Citrus Sinensis ID: 042776

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------
Protein Sequence
LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLTKLMKSEVAEVALEGLVEFLKRKKTEVAEVGNKQKASREAEGDEKIGEFVRKTKKRRSNTKRNRKGL
Secondary Structure (PSIPRED)
ccHHHHHHHHHcccccccccEEEEEEccccccccccccccccccEEEEcccccHHHHHHHHHHHccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHcHHccccccEEEEEEcccHHcccHHHcccccccEEEEEccccHHHHHHHHHHHcccccccHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccccc
Coil and Loop (DISEMBL)
LTLSGLLNFIdglwsscgderIIVFTTnhknrldpallrpgrmdmhihmsycnpsgFRILVSNylgindhnlfPEIDELLTKLMKSEVAEVALEGLVEFLKRKKTEVAEVGnkqkasreaegdeKIGEFVRKTKKRrsntkrnrkgl
Flexible Loop (DISEMBL)
LTLSGLLNFIDGLWSSCGDERIIVFttnhknrldpaLLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLTKLMKSEVAEVALEGLVEFLKRKktevaevgnkqkasreaegdekigefvrktkkrrsntkrnrkgl
Low Complexity Region (SEG)
LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLTKLMKSevaevaleglveFLKRKKTEVAEVGNKQKASREAEGDEKIGEFVrktkkrrsntkrnrkGL
Disordered region (IsUnstruct)
****GLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLTKLMKSEVAEVALEGLVEFLKR*********************************************
Disordered Region (DISOPRED)
LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLTKLMKSEVAEVALEGLVEF************************************************
Disordered Region (DISEMBL)
LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLTKLMKSEVAEVALEGLVEFLKRKKTE******************KIGEFVRK***************
Disordered Region (DISPRO)
LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLTKLMKSEVAEVALEGLVEFLKRKKTEVAEVGNKQK********************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLTKLMKSEVAEVALEGLVEFLKRKKTEVAEVGNKQKASREAEGDEKIGEFVRKTKKRRSNTKRNRKGL
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	147	2.2.26 [Sep-21-2011]
Q9P6Q3	449	Probable mitochondrial ch	yes	no	0.707	0.231	0.366	6e-12
Q5UR45	196	Putative AAA family ATPas	N/A	no	0.503	0.377	0.454	1e-11
Q9Y276	419	Mitochondrial chaperone B	yes	no	0.346	0.121	0.547	2e-10
Q5E9H5	419	Mitochondrial chaperone B	yes	no	0.346	0.121	0.547	3e-10
Q9CZP5	418	Mitochondrial chaperone B	yes	no	0.346	0.122	0.528	1e-09
Q7ZTL7	419	Mitochondrial chaperone B	N/A	no	0.346	0.121	0.528	1e-09
Q7ZV60	420	Mitochondrial chaperone B	yes	no	0.346	0.121	0.528	1e-08
Q54DY9	458	Probable mitochondrial ch	no	no	0.346	0.111	0.509	3e-08
P32839	456	Mitochondrial chaperone B	yes	no	0.353	0.114	0.462	7e-07
Q8TX03	436	Proteasome-activating nuc	yes	no	0.523	0.176	0.4	1e-05

>sp|Q9P6Q3|BCS1_SCHPO Probable mitochondrial chaperone bcs1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC644.07 PE=2 SV=1

 Score = 69.7 bits (169), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 41/112 (36%), Positives = 63/112 (56%), Gaps = 8/112 (7%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
           +T SGLLN +DG+ SS  DERII  TTNH  +LDPAL+RPGR+D+  ++    P   R +
Sbjct: 322 VTFSGLLNALDGVTSS--DERIIFMTTNHPEKLDPALVRPGRVDVKAYLGNATPEQVREM 379

Query: 61  VSNYLGINDHNLFPEI-DELLTKLMKSEVAEVALEGLVEFLKRKKTEVAEVG 111
            + + G   H+  PE+ D+L   +     +  +L+GL    K    +  ++ 
Sbjct: 380 FTRFYG---HS--PEMADDLSDIVCPKNTSMASLQGLFVMNKSSPADAVDMA 426

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q5UR45|YL572_MIMIV Putative AAA family ATPase L572 OS=Acanthamoeba polyphaga mimivirus GN=MIMI_L572 PE=3 SV=1

 Score = 68.2 bits (165), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 35/77 (45%), Positives = 50/77 (64%), Gaps = 3/77 (3%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
           LTLSG+LN +DG+++S G  RI++ TTNH   LDPAL+R GR+DM I  S C+      +
Sbjct: 92  LTLSGILNSLDGIFNSEG--RIVIMTTNHSEVLDPALIRRGRIDMQIEFSNCDRYQIAKM 149

Query: 61  VSNYLGIN-DHNLFPEI 76
             N+ G N D ++  +I
Sbjct: 150 YENFYGKNADSDILSKI 166

Acanthamoeba polyphaga (taxid: 5757)

>sp|Q9Y276|BCS1_HUMAN Mitochondrial chaperone BCS1 OS=Homo sapiens GN=BCS1L PE=1 SV=1

 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/53 (54%), Positives = 41/53 (77%), Gaps = 2/53 (3%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCN 53
           LT SGLLN +DG+ S+  + RI+  TTNH +RLDPAL+RPGR+D+  ++ YC+
Sbjct: 307 LTFSGLLNALDGVAST--EARIVFMTTNHVDRLDPALIRPGRVDLKEYVGYCS 357

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III. Plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex.

Homo sapiens (taxid: 9606)

>sp|Q5E9H5|BCS1_BOVIN Mitochondrial chaperone BCS1 OS=Bos taurus GN=BCS1L PE=2 SV=1

 Score = 63.9 bits (154), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 29/53 (54%), Positives = 41/53 (77%), Gaps = 2/53 (3%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCN 53
           LT SGLLN +DG+ S+  + RI+  TTNH +RLDPAL+RPGR+DM  ++ +C+
Sbjct: 307 LTFSGLLNALDGVAST--EARIVFMTTNHIDRLDPALIRPGRVDMKEYVGHCS 357

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III. Plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex.

Bos taurus (taxid: 9913)

>sp|Q9CZP5|BCS1_MOUSE Mitochondrial chaperone BCS1 OS=Mus musculus GN=Bcs1l PE=1 SV=1

 Score = 62.4 bits (150), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 41/53 (77%), Gaps = 2/53 (3%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCN 53
           LT SGLLN +DG+ S+  + RI+  TTN+ +RLDPAL+RPGR+D+  ++ YC+
Sbjct: 307 LTFSGLLNALDGVAST--EARIVFMTTNYIDRLDPALIRPGRVDLKEYVGYCS 357

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III. Plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex.

Mus musculus (taxid: 10090)

>sp|Q7ZTL7|BCS1_XENLA Mitochondrial chaperone BCS1 OS=Xenopus laevis GN=bcs1l PE=2 SV=1

 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 40/53 (75%), Gaps = 2/53 (3%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCN 53
           LT SGLLN +DG+ S+  + RI+  TTNH +RLDPAL+RPGR+D+  ++ +C 
Sbjct: 307 LTFSGLLNALDGVAST--EARIVFMTTNHIDRLDPALIRPGRVDVKQYVGHCT 357

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.

Xenopus laevis (taxid: 8355)

>sp|Q7ZV60|BCS1_DANRE Mitochondrial chaperone BCS1 OS=Danio rerio GN=bcs1l PE=2 SV=2

 Score = 58.9 bits (141), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 39/53 (73%), Gaps = 2/53 (3%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCN 53
           LT SGLLN +DG+ SS  + RI+  TTN   RLDPAL+RPGR+D+  ++ +C+
Sbjct: 308 LTFSGLLNALDGVASS--EARIVFMTTNFIERLDPALVRPGRVDLKQYVGHCS 358

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.

Danio rerio (taxid: 7955)

>sp|Q54DY9|BCS1B_DICDI Probable mitochondrial chaperone BCS1-B OS=Dictyostelium discoideum GN=bcsl1b PE=3 SV=1

 Score = 57.4 bits (137), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 37/53 (69%), Gaps = 2/53 (3%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCN 53
           LT SGLLN +DG+ +S G  RI+  TTNH  +LD  L+RPGR+D+ I +  C+
Sbjct: 348 LTFSGLLNALDGVAASEG--RILFMTTNHLEKLDKVLIRPGRVDLQIEIGLCS 398

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.

Dictyostelium discoideum (taxid: 44689)

>sp|P32839|BCS1_YEAST Mitochondrial chaperone BCS1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=BCS1 PE=1 SV=2

 Score = 52.8 bits (125), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 35/54 (64%), Gaps = 2/54 (3%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNP 54
           +T SGLLN +DG+ SS  +E I   TTNH  +LD A++RPGR+D  + +    P
Sbjct: 340 VTFSGLLNALDGVTSS--EETITFMTTNHPEKLDAAIMRPGRIDYKVFVGNATP 391

Essential for the expression of the Rieske iron-sulfur protein.

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

>sp|Q8TX03|PAN_METKA Proteasome-activating nucleotidase OS=Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938) GN=pan PE=3 SV=1

 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 34/85 (40%), Positives = 46/85 (54%), Gaps = 8/85 (9%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSG-FRIL 60
           TL+ LL  +DG +    D ++I   TN K+ LDPALLRPGR D HI +   +  G + I 
Sbjct: 302 TLTQLLAEMDG-FDPLDDIKVIA-ATNRKDILDPALLRPGRFDRHIKIPLPDEEGRYEIF 359

Query: 61  VSNYLGINDHNLFPEIDELLTKLMK 85
               +   D NL  ++D  L KL K
Sbjct: 360 ---KIHTRDMNLAEDVD--LQKLAK 379

ATPase which is responsible for recognizing, binding, unfolding and translocation of substrate proteins into the archaeal 20S proteasome core particle. Is essential for opening the gate of the 20S proteasome via an interaction with its C-terminus, thereby allowing substrate entry and access to the site of proteolysis. Thus, the C-termini of the proteasomal ATPase function like a 'key in a lock' to induce gate opening and therefore regulate proteolysis. Unfolding activity requires energy from ATP hydrolysis, whereas ATP binding alone promotes ATPase-20S proteasome association which triggers gate opening, and supports translocation of unfolded substrates.

Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938) (taxid: 190192)

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	147
359473721	486	PREDICTED: mitochondrial chaperone BCS1-	0.986	0.298	0.598	2e-44
359473719	482	PREDICTED: mitochondrial chaperone BCS1-	0.986	0.300	0.598	2e-44
297738387	471	unnamed protein product [Vitis vinifera]	0.897	0.280	0.613	6e-44
359473572	543	PREDICTED: peroxisomal biogenesis factor	0.897	0.243	0.613	7e-44
297738388	479	unnamed protein product [Vitis vinifera]	0.714	0.219	0.715	4e-43
147865124	476	hypothetical protein VITISV_036161 [Viti	0.714	0.220	0.715	6e-43
359473565	516	PREDICTED: ATP-dependent zinc metallopro	0.884	0.251	0.585	3e-42
147782591	513	hypothetical protein VITISV_031444 [Viti	0.843	0.241	0.637	5e-42
297738373	623	unnamed protein product [Vitis vinifera]	0.836	0.197	0.598	6e-42
147766990	492	hypothetical protein VITISV_030608 [Viti	0.918	0.274	0.588	2e-41

>gi|359473721|ref|XP_003631352.1| PREDICTED: mitochondrial chaperone BCS1-like isoform 2 [Vitis vinifera]

 Score =  183 bits (465), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 94/157 (59%), Positives = 110/157 (70%), Gaps = 12/157 (7%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
           LTLSGLLNFIDGLWSSCGDERIIV TTNHK RLDPALLRPGRMDMHIHMSYC P GF+ L
Sbjct: 321 LTLSGLLNFIDGLWSSCGDERIIVLTTNHKERLDPALLRPGRMDMHIHMSYCTPCGFKTL 380

Query: 61  VSNYLGINDHNLFPEIDELLT-----------KLMKSEVAEVALEGLVEFLKRKKTEVAE 109
            SNYLGI DH LFPEI++L+            +LMKSE A++AL  LVEFL R KT   E
Sbjct: 381 ASNYLGIRDHRLFPEIEKLIVEVEVTPAAIAEELMKSEEADIALGRLVEFLTRVKTAQNE 440

Query: 110 VGNKQKASREAEGDEK-IGEFVRKTKKRRSNTKRNRK 145
             + +      +G+E  + +  +K  KR + T RN+K
Sbjct: 441 ATDGKDKEANKKGNESPVVDQSKKKAKRNNPTARNQK 477

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359473719|ref|XP_003631351.1| PREDICTED: mitochondrial chaperone BCS1-like isoform 1 [Vitis vinifera]

 Score =  183 bits (465), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 94/157 (59%), Positives = 110/157 (70%), Gaps = 12/157 (7%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
           LTLSGLLNFIDGLWSSCGDERIIV TTNHK RLDPALLRPGRMDMHIHMSYC P GF+ L
Sbjct: 317 LTLSGLLNFIDGLWSSCGDERIIVLTTNHKERLDPALLRPGRMDMHIHMSYCTPCGFKTL 376

Query: 61  VSNYLGINDHNLFPEIDELLT-----------KLMKSEVAEVALEGLVEFLKRKKTEVAE 109
            SNYLGI DH LFPEI++L+            +LMKSE A++AL  LVEFL R KT   E
Sbjct: 377 ASNYLGIRDHRLFPEIEKLIVEVEVTPAAIAEELMKSEEADIALGRLVEFLTRVKTAQNE 436

Query: 110 VGNKQKASREAEGDEK-IGEFVRKTKKRRSNTKRNRK 145
             + +      +G+E  + +  +K  KR + T RN+K
Sbjct: 437 ATDGKDKEANKKGNESPVVDQSKKKAKRNNPTARNQK 473

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297738387|emb|CBI27588.3| unnamed protein product [Vitis vinifera]

 Score =  181 bits (460), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 92/150 (61%), Positives = 107/150 (71%), Gaps = 18/150 (12%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
           LTLSGLLNFIDGLWSSCGDERIIVFTTNHK+R+DPALLRPGRMDMHIHMSYC P GF+ L
Sbjct: 311 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKDRIDPALLRPGRMDMHIHMSYCTPYGFKTL 370

Query: 61  VSNYLGINDHNLFPEIDELLT-----------KLMKSEVAEVALEGLVEFLKRKKT---- 105
            SNYLG+++H LF EI+ L+T           +LMKSE A+VALEGL+EFLKR K     
Sbjct: 371 ASNYLGVSNHRLFTEIERLITEVEVTPAEIAEELMKSEEADVALEGLIEFLKRAKIAENK 430

Query: 106 ---EVAEVGNKQKASREAEGDEKIGEFVRK 132
              E  EV  +    R+    EK+ E  R+
Sbjct: 431 SNGEGKEVDEQGTERRDVVESEKVVETKRQ 460

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359473572|ref|XP_002265232.2| PREDICTED: peroxisomal biogenesis factor 6-like [Vitis vinifera]

 Score =  181 bits (460), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 92/150 (61%), Positives = 107/150 (71%), Gaps = 18/150 (12%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
           LTLSGLLNFIDGLWSSCGDERIIVFTTNHK+R+DPALLRPGRMDMHIHMSYC P GF+ L
Sbjct: 383 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKDRIDPALLRPGRMDMHIHMSYCTPYGFKTL 442

Query: 61  VSNYLGINDHNLFPEIDELLT-----------KLMKSEVAEVALEGLVEFLKRKKT---- 105
            SNYLG+++H LF EI+ L+T           +LMKSE A+VALEGL+EFLKR K     
Sbjct: 443 ASNYLGVSNHRLFTEIERLITEVEVTPAEIAEELMKSEEADVALEGLIEFLKRAKIAENK 502

Query: 106 ---EVAEVGNKQKASREAEGDEKIGEFVRK 132
              E  EV  +    R+    EK+ E  R+
Sbjct: 503 SNGEGKEVDEQGTERRDVVESEKVVETKRQ 532

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297738388|emb|CBI27589.3| unnamed protein product [Vitis vinifera]

 Score =  179 bits (453), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 83/116 (71%), Positives = 95/116 (81%), Gaps = 11/116 (9%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
           LTLSGLLNFIDGLWSSCGDERIIVFTTNHK+R+DPALLRPGRMDMHIHMSYC P GF+ L
Sbjct: 311 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKDRIDPALLRPGRMDMHIHMSYCTPYGFKTL 370

Query: 61  VSNYLGINDHNLFPEIDELLT-----------KLMKSEVAEVALEGLVEFLKRKKT 105
            SNYLG+++H LF EI+ L+T           +LMKSE A+VALEGL+ FLKR K+
Sbjct: 371 ASNYLGVSNHRLFTEIERLITEVEVTPAEIAEELMKSEEADVALEGLIAFLKRAKS 426

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147865124|emb|CAN79835.1| hypothetical protein VITISV_036161 [Vitis vinifera]

 Score =  178 bits (452), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 83/116 (71%), Positives = 95/116 (81%), Gaps = 11/116 (9%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
           LTLSGLLNFIDGLWSSCGDERIIVFTTNHK+R+DPALLRPGRMDMHIHMSYC P GF+ L
Sbjct: 307 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKDRIDPALLRPGRMDMHIHMSYCTPYGFKTL 366

Query: 61  VSNYLGINDHNLFPEIDELLT-----------KLMKSEVAEVALEGLVEFLKRKKT 105
            SNYLG+++H LF EI+ L+T           +LMKSE A+VALEGL+ FLKR K+
Sbjct: 367 ASNYLGVSNHRLFTEIERLITEVEVTPAEIAEELMKSEEADVALEGLIAFLKRAKS 422

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359473565|ref|XP_002265580.2| PREDICTED: ATP-dependent zinc metalloprotease FTSH, chloroplastic [Vitis vinifera]

 Score =  176 bits (446), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 89/152 (58%), Positives = 110/152 (72%), Gaps = 22/152 (14%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
           LTLSGLLNFIDGLWSSCGDERIIVFTTNHK RLDPALLRPGRMDMHIHMSYC PSGF+IL
Sbjct: 337 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKERLDPALLRPGRMDMHIHMSYCTPSGFKIL 396

Query: 61  VSNYLGINDHNLFPEIDELLT-----------KLMKSEVAEVALEGLVEFLKRKKTEVA- 108
            +NYL IN H LF +I+ L+T           +L+K E  +VALEG+++FL+RKK +V  
Sbjct: 397 AANYLNINTHPLFTKIERLMTEVEVTPAEIAEELLKCEEVDVALEGIIKFLERKKMQVEH 456

Query: 109 ---------EVGNKQKASREAEGDEKIGEFVR 131
                    EV ++Q+ S   +GD+ + E ++
Sbjct: 457 DEKSNEGVKEV-DEQEVSNGIKGDKMVSEDIK 487

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147782591|emb|CAN70582.1| hypothetical protein VITISV_031444 [Vitis vinifera]

 Score =  175 bits (444), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 86/135 (63%), Positives = 98/135 (72%), Gaps = 11/135 (8%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
           LTLSGLLNFIDGLWSSCGDERIIV T+NHK RLDPALLRPGRMDMHIHMSYC P GF+ L
Sbjct: 329 LTLSGLLNFIDGLWSSCGDERIIVLTSNHKERLDPALLRPGRMDMHIHMSYCTPCGFKTL 388

Query: 61  VSNYLGINDHNLFPEIDELLT-----------KLMKSEVAEVALEGLVEFLKRKKTEVAE 109
            SNYLGI DH LFPEI++L+            +LMKSE A++AL  LVEFL R KT   E
Sbjct: 389 ASNYLGIRDHRLFPEIEKLIVEVEVTPAAIAEELMKSEEADIALGRLVEFLTRVKTAQNE 448

Query: 110 VGNKQKASREAEGDE 124
             + +      +G+E
Sbjct: 449 ATDGKDKEANKKGNE 463

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297738373|emb|CBI27574.3| unnamed protein product [Vitis vinifera]

 Score =  175 bits (444), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 88/147 (59%), Positives = 105/147 (71%), Gaps = 24/147 (16%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
           LTLSGLLNFIDGLWSSCGDERIIVFTTNHK RLDPALLRPGRMDMHIHMSYC PSGF+IL
Sbjct: 306 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKERLDPALLRPGRMDMHIHMSYCTPSGFKIL 365

Query: 61  VSNYLGINDHNLFPEIDELLT-----------KLMKSEVAEVALEGLVEFLKRKKTEVAE 109
            +NYL IN H LF +I+ L+T           +L+K E  +VALEG+++FL+RKK +V  
Sbjct: 366 AANYLNINTHPLFTKIERLMTEVEVTPAEIAEELLKCEEVDVALEGIIKFLERKKMQV-- 423

Query: 110 VGNKQKASREAEGDEKIGEFVRKTKKR 136
                      E DEK  E V++  ++
Sbjct: 424 -----------EHDEKSNEGVKEVDEQ 439

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147766990|emb|CAN69873.1| hypothetical protein VITISV_030608 [Vitis vinifera]

 Score =  173 bits (439), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 93/158 (58%), Positives = 111/158 (70%), Gaps = 23/158 (14%)

Query: 1   LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
           LTLSGLLNFIDGLWSSCGDERIIVFT NHK RLDPALLRPGRMDMHIHMSYC PSGF+IL
Sbjct: 331 LTLSGLLNFIDGLWSSCGDERIIVFTXNHKERLDPALLRPGRMDMHIHMSYCTPSGFKIL 390

Query: 61  VSNYLGINDHNLFPEIDELLT-----------KLMKSEVAEVALEGLVEFLKRKKTE--- 106
            +NYL IN H LF +I+ L+T           +L+K E  +VALEG+++FL+RKK +   
Sbjct: 391 AANYLNINTHPLFTKIERLMTEVEVTPAEIAEELLKCEEVDVALEGIIKFLERKKMQVEH 450

Query: 107 -------VAEVGNKQKASREAEGDEKIGEFVRKTKKRR 137
                  V EV ++Q+ S   +GD K+G    K KK R
Sbjct: 451 DEKSNEGVKEV-DEQEVSNGIKGD-KMGVKRNKMKKTR 486

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

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	147
TAIR|locus:2078007	451	AT3G50940 [Arabidopsis thalian	0.564	0.184	0.710	6.9e-31
TAIR|locus:2175986	505	AT5G17760 [Arabidopsis thalian	0.544	0.158	0.75	9.1e-31
TAIR|locus:2053109	494	AT2G18190 [Arabidopsis thalian	0.850	0.253	0.517	6.3e-30
TAIR|locus:2077997	576	BCS1 "cytochrome BC1 synthesis	0.857	0.218	0.521	3.9e-29
TAIR|locus:1005716649	495	AT2G18193 [Arabidopsis thalian	0.850	0.252	0.507	9.7e-29
TAIR|locus:2175956	533	AT5G17740 [Arabidopsis thalian	0.870	0.240	0.5	1.6e-28
TAIR|locus:2175946	470	AT5G17730 [Arabidopsis thalian	0.727	0.227	0.553	4.6e-27
TAIR|locus:2095532	477	AT3G28600 [Arabidopsis thalian	0.802	0.247	0.492	1.5e-26
TAIR|locus:2095537	474	AT3G28610 [Arabidopsis thalian	0.544	0.168	0.637	2.5e-26
TAIR|locus:2095502	451	AT3G28570 [Arabidopsis thalian	0.564	0.184	0.647	1e-25

TAIR|locus:2078007 AT3G50940 [Arabidopsis thaliana (taxid:3702)]

 Score = 340 (124.7 bits), Expect = 6.9e-31, P = 6.9e-31
 Identities = 59/83 (71%), Positives = 73/83 (87%)

Query:     1 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
             +TLSGLLNF+DGLWSSCG+ERIIVFTTN++ +LDPALLRPGRMDMHIHMSYC P+ F++L
Sbjct:   330 VTLSGLLNFVDGLWSSCGNERIIVFTTNYREKLDPALLRPGRMDMHIHMSYCTPAAFKVL 389

Query:    61 VSNYLGINDHNLFPEIDELLTKL 83
              SNYL I DH LF +I+E + ++
Sbjct:   390 ASNYLEIQDHILFEQIEEFIREI 412

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2175986 AT5G17760 [Arabidopsis thaliana (taxid:3702)]

 Score = 340 (124.7 bits), Expect = 9.1e-31, P = 9.1e-31
 Identities = 63/84 (75%), Positives = 73/84 (86%)

Query:     1 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
             LTLSGLLNFIDGLWSSCGDERII+FTTNHK+RLDPALLRPGRMDMHI+M +C+  GF+ L
Sbjct:   339 LTLSGLLNFIDGLWSSCGDERIIIFTTNHKDRLDPALLRPGRMDMHIYMGHCSFQGFKTL 398

Query:    61 VSNYLGIND----HNLFPEIDELL 80
              SNYLG++D    H LFPEI+ L+
Sbjct:   399 ASNYLGLSDAAMPHRLFPEIERLI 422

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM;IDA

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

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

TAIR|locus:2053109 AT2G18190 [Arabidopsis thaliana (taxid:3702)]

 Score = 332 (121.9 bits), Expect = 6.3e-30, P = 6.3e-30
 Identities = 72/139 (51%), Positives = 92/139 (66%)

Query:     1 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
             +TLSGLLNF+DGLWSS GDERIIVFTTNHK RLDPALLRPGRMDMHI+MSYC   GFR L
Sbjct:   330 VTLSGLLNFVDGLWSSFGDERIIVFTTNHKERLDPALLRPGRMDMHINMSYCTGLGFRTL 389

Query:    61 VSNYLGIN--DHNLFPEID-----------ELLTKLMKSXXXXXXXXXXXXFLKRKKTEV 107
             VSNYLG+   +H L  EI+           EL  +LM+             F++ +K E+
Sbjct:   390 VSNYLGLGGLNHPLCEEIEALIDSTEVTPAELAEELMQEDDTDVVLRGVVSFVENRKVEI 449

Query:   108 AEVGNKQKAS-REAEGDEK 125
             ++    + ++ R+ +GD+K
Sbjct:   450 SKTKELEGSTCRKLDGDDK 468

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2077997 BCS1 "cytochrome BC1 synthesis" [Arabidopsis thaliana (taxid:3702)]

 Score = 329 (120.9 bits), Expect = 3.9e-29, P = 3.9e-29
 Identities = 73/140 (52%), Positives = 89/140 (63%)

Query:     1 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
             +TLSGLLNFIDGLWSSCGDERII+FTTN+K +LD ALLRPGRMDMHIHMSYC PS F+ L
Sbjct:   388 VTLSGLLNFIDGLWSSCGDERIIIFTTNYKEKLDAALLRPGRMDMHIHMSYCTPSTFKAL 447

Query:    61 VSNYLGINDHNLFPEIDE-----------LLTKLMKSXXXXXXXXXXXXFLKRKKTEVAE 109
               NYL I +H LF +I+E           +  +LM++            FLK KK E  +
Sbjct:   448 ALNYLEIKEHRLFSKIEEGIEATEVTPAEVAEQLMRNDSVDKVLEGLIEFLKVKKIENEQ 507

Query:   110 VGNKQKASR-EAEGDEKIGE 128
               +K K  + E E  +K  E
Sbjct:   508 --DKAKTEKQELENKKKTKE 525

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0005739 "mitochondrion" evidence=IDA

GO:0009611 "response to wounding" evidence=RCA

GO:0009612 "response to mechanical stimulus" evidence=RCA

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

GO:0010200 "response to chitin" evidence=RCA

GO:0052542 "defense response by callose deposition" evidence=RCA

TAIR|locus:1005716649 AT2G18193 [Arabidopsis thaliana (taxid:3702)]

 Score = 322 (118.4 bits), Expect = 9.7e-29, P = 9.7e-29
 Identities = 70/138 (50%), Positives = 89/138 (64%)

Query:     1 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
             +TLSG+LNFIDGLWSS GDERIIVFTTNHK RLDPALLRPGRMD+HI+MSYC   GFR L
Sbjct:   326 VTLSGILNFIDGLWSSFGDERIIVFTTNHKERLDPALLRPGRMDVHINMSYCTGLGFRTL 385

Query:    61 VSNYLGIN--DHNLFPEID-----------ELLTKLMKSXXXXXXXXXXXXFLKRKKTEV 107
             VSNYLG++  +H L  EI+           EL  +LM+             F++++K E 
Sbjct:   386 VSNYLGLDGLNHPLCEEIEALVDSTEVTPAELAEELMQDDDTDVVLRGVISFVEKRKVER 445

Query:   108 AEVGNKQKASREAEGDEK 125
             ++   +    +  + DEK
Sbjct:   446 SKTKKEVSICKATDDDEK 463

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0005783 "endoplasmic reticulum" evidence=IDA

TAIR|locus:2175956 AT5G17740 [Arabidopsis thaliana (taxid:3702)]

 Score = 322 (118.4 bits), Expect = 1.6e-28, P = 1.6e-28
 Identities = 72/144 (50%), Positives = 91/144 (63%)

Query:     1 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
             LTLSGLLN IDGLWSSCG+ERII+FTTN+K +LDPALLRPGRMDMHI+M +C+  GF+ L
Sbjct:   334 LTLSGLLNCIDGLWSSCGNERIIIFTTNNKEKLDPALLRPGRMDMHIYMGHCSFQGFKTL 393

Query:    61 VSNYLGINDHN-----LFPEIDEL-----LT------KLMKSXXXXXXXXXXXXFLKRKK 104
              SNYLG++D N     L P+I  L     LT      +LMK              LKRK+
Sbjct:   394 ASNYLGLSDENDDTHPLCPDIKHLIDGHVLTPAQVAEELMKDEDADAALEGLVKVLKRKR 453

Query:   105 TEVAEVGNKQKASREAEGDEKIGE 128
              E  +  ++ K  +  EG+E I +
Sbjct:   454 LEPKKCDDESKMKKLKEGEEAIAD 477

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2175946 AT5G17730 [Arabidopsis thaliana (taxid:3702)]

 Score = 306 (112.8 bits), Expect = 4.6e-27, P = 4.6e-27
 Identities = 67/121 (55%), Positives = 81/121 (66%)

Query:     1 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
             LTLSGLL  IDGLWSSCGDERI++FTT HK RLDPALLRPGRMDMHIHM +C    F+ L
Sbjct:   329 LTLSGLLTCIDGLWSSCGDERIVIFTTTHKERLDPALLRPGRMDMHIHMGHCCFDVFKTL 388

Query:    61 VSNYLGIND---HNLFPEID-----ELLT------KLMKSXXXXXXXXXXXXFLKRKKTE 106
              SNYLG++    H+L+PEI+     E+LT      +LMK+             LKRK+ E
Sbjct:   389 ASNYLGLSHDDPHHLYPEIERLIKGEVLTPAQVAEELMKNEDPDVALEGLVKVLKRKRLE 448

Query:   107 V 107
             +
Sbjct:   449 L 449

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2095532 AT3G28600 [Arabidopsis thaliana (taxid:3702)]

 Score = 302 (111.4 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 63/128 (49%), Positives = 84/128 (65%)

Query:     1 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
             +TLSGLLNFIDG+WS+CG ERII+FTTNH  +LDPAL+R GRMDMHI +SYC+   F+IL
Sbjct:   332 VTLSGLLNFIDGIWSACGQERIIIFTTNHFEKLDPALIRRGRMDMHIELSYCSFEAFKIL 391

Query:    61 VSNYLGINDHNLFPEIDELL--TKLMKSXXXXXXXXXXXXFLKRKKTEVAEVGNKQKASR 118
               NYL ++ H LF +I+ LL  TK+  +             L +K TE+   G+ +   +
Sbjct:   392 AKNYLDLDTHPLFKKIESLLKETKIAPADVAEN--------LMKKNTEIDADGSLKDLIQ 443

Query:   119 EAEGDEKI 126
               EG +KI
Sbjct:   444 ALEGKKKI 451

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2095537 AT3G28610 [Arabidopsis thaliana (taxid:3702)]

 Score = 284 (105.0 bits), Expect = 2.5e-26, Sum P(2) = 2.5e-26
 Identities = 51/80 (63%), Positives = 63/80 (78%)

Query:     1 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
             +TLSGLLNFIDG+WS+CG ERIIVFTTNH  +LDPAL+R GRMDMHI +SYC    F+ L
Sbjct:   332 VTLSGLLNFIDGIWSACGQERIIVFTTNHLAKLDPALIRRGRMDMHIELSYCTFEAFKTL 391

Query:    61 VSNYLGINDHNLFPEIDELL 80
               NYL ++ H LF +I+ L+
Sbjct:   392 AKNYLDLDSHPLFSKIESLM 411

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0042991 "transcription factor import into nucleus" evidence=RCA

TAIR|locus:2095502 AT3G28570 [Arabidopsis thaliana (taxid:3702)]

 Score = 293 (108.2 bits), Expect = 1.0e-25, P = 1.0e-25
 Identities = 55/85 (64%), Positives = 67/85 (78%)

Query:     1 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
             +TLSGLLNFIDG+WS+CG ERI+VFTTNH  +LD AL+R GRMDMHI +SYC    F+IL
Sbjct:   323 VTLSGLLNFIDGIWSACGQERILVFTTNHVGKLDQALIRRGRMDMHIELSYCTFGAFKIL 382

Query:    61 VSNYLGINDHNLFPEIDELL--TKL 83
               NYL I+ H+LF EI+ LL  TK+
Sbjct:   383 AKNYLNIDSHHLFGEIESLLKETKI 407

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00035054001 SubName- Full=Chromosome chr1 scaffold_75, whole genome shotgun sequence; (482 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	147
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	6e-07
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	6e-06
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	2e-05
TIGR01241	495	TIGR01241, FtsH_fam, ATP-dependent metalloprotease	4e-05
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	9e-05
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	3e-04
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	7e-04
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	7e-04
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	7e-04
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	0.001
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	0.004
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	0.004
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	0.004

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

 Score = 47.3 bits (113), Expect = 6e-07
 Identities = 31/88 (35%), Positives = 43/88 (48%), Gaps = 13/88 (14%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSG----F 57
           T+  LLN +DG +   G+ ++I   TN  + LDPALLRPGR D  I     +  G     
Sbjct: 274 TMLELLNQLDG-FDPRGNVKVI-MATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEIL 331

Query: 58  RILVSNYLGINDHNLFPEID-ELLTKLM 84
           +I           NL  ++D ELL +L 
Sbjct: 332 KIHTR------KMNLADDVDLELLARLT 353

Length = 406

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

 Score = 42.6 bits (101), Expect = 6e-06
 Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSY 51
            ++ LL  +DG  +S   + I++  TN  ++LDPALLR GR D  I    
Sbjct: 84  VVNQLLTELDGF-TSSLSKVIVIAATNRPDKLDPALLR-GRFDRIIEFPL 131

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

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

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 23/46 (50%), Positives = 31/46 (67%), Gaps = 2/46 (4%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHI 47
           T+  LLN +DG + S GD ++I+  TN    LDPAL+RPGR+D  I
Sbjct: 306 TMLELLNQLDG-FDSRGDVKVIM-ATNRIESLDPALIRPGRIDRKI 349

Length = 438

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

 Score = 41.9 bits (99), Expect = 4e-05
 Identities = 21/49 (42%), Positives = 30/49 (61%), Gaps = 2/49 (4%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMS 50
           TL+ LL  +DG  ++ G   I++  TN  + LDPALLRPGR D  + + 
Sbjct: 177 TLNQLLVEMDGFGTNTG--VIVIAATNRPDVLDPALLRPGRFDRQVVVD 223

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

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

 Score = 40.6 bits (96), Expect = 9e-05
 Identities = 22/47 (46%), Positives = 28/47 (59%), Gaps = 2/47 (4%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIH 48
           TL  LL  +DG +   G+ +II   TN  + LDPA+LRPGR D  I 
Sbjct: 254 TLMQLLAEMDG-FDPRGNVKIIA-ATNRIDILDPAILRPGRFDRIIE 298

Length = 389

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

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 2/60 (3%)

Query: 6   LLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL 65
           LL  IDG+ S   D  I++  +N ++ +DPA+LRPGR+D+ I +   +      + + YL
Sbjct: 321 LLAEIDGVESL--DNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFAKYL 378

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

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

 Score = 38.2 bits (89), Expect = 7e-04
 Identities = 20/46 (43%), Positives = 26/46 (56%), Gaps = 2/46 (4%)

Query: 6   LLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSY 51
           LLN +DG   +   + I+   TN  + LDPALLRPGR+D  I    
Sbjct: 272 LLNQMDGFDQTTNVKVIM--ATNRADTLDPALLRPGRLDRKIEFPL 315

Length = 398

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

 Score = 38.3 bits (89), Expect = 7e-04
 Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 2/43 (4%)

Query: 6   LLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIH 48
           LL  +DG+     +  +++  TN  + LDPALLRPGR D  I+
Sbjct: 366 LLTELDGI--EKAEGVLVIAATNRPDDLDPALLRPGRFDRLIY 406

Length = 494

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

 Score = 38.1 bits (88), Expect = 7e-04
 Identities = 23/47 (48%), Positives = 29/47 (61%), Gaps = 4/47 (8%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFT-TNHKNRLDPALLRPGRMDMHI 47
           TL+ +L  +DG     G+E IIV   TN  + LDPALLRPGR D  +
Sbjct: 274 TLNQMLVEMDGFE---GNEGIIVIAATNRPDVLDPALLRPGRFDRQV 317

Length = 644

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

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 24/47 (51%), Positives = 29/47 (61%), Gaps = 4/47 (8%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFT-TNHKNRLDPALLRPGRMDMHI 47
           TL+ LL  +DG     G+E +IV   TN  + LDPALLRPGR D  I
Sbjct: 272 TLNQLLVEMDG---FGGNEGVIVIAATNRPDVLDPALLRPGRFDRQI 315

Length = 596

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

 Score = 36.4 bits (84), Expect = 0.004
 Identities = 22/46 (47%), Positives = 27/46 (58%), Gaps = 4/46 (8%)

Query: 3   LSGLLNFIDGLWSSCGDERIIVF-TTNHKNRLDPALLRPGRMDMHI 47
           ++ LL  +DGL    G  R+IV   TN  + LDPAL RPGR D  I
Sbjct: 299 VAQLLTLMDGLK---GRGRVIVIGATNRPDALDPALRRPGRFDREI 341

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

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

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 21/46 (45%), Positives = 27/46 (58%), Gaps = 2/46 (4%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHI 47
           TL+ LL  +DG   + G   I++  TN  + LD ALLRPGR D  I
Sbjct: 305 TLNQLLTEMDGFKGNKG--VIVIAATNRVDILDAALLRPGRFDRQI 348

Length = 638

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

 Score = 35.9 bits (83), Expect = 0.004
 Identities = 22/46 (47%), Positives = 28/46 (60%), Gaps = 2/46 (4%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHI 47
           TL  LL  +DG +   G+ ++I   TN  + LDPALLRPGR D  I
Sbjct: 245 TLMQLLAELDG-FDPRGNVKVIA-ATNRPDILDPALLRPGRFDRII 288

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	147
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	99.93
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	99.9
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.86
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	99.84
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.82
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.78
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.77
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	99.77
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	99.76
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	99.75
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.74
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	99.74
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	99.71
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	99.7
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.69
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.69
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.68
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	99.68
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	99.68
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.67
CHL00206	2281	ycf2 Ycf2; Provisional	99.67
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	99.66
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.65
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	99.63
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.63
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.61
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.6
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.58
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.57
CHL00176	638	ftsH cell division protein; Validated	99.56
CHL00195	489	ycf46 Ycf46; Provisional	99.55
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	99.55
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.55
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.51
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	99.49
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.47
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	99.43
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.31
PF00004	132	AAA: ATPase family associated with various cellula	98.45
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	98.42
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	98.05
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	97.86
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	97.31
CHL00181	287	cbbX CbbX; Provisional	97.27
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.06
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.01
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	96.87
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	96.26
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.08
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	96.08
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	95.98
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	95.87
KOG0736	953	consensus Peroxisome assembly factor 2 containing	95.4
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	95.39
COG0714	329	MoxR-like ATPases [General function prediction onl	95.31
PRK00149	450	dnaA chromosomal replication initiation protein; R	95.3
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	95.25
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	95.16
PRK10865	857	protein disaggregation chaperone; Provisional	94.92
PRK07940	394	DNA polymerase III subunit delta'; Validated	94.9
PHA02544	316	44 clamp loader, small subunit; Provisional	94.82
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	94.56
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	94.35
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	94.12
PRK06893	229	DNA replication initiation factor; Validated	94.11
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	93.99
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	93.98
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	93.84
PRK12402	337	replication factor C small subunit 2; Reviewed	93.14
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	93.08
PRK06964	342	DNA polymerase III subunit delta'; Validated	93.01
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	92.95
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	92.87
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	92.67
PRK12422	445	chromosomal replication initiation protein; Provis	92.66
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	92.34
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	92.33
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	91.94
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	91.81
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	91.75
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	91.51
PRK00411	394	cdc6 cell division control protein 6; Reviewed	91.39
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	91.26
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	90.92
PTZ00112	1164	origin recognition complex 1 protein; Provisional	90.91
PRK14088	440	dnaA chromosomal replication initiation protein; P	90.73
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	90.58
PRK14086	617	dnaA chromosomal replication initiation protein; P	90.28
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	90.18
PRK09087	226	hypothetical protein; Validated	89.97
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	89.81
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	89.78
PRK04195	482	replication factor C large subunit; Provisional	89.77
PRK08727	233	hypothetical protein; Validated	89.58
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	89.48
PRK00440	319	rfc replication factor C small subunit; Reviewed	89.15
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	89.15
PRK13342	413	recombination factor protein RarA; Reviewed	88.98
PRK08084	235	DNA replication initiation factor; Provisional	88.5
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	88.42
CHL00095	821	clpC Clp protease ATP binding subunit	88.21
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	88.17
PRK09112	351	DNA polymerase III subunit delta'; Validated	88.12
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	88.07
smart00350	509	MCM minichromosome maintenance proteins.	87.53
PRK06620	214	hypothetical protein; Validated	87.52
PRK08903	227	DnaA regulatory inactivator Hda; Validated	87.3
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	87.2
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	86.99
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	86.96
PRK05642	234	DNA replication initiation factor; Validated	86.33
PRK05707	328	DNA polymerase III subunit delta'; Validated	86.03
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	85.75
PLN03025	319	replication factor C subunit; Provisional	85.63
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	85.5
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	85.13
PRK07471	365	DNA polymerase III subunit delta'; Validated	84.94
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	84.81
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	84.56
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	84.53
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	84.37
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	83.54
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	83.07
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	82.55
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	82.51
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	82.13
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	81.98
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	81.33
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	80.95
PRK14087	450	dnaA chromosomal replication initiation protein; P	80.72
PRK05564	313	DNA polymerase III subunit delta'; Validated	80.49
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	80.4

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.93  E-value=4.8e-26  Score=195.72  Aligned_cols=111  Identities=68%  Similarity=1.109  Sum_probs=102.0

Q ss_pred             CcHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCC-CCCChHHHHHH
Q 042776            1 LTLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIN-DHNLFPEIDEL   79 (147)
Q Consensus         1 ~tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~-~~~~~~~i~~l   79 (147)
                      ||+|+||+++||+||+||+.+|||+||||++.|||||+||||+|++|+|++|+.++.+.|+..||+.. +|.++.+|+++
T Consensus       319 VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDmhI~mgyCtf~~fK~La~nYL~~~~~h~L~~eie~l  398 (457)
T KOG0743|consen  319 VTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDMHIYMGYCTFEAFKTLASNYLGIEEDHRLFDEIERL  398 (457)
T ss_pred             eehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCcceeEEEcCCCCHHHHHHHHHHhcCCCCCcchhHHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999999999999997 59999999988


Q ss_pred             HH-----------HHhccc-hHHHHHHHHHHHHHHhhHHHHhhh
Q 042776           80 LT-----------KLMKSE-VAEVALEGLVEFLKRKKTEVAEVG  111 (147)
Q Consensus        80 ~~-----------~l~~~~-~~~~al~~~~~~l~~~~~~~~~~~  111 (147)
                      ..           .|+-.+ +++.|+++++..+++++.+.++..
T Consensus       399 ~~~~~~tPA~V~e~lm~~~~dad~~lk~Lv~~l~~~~~~~~~~~  442 (457)
T KOG0743|consen  399 IEETEVTPAQVAEELMKNKNDADVALKGLVEALESKKEKRNKDD  442 (457)
T ss_pred             hhcCccCHHHHHHHHhhccccHHHHHHHHHHHHHhhhhhhccch
Confidence            66           555555 899999999999999887666553

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

Probab=99.90  E-value=8.2e-24  Score=178.23  Aligned_cols=107  Identities=23%  Similarity=0.320  Sum_probs=94.1

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC---CChHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH---NLFPEIDE   78 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~---~~~~~i~~   78 (147)
                      |+-|||++|||+...  ++|-||||||||+.|||||+|||||||+|+|++||.++|..||+.|.+....   .++..++.
T Consensus       274 TmleLL~qlDGFD~~--~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~  351 (406)
T COG1222         274 TMLELLNQLDGFDPR--GNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLAR  351 (406)
T ss_pred             HHHHHHHhccCCCCC--CCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHH
Confidence            678999999999988  8899999999999999999999999999999999999999999999876644   44555556


Q ss_pred             HHHHHhccchHHHHHHHHHHHHHHhhHHHHhh
Q 042776           79 LLTKLMKSEVAEVALEGLVEFLKRKKTEVAEV  110 (147)
Q Consensus        79 l~~~l~~~~~~~~al~~~~~~l~~~~~~~~~~  110 (147)
                      ++++++|.+....|.++=+-+++..+.....+
T Consensus       352 ~~~g~sGAdlkaictEAGm~AiR~~R~~Vt~~  383 (406)
T COG1222         352 LTEGFSGADLKAICTEAGMFAIRERRDEVTME  383 (406)
T ss_pred             hcCCCchHHHHHHHHHHhHHHHHhccCeecHH
Confidence            66699999999999999999999887655444

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.86  E-value=6.4e-22  Score=176.12  Aligned_cols=101  Identities=26%  Similarity=0.321  Sum_probs=90.6

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH-
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT-   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~-   81 (147)
                      +|+||++|||+...  .+|+||||||||+.||+||+||||||+.|||++||.++|.+||+.++...+.....++..|+. 
T Consensus       555 lsqLLtEmDG~e~~--k~V~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kkmp~~~~vdl~~La~~  632 (693)
T KOG0730|consen  555 LSQLLTEMDGLEAL--KNVLVIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAKKMPFSEDVDLEELAQA  632 (693)
T ss_pred             HHHHHHHccccccc--CcEEEEeccCChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHHHhcCCCCccccHHHHHHH
Confidence            79999999999887  789999999999999999999999999999999999999999999998776665555555555 


Q ss_pred             --HHhccchHHHHHHHHHHHHHHhhH
Q 042776           82 --KLMKSEVAEVALEGLVEFLKRKKT  105 (147)
Q Consensus        82 --~l~~~~~~~~al~~~~~~l~~~~~  105 (147)
                        +|+|.+....|-++...|+++.-.
T Consensus       633 T~g~SGAel~~lCq~A~~~a~~e~i~  658 (693)
T KOG0730|consen  633 TEGYSGAEIVAVCQEAALLALRESIE  658 (693)
T ss_pred             hccCChHHHHHHHHHHHHHHHHHhcc
Confidence              999999999999999999987654

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=99.84  E-value=2.2e-21  Score=170.25  Aligned_cols=89  Identities=26%  Similarity=0.340  Sum_probs=79.6

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT   81 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~   81 (147)
                      |+||||.+|||+..+  ++||||+|||+|+.||+||+||||||++|.+++||..+|.+||..|+....+....+..-+|.
T Consensus       423 TlNQLLvEmDGF~qN--eGiIvigATNfpe~LD~AL~RPGRFD~~v~Vp~PDv~GR~eIL~~yl~ki~~~~~VD~~iiAR  500 (752)
T KOG0734|consen  423 TLNQLLVEMDGFKQN--EGIIVIGATNFPEALDKALTRPGRFDRHVTVPLPDVRGRTEILKLYLSKIPLDEDVDPKIIAR  500 (752)
T ss_pred             HHHHHHHHhcCcCcC--CceEEEeccCChhhhhHHhcCCCccceeEecCCCCcccHHHHHHHHHhcCCcccCCCHhHhcc
Confidence            799999999999887  899999999999999999999999999999999999999999999999887776666666666


Q ss_pred             ---HHhccchHHHH
Q 042776           82 ---KLMKSEVAEVA   92 (147)
Q Consensus        82 ---~l~~~~~~~~a   92 (147)
                         +|.|.|.....
T Consensus       501 GT~GFsGAdLaNlV  514 (752)
T KOG0734|consen  501 GTPGFSGADLANLV  514 (752)
T ss_pred             CCCCCchHHHHHHH
Confidence               77777776533

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.82  E-value=3.1e-20  Score=164.82  Aligned_cols=101  Identities=22%  Similarity=0.299  Sum_probs=88.2

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhC--CCCCCChHHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLG--INDHNLFPEIDELL   80 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~--~~~~~~~~~i~~l~   80 (147)
                      |||||++|||+...  .+|+||+|||||+.+|||++||||||+.+|+++|+.++|..||+.+..  ..+.....+++.++
T Consensus       632 vNqLLtElDGl~~R--~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~tkn~k~pl~~dVdl~eia  709 (802)
T KOG0733|consen  632 VNQLLTELDGLEER--RGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEERVAILKTITKNTKPPLSSDVDLDEIA  709 (802)
T ss_pred             HHHHHHHhcccccc--cceEEEeecCCCcccchhhcCCCccCceeeecCCCHHHHHHHHHHHhccCCCCCCcccCHHHHh
Confidence            79999999999988  889999999999999999999999999999999999999999999987  33433444455555


Q ss_pred             H-----HHhccchHHHHHHHHHHHHHHhhH
Q 042776           81 T-----KLMKSEVAEVALEGLVEFLKRKKT  105 (147)
Q Consensus        81 ~-----~l~~~~~~~~al~~~~~~l~~~~~  105 (147)
                      .     +|.|.|.+..+-++.+.+|++.-.
T Consensus       710 ~~~~c~gftGADLaaLvreAsi~AL~~~~~  739 (802)
T KOG0733|consen  710 RNTKCEGFTGADLAALVREASILALRESLF  739 (802)
T ss_pred             hcccccCCchhhHHHHHHHHHHHHHHHHHh
Confidence            4     899999999999999998887665

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.78  E-value=6.5e-19  Score=156.51  Aligned_cols=103  Identities=22%  Similarity=0.277  Sum_probs=87.6

Q ss_pred             HHHHHHHhhCCCCC--CCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCC---CCChHHHH
Q 042776            3 LSGLLNFIDGLWSS--CGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIND---HNLFPEID   77 (147)
Q Consensus         3 v~~lL~~lDgl~~~--~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~---~~~~~~i~   77 (147)
                      |+|||+.||++...  .|+.|+||+|||||+.|||||+|+||||+.|.++.|+..+|..||+.....-.   ..++..++
T Consensus       310 VaQLlt~mD~l~~~~~~g~~VlVIgATnRPDslDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~~d~~qlA  389 (802)
T KOG0733|consen  310 VAQLLTSMDELSNEKTKGDPVLVIGATNRPDSLDPALRRAGRFDREICLGVPSETAREEILRIICRGLRLSGDFDFKQLA  389 (802)
T ss_pred             HHHHHHhhhcccccccCCCCeEEEecCCCCcccCHHHhccccccceeeecCCchHHHHHHHHHHHhhCCCCCCcCHHHHH
Confidence            78999999999643  35789999999999999999999999999999999999999999998876443   44455566


Q ss_pred             HHHHHHhccchHHHHHHHHHHHHHHhhH
Q 042776           78 ELLTKLMKSEVAEVALEGLVEFLKRKKT  105 (147)
Q Consensus        78 ~l~~~l~~~~~~~~al~~~~~~l~~~~~  105 (147)
                      .++++|+|.|....|.++..-+++..-.
T Consensus       390 ~lTPGfVGADL~AL~~~Aa~vAikR~ld  417 (802)
T KOG0733|consen  390 KLTPGFVGADLMALCREAAFVAIKRILD  417 (802)
T ss_pred             hcCCCccchhHHHHHHHHHHHHHHHHhh
Confidence            6666999999999999888888877544

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

Probab=99.77  E-value=3.9e-19  Score=158.27  Aligned_cols=104  Identities=27%  Similarity=0.347  Sum_probs=86.9

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCC---hHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNL---FPEIDE   78 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~---~~~i~~   78 (147)
                      |+||||.+|||+.++  ++|+||+|||||+-|||||+||||||+.|.+++||..+|++|++.|....+...   ...+++
T Consensus       272 TLNQlLvEmDGF~~~--~gviviaaTNRpdVlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~~l~~~Vdl~~iAr  349 (596)
T COG0465         272 TLNQLLVEMDGFGGN--EGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVDLKKIAR  349 (596)
T ss_pred             HHHHHHhhhccCCCC--CceEEEecCCCcccchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcCCCCCcCCHHHHhh
Confidence            799999999999966  889999999999999999999999999999999999999999999887664443   334555


Q ss_pred             HHHHHhccchHHHHHHHHHHHHHHhhHHH
Q 042776           79 LLTKLMKSEVAEVALEGLVEFLKRKKTEV  107 (147)
Q Consensus        79 l~~~l~~~~~~~~al~~~~~~l~~~~~~~  107 (147)
                      .++++++.+....+.++.+-+.++.+..-
T Consensus       350 ~tpGfsGAdL~nl~NEAal~aar~n~~~i  378 (596)
T COG0465         350 GTPGFSGADLANLLNEAALLAARRNKKEI  378 (596)
T ss_pred             hCCCcccchHhhhHHHHHHHHHHhcCeeE
Confidence            55588888888777777777776665433

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=99.77  E-value=5.7e-19  Score=160.24  Aligned_cols=103  Identities=27%  Similarity=0.367  Sum_probs=83.7

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCC-ChHHHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHN-LFPEIDELL   80 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~-~~~~i~~l~   80 (147)
                      |+||||.+|||+.++  .+|||+++||||+.||+||+||||||++|++++|+..+|.+||+.|+...... ...++..++
T Consensus       434 tlnQll~emDgf~~~--~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~~a  511 (774)
T KOG0731|consen  434 TLNQLLVEMDGFETS--KGVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSKLA  511 (774)
T ss_pred             HHHHHHHHhcCCcCC--CcEEEEeccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHHHH
Confidence            799999999999888  88999999999999999999999999999999999999999999999766442 334444444


Q ss_pred             H---HHhccchHHHHHHHHHHHHHHhhHH
Q 042776           81 T---KLMKSEVAEVALEGLVEFLKRKKTE  106 (147)
Q Consensus        81 ~---~l~~~~~~~~al~~~~~~l~~~~~~  106 (147)
                      .   ++.|.+....|-++.+.+.++....
T Consensus       512 ~~t~gf~gadl~n~~neaa~~a~r~~~~~  540 (774)
T KOG0731|consen  512 SLTPGFSGADLANLCNEAALLAARKGLRE  540 (774)
T ss_pred             hcCCCCcHHHHHhhhhHHHHHHHHhccCc
Confidence            4   6667777666666666666554443

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]

Probab=99.76  E-value=3.3e-19  Score=148.15  Aligned_cols=107  Identities=24%  Similarity=0.349  Sum_probs=94.1

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT   81 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~   81 (147)
                      |+-+||+++||+.+.  +.|-||+|||+.+.|||||+||||+|++|+|++||...++.||..|...........++.++.
T Consensus       308 tmLELLNQldGFdsr--gDvKvimATnrie~LDPaLiRPGrIDrKIef~~pDe~TkkkIf~IHTs~Mtl~~dVnle~li~  385 (440)
T KOG0726|consen  308 TMLELLNQLDGFDSR--GDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKKIFQIHTSRMTLAEDVNLEELIM  385 (440)
T ss_pred             HHHHHHHhccCcccc--CCeEEEEecccccccCHhhcCCCccccccccCCCchhhhceeEEEeecccchhccccHHHHhh
Confidence            567999999999998  789999999999999999999999999999999999999999998887665555566677766


Q ss_pred             ---HHhccchHHHHHHHHHHHHHHhhHHHHhh
Q 042776           82 ---KLMKSEVAEVALEGLVEFLKRKKTEVAEV  110 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~~l~~~~~~~~~~  110 (147)
                         .++|.+....|-++=+-+++++++..-.+
T Consensus       386 ~kddlSGAdIkAictEaGllAlRerRm~vt~~  417 (440)
T KOG0726|consen  386 TKDDLSGADIKAICTEAGLLALRERRMKVTME  417 (440)
T ss_pred             cccccccccHHHHHHHHhHHHHHHHHhhccHH
Confidence               88999999999999999998888755443

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=99.75  E-value=1.2e-18  Score=143.35  Aligned_cols=107  Identities=29%  Similarity=0.338  Sum_probs=89.1

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCC---ChHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHN---LFPEIDE   78 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~---~~~~i~~   78 (147)
                      |+-+||+++||+.+.  +.+-||+||||.+.|||||+|+||+|++|+||+|+.++|..|++.|.......   .++++++
T Consensus       294 TMLELLNQLDGFss~--~~vKviAATNRvDiLDPALlRSGRLDRKIEfP~Pne~aRarIlQIHsRKMnv~~DvNfeELaR  371 (424)
T KOG0652|consen  294 TMLELLNQLDGFSSD--DRVKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARARILQIHSRKMNVSDDVNFEELAR  371 (424)
T ss_pred             HHHHHHHhhcCCCCc--cceEEEeecccccccCHHHhhcccccccccCCCCChHHHHHHHHHhhhhcCCCCCCCHHHHhh
Confidence            577999999999987  88999999999999999999999999999999999999999999998766444   4455555


Q ss_pred             HHHHHhccchHHHHHHHHHHHHHHhhHHHHhh
Q 042776           79 LLTKLMKSEVAEVALEGLVEFLKRKKTEVAEV  110 (147)
Q Consensus        79 l~~~l~~~~~~~~al~~~~~~l~~~~~~~~~~  110 (147)
                      .+..|-|..-...|+++-+.+++....+..-+
T Consensus       372 sTddFNGAQcKAVcVEAGMiALRr~atev~he  403 (424)
T KOG0652|consen  372 STDDFNGAQCKAVCVEAGMIALRRGATEVTHE  403 (424)
T ss_pred             cccccCchhheeeehhhhHHHHhcccccccHH
Confidence            55577777777888888888887666544433

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=99.74  E-value=5.3e-18  Score=153.49  Aligned_cols=103  Identities=23%  Similarity=0.348  Sum_probs=78.7

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHH-HHHHHHHHh---CCCCCCChHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSG-FRILVSNYL---GINDHNLFPEIDE   78 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~-r~~il~~~l---~~~~~~~~~~i~~   78 (147)
                      |+|||.+|||+...+..+|+||+|||||+.|||||+||||||+.+|++.++..+ +..+|+...   ..++..+..++++
T Consensus       794 VSQLLAELDgls~~~s~~VFViGATNRPDLLDpALLRPGRFDKLvyvG~~~d~esk~~vL~AlTrkFkLdedVdL~eiAk  873 (953)
T KOG0736|consen  794 VSQLLAELDGLSDSSSQDVFVIGATNRPDLLDPALLRPGRFDKLVYVGPNEDAESKLRVLEALTRKFKLDEDVDLVEIAK  873 (953)
T ss_pred             HHHHHHHhhcccCCCCCceEEEecCCCccccChhhcCCCccceeEEecCCccHHHHHHHHHHHHHHccCCCCcCHHHHHh
Confidence            799999999998655689999999999999999999999999999999876554 777777554   3445555556666


Q ss_pred             HHH-HHhccchHHHHHHHHHHHHHHhhH
Q 042776           79 LLT-KLMKSEVAEVALEGLVEFLKRKKT  105 (147)
Q Consensus        79 l~~-~l~~~~~~~~al~~~~~~l~~~~~  105 (147)
                      .++ .+.|.|....|-.+++.+++++-.
T Consensus       874 ~cp~~~TGADlYsLCSdA~l~AikR~i~  901 (953)
T KOG0736|consen  874 KCPPNMTGADLYSLCSDAMLAAIKRTIH  901 (953)
T ss_pred             hCCcCCchhHHHHHHHHHHHHHHHHHHH
Confidence            555 556666666666666666655444

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=99.74  E-value=3.5e-18  Score=140.01  Aligned_cols=107  Identities=25%  Similarity=0.295  Sum_probs=92.1

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT   81 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~   81 (147)
                      |+-+||+++||+.+.  .++-||+||||.+.|||||+||||+|++|+||.|+.++|.+||+.|....+..-..++..+++
T Consensus       270 tmlellnqldgfeat--knikvimatnridild~allrpgridrkiefp~p~e~ar~~ilkihsrkmnl~rgi~l~kiae  347 (404)
T KOG0728|consen  270 TMLELLNQLDGFEAT--KNIKVIMATNRIDILDPALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAE  347 (404)
T ss_pred             HHHHHHHhccccccc--cceEEEEeccccccccHhhcCCCcccccccCCCCCHHHHHHHHHHhhhhhchhcccCHHHHHH
Confidence            577999999999988  779999999999999999999999999999999999999999999988776666667777777


Q ss_pred             ---HHhccchHHHHHHHHHHHHHHhhHHHHhh
Q 042776           82 ---KLMKSEVAEVALEGLVEFLKRKKTEVAEV  110 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~~l~~~~~~~~~~  110 (147)
                         +.+|.+-...|-++-+=++++++-..-.+
T Consensus       348 km~gasgaevk~vcteagm~alrerrvhvtqe  379 (404)
T KOG0728|consen  348 KMPGASGAEVKGVCTEAGMYALRERRVHVTQE  379 (404)
T ss_pred             hCCCCccchhhhhhhhhhHHHHHHhhccccHH
Confidence               66777778888888888888777544433

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=99.71  E-value=5e-18  Score=140.08  Aligned_cols=107  Identities=23%  Similarity=0.322  Sum_probs=90.6

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCC---CCCChHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIN---DHNLFPEIDE   78 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~---~~~~~~~i~~   78 (147)
                      |+-+|+++|||+...  .++-|++|||||+.|||||+||||+|++++|++||.++|.+||+.|....   ...-++-+++
T Consensus       300 tmleli~qldgfdpr--gnikvlmatnrpdtldpallrpgrldrkvef~lpdlegrt~i~kihaksmsverdir~ellar  377 (435)
T KOG0729|consen  300 TMLELINQLDGFDPR--GNIKVLMATNRPDTLDPALLRPGRLDRKVEFGLPDLEGRTHIFKIHAKSMSVERDIRFELLAR  377 (435)
T ss_pred             HHHHHHHhccCCCCC--CCeEEEeecCCCCCcCHhhcCCcccccceeccCCcccccceeEEEeccccccccchhHHHHHh
Confidence            577899999999888  77999999999999999999999999999999999999999999887544   3344556677


Q ss_pred             HHHHHhccchHHHHHHHHHHHHHHhhHHHHhh
Q 042776           79 LLTKLMKSEVAEVALEGLVEFLKRKKTEVAEV  110 (147)
Q Consensus        79 l~~~l~~~~~~~~al~~~~~~l~~~~~~~~~~  110 (147)
                      |++.-.|.+..+.|.++-+=+++.+++..-++
T Consensus       378 lcpnstgaeirsvcteagmfairarrk~atek  409 (435)
T KOG0729|consen  378 LCPNSTGAEIRSVCTEAGMFAIRARRKVATEK  409 (435)
T ss_pred             hCCCCcchHHHHHHHHhhHHHHHHHhhhhhHH
Confidence            77777788889999999888888777654444

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=99.70  E-value=3.5e-17  Score=134.27  Aligned_cols=100  Identities=25%  Similarity=0.418  Sum_probs=86.5

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH-
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT-   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~-   81 (147)
                      +-+||++|||+...  .++-||+||||.+.|||||+||||+|++|+|++||..+++-+|.............+++.++. 
T Consensus       279 l~ellnqmdgfdq~--~nvkvimatnradtldpallrpgrldrkiefplpdrrqkrlvf~titskm~ls~~vdle~~v~r  356 (408)
T KOG0727|consen  279 LIELLNQMDGFDQT--TNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFSTITSKMNLSDEVDLEDLVAR  356 (408)
T ss_pred             HHHHHHhccCcCcc--cceEEEEecCcccccCHhhcCCccccccccCCCCchhhhhhhHHhhhhcccCCcccCHHHHhcC
Confidence            45899999999887  679999999999999999999999999999999999999999998877766666667777766 


Q ss_pred             --HHhccchHHHHHHHHHHHHHHhh
Q 042776           82 --KLMKSEVAEVALEGLVEFLKRKK  104 (147)
Q Consensus        82 --~l~~~~~~~~al~~~~~~l~~~~  104 (147)
                        .++|.+....|-++-+.++++.+
T Consensus       357 pdkis~adi~aicqeagm~avr~nr  381 (408)
T KOG0727|consen  357 PDKISGADINAICQEAGMLAVRENR  381 (408)
T ss_pred             ccccchhhHHHHHHHHhHHHHHhcc
Confidence              67788888888888888877655

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.69  E-value=6.1e-17  Score=145.89  Aligned_cols=99  Identities=17%  Similarity=0.210  Sum_probs=81.0

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHH---HHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEI---DEL   79 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i---~~l   79 (147)
                      |||||++|||+.+.  +||.|+|||.||+.|||||+||||||+.++.++|+..+|..|++........+...++   +..
T Consensus       788 VNQlLTelDG~Egl--~GV~i~aaTsRpdliDpALLRpGRlD~~v~C~~P~~~eRl~il~~ls~s~~~~~~vdl~~~a~~  865 (952)
T KOG0735|consen  788 VNQLLTELDGAEGL--DGVYILAATSRPDLIDPALLRPGRLDKLVYCPLPDEPERLEILQVLSNSLLKDTDVDLECLAQK  865 (952)
T ss_pred             HHHHHHhhcccccc--ceEEEEEecCCccccCHhhcCCCccceeeeCCCCCcHHHHHHHHHHhhccCCccccchHHHhhh
Confidence            89999999999998  8999999999999999999999999999999999999999999977654333334444   444


Q ss_pred             HHHHhccchHHHHHHHHHHHHHHh
Q 042776           80 LTKLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        80 ~~~l~~~~~~~~al~~~~~~l~~~  103 (147)
                      +.++.|.|.-..+..+-+.++++.
T Consensus       866 T~g~tgADlq~ll~~A~l~avh~~  889 (952)
T KOG0735|consen  866 TDGFTGADLQSLLYNAQLAAVHEI  889 (952)
T ss_pred             cCCCchhhHHHHHHHHHHHHHHHH
Confidence            458888888766666655555443

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

Probab=99.69  E-value=8.9e-17  Score=139.97  Aligned_cols=100  Identities=25%  Similarity=0.350  Sum_probs=87.4

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC-----CChHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH-----NLFPEID   77 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~-----~~~~~i~   77 (147)
                      +++||.+|||+...  .+|+||+|||+|+.||||++||||||+.|+|++||..+|..||+.|+.....     .+...+.
T Consensus       363 ~~~lL~~~d~~e~~--~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~~~~~~~~~~~~~~~l~  440 (494)
T COG0464         363 VGQLLTELDGIEKA--EGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELA  440 (494)
T ss_pred             HHHHHHHhcCCCcc--CceEEEecCCCccccCHhhcccCccceEeecCCCCHHHHHHHHHHHhcccCCcchhhhhHHHHH
Confidence            78999999999888  7799999999999999999999999999999999999999999999985433     3334455


Q ss_pred             HHHHHHhccchHHHHHHHHHHHHHHhh
Q 042776           78 ELLTKLMKSEVAEVALEGLVEFLKRKK  104 (147)
Q Consensus        78 ~l~~~l~~~~~~~~al~~~~~~l~~~~  104 (147)
                      ++++++++.+....|.++.+..+.+..
T Consensus       441 ~~t~~~sgadi~~i~~ea~~~~~~~~~  467 (494)
T COG0464         441 EITEGYSGADIAALVREAALEALREAR  467 (494)
T ss_pred             HHhcCCCHHHHHHHHHHHHHHHHHHhc
Confidence            555588999999999999999888775

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.68  E-value=1e-16  Score=145.98  Aligned_cols=100  Identities=23%  Similarity=0.298  Sum_probs=84.4

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHH--
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELL--   80 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~--   80 (147)
                      +++||.+|||+...  .+++||+|||+|+.||||++||||||+.|+|++|+.++|.+||+.++...+.....++..++  
T Consensus       575 ~~~lL~~ldg~~~~--~~v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~~~~~l~~la~~  652 (733)
T TIGR01243       575 VNQLLTEMDGIQEL--SNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEM  652 (733)
T ss_pred             HHHHHHHhhcccCC--CCEEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHH
Confidence            68999999999876  77999999999999999999999999999999999999999999998766554444444444  


Q ss_pred             -HHHhccchHHHHHHHHHHHHHHhh
Q 042776           81 -TKLMKSEVAEVALEGLVEFLKRKK  104 (147)
Q Consensus        81 -~~l~~~~~~~~al~~~~~~l~~~~  104 (147)
                       .++++.+....|-++.+.++++..
T Consensus       653 t~g~sgadi~~~~~~A~~~a~~~~~  677 (733)
T TIGR01243       653 TEGYTGADIEAVCREAAMAALRESI  677 (733)
T ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHh
Confidence             488888888888778777777543

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.

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.68  E-value=5.3e-17  Score=138.58  Aligned_cols=99  Identities=20%  Similarity=0.258  Sum_probs=84.8

Q ss_pred             HHHHHHhhCCCCCCCCc---eEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHH
Q 042776            4 SGLLNFIDGLWSSCGDE---RIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELL   80 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~---vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~   80 (147)
                      ++||.+|||+... .++   |+|+||||.|++||.||+|  ||+++|+++||+.++|..+++..|+..+......++.++
T Consensus       334 sELLvQmDG~~~t-~e~~k~VmVLAATN~PWdiDEAlrR--RlEKRIyIPLP~~~~R~~Li~~~l~~~~~~~~~~~~~la  410 (491)
T KOG0738|consen  334 SELLVQMDGVQGT-LENSKVVMVLAATNFPWDIDEALRR--RLEKRIYIPLPDAEARSALIKILLRSVELDDPVNLEDLA  410 (491)
T ss_pred             HHHHHHhhccccc-cccceeEEEEeccCCCcchHHHHHH--HHhhheeeeCCCHHHHHHHHHHhhccccCCCCccHHHHH
Confidence            7899999999754 255   8899999999999999999  999999999999999999999999877555555555555


Q ss_pred             H---HHhccchHHHHHHHHHHHHHHhhH
Q 042776           81 T---KLMKSEVAEVALEGLVEFLKRKKT  105 (147)
Q Consensus        81 ~---~l~~~~~~~~al~~~~~~l~~~~~  105 (147)
                      +   +|+|.|...+|-++.+..++....
T Consensus       411 e~~eGySGaDI~nvCreAsm~~mRR~i~  438 (491)
T KOG0738|consen  411 ERSEGYSGADITNVCREASMMAMRRKIA  438 (491)
T ss_pred             HHhcCCChHHHHHHHHHHHHHHHHHHHh
Confidence            5   999999999999999988886654

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.68  E-value=5.6e-17  Score=137.11  Aligned_cols=102  Identities=18%  Similarity=0.217  Sum_probs=88.0

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC---CChHHHHHHH
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH---NLFPEIDELL   80 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~---~~~~~i~~l~   80 (147)
                      +||+..|||+.+..+..|+|++|||||.+||.|++|  ||.++++|++|+..+|.+||+.+|...+.   .+...++.++
T Consensus       215 ~eFM~~WDGl~s~~~~rVlVlgATNRP~DlDeAiiR--R~p~rf~V~lP~~~qR~kILkviLk~e~~e~~vD~~~iA~~t  292 (386)
T KOG0737|consen  215 NEFMALWDGLSSKDSERVLVLGATNRPFDLDEAIIR--RLPRRFHVGLPDAEQRRKILKVILKKEKLEDDVDLDEIAQMT  292 (386)
T ss_pred             HHHHHHhccccCCCCceEEEEeCCCCCccHHHHHHH--hCcceeeeCCCchhhHHHHHHHHhcccccCcccCHHHHHHhc
Confidence            789999999999866679999999999999999999  99999999999999999999999987644   4455556666


Q ss_pred             HHHhccchHHHHHHHHHHHHHHhhHHH
Q 042776           81 TKLMKSEVAEVALEGLVEFLKRKKTEV  107 (147)
Q Consensus        81 ~~l~~~~~~~~al~~~~~~l~~~~~~~  107 (147)
                      ++|+|+|..+.|..+....+++--...
T Consensus       293 ~GySGSDLkelC~~Aa~~~ire~~~~~  319 (386)
T KOG0737|consen  293 EGYSGSDLKELCRLAALRPIRELLVSE  319 (386)
T ss_pred             CCCcHHHHHHHHHHHhHhHHHHHHHhc
Confidence            699999999988888887777665543

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.67  E-value=9.9e-17  Score=144.59  Aligned_cols=100  Identities=22%  Similarity=0.283  Sum_probs=84.0

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHH-
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELL-   80 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~-   80 (147)
                      ++++||.+|||+.+.  ++++||+|||+|+.||||++||||||+.|+|++|+.++|.+|++.|+...+.....++..++ 
T Consensus       274 ~ln~lL~~mdg~~~~--~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~~~~~~~l~~~~d~~~la~  351 (644)
T PRK10733        274 TLNQMLVEMDGFEGN--EGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIAR  351 (644)
T ss_pred             HHHHHHHhhhcccCC--CCeeEEEecCChhhcCHHHhCCcccceEEEcCCCCHHHHHHHHHHHhhcCCCCCcCCHHHHHh
Confidence            578999999999876  78999999999999999999999999999999999999999999999766543333444444 


Q ss_pred             --HHHhccchHHHHHHHHHHHHHHh
Q 042776           81 --TKLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        81 --~~l~~~~~~~~al~~~~~~l~~~  103 (147)
                        .++++.+....|-++.+.+++..
T Consensus       352 ~t~G~sgadl~~l~~eAa~~a~r~~  376 (644)
T PRK10733        352 GTPGFSGADLANLVNEAALFAARGN  376 (644)
T ss_pred             hCCCCCHHHHHHHHHHHHHHHHHcC
Confidence              47888888888888887776543

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.67  E-value=9.3e-17  Score=155.57  Aligned_cols=105  Identities=15%  Similarity=0.154  Sum_probs=83.3

Q ss_pred             CcHHHHHHHhhCCCC-CCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCC-----CC-CCCh
Q 042776            1 LTLSGLLNFIDGLWS-SCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGI-----ND-HNLF   73 (147)
Q Consensus         1 ~tv~~lL~~lDgl~~-~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~-----~~-~~~~   73 (147)
                      +|+++||++|||... ....+|+||||||+|+.|||||+||||||+.|+|++|+..+|++++..++..     .+ ..+.
T Consensus      1752 ltL~qLLneLDg~~~~~s~~~VIVIAATNRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl 1831 (2281)
T CHL00206       1752 LSLGLLVNSLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHT 1831 (2281)
T ss_pred             ehHHHHHHHhccccccCCCCCEEEEEeCCCcccCCHhHcCCCCCCeEEEeCCCCchhHHHHHHHHHhhcCCCCCcccccH
Confidence            368999999999842 1237899999999999999999999999999999999999999988754321     11 1234


Q ss_pred             HHHHHHHHHHhccchHHHHHHHHHHHHHHhhH
Q 042776           74 PEIDELLTKLMKSEVAEVALEGLVEFLKRKKT  105 (147)
Q Consensus        74 ~~i~~l~~~l~~~~~~~~al~~~~~~l~~~~~  105 (147)
                      ..++..+.+++|+|....|=++++.++.+.+.
T Consensus      1832 ~~LA~~T~GfSGADLanLvNEAaliAirq~ks 1863 (2281)
T CHL00206       1832 NGFGSITMGSNARDLVALTNEALSISITQKKS 1863 (2281)
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCC
Confidence            55666666888988888888888888876653

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

Probab=99.66  E-value=2.7e-16  Score=134.99  Aligned_cols=100  Identities=24%  Similarity=0.402  Sum_probs=84.5

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCC---ChHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHN---LFPEIDEL   79 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~---~~~~i~~l   79 (147)
                      +.+||++|||+...  .+++||+|||+|+.||||++||||||+.|+|++|+.++|..|++.++......   ....+...
T Consensus       269 l~~LL~~ld~~~~~--~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~~dvd~~~la~~  346 (398)
T PTZ00454        269 LLELLNQMDGFDQT--TNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSR  346 (398)
T ss_pred             HHHHHHHhhccCCC--CCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCCcccCHHHHHHH
Confidence            67899999999876  67999999999999999999999999999999999999999999998755433   33444444


Q ss_pred             HHHHhccchHHHHHHHHHHHHHHhh
Q 042776           80 LTKLMKSEVAEVALEGLVEFLKRKK  104 (147)
Q Consensus        80 ~~~l~~~~~~~~al~~~~~~l~~~~  104 (147)
                      +.++++.+....|-++.+.++++..
T Consensus       347 t~g~sgaDI~~l~~eA~~~A~r~~~  371 (398)
T PTZ00454        347 PEKISAADIAAICQEAGMQAVRKNR  371 (398)
T ss_pred             cCCCCHHHHHHHHHHHHHHHHHcCC
Confidence            4588999999999999888886643

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.65  E-value=4.1e-16  Score=136.36  Aligned_cols=98  Identities=23%  Similarity=0.307  Sum_probs=79.7

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT   81 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~   81 (147)
                      ++++||.+|||+.+.  ++++||+|||+|+.||||++||||||+.|+|++|+.++|.+|++.|+.........++..++.
T Consensus       177 ~~~~lL~~~d~~~~~--~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~~~~~l~~la~  254 (495)
T TIGR01241       177 TLNQLLVEMDGFGTN--TGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVAR  254 (495)
T ss_pred             HHHHHHhhhccccCC--CCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCCcchhHHHHHH
Confidence            478999999999876  779999999999999999999999999999999999999999999997654443444555555


Q ss_pred             ---HHhccchHHHHHHHHHHHHH
Q 042776           82 ---KLMKSEVAEVALEGLVEFLK  101 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~~l~  101 (147)
                         ++.+.+....|-++.....+
T Consensus       255 ~t~G~sgadl~~l~~eA~~~a~~  277 (495)
T TIGR01241       255 RTPGFSGADLANLLNEAALLAAR  277 (495)
T ss_pred             hCCCCCHHHHHHHHHHHHHHHHH
Confidence               66777666666665554443

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.

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=99.63  E-value=5.8e-16  Score=144.23  Aligned_cols=105  Identities=21%  Similarity=0.250  Sum_probs=88.8

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChH-HHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFP-EIDELLT   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~-~i~~l~~   81 (147)
                      |+.||..|||+.+.  .+|+||+|||||+.+||||+||||||+.++|++|+.++|++|+..+-..-..+... -...++.
T Consensus       391 vSTLLaLmdGldsR--gqVvvigATnRpda~dpaLRRPgrfdref~f~lp~~~ar~~Il~Ihtrkw~~~i~~~l~~~la~  468 (1080)
T KOG0732|consen  391 VSTLLALMDGLDSR--GQVVVIGATNRPDAIDPALRRPGRFDREFYFPLPDVDARAKILDIHTRKWEPPISRELLLWLAE  468 (1080)
T ss_pred             HHHHHHhccCCCCC--CceEEEcccCCccccchhhcCCcccceeEeeeCCchHHHHHHHHHhccCCCCCCCHHHHHHHHH
Confidence            68999999999999  88999999999999999999999999999999999999999999887665443332 2344444


Q ss_pred             ---HHhccchHHHHHHHHHHHHHHhhHHHHh
Q 042776           82 ---KLMKSEVAEVALEGLVEFLKRKKTEVAE  109 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~~l~~~~~~~~~  109 (147)
                         ++.|.|....|-++++..++..-...-.
T Consensus       469 ~t~gy~gaDlkaLCTeAal~~~~r~~Pq~y~  499 (1080)
T KOG0732|consen  469 ETSGYGGADLKALCTEAALIALRRSFPQIYS  499 (1080)
T ss_pred             hccccchHHHHHHHHHHhhhhhccccCeeec
Confidence               8889999999999999999876654433

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.63  E-value=8e-16  Score=135.64  Aligned_cols=63  Identities=33%  Similarity=0.551  Sum_probs=59.9

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGI   67 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~   67 (147)
                      +++||++|||+.+.  ++++||+|||+|+.|||||+||||||++|+|++|+.++|.+||+.|+..
T Consensus       318 l~~LL~~LDgl~~~--~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~~  380 (512)
T TIGR03689       318 VPQLLSELDGVESL--DNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYLTD  380 (512)
T ss_pred             HHHHHHHhcccccC--CceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHhhc
Confidence            68999999999877  6799999999999999999999999999999999999999999999864

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.

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

Probab=99.61  E-value=1.4e-15  Score=132.00  Aligned_cols=101  Identities=25%  Similarity=0.325  Sum_probs=83.9

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCC---ChHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHN---LFPEIDE   78 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~---~~~~i~~   78 (147)
                      ++.+||++|||+...  .++.||+|||+++.||||++||||||++|+|++|+.++|.+||+.|+......   +...+..
T Consensus       306 ~ll~LL~~Ldg~~~~--~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~dvdl~~la~  383 (438)
T PTZ00361        306 TMLELLNQLDGFDSR--GDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIM  383 (438)
T ss_pred             HHHHHHHHHhhhccc--CCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCcCcCHHHHHH
Confidence            367899999999766  67999999999999999999999999999999999999999999998655433   3334444


Q ss_pred             HHHHHhccchHHHHHHHHHHHHHHhh
Q 042776           79 LLTKLMKSEVAEVALEGLVEFLKRKK  104 (147)
Q Consensus        79 l~~~l~~~~~~~~al~~~~~~l~~~~  104 (147)
                      .+.++++.+....|.++.+.++++.+
T Consensus       384 ~t~g~sgAdI~~i~~eA~~~Alr~~r  409 (438)
T PTZ00361        384 AKDELSGADIKAICTEAGLLALRERR  409 (438)
T ss_pred             hcCCCCHHHHHHHHHHHHHHHHHhcC
Confidence            44588888888888888888877654

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.60  E-value=2.5e-15  Score=128.20  Aligned_cols=100  Identities=25%  Similarity=0.286  Sum_probs=84.8

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC---CChHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH---NLFPEIDE   78 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~---~~~~~i~~   78 (147)
                      ++.+||+++||+...  .+++||+|||+++.||+|++||||||+.|+|++|+.++|.+||+.|+.....   .....++.
T Consensus       254 ~l~~lL~~ld~~~~~--~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~~~~~~la~  331 (389)
T PRK03992        254 TLMQLLAEMDGFDPR--GNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAE  331 (389)
T ss_pred             HHHHHHHhccccCCC--CCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCCcCCHHHHHH
Confidence            367899999999776  6799999999999999999999999999999999999999999999875533   33445555


Q ss_pred             HHHHHhccchHHHHHHHHHHHHHHh
Q 042776           79 LLTKLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        79 l~~~l~~~~~~~~al~~~~~~l~~~  103 (147)
                      .+.++++.+....|.++.+.+++..
T Consensus       332 ~t~g~sgadl~~l~~eA~~~a~~~~  356 (389)
T PRK03992        332 LTEGASGADLKAICTEAGMFAIRDD  356 (389)
T ss_pred             HcCCCCHHHHHHHHHHHHHHHHHcC
Confidence            5558899999999988888887764

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.58  E-value=5.2e-16  Score=136.63  Aligned_cols=98  Identities=24%  Similarity=0.337  Sum_probs=76.0

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCC-------CCCChHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIN-------DHNLFPE   75 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~-------~~~~~~~   75 (147)
                      |||||+-|||+.+.  ++++||+.|||++.||.||+|||||+.++++++||.++|.+||+.|....       ...+..+
T Consensus       354 VNQLLsKmDGVeqL--NNILVIGMTNR~DlIDEALLRPGRlEVqmEIsLPDE~gRlQIl~IHT~rMre~~~l~~dVdl~e  431 (744)
T KOG0741|consen  354 VNQLLSKMDGVEQL--NNILVIGMTNRKDLIDEALLRPGRLEVQMEISLPDEKGRLQILKIHTKRMRENNKLSADVDLKE  431 (744)
T ss_pred             HHHHHHhcccHHhh--hcEEEEeccCchhhHHHHhcCCCceEEEEEEeCCCccCceEEEEhhhhhhhhcCCCCCCcCHHH
Confidence            79999999999998  88999999999999999999999999999999999999999999886432       2333445


Q ss_pred             HHHHHHHHhccchHHHHHHHHHHHHHHhhHHH
Q 042776           76 IDELLTKLMKSEVAEVALEGLVEFLKRKKTEV  107 (147)
Q Consensus        76 i~~l~~~l~~~~~~~~al~~~~~~l~~~~~~~  107 (147)
                      ++.++..|+|.     -+++++...++-...+
T Consensus       432 lA~lTKNfSGA-----EleglVksA~S~A~nR  458 (744)
T KOG0741|consen  432 LAALTKNFSGA-----ELEGLVKSAQSFAMNR  458 (744)
T ss_pred             HHHHhcCCchh-----HHHHHHHHHHHHHHHh
Confidence            55555445443     3455555444444333

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

Probab=99.57  E-value=1.4e-14  Score=123.70  Aligned_cols=81  Identities=19%  Similarity=0.167  Sum_probs=67.0

Q ss_pred             HHHHHHHhhCC--------C--CCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCC
Q 042776            3 LSGLLNFIDGL--------W--SSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNL   72 (147)
Q Consensus         3 v~~lL~~lDgl--------~--~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~   72 (147)
                      +++||+.|||.        |  ......|+||+|||+|+.|||||+||||||+.|  .+|+.++|..|++.++...... 
T Consensus       241 ~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~VIaTTNrpd~LDpALlRpGRfDk~i--~lPd~e~R~eIL~~~~r~~~l~-  317 (413)
T PLN00020        241 NGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGNDFSTLYAPLIRDGRMEKFY--WAPTREDRIGVVHGIFRDDGVS-  317 (413)
T ss_pred             HHHHHHHhcCCccccccccccccccCCCceEEEeCCCcccCCHhHcCCCCCCcee--CCCCHHHHHHHHHHHhccCCCC-
Confidence            36899999874        2  122367999999999999999999999999975  5899999999999999877555 


Q ss_pred             hHHHHHHHHHHhcc
Q 042776           73 FPEIDELLTKLMKS   86 (147)
Q Consensus        73 ~~~i~~l~~~l~~~   86 (147)
                      ..++..++..+-+.
T Consensus       318 ~~dv~~Lv~~f~gq  331 (413)
T PLN00020        318 REDVVKLVDTFPGQ  331 (413)
T ss_pred             HHHHHHHHHcCCCC
Confidence            68899999955544

>CHL00176 ftsH cell division protein; Validated

Probab=99.56  E-value=7.5e-15  Score=132.47  Aligned_cols=97  Identities=25%  Similarity=0.290  Sum_probs=77.7

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT   81 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~   81 (147)
                      ++++||.+|||+...  .+++||+|||+|+.|||||+||||||+.|+|++|+.++|..|++.|+..........+..++.
T Consensus       305 ~L~~LL~~~dg~~~~--~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~~~d~~l~~lA~  382 (638)
T CHL00176        305 TLNQLLTEMDGFKGN--KGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLSPDVSLELIAR  382 (638)
T ss_pred             HHHHHHhhhccccCC--CCeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhcccchhHHHHHHHh
Confidence            478999999999876  789999999999999999999999999999999999999999999997654444445555555


Q ss_pred             ---HHhccchHHHHHHHHHHHH
Q 042776           82 ---KLMKSEVAEVALEGLVEFL  100 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~~l  100 (147)
                         ++.+++....+-++++...
T Consensus       383 ~t~G~sgaDL~~lvneAal~a~  404 (638)
T CHL00176        383 RTPGFSGADLANLLNEAAILTA  404 (638)
T ss_pred             cCCCCCHHHHHHHHHHHHHHHH
Confidence               5555555555554444433

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.55  E-value=1e-14  Score=128.06  Aligned_cols=96  Identities=16%  Similarity=0.191  Sum_probs=77.7

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCC-----CCChHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIND-----HNLFPEID   77 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~-----~~~~~~i~   77 (147)
                      +++||..|+..    +.+++||+|||+|+.||||++||||||+.|+|++|+.++|.+||+.|+....     ..+...++
T Consensus       347 l~~lL~~l~~~----~~~V~vIaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl~~La  422 (489)
T CHL00195        347 LATFITWLSEK----KSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLS  422 (489)
T ss_pred             HHHHHHHHhcC----CCceEEEEecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcCCCcccccCHHHHH
Confidence            46778888753    2569999999999999999999999999999999999999999999986542     22234455


Q ss_pred             HHHHHHhccchHHHHHHHHHHHHHH
Q 042776           78 ELLTKLMKSEVAEVALEGLVEFLKR  102 (147)
Q Consensus        78 ~l~~~l~~~~~~~~al~~~~~~l~~  102 (147)
                      ..+.+|+|++....|.++...++..
T Consensus       423 ~~T~GfSGAdI~~lv~eA~~~A~~~  447 (489)
T CHL00195        423 KLSNKFSGAEIEQSIIEAMYIAFYE  447 (489)
T ss_pred             hhcCCCCHHHHHHHHHHHHHHHHHc
Confidence            5555999999988888888776643

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.55  E-value=1.9e-15  Score=126.19  Aligned_cols=99  Identities=21%  Similarity=0.262  Sum_probs=83.8

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChH-HHHHHHH-
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFP-EIDELLT-   81 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~-~i~~l~~-   81 (147)
                      ++||.+|.|+... +++++|++|||-|+.||.|++|  ||+++||+++|+..+|..||+.++|..+|.+.. ++..|+. 
T Consensus       254 TEfLVQMqGVG~d-~~gvLVLgATNiPw~LDsAIRR--RFekRIYIPLPe~~AR~~MF~lhlG~tp~~LT~~d~~eL~~k  330 (439)
T KOG0739|consen  254 TEFLVQMQGVGND-NDGVLVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHARARMFKLHLGDTPHVLTEQDFKELARK  330 (439)
T ss_pred             HHHHHhhhccccC-CCceEEEecCCCchhHHHHHHH--HhhcceeccCCcHHHhhhhheeccCCCccccchhhHHHHHhh
Confidence            6899999999765 5899999999999999999999  999999999999999999999999999887654 4555544 


Q ss_pred             --HHhccchHHHHHHHHHHHHHHhhH
Q 042776           82 --KLMKSEVAEVALEGLVEFLKRKKT  105 (147)
Q Consensus        82 --~l~~~~~~~~al~~~~~~l~~~~~  105 (147)
                        +++|+|..-.+-.++++-+++...
T Consensus       331 TeGySGsDisivVrDalmePvRkvqs  356 (439)
T KOG0739|consen  331 TEGYSGSDISIVVRDALMEPVRKVQS  356 (439)
T ss_pred             cCCCCcCceEEEehhhhhhhHHHhhh
Confidence              999988877666777776665543

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

Probab=99.55  E-value=1.6e-14  Score=118.72  Aligned_cols=93  Identities=18%  Similarity=0.251  Sum_probs=80.7

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT   81 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~   81 (147)
                      .||.||++|||+.+.  +||+.|+|||+|+.||||++-  ||+..|+|.+|+.++|..|++.|...-+.+....+..++.
T Consensus       238 iVNALLTelDgi~en--eGVvtIaaTN~p~~LD~aiRs--RFEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~~~~~~~  313 (368)
T COG1223         238 IVNALLTELDGIKEN--EGVVTIAATNRPELLDPAIRS--RFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAA  313 (368)
T ss_pred             HHHHHHHhccCcccC--CceEEEeecCChhhcCHHHHh--hhhheeeeeCCChHHHHHHHHHHHHhCCCccccCHHHHHH
Confidence            379999999999976  999999999999999999999  9999999999999999999999988776555555555554


Q ss_pred             ---HHhccchHHHHHHHHHH
Q 042776           82 ---KLMKSEVAEVALEGLVE   98 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~   98 (147)
                         +++|+|..+..|.....
T Consensus       314 ~t~g~SgRdikekvlK~aLh  333 (368)
T COG1223         314 KTKGMSGRDIKEKVLKTALH  333 (368)
T ss_pred             HhCCCCchhHHHHHHHHHHH
Confidence               99999998888876544

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.51  E-value=5.9e-14  Score=118.28  Aligned_cols=100  Identities=23%  Similarity=0.261  Sum_probs=83.9

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC---CChHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH---NLFPEIDE   78 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~---~~~~~i~~   78 (147)
                      ++.++|.++||+...  .+++||+|||+++.||+|++||||||+.|+|++|+.++|..|++.|+.....   .....++.
T Consensus       245 ~l~~ll~~ld~~~~~--~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~~~~~~la~  322 (364)
T TIGR01242       245 TLMQLLAELDGFDPR--GNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAK  322 (364)
T ss_pred             HHHHHHHHhhCCCCC--CCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCccCCHHHHHH
Confidence            367889999998766  6799999999999999999999999999999999999999999998865432   34555666


Q ss_pred             HHHHHhccchHHHHHHHHHHHHHHh
Q 042776           79 LLTKLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        79 l~~~l~~~~~~~~al~~~~~~l~~~  103 (147)
                      ++.++.+.+....|.++.+.++++.
T Consensus       323 ~t~g~sg~dl~~l~~~A~~~a~~~~  347 (364)
T TIGR01242       323 MTEGASGADLKAICTEAGMFAIREE  347 (364)
T ss_pred             HcCCCCHHHHHHHHHHHHHHHHHhC
Confidence            6668888888888888888887654

Many proteins may score above the trusted cutoff because an internal

>KOG0651 consensus 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones]

Probab=99.49  E-value=9.7e-15  Score=121.99  Aligned_cols=91  Identities=27%  Similarity=0.323  Sum_probs=73.8

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCC---CCCChHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIN---DHNLFPEIDE   78 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~---~~~~~~~i~~   78 (147)
                      |+=+||++|||+...  ..|=+|+|||+|+.|||||+||||+|+.+++|+|+...|..|++.+-...   ..-.+..+.+
T Consensus       255 TLMeLlnqmdgfd~l--~rVk~ImatNrpdtLdpaLlRpGRldrk~~iPlpne~~r~~I~Kih~~~i~~~Geid~eaivK  332 (388)
T KOG0651|consen  255 TLMELLNQMDGFDTL--HRVKTIMATNRPDTLDPALLRPGRLDRKVEIPLPNEQARLGILKIHVQPIDFHGEIDDEAILK  332 (388)
T ss_pred             HHHHHHHhhccchhc--ccccEEEecCCccccchhhcCCccccceeccCCcchhhceeeEeeccccccccccccHHHHHH
Confidence            567899999999887  77889999999999999999999999999999999999999988765322   3344677888


Q ss_pred             HHHHHhccchHHHHHH
Q 042776           79 LLTKLMKSEVAEVALE   94 (147)
Q Consensus        79 l~~~l~~~~~~~~al~   94 (147)
                      +.+++-+.+....|-+
T Consensus       333 ~~d~f~gad~rn~~tE  348 (388)
T KOG0651|consen  333 LVDGFNGADLRNVCTE  348 (388)
T ss_pred             HHhccChHHHhhhccc
Confidence            8876665554444433

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.47  E-value=1.6e-13  Score=122.91  Aligned_cols=97  Identities=23%  Similarity=0.345  Sum_probs=87.1

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH-
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT-   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~-   81 (147)
                      ++||+..|||+.+.  ..++||+|||+|+.||||++| ||||+.+.++.|+..+|..|++.+....++....++..++. 
T Consensus       305 ~sqlltL~dg~~~~--~~vivl~atnrp~sld~alRR-gRfd~ev~IgiP~~~~RldIl~~l~k~~~~~~~~~l~~iA~~  381 (693)
T KOG0730|consen  305 VSQLLTLLDGLKPD--AKVIVLAATNRPDSLDPALRR-GRFDREVEIGIPGSDGRLDILRVLTKKMNLLSDVDLEDIAVS  381 (693)
T ss_pred             HHHHHHHHhhCcCc--CcEEEEEecCCccccChhhhc-CCCcceeeecCCCchhHHHHHHHHHHhcCCcchhhHHHHHHH
Confidence            68999999999866  779999999999999999999 99999999999999999999999998777665566666666 


Q ss_pred             --HHhccchHHHHHHHHHHHHHH
Q 042776           82 --KLMKSEVAEVALEGLVEFLKR  102 (147)
Q Consensus        82 --~l~~~~~~~~al~~~~~~l~~  102 (147)
                        +++|.|....|.++....++.
T Consensus       382 thGyvGaDL~~l~~ea~~~~~r~  404 (693)
T KOG0730|consen  382 THGYVGADLAALCREASLQATRR  404 (693)
T ss_pred             ccchhHHHHHHHHHHHHHHHhhh
Confidence              899999999988888888877

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.43  E-value=1.6e-13  Score=118.51  Aligned_cols=102  Identities=20%  Similarity=0.155  Sum_probs=89.2

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCCh-HHHHHHH-
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLF-PEIDELL-   80 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~-~~i~~l~-   80 (147)
                      .++||.++||..+.+++.|+||+|||+|+.+|.|++|  ||-++++|++|+.++|..++.+++...++.+. .+++.++ 
T Consensus       273 ktefLiq~~~~~s~~~drvlvigaTN~P~e~Dea~~R--rf~kr~yiplPd~etr~~~~~~ll~~~~~~l~~~d~~~l~~  350 (428)
T KOG0740|consen  273 KTEFLLQFDGKNSAPDDRVLVIGATNRPWELDEAARR--RFVKRLYIPLPDYETRSLLWKQLLKEQPNGLSDLDISLLAK  350 (428)
T ss_pred             hhHHHhhhccccCCCCCeEEEEecCCCchHHHHHHHH--HhhceeeecCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHH
Confidence            4689999999998888999999999999999999999  99999999999999999999999987766554 3455444 


Q ss_pred             --HHHhccchHHHHHHHHHHHHHHhhHH
Q 042776           81 --TKLMKSEVAEVALEGLVEFLKRKKTE  106 (147)
Q Consensus        81 --~~l~~~~~~~~al~~~~~~l~~~~~~  106 (147)
                        +++.++|..+.|.++.+.-++.....
T Consensus       351 ~Tegysgsdi~~l~kea~~~p~r~~~~~  378 (428)
T KOG0740|consen  351 VTEGYSGSDITALCKEAAMGPLRELGGT  378 (428)
T ss_pred             HhcCcccccHHHHHHHhhcCchhhcccc
Confidence              49999999999999999888776653

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.31  E-value=6.4e-12  Score=114.71  Aligned_cols=98  Identities=26%  Similarity=0.365  Sum_probs=78.9

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCC---ChHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHN---LFPEIDEL   79 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~---~~~~i~~l   79 (147)
                      +++|++.||++...  ..++||+|||+|+.||||++||||||+.|+|++|+.++|.+|++.++......   ....+...
T Consensus       299 ~~~Ll~~ld~l~~~--~~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~~~l~~d~~l~~la~~  376 (733)
T TIGR01243       299 VAQLLTLMDGLKGR--GRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEV  376 (733)
T ss_pred             HHHHHHHhhccccC--CCEEEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcCCCCccccCHHHHHHh
Confidence            57899999999776  67999999999999999999999999999999999999999999887655433   23344444


Q ss_pred             HHHHhccchHHHHHHHHHHHHHH
Q 042776           80 LTKLMKSEVAEVALEGLVEFLKR  102 (147)
Q Consensus        80 ~~~l~~~~~~~~al~~~~~~l~~  102 (147)
                      +.++.+.+....|.++....++.
T Consensus       377 t~G~~gadl~~l~~~a~~~al~r  399 (733)
T TIGR01243       377 THGFVGADLAALAKEAAMAALRR  399 (733)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHH
Confidence            44777777777666666666654

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

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

Probab=98.45  E-value=2.2e-07  Score=65.73  Aligned_cols=47  Identities=38%  Similarity=0.613  Sum_probs=41.2

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSY   51 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~   51 (147)
                      +++|+..||..... +.+++||+|||+++.|||+++| |||+.+|+|++
T Consensus        86 ~~~L~~~l~~~~~~-~~~~~vI~ttn~~~~i~~~l~~-~rf~~~i~~~~  132 (132)
T PF00004_consen   86 LNQLLSLLDNPSSK-NSRVIVIATTNSPDKIDPALLR-SRFDRRIEFPL  132 (132)
T ss_dssp             HHHHHHHHHTTTTT-SSSEEEEEEESSGGGSCHHHHS-TTSEEEEEE-S
T ss_pred             cceeeecccccccc-cccceeEEeeCChhhCCHhHHh-CCCcEEEEcCC
Confidence            67899999999765 3569999999999999999999 99999999975

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

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

Probab=98.42  E-value=1.2e-06  Score=76.66  Aligned_cols=98  Identities=26%  Similarity=0.310  Sum_probs=75.6

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH-
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT-   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~-   81 (147)
                      +++|+..|||+. . +. ++++++||++..+|+|+.|||||++.+++..|+...+..|+..+..............++. 
T Consensus       104 ~~~l~~~~d~~~-~-~~-v~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~~~~~~~~a~~  180 (494)
T COG0464         104 VAQLLALMDGLK-R-GQ-VIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIHTRLMFLGPPGTGKTLAAR  180 (494)
T ss_pred             HHHHHHhccccc-C-Cc-eEEEeecCCccccChhHhCccccceeeecCCCCHHHHHHHHHHHHhcCCCcccccHHHHHHh
Confidence            689999999999 3 46 8899999999999999999999999999999999999999887765443332334444444 


Q ss_pred             --HHhccchHHHHHHHHHHHHHHh
Q 042776           82 --KLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        82 --~l~~~~~~~~al~~~~~~l~~~  103 (147)
                        ++.+.+....|-+....+++..
T Consensus       181 ~~~~~~~~~~~l~~~~~~~~~~r~  204 (494)
T COG0464         181 TVGKSGADLGALAKEAALRELRRA  204 (494)
T ss_pred             cCCccHHHHHHHHHHHHHHHHHhh
Confidence              5666666666656555555554

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=98.05  E-value=3.5e-06  Score=73.63  Aligned_cols=46  Identities=24%  Similarity=0.330  Sum_probs=43.3

Q ss_pred             CceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhC
Q 042776           19 DERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus        19 ~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      ..++++.|||+|.+||.|+--  |||..|+|++|..++|..||..||.
T Consensus       484 rdivLvlAtNrpgdlDsAV~D--Ride~veFpLPGeEERfkll~lYln  529 (630)
T KOG0742|consen  484 RDIVLVLATNRPGDLDSAVND--RIDEVVEFPLPGEEERFKLLNLYLN  529 (630)
T ss_pred             cceEEEeccCCccchhHHHHh--hhhheeecCCCChHHHHHHHHHHHH
Confidence            568899999999999999998  9999999999999999999998874

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.86  E-value=1.2e-05  Score=68.30  Aligned_cols=59  Identities=19%  Similarity=0.272  Sum_probs=55.5

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      ||.||+|||.+...  .+|++++|+|-.+.||-|+.-  |-|-+.+++.|+.+++..|++..+
T Consensus       282 VNalLTQlDrlK~~--~NvliL~TSNl~~siD~AfVD--RADi~~yVG~Pt~~ai~~Ilksci  340 (423)
T KOG0744|consen  282 VNALLTQLDRLKRY--PNVLILATSNLTDSIDVAFVD--RADIVFYVGPPTAEAIYEILKSCI  340 (423)
T ss_pred             HHHHHHHHHHhccC--CCEEEEeccchHHHHHHHhhh--HhhheeecCCccHHHHHHHHHHHH
Confidence            79999999999998  669999999999999999999  999999999999999999988654

>TIGR00763 lon ATP-dependent protease La

Probab=97.31  E-value=0.0011  Score=61.53  Aligned_cols=44  Identities=25%  Similarity=0.325  Sum_probs=40.5

Q ss_pred             CceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776           19 DERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus        19 ~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      .++++|+|||.++.|+|+|++  ||+ .|+|+.|+.+++.+|++.|+
T Consensus       462 s~v~~I~TtN~~~~i~~~L~~--R~~-vi~~~~~~~~e~~~I~~~~l  505 (775)
T TIGR00763       462 SKVIFIATANSIDTIPRPLLD--RME-VIELSGYTEEEKLEIAKKYL  505 (775)
T ss_pred             CCEEEEEecCCchhCCHHHhC--Cee-EEecCCCCHHHHHHHHHHHH
Confidence            358899999999999999999  996 68999999999999999886

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.

>CHL00181 cbbX CbbX; Provisional

Probab=97.27  E-value=0.0013  Score=54.32  Aligned_cols=65  Identities=17%  Similarity=0.318  Sum_probs=49.0

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCC-----CCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCCh
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKN-----RLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLF   73 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~-----~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~   73 (147)
                      ++.|+..|+...    ..++||+||+...     .++|+|++  ||+..|+|+.++.+++.+|+..++......+.
T Consensus       148 ~~~L~~~me~~~----~~~~vI~ag~~~~~~~~~~~np~L~s--R~~~~i~F~~~t~~el~~I~~~~l~~~~~~l~  217 (287)
T CHL00181        148 IEILLQVMENQR----DDLVVIFAGYKDRMDKFYESNPGLSS--RIANHVDFPDYTPEELLQIAKIMLEEQQYQLT  217 (287)
T ss_pred             HHHHHHHHhcCC----CCEEEEEeCCcHHHHHHHhcCHHHHH--hCCceEEcCCcCHHHHHHHHHHHHHHhcCCCC
Confidence            456777787532    4477888876322     34699999  99999999999999999999999865543333

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.06  E-value=0.0022  Score=51.75  Aligned_cols=67  Identities=13%  Similarity=0.218  Sum_probs=48.1

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCC-----CCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHK-----NRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPE   75 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p-----~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~   75 (147)
                      ++.|+..|+...    ..+++|++++..     ..++|+|++  ||+..|+|+.++.+++.+|++.++.........+
T Consensus       130 i~~Ll~~~e~~~----~~~~vila~~~~~~~~~~~~~p~L~s--Rf~~~i~f~~~~~~el~~Il~~~~~~~~~~l~~~  201 (261)
T TIGR02881       130 IDTLVKGMEDNR----NEFVLILAGYSDEMDYFLSLNPGLRS--RFPISIDFPDYTVEELMEIAERMVKEREYKLTEE  201 (261)
T ss_pred             HHHHHHHHhccC----CCEEEEecCCcchhHHHHhcChHHHh--ccceEEEECCCCHHHHHHHHHHHHHHcCCccCHH
Confidence            456777777642    335566655432     237899999  9999999999999999999999987554443333

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.

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

Probab=97.01  E-value=0.00043  Score=64.34  Aligned_cols=44  Identities=16%  Similarity=0.163  Sum_probs=38.9

Q ss_pred             CceEEEEecCCCC-----CCCccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776           19 DERIIVFTTNHKN-----RLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus        19 ~~vivi~aTN~p~-----~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      ..+.||+|||.++     .+||||.|  ||+ .|+|+.|+.+++..||+.+.
T Consensus       314 g~i~vIgATt~~E~~~~~~~D~AL~r--RFq-~I~v~ePs~~~~~~IL~~~~  362 (758)
T PRK11034        314 GKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLK  362 (758)
T ss_pred             CCeEEEecCChHHHHHHhhccHHHHh--hCc-EEEeCCCCHHHHHHHHHHHH
Confidence            5688999999875     68999999  996 79999999999999998654

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=96.87  E-value=0.0076  Score=49.61  Aligned_cols=63  Identities=11%  Similarity=0.266  Sum_probs=48.8

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCC--CCC---CCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNH--KNR---LDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHN   71 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~--p~~---LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~   71 (147)
                      ++.|+..|+.-.    .+++||+||+.  ++.   ++|+|.+  ||+..|+|+.++.+++..|+.+++......
T Consensus       147 ~~~Ll~~le~~~----~~~~vI~a~~~~~~~~~~~~np~L~s--R~~~~i~fp~l~~edl~~I~~~~l~~~~~~  214 (284)
T TIGR02880       147 IEILLQVMENQR----DDLVVILAGYKDRMDSFFESNPGFSS--RVAHHVDFPDYSEAELLVIAGLMLKEQQYR  214 (284)
T ss_pred             HHHHHHHHhcCC----CCEEEEEeCCcHHHHHHHhhCHHHHh--hCCcEEEeCCcCHHHHHHHHHHHHHHhccc
Confidence            467788887532    45778887763  333   4899999  999999999999999999999998765433

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

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=96.26  E-value=0.018  Score=47.92  Aligned_cols=52  Identities=12%  Similarity=0.111  Sum_probs=45.0

Q ss_pred             eEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChH
Q 042776           21 RIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFP   74 (147)
Q Consensus        21 vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~   74 (147)
                      .++|+|||++..++++|+.  ||...+.|+.|+.+++.+|++...+........
T Consensus       151 ~~li~at~~~~~l~~~L~s--Rf~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~  202 (328)
T PRK00080        151 FTLIGATTRAGLLTSPLRD--RFGIVQRLEFYTVEELEKIVKRSARILGVEIDE  202 (328)
T ss_pred             ceEEeecCCcccCCHHHHH--hcCeeeecCCCCHHHHHHHHHHHHHHcCCCcCH
Confidence            6789999999999999988  999999999999999999999887765444433

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

Probab=96.08  E-value=0.0097  Score=54.96  Aligned_cols=44  Identities=16%  Similarity=0.061  Sum_probs=37.8

Q ss_pred             CceEEEEecCCC-----CCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776           19 DERIIVFTTNHK-----NRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus        19 ~~vivi~aTN~p-----~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      +.+.+|+|||.+     ..+|+||.|  ||. .|+|+.|+.+++..|++.+.
T Consensus       310 g~i~~IgaTt~~e~~~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~il~~~~  358 (731)
T TIGR02639       310 GKLRCIGSTTYEEYKNHFEKDRALSR--RFQ-KIDVGEPSIEETVKILKGLK  358 (731)
T ss_pred             CCeEEEEecCHHHHHHHhhhhHHHHH--hCc-eEEeCCCCHHHHHHHHHHHH
Confidence            458899999963     468999999  997 79999999999999998554

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=96.08  E-value=0.018  Score=46.97  Aligned_cols=60  Identities=17%  Similarity=0.222  Sum_probs=47.5

Q ss_pred             ceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChH-HHHHHHH
Q 042776           20 ERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFP-EIDELLT   81 (147)
Q Consensus        20 ~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~-~i~~l~~   81 (147)
                      ..++|++||++..|+++++.  ||...+.|+.|+.++..++++...+........ .+..++.
T Consensus       129 ~~~li~~t~~~~~l~~~l~s--R~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~  189 (305)
T TIGR00635       129 PFTLVGATTRAGMLTSPLRD--RFGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIAR  189 (305)
T ss_pred             CeEEEEecCCccccCHHHHh--hcceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHH
Confidence            37799999999999999998  999999999999999999999877644333333 3444444

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=95.98  E-value=0.016  Score=54.63  Aligned_cols=44  Identities=18%  Similarity=0.193  Sum_probs=37.2

Q ss_pred             CceEEEEecCCCC-----CCCccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776           19 DERIIVFTTNHKN-----RLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus        19 ~~vivi~aTN~p~-----~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      +.+.+|+||+..+     .+||||+|  ||. .|.|+.|+.+++..||+.+.
T Consensus       315 G~l~~IgaTT~~e~~~~~~~d~AL~r--Rf~-~i~v~eps~~~~~~iL~~~~  363 (852)
T TIGR03345       315 GELRTIAATTWAEYKKYFEKDPALTR--RFQ-VVKVEEPDEETAIRMLRGLA  363 (852)
T ss_pred             CCeEEEEecCHHHHhhhhhccHHHHH--hCe-EEEeCCCCHHHHHHHHHHHH
Confidence            5588999998643     49999999  995 79999999999999976444

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.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=95.87  E-value=0.029  Score=47.98  Aligned_cols=74  Identities=9%  Similarity=0.149  Sum_probs=50.9

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCC---CCccccCCCeeee--EEeecCCCHHHHHHHHHHHhCCCCCCChHHH-H
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNR---LDPALLRPGRMDM--HIHMSYCNPSGFRILVSNYLGINDHNLFPEI-D   77 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~---LD~Al~RpGRfd~--~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i-~   77 (147)
                      .+|+..++.+...  +..+||.+++.|..   +++.|..  ||..  .++|+.|+.+.|..|++..+.........++ .
T Consensus       219 ~~l~~~~n~~~~~--~~~iiits~~~p~~l~~l~~~l~S--Rl~~g~~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~  294 (405)
T TIGR00362       219 EEFFHTFNALHEN--GKQIVLTSDRPPKELPGLEERLRS--RFEWGLVVDIEPPDLETRLAILQKKAEEEGLELPDEVLE  294 (405)
T ss_pred             HHHHHHHHHHHHC--CCCEEEecCCCHHHHhhhhhhhhh--hccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            3466667666544  44566666666765   4577876  9974  7999999999999999998876555444444 4


Q ss_pred             HHHH
Q 042776           78 ELLT   81 (147)
Q Consensus        78 ~l~~   81 (147)
                      .++.
T Consensus       295 ~ia~  298 (405)
T TIGR00362       295 FIAK  298 (405)
T ss_pred             HHHH
Confidence            4443

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).

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=95.40  E-value=0.066  Score=50.30  Aligned_cols=61  Identities=16%  Similarity=0.069  Sum_probs=52.5

Q ss_pred             CceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH
Q 042776           19 DERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT   81 (147)
Q Consensus        19 ~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~   81 (147)
                      .+++||+||+..+.|.+.+.+  -|-..|.++.|+.++|.+||+-|+...........+.++.
T Consensus       532 ~~~ivv~t~~s~~~lp~~i~~--~f~~ei~~~~lse~qRl~iLq~y~~~~~~n~~v~~k~~a~  592 (953)
T KOG0736|consen  532 PPVIVVATTSSIEDLPADIQS--LFLHEIEVPALSEEQRLEILQWYLNHLPLNQDVNLKQLAR  592 (953)
T ss_pred             CceEEEEeccccccCCHHHHH--hhhhhccCCCCCHHHHHHHHHHHHhccccchHHHHHHHHH
Confidence            679999999999999999998  8889999999999999999999998665554555566655

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=95.39  E-value=0.071  Score=50.21  Aligned_cols=44  Identities=16%  Similarity=0.061  Sum_probs=37.7

Q ss_pred             CceEEEEecCCC-----CCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776           19 DERIIVFTTNHK-----NRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus        19 ~~vivi~aTN~p-----~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      ..+.+|+||+.+     ..+|+|+.|  ||. .|.++.|+.+++..|++.+.
T Consensus       301 g~i~~IgaTt~~e~r~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~iL~~~~  349 (852)
T TIGR03346       301 GELHCIGATTLDEYRKYIEKDAALER--RFQ-PVFVDEPTVEDTISILRGLK  349 (852)
T ss_pred             CceEEEEeCcHHHHHHHhhcCHHHHh--cCC-EEEeCCCCHHHHHHHHHHHH
Confidence            457899999977     458999999  996 58999999999999998664

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.

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

Probab=95.31  E-value=0.14  Score=42.59  Aligned_cols=60  Identities=25%  Similarity=0.311  Sum_probs=44.0

Q ss_pred             HHHHHHHhhC----------CCCCCCCceEEEEecC-----CCCCCCccccCCCeeeeEEeecCC-CHHHHHHHHHHHhC
Q 042776            3 LSGLLNFIDG----------LWSSCGDERIIVFTTN-----HKNRLDPALLRPGRMDMHIHMSYC-NPSGFRILVSNYLG   66 (147)
Q Consensus         3 v~~lL~~lDg----------l~~~~~~~vivi~aTN-----~p~~LD~Al~RpGRfd~~i~~~~P-~~~~r~~il~~~l~   66 (147)
                      .+.||..|+.          +.-.  ...+||+|+|     .-..|.+|+++  ||-..+++++| ...+...++..+.+
T Consensus       129 q~aLl~~l~e~~vtv~~~~~~~~~--~~f~viaT~Np~e~~g~~~l~eA~ld--Rf~~~~~v~yp~~~~e~~~i~~~~~~  204 (329)
T COG0714         129 QNALLEALEERQVTVPGLTTIRLP--PPFIVIATQNPGEYEGTYPLPEALLD--RFLLRIYVDYPDSEEEERIILARVGG  204 (329)
T ss_pred             HHHHHHHHhCcEEEECCcCCcCCC--CCCEEEEccCccccCCCcCCCHHHHh--hEEEEEecCCCCchHHHHHHHHhCcc
Confidence            4567777665          2122  5677888889     77889999999  99999999999 55556666655554

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=95.30  E-value=0.047  Score=47.51  Aligned_cols=69  Identities=10%  Similarity=0.188  Sum_probs=49.4

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCC---CCccccCCCeee--eEEeecCCCHHHHHHHHHHHhCCCCCCChHHH
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNR---LDPALLRPGRMD--MHIHMSYCNPSGFRILVSNYLGINDHNLFPEI   76 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~---LD~Al~RpGRfd--~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i   76 (147)
                      .+|+..++.+...  ...+||+++..|..   |+++|.-  ||.  ..+.|..|+.+.|.+|++......+.....++
T Consensus       231 ~~l~~~~n~l~~~--~~~iiits~~~p~~l~~l~~~l~S--Rl~~gl~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~  304 (450)
T PRK00149        231 EEFFHTFNALHEA--GKQIVLTSDRPPKELPGLEERLRS--RFEWGLTVDIEPPDLETRIAILKKKAEEEGIDLPDEV  304 (450)
T ss_pred             HHHHHHHHHHHHC--CCcEEEECCCCHHHHHHHHHHHHh--HhcCCeeEEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            3566667776554  34566666666666   6788887  997  57899999999999999988865544444444

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=95.25  E-value=0.06  Score=43.57  Aligned_cols=83  Identities=17%  Similarity=0.242  Sum_probs=54.0

Q ss_pred             ceEEEEecCCC-----CCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHHHHh-ccchHHHHH
Q 042776           20 ERIIVFTTNHK-----NRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLTKLM-KSEVAEVAL   93 (147)
Q Consensus        20 ~vivi~aTN~p-----~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~~l~-~~~~~~~al   93 (147)
                      +..||+|+|..     ..+++||++  || ..+++++|+.+.-.+|+..+++..+ .....+..++..+- .........
T Consensus       151 ~frvIaTsN~~~~~g~~~l~~aL~~--R~-~~i~i~~P~~~~e~~Il~~~~~~~~-~~~~~iv~~~~~~R~~~~~~~~~~  226 (262)
T TIGR02640       151 EFRVIFTSNPVEYAGVHETQDALLD--RL-ITIFMDYPDIDTETAILRAKTDVAE-DSAATIVRLVREFRASGDEITSGL  226 (262)
T ss_pred             CCEEEEeeCCccccceecccHHHHh--hc-EEEECCCCCHHHHHHHHHHhhCCCH-HHHHHHHHHHHHHHhhCCccCCcH
Confidence            45689999976     367999999  99 6899999999999999998875322 12223333333222 222233346


Q ss_pred             HHHHHHHHHhhHH
Q 042776           94 EGLVEFLKRKKTE  106 (147)
Q Consensus        94 ~~~~~~l~~~~~~  106 (147)
                      +..+.|.+.....
T Consensus       227 r~~i~~~~~~~~~  239 (262)
T TIGR02640       227 RASLMIAEVATQQ  239 (262)
T ss_pred             HHHHHHHHHHHHc
Confidence            6677766655443

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).

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=95.16  E-value=0.064  Score=44.38  Aligned_cols=61  Identities=10%  Similarity=0.178  Sum_probs=47.0

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH   70 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~   70 (147)
                      .+.||..++...    ..+++|++||.++.|.+++..  |+ ..++|+.|+..+...++..++.....
T Consensus       134 ~~~Ll~~le~~~----~~~~lIl~~~~~~~l~~~l~s--r~-~~~~~~~~~~~~l~~~l~~~~~~~g~  194 (355)
T TIGR02397       134 FNALLKTLEEPP----EHVVFILATTEPHKIPATILS--RC-QRFDFKRIPLEDIVERLKKILDKEGI  194 (355)
T ss_pred             HHHHHHHHhCCc----cceeEEEEeCCHHHHHHHHHh--he-eEEEcCCCCHHHHHHHHHHHHHHcCC
Confidence            456777776532    447778888999999999988  77 46899999999999999887755443

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=94.92  E-value=0.023  Score=53.59  Aligned_cols=45  Identities=18%  Similarity=0.111  Sum_probs=39.1

Q ss_pred             CceEEEEecCCCC-----CCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhC
Q 042776           19 DERIIVFTTNHKN-----RLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus        19 ~~vivi~aTN~p~-----~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      +.+.+|+||+.++     .+|+|+.|  ||+ .|.++.|+.+++..|++.+..
T Consensus       306 g~l~~IgaTt~~e~r~~~~~d~al~r--Rf~-~i~v~eP~~~~~~~iL~~l~~  355 (857)
T PRK10865        306 GELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAILRGLKE  355 (857)
T ss_pred             CCCeEEEcCCCHHHHHHhhhcHHHHh--hCC-EEEeCCCCHHHHHHHHHHHhh
Confidence            5688999999887     49999999  998 589999999999999986653

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=94.90  E-value=0.22  Score=43.17  Aligned_cols=56  Identities=11%  Similarity=0.144  Sum_probs=41.7

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhC
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      |.||..|+.-.    .+.++|.+|+.|+.|.|++++  |+ ..|+|+.|+.++..+++....+
T Consensus       135 naLLk~LEep~----~~~~fIL~a~~~~~llpTIrS--Rc-~~i~f~~~~~~~i~~~L~~~~~  190 (394)
T PRK07940        135 NALLKAVEEPP----PRTVWLLCAPSPEDVLPTIRS--RC-RHVALRTPSVEAVAEVLVRRDG  190 (394)
T ss_pred             HHHHHHhhcCC----CCCeEEEEECChHHChHHHHh--hC-eEEECCCCCHHHHHHHHHHhcC
Confidence            56788776532    335555555559999999998  87 6999999999998888864433

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=94.82  E-value=0.055  Score=44.24  Aligned_cols=52  Identities=17%  Similarity=0.190  Sum_probs=40.4

Q ss_pred             HHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHH
Q 042776            6 LLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNY   64 (147)
Q Consensus         6 lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~   64 (147)
                      |...|+...    .+..+|+|||.++.++|+++.  ||. .+.|+.|+.+++..++..+
T Consensus       121 L~~~le~~~----~~~~~Ilt~n~~~~l~~~l~s--R~~-~i~~~~p~~~~~~~il~~~  172 (316)
T PHA02544        121 LRSFMEAYS----KNCSFIITANNKNGIIEPLRS--RCR-VIDFGVPTKEEQIEMMKQM  172 (316)
T ss_pred             HHHHHHhcC----CCceEEEEcCChhhchHHHHh--hce-EEEeCCCCHHHHHHHHHHH
Confidence            344466543    346788899999999999998  885 6899999999998776654

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=94.56  E-value=0.082  Score=47.31  Aligned_cols=51  Identities=24%  Similarity=0.140  Sum_probs=40.7

Q ss_pred             ceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCCh
Q 042776           20 ERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLF   73 (147)
Q Consensus        20 ~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~   73 (147)
                      -++|++|||.|+.|+||+++  |+. .|.|+.++.+++..|++.++........
T Consensus       234 ~rlI~ATt~~p~~L~paLrs--R~~-~I~f~pL~~eei~~Il~~~a~k~~i~is  284 (531)
T TIGR02902       234 FRLIGATTRNPEEIPPALRS--RCV-EIFFRPLLDEEIKEIAKNAAEKIGINLE  284 (531)
T ss_pred             eEEEEEecCCcccCChHHhh--hhh-eeeCCCCCHHHHHHHHHHHHHHcCCCcC
Confidence            36677788899999999999  885 6788888889999999998865544333

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.

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=94.35  E-value=0.55  Score=38.98  Aligned_cols=46  Identities=15%  Similarity=0.164  Sum_probs=39.0

Q ss_pred             CceEEEEecCCCC---CCCccccCCCeee-eEEeecCCCHHHHHHHHHHHhC
Q 042776           19 DERIIVFTTNHKN---RLDPALLRPGRMD-MHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus        19 ~~vivi~aTN~p~---~LD~Al~RpGRfd-~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      ..+.+|++||.++   .|++.+.+  ||. ..|+|+.++.++...|++..+.
T Consensus       164 ~~v~lI~i~n~~~~~~~l~~~~~s--~~~~~~i~f~p~~~~e~~~il~~r~~  213 (365)
T TIGR02928       164 AKVGVIGISNDLKFRENLDPRVKS--SLCEEEIIFPPYDAEELRDILENRAE  213 (365)
T ss_pred             CeEEEEEEECCcchHhhcCHHHhc--cCCcceeeeCCCCHHHHHHHHHHHHH
Confidence            5688999999886   58888877  775 7899999999999999998774

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.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.12  E-value=0.26  Score=43.68  Aligned_cols=59  Identities=12%  Similarity=0.178  Sum_probs=44.9

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCC
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIND   69 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~   69 (147)
                      +.||..|+...    ..+++|++|+.|..|+++++.  |+. .+.|..++.++...+++.......
T Consensus       135 ~~LLk~LE~p~----~~vv~Ilattn~~kl~~~L~S--R~~-vv~f~~l~~~el~~~L~~i~~~eg  193 (472)
T PRK14962        135 NALLKTLEEPP----SHVVFVLATTNLEKVPPTIIS--RCQ-VIEFRNISDELIIKRLQEVAEAEG  193 (472)
T ss_pred             HHHHHHHHhCC----CcEEEEEEeCChHhhhHHHhc--CcE-EEEECCccHHHHHHHHHHHHHHcC
Confidence            45666666432    447777777788999999998  774 799999999999999888765443

>PRK06893 DNA replication initiation factor; Validated

Probab=94.11  E-value=0.1  Score=41.32  Aligned_cols=73  Identities=8%  Similarity=0.096  Sum_probs=48.3

Q ss_pred             HHHHHhhCCCCCCCCc-eEEEEecCCCCCCC---ccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHH
Q 042776            5 GLLNFIDGLWSSCGDE-RIIVFTTNHKNRLD---PALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDEL   79 (147)
Q Consensus         5 ~lL~~lDgl~~~~~~~-vivi~aTN~p~~LD---~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l   79 (147)
                      .|+..++.+...  ++ ++|+.++..|..++   |.|....++...+.++.|+.+.+.+|++............++...
T Consensus       112 ~l~~l~n~~~~~--~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~a~~~~l~l~~~v~~~  188 (229)
T PRK06893        112 AIFDLFNRIKEQ--GKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQRNAYQRGIELSDEVANF  188 (229)
T ss_pred             HHHHHHHHHHHc--CCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            344555555433  33 44555666788776   888884445688999999999999999977754444445444433

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.99  E-value=0.22  Score=46.66  Aligned_cols=64  Identities=14%  Similarity=0.202  Sum_probs=51.1

Q ss_pred             HHHHHHh-hCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCC
Q 042776            4 SGLLNFI-DGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIN   68 (147)
Q Consensus         4 ~~lL~~l-Dgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~   68 (147)
                      +.+|+++ +-+... +..+.|||+.+....|.|-|.-|++|+-.+.++.|+..+|.+||..++...
T Consensus       525 a~flnqvi~~y~~~-~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~ap~~~~R~~IL~~~~s~~  589 (952)
T KOG0735|consen  525 AAFLNQVIKIYLKR-NRKIAVIATGQELQTLNPLLVSPLLFQIVIALPAPAVTRRKEILTTIFSKN  589 (952)
T ss_pred             HHHHHHHHHHHHcc-CcEEEEEEechhhhhcChhhcCccceEEEEecCCcchhHHHHHHHHHHHhh
Confidence            4455443 333333 344679999999999999999999999999999999999999999887643

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=93.98  E-value=0.12  Score=39.26  Aligned_cols=55  Identities=11%  Similarity=0.137  Sum_probs=43.4

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNY   64 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~   64 (147)
                      .+.||..|+...    ...++|++||.+..|.+++..  |+ ..++|..|+.++...++...
T Consensus       113 ~~~Ll~~le~~~----~~~~~il~~~~~~~l~~~i~s--r~-~~~~~~~~~~~~~~~~l~~~  167 (188)
T TIGR00678       113 ANALLKTLEEPP----PNTLFILITPSPEKLLPTIRS--RC-QVLPFPPLSEEALLQWLIRQ  167 (188)
T ss_pred             HHHHHHHhcCCC----CCeEEEEEECChHhChHHHHh--hc-EEeeCCCCCHHHHHHHHHHc
Confidence            456777776532    346677778888999999988  66 47999999999999998876

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

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

Probab=93.84  E-value=0.14  Score=47.96  Aligned_cols=44  Identities=23%  Similarity=0.226  Sum_probs=38.4

Q ss_pred             CceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhC
Q 042776           19 DERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus        19 ~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      .++++|+|||.. .|+|||+.  ||+ .|.|.-++.++..+|++.|+-
T Consensus       464 s~v~~i~TaN~~-~i~~aLl~--R~~-ii~~~~~t~eek~~Ia~~~L~  507 (784)
T PRK10787        464 SDVMFVATSNSM-NIPAPLLD--RME-VIRLSGYTEDEKLNIAKRHLL  507 (784)
T ss_pred             CceEEEEcCCCC-CCCHHHhc--cee-eeecCCCCHHHHHHHHHHhhh
Confidence            468999999987 59999998  997 588998999999999998883

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=93.14  E-value=1.1  Score=36.67  Aligned_cols=70  Identities=7%  Similarity=0.096  Sum_probs=45.1

Q ss_pred             HHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCCh-HHHHHHHH
Q 042776            5 GLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLF-PEIDELLT   81 (147)
Q Consensus         5 ~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~-~~i~~l~~   81 (147)
                      .|+..|+....   . ..+|++|+.+..+.++|..  |+ ..+.|..|+.++...++..++........ ..+..++.
T Consensus       144 ~L~~~le~~~~---~-~~~Il~~~~~~~~~~~L~s--r~-~~v~~~~~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~  214 (337)
T PRK12402        144 ALRRIMEQYSR---T-CRFIIATRQPSKLIPPIRS--RC-LPLFFRAPTDDELVDVLESIAEAEGVDYDDDGLELIAY  214 (337)
T ss_pred             HHHHHHHhccC---C-CeEEEEeCChhhCchhhcC--Cc-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            34455554432   2 3455666677788888876  65 46899999999999999888765443333 33444443

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=93.08  E-value=0.42  Score=43.14  Aligned_cols=60  Identities=12%  Similarity=0.192  Sum_probs=45.3

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIND   69 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~   69 (147)
                      .+.||..|+.-.    ..+++|++|+.|+.|.+.++.  |+. .+.|..|+..+...++...+....
T Consensus       136 ~naLLKtLEepp----~~~ifIlatt~~~ki~~tI~S--Rc~-~~~f~~~~~~ei~~~L~~i~~~eg  195 (559)
T PRK05563        136 FNALLKTLEEPP----AHVIFILATTEPHKIPATILS--RCQ-RFDFKRISVEDIVERLKYILDKEG  195 (559)
T ss_pred             HHHHHHHhcCCC----CCeEEEEEeCChhhCcHHHHh--Hhe-EEecCCCCHHHHHHHHHHHHHHcC
Confidence            456777776543    447777778889999999887  764 578999999998888888775444

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=93.01  E-value=0.21  Score=42.50  Aligned_cols=55  Identities=16%  Similarity=0.271  Sum_probs=46.1

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNY   64 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~   64 (147)
                      -|.||..|+.-    ..++++|.+|++|+.|.|.++.  |. ..|.|+.|+.++..+.|...
T Consensus       149 aNaLLKtLEEP----p~~t~fiL~t~~~~~LLpTI~S--Rc-q~i~~~~~~~~~~~~~L~~~  203 (342)
T PRK06964        149 ANALLKTLEEP----PPGTVFLLVSARIDRLLPTILS--RC-RQFPMTVPAPEAAAAWLAAQ  203 (342)
T ss_pred             HHHHHHHhcCC----CcCcEEEEEECChhhCcHHHHh--cC-EEEEecCCCHHHHHHHHHHc
Confidence            37788888842    2568899999999999999988  88 78999999999998888764

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

Probab=92.95  E-value=1.3  Score=36.28  Aligned_cols=78  Identities=15%  Similarity=0.214  Sum_probs=58.0

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCcccc-C--------------------CCeeeeEEeecCCCHHHHHHHHH
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALL-R--------------------PGRMDMHIHMSYCNPSGFRILVS   62 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~-R--------------------pGRfd~~i~~~~P~~~~r~~il~   62 (147)
                      ..|-+.|||--....++|+|.+|+||-+.+..-.. |                    ..||-..|.|..|+.+.-.+|++
T Consensus       125 k~LKs~LeGgle~~P~NvliyATSNRRHLv~E~~~d~~~~~~~eih~~d~~eEklSLsDRFGL~l~F~~~~q~~YL~IV~  204 (249)
T PF05673_consen  125 KALKSVLEGGLEARPDNVLIYATSNRRHLVPESFSDREDIQDDEIHPSDTIEEKLSLSDRFGLWLSFYPPDQEEYLAIVR  204 (249)
T ss_pred             HHHHHHhcCccccCCCcEEEEEecchhhccchhhhhccCCCccccCcchHHHHHHhHHHhCCcEEEecCCCHHHHHHHHH
Confidence            56778899875444588999999999887765431 1                    24899999999999999999999


Q ss_pred             HHhCCCCCCCh-HHHHHHHH
Q 042776           63 NYLGINDHNLF-PEIDELLT   81 (147)
Q Consensus        63 ~~l~~~~~~~~-~~i~~l~~   81 (147)
                      +|+........ +++..-|.
T Consensus       205 ~~~~~~g~~~~~e~l~~~Al  224 (249)
T PF05673_consen  205 HYAERYGLELDEEELRQEAL  224 (249)
T ss_pred             HHHHHcCCCCCHHHHHHHHH
Confidence            99965554443 34444444

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=92.87  E-value=0.22  Score=42.31  Aligned_cols=46  Identities=15%  Similarity=0.182  Sum_probs=37.7

Q ss_pred             CceEEEEecCCCC-CCCccccCCCeeeeEEeecCCCH-HHHHHHHHHHhC
Q 042776           19 DERIIVFTTNHKN-RLDPALLRPGRMDMHIHMSYCNP-SGFRILVSNYLG   66 (147)
Q Consensus        19 ~~vivi~aTN~p~-~LD~Al~RpGRfd~~i~~~~P~~-~~r~~il~~~l~   66 (147)
                      ..+++|+|+|-.+ .|.++|+.  ||...|.++.|.. +++.+|+.....
T Consensus       170 ~rfiviAt~NP~e~~l~~aLld--RF~~~v~v~~~~~~~e~~~il~~~~~  217 (334)
T PRK13407        170 ARFVLVGSGNPEEGELRPQLLD--RFGLSVEVRSPRDVETRVEVIRRRDA  217 (334)
T ss_pred             CCEEEEecCCcccCCCCHHHHh--hcceEEEcCCCCcHHHHHHHHHHhhc
Confidence            4577888888544 58999999  9999999998877 889999987543

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.67  E-value=0.48  Score=42.30  Aligned_cols=61  Identities=11%  Similarity=0.151  Sum_probs=46.2

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH   70 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~   70 (147)
                      .+.||..|+.-.    ..+++|++|+.++.|.++++.  |+ ..+.|..++.......++..+.....
T Consensus       138 ~NALLKtLEEPp----~~viFILaTte~~kI~~TI~S--RC-q~~~f~~ls~~~i~~~L~~i~~~Egi  198 (484)
T PRK14956        138 FNALLKTLEEPP----AHIVFILATTEFHKIPETILS--RC-QDFIFKKVPLSVLQDYSEKLCKIENV  198 (484)
T ss_pred             HHHHHHHhhcCC----CceEEEeecCChhhccHHHHh--hh-heeeecCCCHHHHHHHHHHHHHHcCC
Confidence            466777775432    458888999999999999998  87 45888888888888888877655433

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=92.66  E-value=0.28  Score=43.12  Aligned_cols=73  Identities=12%  Similarity=0.231  Sum_probs=47.4

Q ss_pred             HHHHHhhCCCCCCCCceEEEEecCCCC---CCCccccCCCeee--eEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHH-
Q 042776            5 GLLNFIDGLWSSCGDERIIVFTTNHKN---RLDPALLRPGRMD--MHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDE-   78 (147)
Q Consensus         5 ~lL~~lDgl~~~~~~~vivi~aTN~p~---~LD~Al~RpGRfd--~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~-   78 (147)
                      +|+..++.+...  ...+||.+++.|.   .+++.|+.  ||.  ..+.+..|+.+.|.+|++............++.. 
T Consensus       223 elf~l~N~l~~~--~k~IIlts~~~p~~l~~l~~rL~S--R~~~Gl~~~l~~pd~e~r~~iL~~k~~~~~~~l~~evl~~  298 (445)
T PRK12422        223 EFFHTFNSLHTE--GKLIVISSTCAPQDLKAMEERLIS--RFEWGIAIPLHPLTKEGLRSFLERKAEALSIRIEETALDF  298 (445)
T ss_pred             HHHHHHHHHHHC--CCcEEEecCCCHHHHhhhHHHHHh--hhcCCeEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            444455555432  3344444444454   56789998  997  7888888999999999998876655555555444 


Q ss_pred             HHH
Q 042776           79 LLT   81 (147)
Q Consensus        79 l~~   81 (147)
                      ++.
T Consensus       299 la~  301 (445)
T PRK12422        299 LIE  301 (445)
T ss_pred             HHH
Confidence            444

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=92.34  E-value=0.51  Score=44.05  Aligned_cols=59  Identities=12%  Similarity=0.191  Sum_probs=45.6

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIN   68 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~   68 (147)
                      .+.||..|+.-+    +.+++|++|+.|+.|.+.++.  |+. .+.|..|+.++...++...+...
T Consensus       135 ~NALLKtLEEPP----~~tifILaTte~~KLl~TI~S--Rcq-~ieF~~L~~eeI~~~L~~il~ke  193 (725)
T PRK07133        135 FNALLKTLEEPP----KHVIFILATTEVHKIPLTILS--RVQ-RFNFRRISEDEIVSRLEFILEKE  193 (725)
T ss_pred             HHHHHHHhhcCC----CceEEEEEcCChhhhhHHHHh--hce-eEEccCCCHHHHHHHHHHHHHHc
Confidence            456777777533    457888888899999999988  774 79999999999888887765433

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.33  E-value=0.99  Score=38.24  Aligned_cols=61  Identities=10%  Similarity=0.157  Sum_probs=45.2

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH   70 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~   70 (147)
                      .+.||..|+-..    ..+.+|++|+.++.|.+++.-  |+ ..++|..|+.++...++...+.....
T Consensus       136 ~naLLk~lEe~~----~~~~fIl~t~~~~~l~~tI~S--Rc-~~~~~~~l~~~el~~~L~~~~~~~g~  196 (363)
T PRK14961        136 FNALLKTLEEPP----QHIKFILATTDVEKIPKTILS--RC-LQFKLKIISEEKIFNFLKYILIKESI  196 (363)
T ss_pred             HHHHHHHHhcCC----CCeEEEEEcCChHhhhHHHHh--hc-eEEeCCCCCHHHHHHHHHHHHHHcCC
Confidence            345666666532    346677788888999999876  76 57899999999999998887755443

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.94  E-value=0.99  Score=37.92  Aligned_cols=61  Identities=11%  Similarity=0.191  Sum_probs=43.2

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH   70 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~   70 (147)
                      ++.||..++...    ...++|++|+.+..+.+++..  |+- .+.|..|+.++...++...+.....
T Consensus       125 ~~~ll~~le~~~----~~~~~Il~~~~~~kl~~~l~s--r~~-~v~~~~~~~~~l~~~l~~~~~~~g~  185 (367)
T PRK14970        125 FNAFLKTLEEPP----AHAIFILATTEKHKIIPTILS--RCQ-IFDFKRITIKDIKEHLAGIAVKEGI  185 (367)
T ss_pred             HHHHHHHHhCCC----CceEEEEEeCCcccCCHHHHh--cce-eEecCCccHHHHHHHHHHHHHHcCC
Confidence            355666666532    345667777888999999987  553 5889999999988888876654433

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=91.81  E-value=0.28  Score=41.61  Aligned_cols=46  Identities=20%  Similarity=0.226  Sum_probs=37.2

Q ss_pred             CceEEEEecCCCC-CCCccccCCCeeeeEEeecCCCH-HHHHHHHHHHhC
Q 042776           19 DERIIVFTTNHKN-RLDPALLRPGRMDMHIHMSYCNP-SGFRILVSNYLG   66 (147)
Q Consensus        19 ~~vivi~aTN~p~-~LD~Al~RpGRfd~~i~~~~P~~-~~r~~il~~~l~   66 (147)
                      ..+++|+|+|-.+ .|.++|+.  ||..++.++.|.. +++.+|++....
T Consensus       173 ~r~iviat~np~eg~l~~~Lld--Rf~l~i~l~~p~~~eer~eIL~~~~~  220 (337)
T TIGR02030       173 ARFVLVGSGNPEEGELRPQLLD--RFGLHAEIRTVRDVELRVEIVERRTE  220 (337)
T ss_pred             CCEEEEeccccccCCCCHHHHh--hcceEEECCCCCCHHHHHHHHHhhhh
Confidence            4467888888544 69999999  9999999999976 888999987543

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.

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.75  E-value=0.66  Score=41.23  Aligned_cols=60  Identities=13%  Similarity=0.209  Sum_probs=44.4

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH   70 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~   70 (147)
                      +.||..|+...    ..+++|++|+.++.|.+++..  |+. .+.|..|+..+...++..++.....
T Consensus       137 naLLk~LEepp----~~~v~Il~tt~~~kl~~tI~S--Rc~-~i~f~~ls~~el~~~L~~i~k~egi  196 (486)
T PRK14953        137 NALLKTLEEPP----PRTIFILCTTEYDKIPPTILS--RCQ-RFIFSKPTKEQIKEYLKRICNEEKI  196 (486)
T ss_pred             HHHHHHHhcCC----CCeEEEEEECCHHHHHHHHHH--hce-EEEcCCCCHHHHHHHHHHHHHHcCC
Confidence            55666666532    346666777778899999887  664 6899999999999999887765443

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=91.51  E-value=0.82  Score=40.96  Aligned_cols=61  Identities=11%  Similarity=0.181  Sum_probs=47.0

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH   70 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~   70 (147)
                      .+.||..|+.-    ...+++|++|+.++.+.+++..  |+ ..++|..++.++...++...+.....
T Consensus       145 ~naLLk~LEep----p~~~vfI~aTte~~kI~~tI~S--Rc-~~~ef~~ls~~el~~~L~~i~~~egi  205 (507)
T PRK06645        145 FNALLKTLEEP----PPHIIFIFATTEVQKIPATIIS--RC-QRYDLRRLSFEEIFKLLEYITKQENL  205 (507)
T ss_pred             HHHHHHHHhhc----CCCEEEEEEeCChHHhhHHHHh--cc-eEEEccCCCHHHHHHHHHHHHHHcCC
Confidence            45566666642    2457888888999999999987  76 57889999999999999988865543

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=91.39  E-value=2.3  Score=35.77  Aligned_cols=58  Identities=12%  Similarity=0.068  Sum_probs=41.1

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCC---CCCccccCCCee-eeEEeecCCCHHHHHHHHHHHhC
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKN---RLDPALLRPGRM-DMHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~---~LD~Al~RpGRf-d~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      ..|+..++.+.   +..+.||+++|.++   .++|.+..  || ...|+|+.++.++...|++..+.
T Consensus       160 ~~l~~~~~~~~---~~~v~vI~i~~~~~~~~~l~~~~~s--~~~~~~i~f~py~~~e~~~il~~r~~  221 (394)
T PRK00411        160 YSLLRAHEEYP---GARIGVIGISSDLTFLYILDPRVKS--VFRPEEIYFPPYTADEIFDILKDRVE  221 (394)
T ss_pred             HHHHHhhhccC---CCeEEEEEEECCcchhhhcCHHHHh--cCCcceeecCCCCHHHHHHHHHHHHH
Confidence            34444444442   23577888888664   57777765  55 36789999999999999988764

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.26  E-value=1.3  Score=39.59  Aligned_cols=61  Identities=15%  Similarity=0.287  Sum_probs=46.7

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH   70 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~   70 (147)
                      ++.||..|+.-.    ..+++|++||.+..|.+++..  |+. .+.|..|+.++...++...+.....
T Consensus       133 ~naLLk~LEep~----~~t~~Il~t~~~~kl~~~I~S--Rc~-~~~f~~ls~~el~~~L~~i~~~egi  193 (504)
T PRK14963        133 FNALLKTLEEPP----EHVIFILATTEPEKMPPTILS--RTQ-HFRFRRLTEEEIAGKLRRLLEAEGR  193 (504)
T ss_pred             HHHHHHHHHhCC----CCEEEEEEcCChhhCChHHhc--ceE-EEEecCCCHHHHHHHHHHHHHHcCC
Confidence            456666666532    447788888999999999987  764 6999999999999999887755443

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=90.92  E-value=1.3  Score=41.99  Aligned_cols=61  Identities=10%  Similarity=0.183  Sum_probs=48.1

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH   70 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~   70 (147)
                      .|.||..|..-.    ..+.+|++||.++.|.+.|+-  |+ .+|.|..++.++...+|..++..+..
T Consensus       136 ~NALLKtLEEPP----~~v~FILaTtd~~KIp~TIrS--RC-q~f~Fk~Ls~eeIv~~L~~Il~~EgI  196 (830)
T PRK07003        136 FNAMLKTLEEPP----PHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPAGHIVSHLERILGEERI  196 (830)
T ss_pred             HHHHHHHHHhcC----CCeEEEEEECChhhccchhhh--he-EEEecCCcCHHHHHHHHHHHHHHcCC
Confidence            466777776543    458889999999999999987  77 68899989999988888888765543

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=90.91  E-value=1.3  Score=42.88  Aligned_cols=81  Identities=14%  Similarity=0.074  Sum_probs=55.9

Q ss_pred             CceEEEEecCC---CCCCCccccCCCeeee-EEeecCCCHHHHHHHHHHHhCCCCCCChHH-HHHHHH-HHhccchHHHH
Q 042776           19 DERIIVFTTNH---KNRLDPALLRPGRMDM-HIHMSYCNPSGFRILVSNYLGINDHNLFPE-IDELLT-KLMKSEVAEVA   92 (147)
Q Consensus        19 ~~vivi~aTN~---p~~LD~Al~RpGRfd~-~i~~~~P~~~~r~~il~~~l~~~~~~~~~~-i~~l~~-~l~~~~~~~~a   92 (147)
                      ..++||++||.   |+.|+|.+..  ||-. .|.|+.++.+++.+||...+.........+ +.-+|. .....+|+-.|
T Consensus       901 SKLiLIGISNdlDLperLdPRLRS--RLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIELIArkVAq~SGDARKA  978 (1164)
T PTZ00112        901 SKLVLIAISNTMDLPERLIPRCRS--RLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQLCARKVANVSGDIRKA  978 (1164)
T ss_pred             CeEEEEEecCchhcchhhhhhhhh--ccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhhcCCHHHHH
Confidence            56889999984   7788898876  5543 589999999999999998876433233333 444444 22345777777


Q ss_pred             HHHHHHHHH
Q 042776           93 LEGLVEFLK  101 (147)
Q Consensus        93 l~~~~~~l~  101 (147)
                      |.-+..+++
T Consensus       979 LDILRrAgE  987 (1164)
T PTZ00112        979 LQICRKAFE  987 (1164)
T ss_pred             HHHHHHHHh
Confidence            777766665

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=90.73  E-value=0.7  Score=40.39  Aligned_cols=71  Identities=15%  Similarity=0.275  Sum_probs=46.7

Q ss_pred             HHHHHhhCCCCCCCCceEEEEecCCCCCC---CccccCCCeee--eEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHH
Q 042776            5 GLLNFIDGLWSSCGDERIIVFTTNHKNRL---DPALLRPGRMD--MHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDEL   79 (147)
Q Consensus         5 ~lL~~lDgl~~~~~~~vivi~aTN~p~~L---D~Al~RpGRfd--~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l   79 (147)
                      +|+..++.+...  ...+||++.+.|..+   ++.++.  ||.  ..+.+..||.+.|..|++............++...
T Consensus       215 elf~~~n~l~~~--~k~iIitsd~~p~~l~~l~~rL~S--R~~~gl~v~i~~pd~e~r~~IL~~~~~~~~~~l~~ev~~~  290 (440)
T PRK14088        215 ELFHTFNELHDS--GKQIVICSDREPQKLSEFQDRLVS--RFQMGLVAKLEPPDEETRKKIARKMLEIEHGELPEEVLNF  290 (440)
T ss_pred             HHHHHHHHHHHc--CCeEEEECCCCHHHHHHHHHHHhh--HHhcCceEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHH
Confidence            466666666554  345555555666664   466766  764  56788899999999999988765544444444333

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=90.58  E-value=0.46  Score=40.63  Aligned_cols=45  Identities=24%  Similarity=0.320  Sum_probs=36.7

Q ss_pred             CceEEEEecCCCC-CCCccccCCCeeeeEEeecCCC-HHHHHHHHHHHh
Q 042776           19 DERIIVFTTNHKN-RLDPALLRPGRMDMHIHMSYCN-PSGFRILVSNYL   65 (147)
Q Consensus        19 ~~vivi~aTN~p~-~LD~Al~RpGRfd~~i~~~~P~-~~~r~~il~~~l   65 (147)
                      ..+++|+|.|-.+ .|.++|+.  ||..+|.++.|+ .+.+.+|++...
T Consensus       186 ~rfiviaT~np~eg~l~~~Lld--Rf~l~i~l~~~~~~~~e~~il~~~~  232 (350)
T CHL00081        186 ARFVLVGSGNPEEGELRPQLLD--RFGMHAEIRTVKDPELRVKIVEQRT  232 (350)
T ss_pred             CCEEEEeccCcccCCCCHHHHH--HhCceeecCCCCChHHHHHHHHhhh
Confidence            4566777777544 59999999  999999999998 589999998754

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=90.28  E-value=1.3  Score=40.72  Aligned_cols=72  Identities=14%  Similarity=0.191  Sum_probs=49.0

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCC----CCCCccccCCCeeee--EEeecCCCHHHHHHHHHHHhCCCCCCChHHHH
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHK----NRLDPALLRPGRMDM--HIHMSYCNPSGFRILVSNYLGINDHNLFPEID   77 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p----~~LD~Al~RpGRfd~--~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~   77 (147)
                      .+|+..++.+...  +.. ||+|+|++    ..|++.|+.  ||..  .+++..||.+.|.+||+.........+..++.
T Consensus       397 eeLF~l~N~l~e~--gk~-IIITSd~~P~eL~~l~~rL~S--Rf~~GLvv~I~~PD~EtR~aIL~kka~~r~l~l~~eVi  471 (617)
T PRK14086        397 EEFFHTFNTLHNA--NKQ-IVLSSDRPPKQLVTLEDRLRN--RFEWGLITDVQPPELETRIAILRKKAVQEQLNAPPEVL  471 (617)
T ss_pred             HHHHHHHHHHHhc--CCC-EEEecCCChHhhhhccHHHHh--hhhcCceEEcCCCCHHHHHHHHHHHHHhcCCCCCHHHH
Confidence            4566667776544  334 44566654    357888988  9864  55778899999999999888766555555544


Q ss_pred             HHH
Q 042776           78 ELL   80 (147)
Q Consensus        78 ~l~   80 (147)
                      .+.
T Consensus       472 ~yL  474 (617)
T PRK14086        472 EFI  474 (617)
T ss_pred             HHH
Confidence            443

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=90.18  E-value=0.99  Score=34.74  Aligned_cols=74  Identities=14%  Similarity=0.171  Sum_probs=44.3

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCC---ccccCCCee--eeEEeecCCCHHHHHHHHHHHhCCCCCCChH-HHH
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLD---PALLRPGRM--DMHIHMSYCNPSGFRILVSNYLGINDHNLFP-EID   77 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD---~Al~RpGRf--d~~i~~~~P~~~~r~~il~~~l~~~~~~~~~-~i~   77 (147)
                      ..|...++.+...  ...+|+.++..+..++   +.|..  ||  ...|.++.|+.+++..+++.+.......... .+.
T Consensus       110 ~~L~~~l~~~~~~--~~~iIits~~~~~~~~~~~~~L~~--r~~~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~l~  185 (226)
T TIGR03420       110 EALFHLYNRVREA--GGRLLIAGRAAPAQLPLRLPDLRT--RLAWGLVFQLPPLSDEEKIAALQSRAARRGLQLPDEVAD  185 (226)
T ss_pred             HHHHHHHHHHHHc--CCeEEEECCCChHHCCcccHHHHH--HHhcCeeEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            3455555554333  3344444444554443   66776  65  4789999999999999999876533333333 344


Q ss_pred             HHHH
Q 042776           78 ELLT   81 (147)
Q Consensus        78 ~l~~   81 (147)
                      .++.
T Consensus       186 ~L~~  189 (226)
T TIGR03420       186 YLLR  189 (226)
T ss_pred             HHHH
Confidence            4444

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.

>PRK09087 hypothetical protein; Validated

Probab=89.97  E-value=0.77  Score=36.51  Aligned_cols=69  Identities=10%  Similarity=0.215  Sum_probs=47.8

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCC---CccccCCCeee--eEEeecCCCHHHHHHHHHHHhCCCCCCChHHH
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRL---DPALLRPGRMD--MHIHMSYCNPSGFRILVSNYLGINDHNLFPEI   76 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~L---D~Al~RpGRfd--~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i   76 (147)
                      .+|...++.+...  +..+||+++..|..+   .|.|+-  ||.  ..+.+..|+.+.+.++++.++.........++
T Consensus       104 ~~lf~l~n~~~~~--g~~ilits~~~p~~~~~~~~dL~S--Rl~~gl~~~l~~pd~e~~~~iL~~~~~~~~~~l~~ev  177 (226)
T PRK09087        104 TGLFHLINSVRQA--GTSLLMTSRLWPSSWNVKLPDLKS--RLKAATVVEIGEPDDALLSQVIFKLFADRQLYVDPHV  177 (226)
T ss_pred             HHHHHHHHHHHhC--CCeEEEECCCChHHhccccccHHH--HHhCCceeecCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            3455566666554  446666666666544   577877  887  78888999999999999988866544444443

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=89.81  E-value=0.9  Score=41.65  Aligned_cols=59  Identities=14%  Similarity=0.230  Sum_probs=45.9

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCC
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIND   69 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~   69 (147)
                      +.||..|+.-.    ..+++|++|+.++.|.++++.  |+. .++|..|+..+...++...+....
T Consensus       137 NaLLKtLEEPp----~~tvfIL~Tt~~~KLl~TI~S--Rcq-~ieF~~Ls~~eL~~~L~~il~keg  195 (605)
T PRK05896        137 NALLKTLEEPP----KHVVFIFATTEFQKIPLTIIS--RCQ-RYNFKKLNNSELQELLKSIAKKEK  195 (605)
T ss_pred             HHHHHHHHhCC----CcEEEEEECCChHhhhHHHHh--hhh-hcccCCCCHHHHHHHHHHHHHHcC
Confidence            55677776533    447788888889999999988  775 689999999999888887775443

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=89.78  E-value=0.67  Score=42.08  Aligned_cols=44  Identities=16%  Similarity=0.177  Sum_probs=36.3

Q ss_pred             ceEEEEecCCCC---CCCccccCCCeeeeEEeec-CCCHHHHHHHHHHHh
Q 042776           20 ERIIVFTTNHKN---RLDPALLRPGRMDMHIHMS-YCNPSGFRILVSNYL   65 (147)
Q Consensus        20 ~vivi~aTN~p~---~LD~Al~RpGRfd~~i~~~-~P~~~~r~~il~~~l   65 (147)
                      ...||+|+|..+   .|.++|+.  ||+.+|.+. +|+..+|.+|++.++
T Consensus       127 ~f~lIAt~np~e~~g~L~~~Lld--Rf~l~v~~~~~~~~~er~eil~~~~  174 (589)
T TIGR02031       127 KFALIATYDPAEGGGGLPDHLLD--RLALHVSLEDVASQDLRVEIVRRER  174 (589)
T ss_pred             ceEEEEecCCccccCCCCHHHHH--hccCeeecCCCCCHHHHHHHHHHHH
Confidence            467889999765   79999999  999998886 567777899988765

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

>PRK04195 replication factor C large subunit; Provisional

Probab=89.77  E-value=2  Score=37.81  Aligned_cols=72  Identities=13%  Similarity=0.098  Sum_probs=46.4

Q ss_pred             eEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCC-hHHHHHHHHHHhccchHHHHHHHH
Q 042776           21 RIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNL-FPEIDELLTKLMKSEVAEVALEGL   96 (147)
Q Consensus        21 vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~-~~~i~~l~~~l~~~~~~~~al~~~   96 (147)
                      ..+|++||.+..+++.-+|  +.-..|.|+.|+..+...+++.++....... ...+..++..  +..+...|+..+
T Consensus       131 ~~iIli~n~~~~~~~k~Lr--sr~~~I~f~~~~~~~i~~~L~~i~~~egi~i~~eaL~~Ia~~--s~GDlR~ain~L  203 (482)
T PRK04195        131 QPIILTANDPYDPSLRELR--NACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAER--SGGDLRSAINDL  203 (482)
T ss_pred             CCEEEeccCccccchhhHh--ccceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH--cCCCHHHHHHHH
Confidence            3467788999999884444  4456799999999999999998875544332 3344444432  233444444444

>PRK08727 hypothetical protein; Validated

Probab=89.58  E-value=0.71  Score=36.67  Aligned_cols=72  Identities=18%  Similarity=0.184  Sum_probs=44.5

Q ss_pred             HHHHhhCCCCCCCCceEEEEecCCCCCC---CccccCCCee--eeEEeecCCCHHHHHHHHHHHhCCCCCCChH-HHHHH
Q 042776            6 LLNFIDGLWSSCGDERIIVFTTNHKNRL---DPALLRPGRM--DMHIHMSYCNPSGFRILVSNYLGINDHNLFP-EIDEL   79 (147)
Q Consensus         6 lL~~lDgl~~~~~~~vivi~aTN~p~~L---D~Al~RpGRf--d~~i~~~~P~~~~r~~il~~~l~~~~~~~~~-~i~~l   79 (147)
                      |+..++.....  ...+|+.+.+.|..+   +|+|..  ||  -..+.++.|+.+.+..|++.+.......... .+..+
T Consensus       115 lf~l~n~~~~~--~~~vI~ts~~~p~~l~~~~~dL~S--Rl~~~~~~~l~~~~~e~~~~iL~~~a~~~~l~l~~e~~~~L  190 (233)
T PRK08727        115 LFDFHNRARAA--GITLLYTARQMPDGLALVLPDLRS--RLAQCIRIGLPVLDDVARAAVLRERAQRRGLALDEAAIDWL  190 (233)
T ss_pred             HHHHHHHHHHc--CCeEEEECCCChhhhhhhhHHHHH--HHhcCceEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            44444444332  223455555577766   799988  87  4678899999999999999765433333333 33444


Q ss_pred             HH
Q 042776           80 LT   81 (147)
Q Consensus        80 ~~   81 (147)
                      +.
T Consensus       191 a~  192 (233)
T PRK08727        191 LT  192 (233)
T ss_pred             HH
Confidence            43

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=89.48  E-value=1.1  Score=41.24  Aligned_cols=60  Identities=15%  Similarity=0.293  Sum_probs=45.6

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIND   69 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~   69 (147)
                      .+.||..|+.-.    ..+++|++||.++.|.+.|+.  |+ ..|.|..++.++...+|...+....
T Consensus       136 ~naLLk~LEEP~----~~~ifILaTt~~~kll~TI~S--Rc-q~i~F~pLs~~eL~~~L~~il~~eg  195 (624)
T PRK14959        136 FNALLKTLEEPP----ARVTFVLATTEPHKFPVTIVS--RC-QHFTFTRLSEAGLEAHLTKVLGREG  195 (624)
T ss_pred             HHHHHHHhhccC----CCEEEEEecCChhhhhHHHHh--hh-hccccCCCCHHHHHHHHHHHHHHcC
Confidence            466777776532    447788889999999998887  76 4689999999998888887665443

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=89.15  E-value=2.2  Score=34.48  Aligned_cols=69  Identities=6%  Similarity=0.038  Sum_probs=46.1

Q ss_pred             HHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCC-hHHHHHHH
Q 042776            5 GLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNL-FPEIDELL   80 (147)
Q Consensus         5 ~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~-~~~i~~l~   80 (147)
                      .|+..++....    ...+|++||.+..+.+++..  |+. .++|+.++.++...++..++....... ...+..++
T Consensus       121 ~L~~~le~~~~----~~~lIl~~~~~~~l~~~l~s--r~~-~~~~~~l~~~ei~~~l~~~~~~~~~~i~~~al~~l~  190 (319)
T PRK00440        121 ALRRTMEMYSQ----NTRFILSCNYSSKIIDPIQS--RCA-VFRFSPLKKEAVAERLRYIAENEGIEITDDALEAIY  190 (319)
T ss_pred             HHHHHHhcCCC----CCeEEEEeCCccccchhHHH--Hhh-eeeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            45555554332    24566777888888888877  665 489999999999999998886554433 33344443

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=89.15  E-value=2  Score=39.32  Aligned_cols=59  Identities=20%  Similarity=0.341  Sum_probs=42.6

Q ss_pred             eEEEE-ecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHHH
Q 042776           21 RIIVF-TTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLTK   82 (147)
Q Consensus        21 vivi~-aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~~   82 (147)
                      +++|+ ||+.++.++++|+.  ||. .++|+..+.++...|++.++......+..++..+...
T Consensus       324 ~VLI~aTt~~~~~l~~aLrS--R~~-~i~~~pls~edi~~Il~~~a~~~~v~ls~eal~~L~~  383 (615)
T TIGR02903       324 FVLIGATTRDPEEINPALRS--RCA-EVFFEPLTPEDIALIVLNAAEKINVHLAAGVEELIAR  383 (615)
T ss_pred             EEEEEeccccccccCHHHHh--cee-EEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            45554 56679999999987  997 5788888999999999998875444444444444433

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.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=88.98  E-value=3.4  Score=35.59  Aligned_cols=45  Identities=18%  Similarity=0.177  Sum_probs=35.7

Q ss_pred             ceEEEEecC--CCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCC
Q 042776           20 ERIIVFTTN--HKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGI   67 (147)
Q Consensus        20 ~vivi~aTN--~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~   67 (147)
                      .+++|++|+  ....++++|+.  |+ ..+.|..++.++...++...+..
T Consensus       120 ~iilI~att~n~~~~l~~aL~S--R~-~~~~~~~ls~e~i~~lL~~~l~~  166 (413)
T PRK13342        120 TITLIGATTENPSFEVNPALLS--RA-QVFELKPLSEEDIEQLLKRALED  166 (413)
T ss_pred             cEEEEEeCCCChhhhccHHHhc--cc-eeeEeCCCCHHHHHHHHHHHHHH
Confidence            466666653  35589999999  88 78999999999999999887653

>PRK08084 DNA replication initiation factor; Provisional

Probab=88.50  E-value=0.96  Score=35.97  Aligned_cols=57  Identities=11%  Similarity=0.103  Sum_probs=40.4

Q ss_pred             eEEEEecCCCCC---CCccccCCCeee--eEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHH
Q 042776           21 RIIVFTTNHKNR---LDPALLRPGRMD--MHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDEL   79 (147)
Q Consensus        21 vivi~aTN~p~~---LD~Al~RpGRfd--~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l   79 (147)
                      .+|+.+++.|..   +.|.|.-  |+.  ..+.+..|+.+++.++++............++...
T Consensus       133 ~li~ts~~~p~~l~~~~~~L~S--Rl~~g~~~~l~~~~~~~~~~~l~~~a~~~~~~l~~~v~~~  194 (235)
T PRK08084        133 RLLITGDRPPRQLNLGLPDLAS--RLDWGQIYKLQPLSDEEKLQALQLRARLRGFELPEDVGRF  194 (235)
T ss_pred             eEEEeCCCChHHcCcccHHHHH--HHhCCceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            456666667666   5799988  987  78899999999999999875543334444444333

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

Probab=88.42  E-value=1.1  Score=42.02  Aligned_cols=62  Identities=21%  Similarity=0.308  Sum_probs=44.7

Q ss_pred             HHHHHHHhh-CCCCCC------CCceEEEEecCCC-------------------------CCCCccccCCCeeeeEEeec
Q 042776            3 LSGLLNFID-GLWSSC------GDERIIVFTTNHK-------------------------NRLDPALLRPGRMDMHIHMS   50 (147)
Q Consensus         3 v~~lL~~lD-gl~~~~------~~~vivi~aTN~p-------------------------~~LD~Al~RpGRfd~~i~~~   50 (147)
                      .+.||+.|| |.-...      -.+.++|+|||.-                         ..+.|.++.  |+|..|.|.
T Consensus       574 ~~~LLq~ld~G~ltd~~g~~vd~rn~iiI~TsN~g~~~~~~~~~g~~~~~~~~~~~~~~~~~f~pefl~--Rid~ii~f~  651 (758)
T PRK11034        574 FNLLLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFD  651 (758)
T ss_pred             HHHHHHHHhcCeeecCCCceecCCCcEEEEeCCcCHHHHhhcccCcccchhhHHHHHHHHHhcCHHHHc--cCCEEEEcC
Confidence            366888887 432110      0367899999932                         125577776  999999999


Q ss_pred             CCCHHHHHHHHHHHhC
Q 042776           51 YCNPSGFRILVSNYLG   66 (147)
Q Consensus        51 ~P~~~~r~~il~~~l~   66 (147)
                      ..+.+...+|+..++.
T Consensus       652 ~L~~~~l~~I~~~~l~  667 (758)
T PRK11034        652 HLSTDVIHQVVDKFIV  667 (758)
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999999887763

>CHL00095 clpC Clp protease ATP binding subunit

Probab=88.21  E-value=1.6  Score=41.11  Aligned_cols=42  Identities=19%  Similarity=0.111  Sum_probs=35.1

Q ss_pred             CceEEEEecCCCC-----CCCccccCCCeeeeEEeecCCCHHHHHHHHHH
Q 042776           19 DERIIVFTTNHKN-----RLDPALLRPGRMDMHIHMSYCNPSGFRILVSN   63 (147)
Q Consensus        19 ~~vivi~aTN~p~-----~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~   63 (147)
                      +.+.+|+||+..+     ..||++.|  ||.. |.+..|+.++...|++.
T Consensus       306 g~l~~IgaTt~~ey~~~ie~D~aL~r--Rf~~-I~v~ep~~~e~~aILr~  352 (821)
T CHL00095        306 GELQCIGATTLDEYRKHIEKDPALER--RFQP-VYVGEPSVEETIEILFG  352 (821)
T ss_pred             CCcEEEEeCCHHHHHHHHhcCHHHHh--cceE-EecCCCCHHHHHHHHHH
Confidence            4577999999764     58999999  9975 89999999998888763

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=88.17  E-value=2.3  Score=37.38  Aligned_cols=58  Identities=10%  Similarity=0.112  Sum_probs=44.0

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCC
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIN   68 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~   68 (147)
                      +.||..|+.-.    +.+++|++||.+..|.++|+.  |+. .++|..++.++...++...+...
T Consensus       139 n~LLk~lEep~----~~~~~Il~t~~~~kl~~tI~s--Rc~-~v~f~~l~~~el~~~L~~~~~~e  196 (451)
T PRK06305        139 NSLLKTLEEPP----QHVKFFLATTEIHKIPGTILS--RCQ-KMHLKRIPEETIIDKLALIAKQE  196 (451)
T ss_pred             HHHHHHhhcCC----CCceEEEEeCChHhcchHHHH--hce-EEeCCCCCHHHHHHHHHHHHHHc
Confidence            45666666532    457788888999999999987  764 58999999999888887766443

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=88.12  E-value=3.8  Score=34.86  Aligned_cols=55  Identities=13%  Similarity=0.236  Sum_probs=43.0

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNY   64 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~   64 (147)
                      .|.||..|..-.    ...++|..|+.|+.|.|.++-  |+ ..+.|+.|+.++...++...
T Consensus       158 anaLLk~LEEpp----~~~~fiLit~~~~~llptIrS--Rc-~~i~l~pl~~~~~~~~L~~~  212 (351)
T PRK09112        158 ANAILKTLEEPP----ARALFILISHSSGRLLPTIRS--RC-QPISLKPLDDDELKKALSHL  212 (351)
T ss_pred             HHHHHHHHhcCC----CCceEEEEECChhhccHHHHh--hc-cEEEecCCCHHHHHHHHHHh
Confidence            466788887633    335666667889999998876  87 69999999999999999874

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.07  E-value=0.99  Score=41.98  Aligned_cols=60  Identities=12%  Similarity=0.277  Sum_probs=46.8

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIND   69 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~   69 (147)
                      .|.||..|+.-    ..++++|++||.++.|.+.|+-  |+ ..+.|..++.++....+..++....
T Consensus       141 aNALLKTLEEP----P~~v~FILaTtep~kLlpTIrS--RC-q~f~f~~ls~eei~~~L~~Il~~Eg  200 (700)
T PRK12323        141 FNAMLKTLEEP----PEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPGHIVSHLDAILGEEG  200 (700)
T ss_pred             HHHHHHhhccC----CCCceEEEEeCChHhhhhHHHH--HH-HhcccCCCChHHHHHHHHHHHHHcC
Confidence            45666666642    2557888999999999999987  87 7899999999998888887775443

>smart00350 MCM minichromosome maintenance proteins

Probab=87.53  E-value=1.4  Score=39.27  Aligned_cols=45  Identities=16%  Similarity=0.194  Sum_probs=36.3

Q ss_pred             CceEEEEecCCCC-------------CCCccccCCCeeeeEEee-cCCCHHHHHHHHHHHh
Q 042776           19 DERIIVFTTNHKN-------------RLDPALLRPGRMDMHIHM-SYCNPSGFRILVSNYL   65 (147)
Q Consensus        19 ~~vivi~aTN~p~-------------~LD~Al~RpGRfd~~i~~-~~P~~~~r~~il~~~l   65 (147)
                      ....||||+|..+             .|+|+++.  |||..+.+ +.|+.+....|+++.+
T Consensus       342 ~~~~viAa~NP~~g~y~~~~~~~~n~~l~~~lLs--RFdLi~~~~d~~~~~~d~~i~~~i~  400 (509)
T smart00350      342 ARCSVLAAANPIGGRYDPKLTPEENIDLPAPILS--RFDLLFVVLDEVDEERDRELAKHVV  400 (509)
T ss_pred             CCcEEEEEeCCCCcccCCCcChhhccCCChHHhC--ceeeEEEecCCCChHHHHHHHHHHH
Confidence            3466899999542             69999999  99986555 7999999999998754

>PRK06620 hypothetical protein; Validated

Probab=87.52  E-value=1.6  Score=34.37  Aligned_cols=70  Identities=17%  Similarity=0.327  Sum_probs=46.9

Q ss_pred             HHHHhhCCCCCCCCceEEEEecCCCCC--CCccccCCCeee--eEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHH
Q 042776            6 LLNFIDGLWSSCGDERIIVFTTNHKNR--LDPALLRPGRMD--MHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELL   80 (147)
Q Consensus         6 lL~~lDgl~~~~~~~vivi~aTN~p~~--LD~Al~RpGRfd--~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~   80 (147)
                      |...++.+...  +..+||++|..|..  | |+|+-  ||.  ..+.+..|+.+.+..+++............++....
T Consensus       102 lf~l~N~~~e~--g~~ilits~~~p~~l~l-~~L~S--Rl~~gl~~~l~~pd~~~~~~~l~k~~~~~~l~l~~ev~~~L  175 (214)
T PRK06620        102 LLHIFNIINEK--QKYLLLTSSDKSRNFTL-PDLSS--RIKSVLSILLNSPDDELIKILIFKHFSISSVTISRQIIDFL  175 (214)
T ss_pred             HHHHHHHHHhc--CCEEEEEcCCCccccch-HHHHH--HHhCCceEeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            33444444444  55778888877775  5 77776  876  358889999999999998887644444444444443

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=87.30  E-value=4.3  Score=31.53  Aligned_cols=73  Identities=15%  Similarity=0.140  Sum_probs=43.5

Q ss_pred             HHHHHhhCCCCCCCCceEEEEecCCCC---CCCccccCCCee--eeEEeecCCCHHHHHHHHHHHhCCCCCCChHH-HHH
Q 042776            5 GLLNFIDGLWSSCGDERIIVFTTNHKN---RLDPALLRPGRM--DMHIHMSYCNPSGFRILVSNYLGINDHNLFPE-IDE   78 (147)
Q Consensus         5 ~lL~~lDgl~~~~~~~vivi~aTN~p~---~LD~Al~RpGRf--d~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~-i~~   78 (147)
                      .|+..++.+...  ...+||+|++.+.   .+.+.|..  ||  ...|+++.|+...+..++..+..........+ +..
T Consensus       109 ~L~~~~~~~~~~--~~~~vl~~~~~~~~~~~l~~~L~s--r~~~~~~i~l~pl~~~~~~~~l~~~~~~~~v~l~~~al~~  184 (227)
T PRK08903        109 ALFNLFNRVRAH--GQGALLVAGPAAPLALPLREDLRT--RLGWGLVYELKPLSDADKIAALKAAAAERGLQLADEVPDY  184 (227)
T ss_pred             HHHHHHHHHHHc--CCcEEEEeCCCCHHhCCCCHHHHH--HHhcCeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            355556655443  3444555555432   24466664  66  47999999999999899887665444444443 344


Q ss_pred             HHH
Q 042776           79 LLT   81 (147)
Q Consensus        79 l~~   81 (147)
                      ++.
T Consensus       185 L~~  187 (227)
T PRK08903        185 LLT  187 (227)
T ss_pred             HHH
Confidence            433

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=87.20  E-value=2.3  Score=38.57  Aligned_cols=59  Identities=14%  Similarity=0.187  Sum_probs=44.3

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIN   68 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~   68 (147)
                      .+.||..|+...    ..+++|++|+.+..|.++|+.  |+. .++|..++.++...++...+...
T Consensus       136 ~naLLK~LEepp----~~~vfI~~tte~~kL~~tI~S--Rc~-~~~f~~l~~~el~~~L~~i~~~e  194 (563)
T PRK06647        136 FNALLKTIEEPP----PYIVFIFATTEVHKLPATIKS--RCQ-HFNFRLLSLEKIYNMLKKVCLED  194 (563)
T ss_pred             HHHHHHhhccCC----CCEEEEEecCChHHhHHHHHH--hce-EEEecCCCHHHHHHHHHHHHHHc
Confidence            456666666422    457788888889999999987  765 58899999999888888776433

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

Probab=86.99  E-value=2.1  Score=33.76  Aligned_cols=74  Identities=18%  Similarity=0.262  Sum_probs=44.7

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCC---ccccCCCeee--eEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHH
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLD---PALLRPGRMD--MHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDE   78 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD---~Al~RpGRfd--~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~   78 (147)
                      ..|...++.+...  ++.+||.+-..|..|.   |.|.-  ||.  ..+.+..|+.+.|..|++.........+..++..
T Consensus       117 ~~lf~l~n~~~~~--~k~li~ts~~~P~~l~~~~~~L~S--Rl~~Gl~~~l~~pd~~~r~~il~~~a~~~~~~l~~~v~~  192 (219)
T PF00308_consen  117 EELFHLFNRLIES--GKQLILTSDRPPSELSGLLPDLRS--RLSWGLVVELQPPDDEDRRRILQKKAKERGIELPEEVIE  192 (219)
T ss_dssp             HHHHHHHHHHHHT--TSEEEEEESS-TTTTTTS-HHHHH--HHHCSEEEEE----HHHHHHHHHHHHHHTT--S-HHHHH
T ss_pred             HHHHHHHHHHHhh--CCeEEEEeCCCCccccccChhhhh--hHhhcchhhcCCCCHHHHHHHHHHHHHHhCCCCcHHHHH
Confidence            3556666666555  5577777767777664   55555  665  3688889999999999998887665556665555


Q ss_pred             HHH
Q 042776           79 LLT   81 (147)
Q Consensus        79 l~~   81 (147)
                      ...
T Consensus       193 ~l~  195 (219)
T PF00308_consen  193 YLA  195 (219)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

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

>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=86.96  E-value=1.1  Score=30.57  Aligned_cols=45  Identities=27%  Similarity=0.347  Sum_probs=30.8

Q ss_pred             HHHHHHhhCCCCC--CCCceEEEEecCCCC--CCCccccCCCeeeeEEeec
Q 042776            4 SGLLNFIDGLWSS--CGDERIIVFTTNHKN--RLDPALLRPGRMDMHIHMS   50 (147)
Q Consensus         4 ~~lL~~lDgl~~~--~~~~vivi~aTN~p~--~LD~Al~RpGRfd~~i~~~   50 (147)
                      .+++..+..+...  ...++.+|++||.+.  .+++.+..  ||+.+|.++
T Consensus       102 ~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~--r~~~~i~~~  150 (151)
T cd00009         102 NALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYD--RLDIRIVIP  150 (151)
T ss_pred             HHHHHHHHhcCceeccCCCeEEEEecCccccCCcChhHHh--hhccEeecC
Confidence            3455555555321  025678899999887  78888887  999888775

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.

>PRK05642 DNA replication initiation factor; Validated

Probab=86.33  E-value=1.9  Score=34.24  Aligned_cols=57  Identities=16%  Similarity=0.210  Sum_probs=41.1

Q ss_pred             HHHHHhhCCCCCCCCceEEEEecCCCCCC---CccccCCCeee--eEEeecCCCHHHHHHHHHHHh
Q 042776            5 GLLNFIDGLWSSCGDERIIVFTTNHKNRL---DPALLRPGRMD--MHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus         5 ~lL~~lDgl~~~~~~~vivi~aTN~p~~L---D~Al~RpGRfd--~~i~~~~P~~~~r~~il~~~l   65 (147)
                      +|...++.+...  +..+||+++..|..+   .|.|.-  ||-  ..+.+..|+.+.+..+++...
T Consensus       118 ~Lf~l~n~~~~~--g~~ilits~~~p~~l~~~~~~L~S--Rl~~gl~~~l~~~~~e~~~~il~~ka  179 (234)
T PRK05642        118 ALFHLFNRLRDS--GRRLLLAASKSPRELPIKLPDLKS--RLTLALVFQMRGLSDEDKLRALQLRA  179 (234)
T ss_pred             HHHHHHHHHHhc--CCEEEEeCCCCHHHcCccCccHHH--HHhcCeeeecCCCCHHHHHHHHHHHH
Confidence            466666666554  556777777667555   578877  875  666778999999999998544

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=86.03  E-value=1.8  Score=36.44  Aligned_cols=56  Identities=13%  Similarity=0.170  Sum_probs=44.4

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      .|.||..|..-.    ++.++|.+|+.|+.|.|.++-  |.-. +.|+.|+.++....+....
T Consensus       123 aNaLLK~LEEPp----~~~~fiL~t~~~~~ll~TI~S--Rc~~-~~~~~~~~~~~~~~L~~~~  178 (328)
T PRK05707        123 ANALLKSLEEPS----GDTVLLLISHQPSRLLPTIKS--RCQQ-QACPLPSNEESLQWLQQAL  178 (328)
T ss_pred             HHHHHHHHhCCC----CCeEEEEEECChhhCcHHHHh--hcee-eeCCCcCHHHHHHHHHHhc
Confidence            466777776532    458888999999999999987  7766 8999999998888877654

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

Probab=85.75  E-value=1.1  Score=39.88  Aligned_cols=29  Identities=28%  Similarity=0.369  Sum_probs=24.4

Q ss_pred             CceEEEEecCCCC----CCCccccCCCeeeeEEeec
Q 042776           19 DERIIVFTTNHKN----RLDPALLRPGRMDMHIHMS   50 (147)
Q Consensus        19 ~~vivi~aTN~p~----~LD~Al~RpGRfd~~i~~~   50 (147)
                      .++.||+|+|..+    .||+||+|  ||.. |++.
T Consensus       324 ~Nl~IIgTMNt~Drs~~~lD~AlrR--RF~f-i~i~  356 (459)
T PRK11331        324 ENVYIIGLMNTADRSLAVVDYALRR--RFSF-IDIE  356 (459)
T ss_pred             CCeEEEEecCccccchhhccHHHHh--hhhe-EEec
Confidence            6699999999988    89999999  9954 4444

>PLN03025 replication factor C subunit; Provisional

Probab=85.63  E-value=3.3  Score=34.25  Aligned_cols=71  Identities=8%  Similarity=0.062  Sum_probs=46.6

Q ss_pred             eEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCC-hHHHHHHHHHHhccchHHHHHHHH
Q 042776           21 RIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNL-FPEIDELLTKLMKSEVAEVALEGL   96 (147)
Q Consensus        21 vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~-~~~i~~l~~~l~~~~~~~~al~~~   96 (147)
                      ..+|++||.++.+.++|+.  |+ ..+.|+.|+.++....+........... ...+..++.  .+.++...|+..+
T Consensus       130 t~~il~~n~~~~i~~~L~S--Rc-~~i~f~~l~~~~l~~~L~~i~~~egi~i~~~~l~~i~~--~~~gDlR~aln~L  201 (319)
T PLN03025        130 TRFALACNTSSKIIEPIQS--RC-AIVRFSRLSDQEILGRLMKVVEAEKVPYVPEGLEAIIF--TADGDMRQALNNL  201 (319)
T ss_pred             ceEEEEeCCccccchhHHH--hh-hcccCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH--HcCCCHHHHHHHH
Confidence            4467788889999999987  66 4789999999999888887775544332 333444433  2334444444433

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=85.50  E-value=3.9  Score=38.86  Aligned_cols=60  Identities=13%  Similarity=0.224  Sum_probs=45.6

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIND   69 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~   69 (147)
                      .|.||..|+-..    ..+++|++|+.++.|-+.|+-  |. ..|.|..++.+....+|..++....
T Consensus       137 ~NaLLK~LEEpP----~~~~fIl~tt~~~kLl~TIrS--Rc-~~v~F~~l~~~~l~~~L~~il~~EG  196 (824)
T PRK07764        137 FNALLKIVEEPP----EHLKFIFATTEPDKVIGTIRS--RT-HHYPFRLVPPEVMRGYLERICAQEG  196 (824)
T ss_pred             HHHHHHHHhCCC----CCeEEEEEeCChhhhhHHHHh--he-eEEEeeCCCHHHHHHHHHHHHHHcC
Confidence            366777777654    347788888889989888876  55 5788998888998888888775443

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=85.13  E-value=2  Score=38.96  Aligned_cols=60  Identities=10%  Similarity=0.095  Sum_probs=44.8

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIND   69 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~   69 (147)
                      .|.||..|+--.    +.+++|++||.|+.|.+.|+-  |+ ..+.|..++.++....+..++....
T Consensus       136 ~naLLk~LEepp----~~~~fIl~t~~~~kl~~tI~S--Rc-~~~~f~~l~~~~i~~~L~~i~~~eg  195 (576)
T PRK14965        136 FNALLKTLEEPP----PHVKFIFATTEPHKVPITILS--RC-QRFDFRRIPLQKIVDRLRYIADQEG  195 (576)
T ss_pred             HHHHHHHHHcCC----CCeEEEEEeCChhhhhHHHHH--hh-hhhhcCCCCHHHHHHHHHHHHHHhC
Confidence            456777777543    458888888999999999876  55 4678888888888888777665443

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=84.94  E-value=2.7  Score=35.98  Aligned_cols=57  Identities=12%  Similarity=0.160  Sum_probs=43.7

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      .|.||..+..-.    .+.++|.+|+.|+.|.|.++.  |+ ..|.|+.|+.++..+++.....
T Consensus       158 anaLLK~LEepp----~~~~~IL~t~~~~~llpti~S--Rc-~~i~l~~l~~~~i~~~L~~~~~  214 (365)
T PRK07471        158 ANALLKVLEEPP----ARSLFLLVSHAPARLLPTIRS--RC-RKLRLRPLAPEDVIDALAAAGP  214 (365)
T ss_pred             HHHHHHHHhcCC----CCeEEEEEECCchhchHHhhc--cc-eEEECCCCCHHHHHHHHHHhcc
Confidence            456676666433    347788899999999988866  65 5789999999999999887654

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=84.81  E-value=6.2  Score=33.57  Aligned_cols=45  Identities=13%  Similarity=0.139  Sum_probs=37.6

Q ss_pred             CceEEEEecCCCC------------CCCccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776           19 DERIIVFTTNHKN------------RLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus        19 ~~vivi~aTN~p~------------~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      ....||||+|..+            .|++|++-  ||-..+.+++|+.+.-.+|+....
T Consensus       177 p~FrviAT~Np~g~Gd~~G~y~Gt~~l~~A~lD--RF~i~~~~~Yp~~e~E~~Il~~~~  233 (327)
T TIGR01650       177 PAFRLFATANTIGLGDTTGLYHGTQQINQAQMD--RWSIVTTLNYLEHDNEAAIVLAKA  233 (327)
T ss_pred             CCeEEEEeeCCCCcCCCCcceeeeecCCHHHHh--heeeEeeCCCCCHHHHHHHHHhhc
Confidence            3466899999765            35788888  999999999999999999987664

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.

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=84.56  E-value=4.1  Score=37.19  Aligned_cols=61  Identities=18%  Similarity=0.333  Sum_probs=46.4

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH   70 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~   70 (147)
                      .|.||..|.-..    ..+++|++|+.++.|-++|+-  |. ..++|..++.+....++..++.....
T Consensus       135 ~NALLK~LEEpp----~~~~fIL~tte~~kll~TI~S--Rc-~~~~F~~l~~~~i~~~L~~i~~~egi  195 (584)
T PRK14952        135 FNALLKIVEEPP----EHLIFIFATTEPEKVLPTIRS--RT-HHYPFRLLPPRTMRALIARICEQEGV  195 (584)
T ss_pred             HHHHHHHHhcCC----CCeEEEEEeCChHhhHHHHHH--hc-eEEEeeCCCHHHHHHHHHHHHHHcCC
Confidence            456777777543    458888888999999999876  64 57899999989888888877765443

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=84.53  E-value=4.6  Score=37.09  Aligned_cols=58  Identities=14%  Similarity=0.183  Sum_probs=41.0

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGI   67 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~   67 (147)
                      .+.||..|+.-.    ..+++|++|+.++.|-|+|+.  |+ ..++|..++.++....+......
T Consensus       138 ~naLLK~LEePp----~~tvfIL~t~~~~~llpTIrS--Rc-~~~~f~~l~~~ei~~~L~~ia~k  195 (620)
T PRK14948        138 FNALLKTLEEPP----PRVVFVLATTDPQRVLPTIIS--RC-QRFDFRRIPLEAMVQHLSEIAEK  195 (620)
T ss_pred             HHHHHHHHhcCC----cCeEEEEEeCChhhhhHHHHh--he-eEEEecCCCHHHHHHHHHHHHHH
Confidence            466777787532    447777888889999999876  65 45788888777766666655543

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=84.37  E-value=5  Score=37.17  Aligned_cols=59  Identities=15%  Similarity=0.273  Sum_probs=45.2

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIN   68 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~   68 (147)
                      .|.||..|.--.    +.+++|++|+.++.|-+.++-  |+ ..++|..++.++....+...+...
T Consensus       136 ~NALLKtLEEPp----~~v~FIL~Tt~~~kLl~TI~S--RC-~~~~f~~Ls~~ei~~~L~~il~~e  194 (647)
T PRK07994        136 FNALLKTLEEPP----EHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRQQLEHILQAE  194 (647)
T ss_pred             HHHHHHHHHcCC----CCeEEEEecCCccccchHHHh--hh-eEeeCCCCCHHHHHHHHHHHHHHc
Confidence            456777666532    457777778889999999887  76 889999999999988888777443

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=83.54  E-value=3.4  Score=36.96  Aligned_cols=61  Identities=7%  Similarity=0.111  Sum_probs=46.0

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH   70 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~   70 (147)
                      .|.||..|+.-.    ..+++|++|+.++.|.+.++.  |+ ..+.|..++.++....+...+.....
T Consensus       133 ~NaLLK~LEePp----~~v~fIlatte~~Kl~~tI~S--Rc-~~~~f~~l~~~el~~~L~~ia~~Egi  193 (491)
T PRK14964        133 FNALLKTLEEPA----PHVKFILATTEVKKIPVTIIS--RC-QRFDLQKIPTDKLVEHLVDIAKKENI  193 (491)
T ss_pred             HHHHHHHHhCCC----CCeEEEEEeCChHHHHHHHHH--hh-eeeecccccHHHHHHHHHHHHHHcCC
Confidence            456777777543    447788888888999999887  66 55899989999988888887765443

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=83.07  E-value=5.7  Score=36.37  Aligned_cols=62  Identities=11%  Similarity=0.146  Sum_probs=45.6

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHN   71 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~   71 (147)
                      .|.||..|....    +.+++|++|+.++.|-+.++-  |+ ..|.|..|+.++...++...+......
T Consensus       149 ~naLLKtLEePp----~~~~fIl~tte~~kll~tI~S--Rc-q~~~f~~l~~~el~~~L~~i~~kegi~  210 (598)
T PRK09111        149 FNALLKTLEEPP----PHVKFIFATTEIRKVPVTVLS--RC-QRFDLRRIEADVLAAHLSRIAAKEGVE  210 (598)
T ss_pred             HHHHHHHHHhCC----CCeEEEEEeCChhhhhHHHHh--he-eEEEecCCCHHHHHHHHHHHHHHcCCC
Confidence            456666666543    447777788888888888876  66 579999999999998888887655433

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=82.55  E-value=6.3  Score=35.68  Aligned_cols=61  Identities=13%  Similarity=0.153  Sum_probs=45.6

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH   70 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~   70 (147)
                      .+.||..|.-..    ..+.+|++|+.|..|.++++-  |. ..++|..++.++....+...+.....
T Consensus       134 ~NALLK~LEEpp----~~t~FIL~ttd~~kL~~tI~S--Rc-~~~~F~~Ls~~ei~~~L~~Il~~EGi  194 (535)
T PRK08451        134 FNALLKTLEEPP----SYVKFILATTDPLKLPATILS--RT-QHFRFKQIPQNSIISHLKTILEKEGV  194 (535)
T ss_pred             HHHHHHHHhhcC----CceEEEEEECChhhCchHHHh--hc-eeEEcCCCCHHHHHHHHHHHHHHcCC
Confidence            356777777643    336677777888999999987  75 58899999999988888877765433

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=82.51  E-value=3.3  Score=38.74  Aligned_cols=61  Identities=8%  Similarity=0.163  Sum_probs=46.0

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH   70 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~   70 (147)
                      .+.||..|+...    +.+.+|++||.+..|.+.++-  |+ ..|.|..++.++...++...+.....
T Consensus       136 ~NALLKtLEEPp----~~v~fILaTtd~~kL~~TIrS--RC-~~f~f~~Ls~eeI~~~L~~Il~kEgi  196 (709)
T PRK08691        136 FNAMLKTLEEPP----EHVKFILATTDPHKVPVTVLS--RC-LQFVLRNMTAQQVADHLAHVLDSEKI  196 (709)
T ss_pred             HHHHHHHHHhCC----CCcEEEEEeCCccccchHHHH--HH-hhhhcCCCCHHHHHHHHHHHHHHcCC
Confidence            456777777543    347788888889999988874  77 66778889999988888888765543

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=82.13  E-value=4.2  Score=38.01  Aligned_cols=59  Identities=12%  Similarity=0.187  Sum_probs=44.3

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIN   68 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~   68 (147)
                      .+.||..|+...    ..+.+|++|+.+..+.+.++.  |+ ..+.|..++..+....+...+...
T Consensus       135 ~NALLKtLEEPP----~~v~FILaTtd~~kIp~TIlS--RC-q~feFkpLs~eEI~k~L~~Il~kE  193 (702)
T PRK14960        135 FNALLKTLEEPP----EHVKFLFATTDPQKLPITVIS--RC-LQFTLRPLAVDEITKHLGAILEKE  193 (702)
T ss_pred             HHHHHHHHhcCC----CCcEEEEEECChHhhhHHHHH--hh-heeeccCCCHHHHHHHHHHHHHHc
Confidence            456777776532    446777888888889888876  77 678899999999888888777544

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=81.98  E-value=6.4  Score=37.99  Aligned_cols=60  Identities=12%  Similarity=0.218  Sum_probs=44.3

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIND   69 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~   69 (147)
                      .+.||..|.--.    ..+.+|++|+.+..|-+.|+.  |+ ..+.|..++.++....+.+.+....
T Consensus       136 qNALLKtLEEPP----~~vrFILaTTe~~kLl~TIlS--RC-q~f~fkpLs~eEI~~~L~~il~~Eg  195 (944)
T PRK14949        136 FNALLKTLEEPP----EHVKFLLATTDPQKLPVTVLS--RC-LQFNLKSLTQDEIGTQLNHILTQEQ  195 (944)
T ss_pred             HHHHHHHHhccC----CCeEEEEECCCchhchHHHHH--hh-eEEeCCCCCHHHHHHHHHHHHHHcC
Confidence            456777776533    346677778888889888876  66 6789998999998888888775543

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=81.33  E-value=3.3  Score=37.12  Aligned_cols=59  Identities=10%  Similarity=0.214  Sum_probs=43.9

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIN   68 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~   68 (147)
                      .|.||..|+...    +.+++|++|+.|+.+.+.++-  |. ..++|..++.++....+...+...
T Consensus       136 ~naLLK~LEepp----~~~~fIL~t~d~~kil~tI~S--Rc-~~~~f~~l~~~~i~~~L~~il~~e  194 (527)
T PRK14969        136 FNAMLKTLEEPP----EHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPPLIVSHLQHILEQE  194 (527)
T ss_pred             HHHHHHHHhCCC----CCEEEEEEeCChhhCchhHHH--HH-HHHhcCCCCHHHHHHHHHHHHHHc
Confidence            466777777643    447777777888888888765  65 678999999999888887777543

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=80.95  E-value=6.9  Score=36.01  Aligned_cols=61  Identities=11%  Similarity=0.202  Sum_probs=44.0

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH   70 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~   70 (147)
                      .|.||..|+.-.    +.+++|++|+.|..+.+.++-  |. ..++|..++.++....+...+.....
T Consensus       141 ~NaLLKtLEEPP----~~~~fIL~Ttd~~kil~TIlS--Rc-~~~~f~~Ls~eei~~~L~~i~~~egi  201 (618)
T PRK14951        141 FNAMLKTLEEPP----EYLKFVLATTDPQKVPVTVLS--RC-LQFNLRPMAPETVLEHLTQVLAAENV  201 (618)
T ss_pred             HHHHHHhcccCC----CCeEEEEEECCchhhhHHHHH--hc-eeeecCCCCHHHHHHHHHHHHHHcCC
Confidence            345666555432    446777788888889888877  66 77899888888888888877755443

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=80.72  E-value=4.5  Score=35.56  Aligned_cols=60  Identities=10%  Similarity=0.293  Sum_probs=39.4

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecC-CCCC---CCccccCCCeee--eEEeecCCCHHHHHHHHHHHhCCC
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTN-HKNR---LDPALLRPGRMD--MHIHMSYCNPSGFRILVSNYLGIN   68 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN-~p~~---LD~Al~RpGRfd--~~i~~~~P~~~~r~~il~~~l~~~   68 (147)
                      .+|...++.+...  +.. +|+|+| .|..   |++.|..  ||.  ..+.+..|+.+.|.+|+++.+...
T Consensus       226 e~lf~l~N~~~~~--~k~-iIltsd~~P~~l~~l~~rL~S--R~~~Gl~~~L~~pd~e~r~~iL~~~~~~~  291 (450)
T PRK14087        226 EIFFTIFNNFIEN--DKQ-LFFSSDKSPELLNGFDNRLIT--RFNMGLSIAIQKLDNKTATAIIKKEIKNQ  291 (450)
T ss_pred             HHHHHHHHHHHHc--CCc-EEEECCCCHHHHhhccHHHHH--HHhCCceeccCCcCHHHHHHHHHHHHHhc
Confidence            3455556665443  334 445555 4544   4677777  775  556678899999999999888643

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=80.49  E-value=23  Score=29.10  Aligned_cols=55  Identities=9%  Similarity=0.098  Sum_probs=41.2

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      |.||..|..-+    ++.++|.+|+.|+.|-|.++-  |. ..++|..|+.++...++...+
T Consensus       111 naLLK~LEepp----~~t~~il~~~~~~~ll~TI~S--Rc-~~~~~~~~~~~~~~~~l~~~~  165 (313)
T PRK05564        111 NAFLKTIEEPP----KGVFIILLCENLEQILDTIKS--RC-QIYKLNRLSKEEIEKFISYKY  165 (313)
T ss_pred             HHHHHHhcCCC----CCeEEEEEeCChHhCcHHHHh--hc-eeeeCCCcCHHHHHHHHHHHh
Confidence            45666666422    457777777889999999876  66 589999999999888877654

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

Probab=80.40  E-value=3.9  Score=37.99  Aligned_cols=62  Identities=19%  Similarity=0.264  Sum_probs=44.5

Q ss_pred             HHHHHHHhhCCCCC--C-----CCceEEEEecCCCC-------------------------CCCccccCCCeeeeEEeec
Q 042776            3 LSGLLNFIDGLWSS--C-----GDERIIVFTTNHKN-------------------------RLDPALLRPGRMDMHIHMS   50 (147)
Q Consensus         3 v~~lL~~lDgl~~~--~-----~~~vivi~aTN~p~-------------------------~LD~Al~RpGRfd~~i~~~   50 (147)
                      .+.||..||.-.-.  .     -.+.++|+|||...                         .+.|.++  +|||..|.|.
T Consensus       570 ~~~Ll~~ld~g~~~d~~g~~vd~~~~iii~Tsn~g~~~~~~~~~~f~~~~~~~~~~~~~~~~f~pef~--~Rid~Vi~F~  647 (731)
T TIGR02639       570 YNILLQVMDYATLTDNNGRKADFRNVILIMTSNAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEFR--NRLDAIIHFN  647 (731)
T ss_pred             HHHHHHhhccCeeecCCCcccCCCCCEEEECCCcchhhhhhccCCcchhhhHHHHHHHHHhhcChHHH--hcCCeEEEcC
Confidence            35678888753110  0     13577999999642                         1455665  4999999999


Q ss_pred             CCCHHHHHHHHHHHhC
Q 042776           51 YCNPSGFRILVSNYLG   66 (147)
Q Consensus        51 ~P~~~~r~~il~~~l~   66 (147)
                      .-+.+....|++.++.
T Consensus       648 pLs~e~l~~Iv~~~L~  663 (731)
T TIGR02639       648 PLSEEVLEKIVQKFVD  663 (731)
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999999988774

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	147
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		2e-05
4b4t_H	467	Near-Atomic Resolution Structural Model Of The Yeas		2e-04
2qz4_A	262	Human Paraplegin, Aaa Domain In Complex With Adp Le		3e-04
4b4t_J	405	Near-Atomic Resolution Structural Model Of The Yeas		4e-04
4b4t_K	428	Near-Atomic Resolution Structural Model Of The Yeas		5e-04
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		6e-04
3h4m_A	285	Aaa Atpase Domain Of The Proteasome- Activating Nuc		7e-04
4b4t_I	437	Near-Atomic Resolution Structural Model Of The Yeas		9e-04

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 34/55 (61%), Gaps = 2/55 (3%)
Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSG 56
           TL  LL  +DG + + G  +II+  TN  + LDPALLRPGR+D  + +   N +G
Sbjct: 304 TLMELLTQMDG-FDNLGQTKIIM-ATNRPDTLDPALLRPGRLDRKVEIPLPNEAG 356

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 25/41 (60%), Gaps = 4/41 (9%)
Query: 23  IVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSG----FRI 59
           ++F TN  N LDPALLRPGR+D  +  S  +  G    FRI
Sbjct: 351 VMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRI 391

>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp Length = 262

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/46 (43%), Positives = 32/46 (69%), Gaps = 2/46 (4%)
Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHI 47
           TL+ LL  +DG+ ++  D  I++ +TN  + LD AL+RPGR+D H+
Sbjct: 129 TLNQLLVEMDGMGTT--DHVIVLASTNRADILDGALMRPGRLDRHV 172

>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 405

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 29/47 (61%), Gaps = 2/47 (4%)
Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIH 48
           T+  LLN +DG  +S   +  I+  TN  + LDPALLRPGR+D  I 
Sbjct: 271 TMLELLNQLDGFETSKNIK--IIMATNRLDILDPALLRPGRIDRKIE 315

>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 428

Iteration: 1
 Score = 40.0 bits (92), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 6   LLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL 65
           LL  +DG   S   +  ++  TN  + LDPALLRPGR+D  I          R L+   +
Sbjct: 299 LLTQMDGFDQSTNVK--VIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTI 356
Query: 66  GINDHNLFPEID 77
             +  +L PE D
Sbjct: 357 A-SKMSLAPEAD 367

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 42/80 (52%), Gaps = 6/80 (7%)
Query: 2   TLSGLLNFIDGLWSSCGDERIIVFT-TNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRIL 60
           TL+ +L  +DG     G+E IIV   TN  + LDPALLRPGR D  + +   +  G   +
Sbjct: 134 TLNQMLVEMDGFE---GNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQI 190
Query: 61  VSNYLGINDHNLFPEIDELL 80
           +  ++      L P+ID  +
Sbjct: 191 LKVHM--RRVPLAPDIDAAI 208

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSG 56
           TL  LL  +DG + + GD +II   TN  + LDPA+LRPGR D  I +   +  G
Sbjct: 140 TLMQLLAEMDG-FDARGDVKII-GATNRPDILDPAILRPGRFDRIIEVPAPDEKG 192

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 22/46 (47%), Positives = 30/46 (65%), Gaps = 2/46 (4%)
Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHI 47
           T+  LLN +DG +   GD ++I+  TN    LDPAL+RPGR+D  I
Sbjct: 305 TMLELLNQLDG-FDDRGDVKVIM-ATNKIETLDPALIRPGRIDRKI 348

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	147
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	9e-07
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	2e-06
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	1e-05
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	4e-06
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	5e-06
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	8e-06
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	1e-05
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	2e-05
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	3e-05
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	3e-05
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	4e-05
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	4e-05
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	3e-04
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	4e-04
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	7e-04

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

 Score = 45.7 bits (109), Expect = 9e-07
 Identities = 23/46 (50%), Positives = 28/46 (60%), Gaps = 2/46 (4%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHI 47
           TL  LL  +DG   + GD +II   TN  + LDPA+LRPGR D  I
Sbjct: 140 TLMQLLAEMDGF-DARGDVKIIG-ATNRPDILDPAILRPGRFDRII 183

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 2/46 (4%)

Query: 3   LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIH 48
           ++ +L  +DG+  S      I+  TN  + +DPA+LRPGR+D  I+
Sbjct: 139 INQILTEMDGM--STKKNVFIIGATNRPDIIDPAILRPGRLDQLIY 182

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

 Score = 43.6 bits (103), Expect = 5e-06
 Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 6/66 (9%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSG----F 57
            +S LL  +DGL        I++  TN  N +DPAL R GR D  + +   + +G     
Sbjct: 324 IVSQLLTLMDGL--KQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEIL 381

Query: 58  RILVSN 63
           +I   N
Sbjct: 382 QIHTKN 387

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

 Score = 42.9 bits (101), Expect = 8e-06
 Identities = 11/40 (27%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 10  IDGLWSSCGDERI-IVFTTNHKNRLDPALLRPGRMDMHIH 48
           + G+++   + R+ I+ T N  + L   L+R GRM+    
Sbjct: 144 LPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYW 183

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

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 19/47 (40%), Positives = 31/47 (65%), Gaps = 2/47 (4%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIH 48
           TL+ LL  +DG+ ++     I++ +TN  + LD AL+RPGR+D H+ 
Sbjct: 129 TLNQLLVEMDGMGTTDH--VIVLASTNRADILDGALMRPGRLDRHVF 173

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 21/47 (44%), Positives = 27/47 (57%), Gaps = 3/47 (6%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVF-TTNHKNRLDPALLRPGRMDMHI 47
           TL+ LL  +DG  S   +  +IV   TN    LDPAL+RPGR D  +
Sbjct: 134 TLNQLLAEMDGFGS--ENAPVIVLAATNRPEILDPALMRPGRFDRQV 178

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

 Score = 41.2 bits (97), Expect = 3e-05
 Identities = 20/46 (43%), Positives = 28/46 (60%), Gaps = 2/46 (4%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHI 47
           TL+ +L  +DG   + G   I++  TN  + LDPALLRPGR D  +
Sbjct: 134 TLNQMLVEMDGFEGNEG--IIVIAATNRPDVLDPALLRPGRFDRQV 177

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

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 8/49 (16%)

Query: 3   LSGLLNFIDGLWSSCGDERIIVF---TTNHKNRLDPALLRPGRMDMHIH 48
           ++ LL  +DGL     + R  VF    TN  + +DPA+LRPGR+D  + 
Sbjct: 131 VNQLLTEMDGL-----EARQQVFIMAATNRPDIIDPAILRPGRLDKTLF 174

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

 Score = 40.8 bits (96), Expect = 4e-05
 Identities = 20/46 (43%), Positives = 26/46 (56%), Gaps = 2/46 (4%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHI 47
           TL+ LL  +DG         +++  TN  + LDPALLRPGR D  I
Sbjct: 162 TLNQLLVEMDGFEKDTA--IVVMAATNRPDILDPALLRPGRFDRQI 205

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

 Score = 40.8 bits (96), Expect = 4e-05
 Identities = 20/46 (43%), Positives = 26/46 (56%), Gaps = 2/46 (4%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHI 47
           TL+ LL  +DG         +++  TN  + LDPALLRPGR D  I
Sbjct: 138 TLNQLLVEMDGFEKDTA--IVVMAATNRPDILDPALLRPGRFDRQI 181

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

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 14/26 (53%), Positives = 18/26 (69%)

Query: 22  IIVFTTNHKNRLDPALLRPGRMDMHI 47
           +++  TN  + LDPALLRPGR D  I
Sbjct: 171 VVMAATNRPDILDPALLRPGRFDRQI 196

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

 Score = 38.3 bits (90), Expect = 4e-04
 Identities = 15/26 (57%), Positives = 18/26 (69%)

Query: 22  IIVFTTNHKNRLDPALLRPGRMDMHI 47
           I++  TN  + LDPALLRPGR D  I
Sbjct: 156 IVMAATNRPDILDPALLRPGRFDKKI 181

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

 Score = 37.3 bits (87), Expect = 7e-04
 Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 4/76 (5%)

Query: 6   LLNFIDGLWSSCGDERIIVF-TTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNY 64
            L   DGL  +   +RI+V   TN    LD A LR  R    +++S  +     +L++  
Sbjct: 144 FLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRL 201

Query: 65  LGINDHNL-FPEIDEL 79
           L      L    +  L
Sbjct: 202 LQKQGSPLDTEALRRL 217

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	147
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	99.86
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	99.85
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	99.85
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	99.84
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	99.83
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	99.83
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.8
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.67
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.64
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.54
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.5
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.46
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.43
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.4
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.4
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.35
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.34
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.32
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.3
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.3
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.3
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.28
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.26
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.26
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.13
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.01
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	98.93
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	98.93
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	98.9
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	98.89
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	98.18
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	97.75
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.64
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.47
2r44_A	331	Uncharacterized protein; putative ATPase, structur	97.37
3kw6_A	78	26S protease regulatory subunit 8; structural geno	97.3
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.19
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	97.16
2chg_A	226	Replication factor C small subunit; DNA-binding pr	97.09
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	97.09
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	97.03
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	96.98
2krk_A	86	26S protease regulatory subunit 8; structural geno	96.94
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.94
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	96.9
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	96.84
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	96.72
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.59
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	96.59
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	96.57
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	96.53
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	96.51
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	96.42
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	96.4
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.33
2chq_A	319	Replication factor C small subunit; DNA-binding pr	96.29
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	96.29
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	96.24
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	96.03
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	95.89
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	95.88
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	95.83
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	95.82
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	95.79
3bos_A	242	Putative DNA replication factor; P-loop containing	95.77
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	95.7
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	95.66
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	95.62
3vlf_B	88	26S protease regulatory subunit 7 homolog; heat re	95.5
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	95.13
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	94.94
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	94.9
3pvs_A	447	Replication-associated recombination protein A; ma	94.54
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	94.54
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	94.46
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	94.16
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	93.93
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	93.91
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	93.22
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	92.28
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	90.83
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	90.61
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	89.48
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	88.21
2dzn_B	82	26S protease regulatory subunit 6B homolog; ankyri	87.73
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	84.46
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	82.03
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	81.41

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

Probab=99.86  E-value=2.7e-22  Score=171.02  Aligned_cols=100  Identities=26%  Similarity=0.289  Sum_probs=87.1

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT   81 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~   81 (147)
                      ++++||++|||+.+.  ++|+||+|||+|+.|||||+||||||++|+|++|+.++|.+||+.|+...+.....++..++.
T Consensus       271 ~l~~lL~~lDg~~~~--~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dvdl~~lA~  348 (405)
T 4b4t_J          271 TMLELLNQLDGFETS--KNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAE  348 (405)
T ss_dssp             HHHHHHHHHHTTTCC--CCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSCCHHHHHH
T ss_pred             HHHHHHHhhhccCCC--CCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHH
Confidence            578999999999887  789999999999999999999999999999999999999999999997665443334555554


Q ss_pred             ---HHhccchHHHHHHHHHHHHHHh
Q 042776           82 ---KLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~~l~~~  103 (147)
                         +++|++....|-++.+.++++.
T Consensus       349 ~t~G~SGADi~~l~~eA~~~Air~~  373 (405)
T 4b4t_J          349 KMNGCSGADVKGVCTEAGMYALRER  373 (405)
T ss_dssp             HCCSCCHHHHHHHHHHHHHHHHHTT
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHcC
Confidence               8999999999999988888654

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

Probab=99.85  E-value=7.8e-22  Score=169.47  Aligned_cols=100  Identities=23%  Similarity=0.318  Sum_probs=86.6

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCC---hHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNL---FPEIDE   78 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~---~~~i~~   78 (147)
                      ++++||++|||+.+.  ++|+||+|||+|+.|||||+||||||++|+|++||.++|.+||+.|+...+...   ...++.
T Consensus       305 ~l~~LL~~lDg~~~~--~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dvdl~~LA~  382 (437)
T 4b4t_I          305 TMLELLNQLDGFDDR--GDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVT  382 (437)
T ss_dssp             HHHHHHHHHHHCCCS--SSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCCCHHHHHH
T ss_pred             HHHHHHHHhhCcCCC--CCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHH
Confidence            578999999999887  789999999999999999999999999999999999999999999997664433   334444


Q ss_pred             HHHHHhccchHHHHHHHHHHHHHHh
Q 042776           79 LLTKLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        79 l~~~l~~~~~~~~al~~~~~~l~~~  103 (147)
                      .+.+|+|++....|.++.+.++++.
T Consensus       383 ~T~GfSGADI~~l~~eA~~~Air~~  407 (437)
T 4b4t_I          383 TKDDLSGADIQAMCTEAGLLALRER  407 (437)
T ss_dssp             HCCSCCHHHHHHHHHHHHHHHHHTT
T ss_pred             hCCCCCHHHHHHHHHHHHHHHHHcC
Confidence            4448999999999999988888654

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

Probab=99.85  E-value=1.3e-21  Score=168.27  Aligned_cols=100  Identities=24%  Similarity=0.316  Sum_probs=86.0

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT   81 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~   81 (147)
                      ++++||++|||+.+.  ++++||+|||+|+.|||||+||||||++|+|++|+.++|.+||+.|+...+.....++..++.
T Consensus       304 ~l~~lL~~lDg~~~~--~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~dl~~lA~  381 (437)
T 4b4t_L          304 TLMELLTQMDGFDNL--GQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVK  381 (437)
T ss_dssp             HHHHHHHHHHSSSCT--TSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCCCHHHHHH
T ss_pred             HHHHHHHHhhcccCC--CCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCcccCHHHHHH
Confidence            478999999999887  789999999999999999999999999999999999999999999987654333334445544


Q ss_pred             ---HHhccchHHHHHHHHHHHHHHh
Q 042776           82 ---KLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~~l~~~  103 (147)
                         +|+|++....|.++.+.+++..
T Consensus       382 ~t~G~sGADi~~l~~eA~~~air~~  406 (437)
T 4b4t_L          382 MSDGFNGADIRNCATEAGFFAIRDD  406 (437)
T ss_dssp             TCCSCCHHHHHHHHHHHHHHHHHTT
T ss_pred             hCCCCCHHHHHHHHHHHHHHHHHcC
Confidence               8999999999999888887653

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

Probab=99.84  E-value=1.7e-21  Score=167.32  Aligned_cols=99  Identities=25%  Similarity=0.308  Sum_probs=85.5

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC---CChHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH---NLFPEIDE   78 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~---~~~~~i~~   78 (147)
                      ++++||++|||+.+.  ++|+||||||+|+.|||||+||||||++|+|++|+.++|.+||+.|+...+.   .+...++.
T Consensus       304 ~~~~lL~~ldg~~~~--~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dvdl~~lA~  381 (434)
T 4b4t_M          304 TMLELLNQLDGFSSD--DRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELAR  381 (434)
T ss_dssp             HHHHHHHHHTTSCSS--CSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCCCHHHHHH
T ss_pred             HHHHHHHHhhccCCC--CCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHH
Confidence            478999999999887  7899999999999999999999999999999999999999999999865433   33445555


Q ss_pred             HHHHHhccchHHHHHHHHHHHHHH
Q 042776           79 LLTKLMKSEVAEVALEGLVEFLKR  102 (147)
Q Consensus        79 l~~~l~~~~~~~~al~~~~~~l~~  102 (147)
                      .+.+|+|++....|.++.+.+++.
T Consensus       382 ~t~G~sGADi~~l~~eA~~~a~r~  405 (434)
T 4b4t_M          382 STDEFNGAQLKAVTVEAGMIALRN  405 (434)
T ss_dssp             HCSSCCHHHHHHHHHHHHHHHHHH
T ss_pred             hCCCCCHHHHHHHHHHHHHHHHHc
Confidence            555899999999999988888764

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

Probab=99.83  E-value=4.5e-21  Score=165.94  Aligned_cols=101  Identities=26%  Similarity=0.345  Sum_probs=87.0

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCC---ChHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHN---LFPEIDE   78 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~---~~~~i~~   78 (147)
                      ++++||++|||+.+.  ++|+||+|||||+.|||||+||||||++|+|++|+.++|.+||+.|+...+..   +...++.
T Consensus       332 ~l~~lL~~lDg~~~~--~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvdl~~LA~  409 (467)
T 4b4t_H          332 TMLELITQLDGFDPR--GNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISR  409 (467)
T ss_dssp             HHHHHHHHHHSSCCT--TTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHH
T ss_pred             HHHHHHHHhhccCCC--CcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHH
Confidence            578999999999887  78999999999999999999999999999999999999999999999766443   3344555


Q ss_pred             HHHHHhccchHHHHHHHHHHHHHHhh
Q 042776           79 LLTKLMKSEVAEVALEGLVEFLKRKK  104 (147)
Q Consensus        79 l~~~l~~~~~~~~al~~~~~~l~~~~  104 (147)
                      .+.+|+|++....|.++.+.+++..+
T Consensus       410 ~T~GfSGADI~~l~~eAa~~Air~~~  435 (467)
T 4b4t_H          410 LCPNSTGAELRSVCTEAGMFAIRARR  435 (467)
T ss_dssp             HCCSCCHHHHHHHHHHHHHHHHHHTC
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHcCC
Confidence            55589999999999999888886543

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

Probab=99.83  E-value=3.7e-21  Score=164.92  Aligned_cols=100  Identities=24%  Similarity=0.330  Sum_probs=85.8

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeec-CCCHHHHHHHHHHHhCCCCC---CChHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMS-YCNPSGFRILVSNYLGINDH---NLFPEID   77 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~-~P~~~~r~~il~~~l~~~~~---~~~~~i~   77 (147)
                      ++++||++|||+.+.  .+|+||||||+|+.|||||+||||||++|+|+ +|+.++|..||+.|+...+.   .+...++
T Consensus       295 ~l~~lL~~ldg~~~~--~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~dl~~lA  372 (428)
T 4b4t_K          295 ILIELLTQMDGFDQS--TNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLI  372 (428)
T ss_dssp             HHHHHHHHHHHSCSS--CSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTCCHHHHH
T ss_pred             HHHHHHHHhhCCCCC--CCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCCcccCHHHHH
Confidence            479999999999987  78999999999999999999999999999995 99999999999999865533   3344455


Q ss_pred             HHHHHHhccchHHHHHHHHHHHHHHh
Q 042776           78 ELLTKLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        78 ~l~~~l~~~~~~~~al~~~~~~l~~~  103 (147)
                      ..+.+|+|++....|-++.+.++++.
T Consensus       373 ~~t~G~sgadi~~l~~eA~~~a~r~~  398 (428)
T 4b4t_K          373 IRNDSLSGAVIAAIMQEAGLRAVRKN  398 (428)
T ss_dssp             HHTTTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHCC
Confidence            55558999999999999988888653

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

Probab=99.80  E-value=2.7e-20  Score=169.87  Aligned_cols=100  Identities=18%  Similarity=0.307  Sum_probs=71.9

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHH---HH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEID---EL   79 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~---~l   79 (147)
                      +|+||++|||+.+.  ++|+||+|||+|+.||||++||||||++|+|++|+.++|.+||+.|+...+.....++.   ..
T Consensus       601 ~~~lL~~mdg~~~~--~~V~vi~aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~~~~dl~~la~~  678 (806)
T 3cf2_A          601 INQILTEMDGMSTK--KNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKM  678 (806)
T ss_dssp             HHHHHHHHHSSCSS--SSEEEECC-CCSSSSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--CCC---------
T ss_pred             HHHHHHHHhCCCCC--CCEEEEEeCCCchhCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHh
Confidence            79999999999887  78999999999999999999999999999999999999999999999876544444444   44


Q ss_pred             HHHHhccchHHHHHHHHHHHHHHhh
Q 042776           80 LTKLMKSEVAEVALEGLVEFLKRKK  104 (147)
Q Consensus        80 ~~~l~~~~~~~~al~~~~~~l~~~~  104 (147)
                      +++|+|++....|-++.+.++++.-
T Consensus       679 t~g~SGadi~~l~~~A~~~a~r~~~  703 (806)
T 3cf2_A          679 TNGFSGADLTEICQRACKLAIRESI  703 (806)
T ss_dssp             -------CHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            5599999999999999888887654

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

Probab=99.67  E-value=5.1e-17  Score=148.29  Aligned_cols=101  Identities=22%  Similarity=0.317  Sum_probs=86.4

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH-
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT-   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~-   81 (147)
                      +++||++|||+.+.  .+|+||+|||+|+.|||||+||||||+.|+|++|+.++|.+||+.|+.........++..++. 
T Consensus       325 v~~LL~~mdg~~~~--~~V~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvdl~~lA~~  402 (806)
T 3cf2_A          325 VSQLLTLMDGLKQR--AHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANE  402 (806)
T ss_dssp             HHHHHTHHHHCCGG--GCEEEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECTTCCHHHHHHH
T ss_pred             HHHHHHHHhccccc--CCEEEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHh
Confidence            78999999999887  779999999999999999999999999999999999999999999997664444444555555 


Q ss_pred             --HHhccchHHHHHHHHHHHHHHhhH
Q 042776           82 --KLMKSEVAEVALEGLVEFLKRKKT  105 (147)
Q Consensus        82 --~l~~~~~~~~al~~~~~~l~~~~~  105 (147)
                        +|++.|....|-++.+.++++...
T Consensus       403 T~GfsgaDL~~Lv~eA~~~A~~r~~~  428 (806)
T 3cf2_A          403 THGHVGADLAALCSEAALQAIRKKMD  428 (806)
T ss_dssp             CCSCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHHHHHhccc
Confidence              888888888888888887776543

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

Probab=99.64  E-value=2.9e-16  Score=126.28  Aligned_cols=99  Identities=20%  Similarity=0.335  Sum_probs=82.6

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCC---CCCChHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIN---DHNLFPEIDEL   79 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~---~~~~~~~i~~l   79 (147)
                      +++++.+|||....  ..++++++||+|+.||||++||||||+.|+|++|+.++|.+|++.++...   +.....++..+
T Consensus       131 ~~~~l~~Lsgg~~~--~~~i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~~~~~~~~~~~~~~~~l  208 (274)
T 2x8a_A          131 VNQLLTEMDGLEAR--QQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAI  208 (274)
T ss_dssp             HHHHHHHHHTCCST--TCEEEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTTTTBTTBBCTTCCHHHH
T ss_pred             HHHHHHhhhccccc--CCEEEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHhcccCCCCccccCHHHH
Confidence            57899999999877  77999999999999999999999999999999999999999999998532   22223345555


Q ss_pred             HH-----HHhccchHHHHHHHHHHHHHHh
Q 042776           80 LT-----KLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        80 ~~-----~l~~~~~~~~al~~~~~~l~~~  103 (147)
                      +.     +|+++|....|-++.+.++++.
T Consensus       209 a~~~~~~g~sgadl~~l~~~a~~~a~~~~  237 (274)
T 2x8a_A          209 AGDLRCDCYTGADLSALVREASICALRQE  237 (274)
T ss_dssp             HTCSGGGSCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhccCCcCHHHHHHHHHHHHHHHHHHH
Confidence            53     7889999988888888877654

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

Probab=99.54  E-value=1.6e-14  Score=116.67  Aligned_cols=98  Identities=19%  Similarity=0.306  Sum_probs=78.1

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH-
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT-   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~-   81 (147)
                      +++||..|||+...  .+++||+|||+|+.||+|++|||||+..|+|++|+.++|.+|++.++...+.....++..++. 
T Consensus       139 ~~~lL~~l~~~~~~--~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~~~~~~~~la~~  216 (301)
T 3cf0_A          139 INQILTEMDGMSTK--KNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKM  216 (301)
T ss_dssp             HHHHHHHHHSSCTT--SSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHT
T ss_pred             HHHHHHHhhcccCC--CCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCCccchHHHHHHH
Confidence            58899999999765  679999999999999999999999999999999999999999999997654332333444544 


Q ss_pred             --HHhccchHHHHHHHHHHHHHH
Q 042776           82 --KLMKSEVAEVALEGLVEFLKR  102 (147)
Q Consensus        82 --~l~~~~~~~~al~~~~~~l~~  102 (147)
                        ++.+.+....|-++++.++..
T Consensus       217 ~~g~sg~dl~~l~~~a~~~a~~~  239 (301)
T 3cf0_A          217 TNGFSGADLTEICQRACKLAIRE  239 (301)
T ss_dssp             CSSCCHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHHHHHH
Confidence              666766666666666655544

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

Probab=99.50  E-value=2.8e-14  Score=123.64  Aligned_cols=97  Identities=25%  Similarity=0.288  Sum_probs=74.9

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT   81 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~   81 (147)
                      ++++||..|||+...  .+++||+|||+|+.||||++||||||+.|+|++|+.++|..|++.|+...+.....++..++.
T Consensus       138 ~l~~LL~~ld~~~~~--~~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v~l~~la~  215 (476)
T 2ce7_A          138 TLNQLLVEMDGFDSK--EGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAK  215 (476)
T ss_dssp             HHHHHHHHHHHSCGG--GTEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHH
T ss_pred             HHHHHHHHHhccCCC--CCEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCcchhhHHHHHH
Confidence            478999999999776  679999999999999999999999999999999999999999999987654332223444444


Q ss_pred             ---HHhccchHHHHHHHHHHHH
Q 042776           82 ---KLMKSEVAEVALEGLVEFL  100 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~~l  100 (147)
                         ++++++....|-++++.+.
T Consensus       216 ~t~G~sgadL~~lv~~Aal~A~  237 (476)
T 2ce7_A          216 RTPGFVGADLENLVNEAALLAA  237 (476)
T ss_dssp             TCTTCCHHHHHHHHHHHHHHHH
T ss_pred             hcCCCcHHHHHHHHHHHHHHHH
Confidence               5555555555544444433

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

Probab=99.46  E-value=2.7e-13  Score=106.14  Aligned_cols=96  Identities=22%  Similarity=0.276  Sum_probs=73.8

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH-
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT-   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~-   81 (147)
                      ++++|..||++...  .+++||+|||+|+.||++++|||||++.|+|++|+.++|.+|++.|+...+......+..++. 
T Consensus       135 ~~~ll~~l~~~~~~--~~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~~~~~~~~la~~  212 (257)
T 1lv7_A          135 LNQMLVEMDGFEGN--EGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARG  212 (257)
T ss_dssp             HHHHHHHHHTCCSS--SCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHT
T ss_pred             HHHHHHHhhCcccC--CCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCCccccHHHHHHH
Confidence            67899999999765  679999999999999999999999999999999999999999999987543332223344444 


Q ss_pred             --HHhccchHHHHHHHHHHHH
Q 042776           82 --KLMKSEVAEVALEGLVEFL  100 (147)
Q Consensus        82 --~l~~~~~~~~al~~~~~~l  100 (147)
                        ++.+++....+-+++..+.
T Consensus       213 ~~G~~~~dl~~l~~~a~~~a~  233 (257)
T 1lv7_A          213 TPGFSGADLANLVNEAALFAA  233 (257)
T ss_dssp             CTTCCHHHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHHHH
Confidence              4455555555555554444

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

Probab=99.43  E-value=3.9e-13  Score=105.05  Aligned_cols=96  Identities=23%  Similarity=0.272  Sum_probs=74.2

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH-
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT-   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~-   81 (147)
                      ++++|..|+|....  ..++++++||+|+.|||+++||||||+.|+|++|+.++|.+|++.++...+.....++..++. 
T Consensus       139 ~~~ll~~l~g~~~~--~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~  216 (254)
T 1ixz_A          139 LNQLLVEMDGFEKD--TAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKR  216 (254)
T ss_dssp             HHHHHHHHHTCCTT--CCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHT
T ss_pred             HHHHHHHHhCCCCC--CCEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHH
Confidence            57899999998766  678999999999999999999999999999999999999999998876543333333445554 


Q ss_pred             --HHhccchHHHHHHHHHHHH
Q 042776           82 --KLMKSEVAEVALEGLVEFL  100 (147)
Q Consensus        82 --~l~~~~~~~~al~~~~~~l  100 (147)
                        ++++++....+-+++..++
T Consensus       217 ~~G~~~~dl~~~~~~a~~~a~  237 (254)
T 1ixz_A          217 TPGFVGADLENLLNEAALLAA  237 (254)
T ss_dssp             CTTCCHHHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHHHH
Confidence              5555555555555554443

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

Probab=99.40  E-value=2.1e-13  Score=118.74  Aligned_cols=95  Identities=24%  Similarity=0.296  Sum_probs=72.2

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT   81 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~   81 (147)
                      ++++||..|||....  ..++||++||+|+.|||+++||||||+.|+|++|+..+|.+|++.|+...+.....++..++.
T Consensus       153 ~l~~LL~~Ldg~~~~--~~viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l~~dv~l~~lA~  230 (499)
T 2dhr_A          153 TLNQLLVEMDGFEKD--TAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAK  230 (499)
T ss_dssp             HHHHHHHHGGGCCSS--CCCEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCCCCSSTTHHHHT
T ss_pred             HHHHHHHHhcccccC--ccEEEEEecCChhhcCcccccccccceEEecCCCCHHHHHHHHHHHHhcCCCChHHHHHHHHH
Confidence            468999999999876  779999999999999999999999999999999999999999999886443332223333333


Q ss_pred             ---HHhccchHHHHHHHHHH
Q 042776           82 ---KLMKSEVAEVALEGLVE   98 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~   98 (147)
                         ++++++....+-++++.
T Consensus       231 ~t~G~~gadL~~lv~~Aa~~  250 (499)
T 2dhr_A          231 RTPGFVGADLENLLNEAALL  250 (499)
T ss_dssp             TSCSCCHHHHHHHHHHHHHH
T ss_pred             hcCCCCHHHHHHHHHHHHHH
Confidence               44555554444444443

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

Probab=99.40  E-value=8.8e-13  Score=107.89  Aligned_cols=99  Identities=17%  Similarity=0.237  Sum_probs=82.9

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCC-ChHHHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHN-LFPEIDELLT   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~-~~~~i~~l~~   81 (147)
                      +++||..|||+... ..+++||+|||+|+.||+|++|  |||+.|++++|+.++|..|++.++...+.. ...++..++.
T Consensus       133 ~~~ll~~ld~~~~~-~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~  209 (322)
T 1xwi_A          133 KTEFLVQMQGVGVD-NDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGR  209 (322)
T ss_dssp             HHHHHHHHHCSSSC-CTTEEEEEEESCTTTSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTCCBCCCHHHHHHHHH
T ss_pred             HHHHHHHHhccccc-CCCEEEEEecCCcccCCHHHHh--hcCeEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Confidence            57899999999643 2779999999999999999999  999999999999999999999999766543 4556777776


Q ss_pred             ---HHhccchHHHHHHHHHHHHHHhh
Q 042776           82 ---KLMKSEVAEVALEGLVEFLKRKK  104 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~~l~~~~  104 (147)
                         ++++++....|-++.+.++++..
T Consensus       210 ~t~G~sgadl~~l~~~A~~~a~r~~~  235 (322)
T 1xwi_A          210 KTDGYSGADISIIVRDALMQPVRKVQ  235 (322)
T ss_dssp             TCTTCCHHHHHHHHHHHHTHHHHHHH
T ss_pred             HcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence               77788888888888877776543

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

Probab=99.35  E-value=2.4e-12  Score=102.22  Aligned_cols=94  Identities=23%  Similarity=0.290  Sum_probs=71.2

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH-
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT-   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~-   81 (147)
                      +++++..|+|....  ..++++++||+|+.|||+++||||||+.|+|++|+.++|.+|++.++.........++..++. 
T Consensus       163 ~~~ll~~lsgg~~~--~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~  240 (278)
T 1iy2_A          163 LNQLLVEMDGFEKD--TAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKR  240 (278)
T ss_dssp             HHHHHHHHTTCCTT--CCEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHT
T ss_pred             HHHHHHHHhCCCCC--CCEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHccCCCCcccCHHHHHHH
Confidence            57889999998765  668899999999999999999999999999999999999999999886543332333444544 


Q ss_pred             --HHhccchHHHHHHHHHH
Q 042776           82 --KLMKSEVAEVALEGLVE   98 (147)
Q Consensus        82 --~l~~~~~~~~al~~~~~   98 (147)
                        ++++++....+-+++..
T Consensus       241 ~~G~~~~dl~~l~~~a~~~  259 (278)
T 1iy2_A          241 TPGFVGADLENLLNEAALL  259 (278)
T ss_dssp             CTTCCHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHH
Confidence              44444444444444433

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

Probab=99.32  E-value=2.5e-12  Score=99.84  Aligned_cols=67  Identities=31%  Similarity=0.442  Sum_probs=60.1

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHN   71 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~   71 (147)
                      +++||..+|++...  .+++||+|||+++.||++++|||||+..|+|++|+.++|.+|++.++......
T Consensus       130 l~~ll~~~~~~~~~--~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~  196 (262)
T 2qz4_A          130 LNQLLVEMDGMGTT--DHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLT  196 (262)
T ss_dssp             HHHHHHHHHTCCTT--CCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHhhCcCCC--CCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCC
Confidence            57899999998765  67999999999999999999999999999999999999999999998654433

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

Probab=99.30  E-value=5.4e-12  Score=99.61  Aligned_cols=97  Identities=24%  Similarity=0.292  Sum_probs=74.4

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH-
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT-   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~-   81 (147)
                      +..+|..+|++...  .+++||+|||+|+.||++++|||||+..++|+.|+.++|.+|++.++.........++..++. 
T Consensus       141 l~~ll~~~~~~~~~--~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~l~~~  218 (285)
T 3h4m_A          141 LMQLLAEMDGFDAR--GDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKM  218 (285)
T ss_dssp             HHHHHHHHHTTCSS--SSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHH
T ss_pred             HHHHHHHhhCCCCC--CCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCCcCCHHHHHHH
Confidence            56788889998776  679999999999999999999999999999999999999999999987554333333444444 


Q ss_pred             --HHhccchHHHHHHHHHHHHH
Q 042776           82 --KLMKSEVAEVALEGLVEFLK  101 (147)
Q Consensus        82 --~l~~~~~~~~al~~~~~~l~  101 (147)
                        ++.+.+....+-.+...++.
T Consensus       219 ~~g~~~~~i~~l~~~a~~~a~~  240 (285)
T 3h4m_A          219 TEGCVGAELKAICTEAGMNAIR  240 (285)
T ss_dssp             CTTCCHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHHHHH
Confidence              55555555555555544444

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

Probab=99.30  E-value=5.3e-12  Score=102.64  Aligned_cols=99  Identities=17%  Similarity=0.191  Sum_probs=81.2

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCC-ChHHHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHN-LFPEIDELLT   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~-~~~~i~~l~~   81 (147)
                      +++||..|||+... ..+++||+|||+|+.||+|++|  ||+..|+|++|+.++|.+|++.++...+.. ....+..++.
T Consensus       138 ~~~ll~~l~~~~~~-~~~v~vi~atn~~~~ld~al~~--Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~l~~la~  214 (322)
T 3eie_A          138 KTELLVQMNGVGND-SQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGA  214 (322)
T ss_dssp             HHHHHHHHGGGGTS-CCCEEEEEEESCGGGSCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHTTCCCCCCHHHHHHHHH
T ss_pred             HHHHHHHhcccccc-CCceEEEEecCChhhCCHHHHc--ccCeEEEeCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence            58899999999643 2679999999999999999999  999999999999999999999999876544 3456677766


Q ss_pred             ---HHhccchHHHHHHHHHHHHHHhh
Q 042776           82 ---KLMKSEVAEVALEGLVEFLKRKK  104 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~~l~~~~  104 (147)
                         ++++++....|-++.+..+++..
T Consensus       215 ~t~g~sg~di~~l~~~a~~~a~r~~~  240 (322)
T 3eie_A          215 MTEGYSGSDIAVVVKDALMQPIRKIQ  240 (322)
T ss_dssp             TTTTCCHHHHHHHHHHHTTHHHHHHH
T ss_pred             HcCCCCHHHHHHHHHHHHHHHHHHHh
Confidence               66777777777777777766554

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

Probab=99.30  E-value=4.9e-12  Score=109.58  Aligned_cols=99  Identities=22%  Similarity=0.328  Sum_probs=80.0

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH-
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT-   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~-   81 (147)
                      +++||..||++...  ..++||+|||+|+.||++++|+|||+..|+|++|+.++|..||+.++.........++..++. 
T Consensus       325 ~~~LL~~ld~~~~~--~~v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~~~~~l~~la~~  402 (489)
T 3hu3_A          325 VSQLLTLMDGLKQR--AHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANE  402 (489)
T ss_dssp             HHHHHHHHHHSCTT--SCEEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBCTTCCHHHHHHT
T ss_pred             HHHHHHHhhccccC--CceEEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCcchhhHHHHHHH
Confidence            57899999998776  679999999999999999999999999999999999999999999987654443334555555 


Q ss_pred             --HHhccchHHHHHHHHHHHHHHh
Q 042776           82 --KLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        82 --~l~~~~~~~~al~~~~~~l~~~  103 (147)
                        ++++.+....|-++...++++.
T Consensus       403 t~g~s~~dL~~L~~~A~~~a~r~~  426 (489)
T 3hu3_A          403 THGHVGADLAALCSEAALQAIRKK  426 (489)
T ss_dssp             CTTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             ccCCcHHHHHHHHHHHHHHHHHhc
Confidence              6667666666666666666543

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

Probab=99.28  E-value=7.7e-12  Score=103.54  Aligned_cols=98  Identities=17%  Similarity=0.192  Sum_probs=80.3

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCC-ChHHHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHN-LFPEIDELLT   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~-~~~~i~~l~~   81 (147)
                      +++||..|||+... ..+++||+|||+|+.||++++|  ||+..|+|++|+.++|..|++.++...+.. ...++..++.
T Consensus       171 ~~~ll~~l~~~~~~-~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~l~~la~  247 (355)
T 2qp9_X          171 KTELLVQMNGVGND-SQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGA  247 (355)
T ss_dssp             HHHHHHHHHHCC----CCEEEEEEESCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTSCBCCCHHHHHHHHH
T ss_pred             HHHHHHHhhccccc-CCCeEEEeecCCcccCCHHHHc--ccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCCHHHHHHHHH
Confidence            68899999999653 2679999999999999999999  999999999999999999999999866543 3456666666


Q ss_pred             ---HHhccchHHHHHHHHHHHHHHh
Q 042776           82 ---KLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~~l~~~  103 (147)
                         ++++++....|-++++.++.+.
T Consensus       248 ~t~G~sg~dl~~l~~~A~~~a~~~~  272 (355)
T 2qp9_X          248 MTEGYSGSDIAVVVKDALMQPIRKI  272 (355)
T ss_dssp             HTTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHHHHHHHHHHHHH
Confidence               6777788888888887777654

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

Probab=99.26  E-value=7.6e-12  Score=106.59  Aligned_cols=99  Identities=16%  Similarity=0.212  Sum_probs=82.0

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCC-ChHHHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHN-LFPEIDELLT   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~-~~~~i~~l~~   81 (147)
                      +++||..|||+... ..+++||+|||+|+.|||+++|  ||+..|+|++|+.++|..|++.++...+.. ...++..++.
T Consensus       255 ~~~lL~~l~~~~~~-~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~  331 (444)
T 2zan_A          255 KTEFLVQMQGVGVD-NDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGR  331 (444)
T ss_dssp             HHHHHTTTTCSSCC-CSSCEEEEEESCGGGSCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCEECCHHHHHHHHH
T ss_pred             HHHHHHHHhCcccC-CCCEEEEecCCCccccCHHHHh--hcceEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Confidence            57899999998643 2679999999999999999999  999999999999999999999999765442 3456666666


Q ss_pred             ---HHhccchHHHHHHHHHHHHHHhh
Q 042776           82 ---KLMKSEVAEVALEGLVEFLKRKK  104 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~~l~~~~  104 (147)
                         ++++++....|-++++..+++..
T Consensus       332 ~t~G~sgadl~~l~~~a~~~a~r~~~  357 (444)
T 2zan_A          332 KTDGYSGADISIIVRDALMQPVRKVQ  357 (444)
T ss_dssp             HTTTCCHHHHHHHHHHHHTHHHHHHH
T ss_pred             HcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence               77788888888888887776643

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

Probab=99.26  E-value=1.5e-11  Score=99.18  Aligned_cols=83  Identities=14%  Similarity=0.145  Sum_probs=65.2

Q ss_pred             HHHHHHHhhCCCC---------CCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCCh
Q 042776            3 LSGLLNFIDGLWS---------SCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLF   73 (147)
Q Consensus         3 v~~lL~~lDgl~~---------~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~   73 (147)
                      .+.||+.||+...         ....+++||+|||+++.||+|++||||||+.|+  +|+.++|.+|++.++.... ...
T Consensus       129 ~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~~ld~al~R~~R~d~~i~--~P~~~~r~~Il~~~~~~~~-~~~  205 (293)
T 3t15_A          129 NATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYW--APTREDRIGVCTGIFRTDN-VPA  205 (293)
T ss_dssp             HHHHHHHHHCCC-----------CCCCCCEEEECSSCCC--CHHHHHHHEEEEEE--CCCHHHHHHHHHHHHGGGC-CCH
T ss_pred             HHHHHHHhccccccccccccccccCCCcEEEEecCCcccCCHHHhCCCCCceeEe--CcCHHHHHHHHHHhccCCC-CCH
Confidence            3789999986641         112569999999999999999999999999997  5899999999998886543 336


Q ss_pred             HHHHHHHHHHhccch
Q 042776           74 PEIDELLTKLMKSEV   88 (147)
Q Consensus        74 ~~i~~l~~~l~~~~~   88 (147)
                      ..++.++.++.+.+.
T Consensus       206 ~~l~~~~~~~~~~~l  220 (293)
T 3t15_A          206 EDVVKIVDNFPGQSI  220 (293)
T ss_dssp             HHHHHHHHHSCSCCH
T ss_pred             HHHHHHhCCCCcccH
Confidence            678888888877665

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

Probab=99.13  E-value=5.9e-12  Score=98.73  Aligned_cols=65  Identities=31%  Similarity=0.400  Sum_probs=57.6

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIN   68 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~   68 (147)
                      +++||..||++.+. ...++||+|||+++.||++++|+|||+..|+|++|+.++|..+++.++...
T Consensus       135 ~~~ll~~l~~~~~~-~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~  199 (268)
T 2r62_A          135 LNQLLAEMDGFGSE-NAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGV  199 (268)
T ss_dssp             TTTTTTTTTCSSCS-CSCCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSS
T ss_pred             HHHHHHHhhCcccC-CCCEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcC
Confidence            56788889988654 245899999999999999999999999999999999999999999998654

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

Probab=99.01  E-value=7.2e-10  Score=91.50  Aligned_cols=98  Identities=18%  Similarity=0.250  Sum_probs=73.8

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCC-ChHHHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHN-LFPEIDELLT   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~-~~~~i~~l~~   81 (147)
                      +++||..|||+.......++||+|||+|+.||++++|  ||+..+++++|+.++|..|+..++...... ....+..++.
T Consensus       204 ~~~lL~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~--Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l~~la~  281 (357)
T 3d8b_A          204 KTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQ  281 (357)
T ss_dssp             HHHHHHHHHC----CCCCEEEEEEESCGGGBCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHHHHHHH
T ss_pred             HHHHHHHHhcccccCCCCEEEEEecCChhhCCHHHHh--hCceEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHHHHHHH
Confidence            4689999999875545779999999999999999999  999999999999999999999988654333 2345566655


Q ss_pred             ---HHhccchHHHHHHHHHHHHHH
Q 042776           82 ---KLMKSEVAEVALEGLVEFLKR  102 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~~l~~  102 (147)
                         ++++.+....|-.+....+++
T Consensus       282 ~t~G~s~~dl~~l~~~a~~~~ir~  305 (357)
T 3d8b_A          282 QSDAFSGADMTQLCREASLGPIRS  305 (357)
T ss_dssp             HTTTCCHHHHHHHHHHHHTHHHHH
T ss_pred             HcCCCCHHHHHHHHHHHHHHHHHH
Confidence               556666666666666655543

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

Probab=98.93  E-value=9.5e-11  Score=100.84  Aligned_cols=56  Identities=14%  Similarity=0.093  Sum_probs=0.0

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEe-cCCCCCCCccccCCCeeeeEEeecCCCHH-HHHHHH
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFT-TNHKNRLDPALLRPGRMDMHIHMSYCNPS-GFRILV   61 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~a-TN~p~~LD~Al~RpGRfd~~i~~~~P~~~-~r~~il   61 (147)
                      .+++||++|||+.+.  .++  +++ ||+|+.|||||+||||||+.|+|++|+.. .|.+||
T Consensus       131 vl~~LL~~~dg~~~~--~~v--~a~~TN~~~~ld~aL~rggr~D~~i~i~lP~~~~~~~ei~  188 (444)
T 1g41_A          131 ILDALLPPAKNQWGE--VEN--HDSHSSTRQAFRKKLREGQLDDKEIEIDVSAGVSMGVEIM  188 (444)
T ss_dssp             --------------------------------------------------------------
T ss_pred             HHHHHHHHhhccccc--ccc--ccccccCHHHHHHHHHcCCCcceEEEEcCCCCccchhhhh
Confidence            378999999999775  333  455 99999999999999999999999999988 677765

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

Probab=98.90  E-value=1.9e-09  Score=89.65  Aligned_cols=96  Identities=24%  Similarity=0.268  Sum_probs=68.6

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCC-hHHHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNL-FPEIDELLT   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~-~~~i~~l~~   81 (147)
                      +++||..|||+.......++||+|||+++.||++++|  ||+..|+|++|+.++|..|++.++......+ ...+..++.
T Consensus       235 ~~~ll~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~--R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~~~~la~  312 (389)
T 3vfd_A          235 KTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLAR  312 (389)
T ss_dssp             HHHHHHHHHHHC-----CEEEEEEESCGGGCCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCCCSCHHHHHHHHH
T ss_pred             HHHHHHHhhcccccCCCCEEEEEecCCchhcCHHHHc--CcceEEEcCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence            4688999999876545779999999999999999999  9999999999999999999999987654433 344555554


Q ss_pred             ---HHhccchHHHHHHHHHHHH
Q 042776           82 ---KLMKSEVAEVALEGLVEFL  100 (147)
Q Consensus        82 ---~l~~~~~~~~al~~~~~~l  100 (147)
                         ++.+.+....+-.+....+
T Consensus       313 ~~~g~~~~~l~~L~~~a~~~~~  334 (389)
T 3vfd_A          313 MTDGYSGSDLTALAKDAALGPI  334 (389)
T ss_dssp             HTTTCCHHHHHHHHHHHTTHHH
T ss_pred             HcCCCCHHHHHHHHHHHHHHHH
Confidence               3344344344433333333

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

Probab=98.89  E-value=1.6e-09  Score=85.94  Aligned_cols=98  Identities=21%  Similarity=0.270  Sum_probs=69.9

Q ss_pred             HHHHHHHhhCCCCC-CCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCC-ChHHHHHHH
Q 042776            3 LSGLLNFIDGLWSS-CGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHN-LFPEIDELL   80 (147)
Q Consensus         3 v~~lL~~lDgl~~~-~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~-~~~~i~~l~   80 (147)
                      .++||..+|++... .+.+++||+|||+|+.||++++|  ||+..+++++|+.++|..|++.++...... ....+..++
T Consensus       141 ~~~ll~~l~~~~~~~~~~~v~vi~~tn~~~~l~~~l~~--R~~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~~la  218 (297)
T 3b9p_A          141 KTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLA  218 (297)
T ss_dssp             HHHHHHHHHHCC------CEEEEEEESCGGGBCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHGGGSCCSCHHHHHHHH
T ss_pred             HHHHHHHHhcccccCCCCcEEEEeecCChhhCCHHHHh--hCCeEEEeCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence            45789999998653 22568999999999999999999  999999999999999999999988654332 234455555


Q ss_pred             H---HHhccchHHHHHHHHHHHHHH
Q 042776           81 T---KLMKSEVAEVALEGLVEFLKR  102 (147)
Q Consensus        81 ~---~l~~~~~~~~al~~~~~~l~~  102 (147)
                      .   ++.+++....|-++....+++
T Consensus       219 ~~~~g~~~~~l~~l~~~a~~~a~r~  243 (297)
T 3b9p_A          219 KITDGYSGSDLTALAKDAALEPIRE  243 (297)
T ss_dssp             HHTTTCCHHHHHHHHHHHTTHHHHT
T ss_pred             HHcCCCCHHHHHHHHHHHHHHHHHH
Confidence            5   444444444544444444443

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

Probab=98.18  E-value=2.5e-07  Score=78.59  Aligned_cols=59  Identities=8%  Similarity=0.047  Sum_probs=42.7

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeee--EEeecCCCH--HHHHHHHH
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDM--HIHMSYCNP--SGFRILVS   62 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~--~i~~~~P~~--~~r~~il~   62 (147)
                      ++++..|+......++.++|++|||+|+.+|+|+.||||||+  .+++++|+.  +.|.+|++
T Consensus       174 ~~ll~~l~~~~~~~~~~v~i~attn~~~~ld~a~~r~~rfd~~~~~~v~~p~~~~~~R~~il~  236 (456)
T 2c9o_A          174 PSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQ  236 (456)
T ss_dssp             HHHHHHHHHTTCCTTEEEEEETTTCCEEEEEEETTSCCTTSCSSSSEECCCCSCSEEEEEEEE
T ss_pred             HHHHHHHhhccCCCCCEEEEEcCCCCcccCChhhcCCcccCcceeEecCCCchhHHHHHHHHH
Confidence            346677763222223667777999999999999999999999  778888854  44555544

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

Probab=97.75  E-value=1.2e-05  Score=70.07  Aligned_cols=44  Identities=18%  Similarity=0.194  Sum_probs=40.7

Q ss_pred             CceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776           19 DERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus        19 ~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      ..++||+|||+++.|||+|++  ||+ .|+|+.|+.+++..|+..|+
T Consensus       223 ~~v~iI~ttN~~~~l~~aL~~--R~~-vi~~~~~~~~e~~~Il~~~l  266 (543)
T 3m6a_A          223 SKVLFIATANNLATIPGPLRD--RME-IINIAGYTEIEKLEIVKDHL  266 (543)
T ss_dssp             SSCEEEEECSSTTTSCHHHHH--HEE-EEECCCCCHHHHHHHHHHTH
T ss_pred             cceEEEeccCccccCCHHHHh--hcc-eeeeCCCCHHHHHHHHHHHH
Confidence            457899999999999999999  996 69999999999999999887

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

Probab=97.64  E-value=6e-05  Score=59.44  Aligned_cols=68  Identities=15%  Similarity=0.294  Sum_probs=53.0

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCC-----CCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKN-----RLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEI   76 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~-----~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i   76 (147)
                      ++.|+..|+...    .+++||+|||.+.     .++|+|++  ||+..|+|+.|+.+++..|++.++.........+.
T Consensus       156 ~~~Ll~~l~~~~----~~~~~i~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~~~~~~~~~il~~~l~~~~~~~~~~~  228 (309)
T 3syl_A          156 IEILLQVMENNR----DDLVVILAGYADRMENFFQSNPGFRS--RIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTPEA  228 (309)
T ss_dssp             HHHHHHHHHHCT----TTCEEEEEECHHHHHHHHHHSTTHHH--HEEEEEEECCCCHHHHHHHHHHHHHHTTCEECHHH
T ss_pred             HHHHHHHHhcCC----CCEEEEEeCChHHHHHHHhhCHHHHH--hCCeEEEcCCcCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            467888888642    4588999998664     36899999  99999999999999999999999865544433333

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

Probab=97.47  E-value=0.00018  Score=57.61  Aligned_cols=60  Identities=12%  Similarity=0.131  Sum_probs=48.1

Q ss_pred             ceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCCh-HHHHHHHH
Q 042776           20 ERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLF-PEIDELLT   81 (147)
Q Consensus        20 ~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~-~~i~~l~~   81 (147)
                      .+++|+|||++..++++|++  ||+..|+|+.|+.+++..++..++........ ..+..++.
T Consensus       154 ~~~~i~atn~~~~l~~~L~~--R~~~~i~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~l~~  214 (338)
T 3pfi_A          154 KFTLIGATTRAGMLSNPLRD--RFGMQFRLEFYKDSELALILQKAALKLNKTCEEKAALEIAK  214 (338)
T ss_dssp             CCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHH
T ss_pred             CeEEEEeCCCccccCHHHHh--hcCEEeeCCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence            47899999999999999999  99999999999999999999988764433322 33444443

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

Probab=97.37  E-value=0.0014  Score=52.36  Aligned_cols=47  Identities=19%  Similarity=0.270  Sum_probs=40.1

Q ss_pred             CceEEEEecCCCC-----CCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCC
Q 042776           19 DERIIVFTTNHKN-----RLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGI   67 (147)
Q Consensus        19 ~~vivi~aTN~p~-----~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~   67 (147)
                      ..++||+|+|.++     .|+++|++  ||+..++|+.|+.+++.+|++.++..
T Consensus       149 ~~~~viat~np~~~~~~~~l~~~l~~--Rf~~~i~i~~p~~~~~~~il~~~~~~  200 (331)
T 2r44_A          149 NPFLVLATQNPVEQEGTYPLPEAQVD--RFMMKIHLTYLDKESELEVMRRVSNM  200 (331)
T ss_dssp             SSCEEEEEECTTCCSCCCCCCHHHHT--TSSEEEECCCCCHHHHHHHHHHHHCT
T ss_pred             CCEEEEEecCCCcccCcccCCHHHHh--heeEEEEcCCCCHHHHHHHHHhcccc
Confidence            4577888888443     39999999  99999999999999999999998764

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens}

Probab=97.30  E-value=0.00018  Score=46.93  Aligned_cols=54  Identities=11%  Similarity=-0.065  Sum_probs=42.9

Q ss_pred             cCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH---HHhccchHHHHHHHHHHHHHHh
Q 042776           50 SYCNPSGFRILVSNYLGINDHNLFPEIDELLT---KLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        50 ~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~---~l~~~~~~~~al~~~~~~l~~~  103 (147)
                      |+|+.++|.+||+.|+...+.....++..++.   +|+|++....|.++.+.++...
T Consensus         1 plPd~~~R~~Il~~~l~~~~~~~~~dl~~la~~t~G~SGADi~~l~~eA~~~a~~~~   57 (78)
T 3kw6_A            1 PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRER   57 (78)
T ss_dssp             CCCCHHHHHHHHHHHHTTSEECTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCCccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhC
Confidence            68999999999999998764433334455554   9999999999999999988763

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

Probab=97.19  E-value=0.0018  Score=51.02  Aligned_cols=60  Identities=15%  Similarity=0.146  Sum_probs=48.1

Q ss_pred             ceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChH-HHHHHHH
Q 042776           20 ERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFP-EIDELLT   81 (147)
Q Consensus        20 ~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~-~i~~l~~   81 (147)
                      .+++|+|||++..++++|++  ||+..+.|+.|+.+++..++..++......... .+..++.
T Consensus       138 ~~~~i~~t~~~~~~~~~l~~--R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~  198 (324)
T 1hqc_A          138 RFTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGR  198 (324)
T ss_dssp             CCEEEEEESCCSSCSCSTTT--TCSCEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHH
T ss_pred             CEEEEEeCCCcccCCHHHHh--cccEEEecCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence            47899999999999999998  999999999999999999999988654433333 3344433

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

Probab=97.16  E-value=0.0012  Score=56.11  Aligned_cols=46  Identities=17%  Similarity=0.080  Sum_probs=41.5

Q ss_pred             CceEEEEecCCCC-----CCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCC
Q 042776           19 DERIIVFTTNHKN-----RLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGI   67 (147)
Q Consensus        19 ~~vivi~aTN~p~-----~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~   67 (147)
                      ..+.||+|||.++     .+|++|.|  ||.. |.|+.|+.+++..|++.++..
T Consensus       290 g~v~vI~at~~~e~~~~~~~~~al~~--Rf~~-i~v~~p~~e~~~~iL~~~~~~  340 (468)
T 3pxg_A          290 GELQCIGATTLDEYRKYIEKDAALER--RFQP-IQVDQPSVDESIQILQGLRDR  340 (468)
T ss_dssp             SSCEEEEECCTTTTHHHHTTCSHHHH--SEEE-EECCCCCHHHHHHHHHHTTTT
T ss_pred             CCEEEEecCCHHHHHHHhhcCHHHHH--hCcc-ceeCCCCHHHHHHHHHHHHHH
Confidence            4688999999998     79999999  9985 999999999999999988754

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

Probab=97.09  E-value=0.0017  Score=47.33  Aligned_cols=56  Identities=7%  Similarity=0.043  Sum_probs=46.2

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhC
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      +.|+..++...    .++.+|++||.+..+++++.+  ||. .++|+.|+.++...++..++.
T Consensus       120 ~~l~~~l~~~~----~~~~~i~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~  175 (226)
T 2chg_A          120 AALRRTMEMYS----KSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEAMKKRLLEICE  175 (226)
T ss_dssp             HHHHHHHHHTT----TTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC----CCCeEEEEeCChhhcCHHHHH--hCc-eeecCCCCHHHHHHHHHHHHH
Confidence            44566666532    457889999999999999999  888 899999999999999998874

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

Probab=97.09  E-value=0.00051  Score=53.66  Aligned_cols=59  Identities=17%  Similarity=0.330  Sum_probs=47.4

Q ss_pred             HHHHHHHhhCCCCC------CCCceEEEEe----cCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHH
Q 042776            3 LSGLLNFIDGLWSS------CGDERIIVFT----TNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSN   63 (147)
Q Consensus         3 v~~lL~~lDgl~~~------~~~~vivi~a----TN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~   63 (147)
                      .+.||..|++....      +...+++|+|    |+.|..++|+|++  ||+..|+|+.|+.+++..|++.
T Consensus       145 ~~~Ll~~le~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~--R~~~~i~~~~~~~~~~~~il~~  213 (310)
T 1ofh_A          145 QRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILTE  213 (310)
T ss_dssp             HHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHS
T ss_pred             HHHHHHHhcCCeEecccccccCCcEEEEEcCCcccCCcccCCHHHHh--hCCceEEcCCcCHHHHHHHHHh
Confidence            46788888875210      1145778888    6789999999998  9999999999999999999984

>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=97.03  E-value=0.0038  Score=45.78  Aligned_cols=72  Identities=14%  Similarity=0.197  Sum_probs=52.7

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCC-hHHHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNL-FPEIDELLT   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~-~~~i~~l~~   81 (147)
                      ++.|+..++...    .++++|++||++..+++++++  |+ ..|+|+.|+.++...++..++....... ...+..++.
T Consensus       143 ~~~l~~~l~~~~----~~~~~i~~t~~~~~~~~~l~~--r~-~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~  215 (250)
T 1njg_A          143 FNALLKTLEEPP----EHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLAR  215 (250)
T ss_dssp             HHHHHHHHHSCC----TTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHH
T ss_pred             HHHHHHHHhcCC----CceEEEEEeCChHhCCHHHHH--Hh-hhccCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence            456777776542    458899999999999999988  75 6899999999999999998885433332 233444443

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

Probab=96.98  E-value=0.0027  Score=51.06  Aligned_cols=51  Identities=10%  Similarity=0.092  Sum_probs=38.8

Q ss_pred             CCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHH-HHHHHH
Q 042776           28 NHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPE-IDELLT   81 (147)
Q Consensus        28 N~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~-i~~l~~   81 (147)
                      |.+..|+++|++  ||.. |+|+.|+.+++..|++.++.........+ +..++.
T Consensus       238 ~~~~~l~~~l~s--R~~~-i~~~~~~~~e~~~il~~~~~~~~~~~~~~~l~~l~~  289 (368)
T 3uk6_A          238 QSPHGIPIDLLD--RLLI-VSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTR  289 (368)
T ss_dssp             EEETTCCHHHHT--TEEE-EEECCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHH
T ss_pred             CCcccCCHHHHh--hccE-EEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            358899999999  9987 89999999999999998876544433333 344433

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens}

Probab=96.94  E-value=0.00039  Score=46.60  Aligned_cols=56  Identities=20%  Similarity=0.065  Sum_probs=44.3

Q ss_pred             eecCCCHHHHHHHHHHHhCCCCC---CChHHHHHHHHHHhccchHHHHHHHHHHHHHHh
Q 042776           48 HMSYCNPSGFRILVSNYLGINDH---NLFPEIDELLTKLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        48 ~~~~P~~~~r~~il~~~l~~~~~---~~~~~i~~l~~~l~~~~~~~~al~~~~~~l~~~  103 (147)
                      +-+.||.++|.+||+.++...+.   .+...++..+.+|+|+|....|-++.+.+++..
T Consensus         7 ~~~~Pd~~~R~~IL~~~l~~~~l~~dvdl~~LA~~T~G~SGADL~~l~~eAa~~alr~~   65 (86)
T 2krk_A            7 HHSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRER   65 (86)
T ss_dssp             CCCCCCHHHHHHHHHHHTTTSEECTTCCCHHHHHTCSSCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHc
Confidence            34689999999999999986543   334445555559999999999999999988764

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

Probab=96.94  E-value=0.0028  Score=56.74  Aligned_cols=46  Identities=17%  Similarity=0.090  Sum_probs=41.2

Q ss_pred             CceEEEEecCCCC-----CCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCC
Q 042776           19 DERIIVFTTNHKN-----RLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGI   67 (147)
Q Consensus        19 ~~vivi~aTN~p~-----~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~   67 (147)
                      ..+.+|+|||.++     .+|||++|  ||. .|+|+.|+.+++..|++.+...
T Consensus       290 ~~v~~I~at~~~~~~~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~il~~~~~~  340 (758)
T 3pxi_A          290 GELQCIGATTLDEYRKYIEKDAALER--RFQ-PIQVDQPSVDESIQILQGLRDR  340 (758)
T ss_dssp             SSCEEEEECCTTTTHHHHTTCSHHHH--SEE-EEECCCCCHHHHHHHHHHTTTT
T ss_pred             CCEEEEeCCChHHHHHHhhccHHHHh--hCc-EEEeCCCCHHHHHHHHHHHHHH
Confidence            5688999999998     79999999  995 5999999999999999977654

>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=96.90  E-value=0.0019  Score=50.26  Aligned_cols=73  Identities=16%  Similarity=0.149  Sum_probs=46.6

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCc-cccCCCeeeeEEeecCCCH-HHHHHHHHHHhCCCCCCChHHHHHHHH
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDP-ALLRPGRMDMHIHMSYCNP-SGFRILVSNYLGINDHNLFPEIDELLT   81 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~-Al~RpGRfd~~i~~~~P~~-~~r~~il~~~l~~~~~~~~~~i~~l~~   81 (147)
                      +.|+..+++.... +..++||+|||+|+.||+ ++.+  ||+..|+++.++. +....++.....    .....+..++.
T Consensus       152 ~~L~~~~~~~~~~-~~~~~ii~ttn~~~~l~~~~l~~--rf~~~i~~p~l~~r~~i~~i~~~~~~----~~~~~~~~l~~  224 (272)
T 1d2n_A          152 QALLVLLKKAPPQ-GRKLLIIGTTSRKDVLQEMEMLN--AFSTTIHVPNIATGEQLLEALELLGN----FKDKERTTIAQ  224 (272)
T ss_dssp             HHHHHHTTCCCST-TCEEEEEEEESCHHHHHHTTCTT--TSSEEEECCCEEEHHHHHHHHHHHTC----SCHHHHHHHHH
T ss_pred             HHHHHHhcCccCC-CCCEEEEEecCChhhcchhhhhc--ccceEEcCCCccHHHHHHHHHHhcCC----CCHHHHHHHHH
Confidence            3455566666433 356889999999999999 4554  9999998875544 555555544321    23445566655


Q ss_pred             HH
Q 042776           82 KL   83 (147)
Q Consensus        82 ~l   83 (147)
                      ..
T Consensus       225 ~~  226 (272)
T 1d2n_A          225 QV  226 (272)
T ss_dssp             HH
T ss_pred             Hh
Confidence            43

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

Probab=96.84  E-value=0.00076  Score=52.96  Aligned_cols=62  Identities=19%  Similarity=0.310  Sum_probs=48.1

Q ss_pred             HHHHHHHhhCCCCCCC-------CceEEEEecCC--------------------------CCCCCccccCCCeeeeEEee
Q 042776            3 LSGLLNFIDGLWSSCG-------DERIIVFTTNH--------------------------KNRLDPALLRPGRMDMHIHM   49 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~-------~~vivi~aTN~--------------------------p~~LD~Al~RpGRfd~~i~~   49 (147)
                      .+.|+..|+.-.-..+       .++++|+|||.                          ...++|+|+.  ||+..+.|
T Consensus       136 ~~~Ll~~le~~~~~~~~~~~~~~~~~iiI~ttn~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~--R~~~~~~~  213 (311)
T 4fcw_A          136 FNILLQMLDDGRLTDSHGRTVDFRNTVIIMTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVF  213 (311)
T ss_dssp             HHHHHHHHHHSEEECTTSCEEECTTEEEEEEESTTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHHHT--TCSEEEEC
T ss_pred             HHHHHHHHhcCEEEcCCCCEEECCCcEEEEecccCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHHHh--cCCeEEEe
Confidence            3567777765321100       25779999998                          5578999997  99999999


Q ss_pred             cCCCHHHHHHHHHHHhC
Q 042776           50 SYCNPSGFRILVSNYLG   66 (147)
Q Consensus        50 ~~P~~~~r~~il~~~l~   66 (147)
                      ..|+.+.+..|++.++.
T Consensus       214 ~p~~~~~~~~i~~~~l~  230 (311)
T 4fcw_A          214 RPLTKEQIRQIVEIQMS  230 (311)
T ss_dssp             CCCCHHHHHHHHHHHTH
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            99999999999998874

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

Probab=96.72  E-value=0.0038  Score=49.79  Aligned_cols=46  Identities=13%  Similarity=0.094  Sum_probs=39.6

Q ss_pred             CceEEEEecCCC---CCCCccccCCCeeee-EEeecCCCHHHHHHHHHHHhC
Q 042776           19 DERIIVFTTNHK---NRLDPALLRPGRMDM-HIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus        19 ~~vivi~aTN~p---~~LD~Al~RpGRfd~-~i~~~~P~~~~r~~il~~~l~   66 (147)
                      .++.+|++||.+   +.+++++.+  ||.. .|+|+.|+.+++..|+..++.
T Consensus       166 ~~~~~I~~t~~~~~~~~l~~~l~~--r~~~~~i~l~~l~~~~~~~il~~~~~  215 (387)
T 2v1u_A          166 VWVSLVGITNSLGFVENLEPRVKS--SLGEVELVFPPYTAPQLRDILETRAE  215 (387)
T ss_dssp             --CEEEEECSCSTTSSSSCHHHHT--TTTSEECCBCCCCHHHHHHHHHHHHH
T ss_pred             ceEEEEEEECCCchHhhhCHHHHh--cCCCeEEeeCCCCHHHHHHHHHHHHH
Confidence            568899999988   789999998  9875 899999999999999998764

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

Probab=96.59  E-value=0.0013  Score=52.36  Aligned_cols=54  Identities=15%  Similarity=0.145  Sum_probs=42.4

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHH
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNY   64 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~   64 (147)
                      +.|+..++...    ..+.+|+|||.+..++++|++  ||. .|+|+.|+.+++..|+..+
T Consensus       124 ~~L~~~le~~~----~~~~iI~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~e~~~il~~~  177 (324)
T 3u61_B          124 RHLRSFMEAYS----SNCSIIITANNIDGIIKPLQS--RCR-VITFGQPTDEDKIEMMKQM  177 (324)
T ss_dssp             HHHHHHHHHHG----GGCEEEEEESSGGGSCTTHHH--HSE-EEECCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCC----CCcEEEEEeCCccccCHHHHh--hCc-EEEeCCCCHHHHHHHHHHH
Confidence            45666666543    347788999999999999999  996 6999999999877765544

>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=96.59  E-value=0.0024  Score=50.80  Aligned_cols=43  Identities=16%  Similarity=0.210  Sum_probs=36.9

Q ss_pred             ceEEEEecCCCC-CCCccccCCCeeeeEEeecCC-CHHHHHHHHHHH
Q 042776           20 ERIIVFTTNHKN-RLDPALLRPGRMDMHIHMSYC-NPSGFRILVSNY   64 (147)
Q Consensus        20 ~vivi~aTN~p~-~LD~Al~RpGRfd~~i~~~~P-~~~~r~~il~~~   64 (147)
                      .++||+|||..+ .|+++|++  ||+..++++.| +.+.+..|+..+
T Consensus       187 ~~~li~~~n~~~~~l~~~L~~--R~~~~~~l~~~~~~~~~~~il~~~  231 (350)
T 1g8p_A          187 RFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPRDVETRVEVIRRR  231 (350)
T ss_dssp             CEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCCSHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCCCCHHHHh--hcceEEEcCCCCcHHHHHHHHHHH
Confidence            588999999744 89999999  99999999998 677787888764

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

Probab=96.57  E-value=0.0022  Score=56.43  Aligned_cols=61  Identities=18%  Similarity=0.244  Sum_probs=46.0

Q ss_pred             HHHHHHhhC---------CCCCCCCceEEEEecCCCC-------------CCCccccCCCeee-eEEeecCCCHHHHHHH
Q 042776            4 SGLLNFIDG---------LWSSCGDERIIVFTTNHKN-------------RLDPALLRPGRMD-MHIHMSYCNPSGFRIL   60 (147)
Q Consensus         4 ~~lL~~lDg---------l~~~~~~~vivi~aTN~p~-------------~LD~Al~RpGRfd-~~i~~~~P~~~~r~~i   60 (147)
                      +.|+..|+.         .....+..+.||+|||.+.             .|++||++  ||| ..+..+.|+.+ ...|
T Consensus       409 ~~Ll~~le~~~i~i~~~g~~~~~~~~~~vIaatNp~~G~~~~~~~~~~ni~l~~aLl~--RFDl~~~~~~~~~~e-~~~i  485 (595)
T 3f9v_A          409 VAIHEAMEQQTVSIAKAGIVAKLNARAAVIAAGNPKFGRYISERPVSDNINLPPTILS--RFDLIFILKDQPGEQ-DREL  485 (595)
T ss_dssp             HHHHHHHHSSSEEEESSSSEEEECCCCEEEEEECCTTCCSCTTSCSCTTTCSCSSSGG--GCSCCEEECCTTHHH-HHHH
T ss_pred             hhhHHHHhCCEEEEecCCcEEEecCceEEEEEcCCcCCccCcccCchhccCCCHHHHh--hCeEEEEeCCCCCHH-HHHH
Confidence            556777763         2211124577999999987             99999999  999 56677899988 8889


Q ss_pred             HHHHhCC
Q 042776           61 VSNYLGI   67 (147)
Q Consensus        61 l~~~l~~   67 (147)
                      +++++..
T Consensus       486 ~~~il~~  492 (595)
T 3f9v_A          486 ANYILDV  492 (595)
T ss_dssp             HHHHHTT
T ss_pred             HHHHHHH
Confidence            8888764

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.53  E-value=0.0091  Score=47.34  Aligned_cols=70  Identities=10%  Similarity=0.017  Sum_probs=50.7

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHH-HHHHH
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPE-IDELL   80 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~-i~~l~   80 (147)
                      +.|+..|+...    ....+|++||+++.++|++++  |+. .|.|+.|+.++...++..++.........+ +..++
T Consensus       151 ~~Ll~~le~~~----~~~~~il~~~~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~  221 (353)
T 1sxj_D          151 SALRRTMETYS----GVTRFCLICNYVTRIIDPLAS--QCS-KFRFKALDASNAIDRLRFISEQENVKCDDGVLERIL  221 (353)
T ss_dssp             HHHHHHHHHTT----TTEEEEEEESCGGGSCHHHHH--HSE-EEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHH
T ss_pred             HHHHHHHHhcC----CCceEEEEeCchhhCcchhhc--cCc-eEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Confidence            45666666543    235677789999999999999  887 899999999999999998875444333333 34443

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

Probab=96.51  E-value=0.00035  Score=49.85  Aligned_cols=40  Identities=20%  Similarity=0.147  Sum_probs=35.1

Q ss_pred             CceEEEEecCCCC-----CCCccccCCCeeeeEEeecCCCHHHHHHHH
Q 042776           19 DERIIVFTTNHKN-----RLDPALLRPGRMDMHIHMSYCNPSGFRILV   61 (147)
Q Consensus        19 ~~vivi~aTN~p~-----~LD~Al~RpGRfd~~i~~~~P~~~~r~~il   61 (147)
                      ..+.+|++||.+.     .+|+++++  ||+ .|+|+.|+.+++.+|+
T Consensus       150 ~~~~~i~~~~~~~~~~~~~~~~~l~~--r~~-~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          150 GELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             TSCCEEEEECHHHHHHHTTTCHHHHT--TEE-EEECCCCCHHHHHTTC
T ss_pred             CCeEEEEeCCHHHHHHHHhcCHHHHH--Hhc-eeecCCCCHHHHHHHh
Confidence            4577899999887     79999999  999 6999999999998875

>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=96.42  E-value=0.0051  Score=48.97  Aligned_cols=75  Identities=17%  Similarity=0.286  Sum_probs=51.2

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCC---CCCccccCCCeee--eEEeecCCCHHHHHHHHHHHhCCCCCCChHH-HH
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKN---RLDPALLRPGRMD--MHIHMSYCNPSGFRILVSNYLGINDHNLFPE-ID   77 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~---~LD~Al~RpGRfd--~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~-i~   77 (147)
                      ..|+..++.+...  +.++||++++.|.   .++++|++  ||+  ..++|+. +.+++..|++.++.........+ +.
T Consensus       118 ~~l~~~l~~~~~~--~~~iii~~~~~~~~l~~l~~~L~s--R~~~~~~i~l~~-~~~e~~~il~~~~~~~~~~l~~~~l~  192 (324)
T 1l8q_A          118 IEFFHIFNTLYLL--EKQIILASDRHPQKLDGVSDRLVS--RFEGGILVEIEL-DNKTRFKIIKEKLKEFNLELRKEVID  192 (324)
T ss_dssp             HHHHHHHHHHHHT--TCEEEEEESSCGGGCTTSCHHHHH--HHHTSEEEECCC-CHHHHHHHHHHHHHHTTCCCCHHHHH
T ss_pred             HHHHHHHHHHHHC--CCeEEEEecCChHHHHHhhhHhhh--cccCceEEEeCC-CHHHHHHHHHHHHHhcCCCCCHHHHH
Confidence            3455555554433  4567777777776   68999998  997  7788988 99999999998875443333333 44


Q ss_pred             HHHHHH
Q 042776           78 ELLTKL   83 (147)
Q Consensus        78 ~l~~~l   83 (147)
                      .++...
T Consensus       193 ~l~~~~  198 (324)
T 1l8q_A          193 YLLENT  198 (324)
T ss_dssp             HHHHHC
T ss_pred             HHHHhC
Confidence            444433

>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=96.40  E-value=0.016  Score=46.43  Aligned_cols=46  Identities=11%  Similarity=0.332  Sum_probs=40.7

Q ss_pred             CceEEEEecCCC---CCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhC
Q 042776           19 DERIIVFTTNHK---NRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus        19 ~~vivi~aTN~p---~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      .++.||+|||.+   +.+++++++  ||...|+|+.|+.++...|+..++.
T Consensus       163 ~~~~iI~~t~~~~~~~~l~~~l~s--r~~~~i~l~~l~~~~~~~il~~~~~  211 (384)
T 2qby_B          163 ANISVIMISNDINVRDYMEPRVLS--SLGPSVIFKPYDAEQLKFILSKYAE  211 (384)
T ss_dssp             SCEEEEEECSSTTTTTTSCHHHHH--TCCCEEEECCCCHHHHHHHHHHHHH
T ss_pred             cceEEEEEECCCchHhhhCHHHHh--cCCCeEEECCCCHHHHHHHHHHHHH
Confidence            348899999988   789999998  9888999999999999999998764

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

Probab=96.33  E-value=0.0045  Score=55.39  Aligned_cols=62  Identities=18%  Similarity=0.202  Sum_probs=45.7

Q ss_pred             HHHHHHHhhCCCCC-------CCCceEEEEecCCCCC------------CCccccCCCeeeeEEeecCCCHHHHHHHHHH
Q 042776            3 LSGLLNFIDGLWSS-------CGDERIIVFTTNHKNR------------LDPALLRPGRMDMHIHMSYCNPSGFRILVSN   63 (147)
Q Consensus         3 v~~lL~~lDgl~~~-------~~~~vivi~aTN~p~~------------LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~   63 (147)
                      .+.||..||.-.-.       .-.+++||+|||.+..            +.|+|+.  |||..|.|+.|+.+.+..|+..
T Consensus       596 ~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~~~~~~~~~~~~~f~p~l~~--Rl~~~i~~~~l~~~~~~~i~~~  673 (758)
T 3pxi_A          596 FNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGASEKDKVMGELKRAFRPEFIN--RIDEIIVFHSLEKKHLTEIVSL  673 (758)
T ss_dssp             HHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTTCCHHHHHHHHHHSCHHHHT--TSSEEEECC--CHHHHHHHHHH
T ss_pred             HHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChhhHHHHHHHHHhhCCHHHHh--hCCeEEecCCCCHHHHHHHHHH
Confidence            46678888752210       0135789999997765            7888887  9999999999999999999988


Q ss_pred             HhC
Q 042776           64 YLG   66 (147)
Q Consensus        64 ~l~   66 (147)
                      ++.
T Consensus       674 ~l~  676 (758)
T 3pxi_A          674 MSD  676 (758)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            764

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=96.29  E-value=0.0078  Score=46.88  Aligned_cols=59  Identities=7%  Similarity=0.093  Sum_probs=45.9

Q ss_pred             CceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCCh-HHHHHHH
Q 042776           19 DERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLF-PEIDELL   80 (147)
Q Consensus        19 ~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~-~~i~~l~   80 (147)
                      ..+++|++||.+..+++++.+  |+. .+.|+.|+.+++..++..++........ ..+..++
T Consensus       131 ~~~~~i~~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~  190 (319)
T 2chq_A          131 KSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALI  190 (319)
T ss_dssp             SSEEEEEEESCGGGSCHHHHT--TCE-EEECCCCCHHHHHHHHHHHHHTTCCCBCHHHHHHHH
T ss_pred             CCCeEEEEeCChhhcchHHHh--hCe-EEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            458889999999999999998  876 8999999999999999988765443333 3344443

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

Probab=96.29  E-value=0.012  Score=52.32  Aligned_cols=54  Identities=22%  Similarity=0.202  Sum_probs=42.4

Q ss_pred             HHHhhCCCCCCCCceEEEEecCCC-----CCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776            7 LNFIDGLWSSCGDERIIVFTTNHK-----NRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus         7 L~~lDgl~~~~~~~vivi~aTN~p-----~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      .+.+..+-..  ..+.+|+|||.+     ..+||+|.|  ||+ .|.|+.|+.+++..|++.+.
T Consensus       304 ~~~L~~~l~~--~~~~~I~at~~~~~~~~~~~d~aL~~--Rf~-~i~v~~p~~~e~~~il~~l~  362 (758)
T 1r6b_X          304 ANLIKPLLSS--GKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLK  362 (758)
T ss_dssp             HHHHSSCSSS--CCCEEEEEECHHHHHCCCCCTTSSGG--GEE-EEECCCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhC--CCeEEEEEeCchHHhhhhhcCHHHHh--Cce-EEEcCCCCHHHHHHHHHHHH
Confidence            3444444444  567889999965     368999999  999 69999999999999998655

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

Probab=96.24  E-value=0.0039  Score=63.38  Aligned_cols=44  Identities=14%  Similarity=0.116  Sum_probs=39.8

Q ss_pred             ceEEEEecCCC-----CCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhC
Q 042776           20 ERIIVFTTNHK-----NRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus        20 ~vivi~aTN~p-----~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      ++.+|||||+|     ..|||+++|  || ..|+++.|+.+++..|+..++.
T Consensus      1384 ~i~lIaA~Npp~~gGR~~l~~rllR--rf-~vi~i~~P~~~~l~~I~~~il~ 1432 (2695)
T 4akg_A         1384 RIHIVGACNPPTDPGRIPMSERFTR--HA-AILYLGYPSGKSLSQIYEIYYK 1432 (2695)
T ss_dssp             SEEEEEEECCTTSTTCCCCCHHHHT--TE-EEEECCCCTTTHHHHHHHHHHH
T ss_pred             CEEEEEecCCCccCCCccCChhhhh--ee-eEEEeCCCCHHHHHHHHHHHHH
Confidence            47899999999     489999999  99 8899999999999999987763

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

Probab=96.03  E-value=0.0055  Score=54.61  Aligned_cols=62  Identities=21%  Similarity=0.273  Sum_probs=48.0

Q ss_pred             HHHHHHHhhCCCC--CCC-----CceEEEEecCCCC-------------------------CCCccccCCCeeeeEEeec
Q 042776            3 LSGLLNFIDGLWS--SCG-----DERIIVFTTNHKN-------------------------RLDPALLRPGRMDMHIHMS   50 (147)
Q Consensus         3 v~~lL~~lDgl~~--~~~-----~~vivi~aTN~p~-------------------------~LD~Al~RpGRfd~~i~~~   50 (147)
                      .+.||..||.-.-  ..+     .+++||+|||.+.                         .++|+|+.  |||..|.|+
T Consensus       574 ~~~Ll~~le~~~~~~~~g~~~~~~~~~iI~tsN~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~  651 (758)
T 1r6b_X          574 FNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFD  651 (758)
T ss_dssp             HHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHHHT--TCSEEEECC
T ss_pred             HHHHHHHhcCcEEEcCCCCEEecCCeEEEEecCcchhhhhhcccCccccchHHHHHHHHHHhcCHHHHh--hCCcceeeC
Confidence            4677888874210  000     3478999999865                         67899998  999999999


Q ss_pred             CCCHHHHHHHHHHHhC
Q 042776           51 YCNPSGFRILVSNYLG   66 (147)
Q Consensus        51 ~P~~~~r~~il~~~l~   66 (147)
                      .|+.+.+..|+..++.
T Consensus       652 ~l~~~~~~~i~~~~l~  667 (758)
T 1r6b_X          652 HLSTDVIHQVVDKFIV  667 (758)
T ss_dssp             CCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999999998874

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=95.89  E-value=0.029  Score=44.71  Aligned_cols=58  Identities=16%  Similarity=0.268  Sum_probs=47.2

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGI   67 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~   67 (147)
                      .+.|+..++...    ..+++|++||.+..++++++.  |+ ..+.|+.|+.++...++..++..
T Consensus       136 ~~~Ll~~le~~~----~~~~~Il~~~~~~~l~~~l~s--r~-~~i~~~~l~~~~~~~~l~~~~~~  193 (373)
T 1jr3_A          136 FNALLKTLEEPP----EHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNE  193 (373)
T ss_dssp             HHHHHHHHHSCC----SSEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCC----CceEEEEEeCChHhCcHHHHh--he-eEeeCCCCCHHHHHHHHHHHHHH
Confidence            456777777542    458888999999999999988  76 78999999999999999988743

>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=95.88  E-value=0.0052  Score=51.91  Aligned_cols=59  Identities=12%  Similarity=0.273  Sum_probs=43.8

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCC---CCccccCCCeee--eEEeecCCCHHHHHHHHHHHhC
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNR---LDPALLRPGRMD--MHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~---LD~Al~RpGRfd--~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      ..|+..++.+...  +..+||++.+.|..   ++++|++  ||+  ..+.++.|+.+++..|+..++.
T Consensus       214 ~~l~~~l~~l~~~--~~~iIitt~~~~~~l~~l~~~L~s--R~~~g~~i~l~~p~~e~r~~iL~~~~~  277 (440)
T 2z4s_A          214 TELFHTFNELHDS--GKQIVICSDREPQKLSEFQDRLVS--RFQMGLVAKLEPPDEETRKSIARKMLE  277 (440)
T ss_dssp             HHHHHHHHHHHTT--TCEEEEEESSCGGGCSSCCHHHHH--HHHSSBCCBCCCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHC--CCeEEEEECCCHHHHHHHHHHHHh--hccCCeEEEeCCCCHHHHHHHHHHHHH
Confidence            3456666655443  34555555555665   8899999  997  8899999999999999998874

>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=95.83  E-value=0.013  Score=46.71  Aligned_cols=57  Identities=7%  Similarity=0.087  Sum_probs=46.7

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCC
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGI   67 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~   67 (147)
                      +.|+..|....    .+..+|++||.++.+.|++..  |+ ..+.|+.|+.++...++..++..
T Consensus       152 ~~L~~~le~~~----~~~~~Il~t~~~~~l~~~l~s--R~-~~~~~~~~~~~~~~~~l~~~~~~  208 (354)
T 1sxj_E          152 AALRRTMEKYS----KNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPSDSEISTILSDVVTN  208 (354)
T ss_dssp             HHHHHHHHHST----TTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhc----CCCEEEEEeCCHHHHHHHHHh--hc-eEEecCCcCHHHHHHHHHHHHHH
Confidence            55666676543    347788999999999999998  88 88999999999999999887643

>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=95.82  E-value=0.017  Score=45.06  Aligned_cols=59  Identities=5%  Similarity=0.011  Sum_probs=46.8

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCC
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIND   69 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~   69 (147)
                      +.|+..|+...    .++.+|++||.++.+++++.+  |+. .+.|+.|+.++...++..++....
T Consensus       128 ~~L~~~le~~~----~~~~~i~~~~~~~~l~~~l~s--r~~-~~~~~~l~~~~~~~~l~~~~~~~~  186 (327)
T 1iqp_A          128 QALRRTMEMFS----SNVRFILSCNYSSKIIEPIQS--RCA-IFRFRPLRDEDIAKRLRYIAENEG  186 (327)
T ss_dssp             HHHHHHHHHTT----TTEEEEEEESCGGGSCHHHHH--TEE-EEECCCCCHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHhcC----CCCeEEEEeCCccccCHHHHh--hCc-EEEecCCCHHHHHHHHHHHHHhcC
Confidence            45666666532    447788899999999999988  887 789999999999999988875443

>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=95.79  E-value=0.022  Score=44.28  Aligned_cols=56  Identities=11%  Similarity=0.102  Sum_probs=43.9

Q ss_pred             HHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCC
Q 042776            5 GLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGI   67 (147)
Q Consensus         5 ~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~   67 (147)
                      .|+..++...    .++.+|++||.+..+++++..  |+. .+.|+.|+.++...++..++..
T Consensus       126 ~L~~~le~~~----~~~~~il~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~~~~~l~~~~~~  181 (323)
T 1sxj_B          126 ALRRTMELYS----NSTRFAFACNQSNKIIEPLQS--QCA-ILRYSKLSDEDVLKRLLQIIKL  181 (323)
T ss_dssp             TTHHHHHHTT----TTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhccC----CCceEEEEeCChhhchhHHHh--hce-EEeecCCCHHHHHHHHHHHHHH
Confidence            3455555422    457788899999999999988  665 8999999999999999887643

>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=95.77  E-value=0.0071  Score=44.90  Aligned_cols=74  Identities=12%  Similarity=0.123  Sum_probs=47.8

Q ss_pred             HHHHHHhhCCCCCCCCce-EEEEecCCCC---CCCccccCCCeee--eEEeecCCCHHHHHHHHHHHhCCCCCCChHH-H
Q 042776            4 SGLLNFIDGLWSSCGDER-IIVFTTNHKN---RLDPALLRPGRMD--MHIHMSYCNPSGFRILVSNYLGINDHNLFPE-I   76 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~v-ivi~aTN~p~---~LD~Al~RpGRfd--~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~-i   76 (147)
                      ..|+..++.+...  ..+ +|+.+++.+.   .+++++.+  ||.  ..|+|+.|+.+++..++..++.........+ +
T Consensus       124 ~~l~~~l~~~~~~--~~~~ii~~~~~~~~~~~~~~~~l~~--r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~  199 (242)
T 3bos_A          124 EAIFDLYNRVAEQ--KRGSLIVSASASPMEAGFVLPDLVS--RMHWGLTYQLQPMMDDEKLAALQRRAAMRGLQLPEDVG  199 (242)
T ss_dssp             HHHHHHHHHHHHH--CSCEEEEEESSCTTTTTCCCHHHHH--HHHHSEEEECCCCCGGGHHHHHHHHHHHTTCCCCHHHH
T ss_pred             HHHHHHHHHHHHc--CCCeEEEEcCCCHHHHHHhhhhhhh--HhhcCceEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            3455666655433  233 4555554554   56788988  886  9999999999999999998875443333333 3


Q ss_pred             HHHHH
Q 042776           77 DELLT   81 (147)
Q Consensus        77 ~~l~~   81 (147)
                      ..++.
T Consensus       200 ~~l~~  204 (242)
T 3bos_A          200 RFLLN  204 (242)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            44433

>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=95.70  E-value=0.054  Score=42.88  Aligned_cols=59  Identities=15%  Similarity=0.120  Sum_probs=44.7

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCC---CCCCccccCCCeee-eEEeecCCCHHHHHHHHHHHhC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHK---NRLDPALLRPGRMD-MHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p---~~LD~Al~RpGRfd-~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      +..|+..++.+.   +.++.+|++||.+   ..+++++.+  ||. +.|+|+.++.++...++..++.
T Consensus       149 l~~l~~~~~~~~---~~~~~~I~~~~~~~~~~~~~~~~~~--r~~~~~i~l~~l~~~~~~~il~~~~~  211 (386)
T 2qby_A          149 LYKLSRINSEVN---KSKISFIGITNDVKFVDLLDPRVKS--SLSEEEIIFPPYNAEELEDILTKRAQ  211 (386)
T ss_dssp             HHHHHHHHHSCC---C--EEEEEEESCGGGGGGCTTHHHH--TTTTEEEEECCCCHHHHHHHHHHHHH
T ss_pred             HHHHhhchhhcC---CCeEEEEEEECCCChHhhhCHHHhc--cCCCeeEEeCCCCHHHHHHHHHHHHH
Confidence            345666676652   2568899999987   578899888  775 5899999999999999988663

>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=95.66  E-value=0.0019  Score=54.04  Aligned_cols=40  Identities=20%  Similarity=0.352  Sum_probs=33.0

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecC
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSY   51 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~   51 (147)
                      +.+.+.+||.       +.|+++||||+.+ ++++||||+|..+++..
T Consensus       245 ~~l~~~ldG~-------v~v~~~tn~~~~l-~alf~pg~ld~~~~~l~  284 (377)
T 1svm_A          245 DNLRDYLDGS-------VKVNLEKKHLNKR-TQIFPPGIVTMNEYSVP  284 (377)
T ss_dssp             HTTHHHHHCS-------SCEEECCSSSCCE-EECCCCEEEEECSCCCC
T ss_pred             HHHHHHhcCC-------CeEeeccCchhhH-HHhhcCcccChhHHhhc
Confidence            4566777763       4578899999999 89999999999988855

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

Probab=95.62  E-value=0.027  Score=48.73  Aligned_cols=60  Identities=22%  Similarity=0.259  Sum_probs=42.1

Q ss_pred             HHHHHHHhh-------CCCCCCCCceEEEEecCCCCC---CCccccCCCeeeeEEeecCCCH-HHHHHHHHHHh
Q 042776            3 LSGLLNFID-------GLWSSCGDERIIVFTTNHKNR---LDPALLRPGRMDMHIHMSYCNP-SGFRILVSNYL   65 (147)
Q Consensus         3 v~~lL~~lD-------gl~~~~~~~vivi~aTN~p~~---LD~Al~RpGRfd~~i~~~~P~~-~~r~~il~~~l   65 (147)
                      .+.||..|+       |.... ....++|+|||.+..   +.+|+++  ||..+|+++.|+. +++..|+..+.
T Consensus       126 q~~LL~~lee~~v~i~G~~~~-~~~~~iI~ATN~lpe~~~~~~aLld--RF~~~i~v~~p~~~ee~~~IL~~~~  196 (500)
T 3nbx_X          126 LNTLLTAINERQFRNGAHVEK-IPMRLLVAASNELPEADSSLEALYD--RMLIRLWLDKVQDKANFRSMLTSQQ  196 (500)
T ss_dssp             HHHHHHHHHSSEEECSSSEEE-CCCCEEEEEESSCCCTTCTTHHHHT--TCCEEEECCSCCCHHHHHHHHTCCC
T ss_pred             HHHHHHHHHHHhccCCCCcCC-cchhhhhhccccCCCccccHHHHHH--HHHHHHHHHHhhhhhhHHHHHhccc
Confidence            356777775       33211 133467888886433   4459999  9999999999997 77889988765

>3vlf_B 26S protease regulatory subunit 7 homolog; heat repeat, chaperone, chaperone-protein binding complex; HET: DNA; 3.80A {Saccharomyces cerevisiae} PDB: 4a3v_B*

Probab=95.50  E-value=0.0065  Score=40.49  Aligned_cols=52  Identities=8%  Similarity=-0.061  Sum_probs=41.2

Q ss_pred             CHHHHHHHHHHHhCCCCCCChHHHHHHHH---HHhccchHHHHHHHHHHHHHHhh
Q 042776           53 NPSGFRILVSNYLGINDHNLFPEIDELLT---KLMKSEVAEVALEGLVEFLKRKK  104 (147)
Q Consensus        53 ~~~~r~~il~~~l~~~~~~~~~~i~~l~~---~l~~~~~~~~al~~~~~~l~~~~  104 (147)
                      |.++|.+||+.|+...+.....++..++.   +|+|+|....|.++.+.+++...
T Consensus         2 d~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~SGADl~~l~~eAa~~a~r~~~   56 (88)
T 3vlf_B            2 DLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRARR   56 (88)
T ss_dssp             CSSHHHHHHHHHHTTSCBCSCCCHHHHHHTCSSCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CHHHHHHHHHHHHCCCCCCCccCHHHHHHHcCCCcHHHHHHHHHHHHHHHHHhcc
Confidence            56789999999998765544445566655   89999999999999999887643

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

Probab=95.13  E-value=0.065  Score=43.11  Aligned_cols=56  Identities=16%  Similarity=0.067  Sum_probs=46.1

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      .+.||..|+.-    ..+.++|++||.|+.|.|+++.  |+. .+.|+.|+.++...++....
T Consensus       125 ~naLLk~lEep----~~~~~~Il~t~~~~~l~~ti~S--Rc~-~~~~~~~~~~~~~~~L~~~~  180 (334)
T 1a5t_A          125 ANALLKTLEEP----PAETWFFLATREPERLLATLRS--RCR-LHYLAPPPEQYAVTWLSREV  180 (334)
T ss_dssp             HHHHHHHHTSC----CTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHC
T ss_pred             HHHHHHHhcCC----CCCeEEEEEeCChHhCcHHHhh--cce-eeeCCCCCHHHHHHHHHHhc
Confidence            46677777753    2558888899999999999998  774 69999999999999998876

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

Probab=94.94  E-value=0.0021  Score=45.80  Aligned_cols=32  Identities=25%  Similarity=0.162  Sum_probs=27.5

Q ss_pred             CceEEEEecCCCC-----CCCccccCCCeeeeEEeecCCC
Q 042776           19 DERIIVFTTNHKN-----RLDPALLRPGRMDMHIHMSYCN   53 (147)
Q Consensus        19 ~~vivi~aTN~p~-----~LD~Al~RpGRfd~~i~~~~P~   53 (147)
                      ..+++|++||.+.     .+|+++++  ||+. |+++.|+
T Consensus       151 ~~~~ii~~~~~~~~~~~~~~~~~l~~--R~~~-i~i~~p~  187 (187)
T 2p65_A          151 GELRCIGATTVSEYRQFIEKDKALER--RFQQ-ILVEQPS  187 (187)
T ss_dssp             TCSCEEEEECHHHHHHHTTTCHHHHH--HEEE-EECCSCC
T ss_pred             CCeeEEEecCHHHHHHHHhccHHHHH--hcCc-ccCCCCC
Confidence            4577999999876     69999999  9995 9999886

>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=94.90  E-value=0.011  Score=53.75  Aligned_cols=44  Identities=18%  Similarity=0.140  Sum_probs=38.1

Q ss_pred             CceEEEEecCCCC----CCCccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776           19 DERIIVFTTNHKN----RLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus        19 ~~vivi~aTN~p~----~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      ..+.+|+|||.++    .+|++|.|  ||+. |+|+.|+.+++..|++.++
T Consensus       298 ~~i~~I~at~~~~~~~~~~d~aL~r--Rf~~-i~l~~p~~~e~~~iL~~~~  345 (854)
T 1qvr_A          298 GELRLIGATTLDEYREIEKDPALER--RFQP-VYVDEPTVEETISILRGLK  345 (854)
T ss_dssp             TCCCEEEEECHHHHHHHTTCTTTCS--CCCC-EEECCCCHHHHHHHHHHHH
T ss_pred             CCeEEEEecCchHHhhhccCHHHHh--CCce-EEeCCCCHHHHHHHHHhhh
Confidence            4577999999775    58999999  9996 9999999999999998655

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

Probab=94.54  E-value=0.075  Score=45.05  Aligned_cols=54  Identities=17%  Similarity=0.183  Sum_probs=41.1

Q ss_pred             HHHHHhhCCCCCCCCceEEEEec--CCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCC
Q 042776            5 GLLNFIDGLWSSCGDERIIVFTT--NHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGI   67 (147)
Q Consensus         5 ~lL~~lDgl~~~~~~~vivi~aT--N~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~   67 (147)
                      .||..|+.      ..+++|++|  |....|+++|++  |+. .+.|..|+.+++..++..++..
T Consensus       125 ~LL~~le~------~~v~lI~att~n~~~~l~~aL~s--R~~-v~~l~~l~~edi~~il~~~l~~  180 (447)
T 3pvs_A          125 AFLPHIED------GTITFIGATTENPSFELNSALLS--RAR-VYLLKSLSTEDIEQVLTQAMED  180 (447)
T ss_dssp             CCHHHHHT------TSCEEEEEESSCGGGSSCHHHHT--TEE-EEECCCCCHHHHHHHHHHHHHC
T ss_pred             HHHHHHhc------CceEEEecCCCCcccccCHHHhC--cee-EEeeCCcCHHHHHHHHHHHHHH
Confidence            34555553      236677666  555689999999  887 6779999999999999998764

>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B* 2dvw_B*

Probab=94.54  E-value=0.009  Score=38.96  Aligned_cols=51  Identities=8%  Similarity=0.160  Sum_probs=39.6

Q ss_pred             CHHHHHHHHHHHhCCCCCCChHHHHHHHH---HHhccchHHHHHHHHHHHHHHh
Q 042776           53 NPSGFRILVSNYLGINDHNLFPEIDELLT---KLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        53 ~~~~r~~il~~~l~~~~~~~~~~i~~l~~---~l~~~~~~~~al~~~~~~l~~~  103 (147)
                      |.++|.+||+.|++..+.....++..++.   +|+|+|....|-++.+..++..
T Consensus         2 d~~~R~~Il~~~l~~~~~~~~vdl~~la~~t~G~SGADi~~l~~eA~~~a~~~~   55 (83)
T 3aji_B            2 DRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQESGMLAVREN   55 (83)
T ss_dssp             CHHHHHHHHHHHHTTSCBCTTCCTHHHHTSSCCCCHHHHHHHHHHHHHGGGTSC
T ss_pred             CHHHHHHHHHHHhCCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhc
Confidence            67899999999998765443444555554   9999999999999988887654

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=94.46  E-value=0.12  Score=42.13  Aligned_cols=46  Identities=9%  Similarity=0.148  Sum_probs=37.4

Q ss_pred             CceEEEEecCCCCC----CCccccCCCeee-eEEeecCCCHHHHHHHHHHHhC
Q 042776           19 DERIIVFTTNHKNR----LDPALLRPGRMD-MHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus        19 ~~vivi~aTN~p~~----LD~Al~RpGRfd-~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      ..++||+++|..+.    |++++..  ||. ..|+|+.++.++...|++..+.
T Consensus       162 s~~~vI~i~n~~d~~~~~L~~~v~S--R~~~~~i~F~pYt~~el~~Il~~Rl~  212 (318)
T 3te6_A          162 SKLSIICVGGHNVTIREQINIMPSL--KAHFTEIKLNKVDKNELQQMIITRLK  212 (318)
T ss_dssp             CCEEEEEECCSSCCCHHHHHTCHHH--HTTEEEEECCCCCHHHHHHHHHHHHH
T ss_pred             CcEEEEEEecCcccchhhcchhhhc--cCCceEEEeCCCCHHHHHHHHHHHHH
Confidence            56889999998875    4555666  786 6899999999999999987764

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

Probab=94.16  E-value=0.11  Score=42.10  Aligned_cols=29  Identities=10%  Similarity=0.241  Sum_probs=26.1

Q ss_pred             CCccccCCCeeeeEEeecCCCHHHHHHHHHH
Q 042776           33 LDPALLRPGRMDMHIHMSYCNPSGFRILVSN   63 (147)
Q Consensus        33 LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~   63 (147)
                      +.|+|+.  |||..+.|..|+.+.+..|+..
T Consensus       239 ~~~~l~~--R~~~~~~~~pl~~~~~~~I~~~  267 (363)
T 3hws_A          239 LIPEFIG--RLPVVATLNELSEEALIQILKE  267 (363)
T ss_dssp             CCHHHHT--TCCEEEECCCCCHHHHHHHHHS
T ss_pred             CCHHHhc--ccCeeeecCCCCHHHHHHHHHH
Confidence            6788886  9999999999999999999876

>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=93.93  E-value=0.18  Score=40.23  Aligned_cols=58  Identities=17%  Similarity=0.201  Sum_probs=43.2

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCC
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIN   68 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~   68 (147)
                      +.|+..|+...    ....+|++||.++.+.|+++.  |+. .+.|..++.++...++...+...
T Consensus       128 ~~L~~~le~~~----~~~~~il~~n~~~~i~~~i~s--R~~-~~~~~~l~~~~~~~~l~~~~~~~  185 (340)
T 1sxj_C          128 NALRRVIERYT----KNTRFCVLANYAHKLTPALLS--QCT-RFRFQPLPQEAIERRIANVLVHE  185 (340)
T ss_dssp             HHHHHHHHHTT----TTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHhcCC----CCeEEEEEecCccccchhHHh--hce-eEeccCCCHHHHHHHHHHHHHHc
Confidence            34555555432    336677889999999999998  886 68898888888888888777433

>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=93.91  E-value=0.1  Score=41.62  Aligned_cols=61  Identities=15%  Similarity=0.057  Sum_probs=45.4

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCC---CCCCccccCCCeeee-EEeecCCCHHHHHHHHHHHhC
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHK---NRLDPALLRPGRMDM-HIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p---~~LD~Al~RpGRfd~-~i~~~~P~~~~r~~il~~~l~   66 (147)
                      ..|+..++.+......++.||++||.+   +.+++.+.+  ||.. .|+|+.++.++...++...+.
T Consensus       143 ~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~--r~~~~~i~~~pl~~~~~~~~l~~~~~  207 (389)
T 1fnn_A          143 STFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTKDQIFDILLDRAK  207 (389)
T ss_dssp             HHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCCBHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCcCCEEEEEEECCchHHHHhCHHhhh--cCCCceEEeCCCCHHHHHHHHHHHHH
Confidence            445555554432000357899999988   788999888  8875 899999999999999987764

>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=93.22  E-value=0.09  Score=42.28  Aligned_cols=44  Identities=11%  Similarity=0.211  Sum_probs=40.1

Q ss_pred             eEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhC
Q 042776           21 RIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus        21 vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      +.++++||++..|++++++  ||...+.|+.|+.+++.+|++.+..
T Consensus       151 ~~li~at~~~~~Ls~~l~s--R~~l~~~Ld~~~~~~l~~iL~~~~~  194 (334)
T 1in4_A          151 FTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAAS  194 (334)
T ss_dssp             CEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             eEEEEecCCcccCCHHHHH--hcCceeeCCCCCHHHHHHHHHHHHH
Confidence            5678899999999999999  9999999999999999999987754

>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=92.28  E-value=0.11  Score=47.10  Aligned_cols=62  Identities=21%  Similarity=0.281  Sum_probs=45.6

Q ss_pred             HHHHHHHhhCCCCC--C-----CCceEEEEecCCC--------------------------CCCCccccCCCeeeeEEee
Q 042776            3 LSGLLNFIDGLWSS--C-----GDERIIVFTTNHK--------------------------NRLDPALLRPGRMDMHIHM   49 (147)
Q Consensus         3 v~~lL~~lDgl~~~--~-----~~~vivi~aTN~p--------------------------~~LD~Al~RpGRfd~~i~~   49 (147)
                      .+.||..||.-.-.  .     -.+.+||+|||.+                          ..+.|+|+.  |||..+.|
T Consensus       677 ~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~tsn~~~~~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~l~~--Rl~~~i~~  754 (854)
T 1qvr_A          677 FNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVF  754 (854)
T ss_dssp             HHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBC
T ss_pred             HHHHHHHhccCceECCCCCEeccCCeEEEEecCcChHHHhhhcccccchHHHHHHHHHHHHhhCCHHHHH--hcCeEEeC
Confidence            46788888843210  0     0357899999973                          245666666  99999999


Q ss_pred             cCCCHHHHHHHHHHHhC
Q 042776           50 SYCNPSGFRILVSNYLG   66 (147)
Q Consensus        50 ~~P~~~~r~~il~~~l~   66 (147)
                      ..|+.+....|+.+++.
T Consensus       755 ~pl~~edi~~i~~~~l~  771 (854)
T 1qvr_A          755 RPLTKEQIRQIVEIQLS  771 (854)
T ss_dssp             CCCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            99999999999988874

>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=90.83  E-value=0.49  Score=39.63  Aligned_cols=34  Identities=15%  Similarity=0.235  Sum_probs=30.3

Q ss_pred             CCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhC
Q 042776           30 KNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus        30 p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      |+.|+|.++-  ||-. +.|+.++.++..++++....
T Consensus       347 ~~~l~~~i~s--R~~~-~~~~~~~~~e~~~iL~~~~~  380 (456)
T 2c9o_A          347 PHGIPLDLLD--RVMI-IRTMLYTPQEMKQIIKIRAQ  380 (456)
T ss_dssp             ETTCCHHHHT--TEEE-EECCCCCHHHHHHHHHHHHH
T ss_pred             cccCChhHHh--hcce-eeCCCCCHHHHHHHHHHHHH
Confidence            8899999999  9987 69999999999999987764

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=90.61  E-value=0.2  Score=40.24  Aligned_cols=54  Identities=22%  Similarity=0.287  Sum_probs=43.8

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      .|.||..|+--.    ...++|++||.|+.|-|+++.  |   .+.|..|+.++...++...+
T Consensus        99 ~naLLk~LEep~----~~t~fIl~t~~~~kl~~tI~S--R---~~~f~~l~~~~i~~~L~~~~  152 (305)
T 2gno_A           99 ANAFLKALEEPP----EYAVIVLNTRRWHYLLPTIKS--R---VFRVVVNVPKEFRDLVKEKI  152 (305)
T ss_dssp             HHHTHHHHHSCC----TTEEEEEEESCGGGSCHHHHT--T---SEEEECCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCC----CCeEEEEEECChHhChHHHHc--e---eEeCCCCCHHHHHHHHHHHh
Confidence            356777777432    457788888889999999998  7   89999999999999988776

>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=89.48  E-value=0.51  Score=38.12  Aligned_cols=28  Identities=14%  Similarity=0.218  Sum_probs=21.3

Q ss_pred             CCccccCCCeeeeEEeecCCCHHHHHHHHH
Q 042776           33 LDPALLRPGRMDMHIHMSYCNPSGFRILVS   62 (147)
Q Consensus        33 LD~Al~RpGRfd~~i~~~~P~~~~r~~il~   62 (147)
                      +.|+|+.  ||+..|.|+.++.+....|+.
T Consensus       256 ~~p~l~~--R~~~~i~~~~l~~~~l~~i~~  283 (376)
T 1um8_A          256 LIPELIG--RLPVLSTLDSISLEAMVDILQ  283 (376)
T ss_dssp             CCHHHHT--TCCEEEECCCCCHHHHHHHHH
T ss_pred             CChHHhc--CCCceeeccCCCHHHHHHHHh
Confidence            3455555  788889999889888888886

>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=88.21  E-value=1.2  Score=37.95  Aligned_cols=55  Identities=11%  Similarity=0.153  Sum_probs=34.7

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhC
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      +.|+..++...    ..+++|+++..+..|.+ +.   |+...|.|+.|+.+++..++..++.
T Consensus       169 ~~L~~~l~~~~----~~iIli~~~~~~~~l~~-l~---~r~~~i~f~~~~~~~~~~~L~~i~~  223 (516)
T 1sxj_A          169 GQLAQFCRKTS----TPLILICNERNLPKMRP-FD---RVCLDIQFRRPDANSIKSRLMTIAI  223 (516)
T ss_dssp             HHHHHHHHHCS----SCEEEEESCTTSSTTGG-GT---TTSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC----CCEEEEEcCCCCccchh-hH---hceEEEEeCCCCHHHHHHHHHHHHH
Confidence            45555555421    23555554444444543 43   5566899999999999999987663

>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} PDB: 2dzo_B

Probab=87.73  E-value=0.028  Score=36.67  Aligned_cols=49  Identities=8%  Similarity=0.014  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHhCCCCC---CChHHHHHHHHHHhccchHHHHHHHHHHHHHHh
Q 042776           55 SGFRILVSNYLGINDH---NLFPEIDELLTKLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        55 ~~r~~il~~~l~~~~~---~~~~~i~~l~~~l~~~~~~~~al~~~~~~l~~~  103 (147)
                      ++|.+||+.|+...+.   .+...++..+.+|+|+|....|-++.+..++..
T Consensus         1 ~~R~~Il~~~l~~~~~~~~vdl~~lA~~t~G~SGADi~~l~~eAa~~ai~~~   52 (82)
T 2dzn_B            1 MERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRKN   52 (82)
T ss_dssp             -------------CEECTTCCSTTTTTSSCCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHcCCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhc
Confidence            4689999999876543   233344444559999999999999999988764

>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=84.46  E-value=1.1  Score=38.26  Aligned_cols=56  Identities=18%  Similarity=0.337  Sum_probs=43.1

Q ss_pred             HHHHHHhhCCCCC------CCCceEEEEec----CCCCCCCccccCCCeeeeEEeecCCCHHHHHHHH
Q 042776            4 SGLLNFIDGLWSS------CGDERIIVFTT----NHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILV   61 (147)
Q Consensus         4 ~~lL~~lDgl~~~------~~~~vivi~aT----N~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il   61 (147)
                      ..||..|||-...      ..+++++|+|.    +.|.++-|.|+-  ||+..|.|+-.+.++..+|+
T Consensus       280 ~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~~~~~dlipel~~--R~~i~i~l~~lt~~e~~~Il  345 (444)
T 1g41_A          280 RDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAADFERIL  345 (444)
T ss_dssp             HHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHT--TCCEEEECCCCCHHHHHHHH
T ss_pred             HHHHHHhcccccccccceecCCcEEEEeccccccCChhhcchHHhc--ccceeeeCCCCCHHHHHHHH
Confidence            3689999984211      12568888886    356666688776  99999999999999999998

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=82.03  E-value=0.58  Score=37.15  Aligned_cols=43  Identities=14%  Similarity=0.282  Sum_probs=25.7

Q ss_pred             ceEEEEecCCC-------CCCCccccCCCeeeeEEeecCCCHHHH----HHHHHHHh
Q 042776           20 ERIIVFTTNHK-------NRLDPALLRPGRMDMHIHMSYCNPSGF----RILVSNYL   65 (147)
Q Consensus        20 ~vivi~aTN~p-------~~LD~Al~RpGRfd~~i~~~~P~~~~r----~~il~~~l   65 (147)
                      .+.||+|||++       ..++++|..  ||. .+.+.+|...+|    ..++.+|+
T Consensus       137 ~~riI~atn~~l~~~v~~g~fr~~L~~--Rl~-~~~i~lPpL~eR~edi~~l~~~~l  190 (304)
T 1ojl_A          137 DVRLIAATHRDLAEEVSAGRFRQDLYY--RLN-VVAIEMPSLRQRREDIPLLADHFL  190 (304)
T ss_dssp             CCEEEEEESSCHHHHHHHTSSCHHHHH--HHS-SEEEECCCSGGGGGGHHHHHHHHH
T ss_pred             CeEEEEecCccHHHHHHhCCcHHHHHh--hcC-eeEEeccCHHHhHhhHHHHHHHHH
Confidence            47799999986       234455555  554 556666765544    34555554

>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=81.41  E-value=0.84  Score=36.50  Aligned_cols=45  Identities=4%  Similarity=0.193  Sum_probs=34.6

Q ss_pred             CceEEEEecCCCC---CCC---ccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776           19 DERIIVFTTNHKN---RLD---PALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus        19 ~~vivi~aTN~p~---~LD---~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      ..+.||++||.++   .++   +.+.+  ||...|+|+.++.++..+++..++
T Consensus       178 ~~v~lI~~~~~~~~~~~l~~~~~~~~~--~~~~~i~l~~l~~~e~~~ll~~~~  228 (412)
T 1w5s_A          178 NRIGFLLVASDVRALSYMREKIPQVES--QIGFKLHLPAYKSRELYTILEQRA  228 (412)
T ss_dssp             CBEEEEEEEEETHHHHHHHHHCHHHHT--TCSEEEECCCCCHHHHHHHHHHHH
T ss_pred             ceEEEEEEeccccHHHHHhhhcchhhh--hcCCeeeeCCCCHHHHHHHHHHHH
Confidence            4578888998776   345   66666  565569999999999999997665

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	147
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	5e-13
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	3e-12
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	9e-12
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	2e-04
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	4e-04

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]} Length = 247

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

 Score = 61.8 bits (150), Expect = 5e-13
 Identities = 23/109 (21%), Positives = 46/109 (42%), Gaps = 5/109 (4%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILV 61
           TL+ LL  +DG         +++  TN  + LDPALLRPGR D  I +   +  G   ++
Sbjct: 131 TLNQLLVEMDGFEKDTA--IVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQIL 188

Query: 62  SNYLGINDHNLFPEIDELLTKLMK---SEVAEVALEGLVEFLKRKKTEV 107
             +          ++  L  +      +++  +  E  +   +  + ++
Sbjct: 189 RIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRRKI 237

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 265

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.8 bits (144), Expect = 3e-12
 Identities = 21/138 (15%), Positives = 56/138 (40%), Gaps = 6/138 (4%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILV 61
            ++ +L  +DG+ +       I+  TN  + +DPA+LRPGR+D  I++   +      ++
Sbjct: 130 VINQILTEMDGMSTKKN--VFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAIL 187

Query: 62  SNYLG---INDHNLFPEIDELLTKLMKSEVAEVALEGLVEFLKRKKTEVAEVGNKQKASR 118
              L    +        + ++      +++ E+        ++           +++ + 
Sbjct: 188 KANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNP 247

Query: 119 EAEGDEKIGEFVRKTKKR 136
            A   E+  + V + ++ 
Sbjct: 248 SAMEVEE-DDPVPEIRRD 264

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]} Length = 256

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

 Score = 58.3 bits (141), Expect = 9e-12
 Identities = 25/109 (22%), Positives = 47/109 (43%), Gaps = 5/109 (4%)

Query: 2   TLSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILV 61
           TL+ +L  +DG   +  +  I++  TN  + LDPALLRPGR D  + +   +  G   ++
Sbjct: 134 TLNQMLVEMDGFEGN--EGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQIL 191

Query: 62  SNY---LGINDHNLFPEIDELLTKLMKSEVAEVALEGLVEFLKRKKTEV 107
             +   + +        I         +++A +  E  +   +  K  V
Sbjct: 192 KVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNKRVV 240

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]} Length = 273

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

 Score = 37.6 bits (86), Expect = 2e-04
 Identities = 16/129 (12%), Positives = 31/129 (24%), Gaps = 5/129 (3%)

Query: 14  WSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCN---PSGFRILVSNYLGINDH 70
             +       + T      +        R              P+    L    L  +  
Sbjct: 142 VMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDIVVKNLPTNLETLHKTGLFSDIR 201

Query: 71  NLFPEIDELLT-KLMKSEVAEVALEGLVEFLKRKKTEVAEVGNKQKASREAEGDEKIGEF 129
               E  +L +     S   +  LE  +   K    E+     + +        ++  EF
Sbjct: 202 LYNREGVKLYSSLETPSISPKETLEKELN-RKVSGKEIQPTLERIEQKMVLNKHQETPEF 260

Query: 130 VRKTKKRRS 138
               +K  S
Sbjct: 261 KAIQQKLES 269

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 258

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.5 bits (83), Expect = 4e-04
 Identities = 19/97 (19%), Positives = 41/97 (42%), Gaps = 3/97 (3%)

Query: 14  WSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFR-ILVSNYLG--INDH 70
                   I++  TN  N +DPAL R GR D  + +   + +G   IL  +     + D 
Sbjct: 134 GLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADD 193

Query: 71  NLFPEIDELLTKLMKSEVAEVALEGLVEFLKRKKTEV 107
               ++       + +++A +  E  ++ +++K   +
Sbjct: 194 VDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLI 230

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	147
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.76
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.75
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	99.74
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.69
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.12
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	98.61
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	97.6
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	97.54
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	97.52
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	96.82
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	96.28
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	95.97
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	95.88
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	95.64
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	95.64
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	94.64
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	94.14
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	93.58
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	93.06
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	91.46
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	88.51
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	86.08
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	84.17

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=99.76  E-value=8.5e-19  Score=138.93  Aligned_cols=97  Identities=22%  Similarity=0.283  Sum_probs=81.7

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH-
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT-   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~-   81 (147)
                      +++||++|||+...  .+++||+|||+|+.||||++||||||.+|+|++|+.++|.+|++.|+...+.....++..++. 
T Consensus       135 ~~~ll~~~d~~~~~--~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~  212 (256)
T d1lv7a_         135 LNQMLVEMDGFEGN--EGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARG  212 (256)
T ss_dssp             HHHHHHHHHTCCSS--SCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHT
T ss_pred             HHHHHHHhhCCCCC--CCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCcccCHHHHHHh
Confidence            68999999999876  779999999999999999999999999999999999999999999998765444445555555 


Q ss_pred             --HHhccchHHHHHHHHHHHHH
Q 042776           82 --KLMKSEVAEVALEGLVEFLK  101 (147)
Q Consensus        82 --~l~~~~~~~~al~~~~~~l~  101 (147)
                        ++++++....+-++...+++
T Consensus       213 t~G~s~adi~~l~~~A~~~a~~  234 (256)
T d1lv7a_         213 TPGFSGADLANLVNEAALFAAR  234 (256)
T ss_dssp             CTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHH
Confidence              78888877777776666554

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=1.6e-18  Score=136.61  Aligned_cols=100  Identities=22%  Similarity=0.317  Sum_probs=83.3

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHH--
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELL--   80 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~--   80 (147)
                      ++.++..+++....  .+++||+|||+|+.||||++||||||++|+|++|+.++|.+|++.|++..+.....++..++  
T Consensus       125 ~~~~~~~~~~~~~~--~~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~  202 (258)
T d1e32a2         125 VSQLLTLMDGLKQR--AHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANE  202 (258)
T ss_dssp             HHHHHHHHHTCCCS--SCEEEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCTTCCHHHHHHH
T ss_pred             HHHhcccccccccc--CCccEEEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCcccccccchhhhhhc
Confidence            67888999999877  77999999999999999999999999999999999999999999999765443333344444  


Q ss_pred             -HHHhccchHHHHHHHHHHHHHHhh
Q 042776           81 -TKLMKSEVAEVALEGLVEFLKRKK  104 (147)
Q Consensus        81 -~~l~~~~~~~~al~~~~~~l~~~~  104 (147)
                       .++++++....|-++.+.++++..
T Consensus       203 t~G~s~adl~~lv~~A~~~a~~~~~  227 (258)
T d1e32a2         203 THGHVGADLAALCSEAALQAIRKKM  227 (258)
T ss_dssp             CTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCHHHHHHHHHHHHHHHHHhhc
Confidence             488888888888888777776544

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=99.74  E-value=2e-18  Score=135.88  Aligned_cols=97  Identities=23%  Similarity=0.278  Sum_probs=79.5

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHH-
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLT-   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~-   81 (147)
                      +++||++|||+...  .+++||+|||+|+.||||++||||||..|+|++|+.++|.+|++.|+...+.....++..++. 
T Consensus       132 ~~~ll~~~d~~~~~--~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~~~~~~~la~~  209 (247)
T d1ixza_         132 LNQLLVEMDGFEKD--TAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKR  209 (247)
T ss_dssp             HHHHHHHHHTCCTT--CCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHT
T ss_pred             HHHHHHHhhCCCCC--CCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCccccCHHHHHHH
Confidence            68899999999776  779999999999999999999999999999999999999999999997654444444555555 


Q ss_pred             --HHhccchHHHHHHHHHHHHH
Q 042776           82 --KLMKSEVAEVALEGLVEFLK  101 (147)
Q Consensus        82 --~l~~~~~~~~al~~~~~~l~  101 (147)
                        ++++++....+-++...++.
T Consensus       210 t~g~s~~di~~lv~~A~l~a~~  231 (247)
T d1ixza_         210 TPGFVGADLENLLNEAALLAAR  231 (247)
T ss_dssp             CTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHH
Confidence              77777766666666555443

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=1.7e-17  Score=131.27  Aligned_cols=99  Identities=18%  Similarity=0.311  Sum_probs=78.7

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCC---CCCChHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGIN---DHNLFPEIDEL   79 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~---~~~~~~~i~~l   79 (147)
                      ++.||+.||++...  .+++||+|||+|+.||||++||||||..|+|++|+.++|.+||+.|+...   .......++..
T Consensus       131 ~~~ll~~l~~~~~~--~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~~~~~l~~la~~  208 (265)
T d1r7ra3         131 INQILTEMDGMSTK--KNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKM  208 (265)
T ss_dssp             HHHHHHTCC--------CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC----CCCCHHHHHH
T ss_pred             HHHHHHHhhCcCCC--CCEEEEEeCCCchhCCHHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCchhhhhHHHHHhc
Confidence            68899999999876  67999999999999999999999999999999999999999999998754   22344566666


Q ss_pred             HHHHhccchHHHHHHHHHHHHHHh
Q 042776           80 LTKLMKSEVAEVALEGLVEFLKRK  103 (147)
Q Consensus        80 ~~~l~~~~~~~~al~~~~~~l~~~  103 (147)
                      +.++++.+....|-++...++++.
T Consensus       209 t~g~s~~di~~lv~~A~~~A~~~~  232 (265)
T d1r7ra3         209 TNGFSGADLTEICQRACKLAIRES  232 (265)
T ss_dssp             HCSSCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHH
Confidence            678888888888877777766543

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=99.12  E-value=4.3e-14  Score=115.32  Aligned_cols=63  Identities=11%  Similarity=0.073  Sum_probs=54.8

Q ss_pred             cHHHHHHHhhCCCCCCCCceEEEEecCC---CCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhC
Q 042776            2 TLSGLLNFIDGLWSSCGDERIIVFTTNH---KNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus         2 tv~~lL~~lDgl~~~~~~~vivi~aTN~---p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      +||+||++|||+.+.  .+++||+|||+   ++.||++++||||||++|+++.||..+|.+||..+..
T Consensus       210 ~v~~lL~e~dg~~~~--~~v~viaatN~~~~~~~i~~~~~r~~Rf~~~v~v~~pd~~~r~~il~~~~~  275 (321)
T d1w44a_         210 GAFDLLSDIGAMAAS--RGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGE  275 (321)
T ss_dssp             HHHHHHHHHHHHHHH--HTCEEEEECCCCCCCHHHHHHHHHHHHHSCSEEEEECSSTTEEEEEEECBT
T ss_pred             hhhhhhhhccccccC--CCeEEEEeCCCcccccchhhhhhccCcccceeecCCCChHHHHHHHHHhcc
Confidence            589999999999887  78999999995   2345666789999999999999999999999987754

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=98.61  E-value=9.9e-09  Score=79.42  Aligned_cols=78  Identities=18%  Similarity=0.146  Sum_probs=52.7

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDELLTK   82 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l~~~   82 (147)
                      +++|+..||+.... +.+++||+|||+|+.||++.+| ||||..|+||  +..+|.+|++.+... ......+...++..
T Consensus       127 ~~~ll~~l~~~~~~-~~~v~vi~tTn~~~~ld~~~~~-~rF~~~i~~P--~~~~r~~il~~l~~~-~~~~~~~~~~i~~~  201 (246)
T d1d2na_         127 LQALLVLLKKAPPQ-GRKLLIIGTTSRKDVLQEMEML-NAFSTTIHVP--NIATGEQLLEALELL-GNFKDKERTTIAQQ  201 (246)
T ss_dssp             HHHHHHHTTCCCST-TCEEEEEEEESCHHHHHHTTCT-TTSSEEEECC--CEEEHHHHHHHHHHH-TCSCHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCcc-ccceeeeeccCChhhccchhhc-CccceEEecC--CchhHHHHHHHHHhc-cCCChHHHHHHHHH
Confidence            57899999999665 4678999999999999987554 6999999984  433444444433211 12234455666665


Q ss_pred             Hhc
Q 042776           83 LMK   85 (147)
Q Consensus        83 l~~   85 (147)
                      +.+
T Consensus       202 ~~g  204 (246)
T d1d2na_         202 VKG  204 (246)
T ss_dssp             HTT
T ss_pred             cCC
Confidence            544

>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=97.60  E-value=2e-05  Score=61.96  Aligned_cols=61  Identities=18%  Similarity=0.346  Sum_probs=47.2

Q ss_pred             HHHHHHHhhCCCCCCC------CceEEEEe----cCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHh
Q 042776            3 LSGLLNFIDGLWSSCG------DERIIVFT----TNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYL   65 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~------~~vivi~a----TN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l   65 (147)
                      +++||..|||...+.+      +++++|++    +|+|..++|+++  ||||..+.|+.|+...+.+|+..+.
T Consensus       144 ~~~LL~~~dg~~~~~~~~~i~~s~ilfi~~ga~~~~~~~~~~p~l~--~R~~~~i~~~~~~~~~~~~Il~~~~  214 (309)
T d1ofha_         144 QRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQ--GRLPIRVELTALSAADFERILTEPH  214 (309)
T ss_dssp             HHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHH--HTCCEEEECCCCCHHHHHHHHHSST
T ss_pred             HHHhhHHhcCCEEecCCeEEEccceeEEeccchhhcCcccchhhhh--hhhheeeeccCCCHHHHHHHHHHHH
Confidence            5779999999643211      23556655    678888888887  5999999999999999999987654

>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=97.54  E-value=1.7e-05  Score=64.27  Aligned_cols=75  Identities=13%  Similarity=-0.067  Sum_probs=45.6

Q ss_pred             EEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHH-HHHHHHhCCCCCC-ChHHHHHHHHHHhccchHHHHHHHHHHHH
Q 042776           23 IVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFR-ILVSNYLGINDHN-LFPEIDELLTKLMKSEVAEVALEGLVEFL  100 (147)
Q Consensus        23 vi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~-~il~~~l~~~~~~-~~~~i~~l~~~l~~~~~~~~al~~~~~~l  100 (147)
                      +|+|||+   +|++++||||||+.|++..|+...+. .++..++...... ....+..++.++.+.|....+-..+..|.
T Consensus       259 ~i~ttN~---~~~~~~r~~Rf~~~i~~~~~~~~~~~~~~l~~i~~~~~l~~~~~~L~~li~~~s~~D~~~~i~~~~~~~~  335 (362)
T d1svma_         259 GIVTMNE---YSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWK  335 (362)
T ss_dssp             EEEEECS---CCCCHHHHTTEEEEEECCCCHHHHHHHHTCTHHHHTTCTTCHHHHHHHHHHHSCGGGSCGGGHHHHHHHH
T ss_pred             ceeeccc---ccccccccccCceEEeecCCCcHHHHHHHHHHHhcccCCCCCHHHHHHHccCCCHHHHHHHHHHHHHHHH
Confidence            7899995   68888999999999999999887765 3333333333222 22233444445555544433333333443

>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=97.52  E-value=0.00013  Score=53.91  Aligned_cols=56  Identities=11%  Similarity=0.178  Sum_probs=49.2

Q ss_pred             CceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChHHH
Q 042776           19 DERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFPEI   76 (147)
Q Consensus        19 ~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i   76 (147)
                      ..+++|+|||++..+++++++  ||+..+.|+.|+...+..+++.+..........+.
T Consensus       133 ~~~~~I~at~~~~~~~~~~~~--r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  188 (238)
T d1in4a2         133 QPFTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAA  188 (238)
T ss_dssp             CCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHH
T ss_pred             CCeEEEEecCCCcccccccee--eeeEEEEecCCCHHHHHHHHHHhhhhccchhhHHH
Confidence            467899999999999999999  99999999999999999999998877666555543

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.82  E-value=0.0012  Score=48.46  Aligned_cols=56  Identities=7%  Similarity=0.104  Sum_probs=44.4

Q ss_pred             HHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCC
Q 042776            5 GLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGI   67 (147)
Q Consensus         5 ~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~   67 (147)
                      .|+..++..    ...+.+|++||+++.++++++.  |+ ..|+|+.|+.++...++...+..
T Consensus       150 ~l~~~~e~~----~~~~~~Il~tn~~~~i~~~l~s--R~-~~i~~~~~~~~~~~~~l~~i~~~  205 (252)
T d1sxje2         150 ALRRTMEKY----SKNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPSDSEISTILSDVVTN  205 (252)
T ss_dssp             HHHHHHHHS----TTTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHH
T ss_pred             hhhcccccc----cccccceeeeccccchhhhhhc--ch-heeeecccchhhHHHHHHHHHHH
Confidence            344445432    2457789999999999999997  88 58999999999999999877643

>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=96.28  E-value=0.014  Score=42.35  Aligned_cols=54  Identities=15%  Similarity=0.177  Sum_probs=45.0

Q ss_pred             CceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChH
Q 042776           19 DERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFP   74 (147)
Q Consensus        19 ~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~   74 (147)
                      ..+++|++||++...+++.+|  |+...+.|..|+.+.+..++...+.........
T Consensus       134 ~~~~~i~~~~~~~~~~~~~l~--~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~~~~  187 (239)
T d1ixsb2         134 PRFTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITE  187 (239)
T ss_dssp             CCCEEEEEESCCSSCSCGGGG--GCSEEEECCCCCHHHHHHHHHHHHGGGCCCBCH
T ss_pred             CCEEEEeeccCcccccchhhc--ccceeeEeeccChhhhhHHHHHHHHHhCCccch
Confidence            457789999999999999999  888999999999999999998777655444333

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=95.97  E-value=0.015  Score=42.75  Aligned_cols=85  Identities=14%  Similarity=0.146  Sum_probs=57.5

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCC-hHHHHHHHH
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNL-FPEIDELLT   81 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~-~~~i~~l~~   81 (147)
                      .+.||..|+...    ....+|++||.++.|.+++..  |+ ..|.|+.|+.++...++........... ...++.++.
T Consensus       132 q~~Llk~lE~~~----~~~~~il~tn~~~~i~~~i~S--Rc-~~i~~~~~~~~~i~~~l~~i~~~e~~~~~~~~l~~i~~  204 (239)
T d1njfa_         132 FNALLKTLEEPP----EHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLAR  204 (239)
T ss_dssp             HHHHHHHHHSCC----TTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHH
T ss_pred             HHHHHHHHhcCC----CCeEEEEEcCCccccChhHhh--hh-cccccccCcHHHhhhHHHHHHhhhccCCCHHHHHHHHH
Confidence            356788887533    447889999999999999998  87 6799999999998888877764333222 233444422


Q ss_pred             HHhccchHHHHHHHH
Q 042776           82 KLMKSEVAEVALEGL   96 (147)
Q Consensus        82 ~l~~~~~~~~al~~~   96 (147)
                        .+.+++-.|+..+
T Consensus       205 --~s~Gd~R~ain~l  217 (239)
T d1njfa_         205 --AAEGSLRDALSLT  217 (239)
T ss_dssp             --HTTTCHHHHHHHH
T ss_pred             --HcCCCHHHHHHHH
Confidence              2335555555443

>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=95.88  E-value=0.013  Score=42.47  Aligned_cols=71  Identities=7%  Similarity=0.029  Sum_probs=53.0

Q ss_pred             HHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCC-hHHHHHHHHH
Q 042776            5 GLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNL-FPEIDELLTK   82 (147)
Q Consensus         5 ~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~-~~~i~~l~~~   82 (147)
                      .|+..++.-.    ..+++|++||++..++++++.  |+. .|.|..|+..+...+++..+....... ...++.++..
T Consensus       128 ~ll~~l~~~~----~~~~~i~~~n~~~~i~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~~~~e~i~i~~~~l~~I~~~  199 (231)
T d1iqpa2         128 ALRRTMEMFS----SNVRFILSCNYSSKIIEPIQS--RCA-IFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYI  199 (231)
T ss_dssp             HHHHHHHHTT----TTEEEEEEESCGGGSCHHHHH--TEE-EEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHH
T ss_pred             HHhhhcccCC----cceEEEeccCChhhchHhHhC--ccc-cccccccchhhHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence            4555555433    347889999999999999987  885 599999999999999998887665432 3445555543

>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=95.64  E-value=0.02  Score=41.17  Aligned_cols=71  Identities=18%  Similarity=0.221  Sum_probs=53.0

Q ss_pred             HHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChH-HHHHHHH
Q 042776            4 SGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFP-EIDELLT   81 (147)
Q Consensus         4 ~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~-~i~~l~~   81 (147)
                      +.|+..|+...    ...+++++||.+..+++++++  |+ ..+.|..|+..+...++...+......... .++.++.
T Consensus       117 ~~Ll~~le~~~----~~~~~~~~~~~~~~i~~~i~s--r~-~~i~~~~~~~~~i~~~l~~I~~~e~i~i~~~~l~~i~~  188 (227)
T d1sxjc2         117 NALRRVIERYT----KNTRFCVLANYAHKLTPALLS--QC-TRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIE  188 (227)
T ss_dssp             HHHHHHHHHTT----TTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHTTTCCBCHHHHHHHHH
T ss_pred             HHHHHHhhhcc----cceeeccccCcHHHhHHHHHH--HH-hhhccccccccccccccccccccccccCCHHHHHHHHH
Confidence            45677776543    347889999999999999998  76 568999999999999998887665444333 3444544

>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=95.64  E-value=0.032  Score=40.40  Aligned_cols=57  Identities=16%  Similarity=0.031  Sum_probs=46.9

Q ss_pred             HHHHHHHhhCCCCCCCCceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhC
Q 042776            3 LSGLLNFIDGLWSSCGDERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus         3 v~~lL~~lDgl~~~~~~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      .+.||..|+.-.    .++++|++||+++.|.|+++-  |+ ..|.|+.|+.+....++.....
T Consensus       125 ~n~Llk~lEep~----~~~~fIl~t~~~~~ll~tI~S--Rc-~~i~~~~~~~~~~~~~L~~~~~  181 (207)
T d1a5ta2         125 ANALLKTLEEPP----AETWFFLATREPERLLATLRS--RC-RLHYLAPPPEQYAVTWLSREVT  181 (207)
T ss_dssp             HHHHHHHHTSCC----TTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHCC
T ss_pred             hHHHHHHHHhhc----ccceeeeeecChhhhhhhhcc--ee-EEEecCCCCHHHHHHHHHHcCC
Confidence            366777777643    558899999999999999987  88 8999999999998888876543

>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=94.64  E-value=0.042  Score=39.73  Aligned_cols=59  Identities=12%  Similarity=0.154  Sum_probs=40.8

Q ss_pred             CceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCC-CChHHHHHHHH
Q 042776           19 DERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDH-NLFPEIDELLT   81 (147)
Q Consensus        19 ~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~-~~~~~i~~l~~   81 (147)
                      ..++++++++....+++  +|  |+...|+|+.|+..++..+++.++..... .....++.++.
T Consensus       155 ~~ii~i~~~~~~~~~~~--l~--~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~~~l~~i~~  214 (253)
T d1sxja2         155 TPLILICNERNLPKMRP--FD--RVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQ  214 (253)
T ss_dssp             SCEEEEESCTTSSTTGG--GT--TTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHH
T ss_pred             ccccccccccccccccc--cc--ceeeeeeccccchhHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            34666666677777775  45  77899999999999999999988743221 12234566654

>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=94.14  E-value=0.066  Score=38.51  Aligned_cols=78  Identities=9%  Similarity=0.112  Sum_probs=48.9

Q ss_pred             CceEEEEecCCCCCCC------ccccCCCeeeeEEeecCCCHHHHHHHHHHHhCC--CCC-CChHHHHHHHHHH----hc
Q 042776           19 DERIIVFTTNHKNRLD------PALLRPGRMDMHIHMSYCNPSGFRILVSNYLGI--NDH-NLFPEIDELLTKL----MK   85 (147)
Q Consensus        19 ~~vivi~aTN~p~~LD------~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~--~~~-~~~~~i~~l~~~l----~~   85 (147)
                      ....+|+.+|.++..+      +++.+  ||+..++|+.++..+..+|++..+..  .+. .....++.++...    ..
T Consensus       172 ~~~~~i~i~~~~~~~~~~~~~~~~~~~--r~~~~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al~~ia~~~~~~~~~  249 (287)
T d1w5sa2         172 NRIGFLLVASDVRALSYMREKIPQVES--QIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGG  249 (287)
T ss_dssp             CBEEEEEEEEETHHHHHHHHHCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTS
T ss_pred             cceeEEeecccHHHHHHHHhhccchhc--ccceeeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHHHHHHHHHhccccC
Confidence            4566777777665443      67777  99999999999999999999876532  122 2234455555422    12


Q ss_pred             cchHHHHHHHHHH
Q 042776           86 SEVAEVALEGLVE   98 (147)
Q Consensus        86 ~~~~~~al~~~~~   98 (147)
                      ..++-.|+.-+..
T Consensus       250 ~gd~R~ai~~l~~  262 (287)
T d1w5sa2         250 DGSARRAIVALKM  262 (287)
T ss_dssp             CCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHH
Confidence            3455555544333

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.58  E-value=0.11  Score=37.02  Aligned_cols=60  Identities=8%  Similarity=-0.016  Sum_probs=46.7

Q ss_pred             CceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChH-HHHHHHH
Q 042776           19 DERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFP-EIDELLT   81 (147)
Q Consensus        19 ~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~-~i~~l~~   81 (147)
                      ...++|.+||.++.+.+++..  |+ ..|.|..|+..+...++...+......... .++.++.
T Consensus       137 ~~~~~i~~~~~~~~~~~~l~s--r~-~~i~f~~~~~~~~~~~L~~i~~~e~i~i~~~~l~~ia~  197 (237)
T d1sxjd2         137 GVTRFCLICNYVTRIIDPLAS--QC-SKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILD  197 (237)
T ss_dssp             TTEEEEEEESCGGGSCHHHHH--HS-EEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHH
T ss_pred             ccccccccccccccccccccc--hh-hhhccccccccccchhhhhhhhhhcCcCCHHHHHHHHH
Confidence            346788899999999999988  88 689999999999999999887765544443 3445544

>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=93.06  E-value=0.13  Score=36.62  Aligned_cols=75  Identities=11%  Similarity=0.139  Sum_probs=51.3

Q ss_pred             CceEEEEecCCCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHHhCCCCCCChH-HHHHHHHHHhccchHHHHHHHHH
Q 042776           19 DERIIVFTTNHKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNYLGINDHNLFP-EIDELLTKLMKSEVAEVALEGLV   97 (147)
Q Consensus        19 ~~vivi~aTN~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~l~~~~~~~~~-~i~~l~~~l~~~~~~~~al~~~~   97 (147)
                      ....++++||..+.+.++|+.  |+ ..|+|+.|+.++...++...+......... .+..++.  .+.+++-.|+..+.
T Consensus       130 ~~~~~i~~~~~~~~i~~~l~s--r~-~~i~~~~~~~~~i~~~l~~i~~~e~~~i~~~~l~~I~~--~s~Gd~R~ai~~Lq  204 (224)
T d1sxjb2         130 NSTRFAFACNQSNKIIEPLQS--QC-AILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIF--TAEGDMRQAINNLQ  204 (224)
T ss_dssp             TTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHH--HHTTCHHHHHHHHH
T ss_pred             cceeeeeccCchhhhhhHHHH--HH-HHhhhcccchhhhHHHHHHHHHhcccCCCHHHHHHHHH--HcCCcHHHHHHHHH
Confidence            447788899999999999998  88 469999999999999998877544433333 3333322  22345445554443


Q ss_pred             H
Q 042776           98 E   98 (147)
Q Consensus        98 ~   98 (147)
                      .
T Consensus       205 ~  205 (224)
T d1sxjb2         205 S  205 (224)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=91.46  E-value=0.13  Score=39.23  Aligned_cols=58  Identities=19%  Similarity=0.230  Sum_probs=40.1

Q ss_pred             HHHHHHHhh---------CCCCCCCCceEEEEecC-CCCCCCccccCCCeeeeEEeecCC-CHHHHHHHHH
Q 042776            3 LSGLLNFID---------GLWSSCGDERIIVFTTN-HKNRLDPALLRPGRMDMHIHMSYC-NPSGFRILVS   62 (147)
Q Consensus         3 v~~lL~~lD---------gl~~~~~~~vivi~aTN-~p~~LD~Al~RpGRfd~~i~~~~P-~~~~r~~il~   62 (147)
                      ++.||..|+         |.........+||+|+| -+..|.++++.  |||..|.++.| +...+..++.
T Consensus       144 ~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~Np~~~~l~~~llD--Rf~~~i~v~~~~~~~~~~~~~~  212 (333)
T d1g8pa_         144 VDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPRDVETRVEVIR  212 (333)
T ss_dssp             HHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCCSHHHHHHHHH
T ss_pred             HHHHhhhhcCCeEEecccCceecCCCCEEEEEecCccccccccchhh--hhcceeeccCcchhhHHHHHHH
Confidence            467777775         33222124467888888 45679999999  99999999877 4455555543

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=88.51  E-value=1.8  Score=32.48  Aligned_cols=86  Identities=16%  Similarity=0.152  Sum_probs=55.8

Q ss_pred             HHhhCCCCCCCCceEEEEecC-----CCCCCCccccCCCeeeeEEeecCCCHHHHHHHHHHH-------hCCCCCCChHH
Q 042776            8 NFIDGLWSSCGDERIIVFTTN-----HKNRLDPALLRPGRMDMHIHMSYCNPSGFRILVSNY-------LGINDHNLFPE   75 (147)
Q Consensus         8 ~~lDgl~~~~~~~vivi~aTN-----~p~~LD~Al~RpGRfd~~i~~~~P~~~~r~~il~~~-------l~~~~~~~~~~   75 (147)
                      +.|-.+-+.  +.+-||+||.     ....-||||.|  ||. .|.+.-|+.++-..|+..+       .+..  .....
T Consensus       137 ~~Lkp~L~r--g~i~vIgatT~eey~~~~e~d~al~r--rF~-~I~V~Eps~e~t~~IL~~~~~~~e~~h~v~--~~~~a  209 (268)
T d1r6bx2         137 NLIKPLLSS--GKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLKPKYEAHHDVR--YTAKA  209 (268)
T ss_dssp             HHHSSCSSS--CCCEEEEEECHHHHHCCCCCTTSSGG--GEE-EEECCCCCHHHHHHHHHHHHHHHHHHHTCC--CCHHH
T ss_pred             HHhhHHHhC--CCCeEEEeCCHHHHHHHHhhcHHHHh--hhc-ccccCCCCHHHHHHHHHHhhHHHhccCCEE--eChHH
Confidence            334444444  5677888877     44567999999  997 4899999999988888642       2221  22333


Q ss_pred             HHHHHH----HHhccchHHHHHHHHHHHH
Q 042776           76 IDELLT----KLMKSEVAEVALEGLVEFL  100 (147)
Q Consensus        76 i~~l~~----~l~~~~~~~~al~~~~~~l  100 (147)
                      +..++.    ++-.+..|+.|++=+-+..
T Consensus       210 l~~~v~ls~ryi~~~~~PdKAIdllDea~  238 (268)
T d1r6bx2         210 VRAAVELAVKYINDRHLPDKAIDVIDEAG  238 (268)
T ss_dssp             HHHHHHHHHHHCTTSCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhccCCCCCcHHHHHHHHHH
Confidence            444433    4456777888888554443

>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=86.08  E-value=0.68  Score=32.58  Aligned_cols=46  Identities=17%  Similarity=0.112  Sum_probs=35.9

Q ss_pred             CceEEEEecCC---CCCCCccccCCCee-eeEEeecCCCHHHHHHHHHHHhC
Q 042776           19 DERIIVFTTNH---KNRLDPALLRPGRM-DMHIHMSYCNPSGFRILVSNYLG   66 (147)
Q Consensus        19 ~~vivi~aTN~---p~~LD~Al~RpGRf-d~~i~~~~P~~~~r~~il~~~l~   66 (147)
                      ..+++|++||.   .+.+++++.+  |+ ...|+|+.|+.++...|+..++.
T Consensus       157 ~~~~~i~~~~~~~~~~~~~~~~~~--r~~~~~i~~~~~~~~e~~~il~~r~~  206 (276)
T d1fnna2         157 FRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTKDQIFDILLDRAK  206 (276)
T ss_dssp             CCEEEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCCBHHHHHHHHHHHHH
T ss_pred             cceEEeecCCchhhhhhcchhhhh--hhcchhccccchhHHHHHHHHHHHHH
Confidence            44778888886   4567888876  54 45789999999999999987764

>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=84.17  E-value=0.69  Score=33.19  Aligned_cols=70  Identities=16%  Similarity=0.301  Sum_probs=45.6

Q ss_pred             HHHHHhhCCCCCCCCceEEEEecCCCCCCC---ccccCCCeee--eEEeecCCCHHHHHHHHHHHhCCCCCCChHHHHHH
Q 042776            5 GLLNFIDGLWSSCGDERIIVFTTNHKNRLD---PALLRPGRMD--MHIHMSYCNPSGFRILVSNYLGINDHNLFPEIDEL   79 (147)
Q Consensus         5 ~lL~~lDgl~~~~~~~vivi~aTN~p~~LD---~Al~RpGRfd--~~i~~~~P~~~~r~~il~~~l~~~~~~~~~~i~~l   79 (147)
                      .|...++.+...  +..+||.+...|..++   |.|.-  ||-  ..+.++ |+.+.+.++++.+.......+..++...
T Consensus       118 ~lf~lin~~~~~--~~~iiits~~~p~~l~~~~~dL~S--RL~~g~~~~i~-p~d~~~~~iL~~~a~~rgl~l~~~v~~y  192 (213)
T d1l8qa2         118 EFFHIFNTLYLL--EKQIILASDRHPQKLDGVSDRLVS--RFEGGILVEIE-LDNKTRFKIIKEKLKEFNLELRKEVIDY  192 (213)
T ss_dssp             HHHHHHHHHHHT--TCEEEEEESSCGGGCTTSCHHHHH--HHHTSEEEECC-CCHHHHHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             HHHHHHHHHhhc--cceEEEecCCcchhccccchHHHH--HhhCceEEEEC-CCcHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            345556655554  5677777777887665   56655  655  344555 6778899999988866655555554433