 2p5t_B           31 QPIAILLGGQSGAGKTTI   48 (253)
T ss_dssp             SCEEEEEESCGGGTTHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            467899999999999743

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=87.62  E-value=0.14  Score=34.86  Aligned_cols=17  Identities=18%  Similarity=0.044  Sum_probs=14.0

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      +..+++.|+|||||+-.
T Consensus        20 ~~~I~l~G~~GsGKST~   36 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQ   36 (201)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            55788999999999743

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=87.43  E-value=0.13  Score=38.70  Aligned_cols=24  Identities=8%  Similarity=-0.182  Sum_probs=19.3

Q ss_pred             ccccccceEEecCCCCCCCCCCce
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      +.+-.|.++++.||||||||-+..
T Consensus       102 GGl~~G~i~~i~G~~GsGKT~la~  125 (324)
T 2z43_A          102 GGIETRTMTEFFGEFGSGKTQLCH  125 (324)
T ss_dssp             TSEETTSEEEEEESTTSSHHHHHH
T ss_pred             CCCCCCcEEEEECCCCCCHhHHHH
Confidence            355678899999999999986643

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=87.25  E-value=0.16  Score=35.29  Aligned_cols=17  Identities=24%  Similarity=0.073  Sum_probs=14.2

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      +..+++.|+|||||+-.
T Consensus         4 ~~~I~l~G~~GsGKsT~   20 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQ   20 (220)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             CcEEEEECCCCCCHHHH
Confidence            56788999999999754

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=87.05  E-value=0.15  Score=37.04  Aligned_cols=17  Identities=12%  Similarity=-0.150  Sum_probs=14.0

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      +..+++.|+|||||+-.
T Consensus         4 ~~lIvl~G~pGSGKSTl   20 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTF   20 (260)
T ss_dssp             CEEEEEECCTTSSHHHH
T ss_pred             CEEEEEEcCCCCCHHHH
Confidence            45789999999999743

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=87.03  E-value=0.14  Score=34.99  Aligned_cols=17  Identities=24%  Similarity=0.184  Sum_probs=14.0

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      ..++++.|+|||||+-.
T Consensus        18 ~~~I~l~G~~GsGKSTl   34 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSV   34 (202)
T ss_dssp             SSCEEEECSTTSCHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            35789999999999744

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=86.90  E-value=0.18  Score=38.55  Aligned_cols=23  Identities=13%  Similarity=-0.050  Sum_probs=18.8

Q ss_pred             cccccceEEecCCCCCCCCCCce
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      .+-.|.++++.||||||||-+.-
T Consensus       118 Gl~~G~i~~I~G~~GsGKTtla~  140 (343)
T 1v5w_A          118 GIESMAITEAFGEFRTGKTQLSH  140 (343)
T ss_dssp             SBCSSEEEEEECCTTCTHHHHHH
T ss_pred             CCCCCeEEEEECCCCCCHHHHHH
Confidence            45568899999999999986643

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=86.75  E-value=0.22  Score=34.51  Aligned_cols=20  Identities=10%  Similarity=0.016  Sum_probs=16.4

Q ss_pred             ccceEEecCCCCCCCCCCce
Q psy2779          70 RGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~   89 (101)
                      .|.++.+.||+|||||-+..
T Consensus        21 ~g~~v~I~G~sGsGKSTl~~   40 (208)
T 3c8u_A           21 GRQLVALSGAPGSGKSTLSN   40 (208)
T ss_dssp             SCEEEEEECCTTSCTHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            47889999999999985443

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=86.64  E-value=0.16  Score=34.18  Aligned_cols=19  Identities=16%  Similarity=0.022  Sum_probs=15.9

Q ss_pred             ccceEEecCCCCCCCCCCc
Q psy2779          70 RGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~   88 (101)
                      .|..+++.|+||||||-..
T Consensus        12 ~~~~i~l~G~~GsGKsT~~   30 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIA   30 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHH
Confidence            4788999999999997543

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=86.53  E-value=0.16  Score=33.95  Aligned_cols=15  Identities=20%  Similarity=-0.064  Sum_probs=12.3

Q ss_pred             eEEecCCCCCCCCCC
Q psy2779          73 RAVAGGRTKCPKPPN   87 (101)
Q Consensus        73 ~ll~~G~p~~g~~~~   87 (101)
                      .+++.|+|||||+-.
T Consensus         6 ~i~i~G~~GsGKsTl   20 (175)
T 1via_A            6 NIVFIGFMGSGKSTL   20 (175)
T ss_dssp             CEEEECCTTSCHHHH
T ss_pred             EEEEEcCCCCCHHHH
Confidence            578999999999743

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=86.46  E-value=0.17  Score=39.83  Aligned_cols=24  Identities=17%  Similarity=0.095  Sum_probs=19.5

Q ss_pred             ccccccceEEecCCCCCCCCCCce
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      +.+-.|..++++|+||+|||-|..
T Consensus       195 gGl~~G~l~ii~G~pg~GKT~lal  218 (444)
T 2q6t_A          195 GTLGPGSLNIIAARPAMGKTAFAL  218 (444)
T ss_dssp             CCCCTTCEEEEEECTTSCHHHHHH
T ss_pred             CCcCCCcEEEEEeCCCCCHHHHHH
Confidence            345678899999999999987643

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=86.26  E-value=0.18  Score=33.81  Aligned_cols=19  Identities=21%  Similarity=0.190  Sum_probs=15.5

Q ss_pred             ccceEEecCCCCCCCCCCc
Q psy2779          70 RGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~   88 (101)
                      .|..+++.|++||||+-..
T Consensus         4 ~g~~i~l~G~~GsGKST~~   22 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVS   22 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4778899999999997543

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=86.22  E-value=0.18  Score=35.95  Aligned_cols=38  Identities=5%  Similarity=-0.073  Sum_probs=24.9

Q ss_pred             ccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      ...-|||.++.-+..   .+.       ++     .|+.+++.||+|+|||-.
T Consensus        10 ~~~~~~gR~~el~~L---~~~-------l~-----~~~~v~i~G~~G~GKT~L   47 (350)
T 2qen_A           10 RREDIFDREEESRKL---EES-------LE-----NYPLTLLLGIRRVGKSSL   47 (350)
T ss_dssp             SGGGSCSCHHHHHHH---HHH-------HH-----HCSEEEEECCTTSSHHHH
T ss_pred             ChHhcCChHHHHHHH---HHH-------Hh-----cCCeEEEECCCcCCHHHH
Confidence            345688887654442   222       11     147999999999999743

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=86.19  E-value=0.18  Score=37.53  Aligned_cols=19  Identities=21%  Similarity=0.181  Sum_probs=16.1

Q ss_pred             cccceEEecCCCCCCCCCC
Q psy2779          69 FRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~~~   87 (101)
                      -.|..+++.||+|||||-.
T Consensus        23 ~~g~~v~i~Gp~GsGKSTl   41 (261)
T 2eyu_A           23 RKMGLILVTGPTGSGKSTT   41 (261)
T ss_dssp             CSSEEEEEECSTTCSHHHH
T ss_pred             CCCCEEEEECCCCccHHHH
Confidence            3688999999999999743

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=86.03  E-value=0.18  Score=38.92  Aligned_cols=18  Identities=11%  Similarity=-0.110  Sum_probs=14.5

Q ss_pred             cceEEecCCCCCCCCCCc
Q psy2779          71 GGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~   88 (101)
                      ...+|+.||||||||=+.
T Consensus       104 ~n~~~l~GppgtGKt~~a  121 (267)
T 1u0j_A          104 RNTIWLFGPATTGKTNIA  121 (267)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            457999999999997543

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=85.99  E-value=0.22  Score=39.26  Aligned_cols=24  Identities=13%  Similarity=0.118  Sum_probs=19.7

Q ss_pred             ccccccceEEecCCCCCCCCCCce
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      ..+-.|..++++|+||+|||-|..
T Consensus       198 gGl~~G~liiI~G~pG~GKTtl~l  221 (454)
T 2r6a_A          198 SGFQRSDLIIVAARPSVGKTAFAL  221 (454)
T ss_dssp             SSBCTTCEEEEECCTTSCHHHHHH
T ss_pred             CCCCCCCEEEEECCCCCCHHHHHH
Confidence            356678999999999999987653

>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=85.65  E-value=0.19  Score=39.09  Aligned_cols=22  Identities=23%  Similarity=0.114  Sum_probs=18.3

Q ss_pred             cccccceEEecCCCCCCCCCCc
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      .+-.|+++++.||||||||-+.
T Consensus        57 Gl~~G~iv~I~G~pGsGKTtLa   78 (349)
T 2zr9_A           57 GLPRGRVIEIYGPESSGKTTVA   78 (349)
T ss_dssp             SEETTSEEEEEESTTSSHHHHH
T ss_pred             CccCCeEEEEECCCCCCHHHHH
Confidence            4556899999999999998653

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=85.57  E-value=0.19  Score=34.04  Aligned_cols=18  Identities=11%  Similarity=-0.080  Sum_probs=14.4

Q ss_pred             cceEEecCCCCCCCCCCc
Q psy2779          71 GGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~   88 (101)
                      ...+++.|+|||||+-..
T Consensus        15 ~~~I~l~G~~GsGKsT~~   32 (203)
T 1ukz_A           15 VSVIFVLGGPGAGKGTQC   32 (203)
T ss_dssp             CEEEEEECSTTSSHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            357889999999997543

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=85.30  E-value=0.17  Score=34.63  Aligned_cols=19  Identities=16%  Similarity=-0.097  Sum_probs=15.3

Q ss_pred             cceEEecCCCCCCCCCCce
Q psy2779          71 GGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~~   89 (101)
                      +.++.+.|+|||||+-...
T Consensus        21 ~~~i~i~G~~GsGKSTl~~   39 (207)
T 2qt1_A           21 TFIIGISGVTNSGKTTLAK   39 (207)
T ss_dssp             CEEEEEEESTTSSHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            6788899999999975443

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=85.29  E-value=0.2  Score=39.21  Aligned_cols=18  Identities=22%  Similarity=0.246  Sum_probs=15.2

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .++.+++.||+|||||-.
T Consensus       122 ~~g~i~I~GptGSGKTTl  139 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTT  139 (356)
T ss_dssp             SSEEEEEECSTTSCHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            467999999999999744

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=85.22  E-value=0.21  Score=33.01  Aligned_cols=17  Identities=18%  Similarity=-0.039  Sum_probs=13.5

Q ss_pred             ceEEecCCCCCCCCCCc
Q psy2779          72 GRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        72 ~~ll~~G~p~~g~~~~~   88 (101)
                      ..+++.|+|||||+-..
T Consensus         8 ~~i~l~G~~GsGKSTva   24 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLA   24 (168)
T ss_dssp             CEEEEESCTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            46889999999997443

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=85.14  E-value=0.2  Score=36.10  Aligned_cols=16  Identities=13%  Similarity=0.067  Sum_probs=13.8

Q ss_pred             eEEecCCCCCCCCCCc
Q psy2779          73 RAVAGGRTKCPKPPNT   88 (101)
Q Consensus        73 ~ll~~G~p~~g~~~~~   88 (101)
                      +.|+.|+||||||=+.
T Consensus         7 i~l~tG~pGsGKT~~a   22 (199)
T 2r2a_A            7 ICLITGTPGSGKTLKM   22 (199)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEEeCCCCCHHHHH
Confidence            6789999999998764

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=85.12  E-value=0.19  Score=35.10  Aligned_cols=17  Identities=29%  Similarity=0.010  Sum_probs=14.0

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      +..+++.|+|||||+-.
T Consensus         7 ~~~I~l~G~~GsGKsT~   23 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTV   23 (227)
T ss_dssp             CCEEEEEECTTSSHHHH
T ss_pred             CcEEEEECCCCCCHHHH
Confidence            46789999999999743

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=85.12  E-value=0.24  Score=33.97  Aligned_cols=19  Identities=11%  Similarity=-0.020  Sum_probs=14.7

Q ss_pred             cceEEecCCCCCCCCCCce
Q psy2779          71 GGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~~   89 (101)
                      +..+.+.|+|||||+-...
T Consensus         5 ~~~i~i~G~~GsGKSTl~~   23 (227)
T 1cke_A            5 APVITIDGPSGAGKGTLCK   23 (227)
T ss_dssp             SCEEEEECCTTSSHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3568899999999975443

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=85.03  E-value=0.23  Score=41.11  Aligned_cols=17  Identities=18%  Similarity=0.108  Sum_probs=15.1

Q ss_pred             ccceEEecCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~   86 (101)
                      .++.+++.|+||||||-
T Consensus       163 ~~~~~vi~G~pGTGKTt  179 (608)
T 1w36_D          163 TRRISVISGGPGTGKTT  179 (608)
T ss_dssp             TBSEEEEECCTTSTHHH
T ss_pred             cCCCEEEEeCCCCCHHH
Confidence            57899999999999983

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=84.85  E-value=0.25  Score=38.74  Aligned_cols=22  Identities=23%  Similarity=0.042  Sum_probs=18.4

Q ss_pred             cccccceEEecCCCCCCCCCCc
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      .+-.|+++++.|+||||||-+.
T Consensus        59 Gl~~G~ii~I~G~pGsGKTtLa   80 (356)
T 1u94_A           59 GLPMGRIVEIYGPESSGKTTLT   80 (356)
T ss_dssp             SEETTSEEEEECSTTSSHHHHH
T ss_pred             CccCCeEEEEECCCCCCHHHHH
Confidence            4557899999999999998654

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=84.76  E-value=0.21  Score=33.47  Aligned_cols=17  Identities=24%  Similarity=0.247  Sum_probs=14.1

Q ss_pred             ccceEEecCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~   86 (101)
                      .|+-+++.+|||||||-
T Consensus        37 ~~~~~li~~~TGsGKT~   53 (207)
T 2gxq_A           37 EGKDLIGQARTGTGKTL   53 (207)
T ss_dssp             TTCCEEEECCTTSCHHH
T ss_pred             CCCCEEEECCCCChHHH
Confidence            35678899999999983

>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=84.68  E-value=0.23  Score=43.67  Aligned_cols=15  Identities=13%  Similarity=-0.039  Sum_probs=12.7

Q ss_pred             cceEEecCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKP   85 (101)
Q Consensus        71 g~~ll~~G~p~~g~~   85 (101)
                      -+-+|+.||||||||
T Consensus       238 p~GILL~GPPGTGKT  252 (806)
T 3cf2_A          238 PRGILLYGPPGTGKT  252 (806)
T ss_dssp             CCEEEEECCTTSCHH
T ss_pred             CCeEEEECCCCCCHH
Confidence            356789999999997

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=84.63  E-value=0.15  Score=40.10  Aligned_cols=23  Identities=17%  Similarity=0.254  Sum_probs=19.4

Q ss_pred             cccccceEEecCCCCCCCCCCce
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      .+-.|..++++|+||+|||-|..
T Consensus        42 Gl~~G~LiiIaG~pG~GKTt~al   64 (338)
T 4a1f_A           42 GFNKGSLVIIGARPSMGKTSLMM   64 (338)
T ss_dssp             SBCTTCEEEEEECTTSCHHHHHH
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHH
Confidence            55678899999999999997753

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=84.62  E-value=0.22  Score=35.26  Aligned_cols=22  Identities=14%  Similarity=-0.108  Sum_probs=16.4

Q ss_pred             ccccceEEecCCCCCCCCCCce
Q psy2779          68 LFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      +-.|.++.+.||+||||+-.-.
T Consensus        20 i~~G~~~~lvGpsGsGKSTLl~   41 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTLIK   41 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHHH
Confidence            3458899999999999974433

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=84.61  E-value=0.3  Score=36.05  Aligned_cols=22  Identities=23%  Similarity=0.170  Sum_probs=13.8

Q ss_pred             cccccceEEecCCCCCCCCCCc
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +|..|..+++.|++||||+-..
T Consensus        21 ~m~~g~~I~~eG~~GsGKsT~~   42 (227)
T 3v9p_A           21 SMARGKFITFEGIDGAGKTTHL   42 (227)
T ss_dssp             --CCCCEEEEECCC---CHHHH
T ss_pred             cccCCeEEEEECCCCCCHHHHH
Confidence            4557899999999999997433

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=84.59  E-value=0.25  Score=34.25  Aligned_cols=19  Identities=21%  Similarity=0.155  Sum_probs=15.4

Q ss_pred             cccceEEecCCCCCCCCCC
Q psy2779          69 FRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~~~   87 (101)
                      ..|.++.+-||+||||+-.
T Consensus        18 ~~Gei~~l~GpnGsGKSTL   36 (207)
T 1znw_A           18 AVGRVVVLSGPSAVGKSTV   36 (207)
T ss_dssp             -CCCEEEEECSTTSSHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            3588999999999998743

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=84.58  E-value=0.24  Score=40.79  Aligned_cols=17  Identities=12%  Similarity=0.040  Sum_probs=14.4

Q ss_pred             ccceEEecCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~   86 (101)
                      ..+..|+.||||||||-
T Consensus       194 ~~~~~li~GppGTGKT~  210 (624)
T 2gk6_A          194 QRPLSLIQGPPGTGKTV  210 (624)
T ss_dssp             TCSEEEEECCTTSCHHH
T ss_pred             cCCCeEEECCCCCCHHH
Confidence            35688999999999984

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=84.56  E-value=0.3  Score=32.86  Aligned_cols=16  Identities=19%  Similarity=0.243  Sum_probs=13.7

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      .|+-+++.+|||+|||
T Consensus        39 ~~~~~lv~apTGsGKT   54 (206)
T 1vec_A           39 SGRDILARAKNGTGKS   54 (206)
T ss_dssp             TTCCEEEECCSSSTTH
T ss_pred             cCCCEEEECCCCCchH
Confidence            3567889999999998

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=84.44  E-value=0.21  Score=39.53  Aligned_cols=22  Identities=18%  Similarity=0.037  Sum_probs=18.1

Q ss_pred             ccccccceEEecCCCCCCCCCC
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +.+-.|.++++.||||||||-+
T Consensus        56 GGi~~G~i~~I~GppGsGKSTL   77 (356)
T 3hr8_A           56 GGYPRGRIVEIFGQESSGKTTL   77 (356)
T ss_dssp             SSEETTEEEEEEESTTSSHHHH
T ss_pred             CCccCCcEEEEECCCCCCHHHH
Confidence            3555688999999999999855

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=84.05  E-value=0.21  Score=34.68  Aligned_cols=17  Identities=12%  Similarity=0.092  Sum_probs=13.8

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      +..+++.|+|||||+-.
T Consensus         5 ~~~I~l~G~~GsGKsT~   21 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQ   21 (222)
T ss_dssp             SCCEEEEESTTSSHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            45688999999999743

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=83.95  E-value=0.26  Score=35.46  Aligned_cols=21  Identities=19%  Similarity=0.126  Sum_probs=15.9

Q ss_pred             ccceEEecCCCCCCCCCCcee
Q psy2779          70 RGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      .+..+++.|+|||||+-...+
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~~   48 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSLN   48 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHH
Confidence            356789999999999754443

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=83.81  E-value=0.27  Score=33.87  Aligned_cols=17  Identities=12%  Similarity=-0.107  Sum_probs=14.0

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      +.++.+.|++||||+-.
T Consensus         4 ~~~I~i~G~~GSGKST~   20 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTV   20 (218)
T ss_dssp             CEEEEEECCTTSCHHHH
T ss_pred             ceEEEEECCCCCCHHHH
Confidence            45788999999999753

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=83.70  E-value=0.26  Score=34.17  Aligned_cols=19  Identities=21%  Similarity=0.113  Sum_probs=15.4

Q ss_pred             ccceEEecCCCCCCCCCCc
Q psy2779          70 RGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~   88 (101)
                      .|..+++.|+|||||+-..
T Consensus        24 ~~~~i~~~G~~GsGKsT~~   42 (211)
T 1m7g_A           24 RGLTIWLTGLSASGKSTLA   42 (211)
T ss_dssp             SCEEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            3778999999999997443

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=83.62  E-value=0.27  Score=39.35  Aligned_cols=24  Identities=13%  Similarity=0.004  Sum_probs=19.9

Q ss_pred             cccccceEEecCCCCCCCCCCcee
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      .+-.|..++++|+||+|||-|..-
T Consensus       193 Gl~~G~liiIaG~pG~GKTtlal~  216 (444)
T 3bgw_A          193 GYKRRNFVLIAARPSMGKTAFALK  216 (444)
T ss_dssp             SBCSSCEEEEEECSSSSHHHHHHH
T ss_pred             CCCCCcEEEEEeCCCCChHHHHHH
Confidence            566789999999999999876543

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=83.52  E-value=0.26  Score=34.42  Aligned_cols=17  Identities=12%  Similarity=0.001  Sum_probs=13.8

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      +..+++.|+|||||+-.
T Consensus         5 ~~~I~l~G~~GsGKsT~   21 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQ   21 (217)
T ss_dssp             CCEEEEEECTTSSHHHH
T ss_pred             ceEEEEECCCCCCHHHH
Confidence            45688999999999754

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=83.44  E-value=0.38  Score=36.36  Aligned_cols=16  Identities=19%  Similarity=0.171  Sum_probs=14.3

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      .|+.+|+.||||+||+
T Consensus        33 ~g~~ilI~GpsGsGKS   48 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKS   48 (205)
T ss_dssp             TTEEEEEECCCTTTTH
T ss_pred             CCEEEEEECCCCCCHH
Confidence            4788999999999996

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=83.37  E-value=0.28  Score=36.30  Aligned_cols=16  Identities=19%  Similarity=0.002  Sum_probs=14.7

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      .|.+.|++|+||+|||
T Consensus        11 ~G~i~litG~mGsGKT   26 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKT   26 (223)
T ss_dssp             CCEEEEEECSTTSCHH
T ss_pred             CcEEEEEECCCCCcHH
Confidence            5889999999999997

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=83.35  E-value=0.27  Score=38.34  Aligned_cols=19  Identities=21%  Similarity=0.181  Sum_probs=15.8

Q ss_pred             cccceEEecCCCCCCCCCC
Q psy2779          69 FRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~~~   87 (101)
                      -.|..+++.||+|||||-.
T Consensus       134 ~~g~~i~ivG~~GsGKTTl  152 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTT  152 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3588999999999999743

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=83.21  E-value=0.3  Score=34.58  Aligned_cols=20  Identities=25%  Similarity=-0.044  Sum_probs=15.6

Q ss_pred             cceEEecCCCCCCCCCCcee
Q psy2779          71 GGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~~~   90 (101)
                      +..+++.|+|||||+-.-.+
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~   46 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQR   46 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            56889999999999754433

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=83.18  E-value=0.31  Score=40.37  Aligned_cols=17  Identities=18%  Similarity=0.038  Sum_probs=14.6

Q ss_pred             ccceEEecCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~   86 (101)
                      ..+.+++.|+||||||-
T Consensus       203 ~~~~~~I~G~pGTGKTt  219 (574)
T 3e1s_A          203 GHRLVVLTGGPGTGKST  219 (574)
T ss_dssp             TCSEEEEECCTTSCHHH
T ss_pred             hCCEEEEEcCCCCCHHH
Confidence            35789999999999983

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=83.02  E-value=0.29  Score=39.29  Aligned_cols=17  Identities=24%  Similarity=0.221  Sum_probs=14.8

Q ss_pred             ccceEEecCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~   86 (101)
                      .|+++++.||+|||||-
T Consensus       166 ~ggii~I~GpnGSGKTT  182 (418)
T 1p9r_A          166 PHGIILVTGPTGSGKST  182 (418)
T ss_dssp             SSEEEEEECSTTSCHHH
T ss_pred             cCCeEEEECCCCCCHHH
Confidence            57899999999999863

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=82.90  E-value=0.28  Score=37.84  Aligned_cols=23  Identities=9%  Similarity=-0.123  Sum_probs=18.2

Q ss_pred             ccccccceEEecCCCCCCCCCCc
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      ...-.|.++++.||||||||-+.
T Consensus       126 ggi~~G~i~~I~G~~GsGKTTL~  148 (349)
T 1pzn_A          126 GGIETQAITEVFGEFGSGKTQLA  148 (349)
T ss_dssp             SSEESSEEEEEEESTTSSHHHHH
T ss_pred             CCCCCCeEEEEECCCCCCHHHHH
Confidence            34557889999999999997543

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=82.83  E-value=0.29  Score=32.62  Aligned_cols=15  Identities=20%  Similarity=0.144  Sum_probs=13.0

Q ss_pred             cceEEecCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKP   85 (101)
Q Consensus        71 g~~ll~~G~p~~g~~   85 (101)
                      .++.++.||+||||+
T Consensus        26 ~g~~~i~G~NGsGKS   40 (182)
T 3kta_A           26 KGFTAIVGANGSGKS   40 (182)
T ss_dssp             SSEEEEEECTTSSHH
T ss_pred             CCcEEEECCCCCCHH
Confidence            448899999999986

>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=82.48  E-value=0.34  Score=45.99  Aligned_cols=20  Identities=20%  Similarity=-0.002  Sum_probs=16.6

Q ss_pred             ccccceEEecCCCCCCCCCC
Q psy2779          68 LFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~~   87 (101)
                      .-.||.+|+.||||||||=+
T Consensus      1079 ~p~g~~~l~~G~~g~GKT~l 1098 (1706)
T 3cmw_A         1079 LPMGRIVEIYGPESSGKTTL 1098 (1706)
T ss_dssp             EETTSEEEEECSTTSSHHHH
T ss_pred             CCCCCEEEEEcCCCCChHHH
Confidence            34688999999999999744

>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=82.33  E-value=0.27  Score=35.04  Aligned_cols=37  Identities=8%  Similarity=-0.022  Sum_probs=24.3

Q ss_pred             ccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          33 NEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        33 ~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .....-|||.++.-+..  .- +       .      . +.+++.||+|+|||-
T Consensus         9 ~~~~~~~~gR~~el~~L--~~-l-------~------~-~~v~i~G~~G~GKT~   45 (357)
T 2fna_A            9 KDNRKDFFDREKEIEKL--KG-L-------R------A-PITLVLGLRRTGKSS   45 (357)
T ss_dssp             CCSGGGSCCCHHHHHHH--HH-T-------C------S-SEEEEEESTTSSHHH
T ss_pred             CCCHHHhcChHHHHHHH--HH-h-------c------C-CcEEEECCCCCCHHH
Confidence            33456789977644432  22 3       1      1 589999999999974

>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=82.03  E-value=0.32  Score=38.29  Aligned_cols=22  Identities=18%  Similarity=0.068  Sum_probs=18.3

Q ss_pred             cccccceEEecCCCCCCCCCCc
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      .+-.|.++++.||||||||-+.
T Consensus        70 Gl~~G~li~I~G~pGsGKTtla   91 (366)
T 1xp8_A           70 GIPRGRITEIYGPESGGKTTLA   91 (366)
T ss_dssp             SEETTSEEEEEESTTSSHHHHH
T ss_pred             CccCCcEEEEEcCCCCChHHHH
Confidence            4556889999999999998654

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=81.97  E-value=0.72  Score=36.18  Aligned_cols=20  Identities=20%  Similarity=0.089  Sum_probs=16.7

Q ss_pred             ccccceEEecCCCCCCCCCC
Q psy2779          68 LFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +..|+-+|+.+|||||||=-
T Consensus         5 l~~g~~vlv~a~TGSGKT~~   24 (440)
T 1yks_A            5 LKKGMTTVLDFHPGAGKTRR   24 (440)
T ss_dssp             TSTTCEEEECCCTTSSTTTT
T ss_pred             hhCCCCEEEEcCCCCCHHHH
Confidence            34688999999999999853

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=81.95  E-value=0.32  Score=33.24  Aligned_cols=16  Identities=19%  Similarity=0.256  Sum_probs=13.8

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      .|+-+++.+|||+|||
T Consensus        50 ~~~~~lv~~pTGsGKT   65 (224)
T 1qde_A           50 EGHDVLAQAQSGTGKT   65 (224)
T ss_dssp             TTCCEEEECCTTSSHH
T ss_pred             cCCCEEEECCCCCcHH
Confidence            3566889999999998

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=81.83  E-value=0.33  Score=33.64  Aligned_cols=16  Identities=19%  Similarity=0.335  Sum_probs=13.9

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      .|+-+++.+|||+|||
T Consensus        61 ~~~~~li~a~TGsGKT   76 (236)
T 2pl3_A           61 QGKDVLGAAKTGSGKT   76 (236)
T ss_dssp             TTCCEEEECCTTSCHH
T ss_pred             CCCCEEEEeCCCCcHH
Confidence            4677889999999998

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=81.70  E-value=0.39  Score=33.86  Aligned_cols=17  Identities=35%  Similarity=0.280  Sum_probs=13.8

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      +..+++.|+|||||+-.
T Consensus        16 ~~~I~l~G~~GsGKsT~   32 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQ   32 (233)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            45688999999999743

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=81.41  E-value=0.31  Score=33.23  Aligned_cols=20  Identities=15%  Similarity=-0.049  Sum_probs=15.7

Q ss_pred             ccceEEecCCCCCCCCCCce
Q psy2779          70 RGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~~~   89 (101)
                      .|.++.+.||+||||+-...
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~   24 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQ   24 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHH
Confidence            46788899999999975443

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=81.33  E-value=0.35  Score=38.59  Aligned_cols=24  Identities=13%  Similarity=-0.015  Sum_probs=19.5

Q ss_pred             ccccccceEEecCCCCCCCCCCce
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      +.+-.|.++++.||||||||-+-.
T Consensus       173 GGI~~Gei~~I~G~sGsGKTTLl~  196 (400)
T 3lda_A          173 GGVETGSITELFGEFRTGKSQLCH  196 (400)
T ss_dssp             TSEETTSEEEEEESTTSSHHHHHH
T ss_pred             CCcCCCcEEEEEcCCCCChHHHHH
Confidence            455678899999999999986654

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=81.25  E-value=0.29  Score=33.88  Aligned_cols=22  Identities=9%  Similarity=-0.117  Sum_probs=17.3

Q ss_pred             cccceEEecCCCCCCCCCCcee
Q psy2779          69 FRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      -.+.++.+.|++|||||-+..+
T Consensus        20 ~~~~~i~i~G~~GsGKstl~~~   41 (201)
T 1rz3_A           20 AGRLVLGIDGLSRSGKTTLANQ   41 (201)
T ss_dssp             SSSEEEEEEECTTSSHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHH
Confidence            3577899999999999865443

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=81.12  E-value=0.42  Score=37.55  Aligned_cols=15  Identities=7%  Similarity=0.042  Sum_probs=13.3

Q ss_pred             ceEEecCCCCCCCCC
Q psy2779          72 GRAVAGGRTKCPKPP   86 (101)
Q Consensus        72 ~~ll~~G~p~~g~~~   86 (101)
                      +.+|+.|+||||||-
T Consensus        46 ~~~li~G~aGTGKT~   60 (459)
T 3upu_A           46 HHVTINGPAGTGATT   60 (459)
T ss_dssp             CEEEEECCTTSCHHH
T ss_pred             CEEEEEeCCCCCHHH
Confidence            389999999999983

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=80.98  E-value=0.37  Score=33.22  Aligned_cols=16  Identities=19%  Similarity=0.140  Sum_probs=14.0

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      .|+-+++.+|||||||
T Consensus        56 ~~~~~l~~apTGsGKT   71 (228)
T 3iuy_A           56 QGIDLIVVAQTGTGKT   71 (228)
T ss_dssp             TTCCEEEECCTTSCHH
T ss_pred             CCCCEEEECCCCChHH
Confidence            4677889999999998

>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=80.93  E-value=0.38  Score=36.08  Aligned_cols=16  Identities=0%  Similarity=-0.199  Sum_probs=13.3

Q ss_pred             cceEEecCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPP   86 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~   86 (101)
                      ..++|+.||||+|||-
T Consensus        24 ~~a~L~~G~~G~GKt~   39 (334)
T 1a5t_A           24 HHALLIQALPGMGDDA   39 (334)
T ss_dssp             CSEEEEECCTTSCHHH
T ss_pred             ceeEEEECCCCchHHH
Confidence            3478999999999864

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=80.90  E-value=0.79  Score=35.86  Aligned_cols=17  Identities=6%  Similarity=-0.031  Sum_probs=14.5

Q ss_pred             ccceEEecCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~   86 (101)
                      ++..+|+.+|||||||=
T Consensus        18 ~~~~~lv~a~TGsGKT~   34 (451)
T 2jlq_A           18 KKRLTIMDLHPGAGKTK   34 (451)
T ss_dssp             TTCEEEECCCTTSSCCT
T ss_pred             cCCeEEEECCCCCCHhh
Confidence            45667999999999996

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=80.62  E-value=0.42  Score=37.94  Aligned_cols=23  Identities=9%  Similarity=-0.025  Sum_probs=18.1

Q ss_pred             ccccceEEecCCCCCCCCCCcee
Q psy2779          68 LFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      .-.|..+++.|||||||+-+..+
T Consensus       166 i~~~~~i~l~G~~GsGKSTl~~~  188 (377)
T 1svm_A          166 IPKKRYWLFKGPIDSGKTTLAAA  188 (377)
T ss_dssp             CTTCCEEEEECSTTSSHHHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHHHH
Confidence            34688999999999999765443

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=80.59  E-value=0.34  Score=32.34  Aligned_cols=19  Identities=11%  Similarity=-0.053  Sum_probs=14.7

Q ss_pred             ceEEecCCCCCCCCCCcee
Q psy2779          72 GRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        72 ~~ll~~G~p~~g~~~~~~~   90 (101)
                      .++.+.|++||||+-...+
T Consensus         9 ~~I~i~G~~GsGKST~~~~   27 (203)
T 1uf9_A            9 IIIGITGNIGSGKSTVAAL   27 (203)
T ss_dssp             EEEEEEECTTSCHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4688999999999755433

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=80.30  E-value=0.24  Score=39.31  Aligned_cols=24  Identities=4%  Similarity=-0.129  Sum_probs=19.8

Q ss_pred             cccccceEEecCCCCCCCCCCcee
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      .+..|..++++|+||+|||-|..-
T Consensus       238 Gl~~G~l~li~G~pG~GKT~lal~  261 (503)
T 1q57_A          238 GARGGEVIMVTSGSGMVMSTFVRQ  261 (503)
T ss_dssp             CCCTTCEEEEEESSCHHHHHHHHH
T ss_pred             ccCCCeEEEEeecCCCCchHHHHH
Confidence            466789999999999999876543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	101
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	97.64
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.56
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	97.37
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	97.27
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	96.69
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	96.56
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.53
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	96.51
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	96.43
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.41
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	96.21
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	96.15
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	96.11
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	96.04
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	95.95
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	95.94
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	95.9
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	95.88
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	95.79
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	95.75
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	95.71
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	95.46
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	95.25
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	95.14
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	95.08
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	95.06
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	94.9
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	94.7
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	94.43
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	94.34
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	94.33
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	94.17
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	94.14
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	93.89
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	93.75
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	93.61
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	93.49
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	93.12
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	92.85
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	92.75
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	92.29
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	92.08
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	91.82
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	91.76
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	91.7
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	91.56
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	91.23
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	90.63
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	90.56
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	90.46
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	89.81
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	88.9
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	88.66
d1okkd2	207	GTPase domain of the signal recognition particle r	88.6
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	88.47
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	87.06
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	86.59
d1j8yf2	211	GTPase domain of the signal sequence recognition p	85.49
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	85.41
d1ls1a2	207	GTPase domain of the signal sequence recognition p	84.98
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	84.32
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	83.95
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	83.01
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	82.95
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	82.6
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	81.2
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	80.57

>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=97.64  E-value=2.4e-06  Score=58.61  Aligned_cols=43  Identities=12%  Similarity=0.063  Sum_probs=28.9

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      -+-+|||+++.+.....++.       .+.+.. .-.-+|+.||||||||-
T Consensus         8 ~~divGqe~~~~~l~~~i~~-------~~~~~~-~~~~~L~~GPpGtGKT~   50 (238)
T d1in4a2           8 LDEFIGQENVKKKLSLALEA-------AKMRGE-VLDHVLLAGPPGLGKTT   50 (238)
T ss_dssp             GGGCCSCHHHHHHHHHHHHH-------HHHHTC-CCCCEEEESSTTSSHHH
T ss_pred             HHHcCChHHHHHHHHHHHHH-------HHhcCC-CCCeEEEECCCCCcHHH
Confidence            46699999999887766554       111110 12347899999999984

>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=97.56  E-value=7.2e-06  Score=56.38  Aligned_cols=42  Identities=14%  Similarity=0.019  Sum_probs=30.6

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      -+-+|||++|.+.....++.       .+.++.. -.-+|+.||||||||
T Consensus         8 ~ddivGq~~~~~~L~~~i~~-------~~~~~~~-~~~~Ll~GPpG~GKT   49 (239)
T d1ixsb2           8 LDEYIGQERLKQKLRVYLEA-------AKARKEP-LEHLLLFGPPGLGKT   49 (239)
T ss_dssp             GGGSCSCHHHHHHHHHHHHH-------HTTSSSC-CCCEEEECCTTSCHH
T ss_pred             HHHhCCHHHHHHHHHHHHHH-------HHhcCCC-CCeEEEECCCCCCHH
Confidence            45689999999998877776       3222222 234779999999997

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=97.37  E-value=8.3e-06  Score=60.23  Aligned_cols=47  Identities=13%  Similarity=0.092  Sum_probs=26.7

Q ss_pred             cccchHHHHhhcceeeecccceeeeeccccc--cccceEEecCCCCCCCC
Q psy2779          38 GLVGQQAAREVSRAVTWEKSFQFERCKSHSL--FRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        38 GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~--~~g~~ll~~G~p~~g~~   85 (101)
                      -.+||.+|.++....|-- .+..++.+....  ...+-+|+.||||||||
T Consensus        15 ~ViGQd~A~~~l~~av~~-~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT   63 (309)
T d1ofha_          15 HIIGQADAKRAVAIALRN-RWRRMQLQEPLRHEVTPKNILMIGPTGVGKT   63 (309)
T ss_dssp             TCCSCHHHHHHHHHHHHH-HHHTTSSCHHHHHHCCCCCEEEECCTTSSHH
T ss_pred             cccChHHHHHHHHHHHHH-HHHHhccCCCCccCCCCceEEEECCCCCCHH
Confidence            359999999988765410 000011111111  02345567899999987

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=97.27  E-value=3.4e-05  Score=56.10  Aligned_cols=41  Identities=15%  Similarity=0.020  Sum_probs=30.0

Q ss_pred             cccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          32 ANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        32 a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      +.+..+..|||+++++|+-+-+=.             .++.-+|+.|+||||||
T Consensus         2 ~~~~f~~I~Gq~~~kral~laa~~-------------~~~h~vLl~G~pG~GKT   42 (333)
T d1g8pa_           2 PVFPFSAIVGQEDMKLALLLTAVD-------------PGIGGVLVFGDRGTGKS   42 (333)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHHC-------------GGGCCEEEECCGGGCTT
T ss_pred             CCCChhhccCcHHHHHHHHHHHhc-------------cCCCeEEEECCCCccHH
Confidence            345567899999999986542211             13456889999999999

>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=96.69  E-value=8e-05  Score=58.61  Aligned_cols=48  Identities=13%  Similarity=0.079  Sum_probs=29.3

Q ss_pred             CcccchHHHHhhcceeeecccceeeee--ccccccccceEEecCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERC--KSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~--~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .-.|||++|++|..+-|-= .|..++.  ....-....=+|+-||||||||
T Consensus        14 ~yVvGQ~~AKk~lsvav~n-hyrR~~~~~~~~~ei~ksNILliGPTGvGKT   63 (443)
T d1g41a_          14 QHIIGQADAKRAVAIALRN-RWRRMQLQEPLRHEVTPKNILMIGPTGVGKT   63 (443)
T ss_dssp             TTCCSCHHHHHHHHHHHHH-HHHHHHSCTTTTTTCCCCCEEEECCTTSSHH
T ss_pred             CcccCcHHHHHHHHHHHHH-HHHHhhcccccccccccccEEEECCCCCCHH
Confidence            4579999999999997721 0100110  0011122345778999999986

>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=96.56  E-value=0.00013  Score=52.36  Aligned_cols=47  Identities=11%  Similarity=0.049  Sum_probs=29.9

Q ss_pred             cccccCcccchHHH----HhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          32 ANEMAAGLVGQQAA----REVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        32 a~~~a~GlVGQ~~A----REAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      +.+.-.|+||+-..    ..-+.++++.       .++.....-+-+|+.||||||||
T Consensus         4 ~~~~~~~~i~~~~~i~~i~~~~~~~~~~-------~~~~~~~p~~~vLL~GppGtGKT   54 (246)
T d1d2na_           4 ASYIMNGIIKWGDPVTRVLDDGELLVQQ-------TKNSDRTPLVSVLLEGPPHSGKT   54 (246)
T ss_dssp             TTTCTTCCCCCSHHHHHHHHHHHHHHHH-------HHHCSSCSEEEEEEECSTTSSHH
T ss_pred             HHhhccCCcCcCHHHHHHHHHHHHHHHH-------HhccCCCCCeEEEEECcCCCCHH
Confidence            45677889996542    3334455555       33333333456889999999986

>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=96.53  E-value=0.0002  Score=45.36  Aligned_cols=16  Identities=19%  Similarity=0.246  Sum_probs=14.9

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      +|+++++.|+|||||+
T Consensus         3 ~g~iI~l~G~~GsGKS   18 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKS   18 (176)
T ss_dssp             TTEEEEEEECTTSCHH
T ss_pred             CCeEEEEECCCCCCHH
Confidence            7999999999999976

>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=96.51  E-value=0.00027  Score=48.03  Aligned_cols=50  Identities=12%  Similarity=-0.050  Sum_probs=30.5

Q ss_pred             ccCcccchHHHHhhcceeeec------ccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          35 MAAGLVGQQAAREVSRAVTWE------KSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        35 ~a~GlVGQ~~AREAaGIVVdm------~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +.+-+|||+++.+..--.+..      ++|+|...  ....-.+.+|+.||||||||-
T Consensus        12 ~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~--~~~~~~~~lll~GPpG~GKTt   67 (253)
T d1sxja2          12 NLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGK--DGSGVFRAAMLYGPPGIGKTT   67 (253)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCT--TSTTSCSEEEEECSTTSSHHH
T ss_pred             CHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcc--cCCCCCceEEEECCCCCCHHH
Confidence            357799999988865443321      12223211  112224679999999999984

>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=96.43  E-value=0.00029  Score=47.79  Aligned_cols=43  Identities=16%  Similarity=0.096  Sum_probs=29.5

Q ss_pred             CCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          30 GEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        30 g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      ..|. +.+-+|||+++.+...-.+          ++.+   -.-+|+.||||||||-
T Consensus        18 y~P~-~~~diig~~~~~~~l~~~i----------~~~~---~~~lll~Gp~G~GKTt   60 (231)
T d1iqpa2          18 YRPQ-RLDDIVGQEHIVKRLKHYV----------KTGS---MPHLLFAGPPGVGKTT   60 (231)
T ss_dssp             TCCC-STTTCCSCHHHHHHHHHHH----------HHTC---CCEEEEESCTTSSHHH
T ss_pred             hCCC-CHHHccCcHHHHHHHHHHH----------HcCC---CCeEEEECCCCCcHHH
Confidence            4455 3567999999998744333          2222   1348899999999983

>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=96.41  E-value=0.00039  Score=46.91  Aligned_cols=16  Identities=19%  Similarity=0.229  Sum_probs=13.4

Q ss_pred             cceEEecCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPP   86 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~   86 (101)
                      .+.+|+.||||||||=
T Consensus        32 P~~ilL~GpPGtGKT~   47 (273)
T d1gvnb_          32 PTAFLLGGQPGSGKTS   47 (273)
T ss_dssp             CEEEEEECCTTSCTHH
T ss_pred             CEEEEEECCCCCCHHH
Confidence            4568899999999974

>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=96.21  E-value=0.00026  Score=51.07  Aligned_cols=53  Identities=11%  Similarity=-0.016  Sum_probs=29.6

Q ss_pred             cccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          32 ANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        32 a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      |.-.-+-++|++++++++-=+++. ..+-.+.+....-.-+-+|+.||||||||
T Consensus         4 p~~~~~di~G~~~~k~~l~~~i~~-l~~~~~~~~~g~~~~~giLl~GppGtGKT   56 (247)
T d1ixza_           4 PKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKT   56 (247)
T ss_dssp             CSCCGGGCCSCHHHHHHHHHHHHH-HHCHHHHHHTTCCCCSEEEEECCTTSSHH
T ss_pred             CCCcHHHHccHHHHHHHHHHHHHH-HHCHHHHHHcCCCCCceEEEecCCCCChh
Confidence            333446689999998876433333 00000011111112345889999999997

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

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, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=96.15  E-value=0.00045  Score=45.91  Aligned_cols=49  Identities=12%  Similarity=-0.049  Sum_probs=30.2

Q ss_pred             CCCcccccCcccchHHHHhh-cceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          29 NGEANEMAAGLVGQQAAREV-SRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        29 ~g~a~~~a~GlVGQ~~AREA-aGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      ...|.+..+-+||+++.-+. ..++-..       .++.+ -..+.+|+.||||||||
T Consensus         8 ~l~~~y~p~~l~~Re~ei~~l~~~l~~~-------l~~~~-~~~~~lll~GppGtGKT   57 (276)
T d1fnna2           8 VFSPSYVPKRLPHREQQLQQLDILLGNW-------LRNPG-HHYPRATLLGRPGTGKT   57 (276)
T ss_dssp             GGSTTCCCSCCTTCHHHHHHHHHHHHHH-------HHSTT-SSCCEEEEECCTTSSHH
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHHHHH-------HhCCC-CCCCceEEECCCCCCHH
Confidence            35566677778999976544 3222222       11111 12467899999999997

>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=96.11  E-value=0.00043  Score=47.02  Aligned_cols=42  Identities=10%  Similarity=0.170  Sum_probs=27.6

Q ss_pred             CcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          31 EANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        31 ~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .|+. .+-+|||+++++..--.++          +++.   .-+|+.||||||||-
T Consensus        10 rP~~-~~d~ig~~~~~~~L~~~~~----------~~~~---~~~ll~Gp~G~GKTt   51 (224)
T d1sxjb2          10 RPQV-LSDIVGNKETIDRLQQIAK----------DGNM---PHMIISGMPGIGKTT   51 (224)
T ss_dssp             CCSS-GGGCCSCTHHHHHHHHHHH----------SCCC---CCEEEECSTTSSHHH
T ss_pred             CCCC-HHHhcCCHHHHHHHHHHHH----------cCCC---CeEEEECCCCCCchh
Confidence            3443 4669999998877543332          2221   127899999999974

>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=96.04  E-value=0.00062  Score=49.42  Aligned_cols=53  Identities=13%  Similarity=-0.039  Sum_probs=29.1

Q ss_pred             cccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          32 ANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        32 a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      ++-+-+=++|.+++.+..-=+|+. ..+..+.+.-+.-..+-+|+.||||||||
T Consensus         7 ~~~t~~Di~Gl~~~k~~l~e~v~~-~~~~~~~~~~g~~~~~~iLL~GppGtGKT   59 (256)
T d1lv7a_           7 IKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKT   59 (256)
T ss_dssp             SCCCGGGSCSCHHHHHHTHHHHHH-HHCGGGC-----CCCCEEEEECCTTSCHH
T ss_pred             CCCCHHHHhchHHHHHHHHHHHHH-HHCHHHHHHcCCCCCCeEEeeCCCCCCcc
Confidence            334446788998888777433433 00001111111112466889999999986

>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=95.95  E-value=0.00056  Score=50.59  Aligned_cols=45  Identities=18%  Similarity=0.013  Sum_probs=29.6

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .=.|||++|-++.-..|..-   +....+..+ ....+|+.||||||||
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~---~~~l~~~~~-p~~~~lf~Gp~GvGKT   66 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMA---RAGLGHEHK-PVGSFLFAGPTGVGKT   66 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHH---HTTCSCTTS-CSEEEEEECSTTSSHH
T ss_pred             CeecChHHHHHHHHHHHHHH---HccCCCCCC-CceEEEEECCCcchhH
Confidence            34799999999987766540   011111111 2347889999999997

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.94  E-value=0.0013  Score=44.27  Aligned_cols=44  Identities=7%  Similarity=-0.103  Sum_probs=27.9

Q ss_pred             CCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          30 GEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        30 g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      -.|.. .+-+|||+++.+...   .+       +.+++.  --.+|+.||||||||-
T Consensus         5 y~P~~-~~diig~~~~~~~L~---~~-------~~~~~~--~~~lll~Gp~G~GKTt   48 (252)
T d1sxje2           5 YRPKS-LNALSHNEELTNFLK---SL-------SDQPRD--LPHLLLYGPNGTGKKT   48 (252)
T ss_dssp             TCCCS-GGGCCSCHHHHHHHH---TT-------TTCTTC--CCCEEEECSTTSSHHH
T ss_pred             cCCCC-HHHccCcHHHHHHHH---HH-------HHcCCC--CCeEEEECCCCCCHHH
Confidence            34554 456999999887653   22       111121  1248899999999964

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

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: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.90  E-value=0.00093  Score=41.53  Aligned_cols=22  Identities=14%  Similarity=0.015  Sum_probs=18.5

Q ss_pred             ccccccceEEecCCCCCCCCCC
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +.+..|.+.+++||||||||=+
T Consensus        18 GGi~~G~v~~i~G~~GsGKT~l   39 (242)
T d1n0wa_          18 GGIETGSITEMFGEFRTGKTQI   39 (242)
T ss_dssp             TSEETTSEEEEECCTTSSHHHH
T ss_pred             CCCcCCEEEEEEeCCCCCHHHH
Confidence            4566799999999999999744

>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=95.88  E-value=0.0007  Score=51.63  Aligned_cols=16  Identities=25%  Similarity=0.389  Sum_probs=12.9

Q ss_pred             cccchHHHHhhcceee
Q psy2779          38 GLVGQQAAREVSRAVT   53 (101)
Q Consensus        38 GlVGQ~~AREAaGIVV   53 (101)
                      =.|||.+|.+|..+-+
T Consensus        18 ~ViGQd~Akkava~Av   33 (364)
T d1um8a_          18 YVIGQEQAKKVFSVAV   33 (364)
T ss_dssp             TCCSCHHHHHHHHHHH
T ss_pred             eecChHHHHHHHHHHH
Confidence            3799999999877654

>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=95.79  E-value=0.00054  Score=45.86  Aligned_cols=38  Identities=21%  Similarity=0.081  Sum_probs=25.2

Q ss_pred             cCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          36 AAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        36 a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+.+|||+++.+..   ..+       +++.+.   .-+|+.||||||||-
T Consensus        11 ~~diig~~~~~~~l---~~~-------i~~~~~---~~lll~Gp~G~GKTt   48 (237)
T d1sxjd2          11 LDEVTAQDHAVTVL---KKT-------LKSANL---PHMLFYGPPGTGKTS   48 (237)
T ss_dssp             TTTCCSCCTTHHHH---HHH-------TTCTTC---CCEEEECSTTSSHHH
T ss_pred             HHHccCcHHHHHHH---HHH-------HHcCCC---CeEEEECCCCCChHH
Confidence            46699999876653   233       222221   238899999999973

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=95.75  E-value=0.001  Score=41.43  Aligned_cols=17  Identities=18%  Similarity=0.071  Sum_probs=15.4

Q ss_pred             cccceEEecCCCCCCCC
Q psy2779          69 FRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~   85 (101)
                      ..|.++++.|+||||||
T Consensus         4 ~~g~~I~l~G~~GsGKT   20 (183)
T d1m8pa3           4 TQGFTIFLTGYMNSGKD   20 (183)
T ss_dssp             TCCEEEEEECSTTSSHH
T ss_pred             CCCeEEEEECCCCCCHH
Confidence            36899999999999998

>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=95.71  E-value=0.00093  Score=44.97  Aligned_cols=44  Identities=14%  Similarity=0.043  Sum_probs=28.2

Q ss_pred             CCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCC
Q psy2779          30 GEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        30 g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      ..|+. .+-+|||+++.+...-.++          +.+. .  -+|+.||||||||-.
T Consensus         8 yrP~~-~~divg~~~~~~~L~~~i~----------~~~~-~--~lLl~Gp~G~GKttl   51 (227)
T d1sxjc2           8 YRPET-LDEVYGQNEVITTVRKFVD----------EGKL-P--HLLFYGPPGTGKTST   51 (227)
T ss_dssp             TCCSS-GGGCCSCHHHHHHHHHHHH----------TTCC-C--CEEEECSSSSSHHHH
T ss_pred             hCCCC-HHHccCcHHHHHHHHHHHH----------cCCC-C--eEEEECCCCCChhHH
Confidence            34554 4569999988776433322          2221 1  278999999999753

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {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: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.46  E-value=0.0015  Score=42.72  Aligned_cols=23  Identities=13%  Similarity=-0.013  Sum_probs=19.0

Q ss_pred             ccccccceEEecCCCCCCCCCCc
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +.+-.|++.+++||||||||=+.
T Consensus        29 GGi~~G~~~li~G~pGsGKT~l~   51 (251)
T d1szpa2          29 GGVETGSITELFGEFRTGKSQLC   51 (251)
T ss_dssp             SSEESSSEEEEEESTTSSHHHHH
T ss_pred             CCCcCCeEEEEEcCCCCCHHHHH
Confidence            44667899999999999998554

>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=95.25  E-value=0.00064  Score=48.51  Aligned_cols=46  Identities=9%  Similarity=-0.093  Sum_probs=24.5

Q ss_pred             ccchHHHHhhcceeee--cccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          39 LVGQQAAREVSRAVTW--EKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        39 lVGQ~~AREAaGIVVd--m~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+|++++-+.+-=.++  ++..+  ..+.....--+-+|+.||||||||=
T Consensus         6 v~G~~~~k~~l~~~i~~~l~~~~--~~~~~g~~~~~giLL~GppGtGKT~   53 (258)
T d1e32a2           6 VGGCRKQLAQIKEMVELPLRHPA--LFKAIGVKPPRGILLYGPPGTGKTL   53 (258)
T ss_dssp             CCSCSHHHHHHHHHHHHHHHCHH--HHHHCCCCCCCEEEEECCTTSSHHH
T ss_pred             hccHHHHHHHHHHHHHHHhcCHH--HHHhCCCCCCceeEEecCCCCCchH
Confidence            5677776665533333  21111  1111122224557899999999973

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {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: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=95.14  E-value=0.0021  Score=40.50  Aligned_cols=19  Identities=21%  Similarity=-0.010  Sum_probs=15.8

Q ss_pred             cceEEecCCCCCCCCCCce
Q psy2779          71 GGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~~   89 (101)
                      ++++++.|+|||||+-...
T Consensus         6 ~~iivl~G~~GsGKsT~a~   24 (171)
T d1knqa_           6 HHIYVLMGVSGSGKSAVAS   24 (171)
T ss_dssp             SEEEEEECSTTSCHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            7899999999999975433

>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=95.08  E-value=0.0019  Score=42.97  Aligned_cols=13  Identities=23%  Similarity=-0.010  Sum_probs=11.8

Q ss_pred             eEEecCCCCCCCC
Q psy2779          73 RAVAGGRTKCPKP   85 (101)
Q Consensus        73 ~ll~~G~p~~g~~   85 (101)
                      .+++.||||||||
T Consensus        48 ~l~l~GppGtGKT   60 (287)
T d1w5sa2          48 IYGSIGRVGIGKT   60 (287)
T ss_dssp             EEECTTCCSSSHH
T ss_pred             EEEeECCCCCCHH
Confidence            5788999999998

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {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: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.06  E-value=0.0021  Score=42.77  Aligned_cols=23  Identities=9%  Similarity=-0.123  Sum_probs=19.2

Q ss_pred             ccccccceEEecCCCCCCCCCCc
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +.+-.|++.+++||||||||=|.
T Consensus        31 GGlp~G~~~li~G~pGsGKT~~~   53 (254)
T d1pzna2          31 GGIETQAITEVFGEFGSGKTQLA   53 (254)
T ss_dssp             SSEESSEEEEEEESTTSSHHHHH
T ss_pred             CCccCCEEEEEEcCCCCCHHHHH
Confidence            34677899999999999998653

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

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: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.90  E-value=0.0032  Score=41.45  Aligned_cols=23  Identities=13%  Similarity=-0.067  Sum_probs=19.4

Q ss_pred             ccccccceEEecCCCCCCCCCCc
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +.+..|.+.+++|+||||||=|.
T Consensus        32 GGip~G~~~~i~G~~GsGKT~la   54 (258)
T d1v5wa_          32 GGIESMAITEAFGEFRTGKTQLS   54 (258)
T ss_dssp             SSBCSSEEEEEECCTTCTHHHHH
T ss_pred             CCCcCCEEEEEECCCCCCHHHHH
Confidence            45677899999999999998664

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

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: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=94.70  E-value=0.0028  Score=39.55  Aligned_cols=13  Identities=15%  Similarity=0.153  Sum_probs=11.0

Q ss_pred             EEecCCCCCCCCC
Q psy2779          74 AVAGGRTKCPKPP   86 (101)
Q Consensus        74 ll~~G~p~~g~~~   86 (101)
                      +++.|+||||||-
T Consensus         7 I~i~G~pGsGKTT   19 (173)
T d1rkba_           7 ILLTGTPGVGKTT   19 (173)
T ss_dssp             EEEECSTTSSHHH
T ss_pred             EEEECCCCCCHHH
Confidence            5689999999974

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.43  E-value=0.0016  Score=41.81  Aligned_cols=16  Identities=25%  Similarity=0.237  Sum_probs=14.6

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      .|.+++|.|+||||||
T Consensus        18 ~g~vI~L~G~pGSGKT   33 (195)
T d1x6va3          18 RGCTVWLTGLSGAGKT   33 (195)
T ss_dssp             CCEEEEEESSCHHHHH
T ss_pred             CCeEEEEECCCCCCHH
Confidence            5889999999999996

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=94.34  E-value=0.011  Score=35.43  Aligned_cols=18  Identities=17%  Similarity=0.086  Sum_probs=15.4

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .|+..+|..|||||||--
T Consensus         6 ~~~~~il~~~tGsGKT~~   23 (140)
T d1yksa1           6 KGMTTVLDFHPGAGKTRR   23 (140)
T ss_dssp             TTCEEEECCCTTSSTTTT
T ss_pred             cCCcEEEEcCCCCChhHH
Confidence            478889999999999953

>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=94.33  E-value=0.003  Score=39.07  Aligned_cols=15  Identities=13%  Similarity=-0.006  Sum_probs=11.8

Q ss_pred             ceEEecCCCCCCCCC
Q psy2779          72 GRAVAGGRTKCPKPP   86 (101)
Q Consensus        72 ~~ll~~G~p~~g~~~   86 (101)
                      +.+++.|+||||||-
T Consensus         8 K~I~i~G~~GsGKTT   22 (192)
T d1lw7a2           8 KTVAILGGESSGKSV   22 (192)
T ss_dssp             EEEEEECCTTSHHHH
T ss_pred             eEEEEECCCCCCHHH
Confidence            446689999999863

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

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: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=94.17  E-value=0.0046  Score=39.95  Aligned_cols=22  Identities=14%  Similarity=-0.099  Sum_probs=18.5

Q ss_pred             ccccccceEEecCCCCCCCCCC
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +.+..|.+.+++|+||+|||=|
T Consensus        29 GGl~~G~l~~i~G~~G~GKT~~   50 (258)
T d2i1qa2          29 GGLESQSVTEFAGVFGSGKTQI   50 (258)
T ss_dssp             SSEETTEEEEEEESTTSSHHHH
T ss_pred             CCccCCeEEEEEeCCCCCHHHH
Confidence            4466799999999999999754

>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=94.14  E-value=0.0047  Score=47.02  Aligned_cols=19  Identities=21%  Similarity=0.496  Sum_probs=15.4

Q ss_pred             ccccceEEecCCCCCCCCC
Q psy2779          68 LFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~   86 (101)
                      +..++.+|+.||||||||.
T Consensus       120 ~~~~g~~l~~G~pG~GKT~  138 (321)
T d1w44a_         120 RYASGMVIVTGKGNSGKTP  138 (321)
T ss_dssp             EEESEEEEEECSSSSCHHH
T ss_pred             ccCCceEEEECCCCccHHH
Confidence            3467788899999999863

>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=93.89  E-value=0.0059  Score=42.12  Aligned_cols=47  Identities=13%  Similarity=0.003  Sum_probs=31.5

Q ss_pred             CCcccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCCCce
Q psy2779          30 GEANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPPNTS   89 (101)
Q Consensus        30 g~a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~~~~   89 (101)
                      ..|. +.+-+|||.++.+...   ..       +++++.  -..+|+.|||||||+...-
T Consensus         6 yrP~-~~~dlig~~~~~~~L~---~~-------i~~~~~--~~~~Ll~Gp~G~GKtt~a~   52 (239)
T d1njfa_           6 WRPQ-TFADVVGQEHVLTALA---NG-------LSLGRI--HHAYLFSGTRGVGKTSIAR   52 (239)
T ss_dssp             TCCS-SGGGSCSCHHHHHHHH---HH-------HHTTCC--CSEEEEECSTTSSHHHHHH
T ss_pred             hCCC-CHHHccChHHHHHHHH---HH-------HHcCCC--CeeEEEECCCCCcHHHHHH
Confidence            3454 4678999999988643   22       233332  3468899999999986543

>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=93.75  E-value=0.006  Score=45.17  Aligned_cols=45  Identities=20%  Similarity=0.068  Sum_probs=27.1

Q ss_pred             CcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~   85 (101)
                      .-++||..|-++.--.+..   .+....+..+ -...+|+.||||+|||
T Consensus        23 ~~v~GQ~~ai~~v~~~i~~---~~~~l~~~~k-p~~~~lf~Gp~G~GKt   67 (315)
T d1qvra3          23 KRVVGQDEAIRAVADAIRR---ARAGLKDPNR-PIGSFLFLGPTGVGKT   67 (315)
T ss_dssp             HHSCSCHHHHHHHHHHHHH---HGGGCSCSSS-CSEEEEEBSCSSSSHH
T ss_pred             CeEeCHHHHHHHHHHHHHH---HhcCCCCCCC-CceEEEEECCCcchHH
Confidence            3479999998876544433   0000111111 1347899999999986

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

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: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=93.61  E-value=0.0064  Score=38.14  Aligned_cols=16  Identities=19%  Similarity=0.179  Sum_probs=13.1

Q ss_pred             cceEEecCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPP   86 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~   86 (101)
                      +-.+++.|+||||||-
T Consensus         5 ~~~I~i~G~~GsGKTT   20 (174)
T d1y63a_           5 GINILITGTPGTGKTS   20 (174)
T ss_dssp             SCEEEEECSTTSSHHH
T ss_pred             CCEEEEEeCCCCCHHH
Confidence            4567899999999874

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

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: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=93.49  E-value=0.0079  Score=40.18  Aligned_cols=25  Identities=24%  Similarity=0.201  Sum_probs=19.9

Q ss_pred             ccccccceEEecCCCCCCCCCCcee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSM   90 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~   90 (101)
                      +.+..|...++.|+||||||=+..-
T Consensus        21 GGi~~gsl~li~G~pGsGKT~l~~q   45 (242)
T d1tf7a2          21 GGFFKDSIILATGATGTGKTLLVSR   45 (242)
T ss_dssp             SSEESSCEEEEEECTTSSHHHHHHH
T ss_pred             CCCcCCeEEEEEeCCCCCHHHHHHH
Confidence            4566799999999999999755433

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

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: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=93.12  E-value=0.0098  Score=38.37  Aligned_cols=23  Identities=17%  Similarity=0.135  Sum_probs=19.3

Q ss_pred             ccccccceEEecCCCCCCCCCCc
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      +.+-.|.+.++.|+||+|||=|+
T Consensus        21 GGi~~G~~~~I~G~~G~GKT~la   43 (242)
T d1tf7a1          21 GGLPIGRSTLVSGTSGTGKTLFS   43 (242)
T ss_dssp             SSEETTSEEEEEESTTSSHHHHH
T ss_pred             CCCcCCeEEEEEeCCCCCHHHHH
Confidence            35667999999999999998664

>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=92.85  E-value=0.0029  Score=45.35  Aligned_cols=48  Identities=8%  Similarity=0.088  Sum_probs=25.6

Q ss_pred             CcccchHHHHhhcceeeec--ccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          37 AGLVGQQAAREVSRAVTWE--KSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        37 ~GlVGQ~~AREAaGIVVdm--~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      +-++|.+++.++.-=.++.  +.-  ...+..++--.+-+|+.||||||||=
T Consensus         7 ~di~G~~~~k~~l~~~i~~~l~~~--~~~~~~g~~~~~giLL~Gp~GtGKT~   56 (265)
T d1r7ra3           7 EDIGGLEDVKRELQELVQYPVEHP--DKFLKFGMTPSKGVLFYGPPGCGKTL   56 (265)
T ss_dssp             SSCSSSSCCCCHHHHHTHHHHHCH--HHHHHCCCCCCCEEEEBCCTTSSHHH
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCH--HHHHhCCCCCCCeEEEECCCCCcchh
Confidence            3356777776665533321  000  00111122234568899999999974

>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=92.75  E-value=0.0062  Score=46.27  Aligned_cols=21  Identities=10%  Similarity=-0.034  Sum_probs=17.0

Q ss_pred             ccccceEEecCCCCCCCCCCc
Q psy2779          68 LFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      .-.++.+|+.||||||||-+.
T Consensus       151 ~~~~~~~~~~g~~~~gk~~~~  171 (362)
T d1svma_         151 IPKKRYWLFKGPIDSGKTTLA  171 (362)
T ss_dssp             CTTCCEEEEECSTTSSHHHHH
T ss_pred             CCCcCeEEEECCCCCCHHHHH
Confidence            345789999999999998653

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

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: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=92.29  E-value=0.015  Score=38.31  Aligned_cols=20  Identities=15%  Similarity=0.034  Sum_probs=15.7

Q ss_pred             ccccceEEecCCCCCCCCCC
Q psy2779          68 LFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        68 ~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +-..+++++-|||||||+-.
T Consensus         5 ~~~~~iI~l~G~pGSGKsT~   24 (194)
T d3adka_           5 LKKSKIIFVVGGPGSGKGTQ   24 (194)
T ss_dssp             HHTSCEEEEEECTTSSHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHH
Confidence            33578899999999998643

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {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: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.08  E-value=0.016  Score=38.67  Aligned_cols=17  Identities=24%  Similarity=0.005  Sum_probs=14.4

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      -.++|+.|+||||||-+
T Consensus        14 p~liil~G~pGsGKST~   30 (172)
T d1yj5a2          14 PEVVVAVGFPGAGKSTF   30 (172)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             CEEEEEECCCCCCHHHH
Confidence            46899999999999743

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {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: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=91.82  E-value=0.019  Score=43.33  Aligned_cols=17  Identities=18%  Similarity=0.108  Sum_probs=15.0

Q ss_pred             ccceEEecCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~   86 (101)
                      .++..++.||||||||=
T Consensus       162 ~~~~~vI~G~pGTGKTt  178 (359)
T d1w36d1         162 TRRISVISGGPGTGKTT  178 (359)
T ss_dssp             TBSEEEEECCTTSTHHH
T ss_pred             cCCeEEEEcCCCCCcee
Confidence            47899999999999974

>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=91.76  E-value=0.025  Score=39.18  Aligned_cols=46  Identities=15%  Similarity=0.027  Sum_probs=29.0

Q ss_pred             CCcccccCccc-c--hHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          30 GEANEMAAGLV-G--QQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        30 g~a~~~a~GlV-G--Q~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      .+++++.+-|| |  .+.|.+|+--+++-       .  +.  .-.-+++.||||||||=
T Consensus         3 ln~~~tFdnF~vg~~N~~a~~~~~~~~~~-------~--~~--~~n~l~l~G~~G~GKTH   51 (213)
T d1l8qa2           3 LNPKYTLENFIVGEGNRLAYEVVKEALEN-------L--GS--LYNPIFIYGSVGTGKTH   51 (213)
T ss_dssp             CCTTCCSSSCCCCTTTHHHHHHHHHHHHT-------T--TT--SCSSEEEECSSSSSHHH
T ss_pred             CCCCCChhhccCCCcHHHHHHHHHHHHhC-------c--CC--CCCcEEEECCCCCcHHH
Confidence            45677777765 4  55566666555444       1  11  12348899999999973

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {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: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.70  E-value=0.018  Score=37.76  Aligned_cols=16  Identities=13%  Similarity=-0.012  Sum_probs=12.8

Q ss_pred             ceEEecCCCCCCCCCC
Q psy2779          72 GRAVAGGRTKCPKPPN   87 (101)
Q Consensus        72 ~~ll~~G~p~~g~~~~   87 (101)
                      .++++.|||||||+--
T Consensus         9 ~iI~i~GppGSGKsT~   24 (196)
T d1ukza_           9 SVIFVLGGPGAGKGTQ   24 (196)
T ss_dssp             EEEEEECSTTSSHHHH
T ss_pred             cEEEEECCCCCCHHHH
Confidence            4677889999999743

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=91.56  E-value=0.019  Score=36.37  Aligned_cols=21  Identities=14%  Similarity=0.192  Sum_probs=15.1

Q ss_pred             ccceEE-ecCCCCCCCCCCcee
Q psy2779          70 RGGRAV-AGGRTKCPKPPNTSM   90 (101)
Q Consensus        70 ~g~~ll-~~G~p~~g~~~~~~~   90 (101)
                      +|+.++ ++|++||||+-+...
T Consensus        20 ~~~~iIgI~G~~GSGKSTla~~   41 (198)
T d1rz3a_          20 AGRLVLGIDGLSRSGKTTLANQ   41 (198)
T ss_dssp             SSSEEEEEEECTTSSHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHH
Confidence            355544 999999999855443

>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=91.23  E-value=0.02  Score=37.45  Aligned_cols=38  Identities=13%  Similarity=0.143  Sum_probs=26.4

Q ss_pred             cccccCcccchHHHHhhcceeeecccceeeeeccccccccceEEecCCCCCCCCC
Q psy2779          32 ANEMAAGLVGQQAAREVSRAVTWEKSFQFERCKSHSLFRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        32 a~~~a~GlVGQ~~AREAaGIVVdm~~~~~~~~~~~~~~~g~~ll~~G~p~~g~~~   86 (101)
                      |..+..=|||.++.-+-      +        ++   ..++.+++.||+|||||-
T Consensus         7 p~~~~~~f~GR~~el~~------l--------~~---~~~~~i~i~G~~G~GKTs   44 (283)
T d2fnaa2           7 PKDNRKDFFDREKEIEK------L--------KG---LRAPITLVLGLRRTGKSS   44 (283)
T ss_dssp             CCCSGGGSCCCHHHHHH------H--------HH---TCSSEEEEEESTTSSHHH
T ss_pred             CCCChhhCCChHHHHHH------H--------Hh---ccCCEEEEEcCCCCcHHH
Confidence            55556779998875433      1        11   136789999999999973

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=90.63  E-value=0.064  Score=36.38  Aligned_cols=16  Identities=6%  Similarity=-0.020  Sum_probs=14.8

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      .|+..|+.+|||||||
T Consensus         8 ~~~~~lv~~~TGsGKT   23 (305)
T d2bmfa2           8 KKRLTIMDLHPGAGKT   23 (305)
T ss_dssp             TTCEEEECCCTTSSTT
T ss_pred             cCCcEEEEECCCCCHH
Confidence            5888999999999999

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

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: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=90.56  E-value=0.034  Score=38.03  Aligned_cols=27  Identities=7%  Similarity=-0.112  Sum_probs=21.2

Q ss_pred             ccccccceEEecCCCCCCCCCCceeee
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPNTSMII   92 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~~~~~~   92 (101)
                      +.+..|.+.+++|+||+|||-|...+.
T Consensus        30 ~G~~~G~l~vi~G~~G~GKT~~~~~la   56 (277)
T d1cr2a_          30 LGARGGEVIMVTSGSGMGKSTFVRQQA   56 (277)
T ss_dssp             CSBCTTCEEEEECSTTSSHHHHHHHHH
T ss_pred             cCCCCCeEEEEEeCCCCCHHHHHHHHH
Confidence            456678899999999999996654433

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

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: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=90.46  E-value=0.024  Score=36.99  Aligned_cols=16  Identities=13%  Similarity=-0.049  Sum_probs=13.5

Q ss_pred             cceEEecCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPP   86 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~   86 (101)
                      -.++++-|||||||+-
T Consensus         6 p~iI~i~G~pGSGKsT   21 (194)
T d1qf9a_           6 PNVVFVLGGPGSGKGT   21 (194)
T ss_dssp             CEEEEEEESTTSSHHH
T ss_pred             CcEEEEECCCCCCHHH
Confidence            4688999999999973

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=89.81  E-value=0.033  Score=37.80  Aligned_cols=14  Identities=14%  Similarity=0.109  Sum_probs=11.3

Q ss_pred             ceEEecCCCCCCCC
Q psy2779          72 GRAVAGGRTKCPKP   85 (101)
Q Consensus        72 ~~ll~~G~p~~g~~   85 (101)
                      +-+|+-|+||||||
T Consensus        15 ~~~lI~g~aGTGKT   28 (306)
T d1uaaa1          15 GPCLVLAGAGSGKT   28 (306)
T ss_dssp             SEEEECCCTTSCHH
T ss_pred             CCEEEEeeCCccHH
Confidence            34677899999997

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=88.90  E-value=0.038  Score=38.16  Aligned_cols=14  Identities=14%  Similarity=0.069  Sum_probs=10.9

Q ss_pred             ceEEecCCCCCCCC
Q psy2779          72 GRAVAGGRTKCPKP   85 (101)
Q Consensus        72 ~~ll~~G~p~~g~~   85 (101)
                      +-+|+-|+||||||
T Consensus        25 g~~lV~g~aGSGKT   38 (318)
T d1pjra1          25 GPLLIMAGAGSGKT   38 (318)
T ss_dssp             SCEEEEECTTSCHH
T ss_pred             CCEEEEecCCccHH
Confidence            34667788999997

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

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: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=88.66  E-value=0.047  Score=36.51  Aligned_cols=15  Identities=20%  Similarity=0.062  Sum_probs=11.1

Q ss_pred             EEecCCCCCCCCCCc
Q psy2779          74 AVAGGRTKCPKPPNT   88 (101)
Q Consensus        74 ll~~G~p~~g~~~~~   88 (101)
                      +++-|||||||+-..
T Consensus         9 IiliG~PGSGKtT~a   23 (189)
T d2ak3a1           9 AAIMGAPGSGKGTVS   23 (189)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            445699999997543

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=88.60  E-value=0.052  Score=38.40  Aligned_cols=17  Identities=18%  Similarity=0.214  Sum_probs=14.4

Q ss_pred             ccceEEecCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~   86 (101)
                      .++++++.||||+|||-
T Consensus         5 ~~~vi~lvGptGvGKTT   21 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTT   21 (207)
T ss_dssp             SSSEEEEECSTTSSHHH
T ss_pred             CCEEEEEECCCCCCHHH
Confidence            36788999999999983

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=88.47  E-value=0.096  Score=32.35  Aligned_cols=14  Identities=21%  Similarity=-0.047  Sum_probs=12.4

Q ss_pred             ceEEecCCCCCCCC
Q psy2779          72 GRAVAGGRTKCPKP   85 (101)
Q Consensus        72 ~~ll~~G~p~~g~~   85 (101)
                      +..|+.+|||+|||
T Consensus         9 ~~~ll~apTGsGKT   22 (136)
T d1a1va1           9 QVAHLHAPTGSGKS   22 (136)
T ss_dssp             EEEEEECCTTSCTT
T ss_pred             CEEEEEeCCCCCHH
Confidence            56789999999999

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {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: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=87.06  E-value=0.067  Score=36.20  Aligned_cols=22  Identities=9%  Similarity=-0.031  Sum_probs=17.9

Q ss_pred             cccccceEEecCCCCCCCCCCc
Q psy2779          67 SLFRGGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        67 ~~~~g~~ll~~G~p~~g~~~~~   88 (101)
                      .+..|.+.+++|+||+||+=|.
T Consensus        25 G~~pg~~~~i~G~~G~GKS~l~   46 (274)
T d1nlfa_          25 NMVAGTVGALVSPGGAGKSMLA   46 (274)
T ss_dssp             TEETTSEEEEEESTTSSHHHHH
T ss_pred             CccCCcEEEEEeCCCCCHHHHH
Confidence            3556899999999999998543

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

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: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=86.59  E-value=0.073  Score=40.14  Aligned_cols=16  Identities=25%  Similarity=0.233  Sum_probs=14.5

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      ..+++|++|||||||+
T Consensus       157 ~~GliLvtGpTGSGKS  172 (401)
T d1p9ra_         157 PHGIILVTGPTGSGKS  172 (401)
T ss_dssp             SSEEEEEECSTTSCHH
T ss_pred             hhceEEEEcCCCCCcc
Confidence            4789999999999986

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=85.49  E-value=0.14  Score=36.27  Aligned_cols=18  Identities=11%  Similarity=-0.149  Sum_probs=11.4

Q ss_pred             ccceEEecCCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~~   87 (101)
                      .-.++++.||||+|||-.
T Consensus        11 ~p~vi~lvGptGvGKTTT   28 (211)
T d1j8yf2          11 IPYVIMLVGVQGTGKATT   28 (211)
T ss_dssp             SSEEEEEECSCCC----H
T ss_pred             CCEEEEEECCCCCCHHHH
Confidence            357888999999999853

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=85.41  E-value=0.09  Score=36.12  Aligned_cols=17  Identities=24%  Similarity=0.173  Sum_probs=15.1

Q ss_pred             ccceEEecCCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~~   86 (101)
                      .|.+++++|.||||||-
T Consensus        23 kg~vIwltGlsGsGKTT   39 (208)
T d1m7ga_          23 RGLTIWLTGLSASGKST   39 (208)
T ss_dssp             SCEEEEEECSTTSSHHH
T ss_pred             CCeEEEEECCCCCCHHH
Confidence            48899999999999984

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=84.98  E-value=0.1  Score=36.67  Aligned_cols=16  Identities=13%  Similarity=-0.114  Sum_probs=13.7

Q ss_pred             cceEEecCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPP   86 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~   86 (101)
                      ++++++.||||+|||-
T Consensus        10 ~~vi~lvGp~GvGKTT   25 (207)
T d1ls1a2          10 RNLWFLVGLQGSGKTT   25 (207)
T ss_dssp             SEEEEEECCTTTTHHH
T ss_pred             CcEEEEECCCCCCHHH
Confidence            5688899999999973

>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=84.32  E-value=0.11  Score=35.21  Aligned_cols=17  Identities=0%  Similarity=-0.246  Sum_probs=13.7

Q ss_pred             cceEEecCCCCCCCCCC
Q psy2779          71 GGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~   87 (101)
                      -.++|+.||||+||+-.
T Consensus        24 ~h~lLl~Gp~G~GKtt~   40 (207)
T d1a5ta2          24 HHALLIQALPGMGDDAL   40 (207)
T ss_dssp             CSEEEEECCTTSCHHHH
T ss_pred             CeEEEEECCCCCcHHHH
Confidence            44689999999999753

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=83.95  E-value=0.045  Score=36.22  Aligned_cols=16  Identities=19%  Similarity=0.115  Sum_probs=13.7

Q ss_pred             ccceEEecCCCCCCCC
Q psy2779          70 RGGRAVAGGRTKCPKP   85 (101)
Q Consensus        70 ~g~~ll~~G~p~~g~~   85 (101)
                      .|+-+++..|||||||
T Consensus        39 ~~~~~il~apTGsGKT   54 (202)
T d2p6ra3          39 SGKNLLLAMPTAAGKT   54 (202)
T ss_dssp             TCSCEEEECSSHHHHH
T ss_pred             cCCCEEEEcCCCCchh
Confidence            4666889999999998

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {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: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=83.01  E-value=0.1  Score=38.62  Aligned_cols=18  Identities=22%  Similarity=0.261  Sum_probs=14.6

Q ss_pred             cceEEecCCCCCCCCCCc
Q psy2779          71 GGRAVAGGRTKCPKPPNT   88 (101)
Q Consensus        71 g~~ll~~G~p~~g~~~~~   88 (101)
                      ++-+|++|+||||||-+-
T Consensus       166 ~~nili~G~tgSGKTT~l  183 (323)
T d1g6oa_         166 GKNVIVCGGTGSGKTTYI  183 (323)
T ss_dssp             TCCEEEEESTTSSHHHHH
T ss_pred             CCCEEEEeeccccchHHH
Confidence            556889999999998543

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-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: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=82.95  E-value=0.16  Score=36.71  Aligned_cols=22  Identities=18%  Similarity=-0.017  Sum_probs=17.8

Q ss_pred             ccccccceEEecCCCCCCCCCC
Q psy2779          66 HSLFRGGRAVAGGRTKCPKPPN   87 (101)
Q Consensus        66 ~~~~~g~~ll~~G~p~~g~~~~   87 (101)
                      +.+-.|++.++.||||||||-+
T Consensus        49 GGi~~g~itei~G~~gsGKTtl   70 (263)
T d1u94a1          49 GGLPMGRIVEIYGPESSGKTTL   70 (263)
T ss_dssp             SSEETTSEEEEECSTTSSHHHH
T ss_pred             CCccCceEEEEecCCCcHHHHH
Confidence            4555678999999999999744

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=82.60  E-value=0.15  Score=34.36  Aligned_cols=17  Identities=24%  Similarity=0.128  Sum_probs=14.8

Q ss_pred             cccceEEecCCCCCCCC
Q psy2779          69 FRGGRAVAGGRTKCPKP   85 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~   85 (101)
                      ..|+-+++.+|||+|||
T Consensus        56 l~g~~~~i~apTGsGKT   72 (237)
T d1gkub1          56 LRKESFAATAPTGVGKT   72 (237)
T ss_dssp             HTTCCEECCCCBTSCSH
T ss_pred             HCCCCEEEEecCCChHH
Confidence            35777889999999999

>d1e69a_ c.37.1.12 (A:) Smc head 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: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=80.57  E-value=0.41  Score=32.45  Aligned_cols=18  Identities=17%  Similarity=0.128  Sum_probs=14.7

Q ss_pred             cccceEEecCCCCCCCCC
Q psy2779          69 FRGGRAVAGGRTKCPKPP   86 (101)
Q Consensus        69 ~~g~~ll~~G~p~~g~~~   86 (101)
                      |..+.-++.||+||||+-
T Consensus        22 f~~~lnvlvG~NgsGKS~   39 (308)
T d1e69a_          22 FSDRVTAIVGPNGSGKSN   39 (308)
T ss_dssp             CCSSEEEEECCTTTCSTH
T ss_pred             CCCCeEEEECCCCCcHHH
Confidence            456688999999999963